Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 62 of 130
Found at i:13097061 original size:23 final size:22
Alignment explanation
Indices: 13097012--13097061 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
13097002 CAAATTATTT
*
13097012 AAAAAATTTATTACTATTTACTA
1 AAAAAATTTATTACTAATTAC-A
13097035 AAAAAATTTATTTGACTAATTACA
1 AAAAAATTTA-TT-ACTAATTACA
13097059 AAA
1 AAA
13097062 GAAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 6 0.25
25 8 0.33
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAATTTATTACTAATTACA
Found at i:13101426 original size:61 final size:60
Alignment explanation
Indices: 13101293--13101573 Score: 324
Period size: 61 Copynumber: 4.8 Consensus size: 60
13101283 TGTTCTTGTG
* * *
13101293 TAAGAAAAATTGATACTTTCAATTTTTTCTCAAAAATA---TTTTTTGAAAATTTATTTT
1 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAAATTTACTTT
13101350 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTGAAAATTTACTTT
1 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTTTGAAAATTTACTTT
*
13101411 TAAGAAAAATTGATACTTTCAACTTTTCC-CTAAAAATA---TTTTTTGGAAATTT-CGATTT
1 TAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTTGAAAATTTAC--TTT
* * * *
13101469 TCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAT-CTTTTTTTT-----TTTATTTT
1 T-AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAAATTTACTTT
13101524 TAAGAAAAATTGATACTTTCAACTTTTCC-CTAAAAATA-TTTTTTTTGAAA
1 TAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTTGAAA
13101574 TTTTTTATTT
Statistics
Matches: 196, Mismatches: 9, Indels: 37
0.81 0.04 0.15
Matches are distributed among these distances:
53 1 0.01
54 40 0.20
55 4 0.02
56 4 0.02
57 49 0.25
58 4 0.02
59 32 0.16
60 2 0.01
61 60 0.31
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (60 bp):
TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAAATTTACTTT
Found at i:13101549 original size:120 final size:116
Alignment explanation
Indices: 13101293--13101567 Score: 338
Period size: 118 Copynumber: 2.4 Consensus size: 116
13101283 TGTTCTTGTG
* *
13101293 TAAGAAAAATTGATACTTTCAA--TTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTTAAGAA
1 TAAGAAAAATTGATACTTTCAACTTTTTTTCCCAAAAATATTTTTTGAAAATTTATTTTCAAGAA
*
13101356 AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTGAAAATTTACTTT
66 AAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTTT----ATTTACTTT
*
13101411 TAAGAAAAATTGATACTTTCAAC---TTTTCCCTAAAAATATTTTTTGGAAATTTCGATTTTCAA
1 TAAGAAAAATTGATACTTTCAACTTTTTTTCCC-AAAAATATTTTTTGAAAATTT--ATTTTCAA
* * *
13101473 GGAAAATTGATACTTTCAACTTTTTCTC-AAAA-ATCTTTTTTTT-TTTATTTT
63 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTTTATTTACTTT
13101524 TAAGAAAAATTGATACTTTCAAC---TTTTCCCTAAAAATATTTTTT
1 TAAGAAAAATTGATACTTTCAACTTTTTTTCCC-AAAAATATTTTTT
13101568 TTGAAATTTT
Statistics
Matches: 146, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
113 51 0.35
117 6 0.04
118 52 0.36
119 4 0.03
120 33 0.23
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (116 bp):
TAAGAAAAATTGATACTTTCAACTTTTTTTCCCAAAAATATTTTTTGAAAATTTATTTTCAAGAA
AAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTTTATTTACTTT
Found at i:13101612 original size:8 final size:8
Alignment explanation
Indices: 13101599--13101662 Score: 67
Period size: 9 Copynumber: 7.5 Consensus size: 8
13101589 TAAAGAAAAT
13101599 AAAATAAA
1 AAAATAAA
13101607 AAAATAAA
1 AAAATAAA
*
13101615 AAATTAAAA
1 AAAAT-AAA
13101624 AAAAGTAAA
1 AAAA-TAAA
13101633 AAAAT-AA
1 AAAATAAA
13101640 AAAATAAAA
1 AAAAT-AAA
13101649 TAAAGATAAA
1 -AAA-ATAAA
13101659 AAAA
1 AAAA
13101663 ATATTAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
7 7 0.15
8 14 0.29
9 18 0.38
10 7 0.15
11 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:13101615 original size:7 final size:7
Alignment explanation
Indices: 13101594--13101648 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
13101584 TTATTTAAAG
13101594 AAAATAA
1 AAAATAA
*
13101601 AATA-AA
1 AAAATAA
13101607 AAAATAA
1 AAAATAA
*
13101614 AAAATTA
1 AAAATAA
13101621 AAAA-AA
1 AAAATAA
**
13101627 AGTA-AA
1 AAAATAA
13101633 AAAATAA
1 AAAATAA
13101640 AAAATAA
1 AAAATAA
13101647 AA
1 AA
13101649 TAAAGATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 12 0.32
7 26 0.68
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:13101623 original size:26 final size:25
Alignment explanation
Indices: 13101594--13101662 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 25
13101584 TTATTTAAAG
13101594 AAAATAAAATAAAAAAATAAAAAATT
1 AAAATAAAATAAAAAAATAAAAAA-T
13101620 AAAA-AAAAGTAAAAAAATAAAAAAT
1 AAAATAAAA-TAAAAAAATAAAAAAT
13101645 AAAATAAAGATAAAAAAA
1 AAAATAAA-ATAAAAAAA
13101663 ATATTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
25 9 0.22
26 30 0.75
27 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (25 bp):
AAAATAAAATAAAAAAATAAAAAAT
Found at i:13101659 original size:11 final size:11
Alignment explanation
Indices: 13101594--13101674 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
13101584 TTATTTAAAG
13101594 AAAATAAAATA
1 AAAATAAAATA
13101605 AAAA-AATAA-A
1 AAAATAA-AATA
* *
13101615 AAATTAAAAAA
1 AAAATAAAATA
*
13101626 AAGTAAAAAAATAA
1 AA--AATAAAAT-A
13101640 AAAATAAAATA
1 AAAATAAAATA
*
13101651 AAGATAAAA-A
1 AAAATAAAATA
*
13101661 AAATATTAAATA
1 AAA-ATAAAATA
13101673 AA
1 AA
13101675 CCTAATCTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
10 11 0.20
11 25 0.46
12 10 0.19
13 5 0.09
14 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:13101670 original size:18 final size:18
Alignment explanation
Indices: 13101594--13101661 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
13101584 TTATTTAAAG
13101594 AAAATAAA-ATAAAAAAAT
1 AAAATAAAGAT-AAAAAAT
** *
13101612 AAAA-AATTAAAAAAAAGT
1 AAAATAAAGATAAAAAA-T
13101630 -AAA-AAA-ATAAAAAAT
1 AAAATAAAGATAAAAAAT
13101645 AAAATAAAGATAAAAAA
1 AAAATAAAGATAAAAAA
13101662 AATATTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
17 16 0.39
18 14 0.34
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATAAAGATAAAAAAT
Found at i:13103263 original size:242 final size:242
Alignment explanation
Indices: 13102838--13103323 Score: 954
Period size: 242 Copynumber: 2.0 Consensus size: 242
13102828 TTCCAGGACA
13102838 TGTTGGATATGCAAAATATTGTGGTGGGACCTCTTGAACAGACTGAACTTGAGATGGGCCAAAAT
1 TGTTGGATATGCAAAATATTGTGGTGGGACCTCTTGAACAGACTGAACTTGAGATGGGCCAAAAT
13102903 CTGAAGGGTACAAAAAGTCAACCACTTCTTGCTGGCTTGTACTTCCTTCAACTCATTTTCCTTTA
66 CTGAAGGGTACAAAAAGTCAACCACTTCTTGCTGGCTTGTACTTCCTTCAACTCATTTTCCTTTA
13102968 TTCATGTTATTAAAGACCTCCAGAATCTTGCTTAGTTCACTTTCAATCTTCTCCTGAGCTTTTTC
131 TTCATGTTATTAAAGACCTCCAGAATCTTGCTTAGTTCACTTTCAATCTTCTCCTGAGCTTTTTC
13103033 TAACTTTTCAAATCTATGAGAACTTTCTTCTTCCATTTGCCTTGCTC
196 TAACTTTTCAAATCTATGAGAACTTTCTTCTTCCATTTGCCTTGCTC
*
13103080 TGTTGGATATGCAAAATGTTGTGGTGGGACCTCTTGAACAGACTGAACTTGAGATGGGCCAAAAT
1 TGTTGGATATGCAAAATATTGTGGTGGGACCTCTTGAACAGACTGAACTTGAGATGGGCCAAAAT
*
13103145 CTGAAGGGTACAAAAAGTCAACCACTTCTTGCTGGCTTGTACTTCCTTTAACTCATTTTCCTTTA
66 CTGAAGGGTACAAAAAGTCAACCACTTCTTGCTGGCTTGTACTTCCTTCAACTCATTTTCCTTTA
13103210 TTCATGTTATTAAAGACCTCCAGAATCTTGCTTAGTTCACTTTCAATCTTCTCCTGAGCTTTTTC
131 TTCATGTTATTAAAGACCTCCAGAATCTTGCTTAGTTCACTTTCAATCTTCTCCTGAGCTTTTTC
13103275 TAACTTTTCAAATCTATGAGAACTTTCTTCTTCCATTTGCCTTGCTC
196 TAACTTTTCAAATCTATGAGAACTTTCTTCTTCCATTTGCCTTGCTC
13103322 TG
1 TG
13103324 GATCTTGTGT
Statistics
Matches: 242, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
242 242 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (242 bp):
TGTTGGATATGCAAAATATTGTGGTGGGACCTCTTGAACAGACTGAACTTGAGATGGGCCAAAAT
CTGAAGGGTACAAAAAGTCAACCACTTCTTGCTGGCTTGTACTTCCTTCAACTCATTTTCCTTTA
TTCATGTTATTAAAGACCTCCAGAATCTTGCTTAGTTCACTTTCAATCTTCTCCTGAGCTTTTTC
TAACTTTTCAAATCTATGAGAACTTTCTTCTTCCATTTGCCTTGCTC
Found at i:13104686 original size:57 final size:59
Alignment explanation
Indices: 13104592--13104704 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 59
13104582 TTGTGTAGGA
* *
13104592 AAAATTGATACTTTCAATTTTTCTTCAAAAATA-TTTTTTGAAAATTT-ATTTTTAAAG
1 AAAATTGATACTTTCAATCTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTTTAAAG
*
13104649 AAAATTGATACTTTCAA-CTTTCCT-AAAAATATTTTTTTTTGAAATTTTGATTTTTA
1 AAAATTGATACTTTCAATCTTTCCTCAAAAATA--TTTTTTTGAAAATTTGATTTTTA
13104705 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
55 7 0.14
56 5 0.10
57 17 0.35
58 13 0.27
59 7 0.14
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.50
Consensus pattern (59 bp):
AAAATTGATACTTTCAATCTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTTTAAAG
Found at i:13104729 original size:7 final size:8
Alignment explanation
Indices: 13104713--13104745 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
13104703 TATTTAAATG
13104713 AAAATAAA
1 AAAATAAA
13104721 AAAATAAA
1 AAAATAAA
13104729 AAAA-ATAA
1 AAAATA-AA
13104737 AAAATAAA
1 AAAATAAA
13104745 A
1 A
13104746 TAAAGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 21 0.91
9 1 0.04
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:13104738 original size:16 final size:17
Alignment explanation
Indices: 13104708--13104761 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 17
13104698 ATTTTTATTT
13104708 AAATGAAAATAAAAAAATA
1 AAAT-AAAAT-AAAAAATA
13104727 AAA-AAAATAAAAAATA
1 AAATAAAATAAAAAATA
13104743 AAATAAAGATAAAAGAATA
1 AAATAAA-ATAAAA-AATA
13104762 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.34
