Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 13 of 160
Found at i:4000892 original size:12 final size:12
Alignment explanation
Indices: 4000875--4000899 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4000865 GATAGAAGGC
4000875 CAATGATCACTG
1 CAATGATCACTG
4000887 CAATGATCACTG
1 CAATGATCACTG
4000899 C
1 C
4000900 TTTCTTTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (12 bp):
CAATGATCACTG
Found at i:4001689 original size:20 final size:20
Alignment explanation
Indices: 4001664--4001726 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
4001654 CACTCTCTGA
4001664 GTGAAAGAAAAAAGAATTAT
1 GTGAAAGAAAAAAGAATTAT
4001684 GTGAAA-AAAAAA-AATGTATT
1 GTGAAAGAAAAAAGAAT-TA-T
* *
4001704 TTGAAAGGAAAAAGAAGTTAT
1 GTGAAAGAAAAAAGAA-TTAT
4001725 GT
1 GT
4001727 ATGGTAGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
18 3 0.09
19 8 0.23
20 12 0.34
21 7 0.20
22 4 0.11
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (20 bp):
GTGAAAGAAAAAAGAATTAT
Found at i:4002404 original size:28 final size:27
Alignment explanation
Indices: 4002372--4002440 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 27
4002362 TAAATAATTC
*
4002372 AAATTTATTTATTAGTTTGTTATATAAT-
1 AAATTTATTT-TTA-TTTATTATATAATA
4002400 AAA-TT-TTTTTATTTATTATATAATA
1 AAATTTATTTTTATTTATTATATAATA
4002425 AAATTTATTTTATATT
1 AAATTTATTTT-TATT
4002441 AAATTAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 12 0.33
25 6 0.17
26 5 0.14
27 6 0.17
28 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (27 bp):
AAATTTATTTTTATTTATTATATAATA
Found at i:4002430 original size:17 final size:17
Alignment explanation
Indices: 4002410--4002443 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4002400 AAATTTTTTT
4002410 ATTTATTATATAATAAA
1 ATTTATTATATAATAAA
* *
4002427 ATTTATTTTATATTAAA
1 ATTTATTATATAATAAA
4002444 TTAGAAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATTATATAATAAA
Found at i:4004350 original size:58 final size:57
Alignment explanation
Indices: 4004233--4004444 Score: 266
Period size: 57 Copynumber: 3.7 Consensus size: 57
4004223 TTGTACAAAA
* ** * ** * *
4004233 AAAATTGATACTTTCAGCTTTTTTTC-AAAATATTTTTCTGAAATTTTAATTTCGAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAG
4004289 AAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTTTGAAAACTTATTTTCAAGG
1 -AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAA-G
* * * *
4004347 AAAATTAATAGTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAACTTATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTC-AAG
*
4004405 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
4004445 TGGAATTTAT
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
57 70 0.52
58 62 0.46
59 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAG
Found at i:4004416 original size:115 final size:115
Alignment explanation
Indices: 4004233--4004444 Score: 295
Period size: 115 Copynumber: 1.8 Consensus size: 115
4004223 TTGTACAAAA
* * * ** *
4004233 AAAATTGATACTTTCAGCTTTTTTTCAAAATATTTTTCTGAAATTTTAATTTCGAGAAAAATTGA
1 AAAATTAATACTTTCAACTTTTTCTCAAAATATTTTTCTGAAAACTTAATTTCAAGAAAAATTGA
4004298 TACTTTCAACTTTTCCTCAAAAAT-TTTTTTTGAAAACTTATTTTCAAGG
66 TACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAGG
* *
4004347 AAAATTAATAGTTTCAACTTTTTCTCAAAAATATTTTT-TAGAAAACTTATTTTCAA-AGAAAAT
1 AAAATTAATACTTTCAACTTTTTCTC-AAAATATTTTTCT-GAAAACTTAATTTCAAGA-AAAAT
*
4004410 TGATACTTTCAACTTTTCCTTAAAAATATTTTTTT
63 TGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
4004445 TGGAATTTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
114 24 0.28
115 54 0.64
116 7 0.08
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (115 bp):
AAAATTAATACTTTCAACTTTTTCTCAAAATATTTTTCTGAAAACTTAATTTCAAGAAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTATTTTCAAGG
Found at i:4004478 original size:9 final size:8
Alignment explanation
Indices: 4004456--4004487 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
4004446 GGAATTTATT
4004456 TAAAGAAAA
1 TAAA-AAAA
4004465 TAAAAAAA
1 TAAAAAAA
4004473 TAAAAAAA
1 TAAAAAAA
4004481 TAAAAAA
1 TAAAAAA
4004488 GAAATACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:4004849 original size:12 final size:12
Alignment explanation
Indices: 4004803--4004854 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
4004793 CAGCAGAATC
4004803 CTCTTTCTCCCTCT
1 CTCTTTCT--CTCT
4004817 CTCTTTACT-TCT
1 CTCTTT-CTCTCT
* *
4004829 TTTTTTCTCTCT
1 CTCTTTCTCTCT
4004841 CTCTTTCTCTCT
1 CTCTTTCTCTCT
4004853 CT
1 CT
4004855 ACCTTCTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.06
12 22 0.69
14 6 0.19
15 2 0.06
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (12 bp):
CTCTTTCTCTCT
Found at i:4005424 original size:4 final size:4
Alignment explanation
Indices: 4005417--4005533 Score: 52
Period size: 4 Copynumber: 30.5 Consensus size: 4
4005407 ATATGGATAG
* * * * * * *
4005417 ATAA AT-A ATAA AAAA ATAT ATTA ATAG ATAA AT-A ATAAA ATAT GTTA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA
* * * *
4005464 ATAG ATTA AT-A ATAA A-AA ATAT ATTA ATAA AT-A AT-A ATAGTA AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA
4005509 ATAA ATAA ATAA ATAA ATAA A-AA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
4005534 TAAAATTAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
3 24 0.29
4 52 0.63
5 3 0.04
6 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (4 bp):
ATAA
Found at i:4005456 original size:24 final size:24
Alignment explanation
Indices: 4005413--4005530 Score: 105
Period size: 24 Copynumber: 4.7 Consensus size: 24
4005403 AGATATATGG
4005413 ATAGATAAATAATAAAAAAATATATTA
1 ATAGATAAATAAT---AAAATATATTA
*
4005440 ATAGATAAATAATAAAATATGTTA
1 ATAGATAAATAATAAAATATATTA
*
4005464 ATAGATTAATAATAAAAAATATATTA
1 ATAGATAAATAAT--AAAATATATTA
* * *
4005490 ATAAAT-AATAATAGTAATA-ATAA
1 ATAGATAAATAATA-AAATATATTA
*
4005513 ATAAATAAATAAATAAAA
1 ATAGATAAAT-AATAAAA
4005531 AATTAAAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
23 10 0.13
24 31 0.39
25 10 0.13
26 15 0.19
27 13 0.16
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAGATAAATAATAAAATATATTA
Found at i:4005798 original size:41 final size:41
Alignment explanation
Indices: 4005697--4006032 Score: 274
Period size: 42 Copynumber: 8.0 Consensus size: 41
4005687 TTTTATCAAA
* * **
4005697 GCTCCTCTAAACAGAGG-TTCAACAACTTTGAGAAACATAAACAAA
1 GCTCTTCTAAACAGAGGCATC-ACAACTTTGA-AAA-AT-AA-ATT
* * *
4005742 GCTCTTCTAATCAGAGGCATTACAACTTTGAAAAATAAATA
1 GCTCTTCTAAACAGAGGCATCACAACTTTGAAAAATAAATT
* * *
4005783 GCTCTTCTAAACAGAGGC-TCAACGACTTTTGAAAAGTAAATG
1 GCTCTTCTAAACAGAGGCATC-ACAAC-TTTGAAAAATAAATT
* * *
4005825 GCTCTTCTAAACAGAGGCAACCACGACTTTTAAAAAATAAATT
1 GCTCTTCTAAACAGAGGC-ATCACAAC-TTTGAAAAATAAATT
* *
4005868 GCTCCTCTAAACAGAGACA-CGACAACTTTTGAAAAATAAATT
1 GCTCTTCTAAACAGAGGCATC-ACAAC-TTTGAAAAATAAATT
* * *
4005910 GCTCCTT-TAAACAGAAGTATCACAACTTTAAAAAATAAATT
1 GCT-CTTCTAAACAGAGGCATCACAACTTTGAAAAATAAATT
* * * *
4005951 GCTCCTT-TAAACAGATGCACCACAACTTTG-AGAGTAAATT
1 GCT-CTTCTAAACAGAGGCATCACAACTTTGAAAAATAAATT
* *
4005991 GCTCCTT-TAATCAGAGGCATCACAACTTTG-AAAGTAAATT
1 GCT-CTTCTAAACAGAGGCATCACAACTTTGAAAAATAAATT
4006031 GC
1 GC
4006033 CCCTTGACAA
Statistics
Matches: 250, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
40 47 0.19
41 64 0.26
42 70 0.28
43 39 0.16
44 4 0.02
45 25 0.10
46 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (41 bp):
GCTCTTCTAAACAGAGGCATCACAACTTTGAAAAATAAATT
Found at i:4007067 original size:25 final size:25
Alignment explanation
Indices: 4007036--4007092 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
4007026 TAAGTCCTCC
4007036 TTTTTCA-TTCATTTTTTTTTCTATT
1 TTTTTCATTTCATTTTTTTTT-TATT
4007061 TTTTTCATTTCATTTTTTTTTTATT
1 TTTTTCATTTCATTTTTTTTTTATT
4007086 TTTTTCA
1 TTTTTCA
4007093 AGCATAGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 18 0.58
26 13 0.42
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTCATTTCATTTTTTTTTTATT
Found at i:4017613 original size:58 final size:57
Alignment explanation
Indices: 4017443--4017622 Score: 213
Period size: 58 Copynumber: 3.1 Consensus size: 57
4017433 TGCTTTTGTA
* * *
4017443 TAAGAAAAATTGATACTTTTAATTTTTTC-CCAAAATATTTTTC-TGAAACTTTAATTT
1 TAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTGAAA-TTT-ATTT
* * * * *
