Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 64
Found at i:531038 original size:21 final size:20
Alignment explanation
Indices: 530973--531041 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
530963 TTTTTATAAT
530973 AATATATAGTATA-ATTT-A
1 AATATATAGTATATATTTAA
*
530991 AA-ATA-AGTATATAATAATAA
1 AATATATAGTATAT-AT-TTAA
*
531011 TATATATAGTATATAGTTTAA
1 AATATATAGTATATA-TTTAA
531032 AATATATAGT
1 AATATATAGT
531042 TTTAGAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 6 0.15
17 3 0.08
18 4 0.10
19 1 0.03
20 2 0.05
21 16 0.40
22 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
AATATATAGTATATATTTAA
Found at i:531215 original size:3 final size:3
Alignment explanation
Indices: 531207--531269 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
531197 GTTTTATTTA
* *
531207 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
531255 TCAT TTT TA- TAT TAT
1 T-AT TAT TAT TAT TAT
531270 ATGATTGAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:539652 original size:10 final size:10
Alignment explanation
Indices: 539637--539661 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
539627 TGCACATCAT
539637 TTTAGTTGCA
1 TTTAGTTGCA
539647 TTTAGTTGCA
1 TTTAGTTGCA
539657 TTTAG
1 TTTAG
539662 GTTATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:556096 original size:9 final size:9
Alignment explanation
Indices: 556082--556154 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
556072 TTCCCTGAGG
556082 AAAAAAAGA
1 AAAAAAAGA
556091 AAAAAAA-A
1 AAAAAAAGA
*
556099 AGGAAAAAGGA
1 A--AAAAAAGA
*
556110 AAAAAGAGA
1 AAAAAAAGA
*
556119 AAAAAGAGA
1 AAAAAAAGA
*
556128 GAAAAGAAGA
1 -AAAAAAAGA
556138 AAAATAAA-A
1 AAAA-AAAGA
556147 ATAAAAAA
1 A-AAAAAA
556155 AAGGATTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.04
9 31 0.60
10 17 0.33
11 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:556112 original size:17 final size:17
Alignment explanation
Indices: 556092--556141 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
556082 AAAAAAAGAA
*
556092 AAAAAAAAGGAAAAAGG
1 AAAAAAAAGAAAAAAGG
*
556109 AAAAAAGAGAAAAAAGAG
1 AAAAAAAAGAAAAAAG-G
*
556127 AGAAAAGAAGAAAAA
1 A-AAAAAAAGAAAAA
556142 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 11 0.41
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAGG
Found at i:556121 original size:26 final size:28
Alignment explanation
Indices: 556083--556155 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 28
556073 TCCCTGAGGA
*
556083 AAAAAAGAAAAAAAAAAG-GAAAA-AGG
1 AAAAAAGAAAAAAAAAAGAGAAAAGAAG
* *
556109 AAAAAAGAGAAAAAAGAGAGAAAAGAAG
1 AAAAAAGAAAAAAAAAAGAGAAAAGAAG
*
556137 AAAAATAAAAATAAAAAAA
1 AAAAA-AGAAA-AAAAAAA
556156 AGGATTCAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 16 0.43
27 5 0.14
28 7 0.19
29 3 0.08
30 6 0.16
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (28 bp):
AAAAAAGAAAAAAAAAAGAGAAAAGAAG
Found at i:557528 original size:136 final size:136
Alignment explanation
Indices: 557378--557884 Score: 673
Period size: 135 Copynumber: 3.7 Consensus size: 136
557368 CTAAATAGTG
* * * *
557378 GTGGAGTGAATCAAATTTTCTCGAGTTTTACCTCCCCTAAAGAGTAGCAGAACAGATTCTTCTTA
1 GTGGAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTC
* *
557443 TTCTTTCAGATTTGATCTTTCTGAAGAGCAGTGAACCAAATCACATTCGATTCAATCTTCCCTGA
66 TTCTTTCAGATTTGATCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCCTGA
* *
557508 ATAGTA
131 AGAGCA
* *
557514 GTGGAGTGAATCAAATTTTTCTCGAGTCTGGCCTCCCCCTAAAGAGTAGCAGAGCATA-T-TT-T
1 GTGGAGTGAATCAAA-TTTTCTCGAGTCTGACCT-CCCCTAAAGAGTAGCAGAGCAGATTCTTCT
* * * *
557576 TCTTTTTTCAAATTT-AGTCTTCCTGAAGAGCAGTGAAGCAAATCAAATTCGATTCAATCTTCCC
64 TCTTCTTTCAGATTTGA-TCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCC
*
557640 TGTAGAGCA
128 TGAAGAGCA
* * *
557649 GTAGAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTATTC
1 GTGGAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTC
* * * *
557714 TTCTTTCGGATTTGATCTTCCTGAAGAGTAGTGAAACAAATCACATTTGATTTAATCTTCCCTGA
66 TTCTTTCAGATTTGATCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCCTGA
557779 AGAGCA
131 AGAGCA
* * * * * *
557785 GT-GAGTGAATCAAATTTTATTGAGTCTGACCTCCGCTAAAGAGTAGCGGGGCAAATTCTTCTTC
1 GTGGAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTC
**
557849 TTCTTTCAGATTCAATCTTCCTTGAAGAGCAGTGAA
66 TTCTTTCAGATTTGATCTTCC-TGAAGAGCAGTGAA
557885 GTGAATCAAA
Statistics
Matches: 326, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
133 21 0.06
134 19 0.06
135 153 0.47
136 95 0.29
137 17 0.05
138 21 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (136 bp):
GTGGAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTCTTC
TTCTTTCAGATTTGATCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCCTGA
AGAGCA
Found at i:557870 original size:271 final size:272
Alignment explanation
Indices: 557381--557896 Score: 736
Period size: 271 Copynumber: 1.9 Consensus size: 272
557371 AATAGTGGTG
* * *
557381 GAGTGAATCAAATTTTCTCGAGTTTTACCTCCCCTAAAGAGTAGCAGAACAGATTCTTCTTATTC
1 GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTCTTATTATTC
* * *
557446 TTTCAGATTTGATCTTTCTGAAGAGCAGTGAACCAAATCACATTCGATTCAATCTTCCCTGAATA
66 TTTCAGATTTGATCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCCTGAAGA
* * *
557511 GTAGTGGAGTGAATCAAATTTTTCTCGAGTCTGGCCTCCCCCTAAAGAGTAGCAGAGCATATTTT
131 GCAGTGGAGTGAATCAAATTTTTCTCGAGTCTGACCTCCCCCTAAAGAGTAGCAGAGCAAATTTT
* * *
557576 TCTTTTTTCAAATTTAGTCTTCC-TGAAGAGCAGTGAAGCAAATCAAATTCGATTCAATCTTCCC
196 TCTTCTTTCAAATTCAATCTTCCTTGAAGAGCAGTGAAGCAAATCAAATTCGATTCAATCTTCCC
557640 TGTAGAGCAGTA
261 TGTAGAGCAGTA
* * *
557652 GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTATTCTTC
1 GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTCTTATTATTC
* * * *
557717 TTTCGGATTTGATCTTCCTGAAGAGTAGTGAAACAAATCACATTTGATTTAATCTTCCCTGAAGA
66 TTTCAGATTTGATCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCCTGAAGA
* * *
557782 GCAGT-GAGTGAATCAAATTTTAT-T-GAGTCTGACCT-CCGCTAAAGAGTAGCGGGGCAAATTC
131 GCAGTGGAGTGAATCAAATTTT-TCTCGAGTCTGACCTCCCCCTAAAGAGTAGCAGAGCAAA-T-
* **
557843 TTCTTCTTCTTTCAGATTCAATCTTCCTTGAAGAGCAGTGAAGTGAATCAAATT
193 TT-TTCTTCTTTCAAATTCAATCTTCCTTGAAGAGCAGTGAAGCAAATCAAATT
557897 TTCTCGAGTC
Statistics
Matches: 215, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
268 19 0.09
269 11 0.05
270 19 0.09
271 142 0.66
272 24 0.11
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (272 bp):
GAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTCTTATTATTC
TTTCAGATTTGATCTTCCTGAAGAGCAGTGAAACAAATCACATTCGATTCAATCTTCCCTGAAGA
GCAGTGGAGTGAATCAAATTTTTCTCGAGTCTGACCTCCCCCTAAAGAGTAGCAGAGCAAATTTT
TCTTCTTTCAAATTCAATCTTCCTTGAAGAGCAGTGAAGCAAATCAAATTCGATTCAATCTTCCC
TGTAGAGCAGTA
Found at i:557918 original size:231 final size:233
Alignment explanation
Indices: 557626--558084 Score: 604
Period size: 231 Copynumber: 2.0 Consensus size: 233
557616 AATCAAATTC
* *
557626 GATTCAATCTTCCCTGTAGAGCAGTAGAGTGAATCAAATTTTCTCGAGTCTGACCTCCCCTAAAG
1 GATTCAATCTTCCCTGAAGAGCAGTAGAGTGAATCAAATTTTCTCGAGTCTAACCTCCCCTAAAG
* * * * *
557691 AGTAGCGGAGCAGATTCTTATTCTTCTTTCGGATTTGATCTTCCTGAAGAGTAGTGAAACAAATC
66 AATAGCGGA-AAAATTCTTATTATTCTTTCAGATTTGATCTTCCTGAAGAGTAGTGAAACAAATC
* * * *
557756 ACATTTGATTTAATCTTCCCTGAAGAGCAGT-GAGTGAATCAAATTTTAT-TGA-GTCTGACCTC
130 ACATTAGATTTAATCTTCCATGAAGAGCAGTGGAGTAAATCAAATTTTATCTCAGGTCTGACCTC
*
557818 CGC-TAAAGAGTAGCGGGGCAAATTCTTCTTCTTCTTTCA
195 C-CTTAAAGAGTAGCGGAGCAAATTCTTCTTCTTCTTTCA
*
557857 GATTCAATCTTCCTTGAAGAGCAGT-GAAGTGAATCAAATTTTCTCGAGTCTAACCTCCCCTAAA
1 GATTCAATCTTCCCTGAAGAGCAGTAG-AGTGAATCAAATTTTCTCGAGTCTAACCTCCCCTAAA
* * * * ** *
557921 TAATAGTGGAAAAATTCTTCTTATTCTTTCATATTTGATCTTCCTGAAGAGTAGTGAAGTAAGTC
65 GAATAGCGGAAAAATTCTTATTATTCTTTCAGATTTGATCTTCCTGAAGAGTAGTGAAACAAATC
* * ** *
557986 ACATTAGATTTAATCTTCCATGAAGAGTATTGGAGTAAATCAGTTTTTTTCCTCAGGTCTGACCT
130 ACATTAGATTTAATCTTCCATGAAGAGCAGTGGAGTAAATCAAATTTTAT-CTCAGGTCTGACCT
* *
558051 CCCTTAAAGAGTAGTGGAGCATATTCTTCTTCTT
194 CCCTTAAAGAGTAGCGGAGCAAATTCTTCTTCTT
558085 TCGGATTTGG
Statistics
Matches: 195, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
230 74 0.38
231 80 0.41
233 3 0.02
234 38 0.19
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (233 bp):
GATTCAATCTTCCCTGAAGAGCAGTAGAGTGAATCAAATTTTCTCGAGTCTAACCTCCCCTAAAG
AATAGCGGAAAAATTCTTATTATTCTTTCAGATTTGATCTTCCTGAAGAGTAGTGAAACAAATCA
CATTAGATTTAATCTTCCATGAAGAGCAGTGGAGTAAATCAAATTTTATCTCAGGTCTGACCTCC
CTTAAAGAGTAGCGGAGCAAATTCTTCTTCTTCTTTCA
Found at i:557942 original size:95 final size:95
Alignment explanation
Indices: 557762--557980 Score: 280
Period size: 95 Copynumber: 2.3 Consensus size: 95
557752 AATCACATTT
* * *
557762 GATTTAATCTTCCCTGAAGAGCAGTG-AGTGAATCAAATTTTATTGAGTCTGACCTCCGCTAAAG
1 GATTTAATCTT-CCTGAAGAGCAGTGAAGTGAATCAAATTTTATCGAGTCTAACCTCCCCTAAAG
* ** *
557826 AGTAGCGGGGCAAATTCTTCTTCTTCTTTCA
65 AATAGCGGGAAAAATTCTTCTTATTCTTTCA
* * *
557857 GATTCAATCTTCCTTGAAGAGCAGTGAAGTGAATCAAATTTTCTCGAGTCTAACCTCCCCTAAAT
1 GATTTAATCTTCC-TGAAGAGCAGTGAAGTGAATCAAATTTTATCGAGTCTAACCTCCCCTAAAG
*
557922 AATAG-TGGAAAAATTCTTCTTATTCTTTCA
65 AATAGCGGGAAAAATTCTTCTTATTCTTTCA
* * *
557952 TATTTGATCTTCCTGAAGAGTAGTGAAGT
1 GATTTAATCTTCCTGAAGAGCAGTGAAGT
557981 AAGTCACATT
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
94 17 0.16
95 53 0.50
96 37 0.35
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (95 bp):
GATTTAATCTTCCTGAAGAGCAGTGAAGTGAATCAAATTTTATCGAGTCTAACCTCCCCTAAAGA
ATAGCGGGAAAAATTCTTCTTATTCTTTCA
Found at i:558405 original size:25 final size:25
Alignment explanation
Indices: 558358--558404 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
558348 GGATTTTGTT
*
558358 TTATTTTATTATAGTTCTATTTTGG
1 TTATTTTATTATACTTCTATTTTGG
*
558383 TTATTTTATTTTACTT-TATTTT
1 TTATTTTATTATACTTCTATTTT
558405 TATAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.70
Consensus pattern (25 bp):
TTATTTTATTATACTTCTATTTTGG
Found at i:558435 original size:12 final size:12
Alignment explanation
Indices: 558418--558535 Score: 61
Period size: 12 Copynumber: 9.9 Consensus size: 12
558408 AATAATTGTA
558418 TATAATATATAG
1 TATAATATATAG
*
558430 TATAATTTAAAATAAG
1 TATAA--T-ATAT-AG
558446 TAT-ATATATA-
1 TATAATATATAG
558456 TATATATATATA-
1 TATA-ATATATAG
*
558468 TATATATATTTAG
1 TATA-ATATATAG
558481 -A-AATATATA-
1 TATAATATATAG
*
558490 TATAGTATATAG
1 TATAATATATAG
* *
558502 TTTAAAATATA-
1 TATAATATATAG
*
558513 TATAGTATATAG
1 TATAATATATAG
* *
558525 TTTAAAATATA
1 TATAATATATA
558536 TAGTTTTTGA
Statistics
Matches: 81, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
10 10 0.12
11 17 0.21
12 43 0.53
13 1 0.01
14 1 0.01
15 4 0.05
16 5 0.06
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (12 bp):
TATAATATATAG
Found at i:558537 original size:2 final size:2
Alignment explanation
Indices: 558446--558523 Score: 77
Period size: 2 Copynumber: 38.0 Consensus size: 2
558436 TTAAAATAAG
* * *
558446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA GA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
558488 TA TA TA GTA TA TA GTT TA -A AA TA TA TA TA GTA TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
558524 GTTTAAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
1 1 0.02
2 58 0.91
3 5 0.08
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:558537 original size:14 final size:14
