Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013900.1 Corchorus capsularis cultivar CVL-1 contig13921, 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: 36171
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:644 original size:32 final size:33
Alignment explanation
Indices: 584--660 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
574 GTTCAGGGGG
*
584 CAAACTGTCCT-GA-ATTTGAAAATTCATGAGA
1 CAAAGTGTCCTCGAGATTTGAAAATTCATGAGA
* * *
615 CAAATTGTCGTCGAGATTTG-AAGTTCATGAGA
1 CAAAGTGTCCTCGAGATTTGAAAATTCATGAGA
647 CAAAGTGTCCTCGA
1 CAAAGTGTCCTCGA
661 CATTGTAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 9 0.23
32 25 0.64
33 5 0.13
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (33 bp):
CAAAGTGTCCTCGAGATTTGAAAATTCATGAGA
Found at i:12330 original size:31 final size:32
Alignment explanation
Indices: 12273--12338 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
12263 AAACTTTATG
12273 TTTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTTCCGATTGTACCCTTATTTTTAAAACATA
*
12305 TTTTCCTATTGTACCCTT-TTTTTAAAACATA
1 TTTTCCGATTGTACCCTTATTTTTAAAACATA
12336 TTT
1 TTT
12339 CTAAATTGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTTCCGATTGTACCCTTATTTTTAAAACATA
Found at i:12398 original size:18 final size:19
Alignment explanation
Indices: 12349--12401 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
12339 CTAAATTGCC
*
12349 ATTACTAAATAATATTTTTA
1 ATTACTAAATTAT-TTTTTA
* **
12369 ATTATTCCATTATTTTTTA
1 ATTACTAAATTATTTTTTA
12388 ATTA-TAAATTATTT
1 ATTACTAAATTATTT
12402 CATTATATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTACTAAATTATTTTTTA
Found at i:12482 original size:22 final size:22
Alignment explanation
Indices: 12465--12557 Score: 134
Period size: 22 Copynumber: 4.2 Consensus size: 22
12455 ATCAAAAATC
12465 CATAGTGTGATTACCAAAATTT
1 CATAGTGTGATTACCAAAATTT
*
12487 CATAGTGTGGTTACCAAAATTT
1 CATAGTGTGATTACCAAAATTT
*
12509 CACAGTGT-AGTTACCAAAATTT
1 CATAGTGTGA-TTACCAAAATTT
* *
12531 CATAGAGTGGTTACCAAAATTT
1 CATAGTGTGATTACCAAAATTT
12553 CATAG
1 CATAG
12558 GATCAGGTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (22 bp):
CATAGTGTGATTACCAAAATTT
Found at i:12505 original size:44 final size:44
Alignment explanation
Indices: 12451--12549 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 44
12441 TCCATGACCA
* * *
12451 GGTTATCAAAAATCCATAGTGT-GATTACCAAAATTTCATAGTGT
1 GGTTACCAAAAATCCACAGTGTAG-TTACCAAAATTTCATAGAGT
* *
12495 GGTTACCAAAATTTCACAGTGTAGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAAATCCACAGTGTAGTTACCAAAATTTCATAGAGT
12539 GGTTACCAAAA
1 GGTTACCAAAA
12550 TTTCATAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
44 48 0.98
45 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (44 bp):
GGTTACCAAAAATCCACAGTGTAGTTACCAAAATTTCATAGAGT
Found at i:12591 original size:22 final size:22
Alignment explanation
Indices: 12480--12611 Score: 111
Period size: 22 Copynumber: 5.9 Consensus size: 22
12470 TGTGATTACC
* **
12480 AAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAGGGTGGTTATT
* * * **
12502 AAAATTTCACAGTGTAGTTACC
1 AAAATTTCATAGGGTGGTTATT
* **
12524 AAAATTTCATAGAGTGGTTACC
1 AAAATTTCATAGGGTGGTTATT
*
12546 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGGT--GGTTATT
* *
12570 AAAATTTCTTAGGTTGGTTATT
1 AAAATTTCATAGGGTGGTTATT
*
12592 GAAATTTCATAGGGTGGTTA
1 AAAATTTCATAGGGTGGTTA
12612 ATTATCACAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 76 0.81
24 18 0.19
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGGGTGGTTATT
Found at i:12702 original size:22 final size:22
Alignment explanation
Indices: 12650--12780 Score: 81
Period size: 22 Copynumber: 6.0 Consensus size: 22
