Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 60 of 297
Found at i:21246928 original size:52 final size:52
Alignment explanation
Indices: 21246872--21246990 Score: 220
Period size: 52 Copynumber: 2.3 Consensus size: 52
21246862 GGGAAATTTC
21246872 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
* *
21246924 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
21246976 TCACTTAGCACAATG
1 TCACTTAGCACAATG
21246991 TCATATACTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:21246949 original size:28 final size:27
Alignment explanation
Indices: 21246872--21246987 Score: 163
Period size: 24 Copynumber: 4.4 Consensus size: 27
21246862 GGGAAATTTC
21246872 TCACTTAGCACAATGCCATGGACTTATT
1 TCACTTAGCAC-ATGCCATGGACTTATT
21246900 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
21246924 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
21246952 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
21246976 TCACTTAGCACA
1 TCACTTAGCACA
21246988 ATGTCATATA
Statistics
Matches: 80, Mismatches: 1, Indels: 15
0.83 0.01 0.16
Matches are distributed among these distances:
24 46 0.57
25 1 0.01
27 2 0.03
28 31 0.39
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:21256583 original size:35 final size:35
Alignment explanation
Indices: 21256522--21256598 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
21256512 TGTAGATCAG
* * *
21256522 TAATCGAGTTCTAAATAGTAAAGAAACACCGCTCT
1 TAATTGAGTTCTAAACAGCAAAGAAACACCGCTCT
*
21256557 TAATTGAGTTCTAAACAGCAAGGAAACACCGCTCT
1 TAATTGAGTTCTAAACAGCAAAGAAACACCGCTCT
*
21256592 TCATTGA
1 TAATTGA
21256599 AGGTAAGTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (35 bp):
TAATTGAGTTCTAAACAGCAAAGAAACACCGCTCT
Found at i:21257534 original size:40 final size:40
Alignment explanation
Indices: 21257473--21257548 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
21257463 CGGTACCTTA
*
21257473 TGGTGTGTAGGATTGGATGGGTTGATTATATCCCCATACT
1 TGGTGTGTAGGATTGGATGGGTCGATTATATCCCCATACT
* * *
21257513 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCCCA
1 TGGTGTGTAGGATTGGATGGGTCGATTATATCCCCA
21257549 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.16, C:0.14, G:0.34, T:0.36
Consensus pattern (40 bp):
TGGTGTGTAGGATTGGATGGGTCGATTATATCCCCATACT
Found at i:21259714 original size:43 final size:43
Alignment explanation
Indices: 21259613--21259915 Score: 349
Period size: 43 Copynumber: 7.1 Consensus size: 43
21259603 AAAGCGCCAT
* *
21259613 TAAAGAACGTGACCTTTAGCGACGCTTTTCACACAAAC-TCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* *
21259655 TAAAGAACGTGACCTTTAGGGGCGCTTTTCACACAAACGCTGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * *
21259698 TAAAGAACGTGACCTTTAGTGGTGCTTTTCACACAAACGCCAC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * *
21259741 TAAAGAACGTGACCTGTAGCGGCGCTTTTCTCAAAAACGCCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * * * *
21259784 TAAAGAACTTGACCTTTAGCGGCGCTTTT-ATAAAAAATGCCGT
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCA-CACAAACGCCGC
* * * * * *
21259827 TAAAGAACATGACCTTTAGCGGCACTTTTCATACTAATGACGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * * * *
21259870 TAAAGAACATGACCTTTAGCGGCGATTTTCTCAAAAACGCCAC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
21259913 TAA
1 TAA
21259916 TTTTAACATA
Statistics
Matches: 222, Mismatches: 36, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 36 0.16
43 185 0.83
44 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
Found at i:21259786 original size:86 final size:86
Alignment explanation
Indices: 21259569--21259915 Score: 344
Period size: 86 Copynumber: 4.0 Consensus size: 86
21259559 AAAAAGGCTG
* * * * **
21259569 CTAAAGAACATGA-CTTTCAGCGGC-CTTTTTTGAGAAAGCGCCATTAAAGAACGTGACCTTTAG
1 CTAAAGAACGTGACCTTT-AGCGGCGCTTTTCTCACAAA-CGCCGCTAAAGAACGTGACCTTTAG
* * * *
21259632 CGACGCTTTTCACACAAAC-TCG
64 CGGCGCTTTTCACAAAAACGCCA
* * * *
21259654 CTAAAGAACGTGACCTTTAGGGGCGCTTTTCACACAAACGCTGCTAAAGAACGTGACCTTTAGTG
1 CTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACGTGACCTTTAGCG
* *
21259719 GTGCTTTTCACACAAACGCCA
66 GCGCTTTTCACAAAAACGCCA
* * *
21259740 CTAAAGAACGTGACCTGTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACTTGACCTTTAGCG
1 CTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACGTGACCTTTAGCG
* * *
21259805 GCGCTTTT-ATAAAAAATGCCG
66 GCGCTTTTCA-CAAAAACGCCA
* * * * * * *
21259826 TTAAAGAACATGACCTTTAGCGGCACTTTTCAT-ACTAATGACGCTAAAGAACATGACCTTTAGC
1 CTAAAGAACGTGACCTTTAGCGGCGCTTTTC-TCACAAACGCCGCTAAAGAACGTGACCTTTAGC
* *
21259890 GGCGATTTTCTCAAAAACGCCA
65 GGCGCTTTTCACAAAAACGCCA
21259912 CTAA
1 CTAA
21259916 TTTTAACATA
Statistics
Matches: 215, Mismatches: 41, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
85 56 0.26
86 158 0.73
87 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (86 bp):
CTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACGTGACCTTTAGCG
GCGCTTTTCACAAAAACGCCA
Found at i:21259833 original size:129 final size:129
Alignment explanation
Indices: 21259557--21259915 Score: 384
Period size: 129 Copynumber: 2.8 Consensus size: 129
21259547 GTGTTTATGT
* * *** * *
21259557 AAAAAAAGGCTGCTAAAGAACATGA-CTTTCAGCGGC-CTTTTTTGAGAAAGCGCCATTAAAGAA
1 AAAAAAACGCCGCTAAAGAACATGACCTTT-AGCGGCACTTTTCACACAAA-CGCCACTAAAGAA
* * * * *
21259620 CGTGACCTTTAGCGACGCTTTTCACACAAAC-TCGCTAAAGAACGTGACCTTTAGGGGCGCTTTT
64 CGTGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTT
21259684 C
129 C
* * * * * **
21259685 ACACAAACGCTGCTAAAGAACGTGACCTTTAGTGGTGCTTTTCACACAAACGCCACTAAAGAACG
1 AAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCACACAAACGCCACTAAAGAACG
* *
21259750 TGACCTGTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACTTGACCTTTAGCGGCGCTTTT-
66 TGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTC
* * * * * * *
21259813 ATAAAAAATGCCGTTAAAGAACATGACCTTTAGCGGCACTTTTCATACTAATGACGCTAAAGAAC
1 A-AAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCACACAAACGCCACTAAAGAAC
* * *
21259878 ATGACCTTTAGCGGCGATTTTCTCAAAAACGCCACTAA
65 GTGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAA
21259916 TTTTAACATA
Statistics
Matches: 191, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
128 65 0.34
129 126 0.66
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (129 bp):
AAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCACACAAACGCCACTAAAGAACG
TGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTC
Found at i:21260647 original size:13 final size:14
Alignment explanation
Indices: 21260614--21260649 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21260604 AATGAATATT
21260614 CCATTATAATTAAA
1 CCATTATAATTAAA
*
21260628 CCATTATGATTAAA
1 CCATTATAATTAAA
21260642 -CATTATAA
1 CCATTATAA
21260650 ATATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (14 bp):
CCATTATAATTAAA
Found at i:21265181 original size:9 final size:9
Alignment explanation
Indices: 21265163--21265204 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
21265153 TATTTATGTA
21265163 TTATGTAAG
1 TTATGTAAG
*
21265172 TTAAGTAAG
1 TTATGTAAG
*
21265181 TTTTGTAAG
1 TTATGTAAG
21265190 TTATGTAAG
1 TTATGTAAG
21265199 TTATGT
1 TTATGT
21265205 TATGATATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:21265308 original size:27 final size:27
Alignment explanation
Indices: 21265227--21265308 Score: 103
Period size: 30 Copynumber: 2.9 Consensus size: 27
21265217 TTATATAAGG
21265227 TATGTAAGTTATGATATGATATATATT
1 TATGTAAGTTATGATATGATATATATT
*
21265254 CATGTATTA-TACTATGATATGATATATATT
1 TATGTA--AGT--TATGATATGATATATATT
*
21265284 TATGTAAGTTATTATATGATATATA
1 TATGTAAGTTATGATATGATATATA
21265309 ATTAACATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 20 0.43
28 2 0.04
29 2 0.04
30 23 0.49
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (27 bp):
TATGTAAGTTATGATATGATATATATT
Found at i:21265524 original size:165 final size:165
Alignment explanation
Indices: 21265339--21266212 Score: 1739
Period size: 165 Copynumber: 5.3 Consensus size: 165
21265329 TATTTCCCTT
21265339 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
1 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
21265404 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
66 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
21265469 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
131 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
21265504 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
1 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
21265569 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
66 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
21265634 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
131 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
21265669 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
1 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
21265734 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
66 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
21265799 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
131 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
21265834 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
1 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
21265899 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
66 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
21265964 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
131 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
21265999 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
1 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
21266064 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
66 TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
21266129 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
131 AAAATAAAATTTGATGATGTGGAAAATCACATGGA
*
21266164 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCTAAATTAT
