Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1024
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1774716
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 201941 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:463100 original size:27 final size:27
Alignment explanation
Indices: 463069--463168 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
463059 ATATCATGAC
* *
463069 TTACAAGTTGATAAGCCTAATAATAAT
1 TTACAAGTTGATAAGGCTAATCATAAT
* *
463096 TTACAATTTGATAAGGCTAATCAT-TT
1 TTACAAGTTGATAAGGCTAATCATAAT
* *
463122 CTTACATGTTGATAAGGCTAATCATAAC
1 -TTACAAGTTGATAAGGCTAATCATAAT
*
463150 TTACAAGTTGATATGGCTA
1 TTACAAGTTGATAAGGCTA
463169 CTCCTTGGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 60 0.98
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (27 bp):
TTACAAGTTGATAAGGCTAATCATAAT
Found at i:464611 original size:4 final size:4
Alignment explanation
Indices: 464602--464661 Score: 63
Period size: 4 Copynumber: 15.0 Consensus size: 4
464592 TACCCTTGTG
*
464602 TGTC TGTC TGTT TGTC TGTCC T-TC TGTC TGT- TCGTC TGTCC T-TC TGTC
1 TGTC TGTC TGTC TGTC TGT-C TGTC TGTC TGTC T-GTC TGT-C TGTC TGTC
464650 TGTC TGTC TGTC
1 TGTC TGTC TGTC
464662 CGTCCGTAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
3 5 0.10
4 38 0.79
5 5 0.10
ACGTcount: A:0.00, C:0.27, G:0.22, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:464629 original size:20 final size:20
Alignment explanation
Indices: 464604--464662 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
464594 CCCTTGTGTG
464604 TCTGTCTGTTTGTCTGTCCT
1 TCTGTCTGTTTGTCTGTCCT
*
464624 TCTGTCTGTTCGTCTGTCCT
1 TCTGTCTGTTTGTCTGTCCT
*
464644 TCTGTCTGTCTGTCTGTCC
1 TCTGTCTGTTTGTCTGTCC
464663 GTCCGTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.00, C:0.29, G:0.20, T:0.51
Consensus pattern (20 bp):
TCTGTCTGTTTGTCTGTCCT
Found at i:465486 original size:166 final size:166
Alignment explanation
Indices: 464692--465486 Score: 1117
Period size: 166 Copynumber: 4.8 Consensus size: 166
464682 GTCGCATTTA
* * * *
464692 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCAAGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* * *
464757 CGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACAACTTTGCTTATTTT
66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTA-TTT
* *
464822 TTAACCAAAATTTTCAAACAAATTTTTGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
464859 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTTACACAATATTTGTATGGGTATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* **
464924 TGTGGGATATATTTTTGTACCAATCGGGCGTCAATTTCCTGTTAAATGACGACTTTGTTTATTTT
66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
464989 TAGCAAAAATTTTCAAACAAATTTTTGTCAAAG-TAT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAT-T
* * * *
465025 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* * *
465090 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTTAATGA-GTACTTTGTTTATTT
66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACG-ACTTTGTTTATTT
* * *
465154 TTAGCCAAAATTTTCAAACAAATTTCCGTCAATGAAT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
465191 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
** * * * *
465256 TGTGGGATATATTTTTGTGTCAATCGGACGTCACCTTCCTGTTAGATAATGACTTTGTTTATTTT
66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT
465321 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
465357 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* *** * * * * *
465422 TGTGGGATATATTTCTGTACCAATCGGATACCAGCTTTCTGTTCAATGTCTACTTTGCTTATTTT
66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT
465487 GCATATTCAT
Statistics
Matches: 560, Mismatches: 64, Indels: 9
0.88 0.10 0.01
Matches are distributed among these distances:
165 2 0.00
166 445 0.79
167 113 0.20
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:469683 original size:15 final size:15
Alignment explanation
Indices: 469663--469692 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
469653 GTTTTTTTTC
469663 ATTATTATTATTATA
1 ATTATTATTATTATA
469678 ATTATTATTATTATA
1 ATTATTATTATTATA
469693 GGAAATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:473425 original size:2 final size:2
Alignment explanation
Indices: 473418--473448 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
473408 GCATACACAA
473418 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
473449 TCTTCACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:480570 original size:25 final size:25
Alignment explanation
Indices: 480542--480594 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
480532 TTATAAAAAC
* * *
480542 ATCACATTGCTATTTATTGAATACT
1 ATCACATTGATATTAATTAAATACT
*
480567 ATCACATTGATATTAATTAAATGCT
1 ATCACATTGATATTAATTAAATACT
480592 ATC
1 ATC
480595 CAGACTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (25 bp):
ATCACATTGATATTAATTAAATACT
Found at i:481268 original size:163 final size:160
Alignment explanation
Indices: 480949--481444 Score: 655
Period size: 163 Copynumber: 3.1 Consensus size: 160
480939 TGTACCAACT
* * * * *
480949 GTTTCCGTTCATTTTCTTCGCAA-AGTATGCACAAAATGAAATGAAATTTAGTATACAGATTTAT
1 GTTTCCGTTCATTTTTTTCG-AAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTAT
* * * * * * *
481013 C--AATA-ATATAGGTCAAGTTCGATTTTGGGTGAGATCGAGCAATTTTCGATAGAGTTGTGCCC
65 CATAATATATCTAGGTCAACTTTGATTTTGAGTGCGATCGAGCAATTTTCGACAGAGTTATGCCC
481075 CTTGGACGTAGAAAAATTCCAATTATTTGCA
130 CTTGGACGTAGAAAAATTCCAATTATTTGCA
* *
481106 GTTTCCATTCATTTTTTTCGAAGAGGATGCACATATTGAAATGAAATTTGGTATACAGGTTTATC
1 GTTTCCGTTCATTTTTTTCGAAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTATC
* *
481171 ATAATAGTATCTAGGTCAACTTTGATTTTGAGTGCG-TCGGGGAGCAATTTTCAACAGAGCTATG
66 ATAATA-TATCTAGGTCAACTTTGATTTTGAGTGCGATC---GAGCAATTTTCGACAGAGTTATG
481235 CCCCTTGGACGTAGAAAAATTCCAATTATTTGCA
127 CCCCTTGGACGTAGAAAAATTCCAATTATTTGCA
* *
481269 GTTTCCGTTCATTTTCTTT-GCAGAGGATGCACATATTAAAATGAAATTTAGTATACAGGTTTAT
1 GTTTCCGTTCATTTT-TTTCGAAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTAT
* *
481333 CATAATAATATCTAGGTCAACTTTGATTTTCGA-TACGATCGAGCAATTTTCGACAGAGTTATGT
65 CATAAT-ATATCTAGGTCAACTTTGATTTT-GAGTGCGATCGAGCAATTTTCGACAGAGTTATGC
* * *
481397 GCCTTGGACTTAGAAAAATTCCAATTATTTGTA
128 CCCTTGGACGTAGAAAAATTCCAATTATTTGCA
*
481430 GGTTCCGTTCATTTT
1 GTTTCCGTTCATTTT
481445 CTATGGAGAT
Statistics
Matches: 299, Mismatches: 28, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
156 2 0.01
157 55 0.18
159 4 0.01
160 2 0.01
161 88 0.29
163 140 0.47
164 8 0.03
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (160 bp):
GTTTCCGTTCATTTTTTTCGAAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTATC
ATAATATATCTAGGTCAACTTTGATTTTGAGTGCGATCGAGCAATTTTCGACAGAGTTATGCCCC
TTGGACGTAGAAAAATTCCAATTATTTGCA
Found at i:487695 original size:166 final size:166
Alignment explanation
Indices: 487485--488184 Score: 1025
Period size: 166 Copynumber: 4.2 Consensus size: 166
487475 TTTTTAAAAA
* *
487485 AAAAATCTTCTTCTCAAGAATCATAA--AGTCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTC-AGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* * *
487548 GGTAGTGTAGATTAAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGTGGCCACAA-TGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGG
*
487612 GCTCGAAGTTTTACATAGGAAAATATAGAGTAAATCTTT
129 G-TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
487651 AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
**
487716 TAGTGTAGATTCAAAGTTGTGAAAATTGTGACCCCCGGGGGTAGGGTGGGGCCACAA-TGGGGGA
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGGG-
*
487780 TCGAAGTTTTACATAGGAATATATAGAGTAAATTTTT
130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
487817 AAAAATCCTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGGAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* ** * *
487882 TAGTGTAGATTCCAAGTTGTGAAAATCATGA-CCATGGGGGTAGGATGGGGCCACAATTGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGGGT
487946 CGAAGTTTTACATAGGAATATATAGAGTAAAT-TTT
131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * * * *
487981 AAAAAATCCTCTTCTCGGAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGTATCCTTAG
1 -AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* *
488046 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGTGGGAAGGGTGGGGCCACCATAGTGGG
65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCA-CA-AGTGGG
* ** *
488111 TGTTAAAGTTTTACATAGGAATGTATAGAGTAAATCTTT
128 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
488150 TAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAA
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAA
488185 TGAAACTCAT
Statistics
Matches: 485, Mismatches: 41, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
164 6 0.01
165 148 0.31
166 259 0.53
167 2 0.00
168 67 0.14
169 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGGGT
CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:488095 original size:331 final size:334
Alignment explanation
Indices: 487514--488184 Score: 1032
Period size: 331 Copynumber: 2.0 Consensus size: 334
487504 ATCATAAAGT
*
487514 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAATTCAT
1 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAAATCAT
* * *
487579 GACCCCCGGGGGTAGGGTGTGGCCACAATGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGTA
66 GACCCACGGGGGTAGGATGGGGCCACAATGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGTA
* * *
487644 AATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCAT
131 AATCTTTAAAAATCCTCTTCTCAAAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGCAT
** *
487709 CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATTGTGACCCCCGGGGGTAGGGTGGGGCCA-CA-
196 CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGAAGGGTGGGGCCACCAT
*
487772 A-TGGGGGATCGAAGTTTTACATAGGAATATATAGAGTAAAT-TTTTAAAAATCCTCTTCTCAGA
261 AGTGGGGG-TCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTT-AAAATCCTCTTCTCAGA
487835 AACTAATCAGC
324 AACTAATCAGC
* **
487846 CAGGAAAGCTGGAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCCAAGTTGTGAAAATCAT
1 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAAATCAT
* *
487911 GA-CCATGGGGGTAGGATGGGGCCACAATTGGGGG-TCGAAGTTTTACATAGGAATATATAGAGT
66 GACCCACGGGGGTAGGATGGGGCCACAA-TGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGT
** *
487974 AAAT-TTTAAAAAATCCTCTTCTCGGAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGT
130 AAATCTTT-AAAAATCCTCTTCTCAAAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGC
* *
488038 ATCCTTAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGTGGGAAGGGTGGGGCCACC
194 ATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGAAGGGTGGGGCCACC
* * * *
488103 ATAGTGGGTGTTAAAGTTTTACATAGGAATGTATAGAGTAAATCTTTTAAAATCTTCTTCTCAGA
259 ATAGTGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTTAAAATCCTCTTCTCAGA
488168 AACTAATCAGC
324 AACTAATCAGC
488179 CAGGAA
1 CAGGAA
488185 TGAAACTCAT
Statistics
Matches: 308, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
330 3 0.01
331 161 0.52
332 71 0.23
333 64 0.21
334 9 0.03
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (334 bp):
CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAAATCAT
GACCCACGGGGGTAGGATGGGGCCACAATGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGTA
AATCTTTAAAAATCCTCTTCTCAAAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGCAT
CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGAAGGGTGGGGCCACCAT
AGTGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTTAAAATCCTCTTCTCAGAAA
CTAATCAGC
Found at i:493205 original size:16 final size:16
Alignment explanation
Indices: 493174--493213 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
493164 CACATTTTTT
493174 TCTGTC-GTCAGGCCG
1 TCTGTCTGTCAGGCCG
* *
493189 TGTGTCTGTCAGTCCG
1 TCTGTCTGTCAGGCCG
493205 TCTGTCTGT
1 TCTGTCTGT
493214 AAACTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.05, C:0.28, G:0.30, T:0.38
Consensus pattern (16 bp):
TCTGTCTGTCAGGCCG
Found at i:494493 original size:15 final size:16
Alignment explanation
Indices: 494475--494512 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
494465 CACTCGATGG
494475 CTCGAACTTC-GATCT
1 CTCGAACTTCTGATCT
*
494490 CTCGAAGTTCTTGATCT
1 CTCGAACTTC-TGATCT
494507 CTCGAA
1 CTCGAA
494513 GTGAACTCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (16 bp):
CTCGAACTTCTGATCT
Found at i:502770 original size:53 final size:54
Alignment explanation
Indices: 502665--502775 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 54
502655 AGCTTAGATT
* *
502665 CTGTAAGAAGACCCTATTTTGTAATTATGTACAATATCAATACACATGTACATCGAA
1 CTGTAAGAAGACACTATTTTG--A-TATGTACAATACCAATACACATGTACATCGAA
* * *
502722 CTGTAAGAAGACACTATTTTG-TATGTATAATACCAATACACATTTACATTGAA
1 CTGTAAGAAGACACTATTTTGATATGTACAATACCAATACACATGTACATCGAA
502775 C
1 C
502776 ACATGGACAG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 29 0.59
57 20 0.41
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
CTGTAAGAAGACACTATTTTGATATGTACAATACCAATACACATGTACATCGAA
Found at i:503061 original size:23 final size:23
Alignment explanation
Indices: 503030--503079 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
503020 TTGAGCCAAT
* *
503030 AAAATATTCACTCACAAAAAAAA
1 AAAATATTCACCCAAAAAAAAAA
*
503053 AAAANATTCACCCAAAAAAAAAA
1 AAAATATTCACCCAAAAAAAAAA
503076 AAAA
1 AAAA
503080 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.70, C:0.16, G:0.00, T:0.12
Consensus pattern (23 bp):
AAAATATTCACCCAAAAAAAAAA
Found at i:503070 original size:1 final size:1
Alignment explanation
