Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006608.1 Hibiscus syriacus cultivar Beakdansim tig00016216_pilon, 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: 74701
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:7684 original size:21 final size:19
Alignment explanation
Indices: 7658--7697 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
7648 TTTTGGGTTT
7658 ATAATAATATATATATATATA
1 ATAATAATA-ATA-ATATATA
7679 ATAATAATAATAATATATA
1 ATAATAATAATAATATATA
7698 GGTAGGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATAATAATATATA
Found at i:11579 original size:23 final size:24
Alignment explanation
Indices: 11537--11585 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
11527 TGTGCCTTAG
* *
11537 TTCATTTGGTTAATGTTGGTCTCC
1 TTCAATTGGTTAATGATGGTCTCC
*
11561 TTCAATTGG-TAATGATGGTTTCC
1 TTCAATTGGTTAATGATGGTCTCC
11584 TT
1 TT
11586 TCTTCTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.49
Consensus pattern (24 bp):
TTCAATTGGTTAATGATGGTCTCC
Found at i:14182 original size:21 final size:21
Alignment explanation
Indices: 14158--14204 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
14148 GAGACTCAAC
*
14158 AAGAATAAGGAAAAAGAAG-AG
1 AAGAACAA-GAAAAAGAAGAAG
14179 AAGAACAAGAAAAAGAAGAAG
1 AAGAACAAGAAAAAGAAGAAG
14200 AAGAA
1 AAGAA
14205 GGTGAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (21 bp):
AAGAACAAGAAAAAGAAGAAG
Found at i:14729 original size:20 final size:21
Alignment explanation
Indices: 14687--14729 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
14677 AGCAAAATAA
***
14687 AATTTTGAAAAAATAATTTTT
1 AATTTTGAAAAAATAAAAATT
14708 AATTTT-AAAAAATAAAAATT
1 AATTTTGAAAAAATAAAAATT
14728 AA
1 AA
14730 GGATTTAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTTTGAAAAAATAAAAATT
Found at i:22251 original size:89 final size:90
Alignment explanation
Indices: 22050--22383 Score: 419
Period size: 89 Copynumber: 3.7 Consensus size: 90
22040 AAATGAATGA
* * * *
22050 ATAAATGAAAATGGATAATGGTGCATTATCGGCATGAAATGATGCTATAAATAAAAAATGCATAA
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAAT-GAAAATGCATAA
*
22115 TGGTGCATTATCGGCATAAAAAGATGTC
65 TGGTGCATTA-C-GCATGAAAAGATGTC
*
22143 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGGTGCCATAAATGAAAATGCATAAT
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
*
22208 GGTGCATTA-GCATGAAATGATGTC
66 GGTGCATTACGCATGAAAAGATGTC
* *
22232 ATAAATGAAAATGCATAATGGTTCATTATCGGCATGAAAGGATGCCAT--A--AAAATGCATAAC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
* *
22293 GGTGCATTATCGATATGAAAGGAT-TCC
66 GGTGCATTA-CG-CATGAAAAGATGT-C
* * * * * *
22320 ATAAATGAATATGCATAACGGTGCATAATTGACATGAAAGGATGCCACAAATGAAAATGCATAA
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA
22384 CAATATATTA
Statistics
Matches: 214, Mismatches: 19, Indels: 17
0.86 0.08 0.07
Matches are distributed among these distances:
85 20 0.09
87 3 0.01
88 51 0.24
89 59 0.28
90 1 0.00
92 32 0.15
93 48 0.22
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (90 bp):
ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
GGTGCATTACGCATGAAAAGATGTC
Found at i:22358 original size:177 final size:179
Alignment explanation
Indices: 22050--22383 Score: 467
Period size: 177 Copynumber: 1.9 Consensus size: 179
22040 AAATGAATGA
* *
22050 ATAAATGAAAATGGATAATGGTGCATTATCGGCATGAAATGATGCTATAAATAAAAAATGCATAA
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGC---AAATAAAAAATGCATAA
* * * * *
22115 TGGTGCATTATCGGCATAAAAAGATGTCATAAATGAAAATGCATAATGGTGCATTATCGGCATGA
63 CGGTGCATTATCGACATAAAAAGATGTCATAAATGAAAATGCATAACGGTGCATAATCGACATGA
* *
22180 AAGGGTGCCATAAATGAAAATGCATAATGGTGCATTAGCATGAAATGATGTC
128 AAGGATGCCACAAATGAAAATGCATAATGGTGCATTAGCATGAAATGATGTC
* *
22232 ATAAATGAAAATGCATAATGGTTCATTATCGGCATGAAAGGATGC-CAT-AAAAATGCATAACGG
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCAAATAAAAAATGCATAACGG
* * * * *
22295 TGCATTATCGATATGAAAGGAT-TCCATAAATGAATATGCATAACGGTGCATAATTGACATGAAA
66 TGCATTATCGACATAAAAAGATGT-CATAAATGAAAATGCATAACGGTGCATAATCGACATGAAA
22359 GGATGCCACAAATGAAAATGCATAA
130 GGATGCCACAAATGAAAATGCATAA
22384 CAATATATTA
Statistics
Matches: 135, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
176 1 0.01
177 90 0.67
178 2 0.01
182 42 0.31
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (179 bp):
ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCAAATAAAAAATGCATAACGG
TGCATTATCGACATAAAAAGATGTCATAAATGAAAATGCATAACGGTGCATAATCGACATGAAAG
GATGCCACAAATGAAAATGCATAATGGTGCATTAGCATGAAATGATGTC
Found at i:22384 original size:46 final size:46
Alignment explanation
Indices: 22050--22383 Score: 421
Period size: 46 Copynumber: 7.4 Consensus size: 46
22040 AAATGAATGA
* * *
22050 ATAAATGAAAATGGATAATGGTGCATTATCGGCATGAAATGATGCT
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* * * *
22096 ATAAATAAAAAATGCATAATGGTGCATTATCGGCATAAAAAGATGTC
1 ATAAAT-GAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
