Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007000.1 Corchorus capsularis cultivar CVL-1 contig07021, 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: 88177
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3774 original size:75 final size:74
Alignment explanation
Indices: 3693--3842 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 74
3683 GGTCCTAAAT
* *
3693 AACCACATATGCTTGTTGCAAAGAAAGCCAGGATTGAACTTTGTAACCAATCATGAAACAAAACA
1 AACCACATATGCTTGTTGCAAAGAAAGCCAAGATTGAACTTTGCAACCAATCATGAAACAAAACA
3758 AACCCAACCC
66 AA-CCAACCC
* *
3768 AACCACATTTGCTTGTTGTAAAGAAAGCCAAGATTGAACTTTGCAACCAATCATGAAACAAAACA
1 AACCACATATGCTTGTTGCAAAGAAAGCCAAGATTGAACTTTGCAACCAATCATGAAACAAAACA
3833 AACCAACCC
66 AACCAACCC
3842 A
1 A
3843 GCAATGATCA
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 8 0.11
75 63 0.89
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.19
Consensus pattern (74 bp):
AACCACATATGCTTGTTGCAAAGAAAGCCAAGATTGAACTTTGCAACCAATCATGAAACAAAACA
AACCAACCC
Found at i:8476 original size:13 final size:13
Alignment explanation
Indices: 8458--8494 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8448 TTTTGTTTTA
8458 TTTTGTATTTTGT
1 TTTTGTATTTTGT
*
8471 TTTTGTTTTTTGT
1 TTTTGTATTTTGT
*
8484 TTTTGTGTTTT
1 TTTTGTATTTT
8495 TCTTAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (13 bp):
TTTTGTATTTTGT
Found at i:12803 original size:12 final size:12
Alignment explanation
Indices: 12788--12816 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12778 TCAAAAATGA
12788 TTTTT-AAAATT
1 TTTTTCAAAATT
12799 TTTTTCAAAATT
1 TTTTTCAAAATT
12811 TTTTTC
1 TTTTTC
12817 TTTTGAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTCAAAATT
Found at i:13326 original size:326 final size:327
Alignment explanation
Indices: 12723--13382 Score: 988
Period size: 326 Copynumber: 2.0 Consensus size: 327
12713 GAAAGGGAGC
*
12723 GAAATGTCTATTATAAAGGTCTATTGTTTGCATTCTTTTTACTAGAGAAGGCTTTTCAAAAATGA
1 GAAATGTCTATTACAAAGGTCTATTGTTTGCATTCTTTTTACTAGAGAAGGCTTTTCAAAAATGA
*
12788 TTTTTAAAATTTTTTTCAAAATTTTTTTCTTTTGAAACCTTTGTTTCTCTAGTTAAATTCTTTTG
66 TTTTTAAAATTTTTTTCAAAATTTTTTTCTTTTGAAACCTTTGCTTCTC-------ATTCTTTTG
12853 CATAATGTTTGTGGATATCGTTCTAATTAAGTAAGCCCTCAGGAGACTATACTCCTCCTCTAGGG
124 CA-AATGTTTGTGGATATCGTTCTAATTAAGTAAGCCCTCAGGAGACTATACTCCTCCTCTAGGG
* * * *
12918 ACACTTAGGAGTTTAAAGGCTTGTGGTTTACGCTAAAAGCCACCGTATGCCTACGAAAGTGGAAA
188 ACACTTAGGAGTTTAAAGGCTTATGATTTACGCTAAAAACCACCGTATGCCTACAAAAGTGGAAA
*
12983 TAAGTCATTTCTTGCATGTGATTTTCCTTTTTGATTTTAGAGTATTTGTTTGCATATGCATTTGT
253 TAAGTCATTTCTTGCATGTGATTTTCCTTTTTGATTTTAGAGTATTTGTTTGAATATGCATTTGT
13048 TTG-TTTAGG
318 TTGCTTTAGG
13057 GAAATGTCTATTACAAAGGTCTATTGTTTGCATTCTTTTTACTAGAGAAGGCTTTTCAAAAATGA
1 GAAATGTCTATTACAAAGGTCTATTGTTTGCATTCTTTTTACTAGAGAAGGCTTTTCAAAAATGA
*
13122 -TTTTAAATTTTTTTTTTTCAAAATTTCTTTTCTTTTGAAACCTTTGCTTCTC-TTCTTTT-C-A
66 TTTTTAAA---ATTTTTTTCAAAATTT-TTTTCTTTTGAAACCTTTGCTTCTCATTCTTTTGCAA
* * * *
13183 GTGTTTGTGGGTATCGTTCTAGTTAAGTAAGTCCTCAGGAGACTATACTCCTCCTCTAGGGACAC
127 ATGTTTGTGGATATCGTTCTAATTAAGTAAGCCCTCAGGAGACTATACTCCTCCTCTAGGGACAC
* * * * *
13248 TTAGGGGTTTAAAGGCTTATGATTTACTCTAAAAACTACCGTGTGCCTACAAAAGTGGAACTAAG
192 TTAGGAGTTTAAAGGCTTATGATTTACGCTAAAAACCACCGTATGCCTACAAAAGTGGAAATAAG
* * * *
13313 TCATTTGTTGCATGTGATTTTCCTTTTTGATTTTATAGTGTTTGTTTGAATATGTATTTGTTTGC
257 TCATTTCTTGCATGTGATTTTCCTTTTTGATTTTAGAGTATTTGTTTGAATATGCATTTGTTTGC
13378 TTTAG
322 TTTAG
13383 TTTAGTTTTC
Statistics
Matches: 300, Mismatches: 21, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
326 177 0.59
327 5 0.02
328 1 0.00
329 7 0.02
333 7 0.02
334 64 0.21
336 15 0.05
337 24 0.08
