Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:1222907 original size:2 final size:2
Alignment explanation
Indices: 1222896--1222940 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
1222886 TGGATTAGTA
*
1222896 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
1222938 AT A
1 AT A
1222941 CATGAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1223160 original size:18 final size:17
Alignment explanation
Indices: 1223137--1223184 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1223127 AATATAGATA
1223137 TAAATATAATAAAATTAT
1 TAAATATAATAAAATT-T
* *
1223155 TAAATATATTTTAAATTT
1 TAAATATA-ATAAAATTT
1223173 TAAATATGAATA
1 TAAATAT-AATA
1223185 TAATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATATAATAAAATTT
Found at i:1224493 original size:6 final size:6
Alignment explanation
Indices: 1224477--1224521 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1224467 GGATTATGGA
* * * *
1224477 ATATGT ATACAT ATACAT ACATAT ATATAT ATATAT ATATAT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
1224522 CAGCCCTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:1224504 original size:4 final size:4
Alignment explanation
Indices: 1224477--1224521 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
1224467 GGATTATGGA
* * * *
1224477 ATAT GTAT ACAT ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1224522 CAGCCCTATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (4 bp):
ATAT
Found at i:1224763 original size:12 final size:12
Alignment explanation
Indices: 1224740--1224773 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1224730 ATTAAAAATT
*
1224740 ATATATAATTAA
1 ATATAAAATTAA
*
1224752 ATTTAAAATTAA
1 ATATAAAATTAA
1224764 ATATAAAATT
1 ATATAAAATT
1224774 TAAACTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAAAATTAA
Found at i:1224768 original size:26 final size:26
Alignment explanation
Indices: 1224739--1224802 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1224729 TATTAAAAAT
1224739 TATATATAATTAAA-TTTAAAATTAAA
1 TATATA-AATTAAACTTTAAAATTAAA
**
1224765 TATA-AAATTTAAACTTTTTAATTAAA
1 TATATAAA-TTAAACTTTAAAATTAAA
*
1224791 TAAATAAATTAA
1 TATATAAATTAA
1224803 TTAATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 2 0.06
25 6 0.19
26 21 0.66
27 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TATATAAATTAAACTTTAAAATTAAA
Found at i:1224825 original size:19 final size:20
Alignment explanation
Indices: 1224769--1224827 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
1224759 ATTAAATATA
*
1224769 AAATTTAAACT-TTTTAATT
1 AAATTTAAACTAATTTAATT
* *
1224788 AAATAAATAAATTAA-TTAATT
1 AAAT--TTAAACTAATTTAATT
1224809 AAATTTAAA-TAATTTAATT
1 AAATTTAAACTAATTTAATT
1224828 TTTAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.09
19 14 0.44
21 15 0.47
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTTAAACTAATTTAATT
Found at i:1224832 original size:26 final size:26
Alignment explanation
Indices: 1224735--1224832 Score: 66
Period size: 26 Copynumber: 3.9 Consensus size: 26
1224725 TTAGTATTAA
* * **
1224735 AAATTATATATAATTAAATTTAAAATT
1 AAATT-TAAATAATTTAATTTTTAATT
*
1224762 AAATAT-AA-AATTTAAACTTTTTAATT
1 AAATTTAAATAATTT-AA-TTTTTAATT
*
1224788 AAA--TAAATAAATTAA---TTAATT
1 AAATTTAAATAATTTAATTTTTAATT
1224809 AAATTTAAATAATTTAATTTTTAA
1 AAATTTAAATAATTTAATTTTTAA
1224833 AAATTAAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
21 9 0.16
23 11 0.20
24 5 0.09
25 7 0.13
26 19 0.35
27 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTTAAATAATTTAATTTTTAATT
Found at i:1224839 original size:23 final size:23
Alignment explanation
Indices: 1224782--1224840 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
1224772 TTTAAACTTT
1224782 TTAATT-AAA-TAAATAAATTAA
1 TTAATTAAAATTAAATAAATTAA
* *
1224803 TTAATTAAATTTAAATAATTTAA
1 TTAATTAAAATTAAATAAATTAA
*
1224826 TT-TTTAAAAATTAAA
1 TTAATT-AAAATTAAA
1224841 CATTATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.19
22 4 0.13
23 21 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAATTAAAATTAAATAAATTAA
Found at i:1225457 original size:2 final size:2
Alignment explanation
Indices: 1225450--1225479 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1225440 AATCAGAAGA
1225450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1225480 CTTTCCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1226249 original size:2 final size:2
Alignment explanation
Indices: 1226242--1226266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1226232 AAATTAATTT
1226242 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1226267 CTTGATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1226745 original size:2 final size:2
Alignment explanation
Indices: 1226738--1226772 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1226728 ATAATTTCTC
1226738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1226773 TCTAAGTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1230467 original size:19 final size:18
Alignment explanation
Indices: 1230441--1230489 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1230431 TCATAATAGT
*
1230441 AAATATTATTTTTATAAA
1 AAATATTATTTTAATAAA
*
1230459 AATATATTAATATTAATAAA
1 AA-ATATT-ATTTTAATAAA
*
1230479 AAATAATATTT
1 AAATATTATTT
1230490 ATCCATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.20
19 9 0.36
20 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTATTTTAATAAA
Found at i:1231002 original size:3 final size:3
Alignment explanation
Indices: 1230988--1231019 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1230978 AGATAAACCT
*
1230988 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1231020 TCCTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1232893 original size:30 final size:30
Alignment explanation
Indices: 1232857--1232916 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1232847 TGCATGAATA
*
1232857 GAGCTCGGATGGTAAACTATGGATCGTGAC
1 GAGCTCGGATGGTAAACTATGGATAGTGAC
1232887 GAGCTCGGATGGTAAACTATGGATAGTGAC
1 GAGCTCGGATGGTAAACTATGGATAGTGAC
1232917 AAACTAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.23
Consensus pattern (30 bp):
GAGCTCGGATGGTAAACTATGGATAGTGAC
Found at i:1233098 original size:19 final size:19
Alignment explanation
Indices: 1233074--1233112 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1233064 GTATATTTAT
1233074 ATTTAACACTTACTTTTGA
1 ATTTAACACTTACTTTTGA
1233093 ATTTAACACTTACTTTTGA
1 ATTTAACACTTACTTTTGA
1233112 A
1 A
1233113 CTGATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTTAACACTTACTTTTGA
Found at i:1243885 original size:2 final size:2
Alignment explanation
Indices: 1243878--1243911 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1243868 TCCACCTTCA
*
1243878 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1243912 CAGAACAAAC
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1244580 original size:27 final size:27
Alignment explanation
Indices: 1244550--1244611 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
1244540 AAGTATTATC
*
1244550 ATTTAATATA-TATTTATTTATGTTTAA
1 ATTTAATATATTAATTATTTA-GTTTAA
*
1244577 ATTTTTAATATATTTAATTATTTAGTTTAT
1 A--TTTAATATA-TTAATTATTTAGTTTAA
1244607 ATTTA
1 ATTTA
1244612 TATTTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
27 1 0.03
28 4 0.14
29 9 0.31
30 6 0.21
31 9 0.31
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (27 bp):
ATTTAATATATTAATTATTTAGTTTAA
Found at i:1244958 original size:28 final size:28
Alignment explanation
Indices: 1244906--1244968 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1244896 ATTAAAAGTG
* *
1244906 TTATATT-TTTATTTATGCTAATCATAC
1 TTATATTAATTATTTATGCTAATCATAA
