Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 140 of 378
Found at i:39929300 original size:29 final size:31
Alignment explanation
Indices: 39929235--39929302 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
39929225 GACTAATAAT
* * *
39929235 AAATTTAATTTCCTAATATTTATATATTTTAT
1 AAATTTAATTT-CTAATATTTATAAATTTAAC
*
39929267 TAATTTAATTT-TAA-ATTTATAAATTTAAC
1 AAATTTAATTTCTAATATTTATAAATTTAAC
39929296 AAATTTA
1 AAATTTA
39929303 GTCCTGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 18 0.58
30 3 0.10
32 10 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (31 bp):
AAATTTAATTTCTAATATTTATAAATTTAAC
Found at i:39948389 original size:38 final size:38
Alignment explanation
Indices: 39948347--39948422 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
39948337 TTGTTTCTTA
* *
39948347 ACTCTTTCGTTTCCCGTGCAAGAATTTTGATCGGTTTT
1 ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGATTTT
39948385 ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGATTTT
1 ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGATTTT
39948423 TCACTGTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (38 bp):
ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGATTTT
Found at i:39954005 original size:43 final size:43
Alignment explanation
Indices: 39953774--39953977 Score: 363
Period size: 43 Copynumber: 4.7 Consensus size: 43
39953764 TTTATTGGAA
* *
39953774 AAAAACGCCGCTAAAGGTCAAGGCTTTTAACGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
39953817 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
39953860 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGAG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
39953903 AAAAGCGCCGCTAAAGGTCAAGGCTTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTGTGGG
*
39953947 AAAAGCGCCGCTAAATGTCAAGGCTTTTAGC
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
39953978 TGCTTTTTTT
Statistics
Matches: 155, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
43 114 0.74
44 41 0.26
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:39954407 original size:21 final size:21
Alignment explanation
Indices: 39954383--39954428 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39954373 GCTCGTGCCT
*
39954383 CTGCCTCTCTCGCTGCAGCCG
1 CTGCCTCCCTCGCTGCAGCCG
* * *
39954404 CTGCCTCCCTCTCTGCTGCCT
1 CTGCCTCCCTCGCTGCAGCCG
39954425 CTGC
1 CTGC
39954429 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.50, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCAGCCG
Found at i:39960080 original size:9 final size:9
Alignment explanation
Indices: 39960066--39960282 Score: 134
Period size: 9 Copynumber: 23.6 Consensus size: 9
39960056 TATTTAAGTA
39960066 TTATGTAAG
1 TTATGTAAG
*
39960075 TTATGTAAT
1 TTATGTAAG
*
39960084 TTATGATATG
1 TTATG-TAAG
* * *
39960094 ATATAT-AT
1 TTATGTAAG
*
39960102 TTATGTAAA
1 TTATGTAAG
* *
39960111 TTATAT-AT
1 TTATGTAAG
*
39960119 TTATCTAAG
1 TTATGTAAG
*
39960128 TTATATAAG
1 TTATGTAAG
39960137 TTATGTAAG
1 TTATGTAAG
*
39960146 TTATGTAAA
1 TTATGTAAG
*
39960155 TTATGATATAAAA
1 TTATG---T-AAG
*
39960168 TATATTTAAG
1 T-TATGTAAG
39960178 TATTATGTAAG
1 --TTATGTAAG
39960189 TTATGTAAG
1 TTATGTAAG
* *
39960198 TTATAT-AT
1 TTATGTAAG
*
39960206 TTATCTAAG
1 TTATGTAAG
*
39960215 TTATATAAG
1 TTATGTAAG
*
39960224 TTATGTATG
1 TTATGTAAG
*
39960233 TTATATAAG
1 TTATGTAAG
39960242 TTATGTAAG
1 TTATGTAAG
* *
39960251 TTATATATG
1 TTATGTAAG
*
39960260 TTATATAAG
1 TTATGTAAG
*
39960269 TTATGTAAA
1 TTATGTAAG
39960278 TTATG
1 TTATG
39960283 ATATCAAATA
Statistics
Matches: 162, Mismatches: 35, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
8 16 0.10
9 122 0.75
10 7 0.04
11 8 0.05
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:39960145 original size:18 final size:18
Alignment explanation
Indices: 39960066--39960282 Score: 162
Period size: 18 Copynumber: 12.3 Consensus size: 18
39960056 TATTTAAGTA
* *
39960066 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
39960084 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
39960102 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
39960119 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
39960137 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
*
39960155 TTATG--A--TATA-AAA
1 TTATGTAAGTTATATAAG
* *
39960168 TATATTTAAGTATTATGTAAG
1 T-TATGTAAG--TTATATAAG
*
39960189 TTATGTAAGTTATAT-AT
1 TTATGTAAGTTATATAAG
*
39960206 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
*
39960224 TTATGTATGTTATATAAG
1 TTATGTAAGTTATATAAG
*
39960242 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
* * *
39960260 TTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
39960278 TTATG
1 TTATG
39960283 ATATCAAATA
Statistics
Matches: 158, Mismatches: 30, Indels: 22
0.75 0.14 0.10
Matches are distributed among these distances:
13 4 0.03
14 6 0.04
16 2 0.01
17 37 0.23
18 89 0.56
19 7 0.04
20 10 0.06
21 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:39960176 original size:114 final size:120
Alignment explanation
Indices: 39960042--39960313 Score: 351
Period size: 123 Copynumber: 2.3 Consensus size: 120
39960032 ACTAGTTATG
* *
39960042 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAA-TT-TATGA-TA-T-GATATAT-A
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATAT-ATTACTAGATATATAA
* * *
39960101 TTTATGTAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
65 GTTATGTAAATTATATAAGTTATCTAAGTTATATAAGTTATATAAGTTATGTAAAT
*
39960156 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATA-TTA-CT-AGATATAT
** * *
39960221 AAGTTATGTATGTTATATAAGTTATGTAAGTTATATATGTTATATAAGTTATGTAAAT
63 AAGTTATGTAAATTATATAAGTTATCTAAGTTATATAAGTTATATAAGTTATGTAAAT
* *
39960279 TATGATATCAAATATATTTATGTATTATGTAAGTT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTT
39960314 TTTTATTTCA
Statistics
Matches: 136, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
114 39 0.29
115 3 0.02
116 3 0.02
117 2 0.01
119 1 0.01
121 6 0.04
122 14 0.10
123 68 0.50
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (120 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTACTAGATATATAAG
TTATGTAAATTATATAAGTTATCTAAGTTATATAAGTTATATAAGTTATGTAAAT
Found at i:39960407 original size:15 final size:15
Alignment explanation
Indices: 39960387--39960442 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
39960377 AAGTAGCGGG
39960387 ATTAAATAATATTTA
1 ATTAAATAATATTTA
39960402 ATTAAATAATATTT-
1 ATTAAATAATATTTA
39960416 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
39960431 ATTAAATAATAT
1 ATTAAATAATAT
39960443 ACATGTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:39960647 original size:24 final size:24
Alignment explanation
Indices: 39960619--39960686 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
39960609 ACTTAAATGG
39960619 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
39960643 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
39960667 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
39960687 CAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:39961000 original size:21 final size:21
Alignment explanation
Indices: 39960975--39961016 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39960965 TAAAGAAATT
*
39960975 TAAAAA-TATTAAATATTAAAA
1 TAAAAATTATT-AATATAAAAA
39960996 TAAAAATTATTAATATAAAAA
1 TAAAAATTATTAATATAAAAA
39961017 AATAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATTATTAATATAAAAA
Found at i:39961094 original size:16 final size:16
Alignment explanation
Indices: 39961073--39961107 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
39961063 TTTTTATAAG
39961073 TAAATTGGAAATAAAT
1 TAAATTGGAAATAAAT
39961089 TAAATTGGAAATAAAT
1 TAAATTGGAAATAAAT
39961105 TAA
1 TAA
39961108 GGTTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (16 bp):
TAAATTGGAAATAAAT
Found at i:39961769 original size:370 final size:371
Alignment explanation
Indices: 39960774--39962069 Score: 2341
Period size: 370 Copynumber: 3.5 Consensus size: 371
39960764 AATTGAAACA
39960774 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
39960839 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
39960904 AATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
39960969 GAAATTTAAAAATATTAAATATTAAAATAAAA-ATTATTAATATAAAAAAATAGTAATTTGAATA
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATAT-AAAAAA-AGTAATTTGAATA
39961033 TAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAATTGGA
259 TAATAATATCAAAAAAGAATCGTAGTTTAA-TTTT-T-A-T-AA---G--------TAAATTGGA
39961098 AATAAATTAAGGTTATATAAATATTCAATAGTAAATGAGCTCGATAGAACT-TTTTCAAGTCTT
308 AATAAATTAAGGTTATATAAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
39961161 TTTGAATTTTTTAA-ATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
39961225 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
39961290 AATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
39961355 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAAGTAATTTGAATATA
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAAGTAATTTGAATATA
39961420 ATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATAT
261 ATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATAT
39961485 AAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
326 AAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
*
39961531 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTATACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
39961596 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTT-A
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
39961660 AATAAGGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
39961725 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAAGTAATTTGAATATA
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAAGTAATTTGAATATA
39961790 ATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATAT
261 ATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATAT
39961855 AAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
326 AAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
* *
39961901 TTTGAATATTTTAAGATTCATCATACGTGGCGTTGTTACGCCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
39961966 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
39962031 AATAAGGTTGGAGAGAAA-GTCAGCTATTGTTGTAATTTT
131 AATAAGGTTGGAGA-AAAGGTCAGCTATTGTTGTAATTTT
39962070 AATGGACAAG
Statistics
Matches: 899, Mismatches: 5, Indels: 26
0.97 0.01 0.03
Matches are distributed among these distances:
369 60 0.07
370 392 0.44
371 148 0.16
372 3 0.00
377 1 0.00
380 2 0.00
381 1 0.00
382 1 0.00
383 1 0.00
384 4 0.00
385 43 0.05
386 218 0.24
387 25 0.03
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (371 bp):
TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
AATAAGGTTGGAGAAAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAAGTAATTTGAATATA
ATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATAT
AAATATTCAATAGTAAATGAGCTCGATAGAACTGTTTTCAAGTCTT
Found at i:39963717 original size:635 final size:635
Alignment explanation
Indices: 39962507--39963780 Score: 2485
Period size: 635 Copynumber: 2.0 Consensus size: 635
39962497 GGTGCTCGAT
39962507 AGTACCTAGAACAGATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATA
1 AGTACCTAGAACAGATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATA
39962572 GAAACTTTACCTATATCAGTTTTGCAAGTGCCCACTTGTACCAGGATCAAAGACACTGCAAATGA
