Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023119.1 Corchorus olitorius cultivar O-4 contig23152, 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: 40316
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1251 original size:37 final size:37
Alignment explanation
Indices: 1201--1275 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1191 TGGTCTGTAT
*
1201 TAGGTTTAGTATTACCTTTGCCAAGCTTAGGTTAATA
1 TAGGTTTAGTATTACCTTTACCAAGCTTAGGTTAATA
1238 TAGGTTTAGTATTACCTTTACCAAGCTTAGGTTAATA
1 TAGGTTTAGTATTACCTTTACCAAGCTTAGGTTAATA
1275 T
1 T
1276 TAGACTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (37 bp):
TAGGTTTAGTATTACCTTTACCAAGCTTAGGTTAATA
Found at i:1841 original size:29 final size:27
Alignment explanation
Indices: 1799--1869 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
1789 GGTAATGGAC
1799 CAAATGACCAAAATGCCCCTCT-AAATG
1 CAAATGACCAAAATGCCCCT-TGAAATG
1826 CACAAATGACCAAAATG-CCCTTGAAATG
1 --CAAATGACCAAAATGCCCCTTGAAATG
*
1854 CAAATAACCAAAATGC
1 CAAATGACCAAAATGC
1870 ACATGGACGT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 14 0.36
27 1 0.03
28 9 0.23
29 15 0.38
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.17
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCTTGAAATG
Found at i:1864 original size:26 final size:27
Alignment explanation
Indices: 1799--1869 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 27
1789 GGTAATGGAC
1799 CAAATGACCAAAATGCCCCTCTAAATGCA
1 CAAATGACCAAAATG-CCCTCTAAATG-A
1828 CAAATGACCAAAATGCCCT-TGAAATG-
1 CAAATGACCAAAATGCCCTCT-AAATGA
*
1854 CAAATAACCAAAATGC
1 CAAATGACCAAAATGC
1870 ACATGGACGT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 15 0.38
27 1 0.03
28 9 0.22
29 15 0.38
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.17
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCTCTAAATGA
Found at i:9694 original size:20 final size:20
Alignment explanation
Indices: 9660--9754 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 20
9650 TTGAGAGTTC
*
9660 AGGGAGAGATGAGGTGTGTG
1 AGGGAGAGTTGAGGTGTGTG
* * * *
9680 AGAGAAAGTTGAGGTGTATC
1 AGGGAGAGTTGAGGTGTGTG
9700 AGGGAGA-TATGAGGTGTGTG
1 AGGGAGAGT-TGAGGTGTGTG
* *
9720 AGGGAGAGTTGAGGTGTATC
1 AGGGAGAGTTGAGGTGTGTG
*
9740 AGGGAGAGATGAGGT
1 AGGGAGAGTTGAGGT
9755 TGAATAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.02
20 59 0.97
21 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.47, T:0.22
Consensus pattern (20 bp):
AGGGAGAGTTGAGGTGTGTG
Found at i:9703 original size:40 final size:40
Alignment explanation
Indices: 9658--9754 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 40
9648 TGTTGAGAGT
9658 TCAGGGAGAGATGAGGTGTGTGAGAGAAAGTTGAGGTGTA
1 TCAGGGAGAGATGAGGTGTGTGAGAGAAAGTTGAGGTGTA
* * *
9698 TCAGGGAGATATGAGGTGTGTGAGGGAGAGTTGAGGTGTA
1 TCAGGGAGAGATGAGGTGTGTGAGAGAAAGTTGAGGTGTA
9738 TCAGGGAGAGATGAGGT
1 TCAGGGAGAGATGAGGT
9755 TGAATAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.28, C:0.03, G:0.46, T:0.23
Consensus pattern (40 bp):
TCAGGGAGAGATGAGGTGTGTGAGAGAAAGTTGAGGTGTA
Found at i:11554 original size:37 final size:37
Alignment explanation
Indices: 11513--11588 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
11503 AGTGTAGCAA
11513 AAACTAATCCACCAAGATTATGAGTTAACAATTGACC
