Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold102
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: 1727112
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 166202 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:718568 original size:43 final size:43
Alignment explanation
Indices: 718379--718555 Score: 189
Period size: 43 Copynumber: 4.2 Consensus size: 43
718369 TCAGTGCCCG
* * *** ***
718379 GTACAGTGGCGTACAGTGAGGTACAGTGCTGGTCAGT-GCCCT
1 GTACAGTGGTGTACAGTGGGGTACAGTGGAAGTCAGTAGAAAT
* * *
718421 GTACAGTGGCGTACAGTGGGGTACAGTGGAAGTCAGTAGGACT
1 GTACAGTGGTGTACAGTGGGGTACAGTGGAAGTCAGTAGAAAT
* **
718464 GTACAGTGGTGTACAGTGGGATACAGT-GCTGTTCAGTAGAAAT
1 GTACAGTGGTGTACAGTGGGGTACAGTGGAAG-TCAGTAGAAAT
*
718507 GTACAGTGGGGTACAGTGGGGTACAGTGGAAGTCAGT-GAAAT
1 GTACAGTGGTGTACAGTGGGGTACAGTGGAAGTCAGTAGAAAT
718549 GTACAGT
1 GTACAGT
718556 CAATGTACAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
42 47 0.41
43 67 0.58
44 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.24
Consensus pattern (43 bp):
GTACAGTGGTGTACAGTGGGGTACAGTGGAAGTCAGTAGAAAT
Found at i:724465 original size:146 final size:145
Alignment explanation
Indices: 724149--724704 Score: 833
Period size: 146 Copynumber: 3.9 Consensus size: 145
724139 TTTGAAACAA
* * * *
724149 TGACCTTGAACTTCCTGAATTGACCTTGGGACAAGGTCATGACACACCCTTGGGTCATAAGCAAT
1 TGACCTTGACCTTCCCGAA-TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * * *
724214 ATTTGTTTGAAGTAAGAACATT-CAATGTTT-TTCATAAGAAAGATTTGGGCCGGACACGAATTT
65 CTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTT
724277 CT-CATTTTTTCTGCCAG
129 -TGCATTTTTTCTGCCAG
* * *
724294 TGACCTTGACCTTGCCCAAATGACCTTTGGTCAAGGTCATGACACACCCTTAGGTAATAAGCAAT
1 TGACCTTGACCTT-CCCGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * *
724359 CTTTGTGCGAAGTAAGAACTTCCAATGTTTCCCCATGAGAAAGATATGGACCGGA-ATCGAATTT
65 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACA-CGAATTT
*
724423 TGCACTTTTTCTGCCAG
129 TGCATTTTTTCTGCCAG
724440 TGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTT-CCCGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
*
724505 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCGTAAGAAAGATATGGACCGGACACGAATTTT
65 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
724570 GCATTTTTTCTGCCAG
130 GCATTTTTTCTGCCAG
*
724586 TGACCTTGA-----CCGAATGACCTTGGGTCAAGGTCAAGACACACCCTTAGGTCATAAGCAATC
1 TGACCTTGACCTTCCCGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATC
724646 TTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGA
66 TTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGA
724705 TTGCTCAGAC
Statistics
Matches: 379, Mismatches: 26, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
140 108 0.28
144 2 0.01
145 79 0.21
146 189 0.50
147 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (145 bp):
TGACCTTGACCTTCCCGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATC
TTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTG
CATTTTTTCTGCCAG
Found at i:724666 original size:286 final size:287
Alignment explanation
Indices: 724149--724699 Score: 851
Period size: 286 Copynumber: 1.9 Consensus size: 287
724139 TTTGAAACAA
* *
724149 TGACCTTGAACTTCCTGAATTGACCTTGGGACAAGGTCATGACACACCCTTGGGTCATAAGCAAT
1 TGACCTTGAACTTCCCGAATTGACCTTGGGACAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * *
724214 ATTTGTTTGAAGTAAGAACATTCAATGTTTTTCATAAGAAAGATTTGGGCCGGACACGAATTTCT
66 ATTTGTGTGAAGTAAGAACATTCAATGTTTTCCATAAGAAAGATATGGACCGGACACGAATTTCT
* *
724279 CATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTTGGTCAAGGTCATGACACACCCT
131 CATTTTTTCTGCCAGTGACCTTGACC-TG--C-AATGACCTTGGGTCAAGGTCAAGACACACCCT
*
724344 TAGGTAATAAGCAATCTTTGTGCGAAGTAAGAACTTCCAATGTTTCCCCATGAGAAAGATATGGA
192 TAGGTAATAAGCAATCTTTGTGCGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGA
724409 CCGGAATCGAATTTTGCACTTTTTCTGCCAG
257 CCGGAATCGAATTTTGCACTTTTTCTGCCAG
* *
724440 TGACCTTGACCTTGCCCGAA-TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
1 TGACCTTGAACTT-CCCGAATTGACCTTGGGACAAGGTCATGACACACCCTTAGGTCATAAGCAA
* *
724504 TCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCGTAAGAAAGATATGGACCGGACACGAATT
65 TATTTGTGTGAAGTAAGAACATT-CAATGTTT-TCCATAAGAAAGATATGGACCGGACACGAATT
724568 T-TGCATTTTTTCTGCCAGTGACCTTGACC-G-AATGACCTTGGGTCAAGGTCAAGACACACCCT
128 TCT-CATTTTTTCTGCCAGTGACCTTGACCTGCAATGACCTTGGGTCAAGGTCAAGACACACCCT
* * *
724630 TAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGA
192 TAGGTAATAAGCAATCTTTGTGCGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGA
724695 CCGGA
257 CCGGA
724700 CACGATTGCT
Statistics
Matches: 240, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
286 96 0.40
290 3 0.01
291 81 0.34
292 60 0.25
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (287 bp):
TGACCTTGAACTTCCCGAATTGACCTTGGGACAAGGTCATGACACACCCTTAGGTCATAAGCAAT
ATTTGTGTGAAGTAAGAACATTCAATGTTTTCCATAAGAAAGATATGGACCGGACACGAATTTCT
CATTTTTTCTGCCAGTGACCTTGACCTGCAATGACCTTGGGTCAAGGTCAAGACACACCCTTAGG
TAATAAGCAATCTTTGTGCGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGG
AATCGAATTTTGCACTTTTTCTGCCAG
Found at i:742900 original size:22 final size:22
Alignment explanation
Indices: 742875--742927 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
742865 TATAAGATAG
*
742875 TCTTTAAGCTGCCTTTAAGCCA
1 TCTTTAAGCTGCCTTTAAACCA
* **
742897 TCTTTACGCTTTCTTTAAACCA
1 TCTTTAAGCTGCCTTTAAACCA
742919 TCTTTAAGC
1 TCTTTAAGC
742928 AACACATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (22 bp):
TCTTTAAGCTGCCTTTAAACCA
Found at i:744212 original size:17 final size:17
Alignment explanation
Indices: 744190--744224 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
744180 CATTAACGTG
744190 CGAGTACCCATTATTGC
1 CGAGTACCCATTATTGC
744207 CGAGTACCCATTATTGC
1 CGAGTACCCATTATTGC
744224 C
1 C
744225 AATCGATTTA
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:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (17 bp):
CGAGTACCCATTATTGC
Found at i:746922 original size:3 final size:3
Alignment explanation
Indices: 746908--746943 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
746898 TTTGTCAACT
* *
746908 TTC TTT TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
746944 ATCCAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:747833 original size:440 final size:440
Alignment explanation
Indices: 746964--748282 Score: 2358
Period size: 440 Copynumber: 3.0 Consensus size: 440
746954 TTCCAGGCCG
* *
746964 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTATATGGTATTAAGAAGG
1 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
747029 AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
66 AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
747094 AAATATTGTCCGGACCATAACACAAGACTCCTTTACATATACATACTTTTAACTTGTATCATAGA
131 AAATATTGTCCGGACCATAACACAAGACTCCTTTAC--ATACATACTTTTAACTTGTATCATAGA
747159 TAGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTC
194 TAGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTC
747224 AAGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAA
259 AAGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAA
* * **
747289 CTTTAAACAAAGAACAATAATAATACACTTAGGTATACAATTGAATAATATTTGACCTTGAGATT
324 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTT
* *
747354 GTTTTACTCAAGGTCAAATTAAG-AAAAAATTAT-AAATTTTGGCTGGGTCT
389 GTTTTACTCAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCT
* * *
747404 TCACTTAAATACCGTTTGACATTAAGTCTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
1 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
747469 AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
66 AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
747534 AAATATTGTCCGGACCATAACACAAGACTCCTTTACATACATACTTTTAACTTGTATCATAGATA
131 AAATATTGTCCGGACCATAACACAAGACTCCTTTACATACATACTTTTAACTTGTATCATAGATA
747599 GATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAA
196 GATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAA
747664 GGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACT
261 GGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACT
747729 TTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTGT
326 TTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTGT
*
747794 TTTACTCAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCA
391 TTTACTCAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCT
*
747844 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
1 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
747909 AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
66 AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
*
747974 AAATATTGTCCGGACCATAACACAAGACTTCTTTAACATACATACTTTTAACTTGTATCATAGAT
131 AAATATTGTCCGGACCATAACACAAGACTCCTTT-ACATACATACTTTTAACTTGTATCATAGAT
* *
748039 AGATGGTGTATAACCTAGTTGAACCTTACCAAAAATTTTGACCTTGACCTAGAA-TTTTATTTCA
195 AGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCA
748103 AGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAA-
260 AGGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAAC
* * * * * * *
748167 TTTAAACAAAGTACAATAATAATTCACTTAGGTGTACTCTTGATTTATATATGACCTTGACCATG
325 TTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTG
* *
748232 TTTTACTTAAGGTCAAATTAAGAAAAAGATAATAAAATTTTGTCTGGGTCT
390 TTTTACTCAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCT
748283 GGGTAACATA
Statistics
Matches: 847, Mismatches: 29, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
438 241 0.28
439 115 0.14
440 409 0.48
441 82 0.10
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (440 bp):
TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG
AGTGCACGCCACCAAAATTTTTGACCTTGACCTATTTTGTTCTTCAAGGTCAAGCTTTTCATAAA