17 8 0.25
18 6 0.19
19 7 0.22
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAATAAAATAAAAAATA
Found at i:13104789 original size:4 final size:4
Alignment explanation
Indices: 13104780--13104806 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13104770 AACCTAATCT
13104780 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
13104807 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:13105827 original size:16 final size:16
Alignment explanation
Indices: 13105798--13105848 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
13105788 ATTTATTATA
13105798 ATATAA-TA-ATAAAT
1 ATATAACTATATAAAT
13105812 ATATAACTATATAAAT
1 ATATAACTATATAAAT
* *
13105828 ATATTAC-ATATAGAT
1 ATATAACTATATAAAT
13105843 AT-TAAC
1 ATATAAC
13105849 AGAGAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.28
15 11 0.34
16 12 0.38
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATAACTATATAAAT
Found at i:13105956 original size:9 final size:9
Alignment explanation
Indices: 13105925--13105956 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
13105915 CGTAAAATAC
13105925 AAAAGAGAAA
1 AAAAGA-AAA
13105935 AAAAGAAAA
1 AAAAGAAAA
13105944 AAAAGAAAA
1 AAAAGAAAA
13105953 AAAA
1 AAAA
13105957 TAACACAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:13106112 original size:21 final size:21
Alignment explanation
Indices: 13106069--13106112 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
13106059 GAAGAAGATT
* *
13106069 ATGTATCAATTTTTAAATTAA
1 ATGTATCAATTATTAAATCAA
* *
13106090 ATGTATCACTTATTGAATCAA
1 ATGTATCAATTATTAAATCAA
13106111 AT
1 AT
13106113 ATTCGGATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (21 bp):
ATGTATCAATTATTAAATCAA
Found at i:13106470 original size:18 final size:19
Alignment explanation
Indices: 13106430--13106468 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13106420 GAAATTAAAC
*
13106430 TTAAATAAAAAGTAGTTAT
1 TTAAATAAAAAATAGTTAT
* *
13106449 TTAATTAAAAAATATTTAT
1 TTAAATAAAAAATAGTTAT
13106468 T
1 T
13106469 AAAACTGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAAATAAAAAATAGTTAT
Found at i:13107060 original size:19 final size:20
Alignment explanation
Indices: 13107026--13107064 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
13107016 TTTGATTTTT
13107026 TTTTCATTTTTCCTATTTAA
1 TTTTCATTTTTCCTATTTAA
13107046 TTTTCATTTTT-CTATTTAA
1 TTTTCATTTTTCCTATTTAA
13107065 AATATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCATTTTTCCTATTTAA
Found at i:13108082 original size:30 final size:30
Alignment explanation
Indices: 13108047--13108117 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
13108037 ATATTTTTAA
* *
13108047 TTATTTAT-TTTATTATATTAAT-AAAATTTT
1 TTATTTATATTT-TAAT-TTAATAAAAATATT
13108077 TTATTTAATATTTTAATTTAATAAAAATATT
1 TTATTT-ATATTTTAATTTAATAAAAATATT
13108108 TTATTTATAT
1 TTATTTATAT
13108118 ATAATTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 15 0.42
31 18 0.50
32 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTATTTATATTTTAATTTAATAAAAATATT
Found at i:13108092 original size:25 final size:26
Alignment explanation
Indices: 13108045--13108093 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
13108035 TTATATTTTT
*
13108045 AATTATTTATTTTATTATATTAATAA
1 AATTATTTATTTTAATATATTAATAA
* *
13108071 AATTTTTTA-TTTAATATTTTAAT
1 AATTATTTATTTTAATATATTAAT
13108094 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
AATTATTTATTTTAATATATTAATAA
Found at i:13108909 original size:6 final size:6
Alignment explanation
Indices: 13108898--13108939 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
13108888 CATTGGTCCT
* *
13108898 TTTTTA TTTTTA TTTTT- TTTTAA TTTTAA TTTTTA TTGTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA
13108940 GATTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
5 4 0.12
6 24 0.75
7 4 0.12
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:13108918 original size:16 final size:17
Alignment explanation
Indices: 13108897--13108931 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13108887 TCATTGGTCC
*
13108897 TTTTTT-ATTTTTATTT
1 TTTTTTAATTTTAATTT
13108913 TTTTTTAATTTTAATTT
1 TTTTTTAATTTTAATTT
13108930 TT
1 TT
13108932 ATTGTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTAATTTTAATTT
Found at i:13109935 original size:22 final size:22
Alignment explanation
Indices: 13109895--13109940 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13109885 AAATAAATAT
*
13109895 AAAAATAAATAAAACTTAATTA
1 AAAAATAAATAAAACTTAAGTA
*
13109917 AAAAATAAA-AATAATTTAAGTA
1 AAAAATAAATAA-AACTTAAGTA
13109939 AA
1 AA
13109941 TATTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATAAATAAAACTTAAGTA
Found at i:13110345 original size:20 final size:18
Alignment explanation
Indices: 13110318--13110374 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
13110308 AATTTAAATT
13110318 TATTATTAAATATTAATA
1 TATTATTAAATATTAATA
*
13110336 TTTTTAATTAAA-ATTCAATA
1 -TATT-ATTAAATATT-AATA
13110356 TATTATTAAATACTTAATA
1 TATTATTAAATA-TTAATA
13110375 ATAAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 14 0.44
20 12 0.38
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATTAAATATTAATA
Found at i:13115445 original size:13 final size:13
Alignment explanation
Indices: 13115427--13115451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13115417 CAGATAATAC
13115427 GTGATTATTCAAG
1 GTGATTATTCAAG
13115440 GTGATTATTCAA
1 GTGATTATTCAA
13115452 TGCATTTTTT
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
GTGATTATTCAAG
Found at i:13116050 original size:34 final size:34
Alignment explanation
Indices: 13115987--13116053 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
13115977 TTCTTGCATT
* * *
13115987 TTGGGTTAAATCCTTAAACTTTATGTTTGATTTA
1 TTGGGTCAAATCCTTAAACTTCATATTTGATTTA
*
13116021 TTGGGTCAAATCCTTAAACTTCCTATTTGATTT
1 TTGGGTCAAATCCTTAAACTTCATATTTGATTT
13116054 GTTACGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.48
Consensus pattern (34 bp):
TTGGGTCAAATCCTTAAACTTCATATTTGATTTA
Found at i:13119549 original size:17 final size:17
Alignment explanation
Indices: 13119527--13119565 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
13119517 TCATAGTTTG
13119527 AGCCATAGGAACAAGTA
1 AGCCATAGGAACAAGTA
13119544 AGCCATAGGAACAAGTA
1 AGCCATAGGAACAAGTA
13119561 AGCCA
1 AGCCA
13119566 ATAGAAGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (17 bp):
AGCCATAGGAACAAGTA
Found at i:13121620 original size:22 final size:22
Alignment explanation
Indices: 13121594--13121640 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13121584 TCCTTTAACC
* *
13121594 TTATTTATGAAATTTAAAAATT
1 TTATTAATGAAATATAAAAATT
* *
13121616 TTATTAATTATATATAAAAATT
1 TTATTAATGAAATATAAAAATT
13121638 TTA
1 TTA
13121641 AATTCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATTAATGAAATATAAAAATT
Found at i:13126369 original size:2 final size:2
Alignment explanation
Indices: 13126362--13126428 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
13126352 AAAGGATTCT
13126362 TA TA TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA
*
13126404 TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13126429 TTTTTTTTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13137079 original size:41 final size:41
Alignment explanation
Indices: 13137017--13137102 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
13137007 TTTGCAAGTT
* **
13137017 TTAAGCCATCTTGGAACAATTGAATACTTATAAACAATTCA
1 TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
13137058 TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
1 TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
13137099 TTAA
1 TTAA
13137103 TTTGACAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (41 bp):
TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
Found at i:13137238 original size:41 final size:41
Alignment explanation
Indices: 13137179--13137264 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
13137169 TTTGCAAGTT
* * ** *
13137179 TTAAATCATCTTGGAACAATTGAATACTTATAAATAATTCA
1 TTAAACCATCTTGAAACAATTGAATACCCATAAACAATTCA
13137220 TTAAACCATCTTGAAACAATTGAATACCCATAAACAATTCA
1 TTAAACCATCTTGAAACAATTGAATACCCATAAACAATTCA
13137261 TTAA
1 TTAA
13137265 TTTGACCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (41 bp):
TTAAACCATCTTGAAACAATTGAATACCCATAAACAATTCA
Found at i:13137389 original size:157 final size:158
Alignment explanation
Indices: 13136984--13137452 Score: 796
Period size: 162 Copynumber: 2.9 Consensus size: 158
13136974 TATAAATAAT
*
13136984 TATATATATATATATATTTGCAATTTGCAAGTTTTAAGCCATCTTGGAACAATTGAATACTTATA
1 TATATATATATATATATTTGCAATTTGCAAGTTTTAAACCATCTTGGAACAATTGAATACTTATA
13137049 AACAATTCATTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCATTAATTTGACAAATG
66 AACAATTCATTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCATTAATTTGACAAATG
13137114 GATGTTTATTATTTAAAGTGTCAAAAAAAAAA
131 GATGTTTATTATTTAAAGTGTC----AAAAAA
*
13137146 TATATATATATATATATTTGCAATTTGCAAGTTTTAAATCATCTTGGAACAATTGAATACTTATA
1 TATATATATATATATATTTGCAATTTGCAAGTTTTAAACCATCTTGGAACAATTGAATACTTATA
* * *
13137211 AATAATTCATTAAACCATCTTGAAACAATTGAATACCCATAAACAATTCATTAATTTGACCAATG
66 AACAATTCATTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCATTAATTTGACAAATG
*
13137276 GATGTTTATTATTTAAAGTGTC-AAATA
131 GATGTTTATTATTTAAAGTGTCAAAAAA
*
13137303 TATATATATATATATATTTGTAATTTGCAAGTTTTAAACCATCTTGGAACAATTGAATACTTATA
