Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold150
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: 1854615
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 196055 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1381336 original size:1 final size:1
Alignment explanation
Indices: 1381330--1381377 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
1381320 TTTCCTTTAG
*** **
1381330 CCCCCCCCCCCCCCNTTCCCCTTCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1381378 TTCCTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.08
Consensus pattern (1 bp):
C
Found at i:1381377 original size:27 final size:27
Alignment explanation
Indices: 1381330--1381381 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1381320 TTTCCTTTAG
***
1381330 CCCCCCCCCCCCCCNTTCCCCTTCCCC
1 CCCCCCCCCCCCCCCCCCCCCTTCCCC
1381357 CCCCCCCCCCCCCCCCCCCCCTTCC
1 CCCCCCCCCCCCCCCCCCCCCTTCC
1381382 TTTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.00, C:0.87, G:0.00, T:0.12
Consensus pattern (27 bp):
CCCCCCCCCCCCCCCCCCCCCTTCCCC
Found at i:1388627 original size:20 final size:20
Alignment explanation
Indices: 1388602--1388642 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1388592 ACAAAATATC
1388602 ATACAATATAATAT-CATTAT
1 ATACAATA-AATATACATTAT
*
1388622 ATACAATAACTATACATTAT
1 ATACAATAAATATACATTAT
1388642 A
1 A
1388643 CTATCATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
ATACAATAAATATACATTAT
Found at i:1388732 original size:15 final size:15
Alignment explanation
Indices: 1388698--1388736 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1388688 GTAACATATA
* *
1388698 ATATTATATTGTGTG
1 ATATTGTATTGTATG
1388713 ATATTGTATTGTATG
1 ATATTGTATTGTATG
*
1388728 CTATTGTAT
1 ATATTGTAT
1388737 CAAATATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.54
Consensus pattern (15 bp):
ATATTGTATTGTATG
Found at i:1390145 original size:18 final size:19
Alignment explanation
Indices: 1390108--1390146 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1390098 GTGAGTGCAA
*
1390108 CAAAATCTTTAACATGCTC
1 CAAAATCTTTAACATCCTC
*
1390127 CAAAA-CTTTAACCTCCTC
1 CAAAATCTTTAACATCCTC
1390145 CA
1 CA
1390147 GCATCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.28
Consensus pattern (19 bp):
CAAAATCTTTAACATCCTC
Found at i:1396612 original size:21 final size:21
Alignment explanation
Indices: 1396588--1396710 Score: 129
Period size: 21 Copynumber: 5.9 Consensus size: 21
1396578 TGGATAATTT
*
1396588 CATTACATGATGATACTTTAA
1 CATTACATGCTGATACTTTAA
* * *
1396609 CATTACATGCTTATATTTTTA
1 CATTACATGCTGATACTTTAA
* * *
1396630 TATAACATGCTGACACTTTAA
1 CATTACATGCTGATACTTTAA
* *
1396651 CATTACATGCTGGTACTTCAA
1 CATTACATGCTGATACTTTAA
* * *
1396672 CAATACATGCTGGTACTTCAA
1 CATTACATGCTGATACTTTAA
*
1396693 CATTACATGCTTATACTT
1 CATTACATGCTGATACTT
1396711 CATTACATGA
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
CATTACATGCTGATACTTTAA
Found at i:1401808 original size:26 final size:26
Alignment explanation
Indices: 1401768--1401827 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1401758 ACATATTAGC
*
1401768 ATATAATGAATTGAAGACGTAACAGCAT
1 ATATAATGAATTGAAGAAGTAACA--AT
*
1401796 ATATAAT-AA-TGAAGAAGTATCAAT
1 ATATAATGAATTGAAGAAGTAACAAT
1401820 ATATAATG
1 ATATAATG
1401828 TTAAAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 9 0.31
26 11 0.38
27 2 0.07
28 7 0.24
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (26 bp):
ATATAATGAATTGAAGAAGTAACAAT
Found at i:1401927 original size:42 final size:42
Alignment explanation
Indices: 1401868--1401959 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
1401858 CATATAATAA
1401868 ATATAATGAAGAAGTATCAGCATATAATGTTGAAGAATCAGC
1 ATATAATGAAGAAGTATCAGCATATAATGTTGAAGAATCAGC
1401910 ATATAATGAAGAAGTATCAGCATATAATGTTGAAGAATCAGC
1 ATATAATGAAGAAGTATCAGCATATAATGTTGAAGAATCAGC
1401952 ATATAATG
1 ATATAATG
1401960 TTAATGCATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (42 bp):
ATATAATGAAGAAGTATCAGCATATAATGTTGAAGAATCAGC
Found at i:1401960 original size:21 final size:21
Alignment explanation
Indices: 1401868--1401961 Score: 134
Period size: 21 Copynumber: 4.5 Consensus size: 21
1401858 CATATAATAA
** *
1401868 ATATAATGAAGAAGTATCAGC
1 ATATAATGTTGAAGAATCAGC
1401889 ATATAATGTTGAAGAATCAGC
1 ATATAATGTTGAAGAATCAGC
** *
1401910 ATATAATGAAGAAGTATCAGC
1 ATATAATGTTGAAGAATCAGC
1401931 ATATAATGTTGAAGAATCAGC
1 ATATAATGTTGAAGAATCAGC
1401952 ATATAATGTT
1 ATATAATGTT
1401962 AATGCATGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.29
Consensus pattern (21 bp):
ATATAATGTTGAAGAATCAGC
Found at i:1405483 original size:2 final size:2
Alignment explanation
Indices: 1405476--1405519 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1405466 CTATTCATAT
1405476 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
1405518 TC
1 TC
1405520 CAAACATGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1406114 original size:3 final size:3
Alignment explanation
Indices: 1406108--1406144 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1406098 AAAAAAAAAG
*
1406108 TCA TCA TCA ACA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1406145 AAAAATCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:1418843 original size:10 final size:10
Alignment explanation
Indices: 1418828--1418860 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
1418818 GTTTTAAAGA
1418828 TGCTTGAATT
1 TGCTTGAATT
1418838 TGCTTGAATTT
1 TGCTTGAA-TT
1418849 TGCTTGAATT
1 TGCTTGAATT
1418859 TG
1 TG
1418861 TATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.52
Consensus pattern (10 bp):
TGCTTGAATT
Found at i:1418852 original size:11 final size:11
Alignment explanation
Indices: 1418828--1418859 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1418818 GTTTTAAAGA
1418828 TGCTTGAA-TT
1 TGCTTGAATTT
1418838 TGCTTGAATTT
1 TGCTTGAATTT
1418849 TGCTTGAATTT
1 TGCTTGAATTT
1418860 GTATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.53
Consensus pattern (11 bp):
TGCTTGAATTT
Found at i:1419175 original size:21 final size:22
Alignment explanation
Indices: 1419149--1419197 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1419139 CATCATATAT
* *
1419149 CGCGTTAT-TTCGCGAAAGTTG
1 CGCGTTATATTAGCAAAAGTTG
*
1419170 CGCGTT-TATTAGCAAAAGTTT
1 CGCGTTATATTAGCAAAAGTTG
1419191 CGCGTTA
1 CGCGTTA
1419198 ATTCATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (22 bp):
CGCGTTATATTAGCAAAAGTTG
Found at i:1423011 original size:24 final size:25
Alignment explanation
Indices: 1422965--1423017 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1422955 AAAATTTTCA
*
1422965 TTTAAGTACATCAAAATCTTAATATT
1 TTTAAGTACATCAAAATCATAAT-TT
*
1422991 TTTATGTACAT-AAAA-CATAATTT
1 TTTAAGTACATCAAAATCATAATTT
1423014 TTTA
1 TTTA
1423018 GATATGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 5 0.20
25 4 0.16
26 10 0.40
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (25 bp):
TTTAAGTACATCAAAATCATAATTT
Found at i:1424596 original size:2 final size:2
Alignment explanation
Indices: 1424589--1424615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1424579 CGTGGATTGA
1424589 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1424616 NNNNNNNNNN
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1426314 original size:2 final size:2
Alignment explanation
Indices: 1426307--1426406 Score: 123
Period size: 2 Copynumber: 50.5 Consensus size: 2
1426297 CAGGTACCGG
*
1426307 TC TC TC TC TC TC TC TC TC TC TC TC GC 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
* * ** *
1426349 TC TG TG GG T- TG TGC T- TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1426390 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1426407 GGGTTGCGCT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.02
2 86 0.97
3 1 0.01
ACGTcount: A:0.00, C:0.44, G:0.07, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1439284 original size:4 final size:4
Alignment explanation
Indices: 1439277--1439319 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
1439267 TTTTGTCTGT
* * *
1439277 CGTC CGTC TGTC CGTC CGTC CGTC TGTC CGTC CGTC TGTC CGT
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGT
1439320 AAACTTTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.33
Consensus pattern (4 bp):
CGTC
Found at i:1439294 original size:12 final size:12
Alignment explanation
Indices: 1439278--1439319 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
1439268 TTTGTCTGTC
* *
1439278 GTCCGTCTGTCC
1 GTCCGTCCGTCT
1439290 GTCCGTCCGTCT
1 GTCCGTCCGTCT
1439302 GTCCGTCCGTCT
1 GTCCGTCCGTCT
1439314 GTCCGT
1 GTCCGT
1439320 AAACTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.33
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:1439298 original size:16 final size:16
Alignment explanation
Indices: 1439277--1439312 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1439267 TTTTGTCTGT
1439277 CGTCCGTCTGTCCGTC
1 CGTCCGTCTGTCCGTC
1439293 CGTCCGTCTGTCCGTC
1 CGTCCGTCTGTCCGTC
1439309 CGTC
1 CGTC
1439313 TGTCCGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.44, G:0.25, T:0.31
Consensus pattern (16 bp):
CGTCCGTCTGTCCGTC
Found at i:1440211 original size:171 final size:171
Alignment explanation
Indices: 1439489--1440366 Score: 1307
Period size: 171 Copynumber: 5.2 Consensus size: 171
1439479 AGATATTTTC
* * *
1439489 AAAAATCTTCTTCTCA-AGAACCAGA-AAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTAA
1 AAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
1439552 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACTCCCGGTGGTAGGGTGGGGCCACAAT-----
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
1439612 GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
129 GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1439655 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGGAACTTGTATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1439720 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAAT----GGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGG
* * *
1439781 GGGGTCAAATTTTTACATAGGAATATATAGATTAAATCTTT
131 GGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1439822 AAAAATCTTCTTCTTAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
1439887 AAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGAG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG-G
* * *
1439952 GGGGGTCGAAGTTTTTCATGGGAATATATAGAGTAAATCTCT
130 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * ** *
1439994 AAAAATCTTCTTCTCAGAAACTAATCTGCCATGATAGCTGAAACTTGCATGGAAGTATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
1440059 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGG
** *
1440124 GGGGTTAAAGTTTTACATAAGAATATATAGAGTAAATCTTT
131 GGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1440165 AAAAATCTTCTTCTCAGAAAATAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCACAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
*
1440230 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGAG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGG-G
1440295 GGGGGGTCGAAGTTTTACATAGG-A-ATATAGAGTAAATCTTT
129 GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
1440336 -AAAATCTTCTTCTCAGAAACTAATCAGCCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1440367 ATGATTCTTT
