Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold619
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: 1099986
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 119690 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:872678 original size:16 final size:16
Alignment explanation
Indices: 872640--872677 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
872630 CTGAGCCCGA
872640 TTTTTTTCCGAAATTT
1 TTTTTTTCCGAAATTT
*
872656 TTTTTTTCC-ACATTT
1 TTTTTTTCCGAAATTT
872671 TTTTTTT
1 TTTTTTT
872678 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTTTCCGAAATTT
Found at i:875308 original size:20 final size:20
Alignment explanation
Indices: 875283--875325 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
875273 TATATAATCA
875283 CCTTCTACATCATTGTTGGT
1 CCTTCTACATCATTGTTGGT
875303 CCTTCTACATCATTGTTGGT
1 CCTTCTACATCATTGTTGGT
875323 CCT
1 CCT
875326 GATGGCCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (20 bp):
CCTTCTACATCATTGTTGGT
Found at i:876117 original size:21 final size:21
Alignment explanation
Indices: 876091--876391 Score: 409
Period size: 21 Copynumber: 14.4 Consensus size: 21
876081 TTAGATGATT
876091 TTATTATATGCTGTGGG-TCTA
1 TTATTATATGCTGTGGGTTC-A
876112 TTATTATATGCTGT-GGTTCTA
1 TTATTATATGCTGTGGGTTC-A
*
876133 TAATTATATGCTGTGGG-TCTA
1 TTATTATATGCTGTGGGTTC-A
876154 TTATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTCA
*
876175 --ATTATATGCTGCGGGTTCA
1 TTATTATATGCTGTGGGTTCA
*
876194 TAATTATATGCTGTGGG-TCTA
1 TTATTATATGCTGTGGGTTC-A
876215 TTATTATATGCTGT-GGTTCTA
1 TTATTATATGCTGTGGGTTC-A
876236 TTATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTCA
* *
876257 TAATTATATGCTGTGGTTTCA
1 TTATTATATGCTGTGGGTTCA
*
876278 TTATTATATGCTGTGGTTTCA
1 TTATTATATGCTGTGGGTTCA
* *
876299 TAATTATATGCCGTGGGTTCA
1 TTATTATATGCTGTGGGTTCA
876320 TTATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTCA
*
876341 TAATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTCA
*
876362 TAATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTCA
*
876383 TAATTATAT
1 TTATTATAT
876392 ATGCTGTCGG
Statistics
Matches: 258, Mismatches: 14, Indels: 16
0.90 0.05 0.06
Matches are distributed among these distances:
19 18 0.07
20 6 0.02
21 225 0.87
22 9 0.03
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (21 bp):
TTATTATATGCTGTGGGTTCA
Found at i:876927 original size:21 final size:21
Alignment explanation
Indices: 876901--877496 Score: 704
Period size: 21 Copynumber: 28.5 Consensus size: 21
876891 CGTGTTTGCT
*
876901 CATATAATCATGAACCCACAG
1 CATATAATAATGAACCCACAG
876922 CATATAATAATGAACCCACAG
1 CATATAATAATGAACCCACAG
*
876943 CATATAATAATGAAACCACAG
1 CATATAATAATGAACCCACAG
* *
876964 CATATAATTATGAAACCACAG
1 CATATAATAATGAACCCACAG
*
876985 CATATAATAATGAAACCACAG
1 CATATAATAATGAACCCACAG
877006 CATATAATAATGAACCCACAG
1 CATATAATAATGAACCCACAG
*
877027 CATATAATTATGAACCCACAG
1 CATATAATAATGAACCCACAG
*
877048 CATATAATAATGAAACCACAG
1 CATATAATAATGAACCCACAG
*
877069 CATATAATTATGAACCCACAG
1 CATATAATAATGAACCCACAG
*
877090 CATATAATAATGAAACCACAG
1 CATATAATAATGAACCCACAG
* *
877111 TATATAATTATGAACCCACAG
1 CATATAATAATGAACCCACAG
* *
877132 CATATAATCAT-AGACCGACAG
1 CATATAATAATGA-ACCCACAG
*
877153 CATATAATAAT-AGACCGACAG
1 CATATAATAATGA-ACCCACAG
* *
877174 CATATAATTATGAACCAACAG
1 CATATAATAATGAACCCACAG
877195 CATATAAT--TGAACCCACAG
1 CATATAATAATGAACCCACAG
*
877214 CATATAATAAT-AGATCCACAG
1 CATATAATAATGA-ACCCACAG
*
877235 CATA-AATTAAT-AGACCAACAG
1 CATATAA-TAATGA-ACCCACAG
*
877256 CATATAATTATAGAA-CCACAG
1 CATATAATAAT-GAACCCACAG
877277 CATATAATAATAGAA-CCACAG
1 CATATAATAAT-GAACCCACAG
877298 CATATAATAATAGAA-CCACAG
1 CATATAATAAT-GAACCCACAG
* * *
877319 CATATAATTATAAAACCACAG
1 CATATAATAATGAACCCACAG
877340 CATATAATAAT-AGACCCACAG
1 CATATAATAATGA-ACCCACAG
*
877361 CATATAATTATAGAA-CCACAG
1 CATATAATAAT-GAACCCACAG
877382 CATATAATAAT-AGACCCACAG
1 CATATAATAATGA-ACCCACAG
*
877403 CATATAATTAT-AGACCCACAG
1 CATATAATAATGA-ACCCACAG
*
877424 CATATAATTAT-AGACCCACAG
1 CATATAATAATGA-ACCCACAG
*
877445 CATATAATTATAGAA-CCACAG
1 CATATAATAAT-GAACCCACAG
877466 CATATAATAAT-AGACCCACAG
1 CATATAATAATGA-ACCCACAG
877487 CATATAATAA
1 CATATAATAA
877497 AATCATCTAA
Statistics
Matches: 520, Mismatches: 36, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
19 20 0.04
20 9 0.02
21 482 0.93
22 6 0.01
23 3 0.01
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (21 bp):
CATATAATAATGAACCCACAG
Found at i:878149 original size:33 final size:33
Alignment explanation
