Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 24 of 214
Found at i:6730771 original size:56 final size:56
Alignment explanation
Indices: 6730708--6730821 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
6730698 GACAAAAAGG
*
6730708 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGATGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
6730764 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
6730820 AA
1 AA
6730822 GAAGCATAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (56 bp):
AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
Found at i:6733015 original size:16 final size:16
Alignment explanation
Indices: 6732976--6733040 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
6732966 CGTTTGGTTC
*
6732976 ATTGTAATGGAATAGG
1 ATTGTAATGGAATAGA
* * *
6732992 ACTATAATGTAATAGA
1 ATTGTAATGGAATAGA
*
6733008 ATTGTAATGGAATACA
1 ATTGTAATGGAATAGA
** *
6733024 GCTGTAATAGAATAGA
1 ATTGTAATGGAATAGA
6733040 A
1 A
6733041 CTTTAATAAG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (16 bp):
ATTGTAATGGAATAGA
Found at i:6733244 original size:26 final size:24
Alignment explanation
Indices: 6733201--6733264 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
6733191 TAATTATTGT
* *
6733201 TATTAAAT--TTTAATAAAATTAT
1 TATTAAATAATTTAATAAAAATAA
6733223 TATTAAATATAATTTAATAAAAATAA
1 TATT-AA-ATAATTTAATAAAAATAA
6733249 TATTAAATAATTTAAT
1 TATTAAATAATTTAAT
6733265 CATGTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.11
23 2 0.06
24 12 0.33
25 2 0.06
26 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTAAATAATTTAATAAAAATAA
Found at i:6733908 original size:5 final size:5
Alignment explanation
Indices: 6733898--6733922 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6733888 CGGATTTATT
6733898 TGTGA TGTGA TGTGA TGTGA TGTGA
1 TGTGA TGTGA TGTGA TGTGA TGTGA
6733923 GTAGCATGTT
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:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGTGA
Found at i:6734152 original size:16 final size:16
Alignment explanation
Indices: 6734131--6734172 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6734121 TTCGCTGTAT
6734131 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
6734147 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
*
6734163 TGAAATAGAG
1 TGGAATAGAG
6734173 TGTAATAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:6734177 original size:15 final size:16
Alignment explanation
Indices: 6734134--6734178 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
6734124 GCTGTATTGG
* *
6734134 AATAGAGGCGTAATGG
1 AATAGAGGTGTAATGA
6734150 AATAGAGGTGTAATGA
1 AATAGAGGTGTAATGA
6734166 AATAGA-GTGTAAT
1 AATAGAGGTGTAAT
6734179 AGCAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (16 bp):
AATAGAGGTGTAATGA
Found at i:6734425 original size:15 final size:15
Alignment explanation
Indices: 6734401--6734443 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
6734391 TTTAAACATA
*
6734401 ATTATTATTAAATAT
1 ATTATAATTAAATAT
6734416 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
6734430 A-TATAATTATAATA
1 ATTATAATTA-AATA
6734444 AAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 5 0.20
15 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:6734429 original size:16 final size:16
Alignment explanation
Indices: 6734392--6734433 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6734382 TTAATCATAT
*
6734392 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
6734408 TT-AAATATATTATAA
1 TTAAAATATATTATAA
6734423 TTAAAATATAT
1 TTAAAATATAT
6734434 AATTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6734433 original size:18 final size:18
Alignment explanation
Indices: 6734412--6734447 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6734402 TTATTATTAA
6734412 ATAT-ATTATAATTAAAAT
1 ATATAATTATAA-TAAAAT
6734430 ATATAATTATAATAAAAT
1 ATATAATTATAATAAAAT
6734448 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATTATAATAAAAT
Found at i:6734436 original size:13 final size:14
Alignment explanation
Indices: 6734401--6734443 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
6734391 TTTAAACATA
*
6734401 ATTATTATTAAATAT
1 ATTATAATTAAA-AT
6734416 ATTATAATTAAAAT
1 ATTATAATTAAAAT
*
6734430 A-TATAATTATAAT
1 ATTATAATTAAAAT
6734443 A
1 A
6734444 AAATTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAATTAAAAT
Found at i:6734554 original size:59 final size:61
Alignment explanation
Indices: 6734395--6734812 Score: 250
Period size: 59 Copynumber: 7.0 Consensus size: 61
6734385 ATCATATTTA
* * *
6734395 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTA-TAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGA-TACTAATAAAATTATAAATT
* * * * * *
6734455 AATCA-ATATTCTTATATGAATTTACTGA-AATCATAATATATGATACT-ATAAAA-TATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATGATACTAATAAAATTATAAATT
* * * *
6734516 AACATAATTATTATTAAATATATTATAATTAAAATATATAAT-TTAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAATT
* * * * * * *
6734575 AATCA-ATATTCTTATATGAATTTACTAAAATTATAATATATGATACT-ATAAAA-TATAATTT
1 AA-CATA-ATTATTAT-TAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAATT
* *
6734636 GAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGAT-TTAATAAAATTCATAATAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATT-AT-A-AATT
* * * * * * * *
6734699 -A-AT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAA-GATAATTT
1 AACATAATTATTAT-TAAATATA-TTATAATTAAAATATATGATACTAATAAAATTATAAATT
* * *
6734756 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGAT-TTAATAAAATT-TAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAA
6734813 ATAATTATAA
Statistics
Matches: 267, Mismatches: 60, Indels: 63
0.68 0.15 0.16
Matches are distributed among these distances:
57 3 0.01
58 7 0.03
59 91 0.34
60 54 0.20
61 82 0.31
62 25 0.09
63 5 0.02
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (61 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATACTAATAAAATTATAAATT
Found at i:6734561 original size:14 final size:15
Alignment explanation
Indices: 6734512--6734563 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
6734502 ATAAAATATA
6734512 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
6734527 TATTAAATATATTAT
1 AATTAAATATATTAT
6734542 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
6734555 AATTTAATA
1 AATTAAATA
6734564 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:6734674 original size:18 final size:17
Alignment explanation
Indices: 6734651--6734687 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
6734641 AATTATTATT
6734651 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
6734667 AAATATATGATTTAATA
1 AAATATATGATTTAATA
6734684 AAAT
1 AAAT
6734688 TCATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:6734819 original size:120 final size:120
Alignment explanation
Indices: 6734398--6734808 Score: 689
Period size: 120 Copynumber: 3.4 Consensus size: 120
6734388 ATATTTAAAC
6734398 ATAATTATTATTAAATATATTATAATTAAAATATATAATTATAATAAAATTCTTAATAATCAATA
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATT-TAATAAAATTCTTAATAATCAATA
* *
6734463 TTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT-AA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
6734518 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
1 -ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
*
6734583 TTCTTATATGAATTTACTAAAATTATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
6734639 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCATAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
* *
6734704 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * *
6734759 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
6734809 TAAAATAATT
Statistics
Matches: 278, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
120 236 0.85
121 42 0.15
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:6734878 original size:26 final size:28
