Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013075.1 Corchorus olitorius cultivar O-4 contig13108, 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: 21746
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2186 original size:34 final size:34
Alignment explanation
Indices: 2143--2210 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2133 TCAATCTAAG
2143 CAAACTGTGAATTTCCTTTAACAGAGCATGCACT
1 CAAACTGTGAATTTCCTTTAACAGAGCATGCACT
2177 CAAACTGTGAATTTCCTTTAACAGAGCATGCACT
1 CAAACTGTGAATTTCCTTTAACAGAGCATGCACT
2211 TCATGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (34 bp):
CAAACTGTGAATTTCCTTTAACAGAGCATGCACT
Found at i:2828 original size:18 final size:19
Alignment explanation
Indices: 2805--2843 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2795 CTAAAGTTAA
*
2805 AATGCCTAA-TGCAAGCCC
1 AATGCCCAAGTGCAAGCCC
2823 AATGCCCAAGTGCAAGCCC
1 AATGCCCAAGTGCAAGCCC
2842 AA
1 AA
2844 AGCTAAGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (19 bp):
AATGCCCAAGTGCAAGCCC
Found at i:2853 original size:18 final size:19
Alignment explanation
Indices: 2808--2854 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2798 AAGTTAAAAT
*
2808 GCCTAA-TGCAAGCCCAAT
1 GCCTAAGTGCAAGCCCAAA
*
2826 GCCCAAGTGCAAGCCCAAA
1 GCCTAAGTGCAAGCCCAAA
2845 G-CTAAGTGCA
1 GCCTAAGTGCA
2855 TCTAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (19 bp):
GCCTAAGTGCAAGCCCAAA
Found at i:3123 original size:28 final size:26
Alignment explanation
Indices: 3092--3182 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 26
3082 AATGACCGAG
* *
3092 ATGCCCTTGAATGTGCAAAATGAGCAAA
1 ATGCCCCTGAACGTGC-AAATGA-CAAA
*
3120 ATGCCCCTGGACGTGCAAATGACAAAA
1 ATGCCCCTGAACGTGCAAATGAC-AAA
*
3147 ATGCCCCTGAACATGCAAATGACCCAAA
1 ATGCCCCTGAACGTGCAAATGA--CAAA
3175 ATGCCCCT
1 ATGCCCCT
3183 AGATGACCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.53
28 24 0.44
29 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (26 bp):
ATGCCCCTGAACGTGCAAATGACAAA
Found at i:3147 original size:27 final size:27
Alignment explanation
Indices: 3081--3182 Score: 114
Period size: 28 Copynumber: 3.7 Consensus size: 27
3071 AGTGAGCTTA
* * * *
3081 AAATGACCGAGATGCCCTTGAATGTGC
1 AAATGACCAAAATGCCCCTGAACGTGC
* *
3108 AAAATGAGCAAAATGCCCCTGGACGTGC
1 -AAATGACCAAAATGCCCCTGAACGTGC
* *
3136 AAATGACAAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACGTGC
3163 AAATGACCCAAAATGCCCCT
1 AAATGA-CCAAAATGCCCCT
3183 AGATGACCTT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
27 29 0.47
28 33 0.53
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACGTGC
Found at i:3770 original size:50 final size:50
Alignment explanation
Indices: 3641--4031 Score: 611
Period size: 50 Copynumber: 7.7 Consensus size: 50
3631 ATGTTTGAAC
* *
3641 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTACGTGGCTTGGATAGT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA--T-G-TT-GATAAT
* *
3696 TGACTCGTACGGAAACGAGTTTGGCTTGTGGAAAAGTCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
3746 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTAATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
3796 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* * * *
3846 TGACTCGTATGCAAACAAATTTGGCTTGTGGAAAAGTCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
3896 TGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
3946 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
3996 TGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
4032 TGATCGAGCC
Statistics
Matches: 313, Mismatches: 23, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
50 272 0.87
51 2 0.01
52 1 0.00
53 1 0.00
55 37 0.12
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:8821 original size:17 final size:17
Alignment explanation
Indices: 8799--8831 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8789 AAGGGTAATT
*
8799 AAAAAATTGTTTTCATA
1 AAAAAAGTGTTTTCATA
8816 AAAAAAGTGTTTTCAT
1 AAAAAAGTGTTTTCAT
8832 GATAGAGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
AAAAAAGTGTTTTCATA