Alignment explanation
Indices: 558495--558541 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
558485 ATATATATAG
558495 TATATAGTTTAAAA
1 TATATAGTTTAAAA
*
558509 TATATA---T--AG
1 TATATAGTTTAAAA
558518 TATATAGTTTAAAA
1 TATATAGTTTAAAA
558532 TATATAGTTT
1 TATATAGTTT
558542 TTGAGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
9 7 0.27
11 1 0.04
12 1 0.04
14 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TATATAGTTTAAAA
Found at i:558580 original size:23 final size:22
Alignment explanation
Indices: 558417--558590 Score: 135
Period size: 23 Copynumber: 7.7 Consensus size: 22
558407 TAATAATTGT
558417 ATATAATATATAGTATAATTTAAA
1 ATAT-ATATATA-TATAATTTAAA
* *
558441 ATA-AGTATATATAT-ATAT-AT
1 ATATA-TATATATATAATTTAAA
558461 ATATATATATATAT-ATTTAGAA
1 ATATATATATATATAATTTA-AA
558483 ATATATATATAGTATATAGTTTAAA
1 ATATATATATA-TATA-A-TTTAAA
*
558508 ATATATATAGTATATAGTTTAAA
1 ATATATATA-TATATAATTTAAA
* * * * *
558531 ATATATAGTTTTTGAGAA-ATAAT
1 ATATATA-TATAT-ATAATTTAAA
558554 ATATATATATAGTATAATTTAAA
1 ATATATATATA-TATAATTTAAA
558577 ATATATATA-ATATA
1 ATATATATATATATA
558591 GTTTTTTAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
20 16 0.13
21 8 0.07
22 22 0.18
23 47 0.39
24 6 0.05
25 16 0.13
26 6 0.05
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (22 bp):
ATATATATATATATAATTTAAA
Found at i:558605 original size:23 final size:26
Alignment explanation
Indices: 558552--558605 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 26
558542 TTGAGAAATA
*
558552 ATATATATATATAGTATAATTTAAAAT
1 ATATATATATATAGTAT-ATTTAAAAC
*
558579 ATATATA-ATATAGT-T-TTTTAAAC
1 ATATATATATATAGTATATTTAAAAC
558602 ATAT
1 ATAT
558606 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 10 0.40
25 1 0.04
26 7 0.28
27 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATATATATATAGTATATTTAAAAC
Found at i:558630 original size:69 final size:68
Alignment explanation
Indices: 558483--558635 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 68
558473 ATATTTAGAA
* *
558483 ATATATATATAGTATATAGTTTAAAATATATATAGTATATAGTTTAAAATATATAGTTTTTGAGA
1 ATATATATATAGTATA-A-TTTAAAATATATATAG-ATATAGTTTAAAATACATAGTTTTTGAAA
558548 AATAAT
63 AATAAT
**
558554 ATATATATATAGTATAATTTAAAATATATATA-ATATAGTTTTTTAA-ACATA-TTTTT-AAAAT
1 ATATATATATAGTATAATTTAAAATATATATAGATATAG-TTTAAAATACATAGTTTTTGAAAA-
558615 ATAATT
64 ATAA-T
*
558621 ATATGTATATA-TATA
1 ATATATATATAGTATA
558636 TAATATGTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
65 3 0.04
66 13 0.18
67 21 0.28
68 5 0.07
69 15 0.20
70 1 0.01
71 16 0.22
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (68 bp):
ATATATATATAGTATAATTTAAAATATATATAGATATAGTTTAAAATACATAGTTTTTGAAAAAT
AAT
Found at i:563323 original size:20 final size:19
Alignment explanation
Indices: 563298--563379 Score: 89
Period size: 20 Copynumber: 4.4 Consensus size: 19
563288 AGGGTGTCAA
563298 AGTGCATCCATGCACCCTGC
1 AGTGCATCCATGCA-CCTGC
*
563318 AGTGCATCTATGCACCTGC
1 AGTGCATCCATGCACCTGC
*
563337 AGTGTATCCATGCA-CT--
1 AGTGCATCCATGCACCTGC
* *
563353 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACC-TGC
563373 AGTGCAT
1 AGTGCAT
563380 TGATGCACTC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
16 12 0.23
17 1 0.02
18 3 0.06
19 17 0.32
20 20 0.38
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:563524 original size:21 final size:20
Alignment explanation
Indices: 563487--563525 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
563477 GAATTTAATG
* *
563487 AATGGGTACCGATGCACCTT
1 AATGGGTACCAAAGCACCTT
563507 AATGGTGTACCAAAGCACC
1 AATGG-GTACCAAAGCACC
563526 CTGTTATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (20 bp):
AATGGGTACCAAAGCACCTT
Found at i:563582 original size:21 final size:21
Alignment explanation
Indices: 563553--563592 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
563543 TTTGAGCAGA
563553 AAAATCATCCCCTAACAGCTCC
1 AAAATCAT-CCCTAACAGCTCC
563575 AAAA-CATCCCTAACAGCT
1 AAAATCATCCCTAACAGCT
563593 ATATACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 3 0.17
22 4 0.22
ACGTcount: A:0.40, C:0.38, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCTAACAGCTCC
Found at i:566542 original size:21 final size:21
Alignment explanation
Indices: 566516--566556 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
566506 TGTTATATTT
566516 TTAACAATTGATATCCTTTTG
1 TTAACAATTGATATCCTTTTG
* *
566537 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCCTTTT
566557 CATTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTAACAATTGATATCCTTTTG
Found at i:566856 original size:20 final size:20
Alignment explanation
Indices: 566831--566868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
566821 GAATGCAATT
*
566831 AGTGCATCGATGCACCCTGC
1 AGTGCATCCATGCACCCTGC
*
566851 AGTGCATCCATGTACCCT
1 AGTGCATCCATGCACCCT
566869 AGCTGCATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:567014 original size:20 final size:22
Alignment explanation
Indices: 566976--567015 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
566966 TTTTGAGCAA
566976 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
566998 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
567016 ATATACATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:567270 original size:34 final size:33
Alignment explanation
Indices: 567231--567301 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
567221 TTTTGTAAAG
* *
567231 GGGAAAGGTTCTAGTTTAGCCTGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCGTG-AAAAACTA
*
567265 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
567298 GGGA
1 GGGA
567302 GTTGTAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (33 bp):
GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
Found at i:570618 original size:43 final size:43
Alignment explanation
Indices: 570558--570653 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
570548 CCTTACTTTA
570558 ACAC-TTCTCCCATTTATCATTTTTAAAACACACTTAAAACAC
1 ACACTTTCTCCCATTTATCATTTTTAAAACACACTTAAAACAC
570600 ACACTTTCTCCCATTTATCATTTTTAAAACACACTTAAAACAC
1 ACACTTTCTCCCATTTATCATTTTTAAAACACACTTAAAACAC
570643 ACA-TTTCTCCC
1 ACACTTTCTCCC
570654 CCTTTTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 12 0.23
43 41 0.77
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.34
Consensus pattern (43 bp):
ACACTTTCTCCCATTTATCATTTTTAAAACACACTTAAAACAC
Found at i:572934 original size:20 final size:21
Alignment explanation
Indices: 572881--572942 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
572871 TTCCCCTGTG
572881 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
572905 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
572925 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
572943 TTCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:579118 original size:2 final size:2
Alignment explanation
Indices: 579111--579139 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
579101 ACGAGAATAG
579111 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 T
579140 TAGGAGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:580156 original size:23 final size:23
Alignment explanation
Indices: 580121--580189 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
580111 ACATCTTATA
*
580121 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGCATTTATACG
** *
580144 TGGCACTTTGGTGCAATTATACG
1 TGGCACTACGGTGCATTTATACG
*
580167 TGGCACTCCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTATACG
580190 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTATACG
Found at i:580978 original size:21 final size:23
Alignment explanation
Indices: 580935--580986 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
580925 AAATAATAAT
*
580935 AATAATAATTAAATATATGAACA
1 AATAATAATTAAATATATAAACA
*
580958 TATAA-AATTAAA-ATATAAACA
1 AATAATAATTAAATATATAAACA
580979 AATAATAA
1 AATAATAA
580987 CTAATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 12 0.48
22 9 0.36
23 4 0.16
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
AATAATAATTAAATATATAAACA
Found at i:582412 original size:3 final size:3
Alignment explanation
Indices: 582406--582463 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
582396 TAATATTTTT
582406 TAA TAA TAA TAA TAA TAA T-A TAA -AA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
582450 -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
582464 CAAATGGATG
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:582417 original size:22 final size:22
Alignment explanation
Indices: 582407--582463 Score: 107
Period size: 21 Copynumber: 2.6 Consensus size: 22
582397 AATATTTTTT
582407 AATAATAATAATAATAATATAA
1 AATAATAATAATAATAATATAA
582429 AATAATAATAATAATAA-ATAA
1 AATAATAATAATAATAATATAA
582450 AATAATAATAATAA
1 AATAATAATAATAA
582464 CAAATGGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAATAATAATAATAATATAA
Found at i:582423 original size:25 final size:25
Alignment explanation
Indices: 582406--582463 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 25
582396 TAATATTTTT
582406 TAATAATAATAATAATAATATAAAA
1 TAATAATAATAATAATAATATAAAA
*
582431 TAATAATAATAATAAATAAAATAATAA
1 TAATAATAATAAT-AATAATATAA-AA
582458 TAATAA
1 TAATAA
582464 CAAATGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 13 0.43
26 9 0.30
27 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
TAATAATAATAATAATAATATAAAA
Found at i:582468 original size:16 final size:15
Alignment explanation
Indices: 582406--582463 Score: 73
Period size: 16 Copynumber: 3.8 Consensus size: 15
582396 TAATATTTTT
*
582406 TAATAATAATAATAA
1 TAATAAAAATAATAA
582421 TAATATAAAATAATAA
1 TAATA-AAAATAATAA
582437 TAATAATAAATAA-AA
1 TAATAA-AAATAATAA
*
582452 TAATAATAATAA
1 TAATAAAAATAA
582464 CAAATGGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.13
15 14 0.36
16 20 0.51
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAATAAAAATAATAA
Found at i:582920 original size:122 final size:120
Alignment explanation
Indices: 582754--583221 Score: 609
Period size: 122 Copynumber: 3.9 Consensus size: 120
582744 TACCTACTTC
* * *
582754 ATCTATATCCTTCTGTGATAGAATCAAT-CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTATGATAGAGTC-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
582818 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAATTTGATACTG
65 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-TTGAT--TG
582877 ATCTATCTCCTTCTATGATAGAGTCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* * *
582941 TTTTCCTCTTCTGATAAGTTCTTATCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-TTGA--TTG
*
582999 ATCTATCTCCTTCTGTGATAGAGTCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
583063 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA--G-TTG
66 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAATTGATTG
* *** * * * * *
583115 ATCCATC-GAGT-GATG--A-ATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* *
583175 TCTTCCTTCTCCAGATGAGTTCTTCTCATTATGAAC-TTCTTCTGGAA
66 TCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTC-TCTGGAA
583222 CAGTTGATCC
Statistics
Matches: 316, Mismatches: 23, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
111 6 0.02
112 43 0.14
113 34 0.11
114 2 0.01
115 1 0.00
116 9 0.03
119 1 0.00
122 196 0.62
123 23 0.07