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (327 bp):
GAAATGTCTATTACAAAGGTCTATTGTTTGCATTCTTTTTACTAGAGAAGGCTTTTCAAAAATGA
TTTTTAAAATTTTTTTCAAAATTTTTTTCTTTTGAAACCTTTGCTTCTCATTCTTTTGCAAATGT
TTGTGGATATCGTTCTAATTAAGTAAGCCCTCAGGAGACTATACTCCTCCTCTAGGGACACTTAG
GAGTTTAAAGGCTTATGATTTACGCTAAAAACCACCGTATGCCTACAAAAGTGGAAATAAGTCAT
TTCTTGCATGTGATTTTCCTTTTTGATTTTAGAGTATTTGTTTGAATATGCATTTGTTTGCTTTA
GG
Found at i:15486 original size:1 final size:1
Alignment explanation
Indices: 15480--15512 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
15470 CGTTTCTTTG
15480 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15513 CCACTTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19376 original size:1 final size:1
Alignment explanation
Indices: 19370--19403 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
19360 GTGTAATGCC
19370 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19404 CTGCTACCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33553 original size:16 final size:16
Alignment explanation
Indices: 33502--33609 Score: 89
Period size: 16 Copynumber: 6.8 Consensus size: 16
33492 AACCCGCCCA
*
33502 ACCCGAGACTCGAATG
1 ACCCGAGACCCGAATG
* * *
33518 ACCCGCAAACCAG-ATA
1 ACCCG-AGACCCGAATG
33534 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
33550 ACCCGTA-ACCC-AGATG
1 ACCCG-AGACCCGA-ATG
*
33566 ACCCGAGACCCAAATG
1 ACCCGAGACCCGAATG
*
33582 ACCCGTA-ACCCGAGTG
1 ACCCG-AGACCCGAATG
*
33598 ACCTGAGACCCG
1 ACCCGAGACCCG
33610 TGTGACGTGT
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
15 8 0.11
16 59 0.80
17 7 0.09
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.09
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:33587 original size:32 final size:32
Alignment explanation
Indices: 33502--33609 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
33492 AACCCGCCCA
* * * *
33502 ACCCGAGACTCGAATGACCCGCAAACCAGATA
1 ACCCGAGACCCGAATGACCCGTAACCCAGATG
33534 ACCCGAGACCCGAATGACCCGTAACCCAGATG
1 ACCCGAGACCCGAATGACCCGTAACCCAGATG
*
33566 ACCCGAGACCCAAATGACCCGTAACCC-GAGTG
1 ACCCGAGACCCGAATGACCCGTAACCCAGA-TG
*
33598 ACCTGAGACCCG
1 ACCCGAGACCCG
33610 TGTGACGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 2 0.03
32 66 0.97
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.09
Consensus pattern (32 bp):
ACCCGAGACCCGAATGACCCGTAACCCAGATG
Found at i:34226 original size:42 final size:42
Alignment explanation
Indices: 34162--34243 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
34152 TGTTGACACA
*
34162 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
* *
34204 TACCTCACCTGATAATCGATTATGTATTTAATATTCAAAA
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAA
34244 TTAATATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.37
Consensus pattern (42 bp):
TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:34489 original size:16 final size:16
Alignment explanation
Indices: 34470--34572 Score: 86
Period size: 16 Copynumber: 6.5 Consensus size: 16
34460 AACCCGTCCA
34470 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* *
34486 ACCCG-GAACTCGTATG
1 ACCCGAG-ACCCGAATG
34502 ACCCGAGACCC-ATATG
1 ACCCGAGACCCGA-ATG
* *
34518 ATCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
* * *
34534 ACCCGAAACCAG-ATT
1 ACCCGAGACCCGAATG
* *
34549 ACCCGAAACCCGAATA
1 ACCCGAGACCCGAATG
34565 ACCCGAGA
1 ACCCGAGA
34573 AAACTGTCTG
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
15 14 0.20
16 53 0.77
17 2 0.03
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.11
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:36010 original size:16 final size:16
Alignment explanation
