Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 5 of 141
Found at i:1232551 original size:36 final size:38
Alignment explanation
Indices: 1232486--1232565 Score: 146
Period size: 36 Copynumber: 2.2 Consensus size: 38
1232476 TAACTTCTAA
1232486 AAACTTAACATTTACATAAAAAAAATTAAAATAAAAAC
1 AAACTTAACATTTACATAAAAAAAATTAAAATAAAAAC
1232524 AAACTT-ACATTTACAT-AAAAAAATTAAAATAAAAAC
1 AAACTTAACATTTACATAAAAAAAATTAAAATAAAAAC
1232560 AAACTT
1 AAACTT
1232566 TTTTCTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 26 0.62
37 10 0.24
38 6 0.14
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (38 bp):
AAACTTAACATTTACATAAAAAAAATTAAAATAAAAAC
Found at i:1232984 original size:19 final size:18
Alignment explanation
Indices: 1232939--1232984 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1232929 AAAATCAATC
1232939 AAATAAATTAAATAAAAGA
1 AAATAAA-TAAATAAAAGA
**
1232958 AACCAAATAAGATAAAAGA
1 AAATAAATAA-ATAAAAGA
1232977 AAATAAAT
1 AAATAAAT
1232985 TTGTGAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (18 bp):
AAATAAATAAATAAAAGA
Found at i:1236267 original size:21 final size:21
Alignment explanation
Indices: 1236240--1236289 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1236230 GTCCACGCCC
*
1236240 AAAATA-AATTAA-AATAAAT
1 AAAATATAATTAATAAAAAAT
1236259 AAAATATAATTAATAAAAAAT
1 AAAATATAATTAATAAAAAAT
1236280 AAAATA-AATT
1 AAAATATAATT
1236290 GGGTTACCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 12 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATATAATTAATAAAAAAT
Found at i:1237277 original size:16 final size:16
Alignment explanation
Indices: 1237252--1237295 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1237242 ATTTAGTTAA
* *
1237252 TTTCTCTTGAGTATAT
1 TTTCTTTTGAATATAT
1237268 TTTCTTTTGAATATAT
1 TTTCTTTTGAATATAT
1237284 TTT-TTTT-AATAT
1 TTTCTTTTGAATAT
1237296 GATCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 5 0.19
15 4 0.15
16 17 0.65
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.64
Consensus pattern (16 bp):
TTTCTTTTGAATATAT
Found at i:1241244 original size:23 final size:23
Alignment explanation
Indices: 1241226--1241270 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1241216 AGCTAATTTT
1241226 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
1241249 TTCTAAATATTATCACTAAATA
1 TTCTAAATATTATCACTAAATA
1241271 TTATCACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (23 bp):
TTCTAAATATTATCACTAAATAA
Found at i:1241246 original size:13 final size:13
Alignment explanation
Indices: 1241228--1241306 Score: 98
Period size: 13 Copynumber: 6.5 Consensus size: 13
1241218 CTAATTTTTT
1241228 CTAAATATTATCA
1 CTAAATATTATCA
*
1241241 CTAAATA--AT-T
1 CTAAATATTATCA
1241251 CTAAATATTATCA
1 CTAAATATTATCA
1241264 CTAAATATTATCA
1 CTAAATATTATCA
*
1241277 CTAAATA--AT-T
1 CTAAATATTATCA
1241287 CTAAATATTATCA
1 CTAAATATTATCA
1241300 CTAAATA
1 CTAAATA
1241307 ATTCAAAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
10 14 0.25
11 4 0.07
12 4 0.07
13 34 0.61
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:1241268 original size:36 final size:36
Alignment explanation
Indices: 1241228--1241306 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
1241218 CTAATTTTTT
1241228 CTAAATATTATCACTAAATAATTCTAAATATTATCA
1 CTAAATATTATCACTAAATAATTCTAAATATTATCA
1241264 CTAAATATTATCACTAAATAATTCTAAATATTATCA
1 CTAAATATTATCACTAAATAATTCTAAATATTATCA
1241300 CTAAATA
1 CTAAATA
1241307 ATTCAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (36 bp):
CTAAATATTATCACTAAATAATTCTAAATATTATCA
Found at i:1241290 original size:23 final size:23
Alignment explanation
Indices: 1241264--1241315 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1241254 AATATTATCA
1241264 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
1241287 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
1241310 CAAAAT
1 CTAAAT
1241316 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:1249165 original size:13 final size:13
Alignment explanation
Indices: 1249141--1249174 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1249131 CAAAAAGGTT
*
1249141 GAAAGTAAAAAAAG
1 GAAAG-AAAAAAAA
1249155 GAAAGAAAAAAAA
1 GAAAGAAAAAAAA
1249168 GAAAGAA
1 GAAAGAA
1249175 TTTATTAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
GAAAGAAAAAAAA
Found at i:1249291 original size:13 final size:13
Alignment explanation
Indices: 1249273--1249315 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1249263 TAGATTTTTC
1249273 CTAAATATTATCA
1 CTAAATATTATCA
*
1249286 CTAAATA--AT-T
1 CTAAATATTATCA
1249296 CTAAATATTATCA
1 CTAAATATTATCA
1249309 CTAAATA
1 CTAAATA
1249316 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:1249303 original size:23 final size:23
Alignment explanation
Indices: 1249273--1249323 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1249263 TAGATTTTTC
1249273 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
1249296 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
1249319 -TAAAT
1 CTAAAT
1249324 TTTAAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:1251864 original size:19 final size:19
Alignment explanation
Indices: 1251840--1251935 Score: 156
Period size: 19 Copynumber: 4.9 Consensus size: 19
1251830 ATAATTTTTG
1251840 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1251859 ATGATATGCAATCCTAGAT
1 ATGATATGCAATCTTAGAT
1251878 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
1251897 ATGATATATGCAATCTTAGAT
1 ATG--ATATGCAATCTTAGAT
*
1251918 ATGATATGTAATCTTAGA
1 ATGATATGCAATCTTAGA
1251936 AGATATGATT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 53 0.74
21 19 0.26
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:1251917 original size:40 final size:38
Alignment explanation
Indices: 1251840--1251942 Score: 156
Period size: 40 Copynumber: 2.7 Consensus size: 38
1251830 ATAATTTTTG
1251840 ATGATATGCAATCTTAGATATGATATGCAATCCTAGAT
1 ATGATATGCAATCTTAGATATGATATGCAATCCTAGAT
*
1251878 ATGATATGCAATCTTAGATATGATATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATG--ATATGCAATCCTAGAT
*
1251918 ATGATATGTAATCTTAGA-A-GATATG
1 ATGATATGCAATCTTAGATATGATATG
1251943 ATTTTGTAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 5 0.08
38 23 0.38
39 1 0.02
40 32 0.52
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
ATGATATGCAATCTTAGATATGATATGCAATCCTAGAT
Found at i:1251961 original size:22 final size:22
Alignment explanation
Indices: 1251874--1251958 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 22
1251864 ATGCAATCCT
*
1251874 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
1251895 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
1251914 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
* *
1251936 AGATATGATTTTGTAATTTTAGA
1 AGATATGA-TATGTAATCTTAGA
1251959 GATTTAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 12 0.23
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:1251968 original size:22 final size:23
Alignment explanation
Indices: 1251924--1251968 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1251914 AGATATGATA
*
1251924 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
* *
1251947 TGTAATTTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
1251969 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:1253248 original size:98 final size:98
Alignment explanation
Indices: 1253079--1253273 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
1253069 NNNNNNNNAA
* *
1253079 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1253144 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
1253177 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1253242 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
1253274 ATTTTATTGT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:1256384 original size:2 final size:2
Alignment explanation
Indices: 1256377--1256409 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1256367 AACTATGTAA
1256377 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 T
1256410 TTGTTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1259250 original size:100 final size:101
Alignment explanation
Indices: 1259076--1259291 Score: 299
Period size: 100 Copynumber: 2.1 Consensus size: 101
1259066 CAATTATTCA
* * *
1259076 AACGTAAGATCATGGTTGGATCATGGCAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATT
1 AACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATT
* * * *
1259141 ATGATGATAAGATCATAA-TTGGTTATGGCACTATG
66 ATGATGATAAGACCATAACTAGGTTATGACACTACG
* * * *
1259176 GACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTGGGTTATGGCATT
