Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 18 of 31
Found at i:8897049 original size:19 final size:19
Alignment explanation
Indices: 8897025--8897061 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8897015 TTATATTTAT
8897025 AAATGTATATTCATTAAAA
1 AAATGTATATTCATTAAAA
*
8897044 AAATGTATATTTATTAAA
1 AAATGTATATTCATTAAA
8897062 TGACTATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AAATGTATATTCATTAAAA
Found at i:8897231 original size:21 final size:21
Alignment explanation
Indices: 8897206--8897263 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
8897196 AATATTTTAA
* *
8897206 ATTAAAATTTTTTAGTTAAAT
1 ATTAATATTTTTTAATTAAAT
* *
8897227 GTTAATATTTTTAAATTAAAT
1 ATTAATATTTTTTAATTAAAT
*
8897248 ATTACTATTTTTTAAT
1 ATTAATATTTTTTAAT
8897264 ATTTAATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTAATATTTTTTAATTAAAT
Found at i:8900025 original size:21 final size:21
Alignment explanation
Indices: 8899996--8900053 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
8899986 ATACAATAAC
*
8899996 AAAATTAAAATGCAAAAAAC-A
1 AAAAATAAAAT-CAAAAAACAA
* *
8900017 AAAAATAAAATCACAAATCAA
1 AAAAATAAAATCAAAAAACAA
8900038 AATAAATAAAAT-AAAA
1 AA-AAATAAAATCAAAA
8900054 GAACCAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 16 0.52
22 9 0.29
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAAATAAAATCAAAAAACAA
Found at i:8900120 original size:19 final size:20
Alignment explanation
Indices: 8900091--8900131 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
8900081 ATCAATGACT
8900091 AAACAAAACAAAAAAAACCA
1 AAACAAAACAAAAAAAACCA
* *
8900111 AAAC-AAACAAAGAAAGCCA
1 AAACAAAACAAAAAAAACCA
8900130 AA
1 AA
8900132 GAAGAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.76, C:0.20, G:0.05, T:0.00
Consensus pattern (20 bp):
AAACAAAACAAAAAAAACCA
Found at i:8900781 original size:30 final size:30
Alignment explanation
Indices: 8900702--8900803 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
8900692 TTAGGAAATT
* *
8900702 TTAAATAAA-TTTTATATTTTT-A-TTATA
1 TTAAATAAATTTTTGTATTTTTAATTTAAA
* * * * *
8900729 TTCAATGAAGTTTTTATTTTTTTATTTTGAAA
1 TTAAAT-AAATTTTTGTATTTTTAATTT-AAA
8900761 -TAAATAAATTTTTGTATTTTTAATTTAAA
1 TTAAATAAATTTTTGTATTTTTAATTTAAA
*
8900790 TTAAATAAGTTTTT
1 TTAAATAAATTTTT
8900804 ATAGTTAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.09
28 2 0.03
29 14 0.24
30 29 0.50
31 6 0.10
32 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (30 bp):
TTAAATAAATTTTTGTATTTTTAATTTAAA
Found at i:8903670 original size:33 final size:33
Alignment explanation
Indices: 8903633--8903700 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
8903623 TTAAACTCTC
8903633 AATATAT-TCTTTATAATATTAATTT-TTAAATAA
1 AATATATAT-TTT-TAATATTAATTTATTAAATAA
* *
8903666 AATATATATTTTTCATATTAATTTATTAATTAA
1 AATATATATTTTTAATATTAATTTATTAAATAA
8903699 AA
1 AA
8903701 ATTTAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.35
33 19 0.61
34 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
AATATATATTTTTAATATTAATTTATTAAATAA
Found at i:8925740 original size:21 final size:20
Alignment explanation
Indices: 8925698--8925740 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
8925688 TAATAGTTAA
*
8925698 AAAAGAAAGAATAAATGGTT
1 AAAAGAAAGAATAAATGATT
8925718 AAAAGAAAAGAATATAA-GATT
1 AAAAG-AAAGAATA-AATGATT
8925739 AA
1 AA
8925741 TGTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 13 0.65
22 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAAGAAAGAATAAATGATT
Found at i:8933227 original size:2 final size:2
Alignment explanation
Indices: 8933217--8933249 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
8933207 TCTTCTCTCC
*
8933217 AT AT A- AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8933250 GTTCATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8934381 original size:43 final size:43
Alignment explanation
Indices: 8934321--8934415 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
8934311 TACAATACAT
* *
8934321 TTTTCTCTACAATTACATTTCA-TATAATCATCACTTTCTCATA
1 TTTTATCTACAATTACA-TTCATTATAATCATCACTTTCTCACA
**
8934364 TTTTATCTACAATTACATTCATTATAATCATTTCTTTCTCACA
1 TTTTATCTACAATTACATTCATTATAATCATCACTTTCTCACA
*
8934407 TTATATCTA
1 TTTTATCTA
8934416 ATACTACAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 4 0.09
43 42 0.91
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (43 bp):
TTTTATCTACAATTACATTCATTATAATCATCACTTTCTCACA
Found at i:8936105 original size:36 final size:37
Alignment explanation
Indices: 8936030--8936105 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
8936020 GCTTTTATAT
* *
8936030 TTGAATAAATCATTATTGTATTTTTTCCCTATTGTGG
1 TTGAATAAATCATTATTGTATTTTTTCCCTATGGAGG
* **
8936067 TTGAATACATCATTATTGTATTTTTT-TTTATGGAGG
1 TTGAATAAATCATTATTGTATTTTTTCCCTATGGAGG
8936103 TTG
1 TTG
8936106 TATTGTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 9 0.26
37 25 0.74
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (37 bp):
TTGAATAAATCATTATTGTATTTTTTCCCTATGGAGG
Found at i:8943631 original size:2 final size:2
Alignment explanation
Indices: 8943624--8943648 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8943614 CATTTGAGAA
8943624 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8943649 AGAATGCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8953938 original size:25 final size:25
Alignment explanation
Indices: 8953881--8953939 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
8953871 CCTAGAAAAG
8953881 TACTAAATTGTAATTGGTAAATTGA
1 TACTAAATTGTAATTGGTAAATTGA
*
8953906 TACAAAATTGTAATT-GT-AATTGTA
1 TACTAAATTGTAATTGGTAAATTG-A
8953930 TTACTAAATT
1 -TACTAAATT
8953940 ACCAGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 3 0.10
25 22 0.73
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (25 bp):
TACTAAATTGTAATTGGTAAATTGA
Found at i:8954937 original size:17 final size:17
Alignment explanation
Indices: 8954915--8954955 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
8954905 TATGTATATA
8954915 TAGATTTGATTATAAA-T
1 TAGATTTGATTA-AAATT
*
8954932 TAGATTGGATTAAAATT
1 TAGATTTGATTAAAATT
8954949 TAGATTT
1 TAGATTT
8954956 AATATATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
TAGATTTGATTAAAATT
Found at i:8955219 original size:39 final size:39
Alignment explanation
Indices: 8955176--8955259 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
8955166 CTAATCTCTT
* * * *
8955176 AAGTTTTGATATCGTTTAGTTTTCCTCATCTCCAAGTCC
1 AAGTTTTGATATCATTTAGTTTTCATCATCTCAAAGTCA
*
8955215 AAGTTTTGATTTCATTTAGTTTTCATCATCTCAAAGTCA
1 AAGTTTTGATATCATTTAGTTTTCATCATCTCAAAGTCA
8955254 AAGTTT
1 AAGTTT
8955260 AGTTTCTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (39 bp):
AAGTTTTGATATCATTTAGTTTTCATCATCTCAAAGTCA
Found at i:8955435 original size:27 final size:26
Alignment explanation
Indices: 8955394--8955484 Score: 92
Period size: 27 Copynumber: 3.4 Consensus size: 26
8955384 ATCAAGTAAA
8955394 TGGATGGATAATTTTACCAACTAGAAG
1 TGGATGGATAATTTTACC-ACTAGAAG
* * * *
8955421 TGAATGGATAGTTTTATCCGCTAGAAA
1 TGGATGGATAATTTTA-CCACTAGAAG
* * *
8955448 TGGATGGATAATTTCACTTACAAGAAG
1 TGGATGGATAATTTTAC-CACTAGAAG
8955475 TGGATGGATA
1 TGGATGGATA
8955485 GCTATACTCG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.02
27 48 0.94
28 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (26 bp):
TGGATGGATAATTTTACCACTAGAAG
Found at i:8955542 original size:27 final size:27
Alignment explanation
Indices: 8955416--8955546 Score: 88
Period size: 27 Copynumber: 4.9 Consensus size: 27
8955406 TTTACCAACT
* ** *
8955416 AGAAGTGAATGGATAGTTTTA-TCCGCT
1 AGAAGTGGATGGATACCTTTACT-CGCA
* * **
8955443 AGAAATGGATGGATA-ATTTCACTTACA
1 AGAAGTGGATGGATACCTTT-ACTCGCA
* *
8955470 AGAAGTGGATGGATAGCTATACTCGCA
1 AGAAGTGGATGGATACCTTTACTCGCA
*** *
8955497 AGAAGCAAATAGATACCTTTA-TCCGCA
1 AGAAGTGGATGGATACCTTTACT-CGCA
8955524 AGAAGTGGATGGATACCTTTACT
1 AGAAGTGGATGGATACCTTTACT
8955547 TAAAAAAAGT
Statistics
Matches: 78, Mismatches: 21, Indels: 9
0.72 0.19 0.08
Matches are distributed among these distances:
26 4 0.05
27 70 0.90
28 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (27 bp):
AGAAGTGGATGGATACCTTTACTCGCA
Found at i:8955598 original size:27 final size:27
Alignment explanation
Indices: 8955568--8955652 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
8955558 GATGAATGCT
8955568 TTTACCCACTAGAAATGGATAGATACC
1 TTTACCCACTAGAAATGGATAGATACC
* * *
8955595 TTTACCCAAC-AGTAATGGATGGATACA
1 TTTACCC-ACTAGAAATGGATAGATACC
* * **
8955622 TTTACCCAATAGAAGTTTATAGATACC
1 TTTACCCACTAGAAATGGATAGATACC
8955649 TTTA
1 TTTA
8955653 TCTATCAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
26 1 0.02
27 43 0.93
28 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (27 bp):
TTTACCCACTAGAAATGGATAGATACC
Found at i:8955670 original size:54 final size:55
Alignment explanation
Indices: 8955553--8955679 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 55
