Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016334.1 Corchorus capsularis cultivar CVL-1 contig16355, 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: 45559
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:15021 original size:21 final size:20
Alignment explanation
Indices: 14995--15036 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
14985 TCTTGAAGGT
*
14995 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
15016 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
15036 T
1 T
15037 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:20961 original size:981 final size:985
Alignment explanation
Indices: 19043--20963 Score: 3404
Period size: 981 Copynumber: 1.9 Consensus size: 985
19033 TGAGTAATGC
*
19043 TGATACGAATCTAGTTGTGTTAGGATCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAAA
1 TGATACGAATCTAGTTGTGTCAGGATCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAAA
19108 CACCAAAACTTCTAGACTTGTAGTAGTCGATAAACCTAACCTAGTCTTCTTCTTCGTTCGTCAGC
66 CACCAAAACTTCTAGACTTGTAGTAGTCGATAAACCTAACCTAGTCTTCTTCTTCGTTCGTCAGC
*
19173 CTTAAACTCTCAATTAGACCTGCAATTGAACACTTAAGATCACAAGATTCACAAACAATTAAGCA
131 CTTAAACTCTCAATTAGACCTGCAATTGAACACTTAAGATCACAAGATTCACAAACAAATAAGCA
19238 ATCACAACCTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCCAAGTTTGCTCAAACTAGA
196 ATCACAACCTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCCAAGTTTGCTCAAACTAGA
*
19303 ACAATGAAGCTAAGATTATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTAA
261 ACAATGAAGCTAAGATAATCAATTTGGG-----AA----CAA---TATTAATC-ACTCAACTTAA
* *
19368 CTTTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCC
313 CTTTTACAAGAGATATTGGTGGCCTAATATAGTGATAGGGTCAACCAAAATCCTAAAATAAACCC
*
19433 TAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCATACCCAACTAGGAAAACGAAATA
378 TAATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAACGAAATA
*
19498 AAAGCATAATTAAATAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAAATAACATCCAAACTT
443 AAAGCATAATTAAACAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAAATAACATCCAAACTT
*
19563 AAAAATAAGCTAATTTAAGATAGAATTAAGCCCAAACAAAGAAAACTAAAGCTAATTGCTCATGC
508 AAAAATAAGCTAATTTAAGATAGAATTAAGCCCAAACAAAGAAAACTAAAGCTAATGGCTCATGC
*
19628 CATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAAAGTGATGAACTTGTAATTGATTTGT
573 CATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAAAGTGATGAACTTGTAATTAATTTGT
*
19693 AATTTCTTGCCCAAATTATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAG
638 AATTTCTTGCCCAAATTATCACCAAACCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAG
*
19758 ATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGTTCTTGTCATCGGAC
703 ATGAGTTCGAAAAAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGTTCTTGTCATCGGAC
*
19823 TAATAAGCATCTTCAATGGATCGAATGGCGTCTTTTTAGTGCTTGGAACATGATTATCGATATCT
768 CAATAAGCATCTTCAATGGATCGAATGGCGTCTTTTTAGTGCTTGGAACATGATTATCGATATCT
* *
19888 CCATGGTCTCAATGCATCTTCATGCTTCCTTGCAGCCCTTGCACATCTTTTCCTTTCTCTCCATA
833 CCATGGTCTCAATGCATCTTCATGCTTCCTTACAGCCCTTGCACATCTTTTCCTTGCTCTCCATA