Found at i:11011 original size:79 final size:82
Alignment explanation
Indices: 10880--11298 Score: 450
Period size: 91 Copynumber: 4.8 Consensus size: 82
10870 ATACCTTTGG
* * * * *
10880 AAAATATCTCTGAATCTGATGCTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
*
10945 TGC-G-G-TCAACTTGA
66 TGCAGTGAACAACTTGA
* * *
10959 AAAATAACTCTGAGTTTGATGTTGTAGCTGAAAGCTTCTTGATTGATGATGAAAGAGGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
11024 TGCAGTCAACTTGAAAAACAACTTGA
66 TGCAG------TG---AACAACTTGA
*
11050 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGAACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
11115 TGCAGTCAACTTGAAAAACAACTTGA
66 TGCAG------TG---AACAACTTGA
* *
11141 AAAATAACTCTGAGTCTGATGTTCTAACTGGAAACTTCTTGATTGATGATGAAAGAGGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
11206 TGCAGTCAACTTGAAAAACAACTTGA
66 TGCAG------TG---AACAACTTGA
*
11232 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAA-AAGACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
11296 TGC
66 TGC
11299 GGTCAATTTT
Statistics
Matches: 309, Mismatches: 19, Indels: 13
0.91 0.06 0.04
Matches are distributed among these distances:
79 60 0.19
80 1 0.00
87 1 0.00
90 12 0.04
91 235 0.76
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (82 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAATT
TGCAGTGAACAACTTGA
Found at i:11070 original size:91 final size:91
Alignment explanation
Indices: 10951--11341 Score: 630
Period size: 91 Copynumber: 4.3 Consensus size: 91
10941 AATGTGCGGT
* * *
10951 CAACTTGAAAAATAACTCTGAGTTTGATGTTGTAGCTGAAAGCTTCTTGATTGATGATGAAAGAG
1 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAG
11016 GACCAATTTGCAGTCAACTTGAAAAA
66 GACCAATTTGCAGTCAACTTGAAAAA
11042 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAG
1 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAG
*
11107 AACCAATTTGCAGTCAACTTGAAAAA
66 GACCAATTTGCAGTCAACTTGAAAAA
* *
11133 CAACTTGAAAAATAACTCTGAGTCTGATGTTCTAACTGGAAACTTCTTGATTGATGATGAAAGAG
1 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAG
11198 GACCAATTTGCAGTCAACTTGAAAAA
66 GACCAATTTGCAGTCAACTTGAAAAA
*
11224 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAA-AA
1 CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAG
* *
11288 GACCAATTTGCGGTCAATTTTG----A
66 GACCAATTTGCAGTCAA-CTTGAAAAA
* * *
11311 TAATTTGAAGAATAACTCTGAGTCTGATGTT
1 CAACTTGAAAAATAACTCTGAGTCTGATGTT
11342 ATGATTAAAA
Statistics
Matches: 284, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
87 29 0.10
90 17 0.06
91 238 0.84
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (91 bp):
CAACTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAG
GACCAATTTGCAGTCAACTTGAAAAA
Found at i:11258 original size:182 final size:178
Alignment explanation
Indices: 10880--11341 Score: 658
Period size: 182 Copynumber: 2.6 Consensus size: 178
10870 ATACCTTTGG
* * * *
10880 AAAATATCTCTGAATCTGATGCTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAA-GACCAATT
* * * *
10945 TGC-G--------GTCAACTTGAAAAATAACTCTGAGTTTGATGTTGTAGCTGAAAGCTTCTTGA
65 TGCAGTCAATCTTGACAACTTGAAAAATAACTCTGAGTCTGATGTTCTAACTGAAAGCTTCTTGA
11001 TTGATGATGAAAGAGGACCAATTTGCAGTCAACTTGAAAAACAACTTGA
130 TTGATGATGAAAGAGGACCAATTTGCAGTCAACTTGAAAAACAACTTGA
*
11050 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGAACCAATT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAG-ACCAATT
11115 TGCAGTCAA-CTTGAAAAACAACTTGAAAAATAACTCTGAGTCTGATGTTCTAACTGGAAA-CTT
65 TGCAGTCAATCTTG----ACAACTTGAAAAATAACTCTGAGTCTGATGTTCTAACT-GAAAGCTT
11178 CTTGATTGATGATGAAAGAGGACCAATTTGCAGTCAACTTGAAAAACAACTTGA
125 CTTGATTGATGATGAAAGAGGACCAATTTGCAGTCAACTTGAAAAACAACTTGA
11232 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGACCAATTT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGACCAATTT
* * * * *
11297 GCGGTCAATTTTGATAATTTGAAGAATAACTCTGAGTCTGATGTT
66 GCAGTCAATCTTGACAACTTGAAAAATAACTCTGAGTCTGATGTT
11342 ATGATTAAAA
Statistics
Matches: 262, Mismatches: 15, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
169 1 0.00
170 61 0.23
171 1 0.00
178 30 0.11
