Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold456
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: 970336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:255215 original size:2 final size:2
Alignment explanation
Indices: 255208--255235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
255198 CTATGTGCGC
255208 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
255236 ATATGCGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:256487 original size:57 final size:57
Alignment explanation
Indices: 256418--256534 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
256408 TTGTATAAAT
256418 ACCCAACTTTACCTTCATTAATTTTTGCATAAATCACTACTTCTGTCTTTCAAATCG
1 ACCCAACTTTACCTTCATTAATTTTTGCATAAATCACTACTTCTGTCTTTCAAATCG
256475 ACCCAACTTTACCTTCATTAATTTTTGCATAAATCACTACTTCTGTCTTTCAAATCG
1 ACCCAACTTTACCTTCATTAATTTTTGCATAAATCACTACTTCTGTCTTTCAAATCG
256532 ACC
1 ACC
256535 ATCATAATCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.28, C:0.27, G:0.05, T:0.39
Consensus pattern (57 bp):
ACCCAACTTTACCTTCATTAATTTTTGCATAAATCACTACTTCTGTCTTTCAAATCG
Found at i:267912 original size:20 final size:20
Alignment explanation
Indices: 267887--267929 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
267877 AAAAAATTAT
267887 TTTAAT-TTTATATTATTAAA
1 TTTAATATTT-TATTATTAAA
*
267907 TTTAATATTTTATTATTATA
1 TTTAATATTTTATTATTAAA
267927 TTT
1 TTT
267930 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAATATTTTATTATTAAA
Found at i:267992 original size:22 final size:21
Alignment explanation
Indices: 267948--267993 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
267938 TATAGTAAAT
*
267948 AAAAAATAATTAATAATGTTA
1 AAAAAATAATTAATAATGATA
* *
267969 AAAAAATATTTAAATGATGATA
1 AAAAAATAATT-AATAATGATA
267991 AAA
1 AAA
267994 TATTAATGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAATAATTAATAATGATA
Found at i:267993 original size:21 final size:20
Alignment explanation
Indices: 267946--267993 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
267936 ATTATAGTAA
267946 ATAAAAAATAATTAATAATG
1 ATAAAAAATAATTAATAATG
* * *
267966 TTAAAAAAATATTTAAATGATG
1 AT-AAAAAATAATT-AATAATG
267988 ATAAAA
1 ATAAAA
267994 TATTAATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (20 bp):
ATAAAAAATAATTAATAATG
Found at i:268143 original size:20 final size:21
Alignment explanation
Indices: 268115--268161 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
268105 CATATCAATA
268115 TTTTATAAT-ATATAAATAAT
1 TTTTATAATAATATAAATAAT
* * *
268135 TTTTTTAATAATATTAATTAT
1 TTTTATAATAATATAAATAAT
268156 TTTTAT
1 TTTTAT
268162 TTATATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATAATATAAATAAT
Found at i:268164 original size:23 final size:24
Alignment explanation
Indices: 268113--268164 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
268103 GACATATCAA
*
268113 TATTTTATAATATATAAATAATTT
1 TATTTAATAATATATAAATAATTT
* *
268137 T-TTTAATAATAT-TAATTATTTT
1 TATTTAATAATATATAAATAATTT
268159 TATTTA
1 TATTTA
268165 TATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.38
23 14 0.58
24 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTAATAATATATAAATAATTT
Found at i:268167 original size:19 final size:18
Alignment explanation
Indices: 268131--268174 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
268121 AATATATAAA
268131 TAATTTTTTTAATAATAT
1 TAATTTTTTTAATAATAT
* *
268149 TAATTATTTTTATTTATAT
1 TAATT-TTTTTAATAATAT
268168 T-ATTTTT
1 TAATTTTT
268175 AAAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATTTTTTTAATAATAT
Found at i:268206 original size:12 final size:14
Alignment explanation
Indices: 268173--268220 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
268163 TATATTATTT
268173 TTAAAATATATAAA
1 TTAAAATATATAAA
268187 TTAAAATAT-TAAA
1 TTAAAATATATAAA
*
268200 TTTAATAATATAAAAA
1 -TTAA-AATATATAAA
268216 TTAAA
1 TTAAA
268221 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 14 0.47
15 9 0.30
16 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATATATAAA
Found at i:272630 original size:26 final size:25
Alignment explanation
Indices: 272601--272653 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
272591 TTTAATACAT
*
272601 ATTTAAAAATAAATATAAAATTATAA
1 ATTTAAAAATAAATAAAAAATTA-AA
** *
272627 ATTTTTAAATATATAAAAAATTAAA
1 ATTTAAAAATAAATAAAAAATTAAA
272652 AT
1 AT
272654 ATATATCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTAAAAATAAATAAAAAATTAAA
Found at i:276653 original size:71 final size:71
Alignment explanation
Indices: 276537--276679 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
276527 GAGGTGATTC
276537 AACGTGAGTTTAGATCAATCATTAATGGGGTTTGCCTTTAACCACCTATGGTTAAACTATCCAAA
1 AACGTGAGTTTAGATCAATCATTAATGGGGTTTGCCTTTAACCACCTATGGTTAAACTATCCAAA
276602 AAAGCT
66 AAAGCT
276608 AACGTGAGTTTAGATCAATCATTAATGGGGTTTGCCTTTAACCACCTATGGTTAAACTATCCAAA
1 AACGTGAGTTTAGATCAATCATTAATGGGGTTTGCCTTTAACCACCTATGGTTAAACTATCCAAA
276673 AAAGCT
66 AAAGCT
276679 A
1 A
276680 TGGCAATAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (71 bp):
AACGTGAGTTTAGATCAATCATTAATGGGGTTTGCCTTTAACCACCTATGGTTAAACTATCCAAA
AAAGCT
Found at i:279057 original size:2 final size:2
Alignment explanation
Indices: 279050--279087 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
279040 TTCGTCTTGC
*
279050 CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
279088 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:290306 original size:2 final size:2
Alignment explanation
Indices: 290299--290327 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
290289 TAAGATAATC
290299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
290328 CACGCTCTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:296403 original size:19 final size:20
Alignment explanation
Indices: 296369--296406 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
296359 CAAAATTTTA
296369 AAAATAAATATAATTTAATT
1 AAAATAAATATAATTTAATT
*
296389 AAAAT-AATATTATTTAAT
1 AAAATAAATATAATTTAAT
296407 CGATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAAATATAATTTAATT
Found at i:297006 original size:2 final size:2
Alignment explanation
Indices: 296999--297029 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
296989 CATTTTGCTA
296999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
297030 GATGTGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:305315 original size:25 final size:25
Alignment explanation
Indices: 305278--305327 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
305268 GCCATGGGTG
*
305278 ATTCTTTTTATGTTCTCGATACTTT
1 ATTCTTTTCATGTTCTCGATACTTT
305303 ATTCTTTTCATGTTCTCGATACTTT
1 ATTCTTTTCATGTTCTCGATACTTT
305328 CTTTCCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (25 bp):
ATTCTTTTCATGTTCTCGATACTTT
Found at i:307429 original size:6 final size:6
Alignment explanation
Indices: 307415--307448 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
307405 TAATTTTGCC
307415 AAAAA- AAAAAG -AAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
307449 CATATGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:309679 original size:19 final size:19
Alignment explanation
Indices: 309651--309687 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