1 AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTAT
21266213 TAAAAATAAG
Statistics
Matches: 708, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 708 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (165 bp):
AAAAAATTATTTTAATTAAATAATATTTAAATAAATTAATCCAAATTATGTAATTTAAAAAATTG
TGTATAAAAAGTTGTAAGCCGTATAATATGAAATGTCAACTTGGTTCCATGAAAAAGAAATAATA
AAAATAAAATTTGATGATGTGGAAAATCACATGGA
Found at i:21266262 original size:14 final size:14
Alignment explanation
Indices: 21266240--21266270 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21266230 CTTGTTTTAA
21266240 TATGATAATGGCAT
1 TATGATAATGGCAT
*
21266254 TATGGTAATGGCAT
1 TATGATAATGGCAT
21266268 TAT
1 TAT
21266271 TGACAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (14 bp):
TATGATAATGGCAT
Found at i:21268540 original size:9 final size:9
Alignment explanation
Indices: 21268522--21268572 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
21268512 GAAACAAATT
*
21268522 CAAAATGCA
1 CAAAACGCA
21268531 CAAAACGCA
1 CAAAACGCA
21268540 CATAAAC-C-
1 CA-AAACGCA
21268548 CAAAACGCA
1 CAAAACGCA
21268557 CAAAACGCA
1 CAAAACGCA
21268566 CATAAAC
1 CA-AAAC
21268573 CCAAACCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 4 0.11
8 3 0.08
9 22 0.59
10 8 0.22
ACGTcount: A:0.55, C:0.31, G:0.08, T:0.06
Consensus pattern (9 bp):
CAAAACGCA
Found at i:21268551 original size:26 final size:26
Alignment explanation
Indices: 21268522--21268577 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
21268512 GAAACAAATT
*
21268522 CAAAATGCACAAAACGCACATAAACC
1 CAAAACGCACAAAACGCACATAAACC
21268548 CAAAACGCACAAAACGCACATAAACC
1 CAAAACGCACAAAACGCACATAAACC
21268574 CAAA
1 CAAA
21268578 CCCAAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.55, C:0.32, G:0.07, T:0.05
Consensus pattern (26 bp):
CAAAACGCACAAAACGCACATAAACC
Found at i:21268577 original size:17 final size:16
Alignment explanation
Indices: 21268531--21268562 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
21268521 TCAAAATGCA
21268531 CAAAACGCACATAAACC
1 CAAAACGCACA-AAACC
21268548 CAAAACGCACAAAAC
1 CAAAACGCACAAAAC
21268563 GCACATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.34, G:0.06, T:0.03
Consensus pattern (16 bp):
CAAAACGCACAAAACC
Found at i:21268700 original size:17 final size:19
Alignment explanation
Indices: 21268659--21268703 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
21268649 GACAGCAGTG
* *
21268659 GAGAGAAGAGGGTGTGACA
1 GAGAGAAGAGGATGCGACA
*
21268678 GAGAGAAGAGGATGCGACG
1 GAGAGAAGAGGATGCGACA
21268697 GAGAGAA
1 GAGAGAA
21268704 AACGAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.47, T:0.07
Consensus pattern (19 bp):
GAGAGAAGAGGATGCGACA
Found at i:21273501 original size:29 final size:29
Alignment explanation
Indices: 21273458--21273532 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
21273448 CATGATTATG
* *
21273458 AATGTGA-CTGGGCCTAACGGGCCATATA
1 AATGTGATTTGGGCCTAACAGGCCATATA
**
21273486 AATGTGATTTGGGCCTAGTAGGCCATATA
1 AATGTGATTTGGGCCTAACAGGCCATATA
* *
21273515 CAGGTGATTTGGGCCTAA
1 AATGTGATTTGGGCCTAA
21273533 TGAGTCATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.18
29 32 0.82
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAACAGGCCATATA
Found at i:21273541 original size:29 final size:29
Alignment explanation
Indices: 21273466--21273542 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
21273456 TGAATGTGAC
* * *
21273466 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGAGCCATATAAAGGTGATT
* *
21273495 TGGGCCTAGT-AGGCCATATACAGGTGATT
1 TGGGCCTAATGA-GCCATATAAAGGTGATT
*
21273524 TGGGCCTAATGAGTCATAT
1 TGGGCCTAATGAGCCATAT
21273543 GAATATGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGAGCCATATAAAGGTGATT
Found at i:21284906 original size:42 final size:43
Alignment explanation
Indices: 21284806--21284955 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 43
21284796 CAATGCCAGG
* ** * *
21284806 GTCCCAGATATGGTCTTACATGTAATCAAATATTGATGCCACT
1 GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
* * * *
21284849 GTCCCTGACAGGGTCTTACACAAAATCATATA-CGATGCCAAT
1 GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
* * *
21284891 GTCCCAGACATGGTCTTACATTTAAATCAAAAATCGATGCCAAC
1 GTCCCAGACATGGTCTTACA-TAAAATCAAATATCGATGCCAAT
**
21284935 GTCCCAGATGTGGTCTTACAT
1 GTCCCAGACATGGTCTTACAT
21284956 GATAACACAC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
42 26 0.30
43 34 0.39
44 27 0.31
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
Found at i:21290182 original size:42 final size:43
Alignment explanation
Indices: 21290117--21290199 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 43
21290107 TCTTCCATGT
* *
21290117 AATCAAATATCGATGCCACTGTCCCTGACAGGGTCCTACACGA
1 AATCAAATATCGATGCCAATGTCCCAGACAGGGTCCTACACGA
* * * *
21290160 AATCATATA-CGATGTCAATGTCCCAGACATGGTCTTACAC
1 AATCAAATATCGATGCCAATGTCCCAGACAGGGTCCTACAC
21290200 ATAAATCACA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 26 0.76
43 8 0.24
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
AATCAAATATCGATGCCAATGTCCCAGACAGGGTCCTACACGA
Found at i:21293335 original size:117 final size:116
Alignment explanation
Indices: 21293139--21293384 Score: 359
Period size: 117 Copynumber: 2.1 Consensus size: 116
21293129 ACAGGCATGC
* * * *
21293139 CACATGCCCATGTGCTAGGCCATGTGGTTAATTAATGTTTTTTGAACCTAGGTGTAGGATTCACA
1 CACACGCCCATGTGCTAGGCCATGTGGTTAATTAATGTTTTTTGAAACTAGGTGCAGGAATCACA
**
21293204 CGACCAAGACACATG-CTCGTGTTCTAGGCTTTGTAGCACACACGGCTAAGA
66 CGACCAAGACACATGCCT-GTGTTCTAGGCCGTGTAGCACACACGGCTAAGA
* * * *
21293255 CACACGCCCGTGTGCTAGGCCGTGTGGTTAATTAACTTTTTTTTGAAATTAGGTGCAGGAATCAC
1 CACACGCCCATGTGCTAGGCCATGTGGTTAATTAA-TGTTTTTTGAAACTAGGTGCAGGAATCAC
*
21293320 ACGACCAAGACACATGCCTGTGTTCTAGGCCGTGTAGCACACACGGCTGAGA
65 ACGACCAAGACACATGCCTGTGTTCTAGGCCGTGTAGCACACACGGCTAAGA
*
21293372 CACACGCCTATGT
1 CACACGCCCATGT
21293385 CTCTGCCCGT
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
116 32 0.28
117 81 0.70
118 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (116 bp):
CACACGCCCATGTGCTAGGCCATGTGGTTAATTAATGTTTTTTGAAACTAGGTGCAGGAATCACA
CGACCAAGACACATGCCTGTGTTCTAGGCCGTGTAGCACACACGGCTAAGA
Found at i:21301031 original size:162 final size:162
Alignment explanation
Indices: 21300762--21301080 Score: 575
Period size: 162 Copynumber: 2.0 Consensus size: 162
21300752 AGTACTTGAA
*
21300762 ATGAATTATCATTGTATAAGATCCTTATACAAAGCAATATGAACCAGAAGTTAAACAGATAATTC
1 ATGAATTATCATTGTATAAGATCCTTATACAAAGAAATATGAACCAGAAGTTAAACAGATAATTC
* *
21300827 ATTTTACAAATCAACTGCTAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
66 ATTTTACAAATCAACTACCAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
*
21300892 GCTAAAAATGTTCCAATACGAATTGATACTCT
131 ACTAAAAATGTTCCAATACGAATTGATACTCT
* *
21300924 ATGAATTATCATTGTATAAGATCCTTGTACAAAGAAATATGAACCAGAAGTTCAACAGATAATTC
1 ATGAATTATCATTGTATAAGATCCTTATACAAAGAAATATGAACCAGAAGTTAAACAGATAATTC
*
21300989 ATTTTACAAATCAACTACCAGATTCATTTATTGACTTAAAGAGAATTACAAAATCTCACATATCA
66 ATTTTACAAATCAACTACCAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
21301054 ACTAAAAATGTTCCAATACGAATTGAT
131 ACTAAAAATGTTCCAATACGAATTGAT
21301081 GTCCCAATAG
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 150 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (162 bp):
ATGAATTATCATTGTATAAGATCCTTATACAAAGAAATATGAACCAGAAGTTAAACAGATAATTC
ATTTTACAAATCAACTACCAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
ACTAAAAATGTTCCAATACGAATTGATACTCT
Found at i:21306695 original size:14 final size:13
Alignment explanation
Indices: 21306672--21306703 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
21306662 GGGATATCAA
21306672 AACAATAATTAAG
1 AACAATAATTAAG
21306685 AACACATAATTAAG
1 AACA-ATAATTAAG
21306699 AACAA
1 AACAA
21306704 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:21316829 original size:47 final size:47
Alignment explanation
Indices: 21316737--21316831 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 47
21316727 ATGGGTAAGG
**
21316737 TGTCGATGCCATGTCCCAGACACGATCTTACACTGGCTTATATCTCA
1 TGTCGATGCCATGTCCCAGACACGATCTTACACTAACTTATATCTCA
* * * *
21316784 TGTCGATGCCATGTTCCAGACATGGTGTTACACTAAC-TATCATCTCA
1 TGTCGATGCCATGTCCCAGACACGATCTTACACTAACTTAT-ATCTCA
21316831 T
1 T
21316832 AGCCTATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 3 0.07
47 38 0.93
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (47 bp):
TGTCGATGCCATGTCCCAGACACGATCTTACACTAACTTATATCTCA
Found at i:21321239 original size:50 final size:50
Alignment explanation
Indices: 21321185--21321285 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
21321175 CGTGTGAGGC
* * **
21321185 ACACGGCCTGCTTGCACAAGCATGTGACATGTGAATGTAATTTTTTTCTA
1 ACACGGCCTGCTTACACAAGCATGTGACATGTGAACGTAAAATTTTTCTA
* * *
21321235 ACACGGCCTGCTTACACAGGCGTGTGACCTGTGAACGTAAAATTTTTCTA
1 ACACGGCCTGCTTACACAAGCATGTGACATGTGAACGTAAAATTTTTCTA
21321285 A
1 A
21321286 GTGTTTGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
ACACGGCCTGCTTACACAAGCATGTGACATGTGAACGTAAAATTTTTCTA
Found at i:21321949 original size:20 final size:20
Alignment explanation
Indices: 21321924--21321971 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
21321914 AAATAGGGTC
21321924 ACACGCCCATGTGGCTAGGG
1 ACACGCCCATGTGGCTAGGG
* *
21321944 ACACGCCGATGTGGCTTGGG
1 ACACGCCCATGTGGCTAGGG
21321964 ACACGCCC
1 ACACGCCC
21321972 GTGTCCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (20 bp):
ACACGCCCATGTGGCTAGGG
Found at i:21335819 original size:43 final size:44
Alignment explanation
Indices: 21335772--21335870 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 44
21335762 CATCAATTTG
*
21335772 TGATTTACATGTAAGAAC-ATGTCTGAGACATTGGCATC-ATATA
1 TGATTTACATGTAAG-ACTATGTCTGAGACAGTGGCATCGATATA
* * * *
21335815 TGATTT-CGTGTAAGACTCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTACATGTAAGACTATGTCTGAGACAGTGGCATCGATATA
21335858 TGA-TTACATGTAA
1 TGATTTACATGTAA
21335871 AACCACGTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.04
42 26 0.55