Alignment explanation
Indices: 6734849--6734909 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6734839 TATGAATTTG
*
6734849 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
6734875 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
6734903 TAAAATT
1 TATAATT
6734910 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:6734985 original size:18 final size:18
Alignment explanation
Indices: 6734958--6734995 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6734948 AAAATAATCA
6734958 AATGAAATATAATTTAAT
1 AATGAAATATAATTTAAT
* *
6734976 AATGATATATAATTTCAT
1 AATGAAATATAATTTAAT
6734994 AA
1 AA
6734996 AATTCTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
AATGAAATATAATTTAAT
Found at i:6735000 original size:90 final size:91
Alignment explanation
Indices: 6734824--6735030 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
6734814 TAATTATAAC
* * * * * * *
6734824 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCATAATGAAATATAATTTAATAAT
*
6734889 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
6734915 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCA-AATGAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCATAATGAAATATAATTTAATAAT
*
6734979 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
6735005 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
6735031 CTAAAATCAA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
90 46 0.44
91 59 0.56
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATCATAATGAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:6735620 original size:14 final size:15
Alignment explanation
Indices: 6735598--6735674 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
6735588 CAATCAAACA
6735598 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
6735612 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
6735627 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
6735647 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
6735661 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
6735675 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:6735639 original size:20 final size:20
Alignment explanation
Indices: 6735614--6735653 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6735604 AATATTTTCC
*
6735614 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
6735634 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
6735654 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:6735659 original size:34 final size:35
Alignment explanation
Indices: 6735602--6735668 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
6735592 CAAACACCAG
*
6735602 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
6735637 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
6735669 TATTTTACTG
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:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:6742335 original size:41 final size:41
Alignment explanation
Indices: 6742276--6742379 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
6742266 TTTAACATAT
* *
6742276 TCACCGGCACTTAGCCTGCTAGGCTAATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
* * *
6742317 TTACCGGCACTTAGCCTGCTAGGTTTACAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
*
6742358 TCACCCGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
6742380 ATTTATGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTAACAACCTGATTCAGA
Found at i:6750102 original size:41 final size:41
Alignment explanation
Indices: 6750045--6750148 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
6750035 TTTAACATAT
* *
6750045 TCACCGGCACTTAGCCTGCTAGGCTTACAGCCTGATTCAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTACAACCTGATTCAGA
* *
6750086 TCACCAGCACTTAGCCTGCTGGGTTTACAACCTGATTCAGA
1 TCACCAGCACTTAGCCTGCTAGGCTTACAACCTGATTCAGA
* *
6750127 TCACCCGCACTTAGCTTGCTAG
1 TCACCAGCACTTAGCCTGCTAG
6750149 ATTTATGGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCAGCACTTAGCCTGCTAGGCTTACAACCTGATTCAGA
Found at i:6753475 original size:18 final size:18
Alignment explanation
Indices: 6753454--6753492 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6753444 GATTGAGAGT
* *
6753454 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
6753472 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
6753490 GAA
1 GAA
6753493 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:6757851 original size:17 final size:17
Alignment explanation
Indices: 6757822--6757864 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
6757812 ATATTATAAT
6757822 ATTATATATTAATTTTGC
1 ATTATA-ATTAATTTTGC
6757840 ATTATAATTAATTTTGC
1 ATTATAATTAATTTTGC
6757857 ATTATAAT
1 ATTATAAT
6757865 AATATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (17 bp):
ATTATAATTAATTTTGC
Found at i:6759095 original size:10 final size:11
Alignment explanation
Indices: 6759069--6759094 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6759059 AAAATCTGTC
6759069 AAAAATAGGAT
1 AAAAATAGGAT
6759080 AAAAATAGGAT
1 AAAAATAGGAT
6759091 AAAA
1 AAAA
6759095 TTCCTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (11 bp):
AAAAATAGGAT
Found at i:6761070 original size:7 final size:7
Alignment explanation
Indices: 6761060--6761118 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
6761050 CCTAAATCTA
*
6761060 TAACTCT
1 TAACCCT
6761067 TAACCCT
1 TAACCCT
6761074 TAA-CCT
1 TAACCCT
6761080 CTAA-CCT
1 -TAACCCT
*
6761087 CTAACCCC
1 -TAACCCT
*
6761095 TAACCCC
1 TAACCCT
6761102 TAACCCT
1 TAACCCT
*
6761109 TAAACCT
1 TAACCCT
6761116 TAA
1 TAA
6761119 ATCCCAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
6 3 0.07
7 41 0.89
8 2 0.04
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (7 bp):
TAACCCT
Found at i:6761084 original size:21 final size:21
Alignment explanation
Indices: 6761042--6761118 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
6761032 GCCCTTGAAT
* * * *
6761042 CTCTAAACCCTAAATCTATAA
1 CTCTTAACCCTTAACCTCTAA
6761063 CTCTTAACCCTTAACCTCTAA
1 CTCTTAACCCTTAACCTCTAA
* *
6761084 C-CTCTAACCCCTAACCCCTAA
1 CTCT-TAACCCTTAACCTCTAA
* *
6761105 CCCTTAAACCTTAA
1 CTCTTAACCCTTAA
6761119 ATCCCAATCC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (21 bp):
CTCTTAACCCTTAACCTCTAA
Found at i:6761136 original size:34 final size:34
Alignment explanation
Indices: 6761093--6761159 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
6761083 ACCTCTAACC
6761093 CCTAACCCCTAACCCT-TAAACCTTAAATCCCAAT
1 CCTAACCCCT-ACCCTCTAAACCTTAAATCCCAAT
*
6761127 CCTAACCCCTAGCCTCTAAACCTTAAATCCCAA
1 CCTAACCCCTACCCTCTAAACCTTAAATCCCAA
6761160 CCCTTAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.22
Consensus pattern (34 bp):
CCTAACCCCTACCCTCTAAACCTTAAATCCCAAT
Found at i:6761636 original size:41 final size:41
Alignment explanation
Indices: 6761579--6761731 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
6761569 AAATGTTTTT
*
6761579 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
* *
6761620 GCGGCGCTTCTCCAAAAACGCCACTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
* *
6761661 GCGGCGCTTCTTCAAAAATGCCGCT--AGGCCAGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
*
6761700 GCGGTGCTTC-CTCAAAAACGCCGCTAAAGGCC
1 GCGGCGCTTCTC-CAAAAACGCCGCTAAAGGCC
6761732 CCAAAAACTC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.34
41 65 0.66
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.17
Consensus pattern (41 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCAGAGCATTA
Found at i:6761716 original size:80 final size:81
Alignment explanation
Indices: 6761579--6761732 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 81
6761569 AAATGTTTTT
6761579 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCAC
1 GCGGCGCTTCTTCAAAAACGCCGCT-AAGGCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCAC
6761644 TAAAGGCCCGAGCATTA
65 TAAAGGCCCGAGCATTA
* * *
6761661 GCGGCGCTTCTTCAAAAATGCCGCT-AGGCCAGAGCATTAGCGGTGCTTC-CTCAAAAACGCCGC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAGGCCAGAGCATTAGCGGCGCTTCTC-CAAAAACGCCAC