Indices: 503066--503094 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
503056 ANATTCACCC
503066 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
503095 TCATTCAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:509789 original size:2 final size:2
Alignment explanation
Indices: 509782--509838 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
509772 CAAGACTGAG
509782 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
509824 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
509839 GCACGTACGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:509869 original size:14 final size:14
Alignment explanation
Indices: 509848--509887 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
509838 CGCACGTACG
*
509848 CACAAACACACGCA
1 CACAAACACACACA
*
509862 CGCAAACACACACA
1 CACAAACACACACA
*
509876 CACACACACACA
1 CACAAACACACA
509888 TATTTAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.45, G:0.05, T:0.00
Consensus pattern (14 bp):
CACAAACACACACA
Found at i:510144 original size:16 final size:16
Alignment explanation
Indices: 510125--510155 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
510115 CACTGCGACA
510125 AGGCATCACCTTTATG
1 AGGCATCACCTTTATG
*
510141 AGGCGTCACCTTTAT
1 AGGCATCACCTTTAT
510156 AAGACCACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (16 bp):
AGGCATCACCTTTATG
Found at i:510338 original size:17 final size:17
Alignment explanation
Indices: 510318--510352 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
510308 AAAATATACA
510318 ATATTGAATCCTATGAT
1 ATATTGAATCCTATGAT
510335 ATATTGAATCCTATGAT
1 ATATTGAATCCTATGAT
510352 A
1 A
510353 CTTACAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
ATATTGAATCCTATGAT
Found at i:515907 original size:12 final size:12
Alignment explanation
Indices: 515890--515925 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
515880 TTCAATTAAG
515890 GTTTTTTTTTTT
1 GTTTTTTTTTTT
*
515902 GTTTTTGTTTTT
1 GTTTTTTTTTTT
515914 GTTTTTTTTTTT
1 GTTTTTTTTTTT
515926 TGCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:515926 original size:6 final size:6
Alignment explanation
Indices: 515890--515924 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
515880 TTCAATTAAG
*
515890 GTTTTT TTTTTT GTTTTT GTTTTT GTTTTT -TTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
515925 TTGCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (6 bp):
GTTTTT
Found at i:516673 original size:18 final size:18
Alignment explanation
Indices: 516630--516664 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
516620 ATGTAAAGTT
*
516630 ACATATACATATATATAA
1 ACATATACAAATATATAA
516648 ACATATACAAATATATA
1 ACATATACAAATATATA
516665 CGCATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
ACATATACAAATATATAA
Found at i:523238 original size:10 final size:11
Alignment explanation
Indices: 523205--523244 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
523195 GGATACCCTA
523205 TTTTAAGACAAC
1 TTTTAA-ACAAC
523217 TTTTAAACAAC
1 TTTTAAACAAC
*
523228 TTTT-TACAAC
1 TTTTAAACAAC
523238 TTTTAAA
1 TTTTAAA
523245 AATATGCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 10 0.40
12 6 0.24
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (11 bp):
TTTTAAACAAC
Found at i:523620 original size:30 final size:30
Alignment explanation
Indices: 523586--523648 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
523576 AGTTATTCAG
* * *
523586 AAAATGGGAAGGTGGAATTCGGATGCTTTT
1 AAAATGAGAAGATGGAATTCAGATGCTTTT
*
523616 AAAATGAGAAGATGGAATTTAGATGCTTTT
1 AAAATGAGAAGATGGAATTCAGATGCTTTT
523646 AAA
1 AAA
523649 CACTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (30 bp):
AAAATGAGAAGATGGAATTCAGATGCTTTT
Found at i:556635 original size:177 final size:176
Alignment explanation
Indices: 556433--556799 Score: 506
Period size: 177 Copynumber: 2.1 Consensus size: 176
556423 GGGTCCTCAA
* ** *
556433 TTTCAGATGCTTGAGAAGGTTAAGGTTTTTGGAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCAGATGCTGGAGAAGGTTAAGGTTTTTAAAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTCT
* *
556498 GATAGCA-ATATCTAAG-TAACTGCTGGT-TCTAACTTCACCAAACTTGCATGGATGGTGTGTCA
66 GAT-G-ATATATCTAAGCT-ACTACTGGTCT-TAACTTCACCAAACTTGCATGGATGGTGCGTCA
* *
556560 TATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCTATGGG
127 TATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
* * * *
556610 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAAAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT
1 TTTCAGATGCTGGAGAAGGTTAAGGTTTTTAAAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTCT
* * *
556675 GATGATTATATCTTAGCTACTACTGGTCTTAACTTCACCAAACTTGCATGGTTGGTGCGTCTTAT
66 GATGA-TATATCTAAGCTACTACTGGTCTTAACTTCACCAAACTTGCATGGATGGTGCGTCATAT
* *
556740 GATACTGATGCTCGAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
130 GATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
*
556787 TTTCAGAGGCTGG
1 TTTCAGATGCTGG
556800 TTGAGGTAAA
Statistics
Matches: 167, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
175 1 0.01
176 1 0.01
177 163 0.98
178 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (176 bp):
TTTCAGATGCTGGAGAAGGTTAAGGTTTTTAAAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTCT
GATGATATATCTAAGCTACTACTGGTCTTAACTTCACCAAACTTGCATGGATGGTGCGTCATATG
ATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG
Found at i:557736 original size:15 final size:15
Alignment explanation
Indices: 557718--557777 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
557708 TATTTTACTA
557718 TATCACATTATATTG
1 TATCACATTATATTG
*
557733 TATCA-TTTGATA-TG
1 TATCACATT-ATATTG
557747 -AT-ACA--ATATTG
1 TATCACATTATATTG
*
557758 TATCAAATTATATTG
1 TATCACATTATATTG
557773 TATCA
1 TATCA
557778 TATGATACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
10 3 0.09
11 2 0.06
12 3 0.09
13 4 0.11
14 4 0.11
15 19 0.54
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (15 bp):
TATCACATTATATTG
Found at i:558278 original size:16 final size:16
Alignment explanation
Indices: 558257--558290 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
558247 TAAAGGTGGT
*
558257 CTAATAAAGGTGATGC
1 CTAATAAAAGTGATGC
558273 CTAATAAAAGTGATGC
1 CTAATAAAAGTGATGC
558289 CT
1 CT
558291 CGTCTCGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (16 bp):
CTAATAAAAGTGATGC
Found at i:560426 original size:46 final size:46
Alignment explanation
Indices: 560345--560464 Score: 215
Period size: 46 Copynumber: 2.6 Consensus size: 46
560335 ACCATTAACT
560345 ATATAAAAGGACTATA-TTTTGGCGGAACTAATTAAAAAATTATCC
1 ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAAAAATTATCC
* *
560390 ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAACAATTATCT
1 ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAAAAATTATCC
560436 ATATAAAAGGACTATATTTTTGGCGGAAC
1 ATATAAAAGGACTATATTTTTGGCGGAAC
560465 ATTGACGTAG
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 16 0.22
46 56 0.78
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (46 bp):
ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAAAAATTATCC
Found at i:563738 original size:2 final size:2
Alignment explanation
Indices: 563731--563783 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
563721 CTTCACCCAC
563731 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
563773 AG AG AG AG AG A
1 AG AG AG AG AG A
563784 TAAGGTCATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:567483 original size:21 final size:20
Alignment explanation
Indices: 567455--567494 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
567445 GTACATAAAT
567455 GTACATACATTCTGTTGATA
1 GTACATACATTCTGTTGATA
567475 GTACGATACATTCTGTTGAT
1 GTAC-ATACATTCTGTTGAT
567495 TATTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
GTACATACATTCTGTTGATA
Found at i:570277 original size:12 final size:12
Alignment explanation
Indices: 570260--570285 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
570250 CCCGTTGTCC
570260 GTCCGTCCGTCT
1 GTCCGTCCGTCT
570272 GTCCGTCCGTCT
1 GTCCGTCCGTCT
570284 GT
1 GT
570286 AAACTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.27, T:0.35
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:570738 original size:166 final size:167
Alignment explanation
Indices: 570435--570775 Score: 495
Period size: 166 Copynumber: 2.0 Consensus size: 167
570425 AATAGGGTGC
* *
570435 ATGTCTTTAAAAATCTTTTTCTCAAGAACCACTGCACCAGAAATGCAAATTTTTACACAAAAGCT
1 ATGT-TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCAAACTTTTACACAAAAGCT
* * *
570500 TGTATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAG
65 TGCATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCAGACCAAAACTGGGCCCCCAG
*
570565 ACGGGGTTCAAAGTTAAACATAGAAATACAT-AGGAAA
130 ACGGGGTTCAAAGTTAAACATAGAAATACATAAGAAAA
* *
570602 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAACTTTTATACAAAAGCTT
1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCAAACTTTTACACAAAAGCTT
* * * * ** *
570667 GCATATATTGTGAAGATTCTAAATTGTAAAAATCGTGATCCTCATACCACTACTGGGCCCCCAGG
66 GCATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCAGACCAAAACTGGGCCCCCAGA
****
570732 CGGGGTTCAAAGTTTTTTATAGAAATACATAAGAAAA
131 CGGGGTTCAAAGTTAAACATAGAAATACATAAGAAAA
570769 ATGTTTT
1 ATGTTTT
570776 CATGACTTTT
Statistics
Matches: 154, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
166 138 0.90
167 16 0.10
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (167 bp):
ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCAAACTTTTACACAAAAGCTT
GCATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCAGACCAAAACTGGGCCCCCAGA
CGGGGTTCAAAGTTAAACATAGAAATACATAAGAAAA
Found at i:572407 original size:165 final size:165
Alignment explanation
Indices: 572157--572564 Score: 439
Period size: 165 Copynumber: 2.5 Consensus size: 165
572147 CGGTATATAT
* * * * * *
572157 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAATTTGTCAGATAACTACGTA
1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCA
* * * *
572221 AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCCGTGA-C-CTCAATCTAATACTGGGG
65 AGCATCCTCAAATAATGTAGATTCCAAATAATTAAAA--CGTGAGCACTCAA-CTAATACTGGGG
* * * *
572283 CCCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG
127 CCCCAAAAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * *
572322 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTATGCAA
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA
* * * ** *
572387 GCATCCTTAAATAATGTAGATTCCAAATAATTAAAACTTTAGCACTGGACTAATACTGTGGCCCC
66 GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACGTGAGCACTCAACTAATACTGGGGCCCC
* *
572452 AAAAGGGGTTCAAAGTTTAACATAGAAAGATATAT
131 AAAAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * *
572487 TGAAAATGTTTTTAAAAA-GTTCTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTACTATGC
1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGC
*
572551 AAGGATCCTCAAAT
64 AAGCATCCTCAAAT
572565 TGTGTAAACT
Statistics
Matches: 200, Mismatches: 37, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
164 6 0.03
165 128 0.64
166 59 0.29
167 7 0.04
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (165 bp):
GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA
GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACGTGAGCACTCAACTAATACTGGGGCCCC
AAAAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
Found at i:573309 original size:2 final size:2
Alignment explanation
Indices: 573302--573343 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
573292 CTCCCCCTCC
573302 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
573344 ACCTCTACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:573349 original size:12 final size:11
Alignment explanation
Indices: 573301--573349 Score: 66
Period size: 10 Copynumber: 4.5 Consensus size: 11
573291 CCTCCCCCTC
573301 CCTCTCTCTCT
1 CCTCTCTCTCT
573312 -CTCTCTCTCT
1 CCTCTCTCTCT
573322 -CTCTCTCTCT
1 CCTCTCTCTCT
573332 CTCTCTCTCTCT
1 C-CTCTCTCTCT
573344 ACCTCT
1 -CCTCT
573350 ACCTCTACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 20 0.57
12 14 0.40
13 1 0.03
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47
Consensus pattern (11 bp):
CCTCTCTCTCT
Found at i:574536 original size:11 final size:11
Alignment explanation
Indices: 574506--574539 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
574496 AGGTGTGTCT
574506 TAAAA-AAGGG
1 TAAAACAAGGG
574516 TAACAACAAGGG
1 TAA-AACAAGGG
574528 TAAAACAAGGG
1 TAAAACAAGGG
574539 T
1 T
574540 TTTAGGGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 11 0.50
12 8 0.36
ACGTcount: A:0.53, C:0.09, G:0.26, T:0.12
Consensus pattern (11 bp):
TAAAACAAGGG
Found at i:576699 original size:15 final size:16
Alignment explanation
Indices: 576671--576701 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
576661 GTCAACACAG
576671 TCAATCAGTTAAATCA
1 TCAATCAGTTAAATCA
576687 TCAATCA-TTAAATCA
1 TCAATCAGTTAAATCA
576702 ATGGTCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (16 bp):
TCAATCAGTTAAATCA
Found at i:576975 original size:24 final size:24
Alignment explanation
Indices: 576942--576987 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
576932 TTTACTTCGT
*
576942 TATAATAGTAATTCGCTATATCGG
1 TATAAGAGTAATTCGCTATATCGG
* *
576966 TATAAGAGTAATTTGTTATATC
1 TATAAGAGTAATTCGCTATATC
576988 AGTCAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (24 bp):
TATAAGAGTAATTCGCTATATCGG
Found at i:577307 original size:65 final size:65
Alignment explanation
Indices: 577225--577541 Score: 431
Period size: 65 Copynumber: 4.9 Consensus size: 65
577215 CGGGCCATTC