1244933 TTA-ATTAATTATATTAT-CTAACTCATAA
1 TTATATTAATTAT-TTATGCTAA-TCATAA
1244961 TTATATTA
1 TTATATTA
1244969 CTCATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.10
27 11 0.37
28 12 0.40
29 4 0.13
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.52
Consensus pattern (28 bp):
TTATATTAATTATTTATGCTAATCATAA
Found at i:1245040 original size:3 final size:3
Alignment explanation
Indices: 1245023--1245060 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
1245013 ATTAATTTTA
1245023 ATT A-T ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1245061 AAAATTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1247084 original size:2 final size:2
Alignment explanation
Indices: 1247079--1247111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1247069 ACACACAAAC
1247079 AT AT 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 AT AT A
1247112 GTGTTCAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1247783 original size:27 final size:26
Alignment explanation
Indices: 1247753--1247820 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
1247743 TATTTATTTT
1247753 ATATTATATTAAATTAAATTTAATTAA
1 ATATTATATTAAATTAAA-TTAATTAA
* * * *
1247780 ATATTTTAATAATTTAAATTAATTTA
1 ATATTATATTAAATTAAATTAATTAA
* *
1247806 ATTTTAAATTAAATT
1 ATATTATATTAAATT
1247821 TATATAATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATTATATTAAATTAAATTAATTAA
Found at i:1247821 original size:27 final size:25
Alignment explanation
Indices: 1247761--1247822 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 25
1247751 TTATATTATA
1247761 TTAAATTAAATTT-AATTAAATATT
1 TTAAATTAAATTTAAATTAAATATT
*
1247785 TT-AA-T-AATTTAAATTAATTTAATT
1 TTAAATTAAATTTAAATTAA-AT-ATT
1247809 TTAAATTAAATTTA
1 TTAAATTAAATTTA
1247823 TATAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
21 5 0.16
22 7 0.23
23 3 0.10
24 7 0.23
25 2 0.06
26 1 0.03
27 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAATTAAATTTAAATTAAATATT
Found at i:1252028 original size:24 final size:24
Alignment explanation
Indices: 1252001--1252052 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1251991 TTGATCTGAC
1252001 AATTCATTAATATATGTATAATCA
1 AATTCATTAATATATGTATAATCA
1252025 AATTCATTAATATATGTATAATCA
1 AATTCATTAATATATGTATAATCA
1252049 AATT
1 AATT
1252053 TTTATCCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
AATTCATTAATATATGTATAATCA
Found at i:1252183 original size:22 final size:22
Alignment explanation
Indices: 1252158--1252204 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1252148 TTTTAAACTC
* * *
1252158 AAACCCACTTTTTTTTTATTTT
1 AAACCCAATATTTTTTTAGTTT
*
1252180 AAACCTAATATTTTTTTAGTTT
1 AAACCCAATATTTTTTTAGTTT
1252202 AAA
1 AAA
1252205 ATGCTCAAAA
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:0.32, C:0.13, G:0.02, T:0.53
Consensus pattern (22 bp):
AAACCCAATATTTTTTTAGTTT
Found at i:1252603 original size:14 final size:14
Alignment explanation
Indices: 1252584--1252624 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1252574 TAATAAATTA
1252584 AAAAAATATATTTT
1 AAAAAATATATTTT
1252598 AAAAAATAT-TTTT
1 AAAAAATATATTTT
*
1252611 ATAAAAATTTATTT
1 A-AAAAATATATTT
1252625 AGAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 16 0.67
15 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:1259591 original size:33 final size:34
Alignment explanation
Indices: 1259529--1259592 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
1259519 TAAAATATAA
*
1259529 AAAAATATATTAATATTTATAATTAAATTTAAAT
1 AAAAATATATTAATATTTATAATAAAATTTAAAT
1259563 AAAAAT-T-TTAATTATTTA-AATAATAATTTA
1 AAAAATATATTAA-TATTTATAATAA-AATTTA
1259593 GATCCAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 8 0.30
33 13 0.48
34 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
AAAAATATATTAATATTTATAATAAAATTTAAAT
Found at i:1259944 original size:35 final size:36
Alignment explanation
Indices: 1259905--1259985 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 36
1259895 TAGTTATACA
1259905 AATATAATATATAAAAAAT-AATTAAAACATA-ATAT
1 AATATAATATA-AAAAAATGAATTAAAACATATATAT
* * * *
1259940 AATATAATATAAATATATGACTTAAAATATATATAT
1 AATATAATATAAAAAAATGAATTAAAACATATATAT
1259976 ATATATAATA
1 A-ATATAATA
1259986 CGATTTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 5 0.13
35 21 0.54
36 5 0.13
37 8 0.21
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (36 bp):
AATATAATATAAAAAAATGAATTAAAACATATATAT
Found at i:1262968 original size:30 final size:29
Alignment explanation
Indices: 1262927--1262984 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1262917 TAAAACTTAA
1262927 TAAAATAATATATAATGT-AATAAATTTTTC
1 TAAAATAATATATAAT-TAAAT-AATTTTTC
*
1262957 TAAAATCATATATAATTAAATAATTTTT
1 TAAAATAATATATAATTAAATAATTTTT
1262985 AACTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAAATAATATATAATTAAATAATTTTTC
Found at i:1263472 original size:24 final size:23
Alignment explanation
Indices: 1263423--1263485 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1263413 AAAATTTTAA
*
1263423 ATTAAATATATCATGTTAAATAT
1 ATTAAATATATCATATTAAATAT
* * *
1263446 ATTTAAATATATTATATTATATTT
1 A-TTAAATATATCATATTAAATAT
*
1263470 ATT-AATATATCGTATT
1 ATTAAATATATCATATT
1263486 TACGTCATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 11 0.33
23 3 0.09
24 19 0.58
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
ATTAAATATATCATATTAAATAT
Found at i:1263485 original size:22 final size:20
Alignment explanation
Indices: 1263443--1263485 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1263433 TCATGTTAAA
*
1263443 TATATTTAAATATATTATAT
1 TATATTTAAATATATCATAT
*
1263463 TATATTTATTAATATATCGTAT
1 TATATTTA--AATATATCATAT
1263485 T
1 T
1263486 TACGTCATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATTTAAATATATCATAT
Found at i:1268341 original size:20 final size:20
Alignment explanation
Indices: 1268295--1268344 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1268285 TTATCCAAAA
* * *
1268295 TATATTTTTTTAATAATATT
1 TATAATTTTATAATAATAGT
*
1268315 TAT-ATTTTATAATACTAGT
1 TATAATTTTATAATAATAGT
1268334 TATAATTTTAT
1 TATAATTTTAT
1268345 TTTTTAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATAATTTTATAATAATAGT
Found at i:1271392 original size:65 final size:65
Alignment explanation
Indices: 1271321--1271452 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
1271311 AATATAAAGG
*
1271321 ATAAACGAATACATAAAAAACATCTCCCCACCTTTGTTGCTCGAACTCGGGGGTGAGTATCTGAT
1 ATAAACGAATACATAAAAAACATCTCCCCACCTTTGTTGCTCGAACACGGGGGTGAGTATCTGAT
1271386 ATAAACGAATACATAAAAAACATCTCCCCACCTTTGTTGCTCGAACACGGGGGTGAGTATCTGAT
1 ATAAACGAATACATAAAAAACATCTCCCCACCTTTGTTGCTCGAACACGGGGGTGAGTATCTGAT
1271451 AT
1 AT
1271453 GGGTATGTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (65 bp):
ATAAACGAATACATAAAAAACATCTCCCCACCTTTGTTGCTCGAACACGGGGGTGAGTATCTGAT
Found at i:1271474 original size:17 final size:17
Alignment explanation
Indices: 1271442--1271475 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1271432 ACGGGGGTGA
* *
1271442 GTATCTGATATGGGTAT
1 GTATCTGACATAGGTAT
1271459 GTATCTGACATAGGTAT
1 GTATCTGACATAGGTAT
1271476 ACTCAATTTT
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:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (17 bp):
GTATCTGACATAGGTAT
Found at i:1275392 original size:5 final size:5
Alignment explanation
Indices: 1275372--1275432 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
1275362 TGATTTTACC
* *
1275372 TTAAT TTTAT TT--T TTAAT TTAAT TTAAT TTAAC TT-AT ATTAAT TTAAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT -TTAAT TT-AAT
*
1275421 TTGAT TTAAT TT
1 TTAAT TTAAT TT
1275433 TTTTATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 35 0.76
