Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023245.1 Corchorus olitorius cultivar O-4 contig23278, 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: 17973
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1861 original size:12 final size:13
Alignment explanation
Indices: 1843--1872 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1833 GTTTTCTTTA
1843 ATTTTCTTGATTG
1 ATTTTCTTGATTG
1856 -TTTTCTTGATTG
1 ATTTTCTTGATTG
1868 ATTTT
1 ATTTT
1873 AATTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:7916 original size:151 final size:151
Alignment explanation
Indices: 7514--7999 Score: 783
Period size: 151 Copynumber: 3.2 Consensus size: 151
7504 CAGATGTGCT
* *
7514 TGTCCCACTGGGCATGCCAAAAAGAGATGTTGGTGCGGCCGAGTCGGCAGTCCAACGTAGCACGA
1 TGTCCCACTGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGCAGTCCAACGTAGCACGA
* * * *
7579 AAAATTGAGAAAAGAGTCGGGGATTGCCGACTTTGAGAGAGAGAGAGCTTATGGAGACGTCGAGT
66 AAAATTGAGAAGAGAGTCGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACGCCGAGT
7644 TGAGAAGACAGGATATTGATG
131 TGAGAAGACAGGATATTGATG
7665 TGTCCCACTGGGCGTGCCAAAAAAGAGATGTTGGTGCGGCCGAGTGGGCAGTCCAACGTAGCACG
1 TGTCCCACTGGGCGTGCC-AAAAAGAGATGTTGGTGCGGCCGAGTGGGCAGTCCAACGTAGCACG
* *
7730 TAAAATTGAGAAGAGAGTAGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACGCCGAG
65 AAAAATTGAGAAGAGAGTCGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACGCCGAG
* *
7795 TTGAGAAGACAAGATATTGTTG
130 TTGAGAAGACAGGATATTGATG
* * * * *
7817 TGTTCCATTGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGCAGTACAACGTAGAACGG
1 TGTCCCACTGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGCAGTCCAACGTAGCACGA
*
7882 AAAATTGAGAAGAGAGTCGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACACCGAGT
66 AAAATTGAGAAGAGAGTCGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACGCCGAGT
*
7947 TGAGAAGACAGGATATTGCTG
131 TGAGAAGACAGGATATTGATG
** *
7968 TGTCCCACCAGGAGTGCCAAAAAGAGATGTTG
1 TGTCCCACTGGGCGTGCCAAAAAGAGATGTTG
8000 CGCCAAAAAT
Statistics
Matches: 310, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 170 0.55
152 140 0.45
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.19
Consensus pattern (151 bp):
TGTCCCACTGGGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTGGGCAGTCCAACGTAGCACGA
AAAATTGAGAAGAGAGTCGGGGATCGCCGACTTTGAGAGAGAGAAAGCTTATGGAGACGCCGAGT
TGAGAAGACAGGATATTGATG
Found at i:9787 original size:11 final size:11
Alignment explanation
Indices: 9767--9819 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
9757 TGTGAGATTT
9767 TTAA-TAATAA
1 TTAATTAATAA
*
9777 TTATTTAATAAA
1 TTAATTAAT-AA
* * *
9789 ATAATTACTAT
1 TTAATTAATAA
9800 TTAATTAATAA
1 TTAATTAATAA
9811 TTAATTAAT
1 TTAATTAAT
9820 TTCAGTCCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 3 0.09
11 22 0.67
12 8 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:9793 original size:19 final size:18
Alignment explanation
Indices: 9769--9817 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
9759 TGAGATTTTT
9769 AATAATAATTATTTAATAA
