Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 172 of 203
Found at i:54624435 original size:53 final size:53
Alignment explanation
Indices: 54624342--54624457 Score: 142
Period size: 53 Copynumber: 2.2 Consensus size: 53
54624332 GAAGCAGGGA
* **
54624342 CACACGGCCATGTCCCAGCATGTGTCTGTGCCCTAAAACTCTTTGACTTGGGT
1 CACACAGCCATGTCCCAGCATGTGTCCATGCCCTAAAACTCTTTGACTTGGGT
* * * **
54624395 CACACAGCCGTGTCCCAGCCTGTGTCCATGTCCTGTAACTCTTTGACTTGGGT
1 CACACAGCCATGTCCCAGCATGTGTCCATGCCCTAAAACTCTTTGACTTGGGT
* *
54624448 TACACGGCCA
1 CACACAGCCA
54624458 AGCCACACGC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.18, C:0.32, G:0.22, T:0.28
Consensus pattern (53 bp):
CACACAGCCATGTCCCAGCATGTGTCCATGCCCTAAAACTCTTTGACTTGGGT
Found at i:54625707 original size:23 final size:23
Alignment explanation
Indices: 54625669--54625719 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
54625659 CGAGCTATTG
*
54625669 TGTAATATCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
54625692 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
54625715 AGTAA
1 TGTAA
54625720 GGAAGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:54636244 original size:235 final size:235
Alignment explanation
Indices: 54635833--54636302 Score: 940
Period size: 235 Copynumber: 2.0 Consensus size: 235
54635823 AAGTTCACAA
54635833 AAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCTATTTCTCTCTTGACTAT
1 AAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCTATTTCTCTCTTGACTAT
54635898 ATCCCTATGTCAATTCAATCGATTAAACAAATCTTAATAGGCAAATATGTTATTGCACATACATA
66 ATCCCTATGTCAATTCAATCGATTAAACAAATCTTAATAGGCAAATATGTTATTGCACATACATA
54635963 CTTATTAAATCGAAATAATCTCTTATACATATCCCTATGTCACTTCAAAAAATTAACTCGATTTA
131 CTTATTAAATCGAAATAATCTCTTATACATATCCCTATGTCACTTCAAAAAATTAACTCGATTTA
54636028 ATAAGTACATAAAAGACTATGTGAGGTAACAAAGTATCCT
196 ATAAGTACATAAAAGACTATGTGAGGTAACAAAGTATCCT
54636068 AAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCTATTTCTCTCTTGACTAT
1 AAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCTATTTCTCTCTTGACTAT
54636133 ATCCCTATGTCAATTCAATCGATTAAACAAATCTTAATAGGCAAATATGTTATTGCACATACATA
66 ATCCCTATGTCAATTCAATCGATTAAACAAATCTTAATAGGCAAATATGTTATTGCACATACATA
54636198 CTTATTAAATCGAAATAATCTCTTATACATATCCCTATGTCACTTCAAAAAATTAACTCGATTTA
131 CTTATTAAATCGAAATAATCTCTTATACATATCCCTATGTCACTTCAAAAAATTAACTCGATTTA
54636263 ATAAGTACATAAAAGACTATGTGAGGTAACAAAGTATCCT
196 ATAAGTACATAAAAGACTATGTGAGGTAACAAAGTATCCT
54636303 TACCTTAAAA
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 235 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (235 bp):
AAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCTATTTCTCTCTTGACTAT
ATCCCTATGTCAATTCAATCGATTAAACAAATCTTAATAGGCAAATATGTTATTGCACATACATA
CTTATTAAATCGAAATAATCTCTTATACATATCCCTATGTCACTTCAAAAAATTAACTCGATTTA
ATAAGTACATAAAAGACTATGTGAGGTAACAAAGTATCCT
Found at i:54646067 original size:23 final size:23
Alignment explanation
Indices: 54646037--54646080 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54646027 CTTTCTCGCT
* *
54646037 GTAGTAATTTTCGGGGTATTATG
1 GTAGTAATTTTCAGGATATTATG
54646060 GTAGTAATTTTCAGGATATTA
1 GTAGTAATTTTCAGGATATTA
54646081 CAACTGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (23 bp):
GTAGTAATTTTCAGGATATTATG
Found at i:54651165 original size:26 final size:26
Alignment explanation
Indices: 54651136--54651244 Score: 101
Period size: 26 Copynumber: 4.2 Consensus size: 26
54651126 CCAAGACACC
* *
54651136 AATATCGTAGCAAAGCTGTCAGTAAT
1 AATATCGCAGCAAAGCTGCCAGTAAT
* *
54651162 AATATCGCAGCAGAGCTGCCAGTAAC
1 AATATCGCAGCAAAGCTGCCAGTAAT
** * * * *
54651188 AGGATCGCAGCAGAGCTTCCAATAAC
1 AATATCGCAGCAAAGCTGCCAGTAAT
* * *
54651214 AGTATCGCACCAAAGCTGCCAGTAAC
1 AATATCGCAGCAAAGCTGCCAGTAAT
54651240 AATAT
1 AATAT
54651245 TCTTCCTCCA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (26 bp):
AATATCGCAGCAAAGCTGCCAGTAAT
Found at i:54651429 original size:27 final size:27
Alignment explanation
Indices: 54651407--54651521 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 27
54651397 GAGTATAACA
*
54651407 GTCATTTTACCCTATAGAGGTATTTGG
1 GTCATTTTACCCTATAGAGGTATTTCG
* * *
54651434 GTTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
*
54651461 ATCATTTTACCCTAT-GAGGGTATTTCG
1 GTCATTTTACCCTATAGA-GGTATTTCG
* *
54651488 GTCATTTTACCCTATAGAGGGATGTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
*
54651515 ATCATTT
1 GTCATTT
54651522 GTTGACCTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 72 0.96
28 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATAGAGGTATTTCG
Found at i:54651495 original size:54 final size:54
Alignment explanation
Indices: 54651408--54651521 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
54651398 AGTATAACAG
* * * *
54651408 TCATTTTACCCTATAGAGGTATTTGGGTTATTTTACCCTAT-GGGGGTATTTCGA
1 TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTATAGAGGG-ATGTCGA
54651462 TCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCCTATAGAGGGATGTCGA
1 TCATTTTACCCTATAGA-GGTATTTCGGTCATTTTACCCTATAGAGGGATGTCGA
54651516 TCATTT
1 TCATTT
54651522 GTTGACCTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
53 2 0.04
54 48 0.89
55 4 0.07
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (54 bp):
TCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCCTATAGAGGGATGTCGA
Found at i:54651637 original size:20 final size:21
Alignment explanation
Indices: 54651598--54651639 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
54651588 TAAATGGGCT
54651598 CAAGGCCCAGTACTCGGCCCAA
1 CAAGGCCCAGTAC-CGGCCCAA
*
54651620 CAAGGCCCATTA-CGGCCCAA
1 CAAGGCCCAGTACCGGCCCAA
54651640 GCCCATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.29, C:0.40, G:0.21, T:0.10
Consensus pattern (21 bp):
CAAGGCCCAGTACCGGCCCAA
Found at i:54652881 original size:182 final size:183
Alignment explanation
Indices: 54652573--54652928 Score: 642
Period size: 182 Copynumber: 2.0 Consensus size: 183
54652563 ACCCCACTTT
*
54652573 CACGATTTTCTCCTAAAATCTCTCCCCTTATCCCTCCTTGGAGTACTCCACCAATTTCTCTTCAA
1 CACGATTTTCTCCTAAAATCTCTCCCCTTATCCCTCCTTGGAGTACTCCACCAATTTCTCCTCAA
54652638 CTCCCTCAACAACTCCATTCAAATTCAAATCAAACCCCCCATAGCTATATTTCAGTCCAACTCCA
66 CTCCCTCAACAACTCCATTCAAATTCAAATCAAACCCCCCATAGCTATATTTCAGTCCAACTCCA
54652703 CTACCTACACAACTCAAGCAACAAAATAAATACTCCATTACACAACATACTCC
131 CTACCTACACAACTCAAGCAACAAAATAAATACTCCATTACACAACATACTCC
*
54652756 CACGATTTTCTCCTAAAATCTCTCCCCTTAT-CCTCCTTGGATTACTCCACCAATTTCTCCTCAA
1 CACGATTTTCTCCTAAAATCTCTCCCCTTATCCCTCCTTGGAGTACTCCACCAATTTCTCCTCAA
*
54652820 CTCCCTCAACAACTCCATTCAAATTCAAATCAAACTCCCCATAGCTATATTTCAGTCCAACTCCA
66 CTCCCTCAACAACTCCATTCAAATTCAAATCAAACCCCCCATAGCTATATTTCAGTCCAACTCCA
* * **
54652885 CTACCTACATAGCTCAAGCAGTAAAATAAATACTCCATTACACA
131 CTACCTACACAACTCAAGCAACAAAATAAATACTCCATTACACA
54652929 GCCCAAGACT
Statistics
Matches: 166, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
182 135 0.81
183 31 0.19
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (183 bp):
CACGATTTTCTCCTAAAATCTCTCCCCTTATCCCTCCTTGGAGTACTCCACCAATTTCTCCTCAA
CTCCCTCAACAACTCCATTCAAATTCAAATCAAACCCCCCATAGCTATATTTCAGTCCAACTCCA
CTACCTACACAACTCAAGCAACAAAATAAATACTCCATTACACAACATACTCC
Found at i:54663496 original size:5 final size:5
Alignment explanation
Indices: 54663486--54663510 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54663476 AACAACTAAG
54663486 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
54663511 AGTTCCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:54666909 original size:19 final size:21
Alignment explanation
Indices: 54666864--54666911 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
54666854 TATTTAGCAC
54666864 ACTTTTTTTTATATTCGAAAT
1 ACTTTTTTTTATATTCGAAAT
*
54666885 AATTTTTTTTA-ATTC-AAA-
1 ACTTTTTTTTATATTCGAAAT
*
54666903 ACCTTTTTT
1 ACTTTTTTT
54666912 AACTTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.29
19 3 0.12
20 4 0.17
21 10 0.42
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.58
Consensus pattern (21 bp):
ACTTTTTTTTATATTCGAAAT
Found at i:54681469 original size:51 final size:51
Alignment explanation
Indices: 54681404--54681749 Score: 324
Period size: 51 Copynumber: 6.8 Consensus size: 51
54681394 ATAAGGTATC
* * *
54681404 GATGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAAT
1 GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT
* * * * * *
54681455 GATGATCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
1 GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-AT
* * * * *
54681507 -TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAT
1 GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT
* * ** * * *
54681557 GATGGTCACATGAATAGTAATAAGTGAAGGCTACTATGTGTACCGA-AAA-
1 GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT
* * * * * *
54681606 GCTTTGGTCACTTGTGTAGTTCTATGTGAAGGCTACTACGTGAACCG-TAAAA
1 G--ATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT
* * * * *
54681658 CATGATCACGTGTGTAGTACAATGTGAAGGCTACTACGTGAACTG-TAAAA
1 GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT
**
54681708 CTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
54681750 TCGAATGATA
Statistics
Matches: 240, Mismatches: 49, Indels: 13
0.79 0.16 0.04
Matches are distributed among these distances:
49 1 0.00
50 86 0.36
51 152 0.63
52 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
GATGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT
Found at i:54681586 original size:102 final size:101
Alignment explanation
Indices: 54681410--54681753 Score: 442
Period size: 102 Copynumber: 3.4 Consensus size: 101
54681400 TATCGATGAA
* * *
54681410 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGATCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAA
*
54681475 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
* * **
54681512 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGAATAGTAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAA
54681577 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * * ** *
