Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010837.1 Corchorus capsularis cultivar CVL-1 contig10858, 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: 34530
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--46 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT 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 AT
43 AT AT
1 AT AT
47 GGGCATGGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3407 original size:6 final size:6
Alignment explanation
Indices: 3398--3432 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3388 TGGTGCGCCA
3398 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGG
1 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGG
3433 TGTAGATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.69, T:0.17
Consensus pattern (6 bp):
TGGGGC
Found at i:5398 original size:144 final size:144
Alignment explanation
Indices: 5138--5429 Score: 575
Period size: 144 Copynumber: 2.0 Consensus size: 144
5128 GAACATCAAG
5138 AGCAGGATTGACAGATAATGCATGAACATCCTTGTTCTTATTGCGTTCTTCTAGAATGGATGCAA
1 AGCAGGATTGACAGATAATGCATGAACATCCTTGTTCTTATTGCGTTCTTCTAGAATGGATGCAA
5203 CCATTTCAGCCAGGGTCGGATGTATAGATGGAGGAGGAACACTCGTGTCCTTCTTGCTATGGTTT
66 CCATTTCAGCCAGGGTCGGATGTATAGATGGAGGAGGAACACTCGTGTCCTTCTTGCTATGGTTT
5268 TCAGCAAAATTCCT
131 TCAGCAAAATTCCT
5282 AGCAGGATTGACAGATAATGCATGAACATCCTTGTTCTTATTGCGTTCTTCTAGAATGGATGCAA
1 AGCAGGATTGACAGATAATGCATGAACATCCTTGTTCTTATTGCGTTCTTCTAGAATGGATGCAA
*
5347 CCATTTCAGCCAGGGTCGGATGTATAGATGGAGGAGGAACACTCTTGTCCTTCTTGCTATGGTTT
66 CCATTTCAGCCAGGGTCGGATGTATAGATGGAGGAGGAACACTCGTGTCCTTCTTGCTATGGTTT
5412 TCAGCAAAATTCCT
131 TCAGCAAAATTCCT
5426 AGCA
1 AGCA
5430 TTCAAATTCT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 147 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (144 bp):
AGCAGGATTGACAGATAATGCATGAACATCCTTGTTCTTATTGCGTTCTTCTAGAATGGATGCAA
CCATTTCAGCCAGGGTCGGATGTATAGATGGAGGAGGAACACTCGTGTCCTTCTTGCTATGGTTT
TCAGCAAAATTCCT
Found at i:22378 original size:2 final size:2
Alignment explanation
Indices: 22371--22411 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22361 TATGATCAGC
22371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22412 GAGCAATGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29007 original size:7 final size:7
Alignment explanation
Indices: 28995--29019 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28985 TAACCACTTC
28995 CACTTTG
1 CACTTTG
29002 CACTTTG
1 CACTTTG
29009 CACTTTG
1 CACTTTG
29016 CACT
1 CACT
29020 ACTACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.12, T:0.40
Consensus pattern (7 bp):
CACTTTG
Found at i:29725 original size:7 final size:7
Alignment explanation
Indices: 29713--29739 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29703 CCAATCTAAC
29713 GTCTCAA
1 GTCTCAA
29720 GTCTCAA
1 GTCTCAA
29727 GTCTCAA
1 GTCTCAA
29734 GTCTCA
1 GTCTCA
29740 TCGAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (7 bp):
GTCTCAA
Found at i:31993 original size:32 final size:32
Alignment explanation
Indices: 31957--32018 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
31947 GAAAAAGTTG
*
31957 TTTAAGCCATGAGCAAATCCAAAATCTATTTT
1 TTTAAGCCATCAGCAAATCCAAAATCTATTTT
* *
31989 TTTAAGCCTTCAGCAAATCCAAGATCTATT
1 TTTAAGCCATCAGCAAATCCAAAATCTATT
32019 AATTACCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (32 bp):
TTTAAGCCATCAGCAAATCCAAAATCTATTTT
Found at i:34040 original size:334 final size:332
