Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010636.1 Corchorus capsularis cultivar CVL-1 contig10657, 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: 31655
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1217 original size:26 final size:26
Alignment explanation
Indices: 1188--1241 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1178 AAGGCCAACG
* *
1188 AATCAAAACTCCTTGAACTCGATCTA
1 AATCAAAACTACTTGAACTCAATCTA
* *
1214 AATCATAATTACTTGAACTCAATCTA
1 AATCAAAACTACTTGAACTCAATCTA
1240 AA
1 AA
1242 CCGAAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (26 bp):
AATCAAAACTACTTGAACTCAATCTA
Found at i:1255 original size:26 final size:26
Alignment explanation
Indices: 1199--1256 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1189 ATCAAAACTC
* * *
1199 CTTGAACTCGATCTAAATCATAATTA
1 CTTGAACTCAATCTAAACCATAATAA
1225 CTTGAACTCAATCTAAACCGA-AATAA
1 CTTGAACTCAATCTAAACC-ATAATAA
*
1251 TTTGAA
1 CTTGAA
1257 TAATTGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (26 bp):
CTTGAACTCAATCTAAACCATAATAA
Found at i:1272 original size:242 final size:244
Alignment explanation
Indices: 845--1329 Score: 839
Period size: 242 Copynumber: 2.0 Consensus size: 244
835 TTTACTTAAA
* * *
845 AGATTATGTTGTCCGTGAACGAGGTGACAAAATAAAACCGAGTTCAAAATCTCGTCAAATTCGAA
1 AGATTATGTTATCAGTGAACGAGGTGACAAAATAAAACCGAGTTCAAAATCTCGTCAAATCCGAA
* *
910 TTTAATTGAACTCGATTTAACTAAAAAAGGCCAACGAATCAAAGCTCCTTGAACTCGATCTAAAC
66 TTTAATTAAACTCGATTTAACTAAAAAAGGCCAACGAATCAAAACTCCTTGAACTCGATCTAAAC
*
975 CATAATTACTTGAACTCAATCTACACCGAAATAATTTAAATAATTATTACTATTCTCAATGTGAC
131 CATAATTACTTGAACTCAATCTAAACCGAAATAATTTAAATAATTATTACTATTCTCAATGTGAC
*
1040 TTCTTAAAAATGAAAATTAACA-TTTTTCTAGTTTGGAAAAAGGCCAAT
196 TTCTTAAAAATGAAAAATAACATTTTTTCTAGTTTGGAAAAAGGCCAAT
**
1088 AGATTATGTTATCAGTGAGTGAGGTGACAAAATAAAACCGAGTTCAAAATCTCGTCAAATCCGAA
1 AGATTATGTTATCAGTGAACGAGGTGACAAAATAAAACCGAGTTCAAAATCTCGTCAAATCCGAA
*
1153 TTTAATTAAACTCGATTTAACT-AAAAAGGCCAACGAATCAAAACTCCTTGAACTCGATCTAAAT
66 TTTAATTAAACTCGATTTAACTAAAAAAGGCCAACGAATCAAAACTCCTTGAACTCGATCTAAAC
* * *
1217 CATAATTACTTGAACTCAATCTAAACCGAAATAATTTGAATAATTGTTGCTATTCTCAATGTGAC
131 CATAATTACTTGAACTCAATCTAAACCGAAATAATTTAAATAATTATTACTATTCTCAATGTGAC
1282 TTCTTAAAAATGAAAAATAACATTTTTTCTAGTTTGGAAAAAGGCCAA
196 TTCTTAAAAATGAAAAATAACATTTTTTCTAGTTTGGAAAAAGGCCAA
1330 ACCTAAATCT
Statistics
Matches: 228, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
242 122 0.54
243 106 0.46
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (244 bp):
AGATTATGTTATCAGTGAACGAGGTGACAAAATAAAACCGAGTTCAAAATCTCGTCAAATCCGAA
TTTAATTAAACTCGATTTAACTAAAAAAGGCCAACGAATCAAAACTCCTTGAACTCGATCTAAAC
CATAATTACTTGAACTCAATCTAAACCGAAATAATTTAAATAATTATTACTATTCTCAATGTGAC
TTCTTAAAAATGAAAAATAACATTTTTTCTAGTTTGGAAAAAGGCCAAT
Found at i:2630 original size:12 final size:14
Alignment explanation
Indices: 2599--2625 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2589 AGATTAAAGA
2599 TAATATATGCGGTG
1 TAATATATGCGGTG
2613 TAATATATGCGGT
1 TAATATATGCGGT
2626 AATATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (14 bp):
TAATATATGCGGTG
Found at i:14896 original size:60 final size:60
Alignment explanation
