Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 75 of 79
Found at i:24988399 original size:3 final size:3
Alignment explanation
Indices: 24988391--24988438 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
24988381 ATCATAAATC
24988391 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24988439 ATNNNNNNNN
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24989250 original size:15 final size:16
Alignment explanation
Indices: 24989212--24989250 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
24989202 AATCCACAAT
*
24989212 ATATTAATATTTTAGA
1 ATATTAATTTTTTAGA
24989228 A-ATTAATTTTTTA-A
1 ATATTAATTTTTTAGA
24989242 ATATTAATT
1 ATATTAATT
24989251 CAAGGTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATATTAATTTTTTAGA
Found at i:24995082 original size:28 final size:26
Alignment explanation
Indices: 24995051--24995124 Score: 69
Period size: 31 Copynumber: 2.6 Consensus size: 26
24995041 GGATATTCAT
24995051 TTTTATTATTTAAAAATAATTTAATAAA
1 TTTTATT-TTTAAAAATAA-TTAATAAA
*
24995079 TTTTAATGTTTTTAAAAATCTAATTAATATA
1 TTTT-A--TTTTTAAAAA--TAATTAATAAA
24995110 TTTTA-TTTTAAAAAT
1 TTTTATTTTTAAAAAT
24995125 CAAATCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
25 1 0.03
27 9 0.22
28 4 0.10
29 1 0.03
30 9 0.22
31 13 0.32
32 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TTTTATTTTTAAAAATAATTAATAAA
Found at i:24998217 original size:21 final size:21
Alignment explanation
Indices: 24998180--24998221 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24998170 ATGAACTAAA
24998180 ATTTTTAATTTAATTTATAATT
1 ATTTTTAATTT-ATTTATAATT
24998202 ATTTTTAAATTT-TTTATAAT
1 ATTTTT-AATTTATTTATAAT
24998222 GTAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAATTTATTTATAATT
Found at i:25004051 original size:21 final size:22
Alignment explanation
Indices: 25004027--25004076 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
25004017 AATTGTGTTA
* *
25004027 ATATTTAAAATTTA-TTTTTAT
1 ATATTAAAAAATTACTTTTTAT
25004048 ATATTAAAAAATTACTTTTTAT
1 ATATTAAAAAATTACTTTTTAT
25004070 ATTATTA
1 A-TATTA
25004077 CTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 8 0.32
23 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTAAAAAATTACTTTTTAT
Found at i:25004056 original size:20 final size:21
Alignment explanation
Indices: 25004027--25004076 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
25004017 AATTGTGTTA
*
25004027 ATAT-TTAAAATTTA-TTTTT
1 ATATATTAAAAATTACTTTTT
25004046 ATATATTAAAAAATTACTTTTT
1 ATATATT-AAAAATTACTTTTT
25004068 ATATTATTA
1 ATA-TATTA
25004077 CTAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 7 0.27
22 9 0.35
23 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATATTAAAAATTACTTTTT
Found at i:25005197 original size:255 final size:256
Alignment explanation
Indices: 25004733--25005248 Score: 1025
Period size: 255 Copynumber: 2.0 Consensus size: 256
25004723 AAATAAATTT
25004733 AAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTACAAACAAATTGAAAAT
1 AAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTACAAACAAATTGAAAAT
25004798 AAATTAAAAAATTTATTTATACTTAAATAACACTGAGATAGATACAACTTAACAAGCAAATACCT
66 AAATTAAAAAATTTATTTATACTTAAATAACACTGAGATAGATACAACTTAACAAGCAAATACCT
25004863 CTAAAATGGTAGTAAAATTAACAATAAAACAAATGTTATACAGTATCCAAATAATAGCAACAAAG
131 CTAAAATGGTAGTAAAATTAACAATAAAACAAATGTTATACAGTATCCAAATAATAGCAACAAAG
25004928 TAGTAGCAATATAATAGCGAAATGACACCAAACAGTGACAAAACAGCAACAAAAACAATGA
196 TAGTAGCAATATAATAGCGAAATGACACCAAACAGTGACAAAACAGCAACAAAAACAATGA
25004989 AAAAAATATAAT-TATCAAATACACTAAAAATATTAAAATAAATGTTTACAAACAAATTGAAAAT
1 AAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTACAAACAAATTGAAAAT
25005053 AAATTAAAAAATTTATTTATACTTAAATAACACTGAGATAGATACAACTTAACAAGCAAATACCT
66 AAATTAAAAAATTTATTTATACTTAAATAACACTGAGATAGATACAACTTAACAAGCAAATACCT
25005118 CTAAAATGGTAGTAAAATTAACAATAAAACAAATGTTATACAGTATCCAAATAATAGCAACAAAG
131 CTAAAATGGTAGTAAAATTAACAATAAAACAAATGTTATACAGTATCCAAATAATAGCAACAAAG
25005183 TAGTAGCAATATAATAGCGAAATGACACCAAACAGTGACAAAACAGCAACAAAAACAATGA
196 TAGTAGCAATATAATAGCGAAATGACACCAAACAGTGACAAAACAGCAACAAAAACAATGA
25005244 AAAAA
1 AAAAA
25005249 GTAGTAAAAA
Statistics
Matches: 260, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
255 248 0.95
256 12 0.05
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.23
Consensus pattern (256 bp):
AAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTACAAACAAATTGAAAAT
AAATTAAAAAATTTATTTATACTTAAATAACACTGAGATAGATACAACTTAACAAGCAAATACCT
CTAAAATGGTAGTAAAATTAACAATAAAACAAATGTTATACAGTATCCAAATAATAGCAACAAAG
TAGTAGCAATATAATAGCGAAATGACACCAAACAGTGACAAAACAGCAACAAAAACAATGA
Found at i:25006568 original size:28 final size:28
Alignment explanation
Indices: 25006532--25006596 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
25006522 TTGAGTAATT
*
25006532 TAATTTTTTTCTTTTATATTT-TTTTAACT
1 TAATTTTTTTC-TTTAT-TTTCTTTTAACG
*
25006561 TTATTTTTTTCTTTATTTTCTTTTAACG
1 TAATTTTTTTCTTTATTTTCTTTTAACG
25006589 TAATTTTT
1 TAATTTTT
25006597 CTATGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.09
28 19 0.59
29 10 0.31
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (28 bp):
TAATTTTTTTCTTTATTTTCTTTTAACG
Found at i:25020115 original size:13 final size:15
Alignment explanation
Indices: 25020093--25020124 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
25020083 TAAAATGTTA
25020093 AAAAATTATA-ATTT
1 AAAAATTATATATTT
25020107 AAAAA-TATATATTT
1 AAAAATTATATATTT
25020121 AAAA
1 AAAA
25020125 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATTATATATTT
Found at i:25020152 original size:22 final size:20
Alignment explanation
Indices: 25020105--25020161 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
25020095 AAATTATAAT
25020105 TTAAAAATATATATTTAAAA
1 TTAAAAATATATATTTAAAA
25020125 TTAAAAATATATATTTAAAA
1 TTAAAAATATATATTTAAAA
25020145 TCTAAAAAATATATATT
1 T-T-AAAAATATATATT
25020162 GTTTAAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 21 0.60
21 1 0.03
22 13 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAAATATATATTTAAAA
Found at i:25025819 original size:3 final size:3
Alignment explanation
Indices: 25025811--25025849 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
25025801 TATTTTCTCC
*
25025811 TTA TTA TTA TTA TTA TTA TTA TTA TTTA GTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
25025850 TTCATGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25035562 original size:14 final size:14
Alignment explanation
Indices: 25035538--25035572 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
25035528 AGCAAAAATA
25035538 ATCATTGTATGATTT
1 ATCA-TGTATGATTT
25035553 ATCATGTATGATTT
1 ATCATGTATGATTT
25035567 A-CATGT
1 ATCATGT
25035573 GGTAGATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 11 0.55
15 4 0.20
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (14 bp):
ATCATGTATGATTT
Found at i:25037747 original size:21 final size:21
Alignment explanation
Indices: 25037721--25037776 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
25037711 AACAGCGGTG
25037721 GCGGTGAGATTA-ATCACTGTA
1 GCGGTGAGATTAGAT-ACTGTA
25037742 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
25037763 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
25037777 AACAATGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.27
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:25039440 original size:18 final size:17
Alignment explanation
Indices: 25039399--25039443 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
25039389 TTTAATTTTG
25039399 TATAAAAATTGTAAAAA
1 TATAAAAATTGTAAAAA
*
25039416 T-TCAAAAATATTTAAAAA
1 TAT-AAAAAT-TGTAAAAA
25039434 TATAAAAATT
1 TATAAAAATT
25039444 CAAGTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 8 0.33
18 14 0.58
19 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TATAAAAATTGTAAAAA
Found at i:25047800 original size:56 final size:56
Alignment explanation
Indices: 25047714--25047881 Score: 336
Period size: 56 Copynumber: 3.0 Consensus size: 56
25047704 TGGCTATGGC
25047714 AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
1 AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
25047770 AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
1 AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
25047826 AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
1 AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
25047882 TTACCAGTTG
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 112 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (56 bp):
AATTGACAAAGCACATCATGCCTTAAACTTTTGTAATTTATCTCACACTCTTTTGT
Found at i:25064546 original size:3 final size:3
Alignment explanation
Indices: 25064538--25064581 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
25064528 GTTTATTTTC
25064538 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25064582 TTAATAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25068370 original size:31 final size:31
Alignment explanation
Indices: 25068330--25068403 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
25068320 TAGTTTGTCC
*
25068330 CCTGAACTTGTCCAGAAGTACCTACTTGATA
1 CCTGAACTTGTCCAGAAGTACCTAATTGATA
* * * *
25068361 CTTGAACTTGTCCGGGAGTACCTAATTGGTA
1 CCTGAACTTGTCCAGAAGTACCTAATTGATA
25068392 CCTGAACTTGTC
1 CCTGAACTTGTC
25068404 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (31 bp):
CCTGAACTTGTCCAGAAGTACCTAATTGATA
Found at i:25068433 original size:20 final size:20
Alignment explanation
Indices: 25068408--25068445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25068398 CTTGTCTAAA