6761724 TAAAGGCCC
65 TAAAGGCCC
6761733 CAAAAACTCA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
79 1 0.01
80 43 0.63
82 24 0.35
ACGTcount: A:0.27, C:0.32, G:0.24, T:0.17
Consensus pattern (81 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAGGCCAGAGCATTAGCGGCGCTTCTCCAAAAACGCCACT
AAAGGCCCGAGCATTA
Found at i:6761882 original size:12 final size:12
Alignment explanation
Indices: 6761867--6761892 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6761857 TTTTTTGTCC
6761867 AAACGCCGCTAA
1 AAACGCCGCTAA
6761879 AAACGCCGCTAA
1 AAACGCCGCTAA
6761891 AA
1 AA
6761893 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:6768794 original size:27 final size:27
Alignment explanation
Indices: 6768764--6768818 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6768754 GGATGCTAAG
6768764 TATGATCATTTTGGATAAGTATTTTGC
1 TATGATCATTTTGGATAAGTATTTTGC
*
6768791 TATGATCGTTTTGGATAAGTATTTTGC
1 TATGATCATTTTGGATAAGTATTTTGC
6768818 T
1 T
6768819 TGGTACGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (27 bp):
TATGATCATTTTGGATAAGTATTTTGC
Found at i:6771106 original size:80 final size:80
Alignment explanation
Indices: 6771022--6771177 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 80
6771012 TTGATGTCTC
* ** *
6771022 AAATCTGTATCAAAAAAGGGTGAGAGTTTTTTTTTGGAGTTCCAATGCAATGCCATAAATAACTA
1 AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
6771087 CTCTTGATAATTTCT
66 CTCTTGATAATTTCT
* * *
6771102 AAATCTATATCAAAAACGGGTGAGAACTTTTTTTTGGAGTTCTAATGCAATGCCATCAAGAACTA
1 AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
6771167 CTCTTGATAAT
66 CTCTTGATAAT
6771178 GATGTTTGGA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (80 bp):
AAATCTATATCAAAAAAGGGTGAGAACTTTTTTTTGGAGTTCCAATGCAATGCCATAAAGAACTA
CTCTTGATAATTTCT
Found at i:6771680 original size:14 final size:13
Alignment explanation
Indices: 6771656--6771700 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
6771646 TTTCCTTTGT
*
6771656 TTTTCTGTTTTTC
1 TTTTCTCTTTTTC
6771669 TGTTTCTCTTTTTC
1 T-TTTCTCTTTTTC
6771683 TTTTCCTCTTTATTC
1 TTTT-CTCTTT-TTC
6771698 TTT
1 TTT
6771701 ATTGTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 18 0.64
15 6 0.21
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTCTCTTTTTC
Found at i:6777327 original size:43 final size:42
Alignment explanation
Indices: 6777280--6777378 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
6777270 TCCCAGACGT
* *
6777280 GGTCTTACATGTAATTA-ATTATCGATGCCACTGTCCCAAACAA
1 GGTCTTACACGTAATTATA-TA-CGATGCCAATGTCCCAAACAA
* * *
6777323 GGTCTTATACGTAATTATATACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATTATATACGATGCCAATGTCCCAAACAA
6777365 GGTCTTACACGTAA
1 GGTCTTACACGTAA
6777379 ATCTCAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 31 0.63
43 17 0.35
44 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (42 bp):
GGTCTTACACGTAATTATATACGATGCCAATGTCCCAAACAA
Found at i:6777406 original size:44 final size:41
Alignment explanation
Indices: 6777261--6777419 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 41
6777251 AGCTCATACA
* *
6777261 ATGCCAACATCCCAGACGTGGTCTTACATGTAATTAATTATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGTAATTAA--ATCG
* * * * *
6777304 ATGCC-ACTGTCCCAAACAAGGTCTTATACGTAATTATATACG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACGTAATTAAAT-CG
**
6777346 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGT-AAT-T-AAATCG
*
6777390 AGGCCAACATCCCAGACATGGTCTTACACG
1 ATGCCAACATCCCAGACATGGTCTTACACG
6777420 ATGTCACATT
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 31 0.33
44 30 0.32
45 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (41 bp):
ATGCCAACATCCCAGACATGGTCTTACACGTAATTAAATCG
Found at i:6778395 original size:15 final size:15
Alignment explanation
Indices: 6778375--6778405 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6778365 ATAAATTAAA
6778375 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
6778390 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
6778405 A
1 A
6778406 AAAGGCCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AGGTATAATTTCAAC
Found at i:6783170 original size:106 final size:108
Alignment explanation
Indices: 6782975--6783178 Score: 324
Period size: 106 Copynumber: 1.9 Consensus size: 108
6782965 TGGATTAAGA
*
6782975 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACGT
*
6783040 TTCCTCGAATTTCCAAACGCAAAATATTGCCTTACTCTGAAAT
66 TTCCTCGAATTCCCAAACGCAAAATATTGCCTTACTCTGAAAT
* * *
6783083 TTTAA-AGGATATTTGGCTATTTGGTCGAATG-AAAAAATCGAAACCCAACACATTAGGGCACGC
1 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACG-
*
6783146 TTT-CTCGAATTCCCAAATGCAAAATATTGCCTT
65 TTTCCTCGAATTCCCAAACGCAAAATATTGCCTT
6783179 TATTATTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
106 58 0.65
107 26 0.29
108 5 0.06
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (108 bp):
TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAACACATTAGGGCACGT
TTCCTCGAATTCCCAAACGCAAAATATTGCCTTACTCTGAAAT
Found at i:6784237 original size:12 final size:12
Alignment explanation
Indices: 6784199--6784237 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6784189 GAAATATATA
*
6784199 AATAATATCAAT
1 AATAATATTAAT
*
6784211 AATAATAGTAAT
1 AATAATATTAAT
*
6784223 AATAATATTATT
1 AATAATATTAAT
6784235 AAT
1 AAT
6784238 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:6790512 original size:19 final size:19
Alignment explanation
Indices: 6790488--6790526 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6790478 AAAGGAAGAG
6790488 ATAGTTAATTCATTTTCCA
1 ATAGTTAATTCATTTTCCA
6790507 ATAGTTAATTCATTTTCCA
1 ATAGTTAATTCATTTTCCA
6790526 A
1 A
6790527 AGAAGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
ATAGTTAATTCATTTTCCA
Found at i:6796940 original size:13 final size:13
Alignment explanation
Indices: 6796922--6796946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6796912 ATTTCTGGTC
6796922 TTTACTCAAGTTT
1 TTTACTCAAGTTT
6796935 TTTACTCAAGTT
1 TTTACTCAAGTT
6796947 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:6801421 original size:13 final size:13
Alignment explanation
Indices: 6801403--6801427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6801393 ATTTCTGGTC
6801403 TTTACTCAAGTTT
1 TTTACTCAAGTTT
6801416 TTTACTCAAGTT
1 TTTACTCAAGTT
6801428 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:6807312 original size:6 final size:6
Alignment explanation
Indices: 6807303--6807357 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
6807293 ATAAAACGTA
6807303 GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT
1 GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT GGGGAT
6807351 GGGGAT G
1 GGGGAT G
6807358 ATGCTGACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.16, C:0.00, G:0.67, T:0.16
Consensus pattern (6 bp):
GGGGAT
Found at i:6807444 original size:46 final size:46
Alignment explanation
Indices: 6807377--6807469 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
6807367 AAGAGACAAG
6807377 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
*
6807423 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
6807469 A
1 A
6807470 ATGCTCCAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.55, C:0.13, G:0.12, T:0.20
Consensus pattern (46 bp):
ACAAAGTCAAAAATAGATGTAGCGACAATCATACATGAAAAAAATT
Found at i:6808100 original size:22 final size:22
Alignment explanation
Indices: 6808075--6808128 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6808065 TTGTTTTTAA
* *
6808075 AAAATTAT-TTAATTTTAATTAT
1 AAAATTATATAAATATTAA-TAT
*
6808097 AAAAGTATATAAATATTAATAT
1 AAAATTATATAAATATTAATAT
*
6808119 AACATTATAT
1 AAAATTATAT
6808129 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAATATTAATAT
Found at i:6808247 original size:29 final size:28
Alignment explanation
Indices: 6808189--6808247 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
6808179 ATGTAAAATT