19953 GCCATCTTCAAGTCCATAATAAGTCCTTGGTACGAATAGAAGGATAGATTTACCGATTGAAGATG
898 GCCATCTTCAAGTCCATAATAAGTCCTTGGTACGAATAGAAGGATAGATTTACCGATTGAAGATG
20018 GCAACCTATGCTCTGATACTAAT
963 GCAACCTATGCTCTGATACTAAT
*
20041 TGATACGAATCTAGTTGTGTCAGGATCAAATCCACCTTTGAGACCCGCTAAAGATCAACTTGAAA
1 TGATACGAATCTAGTTGTGTCAGGATCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAAA
* **
20106 CACCAAAACTTCTAGACTTGTAGTAGTCGATAAACCTAACCTAGTCTTTTTCTTCGTTCGTTGGC
66 CACCAAAACTTCTAGACTTGTAGTAGTCGATAAACCTAACCTAGTCTTCTTCTTCGTTCGTCAGC
*
20171 CTTAAACTCTCAATTAGACCTGCAATTGAACACTTAAGATCACATGATTCACAAACAAATAAGCA
131 CTTAAACTCTCAATTAGACCTGCAATTGAACACTTAAGATCACAAGATTCACAAACAAATAAGCA
* *
20236 ATCACAACCTAATTGTTTGCTAGGACTCTAGAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGA
196 ATCACAACCTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCCAAGTTTGCTCAAACTAGA
*
20301 ACAATGAAGCTAAGATAATCAATTTGGG-A-AA-A-TAATC-CTCAACTTAACTTTTACAAGCGA
261 ACAATGAAGCTAAGATAATCAATTTGGGAACAATATTAATCACTCAACTTAACTTTTACAAGAGA
20361 TATTGGTGGCCTAATATAGTGATAGGGTCAACCAAAATCCTAAAATAAACCCTAATTTTCGTCCA
326 TATTGGTGGCCTAATATAGTGATAGGGTCAACCAAAATCCTAAAATAAACCCTAATTTTCGTCCA
* *
20426 AATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAAGGAAATAAAAGTATAATTAA
391 AATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAACGAAATAAAAGCATAATTAA
20491 ACAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAAATAACATCCAAACTTAAAAATAAGCTAA
456 ACAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAAATAACATCCAAACTTAAAAATAAGCTAA
*
20556 TTTAAGATAGAATTAAGCCCAAACAAAGCAAACTAAAGCTAATGGGCTCATGCCATGATGTCAAT
521 TTTAAGATAGAATTAAGCCCAAACAAAGAAAACTAAAGCTAAT-GGCTCATGCCATGATGTCAAT
* *
20621 CCGGCTATCTAGAATCAATAGCAAGCAAATTGATGAACTTGTAATTAATTTGTAATTTCTTGCCC
585 CCGGCCATCTAGAATCAATAGCAAGCAAAGTGATGAACTTGTAATTAATTTGTAATTTCTTGCCC
20686 AAATTATCACCAAACCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAAA
650 AAATTATCACCAAACCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAAA
20751 AAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGTTCTTGTCATCGGACCAATAAGCATCT
715 AAGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGTTCTTGTCATCGGACCAATAAGCATCT
* *
20816 TCAATGGATCGAATGGCGTCTTTTTAGTGCTTGGAACATGGTTATCGATATCTCCATGGTCTCCA
780 TCAATGGATCGAATGGCGTCTTTTTAGTGCTTGGAACATGATTATCGATATCTCCATGGTCTCAA
20881 TGCATCTTCATGCTTCCTTACAGCCCTTGCACATCCTTTT-CTTGCTCTCCATAGCCATCTTCAA
845 TGCATCTTCATGCTTCCTTACAGCCCTTGCACAT-CTTTTCCTTGCTCTCCATAGCCATCTTCAA
20945 GTCCATAATAAGTCCTTGG
909 GTCCATAATAAGTCCTTGG
20964 CGCATCATTC
Statistics
Matches: 892, Mismatches: 29, Indels: 21
0.95 0.03 0.02
Matches are distributed among these distances:
980 253 0.28
981 347 0.39
982 10 0.01
983 1 0.00
987 2 0.00
992 1 0.00
998 278 0.31
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (985 bp):
TGATACGAATCTAGTTGTGTCAGGATCAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAAA
CACCAAAACTTCTAGACTTGTAGTAGTCGATAAACCTAACCTAGTCTTCTTCTTCGTTCGTCAGC
CTTAAACTCTCAATTAGACCTGCAATTGAACACTTAAGATCACAAGATTCACAAACAAATAAGCA
ATCACAACCTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCCAAGTTTGCTCAAACTAGA
ACAATGAAGCTAAGATAATCAATTTGGGAACAATATTAATCACTCAACTTAACTTTTACAAGAGA
TATTGGTGGCCTAATATAGTGATAGGGTCAACCAAAATCCTAAAATAAACCCTAATTTTCGTCCA
AATATAAGGGCTAGGGAAAAACTAGTCCAAACCCAACTAGGAAAACGAAATAAAAGCATAATTAA
ACAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAAATAACATCCAAACTTAAAAATAAGCTAA
TTTAAGATAGAATTAAGCCCAAACAAAGAAAACTAAAGCTAATGGCTCATGCCATGATGTCAATC
CGGCCATCTAGAATCAATAGCAAGCAAAGTGATGAACTTGTAATTAATTTGTAATTTCTTGCCCA
AATTATCACCAAACCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCGAAAA
AGGCCCATGAGTGCATCCTTGAATCTCTTAGCTCTTGTTCTTGTCATCGGACCAATAAGCATCTT
CAATGGATCGAATGGCGTCTTTTTAGTGCTTGGAACATGATTATCGATATCTCCATGGTCTCAAT
GCATCTTCATGCTTCCTTACAGCCCTTGCACATCTTTTCCTTGCTCTCCATAGCCATCTTCAAGT
CCATAATAAGTCCTTGGTACGAATAGAAGGATAGATTTACCGATTGAAGATGGCAACCTATGCTC
TGATACTAAT
Found at i:23398 original size:21 final size:20
Alignment explanation
Indices: 23372--23413 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
23362 TCTTGAAGGT
*
23372 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
23393 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
23413 T
1 T
23414 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:23858 original size:21 final size:20
Alignment explanation
Indices: 23832--23873 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
23822 TCTTGAAGGT
*
23832 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
23853 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
23873 T
1 T
23874 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:24207 original size:460 final size:460
Alignment explanation
Indices: 23347--24269 Score: 1819
Period size: 460 Copynumber: 2.0 Consensus size: 460
23337 CTTTAACAAG
23347 TCTTGTTCGAAATCATCTTGAAGGTTTGAAGTCCATTGAAGATCAATTGAAGAGCATTGAAGACA
1 TCTTGTTCGAAATCATCTTGAAGGTTTGAAGTCCATTGAAGATCAATTGAAGAGCATTGAAGACA
23412 ATAAGCAAAGGAATATTCCCATCGATTCCAAGTTATGCACCATACTTGAAACCGATGAACCATAA
66 ATAAGCAAAGGAATATTCCCATCGATTCCAAGTTATGCACCATACTTGAAACCGATGAACCATAA
*
23477 TGCTTCCATTGTGTAATTCGGCCATATGGGCCTTAATTCTATCTTAGATTAGTTTATTATGTAGT
131 TGCTTCCATTGTGTAATTCAGCCATATGGGCCTTAATTCTATCTTAGATTAGTTTATTATGTAGT
23542 TTGGACCTTGTTTAAGGTTGGGCCTTGTCTAATTAAGTCCAATCCTTAACTATTTTTCCTATTGG
196 TTGGACCTTGTTTAAGGTTGGGCCTTGTCTAATTAAGTCCAATCCTTAACTATTTTTCCTATTGG
23607 TTGTATTTTAGGATAGTTTCTAGAAGTATTTATGTGTAAATCGCCCTAGACCCTTGCATTGAATG
261 TTGTATTTTAGGATAGTTTCTAGAAGTATTTATGTGTAAATCGCCCTAGACCCTTGCATTGAATG
23672 CCAAGGTCGGTTTAAGGGGGTTATTGCGTTATCTTGGTGCCTATATAAGGCCACCTATAGCTCTT
326 CCAAGGTCGGTTTAAGGGGGTTATTGCGTTATCTTGGTGCCTATATAAGGCCACCTATAGCTCTT
23737 GTAAACACAAGTTAAGTTGATTAAATAAAGTTGAGGTTATTCACCCAATTGATTATCTTAGCTTC
391 GTAAACACAAGTTAAGTTGATTAAATAAAGTTGAGGTTATTCACCCAATTGATTATCTTAGCTTC
23802 ATTAT
456 ATTAT
23807 TCTTGTTCGAAATCATCTTGAAGGTTTGAAGTCCATTGAAGATCAATTGAAGAGCATTGAAGACA
1 TCTTGTTCGAAATCATCTTGAAGGTTTGAAGTCCATTGAAGATCAATTGAAGAGCATTGAAGACA
23872 ATAAGCAAAGGAATATTCCCATCGATTCCAAGTTATGCACCATACTTGAAACCGATGAACCATAA
