Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015899.1 Corchorus olitorius cultivar O-4 contig15932, 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: 31652
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:526 original size:31 final size:32
Alignment explanation
Indices: 491--595 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 32
481 ATATAGGCTG
491 AAATCTCAAAT-AGGTCCCCGAACTTTGTCAT
1 AAATCTCAAATAAGGTCCCCGAACTTTGTCAT
* *
522 AAATCTCAAATAAGG-GCCCGAACTTTAT-A-
1 AAATCTCAAATAAGGTCCCCGAACTTTGTCAT
**
551 AAAGGTCAAATAAGGAT-CCC-AAC-TTGTCAT
1 AAATCTCAAATAAGG-TCCCCGAACTTTGTCAT
581 AAAGTCTCAAATAAG
1 AAA-TCTCAAATAAG
596 TCCATCCATT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.05
29 17 0.28
30 7 0.11
31 31 0.51
32 3 0.05
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (32 bp):
AAATCTCAAATAAGGTCCCCGAACTTTGTCAT
Found at i:1970 original size:31 final size:30
Alignment explanation
Indices: 1932--2036 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
1922 CGAAAAGGAT
1932 TTATTTGAGACTTTCTGACAAGTTGGGGCCC
1 TTATTTGAGA-TTTCTGACAAGTTGGGGCCC
** * *
1963 TTATTTGACCTTT-T-ATAAAGTTCGGGCCC
1 TTATTTGAGATTTCTGA-CAAGTTGGGGCCC
* * *
1992 TTATTTGAGATTTATGACAAAATTCGGGGACC
1 TTATTTGAGATTTCTGAC-AAGTT-GGGGCCC
2024 -TATTTGAGATTTC
1 TTATTTGAGATTTC
2037 AGCCTAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
28 1 0.02
29 23 0.40
30 4 0.07
31 25 0.43
32 5 0.09
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (30 bp):
TTATTTGAGATTTCTGACAAGTTGGGGCCC
Found at i:2816 original size:27 final size:27
Alignment explanation
Indices: 2776--2837 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
2766 TCTAAATTTT
2776 TATTATTTTAATAATGAAATAA-TTA-AAA
1 TATTA-TTTAATAAT--AATAATTTAGAAA
2804 TATTATTTAATAATAATAATTTAGAAA
1 TATTATTTAATAATAATAATTTAGAAA
2831 TA-TATTT
1 TATTATTT
2838 GAAAAAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.16
26 8 0.25
27 14 0.44
28 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
TATTATTTAATAATAATAATTTAGAAA
Found at i:7512 original size:26 final size:27
Alignment explanation
Indices: 7473--7530 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
7463 GAGTCAATGA
*
7473 ATATAGTAGTATAAATCTATTATATAT
1 ATATAATAGTATAAATCTATTATATAT
7500 ATATAATA-TATAAATCTATTATATAT
1 ATATAATAGTATAAATCTATTATATAT
7526 ATATA
1 ATATA
7531 GTAGCTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATAATAGTATAAATCTATTATATAT
Found at i:8878 original size:47 final size:48
Alignment explanation
Indices: 8797--8904 Score: 157
Period size: 47 Copynumber: 2.3 Consensus size: 48
8787 AAAAATAGTC
* *
8797 AATAAAGAAGGATTCCTTTCTTAATTAGAAAATATATAAACG-ATAAA
1 AATAAAGAAGGATTCCATTCTTAATTAGAAAATATATAAACGAAAAAA
* *
8844 AATAAAGAAGGATTCCATTCTT-TTATAGAGAATATATAAACGAAAAAA
1 AATAAAGAAGGATTCCATTCTTAAT-TAGAAAATATATAAACGAAAAAA
8892 AATAAAGAAGGAT
1 AATAAAGAAGGAT
8905 AAAGGATTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
46 1 0.02
47 37 0.67
48 17 0.31
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (48 bp):
AATAAAGAAGGATTCCATTCTTAATTAGAAAATATATAAACGAAAAAA
Found at i:9888 original size:14 final size:13
Alignment explanation
Indices: 9857--9902 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
9847 ATTGGGTTTT
