Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 100 of 129
Found at i:16552639 original size:22 final size:22
Alignment explanation
Indices: 16552613--16552656 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16552603 ATTGATTCTA
*
16552613 TAAGACCTCCGGACATGATTTT
1 TAAGACCTCCGGACATAATTTT
16552635 TAAGACCTCCGGACATAATTTT
1 TAAGACCTCCGGACATAATTTT
16552657 GATTTACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (22 bp):
TAAGACCTCCGGACATAATTTT
Found at i:16552650 original size:155 final size:152
Alignment explanation
Indices: 16552357--16552655 Score: 337
Period size: 155 Copynumber: 1.9 Consensus size: 152
16552347 TTTTAAGACT
* * * * *
16552357 TTCAGGCATAATCTTTAAGACCTCTGGGCGTAATTTCAATTTGCGTGTTGTTTCAATCGATTCTT
1 TTCAGACATAATCTTTAAGACCTCTGGGCATAATTTCAATTTACGTATTGTCTCAATCGATTCTT
* * * * * * *
16552422 TACTTTTCGACTACGGTGTTGTCCCGATCAATTCTGTAAGATCTTCGGACATGATTTCTAAGATC
66 TACTTTTCAACTACGATGTTGTCCCAATCAATTCTATAAGACCTCCGGACATGATTTCTAAGACC
* *
16552487 TTCAGACATGATTTCTAAGATC
131 TCCAGACATAATTTCTAAGATC
** * *
16552509 TTCAGACATAATCTTTAAGACCTCTGGGCATAATTTTGATTTACGGTATTGTCTCGATCGATTTT
1 TTCAGACATAATCTTTAAGACCTCTGGGCATAATTTCAATTTAC-GTATTGTCTCAATCGA-TTC
* * * * ** *
16552574 TTTATTTTTTAACTTGCGATGTTGTCCTAATTGATTCTATAAGACCTCCGGACATGATTTTTAAG
64 TTTACTTTTCAAC-TACGATGTTGTCCCAATCAATTCTATAAGACCTCCGGACATGATTTCTAAG
*
16552639 ACCTCCGGACATAATTT
128 ACCTCCAGACATAATTT
16552656 TGATTTACGA
Statistics
Matches: 118, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
152 39 0.33
153 13 0.11
154 12 0.10
155 54 0.46
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (152 bp):
TTCAGACATAATCTTTAAGACCTCTGGGCATAATTTCAATTTACGTATTGTCTCAATCGATTCTT
TACTTTTCAACTACGATGTTGTCCCAATCAATTCTATAAGACCTCCGGACATGATTTCTAAGACC
TCCAGACATAATTTCTAAGATC
Found at i:16552718 original size:37 final size:37
Alignment explanation
Indices: 16552677--16552747 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
16552667 GTTGTCTCAA
* *
16552677 TCGATTATTTATTTCTCAACTTACAGTGTTGTCCTGG
1 TCGATTATTTACTTCTCAACTCACAGTGTTGTCCTGG
* * *
16552714 TCGATTCTTTACTTCTCGACTCATAGTGTTGTCC
1 TCGATTATTTACTTCTCAACTCACAGTGTTGTCC
16552748 CGATCATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (37 bp):
TCGATTATTTACTTCTCAACTCACAGTGTTGTCCTGG
Found at i:16553014 original size:21 final size:21
Alignment explanation
Indices: 16552990--16553031 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16552980 AATAATAATT
16552990 AAAAAAA-TAAAAAAAATGACA
1 AAAAAAATTAAAAAAAA-GACA
*
16553011 AAAAAAATTTAAAAAAAGACA
1 AAAAAAATTAAAAAAAAGACA
16553032 GAAGTGGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAAAATTAAAAAAAAGACA
Found at i:16554083 original size:9 final size:9
Alignment explanation
Indices: 16554069--16554112 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
16554059 CGATTGAAGT
16554069 ATTTTTTTA
1 ATTTTTTTA
16554078 ATTTTTTTA
1 ATTTTTTTA
*
16554087 ATATTTTTA
1 ATTTTTTTA
** *
16554096 AAATTTTGA
1 ATTTTTTTA
16554105 ATTTTTTT
1 ATTTTTTT
16554113 TATATTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:16554095 original size:18 final size:18
Alignment explanation
Indices: 16554069--16554127 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
16554059 CGATTGAAGT
*
16554069 ATTTTTTTAATTTTTTTA
1 ATTTTTTTAATATTTTTA
* * *
16554087 ATATTTTTAAAATTTTGA
1 ATTTTTTTAATATTTTTA
* *
16554105 ATTTTTTTTATATTATT-
1 ATTTTTTTAATATTTTTA
16554122 ATTTTT
1 ATTTTT
16554128 ATTATTTTGA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTTAATATTTTTA
Found at i:16554246 original size:21 final size:20
Alignment explanation
Indices: 16554213--16554251 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16554203 TTTAATAATA
16554213 ATAAAAATGAAAATAAATAGG
1 ATAAAAATGAAAA-AAATAGG
* *
16554234 ATAATAATTAAAAAAATA
1 ATAAAAATGAAAAAAATA
16554252 CTAAAAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
ATAAAAATGAAAAAAATAGG
Found at i:16554273 original size:3 final size:3
Alignment explanation
Indices: 16554265--16554307 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
16554255 AAAATGCTTA
*
16554265 AAT AAT AAT AAT AAT AAT -CT AAAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
16554308 GAATATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16554287 original size:21 final size:21
Alignment explanation
Indices: 16554234--16554303 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
16554224 AATAAATAGG
16554234 ATAATAAT-TAAA-AA-AATA
1 ATAATAATCTAAATAATAATA
* *
16554252 CTAAAAATGCTTAAATAATAATA
1 ATAATAAT-C-TAAATAATAATA
16554275 ATAATAATCTAAATAATAATA
1 ATAATAATCTAAATAATAATA
16554296 ATAATAAT
1 ATAATAAT
16554304 AATAGAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.14
21 24 0.56
22 3 0.07
23 10 0.23
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (21 bp):
ATAATAATCTAAATAATAATA
Found at i:16554607 original size:14 final size:14
Alignment explanation
Indices: 16554557--16554633 Score: 77
Period size: 15 Copynumber: 5.4 Consensus size: 14
16554547 CTAAAATTTA
16554557 AAAATCCCTAAA-CC
1 AAAA-CCCTAAATCC
*
16554571 AAAACCCTAAAT-T
1 AAAACCCTAAATCC
* *
16554584 GAAACTCTAAATCC
1 AAAACCCTAAATCC
16554598 AAAACCCTAAAATCC
1 AAAACCCT-AAATCC
*
16554613 AAACCCCTAGAATCC
1 AAAACCCTA-AATCC
16554628 AAAACC
1 AAAACC
16554634 TTAGAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
13 17 0.33
14 11 0.22
15 23 0.45
ACGTcount: A:0.49, C:0.32, G:0.03, T:0.16
Consensus pattern (14 bp):
AAAACCCTAAATCC
Found at i:16554612 original size:15 final size:15
Alignment explanation
Indices: 16554535--16554633 Score: 68
Period size: 15 Copynumber: 6.9 Consensus size: 15
16554525 TCATTAAAAT
16554535 TAAAAT-CAAAA-CC
1 TAAAATCCAAAACCC
**
16554548 TAAAATTTAAAAATCCC
1 TAAAA-TCCAAAA-CCC
16554565 T-AAA-CCAAAACCC
1 TAAAATCCAAAACCC
** *
16554578 T-AAAT-TGAAACTC
1 TAAAATCCAAAACCC
16554591 T-AAATCCAAAACCC
1 TAAAATCCAAAACCC
*
16554605 TAAAATCCAAACCCC
1 TAAAATCCAAAACCC
*
16554620 TAGAATCCAAAACC
1 TAAAATCCAAAACC
16554634 TTAGAATTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
13 22 0.33
14 11 0.16
15 28 0.42
16 3 0.04
17 3 0.04
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.18
Consensus pattern (15 bp):
TAAAATCCAAAACCC
Found at i:16554666 original size:59 final size:55
Alignment explanation
Indices: 16554562--16554683 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 55
16554552 ATTTAAAAAT
16554562 CCCTAAACCAAAACCCTAAATTGAAACTCTAAATCCAAAACCCTAAAATCCAAAC
1 CCCTAAACCAAAACCCTAAATTGAAACTCTAAATCCAAAACCCTAAAATCCAAAC
* * * * * *
16554617 CCCTAGAATCCAAAACCTTAGAATTTAAACCTTTAAATTCAAAACCCTAAGATCTAAAC
1 CCCTA-AA-CCAAAACCCTA-AATTGAAA-CTCTAAATCCAAAACCCTAAAATCCAAAC
*
16554676 CCCAAAAC
1 CCCTAAAC
16554684 TTTCGAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 11 0.20
58 9 0.16
59 29 0.52
ACGTcount: A:0.47, C:0.30, G:0.03, T:0.20
Consensus pattern (55 bp):
CCCTAAACCAAAACCCTAAATTGAAACTCTAAATCCAAAACCCTAAAATCCAAAC
Found at i:16554718 original size:22 final size:22
Alignment explanation
Indices: 16554670--16554712 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
16554660 ACCCTAAGAT
16554670 CTAAACCCCAAAACTTTCGAAA
1 CTAAACCCCAAAACTTTCGAAA
*
16554692 CTAAA-CCCAAAA-TTTCTAAA
1 CTAAACCCCAAAACTTTCGAAA
16554712 C
1 C
16554713 CCTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (22 bp):
CTAAACCCCAAAACTTTCGAAA
Found at i:16554733 original size:21 final size:20
Alignment explanation
Indices: 16554709--16554762 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
16554699 CAAAATTTCT
16554709 AAACCCTAAAATAAAAACTCA
1 AAACCCTAAAATAAAAAC-CA
* *
16554730 AAA-CCTCAAACTTTAAAACCA
1 AAACCCT-AAA-ATAAAAACCA
16554751 AAACCCTAAAAT
1 AAACCCTAAAAT
16554763 CTTCAAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 4 0.15
21 14 0.52
22 9 0.33
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (20 bp):
AAACCCTAAAATAAAAACCA
Found at i:16554776 original size:16 final size:16
Alignment explanation
Indices: 16554751--16554808 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
16554741 TTTAAAACCA
*
16554751 AAACCCTAAAATCTTC
1 AAACCTTAAAATCTTC
*
16554767 AAACCTTAAAATC--A
1 AAACCTTAAAATCTTC
*
16554781 AAACCTT-AAACCTTC
1 AAACCTTAAAATCTTC
*
16554796 TATACCTTAAAAT
1 -AAACCTTAAAAT
16554809 TCAAGCCCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.12
14 7 0.22
16 18 0.56
17 3 0.09
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (16 bp):
AAACCTTAAAATCTTC
Found at i:16554786 original size:14 final size:14
Alignment explanation
Indices: 16554737--16554790 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
16554727 TCAAAACCTC
* *
16554737 AAACTTTAAAACCA
1 AAACCTTAAAATCA
* *
16554751 AAACCCTAAAATCTTC
1 AAACCTTAAAATC--A
16554767 AAACCTTAAAATCA
1 AAACCTTAAAATCA
16554781 AAACCTTAAA
1 AAACCTTAAA
16554791 CCTTCTATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 20 0.62
16 12 0.38
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (14 bp):
AAACCTTAAAATCA
Found at i:16556262 original size:34 final size:34
Alignment explanation
Indices: 16556212--16556292 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
16556202 TTTATCATAT
* * * *
16556212 AAACATCACTATATTAGCGATATTTTTTTGATAC
1 AAACGTCACTAAATTAGCAATATTTTTTAGATAC
* *
16556246 AAACGTCACTAAATTAGTAATGTTTTTTAGATAC
1 AAACGTCACTAAATTAGCAATATTTTTTAGATAC
* *
16556280 AAATGTCGCTAAA
1 AAACGTCACTAAA
16556293 ATAATAACAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (34 bp):
AAACGTCACTAAATTAGCAATATTTTTTAGATAC
Found at i:16560093 original size:18 final size:19
Alignment explanation
Indices: 16560061--16560104 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
