Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1179
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1367275
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 72735 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:292145 original size:36 final size:36
Alignment explanation
Indices: 292098--292169 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
292088 TGTAAAGATG
*
292098 GGTGTCCAATAAATCAAAATGATATTGGATGTTCTT
1 GGTGTCCAATAAAACAAAATGATATTGGATGTTCTT
* *
292134 GGTGTCCAATAAAACAATATTATATTGGATGTTCTT
1 GGTGTCCAATAAAACAAAATGATATTGGATGTTCTT
292170 AATGATTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (36 bp):
GGTGTCCAATAAAACAAAATGATATTGGATGTTCTT
Found at i:294009 original size:12 final size:12
Alignment explanation
Indices: 293993--294037 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
293983 CCCCCCCCCC
293993 AAAAAAA-AAAA
1 AAAAAAACAAAA
*
294004 ACAAAAACAAAA
1 AAAAAAACAAAA
**
294016 AAAAAAACCCAA
1 AAAAAAACAAAA
294028 AAAAAAACAA
1 AAAAAAACAA
294038 CTAAGATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 6 0.22
12 21 0.78
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:294033 original size:14 final size:14
Alignment explanation
Indices: 293993--294034 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
293983 CCCCCCCCCC
*
293993 AAAAA-AAAAAAAC
1 AAAAACAAAAAAAA
294006 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
**
294020 AAACCCAAAAAAAA
1 AAAAACAAAAAAAA
294034 A
1 A
294035 CAACTAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:299022 original size:2 final size:2
Alignment explanation
Indices: 299015--299072 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
299005 CACCAACGAT
299015 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
299057 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
299073 AAATAATCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:300294 original size:27 final size:27
Alignment explanation
Indices: 300234--300309 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
300224 TTAAAATTAA
* *
300234 ATCGCAACAAATG-ATAATAAATGAATT
1 ATCGCAACAAATGAAT-ATCAATGAATC
*
300261 ATTGCAACAAATGAATATCAAT-ATATC
1 ATCGCAACAAATGAATATCAATGA-ATC
*
300288 ATCGCAACAAATGATTATCAAT
1 ATCGCAACAAATGAATATCAAT
300310 CAATTAATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 39 0.93
28 2 0.05
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (27 bp):
ATCGCAACAAATGAATATCAATGAATC
Found at i:301146 original size:54 final size:53
Alignment explanation
Indices: 301087--301188 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
301077 ATATATCATT
**
301087 GCAACAAATGATTATCAA-CTAATAAATCATCTTAACAAATGATGAATCATTATC
1 GCAACAAATGATTATCAATC-AATAAATCATCGCAACAAATGA-GAATCATTATC
* *
301141 GCAACAAATGATTATTAATCAATAAATCATCGCAACTAATGAGAATCA
1 GCAACAAATGATTATCAATCAATAAATCATCGCAACAAATGAGAATCA
301189 ATGGATAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
53 6 0.14
54 36 0.84
55 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (53 bp):
GCAACAAATGATTATCAATCAATAAATCATCGCAACAAATGAGAATCATTATC
Found at i:301515 original size:4 final size:4
Alignment explanation
Indices: 301501--301534 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
301491 TCTAATAAAA
301501 TTAT GTTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
301535 GATGTGCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:304006 original size:1 final size:1
Alignment explanation
Indices: 304000--304025 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
303990 TTGATGTGGA
304000 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
304026 TTGTTGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:307473 original size:2 final size:2
Alignment explanation
Indices: 307466--307504 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
307456 TAAATGTCCT
307466 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
307505 TTTTAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:308208 original size:21 final size:20
Alignment explanation
Indices: 308178--308216 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
308168 TTGTTTATTT
308178 TTTAATTTAC-CATTATTTTC
1 TTTAATTTACACA-TATTTTC
308198 TTTATATTTACACATATTT
1 TTTA-ATTTACACATATTT
308217 GTCAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATTTACACATATTTTC
Found at i:310894 original size:2 final size:2
Alignment explanation
Indices: 310889--310958 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
310879 TGTGTGTATA
310889 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
310931 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
310959 TAAATCTAAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:320065 original size:18 final size:18
Alignment explanation
Indices: 320033--320081 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
320023 GGCGATGAAA
320033 AGAAAGAAGGA-GAGGAAG
1 AGAAA-AAGGAGGAGGAAG
*
320051 AGAAAAAGGAGGAGGAGG
1 AGAAAAAGGAGGAGGAAG
* *
320069 TGAAAAAAGAGGA
1 AGAAAAAGGAGGA
320082 ACCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (18 bp):
AGAAAAAGGAGGAGGAAG
Found at i:325499 original size:2 final size:2
Alignment explanation
Indices: 325492--325545 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
325482 AAATTAAAAG
325492 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
325534 TC TC TC TC TC TC
1 TC TC TC TC TC TC
325546 ATTGGATTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:326272 original size:13 final size:13
Alignment explanation
Indices: 326254--326278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326244 TATCTATCAA
326254 AATTAACTAAATG
1 AATTAACTAAATG
326267 AATTAACTAAAT
1 AATTAACTAAAT
326279 AAAAGTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
AATTAACTAAATG
Found at i:330490 original size:166 final size:166
Alignment explanation
Indices: 330209--331078 Score: 1300
Period size: 166 Copynumber: 5.3 Consensus size: 166
330199 GGTGCGACTG
*
330209 TATATAAAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
1 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
* * *
330274 TGTGGATGCAT-TCTCAGGTAGTGTAGATTCAAACTTGTGTAAATCATGACCCCCGGGGGTAGGG
66 TGTGGAAGCATCT-TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGG
*
330338 TGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAA
130 TGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAA
*
330375 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTT
1 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
* *
330440 TGTGAAAGCATCTTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCC-GGGGTAGGGT
66 TGTGGAAGCATCTTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGT
*
330504 GGGGCCACAATGGGGGATCGAAGTTTTACATAGGAA
131 GGGGCCACAATGGGGGATCGAAGTTTAACATAGGAA
330540 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
1 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
*
330605 TGTGGATGCAT-TCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGG
66 TGTGGAAGCATCT-TCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGG
330669 TGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAA
130 TGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAA
* * *
330706 TATATAGAGTAAATCTTTAAAAATCCTCTTCTCAGAAACTAATCGG-CTGGCAAAGCTGAAACTT
1 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGG-AAAGCTGACACTT
* * * * * * *
330770 GTGTGGAAGCATCCTCAGGTAGTGTAGATTCATAGCTGTGAAAATAATAACCCCTGGGGGTATGG
65 GTGTGGAAGCATCTTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGG
* * *
330835 TTGGGCCACAATGGGGGGGTCGAAGTTTAACATATG--
130 TGGGGCCACAAT-GGGGGATCGAAGTTTAACATAGGAA
* *
330871 -AT-T--A-T--ATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTG
1 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
* * * *
330929 TGTGAAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGT
66 TGTGGAAGCATCTTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGT
* * *
330994 GGGGCCACAATGGGGGGTCAAAGTTTAACAAAGGAA
131 GGGGCCACAATGGGGGATCGAAGTTTAACATAGGAA
* *
331030 TATAT-GGGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1 TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAG
331079 ATGATTCTTT
Statistics
Matches: 646, Mismatches: 43, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
157 20 0.03
158 112 0.17
159 3 0.00
160 3 0.00
161 2 0.00
163 2 0.00
164 3 0.00
165 200 0.31
166 279 0.43
167 22 0.03
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (166 bp):
TATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGACACTTG
TGTGGAAGCATCTTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGT
GGGGCCACAATGGGGGATCGAAGTTTAACATAGGAA
Found at i:334796 original size:15 final size:15
Alignment explanation
Indices: 334778--334809 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
334768 GTTGAGATTT
*
334778 TAAAGATTGATTTAA
1 TAAAGATTGATTGAA
334793 TAAAGATTGATTGAA
1 TAAAGATTGATTGAA
334808 TA
1 TA
334810 TATGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (15 bp):
TAAAGATTGATTGAA
Found at i:340607 original size:22 final size:22
Alignment explanation
Indices: 340581--340812 Score: 118
Period size: 22 Copynumber: 10.7 Consensus size: 22
340571 ACAAGATTAT
* *
340581 GTAACCATAAGTGTTACAATAT
1 GTAACCATGAGTGTTACAATAC
* *
340603 TTAACCATGAGTGTTACAGTAC
1 GTAACCATGAGTGTTACAATAC
340625 GTAACCATGAGTGTTACAGAT--
1 GTAACCATGAGTGTTACA-ATAC
* * *
340646 GAAACCATGAATG-TA-ACTAC
1 GTAACCATGAGTGTTACAATAC
* * * *** *
340666 ATAACCATGATTGTAATGGTAT
1 GTAACCATGAGTGTTACAATAC
* * * * **
340688 ATAACAATAAGTGTTACAGTGT
1 GTAACCATGAGTGTTACAATAC
*
340710 GTAACCATGGGTGTTACACAT--
1 GTAACCATGAGTGTTACA-ATAC
* * ***
340731 GTAA-CTTCGAGGGTTATGGTAC
1 GTAACCAT-GAGTGTTACAATAC
* *
340753 ATAACCATGAGTGTTACAGTAC
1 GTAACCATGAGTGTTACAATAC
* *
340775 GTAACCATGAGTGTTACAGTAT
1 GTAACCATGAGTGTTACAATAC
340797 GTAACCATGAGTGTTA
1 GTAACCATGAGTGTTA
340813 TATAGTACAA
Statistics
Matches: 159, Mismatches: 41, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 15 0.09
21 22 0.14
22 116 0.73
23 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (22 bp):
GTAACCATGAGTGTTACAATAC
Found at i:340792 original size:87 final size:85
Alignment explanation
Indices: 340582--340812 Score: 239
Period size: 85 Copynumber: 2.7 Consensus size: 85
340572 CAAGATTATG
* * * * *
340582 TAACCATAAGTGTTACAATATTTAACCATGAGTGTTACAGTACGTAACCATGAGTGTTACAGATG
1 TAACCATGAGTGTTACAGTATATAACCATGAGTGTTACAGTATGTAACCATGAGTGTTACACATG
*
340647 AAACCATGAATGTAACTACA
66 AAACCATGAAGGTAACTACA
* * ** * * * *
340667 TAACCATGATTGTAATGGTATATAACAATAAGTGTTACAGTGTGTAACCATGGGTGTTACACATG
1 TAACCATGAGTGTTACAGTATATAACCATGAGTGTTACAGTATGTAACCATGAGTGTTACACATG
* * * **
340732 TAA-CTTCGAGGGTTATGGTACA
66 AAACCAT-GAAGG-TA-ACTACA
**
340754 TAACCATGAGTGTTACAGTACGTAACCATGAGTGTTACAGTATGTAACCATGAGTGTTA
1 TAACCATGAGTGTTACAGTATATAACCATGAGTGTTACAGTATGTAACCATGAGTGTTA
340813 TATAGTACAA
Statistics
Matches: 114, Mismatches: 29, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
84 2 0.02
85 57 0.50
86 2 0.02
87 53 0.46
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (85 bp):
TAACCATGAGTGTTACAGTATATAACCATGAGTGTTACAGTATGTAACCATGAGTGTTACACATG
AAACCATGAAGGTAACTACA
Found at i:344229 original size:29 final size:29
Alignment explanation
Indices: 344161--344222 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
344151 TGACACTTGA
** *
344161 TAATCAACTTTTAGAGTGTCTGTTTTGGG
1 TAATCAACTTTTAGAGTGTCTGAATAGGG
344190 TAATCAACTTTTAGAGTGTCTGAATAGGG
1 TAATCAACTTTTAGAGTGTCTGAATAGGG
344219 TAAT
1 TAAT
344223 TCTCTTTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (29 bp):
TAATCAACTTTTAGAGTGTCTGAATAGGG
Found at i:351389 original size:11 final size:11
Alignment explanation
Indices: 351375--351407 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
351365 TCAAACAAAG
351375 TTCAAAGTTCA
1 TTCAAAGTTCA
351386 TTCAAAGTTCA
1 TTCAAAGTTCA
*
351397 CTCAAAGTTCA
1 TTCAAAGTTCA
351408 AAGTTCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
TTCAAAGTTCA
Found at i:351396 original size:29 final size:28
Alignment explanation
Indices: 351360--351414 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
351350 CATAATGCAA
351360 CAAATTCAAACAAAGTTCAAAGTTCATT
1 CAAATTCAAACAAAGTTCAAAGTTCATT
**
351388 CAAAGTTCACTCAAAGTTCAAAGTTCA
1 CAAA-TTCAAACAAAGTTCAAAGTTCA
351415 CAGGTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (28 bp):
