Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014037.1 Corchorus capsularis cultivar CVL-1 contig14058, 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: 111756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1788 original size:3 final size:3
Alignment explanation
Indices: 1782--1816 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1772 TCCTAAAAAA
1782 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1817 TGGTGGTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6427 original size:13 final size:13
Alignment explanation
Indices: 6409--6436 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6399 GAGTGATTAA
6409 AACTGTTTAGGAT
1 AACTGTTTAGGAT
6422 AACTGTTTAGGAT
1 AACTGTTTAGGAT
6435 AA
1 AA
6437 ATTTGAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (13 bp):
AACTGTTTAGGAT
Found at i:15797 original size:23 final size:23
Alignment explanation
Indices: 15763--15807 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
15753 GATCTACTAA
*
15763 CTTTGAAGCTGCATTAAAGTGCT
1 CTTTGAAACTGCATTAAAGTGCT
15786 CTTTGAAACTGCATTAAAGTGC
1 CTTTGAAACTGCATTAAAGTGC
15808 ATCTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (23 bp):
CTTTGAAACTGCATTAAAGTGCT
Found at i:17275 original size:206 final size:206
Alignment explanation
Indices: 16921--17333 Score: 781
Period size: 206 Copynumber: 2.0 Consensus size: 206
16911 TTATAAGATT
16921 AACTTTAGCTCAACAGAAGGGTTAAAATAAAGCTGAAAGCTGGAGAAGTATATCAGAATATGGGG
1 AACTTTAGCTCAACAGAAGGGTTAAAATAAAGCTGAAAGCTGGAGAAGTATATCAGAATATGGGG
* *
16986 ATTTTTATTCTACTCTTTATATTTCTCTTTTGAAGTCAAATGAAGTTTAAATACATGTTTAACAT
66 ATTTTTATTCTACTCTTTATATATCTCTTTTGAAGTCAAATGAAGTTTAAATACACGTTTAACAT
*
17051 CATTCAACAGGAATTTTTATATGAATTCATGCACATAGGTCTCTGCAATTCTCAAACATTTAAAT
131 CATTCAACAGGAATTTTTATATGAATTCATGCACATAGGCCTCTGCAATTCTCAAACATTTAAAT
*
17116 ATCAGCACCTC
196 ATCAACACCTC
17127 AACTTTAGCTCAACAGAAGGGTTAAAATAAAGCTGAAAGCTGGAGAAGTATATCAGAATATGGGG
1 AACTTTAGCTCAACAGAAGGGTTAAAATAAAGCTGAAAGCTGGAGAAGTATATCAGAATATGGGG
*
17192 ATTTTTATTCTACTCTTTATATATGTCTTTTGAAGTCAAATGAAGTTTAAATACACGTTTAACAT
66 ATTTTTATTCTACTCTTTATATATCTCTTTTGAAGTCAAATGAAGTTTAAATACACGTTTAACAT
17257 CATTCAACAGGAATTTTTATATGAATTCATGCACATAGGCCTCTGCAATTCTCAAACATTTAAAT
131 CATTCAACAGGAATTTTTATATGAATTCATGCACATAGGCCTCTGCAATTCTCAAACATTTAAAT
17322 ATCAACACCTC
196 ATCAACACCTC
17333 A
1 A
17334 TTGTGCACAG
Statistics
Matches: 202, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
206 202 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (206 bp):
AACTTTAGCTCAACAGAAGGGTTAAAATAAAGCTGAAAGCTGGAGAAGTATATCAGAATATGGGG
ATTTTTATTCTACTCTTTATATATCTCTTTTGAAGTCAAATGAAGTTTAAATACACGTTTAACAT
CATTCAACAGGAATTTTTATATGAATTCATGCACATAGGCCTCTGCAATTCTCAAACATTTAAAT
ATCAACACCTC
Found at i:18873 original size:20 final size:20
Alignment explanation
Indices: 18836--18874 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18826 TATACGCCAA
* **
18836 AAAGAAAGCATATTACAGAG
1 AAAGAAAGCAGAGAACAGAG
18856 AAAGAAAGCAGAGAACAGA
1 AAAGAAAGCAGAGAACAGA
18875 ATAAACAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.10, G:0.23, T:0.08
Consensus pattern (20 bp):
AAAGAAAGCAGAGAACAGAG
Found at i:22834 original size:17 final size:17
Alignment explanation
Indices: 22812--22855 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
22802 TATGATTTTA
*
22812 TATATATATATATATAT
1 TATATATATATATAGAT
22829 TATATA-ATTATATAGAT
1 TATATATA-TATATAGAT
22846 TAT-TATATAT
1 TATATATATAT
22856 TTTATACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TATATATATATATAGAT
Found at i:22842 original size:29 final size:27
Alignment explanation
Indices: 22798--22861 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
22788 CAAGAACCCG
* * *
22798 ATTATATGATTTTATATATATATATATAT
1 ATTATATAATTATATAGAT-TAT-TATAT