Statistics
Matches: 641, Mismatches: 61, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
165 1 0.00
166 111 0.17
167 157 0.24
170 30 0.05
171 165 0.26
172 156 0.24
173 21 0.03
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (171 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGG
GGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:1440281 original size:343 final size:338
Alignment explanation
Indices: 1439489--1440366 Score: 1357
Period size: 343 Copynumber: 2.6 Consensus size: 338
1439479 AGATATTTTC
* *
1439489 AAAAATCTTCTTCTCAAGAACCAGAA--AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTA-
1 AAAAATCTTCTTCTC-AGAA-AATAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCC-AC
*
1439551 AGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACTCCCG-GTGGTAGGGTGGGGCCACAAT---
63 AGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAG-GGTAGGGTGGGGCCACAATGGG
1439612 ---GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAA
127 GGAGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATC-TTAAAAATCTTCTTCTCAGAA
* *
1439674 ACTAATCAGCCAGGAAAGCTGGAACTTGTATGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTG
191 ACTAATCAGCCAGGAAAGCTGAAACTTGCATGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTG
* * *
1439739 TGAAAATCATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGGGTCAAATTTTTACATAGGAA
256 TGAAAATCATGACCCCTGGGGGTAGGGTGAGGCCACAATGGGGGGGTCAAAGTTTTACATAAGAA
*
1439804 TATATAGATTAAATCTTT
321 TATATAGAGTAAATCTTT
* * * *
1439822 AAAAATCTTCTTCTTAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAAG
1 AAAAATCTTCTTCTCAGAAAATAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCACAGG
*
1439887 AAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGAG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGAG
* *
1439952 GGGGGTCGAAGTTTTTCATGGGAATATATAGAGTAAATCTCTAAAAATCTTCTTCTCAGAAACTA
131 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCT-TAAAAATCTTCTTCTCAGAAACTA
* * * *
1440017 ATCTGCCATGATAGCTGAAACTTGCATGGAAGTATCCTCAGGTAGTGTAGATTCAAAGTTGTGAA
195 ATCAGCCAGGAAAGCTGAAACTTGCATGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAA
* * *
1440082 AATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGGGGGGTTAAAGTTTTACATAAGAA
260 AATCATGACCCCTGGGGGTAGGGTGAGGCCACAAT----GGGGGGGTCAAAGTTTTACATAAGAA
1440147 TATATAGAGTAAATCTTT
321 TATATAGAGTAAATCTTT
1440165 AAAAATCTTCTTCTCAGAAAATAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCACAGG
1 AAAAATCTTCTTCTCAGAAAATAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCACAGG
1440230 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGAG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGA-
*
1440295 GGGGGGTCGAAGTTTTACATAGG-A-ATATAGAGTAAATCTTTAAAATCTTCTTCTCAGAAACTA
130 GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTAAAAATCTTCTTCTCAGAAACTA
1440358 ATCAGCCAG
195 ATCAGCCAG
1440367 ATGATTCTTT
Statistics
Matches: 496, Mismatches: 33, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
331 2 0.00
332 4 0.01
333 104 0.21
334 1 0.00
338 1 0.00
339 153 0.31
341 30 0.06
342 15 0.03
343 165 0.33
344 21 0.04
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (338 bp):
AAAAATCTTCTTCTCAGAAAATAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCACAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGAGGGTAGGGTGGGGCCACAATGGGGGAG
GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTAAAAATCTTCTTCTCAGAAACTAA
TCAGCCAGGAAAGCTGAAACTTGCATGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAA
ATCATGACCCCTGGGGGTAGGGTGAGGCCACAATGGGGGGGTCAAAGTTTTACATAAGAATATAT
AGAGTAAATCTTT
Found at i:1441081 original size:23 final size:23
Alignment explanation
Indices: 1441055--1441104 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1441045 GACAAATTAA
*
1441055 TTAAATATCAGATCATTTAATGC
1 TTAAATATCAGATCATGTAATGC
* * **
1441078 TTAACTGTCATCTCATGTAATGC
1 TTAAATATCAGATCATGTAATGC
1441101 TTAA
1 TTAA
1441105 CTGTCATCTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (23 bp):
TTAAATATCAGATCATGTAATGC
Found at i:1441105 original size:23 final size:23
Alignment explanation
Indices: 1441067--1441121 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1441057 AAATATCAGA
*
1441067 TCATTTAATGCTTAACTGTCATC
1 TCATGTAATGCTTAACTGTCATC
1441090 TCATGTAATGCTTAACTGTCATC
1 TCATGTAATGCTTAACTGTCATC
1441113 TCATGTAAT
1 TCATGTAAT
1441122 CGAGCTATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (23 bp):
TCATGTAATGCTTAACTGTCATC
Found at i:1441584 original size:20 final size:20
Alignment explanation
Indices: 1441553--1441985 Score: 577
Period size: 20 Copynumber: 21.7 Consensus size: 20
1441543 GTAAGTAATA
*
1441553 TCATGT-CATGTAACCTATA
1 TCATGTACATGTAACCTATG
* *
1441572 TCATGAACATGTAACCTATT
1 TCATGTACATGTAACCTATG
* *
1441592 TCATGAACATGTAACCTATT
1 TCATGTACATGTAACCTATG
* * * *
1441612 TCATGTATATGTAACATTTA
1 TCATGTACATGTAACCTATG
* *
1441632 TCATGAATATGTAACCTATG
1 TCATGTACATGTAACCTATG
1441652 TCATGTACATGTAACCTATG
1 TCATGTACATGTAACCTATG
1441672 TCATGTACATGTAACCTATG
1 TCATGTACATGTAACCTATG
*
1441692 TCATGTTCATGTAACCTATG
1 TCATGTACATGTAACCTATG
* *
1441712 AT-GTGTACATGTAACCTGTG
1 -TCATGTACATGTAACCTATG
1441732 TCATGTACATGTAACCTATG
1 TCATGTACATGTAACCTATG
*
1441752 TCATGTACATGTAACCTACG
1 TCATGTACATGTAACCTATG
1441772 TCATGTACATGTAACCTATG
1 TCATGTACATGTAACCTATG
* *
1441792 -CTGTGTACATGTAACCTGTG
1 TC-ATGTACATGTAACCTATG
*
1441812 TCATGTACATGTAACCTGTG
1 TCATGTACATGTAACCTATG
* *
1441832 TCGTGTACATGTAACCTGTG
1 TCATGTACATGTAACCTATG
1441852 TCATGTACATGTAACCTATG
1 TCATGTACATGTAACCTATG
*
1441872 TCATGTACATGTAACCTGTG
1 TCATGTACATGTAACCTATG
* *
1441892 TCGTGTACATGTAACCTGTG
1 TCATGTACATGTAACCTATG
1441912 TCATGTACATGTAACCTATG
1 TCATGTACATGTAACCTATG
*
1441932 TCATGTACATGTAATCTATG
1 TCATGTACATGTAACCTATG
* *
1441952 -CTGTGTACATGTAACCTGTG
1 TC-ATGTACATGTAACCTATG
1441972 TCATGTACATGTAA
1 TCATGTACATGTAA
1441986 GAATTATCAT
Statistics
Matches: 371, Mismatches: 36, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.02
20 360 0.97
21 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (20 bp):
TCATGTACATGTAACCTATG
Found at i:1443133 original size:19 final size:19
Alignment explanation
Indices: 1443105--1443166 Score: 115
Period size: 19 Copynumber: 3.3 Consensus size: 19
1443095 ATAGGAACTA
*
1443105 GTGATAATGATTGAATGTT
1 GTGATCATGATTGAATGTT
1443124 GTGATCATGATTGAATGTT
1 GTGATCATGATTGAATGTT
1443143 GTGATCATGATTGAATGTT
1 GTGATCATGATTGAATGTT
1443162 GTGAT
1 GTGAT
1443167 TATGTTATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.42
Consensus pattern (19 bp):
GTGATCATGATTGAATGTT
Found at i:1444770 original size:18 final size:18
Alignment explanation
Indices: 1444734--1444778 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1444724 GGCTGAAAAG
1444734 AAAAAGAAGAAAAAGAACA
1 AAAAAG-AGAAAAAGAACA
*
1444753 AGAAAGAGAAGAAA-AACA
1 AAAAAGAGAA-AAAGAACA
1444771 AAAAAGAG
1 AAAAAGAG
1444779 GACCCCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAAAGAACA
Found at i:1450761 original size:13 final size:13
Alignment explanation
Indices: 1450742--1450838 Score: 103
Period size: 13 Copynumber: 7.5 Consensus size: 13
1450732 CAAATTTACC
*
1450742 AGAGAGATCAAAG
1 AGAGAGATCGAAG
*
1450755 CGAGAGATCGAAG
1 AGAGAGATCGAAG
1450768 AGAGAGATCGAAG
1 AGAGAGATCGAAG
1450781 AGAGAGATCGAAG
1 AGAGAGATCGAAG
1450794 AGAGAGA--GAGAG
1 AGAGAGATCGA-AG
1450806 AGAGAGA--GAGAG
1 AGAGAGATCGA-AG
**
1450818 AGAGAGAGGGGAAG
1 AGAGAGA-TCGAAG
1450832 AGAGAGA
1 AGAGAGA
1450839 GAGGTGGCCT
Statistics
Matches: 77, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
11 2 0.03
12 21 0.27
13 43 0.56
14 9 0.12
15 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.43, T:0.04
Consensus pattern (13 bp):
AGAGAGATCGAAG
Found at i:1450771 original size:2 final size:2
Alignment explanation
Indices: 1450766--1450841 Score: 79
Period size: 2 Copynumber: 40.0 Consensus size: 2
1450756 GAGAGATCGA
* * * *
1450766 AG AG AG AG AT CG A- AG AG AG AG AT CG A- 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
*
1450806 AG AG AG AG AG AG AG AG AG AG -G GG A- 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
1450842 GTGGCCTACT
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
1 4 0.07
2 57 0.93
ACGTcount: A:0.47, C:0.03, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1459123 original size:20 final size:20
Alignment explanation
Indices: 1459100--1459163 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1459090 CGACTTTAAT
1459100 CTATATTTCACATCTGTAAA
1 CTATATTTCACATCTGTAAA
* * * *
1459120 CTATAGTTAAC-GC-GATAAT
1 CTATATTTCACATCTG-TAAA
* *
1459139 CTATGTTTCCCATCTGTAAA
1 CTATATTTCACATCTGTAAA
1459159 CTATA
1 CTATA
1459164 AGTTAACACT
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 17 0.57
21 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (20 bp):
CTATATTTCACATCTGTAAA
Found at i:1459124 original size:40 final size:40
Alignment explanation
Indices: 1459075--1459177 Score: 138
Period size: 39 Copynumber: 2.6 Consensus size: 40
1459065 TTTACGGATC
*
1459075 GTAAACTATAGTTACCGACTTTAATCTATATTTCACATCT
1 GTAAACTATAGTTAACGACTTTAATCTATATTTCACATCT
** * *
1459115 GTAAACTATAGTTAACG-CGATAATCTATGTTTCCCATCT
1 GTAAACTATAGTTAACGACTTTAATCTATATTTCACATCT
1459154 GTAAACTATAAGTTAAC-ACTTTAA
1 GTAAACTAT-AGTTAACGACTTTAA
1459178 ACAATCATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 27 0.50
40 27 0.50
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (40 bp):
GTAAACTATAGTTAACGACTTTAATCTATATTTCACATCT
Found at i:1459662 original size:39 final size:40
Alignment explanation
Indices: 1459596--1459684 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
1459586 AGAGTTGTTT
* * * *
1459596 ACTATAGTTAACAGATGAGAAACATAGATTATCG-CGTTA
1 ACTATAGTTTACAGACGAGAAACATAGATTAACGTCGTAA
* *
1459635 ACTATAGTTTACAGACGTGAAATATAGATTAACGTCGTAA
1 ACTATAGTTTACAGACGAGAAACATAGATTAACGTCGTAA
1459675 ACTATAGTTT
1 ACTATAGTTT
1459685 TCGATCCGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 29 0.67
40 14 0.33
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (40 bp):
ACTATAGTTTACAGACGAGAAACATAGATTAACGTCGTAA
Found at i:1459680 original size:20 final size:19
Alignment explanation
Indices: 1459615--1459681 Score: 50
Period size: 20 Copynumber: 3.5 Consensus size: 19
1459605 AACAGATGAG
*
1459615 AAAC-ATAGATTATCGCGT
1 AAACTATAGATTAACGCGT
* *
1459633 TAACTATAG-TTTACAGACGT
1 AAACTATAGATTAAC-G-CGT
1459653 GAAA-TATAGATTAACGTCGT
1 -AAACTATAGATTAACG-CGT
1459673 AAACTATAG
1 AAACTATAG
1459682 TTTTCGATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 6 0.16
19 8 0.22
20 17 0.46
21 6 0.16
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (19 bp):
AAACTATAGATTAACGCGT
Found at i:1460008 original size:21 final size:21
Alignment explanation
Indices: 1459941--1459997 Score: 89
Period size: 20 Copynumber: 2.8 Consensus size: 21
1459931 TTCCACAGAT
1459941 GTAAACTATAGTTAACGAATC
1 GTAAACTATAGTTAACGAATC
* *
1459962 GT-AACTATAGTTTACGAACC
1 GTAAACTATAGTTAACGAATC
1459982 GTAAACTATAGTTAAC
1 GTAAACTATAGTTAAC
1459998 AGTCGATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (21 bp):
GTAAACTATAGTTAACGAATC
Found at i:1460014 original size:41 final size:41
Alignment explanation