4017500 TGAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTT-TAGAAAACTTATTT
1 TAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTG-AAATTTATTT
*
4017557 TCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTGGAATTTATTT
1 T-AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTGAAATTTATTT
*
4017615 AAAGAAAA
1 TAAGAAAA
4017623 TAAAAAATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
57 37 0.36
58 61 0.59
59 5 0.05
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (57 bp):
TAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTCTTGAAATTTATTT
Found at i:4017698 original size:15 final size:16
Alignment explanation
Indices: 4017678--4017726 Score: 75
Period size: 15 Copynumber: 3.2 Consensus size: 16
4017668 TCTAATCAAT
*
4017678 AAATAATAATAATA-A
1 AAATAATAAAAATATA
4017693 AAATAATAAAAATATA
1 AAATAATAAAAATATA
4017709 AAAT-ATAAAAATATA
1 AAATAATAAAAATATA
4017724 AAA
1 AAA
4017727 AAAAAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 27 0.84
16 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATAAAAATATA
Found at i:4017709 original size:8 final size:8
Alignment explanation
Indices: 4017689--4017727 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
4017679 AATAATAATA
4017689 ATAAAAAT
1 ATAAAAAT
4017697 AATAAAAAT
1 -ATAAAAAT
4017706 AT-AAAAT
1 ATAAAAAT
4017713 ATAAAAAT
1 ATAAAAAT
4017721 ATAAAAA
1 ATAAAAA
4017728 AAAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.24
8 14 0.48
9 8 0.28
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
ATAAAAAT
Found at i:4018703 original size:8 final size:7
Alignment explanation
Indices: 4018644--4018768 Score: 58
Period size: 8 Copynumber: 16.9 Consensus size: 7
4018634 ATATGGATAG
4018644 ATAAATA
1 ATAAATA
4018651 ATAAA-A
1 ATAAATA
*
4018657 ATATATA
1 ATAAATA
*
4018664 TATTAATA
1 -ATAAATA
4018672 GATAAATA
1 -ATAAATA
*
4018680 ATAAAATCT
1 AT-AAAT-A
* *
4018689 GTTAATA
1 ATAAATA
4018696 GATAAATA
1 -ATAAATA
4018704 ATAGAATA
1 ATA-AATA
*
4018712 TATATATTA
1 -ATA-AATA
4018721 ATAAATA
1 ATAAATA
*
4018728 GT-AATA
1 ATAAATA
*
4018734 GT-AATA
1 ATAAATA
4018740 ATAAATAA
1 ATAAAT-A
4018748 ATAAATAA
1 ATAAAT-A
4018756 ATAAATA
1 ATAAATA
*
4018763 AAAAAT
1 ATAAAT
4018769 TAAAATTAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 18
0.72 0.13 0.14
Matches are distributed among these distances:
6 16 0.17
7 24 0.26
8 45 0.49
9 7 0.08
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (7 bp):
ATAAATA
Found at i:4018732 original size:27 final size:27
Alignment explanation
Indices: 4018702--4018754 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4018692 AATAGATAAA
* *
4018702 TAATAG-AATATATATATTAATAAATAG
1 TAATAGTAATA-ATAAATAAATAAATAG
4018729 TAATAGTAATAATAAATAAATAAATA
1 TAATAGTAATAATAAATAAATAAATA
4018755 AATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (27 bp):
TAATAGTAATAATAAATAAATAAATAG
Found at i:4018746 original size:4 final size:4
Alignment explanation
Indices: 4018739--4018768 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4018729 TAATAGTAAT
4018739 AATA AATA AATA AATA AATA AATA AA-A AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
4018769 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:4024562 original size:17 final size:17
Alignment explanation
Indices: 4024540--4024572 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4024530 CAAGAGTGAA
4024540 TTTCTTATTTCTTATTC
1 TTTCTTATTTCTTATTC
4024557 TTTCTTATTTCTTATT
1 TTTCTTATTTCTTATT
4024573 ATTGAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTATTTCTTATTC
Found at i:4024846 original size:638 final size:639
Alignment explanation
Indices: 4023629--4024974 Score: 2092
Period size: 638 Copynumber: 2.1 Consensus size: 639
4023619 CAAGAGTGAA
* * *
4023629 TTTCTTATTTCTTATTATTGAATTTATAGGCGCTTGACGTGGGTCGAACGGTTTAGGGCTAGCTC
1 TTTCTTATTTCTTATTATTGAATTTATAGGCGCTTGACATGGGTCGAACAGTTTAGGACTAGCTC
* * *
4023694 TGATACCACTTATCACGTGTCAAAATTTAAGCTCCAAGACTCGGGTATGGCATCTCAGATCAACC
66 TGATACCACTTATCACGTGTCAAAATTTAAACTCCAAGACCCGGGTATGGCATCCCAGATCAACC
* * * * *
4023759 TACTTACCATGATTCACTACCTCTCTCGAGGCGTTTGGCGTGAGTTGAACGGTTTAGGCCTTTTT
131 TACTTACCACGATTCACTACCTCTCTCAAGGCGCTTGGCGTGAGTTGAACGATTTAGGCCTTTGT
* * * *
4023824 TTTCATTTCATAAATGAATTACTCATATTTTCACATCTAGGATTTACATATACAACATATATTAT
196 TTTCATTTCATAAACGAATTACGCATATTTTCACATATAGGATTTACATATACAACATATATTAC
* * *
4023889 TGTTAAGAGTGAATTTCTTATTTTTTATTCTTTTTTATTTCTTATTATTGAATTTATAGGCGCTT
261 TGTCAAGAGTGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTGAATTTATAGGCGCTT
* * * * *
4023954 GGTGTGGGTCGAACGGTTTAGGGCTAGCTCTGATTTACATATACAACATATATTACTGTCAAGAG
326 GGCGTGAGTCGAACAGTTTAAGGCTAGCTCTGATTTACAAATACAACATATATTACTGTCAAGAG
* *
4024019 TAAATTTCTTATTTCTTATTATTGAATTTATAGGCGCTTGACGTGGGTCGAACGGTTTAGGGCTA
391 TAAATTTCTTATTTCTTATTATTGAATTTATAGGCACTTGACATGGGTCGAACGGTTTAGGGCTA
*
4024084 GCTCTGATACCACTTGTCACGTGTCGAGATTTAAGCTCCAGGACCCGAGTATACACTCATCCGAC
456 GCTCTGATACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGAGTATACACTCATCCGAC
*
4024149 GTCTCAGATCAGCATACTTGCCACGATTCACTACCTCTCTCGAGGCGCTTGGCATGGGTTGAACG
521 GTCTCAGATCAGCATACTTGCCACGATTCACTACCTCTCTCGAGGCGCTTGACATGGGTTGAACG
4024214 GTTTA-AGGCT-GGC-CTGATACCACTTACAAGAATGAATTTCTTATTTCTTATTC
586 GTTTAGA-G-TAGGCTCTGATACCACTTACAAGAATGAATTTCTTATTTCTTATTC
* * * *
4024267 TTTCTTATTTCTTGTTATTGAATTTATAGGCGCTTGGCATGGGTTGAACAGTTTAGGACTAGCTT
1 TTTCTTATTTCTTATTATTGAATTTATAGGCGCTTGACATGGGTCGAACAGTTTAGGACTAGCTC
* * * * * * *
4024332 TGATACCACTTGTCACGTGTCGAGATTTAAACTCTAGGACCCGGGTATGGTATCCCAGATCAGCC
66 TGATACCACTTATCACGTGTCAAAATTTAAACTCCAAGACCCGGGTATGGCATCCCAGATCAACC
* *
4024397 TACTTGCCACGATTCACTACCTTTCTCAAGGCGCTTGGCGTGAGTTGAACGATTTAGGCCTTTGT
131 TACTTACCACGATTCACTACCTCTCTCAAGGCGCTTGGCGTGAGTTGAACGATTTAGGCCTTTGT
*
4024462 TTTCATTTTATAAACGAATTACGCATATTTTCACATATAGGATTTACATATACAACATATATTAC
196 TTTCATTTCATAAACGAATTACGCATATTTTCACATATAGGATTTACATATACAACATATATTAC
*
4024527 TGTCAAGAGTGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTGAATTTATAGGCGTTT
261 TGTCAAGAGTGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTGAATTTATAGGCGCTT
*
4024592 GGCGTGAGTCGAACAGTTTAAGGCTAGCTTTGATTTACAAATACAACATATATTACTGTCAAGAG
326 GGCGTGAGTCGAACAGTTTAAGGCTAGCTCTGATTTACAAATACAACATATATTACTGTCAAGAG
* * * *
4024657 TGAATTTTTTATTTCTTATTATTGAATTTATAGGCACTTGACATGTGTTGAACGGTTTAGGGCTA
391 TAAATTTCTTATTTCTTATTATTGAATTTATAGGCACTTGACATGGGTCGAACGGTTTAGGGCTA
* *
4024722 GCTCTGATACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGGGTATGCACTCATCCGAC
456 GCTCTGATACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGAGTATACACTCATCCGAC
* *
4024787 GT-TCCAGATCAGCCTACTTGTCACGATTCACTACCTCTCTCGAGGCGCTTGACATGGGTTGAAC
521 GTCT-CAGATCAGCATACTTGCCACGATTCACTACCTCTCTCGAGGCGCTTGACATGGGTTGAAC
** *
4024851 GGTTTAGAGTAGGCTCTGATACCACTTGTAAGAGTGAATTTCTTATTTCTTATTC
585 GGTTTAGAGTAGGCTCTGATACCACTTACAAGAATGAATTTCTTATTTCTTATTC
* * *
4024906 TTTCTTATTTTTTATTATTGAATTTATAGGCGCTTGACGTGGATCGAAC-GATTTAAGG-CTAGC
1 TTTCTTATTTCTTATTATTGAATTTATAGGCGCTTGACATGGGTCGAACAG-TTT-AGGACTAGC
4024969 TCTGAT
64 TCTGAT
4024975 TTACATATAC
Statistics
Matches: 641, Mismatches: 61, Indels: 11
0.90 0.09 0.02
Matches are distributed among these distances:
637 2 0.00
638 542 0.85
639 94 0.15
640 3 0.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (639 bp):
TTTCTTATTTCTTATTATTGAATTTATAGGCGCTTGACATGGGTCGAACAGTTTAGGACTAGCTC
TGATACCACTTATCACGTGTCAAAATTTAAACTCCAAGACCCGGGTATGGCATCCCAGATCAACC
TACTTACCACGATTCACTACCTCTCTCAAGGCGCTTGGCGTGAGTTGAACGATTTAGGCCTTTGT
TTTCATTTCATAAACGAATTACGCATATTTTCACATATAGGATTTACATATACAACATATATTAC
TGTCAAGAGTGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTGAATTTATAGGCGCTT
GGCGTGAGTCGAACAGTTTAAGGCTAGCTCTGATTTACAAATACAACATATATTACTGTCAAGAG
TAAATTTCTTATTTCTTATTATTGAATTTATAGGCACTTGACATGGGTCGAACGGTTTAGGGCTA
GCTCTGATACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGAGTATACACTCATCCGAC
GTCTCAGATCAGCATACTTGCCACGATTCACTACCTCTCTCGAGGCGCTTGACATGGGTTGAACG
GTTTAGAGTAGGCTCTGATACCACTTACAAGAATGAATTTCTTATTTCTTATTC
Found at i:4024911 original size:17 final size:17
Alignment explanation
Indices: 4024889--4024921 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4024879 TAAGAGTGAA
4024889 TTTCTTATTTCTTATTC
1 TTTCTTATTTCTTATTC
*
4024906 TTTCTTATTTTTTATT
1 TTTCTTATTTCTTATT
4024922 ATTGAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTATTTCTTATTC
Found at i:4025032 original size:17 final size:17
Alignment explanation
Indices: 4025010--4025042 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4025000 CAAGAGTAAA
4025010 TTTCTTATTTCTTATTC
1 TTTCTTATTTCTTATTC
*
4025027 TTTCTTATTTTTTATT
1 TTTCTTATTTCTTATT
4025043 ATTGAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTATTTCTTATTC
Found at i:4025212 original size:366 final size:360
Alignment explanation
Indices: 4024665--4025334 Score: 1074
Period size: 366 Copynumber: 1.8 Consensus size: 360
4024655 AGTGAATTTT
** *
4024665 TTATTTCTTATTATTGAATTTATAGGCACTTGACATGTGTTGAACGGTTTAGGGCTAGCTCTGAT
1 TTATTTCTTATTATTGAATTTATAGGCACTTGACATAAGTTGAACGATTTAGGGCTAGCTCTGAT
* *
4024730 ACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGGGTATGCACTCATCCGACGTTCCAGA
66 ACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGAGTATACACTCATCCGACGTTCCAGA
* *
4024795 TCAGCCTACTTGTCACGATTCACTACCTCTCTCGAGGCGCTTGACATGGGTTGAACGGTTTAGAG
131 TCAGCCTACTTGTCACGATTCACTACCTCTCTCGAGACGCTTGACATGGGTTGAAC-GATT----
* * *
4024860 TAGGCTCTGATACCACTTGTAAGAGTGAATTTCTTATTTCTTATTCTTTCTTATTTTTTATTATT
191 TAGGC-CTGATACCACTTGCAAGAATGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATT
*
4024925 GAATTTATAGGCGCTTGACGT-GGATCGAACGATTTAAGGCTAGCTCTGATTTACATATACAACA
255 AAATTTATAGGCGCTTGACGTAGG-TCGAACGATTTAAGGCTAGCTCTGATTTACATATACAACA
4024989 TACATTACTGTCAAGAGTAAATTTCTTATTTCTTATTCTTTC
319 TACATTACTGTCAAGAGTAAATTTCTTATTTCTTATTCTTTC
* * *
4025031 TTATTTTTTATTATTGAATTTATAGGCGCTTGACGTAAGTTGAACGATTTAGGGCTAGCTCTGAT
1 TTATTTCTTATTATTGAATTTATAGGCACTTGACATAAGTTGAACGATTTAGGGCTAGCTCTGAT
* * *
4025096 ACCACTTGTCACGTGTCGAGATTTAAGTTCCAAGACCCGAGTATACACTTATCCGACG-TCTTAG
66 ACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGAGTATACACTCATCCGACGTTC-CAG
4025160 ATCAGCCTACTTGTCACGATTCACTACCTCTCTCGAGACGCTTGACATGGGTTGAACGATTTAGG
130 ATCAGCCTACTTGTCACGATTCACTACCTCTCTCGAGACGCTTGACATGGGTTGAACGATTTAGG
4025225 CCTGATACCACTTGCAAGAATGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTAAATT
195 CCTGATACCACTTGCAAGAATGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTAAATT
* * *
4025290 TATAGGCGCTTGACGTAGGTCGAACGGTTTAAGGTTAGCTTTGAT
260 TATAGGCGCTTGACGTAGGTCGAACGATTTAAGGCTAGCTCTGAT
4025335 ACCACTCATT
Statistics
Matches: 282, Mismatches: 20, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
360 99 0.35
361 7 0.02
365 5 0.02
366 171 0.61
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (360 bp):
TTATTTCTTATTATTGAATTTATAGGCACTTGACATAAGTTGAACGATTTAGGGCTAGCTCTGAT
ACCACTTGTCACGTGTCGAGATTTAAGCTCCAAGACCCGAGTATACACTCATCCGACGTTCCAGA
TCAGCCTACTTGTCACGATTCACTACCTCTCTCGAGACGCTTGACATGGGTTGAACGATTTAGGC
CTGATACCACTTGCAAGAATGAATTTCTTATTTCTTATTCTTTCTTATTTCTTATTATTAAATTT
ATAGGCGCTTGACGTAGGTCGAACGATTTAAGGCTAGCTCTGATTTACATATACAACATACATTA
CTGTCAAGAGTAAATTTCTTATTTCTTATTCTTTC
Found at i:4025271 original size:17 final size:17
Alignment explanation
Indices: 4025249--4025281 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4025239 CAAGAATGAA
4025249 TTTCTTATTTCTTATTC
1 TTTCTTATTTCTTATTC
4025266 TTTCTTATTTCTTATT
1 TTTCTTATTTCTTATT
4025282 ATTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTATTTCTTATTC
Found at i:4025991 original size:11 final size:11
Alignment explanation
Indices: 4025975--4026034 Score: 104
Period size: 11 Copynumber: 5.5 Consensus size: 11
4025965 ATTTAAATGT
4025975 AAAATATACTA
1 AAAATATACTA
4025986 AAAATATACTA
1 AAAATATACTA
4025997 AAAATATACTA
1 AAAATATACTA
*
4026008 AAAATATGCTA
1 AAAATATACTA
4026019 AAAA-ATACTA
1 AAAATATACTA
4026029 AAAATA
1 AAAATA
4026035 AAAAATATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.20
11 37 0.80
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (11 bp):
AAAATATACTA
Found at i:4026094 original size:20 final size:20
Alignment explanation
Indices: 4026038--4026082 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4026028 AAAAATAAAA
*
4026038 AATATAGTAATATTATACTT
1 AATATACTAATATTATACTT
*
4026058 AGTATACTAATATTATAC-T
1 AATATACTAATATTATACTT
4026077 AATATA
1 AATATA
4026083 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (20 bp):
AATATACTAATATTATACTT
Found at i:4026154 original size:11 final size:11
Alignment explanation
Indices: 4026100--4026160 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
4026090 ATATAATATT
4026100 AAATAAAATAGA
1 AAATAAAATA-A
*
4026112 CTAATAAAATAA
1 -AAATAAAATAA
* *
4026124 AGATAACAT-A
1 AAATAAAATAA
* *
4026134 TAATAGAATAA
1 AAATAAAATAA
4026145 AAATAAAATAA
1 AAATAAAATAA
4026156 AAATA
1 AAATA
4026161 TATAATATAG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
10 6 0.16
11 21 0.57
12 1 0.03
13 9 0.24
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:4026165 original size:21 final size:21
Alignment explanation
Indices: 4026141--4026217 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 21
4026131 ATATAATAGA
4026141 ATAAAAATAAAATAAAAATAT
1 ATAAAAATAAAATAAAAATAT
*
4026162 ATAATATAGAGATAAATAATAAATAT
1 ATAA-A-A-ATA-AAATAA-AAATAT
*
4026188 ATAAAGATAAATAATAAAAAT-T
1 ATAAAAAT-AA-AATAAAAATAT
4026210 ATAAAAAT
1 ATAAAAAT
4026218 TATAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 7 0.16
24 8 0.18
25 7 0.16
26 10 0.22
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAAAATAAAATAAAAATAT
Found at i:4026177 original size:32 final size:31
Alignment explanation
Indices: 4026113--4026203 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 31
4026103 TAAAATAGAC
* *
4026113 TAATAAAATAAAGATAACATATAATAGAATAAA
1 TAATAAAATAAAAATAATA-AT-ATAGAATAAA
4026146 -AATAAAATAAAAATATATAATATAGAGATAAA
1 TAATAAAATAAAAATA-ATAATATAGA-ATAAA
4026178 TAATAAATATATAAAGATAAATAATA
1 TAATAAA-ATA-AAA-AT-AATAATA
4026204 AAAATTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
31 5 0.10
32 21 0.43
33 8 0.16
34 3 0.06
35 3 0.06
36 8 0.16
37 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.26
Consensus pattern (31 bp):
TAATAAAATAAAAATAATAATATAGAATAAA
Found at i:4026224 original size:8 final size:9
Alignment explanation
Indices: 4026196--4026226 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4026186 ATATAAAGAT
*
4026196 AAATAATAA
1 AAATTATAA
4026205 AAATTATAA
1 AAATTATAA
4026214 AAATTATAA
1 AAATTATAA
4026223 AAAT
1 AAAT
4026227 ATTTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATTATAA
Found at i:4026285 original size:19 final size:19
Alignment explanation
Indices: 4026261--4026314 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 19
4026251 TATAATTATA
4026261 ATTAAATTATAATGATATT
1 ATTAAATTATAATGATATT
4026280 ATTAAAATT-T-A--ATATT
1 ATT-AAATTATAATGATATT
*
4026296 ATTAAA-TATAATGTTATT
1 ATTAAATTATAATGATATT
4026314 A
1 A
4026315 ATATTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
14 1 0.03
15 4 0.14
16 9 0.31
18 6 0.21
19 4 0.14
20 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTAAATTATAATGATATT
Found at i:4026307 original size:15 final size:15
Alignment explanation
Indices: 4026275--4026332 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
4026265 AATTATAATG
*
4026275 ATATTATTAAAATTTA
1 ATATTATT-AAATATA
4026291 ATATTATTAAATATA
1 ATATTATTAAATATA
*
4026306 ATGTTATT-AATATTA
1 ATATTATTAAATA-TA
*
4026321 ATATGATTAAAT
1 ATATTATTAAAT
4026333 TAAAATATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.11
15 21 0.58
16 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATTATTAAATATA
Found at i:4035963 original size:37 final size:37
Alignment explanation
Indices: 4035931--4036026 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
4035921 TATTATTAAT
*
4035931 ATTTAAATTTAATTTAATATTATATAAAATTATATTTG
1 ATTTAAATTTAATATAATATTATATAAAATTATA-TTG
* *
4035969 ATTT-AATTTGATATGATATTATATAAAATTATATTG
1 ATTTAAATTTAATATAATATTATATAAAATTATATTG
*
4036005 ATTTAAA-TTAATAAAATATTAT
1 ATTTAAATTTAATATAATATTAT
4036027 TTTTAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
36 19 0.37
37 28 0.55
38 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (37 bp):
ATTTAAATTTAATATAATATTATATAAAATTATATTG
Found at i:4035967 original size:27 final size:27
Alignment explanation
Indices: 4035910--4035992 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
4035900 TTTGAATTTG
* * *
4035910 ATTTAATTTTATATTAT-TAATATTTAA
1 ATTTAATTTAATATTATATAA-AATTAT
4035937 ATTTAATTTAATATTATATAAAATTAT
1 ATTTAATTTAATATTATATAAAATTAT
* * *