12640 AAAAAGATTT
* *
12650 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* * *
12673 C-GATTTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
12694 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
12715 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* *
12738 CAAAATTTTATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
12760 CAAAATTTCATA-TGAAGGTTA
1 CAAAATTTCATAGTG-AGGTTA
12781 TAAAAGTCTC
Statistics
Matches: 79, Mismatches: 23, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
21 8 0.10
22 66 0.84
23 5 0.06
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:12855 original size:22 final size:23
Alignment explanation
Indices: 12825--12949 Score: 106
Period size: 22 Copynumber: 5.6 Consensus size: 23
12815 TGATAGAAAG
*
12825 TTATC-AAATCTCATATAG-TGA
1 TTATCAAAATTTCATATAGATGA
*
12846 TTATCAAAATTTCATAAAGATATGA
1 TTATCAAAATTTCATATAG--ATGA
*
12871 TTATCAAAATTT-ATAT-GAAGA
1 TTATCAAAATTTCATATAGATGA
*
12892 TTATCAAAATTTCATAGT-GTTG-
1 TTATCAAAATTTCATA-TAGATGA
12914 TTATCAAAATTTCA-A-AG-TGA
1 TTATCAAAATTTCATATAGATGA
12934 GGTTATCAAAATTTCA
1 --TTATCAAAATTTCA
12950 GGGAGGATAC
Statistics
Matches: 88, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 21 0.24
22 42 0.48
23 4 0.05
24 3 0.03
25 15 0.17
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATATAGATGA
Found at i:12888 original size:18 final size:19
Alignment explanation
Indices: 12865--12903 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
12855 TTTCATAAAG
12865 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
12883 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
12904 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:12970 original size:19 final size:19
Alignment explanation
Indices: 12932--13001 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
12922 ATTTCAAAGT
*
12932 GAGGTTATCAAAATTTCAGG
1 GAGGATATCAAAA-TTCAGG
*
12952 GAGGATACCAAAATTCAGG
1 GAGGATATCAAAATTCAGG
* *
12971 GAGGATATTAAAATTCAGT
1 GAGGATATCAAAATTCAGG
12990 GAGGATATCAAA
1 GAGGATATCAAA
13002 GTTTCATATG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 33 0.75
20 11 0.25
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (19 bp):
GAGGATATCAAAATTCAGG
Found at i:13020 original size:22 final size:22
Alignment explanation
Indices: 12995--13509 Score: 122
Period size: 22 Copynumber: 23.7 Consensus size: 22
12985 TCAGTGAGGA
*
12995 TATCAAAGTTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
13017 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
13039 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
13061 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
13082 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
13105 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * ** * * *
13127 TTTTAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
13149 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
13165 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
*
13187 TATCAAAATCTT-ATA-GGAGGTT
1 TATCAAAAT-TTCATATGAAGG-T
*
13209 TATTAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
13231 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
13253 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
13275 TACTAAAAAATTCATATGGAGGT
1 TA-TCAAAATTTCATATGAAGGT
** * *
13298 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
13320 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
13342 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
13365 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * * *
13387 CT-TTAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
