Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006199.1 Corchorus capsularis cultivar CVL-1 contig06218, 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: 68221
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:6294 original size:132 final size:132
Alignment explanation
Indices: 6057--6322 Score: 478
Period size: 132 Copynumber: 2.0 Consensus size: 132
6047 ATATAGCAAT
6057 TTTTTGTGAGATTAATCCTGCATTTACACTCTTTATCCTTATATGAATCTTCTTTAAAAACTTTT
1 TTTTTGTGAGATTAATCCTGCATTTACACTCTTTATCCTTATATGAATCTTCTTTAAAAACTTTT
* *
6122 TCCTCTTCGTTGATCAAAAAAATAGATAAGTTGCACCCTTGTATCCCTAATTGACTATTCTGTAA
66 TCCCCTTCGTTGATCAAAAAAATAGATAAGTCGCACCCTTGTATCCCTAATTGACTATTCTGTAA
6187 AG
131 AG
*
6189 TTTTTGTGAGATTAATCCTGCATTTACACTCTTTATCCTTATATGAATCTTCTTTAAAAAGTTTT
1 TTTTTGTGAGATTAATCCTGCATTTACACTCTTTATCCTTATATGAATCTTCTTTAAAAACTTTT
* * *
6254 TCCCCTTTGTTGATCAACAAAATAGATAAGTCGCGCCCTTGTATCCCTAATTGACTATTCTGTAA
66 TCCCCTTCGTTGATCAAAAAAATAGATAAGTCGCACCCTTGTATCCCTAATTGACTATTCTGTAA
6319 AG
131 AG
6321 TT
1 TT
6323 GGATCCTAAT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (132 bp):
TTTTTGTGAGATTAATCCTGCATTTACACTCTTTATCCTTATATGAATCTTCTTTAAAAACTTTT
TCCCCTTCGTTGATCAAAAAAATAGATAAGTCGCACCCTTGTATCCCTAATTGACTATTCTGTAA
AG
Found at i:13015 original size:83 final size:83
Alignment explanation
Indices: 12920--13077 Score: 316
Period size: 83 Copynumber: 1.9 Consensus size: 83
12910 TTGATTTGAG
12920 TTGAGTTGAGTTTCTGCATCGAGTTCTTCTCTGTGTTGCTTGTCCTATCTTTTCTTGATGCTATC
1 TTGAGTTGAGTTTCTGCATCGAGTTCTTCTCTGTGTTGCTTGTCCTATCTTTTCTTGATGCTATC
12985 TTTGTTATTGTATGAATT
66 TTTGTTATTGTATGAATT
13003 TTGAGTTGAGTTTCTGCATCGAGTTCTTCTCTGTGTTGCTTGTCCTATCTTTTCTTGATGCTATC
1 TTGAGTTGAGTTTCTGCATCGAGTTCTTCTCTGTGTTGCTTGTCCTATCTTTTCTTGATGCTATC
13068 TTTGTTATTG
66 TTTGTTATTG
13078 GAAGTTTTGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (83 bp):
TTGAGTTGAGTTTCTGCATCGAGTTCTTCTCTGTGTTGCTTGTCCTATCTTTTCTTGATGCTATC
TTTGTTATTGTATGAATT
Found at i:15923 original size:1 final size:1
Alignment explanation
Indices: 15917--15956 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
15907 TTAGGTTGTA
*
15917 TTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15957 CGTGAATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:15942 original size:20 final size:21
Alignment explanation
Indices: 15912--15955 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
15902 GTCCTTTAGG
15912 TTGTATTTTTTTTTTTTTTTT
1 TTGTATTTTTTTTTTTTTTTT
*
15933 TTGTTTTTTTTTTTTTTTTTT
1 TTGTATTTTTTTTTTTTTTTT
15954 TT
1 TT
15956 TCGTGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.00, G:0.05, T:0.93
Consensus pattern (21 bp):
TTGTATTTTTTTTTTTTTTTT
Found at i:21816 original size:2 final size:2
Alignment explanation
Indices: 21809--21846 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
21799 TTCTTCTTCT
*
21809 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21847 AATTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:26016 original size:2 final size:2
Alignment explanation
Indices: 26009--26033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25999 GGGTATCTGT
26009 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
26034 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:26038 original size:2 final size:2
Alignment explanation
Indices: 26033--26069 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
26023 TCTCTCTCTC
* *
26033 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26070 GTATGTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29444 original size:33 final size:33
Alignment explanation
Indices: 29330--29433 Score: 154
Period size: 33 Copynumber: 3.2 Consensus size: 33
29320 TTTTTACACT
*
29330 GAGCCTCCCTACTAGGACGGCTCAGCCACGGCG
1 GAGCCTCCCCACTAGGACGGCTCAGCCACGGCG
