Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 90 of 143
Found at i:28144952 original size:4 final size:4
Alignment explanation
Indices: 28144943--28145007 Score: 75
Period size: 4 Copynumber: 16.8 Consensus size: 4
28144933 TCTTATTATT
*
28144943 TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA TTAA TTTTA TTT- TATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA
28144990 TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTT
28145008 TATGAATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
3 10 0.19
4 40 0.74
5 4 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:28144981 original size:35 final size:36
Alignment explanation
Indices: 28144935--28145007 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
28144925 TCCATTTTTC
*
28144935 TTATTATTTTTA-TTTATTTATTTATTTA-TTATTAT
1 TTATTAATTTTATTTTA-TTATTTATTTATTTATTAT
28144970 TTATTAATTTTATTTTATTATTTATTTATTTATTAT
1 TTATTAATTTTATTTTATTATTTATTTATTTATTAT
28145006 TT
1 TT
28145008 TATGAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (36 bp):
TTATTAATTTTATTTTATTATTTATTTATTTATTAT
Found at i:28146318 original size:18 final size:18
Alignment explanation
Indices: 28146295--28146346 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
28146285 GGCAGCGAAG
*
28146295 AAGAAAGATGAAGAAGAT
1 AAGAAAGATGAAGAAGAC
* * *
28146313 AGGAAAAAGTTAGAGAAGAC
1 AAGAAAGA-TGA-AGAAGAC
28146333 AAGAAAGATGAAGA
1 AAGAAAGATGAAGA
28146347 GGCATGCTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
18 9 0.36
19 4 0.16
20 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.29, T:0.10
Consensus pattern (18 bp):
AAGAAAGATGAAGAAGAC
Found at i:28149737 original size:20 final size:20
Alignment explanation
Indices: 28149712--28149749 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28149702 CAACCCATTC
* *
28149712 ACACATTTATTTTCACAACA
1 ACACATGTAATTTCACAACA
28149732 ACACATGTAATTTCACAA
1 ACACATGTAATTTCACAA
28149750 TTTTCACATT
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:0.24, G:0.03, T:0.32
Consensus pattern (20 bp):
ACACATGTAATTTCACAACA
Found at i:28161493 original size:20 final size:21
Alignment explanation
Indices: 28161455--28161495 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28161445 TTGAGTTATG
* *
28161455 TTATATTTTAGTTATTTAATT
1 TTATATTTTAGGTAATTAATT
28161476 TTATA-TTTAGGTAATTAATT
1 TTATATTTTAGGTAATTAATT
28161496 AGGTTAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
TTATATTTTAGGTAATTAATT
Found at i:28174871 original size:6 final size:7
Alignment explanation
Indices: 28174854--28174882 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28174844 ATGCTTGAAA
28174854 AAAAATG
1 AAAAATG
28174861 AAAAATG
1 AAAAATG
28174868 AAAAATG
1 AAAAATG
28174875 AAAAATG
1 AAAAATG
28174882 A
1 A
28174883 TAAGGAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:28175337 original size:17 final size:17
Alignment explanation
Indices: 28175315--28175353 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28175305 CTCTATCTTG
* *
28175315 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
28175332 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
28175349 ACAAG
1 ACAAG
28175354 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:28182477 original size:32 final size:30
Alignment explanation
Indices: 28182416--28182492 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
28182406 TTAGTGGGTG
* *
28182416 TGAGGTCTAGTTTTACATAGTGTCTTAGTTT
1 TGAGGTCTA-TTTTACATAGTGACCTAGTTT
*
28182447 TGAGGTCTATTTTAGATTTAGTGACCTAGTTT
1 TGAGGTCTATTTTACA--TAGTGACCTAGTTT
* *
28182479 TGAAGTTTATTTTA
1 TGAGGTCTATTTTA
28182493 ATTAAAGACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.15
31 9 0.23
32 24 0.62
ACGTcount: A:0.22, C:0.08, G:0.21, T:0.49
Consensus pattern (30 bp):
TGAGGTCTATTTTACATAGTGACCTAGTTT
Found at i:28182505 original size:30 final size:32
Alignment explanation
Indices: 28182441--28182507 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
28182431 CATAGTGTCT
* **
28182441 TAGTTTTGAGGTCTATTTTAGATTTAGTGACC
1 TAGTTTTGAAGTCTATTTTAGATTTAAAGACC
*
28182473 TAGTTTTGAAGTTTATTTTA-A-TTAAAGACC
1 TAGTTTTGAAGTCTATTTTAGATTTAAAGACC
28182503 TAGTT
1 TAGTT
28182508 ATAAGGTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 12 0.39
31 1 0.03
32 18 0.58
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (32 bp):
TAGTTTTGAAGTCTATTTTAGATTTAAAGACC
Found at i:28184700 original size:18 final size:19
Alignment explanation
Indices: 28184668--28184723 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
28184658 GTGATCTAAT
* *
28184668 TTTAAAAATATTAAAAG-A
1 TTTAAAAAAAATAAAAGTA
28184686 TTTAAAAAAAATAAAAGCTATA
1 TTTAAAAAAAATAAAAG---TA
28184708 TTTAAAAAAAATAAAA
1 TTTAAAAAAAATAAAA
28184724 AATAGGGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 15 0.47
22 17 0.53
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
TTTAAAAAAAATAAAAGTA
Found at i:28185669 original size:21 final size:22
Alignment explanation
Indices: 28185629--28185681 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
28185619 TTTAGTTTTG
28185629 AAAT-AAA-AAATAATAATATA
1 AAATAAAATAAATAATAATATA
28185649 AAATAAAATAAATAA-AATATA
1 AAATAAAATAAATAATAATATA
*
28185670 AAGTAAATATAA
1 AAATAAA-ATAA
28185682 GATATATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 15 0.52
22 10 0.34
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (22 bp):
AAATAAAATAAATAATAATATA
Found at i:28185670 original size:16 final size:17
Alignment explanation
Indices: 28185629--28185687 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 17
28185619 TTTAGTTTTG
*
28185629 AAATAAAAAATAATAATAT
1 AAATATAAAAT-A-AATAT
28185648 AAA-ATAAAATAAATA-
1 AAATATAAAATAAATAT
*
28185663 AAATATAAAGTAAATAT
1 AAATATAAAATAAATAT
28185680 AAGATATA
1 AA-ATATA
28185688 TATGTGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 3 0.09
16 15 0.43
17 3 0.09
18 11 0.31
19 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAATATAAAATAAATAT
Found at i:28186953 original size:26 final size:25
Alignment explanation
Indices: 28186924--28186978 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
28186914 ATATCAAATA
*
28186924 TCAACATAT-ACTATCTCATTTCCAAT
1 TCAAAATATAACTATC-CATTTCC-AT
* *
28186950 TCAAAATTTAACTTTCCATTTCCAT
1 TCAAAATATAACTATCCATTTCCAT
28186975 TCAA
1 TCAA
28186979 TTGAATATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 6 0.24
26 14 0.56
27 5 0.20
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
TCAAAATATAACTATCCATTTCCAT
Found at i:28189615 original size:28 final size:30
Alignment explanation
Indices: 28189433--28189687 Score: 152
Period size: 30 Copynumber: 8.7 Consensus size: 30
28189423 CGTAAATTTG
* * *
28189433 GAAAAGTTTAGGGGGTGAAAATATAATTTTG
1 GAAAAGTTTA-AGGGTCAAAATATAATTTTA
** * * **
28189464 GGTAAGCTT--GGGTTAAAATACGATTTTA
1 GAAAAGTTTAAGGGTCAAAATATAATTTTA
* * * *
28189492 GAGAAGTTT-AGGGT-TAAATCATGATTTTT
1 GAAAAGTTTAAGGGTCAAAAT-ATAATTTTA
* * * ** *
28189521 GGAAGGTTTAAGGGTTAAAATGCAATTTTG
1 GAAAAGTTTAAGGGTCAAAATATAATTTTA
* * *
28189551 GAGAAGTTT-AGGAGTTAAAATGA-AATTTTT
1 GAAAAGTTTAAGG-GTCAAAAT-ATAATTTTA
*
28189581 GAAAAGTTT-AGGCTCAAAATATAATTTT-
1 GAAAAGTTTAAGGGTCAAAATATAATTTTA
* *
28189609 GAAAAG-TTAGGGGTCAAAATGTAATTTTA
1 GAAAAGTTTAAGGGTCAAAATATAATTTTA
*
28189638 GAAAAGTTTAAGGGTTAAAA-AGTAATTTTA
1 GAAAAGTTTAAGGGTCAAAATA-TAATTTTA
*
28189668 GAAAAATTTAAGGGTCAAAA
1 GAAAAGTTTAAGGGTCAAAA
28189688 CGTGATTTCT
Statistics
Matches: 176, Mismatches: 37, Indels: 23
0.75 0.16 0.10
Matches are distributed among these distances:
27 2 0.01
28 48 0.27
29 38 0.22
30 78 0.44
31 10 0.06
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
GAAAAGTTTAAGGGTCAAAATATAATTTTA
Found at i:28191794 original size:39 final size:39
Alignment explanation
Indices: 28191751--28192281 Score: 132
Period size: 39 Copynumber: 13.6 Consensus size: 39
28191741 CCTAGCTCAA
* * *
28191751 GGTAAGAGATTGGCTGACGGTGATCTGCCCTACGATCGG
1 GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
* * ** * * *
28191790 GGTAAAAGATCGAATG-C-TTGCAATCTACCCCAGGCTCGA
1 GGTAAGAGATTGGCTGACGGTG--ATCTACCCTAGGCTCGG
*
28191829 GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCGG
1 GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
* * * * * *
28191868 GGTAAGAGATCAGAC-GAC-TTCAATCTTTCCC-AAGCTCGG
1 GGTAAGAGAT-TGGCTGACGGT-GATC-TACCCTAGGCTCGG
* * * *
28191907 GGTAAGAGATTGGCTGATGATGATTTGCTCC-AGGCTCGG
1 GGTAAGAGATTGGCTGACGGTGATCTAC-CCTAGGCTCGG
* * * * **** * * *
28191946 GGTAAAAGATCGGATGGCTACAATCTGTCCC-AAGTTCGG
1 GGTAAGAGATTGGCTGACGGTGATCT-ACCCTAGGCTCGG
* * ** *
28191985 GGTAAGAGATTGGCTGATGGTGATCTACCCCAAACTCGA
1 GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
* * * * * * *
28192024 GGTAAAAGATCGGATGGCTGG-AATCT-GCCTCAGGCTTGG
1 GGTAAGAGATTGGCTGAC-GGTGATCTACCCT-AGGCTCGG
* * * * *
28192063 GGTAAGAGATTAGTTGATGGTGATCTACCCCAAGCTCGG
1 GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
* * ** * * ** * *
28192102 GGTAAAAGATCGAATGGCTGCAATCT-GCCTCAAGCTCGG
1 GGTAAGAGATTGGCTGACGGTGATCTACCCT-AGGCTCGG
** * * * * **
28192141 GGTAAGAGATTGATTGATGGTGATCTGCCCCAAGCTCCA
1 GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
* * * * *
28192180 GGTAAAAGATCGGATG--GTTGCAATCTACCCCAGGCTCGG
1 GGTAAGAGATTGGCTGACGGTG--ATCTACCCTAGGCTCGG
** * * *
28192219 GGTAAGAGATTGGCTGTTGGTGATTTGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
* * * * *
28192258 GATAAAAGATCGGATGACTGTGAT
1 GGTAAGAGATTGGCTGACGGTGAT
28192282 ATGCCCCACG
Statistics
Matches: 343, Mismatches: 127, Indels: 44
0.67 0.25 0.09
Matches are distributed among these distances:
37 5 0.01
38 15 0.04
39 304 0.89
40 14 0.04
41 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
GGTAAGAGATTGGCTGACGGTGATCTACCCTAGGCTCGG
Found at i:28192306 original size:78 final size:78
Alignment explanation
Indices: 28191724--28192273 Score: 616
Period size: 78 Copynumber: 7.1 Consensus size: 78
28191714 TAAGATATTA
* * ** * * * *
28191724 GATGGTTGCAATCTGCCCCTAGCTCAAGGTAAGAGATTGGCTGACGGTGATCTGCCCTACGATCG
1 GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
28191789 GGGTAAAAGATCG
66 GGGTAAAAGATCG
* * * * * * *
28191802 AAT-GCTTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTC
1 GATGGC-TGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC
* *
28191866 GGGGTAAGAGATCA
65 GGGGTAAAAGATCG
* * * ** * * * *
28191880 GACGACTTCAATCTTTCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATTTGCTCCAGGCTCG
1 GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
28191945 GGGTAAAAGATCG
66 GGGTAAAAGATCG
* * * * *
28191958 GATGGCTACAATCTGTCCCAAGTTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAACTCG
1 GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
*
28192023 AGGTAAAAGATCG
66 GGGTAAAAGATCG
* * * * * * *
28192036 GATGGCTGGAATCTGCCTCAGGCTTGGGGTAAGAGATTAGTTGATGGTGATCTACCCCAAGCTCG
1 GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
28192101 GGGTAAAAGATCG
66 GGGTAAAAGATCG
* * ** *
28192114 AATGGCTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTGATTGATGGTGATCTGCCCCAAGCTCC
1 GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
*
28192179 AGGTAAAAGATCG
66 GGGTAAAAGATCG
* * * * * *
28192192 GATGGTTGCAATCTACCCCAGGCTCGGGGTAAGAGATTGGCTGTTGGTGATTTGCCCCAGGCTCG
1 GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
*
28192257 GGATAAAAGATCG
66 GGGTAAAAGATCG
28192270 GATG
1 GATG
28192274 ACTGTGATAT
Statistics
Matches: 398, Mismatches: 72, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
77 1 0.00
78 396 0.99
79 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (78 bp):
GATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG
GGGTAAAAGATCG
Found at i:28204593 original size:60 final size:59
Alignment explanation