25068408 AAATTATACTTTTT-AAAACT
1 AAATTATA-TTTTTCAAAACT
25068428 AAATTATATTTTTCAAAA
1 AAATTATATTTTTCAAAA
25068446 GATTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTATATTTTTCAAAACT
Found at i:25070987 original size:18 final size:18
Alignment explanation
Indices: 25070961--25070997 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25070951 TATATTATTG
*
25070961 TCTATATTTAAATCTAAA
1 TCTAAATTTAAATCTAAA
*
25070979 TCTAAATTTAAATTTAAA
1 TCTAAATTTAAATCTAAA
25070997 T
1 T
25070998 TTAATATTAT
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:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TCTAAATTTAAATCTAAA
Found at i:25070998 original size:6 final size:6
Alignment explanation
Indices: 25070966--25071001 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
25070956 TATTGTCTAT
* *
25070966 ATTTAA ATCTAA ATCTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
25071002 TATTATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:25074469 original size:11 final size:11
Alignment explanation
Indices: 25074455--25074479 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25074445 TCAAATCAAT
25074455 AAATTAAATTA
1 AAATTAAATTA
25074466 AAATTAAATTA
1 AAATTAAATTA
25074477 AAA
1 AAA
25074480 AATTACGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:25080280 original size:15 final size:15
Alignment explanation
Indices: 25080249--25080287 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 15
25080239 ATAGTATATA
25080249 ATATATAATATTTTT
1 ATATATAATATTTTT
25080264 ATAT-TAATATTTATT
1 ATATATAATATTT-TT
25080279 ATAATATAA
1 AT-ATATAA
25080288 AAATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 8 0.38
16 2 0.10
17 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATATAATATTTTT
Found at i:25087295 original size:30 final size:29
Alignment explanation
Indices: 25087237--25087295 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
25087227 GTGTAATGTC
*
25087237 ATACATGAACTTTAATTTTGTGCAATTTT
1 ATACATGAACTTTAATTTGGTGCAATTTT
* * *
25087266 ATACATGAATTCTTGATTTGGTTCAATTTT
1 ATACATGAACT-TTAATTTGGTGCAATTTT
25087296 CAAAAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (29 bp):
ATACATGAACTTTAATTTGGTGCAATTTT
Found at i:25095242 original size:29 final size:30
Alignment explanation
Indices: 25095175--25095251 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
25095165 ATCAAAACTG
25095175 TACATGAATTTTGATCTAATGTACAATGTCA
1 TACATGAATTTTGAT-TAATGTACAATGTCA
* * * *
25095206 TACGTGAATTTTGATT-CTGTGCAATGTTA
1 TACATGAATTTTGATTAATGTACAATGTCA
*
25095235 TACATGAAATTGTGATT
1 TACATG-AATTTTGATT
25095252 TGATTCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 15 0.38
30 10 0.26
31 14 0.36
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (30 bp):
TACATGAATTTTGATTAATGTACAATGTCA
Found at i:25095465 original size:29 final size:29
Alignment explanation
Indices: 25095428--25095483 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
25095418 TATGAATCGT
*
25095428 AATTCAAATTTACGTAT-ATAATTACATCA
1 AATTAAAATTTACGTATGA-AATTACATCA
25095457 AATTAAAATTTACGTATGAAATTACAT
1 AATTAAAATTTACGTATGAAATTACAT
25095484 ATTAAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (29 bp):
AATTAAAATTTACGTATGAAATTACATCA
Found at i:25098601 original size:2 final size:2
Alignment explanation
Indices: 25098594--25098619 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25098584 GGTTATTGTC
25098594 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25098620 CACACTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25109720 original size:2 final size:2
Alignment explanation
Indices: 25109713--25109750 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25109703 ATCAAGTTAC
25109713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25109751 TCAATCTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25109791 original size:24 final size:23
Alignment explanation
Indices: 25109763--25109813 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
25109753 AATCTAGAAG
*
25109763 ATTTAATATTTATGAGTATAATAT
1 ATTTAATATTTATGAGCAT-ATAT
* *
25109787 ATTTAGTATTTATTAGCATATAT
1 ATTTAATATTTATGAGCATATAT
25109810 ATTT
1 ATTT
25109814 GACTTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (23 bp):
ATTTAATATTTATGAGCATATAT
Found at i:25110598 original size:27 final size:27
Alignment explanation
Indices: 25110563--25110624 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
25110553 ACAAAATAAT
* *
25110563 TTTCAAAAATTTA-AAATATTTATAAGAA
1 TTTCTAAAATTTATAAAT-TTTA-AAAAA
25110591 -TTCTAAAATTTATAAATTTTAAAAAA
1 TTTCTAAAATTTATAAATTTTAAAAAA
25110617 TTTCTAAA
1 TTTCTAAA
25110625 GAATATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 22 0.73
28 4 0.13
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (27 bp):
TTTCTAAAATTTATAAATTTTAAAAAA
Found at i:25110654 original size:9 final size:9
Alignment explanation
Indices: 25110560--25110666 Score: 58
Period size: 10 Copynumber: 11.1 Consensus size: 9
25110550 AATACAAAAT
25110560 AATTTTCAAA
1 AATTTT-AAA
25110570 AA-TTTAAA
1 AATTTTAAA
*
25110578 ATATTTATAAG
1 A-ATTT-TAAA
*
25110589 AATTCT-AA
1 AATTTTAAA
*
25110597 AA-TTTATA
1 AATTTTAAA
25110605 AATTTTAAAA
1 AATTTT-AAA
25110615 AATTTCTAAA
1 AATTT-TAAA
*
25110625 GAATATGTAAA
1 -AAT-TTTAAA
*
25110636 TAAATTTAAA
1 -AATTTTAAA
25110646 AATTTTAAAA
1 AATTTT-AAA
25110656 AATTTCTAAA
1 AATTT-TAAA
25110666 A
1 A
25110667 TAATAATTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
7 2 0.03
8 10 0.13
9 13 0.17
10 34 0.45
11 15 0.20
12 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (9 bp):
AATTTTAAA
Found at i:25112535 original size:59 final size:59
Alignment explanation
Indices: 25112390--25112557 Score: 212
Period size: 59 Copynumber: 2.8 Consensus size: 59
25112380 ATATCAGGAT
* * * * * *
25112390 CTAACTTGGACCAAAAAAAGTTTAGG-TTCGAAAGTGGGAACAATTGCCAAGTTTAGGGA
1 CTAACTTAGACAAAAAAAAGTTCAGGCCTC-AATGTGGGAACAATTGCCAAATTTAGGGA
* * *
25112449 CTAACTTGGACAAAAAAAAGTTTAGGCCTTAATGTGGGAACAATTGCCAAATTTAGGGA
1 CTAACTTAGACAAAAAAAAGTTCAGGCCTCAATGTGGGAACAATTGCCAAATTTAGGGA
* * *
25112508 CTAACTTAGACAAAAAAAAGTTCAGGCCTCAATGTGAGAATAGTTGCCAA
1 CTAACTTAGACAAAAAAAAGTTCAGGCCTCAATGTGGGAACAATTGCCAA
25112558 GTTCAAGTTC
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 96 0.99
60 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (59 bp):
CTAACTTAGACAAAAAAAAGTTCAGGCCTCAATGTGGGAACAATTGCCAAATTTAGGGA
Found at i:25115330 original size:29 final size:29
Alignment explanation
Indices: 25115282--25115366 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 29
25115272 ATAAATCTCA
25115282 AAATTATACAT-AAACTTTGATTTGGTGT
1 AAATTATACATGAAACTTTGATTTGGTGT
*
25115310 -AATTATACAGTGAAACTTTGATATTGTGGTTT
1 AAATTATACA-TGAAACTTTG--ATT-TGGTGT
*
25115342 AAATGTATACATGAAACTTTAATTT
1 AAAT-TATACATGAAACTTTGATTT
25115367 TGATTCAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
27 9 0.19
28 1 0.02
29 8 0.17
30 1 0.02
31 6 0.12
32 5 0.10
33 12 0.25
34 6 0.12
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (29 bp):
AAATTATACATGAAACTTTGATTTGGTGT
Found at i:25119113 original size:21 final size:21
Alignment explanation
Indices: 25119074--25119113 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25119064 AACATAAACA
*
25119074 TAAACATTGAACCTCGAACCT
1 TAAACATTGAACATCGAACCT
* *
25119095 TAAACCTTGAACATTGAAC
1 TAAACATTGAACATCGAAC
25119114 ATTGACCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (21 bp):
TAAACATTGAACATCGAACCT
Found at i:25119118 original size:14 final size:14
Alignment explanation
Indices: 25119076--25119125 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
25119066 CATAAACATA
*
25119076 AACATTGAACCTCG
1 AACATTGAACCTTG
* *
25119090 AACCTTAAACCTTG
1 AACATTGAACCTTG
*
25119104 AACATTGAACATTG
1 AACATTGAACCTTG
*
25119118 ACCATTGA
1 AACATTGA
25119126 TCCATAAACC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (14 bp):
AACATTGAACCTTG
Found at i:25119243 original size:20 final size:21
Alignment explanation
Indices: 25119204--25119249 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
25119194 TCAAGGTTTG
25119204 GGGTTCGAGATTTAAGATTTA
1 GGGTTCGAGATTTAAGATTTA
*
25119225 GGGTTCGAG-TTTGAGATTTA
1 GGGTTCGAGATTTAAGATTTA
*
25119245 AGGTT
1 GGGTT
25119250 TAGGGTTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.24, C:0.04, G:0.33, T:0.39
Consensus pattern (21 bp):
GGGTTCGAGATTTAAGATTTA
Found at i:25120227 original size:9 final size:9
Alignment explanation
Indices: 25120210--25120240 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25120200 TCGAGTTGAT
25120210 TCGAATAAC
1 TCGAATAAC
*
25120219 TCGATTAAC
1 TCGAATAAC
25120228 TCGAATAAC
1 TCGAATAAC
25120237 TCGA
1 TCGA
25120241 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:25121065 original size:21 final size:20
Alignment explanation
Indices: 25121025--25121064 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
25121015 TATATATTTT
*
25121025 ATTTTTAATCAATCAAATATA
1 ATTTTTAATCAAT-ATATATA
25121046 ATTTTTAATCAA-ATATATA
1 ATTTTTAATCAATATATATA
25121065 TTTACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTTAATCAATATATATA
Found at i:25123063 original size:5 final size:6
Alignment explanation
Indices: 25123026--25123060 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
25123016 ATTCTTGATT
**
25123026 TTAAAA TTAAAA TTAAAA TTAAAA AGAAAA TTAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
25123061 TTACACAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (6 bp):
TTAAAA
Found at i:25131835 original size:24 final size:24
