Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010104.1 Corchorus capsularis cultivar CVL-1 contig10125, 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: 69071
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1490 original size:11 final size:11
Alignment explanation
Indices: 1470--1499 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1460 ATAATTATAA
1470 AGTATATAAAG
1 AGTATATAAAG
*
1481 AGTGTATAAAG
1 AGTATATAAAG
1492 AGTATATA
1 AGTATATA
1500 CATACACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (11 bp):
AGTATATAAAG
Found at i:2593 original size:19 final size:19
Alignment explanation
Indices: 2569--2613 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
2559 TCTTCCAAAC
2569 TTCAAAAGTCAGCAATACA
1 TTCAAAAGTCAGCAATACA
2588 TTCAAAAGTCAGCAATACA
1 TTCAAAAGTCAGCAATACA
*
2607 TTTAAAA
1 TTCAAAA
2614 TATATAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (19 bp):
TTCAAAAGTCAGCAATACA
Found at i:6230 original size:13 final size:13
Alignment explanation
Indices: 6212--6236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6202 TCCCTCTCAA
6212 GAATGCAGCACAT
1 GAATGCAGCACAT
6225 GAATGCAGCACA
1 GAATGCAGCACA
6237 AGGATTTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (13 bp):
GAATGCAGCACAT
Found at i:10576 original size:29 final size:28
Alignment explanation
Indices: 10535--10596 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
10525 CAAATAGTCC
* * *
10535 CCAAAATTAAAGTTTAGTAGGCAAAATGT
1 CCAAAATTAAAGTTCAATA-GCAAAACGT
* *
10564 CCAAAGTTGAAGTTCAATAGCAAAACGT
1 CCAAAATTAAAGTTCAATAGCAAAACGT
10592 CCAAA
1 CCAAA
10597 CGCTACATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (28 bp):
CCAAAATTAAAGTTCAATAGCAAAACGT
Found at i:15176 original size:14 final size:14
Alignment explanation
Indices: 15159--15217 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
15149 CGATTGTATT
*
15159 TTTTTTAAAATATA
1 TTTTTTAAAAAATA
* *
15173 -TTTTAAAAAAAAA
1 TTTTTTAAAAAATA
*
15186 TATTTTAAAAAATA
1 TTTTTTAAAAAATA
*
15200 TTTTTTAAAATATA
1 TTTTTTAAAAAATA
15214 TTTT
1 TTTT
15218 CAATTGTACC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
13 10 0.28
14 26 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTTTAAAAAATA
Found at i:15178 original size:12 final size:13
Alignment explanation
Indices: 15160--15217 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
15150 GATTGTATTT
*
15160 TTTTTAAAATATA
1 TTTTAAAAATATA
*
15173 TTTTAAAAAAAAATA
1 TTTT--AAAAATATA
15188 TTTTAAAAA-ATA
1 TTTTAAAAATATA
*
15200 TTTTTTAAAATATA
1 -TTTTAAAAATATA
15214 TTTT
1 TTTT
15218 CAATTGTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.08
13 21 0.55
14 3 0.08
15 11 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:15330 original size:27 final size:27
Alignment explanation
Indices: 15278--15342 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
15268 ATATTTTAAC
* *
15278 TATTCCATTA-TTTTTTTACCATAAAT
1 TATTCCATTATTTTTTTTAACAAAAAT
*
15304 TATTCCATTATTTTTTTTAAGAAAAAT
1 TATTCCATTATTTTTTTTAACAAAAAT
