Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011306.1 Corchorus capsularis cultivar CVL-1 contig11327, 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: 47563
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7150 original size:17 final size:17
Alignment explanation
Indices: 7128--7160 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7118 GTGAGTATAA
*
7128 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
7145 AATTTCATCCATATTA
1 AATTTCATCCATATTA
7161 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:8274 original size:13 final size:13
Alignment explanation
Indices: 8256--8280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8246 TTTAATGTTC
8256 TAAATATTATTTA
1 TAAATATTATTTA
8269 TAAATATTATTT
1 TAAATATTATTT
8281 GGAATTCCAA
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:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:12709 original size:2 final size:2
Alignment explanation
Indices: 12704--12743 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
12694 AAATACACAC
* *
12704 AT AT AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12744 GGGGCTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12769 original size:2 final size:2
Alignment explanation
Indices: 12762--12786 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12752 ACCCTATCAA
12762 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12787 CACACACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19559 original size:27 final size:28
Alignment explanation
Indices: 19525--19578 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
19515 TTTATAAATA
19525 TAATTTATATAATACA-A-TATATATTG
1 TAATTTATATAATACATAGTATATATTG
*
19551 TAATGTTATATATTACATAGTATATATT
1 TAAT-TTATATAATACATAGTATATATT
19579 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 11 0.46
28 1 0.04
29 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (28 bp):
TAATTTATATAATACATAGTATATATTG
Found at i:22372 original size:18 final size:18
Alignment explanation
Indices: 22351--22392 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22341 GGATTCATAG
*
22351 GATGATGTTGACCCAGAA
1 GATGATATTGACCCAGAA
* *
22369 GATGATATTGATCCAGAT
1 GATGATATTGACCCAGAA
22387 GATGAT
1 GATGAT
22393 CCCGACGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (18 bp):
GATGATATTGACCCAGAA
Found at i:32888 original size:10 final size:10
Alignment explanation
Indices: 32873--32898 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
32863 AGTTGCTGCC
32873 AAATTCCAGA
1 AAATTCCAGA
32883 AAATTCCAGA
1 AAATTCCAGA
32893 AAATTC
1 AAATTC
32899 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:37072 original size:111 final size:111
Alignment explanation
Indices: 36939--37142 Score: 336
Period size: 111 Copynumber: 1.8 Consensus size: 111
36929 ACACATCAAC
* *
36939 AACACTGTTAATAGCCAAAATAGATGAACTACTGCGGATCCCATGGCAAGATTCGCCGAACATTT
1 AACACTGTTAATAGCCAAAATAGATAAACTACTGCGGATCCCATGGCAAGATCCGCCGAACATTT
*
37004 GAAATCCATCCCTAGGAAGATGTAGCTCACCAAGCAACACACGAGA
