Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022727.1 Corchorus olitorius cultivar O-4 contig22760, 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: 33792
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1751 original size:31 final size:30
Alignment explanation
Indices: 1716--1828 Score: 142
Period size: 28 Copynumber: 3.7 Consensus size: 30
1706 TAAAATTTAA
1716 TTGACACCAGAAGTTGTCATATTAAATTATC
1 TTGACACCAGAAGTTGTCATA-TAAATTATC
1747 TTGACACCAGAAGTTGTCATGA-AAATTA--
1 TTGACACCAGAAGTTGTCAT-ATAAATTATC
1775 TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATAT--AA--ATTATC
*
1809 TTGACACTAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
1829 GCTGAGGAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
27 1 0.01
28 20 0.27
30 8 0.11
31 20 0.27
32 5 0.07
34 19 0.26
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (30 bp):
TTGACACCAGAAGTTGTCATATAAATTATC
Found at i:1802 original size:59 final size:63
Alignment explanation
Indices: 1715--1861 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 63
1705 TTAAAATTTA
*
1715 ATTGACACCAGAAGTTGTCATAT-TAA-ATTATCTTGACACCAGAAGTTGTCA-TGA-AAATT
1 ATTGACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
*
1774 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACTAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATATCAAA-TATTATCTTGACACCAGAAGTTGTCA--CTGA-GAAA
1839 TT
62 TT
1841 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
1862 CCCAAGATTG
Statistics
Matches: 78, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
59 23 0.29
60 2 0.03
62 24 0.31
65 3 0.04
67 26 0.33
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (63 bp):
ATTGACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATT
Found at i:7386 original size:9 final size:10
Alignment explanation
Indices: 7372--7397 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
7362 CAGTTTATGC
7372 TTTTTTTGTT
1 TTTTTTTGTT
7382 TTTTTTTGTT
1 TTTTTTTGTT
7392 TTTTTT
1 TTTTTT
7398 AAAGAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:20144 original size:40 final size:40
Alignment explanation
Indices: 20089--20168 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
20079 GAGAGGTTAC
20089 AATTCTAGATAATTAAGGGGGATAGGATTTATTATAACAT
1 AATTCTAGATAATTAAGGGGGATAGGATTTATTATAACAT
*
20129 AATTCTAGATAATTAAGGGGGATATGATTTATTATAACAT
1 AATTCTAGATAATTAAGGGGGATAGGATTTATTATAACAT
20169 TTATTTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (40 bp):
AATTCTAGATAATTAAGGGGGATAGGATTTATTATAACAT
Found at i:23819 original size:75 final size:74
Alignment explanation
Indices: 23633--23843 Score: 292
Period size: 75 Copynumber: 2.9 Consensus size: 74
23623 ATTTGACATA
* *
23633 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTG-CTTT-CTTTTTTTATGCTTCTGGCTTA
1 AAGATTCCATACTC-GCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTTGT-TGTTTCTGGCTTA
*
23696 TGTAGCCAATC
64 TGTAACCAATC
23707 AAGATTCC--A---GCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTTGTTGTTTCTGGCTTATG
1 AAGATTCCATACTCGCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTTGTTGTTTCTGGCTTATG
23767 TAACCAATC
66 TAACCAATC
* * *
23776 AAGATTCCATACTCGGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGTTTCTGGCCTAT
1 AAGATTCCATACTC-GCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTTGTTGTTTCTGGCTTAT
23841 GTA
65 GTA
23844 GCCCATTAAA
Statistics
Matches: 123, Mismatches: 6, Indels: 15
0.85 0.04 0.10
Matches are distributed among these distances:
68 22 0.18
69 34 0.28
70 7 0.06
71 1 0.01
72 1 0.01
74 8 0.07
75 50 0.41
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (74 bp):
AAGATTCCATACTCGCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTTGTTGTTTCTGGCTTATG
TAACCAATC
Found at i:24013 original size:115 final size:110
Alignment explanation
Indices: 23809--24039 Score: 399
Period size: 115 Copynumber: 2.1 Consensus size: 110
23799 CGTAGCCATA
*
23809 AGTGCCTTTCCTTGTTGATGTTTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTGACTTG
1 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTGACTTG
23874 GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
66 GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
23919 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAGAAAAAAGAATCTATATTTTG
