Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012183.1 Corchorus capsularis cultivar CVL-1 contig12204, 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: 16530
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1507 original size:6 final size:6
Alignment explanation
Indices: 1496--1521 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1486 AAATTTATGA
1496 ATATTT ATATTT ATATTT ATATTT AT
1 ATATTT ATATTT ATATTT ATATTT AT
1522 TTATTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATATTT
Found at i:2818 original size:19 final size:19
Alignment explanation
Indices: 2796--2834 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2786 TGAAATTGTC
2796 AGAA-TTTAATAAAATTAAA
1 AGAATTTTAA-AAAATTAAA
2815 AGAATTTTAAAAAATTAAA
1 AGAATTTTAAAAAATTAAA
2834 A
1 A
2835 ATGGCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AGAATTTTAAAAAATTAAA
Found at i:2900 original size:16 final size:15
Alignment explanation
Indices: 2854--2904 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
2844 TTTCAGTTCT
*
2854 TTCTTTCTTTTCTGC
1 TTCTTTCTTTTCTCC
2869 TT-TTT-TTTTC-CAC
1 TTCTTTCTTTTCTC-C
2882 TTCTTTCTTCTTCTCC
1 TTCTTTCTT-TTCTCC
2898 TTCTTTC
1 TTCTTTC
2905 AGCCAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 8 0.27
14 6 0.20
15 4 0.13
16 11 0.37
17 1 0.03
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (15 bp):
TTCTTTCTTTTCTCC
Found at i:4668 original size:23 final size:23
Alignment explanation
Indices: 4642--4687 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4632 GTTCGATAAA
*
4642 TGTTCATTT-ATTAGCTCGTTTAT
1 TGTTCATTTAAATA-CTCGTTTAT
4665 TGTTCATTTAAATACTCGTTTAT
1 TGTTCATTTAAATACTCGTTTAT
4688 AGCTCGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (23 bp):
TGTTCATTTAAATACTCGTTTAT
Found at i:5793 original size:12 final size:12
Alignment explanation
Indices: 5734--5814 Score: 54
Period size: 12 Copynumber: 6.8 Consensus size: 12
5724 AAGATATTCC
* *
5734 CGTTCCTCAAGT
1 CGTTCCTGACGT
* *
5746 CATTCCTGACCT
1 CGTTCCTGACGT
* *
5758 CGTTCCTAATGT
1 CGTTCCTGACGT
* **
5770 TGTTTTTGACGT
1 CGTTCCTGACGT
5782 CGTTCCTGACGT
1 CGTTCCTGACGT
* *
5794 TGTTCCTGAAGT
1 CGTTCCTGACGT
*
5806 CGATCCTGA
1 CGTTCCTGA
5815 ACAAAAAAAA
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (12 bp):
CGTTCCTGACGT
Found at i:5807 original size:24 final size:24
Alignment explanation
Indices: 5748--5814 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
5738 CCTCAAGTCA
* * *
5748 TTCCTGACCTCGTTCCTAATGTTG
1 TTCCTGACGTCGTTCCTGACGTTG
**
5772 TTTTTGACGTCGTTCCTGACGTTG
1 TTCCTGACGTCGTTCCTGACGTTG
* *
5796 TTCCTGAAGTCGATCCTGA
1 TTCCTGACGTCGTTCCTGA
5815 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40
Consensus pattern (24 bp):
TTCCTGACGTCGTTCCTGACGTTG
Found at i:6448 original size:173 final size:175
Alignment explanation
Indices: 6112--6457 Score: 572
Period size: 174 Copynumber: 2.0 Consensus size: 175
6102 AGTTGATGGG
* * *
6112 TAATGTCTTATAGAACGTAGATTGGTGTTTGTTGCTTGATGTGAGTTTGTATTGCCATGTTAAAA
1 TAATATCTTATAGAACGTAGATTGGTGTTTGTTGCTTGATATGAGTTTGTATTGCCATGTGAAAA
* *
6177 TTGATTTTGTGTTGAATATATGAATGAGGGATGTGAATGCATAGATCTATAAATTAGGGGGATAG
66 TTGATTTTGTGTTGAATATATGAATGAGGGATGTGAATGCATACATCTATAAATAAGGGGGATAG
6242 AATTGAAAAAATGATAAGTTTAGGGACCTAATTG-AAAAAAATTA
131 AATTGAAAAAATGATAAGTTTAGGGACCTAATTGCAAAAAAATTA
*
6286 TAATATCTTATAGAATGTAGATTGGTGTTTGTTGCTTGATATGAGTTTGTATTGCCATGTGAAAA
1 TAATATCTTATAGAACGTAGATTGGTGTTTGTTGCTTGATATGAGTTTGTATTGCCATGTGAAAA
6351 TTGATTTTGTGTT-AATATATGAATGAGGGATGTGAATGCATACATCTATAAATAAGGGGGATAG
66 TTGATTTTGTGTTGAATATATGAATGAGGGATGTGAATGCATACATCTATAAATAAGGGGGATAG
* ** *
6415 ATTTG-AAAAATTCTAAAGTTTAGGGATCTAATTGCAAAAAAAT
131 AATTGAAAAAATGAT-AAGTTTAGGGACCTAATTGCAAAAAAAT
6458 ATATGTTTAG
Statistics
Matches: 160, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