309641 TTCATATAAA
309651 AAATAATTTTAAAAAATAT
1 AAATAATTTTAAAAAATAT
* *
309670 AAATATTTTTTAAAAATA
1 AAATAATTTTAAAAAATA
309688 ACAAAAAAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAATTTTAAAAAATAT
Found at i:315004 original size:6 final size:6
Alignment explanation
Indices: 314987--315067 Score: 81
Period size: 6 Copynumber: 13.5 Consensus size: 6
314977 TGATGATGGT
* * *
314987 GAGGAA GAGGAA GAGGAA GAAGAA GAAGAA GAAGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
** * * * *
315035 GAATAT GAGGAG GAGGAC GAGGAG GAGGAA GAG
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAG
315068 CTTCAGCCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.49, C:0.01, G:0.47, T:0.02
Consensus pattern (6 bp):
GAGGAA
Found at i:315010 original size:3 final size:3
Alignment explanation
Indices: 314990--315037 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
314980 TGATGGTGAG
* * * *
314990 GAA GAG GAA GAG GAA GAA GAA GAA GAA GAA GAA GAG GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
315038 TATGAGGAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:315530 original size:15 final size:15
Alignment explanation
Indices: 315510--315551 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
315500 TTCAGCCGAA
*
315510 AAAAAAAGGAAAGAG
1 AAAAAAAGAAAAGAG
*
315525 AAAAAAAGAAAAGGG
1 AAAAAAAGAAAAGAG
*
315540 AAAGAAAGAAAA
1 AAAAAAAGAAAA
315552 AAATATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAGAG
Found at i:315541 original size:21 final size:20
Alignment explanation
Indices: 315508--315554 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
315498 TGTTCAGCCG
315508 AAAAAAAAAGGAAAG-AGAA
1 AAAAAAAAAGGAAAGAAGAA
315527 AAAAAGAAAAGGGAAAGAAAGAA
1 AAAAA-AAAA-GGAAAG-AAGAA
315550 AAAAA
1 AAAAA
315555 TATTTATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 6 0.25
23 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGGAAAGAAGAA
Found at i:315573 original size:14 final size:15
Alignment explanation
Indices: 315554--315582 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
315544 AAAGAAAAAA
315554 ATATTTATG-TATTT
1 ATATTTATGTTATTT
315568 ATATTTATGTTATTT
1 ATATTTATGTTATTT
315583 TTTATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
ATATTTATGTTATTT
Found at i:315702 original size:20 final size:20
Alignment explanation
Indices: 315679--315743 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
315669 ATATACATAT
315679 AATTTTTATGTTATATTTTA
1 AATTTTTATGTTATATTTTA
**
315699 AATTTTT-T-TTATA-CATA
1 AATTTTTATGTTATATTTTA
*
315716 TCATTTTTATGTTATATTTTA
1 -AATTTTTATGTTATATTTTA
315737 AATTTTT
1 AATTTTT
315744 TTTATAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
17 2 0.06
18 11 0.31
19 2 0.06
20 18 0.51
21 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (20 bp):
AATTTTTATGTTATATTTTA
Found at i:315755 original size:38 final size:38
Alignment explanation
Indices: 315670--315773 Score: 154
Period size: 38 Copynumber: 2.7 Consensus size: 38
315660 ATTCGTGTCA
*
315670 TATACATATAATTTTTATGTTATATTTTAAATTTTTTT
1 TATACATATCATTTTTATGTTATATTTTAAATTTTTTT
315708 TATACATATCATTTTTATGTTATATTTTAAATTTTTTT
1 TATACATATCATTTTTATGTTATATTTTAAATTTTTTT
* * * * *
315746 TATAAATATCGTATTTATATTATTTTTT
1 TATACATATCATTTTTATGTTATATTTT
315774 GTATTGTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (38 bp):
TATACATATCATTTTTATGTTATATTTTAAATTTTTTT
Found at i:316226 original size:16 final size:17
Alignment explanation
Indices: 316202--316234 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
316192 ATTTTTATTA
*
316202 AAAATAATTACAAATGT
1 AAAATAATTAAAAATGT
316219 AAAA-AATTAAAAATGT
1 AAAATAATTAAAAATGT
316235 TGTTAACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAATAATTAAAAATGT
Found at i:318658 original size:2 final size:2
Alignment explanation
Indices: 318651--318682 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
318641 TCTAAAGGGA
318651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318683 CACACCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324830 original size:50 final size:50
Alignment explanation
Indices: 324745--324945 Score: 210
Period size: 50 Copynumber: 4.0 Consensus size: 50
324735 AGATGCTTAG
* ** * *
324745 AGTCAACAATTATGGTCACCTTTCTCGATTATCAAAAGTTGATGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGATGAAGAAT
* * * *
324795 AGTCAACAATTACGACCATCTCTCTCAATTGTCAAAGGTCGATGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGATGAAGAAT
* * * *
324845 AGTCAATAATTACGATCACCTCTCTCGATTGTCAAATGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGATGAAGAAT
* * *
324895 AGTCAACAATTTTA-G-TCACCTCTCTCGATTGTTAAAGGTT-AGTGAAGAAT
1 AGTCAACAA--TTACGACCACCTCTCTCGATTGTCAAAAGTTGA-TGAAGAAT
324945 A
1 A
324946 ATGACGGCCA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
50 124 0.97
51 1 0.01
52 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGATGAAGAAT
Found at i:324941 original size:100 final size:100
Alignment explanation
Indices: 324745--324945 Score: 246
Period size: 100 Copynumber: 2.0 Consensus size: 100
324735 AGATGCTTAG
* * *
324745 AGTCAACAATTATGGTCACCTTTCTCGATTATCAAAAGTTGATGAAGAATAGTCAACAATTACGA
1 AGTCAACAATTACGATCACCTCTCTCGATTATCAAAAGTTGATGAAGAATAGTCAACAATTACGA
* *
324810 CCATCTCTCTCAATTGTCAAAGGTCGATGAAGAAT
66 CCACCTCTCTCAATTGTCAAAGGTAGATGAAGAAT
* * * *
324845 AGTCAATAATTACGATCACCTCTCTCGATTGTCAAATGTTGGTGAAGAATAGTCAACAATTTTA-
1 AGTCAACAATTACGATCACCTCTCTCGATTATCAAAAGTTGATGAAGAATAGTCAACAA--TTAC
* * *
324909 G-TCACCTCTCTCGATTGTTAAAGGTTAG-TGAAGAAT
64 GACCACCTCTCTCAATTGTCAAAGG-TAGATGAAGAAT
324945 A
1 A
324946 ATGACGGCCA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
100 80 0.93
101 3 0.03
102 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (100 bp):
AGTCAACAATTACGATCACCTCTCTCGATTATCAAAAGTTGATGAAGAATAGTCAACAATTACGA
CCACCTCTCTCAATTGTCAAAGGTAGATGAAGAAT
Found at i:328095 original size:35 final size:35
Alignment explanation
Indices: 328048--328118 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
328038 TCCTTTGGAG
*
328048 ATAGGTTTGTATTGTTGGAACCACTCCCTTCTAAA
1 ATAGGTTCGTATTGTTGGAACCACTCCCTTCTAAA
*
328083 ATAGGTTCGTATTGTTGGAACCACTCTCTTCTAAA
1 ATAGGTTCGTATTGTTGGAACCACTCCCTTCTAAA
328118 A
1 A
328119 ATCATGTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (35 bp):
ATAGGTTCGTATTGTTGGAACCACTCCCTTCTAAA
Found at i:329422 original size:50 final size:50
Alignment explanation
Indices: 329363--329522 Score: 153
Period size: 50 Copynumber: 3.2 Consensus size: 50
329353 GCTTAGAGTT
*
329363 AACAATTACGGTCACTTTTCTCTATTGTTAAAGGTTGGTGAAAAATAATC
1 AACAATTACGGTCACTTTTCTCTATTGTCAAAGGTTGGTGAAAAATAATC
** * * * *
329413 AACAATTACGACCACCTCTCT-TGATTGTCAAAGGTTGGTGAAGAATATTC
1 AACAATTACGGTCACTTTTCTCT-ATTGTCAAAGGTTGGTGAAAAATAATC
* * * * * * *
329463 AACAATTATGGTCACCTCTT-TCGATTGTCAAAAGTTGGTGACAAGTAGTC
1 AACAATTACGGTCA-CTTTTCTCTATTGTCAAAGGTTGGTGAAAAATAATC
*
329513 AATAATTACG
1 AACAATTACG
329523 ACTACCTCTC
Statistics
Matches: 86, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
49 1 0.01
50 83 0.97
51 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (50 bp):
AACAATTACGGTCACTTTTCTCTATTGTCAAAGGTTGGTGAAAAATAATC