Indices: 878102--878164 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
878092 TTATGACCCA
* *
878102 CTATACATTTGAAATATCATTTTGTATCCCCTG
1 CTATACATTAGAAATATCATTGTGTATCCCCTG
878135 CTATACATTAGAAATATCATTGTGTATCCC
1 CTATACATTAGAAATATCATTGTGTATCCC
878165 AACAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (33 bp):
CTATACATTAGAAATATCATTGTGTATCCCCTG
Found at i:887877 original size:2 final size:2
Alignment explanation
Indices: 887870--887913 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
887860 ATATTTCTCG
887870 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
887912 GA
1 GA
887914 CGGACAGAGA
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:887922 original size:14 final size:14
Alignment explanation
Indices: 887873--887936 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
887863 TTTCTCGGAG
*
887873 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAC
*
887887 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAC
887901 AGAGAGAGAGAGAC
1 AGAGAGAGAGAGAC
* *
887915 GGACAGAGACG-GAC
1 AGAGAGAGA-GAGAC
*
887929 AGACAGAG
1 AGAGAGAG
887937 TGCATCAGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
14 44 0.98
15 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.45, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGAGAC
Found at i:892693 original size:2 final size:2
Alignment explanation
Indices: 892686--892732 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
892676 ACCTTGAAAA
892686 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
892728 TC TC T
1 TC TC T
892733 TGATAGACGT
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:895560 original size:2 final size:2
Alignment explanation
Indices: 895553--895595 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
895543 CTTGGTCATG
895553 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
895595 G
1 G
895596 TCATACAAGT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:902378 original size:3 final size:3
Alignment explanation
Indices: 902366--902398 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
902356 TGATATATCT
*
902366 TTC TTC -TC TTC TTC TTC TTT TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
902399 GAGAATATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:906329 original size:3 final size:3
Alignment explanation
Indices: 906321--906483 Score: 193
Period size: 3 Copynumber: 54.3 Consensus size: 3
906311 NNNNNNNNNN
906321 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
* ** *
906369 GTG GGG ATG GT- ATTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG A-TG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
** * * * * * *
906414 ATG ATG ATG ATG ATG ATG ATG ATG ATG AAA ACG ACG ACG ACG ACG ACG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
906462 ACG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG A
906484 CTTTACAAAT
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
3 146 0.99
4 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.34, T:0.28
Consensus pattern (3 bp):
ATG
Found at i:906877 original size:3 final size:3
Alignment explanation
Indices: 906869--906949 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
906859 CTACTGTATA
* * *
906869 ACT ACT ACT ACT ACT A-T AATT ACT ACT ACT ACT ACT TCT A-G ATCT
1 ACT ACT ACT ACT ACT ACT -ACT ACT ACT ACT ACT ACT ACT ACT A-CT
* * * *
906914 ACT ACT ACT ACT ACT ACA AGT ACT ACA ACT ATT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
906950 TTTATCATAA
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.03
3 57 0.93
4 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (3 bp):
ACT
Found at i:906886 original size:18 final size:18
Alignment explanation
Indices: 906865--906902 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
906855 TTTCCTACTG
906865 TATAACTACTACTACTAC
1 TATAACTACTACTACTAC
*
906883 TATAATTACTACTACTAC
1 TATAACTACTACTACTAC
906901 TA
1 TA
906903 CTTCTAGATC
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:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAACTACTACTACTAC
Found at i:906895 original size:21 final size:21
Alignment explanation
Indices: 906869--906949 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
906859 CTACTGTATA
906869 ACTACTACTACTACTATAATT
1 ACTACTACTACTACTATAATT
*
906890 ACTACTACTACTACTTCTAGATCT
1 ACTACTACTACTAC-TATA-AT-T
* *
906914 ACTACTACTACTACTACAAGT
1 ACTACTACTACTACTATAATT
* *
906935 ACTACAACTATTACT
1 ACTACTACTACTACT
906950 TTTATCATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 28 0.55
22 4 0.08