66 GAAACTTTACCTATATCAGTTTTGCAAGTGCCCACTTGTACCAGGATCAAAGACACTGCAAATGA
39962637 AGCTATACACCTTAGCAAAATATGGCAAAACTGCACAGTAAACACAGAAGTTGGATAGAAACATG
131 AGCTATACACCTTAGCAAAATATGGCAAAACTGCACAGTAAACACAGAAGTTGGATAGAAACATG
**
39962702 AAAACAGACCAAAAGAGTATCTAAAAAACAAAAATGGAATCACCATTAGTATGTAAACATGAAAA
196 AAAACAGACCAAAAGAACATCTAAAAAACAAAAATGGAATCACCATTAGTATGTAAACATGAAAA
39962767 TGCACAGCTTTAAACAAACCAACTTTGCATGTGCAGAATCATACTCCACAAAACTCATAAACATT
261 TGCACAGCTTTAAACAAACCAACTTTGCATGTGCAGAATCATACTCCACAAAACTCATAAACATT
39962832 AACTTCTCCTAACCAGAATACCAACTTTATGTTTACAGAGGCCTTGATCAAAACTAACATAACTG
326 AACTTCTCCTAACCAGAATACCAACTTTATGTTTACAGAGGCCTTGATCAAAACTAACATAACTG
*
39962897 TTGATTTATAACTTATCTAATAAGAATCATAGAATATGCAGAAAGTACCTGAGCATTTAATTTCA
391 TTGATTTATAACTTATCTAATAAGAATCACAGAATATGCAGAAAGTACCTGAGCATTTAATTTCA
39962962 AGAGAACCATGTATTCGAAGGAAAAGAGCCAGAAAATGATCAATGTATGCAAAACCTGGTCTATA
456 AGAGAACCATGTATTCGAAGGAAAAGAGCCAGAAAATGATCAATGTATGCAAAACCTGGTCTATA
39963027 TTTCAAAACTGGAGTAAAGCTTTCATCTAGTACCAAATACATACATATATAGAGACACAAACACA
521 TTTCAAAACTGGAGTAAAGCTTTCATCTAGTACCAAATACATACATATATAGAGACACAAACACA
*
39963092 CAGGCATACATCTTCCATTACCTAAATCTATTTCTTGCAAATAAAATATA
586 CAGGCATACATCTTCCATTACCTAAATCTATTTCTTGCAAATAAAAGATA
39963142 AGTACCTAGAACAGATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATA
1 AGTACCTAGAACAGATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATA
*
39963207 GAAACTTTACCTATATCAGTTTTGCAAGTGCCCACTTGTACCAGGATCAAAGACACTGCCAATGA
66 GAAACTTTACCTATATCAGTTTTGCAAGTGCCCACTTGTACCAGGATCAAAGACACTGCAAATGA
*
39963272 AGCTATACACCTTAGCAAAATATGGCAAAACTGCACAGTAAACACATAAGTTGGATAGAAACATG
131 AGCTATACACCTTAGCAAAATATGGCAAAACTGCACAGTAAACACAGAAGTTGGATAGAAACATG
39963337 AAAACAGACCAAAAGAACATCTAAAAAACAAAAATGGAATCACCATTAGTATGTAAACATGAAAA
196 AAAACAGACCAAAAGAACATCTAAAAAACAAAAATGGAATCACCATTAGTATGTAAACATGAAAA
39963402 TGCACAGCTTTAAACAAACCAACTTTGCATGTGCAGAATCATACTCCACAAAACTCATAAACATT
261 TGCACAGCTTTAAACAAACCAACTTTGCATGTGCAGAATCATACTCCACAAAACTCATAAACATT
39963467 AACTTCTCCTAACCAGAATACCAACTTTATGTTTACAGAGGCCTTGATCAAAACTAACATAACTG
326 AACTTCTCCTAACCAGAATACCAACTTTATGTTTACAGAGGCCTTGATCAAAACTAACATAACTG
39963532 TTGATTTATAACTTATCTAATAAGAATCACAGAATATGCAGAAAGTACCTGAGCATTTAATTTCA
391 TTGATTTATAACTTATCTAATAAGAATCACAGAATATGCAGAAAGTACCTGAGCATTTAATTTCA
39963597 AGAGAACCATGTATTCGAAGGAAAAGAGCCAGAAAATGATCAATGTATGCAAAACCTGGTCTATA
456 AGAGAACCATGTATTCGAAGGAAAAGAGCCAGAAAATGATCAATGTATGCAAAACCTGGTCTATA
*
39963662 TTTCAAAATTGGAGTAAAGCTTTCATCTAGTACCAAATACATACATATATAGAGACACAAACACA
521 TTTCAAAACTGGAGTAAAGCTTTCATCTAGTACCAAATACATACATATATAGAGACACAAACACA
39963727 CAGGCATACATCTTCCATTACCTAAATCTATTTCTTGCAAATAAAAGATA
586 CAGGCATACATCTTCCATTACCTAAATCTATTTCTTGCAAATAAAAGATA
39963777 AGTA
1 AGTA
39963781 AGCTTCTACA
Statistics
Matches: 632, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
635 632 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (635 bp):
AGTACCTAGAACAGATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATA
GAAACTTTACCTATATCAGTTTTGCAAGTGCCCACTTGTACCAGGATCAAAGACACTGCAAATGA
AGCTATACACCTTAGCAAAATATGGCAAAACTGCACAGTAAACACAGAAGTTGGATAGAAACATG
AAAACAGACCAAAAGAACATCTAAAAAACAAAAATGGAATCACCATTAGTATGTAAACATGAAAA
TGCACAGCTTTAAACAAACCAACTTTGCATGTGCAGAATCATACTCCACAAAACTCATAAACATT
AACTTCTCCTAACCAGAATACCAACTTTATGTTTACAGAGGCCTTGATCAAAACTAACATAACTG
TTGATTTATAACTTATCTAATAAGAATCACAGAATATGCAGAAAGTACCTGAGCATTTAATTTCA
AGAGAACCATGTATTCGAAGGAAAAGAGCCAGAAAATGATCAATGTATGCAAAACCTGGTCTATA
TTTCAAAACTGGAGTAAAGCTTTCATCTAGTACCAAATACATACATATATAGAGACACAAACACA
CAGGCATACATCTTCCATTACCTAAATCTATTTCTTGCAAATAAAAGATA
Found at i:39965997 original size:13 final size:15
Alignment explanation
Indices: 39965959--39965993 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39965949 AAATAATAAT
*
39965959 TTATATATATTTATC
1 TTATATACATTTATC
39965974 TTATATACATTTATC
1 TTATATACATTTATC
39965989 TTATA
1 TTATA
39965994 CATTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:39966433 original size:18 final size:18
Alignment explanation
Indices: 39966410--39966459 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
39966400 TTACACCCTA
39966410 AATATATATTATAA-TCTT
1 AATATATATTATAAGT-TT
*
39966428 AATATATATTAGAAGTTT
1 AATATATATTATAAGTTT
39966446 AATATATATATATA
1 AATATATAT-TATA
39966460 TAACAAGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
AATATATATTATAAGTTT
Found at i:39966799 original size:41 final size:41
Alignment explanation
Indices: 39966754--39967025 Score: 377
Period size: 41 Copynumber: 6.6 Consensus size: 41
39966744 TTACATTTTT
** * * *
39966754 GCGGCGTTTTTGGAAAAACGCCGCTAAAACAT-TGGCCTATA
1 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCT-ACCTATA
* * * **
39966795 GCGGCATTTTTCCAAAAGCGCCGCTAAAACATCGGCCTATA
1 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
39966836 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
1 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
* *
39966877 GCGGCGTTTTTACAGAAGCGCCTCTAAAACCTCTACCTATA
1 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
*
39966918 CCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
1 GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
*
39966959 GCAGCGTTTTT-CAAGAAGCGCCGCTAAAACCTCTACCTATA
1 GCGGCGTTTTTACAA-AAGCGCCGCTAAAACCTCTACCTATA
*
39967000 GCGGCGTTTTTCCAAAAGCGCCGCTA
1 GCGGCGTTTTTACAAAAGCGCCGCTA
39967026 TTGTTCTGTT
Statistics
Matches: 210, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
40 3 0.01
41 204 0.97
42 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (41 bp):
GCGGCGTTTTTACAAAAGCGCCGCTAAAACCTCTACCTATA
Found at i:39967057 original size:41 final size:40
Alignment explanation
Indices: 39966998--39967090 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
39966988 CCTCTACCTA
* *
39966998 TAGCGGCGTTTTTCCAAAAGCGCCGCTATTGTTCTGTTTT
1 TAGCGGCGTTTTTCCAAAAACGCCGCTATTGCTCTGTTTT
**
39967038 TAGCGGCGTTTTGAT-CAAAAACGTTGCTATTGCTCTGTTTT
1 TAGCGGCGTTTT--TCCAAAAACGCCGCTATTGCTCTGTTTT
* *
39967079 TTGCGGCATTTT
1 TAGCGGCGTTTT
39967091 ATTGAAAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 12 0.27
41 32 0.71
42 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (40 bp):
TAGCGGCGTTTTTCCAAAAACGCCGCTATTGCTCTGTTTT
Found at i:39968717 original size:18 final size:18
Alignment explanation
Indices: 39968694--39968729 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39968684 CTACTAATCC
39968694 GATACTTTTTCTTTTCCT
1 GATACTTTTTCTTTTCCT
39968712 GATACTTTTTCTTTTCCT
1 GATACTTTTTCTTTTCCT
39968730 CGATCTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.06, T:0.61
Consensus pattern (18 bp):
GATACTTTTTCTTTTCCT
Found at i:39975849 original size:27 final size:26
Alignment explanation
Indices: 39975801--39975860 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
39975791 GCGAGGCTGC
*
39975801 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
39975828 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
39975854 CAGATAT
1 CAGATAT
39975861 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:39975864 original size:2 final size:2
Alignment explanation
Indices: 39975857--39975890 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39975847 ACCAGAACAG
39975857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39975891 GTGTGTGTGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39975985 original size:27 final size:26
Alignment explanation
Indices: 39975937--39975988 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39975927 GCGAGGCTGC
*
39975937 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
39975963 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
39975989 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:39978021 original size:23 final size:22
Alignment explanation
Indices: 39977993--39978039 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
39977983 AATTATAAAT
*
39977993 TTATAATTGTAAACATCTA-TCAA
1 TTATAATT-CAAA-ATCTAGTCAA
39978016 TTATAATTCAAAATCTAGTCAA
1 TTATAATTCAAAATCTAGTCAA
39978038 TT
1 TT
39978040 TTATGAGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
TTATAATTCAAAATCTAGTCAA
Found at i:39982694 original size:27 final size:27
Alignment explanation
Indices: 39982650--39982712 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
39982640 ATATGCCATG
*
39982650 AAGGCGTTCCTTTCCATAGATCACCACA
1 AAGGC-TTCCTTTCCATAGATCACCAAA
**
39982678 AAGGCTTCCATTT-CATAGATTGCCAAA
1 AAGGCTTCC-TTTCCATAGATCACCAAA
39982705 AAGGCTTC
1 AAGGCTTC
39982713 GATTGCACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (27 bp):
AAGGCTTCCTTTCCATAGATCACCAAA
Found at i:39983290 original size:15 final size:16
Alignment explanation
Indices: 39983270--39983306 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
39983260 AATTGGAAAG
39983270 ATGAAAAGTT-ATTAA
1 ATGAAAAGTTAATTAA
*
39983285 ATG-AAATTTAATTAA
1 ATGAAAAGTTAATTAA
39983300 ATGAAAA
1 ATGAAAA
39983307 ATAAAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 11 0.58
16 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (16 bp):
ATGAAAAGTTAATTAA
Found at i:39990924 original size:48 final size:47
Alignment explanation
Indices: 39990768--39990943 Score: 156
Period size: 48 Copynumber: 3.6 Consensus size: 47
39990758 ATGCCATATC
* * * * * *
39990768 CCAGACATGGTCTTACACT-GACTATTGAAATCGAGGCCGACACCATGT
1 CCAGACATGGTCTTACACTAG-CT-CTCATATCAATGCCGATACCATGT
*** *
39990816 CCCAGACATGGTCTTACACTAGCTCTCACATATTTGTGCCGATGCCATGTT
1 -CCAGACATGGTCTTACACTAGCTCT--CATATCAATGCCGATACCATG-T
* * *
39990867 CCAGGCATGGTCTTACACTAGCTCTCGTCTCAATGCCGATACCATGT
1 CCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATACCATGT
*
39990914 CCTAGACATGGTCTTACACTGGCTCTCATA
1 CC-AGACATGGTCTTACACTAGCTCTCATA
39990944 GACATGTCTT
Statistics
Matches: 102, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
47 3 0.03
48 39 0.38
49 21 0.21
50 38 0.37
51 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (47 bp):
CCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATACCATGT
Found at i:39992396 original size:21 final size:21
Alignment explanation
Indices: 39992370--39992410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39992360 TGACCTATAG
39992370 CACGGGCGTT-TCCCAGGGTCA
1 CACGGGC-TTATCCCAGGGTCA
*
39992391 CACGGGCTTATCCCATGGTC
1 CACGGGCTTATCCCAGGGTC
39992411 CATATGGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.22
Consensus pattern (21 bp):
CACGGGCTTATCCCAGGGTCA
Found at i:40003536 original size:18 final size:17
Alignment explanation
Indices: 40003509--40003543 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40003499 TCTGGTGTTG
40003509 AATAGCAAGGGCGATGA
1 AATAGCAAGGGCGATGA
*
40003526 AATAGGCAAGGTCGATGA
1 AATA-GCAAGGGCGATGA
40003544 CGTGCCCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.11, G:0.34, T:0.14
Consensus pattern (17 bp):
AATAGCAAGGGCGATGA
Found at i:40010210 original size:2 final size:2
Alignment explanation
Indices: 40010203--40010251 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
40010193 ATAAGATAAA
40010203 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
40010245 TC TC TC T
1 TC TC TC T
40010252 TCTGAAGCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40029653 original size:16 final size:16
Alignment explanation
Indices: 40029632--40029673 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
40029622 TTTAATCACT
40029632 TTATTTTAAGTTCAAA
1 TTATTTTAAGTTCAAA