16560051 CTTATTCTTT
*
16560061 TTTTTTTTTTGTTTTTAAC
1 TTTTTATTTTGTTTTTAAC
*
16560080 TTTTTATTTT-TTTTTAAT
1 TTTTTATTTTGTTTTTAAC
16560098 TTTTTAT
1 TTTTTAT
16560105 GCAACAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (19 bp):
TTTTTATTTTGTTTTTAAC
Found at i:16560580 original size:2 final size:2
Alignment explanation
Indices: 16560573--16560597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16560563 CTCGATCGAT
16560573 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16560598 GTATGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16560621 original size:9 final size:9
Alignment explanation
Indices: 16560601--16560629 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16560591 TATATATGTA
16560601 TGTGTG-TG
1 TGTGTGTTG
16560609 TGTGTGTTG
1 TGTGTGTTG
16560618 TGTGTGTTG
1 TGTGTGTTG
16560627 TGT
1 TGT
16560630 TAGATAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (9 bp):
TGTGTGTTG
Found at i:16560655 original size:20 final size:21
Alignment explanation
Indices: 16560630--16560672 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
16560620 TGTGTTGTGT
16560630 TAGATAAT-TGTAATT-TTAAA
1 TAGATAATGT-TAATTATTAAA
16560650 TAGATAATGTTAATTATTAAA
1 TAGATAATGTTAATTATTAAA
16560671 TA
1 TA
16560673 AAAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (21 bp):
TAGATAATGTTAATTATTAAA
Found at i:16563842 original size:26 final size:28
Alignment explanation
Indices: 16563813--16563866 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
16563803 AAAAATTTTG
*
16563813 AGTCA-ATTCATTGTTT-AAAAAATATA
1 AGTCAGATTCACTGTTTGAAAAAATATA
*
16563839 AGTCAGATTCACTGTTTGAAAACATATA
1 AGTCAGATTCACTGTTTGAAAAAATATA
16563867 TTGATCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 10 0.42
28 9 0.38
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (28 bp):
AGTCAGATTCACTGTTTGAAAAAATATA
Found at i:16565160 original size:18 final size:17
Alignment explanation
Indices: 16565137--16565189 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
16565127 ATACACACAT
16565137 TTTATTTATTTTATTGAA
1 TTTATTTATTTTATT-AA
*
16565155 TTTATTATTTTTTATTAA
1 TTTATT-TATTTTATTAA
*
16565173 ATTA-TTATTTTTATTAA
1 TTTATTTA-TTTTATTAA
16565190 AGGAAATAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
18 11 0.37
19 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTATTTATTTTATTAA
Found at i:16565164 original size:21 final size:19
Alignment explanation
Indices: 16565138--16565184 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
16565128 TACACACATT
*
16565138 TTATTTATTTTATTGAATTTA
1 TTATTT-TTTTATT-AAATTA
16565159 TTA-TTTTTTATTAAATTA
1 TTATTTTTTTATTAAATTA
16565177 TTATTTTT
1 TTATTTTT
16565185 ATTAAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 2 0.08
21 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTATTTTTTTATTAAATTA
Found at i:16565184 original size:17 final size:18
Alignment explanation
Indices: 16565145--16565190 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
16565135 ATTTTATTTA
*
16565145 TTTTATTGAATTTATTATT
1 TTTTATT-AAATTATTATT
16565164 TTTTATTAAATTATTA-T
1 TTTTATTAAATTATTATT
16565181 TTTTATTAAA
1 TTTTATTAAA
16565191 GGAAATAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.42
18 8 0.31
19 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATTAAATTATTATT
Found at i:16567319 original size:56 final size:56
Alignment explanation
Indices: 16567242--16567368 Score: 170
Period size: 56 Copynumber: 2.3 Consensus size: 56
16567232 CTTCTTACTC
16567242 GAGGCTCGAA-AACTTTTAAAAATTTAAAATCT-AAAAGAAAAAACCTTT-TCTTGGTA
1 GAGGCT-GAACAACTTTTAAAAATTTAAAATCTGAAAA-AAAAAA-CTTTCTCTTGGTA
* *
16567298 GAGGCTGAACAATTTTTAAAAATTTAAAATCTGAAAAAAAAAAGTTTCTCTTGGTA
1 GAGGCTGAACAACTTTTAAAAATTTAAAATCTGAAAAAAAAAACTTTCTCTTGGTA
* *
16567354 GAAGCTTAACAACTT
1 GAGGCTGAACAACTT
16567369 AAAAAAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
55 6 0.10
56 53 0.84
57 4 0.06
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (56 bp):
GAGGCTGAACAACTTTTAAAAATTTAAAATCTGAAAAAAAAAACTTTCTCTTGGTA
Found at i:16567442 original size:49 final size:49
Alignment explanation
Indices: 16567374--16567675 Score: 261
Period size: 49 Copynumber: 6.1 Consensus size: 49
16567364 AACTTAAAAA
*
16567374 AAAAACTTT-ATCTTGAAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTT
1 AAAAA-TTTCATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTT
* * * * * * * *
16567423 AAAAATTTTATCTTTAAAAAGTTTC-TTTAAACAGAGACTTAATAACTTT
1 AAAAATTTCATCTTGAAAAAG-CTCATCTAAGCAAAGGCTCAATAACTTT
** * * * *
16567472 AAAAAAAATCCCATCTTGAAAAAGCTCATTTAAGTAAAGGTTCAACAACTTT
1 ---AAAAATTTCATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTT
* * * *
16567524 AAAAATTTCATCTTGAAAAGGCTTATCTAAGCAAATGCTTAATAACTTT
1 AAAAATTTCATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTT
*
16567573 AAAAATTTCATCTTGAAAAGGCTTC-TCTAAGCAGAA-GCTCAATAACTTT
1 AAAAATTTCATCTTGAAAAAGC-TCATCTAAGCA-AAGGCTCAATAACTTT
* * * * * * * *
16567622 AAACATTTTATCTTGAAAATGCTCATTTAAGTAGAGGCTCAACAACTTA
1 AAAAATTTCATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTT
16567671 AAAAA
1 AAAAA
16567676 AAAAATCTTT
Statistics
Matches: 203, Mismatches: 40, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
48 6 0.03
49 156 0.77
50 5 0.02
51 2 0.01
52 34 0.17
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (49 bp):
AAAAATTTCATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAATAACTTT
Found at i:16567511 original size:101 final size:97
Alignment explanation
Indices: 16567383--16567640 Score: 286
Period size: 101 Copynumber: 2.6 Consensus size: 97
16567373 AAAAAACTTT
* * *
16567383 ATCTTGAAAAAGCTCCTCTAAGCAAAGGCTCAATAACTTTAAAAATTTTATCTTTAAAAAGTTTC
1 ATCTTGAAAAAGCT-CTCTAAGCAAAGGCTCAATAACTTTAAAAATTTTATCTTGAAAAAGCTTA
* *
16567448 TTTAAACAGA-GACTTAATAACTTTAAAAAAAATCCC
65 TCTAAACAAATG-CTTAATAACTTT---AAAAATCCC
* * * * * *
16567484 ATCTTGAAAAAGCTCATTTAAGTAAAGGTTCAACAACTTTAAAAATTTCATCTTGAAAAGGCTTA
1 ATCTTGAAAAAGCTC-TCTAAGCAAAGGCTCAATAACTTTAAAAATTTTATCTTGAAAAAGCTTA
* **
16567549 TCTAAGCAAATGCTTAATAACTTTAAAAATTTC
65 TCTAAACAAATGCTTAATAACTTTAAAAATCCC
* *
16567582 ATCTTGAAAAGGCTTCTCTAAGCAGAA-GCTCAATAACTTTAAACATTTTATCTTGAAAA
1 ATCTTGAAAAAGC-TCTCTAAGCA-AAGGCTCAATAACTTTAAAAATTTTATCTTGAAAA
16567641 TGCTCATTTA
Statistics
Matches: 132, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
98 53 0.40
99 4 0.03
100 1 0.01
101 73 0.55
102 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.33
Consensus pattern (97 bp):
ATCTTGAAAAAGCTCTCTAAGCAAAGGCTCAATAACTTTAAAAATTTTATCTTGAAAAAGCTTAT
CTAAACAAATGCTTAATAACTTTAAAAATCCC
Found at i:16567678 original size:150 final size:151
Alignment explanation
Indices: 16567351--16567741 Score: 389
Period size: 150 Copynumber: 2.6 Consensus size: 151
16567341 GTTTCTCTTG
* * *
16567351 GTAGAAGCTTAACAACTTAAAAAAAAAACTTTATCTTGAAAAAGCTCCTCTAAGCAAAGGCTCAA
1 GTAGAGGCTCAACAACTT-AAAAAAAAACTTTATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAA
* * * * *
16567416 TAACTTTAAAAATTTTATCTTTAAAAAGTTTCTTTAAACAGAGACTTAATAACTTTAAAAAAAAT
65 TAACTTTAAAAATTTCATCTTGAAAAAGCTTCTCTAAACAGAGACTCAATAACTTT--AAAAAAT
16567481 CCCATCTTGAAAAAGCTCATTTAA
128 CCCATCTTGAAAAAGCTCATTTAA
* * * * * * *
16567505 GTAAAGGTTCAACAACTT---TAAAAA-TTTCATCTTGAAAAGGCTTATCTAAGCAAATGCTTAA
1 GTAGAGGCTCAACAACTTAAAAAAAAACTTT-ATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAA
* * * *
16567566 TAACTTTAAAAATTTCATCTTGAAAAGGCTTCTCTAAGCAGA-AGCTCAATAACTTT-AAACATT
65 TAACTTTAAAAATTTCATCTTGAAAAAGCTTCTCTAAACAGAGA-CTCAATAACTTTAAAAAATC
** *
16567629 TTATCTTGAAAATGCTCATTTAA
129 CCATCTTGAAAAAGCTCATTTAA
* ** * *
16567652 GTAGAGGCTCAACAACTTAAAAAAAAAAATCTTTATTTTGGAAAAAATTCCTTTAAGCAAAGGCT
1 GTAGAGGCTCAACAACTT--AAAAAAAAA-CTTTATCTT-GAAAAAGCTCATCTAAGCAAAGGCT
* *
16567717 CAACAACTTTAAACATTCTCATCTT
62 CAATAACTTTAAAAATT-TCATCTT
16567742 TTCTCGAAAC
Statistics
Matches: 190, Mismatches: 36, Indels: 21
0.77 0.15 0.09
Matches are distributed among these distances:
147 41 0.22
149 4 0.02
150 80 0.42
152 5 0.03
153 4 0.02
154 49 0.26
155 7 0.04
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (151 bp):
GTAGAGGCTCAACAACTTAAAAAAAAACTTTATCTTGAAAAAGCTCATCTAAGCAAAGGCTCAAT
AACTTTAAAAATTTCATCTTGAAAAAGCTTCTCTAAACAGAGACTCAATAACTTTAAAAAATCCC
ATCTTGAAAAAGCTCATTTAA
Found at i:16568569 original size:20 final size:20
Alignment explanation
Indices: 16568544--16568590 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16568534 AGATATGTCA
*
16568544 TTTTTTTC-ACTTTTTTTTAT
1 TTTTTTTCAACTTCTTTTT-T
*
16568564 TTTTTTTCAAGTTCTTTTTT
1 TTTTTTTCAACTTCTTTTTT
16568584 TTTTTTT
1 TTTTTTT
16568591 AAAGTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTTTCAACTTCTTTTTT
Found at i:16568595 original size:20 final size:21
Alignment explanation
Indices: 16568557--16568595 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16568547 TTTTCACTTT
*
16568557 TTTTTATTTTTTTTCAAGTTC
1 TTTTTATTTTTTTTAAAGTTC
16568578 TTTTT-TTTTTTTTAAAGT
1 TTTTTATTTTTTTTAAAGT
16568596 AAAATATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTATTTTTTTTAAAGTTC
Found at i:16571727 original size:6 final size:6
Alignment explanation
Indices: 16571716--16571749 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
16571706 ATAAAATGTA
16571716 ATAATT ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAA
16571750 AAACTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:16572185 original size:18 final size:18
Alignment explanation
Indices: 16572162--16572199 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16572152 ATATTTGAGA
16572162 ATGATACATTTGAGGTGG
1 ATGATACATTTGAGGTGG
