Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 22 of 109
Found at i:3718736 original size:16 final size:16
Alignment explanation
Indices: 3718711--3718753 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
3718701 TACATGGTAC
*
3718711 CACTAGCCACCCACCT
1 CACTAACCACCCACCT
3718727 CACTAACCACCCACCT
1 CACTAACCACCCACCT
3718743 CACTAACCACC
1 CACTAACCACC
3718754 TGCCCCAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.56, G:0.02, T:0.12
Consensus pattern (16 bp):
CACTAACCACCCACCT
Found at i:3719793 original size:3 final size:3
Alignment explanation
Indices: 3719785--3719834 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
3719775 AAAATGCTTA
* *
3719785 AAT AAT AAT AAT AAT AAT -AT AA- AA- AAT GAT AAT AAG AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3719829 AAT AAT
1 AAT AAT
3719835 TTTTTTTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3719816 original size:21 final size:21
Alignment explanation
Indices: 3719783--3719834 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3719773 AAAAAATGCT
* *
3719783 TAAATAATAATAATAATAATA
1 TAAAAAATAATAATAAGAATA
*
3719804 TAAAAAATGATAATAAGAATA
1 TAAAAAATAATAATAAGAATA
*
3719825 -AAATAATAAT
1 TAAAAAATAAT
3719835 TTTTTTTTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAAAATAATAATAAGAATA
Found at i:3719816 original size:24 final size:24
Alignment explanation
Indices: 3719784--3719830 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3719774 AAAAATGCTT
* *
3719784 AAATAATAATAATAATAATATAAA
1 AAATAATAATAAGAATAAAATAAA
*
3719808 AAATGATAATAAGAATAAAATAA
1 AAATAATAATAAGAATAAAATAA
3719831 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATAATAATAAGAATAAAATAAA
Found at i:3720162 original size:28 final size:28
Alignment explanation
Indices: 3720116--3720300 Score: 151
Period size: 28 Copynumber: 6.4 Consensus size: 28
3720106 TTCGTGTTTT
* * *
3720116 TAAAATTTTAAACCCTAAACCCCAAAACC
1 TAAAA-TTAAAACCTTAAACCCCAAACCC
*
3720145 TAAAATTAAAACCTTAAATCCTTCAAACCC
1 TAAAATTAAAACCTTAAA-CC-CCAAACCC
* *
3720175 TAAAATCAAAA-CTCTAAACCTCAAACCC
1 TAAAATTAAAACCT-TAAACCCCAAACCC
* **
3720203 TAAAATCGAAAA-CTTAAATCTTTCAAACCC
1 TAAAAT-TAAAACCTTAAA-C-CCCAAACCC
*
3720233 TAAAACTAAAATCC-TAAACCCCAAACCC
1 TAAAATTAAAA-CCTTAAACCCCAAACCC
* * **
3720261 TAAAATTAAAACCCTATACCCCAAAATC
1 TAAAATTAAAACCTTAAACCCCAAACCC
3720289 TAAAATTAAAAC
1 TAAAATTAAAAC
3720301 ACTAAATCTT
Statistics
Matches: 132, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.02
28 69 0.52
29 23 0.17
30 37 0.28
31 1 0.01
ACGTcount: A:0.50, C:0.28, G:0.01, T:0.22
Consensus pattern (28 bp):
TAAAATTAAAACCTTAAACCCCAAACCC
Found at i:3720191 original size:14 final size:14
Alignment explanation
Indices: 3720169--3720276 Score: 53
Period size: 14 Copynumber: 7.6 Consensus size: 14
3720159 TAAATCCTTC
3720169 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* *
3720183 AAACTCTAAACCTC-
1 AAACCCTAAA-ATCA
3720197 AAACCCTAAAATCGA
1 AAACCCTAAAATC-A
* *
3720212 AAA--CTTAAATCTTTC
1 AAACCCTAAAATC---A
3720227 AAACCCTAAAA-CTA
1 AAACCCTAAAATC-A
* ** *
3720241 AAATCCTAAACCCC
1 AAACCCTAAAATCA
*
3720255 AAACCCTAAAATTA
1 AAACCCTAAAATCA
3720269 AAACCCTA
1 AAACCCTA
3720277 TACCCCAAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
13 9 0.13
14 45 0.65
15 9 0.13
16 1 0.01
17 5 0.07
ACGTcount: A:0.50, C:0.30, G:0.01, T:0.19
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:3720193 original size:58 final size:58
Alignment explanation
Indices: 3720125--3720273 Score: 205
Period size: 58 Copynumber: 2.6 Consensus size: 58
3720115 TTAAAATTTT
* *
3720125 AAACCCTAAACCCCAAAACCTAAAATTAAAACCTTAAATCCTTCAAACCCTAAAA-TCA
1 AAACTCTAAACCCCAAACCCTAAAATTAAAACCTTAAATCCTTCAAACCCTAAAACT-A
* * *
3720183 AAACTCTAAACCTCAAACCCTAAAATCGAAAA-CTTAAATCTTTCAAACCCTAAAACTA
1 AAACTCTAAACCCCAAACCCTAAAAT-TAAAACCTTAAATCCTTCAAACCCTAAAACTA
3720241 AAA-TCCTAAACCCCAAACCCTAAAATTAAAACC
1 AAACT-CTAAACCCCAAACCCTAAAATTAAAACC
3720274 CTATACCCCA
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
57 5 0.06
58 70 0.88
59 5 0.06
ACGTcount: A:0.50, C:0.30, G:0.01, T:0.19
Consensus pattern (58 bp):
AAACTCTAAACCCCAAACCCTAAAATTAAAACCTTAAATCCTTCAAACCCTAAAACTA
Found at i:3720260 original size:86 final size:86
Alignment explanation
Indices: 3720168--3720336 Score: 216
Period size: 86 Copynumber: 2.0 Consensus size: 86
3720158 TTAAATCCTT
* * * *
3720168 CAAACCCTAAAATCAAAACTCTAAACCTCAAACCCTAAAATCGAAAAC-TTAAATCTTTCAAACC
1 CAAACCCTAAAATCAAAACCCTAAACCCCAAAACCTAAAAT-GAAAACACTAAATCTTTCAAACC
3720232 CTAAAACT-AAAATCCTAAACCC
65 CTAAAACTCAAAA-CCTAAACCC
* * * * *
3720254 CAAACCCTAAAATTAAAACCCTATACCCCAAAATCTAAAATTAAAACACTAAATCTTTCAAACCT
1 CAAACCCTAAAATCAAAACCCTAAACCCCAAAACCTAAAATGAAAACACTAAATCTTTCAAACCC
*
3720319 TAAAATTCAAAACCTAAA
66 TAAAACTCAAAACCTAAA
3720337 ACTCTAATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
85 5 0.07
86 62 0.87
87 4 0.06
ACGTcount: A:0.50, C:0.28, G:0.01, T:0.21
Consensus pattern (86 bp):
CAAACCCTAAAATCAAAACCCTAAACCCCAAAACCTAAAATGAAAACACTAAATCTTTCAAACCC
TAAAACTCAAAACCTAAACCC
Found at i:3720272 original size:21 final size:22
Alignment explanation
Indices: 3720240--3720293 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
3720230 CCCTAAAACT
*
3720240 AAAATCCT-AAACCCCAAACCCT
1 AAAAT-CTAAAACCCCAAACCCC
* *
3720262 AAAAT-TAAAACCCTATACCCC
1 AAAATCTAAAACCCCAAACCCC
3720283 AAAATCTAAAA
1 AAAATCTAAAA
3720294 TTAAAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 16 0.59
22 10 0.37
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (22 bp):
AAAATCTAAAACCCCAAACCCC
Found at i:3720370 original size:86 final size:85
Alignment explanation
Indices: 3720168--3720371 Score: 200
Period size: 86 Copynumber: 2.4 Consensus size: 85
3720158 TTAAATCCTT
* *
3720168 CAAACCCTAAAA-TCAAAACTCTAAACCTCAAACCCTAAAATCGAAAACTTAAATCTTTCAAACC
1 CAAACCCTAAAATTCAAAAC-CTAAACC-CAAAACCTAAAATCGAAAACCTAAATCTTTCAAACC
3720232 CTAAAACTAAAATCCTAAACCC
64 CTAAAACTAAAATCCTAAACCC
* * *
3720254 CAAACCCTAAAATT-AAAACCCTATACCCCAAAATCTAAAAT-TAAAACACTAAATCTTTCAAAC
1 CAAACCCTAAAATTCAAAA-CCTA-AACCCAAAACCTAAAATCGAAAAC-CTAAATCTTTCAAAC
* * *
3720317 CTTAAAATTCAAAA-CCTAAAACTC
63 CCTAAAACT-AAAATCCT-AAACCC
* ****
3720341 TAATTTTTAAAATTCAAAACCTAAACCCAAA
1 CAAACCCTAAAATTCAAAACCTAAACCCAAA
3720372 TTTGGCACGC
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
85 5 0.05
86 61 0.63
87 27 0.28
88 4 0.04
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (85 bp):
CAAACCCTAAAATTCAAAACCTAAACCCAAAACCTAAAATCGAAAACCTAAATCTTTCAAACCCT
AAAACTAAAATCCTAAACCC
Found at i:3720985 original size:140 final size:140
Alignment explanation
Indices: 3720733--3721017 Score: 498
Period size: 140 Copynumber: 2.0 Consensus size: 140
3720723 GCATAACATC
* * * *
3720733 TATTAACACATCTGTAGATACTTATCTGTGTTTGAGTTTAATCAAACCATTTTTATTATTTTTGT
1 TATTAACACATCTGTAGATACCTATCTGTGTTCGAGTTCAATCAAACCATTTTTATTATATTTGT
*
3720798 TATATTATAGTATTATCTTATTATTTTTACTATTATTATTGTTATTAGTATAATATACGATACTA
66 TATATTATAGTATTATCTTATTATTTTTACTATTATTATTGTTATTAGTATAATATACGATAATA
3720863 TATTACATTT
131 TATTACATTT
*
3720873 TATTAACACATCTGTAGATACCTATCTGTGTTCGAGTTCAATCAAATCATTTTTATTATATTTGT
1 TATTAACACATCTGTAGATACCTATCTGTGTTCGAGTTCAATCAAACCATTTTTATTATATTTGT
* *
3720938 TATATTATAGTATTATCTTATTATTTTTACTATTATTATTGTTATTAGTATAATATATGGTAATA
66 TATATTATAGTATTATCTTATTATTTTTACTATTATTATTGTTATTAGTATAATATACGATAATA
3721003 TATTACATTT
131 TATTACATTT
3721013 TATTA
1 TATTA
3721018 TTAATATTAA
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (140 bp):
TATTAACACATCTGTAGATACCTATCTGTGTTCGAGTTCAATCAAACCATTTTTATTATATTTGT
TATATTATAGTATTATCTTATTATTTTTACTATTATTATTGTTATTAGTATAATATACGATAATA
TATTACATTT
Found at i:3722629 original size:7 final size:7
Alignment explanation
Indices: 3722602--3722635 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3722592 AATTTTCATG
3722602 AAAAATA
1 AAAAATA
*
3722609 AAAAACA
1 AAAAATA
3722616 AAGAAATA
1 AA-AAATA
3722624 AAAAATA
1 AAAAATA
3722631 AAAAA
1 AAAAA