Found at i:329530 original size:50 final size:49
Alignment explanation
Indices: 329386--329561 Score: 176
Period size: 50 Copynumber: 3.5 Consensus size: 49
329376 ACTTTTCTCT
* *
329386 ATTGTTAAAGGTTGGTGAAAAATAATCAACAATTACGACCACCTCTCTT-G
1 ATTGTCAAAGGTTGGTG-AAAATAATCAACAATTACGACTACCTCT-TTCG
* * *
329436 ATTGTCAAAGGTTGGTGAAGAATATTCAACAATTATG-GTCACCTCTTTCG
1 ATTGTCAAAGGTTGGTGAA-AATAATCAACAATTACGACT-ACCTCTTTCG
* * * * *
329486 ATTGTCAAAAGTTGGTGACAAGTAGTCAATAATTACGACTACCTCTCTCG
1 ATTGTCAAAGGTTGGTGA-AAATAATCAACAATTACGACTACCTCTTTCG
* *
329536 ATTATCAAAGGTTAGTGAAGAATAAT
1 ATTGTCAAAGGTTGGTGAA-AATAAT
329562 TACGATCACC
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
49 5 0.05
50 96 0.93
51 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (49 bp):
ATTGTCAAAGGTTGGTGAAAATAATCAACAATTACGACTACCTCTTTCG
Found at i:329544 original size:100 final size:100
Alignment explanation
Indices: 329363--329559 Score: 261
Period size: 100 Copynumber: 2.0 Consensus size: 100
329353 GCTTAGAGTT
* * * *
329363 AACAATTACGGTCACTTTTCTCTATTGTTAAAGGTTGGTGAAAAATAATCAACAATTACGACCAC
1 AACAATTACGGTCACTCTTCTCGATTGTCAAAAGTTGGTGAAAAATAATCAACAATTACGACCAC
* * *
329428 CTCTCTTGATTGTCAAAGGTTGGTGAAGAATATTC
66 CTCTCTCGATTATCAAAGGTTAGTGAAGAATATTC
* * * * * *
329463 AACAATTATGGTCACCTCTT-TCGATTGTCAAAAGTTGGTGACAAGTAGTCAATAATTACGACTA
1 AACAATTACGGTCA-CTCTTCTCGATTGTCAAAAGTTGGTGAAAAATAATCAACAATTACGACCA
329527 CCTCTCTCGATTATCAAAGGTTAGTGAAGAATA
65 CCTCTCTCGATTATCAAAGGTTAGTGAAGAATA
329560 ATTACGATCA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 79 0.95
101 4 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (100 bp):
AACAATTACGGTCACTCTTCTCGATTGTCAAAAGTTGGTGAAAAATAATCAACAATTACGACCAC
CTCTCTCGATTATCAAAGGTTAGTGAAGAATATTC
Found at i:329574 original size:43 final size:43
Alignment explanation
Indices: 329513--329604 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
329503 ACAAGTAGTC
* *
329513 AATAATTACGACTACCTCTCTCGATTATCAAAGGTTAGTGAAG
1 AATAATTACGACTACCTCTCTCGATTATCAAAGATTAGTGAAA
* *
329556 AATAATTACGA-TCACCTCTTTTGATTATCAAAGATTAGTGAAA
1 AATAATTACGACT-ACCTCTCTCGATTATCAAAGATTAGTGAAA
329599 AATAAT
1 AATAAT
329605 CAAATCACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 1 0.02
43 43 0.98
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (43 bp):
AATAATTACGACTACCTCTCTCGATTATCAAAGATTAGTGAAA
Found at i:334921 original size:11 final size:12
Alignment explanation
Indices: 334907--334936 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
334897 AAGTGTAGAA
334907 AATAATTTAT-T
1 AATAATTTATAT
334918 AATAATTTATAT
1 AATAATTTATAT
334930 AATAATT
1 AATAATT
334937 GTTTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATAATTTATAT
Found at i:335295 original size:20 final size:20
Alignment explanation
Indices: 335272--335321 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
335262 TAATGTATCT
*
335272 TTTAATTTTAAAAATAATTA
1 TTTAATTTAAAAAATAATTA
*
335292 TTTAA-TTAAAAAATTATTA
1 TTTAATTTAAAAAATAATTA
335311 TTTATATTTAA
1 TTTA-ATTTAA
335322 TTTATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 16 0.62
20 6 0.23
21 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAATTTAAAAAATAATTA
Found at i:335766 original size:20 final size:20
Alignment explanation
Indices: 335728--335765 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
335718 ATTTTATGAG
335728 AAAAATATCAAATAAAAAAT
1 AAAAATATCAAATAAAAAAT
*
335748 AAAAATAT-ATATAAAAAA
1 AAAAATATCAAATAAAAAA
335766 AATTATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAATATCAAATAAAAAAT
Found at i:339082 original size:2 final size:2
Alignment explanation
Indices: 339066--339111 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
339056 CGTCAGTATC
339066 AT AT A- AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
339106 AT AT AT
1 AT AT AT
339112 CAGTTTTCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343568 original size:2 final size:2
Alignment explanation
Indices: 343561--343587 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
343551 CTGACATTTT
343561 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
343588 ATGTGGGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:345411 original size:29 final size:29
Alignment explanation
Indices: 345374--345430 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
345364 ACGGGGGAAA
345374 AAGAGAAAATCGAACAAAAATGTACTAAG
1 AAGAGAAAATCGAACAAAAATGTACTAAG
345403 AAGAGAAAATCGAACAAAAATGTACTAA
1 AAGAGAAAATCGAACAAAAATGTACTAA
345431 CAAATTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.14
Consensus pattern (29 bp):
AAGAGAAAATCGAACAAAAATGTACTAAG
Found at i:348217 original size:144 final size:143
Alignment explanation
Indices: 347982--348245 Score: 438
Period size: 144 Copynumber: 1.8 Consensus size: 143
347972 TTCCTTTTAA
* * *
347982 TTGTTTGTCTGTAATTAGGCTTGCACTCTGGTTTGTTTTATCCCTGTTGCAGTGTGTGATGGATT
1 TTGTTTGTCTGTAATTACGCTTGCACTCTAGTTTGTTTTATCCCTGTTACAGTGTGTGATGGATT
348047 CGGATAATCTATTGTCTGTGGGTGGGCTTGAGGTTGCCCATCAAAATGGTGTTTAAGTGTTAAAT
66 CGGATAATCTATTGTCTGTGGGTGGGCTTGAGGTTGCCCATCAAAATGGTGTTTAAGTGTTAAAT
348112 TCCTTTTCATTGT
131 TCCTTTTCATTGT
* * * **
348125 TTGTTTCGTTTGTGATTACGCTTGCACTTTAGTTTGTTTTATTGCTGTTACAGTGTGTGATGGAT
1 TTGTTT-GTCTGTAATTACGCTTGCACTCTAGTTTGTTTTATCCCTGTTACAGTGTGTGATGGAT
*
348190 TCGGATAATCTATTGTCTTTGGGTGGGCTTGAGGTTGCCCATCAAAATGGTGTTTA
65 TCGGATAATCTATTGTCTGTGGGTGGGCTTGAGGTTGCCCATCAAAATGGTGTTTA
348246 TCCGCAACTT
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
143 6 0.05
144 105 0.95
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.44
Consensus pattern (143 bp):
TTGTTTGTCTGTAATTACGCTTGCACTCTAGTTTGTTTTATCCCTGTTACAGTGTGTGATGGATT
CGGATAATCTATTGTCTGTGGGTGGGCTTGAGGTTGCCCATCAAAATGGTGTTTAAGTGTTAAAT
TCCTTTTCATTGT
Found at i:350403 original size:2 final size:2
Alignment explanation
Indices: 350396--350428 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
350386 CTTTCTTGAA
*
350396 TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
350429 ACATGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:351780 original size:2 final size:2
Alignment explanation
Indices: 351773--351797 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
351763 ATTGTTATTC
351773 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
351798 ACACACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:357059 original size:11 final size:12
Alignment explanation
Indices: 357035--357067 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
357025 TTTTGAAAAA
357035 ATAAAATATAAT
1 ATAAAATATAAT
*
357047 ATTAAAT-TAAT
1 ATAAAATATAAT
357058 ATAAAATATA
1 ATAAAATATA
357068 CTAAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:371032 original size:6 final size:6
Alignment explanation
Indices: 371023--371056 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
371013 ATTCCGTTGT
*
371023 AATTTA AATTTA AATTTA AATATTA AATATA AAT
1 AATTTA AATTTA AATTTA AAT-TTA AATTTA AAT
371057 ATATATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:371050 original size:13 final size:13
Alignment explanation
Indices: 371023--371058 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
371013 ATTCCGTTGT
371023 AATTTAAAT-TTA