16572180 ATGATACATTTGAGGTGG
1 ATGATACATTTGAGGTGG
16572198 AT
1 AT
16572200 AATAACCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (18 bp):
ATGATACATTTGAGGTGG
Found at i:16574676 original size:2 final size:2
Alignment explanation
Indices: 16574669--16574705 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16574659 GAAGTCGATC
*
16574669 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16574706 CTGATTCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16576017 original size:27 final size:26
Alignment explanation
Indices: 16575966--16576014 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
16575956 TTTCAAAAAT
*
16575966 TAAATATTTTCAAACTTATATTTTAA
1 TAAATATTTTAAAACTTATATTTTAA
16575992 TAAA-ATTTTAAAACTTATATTTT
1 TAAATATTTTAAAACTTATATTTT
16576015 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (26 bp):
TAAATATTTTAAAACTTATATTTTAA
Found at i:16579568 original size:18 final size:18
Alignment explanation
Indices: 16579545--16579579 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16579535 TGTTGTAACG
*
16579545 TTTCAATAATACATGGTC
1 TTTCAACAATACATGGTC
16579563 TTTCAACAATACATGGT
1 TTTCAACAATACATGGT
16579580 GATATGAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (18 bp):
TTTCAACAATACATGGTC
Found at i:16583964 original size:18 final size:18
Alignment explanation
Indices: 16583941--16583994 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
16583931 ATGCACACAT
* *
16583941 TTTATTAATTTTATTGAC
1 TTTATTATTTTTATTGAA
*
16583959 TTTATTATTTTTTATTAAA
1 TTTATTA-TTTTTATTGAA
16583978 TTT-TTATTTTTATTGAA
1 TTTATTATTTTTATTGAA
16583995 GAAAAAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 10 0.32
18 10 0.32
19 11 0.35
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTATTATTTTTATTGAA
Found at i:16584638 original size:167 final size:167
Alignment explanation
Indices: 16584362--16584699 Score: 667
Period size: 167 Copynumber: 2.0 Consensus size: 167
16584352 GTTTTATTAT
16584362 TTTTGTATTATTATAATAAAGTTTATTTTAAAATTATTTTTCATTATTTTTTAATTATCACTAGG
1 TTTTGTATTATTATAATAAAGTTTATTTTAAAATTATTTTTCATTATTTTTTAATTATCACTAGG
*
16584427 TTTGTTTTTAAAATTAACAAAATTAACCAAAATTTTTAACTATATACTAATTATTTATTTTTTAT
66 TTTATTTTTAAAATTAACAAAATTAACCAAAATTTTTAACTATATACTAATTATTTATTTTTTAT
16584492 TTATTTCAACATAAATTTATTCTAACAAATTAAAATA
131 TTATTTCAACATAAATTTATTCTAACAAATTAAAATA
16584529 TTTTGTATTATTATAATAAAGTTTATTTTAAAATTATTTTTCATTATTTTTTAATTATCACTAGG
1 TTTTGTATTATTATAATAAAGTTTATTTTAAAATTATTTTTCATTATTTTTTAATTATCACTAGG
16584594 TTTATTTTTAAAATTAACAAAATTAACCAAAATTTTTAACTATATACTAATTATTTATTTTTTAT
66 TTTATTTTTAAAATTAACAAAATTAACCAAAATTTTTAACTATATACTAATTATTTATTTTTTAT
16584659 TTATTTCAACATAAATTTATTCTAACAAATTAAAATA
131 TTATTTCAACATAAATTTATTCTAACAAATTAAAATA
16584696 TTTT
1 TTTT
16584700 CACATGCATA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 170 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (167 bp):
TTTTGTATTATTATAATAAAGTTTATTTTAAAATTATTTTTCATTATTTTTTAATTATCACTAGG
TTTATTTTTAAAATTAACAAAATTAACCAAAATTTTTAACTATATACTAATTATTTATTTTTTAT
TTATTTCAACATAAATTTATTCTAACAAATTAAAATA
Found at i:16586275 original size:23 final size:24
Alignment explanation
Indices: 16586244--16586301 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
16586234 TTTTAATGTG
*
16586244 ATATCTTAAAATTTTTATT-TTTTT
1 ATATATTAAAATTTTT-TTATTTTT
16586268 ATAT-TTAAAATTTTTTTATTTTT
1 ATATATTAAAATTTTTTTATTTTT
*
16586291 AAATATTAAAA
1 ATATATTAAAA
16586302 ATCATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.06
23 19 0.61
24 10 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATATTAAAATTTTTTTATTTTT
Found at i:16586294 original size:16 final size:17
Alignment explanation
Indices: 16586260--16586293 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16586250 TAAAATTTTT
16586260 ATTTTTTTATATTTAAA
1 ATTTTTTTATATTTAAA
*
16586277 ATTTTTTTATTTTTAAA
1 ATTTTTTTATATTTAAA
16586294 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTTATATTTAAA
Found at i:16586302 original size:25 final size:25
Alignment explanation
Indices: 16586255--16586303 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
16586245 TATCTTAAAA
** *
16586255 TTTTTATTTTTTTATATTTAAAATT
1 TTTTTATTTTTAAATATTAAAAATT
16586280 TTTTTATTTTTAAATATTAAAAAT
1 TTTTTATTTTTAAATATTAAAAAT
16586304 CATAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATTTTTAAATATTAAAAATT
Found at i:16586713 original size:19 final size:18
Alignment explanation
Indices: 16586668--16586721 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
16586658 TAAAATTATA
*
16586668 TTATTTTTTATATTATTC
1 TTATTTTTAATATTATTC
16586686 TTATATTTTAATATTATGT-
1 TTAT-TTTTAATATTAT-TC
*
16586705 TGTATTTTTAAAATTAT
1 T-TATTTTTAATATTAT
16586722 CAAATTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (18 bp):
TTATTTTTAATATTATTC
Found at i:16601944 original size:13 final size:14
Alignment explanation
Indices: 16601922--16601950 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16601912 TGATATATTT
16601922 TTTAGATAAAAATA
1 TTTAGATAAAAATA
16601936 TTTAG-TAAAAATA
1 TTTAGATAAAAATA
16601949 TT
1 TT
16601951 GATAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTAGATAAAAATA
Found at i:16602121 original size:23 final size:24
Alignment explanation
Indices: 16602095--16602144 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
16602085 TTTAAAAAAT
16602095 TTAACCTAAAAAATTTCA-TAAAC
1 TTAACCTAAAAAATTTCACTAAAC
16602118 TTAACCTAAAAAATTTCACGTAAAC
1 TTAACCTAAAAAATTTCAC-TAAAC
16602143 TT
1 TT
16602145 TATCAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 18 0.72
25 7 0.28
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (24 bp):
TTAACCTAAAAAATTTCACTAAAC
Found at i:16603734 original size:62 final size:61
Alignment explanation
Indices: 16603668--16603882 Score: 156
Period size: 62 Copynumber: 3.5 Consensus size: 61
16603658 ATTTAAGACG
* * *
16603668 TTTTTTATCAAAAACATCTTGAATAATCCTCTCATAAAAATTGAAGGGGATTATTAAAGGTA
1 TTTTTTAGCAAAAACACCTTGAATAATCC-CTCATAAAAATTGAAGGGGATTATTCAAGGTA
*** ** *
16603730 TTTTTT-GCTAAAAATGTCTTGAATAAT-CC-CATTAAATTTTTTTTAA-GGGATTATTCAAGG-
1 TTTTTTAGC-AAAAACACCTTGAATAATCCCTCA-TAAA---AATTGAAGGGGATTATTCAAGGT
16603790 A
61 A
* * * **
16603791 GTTTTTGGCCAAAATGCCTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGT-
1 TTTTTTAGCAAAAACACCTTGAATAAT-CCCTCATAAAAATTGAAGGGGATTATTCAAGGTA
* * *
16603852 TTGTTTAGTCAGAAACACCTTAAATAA-CCCT
1 TTTTTTAG-CAAAAACACCTTGAATAATCCCT
16603883 ATTCAATTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 26
0.72 0.13 0.16
Matches are distributed among these distances:
59 2 0.02
60 13 0.11
61 43 0.36
62 50 0.42
63 10 0.08
64 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (61 bp):
TTTTTTAGCAAAAACACCTTGAATAATCCCTCATAAAAATTGAAGGGGATTATTCAAGGTA
Found at i:16603841 original size:61 final size:62
Alignment explanation
Indices: 16603685--16603851 Score: 182
Period size: 61 Copynumber: 2.7 Consensus size: 62
16603675 TCAAAAACAT
* * * *
16603685 CTTGAATAATCCTCTCATAAAAATTGAAGGGGATTATTAAAGGTATTTTTTGCTAAAAATGT
1 CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGTATTTTTGGCTAAAAATGC
* ** * *
16603747 CTTGAATAATCCCAT--TAAATTTTTTTTAA-GGGATTATTCAAGG-AGTTTTTGGC-CAAAATG
1 CTTGAATAATCCCCTCATAAA---AATTGAAGGGGATTATTCAAGGTA-TTTTTGGCTAAAAATG
16603807 C
62 C
16603808 CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGT
1 CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGT
16603852 TTGTTTAGTC
Statistics
Matches: 84, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
60 8 0.10
61 35 0.42
62 33 0.39
63 8 0.10
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (62 bp):
CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGTATTTTTGGCTAAAAATGC
Found at i:16603878 original size:123 final size:123
Alignment explanation
Indices: 16603685--16603910 Score: 314
Period size: 123 Copynumber: 1.8 Consensus size: 123
16603675 TCAAAAACAT
* * ***
16603685 CTTGAATAATCCTCTCATAAAAATTGAAGGGGATTATTAAAGGTATTTTTTGCTAAAAATGTCTT
1 CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTAAAGGTATTTTTAGCTAAAAACACCTT
* *
16603750 GAATAATCCC-ATTAAATTTTTTTTAAGGGATTATTCAAGGAGTTTTTGGCCAAAATGC
66 AAATAA-CCCTATTAAATTTTTTATAAGGGATTATTCAAGGAGTTTTTGGCCAAAATGC
* *
16603808 CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGT-TTGTTTAG-TCAGAAACACC
1 CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTAAAGGTATT-TTTAGCT-AAAAACACC
*
16603871 TTAAATAACCCTATTCAATTTTTTATAAGGGATTATTCAA
64 TTAAATAACCCTATTAAATTTTTTATAAGGGATTATTCAA
16603911 AATGTTTCAG
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
122 6 0.07
123 84 0.93
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (123 bp):
CTTGAATAATCCCCTCATAAAAATTGAAGGGGATTATTAAAGGTATTTTTAGCTAAAAACACCTT
AAATAACCCTATTAAATTTTTTATAAGGGATTATTCAAGGAGTTTTTGGCCAAAATGC
Found at i:16604218 original size:314 final size:311
Alignment explanation
Indices: 16603684--16604264 Score: 674
Period size: 314 Copynumber: 1.9 Consensus size: 311
16603674 ATCAAAAACA
* * * **** * * *
16603684 TCTTGAATAATCCTCTCATAAAAATTGAAGGGGATTATTAAAGGTATTTTTTGCTAAAAATGTCT
1 TCTTAAATAATCCCCTCATAAAAATTAAAAAAAATTATTAAAGGTATTTTTTACTAAAAACGCCT
* * * *
16603749 TGAATAATCCCATTAAATTTTTTTTAAGGGATTATTCAAGGAGTTTTTGGCCAAAATGCCTTGAA
66 TAAATAAACCCATTAAATTTTTTGTAAGAGATTATTCAAGGAGTTTTTGGCCAAAATGCCTTGAA
* * ** *
16603814 TAATCCCCTCATAAAAATTGAAGGGGATTATTCAAGGTTTGTTTAGTCAGAAACACCTTAAATAA
131 TAAT-CCATCATAAAAATTGAAAGGGATTATTCAAGGAATGTTTAGCCAGAAACACCTTAAATAA
16603879 CCCTATTCAATTTTTTATAAGGGATTATTCAAA-ATGTTTC-AGACAAAAAAAGCCTTAAATAAT
195 CCCTATTCAATTTTTTATAAGGGATTATTCAAAGAT-TTTCTAGACAAAAAAA-CCTTAAATAAT
