Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014332.1 Corchorus capsularis cultivar CVL-1 contig14353, 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: 43855
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:463 original size:33 final size:32
Alignment explanation
Indices: 366--470 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 32
356 TTGAAAAGAG
* *
366 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGACACTAAATC
* * *
399 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGACACTAAATC
*
432 TGTTTTAAGTGTTGTTTGTGATGGA-ACTAAATC
1 TGTTTT-AGTGTTGTTTGCGAT-GACACTAAATC
465 TGTTTT
1 TGTTTT
471 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.05
33 50 0.83
34 7 0.12
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.45
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGACACTAAATC
Found at i:537 original size:33 final size:32
Alignment explanation
Indices: 486--590 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 32
476 CTAATTGTGA
* * *
486 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATCCTATTTTGGTTG-ACATAGCAT
* **
519 TAAAAATAATTTTATTTTGGTTGATCATAGCAT
1 TGAAAATAATCCTATTTTGGTTGA-CATAGCAT
* *
552 TGCAAATAATCCTGTTTTGGTTG--ATAGCAT
1 TGAAAATAATCCTATTTTGGTTGACATAGCAT
582 TGAAAATAA
1 TGAAAATAA
591 ATCTGTTTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 15 0.25
32 1 0.02
33 45 0.74
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGAAAATAATCCTATTTTGGTTGACATAGCAT
Found at i:6603 original size:33 final size:32
Alignment explanation
Indices: 6521--6627 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 32
6511 CGCCAAGCGA
* *
6521 TGGCCGGT-TGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGTCGGACATCTCCA-GTCGCG
* * *
6554 TGACCGGTGATAGTCGGACATCTCCGAGTCGCG
1 TGGCCGGTGTTGGTCGGACATCTCC-AGTCGCG
* * *
6587 TGGCCGGTGTTGGTCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGTCGGACATCTCC-AGTCGCG
6620 TGGCCGGT
1 TGGCCGGT
6628 CACTCGCGCC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
33 59 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.27, G:0.37, T:0.24
Consensus pattern (32 bp):
TGGCCGGTGTTGGTCGGACATCTCCAGTCGCG
Found at i:11901 original size:22 final size:22
Alignment explanation
Indices: 11876--11927 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
11866 TACTCAAATC
**
11876 TGCGAATCGAAGTTGACGGCTT
1 TGCGAATCGAAGAAGACGGCTT
*
11898 TGCGAATCGAAGAAGAGGGCTT
1 TGCGAATCGAAGAAGACGGCTT
*
11920 TGCAAATC
1 TGCGAATC
11928 ATTCTTAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (22 bp):
TGCGAATCGAAGAAGACGGCTT
Found at i:12382 original size:27 final size:27
Alignment explanation
Indices: 12344--12405 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
12334 TCTTGAGGTT
12344 CAGACGCCTCCATTTAGCGGCGTCTCC
1 CAGACGCCTCCATTTAGCGGCGTCTCC
*
12371 CAGACGCCTCCATTTAGCGGTGTCTCC
1 CAGACGCCTCCATTTAGCGGCGTCTCC
*
12398 CAAACGCC
1 CAGACGCC
12406 GCTATCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.40, G:0.21, T:0.21
Consensus pattern (27 bp):
CAGACGCCTCCATTTAGCGGCGTCTCC
Found at i:14378 original size:21 final size:21
Alignment explanation
Indices: 14354--14416 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
14344 TTTCAGGTTG
14354 TTGAGAGTGGTGGAATGAACA
1 TTGAGAGTGGTGGAATGAACA
** * *
14375 TTGA-AGTCGCCGTAATG-ACG
1 TTGAGAGT-GGTGGAATGAACA
14395 TTGAGAGTGGTGGAATGAACA
1 TTGAGAGTGGTGGAATGAACA
14416 T
1 T
14417 GGAAGTCACC
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.30, C:0.10, G:0.35, T:0.25
Consensus pattern (21 bp):
TTGAGAGTGGTGGAATGAACA
Found at i:14410 original size:41 final size:41
Alignment explanation
Indices: 14353--14434 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
14343 GTTTCAGGTT
* *
14353 GTTGAGAGTGGTGGAATGAACATTGAAGTCGCCGTAATGAC
1 GTTGAGAGTGGTGGAATGAACATGGAAGTCACCGTAATGAC
14394 GTTGAGAGTGGTGGAATGAACATGGAAGTCACCGTAATGAC
1 GTTGAGAGTGGTGGAATGAACATGGAAGTCACCGTAATGAC
14435 AAAGGAGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.12, G:0.34, T:0.23
Consensus pattern (41 bp):
GTTGAGAGTGGTGGAATGAACATGGAAGTCACCGTAATGAC
Found at i:14411 original size:20 final size:20
Alignment explanation
Indices: 14353--14412 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
14343 GTTTCAGGTT
14353 GTTGAGAGTGGTGGAATGAAC
1 GTTGAGAGTGGTGGAATG-AC
* ** *
14374 ATTGA-AGTCGCCGTAATGAC
1 GTTGAGAGT-GGTGGAATGAC
14394 GTTGAGAGTGGTGGAATGA
1 GTTGAGAGTGGTGGAATGA
14413 ACATGGAAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.28, C:0.08, G:0.38, T:0.25
Consensus pattern (20 bp):
GTTGAGAGTGGTGGAATGAC
Found at i:18273 original size:20 final size:21
Alignment explanation
Indices: 18222--18274 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
18212 GCACTGGAGT
18222 ACATGGGTCG-CAAGGCAAACC
1 ACATGGG-CGCCAAGGCAAACC
18243 ACATGGGGCGCCAA-GCAAACC
1 ACAT-GGGCGCCAAGGCAAACC
18264 ACATGGGCGCC
1 ACATGGGCGCC
18275 CAGCTAGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.23
21 17 0.57
22 6 0.20
ACGTcount: A:0.30, C:0.32, G:0.30, T:0.08
Consensus pattern (21 bp):
ACATGGGCGCCAAGGCAAACC
Found at i:25569 original size:21 final size:21
Alignment explanation
Indices: 25543--25595 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
25533 GCACTGGAGT
* * *
25543 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
25564 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
25585 ACAT-GGGCGCC
1 ACATGGGGCGCC
25596 CAGCGCTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:27750 original size:21 final size:22
Alignment explanation
Indices: 27729--27770 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27719 TAGAAAGTTC
27729 TAAAAAGATTTT-AAAATTTTCT
1 TAAAAA-ATTTTGAAAATTTTCT
*
27751 TCAAAAATTTTGAAAATTTT
1 TAAAAAATTTTGAAAATTTT
27771 ATCTCTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TAAAAAATTTTGAAAATTTTCT
Found at i:32254 original size:11 final size:10
Alignment explanation
Indices: 32236--32269 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
32226 AATTGTCTTC
32236 AAATCTTCAA
1 AAATCTTCAA
32246 AATATCTTCAA
1 AA-ATCTTCAA
32257 GAAATCTTCAA
1 -AAATCTTCAA
32268 AA
1 AA
32270 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:39337 original size:11 final size:10
Alignment explanation
Indices: 39319--39352 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
39309 AATTGTCTTC
39319 AAATCTTCAA
1 AAATCTTCAA
39329 AATATCTTCAA
1 AA-ATCTTCAA
39340 GAAATCTTCAA
1 -AAATCTTCAA
39351 AA
1 AA
39353 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Done.