3722636 AGAACTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (7 bp):
AAAAATA
Found at i:3723007 original size:23 final size:23
Alignment explanation
Indices: 3722977--3723034 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
3722967 GTGCAAAAAA
* *
3722977 AAAAAAGAAAGCAAAAAAAAGGC
1 AAAAAAGAAAACAAAAAAAAGAC
*
3723000 AAAAAAGATAAATAAAAAAAAGAC
1 AAAAAAGA-AAACAAAAAAAAGAC
*
3723024 AAAAAGGAAAA
1 AAAAAAGAAAA
3723035 AAGAAGACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAAACAAAAAAAAGAC
Found at i:3724230 original size:86 final size:87
Alignment explanation
Indices: 3724028--3724232 Score: 241
Period size: 86 Copynumber: 2.4 Consensus size: 87
3724018 TCTTTCTTGT
* * * *
3724028 GAACTTAAAATTTTTGTGAATCTAAAACATTTACGAAACTTGAAAATCTTACGAATCTGTATTTC
1 GAACCTAAAATCTTTGTGAATCTAAAACCTTTACGAAACTTGAAAATCTTACGAATCTATATTTC
* **
3724093 TTACAAATCTGAAAGTTCTTGT
66 TTACAAATCTGAAAGTCCTTAC
** ** * ** *
3724115 GAACCTAAAATCTTTACGAATCTAAAACCTTTGTGTAACTTGAAAA-CTTGTGAATCTATCTTTC
1 GAACCTAAAATCTTTGTGAATCTAAAACCTTTACGAAACTTGAAAATCTTACGAATCTATATTTC
*
3724179 TTGCAAATCTGAAAGTCCTTAC
66 TTACAAATCTGAAAGTCCTTAC
* *
3724201 GAACCTCAAATCTTTGTGAATCTAGAACCTTT
1 GAACCTAAAATCTTTGTGAATCTAAAACCTTT
3724233 TTGAATTTTG
Statistics
Matches: 98, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
86 60 0.61
87 38 0.39
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (87 bp):
GAACCTAAAATCTTTGTGAATCTAAAACCTTTACGAAACTTGAAAATCTTACGAATCTATATTTC
TTACAAATCTGAAAGTCCTTAC
Found at i:3724627 original size:3 final size:3
Alignment explanation
Indices: 3724619--3724728 Score: 52
Period size: 3 Copynumber: 37.7 Consensus size: 3
3724609 AATCAGACTG
* * * *
3724619 TTA TTA TTA TTT TTG TTA -TA TTA -TA GTA TTA -TA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
3724664 CTA TTA TTA TTG TTG TTA GTA TAA TATA TGGTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T--TA TTA TTA TTA TTA TTA
* *
3724710 -TA TTT TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
3724729 TTTTCTTTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
2 12 0.15
3 65 0.79
4 2 0.02
5 3 0.04
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3724725 original size:17 final size:17
Alignment explanation
Indices: 3724705--3724739 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3724695 TATTATATTA
3724705 TATTATATTTTT-TTTAT
1 TATTAT-TTTTTCTTTAT
3724722 TATTATTTTTTCTTTAT
1 TATTATTTTTTCTTTAT
3724739 T
1 T
3724740 TTTTCCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TATTATTTTTTCTTTAT
Found at i:3725527 original size:14 final size:14
Alignment explanation
Indices: 3725503--3725549 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
3725493 TGATTGTAGG
*
3725503 TTTTTTCTTTTT-T
1 TTTTTTATTTTTAT
*
3725516 TATTTTATTTTTAT
1 TTTTTTATTTTTAT
*
3725530 TTTTTTA-TTTGAT
1 TTTTTTATTTTTAT
3725543 TTTTTTA
1 TTTTTTA
3725550 ACTCATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 22 0.76
14 7 0.24
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:3725532 original size:19 final size:19
Alignment explanation
Indices: 3725504--3725546 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3725494 GATTGTAGGT
* *
3725504 TTTTTCTTTTTTTATTTTA
1 TTTTTATTTTTTTATTTGA
3725523 TTTTTATTTTTTTATTTGA
1 TTTTTATTTTTTTATTTGA
3725542 TTTTT
1 TTTTT
3725547 TTAACTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTTTTATTTGA
Found at i:3725581 original size:23 final size:22
Alignment explanation
Indices: 3725512--3725581 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
3725502 GTTTTTTCTT
3725512 TTTTTATTTT-ATTTTT-ATT-
1 TTTTTATTTTAATTTTTAATTA
* * *
3725531 TTTTTATTTGATTTTTTTAACTCA
1 TTTTTATTTTA-ATTTTTAA-TTA
3725555 -TTTTATTTTAAATTTTTAATTA
1 TTTTTATTTT-AATTTTTAATTA
3725577 TTTTT
1 TTTTT
3725582 TTGGTCTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 9 0.24
21 5 0.13
22 3 0.08
23 20 0.53
24 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTTATTTTAATTTTTAATTA
Found at i:3725790 original size:16 final size:15
Alignment explanation
Indices: 3725748--3725795 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3725738 AAAACAAAAC
3725748 AAATCCTTTCAAA-A
1 AAATCCTTTCAAATA
*
3725762 AAATCTTTTCAAATTA
1 AAATCCTTTCAAA-TA
*
3725778 AAATCCTTACAAAATA
1 AAATCCTTTC-AAATA
3725794 AA
1 AA
3725796 TTTATGAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 12 0.43
16 13 0.46
17 3 0.11
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATCCTTTCAAATA
Found at i:3729886 original size:32 final size:32
Alignment explanation
Indices: 3729777--3729879 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
3729767 TGAATCTATT
3729777 TTTTAAAATGAT-T-TGAAATTTTTATTTAATA
1 TTTTAAAATGATATAT-AAATTTTTATTTAATA
* * *
3729808 TTTTAATATGAGAT-TAAGTTGTTTATTTAATA
1 TTTTAAAATGATATATAAATT-TTTATTTAATA
* *
3729840 TTTTAAATTGATATATAAATTTTTATTTAATT
1 TTTTAAAATGATATATAAATTTTTATTTAATA
3729872 TTTTAAAA
1 TTTTAAAA
3729880 CAATATAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 14 0.23
32 41 0.68
33 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (32 bp):
TTTTAAAATGATATATAAATTTTTATTTAATA
Found at i:3729895 original size:32 final size:32
Alignment explanation
Indices: 3729791--3729895 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 32
3729781 AAAATGATTT
* ** *
3729791 GAAATTTTTATTTAATATTTTAATATGAGAT-
1 GAAATTTTTATTTAATATTTTAAAACAATATA
* * ***
3729822 TAAGTTGTTTATTTAATATTTTAAATTGATATA
1 GAAATT-TTTATTTAATATTTTAAAACAATATA
* *
3729855 TAAATTTTTATTTAATTTTTTAAAACAATATA
1 GAAATTTTTATTTAATATTTTAAAACAATATA
*
3729887 GAATTTTTT
1 GAAATTTTT
3729896 CCAAAAGGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 4 0.07
32 51 0.85
33 5 0.08
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (32 bp):
GAAATTTTTATTTAATATTTTAAAACAATATA
Found at i:3730314 original size:18 final size:18
Alignment explanation
Indices: 3730291--3730332 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3730281 AATTTTAACA
3730291 AACAAATTATATTACAAT
1 AACAAATTATATTACAAT
3730309 AACAAATTATATTACAAT
1 AACAAATTATATTACAAT
3730327 AA-AAAT
1 AACAAAT
3730333 ATAAGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (18 bp):
AACAAATTATATTACAAT
Found at i:3732179 original size:14 final size:16
Alignment explanation
Indices: 3732149--3732181 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3732139 TATTTAGTAC
3732149 TAAAAATAATAAAACT
1 TAAAAATAATAAAACT
3732165 TAAAAAT-AT-AAACT
1 TAAAAATAATAAAACT
3732179 TAA
1 TAA
3732182 TAAAATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATAATAAAACT
Found at i:3732966 original size:21 final size:22
Alignment explanation
Indices: 3732941--3732988 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3732931 TCGATTTGAA
*
3732941 AAATATAATTTAT-AA-TAGTAT
1 AAATATAAATTATAAATTA-TAT
3732962 AAATA-AAATTATAAATTATAT
1 AAATATAAATTATAAATTATAT
3732983 AAATAT
1 AAATAT
3732989 TCTCAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 6 0.26
21 15 0.65
22 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATAAATTATAAATTATAT
Found at i:3733652 original size:89 final size:89
Alignment explanation
Indices: 3733545--3733721 Score: 345
Period size: 89 Copynumber: 2.0 Consensus size: 89
3733535 AAATAAATAA
*
3733545 ATATATATATATATTATCTTTATTAATTGCATGGTTGCCTTTGTTGTCCTTGTAAGATTTTGCTA
1 ATATATATATATATTATCTTTATTAATTGCATGGTTGCCCTTGTTGTCCTTGTAAGATTTTGCTA
3733610 GATTCTGCATTGTCAAGTTGTTAT
66 GATTCTGCATTGTCAAGTTGTTAT
3733634 ATATATATATATATTATCTTTATTAATTGCATGGTTGCCCTTGTTGTCCTTGTAAGATTTTGCTA
1 ATATATATATATATTATCTTTATTAATTGCATGGTTGCCCTTGTTGTCCTTGTAAGATTTTGCTA
3733699 GATTCTGCATTGTCAAGTTGTTA
66 GATTCTGCATTGTCAAGTTGTTA
3733722 ACCTCATGCT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49
Consensus pattern (89 bp):
ATATATATATATATTATCTTTATTAATTGCATGGTTGCCCTTGTTGTCCTTGTAAGATTTTGCTA
GATTCTGCATTGTCAAGTTGTTAT
Found at i:3735332 original size:16 final size:16
Alignment explanation
Indices: 3735296--3735342 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3735286 TTTATAATAA