*
15331 CATTCCATTATT
1 TATTCCATTATT
15343 AATTACTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.29
27 24 0.71
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTCCATTATTTTTTTTAACAAAAAT
Found at i:15749 original size:11 final size:11
Alignment explanation
Indices: 15735--15772 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15725 ATTCATAACA
15735 AATTTATAATT
1 AATTTATAATT
15746 AATTTATAATT
1 AATTTATAATT
15757 -ATTTGATAATT
1 AATTT-ATAATT
*
15768 TATTT
1 AATTT
15773 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:17169 original size:14 final size:15
Alignment explanation
Indices: 17145--17174 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17135 GAGAAAGAAG
17145 TTTGTTTTTTGTTTT
1 TTTGTTTTTTGTTTT
17160 TTTG-TTTTTGTTTT
1 TTTGTTTTTTGTTTT
17174 T
1 T
17175 GGACGGGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
TTTGTTTTTTGTTTT
Found at i:18876 original size:180 final size:180
Alignment explanation
Indices: 18550--18876 Score: 471
Period size: 180 Copynumber: 1.8 Consensus size: 180
18540 TTCGTTAATC
* *
18550 GAAACAACTAATTCTTTGGAAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGTCCTT
1 GAAACAACAAATTCTTTGGAAGCATTTTTTATACCTTAAACATTAAATTTAGTATTCAAGTCCTT
* * *
18615 CATGAAAGTTGTAGATCATGAAACAACCTTTTAAGAGACACTTTAACCATCTCAATCAGACATCT
66 CATGAAAGTTGTAGATCATGAAACAACCTTTTAAGAGACACTTAAACCACCTCAATCAGACAACT
*
18680 GGAGCAAAAGTTATATATAATATTAAGTGGACTGTCTATTCCTGTTAACT
131 GGAGCAAAAATTATATATAATATTAAGTGGACTGTCTATTCCTGTTAACT
* *
18730 GAAACAACAAATT-TTTCGGAAGTATTTTTTATA-CTTGAAACATTAAATTTAGTATTCGAGTCC
1 GAAACAACAAATTCTTT-GGAAGCATTTTTTATACCTT-AAACATTAAATTTAGTATTCAAGTCC
* * * * * * *
18793 TTCATGAAAGTTGTAGATCATGGAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAA
64 TTCATGAAAGTTGTAGATCATGAAACAACCTTTTAAGAGACACTTAAACCACCTCAATCAGACAA
18858 CTGGAG-AGAAAATTATATA
129 CTGGAGCA-AAAATTATATA
18877 ATGTTAAATA
Statistics
Matches: 129, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
179 7 0.05
180 122 0.95
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (180 bp):
GAAACAACAAATTCTTTGGAAGCATTTTTTATACCTTAAACATTAAATTTAGTATTCAAGTCCTT
CATGAAAGTTGTAGATCATGAAACAACCTTTTAAGAGACACTTAAACCACCTCAATCAGACAACT
GGAGCAAAAATTATATATAATATTAAGTGGACTGTCTATTCCTGTTAACT
Found at i:30151 original size:13 final size:13
Alignment explanation
Indices: 30129--30159 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30119 CTATATATGC
30129 AAAA-AAAAAAAA
1 AAAACAAAAAAAA
30141 AAAACAAAAAAAA
1 AAAACAAAAAAAA
30154 AAAACA
1 AAAACA
30160 GTAATCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:34337 original size:140 final size:140
Alignment explanation
Indices: 34085--34363 Score: 486
Period size: 140 Copynumber: 2.0 Consensus size: 140
34075 TTAAAAATTA
*
34085 ATCACATGACACCCGGCATTAATAGAGTCAATGTTGATCGATCTCAAATGCAAATTACTAATATT
1 ATCACATGACACCCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGCAAATTACTAATATT
** *
34150 CAACCAATACTAATACTTCAACAACATTTTCAACAGGATAAAAATGAGGTAATCATAAAAATTCT