Indices: 35975--36009 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
35965 TTAGGGACTC
*
35975 AAATAGAAAACAGAAA
1 AAATAGAAAAAAGAAA
35991 AAATAGAAAAGAAGAAA
1 AAATAGAAAA-AAGAAA
36008 AA
1 AA
36010 TGAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (16 bp):
AAATAGAAAAAAGAAA
Found at i:44938 original size:41 final size:41
Alignment explanation
Indices: 44893--44975 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
44883 TGGCAGAAAA
44893 TACCCACTAAAAAATTTTTGCAATAGAAATACCTACTAGGT
1 TACCCACTAAAAAATTTTTGCAATAGAAATACCTACTAGGT
* * *
44934 TACCCACTAAAAAATTTTTGCGATGGAAATATCTACTAGGT
1 TACCCACTAAAAAATTTTTGCAATAGAAATACCTACTAGGT
44975 T
1 T
44976 GGGTTTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (41 bp):
TACCCACTAAAAAATTTTTGCAATAGAAATACCTACTAGGT
Found at i:51748 original size:22 final size:23
Alignment explanation
Indices: 51710--51762 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
51700 TTAAATGAAG
51710 AAGGTTATACCAATCTTCTTATTC
1 AAGGTTATA-CAATCTTCTTATTC
51734 AAGGTTAT-CAATCTTCTTATTC
1 AAGGTTATACAATCTTCTTATTC
51756 AAGGTTA
1 AAGGTTA
51763 CTAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 21 0.72
24 8 0.28
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (23 bp):
AAGGTTATACAATCTTCTTATTC
Found at i:54641 original size:18 final size:18
Alignment explanation
Indices: 54618--54653 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54608 GGCATTGCCT
54618 TTTAACGGGAAAAAAGAA
1 TTTAACGGGAAAAAAGAA
54636 TTTAACGGGAAAAAAGAA
1 TTTAACGGGAAAAAAGAA
54654 AGTAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (18 bp):
TTTAACGGGAAAAAAGAA
Found at i:55717 original size:68 final size:67
Alignment explanation
Indices: 55640--55774 Score: 225
Period size: 68 Copynumber: 2.0 Consensus size: 67
55630 TTCTTTTTTT
* *
55640 CCCCAAAATTTAATGAAAATTGACAAAATTAATAAATAAATAATTGAGTTTTTTAACGGTGTGCC
1 CCCCAAAATTTAATGAAAATTAACAAAATTAATAAATAAA-AACTGAGTTTTTTAACGGTGTGCC
55705 ACG
65 ACG
* *
55708 CCCCAAAATTTAATGAAAATTAACAAAATTAATAATTAAAAACTGAGTTTTTTCACGGTGTGCCA
1 CCCCAAAATTTAATGAAAATTAACAAAATTAATAAATAAAAACTGAGTTTTTTAACGGTGTGCCA
55773 CG
66 CG
55775 TCACGTCGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 25 0.40
68 38 0.60
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (67 bp):
CCCCAAAATTTAATGAAAATTAACAAAATTAATAAATAAAAACTGAGTTTTTTAACGGTGTGCCA
CG
Found at i:56122 original size:6 final size:6
Alignment explanation
Indices: 56111--56146 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
56101 GGCAATTGGG
*
56111 CGGGTT CGGGTT CGGGTT CGGGTT TGGG-T CGGGTT C
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT C
56147 AGATTCGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
CGGGTT
Found at i:61253 original size:156 final size:158
Alignment explanation
Indices: 61057--61436 Score: 416
Period size: 156 Copynumber: 2.4 Consensus size: 158
61047 GAGCTTCTCA
*
61057 CCTCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
* *
61122 TTTTTCCA-AG-GGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGC
66 TTTTTCCACAGTAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAAC
* * * *
61185 TTCCCTTG-GTAGTGAACTAGGTTTCTCT
131 -TCCCTAGCATAGAGAACTAGGTTTCACT
* ** * **
61213 CC-CCAGGTGGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACAACGCT--
1 CCTCAAACT-GTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA-GCTGA
* * * * *
61274 AA-TTTTCCACCAGTAGACTTATATTATCCCCATAAGGCTATGGGAAAAATTCTAAGTAAAACCG
64 AATTTTTCCA-CAGTAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCG
* * * *
61338 AACTCTCTAGCATAGAGAAGTTGGTTTGACT
128 AACTCCCTAGCATAGAGAACTAGGTTTCACT
* * * ** *