1 AATAATAATTATTTAAT-A
* * *
9788 AATAATTACTATTTAATT
1 AATAATAATTATTTAATA
9806 AATAATTAATTA
1 AATAA-TAATTA
9818 ATTTCAGTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAATAATTATTTAATA
Found at i:13440 original size:15 final size:17
Alignment explanation
Indices: 13420--13454 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13410 CGCTCAAATG
13420 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
13435 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
13452 TCG
1 TCG
13455 ATCGCTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.09, C:0.17, G:0.37, T:0.37
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:14279 original size:21 final size:22
Alignment explanation
Indices: 14255--14298 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
14245 TATTTATTAC
*
14255 TTTAAAATATATATATA-TATA
1 TTTAAAATATACATATATTATA
* *
14276 TTTATAGTATACATATATTATA
1 TTTAAAATATACATATATTATA
14298 T
1 T
14299 AAGAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAAATATACATATATTATA
Found at i:15105 original size:16 final size:17
Alignment explanation
Indices: 15077--15121 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
15067 GTCGAATTGA
*
15077 TCGGGTTCAGGTCATTT
1 TCGGGTTCGGGTCATTT
*
15094 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
15110 TCGGGTTCGGGT
1 TCGGGTTCGGGT
15122 ACCCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:16193 original size:26 final size:26
Alignment explanation
Indices: 16157--16370 Score: 128
Period size: 25 Copynumber: 7.8 Consensus size: 26
16147 ATTTTACCAA
16157 TTACTCTTTAATTACCCAATTTCATT
1 TTACTCTTTAATTACCCAATTTCATT
* * *
16183 TTACTTTTTAATTACCAAGTTGACCGATTTCCTTT
1 TTACTCTTTAATTA-C-------CCAATTT-CATT
* * * * *
16218 TTACTCTTTGATTGCCAAATTTTACT
1 TTACTCTTTAATTACCCAATTTCATT
*
16244 TTACTCTTTAATTA-CCAAATTCATT
1 TTACTCTTTAATTACCCAATTTCATT
* **
16269 TTACT-TCTTAATTACCAAATTTTACAAA
1 TTACTCT-TTAATTACCCAA-TTT-CATT
* * *
16297 TTACTCTCTAATTATCTAA-TTCATT
1 TTACTCTTTAATTACCCAATTTCATT
16322 TTACTCTTTAATTATCCCAATTTCATT
1 TTACTCTTTAATTA-CCCAATTTCATT
* *
16349 TTACTTTCTTAATTACCAAATT
1 TTACTCT-TTAATTACCCAATT
16371 AACCGATTTC
Statistics
Matches: 140, Mismatches: 31, Indels: 33
0.69 0.15 0.16
Matches are distributed among these distances:
24 1 0.01
25 34 0.24
26 34 0.24
27 26 0.19
28 23 0.16
29 1 0.01
34 7 0.05
35 14 0.10
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (26 bp):
TTACTCTTTAATTACCCAATTTCATT
Found at i:16271 original size:25 final size:25
Alignment explanation
Indices: 16216--16370 Score: 132
Period size: 25 Copynumber: 5.9 Consensus size: 25
16206 CCGATTTCCT
* * *
16216 TTTTACTCTTTGATTGCCAAATTTTA
1 TTTTACTCTTTAATTACCAAA-TTCA
*
16242 CTTTACTCTTTAATTACCAAATTCA
1 TTTTACTCTTTAATTACCAAATTCA
16267 TTTTACT-TCTTAATTACCAAATTTTACA
1 TTTTACTCT-TTAATTACCAAA--TT-CA
** * * *
16295 AATTACTCTCTAATTATCTAATTCA
1 TTTTACTCTTTAATTACCAAATTCA
*
16320 TTTTACTCTTTAATTATCCCAATTTCA
1 TTTTACTCTTTAATTA--CCAAATTCA
*
16347 TTTTACTTTCTTAATTACCAAATT
1 TTTTACTCT-TTAATTACCAAATT