*
577225 ACCTCGCGCCTCAAAACCATCCTCAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT
1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT
* * * *
577290 ACCTCGCACCTCAAAACCATCATAAACACCATCAAATACCTAACTAGTGTAAGTAAATGATCGTT
1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT
* * *
577355 ACCTCGCACCTCAAAACCATCATAAACACCATCAAATACCTAACTAGT-TAAGTAAACGATCGTT
1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT
* * * * *
577419 ACCTCGCGCCTCAAAACTATCCTCAACACCATCAAATACATACCCAGTGTAAGAAAACGA-CTGT
1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATC-GT
577483 T
65 T
* * * ** *
577484 CACCTCACGCCTCAAATCCATCCTTAACACCATCAGGTACCTATCCAGTGTAAGTAAA
1 -ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAA
577542 AAACCAGTCA
Statistics
Matches: 226, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
64 57 0.25
65 121 0.54
66 48 0.21
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.21
Consensus pattern (65 bp):
ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT
Found at i:577908 original size:16 final size:16
Alignment explanation
Indices: 577887--577920 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
577877 TATATAGAGG
577887 GTTATTTTTGCCCTGT
1 GTTATTTTTGCCCTGT
577903 GTTATTTTTGCCCTGT
1 GTTATTTTTGCCCTGT
577919 GT
1 GT
577921 AAACTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.21, T:0.56
Consensus pattern (16 bp):
GTTATTTTTGCCCTGT
Found at i:577928 original size:17 final size:16
Alignment explanation
Indices: 577892--577933 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
577882 AGAGGGTTAT
* *
577892 TTTTGCCCTGTGTTAT
1 TTTTGCCCTGTGTAAC
577908 TTTTGCCCTGTGTAAAC
1 TTTTGCCCTGTGT-AAC
577925 TTTTGCCCT
1 TTTTGCCCT
577934 TCTACACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.10, C:0.24, G:0.17, T:0.50
Consensus pattern (16 bp):
TTTTGCCCTGTGTAAC
Found at i:579454 original size:16 final size:16
Alignment explanation
Indices: 579430--579466 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
579420 AGAGGTCAGG
* *
579430 GACAGCCTCATTCTGA
1 GACAACCTCATTCTAA
579446 GACAACCTCATTCTAA
1 GACAACCTCATTCTAA
579462 GACAA
1 GACAA
579467 AGTCCTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (16 bp):
GACAACCTCATTCTAA
Found at i:582147 original size:2 final size:2
Alignment explanation
Indices: 582140--582205 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
582130 GTTTAACAAC
582140 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
582182 AG AG AG AG AG AG -G AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
582206 ACCATATGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:583728 original size:37 final size:39
Alignment explanation
Indices: 583654--583730 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 39
583644 CGCACCTGTT
*
583654 ACAGTCAGGTGGGTATACAGTAAATCTGTGTGGTTAACGTTC
1 ACAGTCAGGTGGGTATA-AG--AATCTGTGTGATTAACGTTC
583696 ACAGTCAGGTGGGTAT-AG-ATCTGTGTGATTAACGT
1 ACAGTCAGGTGGGTATAAGAATCTGTGTGATTAACGT
583731 CCCCAACACA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 16 0.47
40 2 0.06
42 16 0.47
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (39 bp):
ACAGTCAGGTGGGTATAAGAATCTGTGTGATTAACGTTC
Found at i:583914 original size:67 final size:67
Alignment explanation
Indices: 583801--583964 Score: 204
Period size: 67 Copynumber: 2.4 Consensus size: 67
583791 AAGGCAACGC
* * * * * *
583801 GCCTGTTACAGTCAGGTGGGTATAAATCTACTGTAAACAATGAATTTAGCAATGTACTGTACAAC
1 GCCTATTACAATCAGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAC
583866 AT
66 AT
* *
583868 GCCTATTACAATCTGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAT
1 GCCTATTACAATCAGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAC
*
583933 GT
66 AT
* * *
583935 GCCTGTTACAGTCATGTG-GATATAAATCTA
1 GCCTATTACAATCAGGTGAG-TATAAATCTA
583965 GTACATATAC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
66 1 0.01
67 82 0.99
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (67 bp):
GCCTATTACAATCAGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAC
AT
Found at i:587652 original size:18 final size:18
Alignment explanation
Indices: 587631--587672 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
587621 CTCTTGATTT
587631 AGCTATATAGCTTGAAAA
1 AGCTATATAGCTTGAAAA
* *
587649 AGCTATATAGCTTTATAA
1 AGCTATATAGCTTGAAAA
587667 AGCTAT
1 AGCTAT
587673 TCAAAATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (18 bp):
AGCTATATAGCTTGAAAA
Found at i:588235 original size:18 final size:18
Alignment explanation
Indices: 588211--588252 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
588201 GCTACTCTGA
588211 ATAGCTTAATAAAGCTAT
1 ATAGCTTAATAAAGCTAT
* * *
588229 TTAGCTTATTCAAGCTAT
1 ATAGCTTAATAAAGCTAT
588247 ATAGCT
1 ATAGCT
588253 AAATCTGGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
ATAGCTTAATAAAGCTAT
Found at i:589951 original size:2 final size:2
Alignment explanation
Indices: 589938--590689 Score: 390
Period size: 2 Copynumber: 355.5 Consensus size: 2
589928 GGATTGTCTC
* ** ** * *
589938 AG AG AA AG AG AG AG AG AG AG AG AG AG CTC TC AA AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG
* ** **
589981 AG AG AG AG AG CG AG CTC AG AG AG AG AG CTC AG AG AG AG AG AG A-
1 AG AG AG AG AG AG AG -AG AG AG AG AG AG -AG AG AG AG AG AG AG AG
**
590024 AG AG AG AG AG AG AG AG AG AG AG AG AG CTT ATG CAG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG -AG A-G -AG AG AG AG AG
** **
590067 CTC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CTC AG AG AG AG
1 -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG
** * * *
590111 AG AG AG AG AG AG AG AG AG CTC TG AG AG AT AG AG AG AG CTG AG AG
1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG -AG AG AG
** ** *
590155 AG AG AG AG AG AG AG AG CTC AG AG AG AG AG AG AG AG CTC TG AG AG
1 AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG -AG AG AG AG
* * *
590199 AG AG AG AG AG AG AG CTG AG AG AG AG AG AG AG TG GG AG AG AG AG
1 AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * ** * **
590242 AG AG TG GG AG AG AG AG AG AG CTC AG AG AG AT AG AG AG AG CTC AG
1 AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG -AG AG
* ** * * **
590286 AG AG AG AG AG AG AG CTG CTC AG AG AG GG GG AG AG AG CTC AG AG
1 AG AG AG AG AG AG AG -AG -AG AG AG AG AG AG AG AG AG -AG AG AG
** ** **
590329 AG AG AG AG AG AG CTC ATG CAG AG AG AG CTC AG AG AG AG AG AG CTC
1 AG AG AG AG AG AG -AG A-G -AG AG AG AG -AG AG AG AG AG AG AG -AG
**
590374 ATG CAG AG AG AG AG AG AG CTC AG AG AG AG AG AG AG AG AG AG AG
1 A-G -AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG
** *
590417 ATG AG AG AG AG AG AG AG AG AG AG AG AG AG ATG CTC AG AG AG GG
1 A-G AG AG AG AG AG AG AG AG AG AG AG AG AG A-G -AG AG AG AG AG
* ** **
590460 GG AG AG AG CTC AG AG AG AG AG AG AG AG AG AG AG CTC ATG CAG AG
1 AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG -AG A-G -AG AG
* *
590504 AG AG AG AG AG AG AG AG AG AA AG AG AG AG ATC AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG
** * * **
590547 AG AG AG AG AG TAG CTC AG AG AG GG GG AG AG AG CTC AG AG AG AG
1 AG AG AG AG AG -AG -AG AG AG AG AG AG AG AG AG -AG AG AG AG AG
** **
590590 AG AG AG AG AG CTC ATG CAG AG AG AG AG AG AG AG CTC AG AG AG AG
1 AG AG AG AG AG -AG A-G -AG AG AG AG AG AG AG AG -AG AG AG AG AG
* ** * * *
590634 AG AG GG AG AG AG AG CTC AG AG AG AG AG TG GG AG AG AG AG AA AG
1 AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
590677 GG AA AG AG AG AG A
1 AG AG AG AG AG AG A
590690 ATTATCTTGT
Statistics
Matches: 566, Mismatches: 143, Indels: 82
0.72 0.18 0.10
Matches are distributed among these distances:
1 1 0.00
2 544 0.96
3 16 0.03
4 5 0.01
ACGTcount: A:0.42, C:0.08, G:0.44, T:0.06
Consensus pattern (2 bp):
AG
Found at i:589975 original size:31 final size:31
Alignment explanation
Indices: 589934--589997 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
589924 GGTAGGATTG
*
589934 TCTCAGAGAAAGAGAGAGAGAGAGAGAGAGC
1 TCTCAAAGAAAGAGAGAGAGAGAGAGAGAGC
*
589965 TCTCAAAGAAAGAGAGAGAGAGAGAGCGAGC
1 TCTCAAAGAAAGAGAGAGAGAGAGAGAGAGC
589996 TC
1 TC
589998 AGAGAGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.12, G:0.36, T:0.08
Consensus pattern (31 bp):
TCTCAAAGAAAGAGAGAGAGAGAGAGAGAGC
Found at i:590003 original size:13 final size:13
Alignment explanation
Indices: 589985--590660 Score: 117
Period size: 13 Copynumber: 56.8 Consensus size: 13
589975 AGAGAGAGAG
*
589985 AGAGAGCGAGCTC
1 AGAGAGAGAGCTC
589998 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
590011 AGAGAGAGAG---
1 AGAGAGAGAGCTC
590021 AGA-AGAGAG---
1 AGAGAGAGAGCTC
590030 AGAGAGAGAG---
1 AGAGAGAGAGCTC
590040 AGAGAGAGAGCTTATGC
1 AGAGAGAGAGC---T-C
590057 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
590070 AGAGAGAGAG---
1 AGAGAGAGAGCTC
590080 AGAGAGAGAG---
1 AGAGAGAGAGCTC
590090 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
***
590103 AGAGAGAGAGAGAGAG
1 --AGAGAGAGAG-CTC
590119 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
*
590132 TGAGAGATAGAGAGAGCTG
1 ----AG--AGAGAGAGCTC
590151 AGAGAGAGAG---
1 AGAGAGAGAGCTC
590161 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
590174 ----AGAGAG---
1 AGAGAGAGAGCTC
590180 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
*
590193 TGAGAGAGAG---
1 AGAGAGAGAGCTC
*
590203 AGAGAGAGAGCTG
1 AGAGAGAGAGCTC
590216 AGAGAGAGAG---
1 AGAGAGAGAGCTC
* * **
590226 AGAGTGGGAG-AG
1 AGAGAGAGAGCTC
* ***
590238 AGAGAGAGTGGGAG
1 AGAGAGAG-AGCTC
590252 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
590265 --AGAGAGA--T-
1 AGAGAGAGAGCTC
590273 --AGAGAGAGCTC
1 AGAGAGAGAGCTC
590284 AGAGAGAGAG---
1 AGAGAGAGAGCTC
**
590294 AGAGAG-CTGCTC
1 AGAGAGAGAGCTC
**
590306 AGAGAG-G-G-GG
1 AGAGAGAGAGCTC
**
590316 AGAGAGCTCAGAG-AG
1 AGAGAG---AGAGCTC
590331 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
590344 ATGCAGAGAGAGCTC
1 A-G-AGAGAGAGCTC
590359 AGAGAGAGAGAGCTC
1 --AGAGAGAGAGCTC
* *
590374 A-TG-CAGAG---
1 AGAGAGAGAGCTC
590382 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
**
590395 AGAGAGAGAG-AG
1 AGAGAGAGAGCTC
*
590407 AGAGAGAGAGAT-
1 AGAGAGAGAGCTC
590419 -GAGAGAGAG---
1 AGAGAGAGAGCTC
590428 AGAGAGAGAG---
1 AGAGAGAGAGCTC
590438 AGAGAGAGATGCTC
1 AGAGAGAGA-GCTC
590452 AGAGAG-G-G---
1 AGAGAGAGAGCTC
590460 -G-GAGAGAGCTC
1 AGAGAGAGAGCTC
**
590471 AGAGAGAGAG-AG
1 AGAGAGAGAGCTC
590483 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
**
590496 ATGCAGAGAGAG-AG
1 A-G-AGAGAGAGCTC
**
590510 AGAGAGAGAG-AG
1 AGAGAGAGAGCTC
* *
590522 AAAGAGAGAGATC
1 AGAGAGAGAGCTC
***
590535 AGAGAGAGAGAGAG
1 AGAGAGAGAG-CTC
590549 AGAGAGAGTAGCTC
1 AGAGAGAG-AGCTC
590563 AGAGAG-G-G---
1 AGAGAGAGAGCTC
590571 -G-GAGAGAGCTC
1 AGAGAGAGAGCTC
590582 --AGAGAGAG---
1 AGAGAGAGAGCTC
590590 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
*
590603 ATG-CAGAGAG---
1 A-GAGAGAGAGCTC
590613 AGAGAGAGAGCTC
1 AGAGAGAGAGCTC
**
590626 AGAGAGAGAG-AG
1 AGAGAGAGAGCTC
*
590638 GGAGAGAGAGCTC
1 AGAGAGAGAGCTC
590651 AGAGAGAGAG
1 AGAGAGAGAG
590661 TGGGAGAGAG
Statistics
Matches: 509, Mismatches: 58, Indels: 192
0.67 0.08 0.25
Matches are distributed among these distances:
6 6 0.01
7 4 0.01
8 10 0.02
9 19 0.04
10 122 0.24
11 31 0.06
12 66 0.13
13 128 0.25
14 46 0.09
15 52 0.10
16 1 0.00
17 14 0.03
19 10 0.02
ACGTcount: A:0.41, C:0.08, G:0.44, T:0.06
Consensus pattern (13 bp):
AGAGAGAGAGCTC
Found at i:590656 original size:19 final size:19
Alignment explanation
Indices: 589979--590637 Score: 463
Period size: 19 Copynumber: 35.6 Consensus size: 19
589969 AAAGAAAGAG
*
589979 AGAGAGAGAGAGCGAGCTC
1 AGAGAGAGAGAGAGAGCTC
589998 AGAGAGAGAGCTCAGAGAG---
1 AGAGAGAGAG---AGAGAGCTC
590017 AGAGAGAAGAGAGAGAG---
1 AGAGAG-AGAGAGAGAGCTC
*
590034 AGAGAGAGAGAGAGAGCTT
1 AGAGAGAGAGAGAGAGCTC
* *
590053 A-TG-CAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590070 --AGAGAGAGAGAGAG---
1 AGAGAGAGAGAGAGAGCTC
590084 AGAGAGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590103 AGAGAGAGAGAGAGAG---
1 AGAGAGAGAGAGAGAGCTC
* *
590119 AGAGAGAGAGCTCTGAGAGAT-
1 AGAGAGAGAG---AGAGAGCTC
**
590140 AGAGAGAG-CTGAGAG---
1 AGAGAGAGAGAGAGAGCTC
590155 AGAGAGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590174 AGAGAGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
**
590193 TGAGAGAGAGAGAGAGAGAGC
1 --AGAGAGAGAGAGAGAGCTC
*
590214 TGAGAGAGAGAGAGAG-T-
1 AGAGAGAGAGAGAGAGCTC
*
590231 -GGGAGAGAGAGAGAG-T-
1 AGAGAGAGAGAGAGAGCTC
*
590247 -GGGAGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
*
590265 AGAGAGATAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590284 AGAGAGAGAGAGAGAGCTGCTC
1 AGAGAGAGAGAGAGA---GCTC
* *
590306 AGAGAGGGGGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590325 AGAGAGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
* *
590344 --A-TG-CAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590359 ----AGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590374 ATGCAGAGAGAGAGAGAGCTC
1 A-G-AGAGAGAGAGAGAGCTC
**
590395 AGAGAGAGAGAGAGAG-AG
1 AGAGAGAGAGAGAGAGCTC
**
590413 AGAGATGAGAGAGAGAG-AG
1 AGAGA-GAGAGAGAGAGCTC
590432 AGAGAGAGAGAGAGATGCTC
1 AGAGAGAGAGAGAGA-GCTC
* *
590452 AGAGAGGGGGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590471 AGAGAGAGAGAGAGAG---
1 AGAGAGAGAGAGAGAGCTC
**
590487 AGAGAGCTCATGCAGAGAG---
1 AGAGAG-AGA-G-AGAGAGCTC
**
590506 AGAGAGAGAGAGAGAG-AA
1 AGAGAGAGAGAGAGAGCTC
* **
590524 AGAGAGAGATCAGAGAG-AG
1 AGAGAGAGA-GAGAGAGCTC
590543 AGAGAGAGAGAGAGTAGCTC
1 AGAGAGAGAGAGAG-AGCTC
* *
590563 AGAGAGGGGGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590582 AGAGAGAGAGAGAGAGAGCTCATGC