61369 CCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACAAAGTCTGTTTGAGATGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
61434 TTT
66 TTT
61437 CACCTAGATG
Statistics
Matches: 179, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
153 7 0.04
154 2 0.01
155 13 0.07
156 149 0.83
157 4 0.02
158 2 0.01
159 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (158 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
TTTTTCCACAGTAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAAC
TCCCTAGCATAGAGAACTAGGTTTCACT
Found at i:64929 original size:21 final size:21
Alignment explanation
Indices: 64905--64949 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 21
64895 TTTGTTGGGT
64905 CCTAGTCTAGTTTTCATAAGG
1 CCTAGTCTAGTTTTCATAAGG
64926 -C----CTAGTTTTCATAAGG
1 CCTAGTCTAGTTTTCATAAGG
64942 CCTAGTCT
1 CCTAGTCT
64950 TACCAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 10
0.66 0.00 0.34
Matches are distributed among these distances:
16 15 0.79
17 1 0.05
20 1 0.05
21 2 0.11
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
CCTAGTCTAGTTTTCATAAGG
Found at i:64932 original size:16 final size:16
Alignment explanation
Indices: 64911--64947 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
64901 GGGTCCTAGT
64911 CTAGTTTTCATAAGGC
1 CTAGTTTTCATAAGGC
64927 CTAGTTTTCATAAGGC
1 CTAGTTTTCATAAGGC
64943 CTAGT
1 CTAGT
64948 CTTACCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
CTAGTTTTCATAAGGC
Found at i:69659 original size:2 final size:2
Alignment explanation
Indices: 69652--69676 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
69642 CTGCTTTTTG
69652 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
69677 TCTGCTGTTC
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:70025 original size:33 final size:33
Alignment explanation
Indices: 69983--70100 Score: 140
Period size: 33 Copynumber: 3.7 Consensus size: 33
69973 TTGGAATATT
69983 AGAGAGTCATGGTTTTCAAAAATGTTTTTCAAA
1 AGAGAGTCATGGTTTTCAAAAATGTTTTTCAAA
70016 AGAGAGTCATGGTTTTCAAAAATGTTTTTTTC-AA
1 AGAGAGTCATGGTTTTCAAAAATG--TTTTTCAAA
* *
70050 A-A-TGT--T-TTTTTCAAAAGATGTTTTTCAAA
1 AGAGAGTCATGGTTTTCAAAA-ATGTTTTTCAAA
*
70079 AGAAAGTCATGGTTTTCAAAAA
1 AGAGAGTCATGGTTTTCAAAAA
70101 AGAAAAAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
28 6 0.08
29 12 0.17
30 5 0.07
31 2 0.03
32 2 0.03
33 27 0.38
34 12 0.17
35 6 0.08
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (33 bp):
AGAGAGTCATGGTTTTCAAAAATGTTTTTCAAA
Found at i:70048 original size:15 final size:15
Alignment explanation
Indices: 70028--70074 Score: 78
Period size: 14 Copynumber: 3.1 Consensus size: 15
70018 AGAGTCATGG
70028 TTTTCAAAAATGTTT
1 TTTTCAAAAATGTTT
70043 TTTTC-AAAATGTTT
1 TTTTCAAAAATGTTT
70057 TTTTCAAAAGATGTTT
1 TTTTCAAAA-ATGTTT
70073 TT
1 TT
70075 CAAAAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.47
15 8 0.27
16 8 0.27
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (15 bp):
TTTTCAAAAATGTTT
Found at i:70080 original size:14 final size:14
Alignment explanation
Indices: 70028--70081 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
70018 AGAGTCATGG
70028 TTTTCAAAA-ATGTTT
1 TTTTCAAAAGATG--T
*
70043 TTTTCAAAATG-TTT
1 TTTTCAAAA-GATGT
70057 TTTTCAAAAGATGT
1 TTTTCAAAAGATGT
70071 TTTTCAAAAGA
1 TTTTCAAAAGA
70082 AAGTCATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 23 0.68
15 9 0.26
16 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (14 bp):
TTTTCAAAAGATGT
Found at i:70486 original size:24 final size:24
Alignment explanation
Indices: 70459--70504 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
70449 AAAAAGAAAT
*
70459 GAAAATAAAAAG-ATGAAAAAAAGA
1 GAAAA-AAAAAGAAAGAAAAAAAGA