66 GAAATCCATCCCCAGGAAGATGTAGCTCACCAAGCAACACACGAGA
* * * *
37050 AACACTGTTAATAGCCAAAATAGATAAACTACTGCGGATCCCATGGCAGGATCCGTCGGACGTTT
1 AACACTGTTAATAGCCAAAATAGATAAACTACTGCGGATCCCATGGCAAGATCCGCCGAACATTT
*
37115 GAAATTCATCCCCAGGAAGATGTAGCTC
66 GAAATCCATCCCCAGGAAGATGTAGCTC
37143 CCACTCTTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 85 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (111 bp):
AACACTGTTAATAGCCAAAATAGATAAACTACTGCGGATCCCATGGCAAGATCCGCCGAACATTT
GAAATCCATCCCCAGGAAGATGTAGCTCACCAAGCAACACACGAGA
Found at i:38347 original size:488 final size:491
Alignment explanation
Indices: 37422--38509 Score: 1569
Period size: 488 Copynumber: 2.2 Consensus size: 491
37412 GGCTTTAATT
* * *
37422 CCACCTTAAACAGGTTGTCTCCAAAGATACACATCAGTCATCCGGCACAGAAAACAATGATGCCA
1 CCACCTTGAACAGGTTGTCTCC-AAGATACACATCAGCCATCCGGCACAGAAAACGATGATGCCA
* * *
37487 CTGATATTTACAGCCGCCAATCCGCATAGCCATTCTAACAAAATGTAAGTTTTCTCCCGTATCAG
65 CTGATATTCACAGCCGCCAATCCGCATAGCCATTCT---AAAA-GTAAGCTTTCTCCCATATCA-
* * * * *
37552 CCCAATATAGTAAAACATAGCAACCACCAAGGAAAACAGGAGCAACACATTTAATAGCCAAAAGA
125 CACAATATAGTAAAACACAACAACCACAAAGGAAAACAGGAGCAACACAGTTAATAGCCAAAAGA
* * **
37617 GATTAACTACTGCGGATCCCTTGACAGGATTTGCCGGACGAATGAAATTCATCCCCAGGAAGATA
190 GATGAACTACTGCGGATCCCTGGACAGGATCCGCCGGACGAATGAAATTCATCCCCAGGAAGATA
* * * * * * * * *
37682 TAGCTCTCATTCTTAGTCACTGTGAGCGCCTTTATTATGCCTAGTTGGATAATCGGAGACAATTT
255 TAGCTCCCACTCTTAATCACTGCGACCGCATTTAGTATGCCTAATTGGATAATCGGAGACAATGT
* * *
37747 ATAGCTCTTTGATATATCCTTCAAGTTTTTACTCCAATCATCGTCGGTAGAATATTTTTATAACA
320 ATAGCTCTCTGATATATCCTTCAACTTTTTACTCCAATCAACGTCGGTAGAATATTTTTATAACA
* * * *
37812 ATGATAAATCTAAAAAGAAAAGTATATATAGTATCGTTGTCAAATCAAGAAATGTATCAGAGCCA
385 ATGATAAATCTAAAAAGAAAAATATATATAGTATAGTTGTAAAATCAAGAAACGTATCAGAGCCA
* *
37877 TTTTTATCTTTATT-TCCAATTCATTGAAAATGA-AAGTGTCTC
450 ATTTTATCTTTATTAT-CAATTCATTGAAAAGGAGAA-TGTCTC
*
37919 CCACCTTGAACAGGTTGTCTCCAATGATACACATCAGCCATCCCGCACAGAAAACGATGATGCCA
1 CCACCTTGAACAGGTTGTCTCCAA-GATACACATCAGCCATCCGGCACAGAAAACGATGATGCCA
* *
37984 CTGATATTCACAGCCGCCACTCCGCATAGCCATT-T-TAA-T-AGCTTTCTCCCATATCA-ACAA
65 CTGATATTCACAGCCGCCAATCCGCATAGCCATTCTAAAAGTAAGCTTTCTCCCATATCACACAA
* *
38044 GTATAGTAAAACACAACAACCACAAAGTAAAACAGGAGCAACACAGTTAATAGCCAAAATAGATG
130 -TATAGTAAAACACAACAACCACAAAGGAAAACAGGAGCAACACAGTTAATAGCCAAAAGAGATG
* * * *
38109 AACTACTGCGGATCCCTGGGCAGGATCCGCCGGACGTATGAAATTCATCCGCAGGAAGATGTAGC
194 AACTACTGCGGATCCCTGGACAGGATCCGCCGGACGAATGAAATTCATCCCCAGGAAGATATAGC
38174 TCCCACTCTTAATCACTGCGACCGCATTTAGTATGCCTAATTGGATAATCGGAGACAATGTATAG
259 TCCCACTCTTAATCACTGCGACCGCATTTAGTATGCCTAATTGGATAATCGGAGACAATGTATAG
*
38239 CTCTCTGATATATCCTTCAACTTTTTACTCCAATCAACGTCGGTAGAATATTTTTATGACAATGA
324 CTCTCTGATATATCCTTCAACTTTTTACTCCAATCAACGTCGGTAGAATATTTTTATAACAATGA
38304 TAAATCTAAAAAGAAAAATATATATAGTATAGTTGTAAAATCAAGAAACGTATCAGAGCCAATTT
389 TAAATCTAAAAAGAAAAATATATATAGTATAGTTGTAAAATCAAGAAACGTATCAGAGCCAATTT
* *
38369 TATCTTTATTATTAATTCATTGAAAAGGAGCATGTCTC
454 TATCTTTATTATCAATTCATTGAAAAGGAGAATGTCTC