66 CAACCAATACTAATACTTCAACAACATTTTCAACAAAATAAAAATGAGGTAATCACAAAAATTCT
34215 AAATATGTTG
131 AAATATGTTG
*
34225 ATCACATGACACTCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGCAAATTACTAATATT
1 ATCACATGACACCCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGCAAATTACTAATATT
** *
34290 CAACCAATACTAATACTTCAACAACATTTTCAACAAAATTCAAATGAGGTAATCACCAAAATTCT
66 CAACCAATACTAATACTTCAACAACATTTTCAACAAAATAAAAATGAGGTAATCACAAAAATTCT
34355 AAATATGTT
131 AAATATGTT
34364 AACGAAAACT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 131 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (140 bp):
ATCACATGACACCCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGCAAATTACTAATATT
CAACCAATACTAATACTTCAACAACATTTTCAACAAAATAAAAATGAGGTAATCACAAAAATTCT
AAATATGTTG
Found at i:34599 original size:380 final size:383
Alignment explanation
Indices: 33891--34603 Score: 968
Period size: 385 Copynumber: 1.9 Consensus size: 383
33881 CCAGGACGAT
* *** *
33891 AAATTACTAATATTCAATCAATACAAACACTTCAGTGACATTCTCAACAAAATCCAAATGAGGTG
1 AAATTACTAATATTCAACCAATACAAACACTTCAACAACATTCTCAACAAAATCCAAATGAGGTA
**** * * * * *
33956 ATCGTTGAGATTCTGAATTTGTTAACGATAACTTGCTATTTTTGACAATGATAGTTTCTCATTTT
66 ATCACCAAAATTCTAAATATGTTAACGAAAACTTGCTATTCTTGACAATGATAGTTTCTCATTTT
*
34021 GGATTTTCAGACAACATATATACCATCATAGTTTCTTATTTGGGATATATACGTTTAAAAATTAA
131 GGATTTTCAGACAACATATATA-CATCATAGTTTCTTATTTGGGATATATACATTTAAAAATTAA
*
34086 TCACATGACACCCGGCATTAATAGAGTCAATGTTGATCGATCTCAAATGCAAATTACTAATATTC
195 TCACATGACACCCGGCATTAACAGAGTCAATGTT-ATCGATCTCAAATGCAAATTACTAATATTC
**
34151 AACCAATACTAATACTTCAACAACATTTTCAACAGGATAAAAATGAGGTAATCATAAAAATTCTA
259 AACCAATACTAATACTTCAACAACATTTTCAACAAAATAAAAATGAGGTAATCATAAAAATTCTA
34216 AATATGTTGATCACATGACACTCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGC
324 AATATGTTGATCACATGACACTCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGC
* * * *
34276 AAATTACTAATATTCAACCAATACTAATACTTCAACAACATTTTCAACAAAATTCAAATGAGGTA
1 AAATTACTAATATTCAACCAATACAAACACTTCAACAACATTCTCAACAAAATCCAAATGAGGTA
* * **
34341 ATCACCAAAATTCTAAATATGTTAACGAAAACTTGTTATTCTTGACTCATGATAGTTT-TTTTTT
66 ATCACCAAAATTCTAAATATGTTAACGAAAACTTGCTATTCTTGAC-AATGATAGTTTCTCATTT
* * * * *
34405 TGGATTTTCAGACAACATATAT-CATCATAGTTTTTTATTTGGGATATATATATATTTAAGATTG
130 TGGATTTTCAGACAACATATATACATCATAGTTTCTTATTTGGGATATATACAT-TTAAAAATTA
* * * *
34469 ATCACATGACACTCGGTATTAACAGAGTCACTG-T-T-GATCTCAAATGCAAATTACTGATATTC
194 ATCACATGACACCCGGCATTAACAGAGTCAATGTTATCGATCTCAAATGCAAATTACTAATATTC
* ** * * ** *
34531 AACCAATACTAATACTTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCGTCGAGATTCTA
259 AACCAATACTAATACTTCAACAACATTTTCAACAAAATAAAAATGAGGTAATCATAAAAATTCTA
34596 AATATGTT
324 AATATGTT
34604 AATAATAACT
Statistics
Matches: 283, Mismatches: 43, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
380 89 0.31
381 1 0.00
383 29 0.10
384 36 0.13
385 118 0.42
386 10 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (383 bp):
AAATTACTAATATTCAACCAATACAAACACTTCAACAACATTCTCAACAAAATCCAAATGAGGTA
