Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016360.1 Corchorus olitorius cultivar O-4 contig16393, 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: 74900
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17353 original size:27 final size:27
Alignment explanation
Indices: 17315--17400 Score: 145
Period size: 27 Copynumber: 3.2 Consensus size: 27
17305 GATGGCCTAA
17315 CGATGGTCTAAAGTTAATGCTTTAGGC
1 CGATGGTCTAAAGTTAATGCTTTAGGC
17342 CGATGGTCTAAAGTTAATGCTTTAGGC
1 CGATGGTCTAAAGTTAATGCTTTAGGC
* * *
17369 CGATGGCCTAAAATTAATGATTTAGGC
1 CGATGGTCTAAAGTTAATGCTTTAGGC
17396 CGATG
1 CGATG
17401 TCCTTGAATC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (27 bp):
CGATGGTCTAAAGTTAATGCTTTAGGC
Found at i:27637 original size:83 final size:83
Alignment explanation
Indices: 27542--27701 Score: 234
Period size: 83 Copynumber: 1.9 Consensus size: 83
27532 TTTGAGAAAG
* *
27542 TTTTTCTTAAATTTCTAAACCCTATGATTTTTACCGGCGGAAC-ATATGACCCAAATTCATAATA
1 TTTTTCTGAAATTTCAAAACCCTATGATTTTTACCGGCGGAACGA-ATGACCCAAATTCATAATA
27606 TG-TTTTAAAGTGTGACATT
65 TGCTTTT-AAGTGTGACATT
** * *
27625 TTTTTCTGAAATTTCAAAACCCTATGATTTTTAGGGGCGGAGCGAATGACCCAAATTCATATTAT
1 TTTTTCTGAAATTTCAAAACCCTATGATTTTTACCGGCGGAACGAATGACCCAAATTCATAATAT
27690 GCTTTTAAGTGT
66 GCTTTTAAGTGT
27702 TGGTACTCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 64 0.93
84 5 0.07
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (83 bp):
TTTTTCTGAAATTTCAAAACCCTATGATTTTTACCGGCGGAACGAATGACCCAAATTCATAATAT
GCTTTTAAGTGTGACATT
Found at i:28960 original size:167 final size:167
Alignment explanation
Indices: 28684--29016 Score: 605
Period size: 167 Copynumber: 2.0 Consensus size: 167
28674 AAAGTTGGTG
28684 ATGGGAATCTCTATTTGCAGCAAAAGGGATGACATTCCTATTATACATCAAGGTATAATGGTGCA
1 ATGGGAATCTCTATTTGCAGCAAAAGGGATGACATTCCTATTATACATCAAGGTATAATGGTGCA
* *
28749 TCCAAATCAGGGTTGGTAATGAGAATTCTTTTTATGTAGTTAAAGGAACAATGTGGTGGCATTCC
66 TCCAAATAAAGGTTGGTAATGAGAATTCTTTTTATGTAGTTAAAGGAACAATGTGGTGGCATTCC
*
28814 TACTATACATAAAGGTATAGTGGTGTCAGTTCATGTA
131 TACTATACATAAAGGTATAGTGGTGCCAGTTCATGTA
*
28851 ATGGGAATCTCTATTTGCAGCAAAAGGGATGGCATTCCTATTATACATCAAGGTATAATGGTGCA
1 ATGGGAATCTCTATTTGCAGCAAAAGGGATGACATTCCTATTATACATCAAGGTATAATGGTGCA
*
28916 TCCAAATAAAGGTTGGTAATGAGAATAT-TTTTTATGTAGTTAAAGGCACAATGTGGTGGCATTC
66 TCCAAATAAAGGTTGGTAATGAGAAT-TCTTTTTATGTAGTTAAAGGAACAATGTGGTGGCATTC
28980 CTACTATACATAAAGGTATAGTGGTGCCAGTTCATGT
130 CTACTATACATAAAGGTATAGTGGTGCCAGTTCATGT
29017 GCACTGAAAT
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
167 159 0.99
168 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (167 bp):
ATGGGAATCTCTATTTGCAGCAAAAGGGATGACATTCCTATTATACATCAAGGTATAATGGTGCA
TCCAAATAAAGGTTGGTAATGAGAATTCTTTTTATGTAGTTAAAGGAACAATGTGGTGGCATTCC
TACTATACATAAAGGTATAGTGGTGCCAGTTCATGTA
Found at i:29466 original size:29 final size:29
Alignment explanation
Indices: 29411--29466 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
29401 GTGTTGGCAT
* * *
29411 TCCTACTATACATGAAGGTTTAGTGGTAC
1 TCCTACTATACATAAAGGTATAATGGTAC
*
29440 TCCTATTATACATAAAGGTATAATGGT
1 TCCTACTATACATAAAGGTATAATGGT
