Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013886.1 Corchorus olitorius cultivar O-4 contig13919, 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: 48107
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5810 original size:16 final size:17
Alignment explanation
Indices: 5784--5815 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5774 AGTGCAAATT
5784 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
5801 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
5816 ACGCAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:12877 original size:50 final size:50
Alignment explanation
Indices: 12822--13237 Score: 717
Period size: 50 Copynumber: 8.3 Consensus size: 50
12812 CTCATGAAAC
12822 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
* *
12872 TTGGCTCGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
*
12922 TTGGCTTGTGGAAAAGCCTATGTTGATAAATT-ATTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGAT-AATTGACTCGTATGGAAACGAGT
12972 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
* *
13022 TTGGCTTGTGGAAAATCCTATGTTGATAATTGACTCGTATGGAAACGATT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
* *
13072 TTGGCTTATGGAAAAACCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
*
13122 TTGGCTTTTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
*
13172 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGAAAACGAGT
1 TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
* *
13222 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
13238 TCAAAGCATT
Statistics
Matches: 347, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 4 0.01
50 339 0.98
51 4 0.01
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (50 bp):
TTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGT
Found at i:14021 original size:51 final size:51
Alignment explanation
Indices: 13898--14047 Score: 239
Period size: 51 Copynumber: 3.0 Consensus size: 51
13888 CTTCAATGTC
* * * *
13898 CTTTGAAAACCGAATTTTGATCTTGGACTCACAAATGGAATGCAA-TCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTTA
*
13948 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTTA
*
13999 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTT
14048 ATTGTAAAAC
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 41 0.45
51 51 0.55
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (51 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTTA
Found at i:15132 original size:16 final size:16
Alignment explanation
Indices: 15111--15145 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
15101 TTTATTTTCA
15111 TTTTCTTTT-TTCATTT
1 TTTTCTTTTCTTC-TTT
15127 TTTTCTTTTCTTCTTT
1 TTTTCTTTTCTTCTTT
15143 TTT
1 TTT
15146 ATTATTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTCTTCTTT
Found at i:18951 original size:14 final size:15
Alignment explanation
Indices: 18928--18961 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
18918 TTGAAGAATA
18928 ATTA-TGCTTTCT-T
1 ATTATTGCTTTCTCT
18941 ATTATTGCTTTCTCT
1 ATTATTGCTTTCTCT
18956 ATTATT
1 ATTATT
18962 TGCCATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 8 0.42
15 7 0.37
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTATTGCTTTCTCT
Found at i:26274 original size:27 final size:28
Alignment explanation
Indices: 26243--26319 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
26233 ATGTGAACTT
*
26243 AAAATGACTAAAATGCCCCTGAATATG-
1 AAAATGACTAAAATGCCCCTGAACATGA
*
26270 CAAATGACTAAAATGCCCCTGGAACATGA
1 AAAATGACTAAAATGCCCCT-GAACATGA
* *
26299 AAAATGACCAAAATACCCCTG
1 AAAATGACTAAAATGCCCCTG
26320 GGTTTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 19 0.44
28 7 0.16
29 17 0.40
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.18
Consensus pattern (28 bp):
AAAATGACTAAAATGCCCCTGAACATGA
Found at i:26317 original size:29 final size:29
Alignment explanation
Indices: 26243--26347 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 29
26233 ATGTGAACTT
*
26243 AAAATGACTAAAATGCCCCT-GAATATG-
1 AAAATGACCAAAATGCCCCTGGAATATGA
* * *
26270 CAAATGACTAAAATGCCCCTGGAACATGA
1 AAAATGACCAAAATGCCCCTGGAATATGA
* ** * *
26299 AAAATGACCAAAATACCCCTGGGTTTTTA
1 AAAATGACCAAAATGCCCCTGGAATATGA
*
26328 AAAATGACCAAAATTCCCCT
1 AAAATGACCAAAATGCCCCT
26348 AGGTGATCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 19 0.29
28 6 0.09
29 40 0.62
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGAATATGA
Found at i:37768 original size:35 final size:33
Alignment explanation
Indices: 37670--37769 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 33
37660 AAAAATGCTT
* *
37670 TGATGGGAACTTTCCCACTTCGAAAACTAAAAC
1 TGATGGGAACTTTCCCAATTTGAAAACTAAAAC
*
37703 TGAAAGTAACGGGAACTTTCCCTAAATTGAAAACTAAAACC