CAAATTCAAACAAAGTTCAAAGTTCATT
Found at i:352123 original size:11 final size:11
Alignment explanation
Indices: 352109--352141 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
352099 TCAAACAAAG
352109 TTCAAAGTTCA
1 TTCAAAGTTCA
352120 TTCAAAGTTCA
1 TTCAAAGTTCA
*
352131 CTCAAAGTTCA
1 TTCAAAGTTCA
352142 AAGTTCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
TTCAAAGTTCA
Found at i:352130 original size:29 final size:28
Alignment explanation
Indices: 352094--352148 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
352084 CATAATTCAA
352094 CAAATTCAAACAAAGTTCAAAGTTCATT
1 CAAATTCAAACAAAGTTCAAAGTTCATT
**
352122 CAAAGTTCACTCAAAGTTCAAAGTTCA
1 CAAA-TTCAAACAAAGTTCAAAGTTCA
352149 CAGGTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (28 bp):
CAAATTCAAACAAAGTTCAAAGTTCATT
Found at i:359642 original size:16 final size:16
Alignment explanation
Indices: 359617--359651 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
359607 TCAGAGAAAA
*
359617 ATTATCAGATTAACCG
1 ATTATCAGATGAACCG
*
359633 ATTATTAGATGAACCG
1 ATTATCAGATGAACCG
359649 ATT
1 ATT
359652 TAGCGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (16 bp):
ATTATCAGATGAACCG
Found at i:361269 original size:13 final size:13
Alignment explanation
Indices: 361251--361276 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
361241 TTGTGTTTTA
361251 ACACATTCAGGAT
1 ACACATTCAGGAT
361264 ACACATTCAGGAT
1 ACACATTCAGGAT
361277 CTTTTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
ACACATTCAGGAT
Found at i:362511 original size:2 final size:2
Alignment explanation
Indices: 362504--362543 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
362494 TCGAGTACTG
362504 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
362544 AAAAGTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:362715 original size:2 final size:2
Alignment explanation
Indices: 362708--362748 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
362698 ATTTTTCATT
362708 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
362749 CATATACTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:367047 original size:40 final size:41
Alignment explanation
Indices: 367003--367081 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 41
366993 GGAAGACAAT
* *
367003 GTTTATAAAAATG-CTGTAGAAATGA-TGGTAGGATAAAAAA
1 GTTTAGAAAAA-GTCTGTAGAAATGAGTGATAGGATAAAAAA
*
367043 GTTTAGAAACAGTCTGTAGAAATGAGTTGATAGGATAAA
1 GTTTAGAAAAAGTCTGTAGAAATGAG-TGATAGGATAAA
367082 TTTTGTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.03
40 21 0.64
42 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (41 bp):
GTTTAGAAAAAGTCTGTAGAAATGAGTGATAGGATAAAAAA
Found at i:367172 original size:42 final size:42
Alignment explanation
Indices: 367085--367427 Score: 550
Period size: 42 Copynumber: 8.2 Consensus size: 42
367075 GGATAAATTT
* * * *
367085 TGTTAATTACCAGGCTGTAAAGATG--T-GTTAGTAGAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
* *
367124 TGTTTA-TATGCAGGCTGTGGAGATGTTTCGGTAGGAGAACAG
1 TGTTTATTA-GCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
*
367166 TGTTTATTTGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
367208 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
* *
367250 TGTTTATTAGCAGGCTGTAGAGATGTTTTGGTAGGAGAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
367292 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
367334 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
* *
367376 TGTTTATTAGCAGGCTGTAGAGATGTTTCGGTAGGAAAACAG
1 TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
367418 TGTTTATTAG
1 TGTTTATTAG
367428 TGTTTGTTTA
Statistics
Matches: 283, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
38 2 0.01
39 18 0.06
41 1 0.00
42 261 0.92
43 1 0.00
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.34
Consensus pattern (42 bp):
TGTTTATTAGCAGGCTGTAGAGATGTTTCGTTAGGAGAACAG
Found at i:368257 original size:44 final size:44
Alignment explanation
Indices: 368203--369811 Score: 1156
Period size: 44 Copynumber: 35.8 Consensus size: 44
368193 TGTGGCTCTT
368203 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
*
368247 GTATGTAAGTACCGCAGAGAATCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
368291 ATATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
368335 GTATGTAAGTACCACAGAGAACCACACAGTGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
*
368379 GTATGTAAGTACCGCAGAGAACCACACAGAGGGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
*
368423 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* * *
368467 GTATGTAAGTACC-C-GAGAATCACACAGAGGGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
*
368509 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
368553 GTATGTAAGTACCGCAGAGAACCACACAGAAAAGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
*
368597 GTATGTAAGTACCGCAGAGAACAACACAGAG-GGAGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGG-GGTGGCCCTC
*
368641 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* * * *
368685 GTATGTAAGTACTGCAGAGAATCACACAGAGGGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
*
368729 GTATGTAAGTACCGCAGAGAACCACACAGAGA-GGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
368772 GTATGTAAGTACCACAGAGAACCACACAGAGAAGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* * * * * *
368816 GTTTGTAAGTACCACAGAGAACCAGACACAGAGGGATGTCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
368860 GTATGTAAGTACCGCAGAGAATCACACAGAGAGGGGTGGCCCTA
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
** * **** **** *
368904 GTATGTAAGTACCGCAGAGAANTA-AAAGATGAAAAATAATGCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGA-GAGGGGTGGCCCTC
*** ** * ** *** * *
368948 GTA-G-ATA-TA--G--GA-ATTTA-TTAGATA-TTGTTTACATAA
1 GTATGTA-AGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCT-C
* * *** * * * * **** ***
368984 GTTTATTTTAGGTTAATTCTAAATAA-TACATGTATTGATGATAAAT-GTATTC
1 G--TA-TGTAAG-TACCGC-AGAGAACCACA--CA--GA-GAGGGGTGGCCCTC
* * * * * * * ** * * *
369036 ATAAATGATGAA-AACTCTTG-ATAAGAATGCAGTATA-ACTATTTTGATGTCCAGTC
1 GT--ATG-T-AAGTAC-C--GCA-GAGAA-CCA-CACAGA-GA--GGGGTGGCC-CTC
* * * * * * * * *** * *
369091 TGTATGTAGTGTTATTATTCTCAG-GCATTCCTCTTTCCTCGACACCTGT-TCACTAC
1 -GTATGTA-----AGTA-CCGCAGAG-A-ACCAC---AC-AGAGAGGGGTGGCCCT-C
*** * * * * * * ***
369147 G-ATGTACGAG-GGGGAATATGAAAACACGCTGCCGATCCGGCTTTATGGTGTGGCTC
1 GTATGTA--AGTACCGCAGA-G-AACCACACAG-AGA---GG------GGTGGCCCTC
* * * ** *
369203 -T-TGTATGTA-AGTACCGCAG-AGAACCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCG--CAG-AGAACCA-CACAGAGAG--GGGTGGCCCTC
*
369249 GTATGTAAGTACCGCAGAGAATCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* * *
369293 ATATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
369337 GTATGTAAGTACCGCAGAGAATCACACAGAG-GGAGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGG-GGTGGCCCTC
369381 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
369425 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
369469 GTATGTAAGTACCGCAGAGAATCACACAGAG-GGAGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGG-GGTGGCCCTC
*
369513 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTT
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
369557 GTATGTAAGTACCGCAGAGAATCACACGGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
369601 GTATGTAAGTACCACAGAGAATCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* *
369645 GTATGTAAGTACCACAGAGAATCACACAGAGAGGGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* * *
369689 GTATGTAAGTACCACAGAGAATCACACAGAGAGGAGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
* * *
369733 CTATGTAAGTACCTCAGAGAATCACACAGAG-GGAGGTGGCCCTC
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGG-GGTGGCCCTC
* * *
369777 TTATGTAAGTACCGCAGAGAATCACACGGAGAGGG
1 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGG
369812 AAATGGCAAT
Statistics
Matches: 1282, Mismatches: 192, Indels: 182
0.77 0.12 0.11
Matches are distributed among these distances:
35 2 0.00
36 2 0.00
37 6 0.00
38 4 0.00
40 1 0.00
41 1 0.00
42 44 0.03
43 57 0.04
44 1037 0.81
45 8 0.01
46 18 0.01
47 10 0.01
48 8 0.01
49 2 0.00
50 6 0.00
51 7 0.01
52 7 0.01
53 17 0.01
54 13 0.01
55 11 0.01
56 11 0.01
57 6 0.00
58 2 0.00
59 1 0.00
60 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19
Consensus pattern (44 bp):
GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTC
Found at i:368431 original size:132 final size:132
Alignment explanation
Indices: 368203--369811 Score: 1281
Period size: 132 Copynumber: 11.9 Consensus size: 132
368193 TGTGGCTCTT
*
368203 GTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* * *
368268 TCACACAGAGAGGGGTGGCCCTCATATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCC
66 CCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
368333 TC
131 TC
*
368335 GTATGTAAGTACCACAGAGAACCACACAGTGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
*
368400 CCACACAGAGGGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
66 CCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
*
368465 TT
131 TC
* * *
368467 GTATGTAAGTACC-C-GAGAATCACACAGAGGGGGGTGGCCCTTGTATGTAAGTACCGCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* * *
368530 CCACACAGAGAGGGGTGGCCCTTGTATGTAAGTACCGCAGAGAACCACACAGAAAAGGGTGGCCC
66 CCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
368595 TC
131 TC
* *
368597 GTATGTAAGTACCGCAGAGAACAACACAGAG-GGAGGTGGCCCTCGTATGTAAGTACCGCAGAGA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGG-GGTGGCCCTCGTATGTAAGTACCGCAGAGA
* * * *
368661 ACCACACAGAGAGGGGTGGCCCTTGTATGTAAGTACTGCAGAGAATCACACAGAGGGGGGTGGCC
65 ACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCC
*
368726 CTT
130 CTC
* * *
368729 GTATGTAAGTACCGCAGAGAACCACACAGAGA-GGGTGGCCCTTGTATGTAAGTACCACAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* * * * * * *
368793 CCACACAGAGAAGGGTGGCCCTCGTTTGTAAGTACCACAGAGAACCAGACACAGAGGGATGTCCC
66 CCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
368858 TC
131 TC
* * *
368860 GTATGTAAGTACCGCAGAGAATCACACAGAGAGGGGTGGCCCTAGTATGTAAGTACCGCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
** * **** **** * *** ** * ** ***
368925 NTA-AAAGATGAAAAATAATGCTTGTA-G-ATA-TA--G--GA-ATTTA-TTAGATA-TTGTTTA
66 CCACACAGA-GAGGGGTGGCCCTCGTATGTA-AGTACCGCAGAGAACCACACAGAGAGGGGTGGC
* *
368979 CATAA
129 CCT-C
* * *** * * * * **** *** *
368984 GTTTATTTTAGGTTAATTCTAAATAA-TACATGTATTGATGATAAAT-GTATTCATAAATGATGA
1 G--TA-TGTAAG-TACCAC-AGAGAACCACA--CA--GA-GAGGGGTGGCCCTCGT--ATG-T-A
* * * * * * ** * * * *
369047 A-AACTCTTG-ATAAGAATGCAGTATA-ACTATTTTGATGTCCAGTCTGTATGTAGTGTTATTAT
52 AGTAC-C--GCA-GAGAA-CCA-CACAGA-GA--GGGGTGGCC-CTC-GTATGTA-----AGTA-
* * * * * * * *** * *
369109 TCTCAG-GCATTCCTCTTTCCTCGACACCTGT-TCACTAC
100 CCGCAGAG-A-ACCAC---AC-AGAGAGGGGTGGCCCT-C
**** * * * * * * * *
369147 G-ATGTACGAGGGGGAATATGAAAACACGCTGCCGATCCGGCTTTATGGTGTGGCTCTTGTATGT
1 GTATGTA--A-GTACCACA-GAGAAC-CAC-ACAGA----G----A-GGGGTGGCCCTCGTATGT
*
369211 AAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAATCACAC
51 AAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACAC
369276 AGAGAGGGGTGGCCCTC
116 AGAGAGGGGTGGCCCTC
* *
369293 ATATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTTGTATGTAAGTACCGCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* *
369358 TCACACAGAG-GGAGGTGGCCCTTGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCC
66 CCACACAGAGAGG-GGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCC
369422 CTC
130 CTC
*
369425 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTTGTATGTAAGTACCGCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* *
369490 TCACACAGAG-GGAGGTGGCCCTTGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCC
66 CCACACAGAGAGG-GGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCC
*
369554 CTT
130 CTC
* * * *
369557 GTATGTAAGTACCGCAGAGAATCACACGGAGAGGGGTGGCCCTCGTATGTAAGTACCACAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* * *
369622 TCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCACAGAGAATCACACAGAGAGGGGTGGCCC
66 CCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
369687 TC
131 TC
* * * *
369689 GTATGTAAGTACCACAGAGAATCACACAGAGAGGAGTGGCCCTCCTATGTAAGTACCTCAGAGAA
1 GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