124 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (120 bp):
ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAATTGATTG
Found at i:583152 original size:112 final size:113
Alignment explanation
Indices: 583028--583247 Score: 345
Period size: 113 Copynumber: 2.0 Consensus size: 113
583018 AGAGTCATGC
* *
583028 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATAAGTTCTTCTCATT
*
583092 ATGAACTT-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
66 ATGAACTTCT-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCA
* *
583140 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATAAGTTCTTCTCATT
* * *
583205 ATGAACTTCTTCTGGAACAGTTGATCCATTGAATGATGGATTC
66 ATGAACTTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTC
583248 GAATCTTTGC
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
112 39 0.40
113 58 0.59
114 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATAAGTTCTTCTCATT
ATGAACTTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCA
Found at i:584417 original size:21 final size:21
Alignment explanation
Indices: 584388--584428 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
584378 GTTTATGTGA
*
584388 AAAATAAATTGAATTTCAAAC
1 AAAAGAAATTGAATTTCAAAC
584409 AAAAGAAATTGAATTTCAAA
1 AAAAGAAATTGAATTTCAAA
584429 AAGATAGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAGAAATTGAATTTCAAAC
Found at i:588328 original size:9 final size:9
Alignment explanation
Indices: 588316--588347 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
588306 TGAAAATAAT
588316 GAATGTAAA
1 GAATGTAAA
588325 GAATGTAAA
1 GAATGTAAA
588334 GAATGTAAA
1 GAATGTAAA
588343 GAATG
1 GAATG
588348 ATTGCCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (9 bp):
GAATGTAAA
Found at i:596111 original size:29 final size:30
Alignment explanation
Indices: 596049--596112 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
596039 TTCTTAATAT
*
596049 TAAAAAATAAATAAATATTAATAAAATTTT
1 TAAAAAATAAATAAATATTAATAAAATTTA
* *
596079 TAAAAAATAATTAAA-A-TATATATAATTTA
1 TAAAAAATAAATAAATATTA-ATAAAATTTA
596108 TAAAA
1 TAAAA
596113 GTAATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 14 0.47
30 14 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAAAAATAAATAAATATTAATAAAATTTA
Found at i:597722 original size:3 final size:3
Alignment explanation
Indices: 597716--597777 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
597706 TAATATTTTT
*
597716 TAA TAA TAA TAA TAA TAAA TAA T-A TAA -AA TAA TAA TAG TAA TAAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
597761 TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
597778 CAAATGGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 6 0.12
3 40 0.77
4 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:597746 original size:26 final size:27
Alignment explanation
Indices: 597716--597777 Score: 99
Period size: 26 Copynumber: 2.3 Consensus size: 27
597706 TAATATTTTT
*
597716 TAATAATAATAATAATAAATAATATAA
1 TAATAATAATAATAATAAATAAAATAA
*
597743 -AATAATAATAGTAATAAATAAAATAA
1 TAATAATAATAATAATAAATAAAATAA
597769 TAATAATAA
1 TAATAATAA
597778 CAAATGGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
TAATAATAATAATAATAAATAAAATAA
Found at i:598364 original size:18 final size:19
Alignment explanation
Indices: 598331--598369 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
598321 TCACTACAAG
*
598331 AAATTTATATTATTGTGAA
1 AAATTTATATTATTGTCAA
*
598350 AAATTT-TATTTTTGTCAA
1 AAATTTATATTATTGTCAA
598368 AA
1 AA
598370 TTAAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
AAATTTATATTATTGTCAA
Found at i:598876 original size:18 final size:17
Alignment explanation
Indices: 598828--598877 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
598818 AAAATTCAAG
598828 TTTTTTGTAA-TA-AAT
1 TTTTTTGTAACTATAAT
598843 TATTTTTGT-ACTTATATAT
1 T-TTTTTGTAAC-TATA-AT
598862 TTTTTTGTAACTATAA
1 TTTTTTGTAACTATAA
598878 ATGTTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 2 0.07
16 7 0.24
17 3 0.10
18 12 0.41
19 5 0.17
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTTGTAACTATAAT
Found at i:599287 original size:274 final size:275
Alignment explanation
Indices: 598632--599408 Score: 1341
Period size: 276 Copynumber: 2.8 Consensus size: 275
598622 AATAATTATT
598632 ACAAAAAATAATGATATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAAGTTTAACTATA
1 ACAAAAAATAATGATATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAAGTTTAACTATA
* * *
598697 GTGATAGCATATATTGTCATGACTATTTTTCTCCACATTTTTGTTTCAAAAGTTGTATTGATAAT
66 GTGATAGCATATATTGTCATGACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGATAAA
*
598762 TTTTATAATTATAATTTATAGTTATTTTTATAGAAAAAACTATCACATCAAATAATAAAATTCAA
131 TTTTATAATTATAATTTATAGTTATTTTTATAGAAAAAATTATCACATCAAATAATAAAATTCAA
598827 GTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTTTTGTAACTATAAATGTTAATAATTAT
196 GTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTTTTGTAACTATAAATGTTAATAATTAT
* *
598892 TAGAAAAAATATTGTC
261 TA-AAAAAATAGTATC
598908 ACAAAAAATAATGATATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAAGTTTAACTATA
1 ACAAAAAATAATGATATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAAGTTTAACTATA
* *
598973 GTGATAGCATAAATTGTCATGACTATTTTTCTCCACTTTTTTATTTCAAAAGTTATATTGATAAA
66 GTGATAGCATATATTGTCATGACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGATAAA
*
599038 TTTTATAATTATAATTTATAGTTATTTTTATAG-CAAAATTATCACATCAAATAATAAAATTCAA
131 TTTTATAATTATAATTTATAGTTATTTTTATAGAAAAAATTATCACATCAAATAATAAAATTCAA
* * *
599102 GTCTTTTTATAATAAATTACTTTTGTACTTATATATATTTTTTGTAACTATAAGTGTTAATAATT
196 GT-TTTTTGTAATAAATTATTTTTGTACTTATATAT-TTTTTTGTAACTATAAATGTTAATAATT
599167 ATT-AAAAAATAGTATC
259 ATTAAAAAAATAGTATC
*
599183 ACAAAAAA-AATGATATTCACGTTTTTGTGACAAATTATATTTATAGTTATAAAGTTTAACTATA
1 ACAAAAAATAATGATATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAAGTTTAACTATA
* *
599247 GTGATAGCGTATATTGTCATGACTATTTTTCTCTACTTTTTTGTTTCAAAAGTTATATTGAT-AA
66 GTGATAGCATATATTGTCATGACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGATAAA
599311 TTTTATAATTATAATTTATAGTTATTTTTATAGAAAAAATTATCACATCAAATAATAAAATTC-A
131 TTTTATAATTATAATTTATAGTTATTTTTATAGAAAAAATTATCACATCAAATAATAAAATTCAA
*
599375 G-GTTTTGTAATAAATTATTTTTGTACTTATATAT
196 GTTTTTTGTAATAAATTATTTTTGTACTTATATAT
599409 GTTAATCATT
Statistics
Matches: 477, Mismatches: 21, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
271 30 0.06
273 37 0.08
274 141 0.30
275 50 0.10
276 189 0.40
277 30 0.06
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (275 bp):
ACAAAAAATAATGATATTCACGTTTTTGTGACAAATTATATTTGTAGTTATAAAGTTTAACTATA
GTGATAGCATATATTGTCATGACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGATAAA
TTTTATAATTATAATTTATAGTTATTTTTATAGAAAAAATTATCACATCAAATAATAAAATTCAA
GTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTTTTGTAACTATAAATGTTAATAATTAT
TAAAAAAATAGTATC
Found at i:604807 original size:20 final size:21
Alignment explanation
Indices: 604779--604830 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
604769 GATAAAAGTA
* * *
604779 GTATTGATACTGATGTGG-AG
1 GTATCGATACTGAAGAGGAAG
*
604799 GTATCGATAC-CAAGAGGAAG
1 GTATCGATACTGAAGAGGAAG
604819 GTATCGATACTG
1 GTATCGATACTG
604831 TAATTGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (21 bp):
GTATCGATACTGAAGAGGAAG
Found at i:605837 original size:137 final size:135
Alignment explanation
Indices: 605578--605850 Score: 440
Period size: 137 Copynumber: 2.0 Consensus size: 135
605568 GCACTTCAAA
* * *
605578 ATACATTTGTGTATGATGGTTATTGATGATTATTGTTTAATGCATATGTTGCATTTTTTATTAGT
1 ATACATTTGTGTATGATGGTTATCGATGATTATTGTTTAATGCATATGTTGCATTTTGTATCAGT
* * * *
605643 ATATGTGTACTTTCGGCACTATGTGTGCATCCATGGTATTCACAATGAGTTTGTGAATTACCATT
66 ATATATATACTTTCGACACTATGTGTGCATCCATGGAATTCACAATGAGTTTGTGAATTACCATT
605708 TCGAC
131 TCGAC
605713 ATACATTTGTGTATGATGGTTATCGATCGATT-TTGTTTAATGCATATGTTGCATTTTCGTATCA
1 ATACATTTGTGTATGATGGTTATCGAT-GATTATTGTTTAATGCATATGTTGCATTTT-GTATCA
*
605777 GTACTATATATACTTTCGACACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACC
64 GTA-TATATATACTTTCGACACTATGTGTGCATCCATGGAATTCACAATGAGTTTGTGAATTACC
605842 ATTTCGAC
128 ATTTCGAC
605850 A
1 A
605851 CTTAGGTACA
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
135 51 0.40
136 11 0.09
137 65 0.51
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (135 bp):
ATACATTTGTGTATGATGGTTATCGATGATTATTGTTTAATGCATATGTTGCATTTTGTATCAGT
ATATATATACTTTCGACACTATGTGTGCATCCATGGAATTCACAATGAGTTTGTGAATTACCATT
TCGAC
Found at i:609508 original size:21 final size:21
Alignment explanation
Indices: 609482--609521 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
609472 CTTAAAGAAG
609482 AAAATTTTCAAAAAAATATTA
1 AAAATTTTCAAAAAAATATTA
609503 AAAATTTTCAAAAAAATAT
1 AAAATTTTCAAAAAAATAT
609522 CATTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTTTCAAAAAAATATTA
Found at i:615645 original size:2 final size:2
Alignment explanation
Indices: 615638--615663 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
615628 AATGATTTTG
615638 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
615664 TGTTATGGAT
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:620078 original size:45 final size:45
Alignment explanation
Indices: 620027--620397 Score: 498
Period size: 45 Copynumber: 8.3 Consensus size: 45
620017 TAGATCGATA
620027 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
** *
620072 ATTTTCATT-GATGGCACCTTTTATGTTGATAATGCACCGTTATGC
1 ATTTTCATTAG-TGGCACCTTTTATGCCGATAATGCATCGTTATGC
* *
620117 AATTTCATTAATGGCACCTTTTATGCCGATAATGCATCGTTATGC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
* * * *
620162 ATTTTTATTAGTTGCACCTTTTATGTCGATAATGCACCGTTATGC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
* * *
620207 ATTTTCATTAGTGGCA-CATTTATACCGACAATGC-TCTGTTATGC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATC-GTTATGC
* * *
620251 ATTTTCATTAGTGGCACATTTTATGCCAATAATGCA-CAGTTATAC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATC-GTTATGC
* *
620296 ATTTTCATTAGTGGCACCTTTTATGTCGATAATGCACCGTTATGC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
* * * *
620341 ATTTTCATTAGTAGCACCTTTTATGCTGAAAATGCATTGTTATGC
1 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
620386 ATTTTCATTAGT
1 ATTTTCATTAGT
620398 ATTCATCCAT
Statistics
Matches: 282, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.00
44 38 0.13
45 242 0.86
46 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (45 bp):
ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGC
Found at i:620141 original size:26 final size:25
Alignment explanation
Indices: 620066--620142 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
620056 TAATGCATCG
*
620066 TTATGCATTTTCATTGATGGCACCTT
1 TTATGCA-TTTCATTAATGGCACCTT
* *
620092 TTATG---TTGA-TAAT-GCACC-G
1 TTATGCATTTCATTAATGGCACCTT
620111 TTATGCAATTTCATTAATGGCACCTT
1 TTATGC-ATTTCATTAATGGCACCTT
620137 TTATGC
1 TTATGC
620143 CGATAATGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
19 5 0.13
20 5 0.13
21 3 0.08
22 3 0.08
23 3 0.08
24 4 0.10
25 5 0.13
26 11 0.28
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (25 bp):
TTATGCATTTCATTAATGGCACCTT
Found at i:620285 original size:179 final size:180
Alignment explanation
Indices: 620027--620397 Score: 525
Period size: 179 Copynumber: 2.1 Consensus size: 180