ATCACCAAAATTCTAAATATGTTAACGAAAACTTGCTATTCTTGACAATGATAGTTTCTCATTTT
GGATTTTCAGACAACATATATACATCATAGTTTCTTATTTGGGATATATACATTTAAAAATTAAT
CACATGACACCCGGCATTAACAGAGTCAATGTTATCGATCTCAAATGCAAATTACTAATATTCAA
CCAATACTAATACTTCAACAACATTTTCAACAAAATAAAAATGAGGTAATCATAAAAATTCTAAA
TATGTTGATCACATGACACTCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGC
Found at i:34649 original size:240 final size:237
Alignment explanation
Indices: 34222--34949 Score: 806
Period size: 240 Copynumber: 3.1 Consensus size: 237
34212 TCTAAATATG
*
34222 TTGATCACATGACACTCGGCATTAATAAAGTCAATGTTGATCGATCTCAAATGCAAATTACTAAT
1 TTGATCACATGACACTCGG-ATTAATAGAGTCAATG-T--T-GATCTCAAATGCAAATTACT-AT
* * * * * *
34287 ATTCAACCAATACTAATACTTCAACAACATTTTCAACAAAATTCAAATGAGGTAATCACCAAAAT
60 ATTCAACCAATACTAATACTTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCATCGAGAT
* * * * *
34352 TCTAAATATGTTAACGAA-AACTTGTTATTCTTGACTCATGATAGTTT-TTTTTTTGGATTTTCA
125 TCTAAATATGTTAACTAATAACTTGCTATTCTTGAC-AATAATAGTTTCTTATTTTGGATTTTCA
* * *
34415 GACAACATATATCATCATAGTTTTTTATTTGGGATATATATATATTTAAGA
189 GACAA-ATATAT-ATCATAGTTTCTTATTTAGGATATATATATGTTTAAGA
* *
34466 TTGATCACATGACACTCGGTATTAACAGAGTCACTGTTGATCTCAAATGCAAATTACTGATATTC
1 TTGATCACATGACACTCGG-ATTAATAGAGTCAATGTTGATCTCAAATGCAAATTACT-ATATTC
*
34531 AACCAATACTAATACTTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCGTCGAGATTCTA
64 AACCAATACTAATACTTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCATCGAGATTCTA
*
34596 AATATGTTAA-TAATAACTTGCTA-TCATTGACAATAATAGTTTCTTATTTTGGATTTTCAGGC-
129 AATATGTTAACTAATAACTTGCTATTC-TTGACAATAATAGTTTCTTATTTTGGATTTTCAGACA
* * *
34658 AATATA-ATTATTGTTTCTTATTTAGG--ATATATACGTTTAAGA
193 AATATATATCATAGTTTCTTATTTAGGATATATATATGTTTAAGA
* * * * *
34700 TTGATCATATAACGCTCGAGATTAATGGAGTCAATGTTGATCTCAAGTGCAAA-T--TA-ATT--
1 TTGATCACATGACACTCG-GATTAATAGAGTCAATGTTGATCTCAAATGCAAATTACTATATTCA
* *
34759 ---AATACTAATAATTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCATCGAGATTTTAA
65 ACCAATACTAATACTTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCATCGAGATTCTAA
* * * * *
34821 ATATATTAACGATTAACGATAACTTACTATTCTTGGCAATAATATTTTCTTAGTTTGGATTTTCA
130 ATATGTTAAC---T-A--ATAACTTGCTATTCTTGACAATAATAGTTTCTTATTTTGGATTTTCA
* * * *
34886 TACAATATATATTATCATGGTTTCTTATTTAAGATATATATGTGTTTAAGA
189 GACAA-ATATA-TATCATAGTTTCTTATTTAGGATATATATATGTTTAAGA
34937 TTGATCACATGAC
1 TTGATCACATGAC
34950 GCTAAATATA
Statistics
Matches: 418, Mismatches: 48, Indels: 43
0.82 0.09 0.08
Matches are distributed among these distances:
224 67 0.16
228 1 0.00
229 4 0.01
230 1 0.00
231 42 0.10
232 3 0.01
233 6 0.01
234 58 0.14
235 18 0.04
236 16 0.04
237 25 0.06
238 5 0.01
239 14 0.03
240 124 0.30
241 1 0.00
243 1 0.00
244 32 0.08
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (237 bp):
TTGATCACATGACACTCGGATTAATAGAGTCAATGTTGATCTCAAATGCAAATTACTATATTCAA
CCAATACTAATACTTCATCAACATTTTCAACAAAATCCAAATGAGGTGATCATCGAGATTCTAAA
TATGTTAACTAATAACTTGCTATTCTTGACAATAATAGTTTCTTATTTTGGATTTTCAGACAAAT