* * * *
369754 TCACACAGAG-GGAGGTGGCCCTCTTATGTAAGTACCGCAGAGAATCACACGGAGAGGG
66 CCACACAGAGAGG-GGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGG
369812 AAATGGCAAT
Statistics
Matches: 1197, Mismatches: 201, Indels: 158
0.77 0.13 0.10
Matches are distributed among these distances:
123 4 0.00
124 4 0.00
125 2 0.00
126 4 0.00
127 4 0.00
128 6 0.01
129 4 0.00
130 124 0.10
131 129 0.11
132 771 0.64
133 6 0.01
134 3 0.00
135 3 0.00
136 3 0.00
137 2 0.00
138 5 0.00
139 1 0.00
140 2 0.00
141 5 0.00
142 4 0.00
143 6 0.01
144 6 0.01
145 2 0.00
146 7 0.01
147 9 0.01
150 4 0.00
151 7 0.01
152 4 0.00
156 1 0.00
157 8 0.01
158 3 0.00
159 8 0.01
160 4 0.00
161 6 0.01
162 4 0.00
163 14 0.01
164 4 0.00
165 3 0.00
166 3 0.00
167 4 0.00
168 1 0.00
169 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19
Consensus pattern (132 bp):
GTATGTAAGTACCACAGAGAACCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAA
CCACACAGAGAGGGGTGGCCCTCGTATGTAAGTACCGCAGAGAACCACACAGAGAGGGGTGGCCC
TC
Found at i:374233 original size:52 final size:51
Alignment explanation
Indices: 374136--374270 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 51
374126 TAGTGGGGGA
* * * * *
374136 GGGAGGGGGAATAGCCCGATGAATGCATGTGATTTTTAGGGAAGGGAATGG
1 GGGAGGGGGAATAGCCCGATAAATGCATGTGATATCTAAGAAAGGGAATGG
* **
374187 GGGAGGGGGAATAGCCTTGATAAATGCATGTGATATCTAAGAAAGGGGGTGG
1 GGGAGGGGGAATAGCC-CGATAAATGCATGTGATATCTAAGAAAGGGAATGG
*
374239 GGGAGGGGGTCAATAGTCCCGATGAATGCATG
1 GGGAGGGGG--AATAG-CCCGATAAATGCATG
374271 AATCCTAGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
51 16 0.23
52 36 0.51
54 16 0.23
55 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.41, T:0.21
Consensus pattern (51 bp):
GGGAGGGGGAATAGCCCGATAAATGCATGTGATATCTAAGAAAGGGAATGG
Found at i:375544 original size:33 final size:33
Alignment explanation
Indices: 375503--375670 Score: 264
Period size: 33 Copynumber: 5.1 Consensus size: 33
375493 AATACTAGTA
*
375503 TATATATAGAAAGAAGTCCTCAATATTTATATG
1 TATATATAGAAAGAAATCCTCAATATTTATATG
* *
375536 TATATATAGAAAGAAGTTCTCAATATTTATATG
1 TATATATAGAAAGAAATCCTCAATATTTATATG
375569 TATATATAGAAAGAAATCCTCAATATTTATATG
1 TATATATAGAAAGAAATCCTCAATATTTATATG
* *
375602 AATATATAGAAAGAAATCCTCAATATTAATATG
1 TATATATAGAAAGAAATCCTCAATATTTATATG
* * *
375635 CATATATAGAAAGAAATCCTAAATATTTTTATG
1 TATATATAGAAAGAAATCCTCAATATTTATATG
375668 TAT
1 TAT
375671 CGGTATATTG
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 125 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.36
Consensus pattern (33 bp):
TATATATAGAAAGAAATCCTCAATATTTATATG
Found at i:385208 original size:2 final size:2
Alignment explanation
Indices: 385201--385263 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
385191 AATTAATAGA
385201 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
385243 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
385264 ATCACTCTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:392064 original size:2 final size:2
Alignment explanation
Indices: 392057--392137 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
392047 ATTGCTGAAG
392057 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
392099 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
392138 GAAAGCTGAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:396201 original size:189 final size:190
Alignment explanation
Indices: 395881--396260 Score: 710
Period size: 189 Copynumber: 2.0 Consensus size: 190
395871 ATAGCAATGA
395881 ATATCATTTTTGGGAGTTGATTTTAATAAACTCTCCTATGCAGTTACTCTGGCAAACCGAAAGTG
1 ATATCATTTTTGGGAGTTGATTTTAATAAACTCTCCTATGCAGTTACTCTGGCAAACCGAAAGTG
395946 AAACAGTGTTTGGACCTAAGCACAAATCATCACCGCTGACAAGATTTAGTTCTTGAAAATAATCG
66 AAACAGTGTTTGGACCTAAGCACAAATCATCACCGCTGACAAGATTTAGTTCTTGAAAATAATCG
*
396011 ATAAATTCGATGTAATGTATCTAGAAGCATTGGTTTT-AAAAAAAAACTTATTTATGAAT
131 ATAAATTCGATGTAATGTATCTAGAAGCATTGGTTTTAAAAAAAAAACTTATTTAAGAAT
*
396070 ATATCATTTTTGGGAGTTGATTTTAATCAACTCTCCTATGCAGTTACTCTGGCAAACCGAAAGTG
1 ATATCATTTTTGGGAGTTGATTTTAATAAACTCTCCTATGCAGTTACTCTGGCAAACCGAAAGTG
*
396135 AAACAGTGTTTGGGCCTAAGCACAAATCAT-AGCCGCTGACAAGATTTAGTTCTTGAAAATAATC
66 AAACAGTGTTTGGACCTAAGCACAAATCATCA-CCGCTGACAAGATTTAGTTCTTGAAAATAATC
396199 GATAAATTCGATGTAATGTATCTAGAAGCATTGGTTTTAAAAAAAAAACTTATTTAAGAAT
130 GATAAATTCGATGTAATGTATCTAGAAGCATTGGTTTTAAAAAAAAAACTTATTTAAGAAT
396260 A
1 A
396261 CTTTGAAAAT
Statistics
Matches: 186, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
188 1 0.01
189 163 0.88
190 22 0.12
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (190 bp):
ATATCATTTTTGGGAGTTGATTTTAATAAACTCTCCTATGCAGTTACTCTGGCAAACCGAAAGTG
AAACAGTGTTTGGACCTAAGCACAAATCATCACCGCTGACAAGATTTAGTTCTTGAAAATAATCG
ATAAATTCGATGTAATGTATCTAGAAGCATTGGTTTTAAAAAAAAAACTTATTTAAGAAT
Found at i:398024 original size:4 final size:4
Alignment explanation
Indices: 398002--398047 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
397992 ATCACATTTT
*
398002 GTCC GT-C GTCC GTCT GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
398048 TGTAAACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.00, C:0.46, G:0.26, T:0.28
Consensus pattern (4 bp):
GTCC
Found at i:417225 original size:23 final size:23
Alignment explanation
Indices: 417189--417234 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
417179 CAGATAATCC
417189 TTAATAAATAATTTCAAAATAAA
1 TTAATAAATAATTTCAAAATAAA
* * *
417212 TTAATGAATTATTTTAAAATAAA
1 TTAATAAATAATTTCAAAATAAA
417235 GTTTCAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAATAAATAATTTCAAAATAAA
Found at i:418757 original size:11 final size:11
Alignment explanation
Indices: 418738--418774 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
418728 TTATCATGTA
418738 TTTTCAATTAC
1 TTTTCAATTAC
*
418749 TTTTTAATTAC
1 TTTTCAATTAC
*
418760 ATTTCAATTAC
1 TTTTCAATTAC
418771 TTTT
1 TTTT
418775 TTCCAAGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTCAATTAC
Found at i:426263 original size:17 final size:18
Alignment explanation
Indices: 426237--426270 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
426227 TATATAGTAT
426237 ATAATAATATAACAATAA
1 ATAATAATATAACAATAA
*
426255 ATAAT-ATATAATAATA
1 ATAATAATATAACAATA
426271 TAACAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATAATATAACAATAA
Found at i:432382 original size:2 final size:2
Alignment explanation
Indices: 432375--432434 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
432365 TAGGTAAACA
432375 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
432417 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
432435 AGAATTTCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:432823 original size:14 final size:14
Alignment explanation
Indices: 432804--432846 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
432794 TGTAGTATAG
432804 AAGTTTGTATCTAT
1 AAGTTTGTATCTAT
432818 AAGTTTGTATCTAT
1 AAGTTTGTATCTAT
*
432832 ATGTTTGTATCTAT
1 AAGTTTGTATCTAT
432846 A
1 A
432847 TCAGTTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (14 bp):
AAGTTTGTATCTAT
Found at i:439377 original size:2 final size:2
Alignment explanation
Indices: 439370--439414 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
439360 ATCTACACTC
439370 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
439411 AG AG
1 AG AG
439415 GGGGATTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:439726 original size:2 final size:2
Alignment explanation
Indices: 439719--439775 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
439709 AAATGAAATA
439719 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
439761 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
439776 GTTTCTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:439939 original size:70 final size:70
Alignment explanation
Indices: 439816--440011 Score: 266
Period size: 70 Copynumber: 2.8 Consensus size: 70
439806 ATATTGAAAG
* * * * *
439816 TGTCCGATAGAGATGAAGTCAAAAATTTTAAGACAAGATCACGGAAGAAACTTTATTTAAATGTT
1 TGTCTGATAAAGATGAAGTCAAAAATTTTAAGACAAGATCACGGAAGGAACTTTATCTAAACGTT
*
439881 TAAAT
66 TAAAA
** * *
439886 TGTCTGATAAAGATGAAGTCGGATATTTTAAGACAAGATCATGGAAGGAACTTTATCTAAACGTT
1 TGTCTGATAAAGATGAAGTCAAAAATTTTAAGACAAGATCACGGAAGGAACTTTATCTAAACGTT
439951 TAAAA
66 TAAAA
* * * *
439956 TGTCTTATAAAGATTAAGTCAAAAACTTTAAGACAAAATCACGGAAGGAACTTTAT
1 TGTCTGATAAAGATGAAGTCAAAAATTTTAAGACAAGATCACGGAAGGAACTTTAT
440012 ATACCGATCC
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 108 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (70 bp):
TGTCTGATAAAGATGAAGTCAAAAATTTTAAGACAAGATCACGGAAGGAACTTTATCTAAACGTT
TAAAA
Found at i:441410 original size:20 final size:20
Alignment explanation
Indices: 441387--441432 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
441377 ATTTACCTTT
441387 AAAAAT-TAATATCCCATAGG
1 AAAAATATAAT-TCCCATAGG
441407 -AAAATGATAATTCCCATAGG
1 AAAAAT-ATAATTCCCATAGG
*
441427 AGAAAT
1 AAAAAT
441433 GATTCTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (20 bp):
AAAAATATAATTCCCATAGG
Found at i:441432 original size:21 final size:21
Alignment explanation
Indices: 441393--441435 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
441383 CTTTAAAAAT
441393 TAATATCCCATAGGAAAATGA
1 TAATATCCCATAGGAAAATGA
441414 TAAT-TCCCATAGGAGAAATGA
1 TAATATCCCATAGGA-AAATGA
441435 T
1 T
441436 TCTCCTACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (21 bp):
TAATATCCCATAGGAAAATGA
Found at i:441532 original size:18 final size:19
Alignment explanation
Indices: 441486--441532 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
441476 AAAAAAAACC
*
441486 TAGAGGAATTATATTTCCTG
1 TAGA-GAATAATATTTCCTG
441506 TAGGAGAATAATATTTCCTG
1 TA-GAGAATAATATTTCCTG
441526 T-GAGAAT
1 TAGAGAAT
441533 TTGATTCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
20 17 0.68
21 2 0.08
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (19 bp):
TAGAGAATAATATTTCCTG
Found at i:447344 original size:40 final size:40
Alignment explanation
Indices: 447292--447368 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
447282 ACTCTCTCGG
*
447292 ACATAATGTACTCAACATACATGTAAGAGAGAATTAACGA
1 ACATAATATACTCAACATACATGTAAGAGAGAATTAACGA
447332 ACATAATATACTCAACATACATGTAAGAGAGAATTAA
1 ACATAATATACTCAACATACATGTAAGAGAGAATTAA
447369 AAAGATGCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (40 bp):
ACATAATATACTCAACATACATGTAAGAGAGAATTAACGA
Found at i:451479 original size:9 final size:9
Alignment explanation
Indices: 451465--451489 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
451455 TGCGTGAAAA
451465 TGACGTTTT
1 TGACGTTTT
451474 TGACGTTTT
1 TGACGTTTT
451483 TGACGTT
1 TGACGTT
451490 ACCGAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (9 bp):
TGACGTTTT
Found at i:454731 original size:20 final size:20
Alignment explanation
Indices: 454706--454746 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
454696 AACCATTGGA
454706 AGTTCATTATAGTTTAATTT
1 AGTTCATTATAGTTTAATTT
*
454726 AGTTCATTATAGTTTCATTT
1 AGTTCATTATAGTTTAATTT
454746 A
1 A
454747 AGTTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (20 bp):
AGTTCATTATAGTTTAATTT
Found at i:454744 original size:11 final size:11
Alignment explanation
Indices: 454708--454757 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
454698 CCATTGGAAG
454708 TTCATTATAGT
1 TTCATTATAGT
*
454719 TTAATT-TAG-
1 TTCATTATAGT
454728 TTCATTATAGT
1 TTCATTATAGT
454739 TTCATT-TAAGT
1 TTCATTAT-AGT
*
454750 TTAATTAT
1 TTCATTAT
454758 GACAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.16
10 7 0.22
11 19 0.59
12 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (11 bp):
TTCATTATAGT
Found at i:456269 original size:21 final size:22
Alignment explanation
Indices: 456233--456278 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
456223 CTCAATATAC
456233 TACTAGTATCTATTTATTTACAT
1 TACTAGTA-CTATTTATTTACAT
456256 TACTAGTA-TATTTATTTACAT
1 TACTAGTACTATTTATTTACAT
456277 TA
1 TA
456279 GCTGACACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (22 bp):
TACTAGTACTATTTATTTACAT
Found at i:459046 original size:9 final size:9
Alignment explanation
Indices: 459032--459056 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
459022 AAAAATAAAG
459032 AATAAATTA
1 AATAAATTA
459041 AATAAATTA
1 AATAAATTA
459050 AATAAAT
1 AATAAAT