1 --AGAGAGAGAGAGAGAG--C-T-C
590607 AGAGAGAGAGAGAGAGCTC
1 AGAGAGAGAGAGAGAGCTC
590626 AGAGAGAGAGAG
1 AGAGAGAGAGAG
590638 GGAGAGAGAG
Statistics
Matches: 539, Mismatches: 47, Indels: 108
0.78 0.07 0.16
Matches are distributed among these distances:
14 1 0.00
15 30 0.06
16 83 0.15
17 44 0.08
18 31 0.06
19 222 0.41
20 31 0.06
21 56 0.10
22 22 0.04
23 17 0.03
24 1 0.00
25 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.44, T:0.06
Consensus pattern (19 bp):
AGAGAGAGAGAGAGAGCTC
Found at i:590665 original size:25 final size:24
Alignment explanation
Indices: 589999--590672 Score: 235
Period size: 25 Copynumber: 29.4 Consensus size: 24
589989 AGCGAGCTCA
*
589999 GAGAGAGAGCTCAGAGAGAGA-GA
1 GAGAGAGAGCTCAGAGAGAGAGGG
*
590022 GA-AGAGAG---AGAGAGAGA-GA
1 GAGAGAGAGCTCAGAGAGAGAGGG
**
590041 GAGAGAGAGCTTATGCAGAGAGAGAGCT
1 GAGAGAGAGC---T-CAGAGAGAGAGGG
* *
590069 CAGAGAGAG---AGAGAGAGAGAGA
1 GAGAGAGAGCTCAGAGAGAGAG-GG
590091 GAGAGAGAGCTCAGAGAGAGAGAGAGAG
1 GAGAGAGAGCTC--AGAGAGAGAG-G-G
*
590119 AGAGAGAGAGCTC--TGAGAGA---
1 -GAGAGAGAGCTCAGAGAGAGAGGG
* * *
590139 TAGAGAGAGCTGAGAGAGAGA-GA
1 GAGAGAGAGCTCAGAGAGAGAGGG
590162 GAGAGAGAGCTC--AGAGAGA---
1 GAGAGAGAGCTCAGAGAGAGAGGG
* *
590181 GAGAGAGAGCTCTGAGAGAGA-GA
1 GAGAGAGAGCTCAGAGAGAGAGGG
*
590204 GAGAGAGAGCTGAGAGAGAGAGAGAG
1 GAGAGAGAGCTCAGAGAGAGAG-G-G
* *
590230 TGGGAGAGAG---AGAGAGTG-GGAG
1 -GAGAGAGAGCTCAGAGAGAGAGG-G
590252 AGAGAGAGAGCTC--AGAGAGA---
1 -GAGAGAGAGCTCAGAGAGAGAGGG
*
590272 TAGAGAGAGCTCAGAGAGAGA---
1 GAGAGAGAGCTCAGAGAGAGAGGG
*
590293 GAGAGAGCTGCTC----AGAGAGGG
1 GAGAGAG-AGCTCAGAGAGAGAGGG
590314 G-GAGAGAGCTC--AGAGAGA---
1 GAGAGAGAGCTCAGAGAGAGAGGG
*
590332 GAGAGAGAGCTCATGCAGAGAGAGCTCAGA
1 GAGAGAGAGCTCA-G-AGAGAGAG----GG
*
590362 GAGAGAGAGCTCATG-CAGAGA---
1 GAGAGAGAGCTCA-GAGAGAGAGGG
*
590383 GAGAGAGAGCTCAGAGAGAGAGAGA
1 GAGAGAGAGCTCAGAGAGAGAG-GG
* * *
590408 GAGAGAGAGATGAGAGAGAGAGAGA
1 GAGAGAGAGCTCAGAGAGAGAG-GG
**
590433 GAGAGAGAG-AGAGATGCTCAGAGAGGG
1 GAGAGAGAGCTCAGA-G---AGAGAGGG
*
590460 G-GAGAGAGCTCAGAGAGAGAGAGA
1 GAGAGAGAGCTCAGAGAGAGAG-GG
*
590484 GAGAGAGAGCTCATGCAGAGAGA-GA
1 GAGAGAGAGCTCA-G-AGAGAGAGGG
* *
590509 GAGAGAGAG---AGAGAAAGAGAGA
1 GAGAGAGAGCTCAGAGAGAGAG-GG
* *
590531 GATCAGAGAG---AGAGAGAGA-GA
1 GA-GAGAGAGCTCAGAGAGAGAGGG
*
590552 GAGAG-TAGCTC--AGA--GAGGG
1 GAGAGAGAGCTCAGAGAGAGAGGG
590571 G-GAGAGAGCTCAGAGAGAGA---
1 GAGAGAGAGCTCAGAGAGAGAGGG
590591 GAGAGAGAGCTCATGCAGAGAGA---
1 GAGAGAGAGCTCA-G-AGAGAGAGGG
590614 GAGAGAGAGCTCAGAGAGAGAGAGG
1 GAGAGAGAGCTCAGAGAGAGAG-GG
590639 GAGAGAGAGCTCAGAGAGAGAGTGG
1 GAGAGAGAGCTCAGAGAGAGAG-GG
590664 GAGAGAGAG
1 GAGAGAGAG
590673 AAAGGGAAAG
Statistics
Matches: 523, Mismatches: 42, Indels: 170
0.71 0.06 0.23
Matches are distributed among these distances:
18 11 0.02
19 69 0.13
20 24 0.05
21 93 0.18
22 36 0.07
23 86 0.16
24 13 0.02
25 95 0.18
26 9 0.02
27 41 0.08
28 19 0.04
29 12 0.02
30 15 0.03
ACGTcount: A:0.41, C:0.08, G:0.45, T:0.06
Consensus pattern (24 bp):
GAGAGAGAGCTCAGAGAGAGAGGG
Found at i:591123 original size:75 final size:75
Alignment explanation
Indices: 591000--591146 Score: 294
Period size: 75 Copynumber: 2.0 Consensus size: 75
590990 TGAAAATTAA
591000 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG
1 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG
591065 TATCCTTATT
66 TATCCTTATT
591075 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG
1 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG
591140 TATCCTT
66 TATCCTT
591147 GAAACTTTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (75 bp):
AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG
TATCCTTATT
Found at i:592409 original size:21 final size:22
Alignment explanation
Indices: 592374--592415 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
592364 CTGCTCTAGC
* *
592374 TGTCCGATGCTTGGT-AAATAT
1 TGTCCGATCCATGGTGAAATAT
592395 TGTCCGATCCATGGTGAAATA
1 TGTCCGATCCATGGTGAAATA
592416 GTTCAACGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
TGTCCGATCCATGGTGAAATAT
Found at i:598056 original size:2 final size:2
Alignment explanation
Indices: 598051--598150 Score: 193
Period size: 2 Copynumber: 50.5 Consensus size: 2
598041 AGATTTAAAA
598051 TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
598092 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
598134 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
598151 NNNNNNNNNN
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 96 0.99
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:600027 original size:2 final size:2
Alignment explanation
Indices: 600020--600063 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
600010 NNNNNNNNNN
600020 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
600062 CT
1 CT
600064 GTGCTGAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:601489 original size:2 final size:2
Alignment explanation
Indices: 601482--601538 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
601472 AGGATAACAG
* *
601482 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
601524 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
601539 TTTAAACACT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.04, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:604349 original size:79 final size:80
Alignment explanation
Indices: 604209--604358 Score: 248
Period size: 79 Copynumber: 1.9 Consensus size: 80
604199 TTTAGGAAAT
* * * *
604209 ATATTGCCTTGTTTTTTGTTTTCAAAACACATATATAAGTTTTCGTTGTCTTCAGATTTGTCTTT
1 ATATTGCCTTGTTTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTCTTCAAACTTGTCTTT
604274 ACTAAGGTAATTTCC
66 ACTAAGGTAATTTCC
*
604289 ATATTGCCTTG-TTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTTTTCAAACTTGTCTTT
1 ATATTGCCTTGTTTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTCTTCAAACTTGTCTTT
604353 ACTAAG
66 ACTAAG
604359 ATATTTTCTA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 54 0.83
80 11 0.17
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (80 bp):
ATATTGCCTTGTTTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTCTTCAAACTTGTCTTT
ACTAAGGTAATTTCC
Found at i:607705 original size:1 final size:1
Alignment explanation
Indices: 607701--607726 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
607691 CTAACCAAAN
607701 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
607727 GCAATGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:611205 original size:174 final size:171
Alignment explanation
Indices: 610918--611253 Score: 573
Period size: 174 Copynumber: 1.9 Consensus size: 171
610908 AGTGATGAGA
* *
610918 AATTAATCTTTAATATTTTCAACTGTTTTTCAAGTCACTGGTCATAGGGTCTCTCAGATAACTGT
1 AATTAATCTTTAATATTTTCAACTGTTTTACAAGTCACTGGTCAGAGGGTCTCTCAGATAACTGT
*
610983 CCCTCTGAATACAAACGAGCTACTGAGATTCGATTGGCAGACAAGAAGTGTTAAATTGTGCGACC
66 CCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGACAAGAAGTGTTAAATTGTGCGACC
*
611048 CCATCAACAATGTGTGACCTACAGAAGATGTTACCCCAAAG
131 CCATCAACAATGTGTGACCTACAAAAGATGTTACCCCAAAG
*
611089 AATTAATCTTTCATATTTTCAACTGTTTTACAAGTCACTGGTCTTCAGAGGGTCTCTCAGATAAC
1 AATTAATCTTTAATATTTTCAACTGTTTTACAAGTCACTGG---TCAGAGGGTCTCTCAGATAAC
* *
611154 TGTCCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGGCAAGAAGTGTTACATTGTGCG
63 TGTCCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGACAAGAAGTGTTAAATTGTGCG
*
611219 ACCCCATCAACAATGTGTGACCTACAAAAGGTGTT
128 ACCCCATCAACAATGTGTGACCTACAAAAGATGTT
611254 CCTCCAAGGT
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
171 39 0.25
174 115 0.75
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (171 bp):
AATTAATCTTTAATATTTTCAACTGTTTTACAAGTCACTGGTCAGAGGGTCTCTCAGATAACTGT
CCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGACAAGAAGTGTTAAATTGTGCGACC
CCATCAACAATGTGTGACCTACAAAAGATGTTACCCCAAAG
Found at i:615230 original size:34 final size:34
Alignment explanation
Indices: 615187--615373 Score: 123
Period size: 35 Copynumber: 5.5 Consensus size: 34
615177 ATCTACCCGC
* *
615187 TGGTGTCAACCCGGGTCCCTGCAATTAAA-CCTGA
1 TGGTGTCAACCCGGGTCCATGC-ATTAAATCCGGA
* * *
615221 TGGTGTCAACCCAGGTTCCATTCCTTAAATCCGGA
1 TGGTGTCAACCC-GGGTCCATGCATTAAATCCGGA
* * * *
615256 TGGTGTCAACCCGGGAACCATTCCTTAAATCCCGA
1 TGGTGTCAACCCGGG-TCCATGCATTAAATCCGGA
*** * *
615291 TGGTGTCAA-CCGGGGAAATACGCTTTAAATCCCGA
1 TGGTGTCAACCCGGGTCCAT--GCATTAAATCCGGA
* * *
615326 TGGTGTCAACCCGGGAACCAT-TATT-AA-CCCGA
1 TGGTGTCAACCCGGG-TCCATGCATTAAATCCGGA
*
615358 CGGTGTCAACCCGGGT
1 TGGTGTCAACCCGGGT
615374 TTCTTAAGTT
Statistics
Matches: 126, Mismatches: 20, Indels: 17
0.77 0.12 0.10
Matches are distributed among these distances:
32 19 0.15
33 4 0.03
34 26 0.21
35 70 0.56
36 5 0.04
37 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (34 bp):
TGGTGTCAACCCGGGTCCATGCATTAAATCCGGA
Found at i:615265 original size:35 final size:35
Alignment explanation
Indices: 615219--615369 Score: 159
Period size: 35 Copynumber: 4.4 Consensus size: 35
615209 AATTAAACCT
** *
615219 GATGGTGTCAACCCAGGTTCCATTCCTTAAATCCG
1 GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC
*
615254 GATGGTGTCAACCCGGGAACCATTCCTTAAATCCC
1 GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC
** *
615289 GATGGTGTCAACCGGGGAA--ATACGCTTTAAATCCC
1 GATGGTGTCAACCCAGGAACCATTC-C-TTAAATCCC
* *
615324 GATGGTGTCAACCCGGGAACCATT-ATT-AA-CCC
1 GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC
*
615356 GACGGTGTCAACCC
1 GATGGTGTCAACCC
615370 GGGTTTCTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
32 16 0.16
33 5 0.05
34 3 0.03
35 76 0.75
37 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (35 bp):
GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC
Found at i:616356 original size:18 final size:16
Alignment explanation
Indices: 616335--616372 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
616325 ATTGTATTTA
616335 TTTTGTTTTTTGTTTATT
1 TTTTG-TTTTTGTTT-TT
616353 TTTTGTTTTTGTTTTT
1 TTTTGTTTTTGTTTTT
616369 TTTT
1 TTTT
616373 CTAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.87
Consensus pattern (16 bp):
TTTTGTTTTTGTTTTT
Found at i:616361 original size:17 final size:16
Alignment explanation
Indices: 616331--616372 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
616321 AAAAATTGTA
*
616331 TTTATTTTGTTTTTTG
1 TTTATTTTTTTTTTTG
616347 TTTATTTTTTGTTTTTG
1 TTTATTTTTT-TTTTTG
616364 TTT-TTTTTT
1 TTTATTTTTT
616373 CTAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.05, C:0.00, G:0.10, T:0.86
Consensus pattern (16 bp):
TTTATTTTTTTTTTTG
Found at i:617389 original size:141 final size:141
Alignment explanation
Indices: 617184--617517 Score: 461
Period size: 141 Copynumber: 2.4 Consensus size: 141
617174 AAACTAAATA
* *
617184 GCTAACAACTAAAGCTAGCTAGAATAATTTACTAATTAAGCTAGAGGACTAACAACTAGAGCTAG
1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACTAGAGCTAG
* * * *
617249 TTGGAAAATAAAACTAGGTAAGCTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG
66 TTCGAAAATAAAACGAAGTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG
617314 TTAGTTAAAGG
131 TTAGTTAAAGG
* * * * *
617325 GTTAACAACTAAAGCTAGCTAGAATAATATACTAATTCAGCTAGAGGGTTAACAACTTGTGCTAG
1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACTAGAGCTAG
** ** * * * * *
617390 TTCGATTATAATTCGAATTAAACTAAAGGTCTACCAACTATAGCTAGTTAAAAAATAAAACCAGG
66 TTCGAAAATAAAACGAAGTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG
617455 TTAGTTAAAGG
131 TTAGTTAAAGG
* * *
617466 GCTAACAACTAAAGCTAGCTAGAGTAATCTACTAATTAAGCTAAAGGGCTAA
1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAA
617518 AAACCGAAGC
Statistics
Matches: 167, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
141 167 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (141 bp):
GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACTAGAGCTAG
TTCGAAAATAAAACGAAGTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG
TTAGTTAAAGG
Found at i:617511 original size:47 final size:47
Alignment explanation
Indices: 617136--617610 Score: 286
Period size: 47 Copynumber: 10.1 Consensus size: 47
617126 GTAGCTACAA
* * * *
617136 GGCTAACAACTAGAGCTAG-TCAGATTATAA-A-ACGAATTAAACTAAAT
1 GGCTAACAACTAAAGCTAGCT-AGA--ATAATATACTAATTAAGCTAAAG
* * *
617183 AGCTAACAACTAAAGCTAGCTAGAATAATTTACTAATTAAGCTAGAG
1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG
* * * * * **
617230 GACTAACAACTAGAGCTAGTTGGAA-AATAAAACTAGGTAAGCTAAAG
1 GGCTAACAACTAAAGCTAGCTAGAATAAT-ATACTAATTAAGCTAAAG
* * * * * * *
617277 GGCTAACAACTAGAGCTAG-TAAAAAAATAAAACCAGGTT-AGTTAAAG
1 GGCTAACAACTAAAGCTAGCTAGAATAAT-ATACTA-ATTAAGCTAAAG
* * *
617324 GGTTAACAACTAAAGCTAGCTAGAATAATATACTAATTCAGCTAGAG
1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG
* *** * * * *
617371 GGTTAACAACTTGTGCTAGTTCGATTATAAT-T-CGAATTAAACTAAAG
1 GGCTAACAACTAAAGCTAGCTAGA--ATAATATACTAATTAAGCTAAAG
* * * * * * * * *
617418 GTCTACCAACTATAGCTAGTTA-AAAAATAAAACCAGGTT-AGTTAAAG
1 GGCTAACAACTAAAGCTAGCTAGAATAAT-ATACTA-ATTAAGCTAAAG
* *
617465 GGCTAACAACTAAAGCTAGCTAGAGTAATCTACTAATTAAGCTAAAG
1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG
* ** * * *
617512 GGCTAAAAACCGAAGCTAGCTAGAATAATCTACTAATTAGGCTAGAG
1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG
* * * * * * *
617559 AGCTAACAACTAAAACTAGCTAAAATAATCTACTAAATAAACTAAAA
1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG
617606 GGCTA
1 GGCTA
617611 CCAGCTAGAT
Statistics
Matches: 329, Mismatches: 83, Indels: 32
0.74 0.19 0.07
Matches are distributed among these distances:
44 4 0.01
45 4 0.01
46 11 0.03
47 288 0.88
48 17 0.05
49 5 0.02
