Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 78 of 136
Found at i:25444827 original size:31 final size:31
Alignment explanation
Indices: 25444792--25444889 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 31
25444782 CCCAATAGCG
25444792 GCCCAACCCAGCAGACCCAACAACAGCAGTA
1 GCCCAACCCAGCAGACCCAACAACAGCAGTA
* *
25444823 GCCCAATCCAGTCAG-CCCAAC-A-A-TAGTA
1 GCCCAACCCAG-CAGACCCAACAACAGCAGTA
* * * * *
25444851 GACCAACCTAGTAGACCCAACAGCAGCAGCAA
1 GCCCAACCCAGCAGACCCAACAACAGCAG-TA
25444883 GCCCAAC
1 GCCCAAC
25444890 TCAGTTAGCC
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
27 2 0.04
28 18 0.35
29 1 0.02
30 2 0.04
31 18 0.35
32 10 0.20
ACGTcount: A:0.38, C:0.39, G:0.16, T:0.07
Consensus pattern (31 bp):
GCCCAACCCAGCAGACCCAACAACAGCAGTA
Found at i:25456615 original size:75 final size:74
Alignment explanation
Indices: 25456464--25456617 Score: 175
Period size: 76 Copynumber: 2.1 Consensus size: 74
25456454 TCATTTCCTT
* *
25456464 TTTCATTTTTCAAAAATCAACTATAATCTGAGAAGTGAATTGAGCCTCGGGTCACACGTCGAGGT
1 TTTCATTTTTCAAAAATCAACTATAATCTGAGAAGTGAATGGAGCCTCGGGTCACACGCCGAGGT
*
25456529 ATTTTTTAA
66 ATTTTTAAA
* * * * * * ** *
25456538 TTTCTATTTTTCAAAGATCAACTCATGATCTGAGAGGTGAGTGGAGCTTTGGGTTGCATGCCGAG
1 TTTC-ATTTTTCAAAAATCAACT-ATAATCTGAGAAGTGAATGGAGCCTCGGGTCACACGCCGAG
25456603 GTA-TTTTAAA
64 GTATTTTTAAA
25456613 TTTCA
1 TTTCA
25456618 GTCTTTTATT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
74 5 0.08
75 27 0.41
76 34 0.52
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (74 bp):
TTTCATTTTTCAAAAATCAACTATAATCTGAGAAGTGAATGGAGCCTCGGGTCACACGCCGAGGT
ATTTTTAAA
Found at i:25465421 original size:23 final size:23
Alignment explanation
Indices: 25465388--25465439 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
25465378 ATGAGTGCCA
* *
25465388 CACTGATATGTAGTCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
25465411 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
25465434 CACTGA
1 CACTGA
25465440 TCAATAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:25471654 original size:12 final size:10
Alignment explanation
Indices: 25471626--25471670 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
25471616 TTGAAAATAG
25471626 TCAAAATTAA
1 TCAAAATTAA
25471636 TCAAAATTAA
1 TCAAAATTAA
25471646 CTACAAAATTAA
1 -T-CAAAATTAA
* *
25471658 TTAAAATTCA
1 TCAAAATTAA
25471668 TCA
1 TCA
25471671 TGTTCATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (10 bp):
TCAAAATTAA
Found at i:25481362 original size:13 final size:13
Alignment explanation
Indices: 25481344--25481368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25481334 TAGATTGAAT
25481344 TTGATTATGTAAA
1 TTGATTATGTAAA
25481357 TTGATTATGTAA
1 TTGATTATGTAA
25481369 TCTTGTAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:25481791 original size:11 final size:11
Alignment explanation
Indices: 25481763--25481812 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
25481753 CCGTGACACA
*
25481763 ATGGTGGTGAT
1 ATGGTGGTGCT
25481774 A-GGTGGTGCT
1 ATGGTGGTGCT
25481784 ATGGTGGTAG-T
1 ATGGTGGT-GCT
25481795 ATGGTGGTGCT
1 ATGGTGGTGCT
*
25481806 TTGGTGG
1 ATGGTGG
25481813 AGAAGTGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 10 0.29
11 23 0.68
12 1 0.03
ACGTcount: A:0.12, C:0.04, G:0.48, T:0.36
Consensus pattern (11 bp):
ATGGTGGTGCT
Found at i:25481803 original size:22 final size:21
Alignment explanation
Indices: 25481763--25481812 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
25481753 CCGTGACACA
25481763 ATGGTGGTGATAGGTGGTGCT
1 ATGGTGGTGATAGGTGGTGCT
25481784 ATGGTGGT-AGTATGGTGGTGCT
1 ATGGTGGTGA-TA-GGTGGTGCT
*
25481806 TTGGTGG
1 ATGGTGG
25481813 AGAAGTGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 10 0.38
22 15 0.58
ACGTcount: A:0.12, C:0.04, G:0.48, T:0.36
Consensus pattern (21 bp):
ATGGTGGTGATAGGTGGTGCT
Found at i:25481821 original size:22 final size:22
Alignment explanation
Indices: 25481763--25481821 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
25481753 CCGTGACACA
25481763 ATGGTGGT-G-ATAGGTGGTGCT
1 ATGGTGGTAGAAT-GGTGGTGCT
*
25481784 ATGGTGGTAGTATGGTGGTGCT
1 ATGGTGGTAGAATGGTGGTGCT
*
25481806 TTGGTGG-AGAAGTGGT
1 ATGGTGGTAGAA-TGGT
25481822 AGTTTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 11 0.33
22 20 0.61
23 2 0.06
ACGTcount: A:0.15, C:0.03, G:0.47, T:0.34
Consensus pattern (22 bp):
ATGGTGGTAGAATGGTGGTGCT
Found at i:25497195 original size:31 final size:31
Alignment explanation
Indices: 25497138--25497196 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
25497128 ATAGAATTAA
* *
25497138 AATCAAAATTTTATGTATACATTTGAACCAT
1 AATCAAAATTTCATGTATACAATTGAACCAT
* *
25497169 AATCAAAATTTCATGTTTATAATTGAAC
1 AATCAAAATTTCATGTATACAATTGAAC
25497197 AAAATTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
AATCAAAATTTCATGTATACAATTGAACCAT
Found at i:25497380 original size:8 final size:8
Alignment explanation
Indices: 25497367--25497393 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
25497357 CCACCATCTT
25497367 ATATTAAA
1 ATATTAAA
25497375 ATATTAAA
1 ATATTAAA
25497383 ATATTAAA
1 ATATTAAA
25497391 ATA
1 ATA
25497394 CTCGAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATTAAA
Found at i:25498611 original size:44 final size:44
Alignment explanation
Indices: 25498553--25498636 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
25498543 AATTGTATTT
* * *
25498553 TAAATTATATTTATTTTTAAAT-TCGTAATTATCATAACTTGTAC
1 TAAATTATAGTTATTTTTAAATGT-ATAATTATCACAACTTGTAC
25498597 TAAATTATAGTTATTTTTAAATGTATAATTATCACAACTT
1 TAAATTATAGTTATTTTTAAATGTATAATTATCACAACTT
25498637 CTATTTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (44 bp):
TAAATTATAGTTATTTTTAAATGTATAATTATCACAACTTGTAC
Found at i:25504351 original size:27 final size:26
Alignment explanation
Indices: 25504295--25504391 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
25504285 TCGTGCGTCT
* **
25504295 CCTATTTTTCAGATTTTATGGTTTTAC
1 CCTATTTTTCAGATTTTCTAATTTT-C
*
25504322 CCTGATTTTTTAGATTTTCTAATTTTC
1 CCT-ATTTTTCAGATTTTCTAATTTTC
*
25504349 CCTTATTTTTCAAATTTTAC-AATTTTC
1 CC-TATTTTTCAGATTTT-CTAATTTTC
*
25504376 CCT-TTTTTTAGATTTT
1 CCTATTTTTCAGATTTT
25504392 ATAGTTTTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
25 11 0.19
26 1 0.02
27 27 0.46
28 20 0.34
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.59
Consensus pattern (26 bp):
CCTATTTTTCAGATTTTCTAATTTTC
Found at i:25504687 original size:34 final size:34
Alignment explanation
Indices: 25504648--25504724 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
25504638 ATGACTTTTG
* * *
25504648 GCTACTG-AGTTGATCTGTTATAAGCGTATT-ATTT
1 GCTACTGTA-TTGAACTATTATAAGCATATTGA-TT
25504682 GCTACTGTATTGAACTATTATAAGCATATTGATT
1 GCTACTGTATTGAACTATTATAAGCATATTGATT
*
25504716 GCTATTGTA
1 GCTACTGTA
25504725 CTGTTCTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (34 bp):
GCTACTGTATTGAACTATTATAAGCATATTGATT
Found at i:25504797 original size:35 final size:35
Alignment explanation
Indices: 25504726--25504797 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
25504716 GCTATTGTAC
*
25504726 TGTTCTGTTAAAAGCATAATTAAATGATATCATAT
1 TGTTCTGTTAAAAGCATAATTAAATGATACCATAT
* *
25504761 TGTTCTGTTAAAAGCATAATTAAATGCTACCGTAT
1 TGTTCTGTTAAAAGCATAATTAAATGATACCATAT
25504796 TG
1 TG
25504798 ACCTATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (35 bp):
TGTTCTGTTAAAAGCATAATTAAATGATACCATAT
Found at i:25504992 original size:18 final size:18
Alignment explanation
Indices: 25504969--25505026 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
25504959 TTTTATTACT
25504969 AGTGGTTTATCCACAATG
1 AGTGGTTTATCCACAATG
*
25504987 AGTGGTTCATCCACGACGATG
1 AGTGGTTTATCCAC-A--ATG
25505008 AGTGGTTTTATCCACAATG
1 AGTGG-TTTATCCACAATG
25505027 TGGTGTAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
21 9 0.26
22 8 0.24
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (18 bp):
AGTGGTTTATCCACAATG
Found at i:25505991 original size:6 final size:6
Alignment explanation
Indices: 25505986--25506015 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
25505976 ATAATAAATT
25505986 TTAAT- TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA TTAATA T
25506016 GAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:25507937 original size:23 final size:24
Alignment explanation
Indices: 25507900--25507950 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
25507890 AGGGAGTAGC
25507900 AAAAGAAAATAGAAAAT-AAAGAAA
1 AAAAGAAAATAGAAAATGAAA-AAA
* *
25507924 AAAAGAAAA-GGAAAGTGAAAAAA
1 AAAAGAAAATAGAAAATGAAAAAA
25507947 AAAA
1 AAAA
25507951 CATAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAAGAAAATAGAAAATGAAAAAA
Found at i:25517052 original size:26 final size:28
Alignment explanation
Indices: 25516992--25517053 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
25516982 CGGACTTATC
* *
25516992 CTATGTTTACTGTCTCGGTAGACTCTAT
1 CTATGTTTACTGTCTCAGTAGACACTAT
* *
25517020 TTGTGTTTACTGTCTCAGT-GA-ACTAT
1 CTATGTTTACTGTCTCAGTAGACACTAT
25517046 CTATGTTT
1 CTATGTTT