22143 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGGTGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* *
22189 ATAAATGAAAATGCATAATGGTGCATTA---GCATGAAATGATGTC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
22232 ATAAATGAAAATGCATAATGGTTCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* ** *
22278 AT--A--AAAATGCATAACGGTGCATTATCGATATGAAAGGATTCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* * * * *
22320 ATAAATGAATATGCATAACGGTGCATAATTGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
22366 ACAAATGAAAATGCATAA
1 ATAAATGAAAATGCATAA
22384 CAATATATTA
Statistics
Matches: 251, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
42 36 0.14
43 39 0.16
44 2 0.01
46 134 0.53
47 40 0.16
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (46 bp):
ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
Found at i:23397 original size:17 final size:17
Alignment explanation
Indices: 23375--23407 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23365 TCCTTTAAGC
23375 TTGAAA-AAAATAGTGAA
1 TTGAAATAAAAT-GTGAA
23392 TTGAAATAAAATGTGA
1 TTGAAATAAAATGTGA
23408 TTTGGTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (17 bp):
TTGAAATAAAATGTGAA
Found at i:25096 original size:28 final size:26
Alignment explanation
Indices: 25027--25101 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
25017 TTGGACATAA
*
25027 AGAAATGACTAAAATACCCTTGAACT
1 AGAAATGACTAAAATACCCCTGAACT
* * *
25053 ATAAAATGACCAAAATACCCCTGAAGT
1 A-GAAATGACTAAAATACCCCTGAACT
25080 GAGAAATGACGTAAAATACCCC
1 -AGAAATGAC-TAAAATACCCC
25102 CAAGCTCTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.70
28 11 0.28
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (26 bp):
AGAAATGACTAAAATACCCCTGAACT
Found at i:25132 original size:26 final size:26
Alignment explanation
Indices: 25094--25144 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
25084 AATGACGTAA
*
25094 AATACCCCCAAGCTCTGGAATGAATG
1 AATACCCACAAGCTCTGGAATGAATG
* *
25120 AATACCCATAAGCTTTGGAATGAAT
1 AATACCCACAAGCTCTGGAATGAAT
25145 AAATCTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (26 bp):
AATACCCACAAGCTCTGGAATGAATG
Found at i:26201 original size:32 final size:31
Alignment explanation
Indices: 26139--26217 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
26129 CATAAGGTGA
* *
26139 CCTTGGGTAGGCTCTGAGGCCCCAATGTACTT
1 CCTTGGGTAGGCTCTGAGGACCCAAGGTAC-T
* * *
26171 CCTTGTGTAGGCTCTTAGGACCTAAGGTACT
1 CCTTGGGTAGGCTCTGAGGACCCAAGGTACT
*
26202 CCTTTGGATAGGCTCT
1 CC-TTGGGTAGGCTCT
26218 CAGGCCATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 3 0.08
32 36 0.92
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTGAGGACCCAAGGTACT
Found at i:27850 original size:79 final size:80
Alignment explanation
Indices: 27759--27918 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
27749 TTACTATAGT
*
27759 AAGAAGTTACTTCTAATTGCTTATGTTATCATATG-TTTTTTAGATAGTTTTATTTATGATATGA
1 AAGAAGTGACTTCTAATTGCTTATGTTATCATATGTTTTTTTAGATAGTTTTATTTATGATATGA
27823 AAAAGAATAGAACTG
66 AAAAGAATAGAACTG
27838 AAGAAGTGACTTCTAATTGCTTATGTTATCATATGTTTTTTTAGATAGTTTTATTTATGATATGA
1 AAGAAGTGACTTCTAATTGCTTATGTTATCATATGTTTTTTTAGATAGTTTTATTTATGATATGA
27903 AAAAGAATAGAACTG
66 AAAAGAATAGAACTG
27918 A
1 A
27919 CTAGTTGATG
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 34 0.43
80 45 0.57
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (80 bp):
AAGAAGTGACTTCTAATTGCTTATGTTATCATATGTTTTTTTAGATAGTTTTATTTATGATATGA
AAAAGAATAGAACTG
Found at i:30766 original size:24 final size:24
Alignment explanation
Indices: 30739--30784 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
30729 GGTAAGCACG
30739 TATTTATTTTAAAATTTAATTTTT
1 TATTTATTTTAAAATTTAATTTTT
*
30763 TATTTATTTTAAAATTTTATTT
1 TATTTATTTTAAAATTTAATTT
30785 GTGTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTATTTTAAAATTTAATTTTT
Found at i:35486 original size:2 final size:2
Alignment explanation
Indices: 35479--35519 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
35469 TGAGAAAGAA
35479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
35520 TTAAATTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36200 original size:20 final size:20
Alignment explanation
Indices: 36156--36207 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
36146 AAAATATTTA
36156 TTTTAGATAACAAAATTAAT
1 TTTTAGATAACAAAATTAAT
*
36176 ATTTATGATAA-AAAA-TAACT
1 TTTTA-GATAACAAAATTAA-T
*
36196 TTTTAAATAACA
1 TTTTAGATAACA
36208 CTTTACTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (20 bp):
TTTTAGATAACAAAATTAAT
Found at i:37723 original size:31 final size:31
Alignment explanation
Indices: 37688--37746 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
37678 AATATATAAT
* * *
37688 ATTTGATTATTTTCGTTTTTATTTAATTTAA
1 ATTTGATCACTTTCATTTTTATTTAATTTAA
* *
37719 ATTTGGTCGCTTTCATTTTTATTTAATT
1 ATTTGATCACTTTCATTTTTATTTAATT
37747 AAGATGTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.63