1 TATATATATATATATATTTGCAATTTGCAAGTTTTAAACCATCTTGGAACAATTGAATACTTATA
* * *
13137368 AACAATTCATTAAACCATCTTGGAACAATTGAATACCCATAAATAATTCATTAATCTGATAAATG
66 AACAATTCATTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCATTAATTTGACAAATG
*
13137433 GATGTTTATTATTCAAAGTG
131 GATGTTTATTATTTAAAGTG
13137453 ATAAATTTGG
Statistics
Matches: 292, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
157 145 0.50
162 147 0.50
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (158 bp):
TATATATATATATATATTTGCAATTTGCAAGTTTTAAACCATCTTGGAACAATTGAATACTTATA
AACAATTCATTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCATTAATTTGACAAATG
GATGTTTATTATTTAAAGTGTCAAAAAA
Found at i:13137393 original size:41 final size:41
Alignment explanation
Indices: 13137336--13137421 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
13137326 TTTGCAAGTT
**
13137336 TTAAACCATCTTGGAACAATTGAATACTTATAAACAATTCA
1 TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
*
13137377 TTAAACCATCTTGGAACAATTGAATACCCATAAATAATTCA
1 TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
13137418 TTAA
1 TTAA
13137422 TCTGATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (41 bp):
TTAAACCATCTTGGAACAATTGAATACCCATAAACAATTCA
Found at i:13137699 original size:29 final size:30
Alignment explanation
Indices: 13137639--13137703 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
13137629 AATTTTTAAA
* * *
13137639 ATATATATTTATTATTAATAATATAATATT
1 ATATATATTCATTAATAATAATAAAATATT
13137669 ATATA-ATTCATTAATAATATATAAAAT-TT
1 ATATATATTCATTAATAATA-ATAAAATATT
13137698 ATATAT
1 ATATAT
13137704 TTTAAAGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATATATTCATTAATAATAATAAAATATT
Found at i:13137708 original size:26 final size:26
Alignment explanation
Indices: 13137635--13137708 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 26
13137625 TTTAAATTTT
* *
13137635 TAAAATATATAT-TTATTATTAATAA
1 TAAAATTTATATATTATTAATAATAA
*
13137660 TATAATATTATATAATTCATTAATAATATA
1 TAAAAT-TTATAT-ATT-ATTAATAATA-A
13137690 TAAAATTTATATATT-TTAA
1 TAAAATTTATATATTATTAA
13137709 AGTGCGCGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
25 5 0.12
26 9 0.22
28 5 0.12
29 15 0.38
30 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAAATTTATATATTATTAATAATAA
Found at i:13139875 original size:36 final size:35
Alignment explanation
Indices: 13139812--13139913 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 35
13139802 TATAGTCATG
* *
13139812 TTTTCTTATTCAAAAAAAGCTTATTCAAAAAGTTATAT
1 TTTTC-TATTC-AAACATGCTTATTCAAAAA-TTATAT
* *
13139850 TTTTCTATTCAAACATGTTTATTCAAACAATTATGT
1 TTTTCTATTCAAACATGCTTATTCAAA-AATTATAT
*
13139886 TTTTCTATTCAAATATGCTTATTCAAAA
1 TTTTCTATTCAAACATGCTTATTCAAAA
13139914 TAAAAATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
35 1 0.02
36 44 0.77
37 7 0.12
38 5 0.09
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (35 bp):
TTTTCTATTCAAACATGCTTATTCAAAAATTATAT
Found at i:13139902 original size:18 final size:18
Alignment explanation
Indices: 13139849--13139902 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
13139839 AAAAGTTATA
*
13139849 TTTTTCTATTCAAACATG
1 TTTTTCTATTCAAATATG
** *
13139867 TTTATTC-AAACAATTATG
1 TTT-TTCTATTCAAATATG
13139885 TTTTTCTATTCAAATATG
1 TTTTTCTATTCAAATATG
13139903 CTTATTCAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTTCTATTCAAATATG
Found at i:13140605 original size:24 final size:24
Alignment explanation
Indices: 13140551--13140605 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
13140541 TAATTATAGA
*
13140551 CTCCATTAAGACTCTAATCTCAAT
1 CTCCATTAAGACTCTAATCTCAAC
* * * * *
13140575 TTTCATTAAGAGTTTAGTCTCAAC
1 CTCCATTAAGACTCTAATCTCAAC
13140599 CTCCATT
1 CTCCATT
13140606 TATGCAATGG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (24 bp):
CTCCATTAAGACTCTAATCTCAAC
Found at i:13141118 original size:5 final size:5
Alignment explanation
Indices: 13141104--13141297 Score: 72
Period size: 6 Copynumber: 34.8 Consensus size: 5
13141094 TCCAATTTTA
* * *
13141104 TATTT TATTT CATTT TATTT TATTA T-TTT TATCTT TATATT TATAAATG
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TAT-TT TAT---TT
* *
13141153 TA-TT TATCAT TATTT TATATT TATTCT TGTATT TATCTT TATTTT TATTT
1 TATTT TAT-TT TATTT TAT-TT TATT-T TAT-TT TAT-TT TA-TTT TATTT
* *
13141203 CATTC TATCTT TATTCTT TATTT TATTCAT TCATCTT TATTT TACTTT TATTTT
1 TATTT TAT-TT TA-T-TT TATTT TATT--T T-AT-TT TATTT TA-TTT TA-TTT
*
13141257 TATTT TATCTT CATTTT TATTT T-TTT TCA-TT TATTAT TATT
1 TATTT TAT-TT TA-TTT TATTT TATTT T-ATTT TATT-T TATT
13141298 GTTTATAAAA
Statistics
Matches: 147, Mismatches: 19, Indels: 45
0.70 0.09 0.21
Matches are distributed among these distances:
4 11 0.07
5 56 0.38
6 60 0.41
7 13 0.09
8 6 0.04
9 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:13141170 original size:29 final size:29
Alignment explanation
Indices: 13141132--13141202 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
13141122 TTTATTATTT
13141132 TTATCTTTATATTTATAAATGTATTTATCA
1 TTAT-TTTATATTTATAAATGTATTTATCA
*** *
13141162 TTATTTTATATTTATTCTTGTATTTATCT
1 TTATTTTATATTTATAAATGTATTTATCA
13141191 TTATTTT-TATTT
1 TTATTTTATATTT
13141203 CATTCTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.14
29 28 0.76
30 4 0.11
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (29 bp):
TTATTTTATATTTATAAATGTATTTATCA
Found at i:13141207 original size:29 final size:29
Alignment explanation
Indices: 13141151--13141261 Score: 97
Period size: 29 Copynumber: 3.8 Consensus size: 29
13141141 TATTTATAAA
*
13141151 TGTATTTATCATTATTTTATATTT-ATTCT
1 TGTATTTATCTTTATTTT-TATTTCATTCT
13141180 TGTATTTATCTTTATTTTTATTTCATTC-
1 TGTATTTATCTTTATTTTTATTTCATTCT
* *
13141208 TATCTTTATTCTTTA-TTTTA-TTCATTCAT
1 TGTATTTA-TCTTTATTTTTATTTCATTC-T
*
13141237 CTTTATTT-TACTTTTATTTTTATTT
1 -TGTATTTAT-C-TTTATTTTTATTT
13141262 TATCTTCATT
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
27 7 0.10
28 17 0.25
29 28 0.41
30 9 0.13
31 5 0.07
32 2 0.03
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (29 bp):
TGTATTTATCTTTATTTTTATTTCATTCT
Found at i:13141290 original size:48 final size:50
Alignment explanation
Indices: 13141183--13141291 Score: 116
Period size: 54 Copynumber: 2.1 Consensus size: 50
13141173 TTATTCTTGT
* *
13141183 ATTTATCTTTATTTTTATTTCATTCTATCTTTATTCTTTATTTTATTCATTC
1 ATTTAT-TTTACTTTTATTTCATTCTATCTTCATTCTTTATTTTATT-ATTC
* *
13141235 ATCTTTATTTTACTTTTATTTTTATTTTATCTTCATT-TTTATTTT-TT-TTC
1 A--TTTATTTTACTTTTA-TTTCATTCTATCTTCATTCTTTATTTTATTATTC
13141285 ATTTATT
1 ATTTATT
13141292 ATTATTGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
48 6 0.12
50 4 0.08
52 3 0.06
53 17 0.34
54 20 0.40
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (50 bp):
ATTTATTTTACTTTTATTTCATTCTATCTTCATTCTTTATTTTATTATTC
Found at i:13141293 original size:17 final size:17
Alignment explanation
Indices: 13141184--13141294 Score: 86
Period size: 17 Copynumber: 6.4 Consensus size: 17
13141174 TATTCTTGTA
*
13141184 TTTATCTTTATTTTTA-T
1 TTTAT-TTTATTTTCATT
* *
13141201 TTCATTCTATCTTT-ATT
1 TTTATTTTAT-TTTCATT
*
13141218 CTTTATTTTATTCATTCATC
1 -TTTATTTTATT--TTCATT
13141238 TTTATTTTACTTTT-ATT
1 TTTATTTTA-TTTTCATT
*
13141255 TTTATTTTATCTTCATT
1 TTTATTTTATTTTCATT
13141272 TTTATTTT-TTTTCATT
1 TTTATTTTATTTTCATT
13141288 TATTATT
1 T-TTATT
13141295 ATTGTTTATA
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
16 16 0.21
17 36 0.47
18 10 0.13
19 11 0.14
20 4 0.05
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTTTCATT
Found at i:13141294 original size:34 final size:35
Alignment explanation
Indices: 13141212--13141294 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 35
13141202 TCATTCTATC
13141212 TTTATTCTTTATTTTATTCATTCATCTTTATTTTACT
1 TTTATT-TTTATTTTATTCATTCATCTTTATTTTA-T
*
13141249 TTTATTTTTATTTTA-TC-TTCATTTTTATTTT-T
1 TTTATTTTTATTTTATTCATTCATCTTTATTTTAT
13141281 TTTCATTTATTATT
1 TTT-ATTT-TTATT
13141295 ATTGTTTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
34 18 0.42
35 2 0.05
36 9 0.21
37 6 0.14
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (35 bp):
TTTATTTTTATTTTATTCATTCATCTTTATTTTAT
Found at i:13144964 original size:107 final size:107
Alignment explanation
Indices: 13144778--13144992 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
13144768 TCCAAGATCC
13144778 ATGTACTATTGGACATAATTGAGTCTATTTCATCATTAATAGCTTCTTTCTAAAAAGTAATATCT
1 ATGTACTATTGGACATAATTGAGTCTATTTCATCATTAATAGCTTCTTTCTAAAAAGTAATATCT
13144843 TTTGAAGTCATAGCTTCATTAAATGTTTTAGGGTTTTCTTCT
66 TTTGAAGTCATAGCTTCATTAAATGTTTTAGGGTTTTCTTCT
13144885 ATGTACTATTGGACATAATTGAGTCTATTTCATCATTAATAGCTTCTTTCTAAAAAGTAATATCT
1 ATGTACTATTGGACATAATTGAGTCTATTTCATCATTAATAGCTTCTTTCTAAAAAGTAATATCT
13144950 TTTGAAGTCATAGCTTCATTAAATGTTTTAGGGTTTTCTTCT
66 TTTGAAGTCATAGCTTCATTAAATGTTTTAGGGTTTTCTTCT
13144992 A
1 A
13144993 CATTTAGTAG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (107 bp):
ATGTACTATTGGACATAATTGAGTCTATTTCATCATTAATAGCTTCTTTCTAAAAAGTAATATCT
TTTGAAGTCATAGCTTCATTAAATGTTTTAGGGTTTTCTTCT
Found at i:13158095 original size:32 final size:33
Alignment explanation
Indices: 13158058--13158132 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
13158048 TTTTATAAAA
*
13158058 GTTTGAAGAAATGTAGGAAAAAGAA-TCGGTTT
1 GTTTGAAGAAATGAAGGAAAAAGAATTCGGTTT
* * * *
13158090 GTTTGAAGAAATGAAGTAAAGATAATTGGGTTT
1 GTTTGAAGAAATGAAGGAAAAAGAATTCGGTTT
13158123 GTTTGAAGAA
1 GTTTGAAGAA