3735296 TATTT-TAATAT-TTT
1 TATTTGTAATATATTT
*
3735310 TAATTGTAATATATTT
1 TATTTGTAATATATTT
3735326 TATTTGTTAA-ATATTT
1 TATTTG-TAATATATTT
3735342 T
1 T
3735343 TTAATAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 15 0.54
17 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (16 bp):
TATTTGTAATATATTT
Found at i:3741429 original size:32 final size:32
Alignment explanation
Indices: 3741393--3741457 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3741383 AAGAGAAGAG
* *
3741393 GATTGTGAGA-TTTTCATTCCAAGTAGAGCCAA
1 GATTGTGAGACTTCT-ATTACAAGTAGAGCCAA
*
3741425 GATTGTGAGACTTCTATTACAGGTAGAGCCAA
1 GATTGTGAGACTTCTATTACAAGTAGAGCCAA
3741457 G
1 G
3741458 TATGTCTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 26 0.90
33 3 0.10
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (32 bp):
GATTGTGAGACTTCTATTACAAGTAGAGCCAA
Found at i:3742030 original size:65 final size:65
Alignment explanation
Indices: 3741926--3742057 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 65
3741916 GTCTCTTATG
* *
3741926 TGTTTGATTAATTGTTTGATTCTACTTCCTCTAACTTGATTGGATTGGATTTTTTGGTCATGGTT
1 TGTTTGATTAATTGTTTGATTCTACTTCCGCTAACTTGATTGGATTAGATTTTTTGGTCATGGTT
*
3741991 TGTTTGATTAATTGTTTGATTCTACTTCCGCTGACTTGATTGGATTAGATTTTTTGGTCATGGTT
1 TGTTTGATTAATTGTTTGATTCTACTTCCGCTAACTTGATTGGATTAGATTTTTTGGTCATGGTT
3742056 TG
1 TG
3742058 GTCCAATCGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.17, C:0.11, G:0.21, T:0.52
Consensus pattern (65 bp):
TGTTTGATTAATTGTTTGATTCTACTTCCGCTAACTTGATTGGATTAGATTTTTTGGTCATGGTT
Found at i:3750324 original size:19 final size:19
Alignment explanation
Indices: 3750300--3750338 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3750290 GATTGGGTTT
* *
3750300 AAAGTACTTTTTAAATGCA
1 AAAGTAATTTTTAAAGGCA
3750319 AAAGTAATTTTTAAAGGCA
1 AAAGTAATTTTTAAAGGCA
3750338 A
1 A
3750339 TGCTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (19 bp):
AAAGTAATTTTTAAAGGCA
Found at i:3750873 original size:32 final size:32
Alignment explanation
Indices: 3750775--3750887 Score: 88
Period size: 32 Copynumber: 3.4 Consensus size: 32
3750765 ATATATCAAT
*
3750775 CAATAAATATAAATAATATATAAATAAAATATA
1 CAAT-AATATAAATAATATACAAATAAAATATA
* * * *
3750808 -AATGAGA-ATAT-ATATAGCAAAGAATATGCATATA
1 CAATAATATAAATAATATA-CAAATAA-A---ATATA
3750842 CAATAATATAAATAATATACAAATAAAATATA
1 CAATAATATAAATAATATACAAATAAAATATA
* *
3750874 AAAAAATATAAATA
1 CAATAATATAAATA
3750888 TACAAAACAA
Statistics
Matches: 61, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
29 5 0.08
30 8 0.13
31 3 0.05
32 20 0.33
34 5 0.08
35 6 0.10
36 9 0.15
37 5 0.08
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (32 bp):
CAATAATATAAATAATATACAAATAAAATATA
Found at i:3750886 original size:16 final size:16
Alignment explanation
Indices: 3750779--3750894 Score: 56
Period size: 16 Copynumber: 7.1 Consensus size: 16
3750769 ATCAATCAAT
* *
3750779 AAATATAAATAATATAT
1 AAATATAAAT-ATAAAA
3750796 AAATA-AAATATAAATGA
1 AAATATAAATATAAA--A
* * **
3750813 GAATATATATAGCAAA
1 AAATATAAATATAAAA
* ** *
3750829 GAATATGCATATACAA
1 AAATATAAATATAAAA
* * *
3750845 TAATATAAATAATATAC
1 AAATATAAAT-ATAAAA
3750862 AAATA-AAATATAAAA
1 AAATATAAATATAAAA
3750877 AAATATAAATATACAAA
1 AAATATAAATATA-AAA
3750894 A
1 A
3750895 CAAAGTACAT
Statistics
Matches: 74, Mismatches: 19, Indels: 12
0.70 0.18 0.11
Matches are distributed among these distances:
15 13 0.18
16 34 0.46
17 21 0.28
18 6 0.08
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (16 bp):
AAATATAAATATAAAA
Found at i:3751957 original size:21 final size:21
Alignment explanation
Indices: 3751933--3751981 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3751923 AAGTTGAAGT
* *
3751933 AGAAGCACCATAAGTAGTGGC
1 AGAAGCACCATAAATAGTAGC
*
3751954 AGAAGCATCATAAATAGTAGC
1 AGAAGCACCATAAATAGTAGC
3751975 AGAAGCA
1 AGAAGCA
3751982 GTAGTATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.14
Consensus pattern (21 bp):
AGAAGCACCATAAATAGTAGC
Found at i:3753074 original size:20 final size:20
Alignment explanation
Indices: 3753051--3753092 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3753041 TGAAACTAAT
3753051 TAGTA-ATAAGTTTAACTATA
1 TAGTACATAA-TTTAACTATA
*
3753071 TAGTACATAATTTAATTATA
1 TAGTACATAATTTAACTATA
3753091 TA
1 TA
3753093 ATTTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (20 bp):
TAGTACATAATTTAACTATA
Found at i:3753099 original size:18 final size:17
Alignment explanation
Indices: 3753078--3753115 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3753068 ATATAGTACA
3753078 TAATTT-AATTATATAATT
1 TAATTTAAATTA-AT-ATT
3753096 TAATTTAAATTAATATT
1 TAATTTAAATTAATATT
3753113 TAA
1 TAA
3753116 ATATTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTAAATTAATATT
Found at i:3755908 original size:10 final size:10
Alignment explanation
Indices: 3755893--3755920 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3755883 TTTTTTTTGT
3755893 TAAAAATATA
1 TAAAAATATA
3755903 TAAAAATATA
1 TAAAAATATA
3755913 TAAAAATA
1 TAAAAATA
3755921 CTATCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAAATATA
Found at i:3756622 original size:3 final size:3
Alignment explanation
Indices: 3756614--3756646 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3756604 CTTAAATAAA
3756614 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3756647 TTCTAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3756675 original size:14 final size:15
Alignment explanation
Indices: 3756656--3756693 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3756646 TTTCTAACAT
3756656 TTTCTTCC-TTTTTC
1 TTTCTTCCGTTTTTC
3756670 TTTCTTCCCCGTTTTTC
1 TTTCTT--CCGTTTTTC
3756687 TTTCTTC
1 TTTCTTC
3756694 TTTCACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
16 2 0.10
17 12 0.57
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTCTTCCGTTTTTC
Found at i:3757822 original size:19 final size:19
Alignment explanation
Indices: 3757775--3757822 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3757765 TTAGTTTTCC
*
3757775 TTTTCTATTTTATTTTTAT
1 TTTTTTATTTTATTTTTAT
*
3757794 TTTTTGATTTTA-TTTTAT
1 TTTTTTATTTTATTTTTAT
3757812 TTTTGTTATTT
1 TTTT-TTATTT
3757823 GTTTAAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTTTTATTTTATTTTTAT
Found at i:3758145 original size:19 final size:18
Alignment explanation
Indices: 3758130--3758163 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3758120 TGAATAAATC
3758130 TTTTAAA-AAAATATAAA
1 TTTTAAAGAAAATATAAA
3758147 TTTTAAAGAAAAT-TAAA
1 TTTTAAAGAAAATATAAA
3758164 AGAGTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TTTTAAAGAAAATATAAA
Found at i:3769701 original size:28 final size:27
Alignment explanation
Indices: 3769654--3769706 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
3769644 ACCCTTTCAT
* *
3769654 TTTTTTTTCTTTGATTTTTGTTATGGA
1 TTTTTTTTCTTTAATTTTTGCTATGGA
3769681 TTTTTTTT-TTTAATTTCTTTGCTATG
1 TTTTTTTTCTTTAA-TT-TTTGCTATG
3769707 AATTGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
27 10 0.45
28 8 0.36
ACGTcount: A:0.11, C:0.06, G:0.11, T:0.72
Consensus pattern (27 bp):
TTTTTTTTCTTTAATTTTTGCTATGGA
Found at i:3771247 original size:22 final size:22
Alignment explanation
Indices: 3771207--3771249 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3771197 AAATCTTATA
**
3771207 AGAGATTTATTTGGGATTTGTT
1 AGAGATTTATTTGAAATTTGTT
3771229 AGAGATTTATTTGAAATTTGT
1 AGAGATTTATTTGAAATTTGT
3771250 CAAATATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (22 bp):
AGAGATTTATTTGAAATTTGTT
Found at i:3774552 original size:22 final size:20
Alignment explanation
Indices: 3774512--3774553 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3774502 AAATAACATG
3774512 AAAAATTATATATATGTTTA
1 AAAAATTATATATATGTTTA
*
3774532 AAAAATATATAATTTATGTTTA
1 AAAAAT-TAT-ATATATGTTTA
3774554 TTCGTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAAATTATATATATGTTTA
Found at i:3775000 original size:18 final size:17
Alignment explanation
