Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013151.1 Corchorus olitorius cultivar O-4 contig13184, 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: 31095
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:8383 original size:27 final size:28
Alignment explanation
Indices: 8326--8389 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
8316 TTTTCGACGC
*
8326 AAAACACAAAACTCTTTTTTTTAATC-A
1 AAAACGCAAAACTCTTTTTTTTAATCAA
* *
8353 AAAACGCAAAAGTCTTTTTTTT-TTCAAA
1 AAAACGCAAAACTCTTTTTTTTAATC-AA
8381 AAAACGCAA
1 AAAACGCAA
8390 GACTAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 20 0.62
28 10 0.31
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAACGCAAAACTCTTTTTTTTAATCAA
Found at i:8389 original size:28 final size:27
Alignment explanation
Indices: 8326--8382 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
8316 TTTTCGACGC
*
8326 AAAACACAAAACTCTTTTTTTTAATCA
1 AAAACGCAAAACTCTTTTTTTTAATCA
* *
8353 AAAACGCAAAAGTCTTTTTTTT-TTCA
1 AAAACGCAAAACTCTTTTTTTTAATCA
8379 AAAA
1 AAAA
8383 AACGCAAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAACGCAAAACTCTTTTTTTTAATCA
Found at i:8468 original size:29 final size:28
Alignment explanation
Indices: 8419--8474 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
8409 CGCAAGAACA
8419 AATTTTTTTTTTTAGAAAAAAACGCAGAC
1 AATTTTTTTTTTTAG-AAAAAACGCAGAC
**
8448 AATTTTTTTTTTTAGGGAAAACGCAGA
1 AATTTTTTTTTTTAGAAAAAACGCAGA
8475 GACACAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (28 bp):
AATTTTTTTTTTTAGAAAAAACGCAGAC
Found at i:8772 original size:15 final size:16
Alignment explanation
Indices: 8748--8787 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
8738 AGAGGTTGAA
*
8748 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
8763 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
8779 AGAAAACAA
1 AGAAAACAA
8788 AGCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:11017 original size:29 final size:30
Alignment explanation
Indices: 10973--11066 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 30
10963 CTAAATGACG
*
10973 TTTTGTCTCTGAACTT-CAAA-TAAGGACA
1 TTTTGTCCCTGAACTTGCAAATTAAGGACA
* *
11001 TTTTGTCCCATGAACTTGTAAATTCAGGACA
1 TTTTGTCCC-TGAACTTGCAAATTAAGGACA
* * *
11032 TTTTGCCCCTAAACTTCCCAAATTCAA-GACA
1 TTTTGTCCCTGAACTT-GCAAATT-AAGGACA
11063 TTTT
1 TTTT
11067 ACCACCTGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 8 0.15
29 7 0.13
30 9 0.17
31 28 0.53
32 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (30 bp):
TTTTGTCCCTGAACTTGCAAATTAAGGACA
Found at i:11374 original size:17 final size:17
Alignment explanation
Indices: 11352--11387 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11342 TGATTTGTAA
11352 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
11369 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
11386 AG
1 AG
11388 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:13956 original size:18 final size:18
Alignment explanation
Indices: 13933--14001 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
13923 TACAAAATAT
13933 TGTTCCACTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
* * *
13951 TGTTCCACTACTGCAGAA
1 TGTTCCACTGCCGCAGGA
* *
13969 TGTTGCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
*
13987 TGTTCCGCTGCCGCA
1 TGTTCCACTGCCGCA
14002 AGAACCTTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.26
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:19885 original size:27 final size:26
Alignment explanation
Indices: 19855--20012 Score: 117
Period size: 27 Copynumber: 6.3 Consensus size: 26
19845 TTTATAACTA
*
19855 TTATCTATTTATTTACTATTTATCTTT