459057 ACCCCTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAAATTA
Found at i:459125 original size:4 final size:4
Alignment explanation
Indices: 459116--459151 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
459106 TTTCATTGTC
459116 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA
459152 AAATTCAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:459429 original size:16 final size:16
Alignment explanation
Indices: 459408--459443 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
459398 ACGGAAAAAC
459408 TTCGAGGTTTCAAGAG
1 TTCGAGGTTTCAAGAG
*
459424 TTCGAGTTTTCAAGAG
1 TTCGAGGTTTCAAGAG
459440 TTCG
1 TTCG
459444 GAATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (16 bp):
TTCGAGGTTTCAAGAG
Found at i:460189 original size:16 final size:16
Alignment explanation
Indices: 460151--460200 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
460141 GCAGTTTCAC
* *
460151 TTCGAGGAATCAAGGG
1 TTCGAGAAATCAAGAG
*
460167 TTTCGAGAGATCAAGAG
1 -TTCGAGAAATCAAGAG
460184 TTCGAGAAATCAAGAG
1 TTCGAGAAATCAAGAG
460200 T
1 T
460201 AAATTTGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (16 bp):
TTCGAGAAATCAAGAG
Found at i:460285 original size:15 final size:15
Alignment explanation
Indices: 460248--460297 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
460238 CTAGGCTCAC
*
460248 TTCGAGCGATCAAGAAC
1 TTCGAGCGATC--GAAG
460265 TTCGAGCGATCGAAG
1 TTCGAGCGATCGAAG
*
460280 TTCGAGCCATCGAGAG
1 TTCGAGCGATCGA-AG
460296 TT
1 TT
460298 ACCTGTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 15 0.50
16 4 0.13
17 11 0.37
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (15 bp):
TTCGAGCGATCGAAG
Found at i:462651 original size:25 final size:25
Alignment explanation
Indices: 462590--463041 Score: 437
Period size: 25 Copynumber: 18.0 Consensus size: 25
462580 GATCTGGGTA
**
462590 GATACAACCTGTAACACAGAAAAAAG
1 GATACAACCTGTAACACAG-AAAGTG
*
462616 GATACAACCTGTAACATAGAAAG-G
1 GATACAACCTGTAACACAGAAAGTG
* *
462640 AAATACAACCTGTAACATAGAAAGTG
1 -GATACAACCTGTAACACAGAAAGTG
* *
462666 GATACCTTTTACCTGTAACAAAGAAAGTG
1 GATA-C---AACCTGTAACACAGAAAGTG
*
462695 GATACAACCTGTAACACAGAAAATG
1 GATACAACCTGTAACACAGAAAGTG
* *
462720 GATACAACATGTAACGCAGAAAGTG
1 GATACAACCTGTAACACAGAAAGTG
*
462745 GATACAGCCTGT-A-ACAGAAAG-G
1 GATACAACCTGTAACACAGAAAGTG
*
462767 GAATATAACCTGTAACATC-GAAAGTG
1 G-ATACAACCTGTAACA-CAGAAAGTG
462793 GATACAACCTGTAACACAGAAAGTG
1 GATACAACCTGTAACACAGAAAGTG
* *
462818 GATAC-ACCATGTAACACAAAAAATG
1 GATACAACC-TGTAACACAGAAAGTG
*
462843 GATACAACATG-ATACACAGAAAGTG
1 GATACAACCTGTA-ACACAGAAAGTG
* *
462868 GATGCAACCTGTAACACAAAAAGTG
1 GATACAACCTGTAACACAGAAAGTG
*
462893 GATACAGCCTGT-A-ACAGAAAG-G
1 GATACAACCTGTAACACAGAAAGTG
* *
462915 GAGTATAACATGTAACATC-GAAAGTG
1 GA-TACAACCTGTAACA-CAGAAAGTG
*
462941 GATACAACCTGTAATACAGAAAGTG
1 GATACAACCTGTAACACAGAAAGTG
*
462966 GATAC-ACCGTGTAACACAGAAAATG
1 GATACAACC-TGTAACACAGAAAGTG
* *
462991 GATACAACATG-ATACACAAAAAGTAG
1 GATACAACCTGTA-ACACAGAAAGT-G
*
463017 AATACAACCTGTAACACTA-AAAGTG
1 GATACAACCTGTAACAC-AGAAAGTG
463042 AAAAAGAAAC
Statistics
Matches: 356, Mismatches: 42, Indels: 57
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.01
23 30 0.08
24 15 0.04
25 230 0.65
26 51 0.14
27 2 0.01
28 1 0.00
29 22 0.06
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (25 bp):
GATACAACCTGTAACACAGAAAGTG
Found at i:462833 original size:123 final size:124
Alignment explanation
Indices: 462590--463041 Score: 483
Period size: 123 Copynumber: 3.6 Consensus size: 124
462580 GATCTGGGTA
* * *
462590 GATACAACCTGTAACACAGAAAAAAGGATACAACCTGTA-ACATAGAAAG-GAAATACAACCTGT
1 GATACAACATGTAACACAG-AAAATGGATACAACCTGTACACA-A-AAAGTGGAATACAACCTGT
* *
462653 AACATAGAAAGTGGATACCTTTTACCTGTAACAAAGAAAGTGGATACAACCTGTAACACAGAAAA
63 AACAT-GAAAGTGGATA-C---AACCTGTAACACAGAAAGTGGATACAACCTGTAACACAGAAAA
462718 TG
123 TG
* * * * *
462720 GATACAACATGTAACGCAGAAAGTGGATACAGCCTGTA-ACAGAAAG-GGAATATAACCTGTAAC
1 GATACAACATGTAACACAGAAAATGGATACAACCTGTACACAAAAAGTGGAATACAACCTGTAAC
*
462783 ATCGAAAGTGGATACAACCTGTAACACAGAAAGTGGATAC-ACCATGTAACACAAAAAATG
66 AT-GAAAGTGGATACAACCTGTAACACAGAAAGTGGATACAACC-TGTAACACAGAAAATG
* * *
462843 GATACAACATG-ATACACAGAAAGTGGATGCAACCTGTAACACAAAAAGTGG-ATACAGCCTGTA
1 GATACAACATGTA-ACACAGAAAATGGATACAACCTGT-ACACAAAAAGTGGAATACAACCTGTA
* * * *
462906 ACA-GAAAG-GGAGTATAACATGTAACATC-GAAAGTGGATACAACCTGTAATACAGAAAGTG
64 ACATGAAAGTGGA-TACAACCTGTAACA-CAGAAAGTGGATACAACCTGTAACACAGAAAATG
* * * *
462966 GATACACCGTGTAACACAGAAAATGGATACAACATGATACACAAAAAGTAGAATACAACCTGTAA
1 GATACAACATGTAACACAGAAAATGGATACAACCTG-TACACAAAAAGTGGAATACAACCTGTAA
*
463031 CACTAAAAGTG
65 CA-TGAAAGTG
463042 AAAAAGAAAC
Statistics
Matches: 277, Mismatches: 31, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
122 7 0.03
123 153 0.55
124 21 0.08
125 20 0.07
126 7 0.03
127 33 0.12
129 19 0.07
130 17 0.06
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (124 bp):
GATACAACATGTAACACAGAAAATGGATACAACCTGTACACAAAAAGTGGAATACAACCTGTAAC
ATGAAAGTGGATACAACCTGTAACACAGAAAGTGGATACAACCTGTAACACAGAAAATG
Found at i:462894 original size:148 final size:147
Alignment explanation
Indices: 462621--463041 Score: 569
Period size: 148 Copynumber: 2.8 Consensus size: 147
462611 AAAAGGATAC
* * *
462621 AACCTGTAACATAGAAAG-GAAATACAACCTGTAACATAGAAAGTGGATACCTTTTACCTGTAAC
1 AACCTGTAACATCGAAAGTG-GATACAACCTGTAACACAGAAAGTGGATA-C----ACCTGTAAC
* * * * * *
462685 A-AAGAAAGTGGATACAACCTG-TAACACAGAAAATGGATACAACATGTAACGCAGAAAGTGGAT
60 ACAA-AAAATGGATACAACATGAT-ACACAGAAAGTGGATACAACCTGTAACACAAAAAGTGGAT
462748 ACAGCCTGTAACAGAAAGGGAATAT
123 ACAGCCTGTAACAGAAAGGGAATAT
462773 AACCTGTAACATCGAAAGTGGATACAACCTGTAACACAGAAAGTGGATACACCATGTAACACAAA
1 AACCTGTAACATCGAAAGTGGATACAACCTGTAACACAGAAAGTGGATACACC-TGTAACACAAA
*
462838 AAATGGATACAACATGATACACAGAAAGTGGATGCAACCTGTAACACAAAAAGTGGATACAGCCT
65 AAATGGATACAACATGATACACAGAAAGTGGATACAACCTGTAACACAAAAAGTGGATACAGCCT
*
462903 GTAACAGAAAGGGAGTAT
130 GTAACAGAAAGGGAATAT
* * *
462921 AACATGTAACATCGAAAGTGGATACAACCTGTAATACAGAAAGTGGATACACCGTGTAACACAGA
1 AACCTGTAACATCGAAAGTGGATACAACCTGTAACACAGAAAGTGGATACACC-TGTAACACAAA
* * *
462986 AAATGGATACAACATGATACACAAAAAGTAGAATACAACCTGTAACACTAAAAGTG
65 AAATGGATACAACATGATACACAGAAAGT-GGATACAACCTGTAACACAAAAAGTG
463042 AAAAAGAAAC
Statistics
Matches: 245, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
147 3 0.01
148 170 0.69
149 26 0.11
151 1 0.00
152 44 0.18
153 1 0.00
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.18
Consensus pattern (147 bp):
AACCTGTAACATCGAAAGTGGATACAACCTGTAACACAGAAAGTGGATACACCTGTAACACAAAA
AATGGATACAACATGATACACAGAAAGTGGATACAACCTGTAACACAAAAAGTGGATACAGCCTG
TAACAGAAAGGGAATAT
Found at i:465189 original size:2 final size:2
Alignment explanation
Indices: 465182--465226 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
465172 CTTTAAAAAT
* *
465182 GA GA GA GA GA AA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
465224 GA G
1 GA G
465227 TTAATATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:465199 original size:14 final size:14
Alignment explanation
Indices: 465176--465219 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
465166 ATATTGCTTT
465176 AAAAATGAGAGAGAG
1 AAAAA-GAGAGAGAG
465191 AAAAAGAGAGAGAG
1 AAAAAGAGAGAGAG
* *
465205 AGAGAGAGAGAGAG
1 AAAAAGAGAGAGAG
465219 A
1 A
465220 GAGAGAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (14 bp):
AAAAAGAGAGAGAG
Found at i:472496 original size:30 final size:30
Alignment explanation
Indices: 472460--472518 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
472450 TGACCCAGAT
472460 CGTCGACGTGCTGGGGGGTCTACACGTGTC
1 CGTCGACGTGCTGGGGGGTCTACACGTGTC
* *
472490 CGTCGACGTGTTGGGGGGTCTATACGTGT
1 CGTCGACGTGCTGGGGGGTCTACACGTGT
472519 TCCTCGCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.41, T:0.27
Consensus pattern (30 bp):
CGTCGACGTGCTGGGGGGTCTACACGTGTC
Found at i:482359 original size:13 final size:13
Alignment explanation
Indices: 482341--482366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
482331 AATATATATT
482341 TATAAACATCATA
1 TATAAACATCATA
482354 TATAAACATCATA
1 TATAAACATCATA
482367 CGTCGAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TATAAACATCATA
Found at i:484733 original size:18 final size:17
Alignment explanation
Indices: 484686--484733 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
484676 ATATTAGGCC
*
484686 ATAGCATAATGTACATGG
1 ATAGC-TAATGTACATGA
*
484704 ATAGCGATATGTACATGA
1 ATAGCTA-ATGTACATGA
484722 ATAGCTTAATGT
1 ATAGC-TAATGT
484734 GCTTATTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (17 bp):
ATAGCTAATGTACATGA
Found at i:485610 original size:2 final size:2
Alignment explanation
Indices: 485605--485669 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
485595 ATATATTTAA
485605 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
485647 AG AG CG AA AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
485670 TGTATTATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:485870 original size:27 final size:27
Alignment explanation
Indices: 485832--485887 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
485822 GTAATGGGAC
485832 TCGGAACTCGTGGAGCTTTATCAAAGG
1 TCGGAACTCGTGGAGCTTTATCAAAGG
485859 TCGGAACTCGTGGAGCTTTATCAAAGG
1 TCGGAACTCGTGGAGCTTTATCAAAGG
485886 TC
1 TC
485888 AGGTTGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (27 bp):
TCGGAACTCGTGGAGCTTTATCAAAGG
Found at i:489789 original size:18 final size:18
Alignment explanation
Indices: 489758--489792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
489748 TGACGAATCT
* *
489758 GTCTCCAACCAATACAAA
1 GTCTCAAACAAATACAAA
489776 GTCTCAAACAAATACAA
1 GTCTCAAACAAATACAA
489793 TTGACCAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.17
Consensus pattern (18 bp):
GTCTCAAACAAATACAAA
Found at i:492248 original size:60 final size:60
Alignment explanation
Indices: 492175--492655 Score: 593
Period size: 60 Copynumber: 8.0 Consensus size: 60
492165 AAAACTATAG
* * *
492175 CAACGATATCAACATCAGATCACATTAGATTGGAAAGTTCAGTAAAAGGGTCAAGTGACA
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* * * * * * *
492235 CAACAATATCAACATTAGATCACATTGGATTGGACAGTTCAATGAAAAGTTCAAGTGACA
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* **
492295 CAACGATATCAACATCAGAGCACATTAGATTGGAAAGTTCAGTGAAAGATTCAAGTGACA
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* * * * **
492355 CAATGATTTCAACATCAGAGCACTTTAGAATGGACAGTTCAGTGAAAGATTCAAGTGACA
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* * * * * **
492415 CAACGATTTCAATATCAGAGCACTTTAGAATGGATAGTTCAGTGAAAGATTCAAGTGACA
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* * * * * *
492475 CAACGATTTCAACATCAGAGCACTTTAGATTGGATAGTTCAATGAAATGGTCAAGTGACT
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* * * * * *
492535 CAACAATGTCAACATCAGAGCACATTAGATTGGATAGTTCAATGAAATGGTCAAGTGACT
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
* * *
492595 CAACTATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAATGGTCGAGTGACA
1 CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
492655 C
1 C
492656 GGGATCCACT
Statistics
Matches: 381, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 381 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (60 bp):
CAACGATATCAACATCAGAGCACATTAGATTGGACAGTTCAGTGAAAGGGTCAAGTGACA
Found at i:494813 original size:18 final size:18
Alignment explanation
Indices: 494790--494825 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
494780 CACTGACGGA
494790 TATAATTCTGAGAGTGAT
1 TATAATTCTGAGAGTGAT
*
494808 TATAATTGTGAGAGTGAT
1 TATAATTCTGAGAGTGAT
494826 AGTAAAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (18 bp):
TATAATTCTGAGAGTGAT
Found at i:496904 original size:2 final size:2
Alignment explanation
Indices: 496897--496938 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
496887 TTGTTCCCAA
496897 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
496939 ATTTTTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:497243 original size:2 final size:2
Alignment explanation
Indices: 497236--497290 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
497226 GACATTCTTT
497236 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
497278 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