**
40029648 TTATTTTTAA-TTTGAA
1 TTA-TTTTAAGTTCAAA
40029664 TTATTTTAAG
1 TTATTTTAAG
40029674 ATCGTATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (16 bp):
TTATTTTAAGTTCAAA
Found at i:40030098 original size:20 final size:20
Alignment explanation
Indices: 40030073--40030120 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
40030063 ATACCAATTG
*
40030073 AATTAACAACTTTATAAAAT
1 AATTAAAAACTTTATAAAAT
40030093 AATTAAAAACTTTATAAAAT
1 AATTAAAAACTTTATAAAAT
40030113 AATATAAA
1 AAT-TAAA
40030121 TATAGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTAAAAACTTTATAAAAT
Found at i:40030553 original size:2 final size:2
Alignment explanation
Indices: 40030546--40030578 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40030536 CCACCACACT
40030546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40030579 GCATGTGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40032547 original size:29 final size:29
Alignment explanation
Indices: 40032515--40032572 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
40032505 AAAAAATGTG
* * * *
40032515 TGTGTTAGGTCGTGTGGGTCACACGAGCT
1 TGTGTTAGGCCATGTAGGCCACACGAGCT
40032544 TGTGTTAGGCCATGTAGGCCACACGAGCT
1 TGTGTTAGGCCATGTAGGCCACACGAGCT
40032573 GGGCTAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (29 bp):
TGTGTTAGGCCATGTAGGCCACACGAGCT
Found at i:40035881 original size:35 final size:36
Alignment explanation
Indices: 40035842--40035913 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
40035832 TCTGCTCTGT
*
40035842 TCTATTATGCAT-TGTTCTGTTTTGTTATG-TTTTGC
1 TCTATTATG-ATCTGTTCTGTTCTGTTATGCTTTTGC
* *
40035877 TCTATTCTGTTCTGTTCTGTTCTGTTATGCTTTTGC
1 TCTATTATGATCTGTTCTGTTCTGTTATGCTTTTGC
40035913 T
1 T
40035914 TTGTTCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 1 0.03
35 24 0.75
36 7 0.22
ACGTcount: A:0.08, C:0.15, G:0.17, T:0.60
Consensus pattern (36 bp):
TCTATTATGATCTGTTCTGTTCTGTTATGCTTTTGC
Found at i:40035889 original size:5 final size:5
Alignment explanation
Indices: 40035854--40036136 Score: 59
Period size: 5 Copynumber: 56.4 Consensus size: 5
40035844 TATTATGCAT
* * * * * *
40035854 TGTTC TGTTT TGTTA TGTTT TGCTC TATTC TGTTC TGTTC TGTTC TGTTA
1 TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC
* * * ** ** * *
40035904 TGCTTT TGCTT- TGTTC TATTA TGTTC CATTC TGCAC TGCTC TGTTC TGTTT
1 TG-TTC TG-TTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC
* ** * * * * * *
40035955 TGTTA TGTTC TACTC TATTA TGTTC TACTT- TGCTC TGTTC TGTTA TGTTT
1 TGTTC TGTTC TGTTC TGTTC TGTTC T-GTTC TGTTC TGTTC TGTTC TGTTC
* * * * * * * * * * *
40036005 TGCTC TATTC TATTC T-TCTC TATTC TATTT TGCTA TGTTA TGTTA TGTTT
1 TGTTC TGTTC TGTTC TGT-TC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC
* * * * * * * * * ** *
40036055 TGATC TATTC TATTC TGCTC TGCTC TGTTT TGTTA TGCTC TGCTC TACTA
1 TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC
* * *
40036105 TGTTC TGTTA TGTTC TGCTC TGTCC TGTTC TG
1 TGTTC TGTTC TGTTC TGTTC TGTTC TGTTC TG
40036137 GTTGGGTTGT
Statistics
Matches: 203, Mismatches: 69, Indels: 12
0.71 0.24 0.04
Matches are distributed among these distances:
4 4 0.02
5 189 0.93
6 10 0.05
ACGTcount: A:0.10, C:0.19, G:0.15, T:0.57
Consensus pattern (5 bp):
TGTTC
Found at i:40036016 original size:50 final size:49
Alignment explanation
Indices: 40035918--40036066 Score: 138
Period size: 50 Copynumber: 3.0 Consensus size: 49
40035908 TTTGCTTTGT
* * * * * * *
40035918 TCTATTATGTTCCATTCTGCACTGCTCTGTTCTGTTTTGTTATGTTCTAC
1 TCTATTATGTTCTATT-TGCTCTGTTCTGTTATGTTTTGATCTATTCTAC
* *
40035968 TCTATTATGTTCTACTTTGCTCTGTTCTGTTATGTTTTGCTCTATTCTAT
1 TCTATTATGTTCTA-TTTGCTCTGTTCTGTTATGTTTTGATCTATTCTAC
* * * *
40036018 TCT-TCTCTATTCTATTTTGCTATGTTATGTTATGTTTTGATCTATTCTA
1 TCTAT-TATGTTCTA-TTTGCTCTGTTCTGTTATGTTTTGATCTATTCTA
40036067 TTCTGCTCTG
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 80 0.96
51 2 0.02
ACGTcount: A:0.13, C:0.18, G:0.12, T:0.56
Consensus pattern (49 bp):
TCTATTATGTTCTATTTGCTCTGTTCTGTTATGTTTTGATCTATTCTAC
Found at i:40036067 original size:50 final size:50
Alignment explanation
Indices: 40035977--40036075 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
40035967 CTCTATTATG
* * * *
40035977 TTCTACTTTGCTCTGTTCTGTTATGTTTTGCTCTATTCTATTCTTCTCTA
1 TTCTACTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCTA
*
40036027 TTCTATTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCT
1 TTCTACTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCT
40036076 GCTCTGTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.12, C:0.18, G:0.11, T:0.59
Consensus pattern (50 bp):
TTCTACTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCTA
Found at i:40036086 original size:50 final size:50
Alignment explanation
Indices: 40035978--40036091 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
40035968 TCTATTATGT
* * * * * *
40035978 TCTACTTTGCTCTGTTCTGTTATGTTTTGCTCTATTCTATTCTTCTCTAT
1 TCTATTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCTAC
*
40036028 TCTATTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCTGC
1 TCTATTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCTAC
* *
40036078 TCTGTTTTGTTATG
1 TCTATTTTGCTATG
40036092 CTCTGCTCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.11, C:0.18, G:0.13, T:0.58
Consensus pattern (50 bp):
TCTATTTTGCTATGTTATGTTATGTTTTGATCTATTCTATTCTGCTCTAC
Found at i:40036133 original size:25 final size:25
Alignment explanation
Indices: 40036067--40036136 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
40036057 ATCTATTCTA
*
40036067 TTCTGCTCTGCTCTGTTTTGTTATG
1 TTCTGCTCTGCTCTGTTCTGTTATG
* * *
40036092 CTCTGCTCTACTATGTTCTGTTATG
1 TTCTGCTCTGCTCTGTTCTGTTATG
40036117 TTCTGCTCTG-TCCTGTTCTG
1 TTCTGCTCTGCT-CTGTTCTG
40036137 GTTGGGTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.06, C:0.24, G:0.19, T:0.51
Consensus pattern (25 bp):
TTCTGCTCTGCTCTGTTCTGTTATG
Found at i:40037573 original size:10 final size:10
Alignment explanation
Indices: 40037525--40037581 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
40037515 ATTTCACCCA
*
40037525 AATTTTAATT
1 AATTTTGATT
40037535 AATTTT-ATAT
1 AATTTTGAT-T
*
40037545 CAAATTTTTATT
1 --AATTTTGATT
40037557 AATTTTGATT
1 AATTTTGATT
40037567 AATTTTGATT
1 AATTTTGATT
*
40037577 GATTT
1 AATTT
40037582 GCAAAAGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 2 0.05
10 30 0.73
12 7 0.17
13 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (10 bp):
AATTTTGATT
Found at i:40047703 original size:30 final size:29
Alignment explanation
Indices: 40047662--40047721 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
40047652 AATTCATCCA
*
40047662 TGGAAAATAAAATAAAGAAAATGATGA-AAT
1 TGGAAAATAAAA-AAACAAAA-GATGATAAT
*
40047692 TGGAAAGTAAAAAAACAAAAGATGATAAT
1 TGGAAAATAAAAAAACAAAAGATGATAAT
40047721 T
1 T
40047722 AATTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.20
Consensus pattern (29 bp):
TGGAAAATAAAAAAACAAAAGATGATAAT
Found at i:40048869 original size:22 final size:23
Alignment explanation
Indices: 40048828--40048871 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40048818 CCTGTTACAT
40048828 GGCTCTTGATGAGCTTCCCGATA
1 GGCTCTTGATGAGCTTCCCGATA
40048851 GGCTCTTCG-TGA-CTTCCCGAT
1 GGCTCTT-GATGAGCTTCCCGAT
40048872 TAAAGTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 10 0.50
24 1 0.05
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCTCTTGATGAGCTTCCCGATA
Found at i:40048906 original size:25 final size:25
Alignment explanation
Indices: 40048826--40048922 Score: 71
Period size: 24 Copynumber: 4.1 Consensus size: 25
40048816 TTCCTGTTAC
*
40048826 ATGGCTC-TTGATGAGCTTCCCGA-T
1 ATGGCTCTTTG-TGAACTTCCCGATT
*
40048850 A-GGCTCTTCGTG-ACTTCCCGATT
1 ATGGCTCTTTGTGAACTTCCCGATT
** * *
40048873 AAAGTTCTTTGTGAACTTCCTGATT
1 ATGGCTCTTTGTGAACTTCCCGATT
* *
40048898 ATGGCTC-TTATGAGCTTCCCG-TT
1 ATGGCTCTTTGTGAACTTCCCGATT
40048921 AT
1 AT
40048923 ATAGCCCGGA
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
22 8 0.14
23 13 0.23
24 22 0.39
25 14 0.25
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
ATGGCTCTTTGTGAACTTCCCGATT
Found at i:40062894 original size:44 final size:44
Alignment explanation
Indices: 40062709--40062935 Score: 179
Period size: 44 Copynumber: 4.9 Consensus size: 44
40062699 GCGATGTGTG
* * * * *
40062709 TGTGCTAGTGTAAGACATGTCTTGGAAATTCATCGGCCA-CAATA
1 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CATCGAGA
* * *
40062753 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
1 T--GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGA
* * * *
40062801 CGAAAGCTAGTGTAAGACATGTCTGGGACATGTATCAGC-TACGAGA
1 TG--TGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGA
* *
40062847 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATGGATA
1 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGA
*
40062891 TGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 TGT----GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAT
40062936 TATACCCTAT
Statistics
Matches: 148, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
44 39 0.26
45 2 0.01
46 24 0.16
47 28 0.19
48 31 0.21
49 14 0.09
50 10 0.07
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (44 bp):
TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGA
Found at i:40065994 original size:46 final size:46
Alignment explanation
Indices: 40065941--40066116 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40065931 TATTTGGGCA
40065941 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
40065987 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
40066034 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
40066080 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40066117 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:40066096 original size:93 final size:93
Alignment explanation
Indices: 40065937--40066108 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40065927 GGGATATTTG
* *
40065937 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40066002 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
40066030 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40066095 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
40066109 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:40069083 original size:15 final size:15
Alignment explanation
Indices: 40069063--40069131 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
40069053 GTATCTTGGG
40069063 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
40069078 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
40069093 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
40069108 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
40069123 TTTCTTTAT
1 TTTCTTTAT
40069132 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:40069132 original size:30 final size:30
Alignment explanation
Indices: 40069054--40069141 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
40069044 CATAGTATCG
* * * *
40069054 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
40069084 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
40069114 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
40069142 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:40071569 original size:46 final size:46
Alignment explanation
Indices: 40071519--40071694 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40071509 TATTTGGGCA