23 4 0.08
24 15 0.29
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (21 bp):
ACTACTACTACTACTATAATT
Found at i:911633 original size:15 final size:15
Alignment explanation
Indices: 911613--911642 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
911603 TTTTTGTTTT
911613 TGTTACACCAAGGAC
1 TGTTACACCAAGGAC
911628 TGTTACACCAAGGAC
1 TGTTACACCAAGGAC
911643 ATATTTATGA
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:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (15 bp):
TGTTACACCAAGGAC
Found at i:912662 original size:19 final size:19
Alignment explanation
Indices: 912638--912748 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
912628 TACTAGGTTA
912638 TTGTATAATTATAACTTTG
1 TTGTATAATTATAACTTTG
912657 TTGTATAATTATAACTTTG
1 TTGTATAATTATAACTTTG
*
912676 TTGTATAATTGTAACTTTG
1 TTGTATAATTATAACTTTG
912695 TTGTATAATTATAACTTTG
1 TTGTATAATTATAACTTTG
* ****
912714 TTGTATAATTATGACCCAA
1 TTGTATAATTATAACTTTG
912733 TTGTATAATTATAACT
1 TTGTATAATTATAACT
912749 CTGACTTCTT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (19 bp):
TTGTATAATTATAACTTTG
Found at i:913267 original size:15 final size:16
Alignment explanation
Indices: 913240--913269 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
913230 AATTCATGAA
913240 ATAGTATTATACTATT
1 ATAGTATTATACTATT
913256 ATAGTA-TATACTAT
1 ATAGTATTATACTAT
913270 AAATAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
ATAGTATTATACTATT
Found at i:917112 original size:10 final size:11
Alignment explanation
Indices: 917086--917132 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
917076 AACTAAACCC
917086 TGGGTTTACTTTT
1 TGGGTTTAC--TT
917099 TGGGTTTA-TT
1 TGGGTTTACTT
*
917109 TGGGGTTTACTC
1 T-GGGTTTACTT
917121 TGGGTTTACTT
1 TGGGTTTACTT
917132 T
1 T
917133 TTGAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 3 0.10
11 17 0.57
12 2 0.07
13 8 0.27
ACGTcount: A:0.09, C:0.09, G:0.28, T:0.55
Consensus pattern (11 bp):
TGGGTTTACTT
Found at i:926149 original size:329 final size:328
Alignment explanation
Indices: 925547--926418 Score: 1198
Period size: 329 Copynumber: 2.6 Consensus size: 328
925537 CCGCCGGGGG
* * * *
925547 GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAATTTCACAAAGGAATATATAGAGTAAATATT
1 GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAGTTTAACATA-GAATATATAGAGTAAATCTT
* * *
925612 TTAAAATCTTATTCTCAGAAACTAATCAGCCAGGAAAGCTGAAATTTGTGTGAAAGCATTCTCAG
65 TAAAAATC---TTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAG
*
925677 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCCGGGGGTAGGGTGAGGCCACAATAGGGG
127 GTAGTGTAGATTCAAAGTTGTGAAAATCATGA-CCCCCAGGGGTAGGGTGAGGCCACAATAGGGG
* * *
925742 GTCGAAGTTTAACATAGGAATATATAGTGTAAATCTTAAAAATCTTCTTCTCAGAAACTAATCAG
191 GTCAAAGTTTAACATAGGAATATACAGAGTAAATCTTAAAAATCTTCTTCTCAGAAACTAATCAG
*
925807 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
256 CCAAGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA
*
925872 TGACCCCT
321 TGACCCCC
* * * * *
925880 GGGGGTAGGGT-GGGGCCACAATGGGGGGGGGTCGAAGTTTAACGT-GAATATATAGAGTTAATC
1 GGGGGTAGGGTGGGGGCAACAAT---GGGAGGTCAAAGTTTAACATAGAATATATAGAGTAAATC
* *
925943 TTTAAAAATCTTCTCAGAAACTTATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGA
63 TTTAAAAATCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGG
* * *
926008 TAGTGTAGATTGAAAG-TGTGAAAATCATGACCCCTAGGGGTAGGGT-AGGGTTCACAAT-GTGG
128 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGA-GG-CCACAATAG-GG
* * *
926070 GGTCAAAGTTTAACATTGGAATATACAGAGTAAATCTTTAATATCTTCTTCTCAGAAACTAATCA
190 GGTCAAAGTTTAACATAGGAATATACAGAGTAAATCTTAAAAATCTTCTTCTCAGAAACTAATCA
*
926135 GCTAAGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATC
255 GCCAAGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATC
926200 ATGACCCCC
320 ATGACCCCC
926209 GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCTT
1 GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAGTTTAACATA-GAATATATAGAGTAAATCTT
** * * **
926274 TAAAAATCTTCTTCTCAGAAACTAATCAGCCAACAAAGCTTAAACTTGTATGGCAGCATCCTCAG
65 TAAAAA---TCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAG
* * * * * *
926339 GTAATGTAGATTCAAAGTTATGAAAATCATGATCCCCAGGGGTAGGATGGGGCCAGAAT-GGGAG
127 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGAGGCCACAATAGGG-G
*
926403 GTCGAAGTTTAACATA
191 GTCAAAGTTTAACATA
926419 TAAATATGTT
Statistics
Matches: 473, Mismatches: 51, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
327 18 0.04
328 17 0.04
329 188 0.40
330 76 0.16
331 2 0.00
332 94 0.20
333 64 0.14
335 14 0.03