Alignment explanation
Indices: 25131795--25131840 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
25131785 AGGTATCTCT
* *
25131795 CTCCCTTCCCCATTTCTGTCCCCA
1 CTCCCTTCCCCACTTCTCTCCCCA
25131819 CTCCCTTTCCCC-CTTCTCTCCC
1 CTCCC-TTCCCCACTTCTCTCCC
25131841 TCATATGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.04, C:0.59, G:0.02, T:0.35
Consensus pattern (24 bp):
CTCCCTTCCCCACTTCTCTCCCCA
Found at i:25135877 original size:2 final size:2
Alignment explanation
Indices: 25135870--25136414 Score: 1090
Period size: 2 Copynumber: 272.5 Consensus size: 2
25135860 TGGATCATGT
25135870 TA TA TA TA 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 TA TA TA TA
25135912 TA TA TA TA 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 TA TA TA TA
25135954 TA TA TA TA 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 TA TA TA TA
25135996 TA TA TA TA 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 TA TA TA TA
25136038 TA TA TA TA 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 TA TA TA TA
25136080 TA TA TA TA 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 TA TA TA TA
25136122 TA TA TA TA 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 TA TA TA TA
25136164 TA TA TA TA 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 TA TA TA TA
25136206 TA TA TA TA 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 TA TA TA TA
25136248 TA TA TA TA 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 TA TA TA TA
25136290 TA TA TA TA 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 TA TA TA TA
25136332 TA TA TA TA 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 TA TA TA TA
25136374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25136415 GTTCTGATTA
Statistics
Matches: 543, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 543 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25137650 original size:15 final size:15
Alignment explanation
Indices: 25137625--25137666 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
25137615 ATATTTGAGA
25137625 TTTAA-TTTTTATAC
1 TTTAATTTTTTATAC
*
25137639 TTTAATTTTTTATAG
1 TTTAATTTTTTATAC
*
25137654 TTTGATTCTTTTA
1 TTTAATT-TTTTA
25137667 CTTGTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTAATTTTTTATAC
Found at i:25153290 original size:125 final size:126
Alignment explanation
Indices: 25152941--25153277 Score: 498
Period size: 125 Copynumber: 2.7 Consensus size: 126
25152931 TAAGGCCAAG
* * * * *
25152941 CAAGAACTAATGTAGAAAAAGAGCATCCACGTGGGAGTTTTTTTAAGTAATTTTACTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * *
25153006 ATCTTGCTTAAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTTTTTAGAACCATCTTCTCAAAATTATTTTTT
* * * * * *
25153067 CAAGAACTACTATAGAAAAA-AGTGTTCACGTGAGACCTTTTTTCAGTAATTTTGCTGATAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
*
25153131 ATCCTGCTTAAAGCGTTTTTGACACTATTTTTTTAGAACCATTTTCTCAAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTTTTTAGAACCATCTTCTCAAAATTATTTTTT
* *
25153192 -AGGAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
*
25153256 ATCCTACTTAAAGCGTTTTTGA
66 ATCCTGCTTAAAGCGTTTTTGA
25153278 TAGGGTTTTT
Statistics
Matches: 186, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
124 17 0.09
125 151 0.81
126 18 0.10
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (126 bp):
CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTTTTTAGAACCATCTTCTCAAAATTATTTTTT
Found at i:25153630 original size:20 final size:20
Alignment explanation
Indices: 25153605--25153645 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25153595 TGTTGCTGCA
*
25153605 CCACCATGCTGCTATCCCTT
1 CCACCAGGCTGCTATCCCTT
*
25153625 CCACCAGGCTGCTGTCCCTT
1 CCACCAGGCTGCTATCCCTT
25153645 C
1 C
25153646 AATGGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.46, G:0.15, T:0.27
Consensus pattern (20 bp):
CCACCAGGCTGCTATCCCTT
Found at i:25153937 original size:60 final size:59
Alignment explanation
Indices: 25153872--25154020 Score: 149
Period size: 60 Copynumber: 2.5 Consensus size: 59
25153862 ATAGTTTTGG
* * ** *
25153872 ATTAGTATTTTGTATGAATGTAAT-TTTTTTTGCTTTTTATAATTATTTTAAAATTAATTT
1 ATTAGTATTTAGGAT-AATGTAATAAATTTTTG-TGTTTATAATTATTTTAAAATTAATTT
* * * *
25153932 GTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTTAAAATTAATTT
1 ATTAGT-ATTTAGGATAATGTAATAAATTTTTGTGTTTATAATTATTTTAAAATTAATTT
*
25153992 ATTAGTAATTTAGGATTAA-GTTATAAATT
1 ATTAGT-ATTTAGGA-TAATGTAATAAATT
25154021 GTNNNNNNNN
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
60 60 0.80
61 15 0.20
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.55
Consensus pattern (59 bp):
ATTAGTATTTAGGATAATGTAATAAATTTTTGTGTTTATAATTATTTTAAAATTAATTT
Found at i:25154477 original size:15 final size:15
Alignment explanation
Indices: 25154457--25154508 Score: 95
Period size: 15 Copynumber: 3.4 Consensus size: 15
25154447 ATATGAATAT
25154457 TTTTATATAATGTAA
1 TTTTATATAATGTAA
25154472 TTTTATATAATGTAA
1 TTTTATATAATGTAA
25154487 TTTTTATATAATGTAA
1 -TTTTATATAATGTAA
25154503 TTTTAT
1 TTTTAT
25154509 TTGATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 21 0.58
16 15 0.42
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:25154491 original size:16 final size:16
Alignment explanation
Indices: 25154455--25154506 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
25154445 GGATATGAAT
25154455 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
25154471 A-TTTTATATAATGTA
1 ATTTTTATATAATGTA
25154486 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
25154502 ATTTT
1 ATTTT
25154507 ATTTGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.43
16 20 0.57
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTTTTATATAATGTA
Found at i:25160011 original size:27 final size:27
Alignment explanation
Indices: 25159967--25160056 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
25159957 GCCCCACCAT
* ** *
25159967 TCGCGCCTCTGAGTTAGGCACAACTAG
1 TCGCGCCTCTCAAATAGGCTCAACTAG
* *
25159994 TCGTGCCTGC-CAGATAGGCTCAACTAG
1 TCGCGCCT-CTCAAATAGGCTCAACTAG
*
25160021 TCGCGCCTCTGAAATAGGCTCAACTAG
1 TCGCGCCTCTCAAATAGGCTCAACTAG
25160048 TCGCGCCTC
1 TCGCGCCTC
25160057 GTATCTATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.22
Consensus pattern (27 bp):
TCGCGCCTCTCAAATAGGCTCAACTAG
Found at i:25160171 original size:49 final size:49
Alignment explanation
Indices: 25160117--25160224 Score: 171
Period size: 49 Copynumber: 2.2 Consensus size: 49
25160107 TTATTAAACA
*
25160117 AAAAAAATTAATATAAAAAATTGATTCGCGCCTATCAGATAGGCGATATT
1 AAAAAAA-TAATATAAAAAATTGATTCGCGCCTATCAGATAGGCGAGATT
* * *
25160167 AAAAAAATAATATAAAAAATTGATTCGCGCTTGTCAGATAGGCGCGATT
1 AAAAAAATAATATAAAAAATTGATTCGCGCCTATCAGATAGGCGAGATT
25160216 AAAAAAATA
1 AAAAAAATA
25160225 TACCATTCGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 47 0.87
50 7 0.13
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (49 bp):
AAAAAAATAATATAAAAAATTGATTCGCGCCTATCAGATAGGCGAGATT
Found at i:25160508 original size:34 final size:34
Alignment explanation
Indices: 25160468--25160558 Score: 164
Period size: 34 Copynumber: 2.7 Consensus size: 34
25160458 TTTTAAAAAA
25160468 TAAACCCTAATTTAATTAATTTATTTAAAACCCC
1 TAAACCCTAATTTAATTAATTTATTTAAAACCCC
*
25160502 TAAACCCTAATTTAATTAATTTATTTAAAACCCT
1 TAAACCCTAATTTAATTAATTTATTTAAAACCCC
*
25160536 TAAAGCCTAATTTAATTAATTTA
1 TAAACCCTAATTTAATTAATTTA
25160559 AAAAAAATTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.42, C:0.16, G:0.01, T:0.41
Consensus pattern (34 bp):
TAAACCCTAATTTAATTAATTTATTTAAAACCCC
Found at i:25161582 original size:48 final size:48
Alignment explanation
Indices: 25161528--25161621 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
25161518 GCTTTGATTT
*
25161528 TTAAATGTTTTGATATAACAAAATAAAATTTTAAAATTCCCTTAATAA
1 TTAAATGTTTTGATATAACAAAATAAAATTCTAAAATTCCCTTAATAA
25161576 TTAAATGTTTTGATATAACAAAATAAAATTCTAAAATTCCCTTAAT
1 TTAAATGTTTTGATATAACAAAATAAAATTCTAAAATTCCCTTAAT
25161622 CAAATTTTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (48 bp):
TTAAATGTTTTGATATAACAAAATAAAATTCTAAAATTCCCTTAATAA
Found at i:25174629 original size:26 final size:26
Alignment explanation
Indices: 25174593--25174647 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
25174583 GAGTCCGAGT
25174593 CTGATACGAGGTCTACAGCGTCGTAC
1 CTGATACGAGGTCTACAGCGTCGTAC
25174619 CTGATACGAGGTCTACAGCGTCGTAC
1 CTGATACGAGGTCTACAGCGTCGTAC
25174645 CTG
1 CTG
25174648 CTGTCGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (26 bp):
CTGATACGAGGTCTACAGCGTCGTAC
Found at i:25177039 original size:26 final size:26
Alignment explanation
Indices: 25176976--25177041 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
25176966 AGTTCTTCAT
*
25176976 TGCTTTTGAAAAATACTTTCGAAAAG
1 TGCTTTTGAAAAGTACTTTCGAAAAG
* * *
25177002 TGC-TGTGAAAAAGTGCTTTTGAAAAG
1 TGCTTTTG-AAAAGTACTTTCGAAAAG
25177028 TGCTTTTGAAAAGT
1 TGCTTTTGAAAAGT
25177042 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 3 0.09
26 27 0.82
27 3 0.09
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTCGAAAAG
Found at i:25183107 original size:18 final size:18
Alignment explanation
Indices: 25183077--25183116 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
25183067 TTCCTTAATT
*
25183077 TTTTATTTATTATTTT-A
1 TTTTAGTTATTATTTTAA
25183094 TTTTAGTTATTTATTTTAA
1 TTTTAGTTA-TTATTTTAA
25183113 TTTT
1 TTTT
25183117 TTTTATCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTAGTTATTATTTTAA
Found at i:25188899 original size:66 final size:67
Alignment explanation
Indices: 25188773--25188903 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 67