Consensus pattern (31 bp):
ATTTGATCACTTTCATTTTTATTTAATTTAA
Found at i:40898 original size:25 final size:25
Alignment explanation
Indices: 40864--40920 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
40854 TCCTATCTCT
*
40864 CTGGGTCGGACCTGGCACTTGCTCA
1 CTGGGTCGGACCTGACACTTGCTCA
40889 CTGGGTCGGACCTGACACTTGCTCA
1 CTGGGTCGGACCTGACACTTGCTCA
40914 CTGGGTC
1 CTGGGTC
40921 AGGTGAGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.25
Consensus pattern (25 bp):
CTGGGTCGGACCTGACACTTGCTCA
Found at i:41036 original size:2 final size:2
Alignment explanation
Indices: 41013--41303 Score: 157
Period size: 2 Copynumber: 158.0 Consensus size: 2
41003 AATAATAATA
* * *
41013 AT AT A- AT AT AT AC AT AT A- AT AT AT AT AA AT AT A- AC AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
41051 AT A- AT AT AT AT AT -T AG AT AT AT AT AT AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41089 ACT A- AT A- AT AT AT AT AT AT AT AT AT A- AT AT AT AT ACT AT A-
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
41129 AT AT AT AT AT AT A- ACT A- AT AT A- AT AT AT A- AT AT AT GT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
41168 AC A- AT A- AT AT AT A- AT AA AT A- ACT A- AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT
* * *
41207 A- AT AT -T A- AT TT AT -T AT A- AT CT AT AT ACT AT AT GAT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT
41246 -T AT AT A- AT A- AT A- AT AT ACT -T AT AT CAT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT
41283 AT AT ACT AT AT A- AT A- AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT
41304 TAAATGTGTC
Statistics
Matches: 226, Mismatches: 18, Indels: 90
0.68 0.05 0.27
Matches are distributed among these distances:
1 35 0.15
2 175 0.77
3 16 0.07
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:41054 original size:23 final size:23
Alignment explanation
Indices: 41004--41211 Score: 102
Period size: 23 Copynumber: 8.9 Consensus size: 23
40994 TAATTAAATA
41004 ATAATAATA-ATAT-AATATATAC
1 ATAATAATATATATAAATATA-AC
41026 AT-ATAATATATATAAATATAAC
1 ATAATAATATATATAAATATAAC
*
41048 ATAATAATATATATATTAGATAT-AT
1 ATAATAATATATATA--A-ATATAAC
* *
41073 AT-ATATATAATATATAACTAATAAT
1 ATAATA-AT-ATATATAAAT-ATAAC
41098 ATATATATATATATATAATATATATAC
1 ATA-ATA-ATATATATAA-ATATA-AC
41125 -T-ATAATATATAT--ATATAAC
1 ATAATAATATATATAAATATAAC
* *
41144 -TAAT-ATAATATATAATATATGTAT
1 ATAATAAT-ATATATAA-ATAT-AAC
*
41168 ACAATAATATATA-ATAA-ATAAC
1 ATAATAATATATATA-AATATAAC
41190 -TAATATACTATATATATAATAT
1 ATAATA-A-TATATATA-AATAT
41212 TAATTTATTA
Statistics
Matches: 149, Mismatches: 10, Indels: 51
0.71 0.05 0.24
Matches are distributed among these distances:
19 5 0.03
20 13 0.09
21 10 0.07
22 12 0.08
23 39 0.26
24 16 0.11
25 21 0.14
26 25 0.17
27 8 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (23 bp):
ATAATAATATATATAAATATAAC
Found at i:41148 original size:50 final size:50
Alignment explanation
Indices: 41013--41303 Score: 205
Period size: 50 Copynumber: 6.0 Consensus size: 50
41003 AATAATAATA
*
41013 ATATAATATATACA-TATAATATATATAAATATAACATAATA-ATATATATAT
1 ATATAATATATATACTATAATATATAT--ATATAAC-TAATATATATATATAT
* *
41064 -TAGATATATATATA-TATAATATATA-A-CTAA-TAATATATATATATAT
1 ATATA-ATATATATACTATAATATATATATATAACTAATATATATATATAT
41110 ATATAATATATATACTATAATATATATATATAACT-A-ATATA-ATATAT
1 ATATAATATATATACTATAATATATATATATAACTAATATATATATATAT
* * *
41157 A-AT-ATATGTATACAATAATATATAATAAATAACTAATATACTATATATAT
1 ATATAATATATATACTATAATATAT-ATATATAACTAATATA-TATATATAT
* * * * * *
41207 A-ATATTA-ATTTATTATAATCTATATACTAT-A-TGATGTAT-TATATA-
1 ATATAATATATATACTATAATATATATA-TATAACTAATATATATATATAT
41252 ATAATAATATACTTATATCATATAATATATA-ATAT-ACT-ATATA-ATA-ATAT
1 AT-ATAATATA--TATA-C-TATAATATATATATATAACTAATATATATATATAT
41302 AT
1 AT
41304 TAAATGTGTC
Statistics
Matches: 194, Mismatches: 22, Indels: 49
0.73 0.08 0.18
Matches are distributed among these distances:
45 24 0.12
46 36 0.19
47 31 0.16
48 16 0.08
49 13 0.07
50 41 0.21
51 23 0.12
52 10 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (50 bp):
ATATAATATATATACTATAATATATATATATAACTAATATATATATATAT
Found at i:41215 original size:6 final size:7
Alignment explanation
Indices: 41001--41303 Score: 196
Period size: 7 Copynumber: 43.3 Consensus size: 7
40991 AATTAATTAA
41001 ATAATA-
1 ATAATAT
41007 ATAATAAT
1 ATAAT-AT
41015 ATAATAT
1 ATAATAT
41022 ATACATAT
1 ATA-ATAT
41030 A-ATATAT
1 ATA-ATAT
41037 ATAA-AT
1 ATAATAT
*
41043 ATAACAT
1 ATAATAT
41050 AATAATAT
1 -ATAATAT
41058 AT-ATAT
1 ATAATAT
41064 -TAGATAT
1 ATA-ATAT
41071 ATATATAT
1 ATA-ATAT
41079 ATAATAT
1 ATAATAT
41086 ATAACTA-
1 ATAA-TAT
41093 ATAATAT
1 ATAATAT
41100 AT-ATAT
1 ATAATAT
41106 AT-ATAT
1 ATAATAT
41112 ATAATAT
1 ATAATAT
41119 AT-ATACT
1 ATAATA-T
41126 ATAATAT
1 ATAATAT
41133 AT-ATAT
1 ATAATAT
41139 ATAACTAAT
1 ATAA-T-AT
41148 ATAATAT
1 ATAATAT
41155 ATAATAT
1 ATAATAT
* *