16603942 CCAAAAAAATATATAATCCCCTCCAAAAATTTTGACAAGATTATTCCAAAAGCG
258 CCAAAAAAATATATAATCCCCTCCAAAAATTTTGACAAGATTATTCCAAAAGCG
* *
16603996 TCTTAAATAATCCCCTCATAAAAATTAAAAAAAATTATTGAAGGTATTTTTTTACTAGAAACGCC
1 TCTTAAATAATCCCCTCATAAAAATTAAAAAAAATTATTAAAGGTA-TTTTTTACTAAAAACGCC
* * *
16604061 TTAAATAAACCCATTTAA-TTTTTGTAAGAGATTTTTTAA-GATGTTTTCTAGG-CAAAAGTGCC
65 TTAAATAAACCCATTAAATTTTTTGTAAGAGATTATTCAAGGA-GTTTT-T-GGCCAAAA-TGCC
* * *
16604123 TTGAATAAT-CATCAATAAAAAATTGAAAGGGATTATTCAAGGCAAT-TTTGGCCAGAAATACTT
126 TTGAATAATCCATC-AT-AAAAATTGAAAGGGATTATTCAAGG-AATGTTTAGCCAGAAACACCT
* * * * * * * *
16604186 TCAATAACCC-ACTTTAATTTTTTGTGAGGGATTATTCAAAGCTTTTCTAGCCAAAAATACCTTG
188 TAAATAACCCTA-TTCAATTTTTTATAAGGGATTATTCAAAGATTTTCTAGACAAAAAAACCTTA
*
16604250 AATAATTCAAAAAAA
252 AATAATCCAAAAAAA
16604265 ATAACAATGA
Statistics
Matches: 222, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
311 2 0.01
312 63 0.28
313 38 0.17
314 108 0.49
315 11 0.05
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (311 bp):
TCTTAAATAATCCCCTCATAAAAATTAAAAAAAATTATTAAAGGTATTTTTTACTAAAAACGCCT
TAAATAAACCCATTAAATTTTTTGTAAGAGATTATTCAAGGAGTTTTTGGCCAAAATGCCTTGAA
TAATCCATCATAAAAATTGAAAGGGATTATTCAAGGAATGTTTAGCCAGAAACACCTTAAATAAC
CCTATTCAATTTTTTATAAGGGATTATTCAAAGATTTTCTAGACAAAAAAACCTTAAATAATCCA
AAAAAATATATAATCCCCTCCAAAAATTTTGACAAGATTATTCCAAAAGCG
Found at i:16605578 original size:13 final size:13
Alignment explanation
Indices: 16605562--16605591 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16605552 AAATACTATG
16605562 AAAATAAATTAAT
1 AAAATAAATTAAT
16605575 AAAATAAATTAAT
1 AAAATAAATTAAT
16605588 AAAA
1 AAAA
16605592 AATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATAAATTAAT
Found at i:16606539 original size:4 final size:4
Alignment explanation
Indices: 16606530--16606565 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
16606520 AAAATCAAAG
**
16606530 ATAA ATAA ATAA ATGG ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
16606566 TGGGTAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:16606550 original size:16 final size:16
Alignment explanation
Indices: 16606529--16606559 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16606519 AAAAATCAAA
16606529 GATAAATAAATAAATG
1 GATAAATAAATAAATG
16606545 GATAAATAAATAAAT
1 GATAAATAAATAAAT
16606560 AAATAATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
GATAAATAAATAAATG
Found at i:16606913 original size:43 final size:44
Alignment explanation
Indices: 16606836--16606944 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 44
16606826 GCTCAATGAC
* ** *
16606836 TTTGGAAAAGTAAATAAAGCTCTTCTAATCAAAGGCTCCATAAT
1 TTTGGAAAAGTAAACAAAGCTCCCCTAAGCAAAGGCTCCATAAT
* *
16606880 TTTGGAAAA-TAAACGAAGCTCCCCTAAGCAAAGGCTCCATAAC
1 TTTGGAAAAGTAAACAAAGCTCCCCTAAGCAAAGGCTCCATAAT
** *
16606923 TTCAGAAAAGTAAATAAAGCTC
1 TTTGGAAAAGTAAACAAAGCTC
16606945 ATCTAAATAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 35 0.65
44 19 0.35
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (44 bp):
TTTGGAAAAGTAAACAAAGCTCCCCTAAGCAAAGGCTCCATAAT
Found at i:16607093 original size:46 final size:44
Alignment explanation
Indices: 16606812--16607121 Score: 209
Period size: 44 Copynumber: 7.0 Consensus size: 44
16606802 TAAATATGGA
* * *
16606812 TCTTCTAAACATAGGCTCAATGACTTTGGAAA-AGTAAATAAAGC
1 TCTTCTAAACAAAGGCTCAACGACTTTAGAAATA-TAAATAAAGC
* * ** * * **
16606856 TCTTCTAATCAAAGGCTCCATAATTTTGGAAA-ATAAACGAAGC
1 TCTTCTAAACAAAGGCTCAACGACTTTAGAAATATAAATAAAGC
** * * ** *
16606899 TCCCCTAAGCAAAGGCTCCATAACTTCAGAAA-AGTAAATAAAGC
1 TCTTCTAAACAAAGGCTCAACGACTTTAGAAATA-TAAATAAAGC
* * * ** * *
16606943 TCATCTAAATAGAGGCTCGTCGACTTCT-GAAA-ATAAATAAGGG
1 TCTTCTAAACAAAGGCTCAACGACTT-TAGAAATATAAATAAAGC
* * * * * * *
16606986 TCCTCTGAACAAATGTTCAATGACTTTATAAACATAAATAAAGC
1 TCTTCTAAACAAAGGCTCAACGACTTTAGAAATATAAATAAAGC
* *
16607030 TCTTTTAAACAGAGGCTCAACGACTTTA-AAATAATAAATAAAGC
1 TCTTCTAAACAAAGGCTCAACGACTTTAGAAAT-ATAAATAAAGC
*
16607074 ATCTTCTAAACAAAAGGCTCAACAACTTTAGAAATATAAATAAAGC
1 -TCTTCTAAAC-AAAGGCTCAACGACTTTAGAAATATAAATAAAGC
16607120 TC
1 TC
16607122 ATTTAATCAG
Statistics
Matches: 208, Mismatches: 50, Indels: 15
0.76 0.18 0.05
Matches are distributed among these distances:
42 1 0.00
43 66 0.32
44 99 0.48
45 11 0.05
46 27 0.13
47 4 0.02
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (44 bp):
TCTTCTAAACAAAGGCTCAACGACTTTAGAAATATAAATAAAGC
Found at i:16607406 original size:16 final size:16
Alignment explanation
Indices: 16607387--16607418 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16607377 CAAGAATTAA
16607387 ATATTCGTAAAATTTT
1 ATATTCGTAAAATTTT
*
16607403 ATATTCGTAAGATTTT
1 ATATTCGTAAAATTTT
16607419 TCAACTTTGC
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:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (16 bp):
ATATTCGTAAAATTTT
Found at i:16607841 original size:21 final size:21
Alignment explanation
Indices: 16607815--16608017 Score: 271
Period size: 21 Copynumber: 9.6 Consensus size: 21
16607805 GGTTTCACAT
16607815 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
16607836 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
* *
16607857 TTTAAAAGATTCTCATTTGAAA
1 -CTCAAAGATTCTCATTTGAAA
* *
16607879 CTTAAATATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
16607900 CTCAAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTTG-AAA
* *
16607922 CTCAAAGATTCTTATTTGAAT
1 CTCAAAGATTCTCATTTGAAA
*
16607943 CTCAAAGATTCTTATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
*
16607964 CTCAAATATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
* * * *
16607985 TTTAAAGATTTTTATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
*
16608006 TTCAAAGATTCT
1 CTCAAAGATTCT
16608018 TTTTTAAAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
21 122 0.76
22 39 0.24
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:16607879 original size:43 final size:43
Alignment explanation
Indices: 16607813--16608017 Score: 281
Period size: 43 Copynumber: 4.8 Consensus size: 43
16607803 AGGGTTTCAC
16607813 ATCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAA
1 ATCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAA
* * * *
16607856 ATTTAAAAGATTCTCATTTGAAACTTAAATATTCTCATTTGAA
1 ATCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAA
*
16607899 A-CTCAAAGATTCTCATTTGAAAACTCAAAGATTCTTATTTG-A
1 ATCTCAAAGATTCTCATTTG-AAACTCAAAGATTCTCATTTGAA
* *
16607941 ATCTCAAAGATTCTTATTTGAAACTCAAATATTCTCATTTGAA
1 ATCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAA
* * * *
16607984 AT-TTAAAGATTTTTATTTGAAATTCAAAGATTCT
1 ATCTCAAAGATTCTCATTTGAAACTCAAAGATTCT
16608018 TTTTTAAAAA
Statistics
Matches: 143, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
42 65 0.45
43 78 0.55
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (43 bp):
ATCTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAA
Found at i:16607897 original size:64 final size:63
Alignment explanation
Indices: 16607815--16608017 Score: 298
Period size: 64 Copynumber: 3.2 Consensus size: 63
16607805 GGTTTCACAT
*
16607815 CTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAAATTTAAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAAATTT-AAAGATTCTTATTTGAAA
* * * * *
16607879 CTTAAATATTCTCATTTGAAACTCAAAGATTCTCATTTGAAAACTCAAAGATTCTTATTTGAAT
1 CTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTG-AAATTTAAAGATTCTTATTTGAAA
* * *
16607943 CTCAAAGATTCTTATTTGAAACTCAAATATTCTCATTTGAAATTTAAAGATTTTTATTTGAAA
1 CTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAAATTTAAAGATTCTTATTTGAAA
*
16608006 TTCAAAGATTCT
1 CTCAAAGATTCT
16608018 TTTTTAAAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
63 31 0.25
64 88 0.72
65 4 0.03
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (63 bp):
CTCAAAGATTCTCATTTGAAACTCAAAGATTCTCATTTGAAATTTAAAGATTCTTATTTGAAA
Found at i:16609121 original size:18 final size:20
Alignment explanation
Indices: 16609081--16609124 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
16609071 TTATCTCTTT
*
16609081 TTATATTTTTTCATTTTTCCA
1 TTATTTTTTTTCA-TTTTCCA
16609102 TTATTTTTTTTC-TTTT-CA
1 TTATTTTTTTTCATTTTCCA
16609120 TTATT
1 TTATT
16609125 GATGTGTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
21 11 0.50
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (20 bp):
TTATTTTTTTTCATTTTCCA
Found at i:16614822 original size:20 final size:20
Alignment explanation
Indices: 16614794--16614835 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16614784 CAAAAAAAAT
16614794 AAAACAAAT-AATAATAATAA
1 AAAACAAATAAATAA-AATAA
*
16614814 AAAATAAATAAATAAAATAA
1 AAAACAAATAAATAAAATAA
16614834 AA
1 AA
16614836 TCAAGGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAACAAATAAATAAAATAA
Found at i:16618113 original size:29 final size:28
Alignment explanation
Indices: 16618049--16618113 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
16618039 ATTTAAGTTT
* *
16618049 TTAATATTTTATTACAATCAATTGAATCT
1 TTAAT-TTTTATTACAATCAATTGAACCC
* *
16618078 TTAAATTTTTATTTCGACTCAATTGAACCC
1 TT-AATTTTTATTAC-AATCAATTGAACCC
16618108 TTAATT
1 TTAATT
16618114 AGATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.48
Consensus pattern (28 bp):
TTAATTTTTATTACAATCAATTGAACCC
Found at i:16618925 original size:2 final size:2
Alignment explanation
Indices: 16618918--16618956 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16618908 TATCCTTACA
* *
16618918 AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16618957 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:16618961 original size:2 final size:2
Alignment explanation