25517054 TGTGTTTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 10 0.36
27 2 0.07
28 16 0.57
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (28 bp):
CTATGTTTACTGTCTCAGTAGACACTAT
Found at i:25535480 original size:22 final size:22
Alignment explanation
Indices: 25535438--25535480 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25535428 TTTCATCTCT
*
25535438 TGTCTTTTATTTTCACGACATC
1 TGTCTTTTATTTTCACAACATC
* *
25535460 TGTCTTTTTTTTTCCCAACAT
1 TGTCTTTTATTTTCACAACAT
25535481 GTTTACTGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.53
Consensus pattern (22 bp):
TGTCTTTTATTTTCACAACATC
Found at i:25538644 original size:27 final size:27
Alignment explanation
Indices: 25538614--25538704 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
25538604 TTTATTTCAA
25538614 TATTTTACAAACCATAAAAATACTTAT
1 TATTTTACAAACCATAAAAATACTTAT
* * **
25538641 TATTTTAC--TCTCGTAATATAATTGTTCAT
1 TATTTTACAAAC-CATAA-A-AATACTT-AT
25538670 TATTTTACAAACCATAAAAATACTTAT
1 TATTTTACAAACCATAAAAATACTTAT
*
25538697 TGTTTTAC
1 TATTTTAC
25538705 TCTCGTAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 18 0.37
28 10 0.20
29 11 0.22
30 4 0.08
31 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.44
Consensus pattern (27 bp):
TATTTTACAAACCATAAAAATACTTAT
Found at i:25538681 original size:56 final size:56
Alignment explanation
Indices: 25538609--25538720 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
25538599 GATATTTTAT
25538609 TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
1 TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
* *
25538665 TTCATTATTTTACAAACCATAAAAATACTTATTGTTTTACTCTCGTAATATAATTG
1 TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
25538721 ACTTAAAGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (56 bp):
TTCAATATTTTACAAACCATAAAAATACTTATTATTTTACTCTCGTAATATAATTG
Found at i:25547919 original size:20 final size:20
Alignment explanation
Indices: 25547877--25547920 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25547867 TTGAGAGCAA
*
25547877 TTCTCTCTACTAAATAAGAC
1 TTCTCTCTACTAAATAACAC
*
25547897 TTCTCTCATA-TAAATAACCC
1 TTCTCTC-TACTAAATAACAC
25547917 TTCT
1 TTCT
25547921 TGCATGGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (20 bp):
TTCTCTCTACTAAATAACAC
Found at i:25564002 original size:107 final size:106
Alignment explanation
Indices: 25563775--25563988 Score: 331
Period size: 107 Copynumber: 2.0 Consensus size: 106
25563765 CCAAAACCCA
* * * *
25563775 TACTTTGAAACTTTAAGAGGGTATTTGGCTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGACTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
25563840 AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* *
25563881 TACTTTGAAATTTTAAAAGGATATTTGACTATTTGG-TCGAACGAAGAAATCGAAACCTAGCACA
1 TACTTTGAAATTTTAAAAGGATATTTGACTATTTGGCT-AAACG-AGAAATCGAAACCCAGCACA
* *
25563945 TTAGGGCACGTTTTCTCGAATTTCCAAATGTAAAATATTGCCT
64 TTAGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
25563988 T
1 T
25563989 TATTATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 1 0.01
106 36 0.37
107 61 0.62
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (106 bp):
TACTTTGAAATTTTAAAAGGATATTTGACTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
Found at i:25564303 original size:3 final size:3
Alignment explanation
Indices: 25564288--25564354 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
25564278 AAAAGGTATT
* * ** * **
25564288 TAA TAA TAT TAA TAA TGA TGC TAA TAA TAA TAA TAA TAA TAG TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25564336 TAA TAA TATA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA
25564355 AAAATGATAG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:25564319 original size:24 final size:24
Alignment explanation
Indices: 25564288--25564353 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
25564278 AAAAGGTATT
25564288 TAATAATATTAATAAT-GATGCTAA
1 TAATAATATTAATAATAG-TGCTAA
* **
25564312 TAATAATAATAATAATAGTTTTAA
1 TAATAATATTAATAATAGTGCTAA
25564336 TAATAATATATAATAATA
1 TAATAATAT-TAATAATA
25564354 AAAAATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 27 0.75
25 9 0.25
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TAATAATATTAATAATAGTGCTAA
Found at i:25572845 original size:24 final size:26
Alignment explanation
Indices: 25572818--25572876 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
25572808 TAAATGTGTA
25572818 AGCTAATAAAT-AATATATA-AGTTG
1 AGCTAATAAATAAATATATACAGTTG
**
25572842 AGCT-CGAAATAAATATATACAGTTG
1 AGCTAATAAATAAATATATACAGTTG
25572867 AG-TAACTAAA
1 AGCTAA-TAAA
25572877 ATAAGGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 7 0.26
26 3 0.11
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (26 bp):
AGCTAATAAATAAATATATACAGTTG
Found at i:25574940 original size:20 final size:21
Alignment explanation
Indices: 25574905--25574944 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25574895 TCCAAAACAC
25574905 TTCAAGAATAATTTTCTAAAAA
1 TTCAAGAATAATTTTC-AAAAA
25574927 TTCAA-AAT-ATTTTCAAAA
1 TTCAAGAATAATTTTCAAAA
25574945 CCCATTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 3 0.17
22 5 0.28
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
TTCAAGAATAATTTTCAAAAA
Found at i:25575924 original size:18 final size:18
Alignment explanation
Indices: 25575901--25575941 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
25575891 ATTAGCATCG
25575901 ATTGCGGCACTAAACAAT
1 ATTGCGGCACTAAACAAT
25575919 ATTGCGGCACTAAACAAT
1 ATTGCGGCACTAAACAAT
25575937 ATTGC
1 ATTGC
25575942 AACACAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (18 bp):
ATTGCGGCACTAAACAAT
Found at i:25576230 original size:27 final size:27
Alignment explanation
Indices: 25576200--25576578 Score: 472
Period size: 27 Copynumber: 14.1 Consensus size: 27
25576190 TATAACACTA
*
25576200 ATTTTACCCTATGGGGGCATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
25576227 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
25576254 ATTTTACCCTATCGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
** *
25576281 ATTTTACATTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
25576308 ATTTTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
25576335 ATTTTACCCTATGGGGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * **
25576362 ATTTTACCCTCTAGGGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
25576389 ATTTTACCCTATAGAGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
25576416 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
25576443 ATTTTACCATATTGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
25576470 ATTTTACCCTCT-GGGGTATTTCGGCC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
25576496 ATGTTACTCTACGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * **
25576523 ATTTTACCTTATGAGGGTATTTCAATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
25576550 ATTTTACCCTATGGGGGTATATCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
25576577 AT
1 AT
25576579 AAAAGTGTAA
Statistics
Matches: 297, Mismatches: 54, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 20 0.07
27 277 0.93
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:25578733 original size:25 final size:25
Alignment explanation
Indices: 25578705--25578756 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
25578695 CTTTAGATAA
25578705 TTATT-TTCTTTAATTATTGTTTATT
1 TTATTATTCTTT-ATTATTGTTTATT
*
25578730 TTATTATTGTTTATTATTGTTTATT
1 TTATTATTCTTTATTATTGTTTATT
25578755 TT
1 TT
25578757 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (25 bp):
TTATTATTCTTTATTATTGTTTATT
Found at i:25578744 original size:10 final size:10
Alignment explanation
Indices: 25578729--25578754 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
25578719 TATTGTTTAT
25578729 TTTATTATTG
1 TTTATTATTG
25578739 TTTATTATTG
1 TTTATTATTG
25578749 TTTATT
1 TTTATT
25578755 TTTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
TTTATTATTG
Found at i:25579873 original size:20 final size:22
Alignment explanation
Indices: 25579834--25579874 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
25579824 GTGGTTGGAT
25579834 TCAAATTCTAATACTAGATTGTA
1 TCAAATTC-AATACTAGATTGTA
25579857 TCAAATTC-ATA-TAGATTG
1 TCAAATTCAATACTAGATTG
25579875 ATACATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
23 8 0.44
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TCAAATTCAATACTAGATTGTA
Found at i:25583522 original size:31 final size:32
Alignment explanation
Indices: 25583487--25583549 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
25583477 CACTTTCATG
25583487 TTGGAAGTGGGTAA-TTTTAATCTTTCTTTTT
1 TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
25583518 TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
1 TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
25583550 GCTATCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (32 bp):
TTGGAAGTGGGTAATTTTTAATCTTTCTTTTT
Found at i:25588491 original size:101 final size:101
Alignment explanation