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (328 bp):
GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAGTTTAACATAGAATATATAGAGTAAATCTTT
AAAAATCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAG
TGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGAGGCCACAATAGGGGGTCAA
AGTTTAACATAGGAATATACAGAGTAAATCTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAAG
AAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACC
CCC
Found at i:926334 original size:167 final size:166
Alignment explanation
Indices: 925547--926418 Score: 1197
Period size: 166 Copynumber: 5.3 Consensus size: 166
925537 CCGCCGGGGG
* * * * *
925547 GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAATTTCACAAAGGAATATATAGAGTAAATATT
1 GGGGGTAGGGT-GGGGCCACAATGGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCTT
* * * * *
925612 TTAAAATCTTATTCTCAGAAACTAATCAGCCAGGAAAGCTGAAATTTGTGTGAAAGCATTCTCAG
65 TAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
925677 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCC
130 GTAGTGTAGATTCAAAGTTGTGAAAATCATGA-CCCCC
* * *
925715 GGGGGTAGGGTGAGGCCACAATAGGG-GGTCGAAGTTTAACATAGGAATATATAGTGTAAATC-T
1 GGGGGTAGGGTGGGGCCACAAT-GGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCTT
925778 TAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
65 TAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
*
925843 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCT
130 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
* * * *
925880 GGGGGTAGGGTGGGGCCACAATGGGGGGGGGTCGAAGTTTAACGT--GAATATATAGAGTTAATC
1 GGGGGTAGGGTGGGGCCACAAT---GGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATC
* *
925943 TTTAAAAA---TCTTCTCAGAAACTTATCAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTC
63 TTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTC
* * *
926005 AGATAGTGTAGATTGAAAG-TGTGAAAATCATGACCCCT
128 AGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
* ** * *
926043 AGGGGTAGGGTAGGGTTCACAATGTGG-GGTCAAAGTTTAACATTGGAATATACAGAGTAAATCT
1 GGGGGTAGGGT-GGGGCCACAATG-GGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCT
* * *
926107 TT-AATATCTTCTTCTCAGAAACTAATCAGCTAAGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
64 TTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
926171 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
129 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
*
926209 GGGGGTAGGGTGGGGGCAACAATGGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCTT
1 GGGGGTAGGGT-GGGGCCACAATGGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCTT
** * * *
926274 TAAAAATCTTCTTCTCAGAAACTAATCAGCCAACAAAGCTTAAACTTGTATGGCAGCATCCTCAG
65 TAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
* * *
926339 GTAATGTAGATTCAAAGTTATGAAAATCATGATCCCC
130 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
* * * *
926376 AGGGGTAGGATGGGGCCAGAATGGGAGGTCGAAGTTTAACATA
1 GGGGGTAGGGTGGGGCCACAATGGGAGGTCAAAGTTTAACATA
926419 TAAATATGTT
Statistics
Matches: 630, Mismatches: 59, Indels: 32
0.87 0.08 0.04
Matches are distributed among these distances:
161 15 0.02
162 5 0.01
163 48 0.08
164 78 0.12
165 94 0.15
166 212 0.34
167 149 0.24
168 29 0.05
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (166 bp):
GGGGGTAGGGTGGGGCCACAATGGGAGGTCAAAGTTTAACATAGGAATATATAGAGTAAATCTTT
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC
Found at i:927060 original size:1 final size:1
Alignment explanation
Indices: 927056--927093 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
927046 TAAATGTTCA
927056 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
927094 ATTGATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:928639 original size:2 final size:2
Alignment explanation
Indices: 928632--928660 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
928622 CACAAGAAAT
928632 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 T
928661 GTATGACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:930690 original size:75 final size:74
Alignment explanation
Indices: 930566--930715 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 74
930556 TAAAGAAGGA
930566 TAACTCTGACCATGCTCACCGAGCAGGAGTTATCGAAACTTGACATGGCGGACGGGGAATTAAAA
1 TAACTCTGACCATGCTCACCGAGCAGGAGTTATCGAAACTTGACATGGCGGACGGGGAATTAAAA
930631 ACTCCCTTG
66 ACTCCCTTG
*
930640 TNAACTCTGACCATGCTCACCTAGCAGGAGTTATCGAAACTTGACATGGCGGACGGGGAATTAAA
1 T-AACTCTGACCATGCTCACCGAGCAGGAGTTATCGAAACTTGACATGGCGGACGGGGAATTAAA
930705 AACTCCCTTG
65 AACTCCCTTG
930715 T
1 T