Indices: 28204523--28204714 Score: 196
Period size: 60 Copynumber: 3.2 Consensus size: 59
28204513 GCTCAAGGTT
* * *
28204523 AAAATGTAATTTTAGAGAAGTTTAGGGTCAAAAAGTTATTTTTGGAAGGTTTAGGGATC
1 AAAATATAATTTTAGAGAAGTTTAGGGTCAAAAAGTTAATTTTGGAAAGTTTAGGGATC
* * * *
28204582 AAAATTATAATTTTTGAGAAGTTTAAGGGTTAAAATG-TAATTTTGGAGAAGTTTAGGTG-TT
1 AAAA-TATAATTTTAGAGAAGTTT-AGGGTCAAAAAGTTAATTTTGGA-AAGTTTAGG-GATC
* * * *
28204643 AAAATGTAATTTTAGAAAAGTTTTGGGTC-AAAA-TATAATTTTGGAAAAGTTTCGGGATC
1 AAAATATAATTTTAGAGAAGTTTAGGGTCAAAAAGT-TAATTTTGG-AAAGTTTAGGGATC
28204702 -AAATATAATTTTA
1 AAAATATAATTTTA
28204715 AAAAAATTTA
Statistics
Matches: 109, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
58 16 0.15
59 26 0.24
60 43 0.39
61 23 0.21
62 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (59 bp):
AAAATATAATTTTAGAGAAGTTTAGGGTCAAAAAGTTAATTTTGGAAAGTTTAGGGATC
Found at i:28204618 original size:90 final size:89
Alignment explanation
Indices: 28204519--28204694 Score: 237
Period size: 90 Copynumber: 2.0 Consensus size: 89
28204509 GAAAGCTCAA
* * * *
28204519 GGTTAAAATGTAATTTTAGAGAAGTTTAGG-GTCAAAAAGTTATTTTTGGAAGGTTTAGGGATCA
1 GGTTAAAATGTAATTTTAGAGAAGTTTAGGTGTCAAAAAGTAATTTTAGAAAAGTTTAGGG-TCA
* *
28204583 AAATTATAATTTTTGAGAAGTTTAAG
65 AAA-TATAATTTTGGAAAAGTTTAAG
* * * *
28204609 GGTTAAAATGTAATTTTGGAGAAGTTTAGGTGTTAAAATGTAATTTTAGAAAAGTTTTGGGTCAA
1 GGTTAAAATGTAATTTTAGAGAAGTTTAGGTGTCAAAAAGTAATTTTAGAAAAGTTTAGGGTCAA
28204674 AATATAATTTTGGAAAAGTTT
66 AATATAATTTTGGAAAAGTTT
28204695 CGGGATCAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
89 17 0.23
90 35 0.47
91 23 0.31
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (89 bp):
GGTTAAAATGTAATTTTAGAGAAGTTTAGGTGTCAAAAAGTAATTTTAGAAAAGTTTAGGGTCAA
AATATAATTTTGGAAAAGTTTAAG
Found at i:28204625 original size:30 final size:29
Alignment explanation
Indices: 28204523--28204757 Score: 188
Period size: 29 Copynumber: 7.9 Consensus size: 29
28204513 GCTCAAGGTT
28204523 AAAATGTAATTTTAGAGAAGTTTAGGGTC
1 AAAATGTAATTTTAGAGAAGTTTAGGGTC
* * *
28204552 AAAAAGTTATTTTTG-GAAGGTTTAGGGATC
1 AAAATGTAATTTTAGAGAA-GTTTAGGG-TC
* * *
28204582 AAAATTATAATTTTTGAGAAGTTTAAGGGTT
1 AAAA-TGTAATTTTAGAGAAGTTT-AGGGTC
* *
28204613 AAAATGTAATTTTGGAGAAGTTTAGGTGTT
1 AAAATGTAATTTTAGAGAAGTTTAGG-GTC
* *
28204643 AAAATGTAATTTTAGAAAAGTTTTGGGTC
1 AAAATGTAATTTTAGAGAAGTTTAGGGTC
* * * *
28204672 AAAATATAATTTTGGAAAAGTTTCGGGATC
1 AAAATGTAATTTTAGAGAAGTTTAGGG-TC
* * * * *
28204702 -AAATATAATTTTAAAAAAATTTAGGATTC
1 AAAATGTAATTTTAGAGAAGTTTAGG-GTC
* *
28204731 AAAATGTGATTTCTAGA-AAGTTCAGGG
1 AAAATGTAATTT-TAGAGAAGTTTAGGG
28204758 ACCTATTGGG
Statistics
Matches: 169, Mismatches: 27, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
28 3 0.02
29 72 0.43
30 67 0.40
31 20 0.12
32 7 0.04
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAGAAGTTTAGGGTC
Found at i:28204733 original size:59 final size:59
Alignment explanation
Indices: 28204522--28204735 Score: 157
Period size: 60 Copynumber: 3.6 Consensus size: 59
28204512 AGCTCAAGGT
* * * * * *
28204522 TAAAATGTAATTTTAGAGAAGTTTAGGGTCAAAA-AGTTATTTTTGG-AAGGTTTAGG-GA
1 TAAAATATAATTTTAAAAAAATTTAGGGTCAAAATA--TAATTTTGGAAAAGTTTAGGTGA
** * * * * * *
28204580 TCAAAATTATAATTTTTGAGAAGTTTAAGGGTTAAAATGTAATTTTGGAGAAGTTTAGGTGT
1 T-AAAA-TATAATTTTAAAAAAATTT-AGGGTCAAAATATAATTTTGGAAAAGTTTAGGTGA
* * * * *
28204642 TAAAATGTAATTTTAGAAAAGTTTTGGGTCAAAATATAATTTTGGAAAAGTTTCGG-GA
1 TAAAATATAATTTTAAAAAAATTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGTGA
* *
28204700 TCAAATATAATTTTAAAAAAATTTAGGATTCAAAAT
1 TAAAATATAATTTTAAAAAAATTTAGG-GTCAAAAT
28204736 GTGATTTCTA
Statistics
Matches: 126, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
58 24 0.19
59 38 0.30
60 41 0.33
61 21 0.17
62 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (59 bp):
TAAAATATAATTTTAAAAAAATTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGTGA
Found at i:28205452 original size:18 final size:18
Alignment explanation
Indices: 28205431--28205509 Score: 68
Period size: 18 Copynumber: 4.0 Consensus size: 18
28205421 TTTTTTGCTA
*
28205431 TTTTTTGTTGTTTTGGTT
1 TTTTTTATTGTTTTGGTT
28205449 TTTTTTATTGTTTTGGTTGCT
1 TTTTTTATTGTTTTGG-T--T
* *
28205470 ATTTTTTATTTTTTTATGTTAT
1 -TTTTTTA-TTGTTT-TGGT-T
28205492 TTTTTTATTGTTTTGGTT
1 TTTTTTATTGTTTTGGTT
28205510 GCTATTTTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.33
19 4 0.08
20 5 0.10
21 8 0.16
22 8 0.16
23 6 0.12
24 2 0.04
ACGTcount: A:0.08, C:0.01, G:0.15, T:0.76
Consensus pattern (18 bp):
TTTTTTATTGTTTTGGTT
Found at i:28205459 original size:21 final size:20
Alignment explanation
Indices: 28205417--28205505 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 20
28205407 ATTTTGGTGC
*
28205417 TATT-TTTTTTGCTATTTTT
1 TATTGTTTTTTGCTTTTTTT
* *
28205436 TGTTG--TTTTGGTTTTTTT
1 TATTGTTTTTTGCTTTTTTT
*
28205454 TATTGTTTTGGTTGCTATTTTT
1 TATTGTTTT--TTGCTTTTTTT
*
28205476 TATT-TTTTTATGTTATTTTTT
1 TATTGTTTTT-TGCT-TTTTTT
28205497 TATTGTTTT
1 TATTGTTTT
28205506 GGTTGCTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
18 15 0.28
19 4 0.07
20 5 0.09
21 13 0.24
22 17 0.31
ACGTcount: A:0.09, C:0.02, G:0.12, T:0.76
Consensus pattern (20 bp):
TATTGTTTTTTGCTTTTTTT
Found at i:28205474 original size:40 final size:43
Alignment explanation
Indices: 28205425--28205517 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
28205415 GCTATTTTTT
28205425 TTGCTATTTTTT-GTTGTTT-TGGT-TTTTTTTATTGTTTTGG
1 TTGCTATTTTTTAGTTGTTTATGGTATTTTTTTATTGTTTTGG
* * *
28205465 TTGCTATTTTTTATTTTTTTATGTTATTTTTTTATTGTTTTGG
1 TTGCTATTTTTTAGTTGTTTATGGTATTTTTTTATTGTTTTGG
28205508 TTGCTATTTT
1 TTGCTATTTT
28205518 GGTTTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
40 12 0.26
41 5 0.11
42 3 0.06
43 27 0.57
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (43 bp):
TTGCTATTTTTTAGTTGTTTATGGTATTTTTTTATTGTTTTGG
Found at i:28205503 original size:14 final size:13
Alignment explanation
Indices: 28205475--28205499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28205465 TTGCTATTTT
28205475 TTATTTTTTTATG
1 TTATTTTTTTATG
28205488 TTATTTTTTTAT
1 TTATTTTTTTAT
28205500 TGTTTTGGTT
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTATG
Found at i:28205515 original size:23 final size:23
Alignment explanation
Indices: 28205448--28205517 Score: 94
Period size: 21 Copynumber: 3.2 Consensus size: 23
28205438 TTGTTTTGGT
28205448 TTTTTTTATTGTTTTGGTTGCTA
1 TTTTTTTATTGTTTTGGTTGCTA
*
28205471 -TTTTTTATT-TTTT--TATGTTA
1 TTTTTTTATTGTTTTGGT-TGCTA
28205491 TTTTTTTATTGTTTTGGTTGCTA
1 TTTTTTTATTGTTTTGGTTGCTA
28205514 TTTT
1 TTTT
28205518 GGTTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.10
21 13 0.32
22 13 0.32
23 8 0.20
24 1 0.03
ACGTcount: A:0.10, C:0.03, G:0.13, T:0.74
Consensus pattern (23 bp):
TTTTTTTATTGTTTTGGTTGCTA
Found at i:28205532 original size:18 final size:20
Alignment explanation
Indices: 28205511--28205553 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
28205501 GTTTTGGTTG
28205511 CTATTTTGGT-TT-TTTTTA
1 CTATTTTGGTATTATTTTTA
*
28205529 CTATTTTGGTATTATTTTTG
1 CTATTTTGGTATTATTTTTA
28205549 CTATT
1 CTATT
28205554 ATTTTTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (20 bp):
CTATTTTGGTATTATTTTTA
Found at i:28205533 original size:61 final size:59
Alignment explanation
Indices: 28205417--28205562 Score: 143
Period size: 61 Copynumber: 2.4 Consensus size: 59
28205407 ATTTTGGTGC
* * * * *
28205417 TATTTTTTTTGCTATTTTTTGTTGTTTTGGTTTTTTTTATTGTTTTGGTTGCTATTTTT
1 TATTTTTTTTGCTATTTTTTATTGTTTTGGTTCTATTTATGGTTTTGGTTACTATTTTT
* ** *
28205476 TATTTTTTTATGTTATTTTTTTATTGTTTTGGTTGCTATTT-TGGTTTTTTTTACTATTTTGG
1 TATTTTTTT-TGCTA-TTTTTTATTGTTTTGGTT-CTATTTATGGTTTTGGTTACTATTTT-T
* *
28205538 TATTATTTTTGCTATTATTT-TTGTT
1 TATTTTTTTTGCTATTTTTTATTGTT
28205563 GCTATTTTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
59 14 0.20
60 9 0.13
61 36 0.51
62 12 0.17
ACGTcount: A:0.10, C:0.03, G:0.14, T:0.73
Consensus pattern (59 bp):
TATTTTTTTTGCTATTTTTTATTGTTTTGGTTCTATTTATGGTTTTGGTTACTATTTTT
Found at i:28205547 original size:12 final size:12
Alignment explanation
Indices: 28205532--28205633 Score: 50
Period size: 12 Copynumber: 8.8 Consensus size: 12
28205522 TTTTTTACTA
*
28205532 TTTTGGTATTAT
1 TTTTGCTATTAT
28205544 TTTTGCTATTAT
1 TTTTGCTATTAT
* **
28205556 TTTTGTTGCTAT
1 TTTTGCTATTAT
*
28205568 TTTTG---TTGT
1 TTTTGCTATTAT
* * *
28205577 TTTTGTTGTT-G
1 TTTTGCTATTAT
*
28205588 TTTTGCTGTTAT
1 TTTTGCTATTAT
**
28205600 TTTTGCTGCTAT
1 TTTTGCTATTAT
* *
28205612 TTTGGTTATTAT
1 TTTTGCTATTAT
*
28205624 TTTTGTTATT
1 TTTTGCTATT
28205634 TGGATGGTAA
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
9 7 0.10
11 9 0.13
12 55 0.77
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.69
Consensus pattern (12 bp):
TTTTGCTATTAT
Found at i:28205621 original size:21 final size:21
Alignment explanation
Indices: 28205552--28205634 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
28205542 ATTTTTGCTA
*
28205552 TTATTTTTGTTGCTATTTTTG
1 TTATTTTTGTTGCTATTTTGG
* * *
28205573 TTGTTTTTGTTGTTGTTTTGCTG
1 TTATTTTTGTTGCTATTTTG--G
*
28205596 TTATTTTTGCTGCTATTTTGG
1 TTATTTTTGTTGCTATTTTGG
*
28205617 TTATTATTT-TTGTTATTT
1 TTATT-TTTGTTGCTATTT
28205635 GGATGGTAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
21 29 0.59
22 3 0.06
23 17 0.35
ACGTcount: A:0.08, C:0.05, G:0.17, T:0.70
Consensus pattern (21 bp):
TTATTTTTGTTGCTATTTTGG
Found at i:28205630 original size:44 final size:44
Alignment explanation
Indices: 28205544--28205630 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
28205534 TTGGTATTAT
* * *
28205544 TTTTGCTATTATTTTTGTTGCTATTTTTGTTGTTTTTGTTGTTG
1 TTTTGCTATTATTTTTGCTGCTATTTTGGTTATTTTTGTTGTTG
*
28205588 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTATTATTT-TTGTT
1 TTTTGCTATTATTTTTGCTGCTATTTTGGTTATT-TTTGTTGTT
28205631 ATTTGGATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 35 0.92
45 3 0.08
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (44 bp):
TTTTGCTATTATTTTTGCTGCTATTTTGGTTATTTTTGTTGTTG
Found at i:28205807 original size:12 final size:11
Alignment explanation
Indices: 28205765--28205810 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
28205755 ATATAAAGAA
28205765 TTTTTAATG-T
1 TTTTTAATGTT
*
28205775 ATTTTAAT-TT
1 TTTTTAATGTT
*
28205785 TTTTTATTGTT
1 TTTTTAATGTT
28205796 TGTTTTAATGTT
1 T-TTTTAATGTT
28205808 TTT
1 TTT
28205811 AAGTATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 14 0.48
11 5 0.17
12 10 0.34
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTTAATGTT
Found at i:28208584 original size:2 final size:2
Alignment explanation
Indices: 28208577--28208611 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28208567 CTAAATTTGA
28208577 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28208612 ATACTTGTTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28211446 original size:17 final size:17
Alignment explanation
Indices: 28211424--28211484 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
28211414 ATTCATTTTG
* *
28211424 AGTTTAAATTTGATTTA
1 AGTTTAAATTTAAATTA
28211441 AGTTTAAATTTAAATTA
1 AGTTTAAATTTAAATTA
*
28211458 CGTTTAAATTTAAATTGA
1 AGTTTAAATTTAAATT-A
28211476 A-TTTAAATT
1 AGTTTAAATT
28211485 GTATTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 38 0.97
18 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (17 bp):
AGTTTAAATTTAAATTA
Found at i:28211452 original size:6 final size:6
Alignment explanation
Indices: 28211426--28211484 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
28211416 TCATTTTGAG
* * **
28211426 TTTAAA TTT-GA TTTAAG TTTAAA TTTAAA -TTACG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
28211472 -TTGAA TTTAAA TT
1 TTTAAA TTTAAA TT