AAATATTGTCCGGACCATAACACAAGACTCCTTTACATACATACTTTTAACTTGTATCATAGATA
GATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAA
GGTCATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACT
TTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTGT
TTTACTCAAGGTCAAATTAAGAAAAAAATAATAAAATTTTGTCTGGGTCT
Found at i:753081 original size:21 final size:21
Alignment explanation
Indices: 753034--753103 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
753024 TTAGGCTTTT
* *
753034 CTCTTCCCTTTTCCTCTCGGC
1 CTCTTTCCTTTTCCTCTCAGC
753055 CTCTTTCCTTTTCCTCTCAGC
1 CTCTTTCCTTTTCCTCTCAGC
* **
753076 CTCTTTCCTCTTATTCTCAGC
1 CTCTTTCCTTTTCCTCTCAGC
753097 C-CTTTCC
1 CTCTTTCC
753104 CTCCTCTCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 38 0.86
ACGTcount: A:0.04, C:0.44, G:0.06, T:0.46
Consensus pattern (21 bp):
CTCTTTCCTTTTCCTCTCAGC
Found at i:755162 original size:16 final size:16
Alignment explanation
Indices: 755141--755176 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
755131 TTTCCTCTGC
*
755141 GTCCGTCTGTCTGTCT
1 GTCCGTCCGTCTGTCT
755157 GTCCGTCCGTCTGTCT
1 GTCCGTCCGTCTGTCT
755173 GTCC
1 GTCC
755177 CACTTCAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39
Consensus pattern (16 bp):
GTCCGTCCGTCTGTCT
Found at i:765330 original size:38 final size:39
Alignment explanation
Indices: 765274--765837 Score: 176
Period size: 38 Copynumber: 12.9 Consensus size: 39
765264 ATTATAACAA
*
765274 CATTGGTCAAT-AAGTCTACACAGACTACACTATCACCCT
1 CATTGGTC-ATCAACTCTACACAGACTACACTATCACCCT
*
765313 -TTTGGTCATCAACTCTACACAGACTACACTATCACCTACACTATCACCT
1 CATTGGTCATCAACTCTACACAGACTACAC--T-A--T---C-A-C-CCT
765362 CATTGGT-ATCAACTCTACACAGACTACACTATCACCC-
1 CATTGGTCATCAACTCTACACAGACTACACTATCACCCT
* * * *
765399 CATTGGTCATCAACCCTATAAAGACTACACAATCA-CCT
1 CATTGGTCATCAACTCTACACAGACTACACTATCACCCT
* * *
765437 CATCGGTCATCAACTTTA-ATCAGACAACACTATCACCTATACTAT
1 CATTGGTCATCAACTCTACA-CAGACTACACTATCACC----C--T
*
765482 CACCCCTTTGGTCATCAACTCTACACAGACTACATTATCACCTACATCAT
1 CA-----TTGGTCATCAACTCTACACAGACTACACTATCA-C--C--C-T
* * * *
765532 AACAACATTGGTCATCACCCCTACACGGACGACACTATCACCC-
1 -----CATTGGTCATCAACTCTACACAGACTACACTATCACCCT
* *
765575 CATTGGTCATTAACTTTA-ATCAGACTACACTATCACCTATGCTAT
1 CATTGGTCATCAACTCTACA-CAGACTACACTATCACC----C--T
* * *
765620 CACCCCATTGGTCATCAACACAACACAGACTACATTATCACCTACAATAT
1 -----CATTGGTCATCAACTCTACACAGACTACACTATCACC--C----T
*
765670 AACAAGATTGGTCATTAACTCTACACAGACTACACTATCACCC-
1 --C---ATTGGTCATCAACTCTACACAGACTACACTATCACCCT
* * * *
765713 CTTTGGTCTTCAACTCTACAAAGACTACATTATCACCAACACTATCACCT
1 CATTGGTCATCAACTCTACACAGACTACACTAT--------C-A-C-CCT
* * * *
765763 CATTGGTCATCACCTATACACAGACTACATTTTCACCC-
1 CATTGGTCATCAACTCTACACAGACTACACTATCACCCT
*
765801 CATTGGTCATCAACTCTACACAGACTACATTATCACC
1 CATTGGTCATCAACTCTACACAGACTACACTATCACC
765838 TACATTATAA
Statistics
Matches: 401, Mismatches: 56, Indels: 137
0.68 0.09 0.23
Matches are distributed among these distances:
37 13 0.03
38 166 0.41
39 4 0.01
40 3 0.01
41 4 0.01
42 2 0.00
43 2 0.00
44 1 0.00
45 4 0.01
46 3 0.01
47 5 0.01
48 5 0.01
49 28 0.07
50 154 0.38
51 4 0.01
53 1 0.00
55 2 0.00
ACGTcount: A:0.33, C:0.33, G:0.08, T:0.26
Consensus pattern (39 bp):
CATTGGTCATCAACTCTACACAGACTACACTATCACCCT
Found at i:765352 original size:50 final size:49
Alignment explanation
Indices: 765298--765967 Score: 174
Period size: 50 Copynumber: 14.9 Consensus size: 49
765288 TCTACACAGA
*
765298 CTACACTATCACC-CTTTTGGTCATCAACTCTACACAGACTACACTATCAC
1 CTACACTATCACCTC-ATTGGT-ATCAACTCTACACAGACTACACTATCAC
765348 CTACACTATCACCTCATTGGTATCAACTCTACACAGACTACAC--T-A-
1 CTACACTATCACCTCATTGGTATCAACTCTACACAGACTACACTATCAC
* * * *
765393 -T---C-A-C-CC-CATTGGTCATCAACCCTATAAAGACTACACAATCA-
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* *
765434 C--C----TCA--TC---GGTCATCAACTTTA-ATCAGACAACACTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACA-CAGACTACACTATCAC
* * * *
765473 CTATACTATCACCCCTTTGGTCATCAACTCTACACAGACTACATTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* ** * **
765523 CTACA-TCATAACAACATTGG--TC-A-TC-AC-C--CCTACAC--GGA-
1 CTACACT-ATCACCTCATTGGTATCAACTCTACACAGACTACACTATCAC
* * * *
765561 CGACACTATCACCCCATTGGTCATTAACTTTA-ATCAGACTACACTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACA-CAGACTACACTATCAC
** * * * *
765611 CTATGCTATCACCCCATTGGTCATCAACACAACACAGACTACATTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* * *** *
765661 CTACAATATAACAAGATTGGTCATTAACTCTACACAGACTACAC--T-A-
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* * *
765707 -T-CAC---C-CCT--TTGGTCTTCAACTCTACAAAGACTACATTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* * *
765749 CAACACTATCACCTCATTGGTCATCACCTATACACAGACT--AC-AT---
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* *
765793 -T----T-TCACCCCATTGGTCATCAACTCTACACAGACTACATTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* * ** * * *
765837 CTACATTATAACGACATT--TTTCAA---TA-AC--TCTACAC-A--GC
1 CTACACTATCACCTCATTGGTATCAACTCTACACAGACTACACTATCAC
* * * * *
765875 CTACACTATCACCCCATTGATCATCAACTCTACAAAGATTACATTATCAC
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACACTATCAC
* * *
765925 CAACACTATCACCTCATTGGTCATCACCTCTACACAAACTACA
1 CTACACTATCACCTCATTGGT-ATCAACTCTACACAGACTACA
765968 TTATTGCCTC
Statistics
Matches: 450, Mismatches: 94, Indels: 152
0.65 0.14 0.22
Matches are distributed among these distances:
37 8 0.02
38 127 0.28
39 5 0.01
40 7 0.02
41 22 0.05
42 1 0.00
43 4 0.01
44 13 0.03
45 9 0.02
46 2 0.00
47 22 0.05
48 7 0.02
49 25 0.06
50 195 0.43
51 3 0.01
ACGTcount: A:0.34, C:0.33, G:0.07, T:0.27
Consensus pattern (49 bp):
CTACACTATCACCTCATTGGTATCAACTCTACACAGACTACACTATCAC
Found at i:765353 original size:12 final size:12
Alignment explanation
Indices: 765336--765361 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
765326 TCTACACAGA
765336 CTACACTATCAC
1 CTACACTATCAC
765348 CTACACTATCAC
1 CTACACTATCAC
765360 CT
1 CT
765362 CATTGGTATC
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:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (12 bp):
CTACACTATCAC
Found at i:765366 original size:88 final size:88
Alignment explanation
Indices: 765210--765661 Score: 416
Period size: 88 Copynumber: 5.1 Consensus size: 88
765200 TACGGTGTGC
* * ** * * * *
765210 CTACACTATCACCTCATCGGTCATCAACTCTACACAGACCCCACTATTACCTATATTATAACAAC
1 CTACACTATCACCCCATTGGTCATCAACTCTACACAGACTACACTATCACCTACACTATCACAAC
**
765275 ATTGGTCAAT-AAGTCTACACAGA
66 ATTGGTC-ATCAACACTACACAGA
** **
765298 CTACACTATCACCCTTTTGGTCATCAACTCTACACAGACTACACTATCACCTACACTATCACCTC
1 CTACACTATCACCCCATTGGTCATCAACTCTACACAGACTACACTATCACCTACACTATCACAAC
*
765363 ATTGGT-ATCAACTCTACACAGA
66 ATTGGTCATCAACACTACACAGA
* * * * **
765385 CTACACTATCACCCCATTGGTCATCAACCCTATAAAGACTACACAATCACCT-CATCGGTCATCA
1 CTACACTATCACCCCATTGGTCATCAACTCTACACAGACTACACTATCACCTACA-CTATCA-CA
* ** *
765449 ACTTTAATCAGACAACACTATCAC---
64 ACATTGGTCA-TCAACACTA-CACAGA
* * * *
765473 CTATACTATCACCCCTTTGGTCATCAACTCTACACAGACTACATTATCACCTACA-TCATAACAA
1 CTACACTATCACCCCATTGGTCATCAACTCTACACAGACTACACTATCACCTACACT-ATCACAA
* * *
765537 CATTGGTCATCACCCCTACACGGA
65 CATTGGTCATCAACACTACACAGA
* * * ** **
765561 CGACACTATCACCCCATTGGTCATTAACTTTA-ATCAGACTACACTATCACCTATGCTATCACCC
1 CTACACTATCACCCCATTGGTCATCAACTCTACA-CAGACTACACTATCACCTACACTATCACAA
*
765625 CATTGGTCATCAACACAACACAGA
65 CATTGGTCATCAACACTACACAGA
*
765649 CTACATTATCACC
1 CTACACTATCACC
765662 TACAATATAA
Statistics
Matches: 290, Mismatches: 61, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
85 3 0.01
86 10 0.03
87 72 0.25
88 191 0.66
89 4 0.01
90 7 0.02
91 3 0.01
ACGTcount: A:0.33, C:0.33, G:0.08, T:0.26
Consensus pattern (88 bp):
CTACACTATCACCCCATTGGTCATCAACTCTACACAGACTACACTATCACCTACACTATCACAAC
ATTGGTCATCAACACTACACAGA
Found at i:765395 original size:23 final size:23
Alignment explanation
Indices: 765320--765395 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
765310 CCTTTTGGTC
765320 ATCAACTCTACACAGACTACACT
1 ATCAACTCTACACAGACTACACT
* *
765343 ATC-AC-CTACACTATCACCT-CATTGGT
1 ATCAACTCTACAC-A-GA-CTACA---CT
765369 ATCAACTCTACACAGACTACACT
1 ATCAACTCTACACAGACTACACT
765392 ATCA
1 ATCA
765396 CCCCATTGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 11 0.28
24 2 0.05
25 2 0.05
26 7 0.17
27 3 0.08
28 6 0.15
ACGTcount: A:0.36, C:0.34, G:0.05, T:0.25
Consensus pattern (23 bp):
ATCAACTCTACACAGACTACACT
Found at i:765633 original size:138 final size:138
Alignment explanation
Indices: 765399--765799 Score: 511
Period size: 138 Copynumber: 2.9 Consensus size: 138
765389 ACTATCACCC
* * * * * * *
765399 CATTGGTCATCAACCCTATAAAGACTACACAATCACCTCATCGGTCATCAACTTTAATCAGACAA
1 CATTGGTCATCAACCCTACACAGACTACACTATCACCCCATTGGTCATTAACTTTAATCAGACTA
*
765464 CACTATCACCTATACTATCACCCCTTTGGTCATCAACTCTACACAGACTACATTATCACCTAC-A
66 CACTATCACCTATACTATCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACAA
765528 TCATAACAA
131 T-ATAACAA
* * *
765537 CATTGGTCATCACCCCTACACGGACGACACTATCACCCCATTGGTCATTAACTTTAATCAGACTA
1 CATTGGTCATCAACCCTACACAGACTACACTATCACCCCATTGGTCATTAACTTTAATCAGACTA
* * *
765602 CACTATCACCTATGCTATCACCCCATTGGTCATCAACACAACACAGACTACATTATCACCTACAA
66 CACTATCACCTATACTATCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACAA
765667 TATAACAA
131 TATAACAA
* * * * * *
765675 GATTGGTCATTAACTCTACACAGACTACACTATCACCCCTTTGGTC-TTCAACTCTACA-AAGAC
1 CATTGGTCATCAACCCTACACAGACTACACTATCACCCCATTGGTCATT-AACTTTA-ATCAGAC
* * * * * * *
765738 TACATTATCACCAACACTATCACCTCATTGGTCATCACCTATACACAGACTACATTTTCACC
64 TACACTATCACCTATACTATCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACC
765800 CCATTGGTCA
Statistics