Indices: 3774977--3775021 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3774967 ATAATTATAT
3774977 AATATAAATTAAAATTTA
1 AATATAAATT-AAATTTA
*
3774995 AATATATATTAAATTTA
1 AATATAAATTAAATTTA
*
3775012 TATATTAAAT
1 AATA-TAAAT
3775022 GAGTATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATAAATTAAATTTA
Found at i:3775015 original size:13 final size:13
Alignment explanation
Indices: 3774997--3775021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3774987 AAAATTTAAA
3774997 TATATATTAAATT
1 TATATATTAAATT
3775010 TATATATTAAAT
1 TATATATTAAAT
3775022 GAGTATTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATTAAATT
Found at i:3775224 original size:29 final size:29
Alignment explanation
Indices: 3775137--3775230 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
3775127 ATTTTAGTCA
* * *
3775137 TATTCTTGTATATATTTATGTTAGTTATGTC
1 TATTCTTGTATATCTGTA--TTAGTTGTGTC
* * * *
3775168 TATTCGTGTATATCCGTGTTAGTCGTGTC
1 TATTCTTGTATATCTGTATTAGTTGTGTC
* *
3775197 TATTCTTGTATATCTGTATTATTTGTGTT
1 TATTCTTGTATATCTGTATTAGTTGTGTC
3775226 TATTC
1 TATTC
3775231 ATGTCGTGCT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
29 37 0.74
31 13 0.26
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (29 bp):
TATTCTTGTATATCTGTATTAGTTGTGTC
Found at i:3775655 original size:5 final size:5
Alignment explanation
Indices: 3775645--3775680 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
3775635 GAATATCCGC
3775645 ATATT ATATT ATATT ATATT ATATAT ATATAT ATAT
1 ATATT ATATT ATATT ATATT ATAT-T ATAT-T ATAT
3775681 ACATGAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.63
6 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:3775718 original size:22 final size:22
Alignment explanation
Indices: 3775690--3775731 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3775680 TACATGAATG
*
3775690 AATTTATTAATTTTATTGACAA
1 AATTTATCAATTTTATTGACAA
3775712 AATTTATCAATTTTATTGAC
1 AATTTATCAATTTTATTGAC
3775732 GAAAGGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
AATTTATCAATTTTATTGACAA
Found at i:3779404 original size:49 final size:49
Alignment explanation
Indices: 3779332--3779427 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
3779322 TTCTCTAATG
3779332 CTTGATCCAACCCTTGTTATACTAACAGATCTTGAATTATACTTTGCCA
1 CTTGATCCAACCCTTGTTATACTAACAGATCTTGAATTATACTTTGCCA
* *
3779381 CTTGATCCAACCCTTGTTGTACTAACAGATCTTGAATTGTACTTTGC
1 CTTGATCCAACCCTTGTTATACTAACAGATCTTGAATTATACTTTGC
3779428 TATAACATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (49 bp):
CTTGATCCAACCCTTGTTATACTAACAGATCTTGAATTATACTTTGCCA
Found at i:3782401 original size:21 final size:22
Alignment explanation
Indices: 3782359--3782411 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
3782349 CCCGAAATTA
3782359 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
3782381 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
3782402 ATAAATATAT
1 ATAAA-ATAT
3782412 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:3782864 original size:23 final size:24
Alignment explanation
Indices: 3782825--3782882 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
3782815 TTTTTTAATG
* *
3782825 TTTATGATATTTTTGCATGTTTAA
1 TTTAGGATATTTTTGCATATTTAA
*
3782849 TTTAGGAT-TTTTTGCATATTTAT
1 TTTAGGATATTTTTGCATATTTAA
*
3782872 TTTATGATATT
1 TTTAGGATATT
3782883 ATTACATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAGGATATTTTTGCATATTTAA
Found at i:3786022 original size:23 final size:24
Alignment explanation
Indices: 3785981--3786030 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3785971 TACATACTCT
* * *
3785981 AAAAAGAAAGAAAGAAAGAAATGA
1 AAAAAAAAAAAAAGAAAGAAATCA
3786005 AAAAAAAAAAAAAG-AAGAAATCA
1 AAAAAAAAAAAAAGAAAGAAATCA
3786028 AAA
1 AAA
3786031 TCTTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAAAGAAAGAAATCA
Found at i:3796417 original size:12 final size:13
Alignment explanation
Indices: 3796360--3796420 Score: 65
Period size: 12 Copynumber: 4.7 Consensus size: 13
3796350 AATATTATTT
3796360 TAAATATAAATATA
1 TAAAT-TAAATATA
3796374 -AAATTAAATATA
1 TAAATTAAATATA
*
3796386 TAAA-AAATATATA
1 TAAATTAA-ATATA
3796399 TATAATTAAATATA
1 TA-AATTAAATATA
3796413 -AAATTAAA
1 TAAATTAAA
3796421 AAAATAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 17 0.41
13 15 0.37
14 7 0.17
15 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTAAATATA
Found at i:3799748 original size:15 final size:15
Alignment explanation
Indices: 3799728--3799757 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3799718 TCATCTAAGT
3799728 TGGGTTATCTATCTA
1 TGGGTTATCTATCTA
3799743 TGGGTTATCTATCTA
1 TGGGTTATCTATCTA
3799758 ACCTGAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TGGGTTATCTATCTA
Found at i:3802103 original size:24 final size:25
Alignment explanation
Indices: 3802055--3802103 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3802045 TTAATACGAT
** *
3802055 CAGTGGAGTTTTTCTTGACATCTAA
1 CAGTGGAGTTTTTAGTGACAGCTAA
3802080 CAGTGGAGTTTTTAGTGA-AGCTAA
1 CAGTGGAGTTTTTAGTGACAGCTAA
3802104 GAGGGTGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (25 bp):
CAGTGGAGTTTTTAGTGACAGCTAA
Found at i:3802903 original size:2 final size:2
Alignment explanation
Indices: 3802896--3802933 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3802886 TCTTACAGTT
3802896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3802934 GTAGATATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3804434 original size:11 final size:11
Alignment explanation
Indices: 3804418--3804456 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
3804408 TTAACAATTT
3804418 AAAATATATAA
1 AAAATATATAA
3804429 AAAATATATAA
1 AAAATATATAA
3804440 AAAATATA-AA
1 AAAATATATAA
3804450 AATAATA
1 AA-AATA
3804457 CGATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATATATAA
Found at i:3810916 original size:10 final size:10
Alignment explanation
Indices: 3810901--3810928 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3810891 AATTTCCTAA
3810901 AACCCAACTC
1 AACCCAACTC
3810911 AACCCAACTC
1 AACCCAACTC
3810921 AACCCAAC
1 AACCCAAC
3810929 AAAACCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.50, G:0.00, T:0.07
Consensus pattern (10 bp):
AACCCAACTC
Found at i:3811402 original size:29 final size:29
Alignment explanation
Indices: 3811350--3811408 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3811340 CAATTCTTTG
* *
3811350 TTTTATTGTTGTTATAATCAATTTTTTTC
1 TTTTATTGTTATTATAATCAATTTGTTTC
* **
3811379 TTTTGTTGTTATTATAATTTATTTGTTTC
1 TTTTATTGTTATTATAATCAATTTGTTTC
3811408 T
1 T
3811409 CTAACAATCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (29 bp):
TTTTATTGTTATTATAATCAATTTGTTTC
Found at i:3813269 original size:59 final size:58
Alignment explanation
Indices: 3813186--3813706 Score: 683
Period size: 59 Copynumber: 8.7 Consensus size: 58
3813176 TTTTTTTTAG
3813186 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT--ATTTCT-AA
* * ** *
3813245 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGGAAATTTATTTCTAA
* *
3813304 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGAAATTT-TGATTCTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTAT--TTCT-AA
3813364 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTTTTGGAAATTTATTTTTCTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA----TTTTTTTGGAAATTTA--TTTC---T
3813429 AA
57 AA
*
3813431 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTATTTCTAA
* * *
3813490 GGAAAATTGATACTTTCAATTTTTCCCTAAAAATATTTTTTTGAAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTC-TAA
* * *
3813548 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTATTTCTAA
*
3813607 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
*
3813664 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTT
3813707 TAGAATTTTT
Statistics
Matches: 415, Mismatches: 26, Indels: 42
0.86 0.05 0.09
Matches are distributed among these distances:
57 57 0.14
58 65 0.16
59 164 0.40
60 40 0.10
61 13 0.03
62 4 0.01
64 31 0.07
65 3 0.01
67 37 0.09
68 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