Indices: 25588356--25588568 Score: 327
Period size: 101 Copynumber: 2.1 Consensus size: 101
25588346 CATAGCCTTG
* * * * *
25588356 CCATGGTCTTATGTTCATAGTGCCATAACCCAGTTATGGTCTTACCATCAGAATGCCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGACATAACCCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
* *
25588421 GCTATGGTCTTACATATAAACACTACCATGGTCTAA
66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA
* *
25588457 CCATTGTCTTACGTCCATAGTGACATAACTCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
1 CCATGGTCTTACGTCCATAGTGACATAACCCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
* *
25588522 GCAATGGTCTTACATATATACACTGCCATGGTCCAA
66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA
25588558 CCATGGTCTTA
1 CCATGGTCTTA
25588569 AATACTTCAA
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (101 bp):
CCATGGTCTTACGTCCATAGTGACATAACCCAGTTATGGTCTTACCATCAAAATGCCATAACCCA
GCAATGGTCTTACATATAAACACTACCATGGTCCAA
Found at i:25588617 original size:27 final size:27
Alignment explanation
Indices: 25588564--25588636 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
25588554 CCAACCATGG
25588564 TCTTAAATACTTCAA-TTTTTTATTAT
1 TCTTAAATACTTCAATTTTTTTATTAT
*
25588590 TTTTAAATACTTCAATTTTTTTATTAT
1 TCTTAAATACTTCAATTTTTTTATTAT
25588617 TCTTAAATACTTCAATTTTT
1 TCTTAAATACTTCAATTTTT
25588637 AAATTTCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 14 0.32
27 30 0.68
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (27 bp):
TCTTAAATACTTCAATTTTTTTATTAT
Found at i:25589552 original size:11 final size:11
Alignment explanation
Indices: 25589536--25589561 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25589526 ATCAAATTAA
25589536 ATAAATATCCT
1 ATAAATATCCT
25589547 ATAAATATCCT
1 ATAAATATCCT
25589558 ATAA
1 ATAA
25589562 TTTTATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAATATCCT
Found at i:25590033 original size:59 final size:59
Alignment explanation
Indices: 25589941--25590059 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
25589931 TAAATATAAG
25589941 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCA-TCCGAATTAATTGTT
1 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATTCCGAA-TAATTGTT
25590000 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATTCCGAATAATTGTT
1 ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATTCCGAATAATTGTT
25590059 A
1 A
25590060 AAAATAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 53 0.90
60 6 0.10
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (59 bp):
ATTACAATTACACGTATAGGTAATACATATTTAAATAACTATCATTCCGAATAATTGTT
Found at i:25596247 original size:29 final size:29
Alignment explanation
Indices: 25596205--25596277 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
25596195 ACCTCTCAAT
25596205 ACACTTAAATCAATGAGCCGAAACACACA
1 ACACTTAAATCAATGAGCCGAAACACACA
25596234 ACACTTAAATCAATGAGCCGAAACACACA
1 ACACTTAAATCAATGAGCCGAAACACACA
*
25596263 ACACTCAAATCAATG
1 ACACTTAAATCAATG
25596278 GAAGAGCATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.48, C:0.27, G:0.10, T:0.15
Consensus pattern (29 bp):
ACACTTAAATCAATGAGCCGAAACACACA
Found at i:25598413 original size:24 final size:25
Alignment explanation
Indices: 25598386--25598438 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
25598376 GTACATGTAT
*
25598386 GCTCATATGAGCTGTA-AACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
* * *
25598410 GCTCCTCTGAGTTGAATAACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
25598435 GCTC
1 GCTC
25598439 CTTCAAGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (25 bp):
GCTCATATGAGCTGAATAACGGTAA
Found at i:25600888 original size:25 final size:25
Alignment explanation
Indices: 25600860--25600907 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
25600850 GGACAAGATT
25600860 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
25600885 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
25600908 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:25602166 original size:122 final size:123
Alignment explanation
Indices: 25601958--25602247 Score: 393
Period size: 122 Copynumber: 2.4 Consensus size: 123
25601948 AAAAAATGCT
*** * *
25601958 GCTATTGCTTTACCTTTTGCGATGTTTATGGGAAAAACGCCACTATTGCTTTACCTTTTGTGGCG
1 GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTATTGCTTTACCTTTTGTGGCA
25602023 TTTATGGGAAAAACGCCGCTATTGC-TTACCTTTTACAGCGTGTATAGGAAAAACACC
66 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTTACAGCGTGTATAGGAAAAACACC
* *
25602080 GCTATTGCTTTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTGTGGCA
1 GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTATTGCTTTACCTTTTGTGGCA
* * * * * * * * * *
25602145 TTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGCGGTGTTTATGGGCAATATACC
66 TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTTACAGCGTGTATAGGAAAAACACC
* * *
25602203 ACTATTGCTTTACCTTTTGCGGCATTTATAGGAAAAATTCCACTA
1 GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTA
25602248 ATGGTATATA
Statistics
Matches: 145, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
122 81 0.56
123 64 0.44
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (123 bp):
GCTATTGCTTTACCTTTTGCGGCATTTATGGGAAAAATGCCACTATTGCTTTACCTTTTGTGGCA
TTTATGGGAAAAACGCCGCTATTGCTTTACCTTTTACAGCGTGTATAGGAAAAACACC
Found at i:25602247 original size:41 final size:41
Alignment explanation
Indices: 25601932--25602240 Score: 368
Period size: 41 Copynumber: 7.6 Consensus size: 41
25601922 AGTAAATAAA
* * *
25601932 TTTGCGGTGTTTATGGAAAAAATGCTGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
** * *
25601973 TTTGCGATGTTTATGGGAAAAACGCCACTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* *
25602014 TTTGTGGCGTTTATGGGAAAAACGCCGCTATTGC-TTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* * * * **
25602054 TTTACAGCGTGTATAGGAAAAACACCGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* *
25602095 TTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* * *
25602136 TTTGTGGCATTTATGGGCAAAATGCCGCTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* * * * *
25602177 TTTGCGGTGTTTATGGGCAATATACCACTATTGCTTTACCT
1 TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
* *
25602218 TTTGCGGCATTTATAGGAAAAAT
1 TTTGCGGCGTTTATGGGAAAAAT
25602241 TCCACTAATG
Statistics
Matches: 232, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 34 0.15
41 198 0.85
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (41 bp):
TTTGCGGCGTTTATGGGAAAAATGCCGCTATTGCTTTACCT
Found at i:25611519 original size:30 final size:28
Alignment explanation
Indices: 25611485--25611540 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
25611475 GTGATTAAAT
25611485 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
25611515 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
25611541 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:25612979 original size:12 final size:13
Alignment explanation
Indices: 25612955--25612983 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25612945 GGGCTATAAG
25612955 TATTGCATTTATT
1 TATTGCATTTATT
25612968 TATTGC-TTTATT
1 TATTGCATTTATT
25612980 TATT
1 TATT
25612984 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:25625591 original size:26 final size:26
Alignment explanation
Indices: 25625557--25625607 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
25625547 CAGTAGCATC
25625557 GCAACAAAGCTGCCAGCAACAGTATT
1 GCAACAAAGCTGCCAGCAACAGTATT
* *
25625583 GCAATAAAGCTGCCAGTAACAGTAT
1 GCAACAAAGCTGCCAGCAACAGTAT
25625608 ATGTGGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
GCAACAAAGCTGCCAGCAACAGTATT
Found at i:25625629 original size:27 final size:27
Alignment explanation
Indices: 25625599--25625651 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25625589 AAGCTGCCAG
* *
25625599 TAACAGT-ATATGTGGCCAAGCCACCAA
1 TAACAGTGAT-TGTGGCAAAACCACCAA
25625626 TAACAGTGATTGTGGCAAAACCACCA
1 TAACAGTGATTGTGGCAAAACCACCA
25625652 GTATAGTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
TAACAGTGATTGTGGCAAAACCACCAA
Found at i:25625749 original size:11 final size:11
Alignment explanation
Indices: 25625733--25625775 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
25625723 AATCTGCCAT
25625733 ACAAATCACAG
1 ACAAATCACAG
*
25625744 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
25625757 ACCAATCACAG
1 ACAAATCACAG
25625768 ACAAATCA
1 ACAAATCA
25625776 GTCATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:25625750 original size:24 final size:24
Alignment explanation
Indices: 25625723--25625799 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
25625713 TCATGCTCAG
*
25625723 AATCTGCCATACAAATCACAGACA
1 AATCAGCCATACAAATCACAGACA
* *
25625747 AATCAGTCATACCAATCACAGACA
1 AATCAGCCATACAAATCACAGACA
* ** * *
25625771 AATCAGTCATTTAAATCACAAAAA
1 AATCAGCCATACAAATCACAGACA
25625795 AATCA
1 AATCA
25625800 ATCATTTACC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.19
Consensus pattern (24 bp):
AATCAGCCATACAAATCACAGACA
Found at i:25625804 original size:24 final size:24
Alignment explanation