1 TTATTTATTTATTTACTATTTATC-TT
19882 TTATTTA-TTAGTTTAGCTA-TTATC--
1 TTATTTATTTA-TTTA-CTATTTATCTT
19906 -TA-TTATTTATTTACTATTTATC--
1 TTATTTATTTATTTACTATTTATCTT
* * *
19928 TT-TTTATTTA-TTA--GTTTAGCTA
1 TTATTTATTTATTTACTATTTATCTT
*
19950 TTATCTATTTATTTACTATTTATCTTT
1 TTATTTATTTATTTACTATTTATC-TT
*
19977 TTATTTATTAATTTAGCTA-TTATCTAT
1 TTATTTATTTATTTA-CTATTTATCT-T
20004 TTATTTATT
1 TTATTTATT
20013 ATTATCTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
20 5 0.05
21 3 0.03
22 17 0.16
23 20 0.19
24 3 0.03
26 9 0.08
27 44 0.41
28 6 0.06
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (26 bp):
TTATTTATTTATTTACTATTTATCTT
Found at i:19921 original size:49 final size:49
Alignment explanation
Indices: 19860--20012 Score: 267
Period size: 49 Copynumber: 3.2 Consensus size: 49
19850 AACTATTATC
19860 TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAGCTATTATCTAT
1 TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAGCTATTATCTAT
19909 TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAGCTATTATC---
1 TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAGCTATTATCTAT
*
19955 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATCTATT
1 TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAGCTATTATCTA-T
20005 TATTTATT
1 TATTTATT
20013 ATTATCTTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 7
0.93 0.01 0.07
Matches are distributed among these distances:
46 45 0.45
49 46 0.46
50 8 0.08
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (49 bp):
TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAGCTATTATCTAT
Found at i:20024 original size:46 final size:46
Alignment explanation
Indices: 19852--20023 Score: 292
Period size: 46 Copynumber: 3.7 Consensus size: 46
19842 TTTTTTATAA
19852 CTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAGTTTAG
1 CTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAGTTTAG
19898 CTATTATCTATTATTTATTTACTATTTATCTTTTTATTTATTAGTTTAG
1 CTATTATC---TATTTATTTACTATTTATCTTTTTATTTATTAGTTTAG
*
19947 CTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAG
1 CTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAGTTTAG
*
19993 CTATTATCTATTTATTTATTA-TTATCTTTTT
1 CTATTATCTATTTATTTACTATTTATCTTTTT
20024 TTCTTTTACC
Statistics
Matches: 121, Mismatches: 2, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
45 10 0.08
46 65 0.54
49 46 0.38
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.64
Consensus pattern (46 bp):
CTATTATCTATTTATTTACTATTTATCTTTTTATTTATTAGTTTAG
Found at i:24379 original size:14 final size:13
Alignment explanation
Indices: 24360--24406 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
24350 CTGCAAAATT
24360 AACAAAAACACAAA
1 AACAAAAACA-AAA
24374 AACAAAAACAAAA
1 AACAAAAACAAAA
* *
24387 TACGAAAAA-TAAA
1 AAC-AAAAACAAAA
24400 AACAAAA
1 AACAAAA
24407 CTAAAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 4 0.14
13 10 0.34
14 15 0.52
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (13 bp):
AACAAAAACAAAA
Found at i:24385 original size:20 final size:20
Alignment explanation
Indices: 24360--24406 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24350 CTGCAAAATT
24360 AACAAAA-ACACAAAAACAAA
1 AACAAAATAC-CAAAAACAAA
* *
24380 AACAAAATACGAAAAATAAA
1 AACAAAATACCAAAAACAAA
24400 AACAAAA
1 AACAAAA
24407 CTAAAGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (20 bp):
AACAAAATACCAAAAACAAA
Found at i:24386 original size:5 final size:6
Alignment explanation
Indices: 24364--24406 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
24354 AAAATTAACA
*