Indices: 1459941--1460033 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 41
1459931 TTCCACAGAT
1459941 GTAAACTATAGTTAACGAATCGTAACTATAGTTTA-CGAACC
1 GTAAACTATAGTTAACGAATCGTAACTATAGTTTATCG-ACC
* * *
1459982 GTAAACTATAGTTAAC-AGTCGATAAAC-CTAGTTTATCGACT
1 GTAAACTATAGTTAACGAATCG-T-AACTATAGTTTATCGACC
1460023 GTGAAACTATA
1 GT-AAACTATA
1460034 TTTCGCTCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
40 4 0.09
41 28 0.62
42 13 0.29
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (41 bp):
GTAAACTATAGTTAACGAATCGTAACTATAGTTTATCGACC
Found at i:1471597 original size:18 final size:18
Alignment explanation
Indices: 1471574--1471609 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1471564 GCCACCATGC
1471574 TAGCCGTTGCTGTTGCAG
1 TAGCCGTTGCTGTTGCAG
1471592 TAGCCGTTGCTGTTGCAG
1 TAGCCGTTGCTGTTGCAG
1471610 CTGCTGCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TAGCCGTTGCTGTTGCAG
Found at i:1478969 original size:2 final size:2
Alignment explanation
Indices: 1478964--1479054 Score: 121
Period size: 2 Copynumber: 46.0 Consensus size: 2
1478954 TATTCTTAAA
* * * * * *
1478964 TC TC TC TC TG TG TC TG TC TC TC TC TG TC TC TG TT 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
1479006 TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1479047 TC TC TC TC
1 TC TC TC TC
1479055 AAATATGATG
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.00, C:0.44, G:0.05, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1484790 original size:180 final size:180
Alignment explanation
Indices: 1484488--1484856 Score: 686
Period size: 180 Copynumber: 2.0 Consensus size: 180
1484478 ACCCTAGATG
*
1484488 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTAGTATTTTTTTCATAAATTATCG
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTCCAAAAGCTAGTATTTTTTTCATAAATTATCG
1484553 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
1484618 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* * *
1484668 TATATGCAATATTTTGCCAAAAAATGATTAAGTCCAAAAGCTGGTA-TTTTTTCGATAAATTATC
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTCCAAAAGCTAGTATTTTTTTC-ATAAATTATC
1484732 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
65 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
1484797 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
130 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
1484848 TATATGCAA
1 TATATGCAA
1484857 NNNNNNNNNN
Statistics
Matches: 184, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
179 7 0.04
180 177 0.96
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (180 bp):
TATATGCAACATTTTGCCAAAAAATGACTAAGTCCAAAAGCTAGTATTTTTTTCATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:1487636 original size:53 final size:53
Alignment explanation
Indices: 1487565--1487676 Score: 188
Period size: 53 Copynumber: 2.1 Consensus size: 53
1487555 TTTGATTGGC
* *
1487565 TAAACAAATTCATTTGTTTTCCTTTGGACTGAAATGTCACACTTTCATTGGTA
1 TAAACAAATTCATTTGTTTTCCCTCGGACTGAAATGTCACACTTTCATTGGTA
* *
1487618 TAAACAAATTCATTTGTTTTCCCTCGGACTGAAATGTCACACTTTCGTTGGTT
1 TAAACAAATTCATTTGTTTTCCCTCGGACTGAAATGTCACACTTTCATTGGTA
1487671 TAAACA
1 TAAACA
1487677 TAGCACATGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (53 bp):
TAAACAAATTCATTTGTTTTCCCTCGGACTGAAATGTCACACTTTCATTGGTA
Found at i:1489396 original size:2 final size:2
Alignment explanation
Indices: 1489389--1489413 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1489379 TTCAAAGTTC
1489389 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1489414 TGTATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1492226 original size:2 final size:2
Alignment explanation
Indices: 1492221--1492255 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1492211 AAAAAAAAGC
1492221 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 C
1492256 CAAGACACAA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1499491 original size:2 final size:2
Alignment explanation
Indices: 1499484--1499586 Score: 165
Period size: 2 Copynumber: 52.0 Consensus size: 2
1499474 TATATCAACT
1499484 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
*
1499526 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A TA TG-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA
*
1499567 GA GA AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
1499587 TGAATATAGA
Statistics
Matches: 95, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.02
2 93 0.98
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1500213 original size:4 final size:4
Alignment explanation
Indices: 1500204--1500299 Score: 115
Period size: 4 Copynumber: 24.5 Consensus size: 4
1500194 ACAACAAAAC
* * *
1500204 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG ACAG ACAG ACAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * *
1500252 AGAG AGAG ACAG ACAG ACAG AGAG A-AG -GAC AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
1500298 AG
1 AG
1500300 TCCTCAATAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
3 3 0.04
4 81 0.96
ACGTcount: A:0.50, C:0.07, G:0.43, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:1500428 original size:39 final size:39
Alignment explanation
Indices: 1500384--1502734 Score: 2007
Period size: 39 Copynumber: 58.9 Consensus size: 39
1500374 AAATAAAAAT
*
1500384 CTTGTTAACATACTCCTCAGTAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1500423 CTTGTTAACATACTCCTCAATTAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * *
1500462 CTTGTTAACATACTCCTCAATAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1500501 CTTGTTAACATACTCCTCAATAAGGGAGACAACT-GCAGC
1 CTTGTTAACATACTCCTCAATAAGAGAGACAA-TAGCAGG
** * * * *
1500540 CTTGTTAACATACTCCTTGATAAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1500579 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1500618 CTTGTAAACATACTCCTCAACAAGGGAGACAATAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1500657 CTTGTTAACATACTCCTCAA-AGAGAAAAACAATAGCAGG
1 CTTGTTAACATACTCCTCAATA-AGAGAGACAATAGCAGG
* * * * * *
1500696 CTTGTTTACATCCTCCTCAACT-AGGGAGAAAACAGCAAG
1 CTTGTTAACATACTCCTCAA-TAAGAGAGACAATAGCAGG
* * *
1500735 -TTAGTTAATATACTCCTCAATAGGATAGACAATAGCAAACAAATAGAGAG
1 CTT-GTTAACATACTCCTCAATAAGAGAGACAATAG----C------AG-G
* * * * * *
1500785 TTTGTCAACAGACTCCCCAATAAGGGAGACAGA-AGTAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACA-ATAGCAGG
* * * *
1500824 CTTGTTAACATACTCCTCAATAAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1500863 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1500902 CTTGTTAACAGACTCCTCAATGAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1500941 CTTGTAAACATTCTCCTCAATAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
*
1500980 C-TGTTAACATACTCCTCAATGAA-AAAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAAT-AAGAGAGACAATAGCAGG
* *
1501018 CTTGTTAACAGACTCCTCAATGAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * *
1501057 CTTGCTAACATTCTCCTCAAAAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
*
1501096 CTTGTTAACATACTCCTCAGTAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * * *
1501135 CTTGTTAACATACTCCTTAATTAG-GAAGAAAACAGCAAG
1 CTTGTTAACATACTCCTCAATAAGAG-AGACAATAGCAGG
* * *
1501174 -TTAGTTTACATACTCGTCAATAGGAGAGACAATAGCAAACATATAGAGAG
1 CTT-GTTAACATACTCCTCAATAAGAGAGACAATAG----C------AG-G
* * * * * *
1501224 TTTGTCAACAGACTCCTCAATAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * *
1501263 CTTGTTTACATACTCCTCAATAAGGGAGACAACT-GCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAA-TAGCAGG
* * * *
1501302 CTTGTTAACATACTCCTCAATAAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1501341 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * *
1501380 CTTGTTAACATACTCCTCAACAAGGGAGACAATAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1501419 CTTGTTAACATACTCCTCAA-AGAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATA-AGAGAGACAATAGCAGG
* * * * * *
1501458 CTTGTTTACATCCTCCTCAACT-AGGGAGAAAACAGCAAG
1 CTTGTTAACATACTCCTCAA-TAAGAGAGACAATAGCAGG
* * *
1501497 -TTAGTTAATATACTCCTCAATAGGATAGACAATAGCAAACAAATAGAGAG
1 CTT-GTTAACATACTCCTCAATAAGAGAGACAATAG----C------AG-G
* * * * * *
1501547 TTTGTCAACAGACTCCCCAATAAGGGAGACAGA-AGTAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACA-ATAGCAGG
* * * *
1501586 CTTGTTAACATACTCCTCAATAAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1501625 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1501664 CTTGTTAACAGACTCCTCAATGAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1501703 CTTGTAAACATTCTCCTCAATAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
*
1501742 C-TGTTAACATACTCCTCAATGAA-AAAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAAT-AAGAGAGACAATAGCAGG
* *
1501780 CTTGTTAACAGACTCCTCAATGAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * *
1501819 CTTGCTAACATTCTCCTCAAAAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
*
1501858 CTTGTTAACATACTCCTCAGTAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * * *
1501897 CTTGTTAACATACTCCTTAATTAG-GAAGAAAACAGCAAG
1 CTTGTTAACATACTCCTCAATAAGAG-AGACAATAGCAGG
* * *
1501936 -TTAGTTTACATACTCGTCAATAGGAGAGACAATAGCAAACATATAGAGAG
1 CTT-GTTAACATACTCCTCAATAAGAGAGACAATAG----C------AG-G
* * * * * *
1501986 TTTGTCAACAGACTCCTCAATAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * *
1502025 CTTGTTTACATACTCCTCAATAAGGGAGACAACT-GCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAA-TAGCAGG
* * * * *
1502064 CTTGTAAACATACTCCTCAATAAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1502103 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1502142 CTTGTTAACATACTCCTCAACAAGGGAGACAACAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1502181 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1502220 CTTGTTAACATACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1502259 CTTGTTAACATACTCCTCAATGAGAAAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * * *
1502298 CTTGTTTACATCCTCCTCAACTAAG-GAGAAAACAGCAAG
1 CTTGTTAACATACTCCTCAA-TAAGAGAGACAATAGCAGG
*
1502337 -TTAGTTAACATACTCCTCAATAGGAGAGACAATAGCAAACATATAGAGAG
1 CTT-GTTAACATACTCCTCAATAAGAGAGACAATAG----C------AG-G
* * * * * ** *
1502387 TTTGTCAACAGACTCCCCAATAAGGGAGACAGCAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1502426 CTTGTTAACATACTCCTCAATAAGAAAAACAAGAACAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * * *
1502465 CTTGTTAACAAACTCCTCAACAAGGGAGACAACAGCAGA
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* *
1502504 CTTGTTAACAGACTCCTCAATGAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
**
1502543 CTTGTTAACATTTTCCTCAATAAGAGAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
*
1502582 C-TGTTAACATACTCCTCAATGAA-AAAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAAT-AAGAGAGACAATAGCAGG
* * *
1502620 CTTGTTAACAGACTCCTCAATGAGAAAGACAATAGCAGG
1 CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
* * * *
1502659 CTTGTTAACATACTCCTCAACT-AGGGAGAAAACAGCAAG
1 CTTGTTAACATACTCCTCAA-TAAGAGAGACAATAGCAGG
* *
1502698 -TTAGTTAACATACTCTTCAATAGGAGAGACAATAGCA
1 CTT-GTTAACATACTCCTCAATAAGAGAGACAATAGCA
1502735 AACATATAGA
Statistics
Matches: 1881, Mismatches: 330, Indels: 202
0.78 0.14 0.08
Matches are distributed among these distances:
38 123 0.07
39 1592 0.85