1 AACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATT
* *
1259241 CTGATGATAAGACCATAACTAGGTTATTACACTACG
66 ATGATGATAAGACCATAACTAGGTTATGACACTACG
*
1259277 AATGTAAGACCATGG
1 AACGTAAGACCATGG
1259292 CAGGGCCATG
Statistics
Matches: 100, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 74 0.74
101 26 0.26
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (101 bp):
AACGTAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATT
ATGATGATAAGACCATAACTAGGTTATGACACTACG
Found at i:1262014 original size:17 final size:17
Alignment explanation
Indices: 1261992--1262032 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1261982 TGTGGAGGGG
1261992 CACACGCCCGTGTGGGA
1 CACACGCCCGTGTGGGA
*
1262009 CACACGCTCGTGTGGGA
1 CACACGCCCGTGTGGGA
1262026 CACACGC
1 CACACGC
1262033 ACATGTGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.37, G:0.32, T:0.12
Consensus pattern (17 bp):
CACACGCCCGTGTGGGA
Found at i:1262039 original size:17 final size:17
Alignment explanation
Indices: 1261992--1262040 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
1261982 TGTGGAGGGG
*
1261992 CACACGCCCGTGTGGGA
1 CACACGCACGTGTGGGA
*
1262009 CACACGCTCGTGTGGGA
1 CACACGCACGTGTGGGA
*
1262026 CACACGCACATGTGG
1 CACACGCACGTGTGG
1262041 CCACTCGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.14
Consensus pattern (17 bp):
CACACGCACGTGTGGGA
Found at i:1262633 original size:16 final size:16
Alignment explanation
Indices: 1262609--1262639 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1262599 TTTACTTCCA
1262609 AAAAATAAAATAAATT
1 AAAAATAAAATAAATT
*
1262625 AAAATTAAAATAAAT
1 AAAAATAAAATAAAT
1262640 AACTAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:1266272 original size:101 final size:101
Alignment explanation
Indices: 1266097--1266317 Score: 309
Period size: 101 Copynumber: 2.2 Consensus size: 101
1266087 TTCAAACATC
* * *
1266097 AGACCATGGTTGGACCATGATAGTGTTTATATGTAAGACCATAGCTAGGCTATGGCATTATGATG
1 AGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATTATAATG
* *
1266162 ATAAAACCATAACCT-GGTTATAGCACTATGGACGTA
66 ATAAAACCATAA-CTAGGTTATAGCACTACGAACGTA
* * *
1266198 AGACCATGGTTGGACTATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTAATG
1 AGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATTATAATG
* * *
1266263 ATAAGACCATAACTAGGTTATGGCACTACGAATGTA
66 ATAAAACCATAACTAGGTTATAGCACTACGAACGTA
* *
1266299 AGACCATGGTAGGGCCATG
1 AGACCATGGTTGGACCATG
1266318 GCAATGCATA
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
100 2 0.02
101 103 0.98
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (101 bp):
AGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATTATAATG
ATAAAACCATAACTAGGTTATAGCACTACGAACGTA
Found at i:1266273 original size:33 final size:35
Alignment explanation
Indices: 1266195--1266273 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
1266185 CACTATGGAC
* * *
1266195 GTAAGACCATGGTTGGACTATGACAGTGTTTATAT
1 GTAAGACCATAGCTGGACTATGACAGTGTCTATAT
*
1266230 GTAAGACCATAGCTGGGCTATGACA-T-TCTA-AT
1 GTAAGACCATAGCTGGACTATGACAGTGTCTATAT
1266262 GATAAGACCATA
1 G-TAAGACCATA
1266274 ACTAGGTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.08
33 13 0.33
34 1 0.03
35 22 0.56
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (35 bp):
GTAAGACCATAGCTGGACTATGACAGTGTCTATAT
Found at i:1266301 original size:33 final size:32
Alignment explanation
Indices: 1266228--1266305 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
1266218 CAGTGTTTAT
* * * *
1266228 ATGTAAGACCATAGCTGGGCTATGACATTCTA
1 ATGTAAGACCATAACTAGGCTATGACATACGA
* *
1266260 ATGATAAGACCATAACTAGGTTATGGCACTACGA
1 ATG-TAAGACCATAACTAGGCTATGACA-TACGA
1266294 ATGTAAGACCAT
1 ATGTAAGACCAT
1266306 GGTAGGGCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 29 0.76
34 6 0.16
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (32 bp):
ATGTAAGACCATAACTAGGCTATGACATACGA
Found at i:1272198 original size:49 final size:49
Alignment explanation
Indices: 1272144--1272240 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
1272134 AGAAAAGTAA
1272144 TTAATTAAAATTAATTTATAATTTTTATTTTAGAAAATAGAAAAACATG
1 TTAATTAAAATTAATTTATAATTTTTATTTTAGAAAATAGAAAAACATG
1272193 TTAATTAAAATTAATTTATAATTTTTATTTTAGAAAATAGAAAAACAT
1 TTAATTAAAATTAATTTATAATTTTTATTTTAGAAAATAGAAAAACAT
1272241 TTATTGGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (49 bp):
TTAATTAAAATTAATTTATAATTTTTATTTTAGAAAATAGAAAAACATG
Found at i:1275146 original size:28 final size:30
Alignment explanation
Indices: 1275088--1275147 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
1275078 CTTTTCAAAG
* *
1275088 CTCAATTGATTGCTAACTTTCGATTAGAAA
1 CTCAATTGATTGCTAACTTTCAATTAAAAA
*
1275118 CTCAATTGATTG-TGA-TTTCAATTAAAAA
1 CTCAATTGATTGCTAACTTTCAATTAAAAA
1275146 CT
1 CT
1275148 TAATGAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 2 0.07
30 12 0.44
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (30 bp):
CTCAATTGATTGCTAACTTTCAATTAAAAA
Found at i:1278405 original size:18 final size:18
Alignment explanation
Indices: 1278378--1278414 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1278368 CTGGTGCGTT
*
1278378 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
1278396 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
1278414 T
1 T
1278415 TCTTTTCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:1278873 original size:25 final size:25
Alignment explanation
Indices: 1278845--1278892 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1278835 TATTTTGATA
1278845 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
1278870 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
1278893 ATTTTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:1279073 original size:44 final size:44
Alignment explanation
Indices: 1278949--1279401 Score: 425
Period size: 44 Copynumber: 10.0 Consensus size: 44
1278939 AACAATTAAT
* * * * *
1278949 ACCCTTAAGTTAAAAACTCTAACATAATTTAATTAAAAACCTTAA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-A
* *
1278994 ACCATTAACTTAAAAACCTTAGACCTAATTAAATTAAAAACCCTA
1 ACCCTTAACTTAAAAACCCTA-ACCTAATTAAATTAAAAACCCTA
* **
1279039 ACCCTTAACTTAAAAACCATAACCTAATTAAATTAAAAATTCTA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
*
1279083 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * * *
1279127 ACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTA
1 ACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* ***
1279171 ACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAAATTTA
1 ACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * * *
1279217 GCCTAATTAAATTAAAAACCCTAGCCTAATTAAATT-AAAACCCTA
1 ACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* *
1279262 ACCTAATTTAA-TTAAAAA-CCTAAAACCCTAAACCCTAAACTTAAAAACCCTA
1 ACC---CTTAACTTAAAAACCCT--AA-CCT-AA--TTAAA-TTAAAAACCCTA
* * *
1279314 ACCCTTAACTTAAAAACACTAAACC--CTTAACTTAAAAACCCTA
1 ACCCTTAACTTAAAAACCCT-AACCTAATTAAATTAAAAACCCTA
*
1279357 ACCCTTAACTTAAAAACCCTAACCGAATTAAATTAAAAACCCTA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
1279401 A
1 A
1279402 ATGAAATTAA
Statistics
Matches: 347, Mismatches: 43, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
42 4 0.01
43 31 0.09
44 129 0.37
45 52 0.15
46 90 0.26
47 3 0.01
48 2 0.01
49 6 0.02
50 14 0.04
51 4 0.01
52 12 0.03
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (44 bp):
ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
Found at i:1279115 original size:67 final size:67
Alignment explanation
Indices: 1278949--1279401 Score: 426
Period size: 67 Copynumber: 6.7 Consensus size: 67
1278939 AACAATTAAT
* * * * *
1278949 ACCCTTAAGTTAAAAACTCTAACATAATTTAA-TTAAAAACCTTAAACC--ATTAACTTAAAAA-
1 ACCCTTAACTTAAAAACCCTAACCTAA-TTAACTTAAAAACCCT-AACCTAATTAAATTAAAAAT
1279010 CCTTA
64 CC-TA
* * * *
1279015 GACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCATAACCTAATTAAATTAAAAA
1 -ACC--CTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAA
*
1279078 TTCTA
63 TCCTA
*
1279083 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAATCC
1279148 TA
66 TA
1279150 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAAAT-
1 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATT-AAAAATC
*
1279214 TTA
65 CTA
* * * * * *
1279217 GCCTAATTAAATTAAAAACCCTAGCCTAATTAAATT-AAAACCCTAACCTAATTTAATTAAAAAC
1 ACC--CTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAA-
1279281 CTAAAACCCTAA
63 -T-----CCT-A
* * * * * *
1279293 ACCCTAAACTTAAAAACCCTAACC--CTTAACTTAAAAACACTAAACC--CTTAACTTAAAAACC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCT-AACCTAATTAAATTAAAAATC
1279354 CTA
65 CTA
* *