Indices: 25625760--25625807 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25625750 CAGTCATACC
* * *
25625760 AATCACAGACAAATCAGTCATTTA
1 AATCACAAAAAAATCAATCATTTA
25625784 AATCACAAAAAAATCAATCATTTA
1 AATCACAAAAAAATCAATCATTTA
25625808 CCCTATAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (24 bp):
AATCACAAAAAAATCAATCATTTA
Found at i:25625838 original size:27 final size:27
Alignment explanation
Indices: 25625804--25625865 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
25625794 AAATCAATCA
*
25625804 TTTACCCTATAGGGGCATTATGGTCAT
1 TTTACCCTATAGGGGCATTACGGTCAT
25625831 TTTACCCTATAGGGGCATTACGGTCAT
1 TTTACCCTATAGGGGCATTACGGTCAT
25625858 TTTACCCT
1 TTTACCCT
25625866 TCGAGGGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (27 bp):
TTTACCCTATAGGGGCATTACGGTCAT
Found at i:25625886 original size:27 final size:27
Alignment explanation
Indices: 25625856--25625970 Score: 108
Period size: 27 Copynumber: 4.3 Consensus size: 27
25625846 CATTACGGTC
25625856 ATTTTACCCTTCGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCAATA
*
25625883 ATTTTACCCAGT-GAGGGTATTTCAATA
1 ATTTTACCC-TTCGAGGGTATTTCAATA
* * ***
25625910 ATCTTACCCATC-AGGGGTATTTTTGTA
1 ATTTTACCCTTCGA-GGGTATTTCAATA
** * *
25625937 ATTTTACCCTTTAAGGGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCAATA
25625964 ATTTTAC
1 ATTTTAC
25625971 AACCTTTCCG
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.03
27 70 0.95
28 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCAATA
Found at i:25643130 original size:34 final size:33
Alignment explanation
Indices: 25643076--25643139 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 33
25643066 TGCATAATAT
25643076 TTTTAACATATATTAATAC-AACA-TTTACCAC
1 TTTTAACATATATTAATACAAACAGTTTACCAC
*
25643107 TTTTACACATATATACTATTACAAACAGTTTAC
1 TTTTA-ACATATAT--TAATACAAACAGTTTAC
25643140 TGTTTCACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 5 0.19
32 8 0.30
34 5 0.19
35 4 0.15
36 5 0.19
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.39
Consensus pattern (33 bp):
TTTTAACATATATTAATACAAACAGTTTACCAC
Found at i:25645279 original size:51 final size:51
Alignment explanation
Indices: 25645203--25645305 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
25645193 TGATTCATTT
25645203 ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
1 ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
*
25645254 ACTTAAAAATTAATTCTTCTACTACTAGACCAATTGCTCTGAATGCACTGC
1 ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
25645305 A
1 A
25645306 TAAAGGTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (51 bp):
ACTTAAAAATTAATTCATCTACTACTAGACCAATTGCTCTGAATGCACTGC
Found at i:25648398 original size:18 final size:18
Alignment explanation
Indices: 25648375--25648414 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25648365 GATGTGTGCT
* * *
25648375 TTTGTCCTATCTCCTATC
1 TTTGTCCAAACTCCTATA
25648393 TTTGTCCAAACTCCTATA
1 TTTGTCCAAACTCCTATA
25648411 TTTG
1 TTTG
25648415 AACTTCTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTGTCCAAACTCCTATA
Found at i:25650499 original size:12 final size:12
Alignment explanation
Indices: 25650461--25650502 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
25650451 ATTGGTCATA
25650461 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
25650473 GAGGGATATT-TG
1 GAGAGAT-TTGAG
25650485 GAGAGATTTGAG
1 GAGAGATTTGAG
25650497 GAGAGA
1 GAGAGA
25650503 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:25650509 original size:24 final size:24
Alignment explanation
Indices: 25650461--25650507 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
25650451 ATTGGTCATA
*
25650461 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
25650485 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
25650508 GGGATTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:25651207 original size:27 final size:27
Alignment explanation
Indices: 25651173--25651395 Score: 277
Period size: 27 Copynumber: 8.3 Consensus size: 27
25651163 AGAGGTCGAT
*
25651173 AAATGATCGAAATACCCCCATAGGATA
1 AAATGATCGAAATACCCCCATAGGGTA
*
25651200 AAATGATCGAAATACCCCCATAAGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
25651227 AAATGATCGAAATACCTCAATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
25651254 AAATGATTGAAATACCCCCATAGTGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
25651281 AAATGACCGAAATA-CCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
25651307 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * *
25651334 GAATGACCAAAATACCCCTAATAGGGTA
1 AAATGATCGAAATACCCC-CATAGGGTA
* * * *
25651362 AAATGACCAAAATAACCCCATAAGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
25651389 AAATGAT
1 AAATGAT
25651396 TTTTATACCC
Statistics
Matches: 174, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 24 0.14
27 126 0.72
28 24 0.14
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:25651808 original size:28 final size:28
Alignment explanation
Indices: 25651763--25651910 Score: 192
Period size: 28 Copynumber: 5.3 Consensus size: 28
25651753 TGCACTGCAT
25651763 TGTTACTGTATTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
*
25651791 TGATT-CTGTACTGGGCTAAGGCCCACAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
* * * *
25651819 TGATT-TTGTATTGGGCTAAGTCTCATAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
*
25651847 TGTTACTGTATTGGGCTAAGGCCCACAT
1 TGTTACTGTATTGGGCTAAGGCCCACAC
* *
25651875 TGTTACTGTATTAGGCTAAGGCCCAGAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
25651903 TGTTACTG
1 TGTTACTG
25651911 CATGTTGTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
27 2 0.02
28 100 0.96
29 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:25651924 original size:14 final size:14
Alignment explanation
Indices: 25651905--25651942 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
25651895 GCCCAGACTG
* *
25651905 TTACTGCATGTTGT
1 TTACTGAATGCTGT
25651919 TTACTGAATGCTGT
1 TTACTGAATGCTGT
25651933 TTACTGAATG
1 TTACTGAATG
25651943 ACTGATAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (14 bp):
TTACTGAATGCTGT
Found at i:25653645 original size:7 final size:7
Alignment explanation
Indices: 25653633--25653658 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25653623 ATATTTTAAT
25653633 TTTAAAA
1 TTTAAAA
25653640 TTTAAAA
1 TTTAAAA
25653647 TTTAAAA
1 TTTAAAA
25653654 TTTAA
1 TTTAA
25653659 TTTCTAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:25663672 original size:20 final size:21
Alignment explanation
Indices: 25663626--25663672 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
25663616 TTATAGAGTT
*
25663626 ATAAAAACTAAAAATAATTAA
1 ATAAAAACTAAAAATAATGAA
*
25663647 AGAAAAA-T-AAAATAAATGAA
1 ATAAAAACTAAAAAT-AATGAA
25663667 ATAAAA
1 ATAAAA
25663673 TATCAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.23
20 11 0.50
21 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (21 bp):
ATAAAAACTAAAAATAATGAA
Found at i:25681642 original size:13 final size:13
Alignment explanation
Indices: 25681626--25681655 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25681616 ATATAACTGA
25681626 TTCATATAGCCAT
1 TTCATATAGCCAT
*
25681639 TTCATATAGTCAT
1 TTCATATAGCCAT
25681652 TTCA
1 TTCA
25681656 AAGTGCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:25681644 original size:26 final size:25
Alignment explanation
Indices: 25681584--25681646 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
25681574 TCCATGTAAT
*
25681584 CATTTCATATAACACTTCATATAAT
1 CATTTCATATAACACTTCATATAAC
* *
25681609 TATTTCCATATAACTGA-TTCATATAGC
1 CATTT-CATATAAC--ACTTCATATAAC
25681636 CATTTCATATA
1 CATTTCATATA
25681647 GTCATTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.13
26 14 0.45
27 12 0.39
28 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (25 bp):
CATTTCATATAACACTTCATATAAC
Found at i:25686361 original size:19 final size:19
Alignment explanation
Indices: 25686337--25686375 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
25686327 AAATTAGCGG
25686337 TAATTATCGACTT-AGTTAA
1 TAATTA-CGACTTCAGTTAA
*
25686356 TAATTACTACTTCAGTTAA
1 TAATTACGACTTCAGTTAA
25686375 T
1 T
25686376 TCTAGGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (19 bp):
TAATTACGACTTCAGTTAA
Found at i:25692500 original size:437 final size:437
Alignment explanation
Indices: 25691686--25692560 Score: 1750
Period size: 437 Copynumber: 2.0 Consensus size: 437
25691676 TCGAGTTAAA
25691686 ACCATTACAGTTAGTTAGCTTTTATTTAATTCGGAAAAAAATAAGTACTAGTTGATTTGATTTAA
1 ACCATTACAGTTAGTTAGCTTTTATTTAATTCGGAAAAAAATAAGTACTAGTTGATTTGATTTAA
25691751 AACTTGTCTCTTAGCAGAAGATTATGTAACCAATTCATTTAGGGAAAATCATTTCTATTTACGAA
66 AACTTGTCTCTTAGCAGAAGATTATGTAACCAATTCATTTAGGGAAAATCATTTCTATTTACGAA
25691816 AACCTTAGTTTTTAGAAAAACCTTGTTTTGTTTAGTTGCAGTTTAAAAAAATCCATAAAAACAGT
131 AACCTTAGTTTTTAGAAAAACCTTGTTTTGTTTAGTTGCAGTTTAAAAAAATCCATAAAAACAGT
25691881 ATAAAGTCTCAAATTTAAAGACAACCAGTCCATAGTCCAAAAGTTACATAAAAAACCCTAAATAA
196 ATAAAGTCTCAAATTTAAAGACAACCAGTCCATAGTCCAAAAGTTACATAAAAAACCCTAAATAA