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (47 bp):
GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG
Found at i:617550 original size:141 final size:140
Alignment explanation
Indices: 617184--617570 Score: 431
Period size: 141 Copynumber: 2.7 Consensus size: 140
617174 AAACTAAATA
* * *
617184 GCTAACAACTAAAGCTAGCTAGAATAATTTACTAATTAAGCTAGAGGACTAACAA-CTAGAGCTA
1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACCGA-AGCTA
* * ** *
617248 GTTGGAA-AATAAAACTAGGTAAGCTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCA
65 GTTAGAATAAT--TACTAATTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCA
617312 GGTTAGTTAAAGG
128 GGTTAGTTAAAGG
* * * * *
617325 GTTAACAACTAAAGCTAGCTAGAATAATATACTAATTCAGCTAGAGGGTTAACAACTTG-TGCTA
1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAAC-CGAAGCTA
* * * * * *
617389 GTTCGATTATAATT-CGAATTAAACTAAAGGTCTACCAACTATAGCTAGTTAAAAAATAAAACCA
65 GTTAGA--ATAATTACTAATTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCA
617453 GGTTAGTTAAAGG
128 GGTTAGTTAAAGG
* * * *
617466 GCTAACAACTAAAGCTAGCTAGAGTAATCTACTAATTAAGCTAAAGGGCTAAAAACCGAAGCTAG
1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACCGAAGCTAG
* ** * *
617531 CTAGAATAATCTACTAATTAGGCTAGAGAGCTAACAACTA
66 TTAGAATAAT-TACTAATTAAACTAAAGGGCTAACAACTA
617571 AAACTAGCTA
Statistics
Matches: 202, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
139 5 0.02
140 2 0.01
141 191 0.95
143 1 0.00
144 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (140 bp):
GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACCGAAGCTAG
TTAGAATAATTACTAATTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGGT
TAGTTAAAGG
Found at i:620121 original size:28 final size:28
Alignment explanation
Indices: 620089--620344 Score: 275
Period size: 28 Copynumber: 9.1 Consensus size: 28
620079 ATTAGCTAAT
* **
620089 TTATGTTCTGATCGTGAAGTAAACTGAC
1 TTATGTACTGATCGTTTAGTAAACTGAC
** *
620117 TTATGTACTGATCGTGAAGTCAACTGAC
1 TTATGTACTGATCGTTTAGTAAACTGAC
* *
620145 TTATGTTCTAATCGTTTAGTAAACTGAC
1 TTATGTACTGATCGTTTAGTAAACTGAC
*
620173 TT-TAGTACTGATCGTTTAGTAAACATTA-
1 TTAT-GTACTGATCGTTTAGTAAAC-TGAC
* * *
620201 TAATGTACTGATCGTTAAGTAAATTGAC
1 TTATGTACTGATCGTTTAGTAAACTGAC
*
620229 TTATGTACTGATCATTTAGTAAACT-AC
1 TTATGTACTGATCGTTTAGTAAACTGAC
*
620256 GTTATGTACTGATCGTTCAGTAAACTGAC
1 -TTATGTACTGATCGTTTAGTAAACTGAC
* * * *
620285 TAAGGTACTGATCGTTTAGTAAAATAAC
1 TTATGTACTGATCGTTTAGTAAACTGAC
* * *
620313 TTTTATACTGATCGTTTAGAAAACTGAC
1 TTATGTACTGATCGTTTAGTAAACTGAC
620341 TTAT
1 TTAT
620345 AATTATACTT
Statistics
Matches: 189, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
27 5 0.03
28 179 0.95
29 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (28 bp):
TTATGTACTGATCGTTTAGTAAACTGAC
Found at i:620178 original size:14 final size:16
Alignment explanation
Indices: 620155--620196 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
620145 TTATGTTCTA
620155 ATCGTTTAGTAAACTG
1 ATCGTTTAGTAAACTG
620171 A-C-TTTAGT--ACTG
1 ATCGTTTAGTAAACTG
620183 ATCGTTTAGTAAAC
1 ATCGTTTAGTAAAC
620197 ATTATAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
12 5 0.23
13 1 0.05
14 12 0.55
15 1 0.05
16 3 0.14
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (16 bp):
ATCGTTTAGTAAACTG
Found at i:620581 original size:25 final size:25
Alignment explanation
Indices: 620552--620599 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
620542 GCTCATTTTG
* *
620552 AATTAACTCCTGTGTTGCTCTTGAT
1 AATTAACTCCTGTGCTGCACTTGAT
**
620577 AATTAGGTCCTGTGCTGCACTTG
1 AATTAACTCCTGTGCTGCACTTG
620600 TTAAGAAGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (25 bp):
AATTAACTCCTGTGCTGCACTTGAT
Found at i:620996 original size:2 final size:2
Alignment explanation
Indices: 620989--621053 Score: 75
Period size: 2 Copynumber: 34.5 Consensus size: 2
620979 AAACATTGAA
* *
620989 AG AG AG AG AG AG AG A- AA AG -G AG AG AG AG AG AG AG A- AA AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
621028 -G AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
621054 AAGAAATTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:621014 original size:20 final size:20
Alignment explanation
Indices: 620989--621043 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
620979 AAACATTGAA
620989 AGAGAGAGAGAGAGAAAAGG
1 AGAGAGAGAGAGAGAAAAGG
621009 AGAGAGAGAGAGAGAAAAGG
1 AGAGAGAGAGAGAGAAAAGG
621029 AGAGAGAGAGAGAGA
1 AGAGAGAGAGAGAGA
621044 GAGAAAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (20 bp):
AGAGAGAGAGAGAGAAAAGG
Found at i:621058 original size:10 final size:10
Alignment explanation
Indices: 620986--621059 Score: 66
Period size: 10 Copynumber: 7.4 Consensus size: 10
620976 ATAAAACATT
620986 GAAAGAGAGA
1 GAAAGAGAGA
620996 G--AGAGAGA
1 GAAAGAGAGA
621004 -AAAG-GAGA
1 GAAAGAGAGA
*
621012 GAGAGAGAGA
1 GAAAGAGAGA
621022 GAAAAGGAGAGA
1 G-AAA-GAGAGA
621034 GAGAGAGAGAGA
1 GA-A-AGAGAGA
*
621046 GAAAGAGAAA
1 GAAAGAGAGA
621056 GAAA
1 GAAA
621060 TTCTTTCAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
8 11 0.21
9 5 0.09
10 16 0.30
11 4 0.08
12 16 0.30
13 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
GAAAGAGAGA
Found at i:629632 original size:3 final size:3
Alignment explanation
Indices: 629626--629651 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
629616 CGGGGAAAAA
629626 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
629652 AAAGAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:634241 original size:161 final size:161
Alignment explanation
Indices: 633976--634309 Score: 562
Period size: 161 Copynumber: 2.1 Consensus size: 161
633966 AACATCCACA
* * * *
633976 AAGAAAATGAACGTAAACTTCAAATAACTGGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTCA
1 AAGAAAATGAGCGTAAACTGCAAACAACTAGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTCA
634041 AAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATACC
66 AAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATACC
634106 AAATTTCATTTCAATATGTTCATCATCTGCG
131 AAATTTCATTTCAATATGTTCATCATCTGCG
* *
634137 AAGAAAATGAGCAG-AAACTGCAAACAACTAGAATTTTCCTACGTCCATGGGCCATAACTCTGTC
1 AAGAAAATGAGC-GTAAACTGCAAACAACTAGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTC
* * *
634201 GAAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATTATAAACCTGTATAC
65 AAAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATAC
*
634266 CAAATTTCATTTCAATATGTTCATCCTCTGCG
130 CAAATTTCATTTCAATATGTTCATCATCTGCG
634298 AAGAAAATGAGC
1 AAGAAAATGAGC
634310 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
161 161 0.99
162 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (161 bp):
AAGAAAATGAGCGTAAACTGCAAACAACTAGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTCA
AAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATACC
AAATTTCATTTCAATATGTTCATCATCTGCG
Found at i:641490 original size:28 final size:28
Alignment explanation
Indices: 641456--643519 Score: 1998
Period size: 28 Copynumber: 73.8 Consensus size: 28
641446 ATTAGGACTT
*
641456 TTTACAGTACTGTCATTGTGTCAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * **
641484 TTTACAGTACTGGCACTGTGTCAAAACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
641512 -TTACCAGTACTGGCACTGTGTCAGGAC-
1 TTTA-CAGTACTGTCATTGTGTTAGGACA
*
641539 TTTAACTA-TACTGTCATTGTGTTAGGGCA
1 TTT-AC-AGTACTGTCATTGTGTTAGGACA
* * *
641568 TTTACAGTATTTTCATTGTGTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * * *
641596 TTTACAGTATTGCCATCGTGTTCGGACT
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
641624 TTTACTGTACTGTCATTGTGTCAGGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
641652 TTTACAGTACTGTCATTGTGTTATGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
641680 TTTACAGTACTGGCATTGTGTTAAGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
641708 TTTACAGTACTGTCATTGTGTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
641736 TTTACAGTATTTTCATTGTGTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * *
641764 TTTACAGTATTGTCATCGTGTTCGGACT
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
641792 TTTACTGTACTGTCATTGTGTCAGGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
641820 TTAACAGTACTGTCATTGTGTTATGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
641848 TTTACAGTACTGGCATTGTGTTAAGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
641876 TTTACAGTACTGTCATTATGTTAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
641904 TTTACAGTACTGTCATT-T-TTGAAGGAC-
1 TTTACAGTACTGTCATTGTGTT--AGGACA
* * *
641931 TTTACTGTACTGTCATTGTTTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * * * *
641959 TTTAAAGTACTGCCGTTGTATTTGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * * * *
641987 TTTACAGTAATATTATTGTGTAATGA-T
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
642014 TTTACTGTACTGTCATTGTGTCAGGAGA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
642042 TTAACAGTACTATCACTGTGTTAGGAC-
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
642069 TTTAACGGTACTGTCATTGTGTAAGGACT
1 TTT-ACAGTACTGTCATTGTGTTAGGACA
* * * *
642098 TTTCCTGTACTGTCATTTTGTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
642126 TTTACAGTACTGTCATTGTGTTAAGG-CA
1 TTTACAGTACTGTCATTGTGTT-AGGACA
*
642154 TTTACAGTACTGTCATTGTGTTAAGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642182 TTTACAGTGCTGTCATTGTGTAAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
642210 TTTACAGTACTGTCATTATGTTAAGG-CA
1 TTTACAGTACTGTCATTGTGTT-AGGACA
* * *
642238 TTTACAGAACTGTTATTGTGTTATGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
642266 TTTACAGTACTGTCATTATGTTAGGGCT
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642294 TTTACTGTACTGTCATTGTGTCAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
642322 TTAACAGTGCTGTCATTGTGTTAGGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
** *
642350 ACTGCAGTACTGTCATTGTGTTAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642378 TTTACAGTACTGTCGTTGTGGTAAGG-CA
1 TTTACAGTACTGTCATTGT-GTTAGGACA
* * * *
642406 TTAATAGTACTGTTATTGTGTTAGGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * *
642434 TTTACAATACTGTCATTGCGTCAGAACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * *
642462 TTTAAAGTATTGTCATTGTGCTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * **
642490 TTTACTGTACTGTCCTTGTGTTAGGGTA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642518 TTTACAGTACTGGCATTGTGTAAGGA-A
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642545 TTTTACTGTACTGTCATTGTGTCAGGAC-
1 -TTTACAGTACTGTCATTGTGTTAGGACA
* * ** * * *
642573 TTTAACGGTTCTAACATTCTGTAAGGACT
1 TTT-ACAGTACTGTCATTGTGTTAGGACA
* * * * *
642602 TTTAC-TTAAATGTCATTTTGTTAGGGCT
1 TTTACAGT-ACTGTCATTGTGTTAGGACA
* *
642630 TTTACAGTTCTGTCATTGTGTTAAGG-CT
1 TTTACAGTACTGTCATTGTGTT-AGGACA
*
642658 TTTACAGTACTGTCATTGTGGTAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
642686 TTTAACTA-TACTGTCATTGTGTTATGACA
1 TTT-AC-AGTACTGTCATTGTGTTAGGACA
*
642715 TTTACAGTACTGTCATTGTGTAAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
642743 TTTACAGTACTGTCAATGTGTTATGG-CA
1 TTTACAGTACTGTCATTGTGTTA-GGACA
* * *
642771 TTTACAGTACTATTATTGTGTTATGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642799 TTTACAGTGCTGTCATTGCGTTAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
642827 TTTACAGTACTGTCATTGTGTAAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
** *
642855 TTTACAACACTGTCAATGTGTTAAGG-CA
1 TTTACAGTACTGTCATTGTGTT-AGGACA
* * *
642883 TTTAAAGTACTGTTATTGTGTTATGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642911 TTTACAGTACTGTCATTGTGTTAGGGCT
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
642939 TTTACTGTACTGTCATTGTGTCAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * * *
642967 TTAACAGTGCTGTCATTGTGTCAAGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
** * * *
642995 ACTGCAGTACTGTCATTGTGTAAGCACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
643023 TTTAAAGTATTGTCATTGTGTAAGGA-A
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
643050 TTTAACTGTACTGTCATTGTGTTAGGAC-
1 TTT-ACAGTACTGTCATTGTGTTAGGACA
* *
643078 TTTAACAGTACTGGCATTGTGTAAGGA-A
1 TTT-ACAGTACTGTCATTGTGTTAGGACA
** * *
643106 TTTATTGTACTGTCATTGTGTAAGGACT
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * **
643134 TTTACTA-TAATGTCATTTTGTTAGGGTA
1 TTTAC-AGTACTGTCATTGTGTTAGGACA
*
643162 TTTACAGTACTGTCATTGTGTTAGGACT
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * *
643190 TTTACTGCACTGTCATTGTGTCAGGACC
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
643218 TTAACAGTACTGTCATTGTGTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * * *
643246 ATTACAGTGCTGTCATTGTGTCAGGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
643274 TTTGA-AGTACTGTCATTTTGTTAGGACA
1 TTT-ACAGTACTGTCATTGTGTTAGGACA
* * *
643302 TTTACAGTACTGTCAATGTGTTGGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
643330 TTAACAGTAGTGTCATTTTGTTAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
643358 TTTACAATACTGTCATTGTGTCAGGATA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
643386 TTTACAGTACTGTCATTGTGTCAGGACA
1 TTTACAGTACTGTCATTGTGTTAGGACA
* *
643414 TTTACAGTACTGTTATTGTGTAAGGAC-
1 TTTACAGTACTGTCATTGTGTTAGGACA
* * *
643441 TTTCACTGTACTGTCATTATGTCAGGACA
1 TTT-ACAGTACTGTCATTGTGTTAGGACA
* *
643470 TTTACAGTACTGTCTTTGTGTTAGGGCA
1 TTTACAGTACTGTCATTGTGTTAGGACA
*
643498 TTTACAGTACCGTCATTGTGTT
1 TTTACAGTACTGTCATTGTGTT
643520 GAATGTCAGG
Statistics
Matches: 1656, Mismatches: 335, Indels: 90
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.00
27 97 0.06
28 1495 0.90
29 61 0.04
30 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (28 bp):