497291 GATTACTTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:498122 original size:28 final size:28
Alignment explanation
Indices: 498090--498842 Score: 1235
Period size: 28 Copynumber: 27.0 Consensus size: 28
498080 ATAAACAGTT
* * * *
498090 TTACAATACAATGACCAATACCCTATTA
1 TTACAATACAATGACCGACACACAATTA
*** * *
498118 TTACAAT-TGGTGACCAACACACAATTT
1 TTACAATACAATGACCGACACACAATTA
** * *
498145 TTACAAT-CGGTGACCAATACACAATTA
1 TTACAATACAATGACCGACACACAATTA
* **
498172 TTACATTACTCTGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498200 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498228 TTAAAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
* *
498256 TTACAACACAATGACCGACATACAATTA
1 TTACAATACAATGACCGACACACAATTA
* *
498284 TTACAATACAATTACCGACACTCAATTA
1 TTACAATACAATGACCGACACACAATTA
498312 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498340 TTAAAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498368 TTAAAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498396 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498424 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498452 TTAC-ATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498479 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498507 TTACAATACAATGACCGACATACAATTA
1 TTACAATACAATGACCGACACACAATTA
498535 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498563 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498591 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498619 TTAC-ATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498646 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498674 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498702 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498730 TTACAATACAATGACCGACACAGAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498758 TTACAATACAATGACCAACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498786 TTACAATACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
*
498814 TTACACTACAATGACCGACACACAATTA
1 TTACAATACAATGACCGACACACAATTA
498842 T
1 T
498843 CAAAATTCAA
Statistics
Matches: 685, Mismatches: 37, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
27 97 0.14
28 588 0.86
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.23
Consensus pattern (28 bp):
TTACAATACAATGACCGACACACAATTA
Found at i:498810 original size:14 final size:14
Alignment explanation
Indices: 498793--498839 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
498783 TTATTACAAT
498793 ACAATGACCGACAC
1 ACAATGACCGACAC
* **
498807 ACAATTA-TTACAC
1 ACAATGACCGACAC
498820 TACAATGACCGACAC
1 -ACAATGACCGACAC
498835 ACAAT
1 ACAAT
498840 TATCAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.45, C:0.30, G:0.09, T:0.17
Consensus pattern (14 bp):
ACAATGACCGACAC
Found at i:499198 original size:31 final size:30
Alignment explanation
Indices: 499167--499862 Score: 620
Period size: 31 Copynumber: 22.7 Consensus size: 30
499157 TTCAATTTCA
* *
499167 ATTTCGATATGTAACTGACCAATAG-ACTTCA
1 ATTTCAATAT-TAACTGACCAATAGTA-TTCT
*
499198 ATTTCAATATTCAAATGACCAATAGTATTCT
1 ATTTCAATATT-AACTGACCAATAGTATTCT
* * *
499229 ATTTGATTATCAACTGACCAATAGTA---T
1 ATTTCAATATTAACTGACCAATAGTATTCT
* ***
499256 ATTTCAATATTTAACTGGCCAATAGTATAAG
1 ATTTCAATA-TTAACTGACCAATAGTATTCT
* * *
499287 GTGTCAATATTTAACTGACCAATCGTACTTC-
1 ATTTCAATA-TTAACTGACCAATAGTA-TTCT
*
499318 ATTTCAATATCTAACTGACCAATAG-ACTTTT
1 ATTTCAATAT-TAACTGACCAATAGTA-TTCT
* * * *
499349 ACTTCAATATTCAAATAACCAACAGTATTCT
1 ATTTCAATATT-AACTGACCAATAGTATTCT
* * *
499380 ATTTGATTATCAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
* ***
499410 ATTTCAATATTTAAATGACCAATAGTATAAG
1 ATTTCAATA-TTAACTGACCAATAGTATTCT
* * *
499441 GTGTCAATATTTAACTGACCAATCGTACTTC-
1 ATTTCAATA-TTAACTGACCAATAGTA-TTCT
*
499472 ATTTCAATATATAACTGACCAATAG-ACTTTT
1 ATTTCAATAT-TAACTGACCAATAGTA-TTCT
* *
499503 ACTTCAATATTGAAATGACCAATAGTATTCT
1 ATTTCAATATT-AACTGACCAATAGTATTCT
* * *
499534 ATTTGATTATCAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
* * ***
499564 ATTTCAATATTTATCTGGCCAATAGTATAAG
1 ATTTCAATA-TTAACTGACCAATAGTATTCT
* * *
499595 GTGTCAATATTTAACTGACCAATCGTACTTC-
1 ATTTCAATA-TTAACTGACCAATAGTA-TTCT
499626 ATTTCAATATCTAACTGACCAATAG-ACTTCT
1 ATTTCAATAT-TAACTGACCAATAGTA-TTCT
* *
499657 ATTCTAGAATATTCAAATGACCAATAGTATTCT
1 ATT-T-CAATATT-AACTGACCAATAGTATTCT
* * *
499690 ATTTGATTATCAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
* *
499720 ATTTGATTATTAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
* *
499750 ATTTGATTATTAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
*
499780 ATTTCATTATTAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
* *
499810 ATTTGATTATTAACTGACCAATAGTATTCT
1 ATTTCAATATTAACTGACCAATAGTATTCT
499840 ATTTCAATATTAAACTGACCAAT
1 ATTTCAATATT-AACTGACCAAT
499863 GCCAATTGTG
Statistics
Matches: 552, Mismatches: 87, Indels: 52
0.80 0.13 0.08
Matches are distributed among these distances:
27 8 0.01
28 15 0.03
30 225 0.41
31 270 0.49
32 9 0.02
33 24 0.04
34 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (30 bp):
ATTTCAATATTAACTGACCAATAGTATTCT
Found at i:499429 original size:123 final size:123
Alignment explanation
Indices: 499167--499861 Score: 553
Period size: 123 Copynumber: 5.7 Consensus size: 123
499157 TTCAATTTCA
* * * * *
499167 ATTTCGATATGTAACTGACCAATAG-ACTTCAATTTCAATAT-TCAAATGACCAATAGTATTCTA
1 ATTTCAATATTTAACTGACCAATAGTA-TTCTATTTCAATATCT-AACTGACCAATAGTATTTTA
* * * * * * ***
499230 TTTGATTATCAACTGACCAATAGTA----TATTTCAATATTTAACTGGCCAATAGTATAAG
64 TTTCAATATTAACTGACCAACAGTACTTCTATTTCAATA-TCAACTGACCAATAGTATTCT
* * *
499287 GTGTCAATATTTAACTGACCAATCGTACTTC-ATTTCAATATCTAACTGACCAATAG-ACTTTTA
1 ATTTCAATATTTAACTGACCAATAGTA-TTCTATTTCAATATCTAACTGACCAATAGTA-TTTTA
* * * * *
499350 CTTCAATATTCAAATAACCAACAGTA-TTCTATTTGATTATCAACTGACCAATAGTATTCT
64 TTTCAATATT-AACTGACCAACAGTACTTCTATTTCAATATCAACTGACCAATAGTATTCT
* **** * * * * *
499410 ATTTCAATATTTAAATGACCAATAGTATAAGGTGTCAATATTTAACTGACCAATCGTACTTCATT
1 ATTTCAATATTTAACTGACCAATAGTATTCTATTTCAATATCTAACTGACCAATAGTATTTTATT
* * * * *
499475 TCAATATATAACTGACCAATAG-ACTTTTACTTCAATATTGAAATGACCAATAGTATTCT
66 TCAATAT-TAACTGACCAACAGTACTTCTATTTCAATA-TCAACTGACCAATAGTATTCT
* * * * * * **** *
499534 ATTTGATTA-TCAACTGACCAATAGTATTCTATTTCAATATTTATCTGGCCAATAGTATAAGGTG
1 ATTTCAATATTTAACTGACCAATAGTATTCTATTTCAATATCTAACTGACCAATAGTATTTTATT
499598 TCAATATTTAACTGACCAATC-GTACTTC-ATTTCAATATCTAACTGACCAATAG-ACTTCT
66 TCAATA-TTAACTGACCAA-CAGTACTTCTATTTCAATATC-AACTGACCAATAGTA-TTCT
* * * * * *
499657 ATTCTAGAATATTCAAATGACCAATAGTATTCTATTTGATTATC-AACTGACCAATAGTATTCTA
1 ATT-T-CAATATTTAACTGACCAATAGTATTCTATTTCAATATCTAACTGACCAATAGTATTTTA
* * * * * *
499721 TTTGATTATTAACTGACCAATAGTA-TTCTATTTGATTATTAACTGACCAATAGTATTCT
64 TTTCAATATTAACTGACCAACAGTACTTCTATTTCAATATCAACTGACCAATAGTATTCT
* * * *
499780 ATTTCATTA-TTAACTGACCAATAGTATTCTATTTGATTAT-TAACTGACCAATAGTATTCTATT
1 ATTTCAATATTTAACTGACCAATAGTATTCTATTTCAATATCTAACTGACCAATAGTATTTTATT
499843 TCAATATTAAACTGACCAA
66 TCAATATT-AACTGACCAA
499862 TGCCAATTGT
Statistics
Matches: 460, Mismatches: 90, Indels: 49
0.77 0.15 0.08
Matches are distributed among these distances:
119 1 0.00
120 109 0.24
121 31 0.07
122 5 0.01
123 197 0.43
124 66 0.14
125 23 0.05
126 28 0.06
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (123 bp):
ATTTCAATATTTAACTGACCAATAGTATTCTATTTCAATATCTAACTGACCAATAGTATTTTATT
TCAATATTAACTGACCAACAGTACTTCTATTTCAATATCAACTGACCAATAGTATTCT
Found at i:499487 original size:154 final size:154
Alignment explanation
Indices: 499167--499862 Score: 980
Period size: 154 Copynumber: 4.5 Consensus size: 154
499157 TTCAATTTCA
* * * *
499167 ATTTCGATATGTAACTGACCAATAGACTTCAATTTCAATATTCAAATGACCAATAGTATTCTATT
1 ATTTCAATATCTAACTGACCAATAGACTTCTACTTCAATATTCAAATGACCAATAGTATTCTATT
*
499232 TGATTATCAACTGACCAATAGTA---TATTTCAATATTTAACTGGCCAATAGTATAAGGTGTCAA
66 TGATTATCAACTGACCAATAGTATTCTATTTCAATATTTAACTGACCAATAGTATAAGGTGTCAA
499294 TATTTAACTGACCAATCGTACTTC
131 TATTTAACTGACCAATCGTACTTC
* * *
499318 ATTTCAATATCTAACTGACCAATAGACTTTTACTTCAATATTCAAATAACCAACAGTATTCTATT
1 ATTTCAATATCTAACTGACCAATAGACTTCTACTTCAATATTCAAATGACCAATAGTATTCTATT
*
499383 TGATTATCAACTGACCAATAGTATTCTATTTCAATATTTAAATGACCAATAGTATAAGGTGTCAA
66 TGATTATCAACTGACCAATAGTATTCTATTTCAATATTTAACTGACCAATAGTATAAGGTGTCAA
499448 TATTTAACTGACCAATCGTACTTC
131 TATTTAACTGACCAATCGTACTTC
* * *
499472 ATTTCAATATATAACTGACCAATAGACTTTTACTTCAATATTGAAATGACCAATAGTATTCTATT
1 ATTTCAATATCTAACTGACCAATAGACTTCTACTTCAATATTCAAATGACCAATAGTATTCTATT
* *
499537 TGATTATCAACTGACCAATAGTATTCTATTTCAATATTTATCTGGCCAATAGTATAAGGTGTCAA
66 TGATTATCAACTGACCAATAGTATTCTATTTCAATATTTAACTGACCAATAGTATAAGGTGTCAA
499602 TATTTAACTGACCAATCGTACTTC
131 TATTTAACTGACCAATCGTACTTC
499626 ATTTCAATATCTAACTGACCAATAGACTTCTA-TTCTAGAATATTCAAATGACCAATAGTATTCT
1 ATTTCAATATCTAACTGACCAATAGACTTCTACTTC---AATATTCAAATGACCAATAGTATTCT
* * **** *
499690 ATTTGATTATCAACTGACCAATAGTATTCTATTTGATTA-TTAACTGACCAATAGTATTCTATTT
63 ATTTGATTATCAACTGACCAATAGTATTCTATTTCAATATTTAACTGACCAATAGTATAAGGTGT
* * *
499754 GATTA-TTAACTGACCAATAGTA-TTC
128 CAATATTTAACTGACCAATCGTACTTC
* * * * *
499779 TATTTCATTAT-TAACTGACCAATAGTA-TTCTATTTGATTATT-AACTGACCAATAGTATTCTA
1 -ATTTCAATATCTAACTGACCAATAG-ACTTCTACTTCAATATTCAAATGACCAATAGTATTCTA
* * *
499841 TTTCAATATTAAACTGACCAAT
64 TTTGATTA-TCAACTGACCAAT
499863 GCCAATTGTG
Statistics
Matches: 497, Mismatches: 38, Indels: 20
0.90 0.07 0.04
Matches are distributed among these distances:
150 25 0.05
151 98 0.20
153 25 0.05
154 266 0.54
155 21 0.04
156 62 0.12
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (154 bp):
ATTTCAATATCTAACTGACCAATAGACTTCTACTTCAATATTCAAATGACCAATAGTATTCTATT
TGATTATCAACTGACCAATAGTATTCTATTTCAATATTTAACTGACCAATAGTATAAGGTGTCAA
TATTTAACTGACCAATCGTACTTC
Found at i:502182 original size:55 final size:56
Alignment explanation
Indices: 502116--502246 Score: 178
Period size: 55 Copynumber: 2.4 Consensus size: 56
502106 TTACATTGAG
* * *
502116 AGGTCATTGCCCAGTGACGTAGTCAAAATGTGTATATC-CTA-AGCAATCTG-GAAAA
1 AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTAT-TCTCTATAGCAAT-GGAGAAAA
* *
502171 AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTGTTCTCTATCGCAATGGAGAAAA
1 AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTATTCTCTATAGCAATGGAGAAAA
502227 AGGTCATTGCCCAGTGACGT
1 AGGTCATTGCCCAGTGACGT
502247 TTCGTGCATG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
54 2 0.03
55 36 0.53
56 30 0.44
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (56 bp):
AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTATTCTCTATAGCAATGGAGAAAA
Found at i:503801 original size:55 final size:56
Alignment explanation
Indices: 503735--503865 Score: 178
Period size: 55 Copynumber: 2.4 Consensus size: 56
503725 TTACATTGAG
* * *
503735 AGGTCATTGCCCAGTGACGTAGTCAAAATGTGTATATC-CTA-AGCAATCTG-GAAAA
1 AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTAT-TCTCTATAGCAAT-GGAGAAAA
* *
503790 AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTGTTCTCTATCGCAATGGAGAAAA
1 AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTATTCTCTATAGCAATGGAGAAAA
503846 AGGTCATTGCCCAGTGACGT
1 AGGTCATTGCCCAGTGACGT
503866 TTCGTGCATG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
54 2 0.03
55 36 0.53
56 30 0.44
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (56 bp):
AGGTCATTGCCCAGTGACGTAGCCAAAATCTGTATTCTCTATAGCAATGGAGAAAA
Found at i:504544 original size:24 final size:24
Alignment explanation
Indices: 504512--504559 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
504502 GAAACGCTCC
504512 ATTGTGGGTTTATTTTATGAATGG
1 ATTGTGGGTTTATTTTATGAATGG
504536 ATTGTGGGTTTATTTTATGAATGG
1 ATTGTGGGTTTATTTTATGAATGG
504560 GTAGTAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (24 bp):
ATTGTGGGTTTATTTTATGAATGG
Found at i:505641 original size:2 final size:2
Alignment explanation
Indices: 505634--505678 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
505624 CAATCAAAAT
505634 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
505676 AG A
1 AG A
505679 CGTTATGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:509275 original size:51 final size:51
Alignment explanation
Indices: 509215--509349 Score: 252
Period size: 51 Copynumber: 2.6 Consensus size: 51
