Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022401.1 Corchorus olitorius cultivar O-4 contig22434, 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: 95603
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6536 original size:22 final size:22
Alignment explanation
Indices: 6511--6557 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
6501 AAAGTTTTAC
6511 AAAGAT-ATATATTATA-TAAAGA
1 AAAGATAATA-ATT-TAGTAAAGA
*
6533 AAAGGTAATAATTTAGTAAAGA
1 AAAGATAATAATTTAGTAAAGA
6555 AAA
1 AAA
6558 ATTAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 2 0.09
22 17 0.77
23 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (22 bp):
AAAGATAATAATTTAGTAAAGA
Found at i:6567 original size:22 final size:22
Alignment explanation
Indices: 6527--6569 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6517 ATATATTATA
* *
6527 TAAAGAAAAGGTAATAATTTAG
1 TAAAGAAAAAGTAAAAATTTAG
*
6549 TAAAGAAAAATTAAAAATTTA
1 TAAAGAAAAAGTAAAAATTTA
6570 CAGTTTCATC
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:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAAGAAAAAGTAAAAATTTAG
Found at i:7313 original size:13 final size:13
Alignment explanation
Indices: 7292--7327 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
7282 GATAATTCTT
7292 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
7305 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
7318 CTTGACCCTC
1 TTTGACCCTC
7328 ATAATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.42, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:7389 original size:40 final size:40
Alignment explanation
Indices: 7329--7407 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
7319 TTGACCCTCA
* *
7329 TAATAATTAAGGAAATAAATTAAATCTAGGTTTAGCCCCC
1 TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCCC
*
7369 TAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCC
1 TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
7408 TAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (40 bp):
TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCCC
Found at i:8562 original size:18 final size:16
Alignment explanation
Indices: 8541--8633 Score: 68
Period size: 18 Copynumber: 5.7 Consensus size: 16
8531 TTAAGGTAAT
8541 TTCTTAGTTTAGGTTGAA
1 TTCTTA-TTTAGGTTG-A
* *
8559 TTCTCATTTA-GAT-A
1 TTCTTATTTAGGTTGA
8573 TTCTTAGTTTAGGTTGGA
1 TTCTTA-TTTAGGTT-GA
* *
8591 TTCTCATTTA-GAT-A
1 TTCTTATTTAGGTTGA
8605 TTCTTAGTTTAGGTTGGA
1 TTCTTA-TTTAGGTT-GA
8623 TTCTTATTTAG
1 TTCTTATTTAG
8634 ATATTTGGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
14 12 0.20
15 8 0.14
16 8 0.14
17 13 0.22
18 18 0.31
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.52
Consensus pattern (16 bp):
TTCTTATTTAGGTTGA
Found at i:8568 original size:17 final size:16
Alignment explanation
Indices: 8548--8633 Score: 54
Period size: 17 Copynumber: 5.3 Consensus size: 16
8538 AATTTCTTAG
8548 TTTAGGTTGAATTCTCA
1 TTTAGGTTG-ATTCTCA
* *
8565 TTTA-GAT-ATTCTTA
1 TTTAGGTTGATTCTCA
8579 GTTTAGGTTGGATTCTCA
1 -TTTAGGTT-GATTCTCA
* *
8597 TTTA-GAT-ATTCTTA
1 TTTAGGTTGATTCTCA
*
8611 GTTTAGGTTGGATTCTTA
1 -TTTAGGTT-GATTCTCA
8629 TTTAG
1 TTTAG
8634 ATATTTGGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
14 12 0.22
15 8 0.15
16 8 0.15
17 13 0.24
18 13 0.24
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (16 bp):
TTTAGGTTGATTCTCA
Found at i:8578 original size:32 final size:32
Alignment explanation
Indices: 8541--8638 Score: 178
Period size: 32 Copynumber: 3.1 Consensus size: 32
8531 TTAAGGTAAT
*
8541 TTCTTAGTTTAGGTTGAATTCTCATTTAGATA
1 TTCTTAGTTTAGGTTGGATTCTCATTTAGATA
8573 TTCTTAGTTTAGGTTGGATTCTCATTTAGATA
1 TTCTTAGTTTAGGTTGGATTCTCATTTAGATA
*
8605 TTCTTAGTTTAGGTTGGATTCTTATTTAGATA
1 TTCTTAGTTTAGGTTGGATTCTCATTTAGATA
8637 TT
1 TT
8639 TGGGTATATG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.52
Consensus pattern (32 bp):
TTCTTAGTTTAGGTTGGATTCTCATTTAGATA
Found at i:9163 original size:61 final size:61
Alignment explanation
Indices: 9088--9207 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
9078 TCTGGTCATC
* *
9088 ACACTGAATTCGTTATAAAACTCGAATCTTGAATGCTATTTAGGGACATCGATCTCCTTAA
1 ACACTGAATTCGTTACAAAACTCGAATCTTGAATGCTATTTAGAGACATCGATCTCCTTAA
* *