Found at i:3813560 original size:117 final size:118
Alignment explanation
Indices: 3813186--3813707 Score: 731
Period size: 117 Copynumber: 4.4 Consensus size: 118
3813176 TTTTTTTTAG
* *
3813186 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTCGATTT-TCAAGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTT--ATTTCTCAAGGA
* **
3813248 AAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
64 AAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGAAAATTTATTTCTAA
3813304 GGAAAATTGATACTTTCAACTTTTTCCC-AAAAATATTTTTTTT-GAAATTT-TGATTCTCAAGG
1 GGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTTGGAAATTTAT--TTCTCAAGG
*
3813366 AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTTTTGGAAATTTATTTTTCTTTTAA
63 AAAATTGATACTTTCAACTTTTCCCCAAAAATA----TTTTTTTGAAAATTTA--TTTC---TAA
3813431 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCT-AAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTCAAGGAAA
* *
3813495 ATTGATACTTTCAATTTTTCCCTAAAAATATTTTTTTGAAAATTTA-TTCTTAA
66 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTC-TAA
* *
3813548 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCT-GAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTCAAGGAAA
3813612 ATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTCTAA
66 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTCTAA
3813664 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTT
3813708 AGAATTTTTT
Statistics
Matches: 372, Mismatches: 12, Indels: 41
0.88 0.03 0.10
Matches are distributed among these distances:
116 55 0.15
117 104 0.28
118 29 0.08
119 52 0.14
120 6 0.02
122 30 0.08
124 4 0.01
126 42 0.11
127 42 0.11
128 7 0.02
129 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTCAAGGAAA
ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTCTAA
Found at i:3813806 original size:16 final size:16
Alignment explanation
Indices: 3813785--3813827 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3813775 AACCTAATCT
3813785 AATAAATAAAAAATAA
1 AATAAATAAAAAATAA
3813801 AATAAATAAAGAAATAA
1 AATAAATAAA-AAATAA
3813818 AA-AAA-AAAAA
1 AATAAATAAAAA
3813828 CCTGGAGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 13 0.50
17 8 0.31
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (16 bp):
AATAAATAAAAAATAA
Found at i:3814148 original size:20 final size:20
Alignment explanation
Indices: 3814123--3814161 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3814113 AGAACACCGG
*
3814123 TGCCGGATTCTGGAAATTTT
1 TGCCGGAATCTGGAAATTTT
3814143 TGCCGGAATCTGGAAATTT
1 TGCCGGAATCTGGAAATTT
3814162 CGCCGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (20 bp):
TGCCGGAATCTGGAAATTTT
Found at i:3814337 original size:25 final size:25
Alignment explanation
Indices: 3814301--3814348 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3814291 AATCTGGAAA
3814301 TTTCCCAGAAATTTCCAGAAAAATT
1 TTTCCCAGAAATTTCCAGAAAAATT
*
3814326 TTTCGCCA-AAATTTCTAGAAAAA
1 TTTC-CCAGAAATTTCCAGAAAAA
3814349 ATTCTCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (25 bp):
TTTCCCAGAAATTTCCAGAAAAATT
Found at i:3816491 original size:21 final size:21
Alignment explanation
Indices: 3816467--3816507 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3816457 ATGCAATATC
3816467 TTTAAAAATA-AAATAAATAAG
1 TTTAAAAATATAAA-AAATAAG
3816488 TTTAAAAATATAAAAAATAA
1 TTTAAAAATATAAAAAATAA
3816508 TATCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TTTAAAAATATAAAAAATAAG
Found at i:3816741 original size:16 final size:17
Alignment explanation
Indices: 3816705--3816745 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3816695 TTTGGTTTAA
3816705 AAAAATAAAGTATAAAAT
1 AAAAA-AAAGTATAAAAT
*
3816723 AAAAAAAAGT-TATAAT
1 AAAAAAAAGTATAAAAT
3816739 AAAAAAA
1 AAAAAAA
3816746 TAGAAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
17 5 0.23
18 5 0.23
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (17 bp):
AAAAAAAAGTATAAAAT
Found at i:3820935 original size:29 final size:29
Alignment explanation
Indices: 3820893--3820952 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
3820883 ATATCCTTGT
* *
3820893 TCATTACACAAACAAATTGATCATGGTTA
1 TCATTACACAAACAAACTGATCATGATTA
*
3820922 TCATTATACAAACAAACTGATCATGATTA
1 TCATTACACAAACAAACTGATCATGATTA
3820951 TC
1 TC
3820953 CAAAAAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (29 bp):
TCATTACACAAACAAACTGATCATGATTA
Found at i:3822567 original size:18 final size:18
Alignment explanation
Indices: 3822544--3822590 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
3822534 CCTTGAGAAA
3822544 AAGATAAAAATTTAGTAC
1 AAGATAAAAATTTAGTAC
3822562 AAGATAAAAATTTAGTAC
1 AAGATAAAAATTTAGTAC
3822580 AAGATAAAAAT
1 AAGATAAAAAT
3822591 ATTGTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.26
Consensus pattern (18 bp):
AAGATAAAAATTTAGTAC
Found at i:3826416 original size:19 final size:19
Alignment explanation
Indices: 3826392--3826432 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3826382 TGATATAGCT
3826392 TATACCTTTCATGCAAAAC
1 TATACCTTTCATGCAAAAC
3826411 TATACCTTTCATGCAAAAC
1 TATACCTTTCATGCAAAAC
3826430 TAT
1 TAT
3826433 GTGTGCGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (19 bp):
TATACCTTTCATGCAAAAC
Found at i:3827245 original size:27 final size:27
Alignment explanation
Indices: 3827198--3827275 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
3827188 TTGGATTATG
* *
3827198 ATGCATAAATTGAGGGAGAGTTTTGCC
1 ATGCATTAATTAAGGGAGAGTTTTGCC
*
3827225 ATGCATTAATTAAGAGG-GAGTTTTGCT
1 ATGCATTAATTAAG-GGAGAGTTTTGCC
* *
3827252 ATGCATTATTTAAGGGAAAGTTTT
1 ATGCATTAATTAAGGGAGAGTTTT
3827276 TCAAAATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
26 2 0.05
27 40 0.91
28 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.36
Consensus pattern (27 bp):
ATGCATTAATTAAGGGAGAGTTTTGCC
Found at i:3845109 original size:23 final size:21
Alignment explanation
Indices: 3845089--3845148 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
3845079 CGTGAAATCG
3845089 AAAATAAAAATAAATTAAAAT
1 AAAATAAAAATAAATTAAAAT
* *
3845110 ATTAATAAAATATAAATTAAATTT
1 A-AAATAAAA-ATAAATTAAA-AT
3845134 AAAAATAAAAATAAA
1 -AAAATAAAAATAAA
3845149 AATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.03
22 7 0.22
23 15 0.47
24 8 0.25
25 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAAAAATAAATTAAAAT
Found at i:3845118 original size:11 final size:11
Alignment explanation
Indices: 3845090--3845136 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
3845080 GTGAAATCGA
3845090 AAATAAAA-AT
1 AAATAAAATAT
3845100 AAATTAAAATAT
1 AAA-TAAAATAT
*
3845112 TAATAAAATAT
1 AAATAAAATAT
* *
3845123 AAATTAAATTT
1 AAATAAAATAT
3845134 AAA
1 AAA
3845137 AATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 3 0.10
11 24 0.77
12 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:3848350 original size:22 final size:22
Alignment explanation
Indices: 3848316--3848359 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3848306 TGGATCTTTC
* *
3848316 AATTATTATTTTAATTTAAATT
1 AATTATGAATTTAATTTAAATT
* *
3848338 AATTATGAATTTAGTTTTAATT
1 AATTATGAATTTAATTTAAATT
3848360 CAAGGATCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
AATTATGAATTTAATTTAAATT
Found at i:3850094 original size:19 final size:19
Alignment explanation
Indices: 3850056--3850094 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3850046 TATAAATATA
*
3850056 TTATTTTTTAATTAATTTT
1 TTATTTTTTAAATAATTTT
3850075 TTATTTTTTAAATATATTTT
1 TTATTTTTTAAATA-ATTTT
3850095 AAAAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTTTAAATAATTTT
Found at i:3851261 original size:2 final size:2
Alignment explanation
Indices: 3851254--3851282 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3851244 CTTACATGAT
3851254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3851283 TAAAATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3851696 original size:15 final size:15
Alignment explanation