* * **
6808189 ATATTAATATTAATCTTTTATTATGTTA
1 ATATTAAAATTAATATTTTATTATACTA
*
6808217 ATATTAAAATTATATATTTTATTTTACTA
1 ATATTAAAATTA-ATATTTTATTATACTA
6808246 AT
1 AT
6808248 TATCATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAAAATTAATATTTTATTATACTA
Found at i:6813451 original size:22 final size:21
Alignment explanation
Indices: 6813426--6813468 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
6813416 TTGAAAAAAA
* *
6813426 ATTTAATTTTCCTATTATTATT
1 ATTTAATTCTACTATT-TTATT
6813448 ATTTAATTCTACTATTTTATT
1 ATTTAATTCTACTATTTTATT
6813469 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTAATTCTACTATTTTATT
Found at i:6819148 original size:4 final size:4
Alignment explanation
Indices: 6819139--6819163 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6819129 TTAACTAGTT
6819139 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
6819164 ATTTCCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:6825082 original size:14 final size:13
Alignment explanation
Indices: 6825047--6825084 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
6825037 AGTTTTTCTT
6825047 AAATA-TTAAAAA
1 AAATATTTAAAAA
6825059 AAATATTTTATAAAA
1 AAATA-TTTA-AAAA
6825074 AAATATTTAAA
1 AAATATTTAAA
6825085 GCAAAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 7 0.30
15 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATTTAAAAA
Found at i:6845046 original size:7 final size:7
Alignment explanation
Indices: 6844980--6845056 Score: 55
Period size: 7 Copynumber: 11.0 Consensus size: 7
6844970 TCATTTTCAA
*
6844980 CTCAATA
1 CTCAATT
**
6844987 CTCAACC
1 CTCAATT
*
6844994 CTCAGTT
1 CTCAATT
*
6845001 CTAAATT
1 CTCAATT
* *
6845008 CTCACTC
1 CTCAATT
6845015 CTCAATT
1 CTCAATT
* *
6845022 TTCAATC
1 CTCAATT
* *
6845029 CTGAATC
1 CTCAATT
6845036 CTCAATT
1 CTCAATT
6845043 CTCAATT
1 CTCAATT
6845050 CTCAATT
1 CTCAATT
6845057 ATTATTTTTA
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.36
Consensus pattern (7 bp):
CTCAATT
Found at i:6846640 original size:42 final size:42
Alignment explanation
Indices: 6846575--6846681 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
6846565 GAAGCCCGAA
*
6846575 GGTTGAACAGAAGCTCATGAGAGCTAAAAAAAAACCCATAAG
1 GGTTGAACAGAAGCTCATAAGAGCTAAAAAAAAACCCATAAG
* * * * *
6846617 GGTTGAACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAG
1 GGTTGAACAGAAGCTCATAAGAGCTAAAAAAAAACCCATAAG
* *
6846659 GGTTAAACAGAAGCTCAAAAGAG
1 GGTTGAACAGAAGCTCATAAGAG
6846682 ATGAACGATA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (42 bp):
GGTTGAACAGAAGCTCATAAGAGCTAAAAAAAAACCCATAAG
Found at i:6846658 original size:21 final size:21
Alignment explanation
Indices: 6846578--6846658 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 21
6846568 GCCCGAAGGT
* * *
6846578 TGAACAGAAGCTCATGAGAGC
1 TGAACAGAAACCCATAAGAGC
* * * * *
6846599 TAAAAAAAAACCCATAAGGGT
1 TGAACAGAAACCCATAAGAGC
* * * *
6846620 TGAACGGAAGCTCGTAAGAGC
1 TGAACAGAAACCCATAAGAGC
6846641 TGAACAGAAACCCATAAG
1 TGAACAGAAACCCATAAG
6846659 GGTTAAACAG
Statistics
Matches: 39, Mismatches: 21, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (21 bp):
TGAACAGAAACCCATAAGAGC
Found at i:6846667 original size:21 final size:21
Alignment explanation
Indices: 6846606--6846670 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
6846596 AGCTAAAAAA
*
6846606 AAACCCATAAGGGTTGAACGG
1 AAACCCATAAGGGTTGAACAG
* * * * *
6846627 AAGCTCGTAAGAGCTGAACAG
1 AAACCCATAAGGGTTGAACAG
*
6846648 AAACCCATAAGGGTTAAACAG
1 AAACCCATAAGGGTTGAACAG
6846669 AA
1 AA
6846671 GCTCAAAAGA
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (21 bp):
AAACCCATAAGGGTTGAACAG
Found at i:6850124 original size:12 final size:12
Alignment explanation
Indices: 6850107--6850136 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
6850097 ACAACATAAA
6850107 TAAATTGGAAAT
1 TAAATTGGAAAT
6850119 TAAATTGGAAAT
1 TAAATTGGAAAT
6850131 TAAATT
1 TAAATT
6850137 CGAATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (12 bp):
TAAATTGGAAAT
Found at i:6852305 original size:22 final size:22
Alignment explanation
Indices: 6852280--6852341 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
6852270 ATTTGCACTG
6852280 TTGAGTGGTTTATCCACACCGT
1 TTGAGTGGTTTATCCACACCGT
*** * **
6852302 TTGAGCAATTTATCTACATTGT
1 TTGAGTGGTTTATCCACACCGT
6852324 TT-AGTGGTTTATCCACAC
1 TTGAGTGGTTTATCCACAC
6852342 TGTATTAGCA
Statistics
Matches: 29, Mismatches: 11, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (22 bp):
TTGAGTGGTTTATCCACACCGT
Found at i:6852355 original size:22 final size:21
Alignment explanation
Indices: 6852287--6852355 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
6852277 CTGTTGAGTG
*
6852287 GTTTATCCACACCGTTTGAGCA
1 GTTTATCCACACTGTTT-AGCA
* * * **
6852309 ATTTATCTACATTGTTTAGTG
1 GTTTATCCACACTGTTTAGCA
6852330 GTTTATCCACACTGTATTAGCA
1 GTTTATCCACACTGT-TTAGCA
6852352 GTTT
1 GTTT
6852356 TAATCTGCAA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (21 bp):
GTTTATCCACACTGTTTAGCA
Found at i:6857382 original size:13 final size:14
Alignment explanation
Indices: 6857364--6857392 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6857354 TAAAGACTTG
6857364 ATATG-ATTAACCA
1 ATATGAATTAACCA
6857377 ATATGAATTAACCA
1 ATATGAATTAACCA
6857391 AT
1 AT
6857393 GTCACCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
ATATGAATTAACCA
Found at i:6871584 original size:18 final size:18
Alignment explanation
Indices: 6871548--6871592 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
6871538 ACAAATGCCT
6871548 TTAA-AATAGTAACAAAA
1 TTAACAATAGTAACAAAA
6871565 TTAACAATAG-AACAATAA
1 TTAACAATAGTAACAA-AA
6871583 TTATACAATA
1 TTA-ACAATA
6871593 TCCAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAACAATAGTAACAAAA
Found at i:6871615 original size:14 final size:14
Alignment explanation
Indices: 6871596--6871623 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6871586 TACAATATCC
6871596 AAATAATAACAACA
1 AAATAATAACAACA
6871610 AAATAATAACAACA
1 AAATAATAACAACA
6871624 TAATTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:6871709 original size:20 final size:21
Alignment explanation
Indices: 6871657--6871712 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
6871647 AGTGAAAAAA
*
6871657 AAAACAACAATAAAATAGCAAG
1 AAAACAATAA-AAAATAGCAAG
*
6871679 AAAATAATAAAAAATAGCAAG
1 AAAACAATAAAAAATAGCAAG
*
6871700 -AAACAGTAAAAAA
1 AAAACAATAAAAAA
6871713 AGTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 8 0.27
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAACAATAAAAAATAGCAAG
Found at i:6872115 original size:31 final size:31
Alignment explanation
Indices: 6872057--6872115 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
6872047 CGTGTAATTA
* **
6872057 TATACATGAAACTTTAATTGTGGTTCAAATG
1 TATACATGAAACATTAATTGTAATTCAAATG
* *
6872088 TATATATGAAACATTAATTTTAATTCAA
1 TATACATGAAACATTAATTGTAATTCAA
6872116 TTATCCACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (31 bp):
TATACATGAAACATTAATTGTAATTCAAATG
Found at i:6877283 original size:13 final size:13
Alignment explanation
Indices: 6877265--6877292 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6877255 AAAAACACTT
6877265 CTGAAATTTTTAG
1 CTGAAATTTTTAG
6877278 CTGAAATTTTTAG
1 CTGAAATTTTTAG
6877291 CT
1 CT
6877293 TTTCAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (13 bp):
CTGAAATTTTTAG
Found at i:6877823 original size:13 final size:13
Alignment explanation
Indices: 6877807--6877859 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
6877797 TTTAAACCAA
*
6877807 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
* *
6877820 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* * *
6877833 ATTTTTCCACAGC
1 ACTTTTCAAAAGC
6877846 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
6877859 A
1 A
6877860 AAGAAGAACT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:6879024 original size:14 final size:12
Alignment explanation
Indices: 6878996--6879037 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