43 19 0.40
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (44 bp):
TGATTTACATGTAAGACTATGTCTGAGACAGTGGCATCGATATA
Found at i:21335891 original size:85 final size:85
Alignment explanation
Indices: 21335737--21335893 Score: 198
Period size: 85 Copynumber: 1.8 Consensus size: 85
21335727 ATGTGTTATT
* *
21335737 GTGTAAGACTGCGTCTGGGACGTTGCATCAATTTGTGATTTACATGTAAGAACATGTCTGAGACA
1 GTGTAAGACTGCGTCTGGGACGTGGCATCAATTTGTGATTTACATGTAAGAACACGTCTGAGACA
21335802 TTGGCATCATATATGATTTC
66 TTGGCATCATATATGATTTC
*
21335822 GTGTAAGACT-CTGTCTGGGACAGTGGCATCGATATT-TGA-TTACATGTAA-AACCACGTCT-A
1 GTGTAAGACTGC-GTCTGGGAC-GTGGCATCAAT-TTGTGATTTACATGTAAGAA-CACGTCTGA
*
21335882 GGACGTTGGCAT
62 -GACATTGGCAT
21335894 TGTACGAGCT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
84 4 0.06
85 45 0.71
86 12 0.19
87 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (85 bp):
GTGTAAGACTGCGTCTGGGACGTGGCATCAATTTGTGATTTACATGTAAGAACACGTCTGAGACA
TTGGCATCATATATGATTTC
Found at i:21335892 original size:43 final size:42
Alignment explanation
Indices: 21335748--21335893 Score: 113
Period size: 43 Copynumber: 3.4 Consensus size: 42
21335738 TGTAAGACTG
21335748 CGTCTGGGACGTT-GCATCA-ATTTGTGATTTACATGTAAGAA-CA
1 CGTCTGGGACGTTGGCATCATA-TT-TGA-TTACATGTAA-AACCA
* * * * * * *
21335791 TGTCTGAGACATTGGCATCATATATGATTTCGTGTAAGACTC-
1 CGTCTGGGACGTTGGCATCATATTTGATTACATGTAAAAC-CA
*
21335833 TGTCTGGGACAG-TGGCATCGATATTTGATTACATGTAAAACCA
1 CGTCTGGGAC-GTTGGCATC-ATATTTGATTACATGTAAAACCA
*
21335876 CGTCTAGGACGTTGGCAT
1 CGTCTGGGACGTTGGCAT
21335894 TGTACGAGCT
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 26 0.32
43 45 0.56
44 7 0.09
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
CGTCTGGGACGTTGGCATCATATTTGATTACATGTAAAACCA
Found at i:21344084 original size:9 final size:9
Alignment explanation
Indices: 21344070--21344129 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
21344060 TATTTCAAAG
21344070 AGTTATGTA
1 AGTTATGTA
21344079 AGTTATGATA
1 AGTTATG-TA
* * *
21344089 TGATATAT-
1 AGTTATGTA
*
21344097 ATTTATGT-
1 AGTTATGTA
21344105 A-TTATGTA
1 AGTTATGTA
21344113 AGTTATGTA
1 AGTTATGTA
21344122 AGTTATGT
1 AGTTATGT
21344130 TGCAACGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 6 0.15
8 6 0.15
9 23 0.56
10 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
AGTTATGTA
Found at i:21344110 original size:34 final size:35
Alignment explanation
Indices: 21344036--21344119 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 35
21344026 NNNNNNNNNN
21344036 TTATGTAAGTTATGATATGATATATATTTCAAAGAG
1 TTATGTAAGTTATGATATGATATATATTT-AAAGAG
*
21344072 TTATGTAAGTTATGATATGATATATATTT-ATGTA-
1 TTATGTAAGTTATGATATGATATATATTTAAAG-AG
21344106 TTATGTAAGTTATG
1 TTATGTAAGTTATG
21344120 TAAGTTATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
34 16 0.35
35 1 0.02
36 29 0.63
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (35 bp):
TTATGTAAGTTATGATATGATATATATTTAAAGAG
Found at i:21345796 original size:46 final size:45
Alignment explanation
Indices: 21345729--21345884 Score: 151
Period size: 48 Copynumber: 3.4 Consensus size: 45
21345719 GCTAGTATAA
21345729 GACATGCATCGGCCT-CGAGATGTAAG-CTAGTGTAAGA-CATGTCTGG
1 GACATGCATCGG-CTACGAGATGT--GTC-AGTGTAAGACCATGTCTGG
*
21345775 GACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTTTGG
1 GACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTGG
* * * *
21345820 GACATGGTATC-GATACGTATAGAGGTGTCAGTGTAAGACTATGTCTGG
1 GACAT-GCATCGGCTACG---AGATGTGTCAGTGTAAGACCATGTCTGG
21345868 GACATGGCATCGG-TACG
1 GACAT-GCATCGGCTACG
21345885 GATATACGAG
Statistics
Matches: 95, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
44 10 0.11
45 21 0.22
46 24 0.25
48 39 0.41
49 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (45 bp):
GACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTGG
Found at i:21345908 original size:50 final size:48
Alignment explanation
Indices: 21345757--21345925 Score: 163
Period size: 48 Copynumber: 3.6 Consensus size: 48
21345747 GATGTAAGCT
* * *
21345757 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACG---AGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GATACGTATAGAGGTCTC
* * *
21345801 AGTGTAAGACCATGTTTGGGACATGGTATCGATACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATACGTATAGAGGTCTC
* *
21345849 AGTGTAAGACTATGTCTGGGACATGGCATCGGTACGGATATACGAGAG-CT-
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATAC-G-TATA-GAG-GTCTC
*
21345899 AGTGTAAGACCATGTCTGGTACATGGC
1 AGTGTAAGACCATGTCTGGGACATGGC
21345926 GTTGGCCTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
44 9 0.09
45 18 0.17
46 4 0.04
48 39 0.37
49 1 0.01
50 29 0.28
51 4 0.04
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGATACGTATAGAGGTCTC
Found at i:21371161 original size:47 final size:48
Alignment explanation
Indices: 21371092--21371184 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 48
21371082 ATTCCATGTG
* *
21371092 ACATCACCAGATTCGGTCATAACGTTTAGGCCGGGTTT-GGGTGTTTC
1 ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTTTC
21371139 ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTT
1 ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTT
21371185 ACATATGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 36 0.84
48 7 0.16
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (48 bp):
ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTTTC
Found at i:21371303 original size:35 final size:35
Alignment explanation
Indices: 21371264--21371330 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
21371254 TTTTTTTATT
*
21371264 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATATTTATGTAAGTTATGATAATCATAAA
* *
21371299 CTTTAATTATTTATGTAAGTTATGATTATCAT
1 CTTTAAATATTTATGTAAGTTATGATAATCAT
21371331 CTTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (35 bp):
CTTTAAATATTTATGTAAGTTATGATAATCATAAA
Found at i:21371798 original size:35 final size:35
Alignment explanation
Indices: 21371762--21371829 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
21371752 CTATGAAAAT
*
21371762 TTTAACTTTAAAACT-AAATATAA-AAATTAATAAA
1 TTTAAATTTAAAACTCAAA-ATAATAAATTAATAAA
* *
21371796 TTTAAATTTAGAATTCAAAATAATAAATTAATAA
1 TTTAAATTTAAAACTCAAAATAATAAATTAATAA
21371830 CATAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (35 bp):
TTTAAATTTAAAACTCAAAATAATAAATTAATAAA
Found at i:21371896 original size:19 final size:20
Alignment explanation
Indices: 21371872--21371909 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21371862 TATCTTAAAT
21371872 TTTAAAAT-AAAAATAAAAA
1 TTTAAAATCAAAAATAAAAA
*
21371891 TTTAAAATCAAAACTAAAA
1 TTTAAAATCAAAAATAAAA
21371910 TAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
TTTAAAATCAAAAATAAAAA
Found at i:21371910 original size:19 final size:18
Alignment explanation
Indices: 21371867--21371923 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
21371857 CAAGTTATCT
*
21371867 TAAATTTTAAAATAAAAA
1 TAAAATTTAAAATAAAAA
*
21371885 TAAAAATTTAAAATCAAAAC
1 T-AAAATTTAAAAT-AAAAA
*
21371905 TAAAA-TAAATAATAAAAA
1 TAAAATTTAA-AATAAAAA
21371923 T
1 T
21371924 TGAATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.28
19 18 0.56
20 5 0.16
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATTTAAAATAAAAA
Found at i:21372361 original size:72 final size:72
Alignment explanation
Indices: 21372284--21372475 Score: 198
Period size: 72 Copynumber: 2.7 Consensus size: 72
21372274 AAATGGTTCC
* *
21372284 ACTTAATATCAAAATTCAATAAGTTGAACTAAATTAACCTCTTTAAAAAT-TCA-AAATTGA-AC
1 ACTTAATATCAAAATTCAATAAATTGAACTAAATTAACCT-TTTAAAAATGT-ATAAATAGATA-
*
21372346 AAATGTCTT-T
63 AAAGGT-TTCT
* ** * * * *
21372356 ACTTAATATCAAATTTCAATAAATCAAACTAAATTAAGCTTCTAAAAATGTATAACTAGATAAAC
1 ACTTAATATCAAAATTCAATAAATTGAACTAAATTAACCTTTTAAAAATGTATAAATAGATAAAA
21372421 GGTTTCT
66 GGTTTCT
21372428 -CTTAATATCAAAACTT-AATAAATTGAACTAAATTAACCTTTTTAAAAA
1 ACTTAATATCAAAA-TTCAATAAATTGAACTAAATTAACC-TTTTAAAAA
21372476 CACATAATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
71 42 0.42
72 56 0.57
73 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (72 bp):
ACTTAATATCAAAATTCAATAAATTGAACTAAATTAACCTTTTAAAAATGTATAAATAGATAAAA
GGTTTCT
Found at i:21377574 original size:22 final size:22
Alignment explanation
Indices: 21377531--21377574 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21377521 AACATATAAT
*
21377531 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
21377553 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
21377575 CAGCAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:21378413 original size:25 final size:24
Alignment explanation
Indices: 21378379--21378425 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
21378369 GGATAGGATT
21378379 TTGTCAAATGAAATAATAAAAATAA
1 TTGTCAAATGAAATAA-AAAAATAA
*
21378404 TTGTTAAATGAAATAAAAAAAT
1 TTGTCAAATGAAATAAAAAAAT
21378426 TGGGTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (24 bp):
TTGTCAAATGAAATAAAAAAATAA
Found at i:21378520 original size:20 final size:20
Alignment explanation
Indices: 21378495--21378534 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21378485 TGAGAAATGA
21378495 AATAAAACTTGCTTATCATT
1 AATAAAACTTGCTTATCATT
21378515 AATAAAACTTGCTTATCATT
1 AATAAAACTTGCTTATCATT
21378535 CATTTTTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
AATAAAACTTGCTTATCATT
Found at i:21378898 original size:40 final size:40
Alignment explanation
Indices: 21378845--21378945 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
21378835 AAAATGATAC
* **
21378845 TTTGCGGCCTTTTTCTCATAAC-GTAGCTAATGCTTGAAC-T
1 TTTGCGGCGTTTTTCTCATAACACCA-CTAATGCTTG-ACTT
*
21378885 TTTGCAGCGTTTTTCTCATAACACCACTAATGCTTGACTT
1 TTTGCGGCGTTTTTCTCATAACACCACTAATGCTTGACTT
*
21378925 TTTGTGGCGTTTTTCTCATAA
1 TTTGCGGCGTTTTTCTCATAA
21378946 ACGCCAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.04
40 50 0.94
41 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (40 bp):
TTTGCGGCGTTTTTCTCATAACACCACTAATGCTTGACTT