Matches: 227, Mismatches: 33, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
137 2 0.01
138 222 0.98
139 3 0.01
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (138 bp):
CATTGGTCATCAACCCTACACAGACTACACTATCACCCCATTGGTCATTAACTTTAATCAGACTA
CACTATCACCTATACTATCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACAA
TATAACAA
Found at i:765711 original size:88 final size:88
Alignment explanation
Indices: 765616--766013 Score: 431
Period size: 88 Copynumber: 4.5 Consensus size: 88
765606 ATCACCTATG
* * * * * * *
765616 CTATCACCCCATTGGTCATCAACACAACACAGACTACATTATCACCTACAATATAACAAGATTGG
1 CTATCACCCCATTGGTCATCAACTCTACAAAGACTACATTATCACCAACACTATAACCACATTGG
*
765681 TCATTAACTCTACACAGACTACA
66 TCATCAACTCTACACAGACTACA
* * * *
765704 CTATCACCCCTTTGGTCTTCAACTCTACAAAGACTACATTATCACCAACACTATCACCTCATTGG
1 CTATCACCCCATTGGTCATCAACTCTACAAAGACTACATTATCACCAACACTATAACCACATTGG
* *
765769 TCATCACCTATACACAGACTACA
66 TCATCAACTCTACACAGACTACA
* * * * * * **
765792 TTTTCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACATTATAACGACATTTT
1 CTATCACCCCATTGGTCATCAACTCTACAAAGACTACATTATCACCAACACTATAACCACATTGG
*
765857 TCAAT-AACTCTACACAGCCTACA
66 TC-ATCAACTCTACACAGACTACA
* * * *
765880 CTATCACCCCATTGATCATCAACTCTACAAAGATTACATTATCACCAACACTATCACCTCATTGG
1 CTATCACCCCATTGGTCATCAACTCTACAAAGACTACATTATCACCAACACTATAACCACATTGG
* *
765945 TCATCACCTCTACACAAACTACA
66 TCATCAACTCTACACAGACTACA
* ** * * * * *
765968 TTATTGCCTCATTGGTCATTACCTTTACACAGACTA-ATTTATCACC
1 CTATCACCCCATTGGTCATCAACTCTACAAAGACTACA-TTATCACC
766014 TCATTACACT
Statistics
Matches: 253, Mismatches: 54, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
87 3 0.01
88 248 0.98
89 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (88 bp):
CTATCACCCCATTGGTCATCAACTCTACAAAGACTACATTATCACCAACACTATAACCACATTGG
TCATCAACTCTACACAGACTACA
Found at i:765944 original size:176 final size:177
Alignment explanation
Indices: 765619--766019 Score: 585
Period size: 176 Copynumber: 2.3 Consensus size: 177
765609 ACCTATGCTA
* * * *
765619 TCACCCCATTGGTCATCAACACAACACAGACTACATTATCACCTACAATATAACAAGATTGGTCA
1 TCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACATTATAACAACATTGGTCA
* * * *
765684 TTAACTCTACACAGACTACACTATCACCCCTTTGGTCTTCAACTCTACAAAGACTACATTATCAC
66 ATAACTCTACACAGACTACACTATCACCCCATTGATCATCAACTCTACAAAGACTACATTATCAC
*
765749 CAACACTATCACCTCATTGGTCATCACCTATACACAGACTACATT-T
131 CAACACTATCACCTCATTGGTCATCACCTATACACAAACTACATTAT
* **
765795 TCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACATTATAACGACATTTTTCA
1 TCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACATTATAACAACATTGGTCA
* *
765860 ATAACTCTACACAGCCTACACTATCACCCCATTGATCATCAACTCTACAAAGATTACATTATCAC
66 ATAACTCTACACAGACTACACTATCACCCCATTGATCATCAACTCTACAAAGACTACATTATCAC
*
765925 CAACACTATCACCTCATTGGTCATCACCTCTACACAAACTACATTAT
131 CAACACTATCACCTCATTGGTCATCACCTATACACAAACTACATTAT
* * * * *
765972 T-GCCTCATTGGTCATTACCTTTACACAGACTA-ATTTATCACCT-CATTA
1 TCACCCCATTGGTCATCAACTCTACACAGACTACA-TTATCACCTACATTA
766020 CACTATTCCT
Statistics
Matches: 203, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
175 6 0.03
176 195 0.96
177 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (177 bp):
TCACCCCATTGGTCATCAACTCTACACAGACTACATTATCACCTACATTATAACAACATTGGTCA
ATAACTCTACACAGACTACACTATCACCCCATTGATCATCAACTCTACAAAGACTACATTATCAC
CAACACTATCACCTCATTGGTCATCACCTATACACAAACTACATTAT
Found at i:766016 original size:38 final size:38
Alignment explanation
Indices: 765931--766018 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
765921 TCACCAACAC
765931 TATCACCTCATTGGTCATCACCTCTACACAAACTACAT
1 TATCACCTCATTGGTCATCACCTCTACACAAACTACAT
** * * *
765969 TATTGCCTCATTGGTCATTACCTTTACACAGACTA-ATT
1 TATCACCTCATTGGTCATCACCTCTACACAAACTACA-T
766007 TATCACCTCATT
1 TATCACCTCATT
766019 ACACTATTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 1 0.02
38 41 0.98
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (38 bp):
TATCACCTCATTGGTCATCACCTCTACACAAACTACAT
Found at i:791078 original size:42 final size:42
Alignment explanation
Indices: 790997--791150 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
790987 AAGCACATGC
790997 CATAATGAT-ATATGCACATGC-CATAATGA--AAACTGCACATCA
1 CATAATGATGA-ATGCACAT-CACATAAT-ACCAAA-TGCACATCA
* * ** *
791039 CATAAGGATGAATGCACATCACATACTGTCAAATTCACATCA
1 CATAATGATGAATGCACATCACATAATACCAAATGCACATCA
*** *
791081 CATAATGCCAAATGCACATCACATAATACCAAATGCACA-CGC
1 CATAATGATGAATGCACATCACATAATACCAAATGCACATC-A
*
791123 CATAATAATGAATGCACATCACATAATA
1 CATAATGATGAATGCACATCACATAATA
791151 GAAGGAGTAC
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 84 0.93
43 4 0.04
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (42 bp):
CATAATGATGAATGCACATCACATAATACCAAATGCACATCA
Found at i:791150 original size:21 final size:21
Alignment explanation
Indices: 790969--791211 Score: 106
Period size: 21 Copynumber: 11.6 Consensus size: 21
790959 AAGACGGAAC
* * * *
790969 CACATCACATACTTAGAAAAG
1 CACATCACATAATAATAAATG
* *
790990 CACATGC-CATAATGATATATG
1 CACAT-CACATAATAATAAATG
*
791011 CACATGC-CATAATGAA-AACTG
1 CACAT-CACATAAT-AATAAATG
** *
791032 CACATCACATAAGGATGAATG
1 CACATCACATAATAATAAATG
* * *
791053 CACATCACATACT-GTCAAATT
1 CACATCACATAATAAT-AAATG
***
791074 CACATCACATAATGCCAAATG
1 CACATCACATAATAATAAATG
**
791095 CACATCACATAATACCAAATG
1 CACATCACATAATAATAAATG
* *
791116 CACA-CGCCATAATAATGAATG
1 CACATC-ACATAATAATAAATG
*
791137 CACATCACATAATAGA-AGGA-G
1 CACATCACATAATA-ATA-AATG
* * * *
791158 TACACCACATAATGATAAAAG
1 CACATCACATAATAATAAATG
* *
791179 CACACCACATAATGATACAA-G
1 CACATCACATAATAATA-AATG
*
791200 GACATCACATAA
1 CACATCACATAA
791212 CGATTAAAGC
Statistics
Matches: 173, Mismatches: 36, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.03
21 160 0.92
22 7 0.04
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.20
Consensus pattern (21 bp):
CACATCACATAATAATAAATG
Found at i:792301 original size:2 final size:2
Alignment explanation
Indices: 792294--792343 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
792284 AGACAGAAAA
792294 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
792336 TC TC TC TC
1 TC TC TC TC
792344 ATCCTTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:797713 original size:14 final size:13
Alignment explanation
Indices: 797680--797705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
797670 TATTAAGATG
797680 AATTTTTTTTTTT
1 AATTTTTTTTTTT
797693 AATTTTTTTTTTT
1 AATTTTTTTTTTT
797706 GCTTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
AATTTTTTTTTTT
Found at i:800784 original size:13 final size:13
Alignment explanation
Indices: 800765--800804 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
800755 AAAGTCAGCG
800765 ACTGTAAGACGAA
1 ACTGTAAGACGAA
*
800778 GCTGTAAGACGAA
1 ACTGTAAGACGAA
800791 ACTGTAAGACGAA
1 ACTGTAAGACGAA
800804 A
1 A
800805 TTAACAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (13 bp):
ACTGTAAGACGAA
Found at i:801724 original size:1 final size:1
Alignment explanation
Indices: 801720--801752 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
801710 NNNNGGGGGG
801720 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
801753 GGTTCCGACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:802290 original size:21 final size:21
Alignment explanation
Indices: 802266--802305 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
802256 TATAGACATG
*
802266 TAAGCTGCATGTCAACATAGA
1 TAAGCTGCAGGTCAACATAGA
*
802287 TAAGTTGCAGGTCAACATA
1 TAAGCTGCAGGTCAACATA
802306 TTTATCTAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (21 bp):
TAAGCTGCAGGTCAACATAGA
Found at i:808842 original size:28 final size:28
Alignment explanation
Indices: 808759--808842 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
808749 GTAACATTGG
*
808759 TACTTTACATTTACAATCATTTCAATGGT
1 TACTTTACATTTACAATCATTTCAGT-GT
* * * * *
808788 AACTTAACAATAACAATTACTTT-AGTGT
1 TACTTTACATTTACAATCA-TTTCAGTGT
808816 TACTTTACATTTACAATCATTTCAGTG
1 TACTTTACATTTACAATCATTTCAGTG
808843 GAATCTTTTC
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
27 3 0.07
28 20 0.48
29 16 0.38
30 3 0.07
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.42
Consensus pattern (28 bp):
TACTTTACATTTACAATCATTTCAGTGT
Found at i:809358 original size:26 final size:26
Alignment explanation
Indices: 809300--809351 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
809290 AAACAAGCTT
* *
809300 CAAACATTAAACTTATATAAAATGTC
1 CAAACATTAAACTCATATAAAATATC
809326 CAAACATTAAACTCATATAAAATATC
1 CAAACATTAAACTCATATAAAATATC
809352 AGAACATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (26 bp):
CAAACATTAAACTCATATAAAATATC
Found at i:809485 original size:20 final size:20
Alignment explanation
Indices: 809460--809507 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
809450 CTTTCCTCTG
*
809460 CGTCTGTCTGTCCATCCGTC
1 CGTCTGTCTGTCCATCCATC
*
809480 CGTCTGACTGTCCATCCATC
1 CGTCTGTCTGTCCATCCATC
*
809500 TGTCTGTC
1 CGTCTGTC
809508 CCACTTCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.08, C:0.38, G:0.19, T:0.35
Consensus pattern (20 bp):
CGTCTGTCTGTCCATCCATC
Found at i:810030 original size:2 final size:2
Alignment explanation
Indices: 810023--810047 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
810013 TCTTTCAATT
810023 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
810048 ATCTAACCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:814742 original size:2 final size:2
Alignment explanation
Indices: 814735--814781 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
814725 CGTACCGGTG
814735 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
814777 TC TC T
1 TC TC T