70483 GAAAAAAAAAGAAAGAAAAAAA
1 GAAAAAAAAAGAAAGAAAAAAA
70505 AGTGAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (24 bp):
GAAAAAAAAAGAAAGAAAAAAAGA
Found at i:70516 original size:16 final size:14
Alignment explanation
Indices: 70445--70505 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
70435 AAAGTTGCAA
70445 AAAAAAAAAGAAATG
1 AAAAAAAAAGAAA-G
*
70460 AAAATAAAAAG-ATG
1 AAAA-AAAAAGAAAG
70474 --AAAAAAAG--AG
1 AAAAAAAAAGAAAG
70484 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
70498 AAAAAAAA
1 AAAAAAAA
70506 GTGAAAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 10 0.26
14 11 0.28
15 5 0.13
16 6 0.15
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:71778 original size:16 final size:16
Alignment explanation
Indices: 71757--71787 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
71747 GCTCAATTAG
*
71757 CTTCAATTCTTCAATC
1 CTTCAATGCTTCAATC
71773 CTTCAATGCTTCAAT
1 CTTCAATGCTTCAAT
71788 TTATTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (16 bp):
CTTCAATGCTTCAATC
Found at i:71835 original size:8 final size:8
Alignment explanation
Indices: 71807--71913 Score: 60
Period size: 8 Copynumber: 13.4 Consensus size: 8
71797 AATGATCTCT
71807 TTCTTCAA
1 TTCTTCAA
**
71815 TGATTCAA
1 TTCTTCAA
* *
71823 CTCTTCCA
1 TTCTTCAA
71831 TTCTTCAA
1 TTCTTCAA
*
71839 TTATTCAA
1 TTCTTCAA
*
71847 TACTTCAA
1 TTCTTCAA
*
71855 TTCTTCGA
1 TTCTTCAA
71863 TTACTT--A
1 TT-CTTCAA
*
71870 TTGTTTCAAA
1 TT-CTTC-AA
*
71880 AT-TTCAA
1 TTCTTCAA
71887 TTACTT-AA
1 TT-CTTCAA
*
71895 TGCTTCAA
1 TTCTTCAA
71903 TTCTTCAA
1 TTCTTCAA
71911 TTC
1 TTC
71914 ACTTCAATGA
Statistics
Matches: 73, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
7 11 0.15
8 55 0.75
9 5 0.07
10 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:71865 original size:24 final size:24
Alignment explanation
Indices: 71807--71865 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
71797 AATGATCTCT
* *
71807 TTCTTCAATGATTCAACTCTTCCA
1 TTCTTCAATTATTCAACTCTTCAA
71831 TTCTTCAATTATTCAA-TACTTCAA
1 TTCTTCAATTATTCAACT-CTTCAA
*
71855 TTCTTCGATTA
1 TTCTTCAATTA
71866 CTTATTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (24 bp):
TTCTTCAATTATTCAACTCTTCAA
Found at i:71877 original size:24 final size:24
Alignment explanation
Indices: 71825--71922 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
71815 TGATTCAACT
* *
71825 CTTCCATTCTTCAATTA-TTCAATA
1 CTTCAATTCTTCAATTACTT-AATG
* *
71849 CTTCAATTCTTCGATTACTTATTG
1 CTTCAATTCTTCAATTACTTAATG
* *
71873 TTTCAAAAT-TTCAATTACTTAATG
1 CTTC-AATTCTTCAATTACTTAATG
71897 CTTCAATTCTTCAATTCACTTCAATG
1 CTTCAATTCTTCAATT-ACTT-AATG
71923 ACCCAGGGTG
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.05
24 43 0.73
25 9 0.15
26 4 0.07
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (24 bp):
CTTCAATTCTTCAATTACTTAATG
Found at i:71968 original size:58 final size:58
Alignment explanation
Indices: 71898--72029 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
71888 TACTTAATGC
* * * *
71898 TTCAAT-TCTTCAATTCACTTCAATGACCCAGGGTGGTCTTTTTTC-GTTTCTTCAATTA
1 TTCAATGT-TTCAATTCACTTCAATGACACAGGGTGGTCCTTCTTCTG-TTCCTCAATTA
** * *
71956 TTCAATGTTTCAATTTGCTTCAATGATACATGGTGGTCCTTCTTCTGTTCCTCAATTA
1 TTCAATGTTTCAATTCACTTCAATGACACAGGGTGGTCCTTCTTCTGTTCCTCAATTA
**
72014 TTCAATGCCTCAATTC
1 TTCAATGTTTCAATTC
72030 CAAATTTTCA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
58 59 0.97
59 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (58 bp):
TTCAATGTTTCAATTCACTTCAATGACACAGGGTGGTCCTTCTTCTGTTCCTCAATTA
Found at i:72052 original size:14 final size:14
Alignment explanation
Indices: 72035--72305 Score: 114