1279357 ACCCTTAACTTAAAAACCCTAACCGAATTAAATTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAA
1279402 ATGAAATTAA
Statistics
Matches: 323, Mismatches: 39, Indels: 50
0.78 0.09 0.12
Matches are distributed among these distances:
64 24 0.07
65 24 0.07
66 22 0.07
67 119 0.37
68 40 0.12
69 46 0.14
72 16 0.05
73 7 0.02
74 21 0.07
75 1 0.00
76 3 0.01
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (67 bp):
ACCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAATCC
TA
Found at i:1279206 original size:28 final size:23
Alignment explanation
Indices: 1278953--1279401 Score: 403
Period size: 23 Copynumber: 19.8 Consensus size: 23
1278943 ATTAATACCC
* * *
1278953 TTAAGTTAAAAACTCTAACATAA
1 TTAACTTAAAAACCCTAACCTAA
*
1278976 TTTAA-TTAAAAACCTTAAACC--A
1 -TTAACTTAAAAACCCT-AACCTAA
*
1278998 TTAACTTAAAAACCTTAGACCTAA
1 TTAACTTAAAAACCCTA-ACCTAA
* *
1279022 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
1279043 TTAACTTAAAAACCATAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* ** *
1279066 TTAAATTAAAAATTCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
1279087 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
1279110 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
1279133 TTAAATTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
1279154 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
1279177 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *** *
1279200 TTAAATTAAAAAATTTAGCCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
1279223 TTAAATTAAAAACCCTAGCCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
1279246 TTAAATT-AAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
1279268 TTTAA-TTAAAAA-CCTAAAACCCTAAA
1 -TTAACTTAAAAACCCT--AA-CCT-AA
* *
1279294 CCCTAAACTTAAAAACCCTAACC--C
1 ---TTAACTTAAAAACCCTAACCTAA
* *
1279318 TTAACTTAAAAACACTAAACC--C
1 TTAACTTAAAAACCCT-AACCTAA
*
1279340 TTAACTTAAAAACCCTAACC--C
1 TTAACTTAAAAACCCTAACCTAA
*
1279361 TTAACTTAAAAACCCTAACCGAA
1 TTAACTTAAAAACCCTAACCTAA
*
1279384 TTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
1279402 ATGAAATTAA
Statistics
Matches: 362, Mismatches: 39, Indels: 49
0.80 0.09 0.11
Matches are distributed among these distances:
21 98 0.27
22 54 0.15
23 163 0.45
24 25 0.07
25 3 0.01
26 2 0.01
27 2 0.01
28 5 0.01
29 7 0.02
30 3 0.01
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.27
Consensus pattern (23 bp):
TTAACTTAAAAACCCTAACCTAA
Found at i:1279311 original size:22 final size:22
Alignment explanation
Indices: 1279283--1279402 Score: 165
Period size: 21 Copynumber: 5.5 Consensus size: 22
1279273 TTAAAAACCT
*
1279283 AAAACCCTAAACCCTAAACTTA
1 AAAACCCTAAACCCTTAACTTA
1279305 AAAACCCT-AACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
*
1279326 AAAACACTAAACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
1279348 AAAACCCT-AACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
* *
1279369 AAAACCCT-AACCGAATTAAATTA
1 AAAACCCTAAACC--CTTAACTTA
1279392 AAAACCCTAAA
1 AAAACCCTAAA
1279403 TGAAATTAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
21 44 0.49
22 28 0.31
23 15 0.17
24 2 0.02
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (22 bp):
AAAACCCTAAACCCTTAACTTA
Found at i:1279336 original size:43 final size:43
Alignment explanation
Indices: 1279283--1279378 Score: 174
Period size: 43 Copynumber: 2.2 Consensus size: 43
1279273 TTAAAAACCT
1279283 AAAACCCTAAACCCTAAACTTAAAAACCCTAACCCTTAACTTA
1 AAAACCCTAAACCCTAAACTTAAAAACCCTAACCCTTAACTTA
* *
1279326 AAAACACTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTA
1 AAAACCCTAAACCCTAAACTTAAAAACCCTAACCCTTAACTTA
1279369 AAAACCCTAA
1 AAAACCCTAA
1279379 CCGAATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (43 bp):
AAAACCCTAAACCCTAAACTTAAAAACCCTAACCCTTAACTTA
Found at i:1279615 original size:116 final size:116
Alignment explanation
Indices: 1279406--1279645 Score: 392
Period size: 116 Copynumber: 2.1 Consensus size: 116
1279396 CCCTAAATGA
* * **
1279406 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTAGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATGTTTTTGACTAGTACTAACAAT
* *
1279471 TAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATTTATC
66 TAATAATTTTATATAATCTGATAATTTTACTAACCATTAATACAATTTATC
* *
1279522 AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATG-TTTTGACTGGTATTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATGTTTTTGACTAGTACTAACAAT
1279586 TAATAATTTTATATAATCTGATAATTTTTACTAACCATTAATACAATTTATC
66 TAATAATTTTATATAATCTGATAA-TTTTACTAACCATTAATACAATTTATC
1279638 AATTAATA
1 AATTAATA
1279646 GTTTCACAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 39 0.34
116 76 0.66
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGAGTTGGAAAAATGTTTTTGACTAGTACTAACAAT
TAATAATTTTATATAATCTGATAATTTTACTAACCATTAATACAATTTATC
Found at i:1286001 original size:9 final size:10
Alignment explanation
Indices: 1285977--1286005 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
1285967 CACATGTGAC
1285977 AAAAAAATAT
1 AAAAAAATAT
1285987 AAAAAAATA-
1 AAAAAAATAT
1285996 AAAAAAATAT
1 AAAAAAATAT
1286006 TAAACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:1286001 original size:19 final size:19
Alignment explanation
Indices: 1285977--1286029 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1285967 CACATGTGAC
1285977 AAAAAAATATAAAAAAATA
1 AAAAAAATATAAAAAAATA
* ***
1285996 AAAAAAATATTAAACTTTA
1 AAAAAAATATAAAAAAATA
*
1286015 ATAAAAATATAAAAA
1 AAAAAAATATAAAAA
1286030 TATTTAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAAATATAAAAAAATA
Found at i:1286029 original size:28 final size:29
Alignment explanation
Indices: 1285980--1286069 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 29
1285970 ATGTGACAAA
*
1285980 AAAATATAA-AAAAATAAAAAAAATA-TT
1 AAAATTTAATAAAAATAAAAAAAATATTT
* *
1286007 AAACTTTAATAAAAAT-ATAAAAATATTT
1 AAAATTTAATAAAAATAAAAAAAATATTT
*
1286035 AAAATTTACTAAAAATTAGAAAAAAA-ATTGT
1 AAAATTTAATAAAAA-TA-AAAAAAATATT-T
1286066 AAAA
1 AAAA
1286070 ATTGTAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 15 0.29
28 21 0.41
29 1 0.02
30 3 0.06
31 11 0.22
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAATTTAATAAAAATAAAAAAAATATTT
Found at i:1286096 original size:19 final size:19
Alignment explanation
Indices: 1286081--1286118 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1286071 TTGTAAAATT
1286081 TTATGAAAAT-CATAAAAAA
1 TTAT-AAAATGCATAAAAAA
1286100 TTATAAAATGCATAAAAAA
1 TTATAAAATGCATAAAAAA
1286119 AGGTCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
TTATAAAATGCATAAAAAA
Found at i:1286375 original size:10 final size:10
Alignment explanation
Indices: 1286362--1286416 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
1286352 ATTTATAAAA
1286362 TTTTATATAT
1 TTTTATATAT
*
1286372 TTTTCTATAT
1 TTTTATATAT
*
1286382 TTCTATATA-
1 TTTTATATAT
1286391 TTTTATA-AT
1 TTTTATATAT
1286400 TTTTA-ATGAT
1 TTTTATAT-AT
1286410 TTTTATA
1 TTTTATA
1286417 ATCTTTTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
8 2 0.05
9 11 0.30
10 23 0.62
11 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:1294162 original size:22 final size:23
Alignment explanation
Indices: 1294127--1294173 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1294117 ACATATACAT
**
1294127 TGATTCTATGATGTAA-AAAAAA
1 TGATTCTACAATGTAAGAAAAAA
*
1294149 TGATTCTACAATGTAAGAAAGAA
1 TGATTCTACAATGTAAGAAAAAA
1294172 TG
1 TG
1294174 GAGTGATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (23 bp):
TGATTCTACAATGTAAGAAAAAA
Found at i:1304472 original size:236 final size:235
Alignment explanation
Indices: 1304052--1304492 Score: 695
Period size: 236 Copynumber: 1.9 Consensus size: 235
1304042 GAGGGCTGAA
* * *
1304052 TTCAAACAGAAATCAATGATAGACTGGATACAAAGGGCAACTTAACACGAAATTGGTTCATATGA
1 TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
* * * *
1304117 TGGTCAAAAGCAAGCACTGTAGGGCCACTATAAGGATATTAACTGATTTGGTGGGGAATAAATTG
66 TGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
* *
1304182 GAAACTTCGCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAGTTGTTGGCTACTGCAGA
131 GAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGCAGA
*
1304247 TGGCCAGATTCAAAGAGTTGAACTGGCCGAGGAATGTTTC
196 CGGCCAGATTCAAAGAGTTGAACTGGCCGAGGAATGTTTC
*
1304287 TTCAAACAGAAATCAATAATAGACTGGATACAAATGGGCAACTCAACACAAAATTGTTTCATATG
1 TTCAAACAGAAATCAATAATAGACTGGATACAAA-GGGCAACTCAACACAAAATTGGTTCATATG
* * * *
1304352 ATGGTCAAAAGCAAGCACTTTAGGGACACTATAA-CATTTTTATCTGATTTGGAGGTAAATAAAT
65 ATGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCA-TATTAACTGATTTGGAGGGAAATAAAT