54681614 CACTTGTGTAGTTCTATGTGAAGGCTACTACGTGAACCG-TAAAACATGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTA-
* * * * * *
54681678 A-ATGTGAAGGCTACTACGTGAACTGTAAAAC-TTGAT
65 ATAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
*
54681714 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
54681754 ATGATAAAAG
Statistics
Matches: 212, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
100 39 0.18
101 42 0.20
102 130 0.61
103 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAA
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:54682623 original size:54 final size:54
Alignment explanation
Indices: 54682541--54682648 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
54682531 TGTGTGACAG
54682541 CCCAAAATTGACCCTAGTCGGAAAGTGGTTTTGGGACCGCTAAACCGAGTCACT
1 CCCAAAATTGACCCTAGTCGGAAAGTGGTTTTGGGACCGCTAAACCGAGTCACT
54682595 CCCAAAATTGACCCTAGTCGGAAAGTGGTTTTGGGACCGCTAAACCGAGTCACT
1 CCCAAAATTGACCCTAGTCGGAAAGTGGTTTTGGGACCGCTAAACCGAGTCACT
54682649 GAAATGTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (54 bp):
CCCAAAATTGACCCTAGTCGGAAAGTGGTTTTGGGACCGCTAAACCGAGTCACT
Found at i:54693915 original size:47 final size:47
Alignment explanation
Indices: 54693850--54694912 Score: 1874
Period size: 47 Copynumber: 22.4 Consensus size: 47
54693840 CAGCCAAGAG
*
54693850 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * * *
54693897 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * *
54693944 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * *
54693993 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* * *
54694044 AGTATATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AG----TGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694095 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694142 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694189 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694236 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694283 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694330 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694377 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694424 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694471 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694518 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694565 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694612 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694659 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694706 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694753 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
54694800 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
*
54694847 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
* **
54694894 AGTGCATAAATGTGATAAG
1 AGTGTATATGTGTGATAAG
54694913 TCCCGAAAGG
Statistics
Matches: 995, Mismatches: 13, Indels: 16
0.97 0.01 0.02
Matches are distributed among these distances:
47 859 0.86
49 42 0.04
51 90 0.09
53 4 0.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
Found at i:54695087 original size:37 final size:37
Alignment explanation
Indices: 54695031--54695109 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54695021 CCGAGCTCTA
* * *
54695031 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
54695068 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54695105 AAGAC
1 AAGAC
54695110 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54702471 original size:4 final size:4
Alignment explanation
Indices: 54702458--54702545 Score: 56
Period size: 4 Copynumber: 20.5 Consensus size: 4
54702448 ATTTTCCTAC
*
54702458 TTTA -TTA TTTA TTTA TTTA TTCTA -TTA TTTTA TTTTA TTTC TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA -TTTA TTTA TTTA -TTTA
*
54702508 TTT- TATTA TTTGG TTTA TGTTTA TTTCA TTTA TTTA TT
1 TTTA T-TTA TTT-A TTTA --TTTA TTT-A TTTA TTTA TT
54702546 AACCCCAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
3 6 0.09
4 37 0.54
5 22 0.32
6 4 0.06
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:54702489 original size:13 final size:12
Alignment explanation
Indices: 54702458--54702518 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
54702448 ATTTTCCTAC
54702458 TTTATTA-TTTA
1 TTTATTATTTTA
*
54702469 TTTATTTATTCTA
1 TTTA-TTATTTTA
*
54702482 TTATTTTATTTTA
1 TT-TATTATTTTA
*
54702495 TTTCTTTATTTTA
1 TTT-ATTATTTTA
54702508 TTTTATTATTT
1 -TTTATTATTT
54702519 GGTTTATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 29 0.71
14 4 0.10
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:54702496 original size:18 final size:17
Alignment explanation
Indices: 54702458--54702542 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 17
54702448 ATTTTCCTAC
*
54702458 TTTATTATTTA-TTTA-
1 TTTATTCTTTATTTTAT
54702473 TTTATTCTATTATTTTAT
1 TTTATTCT-TTATTTTAT
54702491 TTTATTTCTTTATTTTAT
1 TTTA-TTCTTTATTTTAT
* **
54702509 TTTATTATTTGGTTTAT
1 TTTATTCTTTATTTTAT
54702526 GTTTATTTCATTTATTT
1 -TTTA-TTC-TTTATTT
54702543 ATTAACCCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.12
16 3 0.05
17 14 0.25
18 21 0.38
19 6 0.11
20 5 0.09
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTATTCTTTATTTTAT
Found at i:54702530 original size:23 final size:22
Alignment explanation
Indices: 54702462--54702542 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 22
54702452 TCCTACTTTA
*
54702462 TTATTTATTTATTTATTCTATTATT
1 TTATTTATTTCTTTA-T-T-TTATT
54702487 TTATTTTATTTCTTTATTTTATT
1 TTA-TTTATTTCTTTATTTTATT
*
54702510 TTA-TTATTTGGTTTATGTTTATT
1 TTATTTATTT-CTTTAT-TTTATT
*
54702533 TCATTTATTT
1 TTATTTATTT
54702543 ATTAACCCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.12
22 5 0.10
23 16 0.33
24 7 0.14
25 4 0.08
26 11 0.22
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (22 bp):
TTATTTATTTCTTTATTTTATT
Found at i:54702545 original size:13 final size:13
Alignment explanation
Indices: 54702458--54702545 Score: 51
Period size: 13 Copynumber: 6.8 Consensus size: 13
54702448 ATTTTCCTAC
54702458 TTTA-TTATTT-A
1 TTTATTTATTTCA
54702469 TTTATTTA-TTC-
1 TTTATTTATTTCA
*
54702480 TATTATTTTATTTTA
1 T-TTA-TTTATTTCA
* *
54702495 TTTCTTTATTTTA
1 TTTATTTATTTCA
**
54702508 TTT-TATTATTTGG
1 TTTAT-TTATTTCA
54702521 TTTATGTTTATTTCA
1 TTTA--TTTATTTCA
54702536 TTTATTTATT
1 TTTATTTATT
54702546 AACCCCAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
11 7 0.11
12 7 0.11
13 31 0.51
14 4 0.07
15 11 0.18
16 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTATTTATTTCA
Found at i:54702671 original size:8 final size:8
Alignment explanation
Indices: 54702658--54702682 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54702648 CTATTTGGTA
54702658 TATTATTT
1 TATTATTT
54702666 TATTATTT
1 TATTATTT
54702674 TATTATTT
1 TATTATTT
54702682 T
1 T
54702683 TAGTTATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:54702820 original size:36 final size:36
Alignment explanation
Indices: 54702771--54702855 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
54702761 TGTTACTATT
*
54702771 TTAGTTTATTATTATAGTTACTACTATTATTCGTCC
1 TTAGTTTATTATTATAGTTACTACTATGATTCGTCC
* * *
54702807 TTAGTTTACTATTATAGTTATTATTATGATTCGTCC
1 TTAGTTTATTATTATAGTTACTACTATGATTCGTCC
54702843 TTAGTTTATTATT
1 TTAGTTTATTATT
54702856 TTGAATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (36 bp):
TTAGTTTATTATTATAGTTACTACTATGATTCGTCC
Found at i:54704490 original size:19 final size:20
Alignment explanation
Indices: 54704468--54704509 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
54704458 TTGTTTTCTT
54704468 TTTAAT-TTTAATTTTTATG
1 TTTAATGTTTAATTTTTATG
* *
54704487 TTT-ATGTTTATTTTTTATT
1 TTTAATGTTTAATTTTTATG
54704506 TTTA
1 TTTA
54704510 GTTGTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTAATGTTTAATTTTTATG
Found at i:54704502 original size:32 final size:32
Alignment explanation
Indices: 54704466--54704532 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
54704456 ATTTGTTTTC
54704466 TTTTTAATTTTAATT-TTTATGTTTATGTTTAT
1 TTTTTAATTTTAATTGTTT-TGTTTATGTTTAT
* * * *
54704498 TTTTTATTTTTAGTTGTTTTGTTTTTTTTTAT
1 TTTTTAATTTTAATTGTTTTGTTTATGTTTAT
54704530 TTT
1 TTT
54704533 CTTGTAGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (32 bp):
TTTTTAATTTTAATTGTTTTGTTTATGTTTAT
Found at i:54704525 original size:25 final size:24
Alignment explanation
Indices: 54704452--54704532 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 24
54704442 GGATAATTGA
*
54704452 TTTTATTTGTTTTCTTTTTAATTTTAAT
1 TTTTA-TTGTTTTGTTTTT--TTTT-AT
54704480 TTTTA-TGTTTATGTTTATTTTTTAT
1 TTTTATTGTTT-TGTTT-TTTTTTAT
54704505 TTTTAGTTGTTTTGTTTTTTTTTAT
1 TTTTA-TTGTTTTGTTTTTTTTTAT
54704530 TTT
1 TTT
54704533 CTTGTAGTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
25 18 0.38
26 14 0.29
27 9 0.19
28 7 0.15
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTATTGTTTTGTTTTTTTTTAT
Found at i:54707048 original size:36 final size:36
Alignment explanation
Indices: 54706958--54707065 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
54706948 AATTAGAAAG
*
54706958 AGATTTCAATTAATCAACTTAGAGTCAATTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
* *
54706994 AGATTTC-ATTAATCAACTTAAAGTGAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
54707029 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
54707065 A
1 A
54707066 CTCTCGAAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 32 0.48
36 34 0.52
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (36 bp):
AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
Found at i:54710103 original size:42 final size:42
Alignment explanation
Indices: 54710044--54710128 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
54710034 TGATTACAAG
54710044 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
1 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
54710086 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
1 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
54710128 T
1 T
54710129 AAACCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (42 bp):
TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
Found at i:54718289 original size:46 final size:46
Alignment explanation
Indices: 54718217--54718337 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
54718207 TTTATCATGT
* * * * *
54718217 TTGAAGTGTTAAAGTGTTGCATATTGAAGTATTTATATGCTGTGAA
1 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
* *
54718263 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTATAAA
1 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
* *
54718309 TGGAAGTGTTTTAAA-TACTGCAAATTGAA
1 TTGAAGTG--TTAAAGTGCTGCAAATTGAA
54718338 TTGTTTAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 46 0.72
47 13 0.20
48 5 0.08
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (46 bp):
TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
Found at i:54718309 original size:23 final size:23
Alignment explanation
Indices: 54718217--54718426 Score: 122
Period size: 23 Copynumber: 9.1 Consensus size: 23
54718207 TTTATCATGT
* *
54718217 TTGAAGTG-TTAAAGTGTTGCATA
1 TTGAAGTGTTTAAA-TGCTGCAAA
* * **
54718240 TTGAAGTATTTATATGCTGTGAA
1 TTGAAGTGTTTAAATGCTGCAAA
54718263 TTGAAGTG-TTAAAGTGCTGCAAA
1 TTGAAGTGTTTAAA-TGCTGCAAA
* **
54718286 TTGAAGTGTTTAAATGTTATAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* *
54718309 TGGAAGTGTTTTAAATACTGCAAA
1 TTGAAGTG-TTTAAATGCTGCAAA
* ** *
54718333 TTGAATTGTTTAGTTGCTGAAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* * *
54718356 TTG-AGATGTTTTATTGCTG-TAA
1 TTGAAG-TGTTTAAATGCTGCAAA
* * * * *
54718378 CTGAGGTGTATAAATGTTGTAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* * *
54718401 TTGAAGTGTTTTATTGCTGAAAA
1 TTGAAGTGTTTAAATGCTGCAAA
54718424 TTG
1 TTG
54718427 GATGGTATAA
Statistics
Matches: 138, Mismatches: 42, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
22 18 0.13
23 94 0.68
24 26 0.19
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (23 bp):
TTGAAGTGTTTAAATGCTGCAAA
Found at i:54718333 original size:24 final size:24
Alignment explanation
Indices: 54718261--54718343 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
54718251 ATATGCTGTG
*
54718261 AATTGAAGTG--TTAAAGTGCTGCA
1 AATTGAAGTGTTTTAAA-TACTGCA
** **
54718284 AATTGAAGTG-TTTAAATGTTATA
1 AATTGAAGTGTTTTAAATACTGCA
*
54718307 AATGGAAGTGTTTTAAATACTGCA
1 AATTGAAGTGTTTTAAATACTGCA
*
54718331 AATTGAATTGTTT
1 AATTGAAGTGTTT
54718344 AGTTGCTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 23 0.48
24 25 0.52
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (24 bp):
AATTGAAGTGTTTTAAATACTGCA
Found at i:54719054 original size:16 final size:16
Alignment explanation
Indices: 54719033--54719072 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
54719023 TTGAATTACT
54719033 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
54719049 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
54719065 ATTACAGC
1 ATTACAGC
54719073 GAACCAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:54721156 original size:20 final size:19
Alignment explanation
Indices: 54721101--54721160 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
54721091 GCCCAAATTA
54721101 TATATTAAATATATATTTT
1 TATATTAAATATATATTTT
* * *
54721120 TATTTTTAATCAAATATACTTT
1 TA-TATTAA--ATATATATTTT
54721142 T-TATTAAATATATATTTT
1 TATATTAAATATATATTTT
54721160 T
1 T
54721161 TTTGGACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 10 0.31
22 10 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTAAATATATATTTT
Found at i:54721162 original size:20 final size:20
Alignment explanation
Indices: 54721103--54721163 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
54721093 CCAAATTATA
54721103 TATTAAATATATATTTTTATT
1 TATTAAATATATATTTTT-TT
* **
54721124 T-TT-AATCAAATATACTTTT
1 TATTAAAT-ATATATTTTTTT
54721143 TATTAAATATATATTTTTTT
1 TATTAAATATATATTTTTTT
54721163 T
1 T
54721164 GGACTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 6 0.19
20 21 0.68
21 4 0.13
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTAAATATATATTTTTTT
Found at i:54722124 original size:20 final size:20
Alignment explanation
Indices: 54722099--54722137 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54722089 TGGAGCAGGA
*
54722099 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
54722119 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
54722138 AGTATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:54723631 original size:18 final size:18
Alignment explanation
Indices: 54723591--54723638 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
54723581 ACACCAATTT
**
54723591 GTTATTTGAGCTATTCAA
1 GTTATTTGAATTATTCAA
* *
54723609 ATTATTTGAATTATTCAC
1 GTTATTTGAATTATTCAA
*
54723627 GTTATTCGAATT
1 GTTATTTGAATT
54723639 GTTAAATTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (18 bp):
GTTATTTGAATTATTCAA
Found at i:54723878 original size:14 final size:14
Alignment explanation
Indices: 54723861--54723891 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54723851 AGTAAAATAT
*
54723861 TTTCTGGAAAATGA
1 TTTCTAGAAAATGA
54723875 TTTCTAGAAAATGA
1 TTTCTAGAAAATGA
54723889 TTT
1 TTT
54723892 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (14 bp):
TTTCTAGAAAATGA
Found at i:54723907 original size:19 final size:19
Alignment explanation
Indices: 54723883--54723920 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54723873 GATTTCTAGA
54723883 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
54723902 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
54723921 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:54725491 original size:43 final size:43
Alignment explanation
Indices: 54725384--54725608 Score: 213
Period size: 43 Copynumber: 5.3 Consensus size: 43
54725374 TTATTTTTAT
* **** *
54725384 AAACGCCGCTAAAGGTTATGTTCTTTAGCGGCG-TTACGAAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
* *
54725426 AAATGTCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
* * *
54725469 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
* * * * * * **
54725512 AAATGTCTCTAAAGATCATGTTCTTTAGCGGTGCTTCTTCCGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
* *
54725555 AAACGCCACTAAAGGTCATGTTCTTTTAGCGGC-ATTTTT-ACAC
1 AAACGCCGCTAAAGGTCATGTTC-TTTAGCGGCGCTTTTTCA-AC
*
54725598 AAATGCCGCTA
1 AAACGCCGCTA
54725609 TTTGTTTGGT
Statistics
Matches: 149, Mismatches: 31, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
42 30 0.20
43 111 0.74
44 8 0.05
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
Found at i:54725536 original size:86 final size:86
Alignment explanation
Indices: 54725426--54725608 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 86
54725416 GTTACGAAAA
* * *
54725426 AAATGTCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAACAAACGCCGCTAAAGATCATGTT
1 AAATGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCAACAAACGCCACTAAAGATCATGTT
* *
54725491 C-CTTAGCGGCGCTTTTTCCAC
66 CTCTTAGCGGC-ATTTTTACAC
* * ** *
54725512 AAATGTCTCTAAAGATCATGTTCTTTAGCGGTGCTTCTTCCGCAAACGCCACTAAAGGTCATGTT
1 AAATGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCAACAAACGCCACTAAAGATCATGTT
*
54725577 CTTTTAGCGGCATTTTTACAC
66 CTCTTAGCGGCATTTTTACAC
*
54725598 AAATGCCGCTA
1 AAATGTCGCTA
54725609 TTTGTTTGGT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
86 75 0.90
87 8 0.10
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (86 bp):
AAATGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCAACAAACGCCACTAAAGATCATGTT
CTCTTAGCGGCATTTTTACAC
Found at i:54730513 original size:16 final size:16
Alignment explanation
Indices: 54730492--54730703 Score: 156
Period size: 16 Copynumber: 13.0 Consensus size: 16
54730482 CATCATATAT
54730492 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
54730508 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
54730525 GTTATGT-A-TTAAGTAAA
1 -TTATGTAAGTTATGT--A
54730542 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
54730558 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
* *
54730575 GTTGTGT-A-TTATGAAA
1 -TTATGTAAGTTATG-TA
*
54730591 CTTATGTAAGTTATGTC
1 -TTATGTAAGTTATGTA
*
54730608 TTATGTAGGTTATGTAA
1 TTATGTAAGTTATGT-A
54730625 GTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
*
54730641 GTTATGT-A-TTAAGTAAA
1 -TTATGTAAGTTATGT--A
*
54730658 TTATGTAAG-T-TGTC
1 TTATGTAAGTTATGTA
*
54730672 TTATATAAGTTATGTA
1 TTATGTAAGTTATGTA
54730688 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
54730704 AGTTTTTGTT
Statistics
Matches: 162, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.05
15 1 0.01
16 114 0.70
17 12 0.07
18 27 0.17
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:54730558 original size:50 final size:50
Alignment explanation
Indices: 54730492--54730707 Score: 267
Period size: 50 Copynumber: 4.2 Consensus size: 50
54730482 CATCATATAT
*
54730492 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAA
*
54730542 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTATTATG-AAA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAA
* * *
54730591 CTTATGTAAGTTATGTCTTATGTAGGTTATGTAAGTTATGTATTATGTAAG
1 -TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAA
* * *
54730642 TTATGT-A-TTAAGTAAATTATGTAAGTTGTCTTATATAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGT--ATTATGTAA---G--TTATGTAAGTTATGTATTATGTAAA
54730697 TTATGTAAGTT
1 TTATGTAAGTT
54730708 TTTGTTTTTT
Statistics
Matches: 145, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
48 5 0.03
49 4 0.03
50 100 0.69
51 2 0.01
53 1 0.01
55 30 0.21
56 1 0.01
57 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.47
Consensus pattern (50 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAA
Found at i:54730786 original size:96 final size:96
Alignment explanation
Indices: 54730686--54731342 Score: 1314
Period size: 96 Copynumber: 6.8 Consensus size: 96
54730676 ATAAGTTATG
54730686 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54730751 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
54730782 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54730847 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