8955543 TACTTAAAAA
* * * *
8955553 AAGTAGATGAATGCTTTTACCCACTAGAAATGGATAGATACCTTTACCCAACAGT
1 AAGTAGATGGATACATTTACCCAATAGAAATGGATAGATACCTTTACCCAACAGT
* * ** * * *
8955608 AA-TGGATGGATACATTTACCCAATAGAAGTTTATAGATACCTTTATCTATCAG-
1 AAGTAGATGGATACATTTACCCAATAGAAATGGATAGATACCTTTACCCAACAGT
*
8955661 AAGTAGATGGATACCTTTA
1 AAGTAGATGGATACATTTA
8955680 TGCACCATAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
53 2 0.03
54 54 0.93
55 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (55 bp):
AAGTAGATGGATACATTTACCCAATAGAAATGGATAGATACCTTTACCCAACAGT
Found at i:8971912 original size:137 final size:137
Alignment explanation
Indices: 8971710--8971980 Score: 506
Period size: 137 Copynumber: 2.0 Consensus size: 137
8971700 TCTTTCAATA
* *
8971710 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCGAATTCTGGTCTCCCCAAAGTTT
1 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCTCGTCTCCCCAAAGTTT
8971775 AATAATGAATTTTTATCTTTTCCTAGCATAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
66 AATAATGAATTTTTATCTTTTCCTAGCATAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
8971840 CCAAATG
131 CCAAATG
8971847 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCTCGTCTCCCCAAAGTTT
1 ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCTCGTCTCCCCAAAGTTT
* *
8971912 AATAATGAATTTTTATCTTTTCCTAGTATAGATATCAGTAACCAAATGACAAATTTCAAAAATAT
66 AATAATGAATTTTTATCTTTTCCTAGCATAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
8971977 CCAA
131 CCAA
8971981 CTCATCAGAA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 130 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (137 bp):
ATGGTAGCCACACCTTACATCTAAATTTGATATCCCAATTTCAAATTCTCGTCTCCCCAAAGTTT
AATAATGAATTTTTATCTTTTCCTAGCATAGATATCAGTAACCAAATGACAAATTTCAAAAACAT
CCAAATG
Found at i:8975322 original size:25 final size:23
Alignment explanation
Indices: 8975272--8975322 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
8975262 ATAAATAAAT
* *
8975272 AAAATAAAAAACTAGAAGAAAGA
1 AAAATAAAAAACTAAAAGAAACA
*
8975295 AAAATCAAAATAACTAAAAGGAACA
1 AAAAT-AAAA-AACTAAAAGAAACA
8975320 AAA
1 AAA
8975323 CAATAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 4 0.17
25 14 0.61
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.10
Consensus pattern (23 bp):
AAAATAAAAAACTAAAAGAAACA
Found at i:9014188 original size:2 final size:2
Alignment explanation
Indices: 9014181--9014210 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9014171 TACAAGAGTG
9014181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9014211 GAGTTGACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9024985 original size:2 final size:2
Alignment explanation
Indices: 9024978--9025006 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9024968 CAGTTTGTTT
9024978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9025007 TTGTCTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9025545 original size:15 final size:15
Alignment explanation
Indices: 9025525--9025555 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9025515 GAAGAATATT
9025525 ATTACGACGATGATG
1 ATTACGACGATGATG
*
9025540 ATTACGATGATGATG
1 ATTACGACGATGATG
9025555 A
1 A
9025556 GGAGGAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (15 bp):
ATTACGACGATGATG
Found at i:9025570 original size:18 final size:18
Alignment explanation
Indices: 9025549--9025597 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
9025539 GATTACGATG
*
9025549 ATGATGAGGAGGAATATT
1 ATGATGAGGAAGAATATT
* *
9025567 ATGATGATGAAGATTATT
1 ATGATGAGGAAGAATATT
*
9025585 ATGATGAGAAAGA
1 ATGATGAGGAAGA
9025598 TGAGAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (18 bp):
ATGATGAGGAAGAATATT
Found at i:9025582 original size:15 final size:15
Alignment explanation
Indices: 9025496--9025591 Score: 50
Period size: 15 Copynumber: 6.4 Consensus size: 15
9025486 ATGGCAACGG
9025496 TGATGAAGATGATGA
1 TGATGAAGATGATGA
* *
9025511 AGATGAAGAAT-ATTA
1 TGATGAAG-ATGATGA
* * *
9025526 TTACGACGATGATGA
1 TGATGAAGATGATGA
* * *
9025541 TTACGATGATGATGA
1 TGATGAAGATGATGA
* * * *
9025556 GGAGGAATATTATGA
1 TGATGAAGATGATGA
* *
9025571 TGATGAAGATTATTA
1 TGATGAAGATGATGA
9025586 TGATGA
1 TGATGA
9025592 GAAAGATGAG
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
14 2 0.03
15 57 0.93
16 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (15 bp):
TGATGAAGATGATGA
Found at i:9033424 original size:30 final size:30
Alignment explanation
Indices: 9033378--9033446 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
9033368 ATCAATCATT
* *
9033378 AATTATAAAAATTTATTTAACTCAAAATAA
1 AATTATAAAAACTTATTCAACTCAAAATAA
* *
9033408 AATTATGAAAACTTATTCAATTCAAAATAA
1 AATTATAAAAACTTATTCAACTCAAAATAA
9033438 TAA-TATAAA
1 -AATTATAAA
9033447 TGCTTGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (30 bp):
AATTATAAAAACTTATTCAACTCAAAATAA
Found at i:9035443 original size:2 final size:2
Alignment explanation
Indices: 9035436--9035462 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9035426 TGATGTTAAC
9035436 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9035463 ATCTTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9039125 original size:22 final size:22
Alignment explanation
Indices: 9039100--9039159 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
9039090 ATTTTTCAAA
*
9039100 TTTTTATTATTTATATTTATAT
1 TTTTTATTATTTTTATTTATAT
*
9039122 TTTTTATT-TTTTTAGTTTTTAT
1 TTTTTATTATTTTTA-TTTATAT
*
9039144 TTTAT-TTATTTTTATT
1 TTTTTATTATTTTTATT
9039160 ATTGAGACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 9 0.27
22 24 0.73
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTATTATTTTTATTTATAT
Found at i:9039141 original size:37 final size:38
Alignment explanation
Indices: 9039085--9039158 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
9039075 TCATTTTCTC
9039085 TTTTTATTTTTCAAATTTTTA-TTATTTATATTTATAT
1 TTTTTATTTTTCAAATTTTTATTTATTTATATTTATAT
** * *
9039122 TTTTTATTTTTTTAGTTTTTATTTTATTTATTTTTAT
1 TTTTTATTTTTCAAATTTTTA-TTTATTTATATTTAT
9039159 TATTGAGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 18 0.58
39 13 0.42
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (38 bp):
TTTTTATTTTTCAAATTTTTATTTATTTATATTTATAT
Found at i:9039158 original size:15 final size:15
Alignment explanation
Indices: 9039102--9039159 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
9039092 TTTTCAAATT
9039102 TTTATTATTTATATTTA
1 TTTATT-TTTAT-TTTA
*
9039119 TAT-TTTTTATTTT-
1 TTTATTTTTATTTTA
9039132 TTTAGTTTTTATTTTA
1 TTTA-TTTTTATTTTA
9039148 TTTATTTTTATT
1 TTTATTTTTATT
9039160 ATTGAGACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 2 0.06
14 3 0.08
15 23 0.64
16 6 0.17
17 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTATTTTTATTTTA
Found at i:9042682 original size:88 final size:88
Alignment explanation
Indices: 9042533--9042710 Score: 338
Period size: 88 Copynumber: 2.0 Consensus size: 88
9042523 TATACTATGA
* *
9042533 GTTTCAATAATTTTTATATTTTGTAATATAATCTAGATTCAAATAGCAGGTAATTTTTTTAACAC
1 GTTTCAATAATTCTTATATTTTGTAATACAATCTAGATTCAAATAGCAGGTAATTTTTTTAACAC
9042598 ACTTCTTACTCGAAATAATAGAT
66 ACTTCTTACTCGAAATAATAGAT
9042621 GTTTCAATAATTCTTATATTTTGTAATACAATCTAGATTCAAATAGCAGGTAATTTTTTTAACAC
1 GTTTCAATAATTCTTATATTTTGTAATACAATCTAGATTCAAATAGCAGGTAATTTTTTTAACAC
9042686 ACTTCTTACTCGAAATAATAGAT
66 ACTTCTTACTCGAAATAATAGAT
9042709 GT
1 GT
9042711 AATATAAAGA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (88 bp):
GTTTCAATAATTCTTATATTTTGTAATACAATCTAGATTCAAATAGCAGGTAATTTTTTTAACAC
ACTTCTTACTCGAAATAATAGAT
Found at i:9043517 original size:27 final size:27
Alignment explanation
Indices: 9043433--9043518 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
9043423 TTTCTCTTCA
** *
9043433 GTATTCATCCAC-TTCGGTTGGTTAATT
1 GTATTCATCCACTTTTTG-TGGTTAAAT
* *
9043460 GTACTCATCCACTTTTTGTGATTAAAT
1 GTATTCATCCACTTTTTGTGGTTAAAT
* *
9043487 GTATTCTTCTACTTTTTGTGGTTAAAT
1 GTATTCATCCACTTTTTGTGGTTAAAT
9043514 GTATT
1 GTATT
9043519 ACTACTGTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 46 0.94
28 3 0.06
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (27 bp):
GTATTCATCCACTTTTTGTGGTTAAAT
Found at i:9044017 original size:60 final size:60
Alignment explanation
Indices: 9043907--9044023 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
9043897 GCTTAATCCA
* * * * *
9043907 ATTTAATAAATTAAGAGACCAAATATTATATATACTACTTGATTACAAATTCGCATTCCG
1 ATTTAATAAATTAAGAGACAAAATATAATATATACTACTCGATAACAAATTCACATTCCG
* *
9043967 ATTTAATTAAA-TAAGAGACAAAATATAATATATATTA-TACGATAATAAATTCACATT
1 ATTTAA-TAAATTAAGAGACAAAATATAATATATACTACT-CGATAACAAATTCACATT
9044024 AAAATTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.02
60 43 0.90
61 4 0.08
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (60 bp):
ATTTAATAAATTAAGAGACAAAATATAATATATACTACTCGATAACAAATTCACATTCCG
Found at i:9044121 original size:88 final size:87
Alignment explanation