620017 TAGATCGATA
* * * *
620027 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCATCGTTATGCATTTTCATTGATGGCACCTT
1 ATTTTCATTAGTGGCACCATTTATACCGACAATGCATCGTTATGCATTTTCATTGATGGCACATT
*** * * *
620092 TTATGTTGATAATGCACCGTTATGCAATTTCATTAATGGCACCTTTTATGCCGATAATGCATCGT
66 TTATGCCAATAATGCACAGTTATACAATTTCATTAATGGCACCTTTTATGCCGATAATGCACCGT
* * *
620157 TATGCATTTTTATTAGTTGCACCTTTTATG-TCGATAATGCACCGTTATGC
131 TATGCATTTTCATTAGTAGCACCTTTTATGCT-GAAAATGCACCGTTATGC
620207 ATTTTCATTAGTGGCA-CATTTATACCGACAATGC-TCTGTTATGCATTTTCATT-AGTGGCACA
1 ATTTTCATTAGTGGCACCATTTATACCGACAATGCATC-GTTATGCATTTTCATTGA-TGGCACA
* * *
620269 TTTTATGCCAATAATGCACAGTTATACATTTTCATTAGTGGCACCTTTTATGTCGATAATGCACC
64 TTTTATGCCAATAATGCACAGTTATACAATTTCATTAATGGCACCTTTTATGCCGATAATGCACC
**
620334 GTTATGCATTTTCATTAGTAGCACCTTTTATGCTGAAAATGCATTGTTATGC
129 GTTATGCATTTTCATTAGTAGCACCTTTTATGCTGAAAATGCACCGTTATGC
620386 ATTTTCATTAGT
1 ATTTTCATTAGT
620398 ATTCATCCAT
Statistics
Matches: 170, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
178 3 0.02
179 150 0.88
180 17 0.10
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (180 bp):
ATTTTCATTAGTGGCACCATTTATACCGACAATGCATCGTTATGCATTTTCATTGATGGCACATT
TTATGCCAATAATGCACAGTTATACAATTTCATTAATGGCACCTTTTATGCCGATAATGCACCGT
TATGCATTTTCATTAGTAGCACCTTTTATGCTGAAAATGCACCGTTATGC
Found at i:624693 original size:63 final size:64
Alignment explanation
Indices: 624616--624816 Score: 225
Period size: 63 Copynumber: 3.1 Consensus size: 64
624606 ATAGGAATAT
*
624616 CATTAGCTAGGAAAGCTATTCACCCCTTTGACATCATTTCCTTTGTAGTCATGGCT-GATATCA
1 CATTAGCTAGGAAAGCTATTCACCCCTTTGACATCATTTCCTTTGCAGTCATGGCTCGATATCA
* * *
624679 CATTGGCTAGGAAAGTTATTCACCCCTTTGACATCATTTCCTTTACAGTCACTTCTGGTACTCGA
1 CATTAGCTAGGAAAGCTATTCACCCCTTTGACATCATTTCCTTTGCAGTCA----TGG--CTCGA
624744 GTGTCTATCA
60 -----TATCA
624754 CATTAGCTAGGAAAGCTATTCACCCCTTTG--A-CA-TTCCTTTGCAGTCATGG-TCGATATCA
1 CATTAGCTAGGAAAGCTATTCACCCCTTTGACATCATTTCCTTTGCAGTCATGGCTCGATATCA
624813 CATT
1 CATT
624817 GGATGGTGAT
Statistics
Matches: 119, Mismatches: 7, Indels: 28
0.77 0.05 0.18
Matches are distributed among these distances:
59 9 0.08
63 47 0.39
64 4 0.03
67 6 0.05
69 2 0.02
70 2 0.02
71 13 0.11
72 2 0.02
73 1 0.01
75 33 0.28
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (64 bp):
CATTAGCTAGGAAAGCTATTCACCCCTTTGACATCATTTCCTTTGCAGTCATGGCTCGATATCA
Found at i:626487 original size:45 final size:45
Alignment explanation
Indices: 626436--626651 Score: 254
Period size: 45 Copynumber: 4.8 Consensus size: 45
626426 TAGATCGATA
* * **
626436 ATTTTCATTAGTGACACATTTTATGTCGATAATGAATGGTTATGC
1 ATTTTCATTAGTGACACCTTTTATGTCGATAATGCACCGTTATGC
* * *
626481 ATTTTCATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGA
1 ATTTTCATTAGTGACACCTTTTATGTCGATAATGCACCGTTATGC
** * ** * *
626526 ATTTTTGTTAGTGGCACCTTTTATACCAATAATGCATCGTTATGC
1 ATTTTCATTAGTGACACCTTTTATGTCGATAATGCACCGTTATGC
** **
626571 ATTTTCATTAGT-AGCATATTTTATGTCGATAATGCACAATTATGC
1 ATTTTCATTAGTGA-CACCTTTTATGTCGATAATGCACCGTTATGC
626616 ATTTTCATTAGTGACACCTTTTATGTCGATAATGCA
1 ATTTTCATTAGTGACACCTTTTATGTCGATAATGCA
626652 AATGCATTAG
Statistics
Matches: 143, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
45 142 0.99
46 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (45 bp):
ATTTTCATTAGTGACACCTTTTATGTCGATAATGCACCGTTATGC
Found at i:626650 original size:90 final size:90
Alignment explanation
Indices: 626435--626651 Score: 290
Period size: 90 Copynumber: 2.4 Consensus size: 90
626425 ATAGATCGAT
* * * * *
626435 AATTTTCATTAGTGACACATTTTATGTCGATAATGAATGGTTATGCATTTTCATTAGTGGCACCT
1 AATTTTCATTAGTGACACCTTTTATGTCGATAATGCATCGTTATGCATTTTCATTAGTAGCACAT
**
626500 TTTATGCCGATAATGCACCGTTATG
66 TTTATGCCGATAATGCACAATTATG
** * ** * *
626525 AATTTTTGTTAGTGGCACCTTTTATACCAATAATGCATCGTTATGCATTTTCATTAGTAGCATAT
1 AATTTTCATTAGTGACACCTTTTATGTCGATAATGCATCGTTATGCATTTTCATTAGTAGCACAT
*
626590 TTTATGTCGATAATGCACAATTATG
66 TTTATGCCGATAATGCACAATTATG
*
626615 CATTTTCATTAGTGACACCTTTTATGTCGATAATGCA
1 AATTTTCATTAGTGACACCTTTTATGTCGATAATGCA
626652 AATGCATTAG
Statistics
Matches: 105, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
90 105 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (90 bp):
AATTTTCATTAGTGACACCTTTTATGTCGATAATGCATCGTTATGCATTTTCATTAGTAGCACAT
TTTATGCCGATAATGCACAATTATG
Found at i:626773 original size:45 final size:45
Alignment explanation
Indices: 626656--627019 Score: 545
Period size: 45 Copynumber: 8.1 Consensus size: 45
626646 AATGCAAATG
**
626656 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTTATGCATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
* * *
626701 CATTAG-GTCACATTTTATGTCGATAATGCACCGTTATGCATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
* *
626745 CATTAGTGGCACATTTTATGCCGATAATGCACCATTATGCATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
** * *
626790 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTCATGTATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
626835 CATTAGTGGCACCTTTTAT-CTCGATAATGCACCGTTATGCATTTT
1 CATTAGTGGCACCTTTTATGC-CGATAATGCACCGTTATGCATTTT
*
626880 CATTAGTGGCACCTTTTATGCCGATAATACA-CGTTATGCATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
* **
626924 CATTAGTGGCACCTTTTATGCCGATAATACACCACTATGCATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
* *
626969 CATTAGTGGCACCTTTTATGCAGATAATGCACCATTATGCATTTT
1 CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
627014 CATTAG
1 CATTAG
627020 CATTCATACA
Statistics
Matches: 293, Mismatches: 22, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
44 85 0.29
45 207 0.71
46 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
CATTAGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTT
Found at i:626891 original size:25 final size:24
Alignment explanation
Indices: 626773--626894 Score: 73
Period size: 25 Copynumber: 5.3 Consensus size: 24
626763 TGCCGATAAT
*
626773 GCACCATTATGCATTTTCATTAGTG
1 GCACC-TTATGTATTTTCATTAGTG
* * *
626798 GCACCTT-T-TATGTTGA-TAAT-
1 GCACCTTATGTATTTTCATTAGTG
*
626818 GCACCGTCATGTATTTTCATTAGTG
1 GCACC-TTATGTATTTTCATTAGTG
* *
626843 GCACCTT-T-TA-TCTCGA-TAAT-
1 GCACCTTATGTATTTTC-ATTAGTG
*
626863 GCACCGTTATGCATTTTCATTAGTG
1 GCACC-TTATGTATTTTCATTAGTG
626888 GCACCTT
1 GCACCTT
626895 TTATGCCGAT
Statistics
Matches: 71, Mismatches: 14, Indels: 25
0.65 0.13 0.23
Matches are distributed among these distances:
20 10 0.14
21 12 0.17
22 10 0.14
23 10 0.14
24 14 0.20
25 15 0.21
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (24 bp):
GCACCTTATGTATTTTCATTAGTG
Found at i:626899 original size:26 final size:26
Alignment explanation
Indices: 626779--626900 Score: 67
Period size: 26 Copynumber: 5.2 Consensus size: 26
626769 TAATGCACCA
626779 TTATGCATTTTCATTAGTGGCACCTT
1 TTATGCATTTTCATTAGTGGCACCTT
* * *
626805 TTATG----TTGA-TAAT-GCACC-G
1 TTATGCATTTTCATTAGTGGCACCTT
* *
626824 TCATGTATTTTCATTAGTGGCACCTT
1 TTATGCATTTTCATTAGTGGCACCTT
* *
626850 TTAT-C----TCGA-TAAT-GCACC-G
1 TTATGCATTTTC-ATTAGTGGCACCTT
626869 TTATGCATTTTCATTAGTGGCACCTT
1 TTATGCATTTTCATTAGTGGCACCTT
626895 TTATGC
1 TTATGC
626901 CGATAATACA
Statistics
Matches: 67, Mismatches: 13, Indels: 32
0.60 0.12 0.29
Matches are distributed among these distances:
19 8 0.12
20 11 0.16
21 8 0.12
22 4 0.06
23 4 0.06
24 8 0.12
25 10 0.15
26 14 0.21
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (26 bp):
TTATGCATTTTCATTAGTGGCACCTT
Found at i:626917 original size:134 final size:135
Alignment explanation
Indices: 626656--627019 Score: 556
Period size: 134 Copynumber: 2.7 Consensus size: 135
626646 AATGCAAATG
* * * *
626656 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTTATGCATTTTCATTAG-GTCACATTTTATG
1 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTCATGCATTTTCATTAGTGGCACCTTTTATC
*
626720 TCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATGCACCATTATGC
66 TCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATACACCATTATGC
626785 ATTTT
131 ATTTT
*
626790 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTCATGTATTTTCATTAGTGGCACCTTTTATC
1 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTCATGCATTTTCATTAGTGGCACCTTTTATC
* *
626855 TCGATAATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTATGCCGATAATACA-CGTTATGC
66 TCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATACACCATTATGC
626919 ATTTT
131 ATTTT
** * *
626924 CATTAGTGGCACCTTTTATGCCGATAATACACC-ACTATGCATTTTCATTAGTGGCACCTTTTAT
1 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTC-ATGCATTTTCATTAGTGGCACCTTTTAT
* *
626988 GC-AGATAATGCACCATTATGCATTTTCATTAG
65 -CTCGATAATGCACCGTTATGCATTTTCATTAG
627020 CATTCATACA
Statistics
Matches: 212, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
133 1 0.00
134 146 0.69
135 65 0.31
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (135 bp):
CATTAGTGGCACCTTTTATGTTGATAATGCACCGTCATGCATTTTCATTAGTGGCACCTTTTATC
TCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATACACCATTATGC
ATTTT
Found at i:626965 original size:179 final size:179
Alignment explanation
Indices: 626656--627019 Score: 586
Period size: 179 Copynumber: 2.0 Consensus size: 179
626646 AATGCAAATG
* * * *
626656 CATTAGTGGCACCTTTTATGTTGATAATGCACCGTTATGCATTTTCATTAGGTCACATTTTATGT
1 CATTAGTGGCACCTTTTATCTCGATAATGCACCGTTATGCATTTTCATTAGGGCACATTTTATGC
* * *
626721 CGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATGCACCATTATGCA
66 CGATAATACACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATACACCACTATGCA
** * *
626786 TTTTCATTAGTGGCACCTTTTATGTTGATAATGCACCGTCATGTATTTT
131 TTTTCATTAGTGGCACCTTTTATGCAGATAATGCACCATCATGCATTTT
*
626835 CATTAGTGGCACCTTTTATCTCGATAATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTATG
1 CATTAGTGGCACCTTTTATCTCGATAATGCACCGTTATGCATTTTCATTAG-GGCACATTTTATG
*
626900 CCGATAATACA-CGTTATGCATTTTCATTAGTGGCACCTTTTATGCCGATAATACACCACTATGC
65 CCGATAATACACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATACACCACTATGC
*
626964 ATTTTCATTAGTGGCACCTTTTATGCAGATAATGCACCATTATGCATTTT
130 ATTTTCATTAGTGGCACCTTTTATGCAGATAATGCACCATCATGCATTTT
627014 CATTAG
1 CATTAG
627020 CATTCATACA
Statistics
Matches: 170, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
179 150 0.88
180 20 0.12
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (179 bp):
CATTAGTGGCACCTTTTATCTCGATAATGCACCGTTATGCATTTTCATTAGGGCACATTTTATGC
CGATAATACACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATACACCACTATGCA
TTTTCATTAGTGGCACCTTTTATGCAGATAATGCACCATCATGCATTTT
Found at i:628331 original size:17 final size:17
Alignment explanation
Indices: 628309--628349 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
628299 TATTCAATTT
628309 AATCCTTCAAATTTGTA
1 AATCCTTCAAATTTGTA
628326 AATCCTTCAAATTTGTA
1 AATCCTTCAAATTTGTA
628343 AATCCTT
1 AATCCTT
628350 TCAATATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (17 bp):
AATCCTTCAAATTTGTA
Found at i:641710 original size:304 final size:304
Alignment explanation
Indices: 641153--641928 Score: 891
Period size: 304 Copynumber: 2.6 Consensus size: 304
641143 TGGTAGCACG
* * ** *
641153 TTTTTTAATTTTTAACAATTTACGTTATATGAATGAAACCGTTTATAATATGCAAAACTAAAACA
1 TTTTTTAATTATCAACCGTTTACGTTATATGAATGAAACCGTTTATATTATGCAAAACTAAAACA
** * * * *
641218 AAACAAGTTATGTAGCATAACATTGTAGGTAGCAACTTTTCTACTTGTCAATCATTTAGATTATA