1 AAACTAATCCACCAAGATTATGAGTTAACAATTGACC
11550 AAACTAATCCACCAAGATTATGAGTTAACAATTGACC
1 AAACTAATCCACCAAGATTATGAGTTAACAATTGACC
11587 AA
1 AA
11589 GAATGATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (37 bp):
AAACTAATCCACCAAGATTATGAGTTAACAATTGACC
Found at i:11807 original size:27 final size:28
Alignment explanation
Indices: 11759--11834 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
11749 AAGTGAACTT
11759 AAAATGACCAAAAATGCCCCTGGA-TATG
1 AAAATGACC-AAAATGCCCCTGGATTATG
* *
11787 CAAATGACCAAAATGCCCCTGGATTTTG
1 AAAATGACCAAAATGCCCCTGGATTATG
*
11815 AAAATGACCGAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
11835 AGTTGATCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.33
28 29 0.67
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATTATG
Found at i:13782 original size:54 final size:54
Alignment explanation
Indices: 13627--13934 Score: 289
Period size: 54 Copynumber: 5.9 Consensus size: 54
13617 ATCAGCTATC
* ** * * *
13627 GGAAATTCTGAAAATCATGGAGGAAGGGTGGAATCAACTAATGGAATTGATGCT
1 GGAAATTCTGAAATTCAAAGAAGAAGGGTTGAATCAACTAATGGAGTTGATGCT
* * *
13681 AGAAATTCTGAAATTC-AAGAAGAAAGGTTGAATCAACTATTGGAGTTGATGCT
1 GGAAATTCTGAAATTCAAAGAAGAAGGGTTGAATCAACTAATGGAGTTGATGCT
* * * * *
13734 GGAAATTCTGAAATTCAAAAAAGAAGGGTTGAAACTATTAATGGAGTTGGTGCT
1 GGAAATTCTGAAATTCAAAGAAGAAGGGTTGAATCAACTAATGGAGTTGATGCT
* * *
13788 GGAAATGCTGAAATTCAAAGAGGAAGGGTTGAATCAACTAATGGAG-T--TCCT
1 GGAAATTCTGAAATTCAAAGAAGAAGGGTTGAATCAACTAATGGAGTTGATGCT
* * * *
13839 GG----T-GGAAATTC-AA-AAGAAGGGTTGAATCAACTAATGGAGATGGTGTT
1 GGAAATTCTGAAATTCAAAGAAGAAGGGTTGAATCAACTAATGGAGTTGATGCT
* * * * *
13886 GTAAATGCTGAAATTCAAGGAGGAA-GGTCTCAATCAACTAATGGAGTTG
1 GGAAATTCTGAAATTCAAAGAAGAAGGGT-TGAATCAACTAATGGAGTTG
13935 CTCCAAGCAA
Statistics
Matches: 206, Mismatches: 36, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
44 25 0.12
45 3 0.01
46 7 0.03
47 3 0.01
51 5 0.02
52 7 0.03
53 50 0.24
54 106 0.51
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (54 bp):
GGAAATTCTGAAATTCAAAGAAGAAGGGTTGAATCAACTAATGGAGTTGATGCT
Found at i:13921 original size:98 final size:99
Alignment explanation
Indices: 13743--13933 Score: 278
Period size: 98 Copynumber: 1.9 Consensus size: 99
13733 TGGAAATTCT
* * *
13743 GAAATTCAAAAAAGAAGGGTTGAAACTATTAATGGAGTTGGTGCTGGAAATGCTGAAATTCAAAG
1 GAAATTC-AAAAAGAAGGGTTGAAACAACTAATGGAGATGGTGCTGGAAATGCTGAAATTCAAAG
*
13808 AGGAAGGGTTGAATCAACTAATGGAGTTCCTGGTG
65 AGGAAGGGTTCAATCAACTAATGGAGTTCCTGGTG
* * * *
13843 GAAATTC-AAAAGAAGGGTTGAATCAACTAATGGAGATGGTGTTGTAAATGCTGAAATTCAAGGA
1 GAAATTCAAAAAGAAGGGTTGAAACAACTAATGGAGATGGTGCTGGAAATGCTGAAATTCAAAGA
13907 GGAA-GGTCTCAATCAACTAATGGAGTT
66 GGAAGGGT-TCAATCAACTAATGGAGTT
13934 GCTCCAAGCA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 3 0.04
98 72 0.88
100 7 0.09
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (99 bp):
GAAATTCAAAAAGAAGGGTTGAAACAACTAATGGAGATGGTGCTGGAAATGCTGAAATTCAAAGA
GGAAGGGTTCAATCAACTAATGGAGTTCCTGGTG
Found at i:20365 original size:29 final size:29
Alignment explanation
Indices: 20295--20381 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
20285 CAAAGCTTTG
*
20295 ACACAAGTGCA-AACCCACACTCAAAACAA
1 ACACAAGTGCACAACCCACACT-TAAACAA
* * * *
20324 TCCCAAGT-TACAACCCACACTTGAACAA
