Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014486.1 Corchorus capsularis cultivar CVL-1 contig14507, 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: 46132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5248 original size:115 final size:113
Alignment explanation
Indices: 5046--5271 Score: 364
Period size: 115 Copynumber: 2.0 Consensus size: 113
5036 CAGGGCCCGA
*
5046 GCTCAATTTTGCATGATTTTTGACAGAAAGACTGCTTGAAATATCTATATTCATCGAACTAAATC
1 GCTCAATTTTGCATGATTTTTGACAGAAAGACCGCTTGAAATATCTATATTCATCGAACTAAATC
** *
5111 TCAGCCACATTGGATTTAAGGATGTTTTTTTTTACGAGCATCTGAATCAT
66 TCAGCCACATTGGATTTAAGGA--TTTGCTTTTACGAGCATCTAAATCAT
* *
5161 GCTCAGTTTTGCATGATTTTTGGCAGAAAGACCGCTTGAAATATCTATATTCATCGAA-TCAAAT
1 GCTCAATTTTGCATGATTTTTGACAGAAAGACCGCTTGAAATATCTATATTCATCGAACT-AAAT
5225 CTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAATC
65 CTCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAATC
5272 TTATTTCGAT
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
113 21 0.20
114 1 0.01
115 82 0.79
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (113 bp):
GCTCAATTTTGCATGATTTTTGACAGAAAGACCGCTTGAAATATCTATATTCATCGAACTAAATC
TCAGCCACATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAATCAT
Found at i:5835 original size:294 final size:293
Alignment explanation
Indices: 5306--5891 Score: 841
Period size: 294 Copynumber: 2.0 Consensus size: 293
5296 ATTTGGAAAT
* * * *
5306 AAAAAATGGAAAAACGACATTAGATGCGCGAAAACCCCTCCAATTTTTTTGGCGTTGAATTATAT
1 AAAAAATGGAAAAACGACATTAGAAGCACGAAAACCCCTCCAATATTTTTGGCATTGAATTATAT
* ** *
5371 ATTTTTTCTGAGTATTGTGGCAAAAAATTCAGTAAAAATTTTTTTGAGTCAGTTTTTAACCGAAA
66 ATTTTTTCTGAGTATTGTGGCAAAAAATTCAGGAAAAATAATTTCGAGTCAGTTTTTAACCGAAA
* * * *
5436 TCGTGTACTAACCATCATGGTTTTGGGGCTAAAAATGCATTTCGAGGCCCCGGCTCAGTTTTGCA
131 CCATGTACTAACCATCACGGTTTTGGGGCTAAAAATACATTTCGAGGCCCCGGCTCAGTTTTGCA
* * *
5501 CGATTTTTGGCAGAAAGACTGCTTGAAATATCTATATTCATCTAACCAAATCTCAATCACATTAG
196 CGATTTTTGGCAGAAAGACTACTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATTAG
5566 ACTTAAGGATTTGTTTTTACGAGCATCTAATTCG
261 ACTTAAGGATTTGTTTTT-CGAGCATCTAATTCG
** * *
5600 AAAAAATGGAAAAACGGTATTAGAAGCATGAAAACCCCTTCAATATTTTTGGCATTGAATTATAT
1 AAAAAATGGAAAAACGACATTAGAAGCACGAAAACCCCTCCAATATTTTTGGCATTGAATTATAT
* * * *
5665 ATTTTTTCTGAGTATTGTGGTAAGAAATTCTGGGAAAAA-AATTTCGAGTCAGTTTTTAGCCGAA
66 ATTTTTTCTGAGTATTGTGGCAAAAAATTC-AGGAAAAATAATTTCGAGTCAGTTTTTAACCGAA
* * * * *
5729 ACCATGTACTAATCATCACGGTTTTGGGGCTAAAAATACGTTTTGGGGTCCCGGCTCAGTTTTGC
130 ACCATGTACTAACCATCACGGTTTTGGGGCTAAAAATACATTTCGAGGCCCCGGCTCAGTTTTGC
* * * *
5794 ATGATTTTTGGCAGAAAGACTACTTGAAAAATCTATATTCATCTAATCAAATCTCAGCCACATTG
195 ACGATTTTTGGCAGAAAGACTACTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATTA
* *
5859 GATTTAAGGATTTGTTTTTCGAGCATCTGATTC
260 GACTTAAGGATTTGTTTTTCGAGCATCTAATTC
5892 TTGGTTCGAT
Statistics
Matches: 257, Mismatches: 34, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
293 13 0.05
294 238 0.93
295 6 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (293 bp):
AAAAAATGGAAAAACGACATTAGAAGCACGAAAACCCCTCCAATATTTTTGGCATTGAATTATAT
