Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012476.1 Corchorus olitorius cultivar O-4 contig12509, 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: 2158
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Found at i:325 original size:64 final size:64
Alignment explanation
Indices: 128--675 Score: 697
Period size: 64 Copynumber: 8.6 Consensus size: 64
118 CCGGTGCATC
* * * ** * *
128 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAGCCTTTTGGAGAAACTATCTTCTGGTGTGCT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTT-GAGAAACCATCTTCTGGTGTACT
* * * * * * * * * * *
193 TTTTAACAAGATTGTCATCCGACCGACTTTTGAAAA-TTTTAAGAATCCATCTTCTGGCGTAGT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* *
256 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTTCT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* * *
320 TCTTGACAAGATCATCTTCC-AGTCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTGCT
1 TCTTGACAAGATCGTCTTCCGA-TCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* * ** *
384 TTTTGACGAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* * *
448 TCTTGACAAGATCGTCTTCCAATCAACTCCT-AAAAATTCTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTT-TTGAGAAACCATCTTCTGGTGTACT
* * *
512 TTTTGACAAGATCATCTTCCGATCAACTTCTGAAAACTATTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
* ** *
576 TTTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
*
640 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAA
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAA
676 TTCTTTCTAG
Statistics
Matches: 420, Mismatches: 58, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
63 53 0.13
64 332 0.79
65 35 0.08
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACT
Found at i:460 original size:192 final size:192
Alignment explanation
Indices: 128--680 Score: 804
Period size: 192 Copynumber: 2.9 Consensus size: 192
118 CCGGTGCATC
* * * * ** * *
128 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAGCCTTTTGGAGAAACTATCTTCTGGTGTGCT
1 TCTTGACAAGATCATCTTCCGATCAACTTCTGAAAACTATT-GAGAAACCATCTTCTGGTGTGCT
* * * * * ** * * * *
193 TTTTAACAAGATTGTCATCCGACCGACTTTTGAAAA-TTTTAAGAATCCATCTTCTGGCGTAGTT
65 TTTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTT
* * *
257 CTTGACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTTCT
130 CTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
*
320 TCTTGACAAGATCATCTTCC-AGTCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTGCT
1 TCTTGACAAGATCATCTTCCGA-TCAACTTCTGAAAACTATTGAGAAACCATCTTCTGGTGTGCT
*
384 TTTTGACGAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTT
65 TTTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTT
* * *
449 CTTGACAAGATCGTCTTCCAATCAACTCCTAAAAATTCTTGAGAAACCATCTTCTGGTGTACT
130 CTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
* *
512 TTTTGACAAGATCATCTTCCGATCAACTTCTGAAAACTATTGAGAAACCATCTTCTGGTGTACTT
1 TCTTGACAAGATCATCTTCCGATCAACTTCTGAAAACTATTGAGAAACCATCTTCTGGTGTGCTT
577 TTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTC
66 TTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTC
*
642 TTGACAAGATCGTCTTCCGATCAACTCCTGAAAATTCTT
131 TTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTCTT
681 TCTAGCAAAC
Statistics
Matches: 326, Mismatches: 32, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
191 51 0.16
192 274 0.84
193 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (192 bp):
TCTTGACAAGATCATCTTCCGATCAACTTCTGAAAACTATTGAGAAACCATCTTCTGGTGTGCTT
TTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTC
TTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACT
Found at i:749 original size:54 final size:55
Alignment explanation
Indices: 648--808 Score: 236
Period size: 54 Copynumber: 2.9 Consensus size: 55
638 CTTCTTGACA
* * * *
648 AGATCGTCTTCCGATCAAC-TCCTGAAAATTCTTTCTAGCAAACCGTCTTCCGATG
1 AGATTGTCTTCCAATCAACAT-TTGAAAATTCTTTCTAGCAAACCGTCTTCCGAGG
* *
703 AGATTGTCTTCCAATCAACATTTG-AAATCCTTTCTAGCAAACCGTCTTCCGGGG
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGAGG
*
757 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCG
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCG
809 GTGTTCTCCT
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
54 51 0.53
55 44 0.46
56 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (55 bp):
AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGAGG
Found at i:871 original size:67 final size:67
Alignment explanation
Indices: 756--1074 Score: 530
Period size: 67 Copynumber: 4.8 Consensus size: 67
746 GTCTTCCGGG
* *
756 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTTCTCCTTA
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTA
821 AT
66 AT
* * ** * *
823 AAGATTGTCTTACAATCAATTTTTGAAAATTCTTTCTAGCAAATCGTCTTCCGGTGTACTTCTTA
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTA
888 AT
66 AT
* *
890 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTTCAGTGTACTTCTTA
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTA
955 AT
66 AT
957 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTA
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTA
1022 AT
66 AT
**
1024 GAGATTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTC
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTC
1075 TGTTGTATCT
Statistics
Matches: 232, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 232 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (67 bp):
GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTA
AT
Done.