28211485 GTATTAAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
5 11 0.28
6 29 0.73
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:28211678 original size:38 final size:38
Alignment explanation
Indices: 28211633--28211710 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
28211623 TAAGTTAAAC
*
28211633 CCTAAACAACCAACTTGCACTGCTGCTGCCATCCTCAG
1 CCTAAACAACCAACTTGCACTGCTGCTGCCATCCCCAG
28211671 CCTAAACAACCAACTTGCACTGCTGCTGCCATCCCCAG
1 CCTAAACAACCAACTTGCACTGCTGCTGCCATCCCCAG
28211709 CC
1 CC
28211711 ACTGGGAGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.42, G:0.13, T:0.19
Consensus pattern (38 bp):
CCTAAACAACCAACTTGCACTGCTGCTGCCATCCCCAG
Found at i:28212281 original size:20 final size:19
Alignment explanation
Indices: 28212256--28212297 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
28212246 TTAATAACGG
28212256 TAATTAATAATAACCATTAA
1 TAATTAATAATAA-CATTAA
*
28212276 TAATTAATAATAATATTAA
1 TAATTAATAATAACATTAA
28212295 TAA
1 TAA
28212298 ATAAAAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATTAATAATAACATTAA
Found at i:28213434 original size:30 final size:28
Alignment explanation
Indices: 28213396--28213570 Score: 82
Period size: 29 Copynumber: 6.0 Consensus size: 28
28213386 CTTTGAAGGT
*
28213396 CCCTAAACTGTCTAAAATTTACATTTTTA
1 CCCTAAACTGTCCAAAA-TTACATTTTTA
* *
28213425 CCCTCAAACTTTCCAAAATTCCATTTTTTA
1 CCCT-AAACTGTCCAAAATTACA-TTTTTA
* * ** * *
28213455 CTCTGATTTTTCCAAAAATTATATTTTTA
1 CCCTAAACTGTCC-AAAATTACATTTTTA
* *
28213484 CCCTTGAACT-TCCCAAAATTCCATTTTTA
1 CCC-TAAACTGT-CCAAAATTACATTTTTA
* * ** * *
28213513 ACCTCGATTTTTCTAAAAATTACATTTTTA
1 CCCT-AAACTGTC-CAAAATTACATTTTTA
* * *
28213543 CCCCCAAACTTTCCAAAATTCCATTTTT
1 -CCCTAAACTGTCCAAAATTACATTTTT
28213571 GACCAAGAAT
Statistics
Matches: 111, Mismatches: 26, Indels: 18
0.72 0.17 0.12
Matches are distributed among these distances:
28 1 0.01
29 55 0.50
30 53 0.48
31 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.42
Consensus pattern (28 bp):
CCCTAAACTGTCCAAAATTACATTTTTA
Found at i:28213450 original size:29 final size:29
Alignment explanation
Indices: 28213417--28213746 Score: 142
Period size: 29 Copynumber: 11.2 Consensus size: 29
28213407 CTAAAATTTA
28213417 CATTTTTACCCTCAAACTTTCCAAAATTC
1 CATTTTTACCCTCAAACTTTCCAAAATTC
* * ** *
28213446 CATTTTTTACTCT-GATTTTTCCAAAAATTA
1 CA-TTTTTACCCTCAAACTTTCC-AAAATTC
* ** *
28213476 TATTTTTACCCTTGAACTTCCCAAAATTC
1 CATTTTTACCCTCAAACTTTCCAAAATTC
* * ** * *
28213505 CATTTTTAACCTCGATTTTTCTAAAAATTA
1 CATTTTTACCCTCAAACTTTC-CAAAATTC
*
28213535 CATTTTTACCCCCAAACTTTCCAAAATTC
1 CATTTTTACCCTCAAACTTTCCAAAATTC
* * *
28213564 CATTTTTGA-CC-AAGAATTTTCCCTAAATTAC
1 CATTTTT-ACCCTCA-AACTTT-CCAAAATT-C
* *
28213595 CA-TTTTACCCTTAAAC-TTCTAAAAATTC
1 CATTTTTACCCTCAAACTTTC-CAAAATTC
* * *
28213623 CATTTTCA-ACTCGAAAAC-TTCCACAAATTA
1 CATTTTTACCCTC--AAACTTTCCA-AAATTC
* **
28213653 CAATTTTA-CCTCTGGAC-TTCCAAAAATTC
1 CATTTTTACCCTC-AAACTTTCC-AAAATTC
* * * *
28213682 CATTTTGACCTTGAAACTTTCAAAAATTAC
1 CATTTTTACCCTCAAACTTTCCAAAATT-C
* * *
28213712 CA-TTTTACCCCCAAA-TGTCCAAAAATTT
1 CATTTTTACCCTCAAACTTTCC-AAAATTC
28213740 CATTTTT
1 CATTTTT
28213747 GATCTCTATT
Statistics
Matches: 221, Mismatches: 59, Indels: 42
0.69 0.18 0.13
Matches are distributed among these distances:
28 12 0.05
29 115 0.52
30 90 0.41
31 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (29 bp):
CATTTTTACCCTCAAACTTTCCAAAATTC
Found at i:28213502 original size:59 final size:58
Alignment explanation
Indices: 28213409--28213808 Score: 246
Period size: 59 Copynumber: 6.8 Consensus size: 58
28213399 TAAACTGTCT
* * *
28213409 AAAATTTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTTACTCTGATTTTTCC
1 AAAAATTACATTTTTACCCTCAAACTTCCCAAAATTCCATTTTTAAC-CTGATTTTTCC
* ** *
28213468 AAAAATTATATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTAACCTCGATTTTTCT
1 AAAAATTACATTTTTACCCTCAAACTTCCCAAAATTCCATTTTTAACCT-GATTTTTCC
* * * * *
28213527 AAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCAAGAATTTTCC
1 AAAAATTACATTTTTACCCTCAAACTTCCCAAAATTCCATTTTTAACC-TGATTTTTCC
** * ** * ***
28213586 CTAAATTACCA-TTTTACCCTTAAACTTCTAAAAATTCCATTTTCAA-CTCGAAAACTTCC
1 AAAAATTA-CATTTTTACCCTCAAACTTCCCAAAATTCCATTTTTAACCT-G-ATTTTTCC
* * ** * * **
28213645 ACAAATTACAATTTTA-CCTCTGGACTTCCAAAAATTCCA-TTTTGACCTTGAAACTTT-C
1 AAAAATTACATTTTTACCCTC-AAACTTCCCAAAATTCCATTTTTAACC-TG-ATTTTTCC
* * * * *
28213703 AAAAATTACCA-TTTTACCCCCAAA-TGTCCAAAAATTTCATTTTTGATCTCT-ATTTTTCT
1 AAAAATTA-CATTTTTACCCTCAAACT-TCCCAAAATTCCATTTTT-AAC-CTGATTTTTCC
* * * *
28213762 AAAAATGAC-TGTTTTACCCTCGAA-TGT-CTAAAATTCTATTTTTAACC
1 AAAAATTACAT-TTTTACCCTCAAACT-TCCCAAAATTCCATTTTTAACC
28213809 CCAAACATTC
Statistics
Matches: 268, Mismatches: 55, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
56 1 0.00
57 3 0.01
58 57 0.21
59 201 0.75
60 5 0.02
61 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (58 bp):
AAAAATTACATTTTTACCCTCAAACTTCCCAAAATTCCATTTTTAACCTGATTTTTCC
Found at i:28213620 original size:118 final size:116
Alignment explanation
Indices: 28213406--28213780 Score: 348
Period size: 118 Copynumber: 3.2 Consensus size: 116
28213396 CCCTAAACTG
* * * *
28213406 TCTAAAATTTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTTACTCTGATTTTTCCAAA
1 TCTAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGAC-CTGAATTTTCCAAA
* * *
28213471 AATTA-TATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTAACCTCGATTTT
65 AATTACCA-TTTTACCCTTAAACTTCCAAAAATTCCATTTTTAA-CTCGATTTT
* **
28213524 TCTAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCAAGAATTTTCCCTA
1 TCTAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACC-TGAATTTTCCAAA
* * ***
28213589 AATTACCATTTTACCCTTAAACTTCTAAAAATTCCATTTTCAACTCGAAAACT
65 AATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACTCG-ATTTT
* * * * *** *
28213642 TCCACAAATTACAATTTTACCTCTGGAC-TTCCAAAAATTCCA-TTTTGACCTTGAAACTTT-CA
1 TCTAAAAATTACATTTTTACCCCCAAACTTTCC-AAAATTCCATTTTTGACC-TG-AATTTTCCA
** * * *
28213704 AAAATTACCATTTTACCCCCAAA-TGTCCAAAAATTTCATTTTTGATCTCTATTTT
63 AAAATTACCATTTTACCCTTAAACT-TCCAAAAATTCCATTTTT-AACTCGATTTT
*
28213759 TCTAAAAATGAC-TGTTTTACCC
1 TCTAAAAATTACAT-TTTTACCC
28213781 TCGAATGTCT
Statistics
Matches: 207, Mismatches: 42, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
116 1 0.00
117 72 0.35
118 133 0.64
119 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.40
Consensus pattern (116 bp):
TCTAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTGAATTTTCCAAAA
ATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACTCGATTTT
Found at i:28215497 original size:16 final size:16
Alignment explanation
Indices: 28215474--28215545 Score: 126
Period size: 16 Copynumber: 4.5 Consensus size: 16
28215464 CGTTTGGTTC
28215474 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
28215490 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
28215506 ACTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28215522 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28215538 GCTGTAAT
1 GCTGTAAT
28215546 CAGTAATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:28215586 original size:46 final size:44
Alignment explanation
Indices: 28215527--28215620 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
28215517 ATAGAGCTGT
* *
28215527 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
28215573 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
28215617 AATG
1 AATG
28215621 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:28215784 original size:58 final size:56
Alignment explanation
Indices: 28215715--28215860 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
28215705 AATTTTAATG
*
28215715 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
28215773 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
28215831 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
28215861 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:28223133 original size:49 final size:49
Alignment explanation
Indices: 28222969--28223343 Score: 339
Period size: 49 Copynumber: 7.6 Consensus size: 49
28222959 CGCGATAGTA
* * * * * * *
28222969 GATCCAGGACCACAAAAACACGACGGGAAAGATCTAAGGCTGCAACGGCG
1 GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAA-GCCGGAACGGCG
* * * ** * * * * *
28223019 GATCCAGTACCGCAAAGATACAAAGGGAAAGGTTTAAGTCGCAACAGC-
1 GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGGAACGGCG
* * * *
28223067 GAACCTTA-TACCTCGAAGACATGAAGGGAAAGATCTAAGCCGGAATGGCT
1 GATCC--AGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGGAACGGCG
* * * *
28223117 GATCTAGTACCACGAAGACACGACA-GGAAAGATCTAAGACCGTAACGGTG
1 GATCCAGTACCACGAAGACATGA-AGGGAAAGATCTAAG-CCGGAACGGCG
* *
28223167 GATCCAATACCACGAAGACAT-AAGGGAAAGATCTAAGCCGCAACGGCG
1 GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGGAACGGCG
* * *
28223215 GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCG-ATGACG
1 GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCG-GAACGGCG
* *
28223264 GATCCAGTACCACGAAGACATGAAAGGAAAGATCTAAGTCGCG-ACGGCG
1 GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCG-GAACGGCG
**
28223313 GATCCAGTACCACGAAGATTTGAAGGGAAAG
1 GATCCAGTACCACGAAGACATGAAGGGAAAG
28223344 GTTTAAGTCA
Statistics
Matches: 267, Mismatches: 49, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
48 35 0.13
49 173 0.65
50 59 0.22
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (49 bp):
GATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGGAACGGCG
Found at i:28223372 original size:147 final size:146
Alignment explanation
Indices: 28222969--28223372 Score: 427
Period size: 147 Copynumber: 2.7 Consensus size: 146
28222959 CGCGATAGTA
* * * ** * * * *
28222969 GATCCAGGACCACAAAAACACGACGGGAAAGATCTAAGGCTGCAACGGCGGATCCAGTACCGCAA
1 GATCCAGTACCACGAAGACACGAAAGGAAAGATCTAAGAC-GCGACGGCGGATCCAGTACCACGA
* * * *
28223034 AGATACAAAGGGAAAGGTTTAAGTCGCAACAGCGAACCTTA-TACCTCGAAGACATGAAGGGAAA
65 AGATA-TAAGGGAAAGGTTTAAGTCGCAACGGCGAACC-CAGTACCACGAAGACATGAAGGGAAA
* *
28223098 GATCTAAGCCGGAATGGCT
128 GATCTAAGCCGGAATGACG
* * * *
28223117 GATCTAGTACCACGAAGACACGACAGGAAAGATCTAAGAC-CGTAACGGTGGATCCAATACCACG
1 GATCCAGTACCACGAAGACACGAAAGGAAAGATCTAAGACGCG--ACGGCGGATCCAGTACCACG
* * * * * *
28223181 AAGACATAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACATGAAGGGAAAG
64 AAGATATAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGTACCACGAAGACATGAAGGGAAAG
*
28223246 ATCTAAGCTGCG-ATGACG
129 ATCTAAGCCG-GAATGACG
* *
28223264 GATCCAGTACCACGAAGACATGAAAGGAAAGATCTAAGTCGCGACGGCGGATCCAGTACCACGAA
1 GATCCAGTACCACGAAGACACGAAAGGAAAGATCTAAGACGCGACGGCGGATCCAGTACCACGAA
* * * * *
28223329 GATTTGAAGGGAAAGGTTTAAGTCACAATGGTGAACCCGGTACC
66 GATAT-AAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGTACC
28223373 TTAGAAACAT
Statistics
Matches: 209, Mismatches: 41, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
146 25 0.12
147 126 0.60
148 58 0.28
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14
Consensus pattern (146 bp):
GATCCAGTACCACGAAGACACGAAAGGAAAGATCTAAGACGCGACGGCGGATCCAGTACCACGAA
GATATAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGTACCACGAAGACATGAAGGGAAAGAT
CTAAGCCGGAATGACG
Found at i:28223612 original size:38 final size:38
Alignment explanation
Indices: 28223570--28223651 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 38
28223560 GATTCAAGAA
28223570 GGGCAAAATGAAG-ATTCTAATCTCTTACCCCGAGCCAG
1 GGGCAAAATGAAGCATT-TAATCTCTTACCCCGAGCCAG
* * * * *
28223608 GGGCAGATTGAAGTCATTTGATCTCTTACCCCTAGCCTG
1 GGGCAAAATGAAG-CATTTAATCTCTTACCCCGAGCCAG
28223647 GGGCA
1 GGGCA
28223652 GATCATCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 11 0.30
39 23 0.62
40 3 0.08
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (38 bp):