1 AATTTAAATATTA
371035 AATTTAAATATTA
1 AATTTAAATATTA
*
371048 AATATAAATAT
1 AATTTAAATAT
371059 ATATGATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTAAATATTA
Found at i:371157 original size:11 final size:11
Alignment explanation
Indices: 371133--371173 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
371123 ATATTTTAAA
371133 AAATATAT-TT
1 AAATATATATT
371143 AAATATATATT
1 AAATATATATT
*
371154 AAATATAGATAT
1 AAATATATAT-T
371166 AAA-ATATA
1 AAATATATA
371174 AATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 8 0.30
11 15 0.56
12 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATATATATT
Found at i:377715 original size:15 final size:16
Alignment explanation
Indices: 377689--377721 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
377679 CAGAATCAAA
*
377689 TTAAATTTAAATTTAT
1 TTAAATTTAAATATAT
377705 TTAAA-TTAAATATAT
1 TTAAATTTAAATATAT
377720 TT
1 TT
377722 TCATATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATATAT
Found at i:378444 original size:13 final size:14
Alignment explanation
Indices: 378426--378455 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
378416 TTTATTTTTA
378426 TTTAAATTT-ATTT
1 TTTAAATTTAATTT
378439 TTTAAATTTAATTT
1 TTTAAATTTAATTT
378453 TTT
1 TTT
378456 TGTTTAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAAATTTAATTT
Found at i:378449 original size:19 final size:19
Alignment explanation
Indices: 378425--378463 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
378415 TTTTATTTTT
378425 ATTTAAATTTATTT-TTTAA
1 ATTT-AATTTATTTGTTTAA
*
378444 ATTTAATTTTTTTGTTTAA
1 ATTTAATTTATTTGTTTAA
378463 A
1 A
378464 GCTTACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTTAATTTATTTGTTTAA
Found at i:378552 original size:12 final size:12
Alignment explanation
Indices: 378530--378559 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
378520 AAATTTATTT
378530 TAAATTAATTAAA
1 TAAA-TAATTAAA
378543 TAAATAATTAAA
1 TAAATAATTAAA
378555 TAAAT
1 TAAAT
378560 TTTATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAATAATTAAA
Found at i:378554 original size:36 final size:39
Alignment explanation
Indices: 378514--378591 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 39
378504 AATTTAATTT
378514 TTAAATAAA-TTTAT-TTTA-AATTAATTAAATAAATAA
1 TTAAATAAATTTTATATTTATAATTAATTAAATAAATAA
**
378550 TTAAATAAATTTTATATTTATTAATTAATTATTTAAATAA
1 TTAAATAAATTTTATATTTA-TAATTAATTAAATAAATAA
378590 TT
1 TT
378592 TTAATGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 9 0.25
37 5 0.14
38 4 0.11
40 18 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TTAAATAAATTTTATATTTATAATTAATTAAATAAATAA
Found at i:378555 original size:32 final size:32
Alignment explanation
Indices: 378519--378595 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
378509 AATTTTTAAA
*
378519 TAAATTTATTTTAAATTAATTAAATAAATAAT
1 TAAATTAATTTTAAATTAATTAAATAAATAAT
* * * * * *
378551 TAAATAAATTTTATATTTATTAATTAATTATT
1 TAAATTAATTTTAAATTAATTAAATAAATAAT
378583 TAAA-TAATTTTAA
1 TAAATTAATTTTAA
378596 TGTATAATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 7 0.19
32 29 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAAATTAATTTTAAATTAATTAAATAAATAAT
Found at i:378612 original size:32 final size:32
Alignment explanation
Indices: 378550--378624 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
378540 AAATAAATAA
* *
378550 TTAAATAAATTTTATATTTATTAATTAATT-AT
1 TTAAAT-AATTTTATATGTATAAATTAATTAAT
378582 TTAAATAATTTTA-ATGTATAATATTAAATTAAT
1 TTAAATAATTTTATATGTATAA-ATT-AATTAAT
378615 TTAAATAATT
1 TTAAATAATT
378625 AAATTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
30 6 0.16
31 10 0.26
32 10 0.26
33 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (32 bp):
TTAAATAATTTTATATGTATAAATTAATTAAT
Found at i:378613 original size:18 final size:18
Alignment explanation
Indices: 378592--378629 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
378582 TTAAATAATT
378592 TTAATGTATAAT-ATTAAA
1 TTAATGTA-AATAATTAAA
*
378610 TTAATTTAAATAATTAAA
1 TTAATGTAAATAATTAAA
378628 TT
1 TT
378630 TAAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAATGTAAATAATTAAA
Found at i:379696 original size:2 final size:2
Alignment explanation
Indices: 379689--379718 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
379679 CTTTTTCTTT
379689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
379719 CAGTTCCCTC
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):
TA
Found at i:380888 original size:14 final size:14
Alignment explanation
Indices: 380869--380902 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
380859 TGCTTGCCAT
380869 TGCTGTTGCTTGGA
1 TGCTGTTGCTTGGA
*
380883 TGCTGTTGCTTGGG
1 TGCTGTTGCTTGGA
380897 TGCTGT
1 TGCTGT
380903 GGCTCCAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.03, C:0.15, G:0.38, T:0.44
Consensus pattern (14 bp):
TGCTGTTGCTTGGA
Found at i:387310 original size:2 final size:2
Alignment explanation
Indices: 387303--387336 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
387293 TATAAACTTC
*
387303 AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
387337 AACTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:387318 original size:23 final size:23
Alignment explanation
Indices: 387292--387336 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
387282 AAATATAAAG
387292 ATATAA-ACTTCATATATATATAT
1 ATATAATA-TTCATATATATATAT
*
387315 ATATAATATTTATATATATATA
1 ATATAATATTCATATATATATA
387337 AACTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAATATTCATATATATATAT
Found at i:387323 original size:15 final size:15
Alignment explanation
Indices: 387305--387334 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
387295 TAAACTTCAT
387305 ATATATATATATATA
1 ATATATATATATATA
*
387320 ATATTTATATATATA
1 ATATATATATATATA
387335 TAAACTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:387323 original size:17 final size:17
Alignment explanation
Indices: 387303--387337 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
387293 TATAAACTTC
387303 ATATATATATATATATA
1 ATATATATATATATATA
*
387320 ATATTTATATATATATA
1 ATATATATATATATATA
387337 A
1 A
387338 ACTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:387793 original size:20 final size:20
Alignment explanation
Indices: 387714--387795 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
387704 ATTTTAAATA
*
387714 TAAATATA--ATATATGTAT
1 TAAATATATTATATATTTAT
387732 TAAATATATCATATCATATTTAT
1 TAAATATAT--TAT-ATATTTAT
* *
387755 TATAT-TATTTTTATATTTAT
1 TAAATATA-TTATATATTTAT
*
387775 TAAATATATTATATTTTTAT
1 TAAATATATTATATATTTAT
387795 T
1 T
387796 TTATGTCCGA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
18 8 0.16
20 23 0.45
21 4 0.08
22 4 0.08
23 12 0.24
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (20 bp):
TAAATATATTATATATTTAT
Found at i:388841 original size:51 final size:51
Alignment explanation
Indices: 388781--388881 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
388771 TTCCATTAGC
388781 GAAAATTCGCTAGCTATATATGTATGTAGTATTATTTTAGTGATTAAAGAG
1 GAAAATTCGCTAGCTATATATGTATGTAGTATTATTTTAGTGATTAAAGAG
388832 GAAAATTCGCTAGCTATATATGTATGTAGTATTATTTTAGTGATTAAAGA
1 GAAAATTCGCTAGCTATATATGTATGTAGTATTATTTTAGTGATTAAAGA