22827 ATTATATAATTATATAGATTATTATAT
1 ATTATATAATTATATAGATTATTATAT
*
22854 ATTTTATA
1 ATTATATA
22862 CTGAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 12 0.39
28 3 0.10
29 16 0.52
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
ATTATATAATTATATAGATTATTATAT
Found at i:23221 original size:21 final size:21
Alignment explanation
Indices: 23196--23237 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
23186 CCCGAGGAAT
23196 TGGTGAACCCCGACGCCGACA
1 TGGTGAACCCCGACGCCGACA
23217 TGGTGAACCCCGACGCCGACA
1 TGGTGAACCCCGACGCCGACA
23238 ACACTGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.10
Consensus pattern (21 bp):
TGGTGAACCCCGACGCCGACA
Found at i:25886 original size:22 final size:21
Alignment explanation
Indices: 25851--25907 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
25841 CCTTGATCTC
25851 TGTATATATATGTAGT-TGGTA
1 TGTATATATATGTA-TATGGTA
*
25872 TGTATAGTGTATGTATATGGTA
1 TGTATA-TATATGTATATGGTA
25894 TGTA-AT-TATGTATA
1 TGTATATATATGTATA
25908 CTTAATCTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 1 0.03
21 8 0.24
22 16 0.48
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
TGTATATATATGTATATGGTA
Found at i:35158 original size:2 final size:2
Alignment explanation
Indices: 35151--35209 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
35141 AGAAACCAAA
*
35151 AT AT AT AT AT AT AT AT AG AGT -T ACT -T A- AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT
35191 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
35210 AAAGCCAAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
1 4 0.08
2 44 0.90
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:41994 original size:131 final size:130
Alignment explanation
Indices: 41840--42152 Score: 355
Period size: 131 Copynumber: 2.4 Consensus size: 130
41830 ACCGGCAATG
* * *
41840 ACTAAAGAAGTGTTGTCTAAAATACTATCAAAATTACTTAGACAATGACTTTATAAAGTTGCTAC
1 ACTAAACAAGTGTTGTCTAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGCTAC
* * * *
41905 G-AGCATATTATGATT-TCGCAACGACTTTGTTTTTTTTTGCTACGAAAACTGTAAACATCGGTA
66 GAAG-AAATTATG-TTCCCGCAACGACATTG-TTTTTGTTGCTACGAAAACTGTAAACATCGGTA
41968 ACT
128 ACT
* * *
41971 ACTAAACAGGTGTTGTGTAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGTTAC
1 ACTAAACAAGTGTTGTCTAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGCTAC
* * * * * ** * *
42036 GAAGAAATTATGTTCCCGCAATGACATTGTTTTTGTTGTTACGAAAATTGTAAATATTGACAGCG
66 GAAGAAATTATGTTCCCGCAACGACATTGTTTTTGTTGCTACGAAAACTGTAAACATCGGTAACT
* * *
42101 AC-AAAAAAGT-TAATGTATAAAATACCATCAAAATCACTTAGACAACGACTTT
1 ACTAAACAAGTGT--TGTCTAAAATACCATCAAAATCACTTAGACAATGACTTT
42153 TAATTATTGT
Statistics
Matches: 155, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
128 1 0.01
129 6 0.04
130 68 0.44
131 78 0.50
132 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (130 bp):
ACTAAACAAGTGTTGTCTAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGCTAC
GAAGAAATTATGTTCCCGCAACGACATTGTTTTTGTTGCTACGAAAACTGTAAACATCGGTAACT
Found at i:42151 original size:130 final size:131
Alignment explanation
Indices: 41857--42152 Score: 346
Period size: 130 Copynumber: 2.3 Consensus size: 131
41847 AAGTGTTGTC
* * * *
41857 TAAAATACTATCAAAATTACTTAGACAATGACTTTATAAAGTTGCTACGAGCATATTATGATTTC
1 TAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGCTACGAGCAAATTATGATTCC
* * ** * * * **
41922 GCAACGACTTTGTTTTTTTTTGCTACGAAAACTGTAAACATCGGTAACTACTAAACAGGTGTTGT
66 GCAACGACATTGTTTTTTGTTGCTACGAAAACTGTAAACATCGACAACGACAAAAAAGGTAATGT
*
41987 G
131 A
*
41988 TAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGTTACGAAG-AAATTATG-TTC
1 TAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGCTACG-AGCAAATTATGATT-
* * * * * * *
42051 CCGCAATGACATTG-TTTTTGTTGTTACGAAAATTGTAAATATTGACAGCGACAAAAAAGTTAAT