9149 ACACTGGATTCGTTACAAAACTCGAGTCTTGAATGCTATTTAGAGACATCGATCTCCTT
1 ACACTGAATTCGTTACAAAACTCGAATCTTGAATGCTATTTAGAGACATCGATCTCCTT
9208 CCATTCAGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (61 bp):
ACACTGAATTCGTTACAAAACTCGAATCTTGAATGCTATTTAGAGACATCGATCTCCTTAA
Found at i:9422 original size:14 final size:14
Alignment explanation
Indices: 9403--9435 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
9393 ATTACCAAGT
9403 CTTTCAACATTTTA
1 CTTTCAACATTTTA
9417 CTTTCAACATTTTA
1 CTTTCAACATTTTA
9431 CTTTC
1 CTTTC
9436 CGACCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (14 bp):
CTTTCAACATTTTA
Found at i:14082 original size:122 final size:122
Alignment explanation
Indices: 13865--14093 Score: 343
Period size: 122 Copynumber: 1.9 Consensus size: 122
13855 TATATACAAA
* ** ** * * *
13865 TAAATTACCGTAGTTTCTTTTTTCTTCTATAAATCACATATATCGGCGTATATATTGGTATCTGT
1 TAAATTACCGTAGTTTATTCATTCTTCTATAAATCACATATATCGGCACATATATTAGCATCCGT
13930 TTTAACGGTTTTACGAATAATTCTCTTCGAATCGGGTTAATTAGTTTACTATATGAG
66 TTTAACGGTTTTACGAATAATTCTCTTCGAATCGGGTTAATTAGTTTACTATATGAG
*
13987 TAAATTACCGTAGTTTATTCATTCTTGTTATAAATCACATATATCGGCACATATATTAGCATCCG
1 TAAATTACCGTAGTTTATTCATTCTT-CTATAAATCACATATATCGGCACATATATTAGCATCCG
* *
14052 TTTTAACGG-TTTACGAATAATTTTGTTCGAATCGGGTTAATT
65 TTTTAACGGTTTTACGAATAATTCTCTTCGAATCGGGTTAATT
14094 CACTGTAAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
122 54 0.57
123 41 0.43
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43
Consensus pattern (122 bp):
TAAATTACCGTAGTTTATTCATTCTTCTATAAATCACATATATCGGCACATATATTAGCATCCGT
TTTAACGGTTTTACGAATAATTCTCTTCGAATCGGGTTAATTAGTTTACTATATGAG
Found at i:23597 original size:3 final size:3
Alignment explanation
Indices: 23591--23620 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
23581 AATGGATAAG
23591 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
23621 AACGGCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24343 original size:2 final size:2
Alignment explanation
Indices: 24336--24360 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24326 TCGTTAGACC
24336 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24361 ACATATTGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24560 original size:28 final size:28
Alignment explanation
Indices: 24528--24582 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
24518 GTACCTAACT
* *
24528 TGGAAAGTATTTCTATTAGATTTGCTAA
1 TGGAAAGTATTTATATCAGATTTGCTAA
*
24556 TGGAAAGTATTTATGTCAGATTTGCTA
1 TGGAAAGTATTTATATCAGATTTGCTA
24583 TTGTTTGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (28 bp):
TGGAAAGTATTTATATCAGATTTGCTAA
Found at i:27224 original size:6 final size:6
Alignment explanation
Indices: 27175--27221 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
27165 TGAATGATAA
* *
27175 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTA TCTCTG TCTCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
27222 GTCATGTCGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.62
Consensus pattern (6 bp):
TCTCTT
Found at i:33001 original size:28 final size:30
Alignment explanation
Indices: 32930--33004 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
32920 CGTTTGAGAG
*
32930 GGGGCAAAACGTCCAAAATTGAGAGTTTAT
1 GGGGCAAAACGTCCAAAATTGAGAGTTCAT
*
32960 GGGGCAAAATGTCCAAAATT-AGAGTTCA-
1 GGGGCAAAACGTCCAAAATTGAGAGTTCAT
32988 GGGGCAAAACGTCCAAA
1 GGGGCAAAACGTCCAAA
33005 CGCTACAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 16 0.38
29 7 0.17
30 19 0.45
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (30 bp):
GGGGCAAAACGTCCAAAATTGAGAGTTCAT
Found at i:52630 original size:19 final size:19
Alignment explanation
Indices: 52606--52663 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
52596 CTGTTTAGCA
*
52606 ACTGTACATATGAGATTAC
1 ACTGTACAAATGAGATTAC
* *
52625 ACTGTACAAATTAGATTAGAT
1 ACTGTACAAATGAGATT--AC
52646 ACTGTACAAATGAGATTA
1 ACTGTACAAATGAGATTA
52664 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAC
Found at i:55471 original size:7 final size:7
Alignment explanation
Indices: 55455--55485 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
55445 AAGATGATTG
*
55455 CAGCAGC
1 CAGCACC
55462 CAGCACC
1 CAGCACC
55469 CAGCACC
1 CAGCACC