6 7 0.15
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:1277096 original size:86 final size:86
Alignment explanation
Indices: 1276979--1278081 Score: 651
Period size: 86 Copynumber: 13.1 Consensus size: 86
1276969 TATATCACTC
* * * * * *
1276979 ACTATTTATATTTTAATTACAATGAATATTGATGACAAAAAAATTAAAACCGCAAAATAATTAAA
1 ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAAA
1277044 TTTAACCATTACAAATCATCA
66 TTTAACCATTACAAATCATCA
* * ** *
1277065 ACTATTTACATTTTAATTATAATAAATATTGATGAC-AAAAAATTAAGATCGTAAAATAATTGAA
1 ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAAA
*
1277129 TTTAACCATTATAAATCATCA
66 TTTAACCATTACAAATCATCA
* * ** * * * *** * * *
1277150 TCTGTTTA-ACTTTT-GCTATAATAAATAATGATAACCAAAAAAGTCAAAATGGTATAATAACTG
1 ACTATTTACA-TTTTAATTATAATAAATATTGATAA-CAAAAAAATTAAAATCACAAAATAATTA
* * * *
1277213 AATTTAACCGTTATAAATAATTA
64 AATTTAACCATTACAAATCATCA
* * * ** * * * * *
1277236 ATTATTTATATTTTAATTATAATGAATATCAATAATAAAAAAATTAAAACCATACAATAATTGAA
1 ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAAA
*** * * *
1277301 TTTAAATGTTATAAGTCAACA
66 TTTAACCATTACAAATCATCA
* * ** * * * * * *
1277322 ATTGTTTATGTTTAAATTACAATAAATATTAATAACGAAAACAATTAATATCAC-AAATTATTAA
1 ACTATTTACATTTTAATTATAATAAATATTGATAAC-AAAAAAATTAAAATCACAAAATAATTAA
* * *
1277386 ATCTAAACATTAC-AATC-CCTA
65 ATTTAACCATTACAAATCATC-A
** * ** * * * **
1277407 GTTATGTACACCTTAATTACAATAAATATT-AGCAA-GAAAAAATTAAAATCGTAAAATAATTAA
1 ACTATTTACATTTTAATTATAATAAATATTGA-TAACAAAAAAATTAAAATCACAAAATAATTAA
* * *
1277470 ATTTAACTATTACAAATTACCA
65 ATTTAACCATTACAAATCATCA
* * * * * ** * * * *
1277492 ACTACTTACACTTT-ATCTA-ATTGAATATGGATAATGAAAAAATTAAAACCACATAATGACTAA
1 ACTATTTACATTTTAAT-TATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAA
* *
1277555 ATTTAACTATTACAAATCATTA
65 ATTTAACCATTACAAATCATCA
* * * * * ** *
1277577 ATTATTTATACTTTAATTATAATTAATATTAATGATGAAAAAAAGTAAAATCACAAAATAATTAA
1 ACTATTTACATTTTAATTATAATAAATATTGAT-AACAAAAAAATTAAAATCACAAAATAATTAA
* * *
1277642 ATTTAGCCATTA-TAAT-TTCTA
65 ATTTAACCATTACAAATCATC-A
** * * * * * * *
1277663 ACTATTTACATGATAATTACAATGAATATTAATAGCAGAAAAATTAAAATCACAAAATAACTCAA
1 ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAAA
1277728 TTTAACCATTACAAATCATCA
66 TTTAACCATTACAAATCATCA
* * * *
1277749 ACTATTTACGTTTTAATTATAATAAATATTGAT----AAAAAATT---A-GACAAAATAACTGAA
1 ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAAA
*
1277806 TTTAACAATTACAAATCAAT-A
66 TTTAACCATTACAAATC-ATCA
* ** * * * *
1277827 ACTATTTACACTTTAATTGCAATAGATATTGATAATGAAAAAAATTAAAATTACAAAATAATTGA
1 ACTATTTACATTTTAATTATAATAAATATTGATAA-CAAAAAAATTAAAATCACAAAATAATTAA
* * *
1277892 ATTTAATCATTATAAATCACCA
65 ATTTAACCATTACAAATCATCA
* * **
1277914 ACTATTTACACTTTAATTGTAACGAATATTGATAA-AAAAAAA-TAAAATCACAAAATAACTT-A
1 ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAA-TTAA
* *
1277976 GTTTAACCATTATAAATCA-C-
65 ATTTAACCATTACAAATCATCA
* * * *
1277996 AC--TTTA-A--TT-A-CA-ACT-AATATTGATGACAAAAAAAAATTACAAT-AGCAAAATAATT
1 ACTATTTACATTTTAATTATAATAAATATTGAT-A-ACAAAAAAATTAAAATCA-CAAAATAATT
*
1278051 AAATTTAAACATTAC-AATCATCA
63 AAATTTAACCATTACAAATCATCA
1278074 ACTATTTA
1 ACTATTTA
1278082 TACTTTAGAT
Statistics
Matches: 800, Mismatches: 175, Indels: 90
0.75 0.16 0.08
Matches are distributed among these distances:
73 9 0.01
74 2 0.00
75 1 0.00
76 16 0.02
77 27 0.03
78 60 0.08
79 4 0.00
80 8 0.01
82 9 0.01
83 21 0.03
84 82 0.10
85 199 0.25
86 240 0.30
87 122 0.15
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (86 bp):
ACTATTTACATTTTAATTATAATAAATATTGATAACAAAAAAATTAAAATCACAAAATAATTAAA
TTTAACCATTACAAATCATCA
Found at i:1277819 original size:78 final size:79
Alignment explanation
Indices: 1277714--1277952 Score: 250
Period size: 78 Copynumber: 2.9 Consensus size: 79
1277704 AATTAAAATC
* ** *
1277714 ACAAAATAACTCAATTTAACCATTACAAATCATCAACTATTTACGTTTTAATTATAATAAATATT
1 ACAAAATAACTGAATTTAA-CATTACAAATCATCAACTATTTACACTTTAATTGTAATAAATATT
1277779 GATAAAAAATT-A-G
65 GATAAAAAATTAATG
* *
1277792 ACAAAATAACTGAATTTAACAATTACAAATCAAT-AACTATTTACACTTTAATTGCAATAGATAT
1 ACAAAATAACTGAATTTAAC-ATTACAAATC-ATCAACTATTTACACTTTAATTGTAATAAATAT
*
1277856 TGATAATGAAAAAAATTAAAATT
64 TG---AT--AAAAAATT--AATG
* * * **
1277879 ACAAAATAATTGAATTTAATCATTATAAATCACCAACTATTTACACTTTAATTGTAACGAATATT
1 ACAAAATAACTGAATTTAA-CATTACAAATCATCAACTATTTACACTTTAATTGTAATAAATATT
1277944 GATAAAAAA
65 GATAAAAAA
1277953 AAATAAAATC
Statistics
Matches: 134, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
77 1 0.01
78 55 0.41
79 2 0.01
81 2 0.01
82 6 0.04
83 8 0.06
84 2 0.01
86 2 0.01
87 55 0.41
88 1 0.01
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (79 bp):
ACAAAATAACTGAATTTAACATTACAAATCATCAACTATTTACACTTTAATTGTAATAAATATTG
ATAAAAAATTAATG
Found at i:1277917 original size:87 final size:83
Alignment explanation
Indices: 1277792--1277995 Score: 250
Period size: 87 Copynumber: 2.4 Consensus size: 83
1277782 AAAAAATTAG
* * **
1277792 ACAAAATAACTGAATTTAACAATTACAAATCAATAACTATTTACACTTTAATTGCAATAG-ATAT
1 ACAAAATAATTGAATTTAAC-ATTATAAATCACCAACTATTTACACTTTAATTGCAA-AGAATAT
*
1277856 TGATAATGAAAAAAATTAAAATT
64 TGATAA--AAAAAAA-TAAAATC
* *
1277879 ACAAAATAATTGAATTTAATCATTATAAATCACCAACTATTTACACTTTAATTGTAACGAATATT
1 ACAAAATAATTGAATTTAA-CATTATAAATCACCAACTATTTACACTTTAATTGCAAAGAATATT
1277944 GATAAAAAAAAATAAAATC
65 GATAAAAAAAAATAAAATC
*
1277963 ACAAAATAACTT-AGTTTAACCATTATAAATCAC
1 ACAAAATAA-TTGAATTTAA-CATTATAAATCAC
1277996 ACTTTAATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
84 34 0.32
85 9 0.09
86 1 0.01
87 60 0.57
88 1 0.01
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (83 bp):
ACAAAATAATTGAATTTAACATTATAAATCACCAACTATTTACACTTTAATTGCAAAGAATATTG
ATAAAAAAAAATAAAATC
Found at i:1278064 original size:77 final size:73
Alignment explanation
Indices: 1277921--1278064 Score: 166
Period size: 77 Copynumber: 1.9 Consensus size: 73
1277911 CCAACTATTT
** * *
1277921 ACACTTTAATTGTAACGAATATTGATAAAAAAAAATAAAATCACAAAATAACTTAGTTTAACCAT
1 ACACTTTAATTACAACGAATATTGATAAAAAAAAATAAAATCACAAAATAACTTAATTTAAACAT
1277986 TATAAATC
66 TATAAATC
* *
1277994 ACACTTTAATTACAACTAATATTGATGACAAAAAAAAATTACAAT-AGCAAAATAA-TTAAATTT
1 ACACTTTAATTACAACGAATATTGAT---AAAAAAAAA-TAAAATCA-CAAAATAACTT-AATTT
1278057 AAACATTA
60 AAACATTA
1278065 CAATCATCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
73 23 0.39
76 12 0.20
77 24 0.41
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (73 bp):
ACACTTTAATTACAACGAATATTGATAAAAAAAAATAAAATCACAAAATAACTTAATTTAAACAT
TATAAATC
Found at i:1278286 original size:86 final size:83
Alignment explanation
Indices: 1278145--1278403 Score: 261
Period size: 86 Copynumber: 3.0 Consensus size: 83
1278135 ATTAATGAAA
* * * * * **
1278145 AAATAGTAAAATAATTGAATTTAATCGTTATAAATCATCAACTATTTATATTTTAATTATAACAA
1 AAATAGCAAAATAATTAAATTTAACCATTA-CAA--ATCAACTATTTATATTTTAATTATAATGA
1278210 ATATTGATAGCAAAAAAATTT
63 ATATTGATAGCAAAAAAATTT
* * * * * *
1278231 AAATCA-CAAAATAATTAAATTTTATCATTACAAATCACTGGCTATTTACACTTTAACTATAATG
1 AAAT-AGCAAAATAATTAAATTTAACCATTACAAATCA---ACTATTTATATTTTAATTATAATG
* * *
1278295 AATATTAAT-GACAAAAATATTA
62 AATATTGATAG-CAAAAAAATTT
* *
1278317 AAATAGCAAAATAATTAAATTTAACCATTGCAAATCAACTATTTATATTTTAATTACAATGAATA
1 AAATAGCAAAATAATTAAATTTAACCATTACAAATCAACTATTTATATTTTAATTATAATGAATA
*
1278382 TTGATAACAAAAAAATTT
66 TTGATAGCAAAAAAATTT
1278400 AAAT
1 AAAT
1278404 TGTAAAAAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
83 44 0.31
85 4 0.03
86 91 0.65
87 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (83 bp):
AAATAGCAAAATAATTAAATTTAACCATTACAAATCAACTATTTATATTTTAATTATAATGAATA
TTGATAGCAAAAAAATTT