Indices: 9043983--9044157 Score: 314
Period size: 88 Copynumber: 2.0 Consensus size: 87
9043973 TTAAATAAGA
*
9043983 GACAAAATATAATATATATTATACGATAATAAATTCACATTAAAATTAATTTTTAGAGATGAAAA
1 GACAAAATATAATATATACTATACGATAATAAATTCACATTAAAATTAATTTTTAGAGATGAAAA
9044048 CACTAAAAAGATATTAAATCACT
66 CACT-AAAAGATATTAAATCACT
* *
9044071 GACAAAATATAATATATACTATACGATAATAAATTCACATTAAAGTTAATTTTTAGGGATGAAAA
1 GACAAAATATAATATATACTATACGATAATAAATTCACATTAAAATTAATTTTTAGAGATGAAAA
9044136 CACTAAAAGATATTAAATCACT
66 CACTAAAAGATATTAAATCACT
9044158 TTCCTAATTC
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
87 18 0.21
88 66 0.79
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (87 bp):
GACAAAATATAATATATACTATACGATAATAAATTCACATTAAAATTAATTTTTAGAGATGAAAA
CACTAAAAGATATTAAATCACT
Found at i:9044241 original size:22 final size:22
Alignment explanation
Indices: 9044213--9044256 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9044203 CTTTTTAAAA
9044213 CTTTTAAAGCTTAAAGAAATTG
1 CTTTTAAAGCTTAAAGAAATTG
* *
9044235 CTTTTAATGCTTAGAGAAATTG
1 CTTTTAAAGCTTAAAGAAATTG
9044257 AACTTTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
CTTTTAAAGCTTAAAGAAATTG
Found at i:9052088 original size:45 final size:46
Alignment explanation
Indices: 9051989--9052089 Score: 150
Period size: 48 Copynumber: 2.2 Consensus size: 46
9051979 CAATAGAAAC
* * *
9051989 TCTTAACTCACTCATTGTCTAGATATATTCAGTCTTCAATTAAGTCTT
1 TCTTAACTCACTAATTGTCTAAATATATTCA--CATCAATTAAGTCTT
9052037 TCTTAACTCACTAATTGTCTAAATATATTCA-ATCAATTAAGTCTT
1 TCTTAACTCACTAATTGTCTAAATATATTCACATCAATTAAGTCTT
9052082 TCTTAACT
1 TCTTAACT
9052090 TTTATCTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
45 21 0.42
48 29 0.58
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.44
Consensus pattern (46 bp):
TCTTAACTCACTAATTGTCTAAATATATTCACATCAATTAAGTCTT
Found at i:9059122 original size:2 final size:2
Alignment explanation
Indices: 9059117--9059145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9059107 GGAATAGGAG
9059117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9059146 GTTTAAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9059666 original size:95 final size:94
Alignment explanation
Indices: 9059524--9059756 Score: 263
Period size: 95 Copynumber: 2.5 Consensus size: 94
9059514 AAGAAAATGA
* * * * * *
9059524 AAAAGAGTCAACAGTGTACACCCACATTTTGTTGGCAAAGGATTCATTTATTACTCTCCA-TACT
1 AAAAGAGTCAACATTATACACCCATATTATGTTGACAAAGGGTTCATTTATTAC-CTCCAGTACT
*
9059588 TGCTATCATAGTTTATTTAAAAAG-AAAAAAG
65 CGCTATCATAGTTTATTT--AAAGTAAAAAAG
* *
9059619 AAAAGAGTCAACATTATACACCCATATTATGTTGACAAAGGGTTCATTTGTTACCTTCAGTACTC
1 AAAAGAGTCAACATTATACACCCATATTATGTTGACAAAGGGTTCATTTATTACCTCCAGTACTC
* **
9059684 GCTATCATGGTTTATTTAAAGTTCAAAAG
66 GCTATCATAGTTTATTTAAAGTAAAAAAG
* * * ** *
9059713 AAAAGAATCAACATTATATAACGTTCTTATGTTGACAAAGGGTT
1 AAAAGAGTCAACATTATACACCCATATTATGTTGACAAAGGGTT
9059757 AAAGGATGTT
Statistics
Matches: 118, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
93 4 0.03
94 47 0.40
95 67 0.57
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (94 bp):
AAAAGAGTCAACATTATACACCCATATTATGTTGACAAAGGGTTCATTTATTACCTCCAGTACTC
GCTATCATAGTTTATTTAAAGTAAAAAAG
Found at i:9067260 original size:27 final size:27
Alignment explanation
Indices: 9067222--9067276 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
9067212 AGAAGATGAA
9067222 CAGTGGAGAAACCAGATTACAACAACT
1 CAGTGGAGAAACCAGATTACAACAACT
9067249 CAGTGGAGAAACCAGATTACAACAACT
1 CAGTGGAGAAACCAGATTACAACAACT
9067276 C
1 C
9067277 TCCTGATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.15
Consensus pattern (27 bp):
CAGTGGAGAAACCAGATTACAACAACT
Found at i:9070983 original size:17 final size:18
Alignment explanation
Indices: 9070947--9070984 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9070937 ATATAATAAT
**
9070947 ATATTTTTAAATTTTTTA
1 ATATTTTTAAATTTGATA
9070965 ATATTTTT-AATTTGATA
1 ATATTTTTAAATTTGATA
9070982 ATA
1 ATA
9070985 ATAATAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATATTTTTAAATTTGATA
Found at i:9071245 original size:33 final size:33
Alignment explanation
Indices: 9071208--9071274 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
9071198 ATATATAAGA
* * *
9071208 ATATCATAATTAATAATTATGTTATATGTTAAT
1 ATATCATAACTAATAATAATGTGATATGTTAAT
*
9071241 ATATCATAACTGATAATAATGTGATATGTTAAT
1 ATATCATAACTAATAATAATGTGATATGTTAAT
9071274 A
1 A
9071275 CGGTATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (33 bp):
ATATCATAACTAATAATAATGTGATATGTTAAT
Found at i:9074218 original size:228 final size:228
Alignment explanation
Indices: 9073820--9075158 Score: 1461
Period size: 228 Copynumber: 5.9 Consensus size: 228
9073810 TGACCGACCA
* * * * * *
9073820 GATGCAAATCTTTGTGAAAACCCTTACAGGCAAGACCATCACCCTT-GAGGTTGAGAGCTCTGAC
1 GATGCAAATCTTTGTCAAGACTCTCACAGGAAAGACTATCA-CCTTGGAGGTTGAGAGCTCTGAC
* *
9073884 ACTATTGACAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCCGACCAGCAAAGGCT
65 ACTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGCT
*
9073949 TATTTTTGCTGGCAAACAGCTTGAAGATGGCCGAACCCTAGCTGACTATAACATCCAGAAGGAGT
130 TATTTTTGCTGGCAAACAGCTTGAAGATGGCAGAACCCTAGCTGACTATAACATCCAGAAGGAGT
*
9074014 CCACCCTCCACTTGGTGCTTCGGCTCCGTGGTGG
195 CCACCCTCCACTTGGTGCTTCGTCTCCGTGGTGG
*
9074048 TATGCAAATCTTTGTCAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGACA
1 GATGCAAATCTTTGTCAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGACA
* *
9074113 CTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCTGACCAACAAAGGCTT
66 CTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGCTT
*
9074178 ATTTTTGCTGGCAAACAGCTTGAAGATGGCCGAACCCTAGCTGACTATAACATCCAGAAGGAGTC
131 ATTTTTGCTGGCAAACAGCTTGAAGATGGCAGAACCCTAGCTGACTATAACATCCAGAAGGAGTC
*
9074243 CACCCTCCATTTGGTGCTTCGTCTCCGTGGTGG
196 CACCCTCCACTTGGTGCTTCGTCTCCGTGGTGG
* * *
9074276 TATGCAAATCTTTGTCAAGACACTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGATA
1 GATGCAAATCTTTGTCAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGACA
* * * * *
9074341 CAATTGATAATGTCAAAGCTAAGATCCAAGACAAGGAAGGAATCCCTCCTGATCAACAAAGGCTT
66 CTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGCTT
* * * ********
9074406 ATCTTTGCTGGCAAACAGCTTGAAGACGGTC-GCACCCTAGCTGACTATAACATCCANNNNNNNN
131 ATTTTTGCTGGCAAACAGCTTGAAGATGG-CAGAACCCTAGCTGACTATAACATCCAGAAGGAGT
** * * *
9074470 NNACCCTCCATTTGGTGCTTCGTCTTCGAGGTGG
195 CCACCCTCCACTTGGTGCTTCGTCTCCGTGGTGG
* * * * *
9074504 CATGCAAATCTTTGTCAAGACTCTCACAGGTAAA-ACGATCACTTTGGAGGTAGAGAGCTCAGAC
1 GATGCAAATCTTTGTCAAGACTCTCACAGG-AAAGACTATCACCTTGGAGGTTGAGAGCTCTGAC
* * * * * * * * * *
9074568 ACTATTGACAATGTCAAGGCCAAGATTCAGGATAAAGAGGGTATCCCACCAGACCAGCAGAGG-T
65 ACTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGCT
* * * * * * * * *
9074632 TGATTTTTGCTGGAAAACAACTTGAAGATGGAAGGACACTTGCTGATTATAACATTCAAAAGGAG
130 T-ATTTTTGCTGGCAAACAGCTTGAAGATGGCAGAACCCTAGCTGACTATAACATCCAGAAGGAG
* * * * *
9074697 TCAACCCTTCACTTGGTTCTCCGTCTTCGTGGTGG
194 TCCACCCTCCACTTGGTGCTTCGTCTCCGTGGTGG
* * * * * * * *
9074732 GATGCAAATTTTTGTGAAGACTCTTACGGGAAAGACTATCACATTGGAGGTTGAGAGTTCAGATA
1 GATGCAAATCTTTGTCAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGACA
* * * * * * *
9074797 CCATTGATAATGTGAAGGCAAAGATCCAAGATAAGGAGGGTATCCCACCAGACCAGCAAAGGCTT
66 CTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGCTT
* * * * * * * *
9074862 ATCTTTGCTGGCAAGCAGCTTGAAGATGGGAGAACTCTCGCTGACTATAATATCCAAAAGGAATC
131 ATTTTTGCTGGCAAACAGCTTGAAGATGGCAGAACCCTAGCTGACTATAACATCCAGAAGGAGTC
* * * *
9074927 TACCCTTCACTTGGTG-TTGCGTTTACGTGGTGG
196 CACCCTCCACTTGGTGCTT-CGTCTCCGTGGTGG
* * * * * * * * *
9074960 GATGCAGATATTTGTGAAGAC-CTTGACTGGAAAGAC-AGTAACATTGGAGGTTGAAAGCTCGGA
1 GATGCAAATCTTTGTCAAGACTC-TCACAGGAAAGACTA-TCACCTTGGAGGTTGAGAGCTCTGA
* * * * * *
9075023 CACCATTGATAATGTGAAGGCAAAGATCCAGGACAAGGAAGGGATCCCTCCAGACCAGCAGAGG-
64 CACTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGC
* * * * * * * * * *
9075087 TTGATTTTTGCTGGGAAGCAGCTGGAGGATGGGAGGACTCTGGCAGACTACAACATCCAGAAGGA
129 TT-ATTTTTGCTGGCAAACAGCTTGAAGATGGCAGAACCCTAGCTGACTATAACATCCAGAAGGA
*
9075152 ATCCACC
193 GTCCACC
9075159 TTGCATCTTG
Statistics
Matches: 960, Mismatches: 140, Indels: 22
0.86 0.12 0.02
Matches are distributed among these distances:
227 14 0.01
228 940 0.98
229 6 0.01
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (228 bp):
GATGCAAATCTTTGTCAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGACA
CTATTGATAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCAGACCAGCAAAGGCTT
ATTTTTGCTGGCAAACAGCTTGAAGATGGCAGAACCCTAGCTGACTATAACATCCAGAAGGAGTC
CACCCTCCACTTGGTGCTTCGTCTCCGTGGTGG
Found at i:9078334 original size:35 final size:35
Alignment explanation
Indices: 9078295--9078380 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
9078285 GGTATTCTGT
**
9078295 ATGAAGTAATGTTTCACTTGTTCTAATCGTTTTAC
1 ATGAAGTAATACTTCACTTGTTCTAATCGTTTTAC
* * * *
9078330 ATGAAGTAGTACTTCATTTGTTCTAATTGTTTTGC