40 16 0.01
43 5 0.00
46 3 0.00
49 5 0.00
50 125 0.07
51 12 0.01
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (39 bp):
CTTGTTAACATACTCCTCAATAAGAGAGACAATAGCAGG
Found at i:1502860 original size:90 final size:89
Alignment explanation
Indices: 1502660--1502868 Score: 228
Period size: 90 Copynumber: 2.3 Consensus size: 89
1502650 AATAGCAGGC
* *
1502660 TTGTTAACATACTCCTCAACT-AGGGAGAAAACAGCAAGTTAGTTAACATACTCTTCAATAGGAG
1 TTGTTAACATACTCCT-AAATAAGGGAGAAAACAGCAAGTTAGTTAACATACTCTTCAATAAGAG
*
1502724 AGACAATAGCAAACATATAGAGAGT
65 AGACAATAGCAAACAGATAGAGAGT
* * * * * * *
1502749 TTGTCAATAGACTCCTCAATAAGGGAGACAACAGCAGGCTT-GTTAACATACTCCTTTTAA-AAG
1 TTGTTAACATACTCCTAAATAAGGGAGAAAACAGCAAG-TTAGTTAACATACT-C-TTCAATAAG
* *
1502812 AGAGACAATGGCAGACAGATAGAGAGT
63 AGAGACAATAGCAAACAGATAGAGAGT
* *
1502839 TTGTTTACATACTCCTAAATAA-AGAGAAAA
1 TTGTTAACATACTCCTAAATAAGGGAGAAAA
1502869 TTGCAGACAG
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
88 2 0.02
89 45 0.46
90 46 0.47
91 4 0.04
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (89 bp):
TTGTTAACATACTCCTAAATAAGGGAGAAAACAGCAAGTTAGTTAACATACTCTTCAATAAGAGA
GACAATAGCAAACAGATAGAGAGT
Found at i:1502892 original size:49 final size:50
Alignment explanation
Indices: 1502786--1502915 Score: 131
Period size: 49 Copynumber: 2.6 Consensus size: 50
1502776 ACAACAGCAG
** *
1502786 GCTTGTTAACATACTCCT-TTTAAAAGAGAGACAATGGCAGACAGATAGAGA
1 GCTTGTTAACATACTCCTAAATAAAAGAGA-A-AATGGCAGACAGATAGAAA
* * *
1502837 GTTTGTTTACATACTCCTAAAT-AAAGAGAAAATTGCAGACAGAT-GAAAA
1 GCTTGTTAACATACTCCTAAATAAAAGAGAAAATGGCAGACAGATAG-AAA
* * *
1502886 GCTTGTTAATATCCTCCTGAATAAAAGAGA
1 GCTTGTTAACATACTCCTAAATAAAAGAGA
1502916 CAACATCAGG
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
48 1 0.02
49 32 0.49
50 8 0.12
51 23 0.35
52 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (50 bp):
GCTTGTTAACATACTCCTAAATAAAAGAGAAAATGGCAGACAGATAGAAA
Found at i:1503279 original size:21 final size:21
Alignment explanation
Indices: 1503240--1503309 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
1503230 ACACCATAGT
* *
1503240 ATAGCATTGAAAT-TGCATAGC
1 ATAGCATTGGAATCT-CATACC
1503261 ATAGCATTGGAATCTCATACC
1 ATAGCATTGGAATCTCATACC
* *
1503282 ACAGCATTAGAATCTCATACC
1 ATAGCATTGGAATCTCATACC
1503303 ATAGCAT
1 ATAGCAT
1503310 ACAATCTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (21 bp):
ATAGCATTGGAATCTCATACC
Found at i:1503353 original size:32 final size:30
Alignment explanation
Indices: 1503276--1503353 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 30
1503266 ATTGGAATCT
*
1503276 CATACCACAGCATTAGAATCTCATACCATAG
1 CATACCATAGCA-TAGAATCTCATACCATAG
* ** * *
1503307 CATACAATCTCATAGATTCTCATTCATCATAG
1 CATACCATAGCATAGAATCTCA-T-ACCATAG
1503339 CATACCATAGCATAG
1 CATACCATAGCATAG
1503354 CATACAACAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 9 0.25
31 9 0.25
32 18 0.50
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.27
Consensus pattern (30 bp):
CATACCATAGCATAGAATCTCATACCATAG
Found at i:1503848 original size:50 final size:50
Alignment explanation
Indices: 1503781--1503965 Score: 158
Period size: 50 Copynumber: 3.7 Consensus size: 50
1503771 CTGAAGATAG
* *
1503781 AGAGCTTGTTAATATACTCCTAAAAAAGGGAGACAATGGCAGAGAAATAA
1 AGAGCTTGTTAACATACTCCTAAAAAAGGGAGACAATGGCAGACAAATAA
* * ** * * * *
1503831 AGAGTTTGTTAACATACTCCTCAAAAATAGAAACAA-GAACAGATAGAA-AG
1 AGAGCTTGTTAACATACTCCTAAAAAAGGGAGACAATG-GCAGACA-AATAA
* * * * * *
1503881 AGAACTTGTTTACAAACTCCTAAACAAGGGAGACAATTGCAGACATATAA
1 AGAGCTTGTTAACATACTCCTAAAAAAGGGAGACAATGGCAGACAAATAA
* * **
1503931 AGAGTTTGTTAACATACTCCTTAGGAAGGGAGACA
1 AGAGCTTGTTAACATACTCCTAAAAAAGGGAGACA
1503966 GCAGCAGGCT
Statistics
Matches: 101, Mismatches: 30, Indels: 8
0.73 0.22 0.06
Matches are distributed among these distances:
49 2 0.02
50 97 0.96
51 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (50 bp):
AGAGCTTGTTAACATACTCCTAAAAAAGGGAGACAATGGCAGACAAATAA
Found at i:1504859 original size:37 final size:37
Alignment explanation
Indices: 1504818--1506167 Score: 740
Period size: 37 Copynumber: 37.1 Consensus size: 37
1504808 AACAGGAGAT
* *
1504818 ACAGGAGTAAATGATACCATCAA-CAAGGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATC-AGGGAGACAACA
*
1504855 ACAGGATTAAATGTTACCTTCAA-CAAGGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATC-AGGGAGACAACA
*
1504892 ACAGGAGTAAATGTTACCTTCAATCAGGGGGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * *
1504929 ATA-GAGGTAAATGTTACCATCAA-CAAGGGAGACAAAA
1 ACAGGA-GTAAATGTTACCTTCAATC-AGGGAGACAACA
*
1504966 ACAGGAGTAAATGTTACCTTCAATCAGGGGGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * *
1505003 ATAGGAGTAAATGTAACCTGCAATCAGGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* *
1505040 ATAGGAGTAAATGTTACCATCAATCAGGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * * *
1505077 ATAGAAGTAAATGTAACCTGCAATCAGGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * *
1505114 ATA-GAGGTAAATGTTATCATCAATCAGGGAGACAACA
1 ACAGGA-GTAAATGTTACCTTCAATCAGGGAGACAACA
* *
1505151 ATAGGAGTAAATGTTACCCTT-AATCAGGGAGACACCA
1 ACAGGAGTAAATGTTA-CCTTCAATCAGGGAGACAACA
* *
1505188 ACAAGAGTAAATGTTACCTTCAATCAGGGAGAAAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* *
1505225 ACAGGTGTAAATGTTACCTGCAATCAGGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * *
1505262 ATAGGAGTAAATGTTACCCTT-AATCAGGAAGATAACA
1 ACAGGAGTAAATGTTA-CCTTCAATCAGGGAGACAACA
* *
1505299 ATAGGAGTAAATGTTACCCTT-AATCAGGGAGACACCA
1 ACAGGAGTAAATGTTA-CCTTCAATCAGGGAGACAACA
* *
1505336 ACATGAGTAAATGTTACCTTCAATCAGGGAGAAAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * * * *
1505373 ACAGGTGTAGAAAGTGACCCTCAATCAGTGAGACAAC-
1 ACAGGAGTA-AATGTTACCTTCAATCAGGGAGACAACA
* * * ** *
1505410 A-A--AGTTAGTGTTACCCTCAATCACTGAGACAGCA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * **
1505444 ACAGGACT-AA----A--TT--A-CGGGGAGACAATT
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * * * *
1505471 ACATGAGTAAATGTTACCCTCCATCAGGAAGATAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * * * * *
1505508 ACAGAAGTCAATATTACCCTCAATTAAGGAGACAACA
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * **
1505545 AC-TGAGGTAGATGTTACCCTTC-ATCAGCAAGACAACA
1 ACAGGA-GTAAATGTTA-CCTTCAATCAGGGAGACAACA
* * * * *
1505582 ACAGGAGCAAATGTTGCC-ACAATCAGGGAGAAAACT
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* *
1505618 ACATGAGTAAATG-TA-----GATCAGGGAGACAA-A
1 ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * * *
1505648 ACCAAGGA-TAAATGTTACC-CCAATCTAGAGAAATAA-A
1 A-C-AGGAGTAAATGTTACCTTCAATC-AGGGAGACAACA
* ** * * * ***
1505685 ACAAGGAATAGTTGTTACCATAAACCAATAAGACAA-A
1 AC-AGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* *** * * *
1505722 AC--CA-TAAA-CAAACAC-TAAATCAGGAAGCCAAC-
1 ACAGGAGTAAATGTTAC-CTTCAATCAGGGAGACAACA
** * * * * * ** *
1505754 ACCTGACGGATATCTTACCCTAAATCAGGGAGATGACC
1 ACAGGA-GTAAATGTTACCTTCAATCAGGGAGACAACA
* * * *
1505792 ACAGGGGTAAATGTTACC--CATTATCTGAGAGACACCA
1 ACAGGAGTAAATGTTACCTTCA--ATCAGGGAGACAACA
* * *
1505829 ACAGGAGAAAAAGTTA-CTCTCAACCAGGGAGACAACA
1 ACAGGAGTAAATGTTACCT-TCAATCAGGGAGACAACA
** * * * *
1505866 ATTGAAATAAATGTT-TCTCTCAATCAGGGAGACAACT
1 ACAGGAGTAAATGTTACCT-TCAATCAGGGAGACAACA
* ** * * *
1505903 ACA-GAGGTAAATGCTACTCTT-AAAAAAGTAGGCAAC-
1 ACAGGA-GTAAATGTTAC-CTTCAATCAGGGAGACAACA
* * *
1505939 ACAAGGGGTAAATGTAATCTTCAATCAGGGAGACAACA
1 AC-AGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* ** * * *
1505977 ACAGGAATAAATGTTACCCTT-AAAAAAGTAGGCAAC-
1 ACAGGAGTAAATGTTA-CCTTCAATCAGGGAGACAACA
* * *
1506013 ACAAGGGGTAAATGTTATCTTCAATCAAGGAGA-AGACA
1 AC-AGGAGTAAATGTTACCTTCAATCAGGGAGACA-ACA
* ** * * *
1506051 ACAGGAATAAATGTTACCCTT-AAAAAAGTAGGCAAC-
1 ACAGGAGTAAATGTTA-CCTTCAATCAGGGAGACAACA
* * * *
1506087 ACAAGGGGTAAATGTAATCTTCAATCAGGGAGACAACC
1 AC-AGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
* * *
1506125 ACAGGAGTGAGTGTTACCCTT-AATCAGGGAGAAAACA
1 ACAGGAGTAAATGTTA-CCTTCAATCAGGGAGACAACA
1506162 AGCAGG
1 A-CAGG
1506168 GAAGTTTTAA
Statistics
Matches: 1001, Mismatches: 238, Indels: 147
0.72 0.17 0.11
Matches are distributed among these distances:
27 13 0.01
28 3 0.00
30 2 0.00
31 19 0.02
32 23 0.02
33 25 0.02
34 6 0.01
35 4 0.00
36 70 0.07
37 765 0.76
38 67 0.07
39 4 0.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (37 bp):
ACAGGAGTAAATGTTACCTTCAATCAGGGAGACAACA
Found at i:1509956 original size:32 final size:32
Alignment explanation
Indices: 1509920--1509980 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1509910 ATTTCTTTCA
*
1509920 TTTATGTTGCTATGTCTTTCAAATACATTAGT
1 TTTATGTAGCTATGTCTTTCAAATACATTAGT
1509952 TTTATGTAGCTATGTCTTTCAAATACATT
1 TTTATGTAGCTATGTCTTTCAAATACATT
1509981 GAAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.49
Consensus pattern (32 bp):
TTTATGTAGCTATGTCTTTCAAATACATTAGT
Found at i:1516368 original size:2 final size:2
Alignment explanation
Indices: 1516361--1516414 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1516351 GTTTCTCAAT
1516361 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
1516403 GA GA GA GA GA GA
1 GA GA GA GA GA GA
1516415 TCTATATGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1516526 original size:2 final size:2
Alignment explanation
Indices: 1516514--1516570 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1516504 TACAGTNGGA
*
1516514 AG AG AG GG 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
1516556 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
1516571 TCTATATGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1516567 original size:156 final size:155
Alignment explanation
Indices: 1516365--1516665 Score: 575
Period size: 156 Copynumber: 1.9 Consensus size: 155
1516355 CTCAATGAGA
*
1516365 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTATATGATATATC
1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTATATGATATACC
1516430 TGTGTACATGATTATTAAAAACATAACCACTTTCATTTTTAAATTTATGGTTATGTATCAAGTGG
66 TGTGTACATGATTATTAAAAACATAACCACTTTCATTTTTAAATTTATGGTTATGTATCAAGTGG
1516495 CTGAGCACCTACAGTNGGAAGAGAGG
131 CTGAGCACCTACAGT-GGAAGAGAGG
1516521 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTATATGATATACC
1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTATATGATATACC
*
1516586 TGTGTTCATGATTATTAAAAACATAACCACTTTCATTTTTAAATTTATGGTTATGTATCAAGTGG
66 TGTGTACATGATTATTAAAAACATAACCACTTTCATTTTTAAATTTATGGTTATGTATCAAGTGG
1516651 CTGAGCACCTACAGT
131 CTGAGCACCTACAGT
1516666 CATAATGGGT
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 143 1.00
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (155 bp):
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCTATATGATATACC
TGTGTACATGATTATTAAAAACATAACCACTTTCATTTTTAAATTTATGGTTATGTATCAAGTGG
CTGAGCACCTACAGTGGAAGAGAGG
Found at i:1517452 original size:2 final size:2
Alignment explanation
Indices: 1517445--1517483 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1517435 ACTTTTTAAT
* *
1517445 GA GA GA GA GA GA GA GA AA GA GA GA GA CA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1517484 TTTTCAGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1520929 original size:31 final size:31
Alignment explanation
Indices: 1520894--1521753 Score: 1051
Period size: 31 Copynumber: 27.5 Consensus size: 31