Found at i:1278394 original size:83 final size:83
Alignment explanation
Indices: 1278181--1278403 Score: 268
Period size: 86 Copynumber: 2.7 Consensus size: 83
1278171 GTTATAAATC
** *
1278181 ATCAACTATTTATATTTTAATTATAACAAATATTGATAGCAAAAAAATTTAAATCACAAAATAAT
1 ATCAACTATTTATATTTTAATTATAATGAATATTGATAACAAAAAAATTTAAATCACAAAATAAT
* *
1278246 TAAATTTTATCATTACAA
66 TAAATTTAACCATTACAA
* * * * * * * *
1278264 ATCACTGGCTATTTACACTTTAACTATAATGAATATTAATGACAAAAATATTAAAAT-AGCAAAA
1 ATCA---ACTATTTATATTTTAATTATAATGAATATTGATAACAAAAAAATTTAAATCA-CAAAA
*
1278328 TAATTAAATTTAACCATTGCAA
62 TAATTAAATTTAACCATTACAA
*
1278350 ATCAACTATTTATATTTTAATTACAATGAATATTGATAACAAAAAAATTTAAAT
1 ATCAACTATTTATATTTTAATTATAATGAATATTGATAACAAAAAAATTTAAAT
1278404 TGTAAAAAAA
Statistics
Matches: 113, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
83 45 0.40
85 1 0.01
86 67 0.59
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (83 bp):
ATCAACTATTTATATTTTAATTATAATGAATATTGATAACAAAAAAATTTAAATCACAAAATAAT
TAAATTTAACCATTACAA
Found at i:1278412 original size:17 final size:17
Alignment explanation
Indices: 1278390--1278427 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1278380 TATTGATAAC
*
1278390 AAAAAAATTTAAATTGT
1 AAAAAAATTTAAATCGT
1278407 AAAAAAATTTAAATCGT
1 AAAAAAATTTAAATCGT
1278424 AAAA
1 AAAA
1278428 TAACTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (17 bp):
AAAAAAATTTAAATCGT
Found at i:1278578 original size:81 final size:81
Alignment explanation
Indices: 1278423--1278581 Score: 201
Period size: 81 Copynumber: 2.0 Consensus size: 81
1278413 ATTTAAATCG
* * * * * **
1278423 TAAAATAACTGAATTTAACTATTACAAATCACTAATTATTTATATTTTAATTATAATGAATATCA
1 TAAAACAACTAAATTTAACTATTACAAAGCACTAACTATTTATATTTTAATTACAAAAAATATCA
*
1278488 ATAATAAAAAAAATTA
66 ATAACAAAAAAAATTA
* * **
1278504 TAAAACAACTAAATTTAACTATTATAAAGCATTAACTATTTATATTTTAATTACAAAAAATATTG
1 TAAAACAACTAAATTTAACTATTACAAAGCACTAACTATTTATATTTTAATTACAAAAAATATCA
*
1278569 ATAGCAAAAAAAA
66 ATAACAAAAAAAA
1278582 CTTAAATCAT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (81 bp):
TAAAACAACTAAATTTAACTATTACAAAGCACTAACTATTTATATTTTAATTACAAAAAATATCA
ATAACAAAAAAAATTA
Found at i:1279899 original size:22 final size:22
Alignment explanation
Indices: 1279854--1279896 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1279844 TAAAGGAATG
*
1279854 GACCGAGAAAGAGAAGGTAGAA
1 GACCGAGAAAGAGAAGCTAGAA
*
1279876 GACCTAGAAAG-GAAGCTAGAA
1 GACCGAGAAAGAGAAGCTAGAA
1279897 AGATGGCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.12, G:0.33, T:0.07
Consensus pattern (22 bp):
GACCGAGAAAGAGAAGCTAGAA
Found at i:1280989 original size:21 final size:24
Alignment explanation
Indices: 1280957--1281002 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
1280947 GATATATATG
1280957 AAAAATATTATTAA-AAT-ATTAA
1 AAAAATATTATTAAGAATCATTAA
1280979 AAAAATA-TATTAAGAATCATTAA
1 AAAAATATTATTAAGAATCATTAA
1281002 A
1 A
1281003 TATTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 10 0.45
23 6 0.27
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAATATTATTAAGAATCATTAA
Found at i:1281534 original size:16 final size:19
Alignment explanation
Indices: 1281505--1281540 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1281495 AAATTCAAAT
1281505 TATATTATATTATT-CTTA
1 TATATTATATTATTACTTA
1281523 TATATTA-A-TATTACTTA
1 TATATTATATTATTACTTA
1281540 T
1 T
1281541 CATCCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATTACTTA
Found at i:1281600 original size:79 final size:79
Alignment explanation
Indices: 1281499--1281647 Score: 219
Period size: 79 Copynumber: 1.9 Consensus size: 79
1281489 TTGTCCAAAT
*
1281499 TCAAATTATATTATATTATTCTTATATATTAATATTACTTATCA-TCCCTTCAAGTTTTTCATAT
1 TCAAATTATATTATATTATTCTTATATATTAATATTACTTATCACT-CATTCAAGTTTTTCATAT
1281563 AATAGACATCAGAGA
65 AATAGACATCAGAGA
* * * * * *
1281578 TCAAATTATCTTATGTTGTTCTTGTATATTAATATTATTTGTCACTCATTCAAGTTTTTCATATA
1 TCAAATTATATTATATTATTCTTATATATTAATATTACTTATCACTCATTCAAGTTTTTCATATA
1281643 ATAGA
66 ATAGA
1281648 TAGGGAGTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 61 0.98
80 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.47
Consensus pattern (79 bp):
TCAAATTATATTATATTATTCTTATATATTAATATTACTTATCACTCATTCAAGTTTTTCATATA
ATAGACATCAGAGA
Found at i:1281732 original size:16 final size:15
Alignment explanation
Indices: 1281705--1281735 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1281695 ATATAAAAAT
1281705 ATTAAATTAATAATA
1 ATTAAATTAATAATA
1281720 ATTAAATTTAATAATA
1 ATTAAA-TTAATAATA
1281736 TATAATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAATTAATAATA
Found at i:1281793 original size:20 final size:20
Alignment explanation
Indices: 1281701--1281794 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
1281691 TTTAATATAA
*
1281701 AAATATTAAATTAATAATAATT
1 AAAT-TTAAATAAAT-ATAATT
*
1281723 AAATTT-AATAATATATAATC
1 AAATTTAAATAA-ATATAATT
* *
1281743 AAATATAAATAAAT-TTATT
1 AAATTTAAATAAATATAATT
* *
1281762 --ATTTATTTATAAATATGATT
1 AAATTTA--AATAAATATAATT
1281782 AAATTTAAATAAA
1 AAATTTAAATAAA
1281795 ATTTAATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
17 4 0.07
19 9 0.16
20 25 0.45
21 9 0.16
22 9 0.16
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (20 bp):
AAATTTAAATAAATATAATT
Found at i:1281805 original size:40 final size:41
Alignment explanation
Indices: 1281725--1281807 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 41
1281715 TAATAATTAA
*
1281725 ATTTAATAATATATAATCAAATATAAATAAATTTATTATTT
1 ATTTAATAATATATAATCAAATATAAATAAATTTAATATTT
* * *
1281766 ATTT-ATAA-ATATGATTAAATTTAAATAAAATTTAATATTT
1 ATTTAATAATATATAATCAAATATAAAT-AAATTTAATATTT
1281806 AT
1 AT
1281808 ATTTTAAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 15 0.41
40 18 0.49
41 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
ATTTAATAATATATAATCAAATATAAATAAATTTAATATTT
Found at i:1286872 original size:9 final size:9
Alignment explanation
Indices: 1286849--1286878 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1286839 TTGAAAAGTA
1286849 AAAATAAAT
1 AAAATAAAT
1286858 -AAATAAAT
1 AAAATAAAT
1286866 AAAATAAAT
1 AAAATAAAT
1286875 AAAA
1 AAAA
1286879 CAGGGGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1287546 original size:16 final size:16
Alignment explanation
Indices: 1287527--1287558 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1287517 TTTGAAATTC
1287527 AAAATAATTTAAATAA
1 AAAATAATTTAAATAA
*
1287543 AAAATATTTTAAATAA
1 AAAATAATTTAAATAA
1287559 TTAATCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAATTTAAATAA
Found at i:1287568 original size:23 final size:25
Alignment explanation
Indices: 1287528--1287577 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
1287518 TTGAAATTCA
*
1287528 AAATAATTTAAATAAAAAATATTTT
1 AAATAATTTAAATAAAAAATAATTT
*
1287553 AAATAA-TT-AATCAAAAATAATTT
1 AAATAATTTAAATAAAAAATAATTT
1287576 AA
1 AA
1287578 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 2 0.09
25 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATAATTTAAATAAAAAATAATTT
Found at i:1287715 original size:26 final size:26
Alignment explanation
Indices: 1287689--1287762 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 26
1287679 TGATTTAAAT
1287689 TTAAAATAATTT-AAATTTAAAATAA
1 TTAAAATAATTTAAAATTTAAAATAA
1287714 TTAAAAT--TTTAAATAATTTAAAATAA
1 TTAAAATAATTT-AA-AATTTAAAATAA
1287740 --AAAATAATTTAAAAATTTAAAAT
1 TTAAAATAATTT-AAAATTTAAAAT
1287763 TATTCTATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
23 3 0.07
24 5 0.11
25 18 0.41
26 18 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TTAAAATAATTTAAAATTTAAAATAA
Found at i:1287726 original size:17 final size:17