GGGCAAAATGAAGCATTTAATCTCTTACCCCGAGCCAG
Found at i:28223637 original size:39 final size:39
Alignment explanation
Indices: 28223589--28223731 Score: 139
Period size: 39 Copynumber: 3.7 Consensus size: 39
28223579 GAAGATTCTA
* *
28223589 ATCTCTTACCCCGAGCCAGGGGCAGATTGAAGTCATTTG
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGTCATTCG
* * * *
28223628 ATCTCTTACCCCTAGCCTGGGGCAGATCAT-CA-TCAATCA
1 ATCTCTTACCCCGAGCCAGGGGCAGAT--TGCAGTCATTCG
*
28223667 ATCTCTTACCCCAAGCCAGGGGCAGATTGCAG-CATTCG
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGTCATTCG
* * * **
28223705 ACCTTTTACTCCGAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCCAGGGGCAGAT
28223732 CGTCGTCAAC
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
37 1 0.01
38 27 0.32
39 54 0.64
40 1 0.01
41 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGTCATTCG
Found at i:28223673 original size:78 final size:77
Alignment explanation
Indices: 28223588--28223835 Score: 284
Period size: 78 Copynumber: 3.2 Consensus size: 77
28223578 TGAAGATTCT
* * * *
28223588 AATCTCTTACCCCGAGCCAGGGGCAGATTGAAGTCATTTGATCTCTTACCCCTAGCCTGGGGCAG
1 AATCTCTTACCCCGAGCCAGGGGCAGATTGAAG-CATTCGACCTTTTACCCCTAGCTTGGGGCAG
*
28223653 ATCATCATCAATC
65 ATCATCATCAACC
* * * *
28223666 AATCTCTTACCCCAAGCCAGGGGCAGATTGCAGCATTCGACCTTTTACTCCGAGCTTGGGGCAGA
1 AATCTCTTACCCCGAGCCAGGGGCAGATTGAAGCATTCGACCTTTTACCCCTAGCTTGGGGCAGA
* *
28223731 TCGTCGTCAACC
66 TCATCATCAACC
* * * * * *
28223743 AATCTCTTATCCTGAGCCTA-GGGCAGATTGTAACCATCCGACCTTTTA-CTCTGAGCTTGGAGC
1 AATCTCTTACCCCGAGCC-AGGGGCAGATTG-AAGCATTCGACCTTTTACCCCT-AGCTTGGGGC
28223806 AGATCATCATCAACC
63 AGATCATCATCAACC
*
28223821 AATCTCCTACCCCGA
1 AATCTCTTACCCCGA
28223836 TCACGGGGCG
Statistics
Matches: 141, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
77 61 0.43
78 80 0.57
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (77 bp):
AATCTCTTACCCCGAGCCAGGGGCAGATTGAAGCATTCGACCTTTTACCCCTAGCTTGGGGCAGA
TCATCATCAACC
Found at i:28224210 original size:206 final size:205
Alignment explanation
Indices: 28223916--28224526 Score: 898
Period size: 206 Copynumber: 3.0 Consensus size: 205
28223906 CCAACCTAAG
* * * * * *
28223916 GCTCAATGCGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATATTGAGAAGCAGGACCAAACAA
1 GCTCGATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
* *
28223981 TAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATAC
66 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
28224046 AGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGTGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
**
28224111 TCAAACCCGT
196 TCAAACCCAC
* * *
28224121 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATAAGATACTGAGAAGTAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
28224186 ATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATAAGATA
65 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* *
28224251 CAGAGAAGCGGATTGAAGCAAACGATGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAA
130 CAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
28224316 ATCAAACCCAC
195 ATCAAACCCAC
* * * *
28224327 GCTCGATATGAGCAAATCTTCGAATCCCAGCTTCCTAATGAGATACTGAGAAACAGGTCGAAGTA
1 GCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
28224392 ATAACATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
65 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* ** ** * * *
28224457 CAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTCCTGACGAGATACTGAGAAGAAGGCCAA
130 CAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
*
28224522 GTCAA
195 ATCAA
28224527 TGAAACCAGA
Statistics
Matches: 363, Mismatches: 42, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
205 22 0.06
206 341 0.94
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (205 bp):
GCTCGATGTGAGCAAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:28226896 original size:28 final size:28
Alignment explanation
Indices: 28226865--28226959 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 28
28226855 AGCCCTAAAC
*
28226865 TTTCCAAAATTCCATTTTGACCTTAATT
1 TTTCCAAAATTCCATTTTGACCTCAATT
* * *
28226893 TTTCCAAAAATTACATTTTTACCCCTGAA-T
1 TTTCC-AAAATTCCATTTTGA--CCTCAATT
*
28226923 TTTCCAAAATTCCATTTTGACCCCAATT
1 TTTCCAAAATTCCATTTTGACCTCAATT
28226951 TTTCCAAAA
1 TTTCCAAAA
28226960 ATTATCATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
27 4 0.07
28 15 0.27
29 26 0.46
30 6 0.11
31 5 0.09
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (28 bp):
TTTCCAAAATTCCATTTTGACCTCAATT
Found at i:28226910 original size:29 final size:28
Alignment explanation
Indices: 28226865--28226970 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 28
28226855 AGCCCTAAAC
* *
28226865 TTTCCAAAATTCCATTTTGACCTTAATT
1 TTTCCAAAATTACATTTTGACCTCAATT
* *
28226893 TTTCCAAAAATTACATTTTTACCCCTGAA-T
1 TTTCC-AAAATTACATTTTGA--CCTCAATT
* *
28226923 TTTCCAAAATTCCATTTTGACCCCAATT
1 TTTCCAAAATTACATTTTGACCTCAATT
28226951 TTTCCAAAAATTATCATTTT
1 TTTCC-AAAATTA-CATTTT
28226971 ACCCCCAGAC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.06
28 11 0.17
29 32 0.50
30 12 0.19
31 5 0.08
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTGACCTCAATT
Found at i:28226928 original size:30 final size:29
Alignment explanation
Indices: 28226892--28227147 Score: 138
Period size: 29 Copynumber: 8.7 Consensus size: 29
28226882 TGACCTTAAT
28226892 TTTTCCAAAAATTACATTTTTACCCCTGAA
1 TTTTCCAAAAATTACATTTTTACCCC-GAA
* *
28226922 TTTTCC-AAAATTCCATTTTGACCCC-AA
1 TTTTCCAAAAATTACATTTTTACCCCGAA
*
28226949 TTTTTCCAAAAATTATCA-TTTTACCCCCAGA
1 -TTTTCCAAAAATTA-CATTTTTACCCCGA-A
* *
28226980 CTTT-CAAAAATTCCATTTTTGACCCCGAAA
1 TTTTCCAAAAATTACATTTTT-ACCCCG-AA
* *
28227010 CTTT-CAAAAATTACCA-TTTTACTCTCGAA
1 TTTTCCAAAAATTA-CATTTTTAC-CCCGAA
* * * *
28227039 -TGTCCAAAAATTTCGTTTTTGATCCC-AA
1 TTTTCCAAAAATTACATTTTT-ACCCCGAA
*
28227067 TTTTTCTAAAAATTAC-TATTTTACCCTC-AA
1 -TTTTCCAAAAATTACAT-TTTTACCC-CGAA
* * * * *
28227097 ATGT-CTAAAATTCCATTTTTAACCCCAAA
1 TTTTCCAAAAATTACATTTTT-ACCCCGAA
* *
28227126 CTTTCCCAAAATTACCATTTTT
1 TTTTCCAAAAATTA-CATTTTT
28227148 CCCTCGAGAG
Statistics
Matches: 177, Mismatches: 27, Indels: 43
0.72 0.11 0.17
Matches are distributed among these distances:
27 2 0.01
28 25 0.14
29 76 0.43
30 63 0.36
31 11 0.06
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTTCCAAAAATTACATTTTTACCCCGAA
Found at i:28226974 original size:29 final size:29
Alignment explanation
Indices: 28226889--28227092 Score: 129
Period size: 30 Copynumber: 6.9 Consensus size: 29
28226879 TTTTGACCTT
28226889 AATTTTTCCAAAAATTACATTTTTACCCCTG
1 AATTTTTCCAAAAATTACA-TTTTACCCC-G
*
28226920 AA-TTTTCC-AAAATTCCATTTTGACCCC-
1 AATTTTTCCAAAAATTACATTTT-ACCCCG
*
28226947 AATTTTTCCAAAAATTATCATTTTACCCCC
1 AATTTTTCCAAAAATTA-CATTTTACCCCG
* *
28226977 AGA-CTTT-CAAAAATTCCATTTTTGACCCCG
1 A-ATTTTTCCAAAAATTACA-TTTT-ACCCCG
** *
28227007 AAACTTT-CAAAAATTACCATTTTACTCTCG
1 AATTTTTCCAAAAATTA-CATTTTAC-CCCG
* * * *
28227037 AA--TGTCCAAAAATTTCGTTTTTGATCCC-
1 AATTTTTCCAAAAATTAC-ATTTT-ACCCCG
*
28227065 AATTTTTCTAAAAATTACTATTTTACCC
1 AATTTTTCCAAAAATTAC-ATTTTACCC
28227093 TCAAATGTCT
Statistics
Matches: 139, Mismatches: 18, Indels: 34
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.01
28 17 0.12
29 56 0.40
30 59 0.42
31 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
AATTTTTCCAAAAATTACATTTTACCCCG
Found at i:28227165 original size:58 final size:59
Alignment explanation
Indices: 28226867--28227174 Score: 258
Period size: 58 Copynumber: 5.3 Consensus size: 59
28226857 CCCTAAACTT
** ** *
28226867 TCCAAAATTCCA-TTTTGACCTTAATTTTTCCAAAAATTA-CATTTTTACCC-CTGA-ATTT
1 TCCAAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACCA-TTTTACCCTC-GAGA-TG
** * * *
28226925 TCCAAAATTCCA-TTTTGACCCCAATTTTTCCAAAAATTATCATTTTACCC-CCAGACTT
1 TCCAAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAGA-TG
* *
28226983 TCAAAAATTCCATTTTTGACCCCGAAACTTT-CAAAAATTACCATTTTACTCTCGA-ATG
1 TCCAAAATTCCATTTTTGACCCC-AAACTTTCCAAAAATTACCATTTTACCCTCGAGATG
* * * ** * * *
28227041 TCCAAAAATTTCGTTTTTGATCCCAATTTTTCTAAAAATTACTATTTTACCCTC-AAATG
1 TCC-AAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAGATG
* * * *
28227100 TCTAAAATTCCATTTTTAACCCCAAACTTTCCCAAAATTACCATTTTTCCCTCGAGA-G
1 TCCAAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAGATG
*
28227158 TCCAAAATCACCATTTT
1 TCCAAAAT-TCCATTTT
28227175 ACCCCCGGGT
Statistics
Matches: 206, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
57 1 0.00
58 117 0.57
59 81 0.39
60 7 0.03
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
TCCAAAATTCCATTTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAGATG
Found at i:28227189 original size:28 final size:28
Alignment explanation
Indices: 28227131--28227202 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
28227121 CCAAACTTTC
* * *
28227131 CCAAAATTACCATTTTTCCCTCGAGAGT
1 CCAAAATCACCATTTTACCCCCGAGAGT
*
28227159 CCAAAATCACCATTTTACCCCCGGGTA-T
1 CCAAAATCACCATTTTACCCCCGAG-AGT
28227187 CCAAAAATCA-CATTTT
1 CC-AAAATCACCATTTT
28227203 CAAACCCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 30 0.79
29 8 0.21
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (28 bp):
CCAAAATCACCATTTTACCCCCGAGAGT
Found at i:28229123 original size:23 final size:24
Alignment explanation
Indices: 28229092--28229148 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
28229082 AAAATAATCA
* *
28229092 TTAATTCATTTC-AAAGTTTTCAT
1 TTAAATCATTTCGAAAGTTTTAAT
28229115 TTAAATCA-TTCGAAAGTTTTAAT
1 TTAAATCATTTCGAAAGTTTTAAT
* *
28229138 TTGAATTATTT
1 TTAAATCATTT
28229149 AGTTGTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.11
23 23 0.82
24 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAAATCATTTCGAAAGTTTTAAT
Found at i:28230190 original size:41 final size:41
Alignment explanation
Indices: 28230119--28230477 Score: 294
Period size: 41 Copynumber: 8.8 Consensus size: 41
28230109 AATGTAAAGC
* *
28230119 ATTAGCGGCGC-TTAACAAAAGCGCCGCTAAAGGTTAGGTA
1 ATTAGCGGCGCTTTATCATAAGCGCCGCTAAAGGTTAGGTA
* *
28230159 ATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTTAGTTA
1 ATTAGCGGCGCTTTATCATAAGCGCCGCTAAAGGTTAGGTA
*
28230200 ATTAGCGGCGCTTTCTCA-AATGCGCCGCTAAAGG-TAGGGTA
1 ATTAGCGGCGCTTTATCATAA-GCGCCGCTAAAGGTTA-GGTA
* * * *
28230241 ATTAGCGGCGCTTT-CCCTCAAGCGCCGCTAAAGGTCAGGTC
1 ATTAGCGGCGCTTTATCAT-AAGCGCCGCTAAAGGTTAGGTA
* * * *
28230282 ATTAGCGGCGCTTT-CCCTAAAGCACAGCTAAAGG-TAGGATCA
1 ATTAGCGGCGCTTTATCAT-AAGCGCCGCTAAAGGTTAGG-T-A
* * *
28230324 TTTAGCGGCG-TTT-TCATTTAAGCGCCGCTAAA-GTTCGGGTC
1 ATTAGCGGCGCTTTATCA--TAAGCGCCGCTAAAGGTT-AGGTA
* *
28230365 ATTAGCGGCGCTTATAT-ATAAAGCGCCGCTAAAGGTCAGGTC
1 ATTAGCGGCGCTT-TATCAT-AAGCGCCGCTAAAGGTTAGGTA
* * *
28230407 ATTAGCGGCGCTTTTATAATAAGCGTCACTAAAGG-T--GTGA
1 ATTAGCGGCGC-TTTATCATAAGCGCCGCTAAAGGTTAGGT-A
* **
28230447 ATTAGTGGCGCTTTCCCATAAGCGCCGCTAA
1 ATTAGCGGCGCTTTATCATAAGCGCCGCTAA
28230478 TGTATTTAAA
Statistics
Matches: 265, Mismatches: 34, Indels: 41
0.78 0.10 0.12
Matches are distributed among these distances:
39 17 0.06
40 29 0.11
41 136 0.51
42 71 0.27
43 11 0.04
44 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (41 bp):
ATTAGCGGCGCTTTATCATAAGCGCCGCTAAAGGTTAGGTA
Found at i:28230431 original size:42 final size:41
Alignment explanation
Indices: 28230058--28230442 Score: 281
Period size: 41 Copynumber: 9.4 Consensus size: 41
28230048 TTTGGAAATA
* * * * *
28230058 AAGCGCCGCAAAAGGTAAAG-CATTATCGGCGCTTTTCT-T
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTATAT
* * * * * * *
28230097 AATGCGCCGCAAAATGTAAAG-CATTAGCGGCGC-TTAACAA
1 AA-GCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTATAT
* * *
28230137 AAGCGCCGCTAAAGGTTAGGTAATTAGCGGCGC-TTTATCAC