54730878 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54730943 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
54730974 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54731039 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
54731070 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54731135 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
54731166 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54731231 TATGTATTATTATGTAAGTTATTATGTAGGA
66 TATGTATTATTATGTAAGTTATTATGTAGGA
54731262 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
54731327 TATGTATTATTATGTA
66 TATGTATTATTATGTA
54731343 TTATAAATTT
Statistics
Matches: 561, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 561 1.00
ACGTcount: A:0.27, C:0.01, G:0.18, T:0.54
Consensus pattern (96 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGT
TATGTATTATTATGTAAGTTATTATGTAGGA
Found at i:54731459 original size:21 final size:20
Alignment explanation
Indices: 54731420--54731458 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
54731410 GTAAAGTATC
*
54731420 AATTTTTAAAAATATATATA
1 AATTTTAAAAAATATATATA
54731440 AATTTT-AAAAATATATATA
1 AATTTTAAAAAATATATATA
54731459 TTAAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAAATATATATA
Found at i:54734266 original size:15 final size:15
Alignment explanation
Indices: 54734246--54734318 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 15
54734236 CTTAGCACAT
54734246 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
54734261 CTAACCCTCT-AACCC
1 CTAACCC-CTAAACCC
* * *
54734276 CTAAACCTTAAATCC
1 CTAACCCCTAAACCC
*
54734291 C-AACCCCT-AATCC
1 CTAACCCCTAAACCC
* *
54734304 ATAATCCCTAAACCC
1 CTAACCCCTAAACCC
54734319 ATACTTCCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
13 5 0.11
14 12 0.26
15 27 0.59
16 2 0.04
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:54734282 original size:8 final size:7
Alignment explanation
Indices: 54734246--54734279 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
54734236 CTTAGCACAT
54734246 CTAACCC
1 CTAACCC
54734253 CTAAACCC
1 CT-AACCC
54734261 CTAACCC
1 CTAACCC
54734268 TCTAACCC
1 -CTAACCC
54734276 CTAA
1 CTAA
54734280 ACCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:54734641 original size:41 final size:41
Alignment explanation
Indices: 54734581--54734659 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
54734571 TAAAATATTT
* *
54734581 TTAGCGACGCTTTTCCAAAAACGCCGCTAAAGCTCCCAACA
1 TTAGCGACGCTTTTCCAAAAACGCCGCCAAAGCCCCCAACA
*
54734622 TTAGCGACGCTTTTTCAAAAACGCCGCCAAAGCCCCCA
1 TTAGCGACGCTTTTCCAAAAACGCCGCCAAAGCCCCCA
54734660 GATTTTTGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.19
Consensus pattern (41 bp):
TTAGCGACGCTTTTCCAAAAACGCCGCCAAAGCCCCCAACA
Found at i:54734870 original size:114 final size:114
Alignment explanation
Indices: 54734670--54735318 Score: 1043
Period size: 114 Copynumber: 5.7 Consensus size: 114
54734660 GATTTTTGGC
* ** * * *
54734670 CGCTAAATCCCCGAAAGCTCAGAAAATGGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTA
1 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTC
* * **
54734735 AAAAACGCCGTTAAAGCCCTGAGCGTTAGCGGCATTTTCTTAAAAACGT
66 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
* * * ** *
54734784 CGCTAAATCCCTCGAAAGCTCAGAAAACGGAGTCGTTATGCTTA-GTTTTTTTGTGGCGCTTTCT
1 CGCTAAATCCC-CGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCT
54734848 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
65 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
*
54734898 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGTTTTCTC
1 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTC
54734963 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
66 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
*
54735012 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGTTTTCTC
1 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTC
54735077 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
66 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
*
54735126 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGTTTTCTC
1 CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTC
* * *
54735191 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGGTTTCCTAAAAACGC
66 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
* *
54735240 CGTTAAATCCCCGAAAGCTCACAAAAC-GACGTCGTTGGGCTTAT-TTTTTTTGCGGCACTTTCT
1 CGCTAAATCCCCGAAAGCTCACAAAACAG-CGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCT
54735303 CAAAAACGCCGCTAAA
65 CAAAAACGCCGCTAAA
54735319 TCCCCGAAAG
Statistics
Matches: 509, Mismatches: 23, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
113 61 0.12
114 420 0.83
115 28 0.06
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (114 bp):
CGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTCTC
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGT
Found at i:54735312 original size:72 final size:73
Alignment explanation
Indices: 54735232--54735391 Score: 225
Period size: 72 Copynumber: 2.2 Consensus size: 73
54735222 GCGGTTTCCT
* *
54735232 AAAAACGCCGTTAAATCCCCGAAAGCTCACAAAA-CGACGTCGTTGGGCTTAT-TTTTTTTGCGG
1 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATCG-CGTCGTTGGGCTTATGTTTTTTTGCGA
54735295 CACTTTCTC
65 CACTTTCTC
* * *
54735304 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATTGTGTCGTTGGGCTTATGTTTTTTTGCGAC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATCGCGTCGTTGGGCTTATGTTTTTTTGCGAC
**
54735369 GTTTTCTC
66 ACTTTCTC
*
54735377 AAAAACGCCACTAAA
1 AAAAACGCCGCTAAA
54735392 GCACTGAGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 46 0.59
73 32 0.41
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAATCGCGTCGTTGGGCTTATGTTTTTTTGCGAC
ACTTTCTC
Found at i:54735351 original size:186 final size:186
Alignment explanation
Indices: 54735105--54735569 Score: 657
Period size: 186 Copynumber: 2.5 Consensus size: 186
54735095 CTGAGCATTA
* * *
54735105 GCGGCGCTTTCTTAAAAACGTCGCTAAATCCCCGAAAGCTCACAAAACAGCGTCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
* * *
54735170 GTTTTTTTGCGGCGTTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGGTTTCCTAAA
66 GTTTTTTTGCGGCGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTCCTAAA
** * *
54735235 AACGCCGTTAAATCCCCGAAAGCTCACAAAAC-GACGTCGTTGGGCTTAT-TTTTTTT
131 AACGCCGCAAAATCCCCAAAAGCTCACAAAACAG-CAT-GTTGGGCTTATGTTTTTTT
* ** *
54735291 GCGGCACTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATTGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
* * *
54735356 GTTTTTTTGCGACGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCGCTTTCTTAAA
66 GTTTTTTTGCGGCGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTCCTAAA
* *
54735421 AACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCATGTTGGGCTTATGTTTTTTT
131 AACGCCGCAAAATCCCCAAAAGCTCACAAAACAGCATGTTGGGCTTATGTTTTTTT
** *
54735477 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCTTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
* * **
54735541 GGTTTTTTGCGGCGCTTTCTGGAAAACGC
66 GTTTTTTTGCGGCGTTTTCTCAAAAACGC
54735570 TGCGAAAAAT
Statistics
Matches: 247, Mismatches: 30, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
185 35 0.14
186 211 0.85
187 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (186 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAT
GTTTTTTTGCGGCGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTCCTAAA
AACGCCGCAAAATCCCCAAAAGCTCACAAAACAGCATGTTGGGCTTATGTTTTTTT
Found at i:54735504 original size:113 final size:114
Alignment explanation
Indices: 54735297--54735504 Score: 310
Period size: 113 Copynumber: 1.8 Consensus size: 114
54735287 TTTTGCGGCA
* * ** **
54735297 CTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATTGTGTCGTTGGGCTTATGTTTTT
1 CTTTCTCAAAAACGCCGCAAAATCCCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTATGTTTTT
*
54735362 TTGCGACGTTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCG
66 TTGCGACGCTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCG
* *
54735411 CTTTCTTAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCAT-GTTGGGCTTATGTTTTT
1 CTTTCTCAAAAACGCCGCAAAATCCCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTATGTTTTT
* *
54735475 TTGCGGCGCTTTCTCAAAAACGCCGCTAAA
66 TTGCGACGCTTTCTCAAAAACGCCACTAAA
54735505 TCCTTGAAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
113 44 0.53
114 39 0.47
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (114 bp):
CTTTCTCAAAAACGCCGCAAAATCCCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTATGTTTTT
TTGCGACGCTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGTGGCG
Found at i:54735524 original size:72 final size:72
Alignment explanation
Indices: 54735407--54735569 Score: 213
Period size: 72 Copynumber: 2.3 Consensus size: 72
54735397 GAGCATTAGT
* *
54735407 GGCGCTTTCTTAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCAT-GTTGGGCTTATGT
1 GGCGCTTTCTCAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTA-GG
54735471 TTTTTTGC
65 TTTTTTGC
* ** * *
54735479 GGCGCTTTCTCAAAAACGCCGCTAAATC-CTTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
1 GGCGCTTTCTCAAAAACGCCGCAAAATCTC-CAAAAGCTCAGAAAACAGCATCGTTGGGCTTAGG
54735543 TTTTTTGC
65 TTTTTTGC
**
54735551 GGCGCTTTCTGGAAAACGC
1 GGCGCTTTCTCAAAAACGC
54735570 TGCGAAAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
71 1 0.01
72 69 0.86
73 10 0.12
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (72 bp):
GGCGCTTTCTCAAAAACGCCGCAAAATCTCCAAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGT
TTTTTGC
Found at i:54737345 original size:4 final size:4
Alignment explanation
Indices: 54737329--54737370 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
54737319 CAGTTCGCTT
54737329 TGTC TGT- TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
54737371 TTGTTTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.00, C:0.21, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:54737861 original size:16 final size:18
