Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010120.1 Corchorus capsularis cultivar CVL-1 contig10141, 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: 21304
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:4906 original size:28 final size:27
Alignment explanation
Indices: 4867--4945 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 27
4857 GCATTAGGGT
4867 CATCTAGGGGCATTTTGGTCATTTTCA
1 CATCTAGGGGCATTTTGGTCATTTTCA
**
4894 CATCTAGGAGGCATTTTGGTCATTTTTG
1 CATCTAGG-GGCATTTTGGTCATTTTCA
* *
4922 CATTTAGGGGGTATTTTGGTCATT
1 CATCTA-GGGGCATTTTGGTCATT
4946 CGCAATCTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
27 8 0.17
28 36 0.78
29 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (27 bp):
CATCTAGGGGCATTTTGGTCATTTTCA
Found at i:6424 original size:6 final size:6
Alignment explanation
Indices: 6413--6439 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6403 AAAGCAAAGC
6413 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
6440 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:6454 original size:13 final size:13
Alignment explanation
Indices: 6436--6470 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
6426 AATCTAAATC
*
6436 TAAAGCAGATTAA
1 TAAAGCAAATTAA
6449 TAAAGCAAATTAA
1 TAAAGCAAATTAA
6462 TAAAGCAAA
1 TAAAGCAAA
6471 CAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:7389 original size:10 final size:10
Alignment explanation
Indices: 7374--7398 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7364 GAGGACTCTA
7374 GAATTTTCTG
1 GAATTTTCTG
7384 GAATTTTCTG
1 GAATTTTCTG
7394 GAATT
1 GAATT
7399 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:11778 original size:28 final size:28
Alignment explanation
Indices: 11725--11780 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
11715 AGGGGCATGG
*
11725 TTCTTCTTTAACTTTCCTTTATTTACTA
1 TTCTTCTTTAACTTTCCTTTAGTTACTA
* *
11753 TTCTTGTTTAA-TTTCCTTGTGGTTACTA
1 TTCTTCTTTAACTTTCCTT-TAGTTACTA
11781 ACTTCTCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.59
Consensus pattern (28 bp):
TTCTTCTTTAACTTTCCTTTAGTTACTA
Found at i:15272 original size:3 final size:3
Alignment explanation
Indices: 15264--15319 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
15254 AATTGCATTG
15264 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15312 AAT AAT AA
1 AAT AAT AA
15320 AGGAATAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16039 original size:15 final size:14
Alignment explanation
Indices: 16010--16044 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
16000 AAAATTGATG
16010 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
*
16024 AAAAAGAGAAACGAA
1 AAAAAGA-AAAAGAA
16039 AAAAAG
1 AAAAAG
16045 CAACGATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:17304 original size:16 final size:15
Alignment explanation
Indices: 17264--17304 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
17254 CAAGTGCATG
17264 AAAAAAGA-AAGAAA
1 AAAAAAGAGAAGAAA
17278 AAGAAAA-AGAAGAAA
1 AA-AAAAGAGAAGAAA
17293 AGAAAAAGAGAA
1 A-AAAAAGAGAA
17305 AGAGAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.13
15 15 0.65
16 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAGAAA
Found at i:18357 original size:70 final size:69
Alignment explanation
Indices: 18124--18626 Score: 467
Period size: 69 Copynumber: 7.3 Consensus size: 69
18114 CGAATGCTCC
* * ** * ** ** *
18124 GGCTTTTTCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGTTTTGGTTCCATTTAGGCA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAG-TCAAGCCTTGGTTCCATCCAAGCAT
** *
18188 AGAGA
65 TCAGG
* * ** **
18193 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGA-GATAGTTTC-AGATTTGGTTCCATCCAAGC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGA-AG--TCAAGCCTTGGTTCCATCCAAGC
* *
18256 A-ACAGA
63 ATTCAGG
* * * **
18262 GGCTCTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGATCAAGCTTTGGTTCAATCCAAAAAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAG-TCAAGCCTTGGTTCCATCCAAGCAT
18327 TCAGG
65 TCAGG
** * *
18332 GGCTTTTCCACAAGCCAGTCTCGTTTCCATACCAGGAAGATCAAGCTTTGGTTCCATCCAAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAG-TCAAGCCTTGGTTCCATCCAAGCAT
*
18397 TCATG
65 TCAGG
** **
18402 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCATT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGTCAAGCCTTGGTTCCATCCAAGCATT