Found at i:21378976 original size:41 final size:40
Alignment explanation
Indices: 21378854--21378981 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
21378844 CTTTGCGGCC
** * * *
21378854 TTTTTCTCATAAC-GTAGCTAATGCTTGAACTTTTGCAGCG
1 TTTTTCTCATAACACCA-CTAATGCTTGACCTATTGTAGCG
* * *
21378894 TTTTTCTCATAACACCACTAATGCTTGACTTTTTGTGGCG
1 TTTTTCTCATAACACCACTAATGCTTGACCTATTGTAGCG
* * * *
21378934 TTTTTCTCATAAACGCCAGTACTGCTTTACCTATTGTAGCG
1 TTTTTCTCAT-AACACCACTAATGCTTGACCTATTGTAGCG
21378975 TTTTTCT
1 TTTTTCT
21378982 GTTAGCTCCA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 42 0.58
41 31 0.42
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (40 bp):
TTTTTCTCATAACACCACTAATGCTTGACCTATTGTAGCG
Found at i:21385554 original size:99 final size:99
Alignment explanation
Indices: 21385441--21385639 Score: 389
Period size: 99 Copynumber: 2.0 Consensus size: 99
21385431 ATGATTGCCG
*
21385441 AGGTGTTGAAAGTAAGTATAATTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
1 AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
21385506 GAAAGTATGTAAGTTTGTATATAAATAATACATT
66 GAAAGTATGTAAGTTTGTATATAAATAATACATT
21385540 AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
1 AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
21385605 GAAAGTATGTAAGTTTGTATATAAATAATACATT
66 GAAAGTATGTAAGTTTGTATATAAATAATACATT
21385639 A
1 A
21385640 TCTTTATTAT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (99 bp):
AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
GAAAGTATGTAAGTTTGTATATAAATAATACATT
Found at i:21386017 original size:66 final size:65
Alignment explanation
Indices: 21385860--21386017 Score: 162
Period size: 67 Copynumber: 2.4 Consensus size: 65
21385850 ATTATGATGT
* * * * *
21385860 AGCTAGGTCACATGGGTGATACT-A-TGTGTACACCATGTAGACAAGAGAGCTACGGGATATATG
1 AGCTAGGTCACATGGGTGGTACTAAGTGAGGACACCATGTAGACAAGAGAGCTACGAGATAAATG
* * * * *
21385923 TAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGTA-AGTTACGAGATAA
1 -AGCTAGGTCACATGGGTGGTACTAAGTG-AGGACACCATGTAGACAAG-AGAGCTACGAGATAA
21385987 ACTG
63 A-TG
21385991 -GCTAGGTCACATGGGTGGTACTAAGTG
1 AGCTAGGTCACATGGGTGGTACTAAGTG
21386018 TTCACCATGT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
64 18 0.24
65 1 0.01
66 25 0.33
67 28 0.37
68 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (65 bp):
AGCTAGGTCACATGGGTGGTACTAAGTGAGGACACCATGTAGACAAGAGAGCTACGAGATAAATG
Found at i:21400142 original size:30 final size:29
Alignment explanation
Indices: 21400108--21400171 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
21400098 ATGAATCGGA
21400108 AGCTTTGGCACTAAGTGTGCGATTTAAACT
1 AGCTTTGGCACTAAGTGTGCGATTT-AACT
*
21400138 AGCTTTGGCACTAAGTGTGTGATTTAACT
1 AGCTTTGGCACTAAGTGTGCGATTTAACT
21400167 AGCTT
1 AGCTT
21400172 CGGTTACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCGATTTAACT
Found at i:21401015 original size:87 final size:87
Alignment explanation
Indices: 21400908--21401082 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
21400898 GGTTTATAAG
*
21400908 TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAGCTTAAAGAATGGTTGATT
1 TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
*
21400973 GGGTTGTACATATATGTTTGAT
66 GGGTTGTACATATATGCTTGAT
*
21400995 TATGTAAATTATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
1 TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
*
21401060 GGGTTGTACGTATATGCTTGAT
66 GGGTTGTACATATATGCTTGAT
21401082 T
1 T
21401083 CCTTGTTTGT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (87 bp):
TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
GGGTTGTACATATATGCTTGAT
Found at i:21411130 original size:22 final size:21
Alignment explanation
Indices: 21411100--21411149 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
21411090 TATTTTTATT
*
21411100 TAAATTTAATTATAAA-ATATA
1 TAAATTTAA-AATAAACATATA
21411121 TAAATATTAAAATAAACATATA
1 TAAAT-TTAAAATAAACATATA
*
21411143 TATATTT
1 TAAATTT
21411150 CTTAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAAAATAAACATATA
Found at i:21412772 original size:51 final size:50
Alignment explanation
Indices: 21412703--21412820 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
21412693 TTCAAGTTTT
* *
21412703 TTTCATTTTTCATTTTCATTTTGGAGAAAACCATATTCATTTCCAAATAA
1 TTTCATTTCTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATAA
* * **
21412753 TTTCATTTCTCTATTTTCATTTTGGAGAAAATCATAATCATTTTCAAATGT
1 TTTCATTTCTC-ATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATAA
21412804 TTTCTATTTCTCCATTT
1 TTTC-ATTTCT-CATTT
21412821 CTCTATTTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 10 0.17
51 38 0.64
52 10 0.17
53 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (50 bp):
TTTCATTTCTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATAA
Found at i:21412840 original size:10 final size:10
Alignment explanation
Indices: 21412825--21412858 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
21412815 CCATTTCTCT
21412825 ATTTCTATTC
1 ATTTCTATTC
21412835 ATTTCTATTC
1 ATTTCTATTC
*
21412845 ATTTCTTTTC
1 ATTTCTATTC
21412855 ATTT
1 ATTT
21412859 AATTCAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTCTATTC
Found at i:21414076 original size:12 final size:13
Alignment explanation
Indices: 21414059--21414091 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21414049 TCTTATTTTA
21414059 TTTATTTTGA-TT
1 TTTATTTTGATTT
*
21414071 TTTATTTTTATTT
1 TTTATTTTGATTT
21414084 TTTATTTT
1 TTTATTTT
21414092 ATATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTATTTTGATTT
Found at i:21419700 original size:23 final size:22
Alignment explanation
Indices: 21419654--21419705 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21419644 AAAATTCGGC
21419654 AAAGG-GA-AAAAGGAAAATAA
1 AAAGGAGAGAAAAGGAAAATAA
*
21419674 AAAGGTAGAGAAAAGAGAAAA-AG
1 AAAGG-AGAGAAAAG-GAAAATAA
21419697 AAAGGAGAG
1 AAAGGAGAG
21419706 TTTCAGTAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
22 6 0.22
23 11 0.41
24 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (22 bp):
AAAGGAGAGAAAAGGAAAATAA
Found at i:21433723 original size:13 final size:13
Alignment explanation
Indices: 21433705--21433733 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21433695 GGTTGTTTAT
21433705 TAAACTAATTAAC
1 TAAACTAATTAAC
21433718 TAAACTAATTAAC
1 TAAACTAATTAAC
21433731 TAA
1 TAA
21433734 TTAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:21437715 original size:47 final size:45
Alignment explanation
Indices: 21437550--21437951 Score: 303
Period size: 47 Copynumber: 8.6 Consensus size: 45
21437540 TTACCAATGC
* *
21437550 CATGTCCCAGACATGGTCTTACACTGCCTCTCATATACGCATGCTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAT--G-ATGCCGATG
* * * * *
21437599 CATGTCCCAGACATGTCTTACACTAGCAC-AACTCTTA-GCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCA-TATGATGCCGATG
*** * * * * *
21437643 TGCGTCCCGGAAATGTATTACACTGGCTATCTC-TATCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGC--TCTCATAT-GATGCCGATG
* * *
21437690 CATGTCCCAGACATGTCTTACACTGGCACTAATCTCTG-TGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCA--TATGATGCCGATG
* * * *
21437736 CCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATGCCGATG
1 -CATGTCCCAGACATGTCTTACACTGGCTCTCATAT-GATGCCGATG
* *
21437783 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATGATG-TGGCCAAAG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-ATGAT-GCCGATG
* * * *
21437831 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAT-GATGCCGATG
* *
21437877 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATGATG-TGGCCAAAG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-ATGAT-GCCGATG
21437925 CATGTCCCAGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
21437952 GCACAAATCA
Statistics
Matches: 280, Mismatches: 52, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
44 26 0.09
45 9 0.03
46 44 0.16
47 125 0.45
48 60 0.21
49 16 0.06
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATATGATGCCGATG
Found at i:21437798 original size:94 final size:93
Alignment explanation
Indices: 21437543--21437948 Score: 387
Period size: 94 Copynumber: 4.3 Consensus size: 93
21437533 GGATATATTA
* * *
21437543 CCAATGCCATGTCCCAGACATGGTCTTACACT-GCCTCTCATATACGCATGCTGATGCATGTCCC
1 CCAATG-CATGTCCCAGACAT-GTCTTACACTAGCC-CTCGTAT--GGATGCCGATGCATGTCCC
* * *
21437607 AGACAT-GTCTTACACTAGCAC-AACT-CT-TAG
61 AGACATGGTCTTACACTGGCACTAA-TGATGTGG
* *** * * * * * * * *
21437637 CCGATGTGCGTCCCGGAAATGTATTACACTGGCTATCTC-TATCGAGGCCAATGCATGTCCCAGA
1 CCAATGCATGTCCCAGACATGTCTTACACTAGC--CCTCGTATGGATGCCGATGCATGTCCCAGA
* *
21437701 CAT-GTCTTACACTGGCACTAAT-CTCTGTG
64 CATGGTCTTACACTGGCACTAATGATGTG-G
* *
21437730 CCGATGCCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATGCCGATGCCATGTCCCAGA
1 CCAATG-CATGTCCCAGACATGTCTTACACTAGCCCTCGTATGGATGCCGATG-CATGTCCCAGA
* *
21437795 CATGGTCTTACACTGGCTCTCATGATGTGG
64 CATGGTCTTACACTGGCACTAATGATGTGG
* *
21437825 CCAAAGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATGCCGATGCCATGTCCCAGAC
1 CCAATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTATGGATGCCGATG-CATGTCCCAGAC
* *
21437890 ATGGTCTTACACTGGCTCTCATGATGTGG
65 ATGGTCTTACACTGGCACTAATGATGTGG
*
21437919 CCAAAGCATGTCCCAGACATGTCTTACACT
1 CCAATGCATGTCCCAGACATGTCTTACACT
21437949 GGCGCACAAA
Statistics
Matches: 268, Mismatches: 33, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
91 37 0.14
92 15 0.06
93 31 0.12
94 160 0.60
95 22 0.08
96 3 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (93 bp):
CCAATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTATGGATGCCGATGCATGTCCCAGACA
TGGTCTTACACTGGCACTAATGATGTGG
Found at i:21437929 original size:141 final size:139
Alignment explanation
Indices: 21437682--21437951 Score: 357
Period size: 141 Copynumber: 1.9 Consensus size: 139
21437672 TCTCTATCGA
* * *
21437682 GGCCAATGCATGTCCCAGACATGTCTTACACTGGCACTAATCTCTGTGCCGATGCCATGTCCCAG
1 GGCCAAAGCATGTCCCAGACATGTCTTACACTAGCACTAATCTCGGTGCCGATGCCATGTCCCAG