Alignment explanation
Indices: 54737830--54737868 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
54737820 GATTATGTGA
54737830 TTGTGTCAACATTTATGC
1 TTGTGTCAACATTTATGC
*
54737848 TTGTG-CAA-ATTTATGT
1 TTGTGTCAACATTTATGC
54737864 TTGTG
1 TTGTG
54737869 GAGAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (18 bp):
TTGTGTCAACATTTATGC
Found at i:54740076 original size:26 final size:26
Alignment explanation
Indices: 54740047--54740098 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
54740037 TTTAGTTTCC
**
54740047 TTAATTATAGTTTCTTTTTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
*
54740073 TTAATTTTAGTTTCTTAGTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
54740099 AATAAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.52
Consensus pattern (26 bp):
TTAATTATAGTTTCTTAGTCTACAAG
Found at i:54748567 original size:15 final size:14
Alignment explanation
Indices: 54748540--54748566 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54748530 TTTGACTATC
54748540 AACTTTTTAAAAAT
1 AACTTTTTAAAAAT
54748554 AACTTTTTAAAAA
1 AACTTTTTAAAAA
54748567 AAAGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AACTTTTTAAAAAT
Found at i:54756655 original size:8 final size:8
Alignment explanation
Indices: 54756642--54756668 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
54756632 TTAACTAGTT
54756642 TAATTAAC
1 TAATTAAC
54756650 TAATTAAC
1 TAATTAAC
54756658 TAATTAAC
1 TAATTAAC
54756666 TAA
1 TAA
54756669 CTAGACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
TAATTAAC
Found at i:54761630 original size:13 final size:13
Alignment explanation
Indices: 54761601--54761677 Score: 73
Period size: 13 Copynumber: 5.9 Consensus size: 13
54761591 CAAGTATGGA
**
54761601 GCTAAGTGATATG
1 GCTAAGTGATACC
*
54761614 GCTAAGTGGTACC
1 GCTAAGTGATACC
* * *
54761627 GCTAAGGGGTGCC
1 GCTAAGTGATACC
*
54761640 ACTAAGTGATACC
1 GCTAAGTGATACC
*
54761653 GCTAAGTGACACC
1 GCTAAGTGATACC
*
54761666 GCTAAGTAATAC
1 GCTAAGTGATAC
54761678 TGCGAAATGG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (13 bp):
GCTAAGTGATACC
Found at i:54776275 original size:31 final size:31
Alignment explanation
Indices: 54776233--54776303 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
54776223 TTAAAATCTT
* * *
54776233 TCTTAACAATAATTCTAAAAAAATAAAAAAA
1 TCTTAAAAATAAATATAAAAAAATAAAAAAA
* *
54776264 TCTTAAAAATAAATATAAAATAATAAAAATA
1 TCTTAAAAATAAATATAAAAAAATAAAAAAA
*
54776295 TATTAAAAA
1 TCTTAAAAA
54776304 GTATGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (31 bp):
TCTTAAAAATAAATATAAAAAAATAAAAAAA
Found at i:54782564 original size:17 final size:17
Alignment explanation
Indices: 54782542--54782605 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
54782532 AATCTTAGAG
54782542 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
54782559 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
54782578 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
54782595 TTTTAATTGTA
1 TTCTAATTGTA
54782606 GCCCTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:54782581 original size:36 final size:36
Alignment explanation
Indices: 54782534--54782604 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
54782524 GATTATGTAA
54782534 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
54782570 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
54782605 AGCCCTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:54782583 original size:19 final size:19
Alignment explanation
Indices: 54782533--54782589 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
54782523 TGATTATGTA
54782533 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
54782552 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
54782569 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
54782588 AT
1 AT
54782590 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:54782886 original size:48 final size:48
Alignment explanation
Indices: 54782809--54782904 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
54782799 TGAGGGAATT
* *
54782809 CTGTTGAATCCTTTATCGAGCGAGATTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCATTATCGAGCGAGATTAGGCTGACTTAGGCGTTTTTA
* *
54782857 CTGTTGAATCCATTATC-ATTGCGTG-TTAGGTTGACTTAGGCGTTTTTA
1 CTGTTGAATCCATTATCGA--GCGAGATTAGGCTGACTTAGGCGTTTTTA
54782905 AGCAAAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 1 0.02
48 37 0.88
49 4 0.10
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCATTATCGAGCGAGATTAGGCTGACTTAGGCGTTTTTA
Found at i:54783908 original size:6 final size:6
Alignment explanation
Indices: 54783897--54783925 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
54783887 ATAGTTCCCT
54783897 CACCCC CACCCC CA-CCC CACCCC CACCCC
1 CACCCC CACCCC CACCCC CACCCC CACCCC
54783926 ACCGCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCCC
Found at i:54783916 original size:11 final size:11
Alignment explanation
Indices: 54783900--54783928 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
54783890 GTTCCCTCAC
54783900 CCCCACCCCCA
1 CCCCACCCCCA
54783911 CCCCACCCCCA
1 CCCCACCCCCA
54783922 CCCCACC
1 CCCCACC
54783929 GCAAATACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (11 bp):
CCCCACCCCCA
Found at i:54787218 original size:20 final size:20
Alignment explanation
Indices: 54787193--54787232 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54787183 GATTAATTTT
54787193 TTTTATGAACTTTTTAAAAA
1 TTTTATGAACTTTTTAAAAA
** *
54787213 TTTTATTTATTTTTTAAAAA
1 TTTTATGAACTTTTTAAAAA
54787233 AAGTTTGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATGAACTTTTTAAAAA
Found at i:54787533 original size:25 final size:25
Alignment explanation
Indices: 54787499--54787549 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
54787489 AGACCAGCGA
54787499 ATCGTTATTGACTATTAAAGGACCT
1 ATCGTTATTGACTATTAAAGGACCT
54787524 ATCGTTATTGACTATTAAAGGACCT
1 ATCGTTATTGACTATTAAAGGACCT
54787549 A
1 A
54787550 AATTGATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (25 bp):
ATCGTTATTGACTATTAAAGGACCT
Found at i:54787558 original size:25 final size:25
Alignment explanation
Indices: 54787503--54787558 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
54787493 CAGCGAATCG
**
54787503 TTATTGACTATTAAAGGACCTATCG
1 TTATTGACTATTAAAGGACCTATAA
54787528 TTATTGACTATTAAAGGACCTA-AA
1 TTATTGACTATTAAAGGACCTATAA
54787552 TTGATTG
1 TT-ATTG
54787559 GTTAACAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (25 bp):
TTATTGACTATTAAAGGACCTATAA
Found at i:54792773 original size:39 final size:40
Alignment explanation
Indices: 54792675--54792896 Score: 249
Period size: 40 Copynumber: 5.6 Consensus size: 40
54792665 AATGATGTCT
* * *
54792675 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
* *
54792715 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
54792755 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * *
54792794 GGGTTAAGTCCCGGAGGCATTTGTGCGAGTTACTAAATT-T
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AATTCC
* *
54792834 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
*
54792874 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
54792897 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 35 0.22
40 107 0.68
41 13 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:54792876 original size:80 final size:80
Alignment explanation
Indices: 54792672--54792896 Score: 280
Period size: 80 Copynumber: 2.8 Consensus size: 80
54792662 TTGAATGATG
* * * * *
54792672 TCTGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCTGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
54792735 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAT
* * *
54792752 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGGAGGCATT
1 TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
54792815 TGTGCGAGTTACTAAAT
65 TGTGCGAGATACT-AAT
* *
54792832 T-TGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
54792896 G
66 G
54792897 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 2 0.02
79 52 0.42
80 69 0.55
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAT
Found at i:54813238 original size:11 final size:11
Alignment explanation
Indices: 54813222--54813268 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
54813212 GACCACGGAA
54813222 GAAAGGAAAAT
1 GAAAGGAAAAT
*
54813233 GAAAGGAAACT
1 GAAAGGAAAAT
*
54813244 AGAAAGGAAAAA
1 -GAAAGGAAAAT
*
54813256 GAGA-GAAAAT
1 GAAAGGAAAAT
54813266 GAA
1 GAA
54813269 TGAGAGAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
10 7 0.24
11 13 0.45
12 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.28, T:0.06
Consensus pattern (11 bp):
GAAAGGAAAAT
Found at i:54813250 original size:12 final size:12
Alignment explanation
Indices: 54813221--54813254 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
54813211 AGACCACGGA
54813221 AGAAAGGAAAAT
1 AGAAAGGAAAAT
*
54813233 -GAAAGGAAACT
1 AGAAAGGAAAAT
54813244 AGAAAGGAAAA
1 AGAAAGGAAAA
54813255 AGAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.65, C:0.03, G:0.26, T:0.06
Consensus pattern (12 bp):
AGAAAGGAAAAT
Found at i:54814898 original size:9 final size:9
Alignment explanation
Indices: 54814884--54814909 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54814874 AAATAGGGTT
54814884 TTTTAAGGA
1 TTTTAAGGA
54814893 TTTTAAGGA
1 TTTTAAGGA
54814902 TTTTAAGG
1 TTTTAAGG
54814910 GTTTAGGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (9 bp):
TTTTAAGGA
Found at i:54817719 original size:40 final size:39
Alignment explanation
Indices: 54817649--54817820 Score: 202
Period size: 40 Copynumber: 4.3 Consensus size: 39
54817639 GTCTGCAAAT
* *
54817649 CTGGTGACTTGTCCACAATATTGGCAGTTTATCTCCATTA
1 CTGGTGGCTTGTCCAC-ATTTTGGCAGTTTATCTCCATTA
* * *
54817689 CTAGTGGCTTGTCCACATTTCTGGCGGTTTATCTACATTA
1 CTGGTGGCTTGTCCACATTT-TGGCAGTTTATCTCCATTA
* * * *
54817729 CTGGTGGCTTGTCCACATTATTAGCAGCTTGTCTGCAATT-
1 CTGGTGGCTTGTCCACATT-TTGGCAGTTTATCT-CCATTA
*
54817769 CTGGTGGTTTGTCCACATTTTTGGCAGTTTATCTCCATTA
1 CTGGTGGCTTGTCCACA-TTTTGGCAGTTTATCTCCATTA
54817809 CTGGTGGCTTGT