25691946 GTAATAAATTCTAGACATTAACATAAAACAGTCTAAAATTTATGTGTGGCCACCGTCGAGTCCTC
261 GTAATAAATTCTAGACATTAACATAAAACAGTCTAAAATTTATGTGTGGCCACCGTCGAGTCCTC
25692011 CGCTGTACTGACCTGTCAAATCTAGGGATTACCTGTACAGATTAAACAGAAAAGGGTGAGTTTTT
326 CGCTGTACTGACCTGTCAAATCTAGGGATTACCTGTACAGATTAAACAGAAAAGGGTGAGTTTTT
25692076 GCAAACTCAATGTGTAACCCCCACAGAAAACATGCATACATATATTC
391 GCAAACTCAATGTGTAACCCCCACAGAAAACATGCATACATATATTC
25692123 ACCATTACAGTTAGTTAGCTTTTATTTAATTCGGAAAAAAATAAGTACTAGTTGATTTGATTTAA
1 ACCATTACAGTTAGTTAGCTTTTATTTAATTCGGAAAAAAATAAGTACTAGTTGATTTGATTTAA
25692188 AACTTGTCTCTTAGCAGAAGATTATGTAACCAATTCATTTAGGGAAAATCATTTCTATTTACGAA
66 AACTTGTCTCTTAGCAGAAGATTATGTAACCAATTCATTTAGGGAAAATCATTTCTATTTACGAA
25692253 AACCTTAGTTTTTAGAAAAACCTTGTTTTGTTTAGTTGCAGTTTAAAAAAATCCATAAAAACAGT
131 AACCTTAGTTTTTAGAAAAACCTTGTTTTGTTTAGTTGCAGTTTAAAAAAATCCATAAAAACAGT
25692318 ATAAAGTCTCAAATTTAAAGACAACCAGTCCATAGTCCAAAAGTTACATAAAAAACCCTAAATAA
196 ATAAAGTCTCAAATTTAAAGACAACCAGTCCATAGTCCAAAAGTTACATAAAAAACCCTAAATAA
25692383 GTAATAAATTCTAGACATTAACATAAAACAGTCTAAAATTTATGTGTGGCCACCGTCGAGTCCTC
261 GTAATAAATTCTAGACATTAACATAAAACAGTCTAAAATTTATGTGTGGCCACCGTCGAGTCCTC
25692448 CGCTGTACTGACCTGTCAAATCTAGGGATTACCTGTACAGATTAAACAGAAAAGGGTGAGTTTTT
326 CGCTGTACTGACCTGTCAAATCTAGGGATTACCTGTACAGATTAAACAGAAAAGGGTGAGTTTTT
25692513 GCAAACTCAATGTGTAACCCCCACAGAAAACATGCATACATATATTC
391 GCAAACTCAATGTGTAACCCCCACAGAAAACATGCATACATATATTC
25692560 A
1 A
25692561 ACAACATTCA
Statistics
Matches: 438, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
437 438 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (437 bp):
ACCATTACAGTTAGTTAGCTTTTATTTAATTCGGAAAAAAATAAGTACTAGTTGATTTGATTTAA
AACTTGTCTCTTAGCAGAAGATTATGTAACCAATTCATTTAGGGAAAATCATTTCTATTTACGAA
AACCTTAGTTTTTAGAAAAACCTTGTTTTGTTTAGTTGCAGTTTAAAAAAATCCATAAAAACAGT
ATAAAGTCTCAAATTTAAAGACAACCAGTCCATAGTCCAAAAGTTACATAAAAAACCCTAAATAA
GTAATAAATTCTAGACATTAACATAAAACAGTCTAAAATTTATGTGTGGCCACCGTCGAGTCCTC
CGCTGTACTGACCTGTCAAATCTAGGGATTACCTGTACAGATTAAACAGAAAAGGGTGAGTTTTT
GCAAACTCAATGTGTAACCCCCACAGAAAACATGCATACATATATTC
Found at i:25700532 original size:27 final size:27
Alignment explanation
Indices: 25700502--25700591 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
25700492 TATAACAGTC
25700502 ATTTTACCCTATGGGGGTATTTCGGTA
1 ATTTTACCCTATGGGGGTATTTCGGTA
**
25700529 ATTTTACCC-ATCGAAGGTATTGT-GGTA
1 ATTTTACCCTAT-GGGGGTATT-TCGGTA
* *
25700556 AATTTACCCTTTGGGGGTATTTCGGTA
1 ATTTTACCCTATGGGGGTATTTCGGTA
25700583 ATTTTACCC
1 ATTTTACCC
25700592 ATCAAGGGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.06
27 47 0.90
28 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTA
Found at i:25700600 original size:27 final size:27
Alignment explanation
Indices: 25700516--25700606 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
25700506 TACCCTATGG
25700516 GGGTATTTCGGTAATTTTACCCATCGAA
1 GGGTATTTCGGTAATTTTACCCATC-AA
* * ***
25700544 -GGTATTGT-GGTAAATTTACCCTTTGG
1 GGGTATT-TCGGTAATTTTACCCATCAA
25700570 GGGTATTTCGGTAATTTTACCCATCAA
1 GGGTATTTCGGTAATTTTACCCATCAA
25700597 GGGTATTTCG
1 GGGTATTTCG
25700607 ATCATTTAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.02
27 48 0.96
28 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCATCAA
Found at i:25701903 original size:18 final size:18
Alignment explanation
Indices: 25701869--25701904 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25701859 GAAATGGGAC
**
25701869 GAGAAAGGAAAGGAAATG
1 GAGAAAGGAAAAAAAATG
25701887 GAGAAAGGAAAAAAAATG
1 GAGAAAGGAAAAAAAATG
25701905 ATGAGTAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (18 bp):
GAGAAAGGAAAAAAAATG
Found at i:25703228 original size:25 final size:25
Alignment explanation
Indices: 25703177--25703256 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
25703167 TATCGATTTT
* *
25703177 AGCTCTTATTAGCTTACCGA-TAATC
1 AGCTCATATGAGCTTACC-ATTAATC
*
25703202 AGCTCATATGAGCTTACCATTATTC
1 AGCTCATATGAGCTTACCATTAATC
* *
25703227 AGCTCAGAGGAGCTTACCATTAATC
1 AGCTCATATGAGCTTACCATTAATC
25703252 AGCTC
1 AGCTC
25703257 GGAGGAGCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
24 1 0.02
25 47 0.98
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (25 bp):
AGCTCATATGAGCTTACCATTAATC
Found at i:25703261 original size:25 final size:25
Alignment explanation
Indices: 25703187--25703269 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
25703177 AGCTCTTATT
* *
25703187 AGCTTACCGA-TAATCAGCTCATATG
1 AGCTTACC-ATTAATCAGCTCAGAGG
*
25703212 AGCTTACCATTATTCAGCTCAGAGG
1 AGCTTACCATTAATCAGCTCAGAGG
*
25703237 AGCTTACCATTAATCAGCTCGGAGG
1 AGCTTACCATTAATCAGCTCAGAGG
25703262 AGCTTACC
1 AGCTTACC
25703270 GTTTACAGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 1 0.02
25 51 0.98
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (25 bp):
AGCTTACCATTAATCAGCTCAGAGG
Found at i:25706930 original size:25 final size:25
Alignment explanation
Indices: 25706900--25706948 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
25706890 GTGTAAGGAT
25706900 TCAAACATTATACCAAAGGGTAAGG
1 TCAAACATTATACCAAAGGGTAAGG
25706925 TCAAACATTATACCAAAGGGTAAG
1 TCAAACATTATACCAAAGGGTAAG
25706949 TTGACTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (25 bp):
TCAAACATTATACCAAAGGGTAAGG
Found at i:25710887 original size:14 final size:14
Alignment explanation
Indices: 25710868--25710907 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
25710858 GATTCAAAGA
25710868 TAAATAAAATATCC
1 TAAATAAAATATCC
25710882 TAAATAAAATATCC
1 TAAATAAAATATCC
*
25710896 CAAATAAAATAT
1 TAAATAAAATAT
25710908 ATTAATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATAAAATATCC
Found at i:25712230 original size:30 final size:30
Alignment explanation
Indices: 25712196--25712257 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
25712186 CTTTACTTTA
*
25712196 AACTTCTCAATATGACCATTTAAAGAGTTG
1 AACTTCTCAATATGACCAGTTAAAGAGTTG
**
25712226 AACTTCTCAATATGACTGGTTAAAGAGTTG
1 AACTTCTCAATATGACCAGTTAAAGAGTTG
25712256 AA
1 AA
25712258 GAATCCTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (30 bp):
AACTTCTCAATATGACCAGTTAAAGAGTTG
Found at i:25718893 original size:21 final size:21
Alignment explanation
Indices: 25718860--25718905 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25718850 TTTTCGATTC
* *
25718860 TTTT-CTCTCTTTCAATTTTT
1 TTTTCCTCTCTTTCAATCTCT
*
25718880 TTTTCCTCTTTTTCAATCTCT
1 TTTTCCTCTCTTTCAATCTCT
25718901 TTTTC
1 TTTTC
25718906 TTTTTCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTCCTCTCTTTCAATCTCT
Found at i:25722983 original size:40 final size:40
Alignment explanation
Indices: 25722939--25723018 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
25722929 TGTTCGAATC
25722939 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
1 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
25722979 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
1 CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
25723019 TTATTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (40 bp):
CCTTTGAGTGTTTTTTATATTTATTTGTTTTTATGTTGTT
Found at i:25725779 original size:27 final size:27
Alignment explanation
Indices: 25725749--25725828 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
25725739 GAATTTGAGT
25725749 ATTATTATTATGAGATTATTATAAAAG
1 ATTATTATTATGAGATTATTATAAAAG
* ** *
25725776 ATTATAAGCAT--GA--ATT-T--GAG
1 ATTATTATTATGAGATTATTATAAAAG
25725796 TATTATTATTATGAGATTATTATAAAAG
1 -ATTATTATTATGAGATTATTATAAAAG
25725824 ATTAT
1 ATTAT
25725829 AAGCATGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 16
0.61 0.13 0.26
Matches are distributed among these distances:
20 2 0.05
21 8 0.22
22 1 0.03
23 5 0.14
25 5 0.14
26 1 0.03
27 13 0.35
28 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.44
Consensus pattern (27 bp):
ATTATTATTATGAGATTATTATAAAAG
Found at i:25725793 original size:48 final size:48
Alignment explanation
Indices: 25725722--25725861 Score: 280
Period size: 48 Copynumber: 2.9 Consensus size: 48
25725712 AAAATAAAAT
25725722 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
1 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
25725770 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
1 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
25725818 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATT
1 TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATT
25725862 GGTATTGATA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (48 bp):
TAAAAGATTATAAGCATGAATTTGAGTATTATTATTATGAGATTATTA
Found at i:25725836 original size:27 final size:27
Alignment explanation
Indices: 25725758--25725836 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
25725748 TATTATTATT
25725758 ATGAGATTATTATAAAAGATTATAAGC
1 ATGAGATTATTATAAAAGATTATAAGC
* * **
25725785 AT--GA--ATT-T--GAGTATTATTATT
1 ATGAGATTATTATAAAAG-ATTATAAGC
25725806 ATGAGATTATTATAAAAGATTATAAGC
1 ATGAGATTATTATAAAAGATTATAAGC
25725833 ATGA
1 ATGA
25725837 ATTTGAGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 16
0.60 0.13 0.27