* * * *
21437747 ACATGTCTTACACTAGCCCTCGTCTGGATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGC
66 ACATGTCTTACACTAGCCCTCATATGGA-GCCAAAGCCATGTCCCAGACAT-GTCTTACACTGGC
21437812 TCTCATGATGT
129 TCTCATGATGT
* **
21437823 GGCCAAAGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCT-GGATGCCGATGCCATGTCCCA
1 GGCCAAAGCATGTCCCAGACATGTCTTACACTAGCACTAATCTCGG-TGCCGATGCCATGTCCCA
* *
21437887 GACATGGTCTTACACTGGCTCTCATGATGTG-GCCAAAG-CATGTCCCAGACATGTCTTACACTG
65 GACAT-GTCTTACACTAGCCCTCAT-ATG-GAGCCAAAGCCATGTCCCAGACATGTCTTACACTG
21437950 GC
127 GC
21437952 GCACAAATCA
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
140 14 0.12
141 75 0.66
142 21 0.19
143 2 0.02
144 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (139 bp):
GGCCAAAGCATGTCCCAGACATGTCTTACACTAGCACTAATCTCGGTGCCGATGCCATGTCCCAG
ACATGTCTTACACTAGCCCTCATATGGAGCCAAAGCCATGTCCCAGACATGTCTTACACTGGCTC
TCATGATGT
Found at i:21441696 original size:14 final size:13
Alignment explanation
Indices: 21441673--21441704 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
21441663 GGGATATCAA
21441673 AACAATAATTAAG
1 AACAATAATTAAG
21441686 AACACATAATTAAG
1 AACA-ATAATTAAG
21441700 AACAA
1 AACAA
21441705 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:21442164 original size:52 final size:51
Alignment explanation
Indices: 21442102--21442241 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 51
21442092 GTGTTTGAGC
*
21442102 CTGCCAAATTGACACGGTCGTGTGGTCTGCCCGTGTGAATCATGCTTCGATT
1 CTGCCAAATTGACACGG-CGTGTGGTCTGCCCGTGTGAATCATGCTTCAATT
* *
21442154 TTGCCAAATTGACACGGCTGTGTGGTCTGCCCGTGTGAATCGTGCTTCAATT
1 CTGCCAAATTGACACGGC-GTGTGGTCTGCCCGTGTGAATCATGCTTCAATT
*
21442206 CTACCAAATTGACACGGCCGTGTGAG-CTGCCCGTGT
1 CTGCCAAATTGACACGG-CGTGTG-GTCTGCCCGTGT
21442242 AAGGAAGTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
51 1 0.01
52 77 0.96
53 2 0.03
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (51 bp):
CTGCCAAATTGACACGGCGTGTGGTCTGCCCGTGTGAATCATGCTTCAATT
Found at i:21450247 original size:13 final size:13
Alignment explanation
Indices: 21450229--21450281 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
21450219 GCTTGGCAGG
*
21450229 GACATACCCGTGT
1 GACACACCCGTGT
*
21450242 GACATACCCGTGT
1 GACACACCCGTGT
21450255 GACACACCCGTGT
1 GACACACCCGTGT
*
21450268 GACACGCCCGTGT
1 GACACACCCGTGT
21450281 G
1 G
21450282 CGATTACTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (13 bp):
GACACACCCGTGT
Found at i:21450918 original size:71 final size:71
Alignment explanation
Indices: 21450826--21451603 Score: 1529
Period size: 71 Copynumber: 11.0 Consensus size: 71
21450816 TTATAAGGAC
* *
21450826 TATTTTGTAAAAGATGTAAATGTGTGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21450891 AGAGAA
66 AGAGAA
21450897 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21450962 AGAGAA
66 AGAGAA
21450968 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451033 AGAGAA
66 AGAGAA
21451039 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451104 AGAGAA
66 AGAGAA
21451110 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451175 AGAGAA
66 AGAGAA
21451181 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451246 AGAGAA
66 AGAGAA
21451252 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451317 AGAGAA
66 AGAGAA
21451323 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451388 AGAGAA
66 AGAGAA
21451394 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451459 AGAGAA
66 AGAGAA
21451465 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451530 AGAGAA
66 AGAGAA
*
21451536 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCATA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
21451601 AGA
66 AGA
21451604 AGGAAAAGTG
Statistics
Matches: 704, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 704 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (71 bp):
TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
AGAGAA
Found at i:21452472 original size:21 final size:21
Alignment explanation
Indices: 21452446--21452491 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
21452436 ATTCCATCGG
21452446 GATTTCCTAGAAACTCAACGA
1 GATTTCCTAGAAACTCAACGA
21452467 GATTTCCTAGAAACTCAACGA
1 GATTTCCTAGAAACTCAACGA
21452488 GATT
1 GATT
21452492 AATTGATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (21 bp):
GATTTCCTAGAAACTCAACGA
Found at i:21465570 original size:12 final size:12
Alignment explanation
Indices: 21465555--21465581 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21465545 CTATTTTCAT
21465555 TTTCCATTTCCA
1 TTTCCATTTCCA
21465567 TTTCCATTTCCA
1 TTTCCATTTCCA
21465579 TTT
1 TTT
21465582 TGGAAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTCCATTTCCA
Found at i:21467536 original size:53 final size:54
Alignment explanation
Indices: 21467445--21467662 Score: 215
Period size: 54 Copynumber: 4.0 Consensus size: 54
21467435 TCGGGAACCT
* * * * * * **
21467445 TTTCCTTTTTGAACTTACCATTGCCTTGTCTTGACATGGTCTTATGTGGTATCC
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
* * *
21467499 TTTCCTTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CTT
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATC-C
** * * *
21467552 TTTCCTTATAGTAACTCATTAATGCCATGTCTTGACATGGTCTTACATGATTTCC
1 TTTCCTTATAG-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
* * * * *
21467607 TTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCC
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
21467661 TT
1 TT
21467663 ATCTTACCAA
Statistics
Matches: 136, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
52 1 0.01
53 42 0.31
54 49 0.36
55 43 0.32
56 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (54 bp):
TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
Found at i:21467591 original size:55 final size:53
Alignment explanation
Indices: 21467474--21467654 Score: 197
Period size: 55 Copynumber: 3.4 Consensus size: 53
21467464 ATTGCCTTGT
** * * *
21467474 CTTGACATGGTCTTATGTGGTATCCTTTCCTTAT-GAACTCACCAATGCCATGC
1 CTTGACATGGTCTTACATGGGAT-TTTTCCTTATAGAACTCATCAATGCCATGC
* * *
21467527 CTTGGCATGGTCTTACATGGGACTTTTTCCTTATAGTAACTCATTAATGCCATGT
1 CTTGACATGGTCTTACATGGGA-TTTTTCCTTATAG-AACTCATCAATGCCATGC
*
21467582 CTTGACATGGTCTTACAT--GATTTCCTTACCTTATAGAACTTATCAATGCCATGC
1 CTTGACATGGTCTTACATGGGATTT--TT-CCTTATAGAACTCATCAATGCCATGC
*
21467636 CTTGGCATGGTCTTACATG
1 CTTGACATGGTCTTACATG
21467655 ATATCCTTAT
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
52 3 0.03
53 29 0.27
54 36 0.33
55 40 0.37
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (53 bp):
CTTGACATGGTCTTACATGGGATTTTTCCTTATAGAACTCATCAATGCCATGC
Found at i:21467803 original size:47 final size:47
Alignment explanation
Indices: 21467572--21468045 Score: 173
Period size: 47 Copynumber: 9.8 Consensus size: 47
21467562 GTAACTCATT
* * *
21467572 AATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATC
1 AATGCCATGTCTTGACATGGTCTTACATGATATCCTTA----AT-TAA--TGTC
* * **
21467626 AATGCCATGCCTTGGCATGGTCTTACATGATATCCTT-ATCT--TACC
1 AATGCCATGTCTTGACATGGTCTTACATGATATCCTTAAT-TAATGTC
*** * * ** * *
21467671 AAATGCCATGTTCCAAACATGGTCTT-GATGGTATCCTTGTCTTAGTGCC
1 -AATGCCATG-TCTTGACATGGTCTTACATGATATCCTT-AATTAATGTC
** ** *
21467720 AATGCCACATCTTGATGTGGTCTTACATGGA-GTCCTTAATTAATGTC
1 AATGCCATGTCTTGACATGGTCTTACAT-GATATCCTTAATTAATGTC
* * * *
21467767 GATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATC
1 AATGCCATGTCTTGACATGGTCTTACATGATATCCTTA----AT-TAA--TGTC
* * **
21467821 AATGCCATGCCTTGGCATGGTCTTACATGATATCCTT-ATCT--TACC
1 AATGCCATGTCTTGACATGGTCTTACATGATATCCTTAAT-TAATGTC
*** * * ** * *
21467866 AAATGCCATGTTCCAAACATGGTCTT-GATGGTATCCTTGTCTTAGTGCC
1 -AATGCCATG-TCTTGACATGGTCTTACATGATATCCTT-AATTAATGTC
** ** *
21467915 AATGCCACATCTTGATGTGGTCTTACATGGA-GTCCTTAATTAATGTC
1 AATGCCATGTCTTGACATGGTCTTACAT-GATATCCTTAATTAATGTC
* * ** ** *
21467962 GATGCCATGTCTTGACATGGTCTTACACGGGATCCTTGCCTT-A--CC
1 AATGCCATGTCTTGACATGGTCTTACATGATATCCTT-AATTAATGTC
*
21468007 AATGCCATGTCTTGACATGGTCTTACATGGTATCCTTAA
1 AATGCCATGTCTTGACATGGTCTTACATGATATCCTTAA
21468046 CCGTCAATTC
Statistics
Matches: 311, Mismatches: 83, Indels: 62
0.68 0.18 0.14
Matches are distributed among these distances:
45 41 0.13
46 41 0.13
47 111 0.36
48 32 0.10
49 12 0.04
51 2 0.01
52 2 0.01
54 70 0.23
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (47 bp):
AATGCCATGTCTTGACATGGTCTTACATGATATCCTTAATTAATGTC
Found at i:21467855 original size:195 final size:195
Alignment explanation
Indices: 21467573--21467988 Score: 832
Period size: 195 Copynumber: 2.1 Consensus size: 195
21467563 TAACTCATTA
21467573 ATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCT
1 ATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCT
21467638 TGGCATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGT
66 TGGCATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGT
21467703 ATCCTTGTCTTAGTGCCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCG
131 ATCCTTGTCTTAGTGCCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCG
21467768 ATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCT
1 ATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCT
21467833 TGGCATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGT
66 TGGCATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGT
21467898 ATCCTTGTCTTAGTGCCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCG
131 ATCCTTGTCTTAGTGCCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCG
21467963 ATGCCATGTCTTGACATGGTCTTACA
1 ATGCCATGTCTTGACATGGTCTTACA
21467989 CGGGATCCTT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 221 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (195 bp):
ATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCT
TGGCATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGT
ATCCTTGTCTTAGTGCCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCG
Found at i:21467952 original size:94 final size:94
Alignment explanation