814782 GGGTAGGGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:815617 original size:4 final size:4
Alignment explanation
Indices: 815596--815702 Score: 169
Period size: 4 Copynumber: 26.8 Consensus size: 4
815586 TTACTTATTT
* * * * *
815596 TCTC TCTT TCTC TCTG TCTG TCTC TCTC TCTC TCTG TCTA TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
815644 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
815692 TCTC TCTC TCT
1 TCTC TCTC TCT
815703 TGTATATTAA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 96 1.00
ACGTcount: A:0.01, C:0.45, G:0.03, T:0.51
Consensus pattern (4 bp):
TCTC
Found at i:818228 original size:166 final size:166
Alignment explanation
Indices: 817986--818396 Score: 583
Period size: 166 Copynumber: 2.5 Consensus size: 166
817976 GACTGTGATT
* * * ** * *
817986 TTGAATTTACACTACCCGAGGATGCCTCTACACAAGTTAAAGCTTTTCTGGCCAAA-AGGTCTTT
1 TTGAATCTACACTACCTGAGGATGCCTCCACACAAGTTTGAGCTTTTCAGGCCAAATA-GTTTTT
* * * * *
818050 AAAAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTTATCCCCCAATTGTGG
65 GAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTAGGTAAAAATTCATCCCCCAATTGTGG
818115 CCCCACCCTACCCCCAGGGACCATGATTTGAACAAAC
130 CCCCACCCTACCCCCAGGGACCATGATTTGAACAAAC
* * *** ** *
818152 TTGAATCTACACTACCTGTGGATGCTTCCATTTTAA-TTTGAGCTTTTGTGGCCCAATAGTTTTT
1 TTGAATCTACACTACCTGAGGATGCCTCCA-CACAAGTTTGAGCTTTTCAGGCCAAATAGTTTTT
*
818216 GAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTAGGTAAAAATTCATCCCCCTATTGTGG
65 GAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTAGGTAAAAATTCATCCCCCAATTGTGG
*
818281 CCCCACCCTACCCCCGGGGACCATGATTTGAACAAAC
130 CCCCACCCTACCCCCAGGGACCATGATTTGAACAAAC
*
818318 TTGAATCTACACTACCTGAGGATGCCTCCACACAAGTTTTAGCTTTTCAGGCCAAATAGTTTTTG
1 TTGAATCTACACTACCTGAGGATGCCTCCACACAAGTTTGAGCTTTTCAGGCCAAATAGTTTTTG
818383 AGAAGAAGATTTTT
66 AGAAGAAGATTTTT
818397 GAAAAATACC
Statistics
Matches: 213, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
165 2 0.01
166 208 0.98
167 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (166 bp):
TTGAATCTACACTACCTGAGGATGCCTCCACACAAGTTTGAGCTTTTCAGGCCAAATAGTTTTTG
AGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTAGGTAAAAATTCATCCCCCAATTGTGGC
CCCACCCTACCCCCAGGGACCATGATTTGAACAAAC
Found at i:818576 original size:6 final size:6
Alignment explanation
Indices: 818565--818607 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
818555 GTGAAAAGTT
*
818565 AACGAC AACGAC AACGAC GACGAC AACGAC -A-GAC AACGGAC AA
1 AACGAC AACGAC AACGAC AACGAC AACGAC AACGAC AAC-GAC AA
818608 ATTGTGATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 3 0.09
5 2 0.06
6 22 0.69
7 5 0.16
ACGTcount: A:0.49, C:0.30, G:0.21, T:0.00
Consensus pattern (6 bp):
AACGAC
Found at i:823070 original size:2 final size:2
Alignment explanation
Indices: 823063--823113 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
823053 ACAAATACAT
823063 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
823105 GA GA GA GA G
1 GA GA GA GA G
823114 TAGTTCACAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:828133 original size:2 final size:2
Alignment explanation
Indices: 828128--828216 Score: 155
Period size: 2 Copynumber: 45.5 Consensus size: 2
828118 TCTCCATCTA
*
828128 AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG 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
828169 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G 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
828210 AG AG AG A
1 AG AG AG A
828217 TTACTTGACT
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 81 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:840881 original size:2 final size:2
Alignment explanation
Indices: 840874--840913 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
840864 ATTCAGTATT
840874 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
840914 AGTTTGAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:842128 original size:2 final size:2
Alignment explanation
Indices: 842121--842193 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
842111 TTGAGCTTTT
842121 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
842163 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
842194 TGTATGTATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:845268 original size:2 final size:2
Alignment explanation
Indices: 845261--845314 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
845251 GACATAAAAC
*
845261 GA GA GA GA GA GA GA GA GA GA GA GT 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
845303 GA GA GA GA GA GA
1 GA GA GA GA GA GA
845315 AGGATAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
GA
Found at i:859013 original size:4 final size:4
Alignment explanation
Indices: 859006--859089 Score: 168
Period size: 4 Copynumber: 21.0 Consensus size: 4
858996 CGAAAATGAA
859006 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
859054 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
859090 GCTATGAAGG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:859481 original size:21 final size:21
Alignment explanation
Indices: 859457--859550 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
859447 ATCTGCCACC
859457 ACTTGTCAGATAGTTATGTCG
1 ACTTGTCAGATAGTTATGTCG
859478 ACTTGTCAGAT-GATTATGTCG
1 ACTTGTCAGATAG-TTATGTCG
* * *
859499 AATTGTCAGATATTTATGTCA
1 ACTTGTCAGATAGTTATGTCG
* ** *
859520 ACTTGTAAGATCTTTATGTTG
1 ACTTGTCAGATAGTTATGTCG
859541 ACTTGTCAGA
1 ACTTGTCAGA
859551 AAATAACCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.98
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (21 bp):
ACTTGTCAGATAGTTATGTCG
Found at i:859518 original size:42 final size:42
Alignment explanation
Indices: 859459--859550 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
859449 CTGCCACCAC
* * *
859459 TTGTCAGATAGTTATGTCGACTTGTCAGATGATTATGTCGAA
1 TTGTCAGATAGTTATGTCAACTTGTAAGATCATTATGTCGAA
* * * *
859501 TTGTCAGATATTTATGTCAACTTGTAAGATCTTTATGTTGAC
1 TTGTCAGATAGTTATGTCAACTTGTAAGATCATTATGTCGAA
859543 TTGTCAGA
1 TTGTCAGA
859551 AAATAACCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (42 bp):
TTGTCAGATAGTTATGTCAACTTGTAAGATCATTATGTCGAA
Found at i:859661 original size:21 final size:20
Alignment explanation
Indices: 859624--859684 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
859614 CCATTAACTT
*
859624 GTCATCATAATATCTGACAA
1 GTCAACATAATATCTGACAA
*
859644 GTCGACATAATGATCTGACAA
1 GTCAACATAAT-ATCTGACAA
*
859665 GTTAACATAATTATCTGACA
1 GTCAACATAA-TATCTGACA
859685 GGAAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.26
21 25 0.71
22 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (20 bp):
GTCAACATAATATCTGACAA
Found at i:859873 original size:21 final size:21
Alignment explanation
Indices: 859743--859874 Score: 131
Period size: 21 Copynumber: 6.3 Consensus size: 21
859733 TAAGCCGAGG
* *
859743 TGTCAGATAATGATGTTGACT
1 TGTCAGATAATTATGTCGACT
* *
859764 TGTCAGAT-GTTATGTCGTCT
1 TGTCAGATAATTATGTCGACT
*
859784 TGTCAAATAATTATGTCGACT
1 TGTCAGATAATTATGTCGACT
*
859805 TGTCAAATAATTATGTCGACT
1 TGTCAGATAATTATGTCGACT
*** ** *
859826 TAAAAGATGCTAATGTCGACT
1 TGTCAGATAATTATGTCGACT
**
859847 TGTCAGATCCTTATGTCGACT
1 TGTCAGATAATTATGTCGACT
859868 TGTCAGA
1 TGTCAGA
859875 AAATATTATT
Statistics
Matches: 91, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 15 0.16
21 76 0.84
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (21 bp):
TGTCAGATAATTATGTCGACT
Found at i:859977 original size:21 final size:21
Alignment explanation
Indices: 859951--860042 Score: 112
Period size: 21 Copynumber: 4.4 Consensus size: 21
859941 CGTGGATAAG
* *
859951 TGACAAGTCGACTTAAAGAAC
1 TGACAAGTCGACATAAAGATC
* **
859972 TGACAAGTCCACATAATTATC
1 TGACAAGTCGACATAAAGATC
*
859993 TGACAAGTCGACATCAAGATC
1 TGACAAGTCGACATAAAGATC
**
860014 TGACAAGTCGACATAATTATC
1 TGACAAGTCGACATAAAGATC
860035 TGACAAGT
1 TGACAAGT
860043 GGTGGCAGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (21 bp):
TGACAAGTCGACATAAAGATC
Found at i:860017 original size:42 final size:42
Alignment explanation
Indices: 859951--860042 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
859941 CGTGGATAAG
*
859951 TGACAAGTCGACTTAAAGAACTGACAAGTCCACATAATTATC
1 TGACAAGTCGACATAAAGAACTGACAAGTCCACATAATTATC
* * *
859993 TGACAAGTCGACATCAAGATCTGACAAGTCGACATAATTATC
1 TGACAAGTCGACATAAAGAACTGACAAGTCCACATAATTATC
860035 TGACAAGT
1 TGACAAGT
860043 GGTGGCAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (42 bp):
TGACAAGTCGACATAAAGAACTGACAAGTCCACATAATTATC
Found at i:862763 original size:2 final size:2
Alignment explanation
Indices: 862758--862792 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
862748 GTGTGTGTTT
862758 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
862793 CCTATCGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:864186 original size:11 final size:11
Alignment explanation
Indices: 864170--864202 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
864160 ATTGTCATAG
864170 TGTTTTTTTTT
1 TGTTTTTTTTT
864181 TGTTTTTTTTT
1 TGTTTTTTTTT
864192 TGTTTGTTTTT
1 TGTTT-TTTTT
864203 GTATTGGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:864192 original size:15 final size:15
Alignment explanation
Indices: 864172--864202 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
864162 TGTCATAGTG
864172 TTTTTTT-TTTGTTT
1 TTTTTTTGTTTGTTT
864186 TTTTTTTGTTTGTTT
1 TTTTTTTGTTTGTTT
864201 TT
1 TT
864203 GTATTGGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTGTTTGTTT
Found at i:864421 original size:2 final size:2
Alignment explanation
Indices: 864414--864460 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
864404 CGTGTTTGTC