18467 CAGG
66 CAGG
* ** ** *
18471 GGCTTTTTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCACT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGTCAAGCCTTGGTTCCATCCAAGCATT
18536 CAGG
66 CAGG
* * * * * *
18540 GGGTTTTCCACAAGCCAAACTTGTTTTCATACGAGGTAGTTCAGGCATTGGTTCCATCCAAGCA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAG-TCAAGCCTTGGTTCCATCCAAGCAT
*
18604 ACAGG
65 TCAGG
*
18609 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
18627 GTTCAGTGAG
Statistics
Matches: 372, Mismatches: 56, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
68 2 0.01
69 247 0.66
70 123 0.33
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGTCAAGCCTTGGTTCCATCCAAGCATT
CAGG
Found at i:18395 original size:139 final size:137
Alignment explanation
Indices: 18239--18626 Score: 440
Period size: 139 Copynumber: 2.8 Consensus size: 137
18229 TAGTTTCAGA
* *
18239 TTTGGTTCCATCCAAGCA-ACAGAGGCTCTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGAT
1 TTTGGTTCCATCCAAGCACTCAG-GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAG-T
* * **
18303 CAAGCTTTGGTTCAATCCAAAAATTCAGGGGCTTTTCCACAAGCCAGTCTCGTTTCCATACCAGG
64 CAAGCATTGGTTCCATCCAAAAATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACCAGG
18368 AAGATCAAGC
129 AAG-TCAAGC
* ** *
18378 TTTGGTTCCATCCAAGCATTCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT
1 TTTGGTTCCATCCAAGCACTCA-GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGTC
* * ** * * **
18443 TAGCCTTGGTTCCATCCAAGCATTCAGGGGCTTTTTCACAAGCCAAACTCGTTTCCATACGAGTC
65 AAGCATTGGTTCCATCCAAAAATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACCAGGA
**
18508 AGTTTAGC
130 AGTCAAGC
* * * * *
18516 CTTGGTTCCATCCAAGCACTCAGGGGGTTTTCCACAAGCCAAACTTGTTTTCATACGAGGTAGTT
1 TTTGGTTCCATCCAAGCACTCA-GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAG-T
* * *
18581 CAGGCATTGGTTCCATCCAAGCAA--CAGGGGCTTTTCCATAAGCCAA
64 CAAGCATTGGTTCCATCCAA-AAATTCAGGGGCTTTTCCACAAGCCAA
18627 GTTCAGTGAG
Statistics
Matches: 211, Mismatches: 34, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
138 79 0.37
139 92 0.44
140 39 0.18
141 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (137 bp):
TTTGGTTCCATCCAAGCACTCAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGGAAGTCA
AGCATTGGTTCCATCCAAAAATTCAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACCAGGAA
GTCAAGC
Found at i:18808 original size:47 final size:47
Alignment explanation
Indices: 18736--18973 Score: 359
Period size: 47 Copynumber: 5.0 Consensus size: 47
18726 ATCCAGGCAA
*
18736 TCTTTTCTCGCTTCCATGCGAGTTTTGAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGG
* * *
18783 TCTTTTCTCGCTTCCACGCGGGTTTTCAATTTGGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
18830 TCTTTTCTTGCTTCCATGCGAGTTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
18877 TCTTTTCTCGCTTCCACGCGGGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGG
* * * *
18924 TCTTTCTCTCGCTTCCATGCGAGTATGCAATTCAGTGACCAAAGTTGG
1 TCTTT-TCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGG
18972 TC
1 TC
18974 AACGGGTTTT
Statistics
Matches: 171, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
47 133 0.78
48 38 0.22
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCATGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:19319 original size:28 final size:27
Alignment explanation
Indices: 19280--19358 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 27
19270 GCATTAGGGT
19280 CATCTAGGGGCATTTTGGTCATTTTCA
1 CATCTAGGGGCATTTTGGTCATTTTCA
**
19307 CATCTAGGAGGCATTTTGGTCATTTTTG
1 CATCTAGG-GGCATTTTGGTCATTTTCA
* *
19335 CATTTAGGGGGTATTTTGGTCATT
1 CATCTA-GGGGCATTTTGGTCATT
19359 CGCAATCTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
27 8 0.17
28 36 0.78
29 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (27 bp):
CATCTAGGGGCATTTTGGTCATTTTCA
Found at i:20373 original size:16 final size:16
Alignment explanation
Indices: 20352--20393 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
20342 ACAAAGGTAT
20352 TGCAACAAGGCAACAA
1 TGCAACAAGGCAACAA
* *
20368 TGCAACAAAGCAATAA
1 TGCAACAAGGCAACAA
*
20384 TGCAGCAAGG
1 TGCAACAAGG
20394 TAGTGTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (16 bp):
TGCAACAAGGCAACAA
Done.