Indices: 21467643--21467943 Score: 297
Period size: 94 Copynumber: 3.1 Consensus size: 94
21467633 TGCCTTGGCA
21467643 TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCT
1 TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCT
21467708 TGTCTTAGTGCCAATGCCACATCTTGATG
66 TGTCTTAGTGCCAATGCCACATCTTGATG
* ** * *** * *
21467737 TGGTCTTACATGGA-GTCCTTAAT-TAATGTC-GATGCCATG-TCTTGACATGGTCTTACATGAT
1 TGGTCTTACAT-GATATCCTT-ATCT--TACCAAATGCCATGTTCCAAACATGGTCTT-GATGGT
* ** *** ***
21467798 TTCCTTACCTTA-TAGAACTTATCAATGCCATGCCTTGGCA
61 ATCCTTGTCTTAGT-G--C----CAATGCCACATCTTGATG
21467838 TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCT
1 TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCT
21467903 TGTCTTAGTGCCAATGCCACATCTTGATG
66 TGTCTTAGTGCCAATGCCACATCTTGATG
21467932 TGGTCTTACATG
1 TGGTCTTACATG
21467944 GAGTCCTTAA
Statistics
Matches: 154, Mismatches: 36, Indels: 34
0.69 0.16 0.15
Matches are distributed among these distances:
94 54 0.35
95 26 0.17
96 2 0.01
97 1 0.01
98 1 0.01
99 2 0.01
100 26 0.17
101 42 0.27
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (94 bp):
TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCT
TGTCTTAGTGCCAATGCCACATCTTGATG
Found at i:21476664 original size:28 final size:29
Alignment explanation
Indices: 21476632--21476687 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
21476622 ACTGGTCAAT
*
21476632 ACTGTAAAA-CTAGAAAACAGGGGACAAA
1 ACTGTAAAATCTAAAAAACAGGGGACAAA
* *
21476660 ACTGTAAAATTTAAAAAATAGGGGACAA
1 ACTGTAAAATCTAAAAAACAGGGGACAA
21476688 CTATAAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.16
Consensus pattern (29 bp):
ACTGTAAAATCTAAAAAACAGGGGACAAA
Found at i:21476689 original size:27 final size:28
Alignment explanation
Indices: 21476632--21476704 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
21476622 ACTGGTCAAT
* *
21476632 ACTGTAAAA-CTAGAAAACAGGGGACAAA
1 ACTGTAAAATTTAAAAAACAGGGGAC-AA
*
21476660 ACTGTAAAATTTAAAAAATAGGGGAC-A
1 ACTGTAAAATTTAAAAAACAGGGGACAA
*
21476687 ACTAT-AAATCTTAAAAAA
1 ACTGTAAAAT-TTAAAAAA
21476705 ATAAAGTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 4 0.10
27 13 0.33
28 9 0.23
29 13 0.33
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (28 bp):
ACTGTAAAATTTAAAAAACAGGGGACAA
Found at i:21476750 original size:27 final size:27
Alignment explanation
Indices: 21476657--21476822 Score: 102
Period size: 29 Copynumber: 5.9 Consensus size: 27
21476647 AACAGGGGAC
*
21476657 AAAACTGTAAAATTTAAAAAATAGGGG
1 AAAACTATAAAATTTAAAAAATAGGGG
* * **
21476684 ACAACTAT-AAATCTTAAAAAAATAAAGTC
1 AAAACTATAAAAT-TT-AAAAAAT-AGGGG
* *
21476713 AAAA-TCGTAAAATTTCAAAAATAGGGG
1 AAAACT-ATAAAATTTAAAAAATAGGGG
* * *
21476740 AAAACTATAAAATCTGAAAAGAAAAAAGGGA
1 AAAACTATAAAAT-T--TAA-AAAATAGGGG
* *
21476771 AAAACTATAAAATCTAAAAAATGGGGGGG
1 AAAACTATAAAATTTAAAAAAT--AGGGG
* *
21476800 GAAACTATAAAATCTAAAAAATA
1 AAAACTATAAAATTTAAAAAATA
21476823 AGGAACACAC
Statistics
Matches: 104, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
26 4 0.04
27 24 0.23
28 18 0.17
29 32 0.31
30 5 0.05
31 21 0.20
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (27 bp):
AAAACTATAAAATTTAAAAAATAGGGG
Found at i:21476778 original size:31 final size:32
Alignment explanation
Indices: 21476729--21476790 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
21476719 GTAAAATTTC
* *
21476729 AAAAATAGGGGAAAACTATAAAATCTGAAAAG
1 AAAAATAGGGAAAAACTATAAAATCTAAAAAG
21476761 AAAAA-AGGGAAAAACTATAAAATCTAAAAA
1 AAAAATAGGGAAAAACTATAAAATCTAAAAA
21476791 ATGGGGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (32 bp):
AAAAATAGGGAAAAACTATAAAATCTAAAAAG
Found at i:21480622 original size:14 final size:14
Alignment explanation
Indices: 21480603--21480642 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
21480593 TCAGGTATAT
21480603 TTTATTATAATTTA
1 TTTATTATAATTTA
*
21480617 TTTATTAT-ATCATA
1 TTTATTATAAT-TTA
21480631 TTTATTATAATT
1 TTTATTATAATT
21480643 GGAGATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTATAATTTA
Found at i:21483733 original size:40 final size:40
Alignment explanation
Indices: 21483641--21483752 Score: 97
Period size: 40 Copynumber: 2.8 Consensus size: 40
21483631 GCCATCTCAA
* * *
21483641 ATAACCGAAGCTATCT-CAGTATCGTACACTTAGTGCCTCGT
1 ATAACCGAAGCTAT-TGCAAT-TCGCACACTTAGTGCCTAGT
* * *
21483682 ATAGCCAAAGCTATTGCAATTCGCACACTTAGTG-CTAATT
1 ATAACCGAAGCTATTGCAATTCGCACACTTAGTGCCT-AGT
*
21483722 ATAACCGAAGCTGTTTG-AA-TCGCACACTTAG
1 ATAACCGAAGCT-ATTGCAATTCGCACACTTAG
21483753 CTCCGAACAT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
39 14 0.24
40 27 0.46
41 18 0.31
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (40 bp):
ATAACCGAAGCTATTGCAATTCGCACACTTAGTGCCTAGT
Found at i:21484922 original size:12 final size:12
Alignment explanation
Indices: 21484905--21484937 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
21484895 CTAGACACAC
21484905 GCCCGTGTGTCT
1 GCCCGTGTGTCT
21484917 GCCCGTGTGTCT
1 GCCCGTGTGTCT
*
21484929 ACCCGTGTG
1 GCCCGTGTG
21484938 GACAATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.33, G:0.33, T:0.30
Consensus pattern (12 bp):
GCCCGTGTGTCT
Found at i:21490091 original size:20 final size:20
Alignment explanation
Indices: 21490032--21490096 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
21490022 TTTAATCATA
* *
21490032 TAATAAATTA-TTGATATAAT
1 TAATAAATTATTTAATAT-TT
* **
21490052 TAATATAATTTTTTTTTATTT
1 TAATA-AATTATTTAATATTT
21490073 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
21490093 TAAT
1 TAAT
21490097 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 21 0.58
21 10 0.28
22 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:21490900 original size:14 final size:14
Alignment explanation
Indices: 21490881--21490916 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21490871 AAAAAGTAAG
21490881 TTATTTTCCAGAAA
1 TTATTTTCCAGAAA
21490895 TTATTTTCCAGAAA
1 TTATTTTCCAGAAA
*
21490909 TCATTTTC
1 TTATTTTC
21490917 TGAAAACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATTTTCCAGAAA
Found at i:21495766 original size:16 final size:17
Alignment explanation
Indices: 21495740--21495778 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
21495730 TTTTTTTATT
21495740 ATTTATATATATTTT-AA
1 ATTT-TATATATTTTAAA
21495757 ATTTTATATATTTTAAA
1 ATTTTATATATTTTAAA
21495774 ATTTT
1 ATTTT
21495779 TAAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATATATTTTAAA
Found at i:21495779 original size:18 final size:17
Alignment explanation
Indices: 21495740--21495780 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
21495730 TTTTTTTATT
*
21495740 ATTTATATATATTTTAA
1 ATTTTTATATATTTTAA
21495757 A-TTTTATATATTTTAAA
1 ATTTTTATATATTTT-AA
21495774 ATTTTTA
1 ATTTTTA
21495781 AAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 12 0.57
17 4 0.19
18 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTATATATTTTAA
Found at i:21496355 original size:23 final size:23
Alignment explanation
Indices: 21496327--21496374 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
21496317 CTTTTTGACC
21496327 TTAATTTCAAGTCCCTAGTCATT
1 TTAATTTCAAGTCCCTAGTCATT
21496350 TTAATTTCAAGTCCCTAGTCATT
1 TTAATTTCAAGTCCCTAGTCATT
21496373 TT
1 TT
21496375 TCTTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (23 bp):
TTAATTTCAAGTCCCTAGTCATT
Found at i:21501698 original size:17 final size:18
Alignment explanation
Indices: 21501671--21501705 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
21501661 ATGTGAAAAA
21501671 AATTATATATATTTTATT
1 AATTATATATATTTTATT
21501689 AATT-TATATATTTTATT
1 AATTATATATATTTTATT
21501706 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATATATATTTTATT
Found at i:21502419 original size:18 final size:19
Alignment explanation
Indices: 21502378--21502419 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21502368 AATAGTATTT
*
21502378 AAATTAAATTGAAATTACG
1 AAATTAAATTGAAATGACG
21502397 AAATTAAA-T-AAATGACGG
1 AAATTAAATTGAAATGAC-G
21502415 AAATT
1 AAATT
21502420 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATTAAATTGAAATGACG
Found at i:21503203 original size:27 final size:26
Alignment explanation
Indices: 21503173--21503234 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
21503163 AGATAATTAA
21503173 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
21503200 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
21503227 AATAAAAT
1 AATAAAAT
21503235 GGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:21508544 original size:20 final size:20
Alignment explanation
Indices: 21508521--21508568 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
21508511 TAAATTCTAA
*
21508521 AAAGATAAATACAA-TTAATT
1 AAAGATAAATA-AAGATAATT
21508541 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
21508561 AAA-ATAAA
1 AAAGATAAA
21508569 ATCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:21508593 original size:27 final size:26
Alignment explanation
Indices: 21508563--21508624 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
21508553 AGATAATTAA
21508563 AATAAAATCTTAAAATTAAATAATCCT
1 AATAAAATCTTAAAATT-AATAATCCT
* * *
21508590 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTTAAAATTAATAATCCT
21508617 AATAAAAT
1 AATAAAAT
21508625 GGAGTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 10 0.33
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAAATCTTAAAATTAATAATCCT
Found at i:21510687 original size:52 final size:52
Alignment explanation
Indices: 21510625--21510755 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
21510615 ATCAACCATC
* *
21510625 TAAGAAATAATCATTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
* *
21510677 TAAGATATAATCCTTGATAAATTGAAATATGAAAAATAGAAGAAAACAAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
*
21510729 TAAGATATAATCCTTGACAAATCGAAA
1 TAAGATATAATCCTTGACAAATTGAAA
21510756 ATAAGATGGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.21
Consensus pattern (52 bp):
TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
