Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010322.1 Corchorus olitorius cultivar O-4 contig10354, 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: 7393
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:448 original size:42 final size:42
Alignment explanation
Indices: 362--497 Score: 134
Period size: 42 Copynumber: 3.2 Consensus size: 42
352 CGTACTATAG
* * *
362 TATCAAAAAATTATAGGGAGATTAACAAAATCTCACA-GAGAGGT
1 TATC-AAAAATTATAGGAAGATT-ACAAAATTTCATAGGA-AGGT
*
406 TATCAAAAATCATAGGAAGATTACAAAATTTCATAGGAAGGTT
1 TATCAAAAATTATAGGAAGATTACAAAATTTCATAGGAAGG-T
* * **
449 TATTAAAATTTTATAGGAAGATT--AAAATTTCATAGTTAGGT
1 TATCAAAA-ATTATAGGAAGATTACAAAATTTCATAGGAAGGT
490 TATCAAAA
1 TATCAAAA
498 TTTCATATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
41 8 0.10
42 29 0.37
43 26 0.33
44 16 0.20
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.30
Consensus pattern (42 bp):
TATCAAAAATTATAGGAAGATTACAAAATTTCATAGGAAGGT
Found at i:566 original size:22 final size:22
Alignment explanation
Indices: 538--579 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
528 TCCAAACGTG
538 GTTATCAAAATTTAATAAAGTA
1 GTTATCAAAATTTAATAAAGTA
*
560 GTTATCAAAATTTCATAAAG
1 GTTATCAAAATTTAATAAAG
580 ATATTCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTAATAAAGTA
Found at i:1595 original size:118 final size:118
Alignment explanation
Indices: 1435--1674 Score: 437
Period size: 118 Copynumber: 2.0 Consensus size: 118
1425 TGTTGCAAGT
* *
1435 TCAA-ATCCCACCACAAACAACTCTTTTTTCCAAATTTTAAAATTTTAGATGCAGTCAAATTTGT
1 TCAACATCCCACCACAAACAACTCTTTGTTCCAAATTTTAAAATTTTAGATGCACTCAAATTTGT
* *
1499 CTAAAATTGGTCAAATCAGTCCAGTTTCTCAGTTCAATCGACGGTCAAACCGG
66 CTAAAATCGGTCAAATCAGTCCAGTTTCCCAGTTCAATCGACGGTCAAACCGG
1552 TCAACATCCCACCACAAACAACTCTTTGTTCCAAATTTTAAAATTTTAGATGCACTCAAATTTGT
1 TCAACATCCCACCACAAACAACTCTTTGTTCCAAATTTTAAAATTTTAGATGCACTCAAATTTGT
1617 CTAAAATCGGTCAAATCAGTCCAGTTTCCCAGTTCAATCGACGGTCAAACCGG
66 CTAAAATCGGTCAAATCAGTCCAGTTTCCCAGTTCAATCGACGGTCAAACCGG
1670 TCAAC
1 TCAAC
1675 GTCAATTGTT
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
117 4 0.03
118 114 0.97
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (118 bp):
TCAACATCCCACCACAAACAACTCTTTGTTCCAAATTTTAAAATTTTAGATGCACTCAAATTTGT
CTAAAATCGGTCAAATCAGTCCAGTTTCCCAGTTCAATCGACGGTCAAACCGG
Found at i:2525 original size:100 final size:102
Alignment explanation
Indices: 2307--2563 Score: 308
Period size: 108 Copynumber: 2.5 Consensus size: 102
2297 TATTATAGAA
* *
2307 TTTTAGAAATAGAATATAAAACTAATTTCACTAAGTTTAGTCCCAAAATTAAAATTTTATTTTTA
1 TTTTAGAAATAAAATATAAAACT-ATTTCACTAAGTTTAG-CCCCAAATT--AA-TTTATTTTTA
* * * *
2372 TTTTAAGGGTATATTTCAAAATTAATAATTTATTGTTTCTAGG
61 TTTTAAGAGTAAATTCCAAAATTAATAA-TTATTGTTTATAGG
*
2415 TTTTAGAAATAAAATACAAAACTCATTTCACTAAGTTTAGCCCCAAATTAA-TT-TTTTTATTTT
1 TTTTAGAAATAAAATATAAAACT-ATTTCACTAAGTTTAGCCCCAAATTAATTTATTTTTATTTT
*
2478 AAGAGTAAATTCCATAATTAATAA-TATTG-TTATAGGG
65 AAGAGTAAATTCCAAAATTAATAATTATTGTTTATA-GG
* * *
2515 TTTTATAAATAAAATATATAACTAATTCACTAAGTTTAG-CCCAAATTAA
1 TTTTAGAAATAAAATATAAAACTATTTCACTAAGTTTAGCCCCAAATTAA
2564 AATTAAAATT
Statistics
Matches: 135, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
98 10 0.07
99 19 0.14
100 27 0.20
102 30 0.22
103 2 0.01
105 2 0.01
107 8 0.06
108 37 0.27
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (102 bp):
TTTTAGAAATAAAATATAAAACTATTTCACTAAGTTTAGCCCCAAATTAATTTATTTTTATTTTA
AGAGTAAATTCCAAAATTAATAATTATTGTTTATAGG
Found at i:2597 original size:100 final size:97
Alignment explanation
Indices: 2307--2605 Score: 270
Period size: 100 Copynumber: 2.9 Consensus size: 97
2297 TATTATAGAA
* *
2307 TTTTAGAAATAGAATATAAAACTAATTTCACTAAGTTTAGTCCCAAAATTAAAATTTTATTTTTA
1 TTTTAGAAATAAAATATAAAACTAA-TTCACTAAGTTTAG-CCCCAAATTAAAA--TTATTTTTA
* *
2372 TTTTAAGGGTATATTTCAAAATTAATAATTTATTGTTTCTAGG
62 TTTTAAGGGT-TA---AAAAATTAATAA--TATTG-TTATAGG
* *
2415 TTTTAGAAATAAAATACAAAACTCATTTCACTAAGTTTAGCCCCAAATT--AATT-TTTTTATTT
1 TTTTAGAAATAAAATATAAAACT-AATTCACTAAGTTTAGCCCCAAATTAAAATTATTTTTATTT
*
2477 TAAGAG-TAAATTCCATAATTAATAATATTGTTATAGGG
65 TAAGGGTTAAA----A-AATTAATAATATTGTTATA-GG
* * *
2515 TTTTATAAATAAAATATATAACTAATTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATT
1 TTTTAGAAATAAAATATAAAACTAATTCACTAAGTTTAGCCCCAAATTAAAATT--ATTTTTATT
2579 TTAAGGGTTAGAAAAATTAA-AAT-TTGT
64 TTAAGGGTTA-AAAAATTAATAATATTGT
2606 AAAGGGTGTA
Statistics
Matches: 164, Mismatches: 13, Indels: 38
0.76 0.06 0.18
Matches are distributed among these distances:
97 1 0.01
98 12 0.07
99 22 0.13
100 39 0.24
101 2 0.01
102 23 0.14
103 15 0.09
104 2 0.01
105 4 0.02
107 8 0.05
108 35 0.21
109 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (97 bp):
TTTTAGAAATAAAATATAAAACTAATTCACTAAGTTTAGCCCCAAATTAAAATTATTTTTATTTT
AAGGGTTAAAAAATTAATAATATTGTTATAGG
Done.