388882 AGATTCGAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (51 bp):
GAAAATTCGCTAGCTATATATGTATGTAGTATTATTTTAGTGATTAAAGAG
Found at i:399259 original size:2 final size:2
Alignment explanation
Indices: 399254--399279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
399244 ATGATTACTG
399254 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
399280 ATACTCGAAT
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):
TA
Found at i:400521 original size:2 final size:2
Alignment explanation
Indices: 400514--400554 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
400504 GGCTAAGCTC
400514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400555 TATTTATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:400603 original size:22 final size:24
Alignment explanation
Indices: 400575--400638 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
400565 TTTATTTTTC
400575 TTTAAAATAAT-ATATAAAATAA-
1 TTTAAAATAATGATATAAAATAAT
400597 TTTAAAATAATGA-AT-AAATAAT
1 TTTAAAATAATGATATAAAATAAT
*
400619 TTTTAAATAATGACTATAAA
1 TTTAAAATAATGA-TATAAA
400639 CATTAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 6 0.17
22 25 0.69
23 1 0.03
24 2 0.06
25 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
TTTAAAATAATGATATAAAATAAT
Found at i:400970 original size:21 final size:20
Alignment explanation
Indices: 400915--400970 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
400905 ATTAAATCGA
* *
400915 TTAATTTAATTAAAATATTT
1 TTAATTTAAATAAATTATTT
*
400935 TTAAATATAAA-AAATTATTT
1 TT-AATTTAAATAAATTATTT
400955 TTAATGTTAAATAAAT
1 TTAAT-TTAAATAAAT
400971 ATTAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.10
20 16 0.55
21 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAATTTAAATAAATTATTT
Found at i:400985 original size:16 final size:16
Alignment explanation
Indices: 400964--400994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
400954 TTTAATGTTA
400964 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
400980 AATAAATATTTAATA
1 AATAAATATTAAATA
400995 AAATTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:401027 original size:15 final size:15
Alignment explanation
Indices: 401009--401038 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
400999 TTTTTGATAT
401009 AAAATTAAAATTTTA
1 AAAATTAAAATTTTA
*
401024 AAAATTTAAATTTTA
1 AAAATTAAAATTTTA
401039 TCACTTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTAAAATTTTA
Found at i:401641 original size:22 final size:22
Alignment explanation
Indices: 401613--401656 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
401603 ACAAAAGTAA
*
401613 GCTTTTTTATTGCATATAATTT
1 GCTTTTTTATTACATATAATTT
401635 GCTTTTTTATTACATATAATTT
1 GCTTTTTTATTACATATAATTT
401657 AATCAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (22 bp):
GCTTTTTTATTACATATAATTT
Found at i:403192 original size:21 final size:21
Alignment explanation
Indices: 403139--403192 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
403129 TTATTTAAAT
* * *
403139 TTTAATATAAATTTTTATTATT
1 TTTAATAT-TATTTTTATCATA
* *
403161 TTTTATTTTATTTTTATCATA
1 TTTAATATTATTTTTATCATA
403182 TTTAATATTAT
1 TTTAATATTAT
403193 CATATCAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTAATATTATTTTTATCATA
Found at i:403235 original size:17 final size:18
Alignment explanation
Indices: 403210--403244 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
403200 AAAGATAAAA
403210 TATTGTTATTT-TTTTAT
1 TATTGTTATTTATTTTAT
*
403227 TATTTTTATTTATTTTAT
1 TATTGTTATTTATTTTAT
403245 ACTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TATTGTTATTTATTTTAT
Found at i:405158 original size:27 final size:27
Alignment explanation
Indices: 405086--405209 Score: 96
Period size: 26 Copynumber: 4.7 Consensus size: 27
405076 TAAAAATTAG
* * *
405086 TCACCAATTTTGATAAAC-AACAAG--
1 TCACCATTTTTGACAAACAAAAAAGAA
* *
405110 TCACTATTTTTGACAAATAAAAAA-AA
1 TCACCATTTTTGACAAACAAAAAAGAA
405136 TCACCATTTTTGACAAACAAAAAAGGAA
1 TCACCATTTTTGACAAACAAAAAA-GAA
* * **
405164 -CTACCAATTTTGACAAACACAACGGAA
1 TC-ACCATTTTTGACAAACAAAAAAGAA
* *
405191 CCACCATTTTTGATAAACA
1 TCACCATTTTTGACAAACA
405210 CAAAGAGTGG
Statistics
Matches: 80, Mismatches: 13, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
24 14 0.17
25 4 0.05
26 22 0.28
27 19 0.24
28 21 0.26
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (27 bp):
TCACCATTTTTGACAAACAAAAAAGAA
Found at i:405210 original size:27 final size:27
Alignment explanation
Indices: 405115--405214 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
405105 ACAAGTCACT
* ** *
405115 ATTTTTGACAAATA-AAAAAAATCACC
1 ATTTTTGACAAACACAAAGGAACCACC
* *
405141 ATTTTTGACAAACAAAAAAGGAACTACC
1 ATTTTTGACAAAC-ACAAAGGAACCACC
* *
405169 AATTTTGACAAACACAACGGAACCACC
1 ATTTTTGACAAACACAAAGGAACCACC
*
405196 ATTTTTGATAAACACAAAG
1 ATTTTTGACAAACACAAAG
405215 AGTGGCTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
26 12 0.20
27 28 0.47
28 20 0.33
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAGGAACCACC
Found at i:409124 original size:27 final size:25
Alignment explanation
Indices: 409061--409130 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
409051 TTAACTATCA
* *
409061 ATTTTAATAAATAACAAGAATCATC
1 ATTTTTATAAATAAAAAGAATCATC
* * *
409086 ATTTTTACAAATATAAAAGAATTATT
1 ATTTTTATAAATA-AAAAGAATCATC
409112 ATTTTTCATAAATACAAAA
1 ATTTTT-ATAAATA-AAAA
409131 AGTAACTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 11 0.31
26 15 0.42
27 10 0.28
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (25 bp):
ATTTTTATAAATAAAAAGAATCATC
Found at i:418661 original size:28 final size:28
Alignment explanation
Indices: 418603--418660 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
418593 TAAACTATTT
* *
418603 AATTTTAAATATTTATTTAATATTAAAA
1 AATTTTAAATACTTATTAAATATTAAAA
418631 AATTTTAAATAAACTTATTAAATA-TAAAA
1 AATTTTAAAT--ACTTATTAAATATTAAAA
418660 A
1 A
418661 TAAATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 6 0.23
30 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTTTAAATACTTATTAAATATTAAAA
Found at i:419729 original size:29 final size:29
Alignment explanation
Indices: 419686--419743 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
419676 TATTCCAAGT
419686 CCTACTTGAAACAACACTCCATATATTTG
1 CCTACTTGAAACAACACTCCATATATTTG
*
419715 CCTACTTGAACCAACACTCCATATATTTG
1 CCTACTTGAAACAACACTCCATATATTTG
419744 TTGGAGACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (29 bp):
CCTACTTGAAACAACACTCCATATATTTG
Found at i:429035 original size:38 final size:38
Alignment explanation
Indices: 428993--429080 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
428983 ATTTATTTTA
428993 AAATTCTTTAATCGTAAGTCACCAATCAATTTCAAATT
1 AAATTCTTTAATCGTAAGTCACCAATCAATTTCAAATT
* * * ** * *
429031 AAATTTTTTAATCGTCAGTTATTAATTAATTTTAAATT
1 AAATTCTTTAATCGTAAGTCACCAATCAATTTCAAATT
429069 AAATTCTTTAAT
1 AAATTCTTTAAT
429081 TATCAACAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (38 bp):
AAATTCTTTAATCGTAAGTCACCAATCAATTTCAAATT
Found at i:429076 original size:76 final size:76
Alignment explanation
Indices: 428990--429161 Score: 208
Period size: 76 Copynumber: 2.3 Consensus size: 76
428980 AGAATTTATT