930716 CGACAACGCC
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 1 0.01
75 73 0.99
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (74 bp):
TAACTCTGACCATGCTCACCGAGCAGGAGTTATCGAAACTTGACATGGCGGACGGGGAATTAAAA
ACTCCCTTG
Found at i:931143 original size:16 final size:16
Alignment explanation
Indices: 931101--931143 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
931091 TACAGTCAAG
* *
931101 TCGTACCCAACCCGAC
1 TCGTACCCAAACCAAC
*
931117 TCGCACCCAAACCAAC
1 TCGTACCCAAACCAAC
*
931133 TCGTACTCAAA
1 TCGTACCCAAA
931144 TGGTCAGGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.44, G:0.09, T:0.14
Consensus pattern (16 bp):
TCGTACCCAAACCAAC
Found at i:931229 original size:15 final size:15
Alignment explanation
Indices: 931209--931243 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
931199 AGATCACTTG
*
931209 TTCGCGCTGAGAGGT
1 TTCGCGCCGAGAGGT
*
931224 TTCGCGCCGAGTGGT
1 TTCGCGCCGAGAGGT
931239 TTCGC
1 TTCGC
931244 CCCTTTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.26, G:0.37, T:0.29
Consensus pattern (15 bp):
TTCGCGCCGAGAGGT
Found at i:941839 original size:16 final size:16
Alignment explanation
Indices: 941818--941865 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
941808 ACAGAATGCT
941818 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
941834 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
941850 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
941866 ATTTATCAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Found at i:942669 original size:16 final size:16
Alignment explanation
Indices: 942648--942695 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
942638 TCGGAAATTT
942648 TGTATACGAGTTGACC
1 TGTATACGAGTTGACC
**
942664 TGTATACGAGTTGGTC
1 TGTATACGAGTTGACC
* *
942680 TGTGTACGACTTGACC
1 TGTATACGAGTTGACC
942696 GGACACCGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (16 bp):
TGTATACGAGTTGACC
Found at i:945408 original size:33 final size:32
Alignment explanation
Indices: 945317--945395 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
945307 CCTAGCCATC
945317 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
*
945349 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
945381 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
945396 GCTGACTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:946566 original size:16 final size:15
Alignment explanation
Indices: 946538--946571 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
946528 AAGGGTAATT
*
946538 AAAAAAAACCCAAAA
1 AAAAAAAAACCAAAA
946553 AAAAAACAAACCAAAA
1 AAAAAA-AAACCAAAA
946569 AAA
1 AAA
946572 CAACCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACCAAAA
Found at i:946954 original size:20 final size:20
Alignment explanation
Indices: 946931--946969 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
946921 TGAGATTGAT
*
946931 TGTTTTTTTCATGGATTGTC
1 TGTTGTTTTCATGGATTGTC
*
946951 TGTTGTTTTCATGGTTTGT
1 TGTTGTTTTCATGGATTGT
946970 TTAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (20 bp):
TGTTGTTTTCATGGATTGTC
Found at i:949701 original size:10 final size:10
Alignment explanation
Indices: 949686--949716 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
949676 CGCACTAAAA
949686 AGCGCCCGGG
1 AGCGCCCGGG
*
949696 AGCGCCCGAG
1 AGCGCCCGGG
949706 AGCGCCCGGG
1 AGCGCCCGGG
949716 A
1 A
949717 TTATATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.16, C:0.39, G:0.45, T:0.00
Consensus pattern (10 bp):
AGCGCCCGGG
Found at i:951371 original size:20 final size:21
Alignment explanation
Indices: 951340--951389 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
951330 TCTTTTAATG
951340 TAAAAAATACAAACAG-AAAAA
1 TAAAAAA-ACAAACAGAAAAAA
951361 TAAAAAAACAAACAGAAAAAA
1 TAAAAAAACAAACAGAAAAAA
951382 TAAAAAAA
1 TAAAAAAA
951390 TTAGAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.80, C:0.08, G:0.04, T:0.08
Consensus pattern (21 bp):
TAAAAAAACAAACAGAAAAAA
Found at i:953967 original size:95 final size:94
Alignment explanation
Indices: 953803--953992 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 94
953793 AATACTGTAT
*
953803 ATAATATGCATTTCTATATGGTTACTACCTACGACTAAAAGAATGATTTTTAAGGTGTAAATAAA
1 ATAATATGCATTTCTATATGGTTACCACCTACGACTAAAAGAATGATTTTTAAGGTGTAAATAAA
953868 ATCCATATTAAGCAGTTTCCCATTCTAAA
66 ATCCATATTAAGCAGTTTCCCATTCTAAA
953897 ANTAATATGCATTTCTATATGGTTACCACCTACGACTAAAAGAATGATTTTTAAGGTGTAAATAA
1 A-TAATATGCATTTCTATATGGTTACCACCTACGACTAAAAGAATGATTTTTAAGGTGTAAATAA
953962 AATCCATATTAAGCAGTTTCCCATTCTAAA