** *
1304416 TGGAAACTTCCCAGCAGATTTTAAGGGAAGTCACAATGTTCTTCAAGTAATTGTTGGCTACTGCA
129 TGGAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGCA
1304481 GACGGCCAGATT
194 GACGGCCAGATT
1304493 ACAGGATGCA
Statistics
Matches: 186, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
235 34 0.18
236 152 0.82
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (235 bp):
TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
TGGTCAAAAGCAAGCACTGTAGGGACACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
GAAACTTCCCAGCAGATTGCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGCAGA
CGGCCAGATTCAAAGAGTTGAACTGGCCGAGGAATGTTTC
Found at i:1307494 original size:108 final size:108
Alignment explanation
Indices: 1307300--1307503 Score: 313
Period size: 108 Copynumber: 1.9 Consensus size: 108
1307290 ACCAATAACA
* *
1307300 TTAAATACTACTAGAAACTCAGCATTTACAATAAAGAAAACCAAATAATCAATGAAAATTAACAA
1 TTAAACACTACTAGAAACTCAGCATTTACAATAAAAAAAACCAAATAATCAATGAAAATTAACAA
* *
1307365 TCCTCAGACCAATGATATTCCAATCAGTAAACAGCAGCTAATT
66 TCATCAGACCAATAATATTCCAATCAGTAAACAGCAGCTAATT
* *
1307408 TTAAACACTACTAGAAACTTAGCATTTACAATAAAAAAAACCAAATAATCAATTAAAATTAACAA
1 TTAAACACTACTAGAAACTCAGCATTTACAATAAAAAAAACCAAATAATCAATGAAAATTAACAA
*
1307473 TCAT-AGGACCAATAA-ATTTCCATTCAGTAAA
66 TCATCA-GACCAATAATA-TTCCAATCAGTAAA
1307504 TTTATAAACC
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 2 0.02
108 85 0.98
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (108 bp):
TTAAACACTACTAGAAACTCAGCATTTACAATAAAAAAAACCAAATAATCAATGAAAATTAACAA
TCATCAGACCAATAATATTCCAATCAGTAAACAGCAGCTAATT
Found at i:1309452 original size:27 final size:27
Alignment explanation
Indices: 1309422--1309476 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1309412 AGTAGCAGAA
*
1309422 CAAACATTATATGCAATCTCTCAGTTT
1 CAAACATTATATGCAATCGCTCAGTTT
1309449 CAAACATTATATGCAATCGCTCAGTTT
1 CAAACATTATATGCAATCGCTCAGTTT
1309476 C
1 C
1309477 TCTTATAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (27 bp):
CAAACATTATATGCAATCGCTCAGTTT
Found at i:1310404 original size:13 final size:13
Alignment explanation
Indices: 1310382--1310418 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1310372 TAAAGTACCC
*
1310382 GTGTCTGACACTT
1 GTGTCCGACACTT
1310395 GTGTCCGACACTT
1 GTGTCCGACACTT
*
1310408 GTGTCCAACAC
1 GTGTCCGACAC
1310419 ATGAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (13 bp):
GTGTCCGACACTT
Found at i:1332471 original size:16 final size:16
Alignment explanation
Indices: 1332450--1332489 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1332440 ATGGAATATG
1332450 GCTGTAATAGAATAAA
1 GCTGTAATAGAATAAA
* *
1332466 GTTGTAATAGAATGAA
1 GCTGTAATAGAATAAA
1332482 GCTGTAAT
1 GCTGTAAT
1332490 TAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (16 bp):
GCTGTAATAGAATAAA
Found at i:1332693 original size:56 final size:60
Alignment explanation
Indices: 1332632--1332801 Score: 197
Period size: 56 Copynumber: 2.8 Consensus size: 60
1332622 TTTTTTTACG
* *
1332632 TATAATTATTATTAAATATAATTTAATAAAAAAT-A-A-ATAATTTAATTATACT-TTAA
1 TATAATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAACACTCTTAA
* *
1332688 TATAATTATTATTAAATATAATTTAACAAAGATAATAATATATAATTTAATAACATTCTTAA
1 TATAATTATTATTAAATATAATTTAATAAA-A-AATAATATATAATTTAATAACACTCTTAA
*
1332750 TATAATTATTATCAAAATATGAA-TTAATAAAAATCATAATATATAATATTAA
1 TATAATTATTAT-TAAATAT-AATTTAATAAAAA--ATAATATATAAT-TTAA
1332802 AAAATAATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
56 29 0.30
57 1 0.01
58 3 0.03
59 1 0.01
60 1 0.01
61 14 0.14
62 17 0.18
63 25 0.26
64 6 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (60 bp):
TATAATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAACACTCTTAA
Found at i:1335792 original size:17 final size:18
Alignment explanation
Indices: 1335766--1335800 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1335756 AGGCCAATCT
*
1335766 GGGCGTGTGGG-CCACAC
1 GGGCGCGTGGGCCCACAC
1335783 GGGCGCGTGGGCCCACAC
1 GGGCGCGTGGGCCCACAC
1335801 AGGCATGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.11, C:0.34, G:0.46, T:0.09
Consensus pattern (18 bp):
GGGCGCGTGGGCCCACAC
Found at i:1336267 original size:13 final size:13
Alignment explanation
Indices: 1336251--1336288 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1336241 GGGGGTAGAA
*
1336251 ATCTGTATATCTG
1 ATCTGCATATCTG
1336264 ATCTGCATATCTG
1 ATCTGCATATCTG
1336277 ATCTGCATATCT
1 ATCTGCATATCT
1336289 ATAACTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (13 bp):
ATCTGCATATCTG
Found at i:1339675 original size:20 final size:19
Alignment explanation
Indices: 1339646--1339697 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 19
1339636 CATGAGCCTA
1339646 GGCCGTAATGGGCCACATTG
1 GGCCG-AATGGGCCACATTG
1339666 GGCCGAAATGGGCCACATTG
1 GGCCG-AATGGGCCACATTG
1339686 GGCCGAATGGGC
1 GGCCGAATGGGC
1339698 TCGTGAGTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.15
Consensus pattern (19 bp):
GGCCGAATGGGCCACATTG
Found at i:1340139 original size:26 final size:26
Alignment explanation
Indices: 1340066--1340140 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
1340056 AAGTATACTG
* *
1340066 TACTGGCAGCTTTGCCATA-TATACTGT
1 TACTGGCAGCTTTG-C-TACGATACTAT
* * *
1340093 TACTGGCAGCTTCGTTGCGATACTAT
1 TACTGGCAGCTTTGCTACGATACTAT
*
1340119 TATTGGCAGCTTTGCTACGATA
1 TACTGGCAGCTTTGCTACGATA
1340141 TTGGTGTGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
25 1 0.03
26 24 0.63
27 13 0.34
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTACGATACTAT
Found at i:1342060 original size:10 final size:11
Alignment explanation
Indices: 1342035--1342059 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1342025 GAGTTCTTCT
1342035 AAAAGGCCTAA
1 AAAAGGCCTAA
1342046 AAAAGGCCTAA
1 AAAAGGCCTAA
1342057 AAA
1 AAA
1342060 GAATGTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAGGCCTAA
Found at i:1343466 original size:33 final size:33
Alignment explanation
Indices: 1343418--1343481 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1343408 TGCATTATTG
1343418 CACTATACTGATACTGTATT-GGGCTAAGGCCCA
1 CACTATACTGATACTG-ATTAGGGCTAAGGCCCA
* * *
1343451 CACTGTACTGTTACTGATTAGGGCTCAGGCC
1 CACTATACTGATACTGATTAGGGCTAAGGCC
1343482 TGGACTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (33 bp):
CACTATACTGATACTGATTAGGGCTAAGGCCCA
Found at i:1347737 original size:31 final size:31
Alignment explanation
Indices: 1347702--1347782 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
1347692 TTCATGTATC
1347702 ATTATATTAAATTATTTAAATATTATTCATT
1 ATTATATTAAATTATTTAAATATTATTCATT
* *
1347733 ATTATATTAAATTATTTAAATCTTATTTATT
1 ATTATATTAAATTATTTAAATATTATTCATT
*
1347764 ATTATATTTAATT-TTTAAA
1 ATTATATTAAATTATTTAAA
1347783 ATAGTTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTATTCATT
Found at i:1348917 original size:43 final size:43
Alignment explanation
Indices: 1348856--1348941 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1348846 TATTATATTT
1348856 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
1 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
* * *
1348899 CTATTACGATAATTTAAATGACCTAAATTGATAAGTGTTAAAA
1 CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
1348942 GAAACATGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (43 bp):
CTATTACCATAATATAAATGACCTAAATTGATAAGTGCTAAAA
Found at i:1350257 original size:20 final size:20
Alignment explanation
Indices: 1350234--1350277 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1350224 TAATTTAGCC
*
1350234 ATTTTTATTTTTATTTTAAT
1 ATTTTTATTTTTAATTTAAT
*
1350254 ATTTTTGTTTTTAATTTAAT
1 ATTTTTATTTTTAATTTAAT
1350274 -TTTT
1 ATTTT
1350278 ACATTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTTTATTTTTAATTTAAT
Found at i:1359451 original size:18 final size:18
Alignment explanation
Indices: 1359428--1359469 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1359418 AATGAATTGT
1359428 ATTAAATTGCTTGATGTG
1 ATTAAATTGCTTGATGTG
1359446 ATTAAATTGCTTGATGTG
1 ATTAAATTGCTTGATGTG
1359464 ATTAAA
1 ATTAAA
1359470 AATGCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (18 bp):
ATTAAATTGCTTGATGTG
Found at i:1360661 original size:47 final size:47
Alignment explanation
Indices: 1360608--1360938 Score: 410
Period size: 47 Copynumber: 6.7 Consensus size: 47
1360598 TTAGGATTCT
1360608 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1360655 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1360702 ATGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATG-----T----GA--T---GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
** *
1360763 ATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
