Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016026.1 Corchorus capsularis cultivar CVL-1 contig16047, 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: 15175
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Found at i:184 original size:37 final size:37
Alignment explanation
Indices: 133--249 Score: 180
Period size: 37 Copynumber: 3.1 Consensus size: 37
123 GAGGTGGCCT
*
133 GTGGCGGTCAACACATTTTGTCAGCTTGTCGAGCAAC
1 GTGGCGGTCAACACATTTTGTCAGCTTGTCGAGCGAC
* *
170 GTGGCGGTCCACACATCTTGTCAGCTTGTCGAGCGAC
1 GTGGCGGTCAACACATTTTGTCAGCTTGTCGAGCGAC
* *
207 GTGGCGGTCGACACATTTTGTCAACTTTGTCGAGCGAC
1 GTGGCGGTCAACACATTTTGTCAGC-TTGTCGAGCGAC
245 GTGGC
1 GTGGC
250 ATGAAAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 56 0.77
38 17 0.23
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (37 bp):
GTGGCGGTCAACACATTTTGTCAGCTTGTCGAGCGAC
Found at i:623 original size:2 final size:2
Alignment explanation
Indices: 616--646 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
606 CGCTCGACCC
616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
647 TTTATACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2187 original size:44 final size:43
Alignment explanation
Indices: 1619--2186 Score: 701
Period size: 44 Copynumber: 13.0 Consensus size: 43
1609 TGACCACCTA
* * * * * *
1619 GTTCTTGTCTTCTTGGTTTGATTGTGGTGTGGTGGACCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * * *
1662 GTTGTTTACTTCTTGCTTTGAGTGTGATATGGTCGATCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * * * * *
1705 GTTGTTTACTTCTTGCTTTGAGTGTAATGTAGTCGATCGACCT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
1748 GTT-TCTTTCTTTCTTGCTTTGAATGTGATGTGGTTGATCGACTT
1 GTTCT-TTTC-TTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
1792 TTTCTTGTTCTTCTTGCTTTGAATGTGATATGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
1836 GTTGTTTAT-TTTTTGCTTTTGAATGTGATGTGGTCGATCGACTT
1 GTTCTTT-TCTTCTTGC-TTTGAATGTGATGTGGTCGATCGACTT
1880 GTTCTTGTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
1924 GTTGTTTAT-TTCTTGCTTTTAAATGTGATGTGGTCGATCGACTT
1 GTTCTTT-TCTTCTTGC-TTTGAATGTGATGTGGTCGATCGACTT
1968 GTTCTTGTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
2012 GTTCTTGTTCTTTTTGCTTTGTATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
2056 GTTCTTGTTCTTTTTGCTTTGAATGTGATGTGGTCGATCGACTA
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * *
2100 GTTACTTTTCTTCGTGGTTTGAATGTGATGTGGTCGATCGACTA
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * *
2144 GTTACTTTTCTTCGTGGTTTGAAAGTGATGTGGTCGATCGACT
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACT
2187 ACTTACTTGT
Statistics
Matches: 472, Mismatches: 40, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.00
43 94 0.20
44 355 0.75
45 22 0.05
ACGTcount: A:0.13, C:0.14, G:0.25, T:0.48
Consensus pattern (43 bp):
GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
Found at i:2373 original size:57 final size:57
Alignment explanation
Indices: 2198--2373 Score: 262
Period size: 58 Copynumber: 3.1 Consensus size: 57
2188 CTTACTTGTT
* * * * *
2198 TTCTTTAATCATTTCGACATGAATTTGATTTTGGTCGTTCGACACAATTTTTTCTTTC
1 TTCTTTAACCATTTCGGCATGAATGTGATTTTGGTCGTTCGACAC-ATTTCTCCTTTC
*
2256 TTCTTTAACCATTTCGGCATGAATGTGATTTTTGGTCGTTCGACACATTTCTCATTTC
1 TTCTTTAACCATTTCGGCATGAATGTGA-TTTTGGTCGTTCGACACATTTCTCCTTTC
* *
2314 TTCTTTGACCATTTCGGCATGAATGTGATTTTGGTCGTTCGACGCATTTCTCCTTTC
1 TTCTTTAACCATTTCGGCATGAATGTGATTTTGGTCGTTCGACACATTTCTCCTTTC
2371 TTC
1 TTC
2374 GACTTGGGTG
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
57 30 0.28
58 61 0.56
59 17 0.16
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (57 bp):
TTCTTTAACCATTTCGGCATGAATGTGATTTTGGTCGTTCGACACATTTCTCCTTTC
Found at i:2924 original size:23 final size:21
Alignment explanation
Indices: 2880--2924 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2870 CTCTCGTAGG
**
2880 GAGCATTCTTCTTTCTTTGGA
1 GAGCATTCTTCTTTCTGGGGA
2901 GAGCATTCTTCTCTTCTAGGGGA
1 GAGCATTCTTCT-TTCT-GGGGA
2924 G
1 G
2925 TGAGTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 4 0.20
23 4 0.20
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (21 bp):