1 ATGAAGTAATACTTCACTTGTTCTAATCGTTTTAC
*
9078365 ATGAAGTAGTACTTCA
1 ATGAAGTAATACTTCA
9078381 TGTTTAATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (35 bp):
ATGAAGTAATACTTCACTTGTTCTAATCGTTTTAC
Found at i:9078381 original size:35 final size:35
Alignment explanation
Indices: 9078307--9078381 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
9078297 GAAGTAATGT
*
9078307 TTCACTTGTTCTAATCGTTTTACATGAAGTAGTAC
1 TTCATTTGTTCTAATCGTTTTACATGAAGTAGTAC
* *
9078342 TTCATTTGTTCTAATTGTTTTGCATGAAGTAGTAC
1 TTCATTTGTTCTAATCGTTTTACATGAAGTAGTAC
9078377 TTCAT
1 TTCAT
9078382 GTTTAATTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (35 bp):
TTCATTTGTTCTAATCGTTTTACATGAAGTAGTAC
Found at i:9078484 original size:262 final size:262
Alignment explanation
Indices: 9078013--9078526 Score: 746
Period size: 262 Copynumber: 2.0 Consensus size: 262
9078003 ATTGCTATTT
* *
9078013 GTATGAAGTGGGTGTTCTTCATGAAGTAGTGTTGTACTTGTTCTAATCGTTTTACATGAAGTAGT
1 GTATGAAGTGGGTATTCTTCATGAAGTAATGTTGTACTTGTTCTAATCGTTTTACATGAAGTAGT
* * *
9078078 GCTTCACTTATTCCAATTATTTTGCATGAAGTAGTACTTCACTTTTAACTACTACTCATTCAGGA
66 ACTTCACTTATTCCAATTATTTTGCATGAAGTAGTACTTCACTTTTAACTACCACTCATTCAGAA
* * * * *
9078143 TTACTTTCATTGTTATTCGCAAGAAGTGATTATTTTGCATGAAATATTACTTCACTTGTTCTCAT
131 TTACTTTCATTGCTATTCACAAGAAGTGATTATTTTACATGAAATAATACTTCACTTGTTCTAAT
* * * * * *
9078208 CATTCTATGTGAAGTAGTGCTTCACTTGTTTTAGTTGTTTTGCATGAAGTAGTGCTTTATGTTAT
196 CATTCTACGTGAAGTAGTACTTCACTTATTCTAGTTATTCTGCATGAAGTAGTGCTTTATGTTAT
9078273 CC
261 CC
9078275 GTATGAAGTGGGTATTCTGT-ATGAAGTAATGTT-TCACTTGTTCTAATCGTTTTACATGAAGTA
1 GTATGAAGTGGGTATTCT-TCATGAAGTAATGTTGT-ACTTGTTCTAATCGTTTTACATGAAGTA
* * * * * *
9078338 GTACTTCATTTGTTCTAATTGTTTTGCATGAAGTAGTACTTCA-TGTTTAATTGCCACTCATTCA
64 GTACTTCACTTATTCCAATTATTTTGCATGAAGTAGTACTTCACT-TTTAACTACCACTCATTCA
* * *
9078402 GAATTACTTTCATTGCTATTCATAGGAAGTGATTATTTTACATGAAATAATGCTTCACTTGTTCT
128 GAATTACTTTCATTGCTATTCACAAGAAGTGATTATTTTACATGAAATAATACTTCACTTGTTCT
*
9078467 AATCATTCTACGTGAAGTAGTACTTCATTTATTCTAGTTATTCTGCATGAAGTAGTGCTT
193 AATCATTCTACGTGAAGTAGTACTTCACTTATTCTAGTTATTCTGCATGAAGTAGTGCTT
9078527 CATTTGTAAT
Statistics
Matches: 223, Mismatches: 26, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
261 2 0.01
262 220 0.99
263 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (262 bp):
GTATGAAGTGGGTATTCTTCATGAAGTAATGTTGTACTTGTTCTAATCGTTTTACATGAAGTAGT
ACTTCACTTATTCCAATTATTTTGCATGAAGTAGTACTTCACTTTTAACTACCACTCATTCAGAA
TTACTTTCATTGCTATTCACAAGAAGTGATTATTTTACATGAAATAATACTTCACTTGTTCTAAT
CATTCTACGTGAAGTAGTACTTCACTTATTCTAGTTATTCTGCATGAAGTAGTGCTTTATGTTAT
CC
Found at i:9078502 original size:35 final size:35
Alignment explanation
Indices: 9078440--9078531 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
9078430 GTGATTATTT
* * * * *
9078440 TACATGAAATAATGCTTCACTTGTTCTAATCATTC
1 TACATGAAGTAGTACTTCATTTATTCTAATCATTC
* * *
9078475 TACGTGAAGTAGTACTTCATTTATTCTAGTTATTC
1 TACATGAAGTAGTACTTCATTTATTCTAATCATTC
* *
9078510 TGCATGAAGTAGTGCTTCATTT
1 TACATGAAGTAGTACTTCATTT
9078532 GTAATGGTTA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (35 bp):
TACATGAAGTAGTACTTCATTTATTCTAATCATTC
Found at i:9078542 original size:35 final size:35
Alignment explanation
Indices: 9078479--9078545 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
9078469 TCATTCTACG
**
9078479 TGAAGTAGTACTTCATTTATTCTAGTTATTCTGCA
1 TGAAGTAGTACTTCATTTATAATAGTTATTCTGCA
* * *
9078514 TGAAGTAGTGCTTCATTTGTAATGGTTATTCT
1 TGAAGTAGTACTTCATTTATAATAGTTATTCT
9078546 TATTATTCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (35 bp):
TGAAGTAGTACTTCATTTATAATAGTTATTCTGCA
Found at i:9080026 original size:3 final size:3
Alignment explanation
Indices: 9080011--9080062 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
9080001 TTTCACTCAA
* * *
9080011 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AGT AAT AAAT GATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT
9080058 AAT AA
1 AAT AA
9080063 CAAAATATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 36 0.88
4 5 0.12
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9083018 original size:12 final size:12
Alignment explanation
Indices: 9083001--9083031 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
9082991 AAAAGAAAAG
9083001 ATTAAGAGGCAA
1 ATTAAGAGGCAA
9083013 ATTAAGAGGCAA
1 ATTAAGAGGCAA
9083025 ATTAAGA
1 ATTAAGA
9083032 AATCCAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (12 bp):
ATTAAGAGGCAA
Found at i:9084322 original size:18 final size:18
Alignment explanation
Indices: 9084299--9084342 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
9084289 TTTGAGTTTA
*
9084299 CTCTGATACCTAAATCTG
1 CTCTGATACCCAAATCTG
9084317 CTCTGATACCCAAATCTG
1 CTCTGATACCCAAATCTG
9084335 CTCTGATA
1 CTCTGATA
9084343 TCACTTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (18 bp):
CTCTGATACCCAAATCTG
Found at i:9090660 original size:19 final size:19
Alignment explanation
Indices: 9090636--9090675 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
9090626 ACCTAAACTC
9090636 TAAAGACTTTACTCAAAAA
1 TAAAGACTTTACTCAAAAA
9090655 TAAAGACTTTACTCAAAAA
1 TAAAGACTTTACTCAAAAA
9090674 TA
1 TA
9090676 CAAAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (19 bp):
TAAAGACTTTACTCAAAAA
Found at i:9091262 original size:38 final size:38
Alignment explanation
Indices: 9091211--9091287 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
9091201 CTCATCCTTC
9091211 ATGAACATAGCAACACAAATAAGTTAAAATAGAAAGGA
1 ATGAACATAGCAACACAAATAAGTTAAAATAGAAAGGA
9091249 ATGAACATAGCAACACAAATAAGTTAAAATAGAAAGGA
1 ATGAACATAGCAACACAAATAAGTTAAAATAGAAAGGA
9091287 A
1 A
9091288 AACGATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.16
Consensus pattern (38 bp):
ATGAACATAGCAACACAAATAAGTTAAAATAGAAAGGA
Found at i:9099437 original size:21 final size:21
Alignment explanation
Indices: 9099404--9099453 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
9099394 ATATCAGCCT
9099404 AGCCCACCAAAACATGTTCCC
1 AGCCCACCAAAACATGTTCCC
* *
9099425 AGCCCCCCTAAACATGTT-CC
1 AGCCCACCAAAACATGTTCCC
9099445 AGGCCCACC
1 A-GCCCACC
9099454 CATTTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.28, C:0.46, G:0.12, T:0.14
Consensus pattern (21 bp):
AGCCCACCAAAACATGTTCCC
Found at i:9104651 original size:22 final size:23
Alignment explanation
Indices: 9104608--9104652 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9104598 GCCATGTTGC
*
9104608 GTCTCATTGTTTTGACCTCCTCT
1 GTCTCATTATTTTGACCTCCTCT
9104631 GTCTCATTATTTTG-CCTCCTCT
1 GTCTCATTATTTTGACCTCCTCT
9104653 AAACAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.09, C:0.31, G:0.11, T:0.49
Consensus pattern (23 bp):
GTCTCATTATTTTGACCTCCTCT
Found at i:9108732 original size:42 final size:42
Alignment explanation
Indices: 9108673--9108757 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
9108663 CATGTTGATC
**
9108673 TGGCACTATTAATGAGTAGATTATGTTATTGGTGCAATGAAT
1 TGGCACTATTAATGAGTAGATTATGCCATTGGTGCAATGAAT
* *
9108715 TGGCATTATTAATGAGTAGATTATGCCATTGGTGCACTGAAT
1 TGGCACTATTAATGAGTAGATTATGCCATTGGTGCAATGAAT
9108757 T
1 T
9108758 AATCTTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (42 bp):
TGGCACTATTAATGAGTAGATTATGCCATTGGTGCAATGAAT
Found at i:9116770 original size:64 final size:63
Alignment explanation
Indices: 9116659--9116798 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 63
9116649 ATACTCAAAT
* * * *
9116659 CTTTGATAGATAAAGAAGTTATATATAAGTCATCCTAAAATAGTGTTAAAGGTTCTATTTGAGC
1 CTTTGAAAGATAAAGAAGTTATATATAAG-CATCCTAAAATAATGTTAAAGGTTCTATCTAAGC
* * * * *
9116723 CTTTGAAAGATAAAGAAGTTATACTTTAA-CCTGCTAAAGATAATGTTAGAGGTTCTATCTAAGT
1 CTTTGAAAGATAAAGAAGTTATA-TATAAGCATCCTAAA-ATAATGTTAAAGGTTCTATCTAAGC
*
9116787 TTTTGAAAGATA
1 CTTTGAAAGATA
9116799 GAATTAGGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 7 0.11
64 53 0.83
65 4 0.06
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (63 bp):
CTTTGAAAGATAAAGAAGTTATATATAAGCATCCTAAAATAATGTTAAAGGTTCTATCTAAGC
Found at i:9121714 original size:36 final size:36
Alignment explanation
Indices: 9121671--9121765 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 36
9121661 CTATGTACCC
*
9121671 AAACCTCCAGTTGTAAAGCCTCCACCTTACACACCA
1 AAACCTCCAGTTGTAAAGCCTCCACCCTACACACCA
* *
9121707 AAACCTCCAGTTGTCAAGCCTCCACCCTATACACCA
1 AAACCTCCAGTTGTAAAGCCTCCACCCTACACACCA
*
9121743 AAACCTCCAGTTGTAAAACCTCC
1 AAACCTCCAGTTGTAAAGCCTCC
9121766 CTACGTGCCG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.33, C:0.39, G:0.08, T:0.20
Consensus pattern (36 bp):
AAACCTCCAGTTGTAAAGCCTCCACCCTACACACCA
Found at i:9121714 original size:54 final size:54
Alignment explanation
Indices: 9121512--9121714 Score: 284
Period size: 53 Copynumber: 3.8 Consensus size: 54
9121502 TATCCGTCAC
* * * *
9121512 AACCTCCTGTTGTAAAGCC-CCGCCTCATGCACCGAAGCCTCCCTATGTACCCA
1 AACCTCCTGTAGTAAAGCCTCCACCTTATACACCGAAGCCTCCCTATGTACCCA
*