41162 ATGTATACA
1 AT-AATA-T
41171 ATAATAT
1 ATAATAT
*
41178 ATAATAA
1 ATAATAT
41185 ATAACTA-
1 ATAA-TAT
41192 AT-ATACT
1 ATAATA-T
41199 AT-ATAT
1 ATAATAT
41205 ATAATAT
1 ATAATAT
*
41212 -TAATTT
1 ATAATAT
*
41218 ATTATA-
1 ATAATAT
*
41224 AT-CTAT
1 ATAATAT
*
41230 ATACTAT
1 ATAATAT
* *
41237 ATGATGT
1 ATAATAT
41244 AT--TAT
1 ATAATAT
41249 ATAATA-
1 ATAATAT
41255 ATAATAT
1 ATAATAT
41262 ACTTATATCAT
1 A--TA-AT-AT
41273 ATAATAT
1 ATAATAT
41280 ATAATAT
1 ATAATAT
41287 ACT-ATAT
1 A-TAATAT
41294 AATAATAT
1 -ATAATAT
41302 AT
1 AT
41304 TAAATGTGTC
Statistics
Matches: 245, Mismatches: 16, Indels: 71
0.74 0.05 0.21
Matches are distributed among these distances:
5 9 0.04
6 57 0.23
7 113 0.46
8 49 0.20
9 12 0.05
10 2 0.01
11 3 0.01
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:41224 original size:66 final size:65
Alignment explanation
Indices: 41013--41284 Score: 207
Period size: 66 Copynumber: 4.2 Consensus size: 65
41003 AATAATAATA
* * * * *
41013 ATATAATATAT-A-CATATAATATATATA-AATATAACATAATAATATATATATTAGATATA-TA
1 ATATAATATATAATTATATAATATATATACTATATAATAT-ATAATAAATA-ACTA-ATATACTA
41074 TAT
63 TAT
* *
41077 ATATAATATATAACTA-AT-A-ATATATA-TATAT-ATATATAATATATATACT-ATAATA-TAT
1 ATATAATATATAATTATATAATATATATACTATATAATATATAATAAATA-ACTAAT-ATACTAT
41135 AT
64 AT
41137 ATATAACTAATATAA-TATATAATATATGTATAC-A-ATAATATATAATAAATAACTAATATACT
1 ATATAA-T-ATATAATTATATAATATA--TATACTATATAATATATAATAAATAACTAATATACT
41199 ATAT
62 ATAT
* * * *
41203 ATATAATAT-TAATTTATTATAATCTATATACTATATGATGTATTATATAATAA-TAATATACTT
1 ATATAATATATAA-TTA-TATAATATATATACTATATAATATATAATA-AATAACTAATATAC-T
41266 ATAT
62 ATAT
41270 CATATAATATATAAT
1 -ATATAATATATAAT
41285 ATACTATATA
Statistics
Matches: 176, Mismatches: 9, Indels: 42
0.78 0.04 0.19
Matches are distributed among these distances:
59 2 0.01
60 14 0.08
61 16 0.09
62 11 0.06
63 15 0.09
64 22 0.12
65 15 0.09
66 58 0.33
67 10 0.06
68 10 0.06
69 3 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (65 bp):
ATATAATATATAATTATATAATATATATACTATATAATATATAATAAATAACTAATATACTATAT
Found at i:41278 original size:84 final size:80
Alignment explanation
Indices: 41004--41303 Score: 278
Period size: 82 Copynumber: 3.7 Consensus size: 80
40994 TAATTAAATA
* * * **
41004 ATAATAATAATATAATATATACATATAATATATATAAATATAACATAATAATATATATATTAGAT
1 ATAATAATAATATAATATAT--ATATAATATATATATATATAATATAATAATATATATAATCTAT
*
41069 ATATATATATATAATAT
64 ATATATATATATATTAT
*
41086 ATAACTAATAATAT-ATATATATAT-ATATA-ATATATATACTATAATATATATATATAA-CTAA
1 ATAA-TAATAATATAATATATATATAATATATATATATATAATATAATA-ATATATATAATCT-A
41147 TATAATATATAATATATGTAT
63 TAT-ATATAT-ATATAT-TAT
* * *
41168 ACAATAAT-ATATAATAAATA-ACTAATATACTATATATATAATAT--TAATTTATTATAATCTA
1 ATAATAATAATATAATATATATA-TAATATA-TATATATATAATATAATAATATA-TATAATCTA
*
41229 TATACTATATGATGTATTAT
63 TATA-TATAT-ATATATTAT
*
41249 ATAATAATAATATACTTATATCATATAATATATA-ATATACT-ATATAATAATATAT
1 ATAATAATAATATA-ATATAT-ATATAATATATATATATA-TAATATAATAATATAT
41304 TAAATGTGTC
Statistics
Matches: 180, Mismatches: 17, Indels: 41
0.76 0.07 0.17
Matches are distributed among these distances:
78 14 0.08
79 18 0.10
80 15 0.08
81 31 0.17
82 56 0.31
83 19 0.11
84 26 0.14
85 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (80 bp):
ATAATAATAATATAATATATATATAATATATATATATATAATATAATAATATATATAATCTATAT
ATATATATATATTAT
Found at i:44097 original size:9 final size:9
Alignment explanation
Indices: 44083--44243 Score: 100
Period size: 9 Copynumber: 16.8 Consensus size: 9
44073 CGAATTAAAT
44083 TAATAATAA
1 TAATAATAA
44092 TAATAATAA
1 TAATAATAA
44101 TAATAATAA
1 TAATAATAA
44110 TAATAAT-A
1 TAATAATAA
44118 TAATATATACA
1 TAATA-ATA-A
44129 T-ATAAT-A
1 TAATAATAA
44136 TATATAA-ATA
1 TA-ATAATA-A
*
44146 TAATAGTAA
1 TAATAATAA
*
44155 TAATATATAC
1 TAATA-ATAA
44165 TAAATATATATA
1 T-AATA-ATA-A
*
44177 TACTATATAA
1 TAATA-ATAA
44187 TATATAACTAA
1 TA-ATAA-TAA
44198 TAATAAT-A
1 TAATAATAA
44206 TATATAATATA
1 TA-ATAATA-A
*
44217 TACT-ATAA
1 TAATAATAA
44225 TATATAATATA
1 TA-ATAATA-A
44236 TAACTAAT
1 TAA-TAAT
44244 TTACTATAAA
Statistics
Matches: 124, Mismatches: 8, Indels: 38
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.02
8 12 0.10
9 52 0.42
10 23 0.19
11 34 0.27
12 1 0.01
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (9 bp):
TAATAATAA
Found at i:44103 original size:15 final size:15
Alignment explanation
Indices: 44083--44243 Score: 100
Period size: 15 Copynumber: 10.1 Consensus size: 15
44073 CGAATTAAAT
44083 TAATAATAATAATAA
1 TAATAATAATAATAA
44098 TAATAATAATAATAA
1 TAATAATAATAATAA
44113 TAAT-ATAATATATACA
1 TAATAATAATA-ATA-A
44129 T-ATAAT-ATATATAA
1 TAATAATAATA-ATAA
*
44143 -ATATAATAGTAATAA
1 TA-ATAATAATAATAA
*
44158 TATATACTAAATATATATA
1 TA-ATAAT-AATA-ATA-A
*
44177 TACTATATAATATATAA
1 TAATA-ATAATA-ATAA
44194 CTAATAATAAT-ATATA
1 -TAATAATAATAATA-A
*
44210 TAATATATACT-ATAA
1 TAATA-ATAATAATAA
44225 TATATAATATATAACTAA
1 TA-ATAATA-ATAA-TAA