Indices: 14774--14900 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
14764 ATTACTTATG
* * *
14774 GTGCAAACAAGTACTTGCACAAAATTTCGGGTCATACGGGTCCCTGTACTAATAGGTATT
1 GTGCAAACAAGTACTTGCACAAAATTTCGGATCATACGAGTCCCTGTACCAATAGGTATT
* * * * * * *
14834 GTGCAAACAAGTCCTT-CTACAAAATTTTGGATCATATGAGTCCCTTTACCATTGGGTTTT
1 GTGCAAACAAGTACTTGC-ACAAAATTTCGGATCATACGAGTCCCTGTACCAATAGGTATT
14894 GTGCAAA
1 GTGCAAA
14901 TTTGTCCGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (60 bp):
GTGCAAACAAGTACTTGCACAAAATTTCGGATCATACGAGTCCCTGTACCAATAGGTATT
Found at i:17057 original size:438 final size:431
Alignment explanation
Indices: 16073--16986 Score: 1067
Period size: 438 Copynumber: 2.1 Consensus size: 431
16063 TCTTTTATTT
* * ** * **
16073 TTTTTTGTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTGTTAAAAGGTAATTTCATGATCTA
1 TTTTTTGTTCTATTTGTCCGATCAAGGTGATTCAAGTGTCTACTAAAAAGTAAACTCAT-ATCTA
* ** * * * *
16138 CAACTTTCATGAAGGACTCAAAAACCAATTTTCATGTTTCGGTTCTAAAAAATGCTTTTTAAATT
65 CAACTTTCATAAAAAACTC-AGAA-CAATTTT-AGGTTTTGATTCTAAAAAATGCTTTTTAAATT
* * *
16203 TTGTGATCTTGATTGTCGGTCTATCTAATATTGTATAATTTTCGAACCACTTGTCCGATTGAGGT
127 TTGTGATCTTGATTGCCGGTCTATCTAATATCGTATAATTTTCGAACCACTTGTCCGATTGAAGT
* * *
16268 TGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTTCGTCAAGGGCGTAAAAGTTGA
192 TGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATCAAGGGCATAAAAGTTGA
* * *
16333 ATTTGATTAATGAGTTTCGTGGAGGGTTCGAGAGAGAATTTTTATGTTTGGTCTCCACAAACAAA
257 A--T-ATTAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTTTGGTCTCAACAAACAAA
* * *
16398 TATATTTTTTGCTAGATTATCTATCAAAAGATCCCTATACTTTTATGTTTTATGCTATTTAATCC
319 TATATTTTTTGCTAGATTATCTATCAAAAGATCCCTATACTTTTATGCTTCATGCTATTGAATCC
** *
16463 TTTACATTATGGATTGGACGATTTAACGTTTCGACTTTTATTTTTGTA
384 TTTACATTATGGATCAGACGATTTAACGTTTCGACTTTTATTTTTGAA
* *
16511 TTTTTTGTTCTATTTGTCCGATCAAGGTGATTCAAGTGTCTACTAAAAGGTAATCTCATGATCTA
1 TTTTTTGTTCTATTTGTCCGATCAAGGTGATTCAAGTGTCTACTAAAAAGTAAACTCAT-ATCTA
* *
16576 CAACTTTCATGAAAAACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAATG-TTTCTTAAAT
65 CAACTTTCATAAAAAACTCAGAA--CAATTTT-AGGTTTTGATTCTAAAAAATGCTTT-TTAAAT
* * ** *
16640 TTTGTGGT-TTCGATTGCCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTTCGATTGAA
126 TTTGTGATCTT-GATTGCCGGTCTATCTAATATCGTATAATTTTCGAACCACTTGTCCGATTGAA
* * * *
16704 GTTGTTCAAGTGTCGGTTAAAAGGTTGTTGTGTTATCTACGACTTTCATTAAGGGCATGAAAGTT
190 GTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATCAAGGGCATAAAAGTT
* * * *
16769 G-A-ATT-ATGAGTTTCGTGGAGGATTCAAGGGGGAATTTTTATGTTCT-GTCTCAATAAACTAA
255 GAATATTAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTT-TGGTCTCAACAAACAAA
* * * * * * *
16830 T-TCTTTTTTGCTGGATTATTTATCTAATGA-CCCTCATATTTTTATGCTTCATGCTATTGAATT
319 TATATTTTTTGCTAGATTATCTATCAAAAGATCCCT-ATACTTTTATGCTTCATGCTATTGAATC
*
16893 CTTTACAATTATAGG-TCAGACGATTTAACGCTTT-GACTTTTGTTTTTGAA
383 CTTTAC-ATTAT-GGATCAGACGATTTAACG-TTTCGACTTTTATTTTTGAA
* *
16943 TTTTTGTGTTCTATTTGTCTC-ATTAAGGTGATTTAAGTGTCTAC
1 TTTTT-TGTTCTATTTGTC-CGATCAAGGTGATTCAAGTGTCTAC
16987 ATGAAGAACT
Statistics
Matches: 417, Mismatches: 49, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
430 4 0.01
431 53 0.13
432 85 0.20
433 43 0.10
434 1 0.00
437 9 0.02