864414 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
864456 AG AG A
1 AG AG A
864461 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:865075 original size:16 final size:16
Alignment explanation
Indices: 865054--865120 Score: 125
Period size: 16 Copynumber: 4.2 Consensus size: 16
865044 ATCCAATAGG
865054 ACAGTTAATGAAAAAC
1 ACAGTTAATGAAAAAC
865070 ACAGTTAATGAAAAAC
1 ACAGTTAATGAAAAAC
*
865086 ACAGTTAATGAAATAC
1 ACAGTTAATGAAAAAC
865102 ACAGTTAATGAAAAAC
1 ACAGTTAATGAAAAAC
865118 ACA
1 ACA
865121 CTTAGGTGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.55, C:0.13, G:0.12, T:0.19
Consensus pattern (16 bp):
ACAGTTAATGAAAAAC
Found at i:876093 original size:18 final size:18
Alignment explanation
Indices: 876070--876104 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
876060 ACTTTGAAAT
876070 ATTTTTTCAAAGTGCGTA
1 ATTTTTTCAAAGTGCGTA
876088 ATTTTTTCAAAGTGCGT
1 ATTTTTTCAAAGTGCGT
876105 TGCCACAGCG
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:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTTTTTCAAAGTGCGTA
Found at i:876838 original size:2 final size:2
Alignment explanation
Indices: 876763--876818 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
876753 GTTAACACAC
876763 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
876805 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
876819 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:876839 original size:2 final size:2
Alignment explanation
Indices: 876830--876867 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
876820 NNNNNNNNNN
876830 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
876868 TTTTGCACAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:886031 original size:14 final size:14
Alignment explanation
Indices: 886012--886046 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
886002 GAAAAAAATG
*
886012 AACAATTTATCATA
1 AACAATTTAGCATA
*
886026 AACAATTTAGCATT
1 AACAATTTAGCATA
886040 AACAATT
1 AACAATT
886047 AAGAATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (14 bp):
AACAATTTAGCATA
Found at i:892146 original size:20 final size:19
Alignment explanation
Indices: 892114--892157 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
892104 AAAATTGTTC
892114 ATTTATTTTTTTTTTTTAT
1 ATTTATTTTTTTTTTTTAT
*
892133 TTTTATTATTTTTTTTTTAT
1 ATTTATT-TTTTTTTTTTAT
892153 ATTTA
1 ATTTA
892158 CATCGCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
ATTTATTTTTTTTTTTTAT
Found at i:897164 original size:17 final size:17
Alignment explanation
Indices: 897142--897175 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
897132 AAATTGGCAA
897142 TTGTTTATAAAA-AGTAT
1 TTGTTT-TAAAACAGTAT
897159 TTGTTTTAAAACAGTAT
1 TTGTTTTAAAACAGTAT
897176 ACCATCTGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTGTTTTAAAACAGTAT
Found at i:900362 original size:21 final size:21
Alignment explanation
Indices: 900336--900422 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 21
900326 TTTTTCTATC
* *
900336 AAATATGTCGGCGTGCAAGAT
1 AAATATGTCGACATGCAAGAT
*
900357 AAATATGTTGACATGCAAGAT
1 AAATATGTCGACATGCAAGAT
* ** * *
900378 AATTATAACAACATGCAACAT
1 AAATATGTCGACATGCAAGAT
*
900399 AACTATG-CTGACATGCAAGA-
1 AAATATGTC-GACATGCAAGAT
900419 AAAT
1 AAAT
900423 TACAATCAGA
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 4 0.08
21 47 0.92
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (21 bp):
AAATATGTCGACATGCAAGAT
Found at i:900541 original size:21 final size:21
Alignment explanation
Indices: 900517--900626 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
900507 TTTATGTCGG
900517 CATGCAACTTATTTATGTTAA
1 CATGCAACTTATTTATGTTAA
** ** * *
900538 CATGCAAGATAAATATGCTGA
1 CATGCAACTTATTTATGTTAA
* *
900559 TATGGAACTTATTTATGTTGAA
1 CATGCAACTTATTTATGTT-AA
*
900581 -ATGCAACTTATTTATGTCAA
1 CATGCAACTTATTTATGTTAA
* * *
900601 CCTGCAACTTACTTATGTTGA
1 CATGCAACTTATTTATGTTAA
900622 CATGC
1 CATGC
900627 GAGATAAATA
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 2 0.03
21 63 0.95
22 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
CATGCAACTTATTTATGTTAA
Found at i:900639 original size:42 final size:41
Alignment explanation
Indices: 900518--900639 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
900508 TTATGTCGGC
* *
900518 ATGCAACTTATTTATGTTAACATGCAAGATAAATATGCTGAT
1 ATGCAACTTATTTATGTTGACATGCAAGATAAATATG-TCAT
* * ** **
900560 ATGGAACTTATTTATGTTGAAATGCAACTTATTTATGTCA-
1 ATGCAACTTATTTATGTTGACATGCAAGATAAATATGTCAT
* *
900600 ACCTGCAACTTACTTATGTTGACATGCGAGATAAATATGT
1 A--TGCAACTTATTTATGTTGACATGCAAGATAAATATGT
900640 TGACATGTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
40 1 0.02
41 2 0.03
42 59 0.95
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (41 bp):
ATGCAACTTATTTATGTTGACATGCAAGATAAATATGTCAT
Found at i:900657 original size:29 final size:29
Alignment explanation
Indices: 900615--900675 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
900605 CAACTTACTT
900615 ATGTTGACATGCGAGATAAATATGTTGAC
1 ATGTTGACATGCGAGATAAATATGTTGAC
*
900644 ATGTTTACATGCGAGATAAATATGTTGAC
1 ATGTTGACATGCGAGATAAATATGTTGAC
900673 ATG
1 ATG
900676 CAACTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (29 bp):
ATGTTGACATGCGAGATAAATATGTTGAC
Found at i:900728 original size:21 final size:21
Alignment explanation
Indices: 900697--900862 Score: 197
Period size: 21 Copynumber: 7.9 Consensus size: 21
900687 TTAAATATCA
*
900697 ACATAACTAAGTTGCATGTCG
1 ACATAAATAAGTTGCATGTCG
* *
900718 ACGTAAATAAGTTGCATGTCA
1 ACATAAATAAGTTGCATGTCG
** ** **
900739 ACATATTTATTTTGCATGTTA
1 ACATAAATAAGTTGCATGTCG
*
900760 ACATAACTAAGTTGCATGTCG
1 ACATAAATAAGTTGCATGTCG
* *
900781 ACATAAATATGTTACATGTCG
1 ACATAAATAAGTTGCATGTCG
*
900802 ACATAAATATGTTGCATGTCG
1 ACATAAATAAGTTGCATGTCG
**
900823 ACATAAATAAGTTGCATGTTA
1 ACATAAATAAGTTGCATGTCG
900844 ACATAAATAAGTTGCATGT
1 ACATAAATAAGTTGCATGT
900863 TAACGTCAAT
Statistics
Matches: 123, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 123 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (21 bp):
ACATAAATAAGTTGCATGTCG
Found at i:900768 original size:63 final size:63
Alignment explanation
Indices: 900694--900862 Score: 230
Period size: 63 Copynumber: 2.7 Consensus size: 63
900684 TAGTTAAATA
* ** *
900694 TCAACATAACTAAGTTGCATGTCGACGTAAATAAGTTGCATGTCAACATATTTATTTTGCATG
1 TCAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAATATGTTGCATG
* * * *
900757 TTAACATAACTAAGTTGCATGTCGACATAAATATGTTACATGTCGACATAAATATGTTGCATG
1 TCAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAATATGTTGCATG
* * **
900820 TCGACATAAATAAGTTGCATGTTAACATAAATAAGTTGCATGT
1 TCAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGT
900863 TAACGTCAAT
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 91 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (63 bp):
TCAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAATATGTTGCATG
Found at i:900985 original size:21 final size:21
Alignment explanation
Indices: 900960--901043 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 21
900950 TTGCAGTTTT
*
900960 CTTGCATGTCAACATAGTTAA
1 CTTGCATGTCAACATATTTAA
* * *
900981 GTTGCATGTCAACATCTTTAT
1 CTTGCATGTCAACATATTTAA
* *
901002 CTTGCATGTCAACATCTTTAT
1 CTTGCATGTCAACATATTTAA
* *
901023 CTTGCATGTCGACATAATTAA
1 CTTGCATGTCAACATATTTAA
901044 TACAAAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (21 bp):
CTTGCATGTCAACATATTTAA
Found at i:902633 original size:14 final size:14
Alignment explanation
Indices: 902614--902644 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
902604 TCATTTATTA
902614 AAATCATATTTTAC
1 AAATCATATTTTAC
902628 AAATCATATTTTAC
1 AAATCATATTTTAC
902642 AAA
1 AAA
902645 AATAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATCATATTTTAC
Found at i:910886 original size:29 final size:29
Alignment explanation
Indices: 910854--911069 Score: 389
Period size: 29 Copynumber: 7.4 Consensus size: 29
910844 ATCAAGAACG
910854 TTGTCACAGACAACATATAAAGATAATCA
1 TTGTCACAGACAACATATAAAGATAATCA
910883 TTGTCACAGACAACATATAAAGATAATCA
1 TTGTCACAGACAACATATAAAGATAATCA
910912 TTGTCACAGACAACATATAAAGATAATCA
1 TTGTCACAGACAACATATAAAGATAATCA
*
910941 TTGTCACAGACAACATATAAAGTTAAAT-A
1 TTGTCACAGACAACATATAAAGAT-AATCA
*
910970 TTGTCACATACAACATATAAAGATAATCA
1 TTGTCACAGACAACATATAAAGATAATCA
910999 TTGTCACAGACAACATATAAAGATAATCA
1 TTGTCACAGACAACATATAAAGATAATCA
*
911028 TTGTCACAGACAACATATAAAGTTAATCA
1 TTGTCACAGACAACATATAAAGATAATCA
911057 TTGTCACAGACAA
1 TTGTCACAGACAA
911070 TATCACAGAT
Statistics
Matches: 180, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
28 3 0.02
29 174 0.97
30 3 0.02
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.25
Consensus pattern (29 bp):
TTGTCACAGACAACATATAAAGATAATCA
Found at i:917956 original size:16 final size:16
Alignment explanation
Indices: 917935--917985 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
917925 TAGCGGGACG
917935 TACTAAAGACCTGAAA
1 TACTAAAGACCTGAAA
*
917951 TACTAATGACCTGAAA
1 TACTAAAGACCTGAAA
*
917967 GACCTGAAAGACCTGAAA
1 TA-CT-AAAGACCTGAAA
917985 T
1 T
917986 TTTATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 16 0.55
17 2 0.07
18 11 0.38
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (16 bp):
TACTAAAGACCTGAAA
Found at i:917972 original size:9 final size:9
Alignment explanation
Indices: 917939--917984 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
917929 GGGACGTACT
917939 AAAGACCTG
1 AAAGACCTG
*
917948 AAATA-CT-
1 AAAGACCTG
*
917955 AATGACCTG
1 AAAGACCTG
917964 AAAGACCTG
1 AAAGACCTG
917973 AAAGACCTG
1 AAAGACCTG
917982 AAA
1 AAA
917985 TTTTATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 24 0.77
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (9 bp):
