Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016023.1 Corchorus capsularis cultivar CVL-1 contig16044, 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: 6491
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:853 original size:35 final size:35
Alignment explanation
Indices: 814--1226 Score: 692
Period size: 35 Copynumber: 11.8 Consensus size: 35
804 CGGTCATTTT
*
814 AAGAAGCTTTCAGAGGTCAGAGTTGATCTCATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
*
849 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCGTATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
*
884 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
919 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-TCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATAT-C
954 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-TC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
988 AAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1 -AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1024 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1059 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-TCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATAT-C
1094 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-TCC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATAT-C
1129 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
*
1164 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
* *
1199 AAGAAGTTTCCA-ACGATCAGAGTTGATC
1 AAGAAGTTTTCAGA-GGTCAGAGTTGATC
1227 GCATTTTCAA
Statistics
Matches: 365, Mismatches: 7, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
34 4 0.01
35 358 0.98
36 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (35 bp):
AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATC
Found at i:1232 original size:35 final size:35
Alignment explanation
Indices: 807--1539 Score: 631
Period size: 35 Copynumber: 21.0 Consensus size: 35
797 TCCAGAGCGG
* *
807 TCATTTTAAGAAGCTTT-CAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAG-TTTCCAGAGATCAGAGTTGATC
* * *
842 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * * *
877 TCGTATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* *
912 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
947 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* *
982 TCA-TTCAAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTC-AAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1017 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1052 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1087 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1122 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1157 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
1192 TCATTTCAAGAAGTTTCCA-ACGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * *
1227 GCATTTTCAA-TATTTTCCA-ACGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * * *
1262 GCATTTTC-AGTATTTTCCA-TGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1296 GCATTTTC-AGTAGTTTCCA-ATGATCGGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * * *
1331 GCATTTTC-AGTATTTTCCA-TGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* * *
1365 GCATTTTC-AGTAGTTTCCA-ATGATCGGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * *
1400 CCATTTTC-AGTATTTTCCA-ACGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* *
1435 GCATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * * * * *
1470 ACATTTTAAGTAGTTTCCA-ACAATTAGAGGTGATC
1 TCATTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* *
1505 TCATTTCAAGAAATTTCC-GATGATCAAAGTTGATC
1 TCATTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
1540 CAGAGGAGTT
Statistics
Matches: 640, Mismatches: 48, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
34 73 0.11
35 559 0.87
36 8 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
Found at i:1512 original size:104 final size:106
Alignment explanation
Indices: 1180--1539 Score: 480
Period size: 104 Copynumber: 3.5 Consensus size: 106
1170 TTTTCAGAGG
*
1180 TCAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAATATTTTC
1 TCAGAGTTGATCTCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
*
1244 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC-ATGA
66 CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
* * * *
1284 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAATGATCGGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCTCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
*
1348 C-ATGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
66 CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