6878986 TAAGAAATGC
6878996 TTTTAAAAAGTA
1 TTTTAAAAAGTA
6879008 TTTTGAAAAAGTGA
1 TTTT-AAAAAGT-A
6879022 TTTTAATAAA-TA
1 TTTTAA-AAAGTA
6879034 TTTT
1 TTTT
6879038 TGAAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.33
13 10 0.37
14 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
TTTTAAAAAGTA
Found at i:6887600 original size:18 final size:18
Alignment explanation
Indices: 6887579--6887630 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
6887569 ATAATTATAA
6887579 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
6887597 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
*
6887615 TATTATTTAATTAAAA
1 TATTAATTAA-TAAAA
6887631 AATCATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:6893066 original size:40 final size:42
Alignment explanation
Indices: 6892977--6893067 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 42
6892967 CGTTTGGATA
*
6892977 AAAAACGCCGTTAAAAATTGAGCATTAGCGGCGATTTCAGGG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGGG
* **
6893019 --AAGCGCCGCTAAAAA-TGAGCATTAGCGGC-ATTTGTGGG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGGG
6893057 AAAAACGCCGC
1 AAAAACGCCGC
6893068 AAATGTTAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
38 7 0.17
39 14 0.33
40 21 0.50
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGATTTCAGGG
Found at i:6894925 original size:21 final size:22
Alignment explanation
Indices: 6894899--6894945 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
6894889 AATAGTTGAA
*
6894899 AAAAAATCAAAACTTTT-TTTT
1 AAAAAATCAAAACTTTTCCTTT
**
6894920 AAAAAATTTAAACTTTTCCTTT
1 AAAAAATCAAAACTTTTCCTTT
6894942 AAAA
1 AAAA
6894946 TGACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATCAAAACTTTTCCTTT
Found at i:6895347 original size:17 final size:17
Alignment explanation
Indices: 6895325--6895357 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
6895315 GTTTATGACC
6895325 AAAAAAAAAG--ATAGA
1 AAAAAAAAAGAAATAGA
6895340 AAAAAAAAAGAAATAGA
1 AAAAAAAAAGAAATAGA
6895357 A
1 A
6895358 TGCTTGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.62
17 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAATAGA
Found at i:6900614 original size:23 final size:23
Alignment explanation
Indices: 6900556--6900614 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
6900546 AATTAATAAT
* *
6900556 AAAATTATATATTTTAACTTCTA
1 AAAATTATAAAATTTAACTTCTA
* * * *
6900579 AAAATAATTAAATTTAATTTTTA
1 AAAATTATAAAATTTAACTTCTA
6900602 AAAATTATAAAAT
1 AAAATTATAAAAT
6900615 AATATAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATAAAATTTAACTTCTA
Found at i:6904231 original size:6 final size:6
Alignment explanation
Indices: 6904220--6904252 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
6904210 TAATCTAATC
6904220 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG
6904253 AATTATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:6913064 original size:17 final size:17
Alignment explanation
Indices: 6913044--6913077 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6913034 TAGAATTGGG
*
6913044 TTGAGAAAGTAATTTAA
1 TTGAAAAAGTAATTTAA
*
6913061 TTGAAAAATTAATTTAA
1 TTGAAAAAGTAATTTAA
6913078 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
TTGAAAAAGTAATTTAA
Found at i:6916240 original size:2 final size:2
Alignment explanation
Indices: 6916233--6916260 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6916223 GAGGAGGAAA
6916233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6916261 GAATATTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6918421 original size:105 final size:101
Alignment explanation
Indices: 6918243--6918459 Score: 301
Period size: 105 Copynumber: 2.1 Consensus size: 101
6918233 AATTGATGGA
* * * * *
6918243 TAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTGTGGTATTCTGA
1 TAAGACCATGGTTGGACCATGACAGTATGTATATGTAAGACCATAGCTGGGCTATGGCATCCTGA
*
6918308 TGATAAGACCATAACTGGGTTATGGCACCT-TGAATG
66 TAATAAGACCATAACTGGGTTATGGCA-CTATGAATG
*
6918344 TAAGACCATGGTTGGACCATGGCAGTAAATGTATACGTGTAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATGGTTGGACCATGACAGT--ATGTATA--TGTAAGACCATAGCTGGGCTATGGCATC
* *
6918409 CTGATAATAAGACCATAACTGGGTTATGGCATTATGAGTG
62 CTGATAATAAGACCATAACTGGGTTATGGCACTATGAATG
6918449 TAAGACCATGG
1 TAAGACCATGG
6918460 CAGGGCCATG
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
101 25 0.25
103 5 0.05
104 1 0.01
105 71 0.70
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAGTATGTATATGTAAGACCATAGCTGGGCTATGGCATCCTGA
TAATAAGACCATAACTGGGTTATGGCACTATGAATG
Found at i:6918453 original size:33 final size:33
Alignment explanation
Indices: 6918276--6918457 Score: 100
Period size: 33 Copynumber: 5.3 Consensus size: 33
6918266 AGTGTTTATA
* * *
6918276 TGTAAGACCATAGCTGGGCTGTGGTATTC-TGA-
1 TGTAAGACCATAACTGGGCTATGGCA-TCATGAG
* * * *
6918308 TGATAAGACCATAACTGGGTTATGGCACCTTGAA
1 TG-TAAGACCATAACTGGGCTATGGCATCATGAG
*** * * *
6918342 TGTAAGACCATGGTTGGACCATGGCAGTAAATGTATACG
1 TGTAAGACCATAACTGGGCTATGGCA-T-CATG---A-G
* *
6918381 TGTAAGACCATAGCTGGGCTATGGCATCCTGA-
1 TGTAAGACCATAACTGGGCTATGGCATCATGAG
* * *
6918413 TAATAAGACCATAACTGGGTTATGGCATTATGAG
1 T-GTAAGACCATAACTGGGCTATGGCATCATGAG
6918447 TGTAAGACCAT
1 TGTAAGACCAT
6918458 GGCAGGGCCA
Statistics
Matches: 112, Mismatches: 27, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
32 4 0.04
33 76 0.68
34 4 0.04
35 2 0.02
37 2 0.02
38 2 0.02
39 22 0.20
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (33 bp):
TGTAAGACCATAACTGGGCTATGGCATCATGAG
Found at i:6919902 original size:5 final size:5
Alignment explanation
Indices: 6919894--6919927 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
6919884 TTTAAATTAA
6919894 AAAAT AAAAT AAAAT AAAAT -AAAT AAAACT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAA
6919928 GTAATTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:6922306 original size:12 final size:12
Alignment explanation
Indices: 6922259--6922322 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
6922249 TTTTTATTTT
6922259 ATTTAATATT-A
1 ATTTAATATTAA
6922270 ATATTAATATT-A
1 AT-TTAATATTAA
6922282 ATATTAATATTAA
1 AT-TTAATATTAA
*
6922295 TATTAAAT-TTAA
1 -ATTTAATATTAA
* *
6922307 ATTTATTATTAT
1 ATTTAATATTAA
6922319 ATTT
1 ATTT
6922323 TTTGAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
11 7 0.16
12 31 0.69
13 5 0.11
14 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:6922318 original size:6 final size:6
Alignment explanation
Indices: 6922261--6922300 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
6922251 TTTATTTTAT
6922261 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
6922301 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:6929636 original size:47 final size:44
Alignment explanation
Indices: 6929585--6929792 Score: 120
Period size: 44 Copynumber: 4.9 Consensus size: 44
6929575 TTTGAGTAAA
* *
6929585 TTAATATAAGAATATTATTTATTAAGAATTTTATTAAATTATATAGT
1 TTAAT-TAA-AATA-TATTTAATAAGAATTATATTAAATTATATAGT
* * *
6929632 TTAATTAAAATATATTTAATAATAATTATGTT-AATT-TATATT
1 TTAATTAAAATATATTTAATAAGAATTATATTAAATTATATAGT
* ** *
6929674 TTACAGTATCATATA-TT-AT--G-ATT-TGAGTAAATTA-ATA--
1 TTA-ATTAAAATATATTTAATAAGAATTAT-ATTAAATTATATAGT
* * * * *
6929711 -TAA-GAATAT-TAATTATTAAGAATTTTATTAAATTATATAGT
1 TTAATTAAAATATATTTAATAAGAATTATATTAAATTATATAGT
* * *
6929752 TTAATTAAAATATATTTAATAATAATTATGTTAATTTATAT
1 TTAATTAAAATATATTTAATAAGAATTATATTAAATTATAT
6929793 TTTACAGTAT
Statistics
Matches: 121, Mismatches: 24, Indels: 35
0.67 0.13 0.19
Matches are distributed among these distances:
33 2 0.02
34 5 0.04
35 2 0.02
36 2 0.02
37 2 0.02
38 15 0.12
39 11 0.09
41 2 0.02
42 13 0.11
43 16 0.13
44 39 0.32
45 4 0.03
46 3 0.02
47 5 0.04
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.49
Consensus pattern (44 bp):
TTAATTAAAATATATTTAATAAGAATTATATTAAATTATATAGT
Found at i:6929718 original size:120 final size:120
Alignment explanation
