Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007045.1 Corchorus capsularis cultivar CVL-1 contig07066, 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: 21245
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2983 original size:26 final size:27
Alignment explanation
Indices: 2953--3019 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
2943 GCCCAAGGGT
2953 ATTTTGGTCATTTTTGCAC-CAGGGGC
1 ATTTTGGTCATTTTTGCACTCAGGGGC
2979 ATTTTGGTCATTTTTGCACTCAGGGGC
1 ATTTTGGTCATTTTTGCACTCAGGGGC
*
3006 ATTTTAGTCATTTT
1 ATTTTGGTCATTTT
3020 AAAGTTTACC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 19 0.49
27 20 0.51
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (27 bp):
ATTTTGGTCATTTTTGCACTCAGGGGC
Found at i:6177 original size:51 final size:50
Alignment explanation
Indices: 5960--6337 Score: 506
Period size: 50 Copynumber: 7.4 Consensus size: 50
5950 TCATATCAGG
*
5960 TTTCCTCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTGGTAA
1 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTGGTAA
6010 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTGGTAA
1 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTGGTAA
*
6060 TTTCATCAATAAAAATTGAATCTTTAAATAGTAAATGACAATTTTGGTAA
1 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTGGTAA
6110 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTTGGTAA
1 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAA-TTTTGGTAA
* *
6161 TTTCATCAATAAAAATTGAAATTTTTAAGTAGAAAATGACAATTTTTGGGTAA
1 TTTCATCAATAAAAATTG-AATCTTTAAGTAGTAAATGACAA-TTTT-GGTAA
* * * * * *
6214 TTTCACCAAT-AAAATTGAATCTTGAAGTAGCAAGTGAAAATTTTCGATAA
1 TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTT-GGTAA
* * * * * * * *
6264 TTTCATCAATAAAAATTGGATCTTAAAATAGCAAAATGGCCACTCTTGATAA
1 TTTCATCAATAAAAATTGAATCTTTAAGTAG-TAAAT-GACAATTTTGGTAA
* *
6316 TTTTATCAATGAAAATTGAATC
1 TTTCATCAATAAAAATTGAATC
6338 CTTAGGTGGT
Statistics
Matches: 296, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
50 155 0.52
51 62 0.21
52 60 0.20
53 19 0.06
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (50 bp):
TTTCATCAATAAAAATTGAATCTTTAAGTAGTAAATGACAATTTTGGTAA
Found at i:7276 original size:55 final size:55
Alignment explanation
Indices: 7216--7684 Score: 784
Period size: 55 Copynumber: 8.6 Consensus size: 55
7206 TAAAAAGGGG
*
7216 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGATAATAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
7271 AAATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
* *
7325 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAATTAAGGTAATAGTAATCGGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
*
7380 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAAT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
7435 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
* *
7490 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
* * *
7545 AAATTAGTAATTAAGTAAAAAGAGATTAATTAGAGTTAAGGTAATGGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
*
7600 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG---TCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
* * * *
7652 AAATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAG
7685 TAAATTGATA
Statistics
Matches: 393, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
52 34 0.09
54 53 0.13
55 306 0.78
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (55 bp):
AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGT
Found at i:7682 original size:26 final size:26
Alignment explanation
Indices: 7601--7687 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
7591 GTAATCAGTA
* * * *
7601 AATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAATCAGGTAAAAAGATAGT
* *
7627 AATCAG-AGTCAAGGT-AATAG-TCAGT
1 AATCAGTAATC-AGGTAAAAAGAT-AGT
7652 AAATCAGTAATCAGGTAAAAAGATAGT
1 -AATCAGTAATCAGGTAAAAAGATAGT
7679 AATCAGTAA
1 AATCAGTAA
7688 ATTGATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
25 8 0.17
26 28 0.60
27 10 0.21
28 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (26 bp):
AATCAGTAATCAGGTAAAAAGATAGT
Found at i:7687 original size:34 final size:33
Alignment explanation
Indices: 7647--7760 Score: 106
Period size: 34 Copynumber: 3.3 Consensus size: 33
7637 AAGGTAATAG
*
7647 TCAGTAAATCAGTAATCAGGTAAAAAGATAGTAA
1 TCAGTAAAT-AGTAATAAGGTAAAAAGATAGTAA
* * *
7681 TCAGTAAATTGATAATTAAGAGTCCAGATA-ATAGTAA
1 TCAGTAAATAG-TAA-TAAG-GT--AAAAAGATAGTAA
7718 TCAGTAAATTAGTAATTAA-GTAAAAAGATAGTAA
1 TCAGTAAA-TAGTAA-TAAGGTAAAAAGATAGTAA
7752 TCAGTAAAT
1 TCAGTAAAT
7761 TGATAATTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
33 5 0.08
34 27 0.41
35 5 0.08
36 2 0.03
37 22 0.33
38 5 0.08
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (33 bp):
TCAGTAAATAGTAATAAGGTAAAAAGATAGTAA
Found at i:7715 original size:37 final size:36
Alignment explanation
Indices: 7666--7771 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 36
7656 CAGTAATCAG
7666 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAGA
1 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAGA
* *
7702 GTCCAGATA-ATAGTAATCAGTAAATT-AGTAATT-A-A
1 GT--AAAAAGATAGTAATCAGTAAATTGA-TAATTAAGA
7737 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAG
1 GTAAAAAGATAGTAATCAGTAAATTGATAATTAAG
7772 GGTTAAAGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
33 3 0.05
34 22 0.37
35 5 0.08
36 4 0.07
37 22 0.37
38 3 0.05
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (36 bp):
GTAAAAAGATAGTAATCAGTAAATTGATAATTAAGA
Found at i:8292 original size:16 final size:17
Alignment explanation
Indices: 8271--8312 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
8261 AAGTAAAAAG
8271 AGTAAAAATGGT-ATTA
1 AGTAAAAATGGTAATTA
8287 AGTAAAAAATGGTAATTA
1 AGT-AAAAATGGTAATTA
*
8305 AGCAAAAA
1 AGTAAAAA
8313 AGAGTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 14 0.61
18 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (17 bp):
AGTAAAAATGGTAATTA
Found at i:8294 original size:17 final size:18
Alignment explanation
Indices: 8274--8313 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
8264 TAAAAAGAGT
*
8274 AAAAATGGT-ATTAAGTA
1 AAAAATGGTAATTAAGCA
8291 AAAAATGGTAATTAAGCA
1 AAAAATGGTAATTAAGCA
8309 AAAAA
1 AAAAA
8314 GAGTGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.60, C:0.03, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAAATGGTAATTAAGCA
Found at i:8301 original size:26 final size:26
Alignment explanation
Indices: 8204--8295 Score: 96
Period size: 26 Copynumber: 3.3 Consensus size: 26
8194 GATAAAAATG
*
8204 GTAAAAAAGAGTAAAAATGGCATTAA
1 GTAAAAAAGAGTAAAAATGGTATTAA
*
8230 GTAAAAAAAGGAGAGTAAAAAAATAGTAATTAA
1 GT--AAAAA--AGAGT--AAAAATGGT-ATTAA
8263 GT-AAAAAGAGTAAAAATGGTATTAA
1 GTAAAAAAGAGTAAAAATGGTATTAA
8288 GTAAAAAA
1 GTAAAAAA
8296 TGGTAATTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
25 7 0.13
26 15 0.27
28 10 0.18
30 9 0.16
32 7 0.13
33 7 0.13
ACGTcount: A:0.61, C:0.01, G:0.18, T:0.20
Consensus pattern (26 bp):
GTAAAAAAGAGTAAAAATGGTATTAA
Found at i:11339 original size:42 final size:43
Alignment explanation
Indices: 11292--11374 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
11282 CGTGTTTGGC
*
11292 TTATCGTATCTCTTGTC-TGAATCGTGTC-AGACACGATTAAGA
1 TTATCGTATCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGA
* *
11334 TTATCGTGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
1 TTATCGTATCTCGTGTCGTAATCGTGTCAAGACACGATTAA