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTAT-AT
* * *
28230178 AAGCGCCGCTAAAGGTTAGTTAATTAGCGGCGCTTTCTCA-A-
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT-T-ATAT
* * ** *
28230219 ATGCGCCGCTAAAGGT-AGGGTAATTAGCGGCGCTTTCCCT-C
1 AAGCGCCGCTAAAGGTCA-GGTCATTAGCGGCGCTTT-TATAT
**
28230260 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTCCCTA-
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTT-TATAT
* * *
28230301 AAGCACAGCTAAAGGT-AGGATCATTTAGCGGCG-TTTTCATTT
1 AAGCGCCGCTAAAGGTCAGG-TCA-TTAGCGGCGCTTTT-ATAT
* * *
28230343 AAGCGCCGCTAAAGTTCGGGTCATTAGCGGCGCTTATATAT
1 AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTATAT
28230384 AAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTATAAT
1 -AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTAT-AT
* *
28230427 AAGCGTCACTAAAGGT
1 AAGCGCCGCTAAAGGT
28230443 GTGAATTAGT
Statistics
Matches: 289, Mismatches: 37, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
39 18 0.06
40 48 0.17
41 135 0.47
42 82 0.28
43 5 0.02
44 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTATAT
Found at i:28232804 original size:49 final size:49
Alignment explanation
Indices: 28232761--28233484 Score: 674
Period size: 49 Copynumber: 14.3 Consensus size: 49
28232751 AAGTATCCTT
*
28232761 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* *
28232810 GTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * * *
28232858 GTATATTAATTTAAAAGATATAATTATTTAATTGTATTAAACTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * ** * *
28232907 TTATATTAAATTATTTAATCATG-TTTAATTATGTATTTA-ATTATAAACACTATCGA
1 TTATATTAAATTA---AA--A-GATTTAATTATTTAATTATATTA-AAGTA-AAT-AA
** *
28232963 TTA-ATTAAATATTTAAG-TTGAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAAT-TAAAAGATT--TA-A-----TTATTTAATTATATTAAAGTAAATAA
* *
28233019 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
28233068 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* *
28233117 GTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * * *
28233165 GTATATTAATTTAAAAGATATAATTATTTAATTGTATTAAACTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * * *
28233214 TTATATTAAATTATTTAATCATG-TTTAATTATGTATTTAATTATAAACACTACCGATTAA
1 TTATATTAAATTA---AA--A-GATTTAATTATTTAATT-A-TATTAA-AGTA---AATAA
* *
28233274 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAA
1 TT--ATA-TTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* * * ** *
28233326 TTATATCAAGTTGAAAGATTTAATTATTTAATTATATTAAAGTATCCT-T
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTA-AATAA
* *
28233375 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTTAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
* ** *
28233424 GTATATTAAATT-AATTATTTAATTATTTAATTATATTAAGGTAAATAA
1 TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
28233472 TTATATTAAATTA
1 TTATATTAAATTA
28233485 TTTAATTATA
Statistics
Matches: 561, Mismatches: 72, Indels: 84
0.78 0.10 0.12
Matches are distributed among these distances:
48 136 0.24
49 267 0.48
50 8 0.01
51 1 0.00
52 11 0.02
53 6 0.01
54 30 0.05
55 15 0.03
56 23 0.04
57 16 0.03
58 26 0.05
59 4 0.01
60 8 0.01
62 3 0.01
63 7 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (49 bp):
TTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAA
Found at i:28232872 original size:18 final size:18
Alignment explanation
Indices: 28232793--28232919 Score: 69
Period size: 18 Copynumber: 7.7 Consensus size: 18
28232783 ATTATTTAAT
*
28232793 TATATTAAAGTAAATAAG
1 TATATTAAATTAAATAAG
28232811 TATATTAAATT--A-AA-
1 TATATTAAATTAAATAAG
** *
28232825 TAT-TT-AATTATTTAAT
1 TATATTAAATTAAATAAG
*
28232841 TATATTAAAGTAAATAAG
1 TATATTAAATTAAATAAG
*
28232859 TATATT-AATTTAA-AAG
1 TATATTAAATTAAATAAG
** *
28232875 -ATA-T-AATTATTTAAT
1 TATATTAAATTAAATAAG
* * *
28232890 TGTATTAAACTAAATAAT
1 TATATTAAATTAAATAAG
28232908 TATATTAAATTA
1 TATATTAAATTA
28232920 TTTAATCATG
Statistics
Matches: 81, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
12 4 0.05
13 2 0.02
14 8 0.10
15 9 0.11
16 9 0.11
17 8 0.10
18 41 0.51
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (18 bp):
TATATTAAATTAAATAAG
Found at i:28233003 original size:161 final size:159
Alignment explanation
Indices: 28232815--28233366 Score: 754
Period size: 161 Copynumber: 3.5 Consensus size: 159
28232805 AATAAGTATA
* * *
28232815 TTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATA
1 TTAAGTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATA
*
28232880 ATTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
66 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
28232945 AATTATAAACACTATCGATTAATTAAATAT
131 AATTATAAACACTA-CGATTAATTAAATAT
* *
28232975 TTAAGTTGAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
1 TTAAGTT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATAT
* * * *
28233040 AATTATTTAATTATATTAAAGTAACTAATTATATTAAATTA---AA--A-GATTTAATTATTTAA
65 AATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATG-TTTAATTATGTAT
* * * *
28233099 TT-A-TATTAA-AGTA--AATAAGT--ATA-
129 TTAATTATAAACACTACGATTAATTAAATAT
* * *
28233122 TTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATA
1 TTAAGTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATA
*
28233187 ATTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
66 ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
28233252 AATTATAAACACTACCGATTAATTAAATAT
131 AATTATAAACACTA-CGATTAATTAAATAT
* * * * *
28233282 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATCAAGTTGAAAGATTT
1 TTAAGTT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATAT
28233347 AATTATTTAATTATATTAAA
65 AATTATTTAATTATATTAAA
28233367 GTATCCTTTT
Statistics
Matches: 337, Mismatches: 37, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
146 91 0.27
147 6 0.02
148 3 0.01
149 2 0.01
150 5 0.01
151 14 0.04
152 2 0.01
153 8 0.02
154 8 0.02
155 2 0.01
156 14 0.04
157 5 0.01
158 2 0.01
159 3 0.01
160 12 0.04
161 160 0.47
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (159 bp):
TTAAGTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAGTTAAAAGATATA
ATTATTTAATTATATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
AATTATAAACACTACGATTAATTAAATAT
Found at i:28233288 original size:258 final size:249
Alignment explanation
Indices: 28232761--28233511 Score: 854
Period size: 258 Copynumber: 2.9 Consensus size: 249
28232751 AAGTATCCTT
* * *
28232761 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAT
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAATTAAAG
* *
28232826 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATT
66 ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATTTAATTATTTAATT
* * * *
28232891 GTATTAAACTAAATAATTATATTAAATTATTTAATCATG-TTTAATTATGT-ATTTAATTATAAA
131 ATATTAAAGTAAATAAGTATATT--A--ATTTAA--ATGATTTAATTATTTAATTT-A-T-TAAA
* * * * * * *
28232954 C-ACTATCGATTA-ATTAAA-TATTTAAGTTGAAAGATTTAATTATTTAATT-ATATTAAAGTAA
187 CTA-AAT-AATTATATTAAATTATTTAA--T-AATG-TTTAATTATCTATTTAATATAAAACTAA
28233015 ATAA
246 ATAA
28233019 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAATTAAAA
1 TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAATT-AAA
*
28233084 GATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATT-AAATATTTAATTATTTAAT
65 GATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATTTAATTATTTAAT
* *
28233148 TATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAATTGTATTAAACTAAATA
130 TATATTAAAGTAAATAAGTATATTAATTTAAATGATTTAATTATTTAATT-TATTAAACTAAATA
* * *
28233213 ATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTACCGATTAA
194 ATTATATTAAATTATTTAATAATGTTTAATTATCTATTTAA-TATAAA-ACTA---AATAA
* *
28233274 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATCAAGTTG
1 TT--ATA-TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAATT-
** ** *
28233339 AAAGATTTAATTATTTAATTATATTAAAGTATCCT-TTTATATTAAGTTAAAAGATTTAATTATT
62 AAAGATTTAATTATTTAATTATATTAAAGTA-AATAAGTATATTAAATTAAAAGATTTAATTATT
* * * **
28233403 TAATTATATTAAAGTTAATAAGTATATTAAATT-AATTATTTAATTATTTAATTATATTAAGGTA
126 TAATTATATTAAAGTAAATAAGTATATTAATTTAAATGATTTAATTATTTAATT-TATTAAACTA
* * *
28233467 AATAATTATATTAAATTATTTAATTATATTTAATTAACTATTTAA
190 AATAATTATATTAAATTATTTAATAATGTTTAATTATCTATTTAA
28233512 CTTAAAATGT
Statistics
Matches: 433, Mismatches: 42, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
249 13 0.03
250 3 0.01
251 10 0.02
252 18 0.04
253 18 0.04
254 10 0.02
255 7 0.02
256 1 0.00
257 3 0.01
258 258 0.60
259 92 0.21
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (249 bp):
TTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAATTAAAG
ATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAAATTAAAAGATTTAATTATTTAATT
ATATTAAAGTAAATAAGTATATTAATTTAAATGATTTAATTATTTAATTTATTAAACTAAATAAT
TATATTAAATTATTTAATAATGTTTAATTATCTATTTAATATAAAACTAAATAA
Found at i:28233315 original size:307 final size:307
Alignment explanation
Indices: 28232751--28233480 Score: 1318
Period size: 307 Copynumber: 2.4 Consensus size: 307
28232741 AAACTTAAAT
* *
28232751 AAGTATCCTTTTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
1 AAGTATACTATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
28232816 TAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAA
66 TAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAA
28232881 TTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTA
131 TTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTA
* *
28232946 ATTATAAACACTATCGATTAATTAAATATTTAAGTTGAAAGATTTAATTATTTAATTATATTAAA
196 ATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAA
*
28233011 GTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTA
261 GTAAATAATTATATCAAGTTAAAAGATTTAATTATTTAATTATATTA
*
28233058 AAGTA-ACTAATTATATTAAATTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
1 AAGTATACT-ATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
28233122 TTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATA
65 TTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATA
28233187 ATTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
130 ATTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTT
28233252 AATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAA
195 AATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAA
* *
28233317 AGTAACTAATTATATCAAGTTGAAAGATTTAATTATTTAATTATATTA
260 AGTAAATAATTATATCAAGTTAAAAGATTTAATTATTTAATTATATTA
* * *
28233365 AAGTATCCTTTTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTTAATAAGTATAT
1 AAGTATACTATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
* * *
28233430 TAAATTAATTATTTAATTATTTAATTATATTAAGGTAAATAATTATATTAA
66 TAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAA
28233481 ATTATTTAAT
Statistics
Matches: 406, Mismatches: 15, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
306 2 0.00
307 402 0.99
308 2 0.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (307 bp):
AAGTATACTATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAAGTATAT
TAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAA
TTATTTAATTGTATTAAACTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTA
ATTATAAACACTACCGATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAA
GTAAATAATTATATCAAGTTAAAAGATTTAATTATTTAATTATATTA
Found at i:28233405 original size:8 final size:8
Alignment explanation
Indices: 28233392--28233493 Score: 59
Period size: 8 Copynumber: 12.2 Consensus size: 8
28233382 AAGTTAAAAG
28233392 ATTTAATT
1 ATTTAATT
28233400 ATTTAATT
1 ATTTAATT
28233408 ATATTAAAGTT
1 AT-TT-AA-TT
* *
28233419 A-ATAAGT
1 ATTTAATT
28233426 ATATTAA--
1 AT-TTAATT
28233433 A-TTAATT
1 ATTTAATT
28233440 ATTTAATT
1 ATTTAATT
28233448 ATTTAATT
1 ATTTAATT
*
28233456 ATATTAAGGT
1 AT-TTAA-TT
**
28233466 AAATAATT
1 ATTTAATT