AAAGACCTG
Found at i:918098 original size:17 final size:17
Alignment explanation
Indices: 918070--918124 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
918060 AAATATGAAA
* *
918070 GACCTGAGAATTTGAATT
1 GACCTGA-AATTTCAAAT
918088 GACCTGAAATTTTCAAAT
1 GACCTGAAA-TTTCAAAT
*
918106 GACCTGAAATTTTAAAT
1 GACCTGAAATTTCAAAT
918123 GA
1 GA
918125 TTGATACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (17 bp):
GACCTGAAATTTCAAAT
Found at i:918309 original size:18 final size:18
Alignment explanation
Indices: 918282--918326 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
918272 GAGTACAAAA
* *
918282 GACCTTAAAATTTGAATT
1 GACCTGAAAATTTGAACT
*
918300 GACCTGAAAATTTGAGCT
1 GACCTGAAAATTTGAACT
918318 GACCTGAAA
1 GACCTGAAA
918327 TTATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (18 bp):
GACCTGAAAATTTGAACT
Found at i:918489 original size:18 final size:18
Alignment explanation
Indices: 918463--918503 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
918453 ACGAAAGACT
* *
918463 TGAACATTTGAATTGACC
1 TGAAAATTTGAACTGACC
*
918481 TGAAAATTTGAGCTGACC
1 TGAAAATTTGAACTGACC
918499 TGAAA
1 TGAAA
918504 TTAAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (18 bp):
TGAAAATTTGAACTGACC
Found at i:918662 original size:177 final size:177
Alignment explanation
Indices: 918176--918646 Score: 820
Period size: 177 Copynumber: 2.7 Consensus size: 177
918166 ATATATATAT
* *
918176 GTTCTGTGTCAATATT-AATGTCTATTTGTAAGTTTTT-ATCATATTTCCAGGTATATAAGTGTT
1 GTTCTGTGTCAGT-TTAAATGTCTATTTGTGAGTTTTTAATCATATTTCCAGGTATATAAGTGTT
* *
918239 AAAATATATCATACTGATCAATTATTTATGCAGGAGTACAAAAGACCTTAAAATTTGAATTGACC
65 AAAATATATCATACTGATCAATTATTTATGCAGGAGTACGAAAGACCTGAAAATTTGAATTGACC
*
918304 TGAAAATTTGAGCTGACCTGAAATTATATATAATTGAAACATTTCTAA
130 TGAAAATTTGAGCTGACCTGAAATTAAATATAATTGAAACATTTCTAA
918352 GTTCTGTGTCAGTTTAAATGTCTATTTGTGAGTTTTTAATCATATTTCCAGGTATATAAGTGTTA
1 GTTCTGTGTCAGTTTAAATGTCTATTTGTGAGTTTTTAATCATATTTCCAGGTATATAAGTGTTA
* * *
918417 AAATATATCATACTGATCAATTATTTATGCCGGAGTACGAAAGACTTGAACATTTGAATTGACCT
66 AAATATATCATACTGATCAATTATTTATGCAGGAGTACGAAAGACCTGAAAATTTGAATTGACCT
918482 GAAAATTTGAGCTGACCTGAAATTAAATATAATTGAAACATTTCTAA
131 GAAAATTTGAGCTGACCTGAAATTAAATATAATTGAAACATTTCTAA
*
918529 GTTCTGTGTCAGTTTAAATGTCTATTTGTGAGTTTTTAATCATATTTCCAGGTATATAAGTGTGA
1 GTTCTGTGTCAGTTTAAATGTCTATTTGTGAGTTTTTAATCATATTTCCAGGTATATAAGTGTTA
* *
918594 AAATATATCATACTGATCAATTATTTACGCAGGAATACGAAAGACCTGAAAAT
66 AAATATATCATACTGATCAATTATTTATGCAGGAGTACGAAAGACCTGAAAAT
918647 CTGGGCTGAC
Statistics
Matches: 279, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
175 2 0.01
176 32 0.11
177 245 0.88
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (177 bp):
GTTCTGTGTCAGTTTAAATGTCTATTTGTGAGTTTTTAATCATATTTCCAGGTATATAAGTGTTA
AAATATATCATACTGATCAATTATTTATGCAGGAGTACGAAAGACCTGAAAATTTGAATTGACCT
GAAAATTTGAGCTGACCTGAAATTAAATATAATTGAAACATTTCTAA
Found at i:932774 original size:15 final size:15
Alignment explanation
Indices: 932725--932777 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
932715 TTTGTCCTCC
932725 TTCTCTGCCTTTTCT
1 TTCTCTGCCTTTTCT
*
932740 TTCTC--CATTTTCT
1 TTCTCTGCCTTTTCT
932753 CTCTCTCTGCCTTTTCT
1 -T-TCTCTGCCTTTTCT
932770 TTCTCTGC
1 TTCTCTGC
932778 TTTAACTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 7 0.22
14 1 0.03
15 16 0.50
16 1 0.03
17 7 0.22
ACGTcount: A:0.02, C:0.36, G:0.06, T:0.57
Consensus pattern (15 bp):
TTCTCTGCCTTTTCT
Found at i:932792 original size:30 final size:30
Alignment explanation
Indices: 932726--932795 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
932716 TTGTCCTCCT
* **
932726 TCTCTGCCTTTTCTTTCTCCATTTTCTCTC
1 TCTCTGCCTTTTCTTTCTCCACTTTAACTC
**
932756 TCTCTGCCTTTTCTTTCTCTGCTTTAACTC
1 TCTCTGCCTTTTCTTTCTCCACTTTAACTC
*
932786 TTTCTGCCTT
1 TCTCTGCCTT
932796 CTCTGCAGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.04, C:0.34, G:0.06, T:0.56
Consensus pattern (30 bp):
TCTCTGCCTTTTCTTTCTCCACTTTAACTC
Found at i:936739 original size:11 final size:11
Alignment explanation
Indices: 936720--936775 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
936710 TCTGCTAATG
936720 GCAGACCCAGA
1 GCAGACCCAGA
* *
936731 GCTGACCCAAA
1 GCAGACCCAGA
936742 GCAGACCCCAG-
1 GCAGA-CCCAGA
*
936753 GCTGACCCAGA
1 GCAGACCCAGA
*
936764 GCAGACACAGA
1 GCAGACCCAGA
936775 G
1 G
936776 TGGACAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 5 0.14
11 27 0.75
12 4 0.11
ACGTcount: A:0.34, C:0.36, G:0.27, T:0.04
Consensus pattern (11 bp):
GCAGACCCAGA
Found at i:936748 original size:22 final size:22
Alignment explanation
Indices: 936720--936775 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
936710 TCTGCTAATG
936720 GCAGACCCAGAGCTGACCCAAA
1 GCAGACCCAGAGCTGACCCAAA
*
936742 GCAGACCCCAG-GCTGACCCAGA
1 GCAGA-CCCAGAGCTGACCCAAA
*
936764 GCAGACACAGAG
1 GCAGACCCAGAG
936776 TGGACAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.13
22 21 0.70
23 5 0.17
ACGTcount: A:0.34, C:0.36, G:0.27, T:0.04
Consensus pattern (22 bp):
GCAGACCCAGAGCTGACCCAAA
Found at i:937104 original size:42 final size:42
Alignment explanation
Indices: 937057--937158 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
937047 GTTTATCAGC
*
937057 TGTTAACTATAGTTTACGGATCC-T-AAACTATAGTTAACGAT
1 TGTTAACTATAGTTTAC-GATCCGTGAAACTATAGTTAACGAA
* *
937098 TCGTTAACTATAGTTTAC-ATCCGTGAAACTATATTTCACGAA
1 T-GTTAACTATAGTTTACGATCCGTGAAACTATAGTTAACGAA
*
937140 TGTAAACTATAGTTTACGA
1 TGTTAACTATAGTTTACGA
937159 ATGATAATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 4 0.08
41 17 0.32
42 32 0.60
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (42 bp):
TGTTAACTATAGTTTACGATCCGTGAAACTATAGTTAACGAA
Found at i:937148 original size:20 final size:20
Alignment explanation
Indices: 937061--937175 Score: 85
Period size: 21 Copynumber: 5.6 Consensus size: 20
937051 ATCAGCTGTT
* *
937061 AACTATAGTTTACGGATCCTA
1 AACTATAGTTTACGAAT-GTA
* * *
937082 AACTATAGTTAACGATTCGTT
1 AACTATAGTTTACGAAT-GTA
937103 AACTATAGTTTAC--ATCCGTGA
1 AACTATAGTTTACGAAT--GT-A
937124 AACTATA-TTTCACGAATGTA
1 AACTATAGTTT-ACGAATGTA
937144 AACTATAGTTTACGAATGATA
1 AACTATAGTTTACGAATG-TA
*
937165 ATC-ATAGTTTA
1 AACTATAGTTTA
937176 TCTATCTGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.01
20 29 0.37
21 46 0.59
23 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
AACTATAGTTTACGAATGTA
Found at i:937474 original size:39 final size:40
Alignment explanation
Indices: 937396--937488 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 40
937386 TACGGATCGA
* **
937396 AAACTATAGTTAACGACGTTAATCTATATTTCATGTCTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
* * *
937436 AAACTATAGTTAACG-GGATATTCTATGTTTCACATCTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
*
937475 TAACTATAGTTAAC
1 AAACTATAGTTAAC
937489 AATGAAAACA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 31 0.67
40 15 0.33
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (40 bp):
AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
Found at i:937676 original size:84 final size:84
Alignment explanation
Indices: 937517--937676 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
937507 TGATTGTTAA
* * *
937517 ACATAGCTTATCTGATAAATATAGTTTCACCATTGTGAAACTATAATTAACAACTCTAAACTTTA
1 ACATAGCTTATCTGATAAATATAGTTTCACAATCGTGAAACTATAATTAACAACTCTAAACTATA
* *
937582 GTTCAGGAATGCAAATTGT
66 CTTCACGAATGCAAATTGT
* * * *
937601 ACATAGTTTATCTGATAAATATAGTTTCACAATCGTGAAACTATATTTATCAACTCTTAACTATA
1 ACATAGCTTATCTGATAAATATAGTTTCACAATCGTGAAACTATAATTAACAACTCTAAACTATA
*
937666 CTTTACGAATG
66 CTTCACGAATG
937677 TAAACTATAG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (84 bp):
ACATAGCTTATCTGATAAATATAGTTTCACAATCGTGAAACTATAATTAACAACTCTAAACTATA
CTTCACGAATGCAAATTGT
Found at i:937697 original size:20 final size:20
Alignment explanation
Indices: 937659--937710 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
937649 ATCAACTCTT
937659 AACTATACTTTACGAATGT-A
1 AACTATA-TTTACGAATGTGA
937679 AACTATAGTTTAC-AGATGTGA
1 AACTATA-TTTACGA-ATGTGA
*
937700 ATCTATATTTA
1 AACTATATTTA
937711 TCAGCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 20 0.71
21 7 0.25
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
AACTATATTTACGAATGTGA
Found at i:938042 original size:39 final size:40
Alignment explanation
Indices: 937999--938093 Score: 147
Period size: 39 Copynumber: 2.4 Consensus size: 40
937989 TGCTTTCAGT
* *
937999 GTTAACTATAGTTTACAGATGTGAAACATAGATTATCG-C
1 GTTAACTATAGTTTACAGATGTGAAACACAGATTAACGTC
*
938038 GTTAACTATAGTTTACAGATGTGAAATACAGATTAACGTC
1 GTTAACTATAGTTTACAGATGTGAAACACAGATTAACGTC
*
938078 GGTAACTATAGTTTAC
1 GTTAACTATAGTTTAC
938094 GACCCGTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 35 0.69
40 16 0.31
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (40 bp):
GTTAACTATAGTTTACAGATGTGAAACACAGATTAACGTC
Found at i:942546 original size:16 final size:16
Alignment explanation
Indices: 942522--942552 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
942512 TACTGTAAAC
*
942522 GTATTATATTTAGCGT
1 GTATGATATTTAGCGT
942538 GTATGATATTTAGCG
1 GTATGATATTTAGCG
942553 GAATGTGATT
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:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (16 bp):
GTATGATATTTAGCGT
Found at i:943065 original size:19 final size:19
Alignment explanation
Indices: 943041--943081 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
943031 TCATGCTTGT
**
943041 AACCATATTTTATATTTCA
1 AACCATATTCCATATTTCA
943060 AACCATATTCCATATTTCA
1 AACCATATTCCATATTTCA
943079 AAC
1 AAC
943082 AATTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (19 bp):
AACCATATTCCATATTTCA