4035964 ATTTGATTTAAT-TTGATATGATATTAT
1 ATTTAATTTAATATT-ATATAAAATTAT
4035991 AT
1 AT
4035993 AAAATTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.04
27 43 0.90
28 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTTAATTTAATATTATATAAAATTAT
Found at i:4036039 original size:19 final size:20
Alignment explanation
Indices: 4036015--4036058 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4036005 ATTTAAATTA
4036015 ATAAAATATTA-TTTTTAAT
1 ATAAAATATTATTTTTTAAT
*
4036034 ATAAAATGTTATTTTTTAAT
1 ATAAAATATTATTTTTTAAT
4036054 ATAAA
1 ATAAA
4036059 TATAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTTTTTAAT
Found at i:4036059 original size:19 final size:18
Alignment explanation
Indices: 4036012--4036061 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
4036002 TTGATTTAAA
4036012 TTAATA-AAATATTATTT
1 TTAATATAAATATTATTT
*
4036029 TTAATATAAAATGTTATTTT
1 TTAATAT-AAATATTA-TTT
4036049 TTAATATAAATAT
1 TTAATATAAATAT
4036062 AAATATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.21
19 12 0.43
20 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTAATATAAATATTATTT
Found at i:4043286 original size:2 final size:2
Alignment explanation
Indices: 4043279--4043326 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4043269 CGAATTCAGG
4043279 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4043321 CT CT CT
1 CT CT CT
4043327 TTTCTACAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4046273 original size:23 final size:23
Alignment explanation
Indices: 4046246--4046289 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
4046236 TCAGTTTATC
4046246 TTATTTGCCCTAGGTTTCTCATT
1 TTATTTGCCCTAGGTTTCTCATT
4046269 TTATTTGCCCTAGGTTTCTCA
1 TTATTTGCCCTAGGTTTCTCA
4046290 GCAACCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.50
Consensus pattern (23 bp):
TTATTTGCCCTAGGTTTCTCATT
Found at i:4048267 original size:13 final size:13
Alignment explanation
Indices: 4048249--4048274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4048239 GCCCTCCCCC
4048249 TTTTATAAAAGAA
1 TTTTATAAAAGAA
4048262 TTTTATAAAAGAA
1 TTTTATAAAAGAA
4048275 AAAAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TTTTATAAAAGAA
Found at i:4048377 original size:70 final size:73
Alignment explanation
Indices: 4048258--4048396 Score: 212
Period size: 70 Copynumber: 1.9 Consensus size: 73
4048248 CTTTTATAAA
*
4048258 AGAATTTTATAAAAGAAAAAAAAGAAATAAAGAAATAAAGGAAGTCATGTGTTTAGACTGTGTAT
1 AGAATTTTATAAAAGAAAAAAAAG--A-AAAGAAATAAAAGAAGTCATGTGTTTAGACTGTGTAT
4048323 GTCTTCTCGAG
63 GTCTTCTCGAG
*
4048334 AGAATTTTAT-AAAG-AAAAAAAG-AAAGAAATAAAAGAAGTCATGTTTTTAGACTGTGTATGTC
1 AGAATTTTATAAAAGAAAAAAAAGAAAAGAAATAAAAGAAGTCATGTGTTTAGACTGTGTATGTC
4048396 T
66 T
4048397 CTGGCACTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
70 39 0.64
74 8 0.13
75 4 0.07
76 10 0.16
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.29
Consensus pattern (73 bp):
AGAATTTTATAAAAGAAAAAAAAGAAAAGAAATAAAAGAAGTCATGTGTTTAGACTGTGTATGTC
TTCTCGAG
Found at i:4061880 original size:70 final size:71
Alignment explanation
Indices: 4061788--4061926 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 71
4061778 CTTCTATCTC
*
4061788 AAAAGGGTATATAAAAACAATTTGATTTTGATGTTCTTCAATTACAATAAAATACCCTTCCAAAA
1 AAAAGGGTATATAAAAACAATTTGATTTTGATGTTCTTCAATTACAATAAAATACCCATCCAAAA
4061853 TTGGCA
66 TTGGCA
* * *
4061859 AAAAGGGTATA-CAATACAATTTGATTTTGATGTTCTTCAATTACAATAAAATACCGATCCAAAA
1 AAAAGGGTATATAAAAACAATTTGATTTTGATGTTCTTCAATTACAATAAAATACCCATCCAAAA
4061923 TTGG
66 TTGG
4061927 GATTTAGGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 53 0.83
71 11 0.17
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (71 bp):
AAAAGGGTATATAAAAACAATTTGATTTTGATGTTCTTCAATTACAATAAAATACCCATCCAAAA
TTGGCA
Found at i:4062593 original size:13 final size:13
Alignment explanation
Indices: 4062546--4062593 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
4062536 AATAATTTAT
*
4062546 TTATTAATTAAAA
1 TTATTAATTTAAA
*
4062559 TTATT-TTTTAAA
1 TTATTAATTTAAA
4062571 TTTATATAATTTAAA
1 -TTAT-TAATTTAAA
4062586 TTATTAAT
1 TTATTAAT
4062594 ATAATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 5 0.17
13 13 0.45
14 5 0.17
15 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTAATTTAAA
Found at i:4062599 original size:27 final size:26
Alignment explanation
Indices: 4062544--4062604 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
4062534 AAAATAATTT
* *
4062544 ATTTATTAATTAAAATTATTTTTTAA
1 ATTTATTAATTAAAATTATTATATAA
*
4062570 ATTTATATAATTTAAATTATTA-ATATA
1 ATTTAT-TAATTAAAATTATTATATA-A
4062597 ATTT-TTAA
1 ATTTATTAA
4062605 AAGTATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.10
26 9 0.30
27 18 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTATTAATTAAAATTATTATATAA
Found at i:4065140 original size:10 final size:10
Alignment explanation
Indices: 4065105--4065148 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
4065095 TATATAATCT
4065105 TATATTTTTA
1 TATATTTTTA
4065115 -ATA-TTTTA
1 TATATTTTTA
4065123 T-T-TTTTTA
1 TATATTTTTA
4065131 TATATTTTTA
1 TATATTTTTA
*
4065141 AATATTTT
1 TATATTTT
4065149 AATTACTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
8 12 0.41
9 4 0.14
10 13 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTTA
Found at i:4065221 original size:13 final size:13
Alignment explanation
Indices: 4065205--4065239 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4065195 TATAACTAAA
*
4065205 TTTTTTACCATAT
1 TTTTTTAACATAT
*
4065218 TTTTTAAACATAT
1 TTTTTTAACATAT
4065231 TTTTTTAAC
1 TTTTTTAAC
4065240 TCAAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTTAACATAT
Found at i:4068983 original size:38 final size:38
Alignment explanation
Indices: 4068940--4069012 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
4068930 CCGAAGTATA
*
4068940 TATCTCTATTATTTACCATTTTTAATTGGTCATAATAT
1 TATCTCTATTATTTACCACTTTTAATTGGTCATAATAT
*
4068978 TATCTCTATTATTTATCACTTTTAATTGGTCATAA
1 TATCTCTATTATTTACCACTTTTAATTGGTCATAA
4069013 CATTTTCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (38 bp):
TATCTCTATTATTTACCACTTTTAATTGGTCATAATAT
Found at i:4071219 original size:16 final size:15
Alignment explanation
Indices: 4071198--4071240 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4071188 TTAAACTATT
4071198 AGAAAAAATAAATAAG
1 AGAAAAAA-AAATAAG
* *
4071214 AGAAAAGAAAA-AAT
1 AGAAAAAAAAATAAG
4071228 AGAAAAAAAAATA
1 AGAAAAAAAAATA
4071241 TTGGCTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.52
15 4 0.17
16 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
AGAAAAAAAAATAAG
Found at i:4072744 original size:14 final size:15
Alignment explanation
Indices: 4072725--4072753 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4072715 AATCATTTAA
4072725 TCATTTAA-TTAAAG
1 TCATTTAATTTAAAG
4072739 TCATTTAATTTAAAG
1 TCATTTAATTTAAAG
4072754 ATTCAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (15 bp):
TCATTTAATTTAAAG
Found at i:4078193 original size:23 final size:23
Alignment explanation
Indices: 4078167--4078215 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
4078157 TGTTAAATAC
*
4078167 TTATTTAAGTAAAAATTAAAAAT
1 TTATTTAAATAAAAATTAAAAAT
* *
4078190 TTATTTAAATACAAATTTAAAAT
1 TTATTTAAATAAAAATTAAAAAT
4078213 TTA
1 TTA
4078216 AAAGTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTATTTAAATAAAAATTAAAAAT
Found at i:4081007 original size:20 final size:21
Alignment explanation
Indices: 4080978--4081019 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
4080968 GTGGATTTTA
4080978 TATTAGATAAA-AAAATTTAAT
1 TATTAGATAAATAAAA-TTAAT
4080999 TATTA-ATAAATAAAATTAAT
1 TATTAGATAAATAAAATTAAT
4081019 T
1 T
4081020 TTTATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TATTAGATAAATAAAATTAAT
Found at i:4081084 original size:20 final size:20
Alignment explanation
Indices: 4081045--4081085 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4081035 TTTATATTTT
*
4081045 AAATAATTATATTTGAATAA
1 AAATAATTATATATGAATAA
4081065 AAATAATTATCATATG-ATAA
1 AAATAATTAT-ATATGAATAA
4081085 A
1 A
4081086 TTATCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (20 bp):
AAATAATTATATATGAATAA
Found at i:4081103 original size:42 final size:41
Alignment explanation
Indices: 4081054--4081139 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 41
4081044 TAAATAATTA
* *