1520884 AAAACCTTTT
** * *
1520894 TTCCATGTCTTGTCCATAACATAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
** * * * *
1520925 TTCCATGTCTCATCTGTGACATAACACCATT
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
*
1520956 TTCCATGTCTTGTCTCTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * * * *
1520987 TACTATGTCTTGTCTGTGTCACAATACTCTT
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
*
1521018 TTCCATGTCTTGTCTGTGACACAATACCCTA
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* *
1521049 TTCCATGTCTTGTCTGTGTCACAAGACATAACACCATT
1 TTCCATGTCTTGTCTGTG--AC-ACA-AT-AC-CC-TG
*
1521087 TTCCATGTCTTGTCTCTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * * *
1521118 TACTATGTCTTGTCTGTGTCACAATACTCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* *
1521149 TTCCATGCCTTGTCTGTGACACAATAACCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
1521180 TTCCATGTCTTGTCTGTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
1521211 TTCCATGTCTTGTCTGTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
1521242 TTCCATGTCTTGTCTGTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * *
1521273 TTCCATGTCTTGTCTGTGTCACAAGATCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* *
1521304 TTCCATGTCTTGTCTTTGACATCATAACACCCT-
1 TTCCATGTCTTGTCTGTGACA-C--AATACCCTG
* * *
1521337 ATCCATGTCTTGTCTGTGACACAATACTCTT
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
*
1521368 TTCCATGTCTTGTCTGTGACACAATACCCTA
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * *
1521399 TTCCATGTCTTGTCTGTGTCACAAGATCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * *
1521430 TTCCATGTCTTGCCTATGATACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* ** * *
1521461 TTCTAAAATCTTGTCTGTGTCACAATACCTTG
1 TTC-CATGTCTTGTCTGTGACACAATACCCTG
* * * * *
1521493 TTCTATGTCTTGTATGTGTCACAATACTCTA
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * *
1521524 TTCCATGTCTTGTTTGTGACAAAATATCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
1521555 TTCCATGTCTTGTCTGTGACACAATACCC-G
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
1521585 TTCCATGTCTTGTCTGTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* * *
1521616 TTTCATGTCTTGTATGTAACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
* *
1521647 TTTCATGTCTTGTCTGTGACACAATACCCTA
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
*
1521678 TTCCATGTCTTGTTTGTGACACAATA-CCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
1521708 TTCCATGTCTTGTCTGTGACACAATACCCTG
1 TTCCATGTCTTGTCTGTGACACAATACCCTG
*
1521739 CTCCATGTCTTGTCT
1 TTCCATGTCTTGTCT
1521754 ATGCTGCTTA
Statistics
Matches: 711, Mismatches: 104, Indels: 28
0.84 0.12 0.03
Matches are distributed among these distances:
30 64 0.09
31 559 0.79
32 27 0.04
33 23 0.03
34 10 0.01
35 4 0.01
36 4 0.01
37 2 0.00
38 18 0.03
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (31 bp):
TTCCATGTCTTGTCTGTGACACAATACCCTG
Found at i:1538563 original size:174 final size:168
Alignment explanation
Indices: 1538174--1538608 Score: 525
Period size: 174 Copynumber: 2.5 Consensus size: 168
1538164 CCCCCCATGT
* *
1538174 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGAG-TT-AGTGGACATCA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGG-GCTTCA-TGGACATCA
* * ** ** * * * * *
1538237 TAACCATGTATTCAGTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTTTAAGATTTAA
64 TAACCATGCATTTAGTTTTAACAAATATATATGGGAGAAGAGAAGAAGATTTTTCTAAGATTTAA
1538302 AACATTTTTACTACATGGCCATATTGGCCCCACCCTAGAG
129 AACATTTTTACTACATGGCCATATTGGCCCCACCCTAGAG
* ** * * *
1538342 CCTGAACCCCTAACAAAGGGTTCATGAGTTTCACAATTTTGGTAGAGGGCTTCATGGACATTATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
* *
1538407 ACCAGGCATTTAGTCTTTAACAAATATATATGGGAGAAGAGAAGAAGA-TTTTCTAAGATTTAAT
66 ACCATGCATTTAGT-TTTAACAAATATATATGGGAGAAGAGAAGAAGATTTTTCTAAGATTTAAA
1538471 ACATTTTTACTACATGTATATGGCCATATTGGCCCCACCCTAGAG
130 ACATTTTTACTAC------ATGGCCATATTGGCCCCACCCTAGAG
* * * *
1538516 CCTGATCCCCTGACCCAGGGGTCATGAATTTCACATTTTTTGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
*
1538581 ATCATGCATTTAGTTTTTAACAAATATA
66 ACCATGCATTTAG-TTTTAACAAATATA
1538609 CTGTGGATTC
Statistics
Matches: 224, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
167 1 0.00
168 91 0.41
169 26 0.12
174 105 0.47
175 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (168 bp):
CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
ACCATGCATTTAGTTTTAACAAATATATATGGGAGAAGAGAAGAAGATTTTTCTAAGATTTAAAA
CATTTTTACTACATGGCCATATTGGCCCCACCCTAGAG
Found at i:1540096 original size:165 final size:167
Alignment explanation
Indices: 1539671--1540115 Score: 671
Period size: 168 Copynumber: 2.7 Consensus size: 167
1539661 CTCGGCCTCG
* *
1539671 TTAATACATTTTTTACTATATGGCCATATTGGCCCCACCCTAGAACCTGAACCCCTGACCCAGGG
1 TTAATACA-TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGG
* *
1539736 GTCATGAATTTCATAATTTTTGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTTAA
65 GTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTTAA
1539801 CAAATAAATATGGGAGTAGAGAAGAAGATTTTCTAAGAT
130 CAAATAAATATGGGAGTA-AGAAGAAGATTTTCTAAGAT
* * * * * *
1539840 TTAATAGATTTTAACTTTATGGCCATATTGGCCTCACCCTTGAGCCTGAACCCCTGA-TACAGGG
1 TTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCA-AGGG
* * *
1539904 GTCATGAATTTCACATTTTTAGTAGAGGGCCTCATGGACATCATAATCATGCATTTAGTTTTTAA
65 GTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTTAA
* *
1539969 CAAATATATATGGTAGT-AG-AGAAGATTTTCTAAGAT
130 CAAATAAATATGGGAGTAAGAAGAAGATTTTCTAAGAT
*
1540005 TTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCCTGACCAAGGGG
1 TTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGG
* * *
1540070 CCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAAC
66 TCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATAAC
1540116 TATGCAACCA
Statistics
Matches: 247, Mismatches: 27, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
165 114 0.46
166 3 0.01
168 123 0.50
169 7 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (167 bp):
TTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCAAGGGG
TCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGACATCATAACCAGGCATTTAGTTTTTAAC
AAATAAATATGGGAGTAAGAAGAAGATTTTCTAAGAT
Found at i:1545551 original size:2 final size:2
Alignment explanation
Indices: 1545544--1545577 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1545534 TAAAAGCATA
1545544 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1545578 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1545582 original size:2 final size:2
Alignment explanation
Indices: 1545577--1545636 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1545567 GTGTGTGTGT
1545577 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
1545619 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
1545637 TTTTCAGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1555506 original size:16 final size:16
Alignment explanation
Indices: 1555462--1555506 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1555452 ACCCCAGGAA
*
1555462 TTGGGTACATTGTCTC
1 TTGGGTACATTTTCTC
*
1555478 CTGGGTA-AGTTTTCTC
1 TTGGGTACA-TTTTCTC
1555494 TTGGGTACATTTT
1 TTGGGTACATTTT
1555507 TCCTGATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (16 bp):
TTGGGTACATTTTCTC
Found at i:1579692 original size:13 final size:12
Alignment explanation
Indices: 1579674--1579703 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1579664 AGCCATATTG
1579674 TTTTTGTTTTTGT
1 TTTTTGTTTTT-T
1579687 TTTTTGTTTTTT
1 TTTTTGTTTTTT
1579699 TTTTT
1 TTTTT
1579704 ACACAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:1581998 original size:24 final size:24
Alignment explanation
Indices: 1581973--1582093 Score: 224
Period size: 24 Copynumber: 5.0 Consensus size: 24
1581963 CATGGTAACG
*
1581973 TTACCATGTTAGTACTGTAAAACG
1 TTACCATGTTAGTACTGTAAAACA
1581997 TTACCATGTTAGTACTGTAAAACA
1 TTACCATGTTAGTACTGTAAAACA
*
1582021 TTACCATGTCAGTACTGTAAAACA
1 TTACCATGTTAGTACTGTAAAACA
1582045 TTACCATGTTAGTACTGTAAAACA
1 TTACCATGTTAGTACTGTAAAACA
1582069 TTACCATGTTAGTACTGTAAAACA
1 TTACCATGTTAGTACTGTAAAACA
1582093 T
1 T
1582094 CTGAAGAAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 94 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (24 bp):
TTACCATGTTAGTACTGTAAAACA
Found at i:1582203 original size:4 final size:4
Alignment explanation
Indices: 1582194--1582263 Score: 140
Period size: 4 Copynumber: 17.5 Consensus size: 4
1582184 TTCTTGGATT
1582194 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1582242 TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TA
1582264 ATTTCCCAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:1583803 original size:15 final size:16
Alignment explanation
Indices: 1583776--1583806 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1583766 ACATTTAGTG
1583776 AAATAGAAATAAAATA
1 AAATAGAAATAAAATA
1583792 AAATAG-AATAAAATA
1 AAATAGAAATAAAATA
1583807 CTAGTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (16 bp):
AAATAGAAATAAAATA
Found at i:1585583 original size:2 final size:2
Alignment explanation
Indices: 1585576--1585634 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1585566 AACAATTTTT
1585576 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
1585618 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
1585635 ATAAGTGTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1586626 original size:67 final size:63
Alignment explanation
Indices: 1586410--1586663 Score: 400
Period size: 63 Copynumber: 4.0 Consensus size: 63
1586400 GATAACCCAT
1586410 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
*
1586473 GAAAGCTCTACAAGTGTTTATTCTGGAGCTGATACATGCAGGGAAGCTCCCACCTCACGGGAA
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
*
1586536 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATCCAGGCAGAGAAGCTCCCACCTCACGGG
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACAT----GCAGGGAAGCTCCCACCTCACGGG
1586601 AA
62 AA
* ** * * *
1586603 GAAAGCTCTACAAGTGTTCATTCTAAAGCGAATACATGCAAGGAAGCTCCGACCTCACGGG
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGG
1586664 GTGAACGCAA
Statistics
Matches: 177, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
63 119 0.67
67 58 0.33
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (63 bp):
GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
Found at i:1586639 original size:130 final size:126
Alignment explanation
Indices: 1586410--1586663 Score: 402
Period size: 130 Copynumber: 2.0 Consensus size: 126
1586400 GATAACCCAT
*
1586410 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAAGA
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGAGAAGCTCCCACCTCACGGGAAGA
* ** *
1586475 AAGCTCTACAAGTGTTTATTCTGGAGCTGATACATGCAGGGAAGCTCCCACCTCACGGGAA
66 AAGCTCTACAAGTGTTCATTCTAAAGCTGATACATGCAAGGAAGCTCCCACCTCACGGGAA
1586536 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATCCAGGCAGAGAAGCTCCCACCTCACGGG
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACAT----GCAGAGAAGCTCCCACCTCACGGG
*
1586601 AAGAAAGCTCTACAAGTGTTCATTCTAAAGC-GAATACATGCAAGGAAGCTCCGACCTCACGGG
62 AAGAAAGCTCTACAAGTGTTCATTCTAAAGCTG-ATACATGCAAGGAAGCTCCCACCTCACGGG
1586664 GTGAACGCAA
Statistics
Matches: 117, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