181 15 0.06
182 150 0.57
183 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (178 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGACCAATTT
GCAGTCAATCTTGACAACTTGAAAAATAACTCTGAGTCTGATGTTCTAACTGAAAGCTTCTTGAT
TGATGATGAAAGAGGACCAATTTGCAGTCAACTTGAAAAACAACTTGA
Found at i:11903 original size:50 final size:50
Alignment explanation
Indices: 11757--11906 Score: 228
Period size: 50 Copynumber: 3.0 Consensus size: 50
11747 CTTCAATGTC
* * *
11757 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * *
11807 CTTTGAAAAGCAAATTTTTATCTTGAACTCACAAAGGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* *
11857 CTTTGAAAAGTGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
11907 TTGTAAAACT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:11942 original size:15 final size:16
Alignment explanation
Indices: 11911--11944 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11901 ATTTTATTGT
11911 AAAACTTCTTGTTCTG
1 AAAACTTCTTGTTCTG
*
11927 AAAACTT-TTTTTCTG
1 AAAACTTCTTGTTCTG
11942 AAA
1 AAA
11945 CATGATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (16 bp):
AAAACTTCTTGTTCTG
Found at i:12529 original size:25 final size:26
Alignment explanation
Indices: 12495--12543 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
12485 TCTCTTTTGA
12495 TTTTGATTTGATTTGATTTTTTTGTT
1 TTTTGATTTGATTTGATTTTTTTGTT
* **
12521 TTTTG-TTTGTTTTTTTTTTTTTG
1 TTTTGATTTGATTTGATTTTTTTG
12544 AATTTCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (26 bp):
TTTTGATTTGATTTGATTTTTTTGTT
Found at i:12534 original size:20 final size:20
Alignment explanation
Indices: 12501--12544 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
12491 TTGATTTTGA
12501 TTTGATTTGATTTTTTTGTTT
1 TTTGATTTGATTTTTTT-TTT
12522 TTTG-TTTG-TTTTTTTTTT
1 TTTGATTTGATTTTTTTTTT
12540 TTTGA
1 TTTGA
12545 ATTTCTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 4 0.18
21 4 0.18
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.80
Consensus pattern (20 bp):
TTTGATTTGATTTTTTTTTT
Found at i:13044 original size:14 final size:16
Alignment explanation
Indices: 13025--13056 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
13015 CCTGAGCGAA
13025 TTGATT-TGCACT-CT
1 TTGATTGTGCACTGCT
13039 TTGATTGTGCACTGCT
1 TTGATTGTGCACTGCT
13055 TT
1 TT
13057 TTCGGGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (16 bp):
TTGATTGTGCACTGCT
Found at i:18112 original size:17 final size:18
Alignment explanation
Indices: 18087--18133 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
18077 TTATTGCCTC
*
18087 TTTTAATTTTCAT-GATT
1 TTTTCATTTTCATGGATT
**
18104 TTTTCATTTTTTTGGATT
1 TTTTCATTTTCATGGATT
18122 TTTTCCATTTTC
1 TTTT-CATTTTC
18134 TACCTCTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 8 0.33
19 6 0.25
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTTCATTTTCATGGATT
Found at i:20942 original size:34 final size:34
Alignment explanation
Indices: 20899--20965 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
20889 CAATCTAAGC
20899 AAACTGTGAATTTCCTTTAACAGAGCATGCACTA
1 AAACTGTGAATTTCCTTTAACAGAGCATGCACTA
20933 AAACTGTGAATTTCCTTTAACAGAGCATGCACT
1 AAACTGTGAATTTCCTTTAACAGAGCATGCACT
20966 TCAGGAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (34 bp):
AAACTGTGAATTTCCTTTAACAGAGCATGCACTA
Found at i:21573 original size:18 final size:19
Alignment explanation
Indices: 21550--21588 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21540 CTAAAGTTAA
*
21550 AATGCCTAA-TGCAAGCCC
1 AATGCCCAAGTGCAAGCCC
21568 AATGCCCAAGTGCAAGCCC
1 AATGCCCAAGTGCAAGCCC
21587 AA
1 AA
21589 AGCTAAGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (19 bp):
AATGCCCAAGTGCAAGCCC
Found at i:21598 original size:18 final size:19
Alignment explanation
Indices: 21553--21599 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
21543 AAGTTAAAAT
*
21553 GCCTAA-TGCAAGCCCAAT
1 GCCTAAGTGCAAGCCCAAA
*
21571 GCCCAAGTGCAAGCCCAAA
1 GCCTAAGTGCAAGCCCAAA
21590 G-CTAAGTGCA
1 GCCTAAGTGCA
21600 TCTAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (19 bp):
GCCTAAGTGCAAGCCCAAA
Done.