66 AAACAAGTTATGTAATATAACATTGTAGGTAGCCACTTTTTTAATTGTCAATCGTTTAGATTATA
* *
641283 TGTTTGAAACCGTTTATAATATGAAAAAGTAAGACAAAAAAGTTTATAAGTTTAACATTCTAGGT
131 TGTTTGAAACTGTTTATATTATGAAAAAGTAAGACAAAAAAGTTTATAAGTTTAACATTCTAGGT
*** * * *
641348 CGTGCCTTTTTTTAATCTTCAATTGTTTAGTTTATATGTTTGAAACCGCTTTTATTATGTAAAAG
196 CGTGCCTTTTTTTAATCTTCAACCATTTAGTTTATATGTTGGAAACCGATTTTATTATGCAAAAG
* *
641413 TAAGATAAAAATAGGTTTATAAGTATAATATTATAGGCAGCGC-C
261 TAAGA-AAAAATAGGTTTATAAGTATAACATTATAGGCAACGCTC
* * * * * *
641457 TTTTTTAATTGTCGACCTTTTACGTTATATGCATGAAACCGTTTATGTTATGCAAAACTAAAATA
1 TTTTTTAATTATCAACCGTTTACGTTATATGAATGAAACCGTTTATATTATGCAAAACTAAAACA
* * * *
641522 AAACTAGTTATGTAATACAACATTGTAGGTAGCCCCTTTTTTAATTATCAATCGTTTAGATTATA
66 AAACAAGTTATGTAATATAACATTGTAGGTAGCCACTTTTTTAATTGTCAATCGTTTAGATTATA
* **
641587 TGTTTGAAACTGTTTATATTATGAAAAAGTAAGACAAAAAAGGTTTATAATTTTATTATTCTAGG
131 TGTTTGAAACTGTTTATATTATGAAAAAGTAAGACAAAAAA-GTTTATAAGTTTAACATTCTAGG
* * * *
641652 T-TTCGCCTTTTTTTATTGTT-AACCATTTA-TGTTATATGTTGGAAGCC-ATTTCTATTATGCA
195 TCGT-GCCTTTTTTTAATCTTCAACCATTTAGT-TTATATGTTGGAAACCGATTT-TATTATGCA
* * * ** *
641713 AAAGTAAGACAAAATAGGTTTATAATTATAACATTATAGGTAATTCTT
257 AAAGTAAGAAAAAATAGGTTTATAAGTATAACATTATAGGCAACGCTC
** * * * * *
641761 TTTTTTAATTATCAACCGTTTACGTTATATGTTTGAAAACTTTTATATTATACAAAAGTAAGACA
1 TTTTTTAATTATCAACCGTTTACGTTATATGAATGAAACCGTTTATATTATGCAAAACTAAAACA
* * * * * *
641826 AAACAAGTT-TTTAAGTATAACATTATAGGTAG-CACTTTTTCAATTGTCAACCGCTTACATTAT
66 AAACAAGTTATGTAA-TATAACATTGTAGGTAGCCACTTTTTTAATTGTCAATCGTTTAGATTAT
* * * * *
641889 ATGTATGAAACTGTTTATGTTATGCAAAACTAAAACAAAA
130 ATGTTTGAAACTGTTTATATTATGAAAAAGTAAGACAAAA
641929 TATGTTATCT
Statistics
Matches: 397, Mismatches: 69, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
303 98 0.25
304 264 0.66
305 35 0.09
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (304 bp):
TTTTTTAATTATCAACCGTTTACGTTATATGAATGAAACCGTTTATATTATGCAAAACTAAAACA
AAACAAGTTATGTAATATAACATTGTAGGTAGCCACTTTTTTAATTGTCAATCGTTTAGATTATA
TGTTTGAAACTGTTTATATTATGAAAAAGTAAGACAAAAAAGTTTATAAGTTTAACATTCTAGGT
CGTGCCTTTTTTTAATCTTCAACCATTTAGTTTATATGTTGGAAACCGATTTTATTATGCAAAAG
TAAGAAAAAATAGGTTTATAAGTATAACATTATAGGCAACGCTC
Found at i:641993 original size:202 final size:203
Alignment explanation
Indices: 641234--642131 Score: 739
Period size: 203 Copynumber: 4.4 Consensus size: 203
641224 GTTATGTAGC
* * * * *
641234 ATAACATTGTAGG-TAGCAACTTTTCTACTTGTCAATCATTTA-GATTATATGTTTGAAACCGTT
1 ATAACATTATAGGTTAGC-ACTTTTTTAATTGTCAACCATTTACG-TTATATGTATGAAACCGTT
** * * * * * * * *
641297 TATAATATGAAAAAGTAAGACAAAAAAGTT-TATAAGTTTAACATT-CTAGGTCGTGCCT-TTTT
64 TATGTTATGCAAAACTAAAACAAAATAGTTATATAA-TATAACATTGATAGGT--AGCATCTTTT
** ** * ** * *
641359 TTAATCT-TCAATTGTTTAGTTTATATGTTTGAAACCGCTTT-TATTATGTAAAAGTAAGATAAA
126 TTAAT-TATCAACCGTTTAAATTATATGTTTGAAAACTATTTATATTATGAAAAAGTAAGACAAA
641422 AATAGGTTTATAAGT
190 AA-AGGTTTATAAGT
* * * * * *
641437 ATAATATTATAGG-CAGCGCCTTTTTTAATTGTCGACCTTTTACGTTATATGCATGAAACCGTTT
1 ATAACATTATAGGTTAGC-ACTTTTTTAATTGTCAACCATTTACGTTATATGTATGAAACCGTTT
* * * **
641501 ATGTTATGCAAAACTAAAATAAAACTAGTTATGTAATACAACATTG-TAGGTAGCCCCTTTTTTA
65 ATGTTATGCAAAACTAAAACAAAA-TAGTTATATAATATAACATTGATAGGTAGCATCTTTTTTA
* * *
641565 ATTATCAATCGTTTAGATTATATGTTTG-AAACTGTTTATATTATGAAAAAGTAAGACAAAAAAG
129 ATTATCAACCGTTTAAATTATATGTTTGAAAACTATTTATATTATGAAAAAGTAAGACAAAAAAG
*
641629 GTTTATAATT
194 GTTTATAAGT
* ** * * * * * * *
641639 TTATTATTCTAGGTTTCGC-CTTTTTTTATTGTTAACCATTTATGTTATATGT-TGGAAGCCATT
1 ATAACATTATAGG-TTAGCACTTTTTTAATTGTCAACCATTTACGTTATATGTAT-GAAACCGTT
* * * *
641702 TCTATTATGCAAAAGTAAGACAAAATAGGTT-TATAATTATAACATT-ATAGGTA--ATTCTTTT
64 TATGTTATGCAAAACTAAAACAAAATA-GTTATATAA-TATAACATTGATAGGTAGCA-TC--TT
**
641763 TTTTAATTATCAACCGTTTACGTTATATGTTTGAAAACT-TTTATATTAT-ACAAAAGTAAGACA
124 TTTTAATTATCAACCGTTTAAATTATATGTTTGAAAACTATTTATATTATGA-AAAAGTAAGACA
*
641826 AAACAA-GTTTTTAAGT
188 AAA-AAGGTTTATAAGT
* ** * *
641842 ATAACATTATAGG-TAGCACTTTTTCAATTGTCAACCGCTTACATTATATGTATGAAACTGTTTA
1 ATAACATTATAGGTTAGCACTTTTTTAATTGTCAACCATTTACGTTATATGTATGAAACCGTTTA
* *
641906 TGTTATGCAAAACTAAAACAAAATATGTTATCTAACATAACATTGAT-GGTAGCATCTTTTTTCA
66 TGTTATGCAAAACTAAAACAAAATA-GTTATATAATATAACATTGATAGGTAGCATCTTTTTT-A
* *
641970 ATTGTCAACCGTTTAAATTATATGTTTGAAAA-TATTTATATTATGAAAAAGTAAGATAAAAAA-
129 ATTATCAACCGTTTAAATTATATGTTTGAAAACTATTTATATTATGAAAAAGTAAGACAAAAAAG
642033 GTTTATAAGT
194 GTTTATAAGT
* * * * * **
642043 TTAACAGTT-TAGGTTGAGTA-TTTTTTAAATTGTCAATCATTTAGGTTATATGTTTGAAATTGT
1 ATAACA-TTATAGGTT-AGCACTTTTTT-AATTGTCAACCATTTACGTTATATGTATGAAACCGT
* * *
642106 TTTTGTTATGCAAAAATAAGACAAAA
63 TTATGTTATGCAAAACTAAAACAAAA
642132 AACAAGTTTG
Statistics
Matches: 564, Mismatches: 99, Indels: 64
0.78 0.14 0.09
Matches are distributed among these distances:
201 38 0.07
202 235 0.42
203 260 0.46
204 27 0.05
205 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (203 bp):
ATAACATTATAGGTTAGCACTTTTTTAATTGTCAACCATTTACGTTATATGTATGAAACCGTTTA
TGTTATGCAAAACTAAAACAAAATAGTTATATAATATAACATTGATAGGTAGCATCTTTTTTAAT
TATCAACCGTTTAAATTATATGTTTGAAAACTATTTATATTATGAAAAAGTAAGACAAAAAAGGT
TTATAAGT
Found at i:642000 original size:102 final size:101
Alignment explanation
Indices: 641144--642131 Score: 667
Period size: 101 Copynumber: 9.8 Consensus size: 101
641134 AGTCTTTTTT
* * * ** * ** * *
641144 GGTAGCACGTTTTTTAATTTTTAACAATTTACGTTATATGAATGAAACCGTTTATAATATGCAAA
1 GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
* * * * * ** *
641209 ACTAAAACAAAACAAG-TTATGTAGCATAACATTGTA
66 AGTAAGACAAAATAGGTTTAT-AATTATAACATTATA
* * * * * * * * *
641245 GGTAGCAACTTTTCTACTTGTCAATCATTTAGATTATATGTTTGAAACCGTTTATAATATGAAAA
1 GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
* *
641310 AGTAAGACAAAA-AAGTTTATAAGTT-TAACATTCTA
66 AGTAAGACAAAATAGGTTTATAA-TTATAACATTATA
* ** ** ** * *
641345 GGTCGTGCCTTTTTTTAATCT-TCAATTGTTTAGTTTATATGTTTGAAACCGCTTT-TATTATGT
1 GGTAGCACC-TTTTTTAAT-TGTCAACCGTTTACATTATATGTTTGAAACTG-TTTATATTATGC
* * *
641408 AAAAGTAAGATAAAAATAGGTTTATAAGTATAATATTATA
63 AAAAGTAAGA-CAAAATAGGTTTATAATTATAACATTATA
* * * * * ** * *
641448 GGCAGCGCCTTTTTTAATTGTCGACCTTTTACGTTATATGCATGAAACCGTTTATGTTATGCAAA
1 GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
* * * * * *
641513 ACTAAAATAAAACTA-GTTATGTAA-TACAACATTGTA
66 AGTAAGACAAAA-TAGGTT-TATAATTATAACATTATA
* * * * *
641549 GGTAGCCCCTTTTTTAATTATCAATCGTTTAGATTATATGTTTGAAACTGTTTATATTATGAAAA
1 GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
* * ** *
641614 AGTAAGACAAAAAAGGTTTATAATTTTATTATTCTA
66 AGTAAGACAAAATAGGTTTATAATTATAACATTATA
** * * * * ** * * ** *
641650 GGTTTCGCCTTTTTTTATTGTTAACCATTTATGTTATATGTTGGAAGCCATTTCTATTATGCAAA
1 GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
641715 AGTAAGACAAAATAGGTTTATAATTATAACATTATA
66 AGTAAGACAAAATAGGTTTATAATTATAACATTATA
*** * * * *
641751 GGTAATTCTTTTTTTTAATTATCAACCGTTTACGTTATATGTTTGAAAACT-TTTATATTATACA
1 GGTAGCAC-CTTTTTTAATTGTCAACCGTTTACATTATATGTTTG-AAACTGTTTATATTATGCA
* * * *
641815 AAAGTAAGACAAAACAAGTTTTTAAGTATAACATTATA
64 AAAGTAAGACAAAATAGGTTTATAATTATAACATTATA
* * * *
641853 GGTAGCA-CTTTTTCAATTGTCAACCGCTTACATTATATGTATGAAACTGTTTATGTTATGCAAA
1 GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
* * * * *
641917 ACTAAAACAAAATATGTTATCTAA-CATAACATTGAT-
66 AGTAAGACAAAATAGGTT-TATAATTATAACATT-ATA
* * * * *
641953 GGTAGCATCTTTTTTCAATTGTCAACCGTTTAAATTATATGTTTGAAAATATTTATATTATGAAA
1 GGTAGCACCTTTTTT-AATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAA
* *
642018 AAGTAAGATAAAA-AAGTTTATAAGTT-TAACAGTT-TA
65 AAGTAAGACAAAATAGGTTTATAA-TTATAACA-TTATA
* * * ** * * *
642054 GGTTGAGTA--TTTTTTAAATTGTCAATCATTTAGGTTATATGTTTGAAATTGTTTTTGTTATGC
1 GG-T-AGCACCTTTTTT-AATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGC
*
642117 AAAAATAAGACAAAA
63 AAAAGTAAGACAAAA
642132 AACAAGTTTG
Statistics
Matches: 698, Mismatches: 162, Indels: 54
0.76 0.18 0.06
Matches are distributed among these distances:
99 5 0.01
100 100 0.14
101 371 0.53
102 193 0.28
103 29 0.04
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (101 bp):
GGTAGCACCTTTTTTAATTGTCAACCGTTTACATTATATGTTTGAAACTGTTTATATTATGCAAA
AGTAAGACAAAATAGGTTTATAATTATAACATTATA
Found at i:642872 original size:304 final size:299
Alignment explanation
Indices: 642301--643192 Score: 879
Period size: 304 Copynumber: 2.9 Consensus size: 299
642291 TCTAGGTAGT
* * ** * * *
642301 GCCTTTTTCAATTGTCAATCATTTATGTTATATGTATGAAATTGTTTATGTTATGCAAAACTAAA
1 GCCTTTTTTAATTGTCAATCATTTA-GTTATATGTTTGAAA-CATTTATATTATGCAAAAGTAAG
* * * * *
642366 ACAAAGCAGGTTATGTAA-TATAACATTGTAGGTAGA-GCCTTTTTTAATTG-TCACCGGTTTAG
64 ACAAAACAAGTT-T-TAAGTATAACATTGTAGGTA-ACGTCTTTTTTAATTGTTAATC-GTTTAG
* * *** *
642428 ATTATATGTTTGAAACCGTTTATATTATGAAAAAGTAAGACAAGAAAGGCTTATAAGTTTAAAAT
125 ATTATATGTTTGAAACCGTTTATATTATGAAAAAGTAAGACAAAAAAGGTTTATAAACATAACAT
* * * * * * *
642493 TCTATA-TTGCACCTTTTTTTTAATTGTCAACTATTTAGGTTATATGTTGGAAACCATTT-TTTT
190 TATA-AGTTGCACC--TTTTTTAATTGTTAACTGTTTACGTTATATATTTGAAACC-TTTATATT
* *
642556 ATGCACAAGTAAGACAAAACAAGTTTATAAGCATAACATTA-TAGGTAAC
251 ATGCAAAAGTAAGACAAAACAAGTTTATAAGCATAACA-TAGTAAGTAAC
* *
642605 GCCTTTTTTAATTGTCAATCATTTACGTTATATGTTTGAAACCTTTAATATTATCCAAAAGTAAG
1 GCCTTTTTTAATTGTCAATCATTTA-GTTATATGTTTGAAACATTT-ATATTATGCAAAAGTAAG
* *
642670 ACAAAACATGTTTATAAGTATAACATTGTAGGTAACGTCTTTTTTAATTGTTAATCGTTTCGATT
64 ACAAAACAAGTTT-TAAGTATAACATTGTAGGTAACGTCTTTTTTAATTGTTAATCGTTTAGATT
* *
642735 ATATGTTTGAATCCATTTATATTATGAAAAAGTAAGACAAAAAAGGTTTATAAACATAACATTAT
128 ATATGTTTGAAACCGTTTATATTATGAAAAAGTAAGACAAAAAAGGTTTATAAACATAACATTAT
** *
642800 AAGTTGTGCCTTTTTTAATTTGTTAATTGTTTACGTTATATATTTGAAACCTTTAATATTATTG-
193 AAGTTGCACCTTTTTTAA-TTGTTAACTGTTTACGTTATATATTTGAAACCTTT-ATATTA-TGC
** ** *
642864 AAAAGTAAGA-AAGAA-GGGTTTATAAGTTTAACATAGTAAGTAGC
255 AAAAGTAAGACAA-AACAAGTTTATAAGCATAACATAGTAAGTAAC
** * *
642908 ATCTTTTTTAATTGTCAATCGTTTAGATTATATGTTTGAAGACATTTATATTATGAAAAAGTAAG
1 GCCTTTTTTAATTGTCAATCATTTAG-TTATATGTTTGAA-ACATTTATATTATGCAAAAGTAAG
* * * * * *
642973 ATAAAA-AAGATTTTAAGTTTAACATTATAGGTTACGCCTTTTTTTTAATTGTTAATCGTTTAGG
64 ACAAAACAAG-TTTTAAGTATAACATTGTAGGTAACG--TCTTTTTTAATTGTTAATCGTTTAGA
* * * * * * *
643037 TTATATATTGGAAACCGTTTTTATCATGCAAAAGTTAGACAAAACAGGTTTAT-AACTATAACAT
126 TTATATGTTTGAAACCGTTTATATTATGAAAAAGTAAGACAAAAAAGGTTTATAAAC-ATAACAT
* * * * * *
643101 TATAGGTAGCACCTTTTTAAATTGTTAACCGTGTATGTTATATATTTGAAACCTTTTATATTATG
190 TATAAGTTGCACCTTTTTTAATTGTTAACTGTTTACGTTATATATTTGAAACC-TTTATATTATG
* * *
643166 CGAAAGCAAGACAAAACATGTTTATAA
254 CAAAAGTAAGACAAAACAAGTTTATAA
643193 CAAAGAAGGA
Statistics
Matches: 490, Mismatches: 77, Indels: 42
0.80 0.13 0.07
Matches are distributed among these distances:
302 38 0.08
303 163 0.33
304 284 0.58
305 5 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (299 bp):
GCCTTTTTTAATTGTCAATCATTTAGTTATATGTTTGAAACATTTATATTATGCAAAAGTAAGAC
AAAACAAGTTTTAAGTATAACATTGTAGGTAACGTCTTTTTTAATTGTTAATCGTTTAGATTATA
TGTTTGAAACCGTTTATATTATGAAAAAGTAAGACAAAAAAGGTTTATAAACATAACATTATAAG
TTGCACCTTTTTTAATTGTTAACTGTTTACGTTATATATTTGAAACCTTTATATTATGCAAAAGT
AAGACAAAACAAGTTTATAAGCATAACATAGTAAGTAAC
Found at i:642915 original size:202 final size:202
Alignment explanation
Indices: 642303--643192 Score: 765
Period size: 203 Copynumber: 4.4 Consensus size: 202