1 CTGGTGGCTTGT
54817821 TCGCAAAATA
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 7 0.06
40 96 0.88
41 6 0.06
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (39 bp):
CTGGTGGCTTGTCCACATTTTGGCAGTTTATCTCCATTA
Found at i:54817746 original size:20 final size:20
Alignment explanation
Indices: 54817684--54817787 Score: 77
Period size: 20 Copynumber: 5.2 Consensus size: 20
54817674 AGTTTATCTC
*
54817684 CATTACTAGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCCA
* * * * *
54817704 CATTTCTGGCGGTTTATCTA
1 CATTACTGGTGGCTTGTCCA
54817724 CATTACTGGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCCA
* * **
54817744 CATTATTAGCAGCTTGTCTGCA
1 CATTACTGGTGGCTTGTC--CA
*
54817766 -ATT-CTGGTGGTTTGTCCA
1 CATTACTGGTGGCTTGTCCA
54817784 CATT
1 CATT
54817788 TTTGGCAGTT
Statistics
Matches: 61, Mismatches: 20, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 51 0.84
21 3 0.05
22 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (20 bp):
CATTACTGGTGGCTTGTCCA
Found at i:54817799 original size:80 final size:80
Alignment explanation
Indices: 54817649--54817820 Score: 229
Period size: 80 Copynumber: 2.1 Consensus size: 80
54817639 GTCTGCAAAT
* * * *
54817649 CTGGTGACTTGTCCACAATATTGGCAGTTTATCTCCATTACTAGTGGCTTGTCCACATTTCTGGC
1 CTGGTGGCTTGTCCACAATATTAGCAGCTTATCTCAATTACTAGTGGCTTGTCCACATTTCTGGC
*
54817714 GGTTTATCTACATTA
66 AGTTTATCTACATTA
* * * * *
54817729 CTGGTGGCTTGTCCACATTATTAGCAGCTTGTCTGCAATT-CTGGTGGTTTGTCCACATTTTTGG
1 CTGGTGGCTTGTCCACAATATTAGCAGCTTATCT-CAATTACTAGTGGCTTGTCCACATTTCTGG
*
54817793 CAGTTTATCTCCATTA
65 CAGTTTATCTACATTA
54817809 CTGGTGGCTTGT
1 CTGGTGGCTTGT
54817821 TCGCAAAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 76 0.95
81 4 0.05
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (80 bp):
CTGGTGGCTTGTCCACAATATTAGCAGCTTATCTCAATTACTAGTGGCTTGTCCACATTTCTGGC
AGTTTATCTACATTA
Found at i:54825475 original size:56 final size:56
Alignment explanation
Indices: 54825389--54825497 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
54825379 ATCTTCATTG
54825389 CTGCTGTCTATGATCTTTTCTTCTCTTGGATGGACAGCAATGGTTAAAGAAATTTC
1 CTGCTGTCTATGATCTTTTCTTCTCTTGGATGGACAGCAATGGTTAAAGAAATTTC
*
54825445 CTGCTGTCTATGATTTTTTCTTCTCTTGGATGGACAGCAATGGTTAAAGAAAT
1 CTGCTGTCTATGATCTTTTCTTCTCTTGGATGGACAGCAATGGTTAAAGAAAT
54825498 GGCCCCAGAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (56 bp):
CTGCTGTCTATGATCTTTTCTTCTCTTGGATGGACAGCAATGGTTAAAGAAATTTC
Found at i:54826489 original size:29 final size:29
Alignment explanation
Indices: 54826445--54826510 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
54826435 ATTTGACCTT
* *
54826445 ATTGATTCTTTTTAATAATATAGAGACTAA
1 ATTGA-TCTATTTAATAATAGAGAGACTAA
* *
54826475 ATTGATCTATTTAATAATGGAGGGACTAA
1 ATTGATCTATTTAATAATAGAGAGACTAA
*
54826504 TTTGATC
1 ATTGATC
54826511 CGGTCTCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (29 bp):
ATTGATCTATTTAATAATAGAGAGACTAA
Found at i:54833786 original size:25 final size:25
Alignment explanation
Indices: 54833752--54833803 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
54833742 GGACAAGGTT
54833752 TAATCTTACAACTTCTTAAGATTTC
1 TAATCTTACAACTTCTTAAGATTTC
54833777 TAATCTTACAACTTCTTAAGATTTC
1 TAATCTTACAACTTCTTAAGATTTC
54833802 TA
1 TA
54833804 CCCCAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (25 bp):
TAATCTTACAACTTCTTAAGATTTC
Found at i:54836733 original size:20 final size:20
Alignment explanation
Indices: 54836699--54836751 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
54836689 AAGCCCCATG
**
54836699 GTATCGATA-TTTTACACGA
1 GTATCGATATTTTTACAAAA
54836718 GTATCGATATTTTTACAAAA
1 GTATCGATATTTTTACAAAA
*
54836738 GTACCGATATTTTT
1 GTATCGATATTTTT
54836752 TAGTTGGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATATTTTTACAAAA
Found at i:54869724 original size:11 final size:11
Alignment explanation
Indices: 54869710--54869736 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
54869700 TTTTTTTAAC
54869710 TTTTTATAAAT
1 TTTTTATAAAT
54869721 TTTTTATAAAT
1 TTTTTATAAAT
54869732 TTTTT
1 TTTTT
54869737 GAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTATAAAT
Found at i:54876210 original size:66 final size:65
Alignment explanation
Indices: 54876121--54876287 Score: 176
Period size: 66 Copynumber: 2.6 Consensus size: 65
54876111 ATCCATGTTA
* * * * *
54876121 AAAAAGAAATGGTGTGGCT-AATTCACTAGGGAAGTTCATTCGTTACACCAAGATTAATTCATAC
1 AAAAAGAAATGGTGTAG-TGAATTCACTAAGGAAGTTCATCCGCTACACCAAGATTAATCCATAC
54876185 C
65 C
* * * *
54876186 AAACAAGAAATGGTGTAGTGAATTCACAAAGGAAGTTCATCCGCTACATCAGGATTAATCCATGC
1 AAA-AAGAAATGGTGTAGTGAATTCACTAAGGAAGTTCATCCGCTACACCAAGATTAATCCATAC
54876251 C
65 C
* * * *
54876252 AAAAA-AAAGTGATGTAGCGAATTTACTAAAGAAGTT
1 AAAAAGAAA-TGGTGTAGTGAATTCACTAAGGAAGTT
54876288 AATATGATAA
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
64 3 0.04
65 28 0.33
66 54 0.64
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (65 bp):
AAAAAGAAATGGTGTAGTGAATTCACTAAGGAAGTTCATCCGCTACACCAAGATTAATCCATACC
Found at i:54876500 original size:130 final size:125
Alignment explanation
Indices: 54876190--54876544 Score: 311
Period size: 130 Copynumber: 2.8 Consensus size: 125
54876180 CATACCAAAC
* * *
54876190 AAGAAATGGTGTAGTGAATTCACAAAGGAAGTTCATCCGCTACATCAGGATTAATCCATGCCAAA
1 AAGAAATGGTGTAGTGAATTCACAAAGGAAGCTCATCCGCTACATCGGGATTAATCTATGCCAAA
* * *
54876255 AA-AAAGTGATGTAGCGAATTTACTAAAGAAGTTAATATGATAAACTAGAGTGATCCATGTTA
66 AAGAAA--GATGTAGC-AATTTACTAAAGAAGTTAATACGATAAACTAGAGTGAACCATGTAA
* * * * * * * * *
54876317 AAGAAACGATATAGTGAATTCACTAAGGAAGCCCATTCGTTACATTGGTATTAATCTATGCCAAA
1 AAGAAATGGTGTAGTGAATTCACAAAGGAAGCTCATCCGCTACATCGGGATTAATCTATGCCAAA
** * * * * * *
54876382 GAAGAAACGATGTAGCAAATTTACTATGGACGTTCATCCGATACA-TCGGGTGAACCATGTAAAA
66 -AAGAAA-GATGTAGC-AATTTACTAAAGAAGTTAATACGATAAACTAGAGTGAACCATGT--AA
** * * *
54876446 GAAGAAATGGTGTAGAAAATTCAAAAAGGAAGCTCATCCGCTACACCGGGATTAAT-TCATGCAA
1 -AAGAAATGGTGTAGTGAATTCACAAAGGAAGCTCATCCGCTACATCGGGATTAATCT-ATGC-C
*
54876510 AAAAAGAAAGAATGTAGCAATTTCACTAAGGAAGT
63 AAAAAGAAAG-ATGTAGCAATTT-ACTAAAGAAGT
54876545 ACATGTAATG
Statistics
Matches: 178, Mismatches: 41, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
127 65 0.37
128 31 0.17
129 11 0.06
130 68 0.38
131 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (125 bp):
AAGAAATGGTGTAGTGAATTCACAAAGGAAGCTCATCCGCTACATCGGGATTAATCTATGCCAAA
AAGAAAGATGTAGCAATTTACTAAAGAAGTTAATACGATAAACTAGAGTGAACCATGTAA
Found at i:54879409 original size:22 final size:22
Alignment explanation
Indices: 54879372--54879414 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
54879362 TTATCAAGAT
54879372 AAATATTAGATTAAATTTAATATA
1 AAATATTA-ATTAAA-TTAATATA
54879396 AAATATT-ATTAAATTAATA
1 AAATATTAATTAAATTAATA
54879415 GAATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
24 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATTAATTAAATTAATATA
Found at i:54879451 original size:62 final size:59
Alignment explanation
Indices: 54879343--54879456 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 59
54879333 ATCACTTTAA
* * *
54879343 TATTAAATTAATATAATAGTTATCAAGATAAATATTAGATTAAATTTAATATAAAATAT
1 TATTAAATTAATAGAATAGTTATCAAGATAAACATTAAATTAAATTTAATATAAAATAT
*
54879402 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATAT
1 TATTAAATTAATAGAATAGTTA--T-CAAGATAAACATTAAATTAAATTTAATAT
54879457 TAAGACAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
59 20 0.42
61 1 0.02
62 27 0.56
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (59 bp):
TATTAAATTAATAGAATAGTTATCAAGATAAACATTAAATTAAATTTAATATAAAATAT
Found at i:54879498 original size:25 final size:26
Alignment explanation
Indices: 54879450--54879498 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
54879440 TAAATTAAAT
*
54879450 TTAATATTAAGACAATTACTTTAACA
1 TTAATATTAAGACAAATACTTTAACA
54879476 TTAA-ATTAAGA-AAATACTATTAA
1 TTAATATTAAGACAAATACT-TTAA
54879499 GATAAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (26 bp):
TTAATATTAAGACAAATACTTTAACA
Found at i:54881331 original size:7 final size:8
Alignment explanation
Indices: 54881310--54881339 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
54881300 AATATGAAAG
54881310 ACAAAAAT
1 ACAAAAAT
54881318 ACAAAAAT
1 ACAAAAAT
54881326 ACAAAAAT
1 ACAAAAAT
54881334 ACAAAA
1 ACAAAA
54881340 GACATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (8 bp):
ACAAAAAT
Found at i:54886116 original size:3 final size:3
Alignment explanation
Indices: 54886108--54886951 Score: 1688
Period size: 3 Copynumber: 281.3 Consensus size: 3
54886098 AATTACTTGG
54886108 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886156 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886204 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886252 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886300 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886348 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886396 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886444 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886492 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886540 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886588 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886636 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886684 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886732 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886780 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886828 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886876 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54886924 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54886952 ATTCAATATC
Statistics
Matches: 841, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 841 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:54894775 original size:62 final size:62
Alignment explanation
Indices: 54894642--54894982 Score: 628
Period size: 62 Copynumber: 5.5 Consensus size: 62
54894632 AAAGTAGTAG
*