Indices: 3851676--3851709 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3851666 GTGTTTCCAA
3851676 TAAGATGTTA-AGGTT
1 TAAGATGTTAGA-GTT
3851691 TAAGATGTTAGAGTT
1 TAAGATGTTAGAGTT
3851706 TAAG
1 TAAG
3851710 GTTTAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (15 bp):
TAAGATGTTAGAGTT
Found at i:3852076 original size:7 final size:7
Alignment explanation
Indices: 3852064--3852090 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3852054 TTAATCATCA
3852064 AATTTTG
1 AATTTTG
3852071 AATTTTG
1 AATTTTG
3852078 AATTTTG
1 AATTTTG
3852085 AATTTT
1 AATTTT
3852091 CATTTGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (7 bp):
AATTTTG
Found at i:3853681 original size:9 final size:8
Alignment explanation
Indices: 3853664--3853702 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
3853654 TTAAACTAAG
3853664 AAAAAGAA
1 AAAAAGAA
*
3853672 AAAAAGGA
1 AAAAAGAA
3853680 AAAAAGAA
1 AAAAAGAA
* *
3853688 AGAAAGGA
1 AAAAAGAA
3853696 AAAAAGA
1 AAAAAGA
3853703 GGCACACATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3853685 original size:16 final size:16
Alignment explanation
Indices: 3853664--3853702 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3853654 TTAAACTAAG
3853664 AAAAAGAAAAAAAGGA
1 AAAAAGAAAAAAAGGA
*
3853680 AAAAAGAAAGAAAGGA
1 AAAAAGAAAAAAAGGA
3853696 AAAAAGA
1 AAAAAGA
3853703 GGCACACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAGGA
Found at i:3859930 original size:14 final size:14
Alignment explanation
Indices: 3859913--3859946 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3859903 TTTCTTATTT
*
3859913 AAACAAACTTAATC
1 AAACAAACATAATC
*
3859927 AAACAATCATAATC
1 AAACAAACATAATC
3859941 AAACAA
1 AAACAA
3859947 TCATGTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACAAACATAATC
Found at i:3859947 original size:14 final size:14
Alignment explanation
Indices: 3859922--3859950 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3859912 TAAACAAACT
3859922 TAATCAAACAATCA
1 TAATCAAACAATCA
3859936 TAATCAAACAATCA
1 TAATCAAACAATCA
3859950 T
1 T
3859951 GTTTTCCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (14 bp):
TAATCAAACAATCA
Found at i:3862841 original size:15 final size:15
Alignment explanation
Indices: 3862821--3862851 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3862811 TCATATGGTG
3862821 TCTTCAAGAATTTCT
1 TCTTCAAGAATTTCT
3862836 TCTTCAAGAATTTCT
1 TCTTCAAGAATTTCT
3862851 T
1 T
3862852 TGAAAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (15 bp):
TCTTCAAGAATTTCT
Found at i:3864306 original size:182 final size:178
Alignment explanation
Indices: 3863992--3864347 Score: 660
Period size: 182 Copynumber: 2.0 Consensus size: 178
3863982 TAATTGCAGC
3863992 ATTTTTAAATATATAATTTTTAATAAAATATCATTTCTTTTCACAATGAACTAGATTCTAATAAG
1 ATTTTTAAATATATAATTTTTAATAAAATATCATTTCTTTTCACAATGAACTAGATTCTAATAAG
3864057 TATAGTAGAAAATCTTAAAAAATCCTTAGGTGAGAGAATTTTTCTAAACATATCGTCAAAGAATT
66 TATAGTAGAAAATCTTAAAAAATCCTTAGGTGAGAGAATTTTTCTAAACATATCGTCAAAGAATT
3864122 ATAATATTTAAAATGATTCTCAATACGAAAAA-TTTGTTTATTTCACA
131 ATAATATTTAAAATGATTCTCAATACGAAAAATTTTGTTTATTTCACA
3864169 ATTTTTAAATATATATATATTTTAATATAAAATATCATTTCTTTTCACAATGAACTAGATTCTAA
1 ATTTTTAAATATATA-AT-TTTT-A-ATAAAATATCATTTCTTTTCACAATGAACTAGATTCTAA
3864234 TTAAGTATAGTAGAAAATCTTAAAAAATCCTTAGGTGAGAGAATTTTTCTAAACATATCGTCAAA
62 -TAAGTATAGTAGAAAATCTTAAAAAATCCTTAGGTGAGAGAATTTTTCTAAACATATCGTCAAA
3864299 GAATTATAATATTTAAAATGATTCTCAATACGAAAAATTTTGTTTATTT
126 GAATTATAATATTTAAAATGATTCTCAATACGAAAAATTTTGTTTATTT
3864348 TTCACCTCTA
Statistics
Matches: 173, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
177 15 0.09
178 2 0.01
179 4 0.02
180 1 0.01
181 39 0.23
182 101 0.58
183 11 0.06
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (178 bp):
ATTTTTAAATATATAATTTTTAATAAAATATCATTTCTTTTCACAATGAACTAGATTCTAATAAG
TATAGTAGAAAATCTTAAAAAATCCTTAGGTGAGAGAATTTTTCTAAACATATCGTCAAAGAATT
ATAATATTTAAAATGATTCTCAATACGAAAAATTTTGTTTATTTCACA
Found at i:3870651 original size:186 final size:186
Alignment explanation
Indices: 3870337--3870709 Score: 577
Period size: 186 Copynumber: 2.0 Consensus size: 186
3870327 CAGTGCTCCT
*
3870337 TTTATCTTATCTGTATATTAGTACATGTACAGGCATACGTTTATTTGTAATCATGTGCTTCGTTA
1 TTTATCTTATCTGTATATTAGTACATGTACAGGCATACGTTTATTTATAATCATGTGCTTCGTTA
* * * *
3870402 ACGAGCAGACAGGGCTTAAGCTTAAGTTGTTACTAACTTAACTTTGATGATGGTGGTTTTTTCCT
66 ACGAGCAGACAGGGCTTAAACTTAAATTGTTACTAACTCAACTTTGATGAAGGTGGTTTTTTCCT
* *
3870467 CTGAATTTTTTAGAAATGAATTGGGGAAGGTTTTGGAGTTCT-CAATATCATAAAAC
131 CTGAATTTTTTAGAAATGAATTGGGGAAAGTTTTCGAGTT-TGCAATATCATAAAAC
* * * * *
3870523 TTTATCTTATCTGTATATTATTACATGTACAGGCATATGTTTATTTATAATCTTGTTCTTTGTTA
1 TTTATCTTATCTGTATATTAGTACATGTACAGGCATACGTTTATTTATAATCATGTGCTTCGTTA
* * * *
3870588 ATGAGCAGACAGGGTTTAAATTTAAATTGTTATTAACTCAACTTTGATGAAGGTGGTTTTTTCCT
66 ACGAGCAGACAGGGCTTAAACTTAAATTGTTACTAACTCAACTTTGATGAAGGTGGTTTTTTCCT
*
3870653 CTGAATTTTTTAGAAATGAATTGGGGAAAGTTTTCGAGTTTGTAATATCATAAAAC
131 CTGAATTTTTTAGAAATGAATTGGGGAAAGTTTTCGAGTTTGCAATATCATAAAAC
3870709 T
1 T
3870710 ATCTTAGTTT
Statistics
Matches: 169, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
185 1 0.01
186 168 0.99
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (186 bp):
TTTATCTTATCTGTATATTAGTACATGTACAGGCATACGTTTATTTATAATCATGTGCTTCGTTA
ACGAGCAGACAGGGCTTAAACTTAAATTGTTACTAACTCAACTTTGATGAAGGTGGTTTTTTCCT
CTGAATTTTTTAGAAATGAATTGGGGAAAGTTTTCGAGTTTGCAATATCATAAAAC
Found at i:3875105 original size:35 final size:35
Alignment explanation
Indices: 3875059--3875130 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
3875049 TAACAAAAGA
3875059 AAGGAATTGAACAGCAAAAGCATAGTTCTGAGATG
1 AAGGAATTGAACAGCAAAAGCATAGTTCTGAGATG
* *
3875094 AAGGAATTGAACAGCAAAAGTATGGTTCTGAGATG
1 AAGGAATTGAACAGCAAAAGCATAGTTCTGAGATG
3875129 AA
1 AA
3875131 TATTCATACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (35 bp):
AAGGAATTGAACAGCAAAAGCATAGTTCTGAGATG
Found at i:3877774 original size:2 final size:2
Alignment explanation
Indices: 3877767--3877791 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3877757 TTTCCTTAAA
3877767 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3877792 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3877796 original size:2 final size:2
Alignment explanation
Indices: 3877791--3877817 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3877781 TCTCTCTCTC
3877791 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3877818 CAAAATTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3885483 original size:2 final size:2
Alignment explanation
Indices: 3885476--3885502 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3885466 TTTCAAATCA
3885476 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3885503 ATTATCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3886344 original size:18 final size:18
Alignment explanation
Indices: 3886306--3886345 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3886296 TTTTAAATCA
* * *
3886306 TATTATTTTTATATTTTT
1 TATTATTTTCATATATAT
3886324 TATTATTTTCATATATAT
1 TATTATTTTCATATATAT
3886342 TATT
1 TATT
3886346 TTATCGTATT
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:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTTTCATATATAT
Found at i:3886831 original size:21 final size:20
Alignment explanation
Indices: 3886793--3886833 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3886783 TTTCATAATT
**
3886793 AAATAAAAATGGTGTTTTTA
1 AAATAAAAAACGTGTTTTTA
3886813 AAATAAAAAACGTGATTTTTA
1 AAATAAAAAACGTG-TTTTTA
3886834 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (20 bp):
AAATAAAAAACGTGTTTTTA
Found at i:3887213 original size:40 final size:40
Alignment explanation
Indices: 3887165--3887248 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
3887155 AGAATTCAAC
*
3887165 AAAAATAATG-TTTTTAAAATAAAAACATAGTATTTATTG
1 AAAAATAATGTTTTTTAAAATAAAAACATAATATTTATTG
* * *
3887204 AAAACATAATGTTTTTTAAAATAAAAATATAATTTTTGTTG
1 AAAA-ATAATGTTTTTTAAAATAAAAACATAATATTTATTG
3887245 AAAA
1 AAAA