Period size: 14 Copynumber: 19.9 Consensus size: 14
72025 AATTCCAAAT
*
72035 TTTCAATGCTTCAA
1 TTTCAATTCTTCAA
72049 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
*
72063 ATTCAA-TC--C--
1 TTTCAATTCTTCAA
72072 -TTCAATGT-TTCAA
1 TTTCAAT-TCTTCAA
*
72085 TTTCAATTCCTCAA
1 TTTCAATTCTTCAA
**
72099 TGTTTCAAGGCTTCAA
1 --TTTCAATTCTTCAA
72115 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
*
72129 ATTCAA-TC--C--
1 TTTCAATTCTTCAA
*
72138 -TTCAGTGT-TTCAA
1 TTTCAAT-TCTTCAA
72151 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
* * *
72165 ATTCAAATCTTGAA
1 TTTCAATTCTTCAA
**
72179 CGTTTCAATTC-AAAA
1 --TTTCAATTCTTCAA
* *
72194 TTTCAATGCTTCAG
1 TTTCAATTCTTCAA
72208 TTTCAATTCTTCAA
1 TTTCAATTCTTCAA
*
72222 TGCTTTAA-T-TTCAA
1 T--TTCAATTCTTCAA
72236 TTTCAATTCTTCAAA
1 TTTCAATTCTTC-AA
* * *
72251 TTCCAA-ACGTCAA
1 TTTCAATTCTTCAA
72264 TGTTTCAA-T-TTCAA
1 --TTTCAATTCTTCAA
*
72278 TATGTCAATGCTTCAA
1 T-T-TCAATTCTTCAA
72294 TTTCAATTCTTC
1 TTTCAATTCTTC
72306 CACGCTTCAA
Statistics
Matches: 191, Mismatches: 34, Indels: 64
0.66 0.12 0.22
Matches are distributed among these distances:
8 9 0.05
10 2 0.01
11 4 0.02
12 5 0.03
13 18 0.09
14 109 0.57
15 16 0.08
16 28 0.15
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTCAATTCTTCAA
Found at i:72061 original size:22 final size:21
Alignment explanation
Indices: 72007--72128 Score: 90
Period size: 22 Copynumber: 5.5 Consensus size: 21
71997 CTTCTGTTCC
*
72007 TCAATTATTCAATGCCTCAATT
1 TCAATT-TTCAATGCTTCAATT
*
72029 CCAAATTTTCAATGCTTCAATT
1 TC-AATTTTCAATGCTTCAATT
*
72051 TCAATTCTTCAA--ATTCAATCCT
1 TCAATT-TTCAATGCTTCAAT--T
72073 TCAATGTTTCAAT--TTCAATT
1 TCAAT-TTTCAATGCTTCAATT
*
72093 CCTCAATGTTTCAAGGCTTCAATT
1 --TCAAT-TTTCAATGCTTCAATT
72117 TCAATTCTTCAA
1 TCAATT-TTCAA
72129 ATTCAATCCT
Statistics
Matches: 84, Mismatches: 5, Indels: 22
0.76 0.05 0.20
Matches are distributed among these distances:
20 7 0.08
21 5 0.06
22 60 0.71
23 5 0.06
24 7 0.08
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (21 bp):
TCAATTTTCAATGCTTCAATT
Found at i:72077 original size:66 final size:66
Alignment explanation
Indices: 72022--72159 Score: 217
Period size: 66 Copynumber: 2.1 Consensus size: 66
72012 TATTCAATGC
*
72022 CTCAATTCC-AAAT-TTTCAATGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAA
1 CTCAATTCCTAAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAA
72085 T
66 T
* * *
72086 TTCAATTCCTCAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAGTGTTTCAA
1 CTCAATTCCTAAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAA
72151 T
66 T
*
72152 TTCAATTC
1 CTCAATTC
72160 TTCAAATTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 8 0.12
65 3 0.04
66 57 0.84
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (66 bp):
CTCAATTCCTAAATGTTTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAA
T
Found at i:72141 original size:22 final size:22
Alignment explanation
Indices: 72050--72164 Score: 105
Period size: 22 Copynumber: 5.2 Consensus size: 22
72040 ATGCTTCAAT
72050 TTCAAT-TCTTCAAATTCAATCC
1 TTCAATGT-TTCAAATTCAATCC
*
72072 TTCAATGTTTCAATTTCAATTCC
1 TTCAATGTTTCAAATTCAA-TCC
*
72095 -TCAATGTTTCAAGGCTTCAAT--
1 TTCAATGTTTCAA--ATTCAATCC
72116 TTCAAT-TCTTCAAATTCAATCC
1 TTCAATGT-TTCAAATTCAATCC
* * *
72138 TTCAGTGTTTCAATTTCAATTC
1 TTCAATGTTTCAAATTCAATCC
72160 TTCAA
1 TTCAA
72165 ATTCAAATCT
Statistics
Matches: 77, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
20 6 0.08
21 1 0.01
22 59 0.77
23 6 0.08
24 5 0.06
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (22 bp):
TTCAATGTTTCAAATTCAATCC
Found at i:72184 original size:36 final size:36
Alignment explanation
Indices: 72036--72188 Score: 176
