Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021210.1 Corchorus olitorius cultivar O-4 contig21243, 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: 34956
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5434 original size:19 final size:18
Alignment explanation
Indices: 5401--5436 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5391 TTGAATTAAA
5401 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
5419 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
5437 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:10469 original size:33 final size:31
Alignment explanation
Indices: 10423--10488 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 31
10413 ACAAGAAAAA
*
10423 TTTTTTATTTATGACGCAGAAAACTTTTCTTTT
1 TTTTTTATATATGACGCA-AAAACTTTT-TTTT
*
10456 TTTTTTATATATGATGCAAAAACTTTTTTTT
1 TTTTTTATATATGACGCAAAAACTTTTTTTT
10487 TT
1 TT
10489 CAAAAACACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 6 0.19
32 9 0.29
33 16 0.52
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.58
Consensus pattern (31 bp):
TTTTTTATATATGACGCAAAAACTTTTTTTT
Found at i:10584 original size:30 final size:31
Alignment explanation
Indices: 10479--10585 Score: 82
Period size: 30 Copynumber: 3.6 Consensus size: 31
10469 ATGCAAAAAC
* *
10479 TTTTTTTTTT-C-AAAAACACCACACAAA-A
1 TTTTTTTTTTACGAAAAACACAAAACAAATA
* ** **
10507 TTTTTTTTTAATTAAAAACACAAAAC-CCT-
1 TTTTTTTTTTACGAAAAACACAAAACAAATA
* *
10536 TTTTTTTATGACGCAAAAACACAAAACAAATA
1 TTTTTTTTTTACG-AAAAACACAAAACAAATA
10568 TTTTTTTTTTA-GAAAAAC
1 TTTTTTTTTTACGAAAAAC
10586 GCAGACTCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
28 9 0.15
29 9 0.15
30 30 0.51
31 2 0.03
32 9 0.15
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (31 bp):
TTTTTTTTTTACGAAAAACACAAAACAAATA
Found at i:12351 original size:19 final size:18
Alignment explanation
Indices: 12318--12353 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12308 TTGAATTAAA
12318 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
12336 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
12354 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:13968 original size:17 final size:17
Alignment explanation
Indices: 13924--13956 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13914 CAAAAGGTAA
*
13924 AAAATAAAAAACAAAAC
1 AAAACAAAAAACAAAAC
13941 AAAACAAAAAACAAAA
1 AAAACAAAAAACAAAA
13957 AAACTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAACAAAAAACAAAAC
Found at i:14679 original size:50 final size:50
Alignment explanation
Indices: 14604--14751 Score: 242
Period size: 50 Copynumber: 3.0 Consensus size: 50
14594 GTTTTACAAT
*
14604 AAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTTGCTTTTCAAAGTA
1 AAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAGTA
*
14654 AAATTGCTTTCAATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAGTA
1 AAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAGTA
* * * *
14704 AGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 AAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
14752 GACATTGAAG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (50 bp):
AAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAGTA
Found at i:15444 original size:91 final size:88
Alignment explanation
Indices: 15167--15547 Score: 548
Period size: 91 Copynumber: 4.3 Consensus size: 88
15157 TTTTAATCAT
*
15167 AACATCAGACTCAGAGTTATTCTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
1 AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
15232 TCAATCAAGAAGTTTTCAGTTAC
66 TCAATCAAGAAGTTTTCAGTTAC
* *
15255 AACATCAAACTCAGAGTTATTCTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
1 AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
15320 TCAATCAAGAAGTTTTCAGTTAC
66 TCAATCAAGAAGTTTTCAGTTAC
* * * * * * *
15343 AACATTAGACTCAGAGTTATTTTTCAAGTTGTTTTCCAAGTTGACTGCAAATTGATCCTCTTTCA
1 AACATCAGACTCAGAGTTATTTTTCAA---GTTATCAAAATTGACCGCAAATTGGTCCTTTTTCA
15408 TCATCAATCAAGAAGTTTTCAGTTAC
63 TCATCAATCAAGAAGTTTTCAGTTAC
* * * * *
15434 AGCATCAGACTCAGAATTATTTTTCAAGTTGTTTTTC-AAGTTGACCGCACATTGGTCCTTTTTC
1 AACATCAGACTCAGAGTTATTTTTCAA---G-TTATCAAAATTGACCGCAAATTGGTCCTTTTTC
15498 ATCATCAATCAAGAAGTTTTCAGTTAC
62 ATCATCAATCAAGAAGTTTTCAGTTAC
*
15525 AACATCAGATTCAGAGTTATTTT
1 AACATCAGACTCAGAGTTATTTT
15548 CCAAAGGTAT
Statistics
Matches: 269, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
88 111 0.41
91 153 0.57
92 5 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (88 bp):
AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
TCAATCAAGAAGTTTTCAGTTAC
Found at i:15529 original size:182 final size:176
Alignment explanation
Indices: 15167--15547 Score: 548
Period size: 179 Copynumber: 2.1 Consensus size: 176
15157 TTTTAATCAT
* * *
15167 AACATCAGACTCAGAGTTATTCTTCAAGTTATCAAAATTGACCGCAAATTGGTCCTTTTTCATCA
1 AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGATCCTCTTTCATCA
*
15232 TCAATCAAGAAGTTTTCAGTTACAACATCAAACTCAGAGTTATTCTTCAAGTTATCAAAATTGAC
66 TCAATCAAGAAGTTTTCAGTTACAACATCAAACTCAGAATTATTCTTCAAGTTATCAAAATTGAC
15297 CGCAAATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTAC
131 CGCAAATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTAC
* * * * *
15343 AACATTAGACTCAGAGTTATTTTTCAAGTTGTTTTCCAAGTTGACTGCAAATTGATCCTCTTTCA
1 AACATCAGACTCAGAGTTATTTTTCAA---GTTATCAAAATTGACCGCAAATTGATCCTCTTTCA
* * * *
15408 TCATCAATCAAGAAGTTTTCAGTTACAGCATCAGACTCAGAATTATTTTTCAAGTTGTTTTTC-A
63 TCATCAATCAAGAAGTTTTCAGTTACAACATCAAACTCAGAATTATTCTTCAA---G-TTATCAA
* *
15472 AGTTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTAC
124 AATTGACCGCAAATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTAC
*
15525 AACATCAGATTCAGAGTTATTTT
1 AACATCAGACTCAGAGTTATTTT
15548 CCAAAGGTAT
Statistics
Matches: 181, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
176 25 0.14
179 78 0.43
182 74 0.41
183 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (176 bp):
AACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAATTGACCGCAAATTGATCCTCTTTCATCA
TCAATCAAGAAGTTTTCAGTTACAACATCAAACTCAGAATTATTCTTCAAGTTATCAAAATTGAC
CGCAAATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTAC
Found at i:15709 original size:50 final size:50
Alignment explanation
Indices: 15634--15874 Score: 329
Period size: 50 Copynumber: 4.7 Consensus size: 50
15624 AATGCTTTGA
* * *
15634 CTTTTCCATAAGTCAAACTCGTTTCCATACGAATCAATTATCAACATAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
15684 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
** * *
15734 CTTTTCCACAAGCCACGCTCGTTTCCATACGAGTCAATTATAAACATAGA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
* * *
15784 CTTTTCCACAAGCCAAACTCGTTTCCGTACGAGTTAACTATCCAAGCCACGTAGG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAT-CAA--CA--TAGG
* *
15839 CTTTTCCACAAGCCGAACTCGTTTACATACGAGTCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
15875 GTTCAAACAT
Statistics
Matches: 168, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
50 129 0.77
51 2 0.01
53 2 0.01
55 35 0.21
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGG
Found at i:16430 original size:27 final size:27
Alignment explanation
Indices: 16411--16486 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
16401 GCATGTTCAG
16411 GGGCATTTTAGTCATTTGCACATCCAA
1 GGGCATTTTAGTCATTTGCACATCCAA
* * *
16438 GGGCATTTTGGTCATTTTGCACATCTAGG
1 GGGCATTTTAGTCA-TTTGCACATCCA-A
* *
16467 GGGCATTTTGGTCGTTTGCA
1 GGGCATTTTAGTCATTTGCA
16487 GTTTATTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 13 0.30
28 17 0.40
29 13 0.30
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (27 bp):
GGGCATTTTAGTCATTTGCACATCCAA
Found at i:16477 original size:29 final size:27
Alignment explanation
Indices: 16393--16486 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
16383 GGGATTTTGG
** *
16393 GGTCATTTGCATGTTCAGGGGCATTTT
1 GGTCATTTGCACATCCAGGGGCATTTT
* *
16420 AGTCATTTGCACATCCAAGGGCATTTT
1 GGTCATTTGCACATCCAGGGGCATTTT
*
16447 GGTCATTTTGCACATCTAGGGGGCATTTT
1 GGTCA-TTTGCACATCCA-GGGGCATTTT
*
16476 GGTCGTTTGCA
1 GGTCATTTGCA
16487 GTTTATTGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
27 26 0.46
28 17 0.30
29 13 0.23
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (27 bp):
GGTCATTTGCACATCCAGGGGCATTTT
Found at i:17103 original size:19 final size:18
Alignment explanation
Indices: 17079--17114 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17069 TGAAGATTTA
17079 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
17098 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
17115 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:24311 original size:22 final size:23
Alignment explanation
Indices: 24286--24349 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
24276 TTCAAGGAGA
24286 AAATTTGTCGACTAAAGAGAAG-
1 AAATTTGTCGACTAAAGAGAAGC
*
24308 AAATTAGTCGACTAAAG-GAAGC
1 AAATTTGTCGACTAAAGAGAAGC
** *
24330 AAAACTATCGACTAAAGAGA
1 AAATTTGTCGACTAAAGAGA
24350 GGAGCAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 4 0.11
22 29 0.83
23 2 0.06
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.19
Consensus pattern (23 bp):
AAATTTGTCGACTAAAGAGAAGC
Found at i:26018 original size:18 final size:18
Alignment explanation
Indices: 25995--26031 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25985 AAAGGGTAAT
*
25995 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
26013 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
26031 T
1 T
26032 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:28418 original size:2 final size:2
Alignment explanation
Indices: 28411--28440 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28401 CACTGCACAA
28411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28441 TCCATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.