16371 AACCGATTTC
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
24 1 0.01
25 36 0.35
26 26 0.25
27 16 0.16
28 23 0.22
29 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.01, T:0.50
Consensus pattern (25 bp):
TTTTACTCTTTAATTACCAAATTCA
Found at i:16318 original size:53 final size:52
Alignment explanation
Indices: 16216--16370 Score: 154
Period size: 53 Copynumber: 3.0 Consensus size: 52
16206 CCGATTTCCT
* * * *
16216 TTTTACTCTTTGATT-GCCAAATTTTACTTTACTCTTTAATTACCAAATTCA
1 TTTTACTCTTTAATTATCCAAATTTTACATTACTCTCTAATTACCAAATTCA
* *
16267 TTTTACT-TCTTAATTA-CCAAATTTTACAAATTACTCTCTAATTATCTAATTCA
1 TTTTACTCT-TTAATTATCCAAATTTTAC--ATTACTCTCTAATTACCAAATTCA
* * ** *
16320 TTTTACTCTTTAATTATCCCAATTTCATTTTACTTTCTTAATTACCAAATT
1 TTTTACTCTTTAATTATCCAAATTTTACATTACTCTC-TAATTACCAAATT
16371 AACCGATTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
50 1 0.01
51 23 0.27
52 7 0.08
53 45 0.53
54 9 0.11
ACGTcount: A:0.30, C:0.19, G:0.01, T:0.50
Consensus pattern (52 bp):
TTTTACTCTTTAATTATCCAAATTTTACATTACTCTCTAATTACCAAATTCA
Found at i:16414 original size:52 final size:51
Alignment explanation
Indices: 16352--16526 Score: 260
Period size: 52 Copynumber: 3.4 Consensus size: 51
16342 TTTCATTTTA
*
16352 CTTTCTTAATTACCAAATTAACCGATTTCCTTTCACTCTTTAATTACCAAATT
1 CTTT-TTAATTACCAAATTAACCAATTTCCTTT-ACTCTTTAATTACCAAATT
*
16405 CTTTTTAATTACCAAATTAACCAATTTACTTTTACTCTTTAATTACCAAATT
1 CTTTTTAATTACCAAATTAACCAATTT-CCTTTACTCTTTAATTACCAAATT
* * **
16457 CTTTTTACTTACCAAATTAACCAATTTCCTTGTACTCTTTATTTATAAAATT
1 CTTTTTAATTACCAAATTAACCAATTTCCTT-TACTCTTTAATTACCAAATT
16509 CTTTTTAATTACCAAATT
1 CTTTTTAATTACCAAATT
16527 CTTTTTTCTT
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
51 3 0.03
52 101 0.90
53 8 0.07
ACGTcount: A:0.32, C:0.21, G:0.01, T:0.46
Consensus pattern (51 bp):
CTTTTTAATTACCAAATTAACCAATTTCCTTTACTCTTTAATTACCAAATT
Found at i:16482 original size:26 final size:26
Alignment explanation
Indices: 16393--16480 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
16383 TTCACTCTTT
*
16393 AATTACCAAATTCTTTTTAATTACCA
1 AATTACCAAATTCTTTTTACTTACCA
* **
16419 AATTAACCAATTTAC-TTTTAC-T-CTTT
1 AATT-ACCAAATT-CTTTTTACTTAC-CA
16445 AATTACCAAATTCTTTTTACTTACCA
1 AATTACCAAATTCTTTTTACTTACCA
16471 AATTAACCAA
1 AATT-ACCAA
16481 TTTCCTTGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
24 1 0.02
25 14 0.29
26 14 0.29
27 18 0.38
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTACCAAATTCTTTTTACTTACCA
Found at i:16516 original size:70 final size:70
Alignment explanation
Indices: 16442--16611 Score: 268
Period size: 70 Copynumber: 2.4 Consensus size: 70
16432 ACTTTTACTC
*
16442 TTTAATTACCAAATTCTTTTTACTTACCAAATTAACCAATTTCCTTGTACTCTTTATTTATAAAA
1 TTTAATTACCAAATTCTTTTTACTTACCAAATTAACCAATTTCCTTGTACTCTTTATTTACAAAA
16507 TTCTT
66 TTCTT
* * * * *
16512 TTTAATTACCAAATTCTTTTTTCTTGCCAAATTAACCAATTTTCTTTTACTCTTTATTTACCAAA
1 TTTAATTACCAAATTCTTTTTACTTACCAAATTAACCAATTTCCTTGTACTCTTTATTTACAAAA
16577 TTCTT
66 TTCTT
* *
16582 TTTACTTACCAAATTCTTTTTAATTACCAA