Indices: 16618956--16618980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16618946 ATATATATAT
16618956 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
16618981 CATATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16621692 original size:14 final size:14
Alignment explanation
Indices: 16621673--16621700 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16621663 CACCTTGACA
16621673 AGAGGGGGAGGGGG
1 AGAGGGGGAGGGGG
16621687 AGAGGGGGAGGGGG
1 AGAGGGGGAGGGGG
16621701 GGTGGCCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.79, T:0.00
Consensus pattern (14 bp):
AGAGGGGGAGGGGG
Found at i:16623520 original size:18 final size:18
Alignment explanation
Indices: 16623497--16623532 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16623487 ATCTCAATAA
16623497 AACCTAGGACAAAAATTG
1 AACCTAGGACAAAAATTG
*
16623515 AACCTAGGATAAAAATTG
1 AACCTAGGACAAAAATTG
16623533 CGCTTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (18 bp):
AACCTAGGACAAAAATTG
Found at i:16624995 original size:18 final size:17
Alignment explanation
Indices: 16624972--16625020 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
16624962 CATTACTTCT
16624972 TTTTTTTCAAATATATA
1 TTTTTTTCAAATATATA
* *
16624989 ATTTTTTCAACTGATATA
1 TTTTTTTCAAAT-ATATA
16625007 TTTTTTTCAAATAT
1 TTTTTTTCAAATAT
16625021 TTATACTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTTTTCAAATATATA
Found at i:16625389 original size:15 final size:17
Alignment explanation
Indices: 16625359--16625393 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
16625349 GTATCTTAAA
16625359 ATTATAATTATTTTTAT
1 ATTATAATTATTTTTAT
16625376 ATTATAA-T-TTTTTAT
1 ATTATAATTATTTTTAT
16625391 ATT
1 ATT
16625394 TTTAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATAATTATTTTTAT
Found at i:16641906 original size:2 final size:2
Alignment explanation
Indices: 16641895--16641924 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16641885 ATTTTTATTT
16641895 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16641925 TAGTGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16642410 original size:54 final size:54
Alignment explanation
Indices: 16642324--16642434 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
16642314 TGTATGAGTT
* *
16642324 ATAGGACTCCATGGCAATGGATCAAAAAGTCTTATATGAAGCCCATTCAAAATC
1 ATAGGACTCCATGGCAATGGATCAAAAAGTCTTAAATAAAGCCCATTCAAAATC
* ** *
16642378 ATAGGGCTCCATGGCAATGGATCAAACGGTCTTAAATAAAGCCCATTCAAAGTC
1 ATAGGACTCCATGGCAATGGATCAAAAAGTCTTAAATAAAGCCCATTCAAAATC
16642432 ATA
1 ATA
16642435 TGGCGACGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (54 bp):
ATAGGACTCCATGGCAATGGATCAAAAAGTCTTAAATAAAGCCCATTCAAAATC
Found at i:16648076 original size:31 final size:31
Alignment explanation
Indices: 16648031--16648090 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
16648021 AAATTTACTT
*
16648031 ATTAATGAGATAGCATCATTTGATTCATTTC
1 ATTAATAAGATAGCATCATTTGATTCATTTC
* *
16648062 ATTAATAAGGTAGCATCATTTTATTCATT
1 ATTAATAAGATAGCATCATTTGATTCATT
16648091 GATATTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (31 bp):
ATTAATAAGATAGCATCATTTGATTCATTTC
Found at i:16648123 original size:24 final size:24
Alignment explanation
Indices: 16648087--16648134 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16648077 TCATTTTATT
* * *
16648087 CATTGATATTGTATAAAATCTATA
1 CATTGACAGTGTATAAAATATATA
*
16648111 CATTGACAGTGTATCAAATATATA
1 CATTGACAGTGTATAAAATATATA
16648135 TATATATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (24 bp):
CATTGACAGTGTATAAAATATATA
Found at i:16651752 original size:12 final size:12
Alignment explanation
Indices: 16651735--16651761 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16651725 AGAATCTGCT
16651735 TTATTTTGCTGA
1 TTATTTTGCTGA
16651747 TTATTTTGCTGA
1 TTATTTTGCTGA
16651759 TTA
1 TTA
16651762 GAGATGATAT
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:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (12 bp):
TTATTTTGCTGA
Found at i:16653640 original size:14 final size:14
Alignment explanation
Indices: 16653602--16653642 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
16653592 TAAAAGCATA
* *
16653602 ATTTATTTAATAAA
1 ATTTATTTAATTAT
16653616 ATTTA-TT-ATTAT
1 ATTTATTTAATTAT
16653628 ATTTATTTAATTAT
1 ATTTATTTAATTAT
16653642 A
1 A
16653643 CAAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTAATTAT
Found at i:16655712 original size:19 final size:18
Alignment explanation
Indices: 16655686--16655729 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
16655676 AAATGAAAAT
*
16655686 TTTATTATGTTATACATA
1 TTTATTATGATATACATA
*
16655704 TTTACTTATGATATATATA
1 TTTA-TTATGATATACATA
16655723 TTGTATT
1 TT-TATT
16655730 TTACTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 16 0.73
20 2 0.09
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTATTATGATATACATA
Found at i:16656838 original size:19 final size:20
Alignment explanation
Indices: 16656804--16656842 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
16656794 ATACTTGGTT
16656804 TAGATATGTAAATTATGATTA
1 TAGATATG-AAATTATGATTA
16656825 TAGATATG-AATTATGATT
1 TAGATATGAAATTATGATT
16656843 TAAGTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGATATGAAATTATGATTA
Found at i:16658141 original size:18 final size:16
Alignment explanation
Indices: 16658118--16658202 Score: 55
Period size: 17 Copynumber: 4.9 Consensus size: 16
16658108 ACTTAATAAA
16658118 AAATAAAAAAGTAAAAT
1 AAATAAAAAAG-AAAAT
*
16658135 GAAATAAATAAGAAAAT
1 -AAATAAAAAAGAAAAT
* *
16658152 ATATAAAAAAAATAAAT
1 AAATAAAAAAGA-AAAT
* *
16658169 AAAATGTAAATA-AAAAT
1 -AAAT-AAAAAAGAAAAT
16658186 AAAATAAAAAAAGAAAA
1 -AAAT-AAAAAAGAAAA
16658203 ACATGTGATC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
16 9 0.17
17 22 0.42
18 18 0.34
19 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATAAAAAAGAAAAT
Found at i:16658146 original size:45 final size:40
Alignment explanation
Indices: 16658113--16658203 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 40
16658103 AGAATACTTA
16658113 ATAAAAAATAAAAAAGTAAAATG-AAATAAATAAGAAAATAT
1 ATAAAAAA-AAAAAA-TAAAATGTAAATAAATAAGAAAATAT
* *
16658154 ATAAAAAAAATAAATAAAATGTAAATAAA-AATAAAATA-
1 ATAAAAAAAAAAAATAAAATGTAAATAAATAAGAAAATAT
*
16658192 A-AAAAAGAAAAA
1 ATAAAAAAAAAAA
16658204 CATGTGATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 9 0.20
38 1 0.02
39 15 0.33
40 12 0.27
41 8 0.18
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (40 bp):
ATAAAAAAAAAAAATAAAATGTAAATAAATAAGAAAATAT
Found at i:16658165 original size:13 final size:13
Alignment explanation
Indices: 16658112--16658172 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
16658102 TAGAATACTT
*
16658112 AATAAAAAATAAAA
1 AATAAAAAA-AATA
*
16658126 AAGTAAAATGAAATA
1 AA-TAAAA-AAAATA
*
16658141 AAT-AAGAAAATA
1 AATAAAAAAAATA
*
16658153 TATAAAAAAAATA
1 AATAAAAAAAATA
16658166 AATAAAA
1 AATAAAA
16658173 TGTAAATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
12 7 0.19
13 16 0.43
14 3 0.08
15 10 0.27
16 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AATAAAAAAAATA
Found at i:16658172 original size:11 final size:11
Alignment explanation
Indices: 16658118--16658196 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
16658108 ACTTAATAAA
16658118 AAATAAAAAAGT
1 AAATAAAAAA-T
**
16658130 AAA-ATGAAAT
1 AAATAAAAAAT
16658140 AAATAAGAAAAT
1 AAATAA-AAAAT
*
16658152 ATATAAAAAAAAT
1 A-A-ATAAAAAAT
**
16658165 AAATAAAATGT
1 AAATAAAAAAT
16658176 AAAT-AAAAAT
1 AAATAAAAAAT
16658186 AAAATAAAAAA
1 -AAATAAAAAA
16658197 AGAAAAACAT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
10 8 0.16
11 19 0.37
12 14 0.27
13 7 0.14
14 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:16658190 original size:22 final size:20
Alignment explanation
Indices: 16658155--16658194 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
16658145 AGAAAATATA
16658155 TAAAAAAAATAAATAAAATG
1 TAAAAAAAATAAATAAAATG
16658175 TAAATAAAAATAAAATAAAA
1 TAAA-AAAAAT-AAATAAAA
16658195 AAAGAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (20 bp):
TAAAAAAAATAAATAAAATG
Found at i:16658190 original size:39 final size:41
Alignment explanation
Indices: 16658113--16658191 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 41
16658103 AGAATACTTA
16658113 ATAAAAAATAAAAAAGTAAAATGAAATAAATAAGAAAATAT
1 ATAAAAAATAAAAAAGTAAAATGAAATAAATAAGAAAATAT
* *
16658154 ATAAAAAA-AATAAA-TAAAATGTAAATAAA-AATAAAATA
1 ATAAAAAATAAAAAAGTAAAATG-AAATAAATAAGAAAATA
16658192 AAAAAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 15 0.43
40 12 0.34
41 8 0.23
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (41 bp):
ATAAAAAATAAAAAAGTAAAATGAAATAAATAAGAAAATAT
Found at i:16660795 original size:58 final size:57
Alignment explanation
Indices: 16660607--16660898 Score: 233
Period size: 60 Copynumber: 5.1 Consensus size: 57
16660597 AGTACAGAGA
* ** * * **
16660607 AAAATTGATACTTTCAACTTTTCCCCCCAAA-A---TTTTAGAAATTTCAATTTCGAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTGGAAATTT-TATTTTAAG
* * *
16660661 AAAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTGAAAATTTATTTTTTTAAG
1 -AAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTGGAAA-TT-TTATTTTAAG
* * *
16660721 ACAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGGAACTTTTAATTTCAATG
1 A-AAATTGATACTTTCAACTTTTCCTC-AAAAATACTTTTTTGGAAATTTT-ATTTTAA-G
* ** *
16660781 AAAATTG-TACTTTCAATTTTTTCCTC-AAAACCCTTTTTT-GAAAATTTATTCTTAAG
1 AAAATTGATACTTTCAA-CTTTTCCTCAAAAATACTTTTTTGGAAATTTTATT-TTAAG
* **
16660837 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAAATTTTA-TTTAGAG