* * * * *
38407 CAACCTTGAACAGGTTGTCTCCGAAGATATACATCAGCCATTCGGCGCAGAAAACGATGATACCA
1 CCACCTTGAACAGGTTGTCTCC-AAGATACACATCAGCCATCCGGCACAGAAAACGATGATGCCA
*
38472 CTGATATTCACAGCCACCAATCCGCATAGCCATTCTAA
65 CTGATATTCACAGCCGCCAATCCGCATAGCCATTCTAA
38510 CAATAAAACA
Statistics
Matches: 530, Mismatches: 54, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
487 3 0.01
488 411 0.78
489 20 0.04
490 1 0.00
492 2 0.00
496 3 0.01
497 90 0.17
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (491 bp):
CCACCTTGAACAGGTTGTCTCCAAGATACACATCAGCCATCCGGCACAGAAAACGATGATGCCAC
TGATATTCACAGCCGCCAATCCGCATAGCCATTCTAAAAGTAAGCTTTCTCCCATATCACACAAT
ATAGTAAAACACAACAACCACAAAGGAAAACAGGAGCAACACAGTTAATAGCCAAAAGAGATGAA
CTACTGCGGATCCCTGGACAGGATCCGCCGGACGAATGAAATTCATCCCCAGGAAGATATAGCTC
CCACTCTTAATCACTGCGACCGCATTTAGTATGCCTAATTGGATAATCGGAGACAATGTATAGCT
CTCTGATATATCCTTCAACTTTTTACTCCAATCAACGTCGGTAGAATATTTTTATAACAATGATA
AATCTAAAAAGAAAAATATATATAGTATAGTTGTAAAATCAAGAAACGTATCAGAGCCAATTTTA
TCTTTATTATCAATTCATTGAAAAGGAGAATGTCTC
Found at i:38549 original size:28 final size:28
Alignment explanation
Indices: 38515--38572 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
38505 TCTAACAATA
*
38515 AAACAGAAAACAGGGGATTGTGAATATC
1 AAACAGAAAACAGGGGATTGCGAATATC
38543 AAACAGAAAACAGGGGATTGCGAATATC
1 AAACAGAAAACAGGGGATTGCGAATATC
38571 AA
1 AA
38573 TTTATAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.16
Consensus pattern (28 bp):
AAACAGAAAACAGGGGATTGCGAATATC
Found at i:45383 original size:36 final size:34
Alignment explanation
Indices: 45306--45376 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 34
45296 CGTAAAATAT
*
45306 TTTTTTTTTTAGAAAAATCGGAAAAACGGAAAAAAC
1 TTTTTTTTTTAGAAAAAACGGAAAAAC-G-AAAAAC
45342 TTTTTTTTTTAGAAAAAACGGAAAAAAC-AAAAAC
1 TTTTTTTTTTAGAAAAAACGG-AAAAACGAAAAAC
45376 T
1 T
45377 AATTTTTGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 7 0.21
36 20 0.61
37 6 0.18
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.31
Consensus pattern (34 bp):
TTTTTTTTTTAGAAAAAACGGAAAAACGAAAAAC
Found at i:47225 original size:22 final size:21
Alignment explanation
Indices: 47198--47246 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
47188 AAATACTAGC
47198 AAAATAGGGTAAAACA-TATATA
1 AAAATA-GGTAAAA-AGTATATA
47220 AAAATA-GTAAAAAGTATATA
1 AAAATAGGTAAAAAGTATATA
47240 AAAATAG
1 AAAATAG
47247 CTATAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 18 0.72
22 6 0.24
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAATAGGTAAAAAGTATATA
Found at i:47251 original size:12 final size:11
Alignment explanation
Indices: 47207--47255 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
47197 CAAAATAGGG
47207 TAAAACATA-TA
1 TAAAA-ATAGTA
47218 TAAAAATAGTA
1 TAAAAATAGTA
*
47229 -AAAAGTA-TA
1 TAAAAATAGTA
47238 TAAAAATAGCTA
1 TAAAAATAG-TA
47250 TAAAAA
1 TAAAAA
47256 CATGCATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 2 0.06
10 15 0.47
11 7 0.22
12 8 0.25
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (11 bp):
TAAAAATAGTA
Done.