GAGCATTCTTCTTTCTGGGGA
Found at i:3394 original size:126 final size:126
Alignment explanation
Indices: 3167--3394 Score: 375
Period size: 126 Copynumber: 1.8 Consensus size: 126
3157 GGACGAGGTC
* * *
3167 GATTCATGTCGATCGCCACTTAGTCGATGGCCAAACTAGGTCGAGCTCGGCCTTGCCTGCTTGCC
1 GATTCAAGTCGATCGCCACTTAGTCGATGGCCAAACTAGGTCGAGCTCGGCCTTGCCTGATCGCC
*
3232 CGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
66 CGCCTGTTGGCGTTGGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
* * *
3293 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
1 GATTCAAGTCGATCGCCACTTAGTCGATGGCCAAACTAGGTCGAGCTCGGCCTTGCCTGATCGCC
* *
3358 CGCCTGTTGGCGTTGGGCCCCTTGAGGGTATTATCAT
66 CGCCTGTTGGCGTTGGGCCCCTTGAGGGCATCATCAT
3395 TTCCCAGACT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 93 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.29
Consensus pattern (126 bp):
GATTCAAGTCGATCGCCACTTAGTCGATGGCCAAACTAGGTCGAGCTCGGCCTTGCCTGATCGCC
CGCCTGTTGGCGTTGGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
Found at i:3589 original size:125 final size:126
Alignment explanation
Indices: 3418--3651 Score: 362
Period size: 125 Copynumber: 1.9 Consensus size: 126
3408 TCAGGGATGG
* *
3418 TTCTTGCCAATCACCTGCCGGTCGGGGGCCATGTTAGGTCAAGGTCGATTCTTGTCGATCGCCTA
1 TTCTTGCCAATCACCTGCCAGTCGGGGGCCATGCTAGGTCAAGGTCGATTCTTGTCGATCGCCTA
* * *
3483 GCCTCCTGGCGTTGAGCCCCTTAGGGGCGTTCATCGTTCCCATACTTGTCCAAGGATGGTT
66 GCCTCCTGGCGTTGAGCCCATTAAGGGCGTTCATCATTCCCATACTTGTCCAAGGATGGTT
* * * *
3544 TTCTT-CCAATCTCCTGTCAGTTGGGGGCCATGCTAGGTCAAGGTCGATTCTTGTCGATCGCCTC
1 TTCTTGCCAATCACCTGCCAGTCGGGGGCCATGCTAGGTCAAGGTCGATTCTTGTCGATCGCCTA
* *
3608 GCCTGCTGGCGTTGAGCCCATTAAGGGCGTTCGTCATTCCCATA
66 GCCTCCTGGCGTTGAGCCCATTAAGGGCGTTCATCATTCCCATA
3652 AGTTGGGGGC
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
125 92 0.95
126 5 0.05
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.30
Consensus pattern (126 bp):
TTCTTGCCAATCACCTGCCAGTCGGGGGCCATGCTAGGTCAAGGTCGATTCTTGTCGATCGCCTA
GCCTCCTGGCGTTGAGCCCATTAAGGGCGTTCATCATTCCCATACTTGTCCAAGGATGGTT
Found at i:5742 original size:15 final size:15
Alignment explanation
Indices: 5722--5751 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5712 TTGCTGACTC
5722 ACTCGTATTTTTGGG
1 ACTCGTATTTTTGGG
5737 ACTCGTATTTTTGGG
1 ACTCGTATTTTTGGG
5752 CGGGGGCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (15 bp):
ACTCGTATTTTTGGG
Found at i:7873 original size:2 final size:2
Alignment explanation
Indices: 7866--7905 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
7856 AGCTATATCT
*
7866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7906 CTTAGTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:7879 original size:33 final size:33
Alignment explanation
Indices: 7837--7905 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
7827 CACAGGTACG
* *
7837 TATATATATATATGCTATA-AGCTATATCTTATA
1 TATATATATATAT-ATATATAGATATATCTTATA
*
7870 TATATATATATATATATATATATATATCTTATA
1 TATATATATATATATATATAGATATATCTTATA
7903 TAT
1 TAT
7906 CTTAGTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 4 0.12
33 28 0.88
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (33 bp):
TATATATATATATATATATAGATATATCTTATA
Found at i:12679 original size:27 final size:26
Alignment explanation
Indices: 12641--12700 Score: 111
Period size: 27 Copynumber: 2.3 Consensus size: 26
12631 AAATAAATCC
12641 TAGGGTATTGTATAATCGGGTTAGGG
1 TAGGGTATTGTATAATCGGGTTAGGG
12667 TTAGGGTATTGTATAATCGGGTTAGGG
1 -TAGGGTATTGTATAATCGGGTTAGGG
12694 TAGGGTA
1 TAGGGTA
12701 CGGGTAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 7 0.21
27 26 0.79
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.35
Consensus pattern (26 bp):
TAGGGTATTGTATAATCGGGTTAGGG
Found at i:13662 original size:7 final size:7
Alignment explanation
Indices: 13650--13693 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
13640 GTAGCTTTAT
13650 TAATTAA
1 TAATTAA
13657 TAATTAA
1 TAATTAA
13664 TAATTAA
1 TAATTAA
13671 TAATTAA
1 TAATTAA
13678 TAATTAA
1 TAATTAA
*
13685 AAATTAA
1 TAATTAA
13692 TA
1 TA
13694 TATACGTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATTAA
Done.