Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005347.1 Corchorus capsularis cultivar CVL-1 contig05365, 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: 20518
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:1193 original size:94 final size:93
Alignment explanation
Indices: 1085--1311 Score: 312
Period size: 94 Copynumber: 2.4 Consensus size: 93
1075 ATTTTTTTTG
* * * *
1085 AGAAATTTTCTTTTATTTCAGATATTCTTATATAGATCTAGAAATATCTGGCAAAAAAAAAAAGA
1 AGAATTTTTCTTTTATTTCCGATATTCTTAT-TAGATCTAAAAAAATCTGGCAAAAAAAAAAAGA
1150 TCCAATAGATATTTGATTCTATTTCACAA
65 TCCAATAGATATTTGATTCTATTTCACAA
*
1179 AGAATTTTTCTTTTATTTCCGATATTCTTATGTAGATCTAAAAAAATCTGGCCAAAAAAAAAAGA
1 AGAATTTTTCTTTTATTTCCGATATTCTTAT-TAGATCTAAAAAAATCTGGCAAAAAAAAAAAGA
* * * *
1244 TTCGATAGATATTTGATTCTCTTTCACAG
65 TCCAATAGATATTTGATTCTATTTCACAA
* * * *
1273 AGATTTTTTC-TTGATTTCCGATTTTCATATTAGATCTAA
1 AGAATTTTTCTTTTATTTCCGATATTCTTATTAGATCTAA
1312 TAATAGAGGG
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
92 9 0.08
93 17 0.14
94 93 0.78
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (93 bp):
AGAATTTTTCTTTTATTTCCGATATTCTTATTAGATCTAAAAAAATCTGGCAAAAAAAAAAAGAT
CCAATAGATATTTGATTCTATTTCACAA
Found at i:1603 original size:9 final size:9
Alignment explanation
Indices: 1586--1640 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
1576 GGGCTTTTGA
*
1586 CCCACCTGG
1 CCCATCTGG
1595 CCCATCTGG
1 CCCATCTGG
* *
1604 ACAATCTGG
1 CCCATCTGG
*
1613 CCCATCTAG
1 CCCATCTGG
1622 CCCATCTGG
1 CCCATCTGG
*
1631 CCCACCTGG
1 CCCATCTGG
1640 C
1 C
1641 GCGCCTGACC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.18
Consensus pattern (9 bp):
CCCATCTGG
Found at i:5488 original size:75 final size:75
Alignment explanation
Indices: 5357--5520 Score: 197
Period size: 75 Copynumber: 2.2 Consensus size: 75
5347 CTGGTATCTA
* *
5357 ATTCGAATTCAAATAATGAGTTTTCTGATGGTGTTAGGCAAAATCTTGAAAATGATTCACCTGAT
1 ATTCGAATTCAAATAATAAGTTTTCTGATGATGTTAGGCAAAATCTTGAAAATGATTCACCTGAT
5422 TA-GTTTCCTG
66 TAGGTTT-CTG
* * * * * ** * *
5432 TTTTGAATTCAAATACTAAGTTTTCTGATGATGATT-TGCAACATCTTGAAGCTGATTCACTTTA
1 ATTCGAATTCAAATAATAAGTTTTCTGATGATG-TTAGGCAAAATCTTGAAAATGATTCACCTGA
5496 TTAGGTTTCTG
65 TTAGGTTTCTG
5507 ATTCGAATTCAAAT
1 ATTCGAATTCAAAT
5521 TTTGAGCATC
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
75 68 0.92
76 6 0.08
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (75 bp):
ATTCGAATTCAAATAATAAGTTTTCTGATGATGTTAGGCAAAATCTTGAAAATGATTCACCTGAT
TAGGTTTCTG
Found at i:8765 original size:7 final size:7
Alignment explanation
Indices: 8751--8785 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
8741 CCGTTTGATT
8751 CCTATTG
1 CCTATTG
*
8758 CGTATTG
1 CCTATTG
8765 CCTATTG
1 CCTATTG
8772 CCTATTG
1 CCTATTG
8779 CCTATTG
1 CCTATTG
8786 GTAGCTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (7 bp):
CCTATTG
Found at i:9594 original size:26 final size:26
Alignment explanation
Indices: 9543--9594 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
9533 CTTAATATCT
**
9543 AAAAATATCCTAATCTTATAGTAAAA
1 AAAAATATCCTAATCTTATACAAAAA
*
9569 AAAAAT-TCCTAATCCTTTTACAAAAA
1 AAAAATATCCTAAT-CTTATACAAAAA
9595 CTAAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAATATCCTAATCTTATACAAAAA
Found at i:10355 original size:3 final size:3
Alignment explanation
Indices: 10347--10395 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
10337 GTTTAAATCT
10347 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10395 T
1 T
10396 ATATGTTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16298 original size:22 final size:22
Alignment explanation
Indices: 16270--16313 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16260 ATAAGAGTTT
*
16270 TTCTTATGAAGAAAGGGTTGGC
1 TTCTTATAAAGAAAGGGTTGGC
16292 TTCTTATAAAGAAAGGGTTGGC
1 TTCTTATAAAGAAAGGGTTGGC
16314 AAATTCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (22 bp):
TTCTTATAAAGAAAGGGTTGGC
Found at i:16410 original size:19 final size:19
Alignment explanation
Indices: 16386--16423 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
16376 CTTAGAATTA
16386 GAGTAG-TCTTGTAACTTAG
1 GAGTAGTTCTT-TAACTTAG
16405 GAGTAGTTCTTTAACTTAG
1 GAGTAGTTCTTTAACTTAG
16424 CATTTTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (19 bp):