Matches are distributed among these distances:
20 2 0.06
21 8 0.22
22 1 0.03
23 5 0.14
25 5 0.14
26 1 0.03
27 12 0.33
28 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (27 bp):
ATGAGATTATTATAAAAGATTATAAGC
Found at i:25735281 original size:25 final size:26
Alignment explanation
Indices: 25735239--25735287 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
25735229 AGTTGTAAAT
25735239 TAGAAAAATATCTCTAGA-AATTTTC
1 TAGAAAAATATCTCTAGAGAATTTTC
* * *
25735264 TAGAATAATCTCTTTAGAGAATTT
1 TAGAAAAATATCTCTAGAGAATTT
25735288 CTCTTTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (26 bp):
TAGAAAAATATCTCTAGAGAATTTTC
Found at i:25751031 original size:21 final size:21
Alignment explanation
Indices: 25750984--25751032 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25750974 CAACACGCTT
*
25750984 GTGTGGGAGGAGGCACACGACT
1 GTGT-GGAGGAGGCACACGACC
* * *
25751006 ATGTGGATGAGGCACACGCCC
1 GTGTGGAGGAGGCACACGACC
25751027 GTGTGG
1 GTGTGG
25751033 GCCAAGGACA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.16
Consensus pattern (21 bp):
GTGTGGAGGAGGCACACGACC
Found at i:25757244 original size:20 final size:18
Alignment explanation
Indices: 25757197--25757245 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
25757187 CAAGATAAAC
25757197 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
25757214 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
25757234 ATTAAATTAATA
1 ATTAAATTAATA
25757246 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:25758065 original size:35 final size:35
Alignment explanation
Indices: 25758019--25758088 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
25758009 CATTAACTCT
*
25758019 TTAATTGAGCTATGGATTCCACTGTTGCTAGTAAA
1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
25758054 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
25758089 GTCATGCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (35 bp):
TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA
Found at i:25760855 original size:51 final size:50
Alignment explanation
Indices: 25760724--25760874 Score: 196
Period size: 50 Copynumber: 3.0 Consensus size: 50
25760714 GTGAAAGTGA
* * * *
25760724 AAGTGATGGTCACGTGTGTAGTACTATGTGCATGCTACTACGTGTACCAG
1 AAGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
* * *
25760774 AA-TAATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
1 AAGTGAT-GGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
* *
25760824 ATAGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTATGTGAATCGG
1 A-AGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
25760875 TATCATTAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.03
50 41 0.47
51 40 0.46
52 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
AAGTGATGGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTATCGG
Found at i:25760868 original size:26 final size:26
Alignment explanation
Indices: 25760787--25760868 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
25760777 AATAGGTCGC
*
25760787 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGCAAGCTACT
* * * *
25760813 ACGTGTA-T-CGGATAGTG-ATGGTCAC-
1 ATGTGTAGTAC-TAT-GTGCAAGCT-ACT
25760838 ATGTGTAGTACTATGTGCAAGCTACT
1 ATGTGTAGTACTATGTGCAAGCTACT
25760864 ATGTG
1 ATGTG
25760869 AATCGGTATC
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGCAAGCTACT
Found at i:25761113 original size:16 final size:16
Alignment explanation
Indices: 25761092--25761123 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25761082 TGATTGAAAG
*
25761092 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
25761108 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
25761124 ACAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:25768025 original size:19 final size:20
Alignment explanation
Indices: 25767981--25768025 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
25767971 ATAATATAGT
*
25767981 TATATTTAAAAATTAAAATA
1 TATATTCAAAAATTAAAATA
25768001 TATATTCAAAAATTAAAATA
1 TATATTCAAAAATTAAAATA
25768021 T-TATT
1 TATATT
25768026 ATTGTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATTCAAAAATTAAAATA
Found at i:25768725 original size:31 final size:31
Alignment explanation
Indices: 25768660--25768734 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
25768650 TACAAAATCA
*
25768660 TCACTAAATTATTTGAAAATTTTCATTTAAG
1 TCACTAAATTATTTGAAAATTTTCATTCAAG
* * *
25768691 TCACTGAATTATTTGAAAATTTTTATTCATG
1 TCACTAAATTATTTGAAAATTTTCATTCAAG
* *
25768722 TCACCAAACTATT
1 TCACTAAATTATT
25768735 AAGTTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (31 bp):
TCACTAAATTATTTGAAAATTTTCATTCAAG
Found at i:25769135 original size:3 final size:3
Alignment explanation
Indices: 25769127--25769162 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
25769117 AGGTTACCTC
25769127 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25769163 CCAAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25771046 original size:50 final size:50
Alignment explanation
Indices: 25770987--25771155 Score: 230
Period size: 50 Copynumber: 3.4 Consensus size: 50
25770977 GGTCTTACGG
*
25770987 GGTCTTACATGGGACCTTTCATCTCGGTGCCAACGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
* ** * *
25771037 GGTCTTACATGAGACCTCTCATCTCGGTGTTATCGCCATGTCCAAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
* ** *
25771087 GGTCTTATATGGGACCTCTCATCTCGGTGCCAATTCCATGTCCCATACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
* *
25771137 GGTATTACATGGGATCTCT
1 GGTCTTACATGGGACCTCT
25771156 TTACCCAAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 101 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (50 bp):
GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
Found at i:25773987 original size:20 final size:20
Alignment explanation
Indices: 25773959--25774011 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
25773949 TTAACTTTTG
* *
25773959 GAATCATAAAAATCCAACAA
1 GAATTATAAAAATCCAAAAA
* * *
25773979 GAATTATAAGATTTCAAAAA
1 GAATTATAAAAATCCAAAAA
*
25773999 GAATTCTAAAAAT
1 GAATTATAAAAAT
25774012 AGTCAATTTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (20 bp):
GAATTATAAAAATCCAAAAA
Found at i:25776520 original size:18 final size:18
Alignment explanation
Indices: 25776497--25776541 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
25776487 TCAATCATCT
25776497 ACACCGATGCAAGAATCA
1 ACACCGATGCAAGAATCA
*
25776515 ACACCGATGCAAGAATCG
1 ACACCGATGCAAGAATCA
*
25776533 ATACCGATG
1 ACACCGATG
25776542 GTCCCACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (18 bp):
ACACCGATGCAAGAATCA
Found at i:25779973 original size:23 final size:23
Alignment explanation
Indices: 25779947--25779992 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25779937 AATTGTTAAC
* * *
25779947 TTTACATCTCAAAAATTATAAAT
1 TTTACATATAAAAAATTAAAAAT
*
25779970 TTTATATATAAAAAATTAAAAAT
1 TTTACATATAAAAAATTAAAAAT
25779993 ATATATAGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTACATATAAAAAATTAAAAAT
Found at i:25779997 original size:22 final size:23
Alignment explanation
Indices: 25779957--25779999 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
25779947 TTTACATCTC
* *
25779957 AAAAATTATAAATTTTATATATA
1 AAAAATTATAAAATATATATATA
25779980 AAAAATTA-AAAATATATATA
1 AAAAATTATAAAATATATATA
25780000 GCAAACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATTATAAAATATATATATA
Found at i:25780103 original size:18 final size:18
Alignment explanation
Indices: 25780063--25780108 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
25780053 CTAATTTTAA
**
25780063 AAAATAAAACCCTAACTT
1 AAAATAAAACCCTAACCC
25780081 AAAATAAAACCCTAACCC
1 AAAATAAAACCCTAACCC
*
25780099 GAAATAAAAC
1 AAAATAAAAC
25780109 TTTACACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.59, C:0.24, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAATAAAACCCTAACCC
Found at i:25783160 original size:28 final size:28
Alignment explanation
Indices: 25783115--25783492 Score: 173
Period size: 28 Copynumber: 13.6 Consensus size: 28
25783105 GGGTGTTACA
* *
25783115 GTACCCATCCACGATACAACTCCTAAAG
1 GTACCCATCCATGGTACAACTCCTAAAG
*
25783143 GTACCCATCCATGGTACAACTCCTAATG
1 GTACCCATCCATGGTACAACTCCTAAAG
* *
25783171 GTACCCATCCACGATACAACT-CTGAAAG
1 GTACCCATCCATGGTACAACTCCT-AAAG
* ** * *
25783199 GTACCTATCCATGGTATGACTTCTAACG
1 GTACCCATCCATGGTACAACTCCTAAAG
*
25783227 GTA-CCATCCA-CG-ACATGACTCCTAATA-
1 GTACCCATCCATGGTACA--ACTCCTAA-AG
* *** * *
25783254 GTAGCCATCCACAATAAAACTCCTAATG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * **
25783282 GTTCCCCTCCATGGTACAACTCCTAGTG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * *
25783310 GTATCCATCTA-CG-ACATGACTCCTAAAG
1 GTACCCATCCATGGTACA--ACTCCTAAAG
* ** *
25783338 GTACCTATCCATGGTATGACTCATAATA-
1 GTACCCATCCATGGTACAACTCCTAA-AG
** * ** *
25783366 GTATTCATCCATGGCATGACTCCTATAG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * * **
25783394 GTACCTACCCACGGTATGACTCCTAAAG
1 GTACCCATCCATGGTACAACTCCTAAAG
* * * * *
25783422 GTACGCATCTACGGTAAAACTCCTAATG