25188763 AATTCGGTCT
* * * *
25188773 ATTATCGTTTTGTTGAATCCCCAAATTCAACTTGACCAAAAAATTTGATTTATTTTATATTATTT
1 ATTATCGTTTTGTTGAATCCCCAAATTAAACTTCACCAAAAAATTTAATTTATTTGATATTATTT
25188838 TG
66 TG
* * *
25188840 ATTATCTTTTTTTTGAATTCCCAAATTAAAC-TCACCAAAAACA-TTAATTTATTTGATATTATT
1 ATTATCGTTTTGTTGAATCCCCAAATTAAACTTCACCAAAAA-ATTTAATTTATTTGATATTATT
25188903 T
65 T
25188904 AAAATTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
66 28 0.50
67 28 0.50
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.47
Consensus pattern (67 bp):
ATTATCGTTTTGTTGAATCCCCAAATTAAACTTCACCAAAAAATTTAATTTATTTGATATTATTT
TG
Found at i:25188911 original size:67 final size:67
Alignment explanation
Indices: 25188773--25188911 Score: 165
Period size: 67 Copynumber: 2.1 Consensus size: 67
25188763 AATTCGGTCT
* * * *
25188773 ATTATCGTTTTGTTGAATCCCCAAATTCAACTTGACCAAAAAATTTGATTTATTTTATATTATTT
1 ATTATCGTTTTGTTGAATCCCCAAATTAAACTTCACCAAAAAATTTAATTTATTTGATATTATTT
**
25188838 TG
66 AA
* * *
25188840 ATTATCTTTTTTTTGAATTCCCAAATTAAAC-TCACCAAAAACA-TTAATTTATTTGATATTATT
1 ATTATCGTTTTGTTGAATCCCCAAATTAAACTTCACCAAAAA-ATTTAATTTATTTGATATTATT
25188903 TAAA
65 T-AA
25188907 ATTAT
1 ATTAT
25188912 TTAAAATATA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
66 28 0.46
67 33 0.54
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (67 bp):
ATTATCGTTTTGTTGAATCCCCAAATTAAACTTCACCAAAAAATTTAATTTATTTGATATTATTT
AA
Found at i:25198130 original size:2 final size:2
Alignment explanation
Indices: 25198123--25198147 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25198113 CTATGTACTT
25198123 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25198148 TTGTAGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25199089 original size:18 final size:18
Alignment explanation
Indices: 25199050--25199089 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25199040 CTTTTTATTT
*
25199050 TTTTTAGGATTAGAGGTT
1 TTTTTAGGATTAGAGGTA
25199068 TTTTTAGGATTTA-AGGTA
1 TTTTTAGGA-TTAGAGGTA
25199086 TTTT
1 TTTT
25199090 GAAAGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (18 bp):
TTTTTAGGATTAGAGGTA
Found at i:25202704 original size:26 final size:27
Alignment explanation
Indices: 25202675--25202740 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 27
25202665 ACATACCACA
* *
25202675 GCTCTTTGTGAGCGTCCCGTTACA-TG
1 GCTCTTTGTGAGCGTCCCATTAAATTG
** * *
25202701 GCTCTTCATGAGCTTTCCATTAAATTG
1 GCTCTTTGTGAGCGTCCCATTAAATTG
25202728 GCTCTTTGTGAGC
1 GCTCTTTGTGAGC
25202741 TTCCTGATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
GCTCTTTGTGAGCGTCCCATTAAATTG
Found at i:25210299 original size:14 final size:14
Alignment explanation
Indices: 25210276--25210306 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25210266 TGTCGGGTTC
*
25210276 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
25210290 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
25210304 TTA
1 TTA
25210307 AAATAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:25215004 original size:36 final size:36
Alignment explanation
Indices: 25214939--25215009 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
25214929 ATTAAACTTA
* * * * *
25214939 TAAGTGATTCGGCCTATTGATGTATTTGTAATATTG
1 TAAGTGATTCGACATAATGATATAGTTGTAATATTG
25214975 TAAGTGATTCGACATAATGATATAGTTGTAATATT
1 TAAGTGATTCGACATAATGATATAGTTGTAATATT
25215010 TAAAAGTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (36 bp):
TAAGTGATTCGACATAATGATATAGTTGTAATATTG
Found at i:25219223 original size:10 final size:10
Alignment explanation
Indices: 25219208--25219275 Score: 64
Period size: 12 Copynumber: 6.1 Consensus size: 10
25219198 CCATTTAGTC
*
25219208 TATTTTGTTT
1 TATTTTATTT
25219218 TATTTTATTT
1 TATTTTATTT
25219228 TATTTTTATTTT
1 TA-TTTTA-TTT
25219240 TATTTTTATTTT
1 TA-TTTTA-TTT
25219252 TATTTTTATGTT
1 TA-TTTTAT-TT
25219264 TATTGTTATTT
1 TATT-TTATTT
25219275 T
1 T
25219276 CTTCTATTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
10 11 0.21
11 11 0.21
12 31 0.58
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.79
Consensus pattern (10 bp):
TATTTTATTT
Found at i:25219236 original size:6 final size:6
Alignment explanation
Indices: 25219215--25219275 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
25219205 GTCTATTTTG
25219215 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
25219261 GTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTT
25219276 CTTCTATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 10 0.20
6 41 0.80
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:25220273 original size:9 final size:9
Alignment explanation
Indices: 25220247--25220286 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
25220237 AATTCATGTT
*
25220247 GAAAAAAAA
1 GAAAGAAAA
25220256 GAAAG-AAA
1 GAAAGAAAA
25220264 GAAAGAAAA
1 GAAAGAAAA
25220273 GAAAAGAAAA
1 G-AAAGAAAA
25220283 GAAA
1 GAAA
25220287 AGTATATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.29
9 11 0.39
10 9 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:25220275 original size:5 final size:5
Alignment explanation
Indices: 25220247--25220288 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
25220237 AATTCATGTT
25220247 GAAAA -AAAA G-AAA G-AAA G-AAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
25220289 TATATCTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 16 0.46
5 19 0.54
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:25222022 original size:14 final size:14
Alignment explanation
Indices: 25221999--25222029 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25221989 TGTCGGGTTC
*
25221999 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
25222013 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
25222027 TTA
1 TTA
25222030 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:25223374 original size:27 final size:26
Alignment explanation
Indices: 25223309--25223379 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
25223299 GACATACCAC
* *
25223309 AGCTCTTTGTGAGCGTCCCGTTACAT
1 AGCTCTTTGTGAGCTTCCCGTTAAAT
* *
25223335 GGCTCTTCGTGAGCTTCCCGTTAAATT
1 AGCTCTTTGTGAGCTTCCCGTTAAA-T
25223362 AGCTCTTTGTGAGCTTCC
1 AGCTCTTTGTGAGCTTCC
25223380 TGATTAATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.37
Consensus pattern (26 bp):
AGCTCTTTGTGAGCTTCCCGTTAAAT
Found at i:25225594 original size:14 final size:14
Alignment explanation
Indices: 25225575--25225609 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
25225565 TTCTGCTGCG
25225575 TTTCCAAACCTATT
1 TTTCCAAACCTATT
25225589 TTTCCAAACCTATT
1 TTTCCAAACCTATT
25225603 TTTCCAA
1 TTTCCAA
25225610 CAATCCCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCCAAACCTATT
Found at i:25232989 original size:5 final size:5
Alignment explanation
Indices: 25232979--25233011 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
25232969 CAATTCCCTC
*
25232979 CTTTT CTTTT CCTTT CTTTT CTTTT CTTTT CTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTT
25233012 GCTGTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:25233074 original size:14 final size:15
Alignment explanation
Indices: 25233055--25233083 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25233045 GTCTGTCGTC
25233055 TCTTT-CTCTCCTTT
1 TCTTTCCTCTCCTTT
25233069 TCTTTCCTCTCCTTT
1 TCTTTCCTCTCCTTT
25233084 GTAGCAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTTCCTCTCCTTT
Found at i:25233703 original size:22 final size:23
Alignment explanation
Indices: 25233678--25233721 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25233668 TTAGTTGATG
*
25233678 TATTGAAAGTG-AATAAATTATA
1 TATTGAAAGCGAAATAAATTATA
*
25233700 TATTGCAAGCGAAATAAATTAT
1 TATTGAAAGCGAAATAAATTAT
25233722 GTCGTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (23 bp):
TATTGAAAGCGAAATAAATTATA
Found at i:25238001 original size:17 final size:17
Alignment explanation
Indices: 25237976--25238020 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
25237966 AAATTTAAAA
25237976 ATATTTTTTATACTTTTT
1 ATATTTTTTAT-CTTTTT
*
25237994 AT-TTTTTTGATTTTTTT
1 ATATTTTTT-ATCTTTTT
25238011 ATATTTTTTA
1 ATATTTTTTA
25238021 AAAAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
ATATTTTTTATCTTTTT
Found at i:25238020 original size:9 final size:9
Alignment explanation
Indices: 25237976--25238020 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
25237966 AAATTTAAAA
25237976 ATATTTTTT
1 ATATTTTTT
*
25237985 ATACTTTTT
1 ATATTTTTT
25237994 AT-TTTTTT
1 ATATTTTTT
25238002 GAT-TTTTTT
1 -ATATTTTTT
25238011 ATATTTTTT
1 ATATTTTTT
25238020 A
1 A
25238021 AAAAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (9 bp):
ATATTTTTT
Found at i:25243517 original size:29 final size:27
Alignment explanation
Indices: 25243452--25243517 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
25243442 ATTTAATGCG
25243452 AATTTT-AAAAATTGGGGTCTAATAAA
1 AATTTTAAAAAATTGGGGTCTAATAAA
*
25243478 TATTTTCAAAAAATTGGGAG-CTTAATGAAA
1 AATTTT-AAAAAATTGGG-GTC-TAAT-AAA
25243508 AATTTTAAAA
1 AATTTTAAAA
25243518 GATTTTTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.15
28 11 0.33
29 9 0.27
30 8 0.24
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (27 bp):
AATTTTAAAAAATTGGGGTCTAATAAA
Found at i:25248097 original size:29 final size:30
Alignment explanation
Indices: 25248029--25248097 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
25248019 AAAATTTGGC
* * *
25248029 CTAATTTGATTCTTGTTAGTAGTATATGGA
1 CTAATTTGATTATTGTTAGTACTATAAGGA
**
25248059 CTAAACTGATTATT-TTAGTACTA-AAGAGA