1 ACACAAGTGCACAACCCACACTTAAACAA
*
20352 ACACAAGTGCACAACCCGCACTTAAACAA
1 ACACAAGTGCACAACCCACACTTAAACAA
20381 A
1 A
20382 ATCAGAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
28 12 0.26
29 34 0.74
ACGTcount: A:0.46, C:0.34, G:0.08, T:0.11
Consensus pattern (29 bp):
ACACAAGTGCACAACCCACACTTAAACAA
Found at i:26416 original size:2 final size:2
Alignment explanation
Indices: 26409--26478 Score: 69
Period size: 2 Copynumber: 37.5 Consensus size: 2
26399 GACCCTTTTA
* *
26409 AT AT AT AT AT AT AT AT AT AT AT -T AT AT A- AA AT AT AT -T CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
26448 GT TT AT A- AT -T 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 AT AT AT A
26479 ATAACCCTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
1 5 0.08
2 54 0.92
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28205 original size:31 final size:31
Alignment explanation
Indices: 28134--28206 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
28124 GTCTATCAGC
*
28134 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
** * *
28165 TAATGATTTGTTTAATTTAATGC-TTAATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
28195 GTTTTAATTTGT
1 -TTTTAATTTGT
28207 AATAATTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:28209 original size:24 final size:21
Alignment explanation
Indices: 28170--28218 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
28160 CATTTTAATG
**
28170 ATTTGTTTAATTTAATGCTTA
1 ATTTGTTTAATTTAATAATTA
28191 ATTTGTTTTAATTTGTAATAATTA
1 ATTTG-TTTAA-TT-TAATAATTA
28215 ATTT
1 ATTT
28219 AAATTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 2 0.09
24 11 0.48
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (21 bp):
ATTTGTTTAATTTAATAATTA
Found at i:28704 original size:16 final size:16
Alignment explanation
Indices: 28685--28724 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28675 ACAGAGCCCG
* *
28685 AACCCAAATGAATCCA
1 AACCCAAATAAACCCA
*
28701 AACCCAAATAAACCCG
1 AACCCAAATAAACCCA
28717 AACCCAAA
1 AACCCAAA
28725 GTACCGGGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.35, G:0.05, T:0.07
Consensus pattern (16 bp):
AACCCAAATAAACCCA
Found at i:29031 original size:16 final size:16
Alignment explanation
Indices: 29009--29046 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
28999 GGTGATGGTT
29009 CCGGTCGACGGTTTGA
1 CCGGTCGACGGTTTGA
*
29025 TCGGTCGACGGTTTGA
1 CCGGTCGACGGTTTGA
29041 CCGGTC
1 CCGGTC
29047 CGACCGGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (16 bp):
CCGGTCGACGGTTTGA
Found at i:31001 original size:7 final size:7
Alignment explanation
Indices: 30989--31015 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30979 GATGGTTCGG
30989 TTGCAAT
1 TTGCAAT
30996 TTGCAAT
1 TTGCAAT
31003 TTGCAAT
1 TTGCAAT
31010 TTGCAA
1 TTGCAA
31016 ATCCACCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (7 bp):
TTGCAAT
Found at i:33595 original size:2 final size:2
Alignment explanation
Indices: 33588--33625 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
33578 CTAAGGTTTA
33588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33626 CTACTACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33632 original size:3 final size:3
Alignment explanation