1 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATT----AAAAA-AATCTATATTTTG
*
23984 ACTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAGG
61 ACTTGGAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
24034 AGTGCC
1 AGTGCC
24040 CTTCAGCTTA
Statistics
Matches: 114, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
110 41 0.36
114 5 0.04
115 68 0.60
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (110 bp):
AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTGACTTG
GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
Found at i:24575 original size:39 final size:40
Alignment explanation
Indices: 24506--24581 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
24496 TTCGCTTCAA
* *
24506 ACATCAAAAGGCATGTCGTATTTGCAATGTGGTATTCGCG
1 ACATCAAAAGGCATGTCGCATTCGCAATGTGGTATTCGCG
* *
24546 ACATC-AAAGGCATGTGGCATTCGCGATGTGGTATTC
1 ACATCAAAAGGCATGTCGCATTCGCAATGTGGTATTC
24582 ACAATGTGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 27 0.84
40 5 0.16
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (40 bp):
ACATCAAAAGGCATGTCGCATTCGCAATGTGGTATTCGCG
Found at i:24600 original size:14 final size:14
Alignment explanation
Indices: 24557--24600 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
24547 CATCAAAGGC
* *
24557 ATGTGGCATTCGCG
1 ATGTGGTATTCGCA
*
24571 ATGTGGTATTCACA
1 ATGTGGTATTCGCA
*
24585 ATGTGGTATTTGCA
1 ATGTGGTATTCGCA
24599 AT
1 AT
24601 ATAGTATTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (14 bp):
ATGTGGTATTCGCA
Found at i:24782 original size:42 final size:42
Alignment explanation
Indices: 24721--24803 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
24711 GAGATGGCAT
* *
24721 ATGGTACTCGCGATGTGGTATGGTATTCGCGAC-GCTAAAGGC
1 ATGGTACTCGCAATATGGTATGGTATTCGCGACAG-TAAAGGC
*
24763 ATGGTACTTGCAATATGGTATGGTATTCGCGACAGTAAAGG
1 ATGGTACTCGCAATATGGTATGGTATTCGCGACAGTAAAGG
24804 AATTTGGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (42 bp):
ATGGTACTCGCAATATGGTATGGTATTCGCGACAGTAAAGGC
Found at i:25054 original size:44 final size:43
Alignment explanation
Indices: 24991--25142 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 43
24981 TCTTTCAATG
* *
24991 TCAATGTCAAAGGCTTATGGTGTTCGCGAGACTATCGCTCTCTT
1 TCAATGTCAAAGACATATGGTGTTCGCGA-ACTATCGCTCTCTT
*
25035 TCAATGTCAAAGACATATGGTGTT-------TGT-G-TCTCTT
1 TCAATGTCAAAGACATATGGTGTTCGCGAACTATCGCTCTCTT
* * * *
25069 TCAATGTCAAAGGCATATGGTGTTCGTGAAACTATCACCCTCTT
1 TCAATGTCAAAGACATATGGTGTTCGCG-AACTATCGCTCTCTT
25113 TCAATGTCAAA-AGCATATGGTGTTCGCGAA
1 TCAATGTCAAAGA-CATATGGTGTTCGCGAA
25143 GTACTACCTC
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
34 29 0.33
35 1 0.01
36 2 0.02
42 2 0.02
43 2 0.02
44 52 0.59
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (43 bp):
TCAATGTCAAAGACATATGGTGTTCGCGAACTATCGCTCTCTT
Found at i:25088 original size:78 final size:78
Alignment explanation
Indices: 24991--25136 Score: 231
Period size: 78 Copynumber: 1.9 Consensus size: 78
24981 TCTTTCAATG
* * * *
24991 TCAATGTCAAAGGCTTATGGTGTTCGCGAGACTATCGCTCTCTTTCAATGTC-AAAGACATATGG
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAG-CATATGG
25055 TGTTTGTGTCTCTT
65 TGTTTGTGTCTCTT
*
25069 TCAATGTCAAAGGCATATGGTGTTCGTGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
25134 GTT
66 GTT
25137 CGCGAAGTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 58 0.94
79 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (78 bp):
TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
GTTTGTGTCTCTT
Found at i:25165 original size:30 final size:30
Alignment explanation
Indices: 25129--25189 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
25119 TCAAAAGCAT
* *
25129 ATGGTGTTCGCGAAGTACT-ACCTCCTTCCA
1 ATGGTGTTAGAGAAGT-CTCACCTCCTTCCA
25159 ATGGTGTTAGAGAAGTCTCACCTCCTTCCA
1 ATGGTGTTAGAGAAGTCTCACCTCCTTCCA
25189 A
1 A
25190 CGTCCTGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (30 bp):
ATGGTGTTAGAGAAGTCTCACCTCCTTCCA
Found at i:25266 original size:51 final size:51
Alignment explanation
Indices: 25203--25342 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 51
25193 CCTGAGCCTC
* *
25203 TTGCATATGGTGTTCGCAAAATATCAACTCTTTCCAATATTATAAAGTCTT