44243 T
1 T
44244 TTACTATAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
14 7 0.06
15 54 0.45
16 24 0.20
17 10 0.08
18 21 0.17
19 4 0.03
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (15 bp):
TAATAATAATAATAA
Found at i:44115 original size:24 final size:26
Alignment explanation
Indices: 44084--44325 Score: 147
Period size: 26 Copynumber: 9.3 Consensus size: 26
44074 GAATTAAATT
44084 AATAATAATAATAATA-ATAATA-AT
1 AATAATAATAATAATATATAATATAT
*
44108 AATAATAAT-ATAATATAT-ACATAT
1 AATAATAATAATAATATATAATATAT
44132 AAT-AT-AT-ATAA-ATATAATAGTAAT
1 AATAATAATAATAATATATAATA-T-AT
* *
44156 AATATATACTAAATATATATATACTATAT
1 AATA-ATAAT-AATA-ATATATAATATAT
44185 AATATATAACTAATAATA-AT-ATATAT
1 AATA-ATAA-TAATAATATATAATATAT
*
44211 AATATATACT-ATAATATATAATATAT
1 AATA-ATAATAATAATATATAATATAT
*
44237 AACTAAT-TTACTATAA-ATATAATAT-T
1 AA-TAATAATA--ATAATATATAATATAT
* * *
44263 AATATGTTATAAT-ATATATACTATAT
1 AATA-ATAATAATAATATATAATATAT
44289 AATAATAATATACTTATATCATATAATATAT
1 AATAATAATA-A--TA-AT-ATATAATATAT
44320 -ATAATA
1 AATAATA
44326 TACTATAAAA
Statistics
Matches: 175, Mismatches: 14, Indels: 52
0.73 0.06 0.22
Matches are distributed among these distances:
21 4 0.02
22 8 0.05
23 11 0.06
24 28 0.16
25 20 0.11
26 35 0.20
27 16 0.09
28 8 0.05
29 17 0.10
30 11 0.06
31 17 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (26 bp):
AATAATAATAATAATATATAATATAT
Found at i:44138 original size:2 final size:2
Alignment explanation
Indices: 44115--44332 Score: 101
Period size: 2 Copynumber: 116.5 Consensus size: 2
44105 AATAATAATA
* *
44115 AT AT A- AT AT AT AC AT AT A- AT AT AT AT AA AT AT A- AT AGT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
44154 AT A- AT AT AT ACT AA AT AT AT AT AT ACT AT AT A- AT AT AT A- ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
44196 A- AT A- AT A- AT AT AT AT A- AT AT AT ACT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
44233 AT AT A- ACT A- AT TT ACT AT AA AT AT A- AT AT -T A- AT AT GT -T
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
44271 AT A- AT AT AT AT ACT AT AT A- AT A- AT A- AT AT ACT -T AT AT CAT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT
44311 AT A- AT AT AT AT A- AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT A
44333 AAATAATATA
Statistics
Matches: 168, Mismatches: 11, Indels: 74
0.66 0.04 0.29
Matches are distributed among these distances:
1 26 0.15
2 123 0.73
3 19 0.11
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:44149 original size:45 final size:45
Alignment explanation
Indices: 44088--44342 Score: 225
Period size: 45 Copynumber: 5.8 Consensus size: 45
44078 TAAATTAATA
44088 ATAATA-ATA-ATA-ATAATAATAATAATAATATAATATATACAT
1 ATAATATATATATATATAATAATAATAATAATATAATATATACAT
* * *
44130 ATAATATATATAAATATAATAGTAATAATATATACTAA-ATATATAT
1 ATAATATATATATATATAATAATAATAATA-ATA-TAATATATACAT
*
44176 ATACTATATA-ATATATAACTAATAATAATATATATAATATATAC-T
1 ATAATATATATATATATAA-TAATAATAATA-ATATAATATATACAT
*
44221 ATAATATATA-ATATATAACTAAT-TTACTATAAATATAATAT-TA-AT
1 ATAATATATATATATATAA-TAATAATA--AT-AATATAATATATACAT
** * *
44266 ATGTTATA-ATATATATACTATATAATAATAATATACT-TATATCAT
1 ATAATATATATATATATAATA-ATAATAATAATATAATATATA-CAT
*
44311 ATAATATATATA-ATATACT-ATAA-AATAATATA
1 ATAATATATATATATATAATAATAATAATAATATA
44343 TTAAATGTGT
Statistics
Matches: 179, Mismatches: 16, Indels: 36
0.77 0.07 0.16
Matches are distributed among these distances:
42 16 0.09
43 16 0.09
44 9 0.05
45 80 0.45
46 54 0.30
47 4 0.02
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (45 bp):
ATAATATATATATATATAATAATAATAATAATATAATATATACAT
Found at i:44199 original size:40 final size:38
Alignment explanation
Indices: 44118--44343 Score: 146
Period size: 43 Copynumber: 5.6 Consensus size: 38
44108 AATAATAATA
* * * *
44118 TAATATATACATATAATATATATAAATATAATA-GTAA-
1 TAATATATATAAAT-ATATATATATATATAATATATAAC
44155 TAATATATACTAAATATATATATACTATATAATATATAAC
1 TAATATATA-TAAATATATATATA-TATATAATATATAAC
44195 TAATAATAATATATATAATATATACTATAATATATAATATATAAC
1 ---TAAT-ATATATA-AATATATA-TAT-ATATATAATATATAAC
* *
44240 TAATTTACTATAAATATAATATTAATATGTTATAATATATATAC
1 TAATATA-TATAAATAT-ATA-T-ATAT-ATATAATATATA-AC
44284 T-ATATA-AT-AATAATATACTTATATCATATAATATAT-A-
1 TAATATATATAAAT-ATATA--TATAT-ATATAATATATAAC
44321 TAATATACTATAAA-ATA-ATATAT
1 TAATATA-TATAAATATATATATAT
44344 TAAATGTGTC
Statistics
Matches: 157, Mismatches: 10, Indels: 45
0.74 0.05 0.21
Matches are distributed among these distances:
36 5 0.03
37 19 0.12
38 18 0.11
39 6 0.04
40 22 0.14
41 15 0.10
42 14 0.09
43 23 0.15
44 16 0.10
45 18 0.11
46 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (38 bp):
TAATATATATAAATATATATATATATATAATATATAAC
Found at i:44278 original size:88 final size:92
Alignment explanation
Indices: 44092--44343 Score: 145
Period size: 102 Copynumber: 2.6 Consensus size: 92
44082 TTAATAATAA
*
44092 TAATAATAATAATAATAATA-ATA-ATAT-A-ATATATACATATAAT-ATATATAA-ATATAATA