172 7 0.04
173 71 0.44
174 82 0.51
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (175 bp):
TAATATCTTATAGAACGTAGATTGGTGTTTGTTGCTTGATATGAGTTTGTATTGCCATGTGAAAA
TTGATTTTGTGTTGAATATATGAATGAGGGATGTGAATGCATACATCTATAAATAAGGGGGATAG
AATTGAAAAAATGATAAGTTTAGGGACCTAATTGCAAAAAAATTA
Found at i:8788 original size:31 final size:31
Alignment explanation
Indices: 8750--8810 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
8740 TATTTTGACA
8750 TATTGTAAATTTAAATTTACAAACCTTGAAG
1 TATTGTAAATTTAAATTTACAAACCTTGAAG
*
8781 TATTGTAAATTTTAATTTACAAACCTTGAA
1 TATTGTAAATTTAAATTTACAAACCTTGAA
8811 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTGTAAATTTAAATTTACAAACCTTGAAG
Found at i:10493 original size:19 final size:19
Alignment explanation
Indices: 10469--10506 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10459 TAATTTTACA
*
10469 TAATTTAGGTAGGGAGAAT
1 TAATTTAGGCAGGGAGAAT
10488 TAATTTAGGCAGGGAGAAT
1 TAATTTAGGCAGGGAGAAT
10507 GTTAAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.32, T:0.29
Consensus pattern (19 bp):
TAATTTAGGCAGGGAGAAT
Found at i:12489 original size:36 final size:37
Alignment explanation
Indices: 12446--12516 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
12436 CTCCGGTATG
*
12446 AAAATCTCC-TTCCATGAGTAACGCAAAAACCAGAAA
1 AAAATCTCCATTCCATGAGTAAAGCAAAAACCAGAAA
*
12482 AAAATCTCCAATTCGATGAGTAAAGCAAAAACCAG
1 AAAATCTCC-ATTCCATGAGTAAAGCAAAAACCAG
12517 GGGGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 9 0.29
38 22 0.71
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.17
Consensus pattern (37 bp):
AAAATCTCCATTCCATGAGTAAAGCAAAAACCAGAAA
Found at i:14803 original size:31 final size:31
Alignment explanation
Indices: 14758--14820 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
14748 TAGAACTTTC
14758 AACACTAATTTGTTTCCAACAGATTAATTGA
1 AACACTAATTTGTTTCCAACAGATTAATTGA
** *
14789 AACACT-ATTGTGTTTCTGACAGTTTAATTGA
1 AACACTAATT-TGTTTCCAACAGATTAATTGA
14820 A
1 A
14821 GATTTGTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (31 bp):
AACACTAATTTGTTTCCAACAGATTAATTGA
Found at i:15059 original size:44 final size:44
Alignment explanation
Indices: 14996--15087 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
14986 ATATAACACA
*
14996 ATATTAATATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTC
1 ATATTAAAATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTC
*
15040 ATATTAAAATCTTCTTTTGTATTTTTATCAGATTGCTTCTAGTC
1 ATATTAAAATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTC
15084 ATAT
1 ATAT
15088 CCCTTGTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (44 bp):
ATATTAAAATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTC
Found at i:15152 original size:72 final size:72
Alignment explanation
Indices: 15034--15177 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
15024 CAGACTGCTT
*
15034 CTAGTCATATTAAAATCTTCTTTTGTATTTTTATCAGATTGCTTCTAGTCATATCCCTTGTCAAA
1 CTAGTCATATTAAAATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTCATATCCCTTGTCAAA
15099 TGAAATG
66 TGAAATG
* *
15106 CTAGTCATATTAACATCTTCTTTTGTATTTTTATCAGACTGTTTCTAGTCATATCCCTTGTCAAA
1 CTAGTCATATTAAAATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTCATATCCCTTGTCAAA
15171 TGAAATG
66 TGAAATG
15178 GCCTGGAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.44
Consensus pattern (72 bp):
CTAGTCATATTAAAATCTTCTTTTGTATTTTTATCAGACTGCTTCTAGTCATATCCCTTGTCAAA
TGAAATG
Found at i:15444 original size:7 final size:7
Alignment explanation
Indices: 15432--15457 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
15422 AGCTAAGCTC
15432 CAAAGGG
1 CAAAGGG
15439 CAAAGGG
1 CAAAGGG
15446 CAAAGGG
1 CAAAGGG
15453 CAAAG
1 CAAAG
15458 AGTAGTCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.38, T:0.00
Consensus pattern (7 bp):
CAAAGGG
Done.