64 CCGCAACGACATTGTTTTTTGTTGCTACGAAAACTGTAAACATCGACAACGACAAAAAAGGTAAT
42115 GTA
129 GTA
*
42118 TAAAATACCATCAAAATCACTTAGACAACGACTTT
1 TAAAATACCATCAAAATCACTTAGACAATGACTTT
42153 TAATTATTGT
Statistics
Matches: 140, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
130 74 0.53
131 64 0.46
132 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (131 bp):
TAAAATACCATCAAAATCACTTAGACAATGACTTTATAAAGTTGCTACGAGCAAATTATGATTCC
GCAACGACATTGTTTTTTGTTGCTACGAAAACTGTAAACATCGACAACGACAAAAAAGGTAATGT
A
Found at i:42454 original size:2 final size:2
Alignment explanation
Indices: 42447--42478 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42437 GATTAAATCT
*
42447 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42479 AAAGATTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:56397 original size:18 final size:19
Alignment explanation
Indices: 56351--56400 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
56341 TTATTAAATT
56351 TTTTATTTTAAAATTTAAA
1 TTTTATTTTAAAATTTAAA
*
56370 CTTTATTTTAAAA-TTAATA
1 TTTTATTTTAAAATTTAA-A
56389 TTTTA-TTTAAAA
1 TTTTATTTTAAAA
56401 AAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATTTTAAAATTTAAA
Found at i:63173 original size:109 final size:109
Alignment explanation
Indices: 62985--63280 Score: 372
Period size: 109 Copynumber: 2.8 Consensus size: 109
62975 AGAAAATTAT
* * * * *
62985 AAAATTAA-AAGTTTTTTATTATAGAGTTTTAGAAAT--AATTATATAAAACTAATTTTACTAAA
1 AAAATTAATAA-TTTATTGTTATAGGGTTTTAGAAATAAAATTA-ATAAAACTAATTTCACTAAG
* *
63047 TTTAGCTCCAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTTC
64 TTTAGCCCCAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCC
*
63093 AAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATTAAAAAAACTAATTTCACTAAGTT
1 AAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATTAATAAAACTAATTTCACTAAGTT
* * *
63158 TAGCCCCAAATTAAAATCTTATTTTTATTTTAATGGTAAATTCC
66 TAGCCCCAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCC
** * * * *
63202 ATGATTAATAATTTACTGTTTTCGGGTTTTAGAAATAAAA-T-ATATAACTAA-TTCACTAAGTT
1 AAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATTAATAAAACTAATTTCACTAAGTT
63264 TAG-CCCAAATTAAAATT
66 TAGCCCCAAATTAAAATT
63281 AAAATTTTAT
Statistics
Matches: 166, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
105 13 0.08
106 14 0.08
107 8 0.05
108 31 0.19
109 95 0.57
110 5 0.03
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (109 bp):
AAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATTAATAAAACTAATTTCACTAAGTT
TAGCCCCAAATTAAAATTTTATTTCTATTTTAAGGGTAAATTCC
Found at i:71345 original size:31 final size:31
Alignment explanation
Indices: 71310--71370 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
71300 AAATAACTTG
*
71310 AATTTGGGAAGTTCA-CGGACAAAATGTCCTA
1 AATTT-GGAAATTCATCGGACAAAATGTCCTA
* *
71341 AATTTGGAAATTCATGGGGCAAAATGTCCT
1 AATTTGGAAATTCATCGGACAAAATGTCCT
71371 TTACGCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (31 bp):
AATTTGGAAATTCATCGGACAAAATGTCCTA
Found at i:75312 original size:26 final size:26
Alignment explanation
Indices: 75273--75326 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
75263 CCCAGCTGGC
*
75273 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCACACATGACCTCCAACGTACG
*
75299 ACTCTACACATGACCTCCAACGTACG
1 ACTCCACACATGACCTCCAACGTACG
75325 AC
1 AC
75327 CCGTACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.41, G:0.13, T:0.17
Consensus pattern (26 bp):
ACTCCACACATGACCTCCAACGTACG
Found at i:77609 original size:88 final size:88
Alignment explanation
Indices: 77451--77621 Score: 245
Period size: 88 Copynumber: 1.9 Consensus size: 88
77441 GCTCGAACCT
* * * * *
77451 AATAATTTTCATTATAAATTTAAATATTTACCTATTATATGAAAGATTCAAACCTGATGAAAACT
1 AATAATTTTCATCACAAATTTAAACATTTACCTATTATATGAAAGATTCAAACCTAACGAAAACT