1 TTGCATATGGTGTTCGCAAAATATCACCTCCTTCCAATATTATAAAGTCTT
* * *
25254 TTGCATATGGTGTTTGCAAAATATCACCTCCTTCCAATATTATGAAGTTTT
1 TTGCATATGGTGTTCGCAAAATATCACCTCCTTCCAATATTATAAAGTCTT
* * * * *
25305 TTGTATATGGCGTTGGCGAACTATCACCTCCTTCCAAT
1 TTGCATATGGTGTTCGCAAAATATCACCTCCTTCCAAT
25343 GTCGAAGGGT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 79 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (51 bp):
TTGCATATGGTGTTCGCAAAATATCACCTCCTTCCAATATTATAAAGTCTT
Found at i:25416 original size:31 final size:32
Alignment explanation
Indices: 25351--25438 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 32
25341 ATGTCGAAGG
* *
25351 GTACATCCTCTTCCATATGGTGTTATCAAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
*
25383 GTACACCCTCTTCCATATGATGTTGT-AAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
* *
25414 GTACACCATCTTCCACATGGTGTTG
1 GTACACCCTCTTCCATATGGTGTTG
25439 GCAAACTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (32 bp):
GTACACCCTCTTCCATATGGTGTTGTCAAGAA
Found at i:25649 original size:36 final size:36
Alignment explanation
Indices: 25609--25746 Score: 195
Period size: 36 Copynumber: 3.8 Consensus size: 36
25599 ATAATGTTGA
* *
25609 TGGCCTAAGTCGCCTAATAATTTGCTATAAAGCCGC
1 TGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGC
* * * *
25645 TGGCCTTAGTCGCCCAATACTTGGCTATAATGCCGA
1 TGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGC
25681 TGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGC
1 TGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGC
* * *
25717 TGGCCTTAGTTGCCCAATATTTGGCTATAA
1 TGGCCTAAGTCGCCCAATAATTGGCTATAA
25747 TGCTGCTTGT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (36 bp):
TGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGC
Found at i:25710 original size:72 final size:72
Alignment explanation
Indices: 25593--25749 Score: 260
Period size: 72 Copynumber: 2.2 Consensus size: 72
25583 TGCTCTGTCT
** * *
25593 TTGGCTATAATGTTGATGGCCTAAGTCGCCTAATAATTTGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
25658 CCAATAC
66 CCAATAC
*
25665 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTTGC
1 TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
*
25730 CCAATAT
66 CCAATAC
25737 TTGGCTATAATGC
1 TTGGCTATAATGC
25750 TGCTTGTCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 79 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (72 bp):
TTGGCTATAATGCCGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
CCAATAC
Found at i:26057 original size:46 final size:46
Alignment explanation
Indices: 25922--26063 Score: 185
Period size: 46 Copynumber: 3.1 Consensus size: 46
25912 GAGATGCATT
* * * *
25922 TTATGTGAGCACCCTTCTTCCGAAAGAATACTCTATACAATATCTT
1 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACAGTAGCTC
* *
25968 TTATGTGAGCACACTTCTTCAGAAAGAATACTCTACACAGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACAGTAGCTC
* * * *
26014 TTATGTGATCACCCATCTTCAGAAAGAATTCTCTATACGGTAGCTTC
1 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACAGTAGC-TC
26061 TTA
1 TTA
26064 CAAAGCATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
46 78 0.94
47 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (46 bp):
TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACAGTAGCTC
Found at i:26611 original size:45 final size:45
Alignment explanation
Indices: 26547--26648 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
26537 CTCCAAGGAG
* * * *
26547 TTGAACATGGGAGATACACAAATGGT-TTCCACCATGATAAAGGCA
1 TTGAACCTGAGAGATACACAAATGGTCTT-CACCATGACAAAGACA
*
26592 TTGAACCTGAGAGATACACAAATTGTCTTCACCATGACAAAGACA
1 TTGAACCTGAGAGATACACAAATGGTCTTCACCATGACAAAGACA
* *
26637 CTAAACCTGAGA
1 TTGAACCTGAGA
26649 AATAAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (45 bp):
TTGAACCTGAGAGATACACAAATGGTCTTCACCATGACAAAGACA
Found at i:27795 original size:27 final size:27
Alignment explanation
Indices: 27764--27827 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
27754 TAGGTATTGA
*
27764 TATTGCTAGAAGGTAATTGCCACATAG-
1 TATTGCAAGAAGGTAATTGCCACAT-GT
*
27791 TATTGCAAGAGGGTAATTGCCACATGT
1 TATTGCAAGAAGGTAATTGCCACATGT
27818 TATTGCAAGA
1 TATTGCAAGA
27828 TGGTGCAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (27 bp):
TATTGCAAGAAGGTAATTGCCACATGT
Done.