4081054 TATTTGAATAAAAAT-AATTATCATATGATAAATTATCATAAT
1 TATTTGAATAAAAATAAATTATCAT-TCATAAA-GATCATAAT
* *
4081096 TATTTGAATATAAATAAATTATTATTCATAAAGATCATAAT
1 TATTTGAATAAAAATAAATTATCATTCATAAAGATCATAAT
4081137 TAT
1 TAT
4081140 ATAGAAGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 11 0.28
42 20 0.51
43 8 0.21
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (41 bp):
TATTTGAATAAAAATAAATTATCATTCATAAAGATCATAAT
Found at i:4081168 original size:22 final size:22
Alignment explanation
Indices: 4081088--4081168 Score: 70
Period size: 18 Copynumber: 4.0 Consensus size: 22
4081078 ATGATAAATT
* *
4081088 ATCATAATTATTTGAATATAA-
1 ATCATAATTATTTTAATAGAAG
*
4081109 AT-A-AATTATTATTCATA-AAG
1 ATCATAATTATT-TTAATAGAAG
4081129 ATCATAATTA---T-ATAGAAG
1 ATCATAATTATTTTAATAGAAG
4081147 ATCATAATTATTTTAATAGAAG
1 ATCATAATTATTTTAATAGAAG
4081169 TTTATGTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
17 3 0.06
18 14 0.29
19 9 0.18
20 7 0.14
21 4 0.08
22 12 0.24
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
ATCATAATTATTTTAATAGAAG
Found at i:4082186 original size:15 final size:14
Alignment explanation
Indices: 4082166--4082231 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
4082156 AATACATATT
4082166 AATAATAAATAGATA
1 AATAATAAATA-ATA
4082181 AATAATAAAT-ATA
1 AATAATAAATAATA
*
4082194 TATTAATAAATAATA
1 -AATAATAAATAATA
*
4082209 ATAAAATAAAATAA-A
1 A-ATAAT-AAATAATA
4082224 AAT-ATAAA
1 AATAATAAA
4082232 ATGGGCTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.07
13 5 0.12
14 11 0.26
15 18 0.42
16 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AATAATAAATAATA
Found at i:4082227 original size:11 final size:11
Alignment explanation
Indices: 4082143--4082224 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 11
4082133 ATCAATCAAG
4082143 ATAAAATAA-A
1 ATAAAATAATA
4082153 A-AAAATACATA
1 ATAAAATA-ATA
*
4082164 TTAATAATAAATA
1 ATAA-AAT-AATA
4082177 GAT-AAATAATA
1 -ATAAAATAATA
* *
4082188 A-ATATATATTA
1 ATA-AAATAATA
4082199 AT-AAATAATA
1 ATAAAATAATA
4082209 ATAAAATAA-A
1 ATAAAATAATA
4082219 ATAAAA
1 ATAAAA
4082225 ATATAAAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
9 6 0.11
10 18 0.32
11 18 0.32
12 5 0.09
13 7 0.12
14 2 0.04
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:4082230 original size:24 final size:24
Alignment explanation
Indices: 4082143--4082230 Score: 60
Period size: 24 Copynumber: 3.7 Consensus size: 24
4082133 ATCAATCAAG
4082143 ATAAAATAAAAAA-AATACAT--AT
1 ATAAAATAAAAAATAATA-ATAAAT
*
4082165 -TAATAATAAATAGATAAATAATAAAT
1 ATAA-AATAAA-AAAT-AATAATAAAT
* * *
4082191 ATATATTAATAAATAATAATAAA-
1 ATAAAATAAAAAATAATAATAAAT
4082214 ATAAAATAAAAATATAA
1 ATAAAATAAAAA-ATAA
4082231 AATGGGCTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
21 3 0.06
22 6 0.12
23 11 0.22
24 15 0.30
25 7 0.14
26 6 0.12
27 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (24 bp):
ATAAAATAAAAAATAATAATAAAT
Found at i:4086165 original size:20 final size:20
Alignment explanation
Indices: 4086126--4086166 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4086116 ATTCATATTT
*
4086126 AAATAATTATATTTGAACAA
1 AAATAATTATATATGAACAA
4086146 AAATAATTATCATATG-ACAA
1 AAATAATTAT-ATATGAACAA
4086166 A
1 A
4086167 TAGTCATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATAATTATATATGAACAA
Found at i:4087621 original size:21 final size:21
Alignment explanation
Indices: 4087595--4087656 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
4087585 CACGTAGTTA
*
4087595 TTTATTTTTTTTCATTTTA-TT
1 TTTATTTTTTAT-ATTTTATTT
* *
4087616 TTTATTTTTTATTTTTTATAT
1 TTTATTTTTTATATTTTATTT
* *
4087637 TTTACTTTTTA-ATTTAATTT
1 TTTATTTTTTATATTTTATTT
4087657 AATTTAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTTTTATATTTTATTT
Found at i:4087623 original size:5 final size:5
Alignment explanation
Indices: 4087595--4087696 Score: 59
Period size: 5 Copynumber: 19.8 Consensus size: 5
4087585 CACGTAGTTA
* *
4087595 TTTAT TTT-T TTTCAT TTTAT TTT-T ATT-T TTTAT TTT-T TATAT TTTACTT
1 TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA--T
* * * *
4087644 TTTAA TTTAA TTTAA TTTAA TTTAT TTTACT TATTAT TATTAT TATTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T T-TTAT T-TTAT T-TTAT
4087693 TTTA
1 TTTA
4087697 CTCATTATTT
Statistics
Matches: 83, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
4 13 0.16
5 42 0.51
6 20 0.24
7 8 0.10
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:4087624 original size:7 final size:7
Alignment explanation
Indices: 4087595--4087647 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
4087585 CACGTAGTTA
4087595 TTTATTT
1 TTTATTT
4087602 TTT-TTCAT
1 TTTATT--T
4087610 TTTA-TT
1 TTTATTT
4087616 TTTATTT
1 TTTATTT
4087623 TTTATTT
1 TTTATTT
*
4087630 TTTATAT
1 TTTATTT
*
4087637 TTTACTT
1 TTTATTT
4087644 TTTA
1 TTTA
4087648 ATTTAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 7 0.18
7 27 0.69
8 5 0.13
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTATTT
Found at i:4087647 original size:14 final size:13
Alignment explanation
Indices: 4087608--4087656 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
4087598 ATTTTTTTTC
4087608 ATTTTATTTTTAT
1 ATTTTATTTTTAT
*
4087621 TTTTTATTTTTTAT
1 ATTTTA-TTTTTAT
4087635 ATTTTACTTTTTA-
1 ATTTTA-TTTTTAT
*
4087648 ATTTAATTT
1 ATTTTATTT
4087657 AATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 3 0.10
13 10 0.32
14 18 0.58
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTATTTTTAT
Found at i:4087656 original size:27 final size:27
Alignment explanation
Indices: 4087593--4087652 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
4087583 TTCACGTAGT
*
4087593 TATTTATTTTTTTTCATTTTATTTTTA
1 TATTTATTTTTTATCATTTTATTTTTA
*
4087620 TTTTTTATTTTTTAT-ATTTTACTTTTTA
1 -TATTTATTTTTTATCATTTTA-TTTTTA
4087648 -ATTTA
1 TATTTA
4087653 ATTTAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 18 0.64
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (27 bp):
TATTTATTTTTTATCATTTTATTTTTA
Found at i:4087703 original size:12 final size:12
Alignment explanation
Indices: 4087665--4087708 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
4087655 TTAATTTAAT
4087665 TTATTTTACTTA
1 TTATTTTACTTA
4087677 TTATTATTA-TTA
1 TTATT-TTACTTA
*
4087689 TTATTTTACTCA
1 TTATTTTACTTA
4087701 TTATTTTA
1 TTATTTTA
4087709 AATTGAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTTTACTTA
Found at i:4088310 original size:185 final size:185
Alignment explanation
Indices: 4088000--4088339 Score: 452
Period size: 185 Copynumber: 1.8 Consensus size: 185
4087990 AATTATTGAA
* *
4088000 AGATTTGCATCAAAATAAATTTTACCAAACTATTAGAAAAGTTTACTAATTATTTTTTCAAATAA
1 AGATTTGCATCAAAATAAATCTTACCAAACTATTAGAAAAGTTTACCAATTATTTTTTCAAATAA
* * * * * *
4088065 AATATATTAATGAATCCGACGACGGAGCCTCTTTAGAATATGATACTAATTTTCATGAATACTCT
66 AATATATTAATGAATCCGACGACGAAGCCTCTTCAGAATAGGACACTAATTCTCATGAATACTCA
4088130 TAAAATGAAAAAATTATCTT-AAATTGCTATCAAACTATTAGAGTAAATTATTAGG
131 TAAAATGAAAAAATTAT-TTCAAATTGCTATCAAACTATTAGAGTAAATTATTAGG
* * *
4088185 AGATTTGCATTAAAGTAAATCTTACCAAACTATTAGAAGAA-TTTACCAATTATTTTTTCGAATA
1 AGATTTGCATCAAAATAAATCTTACCAAACTATTAGAA-AAGTTTACCAATTATTTTTTCAAATA
* * ** * *
4088249 AAATATATTAATGAATCCGATGATGAAGTTTCTTCAGAGTGGGACACTAA-TCTCTATGAATACT
65 AAATATATTAATGAATCCGACGACGAAGCCTCTTCAGAATAGGACACTAATTCTC-ATGAATACT
** *
4088313 CATAAGGTGAGAAAATTATTTCAAATT
129 CATAAAATGAAAAAATTATTTCAAATT
4088340 ACTACTAGAC
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
184 5 0.04
185 125 0.95
186 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (185 bp):
AGATTTGCATCAAAATAAATCTTACCAAACTATTAGAAAAGTTTACCAATTATTTTTTCAAATAA
AATATATTAATGAATCCGACGACGAAGCCTCTTCAGAATAGGACACTAATTCTCATGAATACTCA
TAAAATGAAAAAATTATTTCAAATTGCTATCAAACTATTAGAGTAAATTATTAGG
Found at i:4089954 original size:27 final size:27
Alignment explanation
Indices: 4089924--4089975 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4089914 ATTTTTACGT
4089924 CTTTCTAT-TTTTTTTATTTCACATGTA
1 CTTT-TATATTTTTTTATTTCACATGTA
* *
4089951 CTTTTTTATTTTTTTATTTTACATG
1 CTTTTATATTTTTTTATTTCACATG
4089976 CAATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (27 bp):
CTTTTATATTTTTTTATTTCACATGTA
Found at i:4089982 original size:27 final size:27
Alignment explanation
Indices: 4089932--4089983 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4089922 GTCTTTCTAT