Alignment explanation
Indices: 1287681--1287762 Score: 107
Period size: 16 Copynumber: 4.9 Consensus size: 17
1287671 ATATTAATTG
1287681 ATTT-AAATTTAAAATA
1 ATTTAAAATTTAAAATA
1287697 ATTT-AAATTTAAAATA
1 ATTTAAAATTTAAAATA
*
1287713 A-TTAAAATTTTAAATA
1 ATTTAAAATTTAAAATA
**
1287729 ATTTAAAATAAAAAATA
1 ATTTAAAATTTAAAATA
1287746 ATTTAAAAATTTAAAAT
1 ATTT-AAAATTTAAAAT
1287763 TATTCTATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
15 2 0.04
16 29 0.51
17 16 0.28
18 10 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAAATTTAAAATA
Found at i:1288386 original size:25 final size:25
Alignment explanation
Indices: 1288338--1288386 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1288328 CATTATATAT
*
1288338 AATTAAATTAATAAAAATTTATTTA
1 AATTAAATTAATAAAAATTAATTTA
*
1288363 AATTTAATT-ATAAAAATATAATTT
1 AATTAAATTAATAAAAAT-TAATTT
1288387 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTAAATTAATAAAAATTAATTTA
Found at i:1291165 original size:16 final size:17
Alignment explanation
Indices: 1291127--1291167 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1291117 ATGATAAATG
*
1291127 AATTTAAATATTATATA
1 AATTTAAATATAATATA
*
1291144 AA-TTAAATA-AATTTA
1 AATTTAAATATAATATA
1291159 AATTTAAAT
1 AATTTAAAT
1291168 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATATAATATA
Found at i:1291682 original size:20 final size:19
Alignment explanation
Indices: 1291632--1291683 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1291622 TTCTTTTATT
* * *
1291632 TAATTTTAAATTTAATTAT
1 TAATATTAAATTTAACTAA
*
1291651 TTATATTAAAATTTAACTAA
1 TAATATT-AAATTTAACTAA
1291671 TAATAATTAAATT
1 TAAT-ATTAAATT
1291684 AAAATAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATATTAAATTTAACTAA
Found at i:1293678 original size:3 final size:3
Alignment explanation
Indices: 1293670--1293704 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1293660 TTGTCTAAAA
*
1293670 AAT AAT AAT AAT AAT AAT AAA AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1293705 ATAGGCTAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1293838 original size:2 final size:2
Alignment explanation
Indices: 1293831--1293866 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1293821 TTTGGATTGA
1293831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1293867 TAAATTGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1294333 original size:19 final size:20
Alignment explanation
Indices: 1294309--1294346 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1294299 GTATGAATTA
1294309 AAAATTATTTATA-TATTTC
1 AAAATTATTTATATTATTTC
*
1294328 AAAATTTTTTATATTATTT
1 AAAATTATTTATATTATTT
1294347 GCATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAATTATTTATATTATTTC
Found at i:1294608 original size:27 final size:27
Alignment explanation
Indices: 1294550--1294607 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1294540 TAATTTAAAA
**
1294550 TTTTTAAATTATATTTTTTTATCATAT
1 TTTTTAAATTATATTTTTCAATCATAT
1294577 TTTTTAAATT-TATTTTTCAATCCA-AT
1 TTTTTAAATTATATTTTTCAAT-CATAT
1294603 TTTTT
1 TTTTT
1294608 TTTTAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTTAAATTATATTTTTCAATCATAT
Found at i:1294739 original size:22 final size:22
Alignment explanation
Indices: 1294692--1294739 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1294682 ATATATTAAA
* * *
1294692 AAATATTTTTATATTAATATTT
1 AAATACTTTTATAATAAAATTT
1294714 -AATACTTTTATAATAAAATTT
1 AAATACTTTTATAATAAAATTT
1294735 AAATA
1 AAATA
1294740 AAATTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATACTTTTATAATAAAATTT
Found at i:1295267 original size:2 final size:2
Alignment explanation
Indices: 1295260--1295285 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1295250 ATTTATTCAA
1295260 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1295286 TTGAAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1295628 original size:21 final size:20
Alignment explanation
Indices: 1295586--1295633 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
1295576 TTTAAAATTC
* **
1295586 ATATTTATAATAATTATTAT
1 ATATTTATAATAAATACCAT
1295606 ATATTATATAATAAATACCAT
1 ATATT-TATAATAAATACCAT
*
1295627 ATCTTTA
1 ATATTTA
1295634 ATTATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTATAATAAATACCAT
Found at i:1295876 original size:5 final size:5
Alignment explanation
Indices: 1295852--1295961 Score: 53
Period size: 5 Copynumber: 20.6 Consensus size: 5
1295842 GGTTCCATAC
* * **
1295852 ATTTA GTTTAA ATTAA ATTTA ATTTA AAATA ATTT- -TTTA ATGATATA
1 ATTTA ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT--T-TA
* * * *
1295899 ATTTG ATTTG ATTTA ATTTA ATTTA AATTA TATTAAAA ATTTAAA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA -ATT--TA ATTT--A ATTTA
1295949 ATTTA ATTTA ATT
1 ATTTA ATTTA ATT
1295962 ATAAAATTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
3 3 0.04
5 57 0.71
6 6 0.08
7 9 0.11
8 5 0.06
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (5 bp):
ATTTA
Found at i:1295948 original size:30 final size:30
Alignment explanation
Indices: 1295913--1295969 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1295903 GATTTGATTT
1295913 AATTTAATTTAAATTATATTA-AAAATTTAA
1 AATTTAATTTAAATTA-ATTATAAAATTTAA
*
1295943 AATTTAATTTAATTTAATTATAAAATT
1 AATTTAATTTAAATTAATTATAAAATT
1295970 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTTAATTTAAATTAATTATAAAATTTAA
Found at i:1296034 original size:15 final size:16
Alignment explanation
Indices: 1296002--1296034 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1295992 TAAATTTAAA
1296002 TTTAAAATTTTATATT
1 TTTAAAATTTTATATT
*
1296018 TTTAATATTTT-TATT
1 TTTAAAATTTTATATT
1296033 TT
1 TT
1296035 CATATTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAAAATTTTATATT
Found at i:1297220 original size:3 final size:3
Alignment explanation
Indices: 1297212--1297252 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1297202 TTTATGAAAA
1297212 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1297253 AAAGGTGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1297370 original size:3 final size:3
Alignment explanation
Indices: 1297362--1297393 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1297352 GTGCTTTGCT
*
1297362 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1297394 TTCATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1297764 original size:9 final size:9
Alignment explanation
Indices: 1297750--1297783 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1297740 TAATGTTAAA
1297750 ATTTTTTAT
1 ATTTTTTAT
1297759 ATTTTTTAT
1 ATTTTTTAT
* *
1297768 ATATTTTAA
1 ATTTTTTAT
1297777 ATTTTTT
1 ATTTTTT
1297784 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:1304143 original size:27 final size:25
Alignment explanation
Indices: 1304083--1304143 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
1304073 TCGATTTTAA
*
1304083 TTATTATTTAATAATAAAAATATTT
1 TTATAATTTAATAATAAAAATATTT
*
1304108 TTATTTAATTTAATTATAAAAATAATATT
1 TTA--TAATTTAATAATAAAAAT-AT-TT
1304137 TTATAAT
1 TTATAAT
1304144 ATTATCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 3 0.10
27 20 0.67
28 2 0.07
29 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATAATTTAATAATAAAAATATTT
Found at i:1311908 original size:18 final size:18
Alignment explanation
Indices: 1311866--1311910 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1311856 AATGATGGAC
1311866 CACCATCATCATCAACAA
1 CACCATCATCATCAACAA
* * *
1311884 CAACATCATCATCACCAT
1 CACCATCATCATCAACAA
1311902 CACCATCAT
1 CACCATCAT
1311911 AGCAGCAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (18 bp):
CACCATCATCATCAACAA
Found at i:1313783 original size:24 final size:24