77516 CGAACCCGATAACTTTCATCACG
66 CGAACCCGATAACTTTCATCACG
* *
77539 AATAATTTTCATCACAAATTTAAACATTTACCTATTATATGAAAGACTT-GAACCTAACGAAGAC
1 AATAATTTTCATCACAAATTTAAACATTTACCTATTATATGAAAGA-TTCAAACCTAACGAAAAC
* *
77603 TTGAACCCGATACCTTTCA
65 TCGAACCCGATAACTTTCA
77622 CCACAAATCT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 71 0.97
89 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (88 bp):
AATAATTTTCATCACAAATTTAAACATTTACCTATTATATGAAAGATTCAAACCTAACGAAAACT
CGAACCCGATAACTTTCATCACG
Found at i:85923 original size:21 final size:21
Alignment explanation
Indices: 85886--85925 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
85876 AAATAACTTA
*
85886 CCAAATTGGTTGCTTTTTACC
1 CCAAATTAGTTGCTTTTTACC
85907 CCAAATTAGTT-CATTTTTA
1 CCAAATTAGTTGC-TTTTTA
85926 AGTTCTATAA
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:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (21 bp):
CCAAATTAGTTGCTTTTTACC
Found at i:93885 original size:7 final size:7
Alignment explanation
Indices: 93873--93899 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
93863 TTGATTTTGG
93873 TTTTGAT
1 TTTTGAT
93880 TTTTGAT
1 TTTTGAT
93887 TTTTGAT
1 TTTTGAT
93894 TTTTGA
1 TTTTGA
93900 ATGAATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (7 bp):
TTTTGAT
Found at i:95181 original size:80 final size:80
Alignment explanation
Indices: 95048--95205 Score: 226
Period size: 80 Copynumber: 2.0 Consensus size: 80
95038 ACTTAAAACC
* * ** * *
95048 AATTAGCAATAGATGGAGAAGCTCGACTTGAATGTTAGTTATTCAGTAATGTCAAACTTATCAGA
1 AATTAGCAATAGATGGAGAAGCCCGACTTAAATGACAATTATTCAGTAATGTCAAACTTAACAGA
95113 TGTGGGATATTACCA
66 TGTGGGATATTACCA
* * * *
95128 AATTAGTAATAGGTGGAGAGGCCCGACTTAAATGACAATTATTTAGTAATGTCAAACTTAACAGA
1 AATTAGCAATAGATGGAGAAGCCCGACTTAAATGACAATTATTCAGTAATGTCAAACTTAACAGA
95193 TGTGGGATATTAC
66 TGTGGGATATTAC
95206 AACACTTTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (80 bp):
AATTAGCAATAGATGGAGAAGCCCGACTTAAATGACAATTATTCAGTAATGTCAAACTTAACAGA
TGTGGGATATTACCA
Found at i:96524 original size:29 final size:29
Alignment explanation
Indices: 96482--96541 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
96472 ACCTTTCTTA
96482 ATCAAAAATCTCACTAATTGATTTAACTT
1 ATCAAAAATCTCACTAATTGATTTAACTT
96511 ATCAAAAATCTCACTAATTGATTTAACTT
1 ATCAAAAATCTCACTAATTGATTTAACTT
96540 AT
1 AT
96542 TGGCTAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (29 bp):
ATCAAAAATCTCACTAATTGATTTAACTT
Found at i:102873 original size:21 final size:19
Alignment explanation
Indices: 102840--102883 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
102830 GGCAATATTT
*
102840 ATAATGTAAAATTGTGCAA
1 ATAATGTAAAATTATGCAA
*
102859 ATAATAGTATAAATTATGTAA
1 ATAAT-GTA-AAATTATGCAA
102880 ATAA
1 ATAA
102884 CTTTCATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (19 bp):
ATAATGTAAAATTATGCAA
Found at i:105044 original size:15 final size:15
Alignment explanation
Indices: 105024--105054 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
105014 CAACCCCGCG
105024 TTCCATCCACATTTT
1 TTCCATCCACATTTT
105039 TTCCATCCACATTTT
1 TTCCATCCACATTTT
105054 T
1 T
105055 AATATTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
TTCCATCCACATTTT
Found at i:108823 original size:31 final size:29
Alignment explanation
Indices: 108788--108862 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 29
108778 ACTTAAATAC
108788 CAAATAAATCCCTTACCTTTTTATTTTGAGA
1 CAAATAAATCCCTTACCTTTTT-TTTTGA-A
* * *
108819 CAAATAAATCCCTGATCTTTTTTTTTGAC
1 CAAATAAATCCCTTACCTTTTTTTTTGAA
108848 CAAATAAATCCCTTA
1 CAAATAAATCCCTTA
108863 GCTACCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.35
30 6 0.15
31 20 0.50
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (29 bp):
CAAATAAATCCCTTACCTTTTTTTTTGAA
Done.