Found at i:21520529 original size:17 final size:18
Alignment explanation
Indices: 21520489--21520530 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
21520479 TATAAAATAC
*
21520489 AAATTATAAAAATATAAT
1 AAATAATAAAAATATAAT
* *
21520507 ATATAATAAAATTAT-AT
1 AAATAATAAAAATATAAT
21520524 AAATAAT
1 AAATAAT
21520531 TTAATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATAAAAATATAAT
Found at i:21520537 original size:29 final size:26
Alignment explanation
Indices: 21520477--21520528 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
21520467 TGTTAAAAAG
*
21520477 AATATAAAATACAAATTATAAAAATAT
1 AATATATAATA-AAATTATAAAAATAT
*
21520504 AATATATAATAAAATTATATAAATA
1 AATATATAATAAAATTATAAAAATA
21520529 ATTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATATATAATAAAATTATAAAAATAT
Found at i:21520547 original size:29 final size:28
Alignment explanation
Indices: 21520477--21520545 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
21520467 TGTTAAAAAG
*
21520477 AATATAAAATACAAA-T-TATAAAAATAT
1 AATATATAATA-AAATTATATAAAAATAT
*
21520504 AATATATAATAAAATTATATAAATAATTT
1 AATATATAATAAAATTATATAAA-AATAT
*
21520533 AATAT-TTATAAAA
1 AATATATAATAAAA
21520546 ATAATTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.08
27 11 0.31
28 13 0.36
29 9 0.25
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATATAATAAAATTATATAAAAATAT
Found at i:21531823 original size:27 final size:29
Alignment explanation
Indices: 21531788--21531842 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
21531778 TTATTACAGA
*
21531788 TAAATAATATTATAATTA-ATTATAAATT
1 TAAATAATATTATAATTATAATATAAATT
*
21531816 TAAA-AATATTTTAATTATAATATAAAT
1 TAAATAATATTATAATTATAATATAAAT
21531843 ATTATCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAATAATATTATAATTATAATATAAATT
Found at i:21532165 original size:28 final size:29
Alignment explanation
Indices: 21532133--21532187 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
21532123 TAAATTTTAA
* *
21532133 TTCAATTATATACATT-TAAAAATAAAAT
1 TTCAATTATACACATTAAAAAAATAAAAT
21532161 TTCAATTATACACATTAAAAAAATAAA
1 TTCAATTATACACATTAAAAAAATAAA
21532188 TTTATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (29 bp):
TTCAATTATACACATTAAAAAAATAAAAT
Found at i:21533013 original size:17 final size:17
Alignment explanation
Indices: 21532991--21533025 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21532981 GAAGAATAAG
*
21532991 TAATATTTATAAATTAA
1 TAATATATATAAATTAA
*
21533008 TAATATATATATATTAA
1 TAATATATATAAATTAA
21533025 T
1 T
21533026 TTTAGGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATATATAAATTAA
Found at i:21533017 original size:21 final size:21
Alignment explanation
Indices: 21532985--21533026 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21532975 ATTTAAGAAG
*
21532985 AATAAGTAATATTTATAAATT
1 AATAAGTAATATATATAAATT
*
21533006 AATAA-TATATATATATTAATT
1 AATAAGTA-ATATATATAAATT
21533027 TTAGGGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATAAGTAATATATATAAATT
Found at i:21539369 original size:23 final size:23
Alignment explanation
Indices: 21539343--21539388 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
21539333 ACTATGTCCA
21539343 CAAATTAGGTTTAAATTATGATT
1 CAAATTAGGTTTAAATTATGATT
*
21539366 CAAATTAGGTTTAATTTATGATT
1 CAAATTAGGTTTAAATTATGATT
21539389 TGGCTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (23 bp):
CAAATTAGGTTTAAATTATGATT
Found at i:21540489 original size:15 final size:15
Alignment explanation
Indices: 21540469--21540518 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
21540459 AAAACAAATG
21540469 ATAAGATGAAAGAAA
1 ATAAGATGAAAGAAA
**
21540484 ATAAGA-GACAA-ATG
1 ATAAGATGA-AAGAAA
21540498 ATAAGATGAAAGAAA
1 ATAAGATGAAAGAAA
21540513 ATAAGA
1 ATAAGA
21540519 GACGAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (15 bp):
ATAAGATGAAAGAAA
Found at i:21540504 original size:29 final size:29
Alignment explanation
Indices: 21540462--21540521 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
21540452 TCATTCCAAA
21540462 ACAAATGATAAGATGAAAGAAAATAAGAG
1 ACAAATGATAAGATGAAAGAAAATAAGAG
21540491 ACAAATGATAAGATGAAAGAAAATAAGAG
1 ACAAATGATAAGATGAAAGAAAATAAGAG
21540520 AC
1 AC
21540522 GAGTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.62, C:0.05, G:0.20, T:0.13
Consensus pattern (29 bp):
ACAAATGATAAGATGAAAGAAAATAAGAG
Found at i:21540711 original size:16 final size:16
Alignment explanation
Indices: 21540690--21540727 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
21540680 ATATATTTAT
21540690 TTTTCTATCCCTTCAA
1 TTTTCTATCCCTTCAA
**
21540706 TTTTCTATCTTTTCAA
1 TTTTCTATCCCTTCAA
21540722 TTTTCT
1 TTTTCT
21540728 TTCCACCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCTATCCCTTCAA
Found at i:21540967 original size:17 final size:17
Alignment explanation
Indices: 21540945--21540986 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
21540935 CAAATACCAA
21540945 TATATATTATAATTT-TT
1 TATATATT-TAATTTATT
21540962 TATATATTTAATTTATT
1 TATATATTTAATTTATT
21540979 TCATATAT
1 T-ATATAT
21540987 GTATTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 11 0.48
18 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTTAATTTATT
Found at i:21546071 original size:40 final size:40
Alignment explanation
Indices: 21545994--21546249 Score: 342
Period size: 40 Copynumber: 6.4 Consensus size: 40
21545984 AAACCAAGTA
* * * *
21545994 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGAATATAG-TAACTCGCACAAATG
** *
21546033 CCTTCGGGACTTAGCCCGAATATAGTAGTTTGCACAAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
*
21546073 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
*
21546113 CCTTCGGGACTTAGCCCGAA-ATTAGTAACTCGCAAAAATG
1 CCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCACAAATG
21546153 CCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATG
* *
21546193 CCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATG
21546233 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
21546250 CGTTATCATC
Statistics
Matches: 196, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
39 14 0.07
40 179 0.91
41 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
Found at i:21549812 original size:35 final size:35
Alignment explanation
Indices: 21549761--21549836 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
21549751 TATTGATATT
21549761 AGAATGGGTTTATCTATCAACTATAAAATGTTAAAA
1 AGAA-GGGTTTATCTATCAACTATAAAATGTTAAAA
*
21549797 AGAAGGGTTTATCTATCAGCTATAAAATGTTAAAA
1 AGAAGGGTTTATCTATCAACTATAAAATGTTAAAA
21549832 AGAAG
1 AGAAG
21549837 TGTAGGATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (35 bp):
AGAAGGGTTTATCTATCAACTATAAAATGTTAAAA
Found at i:21555282 original size:2 final size:2
Alignment explanation
Indices: 21555271--21555305 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
21555261 AGGCATTTAT
*
21555271 CA CA CA -A CA CA CA CA CA CA CA CA CA TA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21555306 TATAATACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:21564648 original size:42 final size:41
Alignment explanation
Indices: 21564565--21564709 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 41
21564555 GTCCTGGACG
* * *
21564565 TGGTCTTACATGTAAT-TCAATGTCGATGCCTCTGTCTCAGACA
1 TGGTCTTACACG-AATATCAA--TCGATGCCTATGTCCCAGACA
* *
21564608 AGGTCTTACACGAA-ATCAGATACGATGCCAATGTCCCAGACA
1 TGGTCTTACACGAATATCA-AT-CGATGCCTATGTCCCAGACA
* * * *
21564650 TGGTCTTATACGTGAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TGGTCTTACAC--GAATATCAATCGATGCCTATGTCCCAGACA
21564693 TGGTCTTACACG-ATATC
1 TGGTCTTACACGAATATC
21564710 TCAGATAGAT
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
40 4 0.05
41 2 0.02
42 31 0.37
43 38 0.46
44 5 0.06
45 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (41 bp):
TGGTCTTACACGAATATCAATCGATGCCTATGTCCCAGACA
Found at i:21566827 original size:13 final size:13
Alignment explanation
Indices: 21566809--21566855 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
21566799 TCGAATAAAG
21566809 GGCACACGGCCAA
1 GGCACACGGCCAA
*
21566822 GGCACACAGCCAA
1 GGCACACGGCCAA
21566835 GGCACACGGCCAA
1 GGCACACGGCCAA
21566848 GGCACACG
1 GGCACACG
21566856 CCCATGGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.32, C:0.38, G:0.30, T:0.00
Consensus pattern (13 bp):
GGCACACGGCCAA
Found at i:21568040 original size:46 final size:45
Alignment explanation
Indices: 21567779--21568146 Score: 215
Period size: 46 Copynumber: 7.8 Consensus size: 45
21567769 ATAGGTTAAG
* * *
21567779 ATGCCGACGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAGC
1 ATGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCT--C
* * *
21567828 GAGGCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATC
1 -ATGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCATC--TC
* ** * * * * * * *
21567877 GGTGTTGATGCCATATCCTAGACAGGTCTTACACT-G-ACACACCAC
1 -ATGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
* * * * *
21567922 ATGCTGACGCCATGTCCCAGACAGGTCTTACACTAGCT-TGTATATTAC
1 ATGCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCT-CAT-CT-C
*
21567970 GAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
1 -ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
* *
21568016 AATACCGATGCATGTCCCAGACATGTCTTACACTAGCT-TAAATATCTC
1 -ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT---CATCTC
* * * * * *
21568064 GAGGCCAATGCATGTCCCAAACATGCCATACACTGGCTCTCATGCT-
1 -ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCAT-CTC
* *
21568110 GTGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 AT-GCCGATGCATGTCCCAGACATGTCTTACACTAGC
21568147 ACACATATCA
Statistics
Matches: 251, Mismatches: 52, Indels: 34
0.74 0.15 0.10
Matches are distributed among these distances:
44 29 0.12
45 3 0.01
46 67 0.27
47 7 0.03
48 66 0.26
49 57 0.23
50 21 0.08
51 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (45 bp):
ATGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTC
Found at i:21568155 original size:94 final size:94
Alignment explanation
Indices: 21567932--21568146 Score: 283
Period size: 94 Copynumber: 2.3 Consensus size: 94
21567922 ATGCTGACGC
* ** * * *
21567932 CATGTCCCAGACAGGTCTTACACTAGCTTGTATAT-TACGAGGCCGATGCATGTCCCAGACATGT
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTACGAGGCCAATGCATGTCCCAAACATGC
*
21567996 CTTACACTAGCTCTCATCTCAATACCGATG
66 CATACACTAGCTCTCATCT-AATACCGATG
21568026 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCT-CGAGGCCAATGCATGTCCCAAACATGC
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTACGAGGCCAATGCATGTCCCAAACATGC
* * * *
21568090 CATACACTGGCTCTCATGCT-GTGGCTGATG
66 CATACACTAGCTCTCAT-CTAAT-ACCGATG
21568120 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
21568147 ACACATATCA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
93 1 0.01
94 103 0.96
95 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCTACGAGGCCAATGCATGTCCCAAACATGC
CATACACTAGCTCTCATCTAATACCGATG
Found at i:21576580 original size:6 final size:6
Alignment explanation
Indices: 21576569--21576600 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
21576559 CACTGAAACT
*
21576569 TACACA TACACA TACACA TACGCA TACACA TA
1 TACACA TACACA TACACA TACACA TACACA TA
21576601 TAACATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (6 bp):
TACACA
Found at i:21578559 original size:42 final size:43
Alignment explanation
Indices: 21578459--21578572 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
21578449 CAATGCCAAC
* * *
21578459 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCAATT
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCAATT
* * *
21578502 GTCCCAGACAGGGTCTTACACGAAATCCAATAT-GATATCAA-T
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGAT-GCAATT
*
21578544 GTCCTAGACATGGTCTTACACGTAAATCA
1 GTCCCAGACATGGTCTTACACG-AAATCA
21578573 TAAGTCGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 24 0.40
43 36 0.60
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCAATT
Found at i:21584156 original size:27 final size:27
Alignment explanation
Indices: 21584113--21584171 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
21584103 AAAGACGTTC
*
21584113 CTTTCATATTATGCTACAAAGG-TTCTT
1 CTTTCATATTATACTACAAAGGCTT-TT
21584140 CTTTCATATT-TCACTACAAAGGCTTTT
1 CTTTCATATTAT-ACTACAAAGGCTTTT
21584167 CTTTC
1 CTTTC
21584172 TTGATATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 1 0.03
27 26 0.90
28 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (27 bp):
CTTTCATATTATACTACAAAGGCTTTT
Found at i:21586961 original size:119 final size:119
Alignment explanation
Indices: 21586750--21586987 Score: 320
Period size: 119 Copynumber: 2.0 Consensus size: 119
21586740 GGTTAGTAAC
* * * *
21586750 ATTGGCGAACTCAATCAAAAGACTAAGGATGGCTAGAGGAGGGAATGAAGAGAGTGATGGATGGT
1 ATTGGCGAACTCAATCAAAAGACTAAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGATGGT
* *
21586815 CAAGCGTGGGGAGTGTGGTATTGGGCACAAAAT-AAGGAATAGAAATTTCATCCT
66 CAAGCGCGGGGAGTGTGGTATTGGGCACAAAATGAA-GAACAGAAATTTCATCCT
* *
21586869 ATTGGCGAACTCAA-CTAGAAGACTGAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGA-GA
1 ATTGGCGAACTCAATC-AAAAGACTAAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGATG-
* * * *
21586932 GTCAAGTGCGGGGATTGTGGTATTGGGCACAAACTGAAGAACATAAATTTCATCCT
64 GTCAAGCGCGGGGAGTGTGGTATTGGGCACAAAATGAAGAACAGAAATTTCATCCT
21586988 CTAGATGGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
118 2 0.02
119 100 0.96
120 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.21
Consensus pattern (119 bp):
ATTGGCGAACTCAATCAAAAGACTAAGCATGGCTAGAGAAGGAAATGAAGAGAGCGATGGATGGT
CAAGCGCGGGGAGTGTGGTATTGGGCACAAAATGAAGAACAGAAATTTCATCCT
Found at i:21593841 original size:40 final size:40
Alignment explanation
Indices: 21593752--21593931 Score: 197
Period size: 40 Copynumber: 4.5 Consensus size: 40
21593742 ACCCAAGTAT
** * *
21593752 CTTCGGGAT-TTAG-CCGGATATAACCACTAGCA-CAAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCATAAATGC
* *
21593790 CTTCGGGTCTTAGCCTGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
* * *
21593830 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGTACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATAAATGC
* * *
21593870 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
*
21593910 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
21593932 CATTCGAATA
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
37 1 0.01
38 11 0.09
39 16 0.14
40 88 0.75
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
Found at i:21601413 original size:26 final size:26
Alignment explanation
Indices: 21601384--21601465 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
21601374 TGGTACAAAT
*
21601384 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
21601410 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
21601436 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
21601462 TGAT
1 TGAT
21601466 GGACATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:21604509 original size:25 final size:25
Alignment explanation
Indices: 21604455--21604512 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
21604445 TTAATTTAAT
* *
21604455 TTAATACTTATATTAATAGTATTTTA
1 TTAATA-TAATATTAATAGTATTATA
*
21604481 TTAATATAATATTAA-AGTGATTATC
1 TTAATATAATATTAATAGT-ATTATA
21604506 TTAATAT
1 TTAATAT
21604513 TAAATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 19 0.68
26 6 0.21
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (25 bp):
TTAATATAATATTAATAGTATTATA
Found at i:21604590 original size:11 final size:11
Alignment explanation
Indices: 21604576--21604624 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
21604566 ATAATATTAA
21604576 ATTTATATAAT
1 ATTTATATAAT
21604587 ATTTATATAAT
1 ATTTATATAAT
*
21604598 AAATTTAATCTAAT
1 --ATTT-ATATAAT
21604612 ATTTATATTAAT
1 ATTTATA-TAAT
21604624 A
1 A
21604625 AATATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 13 0.41
12 9 0.28
13 4 0.12
14 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTTATATAAT
Found at i:21604593 original size:25 final size:25
Alignment explanation
Indices: 21604565--21604634 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
21604555 ATTTTAATAA
*
21604565 TATAATATTAAATTTATATAATATT
1 TATAATAATAAATTTATATAATATT
*
21604590 TAT-ATAATAAATTTAATCTAATATT
1 TATAATAATAAATTT-ATATAATATT
*
21604615 TATATTAATAAATATTATAT
1 TATAATAATAAAT-TTATAT
21604635 TAATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 10 0.26
25 15 0.39
26 11 0.29
27 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
TATAATAATAAATTTATATAATATT
Found at i:21604640 original size:25 final size:25
Alignment explanation
Indices: 21604573--21604648 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
21604563 AATATAATAT
*
21604573 TAAATTTATATAATATTTATA-TAA
1 TAAATTTATATTATATTTATATTAA
21604597 TAAATTTA-ATCTAATATTTATATTAA
1 TAAATTTATAT-T-ATATTTATATTAA
21604623 TAAATATTATATTA-ATTTAATATTAA
1 TAAAT-TTATATTATATTT-ATATTAA
21604649 AGTGATTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
23 2 0.04
24 8 0.18
25 13 0.29
26 16 0.36
27 4 0.09
28 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAATTTATATTATATTTATATTAA
Found at i:21605506 original size:33 final size:33
Alignment explanation
Indices: 21605462--21605534 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
21605452 GGACATGCTT
* * *
21605462 AACATGTGAATCAGATTTATAGTCAACACAGCC
1 AACATGCGAATCAAATTTATAGTCAACACAACC
*
21605495 AACATGCGAATCAAATTTATAGTCAACACAATC
1 AACATGCGAATCAAATTTATAGTCAACACAACC
21605528 AACATGC
1 AACATGC
21605535 TCAACATGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.23
Consensus pattern (33 bp):
AACATGCGAATCAAATTTATAGTCAACACAACC
Found at i:21610504 original size:38 final size:38
Alignment explanation
Indices: 21610462--21610598 Score: 159
Period size: 38 Copynumber: 3.6 Consensus size: 38
21610452 GTAGGCTTTA
*
21610462 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTCCG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTCCG
*
21610500 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGC-CTAG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTC-CG
* * * *
21610538 TGCTGGTATTATATCTGAGTTTAAAGTCCCGTAGGCTTCG
1 TGCTGGTATTATATCCG-GGTTAAA-TCCCGCAGGCTCCG
* * *
21610578 TGCTGGTGTTATGTTCGGGTT
1 TGCTGGTATTATATCCGGGTT
21610599 TTATACCTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.01
38 50 0.60
39 9 0.11
40 23 0.28
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (38 bp):
TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTCCG
Found at i:21615086 original size:39 final size:40
Alignment explanation
Indices: 21615041--21615151 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
21615031 CGGGGTTTAG
* * *
21615041 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
21615080 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
21615120 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
21615152 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:21615111 original size:40 final size:40
Alignment explanation
Indices: 21615064--21615208 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
21615054 CTCGCACAAG
* * * * *
21615064 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
21615104 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
21615144 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
*
21615185 GCGTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
21615209 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.65
41 26 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:21616439 original size:38 final size:38
Alignment explanation
Indices: 21616397--21616472 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
21616387 CAAGAACTAC
21616397 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
21616435 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
21616473 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Done.