13158133 TTGCTTTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 21 0.57
33 16 0.43
ACGTcount: A:0.40, C:0.01, G:0.28, T:0.31
Consensus pattern (33 bp):
GTTTGAAGAAATGAAGGAAAAAGAATTCGGTTT
Found at i:13160884 original size:2 final size:2
Alignment explanation
Indices: 13160877--13160905 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13160867 ATTATTCTTC
13160877 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13160906 CAACAGCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13161974 original size:19 final size:19
Alignment explanation
Indices: 13161946--13162012 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
13161936 TTATATTTAT
*
13161946 ATAAAAAAATTTAAAATAA
1 ATAAATAAATTTAAAATAA
13161965 ATAAATAAATAAATTAAAATATA
1 ATAAATAAAT---TTAAAATA-A
* *
13161988 ATTAAATAAATCTAATATAA
1 A-TAAATAAATTTAAAATAA
*
13162008 TTAAA
1 ATAAA
13162013 CCAAACCCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 13 0.33
20 1 0.03
21 6 0.15
22 8 0.21
23 2 0.05
24 9 0.23
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAATAAATTTAAAATAA
Found at i:13162007 original size:11 final size:9
Alignment explanation
Indices: 13161957--13162012 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 9
13161947 TAAAAAAATT
*
13161957 TAAAATAAA
1 TAAATTAAA
13161966 TAAA-TAAA
1 TAAATTAAA
13161974 TAAATTAAAA
1 TAAATT-AAA
13161984 TATAATTAAA
1 TA-AATTAAA
13161994 TAAATCT-AA
1 TAAAT-TAAA
13162003 TATAATTAAA
1 TA-AATTAAA
13162013 CCAAACCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.20
9 13 0.32
10 16 0.39
11 4 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAATTAAA
Found at i:13162718 original size:2 final size:2
Alignment explanation
Indices: 13162713--13162766 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
13162703 TAAATTAATT
* * *
13162713 TA TA TA TA -A TT TA TA TA TA -A TT TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
13162753 TA AA T- TA TA TA TA T
1 TA TA TA TA TA TA TA T
13162767 GTGAATTTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13162724 original size:11 final size:11
Alignment explanation
Indices: 13162691--13162765 Score: 82
Period size: 11 Copynumber: 6.9 Consensus size: 11
13162681 AACTTTAATT
13162691 TTTATATAT-A
1 TTTATATATAA
* *
13162701 TGTAAAT-TAA
1 TTTATATATAA
13162711 TTTATATATAA
1 TTTATATATAA
13162722 TTTATATATAA
1 TTTATATATAA
13162733 TTTATATATATA
1 TTTATATATA-A
**
13162745 TAAATATATAA
1 TTTATATATAA
*
13162756 ATTATATATA
1 TTTATATATA
13162766 TGTGAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
9 1 0.02
10 11 0.21
11 32 0.60
12 9 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (11 bp):
TTTATATATAA
Found at i:13164769 original size:16 final size:18
Alignment explanation
Indices: 13164743--13164776 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
13164733 TTTTATAATA
13164743 AAATATAATAAAT-TATT
1 AAATATAATAAATATATT
13164760 AAAT-TAATAAATATATT
1 AAATATAATAAATATATT
13164777 TATTGATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATAATAAATATATT
Found at i:13164976 original size:24 final size:25
Alignment explanation
Indices: 13164936--13164982 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
13164926 TTTGAACTTG
*
13164936 ATAAAATAAATATTAATTTAAAAAT
1 ATAAAATAAATATTAATATAAAAAT
13164961 ATAAAA-AAAT-TATAATATAAAA
1 ATAAAATAAATAT-TAATATAAAA
13164983 TAATTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 13 0.65
25 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAAAATAAATATTAATATAAAAAT
Found at i:13164979 original size:16 final size:16
Alignment explanation
Indices: 13164958--13164988 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13164948 TTAATTTAAA
13164958 AATATAAAAAAATTAT
1 AATATAAAAAAATTAT
*
13164974 AATATAAAATAATTA
1 AATATAAAAAAATTA
13164989 CAATTTTAAG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATATAAAAAAATTAT
Found at i:13166125 original size:6 final size:6
Alignment explanation
Indices: 13166114--13166141 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13166104 TGAGCTTGGA
13166114 TTGCAT TTGCAT TTGCAT TTGCAT TTGC
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGC
13166142 TGCCTAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (6 bp):
TTGCAT
Found at i:13172215 original size:24 final size:22
Alignment explanation
Indices: 13172154--13172217 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 22
13172144 TTTTATTAAA
13172154 TTTATTTATAAT-TTTTTAAAAT
1 TTTA-TTATAATATTTTTAAAAT
* *
13172176 TTTAAATTATATTATTTTTATATAT
1 TTT--ATTATAATATTTTTA-AAAT
13172201 TTTATTCATAATATTTT
1 TTTATT-ATAATATTTT
13172218 AGTGCCAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 3 0.09
23 9 0.26
24 16 0.47
25 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTATAATATTTTTAAAAT
Found at i:13172243 original size:12 final size:12
Alignment explanation
Indices: 13172226--13172252 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13172216 TTAGTGCCAA
13172226 TCATATTATATT
1 TCATATTATATT
13172238 TCATATTATATT
1 TCATATTATATT
13172250 TCA
1 TCA
13172253 GTTCTGTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (12 bp):
TCATATTATATT
Found at i:13189346 original size:19 final size:18
Alignment explanation
Indices: 13189306--13189348 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13189296 CCTAAATCAG
* **
13189306 CAAAAAGGACATGTACTT
1 CAAAAAGGACATGGACCA
13189324 CAAAAAGGACATTGGACCA
1 CAAAAAGGACA-TGGACCA
13189343 CAAAAA
1 CAAAAA
13189349 ATAAAAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (18 bp):
CAAAAAGGACATGGACCA
Found at i:13200477 original size:60 final size:61
Alignment explanation
Indices: 13200407--13200578 Score: 165
Period size: 60 Copynumber: 2.8 Consensus size: 61
13200397 TTATAAAAGG
* *
13200407 CATTTATGTAATTATAATAAAAGAGTATTATAGTAATTTTGATCAATTATGGT-GGA-GTGA
1 CATTTATGTAATTATGATAAAAGAGTATTATAATAATTTTGATCAATTATGGTGGGATG-GA
* * * ** * *
13200467 CATTTTTGTAAGTATGGT-AGGGAGATATTATAATAATTTTGGTCAATTATGGTGGGATGGG
1 CATTTATGTAATTATGATAAAAGAG-TATTATAATAATTTTGATCAATTATGGTGGGATGGA
* * *
13200528 CATTTCTATAATTATGATAAAATG-GTATTACAATAATTTTGA-CTAATTATG
1 CATTTATGTAATTATGATAAAA-GAGTATTATAATAATTTTGATC-AATTATG
13200579 AAAAAAGCGA
Statistics
Matches: 89, Mismatches: 17, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
59 4 0.04
60 41 0.46
61 40 0.45
62 3 0.03
63 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.41
Consensus pattern (61 bp):
CATTTATGTAATTATGATAAAAGAGTATTATAATAATTTTGATCAATTATGGTGGGATGGA
Found at i:13203356 original size:22 final size:22
Alignment explanation
Indices: 13203331--13203375 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
13203321 TTTTTTCTTG
*
13203331 ATTTATTTTTCAAGTTTTTAAT
1 ATTTATTTTTCAAGCTTTTAAT
13203353 ATTTATTTTTCAAGCTTTTAAT
1 ATTTATTTTTCAAGCTTTTAAT
13203375 A
1 A
13203376 CTCTATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTTATTTTTCAAGCTTTTAAT
Found at i:13206899 original size:20 final size:17
Alignment explanation
Indices: 13206828--13206886 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
13206818 AATGAAGTGA
*
13206828 AAAAGAAATGATAAAAAT
1 AAAA-AAATGAAAAAAAT
* *
13206846 AAGAATAAGGAAAATAAAT
1 AA-AAAAATGAAAA-AAAT
13206865 AAAAAAATG-AAAAAAT
1 AAAAAAATGAAAAAAAT
13206881 AAAAAA
1 AAAAAA
13206887 GATGTGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 10 0.29
17 3 0.09
18 13 0.38
19 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (17 bp):
AAAAAAATGAAAAAAAT
Found at i:13208327 original size:44 final size:46
Alignment explanation
Indices: 13208255--13208361 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 46
13208245 GGAGCCATTA
* *
13208255 TTTTTAAAGTTGTGAGCCTCTATTTAAAA-GAACTTTTTATATATG
1 TTTTTAAAGTTGTAAGCCTCTATATAAAATGAACTTTTTATATATG
*
13208300 TTTTT-AAGTTGTTAAGCCTCTA-ATAAAATGAGC-TTTT-TATAT-
1 TTTTTAAAGTTG-TAAGCCTCTATATAAAATGAACTTTTTATATATG
*
13208342 TTTTCAAAGTTGCTAAGCCT
1 TTTTTAAAGTTG-TAAGCCT
13208362 TTGTCCATGG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.07
43 18 0.33
44 15 0.28
45 17 0.31
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (46 bp):
TTTTTAAAGTTGTAAGCCTCTATATAAAATGAACTTTTTATATATG
Found at i:13208742 original size:44 final size:43
Alignment explanation
Indices: 13208675--13208855 Score: 177
Period size: 44 Copynumber: 4.1 Consensus size: 43
13208665 TTTTTAAATA
* * * **
13208675 TGAATCTTTGACGTGAATATTTAAAATTTTCAAATGAAAACCTT
1 TGAATCTTGGATGTGAATCTTTAAAATTTT-AAATGTGAACCTT
* *
13208719 TGAATCTTGGATGTGAATTTTTAAGAA-TTTGAATGTGAACCTT
1 TGAATCTTGGATGTGAATCTTTAA-AATTTTAAATGTGAACCTT
* *
13208762 TGAA-CTTTGGATGTAAATCTTTAAAAGTTTTGAATGTGAACCTT
1 TGAATC-TTGGATGTGAATCTTTAAAA-TTTTAAATGTGAACCTT
* * * **
13208806 TGAATCTTAGATGTGAACCTTTAAGATTTTCAAATGTGAATATT
1 TGAATCTTGGATGTGAATCTTTAAAATTTT-AAATGTGAACCTT
13208850 TGAATC
1 TGAATC
13208856 CTTGCGAATA
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
42 3 0.03
43 34 0.29
44 76 0.66
45 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (43 bp):
TGAATCTTGGATGTGAATCTTTAAAATTTTAAATGTGAACCTT
Found at i:13208775 original size:21 final size:20
Alignment explanation
Indices: 13208713--13208827 Score: 86
Period size: 21 Copynumber: 5.3 Consensus size: 20
13208703 TTCAAATGAA
13208713 AACCTTTGAATCTTGGATGTG
1 AACCTTTGAAT-TTGGATGTG
** *
13208734 AATTTTTAAGAATTTGAATGTG
1 AACCTTT--GAATTTGGATGTG
*
13208756 AACCTTTGAACTTTGGATGTA
1 AACCTTTGAA-TTTGGATGTG
* * *
13208777 AATCTTTAAAAGTTTTGAATGTG
1 AACCTTT-GAA--TTTGGATGTG