1 CTAATTTGATTATTGTTAGTACTATAAG-GA
25248088 CTAATTTGAT
1 CTAATTTGAT
25248098 AGGATCCCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 2 0.06
29 18 0.58
30 11 0.35
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (30 bp):
CTAATTTGATTATTGTTAGTACTATAAGGA
Found at i:25250396 original size:14 final size:15
Alignment explanation
Indices: 25250372--25250400 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25250362 TTGCATACGT
25250372 AATTGAAAATTAAAA
1 AATTGAAAATTAAAA
25250387 AATT-AAAATTAAAA
1 AATTGAAAATTAAAA
25250401 TTGTTGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AATTGAAAATTAAAA
Found at i:25250590 original size:10 final size:10
Alignment explanation
Indices: 25250577--25250620 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
25250567 CCTATAAAAG
25250577 TTTTAAAATT
1 TTTTAAAATT
*
25250587 TTTTATTAAATA
1 TTTTA--AAATT
25250599 TTTTAAAATT
1 TTTTAAAATT
*
25250609 TTTAAAAATT
1 TTTTAAAATT
25250619 TT
1 TT
25250621 AGTGGGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 20 0.69
12 9 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:25255047 original size:25 final size:26
Alignment explanation
Indices: 25255014--25255070 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
25255004 AGCTAACCCA
25255014 TTTTT-GGT-ATATGATCTTTACACT
1 TTTTTGGGTAATATGATCTTTACACT
*
25255038 TTTTTGGGTAGATATGATGTTTACACT
1 TTTTTGGGTA-ATATGATCTTTACACT
25255065 TTTTTG
1 TTTTTG
25255071 AAAACTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
27 21 0.72
ACGTcount: A:0.19, C:0.09, G:0.18, T:0.54
Consensus pattern (26 bp):
TTTTTGGGTAATATGATCTTTACACT
Found at i:25279419 original size:15 final size:15
Alignment explanation
Indices: 25279399--25279431 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
25279389 TATTATCAAA
25279399 TATGTTTACTGAATT
1 TATGTTTACTGAATT
25279414 TATGTTTACTGAATT
1 TATGTTTACTGAATT
25279429 TAT
1 TAT
25279432 AATAATTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (15 bp):
TATGTTTACTGAATT
Found at i:25282190 original size:15 final size:16
Alignment explanation
Indices: 25282167--25282212 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
25282157 TTCCTTTATT
* *
25282167 TTATCTTTT-TATCCC
1 TTATATTTTATATACC
25282182 TTATATTTTTATATACC
1 TTATA-TTTTATATACC
25282199 TTATATTTTATATA
1 TTATATTTTATATA
25282213 TACGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTTATATACC
Found at i:25282202 original size:17 final size:18
Alignment explanation
Indices: 25282180--25282215 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
25282170 TCTTTTTATC
25282180 CCTTATATTTT-TATATA
1 CCTTATATTTTATATATA
25282197 CCTTATATTTTATATATA
1 CCTTATATTTTATATATA
25282215 C
1 C
25282216 GTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTTATATTTTATATATA
Found at i:25291447 original size:220 final size:220
Alignment explanation
Indices: 25291065--25292202 Score: 2186
Period size: 220 Copynumber: 5.2 Consensus size: 220
25291055 NNNNNNNNNN
* * *
25291065 CGAAGACACCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTACAGATCTTATCTC
1 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
* * * * * * *
25291130 CCTAAGCAGTAGTGGAGTAGATCGAAGATGGCCGATTTTACCTCCTTGAGGTTACAGTGGAGTAC
66 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
25291195 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
131 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
25291260 TTCCTGCATCGACAGTGAAGCAGAT
196 TTCCTGCATCGACAGTGAAGCAGAT
25291285 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
1 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
25291350 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
66 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
25291415 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
131 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
25291480 TTCCTGCATCGACAGTGAAGCAGAT
196 TTCCTGCATCGACAGTGAAGCAGAT
25291505 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
1 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
25291570 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
66 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
25291635 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
131 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
25291700 TTCCTGCATCGACAGTGAAGCAGAT
196 TTCCTGCATCGACAGTGAAGCAGAT
25291725 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
1 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
25291790 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
66 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
25291855 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
131 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
25291920 TTCCTGCATCGACAGTGAAGCAGAT
196 TTCCTGCATCGACAGTGAAGCAGAT
25291945 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
1 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
25292010 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
66 CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
25292075 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
131 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
25292140 TTCCTGCATCGACAGTGAAGCAGAT
196 TTCCTGCATCGACAGTGAAGCAGAT
25292165 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAG
1 CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAG
25292203 ATCAATCCTA
Statistics
Matches: 908, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
220 908 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (220 bp):
CGAAGACATCAACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAAGATTTCAGATCTTGTCTC
CCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTTTACCTCCTCGTGGTTACAGTGGAGTAC
ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTGTC
TTCCTGCATCGACAGTGAAGCAGAT
Found at i:25293907 original size:15 final size:16
Alignment explanation
Indices: 25293884--25293929 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
25293874 TTCCTTTATT
* *
25293884 TTATCTTTT-TATCCC
1 TTATATTTTATATACC
25293899 TTATATTTTTATATACC
1 TTATA-TTTTATATACC
25293916 TTATATTTTATATA
1 TTATATTTTATATA
25293930 TACGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTTATATACC
Found at i:25293919 original size:17 final size:18
Alignment explanation
Indices: 25293897--25293932 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
25293887 TCTTTTTATC
25293897 CCTTATATTTT-TATATA
1 CCTTATATTTTATATATA
25293914 CCTTATATTTTATATATA
1 CCTTATATTTTATATATA
25293932 C
1 C
25293933 GTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTTATATTTTATATATA
Found at i:25296998 original size:85 final size:84
Alignment explanation
Indices: 25296905--25297077 Score: 265
Period size: 85 Copynumber: 2.0 Consensus size: 84
25296895 ATCCTTGTCT
* * *
25296905 TCAACTCTTTTACTTCAAACTCTCACTTTACGACTCTCAACCCATCGAATGAATTGTCTTACAAG
1 TCAACTCTTTTACTTCAAACCCTCACTTTACGACTCTCAACCCACCGAATGAACTGTCTTACAAG
*
25296970 TCCCCATTCTCCTCAATCCA
66 T-CCCATCCTCCTCAATCCA
* *
25296990 TCAACTCTTTTACTTCAAACCCTCACTTTACGACTCTCAACCCACCGGATGAACTGTTTTACAAG
1 TCAACTCTTTTACTTCAAACCCTCACTTTACGACTCTCAACCCACCGAATGAACTGTCTTACAAG
* *
25297055 TCCCATCCTCCTCAGTCTA
66 TCCCATCCTCCTCAATCCA
25297074 TCAA
1 TCAA
25297078 TAGATATGTC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 19 0.24
85 61 0.76
ACGTcount: A:0.27, C:0.35, G:0.07, T:0.32
Consensus pattern (84 bp):
TCAACTCTTTTACTTCAAACCCTCACTTTACGACTCTCAACCCACCGAATGAACTGTCTTACAAG
TCCCATCCTCCTCAATCCA
Found at i:25303404 original size:39 final size:38
Alignment explanation
Indices: 25303361--25303519 Score: 215
Period size: 39 Copynumber: 4.3 Consensus size: 38
25303351 TGGTCCAATG
25303361 GCATTTAATGACTATTTGTATTTGGGTATAACTTTTAAA
1 GCATTTAAT-ACTATTTGTATTTGGGTATAACTTTTAAA
25303400 GCATTTAATGACTATTTGTATTTGGGTATAACTTTTAAA
1 GCATTTAAT-ACTATTTGTATTTGGGTATAACTTTTAAA
* *
25303439 GCATTTAATA-TTTTAATATATTTGGGTATAAC------A
1 GCATTTAATACTATT--TGTATTTGGGTATAACTTTTAAA
25303472 GCATTTAATACTATTTGTATTTGGGTATAACTTTTAAA
1 GCATTTAATACTATTTGTATTTGGGTATAACTTTTAAA
25303510 GCATTTAATA
1 GCATTTAATA
25303520 TTTGTATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
32 15 0.14
33 11 0.10
34 3 0.03
37 3 0.03
38 12 0.11
39 63 0.59
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.46
Consensus pattern (38 bp):
GCATTTAATACTATTTGTATTTGGGTATAACTTTTAAA
Found at i:25307506 original size:45 final size:45
Alignment explanation
Indices: 25307385--25307707 Score: 281
Period size: 45 Copynumber: 7.2 Consensus size: 45
25307375 GTAGCAGTAA
* *
25307385 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGGAA-AAAGTAG
1 ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATC-GAAGAAAGCAG
* * * * * *
25307430 ATATTATCTT--CAT-GTACTGGCGTGAAGTAGATCAAAGATAA-CAT
1 ATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGA-AAGCAG
25307474 ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAG
* * * * * *
25307519 ATCTTGT-TT-TCAT-GTACTGGCGTGAAGTAGATCAAAGATAGCAA
1 ATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGAAAGCAG
* * * *
25307563 ATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAGGAG
1 ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAG
* * *
25307608 ATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATCGAGGAAAGCAG
1 ATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGAAAGCAG
* * *
25307652 ATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAG
1 ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAG
25307697 ATCTTGTCTTC
1 ATCTTGTCTTC
25307708 ATGTATTGGC
Statistics
Matches: 218, Mismatches: 42, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