1 TAATAATAATAAT-ATAATATATACATATAATATATATAAATATAATAATA-ATAATATATAATA
*
44151 GTAATA-ATATATACTAAAT-ATATATATAC
64 --AATATATATATACTATATAATATATATAC
*
44180 TATATAATATATAACTAATAATA-ATATATATAATATATACTATAATAT-ATAATATATAACTAA
1 TA-ATAATA-ATAA-T-ATAATATATACATATAATATATA-TA-AATATAATAATA-ATAA-T-A
* *
44243 TTTACTATAAATATAATATTAATA-TGTTATAATATATATAC
57 TATA--ATAAATAT-ATA-T-ATACT-ATATAATATATATAC
*
44284 TATATAATAATAATATACT-TATATCATATAATATATAT-AATATACTATAA-AATAATATAT
1 TA-ATAATAATAATATAATATATA-CATATAATATATATAAATATA--ATAATAATAATATAT
44344 TAAATGTGTC
Statistics
Matches: 132, Mismatches: 7, Indels: 40
0.74 0.04 0.22
Matches are distributed among these distances:
88 2 0.02
89 6 0.05
90 4 0.03
91 11 0.08
92 4 0.03
93 1 0.01
94 5 0.04
95 4 0.03
96 12 0.09
98 3 0.02
99 14 0.11
100 4 0.03
101 15 0.11
102 19 0.14
103 9 0.07
104 19 0.14
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (92 bp):
TAATAATAATAATATAATATATACATATAATATATATAAATATAATAATAATAATATATAATAAA
TATATATATACTATATAATATATATAC
Found at i:46335 original size:77 final size:79
Alignment explanation
Indices: 46241--46386 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 79
46231 CACAGTTTCC
* * * ** * *
46241 CCCAATAATGTCGTGGTTCACTAAGAAA-TAGGTTGTGATATGTAATGTTAATATTTTTAT-TAA
1 CCCAATAATATCATGGTTCACTAAGAAAGGAGGTTGCAATATGGAATCTTAATATTTTTATATAA
46304 TAAAGCAGGTTAAA
66 TAAAGCAGGTTAAA
* *
46318 CCCAATAATATCATGGTTCACTAAGAAAGGAGGTTGCAATTTGGAATCTTAATATTTTTTTATAA
1 CCCAATAATATCATGGTTCACTAAGAAAGGAGGTTGCAATATGGAATCTTAATATTTTTATATAA
46383 TAAA
66 TAAA
46387 ATGGGTTGTG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 26 0.45
78 25 0.43
79 7 0.12
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (79 bp):
CCCAATAATATCATGGTTCACTAAGAAAGGAGGTTGCAATATGGAATCTTAATATTTTTATATAA
TAAAGCAGGTTAAA
Found at i:46608 original size:265 final size:264
Alignment explanation
Indices: 46125--46745 Score: 731
Period size: 265 Copynumber: 2.3 Consensus size: 264
46115 TAACATTTTA
* * * ** *
46125 GGTTGCGCCTAAAAGGTTACCAGAGTTTAAGCTGATGGGGCCTTAGACATTCACATGATAAGAAA
1 GGTTGCGCCTAAAAAGTTATCAGAGTTTAAGCTGATGGAGCCTTAGATTTTCACACGATAAGAAA
** * *
46190 ATAAGTTAAAAGCTGAAAATATTATGAATATATATAAGAAACACAGTTTCCCCCAATAATGTCGT
66 ATAAGTTAAAAGCTGAAAACGTTATGAAAATATATAAGAAACACAGTTTCCCCCAATAATGTCAT
** *** *
46255 GGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAAGCAGGTTAAACC
131 GGTTCACTAAGAAATAAATTACAATATGTAATGTTAATATTTTTATTAATAAAGCAGGTCAAACC
* ** * * *
46320 CAATAATATCATGGTTCACTAAGAAAGGAGGTTGCAATTTGGAATCTTAATATTTTTTTATAATA
196 CAAGAATATCACAGTTCACTAAGAAAGCAGGTTGCAATATGGAATCTTAATA-TTTTTAATAATA
46385 AAATG
260 AAATG
* * * * * * *
46390 GGTTGTGCCTAAAATGTTATTAGAGTTTAAGCTGATAGAGTCTTAGATTTTCCCACGGTAAGAAA
1 GGTTGCGCCTAAAAAGTTATCAGAGTTTAAGCTGATGGAGCCTTAGATTTTCACACGATAAGAAA
* **** ** *
46455 ATAATTTAAAAGCTGAAAACGTTATGAAAATATATAAGAAATGTGGTTTTGCCCAATAATGTTAT
66 ATAAGTTAAAAGCTGAAAACGTTATGAAAATATATAAGAAACACAGTTTCCCCCAATAATGTCAT
* * * * ** *
46520 GGTTCACTAAGAAATAAATTACAATTTGTAATTTTAATATTTTTATTATTAAAGTAGGTCACGCT
131 GGTTCACTAAGAAATAAATTACAATATGTAATGTTAATATTTTTATTAATAAAGCAGGTCAAACC
* * *
46585 CAAGAATGTCACAGTTTACTAAGAAATCAGGTTGCAATATGGAATCTTAATATTTTTAATAATAA
196 CAAGAATATCACAGTTCACTAAGAAAGCAGGTTGCAATATGGAATCTTAATATTTTTAATAATAA
46650 AATG
261 AATG
* * * * * * *
46654 TGTTACGCCTAAAAAATTATCAGAGTTTAAGTTGATGGAACCTTGGATTTTCTCACGATAAGAAA
1 GGTTGCGCCTAAAAAGTTATCAGAGTTTAAGCTGATGGAGCCTTAGATTTTCACACGATAAGAAA
46719 ATAAGTTAAAAGCTG-AAACTGTTATGA
66 ATAAGTTAAAAGCTGAAAAC-GTTATGA
46746 TGAAAATGTT
Statistics
Matches: 295, Mismatches: 60, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
263 4 0.01
264 89 0.30
265 202 0.68
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (264 bp):
GGTTGCGCCTAAAAAGTTATCAGAGTTTAAGCTGATGGAGCCTTAGATTTTCACACGATAAGAAA
ATAAGTTAAAAGCTGAAAACGTTATGAAAATATATAAGAAACACAGTTTCCCCCAATAATGTCAT
GGTTCACTAAGAAATAAATTACAATATGTAATGTTAATATTTTTATTAATAAAGCAGGTCAAACC
CAAGAATATCACAGTTCACTAAGAAAGCAGGTTGCAATATGGAATCTTAATATTTTTAATAATAA
AATG
Found at i:46879 original size:77 final size:76
Alignment explanation
Indices: 46792--47018 Score: 210
Period size: 77 Copynumber: 2.9 Consensus size: 76
46782 AGCCTTTACT
*
46792 AATGTCATGGTTCACTAAGAAATAGATTATCATATGTAATGTTAATATTTTTATTAATAAAATAT
1 AATGTCATGGTTCACTAAGAAATAG-TTATCATATGTAATGTTAATATTTTTATTAATAAAATAG
*
46857 GTTACT-CCTAAG
65 GTT-CTGCCCAAG
* * *
46869 AATGTTATGGTTCACTAAGAAAGTATGTTGCAATCTGTAATTTAATGTTAATATTTTT-TTAATA
1 AATGTCATGGTTCACTAAGAAA-TA-GTT---ATC-AT-ATGTAATGTTAATATTTTTATTAATA
*
46933 AAATAGGTTGTGCCCAAG
59 AAATAGGTTCTGCCCAAG
* * * * * *
46951 AATGTCATGGTTTTGAAT-AGAAATAGGTT-TGATGTGTTATATTAATATTTTTATTAATAAAAT
1 AATGTCATGG--TTCACTAAGAAATA-GTTATCATATGTAATGTTAATATTTTTATTAATAAAAT
47014 AGGTT
63 AGGTT
47019 GCGCCAAAAA
Statistics
Matches: 123, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
76 15 0.12
77 37 0.30
78 5 0.04
79 1 0.01
81 4 0.03