126 37 0.32
129 1 0.01
130 79 0.68
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (126 bp):
GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGAGAAGCTCCCACCTCACGGGAAGA
AAGCTCTACAAGTGTTCATTCTAAAGCTGATACATGCAAGGAAGCTCCCACCTCACGGGAA
Found at i:1586886 original size:77 final size:77
Alignment explanation
Indices: 1586807--1587088 Score: 395
Period size: 77 Copynumber: 3.7 Consensus size: 77
1586797 CAAGGCAATG
* **
1586807 GAGAGATAGATTTATTTGGTATCATGAAATCATACATATAAATAGACATACACAAGGACACTATG
1 GAGAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACACAAGGACTGTATG
* *
1586872 AACATTGCCATG
66 AACACTGCCATA
* * * * *
1586884 GAGAGATATATTTATTTGGTGTCATGAAATCATACATATAAATATACATACACATGGGCTGTATA
1 GAGAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACACAAGGACTGTATG
*
1586949 AACACTGACATA
66 AACACTGCCATA
* * * ** *
1586961 GATAGATAGATTTTTTTGGTGTCATG-AATCATACATACGAATATACATACACAAGGATTGTATG
1 GAGAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACACAAGGACTGTATG
1587025 AACACTGCCATA
66 AACACTGCCATA
*
1587037 GAAAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACA
1 GAGAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACA
1587089 ATTATTTGGG
Statistics
Matches: 178, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
76 66 0.37
77 112 0.63
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (77 bp):
GAGAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACACAAGGACTGTATG
AACACTGCCATA
Found at i:1587068 original size:153 final size:154
Alignment explanation
Indices: 1586810--1587088 Score: 434
Period size: 153 Copynumber: 1.8 Consensus size: 154
1586800 GGCAATGGAG
*
1586810 AGATAGATTTATTTGGTATCATGAAATCATACATATAAATAGACATACACAAGGACACTATGAAC
1 AGATAGATTTATTTGGTATCATGAAATCATACATACAAATAGACATACACAAGGACACTATGAAC
* * * * *
1586875 ATTGCCATGGAGAGATATATTTATTTGGTGTCATGAAATCATACATATAAATATACATACACATG
66 ACTGCCATAGAAAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACACATG
1586940 GGCTGTATAAACACTGACATAGAT
131 GGCTGTATAAACACTGACATAGAT
* * * * ***
1586964 AGATAGATTTTTTTGGTGTCATG-AATCATACATACGAATATACATACACAAGGATTGTATGAAC
1 AGATAGATTTATTTGGTATCATGAAATCATACATACAAATAGACATACACAAGGACACTATGAAC
1587028 ACTGCCATAGAAAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACA
66 ACTGCCATAGAAAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACA
1587089 ATTATTTGGG
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
153 91 0.81
154 21 0.19
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (154 bp):
AGATAGATTTATTTGGTATCATGAAATCATACATACAAATAGACATACACAAGGACACTATGAAC
ACTGCCATAGAAAGATAGATTTATTTGGTATCATGAAATCATACATATAAATATACATACACATG
GGCTGTATAAACACTGACATAGAT
Found at i:1587637 original size:54 final size:54
Alignment explanation
Indices: 1587563--1587798 Score: 357
Period size: 54 Copynumber: 4.4 Consensus size: 54
1587553 GAAATACATA
* * * *
1587563 ACAGGTAAGGGTCAAGGTCAA-GGTCAAAACAGTAAAGGTAAGTAATAATACGAC
1 ACAGGTGAGAGTCAAGGTCAATGG-AAAAACAGTAAAGGTCAGTAATAATACGAC
*
1587617 ACAGGTGAGAGTCAATGTCAATGGAAAAACAGTAAAGGTCAGTAATAATACGAC
1 ACAGGTGAGAGTCAAGGTCAATGGAAAAACAGTAAAGGTCAGTAATAATACGAC
* *
1587671 ACAGGTGAGTGTCGAGGTCAATGGAAAAACAGTAAAGGTCAGTAATAATACGAC
1 ACAGGTGAGAGTCAAGGTCAATGGAAAAACAGTAAAGGTCAGTAATAATACGAC
* * *
1587725 ACAGGTGAGAGTCAGGGTCAATGGAAAAACAGTAAAGGTTAGTCATAATACGAC
1 ACAGGTGAGAGTCAAGGTCAATGGAAAAACAGTAAAGGTCAGTAATAATACGAC
*
1587779 ACAGGTGAGAGTCAGGGTCA
1 ACAGGTGAGAGTCAAGGTCA
1587799 CAAGTAAGAG
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
54 166 0.99
55 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.28, T:0.18
Consensus pattern (54 bp):
ACAGGTGAGAGTCAAGGTCAATGGAAAAACAGTAAAGGTCAGTAATAATACGAC
Found at i:1587991 original size:33 final size:33
Alignment explanation
Indices: 1587885--1588194 Score: 230
Period size: 33 Copynumber: 9.4 Consensus size: 33
1587875 TACATTTCAG
* ** * *
1587885 GTAAGAGTCAAGGTCAATATAAATACGTCACAG
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
* * *
1587918 GTAAGAGTGAAGGTCAGTGGGAAA-ATAT-ACCAG
1 GTAAGAGTCAAGGTCAGT-GGAAATACATCA-CAA
* * **
1587951 GTTAGAGTCAGGGTCTTTGGAAATACATCACAA
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
* *
1587984 GTAAGAGTCAAGGTCAGTAGAAATACATCAAAA
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
* ** *
1588017 TTAA-AGGTCATTGTCAGTGGAAATACATCACAG
1 GTAAGA-GTCAAGGTCAGTGGAAATACATCACAA
* * * * * *
1588050 GTAGGGGTAAAGGTCAGTGAAAATATATCACAT
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
* * *
1588083 GTTACAGTCAAGGTCAGTGGAAATACATCTCAA
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
* * * ** * *
1588116 GTTAGAGCCAATGTCTTTGGAAATACATCATAG
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
* * *
1588149 GTAAGAGTCACGGTCAGTGGAAATTCATCACAT
1 GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
*
1588182 GTAACAGTCAAGG
1 GTAAGAGTCAAGG
1588195 ACGATGGAAA
Statistics
Matches: 209, Mismatches: 62, Indels: 12
0.74 0.22 0.04
Matches are distributed among these distances:
32 7 0.03
33 198 0.95
34 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (33 bp):
GTAAGAGTCAAGGTCAGTGGAAATACATCACAA
Found at i:1588051 original size:99 final size:99
Alignment explanation
Indices: 1587948--1588194 Score: 264
Period size: 99 Copynumber: 2.5 Consensus size: 99
1587938 GAAAATATAC
* ** * *
1587948 CAGGTTAGAGTCAGGGTCTTTGGAAATACATCACAAGTAAGAGTCAAGGTCAGTAGAAATACATC
1 CAGGTTAGAGTCAAGGTCAGTGGAAATACATCACATGTAACAGTCAAGGTCAGTAGAAATACATC
* *
1588013 -AAAATTAAAGGTCATTGTCAGTGGAAATACATCA
66 TAAAATTAAA-GCCAATGTCAGTGGAAATACATCA
* * * * * *
1588047 CAGG-TAGGGGTAAAGGTCAGTGAAAATATATCACATGTTACAGTCAAGGTCAGTGGAAATACAT
1 CAGGTTA-GAGTCAAGGTCAGTGGAAATACATCACATGTAACAGTCAAGGTCAGTAGAAATACAT
* * * **
1588111 CTCAAGTTAGAGCCAATGTCTTTGGAAATACATCA
65 CTAAAATTAAAGCCAATGTCAGTGGAAATACATCA
* * * *
1588146 TAGGTAAGAGTCACGGTCAGTGGAAATTCATCACATGTAACAGTCAAGG
1 CAGGTTAGAGTCAAGGTCAGTGGAAATACATCACATGTAACAGTCAAGG
1588195 ACGATGGAAA
Statistics
Matches: 118, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
98 2 0.02
99 109 0.92
100 7 0.06
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (99 bp):
CAGGTTAGAGTCAAGGTCAGTGGAAATACATCACATGTAACAGTCAAGGTCAGTAGAAATACATC
TAAAATTAAAGCCAATGTCAGTGGAAATACATCA
Found at i:1589611 original size:2 final size:2
Alignment explanation
Indices: 1589604--1589657 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1589594 AGGCATGTAA
*
1589604 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA 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
1589646 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1589658 ATTTTTCCTC
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:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1589746 original size:2 final size:2
Alignment explanation
Indices: 1589734--1589771 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1589724 CCTATTTTTA
*
1589734 CT CT TT 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
1589772 TCTTCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1589777 original size:3 final size:3
Alignment explanation
Indices: 1589769--1589803 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1589759 TCTCTCTCTC
1589769 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1589804 CTCTAACTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1589878 original size:11 final size:10
Alignment explanation
Indices: 1589842--1589922 Score: 71
Period size: 11 Copynumber: 7.9 Consensus size: 10
1589832 GTTTTTCTTC
1589842 TTTTCTGTTT-
1 TTTT-TGTTTG
1589852 TTTTTGTTTG
1 TTTTTGTTTG
1589862 --TTTGTTTG
1 TTTTTGTTTG
1589870 TTATTTGTTTG
1 TT-TTTGTTTG
1589881 TTTTCT-TTTG
1 TTTT-TGTTTG
1589891 ATTTCTTGTTTGG
1 -TTT-TTGTTT-G
1589904 TTTTTGTTTG
1 TTTTTGTTTG
*
1589914 TTTTAGTTT
1 TTTTTGTTT
1589923 TTTATCATCC
Statistics
Matches: 61, Mismatches: 1, Indels: 18
0.76 0.01 0.22
Matches are distributed among these distances:
8 8 0.13
9 5 0.08
10 19 0.31
11 21 0.34
12 7 0.11
13 1 0.02
ACGTcount: A:0.04, C:0.04, G:0.17, T:0.75
Consensus pattern (10 bp):
TTTTTGTTTG
Found at i:1590442 original size:26 final size:26
Alignment explanation
Indices: 1590413--1590484 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
1590403 CAGTACGTCC
*
1590413 AGGTATTTAATAGGCTCAGTACTGCA
1 AGGTATATAATAGGCTCAGTACTGCA
* **
1590439 AGGTATGTAATAGTG-TCAGTACTGTT
1 AGGTATATAATAG-GCTCAGTACTGCA
*
1590465 AGGTATATAATAGACTCAGT
1 AGGTATATAATAGGCTCAGT
1590485 GCCGCCAGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 38 0.97
27 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (26 bp):
AGGTATATAATAGGCTCAGTACTGCA
Found at i:1590646 original size:40 final size:40
Alignment explanation
Indices: 1590576--1592947 Score: 3358
Period size: 40 Copynumber: 59.1 Consensus size: 40
1590566 CCCGATTTCG
* * *
1590576 AGCCTAGTTGTGGTCGTTCCTCCTCCTT-TATTACAATAGT
1 AGCCTAGTTGTGGTCATTCCTTCT-CTTGTATTACAATACT
* ** * * **
1590616 AGCCTAGTTGTGGTAATGGCTTCTTTTTTATTACAATTTT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * * * * *
1590656 AGCCTAGTTGTTGTTAATCCTCCTCTTTTATTACAACACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * * * * *
1590696 ATCCTAGTTGTGGT-TTTCCATCTTATTTTATAACAATACT
1 AGCCTAGTTGTGGTCATTCCTTC-TCTTGTATTACAATACT
* * * * ** *
1590736 GGCCTAGCTGTTTGTCATTCCTTCACTTCCATTACCAATTAATGT
1 AGCCTAGTTG-TGGTCATTCCTTCTCTTGTATTA-CAA-T-A-CT
* * * * * *
1590781 AGCCTAGTTGTGGCCA-TCTCTCCTCTTCTGTTACACTACA
1 AGCCTAGTTGTGGTCATTC-CTTCTCTTGTATTACAATACT
* *
1590821 AGCCTAGTTTTGGTCATT-CTTCTTCTTCTATTACAAATACT
1 AGCCTAGTTGTGGTCATTCCTTC-TCTTGTATTAC-AATACT
* *
1590862 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTTCAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * *
1590902 AGCCTAGTTTTGGTCATTCCTTCACTTCTATTACAA-ATCT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATA-CT
* * * * * * * *
1590942 GGCCTAGTTGTGGCCATCCCTCCTCTTCTGTTACACTACA
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* **
1590982 AGCCTAGTTGTGGTTATGGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* **
1591022 AGCCTAGTTGTTGTCATAGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * **
1591062 AGCCTAGTTGCGGTTATAGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1591102 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * * *
1591142 AGCCTAGTTATGGTCATTCCTACTCCTGTATTACAATACA
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * *
1591182 AGCCTAGTTGTGGCCATTCCTCCTCTTGTATTATAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1591222 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* ***
1591262 AGCCTAGTTGCGGTCATAGATTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* **
1591302 AGCCTAGTTGTTGTCATAGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* **
1591342 AGCCTAGTTGCGGTCATAGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* **
1591382 AGCCTAGTTGCGGTCATAGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1591422 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* *
1591462 AGCCTAGTTGTTGTCATTCCTTCTCTTGCATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * *
1591502 AGCCTAGTTGTTGTCATTCCTTCTCTTCTTTTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1591542 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1591582 AGCCTAGTTGTGGTCATTCCTACTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1591622 AGCCTAGTTGTGGCCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1591662 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* *