9857 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
9870 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
9884 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
9899 AGTC
1 AGTC
9903 TGAGTCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:10637 original size:31 final size:30
Alignment explanation
Indices: 10540--10639 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 30
10530 CTAAAAAGTT
* * *
10540 TATTTTGACAATAAAAAAGATTTCACATGGT
1 TATTTTTAAAATAAAAAA-ATTTCACATGGA
* *
10571 TATTTTTAAAGTAAAAAAA--TCACATGGC
1 TATTTTTAAAATAAAAAAATTTCACATGGA
10599 TACTTTTTAAAATATAAAAAATTTCACATGGA
1 TA-TTTTTAAAATA-AAAAAATTTCACATGGA
10631 TATTTTTAA
1 TATTTTTAA
10640 GAGTGATTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 10 0.17
29 10 0.17
30 7 0.12
31 22 0.37
32 10 0.17
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (30 bp):
TATTTTTAAAATAAAAAAATTTCACATGGA
Found at i:11889 original size:3 final size:3
Alignment explanation
Indices: 11881--11906 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11871 AGGTCAAACT
11881 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
11907 TCTCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16464 original size:2 final size:2
Alignment explanation
Indices: 16459--16499 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16449 TCTCTCTCTC
16459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16500 CTATCTATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23043 original size:19 final size:18
Alignment explanation
Indices: 23006--23045 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
22996 TTCTTGAAAT
*
23006 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
23024 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
23043 AAT
1 AAT
23046 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:26223 original size:270 final size:271
Alignment explanation
Indices: 25739--26236 Score: 847
Period size: 270 Copynumber: 1.8 Consensus size: 271
25729 ACTGCCCGGG
25739 AATAAGAAAGATAAACAAATGACTGATCACGACATAGGAATCAATGAGAGAATGGAACAAGATGG
1 AATAAGAAAGATAAACAAATGACTGATCACGACATAGGAATCAATGAGAGAATGGAACAAGATGG
* * *
25804 AGGATTGTCTTTCATCAGTACTTCCGTCAGCTCTGATAAAGGAGCAATATTGTTCGCCTTAACCT
66 AGGATTGTCTTTAATCAGTACTTCCGTCAGCTCTGATAAAGGAGCAACATTGTTCACCTTAACCT
*
25869 TCTTGGTTTGCCGAGCAAGGCGTGCTAGCGGATTCCCTGTTGCAACTTTGGCCATTGAATTCAGT
131 TCTTGGTTTGCCGAGCAAGGCGTGCTAGCGGATTCCCTGTTACAACTTTGGCCATTGAATTCAGT
* *
25934 TAGGTATGACTAAGAATAAATCGCACACAACATTGCCCCTGCTGCCCCCTATTTCGCTACTGAGT
196 TAGGTACGACTAAGAATAAACCGCACACAACATTGCCCCTGCTGCCCCCTATTTCGCTACTGAGT
25999 TTAGGTAGGGA
261 TTAGGTAGGGA
* *
26010 AATAAGAAAGATAAACAAATGACTGATCACGA-ATAGGAATCAATGGGAGAATGGAACGAGATGG
1 AATAAGAAAGATAAACAAATGACTGATCACGACATAGGAATCAATGAGAGAATGGAACAAGATGG
* * * *
26074 TGGATTGTTTTTAATCAGTACTTCCGTTAGCT-TCGATAAAGGAGCAACATTGTTCACCTTGACC
66 AGGATTGTCTTTAATCAGTACTTCCGTCAGCTCT-GATAAAGGAGCAACATTGTTCACCTTAACC
*
26138 TTCTTGGTTTGTCGAGCAAGGCGTGCTAGCGGATTCCCTGTTACAACTTTGGCCATTGAATTCAG
130 TTCTTGGTTTGCCGAGCAAGGCGTGCTAGCGGATTCCCTGTTACAACTTTGGCCATTGAATTCAG
*
26203 TTAGGTACGACTAGGAATAAACCGCACACAACAT
195 TTAGGTACGACTAAGAATAAACCGCACACAACAT
26237 CCTCCATACA
Statistics
Matches: 212, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