66 ATAAGCAAAGGAATATTCCCATCGATTCCAAGTTATGCACCATACTTGAAACCGATGAACCATAA
23937 TGCTTCCATTGTGTAATTCAGCCATATGGGCCTTAATTCTATCTTAGATTAGTTTATTATGTAGT
131 TGCTTCCATTGTGTAATTCAGCCATATGGGCCTTAATTCTATCTTAGATTAGTTTATTATGTAGT
*
24002 TTGGACCTTGTTTAAGGTTGGGCCTTGTCTAATTAAGTCCAATCCTTAGCTATTTTTCCTATTGG
196 TTGGACCTTGTTTAAGGTTGGGCCTTGTCTAATTAAGTCCAATCCTTAACTATTTTTCCTATTGG
24067 TTGTATTTTAGGATAGTTTCTAGAAGTATTTATGTGTAAATCGCCCTAGACCCTTGCATTGAATG
261 TTGTATTTTAGGATAGTTTCTAGAAGTATTTATGTGTAAATCGCCCTAGACCCTTGCATTGAATG
*
24132 CTAAGGTCGGTTTAAGGGGGTTATTGCGTTATCTTGGTGCCTATATAAGGCCACCTATAGCTCTT
326 CCAAGGTCGGTTTAAGGGGGTTATTGCGTTATCTTGGTGCCTATATAAGGCCACCTATAGCTCTT
24197 GTAAACACAAGTTAAGTTGATTAAATAAAGTTGAGGTTATTCACCCAATTGATTATCTTAGCTTC
391 GTAAACACAAGTTAAGTTGATTAAATAAAGTTGAGGTTATTCACCCAATTGATTATCTTAGCTTC
24262 ATTAT
456 ATTAT
24267 TCT
1 TCT
24270 AGTTTGAGCA
Statistics
Matches: 460, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
460 460 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (460 bp):
TCTTGTTCGAAATCATCTTGAAGGTTTGAAGTCCATTGAAGATCAATTGAAGAGCATTGAAGACA
ATAAGCAAAGGAATATTCCCATCGATTCCAAGTTATGCACCATACTTGAAACCGATGAACCATAA
TGCTTCCATTGTGTAATTCAGCCATATGGGCCTTAATTCTATCTTAGATTAGTTTATTATGTAGT
TTGGACCTTGTTTAAGGTTGGGCCTTGTCTAATTAAGTCCAATCCTTAACTATTTTTCCTATTGG
TTGTATTTTAGGATAGTTTCTAGAAGTATTTATGTGTAAATCGCCCTAGACCCTTGCATTGAATG
CCAAGGTCGGTTTAAGGGGGTTATTGCGTTATCTTGGTGCCTATATAAGGCCACCTATAGCTCTT
GTAAACACAAGTTAAGTTGATTAAATAAAGTTGAGGTTATTCACCCAATTGATTATCTTAGCTTC
ATTAT
Found at i:34789 original size:21 final size:21
Alignment explanation
Indices: 34763--34808 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
34753 TCACTTCCCT
34763 TGATCTCCCTCTCCGAAGGGC
1 TGATCTCCCTCTCCGAAGGGC
** *
34784 TGATCTGTCTGTCCGAAGGGC
1 TGATCTCCCTCTCCGAAGGGC
34805 TGAT
1 TGAT
34809 TTTAAAAGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
TGATCTCCCTCTCCGAAGGGC
Found at i:38519 original size:99 final size:99
Alignment explanation
Indices: 38348--38547 Score: 400
Period size: 99 Copynumber: 2.0 Consensus size: 99
38338 TACTAGCATG
38348 CATTCCTCACAAATATGACATTTACCCCACTCATTCATATCTATGCAAGCACACCACCCGCGCCA
1 CATTCCTCACAAATATGACATTTACCCCACTCATTCATATCTATGCAAGCACACCACCCGCGCCA
38413 ATTGGCGCGGGCATGAATCTAGTACTAATCAAAA
66 ATTGGCGCGGGCATGAATCTAGTACTAATCAAAA
38447 CATTCCTCACAAATATGACATTTACCCCACTCATTCATATCTATGCAAGCACACCACCCGCGCCA
1 CATTCCTCACAAATATGACATTTACCCCACTCATTCATATCTATGCAAGCACACCACCCGCGCCA
38512 ATTGGCGCGGGCATGAATCTAGTACTAATCAAAA
66 ATTGGCGCGGGCATGAATCTAGTACTAATCAAAA
38546 CA
1 CA
38548 GCCCCCAAAT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.23
Consensus pattern (99 bp):
CATTCCTCACAAATATGACATTTACCCCACTCATTCATATCTATGCAAGCACACCACCCGCGCCA
ATTGGCGCGGGCATGAATCTAGTACTAATCAAAA
Found at i:42012 original size:12 final size:12
Alignment explanation
Indices: 41995--42019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41985 TTAGGAAAAA
41995 CATAATTTTTCT
1 CATAATTTTTCT
42007 CATAATTTTTCT
1 CATAATTTTTCT
42019 C
1 C
42020 TCTTGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (12 bp):
CATAATTTTTCT
Done.