TTTACAGTACTGTCATTGTGTTAGGACA
Found at i:646197 original size:18 final size:19
Alignment explanation
Indices: 646162--646197 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
646152 CCCCATGTGG
646162 GGCCAAATATGCAAAAAAA
1 GGCCAAATATGCAAAAAAA
*
646181 GGCCAAATTTG-AAAAAA
1 GGCCAAATATGCAAAAAA
646198 TCTTCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (19 bp):
GGCCAAATATGCAAAAAAA
Found at i:646436 original size:168 final size:167
Alignment explanation
Indices: 646250--646977 Score: 907
Period size: 168 Copynumber: 4.4 Consensus size: 167
646240 CATAGTCATA
*
646250 ATGTCCATGAAA-CCCTCTACCACAATTGTGAAATTCATGCCCCCTGGGTCAGGGGTTCAGGCTC
1 ATGTCCAT-AAAGCCCTCTACCA-AATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTC
* * * *
646314 TAGGGTAGGGCCAATATTGCCATAAAGTTAAAATGTATTAAATCTTAGAAAATCTACTTCTCTAC
64 TAGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTAC
*
646379 TCCCATATATATTTGTTAAAAACTAAATGCATAATTATA
129 TCCCATATATATTTGTTAAAAACTAAATGCATAATTATG
* *
646418 ATGTCCATAAAGCCCTCTACCTAAATCGTGAAATTCATGACCCCTGGGTCAAGGGTTCAGGCTCT
1 ATGTCCATAAAGCCCTCTACC-AAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCT
*
646483 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTTC
65 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAG-AAAATCTTCTTCTCTAC
646548 TCCCATATATATTTGTTAAAAACTAAATGCA-AA--ATG
129 TCCCATATATATTTGTTAAAAACTAAATGCATAATTATG
* * * *
646584 ATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCGTGACCCCTGGGTCAGGGGTTCAGGATCT
1 ATGTCCATAAAGCCCTCTAC-CAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCT
*
646649 AGGGTGGGGTCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT
65 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT
* * **
646714 CCCATATACATTTGTTAAAAACTAAATGCCTGGTTATG
130 CCCATATATATTTGTTAAAAACTAAATGCATAATTATG
* * * * * ** *
646752 ATGTCCATGAGGCCCTCTAACAAAATTGTGAAATTCTTAACCCCTTTGTTAGGGGTTCAGGCTCT
1 ATGTCCATAAAGCCCTCT-ACCAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCT
* * * * * *
646817 AGGGTTGAGCCAATATGGCCTTATAG--AAAATGTTTTTAATCTTAAAAAATCTTCTTCTCTACT
65 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT
* * * ** ** * **
646880 CCC-CACATGTGAGCAAAAAACTAAATACATGGTTATG
130 CCCATATATATTTGTTAAAAACTAAATGCATAATTATG
* * *
646917 ATGTCCACT-AA-CTCCTCTACCTAAATTATGAAATTCATGGCCCCTGGGTCGGGGGTTCAGG
1 ATGTCCA-TAAAGC-CCTCTACC-AAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG
646978 ACATCGGGGG
Statistics
Matches: 494, Mismatches: 55, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
164 3 0.01
165 113 0.23
166 144 0.29
167 3 0.01
168 182 0.37
169 49 0.10
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (167 bp):
ATGTCCATAAAGCCCTCTACCAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTA
GGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTC
CCATATATATTTGTTAAAAACTAAATGCATAATTATG
Found at i:647069 original size:333 final size:332
Alignment explanation
Indices: 646250--647066 Score: 866
Period size: 334 Copynumber: 2.5 Consensus size: 332
646240 CATAGTCATA
* * * * * *
646250 ATGTCCATGAAACCCTCTACCACAATTGTGAAATTCATGCCCCCTGGGTCAGGGGTTCAGGCTCT
1 ATGTCCATGAAGCCCTCTACTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGATCT
* * * * * * *
646315 AGGGTAGGGCCAATATTGCCATAAAGTTAAAATGTATTAAATCTTAGAAAATCTACTTCTCTACT
66 AGGGTGGGGACAATATGGCAATATAGTTAAAATGCATTAAATCTTAGAAAATCTTCTTCTCTACT
* * * * *
646380 CCCATATATATTTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTACCTAAATC
131 CCCA-ACACATCTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTAACAAAATC
* *
646445 GTGAAATTCATGACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGT
195 GTGAAATTCATAACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGAGCCAATATGGCCATATAG-
* * * ** **
646510 TAAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTTCTCCCATATATATTTGTTAAAAACTAAA
259 TAAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTACTCCCACACATATGAGCAAAAAACTAAA
*
646575 TGCAAAATG
324 TACAAAATG
* *
646584 ATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCGTGACCCCTGGGTCAGGGGTTCAGGATCT
1 ATGTCCATGAAGCCCTCTACTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGATCT
* * *
646649 AGGGTGGGGTCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT
66 AGGGTGGGGACAATATGGCAATATAGTTAAAATGCATTAAATCTTAGAAAATCTTCTTCTCTACT
* * * ** * * * *
646714 CCCATATACATTTGTTAAAAACTAAATGCCTGGTTATGATGTCCATGAGGCCCTCTAACAAAATT
131 CCCA-ACACATCTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTAACAAAATC
* ** * * * *
646779 GTGAAATTCTTAACCCCTTTGTTAGGGGTTCAGGCTCTAGGGTTGAGCCAATATGGCCTTATAG-
195 GTGAAATTCATAACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGAGCCAATATGGCCATATAGT
* * *
646843 AAAATGTTTTTAATCTTA-AAAAATCTTCTTCTCTACTCCC-CACATGTGAGCAAAAAACTAAAT
260 AAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTACTCCCACACATATGAGCAAAAAACTAAAT
**
646906 ACATGGTTATG
325 ACA---AAATG
* *
646917 ATGTCCACT-AA-CTCCTCTACCT-AAATTATGAAATTCATGGCCCCTGGGTCGGGGGTTCAGGA
1 ATGTCCA-TGAAGC-CCTCTA-CTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGA
* * *
646979 -CATCGGG-GGAGGACAATATGGCAATATAGTGT-AAATGCA-TATAATGTTTA-AAAATTTTCT
63 TC-TAGGGTGG-GGACAATATGGCAATATAGT-TAAAATGCATTA-AAT-CTTAGAAAATCTTCT
* *
647039 TCTCTATTCTC-ACACATCTGTATAAAAA
123 TCTCTACTCCCAACACATCTGT-TAAAAA
647067 ACTGACTAAT
Statistics
Matches: 414, Mismatches: 57, Indels: 26
0.83 0.11 0.05
Matches are distributed among these distances:
330 18 0.04
331 29 0.07
332 28 0.07
333 103 0.25
334 236 0.57
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (332 bp):
ATGTCCATGAAGCCCTCTACTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGATCT
AGGGTGGGGACAATATGGCAATATAGTTAAAATGCATTAAATCTTAGAAAATCTTCTTCTCTACT
CCCAACACATCTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTAACAAAATCG
TGAAATTCATAACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGAGCCAATATGGCCATATAGTA
AAATGTATTAAATCTTAGAAAAATCTTCTTCTCTACTCCCACACATATGAGCAAAAAACTAAATA
CAAAATG
Found at i:647766 original size:29 final size:29
Alignment explanation
Indices: 647724--647879 Score: 249
Period size: 29 Copynumber: 5.4 Consensus size: 29
647714 GCCAAAAAAC
647724 TATCGTGATACTGAGAAATATCTATACAT
1 TATCGTGATACTGAGAAATATCTATACAT
* *
647753 TATCGTGATACTGAGATATATCTATACCT
1 TATCGTGATACTGAGAAATATCTATACAT
*
647782 AATCGTGATACTGAGAAATATCTATACAT
1 TATCGTGATACTGAGAAATATCTATACAT
* *
647811 TATCGTGATACGGACAAATATCTATACAT
1 TATCGTGATACTGAGAAATATCTATACAT
* *
647840 TATCGTGATACGGACAAATATCTATACAT
1 TATCGTGATACTGAGAAATATCTATACAT
647869 TATCGTGATAC
1 TATCGTGATAC
647880 GGACAATCGT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 119 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (29 bp):
TATCGTGATACTGAGAAATATCTATACAT
Found at i:647918 original size:29 final size:29
Alignment explanation
Indices: 647885--648488 Score: 709
Period size: 29 Copynumber: 21.0 Consensus size: 29
647875 GATACGGACA
* *
647885 ATCGTAATACTGACAAATATCTAAACATT
1 ATCGTGATACTGACAAATATCTATACATT
*
647914 ATCGTGATACTGAAAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
* *
647943 ATCGTGATACTTACAAATATCTATACATC
1 ATCGTGATACTGACAAATATCTATACATT
* *
647972 ATCGTGATACGGAC--A-ATCGTGATAC-TG
1 ATCGTGATACTGACAAATATC-T-ATACATT
** * * **
647999 A-C-AAATATCT-ATACATCATCGTGATACGGACA
1 ATCGTGATA-CTGACAAAT-ATC-T-ATAC--ATT
648031 ATCGTGATACTGACAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
* *
648060 ATCGTAATACTGACAAATATCTAAACATT
1 ATCGTGATACTGACAAATATCTATACATT
* *
648089 ATCGTGATACTGAAAAATATATATACATT
1 ATCGTGATACTGACAAATATCTATACATT
*
648118 ATCGTGATACTGACAAATATCTATACATC
1 ATCGTGATACTGACAAATATCTATACATT
*
648147 ATCGTGATACTGACAAATATCTATACATC
1 ATCGTGATACTGACAAATATCTATACATT
* * *
648176 ATCGTGATACGGAC--A-ATC-GT-GA-T
1 ATCGTGATACTGACAAATATCTATACATT
* * *
648199 A-CG-GACAAAT-ACAATGTATCTATACATT
1 ATCGTGA-TACTGACAA-ATATCTATACATT
*
648227 ATCGTGATACGGACAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
648256 ATCGTGATACTGACAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
*
648285 ATCGTGATACGGACAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
648314 ATCGTGATACTGACAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
648343 ATCGTGATACTGACAAATATCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
*
648372 ATCGTGATACTGACAAATAGCTATACATT
1 ATCGTGATACTGACAAATATCTATACATT
*
648401 ATCGTGATACTGACAAATATCTATGCATT
1 ATCGTGATACTGACAAATATCTATACATT
* *
648430 ATCGTCATACTGACAAATATCTATGCATT
1 ATCGTGATACTGACAAATATCTATACATT
* *
648459 ATCGTCATACTGACAAATATCTATGCATT
1 ATCGTGATACTGACAAATATCTATACATT
648488 A
1 A
648489 ATAAAAATGA
Statistics
Matches: 500, Mismatches: 51, Indels: 48
0.83 0.09 0.08
Matches are distributed among these distances:
21 4 0.01
22 3 0.01
23 1 0.00
24 1 0.00
25 8 0.02
26 9 0.02
27 7 0.01
28 6 0.01
29 436 0.87
30 6 0.01
31 4 0.01
32 2 0.00
33 6 0.01
34 7 0.01
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (29 bp):
ATCGTGATACTGACAAATATCTATACATT
Found at i:647932 original size:73 final size:73
Alignment explanation
Indices: 647812--648098 Score: 359
Period size: 73 Copynumber: 3.9 Consensus size: 73
647802 TCTATACATT
* *
647812 ATCGTGATACGGACAAATATCTATACATTATCGTGATACGGACAAATATCTATACATTATCGTGA
1 ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA
647877 TACGGACA
66 TACGGACA
* * *
647885 ATCGTAATACTGACAAATATCTAAACATTATCGTGATACTGAAAAATATCTATACATTATCGTGA
1 ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA
**
647950 TACTTACA
66 TACGGACA
* * * ** *
647958 A--AT-AT-CT-ATACATCATCGTGATACGGACAATCGTGATACTGACAAATATCTATACATCAT
1 ATCGTGATACTGACAAAT-ATC-T-ATAC--ATTATCGTGATACTGACAAATATCTATACATTAT
648018 CGTGATACGGACA
61 CGTGATACGGACA
* *
648031 ATCGTGATACTGACAAATATCTATACATTATCGTAATACTGACAAATATCTAAACATTATCGTGA
1 ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA
648096 TAC
66 TAC
648099 TGAAAAATAT
Statistics
Matches: 179, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
68 4 0.02
69 5 0.03
70 3 0.02
71 4 0.02
73 146 0.82
75 5 0.03
76 3 0.02
77 5 0.03
78 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (73 bp):
ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA
TACGGACA
Found at i:647992 original size:15 final size:15
Alignment explanation
Indices: 647972--648046 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
647962 TCTATACATC
647972 ATCGTGATACGGACA
1 ATCGTGATACGGACA
*
647987 ATCGTGATACTGACAAA
1 ATCGTGATACGGAC--A
648004 TATC-T-ATAC--ATC-
1 -ATCGTGATACGGA-CA
648016 ATCGTGATACGGACA
1 ATCGTGATACGGACA
*
648031 ATCGTGATACTGACA
1 ATCGTGATACGGACA
648046 A
1 A
648047 ATATCTATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
11 3 0.06
12 1 0.02
13 4 0.08
14 2 0.04
15 30 0.61
16 4 0.08
17 2 0.04
18 3 0.06
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (15 bp):
ATCGTGATACGGACA
Found at i:648006 original size:44 final size:44
Alignment explanation
Indices: 647943--648075 Score: 230
Period size: 44 Copynumber: 3.0 Consensus size: 44
647933 TCTATACATT
*
647943 ATCGTGATACTTACAAATATCTATACATCATCGTGATACGGACA
1 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA
647987 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA
1 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA
* * *
648031 ATCGTGATACTGACAAATATCTATACATTATCGTAATACTGACA
1 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA
648075 A
1 A
648076 ATATCTAAAC
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 85 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (44 bp):
ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA
Found at i:648107 original size:146 final size:146
Alignment explanation
Indices: 647841--648133 Score: 478
Period size: 146 Copynumber: 2.0 Consensus size: 146
647831 TCTATACATT
*
647841 ATCGTGATACGGACAAATATCTATACATTATCGTGATACGGACAATCGTAATACTGACAAATATC
1 ATCGTGATACGGACAAATATCTATACATCATCGTGATACGGACAATCGTAATACTGACAAATATC
* * * * *
647906 TAAACATTATCGTGATACTGAAAAATATCTATACATTATCGTGATACTTACAAATATCTATACAT
66 TAAACATTATCGTAATACTGAAAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT
647971 CATCGTGATACGGACA
131 CATCGTGATACGGACA
* *
647987 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACAATCGTGATACTGACAAATATC
1 ATCGTGATACGGACAAATATCTATACATCATCGTGATACGGACAATCGTAATACTGACAAATATC
* *
648052 TATACATTATCGTAATACTGACAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT
66 TAAACATTATCGTAATACTGAAAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT
* *
648117 TATCGTGATACTGACA
131 CATCGTGATACGGACA
648133 A
1 A
648134 ATATCTATAC
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
146 135 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (146 bp):
ATCGTGATACGGACAAATATCTATACATCATCGTGATACGGACAATCGTAATACTGACAAATATC
TAAACATTATCGTAATACTGAAAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT
CATCGTGATACGGACA
Found at i:648196 original size:15 final size:15
Alignment explanation
Indices: 648176--648206 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
648166 TCTATACATC
648176 ATCGTGATACGGACA
1 ATCGTGATACGGACA
648191 ATCGTGATACGGACA
1 ATCGTGATACGGACA
648206 A
1 A
648207 ATACAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (15 bp):
ATCGTGATACGGACA
Found at i:655000 original size:2 final size:2
Alignment explanation
Indices: 654958--654982 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
654948 AAAATCCAAT
654958 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
654983 CTCTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:663362 original size:18 final size:18
Alignment explanation
Indices: 663339--663373 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