82 34 0.28
83 23 0.19
84 4 0.03
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (76 bp):
AATGTCATGGTTCACTAAGAAATAGTTATCATATGTAATGTTAATATTTTTATTAATAAAATAGG
TTCTGCCCAAG
Found at i:51356 original size:99 final size:99
Alignment explanation
Indices: 51085--51356 Score: 316
Period size: 99 Copynumber: 2.7 Consensus size: 99
51075 ATTTAATTAA
* * * * *
51085 TTTGTATTACTCTTTCATAATAGACATGGTTT-TGCCCTATAACTTAACCAATTAACATAACAAC
1 TTTGTATTACTTTTTCATAATATAAACGGTTTAAG-CCTATAACTTAACCAATTAACATAACAAC
** *
51149 AAGGCATAACCTATAATGTTATCCAGGAAACTAGG
65 AAGGCGCAACCTATAATGTTATCCAGGAAACCAGG
* * * * * * *
51184 TTTGTATTGCTTTTTCATAATATACATGGTTTAAGCCTATAACTTAACCAGTCAACATAAAAATA
1 TTTGTATTACTTTTTCATAATATAAACGGTTTAAGCCTATAACTTAACCAATTAACATAACAACA
*** *
51249 AAATGCAACCTATAATGTTATCCTA-TAAACCAGG
66 AGGCGCAACCTATAATGTTATCC-AGGAAACCAGG
*
51283 TTTGTTTTACTTTTTCATAATATAAACGGTTTCAA-CCTATAACTTAACCAATTAACATAACAAC
1 TTTGTATTACTTTTTCATAATATAAACGGTTT-AAGCCTATAACTTAACCAATTAACATAACAAC
51347 AAGGCGCAAC
65 AAGGCGCAAC
51357 TGGTAACGTT
Statistics
Matches: 144, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
99 140 0.97
100 4 0.03
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (99 bp):
TTTGTATTACTTTTTCATAATATAAACGGTTTAAGCCTATAACTTAACCAATTAACATAACAACA
AGGCGCAACCTATAATGTTATCCAGGAAACCAGG
Found at i:55112 original size:16 final size:16
Alignment explanation
Indices: 55062--55127 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
55052 GGTATTATCC
55062 GACATGTT-TTCAACCT
1 GACATGTTGTT-AACCT
* * *
55078 GACCTG-TGATGAACAT
1 GACATGTTG-TTAACCT
55094 GACATGTTGTTAACCT
1 GACATGTTGTTAACCT
* *
55110 GACCTGTTTTTAACCT
1 GACATGTTGTTAACCT
55126 GA
1 GA
55128 TCTGTAAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 1 0.03
16 35 0.90
17 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (16 bp):
GACATGTTGTTAACCT
Found at i:55132 original size:16 final size:16
Alignment explanation
Indices: 55073--55132 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
55063 ACATGTTTTC
*
55073 AACCTGACCTG-TGATG
1 AACCTGACCTGTTG-TT
* *
55089 AACATGACATGTTGTT
1 AACCTGACCTGTTGTT
*
55105 AACCTGACCTGTTTTT
1 AACCTGACCTGTTGTT
*
55121 AACCTGATCTGT
1 AACCTGACCTGT
55133 AAATGATCCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 34 0.94
17 2 0.06
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (16 bp):
AACCTGACCTGTTGTT
Found at i:55204 original size:16 final size:16
Alignment explanation
Indices: 55162--55194 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55152 TGACCTGATC
55162 TGATATTTACCTGACT
1 TGATATTTACCTGACT
55178 TGATATTTACCTGACT
1 TGATATTTACCTGACT
55194 T
1 T
55195 CTATATTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (16 bp):
TGATATTTACCTGACT
Found at i:55843 original size:24 final size:23
Alignment explanation
Indices: 55811--55879 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 23
55801 TAATTTACTT
55811 TATATAGTTTATATATATATATGA
1 TATATAGTTTATATATATATAT-A
55835 TATATAGTTTATATATATATATA
1 TATATAGTTTATATATATATATA
55858 TATATAGTTTATATATACTATA
1 TATATAGTTTATATATA-TATA
55880 CATGGTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.41
24 26 0.59
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (23 bp):
TATATAGTTTATATATATATATA
Found at i:55859 original size:43 final size:43
Alignment explanation
Indices: 55822--55905 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
55812 ATATAGTTTA
* *
55822 TATATATATA-TGATATATAGTTTATATATATATATATATATAG
1 TATATATATACT-ATACATAGTTTATACATATATATATATATAG
* *
55865 TTTATATATACTATACATGGTTTATACATATATAT-TATATA
1 TATATATATACTATACATAGTTTATACATATATATATATATA
55906 AAATTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 6 0.17
43 29 0.81
44 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (43 bp):
TATATATATACTATACATAGTTTATACATATATATATATATAG
Found at i:55887 original size:20 final size:19
Alignment explanation
Indices: 55848--55898 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
55838 ATAGTTTATA
*
55848 TATATATATATATATAGTT
1 TATATATATATACATAGTT
*
55867 TATATATACTATACATGGTT
1 TATATATA-TATACATAGTT
*
55887 TATACATATATA
1 TATATATATATA
55899 TTATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (19 bp):
TATATATATATACATAGTT
Found at i:55899 original size:2 final size:2
Alignment explanation
Indices: 55820--55879 Score: 66
Period size: 2 Copynumber: 28.0 Consensus size: 2
55810 TTATATAGTT
*
55820 TA TA TA TA TA TA TGA TA TA TA GTT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
55864 GTT TA TA TA TA CTA TA
1 -TA TA TA TA TA -TA TA
55880 CATGGTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 44 0.88
3 6 0.12
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56270 original size:7 final size:7
Alignment explanation
Indices: 56248--56284 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
56238 TCCATTTATA
56248 TTAGGGT
1 TTAGGGT
**
56255 TTAATGT
1 TTAGGGT
56262 TTAGGGT
1 TTAGGGT
56269 TTAGGGT
