Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008090.1 Corchorus capsularis cultivar CVL-1 contig08111, 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: 28197
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:432 original size:48 final size:45
Alignment explanation
Indices: 378--470 Score: 141
Period size: 48 Copynumber: 2.0 Consensus size: 45
368 AGCACAGGAG
* *
378 GAGCAATTGATTGGCTTGGGAAAAAATTCCCTTTTTTTTTAATACTAA
1 GAGCAATTGATTGGCTAGGGAAAAAA-T-CC-TTTTTTATAATACTAA
426 GAGCAATTGATTGGCTAGGGAAAAAATCCTTTTTTATAATACTAA
1 GAGCAATTGATTGGCTAGGGAAAAAATCCTTTTTTATAATACTAA
471 CTCTCTGATA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 15 0.35
46 2 0.05
47 1 0.02
48 25 0.58
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (45 bp):
GAGCAATTGATTGGCTAGGGAAAAAATCCTTTTTTATAATACTAA
Found at i:7508 original size:420 final size:419
Alignment explanation
Indices: 6727--7520 Score: 1024
Period size: 420 Copynumber: 1.9 Consensus size: 419
6717 TAAATCGAGT
** * * *
6727 AAGATAGAATTTGTAAAGGACAAAGTAGTATAAATTAAAAAAGTATGAGGATCATTTAATAAATA
1 AAGATAGAATCAGTAAAGGACAAAGTAGTATAAAGTAAAAAAGTATGAGGATCATCTAAAAAATA
* *
6792 ATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGAAATATAAAAATTCCCTTTTGAACCATTC
66 ATCCAAATAAAAAAATGTTTGTTGATGGAAATCTTGAAATATAAAAATTCCCTTTTGAACCATTC
* * * * * *
6857 ATGAAACTTTAGATCAAATTTAGCTTTCGGGTCTTTCATAAAGATTGTAGCTCATGCAATAACTT
131 ATGAAACTGTAAATCAAATTTAGCTTTCGGATCCTTCATAAAGATCGTAGATCATGCAATAACTT
* * *
6922 TTTAACCAACACTTGAATAACTTTAATCAGACATGTAGATCAAAAATTATATGCTATTAAATAGA
196 TCTAACCAACACTTGAATAACTTTAATCAGACATGTAGATCAAAAATTATATGATATGAAATAGA
* * * * *
6987 CCGGCAACCGAAACCGCCAAATTTGAAAAGCATTTTTTTGAATTGAAACATAAAAATTGACTTTT
261 CCGGCAACCGAAACCACAAAATTTGAAAAGCATTTTTTTGAAATGAAACAGAAAAATTGACTTGT
*
7052 GAGTCATTAGTGGAAATTATAGATCATGAAATTACCTTTTAATAGACACCTTAATCGGACAAATA
326 GAGTCATTAATGGAAATTATAGATCATGAAATTACCTTTTAATAGACACCTTAATCGGACAAATA
7117 TAGTAAAAAATAAAAAAATCTGATCAATC
391 TAGTAAAAAATAAAAAAATCTGATCAATC
* * *
7146 AAGATAGAATCAGTAAAGGACTATA-TAGTATAAAGTACTAAAA-TATGTGGATCATCTAAAAAA
1 AAGATAGAATCAGTAAAGGAC-AAAGTAGTATAAAGTA-AAAAAGTATGAGGATCATCTAAAAAA
* * * * * *
7209 TAATCCAAATAAAAAAATGTTTGTTGATGGAAATCTTGGAGTATAAAACTTCTCTTTTGAGCCCT
64 TAATCCAAATAAAAAAATGTTTGTTGATGGAAATCTTGAAATATAAAAATTCCCTTTTGAACCAT
7274 TCATGAAACTCGTAAATCAAATTTAGCTTTCGGATCCTTCATGAAAGA-CGTAGATCATGCAATA
129 TCATGAAACT-GTAAATCAAATTTAGCTTTCGGATCCTTCAT-AAAGATCGTAGATCATGCAATA
** ** * * * * *
7338 A-TCTTCTAACCGGCACTTTCATAACTTTAATCGGACATGTGGATCGAAAGTTTTATGATATGAA
192 ACT-TTCTAACCAACACTTGAATAACTTTAATCAGACATGTAGATCAAAAATTATATGATATGAA
** * * *
7402 ATAGATGGGCAATCGAAACCACAAAATTTCG-GAAGCATTTTTTTGAAATGAAACGGAAAAATTG
256 ATAGACCGGCAACCGAAACCACAAAATTT-GAAAAGCATTTTTTTGAAATGAAACAGAAAAATTG
** * * * *
7466 GGTTGTGGGTCCTTAAT-GAAAGTTGTAGATCATGACATTACCTTTTAATAGACAC
320 ACTTGTGAGTCATTAATGGAAA-TTATAGATCATGAAATTACCTTTTAATAGACAC
7521 ATGAATTATC
Statistics