* * * *
428990 TTAAAATTCTTTAATCGT-A-AGTCACCAATCAATTTCAAATTAAATTTTTTAATCGTCAGTTAT
1 TTAAAATTCTTTAATCATAACAGT-A--AATCAATTTCAAATTAAATTTTTTAATCATAAATTAT
429053 TAATTAATTTTAAA
63 TAATTAATTTTAAA
* *
429067 TT-AAATTCTTTAATTATCAACAGTAAATCAATTTTAAATTAAATTTTTTAATCATAAATTATTA
1 TTAAAATTCTTTAATCAT-AACAGTAAATCAATTTCAAATTAAATTTTTTAATCATAAATTATTA
*
429131 ATTAATTTTTAA
65 ATTAATTTTAAA
*
429143 TTAAAATT-TTTAATTATAA
1 TTAAAATTCTTTAATCATAA
429162 TTAATTTAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
75 2 0.02
76 70 0.83
77 7 0.08
78 2 0.02
79 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (76 bp):
TTAAAATTCTTTAATCATAACAGTAAATCAATTTCAAATTAAATTTTTTAATCATAAATTATTAA
TTAATTTTAAA
Found at i:429138 original size:38 final size:36
Alignment explanation
Indices: 429020--429184 Score: 145
Period size: 38 Copynumber: 4.5 Consensus size: 36
429010 GTCACCAATC
* * * *
429020 AATTTCAAATTAAATTTTTTAATCGTCAGTTATTAATT
1 AATTTTAAATTAAATTTTTTAATCATAAATTA--AATT
* * * *
429058 AATTTTAAATTAAATTCTTTAATTATCAACAGTAAATC
1 AATTTTAAATTAAATTTTTTAATCAT-AA-ATTAAATT
429096 AATTTTAAATTAAATTTTTTAATCATAAATTATTAATT
1 AATTTTAAATTAAATTTTTTAATCATAAATTA--AATT
* * * *
429134 AATTTTTAATTAAAATTTTTAATTAT-AATTAATTT
1 AATTTTAAATTAAATTTTTTAATCATAAATTAAATT
*
429169 AA-TTTAAATTTAATTT
1 AATTTTAAATTAAATTT
429185 GATTCATGCT
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
34 11 0.11
35 5 0.05
36 3 0.03
37 7 0.07
38 75 0.72
39 1 0.01
40 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (36 bp):
AATTTTAAATTAAATTTTTTAATCATAAATTAAATT
Found at i:429139 original size:24 final size:24
Alignment explanation
Indices: 429111--429158 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
429101 TAAATTAAAT
429111 TTTTTAATCATAAATTATTAATTAA
1 TTTTTAATCA-AAATTATTAATTAA
* *
429136 TTTTTAATTAAAATTTTTAATTA
1 TTTTTAATCAAAATTATTAATTA
429159 TAATTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTAATCAAAATTATTAATTAA
Found at i:429170 original size:28 final size:30
Alignment explanation
Indices: 429123--429179 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
429113 TTTAATCATA
429123 AATTATTAATTAATTTTTAATTAAAATTTTT
1 AATTATTAATTAA-TTTTAATTAAAATTTTT
*
429154 AATTA-TAATTAA-TTTAATTTAAATTT
1 AATTATTAATTAATTTTAATTAAAATTT
429180 AATTTGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 13 0.52
30 7 0.28
31 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTATTAATTAATTTTAATTAAAATTTTT
Found at i:429651 original size:10 final size:10
Alignment explanation
Indices: 429636--429671 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
429626 GGCTGAGAAG
429636 ATATATATAC
1 ATATATATAC
429646 ATATATATAC
1 ATATATATAC
429656 ATATATATAC
1 ATATATATAC
429666 ATATAT
1 ATATAT
429672 CCTTCTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAC
Found at i:438871 original size:89 final size:88
Alignment explanation
Indices: 438713--438940 Score: 264
Period size: 89 Copynumber: 2.6 Consensus size: 88
438703 ATTATGAATT
* * *
438713 AATTAAA-TTAAATTTTAAATTTAATTAATCTTGA-TTTAAAATAATTATTTTTCTATCACTTTT
1 AATTAAATTTAAA-TTTAAATATAATTAAT-TTTATTTTAAAATAATTATTTTTCGATCACTTTT
**
438776 TAAAAATTGTATCATAAATCAAC-G
64 TAAAAATAATATCATAAATCAACTG
438800 AATTAAATTTTAAATTTAATATATAATTAATTTTATTTTAAAATAATTATTTTTCGATCACTTTT
1 AATTAAA-TTTAAATTTAA-ATATAATTAATTTTATTTTAAAATAATTATTTTTCGATCACTTTT
* *
438865 TAAAAATAATATTATAAATTAACTG
64 TAAAAATAATATCATAAATCAACTG
* * ** * *
438890 AATTAAACTTCAAATCTAACATATAATTAACCTTGTTTTAGAATAATTATT
1 AATTAAA-TTTAAATTTAA-ATATAATTAATTTTATTTTAAAATAATTATT
438941 CTTCTATTGG
Statistics
Matches: 121, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
87 7 0.06
88 8 0.07
89 62 0.51
90 44 0.36
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (88 bp):
AATTAAATTTAAATTTAAATATAATTAATTTTATTTTAAAATAATTATTTTTCGATCACTTTTTA
AAAATAATATCATAAATCAACTG
Found at i:439868 original size:2 final size:2
Alignment explanation
Indices: 439861--439903 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
439851 ATAGACAGTT
439861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
439903 T
1 T
439904 GAATTGATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:444289 original size:21 final size:20
Alignment explanation
Indices: 444257--444297 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
444247 ATATATATAA
*
444257 AAATTTATTATTTAAAATTT
1 AAATTTAATATTTAAAATTT
*
444277 AAATCTTAATATTTATAATTT
1 AAAT-TTAATATTTAAAATTT
444298 TTTTATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTAATATTTAAAATTT
Found at i:448614 original size:45 final size:45
Alignment explanation
Indices: 448559--448669 Score: 186
Period size: 45 Copynumber: 2.4 Consensus size: 45
448549 CATCTAAAAT
448559 TCTCATCTCATCTCATTCATATTCCTACGTGCATCTTCTTAGGCA
1 TCTCATCTCATCTCATTCATATTCCTACGTGCATCTTCTTAGGCA
* * *
448604 TCTGATCTCATCTCATTCATATTCCTACGTGCATTTTCTTGGGCA
1 TCTCATCTCATCTCATTCATATTCCTACGTGCATCTTCTTAGGCA
448649 TCTCATCTCATCTCATCTCAT
1 TCTCATCTCATCTCAT-TCAT
448670 CTCATTCACA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 57 0.93
46 4 0.07
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (45 bp):
TCTCATCTCATCTCATTCATATTCCTACGTGCATCTTCTTAGGCA
Found at i:448657 original size:5 final size:5
Alignment explanation
Indices: 448647--448674 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
448637 TTTTCTTGGG
448647 CATCT CATCT CATCT CATCT CATCT CAT
1 CATCT CATCT CATCT CATCT CATCT CAT
448675 TCACATTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (5 bp):
CATCT
Found at i:448668 original size:55 final size:54
Alignment explanation
Indices: 448602--448713 Score: 197
Period size: 55 Copynumber: 2.1 Consensus size: 54
448592 TCTTCTTAGG
* *
448602 CATCTGATCTCATCTCATTCATATTCCTACGTGCATTTTCTTGGGCATCTCATCT
1 CATCTCATCTCATCTCATTCACATTCCTACGTGCATTTTCTTGGGCATCTCAT-T
448657 CATCTCATCTCATCTCATTCACATTCCTACGTGCATTTTCTTGGGCATCTCATT
1 CATCTCATCTCATCTCATTCACATTCCTACGTGCATTTTCTTGGGCATCTCATT
448711 CAT
1 CAT
448714 ACTCCTACGT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
54 4 0.07
55 51 0.93
ACGTcount: A:0.19, C:0.30, G:0.10, T:0.41
Consensus pattern (54 bp):
CATCTCATCTCATCTCATTCACATTCCTACGTGCATTTTCTTGGGCATCTCATT
Found at i:448720 original size:35 final size:35
Alignment explanation
Indices: 448667--448749 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
448657 CATCTCATCT
* * **
448667 CATCTCATTCACATTCCTACGTGCATTTTCTTGGG
1 CATCTCATTCATACTCCTACGTGCATTTTCCAGGG
448702 CATCTCATTCATACTCCTACGTGCATTTTCCAGGG
1 CATCTCATTCATACTCCTACGTGCATTTTCCAGGG
448737 CATCTCATCTCAT
1 CATCTCAT-TCAT
448750 CTAATCTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 39 0.91
36 4 0.09
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.37
Consensus pattern (35 bp):
CATCTCATTCATACTCCTACGTGCATTTTCCAGGG
Found at i:448751 original size:45 final size:45
Alignment explanation
Indices: 448559--448751 Score: 155
Period size: 45 Copynumber: 4.3 Consensus size: 45
448549 CATCTAAAAT
* * *
448559 TCTCATCTCATCTCATTCATATTCCTACGTGCATCTTCTTA-GGCA
1 TCTCATCTCATCTCATTCATACTCCTACGTGCATTTTC-CAGGGCA
* * **
448604 TCTGATCTCATCTCATTCATATTCCTACGTGCATTTTCTTGGGCA
1 TCTCATCTCATCTCATTCATACTCCTACGTGCATTTTCCAGGGCA
* ** *