*
13208800 AACCTTTGAATCTTAGATGTG
1 AACCTTTGAAT-TTGGATGTG
13208821 AACCTTT
1 AACCTTT
13208828 AAGATTTTCA
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
20 4 0.06
21 33 0.46
22 17 0.24
23 18 0.25
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
AACCTTTGAATTTGGATGTG
Found at i:13208969 original size:89 final size:89
Alignment explanation
Indices: 13208865--13209121 Score: 363
Period size: 89 Copynumber: 2.9 Consensus size: 89
13208855 CCTTGCGAAT
* * *
13208865 ATTTGAATCTCTTTGAAATCTTTGCAAATCTTGAATCACTTACGAATATTTGAATCGTAAATTTT
1 ATTTGAATCTATTTGAAATCTTTGCAAATCTTGAATCACTTACGAATCTTTGAATCTTAAATTTT
* *
13208930 TGTGAATTTTTTAACTTTTGA-AA
66 TGTGAATCTTTGAACTTTTGAGAA
* * * *
13208953 ATTTTGAATCTATTTGAAATCTTTGCAAATCTTGAATCACTTGCAAATCTTTGAATATTAAAATT
1 A-TTTGAATCTATTTGAAATCTTTGCAAATCTTGAATCACTTACGAATCTTTGAATCTTAAATTT
*
13209018 TTGTGAATCTTTGAATTTTTGAGAA
65 TTGTGAATCTTTGAACTTTTGAGAA
* * * * *
13209043 ATTTGAATCTTTTTGAAATCTTTGAAAATCTTAAATCATTTATGAATCTTTGAATCTTAAATTTT
1 ATTTGAATCTATTTGAAATCTTTGCAAATCTTGAATCACTTACGAATCTTTGAATCTTAAATTTT
13209108 TGTGAATCTTTGAA
66 TGTGAATCTTTGAA
13209122 ATCCTCATGA
Statistics
Matches: 148, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
88 1 0.01
89 144 0.97
90 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (89 bp):
ATTTGAATCTATTTGAAATCTTTGCAAATCTTGAATCACTTACGAATCTTTGAATCTTAAATTTT
TGTGAATCTTTGAACTTTTGAGAA
Found at i:13208977 original size:28 final size:28
Alignment explanation
Indices: 13208946--13209007 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
13208936 TTTTTTAACT
* *
13208946 TTTGAAAATTTTGAATCTATTTG-AAATC
1 TTTGAAAATCTTGAATC-ACTTGCAAATC
*
13208974 TTTGCAAATCTTGAATCACTTGCAAATC
1 TTTGAAAATCTTGAATCACTTGCAAATC
13209002 TTTGAA
1 TTTGAA
13209008 TATTAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (28 bp):
TTTGAAAATCTTGAATCACTTGCAAATC
Found at i:13209066 original size:19 final size:18
Alignment explanation
Indices: 13209016--13209068 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
13209006 AATATTAAAA
*
13209016 TTTTGTGAATCTTTGAAT
1 TTTTGAGAATCTTTGAAT
*
13209034 TTTTGAGAA-ATTTGAATCT
1 TTTTGAGAATCTTTGAA--T
13209053 TTTTGA-AATCTTTGAA
1 TTTTGAGAATCTTTGAA
13209069 AATCTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.21
18 10 0.34
19 13 0.45
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (18 bp):
TTTTGAGAATCTTTGAAT
Found at i:13209066 original size:28 final size:28
Alignment explanation
Indices: 13209027--13209122 Score: 96
Period size: 28 Copynumber: 3.5 Consensus size: 28
13209017 TTTGTGAATC
* *
13209027 TTTGAATTTTTGAGAAAT-TTGAATC-TT
1 TTTGAATCTTTGA-AAATCTTAAATCATT
13209054 TTTGAAATCTTTGAAAATCTTAAATCATT
1 TTTG-AATCTTTGAAAATCTTAAATCATT
*
13209083 TATGAATCTTTG--AATCTTAAAT--TT
1 TTTGAATCTTTGAAAATCTTAAATCATT
13209107 TTGTGAATCTTTGAAA
1 TT-TGAATCTTTGAAA
13209123 TCCTCATGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.05
25 10 0.17
26 10 0.17
27 9 0.15
28 22 0.37
29 5 0.08
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (28 bp):
TTTGAATCTTTGAAAATCTTAAATCATT
Found at i:13209071 original size:10 final size:9
Alignment explanation
Indices: 13208965--13209176 Score: 51
Period size: 10 Copynumber: 23.3 Consensus size: 9
13208955 TTTGAATCTA
13208965 TTTGAAATC
1 TTTGAAATC
13208974 TTTGCAAATC
1 TTTG-AAATC
13208984 -TTG-AATC
1 TTTGAAATC
*
13208991 ACTTGCAAATC
1 -TTTG-AAATC
13209002 TTTG-AAT-
1 TTTGAAATC
* *
13209009 ATTAAAAT-
1 TTTGAAATC
*
13209017 TTTGTGAATC
1 TTTG-AAATC
*
13209027 TTTG-AATT
1 TTTGAAATC
*
13209035 TTTGAGAA-A
1 TTTGA-AATC
13209044 TTTG-AATC
1 TTTGAAATC
13209052 TTTTTGAAATC
1 --TTTGAAATC
13209063 TTTGAAAATC
1 TTTG-AAATC
13209073 -TT-AAATC
1 TTTGAAATC
13209080 ATTT-ATGAATC
1 -TTTGA--AATC
13209091 TTTG-AATC
1 TTTGAAATC
*
13209099 -TT-AAATT
1 TTTGAAATC
*
13209106 TTTGTGAATC
1 TTTG-AAATC
13209116 TTTGAAATCC
1 TTTGAAAT-C
*
13209126 TCATG-AATC
1 T-TTGAAATC
*
13209135 TTTTATGAATC
1 TTTGA--AATC
13209146 TTTG-AATC
1 TTTGAAATC
*
13209154 TTTTACAACTC
1 TTTGA-AA-TC
13209165 TTTGAAATC
1 TTTGAAATC
13209174 TTT
1 TTT
13209177 TATGGATTTT
Statistics
Matches: 152, Mismatches: 19, Indels: 64
0.65 0.08 0.27
Matches are distributed among these distances:
7 18 0.12
8 29 0.19
9 36 0.24
10 42 0.28
11 27 0.18
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (9 bp):
TTTGAAATC
Found at i:13209151 original size:19 final size:20
Alignment explanation
Indices: 13209129--13209180 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
13209119 GAAATCCTCA
13209129 TGAATCTTTTATGAA-TCTT
1 TGAATCTTTTATGAACTCTT
*
13209148 TGAATCTTTTA-CAACTCTT
1 TGAATCTTTTATGAACTCTT
13209167 TGAAATCTTTTATG
1 TG-AATCTTTTATG
13209181 GATTTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 17 0.61
20 9 0.32
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (20 bp):
TGAATCTTTTATGAACTCTT
Found at i:13209264 original size:17 final size:19
Alignment explanation
Indices: 13209129--13209277 Score: 77
Period size: 18 Copynumber: 8.3 Consensus size: 19
13209119 GAAATCCTCA
* *
13209129 TGAATCTTTTATGAATCTT
1 TGAATCTTTTGTAAATCTT
** *
13209148 TGAATCTTTTACAACTCTT
1 TGAATCTTTTGTAAATCTT
* **
13209167 TGAAATCTTTTATGGAT-TT
1 TG-AATCTTTTGTAAATCTT
**
13209186 TTCAT-TTTT-TCAAAT-TT
1 TGAATCTTTTGT-AAATCTT
* *
13209203 TGAATCATTTGCAAATC-T
1 TGAATCTTTTGTAAATCTT
13209221 T-AAT-TTTTG-ATAATC-T
1 TGAATCTTTTGTA-AATCTT
*
13209237 TGAATCTTTTGTGAA-CTT
1 TGAATCTTTTGTAAATCTT
13209255 TGAA-CTTTTGTAAATCTT
1 TGAATCTTTTGTAAATCTT
13209273 TGAAT
1 TGAAT
13209278 TCAATTTATT
Statistics
Matches: 100, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
15 1 0.01
16 11 0.11
17 27 0.27
18 30 0.30
19 21 0.21
20 10 0.10
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (19 bp):
TGAATCTTTTGTAAATCTT
Found at i:13209444 original size:22 final size:22
Alignment explanation
Indices: 13209366--13209446 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
13209356 TGAATTTGGT
* * *
13209366 GAACTTTTGAACTTTAAGTTGA
1 GAACTTTTGAATTTTCAGTTGC
*
13209388 GAA-TTCTTGAA-TTTCAAATTGC
1 GAACTT-TTGAATTTTC-AGTTGC
* *
13209410 G-ATTGTTTAAATTTTCAGTTGC
1 GAACT-TTTGAATTTTCAGTTGC
13209432 GAACTTTTGAATTTT
1 GAACTTTTGAATTTT
13209447 AGCTGCAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 6 0.13
22 33 0.72
23 7 0.15
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (22 bp):
GAACTTTTGAATTTTCAGTTGC
Found at i:13209935 original size:21 final size:20
Alignment explanation
Indices: 13209909--13209948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
13209899 CCCATTAGGG
13209909 TCAATTAGAAACAATCAAGAA
1 TCAATTAGAAA-AATCAAGAA
*
13209930 TCAATTAGAAAAATGAAGA
1 TCAATTAGAAAAATCAAGA
13209949 GAGAAAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (20 bp):
TCAATTAGAAAAATCAAGAA
Found at i:13211813 original size:132 final size:127
Alignment explanation
Indices: 13211601--13212069 Score: 445
Period size: 132 Copynumber: 3.7 Consensus size: 127
13211591 TTGATATGAA
* ** *
13211601 AGTATTATAATAAATAATTATAAGAGAAGATGTATTTTATAATTATGGTAAAAGGGCATAACAGT
1 AGTATTATAGTAAATAATTATAAGAGAAGATGTATTTTATAATTAT-GTATGA-GGCATAATAGT
* *
13211666 CAATTTGGTTACATGTCAATTTCTTATCAAATAATAAAAAATGTATTTTGGTAATTTGGTAGGAA
64 CAATTTGGTCACATGTCAATTTCTTATCAAATAATAGAAAATGTATTTTGGTAATTT-GTA--AA
13211731 AG
126 AG
*
13211733 A-TATTATAGTAAATAATTATAAGAGAAGATGTATTTTCATAATTATAGTATGATTGCATAATAG
1 AGTATTATAGTAAATAATTATAAGAGAAGATGTATTTT-ATAATTAT-GTATGA-GGCATAATAG
** * * * *
13211797 TCAATTTGACCACATGTCAATTTTTTATCAAATGAT-GGAAATGATATTTTGGTAATTTCTTAAA
63 TCAATTTGGTCACATGTCAATTTCTTATCAAATAATAGAAAATG-TATTTTGGTAATTT-GTAAA
13211861 AG
126 AG
* * * *
13211863 AGGTATTATAGTAAATAA-TATAAAAGAAAAAGTATTTTGT-A--AT-TAT--GGCAT--T-G--
1 A-GTATTATAGTAAATAATTATAAGAGAAGATGTATTTTATAATTATGTATGAGGCATAATAGTC
* *
13211916 AATTTGGTCACATGTCAATTTCTTATCATATAATAGAAAAGGTATTTTGGTAATTT-TAAAAGG
65 AATTTGGTCACATGTCAATTTCTTATCAAATAATAGAAAATGTATTTTGGTAATTTGTAAAA-G
*
13211979 ATTATT-TAGTAAATAATTATAA-A-AA-ATGGATATTTTTATAATTATGTTATGAAGGCATAAT
1 AGTATTATAGTAAATAATTATAAGAGAAGAT-G-TA-TTTTATAATTATG-TATG-AGGCATAAT
* * *
13212040 ATTCCATTTGTTCACATGTCAATTTCTTAT
61 AGTCAATTTGGTCACATGTCAATTTCTTAT
13212070 TATAAATGGA
Statistics
Matches: 280, Mismatches: 34, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
112 1 0.00
113 3 0.01
114 13 0.05
115 19 0.07
116 3 0.01
117 43 0.15
118 7 0.03
119 1 0.00
120 4 0.01
122 4 0.01
123 5 0.02
125 4 0.01
127 2 0.01
128 24 0.09
129 1 0.00
130 6 0.02
131 57 0.20
132 83 0.30
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.39
Consensus pattern (127 bp):
AGTATTATAGTAAATAATTATAAGAGAAGATGTATTTTATAATTATGTATGAGGCATAATAGTCA
ATTTGGTCACATGTCAATTTCTTATCAAATAATAGAAAATGTATTTTGGTAATTTGTAAAAG
Found at i:13212121 original size:127 final size:126
Alignment explanation
Indices: 13211917--13212201 Score: 335
Period size: 125 Copynumber: 2.3 Consensus size: 126
13211907 ATGGCATTGA
* *
13211917 ATTTGGTCACATGTCAATTTCTTATCATATAATAGAAAAGGTATTTTGGTAATTTTAAAAGGATT
1 ATTTGGTCACATGTCAATTTCTTATCATATAATAGAAAAGGTAATTTGATAATTTTAAAAGGATT
* ** *
13211982 ATTTAGTAAATAATTATAAAAAATGGATATTTTTATAATTATGTTATGAAGGCATAATATTCC
66 ATTTAATAAATAATTATAAAAAA-GG-TATTTTTATAATTATAATATGAAGGCATAATAATCC
* * * * *
13212045 ATTTGTTCACATGTCAATTTCTTATTATA-AAT-GGAAAGG-ACATTTGAATAATTTTTAAGGGA
1 ATTTGGTCACATGTCAATTTCTTATCATATAATAGAAAAGGTA-ATTTG-ATAATTTTAAAAGGA
* * *
13212107 TTATTTAATAAATAATTATATAAAAGGTATTTTTGTAATTATAATATGATGGCATAATAATCC