1 TTTAATTACCAAATTCTTTTTACTTACCAA
16612 TTTACTTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 90 1.00
ACGTcount: A:0.30, C:0.19, G:0.01, T:0.49
Consensus pattern (70 bp):
TTTAATTACCAAATTCTTTTTACTTACCAAATTAACCAATTTCCTTGTACTCTTTATTTACAAAA
TTCTT
Found at i:16607 original size:62 final size:64
Alignment explanation
Indices: 16541--16665 Score: 166
Period size: 62 Copynumber: 2.0 Consensus size: 64
16531 TTTCTTGCCA
* * * * *
16541 AATTAACCAATTTTC-TTTTACTCTTTATTTACCAAATTC-TTTTTACTTACCAAATT-CTTTTT
1 AATT-ACCAATTTACTTTTTAATCTTGAATTACCAAATTCTTTTTTAATTACCAAATTACTTTTT
*
16603 AATTACCAATTTACTTTTTAATCTTGAATTACCAAATTCTTTTTTAATTACCAATTTACTTTT
1 AATTACCAATTTACTTTTTAATCTTGAATTACCAAATTCTTTTTTAATTACCAAATTACTTTT
16666 AGTTTTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
61 9 0.17
62 25 0.46
63 15 0.28
64 5 0.09
ACGTcount: A:0.30, C:0.18, G:0.01, T:0.52
Consensus pattern (64 bp):
AATTACCAATTTACTTTTTAATCTTGAATTACCAAATTCTTTTTTAATTACCAAATTACTTTTT
Found at i:16619 original size:19 final size:18
Alignment explanation
Indices: 16564--16624 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
16554 TCTTTTACTC
*
16564 TTTATTTACCAAATTCTT
1 TTTAATTACCAAATTCTT
*
16582 TTTACTTACCAAATTCTT
1 TTTAATTACCAAATTCTT
*
16600 TTTAATTACCAATTTACTT
1 TTTAATTACCAAATT-CTT
16619 TTTAAT
1 TTTAAT
16625 CTTGAATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 30 0.77
19 9 0.23
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATTACCAAATTCTT
Found at i:16698 original size:47 final size:45
Alignment explanation
Indices: 16580--16713 Score: 189
Period size: 47 Copynumber: 2.9 Consensus size: 45
16570 TACCAAATTC
*
16580 TTTTTACTTACCAAATTCTTTTTAATTACCAATTTACTTTT-TAA
1 TTTTTAATTACCAAATTCTTTTTAATTACCAATTTACTTTTATAA
* * **
16624 TCTTGAATTACCAAATTCTTTTTTAATTACCAATTTACTTTTAGTTT
1 TTTTTAATTACCAAATTC-TTTTTAATTACCAATTTACTTTTA-TAA
16671 TTTTTAATTACCAAATTTCTTTTTAATTACCAATTTACTTTTA
1 TTTTTAATTACCAAA-TTCTTTTTAATTACCAATTTACTTTTA
16714 CTCTTTAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
44 15 0.19
45 23 0.29
47 38 0.48
48 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.01, T:0.54
Consensus pattern (45 bp):
TTTTTAATTACCAAATTCTTTTTAATTACCAATTTACTTTTATAA
Found at i:16713 original size:18 final size:19
Alignment explanation
Indices: 16671--16712 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
16661 CTTTTAGTTT
16671 TTTTTAATTACCAAATTTC
1 TTTTTAATTACCAAATTTC
16690 TTTTTAATTACC-AATTTAC
1 TTTTTAATTACCAAATTT-C
16709 TTTT
1 TTTT
16713 ACTCTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAATTACCAAATTTC
Found at i:17476 original size:23 final size:20
Alignment explanation
Indices: 17440--17488 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
17430 AGAGGCCCAT
*
17440 AAGGCCCAACAACACCATAG
1 AAGGCCCAACAACAACATAG
17460 AAGGCCCAACAACAACATAG
1 AAGGCCCAACAACAACATAG
17480 AAGGCCCAA
1 AAGGCCCAA
17489 AATCAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.33, G:0.16, T:0.04
Consensus pattern (20 bp):
AAGGCCCAACAACAACATAG
Done.