* * * * *
1388 TCGGAGTTGATCCCATTTTC-AGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC
1 TCAGAGTTGATCTCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
* * **
1452 CAACGATCAGAGTTGATCACATTTTAAGTAGTTTCCAACAA
66 CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
* * * * * *
1493 TTAGAGGTGATCTCA-TTTCAAGAAATTTCCGATGATCAAAGTTGATC
1 TCAGAGTTGATCTCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATC
1540 CAGAGGAGTT
Statistics
Matches: 225, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
103 32 0.14
104 122 0.54
105 71 0.32
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (106 bp):
TCAGAGTTGATCTCATTTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
CAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
Found at i:1522 original size:70 final size:70
Alignment explanation
Indices: 1180--1539 Score: 467
Period size: 69 Copynumber: 5.2 Consensus size: 70
1170 TTTTCAGAGG
* * * * *
1180 TCAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAATATTTTC
1 TCAGAGTTGATCGCATTTTC-AGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC
*
1244 CAACGA
65 CAATGA
*
1250 TCAGAGTTGATCGCATTTTCAGTATTTTCC-ATGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1314 AATGA
66 AATGA
* *
1319 TCGGAGTTGATCGCATTTTCAGTATTTTCC-ATGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1383 AATGA
66 AATGA
* *
1388 TCGGAGTTGATCCCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
*
1453 AACGA
66 AATGA
* * * * * * * * *
1458 TCAGAGTTGATCACATTTTAAGTAGTTTCCAACAATTAGAGGTGATCTCA-TTTCAAGAAATTTC
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTC-AGTAGTTTC
*
1522 CGATGA
65 CAATGA
*
1528 TCAAAGTTGATC
1 TCAGAGTTGATC
1540 CAGAGGAGTT
Statistics
Matches: 263, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
69 136 0.52
70 123 0.47
71 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (70 bp):
TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
AATGA
Found at i:2896 original size:75 final size:75
Alignment explanation
Indices: 2787--2977 Score: 260
Period size: 75 Copynumber: 2.5 Consensus size: 75
2777 ATAATAATGG
*
2787 GAATATTTTCTAAATCTTGCCAAATTGTGAGAGATTTTGGAGATATTTTAAGAAATAAA-ATAAT
1 GAATATTTTCTAAATCTTGCCAAATTGTG-GAGATTTAGGAGATATTTTAAGAAATAAATA-AAT
* *
2851 AATAAAG-TTGA
64 AATAAAGAATAA
* *
2862 GAATATTTTCTAAATCTTGCCAAATTGTAGGAGATTTAGGAGATATTTTACGAAATAAATAAATT
1 GAATATTTTCTAAATCTTGCCAAATTGT-GGAGATTTAGGAGATATTTTAAGAAATAAATAAATA
2927 ATAAAGAATAA
65 ATAAAGAATAA
* *
2938 GAATATTTCTCTAAATCTTGTCAGATTGTGGGAGATTTAG
1 GAATATTT-TCTAAATCTTGCCAAATTGT-GGAGATTTAG
2978 AAAATATCAA
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
75 64 0.62
76 12 0.12
77 28 0.27
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (75 bp):
GAATATTTTCTAAATCTTGCCAAATTGTGGAGATTTAGGAGATATTTTAAGAAATAAATAAATAA
TAAAGAATAA
Found at i:5377 original size:27 final size:28
Alignment explanation
Indices: 5321--5379 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
5311 TACCCGATGC
* *
5321 TCCAGCAGAGGCCGATGAACAGTGATCT
1 TCCAGCAGAGGCCGATGAACAGTAAACT
* *
5349 TCCAGCAGAGGTCG-TGAATAGTAAACT
1 TCCAGCAGAGGCCGATGAACAGTAAACT
5376 TCCA
1 TCCA
5380 TATTAGTGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (28 bp):
TCCAGCAGAGGCCGATGAACAGTAAACT
Found at i:5433 original size:148 final size:148
Alignment explanation
Indices: 5164--5540 Score: 540
Period size: 148 Copynumber: 2.5 Consensus size: 148
5154 CCTCAACGGG
* * * *
5164 ACCCGATGCTCCAGCA-ACGGCCTATGAACAGTAATCTTCCAGCATAGGTCACGAATAGTAAAGT
1 ACCCGATGCTCCAGCAGA-GGCCGATGAACAGTGATCTTCCAGCATAGGTCATGAATAGTAAACT
* * * * *
5228 TCCCTATTAGTGAGCCCCACGGACAATATGCCTCTTGTGTTGCCACGTCAGCCTGCTGTGGGCCC
65 TCCATATTAGTGGGCCCCACGGACAATATGCCTCCTGTGCTGCCACGTCAGCATGCTGTGGGCCC
5293 CAACAGTACCCGATGGTTT
130 CAACAGTACCCGATGGTTT
* *
5312 ACCCGATGCTCCAGCAGAGGCCGATGAACAGTGATCTTCCAGCAGAGGTCGTGAATAGTAAACTT
1 ACCCGATGCTCCAGCAGAGGCCGATGAACAGTGATCTTCCAGCATAGGTCATGAATAGTAAACTT
* *
5377 CCATATTAGTGGGCCCCACGGGCAATATGCCTCCTGTGCTGCCACGTCAGCATGCTGTGGGCCTC
66 CCATATTAGTGGGCCCCACGGACAATATGCCTCCTGTGCTGCCACGTCAGCATGCTGTGGGCCCC
*
5442 AACAGTACCTGATGGTTT
131 AACAGTACCCGATGGTTT
* * ** * * * *
5460 GCCCGATGCTCTAGCAGAGGTTGATGAACAGTGATCTTCCAACATAGGCCATGAACAATAAACTT
1 ACCCGATGCTCCAGCAGAGGCCGATGAACAGTGATCTTCCAGCATAGGTCATGAATAGTAAACTT
5525 CCATATTAGTGGGCCC
66 CCATATTAGTGGGCCC
5541 AATGAATAGT
Statistics
Matches: 204, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 203 1.00
149 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (148 bp):
ACCCGATGCTCCAGCAGAGGCCGATGAACAGTGATCTTCCAGCATAGGTCATGAATAGTAAACTT
CCATATTAGTGGGCCCCACGGACAATATGCCTCCTGTGCTGCCACGTCAGCATGCTGTGGGCCCC
AACAGTACCCGATGGTTT
Done.