28233474 ATATTAAATT
1 AT-TT-AATT
28233484 ATTTAATT
1 ATTTAATT
28233492 AT
1 AT
28233494 ATTTAATTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
5 4 0.05
7 4 0.05
8 36 0.49
9 16 0.22
10 10 0.14
11 3 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (8 bp):
ATTTAATT
Found at i:28233567 original size:8 final size:8
Alignment explanation
Indices: 28233531--28233624 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
28233521 TGGTCGTAAA
28233531 TAATTATAT
1 TAATTAT-T
28233540 ATAATTATT
1 -TAATTATT
28233549 TAAGCTTATT
1 TAA--TTATT
28233559 TAATTATT
1 TAATTATT
28233567 TAATTGA--
1 TAATT-ATT
**
28233574 -AAAAATT
1 TAATTATT
28233581 TAATTATT
1 TAATTATT
28233589 TAATTATAT
1 TAATTAT-T
28233598 TAA--A-T
1 TAATTATT
*
28233603 TAAATATT
1 TAATTATT
28233611 TAATTATT
1 TAATTATT
28233619 TAATTA
1 TAATTA
28233625 ATAAAAACAG
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
5 5 0.07
6 2 0.03
7 2 0.03
8 39 0.57
9 6 0.09
10 15 0.22
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (8 bp):
TAATTATT
Found at i:28233605 original size:22 final size:22
Alignment explanation
Indices: 28233558--28233626 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
28233548 TTAAGCTTAT
*
28233558 TTAATTATTTAATTGA-A-AAAA
1 TTAATTATTTAATT-ATATTAAA
28233579 TTTAATTATTTAATTATATTAAA
1 -TTAATTATTTAATTATATTAAA
*
28233602 TTAAATATTTAATTAT-TT-AA
1 TTAATTATTTAATTATATTAAA
28233622 TTAAT
1 TTAAT
28233627 AAAAACAGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 6 0.14
21 3 0.07
22 30 0.71
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TTAATTATTTAATTATATTAAA
Found at i:28239251 original size:66 final size:66
Alignment explanation
Indices: 28239145--28239301 Score: 226
Period size: 66 Copynumber: 2.4 Consensus size: 66
28239135 CAAATTGCTC
*
28239145 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
28239209 AA
65 AA
* * *
28239211 AACTTAAAGAGGAGGTTGCAATGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
28239276 C
66 A
* * *
28239277 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
28239302 GCAAGCCGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 1 0.01
66 79 0.99
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:28239317 original size:21 final size:21
Alignment explanation
Indices: 28239288--28239328 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28239278 ACTTAAAGTG
28239288 GAGGCAGCAGCGAGGCAAGCC
1 GAGGCAGCAGCGAGGCAAGCC
*
28239309 GAGGTAGCAGCGAGGCAAGC
1 GAGGCAGCAGCGAGGCAAGC
28239329 GAAGGAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.44, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGCAAGCC
Found at i:28239338 original size:21 final size:21
Alignment explanation
Indices: 28239288--28239339 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28239278 ACTTAAAGTG
*
28239288 GAGGCAGCAGCGAGGCAAGCC
1 GAGGAAGCAGCGAGGCAAGCC
*
28239309 GAGGTAGCAGCGAGGCAAG-C
1 GAGGAAGCAGCGAGGCAAGCC
28239329 GAAGGAAGCAG
1 G-AGGAAGCAG
28239340 AGGCTACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.33, C:0.21, G:0.44, T:0.02
Consensus pattern (21 bp):
GAGGAAGCAGCGAGGCAAGCC
Found at i:28239700 original size:43 final size:43
Alignment explanation
Indices: 28239639--28239760 Score: 201
Period size: 43 Copynumber: 2.8 Consensus size: 43
28239629 TCTGTTATAT
*
28239639 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAG
1 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
28239682 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
1 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
* *
28239725 AAAGCGCCGCTAAAGACCATTGG-CTTCAGCGGCGCT
1 AAAGCGCCGCTGAAGAACA-TGGCCTTCAGCGGCGCT
28239761 CTTTAGCGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
43 72 0.96
44 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.32, T:0.16
Consensus pattern (43 bp):
AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
Found at i:28239975 original size:43 final size:43
Alignment explanation
Indices: 28239914--28240035 Score: 201
Period size: 43 Copynumber: 2.8 Consensus size: 43
28239904 TCTGTTATAT
*
28239914 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAG
1 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
28239957 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
1 AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
* *
28240000 AAAGCGCCGCTAAAGACCATTGG-CTTCAGCGGCGCT
1 AAAGCGCCGCTGAAGAACA-TGGCCTTCAGCGGCGCT
28240036 CTTTAGCGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
43 72 0.96
44 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.32, T:0.16
Consensus pattern (43 bp):
AAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAA
Found at i:28239989 original size:275 final size:275
Alignment explanation
Indices: 28239498--28240048 Score: 1102
Period size: 275 Copynumber: 2.0 Consensus size: 275
28239488 AAATCATATG
28239498 TATATTTCTATCATTTATCATTTACCTTTAAGATTTGAAGTTATTGGTTGGATTTGCATTGGTTG
1 TATATTTCTATCATTTATCATTTACCTTTAAGATTTGAAGTTATTGGTTGGATTTGCATTGGTTG
28239563 GATTTCCTATTTACAGGAAAAATGCTGAAATTCGGGTTTTATGTGAATTAAAAAGGGTTGTCAAA
66 GATTTCCTATTTACAGGAAAAATGCTGAAATTCGGGTTTTATGTGAATTAAAAAGGGTTGTCAAA
28239628 ATCTGTTATATAAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAGAAAGCGCCGCT
131 ATCTGTTATATAAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAGAAAGCGCCGCT
28239693 GAAGAACATGGCCTTCAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGACCATTGGCTTCAGCGGC
196 GAAGAACATGGCCTTCAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGACCATTGGCTTCAGCGGC
28239758 GCTCTTTAGCGGCGC
261 GCTCTTTAGCGGCGC
28239773 TATATTTCTATCATTTATCATTTACCTTTAAGATTTGAAGTTATTGGTTGGATTTGCATTGGTTG
1 TATATTTCTATCATTTATCATTTACCTTTAAGATTTGAAGTTATTGGTTGGATTTGCATTGGTTG
28239838 GATTTCCTATTTACAGGAAAAATGCTGAAATTCGGGTTTTATGTGAATTAAAAAGGGTTGTCAAA
66 GATTTCCTATTTACAGGAAAAATGCTGAAATTCGGGTTTTATGTGAATTAAAAAGGGTTGTCAAA
28239903 ATCTGTTATATAAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAGAAAGCGCCGCT
131 ATCTGTTATATAAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAGAAAGCGCCGCT
28239968 GAAGAACATGGCCTTCAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGACCATTGGCTTCAGCGGC
196 GAAGAACATGGCCTTCAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGACCATTGGCTTCAGCGGC
28240033 GCTCTTTAGCGGCGC
261 GCTCTTTAGCGGCGC
28240048 T
1 T
28240049 TTTTCGCATA
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
275 276 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (275 bp):
TATATTTCTATCATTTATCATTTACCTTTAAGATTTGAAGTTATTGGTTGGATTTGCATTGGTTG
GATTTCCTATTTACAGGAAAAATGCTGAAATTCGGGTTTTATGTGAATTAAAAAGGGTTGTCAAA
ATCTGTTATATAAAGCGCCGCTGAAGAACATGGCCTTCAGCGGCGCTTGTGGAGAAAGCGCCGCT
GAAGAACATGGCCTTCAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGACCATTGGCTTCAGCGGC
GCTCTTTAGCGGCGC
Found at i:28243086 original size:19 final size:21
Alignment explanation
Indices: 28243044--28243086 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
28243034 TTCAACTAGG
*
28243044 ATTAGAATTAATCACAATAAT
1 ATTAGAATTAATCAAAATAAT
*
28243065 ATTA-AATTAAT-AAAATATT
1 ATTAGAATTAATCAAAATAAT
28243084 ATT
1 ATT
28243087 TAGATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTAGAATTAATCAAAATAAT
Found at i:28243164 original size:32 final size:30
Alignment explanation
Indices: 28243062--28243167 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 30
28243052 TAATCACAAT
*
28243062 AATATTAAATTAATAAAATATTATTTAGATA
1 AATATTAAATTAATAAAATA-TATCTAGATA
** * * *
28243093 AATATTAAATTAAATTTAATATTTC-ATATT
1 AATATTAAATT-AATAAAATATATCTAGATA
28243123 AATATTAAATTAATAAAATACTATCTAGATAA
1 AATATTAAATTAATAAAATA-TATCTAGAT-A
28243155 AATATTAAATTAA
1 AATATTAAATTAA
28243168 ATTTAAAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 7 0.12
30 17 0.28
31 16 0.27
32 20 0.33
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
AATATTAAATTAATAAAATATATCTAGATA
Found at i:28244799 original size:30 final size:29
Alignment explanation
Indices: 28244650--28245033 Score: 362
Period size: 30 Copynumber: 13.0 Consensus size: 29
28244640 ATTCGAGGTC
*
28244650 AAAATGTAATTTTGGAAAAGTTTGAGGGGTA
1 AAAATGTAATTTTGGAAAAGTTT-A-GGGTT
* * *
28244681 AAAATGTAATTTTAGAAAATTTTAAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
* **
28244710 AAAATGTGATTTTGGTGAAGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
** *
28244739 AAAATGCGATTTTGGAGAAGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
* *
28244768 AAAATG-AGATTTTAGAGAAGTTTAGGGGTT
1 AAAATGTA-ATTTTGGAAAAGTTTA-GGGTT
* *
28244798 AAAATGTAATTTTGGAAAAGTATAAGGGTC
1 AAAATGTAATTTTGGAAAAGT-TTAGGGTT
28244828 AAAATGTAATTTTGGAAAAGTTTAGAGG-T
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTT
* * *
28244857 -CAATTTAATTTTGGAAAGGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
*
28244885 CAAAATGTAATTTTGGAAAAATTTAAGGGTT
1 -AAAATGTAATTTTGGAAAAGTTT-AGGGTT
** *
28244916 AAAATGTAATTTTGGAAAAGTTTGAAAGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
* * *
28244946 AGAATGTAATTTTGGAAAAATTTGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
* ** *
28244976 AAAATGTAATTTTAGAGTAGTTCAAGGGTT
1 AAAATGTAATTTTGGAAAAGTT-TAGGGTT
* *
28245006 AAAATATAATTTCTAG-AAAGTTTAGGGT
1 AAAATGTAATTT-TGGAAAAGTTTAGGGT
28245034 CCTTTTGGGT
Statistics
Matches: 295, Mismatches: 47, Indels: 24
0.81 0.13 0.07
Matches are distributed among these distances:
27 2 0.01
28 22 0.07
29 82 0.28
30 156 0.53
31 33 0.11
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTT
Found at i:28244802 original size:88 final size:85
Alignment explanation
Indices: 28244650--28245033 Score: 331
Period size: 88 Copynumber: 4.3 Consensus size: 85
28244640 ATTCGAGGTC
* * *
28244650 AAAATGTAATTTTGGAAAAGTTTGAGGGGTAAAAATGTAATTTTAGAAAATTTTAAGGTTAAAAT
1 AAAATGTAATTTTGGAAAAGTTT-A-GGGTTAAAATG-AATTTTAG-AAAGTTTAGGGTTAAAAT
* **
28244715 GTGATTTTGGTGAAGTTTAGGGTT
62 GTAATTTTGGAAAAGTTTAGGGTT
** *
28244739 AAAATGCGATTTTGGAGAAGTTTAGGGTTAAAATGAGATTTTAGAGAAGTTTAGGGGTTAAAATG
1 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGA-ATTTTAGA-AAGTTTA-GGGTTAAAATG
* *
28244804 TAATTTTGGAAAAGTATAAGGGTC
63 TAATTTTGGAAAAGT-TTAGGGTT
* * * *
28244828 AAAATGTAATTTTGGAAAAGTTTAGAGG-TCAATTTAATTTTGGAAAGGTTTAGGGTTCAAAATG
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTTAAAATGAATTTTAGAAA-GTTTAGGGTT-AAAATG
*
28244892 TAATTTTGGAAAAATTTAAGGGTT
63 TAATTTTGGAAAAGTTT-AGGGTT
** * * * * *
28244916 AAAATGTAATTTTGGAAAAGTTTGAAAGTCAGAATGTAATTTTGGAAAAATTTGAGGGTCAAAAT
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATG-AATTTTAG-AAAGTTT-AGGGTTAAAAT
* ** *
28244981 GTAATTTTAGAGTAGTTCAAGGGTT
62 GTAATTTTGGAAAAGTT-TAGGGTT
* *
28245006 AAAATATAATTTCTAG-AAAGTTTAGGGT
1 AAAATGTAATTT-TGGAAAAGTTTAGGGT
28245034 CCTTTTGGGT
Statistics
Matches: 241, Mismatches: 39, Indels: 30
0.78 0.13 0.10
Matches are distributed among these distances:
86 2 0.01
87 31 0.13
88 84 0.35
89 59 0.24
90 55 0.23
91 10 0.04
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (85 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGAATTTTAGAAAGTTTAGGGTTAAAATGTAA
TTTTGGAAAAGTTTAGGGTT
Found at i:28244935 original size:118 final size:117
Alignment explanation
Indices: 28244648--28245032 Score: 388
Period size: 118 Copynumber: 3.2 Consensus size: 117
28244638 GAATTCGAGG
* * * *
28244648 TCAAAATGTAATTTTGGAAAAGTTTGAGGGGTAAAAATGTAATTTTAGAAAATTTTAAGGTTAAA
1 TCAAAATGTAATTTTGGAAAAGTTT-AGGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTCAAA
* ** * *
28244713 ATGTGATTTTGGTGAAGTTTAG-GGTTAAAATGCGATTTTGGAGAAGTTTAGGGT
65 ATGTAATTTTGGAAAAGTTTAGAGG-T-CAATGCAATTTTGGAGAAGTTTAGGGT
* * *
28244767 T-AAAATG-AGATTTTAGAGAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTATAAGGGTCAA
1 TCAAAATGTA-ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAA-GGTCAA