42 15 0.07
43 11 0.05
44 77 0.35
45 91 0.42
46 9 0.04
47 15 0.07
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (45 bp):
ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAG
Found at i:25307742 original size:89 final size:89
Alignment explanation
Indices: 25307385--25307745 Score: 519
Period size: 89 Copynumber: 4.1 Consensus size: 89
25307375 GTAGCAGTAA
* *
25307385 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGGAA-AAAGTAGATATTATCTTCATGTACTG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-GAAGAAAGTAGATCTTGTCTTCATGTACTG
* *
25307449 GCGTGAAGTAGATCAAAGATAACAT
65 GCGTGAAGTAGATCAAAGATAGCAG
* * *
25307474 ATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTTTTCATGTACTGG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGG
*
25307539 CGTGAAGTAGATCAAAGATAGCAA
66 CGTGAAGTAGATCAAAGATAGCAG
* * * *
25307563 ATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAGGAGATCTTGTCTTCATGTATTGG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGG
* * *
25307628 CGTGAAGTAGATCGAGGAAAGCAG
66 CGTGAAGTAGATCAAAGATAGCAG
* *
25307652 ATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGG
* *
25307717 CGTGAAGTATATCGAAGAGTA-CAG
66 CGTGAAGTAGATCAAAGA-TAGCAG
25307741 ATCTT
1 ATCTT
25307746 ATCTCCCTAA
Statistics
Matches: 245, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
88 3 0.01
89 241 0.98
90 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (89 bp):
ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGG
CGTGAAGTAGATCAAAGATAGCAG
Found at i:25307743 original size:44 final size:44
Alignment explanation
Indices: 25307409--25307745 Score: 304
Period size: 44 Copynumber: 7.6 Consensus size: 44
25307399 TACTGGTGGC
* * * *
25307409 GAAGTAGATCGGAA-AAAGTAGATATTATCTTCATGTACTGGCGT
1 GAAGTAGATC-GAAGATAGCAGATCTTGTCTTCATGTACTGGCGT
* * * * *
25307453 GAAGTAGATCAAAGATAACATATCTTGTCTTCCCATACTAGTGGC--
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTT--CAT-GTACTGGCGT
* *
25307498 GAAGTAGATCGAAGAAAGCAGATCTTGTTTTCATGTACTGGCGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGT
* * ** *
25307542 GAAGTAGATCAAAGATAGCAAATCTTGTCTTCACATACTGGTGGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGG-CGT
* * *
25307587 GAAGTAGATCGAAGAAAGGAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGT
* * * *** * *
25307631 GAAGTAGATCGAGGAAAGCAGATATTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGG-CGT
* * *
25307676 GAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGT
*
25307720 GAAGTATATCGAAGAGTA-CAGATCTT
1 GAAGTAGATCGAAGA-TAGCAGATCTT
25307746 ATCTCCCTAA
Statistics
Matches: 232, Mismatches: 52, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
42 6 0.03
43 5 0.02
44 114 0.49
45 98 0.42
46 3 0.01
47 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (44 bp):
GAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTACTGGCGT
Found at i:25308092 original size:100 final size:100
Alignment explanation
Indices: 25307972--25308732 Score: 1122
Period size: 100 Copynumber: 7.6 Consensus size: 100
25307962 TTCTATCTTA
* *
25307972 TTAGCAGTACAATGGAACAGATTGAAGCTATGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
25308037 AAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCC
66 AAAAGATTGAAGCCACAACGGCGGATCTTATC-TCC
*
25308072 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATAA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
* *
25308137 AAAAGCTTGAAGCCACAACGACGGATCTTATCTCC
66 AAAAGATTGAAGCCACAACGGCGGATCTTATCTCC
25308172 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
25308237 AAAA-ACTTGAAGCCACAACGGCGGATCTTATCTCC
66 AAAAGA-TTGAAGCCACAACGGCGGATCTTATCTCC
* * *
25308272 TTAGTAGTACAGTGGAACAGATTGAAGCTACGACGGCGGGTCTGGTTTCCCTGATATGGCAATAA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
25308337 AAAA-ACTTGAAGCCACAACGGCGGATCTTATCTCC
66 AAAAGA-TTGAAGCCACAACGGCGGATCTTATCTCC
* * * *
25308372 TTAGTAGTACAGTGGAACAGACTGAAGCTACGACGGCGGGTCTGGTTTCCCTGATATGGCAATAA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
25308437 AAAA-ACTTGAAGCCACAACGGCGGATCTTATCTCC
66 AAAAGA-TTGAAGCCACAACGGCGGATCTTATCTCC
* * * * *
25308472 TTAGTAGTACAGTGGAACAGACTGAAGCTACGACGGCGGGTCTGGTTTCCCTGATATTGTAATTA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
* *
25308537 AAAAGATTGAAGCCACAACGACGGATCTTA-CTTTC
66 AAAAGATTGAAGCCACAACGGCGGATCTTATC-TCC
* * * * * * * *
25308572 TTAGCAGTGCAATGGAATAGATTAAAGCTACGACGGCGGATCTAGTTTTCCTGACATTGCAATTA
1 TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
*
25308637 AAAAGATTGAAGCCACAACGGTGGATCTTA-CTTCC
66 AAAAGATTGAAGCCACAACGGCGGATCTTATC-TCC
* * * *
25308672 CT-GACGGTACGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCA
1 TTAG-CAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCA
25308733 GTAGAGCAAA
Statistics
Matches: 616, Mismatches: 40, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
99 2 0.00
100 612 0.99
101 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (100 bp):
TTAGCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATAA
AAAAGATTGAAGCCACAACGGCGGATCTTATCTCC
Found at i:25308722 original size:50 final size:50
Alignment explanation
Indices: 25307976--25308727 Score: 316
Period size: 50 Copynumber: 15.0 Consensus size: 50
25307966 ATCTTATTAG
* * *
25307976 CAGTACAATGGAACAGATTGAAGCTATGACGGCGGATCTGGTTTCCCTGA
1 CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * * ** * * * *
25308026 TATTGCAATAAAAAAGATTGAAGCCACAACGGCGGATCTTA-CTT-CCTTA
1 CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATC-TAGTTTCCCTGA
* * * *
25308075 GCAGTACAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGA
1 -CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * * ** * * * * * *
25308126 TATTGCAATAAAAAAGCTTGAAGCCACAACGACGGATCT--TATCTCCTTA
1 CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTC-CCTGA
* * *
25308175 GCAGTACAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 -CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * * * * * * * *
25308226 TATTGCAAT-AAAAAAACTTGAAGCCACAACGGCGGATCT--TATCTCCTTA
1 CAGTACAATGGAAAAGA-TTGAAGCTACGACGGCGGATCTAGTTTC-CCTGA
* * * * *
25308275 GTAGTACAGTGGAACAGATTGAAGCTACGACGGCGGGTCTGGTTTCCCTGA
1 -CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * * * * * * *
25308326 TA-TGGCAAT-AAAAAAACTTGAAGCCACAACGGCGGATCT--TATCTCCTTA
1 CAGT-ACAATGGAAAAGA-TTGAAGCTACGACGGCGGATCTAGTTTC-CCTGA
* * * * * *
25308375 GTAGTACAGTGGAACAGACTGAAGCTACGACGGCGGGTCTGGTTTCCCTGA
1 -CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * * * * * * *
25308426 TA-TGGCAAT-AAAAAAACTTGAAGCCACAACGGCGGATCT--TATCTCCTTA
1 CAGT-ACAATGGAAAAGA-TTGAAGCTACGACGGCGGATCTAGTTTC-CCTGA
* * * * * *
25308475 GTAGTACAGTGGAACAGACTGAAGCTACGACGGCGGGTCTGGTTTCCCTGA
1 -CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * ** ** * * * * *
25308526 TATTGTAATTAAAAAGATTGAAGCCACAACGACGGATCTTACTTT--CTTA
1 CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATC-TAGTTTCCCTGA
* * * *
25308575 GCAGTGCAATGGAATAGATTAAAGCTACGACGGCGGATCTAGTTTTCCTGA
1 -CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
* * ** * * * *
25308626 CATTGCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTA-CTTCCCTGA
1 CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATC-TAGTTTCCCTGA
* ** * *
25308676 CGGTACGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
1 CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
25308726 CA
1 CA
25308728 TTGCAGTAGA
Statistics
Matches: 498, Mismatches: 168, Indels: 72
0.67 0.23 0.10
Matches are distributed among these distances:
48 12 0.02
49 44 0.09
50 386 0.78
51 44 0.09
52 12 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
CAGTACAATGGAAAAGATTGAAGCTACGACGGCGGATCTAGTTTCCCTGA
Found at i:25310069 original size:3 final size:3
Alignment explanation
Indices: 25310061--25310146 Score: 104
Period size: 3 Copynumber: 28.7 Consensus size: 3
25310051 ATTTTTCATG
* * * *
25310061 TTA TTA TTA TAA TTA -TA TTA TAA TTA TT- TTT TTGA GTTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA
25310106 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25310147 CCTATTGCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
2 4 0.06
3 65 0.90
4 1 0.01
5 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:25315856 original size:31 final size:31
Alignment explanation
Indices: 25315821--25315879 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
25315811 AAAAACCATA
*
25315821 AAAATGTGAAGTAAGATGATATAGTTAGTAT
1 AAAATGTGAAATAAGATGATATAGTTAGTAT
* *
25315852 AAAATGTGAAATAAGTTGATATGGTTAG
1 AAAATGTGAAATAAGATGATATAGTTAG
25315880 GAAATTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (31 bp):
AAAATGTGAAATAAGATGATATAGTTAGTAT
Found at i:25323862 original size:29 final size:29
Alignment explanation
Indices: 25323824--25323909 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
25323814 AACATTTGTT
* *
25323824 AATATGCATTAATTAAAACAAATATATAA
1 AATATACATTAATTATAACAAATATATAA
* *
25323853 AATATACATTAATTATACCAAATGTATAA
1 AATATACATTAATTATAACAAATATATAA
*
25323882 AATATACATTAGTTATAACAAATATATA
1 AATATACATTAATTATAACAAATATATA
25323910 TTATTATTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (29 bp):
AATATACATTAATTATAACAAATATATAA
Found at i:25324128 original size:31 final size:31
Alignment explanation
Indices: 25324064--25324200 Score: 213
Period size: 31 Copynumber: 4.5 Consensus size: 31
25324054 AGATAAGCTC
25324064 GAACCGGGATATCCTAAACTGGAATA-CATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
* * *
25324094 GAACCGGGACATCCTAAACTGGAAAATCATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