438 222 0.53
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (431 bp):
TTTTTTGTTCTATTTGTCCGATCAAGGTGATTCAAGTGTCTACTAAAAAGTAAACTCATATCTAC
AACTTTCATAAAAAACTCAGAACAATTTTAGGTTTTGATTCTAAAAAATGCTTTTTAAATTTTGT
GATCTTGATTGCCGGTCTATCTAATATCGTATAATTTTCGAACCACTTGTCCGATTGAAGTTGTT
CAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCATCAAGGGCATAAAAGTTGAATAT
TAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTTTGGTCTCAACAAACAAATATATTT
TTTGCTAGATTATCTATCAAAAGATCCCTATACTTTTATGCTTCATGCTATTGAATCCTTTACAT
TATGGATCAGACGATTTAACGTTTCGACTTTTATTTTTGAA
Found at i:22992 original size:94 final size:94
Alignment explanation
Indices: 22831--23018 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
22821 AAATAGAAAG
*
22831 GGTCTAGTTGCAAAAGCAAATTCAAGATTTTGAGGTATGCCTTATTTTCTATCTTCATTGTTTGT
1 GGTCTAGTTGCAAAAGCAAATTCAAGATTTTGAGGTATGCCTGATTTTCTATCTTCATTGTTTGT
22896 GACATAGCCTTGTTACAGCTTACAGGCAT
66 GACATAGCCTTGTTACAGCTTACAGGCAT
22925 GGTCTAGTTGCAAAAGCAAATTCAAGATTTTGAGGTATGCCTGATTTTCTATCTTCATTGTTTGT
1 GGTCTAGTTGCAAAAGCAAATTCAAGATTTTGAGGTATGCCTGATTTTCTATCTTCATTGTTTGT
22990 GACATAGCCTTGTTACAGCTTACAGGCAT
66 GACATAGCCTTGTTACAGCTTACAGGCAT
23019 TCGTCCTTTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (94 bp):
GGTCTAGTTGCAAAAGCAAATTCAAGATTTTGAGGTATGCCTGATTTTCTATCTTCATTGTTTGT
GACATAGCCTTGTTACAGCTTACAGGCAT
Found at i:23978 original size:29 final size:29
Alignment explanation
Indices: 23935--23990 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
23925 TAGGGGACAT
23935 CTTCTTCTTTGAAGTGGATCTTAGTCACG
1 CTTCTTCTTTGAAGTGGATCTTAGTCACG
*
23964 CTTCTTCTCTT-AAGTGGGTCTTAGTCA
1 CTTCTTCT-TTGAAGTGGATCTTAGTCA
23991 TGTAATCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (29 bp):
CTTCTTCTTTGAAGTGGATCTTAGTCACG
Found at i:24244 original size:19 final size:21
Alignment explanation
Indices: 24215--24256 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
24205 ATAAACTATG
24215 AACTAAAATTG-AAATAATTA
1 AACTAAAATTGCAAATAATTA
*
24235 AACT-AAATTGCAAGTAATTA
1 AACTAAAATTGCAAATAATTA
24255 AA
1 AA
24257 ATAGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AACTAAAATTGCAAATAATTA
Found at i:25901 original size:96 final size:94
Alignment explanation
Indices: 25737--25996 Score: 306
Period size: 96 Copynumber: 2.7 Consensus size: 94
25727 ATTTAGTTGA
* * * * * *
25737 ACCCTTTAGAA-GGCGTTGGACCTTGTTGGTCAGGGAACGTATCTCGTCGATTGACCGCTAACAT
1 ACCCTTTA-AAGGGCTTTGGACCTTGTTGGTCAGGGAACGTATCTTGTCGATCG-CCGCCAATAG
* *
25801 GTTTATGACATGGGCCCTTTAGCGGGCGTTAG
64 GTTTATAACATGAGCCCTTTAG-GGGCGTTAG
* *
25833 ACCCTTTAAAGGGCTTTGGACCTTTTTGGTCAGGGAACATATCTTGTCGATCGCCTGCCAATAGG
1 ACCCTTTAAAGGGCTTTGGACCTTGTTGGTCAGGGAACGTATCTTGTCGATCGCC-GCCAATAGG
* * *
25898 TTTATAACTTGAGCCCTTTAGTGGCGTTGG
65 TTTATAACATGAGCCCTTTAGGGGCGTTAG
* * * * *
25928 ACCCTTTGAAGGGCTATGGACCTTGTTGGTCAAGGAACGGATCATTGTCAATCGCCGCCAATAGG
1 ACCCTTTAAAGGGCTTTGGACCTTGTTGGTCAGGGAACGTATC-TTGTCGATCGCCGCCAATAGG
25993 TTTA
65 TTTA
25997 GAAATTGAGC
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
95 61 0.43
96 80 0.57
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (94 bp):
ACCCTTTAAAGGGCTTTGGACCTTGTTGGTCAGGGAACGTATCTTGTCGATCGCCGCCAATAGGT
TTATAACATGAGCCCTTTAGGGGCGTTAG
Done.