ATATATCATAGTTTCTTATTTAGGATATATATATGTTTAAGA
Found at i:34997 original size:38 final size:36
Alignment explanation
Indices: 34919--34988 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
34909 CTTATTTAAG
34919 ATATATATGTGTTTAAGATTGATCACATGACGCTAA
1 ATATATATGTGTTTAAGATTGATCACATGACGCTAA
34955 ATATATATGTGTTTAAGATTGATCACATGACGCT
1 ATATATATGTGTTTAAGATTGATCACATGACGCT
34989 TGGCATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (36 bp):
ATATATATGTGTTTAAGATTGATCACATGACGCTAA
Found at i:35686 original size:21 final size:22
Alignment explanation
Indices: 35660--35715 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
35650 TTAGGTTTTA
*
35660 ATTATTAAAAATAATTA-AATT
1 ATTATTAAAAATAATTATAAAT
35681 ATTATT-AAAA-AATTATAAAT
1 ATTATTAAAAATAATTATAAAT
35701 ATTATTAAGAAATAA
1 ATTATTAA-AAATAA
35716 ATTACACACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.17
20 13 0.43
21 7 0.23
22 3 0.10
23 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTATTAAAAATAATTATAAAT
Found at i:42600 original size:1 final size:1
Alignment explanation
Indices: 42594--42635 Score: 75
Period size: 1 Copynumber: 42.0 Consensus size: 1
42584 ATAATGATTG
*
42594 TTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42636 ATGAGATCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:53980 original size:14 final size:14
Alignment explanation
Indices: 53961--53990 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53951 TTTAATTTCT
53961 TTTCAAATAAGTCC
1 TTTCAAATAAGTCC
*
53975 TTTCAATTAAGTCC
1 TTTCAAATAAGTCC
53989 TT
1 TT
53991 GAAACTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTCAAATAAGTCC
Found at i:58668 original size:13 final size:13
Alignment explanation
Indices: 58652--58704 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
58642 TATTCTTTAT
*
58652 TTTTTTAGATTAA
1 TTTTTTATATTAA
*
58665 TTTTTCATATTAA
1 TTTTTTATATTAA
58678 TTTTTT-TATTAA
1 TTTTTTATATTAA
*
58690 TATTTTATATATAA
1 TTTTTTATAT-TAA
58704 T
1 T
58705 GAATGATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.32
13 19 0.56
14 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (13 bp):
TTTTTTATATTAA
Found at i:58701 original size:27 final size:26
Alignment explanation
Indices: 58650--58704 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
58640 TTTATTCTTT
58650 ATTTTTTTAGATTAATTTTTCATATTA
1 ATTTTTTTA-ATTAATTTTTCATATTA
58677 ATTTTTTT-ATTAATATTTT-ATATATA
1 ATTTTTTTAATTAAT-TTTTCATAT-TA
58703 AT
1 AT
58705 GAATGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 10 0.38
26 8 0.31
27 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTTTTTTAATTAATTTTTCATATTA
Found at i:59506 original size:16 final size:18
Alignment explanation
Indices: 59477--59513 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
59467 GCTAGTACTC
59477 AATTTTTTAATTCAAA-A
1 AATTTTTTAATTCAAATA
*
59494 AATTTTTT-TTTCAAATA
1 AATTTTTTAATTCAAATA
59511 AAT
1 AAT
59514 GCTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTTTTAATTCAAATA
Done.