642293 TAGGTAGTGC
* * * *** * * * *
642303 CTTTTTCAATTGTCAATCATTTATG-TTATATGTATGAAATTGTTTATGTTATGCAAAACTAAAA
1 CTTTTTTAATTGTCAATCGTTTA-GATTATATGTTTGAAACCATTTATATTATGAAAAAGTAAGA
** * * * * * *
642367 CAAAGCAGGTTATGTAA-TATAACATTGTAGG-TAGAGCCTTTTTTAATTG-TCACCGGTTTA-G
65 CAAAAAAGGTT-TATAAGCATAACATTATAGGTTA-CGCCTTTTTTAATTGTTAATC-GTTTACG
* * * *
642428 ATTATATGTTTGAAACCGTTTATATTATGAAAAAGTAAGACAAGAA-AGGCTTATAAGTTTAAAA
127 -TTATATATTTGAAACCGTTTATATTATGAAAAAGTAAGACAA-AACAGGTTTATAAGTATAACA
** *
642492 TTCTATA-TTGCACCT
190 TAGTA-AGTAGCA--T
* * * * * * *
642507 TTTTTTTAATTGTCAA-CTATTTAGGTTATATGTTGGAAACCATTT-TTTTATGCACAAGTAAGA
1 CTTTTTTAATTGTCAATC-GTTTAGATTATATGTTTGAAACCATTTATATTATGAAAAAGTAAGA
* * *
642570 CAAAACAA-GTTTATAAGCATAACATTATAGGTAACGCCTTTTTTAATTGTCAATCATTTACGTT
65 CAAAA-AAGGTTTATAAGCATAACATTATAGGTTACGCCTTTTTTAATTGTTAATCGTTTACGTT
* ** * *
642634 ATATGTTTGAAACC-TTTAATATTATCCAAAAGTAAGACAAAACATGTTTATAAGTATAACATTG
129 ATATATTTGAAACCGTTT-ATATTATGAAAAAGTAAGACAAAACAGGTTTATAAGTATAACATAG
* * *
642698 TAGGTAACGT
193 TAAGTAGCAT
* * *
642708 CTTTTTTAATTGTTAATCGTTTCGATTATATGTTTGAATCCATTTATATTATGAAAAAGTAAGAC
1 CTTTTTTAATTGTCAATCGTTTAGATTATATGTTTGAAACCATTTATATTATGAAAAAGTAAGAC
* * ** *
642773 AAAAAAGGTTTATAAACATAACATTATAAGTTGTGCCTTTTTTAATTTGTTAATTGTTTACGTTA
66 AAAAAAGGTTTATAAGCATAACATTATAGGTTACGCCTTTTTTAA-TTGTTAATCGTTTACGTTA
* *
642838 TATATTTGAAACC-TTTAATATTATTG-AAAAGTAAGA-AAGAA-GGGTTTATAAGTTTAACATA
130 TATATTTGAAACCGTTT-ATATTA-TGAAAAAGTAAGACAA-AACAGGTTTATAAGTATAACATA
642899 GTAAGTAGCAT
192 GTAAGTAGCAT
642910 CTTTTTTAATTGTCAATCGTTTAGATTATATGTTTGAAGA-CATTTATATTATGAAAAAGTAAGA
1 CTTTTTTAATTGTCAATCGTTTAGATTATATGTTTGAA-ACCATTTATATTATGAAAAAGTAAGA
* * ** *
642974 TAAAAAAGATTT-TAAGTTTAACATTATAGGTTACGCCTTTTTTTTAATTGTTAATCGTTTAGGT
65 CAAAAAAGGTTTATAAGCATAACATTATAGGTTACGCC--TTTTTTAATTGTTAATCGTTTACGT
* * * * * *
643038 TATATATTGGAAACCGTTTTTATCATGCAAAAGTTAGACAAAACAGGTTTATAACTATAACATTA
128 TATATATTTGAAACCGTTTATATTATGAAAAAGTAAGACAAAACAGGTTTATAAGTATAACA-TA
* *
643103 -TAGGTAGCAC
192 GTAAGTAGCAT
* * * * * * ** *
643113 CTTTTTAAATTGTTAACCGTGTATG-TTATATATTTGAAACCTTTTATATTATGCGAAAGCAAGA
1 CTTTTTTAATTGTCAATCGTTTA-GATTATATGTTTGAAACCATTTATATTATGAAAAAGTAAGA
* *
643177 CAAAACATGTTTATAA
65 CAAAAAAGGTTTATAA
643193 CAAAGAAGGA
Statistics
Matches: 564, Mismatches: 95, Indels: 54
0.79 0.13 0.08
Matches are distributed among these distances:
201 60 0.11
202 204 0.36
203 254 0.45
204 46 0.08
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (202 bp):
CTTTTTTAATTGTCAATCGTTTAGATTATATGTTTGAAACCATTTATATTATGAAAAAGTAAGAC
AAAAAAGGTTTATAAGCATAACATTATAGGTTACGCCTTTTTTAATTGTTAATCGTTTACGTTAT
ATATTTGAAACCGTTTATATTATGAAAAAGTAAGACAAAACAGGTTTATAAGTATAACATAGTAA
GTAGCAT
Found at i:643193 original size:101 final size:101
Alignment explanation
Indices: 642293--643193 Score: 735
Period size: 101 Copynumber: 8.9 Consensus size: 101
642283 ATCGTATGTC
* * * * * * * *
642293 TAGGTAGTGCCTTTTTCAATTGTCAATCATTTATGTTATATGTATGAAA-TTGTTTATGTTATGC
1 TAGGTAGCGCCTTTTTTAATTGTTAATCGTTTACGTTATATGTTTGAAACCT-TTTATATTATGC
* * * * *
642357 AAAACTAAAACAAAGCAGGTTATGTAA-TATAACATTG
65 AAAAGTAAGACAAAACAGGTT-TATAACTATAACATTA
* * * *
642394 TAGGTAGAGCCTTTTTTAATTG-TCACCGGTTTA-GATTATATGTTTGAAACCGTTTATATTATG
1 TAGGTAGCGCCTTTTTTAATTGTTAATC-GTTTACG-TTATATGTTTGAAACCTTTTATATTATG
* * * * * *
642457 AAAAAGTAAGACAAGAA-AGGCTTATAAGTTTAAAATTC
64 CAAAAGTAAGACAA-AACAGGTTTATAACTATAACATTA
** * * * * * *
642495 TATATTGCACCTTTTTTTTAATTGTCAA-CTATTTAGGTTATATGTTGGAAACCATTTT-T-TTA
1 TAGGTAGCGCC--TTTTTTAATTGTTAATC-GTTTACGTTATATGTTTGAAACC-TTTTATATTA
* *
642557 TGCACAAGTAAGACAAAACAAGTTTATAAGC-ATAACATTA
62 TGCAAAAGTAAGACAAAACAGGTTTATAA-CTATAACATTA
* * * * *
642597 TAGGTAACGCCTTTTTTAATTGTCAATCATTTACGTTATATGTTTGAAACCTTTAATATTATCCA
1 TAGGTAGCGCCTTTTTTAATTGTTAATCGTTTACGTTATATGTTTGAAACCTTTTATATTATGCA
* * *
642662 AAAGTAAGACAAAACATGTTTATAAGTATAACATTG
66 AAAGTAAGACAAAACAGGTTTATAACTATAACATTA
* * * * *
642698 TAGGTAACGTCTTTTTTAATTGTTAATCGTTT-CGATTATATGTTTGAATCCATTTATATTATGA
1 TAGGTAGCGCCTTTTTTAATTGTTAATCGTTTACG-TTATATGTTTGAAACCTTTTATATTATGC
*
642762 AAAAGTAAGACAAAAAAGGTTTATAAAC-ATAACATTA
65 AAAAGTAAGACAAAACAGGTTTAT-AACTATAACATTA
* * * * * *
642799 TAAGTTGTGCCTTTTTTAATTTGTTAATTGTTTACGTTATATATTTGAAACCTTTAATATTATTG
1 TAGGTAGCGCCTTTTTTAA-TTGTTAATCGTTTACGTTATATGTTTGAAACCTTTTATATTA-TG
* * *
642864 -AAAAGTAAGA-AAGAA-GGGTTTATAAGTTTAACA-TA
64 CAAAAGTAAGACAA-AACAGGTTTATAACTATAACATTA
* ** * *
642899 GTAAGTAGCATCTTTTTTAATTGTCAATCGTTTA-GATTATATGTTTGAAGA-CATTTATATTAT
1 -TAGGTAGCGCCTTTTTTAATTGTTAATCGTTTACG-TTATATGTTTGAA-ACCTTTTATATTAT
* * * * * *
642962 GAAAAAGTAAGATAAAAAAGATTT-TAAGTTTAACATTA
63 GCAAAAGTAAGACAAAACAGGTTTATAACTATAACATTA
* * * *
643000 TAGGTTA-CGCCTTTTTTTTAATTGTTAATCGTTTAGGTTATATATTGGAAACCGTTTT-TATCA
1 TAGG-TAGCGCC--TTTTTTAATTGTTAATCGTTTACGTTATATGTTTGAAACC-TTTTATATTA
*
643063 TGCAAAAGTTAGACAAAACAGGTTTATAACTATAACATTA
62 TGCAAAAGTAAGACAAAACAGGTTTATAACTATAACATTA
* * * * * * *
643103 TAGGTAGCACCTTTTTAAATTGTTAACCGTGTATGTTATATATTTGAAACCTTTTATATTATGCG
1 TAGGTAGCGCCTTTTTTAATTGTTAATCGTTTACGTTATATGTTTGAAACCTTTTATATTATGCA
* *
643168 AAAGCAAGACAAAACATGTTTATAAC
66 AAAGTAAGACAAAACAGGTTTATAAC
643194 AAAGAAGGAG
Statistics
Matches: 648, Mismatches: 113, Indels: 78
0.77 0.13 0.09
Matches are distributed among these distances:
99 6 0.01
100 115 0.18
101 318 0.49
102 145 0.22
103 59 0.09
104 5 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (101 bp):
TAGGTAGCGCCTTTTTTAATTGTTAATCGTTTACGTTATATGTTTGAAACCTTTTATATTATGCA
AAAGTAAGACAAAACAGGTTTATAACTATAACATTA
Found at i:644858 original size:45 final size:45
Alignment explanation
Indices: 644768--644877 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 45
644758 ATGTTGGATT
* * * *
644768 CCCAACTTATTTC-TCACACTTTGTTGGAGCTATTACCAAAATTA
1 CCCAACTTATTTCTTAAAACTATGTTGAAGCTATTACCAAAATTA
* ***
644812 CCCAACTTATTTCTTAAAACTATGTTGAAGTTATTACCAGTGTTA
1 CCCAACTTATTTCTTAAAACTATGTTGAAGCTATTACCAAAATTA
644857 CCCAACTTATTTCTTAAAACT
1 CCCAACTTATTTCTTAAAACT
644878 CTCTCTTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 13 0.23
45 44 0.77
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CCCAACTTATTTCTTAAAACTATGTTGAAGCTATTACCAAAATTA
Found at i:646656 original size:8 final size:8
Alignment explanation
Indices: 646643--646676 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
646633 AAAGTTATGA
646643 TTTAAAAT
1 TTTAAAAT
646651 TTTAAAAT
1 TTTAAAAT
646659 TTTAAAAT
1 TTTAAAAT
646667 TTTAAAAT
1 TTTAAAAT
646675 TT
1 TT
646677 AAGGGTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:653528 original size:23 final size:23
Alignment explanation
Indices: 653498--653549 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
653488 CTAGCTTCGG
653498 TGACCAGTCCTTTCGACTTGGGT
1 TGACCAGTCCTTTCGACTTGGGT
653521 TGACCAGTCCTTTCGACTTGGGT
1 TGACCAGTCCTTTCGACTTGGGT
653544 TGACCA
1 TGACCA
653550 ATTTCTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.27, G:0.25, T:0.33
Consensus pattern (23 bp):
TGACCAGTCCTTTCGACTTGGGT
Found at i:679462 original size:16 final size:16
Alignment explanation
Indices: 679441--679472 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
679431 CGCAAATAGA
679441 ATACAACTTAATGGAT
1 ATACAACTTAATGGAT
679457 ATACAACTTAATGGAT
1 ATACAACTTAATGGAT
679473 CTTATCTCCC
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:0.12, G:0.12, T:0.31
Consensus pattern (16 bp):
ATACAACTTAATGGAT
Found at i:682464 original size:25 final size:25
Alignment explanation
Indices: 682399--682475 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
682389 TTTAATTAAG
* * *
682399 TAAAATATTAATAAATTTAAATATT
1 TAAAATATTAATTATTTTTAATATT
*
682424 TAAAATTATTTA-TATTTTTAATATT
1 TAAAA-TATTAATTATTTTTAATATT
* *
682449 TAATATATTAATTATTTGTAAT-TT
1 TAAAATATTAATTATTTTTAATATT
682473 TAA
1 TAA
682476 GATGTAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
24 10 0.23
25 28 0.65
26 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAAATATTAATTATTTTTAATATT
Found at i:682516 original size:16 final size:17
Alignment explanation
Indices: 682478--682523 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
682468 AATTTTAAGA
682478 TGTAAAAATAATATTAT
1 TGTAAAAATAATATTAT
682495 TGTAAAAAT-ATAATTAT
1 TGTAAAAATAAT-ATTAT
682512 T-T-AAAATAATAT
1 TGTAAAAATAATAT
682524 ATAACTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.26
16 5 0.19
17 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
TGTAAAAATAATATTAT
Found at i:682635 original size:22 final size:21
Alignment explanation
Indices: 682610--682650 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
682600 TTTTTATATT
* *
682610 ATATTATATTTTATATAAATAA
1 ATATGATA-TTTATAAAAATAA
682632 ATATGATATTTATAAAAAT
1 ATATGATATTTATAAAAAT
682651 TGTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATGATATTTATAAAAATAA
Found at i:684876 original size:18 final size:18
Alignment explanation
Indices: 684853--684891 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
684843 ACCGGTTATA
684853 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
684871 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
684889 ACC
1 ACC
684892 GTTGACCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:689161 original size:23 final size:23
Alignment explanation
Indices: 689135--689183 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
689125 GAACGACCAT
*
689135 ATAGGTTTGCACCGAAGTGCCAC
1 ATAGGTTTGCACCGAAATGCCAC
689158 ATAGGTTTGCACCGAAATGCCAC
1 ATAGGTTTGCACCGAAATGCCAC
689181 ATA
1 ATA
689184 TTTGTCCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
ATAGGTTTGCACCGAAATGCCAC
Found at i:696376 original size:407 final size:407
Alignment explanation
Indices: 695621--696403 Score: 1485
Period size: 407 Copynumber: 1.9 Consensus size: 407
695611 TCAGAGCATT
695621 TCAAATTAAAAGTATAATACACGCCAACAGTTTACAAAATTAATAAAAACCTACATTTAATTTGT
1 TCAAATTAAAAGTATAATACACGCCAACAGTTTACAAAATTAATAAAAACCTACATTTAATTTGT
695686 CCTGATATGATCTTCAAGTGGTATGTTATCCTCCACAACTCAGTCTTCAGCTTTCTTGAAACCTA
66 CCTGATATGATCTTCAAGTGGTATGTTATCCTCCACAACTCAGTCTTCAGCTTTCTTGAAACCTA
*
695751 CGCGTGAGGAAATCACACACTAAGTCGATGACTTAGTGAGGCAAATACTAATAGTACTAACTTAG
131 CGCGTGAGGAAATCAAACACTAAGTCGATGACTTAGTGAGGCAAATACTAATAGTACTAACTTAG
695816 TAAACAAAATCTTATTTGTTTTTATCAAAATGTTTTACAAATAACTCTAATTATTTTCCATATCA
196 TAAACAAAATCTTATTTGTTTTTATCAAAATGTTTTACAAATAACTCTAATTATTTTCCATATCA
695881 AAAAGTATACTTATGAATAGTATTAACTTTGTATATCTTTGCTCAAAATACCCAAAGTATACTAC
261 AAAAGTATACTTATGAATAGTATTAACTTTGTATATCTTTGCTCAAAATACCCAAAGTATACTAC
*
695946 TAAGAATGCTATGTATTTGAGTACATTGAGGTTGTGCACTAATGATGTAACAGTTTACTTTGTAT
326 TAAGAATGCTATATATTTGAGTACATTGAGGTTGTGCACTAATGATGTAACAGTTTACTTTGTAT
696011 ATCTTTGCTCCAAATAC
391 ATCTTTGCTCCAAATAC
* * *
696028 TCAAATTAAAAGTATAATGCATGCCAACAGTTTACAAAATTAATAAAAACTTACATTTAATTTGT
1 TCAAATTAAAAGTATAATACACGCCAACAGTTTACAAAATTAATAAAAACCTACATTTAATTTGT
696093 CCTGATATGATCTTCAAGTGGTATGTTATCCTCCACAACTCAGTCTTCAGCTTTCTTGAAACCTA
66 CCTGATATGATCTTCAAGTGGTATGTTATCCTCCACAACTCAGTCTTCAGCTTTCTTGAAACCTA
696158 CGCGTGAGGAAATCAAACACTAAGTCGATGACTTAGTGAGGCAAATACTAATAGTACTAACTTAG
131 CGCGTGAGGAAATCAAACACTAAGTCGATGACTTAGTGAGGCAAATACTAATAGTACTAACTTAG
*
696223 TAAACAAAATTTTATTTGTTTTTATCAAAATGTTTTACAAATAACTCTAATTATTTTCCATATCA