Indices: 6929521--6929903 Score: 721
Period size: 120 Copynumber: 3.2 Consensus size: 120
6929511 TTTTCAAGTT
6929521 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
6929586 TAATATAAGAATATTATTTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
6929641 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
6929706 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
6929761 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* * * *
6929826 TAATATAAGAATATTAATTATTAAGAATTTTAATAAAATAAATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
6929881 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
6929904 TAAATATGAT
Statistics
Matches: 258, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 258 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Found at i:6929888 original size:16 final size:16
Alignment explanation
Indices: 6929852--6929893 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
6929842 ATTATTAAGA
6929852 ATTTTAATAAAATAAAT
1 ATTTTAATAAAAT-AAT
6929869 ATTTTAATTAAAAT-AT
1 ATTTTAA-TAAAATAAT
6929885 A-TTTAATAA
1 ATTTTAATAA
6929894 TAATTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 5 0.21
16 3 0.12
17 7 0.29
18 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAATAAAATAAT
Found at i:6930143 original size:16 final size:16
Alignment explanation
Indices: 6930122--6930189 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
6930112 GATTTGCTAT
6930122 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6930138 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
6930154 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
6930170 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
6930186 TACA
1 TACA
6930190 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:6937172 original size:21 final size:21
Alignment explanation
Indices: 6937115--6937192 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
6937105 ACTTGGATTT
* * *
6937115 AAATTAAATAATTTTTATATA
1 AAATTATATAAATTTAATATA
* * * *
6937136 TATTTATTTATATTTAATTATA
1 AAATTATATAAATTTAA-TATA
6937158 AAA-TATATAAATTTAATATA
1 AAATTATATAAATTTAATATA
*
6937178 AAATTATATATATTT
1 AAATTATATAAATTT
6937193 TTTATTATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 7 0.16
21 31 0.72
22 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTATATAAATTTAATATA
Found at i:6937179 original size:20 final size:22
Alignment explanation
Indices: 6937147--6937192 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
6937137 ATTTATTTAT
6937147 ATTTAATTATAAAA-TATATAA
1 ATTTAATTATAAAATTATATAA
*
6937168 ATTTAA-TATAAAATTATATAT
1 ATTTAATTATAAAATTATATAA
6937189 ATTT
1 ATTT
6937193 TTTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAATTATAAAATTATATAA
Found at i:6937730 original size:20 final size:22
Alignment explanation
Indices: 6937701--6937745 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
6937691 TTGCTTGTAC
*
6937701 TTTAGTACATCTT-GTTA-CAT
1 TTTAGGACATCTTAGTTAGCAT
*
6937721 TTTAGGACATTTTAGTTAGCAT
1 TTTAGGACATCTTAGTTAGCAT
6937743 TTT
1 TTT
6937746 TAATATTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.51
Consensus pattern (22 bp):
TTTAGGACATCTTAGTTAGCAT
Found at i:6942856 original size:39 final size:39
Alignment explanation
Indices: 6942764--6942898 Score: 105
Period size: 39 Copynumber: 3.4 Consensus size: 39
6942754 AGTTTGGATA
* * * *
6942764 AAAAACGCCGTTAAAAATC-AATCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAAATCGAGT-ATTAGC-GCGCTTTCTG
* * * *
6942804 TAAAGCGCTGCTAAAGATCGAGTATTAGCGCGCTTTCTG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGCGCTTTCTG
* *
6942843 AAAAACGCCGCTAAAAAT-GAGCATTAGCCGCGTTTTCT-
1 AAAAACGCCGCTAAAAATCGAGTATTAG-CGCGCTTTCTG
* *
6942881 AATAAGCGCCGCAAAAAA
1 AA-AAACGCCGCTAAAAA
6942899 CCTAAGCCCA
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
38 10 0.13
39 44 0.58
40 20 0.26
41 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCGAGTATTAGCGCGCTTTCTG
Found at i:6943038 original size:38 final size:41
Alignment explanation
Indices: 6942949--6943042 Score: 122
Period size: 41 Copynumber: 2.4 Consensus size: 41
6942939 TAGTAGCGTT
* * *
6942949 TTTTTTAAAAAGCGCCGCTAATGCTTGTGTCTTTAGCGGCG
1 TTTTTAAAAAAGCGCCGCTAATGCTTCTATCTTTAGCGGCG
*
6942990 TTTTTAAAAAAGCGCCGCTAATGC-TCTAT-TTTA-TGGCG
1 TTTTTAAAAAAGCGCCGCTAATGCTTCTATCTTTAGCGGCG
*
6943028 TTTTTGAAAAAGCGC
1 TTTTTAAAAAAGCGC
6943043 TGCAAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 18 0.38
39 4 0.08
40 3 0.06
41 23 0.48
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTTTAAAAAAGCGCCGCTAATGCTTCTATCTTTAGCGGCG
Found at i:6943432 original size:22 final size:21
Alignment explanation
Indices: 6943361--6943460 Score: 58
Period size: 22 Copynumber: 4.7 Consensus size: 21
6943351 TTAAGGTTTT
* * *
6943361 TGGTTTAGGGTATATGGTTTA
1 TGGTTTAAGGTTTATGATTTA
** * *
6943382 AAGTTTAAGGTTTAGGAGTTA
1 TGGTTTAAGGTTTATGATTTA
**
6943403 CTATTTTAAGGTTTATGGA-TTA
1 -TGGTTTAAGGTTTAT-GATTTA
* *
6943425 TGGGTTTAGGGGTTATGATTTA
1 T-GGTTTAAGGTTTATGATTTA
*
6943447 TGGTTTATGGTTTA
1 TGGTTTAAGGTTTA
6943461 AAGGCTGGGG
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
21 28 0.47
22 29 0.49
23 2 0.03
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (21 bp):
TGGTTTAAGGTTTATGATTTA
Found at i:6943453 original size:7 final size:7
Alignment explanation
Indices: 6943349--6943460 Score: 57
Period size: 7 Copynumber: 15.7 Consensus size: 7
6943339 TATCACTATA
*
6943349 GTTTAAG
1 GTTTATG
*
6943356 GTTTTTG
1 GTTTATG
*
6943363 GTTTAGG
1 GTTTATG
*
6943370 GTATATG
1 GTTTATG
**
6943377 GTTTAAA
1 GTTTATG
*
6943384 GTTTAAG
1 GTTTATG
*
6943391 GTTTAGG
1 GTTTATG
6943398 AGTTACTAT-
1 -GTT--TATG
*
6943407 -TTTAAG
1 GTTTATG
6943413 GTTTATG
1 GTTTATG
*
6943420 GATTATGG
1 GTTTAT-G
*
6943428 GTTTAGG
1 GTTTATG
*
6943435 GGTTATG
1 GTTTATG
*
6943442 ATTTATG
1 GTTTATG
6943449 GTTTATG
1 GTTTATG
6943456 GTTTA
1 GTTTA
6943461 AAGGCTGGGG
Statistics
Matches: 77, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
5 2 0.03
7 65 0.84
8 8 0.10
10 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (7 bp):
GTTTATG
Found at i:6944222 original size:13 final size:15
Alignment explanation
Indices: 6944194--6944225 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
6944184 CTCGTATTAT
6944194 TATTAATTTAATATA
1 TATTAATTTAATATA
6944209 TATTAA-TT-ATATA
1 TATTAATTTAATATA
6944222 TATT
1 TATT
6944226 TTTCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATTTAATATA
Found at i:6947700 original size:43 final size:43
Alignment explanation
Indices: 6947633--6947719 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
6947623 CAATGATGTA
* * *
6947633 CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* * *
6947676 CAAGATTTACTTGATTAGGAAAATGCATTGTATGTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
6947719 C
1 C
6947720 TTGCATATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:6948043 original size:42 final size:43
Alignment explanation
Indices: 6947980--6948248 Score: 280
Period size: 43 Copynumber: 6.3 Consensus size: 43
6947970 AAGATATGTT
* *
6947980 TTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGT-TTGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
* * * *
6948022 TTTAGCGGCGTTTGTGGGAAAAGTGTCGTTAAAGGTC-TG-TT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
* * * *
6948063 TTATAACGGCGTTTGTGGGAAAAGCGTCGCTAAAAGTGATGATC
1 TT-TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
* * *
6948107 TATAGTGGCGTTTGTGGGAAAAGCGCCGTTACAA-GTCATGA-C
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTA-AAGGTCATGATC
* * * *
6948149 TTATAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGGTCGTGTTC
1 TT-TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
* * *
6948193 TTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCCTG-TT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
6948235 TTATAGCGGCGTTT
1 TT-TAGCGGCGTTT
6948249 ATTTCTAAAA
Statistics