54894642 TAAGCAGATAAGGAGGAATCTGCTTTTTCAAACATAAAGGACATGACTCATACATAAAGGACA
1 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACAT-AAGGACATGACTCATACATAAAGGACA
*
54894705 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCGTACATAAAGGACA
1 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
*
54894767 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCGTACATAAAGGACA
1 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
*
54894829 TAAGCAGATAAGGAGGAATATGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
1 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
*
54894891 TAAGCAGATAAGAAGGAATCTGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
1 TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
54894953 TAAGCAGATAAGGAGGAATCTGCTTTTACA
1 TAAGCAGATAAGGAGGAATCTGCTTTTACA
54894983 TTAATTTATC
Statistics
Matches: 271, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
62 237 0.87
63 34 0.13
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (62 bp):
TAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAGGACATGACTCATACATAAAGGACA
Found at i:54902337 original size:47 final size:47
Alignment explanation
Indices: 54902274--54903404 Score: 1976
Period size: 47 Copynumber: 24.1 Consensus size: 47
54902264 GAAATGATAG
*
54902274 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
54902321 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
54902368 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
54902415 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
54902462 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902509 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902556 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902603 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902650 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902697 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902744 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902791 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902838 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902885 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902932 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54902979 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54903026 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54903073 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54903120 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54903167 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
54903214 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54903261 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54903308 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
54903354 CAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
54903401 TAAG
1 TAAG
54903405 TCCCGAAGGG
Statistics
Matches: 1035, Mismatches: 48, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
46 40 0.04
47 995 0.96
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:54903579 original size:37 final size:37
Alignment explanation
Indices: 54903523--54903601 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
54903513 CCGAGCTCTA
* * * *
54903523 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
*
54903560 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGAGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
54903597 AAGAC
1 AAGAC
54903602 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
Found at i:54911586 original size:29 final size:29
Alignment explanation
Indices: 54911523--54911590 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
54911513 TAATCAACCG
54911523 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
54911552 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
54911581 CGCACACTTA
1 CGCACACTTA
54911591 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:54911703 original size:174 final size:174
Alignment explanation
Indices: 54911412--54911739 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
54911402 AACTCAAGGT
* *
54911412 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
54911477 GAAAATATATATTGGGTTCGTACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
54911542 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
54911586 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
54911651 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
54911716 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
54911740 TGTACAATTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:54911731 original size:29 final size:29
Alignment explanation
Indices: 54911697--54911770 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
54911687 TAATCAACCA
54911697 CGCACACTTAGTGCCATGTAC-TTTAAAC
1 CGCACACTTAGTGCCATGTACATTTAAAC
54911725 TCGCACACTTAGTG-C-TGTACAATTTAAAC
1 -CGCACACTTAGTGCCATGTAC-ATTTAAAC
54911754 CTGCACACTTAGTGCCA
1 C-GCACACTTAGTGCCA
54911771 ATCTCATGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.12
28 2 0.05
29 32 0.80
30 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGTACATTTAAAC
Found at i:54915449 original size:47 final size:47
Alignment explanation
Indices: 54915386--54915764 Score: 598
Period size: 47 Copynumber: 8.1 Consensus size: 47
54915376 GAAATGATAG
*
54915386 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
54915433 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
54915480 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54915527 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
54915574 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54915621 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
54915668 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
54915714 CAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
54915761 TAAG
1 TAAG
54915765 TCCCGAAGGG
Statistics
Matches: 311, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 40 0.13
47 271 0.87
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:54915939 original size:37 final size:37
Alignment explanation
Indices: 54915883--54915961 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
54915873 CCGAGCTCTA
* * * *
54915883 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
*
54915920 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGAGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
54915957 AAGAC
1 AAGAC
54915962 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGAGT
Found at i:54930239 original size:32 final size:32
Alignment explanation
Indices: 54930203--54930265 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
54930193 TATGGCTTTT
54930203 ATATTATTATTGGATGTAATTATAATATTATA
1 ATATTATTATTGGATGTAATTATAATATTATA
54930235 ATATTATTATTGGATGTAATTATAATATTAT
1 ATATTATTATTGGATGTAATTATAATATTAT
54930266 TCTATCTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (32 bp):
ATATTATTATTGGATGTAATTATAATATTATA
Found at i:54932624 original size:16 final size:16
Alignment explanation
Indices: 54932603--54932638 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
54932593 TTTTACATAA
*
54932603 ATATAAATATTTGTTT
1 ATATAAATATTTGCTT
54932619 ATATAAATATTTGCTT
1 ATATAAATATTTGCTT
54932635 ATAT
1 ATAT
54932639 TAATTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATAAATATTTGCTT
Found at i:54932669 original size:16 final size:16
Alignment explanation
Indices: 54932648--54932678 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54932638 TTAATTTGTT
54932648 TTATTTATATATATAA
1 TTATTTATATATATAA
*
54932664 TTATTTATATTTATA
1 TTATTTATATATATA
54932679 TTGTTCACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTATATATATAA
Found at i:54932931 original size:82 final size:84
Alignment explanation
Indices: 54932814--54933180 Score: 302
Period size: 82 Copynumber: 4.4 Consensus size: 84
54932804 AAATAAAATC
* * *
54932814 TGTTTCGGGATTTATTCCTGCCATTCAACAGATTTTATTC-ATTTTTTGA-TTTGTTCCCAAATA
1 TGTTTCGGGATTTATTCCCGCCATTCAACAGATTTTATTCGATTTTTTGATTTTGTTTCCAAACA
54932877 AGAATTAAATTGAATAA-TA
66 AGAATT-AATTGAATAATTA
* * * *
54932896 TGTTTCGGGATTTATTCCCGTCGTTTAACATATTTTATT---TTATTTTGATTTTGTTTCCAAAC
1 TGTTTCGGGATTTATTCCCGCCATTCAACAGATTTTATTCGATT-TTTTGATTTTGTTTCCAAAC
** * *
54932958 GTGAAATAATTGAATAATTC
65 AAGAATTAATTGAATAATTA
* * * * *
54932978 TATTTCAGGATTCATTCCCGCCATTCAACAGATTTTATTCGA--TTGTGATTTTGTTTCTAAACA
1 TGTTTCGGGATTTATTCCCGCCATTCAACAGATTTTATTCGATTTTTTGATTTTGTTTCCAAACA
* * *
54933041 ATGATTTAATTAAATAATTT
66 A-GAATTAATTGAATAATTA
* * * * * * *
54933061 TGTTTCGGGATTTATTCCCACCGTTTAACATATTTAATTCGATTTTGATTTTGATTTTTTTTGCA
1 TGTTTCGGGATTTATTCCCGCCATTCAACAGATTTTATTCGA--TT--TTTTGATTTTGTTTCCA
* *
54933126 AACGAAGATTTAATTAAATAATT-
62 AAC-AAGAATTAATTGAATAATTA
* * * * *
54933149 TTTTTCGGGATTTAATCCTGCCGTTCAGCAGA
1 TGTTTCGGGATTTATTCCCGCCATTCAACAGA
54933181 ATTGATTTTG
Statistics
Matches: 226, Mismatches: 45, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
80 2 0.01
81 16 0.07
82 100 0.44
83 48 0.21
88 25 0.11
89 33 0.15
90 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.46
Consensus pattern (84 bp):
TGTTTCGGGATTTATTCCCGCCATTCAACAGATTTTATTCGATTTTTTGATTTTGTTTCCAAACA
AGAATTAATTGAATAATTA
Found at i:54933007 original size:164 final size:165
Alignment explanation
Indices: 54932816--54933113 Score: 406
Period size: 164 Copynumber: 1.8 Consensus size: 165
54932806 ATAAAATCTG
* * * * *
54932816 TTTCGGGATTTATTCCTGCCATTCAACAGATTTTATTC-ATTTTTTGA-TTTGTTCCCAAATAA-
1 TTTCAGGATTCATTCCCGCCATTCAACAGATTTTATTCGA--TTGTGATTTTGTTCCCAAACAAT
* ** * **
54932878 GAATTAAATTGAATAA-TATGTTTCGGGATTTATTCCCGTCGTTTAACATATTTTATTTTATTTT
64 G-ATTAAATTAAATAATTATGTTTCGGGATTTATTCCCACCGTTTAACATATTTAATTCGATTTT
54932942 GATTTTGTTTCCAAACGTGAAATAATTGAATAATTCTA
128 GATTTTGTTTCCAAACGTGAAATAATTGAATAATTCTA
* *
54932980 TTTCAGGATTCATTCCCGCCATTCAACAGATTTTATTCGATTGTGATTTTGTTTCTAAACAATGA
1 TTTCAGGATTCATTCCCGCCATTCAACAGATTTTATTCGATTGTGATTTTGTTCCCAAACAATGA
* *
54933045 TTTAATTAAATAATTTTGTTTCGGGATTTATTCCCACCGTTTAACATATTTAATTCGATTTTGAT