**
28244830 AATGTAATTTTGGAAAAGTTTAGAGGTCAATTTAATTTTGGA-AAGGTTTAGGGT
64 AATGTAATTTTGGAAAAGTTTAGAGGTCAATGCAATTTTGGAGAA-GTTTAGGGT
* * * *
28244884 TCAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTGAAAGTCAGA
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTT-AAGGTCAAA
* * * * *
28244949 ATGTAATTTTGGAAAAATTT-GAGGGTCAAAATGTAATTTTAGAGTAGTTCAAGGGT
65 ATGTAATTTTGGAAAAGTTTAGA-GGTC--AATGCAATTTTGGAGAAGTT-TAGGGT
* *
28245005 T-AAAATATAATTTCTAG-AAAGTTTAGGG
1 TCAAAATGTAATTT-TGGAAAAGTTTAGGG
28245033 TCCTTTTGGG
Statistics
Matches: 223, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
116 2 0.01
117 52 0.23
118 119 0.53
119 6 0.03
120 35 0.16
121 9 0.04
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (117 bp):
TCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTCAAAA
TGTAATTTTGGAAAAGTTTAGAGGTCAATGCAATTTTGGAGAAGTTTAGGGT
Found at i:28245575 original size:17 final size:17
Alignment explanation
Indices: 28245543--28245574 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28245533 AAAAATCATT
28245543 TCTTCTCTCTCTTTTTC
1 TCTTCTCTCTCTTTTTC
28245560 TCTTCTCTCT-TTTTT
1 TCTTCTCTCTCTTTTT
28245575 TGAGTGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTCTCTCTCTTTTTC
Found at i:28246926 original size:14 final size:14
Alignment explanation
Indices: 28246904--28246937 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28246894 CTTTAAATGC
*
28246904 ATTTTGAATGGTTG
1 ATTTGGAATGGTTG
28246918 ATTTGGAATGGTTG
1 ATTTGGAATGGTTG
*
28246932 AATTGG
1 ATTTGG
28246938 TACAAATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (14 bp):
ATTTGGAATGGTTG
Found at i:28247377 original size:10 final size:10
Alignment explanation
Indices: 28247356--28247390 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
28247346 GTGACCCTTG
28247356 TTTTC-AAAT
1 TTTTCTAAAT
28247365 TTTT-TAAAT
1 TTTTCTAAAT
28247374 TTTTCTAAAT
1 TTTTCTAAAT
28247384 TTTTCTA
1 TTTTCTA
28247391 TTTTGCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 12 0.50
10 12 0.50
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTCTAAAT
Found at i:28250768 original size:21 final size:20
Alignment explanation
Indices: 28250742--28250799 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
28250732 AACAATAATG
28250742 AATCGATTCAAACAGAAAAAC
1 AATCGATTCAAA-AGAAAAAC
*
28250763 AATCGATTCAATAAAAAAAAC
1 AATCGATTCAA-AAGAAAAAC
*
28250784 AATTGATTCAAAAGAA
1 AATCGATTCAAAAGAA
28250800 GAGTATTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 28 0.85
22 1 0.03
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.19
Consensus pattern (20 bp):
AATCGATTCAAAAGAAAAAC
Found at i:28254879 original size:30 final size:28
Alignment explanation
Indices: 28254829--28254897 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 28
28254819 AGTATAGCTG
*
28254829 GAGCTTTGCAATATGTTGTCATCACTCGACTT
1 GAGC-TTGC-ATATGCTGTCA--ACTCGACTT
28254861 GAGCTTGCATATGCTGTCAACTCGACTT
1 GAGCTTGCATATGCTGTCAACTCGACTT
* *
28254889 AAGCATGCA
1 GAGCTTGCA
28254898 CCCTTGGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.47
30 10 0.29
31 4 0.12
32 4 0.12
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (28 bp):
GAGCTTGCATATGCTGTCAACTCGACTT
Found at i:28262504 original size:3 final size:3
Alignment explanation
Indices: 28262496--28262535 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
28262486 AAGATTCTCA
28262496 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
28262536 ATTAGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28263652 original size:12 final size:12
Alignment explanation
Indices: 28263635--28263659 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28263625 CTGATCTGAA
28263635 AGCTGCTTCAAC
1 AGCTGCTTCAAC
28263647 AGCTGCTTCAAC
1 AGCTGCTTCAAC
28263659 A
1 A
28263660 ATGACGGATG
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:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
AGCTGCTTCAAC
Found at i:28263815 original size:21 final size:21
Alignment explanation
Indices: 28263760--28263823 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
28263750 TTGCTTCCTT
*
28263760 AACACGCTCCAGGATTTCTTG
1 AACACGCTCCAGGATTTCTTC
* * **
28263781 TACATGCTTAAGGATTTCTTC
1 AACACGCTCCAGGATTTCTTC
*
28263802 AACGCGCTCCAGGATTTTCTTC
1 AACACGCTCCAGGA-TTTCTTC
28263824 TGCAGTTCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (21 bp):
AACACGCTCCAGGATTTCTTC
Found at i:28266353 original size:3 final size:3
Alignment explanation
Indices: 28266347--28266371 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28266337 TCATCATCAC
28266347 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
28266372 ATCATCATCA
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:28267526 original size:19 final size:18
Alignment explanation
Indices: 28267479--28267530 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
28267469 GGTTTCCGAA
*
28267479 AAATAATTTTTGGAAAAT
1 AAATATTTTTTGGAAAAT
28267497 AAATTACTTTTTTGGAAAAGT
1 AAA-TA-TTTTTTGGAAAA-T
*
28267518 TAATATTTTTTGG
1 AAATATTTTTTGG
28267531 TGTTTGGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 10 0.34
20 13 0.45
21 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (18 bp):
AAATATTTTTTGGAAAAT
Found at i:28267856 original size:46 final size:46
Alignment explanation
Indices: 28267788--28267875 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
28267778 AAGCGAATTG
* ** * *
28267788 ATGATAACTACAATATTTTCCAAGTGTATAACTAGTATTACACCAC
1 ATGATAACTACAACATCATCCAAGTGCATAACTAATATTACACCAC
28267834 ATGATAACTACAACATCATCCAAGTGCATAACTAATATTACA
1 ATGATAACTACAACATCATCCAAGTGCATAACTAATATTACA
28267876 AATTAGTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (46 bp):
ATGATAACTACAACATCATCCAAGTGCATAACTAATATTACACCAC
Found at i:28271209 original size:17 final size:18
Alignment explanation
Indices: 28271187--28271236 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
28271177 TATTATTTCA
28271187 TAAAAATATTTTTA-TTT
1 TAAAAATATTTTTATTTT
28271204 TAAAAAGT-TTTTTATTTT
1 TAAAAA-TATTTTTATTTT
28271222 TAAACAATATTTTTA
1 TAAA-AATATTTTTA
28271237 CATACACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 12 0.41
18 9 0.31
19 8 0.28
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TAAAAATATTTTTATTTT
Found at i:28283352 original size:6 final size:6
Alignment explanation
Indices: 28283327--28283383 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
28283317 ACAATTCATA
* * * * * *
28283327 TCACTT TCAATT CCAATT TCACTT TCAATT CCAATT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
28283375 TCACTT TCA
1 TCACTT TCA
28283384 ATTTTGATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:28283355 original size:12 final size:12
Alignment explanation
Indices: 28283327--28283387 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
28283317 ACAATTCATA
28283327 TCACTTTCAATT
1 TCACTTTCAATT
* * *
28283339 CCAATTTCACTT
1 TCACTTTCAATT
* *
28283351 TCAATTCCAATT
1 TCACTTTCAATT
*
28283363 TCACTTTCACTT
1 TCACTTTCAATT
28283375 TCACTTTCAATT
1 TCACTTTCAATT
28283387 T
1 T
28283388 TGATCACAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:28283383 original size:18 final size:18
Alignment explanation
Indices: 28283327--28283371 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
28283317 ACAATTCATA
28283327 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
28283345 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
28283363 TCACTTTCA
1 TCACTTTCA
28283372 CTTTCACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:28293313 original size:26 final size:26
Alignment explanation
Indices: 28293271--28293417 Score: 197
Period size: 26 Copynumber: 5.7 Consensus size: 26
28293261 GGTTCATACA
*
28293271 AGCCTAGTT-AGTTTATCGCTCTTACG
1 AGCC-AGTTCAGTATATCGCTCTTACG
28293297 AGCCAGTTCAGTATATCGCTCTTACG
1 AGCCAGTTCAGTATATCGCTCTTACG
* * *
28293323 AGCCAGTTCAATATATCTCTCTTTCG
1 AGCCAGTTCAGTATATCGCTCTTACG
*
28293349 AGCCAGTTCAATATATCGCTCTTACG
1 AGCCAGTTCAGTATATCGCTCTTACG
* *
28293375 AGCCAATTCAGTATATCGCTCTTTCG
1 AGCCAGTTCAGTATATCGCTCTTACG
* *
28293401 AGCTAGTTTAGTATATC
1 AGCCAGTTCAGTATATC
28293418 TTCAAAGTCT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
25 4 0.04
26 104 0.96
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (26 bp):
AGCCAGTTCAGTATATCGCTCTTACG
Found at i:28301042 original size:36 final size:36
Alignment explanation
Indices: 28300995--28301134 Score: 246
Period size: 36 Copynumber: 3.9 Consensus size: 36
28300985 TGGTAACAGG
28300995 CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
28301031 CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
28301067 CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
* *
28301103 TATGACTTTTGGGTC-ATCAGGGAGTAAAACGA
1 CATGACCTTTGGGTCAAT-AGGGAGTAAAACGA
28301135 ATAACGAACG
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
35 2 0.02
36 99 0.98
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAACGATCAT
Found at i:28315310 original size:24 final size:23
Alignment explanation
Indices: 28315275--28315322 Score: 55
Period size: 24 Copynumber: 2.0 Consensus size: 23
28315265 ATCCTAAAAT
28315275 GGAGAGAAAAGGATGGTGAGA-GAA
1 GGAGAGAAAAGG--GGTGAGATGAA
28315299 GGAGA-AATAAGGGGTGAGATGAA
1 GGAGAGAA-AAGGGGTGAGATGAA
28315322 G
1 G
28315323 TGGGACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (23 bp):
GGAGAGAAAAGGGGTGAGATGAA
Found at i:28320110 original size:24 final size:24
Alignment explanation
Indices: 28320083--28320337 Score: 178
Period size: 24 Copynumber: 10.6 Consensus size: 24
28320073 TTTATATACA
* *
28320083 TTTACGCTCGTCAACTTACAGACG
1 TTTACGCTCGTCAGCTTGCAGACG
28320107 TTTACGCTCGTCAGCTTGC-GCACG
1 TTTACGCTCGTCAGCTTGCAG-ACG
** *
28320131 TTTACGCTCACCAGCTT--ATGTACA
1 TTTACGCTCGTCAGCTTGCA-G-ACG
** * *
28320155 TTTACGCTCACCAGCTTGTACACG
1 TTTACGCTCGTCAGCTTGCAGACG
* * ** *
28320179 TTTACACTTGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTGCAGACG
*
28320203 TTTACGCTCGTTAGCTTGCA-AGCG
1 TTTACGCTCGTCAGCTTGCAGA-CG
* ** *
28320227 TTTAAGCTCGTCAGCTT-TTGTACA
1 TTTACGCTCGTCAGCTTGCAG-ACG
* ** * *
28320251 TTTACGCTCATCAGCTTATATACC
1 TTTACGCTCGTCAGCTTGCAGACG
* * *
28320275 TTTACGCTCATCAGCTTGCACACA
1 TTTACGCTCGTCAGCTTGCAGACG
*
28320299 TTTACGCTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTGCAGACG
28320323 TTTACGCTCGTCAGC
1 TTTACGCTCGTCAGC
28320338 ATATATATGT
Statistics
Matches: 187, Mismatches: 35, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
23 2 0.01
24 182 0.97
25 2 0.01
26 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTGCAGACG
Found at i:28320204 original size:72 final size:71
Alignment explanation
Indices: 28320080--28320353 Score: 250
Period size: 72 Copynumber: 3.8 Consensus size: 71
28320070 TAGTTTATAT
* ** * **** *
28320080 ACATTTACGCTCGTCAACTTACAGACGTTTACGCTCGTCAGCTTGCGCACGTTTACGCTCACCAG
1 ACATTTACGCTCGTCAGCTTGTACACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAG
*
28320145 CTTATGT
66 CTT-TGA
** * * * *
28320152 ACATTTACGCTCACCAGCTTGTACACGTTTACACTTGTCAGCTTATATACGTTTACGCTCGTTAG
1 ACATTTACGCTCGTCAGCTTGTACACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAG
28320217 C-TTGCA
66 CTTTG-A
* * * *
28320223 AGCGTTTAAGCTCGTCAGCTTTTGTACA--TTTACGCTCATCAGCTTATATACCTTTACGCTCAT
1 A-CATTTACGCTCGTCAGC--TTGTACACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCAT
28320286 CAGC-TTGCA
63 CAGCTTTG-A
* * *
28320295 CACATTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCATATATATGTTTACGC
1 -ACATTTACGCTCGTCAGCTTGTACACGTTTACGCTCGTCAGCTTATATACGTTTACGC
28320354 AGTTCAATGA
Statistics
Matches: 162, Mismatches: 33, Indels: 14
0.78 0.16 0.07
Matches are distributed among these distances:
70 8 0.05
71 2 0.01
72 144 0.89
73 1 0.01
74 7 0.04