40071519 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
40071565 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
40071612 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
40071658 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40071695 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:40071674 original size:93 final size:93
Alignment explanation
Indices: 40071515--40071686 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40071505 TGGATATTTG
* *
40071515 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40071580 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
40071608 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40071673 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
40071687 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:40086296 original size:21 final size:21
Alignment explanation
Indices: 40086272--40086316 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
40086262 AAAAAAATTT
40086272 GCACTTAGCAAAACAGAATAG
1 GCACTTAGCAAAACAGAATAG
*
40086293 GCACTTAGCAAAACAGAATGG
1 GCACTTAGCAAAACAGAATAG
40086314 GCA
1 GCA
40086317 TTTGGTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (21 bp):
GCACTTAGCAAAACAGAATAG
Found at i:40086374 original size:19 final size:20
Alignment explanation
Indices: 40086337--40086381 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40086327 ACACTGATAC
40086337 AAAAATATAGATACTTTAT-
1 AAAAATATAGATACTTTATG
*
40086356 AAAAAGTATTGATAC-TTATG
1 AAAAA-TATAGATACTTTATG
40086376 AAAAAT
1 AAAAAT
40086382 TGTCGATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (20 bp):
AAAAATATAGATACTTTATG
Found at i:40088934 original size:134 final size:134
Alignment explanation
Indices: 40088695--40088954 Score: 297
Period size: 134 Copynumber: 1.9 Consensus size: 134
40088685 ATATTCACAA
* * * * ** *
40088695 ATTTATTGATACCTTTTTTGATATCGATACAAAAATGGCATTCTATTTTTTAAAATATTTACCAA
1 ATTTATCGATACCTTCTTTAATATCGATACAAAAATGGCATTCTATCTTCCAAAAGATTTACCAA
* * ** *
40088760 GTATCAATATGGTATCGATACGTTTTGCTTGGTATTGATAAAATTATTTAAGTATCGATAGACGT
66 GTATCAATATAGTATCGATACCTTTTGCTTGAAATCGATAAAATTATTTAAGTATCGATAGACGT
40088825 ACAC
131 ACAC
* * * **
40088829 ATTTATCGATACCTTCTTTAATATCGATACCAAATTGGCATTCTGA-CTTCCAAAGGATTTATTA
1 ATTTATCGATACCTTCTTTAATATCGATACAAAAATGGCATTCT-ATCTTCCAAAAGATTTACCA
* * * * **
40088893 AGTATCGATATAGTATCGATACCTTTTGTTTGAAATCGATAAATTTCTTTTGGTATCGATAG
65 AGTATCAATATAGTATCGATACCTTTTGCTTGAAATCGATAAAATTATTTAAGTATCGATAG
40088955 TTTTAGTTCC
Statistics
Matches: 102, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
134 101 0.99
135 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (134 bp):
ATTTATCGATACCTTCTTTAATATCGATACAAAAATGGCATTCTATCTTCCAAAAGATTTACCAA
GTATCAATATAGTATCGATACCTTTTGCTTGAAATCGATAAAATTATTTAAGTATCGATAGACGT
ACAC
Found at i:40089486 original size:120 final size:120
Alignment explanation
Indices: 40089273--40089512 Score: 480
Period size: 120 Copynumber: 2.0 Consensus size: 120
40089263 TCAAGTGTTC
40089273 TTCTTTGTAATTGTGTTTAATTGGTAAACACTTTGATCTGGTAAGGGTTATTTCTTTGTTTGCTT
1 TTCTTTGTAATTGTGTTTAATTGGTAAACACTTTGATCTGGTAAGGGTTATTTCTTTGTTTGCTT
40089338 ATTTATTTCTTTTTGAGAGGGTTTGAGTATTAAGATTTGTGTAGAAATCTAAAGG
66 ATTTATTTCTTTTTGAGAGGGTTTGAGTATTAAGATTTGTGTAGAAATCTAAAGG
40089393 TTCTTTGTAATTGTGTTTAATTGGTAAACACTTTGATCTGGTAAGGGTTATTTCTTTGTTTGCTT
1 TTCTTTGTAATTGTGTTTAATTGGTAAACACTTTGATCTGGTAAGGGTTATTTCTTTGTTTGCTT
40089458 ATTTATTTCTTTTTGAGAGGGTTTGAGTATTAAGATTTGTGTAGAAATCTAAAGG
66 ATTTATTTCTTTTTGAGAGGGTTTGAGTATTAAGATTTGTGTAGAAATCTAAAGG
40089513 AAGTTGTAAG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.48
Consensus pattern (120 bp):
TTCTTTGTAATTGTGTTTAATTGGTAAACACTTTGATCTGGTAAGGGTTATTTCTTTGTTTGCTT
ATTTATTTCTTTTTGAGAGGGTTTGAGTATTAAGATTTGTGTAGAAATCTAAAGG
Found at i:40089684 original size:13 final size:12
Alignment explanation
Indices: 40089645--40089697 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
40089635 AGTTTGGCAA
40089645 TGCTTTTGAAAAG
1 TGCTTTT-AAAAG
**
40089658 TGCTGTGAAAAAG
1 TGCT-TTTAAAAG
40089671 TGCTTTTAAGAAG
1 TGCTTTTAA-AAG
40089684 TGCTTTTGAAAAG
1 TGCTTTT-AAAAG
40089697 T
1 T
40089698 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.09
13 27 0.82
14 3 0.09
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
TGCTTTTAAAAG
Found at i:40090497 original size:20 final size:20
Alignment explanation
Indices: 40090474--40090513 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40090464 TTTTCTATCA
40090474 TTTCTAAATTTTT-ATAATAT
1 TTTC-AAATTTTTCATAATAT
*
40090494 TTTCATATTTTTCATAATAT
1 TTTCAAATTTTTCATAATAT
40090514 ACTAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCAAATTTTTCATAATAT
Found at i:40090584 original size:18 final size:19
Alignment explanation
Indices: 40090553--40090602 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
40090543 TTTAATAGTA
* *
40090553 TTTTATAATTTTTC-CATGT
1 TTTTATAATATTTCAAAT-T
40090572 TTTTAT-ATATTTCAAATT
1 TTTTATAATATTTCAAATT
40090590 TTTTATAATATTT
1 TTTTATAATATTT
40090603 TTATATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATATTTCAAATT
Found at i:40090611 original size:19 final size:19
Alignment explanation
Indices: 40090589--40090653 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
40090579 TATTTCAAAT
*
40090589 TTTTTATAATATTTTTA-TA
1 TTTTCATAA-ATTTTTATTA
*
40090608 TTTTCATTAATTTTTATTA
1 TTTTCATAAATTTTTATTA
* * *
40090627 TTTTCCT-AAGTTTTATAA
1 TTTTCATAAATTTTTATTA
40090645 TTTT-ATAAA
1 TTTTCATAAA
40090654 CTTGTTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 1 0.03
18 22 0.58
19 15 0.39
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTCATAAATTTTTATTA
Found at i:40091353 original size:10 final size:10
Alignment explanation
Indices: 40091338--40091420 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
40091328 AAATTATGAA
40091338 AAAAATATAT
1 AAAAATATAT
*
40091348 AAAAATGT-T
1 AAAAATATAT
** *
40091357 AAAGTTATGAA
1 AAAAATAT-AT
*
40091368 AAATAATATTT
1 AAA-AATATAT
40091379 AAAAATATA-
1 AAAAATATAT
40091388 AAAAATAT-T
1 AAAAATATAT
40091397 ACAAAATCATA-
1 A-AAAAT-ATAT
40091408 AAAAAT-TAT
1 AAAAATATAT
40091417 AAAA
1 AAAA
40091421 CAAATTTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 17
0.67 0.12 0.21
Matches are distributed among these distances:
8 2 0.04
9 19 0.35
10 22 0.40
11 9 0.16
12 3 0.05
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAATATAT
Found at i:40091367 original size:30 final size:30
Alignment explanation
Indices: 40091327--40091384 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
40091317 TTAAATTATA
40091327 TAAATTATGAAAAA-AATATATAAAAATGT
1 TAAATTATGAAAAATAATATATAAAAATGT
*
40091356 TAAAGTTATGAAAAATAATATTTAAAAAT
1 TAAA-TTATGAAAAATAATATATAAAAAT
40091385 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 10 0.38
31 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTATGAAAAATAATATATAAAAATGT
Found at i:40091396 original size:19 final size:20
Alignment explanation
Indices: 40091367--40091413 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
40091357 AAAGTTATGA
40091367 AAAATAATATTTA-AAAAT-AT
1 AAAA-AATA-TTACAAAATCAT
40091387 AAAAAATATTACAAAATCAT
1 AAAAAATATTACAAAATCAT
40091407 AAAAAAT
1 AAAAAAT
40091414 TATAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.12
19 9 0.36
20 13 0.52
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAATATTACAAAATCAT
Found at i:40092097 original size:19 final size:20
Alignment explanation
Indices: 40092063--40092104 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
40092053 TTTTTCAATT
*
40092063 TTTATAATATATTTTTGTAA
1 TTTATAATATATTTTTATAA
40092083 TTTATAATA-ATTTTTATAA
1 TTTATAATATATTTTTATAA
40092102 TTT
1 TTT
40092105 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATAATATATTTTTATAA
Found at i:40092156 original size:27 final size:26
Alignment explanation
Indices: 40092126--40092187 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
40092116 CACTTTCATA
* * **
40092126 TATATTTTTTCATTTTTTACTATTCTT
1 TATATTTTTT-AGTATTTACTATAATT
*
40092153 TATAATTTTTAGTATTTACTATAATT
1 TATATTTTTTAGTATTTACTATAATT
40092179 T-TATTTTTT
1 TATATTTTTT
40092188 TAAGTTAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 7 0.24
26 13 0.45
27 9 0.31
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (26 bp):
TATATTTTTTAGTATTTACTATAATT
Found at i:40097492 original size:24 final size:26
Alignment explanation
Indices: 40097447--40097494 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40097437 TATAAAAAAA
40097447 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAATATAATAAATCAAATATAT
*
40097473 TTAAAAATATTA-AAAT-AAATAT
1 TTAAAAATATAATAAATCAAATAT
40097495 TAAAACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAAAAATATAATAAATCAAATATAT
Found at i:40098931 original size:523 final size:523
Alignment explanation
Indices: 40097947--40098991 Score: 2072
Period size: 523 Copynumber: 2.0 Consensus size: 523
40097937 AATTGAAATT
*
40097947 TAACTTAATCAAAAATAACAAAAATTAAATTTTCGTCTTACCATAACTACTTGAGTGGTGAAAAT
1 TAACTTAATCAAAAATAACAAAAATTAAATTTTCGTCTTACCATAACTACTTGAGTGGCGAAAAT
40098012 GTGATTGTCATCGAAACGGATTAGAGATGTTGTCATTTGTGAAAACTTAATCTGAACGAATAAAA
66 GTGATTGTCATCGAAACGGATTAGAGATGTTGTCATTTGTGAAAACTTAATCTGAACGAATAAAA
40098077 TACAGAATAATTAAAAAAAGCTAATATTTTTAAACGAGAATGTAAAAAAAATTAGAACAAGAACT
131 TACAGAATAATTAAAAAAAGCTAATATTTTTAAACGAGAATGTAAAAAAAATTAGAACAAGAACT
40098142 TGAGAAAATTGAGAAAGTTGAGAGAGTTAGTGTAACAGCTCATTTTCAGTGAAATCAGAATAGTA
196 TGAGAAAATTGAGAAAGTTGAGAGAGTTAGTGTAACAGCTCATTTTCAGTGAAATCAGAATAGTA
40098207 GTTTCGGGACTACAAATCCGACCCAAAAATATAATTTATTTTTATTTCATTATATGGTTCGTATT
261 GTTTCGGGACTACAAATCCGACCCAAAAATATAATTTATTTTTATTTCATTATATGGTTCGTATT
40098272 ATAATATGCATGTCATTTGAAAATTTTGAAACGAAAATTTTATCGATTAAGTGCTTAATTACTAG
326 ATAATATGCATGTCATTTGAAAATTTTGAAACGAAAATTTTATCGATTAAGTGCTTAATTACTAG
40098337 AATGACTAAATCGTATAAAATGTGAAAGTTGAATTCTAGTAGCTATAAGGATCAAATAGCTATGG
391 AATGACTAAATCGTATAAAATGTGAAAGTTGAATTCTAGTAGCTATAAGGATCAAATAGCTATGG
*
40098402 AATTCAAAACTTAAGGCTCTTATATGGTAATTAGACCATTAAGAAAAGTATGTAGATTTTTGTTG
456 AATTCAAAACTTAAGGCTCTTATATGGTAATTAGACCATTAAGAAAAGTATGTAGATTTTTCTTG
40098467 ATC
521 ATC
40098470 TAACTTAATCAAAAATAACAAAAATTAAATTTTCGTCTTACCATAACTACTTGAGTGGCGAAAAT
1 TAACTTAATCAAAAATAACAAAAATTAAATTTTCGTCTTACCATAACTACTTGAGTGGCGAAAAT
40098535 GTGATTGTCATCGAAACGGATTAGAGATGTTGTCATTTGTGAAAACTTAATCTGAACGAATAAAA
66 GTGATTGTCATCGAAACGGATTAGAGATGTTGTCATTTGTGAAAACTTAATCTGAACGAATAAAA
40098600 TACAGAATAATTAAAAAAAGCTAATATTTTTAAACGAGAATGTAAAAAAAATTAGAACAAGAACT
131 TACAGAATAATTAAAAAAAGCTAATATTTTTAAACGAGAATGTAAAAAAAATTAGAACAAGAACT
40098665 TGAGAAAATTGAGAAAGTTGAGAGAGTTAGTGTAACAGCTCATTTTCAGTGAAATCAGAATAGTA
196 TGAGAAAATTGAGAAAGTTGAGAGAGTTAGTGTAACAGCTCATTTTCAGTGAAATCAGAATAGTA
40098730 GTTTCGGGACTACAAATCCGACCCAAAAATATAATTTATTTTTATTTCATTATATGGTTCGTATT
261 GTTTCGGGACTACAAATCCGACCCAAAAATATAATTTATTTTTATTTCATTATATGGTTCGTATT
40098795 ATAATATGCATGTCATTTGAAAATTTTGAAACGAAAATTTTATCGATTAAGTGCTTAATTACTAG
326 ATAATATGCATGTCATTTGAAAATTTTGAAACGAAAATTTTATCGATTAAGTGCTTAATTACTAG
40098860 AATGACTAAATCGTATAAAATGTGAAAGTTGAATTCTAGTAGCTATAAGGATCAAATAGCTATGG
391 AATGACTAAATCGTATAAAATGTGAAAGTTGAATTCTAGTAGCTATAAGGATCAAATAGCTATGG
40098925 AATTCAAAACTTAAGGCTCTTATATGGTAATTAGACCATTAAGAAAAGTATGTAGATTTTTCTTG
456 AATTCAAAACTTAAGGCTCTTATATGGTAATTAGACCATTAAGAAAAGTATGTAGATTTTTCTTG