509205 CTACACCTTG
* *
509215 TCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCC
1 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
509266 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
1 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
509317 TCCCCAAGATCCAGATCCACCACTAGAAAATCC
1 TCCCCAAGATCCAGATCCACCACTAGAAAATCC
509350 GGGATCGACT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.33, C:0.36, G:0.14, T:0.17
Consensus pattern (51 bp):
TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
Found at i:509666 original size:51 final size:51
Alignment explanation
Indices: 509606--509740 Score: 252
Period size: 51 Copynumber: 2.6 Consensus size: 51
509596 CTACACCTTG
* *
509606 TCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCC
1 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
509657 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
1 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
509708 TCCCCAAGATCCAGATCCACCACTAGAAAATCC
1 TCCCCAAGATCCAGATCCACCACTAGAAAATCC
509741 GGGATCGACT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.33, C:0.36, G:0.14, T:0.17
Consensus pattern (51 bp):
TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCC
Found at i:509793 original size:391 final size:390
Alignment explanation
Indices: 509072--509854 Score: 1557
Period size: 391 Copynumber: 2.0 Consensus size: 390
509062 AAACGCCAAC
509072 AATGCTGATCAATAAATTGGTGATGATGAAGAGGAGCCTTGTGACCACGAGTTCGAGGATCCACC
1 AATGCTGATCAATAAATTGGTGATGATGAAGAGGAGCCTTGTGACCACGAGTTCGAGGATCCACC
509137 GGAAAATCCAGAGTTCATTCCGACGCCGCTTGACCAAGAATTAGATGCGCCAAAGGAAAATCCGG
66 GGAAAATCCAGAGTTCATTCCGACGCCGCTTGACCAAGAATTAGATGCGCCAAAGGAAAATCCGG
509202 GATCTACACCTTGTCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCCT
131 GATCTACACCTTGTCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCCT
509267 CCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCCTCCCCAAGATCCAGA
196 CCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCCTCCCCAAGATCCAGA
509332 TCCACCACTAGAAAATCCGGGATCGACTCCATCACTTCCCCAGGAGATATCGCCTCGGGAAAATC
261 TCCACCACTAGAAAATCCGGGATCGACTCCATCACTTCCCCAGGAGATATCGCCTCGGGAAAATC
509397 CGGAATCGCCAGCAGGTCCGCCAAAGTCGTTGTTACCCTGGAGGAAACCTGGTTCAGGCCCTATG
326 CGGAATCGCCAGCAGGTCCGCCAAAGTCGTTGTTACCCTGGAGGAAACCTGGTTCAGGCCCTATG
509462 NAATGCTGATCAATAAATTGGTGATGATGAAGAGGAGCCTTGTGACCACGAGTTCGAGGATCCAC
1 -AATGCTGATCAATAAATTGGTGATGATGAAGAGGAGCCTTGTGACCACGAGTTCGAGGATCCAC
509527 CGGAAAATCCAGAGTTCATTCCGACGCCGCTTGACCAAGAATTAGATGCGCCAAAGGAAAATCCG
65 CGGAAAATCCAGAGTTCATTCCGACGCCGCTTGACCAAGAATTAGATGCGCCAAAGGAAAATCCG
509592 GGATCTACACCTTGTCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCC
130 GGATCTACACCTTGTCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCC
509657 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCCTCCCCAAGATCCAG
195 TCCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCCTCCCCAAGATCCAG
509722 ATCCACCACTAGAAAATCCGGGATCGACTCCATCACTTCCCCAGGAGATATCGCCTCGGGAAAAT
260 ATCCACCACTAGAAAATCCGGGATCGACTCCATCACTTCCCCAGGAGATATCGCCTCGGGAAAAT
509787 CCGGAATCGCCAGCAGGTCCGCCAAAGTCGTTGTTACCCTGGAGGAAACCTGGTTCAGGCCCTAT
325 CCGGAATCGCCAGCAGGTCCGCCAAAGTCGTTGTTACCCTGGAGGAAACCTGGTTCAGGCCCTAT
509852 G
390 G
509853 AA
1 AA
509855 GGACCCAAAG
Statistics
Matches: 392, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
390 2 0.01
391 390 0.99
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (390 bp):
AATGCTGATCAATAAATTGGTGATGATGAAGAGGAGCCTTGTGACCACGAGTTCGAGGATCCACC
GGAAAATCCAGAGTTCATTCCGACGCCGCTTGACCAAGAATTAGATGCGCCAAAGGAAAATCCGG
GATCTACACCTTGTCCCCAAGATCCAGATCCGCCACTAGAGAATCCAGAACCCATAGTTGGTCCT
CCCCAAGATCCAGATCCACCACTAGAAAATCCAGAACCCATAGTTGGTCCTCCCCAAGATCCAGA
TCCACCACTAGAAAATCCGGGATCGACTCCATCACTTCCCCAGGAGATATCGCCTCGGGAAAATC
CGGAATCGCCAGCAGGTCCGCCAAAGTCGTTGTTACCCTGGAGGAAACCTGGTTCAGGCCCTATG
Found at i:515295 original size:2 final size:2
Alignment explanation
Indices: 515290--515358 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
515280 CACACACACA
515290 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
515332 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
515359 ATTCAAATTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:515380 original size:12 final size:12
Alignment explanation
Indices: 515363--515398 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
515353 TCTCTCATTC
515363 AAATTCTTATTT
1 AAATTCTTATTT
* *
515375 AAATTCTCATTC
1 AAATTCTTATTT
515387 AAATTCTTATTT
1 AAATTCTTATTT
515399 GAAAAACTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATTCTTATTT
Found at i:526624 original size:45 final size:45
Alignment explanation
Indices: 526557--526656 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 45
526547 GAACTTCAAC
* * * *
526557 GACTATTACAGAGATAGTTAGAAATGTCTACTAAGTGATTTCAGT
1 GACTATTACAGAGACAGCTAGAAATGTCTACTAAGTAACTTCAGT
*
526602 GGCTATTACAGAGACAGCTAGAAATGTCTACTAAGTAACTTCAGT
1 GACTATTACAGAGACAGCTAGAAATGTCTACTAAGTAACTTCAGT
526647 GACTATTACA
1 GACTATTACA
526657 CGACTATTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (45 bp):
GACTATTACAGAGACAGCTAGAAATGTCTACTAAGTAACTTCAGT
Found at i:526674 original size:56 final size:56
Alignment explanation
Indices: 526604--526742 Score: 215
Period size: 56 Copynumber: 2.5 Consensus size: 56
526594 ATTTCAGTGG
* **
526604 CTATTACAGAGACAGCTAGAAATGTCTACTAAGTAACTTCAGTGACTATTACACGA
1 CTATTACAGAGACAGTTAGAAATGTCTACTAAGTAACTTCAGTGACTATTACAAAA
* * *
526660 CTATTACAGAGACAGTTAGAAATATGTACTTAGTAACTTCAGTGACTATTACAAAA
1 CTATTACAGAGACAGTTAGAAATGTCTACTAAGTAACTTCAGTGACTATTACAAAA
*
526716 CTATTATAGAGACAGTTAGAAATGTCT
1 CTATTACAGAGACAGTTAGAAATGTCT
526743 CCAAATCCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (56 bp):
CTATTACAGAGACAGTTAGAAATGTCTACTAAGTAACTTCAGTGACTATTACAAAA
Found at i:527975 original size:14 final size:15
Alignment explanation
Indices: 527956--527992 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
527946 TATTATTAGT
527956 TTTCTTTCTTCT-CC
1 TTTCTTTCTTCTGCC
*
527970 TTTCTTTCCTCTGCC
1 TTTCTTTCTTCTGCC
527985 TTT-TTTCT
1 TTTCTTTCT
527993 GGCATTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTCTTTCTTCTGCC
Found at i:528847 original size:78 final size:78
Alignment explanation
Indices: 528708--528851 Score: 191
Period size: 78 Copynumber: 1.8 Consensus size: 78
528698 ATTGGTTTTA
* *** * * *
528708 AATTACTCAAATTCAGAAAATATATGTTTTGATGATGCACAAAACTGGTCAAAGAAGTTTTTATG
1 AATTACTCAAATTAAGAAAATATATGAACTAATGATGCACAAAACTGATCAAAGAACTTTTTATG
528773 GTATGCATTCCTT
66 GTATGCATTCCTT
**
528786 AATTACTCAAATTAAGAAAATATATGAACTAATGATGCACTTAACTGATCAATA-AACTTTTTAT
1 AATTACTCAAATTAAGAAAATATATGAACTAATGATGCACAAAACTGATCAA-AGAACTTTTTAT
528850 GG
65 GG
528852 CGCATACTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 55 0.98
79 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (78 bp):
AATTACTCAAATTAAGAAAATATATGAACTAATGATGCACAAAACTGATCAAAGAACTTTTTATG
GTATGCATTCCTT
Found at i:543182 original size:306 final size:302
Alignment explanation
Indices: 542633--543184 Score: 924
Period size: 302 Copynumber: 1.8 Consensus size: 302
542623 AAAATAGTGC
*
542633 CCATTGTCAACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTT
1 CCATTGTCAACCGACGAGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTT
* *
542698 ACCCTCCCAAACAGGGACTATTAATTTTATTATATTAAATGTCTTAATTTTAAAGAAAATTTTAG
66 ACCCTCCCAAACAGGCACTATTAATTTTATTATACTAAATGTCTTAATTTTAAAGAAAATTTTAG
* *
542763 TTTTATATAGAAATGAAGTGAATTTTACGGCGAACCGTACGCGCATAATTTACGCGCATGTAACA
131 TTTTATATAGAAACGAAGTGAATTCTACGGCGAACCGTACGCGCATAATTTACGCGCATGTAACA
*
542828 ATTCGTTGTGTTACCCGTTGCCAAGTGTGTTGTTAACGCTGAGGGTAATAGTATATATATAGTGC
196 ATTCGTTGTGTTACCCGTTGCCAAGTGTGTTGCTAACGCTGAGGGTAATAGTATATATATAGTGC
542893 CTGTTTGGGAGGGTAACAGTTGAAATTGACACCCCGAGGAAA
261 CTGTTTGGGAGGGTAACAGTTGAAATTGACACCCCGAGGAAA
*
542935 CCATTGTCAACCGACGAGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACTGTT
1 CCATTGTCAACCGACGAGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTT
* * * * * *
543000 ATCCTCCCAAACAGGCATTATTTATTTTATTATACTGAATGTCTTAATTTTAGAGAATATTTTTA
66 ACCCTCCCAAACAGGCACTATTAATTTTATTATACTAAATGTCTTAATTTTAAAGAA-AATTTTA
*
543065 CTGCTTTTATATAGAAACGACGTGAATTCTACGGCGAACCGTACGCGCATAATTTACGCGCATGT
130 --G-TTTTATATAGAAACGAAGTGAATTCTACGGCGAACCGTACGCGCATAATTTACGCGCATGT
**
543130 AACAATTCGTTGTGTTACCCGTTGTTAAGTGTGTTGCTAACGCTGAGGGTAATAG
192 AACAATTCGTTGTGTTACCCGTTGCCAAGTGTGTTGCTAACGCTGAGGGTAATAG
543185 AACGGATTAT
Statistics
Matches: 230, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
302 113 0.49
303 6 0.03
305 1 0.00
306 110 0.48
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (302 bp):
CCATTGTCAACCGACGAGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGTCAATTTCAACAGTT
ACCCTCCCAAACAGGCACTATTAATTTTATTATACTAAATGTCTTAATTTTAAAGAAAATTTTAG
TTTTATATAGAAACGAAGTGAATTCTACGGCGAACCGTACGCGCATAATTTACGCGCATGTAACA
ATTCGTTGTGTTACCCGTTGCCAAGTGTGTTGCTAACGCTGAGGGTAATAGTATATATATAGTGC
CTGTTTGGGAGGGTAACAGTTGAAATTGACACCCCGAGGAAA
Found at i:545897 original size:54 final size:53
Alignment explanation
Indices: 545823--546179 Score: 310
Period size: 54 Copynumber: 6.7 Consensus size: 53
545813 TTCAGTGATA
* * * *
545823 TCACTGTTTGTAAGGATGTACAAAGCAGGGCAATACATTCTACCTGAAGTAATG
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATA-ATCCTACCTGAAGTAATG
* * * * *
545877 TCACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGCTCAGTGATA
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTG--AAGTAATG
* * * * *
545932 TCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATG
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATA-ATCCTACCTGAAGTAATG
* * * * *
545986 TCACTGTTAGCAAGGGTGTACAAGGCAGGGCAAT-ATAC--CCTCACAGTGATA
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTGA-AGTAATG
* * * * *
546037 TCACTGTCAGCAAGGATATACTATGCAGGGCAATATATCCTACCAGAAGTAATG
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATA-ATCCTACCTGAAGTAATG
* * * * * *
546091 TCAATGTTATCAAGGATGTACAAGGCAGGGCAATAATCCTTCCTGCTCAGTGATA
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTG--AAGTAATG
* *
546146 TCAAT-TTCAGCAAGGATGTA-AAGACAGGGCAATA
1 TCACTGTT-AGCAAGGATGTACAAGGCAGGGCAATA
546180 CAAATGTACA
Statistics
Matches: 241, Mismatches: 51, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
50 4 0.02
51 34 0.14
52 3 0.01
53 19 0.08
54 114 0.47
55 59 0.24
56 8 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (53 bp):
TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTGAAGTAATG
Found at i:546005 original size:109 final size:109
Alignment explanation
Indices: 545814--546162 Score: 526
Period size: 109 Copynumber: 3.2 Consensus size: 109
545804 CAATATCCTT
** * * * *
545814 TCAGTGATATCACTGTTTGTAAGGATGTACAAAGCAGGGCAATACATTCTACCTGAAGTAATGTC
1 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
545879 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
66 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
545923 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
1 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
*
545988 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAAT-ATAC--CCT-C
66 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
* * * *
546028 ACAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATATCCTACCAGAAGTAATGTC
1 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
* * *
546093 AATGTTATCAAGGATGTACAAGGCAGGGCAATAATCCTTCCTGC
66 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
* *
546137 TCAGTGATATCAATTTCAGCAAGGAT
1 TCAGTGATATCACTGTCAGCAAGGAT
546163 GTAAAGACAG
Statistics
Matches: 218, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
105 91 0.42
106 6 0.03
108 6 0.03
109 115 0.53
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (109 bp):
TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
Found at i:546065 original size:51 final size:52
Alignment explanation
Indices: 545924--546073 Score: 178
Period size: 51 Copynumber: 2.9 Consensus size: 52
545914 CCTTCCTGCT
* *
545924 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGA
1 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAAT--ATAC-ACCTCA
* * * * * * *
545979 -AGTAATGTCACTGTTAGCAAGGGTGTACAAGGCAGGGCAATATAC-CCTCA
1 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATACACCTCA
546029 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATA
1 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATA
546074 TCCTACCAGA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
50 4 0.05
51 37 0.47
52 3 0.04
54 34 0.44
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (52 bp):
CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATACACCTCA
Found at i:564385 original size:54 final size:53
Alignment explanation
Indices: 564311--564667 Score: 310
Period size: 54 Copynumber: 6.7 Consensus size: 53
564301 TTCAGTGATA
* * * *
564311 TCACTGTTTGTAAGGATGTACAAAGCAGGGCAATACATTCTACCTGAAGTAATG
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATA-ATCCTACCTGAAGTAATG
* * * * *
564365 TCACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGCTCAGTGATA
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTG--AAGTAATG
* * * * *
564420 TCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATG
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATA-ATCCTACCTGAAGTAATG
* * * * *
564474 TCACTGTTAGCAAGGGTGTACAAGGCAGGGCAAT-ATAC--CCTCACAGTGATA
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTGA-AGTAATG
* * * * *
564525 TCACTGTCAGCAAGGATATACTATGCAGGGCAATATATCCTACCAGAAGTAATG
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATA-ATCCTACCTGAAGTAATG
* * * * * *
564579 TCAATGTTATCAAGGATGTACAAGGCAGGGCAATAATCCTTCCTGCTCAGTGATA
1 TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTG--AAGTAATG
* *
564634 TCAAT-TTCAGCAAGGATGTA-AAGACAGGGCAATA
1 TCACTGTT-AGCAAGGATGTACAAGGCAGGGCAATA
564668 CAAATGTACA
Statistics
Matches: 241, Mismatches: 51, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
50 4 0.02
51 34 0.14
52 3 0.01
53 19 0.08
54 114 0.47
55 59 0.24
56 8 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (53 bp):
TCACTGTTAGCAAGGATGTACAAGGCAGGGCAATAATCCTACCTGAAGTAATG
Found at i:564493 original size:109 final size:109
Alignment explanation
Indices: 564302--564650 Score: 526
Period size: 109 Copynumber: 3.2 Consensus size: 109
564292 CAATATCCTT
** * * * *
564302 TCAGTGATATCACTGTTTGTAAGGATGTACAAAGCAGGGCAATACATTCTACCTGAAGTAATGTC
1 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
564367 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
66 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
564411 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
1 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
*
564476 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAAT-ATAC--CCT-C
66 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
* * * *
564516 ACAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATATCCTACCAGAAGTAATGTC
1 TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
* * *
564581 AATGTTATCAAGGATGTACAAGGCAGGGCAATAATCCTTCCTGC
66 ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
* *
564625 TCAGTGATATCAATTTCAGCAAGGAT
1 TCAGTGATATCACTGTCAGCAAGGAT
564651 GTAAAGACAG
Statistics
Matches: 218, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
105 91 0.42
106 6 0.03
108 6 0.03
109 115 0.53
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (109 bp):
TCAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGAAGTAATGTC
ACTGTTAGCAAGGGTGTACAAGGCAGGGCAATAATCCTTCCTGC
Found at i:564553 original size:51 final size:52
Alignment explanation
Indices: 564412--564561 Score: 178
Period size: 51 Copynumber: 2.9 Consensus size: 52
564402 CCTTCCTGCT
* *
564412 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATACATTCTACCTGA
1 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAAT--ATAC-ACCTCA
* * * * * * *
564467 -AGTAATGTCACTGTTAGCAAGGGTGTACAAGGCAGGGCAATATAC-CCTCA
1 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATACACCTCA
564517 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATA
1 CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATA
564562 TCCTACCAGA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
50 4 0.05
51 37 0.47
52 3 0.04
54 34 0.44
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (52 bp):
CAGTGATATCACTGTCAGCAAGGATATACTATGCAGGGCAATATACACCTCA
Found at i:574343 original size:29 final size:29
Alignment explanation
Indices: 574296--574355 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
574286 AAAACATGAA
574296 AATCAACATGAATTGGATTAATTAACTTC
1 AATCAACATGAATTGGATTAATTAACTTC
** * *
574325 AATCAACATGTTTTTGATTAATTCACTTC
1 AATCAACATGAATTGGATTAATTAACTTC
574354 AA
1 AA
574356 ATTTTAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (29 bp):
AATCAACATGAATTGGATTAATTAACTTC
Found at i:576112 original size:40 final size:40
Alignment explanation
Indices: 576059--576228 Score: 195
Period size: 40 Copynumber: 4.3 Consensus size: 40
576049 CTAATTTTTT
* *
576059 AACCTTTCT-CTAATACCCACTTCATAGCACTTACTAACAA
1 AACCTTT-TACTAATGCCCACTTCATAGCACTTACCAACAA
*
576099 AACCTTTTACTAATGCCCACTTCATAGCACTTACCAATAA
1 AACCTTTTACTAATGCCCACTTCATAGCACTTACCAACAA
* * * * *
576139 ATCCTCGCTT--TAATGCCCATTTCATAGAATTTACCAACAA
1 AACCT--TTTACTAATGCCCACTTCATAGCACTTACCAACAA
*
576179 AACCTTTTACTAATGCCCACTTCATAGCACTAACCAAC-A
1 AACCTTTTACTAATGCCCACTTCATAGCACTTACCAACAA
*
576218 AACTTTTTACT
1 AACCTTTTACT
576229 TCAGAGCACT
Statistics
Matches: 109, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 12 0.11
40 93 0.85
42 2 0.02
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (40 bp):
AACCTTTTACTAATGCCCACTTCATAGCACTTACCAACAA
Found at i:576121 original size:87 final size:88
Alignment explanation
Indices: 575973--576135 Score: 242
Period size: 87 Copynumber: 1.9 Consensus size: 88
575963 ACAAGCAAAT
* *
575973 CCTTTCTCCAATGCCCACTTCATAGCATTTTACCAACAAAACTTGTCTCTAATGCCCACTTCATA
1 CCTTTCTCCAATACCCACTTCATAGCATCTTACCAACAAAACTTGTCTCTAATGCCCACTTCATA
*
576038 GCATTTACCAACTAATTTTTTAA
66 GCACTTACCAACTAATTTTTTAA
* *
576061 CCTTTCTCTAATACCCACTTCATAGCA-CTTACTAACAAAACCTT-T-TACTAATGCCCACTTCA
1 CCTTTCTCCAATACCCACTTCATAGCATCTTACCAACAAAA-CTTGTCT-CTAATGCCCACTTCA
576123 TAGCACTTACCAA
64 TAGCACTTACCAA
576136 TAAATCCTCG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
86 1 0.01
87 39 0.57
88 28 0.41
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (88 bp):
CCTTTCTCCAATACCCACTTCATAGCATCTTACCAACAAAACTTGTCTCTAATGCCCACTTCATA
GCACTTACCAACTAATTTTTTAA
Found at i:578731 original size:40 final size:40
Alignment explanation
Indices: 578618--578936 Score: 214
Period size: 40 Copynumber: 8.2 Consensus size: 40
578608 TTCTTTAATA
* *
578618 AGCACTTACCAACAAAACGTTT-TACTAATGTCCACTAT-AT
1 AGCACTTACCAACAAAACCTTTCT-CTAATGCCCACT-TCAT
* ** * ** *
578658 AGCGCTTAAAAACAAAACATCCCTCAAATGCCCACTTCAT
1 AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
* * ** * *
578698 AACACTTACTAACAAAACCTTTAACTAACGCCCACTTGAT
1 AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
*
578738 AGCACTAACCAACAAAA-C--TCT-T--T----ACTTCAT
1 AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
* * * * *
578768 AGCACTTTCAAACAATACCTTTTTCTAATGCCCACTTGAT
1 AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
* *
578808 AGCACTTACCAACTAAGCCTTT-TACTAATGCCCACTTCAT
1 AGCACTTACCAACAAAACCTTTCT-CTAATGCCCACTTCAT
* * * *
578848 GGCACTTACCAACTAAGCCTTTCTCTAATGTCCACTTCAT
1 AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
* ** * * *
578888 AGCCCTTACTTACAAAACCTTTCTCTAACGACCACTTGAT
1 AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
*
578928 AACACTTAC
1 AGCACTTAC
578937 ATGTAACAGC
Statistics
Matches: 213, Mismatches: 52, Indels: 28
0.73 0.18 0.10
Matches are distributed among these distances:
30 19 0.09
31 1 0.00
33 2 0.01
34 1 0.00
36 2 0.01
37 1 0.00
39 3 0.01
40 182 0.85
41 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.29
Consensus pattern (40 bp):
AGCACTTACCAACAAAACCTTTCTCTAATGCCCACTTCAT
Found at i:579662 original size:180 final size:180
Alignment explanation
Indices: 579344--579889 Score: 941
Period size: 180 Copynumber: 3.0 Consensus size: 180
579334 GTGAAATGGT
579344 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* * *
579408 TTACCGGAAATCAAAATCCTATCAATGTGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
66 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
579473 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
131 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
*
579523 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTTATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* * * * ** *
579588 TTATCAGTAATCAAAATCCTAGCAATACGCACACCTCTGAAATATGTTTAATTGATCTGAAAAAG
66 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
579653 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
131 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
* * *
579703 GTACACTATATGCAATATTTTGCCAAAAAAGGACTAAATTCAAAAGCTGGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
*
579768 TTATTGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
66 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
*
579833 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCTGTACAATGAGG
131 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
579883 GTACCCT
1 GTACCCT
579890 TTTGGCAGCC
Statistics
Matches: 341, Mismatches: 25, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
179 52 0.15
180 289 0.85
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (180 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
Found at i:580837 original size:43 final size:42
Alignment explanation
Indices: 580774--581266 Score: 422
Period size: 43 Copynumber: 11.2 Consensus size: 42
580764 TTATAATGAC
*
580774 TTGACTTACCAGTATAACTTCTATCAAGTACCCTAGTTTCTTT
1 TTGACTTACCAGTATAACTTCTATCAA-TACCCTAGTTTCTCT
* * *
580817 TTGACTTACCAGTATGACTTCCATGGAATACCCTAGTTTCTC-
1 TTGACTTACCAGTATAACTTCTAT-CAATACCCTAGTTTCTCT
* * * *
580859 TTGACTTTCCAGTATAACTTCCGT-TTAATACCCTAGTTCCTTT
1 TTGACTTACCAGTATAACTT-C-TATCAATACCCTAGTTTCTCT
* * *
580902 TTGACTTACCAGTATAACTTATATCAATTACCCTAATTCCTCT
1 TTGACTTACCAGTATAACTTCTATCAA-TACCCTAGTTTCTCT
* ** * * *
580945 TTGACTTACCAGTATTACTTCCGTGGAATACCTTAGTTCCTCT
1 TTGACTTACCAGTATAACTTCTAT-CAATACCCTAGTTTCTCT
* *
580988 TTCACTTACCAGTATAGCTTCTATCGAGTACCGGTACCCTAGTTTCAT-T
1 TTGACTTACCAGTATAACTTCTATC-A--A----TACCCTAGTTTC-TCT
* * *
581037 TTGACTTACCAGTA-AGACTTCCATGAAATACCCTAGTTCCTCT
1 TTGACTTACCAGTATA-ACTTCTAT-CAATACCCTAGTTTCTCT
*
581080 TTGACTTACCAGTAATGAGTATAACTTCTATTGAATACCCTAGTTTCTCT
1 TTGACTTACC-------AGTATAACTTCTA-TCAATACCCTAGTTTCTCT
*
581130 TTGACTTACCAGTATAACTTCTATCGAGTACCCTAGTTTCTCT
1 TTGACTTACCAGTATAACTTCTATC-AATACCCTAGTTTCTCT
* *
581173 TTGACTTACCAGTAAAACTTCTATCGAGA-ACTCTAGTTTCTCT
1 TTGACTTACCAGTATAACTTCTATC-A-ATACCCTAGTTTCTCT
* * *
581216 TTGACTTACCAGTATACCTTC-AGTGGAATACCCTAGTTCCTCT
1 TTGACTTACCAGTATAACTTCTA-T-CAATACCCTAGTTTCTCT
581259 TTGACTTA
1 TTGACTTA
581267 TATTTGACTT
Statistics
Matches: 370, Mismatches: 48, Indels: 64
0.77 0.10 0.13
Matches are distributed among these distances:
41 1 0.00
42 39 0.11
43 253 0.68
44 4 0.01
45 1 0.00
47 1 0.00
48 1 0.00
49 31 0.08
50 37 0.10
51 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (42 bp):
TTGACTTACCAGTATAACTTCTATCAATACCCTAGTTTCTCT
Found at i:580982 original size:86 final size:85
Alignment explanation
Indices: 580774--581266 Score: 476
Period size: 86 Copynumber: 5.6 Consensus size: 85
580764 TTATAATGAC
* * * * *
580774 TTGACTTACCAGTATAACTTCTAT-CAAGTACCCTAGTTTCTTTTTGACTTACCAGTATGACTTC
1 TTGACTTACCAGTATAACTTCCATGGAA-TACCCTAGTTCCTCTTTGACTTACCAGTATAACTTC
* *
580838 CATGGAATACCCTAGTTTCTC-
65 TAT-CAATACCCTAGTTTCTCT
* * ** * *
580859 TTGACTTTCCAGTATAACTTCCGTTTAATACCCTAGTTCCTTTTTGACTTACCAGTATAACTTAT
1 TTGACTTACCAGTATAACTTCCATGGAATACCCTAGTTCCTCTTTGACTTACCAGTATAACTTCT
* *
580924 ATCAATTACCCTAATTCCTCT
66 ATCAA-TACCCTAGTTTCTCT
* * * * *
580945 TTGACTTACCAGTATTACTTCCGTGGAATACCTTAGTTCCTCTTTCACTTACCAGTATAGCTTCT
1 TTGACTTACCAGTATAACTTCCATGGAATACCCTAGTTCCTCTTTGACTTACCAGTATAACTTCT
581010 ATCGAGTACCGGTACCCTAGTTTCAT-T
66 ATC-A--A----TACCCTAGTTTC-TCT
*
581037 TTGACTTACCAGTA-AGACTTCCATGAAATACCCTAGTTCCTCTTTGACTTACCAGTAATGAGTA
1 TTGACTTACCAGTATA-ACTTCCATGGAATACCCTAGTTCCTCTTTGACTTACC-------AGTA
*
581101 TAACTTCTATTGAATACCCTAGTTTCTCT
58 TAACTTCTA-TCAATACCCTAGTTTCTCT
* * * * *
581130 TTGACTTACCAGTATAACTTCTATCGAGTACCCTAGTTTCTCTTTGACTTACCAGTAAAACTTCT
1 TTGACTTACCAGTATAACTTCCATGGAATACCCTAGTTCCTCTTTGACTTACCAGTATAACTTCT
*
581195 ATCGAGA-ACTCTAGTTTCTCT