* *
4089932 TTTTTTTATTTCACATGTACTTTTTTA
1 TTTTTTTATTTCACATGCAATTTTTTA
*
4089959 TTTTTTTATTTTACATGCAATTTTT
1 TTTTTTTATTTCACATGCAATTTTT
4089984 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTTTTATTTCACATGCAATTTTTTA
Found at i:4095639 original size:17 final size:17
Alignment explanation
Indices: 4095617--4095656 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4095607 AAACTGGGTG
*
4095617 AAAAAAATGATATTTTA
1 AAAAAAATGATATATTA
*
4095634 AAAAAAATGCTATATTA
1 AAAAAAATGATATATTA
4095651 AAAAAA
1 AAAAAA
4095657 TAATATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
AAAAAAATGATATATTA
Found at i:4095669 original size:16 final size:16
Alignment explanation
Indices: 4095617--4095669 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
4095607 AAACTGGGTG
*
4095617 AAAAAAATGATATTTTA
1 AAAAAAATGATA-TATA
* *
4095634 AAAAAAATGCTATATT
1 AAAAAAATGATATATA
* *
4095650 AAAAAAATAATATGTA
1 AAAAAAATGATATATA
4095666 AAAA
1 AAAA
4095670 TGGTAGATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAAAAATGATATATA
Found at i:4098688 original size:11 final size:11
Alignment explanation
Indices: 4098672--4098699 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4098662 ATAAAAAGCC
4098672 AAAATTTTTAT
1 AAAATTTTTAT
4098683 AAAATTTTTAT
1 AAAATTTTTAT
4098694 AAAATT
1 AAAATT
4098700 AATATCTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATTTTTAT
Found at i:4105445 original size:17 final size:18
Alignment explanation
Indices: 4105423--4105456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4105413 ATGACAAATT
*
4105423 CTTTTA-CTGTTGAAGCC
1 CTTTTAGCTGTTCAAGCC
4105440 CTTTTAGCTGTTCAAGC
1 CTTTTAGCTGTTCAAGC
4105457 ATTGGAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (18 bp):
CTTTTAGCTGTTCAAGCC
Found at i:4109838 original size:8 final size:8
Alignment explanation
Indices: 4109821--4109854 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
4109811 ATTTGAAGAG
*
4109821 AAAACCAA
1 AAAAACAA
4109829 AAAAA-AA
1 AAAAACAA
4109836 AAAAACAA
1 AAAAACAA
4109844 AAAAACAA
1 AAAAACAA
4109852 AAA
1 AAA
4109855 GCTTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:4109844 original size:15 final size:16
Alignment explanation
Indices: 4109821--4109854 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4109811 ATTTGAAGAG
*
4109821 AAAACCAAAAAAA-AA
1 AAAAACAAAAAAACAA
4109836 AAAAACAAAAAAACAA
1 AAAAACAAAAAAACAA
4109852 AAA
1 AAA
4109855 GCTTTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAACAA
Found at i:4111498 original size:49 final size:49
Alignment explanation
Indices: 4111421--4111518 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
4111411 GGTAATAGAA
*
4111421 CCAAGAATGCTTTGAGTTGTATATCCATCATATTTCCTTGATTTCGTGT
1 CCAAGAATGCTTTGAGTTGTATAACCATCATATTTCCTTGATTTCGTGT
4111470 CCAAGAATGCTTTGAGTTGTATAACCATCATATTTCCTTGATTTCGTGT
1 CCAAGAATGCTTTGAGTTGTATAACCATCATATTTCCTTGATTTCGTGT
4111519 TTATCTCTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (49 bp):
CCAAGAATGCTTTGAGTTGTATAACCATCATATTTCCTTGATTTCGTGT
Found at i:4124059 original size:20 final size:19
Alignment explanation
Indices: 4124034--4124073 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4124024 AAATGTTAAA
*
4124034 TTATTTAATATTTATAAATT
1 TTATTTAATATATA-AAATT
*
4124054 TTATTTATTATATAAAATT
1 TTATTTAATATATAAAATT
4124073 T
1 T
4124074 ATAAAACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTTAATATATAAAATT
Found at i:4124067 original size:18 final size:17
Alignment explanation
Indices: 4124042--4124075 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4124032 AATTATTTAA
*
4124042 TATTTATAAATTTTATT
1 TATTTATAAAATTTATT
4124059 TATTATATAAAATTTAT
1 TATT-TATAAAATTTAT
4124076 AAAACTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTATAAAATTTATT
Found at i:4125575 original size:19 final size:20
Alignment explanation
Indices: 4125553--4125596 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
4125543 AGTACAAAAT
*
4125553 TATATAGATT-ATACATGCA
1 TATATAGATTAATACATACA
4125572 TATAT-GATTAATACATACA
1 TATATAGATTAATACATACA
4125591 TATATA
1 TATATA
4125597 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (20 bp):
TATATAGATTAATACATACA
Found at i:4125684 original size:2 final size:2
Alignment explanation
Indices: 4125677--4125701 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4125667 GATTATATGC
4125677 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 A
4125702 ATTGTATCAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4128749 original size:20 final size:19
Alignment explanation
Indices: 4128701--4128749 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
4128691 TTAGTACATG
*
4128701 ATTTATTAAACAAGAACTA
1 ATTTATTAAACAAGAAATA
4128720 ATTTATTTAAACTAA-AAATA
1 ATTTA-TTAAAC-AAGAAATA
4128740 ACTTTATTAA
1 A-TTTATTAA
4128750 TTTTCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 15 0.58
21 6 0.23
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTTATTAAACAAGAAATA
Found at i:4134450 original size:13 final size:13
Alignment explanation
Indices: 4134423--4134457 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4134413 AAAAATGAGT
*
4134423 AAATT-AAAATTA
1 AAATTAAAAATCA
4134435 AAATTAAAAATCA
1 AAATTAAAAATCA
4134448 AAATTAAAAA
1 AAATTAAAAA
4134458 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATTAAAAATCA
Found at i:4134464 original size:6 final size:6
Alignment explanation
Indices: 4134423--4134456 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
4134413 AAAAATGAGT
*
4134423 AAATTA AAATTA AAATTAA AAATCA AAATTA AAA
1 AAATTA AAATTA AAATT-A AAATTA AAATTA AAA
4134457 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (6 bp):
AAATTA
Found at i:4144783 original size:9 final size:9
Alignment explanation
Indices: 4144769--4144798 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4144759 GTGTATATAG
*
4144769 GGAAGATGT
1 GGAAGATGA
4144778 GGAAGATGA
1 GGAAGATGA
4144787 GGAAGATGA
1 GGAAGATGA
4144796 GGA
1 GGA
4144799 GACAACAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.47, T:0.13
Consensus pattern (9 bp):
GGAAGATGA
Found at i:4146346 original size:2 final size:2
Alignment explanation
Indices: 4146341--4146377 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4146331 TTATGAATTT
4146341 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 T
4146378 CAAACCAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4153391 original size:9 final size:9
Alignment explanation
Indices: 4153352--4153385 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
4153342 AATCTATATA
*
4153352 TTTTTTATT
1 TTTTTTGTT
4153361 TTTTTTGTT
1 TTTTTTGTT
4153370 TTTTTTGTT
1 TTTTTTGTT
4153379 TATTTTT
1 T-TTTTT
4153386 TTTATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:4153650 original size:16 final size:16
Alignment explanation
Indices: 4153612--4153652 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4153602 TTTAATTTTA
4153612 TATTTAA-AATAATAT
1 TATTTAATAATAATAT
4153627 TATGTTAATAA-AATTAT
1 TAT-TTAATAATAA-TAT
4153644 TATTTAATA
1 TATTTAATA
4153653 TTTTAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TATTTAATAATAATAT
Found at i:4154214 original size:18 final size:19
Alignment explanation
Indices: 4154159--4154219 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 19
4154149 CTTTATTTTA
4154159 ATAAAAATATATATTTATAT
1 ATAAAAATA-ATATTTATAT
4154179 ATAATTAAGAT-ATAATTTATAT
1 ATAA--AA-ATAAT-ATTTATAT
*
4154201 -TAAAAATAATATTTTTAT
1 ATAAAAATAATATTTATAT
4154219 A
1 A
4154220 AACATTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 4 0.12
21 5 0.15
22 10 0.29
23 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAAAAATAATATTTATAT
Found at i:4154278 original size:2 final size:2
Alignment explanation
Indices: 4154271--4154304 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4154261 AAATGTTGGT
*
4154271 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4154305 AGATAGGCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4154524 original size:16 final size:16
Alignment explanation
Indices: 4154505--4154535 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4154495 TTAGGTTTTT
4154505 TTTTTTTAGTTTTAAC
1 TTTTTTTAGTTTTAAC
*
4154521 TTTTTTTATTTTTAA
1 TTTTTTTAGTTTTAA
4154536 TTATCTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTTAGTTTTAAC
Found at i:4154648 original size:24 final size:24
Alignment explanation
Indices: 4154603--4154666 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
4154593 CTAGCACCCA
*
4154603 TTTTGCTTT-TTTTTTTTCCAACC
1 TTTTCCTTTGTTTTTTTTCCAACC
4154626 TTTTCCTTTGTTTTCTTTT-CAACC
1 TTTTCCTTTGTTTT-TTTTCCAACC
*
4154650 CTTTCCTTTGTTTTTTT
1 TTTTCCTTTGTTTTTTT
4154667 AGTTTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.30
24 22 0.59
25 4 0.11
ACGTcount: A:0.06, C:0.22, G:0.05, T:0.67
Consensus pattern (24 bp):
TTTTCCTTTGTTTTTTTTCCAACC
Found at i:4155945 original size:16 final size:18
Alignment explanation
Indices: 4155924--4155960 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4155914 AATTTATTTT
4155924 TTTAAATT-TT-ATATAA
1 TTTAAATTATTAATATAA
4155940 TTTAAATTATTAATATAA
1 TTTAAATTATTAATATAA
4155958 TTT
1 TTT
4155961 TTAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTATTAATATAA
Found at i:4159395 original size:26 final size:26
Alignment explanation
Indices: 4159365--4159418 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
4159355 TGGAGTCAAG
* *
4159365 TCACCAAGAACGAATGGCTAAAGGGT
1 TCACCAAGAAAGAATGGCAAAAGGGT
4159391 TCACCAAGAAAGAATGGCAAAAGGGT
1 TCACCAAGAAAGAATGGCAAAAGGGT
4159417 TC
1 TC
4159419 TCATTATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.15
Consensus pattern (26 bp):
TCACCAAGAAAGAATGGCAAAAGGGT
Found at i:4160364 original size:19 final size:18
Alignment explanation
Indices: 4160337--4160379 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4160327 AATGATATCA
4160337 TTTTATTAATAAATAAATT
1 TTTTATTAA-AAATAAATT
* * *
4160356 TTTTTTTAAATATTAATT
1 TTTTATTAAAAATAAATT
4160374 TTTTAT
1 TTTTAT
4160380 ACATTCATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATTAAAAATAAATT
Found at i:4162139 original size:68 final size:65
Alignment explanation
Indices: 4162033--4162166 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 65
4162023 TGTGGCCTGC
4162033 TTAATCCTTCTCTTATCATCATTATTGTGCCAAGCATTCTATACTTGGACAAAGCTCAAGTGAGA
1 TTAATCCTTCTCTTATCATCATTATTGTGCCAAGCATTCTATACTTGGACAAAGCTCAAGTGAGA
4162098 TTAATCCTTCTCTTATTATCATCATTATTGTGCCAAGCATTCTATACTTGGACAAAGCTCAAGTG
1 TTAATCCTTCTC---TTATCATCATTATTGTGCCAAGCATTCTATACTTGGACAAAGCTCAAGTG
4162163 AGA
63 AGA
4162166 T
1 T
4162167 CTATGATCTC
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
65 12 0.18
68 54 0.82
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (65 bp):
TTAATCCTTCTCTTATCATCATTATTGTGCCAAGCATTCTATACTTGGACAAAGCTCAAGTGAGA
Found at i:4167908 original size:2 final size:2
Alignment explanation
Indices: 4167901--4167927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4167891 AAACCCCCAG
4167901 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4167928 GTCTTCCTCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4194241 original size:2 final size:2
Alignment explanation
Indices: 4194234--4194286 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
4194224 AGGTATTTCC
*
4194234 TA TA TA TA AA TA TA TA TA -A TA TA -A TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4194273 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
4194287 ACTTTTATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4194371 original size:6 final size:6
Alignment explanation
Indices: 4194352--4194422 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
4194342 TAGTCTGTTC
* * *
4194352 TTTA-T TTTATTT TTTATT TTT-TT ATTAAT TTTATT TTTATT TTTA-A
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
4194398 TTAATT AATTATT TTTATT TTTATT
1 TTTATT -TTTATT TTTATT TTTATT
4194423 AAATAAATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
5 11 0.22
6 31 0.61
7 9 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:4194376 original size:15 final size:16
Alignment explanation
Indices: 4194356--4194389 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4194346 CTGTTCTTTA
4194356 TTTTATT-TTTTATTT
1 TTTTATTATTTTATTT
4194371 TTTTATTAATTTTATTT
1 TTTTATT-ATTTTATTT
4194388 TT
1 TT
4194390 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTATTTTATTT
Found at i:4194387 original size:24 final size:23
Alignment explanation
Indices: 4194355--4194419 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 23
4194345 TCTGTTCTTT
*
4194355 ATTTTATTTTTTATTTTTTTATTA
1 ATTTTA-TTTTTATTTTTTAATTA
4194379 ATTTTATTTTTA-TTTTTAATTA
1 ATTTTATTTTTATTTTTTAATTA
4194401 ATTAATTATTTTTATTTTT
1 ATT--TTATTTTTATTTTT
4194420 ATTAAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 12 0.32
23 6 0.16
24 15 0.41
25 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (23 bp):
ATTTTATTTTTATTTTTTAATTA
Found at i:4194392 original size:30 final size:30
Alignment explanation
Indices: 4194352--4194422 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
4194342 TAGTCTGTTC
* ** *
4194352 TTTA-TTTTATTTTTTATTTTTTTATTAAT
1 TTTATTTTTATTTTTAATTAATTAATTAAT
*
4194381 TTTATTTTTATTTTTAATTAATTAATTATT
1 TTTATTTTTATTTTTAATTAATTAATTAAT
4194411 TTTATTTTTATT
1 TTTATTTTTATT
4194423 AAATAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTATTTTTATTTTTAATTAATTAATTAAT
Found at i:4194431 original size:24 final size:24
Alignment explanation
Indices: 4194382--4194431 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4194372 TTTATTAATT
*
4194382 TTATTTTTATTTTTAATTAATTAA
1 TTATTTTTATTTTTAATTAATAAA
4194406 TTATTTTTATTTTT-ATTAAATAAA
1 TTATTTTTATTTTTAATT-AATAAA
4194430 TT
1 TT
4194432 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTTTTATTTTTAATTAATAAA
Found at i:4194468 original size:14 final size:16
Alignment explanation
Indices: 4194438--4194469 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
4194428 AATTTTATAA
4194438 AAAAATTAATGAAAAT
1 AAAAATTAATGAAAAT
4194454 AAAAA-TAAT-AAAAT
1 AAAAATTAATGAAAAT
4194468 AA
1 AA
4194470 TTCATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAAATTAATGAAAAT
Found at i:4195555 original size:58 final size:58
Alignment explanation
Indices: 4195464--4195582 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
4195454 TCGAGTTTGA
* *
4195464 AATGTTTTGTCTTGATCCTTCTTGATATATATAAAAGAGTATATTTTAATATTTATTT
1 AATGTTTTGCCTTGATCCTCCTTGATATATATAAAAGAGTATATTTTAATATTTATTT
*
4195522 AATGTTTTGCCTTGATCCTCCTTGATATTTATAAAAGAGTATATTTTAATATTTATTT
1 AATGTTTTGCCTTGATCCTCCTTGATATATATAAAAGAGTATATTTTAATATTTATTT
4195580 AAT
1 AAT
4195583 TTATATTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (58 bp):
AATGTTTTGCCTTGATCCTCCTTGATATATATAAAAGAGTATATTTTAATATTTATTT
Found at i:4195657 original size:28 final size:26
Alignment explanation
Indices: 4195612--4195680 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
4195602 TTATATTAAT
*
4195612 AAAAATATTAT-TTAATATCTTAATTA
1 AAAAATATTATATTAATAT-ATAATTA
*
4195638 AATAAATATTATATTTATATATAATTA
1 AA-AAATATTATATTAATATATAATTA
4195665 AAATAAT-TTATATTAA
1 AAA-AATATTATATTAA
4195681 AAAATATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.30
27 20 0.54
28 6 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
AAAAATATTATATTAATATATAATTA
Found at i:4195668 original size:24 final size:23
Alignment explanation
Indices: 4195602--4195678 Score: 57
Period size: 27 Copynumber: 3.0 Consensus size: 23
4195592 TATATAAGTA
*
4195602 TTATATTAATAAAAATATTAT-T
1 TTATATTAATTAAAATATTATAT
*
4195624 TAATATCTTAATTAAATAAATATTATAT
1 T--TATATTAATT--A-AAATATTATAT
4195652 TTATATATAATTAAAATAATTTATAT
1 TTATAT-TAATTAAAAT-A-TTATAT
4195678 T
1 T
4195679 AAAAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
22 1 0.02
24 12 0.28
25 2 0.05
26 12 0.28
27 14 0.33
28 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATATTAATTAAAATATTATAT
Found at i:4195691 original size:18 final size:19
Alignment explanation
Indices: 4195647--4195696 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
4195637 AAATAAATAT
4195647 TATATTTATATATAATTAAAA
1 TATATTTATAT-TAA-TAAAA
4195668 TA-ATTTATATTAA-AAAA
1 TATATTTATATTAATAAAA
4195685 TATATTTATATT
1 TATATTTATATT
4195697 CATATGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 3 0.11
20 8 0.29
21 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATTTATATTAATAAAA
Found at i:4201198 original size:24 final size:25
Alignment explanation
Indices: 4201150--4201203 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
4201140 ACATAAAATT
*
4201150 AATAAAATATTATTTTTAATATAAA
1 AATAAAATATTATTATTAATATAAA