** *
1360810 ATGTGATGAATGTGAAAGTGTATATGCGTGATAAGGCTTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
1360857 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
1360904 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1360939 TCCCGAAGGG
Statistics
Matches: 254, Mismatches: 16, Indels: 28
0.85 0.05 0.09
Matches are distributed among these distances:
47 203 0.80
50 1 0.00
52 3 0.01
56 3 0.01
58 1 0.00
61 43 0.17
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:1360709 original size:14 final size:14
Alignment explanation
Indices: 1360690--1360718 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1360680 ATGTGATAAG
1360690 GCCTAATGGCCGAT
1 GCCTAATGGCCGAT
1360704 GCCTAATGGCCGAT
1 GCCTAATGGCCGAT
1360718 G
1 G
1360719 TGATGAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.31, T:0.21
Consensus pattern (14 bp):
GCCTAATGGCCGAT
Found at i:1360717 original size:61 final size:61
Alignment explanation
Indices: 1360643--1360765 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
1360633 ATGTGATAAG
1360643 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1360704 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1360765 G
1 G
1360766 TGATGAATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28
Consensus pattern (61 bp):
GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
Found at i:1377823 original size:11 final size:10
Alignment explanation
Indices: 1377805--1377853 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
1377795 GAGCATTTGA
1377805 GAGC-AAAAT
1 GAGCAAAAAT
*
1377814 GAGCGAAAAAC
1 GAGC-AAAAAT
1377825 GAGC-AAAAT
1 GAGCAAAAAT
1377834 GAGCACAAAAT
1 GAGCA-AAAAT
1377845 GAGCAAAAA
1 GAGCAAAAA
1377854 CCAAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 12 0.35
10 4 0.12
11 18 0.53
ACGTcount: A:0.57, C:0.14, G:0.22, T:0.06
Consensus pattern (10 bp):
GAGCAAAAAT
Found at i:1377830 original size:20 final size:20
Alignment explanation
Indices: 1377805--1377852 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1377795 GAGCATTTGA
1377805 GAGCAAAATGAGCGA-AAAAC
1 GAGCAAAATGAGC-ACAAAAC
*
1377825 GAGCAAAATGAGCACAAAAT
1 GAGCAAAATGAGCACAAAAC
1377845 GAGCAAAA
1 GAGCAAAA
1377853 ACCAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.56, C:0.15, G:0.23, T:0.06
Consensus pattern (20 bp):
GAGCAAAATGAGCACAAAAC
Found at i:1377985 original size:17 final size:17
Alignment explanation
Indices: 1377965--1378011 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1377955 ACCACACGGC
*
1377965 CATGTGAGCTACACAGT
1 CATGTGAGCCACACAGT
*
1377982 CATGTGAGCCACACGGT
1 CATGTGAGCCACACAGT
*
1377999 CGTGTGAGCCACA
1 CATGTGAGCCACA
1378012 TGGGCTACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (17 bp):
CATGTGAGCCACACAGT
Found at i:1378174 original size:9 final size:9
Alignment explanation
Indices: 1378157--1378193 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1378147 TGAGTTTTCG
1378157 AATTCGAAT
1 AATTCGAAT
*
1378166 AACTCGAAT
1 AATTCGAAT
1378175 AATTCGAAT
1 AATTCGAAT
1378184 AATTCGAAT
1 AATTCGAAT
1378193 A
1 A
1378194 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1378457 original size:30 final size:30
Alignment explanation
Indices: 1378410--1378468 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1378400 AACCTTTTAT
* *
1378410 TTTTCTCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCAC
*
1378439 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCC-AAAACTTTTACTCCCTTCCCA
1378469 TCTCACCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:1378575 original size:17 final size:17
Alignment explanation
Indices: 1378548--1378605 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
1378538 CTCCCCCCTA
*
1378548 TTTACTTTCCCTTAAACT
1 TTTATTTTCCC-TAAACT
*
1378566 TTTA-TTTCCCAAAACTT
1 TTTATTTTCCCTAAAC-T
1378583 TTTATTTTTCCCCTAAACT
1 TTTA-TTTT-CCCTAAACT
1378602 TTTA
1 TTTA
1378606 CTTCTCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 4 0.12
19 8 0.24
20 7 0.21
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATTTTCCCTAAACT
Found at i:1380920 original size:20 final size:20
Alignment explanation
Indices: 1380897--1380945 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1380887 AAGATTTAGT
1380897 AAAGAACTTAAAGTTCTATG
1 AAAGAACTTAAAGTTCTATG
*
1380917 AAAGAACTTAAAGTTTTATG
1 AAAGAACTTAAAGTTCTATG
*
1380937 AAAAAACTT
1 AAAGAACTT
1380946 GAGAAGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (20 bp):
AAAGAACTTAAAGTTCTATG
Found at i:1385783 original size:3 final size:3
Alignment explanation
Indices: 1385775--1385800 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1385765 TTTTGTGATT
1385775 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1385801 GAATTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1386572 original size:17 final size:17
Alignment explanation
Indices: 1386550--1386584 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1386540 GCGTTTTTAG
*
1386550 GAGAGAGAAATGAAAAC
1 GAGAGAAAAATGAAAAC
1386567 GAGAGAAAAATGAAAAC
1 GAGAGAAAAATGAAAAC
1386584 G
1 G
1386585 CGTCCTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.06, G:0.29, T:0.06
Consensus pattern (17 bp):
GAGAGAAAAATGAAAAC
Found at i:1386579 original size:58 final size:58
Alignment explanation
Indices: 1386509--1386625 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
1386499 GTTGTTTTTG
* * * *
1386509 GAGAGAGAAATGAAAACGCATCATGTAGGACGCGTTTTTAGGAGAGAGAAATGAAAAC
1 GAGAGAAAAATGAAAACGCATCATGAAGAACGCGTTTTTAGGAGAGAAAAATGAAAAC
* * *
1386567 GAGAGAAAAATGAAAACGCGTCCTGAAGAACGTGTTTTTAGGAGAGAAAAATGAAAAC
1 GAGAGAAAAATGAAAACGCATCATGAAGAACGCGTTTTTAGGAGAGAAAAATGAAAAC
1386625 G
1 G
1386626 CGTCCTGCAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.17
Consensus pattern (58 bp):
GAGAGAAAAATGAAAACGCATCATGAAGAACGCGTTTTTAGGAGAGAAAAATGAAAAC
Found at i:1391696 original size:12 final size:11
Alignment explanation
Indices: 1391668--1391708 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
1391658 AGAAGGGGCG
1391668 TTTT-TTTTTA
1 TTTTCTTTTTA
*
1391678 TGTT-TTTTTA
1 TTTTCTTTTTA
1391688 TTTTCTTTTTA
1 TTTTCTTTTTA
1391699 TTTTCGTTTT
1 TTTTC-TTTT
1391709 GAAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 12 0.44
11 11 0.41
12 4 0.15
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTA
Found at i:1391703 original size:11 final size:10
Alignment explanation
Indices: 1391668--1391702 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1391658 AGAAGGGGCG
1391668 TTTTTTTTTA
1 TTTTTTTTTA
*
1391678 TGTTTTTTTA
1 TTTTTTTTTA
1391688 TTTTCTTTTTA
1 TTTT-TTTTTA
1391699 TTTT
1 TTTT
1391703 CGTTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:1394704 original size:20 final size:21
Alignment explanation
Indices: 1394671--1394714 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1394661 GTACTCGTCG
1394671 AAAGACTAAGGAAA-TGGACC
1 AAAGACTAAGGAAACTGGACC
*
1394691 AAAGACT-AGAGAAACTGGAGC
1 AAAGACTAAG-GAAACTGGACC
1394712 AAA
1 AAA
1394715 TGCAAAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 11 0.52
21 8 0.38
ACGTcount: A:0.52, C:0.14, G:0.25, T:0.09
Consensus pattern (21 bp):
AAAGACTAAGGAAACTGGACC
Found at i:1397122 original size:20 final size:19
Alignment explanation
Indices: 1397093--1397141 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1397083 AGATTCAATC
1397093 AAAAAAAAATCAAAAA-CAA
1 AAAAAAAAAT-AAAAATCAA
1397112 AAAATAAAAATAAAAATCAA
1 AAAA-AAAAATAAAAATCAA
1397132 AAACAAAAAA
1 AAA-AAAAAA
1397142 GGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.33
20 17 0.63
21 1 0.04
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAAAAAATAAAAATCAA
Found at i:1397130 original size:26 final size:25
Alignment explanation
Indices: 1397093--1397151 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
1397083 AGATTCAATC
1397093 AAAAAAAAATCAAAAACAAAAAATA
1 AAAAAAAAATCAAAAACAAAAAATA
**
1397118 AAAATAAAAATCAAAAACAAAAAAGG
1 AAAA-AAAAATCAAAAACAAAAAATA
1397144 AAAAAAAA
1 AAAAAAAA
1397152 TTTCAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (25 bp):
AAAAAAAAATCAAAAACAAAAAATA
Found at i:1403206 original size:32 final size:33
Alignment explanation
Indices: 1403134--1403210 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
1403124 AATGAATCAA
**
1403134 AGTTAATTGGTTCATGTAACAACAAAAAAAAATT
1 AGTTAATTGGTTCATGTAAC-ACAAAAAAAAAAG
*
1403168 AATTAATTGGTTCATGTAAC-CAAAAAAAAAAG
1 AGTTAATTGGTTCATGTAACACAAAAAAAAAAG
1403200 AGTTAA-TGGTT
1 AGTTAATTGGTT
1403211 TCAAAATCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 5 0.13
32 15 0.38
34 19 0.49