9121565 AACCTCCTGTAGTAAAACCTCCACCTTATAC-CCGAAGCCTCCCTATGTACCCA
1 AACCTCCTGTAGTAAAGCCTCCACCTTATACACCGAAGCCTCCCTATGTACCCA
* *
9121618 AACCTCCGGTAGTAAAGCCTCCACCTTATACGCCGAAGCCTCCCTATGTACCCA
1 AACCTCCTGTAGTAAAGCCTCCACCTTATACACCGAAGCCTCCCTATGTACCCA
* * * * *
9121672 AACCTCCAGTTGTAAAGCCTCCACCTTACACACCAAAACCTCC
1 AACCTCCTGTAGTAAAGCCTCCACCTTATACACCGAAGCCTCC
9121715 AGTTGTCAAG
Statistics
Matches: 135, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
53 68 0.50
54 67 0.50
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (54 bp):
AACCTCCTGTAGTAAAGCCTCCACCTTATACACCGAAGCCTCCCTATGTACCCA
Found at i:9121995 original size:63 final size:63
Alignment explanation
Indices: 9121894--9122080 Score: 293
Period size: 63 Copynumber: 3.0 Consensus size: 63
9121884 CCAGTCATAT
*
9121894 CACCACCAATTCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCTATTGTGAAGCCACCAA
1 CACCACCAATTCTGCCTCCAACGCCTCCTGTATATCCGAGTCCTCCTATTGTGAAGCCACCAA
* * *
9121957 CGCCACCAATTCTGCCTCCAACGCCTCCTGTCTATCCGAGTCCTCCGATTGTGAAGCCACCAA
1 CACCACCAATTCTGCCTCCAACGCCTCCTGTATATCCGAGTCCTCCTATTGTGAAGCCACCAA
* * * * *
9122020 CACCGCCAATCCTGCCTCCAACCCCTCCTATATATCCAAGTCCTCCTATTGTGAAGCCACC
1 CACCACCAATTCTGCCTCCAACGCCTCCTGTATATCCGAGTCCTCCTATTGTGAAGCCACC
9122081 TCCAATCGAG
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 112 1.00
ACGTcount: A:0.23, C:0.41, G:0.13, T:0.23
Consensus pattern (63 bp):
CACCACCAATTCTGCCTCCAACGCCTCCTGTATATCCGAGTCCTCCTATTGTGAAGCCACCAA
Found at i:9123240 original size:71 final size:71
Alignment explanation
Indices: 9123159--9123302 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 71
9123149 TTTGAAATAA
9123159 TTTTTAATTAGATCAATTCGAAACTTAGACA-TCAATAAACTCAAGAATTTAAAATTTAAAAACT
1 TTTTTAATTAGATCAATTCGAAACTTAGACACT-AATAAACTCAAGAATTTAAAATTTAAAAACT
9123223 TAAGATT
65 TAAGATT
* * * *
9123230 TTTTTAATTAGATCAATTCGGAACTTAGACACTAATAAATTCAAGAATTTGAAATTTATAAACTT
1 TTTTTAATTAGATCAATTCGAAACTTAGACACTAATAAACTCAAGAATTTAAAATTTAAAAACTT
9123295 AAGATT
66 AAGATT
9123301 TT
1 TT
9123303 AAAGAGAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 67 0.99
72 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (71 bp):
TTTTTAATTAGATCAATTCGAAACTTAGACACTAATAAACTCAAGAATTTAAAATTTAAAAACTT
AAGATT
Found at i:9123350 original size:15 final size:15
Alignment explanation
Indices: 9123330--9123361 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9123320 ATTTTTAGTC
9123330 GAAATAGGTGTTTTA
1 GAAATAGGTGTTTTA
9123345 GAAATAGGTGTTTTA
1 GAAATAGGTGTTTTA
9123360 GA
1 GA
9123362 TAAGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (15 bp):
GAAATAGGTGTTTTA
Found at i:9123522 original size:30 final size:29
Alignment explanation
Indices: 9123481--9123552 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
9123471 TATTAAAATG
*
9123481 TAATAAAATTTTGTTGAATATGACATGTAA
1 TAATAAAATTTT-TTGAATATAACATGTAA
* * *
9123511 TAATAACATTTTTTTAATATAATATGTAA
1 TAATAAAATTTTTTGAATATAACATGTAA
* *
9123540 CAATAATATTTTT
1 TAATAAAATTTTT
9123553 CTTAACATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (29 bp):
TAATAAAATTTTTTGAATATAACATGTAA
Found at i:9123539 original size:29 final size:29
Alignment explanation
Indices: 9123481--9123574 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 29
9123471 TATTAAAATG
* * *
9123481 TAATAAAATTTTGTTGAATATGACATGTAA
1 TAATAAAATTTT-TTTAATATAATATGTAA
*
9123511 TAATAACATTTTTTTAATATAATATGTAA
1 TAATAAAATTTTTTTAATATAATATGTAA
* * *
9123540 CAATAATATTTTTCTTAACATGAAT-TGTAA
1 TAATAAAATTTTT-TTAATAT-AATATGTAA
9123570 TAATA
1 TAATA
9123575 TTTTTTAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.46
30 26 0.48
31 3 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (29 bp):
TAATAAAATTTTTTTAATATAATATGTAA
Found at i:9125123 original size:27 final size:28
Alignment explanation
Indices: 9125087--9125139 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
9125077 AATATGTTAA
9125087 AATTTATAAATTAAA-A-AAATTTAATATT
1 AATTTATAAA--AAATATAAATTTAATATT
9125115 AATTT-TAAAAAATATAAATTTAATA
1 AATTTATAAAAAATATAAATTTAATA
9125140 CATTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 3 0.13
26 1 0.04
27 14 0.61
28 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATTTATAAAAAATATAAATTTAATATT
Found at i:9127860 original size:24 final size:24
Alignment explanation
Indices: 9127823--9127876 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
9127813 TGAATTTTTT
9127823 ATATT-AAATAGCCTCATTCTAGA
1 ATATTCAAATAGCCTCATTCTAGA
* * *
9127846 ATTTTCAAATAGCCTTATTTTAGA
1 ATATTCAAATAGCCTCATTCTAGA
9127870 ATATTCA
1 ATATTCA
9127877 GTGCAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (24 bp):
ATATTCAAATAGCCTCATTCTAGA
Found at i:9128335 original size:18 final size:17
Alignment explanation
Indices: 9128312--9128349 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
9128302 TTATTCAAAT
9128312 GTGATTATTCAAATTATA
1 GTGATTATTCAAATTA-A
*
9128330 GTGATTATTTAAATTAA
1 GTGATTATTCAAATTAA
9128347 GTG
1 GTG
9128350 TCTATTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (17 bp):
GTGATTATTCAAATTAA
Found at i:9128355 original size:17 final size:17
Alignment explanation
Indices: 9128312--9128363 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
9128302 TTATTCAAAT
*
9128312 GTGATTATTCAAATTATA
1 GTGATTATTTAAATTA-A
9128330 GTGATTATTTAAATTAA
1 GTGATTATTTAAATTAA
*
9128347 GTG-TCTATTTAGATTAA
1 GTGAT-TATTTAAATTAA
9128364 CACATGATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 1 0.03
17 15 0.48
18 15 0.48
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (17 bp):
GTGATTATTTAAATTAA
Found at i:9129264 original size:28 final size:27
Alignment explanation
Indices: 9129240--9129443 Score: 182
Period size: 27 Copynumber: 7.6 Consensus size: 27
9129230 GTTATGTTTT
9129240 AAAATTTAGTTGTTACATGTCATGTTG
1 AAAATTTAGTTGTTACATGTCATGTTG
* ** *
9129267 AAAA--TAATTGTTACACATCATCTT-
1 AAAATTTAGTTGTTACATGTCATGTTG
* * *
9129291 AAGAATATAGTTGTTACAAGTCATATTG
1 AA-AATTTAGTTGTTACATGTCATGTTG
* ** *
9129319 AAAATTTAGTTGTGACAAATTATGTTG
1 AAAATTTAGTTGTTACATGTCATGTTG
* *
9129346 AAAATTTACTTGTTACATGCCATGTTG
1 AAAATTTAGTTGTTACATGTCATGTTG
* *
9129373 AAAAATTTAGTTATTACAT-ACTATGTTG
1 -AAAATTTAGTTGTTACATGTC-ATGTTG
* * *
9129401 AAAATTGTAGTTGTTATATGACATGTTA
1 AAAATT-TAGTTGTTACATGTCATGTTG
9129429 AAAATTTAGTTGTTA
1 AAAATTTAGTTGTTA
9129444 TATGCTATGC
Statistics
Matches: 144, Mismatches: 25, Indels: 16
0.78 0.14 0.09
Matches are distributed among these distances:
24 2 0.01
25 18 0.12
27 77 0.53
28 45 0.31
29 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (27 bp):
AAAATTTAGTTGTTACATGTCATGTTG
Found at i:9129267 original size:55 final size:54
Alignment explanation
Indices: 9129201--9129445 Score: 198
Period size: 55 Copynumber: 4.5 Consensus size: 54
9129191 AAAAATATTA
* * * *
9129201 ATGTCGTGTTGAAAAATGTAGTGTTATACGTTATGTTTTAAAATTTAGTTGTTAC
1 ATGTCATGTTGAAAAATTTAGTGTTATACATTATG-TTGAAAATTTAGTTGTTAC
* * * * * *
9129256 ATGTCATGTTG-AAAA-TAATTGTTACACATCATCTT-AAGAATATAGTTGTTAC
1 ATGTCATGTTGAAAAATTTAGTGTTATACATTATGTTGAA-AATTTAGTTGTTAC
* * * * * *
9129308 AAGTCATATTG-AAAATTTAGTTGTGACAAATTATGTTGAAAATTTACTTGTTAC
1 ATGTCATGTTGAAAAATTTAG-TGTTATACATTATGTTGAAAATTTAGTTGTTAC
* *
9129362 ATGCCATGTTGAAAAATTTA--GTTATTACATACTATGTTGAAAATTGTAGTTGTTAT
1 ATGTCATGTTGAAAAATTTAGTGTTA-TACAT--TATGTTGAAAATT-TAGTTGTTAC
*
9129418 ATGACATGTT-AAAAATTTAGTTGTTATA
1 ATGTCATGTTGAAAAATTTAG-TGTTATA
9129446 TGCTATGCTG
Statistics
Matches: 150, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
51 2 0.01
52 31 0.21
53 16 0.11
54 36 0.24
55 42 0.28
56 17 0.11
57 2 0.01
58 4 0.03
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (54 bp):
ATGTCATGTTGAAAAATTTAGTGTTATACATTATGTTGAAAATTTAGTTGTTAC
Found at i:9129459 original size:28 final size:28
Alignment explanation
Indices: 9129207--9129460 Score: 149
Period size: 27 Copynumber: 9.4 Consensus size: 28
9129197 ATTAATGTCG
* * * *
9129207 TGTTGAAAAATGTAG-TGTTATACGTTA
1 TGTTGAAAAATTTAGTTGTTACATGCTA
**
9129234 TGTTTTAAAATTTAGTTGTTACATG-TCA
1 TGTTGAAAAATTTAGTTGTTACATGCT-A
*
9129262 TGTTG-AAAA--TAATTGTTACA--CATCA
1 TGTTGAAAAATTTAGTTGTTACATGC-T-A
* * * *
9129287 TCTT-AAGAATATAGTTGTTACAAG-TCA
1 TGTTGAAAAATTTAGTTGTTACATGCT-A
* * ***
9129314 TATTG-AAAATTTAGTTGTGACAAATTA
1 TGTTGAAAAATTTAGTTGTTACATGCTA
* *
9129341 TGTTG-AAAATTTACTTGTTACATGCCA
1 TGTTGAAAAATTTAGTTGTTACATGCTA
* *
9129368 TGTTGAAAAATTTAGTTATTACATACTA
1 TGTTGAAAAATTTAGTTGTTACATGCTA
*
9129396 TGTTG-AAAATTGTAGTTGTTATATGAC-A
1 TGTTGAAAAATT-TAGTTGTTACATG-CTA
*
9129424 TGTT-AAAAATTTAGTTGTTATATGCTA
1 TGTTGAAAAATTTAGTTGTTACATGCTA
*
9129451 TGCTGAAAAA
1 TGTTGAAAAA
9129461 GTTATTATAC
Statistics
Matches: 180, Mismatches: 30, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
25 19 0.11
26 1 0.01
27 97 0.54
28 62 0.34
29 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (28 bp):
TGTTGAAAAATTTAGTTGTTACATGCTA
Found at i:9140414 original size:2 final size:2
Alignment explanation