Alignment explanation
Indices: 33424--34519 Score: 1862
Period size: 334 Copynumber: 3.3 Consensus size: 332
33414 TTCTAATAAA
33424 CACAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTTAAGGACTTTTCATGCTTAAAA
1 CACAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTTAAGGACTTTTCATGCTTAAAA
33489 TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTCAGATGCTCG
66 TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTCAGATGCTCG
33554 TAAAAACATATCCTTAAATCCATTGTGGCTGAGATTTGATTGGATAAACATAGATATTTCAAGGA
131 TAAAAACATATCCTTAAATCCATTGTGGCTGAGATTTGATTGGATAAACATAGATATTTCAAGGA
33619 GTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAGAAACC
196 GTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAGAAACC
* *
33684 GTGATGGTTAGTACATGATTTCGGCTAAAATTTTA-ATAAATCTGGCTCGAAAAATTATTTCCTC
261 GT-AT-GTTAGTACACGATTTCGGCTAAAATTTTACA-AAATCTGGCCCGAAAAATTATTTCCTC
33748 CATTTTTGGC
323 CATTTTTGGC
*
33758 CACAATACTCATAAAAAATATATAATTCAACGTCAAAAATATTTAAGGACTTTTCATGCTTAAAA
1 CACAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTTAAGGACTTTTCATGCTTAAAA
*
33823 TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCG
66 TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTCAGATGCTCG
* * **
33888 TAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATAATTATAGATATTTCAAGGA
131 TAAAAACATATCCTTAAATCCATTGTGGCTGAGATTTGATTGGATAAACATAGATATTTCAAGGA
* * * ** * *
33953 GTCTTGGCGCCAAAAATCATGCAAAACAGAGCCAGGGCCCCGGAACGCGTTTTTAGCTAGAAATC
196 GTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAGAAACC
* *
34018 GTTATAGTTAGTACACGATTTCGACTAAAATTTTACAAAATCTGGCCCGAAAAATTATTCCCTCC
261 G-TAT-GTTAGTACACGATTTCGGCTAAAATTTTACAAAATCTGGCCCGAAAAATTATTTCCTCC
*
34083 ATTTTTGGT
324 ATTTTTGGC
* *
34092 CACAATACTCATAAAAAATATATAATT-AACCGCCAAAAATATTTAAGGGCATTTCATGCTTAAA
1 CACAATACTCATAAAAAATATATAATTCAA-CGCCAAAAATATTTAAGGACTTTTCATGCTTAAA
*
34156 ATATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTCAGATTCTC
65 ATATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTCAGATGCTC
*
34221 GTAAAAACATATCCTTAAATCCATTGTGGCTGAGATTTGATTGGATAAACATAGATATTTCATGG
130 GTAAAAACATATCCTTAAATCCATTGTGGCTGAGATTTGATTGGATAAACATAGATATTTCAAGG
*
34286 TGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAGAAAC
195 AGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAGAAAC
* *
34351 CG--TG--AGTACACGATTTCGGCTAAAATTTTACAAAATATGGCCCGAAAAATTATTTCCTTCA
260 CGTATGTTAGTACACGATTTCGGCTAAAATTTTACAAAATCTGGCCCGAAAAATTATTTCCTCCA
34412 TTTTTGGC
325 TTTTTGGC
*
34420 TACAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTTAAGGACTTTTCATGCTTAAAA
1 CACAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTTAAGGACTTTTCATGCTTAAAA
34485 TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCT
66 TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCT
34520 TATATAATCG
Statistics
Matches: 713, Mismatches: 45, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
328 154 0.22
329 2 0.00
330 1 0.00
331 1 0.00
333 2 0.00
334 551 0.77
335 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (332 bp):
CACAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTTAAGGACTTTTCATGCTTAAAA
TATGGTTTTTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAAGATTCAGATGCTCG
TAAAAACATATCCTTAAATCCATTGTGGCTGAGATTTGATTGGATAAACATAGATATTTCAAGGA
GTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTTCGGAACGCGTTTTTAGCCAGAAACC
GTATGTTAGTACACGATTTCGGCTAAAATTTTACAAAATCTGGCCCGAAAAATTATTTCCTCCAT
TTTTGGC
Done.