Period size: 36 Copynumber: 4.4 Consensus size: 36
72026 ATTCCAAATT
*
72036 TTCAATGCTTCAATTTCAATTCTTCAAATTCAATCC
1 TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
**
72072 TTCAATGTTTCAATTTCAATTC--C----TCAATGT
1 TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
* *
72102 TTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCC
1 TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
*
72138 TTCAGTGTTTCAATTTCAATTCTTCAAATTCAAAT-C
1 TTCAATGTTTCAATTTCAATTCTTCAAATTC-AATCC
* *
72174 TTGAACGTTTCAATT
1 TTCAATGTTTCAATT
72189 CAAAATTTCA
Statistics
Matches: 97, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
30 25 0.26
32 1 0.01
34 1 0.01
36 67 0.69
37 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (36 bp):
TTCAATGTTTCAATTTCAATTCTTCAAATTCAATCC
Found at i:72185 original size:66 final size:65
Alignment explanation
Indices: 72036--72278 Score: 215
Period size: 66 Copynumber: 3.9 Consensus size: 65
72026 ATTCCAAATT
*
72036 TTCAATGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTCCTCAATG
1 TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTCCTCAA-G
*
72101 T
65 A
* * *
72102 TTCAAGGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAGTGTTTCAATTTCAATTCTTCAA-A
1 TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTCCTCAAGA
* * * * *
72166 TTCAAATCTTGAACGTTTCAA---TTC-AA---AAT--TTCAATGCTTCAGTTTCAATTCTTCAA
1 TTCAAAGCTTCAA--TTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTCCTCAA
*
72222 TGC
64 -GA
* * * *
72225 TT-TAA-TTTCAATTTCAATTCTTCAAATTCCAA-ACGTCAATGTTTCAATTTCAAT
1 TTCAAAGCTTCAATTTCAATTCTTCAAATT-CAATCCTTCAATGTTTCAATTTCAAT
72279 ATGTCAATGC
Statistics
Matches: 146, Mismatches: 17, Indels: 30
0.76 0.09 0.16
Matches are distributed among these distances:
55 6 0.04
57 28 0.19
58 5 0.03
59 7 0.05
62 2 0.01
63 5 0.03
64 27 0.18
66 66 0.45
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (65 bp):
TTCAAAGCTTCAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTCCTCAAGA
Found at i:72212 original size:22 final size:22
Alignment explanation
Indices: 72149--72321 Score: 106
Period size: 22 Copynumber: 8.0 Consensus size: 22
72139 TCAGTGTTTC
* *
72149 AATTTCAATTCTTCAAATTC-A
1 AATTTCAATGCTTCAATTTCAA
* * *
72170 AATCTTGAACGTTTCAA-TTCAA
1 AAT-TTCAATGCTTCAATTTCAA
*
72192 AATTTCAATGCTTCAGTTTC-A
1 AATTTCAATGCTTCAATTTCAA
* *
72213 ATTCTTCAATGCTTTAATTTC--
1 AAT-TTCAATGCTTCAATTTCAA
* * *
72234 AATTTCAATTCTTCAAATTCCA
1 AATTTCAATGCTTCAATTTCAA
** *
72256 AACGTCAATGTTTCAATTTCAA
1 AATTTCAATGCTTCAATTTCAA
* *
72278 TATGTCAATGCTTCAATTTC-A
1 AATTTCAATGCTTCAATTTCAA
* * *
72299 ATTCTTCCACGCTTCAATTTCAA
1 AAT-TTCAATGCTTCAATTTCAA
72322 TTCTTCGAAT
Statistics
Matches: 115, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
20 14 0.12
21 22 0.19
22 78 0.68
23 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (22 bp):
AATTTCAATGCTTCAATTTCAA
Found at i:72357 original size:20 final size:20
Alignment explanation
Indices: 72289--72342 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
72279 ATGTCAATGC
* *
72289 TTCAATTTCAATTCTTCCACGC
1 TTCAATTTCAATTCTTCGA--A
72311 TTCAATTTCAATTCTTCGAA
1 TTCAATTTCAATTCTTCGAA
72331 TTCAATTTCAAT
1 TTCAATTTCAAT
72343 GTTTTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (20 bp):
TTCAATTTCAATTCTTCGAA
Found at i:75473 original size:16 final size:16
Alignment explanation
Indices: 75456--75523 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
75446 TTGTCCTAGT
* *
75456 CTAGTTTTTATAAGGT
1 CTAGTTTTCATAAGGC
75472 CTAG-TTTCATAAGGC
1 CTAGTTTTCATAAGGC
75487 CTAGTTTTCATAAGGC
1 CTAGTTTTCATAAGGC
75503 CTAGTTTTCATAAGGC
1 CTAGTTTTCATAAGGC
75519 CTAGT
1 CTAGT