3887249 TATGAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.10
40 6 0.15
41 29 0.74
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (40 bp):
AAAAATAATGTTTTTTAAAATAAAAACATAATATTTATTG
Found at i:3897880 original size:126 final size:126
Alignment explanation
Indices: 3897655--3897906 Score: 477
Period size: 126 Copynumber: 2.0 Consensus size: 126
3897645 AACAAAATGG
3897655 GTCCGATCACAACTCTGGAGGACTGGATTGTGGTGGCTTAAAGCAAAAAGATGGTATATATGAAA
1 GTCCGATCACAACTCTGGAGGACTGGATTGTGGTGGCTTAAAGCAAAAAGATGGTATATATGAAA
*
3897720 AGAATAGAACAGTATGAAAAGGCACTATCATTTTCTTTTTCTCTTTTCAATCAGTCATCTC
66 AGAATAGAACAGTATGAAAAGGCACTATCATTTTCTTTTTCTCTTTTCAATCAGCCATCTC
3897781 GTCCGATCACAACTCTGGAGGACTGGATTGTGGTGGCTTAAAGCAAAAAGATGGTATATATGAAA
1 GTCCGATCACAACTCTGGAGGACTGGATTGTGGTGGCTTAAAGCAAAAAGATGGTATATATGAAA
* *
3897846 AGAATAGAACAGTGTGGAAAGGCACTATCATTTTCTTTTTCTCTTTTCAATCAGCCATCTC
66 AGAATAGAACAGTATGAAAAGGCACTATCATTTTCTTTTTCTCTTTTCAATCAGCCATCTC
3897907 ACTTTGTTGA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (126 bp):
GTCCGATCACAACTCTGGAGGACTGGATTGTGGTGGCTTAAAGCAAAAAGATGGTATATATGAAA
AGAATAGAACAGTATGAAAAGGCACTATCATTTTCTTTTTCTCTTTTCAATCAGCCATCTC
Found at i:3903189 original size:19 final size:19
Alignment explanation
Indices: 3903161--3903205 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3903151 TAAAAAGGGA
*
3903161 GGCCCGGCAGGCCCGAACT
1 GGCCCTGCAGGCCCGAACT
3903180 GGCCCTGCAGGCCCGAACT
1 GGCCCTGCAGGCCCGAACT
3903199 GGCCCTG
1 GGCCCTG
3903206 GCCATAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.42, G:0.36, T:0.09
Consensus pattern (19 bp):
GGCCCTGCAGGCCCGAACT
Found at i:3904913 original size:22 final size:22
Alignment explanation
Indices: 3904888--3904945 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
3904878 TTTGATAAAT
3904888 AAAAATA-AAAATTATTTTTTA
1 AAAAATACAAAATTATTTTTTA
3904909 AAAAATACAAAATTATTTTTTA
1 AAAAATACAAAATTATTTTTTA
3904931 AAAAATACAAAATTA
1 AAAAATACAAAATTA
3904946 AGGAAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATACAAAATTATTTTTTA
Found at i:3913245 original size:11 final size:11
Alignment explanation
Indices: 3913220--3913257 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3913210 AGTAAGTTGT
3913220 CTTTTTGTTTG
1 CTTTTTGTTTG
3913231 -TTTTTGTTTG
1 CTTTTTGTTTG
* *
3913241 CTTTTTCTTTT
1 CTTTTTGTTTG
3913252 CTTTTT
1 CTTTTT
3913258 TTAAAGCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (11 bp):
CTTTTTGTTTG
Found at i:3916920 original size:16 final size:15
Alignment explanation
Indices: 3916896--3916949 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
3916886 ATGATTTGTT
3916896 TATTTATTTATGAATA
1 TATTTATTTATG-ATA
*
3916912 TATTCATTTAT-ATA
1 TATTTATTTATGATA
3916926 TA--TATTTATGCATA
1 TATTTATTTATG-ATA
3916940 TATTTATTTA
1 TATTTATTTA
3916950 ATATTCATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 6 0.19
14 10 0.31
16 16 0.50
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (15 bp):
TATTTATTTATGATA
Found at i:3916931 original size:28 final size:27
Alignment explanation
Indices: 3916900--3916953 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
3916890 TTTGTTTATT
3916900 TATTTATGAATATATTCATTTATATATA
1 TATTTATGAATATATTCATTTA-ATATA
* *
3916928 TATTTATGCATATATTTATTTAATAT
1 TATTTATGAATATATTCATTTAATAT
3916954 TCATGAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
TATTTATGAATATATTCATTTAATATA
Found at i:3917295 original size:19 final size:19
Alignment explanation
Indices: 3917273--3917309 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3917263 TTTTTTGTTA
3917273 TTTGGTTGTTTTTTAAAAT
1 TTTGGTTGTTTTTTAAAAT
* *
3917292 TTTGTTTTTTTTTTAAAA
1 TTTGGTTGTTTTTTAAAA
3917310 GGTATTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (19 bp):
TTTGGTTGTTTTTTAAAAT
Found at i:3917374 original size:26 final size:26
Alignment explanation
Indices: 3917322--3917389 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
3917312 TATTAATATA
*
3917322 ATTATTAAAATAT-TAAAAATTATTT
1 ATTATTAAAATATATTAAAATTATTT
*
3917347 ATTATTAAAATATATTGAAATTATTT
1 ATTATTAAAATATATTAAAATTATTT
*
3917373 ATTACTAAAAT-TATTAA
1 ATTATTAAAATATATTAA
3917390 TATTCAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
ATTATTAAAATATATTAAAATTATTT
Found at i:3917443 original size:19 final size:18
Alignment explanation
Indices: 3917408--3917459 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3917398 AGTAACTATT
3917408 TTAATAATAATATTTAATA
1 TTAA-AATAATATTTAATA
*
3917427 TTAAAATATTATATTAATA
1 TTAAAATAATAT-TTAATA
*
3917446 -TAAAA-AATACTTAA
1 TTAAAATAATATTTAA
3917460 AATAAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 3 0.10
18 12 0.41
19 10 0.34
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAATAATATTTAATA
Found at i:3917520 original size:23 final size:23
Alignment explanation
Indices: 3917487--3917657 Score: 145
Period size: 23 Copynumber: 7.4 Consensus size: 23
3917477 TTTTTATGTC
3917487 ATTTA-TAATATATTATAATATT
1 ATTTATTAATATATTATAATATT
* * *
3917509 ATTCATTAATATATTATATTAAT
1 ATTTATTAATATATTATAATATT
** *
3917532 AGCATATT-ATTTATTAATGATATATT
1 A-TTTATTAATATATT-AT-A-ATATT
* *
3917558 ATTTATTAATATATTATTATAAT
1 ATTTATTAATATATTATAATATT
*
3917581 ATTTATTAAT-TAATATAATAATT
1 ATTTATTAATATATTATAAT-ATT
*
3917604 A-TTATTAATTTATTATAATATT
1 ATTTATTAATATATTATAATATT
* * *
3917626 ATTTATTAATATAATGTTAT-TT
1 ATTTATTAATATATTATAATATT
3917648 ATTTATTAAT
1 ATTTATTAAT
3917658 GTAATATTAT
Statistics
Matches: 118, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
22 35 0.30
23 61 0.52
24 5 0.04
25 7 0.06
26 10 0.08
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTATTAATATATTATAATATT
Found at i:3917521 original size:28 final size:30
Alignment explanation
Indices: 3917490--3917549 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
3917480 TTATGTCATT
3917490 TATAATATATT-ATA-ATATTATTCATTAA
1 TATAATATATTAATACATATTATTCATTAA
* *
3917518 TATATTATATTAATAGCATATTATTTATTAA
1 TATAATATATTAATA-CATATTATTCATTAA
3917549 T
1 T
3917550 GATATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 10 0.37
29 3 0.11
31 14 0.52
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (30 bp):
TATAATATATTAATACATATTATTCATTAA
Found at i:3917522 original size:15 final size:14
Alignment explanation
Indices: 3917504--3917638 Score: 86
Period size: 15 Copynumber: 9.2 Consensus size: 14
3917494 ATATATTATA
3917504 ATATTATTCATTAAT
1 ATATTATT-ATTAAT
3917519 ATATTA-TATTAAT
1 ATATTATTATTAAT
3917532 AGCATATTATTTATTAATGAT
1 ---ATATTA-TTATT-A--AT
3917553 ATATTATTTATTAAT
1 ATATTA-TTATTAAT
3917568 ATATTATTA-TAAT
1 ATATTATTATTAAT
3917581 AT-TTATTAATTAAT
1 ATATTATT-ATTAAT
*
3917595 ATAATAATTATT-AT
1 AT-ATTATTATTAAT
*
3917609 -TAAT-TTATT-AT
1 ATATTATTATTAAT
3917620 AATATTATTTATTAAT
1 -ATATTA-TTATTAAT
3917636 ATA
1 ATA
3917639 ATGTTATTTA
Statistics
Matches: 99, Mismatches: 4, Indels: 34
0.72 0.03 0.25
Matches are distributed among these distances:
11 7 0.07
12 6 0.06
13 17 0.17
14 12 0.12
15 25 0.25
16 12 0.12
17 1 0.01
18 16 0.16
19 1 0.01
21 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
ATATTATTATTAAT
Found at i:3917564 original size:22 final size:21
Alignment explanation
Indices: 3917538--3917671 Score: 103
Period size: 22 Copynumber: 6.2 Consensus size: 21
3917528 TAATAGCATA
3917538 TTATTTATTAATGATATATTAT
1 TTATTTATTAAT-ATATATTAT
* * *
3917560 TTATTAATATATTATTATAATAT
1 TTATTTAT-TAATA-TATATTAT
* *
3917583 TTATTAATTAATATA-A-TAA
1 TTATTTATTAATATATATTAT
* *
3917602 TTA-TTATTAATTTATTATAAT
1 TTATTTATTAATATA-TATTAT
*
3917623 ATTATTTATTAATATAATGTTAT
1 -TTATTTATTAATAT-ATATTAT
*
3917646 TTATTTATTAATGTAATATTAT
1 TTATTTATTAATAT-ATATTAT
3917668 TTAT
1 TTAT
3917672 AATTAAAATT
Statistics
Matches: 90, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
18 9 0.10
19 5 0.06
20 2 0.02
21 3 0.03
22 39 0.43
23 31 0.34
24 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATTTATTAATATATATTAT
Found at i:3917640 original size:18 final size:18
Alignment explanation
Indices: 3917487--3917671 Score: 104