64 TTATTTAATAAATAATTATAAAAAAGGTATTTTTATAATTATAATATGAAGGCATAATAATCC
* * * *
13212170 ATTTGGCCA-AGTGTCACTTTCTCATCAAATAA
1 ATTTGGTCACA-TGTCAATTTCTTATCATATAA
13212202 GGGGAATGAT
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
124 1 0.01
125 53 0.40
126 14 0.11
127 38 0.29
128 27 0.20
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (126 bp):
ATTTGGTCACATGTCAATTTCTTATCATATAATAGAAAAGGTAATTTGATAATTTTAAAAGGATT
ATTTAATAAATAATTATAAAAAAGGTATTTTTATAATTATAATATGAAGGCATAATAATCC
Found at i:13214353 original size:23 final size:23
Alignment explanation
Indices: 13214314--13214386 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 23
13214304 ATTCAATTAA
*
13214314 ATTAAATGAAC-TCGTTCATGAAT
1 ATTAAATGATCAT-GTTCATGAAT
*
13214337 ATTAAATGATCATGTTCACGAACAT
1 ATTAAATGATCATGTTCATG-A-AT
*
13214362 ATATAAATGAAT-ATGTCCATGAAT
1 AT-TAAATG-ATCATGTTCATGAAT
13214386 A
1 A
13214387 ATGAACAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
23 16 0.39
24 5 0.12
25 5 0.12
26 13 0.32
27 2 0.05
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
ATTAAATGATCATGTTCATGAAT
Found at i:13219405 original size:21 final size:20
Alignment explanation
Indices: 13219361--13219408 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
13219351 CTTATTTATT
*
13219361 TATAAAAAATTATATATTAA
1 TATATAAAATTATATATTAA
13219381 -ATATAAAATT-TCATATTAAA
1 TATATAAAATTAT-ATATT-AA
13219401 TATATAAA
1 TATATAAA
13219409 TAATCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 2 0.08
21 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATAAAATTATATATTAA
Found at i:13220396 original size:189 final size:189
Alignment explanation
Indices: 13220076--13220646 Score: 964
Period size: 189 Copynumber: 3.0 Consensus size: 189
13220066 TTTTGTTTTG
* *
13220076 AAATAATTTGTTGGACAAACAAAGCTCCAAACACCCCTAACATGGCCAAGTATGTCTTTAGAGCT
1 AAATAATTTGTTGGACAAACAAAGCTCCAAACACCCCTAACATGGCCAGGTATGTCTTTAGAACT
* *
13220141 GAAAGCTAAGGTTAGCACATCTACACCATCACTAATTTCAATTTCATTGAACA-TGCATCTCATA
66 GAAAGCTAAGGTTAGCACATCTACATCATCACCAATTTCAATTTCATTGAA-AGTGCATCTCATA
13220205 GTTATGTCATTTTAAAACATAAAATGCTTACATAAATAAATACGATATATTAAGATGCAT
130 GTTATGTCATTTTAAAACATAAAATGCTTACATAAATAAATACGATATATTAAGATGCAT
* *
13220265 AAATAATTTGTTGGACAAACAAAGCTTCAAACACCCCTAACATGGCCAGGTTTGTCTTTAGAACT
1 AAATAATTTGTTGGACAAACAAAGCTCCAAACACCCCTAACATGGCCAGGTATGTCTTTAGAACT
13220330 GAAAGCTAAGGTTAGCACATCTACATCATCACCAATTTCAATTTCATTGAAAGTGCATCTCATAG
66 GAAAGCTAAGGTTAGCACATCTACATCATCACCAATTTCAATTTCATTGAAAGTGCATCTCATAG
* *
13220395 TTATGTCGTTTTAAAACATAAAATGCTTAGATAAATAAATACGATATATTAAGATGCAT
131 TTATGTCATTTTAAAACATAAAATGCTTACATAAATAAATACGATATATTAAGATGCAT
* * *
13220454 AAATAATTTGTTGGACAAACAAAGCTCCAAACACCCCTAACATGGCTAGGTCTGTCTTTAGAACA
1 AAATAATTTGTTGGACAAACAAAGCTCCAAACACCCCTAACATGGCCAGGTATGTCTTTAGAACT
* * * * *
13220519 AAAAGCTAAGGTTAGCATATCTACATCATCATCAATTTCAATTTCATTGAACGCGCATCTCATAG
66 GAAAGCTAAGGTTAGCACATCTACATCATCACCAATTTCAATTTCATTGAAAGTGCATCTCATAG
* *
13220584 TTATGTCATTTTAAAACATAAAATGCTTACATAAATAAATAAGATATATTAAAATGCAT
131 TTATGTCATTTTAAAACATAAAATGCTTACATAAATAAATACGATATATTAAGATGCAT
13220643 AAAT
1 AAAT
13220647 GAGAAAGTAG
Statistics
Matches: 360, Mismatches: 21, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 1 0.00
189 359 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (189 bp):
AAATAATTTGTTGGACAAACAAAGCTCCAAACACCCCTAACATGGCCAGGTATGTCTTTAGAACT
GAAAGCTAAGGTTAGCACATCTACATCATCACCAATTTCAATTTCATTGAAAGTGCATCTCATAG
TTATGTCATTTTAAAACATAAAATGCTTACATAAATAAATACGATATATTAAGATGCAT
Found at i:13223443 original size:27 final size:27
Alignment explanation
Indices: 13223401--13223453 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
13223391 AAGGGAAACA
* *
13223401 AAATTATAGATTTATATATGTTAAAAG
1 AAATTATAGATATATAAATGTTAAAAG
13223428 AAATTATAGATATATAAATGTTAAAA
1 AAATTATAGATATATAAATGTTAAAA
13223454 ATATGAGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (27 bp):
AAATTATAGATATATAAATGTTAAAAG
Found at i:13224666 original size:14 final size:14
Alignment explanation
Indices: 13224625--13224672 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
13224615 AAAGTTACAT
13224625 ATTAAA-TATA-TA
1 ATTAAATTATATTA
* * *
13224637 AATAATTTAAATTA
1 ATTAAATTATATTA
13224651 ATTAAATTATATTA
1 ATTAAATTATATTA
13224665 ATTAAATT
1 ATTAAATT
13224673 TTATATTAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 21 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAAATTATATTA
Found at i:13225677 original size:14 final size:14
Alignment explanation
Indices: 13225660--13225686 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13225650 CACAGTATTA
13225660 GATAAAATATTTAT
1 GATAAAATATTTAT
13225674 GATAAAATATTTA
1 GATAAAATATTTA
13225687 AGAATGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
GATAAAATATTTAT
Found at i:13229419 original size:128 final size:128
Alignment explanation
Indices: 13229179--13229419 Score: 281
Period size: 128 Copynumber: 1.9 Consensus size: 128
13229169 AATTTTACAT
* * *
13229179 AAAATTGACAAAGTTCAATTTAAAATTTGAAGTACAAACACATATTACATTTTTAACATAAAAAT
1 AAAATTGACAAAGTTCAATTTAAAATATGAAGAACAAACAAATATTACATTTTTAACATAAAAAT
** * * **
13229244 GTTGTCATTGTAAACGAACATTGCATTTTTAACATAAAAAATGTCGTCATTGTTAGTTAACAC
66 GTCATCATTGTAAAAGAAAATTGCATTTTTAACATAAAAAACATCGTCATTGTTAGTTAACAC
* * * *
13229307 AAAATTGACCAATTTCAATTTAAAATATGAGGAACTAACAAATATTACATTTTTAACATAAAAAT
1 AAAATTGACAAAGTTCAATTTAAAATATGAAGAACAAACAAATATTACATTTTTAACATAAAAAT
* ** *
13229372 GTCATC-TT-TAAATATATAAATTGTGTTTTTTAACA-AAGAAACATCGTC
66 GTCATCATTGTAAA-AGA-AAATTG-CATTTTTAACATAAAAAACATCGTC
13229420 TTTAATACAT
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
126 4 0.04
127 3 0.03
128 77 0.83
129 9 0.10
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (128 bp):
AAAATTGACAAAGTTCAATTTAAAATATGAAGAACAAACAAATATTACATTTTTAACATAAAAAT
GTCATCATTGTAAAAGAAAATTGCATTTTTAACATAAAAAACATCGTCATTGTTAGTTAACAC
Found at i:13229662 original size:24 final size:23
Alignment explanation
Indices: 13229581--13229701 Score: 90
Period size: 24 Copynumber: 5.3 Consensus size: 23
13229571 TATATGAATG
*
13229581 ATGAAAA--TTAGATTTGTATAT
1 ATGAAAATTTTAGATTTGTATAA
* * *
13229602 ATGATAAATTTTGGAATTGCATAA
1 ATGA-AAATTTTAGATTTGTATAA
*
13229626 ATGATAAAATTTAGATTTGTATAA
1 ATGA-AAATTTTAGATTTGTATAA
* *
13229650 ATGAAAATTTTTA-ATGTGTATTA
1 ATGAAAA-TTTTAGATTTGTATAA
*
13229673 ATGAAAAATTTGTA-A-TTGTACAA
1 ATG-AAAATTT-TAGATTTGTATAA
13229696 ATGAAA
1 ATGAAA
13229702 CAATTTGGAA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
21 4 0.05
22 6 0.08
23 25 0.31
24 45 0.56
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.40
Consensus pattern (23 bp):
ATGAAAATTTTAGATTTGTATAA
Found at i:13229706 original size:24 final size:24
Alignment explanation
Indices: 13229643--13229723 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 24
13229633 AATTTAGATT
* * *
13229643 TGTATAAATG-AAAATTTTTAATG
1 TGTACAAATGAAAAATTTGTAATC
**
13229666 TGTATTAATGAAAAATTTGTAAT-
1 TGTACAAATGAAAAATTTGTAATC
*
13229689 TGTACAAATGAAACAATTTGGAATTC
1 TGTACAAATGAAA-AATTTGTAA-TC
13229715 TGTACAAAT
1 TGTACAAAT
13229724 TATATGTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
23 20 0.41
24 19 0.39
25 1 0.02
26 9 0.18
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (24 bp):
TGTACAAATGAAAAATTTGTAATC
Found at i:13231842 original size:25 final size:25
Alignment explanation
Indices: 13231813--13231869 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
13231803 TATTTTATAC
*
13231813 AACAAAAAATTTTAAGAACTCATAA
1 AACAAAAAATTTTAAGAACACATAA
* * *
13231838 AACAAATAATTTTAATAACACATGA
1 AACAAAAAATTTTAAGAACACATAA
13231863 AACAAAA
1 AACAAAA
13231870 TTCCTATCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.23
Consensus pattern (25 bp):
AACAAAAAATTTTAAGAACACATAA
Found at i:13235577 original size:10 final size:10
Alignment explanation
Indices: 13235550--13235638 Score: 62
Period size: 10 Copynumber: 8.7 Consensus size: 10
13235540 CATCAAATAA
13235550 AAAAATATAT
1 AAAAATATAT
13235560 AAAAATATA-
1 AAAAATATAT
13235569 AAAATATATAAT
1 AAAA-ATAT-AT
*
13235581 AGTAAATATA-
1 A-AAAATATAT
13235591 ATAAAATAGTAAT
1 A-AAAATA-T-AT
13235604 AAAAATA-AT
1 AAAAATATAT
13235613 AAATAATA-AT
1 AAA-AATATAT
*
13235623 AAAAA-AAAT
1 AAAAATATAT
13235632 AAAAATA
1 AAAAATA
13235639 AAAATTAGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
8 1 0.02
9 18 0.27
10 29 0.44
11 3 0.05
12 12 0.18
13 3 0.05
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAAATATAT
Found at i:13235590 original size:22 final size:21
Alignment explanation
Indices: 13235546--13235638 Score: 88
Period size: 22 Copynumber: 4.4 Consensus size: 21
13235536 AAGTCATCAA
*
13235546 ATAAAAAAATAT-ATAAAAAT
1 ATAAAAATATATAATAAAAAT
*
13235566 ATAAAAATATATAATAGTAAAT
1 ATAAAAATATATAATA-AAAAT
13235588 ATAATAAA-ATAGTAATAAAAAT
1 ATAA-AAATATA-TAATAAAAAT
13235610 AATAAATAATA-ATAA-AAAAA-
1 -ATAAA-AATATATAATAAAAAT
13235630 ATAAAAATA
1 ATAAAAATA
13235639 AAAATTAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
18 4 0.06
19 5 0.08
20 11 0.17
21 8 0.13
22 19 0.30
23 15 0.24
24 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
ATAAAAATATATAATAAAAAT
Found at i:13235610 original size:6 final size:6
Alignment explanation
Indices: 13235601--13235656 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
13235591 ATAAAATAGT
*
13235601 AATAAA AATAATA AATAAT AAT--A AA-AAA AATAAA AATAAA AATTAGAA