269 1 0.00
270 179 0.84
271 32 0.15
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (271 bp):
AATAAGAAAGATAAACAAATGACTGATCACGACATAGGAATCAATGAGAGAATGGAACAAGATGG
AGGATTGTCTTTAATCAGTACTTCCGTCAGCTCTGATAAAGGAGCAACATTGTTCACCTTAACCT
TCTTGGTTTGCCGAGCAAGGCGTGCTAGCGGATTCCCTGTTACAACTTTGGCCATTGAATTCAGT
TAGGTACGACTAAGAATAAACCGCACACAACATTGCCCCTGCTGCCCCCTATTTCGCTACTGAGT
TTAGGTAGGGA
Found at i:30571 original size:48 final size:48
Alignment explanation
Indices: 30497--30789 Score: 362
Period size: 48 Copynumber: 6.1 Consensus size: 48
30487 TTGAAGACAT
* *
30497 GAATGAAATATTGAAAACGACACCTTCCGACCGAGAAGGGCAAAACAG
1 GAATGAAATATTGAAAACAACACCTTCCGACCGAGAAGGGCAAAACGG
* *
30545 GAATGAAATATTGAAGACAA-ACCCTTCCGACCGGGAAGGGCAAAACGG
1 GAATGAAATATTGAAAACAACA-CCTTCCGACCGAGAAGGGCAAAACGG
* *
30593 GAATGAAACATTGAAAACCACACCTTCCGACC-AGGAAGGGCAAAACGG
1 GAATGAAATATTGAAAACAACACCTTCCGACCGA-GAAGGGCAAAACGG
* *
30641 GAATGAAACATCGAAAACAACACCTTCCGACC-AGGAAGGGCAAAACGG
1 GAATGAAATATTGAAAACAACACCTTCCGACCGA-GAAGGGCAAAACGG
* **
30689 GAATGAAA-ACTTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAA
1 GAATGAAATA--TTGAAAACAACACCTTCCGACCGAGAAGGGCAAAACGG
* * * *
30738 GAATGAACTATTGAAGATAACACCTTCCGACCGGGAAGGGC-AAACTGG
1 GAATGAAATATTGAAAACAACACCTTCCGACCGAGAAGGGCAAAAC-GG
30786 GAAT
1 GAAT
30790 TTAAAACAAC
Statistics
Matches: 218, Mismatches: 19, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
47 6 0.03
48 170 0.78
49 41 0.19
50 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (48 bp):
GAATGAAATATTGAAAACAACACCTTCCGACCGAGAAGGGCAAAACGG
Found at i:30648 original size:40 final size:42
Alignment explanation
Indices: 30604--30822 Score: 131
Period size: 48 Copynumber: 4.8 Consensus size: 42
30594 AATGAAACAT
30604 TGAAAAC-C-ACACCTTCCGACCAGGAAGGGCAAAACGGGAA
1 TGAAAACACAACACCTTCCGACCAGGAAGGGCAAAACGGGAA
30644 TGAAACATCGAAAACAACACCTTCCGACCAGGAAGGGCAAAACGGGAA
1 TGAAA-A-C----ACAACACCTTCCGACCAGGAAGGGCAAAACGGGAA
* **
30692 TGAAAACTTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAAGAA
1 TGAAAAC-------ACAACACCTTCCGACCAGGAAGGGCAAAACGGGAA
* * *
30741 TGAACTATTGAAGATAACACCTTCCGACCGGGAAGGGC-AAACTGGGAA
1 TG-A--A---AACACAACACCTTCCGACCAGGAAGGGCAAAAC-GGGAA
** * **
30789 TTTAAA-ACAACACCTTTCGATAAGGAAGGGCAAA
1 TGAAAACACAACACCTTCCGACCAGGAAGGGCAAA
30823 CTGGGGATTA
Statistics
Matches: 146, Mismatches: 14, Indels: 36
0.74 0.07 0.18
Matches are distributed among these distances:
40 5 0.03
41 21 0.14
42 5 0.03
45 1 0.01
46 1 0.01
47 6 0.04
48 65 0.45
49 38 0.26
50 1 0.01
52 1 0.01
55 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.13
Consensus pattern (42 bp):
TGAAAACACAACACCTTCCGACCAGGAAGGGCAAAACGGGAA
Found at i:30744 original size:97 final size:96
Alignment explanation
Indices: 30497--30789 Score: 412
Period size: 96 Copynumber: 3.0 Consensus size: 96
30487 TTGAAGACAT
* * * *
30497 GAATGAAATATTGAAAACGACACCTTCCGACCGAGAAGGGCAAAACAGGAATGAAATATTGAAGA
1 GAATGAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAACATTGAAGA
30562 CAA-ACCCTTCCGACCGGGAAGGGCAAAACGG
66 CAACA-CCTTCCGACCGGGAAGGGCAAAACGG
* * * * *
30593 GAATGAAACATTGAAAACCACACCTTCCGACCAGGAAGGGCAAAACGGGAATGAAACATCGAAAA
1 GAATGAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAACATTGAAGA