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (33 bp):
AGTTAATTGGTTCATGTAACACAAAAAAAAAAG
Found at i:1406170 original size:20 final size:19
Alignment explanation
Indices: 1406144--1406201 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1406134 ATAAAAGCAA
1406144 ATGAGCTTAAAATGAGCT-G
1 ATGAGC-TAAAATGAGCTCG
*
1406163 ATTGAGCTAAGAGTGAGCTCG
1 A-TGAGCTAA-AATGAGCTCG
1406184 ATGAGCTAAAATTGAGCT
1 ATGAGCTAAAA-TGAGCT
1406202 AAATGAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 5 0.15
20 26 0.79
21 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (19 bp):
ATGAGCTAAAATGAGCTCG
Found at i:1406207 original size:20 final size:19
Alignment explanation
Indices: 1406142--1406207 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
1406132 ATATAAAAGC
1406142 AAATGAGCTTAAAATGAGCT
1 AAATGAGC-TAAAATGAGCT
* * *
1406162 GATTGAGCTAAGAGTGAGCT
1 AAATGAGCTAA-AATGAGCT
**
1406182 CGATGAGCTAAAATTGAGCT
1 AAATGAGCTAAAA-TGAGCT
1406202 AAATGA
1 AAATGA
1406208 ACTTGAAGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (19 bp):
AAATGAGCTAAAATGAGCT
Found at i:1407450 original size:18 final size:19
Alignment explanation
Indices: 1407429--1407464 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1407419 AAAGCGAAAA
*
1407429 GAGATTGA-AAAAGAATTT
1 GAGATTGAGAAAAAAATTT
1407447 GAGATTGAGAAAAAAATT
1 GAGATTGAGAAAAAAATT
1407465 GACAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGATTGAGAAAAAAATTT
Found at i:1411802 original size:8 final size:8
Alignment explanation
Indices: 1411791--1411833 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
1411781 ATTTTAAAAT
1411791 TTTTTATA
1 TTTTTATA
1411799 TTTTTATA
1 TTTTTATA
1411807 TTTTTGA-A
1 TTTTT-ATA
1411815 -TTTTATA
1 TTTTTATA
*
1411822 TTTATATA
1 TTTTTATA
1411830 TTTT
1 TTTT
1411834 AAAATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 1 0.03
7 5 0.17
8 23 0.77
9 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTATA
Found at i:1411832 original size:15 final size:15
Alignment explanation
Indices: 1411793--1411834 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1411783 TTTAAAATTT
1411793 TTTATAT-TTTTATA
1 TTTATATATTTTATA
*
1411807 TTTTTGA-ATTTTATA
1 TTTAT-ATATTTTATA
1411822 TTTATATATTTTA
1 TTTATATATTTTA
1411835 AAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATATATTTTATA
Found at i:1415308 original size:62 final size:62
Alignment explanation
Indices: 1415235--1415361 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
1415225 ATTTTTTTCC
1415235 ATTTTTTCTTTTTCACTTTCTTTCCCATTTCTCCTCTCAATCAAGCATACCCTAAAGATTTA
1 ATTTTTTCTTTTTCACTTTCTTTCCCATTTCTCCTCTCAATCAAGCATACCCTAAAGATTTA
1415297 ATTTTTTCTTTTTCACTTTCTTTCCCATTTCTCCTCTCAATCAAGCATACCCTAAAGATTTA
1 ATTTTTTCTTTTTCACTTTCTTTCCCATTTCTCCTCTCAATCAAGCATACCCTAAAGATTTA
1415359 ATT
1 ATT
1415362 GATAAAGTGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (62 bp):
ATTTTTTCTTTTTCACTTTCTTTCCCATTTCTCCTCTCAATCAAGCATACCCTAAAGATTTA
Found at i:1415504 original size:19 final size:21
Alignment explanation
Indices: 1415471--1415509 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1415461 TAGAGTTTGT
1415471 AAAATGAGATGAATTTTAAAA
1 AAAATGAGATGAATTTTAAAA
1415492 AAAAT-AGAT-AATTTTAAA
1 AAAATGAGATGAATTTTAAA
1415510 TTAACATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATGAGATGAATTTTAAAA
Found at i:1430287 original size:106 final size:106
Alignment explanation
Indices: 1430102--1430308 Score: 292
Period size: 106 Copynumber: 2.0 Consensus size: 106
1430092 AGTTTGGCCT
* *
1430102 TTATTATATGCTTTTTCCTGGGGTAGCTATCATTTTGGTTAAAAAAACTTATACTCAATGGTCTC
1 TTATTATATGCTTTTTCATGGGGTAGCTACCATTTTGGTTAAAAAAACTTATACTCAATGGTCTC
* *
1430167 TCCTCTTTGCTTTTGGCAAAACATAGTGATAGCTTTAGCCA
66 TCATCTTTGCTTTTGGCAAAACATAATGATAGCTTTAGCCA
*** *
1430208 TTATTATATGCTTTTTCAT-GGGTGAGCTACCATTTTGGTTAAAATTGCTT-TAACTTAATGGTC
1 TTATTATATGCTTTTTCATGGGGT-AGCTACCATTTTGGTTAAAAAAACTTAT-ACTCAATGGTC
* *
1430271 TCTTATCTTTGCTTTTGGCAAAGCATAATGATAGCTTT
64 TCTCATCTTTGCTTTTGGCAAAACATAATGATAGCTTT
1430309 GGTTGAGGCC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 5 0.06
106 84 0.94
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (106 bp):
TTATTATATGCTTTTTCATGGGGTAGCTACCATTTTGGTTAAAAAAACTTATACTCAATGGTCTC
TCATCTTTGCTTTTGGCAAAACATAATGATAGCTTTAGCCA
Found at i:1432114 original size:91 final size:91
Alignment explanation
Indices: 1431981--1432188 Score: 301
Period size: 91 Copynumber: 2.3 Consensus size: 91
1431971 TTGATTTTAG
* *
1431981 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
1432046 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
1432073 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
1432138 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
1432164 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
1432189 GTTATAATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 86 0.82
92 19 0.18
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:1432222 original size:28 final size:27
Alignment explanation
Indices: 1432191--1432266 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
1432181 ATTTATTAGT
1432191 TATAATTATTTTAAATTTTATTAAATCA
1 TATAATTATTTTAAATTTTATTAAAT-A
* * *
1432219 TAT-ATT-TTAATTAAAATATATTTAATA
1 TATAATTATT--TTAAATTTTATTAAATA
*
1432246 T-TAATTATTTCAAATTTTATT
1 TATAATTATTTTAAATTTTATT
1432267 TTATAGTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
26 12 0.32
27 8 0.21
28 18 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
TATAATTATTTTAAATTTTATTAAATA
Found at i:1432328 original size:66 final size:64
Alignment explanation
Indices: 1432242--1432452 Score: 194
Period size: 66 Copynumber: 3.4 Consensus size: 64
1432232 AAATATATTT
*
1432242 AATATTAATTATTTCAAATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTA-TTAAAATTTTATTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
1432307 G
64 G
* * * **
1432308 AATATTAATTATTAAGAATTTTA--TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTAA-AATTTTATTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
1432362 AATAATAATTATGT-TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TAAAATTT-TATTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
1432426 AG
63 AG
*
1432428 AATATTAATTCTTAAGAATTTTATT
1 AATATTAATTATTAA-AATTTTATT
1432453 AAATTATATA
Statistics
Matches: 112, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 8 0.07
66 32 0.29
67 5 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTAAAATTTTATTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:1432328 original size:120 final size:120
Alignment explanation
Indices: 1432204--1432496 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 120
1432194 AATTATTTTA
* *
1432204 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
1432267 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
1432324 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
1432389 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTCTTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
1432444 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1432497 TAAATATGAT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 5 0.03
120 158 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:1432364 original size:15 final size:15
Alignment explanation
Indices: 1432329--1432380 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1432319 TTAAGAATTT
*
1432329 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1432343 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1432357 TATTTAATAATAAT-
1 TATTTAATTATAATA
1432371 TATGTTAATT
1 TAT-TTAATT
1432381 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1432473 original size:18 final size:17
Alignment explanation
Indices: 1432445--1432479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1432435 ATTCTTAAGA
*
1432445 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1432462 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1432480 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1432670 original size:39 final size:40
Alignment explanation
Indices: 1432627--1432731 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
1432617 TTCCATTATG
1432627 CTATTACACCTCTATTCCATTCAACCAAACACTAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACTAGATTTA
** * * *
1432666 CTATTATGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACTAGATTTA
1432711 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
1432732 ACACCTCTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
39 14 0.26
40 5 0.09
44 18 0.34
45 16 0.30
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACTAGATTTA
Found at i:1432726 original size:45 final size:44