* *
25324125 GAACAGGGATATCCTAAACTGGAACACCATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
*
25324156 GAACCGGGATACCCTAAACTGGAATACCATT
1 GAACCGGGATATCCTAAACTGGAATACCATT
25324187 GAACCGGGATATCC
1 GAACCGGGATATCC
25324201 GCATAACGGG
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 24 0.25
31 72 0.75
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
GAACCGGGATATCCTAAACTGGAATACCATT
Found at i:25325453 original size:66 final size:66
Alignment explanation
Indices: 25325381--25325581 Score: 343
Period size: 66 Copynumber: 3.1 Consensus size: 66
25325371 AAAAAAAAAG
* *
25325381 AAAAAGAATATACAATTTATTGTTTACTACTATTATTTCCATTATTTAGTTATTAATATCTACAA
1 AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
25325446 A
66 A
*
25325447 AAAAAGAATATTCATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
1 AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
25325512 A
66 A
* *
25325513 AAAAAG--TATACATTTTATTGTTTACTAATATTATTTCCATTTTTTAGCTATTAATATCTACAA
1 AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
25325576 A
66 A
25325577 AAAAA
1 AAAAA
25325582 AAGAAAAAAG
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
64 60 0.47
66 69 0.53
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (66 bp):
AAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACAA
A
Found at i:25343891 original size:24 final size:24
Alignment explanation
Indices: 25343864--25343915 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
25343854 CCTAGCTACC
**
25343864 CACACCCACACACTTGCACTCACT
1 CACACCCACACACACGCACTCACT
**
25343888 CACATGCACACACACGCACTCACT
1 CACACCCACACACACGCACTCACT
25343912 CACA
1 CACA
25343916 TATACACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.13
Consensus pattern (24 bp):
CACACCCACACACACGCACTCACT
Found at i:25343916 original size:24 final size:24
Alignment explanation
Indices: 25343870--25343987 Score: 87
Period size: 24 Copynumber: 4.8 Consensus size: 24
25343860 TACCCACACC
** *
25343870 CACACACTTGCACTCACTCACATG
1 CACACACACGCACACACTCACATG
*
25343894 CACACACACGCACTCACTCACAT-
1 CACACACACGCACACACTCACATG
* * * **
25343917 -ATACACATGCATACACACACACACA
1 CACACACACGC--ACACACTCACATG
*
25343942 CACACACACACACACACTCACATG
1 CACACACACGCACACACTCACATG
*
25343966 CACACATGCATGCACACACTCA
1 CACACA--CACGCACACACTCA
25343988 TTTTTAAAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
22 8 0.11
24 46 0.63
26 19 0.26
ACGTcount: A:0.38, C:0.42, G:0.06, T:0.14
Consensus pattern (24 bp):
CACACACACGCACACACTCACATG
Found at i:25343983 original size:2 final size:2
Alignment explanation
Indices: 25343929--25343963 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
25343919 ACACATGCAT
*
25343929 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC TC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
25343964 TGCACACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:25345003 original size:54 final size:54
Alignment explanation
Indices: 25344933--25345035 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
25344923 AATATACCTA
* * *
25344933 TTTCATCGCAAGCAGAGGCTATGAATGTTGATAATCAGGTAATATGAACAATCT
1 TTTCATCGCAAGCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
* * * *
25344987 TTTCATCTCAATCAGAGTATATGGATGTTGAGAATCAGGTAACATGAAC
1 TTTCATCGCAAGCAGAGGATATGAATGTTGAGAATCAGGTAACATGAAC
25345036 TTTCTTCCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (54 bp):
TTTCATCGCAAGCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
Found at i:25347946 original size:27 final size:27
Alignment explanation
Indices: 25347906--25347963 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
25347896 GACTTTGGAA
25347906 TTTATAATATAAAAATATATAAATTTATT
1 TTTATAATATAAAAATATAT-AATTT-TT
* *
25347935 TTTATAA-A-AAAATTGTATAATTTTT
1 TTTATAATATAAAAATATATAATTTTT
25347960 TTTA
1 TTTA
25347964 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 5 0.19
27 8 0.30
28 1 0.04
29 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTATAATATAAAAATATATAATTTTT
Found at i:25348176 original size:23 final size:24
Alignment explanation
Indices: 25348145--25348189 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25348135 TCTACTTTAA
*
25348145 AATTGTTAA-AAAAATATTAAAGC
1 AATTATTAAGAAAAATATTAAAGC
*
25348168 AATTATTAAGAAAAGTATTAAA
1 AATTATTAAGAAAAATATTAAA
25348190 AATACCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (24 bp):
AATTATTAAGAAAAATATTAAAGC
Found at i:25348430 original size:3 final size:3
Alignment explanation
Indices: 25348422--25348474 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
25348412 CTGAGTAGAG
25348422 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25348470 ATA AT
1 ATA AT
25348475 GTGCGGTGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:25351049 original size:18 final size:18
Alignment explanation
Indices: 25351026--25351061 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
25351016 AAAAAGAAAT
25351026 TCAAAATAATTTT-TAAAA
1 TCAAAAT-ATTTTATAAAA
25351044 TCAAAATATTTTATAAAA
1 TCAAAATATTTTATAAAA
25351062 ATTTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (18 bp):
TCAAAATATTTTATAAAA
Found at i:25355009 original size:4 final size:4
Alignment explanation
Indices: 25355000--25355031 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
25354990 TTGCTAGCTC
25355000 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
25355032 ATATTCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:25359409 original size:20 final size:19
Alignment explanation
Indices: 25359371--25359409 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25359361 ATATTAATTT
* *
25359371 TTTTAAAAAAATTATATAA
1 TTTTAAAAAAAATAAATAA
25359390 TTTTAAAAAAAATACAATAA
1 TTTTAAAAAAAATA-AATAA
25359410 ACTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTTAAAAAAAATAAATAA
Found at i:25361528 original size:47 final size:47
Alignment explanation
Indices: 25361433--25361562 Score: 127
Period size: 47 Copynumber: 2.8 Consensus size: 47
25361423 AGTCAGTAAT
* * * *
25361433 TCATCTACTTGACTAGTGGTTTATCCACAACGTATTCTAATCAGTAG
1 TCATCTGCTTGACCAATAGTTTATCCACAACGTATTCTAATCAGTAG
* * *
25361480 TCATCTGTTTGACCAATAGTTTATCCACAACGTATTCTACT-TGATAG
1 TCATCTGCTTGACCAATAGTTTATCCACAACGTATTCTAATCAG-TAG
* * * * * *
25361527 TCATTTGCTTGACTAGTGGTTTACCCACAACATATT
1 TCATCTGCTTGACCAATAGTTTATCCACAACGTATT
25361563 AGTGACTTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
46 1 0.01
47 67 0.99
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (47 bp):
TCATCTGCTTGACCAATAGTTTATCCACAACGTATTCTAATCAGTAG
Found at i:25361648 original size:91 final size:91
Alignment explanation
Indices: 25361532--25361700 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 91
25361522 GATAGTCATT
* * * * *
25361532 TGCTTGACTAGTGGTTTACCCACAACATATTAG-TGACTTTTATCTGCACAAATGGATGATTCAT
1 TGCTCGACCAGTGGTTTACCCACAACATATTAGCAG-CTTTTATATGCACAAA-GGATGATTCAC
25361596 CCACCAATAT-TTTAGTCGGTAGACATA
64 CCACCAATATATTTAGTCGGTAGACATA
* * *
25361623 TGCTCGACCAGTGGTTTATCCACAACATATTAGCAGCTTTTATATGCACAGAGGATGGTTCACCC
1 TGCTCGACCAGTGGTTTACCCACAACATATTAGCAGCTTTTATATGCACAAAGGATGATTCACCC
*
25361688 ATCAATATATTTA
66 ACCAATATATTTA
25361701 TCATTAGCAG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 18 0.27
91 48 0.72
92 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (91 bp):
TGCTCGACCAGTGGTTTACCCACAACATATTAGCAGCTTTTATATGCACAAAGGATGATTCACCC
ACCAATATATTTAGTCGGTAGACATA
Found at i:25370622 original size:88 final size:88
Alignment explanation
Indices: 25370472--25370649 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
25370462 TGTTGGACCG
25370472 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
1 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
25370537 TTTTAAAACTGGTGTTTAATTAT
66 TTTTAAAACTGGTGTTTAATTAT
*
25370560 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATGTTTAATC
1 TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
25370625 TTTTAAAACTGGTGTTTAATTAT
66 TTTTAAAACTGGTGTTTAATTAT
25370648 TG
1 TG
25370650 TTATCTTTTT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (88 bp):
TGACAGAATTAGATCATTATGTGAAGAAAAGGATACTGCTCTTCAGGCTAGTCTTATATTTAATC
TTTTAAAACTGGTGTTTAATTAT
Found at i:25375225 original size:17 final size:17
Alignment explanation
Indices: 25375203--25375236 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
25375193 TTAATGGTAA
25375203 ATTATACCAACAGTCAC
1 ATTATACCAACAGTCAC
25375220 ATTATACCAACAGTCAC
1 ATTATACCAACAGTCAC
25375237 TCAACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
ATTATACCAACAGTCAC
Found at i:25377023 original size:22 final size:22
Alignment explanation
Indices: 25376982--25377025 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
25376972 CATCAAAATA
*
25376982 ATAAAATAAGATTCACAAGTTT
1 ATAAAATAAGATTCAAAAGTTT
25377004 ATAAAATAAGATT-ATAAAGTTT
1 ATAAAATAAGATTCA-AAAGTTT
25377026 CCTCAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
ATAAAATAAGATTCAAAAGTTT
Found at i:25377452 original size:2 final size:2
Alignment explanation
Indices: 25377447--25377487 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
25377437 TTAACTGGTT
* *
25377447 TA TA TA TA TA TA TA TA TT TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25377488 TCCTTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:25377554 original size:136 final size:137
Alignment explanation
Indices: 25377367--25377640 Score: 541
Period size: 136 Copynumber: 2.0 Consensus size: 137
25377357 GCCTTTCAGT
25377367 TTAATTTGTTTTCTTGAATCTGTTATATATCTTCATCTTTATAAAAGGGTGTTCGGGTTTTCCTT