Found at i:968680 original size:2 final size:2
Alignment explanation
Indices: 968673--968706 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
968663 ACGAAATATT
*
968673 GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
968707 TGCCCGTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:973009 original size:42 final size:41
Alignment explanation
Indices: 972920--973009 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
972910 AACAGAATTT
* *
972920 TATAAAG-AGTACTTTGGAGTTTAAAAAAACCCCACTGCAA
1 TATAAAGTAGTACTTTGGAGTTAAAAAAAACCCCACTGAAA
* *
972960 TAAAAAGTAGTACTTTGGAGTTGAAAAAAAACCCCTCTGAAA
1 TATAAAGTAGTACTTTGGAGTT-AAAAAAAACCCCACTGAAA
973002 TATAAAGT
1 TATAAAGT
973010 TGTATGTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 6 0.14
41 14 0.33
42 23 0.53
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (41 bp):
TATAAAGTAGTACTTTGGAGTTAAAAAAAACCCCACTGAAA
Found at i:981965 original size:2 final size:2
Alignment explanation
Indices: 981958--982000 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
981948 AATGATGATA
981958 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
982000 C
1 C
982001 CACACACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:986209 original size:2 final size:2
Alignment explanation
Indices: 986202--986226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
986192 NNNNNNNNNN
986202 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
986227 TGTGACTACC
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:993140 original size:2 final size:2
Alignment explanation
Indices: 993135--993169 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
993125 CCCCCCCCAT
993135 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
993170 AGTTGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:994485 original size:2 final size:2
Alignment explanation
Indices: 994480--994514 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
994470 CCCCCCCCAT
994480 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
994515 AGTTGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:998575 original size:34 final size:33
Alignment explanation
Indices: 998526--998617 Score: 89
Period size: 34 Copynumber: 2.7 Consensus size: 33
998516 AATACAGTTG
998526 TGAAATCATA-AAGACAACAATCCAT-ACACAGCAA
1 TGAAATCA-AGAAGACAACAAT-CATGA-ACAGCAA
* *
998560 TGAAATCAAGTAGACAAAAATCATGGAACAGCAA
1 TGAAATCAAGAAGACAACAATCAT-GAACAGCAA
* * *
998594 TGCAATCAGGAAGACAACGATCAT
1 TGAAATCAAGAAGACAACAATCAT
998618 TTTATACTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
33 4 0.08
34 43 0.90
35 1 0.02
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (33 bp):
TGAAATCAAGAAGACAACAATCATGAACAGCAA
Found at i:998907 original size:32 final size:32
Alignment explanation
Indices: 998866--998930 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
998856 ACAATTGTTC
998866 TGCAATGTCGCCTCCTTCATATCCTGCATGAA
1 TGCAATGTCGCCTCCTTCATATCCTGCATGAA
998898 TGCAATGTCGCCTCCTTCATATCCTGCATGAA
1 TGCAATGTCGCCTCCTTCATATCCTGCATGAA
998930 T
1 T
998931 CACCAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (32 bp):
TGCAATGTCGCCTCCTTCATATCCTGCATGAA
Found at i:1009655 original size:12 final size:12
Alignment explanation
Indices: 1009638--1009671 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1009628 ATCAGAGACA
1009638 GACAGACAGATG
1 GACAGACAGATG
1009650 GACAGACAGATG
1 GACAGACAGATG
*
1009662 GATAGACAGA
1 GACAGACAGA
1009672 GTACAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.32, T:0.09
Consensus pattern (12 bp):
GACAGACAGATG
Found at i:1009669 original size:16 final size:16
Alignment explanation
Indices: 1009633--1009671 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1009623 CATTGATCAG
1009633 AGACAGACAGACAGAT
1 AGACAGACAGACAGAT
* **
1009649 GGACAGACAGATGGAT
1 AGACAGACAGACAGAT
1009665 AGACAGA
1 AGACAGA
1009672 GTACAATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.31, T:0.08
Consensus pattern (16 bp):
AGACAGACAGACAGAT
Found at i:1020694 original size:16 final size:17
Alignment explanation
Indices: 1020673--1020705 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1020663 CTTTTTTGGA
1020673 TCAAATTAGTG-TATGT
1 TCAAATTAGTGTTATGT
*
1020689 TCAAATTTGTGTTATGT
1 TCAAATTAGTGTTATGT
1020706 GATGAATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (17 bp):
TCAAATTAGTGTTATGT
Found at i:1020825 original size:54 final size:54
Alignment explanation
Indices: 1020765--1020999 Score: 373
Period size: 54 Copynumber: 4.3 Consensus size: 54
1020755 ATGAAATCTG
* * *
1020765 ATGAAAGTTCTATTTTGTAATGAATCCTGAGTGTTCTATTTTTTGACGACCTTA
1 ATGAAAGTTCTATTTTGTAATGAATCCTGATTGTTATATTTTTTGATGACCTTA
1020819 ATGAAAGTTCTATTTTGTAATGAATCCTGATTGTTATATTTTTTGATGACCTTA
1 ATGAAAGTTCTATTTTGTAATGAATCCTGATTGTTATATTTTTTGATGACCTTA
* *
1020873 ATGAAAGTTCTATTTTGTAATGAATCCTGATCGTTATATTTTTTGATGACCTTG
1 ATGAAAGTTCTATTTTGTAATGAATCCTGATTGTTATATTTTTTGATGACCTTA
* *
1020927 ATGAAAGTTCTATTTTGTAATGAATCCT-ATTTGTTCTATTTTTTGATGAACCTTG
1 ATGAAAGTTCTATTTTGTAATGAATCCTGA-TTGTTATATTTTTTGATG-ACCTTA
*
1020982 ATGAAAGTTCTGTTTTGT
1 ATGAAAGTTCTATTTTGT
1021000 TTCAGAACAA
Statistics
Matches: 171, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
53 1 0.01
54 147 0.86
55 23 0.13
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (54 bp):
ATGAAAGTTCTATTTTGTAATGAATCCTGATTGTTATATTTTTTGATGACCTTA
Found at i:1020828 original size:28 final size:28
Alignment explanation
Indices: 1020797--1020997 Score: 103
Period size: 26 Copynumber: 7.4 Consensus size: 28
1020787 AATCCTGAGT
*
1020797 GTTCTATTTTTTGACGACCTTAATGAAA
1 GTTCTATTTTTTGATGACCTTAATGAAA
* * * ** **
1020825 GTTCTATTTTGTAATGA--ATCCTGATT
1 GTTCTATTTTTTGATGACCTTAATGAAA
*
1020851 GTTATATTTTTTGATGACCTTAATGAAA
1 GTTCTATTTTTTGATGACCTTAATGAAA
* * * ** **
1020879 GTTCTATTTTGTAATGA--ATCCTGATC
1 GTTCTATTTTTTGATGACCTTAATGAAA
* *
1020905 GTTATATTTTTTGATGACCTTGATGAAA
1 GTTCTATTTTTTGATGACCTTAATGAAA
* * **
1020933 GTTCTATTTTGTAATGAATCC-T-AT--TT
1 GTTCTATTTTTTGATG-A-CCTTAATGAAA
*
1020959 GTTCTATTTTTTGATGAACCTTGATGAAA
1 GTTCTATTTTTTGATG-ACCTTAATGAAA
*
1020988 GTTCTGTTTT
1 GTTCTATTTT
1020998 GTTTCAGAAC
Statistics
Matches: 121, Mismatches: 42, Indels: 19
0.66 0.23 0.10
Matches are distributed among these distances:
25 2 0.02
26 53 0.44
27 2 0.02
28 51 0.42
29 11 0.09
30 2 0.02
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.48
Consensus pattern (28 bp):
GTTCTATTTTTTGATGACCTTAATGAAA
Found at i:1022346 original size:15 final size:16
Alignment explanation
Indices: 1022326--1022356 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1022316 GTGCTTCCAG
1022326 TATGAAATAA-AAAAC
1 TATGAAATAACAAAAC
1022341 TATGAAATAACAAAAC
1 TATGAAATAACAAAAC
1022357 AGCTGTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (16 bp):
TATGAAATAACAAAAC
Found at i:1023944 original size:2 final size:2
Alignment explanation
Indices: 1023939--1023975 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1023929 CCTGATCCAT
1023939 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1023976 GGACGATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1025741 original size:4 final size:4
Alignment explanation
Indices: 1025723--1025784 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
1025713 ATCACATTTT
* * * * *
1025723 GTCC GT-C GTCC GTCT GTCT GTCC GTCC GTCC GTCT GTCT GTCC GTCA
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
*
1025770 GTCC GTCT GTCC GTC
1 GTCC GTCC GTCC GTC
1025785 TGTAAACTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.02, C:0.39, G:0.26, T:0.34
Consensus pattern (4 bp):
GTCC
Found at i:1025750 original size:16 final size:16
Alignment explanation
Indices: 1025730--1025784 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1025720 TTTGTCCGTC
* *
1025730 GTCCGTCTGTCTGTCC
1 GTCCGTCAGTCTGTCT
*
1025746 GTCCGTCCGTCTGTCT
1 GTCCGTCAGTCTGTCT
*
1025762 GTCCGTCAGTCCGTCT
1 GTCCGTCAGTCTGTCT
1025778 GTCCGTC
1 GTCCGTC
1025785 TGTAAACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.02, C:0.38, G:0.25, T:0.35
Consensus pattern (16 bp):
GTCCGTCAGTCTGTCT
Found at i:1025754 original size:20 final size:20
Alignment explanation
Indices: 1025722--1025780 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
1025712 GATCACATTT
1025722 TGTCCGT-CGTCCGTCTGTC
1 TGTCCGTCCGTCCGTCTGTC
1025741 TGTCCGTCCGTCCGTCTGTC
1 TGTCCGTCCGTCCGTCTGTC
*
1025761 TGTCCGTCAGTCCGTCTGTC
1 TGTCCGTCCGTCCGTCTGTC
1025781 CGTCTGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.02, C:0.37, G:0.25, T:0.36
Consensus pattern (20 bp):
TGTCCGTCCGTCCGTCTGTC
Found at i:1034097 original size:166 final size:167
Alignment explanation
Indices: 1033814--1034188 Score: 489
Period size: 166 Copynumber: 2.3 Consensus size: 167
1033804 NNNNNNNNAT
*
1033814 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAAC----CAGCCAGGAAAACTGAAACTTGTGTGG
1 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAACTGAAACTTGTGTGA
* * * * *
1033875 AAGCATCCTCAGGTAGTATAGATTCAAATTTGTGAAAATCATGACCCCTTGGGGTAGGTTTGGGC
66 AAGCATCCTCAGGTAGTATAGATTCAAAGTTGTGAAAATAATGACCCCTAGGGGTAGGGTGGGGC
* * * *
1033940 CACAAT-GGGAGGTCGATGTTTTACATAGGAATAAAC
131 CACAATGGGGAGGTCAAAGTTTAACAAAGGAATAAAC
*
1033976 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGA
1 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAACTGAAACTTGTGTGA
* *
1034041 AAGCATCCTCAGGTAGTGTAGATTCAGAGTTGTGAAAATAATGATCCCC-AGGGGTAGGGTGGGG
66 AAGCATCCTCAGGTAGTATAGATTCAAAGTTGTGAAAATAATGA-CCCCTAGGGGTAGGGTGGGG
* * *
1034105 CCACAATGGGGGGGGGGGTCAAAGTTTAACAAAGGAATATAT
130 CCACAAT----GGGGAGGTCAAAGTTTAACAAAGGAATAAAC
*
1034147 AGGGTAAATCTTTAAAAA---TCTTCTCAGAAACTAATCAGCCAG