* * * *
29363 GAGCCTCCCCACTAGGGCGGCTCAACCACAGTG
1 GAGCCTCCCCACTAGGACGGCTCAGCCACGGCG
*
29396 GAGCCTCCCCACTAGGACGGCTTAGCCACGGCG
1 GAGCCTCCCCACTAGGACGGCTCAGCCACGGCG
29429 GAGCC
1 GAGCC
29434 GTCCTACTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.19, C:0.39, G:0.30, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGACGGCTCAGCCACGGCG
Found at i:33170 original size:12 final size:12
Alignment explanation
Indices: 33153--33182 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
33143 CCATTGCAGC
33153 TTTTTTTCCTTT
1 TTTTTTTCCTTT
33165 TTTTTTTCCTTT
1 TTTTTTTCCTTT
33177 TTTTTT
1 TTTTTT
33183 GTTTGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTCCTTT
Found at i:48405 original size:21 final size:21
Alignment explanation
Indices: 48381--48489 Score: 91
Period size: 21 Copynumber: 5.2 Consensus size: 21
48371 CTGCTTCTAT
*
48381 TTGTCATAATGATGTTTCTAA
1 TTGTCATAATGATGTTTCTGA
* * *
48402 TTGT-ATTGCATCATCTTT-TGA
1 TTGTCA-T-AATGATGTTTCTGA
48423 TTGTCATAATGATGTTTCTGA
1 TTGTCATAATGATGTTTCTGA
* * *
48444 TTGT-ATTGCATCATCTTT-TGA
1 TTGTCA-T-AATGATGTTTCTGA
48465 TTGTCATAATGATGTTTCTGA
1 TTGTCATAATGATGTTTCTGA
48486 TTGT
1 TTGT
48490 ATTGCATCAT
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
20 16 0.24
21 35 0.52
22 16 0.24
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (21 bp):
TTGTCATAATGATGTTTCTGA
Found at i:48440 original size:42 final size:42
Alignment explanation
Indices: 48381--48510 Score: 251
Period size: 42 Copynumber: 3.1 Consensus size: 42
48371 CTGCTTCTAT
*
48381 TTGTCATAATGATGTTTCTAATTGTATTGCATCATCTTTTGA
1 TTGTCATAATGATGTTTCTGATTGTATTGCATCATCTTTTGA
48423 TTGTCATAATGATGTTTCTGATTGTATTGCATCATCTTTTGA
1 TTGTCATAATGATGTTTCTGATTGTATTGCATCATCTTTTGA
48465 TTGTCATAATGATGTTTCTGATTGTATTGCATCATCTTTTGA
1 TTGTCATAATGATGTTTCTGATTGTATTGCATCATCTTTTGA
48507 TTGT
1 TTGT
48511 ACTGCTATTC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.51
Consensus pattern (42 bp):
TTGTCATAATGATGTTTCTGATTGTATTGCATCATCTTTTGA
Found at i:48507 original size:21 final size:21
Alignment explanation
Indices: 48401--48511 Score: 104
Period size: 21 Copynumber: 5.3 Consensus size: 21
48391 GATGTTTCTA
48401 ATTGTATTGCATCATCTTTTG
1 ATTGTATTGCATCATCTTTTG
* * *
48422 ATTGTCA-T-AATGATGTTTCTG
1 ATTGT-ATTGCATCATCTTT-TG
48443 ATTGTATTGCATCATCTTTTG
1 ATTGTATTGCATCATCTTTTG
* * *
48464 ATTGTCA-T-AATGATGTTTCTG
1 ATTGT-ATTGCATCATCTTT-TG
48485 ATTGTATTGCATCATCTTTTG
1 ATTGTATTGCATCATCTTTTG
48506 ATTGTA
1 ATTGTA
48512 CTGCTATTCC
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
20 16 0.23
21 38 0.54
22 16 0.23
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (21 bp):
ATTGTATTGCATCATCTTTTG
Found at i:65008 original size:32 final size:32
Alignment explanation
Indices: 64973--65083 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 32
64963 CCGCCCAGCC
* ** *
64973 TGGGCGGC-ATGCCATGGGCAACCCGCCCAAAC
1 TGGGCGGCAAGGCCAT-GGCATGCCGCCCAAAA
* *
65005 TGGGTGGCAAGGCCATGGCATGCCACCCAAAA
1 TGGGCGGCAAGGCCATGGCATGCCGCCCAAAA
*
65037 TGGGCGGCAAGGCCATGGCATGCCGCCTAAAA
1 TGGGCGGCAAGGCCATGGCATGCCGCCCAAAA
*
65069 TGGGCGGCAAAGCCA
1 TGGGCGGCAAGGCCA
65084 ATTTTCTTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 62 0.91
33 6 0.09
ACGTcount: A:0.25, C:0.31, G:0.33, T:0.11
Consensus pattern (32 bp):
TGGGCGGCAAGGCCATGGCATGCCGCCCAAAA
Found at i:65146 original size:22 final size:23
Alignment explanation
Indices: 65107--65160 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
65097 AAAATAATTT
*
65107 TTAATTAATTAGCATTTAATTAC
1 TTAATTTATTAGCATTTAATTAC
* *
65130 TTAATTTATTAG-TTTTAATTAG
1 TTAATTTATTAGCATTTAATTAC
65152 TTAATTTAT
1 TTAATTTAT
65161 GATTGATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TTAATTTATTAGCATTTAATTAC
Done.