1591702 AGCCTAGTTGTGGTCATTCCTACTCTTGTATTACAATACA
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * *
1591742 AGCCAAGTTGTGGCCATTCCTCCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* * *
1591782 ACCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAAAACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* *
1591822 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATAATAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* ** *
1591862 AGCCTAGTTGCGGTCATAGCTTCTCTTGTATTACAATACA
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* *
1591902 AGCCTAGTTGTGGCCATTCCTCCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* **
1591942 AGCCTAGTTGTTGTCATAGCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1591982 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
* *
1592022 ACCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592062 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592102 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592142 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592182 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592222 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592262 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592302 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592342 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592382 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592422 AGCCTAGTTGTGGTCATTCCTACTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592462 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592502 AGCCTAGTTATGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592542 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592582 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592622 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592662 AGCCTAGTTGTTGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1592702 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
** * *
1592742 AGCCTAGTAATTGTCATTCCTCCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592782 AGCCTAGTTGTGGTCATTCCTCCTCTTGTATTACAA-ATCT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATA-CT
* * *
1592822 AGCCTAGTTGTGG-CAATTCTCCTTTTCTTCTATTAAAATACT
1 AGCCTAGTTGTGGTC-A-T-TCCTTCTCTTGTATTACAATACT
1592864 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
1 AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
*
1592904 AGCCTAATTGTGGTCATTCCCCTTCTC--GTATTACAATACT
1 AGCCTAGTTGTGGTCATT--CCTTCTCTTGTATTACAATACT
1592944 AGCC
1 AGCC
1592948 CCGAGCACAT
Statistics
Matches: 2104, Mismatches: 205, Indels: 46
0.89 0.09 0.02
Matches are distributed among these distances:
39 12 0.01
40 1967 0.93
41 42 0.02
42 52 0.02
43 7 0.00
44 15 0.01
45 9 0.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (40 bp):
AGCCTAGTTGTGGTCATTCCTTCTCTTGTATTACAATACT
Found at i:1594659 original size:26 final size:26
Alignment explanation
Indices: 1594630--1594736 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
1594620 CGATATGAGC
1594630 GATGGACTGTAGGTTGAGTTTTTGTG
1 GATGGACTGTAGGTTGAGTTTTTGTG
*
1594656 GATGGACTGTAGGTTGAGTTTTCGTG
1 GATGGACTGTAGGTTGAGTTTTTGTG
* *
1594682 GATGTACTGTAGGTTGAGTTTTTGGG
1 GATGGACTGTAGGTTGAGTTTTTGTG
*
1594708 GAT-GACTGTAGGTTGAGCTTTTGTG
1 GATGGACTGTAGGTTGAGTTTTTGTG
1594733 GATG
1 GATG
1594737 TAAGGCACTC
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
25 22 0.30
26 51 0.70
ACGTcount: A:0.16, C:0.06, G:0.38, T:0.40
Consensus pattern (26 bp):
GATGGACTGTAGGTTGAGTTTTTGTG
Found at i:1595467 original size:18 final size:18
Alignment explanation
Indices: 1595444--1595526 Score: 109
Period size: 18 Copynumber: 4.8 Consensus size: 18
1595434 AAATTTACAT
* *
1595444 ACGACAACTTTAGCAACA
1 ACGACAACTTTACCGACA
1595462 ACGACAACTTTACCGACA
1 ACGACAACTTTACCGACA
* *
1595480 ACGACACCTCTACCGAC-
1 ACGACAACTTTACCGACA
1595497 A--ACAACTTTACCGACA
1 ACGACAACTTTACCGACA
1595513 ACGACAACTTTACC
1 ACGACAACTTTACC
1595527 ACCGACGACA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.21
16 1 0.02
17 1 0.02
18 42 0.75
ACGTcount: A:0.39, C:0.35, G:0.10, T:0.17
Consensus pattern (18 bp):
ACGACAACTTTACCGACA
Found at i:1595510 original size:15 final size:15
Alignment explanation
Indices: 1595465--1595514 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
1595455 AGCAACAACG
1595465 ACAACTTTACCGACA
1 ACAACTTTACCGACA
*
1595480 ACGACACCTCTACCGACA
1 AC-A-A-CTTTACCGACA
1595498 ACAACTTTACCGACA
1 ACAACTTTACCGACA
1595513 AC
1 AC
1595515 GACAACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 14 0.47
16 2 0.07
17 2 0.07
18 12 0.40
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.16
Consensus pattern (15 bp):
ACAACTTTACCGACA
Found at i:1595960 original size:9 final size:9
Alignment explanation
Indices: 1595945--1595992 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
1595935 AATAAAGATG
1595945 ACATCAACA
1 ACATCAACA
*
1595954 TCATCAACA
1 ACATCAACA
*
1595963 ACAACAACA
1 ACATCAACA
**
1595972 ACATCAATG
1 ACATCAACA
1595981 ACATCAACA
1 ACATCAACA
1595990 ACA
1 ACA
1595993 ATGACAGCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.54, C:0.31, G:0.02, T:0.12
Consensus pattern (9 bp):
ACATCAACA
Found at i:1596530 original size:18 final size:18
Alignment explanation
Indices: 1596488--1596531 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1596478 TAAACCGACA
*
1596488 ACAACAACTAGCCAACCG
1 ACAACAACAAGCCAACCG
* **
1596506 ACGACAACAAGCCAACTT
1 ACAACAACAAGCCAACCG
1596524 ACAACAAC
1 ACAACAAC
1596532 CCGTAAACCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.36, G:0.09, T:0.07
Consensus pattern (18 bp):
ACAACAACAAGCCAACCG
Found at i:1596569 original size:21 final size:18
Alignment explanation
Indices: 1596524--1596558 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1596514 AAGCCAACTT
*
1596524 ACAACAACCCGTAAACCG
1 ACAACAACCCATAAACCG
1596542 ACAACAACCCATAAACC
1 ACAACAACCCATAAACC
1596559 CGTCACAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.40, G:0.06, T:0.06
Consensus pattern (18 bp):
ACAACAACCCATAAACCG
Found at i:1598771 original size:15 final size:15
Alignment explanation
Indices: 1598751--1598803 Score: 106
Period size: 15 Copynumber: 3.5 Consensus size: 15
1598741 ACGACAACGC
1598751 CGACAACAAAACAAA
1 CGACAACAAAACAAA
1598766 CGACAACAAAACAAA
1 CGACAACAAAACAAA
1598781 CGACAACAAAACAAA
1 CGACAACAAAACAAA
1598796 CGACAACA
1 CGACAACA
1598804 CCACAGCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.64, C:0.28, G:0.08, T:0.00
Consensus pattern (15 bp):
CGACAACAAAACAAA
Found at i:1600221 original size:2 final size:2
Alignment explanation
Indices: 1600214--1600247 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1600204 TGATGACACT
1600214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1600248 CTTCATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1600666 original size:47 final size:47
Alignment explanation
Indices: 1600577--1600716 Score: 248
Period size: 47 Copynumber: 3.0 Consensus size: 47
1600567 CTCAGTTATT
1600577 CAACGTAATGATTGGCTTAG--TATATACACCAACATCTATAATATA
1 CAACGTAATGATTGGCTTAGTATATATACACCAACATCTATAATATA
*
1600622 CAACGTAATGATTGACTTAGTATATATACACCAACATCTATAATATA
1 CAACGTAATGATTGGCTTAGTATATATACACCAACATCTATAATATA
*
1600669 CAACGTAATGAGTGGCTTAGTATATATACACCAACATCTATAATATA
1 CAACGTAATGATTGGCTTAGTATATATACACCAACATCTATAATATA
1600716 C
1 C
1600717 TTCGTATAGG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
45 19 0.21
47 71 0.79
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (47 bp):
CAACGTAATGATTGGCTTAGTATATATACACCAACATCTATAATATA
Found at i:1601647 original size:16 final size:15
Alignment explanation
Indices: 1601626--1601656 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1601616 TGTACATATC
1601626 TATATAGATAGATGGA
1 TATATAGATA-ATGGA
1601642 TATATAGATAATGGA
1 TATATAGATAATGGA
1601657 ATTTCCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (15 bp):
TATATAGATAATGGA
Found at i:1601725 original size:100 final size:100
Alignment explanation
Indices: 1601552--1601737 Score: 363
Period size: 100 Copynumber: 1.9 Consensus size: 100
1601542 GATACTACGT
1601552 ATGGAATTTCCTTTATAATCTTCTTGAAATTACACTTAAATTGCTGATATAAACATTTTTGGAAT
1 ATGGAATTTCCTTTATAATCTTCTTGAAATTACACTTAAATTGCTGATATAAACATTTTTGGAAT
*
1601617 GTACATATCTATATAGATAGATGGATATATAGATA
66 GTACATATCCATATAGATAGATGGATATATAGATA
1601652 ATGGAATTTCCTTTATAATCTTCTTGAAATTACACTTAAATTGCTGATATAAACATTTTTGGAAT
1 ATGGAATTTCCTTTATAATCTTCTTGAAATTACACTTAAATTGCTGATATAAACATTTTTGGAAT
1601717 GTACATATCCATATAGATAGA
66 GTACATATCCATATAGATAGA
1601738 CATATTAAGA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (100 bp):
ATGGAATTTCCTTTATAATCTTCTTGAAATTACACTTAAATTGCTGATATAAACATTTTTGGAAT
GTACATATCCATATAGATAGATGGATATATAGATA
Found at i:1601886 original size:21 final size:21
Alignment explanation
Indices: 1601862--1601906 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1601852 CTGTATACAT
*
1601862 TTATGAATAAAATT-TAAATCA
1 TTATGAA-AAAATTATAAATAA
*
1601883 TTATGAAATAATTATAAATAA
1 TTATGAAAAAATTATAAATAA
1601904 TTA
1 TTA
1601907 AAATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
TTATGAAAAAATTATAAATAA
Found at i:1605620 original size:11 final size:11
Alignment explanation
Indices: 1605604--1605644 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
1605594 TAAGCAAGTC
1605604 CTTAAAGGTGG
1 CTTAAAGGTGG
1605615 CTTAAAGGTGG
1 CTTAAAGGTGG
*
1605626 CGTAAAGGTGG
1 CTTAAAGGTGG
1605637 CTTAAAGG
1 CTTAAAGG
1605645 ATATAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1605670 original size:11 final size:11
Alignment explanation
Indices: 1605654--1605683 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1605644 GATATAAAAT
1605654 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1605665 CTTTAAGTCAC
1 CTTTAAGCCAC
1605676 CTTTAAGC
1 CTTTAAGC
1605684 TGAGCTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1605730 original size:11 final size:11
Alignment explanation
Indices: 1605714--1605763 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
1605704 GTCCAAACTT
*
1605714 CTTTAAGTCAC
1 CTTTAAGCCAC
*
1605725 CTTTAAGCCAT
1 CTTTAAGCCAC
1605736 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1605747 CTTTAAG-CAT
1 CTTTAAGCCAC
1605757 CTTTAAG
1 CTTTAAG
1605764 TGGCATTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1605759 original size:21 final size:22
Alignment explanation
Indices: 1605713--1605763 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1605703 TGTCCAAACT
*
1605713 TCTTTAAGTCACCTTTAAGCCA
1 TCTTTAAGCCACCTTTAAGCCA
1605735 TCTTTAAGCCACCTTTAAG-CA
1 TCTTTAAGCCACCTTTAAGCCA
1605756 TCTTTAAG
1 TCTTTAAG
1605764 TGGCATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (22 bp):
TCTTTAAGCCACCTTTAAGCCA
Found at i:1606148 original size:2 final size:2
Alignment explanation
Indices: 1606143--1606180 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1606133 GTGAAAAAAA
1606143 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
1606181 AGTTCATCTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1607406 original size:1 final size:1