1 GTACCCATCCATGGTACAACTCCTAAAG
* ** *
25783450 GTACCTATCCACT-ACACAACTCTTAAAG
1 GTACCCATCCA-TGGTACAACTCCTAAAG
*
25783478 GTA-TCATCCATGGTA
1 GTACCCATCCATGGTA
25783493 TGGCTCCTAA
Statistics
Matches: 256, Mismatches: 77, Indels: 35
0.70 0.21 0.10
Matches are distributed among these distances:
25 1 0.00
26 5 0.02
27 26 0.10
28 217 0.85
29 4 0.02
30 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (28 bp):
GTACCCATCCATGGTACAACTCCTAAAG
Found at i:25783183 original size:56 final size:56
Alignment explanation
Indices: 25783115--25783529 Score: 257
Period size: 56 Copynumber: 7.4 Consensus size: 56
25783105 GGGTGTTACA
*
25783115 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATG
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* * * *
25783171 GTACCCATCCACGATACAACT-CTGAAAGGTACCTATCCATGGTATGACTTCTAACG
1 GTACCCATCCACGATACAACTCCT-AAAGGTACCCATCCATGGTATAACTCCTAATG
* ** * *** *
25783227 GTA-CCATCCACGACATGACTCCTAATA-GTAGCCATCCACAATAAAACTCCTAATG
1 GTACCCATCCACGATACAACTCCTAA-AGGTACCCATCCATGGTATAACTCCTAATG
* * * * ** * * * ** * *
25783282 GTTCCCCTCCATGGTACAACTCCTAGTGGTATCCATCTACGACATGACTCCTAAAG
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* * * ** * ** * *
25783338 GTACCTATCCATGGTATGACTCATAATA-GTATTCATCCATGGCATGACTCCT-ATAG
1 GTACCCATCCACGATACAACTCCTAA-AGGTACCCATCCATGGTATAACTCCTAAT-G
* * * ** * * * *
25783394 GTACCTACCCACGGTATGACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATG
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* * * * * ** *
25783450 GTACCTATCCACTACACAACTCTTAAAGGTA-TCATCCATGGTATGGCTCCTAATA
1 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
* *
25783505 GTACCCCTCCACGATACGACTCCTA
1 GTACCCATCCACGATACAACTCCTA
25783530 TTGGCACTCA
Statistics
Matches: 274, Mismatches: 76, Indels: 19
0.74 0.21 0.05
Matches are distributed among these distances:
55 77 0.28
56 195 0.71
57 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (56 bp):
GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTATAACTCCTAATG
Found at i:25783262 original size:83 final size:84
Alignment explanation
Indices: 25783115--25783348 Score: 217
Period size: 83 Copynumber: 2.8 Consensus size: 84
25783105 GGGTGTTACA
* * * * * *
25783115 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTACA--ACTCCTAATGGTACCCA
1 GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCA-CG-ACATGACTCCTAATAGTACCCA
* *
25783178 TCCACGATACAACT-CTGAAAG
64 TCCACAATAAAACTCCT-AAAG
* ** * *
25783199 GTACCTATCCATGGTATGACTTCTAACGGTA-CCATCCACGACATGACTCCTAATAGTAGCCATC
1 GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCACGACATGACTCCTAATAGTACCCATC
*
25783263 CACAATAAAACTCCTAATG
66 CACAATAAAACTCCTAAAG
* * ** * *
25783282 GTTCCCCTCCATGGTACAACTCCTAGTGGTATCCATCTACGACATGACTCCTAA-AGGTACCTAT
1 GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCACGACATGACTCCTAATA-GTACCCAT
25783346 CCA
65 CCA
25783349 TGGTATGACT
Statistics
Matches: 121, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
81 3 0.02
82 1 0.01
83 61 0.50
84 56 0.46
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.24
Consensus pattern (84 bp):
GTACCCATCCATGGTACAACTCCTAACGGTATCCATCCACGACATGACTCCTAATAGTACCCATC
CACAATAAAACTCCTAAAG
Found at i:25783460 original size:84 final size:83
Alignment explanation
Indices: 25783161--25783460 Score: 245
Period size: 84 Copynumber: 3.6 Consensus size: 83
25783151 CCATGGTACA
* * * * *
25783161 ACTCCTAATGGTACCCATCCACGATACAACT-CTGAAAGGTACCTATCCATGGTATGACTTCTA-
1 ACTCCTAAAGGTACGCATCCACGATAAAACTCCT-AATGGTACCTATCCATGGTATGACTCCTAT
25783224 ACGGTACCATCCACGACATG
65 A-GGTACCATCCACGACATG
* * ** **
25783244 ACTCCTAATA-GTA-GCCATCCACAATAAAACTCCTAATGGTTCCCCTCCATGGTACAACTCCTA
1 ACTCCTAA-AGGTACG-CATCCACGATAAAACTCCTAATGGTACCTATCCATGGTATGACTCCTA
*
25783307 GT-GGTATCCATCTACGACATG
64 -TAGGTA-CCATCCACGACATG
* * ** * * * *
25783328 ACTCCTAAAGGTAC-CTATCCATGGTATGACTCATAATAGTA-TTCATCCATGGCATGACTCCTA
1 ACTCCTAAAGGTACGC-ATCCACGATAAAACTCCTAATGGTACCT-ATCCATGGTATGACTCCTA
* **
25783391 TAGGTACCTACCCACGGTATG
64 TAGGTACC-ATCCACGACATG
* *
25783412 ACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATGGTACCTATCCA
1 ACTCCTAAAGGTACGCATCCACGATAAAACTCCTAATGGTACCTATCCA
25783461 CTACACAACT
Statistics
Matches: 166, Mismatches: 37, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
83 56 0.34
84 108 0.65
85 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (83 bp):
ACTCCTAAAGGTACGCATCCACGATAAAACTCCTAATGGTACCTATCCATGGTATGACTCCTATA
GGTACCATCCACGACATG
Found at i:25783530 original size:139 final size:138
Alignment explanation
Indices: 25783115--25783591 Score: 458
Period size: 139 Copynumber: 3.4 Consensus size: 138
25783105 GGGTGTTACA
* **
25783115 GTACCCATCCACGATACAACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCCATC
1 GTACCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCATC
* * * **
25783180 CACGATACAACTCTGAAAGGTACCTATCCATGGTATGACTTCTAACGGTACCATCCACGACATGA
65 CACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGACATGA
25783245 CTCCTAATA-
130 CTCCT-ATAG
* ** * * * *
25783254 GTAGCC-ATCCACAATAAAACTCCTAATGGTTCCCCTCCATGGTACAACTCCTAGTGGTATCCAT
1 GTA-CCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCAT
* ** * * * * *
25783318 CTACGACATGACTCCTAAAGGTACCTATCCATGGTATGACTCATAATAGTATTCATCCATGGCAT
64 CCACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCACGACAT
25783383 GACTCCTATAG
128 GACTCCTATAG
* * * * * *
25783394 GTACCTACCCACGGTATGACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATGGTACCTATC
1 GTACCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACC-ATC
* * * * * *
25783459 CACTACACAACTCTTAAAGGTATC-ATCCATGGTATGGCTCCTAATAGTACCCCTCCACGATACG
65 CACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCACGACATG
*
25783523 ACTCCTATTG
129 ACTCCTATAG
* * * * * ** *
25783533 GCA-CTCATCCACGATATGACTCTTAAAGGTATCTATCTATTATACAACTCCTACTGGTA
1 GTACCT-ATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA
25783592 TTCTTTACGG
Statistics
Matches: 271, Mismatches: 61, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
138 2 0.01
139 186 0.69
140 83 0.31
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (138 bp):
GTACCTATCCACGATATGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCATCC
ACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGACATGAC
TCCTATAG
Found at i:25786254 original size:30 final size:30
Alignment explanation
Indices: 25786219--25786278 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
25786209 CTAAACTTAA
25786219 ATAAACTCTAATCACTTAATTAGAAAACAT
1 ATAAACTCTAATCACTTAATTAGAAAACAT
25786249 ATAAACTCTAATCACTTAATTAGAAAACAT
1 ATAAACTCTAATCACTTAATTAGAAAACAT
25786279 GAAAGAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (30 bp):
ATAAACTCTAATCACTTAATTAGAAAACAT
Found at i:25794866 original size:27 final size:27
Alignment explanation
Indices: 25794811--25794867 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
25794801 ATATACAATG
*
25794811 TATTGAATGAATGTGAAAATGATTATAT
1 TATTGAATGAATGT-AAAATGATGATAT
*
25794839 TATTGAATGATATGT-ATATGATGATAT
1 TATTGAATGA-ATGTAAAATGATGATAT
25794866 TA
1 TA
25794868 CAATATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
28 10 0.38
29 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (27 bp):
TATTGAATGAATGTAAAATGATGATAT
Found at i:25802567 original size:9 final size:9
Alignment explanation
Indices: 25802555--25802617 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
25802545 ATATTAAAAG
25802555 TGAGAGAGT
1 TGAGAGAGT
*
25802564 TGAGAGACT
1 TGAGAGAGT
*
25802573 TGAGAGTGTT
1 TGAGAGAG-T
*
25802583 TGAGAGAATT
1 TGAGAG-AGT
* *
25802593 TGAAAGAAT
1 TGAGAGAGT
25802602 TGAGAGAGT
1 TGAGAGAGT
25802611 TGAGAGA
1 TGAGAGA
25802618 AGGATGTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 30 0.70
10 13 0.30
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.25
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:25808560 original size:13 final size:13
Alignment explanation
Indices: 25808525--25808563 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 13
25808515 AATCTCGAAA
25808525 CCAAAATACTTAC
1 CCAAAATACTTAC
25808538 CCATAAAATACTTAC
1 CC--AAAATACTTAC
25808553 CCAAAATACTT
1 CCAAAATACTT
25808564 CAAATAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (13 bp):
CCAAAATACTTAC
Found at i:25820406 original size:49 final size:49
Alignment explanation
Indices: 25820344--25820452 Score: 157
Period size: 49 Copynumber: 2.2 Consensus size: 49
25820334 TTGTAGGCCG
* * *
25820344 TGTGGGTAAGCCTTGTAGGACACACGATCC-TTTGAAATAATGCAAGCCA
1 TGTGGGTAGGCCTTGTAGGACACACG-GCCGTTTGAAATAAAGCAAGCCA
* *
25820393 TGTGGGTAGGCCTTGTAGGGCACATGGCCGTTTGAAATAAAGCAAGCCA
1 TGTGGGTAGGCCTTGTAGGACACACGGCCGTTTGAAATAAAGCAAGCCA
25820442 TGTGGGTAGGC
1 TGTGGGTAGGC
25820453 GTGTGGGGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
48 2 0.04
49 52 0.96
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (49 bp):
TGTGGGTAGGCCTTGTAGGACACACGGCCGTTTGAAATAAAGCAAGCCA
Found at i:25821176 original size:27 final size:28
Alignment explanation
