Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022765.1 Corchorus olitorius cultivar O-4 contig22798, 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: 52896
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Found at i:1378 original size:11 final size:11
Alignment explanation
Indices: 1359--1388 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1349 CTACTTTCTA
1359 CTTTCTTCTTT
1 CTTTCTTCTTT
*
1370 CTTTTTTCTTT
1 CTTTCTTCTTT
1381 CTTTCTTC
1 CTTTCTTC
1389 CTCCGTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
CTTTCTTCTTT
Found at i:3750 original size:65 final size:67
Alignment explanation
Indices: 3617--3758 Score: 207
Period size: 65 Copynumber: 2.1 Consensus size: 67
3607 TCGATATGTT
* *
3617 CGTCGATATATCCGAAATCTGTACCCCTCGATATAAATATCCAAAAAAATTTCAATGTCACCGGA
1 CGTCGATATATCCGAAATCTGTACCCCT--ATATAAATATCCAAAAAAATTTCAATATCACCGAA
3682 TATC
64 TATC
* * *
3686 CGTGGATATATCCGATATCTGTACCCCT-TA-ATATATCCAAAAAAATTTCAATATCACCGAATA
1 CGTCGATATATCCGAAATCTGTACCCCTATATAAATATCCAAAAAAATTTCAATATCACCGAATA
3749 TC
66 TC
3751 CGTCGATA
1 CGTCGATA
3759 CATTCGTGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 39 0.58
66 2 0.03
69 26 0.39
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (67 bp):
CGTCGATATATCCGAAATCTGTACCCCTATATAAATATCCAAAAAAATTTCAATATCACCGAATA
TC
Found at i:7545 original size:23 final size:23
Alignment explanation
Indices: 7519--7568 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
7509 GTTTTGGGTT
*
7519 TTTTA-GTTATTTTGGACTTTTAA
1 TTTTATGTTATTTGGGA-TTTTAA
*
7542 TTTTATTTTATTTGGGATTTTAA
1 TTTTATGTTATTTGGGATTTTAA
7565 TTTT
1 TTTT
7569 CTTTATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (23 bp):
TTTTATGTTATTTGGGATTTTAA
Found at i:7545 original size:24 final size:24
Alignment explanation
Indices: 7518--7568 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
7508 TGTTTTGGGT
*
7518 TTTTTA-GTTATTTTGGACTTTTAA
1 TTTTTATGTTATTTGGGA-TTTTAA
*
7542 -TTTTATTTTATTTGGGATTTTAA
1 TTTTTATGTTATTTGGGATTTTAA
7565 TTTT
1 TTTT
7569 CTTTATGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.67
Consensus pattern (24 bp):
TTTTTATGTTATTTGGGATTTTAA
Found at i:8200 original size:14 final size:15
Alignment explanation
Indices: 8181--8209 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8171 AAAATTCAGA
8181 TCAAAAATT-AAAAT
1 TCAAAAATTCAAAAT
8195 TCAAAAATTCAAAAT
1 TCAAAAATTCAAAAT
8210 AACAGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
TCAAAAATTCAAAAT
Found at i:8309 original size:49 final size:49
Alignment explanation
Indices: 8251--8491 Score: 155
Period size: 49 Copynumber: 5.1 Consensus size: 49
8241 CAAACGGAGA
* *
8251 GCGTTAGTTTTTACTTGCTTTTCCCCAAAACGCCATTTCTAGTCGAAAG
1 GCGTTAGTTTTTACTTGCTTTTCCCCAAAACGCCCTTTCCAGTCGAAAG
* * * *
8300 GCGTCAG---TT--TTG-TATTT-CCCAAAACGCCC-CTCCTAGACG-GAG
1 GCGTTAGTTTTTACTTGCT-TTTCCCCAAAACGCCCTTTCC-AGTCGAAAG
* * ** * *
8342 AGCGTTAGTTCTTACTTGATAATCCTCAAAACGCCCTTTCCGGTCGAAAG
1 -GCGTTAGTTTTTACTTGCTTTTCCCCAAAACGCCCTTTCCAGTCGAAAG
* * * * * *
8392 GCG-CAGGTTTTACTTGCTATTACCCAAAACGCCC-CTCCAAGACG-AAG
1 GCGTTAGTTTTTACTTGCTTTTCCCCAAAACGCCCTTTCC-AGTCGAAAG
* * * *
8439 AGCGTTAGTTTTTACTTGTTTTTCCCCAAAACGGCATTTCCGGTCGAAAG
1 -GCGTTAGTTTTTACTTGCTTTTCCCCAAAACGCCCTTTCCAGTCGAAAG
8489 GCG
1 GCG
8492 CGGGTTTTTG
Statistics
Matches: 141, Mismatches: 34, Indels: 34
0.67 0.16 0.16
Matches are distributed among these distances:
42 4 0.03
43 22 0.16
44 6 0.04
46 4 0.03