29467 GCCAATTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (29 bp):
TCCTACTATACATAAAGGTATAATGGTAC
Found at i:32834 original size:19 final size:19
Alignment explanation
Indices: 32810--32851 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
32800 AGAGCTCTAT
32810 GCATATGAAAAAATGTGCA
1 GCATATGAAAAAATGTGCA
32829 GCATATGAAAAAATGTGCA
1 GCATATGAAAAAATGTGCA
32848 GCAT
1 GCAT
32852 TGTGTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (19 bp):
GCATATGAAAAAATGTGCA
Found at i:36808 original size:21 final size:21
Alignment explanation
Indices: 36782--36823 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36772 TATGCACTAG
*
36782 TATGTTTAAA-TTGTGGTTATC
1 TATG-TTAAAGTTATGGTTATC
36803 TATGTTAAAGTTATGGTTATC
1 TATGTTAAAGTTATGGTTATC
36824 CAGAGGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (21 bp):
TATGTTAAAGTTATGGTTATC
Found at i:39144 original size:42 final size:43
Alignment explanation
Indices: 39042--39127 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 43
39032 TAATACGCTT
*
39042 TGGAATTCTTTTT-CAATTGGTAAGATTATTCAACGTTAATAC
1 TGGAATTCTTTTTAAAATTGGTAAGATTATTCAACGTTAATAC
* *
39084 TGGAATTCTTTTTAAAATTGGTAATATTATTCAAC-TTTATAC
1 TGGAATTCTTTTTAAAATTGGTAAGATTATTCAACGTTAATAC
39126 TG
1 TG
39128 ATTTTTGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 21 0.52
43 19 0.47
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (43 bp):
TGGAATTCTTTTTAAAATTGGTAAGATTATTCAACGTTAATAC
Found at i:42182 original size:63 final size:63
Alignment explanation
Indices: 42083--42224 Score: 257
Period size: 63 Copynumber: 2.3 Consensus size: 63
42073 TGGGGACCCT
* *
42083 CAACATAGCTTCGTGTGAAACCTCTATAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
1 CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
42146 CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
1 CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
*
42209 CAACATAGCTTGGTGC
1 CAACATAGCTTCGTGC
42225 TGCTTCTCAG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 76 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (63 bp):
CAACATAGCTTCGTGCGAAACCTCTACAGCTCTTCTACCGAACCAAGCTATACTTTTACCGAA
Found at i:42361 original size:61 final size:62
Alignment explanation
Indices: 42288--42409 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 62
42278 AATGTATTTT
*
42288 GATAATATACTAAGCTTTAACTTCTAATTAAT-ATATTCATTGTTATTTAAATATTTGTTTG
1 GATAATATACTAAGCTTTAACTTCTAATTAATAATATTCATTATTATTTAAATATTTGTTTG
**
42349 GATAATATACTAAGCTTTCGCTTCTAATTAATAATATTCATTATTATTTAAATATTTGTTT
1 GATAATATACTAAGCTTTAACTTCTAATTAATAATATTCATTATTATTTAAATATTTGTTT
42410 TAATTAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 30 0.53
62 27 0.47
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.49
Consensus pattern (62 bp):
GATAATATACTAAGCTTTAACTTCTAATTAATAATATTCATTATTATTTAAATATTTGTTTG
Found at i:42471 original size:79 final size:76
Alignment explanation
Indices: 42334--42497 Score: 267
Period size: 79 Copynumber: 2.1 Consensus size: 76
42324 TCATTGTTAT
*
42334 TTAAATATTTGTTTGGATAATATACTAAGCTTTCGCTTCTAATTAATAATATTCATTATTATTTA