66 TTAAATTAAATAATTATGTTTCGGGATTTATTCCCACCGTTTAACATATTTAATTCGATTTTGAT
54933110 TTTG
131 TTTG
54933114 ATTTTTTTTG
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
163 5 0.04
164 59 0.51
165 51 0.44
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (165 bp):
TTTCAGGATTCATTCCCGCCATTCAACAGATTTTATTCGATTGTGATTTTGTTCCCAAACAATGA
TTAAATTAAATAATTATGTTTCGGGATTTATTCCCACCGTTTAACATATTTAATTCGATTTTGAT
TTTGTTTCCAAACGTGAAATAATTGAATAATTCTA
Found at i:54933194 original size:89 final size:89
Alignment explanation
Indices: 54933018--54933196 Score: 211
Period size: 89 Copynumber: 2.0 Consensus size: 89
54933008 GATTTTATTC
*
54933018 GATTGTGATTTTGTTTCTAAACAATGATTTAATTAAATAATTTTGTTTCGGGATTTATTCCCACC
1 GATTGTGATTTTGTTTCTAAACAATGATTTAATTAAATAATTTTGTTTCGGGATTTAATCCCACC
* * *
54933083 GTTTAACATATTTAATTCGATTTT
66 GTTCAACAAATTGAATTCGATTTT
* * **
54933107 GATTTTGATTTTTTTTGC-AAACGAA-GATTTAATTAAATAATTTT-TTTCGGGATTTAATCCTG
1 GATTGTGATTTTGTTT-CTAAAC-AATGATTTAATTAAATAATTTTGTTTCGGGATTTAATCCCA
* * *
54933169 CCGTTCAGCAGAATTGATTTTGATTTT
64 CCGTTCAACA-AATTGAATTCGATTTT
54933196 G
1 G
54933197 TTTCAGAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
88 23 0.30
89 50 0.66
90 3 0.04
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (89 bp):
GATTGTGATTTTGTTTCTAAACAATGATTTAATTAAATAATTTTGTTTCGGGATTTAATCCCACC
GTTCAACAAATTGAATTCGATTTT
Found at i:54938241 original size:22 final size:24
Alignment explanation
Indices: 54938199--54938245 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
54938189 ATTTTTTATT
54938199 TAAATATTGTGTTTTACATAAATA
1 TAAATATTGTGTTTTACATAAATA
*
54938223 TAAATATT-TG-TTTATATAAATA
1 TAAATATTGTGTTTTACATAAATA
54938245 T
1 T
54938246 TTACTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.55
23 2 0.09
24 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
TAAATATTGTGTTTTACATAAATA
Found at i:54938253 original size:16 final size:16
Alignment explanation
Indices: 54938220--54938255 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54938210 TTTTACATAA
**
54938220 ATATAAATATTTGTTT
1 ATATAAATATTTACTT
54938236 ATATAAATATTTACTT
1 ATATAAATATTTACTT
54938252 ATAT
1 ATAT
54938256 TAATTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATAAATATTTACTT
Found at i:54938269 original size:6 final size:6
Alignment explanation
Indices: 54938250--54938293 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
54938240 AAATATTTAC
54938250 TTATA- TTA-AT TTATAT TTATAT TTATAT TTATAT TTATAT TTAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTAT
54938294 TTGCTAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
4 1 0.03
5 6 0.16
6 30 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTATAT
Found at i:54939720 original size:9 final size:9
Alignment explanation
Indices: 54939706--54939769 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
54939696 GAAATTATAA
54939706 AAAAATTAT
1 AAAAATTAT
*
54939715 AAAAATTACA
1 AAAAATTA-T
*
54939725 AAGAAATCAT
1 AA-AAATTAT
*
54939735 TAAAATTAT
1 AAAAATTAT
54939744 -AAAATTAT
1 AAAAATTAT
*
54939752 TAAAATT-T
1 AAAAATTAT
54939760 ATAAAATTAT
1 A-AAAATTAT
54939770 TAGAAAGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 9 0.20
9 26 0.59
10 4 0.09
11 5 0.11
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54939722 original size:20 final size:20
Alignment explanation
Indices: 54939697--54939747 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
54939687 GTTTATTATG
*
54939697 AAATTATAAAAAAATTATAA
1 AAATTATAAAAAAATCATAA
* * *
54939717 AAATTACAAAGAAATCATTA
1 AAATTATAAAAAAATCATAA
54939737 AAATTATAAAA
1 AAATTATAAAA
54939748 TTATTAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATTATAAAAAAATCATAA
Found at i:54939748 original size:8 final size:8
Alignment explanation
Indices: 54939735--54939769 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
54939725 AAGAAATCAT
54939735 TAAAATTA
1 TAAAATTA
54939743 TAAAATTA
1 TAAAATTA
54939751 TTAAAATTTA
1 -TAAAA-TTA
54939761 TAAAATTA
1 TAAAATTA
54939769 T
1 T
54939770 TAGAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 12 0.48
9 10 0.40
10 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TAAAATTA
Found at i:54939763 original size:18 final size:17
Alignment explanation
Indices: 54939728--54939771 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
54939718 AATTACAAAG
*
54939728 AAATCATTAAAATTATA
1 AAATTATTAAAATTATA
54939745 AAATTATTAAAATTTATA
1 AAATTATTAAAA-TTATA
54939763 AAATTATTA
1 AAATTATTA
54939772 GAAAGTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTATTAAAATTATA
Found at i:54943838 original size:20 final size:21
Alignment explanation
Indices: 54943791--54943841 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
54943781 ATAAAGTTTT
54943791 GGTATCGATAAAATTTTAATA
1 GGTATCGATAAAATTTTAATA
* * *
54943812 AGTATCGATATAATTTTCA-A
1 GGTATCGATAAAATTTTAATA
54943832 GGTATCGATA
1 GGTATCGATA
54943842 CTTATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
GGTATCGATAAAATTTTAATA
Found at i:54948732 original size:18 final size:18
Alignment explanation
Indices: 54948701--54948737 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54948691 ACAAACAAAA
* *
54948701 ATAAACACAGAAATAAAC
1 ATAAAAACAAAAATAAAC
54948719 ATAAAAACAAAAATAAAC
1 ATAAAAACAAAAATAAAC
54948737 A
1 A
54948738 CACATAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.14, G:0.03, T:0.11
Consensus pattern (18 bp):
ATAAAAACAAAAATAAAC
Found at i:54953141 original size:16 final size:16
Alignment explanation
Indices: 54953120--54953161 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
54953110 GAATTTAGAA
54953120 GAATTTTTGAATTAGT
1 GAATTTTTGAATTAGT
* *
54953136 GAATTTTGCGATTTAGT
1 GAATTTT-TGAATTAGT
54953153 GAATTTTTG
1 GAATTTTTG
54953162 CGATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.50
Consensus pattern (16 bp):
GAATTTTTGAATTAGT
Found at i:54953151 original size:17 final size:18
Alignment explanation
Indices: 54953131--54953168 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
54953121 AATTTTTGAA
54953131 TTAGTGAA-TTTTGCGAT
1 TTAGTGAATTTTTGCGAT
54953148 TTAGTGAATTTTTGCGAT
1 TTAGTGAATTTTTGCGAT
54953166 TTA
1 TTA
54953169 AAAAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (18 bp):
TTAGTGAATTTTTGCGAT
Found at i:54954460 original size:46 final size:46
Alignment explanation
Indices: 54954389--54954573 Score: 291
Period size: 46 Copynumber: 4.0 Consensus size: 46
54954379 CATGGCAAAG
*
54954389 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGATTCGGTGAAGAAAACCATACTGAGT
54954435 TGTGAAAAGTAGGTATGGTGATTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGATTCGGTGAAGAAAACCATACTGAGT
* * *
54954481 TATGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGATTCGGTGAAGAAAACCATACTGAGT
* * *
54954527 TGTGAAAACTAGGTATGGT-ATTTCCGTGAAGAAAGCCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGA-TTCGGTGAAGAAAACCATACTGAGT
54954573 T
1 T
54954574 ATAGCAATGT
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGATTCGGTGAAGAAAACCATACTGAGT
Found at i:54956636 original size:29 final size:29
Alignment explanation
Indices: 54956599--54956707 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 29
54956589 CAATCAGAGA
*
54956599 TAGATAGCCAGTAAGGCATCCACGGATAG
1 TAGATAGCCAGTAAGACATCCACGGATAG
* * ** *
54956628 TAGATAGCCAATAAGGCATCCATAGATAA
1 TAGATAGCCAGTAAGACATCCACGGATAG
** ** *
54956657 TAGATAGTAAGTAAGATGTCCACGAAT-G
1 TAGATAGCCAGTAAGACATCCACGGATAG
*
54956685 ATAGATAGCTAGTAAGACATCCA
1 -TAGATAGCCAGTAAGACATCCA
54956708 TTCACAAATA
Statistics
Matches: 61, Mismatches: 18, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (29 bp):
TAGATAGCCAGTAAGACATCCACGGATAG
Found at i:54956922 original size:26 final size:26
Alignment explanation
Indices: 54956893--54956978 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
54956883 GCCACAGAGG
*
54956893 CTCTTTAATAGAATCAGCTAAAAAAA
1 CTCTTTAATAGAATCAGCCAAAAAAA
* * * **
54956919 CTCTTTAATAGGATTAGCCAGAAAGG
1 CTCTTTAATAGAATCAGCCAAAAAAA
* * **
54956945 CTCTTTAATAGAATAAGCCACAAAGG
1 CTCTTTAATAGAATCAGCCAAAAAAA
54956971 CTCTTTAA
1 CTCTTTAA
54956979 CAGGAAATGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (26 bp):
CTCTTTAATAGAATCAGCCAAAAAAA
Found at i:54956975 original size:52 final size:52
Alignment explanation
Indices: 54956880--54956983 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
54956870 TATAACATAG
* * * *
54956880 TTAGCCACAGAGGCTCTTTAATAGAATCAGCTAAAAAAACTCTTTAATAGGA
1 TTAGCCACAAAGGCTCTTTAATAGAATAAGCCAAAAAAACTCTTTAACAGGA
* * **
54956932 TTAGCCAGAAAGGCTCTTTAATAGAATAAGCCACAAAGGCTCTTTAACAGGA
1 TTAGCCACAAAGGCTCTTTAATAGAATAAGCCAAAAAAACTCTTTAACAGGA
54956984 AATGGTGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (52 bp):
TTAGCCACAAAGGCTCTTTAATAGAATAAGCCAAAAAAACTCTTTAACAGGA
Found at i:54960129 original size:26 final size:26
Alignment explanation
Indices: 54960077--54960170 Score: 125
Period size: 26 Copynumber: 3.6 Consensus size: 26
54960067 ACACTATTTC
* * * *
54960077 CTATTAAATAGCCTTTGTGGCTAATT
1 CTATTAAAGAGCCTTTGTTGTTGATT
* *
54960103 CTGTCAAAGAGCCTTTGTTGTTGATT
1 CTATTAAAGAGCCTTTGTTGTTGATT
54960129 CTATTAAAGAGCCTTTGTTGTTGATT
1 CTATTAAAGAGCCTTTGTTGTTGATT
*
54960155 CTATTAAAAAGCCTTT
1 CTATTAAAGAGCCTTT
54960171 ATGACTAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (26 bp):
CTATTAAAGAGCCTTTGTTGTTGATT
Found at i:54966527 original size:18 final size:18
Alignment explanation
Indices: 54966504--54966538 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54966494 CAAAAGTAGT
*
54966504 AAGCATCAAAATAGTTTC
1 AAGCATAAAAATAGTTTC
54966522 AAGCATAAAAATAGTTT
1 AAGCATAAAAATAGTTT
54966539 GGAGCGTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
AAGCATAAAAATAGTTTC
Found at i:54971310 original size:34 final size:35
Alignment explanation
Indices: 54971266--54971332 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
54971256 CAGTAAAATA
54971266 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
54971300 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
54971333 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Done.