196 TAAACAAAATCTTATTTGTTTTTATCAAAATGTTTTACAAATAACTCTAATTATTTTCCATATCA
* *
696288 AAAAGTATACTTATGAATAGTATTAACTTTGTATATCTTTGCTCCAAATACCCAAGGTATACTAC
261 AAAAGTATACTTATGAATAGTATTAACTTTGTATATCTTTGCTCAAAATACCCAAAGTATACTAC
*
696353 TGAGAATGCTATATATTTGAGTACATTGAGGTTGTGCACTAATGATGTAAC
326 TAAGAATGCTATATATTTGAGTACATTGAGGTTGTGCACTAATGATGTAAC
696404 CACATCTCGT
Statistics
Matches: 367, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
407 367 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (407 bp):
TCAAATTAAAAGTATAATACACGCCAACAGTTTACAAAATTAATAAAAACCTACATTTAATTTGT
CCTGATATGATCTTCAAGTGGTATGTTATCCTCCACAACTCAGTCTTCAGCTTTCTTGAAACCTA
CGCGTGAGGAAATCAAACACTAAGTCGATGACTTAGTGAGGCAAATACTAATAGTACTAACTTAG
TAAACAAAATCTTATTTGTTTTTATCAAAATGTTTTACAAATAACTCTAATTATTTTCCATATCA
AAAAGTATACTTATGAATAGTATTAACTTTGTATATCTTTGCTCAAAATACCCAAAGTATACTAC
TAAGAATGCTATATATTTGAGTACATTGAGGTTGTGCACTAATGATGTAACAGTTTACTTTGTAT
ATCTTTGCTCCAAATAC
Found at i:697129 original size:20 final size:24
Alignment explanation
Indices: 697106--697162 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 24
697096 CATCCCCCTG
697106 GTATCGATACTACC-C-TC-AC-A
1 GTATCGATACTACCTCTTCAACTA
697126 GTATCGATAC--CCTCTTCAACTA
1 GTATCGATACTACCTCTTCAACTA
697148 GTATCGATACTACCT
1 GTATCGATACTACCT
697163 TTAAGAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 12 0.39
21 2 0.06
22 11 0.35
24 3 0.10
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.30
Consensus pattern (24 bp):
GTATCGATACTACCTCTTCAACTA
Found at i:698719 original size:34 final size:30
Alignment explanation
Indices: 698681--698749 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
698671 TTGATATAAC
698681 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
698715 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
698744 AATTTA
1 AATTTA
698750 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:698760 original size:29 final size:30
Alignment explanation
Indices: 698690--698749 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
698680 CAATTTAAGG
698690 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
698721 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
698750 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:698878 original size:20 final size:21
Alignment explanation
Indices: 698826--698866 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
698816 TAAAGGGTGT
698826 CACAGTGCATCCATGCACCTA
1 CACAGTGCATCCATGCACCTA
*
698847 CACTAGTGCATCGATGCACC
1 CAC-AGTGCATCCATGCACC
698867 ATGCAGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.20
Consensus pattern (21 bp):
CACAGTGCATCCATGCACCTA
Found at i:698931 original size:20 final size:20
Alignment explanation
Indices: 698906--698979 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
698896 AATGAAATTA
*
698906 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
698926 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
*
698947 GTGCATCAATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
698967 GTGCATCCATGCA
1 GTGCATCGATGCA
698980 CGAAGGTTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:699059 original size:21 final size:21
Alignment explanation
Indices: 699035--699088 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
699025 GAAGGGGTAT
699035 CGATGCACCATGATTGTGCAC
1 CGATGCACCATGATTGTGCAC
699056 CGATGCACCATGATTGTGCAC
1 CGATGCACCATGATTGTGCAC
699077 CGATGCACCATG
1 CGATGCACCATG
699089 TTATGGGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (21 bp):
CGATGCACCATGATTGTGCAC
Found at i:699151 original size:20 final size:22
Alignment explanation
Indices: 699113--699152 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
699103 TTTTAGTAGA
699113 AAAATCATCCCCAAATGGCTCC
1 AAAATCATCCCCAAATGGCTCC
699135 AAAA-CATCCCC-AATGGCT
1 AAAATCATCCCCAAATGGCT
699153 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATCATCCCCAAATGGCTCC
Found at i:699436 original size:32 final size:33
Alignment explanation
Indices: 699369--699438 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
699359 TTTTGTAAAG
* *
699369 GGGAAAGGTTCTAGTTTATCCCATGTAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCA-GAAAAAACTA
699403 GGGAAAGGTTCTAGTTTAGCCC-GAAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCAGAAAAAACTA
699435 GGGA
1 GGGA
699439 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 13 0.38
34 21 0.62
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGTTTAGCCCAGAAAAAACTA
Found at i:700912 original size:20 final size:19
Alignment explanation
Indices: 700884--700924 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
700874 TGAGACCATG
700884 AATTCCAAATACACAAAATT
1 AATTCCAAA-ACACAAAATT
* *
700904 AATTTCAAAACTCAAAATT
1 AATTCCAAAACACAAAATT
700923 AA
1 AA
700925 AGATAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (19 bp):
AATTCCAAAACACAAAATT
Found at i:700968 original size:19 final size:19
Alignment explanation
Indices: 700932--700968 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
700922 TAAAGATAAT
*
700932 TTGATTTTGAAAGCAAAAG
1 TTGATTTTGAAAACAAAAG
*
700951 TTGATTTTGAAAATAAAA
1 TTGATTTTGAAAACAAAA
700969 AATGAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACAAAAG
Found at i:702456 original size:22 final size:21
Alignment explanation
Indices: 702404--702484 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
702394 TAAAGGGTGT
702404 CACAGTGCATCCATGCATCCCTG
1 CACAGTGCATCCATGCA--CCTG
702427 --CAGTGCATCCATGCACCTG
1 CACAGTGCATCCATGCACCTG
*
702446 CACTAGTGCATCGATGCACCATG
1 CAC-AGTGCATCCATGCACC-TG
*
702469 --CAGTGCATCCGTGCAC
1 CACAGTGCATCCATGCAC
702485 TCAAACACCG
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.08
20 13 0.25
21 17 0.33
22 15 0.29
23 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (21 bp):
CACAGTGCATCCATGCACCTG
Found at i:702533 original size:20 final size:20
Alignment explanation
Indices: 702505--702579 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
702495 AATGCAATTA
*
702505 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* **
702525 GTGCTTCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
702546 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
702566 GTGCATCCATGCAT
1 GTGCATCGATGCAT
702580 GAAGGTTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:702552 original size:41 final size:41
Alignment explanation
Indices: 702505--702584 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
702495 AATGCAATTA
* * *
702505 GTGCATCGATGCATCCTTCTGTGCTTCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
*
702546 GTGCATCGATGCATCCTGCTGTGCATCCATGCATGAAGG
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGG
702585 TTGCAACAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
Found at i:703685 original size:20 final size:20
Alignment explanation
Indices: 703660--703698 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
703650 AAAATATATT
703660 TTCATTTATGTTCGTTTATG
1 TTCATTTATGTTCGTTTATG
*
703680 TTCATTTATTTTCGTTTAT
1 TTCATTTATGTTCGTTTAT
703699 TATGTTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.64
Consensus pattern (20 bp):
TTCATTTATGTTCGTTTATG
Found at i:703699 original size:10 final size:10
Alignment explanation
Indices: 703656--703699 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
703646 AGAAAAAATA
703656 TATTTTCATT
1 TATTTTCATT
* *
703666 TATGTTCGTT
1 TATTTTCATT
*
703676 TATGTTCATT
1 TATTTTCATT
*
703686 TATTTTCGTT
1 TATTTTCATT
703696 TATT
1 TATT
703700 ATGTTCGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.66
Consensus pattern (10 bp):
TATTTTCATT
Found at i:703707 original size:33 final size:35
Alignment explanation
Indices: 703660--703750 Score: 114
Period size: 37 Copynumber: 2.6 Consensus size: 35
703650 AAAATATATT
*
703660 TTCATTTATGTTCGTTTAT-GTTCATTTATTTTCG
1 TTCATTTATGTTCGTTTATCGTTCATTTATGTTCG
*
703694 TTTA-TTATGTTCGTTTACATCCGTTCATTTATGTTCG
1 TTCATTTATGTTCGTTT--AT-CGTTCATTTATGTTCG
*
703731 TTCATTTGTGTTCGTTTATC
1 TTCATTTATGTTCGTTTATC
703751 ATTTAAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
33 12 0.25
34 3 0.06
35 3 0.06
36 2 0.04
37 17 0.35
38 11 0.23
ACGTcount: A:0.14, C:0.14, G:0.13, T:0.58
Consensus pattern (35 bp):
TTCATTTATGTTCGTTTATCGTTCATTTATGTTCG
Found at i:703732 original size:14 final size:14
Alignment explanation
Indices: 703715--703746 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
703705 CGTTTACATC
703715 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
703729 CGTTCATTTGTGTT
1 CGTTCATTTATGTT
703743 CGTT
1 CGTT
703747 TATCATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.19, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:704821 original size:27 final size:28
Alignment explanation
Indices: 704791--704843 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
704781 TTAAATTTAA
704791 ATTAATATGAATC-AATTTA-TCTTAATG
1 ATTAA-ATGAATCGAATTTATTCTTAATG
*
704818 ATTAAATGAATCGTATTTATTCTTAA
1 ATTAAATGAATCGAATTTATTCTTAA
704844 AAATCATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 10 0.43
28 6 0.26
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (28 bp):
ATTAAATGAATCGAATTTATTCTTAATG
Found at i:705085 original size:24 final size:24
Alignment explanation
Indices: 705051--705096 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
705041 ATATAAAAAA
* *
705051 ATCTACCCACTATTAGGTTTTTCT
1 ATCTACCCACTACTAGGGTTTTCT
*
705075 ATCTACTCACTACTAGGGTTTT
1 ATCTACCCACTACTAGGGTTTT
705097 ATCCGTCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (24 bp):
ATCTACCCACTACTAGGGTTTTCT
Found at i:710686 original size:36 final size:37
Alignment explanation
Indices: 710633--710703 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
710623 TAGTAATATA
*
710633 TTCTGATCTGAATGCACTTTGTGTGCGTAT-TGTTAT
1 TTCTGATCTGAATGCACTGTGTGTGCGTATCTGTTAT
* *
710669 TTCTGATGTG-ATAGCACTGTGTGTGCTTATCTGTT
1 TTCTGATCTGAAT-GCACTGTGTGTGCGTATCTGTT
710704 CTGACTCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 2 0.07
36 24 0.80
37 4 0.13
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.46
Consensus pattern (37 bp):
TTCTGATCTGAATGCACTGTGTGTGCGTATCTGTTAT
Found at i:713029 original size:28 final size:28
Alignment explanation
Indices: 712987--713053 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
712977 CATTTATGGA
*
712987 TTTGATGAATCGGGTGTTTCAGCCGTAT
1 TTTGATGAATTGGGTGTTTCAGCCGTAT
713015 TTTGATGAATTGGGTGTTTCAGCCGTAT
1 TTTGATGAATTGGGTGTTTCAGCCGTAT
* *
713043 TTAGATAAATT
1 TTTGATGAATT
713054 TGTGGTCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.42
Consensus pattern (28 bp):
TTTGATGAATTGGGTGTTTCAGCCGTAT
Found at i:725678 original size:20 final size:20
Alignment explanation
Indices: 725653--725705 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
725643 TTTCAGAGTA
725653 ATGCATCGATGCACCA-ATCC
1 ATGCATCGATGCACCATA-CC
725673 ATGCATCGATGCA-CATACC
1 ATGCATCGATGCACCATACC
*
725692 ATGCACCGATGCAC
1 ATGCATCGATGCAC
725706 TGAGGATTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACCATACC
Found at i:725786 original size:65 final size:64
Alignment explanation
Indices: 725673--725806 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 64
725663 GCACCAATCC
* *
725673 ATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTCTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTCTATG-AAACATCGAATGCACTTG
