Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015995.1 Corchorus capsularis cultivar CVL-1 contig16016, 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: 54185
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:165 original size:35 final size:35
Alignment explanation
Indices: 126--229 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 35
116 TGAATATATG
126 AAATTCTTAATAAGGTAAAAAATCATACAATTTAC
1 AAATTCTTAATAAGGTAAAAAATCATACAATTTAC
* * * ** * *
161 AAATT-TGTAGTTA-G-AAAAAATTATTGAATGT-G
1 AAATTCT-TAATAAGGTAAAAAATCATACAATTTAC
*
193 AAATCCTTAATAAGGTAAAAAATCATACAATTTAC
1 AAATTCTTAATAAGGTAAAAAATCATACAATTTAC
228 AA
1 AA
230 TGTGATTTCT
Statistics
Matches: 49, Mismatches: 15, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
32 8 0.16
33 15 0.31
34 15 0.31
35 11 0.22
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.32
Consensus pattern (35 bp):
AAATTCTTAATAAGGTAAAAAATCATACAATTTAC
Found at i:1406 original size:2 final size:2
Alignment explanation
Indices: 1399--1452 Score: 76
Period size: 2 Copynumber: 27.0 Consensus size: 2
1389 GCTTTAATAG
1399 TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA GTA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA
1441 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1453 GTGTTGGTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.04
2 42 0.88
3 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1854 original size:74 final size:74
Alignment explanation
Indices: 1776--1925 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 74
1766 GTTTCCTGTT
* *
1776 TTCTGTTGTCAATTTCCTGTTTTTAGAAACAAAACAGTGAAAACATGTTTGACAGGCTGTTTCTG
1 TTCTGTTGCCAATTTCCTATTTTTAGAAACAAAACAGTGAAAACATGTTTGACAGGCTGTTTCTG
1841 TTTCCAAAA
66 TTTCCAAAA
*
1850 TTCTGTTGCCAATTTCCTATTTTTAGAAACAAAACAGTGAAAACATGTTTGGCAGGCTGTTTCTG
1 TTCTGTTGCCAATTTCCTATTTTTAGAAACAAAACAGTGAAAACATGTTTGACAGGCTGTTTCTG
1915 TTTCCAAAA
66 TTTCCAAAA
1924 TT
1 TT
1926 TTGGAAACAG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (74 bp):
TTCTGTTGCCAATTTCCTATTTTTAGAAACAAAACAGTGAAAACATGTTTGACAGGCTGTTTCTG
TTTCCAAAA
Found at i:2158 original size:11 final size:11
Alignment explanation
Indices: 2134--2168 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2124 TTGGCAGCGC
2134 AACAAAAACAA
1 AACAAAAACAA
* *
2145 AACGAAAACGA
1 AACAAAAACAA
2156 AACAAAAACAA
1 AACAAAAACAA
2167 AA
1 AA
2169 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:17276 original size:31 final size:31
Alignment explanation
Indices: 17179--17277 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
17169 TTTTGTGCAC
* * **
17179 GTGGCATGCCACGTG-CAATTTTTTGAAACAT
1 GTGGCATGACACGTGTC-ACTTTTTGGTACAT
* *
17210 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAT
* * *
17241 GTGGCGTGACATGTGTCACTTTTTGGTATAT
1 GTGGCATGACACGTGTCACTTTTTGGTACAT
17272 GTGGCA
1 GTGGCA
17278 CGACTTTTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 56 0.98
32 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (31 bp):
GTGGCATGACACGTGTCACTTTTTGGTACAT
Found at i:18406 original size:29 final size:30
Alignment explanation
Indices: 18354--18415 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
18344 TTTCTTAAGA
*
18354 AAAAACTTTCTAGTCTTAAACTTTCTATAG
1 AAAAACTTTCTAGCCTTAAACTTTCTATAG
**
18384 AAAAACTTTCTA-CCTTTTACTTTCTATAG
1 AAAAACTTTCTAGCCTTAAACTTTCTATAG
18413 AAA
1 AAA
18416 CTTCCAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAAACTTTCTAGCCTTAAACTTTCTATAG
Found at i:29749 original size:50 final size:50