ATTTTTTCTGAGTATTGTGGCAAAAAATTCAGGAAAAATAATTTCGAGTCAGTTTTTAACCGAAA
CCATGTACTAACCATCACGGTTTTGGGGCTAAAAATACATTTCGAGGCCCCGGCTCAGTTTTGCA
CGATTTTTGGCAGAAAGACTACTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATTAG
ACTTAAGGATTTGTTTTTCGAGCATCTAATTCG
Found at i:6516 original size:326 final size:318
Alignment explanation
Indices: 5600--6531 Score: 873
Period size: 326 Copynumber: 2.8 Consensus size: 318
5590 ATCTAATTCG
* * * *
5600 AAAAAATGGAAAAACGGTATTAGAAGCATGAAAACCCCTTCAATATTTTTGGCATTGAATTATAT
1 AAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATATTTTTAGCGTTGAATTATAT
* * *
5665 ATTTTTTCTGAGTATTGTGGTAAGAAATTCTG-GGAAAAAAATTTCGAGTCAGTTTTTAGCCGAA
66 -TTTTTT-TGAGTATTGTGGCAA-AAAAT-TGAGGAAAAAAATTTCG-GTCAGTTTTTAGCCAAA
* * * *
5729 ACCATGTACTAATCATCACGGTTTTGGGGCTAAAAATACGTTTTGGGGTCCCGGCTCAGTTTTGC
126 ACCAAGTACTAA-CATCACGGTTTT--TGCTAAAAATGCG-TTTCGGGTCCCGGCTCAGTTTTGC
* * * *
5794 ATGATTTTTGGCAGAAAGACTACTTGAAAAATCTATATTCATCTAATCAAATCTCAGCCACATTG
187 ATGATTTTTGGCATAAAGACTACTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTG
* **
5859 GATTTAAGGATTTGTTTTTCGAGCATCTGATTCTTGGTTCGATTTAATTTTAAATAAATTCGAAA
252 GATTTAAGGATTTGTTTTACGAGCATCTGATTCTTGGTTCGATTTAATTAGAAATAAATTCGAAA
5924 AA
317 AA
* * * * ** *
5926 AAAAAGAAGGAAAAACAATATTAGAAGCATGAAAAACCCTACAAATTTTTTTTTCGTTTAATTAT
1 AAAAA-ATGGAAAAACGATATTAGAAGCATGAAAAACCCTTC-AATATTTTTAGCGTTGAATTAT
* ** ** * *
5991 ATTTTTTTTG-TTATTACGGCAAGGAATTGAGGAAAAAAATTTCGGGTCAGTTTTT-TCAAAAAT
64 ATTTTTTTTGAGTATTGTGGCAAAAAATTGAGGAAAAAAATTTC-GGTCAGTTTTTAGCCAAAA-
* * ** * * * *
6054 TTTGCTGAAAATTGTGAACATCACGGTTTTTTACTCAAAACGCGTTCCGGGATCCCGGCTCAGTT
127 ----C--CAAGTACT-AACATCACGG-TTTTTGCTAAAAATGCGTTTCGGG-TCCCGGCTCAGTT
* * * * * ** * *
6119 TCGCATGGTTTTGGGCGTAAAGACTTCTTGAAATATCTATATTCATCGGACCAAATCCCAACCAA
183 TTGCATGATTTTTGGCATAAAGACTACTTGAAATATCTATATTCATCTAACCAAATCTCAACCAC
* * *
6184 ATTGGATTTAAGGATTTGCTTTTACGAGCATCTGAATT-TTGTTTCGATTTAGTTAGAAATTAAT
248 ATTGGATTTAAGGATTTG-TTTTACGAGCATCTG-ATTCTTGGTTCGATTTAATTAGAAATAAAT
***
6248 TCGGAATTTT
311 TC-GAA-AAA
* * * * *
6258 AAAAAATGGAAAAACGATATTTGAAGCGTGAAAAACGCTTCAATCTTTCTAGCGTTGAATTATAT
1 AAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATATTTTTAGCGTTGAATTATAT
* *
6323 TTTTTTATGAGTATTGTGACAAAAAATTGAGAAAAAAAATTTCGGCTCAGTTTTTAGCCAAAACC
66 TTTTTT-TGAGTATTGTGGCAAAAAATTGAGGAAAAAAATTTCGG-TCAGTTTTTAGCCAAAACC
* ** * * * *
6388 AGGTACTAACCATCACAATTTCTTGCTAAAAATGCGTTTCAGGTCCTCGACTTAATTTTGCATGA
129 AAGTACTAA-CATCACGGTTT-TTGCTAAAAATGCGTTTCGGGTCC-CGGCTCAGTTTTGCATGA
* * * * *
6453 TTTTTGGAATAAAAAATCCTTGAAATATTTATATTCATCTAACCAAATCTCAACCACATTGGATT
191 TTTTTGGCATAAAGACTACTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATT
* *
6518 TAAAGATTTTTTTT
256 TAAGGATTTGTTTT
6532 GACAAATTAC
Statistics
Matches: 477, Mismatches: 104, Indels: 51
0.75 0.16 0.08
Matches are distributed among these distances:
323 6 0.01
324 25 0.05
325 21 0.04
326 107 0.22
327 37 0.08
328 26 0.05
329 91 0.19
330 73 0.15
331 46 0.10
332 40 0.08
333 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (318 bp):
AAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATATTTTTAGCGTTGAATTATAT
TTTTTTTGAGTATTGTGGCAAAAAATTGAGGAAAAAAATTTCGGTCAGTTTTTAGCCAAAACCAA
GTACTAACATCACGGTTTTTGCTAAAAATGCGTTTCGGGTCCCGGCTCAGTTTTGCATGATTTTT
GGCATAAAGACTACTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGG
ATTTGTTTTACGAGCATCTGATTCTTGGTTCGATTTAATTAGAAATAAATTCGAAAAA
Found at i:14606 original size:63 final size:63
Alignment explanation
Indices: 14528--14654 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
14518 TACCATTCTC
14528 AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAG-CTTTTTGTA
1 AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGAC-TTTTGTA
* *
14591 AGAAGCATCTGCAGACTCTGTACTTAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
1 AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
14654 A
1 A
14655 CTTTCACATG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 60 0.98
64 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (63 bp):
AGAAGCATCTGCAGACTCAGTACTCAACTTAGATCCATCACTTATCTCACTGAGACTTTTGTA
Found at i:16632 original size:21 final size:22
Alignment explanation
Indices: 16608--16652 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
16598 GAAGTCATAT
*
16608 ATATGCAAT-TTTATATACTTG
1 ATATGAAATGTTTATATACTTG
* *
16629 ATATTAAATGTTTCTATACTTG
1 ATATGAAATGTTTATATACTTG
16651 AT
1 AT
16653 TTTGCATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
ATATGAAATGTTTATATACTTG
Found at i:34688 original size:18 final size:19
Alignment explanation
Indices: 34654--34694 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
34644 GCTTTTTTTC
*
34654 CTTC-TCTTTCTCTTTCAA
1 CTTCTTCTTTATCTTTCAA
34672 CTTCTTCTTTATC-TTCAA
1 CTTCTTCTTTATCTTTCAA
34690 -TTCTT
1 CTTCTT
34695 GCAGCAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (19 bp):
CTTCTTCTTTATCTTTCAA
Found at i:37743 original size:23 final size:23
Alignment explanation
Indices: 37717--37762 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
37707 GAATGGAGTC
*
37717 AATATTTAAAAGAAAT-TTTAATT
1 AATATATAAAA-AAATATTTAATT
*
37740 AATATATAGAAAAATATTTAATT
1 AATATATAAAAAAATATTTAATT
37763 TTTAATCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AATATATAAAAAAATATTTAATT
Found at i:43674 original size:1 final size:1
Alignment explanation
Indices: 43664--43712 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
43654 TGAGACAAAG
* * * **
43664 AAAAAGAAAAAGAAAAAAAAGAATTAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43713 GGTTAAGAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.04
Consensus pattern (1 bp):
A
Found at i:45997 original size:31 final size:31
Alignment explanation
Indices: 45962--46059 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
45952 TTTTGTGCAC
*
45962 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGCCACTTTTTGAAACAT
* **
45993 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGCCACTTTTTGAAACAT
* * * * **
46024 GTGGCGTGACATGTGTCAC-TTTTGGTACAT
1 GTGGCATGCCACGTGCCACTTTTTGAAACAT
46054 GTGGCA
1 GTGGCA
46060 CGACTTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 16 0.27
31 43 0.73
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGCCACTTTTTGAAACAT
Done.