Alignment explanation
Indices: 1607400--1607435 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
1607390 CGTGGGCGGG
**
1607400 TTTTTTTTTTTTTTTTTTTTTTTTTTCATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1607436 GTCTAGAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.03, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:1607543 original size:11 final size:11
Alignment explanation
Indices: 1607529--1607593 Score: 112
Period size: 11 Copynumber: 5.9 Consensus size: 11
1607519 AATTTTTTAA
1607529 TGGCTTAAAGG
1 TGGCTTAAAGG
1607540 TGGCTTAAAGG
1 TGGCTTAAAGG
*
1607551 TAGCTTAAAGG
1 TGGCTTAAAGG
1607562 TGGCTTAAAGG
1 TGGCTTAAAGG
*
1607573 TAGCTTAAAGG
1 TGGCTTAAAGG
1607584 TGGCTTAAAG
1 TGGCTTAAAG
1607594 AAGTTTGGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 50 1.00
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.28
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:1607557 original size:22 final size:22
Alignment explanation
Indices: 1607531--1607593 Score: 126
Period size: 22 Copynumber: 2.9 Consensus size: 22
1607521 TTTTTTAATG
1607531 GCTTAAAGGTGGCTTAAAGGTA
1 GCTTAAAGGTGGCTTAAAGGTA
1607553 GCTTAAAGGTGGCTTAAAGGTA
1 GCTTAAAGGTGGCTTAAAGGTA
1607575 GCTTAAAGGTGGCTTAAAG
1 GCTTAAAGGTGGCTTAAAG
1607594 AAGTTTGGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (22 bp):
GCTTAAAGGTGGCTTAAAGGTA
Found at i:1612127 original size:13 final size:13
Alignment explanation
Indices: 1612109--1612137 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1612099 TGCAATAAAT
1612109 AATGTTTACACTA
1 AATGTTTACACTA
1612122 AATGTTTACACTA
1 AATGTTTACACTA
1612135 AAT
1 AAT
1612138 AAAATAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (13 bp):
AATGTTTACACTA
Found at i:1612880 original size:16 final size:16
Alignment explanation
Indices: 1612855--1612894 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1612845 AAATGCCGGG
1612855 CGTCCGTCCGTGTGTC
1 CGTCCGTCCGTGTGTC
* *
1612871 CGTGCGTCCGTGTTTC
1 CGTCCGTCCGTGTGTC
1612887 CGTCCGTC
1 CGTCCGTC
1612895 ACACTTTTTT
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:0.00, C:0.38, G:0.30, T:0.33
Consensus pattern (16 bp):
CGTCCGTCCGTGTGTC
Found at i:1613496 original size:16 final size:16
Alignment explanation
Indices: 1613475--1613505 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1613465 GAATTCGTTA
*
1613475 TACGGATCTAACGAAT
1 TACGGATATAACGAAT
1613491 TACGGATATAACGAA
1 TACGGATATAACGAA
1613506 ATAAATCTAT
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:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (16 bp):
TACGGATATAACGAAT
Found at i:1614869 original size:12 final size:12
Alignment explanation
Indices: 1614848--1614877 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1614838 ATATTGTCAA
1614848 TATTTAATGTAT
1 TATTTAATGTAT
*
1614860 TATTTTATGTAT
1 TATTTAATGTAT
1614872 TATTTA
1 TATTTA
1614878 TTTAAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TATTTAATGTAT
Found at i:1624471 original size:13 final size:13
Alignment explanation
Indices: 1624453--1624487 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1624443 CAACTAAACC
1624453 CTGGGTTTACTTT
1 CTGGGTTTACTTT
1624466 CTGGGTTTAC-TT
1 CTGGGTTTACTTT
1624478 C-GGGTTTACT
1 CTGGGTTTACT
1624488 AGAGTGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 3 0.14
13 10 0.48
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (13 bp):
CTGGGTTTACTTT
Found at i:1624702 original size:11 final size:11
Alignment explanation
Indices: 1624688--1624788 Score: 51
Period size: 11 Copynumber: 9.1 Consensus size: 11
1624678 AAAGCAATTT
1624688 CAAAGTAAACC
1 CAAAGTAAACC
1624699 CAAAGTAAACC
1 CAAAGTAAACC
**
1624710 CCGAGTAAACC
1 CAAAGTAAACC
** **
1624721 CCGAGTGGACC
1 CAAAGTAAACC
*** *
1624732 CAAA-TTTTCA
1 CAAAGTAAACC
* *
1624742 AAAAATAAACC
1 CAAAGTAAACC
*
1624753 CAGAGTAAACC
1 CAAAGTAAACC
*
1624764 CAAAGTAGACC
1 CAAAGTAAACC
1624775 CAAAAAGTAAACC
1 C--AAAGTAAACC
1624788 C
1 C
1624789 GGGGTATAGT
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
10 5 0.08
11 51 0.77
13 10 0.15
ACGTcount: A:0.48, C:0.28, G:0.13, T:0.12
Consensus pattern (11 bp):
CAAAGTAAACC
Found at i:1625709 original size:85 final size:85
Alignment explanation
Indices: 1625556--1625722 Score: 280
Period size: 85 Copynumber: 2.0 Consensus size: 85
1625546 CAATTTGTTC
*
1625556 TATTATACCCCATTATAATAATTCTATGTAACGCGTTATCTGACTGGTTCTAGACAATCACGTGC
1 TATTATACCCCATTATAATAATTCTATGTAACGCGTTATCTGACTGGTACTAGACAATCACGTGC
1625621 CAGGGCAACAAAACTTCTTA
66 CAGGGCAACAAAACTTCTTA
* * * * *
1625641 TATTGTACCTCATTATAATAATTCTATGTAACGCGTTATTTGATTGGTACTATACAATCACGTGC
1 TATTATACCCCATTATAATAATTCTATGTAACGCGTTATCTGACTGGTACTAGACAATCACGTGC
1625706 CAGGGCAACAAAACTTC
66 CAGGGCAACAAAACTTC
1625723 ATATTTCCCC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (85 bp):
TATTATACCCCATTATAATAATTCTATGTAACGCGTTATCTGACTGGTACTAGACAATCACGTGC
CAGGGCAACAAAACTTCTTA
Found at i:1628295 original size:16 final size:16
Alignment explanation
Indices: 1628274--1628318 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1628264 TCTTTGTATG
1628274 AGACAAATTCATTGTC
1 AGACAAATTCATTGTC
*
1628290 AGACAAATTTATTGTC
1 AGACAAATTCATTGTC
1628306 AGACAAATTCATT
1 AGACAAATTCATT
1628319 TGCTGGCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (16 bp):
AGACAAATTCATTGTC
Found at i:1639156 original size:22 final size:22
Alignment explanation
Indices: 1639131--1639180 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1639121 AATTTAGTAA
1639131 AGGATGCATTACTTACAGGAGT
1 AGGATGCATTACTTACAGGAGT
1639153 AGGATGCATTACTTACAGGAGT
1 AGGATGCATTACTTACAGGAGT
1639175 AGGATG
1 AGGATG
1639181 TCCCTCCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (22 bp):
AGGATGCATTACTTACAGGAGT
Found at i:1651564 original size:18 final size:18
Alignment explanation
Indices: 1651541--1651577 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1651531 ACATTAAGAT
*
1651541 TGTACATACAACATCCAA
1 TGTACATAAAACATCCAA
*
1651559 TGTACATAAAACATTCAA
1 TGTACATAAAACATCCAA
1651577 T
1 T
1651578 AAACATGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (18 bp):
TGTACATAAAACATCCAA
Found at i:1651876 original size:2 final size:2
Alignment explanation
Indices: 1651869--1651933 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1651859 GTACTTCGAA
1651869 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
1651911 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1651934 AAATTTAGCA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1658192 original size:3 final size:3
Alignment explanation
Indices: 1658184--1658231 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1658174 GGAAGTCACA
1658184 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1658232 ATTTTAGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1659384 original size:25 final size:26
Alignment explanation
Indices: 1659356--1659405 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1659346 ATCTACAGTA
* *
1659356 TAAGGGG-TGTAAAAGAAGGGAATTC
1 TAAGGGGATATAAAAGAAAGGAATTC
*
1659381 TAAGGGGATATAAAGGAAAGGAATT
1 TAAGGGGATATAAAAGAAAGGAATT
1659406 TTAGGAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.34, T:0.20
Consensus pattern (26 bp):
TAAGGGGATATAAAAGAAAGGAATTC
Found at i:1668628 original size:110 final size:110
Alignment explanation
Indices: 1668491--1668714 Score: 412
Period size: 110 Copynumber: 2.0 Consensus size: 110
1668481 CTTTCGACAG
* *
1668491 GTGTATGCTCACTCTCTACATAAATTCAGACTGCATTTATTGAAATTTGTACATGTGAAATATTT
1 GTGTATGCTCACTCTCTACATAAATTCAGACTGCATATATTGAAATTTCTACATGTGAAATATTT
* *
1668556 GGAATTTAAGTTTTATTTTATATTTTAATTTTGCATCTGACAATT
66 AGAATTTAAGTTTTATTTTATATTTTAATTTTGCATCTGACAATA
1668601 GTGTATGCTCACTCTCTACATAAATTCAGACTGCATATATTGAAATTTCTACATGTGAAATATTT
1 GTGTATGCTCACTCTCTACATAAATTCAGACTGCATATATTGAAATTTCTACATGTGAAATATTT
1668666 AGAATTTAAGTTTTATTTTATATTTTAATTTTGCATCTGACAATA
66 AGAATTTAAGTTTTATTTTATATTTTAATTTTGCATCTGACAATA
1668711 GTGT
1 GTGT
1668715 GATCTCATTA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (110 bp):
GTGTATGCTCACTCTCTACATAAATTCAGACTGCATATATTGAAATTTCTACATGTGAAATATTT
AGAATTTAAGTTTTATTTTATATTTTAATTTTGCATCTGACAATA
Found at i:1689213 original size:12 final size:12
Alignment explanation
Indices: 1689196--1689222 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1689186 AGTCCGTAAA
1689196 TTTTTTTTTATT
1 TTTTTTTTTATT
1689208 TTTTTTTTTATT
1 TTTTTTTTTATT
1689220 TTT
1 TTT
1689223 GACAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:1694748 original size:23 final size:22
Alignment explanation
Indices: 1694675--1694755 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
1694665 ACAAATGATT
*
1694675 TTAGGTTAGGATTAGGTTTGGGG
1 TTAGGTTAGGGTTA-GTTTGGGG
* *
1694698 TTAAGGTTA-GGTTCGTTT-AGG
1 TT-AGGTTAGGGTTAGTTTGGGG
*
1694719 TTTGGATTAGGGTTAGTTTGGGG
1 TTAGG-TTAGGGTTAGTTTGGGG
1694742 TTAGGATTAGGGTT
1 TTAGG-TTAGGGTT
1694756 TAGGACCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.04
21 7 0.15
22 12 0.26
23 20 0.43
24 6 0.13
ACGTcount: A:0.17, C:0.01, G:0.40, T:0.42
Consensus pattern (22 bp):
TTAGGTTAGGGTTAGTTTGGGG
Found at i:1694966 original size:18 final size:18
Alignment explanation
Indices: 1694912--1694968 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1694902 GTTACAAATG
*
1694912 GGTTTA-GGTTAAGGTTA
1 GGTTTAGGGTTAGGGTTA
* * *
1694929 GGTTTTGGATTAGGGATA
1 GGTTTAGGGTTAGGGTTA
* *
1694947 GGGTTAGGGTTAGGTTTA
1 GGTTTAGGGTTAGGGTTA
1694965 GGTT
1 GGTT
1694969 AGGTTCGGAT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (18 bp):
GGTTTAGGGTTAGGGTTA
Found at i:1695288 original size:2 final size:2
Alignment explanation
Indices: 1695281--1695328 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1695271 GATATTTTTC
1695281 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
1695323 AG AG AG
1 AG AG AG
1695329 TTTGGGCATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1704456 original size:12 final size:12
Alignment explanation
Indices: 1704439--1704469 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1704429 GTTTACAGTA
1704439 ACCATCCCTCTC
1 ACCATCCCTCTC
1704451 ACCATCCCTCTC
1 ACCATCCCTCTC
1704463 ACCATCC
1 ACCATCC
1704470 TTCACAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.58, G:0.00, T:0.23
Consensus pattern (12 bp):
ACCATCCCTCTC
Found at i:1724575 original size:27 final size:27
Alignment explanation
Indices: 1724537--1724591 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1724527 NNNNNNNNNN
1724537 CAACCAAATAAAGTGATACCCATCGCA
1 CAACCAAATAAAGTGATACCCATCGCA
1724564 CAACCAAATAAAGTGATACCCATCGCA
1 CAACCAAATAAAGTGATACCCATCGCA
1724591 C
1 C
1724592 CCAAGATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.31, G:0.11, T:0.15
Consensus pattern (27 bp):
CAACCAAATAAAGTGATACCCATCGCA
Found at i:1738927 original size:16 final size:16
Alignment explanation
Indices: 1738906--1738937 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1738896 TTTGAATGCT
1738906 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
1738922 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
1738938 ATTTATAGGG
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:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Done.