Alignment explanation
Indices: 1313741--1313795 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1313731 ATGAATAAAA
*
1313741 TATATATTAAATCTGTTATATTAAT
1 TATAT-TTAAATCTATTATATTAAT
* *
1313766 TATATTTAAATGTATTATATTTAT
1 TATATTTAAATCTATTATATTAAT
1313790 TATATT
1 TATATT
1313796 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATTTAAATCTATTATATTAAT
Found at i:1314226 original size:3 final size:3
Alignment explanation
Indices: 1314218--1314262 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
1314208 AAAAAGTTAC
* *
1314218 CTT CTT CTT CTT CTT CTT CTT CTT CTT CGT CTT CTT CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1314263 TCAATTTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:1315154 original size:42 final size:42
Alignment explanation
Indices: 1315095--1315178 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
1315085 AGTCTAAATT
*
1315095 TATTTGCAAAGTTTTGATAAATTTTTAATGTTTTCTTTTTTG
1 TATTTGCAAAATTTTGATAAATTTTTAATGTTTTCTTTTTTG
1315137 TATTTGCAAAATTTTGATAAATTTTTAATGTTTTCTTTTTTG
1 TATTTGCAAAATTTTGATAAATTTTTAATGTTTTCTTTTTTG
1315179 CCTCTGATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.60
Consensus pattern (42 bp):
TATTTGCAAAATTTTGATAAATTTTTAATGTTTTCTTTTTTG
Found at i:1318820 original size:15 final size:16
Alignment explanation
Indices: 1318783--1318814 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1318773 TTAGTCCCTG
1318783 ACCTTTTTATAAAGTT
1 ACCTTTTTATAAAGTT
1318799 ACCTTTTTATAAAGTT
1 ACCTTTTTATAAAGTT
1318815 TGTTTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
ACCTTTTTATAAAGTT
Found at i:1322510 original size:2 final size:2
Alignment explanation
Indices: 1322503--1322527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1322493 GGCTTCTAGG
1322503 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1322528 TTTTGCCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1329294 original size:2 final size:2
Alignment explanation
Indices: 1329281--1329317 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1329271 CTCTCCTGCA
*
1329281 AT AT AT AC 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 AT AT AT AT A
1329318 GTTGAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1331408 original size:29 final size:29
Alignment explanation
Indices: 1331374--1331451 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
1331364 TAACTAAATT
1331374 TAAAAATTTATTTTATAATTTATAAAATAA
1 TAAAAATTTATTTTATAATTTAT-AAATAA
*
1331404 TAAAAA-TTAATTTATAATTTATAAATAA
1 TAAAAATTTATTTTATAATTTATAAATAA
*
1331432 TAAAAATTAATTTTATAATT
1 TAAAAATTTATTTTATAATT
1331452 AAATTTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 12 0.27
29 26 0.59
30 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAAATTTATTTTATAATTTATAAATAA
Found at i:1331687 original size:2 final size:2
Alignment explanation
Indices: 1331680--1331708 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1331670 TCATTACATA
1331680 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
1331709 CAAGAATTAT
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:1331883 original size:24 final size:23
Alignment explanation
Indices: 1331838--1331883 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1331828 ATTGATATAT
*
1331838 TTTTAAATATAAATTTATAAATA
1 TTTTAAATATAAAATTATAAATA
1331861 TTTTAATATATAATAATTA-AAAT
1 TTTTAA-ATATAA-AATTATAAAT
1331884 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTTAAATATAAAATTATAAATA
Found at i:1331893 original size:10 final size:10
Alignment explanation
Indices: 1331875--1331925 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 10
1331865 AATATATAAT
1331875 AATTAAAATTA
1 AATT-AAATTA
1331886 AATTAAATTA
1 AATTAAATTA
1331896 AATT-AATTA
1 AATTAAATTA
1331905 AATATAAAAATT-
1 AAT-T--AAATTA
1331917 AATTAAATT
1 AATTAAATT
1331926 TTAAAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 13 0.36
10 11 0.31
11 5 0.14
12 3 0.08
13 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTAAATTA
Found at i:1331905 original size:4 final size:5
Alignment explanation
Indices: 1331875--1331925 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
1331865 AATATATAAT
1331875 AATTAA AATTA AATTA AATTA AATT- AATTA AATATAAA AATT- AATTA
1 AATT-A AATTA AATTA AATTA AATTA AATTA AAT-T--A AATTA AATTA
1331922 AATT
1 AATT
1331926 TTAAAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
4 8 0.20
5 22 0.55
6 5 0.12
7 1 0.03
8 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:1331905 original size:9 final size:9
Alignment explanation
Indices: 1331881--1331925 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
1331871 TAATAATTAA
1331881 AATTAAATT
1 AATTAAATT
1331890 AAATTAAATT
1 -AATTAAATT
1331900 AATTAAATAT
1 AATTAAAT-T
1331910 AA--AAATT
1 AATTAAATT
1331917 AATTAAATT
1 AATTAAATT
1331926 TTAAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 13 0.41
10 12 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:1331931 original size:17 final size:16
Alignment explanation
Indices: 1331877--1331933 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
1331867 TATATAATAA
1331877 TTAAAATTAAATTAAA-
1 TTAAAATT-AATTAAAT
1331893 TT-AAATTAATTAAAT
1 TTAAAATTAATTAAAT
*
1331908 ATAAAAATTAATTAAATT
1 -TTAAAATTAATTAAA-T
1331926 TTAAAATT
1 TTAAAATT
1331934 TTTAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 7 0.20
15 5 0.14
16 3 0.09
17 19 0.54
18 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAATTAATTAAAT
Found at i:1333625 original size:3 final size:3
Alignment explanation
Indices: 1333617--1333679 Score: 110
Period size: 3 Copynumber: 21.0 Consensus size: 3
1333607 TGCAGTTCAA
1333617 TAT TAT TAT CT-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1333662 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
1333680 GTCTCTCAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1337649 original size:26 final size:25
Alignment explanation
Indices: 1337628--1337716 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
1337618 TTAAATAGAG
1337628 TATTATAAATATAATA-AAAAATATA
1 TATTATAAATATAATATAAAAATA-A
* * *
1337653 AAATATTAATA-AATATAAAAATAA
1 TATTATAAATATAATATAAAAATAA
*
1337677 TATAATAAATATAATAT---AAT-A
1 TATTATAAATATAATATAAAAATAA
1337698 TATT-TAAATATAAT-TAAAA
1 TATTATAAATATAATATAAAA
1337717 CGACACATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.02
20 10 0.20
21 4 0.08
22 4 0.08
24 12 0.24
25 20 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TATTATAAATATAATATAAAAATAA
Found at i:1337681 original size:40 final size:40
Alignment explanation
Indices: 1337635--1337710 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1337625 GAGTATTATA
1337635 AATATAATAAA-A-AATATAAAATATTAATAAATATAAAAAT
1 AATATAATAAATATAATATAAAATATT--TAAATATAAAAAT
*
1337675 AATATAATAAATATAATATAATATATTTAAATATAA
1 AATATAATAAATATAATATAAAATATTTAAATATAA
1337711 TTAAAACGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
40 20 0.61
41 1 0.03
42 12 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (40 bp):
AATATAATAAATATAATATAAAATATTTAAATATAAAAAT
Found at i:1337692 original size:17 final size:18
Alignment explanation
Indices: 1337631--1337710 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 18
1337621 AATAGAGTAT
*
1337631 TATAAAT-ATAATAAAAAA
1 TATAAATAAT-ATAATAAA
1337649 TAT-AA-AATATTAATAAA
1 TATAAATAATA-TAATAAA
1337666 TATAAAAATAATATAATAAA
1 TAT--AAATAATATAATAAA
*
1337686 TATAATATAATATATTTAAA
1 TATAA-ATAATATA-ATAAA
1337706 TATAA
1 TATAA
1337711 TTAAAACGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.02
17 13 0.25
18 5 0.10
19 8 0.15
20 21 0.40
21 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAATAATATAATAAA
Found at i:1337705 original size:20 final size:20
Alignment explanation
Indices: 1337647--1337711 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
1337637 TATAATAAAA
*
1337647 AATATAAAATATTAATAAATAT
1 AATATAATATATT--TAAATAT
* *
1337669 AAAAATAATATA-ATAAATAT
1 -AATATAATATATTTAAATAT
1337689 AATATAATATATTTAAATAT
1 AATATAATATATTTAAATAT
1337709 AAT
1 AAT
1337712 TAAAACGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 10 0.28
20 17 0.47
23 9 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATAATATATTTAAATAT
Found at i:1337707 original size:10 final size:10
Alignment explanation
Indices: 1337633--1337715 Score: 57
Period size: 10 Copynumber: 8.4 Consensus size: 10
1337623 TAGAGTATTA
1337633 TAAATATAAT
1 TAAATATAAT
* *
1337643 AAAAAAT-AT
1 TAAATATAAT
*
1337652 AAAATATTAA-
1 TAAATA-TAAT
*
1337662 TAAATATAAA
1 TAAATATAAT
*
1337672 AATAATATAA-
1 TA-AATATAAT
1337682 TAAATATAA-
1 TAAATATAAT
*
1337691 TATAATATATT
1 TA-AATATAAT
1337702 TAAATATAAT
1 TAAATATAAT
1337712 TAAA
1 TAAA
1337716 ACGACACATA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
9 19 0.32
10 30 0.51
11 10 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAATATAAT
Found at i:1423400 original size:21 final size:20
Alignment explanation
Indices: 1423359--1423402 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1423349 TTTTGTAATT
*
1423359 AATTTTTTTCATATAATTAA
1 AATTTTTTTCATACAATTAA
1423379 AATTTTTTT-ATAACAATATAA
1 AATTTTTTTCAT-ACAAT-TAA
1423400 AAT
1 AAT
1423403 ATAATCACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.62
21 6 0.29
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTTTTTCATACAATTAA
Found at i:1424015 original size:2 final size:2
Alignment explanation
Indices: 1423956--1423995 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
1423946 ATTCGAATAA
*
1423956 AT AT CAT AT AT AT AT AT AT AT AT AT AT TT A- AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423996 TTAATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1424391 original size:29 final size:28
Alignment explanation
Indices: 1424356--1424423 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 28
1424346 TTAAAATACG
1424356 ATATAAAAA-ATAAAATAAATATATTAAT
1 ATATAAAAATATAAAATAAAT-TATTAAT
1424384 ATATTAAAATTAATATAAAATAAATTATTAAT
1 ATA-T-AAA--AATATAAAATAAATTATTAAT
*
1424416 GTATAAAA
1 ATATAAAA
1424424 TTTTATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
28 4 0.12
29 1 0.03
30 6 0.18
31 1 0.03
32 11 0.32
33 11 0.32
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
ATATAAAAATATAAAATAAATTATTAAT
Found at i:1424432 original size:32 final size:33
Alignment explanation
Indices: 1424365--1424434 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
1424355 GATATAAAAA
1424365 ATAAAATAAATATATTAATATATTAAAATTAAT
1 ATAAAATAAATATATTAATATATTAAAATTAAT
* *
1424398 ATAAAATAAAT-TATTAATGTA-TAAAATTTTAT
1 ATAAAATAAATATATTAATATATTAAAA-TTAAT
1424430 ATAAA
1 ATAAA
1424435 TTTATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 5 0.15
32 18 0.53
33 11 0.32
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (33 bp):
ATAAAATAAATATATTAATATATTAAAATTAAT
Found at i:1424641 original size:22 final size:20
Alignment explanation
Indices: 1424613--1424655 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
1424603 ATAACACGTA
1424613 AAAAATAATTAAAATATAATAT
1 AAAAATAA--AAAATATAATAT
*
1424635 AAAAATAAAATATATAATAT
1 AAAAATAAAAAATATAATAT
1424655 A
1 A
1424656 TTAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATAAAAAATATAATAT
Found at i:1424679 original size:21 final size:22
Alignment explanation
Indices: 1424650--1424693 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1424640 TAAAATATAT
*
1424650 AATATATTA-AAATATATAAAA
1 AATAAATTATAAATATATAAAA
* *
1424671 AATAAATTATTAATATTTAAAA
1 AATAAATTATAAATATATAAAA
1424693 A
1 A
1424694 TTTTATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAATTATAAATATATAAAA
Found at i:1424685 original size:32 final size:31
Alignment explanation
Indices: 1424616--1424738 Score: 117
Period size: 28 Copynumber: 3.9 Consensus size: 31
1424606 ACACGTAAAA
* *
1424616 AATAATTAAAATATAATATAAAAATAAAATATAT
1 AATATTTAAAATAT-ATA-AAAAATAAATTAT-T
1424650 AATATATTAAAATATATAAAAAATAAATTATT
1 AATAT-TTAAAATATATAAAAAATAAATTATT
** * *
1424682 AATATTTAAAA-AT-T-TTATATAAATTAAT
1 AATATTTAAAATATATAAAAAATAAATTATT
*
1424710 AATATTTTAAATATATAAAAATATAAATT
1 AATATTTAAAATATATAAAAA-ATAAATT
1424739 TTTTACGCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
28 20 0.27
29 3 0.04
30 3 0.04
31 7 0.09
32 13 0.18
33 12 0.16
34 7 0.09
35 9 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
AATATTTAAAATATATAAAAAATAAATTATT
Found at i:1424723 original size:37 final size:35
Alignment explanation
Indices: 1424631--1424731 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 35
1424621 TTAAAATATA
* *
1424631 ATAT-AAAAATAAAATATATAATATATTAAAA---T
1 ATATAAAAAATAAATTAT-TAATATATAAAAATTTT
*
1424663 ATATAAAAAATAAATTATTAATATTTAAAAATTTT
1 ATATAAAAAATAAATTATTAATATATAAAAATTTT
*
1424698 ATATAAATTAATAATATT-TTAAATATATAAAAAT
1 ATATAAA-AAATAA-ATTATT-AATATATAAAAAT
1424732 ATAAATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
32 15 0.26
33 12 0.21
35 8 0.14
36 7 0.12
37 15 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
ATATAAAAAATAAATTATTAATATATAAAAATTTT
Found at i:1427046 original size:28 final size:28
Alignment explanation
Indices: 1426994--1427072 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 28
1426984 ATATTAATCA
*
1426994 AAAATAATTCAAATTTGATTAATTTAAATATT
1 AAAATAATT-AAATTT-A-AAATTTAAA-ATT
* *
1427026 AAATCTAATT-AA-TTAAAATTTTAAATT
1 AAA-ATAATTAAATTTAAAATTTAAAATT
1427053 AAAATAATTAAATTTAAAAT
1 AAAATAATTAAATTTAAAAT
1427073 AATTTAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
26 5 0.12
27 8 0.20
28 14 0.35
29 1 0.03
30 2 0.05
31 2 0.05
32 3 0.08
33 5 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (28 bp):
AAAATAATTAAATTTAAAATTTAAAATT
Found at i:1427067 original size:21 final size:21
Alignment explanation
Indices: 1427017--1427072 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1427007 TTTGATTAAT
* *
1427017 TTAAATATTAAATCTAATTAA
1 TTAAATTTTAAATCTAAATAA
1427038 TTAAAATTTTAAAT-TAAAATAA
1 TT-AAATTTTAAATCT-AAATAA
*
1427060 TTAAATTTAAAAT
1 TTAAATTTTAAAT
1427073 AATTTAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATTTTAAATCTAAATAA
Found at i:1427071 original size:15 final size:15
Alignment explanation
Indices: 1426994--1427091 Score: 62
Period size: 16 Copynumber: 6.5 Consensus size: 15
1426984 ATATTAATCA
1426994 AAAATAATTCAAATTT
1 AAAATAATT-AAATTT
* *
1427010 -GATTAATTTAAATATT
1 AAAATAA-TTAAAT-TT
*
1427026 AAATCTAATT-AA-TT
1 AAA-ATAATTAAATTT
*
1427040 AAAAT-TTTAAA-TT
1 AAAATAATTAAATTT
1427053 AAAATAATTAAATTT
1 AAAATAATTAAATTT
* *
1427068 AAAATAATTTAACTTA
1 AAAATAA-TTAAATTT
1427084 AAAATAAT
1 AAAATAAT
1427092 CTATTTTGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.03
13 10 0.15
14 10 0.15
15 18 0.28
16 19 0.29
17 3 0.05
18 3 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AAAATAATTAAATTT
Found at i:1427526 original size:18 final size:18
Alignment explanation
Indices: 1427505--1427566 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
1427495 ATTATATTAC
1427505 ATTAATATAATTTTATAT
1 ATTAATATAATTTTATAT
1427523 ATT-ATAATAAATTTTA-AT
1 ATTAAT-AT-AATTTTATAT
**
1427541 ATTTGTATTAATTTTATTAT
1 ATTAATA-TAATTTTA-TAT
1427561 ATTAAT
1 ATTAAT
1427567 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 2 0.06
18 18 0.51
19 9 0.26
20 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTAATATAATTTTATAT
Found at i:1435171 original size:18 final size:18
Alignment explanation
Indices: 1435150--1435189 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1435140 TGTTTAATAT
*
1435150 TTATAAAATTAATTTAAA
1 TTATAAAATAAATTTAAA
* *
1435168 TTATAATATAAATTTTAA
1 TTATAAAATAAATTTAAA
1435186 TTAT
1 TTAT
1435190 GTTTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAAAATAAATTTAAA
Found at i:1435986 original size:40 final size:38
Alignment explanation
Indices: 1435941--1436031 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 38
1435931 TAAACATAAT
*
1435941 AAATTTTAAATATAT-ATTATATAAATATACTAATATTTAA
1 AAATTTT-AATATATCATTATATAAATATA--AAAATTTAA
* * *
1435981 AAATTTTTATATATCATTATTTACATATAAAAATTTAA
1 AAATTTTAATATATCATTATATAAATATAAAAATTTAA
*
1436019 AAATATATAATAT
1 AAAT-TTTAATAT
1436032 TAATACATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 12 0.28
39 12 0.28
40 19 0.44
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (38 bp):
AAATTTTAATATATCATTATATAAATATAAAAATTTAA
Found at i:1436497 original size:18 final size:21
Alignment explanation
Indices: 1436449--1436504 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 21
1436439 ACATTAATTA
1436449 ATTAAAATACTTAAATAATAT
1 ATTAAAATACTTAAATAATAT
1436470 ATACTAAAATA-TTAAAT-AT-T
1 AT--TAAAATACTTAAATAATAT
*
1436490 ATTAAAATACATAAA
1 ATTAAAATACTTAAA
1436505 AGTAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 3 0.10
21 4 0.13
22 6 0.19
23 7 0.23
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTAAAATACTTAAATAATAT
Found at i:1436613 original size:26 final size:26
Alignment explanation
Indices: 1436584--1436635 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1436574 CTAAATAAAA
*
1436584 TATTTTAATATTAATTTTAATT-TTAT
1 TATTATAATATTAA-TTTAATTATTAT
1436610 TATTATAATATTAATTTAATTATTAT
1 TATTATAATATTAATTTAATTATTAT
1436636 AATGAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTATAATATTAATTTAATTATTAT
Found at i:1436623 original size:20 final size:20
Alignment explanation
Indices: 1436595--1436649 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1436585 ATTTTAATAT
*
1436595 TAATTTTAATTTTATTATTA
1 TAATATTAATTTTATTATTA
*
1436615 TAATATTAATTTAATTATTA
1 TAATATTAATTTTATTATTA
*
1436635 TAATGAATAATTTTA
1 TAAT-ATTAATTTTA
1436650 CTCTCACGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TAATATTAATTTTATTATTA
Found at i:1436816 original size:28 final size:29
Alignment explanation
Indices: 1436783--1436844 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
1436773 TCTTTTAGGA
1436783 AAATAAATATATAATAAACTTTA-TTAT-TAT
1 AAATAAATATAT-A-AAA-TTTATTTATATAT
1436813 ATAATAAATATATAAAATTTATTTATATAT
1 A-AATAAATATATAAAATTTATTTATATAT
1436843 AA
1 AA
1436845 TGATCTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
28 4 0.14
29 8 0.28
30 6 0.21
31 11 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATAAATATATAAAATTTATTTATATAT
Found at i:1441028 original size:2 final size:2
Alignment explanation
Indices: 1441021--1441049 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1441011 TGTTTCGTTC
1441021 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
1441050 ACATAAATAC
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:1442258 original size:2 final size:2
Alignment explanation
Indices: 1442251--1442282 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1442241 ATAATTGCGC
1442251 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1442283 GGGCCGGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1442510 original size:18 final size:18
Alignment explanation
Indices: 1442462--1442510 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1442452 TTATCCGTTC
1442462 TTATTTAAATA-AAAAAT
1 TTATTTAAATATAAAAAT
* * *
1442479 TAATTTATAT-TAAAATT
1 TTATTTAAATATAAAAAT
1442496 TTATTTAAATATAAA
1 TTATTTAAATATAAA
1442511 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTTAAATATAAAAAT
Found at i:1445160 original size:22 final size:22
Alignment explanation
Indices: 1445142--1445201 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 22
1445132 CTCAAATTGA
1445142 TATTT-AA-TAATTAAAAAATT
1 TATTTAAATTAATTAAAAAATT
*
1445162 TATTTAAATTAATTATAAAA--
1 TATTTAAATTAATTAAAAAATT
*
1445182 TATATAAATT-ATTAAAAAAT
1 TATTTAAATTAATTAAAAAAT
1445202 AAGAGATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.24
20 14 0.41
21 2 0.06
22 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTTAAATTAATTAAAAAATT
Found at i:1445167 original size:20 final size:20
Alignment explanation
Indices: 1445141--1445202 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
1445131 ACTCAAATTG
1445141 ATATTTAATAATTAAAAAAT
1 ATATTTAATAATTAAAAAAT
* *
1445161 TTATTTAAATTAATTATAAAAT
1 ATATTT-AA-TAATTAAAAAAT
* *
1445183 ATA-TAAATTATTAAAAAAT
1 ATATTTAATAATTAAAAAAT
1445202 A
1 A
1445203 AGAGATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 11 0.32
20 7 0.21
21 3 0.09
22 13 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATTTAATAATTAAAAAAT
Found at i:1446889 original size:32 final size:33
Alignment explanation
Indices: 1446853--1446924 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
1446843 TATTATAAAA
1446853 TTATATAAATTTT-TACATATTGATAATTCAT-T
1 TTATATAAATTTTATACAT-TTGATAATTCATAT
* * *
1446885 TTATATAGATTTTAATACGTTTGTTAATTCATAT
1 TTATATAAATTTT-ATACATTTGATAATTCATAT
1446919 TTATAT
1 TTATAT
1446925 TATTTTTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 12 0.35
33 11 0.32
34 11 0.32
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (33 bp):
TTATATAAATTTTATACATTTGATAATTCATAT
Found at i:1447195 original size:33 final size:33
Alignment explanation
Indices: 1447141--1447207 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1447131 AAAAAGGATA
* *
1447141 TATTTTAGTATTAATAAAACTTAAGCCCAAGAT
1 TATTCTAGTATTAACAAAACTTAAGCCCAAGAT
* *
1447174 TATTCTAGTATTAACAGAACTTAAGCCGAAGAT
1 TATTCTAGTATTAACAAAACTTAAGCCCAAGAT
1447207 T
1 T
1447208 TTAAGGTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
TATTCTAGTATTAACAAAACTTAAGCCCAAGAT
Found at i:1448508 original size:25 final size:26
Alignment explanation
Indices: 1448466--1448515 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1448456 TGAGCATAAT
*
1448466 ATAAATAAAATAGTTAAA-ATAAAAC
1 ATAAATAAAATAATTAAATATAAAAC
1448491 ATAAA-AAAATAATATAAATATAAAA
1 ATAAATAAAATAAT-TAAATATAAAA
1448516 AAATATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 9 0.41
26 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (26 bp):
ATAAATAAAATAATTAAATATAAAAC
Found at i:1448521 original size:10 final size:10
Alignment explanation
Indices: 1448463--1448554 Score: 51
Period size: 10 Copynumber: 8.4 Consensus size: 10
1448453 ATATGAGCAT
1448463 AATATAAATAA
1 AATATAAA-AA
1448474 AATAGTTAAAATAA
1 AATA--T-AAA-AA
*
1448488 AACATAAAAA
1 AATATAAAAA
* *
1448498 AATA-ATATA
1 AATATAAAAA
1448507 AATATAAAAA
1 AATATAAAAA
1448517 AATATATCAAAA
1 AATATA--AAAA
*
1448529 TATATCAAAAA
1 AATAT-AAAAA
*
1448540 AGATATAAATA
1 A-ATATAAAAA
1448551 AATA
1 AATA
1448555 ATTAACGTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
9 7 0.11
10 17 0.27
11 16 0.25
12 13 0.20
13 2 0.03
14 9 0.14
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (10 bp):
AATATAAAAA
Found at i:1448529 original size:20 final size:18
Alignment explanation
Indices: 1448483--1448532 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
1448473 AAATAGTTAA
*
1448483 AATAAAACATAAAAAAAT
1 AATAAAATATAAAAAAAT
1448501 AATATAAATATAAAAAAAT
1 AATA-AAATATAAAAAAAT
1448520 ATATCAAAATATA
1 A-AT-AAAATATA
1448533 TCAAAAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 14 0.50
20 9 0.32
21 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAAATATAAAAAAAT
Done.