1 TTAATTTGTTTTCTTGAATCTGTTATATATCTTCATCTTTATAAAAGGGTGTTCGGGTTTTCCTT
25377432 TTTTGTTAACTGGTTTATATATATATATATATTTATTTATATATATATATATATATTCC-TTTTC
66 TTTTGTTAACTGGTTTATATATATATATATATTTATTTATATATATATATATATATTCCTTTTTC
25377496 TTTCTAA
131 TTTCTAA
25377503 TTAATTTGTTTTCTTGAATCTGTTATATATCTTCATCTTTATAAAAGGGTGTTCGGGTTTTCCTT
1 TTAATTTGTTTTCTTGAATCTGTTATATATCTTCATCTTTATAAAAGGGTGTTCGGGTTTTCCTT
25377568 TTTTGTTAACTGGTTTATATATATATATATATTTATTTATATATATATATATATATTCCTTTTTC
66 TTTTGTTAACTGGTTTATATATATATATATATTTATTTATATATATATATATATATTCCTTTTTC
25377633 TTTCTAA
131 TTTCTAA
25377640 T
1 T
25377641 CAATGCCTTG
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
136 124 0.91
137 13 0.09
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.55
Consensus pattern (137 bp):
TTAATTTGTTTTCTTGAATCTGTTATATATCTTCATCTTTATAAAAGGGTGTTCGGGTTTTCCTT
TTTTGTTAACTGGTTTATATATATATATATATTTATTTATATATATATATATATATTCCTTTTTC
TTTCTAA
Found at i:25377588 original size:2 final size:2
Alignment explanation
Indices: 25377583--25377623 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
25377573 TTAACTGGTT
* *
25377583 TA TA TA TA TA TA TA TA TT TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25377624 TCCTTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:25384507 original size:4 final size:4
Alignment explanation
Indices: 25384498--25384522 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25384488 GGAAAAGGTA
25384498 TAGC TAGC TAGC TAGC TAGC TAGC T
1 TAGC TAGC TAGC TAGC TAGC TAGC T
25384523 CTAAAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (4 bp):
TAGC
Found at i:25394490 original size:153 final size:153
Alignment explanation
Indices: 25394212--25394522 Score: 606
Period size: 153 Copynumber: 2.0 Consensus size: 153
25394202 AAACTAGACT
25394212 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
1 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
25394277 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTGTGCAAAATGGTTGATAACCAAGTTTAT
66 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTGTGCAAAATGGTTGATAACCAAGTTTAT
25394342 TACACTCTCCTTTCTTTTCTCTA
131 TACACTCTCCTTTCTTTTCTCTA
25394365 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
1 CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
25394430 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTAGTGCAAAAT-GTTGATAACCAAGTTTA
66 TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTT-GTGCAAAATGGTTGATAACCAAGTTTA
25394494 TTACACTCTCCTTTCTTTTCTCTA
130 TTACACTCTCCTTTCTTTTCTCTA
25394518 CAATA
1 CAATA
25394523 TTTCTCATCA
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 148 0.94
154 9 0.06
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (153 bp):
CAATAGGCTTTAATTTCATACTTTAATTAACCTCTAATTCAATTTATACAATTTTTGGTGAATTT
TCAAAGTTAGACTACTACTGCTGTCTAAAACTGTTTTGTGCAAAATGGTTGATAACCAAGTTTAT
TACACTCTCCTTTCTTTTCTCTA
Found at i:25399979 original size:557 final size:558
Alignment explanation
Indices: 25398919--25400037 Score: 2231
Period size: 557 Copynumber: 2.0 Consensus size: 558
25398909 TATTCACAAC
25398919 TGCAGGCCTTCCAGAAACGTTTGCTTTCAGTGGAAGACCATTGCACACGATCATAGACGTCAGAA
1 TGCAGGCCTTCCAGAAACGTTTGCTTTCAGTGGAAGACCATTGCACACGATCATAGACGTCAGAA
25398984 GCCATAGGATGATATTCATGGTAAATTGCTGCCGCTGCTGCTTCATTAGAGTTGCTCCGACTCTG
66 GCCATAGGATGATATTCATGGTAAATTGCTGCCGCTGCTGCTTCATTAGAGTTGCTCCGACTCTG
25399049 ATAAAAATAGATCAGCAGAAAATGATACGTTGACTAAAGCTAAACCACGACAAGGCAATCAAACA
131 ATAAAAATAGATCAGCAGAAAATGATACGTTGACTAAAGCTAAACCACGACAAGGCAATCAAACA
25399114 ATAGAATTAATAATAGCAGATCTGAAATAAGAAATCAGGATGAGGAAAACATAAGATCTTGTGCT
196 ATAGAATTAATAATAGCAGATCTGAAATAAGAAATCAGGATGAGGAAAACATAAGATCTTGTGCT
25399179 CCGCTAATTTGCAAAACCCAAGAAAGGACCCAAGAAGGGTAATAAATAAATAAAACTAAAACTGA
261 CCGCTAATTTGCAAAACCCAAGAAAGGACCCAAGAAGGGTAATAAATAAATAAAACTAAAACTGA
25399244 CAAAGCAAGTGCCAGGCAAGCTATCAAATCACATAGTTGTAGCAGTAGTTAACATGAAAAAAAGA
326 CAAAGCAAGTGCCAGGCAAGCTATCAAATCACATAGTTGTAGCAGTAGTTAACATGAAAAAAAGA
25399309 GGTTTAATTCAATTGACAAGATTGTAGAAGAAGCTTGGTACAAATATGAAAAGCGAAAACGACTT
391 GGTTTAATTCAATTGACAAGATTGTAGAAGAAGCTTGGTACAAATATGAAAAGCGAAAACGACTT
25399374 TTGGACCATAACTCACAGTAGCAGAGTAGGTGTAGCGTAGCAGCCATGAATTTCAAGTAAGAAAC
456 TTGGACCATAACTCACAGTAGCAGAGTAGGTGTAGCGTAGCAGCCATGAATTTCAAGTAAGAAAC
25399439 CCTGTCTGTTGTGATGATTTTAATGAAGGTGAGACTAG
521 CCTGTCTGTTGTGATGATTTTAATGAAGGTGAGACTAG
25399477 TGCA-GCCTTCCAGAAACGTTTGCTTTCAGTGGAAGACCATTGCACACGATCATAGACGTCAGAA
1 TGCAGGCCTTCCAGAAACGTTTGCTTTCAGTGGAAGACCATTGCACACGATCATAGACGTCAGAA
25399541 GCCATAGGATGATATTCATGGTAAATTGCTGCCGCTGCTGCTTCATTAGAGTTGCTCCGACTCTG
66 GCCATAGGATGATATTCATGGTAAATTGCTGCCGCTGCTGCTTCATTAGAGTTGCTCCGACTCTG
25399606 ATAAAAATAGATCAGCAGAAAATGATACGTTGACTAAAGCTAAACCACGACAAGGCAATCAAACA
131 ATAAAAATAGATCAGCAGAAAATGATACGTTGACTAAAGCTAAACCACGACAAGGCAATCAAACA
25399671 ATAGAATTAATAATAGCAGATCTGAAATAAGAAATCAGGATGAGGAAAACATAAGATCTTGTGCT
196 ATAGAATTAATAATAGCAGATCTGAAATAAGAAATCAGGATGAGGAAAACATAAGATCTTGTGCT
25399736 CCGCTAATTTGCAAAACCCAAGAAAGGACCCAAGAAGGGTAATAAATAAATAAAACTAAAACTGA
261 CCGCTAATTTGCAAAACCCAAGAAAGGACCCAAGAAGGGTAATAAATAAATAAAACTAAAACTGA
25399801 CAAAGCAAGTGCCAGGCAAGCTATCAAATCACATAGTTGTAGCAGTAGTTAACATGAAAAAAAGA
326 CAAAGCAAGTGCCAGGCAAGCTATCAAATCACATAGTTGTAGCAGTAGTTAACATGAAAAAAAGA
25399866 GGTTTAATTCAATTGACAAGATTGTAGAAGAAGCTTGGTACAAATATGAAAAGCGAAAACGACTT
391 GGTTTAATTCAATTGACAAGATTGTAGAAGAAGCTTGGTACAAATATGAAAAGCGAAAACGACTT
25399931 TTGGACCATAACTCACAGTAGCAGAGTAGGTGTAGCGTAGCAGCCATGAATTTCAAGTAAGAAAC
456 TTGGACCATAACTCACAGTAGCAGAGTAGGTGTAGCGTAGCAGCCATGAATTTCAAGTAAGAAAC
25399996 CCTGTCTGTTGTGATGATTTTAATGAAGGTGAGACTAG
521 CCTGTCTGTTGTGATGATTTTAATGAAGGTGAGACTAG
25400034 TGCA
1 TGCA
25400038 AAAAAAAAAA
Statistics
Matches: 561, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
557 557 0.99
558 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (558 bp):
TGCAGGCCTTCCAGAAACGTTTGCTTTCAGTGGAAGACCATTGCACACGATCATAGACGTCAGAA
GCCATAGGATGATATTCATGGTAAATTGCTGCCGCTGCTGCTTCATTAGAGTTGCTCCGACTCTG
ATAAAAATAGATCAGCAGAAAATGATACGTTGACTAAAGCTAAACCACGACAAGGCAATCAAACA
ATAGAATTAATAATAGCAGATCTGAAATAAGAAATCAGGATGAGGAAAACATAAGATCTTGTGCT
CCGCTAATTTGCAAAACCCAAGAAAGGACCCAAGAAGGGTAATAAATAAATAAAACTAAAACTGA
CAAAGCAAGTGCCAGGCAAGCTATCAAATCACATAGTTGTAGCAGTAGTTAACATGAAAAAAAGA
GGTTTAATTCAATTGACAAGATTGTAGAAGAAGCTTGGTACAAATATGAAAAGCGAAAACGACTT
TTGGACCATAACTCACAGTAGCAGAGTAGGTGTAGCGTAGCAGCCATGAATTTCAAGTAAGAAAC
CCTGTCTGTTGTGATGATTTTAATGAAGGTGAGACTAG
Found at i:25401111 original size:5 final size:5
Alignment explanation
Indices: 25401101--25401125 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25401091 GTCCATATTC
25401101 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
25401126 GTGGGTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:25408458 original size:69 final size:69
Alignment explanation
Indices: 25408340--25408587 Score: 257
Period size: 69 Copynumber: 3.6 Consensus size: 69
25408330 AGGGGTACCT
** ** *
25408340 GGAACAGAATCAGCAAAAATAGACGAGGT-TTGCCCCTTGAACAACTTATCCT-CATAGACAGGA
1 GGAACAGAATCAGCAAAAATAGACGAACTCTT-CCCCTTGAACATGTTAT-CTGCATAGGCAGGA
*
25408403 GAGCTT
64 GAGCTA
* * * * * * * * *
25408409 GGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACATGTTATCTGTATAGGCAGGAGT
1 GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
25408474 GCTA
66 GCTA
* * *
25408478 GGAACAGAATCAGCAAAAATAGATGAGCTCTTTCCCTTGAACATGTTATCTGCATAGGCAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
**
25408543 ATTA
66 GCTA
* * *
25408547 GGAACAGAATCTGCAAAAATAGATGAGCTCTTCCCCTTGAA
1 GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAA
25408588 GACTTTGTTT
Statistics
Matches: 147, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
68 2 0.01
69 143 0.97
70 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (69 bp):
GGAACAGAATCAGCAAAAATAGACGAACTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
GCTA
Found at i:25408579 original size:138 final size:137
Alignment explanation
Indices: 25408340--25408661 Score: 337
Period size: 138 Copynumber: 2.3 Consensus size: 137
25408330 AGGGGTACCT
* * **
25408340 GGAACAGAATCAGCAAAAATAGACGAGGTTTGCCCCTTGAACAACTTATCCTCATAGACAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAGCTTT-TCCCTTGAACATGTTATCCTCATAGACAGGAGA
* * * * * * * *
25408405 GCTTGGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACA-TGTTATCTGTATAGGCA
65 GATTGGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACT-TTATCTGTATAAGCA
25408469 GGAG-TGCTA
129 GG-GCTGCTA
* *
25408478 GGAACAGAATCAGCAAAAATAGATGAGCTCTTTCCCTTGAACATGTTAT-CTGCATAGGCAGGAG
1 GGAACAGAATCAGCAAAAATAGACGAGCT-TTTCCCTTGAACATGTTATCCT-CATAGACAGGAG
* * * * * *
25408542 A-ATTAGGAACAGAATCTGCAAAAATAGATGAGCTCTTCCCCTTGAAGACTTTGTTTTTATAAGC
64 AGATT-GGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACTTTATCTGTATAAGC
*
25408606 AGGGCTGCTT
128 AGGGCTGCTA
* * *
25408616 GGAATAGAATCCGCAAAAATAGACGAGCTTTTCCCGTGGAACATGT
1 GGAACAGAATCAGCAAAAATAGACGAGCTTTTCCC-TTGAACATGT
25408662 CCCCTATGTA
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
137 11 0.07
138 139 0.91
139 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (137 bp):
GGAACAGAATCAGCAAAAATAGACGAGCTTTTCCCTTGAACATGTTATCCTCATAGACAGGAGAG
ATTGGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACTTTATCTGTATAAGCAGG
GCTGCTA
Found at i:25414625 original size:4 final size:4
Alignment explanation
Indices: 25414616--25414642 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25414606 CCCACTATTA
25414616 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
25414643 ATTTATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Done.