* * *
725738 ATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATT-T-TGAAACATCGAATGCACT
1 ATGCATCGATGCA-CATACCATGCACCGATGCACTCAGG--ATTCTATGAAACATCGAATGCACT
725800 TG
63 TG
725802 ATGCA
1 ATGCA
725807 CTCTTAGTGC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
64 22 0.36
65 33 0.54
66 3 0.05
67 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (64 bp):
ATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTCTATGAAACATCGAATGCACTTG
Found at i:731569 original size:24 final size:24
Alignment explanation
Indices: 731537--731617 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
731527 ACACTTAACA
731537 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
731561 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
731583 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
731605 GTGCATCGATGCA
1 GTGCATCGATGCA
731618 CGGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:737415 original size:2 final size:2
Alignment explanation
Indices: 737410--737439 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
737400 TTATTTTTTA
737410 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
737440 TTATTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:739266 original size:37 final size:36
Alignment explanation
Indices: 739203--739322 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
739193 TTTCCATTAT
* * *
739203 CATTTTTC-AACAAACATCTACTAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
739239 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
739275 CATTTTT-AAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
739310 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
739323 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 30 0.39
36 23 0.30
37 23 0.30
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:739278 original size:21 final size:21
Alignment explanation
Indices: 739254--739314 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
739244 TTCAAAGAAA
739254 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
**
739275 CATTT-TTAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
739289 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
739310 CATTT
1 CATTT
739315 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 1 0.03
19 1 0.03
20 6 0.21
21 10 0.34
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:739331 original size:35 final size:35
Alignment explanation
Indices: 739225--739349 Score: 130
Period size: 35 Copynumber: 3.5 Consensus size: 35
739215 AACATCTACT
* * *
739225 AAACTTTGAAAAACTATTTTTCAAAGAAACATTTACC
1 AAACTTTG-AAAACCATTTTTTAAAG-AACAGTTACC
*
739262 AAACTTTGAAAACCA-TTTTTAAAGAAACATTTACC
1 AAACTTTGAAAACCATTTTTTAAAG-AACAGTTACC
***
739297 AAACTTTGAAAACCATTTTTTCAAAG-TTGGTTACC
1 AAACTTTGAAAACCATTTTTT-AAAGAACAGTTACC
739332 AAAC-TTGAAAACCATTTT
1 AAACTTTGAAAACCATTTT
739350 AATAATTTCA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 14 0.17
35 43 0.54
36 11 0.14
37 12 0.15
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (35 bp):
AAACTTTGAAAACCATTTTTTAAAGAACAGTTACC
Found at i:743882 original size:37 final size:36
Alignment explanation
Indices: 743823--743942 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
743813 ATCCCATTAT
* *
743823 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
743859 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
743895 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
743930 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
743943 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:743898 original size:21 final size:21
Alignment explanation
Indices: 743874--743934 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
743864 TTCAAAGAAA
743874 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
743895 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
743909 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
743930 CATTT
1 CATTT
743935 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:743951 original size:35 final size:36
Alignment explanation
Indices: 743825--743969 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
743815 CCCATTATCA
*
743825 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
743860 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
743897 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*** *
743933 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAATCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
743967 TTT
1 TTT
743970 AATAATTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 13 0.13
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:753209 original size:14 final size:15
Alignment explanation
Indices: 753190--753218 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
753180 TATAACTACT
753190 TTAGTTTA-TTTTAC
1 TTAGTTTAGTTTTAC
753204 TTAGTTTAGTTTTAC
1 TTAGTTTAGTTTTAC
753219 CAGTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (15 bp):
TTAGTTTAGTTTTAC
Found at i:759026 original size:20 final size:20
Alignment explanation
Indices: 758949--759039 Score: 82
Period size: 20 Copynumber: 4.6 Consensus size: 20
758939 AAATGACCAA
758949 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAAT-T-T
** *
758971 -AAATT-GCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
*
758989 CCAAATTCGCAAC-TGAATTT
1 -CAAATTCGCAACGCGAATTT
759009 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
759029 -AATTTCGCAAC
1 CAAATTCGCAAC
759040 AGGTTTTAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 23 0.41
20 24 0.43
21 8 0.14
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:762625 original size:20 final size:21
Alignment explanation
Indices: 762600--762648 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
762590 GCAACGCGAA
*
762600 ATCGCAAAT-CGAATTTGACT
1 ATCGCAAATACAAATTTGACT
**
762620 ATCGCACGTTACAAATTTGACT
1 ATCGCA-AATACAAATTTGACT
762642 ATCGCAA
1 ATCGCAA
762649 CGCTTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (21 bp):
ATCGCAAATACAAATTTGACT
Found at i:763125 original size:24 final size:23
Alignment explanation
Indices: 763094--763138 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
763084 TTCATTTCAT
763094 ATTTAATTAGAGTTTGAATTTAA
1 ATTTAATTAGAGTTTGAATTTAA
*
763117 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTAGAGTTTGAATTT
763139 CAATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTAATTAGAGTTTGAATTTAA
Found at i:763127 original size:18 final size:18
Alignment explanation
Indices: 763106--763142 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
763096 TTAATTAGAG
763106 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
763124 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
763142 T
1 T
763143 ATAAATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:763149 original size:24 final size:24
Alignment explanation
Indices: 763098--763150 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
763088 TTTCATATTT
* * *
763098 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
763122 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
763146 AATTT
1 AATTT
763151 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:763501 original size:39 final size:39
Alignment explanation
Indices: 763454--763540 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
763444 TCCGATGCTT
763454 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
763493 ATCCAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
763532 ATCAAAATC
1 ATCAAAATC
763541 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:763868 original size:65 final size:60
Alignment explanation
Indices: 763788--763926 Score: 172
Period size: 61 Copynumber: 2.2 Consensus size: 60
763778 TTTTAGAAAC
* *
763788 AACAAATCAAGTTTTACAAAT-AATTAAAAAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACACATC-AATT
763852 A
60 A
* * *
763853 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
763913 AACAAATCAACTTT
1 AACAAATCAACTTT
763927 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 19 0.28
61 22 0.32
62 3 0.04
65 20 0.29
66 4 0.06
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
Found at i:765305 original size:21 final size:21
Alignment explanation
Indices: 765281--765333 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
765271 GTGAATCGGG
765281 CTCTTGAACGGCGA-ACGGGAC
1 CTCTTGAACGGCGACA-GGGAC
** *
765302 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGCGACAGGGAC
765323 CTCTTGAACGG
1 CTCTTGAACGG
765334 TGGGAGGGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGCGACAGGGAC
Found at i:765341 original size:21 final size:21
Alignment explanation
Indices: 765301--765399 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
765291 GCGAACGGGA
*
765301 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
765322 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
765343 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
**
765364 CCTCTTGAACGAT-AGGAGGCA
1 CCTCTTGAACGATGA-GAGGGG
*
765385 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
765400 TAGGTGCATC
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:765397 original size:42 final size:42
Alignment explanation
Indices: 765300--765399 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
765290 GGCGAACGGG
* * * *
765300 ACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGG
1 ACCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGC
* * *
765342 GCTTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGC
1 ACCTCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGC
765384 ACCTCTTGAATGATGA
1 ACCTCTTGAATGATGA
765400 TAGGTGCATC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (42 bp):
ACCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGC
Found at i:765564 original size:4 final size:4
Alignment explanation
Indices: 765543--765576 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
765533 GGGCCGCTGA
* *
765543 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
765577 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:765818 original size:63 final size:63
Alignment explanation
Indices: 765724--765845 Score: 138
Period size: 63 Copynumber: 1.9 Consensus size: 63
765714 ACCGCGTAGC
* * * * * *
765724 GCACCATTGTCATCGCGTAAAAAATCTACCTCACCACGTAAAG-ATCGAACCTCATCACGCCAT
1 GCACCATTATCATCACGTAAAAAACCGACCTCACCACGCAAAGCACCG-ACCTCATCACGCCAT
* * **
765787 GCACCATTATCTTCACGTAAAATACCGACCTCATGACGCAAAGCACCGACCTCATCACG
1 GCACCATTATCATCACGTAAAAAACCGACCTCACCACGCAAAGCACCGACCTCATCACG
765846 TAATTCCCCT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
63 45 0.94
64 3 0.06
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.20
Consensus pattern (63 bp):
GCACCATTATCATCACGTAAAAAACCGACCTCACCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:767550 original size:20 final size:20
Alignment explanation
Indices: 767527--767577 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
767517 AAAAGTTTCT
*
767527 GAAACTTAAATTCGCAACGC
1 GAAACTAAAATTCGCAACGC
*
767547 GAAAATGAAAA-TCGCAACGC
1 GAAACT-AAAATTCGCAACGC
*
767567 AAAACTAAAAT
1 GAAACTAAAAT
767578 CGCGTTGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.16
20 18 0.72
21 3 0.12
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTAAAATTCGCAACGC
Done.