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (71 bp):
ACATTTACGCTCGTCAGCTTGTACACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAG
CTTTGA
Found at i:28320351 original size:48 final size:48
Alignment explanation
Indices: 28320083--28320353 Score: 256
Period size: 48 Copynumber: 5.6 Consensus size: 48
28320073 TTTATATACA
* * * * *
28320083 TTTACGCTCGTCAACTTACAGACGTTTACGCTCGTCAGCTTGCGCACG
1 TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAGCTTGCACACG
** * ** *
28320131 TTTACGCTCACCAGCTTATGTACATTTACGCTCACCAGCTTGTACACG
1 TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAGCTTGCACACG
* * * *
28320179 TTTACACTTGTCAGCTTATATACGTTTACGCTCGTTAGCTTGCA-AGCG
1 TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAGCTTGCACA-CG
* * * * ** * *
28320227 TTTAAGCTCGTCAGCTTTTGTACATTTACGCTCATCAGCTTATATACC
1 TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAGCTTGCACACG
* ** *
28320275 TTTACGCTCATCAGCTTGCACACATTTACGCTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAGCTTGCACACG
* **
28320323 TTTACGCTCGTCAGCATATATATGTTTACGC
1 TTTACGCTCGTCAGCTTATATACATTTACGC
28320354 AGTTCAATGA
Statistics
Matches: 171, Mismatches: 50, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
47 1 0.01
48 169 0.99
49 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTATATACATTTACGCTCGTCAGCTTGCACACG
Found at i:28327966 original size:17 final size:17
Alignment explanation
Indices: 28327946--28327978 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28327936 TATTCATGAT
28327946 AAAAAATAA-TGGAAAGG
1 AAAAAA-AAGTGGAAAGG
28327963 AAAAAAAAGTGGAAAG
1 AAAAAAAAGTGGAAAG
28327979 TAATTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGTGGAAAGG
Found at i:28332575 original size:16 final size:16
Alignment explanation
Indices: 28332551--28332583 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28332541 AAAATTTCAC
*
28332551 AAAATTTAAAAATAAA
1 AAAAATTAAAAATAAA
28332567 AAAAATTAAAAATAAA
1 AAAAATTAAAAATAAA
28332583 A
1 A
28332584 TTTTATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAAATAAA
Found at i:28336336 original size:3 final size:3
Alignment explanation
Indices: 28336328--28336353 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28336318 GAATATTTTA
28336328 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
28336354 AGTAGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:28337089 original size:31 final size:31
Alignment explanation
Indices: 28337031--28337089 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
28337021 ATGGTCATTT
**
28337031 AACTATTTGAAAGTTTTCATTTAAGTCACTG
1 AACTATTCAAAAGTTTTCATTTAAGTCACTG
*
28337062 AACTATTCAAAAGCTTTT-ATTTGAGTCA
1 AACTATTCAAAAG-TTTTCATTTAAGTCA
28337090 TTGGGTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCACTG
Found at i:28338170 original size:21 final size:23
Alignment explanation
Indices: 28338134--28338178 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
28338124 CAGCAAATGA
28338134 TTTTAAAACTATTAAAATTATTT
1 TTTTAAAACTATTAAAATTATTT
28338157 TTTTAAAA-TA-TAAAATTATTT
1 TTTTAAAACTATTAAAATTATTT
28338178 T
1 T
28338179 AAAATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAACTATTAAAATTATTT
Found at i:28338183 original size:11 final size:12
Alignment explanation
Indices: 28338167--28338195 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28338157 TTTTAAAATA
28338167 TAAAATT-ATTT
1 TAAAATTAATTT
28338178 TAAAATTAATTT
1 TAAAATTAATTT
28338190 TAAAAT
1 TAAAAT
28338196 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAAATTAATTT
Found at i:28339137 original size:20 final size:20
Alignment explanation
Indices: 28339112--28339194 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
28339102 AAATAATTTT
28339112 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
* **
28339132 AATAATTTTA-A-ATTAATTTT
1 AATAATTTTATATTTTAA--AA
*
28339152 AATAATTTTATATTTTTTAAA
1 AATAATTTTATA-TTTTAAAA
*
28339173 AATATTTTTAATAATTTTAAAA
1 AATAATTTT-AT-ATTTTAAAA
28339195 TCATTTACTG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 4 0.09
19 1 0.02
20 20 0.43
21 9 0.19
22 9 0.19
23 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:28339149 original size:40 final size:39
Alignment explanation
Indices: 28339093--28339192 Score: 141
Period size: 40 Copynumber: 2.6 Consensus size: 39
28339083 GATGATGATT
*
28339093 AAAATA-TTAAAATAATTTTAATAATTTTATA-TTTTAA
1 AAAATATTTTAAATAATTTTAATAATTTTATATTTTTAA
*
28339130 AAAATAATTTTAAATTAATTTTAATAATTTTATATTTTTTA
1 AAAAT-ATTTTAAA-TAATTTTAATAATTTTATATTTTTAA
*
28339171 AAAATATTTTTAATAATTTTAA
1 AAAATATTTTAAATAATTTTAA
28339193 AATCATTTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
37 5 0.09
38 1 0.02
39 14 0.25
40 26 0.46
41 10 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
AAAATATTTTAAATAATTTTAATAATTTTATATTTTTAA
Found at i:28339150 original size:11 final size:10
Alignment explanation
Indices: 28339102--28339193 Score: 61
Period size: 9 Copynumber: 9.3 Consensus size: 10
28339092 TAAAATATTA
28339102 AAATAATTTT
1 AAATAATTTT
28339112 -AATAATTTT
1 AAATAATTTT
28339121 --AT-ATTTT
1 AAATAATTTT
28339128 AAAAAATAATTTT
1 ---AAATAATTTT
28339141 AAATTAATTTT
1 AAA-TAATTTT
28339152 -AATAATTTT
1 AAATAATTTT
* *
28339161 ATAT-TTTTT
1 AAATAATTTT
*
28339170 AAAAATATTTT
1 AAATA-ATTTT
*
28339181 TAATAATTTT
1 AAATAATTTT
28339191 AAA
1 AAA
28339194 ATCATTTACT
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 22 0.34
10 14 0.22
11 14 0.22
12 2 0.03
13 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AAATAATTTT
Found at i:28351411 original size:24 final size:24
Alignment explanation
Indices: 28351361--28351411 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28351351 AGGCCCGAGC
*
28351361 AAAATCCCTCAGCCAAAAACTATG
1 AAAATCCCTCAGCCAAAAACCATG
* *
28351385 AAAATTCCTCAG-CAAATACCATCG
1 AAAATCCCTCAGCCAAAAACCAT-G
28351409 AAA
1 AAA
28351412 TACATCAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.47, C:0.27, G:0.08, T:0.18
Consensus pattern (24 bp):
AAAATCCCTCAGCCAAAAACCATG
Found at i:28359968 original size:77 final size:77
Alignment explanation
Indices: 28359860--28360013 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
28359850 TTATGTGAAA
28359860 TAGTTTGGGGGAAATATAAACCATACCTTTATCCGTCAAGATAGGTTTTATAAATTGAATTCAAC
1 TAGTTTGGGGGAAATATAAACCATACCTTTATCCGTCAAGATAGGTTTTATAAATTGAATTCAAC
28359925 ATCTAATTTTGC
66 ATCTAATTTTGC
28359937 TAGTTTGGGGGAAATATAAACCATACCTTTATCCGTCAAGATAGGTTTTATAAATTGAATTCAAC
1 TAGTTTGGGGGAAATATAAACCATACCTTTATCCGTCAAGATAGGTTTTATAAATTGAATTCAAC
28360002 ATCTAATTTTGC
66 ATCTAATTTTGC
28360014 ATTGTCGAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (77 bp):
TAGTTTGGGGGAAATATAAACCATACCTTTATCCGTCAAGATAGGTTTTATAAATTGAATTCAAC
ATCTAATTTTGC
Found at i:28362598 original size:40 final size:40
Alignment explanation
Indices: 28362541--28362621 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
28362531 CGACCTTATC
*
28362541 TCCCCAAAGTCGCTTATCAAATCTACATATCTCTTTCATT
1 TCCCCAAAGTCACTTATCAAATCTACATATCTCTTTCATT
* * *
28362581 TCCCCAAAGTCATTTATCGAATCTGCATATCTCTTTCATT
1 TCCCCAAAGTCACTTATCAAATCTACATATCTCTTTCATT
28362621 T
1 T
28362622 ACTTTACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (40 bp):
TCCCCAAAGTCACTTATCAAATCTACATATCTCTTTCATT
Found at i:28364522 original size:25 final size:25
Alignment explanation
Indices: 28364494--28364553 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
28364484 TGACTTATTA
*
28364494 CATATCTTTTAAGAAATGGAGTTTG
1 CATATTTTTTAAGAAATGGAGTTTG
28364519 CATATTTTTTAAGAAATGGAGTTTG
1 CATATTTTTTAAGAAATGGAGTTTG
28364544 CATATTTTTT
1 CATATTTTTT
28364554 TATATAATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (25 bp):
CATATTTTTTAAGAAATGGAGTTTG
Found at i:28366127 original size:26 final size:26
Alignment explanation
Indices: 28366098--28366155 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
28366088 GAGTAATTTC
* *
28366098 TTTATCCTTTTTCATTTA-TTCTTTTA
1 TTTATACTTTTTCATTAACTT-TTTTA
* *
28366124 TTTATATTTTTTCGTTAACTTTTTTA
1 TTTATACTTTTTCATTAACTTTTTTA
28366150 TTTATA
1 TTTATA
28366156 TTTGGCATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTATACTTTTTCATTAACTTTTTTA
Found at i:28373303 original size:3 final size:3
Alignment explanation
Indices: 28373295--28373319 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28373285 CTTTATTTAT
28373295 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
28373320 ATTTTTTTCT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28375706 original size:20 final size:20
Alignment explanation
Indices: 28375683--28375721 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28375673 AAGCCCATGG
*
28375683 TCAACCTAAAAAGTCAACGA
1 TCAACCCAAAAAGTCAACGA
28375703 TCAACCCAAAAAGTCAACG
1 TCAACCCAAAAAGTCAACG
28375722 GTTAACGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.28, G:0.10, T:0.13
Consensus pattern (20 bp):
TCAACCCAAAAAGTCAACGA
Found at i:28380388 original size:15 final size:15
Alignment explanation
Indices: 28380368--28380397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28380358 TATTTAACTG
28380368 AATTAACCAAATTAA
1 AATTAACCAAATTAA
*
28380383 AATTAATCAAATTAA
1 AATTAACCAAATTAA
28380398 CCAAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAACCAAATTAA
Found at i:28381868 original size:2 final size:2
Alignment explanation
Indices: 28381861--28381892 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28381851 GGAAATATGA
28381861 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
28381893 TAATTGTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28384491 original size:21 final size:21
Alignment explanation
Indices: 28384445--28384491 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28384435 AGATCTATGG
* *
28384445 CTTCTACCGATACAACTCTGA
1 CTTCTACCGATACAACCCAGA
* *
28384466 GTTCTATCGATACAACCCAGA
1 CTTCTACCGATACAACCCAGA
28384487 CTTCT
1 CTTCT
28384492 TTTAGTAGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.30
Consensus pattern (21 bp):
CTTCTACCGATACAACCCAGA
Found at i:28386521 original size:3 final size:3
Alignment explanation
Indices: 28386513--28386557 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
28386503 TATATCCCAA
28386513 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28386558 GAATAGAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28387605 original size:7 final size:7
Alignment explanation
Indices: 28387593--28387687 Score: 88
Period size: 7 Copynumber: 14.0 Consensus size: 7
28387583 TTCGAAAAAA
28387593 GTCAACG
1 GTCAACG
28387600 GTCAACG
1 GTCAACG
28387607 GTCAACG
1 GTCAACG
*
28387614 GTCAA-T
1 GTCAACG
28387620 GTCAACG
1 GTCAACG
**
28387627 GTCAGTG
1 GTCAACG
28387634 GTCAACG
1 GTCAACG
*
28387641 GTCAA-A
1 GTCAACG
28387647 GTCAACG
1 GTCAACG
* *
28387654 GTTAATG
1 GTCAACG
*
28387661 GTCAA-A
1 GTCAACG
28387667 GTCAACG
1 GTCAACG
**
28387674 GTCAGTG
1 GTCAACG
28387681 GTCAACG
1 GTCAACG
28387688 CCGGTCAACG
Statistics
Matches: 68, Mismatches: 17, Indels: 6
0.75 0.19 0.07
Matches are distributed among these distances:
6 15 0.22
7 53 0.78
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:28387625 original size:20 final size:21
Alignment explanation
Indices: 28387593--28387687 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 21
28387583 TTCGAAAAAA
*
28387593 GTCAACGGTCAACGGTCAACG
1 GTCAATGGTCAACGGTCAACG
**
28387614 GTCAAT-GTCAACGGTCAGTG
1 GTCAATGGTCAACGGTCAACG
* *
28387634 GTCAACGGTCAA-AGTCAACG
1 GTCAATGGTCAACGGTCAACG
* *
28387654 GTTAATGGTCAA-AGTCAACG
1 GTCAATGGTCAACGGTCAACG
*
28387674 GTCAGTGGTCAACG
1 GTCAATGGTCAACG
28387688 CCGGTCAACG
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 50 0.83
21 10 0.17
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (21 bp):
GTCAATGGTCAACGGTCAACG
Done.