40098990 AT
521 AT
40098992 GACTCATCCA
Statistics
Matches: 520, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
523 520 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (523 bp):
TAACTTAATCAAAAATAACAAAAATTAAATTTTCGTCTTACCATAACTACTTGAGTGGCGAAAAT
GTGATTGTCATCGAAACGGATTAGAGATGTTGTCATTTGTGAAAACTTAATCTGAACGAATAAAA
TACAGAATAATTAAAAAAAGCTAATATTTTTAAACGAGAATGTAAAAAAAATTAGAACAAGAACT
TGAGAAAATTGAGAAAGTTGAGAGAGTTAGTGTAACAGCTCATTTTCAGTGAAATCAGAATAGTA
GTTTCGGGACTACAAATCCGACCCAAAAATATAATTTATTTTTATTTCATTATATGGTTCGTATT
ATAATATGCATGTCATTTGAAAATTTTGAAACGAAAATTTTATCGATTAAGTGCTTAATTACTAG
AATGACTAAATCGTATAAAATGTGAAAGTTGAATTCTAGTAGCTATAAGGATCAAATAGCTATGG
AATTCAAAACTTAAGGCTCTTATATGGTAATTAGACCATTAAGAAAAGTATGTAGATTTTTCTTG
ATC
Found at i:40099410 original size:20 final size:20
Alignment explanation
Indices: 40099385--40099429 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
40099375 AGGGACTAAA
* *
40099385 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
40099405 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
40099425 ATGAA
1 ATGAA
40099430 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:40106589 original size:48 final size:48
Alignment explanation
Indices: 40106474--40106736 Score: 205
Period size: 48 Copynumber: 5.6 Consensus size: 48
40106464 TGATATGTGT
* * * * *
40106474 GCTAGTGTAAGACATGTCTGAGACATGCATTAGCCAC-AG-CA-TGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTA-A
*
40106520 GATAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAA
** *
40106568 GCTAGTGTAAGACATACCTGGGACATGCATCGGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAA
* * * * ** ** * *
40106616 GCCAATGTAAGACATGTCTGGGACGTGGATCAGTATTAAGACGA---GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGA-TATTTAA
* * * * **
40106662 GCTAGTGTAAGATATGTCTAGGACATGCATCGGCCTCGTGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAA
* * * *
40106710 GCTAATGTAAGACCTGGCTAGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
40106737 GCGTCAGCTT
Statistics
Matches: 169, Mismatches: 41, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
45 1 0.01
46 63 0.37
47 2 0.01
48 100 0.59
49 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATTTAA
Found at i:40110047 original size:69 final size:68
Alignment explanation
Indices: 40109885--40110058 Score: 215
Period size: 69 Copynumber: 2.5 Consensus size: 68
40109875 GGGTGTTACA
* * * * *
40109885 CAACTTTTTTCAGCTTGTCTGACTAGTGTTGGGCAAACAATTTTGGTCAATCTAATTAGCATTAG
1 CAACTTTTGTCAGCTTGTCTGACTAGTGCTGGGCACACAATTTAGGTCAATCTAATTAGCACTAG
40109950 GCG
66 GCG
* * * * *
40109953 CAGCCTTTGTCAGCTTGTCTGACTAGTGCTGGGCACACAATTGTCAGTTCATTC-GATTAGCACT
1 CAACTTTTGTCAGCTTGTCTGACTAGTGCTGGGCACACAATT-T-AGGTCAATCTAATTAGCACT
*
40110017 GGGCG
64 AGGCG
*
40110022 CAACTTTTGTCAGCTTGTCTAACTAGTGCTGGGCACA
1 CAACTTTTGTCAGCTTGTCTGACTAGTGCTGGGCACA
40110059 GAATCATCGA
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
68 37 0.41
69 47 0.52
70 6 0.07
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (68 bp):
CAACTTTTGTCAGCTTGTCTGACTAGTGCTGGGCACACAATTTAGGTCAATCTAATTAGCACTAG
GCG
Found at i:40110086 original size:69 final size:69
Alignment explanation
Indices: 40109949--40110093 Score: 166
Period size: 69 Copynumber: 2.1 Consensus size: 69
40109939 ATTAGCATTA
* * ** ** * * *
40109949 GGCGCAGCCTTTGTCAGCTTGTCTGACTAGTGCTGGGCACACAATTGTCAGTTCATTCGATTAGC
1 GGCGCAACCTTTGTCAGCTTGTCTAACTAGTGCTGGGCACACAATCATCAGTTCAACCAACTAAC
40110014 ACTG
66 ACTG
* * *
40110018 GGCGCAACTTTTGTCAGCTTGTCTAACTAGTGCTGGGCACAGAATCATC-GATTTAACCAACTAA
1 GGCGCAACCTTTGTCAGCTTGTCTAACTAGTGCTGGGCACACAATCATCAG-TTCAACCAACTAA
40110082 CACTG
65 CACTG
40110087 GGCGCAA
1 GGCGCAA
40110094 ACATCGTTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
68 1 0.02
69 62 0.98
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (69 bp):
GGCGCAACCTTTGTCAGCTTGTCTAACTAGTGCTGGGCACACAATCATCAGTTCAACCAACTAAC
ACTG
Found at i:40118506 original size:69 final size:69
Alignment explanation
Indices: 40118394--40118803 Score: 244
Period size: 69 Copynumber: 6.0 Consensus size: 69
40118384 ACAACATTCG
* * * **
40118394 TGTCATATTAAGGCTCGTAGGTGAAAATCCGTAATCTCTAACACAGTTAGTGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTAGTAGGCGAAAATCCGTAATCTCCAACACAGTTAACGAGAGCAAAGCTCC
* *
40118459 TAGT
66 CAGC
* *
40118463 TGTCATATTAAGGCTTGTAGGCGAAAATCTGTAATCTCCAACACAGTTAACGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTAGTAGGCGAAAATCCGTAATCTCCAACACAGTTAACGAGAGCAAAGCTCC
40118528 CAGC
66 CAGC
** * * * * * * *
40118532 TGTCATATTAAGGCTAGTAGGCGAGGAGCTG-CAGC-CCTAGCATAGTTAGA-AAGAGCAAAGCT
1 TGTCATATTAAGGCTAGTAGGCGAAAATCCGTAATCTCC-AACACAGTTA-ACGAGAGCAAAGCT
* *
40118594 TCCAAC
64 CCCAGC
* * ** * * *
40118600 TGTCATATTAAGGCTCGTAGGCGAAGAGTCAC--AGCCTCAAACACAGTTAATGAGAGAAAAGCT
1 TGTCATATTAAGGCTAGTAGGCGAA-AATC-CGTAATCTCCAACACAGTTAACGAGAGCAAAGCT
*
40118663 CCCAGT
64 CCCAGC
* * * ** * * ** * *
40118669 TGTCACATTAAGGTTCA-CA-ATGAAGAGCCGTAGCCTCCAACACAGTTAGCGAGAGCAGAGCTC
1 TGTCATATTAAGGCT-AGTAGGCGAAAATCCGTAATCTCCAACACAGTTAACGAGAGCAAAGCTC
*
40118732 CTAGC
65 CCAGC
* ** * * * * * * *
40118737 TATCATACCAAGGCTCGCAGGCGAAAAGCC--ACTGCCTCCAACATAGTTAGCAAGAGCAAAGCT
1 TGTCATATTAAGGCTAGTAGGCGAAAATCCGTAAT--CTCCAACACAGTTAACGAGAGCAAAGCT
40118800 CCCA
64 CCCA
40118804 ACTGATTATC
Statistics
Matches: 261, Mismatches: 67, Indels: 26
0.74 0.19 0.07
Matches are distributed among these distances:
66 1 0.00
67 4 0.02
68 94 0.36
69 161 0.62
70 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (69 bp):
TGTCATATTAAGGCTAGTAGGCGAAAATCCGTAATCTCCAACACAGTTAACGAGAGCAAAGCTCC
CAGC
Found at i:40120876 original size:21 final size:21
Alignment explanation
Indices: 40120852--40120919 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
40120842 AACCCAAACC
40120852 CATTGGTGAACCTACATTTCA
1 CATTGGTGAACCTACATTTCA
* * ****
40120873 CATTGAT-ATACTTACCCAACA
1 CATTGGTGA-ACCTACATTTCA
40120894 CATTGGTGAACCTACATTTCA
1 CATTGGTGAACCTACATTTCA
*
40120915 TATTG
1 CATTG
40120920 ATATACTTAC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (21 bp):
CATTGGTGAACCTACATTTCA
Found at i:40120903 original size:42 final size:43
Alignment explanation
Indices: 40120843--40120929 Score: 149
Period size: 42 Copynumber: 2.0 Consensus size: 43
40120833 TTTGTGGGAA
*
40120843 ACCCAAACCCATTGGTGAACCTACATTTCACATTGATATACTT
1 ACCCAAACACATTGGTGAACCTACATTTCACATTGATATACTT
*
40120886 ACCC-AACACATTGGTGAACCTACATTTCATATTGATATACTT
1 ACCCAAACACATTGGTGAACCTACATTTCACATTGATATACTT
40120928 AC
1 AC
40120930 TCCAGTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.31
Consensus pattern (43 bp):
ACCCAAACACATTGGTGAACCTACATTTCACATTGATATACTT
Found at i:40126143 original size:21 final size:21
Alignment explanation
Indices: 40126119--40126173 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
40126109 TTAATCCTAT
*
40126119 TTAATTTAAATTTAATTAAGA
1 TTAATTTAAATTTAAATAAGA
* * *
40126140 TTAAATTAAAATTAAATAGGA
1 TTAATTTAAATTTAAATAAGA
*
40126161 TTAAATTGAAATT
1 TT-AATTTAAATT
40126174 AAAGTAAATC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
TTAATTTAAATTTAAATAAGA
Found at i:40126979 original size:15 final size:15
Alignment explanation
Indices: 40126959--40127015 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
40126949 CGATGAATTT
40126959 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
40126974 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
40126989 ATTGAATTTATATTG
1 ATTGAATTTATATTG
40127004 ATTGAA-TTATAT
1 ATTGAATTTATAT
40127016 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:40127425 original size:23 final size:23
Alignment explanation
Indices: 40127399--40127450 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
40127389 AGGCACTTTA
*
40127399 TGTGTCGTGTACCAGGCACCTCG
1 TGTGTCGTGTACCAAGCACCTCG
* *
40127422 TGTGTC--GTATCAAGCACCTCT
1 TGTGTCGTGTACCAAGCACCTCG
40127443 TGTGTCGT
1 TGTGTCGT
40127451 TTTAGGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 18 0.75
23 6 0.25
ACGTcount: A:0.13, C:0.27, G:0.27, T:0.33
Consensus pattern (23 bp):
TGTGTCGTGTACCAAGCACCTCG
Found at i:40127459 original size:21 final size:21
Alignment explanation
Indices: 40127411--40127473 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
40127401 TGTCGTGTAC
40127411 CAGGCACCTCGTGTGTCGTAT
1 CAGGCACCTCGTGTGTCGTAT
* * *
40127432 CAAGCACCTCTTGTGTCGTTT
1 CAGGCACCTCGTGTGTCGTAT
* * **
40127453 TAGGCACTTTATGTGTCGTAT
1 CAGGCACCTCGTGTGTCGTAT
40127474 ACTGATCAGG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.37
Consensus pattern (21 bp):
CAGGCACCTCGTGTGTCGTAT
Found at i:40135023 original size:30 final size:30
Alignment explanation
Indices: 40134987--40135054 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
40134977 GGTTTCATTT
* *
40134987 CAGTCACCTAAC-TTTTGAAAAATAACAAAG
1 CAGTCA-CTAACGTTATAAAAAATAACAAAG
* *
40135017 CAGTCACTAACGTTATAAAAAATGACAAAA
1 CAGTCACTAACGTTATAAAAAATAACAAAG
*
40135047 TAGTCACT
1 CAGTCACT
40135055 GACTAACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.47, C:0.19, G:0.10, T:0.24
Consensus pattern (30 bp):
CAGTCACTAACGTTATAAAAAATAACAAAG
Found at i:40135115 original size:21 final size:21
Alignment explanation
Indices: 40135089--40135129 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40135079 TAACAGAACC
*
40135089 GCTGATGTGGCAAGTTAACTA
1 GCTGATATGGCAAGTTAACTA
*
40135110 GCTGATATGGCCAGTTAACT
1 GCTGATATGGCAAGTTAACT
40135130 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
GCTGATATGGCAAGTTAACTA
Found at i:40139290 original size:27 final size:29
Alignment explanation
Indices: 40139260--40139345 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 29
40139250 ATACAAGAGC
*
40139260 ATATA-GTGAATC-CGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
40139287 ATATATTTTCAGCTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
40139316 ATATAATTTTCAGCTCGCACACTTAGTGCT
1 ATAT-ATGTGAAGCTCGCACACTTAGTGCT
40139346 GTACAATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 19 0.37
30 25 0.48
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (29 bp):
ATATATGTGAAGCTCGCACACTTAGTGCT
Found at i:40139327 original size:30 final size:30
Alignment explanation
Indices: 40139272--40139374 Score: 154
Period size: 30 Copynumber: 3.5 Consensus size: 30
40139262 ATAGTGAATC
40139272 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40139301 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* * * * *
40139331 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40139361 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40139375 CAATCTTGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 19 0.28
30 49 0.72
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:40147205 original size:27 final size:29
Alignment explanation
Indices: 40147175--40147263 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 29
40147165 ATACAAGAGC
*
40147175 ATATA-GTGAATC-CGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
40147202 ATATATTTTCAGCTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
40147231 ATATAATTTTCAGCTCGCACACTTAGTGCT
1 ATAT-ATGTGAAGCTCGCACACTTAGTGCT
40147261 ATA
1 ATA
40147264 CAATTTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
27 5 0.09
28 3 0.05
29 19 0.35
30 28 0.51
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (29 bp):
ATATATGTGAAGCTCGCACACTTAGTGCT