Matches: 317, Mismatches: 51, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
419 119 0.38
420 192 0.61
421 6 0.02
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (419 bp):
AAGATAGAATCAGTAAAGGACAAAGTAGTATAAAGTAAAAAAGTATGAGGATCATCTAAAAAATA
ATCCAAATAAAAAAATGTTTGTTGATGGAAATCTTGAAATATAAAAATTCCCTTTTGAACCATTC
ATGAAACTGTAAATCAAATTTAGCTTTCGGATCCTTCATAAAGATCGTAGATCATGCAATAACTT
TCTAACCAACACTTGAATAACTTTAATCAGACATGTAGATCAAAAATTATATGATATGAAATAGA
CCGGCAACCGAAACCACAAAATTTGAAAAGCATTTTTTTGAAATGAAACAGAAAAATTGACTTGT
GAGTCATTAATGGAAATTATAGATCATGAAATTACCTTTTAATAGACACCTTAATCGGACAAATA
TAGTAAAAAATAAAAAAATCTGATCAATC
Found at i:10721 original size:18 final size:18
Alignment explanation
Indices: 10646--10717 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 18
10636 ATCCGCTACT
*
10646 CAAAATCCAAAGAAGCTA
1 CAAAATCCAAAGAAACTA
10664 CAAAAT-CAAAGAAAACTAA
1 CAAAATCCAAAG-AAACT-A
10683 CTAGAACATCCAAAGAAACTA
1 C-A-AA-ATCCAAAGAAACTA
10704 CAAAAT-CAAAGAAA
1 CAAAATCCAAAGAAA
10718 ACTAACTCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
17 13 0.28
18 12 0.26
19 4 0.09
20 2 0.04
21 4 0.09
22 7 0.15
23 5 0.11
ACGTcount: A:0.61, C:0.19, G:0.08, T:0.11
Consensus pattern (18 bp):
CAAAATCCAAAGAAACTA
Found at i:10724 original size:22 final size:22
Alignment explanation
Indices: 10661--10724 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
10651 TCCAAAGAAG
10661 CTACAAAATCAAAGAAAACTAA
1 CTACAAAATCAAAGAAAACTAA
* *
10683 CTAGAACATCCAAAG---A--AA
1 CTACAAAAT-CAAAGAAAACTAA
10701 CTACAAAATCAAAGAAAACTAA
1 CTACAAAATCAAAGAAAACTAA
10723 CT
1 CT
10725 CTCAGGCTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 5 0.16
18 9 0.28
20 2 0.06
22 11 0.34
23 5 0.16
ACGTcount: A:0.59, C:0.20, G:0.06, T:0.14
Consensus pattern (22 bp):
CTACAAAATCAAAGAAAACTAA
Found at i:19118 original size:3 final size:3
Alignment explanation
Indices: 19112--19144 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
19102 ATATATATAT
19112 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19145 TAAAAAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19275 original size:13 final size:13
Alignment explanation
Indices: 19257--19282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19247 ATTAATTTTC
19257 TTTTTTTGAGGAA
1 TTTTTTTGAGGAA
19270 TTTTTTTGAGGAA
1 TTTTTTTGAGGAA
19283 ATAATTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
TTTTTTTGAGGAA
Found at i:19556 original size:2 final size:2
Alignment explanation
Indices: 19511--19544 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
19501 GTTTGAAGGC
*
19511 TA TA CA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19545 GCAATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19688 original size:2 final size:2
Alignment explanation
Indices: 19681--19710 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19671 TTTTTGAAGA
19681 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19711 AAGATCATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.