55476 CAGCACC
1 CAGCACC
55483 CAG
1 CAG
55486 TAGGCATGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.52, G:0.19, T:0.00
Consensus pattern (7 bp):
CAGCACC
Found at i:62018 original size:45 final size:45
Alignment explanation
Indices: 61969--62064 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
61959 CTGGATATCC
61969 TCCTCCTGCCCAGTACCCTCCAGCTGCTTACCCACCATCCGGCTA
1 TCCTCCTGCCCAGTACCCTCCAGCTGCTTACCCACCATCCGGCTA
*
62014 TCCTCCTGCCCAGTACCCTCCAGCTGCTTACCCGCCATCCGGCTA
1 TCCTCCTGCCCAGTACCCTCCAGCTGCTTACCCACCATCCGGCTA
62059 TCCTCC
1 TCCTCC
62065 CAAGTAATAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.14, C:0.50, G:0.14, T:0.23
Consensus pattern (45 bp):
TCCTCCTGCCCAGTACCCTCCAGCTGCTTACCCACCATCCGGCTA
Found at i:64705 original size:19 final size:19
Alignment explanation
Indices: 64681--64738 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
64671 CTGTTTAGCA
*
64681 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
64700 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
64721 ACTATACAGATGAGATTA
1 ACTGTACAGATGAGATTA
64739 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:65390 original size:6 final size:6
Alignment explanation
Indices: 65376--65409 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
65366 TATAAAAGGG
*
65376 AAAATT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
65410 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:66455 original size:82 final size:82
Alignment explanation
Indices: 66318--66481 Score: 258
Period size: 82 Copynumber: 2.0 Consensus size: 82
66308 GTATCGAGTT
* * * *
66318 TGAGTCTTGTAAGTTGAGAAAACAATTAGTTCTGGAAGACTTTTCCCTCAATTGAATTCCGGCAC
1 TGAGTCTTGTAAATTGAGAAAACAATTAGCTCTGGAAGACTTTTCCCTCAATTGAATCCCGACAC
66383 GCCTCGATACAGGATTA
66 GCCTCGATACAGGATTA
*
66400 TGAGTCTTGTAAATTGAGAAAATAATTAGCTCTAGG-AGACTTTTCCCTCAATTGAATCCCGACA
1 TGAGTCTTGTAAATTGAGAAAACAATTAGCTCT-GGAAGACTTTTCCCTCAATTGAATCCCGACA
*
66464 CGCCTCGATTCAGGATTA
65 CGCCTCGATACAGGATTA
66482 GTCAGGTCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
82 73 0.97
83 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (82 bp):
TGAGTCTTGTAAATTGAGAAAACAATTAGCTCTGGAAGACTTTTCCCTCAATTGAATCCCGACAC
GCCTCGATACAGGATTA
Found at i:70787 original size:19 final size:20
Alignment explanation
Indices: 70763--70820 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
70753 CGATTTAGTA
70763 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* * *
70782 ACTGTACATATTAGATTAAGT
1 ACTGTACAGATGAGATT-AGC
*
70803 ACTATACAGATGAGATTA
1 ACTGTACAGATGAGATTA
70821 TTAGACCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 15 0.48
20 2 0.06
21 14 0.45
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:70818 original size:21 final size:20
Alignment explanation
Indices: 70767--70820 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
70757 TTAGTAACTG
*
70767 TACAGATGAGATT-ACACTG
1 TACAGATGAGATTAACACTA
* * *
70786 TACATATTAGATTAAGTACTA
1 TACAGATGAGATTAA-CACTA
70807 TACAGATGAGATTA
1 TACAGATGAGATTA
70821 TTAGACCAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 15 0.56
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
TACAGATGAGATTAACACTA
Found at i:72097 original size:2 final size:2
Alignment explanation
Indices: 72060--72086 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72050 GTTAGTTTAC
72060 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
72087 ACCATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84002 original size:12 final size:12
Alignment explanation
Indices: 83981--84010 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
83971 TTTCATGGCA
83981 ACAACAACAACT
1 ACAACAACAACT
*
83993 ACAACTACAACT
1 ACAACAACAACT
84005 ACAACA
1 ACAACA
84011 TCAATTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.33, G:0.00, T:0.10
Consensus pattern (12 bp):
ACAACAACAACT
Found at i:93512 original size:19 final size:18
Alignment explanation
Indices: 93470--93512 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
93460 GCCAAATGCA
* *
93470 TTTTTTTTTATATATTTT
1 TTTTTTATTATATATTTG
93488 TATTTTTATTATATACTTTG
1 T-TTTTTATTATATA-TTTG
93508 TTTTT
1 TTTTT
93513 CTGGTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTATTATATATTTG
Done.