Indices: 9140407--9140457 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
9140397 CATGTGACTG
9140407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9140449 AT AT GT AT A
1 AT AT AT AT A
9140458 CTAGTATTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9144133 original size:5 final size:5
Alignment explanation
Indices: 9144119--9144148 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
9144109 GGCTTTTAGC
9144119 TGCC- TGCCT TGCCT TGCCT TGCCT TGCCT T
1 TGCCT TGCCT TGCCT TGCCT TGCCT TGCCT T
9144149 ATAGGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
TGCCT
Found at i:9145322 original size:23 final size:24
Alignment explanation
Indices: 9145279--9145323 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
9145269 TTATCAATTG
* *
9145279 AACTAACCTTTCCTTGGTTCTACA
1 AACTAACCTCTCCTTGATTCTACA
9145303 AACTAA-CTCTCCTTGATTCTA
1 AACTAACCTCTCCTTGATTCTA
9145324 TAAGTAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.38
Consensus pattern (24 bp):
AACTAACCTCTCCTTGATTCTACA
Found at i:9146950 original size:12 final size:12
Alignment explanation
Indices: 9146933--9146958 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9146923 GAGGGAAGCT
9146933 CATCATATTCAA
1 CATCATATTCAA
9146945 CATCATATTCAA
1 CATCATATTCAA
9146957 CA
1 CA
9146959 AAATGTCCTT
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:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (12 bp):
CATCATATTCAA
Found at i:9147502 original size:15 final size:16
Alignment explanation
Indices: 9147437--9147506 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 16
9147427 TTTATACTAT
*
9147437 TATAATTAAAATAAAATA
1 TATAAATAAAAT-AAA-A
9147455 TATAATATAAGAATCAAAAA
1 TATAA-ATAA-AAT--AAAA
*
9147475 TTTAAATAAAATAAAA
1 TATAAATAAAATAAAA
9147491 TATAAA-AAAATAAAA
1 TATAAATAAAATAAAA
9147506 T
1 T
9147507 TTATATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 10 0.22
16 9 0.20
18 8 0.17
19 7 0.15
20 8 0.17
21 4 0.09
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (16 bp):
TATAAATAAAATAAAA
Found at i:9147506 original size:31 final size:33
Alignment explanation
Indices: 9147440--9147514 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 33
9147430 ATACTATTAT
* **
9147440 AATTAAAATAAAATATATAATATAAGAATCAAA
1 AATTTAAATAAAATATATAATATAAGAAAAAAA
9147473 AATTTAAATAAAATA-A-AATATAA-AAAAATAA
1 AATTTAAATAAAATATATAATATAAGAAAAA-AA
*
9147504 AATTTATATAA
1 AATTTAAATAA
9147515 TATAGGTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 19 0.51
32 1 0.03
33 14 0.38
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (33 bp):
AATTTAAATAAAATATATAATATAAGAAAAAAA
Found at i:9147518 original size:55 final size:55
Alignment explanation
Indices: 9147444--9147555 Score: 142
Period size: 55 Copynumber: 2.0 Consensus size: 55
9147434 TATTATAATT
*
9147444 AAAATAAAATATATAATATAAG-AATCAA-AAATTTAAATAAAATA-A-AATATAAA
1 AAAATAAAATATATAATATAAGTAA--AACAAATTAAAATAAAATATATAATATAAA
*
9147497 AAAATAAAATTTATATAATATAGGTAAAACAAATTAAAATAAAATATATAATATAAA
1 AAAATAAAA--TATATAATATAAGTAAAACAAATTAAAATAAAATATATAATATAAA
9147554 AA
1 AA
9147556 TATATTAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
53 9 0.18
54 2 0.04
55 27 0.53
56 3 0.06
57 10 0.20
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (55 bp):
AAAATAAAATATATAATATAAGTAAAACAAATTAAAATAAAATATATAATATAAA
Found at i:9147555 original size:15 final size:15
Alignment explanation
Indices: 9147537--9147771 Score: 62
Period size: 15 Copynumber: 16.0 Consensus size: 15
9147527 AAATTAAAAT
9147537 AAAATATATAATATA
1 AAAATATATAATATA
9147552 AAAATATATTAGATTATA
1 AAAATATA-TA-A-TATA
* * *
9147570 ATAATAAATGAAAAT-
1 AAAATATAT-AATATA
9147585 AAAATATATGACAT-TA
1 AAAATATAT-A-ATATA
*
9147601 AAAATAT-T--TTTA
1 AAAATATATAATATA
* *
9147613 AGAGATGATATTATATA
1 A-AAAT-ATATAATATA
9147630 AAAAT-TAATAATA-A
1 AAAATAT-ATAATATA
9147644 AAAATATA-AATATA
1 AAAATATATAATATA
*
9147658 TTAAAA-ATAAAATATA
1 --AAAATATATAATATA
*
9147674 TAAGAT-TATAATA-A
1 -AAAATATATAATATA
* *
9147688 TAAAT-GA-AA-AT-
1 AAAATATATAATATA
*
9147699 AAAATATATGATATTA
1 AAAATATATAATA-TA
9147715 AAAATATAT--T-TA
1 AAAATATATAATATA
* *
9147727 AGAGATGATATTATATA
1 A-AAAT-ATATAATATA
9147744 AAAAT-TAATAATA-A
1 AAAATAT-ATAATATA
9147758 AAAATATA-AATATA
1 AAAATATATAATATA
9147772 TTAAACTTGT
Statistics
Matches: 166, Mismatches: 21, Indels: 67
0.65 0.08 0.26
Matches are distributed among these distances:
11 6 0.04
12 9 0.05
13 19 0.11
14 27 0.16
15 46 0.28
16 38 0.23
17 10 0.06
18 11 0.07
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (15 bp):
AAAATATATAATATA
Found at i:9147607 original size:114 final size:111
Alignment explanation
Indices: 9147487--9147776 Score: 282
Period size: 114 Copynumber: 2.5 Consensus size: 111
9147477 TAAATAAAAT
*
9147487 AAAATATAAAAAAATAAAATTTATATAATATAGGTAA-AACAAATTAAAATA-AAATATA-T-AA
1 AAAATATAAAAAAATAAAA-TTATATAA-A-AAGTAATAA-AAA--AAAATATAAATATATTAAA
* *
9147548 TATAAAAATATATTAGATTATAATAATAAATGAAAATAAAATATATGACATTA
60 AAT-AAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTA
* * * * * * *
9147601 AAAATATTTTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAAAAAT
1 AAAATA---TAAAAAAATAAAATTATATAAAAAGTAATAAAAAAAAATATAAATATATTAAAAAT
*
9147666 AAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGATATTA
63 AAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTA
* * * * * *
9147715 AAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
1 AAAATATA---AAAAAATAAAATTATATAAAAAGTAATAAAAAAAAATATAAATATATTAAA
9147777 CTTGTATTTT
Statistics
Matches: 154, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
111 1 0.01
112 6 0.04
113 7 0.05
114 117 0.76
115 7 0.05
116 8 0.05
117 8 0.05
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (111 bp):
AAAATATAAAAAAATAAAATTATATAAAAAGTAATAAAAAAAAATATAAATATATTAAAAATAAA
ATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTA
Found at i:9147640 original size:54 final size:54
Alignment explanation
Indices: 9147582--9147754 Score: 158
Period size: 54 Copynumber: 3.1 Consensus size: 54
9147572 AATAAATGAA
* *
9147582 AATAAAATATATGACATTAAAAATATTTTTAAGAGATGATATTATATAAAAATTAAT
1 AATAAAATATATGATATTAAAAATATATTTAAGAGATGATATTATATAAAAA-T--T
* * * *
9147639 AATAAAAAATATAAAT-ATATTAAAAATAAAATATATA-AGATTATAATA-ATAAATGAA--
1 AAT--AAAATAT--ATGATATTAAAAAT-ATATTTA-AGAGATGATATTATATAAA--AATT
9147696 AATAAAATATATGATATTAAAAATATATTTAAGAGATGATATTATATAAAAATT
1 AATAAAATATATGATATTAAAAATATATTTAAGAGATGATATTATATAAAAATT
9147750 AATAA
1 AATAA
9147755 TAAAAAATAT
Statistics
Matches: 93, Mismatches: 10, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
52 3 0.03
53 16 0.17
54 21 0.23
55 7 0.08
57 6 0.06
59 7 0.08
60 15 0.16
61 15 0.16
62 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.34
Consensus pattern (54 bp):
AATAAAATATATGATATTAAAAATATATTTAAGAGATGATATTATATAAAAATT
Found at i:9147651 original size:24 final size:24
Alignment explanation
Indices: 9147624--9147691 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
9147614 GAGATGATAT
9147624 TATATAAAAATTAATAATAAAAAA
1 TATATAAAAATTAATAATAAAAAA
* *
9147648 TATA-AATATATTAA-AA-ATAAAA
1 TATATAA-AAATTAATAATAAAAAA
* *
9147670 TATATAAGATTATAATAATAAA
1 TATATAAAAAT-TAATAATAAA
9147692 TGAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
24 12 0.36
25 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
TATATAAAAATTAATAATAAAAAA
Found at i:9147663 original size:16 final size:16
Alignment explanation
Indices: 9147643--9147674 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
9147633 ATTAATAATA
9147643 AAAAATATAAATATATT
1 AAAAATA-AAATATATT
9147660 AAAAATAAAATATAT
1 AAAAATAAAATATAT
9147675 AAGATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAAAATATATT
Found at i:9148974 original size:19 final size:19
Alignment explanation
Indices: 9148936--9148975 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9148926 ATTAGTGCTT
*
9148936 TTAAGAATTTCTTTAGTTC
1 TTAAGAATTTCTTTAATTC
9148955 TTAAGAATTT-TTTCAATTC
1 TTAAGAATTTCTTT-AATTC
9148974 TT
1 TT
9148976 CAGAGCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (19 bp):
TTAAGAATTTCTTTAATTC
Found at i:9149628 original size:3 final size:3
Alignment explanation
Indices: 9149620--9149676 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
9149610 TGAAACTTGC
9149620 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9149668 TAT TAT TAT
1 TAT TAT TAT
9149677 GGATTTGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9152497 original size:50 final size:50
Alignment explanation
Indices: 9152421--9152520 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
9152411 AATAGTTGGC
* * * *
9152421 ATGTTATAGCTGCAGCACTAAGAAGAATCAAAGGCATAAGAAGAAAAAGA
1 ATGTTACAGCTGCAGCACTAAAAAGAATCAAAGACAAAAGAAGAAAAAGA
* *
9152471 ATGTTACAGCTGCGGCACTAAAAAGAATCAAAGACAAAAGAAGAAGAAGA
1 ATGTTACAGCTGCAGCACTAAAAAGAATCAAAGACAAAAGAAGAAAAAGA