448649 TCTCATCTCATCTCATCTCAT-CT-C-A--TTCACATTCCTACGTGCA
1 TCTCATCTCATCTCAT-TCATACTCCTACGTGCATTTTCC-A-GGGCA
* * **
448692 TTTTCTTGGGCATCTCATTCATACTCCTACGTGCATTTTCCAGGGCA
1 -TCTCAT-CTCATCTCATTCATACTCCTACGTGCATTTTCCAGGGCA
448739 TCTCATCTCATCT
1 TCTCATCTCATCT
448752 AATCTTAGCG
Statistics
Matches: 114, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
41 6 0.05
43 5 0.04
44 10 0.09
45 71 0.62
46 9 0.08
47 5 0.04
48 1 0.01
49 7 0.06
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (45 bp):
TCTCATCTCATCTCATTCATACTCCTACGTGCATTTTCCAGGGCA
Found at i:449157 original size:23 final size:23
Alignment explanation
Indices: 449122--449197 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
449112 TTGATGGTGC
* *
449122 AAATTAAAATATATCAATATAATA
1 AAATTAAATTATAT-AATAAAATA
*
449146 AAA-TAAATTATAT-ATAGAATTA
1 AAATTAAATTATATAATA-AAATA
449168 AAATTAAATTATAATAATAAAAT-
1 AAATTAAATTAT-ATAATAAAATA
449191 AAATTAA
1 AAATTAA
449198 GAGTGCAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.07
22 6 0.14
23 24 0.55
24 8 0.18
25 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (23 bp):
AAATTAAATTATATAATAAAATA
Found at i:449757 original size:17 final size:17
Alignment explanation
Indices: 449731--449768 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
449721 TATACTCAAG
*
449731 TAAATATTTTATATTTT
1 TAAATATTTTATATATT
*
449748 TAAATTTTTTATATATT
1 TAAATATTTTATATATT
449765 TAAA
1 TAAA
449769 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAAATATTTTATATATT
Found at i:450601 original size:2 final size:2
Alignment explanation
Indices: 450589--450618 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
450579 TTCACTAAGC
*
450589 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
450619 ATAGAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:450892 original size:26 final size:28
Alignment explanation
Indices: 450863--450927 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
450853 TACCTATTCA
*
450863 TAATTTTTTTTTATCA-TATTTAT-AT-T
1 TAATTTTTTTTTA-AATTATTTATAATAT
*
450889 TAATATTTTTTTAAATTATTTATAATAAT
1 TAATTTTTTTTTAAATTATTTATAAT-AT
450918 TAATTTTTTT
1 TAATTTTTTT
450928 ATATTTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 1 0.03
26 19 0.59
27 2 0.06
29 10 0.31
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TAATTTTTTTTTAAATTATTTATAATAT
Found at i:450935 original size:25 final size:25
Alignment explanation
Indices: 450862--450935 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
450852 TTACCTATTC
*
450862 ATAATTTTTTTTTATCATATTTATAT
1 ATAATATTTTTTTAT-ATATTTATAT
* *
450888 TTAATATTTTTTTAAATTATTTATA-
1 ATAATATTTTTTTATA-TATTTATAT
450913 ATAATTAATTTTTTTATAT-TTTA
1 ATAA-T-ATTTTTTTATATATTTA
450936 CTTTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 8 0.20
26 22 0.55
27 10 0.25
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (25 bp):
ATAATATTTTTTTATATATTTATAT
Found at i:450959 original size:19 final size:19
Alignment explanation
Indices: 450921--450959 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
450911 TAATAATTAA
* * *
450921 TTTTTTTATATTTTACTTT
1 TTTTTTTAAATATTAATTT
450940 TTTTTTTAAATATTAATTT
1 TTTTTTTAAATATTAATTT
450959 T
1 T
450960 ATTTAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTAAATATTAATTT
Found at i:453252 original size:2 final size:2
Alignment explanation
Indices: 453245--453272 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
453235 AATCCATGAA
453245 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
453273 TCTAATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:457455 original size:2 final size:2
Alignment explanation
Indices: 457448--457474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
457438 CATGTTCAGA
457448 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
457475 GGAGCAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:459633 original size:105 final size:105
Alignment explanation
Indices: 459349--459727 Score: 380
Period size: 105 Copynumber: 3.6 Consensus size: 105
459339 AATGTTATCC
* ** * * *
459349 TATTTAAATACGTAATTTTA-TAAAGTATTTAAATTAAAATTAATAAATATTTCAAAATAGAGTT
1 TATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAATAAATAAATATTTAAAAATAGAGTT
*
459413 TACATTATATTAATCTACTTTAAAATTAATAAAAAAATTTC-
66 TACATTATATTAATCCACTTTAAAATTAAT--AAAAATTTCT
* * * *
459454 TATTTAAATATATAATTTTATT-A-TT-TTAAAATTTAAATCTATATAAATGTTTAAAAATTA-A
1 TATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAA--TAAATAAATATTTAAAAA-TAGA
*
459515 GTTTACATTATATTAATCCA-TATTAAAATTAATAAAATTTTCT
63 GTTTACATTATATTAATCCACT-TTAAAATTAATAAAAATTTCT
* *
459558 TATTTTAATATGTAATTTTATTAATTTATTTAAATTTAAATAAATAAATATTTAAAAATAGAGTC
1 TATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAATAAATAAATATTTAAAAATAGAGTT
* * * * **
459623 CAAATGATATTATTAAACGACTTTAAAATTAAT-AAACCTTCT
66 TACAT--TA-TATTAATCCACTTTAAAATTAATAAAAATTTCT
* *
459665 TATTTTAAATATGTAATTTTTATTAATTTTTTTCAATTTAAATGAACA-AAATATTTAAAAATA
1 TA-TTTAAATATGTAA-TTTTATTAATTTATTTAAATTTAAAT-AA-ATAAATATTTAAAAATA
459728 AAATCCACAT
Statistics
Matches: 230, Mismatches: 26, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
103 18 0.08
104 24 0.10
105 87 0.38
106 5 0.02
107 22 0.10
108 31 0.13
109 25 0.11
110 17 0.07
111 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (105 bp):
TATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAATAAATAAATATTTAAAAATAGAGTT
TACATTATATTAATCCACTTTAAAATTAATAAAAATTTCT
Found at i:459802 original size:65 final size:67
Alignment explanation
Indices: 459670--459794 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 67
459660 CTTCTTATTT
* *
459670 TAAATATGTAATTTTTATTAATTTTTTTCAATTTAAATGAACAAAATATTTAAAAATAAAATCCA
1 TAAATATGTAATTTTTATTAATTTATTTAAATTTAAATGAACAAAATATTTAAAAATAAAATCCA
459735 CA
66 CA
* *
459737 TAAATATGTAA-TTTTATT-ATATTATTTAAATTTAAATTAA-TAAATATTTAAAAATAAA
1 TAAATATGTAATTTTTATTAAT-TTATTTAAATTTAAATGAACAAAATATTTAAAAATAAA
459795 TTTCACATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
65 19 0.36
66 23 0.43
67 11 0.21
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (67 bp):
TAAATATGTAATTTTTATTAATTTATTTAAATTTAAATGAACAAAATATTTAAAAATAAAATCCA
CA
Found at i:464772 original size:5 final size:5
Alignment explanation
Indices: 464762--464803 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
464752 TATTTATTAC
*
464762 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAGT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
464804 GTCCATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:471561 original size:21 final size:19
Alignment explanation
Indices: 471536--471591 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
471526 AATAATTTAA
*
471536 ATATTAAATATTTATTTATTT
1 ATATTAAATA-TTAATT-TTT
*
471557 ATATTATATATTAATTTTT
1 ATATTAAATATTAATTTTT
* *
471576 ATATTATATTTTAATT
1 ATATTAAATATTAATT
471592 ATAAATGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 18 0.56
20 5 0.16
21 9 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTAAATATTAATTTTT
Found at i:471565 original size:19 final size:18
Alignment explanation
Indices: 471543--471591 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
471533 TAAATATTAA
*
471543 ATATTTATTTATTTATATT