1 -AAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTGGAAATTTTATTTTA-AG
16660895 AAAA
1 AAAA
16660899 ATAAAATAAA
Statistics
Matches: 191, Mismatches: 28, Indels: 34
0.75 0.11 0.13
Matches are distributed among these distances:
55 28 0.15
56 5 0.03
57 31 0.16
58 43 0.23
59 35 0.18
60 48 0.25
61 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTGGAAATTTTATTTTAAG
Found at i:16660887 original size:116 final size:117
Alignment explanation
Indices: 16660604--16660900 Score: 344
Period size: 116 Copynumber: 2.6 Consensus size: 117
16660594 TTTAGTACAG
** * *
16660604 AGAAAAATTGATACTTTCAACTTTTCCCCCCAAA-A---TTTTAGAAATTTCAATTTCGAGAAAA
1 AGAAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTAGAAATTTTAATTTCAAGAAAA
*
16660665 ATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTGAAAATTTATTTTTTTA
65 ATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTGAAAATTTA-TTTCTTA
* * *
16660719 AGACAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAACTTTTAATTTCAATG-AA
1 AGAAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTAGAAATTTTAATTTCAA-GAAA
* **
16660783 AATTG-TACTTTCAATTTTTTCCTC-AAAACCCTTTTTTGAAAATTTA-TTCTTA
64 AATTGATACTTTCAA-CTTTTCCTCAAAAAAACTTTTTTGAAAATTTATTTCTTA
**
16660835 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAAATTTT-ATTT-AGAGAAA
1 AGAAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTAGAAATTTTAATTTCA-AGAAA
16660898 AAT
64 AAT
16660901 AAAATAAATA
Statistics
Matches: 157, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
114 5 0.03
115 37 0.24
116 52 0.33
117 1 0.01
118 29 0.18
119 32 0.20
120 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.43
Consensus pattern (117 bp):
AGAAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTAGAAATTTTAATTTCAAGAAAAA
TTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTGAAAATTTATTTCTTA
Found at i:16660899 original size:58 final size:56
Alignment explanation
Indices: 16660604--16660900 Score: 239
Period size: 58 Copynumber: 5.1 Consensus size: 56
16660594 TTTAGTACAG
* ** * * *
16660604 AGAAAAATTGATACTTTCAACTTTTCCCCCCAAAA---TTTTAGAAATTTCAATTTCG
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTGGAAATTT-TATTT-A
* *
16660659 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTGAAAATTTATTTTTTTA
1 AGAAAAATTGATACTTTCAACTTTTCCTC-AAAAAACTTTTTTGGAAA--T-TTTATTTA
* * *
16660719 AGACAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGGAACTTTTAATTTCA
1 AGAAAAATTGATACTTTCAACTTTTCCTC-AAAAA-ACTTTTTTGGAAATTTT-ATTT-A
* ** *
16660778 ATG-AAAATTG-TACTTTCAATTTTTTCCTCAAAACCCTTTTTT-GAAAATTTATTCTTA
1 A-GAAAAATTGATACTTTCAA-CTTTTCCTCAAAAAACTTTTTTGGAAATTTTA-T-TTA
* **
16660835 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAAATTTTATTTA
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-ACTTTTTTGGAAATTTTATTTA
16660892 GAGAAAAAT
1 -AGAAAAAT
16660901 AAAATAAATA
Statistics
Matches: 195, Mismatches: 27, Indels: 37
0.75 0.10 0.14
Matches are distributed among these distances:
55 28 0.14
56 6 0.03
57 34 0.17
58 45 0.23
59 38 0.19
60 38 0.19
61 4 0.02
62 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.43
Consensus pattern (56 bp):
AGAAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTGGAAATTTTATTTA
Found at i:16660930 original size:9 final size:9
Alignment explanation
Indices: 16660897--16660926 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16660887 ATTTAGAGAA
16660897 AAATAAAAT
1 AAATAAAAT
16660906 AAATAAAAT
1 AAATAAAAT
16660915 AAATAAAA-
1 AAATAAAAT
16660923 AAAT
1 AAAT
16660927 TAAACAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:16661891 original size:21 final size:21
Alignment explanation
Indices: 16661867--16661960 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 21
16661857 TAATTAGACA
16661867 AAAAATAATAATA-AAATAAAT
1 AAAAA-AATAATACAAATAAAT
*
16661888 -AAAAAATATTACAAGATAAAT
1 AAAAAAATAATACAA-ATAAAT
* *
16661909 AAAAAAATCATA-ATAATAGAT
1 AAAAAAATAATACA-AATAAAT
* *
16661930 AAATTATAAT-ATACAAATGAAT
1 AAA--AAAATAATACAAATAAAT
*
16661952 AAATAAATA
1 AAAAAAATA
16661961 TATAACTGCA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
19 6 0.11
20 9 0.16
21 15 0.27
22 21 0.38
23 5 0.09
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAAAAATAATACAAATAAAT
Found at i:16661922 original size:47 final size:48
Alignment explanation
Indices: 16661832--16661926 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 48
16661822 AAAATCAGAT
*
16661832 AAATAAAAAAAAAAATATTAATAGATAATTAGACAAAAAATAATAATA
1 AAATAAAAAAAAAAATATTAATAGATAAATAGACAAAAAATAATAATA
*
16661880 AAAT-AAATAAAAAATATTACA-AGATAAATA-A-AAAAATCATAATAATA
1 AAATAAAAAAAAAAATATTA-ATAGATAAATAGACAAAAA--ATAATAATA
16661927 GATAAATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
45 5 0.12
46 1 0.02
47 31 0.74
48 5 0.12
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (48 bp):
AAATAAAAAAAAAAATATTAATAGATAAATAGACAAAAAATAATAATA
Found at i:16661929 original size:25 final size:24
Alignment explanation
Indices: 16661834--16661933 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 24
16661824 AATCAGATAA
*
16661834 ATAAA-AAAAAAA-ATATTAATAG
1 ATAAATAAAAAAATATAATAATAG
* *
16661856 ATAATTAGACAAAAA-ATAATAATAAA
1 ATAAATA-A-AAAAATATAATAAT-AG
16661882 ATAAAT-AAAAAATAT--TACA-AG
1 ATAAATAAAAAAATATAATA-ATAG
16661903 ATAAATAAAAAAATCATAATAATAG
1 ATAAATAAAAAAAT-ATAATAATAG
16661928 ATAAAT
1 ATAAAT
16661934 TATAATATAC
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
21 7 0.11
22 13 0.21
23 9 0.15
24 5 0.08
25 22 0.35
26 6 0.10
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (24 bp):
ATAAATAAAAAAATATAATAATAG
Found at i:16661962 original size:20 final size:20
Alignment explanation
Indices: 16661880--16661962 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 20
16661870 AATAATAATA
16661880 AAATAAATAAA-AAATATTAC
1 AAATAAATAAATAAATA-TAC
*
16661900 AAGATAAATAAAAAAATCATA-
1 AA-ATAAATAAATAAAT-ATAC
*
16661921 ATAATAGATAAATTATAATATAC
1 A-AATAAATAAA-TA-AATATAC
*
16661944 AAATGAATAAATAAATATA
1 AAATAAATAAATAAATATA
16661963 TAACTGCATA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
20 8 0.15
21 20 0.38
22 19 0.37
23 5 0.10
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
AAATAAATAAATAAATATAC
Found at i:16662134 original size:23 final size:23
Alignment explanation
Indices: 16662107--16662152 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16662097 ATATATACAT
*
16662107 AAAATATAAATTA-AAAATTAAAA
1 AAAATATAAAATACAAAA-TAAAA
16662130 AAAATATAAAATACAAAATAAAA
1 AAAATATAAAATACAAAATAAAA
16662153 GCAAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAATATAAAATACAAAATAAAA
Found at i:16662391 original size:46 final size:45
Alignment explanation
Indices: 16662338--16662537 Score: 264
Period size: 46 Copynumber: 4.5 Consensus size: 45
16662328 AAGATTTGAT
*
16662338 CAAGGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAATGAATAAA
1 CAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA-GAATAAA
16662384 CAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATGAATAAA
1 CAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA-GAATAAA
* * * *
16662430 CAACGCTCCCCTAATCAGAGGCTCGACGACTTTGGAAA-AAT-AA
1 CAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGAATAAA
* * *
16662473 -ATGACTCCTCTAATCAGAGGCTCAATGACTTTGAAAAG-ATAAA
1 CAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGAATAAA
* *
16662516 CAAAGCTCCTTTAATCAGAGGC
1 CAAGGCTCCTCTAATCAGAGGC
16662538 ATTTTTTTGT
Statistics
Matches: 135, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.24
43 4 0.03
44 20 0.15
46 79 0.59
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (45 bp):
CAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGAATAAA
Found at i:16662503 original size:42 final size:40
Alignment explanation
Indices: 16662342--16662973 Score: 304
Period size: 41 Copynumber: 15.0 Consensus size: 40
16662332 TTTGATCAAG
* * *
16662342 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAATGAATAAACAAG
1 GCTCCTCTAATCAGAGGCTCCACGACTTTG-AAA--AAT--A-AAT
* *
16662388 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATGAATAAACAAC
1 GCTCCTCTAATCAGAGGCTCCACGACTTTG-AAA--AAT--A-AAT
* *
16662434 GCTCCCCTAATCAGAGGCTCGACGACTTTGGAAAAATAAAT
1 GCTCCTCTAATCAGAGGCTCCACGACTTT-GAAAAATAAAT
* * *
16662475 GACTCCTCTAATCAGAGGCTCAATGACTTTGAAAAGATAAACAAA
1 G-CTCCTCTAATCAGAGGCTCCACGACTTTGAAAA-AT--A-AAT
* **** ** *****
16662520 GCTCCTTTAATCAGAGGCATTTTTTTGTTTTTTTTTTATCAAA-
1 GCTCCTCTAATCAGAGGC---TCCACGACTTTGAAAAAT-AAAT
* ** * *
16662563 GCTCCTCTAAGCAGAAACTCAACGACTTGGAAAAATAAAT
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAAT
* * * ** * * *
16662603 GAGTTCTCTAAGCAGAAACACCATGAC-TTCAAAAATAAAT
1 G-CTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAAT
* * * *
16662643 ACTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAA-T
* *
16662684 GCTCCTCTAATCAAAGG-TAACCACAACTTTGAAAAATAAATT
1 GCTCCTCTAATCAGAGGCT--CCACGACTTTGAAAAATAAA-T
* * *
16662726 GCTCCTCTAAACAGAGGCACCATGACTTT-AAAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAA-TAAA-T
* *
16662767 GCTCCTCTAAACAGAGGCAACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAATCAGAGGC-TCCACGACTTTGAAAAATAAA-T
* ** * *
16662809 GCTCCTCTACA-CAGAGGCACCATAACTTTGAAAAGTAGATT
1 GCTCCTCTA-ATCAGAGGCTCCACGACTTTGAAAAATA-AAT
* * * *
16662850 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAA-T
* * * * * * *
16662891 GCTCCTCTAAACAAAGGCACCTCAACTTTTGGAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCCACGAC-TTTGAAAAATAAA-T
* * *
16662933 GCTCCTCTAAAT-AGAGGCACCACAACTTTGAAAAGTAAAT
1 GCTCCTCT-AATCAGAGGCTCCACGACTTTGAAAAATAAAT
16662973 G
1 G
16662974 ACTCATTGAC
Statistics