Matches: 190, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.02
42 71 0.37
43 109 0.57
44 7 0.04
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATC
Found at i:6948203 original size:86 final size:84
Alignment explanation
Indices: 6947982--6948248 Score: 320
Period size: 86 Copynumber: 3.1 Consensus size: 84
6947972 GATATGTTTT
* * *
6947982 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTTTGATCTTTAGCGGCGTTTGTGGGAAAAGTG
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTGTGATCTTTAGCGGCGTTTGTGGGAAAAGCG
* **
6948047 TCGTTAAAGGTCTGTTTTA
66 CCGTTAAAGGTCTGACTTA
* * * * * *
6948066 TAACGGCGTTTGTGGGAAAAGCGTCGCTAAAAGTGATGATCTATAGTGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTG-TGATCTTTAGCGGCGTTTGTGGGAAAAGC
6948131 GCCGTTACAA-GTCATGACTTA
65 GCCGTTA-AAGGTC-TGACTTA
* * *
6948152 TAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGGTCGTGTTCTTTAGCGGCGTTTGTGTGAAAAGC
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGT-GTGATCTTTAGCGGCGTTTGTGGGAAAAGC
* **
6948217 GCCGCTAAAGGTCCTGTTTTA
65 GCCGTTAAAGGT-CTGACTTA
6948238 TAGCGGCGTTT
1 TAGCGGCGTTT
6948249 ATTTCTAAAA
Statistics
Matches: 153, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
84 30 0.20
85 37 0.24
86 84 0.55
87 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (84 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTGTGATCTTTAGCGGCGTTTGTGGGAAAAGCG
CCGTTAAAGGTCTGACTTA
Found at i:6953137 original size:15 final size:15
Alignment explanation
Indices: 6953117--6953147 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6953107 ACATCTACCG
6953117 AAATAGACGAATTAC
1 AAATAGACGAATTAC
6953132 AAATAGACGAATTAC
1 AAATAGACGAATTAC
6953147 A
1 A
6953148 TACAACACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (15 bp):
AAATAGACGAATTAC
Found at i:6963199 original size:24 final size:22
Alignment explanation
Indices: 6963160--6963207 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
6963150 TTATTTATAT
*
6963160 AATTTTAAAAATACACATTAAA
1 AATTTTAAAAAAACACATTAAA
6963182 AATTATTAAAAAGAACACATTAAA
1 AATT-TTAAAAA-AACACATTAAA
6963206 AA
1 AA
6963208 ACTATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.17
23 7 0.30
24 12 0.52
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (22 bp):
AATTTTAAAAAAACACATTAAA
Found at i:6963213 original size:25 final size:23
Alignment explanation
Indices: 6963164--6963218 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
6963154 TTATATAATT
* *
6963164 TTAAAAATACACATTAAAAATTA
1 TTAAAAAAACACATTAAAAACTA
6963187 TTAAAAAGAACACATTAAAAAACTA
1 TTAAAAA-AACACATT-AAAAACTA
*
6963212 TTTAAAA
1 TTAAAAA
6963219 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 13 0.48
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (23 bp):
TTAAAAAAACACATTAAAAACTA
Found at i:6963216 original size:26 final size:24
Alignment explanation
Indices: 6963163--6963218 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
6963153 TTTATATAAT
* *
6963163 TTTAAAAATACACATTAAAAATTA
1 TTTAAAAAAACACATTAAAAACTA
6963187 -TTAAAAAGAACACATTAAAAAACTA
1 TTTAAAAA-AACACATT-AAAAACTA
6963212 TTTAAAA
1 TTTAAAA
6963219 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 7 0.26
26 6 0.22
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.29
Consensus pattern (24 bp):
TTTAAAAAAACACATTAAAAACTA
Found at i:6963672 original size:29 final size:29
Alignment explanation
Indices: 6963640--6963701 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6963630 TTAAAATTTT
6963640 AAAAATAAAAAATATAAATATAAAT-TAAA
1 AAAAATAAAAAATATAAATA-AAATATAAA
* * * *
6963669 AAAAATCAAAATTTTATATAAAATATAAA
1 AAAAATAAAAAATATAAATAAAATATAAA
6963698 AAAA
1 AAAA
6963702 TCATATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAAATAAAAAATATAAATAAAATATAAA
Found at i:6963699 original size:20 final size:21
Alignment explanation
Indices: 6963676--6963721 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6963666 AAAAAAAATC
*
6963676 AAAATTTTATATAAAATATAAA
1 AAAATTATATATAAAATAT-AA
* *
6963698 AAAATCATATATAATATATAA
1 AAAATTATATATAAAATATAA
6963719 AAA
1 AAA
6963722 TTCAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTATATATAAAATATAA
Found at i:6963722 original size:20 final size:20
Alignment explanation
Indices: 6963684--6963722 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6963674 TCAAAATTTT
6963684 ATATAAAATATAAAAAAATC
1 ATATAAAATATAAAAAAATC
* *
6963704 ATATATAATATATAAAAAT
1 ATATAAAATATAAAAAAAT
6963723 TCAAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATAAAATATAAAAAAATC
Found at i:6963852 original size:29 final size:29
Alignment explanation
Indices: 6963794--6963855 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6963784 ATATCAAAAT
** *
6963794 ATTATATAAAAATTGAAATTTTTAACAAA
1 ATTATATAAAAATCAAAATTTATAACAAA
6963823 ATTATATAAAAATCAAAATATTATATA-AAA
1 ATTATATAAAAATCAAAAT-TTATA-ACAAA
6963853 ATT
1 ATT
6963856 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 17 0.61
30 10 0.36
31 1 0.04
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTATATAAAAATCAAAATTTATAACAAA
Found at i:6963860 original size:19 final size:19
Alignment explanation
Indices: 6963777--6963854 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 19
6963767 AATATATAAA
*
6963777 TATATAAATATCAAAATAT
1 TATATAAAAATCAAAATAT
**
6963796 TATATAAAAATTGAAAT-T
1 TATATAAAAATCAAAATAT
6963814 T-T-T---AA-C-AAA-AT
1 TATATAAAAATCAAAATAT
6963825 TATATAAAAATCAAAATAT
1 TATATAAAAATCAAAATAT
6963844 TATATAAAAAT
1 TATATAAAAAT
6963855 TTAAATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
11 5 0.11
12 1 0.02
13 3 0.07
16 3 0.07
17 2 0.04
18 5 0.11
19 27 0.59
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (19 bp):
TATATAAAAATCAAAATAT
Found at i:6963878 original size:32 final size:32
Alignment explanation
Indices: 6963830--6963892 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
6963820 AAAATTATAT
*
6963830 AAAAATCAAAATATTATATAAAAATTTAAATTA
1 AAAAATCAAAATATTATA-AAAAATATAAATTA
* *
6963863 AAAAATCTAAA-ATTATAAAACATATAAATT
1 AAAAATCAAAATATTATAAAAAATATAAATT
6963893 GAAATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
32 6 0.22
33 10 0.37
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (32 bp):
AAAAATCAAAATATTATAAAAAATATAAATTA
Found at i:6963881 original size:17 final size:18
Alignment explanation
Indices: 6963820--6963879 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 18
6963810 AATTTTTAAC
*
6963820 AAAATTATATAAAAATCA
1 AAAATTATATAAAAATCT
6963838 AAATATTATATAAAAAT-T
1 AAA-ATTATATAAAAATCT
*
6963856 TAAA-T-TA-AAAAATCT
1 AAAATTATATAAAAATCT
6963871 AAAATTATA
1 AAAATTATA
6963880 AAACATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 6 0.17
15 6 0.17
16 2 0.06
17 3 0.09
18 5 0.14
19 13 0.37
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATATAAAAATCT
Found at i:6972703 original size:64 final size:64
Alignment explanation
Indices: 6972635--6972762 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
6972625 ATTAATGGAC
* *
6972635 TCTTCTTCTGAGTTGCATAAAAAGTAGATATTACTTACTTGGAGATTTTTCCTTTGTAAATTAT
1 TCTTCCTCTAAGTTGCATAAAAAGTAGATATTACTTACTTGGAGATTTTTCCTTTGTAAATTAT
6972699 TCTTCCTCTAAGTTGCATAAAAAGTAGATATTACTTACTTGGAGATTTTTCCTTTGTAAATTAT
1 TCTTCCTCTAAGTTGCATAAAAAGTAGATATTACTTACTTGGAGATTTTTCCTTTGTAAATTAT
6972763 CAAAAGCACG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (64 bp):
TCTTCCTCTAAGTTGCATAAAAAGTAGATATTACTTACTTGGAGATTTTTCCTTTGTAAATTAT
Found at i:6984024 original size:15 final size:15
Alignment explanation
Indices: 6984004--6984063 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 15
6983994 CATTTAATTT
6984004 TTTTTTAAATTTTTA
1 TTTTTTAAATTTTTA
*
6984019 TTTTTTTAATATTTTA
1 TTTTTTAAAT-TTTTA
*
6984035 TTTTTGAATATTTTTA
1 TTTTTTAA-ATTTTTA
6984051 TAATTTTTAAATT
1 T--TTTTTAAATT
6984064 ATTTGTTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 9 0.24
16 17 0.46
17 5 0.14
18 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTTTAAATTTTTA
Found at i:6986144 original size:44 final size:44