65 AATCCATATTAAGCAGTTTCCCATTCTAAA
953992 A
1 A
953993 ATTATCAGAT
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 1 0.01
95 93 0.99
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (94 bp):
ATAATATGCATTTCTATATGGTTACCACCTACGACTAAAAGAATGATTTTTAAGGTGTAAATAAA
ATCCATATTAAGCAGTTTCCCATTCTAAA
Found at i:957011 original size:42 final size:40
Alignment explanation
Indices: 956974--957101 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 40
956964 GAATTCATTG
956974 AATTTATTATAACATATTAAATTCGTTATAACAAATTCCAAAA
1 AATTT-TTATAACATATTAAATTCGTTATAACAAATT-C-AAA
* * * * *
957017 AATTTTTATTACAAATTTAATTCGTTATAACAGATTCAAC
1 AATTTTTATAACATATTAAATTCGTTATAACAAATTCAAA
* * *
957057 AATTCGTCATAACGAT-TTAAATTCGTTTTAACAAATTCAAA
1 AATT-TTTATAAC-ATATTAAATTCGTTATAACAAATTCAAA
957098 AATT
1 AATT
957102 CATTATATCA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
40 6 0.09
41 31 0.44
42 28 0.40
43 5 0.07
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (40 bp):
AATTTTTATAACATATTAAATTCGTTATAACAAATTCAAA
Found at i:957060 original size:22 final size:21
Alignment explanation
Indices: 956980--957120 Score: 89
Period size: 19 Copynumber: 6.8 Consensus size: 21
956970 ATTGAATTTA
*
956980 TTATAACATATT--AAATTCG
1 TTATAACAAATTCAAAATTCG
*
956999 TTATAACAAATTCCAAAAAATT-T
1 TTATAACAAATT-C--AAAATTCG
* *
957022 TTATTACAAATT--TAATTCG
1 TTATAACAAATTCAAAATTCG
*
957041 TTATAACAGATTCAACAATTCG
1 TTATAACAAATTCAA-AATTCG
* * *
957063 TCATAAC-GATT-TAAATTCG
1 TTATAACAAATTCAAAATTCG
* *
957082 TTTTAACAAATTCAAAAATTCA
1 TTATAACAAATTC-AAAATTCG
*
957104 TTATATCAAATTCAAAA
1 TTATAACAAATTCAAAA
957121 ATATTTTTGA
Statistics
Matches: 93, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
18 4 0.04
19 32 0.34
20 4 0.04
21 8 0.09
22 29 0.31
23 11 0.12
24 5 0.05
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (21 bp):
TTATAACAAATTCAAAATTCG
Found at i:957918 original size:1 final size:1
Alignment explanation
Indices: 957902--957946 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
957892 TTGATTCTTG
* * * *
957902 TTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
957947 ACAATAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:957925 original size:22 final size:22
Alignment explanation
Indices: 957899--957944 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
957889 TTGTTGATTC
957899 TTGTTTTGTTTTGTTTTTTTTT
1 TTGTTTTGTTTTGTTTTTTTTT
*
957921 TTGTTTTTTTTTGTTTTTTTTT
1 TTGTTTTGTTTTGTTTTTTTTT
957943 TT
1 TT
957945 TTACAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (22 bp):
TTGTTTTGTTTTGTTTTTTTTT
Found at i:960871 original size:157 final size:152
Alignment explanation
Indices: 960581--960872 Score: 437
Period size: 161 Copynumber: 1.9 Consensus size: 152
960571 GGGATTTTTC
*
960581 GACGAGCTGTCTTTCGATGAGATGTAGACCAACAAATTATTGAGCTCAGATTTGCAAAACGGGAA
1 GACGAGCTGTCTTTCGATGAGATGTAGACCAACAAATTATTGACCTCAGATTTGCAAAACGGGAA
960646 CAAACCCAAAATTCATTTTCCATAAAAAAAATGCATGCTTACAAAAAAAAAGAACGTCCACCCCC
66 CAAACCCAAAATTCATTTTCCAT-AAAAAAATGCATGCTT---AAAAAAAAGAACGTCCACCCCC
960711 CCCCCCCCCCCTTTACCCCCAAACCA
127 CCCCCCCCCCCTTTACCCCCAAACCA
960737 NGACGAGCTGTCTTTCGATGAGATGTAGACCAACAAACTTATTATTGACCTCAGATTTGCAAAAC
1 -GACGAGCTGTCTTTCGATGAGATGTAGACCAAC-AA---ATTATTGACCTCAGATTTGCAAAAC
* * *
960802 GGGAACAAACCC-AAATTCATTTTCCAT-AAAAAATGCGTGCTT-AAAAAAAGCACGTCCACACC
61 GGGAACAAACCCAAAATTCATTTTCCATAAAAAAATGCATGCTTAAAAAAAAGAACGTCCACCCC
*
960864 CCACCCCCC
126 CCCCCCCCC
960873 TCTTTTAACC
Statistics
Matches: 126, Mismatches: 5, Indels: 11
0.89 0.04 0.08
Matches are distributed among these distances:
154 26 0.21
157 33 0.26
158 16 0.13
160 15 0.12
161 36 0.29
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (152 bp):
GACGAGCTGTCTTTCGATGAGATGTAGACCAACAAATTATTGACCTCAGATTTGCAAAACGGGAA
CAAACCCAAAATTCATTTTCCATAAAAAAATGCATGCTTAAAAAAAAGAACGTCCACCCCCCCCC
CCCCCCCTTTACCCCCAAACCA
Found at i:963931 original size:2 final size:2
Alignment explanation
Indices: 963924--963968 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
963914 AATCGTGCGC
963924 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
963966 CT C
1 CT C
963969 AGATTTTGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:964744 original size:2 final size:2
Alignment explanation
Indices: 964739--964795 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
964729 AGGACCCCCC
964739 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
964781 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
964796 AGATTGGGTT