47 6 0.04
48 34 0.24
49 54 0.38
50 11 0.08
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (49 bp):
GCGTTAGTTTTTACTTGCTTTTCCCCAAAACGCCCTTTCCAGTCGAAAG
Found at i:8372 original size:92 final size:91
Alignment explanation
Indices: 8212--8492 Score: 348
Period size: 92 Copynumber: 3.0 Consensus size: 91
8202 TTCAAAATAA
* * *
8212 CAGTTTTGTATTTTCCAAAACGCCCTTCCCAA-ACGGAGAGCGTTAGTTTTTACTTGCTTTTCCC
1 CAGTTTTGTATTTCCCAAAACGCCCCT-CCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCC
**
8276 CAAAACGCCATTTCTAGTCGAAAGGCG
65 CAAAACGCCATTTCCGGTCGAAAGGCG
* * ** *
8303 TCAGTTTTGTATTTCCCAAAACGCCCCTCCTAGACGGAGAGCGTTAGTTCTTACTTGATAATCCT
1 -CAGTTTTGTATTTCCCAAAACGCCCCTCCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCC
*
8368 CAAAACGCCCTTTCCGGTCGAAAGGCG
65 CAAAACGCCATTTCCGGTCGAAAGGCG
* * *
8395 CAGGTTTTACTTGCTATTACCCAAAACGCCCCTCCAAGACGAAGAGCGTTAGTTTTTACTTGTTT
1 CA-G--TT--TTG-TATTTCCCAAAACGCCCCTCCAAGACGGAGAGCGTTAGTTTTTACTTGATT
*
8460 TTCCCCAAAACGGCATTTCCGGTCGAAAGGCG
60 TTCCCCAAAACGCCATTTCCGGTCGAAAGGCG
8492 C
1 C
8493 GGGTTTTTGC
Statistics
Matches: 161, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
91 5 0.03
92 77 0.48
94 2 0.01
96 3 0.02
97 74 0.46
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (91 bp):
CAGTTTTGTATTTCCCAAAACGCCCCTCCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCCC
AAAACGCCATTTCCGGTCGAAAGGCG
Found at i:8447 original size:97 final size:94
Alignment explanation
Indices: 8215--8500 Score: 346
Period size: 97 Copynumber: 3.0 Consensus size: 94
8205 AAAATAACAG
** * *
8215 TTTTGTATTTTCCAAAACGCCCTTCCCAA-ACGGAGAGCGTTAGTTTTTACTTGCTTTTCCCCAA
1 TTTTGTATTACCCAAAACGCCCCT-CCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCCCAA
**
8279 AACGCCATTTCTAGTCGAAAGGCGTCA-G--
65 AACGCCATTTCCGGTCGAAAGGCG-CAGGTT
* * * ** *
8307 TTTTGTATTTCCCAAAACGCCCCTCCTAGACGGAGAGCGTTAGTTCTTACTTGATAATCCTCAAA
1 TTTTGTATTACCCAAAACGCCCCTCCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCCCAAA
*
8372 ACGCCCTTTCCGGTCGAAAGGCGCAGGTT
66 ACGCCATTTCCGGTCGAAAGGCGCAGGTT
* *
8401 TTACTTGCTATTACCCAAAACGCCCCTCCAAGACGAAGAGCGTTAGTTTTTACTTGTTTTTCCCC
1 TT--TTG-TATTACCCAAAACGCCCCTCCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCCC
* *
8466 AAAACGGCATTTCCGGTCGAAAGGCGCGGGTT
63 AAAACGCCATTTCCGGTCGAAAGGCGCAGGTT
8498 TTT
1 TTT
8501 GCTTATATTT
Statistics
Matches: 165, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
91 5 0.03
92 74 0.45
94 2 0.01
95 1 0.01
96 3 0.02
97 80 0.48
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (94 bp):
TTTTGTATTACCCAAAACGCCCCTCCAAGACGGAGAGCGTTAGTTTTTACTTGATTTTCCCCAAA
ACGCCATTTCCGGTCGAAAGGCGCAGGTT
Found at i:8581 original size:47 final size:47
Alignment explanation
Indices: 8508--8821 Score: 423
Period size: 47 Copynumber: 6.7 Consensus size: 47
8498 TTTGCTTATA
* *
8508 TTTCCCAAAATGCCCTT-CTGGTCGGAAGGTGCCAGTTTTCTTTACT
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
*
8554 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGTCAGTTTTCTTTACT
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
* * * * *
8601 CTCCCCAAAATGCCCTTCCCGATCGGAAGGTGTCAGTTTTCTTTACT
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
* * * *
8648 TTTCCAAAAATGCCCTTCTCGGTCGAAAGGTGTCAATTTTCTTTACT
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
* * * *
8695 TTTCCAAAAATGCCCTTCTCAGTCGGAAGATGCCAGTTTTCTTTGCT
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
* * **