1 AATAAA AATAA-A AATAAA AATAAA AATAAA AATAAA AATAAA AA-TA-AA
13235649 AATAAA AA
1 AATAAA AA
13235657 AGAGAAATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 2 0.05
5 3 0.07
6 23 0.55
7 10 0.24
8 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:13235612 original size:32 final size:32
Alignment explanation
Indices: 13235552--13235638 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 32
13235542 TCAAATAAAA
13235552 AAATATATAAAAATATAAAAATATATAATAGT
1 AAATATATAAAAATATAAAAATATATAATAGT
13235584 AAATATAATAAAATAGTAATAAAAATA-ATAA-A-T
1 AAATAT-ATAAAA-A-T-ATAAAAATATATAATAGT
*
13235617 -AATA-ATAAAAAAAATAAAAATA
1 AAATATAT-AAAAATATAAAAATA
13235639 AAAATTAGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
28 9 0.18
30 3 0.06
31 4 0.08
32 10 0.20
33 7 0.14
34 2 0.04
35 5 0.10
36 9 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (32 bp):
AAATATATAAAAATATAAAAATATATAATAGT
Found at i:13235652 original size:54 final size:54
Alignment explanation
Indices: 13235550--13235652 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 54
13235540 CATCAAATAA
* * * * *
13235550 AAAAATATATAAAAATATAAAAATATATAATAGTAAATATAATAAAATAGTAAT
1 AAAAATATATAAAAATATAAAAATAAATAAAAATAAAAATAAGAAAATAGTAAT
*
13235604 AAAAATA-ATAAATAATAATAAAAA-AAATAAAAATAAAAATTAGAAAATA
1 AAAAATATATAAA-AAT-ATAAAAATAAATAAAAATAAAAATAAGAAAATA
13235653 AAAAAGAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
53 5 0.12
54 29 0.71
55 7 0.17
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (54 bp):
AAAAATATATAAAAATATAAAAATAAATAAAAATAAAAATAAGAAAATAGTAAT
Found at i:13243639 original size:3 final size:3
Alignment explanation
Indices: 13243631--13243668 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
13243621 TTAACAAAAG
*
13243631 TAA TAA TAA TAA TAA TTAA TAT TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA T
13243669 GTAATGACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:13243658 original size:22 final size:23
Alignment explanation
Indices: 13243631--13243673 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
13243621 TTAACAAAAG
13243631 TAATAATAATAATAAT-TAATAT
1 TAATAATAATAATAATGTAATAT
13243653 TAATAATAATAATAATGTAAT
1 TAATAATAATAATAATGTAAT
13243674 GACAATAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATAATAATAATAATGTAATAT
Found at i:13250741 original size:13 final size:14
Alignment explanation
Indices: 13250725--13250756 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
13250715 AAAAGAGATA
13250725 AAAAATAAAAAAT-
1 AAAAATAAAAAATG
13250738 AAAAATAAAAAATG
1 AAAAATAAAAAATG
13250752 AAAAA
1 AAAAA
13250757 GATTTAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAAATG
Found at i:13252022 original size:35 final size:35
Alignment explanation
Indices: 13251982--13252101 Score: 111
Period size: 35 Copynumber: 3.4 Consensus size: 35
13251972 CTCGTTGTTC
* *
13251982 TTTATTTCCTGACTTATCGCTTTGTCCCAGTCATT
1 TTTATTTCCTGACTTATGGCTTAGTCCCAGTCATT
* *
13252017 TTTATTTTCTGACTTGTGGCTTAGTCCCAGTC-TT
1 TTTATTTCCTGACTTATGGCTTAGTCCCAGTCATT
* * * *
13252051 TGTTGTTTCTTAACTTATGGCTTCA-TCCC-GATCATC
1 T-TTATTTCCTGACTTATGGCTT-AGTCCCAG-TCATT
*
13252087 TTTATTTTCTGACTT
1 TTTATTTCCTGACTT
13252102 GCGACTCAGT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
34 4 0.06
35 60 0.90
36 3 0.04
ACGTcount: A:0.14, C:0.23, G:0.13, T:0.50
Consensus pattern (35 bp):
TTTATTTCCTGACTTATGGCTTAGTCCCAGTCATT
Found at i:13252159 original size:36 final size:35
Alignment explanation
Indices: 13252082--13252202 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 35
13252072 TTCATCCCGA
* * * *
13252082 TCATC-TTTATTTTCTGACTTGCGACTCAGTCTCGG
1 TCATCTTTTATTTT-TAACTTGCGATTTAGTCTCAG
* *
13252117 TTATCTTTTATTTTCTAACTTGTGATTTAGTC-CTAG
1 TCATCTTTTATTTT-TAACTTGCGATTTAGTCTC-AG
* *
13252153 TCATCTTGTATCTTTTTACTTGCGATTTAGTCTCAG
1 TCATCTTTTAT-TTTTAACTTGCGATTTAGTCTCAG
13252189 TCAT-TTTTATTTTT
1 TCATCTTTTATTTTT
13252203 GATTTGTAGC
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
34 4 0.06
35 10 0.14
36 53 0.75
37 4 0.06
ACGTcount: A:0.17, C:0.18, G:0.12, T:0.53
Consensus pattern (35 bp):
TCATCTTTTATTTTTAACTTGCGATTTAGTCTCAG
Found at i:13252315 original size:21 final size:17
Alignment explanation
Indices: 13252289--13252347 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
13252279 GTTTTCAACT
13252289 AAAAAAAACTAAGCAAACA
1 AAAAAAAACTAA--AAACA
13252308 AAAAAAAACTAAAAACA
1 AAAAAAAACTAAAAACA
**
13252325 AAATAAAAAAAACAAAACA
1 AAA-AAAAACTA-AAAACA
13252344 AAAA
1 AAAA
13252348 CAATTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 8 0.22
18 7 0.19
19 21 0.58
ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05
Consensus pattern (17 bp):
AAAAAAAACTAAAAACA
Found at i:13252327 original size:14 final size:14
Alignment explanation
Indices: 13252318--13252347 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13252308 AAAAAAAACT
13252318 AAAAACAAAATAAA
1 AAAAACAAAATAAA
*
13252332 AAAAACAAAACAAA
1 AAAAACAAAATAAA
13252346 AA
1 AA
13252348 CAATTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAACAAAATAAA
Found at i:13252749 original size:30 final size:31
Alignment explanation
Indices: 13252715--13252773 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
13252705 AACAAATAAA
*
13252715 AAATAT-ATAAAATTA-TAAAAATATAATAGC
1 AAATATAATAAAA-TAGTAAAAAAATAATAGC
13252745 AAATATAATAAAATAGTAAAAAAATAATA
1 AAATATAATAAAATAGTAAAAAAATAATA
13252774 AATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (31 bp):
AAATATAATAAAATAGTAAAAAAATAATAGC
Found at i:13252827 original size:14 final size:13
Alignment explanation
Indices: 13252810--13252855 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
13252800 AAGAAAAAGG
13252810 AAAAGAGAAATTAA
1 AAAAGAGAAA-TAA
13252824 AAAA-AGAAATAA
1 AAAAGAGAAATAA
13252836 AAATTAG-GAAATAA
1 AAA--AGAGAAATAA
13252850 AAAAGA
1 AAAAGA
13252856 AATGGGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 8 0.29
13 5 0.18
14 15 0.54
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAAGAGAAATAA
Found at i:13253377 original size:1 final size:1
Alignment explanation
Indices: 13253371--13253405 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
13253361 CAACGAAATT
13253371 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13253406 GAGAAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13254417 original size:18 final size:18
Alignment explanation
Indices: 13254394--13254428 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13254384 ACTAAGATTG
13254394 CAAAAG-CAAAAGTAAAAA
1 CAAAAGCCAAAAG-AAAAA
13254412 CAAAAGCCAAAAGAAAA
1 CAAAAGCCAAAAGAAAA
13254429 GAAAACTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.71, C:0.14, G:0.11, T:0.03
Consensus pattern (18 bp):
CAAAAGCCAAAAGAAAAA
Found at i:13255216 original size:22 final size:22
Alignment explanation
Indices: 13255190--13255241 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
13255180 TTTGATTTTG
13255190 TTATTTATTAATTT-ATAATTT
1 TTATTTATTAATTTAATAATTT
13255211 TATATTTGA--AATTTAATAATTT
1 T-TATTT-ATTAATTTAATAATTT
13255233 TT-TTTATTA
1 TTATTTATTA
13255242 TTTTGGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 8 0.31
22 13 0.50
23 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTATTAATTTAATAATTT
Found at i:13255218 original size:29 final size:28
Alignment explanation
Indices: 13255174--13255232 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
13255164 AAATTAAATA
** *
13255174 TTATATTTTGATTTTGTTATTTATTAAT
1 TTATATTTTGATTTTGAAATTTAATAAT
13255202 TTATAATTTT-ATATTTGAAATTTAATAAT
1 TTAT-ATTTTGAT-TTTGAAATTTAATAAT
13255231 TT
1 TT
13255233 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TTATATTTTGATTTTGAAATTTAATAAT
Found at i:13256600 original size:14 final size:14
Alignment explanation
Indices: 13256522--13256613 Score: 50
Period size: 14 Copynumber: 6.9 Consensus size: 14
13256512 ACTAAAAACC
*
13256522 TAAAACCCTAAAGT
1 TAAAACCCTAAAAT
*
13256536 TAAAA-CCTTAAA-
1 TAAAACCCTAAAAT
* *
13256548 TATAA-CCTTAAAT
1 TAAAACCCTAAAAT
* * *
13256561 GAAACCCCAAAAAT
1 TAAAACCCTAAAAT
* * *
13256575 CAAAATCTTAAAAT
1 TAAAACCCTAAAAT
13256589 TAAAACCCT-AAA-
1 TAAAACCCTAAAAT
*
13256601 TATAACCCTAAAA
1 TAAAACCCTAAAA
13256614 CCCTAGGTGA
Statistics
Matches: 58, Mismatches: 17, Indels: 7
0.71 0.21 0.09
Matches are distributed among these distances:
12 19 0.33
13 13 0.22
14 26 0.45
ACGTcount: A:0.54, C:0.21, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAAACCCTAAAAT
Found at i:13257647 original size:7 final size:7
Alignment explanation
Indices: 13257635--13257659 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13257625 TCTTAAAAAT
13257635 AATAATA
1 AATAATA
13257642 AATAATA
1 AATAATA
13257649 AATAATA
1 AATAATA
13257656 AATA
1 AATA
13257660 TATATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:13267853 original size:262 final size:260
Alignment explanation
Indices: 13267332--13267854 Score: 791
Period size: 262 Copynumber: 2.0 Consensus size: 260
13267322 CATTACTAAA
*
13267332 ACATGATGATTTGAGCATAGATTAGGGCAGTCCTTAAGGTTAGCTTGGTCTTTTAAACTCTTCAT
1 ACATGATGATTTGAGCATAAATTAGGGCAGTCCTTAAGGTTAGCTTGGTCTTTTAAACTCTTCAT
* *
13267397 CACATCTTTTGGGGTTATGTCTAAGGTACTAGGGGTGTAAAAAATAGAGAGAGTTATCATTGTCA
66 CACATCTTTTGGGGTTATGCCTAAGGTACTAGGGGTGTAAAAAATAGAGAGAGTTATCATTATCA
* * *
13267462 TTAAAACCTCATGTTCTTTCATCACCATCATTATTCTCATCACCTTGGTTGGACATTTTGGTCTA