24364 AAAACAC AAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
24407 CTAAAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.79, C:0.14, G:0.02, T:0.05
Consensus pattern (6 bp):
AAAAAC
Found at i:25971 original size:54 final size:54
Alignment explanation
Indices: 25889--25997 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
25879 CCCCAAATGG
25889 TCGATTTTCATCAAGAACAAAGAGATGAATCCTTGCGCCGTGGTTGTTTGATTC
1 TCGATTTTCATCAAGAACAAAGAGATGAATCCTTGCGCCGTGGTTGTTTGATTC
* *
25943 TCGATTTTCATCAAGAACAAAGAGATGAATTCTTGTGCCGTGGTTGTTTGATTC
1 TCGATTTTCATCAAGAACAAAGAGATGAATCCTTGCGCCGTGGTTGTTTGATTC
25997 T
1 T
25998 TCGTTATTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (54 bp):
TCGATTTTCATCAAGAACAAAGAGATGAATCCTTGCGCCGTGGTTGTTTGATTC
Found at i:28565 original size:15 final size:15
Alignment explanation
Indices: 28528--28559 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28518 AGAAGGAATT
28528 CACCAAAATTAACTA
1 CACCAAAATTAACTA
28543 CACCAAAATTAACTA
1 CACCAAAATTAACTA
28558 CA
1 CA
28560 GGAAAAGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (15 bp):
CACCAAAATTAACTA
Found at i:29839 original size:29 final size:30
Alignment explanation
Indices: 29779--29858 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
29769 GCTAAATACC
* *
29779 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
*
29810 CAAAATAATCCTTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* * *
29839 CAAATTAATCTCTTACGTTT
1 CAAAATAATCCCTTATGTTT
29859 CAAAAATGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 23 0.55
31 19 0.45
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:30063 original size:31 final size:32
Alignment explanation
Indices: 30007--30097 Score: 150
Period size: 31 Copynumber: 2.9 Consensus size: 32
29997 CTAATTTGTT
*
30007 CAAAAA-AAAAACATAAGGGATTTTTTTGTCC
1 CAAAAAGAAAAACATAAGGGATTTTTTTATCC
30038 CAAAAAGAAAAACATAAGGGATTTTTTTATCC
1 CAAAAAGAAAAACATAAGGGATTTTTTTATCC
*
30070 C-AAAAGAAAAACATTAGGGATTTTTTTA
1 CAAAAAGAAAAACATAAGGGATTTTTTTA
30098 GTATTTGTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 32 0.56
32 25 0.44
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (32 bp):
CAAAAAGAAAAACATAAGGGATTTTTTTATCC
Found at i:30150 original size:8 final size:8
Alignment explanation
Indices: 30137--30169 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
30127 AAAAAATTGA
30137 TTTTTTCC
1 TTTTTTCC
*
30145 TTTTTTTC
1 TTTTTTCC
30153 TTTTTT-C
1 TTTTTTCC
30160 TTTTTTCC
1 TTTTTTCC
30168 TT
1 TT
30170 CTCCTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCC
Found at i:30483 original size:126 final size:126
Alignment explanation
Indices: 30256--30495 Score: 326
Period size: 126 Copynumber: 1.9 Consensus size: 126
30246 TTCCCTAAAA
* **
30256 AAAATGGTAAAGATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAATTTTCGG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAATTTTCAA
* *
30321 TAAAATAAAACTGTAAAAGTTTTTAAAATGTCATTTAAGAAATATATTTAATTAAAATAGT
66 TAAAATAAAACTGTAAAAGTTTTAAAAATGTCATTTAAAAAATATATTTAATTAAAATAGT
*
30382 AAAATGGTAAAAATAAAATAGTTATAAAATATATT-AGATTTGATTAAATAAAAATAGAGATTTT
1 AAAATGGTAAAAATAAAATAGTTATAAAA-ATATTGA-ATTTAATTAAATAAAAATAGA-ATTTT
** * *
30446 -AATTGAGTAAAATTGTAAAAG-TTTAAAAATGGT-ATTTAAAAAATATATTT
63 CAATAAAATAAAACTGTAAAAGTTTTAAAAAT-GTCATTTAAAAAATATATTT
30496 GAAAAATAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
126 53 0.53
127 42 0.42
128 5 0.05
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.35
Consensus pattern (126 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAATTTTCAA
TAAAATAAAACTGTAAAAGTTTTAAAAATGTCATTTAAAAAATATATTTAATTAAAATAGT
Done.