Indices: 33624--33653 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
33614 ATTATATATA
*
33624 TAC TAC TAC TAC TAC TAC TAC TAA TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
33654 AACTTTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:34235 original size:21 final size:21
Alignment explanation
Indices: 34210--34249 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
34200 TGGGCCATTT
34210 GATAGTATTGACTTTTTTTGA
1 GATAGTATTGACTTTTTTTGA
34231 GATAGTATTGACTTTTTTT
1 GATAGTATTGACTTTTTTT
34250 TCTTTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.05, G:0.17, T:0.55
Consensus pattern (21 bp):
GATAGTATTGACTTTTTTTGA
Found at i:34597 original size:14 final size:14
Alignment explanation
Indices: 34578--34605 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34568 CCAATACCCG
34578 AACCCGAACCCGAT
1 AACCCGAACCCGAT
34592 AACCCGAACCCGAT
1 AACCCGAACCCGAT
34606 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (14 bp):
AACCCGAACCCGAT
Found at i:36914 original size:25 final size:23
Alignment explanation
Indices: 36883--36941 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
36873 TATTATATTA
* *
36883 TATTATTATTAAACTAT-AAAAAC
1 TATT-TTATTATACAATAAAAAAC
36906 TATTTTATTATACAATAAAAAAC
1 TATTTTATTATACAATAAAAAAC
36929 TATTTTATATATA
1 TATTTTAT-TATA
36942 ATTATTATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 10 0.31
23 18 0.56
24 4 0.12
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTTATTATACAATAAAAAAC
Found at i:36946 original size:55 final size:55
Alignment explanation
Indices: 36871--37005 Score: 177
Period size: 55 Copynumber: 2.4 Consensus size: 55
36861 CAACATCTAC
* * *
36871 ACTATTATATTATATTATTATTAAACTATAAAAACTA-TTT--TATTATACAATAAAAA
1 ACTATTTTA-TATATAATTATTAAACAATAAAAACTATTTTCATATTAT-C-A-AAAAA
*
36927 ACTATTTTATATATAATTATTATACAATAAAAACTATTTTCATATTATCAAAAAA
1 ACTATTTTATATATAATTATTAAACAATAAAAACTATTTTCATATTATCAAAAAA
36982 ACTATTTTATATATAATTATTAAA
1 ACTATTTTATATATAATTATTAAA
37006 TGTACATTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
55 52 0.73
56 12 0.17
57 1 0.01
58 6 0.08
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (55 bp):
ACTATTTTATATATAATTATTAAACAATAAAAACTATTTTCATATTATCAAAAAA
Found at i:36993 original size:22 final size:25
Alignment explanation
Indices: 36944--36993 Score: 79
Period size: 23 Copynumber: 2.1 Consensus size: 25
36934 TATATATAAT
36944 TATTATACAATAAAAACTATTTTCA
1 TATTATACAATAAAAACTATTTTCA
36969 TATTAT-CAA-AAAAACTATTTT-A
1 TATTATACAATAAAAACTATTTTCA
36991 TAT
1 TAT
36994 ATAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.16
23 12 0.48
24 3 0.12
25 6 0.24
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (25 bp):
TATTATACAATAAAAACTATTTTCA
Found at i:37462 original size:21 final size:21
Alignment explanation
Indices: 37436--37527 Score: 134
Period size: 21 Copynumber: 4.4 Consensus size: 21
37426 TGCTAGGAGT
37436 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
37457 TCATTGGAGCAA-GTTCCAAAC
1 TCATTGGAG-AAGGTTCCAAGC
37478 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
37499 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
37520 TCATTGGA
1 TCATTGGA
37528 ATTGCCTAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.