Alignment explanation
Indices: 6986096--6986188 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
6986086 GAACATAAAA
* * *
6986096 GAATGAAAATGATGAAGTTATAGATATGAGTTGTACTAACAAAT
1 GAATGAAAATGATGAAGTTAGAGAAATGAGTCGTACTAACAAAT
* * *
6986140 GAATGGAAATGATGAAGTTAGAGAAATGAGTCGTATTCACAAAT
1 GAATGAAAATGATGAAGTTAGAGAAATGAGTCGTACTAACAAAT
6986184 GAATG
1 GAATG
6986189 CATTTTCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (44 bp):
GAATGAAAATGATGAAGTTAGAGAAATGAGTCGTACTAACAAAT
Found at i:6992763 original size:4 final size:4
Alignment explanation
Indices: 6992754--6992782 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
6992744 ATCATTGGCA
6992754 TGTT TGTT TGTT TGTT TGTT TGTT T-TT TG
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TG
6992783 CAGTCTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TGTT
Found at i:6993253 original size:16 final size:16
Alignment explanation
Indices: 6993228--6993280 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
6993218 TTGGTTCGCT
*
6993228 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
*
6993244 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
6993260 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
6993276 GTAAT
1 GTAAT
6993281 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.04, G:0.34, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:6993531 original size:16 final size:16
Alignment explanation
Indices: 6993494--6993535 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6993484 TTAATCATAT
*
6993494 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
6993510 TT-AAATATATTATAA
1 TTAAAATATATTATAA
6993525 TTAAAATATAT
1 TTAAAATATAT
6993536 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6993542 original size:14 final size:15
Alignment explanation
Indices: 6993503--6993544 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6993493 TTTAAACATA
*
6993503 ATTATTATTAAATAT
1 ATTATAATTAAATAT
6993518 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
6993532 A-TATAATTTAATA
1 ATTATAATTAAATA
6993545 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:6993640 original size:120 final size:120
Alignment explanation
Indices: 6993492--6994120 Score: 1145
Period size: 120 Copynumber: 5.2 Consensus size: 120
6993482 ATTTAATCAT
6993492 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATA
*
6993557 ATCAATATTCTTATATGAATTTACTCAAATCAAAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
6993613 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
6993678 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
**
6993733 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCCTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
*
6993798 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
*
6993853 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
*
6993918 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
*
6993973 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
*
6994038 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
*
6994093 ATTTGAA-ATAATTAATATTAAATA-ATTA
1 ATTT-AACATAATTATTATTAAATATATTA
6994121 ATGTTGACAA
Statistics
Matches: 497, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
119 4 0.01
120 487 0.98
121 6 0.01
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:6993653 original size:16 final size:16
Alignment explanation
Indices: 6993609--6993655 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6993599 TACTATAAAA
*
6993609 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
6993625 TATTATT-AAATATAT
1 TATAATTAAAATATAT
6993640 TATAATTAAAATATAT
1 TATAATTAAAATATAT
6993656 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:6993773 original size:16 final size:16
Alignment explanation
Indices: 6993729--6993775 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6993719 TACTATAAAA
*
6993729 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
6993745 TATTATT-AAATATAT
1 TATAATTAAAATATAT
6993760 TATAATTAAAATATAT
1 TATAATTAAAATATAT
6993776 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:6993893 original size:16 final size:16
Alignment explanation
Indices: 6993849--6993895 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6993839 TACTATAAAA
*
6993849 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
6993865 TATTATT-AAATATAT
1 TATAATTAAAATATAT
6993880 TATAATTAAAATATAT
1 TATAATTAAAATATAT
6993896 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:6994013 original size:16 final size:16
Alignment explanation
Indices: 6993969--6994015 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6993959 TACTATAAAA
*
6993969 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
6993985 TATTATT-AAATATAT
1 TATAATTAAAATATAT
6994000 TATAATTAAAATATAT
1 TATAATTAAAATATAT
6994016 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:6994475 original size:30 final size:30
Alignment explanation
Indices: 6994441--6994499 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6994431 GGCCCATTTT
6994441 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAG
*
6994471 TATTTTAAAAATATTTTAAAATTAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAA
6994500 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAG
Found at i:6994480 original size:11 final size:10
Alignment explanation
Indices: 6994441--6994492 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
6994431 GGCCCATTTT
6994441 TATTTTAAAA
1 TATTTTAAAA
6994451 -ATTTTAAAA
1 TATTTTAAAA
* **
6994460 AATTAAAAAA
1 TATTTTAAAA
6994470 GTATTTTAAAAA
1 -TATTTT-AAAA
6994482 TATTTTAAAA
1 TATTTTAAAA
6994492 T
1 T
6994493 TAAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.26
10 12 0.35
11 9 0.26
12 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:6994487 original size:41 final size:41
Alignment explanation
Indices: 6994441--6994624 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 41
6994431 GGCCCATTTT
*
6994441 TATTTTAAAAATTTTAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
6994482 TATTTT-AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAT
1 TATTTTAAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
6994522 TATTTT-AAAATTAAAAAGAATTAAAAAAATTATTTTAAAAA
1 TATTTTAAAAATTAAAAA-AATTAAAAAAAGTATTTTAAAAA
**
6994563 TA-TTTAAAAATTTAAAAAAAATT-AAAAAAGTATGTAAAAAAA
1 TATTTTAAAAA-TT-AAAAAAATTAAAAAAAGTAT-TTTAAAAA
6994605 TATTTT-AAAATTAAAAAAAT
1 TATTTTAAAAATTAAAAAAAT
6994625 AAATATATTT
Statistics
Matches: 129, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
39 10 0.08
40 49 0.38
41 44 0.34
42 18 0.14
43 8 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (41 bp):
TATTTTAAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:6994532 original size:11 final size:11
Alignment explanation
Indices: 6994440--6994534 Score: 51
Period size: 11 Copynumber: 9.3 Consensus size: 11
6994430 CGGCCCATTT
6994440 TTATTTTAAAA
1 TTATTTTAAAA
6994451 --ATTTTAAAA
1 TTATTTTAAAA
* **
6994460 -AATTAAAAAA
1 TTATTTTAAAA
*
6994470 GTATTTTAAAA
1 TTATTTTAAAA
*
6994481 ATATTTTAAAA
1 TTATTTTAAAA
**
6994492 TTA--AAAAAA
1 TTATTTTAAAA
**
6994501 TTA--AAAAAA
1 TTATTTTAAAA
*
6994510 GTATTTTAAAA
1 TTATTTTAAAA
6994521 TTATTTTAAAA
1 TTATTTTAAAA
6994532 TTA
1 TTA
6994535 AAAAGAATTA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
9 24 0.36
10 7 0.10
11 36 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:6994537 original size:29 final size:29
Alignment explanation
Indices: 6994475--6994561 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
6994465 AAAAAGTATT
**
6994475 TTAAAAA-TATTTTAAAATTA--AAAAAA
1 TTAAAAAGTATTTTAAAATTATTTTAAAA
6994501 TTAAAAAAAGTATTTTAAAATTATTTTAAAA
1 TT--AAAAAGTATTTTAAAATTATTTTAAAA
* **
6994532 TTAAAAAGAATTAAAAAAATTATTTTAAAA
1 TTAAAAAGTATT-TTAAAATTATTTTAAAA
6994562 ATATTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.04
28 5 0.10
29 22 0.44
30 15 0.30
31 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAAAAGTATTTTAAAATTATTTTAAAA
Done.