Found at i:40147242 original size:30 final size:30
Alignment explanation
Indices: 40147187--40147289 Score: 163
Period size: 30 Copynumber: 3.5 Consensus size: 30
40147177 ATAGTGAATC
40147187 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40147216 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* * * *
40147246 CGCACACTTAGTGCTATACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
40147276 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40147290 CAATCTTGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 19 0.28
30 50 0.72
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:40150728 original size:26 final size:26
Alignment explanation
Indices: 40150699--40150751 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40150689 CATTGCAGCA
40150699 ACTTGCTATGAAATTCTTAGAACGTG
1 ACTTGCTATGAAATTCTTAGAACGTG
*
40150725 ACTTGGTATGAAATTCTTAGAACGTG
1 ACTTGCTATGAAATTCTTAGAACGTG
40150751 A
1 A
40150752 GGAGATCGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (26 bp):
ACTTGCTATGAAATTCTTAGAACGTG
Found at i:40151686 original size:21 final size:21
Alignment explanation
Indices: 40151660--40151708 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
40151650 AGATTATGGC
40151660 TATATATTATT-TT-TCTAATAT
1 TATATATTATTATTGT-TAA-AT
40151681 TATATATTATTATTGTTAAAT
1 TATATATTATTATTGTTAAAT
40151702 TATATAT
1 TATATAT
40151709 AATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 20 0.77
22 5 0.19
23 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATATATTATTATTGTTAAAT
Found at i:40151760 original size:59 final size:58
Alignment explanation
Indices: 40151677--40151787 Score: 159
Period size: 59 Copynumber: 1.9 Consensus size: 58
40151667 TATTTTTCTA
* *
40151677 ATATTATATATTATTATTGTTAAATTATATATAATAATAATTTTATAAAAATATGATT
1 ATATTATATATTATTATTATTAAATTATATATAATAATAATGTTATAAAAATATGATT
* * * *
40151735 ATATTATTTATTATATTTTATTAAATTATATTTAATAATAATGTTATTAAAAT
1 ATATTATATATTAT-TATTATTAAATTATATATAATAATAATGTTATAAAAAT
40151788 TTAAAAACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 13 0.28
59 33 0.72
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (58 bp):
ATATTATATATTATTATTATTAAATTATATATAATAATAATGTTATAAAAATATGATT
Found at i:40155077 original size:8 final size:7
Alignment explanation
Indices: 40155050--40155075 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40155040 AGCTAAACTC
40155050 TTTTTAT
1 TTTTTAT
40155057 TTTTTAT
1 TTTTTAT
40155064 TTTTTAT
1 TTTTTAT
40155071 TTTTT
1 TTTTT
40155076 TAATATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:40158193 original size:13 final size:13
Alignment explanation
Indices: 40158172--40158240 Score: 102
Period size: 13 Copynumber: 5.3 Consensus size: 13
40158162 AAATTTTTCT
40158172 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
40158185 AAAGTACTTCTCA
1 AAAGCACTTCTCA
40158198 AAAGCACTTCTCA
1 AAAGCACTTCTCA
* *
40158211 AAAGTACTTTTCA
1 AAAGCACTTCTCA
*
40158224 AAAACACTTCTCA
1 AAAGCACTTCTCA
40158237 AAAG
1 AAAG
40158241 TATTGCCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:40158201 original size:26 final size:26
Alignment explanation
Indices: 40158172--40158242 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
40158162 AAATTTTTCT
40158172 AAAGCACTTCTCAAAAGTACTTCTCA
1 AAAGCACTTCTCAAAAGTACTTCTCA
*
40158198 AAAGCACTTCTCAAAAGTACTTTTCA
1 AAAGCACTTCTCAAAAGTACTTCTCA
*
40158224 AAAACACTTCTCAAAAGTA
1 AAAGCACTTCTCAAAAGTA
40158243 TTGCCAAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (26 bp):
AAAGCACTTCTCAAAAGTACTTCTCA
Found at i:40158589 original size:51 final size:51
Alignment explanation
Indices: 40158505--40158603 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
40158495 TTTGAATGCA
* * * *
40158505 CACTCATTTTCTTAGGAGACTAGATGAATTAAAGTTTTAAGTGGACTTGCC
1 CACTCACTTTCTTAGGAGACTAGATAAAATAAAGTTTCAAGTGGACTTGCC
* *
40158556 CACTCACTTTCTTTGGAGACTATATAAAATAAAGTTTCAAGTGGACTT
1 CACTCACTTTCTTAGGAGACTAGATAAAATAAAGTTTCAAGTGGACTT
40158604 AGACATGCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (51 bp):
CACTCACTTTCTTAGGAGACTAGATAAAATAAAGTTTCAAGTGGACTTGCC
Found at i:40170959 original size:30 final size:30
Alignment explanation
Indices: 40170925--40170984 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
40170915 ACTTAACAAG
40170925 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAATTAA
* *
40170955 CAAATTCCTTTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAATTAA
40170985 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAATAAAATTAA
Found at i:40170987 original size:12 final size:12
Alignment explanation
Indices: 40170965--40170993 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40170955 CAAATTCCTT
40170965 TAAAA-TAATAA
1 TAAAATTAATAA
40170976 TAAAATTAATAA
1 TAAAATTAATAA
40170988 TAAAAT
1 TAAAAT
40170994 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:40174363 original size:127 final size:125
Alignment explanation
Indices: 40174097--40174538 Score: 580
Period size: 127 Copynumber: 3.5 Consensus size: 125
40174087 AACATAAAGA
** * * *
40174097 AATATTTCGTGTTTGGGAGTATGAGAGATCGTGCCCAATTGTGCTGGGTTTCGATTTTTCATTTG
1 AATATTTCGAATTTGGGAGT-TGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTCG
* * * * * *
40174162 ACTAAAATACAAAATA-TCCTTTTGGAATTTTGTCTATGTTTTCTTAAATTAAAACGAGGC
65 ACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAAAACGAGGC
40174222 AATATTTCGAATTTGGGGAGCTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
1 AATATTTCGAATTT-GGGAG-TTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
* *
40174287 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCATCCATGTTTTCTTAAATTAAAACGAGGC
64 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAAAACGAGGC
* * * *
40174349 AATATTTCGAATTTGGGGAGTTTGAGAGATCATGCCCAATCATGCTGGGTTTCAATTTTTCATTC
1 AATATTTCGAATTT-GGGAG-TTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTC
* *
40174414 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAACATGAGGC
64 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAAAACGAGGC
* * * * * * * *
40174476 AATATTTCGTATTTGGAAATTCGATAAATCGTGTCCAATCGTGCTAGGTTTCGATTTACCATT
1 AATATTTCGAATTTGGGAGTT-GAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATT
40174539 TGGCAAAATA
Statistics
Matches: 279, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
125 14 0.05
126 93 0.33
127 172 0.62
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (125 bp):
AATATTTCGAATTTGGGAGTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTCCATTCGA
CTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAAAACGAGGC
Found at i:40175072 original size:40 final size:40
Alignment explanation
Indices: 40175028--40175103 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
40175018 TCCGCTGGGG
40175028 ACAATAAGAGAGTCAAGCCGTAAAATTGACTATTTTTTAT
1 ACAATAAGAGAGTCAAGCCGTAAAATTGACTATTTTTTAT
*
40175068 ACAATAAGAGAGTCAAGCCGTAAAATTGATTATTTT
1 ACAATAAGAGAGTCAAGCCGTAAAATTGACTATTTT
40175104 CTATCCTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (40 bp):
ACAATAAGAGAGTCAAGCCGTAAAATTGACTATTTTTTAT
Found at i:40185821 original size:64 final size:64
Alignment explanation
Indices: 40185765--40185887 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 64
40185755 CATTTATAGT
* * * * *
40185765 ACATCTAGTTAGGAGCATTTGATTCATTTTGATTATAGCATCCTAATTATTTGACATAAATATC
1 ACATCTAGCTAGGAACATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAATATC
*
40185829 ACATCTAGCTAGGAACATTTGATTCATTTCGATCATAACATCCTAATTATTTGGCATAA
1 ACATCTAGCTAGGAACATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAA
40185888 GCATAGATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (64 bp):
ACATCTAGCTAGGAACATTTGATTCATTTCGATCATAACATCCTAATTATTTGACATAAATATC
Found at i:40186269 original size:177 final size:177
Alignment explanation
Indices: 40185961--40186715 Score: 1176
Period size: 177 Copynumber: 4.3 Consensus size: 177
40185951 GAAGTCACGT
* * *
40185961 GCCTTAACCCCCTAAACAGTAGGGTAACAGACTAAAAATTATAGATCTTATCTCCATGTATCGGC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
* * * * *
40186026 TATAGAGTAGATAAAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCA
66 TATGGAGCAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
* *
40186091 CC-AGCTTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTAAAGATACGA
131 CCGA-CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
* *
40186138 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTGCAAATCTTATCTCCATGTATCGGC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
* * *
40186203 TATGGAGTAGATTGAAA-ATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTAAGCC
66 TATGGAGCAGA-TCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * * *
40186267 ACCGGCCTTATCTCTCTGAGATAACAAGAGAGCAGATTGAAGATACGA
130 ACCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
*
40186315 GCCTTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
*
40186380 TATGGAGCAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGACTATGGAGCAGATTTTAGCCA
66 TATGGAGCAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
*
40186445 CCGACCTTATCTCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATACGA
131 CCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
* * * *
40186492 GTCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTTCATGTATCGAC
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
* *
40186557 TATGGAGCAGATCAAAGATGGCGAG-CTTATCTCCATGTATCAGCTATGGAGTAGATTTTAGCCA
66 TATGGAGCAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
*
40186621 CTGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
131 CCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
* *
40186668 GCCTTAACTCCCTAAGCAGTAGGGTAATAGGCTAGAAAA-TACAGATCT
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTA-AAAATTACAGATCT
40186716 CCCCTAAACA
Statistics
Matches: 533, Mismatches: 41, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
176 124 0.23
177 405 0.76
178 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (177 bp):
GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCATGTATCGGC
TATGGAGCAGATCAAAGATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
CCGACCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATACGA
Found at i:40186938 original size:84 final size:83
Alignment explanation
Indices: 40186667--40186950 Score: 388
Period size: 84 Copynumber: 3.4 Consensus size: 83
40186657 TGAAGATACG
* * *
40186667 AGCCTTAACTCCCTAAGCAGTAGGGTAATAGGCTAGAAAATACAGATCTCCCCTAAACAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAATAGGTTGGAAAATACAGATCT-CCCTAAACAGTAGTG
* *
40186732 GAGCAGAACAAAGACAGTA
65 GAGCAGATCGAAGACAGTA
* * * * *
40186751 AGCCTTAACCTCTTAAGTAATAGGGTAATAGGTTGGAAAATACAAATCTCTCCTAAACAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAATAGGTTGGAAAATACAGATCTC-CCTAAACAGTAGTG
40186816 GAGCAGATCGAAGACAGTA
65 GAGCAGATCGAAGACAGTA
* * *
40186835 AGCCTTAACCCCTTAAGCAGTAGGGTAACATGTTGGAAAATACAGATCTCCCTTAAACAGTAGTG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAATAGGTTGGAAAATACAGATCTCCC-TAAACAGTAGTG
* *
40186900 GAACAGATCGAAGACAGCA
65 GAGCAGATCGAAGACAGTA
* *
40186919 AGCCTTAACCCCCTAAGCAGCAGGGTATTAGG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAATAGG
40186951 CTTCTCGAAG
Statistics
Matches: 175, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
83 3 0.02
84 172 0.98
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (83 bp):