75524 CTTACCAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.27
16 36 0.73
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (16 bp):
CTAGTTTTCATAAGGC
Found at i:75492 original size:31 final size:32
Alignment explanation
Indices: 75456--75523 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
75446 TTGTCCTAGT
* *
75456 CTAGTTTTTATAAGGTCTAG-TTTCATAAGGC
1 CTAGTTTTCATAAGGCCTAGTTTTCATAAGGC
75487 CTAGTTTTCATAAGGCCTAGTTTTCATAAGGC
1 CTAGTTTTCATAAGGCCTAGTTTTCATAAGGC
75519 CTAGT
1 CTAGT
75524 CTTACCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 18 0.53
32 16 0.47
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (32 bp):
CTAGTTTTCATAAGGCCTAGTTTTCATAAGGC
Found at i:77483 original size:20 final size:21
Alignment explanation
Indices: 77455--77509 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
77445 CTTGATCTTG
*
77455 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
* *
77475 AGTCGTTTGACTCCTTAAGTTG
1 AGTCATTTGACTCCTTAAG-TA
77497 AG-CATTTGACTCC
1 AGTCATTTGACTCC
77510 ATTACTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:82728 original size:156 final size:155
Alignment explanation
Indices: 82421--82783 Score: 394
Period size: 156 Copynumber: 2.3 Consensus size: 155
82411 GAGCTTCTCA
* ** *
82421 CCTCAAACTATCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGAGCT-AAA
* *
82486 TTTTGCCAAGGGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTT
65 TTTTGCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTT
** * * * *
82551 CCCTTGGTAGTGAAATAGGTTTCTCT
130 CAATAGATAGAGAAATAGGTTTCACT
* **
82577 CC-CCAGGTGGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAACAAG-GCT-A
1 CCTCAAACT-GTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAA-AAGAGCTAA
* * * * *
82639 ATTTT-CCACCAGTAGACTTATATTATCCCCATAAGGCTATGGGAAAAATTCTAAGTAAAACCGA
64 ATTTTGCCA--AG-AGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGA
* * *
82703 AC-TCAATAGCATAGAGAAGTTGGTTTGACT
126 ACTTCAATAG-ATAGAGAAATAGGTTTCACT
* * *
82733 CCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTTATACTAAGTC
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC
82784 TGTTTGAGAT
Statistics
Matches: 171, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
153 3 0.02
154 6 0.04
155 9 0.05
156 148 0.87
157 5 0.03
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (155 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGAGCTAAAT
TTTGCCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTTC
AATAGATAGAGAAATAGGTTTCACT
Found at i:83340 original size:19 final size:19
Alignment explanation
Indices: 83313--83349 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
83303 ACATAGGGAG
*
83313 TAATTAATAATAATTATTT
1 TAATAAATAATAATTATTT
*
83332 TAATAAATAATTATTATT
1 TAATAAATAATAATTATT
83350 AATTAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAAATAATAATTATTT
Found at i:83361 original size:19 final size:17
Alignment explanation
Indices: 83315--83366 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
83305 ATAGGGAGTA
83315 ATTAAT-AATAATTATT
1 ATTAATAAATAATTATT
83331 -TTAATAAATAATTATT
1 ATTAATAAATAATTATT
*
83347 ATTAATTAACTTAATTATT
1 ATTAA-TAA-ATAATTATT
83366 A
1 A
83367 ATTTTGGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 5 0.16
16 10 0.32
17 4 0.13
18 3 0.10
19 9 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATAAATAATTATT
Found at i:84627 original size:2 final size:2
Alignment explanation
Indices: 84620--84650 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
84610 GGAGTCCAAT
*
84620 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
84651 GAGGGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Done.