131 TCAAAACCTCATGCTCTTTCATCACCATCATTATTCTCATCACATTGGTTGGACATTTTGGTCTA
* * * *
13267527 TTTAAAACTCTAAGCTTGCTAGGCCCAAAAAGCCTTTTCGCTTGTTTACTTGGCTTTTAGAGTTT
196 CTTAAAACTCTAAACTTACTAGGCCCAAAAAGCCTTCTCGCTTGTTTACTTGGCTTTTAGAGTTT
*
13267592 ACATGATGA-TTGCAGCATAAATTAGGGCAGTCCTTAAGGTTAGCTTGGTCTTTTAAGCTCTTCA
1 ACATGATGATTTG-AGCATAAATTAGGGCAGTCCTTAAGGTTAGCTTGGTCTTTTAAACTCTTCA
*
13267656 TCACATCTTTTGGGGTTATGCCTAAGGTATTAGGGGTGTAAAAAGGA-ATGA-ACGAGTTATCAT
65 TCACATCTTTTGGGGTTATGCCTAAGGTACTAGGGGTGTAAAAA--ATA-GAGA-GAGTTATCAT
* ** * * *
13267719 TATCATCAAAACCTCCTGCTCTTTTTTCATCATCATTATTCTTATCACATTTGTTGGACATTTTG
126 TATCATCAAAACCTCATGCTCTTTCATCACCATCATTATTCTCATCACATTGGTTGGACATTTTG
* * *
13267784 GTCTACTTAAAACTCTAAACTTACTAGGCCCCAAAAGGCTTCTCGCTTGTTTGCTTGGCTTTTAG
191 GTCTACTTAAAACTCTAAACTTACTAGGCCCAAAAAGCCTTCTCGCTTGTTTACTTGGCTTTTAG
13267849 AGTTT
256 AGTTT
13267854 A
1 A
13267855 AGACGACCCT
Statistics
Matches: 237, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
259 3 0.01
260 100 0.42
261 2 0.01
262 132 0.56
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (260 bp):
ACATGATGATTTGAGCATAAATTAGGGCAGTCCTTAAGGTTAGCTTGGTCTTTTAAACTCTTCAT
CACATCTTTTGGGGTTATGCCTAAGGTACTAGGGGTGTAAAAAATAGAGAGAGTTATCATTATCA
TCAAAACCTCATGCTCTTTCATCACCATCATTATTCTCATCACATTGGTTGGACATTTTGGTCTA
CTTAAAACTCTAAACTTACTAGGCCCAAAAAGCCTTCTCGCTTGTTTACTTGGCTTTTAGAGTTT
Found at i:13268366 original size:15 final size:15
Alignment explanation
Indices: 13268341--13268382 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
13268331 TGTTTAAATA
*
13268341 GAAGGTCAAACAAAG
1 GAAGCTCAAACAAAG
*
13268356 GTAGCTCAAACAAAG
1 GAAGCTCAAACAAAG
13268371 GAAGCTCAAACA
1 GAAGCTCAAACA
13268383 GAAGCTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (15 bp):
GAAGCTCAAACAAAG
Found at i:13273500 original size:3 final size:3
Alignment explanation
Indices: 13273492--13273522 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
13273482 TTAGAAAAAC
*
13273492 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13273523 CATGAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:13284225 original size:19 final size:19
Alignment explanation
Indices: 13284201--13284315 Score: 63
Period size: 19 Copynumber: 5.9 Consensus size: 19
13284191 TAAACACGAT
13284201 ACGAATAAATATAAATAAC
1 ACGAATAAATATAAATAAC
* *
13284220 ACGAATATACATAAATAAAC
1 ACGAATAAATATAAAT-AAC
* ** *
13284240 ACGACT-AATATGGATATAT
1 ACGAATAAATATAAATA-AC
* * * *
13284259 ACGAATAGACATGACTAAC
1 ACGAATAAATATAAATAAC
* *
13284278 ACGAATATATACAAA-AAC
1 ACGAATAAATATAAATAAC
*
13284296 ACGACTAAAATAATAAATAA
1 ACGAAT-AAAT-ATAAATAA
13284316 TTATAAATTA
Statistics
Matches: 68, Mismatches: 22, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
18 9 0.13
19 39 0.57
20 18 0.26
21 2 0.03
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.21
Consensus pattern (19 bp):
ACGAATAAATATAAATAAC
Found at i:13284265 original size:29 final size:28
Alignment explanation
Indices: 13284216--13284303 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
13284206 TAAATATAAA
13284216 TAACACGAATATACATA-AATAAACACGAC
1 TAACACGAATAT--ATACAATAAACACGAC
* * * * *
13284245 TAATATGGATATATACGAATAGACATGAC
1 TAACACGAATATATAC-AATAAACACGAC
13284274 TAACACGAATATATACAA-AAACACGAC
1 TAACACGAATATATACAATAAACACGAC
13284301 TAA
1 TAA
13284304 AATAATAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
27 13 0.28
28 2 0.04
29 32 0.68
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.20
Consensus pattern (28 bp):
TAACACGAATATATACAATAAACACGAC
Found at i:13306148 original size:102 final size:102
Alignment explanation
Indices: 13305965--13306165 Score: 291
Period size: 102 Copynumber: 2.0 Consensus size: 102
13305955 AATATTAGTA
*
13305965 AATTAATTTTAAAAGATAAAAAGATACATATTTAAATTATATATAAATTATTAGAAAAATAATTT
1 AATTAATTTTAAAAGATAAAAAGATACATATTTAAACTATATATAAATTATTAGAAAAATAATTT
* *
13306030 TGGATAACTTAAAATTTTTAAATATTTTTATTTAATT
66 TGGATAACTTAAAATTTTAAAATAATTTTATTTAATT
* * * *
13306067 AATTAATTTTATAAGATAAAAAGATATATATTTAAACTATATATATAA-TATTTA-AAAATTACT
1 AATTAATTTTAAAAGATAAAAAGATACATATTTAAACTATATATA-AATTA-TTAGAAAAATAAT
13306130 TTTGGATAAC-TAATAATTTTAAAATAATTTTATTTA
64 TTTGGATAACTTAA-AATTTTAAAATAATTTTATTTA
13306166 TGTGATAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
101 3 0.03
102 81 0.91
103 5 0.06
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (102 bp):
AATTAATTTTAAAAGATAAAAAGATACATATTTAAACTATATATAAATTATTAGAAAAATAATTT
TGGATAACTTAAAATTTTAAAATAATTTTATTTAATT
Found at i:13307103 original size:24 final size:24
Alignment explanation
Indices: 13307076--13307122 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13307066 AAATTGTTTT
*
13307076 TAAATCAAATAATATT-TTTATTAA
1 TAAAT-AAATAAAATTATTTATTAA
*
13307100 TAAATAATTAAAATTATTTATTA
1 TAAATAAATAAAATTATTTATTA
13307123 GTTTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATAAATAAAATTATTTATTAA
Found at i:13307104 original size:19 final size:19
Alignment explanation
Indices: 13307041--13307107 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
13307031 TATTTATAAA
*
13307041 ATTAATAAATAATTAATTTT
1 ATTAATAAATAA-TATTTTT
* *
13307061 -TTATTAAAT--TGTTTTT
1 ATTAATAAATAATATTTTT
13307077 A--AATCAAATAATATTTTT
1 ATTAAT-AAATAATATTTTT
13307095 ATTAATAAATAAT
1 ATTAATAAATAAT
13307108 TAAAATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
15 2 0.06
16 9 0.25
18 7 0.19
19 15 0.42
20 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
ATTAATAAATAATATTTTT
Found at i:13307168 original size:32 final size:32
Alignment explanation
Indices: 13307092--13307170 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
13307082 AAATAATATT
*
13307092 TTTATTA-ATAAATAATTAAAATTATTTATTAG
1 TTTATTATAT-AATAATTAAAATTATTTATTAA
*
13307124 TTTATTATATAATAA-TAAATTTTATTTATTAA
1 TTTATTATATAATAATTAAA-ATTATTTATTAA
13307156 TTTATTATATAATAA
1 TTTATTATATAATAA
13307171 AATTCATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 4 0.09
32 37 0.86
33 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTATTATATAATAATTAAAATTATTTATTAA
Found at i:13307179 original size:29 final size:28
Alignment explanation
Indices: 13307103--13307179 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 28
13307093 TTATTAATAA
*
13307103 ATAATTAAAATTATTTATTAGTTTATTAT
1 ATAA-TAAAATTATTTATTAATTTATTAT
13307132 ATAATAATAAATTTTATTTATTAATTTATTAT
1 ATAAT-A-AAA--TTATTTATTAATTTATTAT
13307164 ATAATAAAATTCATTT
1 ATAATAAAATT-ATTT
13307180 TTATATTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 3 0.07
29 9 0.21
30 6 0.14
31 1 0.02
32 23 0.55
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
ATAATAAAATTATTTATTAATTTATTAT
Found at i:13307432 original size:2 final size:2
Alignment explanation
Indices: 13307425--13307453 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13307415 GTTATTTTTA
13307425 AT 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 AT A
13307454 AAACTATCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13308360 original size:57 final size:54
Alignment explanation
Indices: 13308296--13308411 Score: 128
Period size: 57 Copynumber: 2.1 Consensus size: 54
13308286 AATATCCCCC
* *
13308296 TTATAAATG-TCAAATCATTATAATACCTTTATATCTTA-AATGATGAAAATACTTCTT
1 TTATAAATGAT-AAATCACTATAATA--TTTATATATTATAATGATGAAAATA--TCTT
* * *
13308353 TTATAAATGATAAATTACTATAATATTTTTATATTATAATTATGAAAATATCTT
1 TTATAAATGATAAATCACTATAATATTTATATATTATAATGATGAAAATATCTT
13308407 TTATA
1 TTATA
13308412 CCATAATTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
54 9 0.17
55 9 0.17
56 12 0.23
57 21 0.40
58 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (54 bp):
TTATAAATGATAAATCACTATAATATTTATATATTATAATGATGAAAATATCTT
Found at i:13309088 original size:9 final size:9
Alignment explanation
Indices: 13309076--13309235 Score: 61
Period size: 9 Copynumber: 16.7 Consensus size: 9
13309066 CTAAGTTTTT
13309076 TTTAAAAAA
1 TTTAAAAAA
**
13309085 TTTAAAATTT
1 TTTAAAA-AA
* *
13309095 TTTTAAAGA
1 TTTAAAAAA
13309104 -TTAAAAAA
1 TTTAAAAAA
*
13309112 TTCTAAAAAT
1 TT-TAAAAAA
*
13309122 TTTAAATAAT
1 TTTAAA-AAA
*
13309132 TCTTAAAATA
1 T-TTAAAAAA
*
13309142 TTAAAAAAA
1 TTTAAAAAA
**
13309151 TTTTAAAACT
1 -TTTAAAAAA
**
13309161 TTTTTAAAA
1 TTTAAAAAA
13309170 TTTAAAAAA
1 TTTAAAAAA
* *
13309179 GTAAAAAAA
1 TTTAAAAAA
*
13309188 GTGTAAAAAAA
1 -T-TTAAAAAA
13309199 TATTAAAAATA
1 T-TTAAAAA-A
*
13309210 TTAAAAAAAA
1 TT-TAAAAAA
*
13309220 TTTTAAAAA
1 TTTAAAAAA
13309229 TTCTAAA
1 TT-TAAA
13309236 CTTTTTTTAA
Statistics
Matches: 110, Mismatches: 30, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
8 6 0.05
9 44 0.40
10 40 0.36
11 20 0.18
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:13309109 original size:18 final size:20
Alignment explanation
Indices: 13309058--13309101 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13309048 TTTTAAATTC
* **
13309058 TAAAAAATCTAAGTTTTTTT
1 TAAAAAATTTAAAATTTTTT
13309078 TAAAAAATTTAAAATTTTTT
1 TAAAAAATTTAAAATTTTTT
13309098 TAAA
1 TAAA
13309102 GATTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAAAAATTTAAAATTTTTT
Found at i:13309110 original size:19 final size:20
Alignment explanation
Indices: 13309072--13309110 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
13309062 AAATCTAAGT
*
13309072 TTTTTTTAAAAAATTTAAAA
1 TTTTTTTAAAAAATTAAAAA
*
13309092 TTTTTTT-AAAGATTAAAAA
1 TTTTTTTAAAAAATTAAAAA
13309111 ATTCTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TTTTTTTAAAAAATTAAAAA
Done.