GAGTAGTTCTTTAACTTAG
Found at i:16746 original size:20 final size:21
Alignment explanation
Indices: 16721--16760 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16711 TATTAAAGAT
16721 TTATATAATATA-AAAATTAA
1 TTATATAATATATAAAATTAA
*
16741 TTATATGATATATAAAATTA
1 TTATATAATATATAAAATTA
16761 TATATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATATAATATATAAAATTAA
Found at i:19607 original size:24 final size:24
Alignment explanation
Indices: 19580--19646 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 24
19570 GTCTTCTCTA
19580 ACCCACAAATAAATTACATGTCAT
1 ACCCACAAATAAATTACATGTCAT
* ** *
19604 ACCCAAAAATATCTT-C-T-TTAT
1 ACCCACAAATAAATTACATGTCAT
*
19625 -CCCACAAATAAATTATATGTCA
1 ACCCACAAATAAATTACATGTCA
19647 GTATCCAAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 7
0.66 0.19 0.15
Matches are distributed among these distances:
20 11 0.35
21 3 0.10
22 2 0.06
23 3 0.10
24 12 0.39
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (24 bp):
ACCCACAAATAAATTACATGTCAT
Found at i:19611 original size:44 final size:44
Alignment explanation
Indices: 19556--19810 Score: 280
Period size: 44 Copynumber: 5.8 Consensus size: 44
19546 ATTTATTATT
* *
19556 TCATCCCCAAAAATGTCTTCTCTAACCCACAAATAAATTACATG
1 TCATACCCAAAAATGTCTTCTCTATCCCACAAATAAATTACATG
* * *
19600 TCATACCCAAAAATATCTTCTTTATCCCACAAATAAATTATATG
1 TCATACCCAAAAATGTCTTCTCTATCCCACAAATAAATTACATG
* * * * **
19644 TCAGTATCCAAAAAAGTCTTAT-TGATCTCACATTTAAATTACATG
1 TCA-TACCCAAAAATGTCTTCTCT-ATCCCACAAATAAATTACATG
**
19689 TCATACCCCCAAATGTCTTCTCTATCCCACAAATAAATTACATG
1 TCATACCCAAAAATGTCTTCTCTATCCCACAAATAAATTACATG
* * * * *
19733 TCATCCCCAAATATTTCTTCTTTAACCCACAAATAAATTACATG
1 TCATACCCAAAAATGTCTTCTCTATCCCACAAATAAATTACATG
* * *
19777 TTATCCCCAAACCATGTCTTCTCTATCCC-CAAAT
1 TCATACCCAAA-AATGTCTTCTCTATCCCACAAAT
19811 CTCCAACATG
Statistics
Matches: 174, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
44 126 0.72
45 48 0.28
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.32
Consensus pattern (44 bp):
TCATACCCAAAAATGTCTTCTCTATCCCACAAATAAATTACATG
Found at i:19663 original size:89 final size:87
Alignment explanation
Indices: 19556--19810 Score: 287
Period size: 89 Copynumber: 2.9 Consensus size: 87
19546 ATTTATTATT
* *
19556 TCATCCCCAAAAATGTCTTCTCTAACCCACAAATAAATTACATGTCATACCCAAAAATATCTTCT
1 TCATACCCAAAAATGTCTTCT-TAACCCACAAATAAATTACATGTCATACCCAAAAATGTCTTCT
* *
19621 TTATCCCACAAATAAATTATATG
65 CTATCCCACAAATAAATTACATG
* * * * * ** **
19644 TCAGTATCCAAAAAAGTCTTATTGATCTCACATTTAAATTACATGTCATACCCCCAAATGTCTTC
1 TCA-TACCCAAAAATGTCTTCTT-AACCCACAAATAAATTACATGTCATACCCAAAAATGTCTTC
19709 TCTATCCCACAAATAAATTACATG
64 TCTATCCCACAAATAAATTACATG
* * * * * *
19733 TCATCCCCAAATATTTCTTCTTTAACCCACAAATAAATTACATGTTATCCCCAAACCATGTCTTC
1 TCATACCCAAAAATGTCTTC-TTAACCCACAAATAAATTACATGTCATACCCAAA-AATGTCTTC
19798 TCTATCCC-CAAAT
64 TCTATCCCACAAAT
19811 CTCCAACATG
Statistics
Matches: 135, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
88 44 0.33
89 91 0.67
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.32
Consensus pattern (87 bp):
TCATACCCAAAAATGTCTTCTTAACCCACAAATAAATTACATGTCATACCCAAAAATGTCTTCTC
TATCCCACAAATAAATTACATG
Found at i:19787 original size:22 final size:23
Alignment explanation
Indices: 19711--19787 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 23
19701 ATGTCTTCTC
19711 TATCCCACAAATAAATTACATGT
1 TATCCCACAAATAAATTACATGT
* * * *
19734 CATCCC-CAAAT--ATTTCTTCTT
1 TATCCCACAAATAAATTACAT-GT
*
19755 TAACCCACAAATAAATTACATGT
1 TATCCCACAAATAAATTACATGT
19778 TATCCC-CAAA
1 TATCCCACAAA
19788 CCATGTCTTC
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
20 5 0.12
21 5 0.12
22 14 0.35
23 11 0.28
24 5 0.12
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.31
Consensus pattern (23 bp):
TATCCCACAAATAAATTACATGT
Found at i:20270 original size:8 final size:8
Alignment explanation
Indices: 20259--20296 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
20249 ATGATATATC
20259 TATATCTA
1 TATATCTA
20267 TATATCTA
1 TATATCTA
20275 TATATCTA
1 TATATCTA
*
20283 TCTATACTA
1 TATAT-CTA
20292 TATAT
1 TATAT
20297 AAAAGTACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATCTA
Done.