1 TG--A-T---GGGAACTTTCCC-AATTTGAAAACTAAAA-C
37744 TGATGGGAACTTTCCCAATTTTGAAA
1 TGATGGGAACTTTCCCAA-TTTGAAA
37770 GAGCTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
33 2 0.04
34 2 0.04
35 19 0.35
36 1 0.02
38 1 0.02
39 13 0.24
40 13 0.24
41 3 0.06
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (33 bp):
TGATGGGAACTTTCCCAATTTGAAAACTAAAAC
Found at i:38566 original size:81 final size:81
Alignment explanation
Indices: 38454--38620 Score: 316
Period size: 81 Copynumber: 2.1 Consensus size: 81
38444 TAGAAAGGTC
*
38454 AAGCCCAAATAACTAAAACAAGCAAAGCCCAAATACAACTCTATCAAACACAAATAAAGCCCAAC
1 AAGCCCAAATAACTAAAACAAACAAAGCCCAAATACAACTCTATCAAACACAAATAAAGCCCAAC
38519 AGAAAACTATAACTCT
66 AGAAAACTATAACTCT
*
38535 AAGCCCAAATAACTAAAGCAAACAAAGCCCAAATACAACTCTATCAAACACAAATAAAGCCCAAC
1 AAGCCCAAATAACTAAAACAAACAAAGCCCAAATACAACTCTATCAAACACAAATAAAGCCCAAC
38600 AGAAAACTATAACTCT
66 AGAAAACTATAACTCT
38616 AAGCC
1 AAGCC
38621 TAAACATAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.53, C:0.28, G:0.07, T:0.13
Consensus pattern (81 bp):
AAGCCCAAATAACTAAAACAAACAAAGCCCAAATACAACTCTATCAAACACAAATAAAGCCCAAC
AGAAAACTATAACTCT
Found at i:38616 original size:39 final size:39
Alignment explanation
Indices: 38490--38616 Score: 116
Period size: 39 Copynumber: 3.2 Consensus size: 39
38480 GCCCAAATAC
38490 AACTCTATCAAACACAAATAAAGCCCAACAGAAAACTAT
1 AACTCTATCAAACACAAATAAAGCCCAACAGAAAACTAT
* * * * * * *
38529 AACTCTAAGCCCAA-ATAACTAAAG-CAAACA-AAGCCCAAATAC
1 AACTCT-A-TCAAACACAAATAAAGCCCAACAGAA----AACTAT
38571 AACTCTATCAAACACAAATAAAGCCCAACAGAAAACTAT
1 AACTCTATCAAACACAAATAAAGCCCAACAGAAAACTAT
38610 AACTCTA
1 AACTCTA
38617 AGCCTAAACA
Statistics
Matches: 65, Mismatches: 14, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
38 2 0.03
39 22 0.34
40 12 0.18
41 12 0.18
42 15 0.23
43 2 0.03
ACGTcount: A:0.53, C:0.27, G:0.06, T:0.15
Consensus pattern (39 bp):
AACTCTATCAAACACAAATAAAGCCCAACAGAAAACTAT
Found at i:38632 original size:42 final size:41
Alignment explanation
Indices: 38498--38633 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 41
38488 ACAACTCTAT
38498 CAAACACAAATAAAGCCCAACAGAAAACTATAACTCTAAGC
1 CAAACACAAATAAAGCCCAACAGAAAACTATAACTCTAAGC
* * * * * * *
38539 CCAA-ATAACTAAAG-CAAACA-AAGCCCAAATACAACTCT-A-T
1 CAAACACAAATAAAGCCCAACAGAA----AACTATAACTCTAAGC
38579 CAAACACAAATAAAGCCCAACAGAAAACTATAACTCTAAGC
1 CAAACACAAATAAAGCCCAACAGAAAACTATAACTCTAAGC
*
38620 CTAAACATAAATAA
1 C-AAACACAAATAA
38634 TAAACCCAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 19
0.67 0.14 0.18
Matches are distributed among these distances:
38 2 0.03
39 15 0.21
40 12 0.17
41 13 0.19
42 26 0.37
43 2 0.03
ACGTcount: A:0.54, C:0.26, G:0.06, T:0.14
Consensus pattern (41 bp):
CAAACACAAATAAAGCCCAACAGAAAACTATAACTCTAAGC
Found at i:44031 original size:52 final size:52
Alignment explanation
Indices: 43966--44154 Score: 297
Period size: 52 Copynumber: 3.6 Consensus size: 52
43956 ATTGTAAACT
*
43966 AAAACCTGATGGGAACTTTCTCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* * *
44019 AAAACTGATGGGAACTCTCCCAATTGGAAAAAGAGCTAAATCGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* *
44071 AAAACAGATGGGAAATTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
*
44123 AAGACTTGATGGGAACTTTCCCAATTTGAAAA
1 AAAAC-TGATGGGAACTTTCCCAATTTGAAAA
44155 CTTAAAAACT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 95 0.77
53 28 0.23
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
Found at i:44252 original size:18 final size:17
Alignment explanation
Indices: 44212--44260 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 17
44202 TGAAATTCTT
44212 TTTTTGATTTTTG---A
1 TTTTTGATTTTTGAAAA
44226 TTTTTGATTTTTGAAAA
1 TTTTTGATTTTTGAAAA
44243 TTTTTGGATTTTTGAAAA
1 TTTTT-GATTTTTGAAAA
44261 CATTTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.42
17 6 0.19
18 12 0.39
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.61
Consensus pattern (17 bp):
TTTTTGATTTTTGAAAA
Found at i:44254 original size:7 final size:7
Alignment explanation
Indices: 44212--44239 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
44202 TGAAATTCTT
44212 TTTTTGA
1 TTTTTGA
44219 TTTTTGA
1 TTTTTGA
44226 TTTTTGA
1 TTTTTGA
44233 TTTTTGA
1 TTTTTGA
44240 AAATTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (7 bp):
TTTTTGA
Found at i:48054 original size:15 final size:15
Alignment explanation
Indices: 48024--48065 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
48014 TTACTTTGTT
48024 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
48040 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
48055 TTGTTTTCTGT
1 TTGTTTTCTGT
48066 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.