9152521 GGAAGAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.51, C:0.13, G:0.22, T:0.14
Consensus pattern (50 bp):
ATGTTACAGCTGCAGCACTAAAAAGAATCAAAGACAAAAGAAGAAAAAGA
Found at i:9153017 original size:2 final size:2
Alignment explanation
Indices: 9153010--9153037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9153000 TAAGTGGAAC
9153010 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
9153038 GCTAAATGGT
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:9154904 original size:2 final size:2
Alignment explanation
Indices: 9154897--9154924 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9154887 TTTAAACGGA
9154897 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
9154925 GTAATCTCAT
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:9161965 original size:2 final size:2
Alignment explanation
Indices: 9161960--9161994 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9161950 GTGTGTGTGT
9161960 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
9161995 GTAGCAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9170242 original size:12 final size:12
Alignment explanation
Indices: 9170220--9170255 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
9170210 GAAGAGCTTT
9170220 AGAGAAGAGAGGG
1 AGAG-AGAGAGGG
9170233 AGAGAGAGAGGG
1 AGAGAGAGAGGG
9170245 AGAGAGAGAGG
1 AGAGAGAGAGG
9170256 TTAAGAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGGG
Found at i:9173612 original size:12 final size:12
Alignment explanation
Indices: 9173595--9173619 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9173585 CCCACAAAGC
9173595 CTCCAACCCCAA
1 CTCCAACCCCAA
9173607 CTCCAACCCCAA
1 CTCCAACCCCAA
9173619 C
1 C
9173620 CAGACTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.60, G:0.00, T:0.08
Consensus pattern (12 bp):
CTCCAACCCCAA
Found at i:9187386 original size:27 final size:27
Alignment explanation
Indices: 9187344--9187398 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
9187334 ACCTCATCAT
* *
9187344 TGCCATTCGAAATCTCTAATTTCTCAA
1 TGCCATTCGAAATCTCTAACTCCTCAA
* *
9187371 TGCCATTTGAAGTCTCTAACTCCTCAA
1 TGCCATTCGAAATCTCTAACTCCTCAA
9187398 T
1 T
9187399 TTCCCCCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (27 bp):
TGCCATTCGAAATCTCTAACTCCTCAA
Found at i:9200665 original size:18 final size:21
Alignment explanation
Indices: 9200638--9200680 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
9200628 AATCAAATTA
9200638 TTTTATTATT-TATT-TCTTT
1 TTTTATTATTCTATTATCTTT
*
9200657 TTTTA-TATTCTATTATGTTT
1 TTTTATTATTCTATTATCTTT
9200677 TTTT
1 TTTT
9200681 GTTTTGAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 9 0.43
20 8 0.38
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTATTATTCTATTATCTTT
Found at i:9213407 original size:21 final size:19
Alignment explanation
Indices: 9213369--9213427 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
9213359 TAATTTTTAA
* *
9213369 TTATT-ATTTTACACAAAT
1 TTATTAATTTTAAAAAAAT
9213387 TTATTAATTTTTAAAATAAA-
1 TTATTAA-TTTTAAAA-AAAT
* *
9213407 TAATTTATTTTAAAAAAAT
1 TTATTAATTTTAAAAAAAT
9213426 TT
1 TT
9213428 TCATTAGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 8 0.25
19 10 0.31
20 11 0.34
21 3 0.09
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTAATTTTAAAAAAAT
Found at i:9213964 original size:2 final size:2
Alignment explanation
Indices: 9213957--9213987 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9213947 AAACTCATAA
9213957 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9213988 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9222086 original size:344 final size:344
Alignment explanation
Indices: 9221444--9222099 Score: 1107
Period size: 344 Copynumber: 1.9 Consensus size: 344
9221434 AAGTAGAAAT
* *
9221444 ATAATTGCAGAACATGCTCGCATAGGTAAAATTACTTTAACTTTTATTTTGCTTTATTATTTTAT
1 ATAATTGCAAAACATGCTCGCATAGATAAAATTACTTTAACTTTTATTTT-CTTTATTATTTTAT
9221509 TATTTTATCTCACTAGCGATGCATGAGAATTTCTTTCACTAAGATTTCTCAAGCAATAAGTAAAT
65 TATTTTATCTCACTAGCGATGCATGAGAATTTCTTTCACTAAGATTTCTCAAGCAATAAGTAAAT
* * *
9221574 TGTAGATACTTGATTTTGACTACTAATTTATTATTTTTCTAAAAATTGTTTCATAGCAAGTATAA
130 TGTAGATACTTGATTTTAACTACTAACTTACTATTTTTCTAAAAATTGTTTCATAGCAAGTATAA
*
9221639 TGTTATATAGAAAGTAATAAGAATGATTAAAGCAAGAAAAACAACTATATCACGTGAAAAGTATT
195 TGTTATATAGAAAGTAATAAGAATGATTAAAGCAAGAAAAACAACTATATCACGTGAAAAGCATT
* *
9221704 GAAAGTAACTAAGAGTAAGTGACAGAATTTAAATGTTAGTTTTATCCTTGAAAAGTTTGGTTTAG
260 GAAAGTAACTAAGAGTAAGTGAAAAAATTTAAATGTTAGTTTTA-CCTTGAAAAGTTTGGTTTAG
9221769 TGACTCAGAAATGAAAAAAAC
324 TGACTCAGAAATGAAAAAAAC
* *
9221790 ATAATTGCAAAACATGCTTGCATAGATCAAATTACTTTAACTTTTATTTT-TTTATTATTTTATT
1 ATAATTGCAAAACATGCTCGCATAGATAAAATTACTTTAACTTTTATTTTCTTTATTATTTTATT
* *
9221854 ATTTTGTCTCACTAGCGATGCATGAGAATTTCTTTCACTAAGATTTCTCAAGCAATTAGTAAATT
66 ATTTTATCTCACTAGCGATGCATGAGAATTTCTTTCACTAAGATTTCTCAAGCAATAAGTAAATT
9221919 GTAGATACTTGATTTTAACTACTAACTTACTATTTTTCTAAAAATTGTTTCATAGCAAGTATAAT
131 GTAGATACTTGATTTTAACTACTAACTTACTATTTTTCTAAAAATTGTTTCATAGCAAGTATAAT
** *
9221984 GTTATATAGAAAGTAATAAGAATGATTAAAGCGGGTAAAACAACTATATCACGTGAAAAGCATTG
196 GTTATATAGAAAGTAATAAGAATGATTAAAGCAAGAAAAACAACTATATCACGTGAAAAGCATTG
** * * *
9222049 AAAGTAACTCTGAGTGAGTGAAAAAATTTACATGTTAGTTTTACTTTGAAA
261 AAAGTAACTAAGAGTAAGTGAAAAAATTTAAATGTTAGTTTTACCTTGAAA
9222100 TATTTTACAA
Statistics
Matches: 290, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
343 7 0.02
344 237 0.82
346 46 0.16
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (344 bp):
ATAATTGCAAAACATGCTCGCATAGATAAAATTACTTTAACTTTTATTTTCTTTATTATTTTATT
ATTTTATCTCACTAGCGATGCATGAGAATTTCTTTCACTAAGATTTCTCAAGCAATAAGTAAATT
GTAGATACTTGATTTTAACTACTAACTTACTATTTTTCTAAAAATTGTTTCATAGCAAGTATAAT
GTTATATAGAAAGTAATAAGAATGATTAAAGCAAGAAAAACAACTATATCACGTGAAAAGCATTG
AAAGTAACTAAGAGTAAGTGAAAAAATTTAAATGTTAGTTTTACCTTGAAAAGTTTGGTTTAGTG
ACTCAGAAATGAAAAAAAC
Found at i:9229295 original size:103 final size:103
Alignment explanation
Indices: 9229116--9229324 Score: 409
Period size: 103 Copynumber: 2.0 Consensus size: 103
9229106 TGTGATATGT
9229116 TGGTTCCAATGATTAGTTCAATCTTTGGGCAAGAATAATGATTCTGGTCCACGAGTCTATTCCAG
1 TGGTTCCAATGATTAGTTCAATCTTTGGGCAAGAATAATGATTCTGGTCCACGAGTCTATTCCAG
*
9229181 TCAAACTCAATAATAGCCATTCTTTACTCACCTCAGAA
66 TCAAACCCAATAATAGCCATTCTTTACTCACCTCAGAA
9229219 TGGTTCCAATGATTAGTTCAATCTTTGGGCAAGAATAATGATTCTGGTCCACGAGTCTATTCCAG
1 TGGTTCCAATGATTAGTTCAATCTTTGGGCAAGAATAATGATTCTGGTCCACGAGTCTATTCCAG
9229284 TCAAACCCAATAATAGCCATTCTTTACTCACCTCAGAA
66 TCAAACCCAATAATAGCCATTCTTTACTCACCTCAGAA
9229322 TGG
1 TGG
9229325 CTATTCCTCA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (103 bp):
TGGTTCCAATGATTAGTTCAATCTTTGGGCAAGAATAATGATTCTGGTCCACGAGTCTATTCCAG
TCAAACCCAATAATAGCCATTCTTTACTCACCTCAGAA
Found at i:9237418 original size:23 final size:23
Alignment explanation
Indices: 9237392--9237465 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
9237382 GCAATGTCTA
9237392 AGTCACACAATACCTTACTAACT
1 AGTCACACAATACCTTACTAACT
** * *
9237415 AGTCACGTAATGCCTTACTAACA
1 AGTCACACAATACCTTACTAACT
9237438 AGTCACACAATACC-TA-TCAACT
1 AGTCACACAATACCTTACT-AACT
9237460 AGTCAC
1 AGTCAC
9237466 GTAATGTCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 11 0.26
23 30 0.71
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.24
Consensus pattern (23 bp):
AGTCACACAATACCTTACTAACT
Found at i:9237487 original size:45 final size:46
Alignment explanation
Indices: 9237391--9237495 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 46
9237381 AGCAATGTCT
*
9237391 AAGTCACACAATACCTTACTAACTAGTCACGTAATGCCTTACTAAC
1 AAGTCACACAATACCTTACTAACTAGTCACGTAATGCCATACTAAC
*
9237437 AAGTCACACAATACC-TA-TCAACTAGTCACGTAATGTCATA-TCAAC
1 AAGTCACACAATACCTTACT-AACTAGTCACGTAATGCCATACT-AAC
* *
9237482 CAGTCATACAATAC
1 AAGTCACACAATAC
9237496 TTAGTCAAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
44 2 0.04
45 36 0.68
46 15 0.28
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.25
Consensus pattern (46 bp):
AAGTCACACAATACCTTACTAACTAGTCACGTAATGCCATACTAAC
Found at i:9238451 original size:20 final size:20
Alignment explanation
Indices: 9238409--9238453 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9238399 TTAAATATTA
* * *
9238409 TTTTTTAGGATTTTTTTCTT
1 TTTTTTAGGATTTTCTACGT
*
9238429 TTTTTTAGGGTTTTCTACGT
1 TTTTTTAGGATTTTCTACGT
9238449 TTTTT
1 TTTTT
9238454 CGGATCTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.71
Consensus pattern (20 bp):
TTTTTTAGGATTTTCTACGT
Found at i:9254745 original size:57 final size:57
Alignment explanation
Indices: 9254682--9254796 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
9254672 TCAATTAAGT
9254682 TGGACTTAATTGGAATAGATTAAAATAAAGTTAGAAATTAATTAAGTTCACAAAGAC
1 TGGACTTAATTGGAATAGATTAAAATAAAGTTAGAAATTAATTAAGTTCACAAAGAC
*
9254739 TGGACTTAATTGGAATATATTAAAATAAAGTTAGAAATTAATTAAGTTCACAAAGAC
1 TGGACTTAATTGGAATAGATTAAAATAAAGTTAGAAATTAATTAAGTTCACAAAGAC
9254796 T
1 T