*
30658 CAACACCTTCCGACCAGGAAGGGCAAAACGG
66 CAACACCTTCCGACCGGGAAGGGCAAAACGG
* *
30689 GAATGAAAACTTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAAGAATG-AACTATTGAA
1 GAATG-AAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAC-ATTGAA
*
30753 GATAACACCTTCCGACCGGGAAGGGC-AAACTGG
64 GACAACACCTTCCGACCGGGAAGGGCAAAAC-GG
30786 GAAT
1 GAAT
30790 TTAAAACAAC
Statistics
Matches: 175, Mismatches: 18, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
96 97 0.55
97 78 0.45
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (96 bp):
GAATGAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAACATTGAAGA
CAACACCTTCCGACCGGGAAGGGCAAAACGG
Found at i:30892 original size:43 final size:43
Alignment explanation
Indices: 30839--30962 Score: 176
Period size: 43 Copynumber: 2.9 Consensus size: 43
30829 ATTAACGAAG
* *
30839 GAAAACTGGGACCTTCCGACCGGGATGGGGCATTTTTGGAAAT
1 GAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAT
* * *
30882 GAAATCTGGGACCATCCGACTGGGAAGGGGTATTTTTGGAAAT
1 GAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAT
** *
30925 GAAAACAAGGACCTTCCGACTAGGAAGGGGCATTTTTG
1 GAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTG
30963 AAAAGACAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.23
Consensus pattern (43 bp):
GAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAAT
Found at i:30993 original size:42 final size:43
Alignment explanation
Indices: 30848--30997 Score: 122
Period size: 43 Copynumber: 3.5 Consensus size: 43
30838 GGAAAACTGG
* * * * * ***
30848 GACCTTCCGACCGGGATGGGGCATTTTTGGAAATGAAATCTGG
1 GACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAACAAA
* * ** * * *
30891 GACCATCCGACTGGGAAGGGGTATTTTTGGAAATGAAAACAAG
1 GACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAACAAA
* * * *
30934 GACCTTCCGACTAGGAAGGGGCATTTTT-GAAAAGACAATAAA
1 GACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAACAAA
30976 GACCTTCCAACCAGGAAGGGGC
1 GACCTTCCAACCAGGAAGGGGC
30998 TGATAAGTGT
Statistics
Matches: 91, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 30 0.33
43 61 0.67
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (43 bp):
GACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAGAAAACAAA
Found at i:31399 original size:69 final size:68
Alignment explanation
Indices: 31263--31489 Score: 332
Period size: 69 Copynumber: 3.3 Consensus size: 68
31253 CAGATCTTGG
* * *
31263 CCAAGTCCTGTCCAGGACTTGGGCTATTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCT-TTGAGGAACGC-AAATTACAGGACAAGACCTGGGCAGGA
31328 GTTAC
64 GTTAC
* * * *
31333 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAAGAGCGCAAATTACAGGACAAGACCTGGGCGGGAG
1 CCAAGTCCTGTCCAGGACTTGTGCT-TTGAGGAACGCAAATTACAGGACAAGACCTGGGCAGGAG
31398 TTAC
65 TTAC
*
31402 CCAAGTCCTGTCCCGGACTTGTGC-TTGAGGAACGCAAATTACAGGACAAGACCT-GGCAGGAGT
1 CCAAGTCCTGTCCAGGACTTGTGCTTTGAGGAACGCAAATTACAGGACAAGACCTGGGCAGGAGT
31465 TAC
66 TAC
*
31468 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
31490 TGCGGGAAAT
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
66 31 0.22
67 28 0.19
69 54 0.38
70 31 0.22
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (68 bp):
CCAAGTCCTGTCCAGGACTTGTGCTTTGAGGAACGCAAATTACAGGACAAGACCTGGGCAGGAGT
TAC
Done.