8742 TTTCCAAAAATTCCCTTCCCAGTCGGAAGGTGCCAACTTTCTTTACT
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
* *
8789 TTTCCCAAAATGCCCTTCCCGGTTGGAAGGTGC
1 TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGC
8822 ACATTTGACT
Statistics
Matches: 237, Mismatches: 30, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
46 16 0.07
47 221 0.93
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (47 bp):
TTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGCCAGTTTTCTTTACT
Found at i:12520 original size:27 final size:27
Alignment explanation
Indices: 12490--12553 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
12480 ATGTGGCGCC
*
12490 ACCCCAAGTGGCCGCGCTTCATCCGCA
1 ACCCCAAGTGGCCACGCTTCATCCGCA
12517 ACCCCAAGTGGCCACGCTTCATCCGCA
1 ACCCCAAGTGGCCACGCTTCATCCGCA
12544 ACCCCAAGTG
1 ACCCCAAGTG
12554 AATGGCCGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.44, G:0.20, T:0.14
Consensus pattern (27 bp):
ACCCCAAGTGGCCACGCTTCATCCGCA
Found at i:12659 original size:18 final size:15
Alignment explanation
Indices: 12613--12708 Score: 84
Period size: 15 Copynumber: 6.0 Consensus size: 15
12603 AAAAATTGGC
12613 ACCGTTTCAGAAACA
1 ACCGTTTCAGAAACA
* *
12628 ACCGTTGCAAAAACA
1 ACCGTTTCAGAAACA
12643 TCATCCGTTTCAGAAACA
1 --A-CCGTTTCAGAAACA
* *
12661 ACCGTTGCAAAAACA
1 ACCGTTTCAGAAACA
12676 TCATCCGTTTCAGAAACA
1 --A-CCGTTTCAGAAACA
* *
12694 ACCATTGCAGAAACA
1 ACCGTTTCAGAAACA
12709 CCATCTGGTG
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
15 37 0.57
16 2 0.03
17 2 0.03
18 24 0.37
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (15 bp):
ACCGTTTCAGAAACA
Found at i:12724 original size:33 final size:33
Alignment explanation
Indices: 12614--12713 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
12604 AAAATTGGCA
12614 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
1 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
12647 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
1 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
* * *
12680 CCGTTTCAGAAACAACCATTGCAGAAACACCAT
1 CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
12713 C
1 C
12714 TGGTGCAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (33 bp):
CCGTTTCAGAAACAACCGTTGCAAAAACATCAT
Found at i:29332 original size:18 final size:18
Alignment explanation
Indices: 29309--29345 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29299 AGATAAACAT
29309 TCAACTTGAAACCCCTCA
1 TCAACTTGAAACCCCTCA
29327 TCAACTTGAAACCCCTCA
1 TCAACTTGAAACCCCTCA
29345 T
1 T
29346 ACAAAGGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.38, G:0.05, T:0.24
Consensus pattern (18 bp):
TCAACTTGAAACCCCTCA
Found at i:46682 original size:30 final size:30
Alignment explanation
Indices: 46646--46705 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
46636 AAGCCTAGAA
46646 GTCATGGAACTTCAATTGCAAAGTTCGTTT
1 GTCATGGAACTTCAATTGCAAAGTTCGTTT
46676 GTCATGGAACTTCAATTGCAAAGTTCGTTT
1 GTCATGGAACTTCAATTGCAAAGTTCGTTT
46706 CCGTTTCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (30 bp):
GTCATGGAACTTCAATTGCAAAGTTCGTTT
Found at i:52209 original size:18 final size:18
Alignment explanation
Indices: 52168--52213 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
52158 CACTAGAAAT
*
52168 TTAATAATAATTATTCAA
1 TTAATAATTATTATTCAA
** *
52186 AAAATAATTATTATTTAA
1 TTAATAATTATTATTCAA
52204 TTAATAATTA
1 TTAATAATTA
52214 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATAATTATTATTCAA
Done.