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:965021 original size:2 final size:2
Alignment explanation
Indices: 965014--965052 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
965004 CTCACAAGTG
965014 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
965053 GTTCAAGCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:965109 original size:2 final size:2
Alignment explanation
Indices: 965102--965134 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
965092 AAGTGAAATC
965102 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
965135 ATTTCTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:971750 original size:2 final size:2
Alignment explanation
Indices: 971743--971769 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
971733 TAGGTTCAAG
971743 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 G
971770 CACTTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:975306 original size:35 final size:35
Alignment explanation
Indices: 975264--975344 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
975254 AGACTACTGC
* *
975264 ATCTTCAAGAACTCC-ATTGTGTTAGTTCTGGAAGA
1 ATCTTCAAGAACTCCTA-TGTGTTAGTTCCGAAAGA
* * *
975299 ATTTTCAAGAACTTCTATGTGTTATTTCCGAAAGA
1 ATCTTCAAGAACTCCTATGTGTTAGTTCCGAAAGA
975334 ATCTTCAAGAA
1 ATCTTCAAGAA
975345 ATTCTTTGCG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (35 bp):
ATCTTCAAGAACTCCTATGTGTTAGTTCCGAAAGA
Found at i:988521 original size:10 final size:10
Alignment explanation
Indices: 988506--988535 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
988496 AGTATTTTGA
988506 TTGAAAACTC
1 TTGAAAACTC
988516 TTGAAAACTC
1 TTGAAAACTC
988526 TTGAAAACTC
1 TTGAAAACTC
988536 GTAATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (10 bp):
TTGAAAACTC
Found at i:992411 original size:2 final size:2
Alignment explanation
Indices: 992404--992431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
992394 CCCCTACCCC
992404 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
992432 CCGGTTCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1001392 original size:34 final size:34
Alignment explanation
Indices: 1001354--1001534 Score: 202
Period size: 34 Copynumber: 5.3 Consensus size: 34
1001344 AATGGCAGAG
** * * *
1001354 GTTTATAATACCCAGCACTTTTCAAGTAGCAGAA
1 GTTTATAATACTTAGCTCTTTGCAAGTAGTAGAA
* *
1001388 GTTTATAGTACTTAGCTCTTTGCAAGTAGTGGAA
1 GTTTATAATACTTAGCTCTTTGCAAGTAGTAGAA
* * * * *
1001422 GTTTGTAATACTTACCACTTTGAAAGTAGTGGAA
1 GTTTATAATACTTAGCTCTTTGCAAGTAGTAGAA
* * *
1001456 GTTTGTAATACTTAGCTCTTTGAAAGTAGTGGAA
1 GTTTATAATACTTAGCTCTTTGCAAGTAGTAGAA
*
1001490 GTTTATAATACTTAACTCTTTGCAAGTAG-AGGAA
1 GTTTATAATACTTAGCTCTTTGCAAGTAGTA-GAA
1001524 GTTTATAATAC
1 GTTTATAATAC
1001535 CTGTACAGTT
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
34 128 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (34 bp):
GTTTATAATACTTAGCTCTTTGCAAGTAGTAGAA
Found at i:1001468 original size:68 final size:68
Alignment explanation
Indices: 1001354--1001534 Score: 229
Period size: 68 Copynumber: 2.7 Consensus size: 68
1001344 AATGGCAGAG
** * ** * *
1001354 GTTTATAATACCCAGCACTTTTCAAGTAGCA-GAAGTTTATAGTACTTAGCTCTTTGCAAGTAGT
1 GTTTATAATACTTAACACTTTGAAAGTAG-AGGAAGTTTATAATACTTAGCTCTTTGAAAGTAGT
1001418 GGAA
65 GGAA
* * * *
1001422 GTTTGTAATACTTACCACTTTGAAAGTAGTGGAAGTTTGTAATACTTAGCTCTTTGAAAGTAGTG
1 GTTTATAATACTTAACACTTTGAAAGTAGAGGAAGTTTATAATACTTAGCTCTTTGAAAGTAGTG
1001487 GAA
66 GAA
* *
1001490 GTTTATAATACTTAACTCTTTGCAAGTAGAGGAAGTTTATAATAC
1 GTTTATAATACTTAACACTTTGAAAGTAGAGGAAGTTTATAATAC
1001535 CTGTACAGTT
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 96 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (68 bp):
GTTTATAATACTTAACACTTTGAAAGTAGAGGAAGTTTATAATACTTAGCTCTTTGAAAGTAGTG
GAA
Found at i:1004811 original size:16 final size:16
Alignment explanation
Indices: 1004790--1004821 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1004780 GAGATATGTC
1004790 AAAATGACCTTGTTTA
1 AAAATGACCTTGTTTA
1004806 AAAATGACCTTGTTTA
1 AAAATGACCTTGTTTA
1004822 CAACAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAATGACCTTGTTTA
Found at i:1039753 original size:3 final size:3
Alignment explanation
Indices: 1039729--1039791 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
1039719 TGTAGTAACA
* * * *
1039729 AAT ATAT AAA AAT AAT ACT AAT AAT AAT AAA AATT AAT -AT AAT AGT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
*
1039775 GAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1039792 GAGTAATAGT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1039798 original size:27 final size:27
