Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010015.1 Corchorus capsularis cultivar CVL-1 contig10036, 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: 17720
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:541 original size:13 final size:13
Alignment explanation
Indices: 520--552 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
510 TCTGACATAT
*
520 GCCATGTTGGATG
1 GCCACGTTGGATG
533 GCCACGTTGGATG
1 GCCACGTTGGATG
546 GCCACGT
1 GCCACGT
553 CATCTAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.36, T:0.24
Consensus pattern (13 bp):
GCCACGTTGGATG
Found at i:1811 original size:25 final size:25
Alignment explanation
Indices: 1777--1928 Score: 178
Period size: 25 Copynumber: 5.7 Consensus size: 25
1767 AATTTGCATA
1777 TAGCGGCGTCTAGACGCCACTATTT
1 TAGCGGCGTCTAGACGCCACTATTT
1802 TAGCGGCGTCAGGACTTCAGGACGCCACTATTT
1 TAGCGGCGT-----C-T-A-GACGCCACTATTT
* * *
1835 TAGCGACGTCAAGACGCCACTACTT
1 TAGCGGCGTCTAGACGCCACTATTT
1860 TAGCGGCGTCTAGACGCCACTATTTT
1 TAGCGGCGTCTAGACGCCACTA-TTT
* *
1886 TAGAGGCGTCTAGACGCTACTATTT
1 TAGCGGCGTCTAGACGCCACTATTT
1911 TAGCGGCGTCTAGACGCC
1 TAGCGGCGTCTAGACGCC
1929 GCTACTTATA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
25 60 0.56
26 23 0.21
28 1 0.01
30 1 0.01
31 1 0.01
32 1 0.01
33 21 0.19
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.26
Consensus pattern (25 bp):
TAGCGGCGTCTAGACGCCACTATTT
Found at i:1913 original size:51 final size:50
Alignment explanation
Indices: 1822--1928 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 50
1812 AGGACTTCAG
*
1822 GACGCCACTATTTTAGCGACGTCAAGACGCCACTACTTTAGCGGCGTCTA
1 GACGCCACTATTTTAGAGACGTCAAGACGCCACTACTTTAGCGGCGTCTA
* * * *
1872 GACGCCACTATTTTTAGAGGCGTCTAGACGCTACTATTTTAGCGGCGTCTA
1 GACGCCACTA-TTTTAGAGACGTCAAGACGCCACTACTTTAGCGGCGTCTA
1923 GACGCC
1 GACGCC
1929 GCTACTTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 10 0.20
51 41 0.80
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
GACGCCACTATTTTAGAGACGTCAAGACGCCACTACTTTAGCGGCGTCTA
Found at i:4773 original size:21 final size:21
Alignment explanation
Indices: 4713--4773 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
4703 TTAGAGTTGA
* * * *
4713 TGAACAAGAATTGGATGACTC
1 TGAAGAAGAATGGGAAGAATC
* *
4734 TGATGAAGAATGGGTAGAATC
1 TGAAGAAGAATGGGAAGAATC
4755 TGAAGAAGAA-GAGGAAGAA
1 TGAAGAAGAATG-GGAAGAA
4774 AACCAAGTGA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.44, C:0.07, G:0.31, T:0.18
Consensus pattern (21 bp):
TGAAGAAGAATGGGAAGAATC
Found at i:5098 original size:49 final size:49
Alignment explanation
Indices: 5026--5253 Score: 413
Period size: 49 Copynumber: 4.7 Consensus size: 49
5016 TCAATAATAT
5026 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
1 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
*
5075 GAATCTCTTTTGTGAACTCTTAACAATCAGTGTATTTAGTGATGGTATG
1 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
5124 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
1 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
** *
5173 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATAAT-TT
1 GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
5221 GAATCTCTTTTGTGAACTCTTAACAATCATTGT
1 GAATCTCTTTTGTGAACTCTTAACAATCATTGT
5254 TATTGTGTTC
Statistics
Matches: 174, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
48 34 0.20
49 140 0.80
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (49 bp):
GAATCTCTTTTGTGAACTCTTAACAATCATTGTATTTAGTGATGGTATG
Found at i:5387 original size:22 final size:22
Alignment explanation
Indices: 5362--5404 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5352 AAAGGACCCT
* *
5362 GAGCAAGTCATGCGCATGACCA
1 GAGCAAGTCATACCCATGACCA
*
5384 GAGCAGGTCATACCCATGACC
1 GAGCAAGTCATACCCATGACC
5405 TCCATATGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (22 bp):
GAGCAAGTCATACCCATGACCA
Found at i:5482 original size:73 final size:73
Alignment explanation
Indices: 5359--5622 Score: 388
Period size: 73 Copynumber: 3.6 Consensus size: 73
5349 AGAAAAGGAC
* * * * *
5359 CCTGAGCAAGTCATGCGCATGACC-AGAGCAGGTCATACCCATGACCTCCATATGCGTTTTAGCC
1 CCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCCATATGCGTTTTAGCC
5423 TTCTTGCA
66 TTCTTGCA
* * *
5431 CCTGAGGAAGTCATGCACATGATCAACAGAAGGTCATGCCCATGACATCCATATGCGTTTTAGCC
1 CCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCCATATGCGTTTTAGCC
5496 TTCTTGCA
66 TTCTTGCA
* * *
5504 CCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCTAAAGGCGTTTTAGCC
1 CCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCCATATGCGTTTTAGCC
5569 TTCTTGCA
66 TTCTTGCA
* **
5577 CCTGAGTAAGTCATGCACATGACCAACACAA-GTCATGTGCATGACC
1 CCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACC
5623 AGGACGGACA
Statistics
Matches: 175, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
72 34 0.19
73 141 0.81
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (73 bp):
CCTGAGTAAGTCATGCACATGACCAACAGAAGGTCATGCCCATGACCTCCATATGCGTTTTAGCC
TTCTTGCA
Found at i:14166 original size:1 final size:1
Alignment explanation
Indices: 14160--14195 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
14150 AACCGTCAAG
14160 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14196 CGAATCTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15162 original size:349 final size:350
Alignment explanation
Indices: 14516--15221 Score: 1229
Period size: 349 Copynumber: 2.0 Consensus size: 350
14506 TTATACCCTT
14516 ATTTTTCAAACATATTTCTTAAATGTCATTGCTTAACTATTGTAGTTTTATTCTACTAAAACTCT
1 ATTTTTCAAACATATTTCTTAAATGTCATTGCTTAACTATTGTAGTTTTATTCTACTAAAACTCT
* *
14581 ATTTTTATTCAACTAAATCTAATATCTTTATAATTACTTTTTTTTTTTACCATTTCACTATTTTT
66 ATTTTTATTCAACTAAATCTAATATCTTTATAATTAC-TTTTATTTTTACCATTTCAATATTTTT
*
14646 CAATAAAAATTTGGATATTAAAATCTTTTAATATACAGTTTTATTCTATTAAAAACTCTATTTTC
130 CAATAAAAATTTGGATATTAAAATCTTTTAACATACAGTTTTATTCTATTAAAAACTCTATTTTC
* *
14711 ATTTAATTAAATTCAATATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAAGTTATTGT
195 ATTTAATTAAATTCAATATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAACTTACTGT
*
14776 GATTGACATCTTTCTATTTGATAGTTTAATGTATTATGATTAAAATTTATCATATCACTAACGT-
260 GATTGACATCTTTCTATTTGATAGTTTAATATATTATGATTAAAATTTATCATATCACTAACGTG
14840 GCAGTTATTTTATTTGACTTATAATTA
325 GC-GTTATTTTATTTGACTTATAATTA
14867 ATTTTTCAAACATATTTCTTAAATGTCATTGCTTAACTATTGTAGTTTTATTCTACTAAAAACTC
1 ATTTTTCAAACATATTTCTTAAATGTCATTGCTTAACTATTGTAGTTTTATTCTACT-AAAACTC
*
14932 TATTTTTATTCAATTAAATCTAATATCTTTATAATTAC-TTTATTTTTACCATTT-AATATTTTT
65 TATTTTTATTCAACTAAATCTAATATCTTTATAATTACTTTTATTTTTACCATTTCAATATTTTT
* * *
14995 CAATAAAAATTTGGATATTAAAATGTTTTAACATACAGTTTTATTCTCTTAAAAACTGTATTTTC
130 CAATAAAAATTTGGATATTAAAATCTTTTAACATACAGTTTTATTCTATTAAAAACTCTATTTTC
*
15060 ATTTAATTAAATTCAATATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAACTTGCTGT
195 ATTTAATTAAATTCAATATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAACTTACTGT
* * * *
15125 GATTGACATCTTTTTATTTGATAGTTTAATATATTATGATTAAAATTTATTATTTCCCTAACGTG
260 GATTGACATCTTTCTATTTGATAGTTTAATATATTATGATTAAAATTTATCATATCACTAACGTG
15190 GCGTTATTTTATTTGACTTATAATTA
325 GCGTTATTTTATTTGACTTATAATTA
15216 ATTTTT
1 ATTTTT
15222 TGCTTGATAA
Statistics
Matches: 338, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
349 220 0.65
350 17 0.05
351 57 0.17
352 44 0.13
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (350 bp):
ATTTTTCAAACATATTTCTTAAATGTCATTGCTTAACTATTGTAGTTTTATTCTACTAAAACTCT
ATTTTTATTCAACTAAATCTAATATCTTTATAATTACTTTTATTTTTACCATTTCAATATTTTTC
AATAAAAATTTGGATATTAAAATCTTTTAACATACAGTTTTATTCTATTAAAAACTCTATTTTCA
TTTAATTAAATTCAATATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAACTTACTGTG
ATTGACATCTTTCTATTTGATAGTTTAATATATTATGATTAAAATTTATCATATCACTAACGTGG
CGTTATTTTATTTGACTTATAATTA
Found at i:17585 original size:49 final size:49
Alignment explanation
Indices: 17513--17611 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
17503 ACGTGACTAA
* *
17513 CGGTGCCACATATGTGATTGCACATCACTAATGGGGCTGATGTGGCATG
1 CGGTGCCACATATGTGACTGCACATCACTAACGGGGCTGATGTGGCATG
17562 CGGTGCCACATATGTGACTGCACATCACTAACGGGGCTGATGTGGCATG
1 CGGTGCCACATATGTGACTGCACATCACTAACGGGGCTGATGTGGCATG
17611 C
1 C
17612 CACGTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.24
Consensus pattern (49 bp):
CGGTGCCACATATGTGACTGCACATCACTAACGGGGCTGATGTGGCATG
Found at i:17652 original size:27 final size:27
Alignment explanation
Indices: 17622--17675 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17612 CACGTTTGAT
17622 GGCTTAATGCCCTTTTTGCCTCATGAA
1 GGCTTAATGCCCTTTTTGCCTCATGAA
17649 GGCTTAATGCCCTTTTTGCCTCATGAA
1 GGCTTAATGCCCTTTTTGCCTCATGAA
17676 CTTGTGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (27 bp):
GGCTTAATGCCCTTTTTGCCTCATGAA
Done.