Alignment explanation
Indices: 29674--29771 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
29664 GAAAATTCTA
29674 TTAGGTGACCTATAAAACCTATATTTTACACCCTCCAATGATATTATGCT
1 TTAGGTGACCTATAAAACCTATATTTTACACCCTCCAATGATATTATGCT
*
29724 TTAGGTGGCCTATAAAACCTATATTTTACACCCTCCAATGATATTATG
1 TTAGGTGACCTATAAAACCTATATTTTACACCCTCCAATGATATTATG
29772 TCATATAGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (50 bp):
TTAGGTGACCTATAAAACCTATATTTTACACCCTCCAATGATATTATGCT
Found at i:32292 original size:62 final size:62
Alignment explanation
Indices: 32195--32380 Score: 372
Period size: 62 Copynumber: 3.0 Consensus size: 62
32185 CTGTTTTATT
32195 TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
1 TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
32257 TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
1 TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
32319 TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
1 TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
32381 ACAAAGAGAG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 124 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (62 bp):
TTATAGATTCTTTTAAGAAAATTCAGTTAACAAATGAAATTTTGTTGTTAAATGATAACAAA
Found at i:32680 original size:11 final size:11
Alignment explanation
Indices: 32666--32698 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
32656 ATTCATAACA
32666 AATTTATAATT
1 AATTTATAATT
32677 AATTTATAATT
1 AATTTATAATT
32688 -ATTTGATAATT
1 AATTT-ATAATT
32699 TACTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:36579 original size:3 final size:3
Alignment explanation
Indices: 36573--36619 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
36563 CTTCTATTAT
36573 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
36620 CTATACTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:37127 original size:28 final size:28
Alignment explanation
Indices: 37064--37143 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
37054 GCTTAATACC
* *
37064 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T--TTTTTGGGA
*
37095 CAAATTGGCCCCTTAACTTTTTTTTGGA
1 CAAATTGGCCCCTTAACTTTTTTTGGGA
* *
37123 CAAATTGACCCTTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
37144 AAACACGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 26 0.59
30 1 0.02
31 17 0.39
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (28 bp):
CAAATTGGCCCCTTAACTTTTTTTGGGA
Found at i:37866 original size:31 final size:31
Alignment explanation
Indices: 37831--37913 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
37821 TCTTGTTTTT
*
37831 AAAAGTTAAGGGGTCAATTTGTCCCAAAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAAAA
**
37862 AAAAGTTAAGGGGCCAATTTGTCCCAAAATG
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAAAA
* * *
37893 GATAGTTAAGGGGCTAATTTG
1 AAAAGTTAAGGGGCCAATTTG
37914 GGTATTAAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (31 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAAAA
Found at i:41806 original size:20 final size:20
Alignment explanation
Indices: 41767--41807 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41757 ATGAATACAA
**
41767 GGCATTTGATTTACGGATTG
1 GGCATTTGATTTACAAATTG
*
41787 GGCATTTGATTTGCAAATTG
1 GGCATTTGATTTACAAATTG
41807 G
1 G
41808 CGCTTTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (20 bp):
GGCATTTGATTTACAAATTG
Found at i:42379 original size:19 final size:19
Alignment explanation
Indices: 42355--42391 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42345 TTTGCAGCAC