13409 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* *
13431 T-TAAAAAATTT-ATA-AAAGGAT
1 TAT-CAAAATTTCATATGAAGG-T
* ** * **
13452 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
* *
13474 TATCAAAATTTCATA-GGAGCT
1 TATCAAAATTTCATATGAAGGT
13495 TATCAAAATTTCATA
1 TATCAAAATTTCATA
13510 ATTGGATCAT
Statistics
Matches: 358, Mismatches: 103, Indels: 65
0.68 0.20 0.12
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 9 0.03
21 46 0.13
22 234 0.65
23 52 0.15
24 5 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:13261 original size:44 final size:44
Alignment explanation
Indices: 12839--13263 Score: 202
Period size: 44 Copynumber: 10.0 Consensus size: 44
12829 CAAATCTCAT
*
12839 ATAGTGA--TTATCAAAATTTCATAAAGATATGATTATCAAAATTT-
1 ATAGTGAGGTTATCAAAATTTCAT--AG-TGTGATTATCAAAATTTC
*
12883 ATA-TGAAGATTATCAAAATTTCATAGTGTTG-TTATCAAAATTTC
1 ATAGTG-AGGTTATCAAAATTTCATAGTG-TGATTATCAAAATTTC
* ** * *
12927 AAAGTGAGGTTATCAAAATTTCAGGGAG-GA-TACCAAAA-TTC
1 ATAGTGAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTC
* * * * *
12968 --AGGGAGGATATTAAAA-TTC--AGTGAGGA-TATCAAAGTTTC
1 ATAGTGAGGTTATCAAAATTTCATAGTG-TGATTATCAAAATTTC
* * *
13007 ATA-TGAAGGTTATCAAATTTTCATAGT-TTAGTTTTCAAAATTTC
1 ATAGTG-AGGTTATCAAAATTTCATAGTGTGA-TTATCAAAATTTC
* * *
13051 ATA-AGAGGGTTATCAAAATTTCATAGTATG-TAGATCAAAATTTC
1 ATAGTGA-GGTTATCAAAATTTCATAGTGTGAT-TATCAAAATTTC
* * * * * * * * **
13095 ATAGGGAGATTAACAAAATTTCATAATGAGGTTTTTAAAAAATC
1 ATAGTGAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTC
* * * *
13139 ATAGGGAGCTTATCAAAA-TT--T-GT-AG-TTATCAAGATTTC
1 ATAGTGAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTC
* * * * *
13177 ATAAG-AAAGTTATCAAAATCTT-ATAG-GAGGTTTATTAAAATTTC
1 AT-AGTGAGGTTATCAAAAT-TTCATAGTG-TGATTATCAAAATTTC
*
13221 ATAGTGAGGTTATCACAATTTCATAGTGTGATTATCAAAATTT
1 ATAGTGAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTT
13264 TAAAGTGTGA
Statistics
Matches: 289, Mismatches: 58, Indels: 68
0.70 0.14 0.16
Matches are distributed among these distances:
36 2 0.01
38 31 0.11
39 20 0.07
40 4 0.01
41 15 0.05
42 13 0.04
43 24 0.08
44 158 0.55
45 7 0.02
46 15 0.05
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
ATAGTGAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTC
Found at i:30314 original size:217 final size:217
Alignment explanation
Indices: 29914--30325 Score: 653
Period size: 217 Copynumber: 1.9 Consensus size: 217
29904 TTTATTAATT
* * *
29914 GGGTAATTATTTGATACACAGTCGGTGTAAATTTGGGACTCCACAAGCGGGTTGTGGAGTTGACA
1 GGGTAATTATATGATACACAGGCGGTGTAAATTTGGGACTCCACAAGCGGCTTGTGGAGTTGACA
29979 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTC
66 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTC
* * * *
30044 ACCCTTCAGGACACATTTGTGTAGCCTGCTAAACTCTACTGACGGTATATTGTATAATTTGCCTT
131 ACCCTTCAGGACACACTTGTGTAACCTGCTAAACTCCACCGACGGTATATTGTATAATTTGCCTT
30109 ATTAATTTATACATTTTTTTTG
196 ATTAATTTATACATTTTTTTTG
* * *
30131 GGGTGATTATATGATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGCTTGTGGAGTTGACA
1 GGGTAATTATATGATACACAGGCGGTGTAAATTTGGGACTCCACAAGCGGCTTGTGGAGTTGACA
*
30196 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTC
66 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTC
* * * ** * * *
30261 ACCCTTTAGGACCCGCTTGTGTAATTTTCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCTT
131 ACCCTTCAGGACACACTTGTGTAACCTGCTAAACTCCACCGACGGTATATTGTATAATTTGCCTT
30326 TTTTTTTAGG
Statistics
Matches: 176, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
217 176 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (217 bp):
GGGTAATTATATGATACACAGGCGGTGTAAATTTGGGACTCCACAAGCGGCTTGTGGAGTTGACA
CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACACATGTC
ACCCTTCAGGACACACTTGTGTAACCTGCTAAACTCCACCGACGGTATATTGTATAATTTGCCTT
ATTAATTTATACATTTTTTTTG
Found at i:31568 original size:2 final size:2
Alignment explanation
Indices: 31556--31585 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31546 GTACGTGAAT
*
31556 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31586 CTAGTAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31780 original size:25 final size:25
Alignment explanation
Indices: 31752--31801 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
31742 CATTTTGAAC
31752 AAATTAGTATTGATTAGTAACCAAG
1 AAATTAGTATTGATTAGTAACCAAG
*
31777 AAATTAGTATTGATTAGTATCCAAG
1 AAATTAGTATTGATTAGTAACCAAG
31802 CACACGTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (25 bp):
AAATTAGTATTGATTAGTAACCAAG
Found at i:33923 original size:41 final size:42
Alignment explanation
Indices: 33866--33949 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
33856 CGTATGGCTG
33866 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
*
33907 TTTTATTTTCTAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
33949 T
1 T
33950 GAAATTATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 23 0.56
42 18 0.44
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (42 bp):
TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
Found at i:34271 original size:11 final size:11
Alignment explanation
Indices: 34257--34294 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
34247 ATTCATAACA
34257 AATTTATAATT
1 AATTTATAATT
34268 AATTTATAATT
1 AATTTATAATT
34279 -ATTTGATAATT
1 AATTT-ATAATT
*
34290 TATTT
1 AATTT
34295 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:34515 original size:14 final size:14
Alignment explanation
Indices: 34496--34522 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34486 TAGTATTTTT
34496 ATTTTATTAGAAAC
1 ATTTTATTAGAAAC
34510 ATTTTATTAGAAA
1 ATTTTATTAGAAA
34523 TTACGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
ATTTTATTAGAAAC
Found at i:35490 original size:166 final size:166
Alignment explanation
Indices: 35216--35531 Score: 469
Period size: 166 Copynumber: 1.9 Consensus size: 166
35206 AACATATGGA
* * *
35216 AATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTC
1 AATTACTAAAAAATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCATCTTTAC
* *
35281 ACACTTGACCGATTACTTAAATGCCCTAACTTTTGATTCTTGAGGTG-ATTAAATAACTAGACTT
66 ACACTTGACAGATTACTTAAATGCCCTAACTTTTGATTCTTGAGG-GAATTAAATAACTAAACTT
35345 TTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGG
130 TTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGG
* *
35382 AATTACTAAAAAATCCCTACCCCGGATTAATGATGAGCTG-GAGAAGT-ATTCTTTTTCATCTTT
1 AATTACTAAAAAATCCCTACCCCGGATTAATGAGGAGC-GAGAGAACTAATT-TTTTTCATCTTT
* * * *
35445 AC-CTACTTGACATATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGAATTAAATATCTAAAC
64 ACAC-ACTTGACAGATTACTTAAATGCCCTAACTTTTGATTCTTGAGGGAATTAAATAACTAAAC
35509 TTTTTGGTCATTTCTCAATTGAC
128 TTTTTGGTCATTTCTCAATTGAC
35532 AAATGACTCA
Statistics
Matches: 135, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
165 5 0.04
166 129 0.96
167 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (166 bp):
AATTACTAAAAAATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCATCTTTAC
ACACTTGACAGATTACTTAAATGCCCTAACTTTTGATTCTTGAGGGAATTAAATAACTAAACTTT
TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGG
Found at i:35841 original size:2 final size:2
Alignment explanation
Indices: 35836--35866 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35826 TGAAGATAGT
35836 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35867 AATGAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.