Indices: 25821138--25821198 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
25821128 TTGCATGATA
*
25821138 TGATATGTTATGATTTATAATATG-TTT
1 TGATATGGTATGATTTATAATATGCTTT
25821165 TGATATGGTATGATTTATAATATGCTTT
1 TGATATGGTATGATTTATAATATGCTTT
25821193 T-ATATG
1 TGATATG
25821199 TTAAGATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.52
Consensus pattern (28 bp):
TGATATGGTATGATTTATAATATGCTTT
Found at i:25821666 original size:11 final size:11
Alignment explanation
Indices: 25821650--25821674 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25821640 AACCCTTAAG
25821650 TGTTTTTTTTT
1 TGTTTTTTTTT
25821661 TGTTTTTTTTT
1 TGTTTTTTTTT
25821672 TGT
1 TGT
25821675 AAATAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:25822191 original size:87 final size:87
Alignment explanation
Indices: 25821993--25822183 Score: 229
Period size: 87 Copynumber: 2.2 Consensus size: 87
25821983 CAGACACTCC
* * * *
25821993 AATTTGTAGATGAACCACCAGTGTTTGCAGATAAACTATCAGTAGGTTATGAATACACAACGTGT
1 AATTTGTGGATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
* **
25822058 TTGCAAATAAAAGTTTTCAGTA
66 TTGCAAATAAAAGCTGCCAGTA
* * * * * * * *
25822080 AGTTTTTGGATGAACCACCAGTGTTTGTAGATAAATTGCCAGTAGGATGTGAGTGCACAACATGT
1 AATTTGTGGATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
*
25822145 TTGCAAATAAGAGCTGCCAGTA
66 TTGCAAATAAAAGCTGCCAGTA
*
25822167 AATTTGTGGATAAACCA
1 AATTTGTGGATGAACCA
25822184 TTAGTGTTGC
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (87 bp):
AATTTGTGGATGAACCACCAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT
TTGCAAATAAAAGCTGCCAGTA
Found at i:25825495 original size:32 final size:29
Alignment explanation
Indices: 25825430--25825499 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
25825420 TTAAAACAAT
* * *
25825430 TTTAAAACATGTATATTATTATTATTTAT
1 TTTAAAATATGTATATTATTATTACTTAA
*
25825459 TTTAAAATATTTATATTATTAATAGTACTTAA
1 TTTAAAATATGTATATTATT-AT--TACTTAA
25825491 TTTAAAATA
1 TTTAAAATA
25825500 ATAAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.53
30 2 0.06
32 14 0.41
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAAAATATGTATATTATTATTACTTAA
Found at i:25832938 original size:27 final size:26
Alignment explanation
Indices: 25832885--25832938 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
25832875 AGAACAAAAG
*
25832885 AAAGAAAGAAAAAGAAATGGTAGGAA
1 AAAGAAAGAAAAAGAAATGGTAAGAA
* **
25832911 AAAGAAACGTAAAAGAAATTTTAAGAA
1 AAAGAAA-GAAAAAGAAATGGTAAGAA
25832938 A
1 A
25832939 GAAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.20, T:0.13
Consensus pattern (26 bp):
AAAGAAAGAAAAAGAAATGGTAAGAA
Found at i:25833819 original size:29 final size:31
Alignment explanation
Indices: 25833786--25833852 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
25833776 ATAGGGATTT
25833786 GATCAAATTTG-TCGC-TCTACTATT-AAATG
1 GATCAAATTTGATC-CTTCTACTATTAAAATG
*
25833815 GATC-AATTTGATCCTTGTACTATTAAAATG
1 GATCAAATTTGATCCTTCTACTATTAAAATG
*
25833845 AATCAAAT
1 GATCAAAT
25833853 AAGACAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 7 0.22
29 14 0.44
30 8 0.25
31 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (31 bp):
GATCAAATTTGATCCTTCTACTATTAAAATG
Found at i:25834061 original size:30 final size:30
Alignment explanation
Indices: 25834027--25834105 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
25834017 ATAGACTTAT
** * *
25834027 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGATTCCATTTAATAATAGAGGGACTAAA
*
25834057 TTGA-TCCATTTAATAATAGAGGGACTAAT
1 TTGATTCCATTTAATAATAGAGGGACTAAA
25834086 TTGA-TCCAGTTTCAATAATA
1 TTGATTCCA-TTT-AATAATA
25834106 TGGGGACCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 28 0.67
30 7 0.17
31 7 0.17
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (30 bp):
TTGATTCCATTTAATAATAGAGGGACTAAA
Found at i:25834069 original size:29 final size:30
Alignment explanation
Indices: 25834036--25834112 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
25834026 TTTGATTCTT
*
25834036 TTTAATAGTATAGGGACTAAATTGATCCA-
1 TTTAATAATATAGGGACTAAATTGATCCAG
* *
25834065 TTTAATAATAGAGGGACTAATTTGATCCAG
1 TTTAATAATATAGGGACTAAATTGATCCAG
*
25834095 TTTCAATAATATGGGGAC
1 TTT-AATAATATAGGGAC
25834113 CTCCTAAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 26 0.63
30 3 0.07
31 12 0.29
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (30 bp):
TTTAATAATATAGGGACTAAATTGATCCAG
Found at i:25835607 original size:45 final size:45
Alignment explanation
Indices: 25835543--25835730 Score: 238
Period size: 45 Copynumber: 4.2 Consensus size: 45
25835533 TACTACGTGT
* * * *
25835543 ACCGGGTACCATTGATTATAAAGGCGGTTGCTGTGTACTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* *
25835588 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * *
25835633 ACCAGGTA-CTATTGATTATGAAGGTTGTTGCTATGTGCTGATTCC
1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* *
25835678 ACCGAGTATCATTGACTATAAAGGTGG-TGCTATGTGCTGA-TCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
*
25835721 ACCGTGTATC
1 ACCGGGTATC
25835731 TGTTATTCTT
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 12 0.10
44 14 0.11
45 99 0.79
46 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (45 bp):
ACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
Found at i:25837845 original size:69 final size:68
Alignment explanation
Indices: 25837735--25837869 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 68
25837725 GTTTTTGTGA
*
25837735 AATTTGTCATAAATAAGTATCTACTTCGGTGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTGG
1 AATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTGG
25837800 GGT
66 GGT
*
25837803 AATTTGTCATAAATAAGTAATCTACTTCGATGGTTAGGTGTTCTGATTGTGTGTTTAAAGTCTTG
1 AATTTGTCATAAATAAGT-ATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTG
25837868 GG
65 GG
25837870 TTCAAGTCCC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 18 0.28
69 46 0.72
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (68 bp):
AATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTTGG
GGT
Found at i:25842309 original size:18 final size:19
Alignment explanation
Indices: 25842270--25842313 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
25842260 AAATCTCTTA
*
25842270 AATTTTT-TCCTAAATTCT
1 AATTTTTATCCTAAATTAT
25842288 -ATTTTTAT-CTAAATTAT
1 AATTTTTATCCTAAATTAT
25842305 AATTTTTAT
1 AATTTTTAT
25842314 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTATCCTAAATTAT
Found at i:25842470 original size:31 final size:31
Alignment explanation
Indices: 25842435--25842493 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
25842425 TCTGTCAACT
25842435 AATTGCAAATGGTAAGAATAAATTTTAAACC
1 AATTGCAAATGGTAAGAATAAATTTTAAACC
25842466 AATTGCAAATGGTAAGAATAAATTTTAA
1 AATTGCAAATGGTAAGAATAAATTTTAA
25842494 TCTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (31 bp):
AATTGCAAATGGTAAGAATAAATTTTAAACC
Found at i:25845071 original size:42 final size:44
Alignment explanation
Indices: 25844962--25845120 Score: 121
Period size: 43 Copynumber: 3.7 Consensus size: 44
25844952 AGCTCGTACA
* * * * **
25844962 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCAAATAAT-G
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCA-AATCG
* * * * * *
25845005 ACGCCACTGTCCTAGACAGGGTCTTACACGT-AA--TCATATACG
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAAT-CG
* *
25845047 GTGCTAATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCG
* *
25845091 ATGCCAATGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAAACATGGTCTTACACG
25845121 ATATCACATT
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
40 2 0.02
41 1 0.01
42 25 0.28
43 28 0.31
44 28 0.31
45 5 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCG
Found at i:25847624 original size:3 final size:3
Alignment explanation
Indices: 25847616--25847653 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
25847606 TTCCATTTCT
25847616 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25847654 TTAGAATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25853456 original size:26 final size:26
Alignment explanation
Indices: 25853397--25853454 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
25853387 TGCAACGATC
* *
25853397 ATTTTTTAGTTACATGACTACCAACT
1 ATTTTTTAGTTACATAAATACCAACT
* *
25853423 ATTTTTTAG-TACATAAATACCGAGT
1 ATTTTTTAGTTACATAAATACCAACT
25853448 ATTTTTT
1 ATTTTTT
25853455 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (26 bp):
ATTTTTTAGTTACATAAATACCAACT
Found at i:25853775 original size:23 final size:27
Alignment explanation
Indices: 25853745--25853801 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
25853735 TTATTATTTT
25853745 TAAAATTTATT-T-AA-A-AATAAAAA
1 TAAAATTTATTATCAATATAATAAAAA
*
25853768 TAAAATTTATTATCAATATAATAAAAT
1 TAAAATTTATTATCAATATAATAAAAA
25853795 TAAAATT
1 TAAAATT
25853802 ATCTATTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.38
24 1 0.03
25 2 0.07
26 1 0.03
27 14 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAAATTTATTATCAATATAATAAAAA
Done.