Matches: 483, Mismatches: 78, Indels: 56
0.78 0.13 0.09
Matches are distributed among these distances:
39 21 0.04
40 38 0.08
41 161 0.33
42 132 0.27
43 22 0.05
44 22 0.05
45 4 0.01
46 76 0.16
47 7 0.01
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (40 bp):
GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAAT
Found at i:16662743 original size:83 final size:82
Alignment explanation
Indices: 16662633--16662972 Score: 441
Period size: 83 Copynumber: 4.1 Consensus size: 82
16662623 CCATGACTTC
* *
16662633 AAAAATAAA-TACTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAATCA
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAAACA
*
16662697 AAGGTAACCACAACTTTG
66 GAGG-AACCACAACTTTG
**
16662715 AAAAATAAATTGCTCCTCTAAACAGAGGCACCATGACTTT-AAAAAGTAAATTGCTCCTCTAAAC
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAA-TAAATTGCTCCTCTAAAC
*
16662779 AGAGGCAACCACGACTTTG
65 AGAGG-AACCACAACTTTG
* * * *
16662798 AAAAATAAATTGCTCCTCTACACAGAGGCACCATAACTTTGAAAAGTAGATTGCTCCTCTAAACA
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAAACA
* **
16662863 GAGGCACCATGACTTTG
66 GAGGAACCACAACTTTG
* * * * * *
16662880 AAAAGTAAATTGCTCCTCTAAACAAAGGCACCTCAACTTTTGGAAAGTAAATTGCTCCTCTAAAT
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAAC-TTTGAAAAATAAATTGCTCCTCTAAAC
*
16662945 AGAGGCACCACAACTTTG
65 AGAGGAACCACAACTTTG
*
16662963 AAAAGTAAAT
1 AAAAATAAAT
16662973 GACTCATTGA
Statistics
Matches: 231, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
82 57 0.25
83 170 0.74
84 4 0.02
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (82 bp):
AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTAAACA
GAGGAACCACAACTTTG
Found at i:16662837 original size:41 final size:41
Alignment explanation
Indices: 16662633--16662972 Score: 450
Period size: 41 Copynumber: 8.2 Consensus size: 41
16662623 CCATGACTTC
*
16662633 AAAAATAAA-TACTCCTCTAAACAGAGGCACCACAACTTTG
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG
* * *
16662673 AAAAATAAATTGCTCCTCTAATCAAAGGTAACCACAACTTTG
1 AAAAATAAATTGCTCCTCTAAACAGAGG-CACCACAACTTTG
**
16662715 AAAAATAAATTGCTCCTCTAAACAGAGGCACCATGACTTT-
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG
*
16662755 AAAAAGTAAATTGCTCCTCTAAACAGAGGCAACCACGACTTTG
1 AAAAA-TAAATTGCTCCTCTAAACAGAGGC-ACCACAACTTTG
* *
16662798 AAAAATAAATTGCTCCTCTACACAGAGGCACCATAACTTTG
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG
* * **
16662839 AAAAGTAGATTGCTCCTCTAAACAGAGGCACCATGACTTTG
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG
* * *
16662880 AAAAGTAAATTGCTCCTCTAAACAAAGGCACCTCAACTTTTG
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAAC-TTTG
* * *
16662922 GAAAGTAAATTGCTCCTCTAAATAGAGGCACCACAACTTTG
1 AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG
*
16662963 AAAAGTAAAT
1 AAAAATAAAT
16662973 GACTCATTGA
Statistics
Matches: 267, Mismatches: 27, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
40 14 0.05
41 140 0.52
42 108 0.40
43 5 0.02
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (41 bp):
AAAAATAAATTGCTCCTCTAAACAGAGGCACCACAACTTTG
Found at i:16662851 original size:124 final size:122
Alignment explanation
Indices: 16662621--16662972 Score: 510
Period size: 124 Copynumber: 2.9 Consensus size: 122
16662611 TAAGCAGAAA
* *
16662621 CACCATGACTTCAAAAA-TAAA-TACTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
1 CACCATGACTTTAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
* * *
16662684 GCTCCTCTAATCAAAGGTAACCACAACTTTGAAAAATAAATTGCTCCTCTAAACAGAGG
66 GCTCCTCTAA-CAGAGG-CACCACAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
*
16662743 CACCATGACTTTAAAAAGTAAATTGCTCCTCTAAACAGAGGCAACCACGACTTTGAAAAATAAAT
1 CACCATGACTTTAAAAAGTAAATTGCTCCTCTAAACAGAGGC-ACCACAACTTTGAAAAATAAAT
* *
16662808 TGCTCCTCTACACAGAGGCACCATAACTTTGAAAAGTAGATTGCTCCTCTAAACAGAGG
65 TGCTCCTCTA-ACAGAGGCACCACAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
* * * * *
16662867 CACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCTCAACTTTTGGAAAGTAAAT
1 CACCATGACTTTAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACAAC-TTTGAAAAATAAAT
*
16662932 TGCTCCTCTAAATAGAGGCACCACAACTTTGAAAAGTAAAT
65 TGCTCCTCT-AACAGAGGCACCACAACTTTGAAAAGTAAAT
16662973 GACTCATTGA
Statistics
Matches: 207, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
122 16 0.08
123 10 0.05
124 143 0.69
125 37 0.18
126 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (122 bp):
CACCATGACTTTAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
GCTCCTCTAACAGAGGCACCACAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
Found at i:16663306 original size:44 final size:44
Alignment explanation
Indices: 16663256--16663349 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 44
16663246 TCAAAAGTTC
* *
16663256 TCATTTGGCAAACTTG-GAATTCATATCCAAAAA-TCTAAAGCTTT
1 TCATTTGG-AAACTTGAAAATTCACATCCAAAAATTC-AAAGCTTT
**
16663300 TCATTT-GAATTTTGAAAATTCACATCCAAAAATTCAAAGCTTT
1 TCATTTGGAAACTTGAAAATTCACATCCAAAAATTCAAAGCTTT
16663343 TCATTTG
1 TCATTTG
16663350 AGTTCAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
42 5 0.12
43 30 0.70
44 8 0.19
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (44 bp):
TCATTTGGAAACTTGAAAATTCACATCCAAAAATTCAAAGCTTT
Found at i:16664731 original size:12 final size:12
Alignment explanation
Indices: 16664701--16664749 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
16664691 TCTTTTTTCA
* *
16664701 TTTTTTCCTTCT
1 TTTTTTCTTTTT
*
16664713 TTCTTTCTTTTT
1 TTTTTTCTTTTT
16664725 TTTTTTCTTTTT
1 TTTTTTCTTTTT
16664737 TTTTATT-TTTTT
1 TTTT-TTCTTTTT
16664749 T
1 T
16664750 CATCATCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 30 0.94
13 2 0.06
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:16668856 original size:1 final size:1
Alignment explanation
Indices: 16668852--16668912 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
16668842 TTATTTAGAG
* * * * * * * *
16668852 AAAAATAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAATAAAAAAAATAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16668913 TATTAAACAA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.00, G:0.02, T:0.11
Consensus pattern (1 bp):
A
Found at i:16668871 original size:8 final size:8
Alignment explanation
Indices: 16668858--16668911 Score: 90
Period size: 8 Copynumber: 6.5 Consensus size: 8
16668848 AGAGAAAAAT
16668858 AAAATAAA
1 AAAATAAA
16668866 AAAATAAA
1 AAAATAAA
16668874 AAAATAAA
1 AAAATAAA
16668882 AAAATAAA
1 AAAATAAA
16668890 AAAATAAAA
1 AAAAT-AAA
16668899 AAAATAGAA
1 AAAATA-AA
16668908 AAAA
1 AAAA
16668912 ATATTAAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
8 30 0.68
9 14 0.32
ACGTcount: A:0.87, C:0.00, G:0.02, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:16668890 original size:24 final size:26
Alignment explanation
Indices: 16668864--16668914 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
16668854 AAATAAAATA
16668864 AAAAAATAAAAAAAT-AAAAAAATA-
1 AAAAAATAAAAAAATAAAAAAAATAG
16668888 AAAAAATAAAAAAAATAGAAAAAAATA
1 AAAAAAT-AAAAAAATA-AAAAAAATA
16668915 TTAAACAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
27 9 0.38
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.12
Consensus pattern (26 bp):
AAAAAATAAAAAAATAAAAAAAATAG
Found at i:16668979 original size:20 final size:23
Alignment explanation
Indices: 16668885--16668966 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
16668875 AAATAAAAAA
16668885 ATAAAAA-AATAAA-AAA-AATAG
1 ATAAAAATAATAAATAAATAAT-G
* * *
16668906 AAAAAAATATTAAACAATCATAAT-
1 ATAAAAATAATAAATAA--ATAATG
*
16668930 ATAATAATAATAAATAAATAATG
1 ATAAAAATAATAAATAAATAATG
16668953 ATAAAAATAATAAA
1 ATAAAAATAATAAA
16668967 AGAAATGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
21 6 0.12
22 10 0.21
23 15 0.31
24 13 0.27
25 1 0.02
26 3 0.06
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (23 bp):
ATAAAAATAATAAATAAATAATG
Found at i:16669031 original size:10 final size:10
Alignment explanation
Indices: 16669005--16669039 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
16668995 CTCGGCTTAC
* *
16669005 GGCTCGGCTC
1 GGCTCGACTT
16669015 GGCTCGACTT
1 GGCTCGACTT
16669025 GGCTCGACTT
1 GGCTCGACTT
16669035 GGCTC
1 GGCTC
16669040 AAGGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.06, C:0.34, G:0.34, T:0.26
Consensus pattern (10 bp):
GGCTCGACTT
Found at i:16669986 original size:21 final size:21
Alignment explanation
Indices: 16669884--16669989 Score: 74
Period size: 21 Copynumber: 4.9 Consensus size: 21
16669874 AGAAAAAAAA
* * *
16669884 AGATAAATAAAAAATATTACA
1 AGATAAATAAAATATATAACT
16669905 AGATAAATAAAAAAATCATAATAA-T
1 AGATAAAT---AAAAT-AT-ATAACT
* * *
16669930 AGATAAATTATAATATACAAAT
1 AGATAAA-TAAAATATATAACT
16669952 -GAATAAAT-AAATATATAACT
1 AG-ATAAATAAAATATATAACT
16669972 AGATAAATAAAATATATA
1 AGATAAATAAAATATATA
16669990 TATAAATATT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
20 15 0.22
21 23 0.34
22 8 0.12
23 4 0.06
24 4 0.06
25 9 0.13
26 4 0.06
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (21 bp):
AGATAAATAAAATATATAACT
Found at i:16670085 original size:7 final size:7
Alignment explanation
Indices: 16670053--16670152 Score: 55
Period size: 7 Copynumber: 13.7 Consensus size: 7
16670043 ATACATATAT
16670053 TAATAAA
1 TAATAAA
*
16670060 TAGT-AA
1 TAATAAA
16670066 TAATAAA
1 TAATAAA
16670073 TAAATAAA
1 T-AATAAA
16670081 TAATAAA
1 TAATAAA
16670088 TACATAAGA
1 TA-ATAA-A
*
16670097 TACAAAGAA
1 TA-ATA-AA
* *
16670106 AAATATA
1 TAATAAA
16670113 TACATAAA
1 TA-ATAAA
16670121 -ATATAAAA
1 TA-AT-AAA
16670129 TAA-AAA
1 TAATAAA
16670135 TAA-AAA