9254797 TAACTAAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (57 bp):
TGGACTTAATTGGAATAGATTAAAATAAAGTTAGAAATTAATTAAGTTCACAAAGAC
Found at i:9255274 original size:11 final size:11
Alignment explanation
Indices: 9255258--9255282 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9255248 TTCATAATTA
9255258 ACATGAAAAAT
1 ACATGAAAAAT
9255269 ACATGAAAAAT
1 ACATGAAAAAT
9255280 ACA
1 ACA
9255283 AACATTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (11 bp):
ACATGAAAAAT
Found at i:9266993 original size:10 final size:10
Alignment explanation
Indices: 9266980--9267006 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9266970 GAACTCATTT
9266980 TATATATGTA
1 TATATATGTA
9266990 TATATATGTA
1 TATATATGTA
9267000 TATATAT
1 TATATAT
9267007 ACACACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATGTA
Found at i:9267614 original size:2 final size:2
Alignment explanation
Indices: 9267607--9267632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9267597 GTATAAAGCA
9267607 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
9267633 GTAAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9274029 original size:15 final size:15
Alignment explanation
Indices: 9274009--9274037 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9273999 AGTCTTTAAA
9274009 CTATGTCTTTATTTG
1 CTATGTCTTTATTTG
9274024 CTATGTCTTTATTT
1 CTATGTCTTTATTT
9274038 TGGTGTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (15 bp):
CTATGTCTTTATTTG
Found at i:9274212 original size:17 final size:17
Alignment explanation
Indices: 9274163--9274204 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
9274153 TTTATTAGGG
9274163 CACATATTTAAGGGGAA
1 CACATATTTAAGGGGAA
9274180 CACATATTTAAGGGGAA
1 CACATATTTAAGGGGAA
9274197 CACATATT
1 CACATATT
9274205 CAGGGGGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (17 bp):
CACATATTTAAGGGGAA
Found at i:9282980 original size:65 final size:65
Alignment explanation
Indices: 9282888--9283043 Score: 179
Period size: 65 Copynumber: 2.4 Consensus size: 65
9282878 TCTTCGATCA
** * * *
9282888 GTTGTGTTG-CATGCTTTATATAATTGATATGTGATTCCAAGCACAATGCTTGATATCCTTAATT
1 GTTGTGTTGTC-TGCTTTATATCCTTGATATATGATTCCAAGCACAATGCTTGAAATCCTTAATC
9282952 T
65 T
* * * * * *
9282953 GTTGTGTTGTCTGCTTGATATCCTTGATTTATGGTTCTAAGCAGAATGCTTGAAATCCTTGATCT
1 GTTGTGTTGTCTGCTTTATATCCTTGATATATGATTCCAAGCACAATGCTTGAAATCCTTAATCT
* *
9283018 GTTTTGTTATCTGCTTTATATCCTTG
1 GTTGTGTTGTCTGCTTTATATCCTTG
9283044 TCCCTGATCC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 75 0.99
66 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (65 bp):
GTTGTGTTGTCTGCTTTATATCCTTGATATATGATTCCAAGCACAATGCTTGAAATCCTTAATCT
Found at i:9283215 original size:56 final size:55
Alignment explanation
Indices: 9283120--9283244 Score: 171
Period size: 56 Copynumber: 2.2 Consensus size: 55
9283110 GATATTGTCT
9283120 TTTCAAGCATAATATTCATTATCTTGTGTTGTCTACTTGATATATTAAATTTGTG
1 TTTCAAGCATAATATTCATTATCTTGTGTTGTCTACTTGATATATTAAATTTGTG
* * * *
9283175 TTTCCAAGCATAATCTTCGA-TATCTTGTGTTGTTTCCTTGATATCTTAAATTTGTGG
1 TTT-CAAGCATAATATTC-ATTATCTTGTGTTGTCTACTTGATATATTAAATTTGT-G
*
9283232 TTTCAAGTATAAT
1 TTTCAAGCATAAT
9283245 GCTCAATAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
55 3 0.05
56 54 0.87
57 5 0.08
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.48
Consensus pattern (55 bp):
TTTCAAGCATAATATTCATTATCTTGTGTTGTCTACTTGATATATTAAATTTGTG
Found at i:9283486 original size:20 final size:20
Alignment explanation
Indices: 9283458--9283495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9283448 TGCCTTGATG
*
9283458 AAGAATTATATTCTTGAAGA
1 AAGAATTATATCCTTGAAGA
*
9283478 AAGAGTTATATCCTTGAA
1 AAGAATTATATCCTTGAA
9283496 AAAAATATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (20 bp):
AAGAATTATATCCTTGAAGA
Found at i:9288491 original size:20 final size:20
Alignment explanation
Indices: 9288446--9288492 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
9288436 TTGCTGATGA
*
9288446 TTTTCAAAATGAAAGATTGTC
1 TTTTC-AAATGAAAGATTATC
*
9288467 CTTTCAAATGAAA-AGTTATC
1 TTTTCAAATGAAAGA-TTATC
9288487 TTTTCA
1 TTTTCA
9288493 TCTTATATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
TTTTCAAATGAAAGATTATC
Found at i:9296130 original size:29 final size:31
Alignment explanation
Indices: 9296066--9296130 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
9296056 TTATTAAACA
9296066 TTTATATATTTAATTTGAGTCAAATAACCTC
1 TTTATATATTTAATTTGAGTCAAATAACCTC
* * *
9296097 ATTATAT-TTTATTTTGAGTCAAATAA-GTC
1 TTTATATATTTAATTTGAGTCAAATAACCTC
9296126 TTTAT
1 TTTAT
9296131 GACTAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 6 0.20
30 18 0.60
31 6 0.20
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTATATATTTAATTTGAGTCAAATAACCTC
Found at i:9298571 original size:3 final size:3
Alignment explanation
Indices: 9298563--9298589 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9298553 ATGGTTTCTA
9298563 AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG
9298590 GATTAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:9304891 original size:24 final size:24
Alignment explanation
Indices: 9304850--9304895 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9304840 TTGAACAATG
**
9304850 AGGAAGATTGACTGAAAAAAAACA
1 AGGAAGATTGACCAAAAAAAAACA
*
9304874 AGGAAGATTGGCCAAAAAAAAA
1 AGGAAGATTGACCAAAAAAAAA
9304896 AAGAAGTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.22, T:0.11
Consensus pattern (24 bp):
AGGAAGATTGACCAAAAAAAAACA
Found at i:9319248 original size:90 final size:90
Alignment explanation
Indices: 9319095--9319274 Score: 290
Period size: 90 Copynumber: 2.0 Consensus size: 90
9319085 TAGAACGTGT
*
9319095 CTCTTTTTTAAACCATGAAAGAAAAAATCTTAAAAGAGTATACAATTGTCTTATTGTACTGTTTT
1 CTCTTTTTTAAACCATGAAAGAAAAAATCTTAAAAGAGTATACAATTATCTTATTGTACTGTTTT
*
9319160 GATATATTCTTTATAATCTGCTTAA
66 GATATATTCTTTATAATATGCTTAA
* * *
9319185 CTCTTTTTTCAAA-CATGAAAGAAAAAATCTTAAAAGAGTGTACAATTATTTTATTTTACTGTTT
1 CTCTTTTTT-AAACCATGAAAGAAAAAATCTTAAAAGAGTATACAATTATCTTATTGTACTGTTT
*
9319249 TGATATATTCTTTATTATATGCTTAA
65 TGATATATTCTTTATAATATGCTTAA
9319275 TTTGGGGCCA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
90 80 0.96
91 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (90 bp):
CTCTTTTTTAAACCATGAAAGAAAAAATCTTAAAAGAGTATACAATTATCTTATTGTACTGTTTT
GATATATTCTTTATAATATGCTTAA
Found at i:9335748 original size:5 final size:5
Alignment explanation
Indices: 9335738--9335768 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
9335728 TACTTAATCG
*
9335738 AATAT AATAT AATAT AATAT AACAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A
9335769 TATGATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:9335822 original size:18 final size:17
Alignment explanation
Indices: 9335795--9335828 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9335785 CATATCATAT
*
9335795 TGTATTATACATATATTA
1 TGTATCATACA-ATATTA
9335813 TGTATCATACAATATT
1 TGTATCATACAATATT
9335829 GATAACTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (17 bp):
TGTATCATACAATATTA
Found at i:9338205 original size:3 final size:3
Alignment explanation
Indices: 9338197--9338221 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9338187 CACTAAAATC
9338197 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
9338222 CAAACAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9341011 original size:20 final size:19
Alignment explanation
Indices: 9340984--9341033 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
9340974 TATTTAATTT
9340984 AAAA-TAAAAAT-ATAAAA
1 AAAATTAAAAATAATAAAA
*
9341001 TAATAATTAAATATAATAAAA
1 -AA-AATTAAAAATAATAAAA
*
9341022 AAAATTTAAAAT
1 AAAATTAAAAAT
9341034 TTTTGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 10 0.38
20 8 0.31
21 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATTAAAAATAATAAAA
Found at i:9347328 original size:2 final size:2
Alignment explanation
Indices: 9347321--9347346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9347311 AAACTGGAGT
9347321 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
9347347 TAAGCTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9350715 original size:16 final size:16
Alignment explanation
Indices: 9350691--9350721 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9350681 ATTCTTATTT
*
9350691 AAATTTTTTTTTAAAA
1 AAATGTTTTTTTAAAA
9350707 AAATGTTTTTTTAAA
1 AAATGTTTTTTTAAA
9350722 GTTATCAAAA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AAATGTTTTTTTAAAA
Found at i:9356729 original size:23 final size:24
Alignment explanation
Indices: 9356703--9356747 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
9356693 CAAAAATTTA
* *
9356703 AATTCAGC-AGGCTAATTGAAAAG
1 AATTAAGCGAGGCCAATTGAAAAG
*
9356726 AATTAAGCGTGGCCAATTGAAA
1 AATTAAGCGAGGCCAATTGAAA
9356748 TATTGGGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (24 bp):
AATTAAGCGAGGCCAATTGAAAAG
Done.