Alignment explanation
Indices: 1039749--1039801 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1039739 AATAATACTA
*
1039749 ATAATAATAAAAATTAATATAATAGTG
1 ATAATAATAAAAATTAAGATAATAGTG
*
1039776 ATAATAATAATAA-TAAGAGTAATAGT
1 ATAATAATAAAAATTAAGA-TAATAGT
1039802 AGTAGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (27 bp):
ATAATAATAAAAATTAAGATAATAGTG
Found at i:1044291 original size:2 final size:2
Alignment explanation
Indices: 1044284--1044325 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1044274 GCATAAATAT
1044284 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
1044326 AGGGTAAAAT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1049147 original size:12 final size:12
Alignment explanation
Indices: 1049130--1049154 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1049120 AAACCCTTAT
1049130 AAATACATATAA
1 AAATACATATAA
1049142 AAATACATATAA
1 AAATACATATAA
1049154 A
1 A
1049155 GTACTACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATACATATAA
Found at i:1057073 original size:2 final size:2
Alignment explanation
Indices: 1057066--1057101 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1057056 TTAATCTCAA
1057066 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
1057102 ATTAAAGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1080684 original size:180 final size:179
Alignment explanation
Indices: 1080380--1080744 Score: 570
Period size: 180 Copynumber: 2.0 Consensus size: 179
1080370 GTGAAATGGA
1080380 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
* * * *
1080445 AATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACATTTAATCTGCAAAAGA
66 AACCAGAAATCAAAATCCTAGCAATATGCACACATCGGATATATGTACAATTAATCTGCAAAAGA
* * *
1080510 ACAA-CTTCGTATCTTAAAAACTGTAGGAATAGTTATCCGTACAATGAGG
131 ACAACCTAC-TATCTTAAAAACTGTAGGAAGAATTATCCGTACAATGAGG
* **
1080559 GTACCCTATATGCAATATTTTGCCAAAAAATGACTCAGTTCAAAAGCTGGTATTTTTTTCATATT
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCATAAA
* * *
1080624 TTACCAGAAATCAAAATCCTAGCAATATGCACACATCGGATATATGTACAATTGATCTGCAAAAT
65 TAACCAGAAATCAAAATCCTAGCAATATGCACACATCGGATATATGTACAATTAATCTGCAAAAG
* *
1080689 AACAACCTACTATCTTTAAAACTGTAGGAGGAATTATCCGTACAATGAGG
130 AACAACCTACTATCTTAAAAACTGTAGGAAGAATTATCCGTACAATGAGG
1080739 GTACCC
1 GTACCC
1080745 ATTTGGCAGC
Statistics
Matches: 169, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
179 51 0.30
180 115 0.68
181 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (179 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
AACCAGAAATCAAAATCCTAGCAATATGCACACATCGGATATATGTACAATTAATCTGCAAAAGA
ACAACCTACTATCTTAAAAACTGTAGGAAGAATTATCCGTACAATGAGG
Found at i:1083791 original size:2 final size:2
Alignment explanation
Indices: 1083784--1083814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1083774 CCATTACCTA
1083784 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1083815 ATTAAAGCTG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1084501 original size:12 final size:12
Alignment explanation
Indices: 1084484--1084511 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1084474 TTAAAACCCT
1084484 TAAAAATACATA
1 TAAAAATACATA
1084496 TAAAAATACATA
1 TAAAAATACATA
1084508 TAAA
1 TAAA
1084512 GTACTACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAAAATACATA
Found at i:1094858 original size:27 final size:27
Alignment explanation
Indices: 1094826--1094881 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1094816 ACAAATTTAA
* * **
1094826 TAATTTGTACATGAAAATTATGTTTTG
1 TAATTTGTAAATAAAAACAATGTTTTG
1094853 TAATTTGTAAATAAAAACAATGTTTTG
1 TAATTTGTAAATAAAAACAATGTTTTG
1094880 TA
1 TA
1094882 TATATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (27 bp):
TAATTTGTAAATAAAAACAATGTTTTG
Found at i:1097390 original size:17 final size:15
Alignment explanation
Indices: 1097357--1097385 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1097347 GTATATATTT
1097357 TAATTGCAATTTTTA
1 TAATTGCAATTTTTA
1097372 TAATTGCAATTTTT
1 TAATTGCAATTTTT
1097386 TTATATAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
TAATTGCAATTTTTA
Found at i:1099673 original size:12 final size:12
Alignment explanation
Indices: 1099656--1099680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1099646 TTAAAGGATT
1099656 TGAGTTGAGGAA
1 TGAGTTGAGGAA
1099668 TGAGTTGAGGAA
1 TGAGTTGAGGAA
1099680 T
1 T
1099681 TTGAAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (12 bp):
TGAGTTGAGGAA
Done.