1 TAATAAA
16670141 TAATAAA
1 TAATAAA
*
16670148 AAATA
1 TAATA
16670153 TAAAATACAA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
6 17 0.23
7 26 0.35
8 21 0.28
9 9 0.12
10 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (7 bp):
TAATAAA
Found at i:16670133 original size:12 final size:12
Alignment explanation
Indices: 16670105--16670169 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
16670095 GATACAAAGA
*
16670105 AAAATATATACAT
1 AAAATATA-AAAT
16670118 AAAATATAAAAT
1 AAAATATAAAAT
16670130 AAAA-ATAAAAAT
1 AAAATAT-AAAAT
16670142 AATAA-A-AAATAT
1 AA-AATATAAA-AT
*
16670154 AAAATACAAAAT
1 AAAATATAAAAT
16670166 AAAA
1 AAAA
16670170 GCAAAATTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
11 7 0.15
12 25 0.54
13 14 0.30
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATATAAAAT
Found at i:16670133 original size:25 final size:25
Alignment explanation
Indices: 16670082--16670138 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
16670072 ATAAATAAAT
*
16670082 AATAAATACATAAGATACAAAGAAA
1 AATAAATACATAAAATACAAAGAAA
* * *
16670107 AATATATACATAAAATATAAAATAAA
1 AATAAATACATAAAATA-CAAAGAAA
16670133 AATAAA
1 AATAAA
16670139 AATAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (25 bp):
AATAAATACATAAAATACAAAGAAA
Found at i:16670157 original size:7 final size:7
Alignment explanation
Indices: 16670116--16670166 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
16670106 AAATATATAC
16670116 ATAAAAT
1 ATAAAAT
16670123 ATAAAAT
1 ATAAAAT
16670130 A-AAAAT
1 ATAAAAT
16670136 A-AAAAT
1 ATAAAAT
16670142 AATAAAAAAT
1 -AT--AAAAT
16670152 ATAAAAT
1 ATAAAAT
*
16670159 ACAAAAT
1 ATAAAAT
16670166 A
1 A
16670167 AAAGCAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 11 0.28
7 21 0.54
9 2 0.05
10 5 0.13
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (7 bp):
ATAAAAT
Found at i:16676316 original size:19 final size:20
Alignment explanation
Indices: 16676279--16676319 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16676269 TTCATCCTAC
*
16676279 CTAGAAAAATCCAATTTTTT
1 CTAGAAAAATCCAAGTTTTT
*
16676299 CTAGAAAAA-CCTAGTTTTT
1 CTAGAAAAATCCAAGTTTTT
16676318 CT
1 CT
16676320 CAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (20 bp):
CTAGAAAAATCCAAGTTTTT
Found at i:16676791 original size:3 final size:3
Alignment explanation
Indices: 16676775--16676831 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
16676765 CATTTTTTTG
*
16676775 AAT AAGT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16676821 AAT AAT AAT AA
1 AAT AAT AAT AA
16676832 CAACAACAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:16685567 original size:18 final size:18
Alignment explanation
Indices: 16685535--16685569 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16685525 ATGGTTTAAG
16685535 AAAAAGAGAAAAGAAAAC
1 AAAAAGAGAAAAGAAAAC
16685553 AAAAA-AGAAAGAGAAAA
1 AAAAAGAGAAA-AGAAAA
16685570 GACTGATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAGAAAAGAAAAC
Found at i:16691659 original size:10 final size:10
Alignment explanation
Indices: 16691602--16691661 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
16691592 GGGGCATGGT
*
16691602 AAAAAAATGA
1 AAAAAAAAGA
16691612 AAAAAAAA-A
1 AAAAAAAAGA
16691621 ACAAACAAAA-A
1 A-AAA-AAAAGA
*
16691632 TAAAAAAA-A
1 AAAAAAAAGA
16691641 AAAAAAAAGA
1 AAAAAAAAGA
*
16691651 GAAAAAAAGA
1 AAAAAAAAGA
16691661 A
1 A
16691662 GACTTAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 14 0.33
10 23 0.55
11 5 0.12
ACGTcount: A:0.87, C:0.03, G:0.07, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:16691676 original size:1 final size:1
Alignment explanation
Indices: 16691611--16691658 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
16691601 TAAAAAAATG
* * * * *
16691611 AAAAAAAAAAACAAACAAAAATAAAAAAAAAAAAAAAAGAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16691659 GAAGACTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.04, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:16692330 original size:11 final size:11
Alignment explanation
Indices: 16692316--16692350 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
16692306 TTGTATTACA
*
16692316 TACATTGTGTT
1 TACATTGTATT
16692327 TACATTGTATT
1 TACATTGTATT
16692338 TACATTGTATT
1 TACATTGTATT
16692349 TA
1 TA
16692351 AATCCTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (11 bp):
TACATTGTATT
Found at i:16692391 original size:24 final size:24
Alignment explanation
Indices: 16692364--16692421 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
16692354 CCTTGATAAT
16692364 TGCATTTGCATCAATGTTGGAGAA
1 TGCATTTGCATCAATGTTGGAGAA
* *
16692388 TGCATTTACATCAATGTTGGAGCA
1 TGCATTTGCATCAATGTTGGAGAA
16692412 TGCATTTGCA
1 TGCATTTGCA
16692422 CCATGTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (24 bp):
TGCATTTGCATCAATGTTGGAGAA
Found at i:16692748 original size:44 final size:44
Alignment explanation
Indices: 16692698--16692865 Score: 169
Period size: 44 Copynumber: 3.8 Consensus size: 44
16692688 CAAAAACGAC
*
16692698 TCTTTAAATTTTGGATGCGAAACCCTAAAATTTTTCAATGAAAA
1 TCTTTAAATTTTGGATGTGAAACCCTAAAATTTTTCAATGAAAA
* * * * *
16692742 TCTTTAACTTTCGGATGTGAATCCC-AAAATTTTTTGAATGAGAA
1 TCTTTAAATTTTGGATGTGAAACCCTAAAA-TTTTTCAATGAAAA
* * *
16692786 TATTTGAAATTTTGGATGTG-AATCTTAAAATTTTTCAAATGAAAA
1 TCTTT-AAATTTTGGATGTGAAACCCTAAAATTTTTC-AATGAAAA
* * * * *
16692831 TCTTTAACTGTTGGAAGTGAAACCTTGAAATTTTT
1 TCTTTAAATTTTGGATGTGAAACCCTAAAATTTTT
16692866 TAAATAAGAA
Statistics
Matches: 99, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
43 4 0.04
44 55 0.56
45 40 0.40
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (44 bp):
TCTTTAAATTTTGGATGTGAAACCCTAAAATTTTTCAATGAAAA
Found at i:16692820 original size:22 final size:22
Alignment explanation
Indices: 16692754--16692820 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
16692744 TTTAACTTTC
**
16692754 GGATGTGAATCCCAAAATTTTTT
1 GGATGTGAATCTTAAAA-TTTTT
* * * *
16692777 GAATGAGAATATTTGAAA-TTTT
1 GGATGTGAAT-CTTAAAATTTTT
16692799 GGATGTGAATCTTAAAATTTTT
1 GGATGTGAATCTTAAAATTTTT
16692821 CAAATGAAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 5
0.68 0.21 0.11
Matches are distributed among these distances:
21 5 0.16
22 16 0.50
23 8 0.25
24 3 0.09
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (22 bp):
GGATGTGAATCTTAAAATTTTT
Found at i:16692827 original size:89 final size:90
Alignment explanation
Indices: 16692703--16692883 Score: 233
Period size: 89 Copynumber: 2.0 Consensus size: 90
16692693 ACGACTCTTT
* *
16692703 AAATTTTGGATGCGAAACCCTAAAATTTTTCAATGAAAATCTTTAACT-TTCGGATGTGAATCC-
1 AAATTTTGGATGCGAAACCCTAAAATTTTTCAATGAAAATCTTTAACTGTT-GGAAGTGAAACCT
* *
16692766 CAAAATTTTTTGAATGAGAATATTTG
65 CAAAATTTTTTAAATAAGAATATTTG
* * *
16692792 AAATTTTGGATGTG-AATCTTAAAATTTTTCAAATGAAAATCTTTAACTGTTGGAAGTGAAACCT
1 AAATTTTGGATGCGAAACCCTAAAATTTTTC-AATGAAAATCTTTAACTGTTGGAAGTGAAACCT
** *
16692856 TGAAATTTTTTAAATAAGAATCTTTG
65 CAAAATTTTTTAAATAAGAATATTTG
16692882 AA
1 AA
16692884 CTTTAAAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 14 0.18
89 40 0.51
90 25 0.32
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (90 bp):
AAATTTTGGATGCGAAACCCTAAAATTTTTCAATGAAAATCTTTAACTGTTGGAAGTGAAACCTC
AAAATTTTTTAAATAAGAATATTTG
Found at i:16692862 original size:45 final size:45
Alignment explanation
Indices: 16692698--16692887 Score: 181
Period size: 45 Copynumber: 4.2 Consensus size: 45
16692688 CAAAAACGAC
* * *
16692698 TCTTTAAATTTTGGATGCGAAACCCTAAAATTTTTC-AATGAAAA
1 TCTTTAACTTTTGGATGTGAAACCTTAAAATTTTTCAAATGAAAA
* * * ** *
16692742 TCTTTAACTTTCGGATGTGAATCC-CAAAATTTTTTGAATGAGAA
1 TCTTTAACTTTTGGATGTGAAACCTTAAAATTTTTCAAATGAAAA
* * *
16692786 TATTTGAAATTTTGGATGTG-AATCTTAAAATTTTTCAAATGAAAA
1 TCTTT-AACTTTTGGATGTGAAACCTTAAAATTTTTCAAATGAAAA
* * * *
16692831 TCTTTAACTGTTGGAAGTGAAACCTTGAAATTTTTTAAAT-AAGAA
1 TCTTTAACTTTTGGATGTGAAACCTTAAAATTTTTCAAATGAA-AA
16692876 TCTTTGAACTTT
1 TCTTT-AACTTT
16692888 AAAATTTTTT
Statistics
Matches: 116, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
43 9 0.08
44 46 0.40
45 56 0.48
46 5 0.04
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (45 bp):
TCTTTAACTTTTGGATGTGAAACCTTAAAATTTTTCAAATGAAAA
Found at i:16693001 original size:17 final size:17
Alignment explanation
Indices: 16692962--16693022 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
16692952 TGTGAACCTT
*
16692962 TGAATTTATTGTGAA-A
1 TGAATTTTTTGTGAATA
*
16692978 CTAAATTTTTTGTGAATA
1 -TGAATTTTTTGTGAATA
* *
16692996 TGAATTTCTTGCGAACT-
1 TGAATTTTTTGTGAA-TA
16693013 TGAATTTTTT
1 TGAATTTTTT
16693023 ACGAACCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 34 0.94
18 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.49
Consensus pattern (17 bp):
TGAATTTTTTGTGAATA
Found at i:16693758 original size:15 final size:16
Alignment explanation
Indices: 16693739--16693784 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
16693729 GTCAAAAGTA
16693739 AAAAAAAATCAAGAAT
1 AAAAAAAATCAAGAAT
* *
16693755 AAAAAATAT-AATAAT
1 AAAAAAAATCAAGAAT
16693770 AAAAAAAATCAAGAA
1 AAAAAAAATCAAGAA
16693785 ACCCAAAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (16 bp):
AAAAAAAATCAAGAAT
Found at i:16703484 original size:12 final size:12
Alignment explanation
Indices: 16703467--16703496 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16703457 TGTCAATTAG
16703467 CTTCCTAAGCTA
1 CTTCCTAAGCTA
*
16703479 CTTCCTGAGCTA
1 CTTCCTAAGCTA
16703491 CTTCCT
1 CTTCCT
16703497 CAACTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.37, G:0.10, T:0.37
Consensus pattern (12 bp):
CTTCCTAAGCTA
Done.