42355 GGATTTTACAATAGGAGAT
1 GGATTTTACAATAGGAGAT
42374 GGATTTTACAATAGGAGA
1 GGATTTTACAATAGGAGA
42392 AAAGGGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (19 bp):
GGATTTTACAATAGGAGAT
Found at i:44792 original size:390 final size:390
Alignment explanation
Indices: 44073--44855 Score: 1566
Period size: 390 Copynumber: 2.0 Consensus size: 390
44063 GTTCAAATTT
44073 TTGAACTAAAATTAGCTTGAAAATTTAAAAGTCATTTTTGAGCTAATTTTAGTTTGAAAATAAAC
1 TTGAACTAAAATTAGCTTGAAAATTTAAAAGTCATTTTTGAGCTAATTTTAGTTTGAAAATAAAC
44138 TTTGAAATAAAGGATTTGACTTTTTTAAATTGGAAGTGACTTAAAATGGAATTGACGAATTAATT
66 TTTGAAATAAAGGATTTGACTTTTTTAAATTGGAAGTGACTTAAAATGGAATTGACGAATTAATT
44203 TGGATTAGTATTTACTTAAAAATTAAGCCTTTGGTTAGAATTTTGGTCTCTTTTAGGTATAAGCT
131 TGGATTAGTATTTACTTAAAAATTAAGCCTTTGGTTAGAATTTTGGTCTCTTTTAGGTATAAGCT
44268 AATTAAGGAGTGGATTTAATTTTCTCATGCCAAGTTCATTTTATTTGACCATCTTGATTTTTTGA
196 AATTAAGGAGTGGATTTAATTTTCTCATGCCAAGTTCATTTTATTTGACCATCTTGATTTTTTGA
44333 CTTATTGTGATGAACGTGGTTGATTTGTGTTTTGTGCCCCTGAATGTCACTAATCGTTTGCTTTA
261 CTTATTGTGATGAACGTGGTTGATTTGTGTTTTGTGCCCCTGAATGTCACTAATCGTTTGCTTTA
44398 GTGTGCAGAAGTCCCCGGAATTATCCAGTTGACCCATAGTTTTTTAATTTATTTTTATTTGGGGC
326 GTGTGCAGAAGTCCCCGGAATTATCCAGTTGACCCATAGTTTTTTAATTTATTTTTATTTGGGGC
44463 TTGAACTAAAATTAGCTTGAAAATTTAAAAGTCATTTTTGAGCTAATTTTAGTTTGAAAATAAAC
1 TTGAACTAAAATTAGCTTGAAAATTTAAAAGTCATTTTTGAGCTAATTTTAGTTTGAAAATAAAC
44528 TTTGAAATAAAGGATTTGACTTTTTTAAATTGGAAGTGACTTAAAATGGAATTGACGAATTAATT
66 TTTGAAATAAAGGATTTGACTTTTTTAAATTGGAAGTGACTTAAAATGGAATTGACGAATTAATT
44593 TGGATTAGTATTTACTTAAAAATTAAGCCTTTGGTTAGAATTTTGGTCTCTTTTAGGTATAAGCT
131 TGGATTAGTATTTACTTAAAAATTAAGCCTTTGGTTAGAATTTTGGTCTCTTTTAGGTATAAGCT
44658 AATTAAGGAGTGGATTTAATTTTCTCATGCCAAGTTCATTTTATTTGACCATCTTGATTTTTTGA
196 AATTAAGGAGTGGATTTAATTTTCTCATGCCAAGTTCATTTTATTTGACCATCTTGATTTTTTGA
44723 CTTATTGTGATGAACGTGGTTGATTTGTGTTTTGTGCCCCTGAATGTCACTAATCGTTTGCTTTA
261 CTTATTGTGATGAACGTGGTTGATTTGTGTTTTGTGCCCCTGAATGTCACTAATCGTTTGCTTTA
44788 GTGTGCAGAAGTCCCCGGAATTATCCAGTTGACCCATAGTTTTTTAATTTATTTTTATTTGGGGC
326 GTGTGCAGAAGTCCCCGGAATTATCCAGTTGACCCATAGTTTTTTAATTTATTTTTATTTGGGGC
44853 TTG
1 TTG
44856 TAATAATTTA
Statistics
Matches: 393, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
390 393 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (390 bp):
TTGAACTAAAATTAGCTTGAAAATTTAAAAGTCATTTTTGAGCTAATTTTAGTTTGAAAATAAAC
TTTGAAATAAAGGATTTGACTTTTTTAAATTGGAAGTGACTTAAAATGGAATTGACGAATTAATT
TGGATTAGTATTTACTTAAAAATTAAGCCTTTGGTTAGAATTTTGGTCTCTTTTAGGTATAAGCT
AATTAAGGAGTGGATTTAATTTTCTCATGCCAAGTTCATTTTATTTGACCATCTTGATTTTTTGA
CTTATTGTGATGAACGTGGTTGATTTGTGTTTTGTGCCCCTGAATGTCACTAATCGTTTGCTTTA
GTGTGCAGAAGTCCCCGGAATTATCCAGTTGACCCATAGTTTTTTAATTTATTTTTATTTGGGGC
Found at i:45316 original size:15 final size:13
Alignment explanation
Indices: 45285--45309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45275 CAATAAAAGG
45285 TGTTTTCAAAAAA
1 TGTTTTCAAAAAA
45298 TGTTTTCAAAAA
1 TGTTTTCAAAAA
45310 TCATGTTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TGTTTTCAAAAAA
Found at i:50635 original size:27 final size:27
Alignment explanation
Indices: 50605--50658 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
50595 CATTCATGTT
* *
50605 ATATTATTGTTTCCTCTATTGTTGCAG
1 ATATTATTCTTTCCTCTATTATTGCAG
50632 ATATTATTCTTTCCTCTATTATTGCAG
1 ATATTATTCTTTCCTCTATTATTGCAG
50659 CAGCAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (27 bp):
ATATTATTCTTTCCTCTATTATTGCAG
Done.