Alignment explanation
Indices: 1432625--1432734 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
1432615 TTTTCCATTA
1432625 TGCTATTACACCTCTATT-C----CATTCAACCAAACACTAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACTAGAT
* ** * *
1432664 TACTATTATGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACTAGA-T
1432709 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
1432735 CCTCTATTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 15 0.26
40 1 0.02
44 17 0.30
45 24 0.42
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACTAGAT
Found at i:1432734 original size:16 final size:16
Alignment explanation
Indices: 1432713--1432766 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
1432703 TTGATTTGCT
1432713 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
1432729 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
1432745 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
1432761 AATACA
1 ATTACA
1432767 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:1434452 original size:25 final size:25
Alignment explanation
Indices: 1434424--1434506 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
1434414 CAGCTCTTAT
*
1434424 GAGCGTCCTGA-TATATGGCTCTTCG
1 GAGCTTCCTGATTA-ATGGCTCTTCG
* * *
1434449 GAGCTTCCCGATTAAAGGCTCTTTCAT
1 GAGCTTCCTGATTAATGGCTC-TTC-G
*
1434476 GAGCTTCCTGATTAATGGCTCTCCG
1 GAGCTTCCTGATTAATGGCTCTTCG
1434501 GAGCTT
1 GAGCTT
1434507 TCGATATTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 21 0.45
26 7 0.15
27 19 0.40
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTTCG
Found at i:1434602 original size:14 final size:14
Alignment explanation
Indices: 1434583--1434611 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1434573 GGGCTTCCCG
1434583 TTTACATGTTTTCA
1 TTTACATGTTTTCA
1434597 TTTACATGTTTTCA
1 TTTACATGTTTTCA
1434611 T
1 T
1434612 GAGCATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTACATGTTTTCA
Found at i:1437028 original size:62 final size:61
Alignment explanation
Indices: 1436942--1437069 Score: 175
Period size: 62 Copynumber: 2.1 Consensus size: 61
1436932 GTACACGCTT
* * * * *
1436942 GTGTCCCTAGCCGTGTGGTTTTGTACAAAAAATAGTGAGTTACACGGCCTGGACATATGCCC
1 GTGTCCCTAGCCGTGTGGTATTGTACAAAAAACAGTGAGTTACA-GGCCTAGACACACGCCC
* * *
1437004 GTGTCCCTAGCCGTGTGGTATTGTACCACAAACAGTGAGTTACATGCCTAGACACACGCCC
1 GTGTCCCTAGCCGTGTGGTATTGTACAAAAAACAGTGAGTTACAGGCCTAGACACACGCCC
1437065 GTGTC
1 GTGTC
1437070 TATTGCCCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
61 18 0.31
62 40 0.69
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (61 bp):
GTGTCCCTAGCCGTGTGGTATTGTACAAAAAACAGTGAGTTACAGGCCTAGACACACGCCC
Found at i:1439807 original size:19 final size:19
Alignment explanation
Indices: 1439783--1439819 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1439773 ATTTTGATGT
1439783 TGTGGTATG-ATAGTTTAAA
1 TGTGGTATGTAT-GTTTAAA
1439802 TGTGGTATGTATGTTTAA
1 TGTGGTATGTATGTTTAA
1439820 TTCCATGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (19 bp):
TGTGGTATGTATGTTTAAA
Found at i:1446468 original size:13 final size:12
Alignment explanation
Indices: 1446450--1446508 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
1446440 TGGGAAAGAA
1446450 AAAGATATGAGAG
1 AAAGATA-GAGAG
1446463 AAAGATAGAG-G
1 AAAGATAGAGAG
* *
1446474 AACGAGAGAGA-
1 AAAGATAGAGAG
*
1446485 AAGAGATATGGGAG
1 AA-AGATA-GAGAG
1446499 AAAGATAGAG
1 AAAGATAGAG
1446509 GGTTAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 11 0.31
12 8 0.22
13 15 0.42
14 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.36, T:0.10
Consensus pattern (12 bp):
AAAGATAGAGAG
Found at i:1446508 original size:19 final size:19
Alignment explanation
Indices: 1446452--1446508 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1446442 GGAAAGAAAA
1446452 AGATATGAGAGAAAGATAG
1 AGATATGAGAGAAAGATAG
* *
1446471 AGGA-ACGAGAG--AGAAAG
1 A-GATATGAGAGAAAGATAG
*
1446488 AGATATGGGAGAAAGATAG
1 AGATATGAGAGAAAGATAG
1446507 AG
1 AG
1446509 GGTTAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.07
17 11 0.38
19 14 0.48
20 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.37, T:0.11
Consensus pattern (19 bp):
AGATATGAGAGAAAGATAG
Found at i:1447451 original size:35 final size:35
Alignment explanation
Indices: 1447405--1447475 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1447395 AAAAAATTCA
*
1447405 AGCCAATATTTTAATAATAATAAAGTATTTAAACT
1 AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
* *
1447440 AGCCAATATTTTAATAAGATTAAATTATTTAAACT
1 AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
1447475 A
1 A
1447476 ACTAATGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (35 bp):
AGCCAATATTTTAATAAGAATAAAGTATTTAAACT
Found at i:1449450 original size:34 final size:34
Alignment explanation
Indices: 1449412--1449489 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
1449402 GCAATATGAC
* * *
1449412 ATGCTTATAACAGA-TCAATATGGTAGCAATTTAT
1 ATGCTTATAACA-ATTCAATACGGTAGCAAATAAT
* *
1449446 ATGCTAATAACAATTCGATACGGTAGCAAATAAT
1 ATGCTTATAACAATTCAATACGGTAGCAAATAAT
1449480 ATGCTTATAA
1 ATGCTTATAA
1449490 TGGACCAACG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (34 bp):
ATGCTTATAACAATTCAATACGGTAGCAAATAAT
Found at i:1460450 original size:21 final size:21
Alignment explanation
Indices: 1460424--1460465 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1460414 TACACATGTG
1460424 GAGTATTTAGGACACATCATC
1 GAGTATTTAGGACACATCATC
1460445 GAGTATTTAGGACACATCATC
1 GAGTATTTAGGACACATCATC
1460466 TCGAAGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
GAGTATTTAGGACACATCATC
Found at i:1466252 original size:45 final size:47
Alignment explanation
Indices: 1466163--1466255 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 47
1466153 TATAAACAAA
*
1466163 TATTTATATTTATGTAAAAACACCAGATTTAAATAAAAAATTAAATAAT
1 TATTTATATTTATGTAAAAACACCAGATTT--AGAAAAAATTAAATAAT
* *
1466212 TATTTGTATTTATGT-AAAACACCAGATTT-GAAACAATTAAATAA
1 TATTTATATTTATGTAAAAACACCAGATTTAGAAAAAATTAAATAA
1466256 ACCAGGTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 13 0.32
48 14 0.34
49 14 0.34
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (47 bp):
TATTTATATTTATGTAAAAACACCAGATTTAGAAAAAATTAAATAAT
Found at i:1474468 original size:12 final size:11
Alignment explanation
Indices: 1474439--1474474 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1474429 TTTTGAATAA
1474439 AATATTTTTTT
1 AATATTTTTTT
*
1474450 TATATTTTTTT
1 AATATTTTTTT
1474461 AATAATTTTTTT
1 AAT-ATTTTTTT
1474473 AA
1 AA
1474475 AAAAATACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:1474515 original size:5 final size:5
Alignment explanation
Indices: 1474505--1474530 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1474495 GGTCAACGGA
1474505 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1474531 GGCGCCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1474575 original size:27 final size:27
Alignment explanation
Indices: 1474545--1474611 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
1474535 CCTATTAGGT
1474545 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
1474572 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
1474599 AGGCCCCAATGAA
1 AGGCGCCAATGAA
1474612 TATTGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.31, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:1474710 original size:21 final size:21
Alignment explanation
Indices: 1474681--1474724 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1474671 TGGATTAGTA
*
1474681 TTTTGTATGAATACTGTAATT
1 TTTTATATGAATACTGTAATT
*
1474702 TTTTATATGAATATTGTAATT
1 TTTTATATGAATACTGTAATT
1474723 TT
1 TT
1474725 GTGTTTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTATATGAATACTGTAATT
Found at i:1474857 original size:16 final size:16
Alignment explanation
Indices: 1474812--1474857 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1474802 ACAAAATAAA
*
1474812 ATAAAAAAT-AATTAT
1 ATAAAAATTAAATTAT
* *
1474827 ATAAAAGTTACATTAT
1 ATAAAAATTAAATTAT
1474843 ATAAAAATTAAATTA
1 ATAAAAATTAAATTA
1474858 GTTAACAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
ATAAAAATTAAATTAT
Found at i:1474933 original size:38 final size:38
Alignment explanation
Indices: 1474890--1474971 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
1474880 AAAAAGTCAG
1474890 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
1474928 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1474966 TTATAA
1 TTATAA
1474972 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:1475097 original size:60 final size:60
