Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004183.1 Corchorus capsularis cultivar CVL-1 contig04191, 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: 2346
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:52 original size:20 final size:20
Alignment explanation
Indices: 23--126 Score: 61
Period size: 22 Copynumber: 5.0 Consensus size: 20
13 GTTGACCCCT
23 TTATGAAATTCTT-ATAATCA
1 TTATGAAATT-TTGATAATCA
*
43 TTATGTAATTTTGATAATC-
1 TTATGAAATTTTGATAATCA
* * *
62 TCGCTTTGAATTTTTGATAATAACG
1 T---TATGAAATTTTGATAAT--CA
* *
87 CTATGAAATTTTGATAATCTT
1 TTATGAAATTTTGATAATC-A
108 TCTAT-AAATTTTGATAATC
1 T-TATGAAATTTTGATAATC
127 CGATCTCTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 3 0.05
20 16 0.24
21 14 0.21
22 32 0.48
24 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (20 bp):
TTATGAAATTTTGATAATCA
Found at i:142 original size:25 final size:23
Alignment explanation
Indices: 44--349 Score: 112
Period size: 22 Copynumber: 13.7 Consensus size: 23
34 TTATAATCAT
* *
44 TATGTAATTTTGATAAT-CTCGC
1 TATGAAATTTTGATAATCCTCTC
* * ** *
66 TTTGAATTTTTGATAAT-AACGC
1 TATGAAATTTTGATAATCCTCTC
*
88 TATGAAATTTTGATAAT-CTTTC
1 TATGAAATTTTGATAATCCTCTC
110 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAATCC--TCTC
* *
134 TATGAAATTTCGATAAT-CACTC
1 TATGAAATTTTGATAATCCTCTC
* *
156 TATGAGA-TTGGATAA-CCT-TC
1 TATGAAATTTTGATAATCCTCTC
* * * *
176 TATCAAATTTTGGTACTCCT-TA
1 TATGAAATTTTGATAATCCTCTC
*
198 TGAAATTGAGACTTTT-ATAA-CCT-TC
1 T---A-TGA-AATTTTGATAATCCTCTC
* **
223 ATATGAAATTTTGATAA-CCACAA
1 -TATGAAATTTTGATAATCCTCTC
* *
246 TATAAAATTTTGATAA-CCTCCC
1 TATGAAATTTTGATAATCCTCTC
* *
268 CATGAAATATT-AGTAA-CCTC-C
1 TATGAAATTTTGA-TAATCCTCTC
* * *
289 TAATGAAATTTTGTTAA-CCACAC
1 T-ATGAAATTTTGATAATCCTCTC
*
312 TATGAAATTCTT-ATAA-CCTCGC
1 TATGAAATT-TTGATAATCCTCTC
*
334 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
350 CATCTTTGAT
Statistics
Matches: 216, Mismatches: 47, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
20 7 0.03
21 35 0.16
22 135 0.62
23 5 0.02
24 7 0.03
25 17 0.08
26 5 0.02
27 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (23 bp):
TATGAAATTTTGATAATCCTCTC
Found at i:495 original size:44 final size:44
Alignment explanation
Indices: 439--544 Score: 185
Period size: 44 Copynumber: 2.4 Consensus size: 44
429 TGACATGGTC
439 CTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCACA
*
483 CTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCACG
1 CTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCACA
* *
527 CTATGGAATTTTGATAAC
1 CTATGAAATTTTGGTAAC
545 CTCCTCATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCACA
Found at i:531 original size:22 final size:21
Alignment explanation
Indices: 438--591 Score: 137
Period size: 22 Copynumber: 7.0 Consensus size: 21
428 ATGACATGGT
**
438 CCTATGAAATTTTGGTAACTT
1 CCTATGAAATTTTGGTAACCA
459 CCATATGAAATTTTGGTAACCA
1 CC-TATGAAATTTTGGTAACCA
**
481 CACTATGAAATTTTGGTAACTT
1 C-CTATGAAATTTTGGTAACCA
503 CCATATGAAATTTTGGTAACCA
1 CC-TATGAAATTTTGGTAACCA
* * *
525 CGCTATGGAATTTTGATAACCT
1 C-CTATGAAATTTTGGTAACCA
* * **
547 CCTCATAAAATTATAATAACCA
1 CCT-ATGAAATTTTGGTAACCA
* *
569 TCTTATGAAATTTTGATAACCA
1 -CCTATGAAATTTTGGTAACCA
591 C
1 C
592 ATAGAGACAA
Statistics
Matches: 109, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
21 6 0.06
22 99 0.91
23 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (21 bp):
CCTATGAAATTTTGGTAACCA
Found at i:558 original size:44 final size:43
Alignment explanation
Indices: 438--589 Score: 171
Period size: 44 Copynumber: 3.5 Consensus size: 43
428 ATGACATGGT
* *
438 CCTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCA
1 CCTATGAAATTTTGATAACCTCCATATGAAATTTTGGTAACCA
* *
481 CACTATGAAATTTTGGTAACTTCCATATGAAATTTTGGTAACCA
1 C-CTATGAAATTTTGATAACCTCCATATGAAATTTTGGTAACCA
* * * **
525 CGCTATGGAATTTTGATAACCTCC-TCATAAAATTATAATAACCA
1 C-CTATGAAATTTTGATAACCTCCAT-ATGAAATTTTGGTAACCA
*
569 TCTTATGAAATTTTGATAACC
1 -CCTATGAAATTTTGATAACC
590 ACATAGAGAC
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.02
44 93 0.97
45 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (43 bp):
CCTATGAAATTTTGATAACCTCCATATGAAATTTTGGTAACCA
Found at i:792 original size:20 final size:19
Alignment explanation
Indices: 755--792 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
745 TACTGGCATT
755 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
774 TAAAATATT-AAATTTAAAA
1 TAAAA-ATTGAAA-TTAAAA
793 AACAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:2054 original size:20 final size:21
Alignment explanation
Indices: 2029--2076 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2019 AAAAACTTTA
*
2029 TATATATATATAA-ATTTTTT
1 TATATATATACAACATTTTTT
2049 TATATATATACAACATTTTTT
1 TATATATATACAACATTTTTT
*
2070 TGTATAT
1 TATATAT
2077 TCTTCGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TATATATATACAACATTTTTT
Found at i:2127 original size:74 final size:75
Alignment explanation
Indices: 2043--2187 Score: 283
Period size: 75 Copynumber: 1.9 Consensus size: 75
2033 TATATATAAA
2043 TTTTTTTATATATATACAACA-TTTTTTTGTATATTCTTCGTATTTTCTGACTTACTAAAATTTT
1 TTTTTTTATATATATACAACATTTTTTTTGTATATTCTTCGTATTTTCTGACTTACTAAAATTTT
2107 GGAAATAATC
66 GGAAATAATC
2117 TTTTTTTATATATATACAACATTTTTTTTGTATATTCTTCGTATTTTCTGACTTACTAAAATTTT
1 TTTTTTTATATATATACAACATTTTTTTTGTATATTCTTCGTATTTTCTGACTTACTAAAATTTT
2182 GGAAAT
66 GGAAAT
2188 TCCCAAGAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 21 0.30
75 49 0.70
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (75 bp):
TTTTTTTATATATATACAACATTTTTTTTGTATATTCTTCGTATTTTCTGACTTACTAAAATTTT
GGAAATAATC
Done.