Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007876.1 Corchorus capsularis cultivar CVL-1 contig07897, 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: 30398
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1117 original size:335 final size:338
Alignment explanation
Indices: 607--1262 Score: 837
Period size: 343 Copynumber: 1.9 Consensus size: 338
597 TATTGGTTAT
* * *
607 TGATTTTCTTATCTAAGATTACTTAAAGTTATAAAGGTTATGGAAAACATTATAGTTCTATCTAC
1 TGATTTTCTTACCTAAGATTACTTAAAGTTATAAAGGTTATGAAAAACATTATAGTACTATCTAC
* * * * **
672 ATTCAAGTAATCTTACATCCTTATTAATTTTAGCAACTTTTAATCAATAATGGAAGTTACCAATT
66 ATTCAAATAACCTTACATCCTTAATAAGTTTAGCAACTTTTAATCAATAATAAAAGTTACCAATT
* * *
737 TTATTACTTAAGTGATCTACTGAAACACCTATAAAAGTTATTAAAATTGTA-TT-T-A-CC-A-A
131 TTATTACTTAAGT-ATCTACTAAAAAACCTATAAAAGTAATTAAAATTGTATTTATAATCCTACA
* * *
796 TCCTTAATAAGATTAGTAAATTTTCATCAATGGT-AATGATTTA-CCTTTTTTCTCTCAAAAGTT
195 TCCTTAATAACATGAGTAAACTTTCATCAATGGTAAAT-ATTTACCCTTTTTT-TCTCAAAAGTT
* * ** * * * *
859 ACTGAAAACCCTATAATTTTTATAAAAAATGTATGGTACTATCAACTAATTCAATGACCTTATAT
258 ACTAAAAAACCTATAATGATCATAAAAAATGTATAGTACTAACAACTAATTCAATAACCTTATAT
924 TATGAAGGTAAAGTAC
323 TATGAAGGTAAAGTAC
* *
940 TGATTTTTTTACCTAAGATTACTTAAAAGGTTATAAAGGTTATGAAAAACTTTATAGTACTATCT
1 TGATTTTCTTACCTAAGATTACTT-AAA-GTTATAAAGGTTATGAAAAACATTATAGTACTATCT
* * * * * *
1005 AGATTGAAATAACCTTACACGTTCTTAATAAGTTTAGTAACTTTTCATCATTAATAAAAGTTACC
64 ACATTCAAATAACCTTACA--TCCTTAATAAGTTTAGCAACTTTTAATCAATAATAAAAGTTACC
*
1070 AATTTTATTACTTAAGT-T-TACTAAAAAAGCTATAAAAGTAAATTAAAATTGTATTTACTAATC
127 AATTTTATTACTTAAGTATCTACTAAAAAACCTATAAAAGT-AATTAAAATTGTATTTA-TAATC
*
1133 CTTACATTCTTAATAACATGAGTAAACTTTCATCAATGGTAAATATTTACCCTTTTTTTCTCAAA
190 C-TACATCCTTAATAACATGAGTAAACTTTCATCAATGGTAAATATTTACCCTTTTTTTCTCAAA
* *
1198 AGTTATTAAAAAACCTATAATGATCATAAAAGATGTATAGTACTAACAACTAATTCAATAACCTT
254 AGTTACTAAAAAACCTATAATGATCATAAAAAATGTATAGTACTAACAACTAATTCAATAACCTT
1263 GCATTTTTTG
Statistics
Matches: 273, Mismatches: 35, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
333 22 0.08
334 21 0.08
335 61 0.22
336 2 0.01
337 53 0.19
338 1 0.00
339 1 0.00
340 2 0.01
342 1 0.00
343 98 0.36
344 11 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (338 bp):
TGATTTTCTTACCTAAGATTACTTAAAGTTATAAAGGTTATGAAAAACATTATAGTACTATCTAC
ATTCAAATAACCTTACATCCTTAATAAGTTTAGCAACTTTTAATCAATAATAAAAGTTACCAATT
TTATTACTTAAGTATCTACTAAAAAACCTATAAAAGTAATTAAAATTGTATTTATAATCCTACAT
CCTTAATAACATGAGTAAACTTTCATCAATGGTAAATATTTACCCTTTTTTTCTCAAAAGTTACT
AAAAAACCTATAATGATCATAAAAAATGTATAGTACTAACAACTAATTCAATAACCTTATATTAT
GAAGGTAAAGTAC
Found at i:1777 original size:3 final size:3
Alignment explanation
Indices: 1769--1805 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1759 TTTCAACAAT
1769 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1806 ATTTTGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5047 original size:9 final size:9
Alignment explanation
Indices: 5027--5057 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5017 CAATTAAATA
5027 ATATACTAGT
1 ATATA-TAGT
5037 ATATATAGT
1 ATATATAGT
5046 ATATATAGT
1 ATATATAGT
5055 ATA
1 ATA
5058 AAATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (9 bp):
ATATATAGT
Found at i:15566 original size:21 final size:22
Alignment explanation
Indices: 15540--15584 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
15530 AATTACTGAA
15540 TTGCTAAACACCGCCCCA-TTT
1 TTGCTAAACACCGCCCCACTTT
** *
15561 TTGCTATTCACCGCCTCACTTT
1 TTGCTAAACACCGCCCCACTTT
15583 TT
1 TT
15585 ACACTTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCACTTT
Found at i:19995 original size:35 final size:35
Alignment explanation
Indices: 19954--20025 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
19944 ACACGAACTC
*
19954 AAAAATCTTAATTAGTCAATTACTAAAATATCCTT
1 AAAAATCTTAATTAGTAAATTACTAAAATATCCTT
19989 AAAAATCTTAATTAGTAAATTACTAAAATATCCTT
1 AAAAATCTTAATTAGTAAATTACTAAAATATCCTT
20024 AA
1 AA
20026 TATTATAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (35 bp):
AAAAATCTTAATTAGTAAATTACTAAAATATCCTT
Found at i:20200 original size:30 final size:30
Alignment explanation
Indices: 20166--20227 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
20156 TATAATTTTT
*
20166 AATCATTAAACTTTTATCTATTAATTATAA
1 AATCATTAAAATTTTATCTATTAATTATAA
*
20196 AATCATTAAAATTTTATTTATTAATTATAA
1 AATCATTAAAATTTTATCTATTAATTATAA
20226 AA
1 AA
20228 AGATACTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (30 bp):
AATCATTAAAATTTTATCTATTAATTATAA
Found at i:24491 original size:27 final size:28
Alignment explanation
Indices: 24451--24525 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
24441 ATGACATGGC
24451 TTTTTTTT-TT-TTTC-CCTCTTTTATT
1 TTTTTTTTCTTCTTTCTCCTCTTTTATT
* *
24476 TTTTTTTTCTTCTTTCTTTCTCTTTTCTT
1 TTTTTTTTCTTCTTTC-TCCTCTTTTATT
*
24505 TTTTCTCTTCTTC-TTCTCCTC
1 TTTT-TTTTCTTCTTTCTCCTC
24526 AACGCCAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.20
26 2 0.05
27 4 0.10
28 4 0.10
29 16 0.39
30 7 0.17
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTTTTTCTTCTTTCTCCTCTTTTATT
Found at i:24493 original size:23 final size:24
Alignment explanation
Indices: 24451--24510 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
24441 ATGACATGGC
*
24451 TTTTTTTTTTTTTCCCTCTTT-TA
1 TTTTTTTTTTCTTCCCTCTTTCTA
** *
24474 TTTTTTTTTTCTTCTTTCTTTCTC
1 TTTTTTTTTTCTTCCCTCTTTCTA
24498 TTTTCTTTTTTCT
1 TTTT-TTTTTTCT
24511 CTTCTTCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 18 0.58
24 5 0.16
25 8 0.26
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTTTTCTTCCCTCTTTCTA
Found at i:24503 original size:18 final size:19
Alignment explanation
Indices: 24480--24515 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24470 TTTATTTTTT
24480 TTTTCTTCTTTCT-TTCTC
1 TTTTCTTCTTTCTCTTCTC
*
24498 TTTTCTTTTTTCTCTTCT
1 TTTTCTTCTTTCTCTTCT
24516 TCTTCTCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCTTCTTTCTCTTCTC
Found at i:24515 original size:23 final size:21
Alignment explanation
Indices: 24454--24516 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
24444 ACATGGCTTT
*
24454 TTTTTTTTTTC-CCTCTTTTA
1 TTTTTTTTTTCTCTTCTTTTA
*
24474 TTTTTTTTTTCTTCTTTCTTTCTC
1 TTTTTTTTTTC-TC-TTCTTT-TA
24498 TTTTCTTTTTTCTCTTCTT
1 TTTT-TTTTTTCTCTTCTT
24517 CTTCTCCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 11 0.31
22 1 0.03
23 10 0.28
24 7 0.19
25 7 0.19
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTTTTTCTCTTCTTTTA
Found at i:24521 original size:18 final size:16
Alignment explanation
Indices: 24482--24519 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
24472 TATTTTTTTT
24482 TTCTTCTTTCTTTCTC
1 TTCTTCTTTCTTTCTC
24498 TT-TTCTTT-TTTCTC
1 TTCTTCTTTCTTTCTC
24512 TTCTTCTT
1 TTCTTCTT
24520 CTCCTCAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 11 0.52
16 2 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTCTTTCTTTCTC
Found at i:25929 original size:3 final size:3
Alignment explanation
Indices: 25921--25970 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
25911 TGATGAGATG
25921 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25969 AA
1 AA
25971 ACTATTTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.