1 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1034189 ATGATTCTTT
Statistics
Matches: 186, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
162 34 0.18
166 84 0.45
167 4 0.02
168 24 0.13
171 40 0.22
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (167 bp):
AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAACTGAAACTTGTGTGA
AAGCATCCTCAGGTAGTATAGATTCAAAGTTGTGAAAATAATGACCCCTAGGGGTAGGGTGGGGC
CACAATGGGGAGGTCAAAGTTTAACAAAGGAATAAAC
Found at i:1035736 original size:17 final size:17
Alignment explanation
Indices: 1035716--1035749 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1035706 CATGTCACAA
1035716 TCATAAAATACTTACTT
1 TCATAAAATACTTACTT
1035733 TCATAAAATACTTACTT
1 TCATAAAATACTTACTT
1035750 ACTCTAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATAAAATACTTACTT
Found at i:1036175 original size:16 final size:16
Alignment explanation
Indices: 1036156--1036199 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1036146 CTTTAGTCAT
1036156 GGGTACGTTTTCACCA
1 GGGTACGTTTTCACCA
*
1036172 GGGTACGTTTTCACCT
1 GGGTACGTTTTCACCA
1036188 GGGTACGTTTTC
1 GGGTACGTTTTC
1036200 TTTGGTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (16 bp):
GGGTACGTTTTCACCA
Found at i:1037699 original size:23 final size:22
Alignment explanation
Indices: 1037672--1037716 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1037662 CTACTTTGAA
*
1037672 GTTTTGGGTTGTTTTTGTTTTTT
1 GTTTTGGGTTGTTGTT-TTTTTT
**
1037695 GTTTTTTGTTGTTGTTTTTTTT
1 GTTTTGGGTTGTTGTTTTTTTT
1037717 ATTGAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (22 bp):
GTTTTGGGTTGTTGTTTTTTTT
Found at i:1043579 original size:13 final size:13
Alignment explanation
Indices: 1043561--1043586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1043551 ACATGTCACA
1043561 ATCATAAAATACT
1 ATCATAAAATACT
1043574 ATCATAAAATACT
1 ATCATAAAATACT
1043587 TACTTACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATAAAATACT
Found at i:1044037 original size:16 final size:16
Alignment explanation
Indices: 1044018--1044057 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1044008 AGTCATGGGT
*
1044018 ACGTTTTTACCAGGGA
1 ACGTTTTCACCAGGGA
* *
1044034 ACGTTTTCACCTGGGT
1 ACGTTTTCACCAGGGA
1044050 ACGTTTTC
1 ACGTTTTC
1044058 TTTGGTTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (16 bp):
ACGTTTTCACCAGGGA
Found at i:1047152 original size:30 final size:30
Alignment explanation
Indices: 1047116--1047177 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1047106 ACTTCGGGAA
*
1047116 TATCATAGTGGGAACAGACCCTGCAGCCTC
1 TATCATAGTGGGAACAGACCCTCCAGCCTC
*
1047146 TATCATAGTGGGAACAGATCCTCCAGCCTC
1 TATCATAGTGGGAACAGACCCTCCAGCCTC
1047176 TA
1 TA
1047178 AGATTGTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (30 bp):
TATCATAGTGGGAACAGACCCTCCAGCCTC
Found at i:1050574 original size:17 final size:17
Alignment explanation
Indices: 1050554--1050587 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1050544 CATGTCACAA
1050554 TCATAAAATACTTACTT
1 TCATAAAATACTTACTT
1050571 TCATAAAATACTTACTT
1 TCATAAAATACTTACTT
1050588 ACTTACTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATAAAATACTTACTT
Found at i:1072190 original size:20 final size:20
Alignment explanation
Indices: 1072165--1072205 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1072155 TTTAGAAACG
1072165 ATCATTGTTATAAATCTACA
1 ATCATTGTTATAAATCTACA
1072185 ATCATTGTTATAAATCTACA
1 ATCATTGTTATAAATCTACA
1072205 A
1 A
1072206 ACAACCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (20 bp):
ATCATTGTTATAAATCTACA
Found at i:1072788 original size:96 final size:96
Alignment explanation
Indices: 1072680--1072996 Score: 361
Period size: 96 Copynumber: 3.2 Consensus size: 96
1072670 CTGGAATCCT
*
1072680 TGACTAAATCTTCCACACTTACTTGACTAAATCTGTCTAAACTATCTGAAATATTTGACTAAACA
1 TGACTAAATCTTCCACACTTACTTGACTAAATCTGACTAAACTATCTGAAATATTTGACTAAACA
*
1072745 TGCTAAATTTGTTCAAATCAAGTGGAGTACC
66 TGCTAAATTTGTTCAAATCATGTGGAGTACC
* *
1072776 TGACTAAATCTTCCACAGTTAAGGTACTTGGACTAAACACATACTTGACTAAATCTGTCT-AAAC
1 TGACTAAATCTTCCACA-CT----TACTT-GACT--A-A-AT-C-TGACTAAA-CTATCTGAAA-
* * * *
1072840 TATCTGGA--ATACTTGACTAAATTTGTTCAAATCATGTGGTGTACC
52 TAT-TTGACTAAACATG-CTAAATTTGTTCAAATCATGTGGAGTACC
* *
1072885 TGACTAAATCTTCAACACTTACATGACTAAATCTGACTAAACTATCTGAAATATTTGACTAAACA
1 TGACTAAATCTTCCACACTTACTTGACTAAATCTGACTAAACTATCTGAAATATTTGACTAAACA
* *
1072950 TGCTAAATTTGTTCAAATCATCTGCAGTACC
66 TGCTAAATTTGTTCAAATCATGTGGAGTACC
1072981 TGACTAAATCTTCCAC
1 TGACTAAATCTTCCAC
1072997 CTCCAGAACG
Statistics
Matches: 183, Mismatches: 19, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
95 3 0.02
96 66 0.36
97 17 0.09
98 1 0.01
99 2 0.01
100 1 0.01
101 6 0.03
102 4 0.02
103 4 0.02
104 5 0.03
105 1 0.01
106 2 0.01
107 1 0.01
108 16 0.09
109 51 0.28
110 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (96 bp):
TGACTAAATCTTCCACACTTACTTGACTAAATCTGACTAAACTATCTGAAATATTTGACTAAACA
TGCTAAATTTGTTCAAATCATGTGGAGTACC
Found at i:1073716 original size:14 final size:14
Alignment explanation
Indices: 1073697--1073726 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1073687 AAACCAAAAG
1073697 CAGATGTTCATCAA
1 CAGATGTTCATCAA
*
1073711 CAGATGTTCATTAA
1 CAGATGTTCATCAA
1073725 CA
1 CA
1073727 TATTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (14 bp):
CAGATGTTCATCAA
Found at i:1074191 original size:12 final size:12
Alignment explanation
Indices: 1074174--1074199 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1074164 TTAAGATGTA
1074174 ACTGTATAATTT
1 ACTGTATAATTT
1074186 ACTGTATAATTT
1 ACTGTATAATTT
1074198 AC
1 AC
1074200 AACTACCAAG
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:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (12 bp):
ACTGTATAATTT
Found at i:1081709 original size:31 final size:30
Alignment explanation
Indices: 1081674--1081734 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1081664 GCAACCATTT
* *
1081674 TTGAAAAAATTTAATTATCATGGAGTTGCC
1 TTGAAAAAAATTAATTAACATGGAGTTGCC
*
1081704 NTTGAAAAAAATTAATTAACATGGGGTTGCC
1 -TTGAAAAAAATTAATTAACATGGAGTTGCC
1081735 CCCCCCCCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (30 bp):
TTGAAAAAAATTAATTAACATGGAGTTGCC
Found at i:1090630 original size:5 final size:5
Alignment explanation
Indices: 1090620--1090706 Score: 90
Period size: 5 Copynumber: 17.8 Consensus size: 5
1090610 CTGTAAAGTG
* *
1090620 CGAAA CGAAA CGAAA CCG-AA CGAAA CGAAA CCAAT CGAAA CGAAA CGAAA
1 CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
* * * *
1090670 CCAAA CGAAA CGAAA CCAAA --AAT CGAAA CGGAA CGAA
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAA
1090707 TTATATAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 61 0.91
6 2 0.03
ACGTcount: A:0.56, C:0.24, G:0.17, T:0.02
Consensus pattern (5 bp):
CGAAA
Found at i:1090872 original size:5 final size:5
Alignment explanation
Indices: 1090864--1090989 Score: 132
Period size: 5 Copynumber: 25.4 Consensus size: 5
1090854 GTTTAAATTC
* * * * *
1090864 CGTTT CGTTT CGTCT CGATT --TTT GGTTT CGTTT CGTTT GGTTT GGTTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT
* * * *
1090912 CGTTT CGATT GGTTT CGTTT CGTTT CGATT GGTTT CGTTT CG-TT CGATTT
1 CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT
1090962 CGTTT CGTTT CGTTT CGATTT CGTTT CG
1 CGTTT CGTTT CGTTT CG-TTT CGTTT CG
1090990 CACTTTACAG
Statistics
Matches: 101, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
3 2 0.02
4 4 0.04
5 86 0.85
6 9 0.09
ACGTcount: A:0.04, C:0.17, G:0.24, T:0.56
Consensus pattern (5 bp):
CGTTT
Found at i:1090909 original size:20 final size:20
Alignment explanation
Indices: 1090865--1090981 Score: 159
Period size: 20 Copynumber: 6.0 Consensus size: 20
1090855 TTTAAATTCC
*
1090865 GTTTCGTTTCGTCTCGATT-
1 GTTTCGTTTCGTTTCGATTG
* *
1090884 -TTTGGTTTCGTTTCGTTTG
1 GTTTCGTTTCGTTTCGATTG
*
1090903 GTTTGGTTTCGTTTCGATTG
1 GTTTCGTTTCGTTTCGATTG
1090923 GTTTCGTTTCGTTTCGATTG
1 GTTTCGTTTCGTTTCGATTG
*
1090943 GTTTCGTTTCG-TTCGATTTC
1 GTTTCGTTTCGTTTCGA-TTG
1090963 GTTTCGTTTCGTTTCGATT
1 GTTTCGTTTCGTTTCGATT
1090982 TCGTTTCGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
18 15 0.17
19 5 0.06
20 63 0.72
21 5 0.06
ACGTcount: A:0.04, C:0.15, G:0.24, T:0.56
Consensus pattern (20 bp):
GTTTCGTTTCGTTTCGATTG
Found at i:1091484 original size:39 final size:39
Alignment explanation
Indices: 1091430--1091505 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1091420 TTTGCTCCCC
1091430 AGCAAAGCGGACCGAAAACCCTTGGCTAGCGAAGATGGG
1 AGCAAAGCGGACCGAAAACCCTTGGCTAGCGAAGATGGG
1091469 AGCAAAGCGGACCGAAAACCCTTGGCTAGCGAAGATG
1 AGCAAAGCGGACCGAAAACCCTTGGCTAGCGAAGATG
1091506 CCTATTAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.32, T:0.11
Consensus pattern (39 bp):
AGCAAAGCGGACCGAAAACCCTTGGCTAGCGAAGATGGG
Found at i:1097865 original size:4 final size:4
Alignment explanation
Indices: 1097850--1097899 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
1097840 ATCACTTTTT
* * *
1097850 GTCC GT-C GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTCT GTCT GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
1097897 GTC
1 GTC
1097900 TGTAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32
Consensus pattern (4 bp):
GTCC
Found at i:1097900 original size:12 final size:12
Alignment explanation
Indices: 1097856--1097902 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1097846 TTTTGTCCGT
*
1097856 CGTCCGTCCGTC
1 CGTCCGTCTGTC
1097868 CGTCCGTCTGTC
1 CGTCCGTCTGTC
1097880 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
1097892 TGTCCGTCTGT
1 CGTCCGTCTGT
1097903 AAACTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.34
Consensus pattern (12 bp):
CGTCCGTCTGTC
Done.