1 ATATTTAATT-TTTATATT
471562 ATATATTAATTTTTATATT
1 ATAT-TTAATTTTTATATT
471581 ATATTTTAATT
1 ATA-TTTAATT
471592 ATAAATGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTAATTTTTATATT
Found at i:471612 original size:2 final size:2
Alignment explanation
Indices: 471605--471634 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
471595 AATGTACGTC
*
471605 AT AT AT AT AT TT 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
471635 TGTAGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:473513 original size:4 final size:4
Alignment explanation
Indices: 473504--473529 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
473494 TCAATTCTTG
473504 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
473530 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:479112 original size:91 final size:92
Alignment explanation
Indices: 478955--479140 Score: 347
Period size: 91 Copynumber: 2.0 Consensus size: 92
478945 GGTTGAACTT
478955 TGATGTATGCAGAACGTCATGTATTGTCTATACATGCTCTGTGGTATCATCTTTAAGTGTTGGAG
1 TGATGTATGCAGAACGTCATGTATTGTCTATA-ATGCTCTGTGGTATCATCTTTAAGTGTTGGAG
479020 GGGATGGGTACAGAGAGTGGAGGAAAGG
65 GGGATGGGTACAGAGAGTGGAGGAAAGG
*
479048 TGATGTATGCAGAACGTCATGTATTGTCTAT-ATGCTTTGTGGTATCATCTTTAAGTGTTGGAGG
1 TGATGTATGCAGAACGTCATGTATTGTCTATAATGCTCTGTGGTATCATCTTTAAGTGTTGGAGG
479112 GGATGGGTACAGAGAGTGGAGGAAAGG
66 GGATGGGTACAGAGAGTGGAGGAAAGG
479139 TG
1 TG
479141 TTTGGGATAT
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
91 61 0.66
93 31 0.34
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (92 bp):
TGATGTATGCAGAACGTCATGTATTGTCTATAATGCTCTGTGGTATCATCTTTAAGTGTTGGAGG
GGATGGGTACAGAGAGTGGAGGAAAGG
Found at i:482967 original size:23 final size:24
Alignment explanation
Indices: 482917--482971 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
482907 AATAATAAAA
*
482917 ATAATATTTTTATTTAAATTTAATT
1 ATAAAATTTTTA-TTAAATTTAATT
482942 ATAAAATTTTTA-TAAATATTAA-T
1 ATAAAATTTTTATTAAAT-TTAATT
482965 ATAAAAT
1 ATAAAAT
482972 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 13 0.46
24 4 0.14
25 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAAATTTTTATTAAATTTAATT
Found at i:483518 original size:2 final size:2
Alignment explanation
Indices: 483511--483553 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
483501 ATTGCCACAA
*
483511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
483552 AT
1 AT
483554 GTCGTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:487731 original size:13 final size:13
Alignment explanation
Indices: 487715--487744 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
487705 ATTTTTAAAA
*
487715 AATATTTATATTT
1 AATATTTATATAT
487728 AATATTTATATAT
1 AATATTTATATAT
487741 AATA
1 AATA
487745 AATAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTATATAT
Found at i:487757 original size:19 final size:19
Alignment explanation
Indices: 487734--487772 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
487724 ATTTAATATT
487734 TATATATAATAAATAATTAAA
1 TATATAT-ATAAAT-ATTAAA
487755 TATATATATAAATATTAA
1 TATATATATAAATATTAA
487773 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATATATAAATATTAAA
Found at i:487805 original size:17 final size:18
Alignment explanation
Indices: 487774--487809 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
487764 AAATATTAAT
487774 TTTTAAAAAAATAAAAAA
1 TTTTAAAAAAATAAAAAA
*
487792 TTTT-AAAAATTAAAAAA
1 TTTTAAAAAAATAAAAAA
487809 T
1 T
487810 ATATCTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTTAAAAAAATAAAAAA
Found at i:491362 original size:2 final size:2
Alignment explanation
Indices: 491355--491383 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
491345 AATATTCATA
491355 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
491384 GCATCTGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:491602 original size:2 final size:2
Alignment explanation
Indices: 491597--491644 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
491587 AAATGAAAAA
* * *
491597 AT AT AT AT AT AT AT AT A- AT -T CT CT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
491637 AT AT AT AT
1 AT AT AT AT
491645 GGTTAGAGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:492469 original size:2 final size:2
Alignment explanation
Indices: 492462--492489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
492452 TTAAATCTTA
492462 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
492490 TTGTGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:498571 original size:19 final size:20
Alignment explanation
Indices: 498549--498596 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
498539 ATATTTCGAA
*
498549 TTAATTTAAAATAGTA-ATT
1 TTAATTTAAAATAATATATT
*
498568 TTAAATTAAAATAATATATT
1 TTAATTTAAAATAATATATT
498588 TT-ATTTAAA
1 TTAATTTAAA
498597 TTTAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAATTTAAAATAATATATT
Found at i:499022 original size:41 final size:39
Alignment explanation
Indices: 498968--499090 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 39
498958 ATATACTATT
*
498968 AATAAAT-TAAATAATTTT-ATCTAATTAAAATTTATTTAAA
1 AATAAATATAAATAATTTTAAT-TAAATAAAA-TTA-TTAAA
*
499008 AATAAATATAAATAATTTTAATTAAATAATATTATTAAA
1 AATAAATATAAATAATTTTAATTAAATAAAATTATTAAA
* *
499047 AATATATTTATAAATAATTAATATATTAAATATAAATTTATTAA
1 AATA-A-ATATAAATAATT-TTA-ATTAAATA-AAA-TTATTAA
499091 TAATCGAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
39 9 0.13
40 11 0.16
41 29 0.41
42 4 0.06
43 8 0.11
44 2 0.03
45 7 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
AATAAATATAAATAATTTTAATTAAATAAAATTATTAAA
Found at i:499076 original size:30 final size:30
Alignment explanation
Indices: 499017--499094 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
499007 AAATAAATAT
* *
499017 AAATAATTT-TAATTAAATAATATTATTAA
1 AAATAATTTATAAATAATTAATATTATTAA
499046 AAATATATTTATAAATAATTAATA-TATTAA
1 AAATA-ATTTATAAATAATTAATATTATTAA
* *
499076 ATATAAATTTATTAATAAT
1 AAAT-AATTTATAAATAAT
499095 CGAAATGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.12
30 25 0.60
31 12 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATAATTTATAAATAATTAATATTATTAA
Found at i:499491 original size:31 final size:31
Alignment explanation
Indices: 499450--499527 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
499440 TTTAAAATCA
* *
499450 TAAATTAATTTATATTAATTTAATA-AAAAAT
1 TAAATAAATTTATATTAA-TAAATATAAAAAT
* *
499481 TTAATAAATTTATTTTAATAAATATAAAAAT
1 TAAATAAATTTATATTAATAAATATAAAAAT
* *
499512 TAAATATATTTTTATT
1 TAAATAAATTTATATT
499528 TTTTAAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAATAAATTTATATTAATAAATATAAAAAT
Found at i:499556 original size:32 final size:33
Alignment explanation
Indices: 499489--499556 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
499479 ATTTAATAAA
*
499489 TTTATTTTAATAAATATAAAAATTAAATATATT
1 TTTATTTTAATAAATATAAAAAATAAATATATT
* * *
499522 TTTATTTT-TTAAAT-TAAAATAATAATTATTTT
1 TTTATTTTAATAAATATAAAA-AATAAATATATT
499554 TTT
1 TTT
499557 TAAAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 5 0.17
32 17 0.57
33 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTATTTTAATAAATATAAAAAATAAATATATT
Done.