*
4201175 TATAAAAT-TTATTAATTAAT-TAAA
1 AATAAAATATTATT-ATTAATATAAA
4201199 AATAA
1 AATAA
4201204 TTTTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAAAATATTATTATTAATATAAA
Found at i:4204801 original size:10 final size:10
Alignment explanation
Indices: 4204778--4204881 Score: 54
Period size: 10 Copynumber: 9.9 Consensus size: 10
4204768 TACAAAACAA
* *
4204778 AAATAAAAAA
1 AAATAATAAT
4204788 AAATAATAAT
1 AAATAATAAT
4204798 AAATATATAACT
1 AAATA-ATAA-T
*
4204810 ATATACAT-AT
1 AAATA-ATAAT
*
4204820 AAAT-CTAAT
1 AAATAATAAT
*
4204829 CTAATAATAA-
1 -AAATAATAAT
4204839 AAATATATATAT
1 AAATA-ATA-AT
4204851 ATTAATACATAAT
1 A--AATA-ATAAT
4204864 -AATAATAAT
1 AAATAATAAT
4204873 AAATAATAA
1 AAATAATAA
4204882 AATACATAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
8 1 0.01
9 11 0.15
10 35 0.48
11 9 0.12
12 8 0.11
13 2 0.03
14 7 0.10
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATAATAAT
Found at i:4204838 original size:3 final size:3
Alignment explanation
Indices: 4204830--4204894 Score: 53
Period size: 3 Copynumber: 20.7 Consensus size: 3
4204820 AAATCTAATC
* *
4204830 TAA TAA TAA AAA TATA TATA TAT TAA TACA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TA-A TAA TAA TAA TAA T-AA TAA
4204879 TAA -AA TACA TAA -AA TA
1 TAA TAA TA-A TAA TAA TA
4204895 CAAAAGAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 4 0.08
3 32 0.62
4 16 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4204847 original size:33 final size:37
Alignment explanation
Indices: 4204789--4204896 Score: 109
Period size: 36 Copynumber: 3.0 Consensus size: 37
4204779 AATAAAAAAA
*
4204789 AATAATAATAAATATATAACTATATACATATAAAT-C-T
1 AATAATAAT-AATAAATAA-TATATACATATAAATACAT
* * *
4204826 AAT-CTAATAATAAA-AATATATATATATTAATACAT
1 AATAATAATAATAAATAATATATACATATAAATACAT
*
4204861 AATAATAATAATAAATAATAAAATACATA-AAATACA
1 AATAATAATAATAAATAAT-ATATACATATAAATACA
4204897 AAAGAAACAG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
33 13 0.22
34 3 0.05
35 9 0.16
36 14 0.24
37 12 0.21
38 7 0.12
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (37 bp):
AATAATAATAATAAATAATATATACATATAAATACAT
Found at i:4204866 original size:30 final size:28
Alignment explanation
Indices: 4204830--4204899 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
4204820 AAATCTAATC
* *
4204830 TAATAATAAAAATATATATATATTAATACA
1 TAATAATAAAAATAAATA-ATA-AAATACA
*
4204860 TAATAATAATAATAAATAATAAAATACA
1 TAATAATAAAAATAAATAATAAAATACA
4204888 TAA-AATACAAAA
1 TAATAATA-AAAA
4204900 GAAACAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.11
28 12 0.34
29 3 0.09
30 16 0.46
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
TAATAATAAAAATAAATAATAAAATACA
Found at i:4204878 original size:16 final size:16
Alignment explanation
Indices: 4204830--4204891 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
4204820 AAATCTAATC
4204830 TAATAATAA-AAATATA
1 TAATAATAATAAATA-A
* *
4204846 TATATATTAATACATAA
1 TA-ATAATAATAAATAA
4204863 TAATAATAATAAATAA
1 TAATAATAATAAATAA
4204879 TAA-AATACATAAA
1 TAATAATA-ATAAA
4204892 ATACAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 4 0.10
16 22 0.56
17 9 0.23
18 4 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:4207031 original size:21 final size:21
Alignment explanation
Indices: 4207006--4207045 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4206996 AGTGAACATG
4207006 ATATATACA-AAGAACAATATA
1 ATATATACACAA-AACAATATA
4207027 ATATATACACAAAACAATA
1 ATATATACACAAAACAATA
4207046 GAAAGGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.23
Consensus pattern (21 bp):
ATATATACACAAAACAATATA
Found at i:4207460 original size:4 final size:4
Alignment explanation
Indices: 4207453--4207477 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4207443 TGATAGATAT
4207453 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
4207478 ATACAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:4208177 original size:21 final size:21
Alignment explanation
Indices: 4208138--4208203 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
4208128 GTCATGCAAA
*
4208138 ATAATATTATGCAAATAATAAT
1 ATAATATAATGC-AATAATAAT
*
4208160 ATAATATCATGCAATAATAAT
1 ATAATATAATGCAATAATAAT
*
4208181 ATGATATAATGCAAT--TAAT
1 ATAATATAATGCAATAATAAT
4208200 ATAA
1 ATAA
4208204 ACTATCTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.17
21 22 0.55
22 11 0.28
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (21 bp):
ATAATATAATGCAATAATAAT
Found at i:4209297 original size:29 final size:31
Alignment explanation
Indices: 4209265--4209333 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
4209255 AAAATTTTTT
4209265 AATTAGATAA-TTTT-TTCAAAAAAATGATA
1 AATTAGATAACTTTTCTTCAAAAAAATGATA
* *
4209294 AATTAGGTAACTTTTCTTTAAAAAAATGATA
1 AATTAGATAACTTTTCTTCAAAAAAATGATA
4209325 AATATAGAT
1 AAT-TAGAT
4209334 GACAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 9 0.26
30 4 0.12
31 17 0.50
32 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (31 bp):
AATTAGATAACTTTTCTTCAAAAAAATGATA
Found at i:4215917 original size:6 final size:6
Alignment explanation
Indices: 4215906--4215937 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4215896 GTCAGCATCT
*
4215906 GCGTTG GCGTTG GCGTTG GCGTTG GAGTTG GC
1 GCGTTG GCGTTG GCGTTG GCGTTG GCGTTG GC
4215938 ATAACAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.16, G:0.50, T:0.31
Consensus pattern (6 bp):
GCGTTG
Found at i:4218546 original size:16 final size:16
Alignment explanation
Indices: 4218513--4218546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4218503 AAGGTTCATG
**
4218513 TTTTTTTTTTCTTTTT
1 TTTTTTTTTTCTGGTT
4218529 TTTTTTTTTTCTGGTT
1 TTTTTTTTTTCTGGTT
4218545 TT
1 TT
4218547 GATGTTCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTCTGGTT
Found at i:4219735 original size:19 final size:20
Alignment explanation
Indices: 4219711--4219758 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
4219701 AATTTGTGAG
4219711 TTTAATTAAATTTATA-AAT
1 TTTAATTAAATTTATATAAT
* * *
4219730 TTTAA-TATATTTTTATTAT
1 TTTAATTAAATTTATATAAT
4219749 TTTAATTAAA
1 TTTAATTAAA
4219759 AATTATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTAAATTTATATAAT
Found at i:4227403 original size:29 final size:29
Alignment explanation
Indices: 4227361--4227416 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
4227351 TTTGCTGATG
4227361 TGTTACCCTTTGACTTTTGAGTGTTTTGC
1 TGTTACCCTTTGACTTTTGAGTGTTTTGC
*
4227390 TGTTACCTTTTGACTTTTGAGTGTTTT
1 TGTTACCCTTTGACTTTTGAGTGTTTT
4227417 CACGTTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (29 bp):
TGTTACCCTTTGACTTTTGAGTGTTTTGC
Found at i:4234805 original size:147 final size:147
Alignment explanation
Indices: 4234523--4234814 Score: 507
Period size: 147 Copynumber: 2.0 Consensus size: 147
4234513 ATTTCAAGTA
4234523 CTTCTTTTTCTAACAAATTACCATGGCAAAGGCCCTCAATATATATCTGTCCAACATATGATGTT
1 CTTCTTTTTCTAACAAATTACCATGGCAAAGGCCCTCAATATATATCTGTCCAACATATGATGTT
* *
4234588 AGAAATTAAATAAACTACGATAAATGTCCATTAAGAATTAGGGAGAAGTGAGACAACCAGACAAA
66 AGAAATTAAACAAACTACGATAAATGTCCATTAAGAATTAGGGAGAAGCGAGACAACCAGACAAA
4234653 GACCCAACAATTAAATT
131 GACCCAACAATTAAATT
*
4234670 CTTCTTTTTCTAACAAATTACTATGGCAAAGGCCCTCAATATATATCTGTCCAACATATGCA-GT
1 CTTCTTTTTCTAACAAATTACCATGGCAAAGGCCCTCAATATATATCTGTCCAACATATG-ATGT
**
4234734 TAGAAATTAAACAAACTGGGATAAATGTCCATTAAGAATTAGGGAG-AGCGAGACAACCAGACAA
65 TAGAAATTAAACAAACTACGATAAATGTCCATTAAGAATTAGGGAGAAGCGAGACAACCAGACAA
4234798 AGAACCCAACAATTAAA
130 AG-ACCCAACAATTAAA
4234815 CTAGGTGATT
Statistics
Matches: 138, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
146 19 0.14
147 118 0.86
148 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (147 bp):
CTTCTTTTTCTAACAAATTACCATGGCAAAGGCCCTCAATATATATCTGTCCAACATATGATGTT
AGAAATTAAACAAACTACGATAAATGTCCATTAAGAATTAGGGAGAAGCGAGACAACCAGACAAA
GACCCAACAATTAAATT
Found at i:4241538 original size:12 final size:12
Alignment explanation
Indices: 4241523--4241565 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
4241513 GGTGTCATCT
*
4241523 TCTTCTTCTTCC
1 TCTTCTTCTTCA
*
4241535 TCTTCCTCTTCA
1 TCTTCTTCTTCA
* *
4241547 TCTTCGTCTTCG
1 TCTTCTTCTTCA
4241559 TCTTCTT
1 TCTTCTT
4241566 TGTCGTCATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.02, C:0.37, G:0.05, T:0.56
Consensus pattern (12 bp):
TCTTCTTCTTCA
Done.