Period size: 18 Copynumber: 10.3 Consensus size: 18
3917477 TTTTTATGTC
* *
3917487 ATTTA-TAATATATTATA
1 ATTTATTAATATAATATT
*
3917504 ATATTATTCAT-TAATA-T
1 AT-TTATTAATATAATATT
**
3917521 ATTATATTAATAGCATATT
1 ATT-TATTAATATAATATT
3917540 ATTTATTAATGAT-ATATT
1 ATTTATTAAT-ATAATATT
3917558 ATTTATT-A-AT-ATATT
1 ATTTATTAATATAATATT
*
3917573 A-TTA-TAATAT-TTATT
1 ATTTATTAATATAATATT
* *
3917588 AATTAATATAATA-ATTATT
1 -ATTTAT-TAATATAATATT
* *
3917607 ATTAATTTATTATAATATT
1 ATTTA-TTAATATAATATT
3917626 ATTTATTAATATAATGTTATTT
1 ATTTATTAATATAA---TA-TT
*
3917648 ATTTATTAATGTAATATT
1 ATTTATTAATATAATATT
3917666 ATTTAT
1 ATTTAT
3917672 AATTAAAATT
Statistics
Matches: 135, Mismatches: 14, Indels: 37
0.73 0.08 0.20
Matches are distributed among these distances:
13 1 0.01
14 4 0.03
15 14 0.10
16 2 0.01
17 13 0.10
18 54 0.40
19 30 0.22
21 2 0.01
22 15 0.11
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTATTAATATAATATT
Found at i:3917654 original size:45 final size:44
Alignment explanation
Indices: 3917492--3917682 Score: 53
Period size: 45 Copynumber: 4.2 Consensus size: 44
3917482 ATGTCATTTA
* *
3917492 TAATA-TATTATAATATTATTCATTAATAT-ATTATATTAATAGCATAT
1 TAATATTATTATAATATTATTTATTAATATAATT-TATT--TA--TTAT
*
3917539 T-AT-TTATTAATGATATATTATTTATTAATAT-A-TTATTATAATATT
1 TAATATTATT-AT-A-ATATTATTTATTAATATAATTTATT-TATTA-T
* * *
3917584 TATTAATTAATATAATAATTA-TTATTAAT-TTATTATAATATTATTTAT
1 TAAT-ATTATTATAAT-ATTATTTATTAATATAATT-T-AT-TTA-TTAT
* * *
3917632 TAATATAATGT-T-AT-TTATTTATTAATGTAATATTATTTATAAT
1 TAATATTAT-TATAATATTATTTATTAATATAAT-TTATTTATTAT
*
3917675 TAAAATTA
1 TAATATTA
3917683 GGCTAAAAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 42
0.68 0.07 0.25
Matches are distributed among these distances:
43 9 0.08
44 10 0.09
45 23 0.20
46 22 0.19
47 15 0.13
48 15 0.13
49 20 0.18
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (44 bp):
TAATATTATTATAATATTATTTATTAATATAATTTATTTATTAT
Found at i:3920365 original size:10 final size:10
Alignment explanation
Indices: 3920350--3920383 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3920340 ATTAAATTTA
3920350 ATAAATAAAT
1 ATAAATAAAT
3920360 ATAAATAAAT
1 ATAAATAAAT
*
3920370 AAAAATCAAAT
1 ATAAAT-AAAT
3920381 ATA
1 ATA
3920384 TTCATAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:3920723 original size:10 final size:10
Alignment explanation
Indices: 3920700--3920732 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3920690 TATTTTATTT
3920700 TATAAAAAT-
1 TATAAAAATA
3920709 T-TAAAAATA
1 TATAAAAATA
3920718 TATAAAAATA
1 TATAAAAATA
3920728 TATAA
1 TATAA
3920733 TTAAGTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.32
9 2 0.09
10 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TATAAAAATA
Found at i:3920817 original size:38 final size:36
Alignment explanation
Indices: 3920750--3920825 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 36
3920740 CCATTTATTT
*
3920750 TTTAATTTGAAATTTAATATGAACTAAATATAAAAAA
1 TTTAATTTCAAATTTAATATGAACTAAATA-AAAAAA
* *
3920787 TTTAATATTCAAATTTAATTTTAA-TCAAATAAAAAAA
1 TTTAAT-TTCAAATTTAATATGAACT-AAATAAAAAAA
3920824 TT
1 TT
3920826 GATTTAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (36 bp):
TTTAATTTCAAATTTAATATGAACTAAATAAAAAAA
Found at i:3930369 original size:2 final size:2
Alignment explanation
Indices: 3930362--3930390 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3930352 CTTTGAATTT
3930362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3930391 TAAATCTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3934467 original size:16 final size:18
Alignment explanation
Indices: 3934448--3934491 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
3934438 TATTTAATTT
3934448 TATATTTAT-ATAT-TAA
1 TATATTTATAATATATAA
*
3934464 TATATTTAATAATATATAT
1 TATATTT-ATAATATATAA
3934483 TATATTTAT
1 TATATTTAT
3934492 GTATAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 6 0.25
19 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTATAATATATAA
Found at i:3934497 original size:22 final size:22
Alignment explanation
Indices: 3934454--3934498 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3934444 ATTTTATATT
*
3934454 TATATATTAATATATTTAATAA
1 TATATATTAATATATGTAATAA
*
3934476 TATATATTATATTTATGT-ATAA
1 TATATATTA-ATATATGTAATAA
3934498 T
1 T
3934499 TAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATATTAATATATGTAATAA
Found at i:3934500 original size:16 final size:16
Alignment explanation
Indices: 3934447--3934500 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
3934437 TTATTTAATT
3934447 TTATATTTATATATTAA
1 TTATATTTATATA-TAA
3934464 -TATATTTAATAATATATA
1 TTATATTT-AT-ATATA-A
*
3934482 TTATATTTATGTATAA
1 TTATATTTATATATAA
3934498 TTA
1 TTA
3934501 AAATATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 11 0.34
17 8 0.25
18 6 0.19
19 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTATATTTATATATAA
Found at i:3934505 original size:28 final size:29
Alignment explanation
Indices: 3934448--3934516 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
3934438 TATTTAATTT
*
3934448 TATAT-TTATATATTAATATATTTAATAA
1 TATATATTATATATTAATATAATTAATAA
*
3934476 TATATATTATAT-TTATGTATAATTAA-AA
1 TATATATTATATATTA-ATATAATTAATAA
3934504 TATA-ATTTATATA
1 TATATA-TTATATA
3934517 CAAAATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 20 0.57
29 14 0.40
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TATATATTATATATTAATATAATTAATAA
Found at i:3943736 original size:22 final size:21
Alignment explanation
Indices: 3943697--3943739 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3943687 TGTATATTTA
*
3943697 TATTTTATCTCTAAAATTAAG
1 TATTTTATCCCTAAAATTAAG
*
3943718 TATTTGTATCCCTAGAATTAAG
1 TATTT-TATCCCTAAAATTAAG
3943740 GACAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (21 bp):
TATTTTATCCCTAAAATTAAG
Found at i:3943922 original size:25 final size:25
Alignment explanation
Indices: 3943881--3943930 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
3943871 CACATACATT
3943881 CAGTTTTACTCTTAG-TTTTCCACA
1 CAGTTTTACTCTTAGTTTTTCCACA
*
3943905 CAGTTTTATTTCTTAGTTTTTCCACA
1 CAGTTTTA-CTCTTAGTTTTTCCACA
3943931 TATTTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.35
25 6 0.26
26 9 0.39
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.50
Consensus pattern (25 bp):
CAGTTTTACTCTTAGTTTTTCCACA
Found at i:3948740 original size:2 final size:2
Alignment explanation
Indices: 3948733--3948771 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3948723 GGAGTTCTTT
3948733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3948772 GTTGAAGGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3952739 original size:8 final size:7
Alignment explanation
Indices: 3952728--3952769 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
3952718 ATAAATAAAC
3952728 AAAAAAGG
1 AAAAAA-G
3952736 AAAAAAG
1 AAAAAAG
3952743 AAAAAAG
1 AAAAAAG
3952750 AGAAAAAG
1 A-AAAAAG
3952758 AAAAAAG
1 AAAAAAG
*
3952765 GAAAA
1 AAAAA
3952770 TGAAGCTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 19 0.59
8 13 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3952745 original size:7 final size:7
Alignment explanation
Indices: 3952728--3952769 Score: 57
Period size: 8 Copynumber: 5.6 Consensus size: 7
3952718 ATAAATAAAC
3952728 AAAAAAGG
1 AAAAAA-G
3952736 AAAAAAG
1 AAAAAAG
3952743 AAAAAAG
1 AAAAAAG
3952750 AGAAAAAG
1 A-AAAAAG
3952758 AAAAAAGG
1 AAAAAA-G
3952766 AAAA
1 AAAA
3952770 TGAAGCTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.44
8 18 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3952748 original size:15 final size:15
Alignment explanation
Indices: 3952728--3952769 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
3952718 ATAAATAAAC
3952728 AAAAAAGGAAAAAAG
1 AAAAAAGGAAAAAAG
3952743 AAAAAA-GAGAAAAAG
1 AAAAAAGGA-AAAAAG
3952758 AAAAAAGGAAAA
1 AAAAAAGGAAAA
3952770 TGAAGCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAAAAG
Done.