663329 CCCCCACCCC
663339 CTCCAAAGAAA-CTGAAAT
1 CTCCAAA-AAAGCTGAAAT
663357 CTCCAAAAAAGCTGAAA
1 CTCCAAAAAAGCTGAAA
663374 ACAAACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.14
Consensus pattern (18 bp):
CTCCAAAAAAGCTGAAAT
Found at i:672165 original size:17 final size:17
Alignment explanation
Indices: 672140--672178 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
672130 GCTGATGAAA
*
672140 TGATCCAAGGACTTCAC
1 TGATTCAAGGACTTCAC
672157 TGATTCAAGGACTTCAC
1 TGATTCAAGGACTTCAC
672174 TGATT
1 TGATT
672179 TGACAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (17 bp):
TGATTCAAGGACTTCAC
Found at i:683323 original size:18 final size:18
Alignment explanation
Indices: 683300--683334 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
683290 CCTTTCAGGC
683300 AGCATTTAGATACTTATT
1 AGCATTTAGATACTTATT
683318 AGCATTTAGATACTTAT
1 AGCATTTAGATACTTAT
683335 GTTAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
AGCATTTAGATACTTATT
Found at i:683564 original size:14 final size:14
Alignment explanation
Indices: 683545--683573 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
683535 TGCAGTCAAC
683545 ATAAATATATATAT
1 ATAAATATATATAT
683559 ATAAATATATATAT
1 ATAAATATATATAT
683573 A
1 A
683574 ACTACTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATATATAT
Found at i:685972 original size:18 final size:18
Alignment explanation
Indices: 685949--685986 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
685939 CCGATTGATA
685949 CAGATATTTAGAGTCCTT
1 CAGATATTTAGAGTCCTT
*
685967 CAGATATTTCGAGTCCTT
1 CAGATATTTAGAGTCCTT
685985 CA
1 CA
685987 ATTTCTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (18 bp):
CAGATATTTAGAGTCCTT
Found at i:709086 original size:2 final size:2
Alignment explanation
Indices: 709079--709144 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
709069 AGGAAACAAA
709079 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
709121 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
709145 GGGGGACACC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:709518 original size:49 final size:48
Alignment explanation
Indices: 709446--709544 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 48
709436 ACCAGGTACA
*
709446 ATTTAAGCTCTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT
1 ATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT
709494 NATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT
1 -ATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT
709543 AT
1 AT
709545 ACATGTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 2 0.04
49 47 0.96
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.32
Consensus pattern (48 bp):
ATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT
Found at i:714562 original size:2 final size:2
Alignment explanation
Indices: 714555--714619 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
714545 GAGTGAAATT
714555 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
714597 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
714620 ACGTTTCACA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:718699 original size:140 final size:140
Alignment explanation
Indices: 718311--719081 Score: 802
Period size: 140 Copynumber: 5.5 Consensus size: 140
718301 TGCATGTAAA
718311 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA
1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA
718376 ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG
66 ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG
718441 TACATATATC
131 TACATATATC
718451 ATATAGTTAACTCGACAGTAAATGCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATA
1 ATATAGTTAACTCGACAGT---T-CATGTATCATATAGATAACTTGACAGTATTTCTTTCATATA
*
718516 GTTAACTTGGCGGTATATGTGTTATAAAGGTAAATCGACAGTACATGTATCATACAGTAAACTCG
62 GTTAACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCG
718581 ATAGTACATATATC
127 ATAGTACATATATC
* *
718595 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTAACAGTATTTCTTTCATATAGTAA
1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA
* * * * *
718660 ACTTGGCGGCATATGTGTCATATAGTTTAATCGAGAGTACATGTATCATACAGTAAACTCGATAG
66 ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG
718725 TACATATATC
131 TACATATATC
* * * * * ** * *
718735 ATATAGTTAAATCGACAGTACATGTATCATACAG-TAAACTCGATAGTACATATATCATATAGTT
1 ATATAGTTAACTCGACAGTTCATGTATCATATAGAT-AACTTGACAGTATTTCTTTCATATAGTT
* * * * * * * * *
718799 AAATCGAG-AGTACATGTATCATACAA--TAAACTCGATAG-A-ATATATCATATTATAGTTAAA
65 AACTTG-GCGGTATATGTGTTATA-AAGTTAAA-TCGACAGTACATGTATC--A-TACAG-TAAA
* *
718859 -TCGACAGTACATGTATC
123 CTCGATAGTACATATATC
* * * * * * * * * ** * * * * *
718876 ATACAGTAAACTCGATAGTACATATATCATATAGTTAAATCGAGAGTACATGTATCATACAATAA
1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA
* *** * * ** * *
718941 ACTCGATAGAATATATCATATTATAGTTAAATCGACAGTACATATATCATACAGTAAACTCGATA
66 ACTTGGCGGTATATGTGTTA-TAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATA
719006 GTACATATATC
130 GTACATATATC
* * * * * * * * *
719017 ATATAGTTAAATCGACAATACATATATCATACAG-TAACTTGACGGTATATGTGTCATATAGTTA
1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA
719081 A
66 A
719082 ATTGACAGTA
Statistics
Matches: 538, Mismatches: 73, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
138 6 0.01
139 5 0.01
140 230 0.43
141 132 0.25
142 14 0.03
143 6 0.01
144 145 0.27
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (140 bp):
ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA
ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG
TACATATATC
Found at i:719294 original size:142 final size:141
Alignment explanation
Indices: 718705--719379 Score: 478
Period size: 142 Copynumber: 4.8 Consensus size: 141
718695 AGTACATGTA
* * * * * * *
718705 TCATACAG-TAAACTCGATAGTACATATATCATATAGTTAAATCGACAGTACATGTATCATACA-
1 TCATACAGTTAAACT-GACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAG
* * * * *
718768 GTAAACTCGATAGTACATATATCATATAGTTAAATCGAGAGTACATG--TATCATACAATAAACT
65 GT-AACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAGT-AACT
* * *
718831 CGATAGAATATATC-A
128 TG--ACAATATATCTG
* * * * * * *
718846 T-ATTATAGTTAAA-TCGACAGTACATGTATCATACAG-TAAACTCGATAGTACATATATCATAT
1 TCA-TACAGTTAAACT-GACAGTACATGTGTCATAAAGTTAAA-TCGACAATACATATATAATAC
* * * * * * * * * * *
718908 AGTTAAATCGAGAGTACATGTATCATACAATAAACTCGATAG-A-ATATATCATATTATAGTTAA
63 AGGTAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTAT-ATAATACAG-TAA
* * * * * *
718971 ATCGACAGTACATATA
126 CTTGACAATATATCTG
* * * * *
718987 TCATACAG-TAAACTCGATAGTACATATATCATATAGTTAAATCGACAATACATATATCATACA-
1 TCATACAGTTAAACT-GACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAG
* * * * * * * *
719050 GTAACTTGACGGTATATGTGTCATATAGTTAAATTGACAGTACA--TATATCATACAGTAACTTG
65 GTAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAGTAACTTG
** *
719113 ACGGTATATGTG
130 ACAATATATCTG
* * * * * * *
719125 TCATATAGTTAAATTGACAGTATATGTGTTATAAAGTTAAGTCGACAACACATGTATAATACAGG
1 TCATACAGTTAAACTGACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAGG
* *
719190 TAACTCGATAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATATAGTTAACTTG
66 TAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAG-TAACTTG
*
719255 ACAATATATCTT
130 ACAATATATCTG
* * * * * * * *
719267 TCATACAGTTAACCTGACGGTACATGTGTCATATAGTTAACTCGACAGTACATATATTATATAGT
1 TCATACAGTTAAACTGACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAGG
*
719332 TAACTCGACAGTACATATATTATATAGTTAACTCGACAGTACATGTAT
66 TAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTAT
719380 CATACAGTTA
Statistics
Matches: 418, Mismatches: 97, Indels: 37
0.76 0.18 0.07
Matches are distributed among these distances:
138 58 0.14
139 49 0.12
140 46 0.11
141 131 0.31
142 133 0.32
143 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (141 bp):
TCATACAGTTAAACTGACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAGG
TAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAGTAACTTGA
CAATATATCTG
Found at i:719395 original size:28 final size:28
Alignment explanation
Indices: 718249--719529 Score: 718
Period size: 28 Copynumber: 45.6 Consensus size: 28
718239 ATGAATGTAT
* * *
718249 ATGTATCATATTGTTAACTTGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * ** *
718277 ATGTATCATAT-GGTAACTTGAGGGTGC
1 ATGTATCATATAGTTAAATCGACAGTAC
** * *
718304 ATGTAAAATATAGTTAACTCGACAGTTC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * *
718332 ATGTATCATATAGATAACTTGACAGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * * * * *
718360 TTCTTTCATATAGTTAACTTGGCGGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * *
718388 ATGTGTTATAAAGTTAAATCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
718416 ATGTATCATACAG-TAAACTCGATAGTAC
1 ATGTATCATATAGTTAAA-TCGACAGTAC
* *
718444 ATATATCATATAGTTAACTCGACAGTAAATGC
1 ATGTATCATATAGTTAAATCGACAGT--A--C
* * * *
718476 ATGTATCATATAGATAACTTGACAGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * * * * *
718504 TTCTTTCATATAGTTAACTTGGCGGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * *
718532 ATGTGTTATAAAGGTAAATCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
718560 ATGTATCATACAG-TAAACTCGATAGTAC
1 ATGTATCATATAGTTAAA-TCGACAGTAC
* * *
718588 ATATATCATATAGTTAACTCGACAGTTC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * ** *
718616 ATGTATCATATAGATAACTTAACAGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * * * * *
718644 TTCTTTCATATAG-TAAACTTGGCGGCAT
1 ATGTATCATATAGTTAAA-TCGACAGTAC
* * *
718672 ATGTGTCATATAGTTTAATCGAGAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
718700 ATGTATCATACAG-TAAACTCGATAGTAC
1 ATGTATCATATAGTTAAA-TCGACAGTAC
*
718728 ATATATCATATAGTTAAATCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
718756 ATGTATCATACAG-TAAACTCGATAGTAC
1 ATGTATCATATAGTTAAA-TCGACAGTAC
* *
718784 ATATATCATATAGTTAAATCGAGAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * *
718812 ATGTATCATACA-ATAAACTCGATAG-A-
1 ATGTATCATATAGTTAAA-TCGACAGTAC
*
718838 ATATATCATATTATAGTTAAATCGACAGTAC
1 ATGTATC--A-TATAGTTAAATCGACAGTAC
* *
718869 ATGTATCATACAG-TAAACTCGATAGTAC
1 ATGTATCATATAGTTAAA-TCGACAGTAC
* *
718897 ATATATCATATAGTTAAATCGAGAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * *
718925 ATGTATCATACA-ATAAACTCGATAG-A-
1 ATGTATCATATAGTTAAA-TCGACAGTAC
*
718951 ATATATCATATTATAGTTAAATCGACAGTAC
1 ATGTATC--A-TATAGTTAAATCGACAGTAC
* * *
718982 ATATATCATACAG-TAAACTCGATAGTAC
1 ATGTATCATATAGTTAAA-TCGACAGTAC
* *
719010 ATATATCATATAGTTAAATCGACAATAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * * *
719038 ATATATCATACAG-TAACTTGACGGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
719065 ATGTGTCATATAGTTAAATTGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * * *
719093 ATATATCATACAG-TAACTTGACGGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * *
719120 ATGTGTCATATAGTTAAATTGACAGTAT
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * **
719148 ATGTGTTATAAAGTTAAGTCGACAACAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * *
719176 ATGTATAATACAGGTAACTCGATAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
719204 ATATATCATATAGTTAACTCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * * * *
719232 ATGTATATAATATAGTTAACTTGACAATAT
1 ATG--TATCATATAGTTAAATCGACAGTAC
* * * * *
719262 ATCTTTCATACAGTT-AACCTGACGGTAC
1 ATGTATCATATAGTTAAATC-GACAGTAC
* *
719290 ATGTGTCATATAGTTAACTCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * *
719318 ATATATTATATAGTTAACTCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* * *
719346 ATATATTATATAGTTAACTCGACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
* *
719374 ATGTATCATACAGTTAAATCGACATGT-G
1 ATGTATCATATAGTTAAATCGACA-GTAC
* ** *
719402 ATACTAGAATATAGTTAAATCGCCAGTAC
1 AT-GTATCATATAGTTAAATCGACAGTAC
* * * * * *
719431 ACG-ATCACACAGCTAACTCGATAAG-AC
1 ATGTATCATATAGTTAAATCGA-CAGTAC
* * *
719458 ATATATCATACT-GTTAACCTCAACAGTAC
1 ATGTATCATA-TAGTTAA-ATCGACAGTAC
** * *
719487 ATGTAT--TCGAGTTAACTCAACAGTAC
1 ATGTATCATATAGTTAAATCGACAGTAC
719513 ATGTATCATATAGTTAA
1 ATGTATCATATAGTTAA
719530 CTCGGGAGTT
Statistics
Matches: 968, Mismatches: 235, Indels: 100
0.74 0.18 0.08
Matches are distributed among these distances:
26 29 0.03
27 118 0.12
28 671 0.69
29 78 0.08
30 35 0.04
31 13 0.01
32 24 0.02
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (28 bp):
ATGTATCATATAGTTAAATCGACAGTAC
Found at i:726767 original size:16 final size:16
Alignment explanation
Indices: 726748--726796 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
726738 AACGAATGCT
726748 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
726764 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
726780 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
726796 G
1 G
726797 TTTATAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.43, C:0.24, G:0.27, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Found at i:727214 original size:31 final size:31
Alignment explanation
Indices: 727176--727237 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
727166 GATTTTCATA
*
727176 GGGTACGTTTTCTCTTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
727207 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
727238 TAGAGATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGTACGTTTTCTCCTGGAGAAAACGTACCC
Found at i:727264 original size:16 final size:16
Alignment explanation
Indices: 727245--727294 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
727235 CCCTAGAGAT
727245 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