66 ATC-A-ATACCCTAGTTTCTCT
*
581216 TTGACTTACCAGTATACCTT-CAGTGGAATACCCTAGTTCCTCTTTGACTTA
1 TTGACTTACCAGTATAACTTCCA-TGGAATACCCTAGTTCCTCTTTGACTTA
581267 TATTTGACTT
Statistics
Matches: 341, Mismatches: 43, Indels: 47
0.79 0.10 0.11
Matches are distributed among these distances:
84 2 0.01
85 70 0.21
86 131 0.38
87 2 0.01
89 1 0.00
92 59 0.17
93 60 0.18
94 1 0.00
97 1 0.00
99 13 0.04
100 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (85 bp):
TTGACTTACCAGTATAACTTCCATGGAATACCCTAGTTCCTCTTTGACTTACCAGTATAACTTCT
ATCAATACCCTAGTTTCTCT
Found at i:581139 original size:21 final size:21
Alignment explanation
Indices: 581115--581182 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
581105 TTCTATTGAA
581115 TACCCTAGTTTCTCTTTGACT
1 TACCCTAGTTTCTCTTTGACT
* * *
581136 TA-CC-AGTATAACTTCTATCGA-G
1 TACCCTAGT-T-TC-TCT-TTGACT
581158 TACCCTAGTTTCTCTTTGACT
1 TACCCTAGTTTCTCTTTGACT
581179 TACC
1 TACC
581183 AGTAAAACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 10 0.29
22 6 0.18
23 6 0.18
24 3 0.09
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (21 bp):
TACCCTAGTTTCTCTTTGACT
Found at i:581225 original size:228 final size:214
Alignment explanation
Indices: 580774--581236 Score: 552
Period size: 228 Copynumber: 2.1 Consensus size: 214
580764 TTATAATGAC
* *
580774 TTGACTTACCAGTATAACTTCTATCAAGTACCCTAGTTTCTTTTTGACTTACCAGTATGACTTCC
1 TTGACTTACCAGTATAACTTCTATCAAGTACCCTAGTTTCATTTTGACTTACCAGTAAGACTTCC
* * * * * *
580839 ATGGAATACCCTAGTTTCTCTTGACTTTCCAGTATAACTTCCGTTTAATACCCTAGTTCCTTTTT
66 ATGAAATACCCTAGTTCCTCTTGACTTACCAGTATAACTTCCATTGAATACCCTAGTTCCTCTTT
* ** *
580904 GACTTACCAGTATAACTTATATCAATTACCCTAATTCCTCTTTGACTTACCAGTATTACTTCCGT
131 GACTTACCAGTATAACTTATATCAAGTACCCTAATTCCTCTTTGACTTACCAGTAAAACTTCCAT
*
580969 GGAATACCTTAGTTCCTCT
196 CGAATACCTTAGTTCCTCT
* *
580988 TTCACTTACCAGTATAGCTTCTATCGAGTACCGGTACCCTAGTTTCATTTTGACTTACCAGTAAG
1 TTGACTTACCAGTATAACTTCTATC-A--A---GTACCCTAGTTTCATTTTGACTTACCAGTAAG
*
581053 ACTTCCATGAAATACCCTAGTTCCTCTTTGACTTACCAGTAATGAGTATAACTTCTATTGAATAC
60 ACTTCCATGAAATACCCTAGTTCCTC-TTGACTTACC-------AGTATAACTTCCATTGAATAC
* * * * *
581118 CCTAGTTTCTCTTTGACTTACCAGTATAACTTCTATCGAGTACCCTAGTTTCTCTTTGACTTACC
117 CCTAGTTCCTCTTTGACTTACCAGTATAACTTATATCAAGTACCCTAATTCCTCTTTGACTTACC
* *
581183 AGTAAAACTTCTATCGAGA-A-CTCTAGTTTCTCT
182 AGTAAAACTTCCATCGA-ATACCT-TAGTTCCTCT
*
581216 TTGACTTACCAGTATACCTTC
1 TTGACTTACCAGTATAACTTC
581237 AGTGGAATAC
Statistics
Matches: 208, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
214 23 0.11
215 1 0.00
217 1 0.00
220 54 0.26
221 9 0.04
227 2 0.01
228 117 0.56
229 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (214 bp):
TTGACTTACCAGTATAACTTCTATCAAGTACCCTAGTTTCATTTTGACTTACCAGTAAGACTTCC
ATGAAATACCCTAGTTCCTCTTGACTTACCAGTATAACTTCCATTGAATACCCTAGTTCCTCTTT
GACTTACCAGTATAACTTATATCAAGTACCCTAATTCCTCTTTGACTTACCAGTAAAACTTCCAT
CGAATACCTTAGTTCCTCT
Found at i:587950 original size:2 final size:2
Alignment explanation
Indices: 587943--587976 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
587933 AGTTATCAAC
587943 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
587977 TTTTTAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:590211 original size:10 final size:10
Alignment explanation
Indices: 590196--590226 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
590186 TATAGTTCTG
590196 AAACATACAC
1 AAACATACAC
*
590206 AAACATACAT
1 AAACATACAC
590216 AAACATACAC
1 AAACATACAC
590226 A
1 A
590227 TCACAAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (10 bp):
AAACATACAC
Found at i:590244 original size:25 final size:25
Alignment explanation
Indices: 590198--590254 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
590188 TAGTTCTGAA
* *
590198 ACATACACAAACATACATAAACATAC
1 ACAT-CACAAACATACACAAACACAC
590224 ACATCACAAGACA-ACACAAACACAC
1 ACATCACAA-ACATACACAAACACAC
*
590249 ATATCA
1 ACATCA
590255 AGTACACTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.56, C:0.30, G:0.02, T:0.12
Consensus pattern (25 bp):
ACATCACAAACATACACAAACACAC
Found at i:593811 original size:14 final size:14
Alignment explanation
Indices: 593792--593818 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
593782 ATTAATTAAT
593792 GAAAAAGATAAAAG
1 GAAAAAGATAAAAG
593806 GAAAAAGATAAAA
1 GAAAAAGATAAAA
593819 TAAAATCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (14 bp):
GAAAAAGATAAAAG
Found at i:594108 original size:24 final size:24
Alignment explanation
Indices: 594080--594158 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
594070 CAAAATCGCA
* *
594080 TGCCCACAAATTGTAGCGATCTTG
1 TGCCCACAAACTGTAGCGATCGTG
*
594104 TGCCCACAAACTGTAGTGATCGTG
1 TGCCCACAAACTGTAGCGATCGTG
594128 TGCCCACAAACTGTAGCGATCGTG
1 TGCCCACAAACTGTAGCGATCGTG
594152 TGCCCAC
1 TGCCCAC
594159 TATCAGGTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (24 bp):
TGCCCACAAACTGTAGCGATCGTG
Found at i:594234 original size:36 final size:37
Alignment explanation
Indices: 594187--594263 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
594177 GAATTGACCG
* *
594187 GGTGGCAGTAAATACAAAATCTAC-ACATGACAATTA
1 GGTGGCAGTAAACACAAAATCTACAACATGACAACTA
*
594223 GGTGGCAGTAAACATAAAATCTACAACATGACAACTA
1 GGTGGCAGTAAACACAAAATCTACAACATGACAACTA
594260 GGTG
1 GGTG
594264 TCATGCCACC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 22 0.59
37 15 0.41
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (37 bp):
GGTGGCAGTAAACACAAAATCTACAACATGACAACTA
Found at i:595803 original size:2 final size:2
Alignment explanation
Indices: 595796--595948 Score: 227
Period size: 2 Copynumber: 77.0 Consensus size: 2
595786 TTGTAACTAA
* *
595796 CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
595838 CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* ** **
595880 -T GT AA CT AA CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
595921 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
595949 TAAGATTTTC
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
1 1 0.01
2 135 0.99
ACGTcount: A:0.03, C:0.46, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:596326 original size:3 final size:3
Alignment explanation
Indices: 596318--596390 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
596308 TGTTTAAAAA
596318 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
596366 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
596391 AATATATTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:604147 original size:22 final size:22
Alignment explanation
Indices: 604100--604147 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
604090 ATCGGTGAGT
* *
604100 GCGAAGATGCGAAGGCGAGAGT
1 GCGAAGATGCGAAGACGAGAGA
*
604122 GCGAAGTTGCGAAGACG-GAGGA
1 GCGAAGATGCGAAGACGAGA-GA
604144 GCGA
1 GCGA
604148 TAGTAGTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.31, C:0.15, G:0.46, T:0.08
Consensus pattern (22 bp):
GCGAAGATGCGAAGACGAGAGA
Found at i:604211 original size:22 final size:22
Alignment explanation
Indices: 604170--604232 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
604160 TTCTTTGCCT
* * *
604170 TCGCATCTTCGCGC-TTCGCCG
1 TCGCAACTTCGCACTTTCGCCA
* *
604191 TTGCACCTTCGCACTTTCGCCA
1 TCGCAACTTCGCACTTTCGCCA
*
604213 TCGCAACTTCGCACTCTCGC
1 TCGCAACTTCGCACTTTCGC
604233 ATCTTCGCCC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 11 0.32
22 23 0.68
ACGTcount: A:0.11, C:0.43, G:0.17, T:0.29
Consensus pattern (22 bp):
TCGCAACTTCGCACTTTCGCCA
Found at i:606431 original size:4 final size:4
Alignment explanation
Indices: 606422--606465 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
606412 TACCCTTGTG
* * *
606422 TGTC TGTC TGTC TGTC CGTC TGTC TGTA TGTC TGTC TATC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
606466 CGTAACAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.05, C:0.25, G:0.23, T:0.48
Consensus pattern (4 bp):
TGTC
Found at i:606770 original size:167 final size:168
Alignment explanation
Indices: 606492--607121 Score: 848
Period size: 167 Copynumber: 3.8 Consensus size: 168
606482 GTCGCATTTA
* * *
606492 TCTCAGCAACTATTTTTCGCAGATGCTTGAAA-TTTT-TACACAGTGTTTGTGA-AGGCATGCCA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTATACACACTATTTGT-ATAGGCATGCCA
* *
606554 TATCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTGCTGTTAAATGACGACTTTGCTTAT
65 TATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTA-
*
606619 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
129 TTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
606659 TCTCAGCAACTATTTATCGCAGATGCTTTAAATTTTTATA-ATA-TATTTGTATAGGCATGCCAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTATACACACTATTTGTATAGGCATGCCAT
* * *
606722 ATCGTGGGATATATTTTTGTACCAATCAGACGTCAAGTTCCAGTTAAATGACGACTTTGTTTATT
66 ATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT
* *
606787 TTTAGCAAAAATTTTCAAACAAATATTT-GTCAAAGAAT
131 TTTAGCCAAAATTTTCAAACAAAT-TTTCGTCAAAGATT
* * *
606825 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTT-TACACAGTATTTGTATAGGCATGCTAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTATACACACTATTTGTATAGGCATGCCAT
* * * * *
606889 ATCGTGGGATGTAATTTTGTACCAATCAGACGTCAACTTCCTGTTTATTGA-GTACTTTGTTTAT
66 ATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTAT
*
606953 TTTTGGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
606992 TCTCAGCAGCTATTTATCGCAGATGCTTGAAA-TCTTA-ACACACTATTTGTTTAGGCATGCCAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTATACACACTATTTGTATAGGCATGCCAT
* * * * * ** * *
607055 ATTGTGGGATATATTTCTGTACCAATCGGATGCCAGTTTTCTGTTAAATGTCGACTTTGCTTATT
66 ATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT
607120 TT
131 TT
607122 GCATATTCAC
Statistics
Matches: 408, Mismatches: 45, Indels: 21
0.86 0.09 0.04
Matches are distributed among these distances:
165 2 0.00
166 152 0.37
167 246 0.60
168 6 0.01
169 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (168 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTATACACACTATTTGTATAGGCATGCCAT
ATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT
TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:607103 original size:333 final size:333
Alignment explanation
Indices: 606492--607121 Score: 921
Period size: 333 Copynumber: 1.9 Consensus size: 333
606482 GTCGCATTTA
* *
606492 TCTCAGCAACTATTTTTCGCAGATGCTTGAAATTTTTACACAGTGTTTGTGAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTGAAGGCATGCCATAT
* * *
606557 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTGCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATAATTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
606622 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
* * * *
606687 TAAATTTTTATAATATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
196 GAAATTCTTATAACATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCAGA
*
606752 CGTCAAGTTCCAGTTAAATGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATATTTGT
261 CGTCAAGTTCCAGTTAAATGACGACTTTGCTTATTTTTAGCAAAAATTTTCAAACAAATATTTGT
606817 CAAAGAAT
326 CAAAGAAT
* *
606825 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTTACACAGTATTTGT-ATAGGCATGCTAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAA-TTTTTACACAGTATTTGTGA-AGGCATGCCAT
* * * *
606889 ATCGTGGGATGTAATTTTGTACCAATCAGACGTCAACTTCCTGTTTATTGA-GTACTTTGTTTA-
64 ATCGTGGGATATAATTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTAT
** *
606952 TTTTTGGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG
128 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATG
* *
607017 CTTGAAA-TCTTA-ACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAA
193 CTTGAAATTCTTATA-ACA-TATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAA
* * * * * *
607080 TCGGATG-CCAGTTTTCTGTTAAATGTCGACTTTGCTTATTTT
256 TCAGACGTCAAG-TTCCAGTTAAATGACGACTTTGCTTATTTT
607122 GCATATTCAC
Statistics
Matches: 264, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
331 1 0.00
332 9 0.03
333 173 0.66
334 81 0.31
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (333 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTGAAGGCATGCCATAT
CGTGGGATATAATTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
GAAATTCTTATAACATATTTGTATAGGCATGCCATATCGTGGGATATATTTCTGTACCAATCAGA
CGTCAAGTTCCAGTTAAATGACGACTTTGCTTATTTTTAGCAAAAATTTTCAAACAAATATTTGT
CAAAGAAT
Done.