1 TTAGGGT
56276 TTAGGGT
1 TTAGGGT
56283 TT
1 TT
56285 TTATAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (7 bp):
TTAGGGT
Found at i:56377 original size:20 final size:20
Alignment explanation
Indices: 56354--56406 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
56344 ATATGTAATT
*
56354 TACTTTATATAGTTTATATA
1 TACTTTATATAGTTTATAAA
* * *
56374 TACTATACATGGTTTATAAA
1 TACTTTATATAGTTTATAAA
56394 TACATATTATATA
1 TAC-T-TTATATA
56407 AAATTATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 19 0.79
21 1 0.04
22 4 0.17
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (20 bp):
TACTTTATATAGTTTATAAA
Found at i:56425 original size:23 final size:25
Alignment explanation
Indices: 56399--56457 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 25
56389 ATAAATACAT
56399 ATTATATAAAATTATTT-AAT-AAA
1 ATTATATAAAATTATTTAAATGAAA
*
56422 ATTA-ATAAAAATTATTTAAATGTAA
1 ATTATAT-AAAATTATTTAAATGAAA
56447 ATTATATAAAA
1 ATTATATAAAA
56458 CATGATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 2 0.06
23 14 0.45
24 3 0.10
25 10 0.32
26 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTATATAAAATTATTTAAATGAAA
Found at i:56767 original size:21 final size:21
Alignment explanation
Indices: 56735--56774 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56725 TTAAATTAGA
56735 GTTTGTGATTTAGGGTTTAAT
1 GTTTGTGATTTAGGGTTTAAT
*
56756 GTTTAGTG-TTTATGGTTTA
1 GTTT-GTGATTTAGGGTTTA
56775 GGATTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (21 bp):
GTTTGTGATTTAGGGTTTAAT
Found at i:56938 original size:2 final size:2
Alignment explanation
Indices: 56864--56923 Score: 75
Period size: 2 Copynumber: 29.0 Consensus size: 2
56854 TTATATAGTT
* * *
56864 TA TA TA TA TA TG GA TA TA TA TA TA TA AA 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
56906 TA TA TA TA CTA TA CTA TA
1 TA TA TA TA -TA TA -TA TA
56924 CATGGTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:57100 original size:13 final size:13
Alignment explanation
Indices: 57078--57107 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57068 TAAATAGACA
*
57078 TATTATATAAAAT
1 TATTAAATAAAAT
57091 TATTAAATAAAAT
1 TATTAAATAAAAT
57104 TATT
1 TATT
57108 TTAATGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTAAATAAAAT
Found at i:57337 original size:20 final size:20
Alignment explanation
Indices: 57312--57349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57302 TAAAAAAAAT
*
57312 AAGTCCATTTGCATTAGTGC
1 AAGTCCATTTACATTAGTGC
57332 AAGTCCATTTACATTAGT
1 AAGTCCATTTACATTAGT
57350 TTACATAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
AAGTCCATTTACATTAGTGC
Found at i:57567 original size:2 final size:2
Alignment explanation
Indices: 57562--57586 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57552 TTATATAGTT
57562 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
57587 TAGTATGCCA
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:57620 original size:12 final size:12
Alignment explanation
Indices: 57603--57634 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
57593 GCCATATTGC
57603 ATAATATAGTTT
1 ATAATATAGTTT
57615 ATAATATAGTTT
1 ATAATATAGTTT
57627 ATACATAT
1 ATA-ATAT
57635 TATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (12 bp):
ATAATATAGTTT
Found at i:58890 original size:15 final size:15
Alignment explanation
Indices: 58870--58901 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58860 CCCCCTTACT
58870 TTAACACTACTCCTC
1 TTAACACTACTCCTC
58885 TTAACACTACTCCTC
1 TTAACACTACTCCTC
58900 TT
1 TT
58902 TAAAACGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAACACTACTCCTC
Found at i:61210 original size:19 final size:19
Alignment explanation
Indices: 61182--61239 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
61172 AAAACCAGAA
61182 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGTATCGATT
* *
61200 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGTATCGATT
*
61219 -CCCTCATGAGGGTATCGATT
1 CCCCT-A-GGGGGTATCGATT
61239 C
1 C
61240 TCTCTGCACC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.26
19 13 0.42
20 10 0.32
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.24
Consensus pattern (19 bp):
CCCCTAGGGGGTATCGATT
Found at i:73515 original size:19 final size:19
Alignment explanation
Indices: 73487--73523 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73477 ATTTTACACC
73487 TAGGGAACCGATTCCCCAT
1 TAGGGAACCGATTCCCCAT
*
73506 TAGGGTACCGATTCCCCA
1 TAGGGAACCGATTCCCCA
73524 CACCTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (19 bp):
TAGGGAACCGATTCCCCAT
Found at i:74659 original size:22 final size:21
Alignment explanation
Indices: 74617--74656 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
74607 AAGTTTATTT
*
74617 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
74638 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
74657 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Done.