*
727261 TGGGTACGTTTTCTCT
1 TGGGTACGTTTTCTCC
727277 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
727293 TG
1 TG
727295 ATACCGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.06, C:0.22, G:0.26, T:0.46
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:727620 original size:2 final size:2
Alignment explanation
Indices: 727615--727676 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
727605 CATCTCTCGC
727615 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
727657 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
727677 GAAGTACACG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:736651 original size:22 final size:21
Alignment explanation
Indices: 736468--736651 Score: 69
Period size: 22 Copynumber: 9.0 Consensus size: 21
736458 TTGCTGACAC
736468 ATCACTGAAATCTTAATGAG-
1 ATCACTGAAATCTTAATGAGA
* * * ** *
736488 -TCAGTGAGATATTGCTGACA
1 ATCACTGAAATCTTAATGAGA
736508 CATCACTGAAATCTTAAT--GA
1 -ATCACTGAAATCTTAATGAGA
* * ** ** *
736528 ATCAGTGAGATAATGCTGACA
1 ATCACTGAAATCTTAATGAGA
736549 CATCACTGAAATCTTAATGAG-
1 -ATCACTGAAATCTTAATGAGA
* * * ** *
736570 -TCAGTGAGATATTGCTGACA
1 ATCACTGAAATCTTAATGAGA
736590 CATCACTGAAATCTTAAT--GA
1 -ATCACTGAAATCTTAATGAGA
* * **
736610 ATCAGTGAAATATTGCTGAGA
1 ATCACTGAAATCTTAATGAGA
736631 TATCACTGAAATCTTAATGAG
1 -ATCACTGAAATCTTAATGAG
736652 TCAGGGAGAT
Statistics
Matches: 106, Mismatches: 46, Indels: 22
0.61 0.26 0.13
Matches are distributed among these distances:
19 50 0.47
20 2 0.02
21 3 0.03
22 51 0.48
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (21 bp):
ATCACTGAAATCTTAATGAGA
Found at i:736929 original size:41 final size:41
Alignment explanation
Indices: 736458--736912 Score: 802
Period size: 41 Copynumber: 11.1 Consensus size: 41
736448 AATGATGAGT
*
736458 TTGCTGACACATCACTGAAATCTTAATGAGTCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
736499 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
* *
736540 ATGCTGACACATCACTGAAATCTTAATGAGTCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
*
736581 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAAATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
* * * *
736622 TTGCTGAGATATCACTGAAATCTTAATGAGTCAGGGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
*
736663 TTGCTGACACATCACTGAAATCTTAATGCATCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
*
736704 TTGCTGACACATCACTGAAATCTTAATGAACCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
736745 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
*
736786 TTGCTGACACATCACTGAAATCTTAATGAACCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
*
736827 TTGCTGACACATCACTGAAATCTTAATGAGTCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
736868 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
736909 TTGC
1 TTGC
736913 CGAGATATCA
Statistics
Matches: 391, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 391 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (41 bp):
TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA
Found at i:743094 original size:47 final size:47
Alignment explanation
Indices: 743025--743155 Score: 253
Period size: 47 Copynumber: 2.8 Consensus size: 47
743015 ACAACTATTG
*
743025 TATACACAAGAAGTCTACTCTGAAATCTATTTCACTATACTGCAACA
1 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA
743072 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA
1 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA
743119 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTA
1 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTA
743156 CTACCAGGAG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 83 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.32
Consensus pattern (47 bp):
TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA
Found at i:767386 original size:1 final size:1
Alignment explanation
Indices: 767380--767407 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
767370 CCTCTCCCGA
767380 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
767408 GGGGAGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:769264 original size:2 final size:2
Alignment explanation
Indices: 769257--769302 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
769247 TATCTTATAT
769257 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
769299 GA GA
1 GA GA
769303 TATTTTCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:776056 original size:17 final size:17
Alignment explanation
Indices: 776030--776067 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
776020 TCTAAATATC
*
776030 AAAATCTGAAACATTACA
1 AAAATCTGAAA-AATACA
776048 AAAAT-TGAAAAATACA
1 AAAATCTGAAAAATACA
776064 AAAA
1 AAAA
776068 AGGAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATCTGAAAAATACA
Found at i:785624 original size:1 final size:1
Alignment explanation
Indices: 785618--785669 Score: 104
Period size: 1 Copynumber: 52.0 Consensus size: 1
785608 AGCTAAAGCT
785618 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
785670 GATCCAAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:797827 original size:1 final size:1
Alignment explanation
Indices: 797821--797855 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
797811 TACTTATTTA
* *
797821 TTTTTTTTTTATTTATTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
797856 ACAAAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:797834 original size:15 final size:15
Alignment explanation
Indices: 797814--797855 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
797804 ATAATCTTAC
797814 TTATTTATTTTTTTT
1 TTATTTATTTTTTTT
797829 TTATTTATTTTTTTT
1 TTATTTATTTTTTTT
797844 TT-TTT-TTTTTTT
1 TTATTTATTTTTTT
797856 ACAAAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 7 0.26
14 3 0.11
15 17 0.63
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTATTTATTTTTTTT
Found at i:798114 original size:2 final size:2
Alignment explanation
Indices: 798107--798131 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
798097 ACGATCAGCC
798107 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
798132 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:799216 original size:19 final size:19
Alignment explanation
Indices: 799138--799216 Score: 52
Period size: 19 Copynumber: 3.9 Consensus size: 19
799128 CGATAGGAAA
799138 ATAACTCTAGGAATATCTC
1 ATAACTCTAGGAATATCTC
* *
799157 AAAACTCGATCTATGG-ATATTTC
1 ATAA--C--TCTA-GGAATATCTC
* * *
799180 ATAACTTTCGGAAAATCTC
1 ATAACTCTAGGAATATCTC
*
799199 ATAACTCTAGGGATATCT
1 ATAACTCTAGGAATATCT
799217 TAAGAGGCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
18 2 0.05
19 24 0.56
21 2 0.05
23 13 0.30
24 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
ATAACTCTAGGAATATCTC
Found at i:808463 original size:38 final size:38
Alignment explanation
Indices: 808420--808593 Score: 131
Period size: 38 Copynumber: 4.4 Consensus size: 38
808410 CAAAACACTA
* *
808420 GAAAATCTCATAACTAAAGTGATATCTCGAATTGCTAG
1 GAAAATCTCATAACTAAAGTGATATCTCAAAATGCTAG
* *
808458 GAAAATCTCATATTTCGAGCAAATAG-GATATCTCAAAACGCTAG
1 GAAAATCTCATA-----A-CTAA-AGTGATATCTCAAAATGCTAG
**
808502 GAAAATCTCATAACTCTA-TGGATATCTCAAAATGCTAG
1 GAAAATCTCATAACTAAAGT-GATATCTCAAAATGCTAG
** *
808540 GAAAATCTCATAACTCTAG-GAATATCTCATAACT-CTAG
1 GAAAATCTCATAACTAAAGTG-ATATCTCA-AAATGCTAG
* *
808578 AAAAATCTAATAACTA
1 GAAAATCTCATAACTA
808594 TTTAAGAACA
Statistics
Matches: 112, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
37 2 0.02
38 73 0.65
39 4 0.04
43 1 0.01
44 30 0.27
45 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (38 bp):
GAAAATCTCATAACTAAAGTGATATCTCAAAATGCTAG
Found at i:808511 original size:19 final size:19
Alignment explanation
Indices: 808487--808592 Score: 117
Period size: 19 Copynumber: 5.6 Consensus size: 19
808477 CAAATAGGAT
* *
808487 ATCTCAAAACGCTAGGAAA
1 ATCTCATAACTCTAGGAAA
*
808506 ATCTCATAACTCTATGG-AT
1 ATCTCATAACTCTA-GGAAA
*
808525 ATCTCA-AAATGCTAGGAAA
1 ATCTCATAACT-CTAGGAAA
*
808544 ATCTCATAACTCTAGGAAT
1 ATCTCATAACTCTAGGAAA
*
808563 ATCTCATAACTCTAGAAAA
1 ATCTCATAACTCTAGGAAA
*
808582 ATCTAATAACT
1 ATCTCATAACT
808593 ATTTAAGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
18 5 0.07
19 63 0.86
20 5 0.07
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (19 bp):
ATCTCATAACTCTAGGAAA
Found at i:808515 original size:82 final size:81
Alignment explanation
Indices: 808401--808551 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
808391 TAAAACGCTA
* *
808401 AGGATATCGCAAAACACTAGAAAATCTCATAACTAAA-GTGATATCTCGAATTGCTAGGAAAATC
1 AGGATATCGCAAAACACTAGAAAATCTCATAACTAAATG-GATATCTCAAAATGCTAGGAAAATC
808465 TCATATTTCGAGCAAAT
65 TCATATTTCGAGCAAAT
* * **
808482 AGGATATCTCAAAACGCTAGGAAAATCTCATAACTCTATGGATATCTCAAAATGCTAGGAAAATC
1 AGGATATCGCAAAACACTA-GAAAATCTCATAACTAAATGGATATCTCAAAATGCTAGGAAAATC
808547 TCATA
65 TCATA
808552 ACTCTAGGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 17 0.27
82 44 0.71
83 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (81 bp):
AGGATATCGCAAAACACTAGAAAATCTCATAACTAAATGGATATCTCAAAATGCTAGGAAAATCT
CATATTTCGAGCAAAT
Found at i:808923 original size:48 final size:48
Alignment explanation
Indices: 808848--809257 Score: 525
Period size: 48 Copynumber: 8.2 Consensus size: 48
808838 AAATGGTTAG
* *
808848 TTTATACGTTGATTTGTACATTAGGGGACATGTTGATACCTTGGTGAA
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA
*
808896 TTTATACGTTGATTTGTACATTTGGGGACATGTTGATACCTTGGTGAA
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA
* *
808944 TTTATACGTTGATTTGTACATTAGGGGACATGTTGATACCTTGGTGAGA
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGA-A
*
808993 -TTATACGTTGATTTGCACATTTGGGAACATGTTGATACCTTGGTGAA
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA
* *
809040 TTTATACGTTGATTTGCACATTTGTGGACATGTTGATACCTTGTTGAA
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA
* *
809088 TTTATACGTTGATTTGCACATTTAGGGACATGTTGATACCTTCAAAAATGGTGAG
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACC-T------TGGTGAA
* * *
809143 TTTATACGTTGATTTGTACATTAGGGGACATGTTGATACCTTGGCGAGA
1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGA-A
* *
809192 TTATACAAAATGTAGGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAG
1 TT-T-----A--TACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA
809248 TTTATACGTT
1 TTTATACGTT
809258 TATACCTAAA
Statistics
Matches: 321, Mismatches: 23, Indels: 36
0.84 0.06 0.09
Matches are distributed among these distances:
47 1 0.00
48 228 0.71
49 4 0.01
50 2 0.01
54 1 0.00
55 44 0.14
56 2 0.01
57 39 0.12
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.39
Consensus pattern (48 bp):
TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA
Found at i:809456 original size:2 final size:2
Alignment explanation
Indices: 809449--809492 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
809439 CCTCAGCCCA
809449 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
809491 TC
1 TC
809493 ATTAATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:810778 original size:46 final size:46
Alignment explanation
Indices: 810725--811362 Score: 705
Period size: 46 Copynumber: 13.8 Consensus size: 46
810715 AAAAAAGTCC
* * * **
810725 TCCATAACGTGGACTTCTTTGGAAGTCTATATGACTTTATTGCACG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
* *
810771 TCCATAACATGGAC-T-TTTGAGAAAGTCTATTTGATTACATTGCACG
1 TCCATAACATGGACTTCTTTG-G-GAGTCTATTTGACTACATTGCACG
* * * *
810817 TCCTTAAAATGGACTTCTTTGGGAGTCTATTTGATTTCATTGCACG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
*
810863 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCATG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
* * *
810909 TCCATAACATGGACTT-TAGTGGAAGTCTATTTGACTAAATTGCACG
1 TCCATAACATGGACTTCT-TTGGGAGTCTATTTGACTACATTGCACG
* **
810955 TCCATAATAT-GTTTTCTTTGGGAGTCTATTTGACTACATTGCACG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
* * * *
811000 TCCATAACATGGATTTCTTTGGGAGTTTATTTAACAACATTGCACG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
* * ** * *
811046 TCTATAAAACAGACTTCTTTTGGAGTCTATTTGACTAAATTGCACG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
* * *
811092 TCCATAACACGGACTT-TTGTGGAAGTCTATTTGACTACATTGCATG
1 TCCATAACATGGACTTCTT-TGGGAGTCTATTTGACTACATTGCACG
* * *
811138 TCCATAAGATGGACTTCTTTGGGAGTCTATTTGACTACACTGTACG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
* * *
811184 TCCATAACATGGATTTTTTTGGGAGTCTATTTGACTACATTGCATG
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
*
811230 TCCATAACATGGACTT-TTGTGGAAGTCTATTTGACTACATTGCACG
1 TCCATAACATGGACTTCTT-TGGGAGTCTATTTGACTACATTGCACG
* * * *
811276 TCCATAAAATGGACTTCTTTAGTTAGGTAGTCTTTTTGACTACATTTCATG
1 TCCATAACATGGACTTCTTT-G---GG-AGTCTATTTGACTACATTGCACG
* ** * * *
811327 TCCAAAAGGTGGACTTC-TTGGTAGTCTCTCTGACTA
1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTA
811363 TGTTGTGAGT
Statistics
Matches: 504, Mismatches: 72, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
44 4 0.01
45 56 0.11
46 395 0.78
47 7 0.01
48 4 0.01
49 1 0.00
50 3 0.01
51 34 0.07
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (46 bp):
TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG
Found at i:815358 original size:12 final size:12
Alignment explanation
Indices: 815343--815382 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
815333 TCAATGAACT
815343 AGAATATGATAA
1 AGAATATGATAA
815355 AGAATATGATAA
1 AGAATATGATAA
815367 AGAATATGATAA
1 AGAATATGATAA
815379 AGAA
1 AGAA
815383 AACAGATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (12 bp):
AGAATATGATAA
Done.