11375 CACGTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 23 0.64
43 13 0.36
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (43 bp):
TTATCGTATCTCGTGTCGTAATCGTGTCAAGACACGATTAAGA
Found at i:11563 original size:14 final size:14
Alignment explanation
Indices: 11544--11571 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11534 CAATTATCTT
11544 TAATTATATATATA
1 TAATTATATATATA
11558 TAATTATATATATA
1 TAATTATATATATA
11572 GTTTAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:11798 original size:12 final size:12
Alignment explanation
Indices: 11781--11808 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11771 TACCCTATGT
11781 AAACACGACACG
1 AAACACGACACG
11793 AAACACGACACG
1 AAACACGACACG
11805 AAAC
1 AAAC
11809 CCGAATTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.32, G:0.14, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:14162 original size:2 final size:2
Alignment explanation
Indices: 14155--14197 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
14145 CAAACCCAGT
14155 TA TA TA TA -A TA TA -A TA TA -A 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 TA TA TA TA TA TA
14194 TA TA
1 TA TA
14198 ATACTATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:14205 original size:10 final size:9
Alignment explanation
Indices: 14155--14205 Score: 70
Period size: 8 Copynumber: 5.7 Consensus size: 9
14145 CAAACCCAGT
14155 TATATATAA
1 TATATATAA
14164 TATAATATAA
1 TAT-ATATAA
14174 TATATAT-A
1 TATATATAA
14182 TATATAT-A
1 TATATATAA
14190 TATATATAA
1 TATATATAA
14199 TACTATA
1 TA-TATA
14206 AAACATGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
8 16 0.41
9 10 0.26
10 13 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATATAA
Found at i:17312 original size:16 final size:16
Alignment explanation
Indices: 17287--17346 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
17277 CGCAAACCCG
17287 AAATGACCCGAATCCA
1 AAATGACCCGAATCCA
* * *
17303 AAACGACCCGAACCCG
1 AAATGACCCGAATCCA
* *
17319 AAATGATCCAAATCCA
1 AAATGACCCGAATCCA
17335 AAATGACCCGAA
1 AAATGACCCGAA
17347 CCCGATCAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.45, C:0.32, G:0.13, T:0.10
Consensus pattern (16 bp):
AAATGACCCGAATCCA
Found at i:17317 original size:32 final size:32
Alignment explanation
Indices: 17281--17351 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
17271 TGGGTACGCA
*
17281 AACCCGAAATGACCCGAATCCAAAACGACCCG
1 AACCCGAAATGACCCAAATCCAAAACGACCCG
* *
17313 AACCCGAAATGATCCAAATCCAAAATGACCCG
1 AACCCGAAATGACCCAAATCCAAAACGACCCG
17345 AACCCGA
1 AACCCGA
17352 TCAACCCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.42, C:0.35, G:0.14, T:0.08
Consensus pattern (32 bp):
AACCCGAAATGACCCAAATCCAAAACGACCCG
Found at i:17728 original size:30 final size:28
Alignment explanation
Indices: 17694--17753 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
17684 TTATAAGTTA
*
17694 TATAAGTTTGAAAATGTAAATAAAATGGAT
1 TATAAG-TT-AAAATATAAATAAAATGGAT
*
17724 TATAAGTTATAATATAAATAAAATGGAT
1 TATAAGTTAAAATATAAATAAAATGGAT
17752 TA
1 TA
17754 AATTATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.71
29 2 0.07
30 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (28 bp):
TATAAGTTAAAATATAAATAAAATGGAT
Found at i:19658 original size:33 final size:32
Alignment explanation
Indices: 19582--19647 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
19572 TAATTACCAA
19582 TTACTAAGCTTAAATAGGTGGTTTTCTTAATT
1 TTACTAAGCTTAAATAGGTGGTTTTCTTAATT
19614 TTACTAAGCTTAAATAGGTGGTTTTCTTAATT
1 TTACTAAGCTTAAATAGGTGGTTTTCTTAATT
19646 TT
1 TT
19648 TATTTGGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (32 bp):
TTACTAAGCTTAAATAGGTGGTTTTCTTAATT
Done.