AGCCTTAACCCCCTAAGCAGTAGGGTAATAGGTTGGAAAATACAGATCTCCCTAAACAGTAGTGG
AGCAGATCGAAGACAGTA
Found at i:40189449 original size:127 final size:127
Alignment explanation
Indices: 40189184--40189619 Score: 599
Period size: 127 Copynumber: 3.5 Consensus size: 127
40189174 AACATAAGGA
** * * *
40189184 AATATTTCGTGTTTGGG-AGTTTGAGAGATCATGCCCAATCGTGCTGGGTTTTGATTTTTCATTT
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
* * * * * * *
40189248 GACTAAAATACAAAATA-TCCTTTTGGAATTTCGTTTATGTTTCCTTAAATTAAAATGAGGC
66 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
* * *
40189309 AATATTTCAAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTTGATTTTCCATTC
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
* *
40189374 GACTAAAGTGCGGAATATTCCTTTTGAAATTTCGTCCATGTTTTCTTAAATTAAAACGAGGC
66 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
* *
40189436 AATATTTCGAATTTGGGGAGTTTGAGAGATCGTGCCTAATCGTGCTGGGTTTCGATTTTTCATTC
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
* *
40189501 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAACAGGAGGC
66 GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
* * * * * * *
40189563 AATATTTAGTATTT-GGAAATTCGATAAATCGTGCCCAATCGTGCTAGGTTTCGATTT
1 AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTT
40189620 ACCGTTTGGC
Statistics
Matches: 276, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
125 14 0.05
126 93 0.34
127 169 0.61
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (127 bp):
AATATTTCGAATTTGGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTCATTC
GACTAAAGTGCAGAATATTCCTTTTGAAATTTCGTCTATGTTTTCTTAAATTAAAACGAGGC
Found at i:40190690 original size:31 final size:31
Alignment explanation
Indices: 40190649--40190712 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40190639 CCTTTTCATA
*
40190649 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40190680 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40190711 TT
1 TT
40190713 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40190961 original size:25 final size:25
Alignment explanation
Indices: 40190897--40191097 Score: 290
Period size: 25 Copynumber: 8.2 Consensus size: 25
40190887 AGCATAGCTG
*
40190897 CTTTATCATATAACTGGAGGCCT-AGCC
1 CTTTATC--ATAACTGG-GGCATAAGCC
40190924 TCTTT-T-ATAACTGGGGCATAAGCC
1 -CTTTATCATAACTGGGGCATAAGCC
*
40190948 CTTTATCACAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
*
40190973 CTTCATCATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
40190998 CTTTATCATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
40191023 CTTTA--ATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
40191046 CTTTATCATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
40191071 CTTTA--ATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
40191094 CTTT
1 CTTT
40191098 TGCACTTCCT
Statistics
Matches: 163, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
23 53 0.33
24 13 0.08
25 92 0.56
27 1 0.01
28 4 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (25 bp):
CTTTATCATAACTGGGGCATAAGCC
Found at i:40191051 original size:48 final size:48
Alignment explanation
Indices: 40190897--40191097 Score: 305
Period size: 48 Copynumber: 4.1 Consensus size: 48
40190887 AGCATAGCTG
* *
40190897 CTTTATCATATAACTGGAGGCCT-AGCCTCTTTTATAACTGGGGCATAAGCC
1 CTTTATC--ATAACTGG-GGCATAAGCC-CTTTAATAACTGGGGCATAAGCC
* *
40190948 CTTTATCACAACTGGGGCATAAGCCCTTCATCATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCCCTT--TAATAACTGGGGCATAAGCC
40190998 CTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
40191046 CTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
40191094 CTTT
1 CTTT
40191098 TGCACTTCCT
Statistics
Matches: 142, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
48 78 0.55
49 11 0.08
50 46 0.32
51 7 0.05
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (48 bp):
CTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
Found at i:40191054 original size:73 final size:73
Alignment explanation
Indices: 40190897--40191097 Score: 293
Period size: 73 Copynumber: 2.7 Consensus size: 73
40190887 AGCATAGCTG
*
40190897 CTTTATCATATAACTGGAGGCCT-AGCCTCTTT-TATAACTGGGGCATAAGCCCTTTATCACAAC
1 CTTTATC--ATAACTGG-GGCATAAGCC-CTTTATATAACTGGGGCATAAGCCCTTTA-CACAAC
40190960 TGGGGCATAAGCC
61 TGGGGCATAAGCC
* *
40190973 CTTCATCATAACTGGGGCATAAGCCCTTTATCATAACTGGGGCATAAGCCCTTTA-ATAACTGGG
1 CTTTATCATAACTGGGGCATAAGCCCTTTAT-ATAACTGGGGCATAAGCCCTTTACACAACTGGG
40191037 GCATAAGCC
65 GCATAAGCC
40191046 CTTTATCATAACTGGGGCATAAGCCCTTTA-ATAACTGGGGCATAAGCCCTTT
1 CTTTATCATAACTGGGGCATAAGCCCTTTATATAACTGGGGCATAAGCCCTTT
40191098 TGCACTTCCT
Statistics
Matches: 118, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
71 22 0.19
73 54 0.46
74 13 0.11
75 23 0.19
76 6 0.05
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (73 bp):
CTTTATCATAACTGGGGCATAAGCCCTTTATATAACTGGGGCATAAGCCCTTTACACAACTGGGG
CATAAGCC
Found at i:40191172 original size:20 final size:20
Alignment explanation
Indices: 40191144--40191214 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40191134 GCATTTATGA
*
40191144 ACATCTCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
*
40191164 ACATATCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
40191184 ACATGTCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
40191204 ACATGTCATGT
1 ACATGTCATGT
40191215 TTATCAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (20 bp):
ACATGTCATGTGCATATCAT
Found at i:40191179 original size:11 final size:11
Alignment explanation
Indices: 40191149--40191203 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40191139 TATGAACATC
40191149 TCATGTGCATA
1 TCATGTGCATA
*
40191160 TCA--TACATA
1 TCATGTGCATA
40191169 TCATGTGCATA
1 TCATGTGCATA
* *
40191180 TCA--TACATG
1 TCATGTGCATA
40191189 TCATGTGCATA
1 TCATGTGCATA
40191200 TCAT
1 TCAT
40191204 ACATGTCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40192496 original size:27 final size:27
Alignment explanation
Indices: 40192434--40192511 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
40192424 GGGCATATTC
* *
40192434 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTATAGGGGTATTACG
*
40192461 GTCACTTTACCCTATAGGGGCT-TTACG
1 GTCATTTTACCCTATAGGGG-TATTACG
*
40192488 GTCTTTTTA-CCTAATAGGGGTATT
1 GTCATTTTACCCT-ATAGGGGTATT
40192512 TTAGTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 38 0.88
28 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTACG
Found at i:40192582 original size:27 final size:27
Alignment explanation
Indices: 40192549--40192767 Score: 183
Period size: 27 Copynumber: 8.0 Consensus size: 27
40192539 TTGGTAAATC
*
40192549 TACAAACTAAGGGTATTTCAGTAATTT
1 TACAAACTAAGGGTATTTCGGTAATTT
** * * **
40192576 TGTAAACCAATGGTATTTCTATAATTTT
1 TACAAACTAAGGGTATTTCGGTAA-TTT
* * *
40192604 TAAAAAGTCAAGGGTATTTCTGTAACTTT
1 TACAAACT-AAGGGTATTTCGGTAA-TTT
* * *
40192633 GTA-AATC-AGGGGTATTTTGGTAATTT
1 -TACAAACTAAGGGTATTTCGGTAATTT
*
40192659 TACAAATTGAA-GGTATTTCGGTAATTT
1 TACAAACT-AAGGGTATTTCGGTAATTT
* * *
40192686 CACAAACCAAGGGTATTTTGGTAATTT
1 TACAAACTAAGGGTATTTCGGTAATTT
* *
40192713 TACAAACTAGGGGTATTTTGGTAATTT
1 TACAAACTAAGGGTATTTCGGTAATTT
**
40192740 TACAAACTAAGGGTATTTTAGTAATTT
1 TACAAACTAAGGGTATTTCGGTAATTT
40192767 T
1 T
40192768 GTAAATCGAG
Statistics
Matches: 154, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
25 2 0.01
26 7 0.05
27 116 0.75
28 8 0.05
29 19 0.12
30 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
TACAAACTAAGGGTATTTCGGTAATTT
Found at i:40192755 original size:81 final size:81
Alignment explanation
Indices: 40192537--40192766 Score: 218
Period size: 81 Copynumber: 2.8 Consensus size: 81
40192527 TACAAAGGTG
* * * ** ** *
40192537 TTTTGGTAAATCTACAAACTAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCTA-TAAT
1 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAA-GGTATTTC-AGTAA-
* *
40192601 TTTTAAAAAGTCAAGGGTA
63 TTTCAAAAAGCCAAGGGTA
* * *
40192620 TTTCT-GTAACTTTGTA-AATC-AGGGGTATTTTGGTAATTTTACAAATTGAAGGTATTTCGGTA
1 TTT-TGGTAA-TTT-TACAAACTAGGGGTATTTTGGTAATTTTACAAACT-AAGGTATTTCAGTA
*
40192682 ATTTCACAAA-CCAAGGGTA
62 ATTTCAAAAAGCCAAGGGTA
*
40192701 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTAGTAATT
1 TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAA-GGTATTTCAGTAATT
40192766 T
65 T
40192767 TGTAAATCGA
Statistics
Matches: 120, Mismatches: 18, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
79 2 0.02
80 9 0.08
81 55 0.46
82 7 0.06
83 38 0.32
84 7 0.06
85 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (81 bp):
TTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAAGGTATTTCAGTAATTT
CAAAAAGCCAAGGGTA
Found at i:40192779 original size:27 final size:27
Alignment explanation
Indices: 40192557--40192800 Score: 147
Period size: 27 Copynumber: 9.0 Consensus size: 27
40192547 TCTACAAACT
* * *
40192557 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTATAAATC
* *
40192584 AATGGTATTTCTA-TAATTTTTAAAAAGTC
1 AAGGGTATTT-TAGTAA-TTTTATAAA-TC
* *
40192613 AAGGGTATTTCT-GTAACTTTGTAAATC
1 AAGGGTATTT-TAGTAATTTTATAAATC
* * * *
40192640 AGGGGTATTTTGGTAATTTTACAAATTG
1 AAGGGTATTTTAGTAATTTTATAAA-TC
** * * *
40192668 AA-GGTATTTCGGTAATTTCACAAACC
1 AAGGGTATTTTAGTAATTTTATAAATC
* *
40192694 AAGGGTATTTTGGTAATTTTACAAA-C
1 AAGGGTATTTTAGTAATTTTATAAATC
* * *
40192720 TAGGGGTATTTTGGTAATTTTACAAA-C
1 -AAGGGTATTTTAGTAATTTTATAAATC
*
40192747 TAAGGGTATTTTAGTAATTTTGTAAATC
1 -AAGGGTATTTTAGTAATTTTATAAATC
* *** *
40192775 GAGGGTAAAATAGTAATTCTATAAAT
1 AAGGGTATTTTAGTAATTTTATAAAT
40192801 TGAGGGTAAA
Statistics
Matches: 176, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.02
27 140 0.80
28 17 0.10
29 15 0.09
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTATAAATC
Found at i:40192791 original size:54 final size:54
Alignment explanation
Indices: 40192733--40192946 Score: 137
Period size: 54 Copynumber: 4.0 Consensus size: 54
40192723 GGGTATTTTG
* * *
40192733 GTAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTTTACAAACTAAGGGTATTATAGTAATTCTATAAATCGAGGGTAAAATA
* * * * * * * **
40192787 GTAATTCTATAAATTGAGGGTA--AAACGATAATTCTGTAAATCGAAGGTAAAACG
1 GTAATTTTACAAACTAAGGGTATTATA-G-TAATTCTATAAATCGAGGGTAAAATA
* ** **
40192841 GTAATTTTACAAA-TCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTTTACAAACT-AAGGGTATTATAGTAATTCTATAAATCGAGGGTAAAATA
* ** * ** ** * *
40192895 GTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAA
1 GTAATTTTACAAACTAAGGGTATTATAGTAATTCTATAAATCGAGGGTAAAA
40192947 CGGTAATTCT
Statistics
Matches: 131, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 125 0.95
55 2 0.02
56 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (54 bp):
GTAATTTTACAAACTAAGGGTATTATAGTAATTCTATAAATCGAGGGTAAAATA
Found at i:40192791 original size:81 final size:81
Alignment explanation
Indices: 40192640--40192792 Score: 182
Period size: 81 Copynumber: 1.9 Consensus size: 81
40192630 TTTGTAAATC
* * ***
40192640 AGGGGTATTTTGGTAATTTTACAAATTGAAGGTATTTCGGTAATTTCACAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACTGAAGGTATTTCAGTAATTTCACAAACCAAGGGTAAAAT
*
40192705 GGTAATTTTACAAACT
66 AGTAATTTTACAAACT
* *** * *
40192721 AGGGGTATTTTGGTAATTTTACAAACT-AAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAA
1 AGGGGTATTTTGGTAATTTTACAAACTGAA-GGTATTTCAGTAATTTCACAAACCAAGGGTAAAA
40192785 TAGTAATT
65 TAGTAATT
40192793 CTATAAATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 2 0.03