Alignment explanation
Indices: 1475004--1475125 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
1474994 ATATTAAACT
* * * *
1475004 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATTT-T-AAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT--ATTTATAAAATAATTAC
*
1475064 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
1475124 AA
1 AA
1475126 TATTCATACA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 4 0.07
59 1 0.02
60 50 0.91
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
Found at i:1475144 original size:21 final size:21
Alignment explanation
Indices: 1475113--1475279 Score: 104
Period size: 27 Copynumber: 7.2 Consensus size: 21
1475103 AATTATTTAT
1475113 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
1475135 AAAAAATTACAATATTACAATATATC
1 AAAAAATTACAATATT-C---ATA-C
*** *
1475161 TCGACATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
1475182 --AAAATTACAATATTACAATATTC
1 AAAAAATTACAATATT-C-ATA--C
*
1475205 ATACAAAATTATAATATTACAATATTC
1 A-A-AAAATTACAATATT-C-ATA--C
*
1475232 ATACAAAATTACAATATTCATAT
1 A-A-AAAATTACAATATTCATAC
1475255 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
1475276 AAAA
1 AAAA
1475280 TACTAATCCA
Statistics
Matches: 122, Mismatches: 10, Indels: 27
0.77 0.06 0.17
Matches are distributed among these distances:
19 12 0.10
20 1 0.01
21 38 0.31
22 9 0.07
23 2 0.02
25 7 0.06
26 14 0.11
27 39 0.32
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:1475153 original size:8 final size:8
Alignment explanation
Indices: 1475140--1475270 Score: 61
Period size: 8 Copynumber: 15.4 Consensus size: 8
1475130 CATACAAAAA
1475140 ATTACAAT
1 ATTACAAT
1475148 ATTACAAT
1 ATTACAAT
* * *
1475156 ATATCTCGAC
1 AT-T-ACAAT
1475166 ATTACAAT
1 ATTACAAT
*
1475174 ATTCATACAAA
1 A-T--TACAAT
1475185 ATTACAAT
1 ATTACAAT
1475193 ATTACAAT
1 ATTACAAT
*
1475201 ATTCATACAAA
1 A-T--TACAAT
*
1475212 ATTATAAT
1 ATTACAAT
1475220 ATTACAAT
1 ATTACAAT
*
1475228 ATTCATACAAA
1 A-T--TACAAT
1475239 ATTACAAT
1 ATTACAAT
1475247 ATT-C-AT
1 ATTACAAT
* *
1475253 A-TAAAAA
1 ATTACAAT
1475260 ATTACAAT
1 ATTACAAT
1475268 ATT
1 ATT
1475271 CATACAAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 28
0.66 0.13 0.20
Matches are distributed among these distances:
5 1 0.01
6 3 0.03
7 3 0.03
8 54 0.59
9 5 0.05
10 7 0.08
11 18 0.20
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (8 bp):
ATTACAAT
Found at i:1475190 original size:19 final size:19
Alignment explanation
Indices: 1475166--1475353 Score: 108
Period size: 19 Copynumber: 9.7 Consensus size: 19
1475156 ATATCTCGAC
1475166 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
1475185 ATTACAATA-T--TACAATA
1 ATTACAATATTCATACAA-A
* * *
1475202 TTCATACAAAATT-AT--AAT
1 AT--TACAATATTCATACAAA
1475220 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
1475239 ATTACAATATTCATATAAAAA
1 ATTACAATATTC--ATACAAA
1475260 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
1475279 A-TACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
1475299 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
1475321 ATTACAATATTAATACAAA
1 ATTACAATATTCATACAAA
1475340 ATTACAATATTCAT
1 ATTACAATATTCAT
1475354 TGGCGCCTCT
Statistics
Matches: 131, Mismatches: 17, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
16 13 0.10
17 7 0.05
18 9 0.07
19 56 0.43
20 13 0.10
21 21 0.16
22 5 0.04
23 5 0.04
25 2 0.02
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:1475202 original size:27 final size:27
Alignment explanation
Indices: 1475166--1475270 Score: 159
Period size: 27 Copynumber: 4.1 Consensus size: 27
1475156 ATATCTCGAC
1475166 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
1475193 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1475220 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
1475247 ATT-C-ATA-T-A-A-AAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
1475268 ATT
1 ATT
1475271 CATACAAAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
21 14 0.18
22 1 0.01
23 1 0.01
24 1 0.01
25 3 0.04
26 1 0.01
27 55 0.72
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:1475303 original size:67 final size:60
Alignment explanation
Indices: 1475193--1475341 Score: 138
Period size: 67 Copynumber: 2.4 Consensus size: 60
1475183 AAATTACAAT
** * **
1475193 ATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAATTACAATATTCATATAAA
1 ATTACAATATTCATACAAAA-TATAATACCAAAATATAAATAC-AAATT--AA-ATT-ATA-AAA
1475258 AA
59 AA
* *
1475260 ATTACAATATTCATACAAAATACTAAT-CCAAAACTATAAATACAAATTTAATTATAAAATA
1 ATTACAATATTCATACAAAATA-TAATACCAAAA-TATAAATACAAATTAAATTATAAAAAA
*
1475321 ATTACAATATTAATACAAAAT
1 ATTACAATATTCATACAAAAT
1475342 TACAATATTC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
61 24 0.33
62 3 0.04
63 3 0.04
64 1 0.01
66 10 0.14
67 31 0.43
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (60 bp):
ATTACAATATTCATACAAAATATAATACCAAAATATAAATACAAATTAAATTATAAAAAA
Found at i:1475387 original size:27 final size:27
Alignment explanation
Indices: 1475349--1475415 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
1475339 AATTACAATA
*
1475349 TTCATTGGCGCCTCTGTATGAGACACC
1 TTCATTGGCGCCTCTCTATGAGACACC
* *
1475376 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGACACC
1475403 TTCATTGGCGCCT
1 TTCATTGGCGCCT
1475416 ACCTGATAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.13, C:0.31, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGACACC
Found at i:1475426 original size:27 final size:27
Alignment explanation
Indices: 1475349--1475426 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
1475339 AATTACAATA
*
1475349 TTCATTGGCGCCT-CTGTATGAGACACC
1 TTCATTGGCGCCTCCTG-ATGAGGCACC
1475376 TTCATTGGCGCCTCTCTG-TGAGGCACC
1 TTCATTGGCGCCTC-CTGATGAGGCACC
1475403 TTCATTGGCGCCTACCTGAT-AGGC
1 TTCATTGGCGCCT-CCTGATGAGGC
1475427 GCCACCCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
27 41 0.89
28 2 0.04
29 3 0.07
ACGTcount: A:0.15, C:0.31, G:0.24, T:0.29
Consensus pattern (27 bp):
TTCATTGGCGCCTCCTGATGAGGCACC
Found at i:1475782 original size:15 final size:15
Alignment explanation
Indices: 1475758--1475787 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1475748 TAAAATTATA
1475758 AAAAAATTGAATATT
1 AAAAAATTGAATATT
*
1475773 AAAAATTTGAATATT
1 AAAAAATTGAATATT
1475788 TTTATACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAAAATTGAATATT
Found at i:1476922 original size:34 final size:34
Alignment explanation
Indices: 1476857--1476922 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1476847 TTAGAGTTTT
* *
1476857 TTTTAAATAATTATAAAAATTATTTAATTTTAAA
1 TTTTAAATAATTATAAAAATAATATAATTTTAAA
* *
1476891 TTTTAAATAAATTTTAAAAA-AATATATTTTTA
1 TTTTAAAT-AATTATAAAAATAATATAATTTTA
1476923 GGATTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 17 0.63
35 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTTAAATAATTATAAAAATAATATAATTTTAAA
Found at i:1477587 original size:3 final size:3
Alignment explanation
Indices: 1477579--1477604 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1477569 GCAAAAAGTG
1477579 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1477605 GGGTACGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1478924 original size:40 final size:40
Alignment explanation
Indices: 1478753--1479068 Score: 298
Period size: 41 Copynumber: 7.8 Consensus size: 40
1478743 TAACCTTTCG
* *
1478753 GGGCTTTAGCGGCGCTTTTAAAGAAGCGCCGCTAGTGCTCA
1 GGGCTTTAGCGGCGTTTTTAAA-AAGCGCCGCTAATGCTCA
* * *
1478794 GAGCTTTAGCAGCGTTTTTAAAGAAGCGTCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTAAA-AAGCGCCGCTAATGCTCA
* * * * * *
1478835 GAGCTTTAGCGGCATTTTTGAAGAAGCGCTGCTAATGTTCG
1 GGGCTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTCA
*
1478876 GGGTTTTAGCGGCGTTTTTAAAAAGCGCCGC-AACTGCTCA
1 GGGCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAA-TGCTCA
** * * * *
1478916 AAGCTTTAGCGCCGTTTTTAAGGAAGCGCCACTAATACTC-
1 GGGCTTTAGCGGCGTTTTTAA-AAAGCGCCGCTAATGCTCA
* **
1478956 GAGGTTTTAGCGGCGTTTTTGGAAAGCGCCGCTAATGCTC-
1 G-GGCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCA
* * *
1478996 GTGGTTTTAGCGGCGTTTTTTGAAAAGCGCCGTTAATGCTC-
1 G-GGCTTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTCA
*
1479037 GGGATTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 GGGCTTTAGCGGCGTTTTT-AAAAAGCGCCGC
1479069 AAAAACATTT
Statistics
Matches: 227, Mismatches: 41, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
39 7 0.03
40 82 0.36
41 134 0.59
42 4 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
GGGCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCA
Done.