81 57 0.97
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAACTGAAGGTATTTCAGTAATTTCACAAACCAAGGGTAAAAT
AGTAATTTTACAAACT
Found at i:40193062 original size:27 final size:27
Alignment explanation
Indices: 40192760--40193047 Score: 400
Period size: 27 Copynumber: 10.7 Consensus size: 27
40192750 GGGTATTTTA
* **
40192760 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40192787 GTAATTCTATAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40192814 ATAATTCTGTAAATCGAAGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
40192841 GTAATTTTACAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
40192868 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
40192895 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
*
40192922 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40192949 GTAATTCTGTAAA-CTGAGGTTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
*
40192976 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
40193003 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
40193030 GTAATTCTGTAAATCGAG
1 GTAATTCTGTAAATCGAG
40193048 AGTACTTTGG
Statistics
Matches: 230, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.00
27 228 0.99
28 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:40194318 original size:13 final size:13
Alignment explanation
Indices: 40194300--40194324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40194290 TATAATTTTT
40194300 AAGCACTTTCTTG
1 AAGCACTTTCTTG
40194313 AAGCACTTTCTT
1 AAGCACTTTCTT
40194325 TGAGGCAATG
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
AAGCACTTTCTTG
Found at i:40196077 original size:15 final size:15
Alignment explanation
Indices: 40196059--40196099 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
40196049 TCTATTTGAT
40196059 TTTATTCTATATGTG
1 TTTATTCTATATGTG
*
40196074 TTTATGCTATATGTG
1 TTTATTCTATATGTG
40196089 TTTATT-TATAT
1 TTTATTCTATAT
40196100 TTAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.22, C:0.05, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTATTCTATATGTG
Found at i:40196486 original size:88 final size:87
Alignment explanation
Indices: 40196389--40196646 Score: 274
Period size: 88 Copynumber: 3.0 Consensus size: 87
40196379 TTTTGTTTCC
* * *
40196389 AAATTAAAAGTAAATAAAATATGTTTCAAGATCTATTCCCGCTGTTCAATGGATTTTATTCCATT
1 AAATTAAAAGTAAATAAAATCTGTTTCGAGAT-TATTCCCGCTATTCAATGGATTTTATTCCATT
40196454 ATTTTTATTTATTTCCAAACGAG
65 ATTTTTATTTATTTCCAAACGAG
* ** * ** * *
40196477 AAATTAAAAGTAAA-AAGATCCATTTCGGGATTTATTCCCGCCCTACAACGGATTTTATTCCATT
1 AAATTAAAAGTAAATAAAATCTGTTTCGAGA-TTATTCCCGCTATTCAATGGATTTTATTCCATT
* * *
40196541 ATTTTGATTTTATTTCCAAATGGG
65 ATTTTTA-TTTATTTCCAAACGAG
* *
40196565 AAATTAAAGGTAAATAAAATCTGTTTCGAGATTGATTCCCG-TCATTCAAT-GAATTTATTCCA-
1 AAATTAAAAGTAAATAAAATCTGTTTCGAGATT-ATTCCCGCT-ATTCAATGGATTTTATTCCAT
*
40196627 AATTTTGT-TTTATTTCCAAA
64 TATTTT-TATTTATTTCCAAA
40196647 AACGAGTAAA
Statistics
Matches: 139, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
86 12 0.09
87 49 0.35
88 55 0.40
89 23 0.17
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
AAATTAAAAGTAAATAAAATCTGTTTCGAGATTATTCCCGCTATTCAATGGATTTTATTCCATTA
TTTTTATTTATTTCCAAACGAG
Found at i:40196515 original size:87 final size:85
Alignment explanation
Indices: 40196423--40196781 Score: 286
Period size: 79 Copynumber: 4.3 Consensus size: 85
40196413 TTCAAGATCT
* *
40196423 ATTCCCG-CTGTTCAATGGATTTTATTCCATTATTTTTATTTATTTCCAAACGAGAAATTAAAAG
1 ATTCCCGTC-GTTCAATGGATTTTATTCCA-AATTTTGATTTATTTCCAAACGAGAAATTAAAAG
*
40196487 TAAAAAGATCCATTTCGGGATTT
64 TAAAAA-ATCCATTTCGGGATTG
* * * * * * * *
40196510 ATTCCCGCCCTACAACGGATTTTATTCCATTATTTTGATTTTATTTCCAAATGGGAAATTAAAGG
1 ATTCCCGTCGTTCAATGGATTTTATTCCA-AATTTTGA-TTTATTTCCAAACGAGAAATTAAAAG
** *
40196575 TAAATAAAATCTGTTTCGAGATTG
64 T-AA-AAAATCCATTTCGGGATTG
* * *
40196599 ATTCCCGTCATTCAAT-GAATTTATTCCAAATTTTGTTTTATTTCCAAAAACGAG----TAAAA-
1 ATTCCCGTCGTTCAATGGATTTTATTCCAAATTTTGATTTATTTCC--AAACGAGAAATTAAAAG
* *
40196658 T--AAAATTCATTTCGGAATTG
64 TAAAAAATCCATTTCGGGATTG
*
40196678 ATTCCCGTCGTTCAA-CGATTTTATTCCAAATTTTGATTTATTTCCAAAAACGAG----TAAAA-
1 ATTCCCGTCGTTCAATGGATTTTATTCCAAATTTTGATTTATTTCC--AAACGAGAAATTAAAAG
40196737 T--AAAATCCATTTCGGGATTG
64 TAAAAAATCCATTTCGGGATTG
* * *
40196757 ATACTCGCCGTTCAAT-GATTTTATT
1 ATTCCCGTCGTTCAATGGATTTTATT
40196782 TCAGTTTCGA
Statistics
Matches: 230, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
79 108 0.47
83 1 0.00
84 4 0.02
86 9 0.04
87 38 0.17
88 41 0.18
89 26 0.11
90 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (85 bp):
ATTCCCGTCGTTCAATGGATTTTATTCCAAATTTTGATTTATTTCCAAACGAGAAATTAAAAGTA
AAAAATCCATTTCGGGATTG
Found at i:40196812 original size:79 final size:80
Alignment explanation
Indices: 40196576--40196805 Score: 304
Period size: 79 Copynumber: 2.9 Consensus size: 80
40196566 AATTAAAGGT
** * * *
40196576 AAATAAAATCTGTTTCGAGATTGATTCCCGTCATTCAATGAATTTATTCCAAATTTTG-TTTTAT
1 AAATAAAATCCATTTCGGGATTGATTCCCGTCGTTCAATGATTTTATTCCAAATTTTGATTTTAT
40196640 TTCCAAAAACGAGTA
66 TTCCAAAAACGAGTA
* * *
40196655 AAATAAAATTCATTTCGGAATTGATTCCCGTCGTTCAACGATTTTATTCCAAATTTTGA-TTTAT
1 AAATAAAATCCATTTCGGGATTGATTCCCGTCGTTCAATGATTTTATTCCAAATTTTGATTTTAT
40196719 TTCCAAAAACGAGTA
66 TTCCAAAAACGAGTA
* * * * * *
40196734 AAATAAAATCCATTTCGGGATTGATACTCGCCGTTCAATGATTTTATTTC-AGTTTCGATTTTAT
1 AAATAAAATCCATTTCGGGATTGATTCCCGTCGTTCAATGATTTTATTCCAAATTTTGATTTTAT
*
40196798 TTTCAAAA
66 TTCCAAAA
40196806 CTGAGTATTA
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
78 6 0.05
79 125 0.95
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (80 bp):
AAATAAAATCCATTTCGGGATTGATTCCCGTCGTTCAATGATTTTATTCCAAATTTTGATTTTAT
TTCCAAAAACGAGTA
Found at i:40197030 original size:84 final size:85
Alignment explanation
Indices: 40196899--40197064 Score: 196
Period size: 84 Copynumber: 2.0 Consensus size: 85
40196889 AAAAACTAGA
* * * * **
40196899 AATTAAAAATAAATAAATTCTGTTTTGGGATTTATTCCTGTCATTTAACAATATTTTATTTTAT-
1 AATTAAAAATAAATAAAATCTATTTCGGGATTTATTCCTGTCATTTAACAAGATTTTATTCGATA
*
40196963 TTTATTTTGTTTCCAAATTCG
66 TTT-TTCTGTTTCCAAATTCG
* *
40196984 AATT-AAATTAAATAAAATCTATTTCGGGATTTATT-CTCG-CTGTTTAACAAGATTTTATTCGA
1 AATTAAAAATAAATAAAATCTATTTCGGGATTTATTCCT-GTC-ATTTAACAAGATTTTATTCGA
40197046 TATTTTTCTGTTTCCAAAT
64 TATTTTTCTGTTTCCAAAT
40197065 AAAGACGTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
83 3 0.04
84 59 0.86
85 7 0.10
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (85 bp):
AATTAAAAATAAATAAAATCTATTTCGGGATTTATTCCTGTCATTTAACAAGATTTTATTCGATA
TTTTTCTGTTTCCAAATTCG
Found at i:40211155 original size:180 final size:179
Alignment explanation
Indices: 40210885--40211237 Score: 562
Period size: 180 Copynumber: 2.0 Consensus size: 179
40210875 GAGCTACGGA
*** *
40210885 ACTCCAAATTAAGATTGTTAATTTTCCCAGAAACTAGACTCATATATATTCTTACCATAAAATTT
1 ACTCCAAATTAAGATCACTAATTTTCCCAGAAACTAGACTAATATATATTCTTACCATAAAATTT
* *
40210950 TTAGAATTTTTGGTTTAGCCAATTAGTACAGTTTATTCATTAAAGTTACCCCTATTTCACTGTCC
66 TTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTGTCC
* *
40211015 AATAGTTCCGACCTCTCTTCACTAAAAATTATTTATCTCATGGAAAGCG
131 AACAGTTCCAACCTCTCTTCACTAAAAATTATTTATCTCATGGAAAGCG
* *
40211064 ACTCCAAATTAAGAATCACTAATTTTCTCAGAAACTAGACTAATATATTTTCTTACCATAAAATT
1 ACTCCAAATTAAG-ATCACTAATTTTCCCAGAAACTAGACTAATATATATTCTTACCATAAAATT
* *
40211129 TTTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACTCCTGTTTCACTGTC
65 TTTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTGTC
* * *
40211194 CGACAGTTCCAATCTTTCTTCACTAAAAATTATTTATCTCATGG
130 CAACAGTTCCAACCTCTCTTCACTAAAAATTATTTATCTCATGG
40211238 TACAGATCTC
Statistics
Matches: 158, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
179 13 0.08
180 145 0.92
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (179 bp):
ACTCCAAATTAAGATCACTAATTTTCCCAGAAACTAGACTAATATATATTCTTACCATAAAATTT
TTAGAATTTTTGATTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTGTCC
AACAGTTCCAACCTCTCTTCACTAAAAATTATTTATCTCATGGAAAGCG
Found at i:40212060 original size:151 final size:151
Alignment explanation
Indices: 40211786--40212075 Score: 418
Period size: 151 Copynumber: 1.9 Consensus size: 151
40211776 GAAGCTCTCT
* * * * *
40211786 GGTACGCATAGTAGCCTGCACTTAGTACTTCACATGCGACCTATCAATCTGGTATACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGC
* * ** * * **
40211851 CTGCACTTAGTACTACAGACGTGATTTATCCATCTAATGTACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGCGACCTAACAATCTAATCCACGTAGTAGCCTGCACTTAGTACTA
40211916 CACACGTGATCAAAGTTAACG
131 CACACGTGATCAAAGTTAACG
* *
40211937 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATTTGATACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGC
* *
40212002 CTGCACTTAGTACTACACATGCGACCTAACAATCTGATCCACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGCGACCTAACAATCTAATCCACGTAGTAGCCTGCACTTAGTACTA
*
40212067 CATACGTGA
131 CACACGTGA
40212076 CCTAAAACTA
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
151 121 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGC
CTGCACTTAGTACTACACACGCGACCTAACAATCTAATCCACGTAGTAGCCTGCACTTAGTACTA
CACACGTGATCAAAGTTAACG
Found at i:40212080 original size:50 final size:50
Alignment explanation
Indices: 40211794--40212122 Score: 318
Period size: 50 Copynumber: 6.5 Consensus size: 50
40211784 CTGGTACGCA
* * * * * *
40211794 TAGTAGCCTGCACTTAGTACTTCACATGCGACCTATCAATCTGGTATACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
* ** * * * **
40211844 TAGTAGCCTGCACTTAGTACTACAGACGTGATTTATCCATCTAATGTACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
* * * * * * *
40211894 TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA-CGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAATCTGATACACG
*
40211945 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
* * *
40211995 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATCCACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
* * * * * *
40212045 TAGTAGCCTGCACTTAGTACTACATACGTGACCTAAAACTATCTTAAACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACAATCTGATACACG
* *
40212097 TAGTAGACTGCACATAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
40212123 TGTGTTCTCA
Statistics
Matches: 227, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
49 2 0.01
50 154 0.68
51 37 0.16
52 34 0.15
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGATACACG
Found at i:40212529 original size:28 final size:28
Alignment explanation
Indices: 40212485--40212562 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
40212475 CATCCTATGG
*
40212485 CAAAATTTAAAATTTTGCCCCTAAAGTTT
1 CAAAA-TTACAATTTTGCCCCTAAAGTTT
*
40212514 CAAAATTACAATTTTGCCCTTAAAGTTT
1 CAAAATTACAATTTTGCCCCTAAAGTTT
40212542 CAAAATTACAATTTT-CCCCTA
1 CAAAATTACAATTTTGCCCCTA
40212563 GGTTCGGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 5 0.11
28 36 0.78
29 5 0.11
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (28 bp):
CAAAATTACAATTTTGCCCCTAAAGTTT
Found at i:40215811 original size:15 final size:15
Alignment explanation
Indices: 40215791--40215835 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
40215781 AGAACCTTTT
40215791 GTATTCATATAACAA
1 GTATTCATATAACAA
40215806 GTATTCATATAACAA
1 GTATTCATATAACAA
40215821 GTATTCATATAACAA
1 GTATTCATATAACAA
40215836 CCTTCAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
GTATTCATATAACAA
Done.