1 TTAAATATTTGTTTGGATAATATACTAAGCTTTCACTTCTAATTAAT-AT-TTCATTATTATTTA
42399 AATATTTGTTTTAA
64 AATATTTG-TTTAA
*
42413 TTAAATATTTGTTTTGATAATATACTAAGCTTTCACTTCTAATTAATATTT-ATTATTATTTAAA
1 TTAAATATTTGTTTGGATAATATACTAAGCTTTCACTTCTAATTAATATTTCATTATTATTTAAA
42477 TATTTGTTTAA
66 TATTTGTTTAA
*
42488 TTGAATATTT
1 TTAAATATTT
42498 TAATTTCTTA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
75 14 0.17
76 19 0.23
77 2 0.02
78 2 0.02
79 45 0.55
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (76 bp):
TTAAATATTTGTTTGGATAATATACTAAGCTTTCACTTCTAATTAATATTTCATTATTATTTAAA
TATTTGTTTAA
Found at i:42892 original size:19 final size:17
Alignment explanation
Indices: 42868--42909 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
42858 CTAAAAGTTC
42868 CAAGAAAAGAAAGAGAGGG
1 CAAGAAAAG--AGAGAGGG
*
42887 CAAGAACAGAGAGAGGG
1 CAAGAAAAGAGAGAGGG
42904 CAAGAA
1 CAAGAA
42910 CGCGCAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.64
19 8 0.36
ACGTcount: A:0.55, C:0.10, G:0.36, T:0.00
Consensus pattern (17 bp):
CAAGAAAAGAGAGAGGG
Found at i:44039 original size:154 final size:155
Alignment explanation
Indices: 43759--44061 Score: 536
Period size: 154 Copynumber: 2.0 Consensus size: 155
43749 CAAAACAATG
*
43759 GCATTCCTATTATACATTGAGGTATAATGGTGCATATGAATAAAGGTTGGCAATGGGAATTTTTA
1 GCATTCCTATTATACATTAAGGTATAATGGTGCATATGAATAAAGGTTGGCAATGGGAATTTTTA
* *
43824 TTATGCAGTAAAAGACACAATGTGTTGGCATTCCTATTATACATAAAGGTATAGTGGTGCCA-TT
66 TTATGCAGTAAAAGACACAATGTGGTGGCATTCCTATTATACATAAAGGTATAGTGGTGCCACCT
*
43888 TGAGTAATATACTTTAATAACAGTA
131 CGAGTAATATACTTTAATAACAGTA
* *
43913 GCATTCCTATTATACATTAAGGTATAATGGTGCATCTGAATAAAGGTTGGCAGTGGGAATTTTTA
1 GCATTCCTATTATACATTAAGGTATAATGGTGCATATGAATAAAGGTTGGCAATGGGAATTTTTA
*
43978 TTATGCAGTAAAAGGCACAATGTGGTGGCATTCCTATTATACATAAAGGTATAGTGGTGCCACCT
66 TTATGCAGTAAAAGACACAATGTGGTGGCATTCCTATTATACATAAAGGTATAGTGGTGCCACCT
44043 CGAGTAATATACTTTAATA
131 CGAGTAATATACTTTAATA
44062 CATCGCACTT
Statistics
Matches: 141, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
154 122 0.87
155 19 0.13
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (155 bp):
GCATTCCTATTATACATTAAGGTATAATGGTGCATATGAATAAAGGTTGGCAATGGGAATTTTTA
TTATGCAGTAAAAGACACAATGTGGTGGCATTCCTATTATACATAAAGGTATAGTGGTGCCACCT
CGAGTAATATACTTTAATAACAGTA
Found at i:48374 original size:28 final size:28
Alignment explanation
Indices: 48342--48401 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
48332 TGGAACTTGA
* * *
48342 ATTATGATGGAGCTATTGACATGGTTGG
1 ATTATGATCGAGCTATTGACATCGCTGG
*
48370 ATTATGATCGAGTTATTGACATCGCTGG
1 ATTATGATCGAGCTATTGACATCGCTGG
48398 ATTA
1 ATTA
48402 ACACTACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (28 bp):
ATTATGATCGAGCTATTGACATCGCTGG
Found at i:63720 original size:14 final size:14
Alignment explanation
Indices: 63703--63737 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
63693 GATTATTGTT
63703 TTTTTCATGCTCTG
1 TTTTTCATGCTCTG
*
63717 TTTTTAATGCTCTG
1 TTTTTCATGCTCTG
63731 TATTTTC
1 T-TTTTC
63738 TTTCCTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.60
Consensus pattern (14 bp):
TTTTTCATGCTCTG
Found at i:65032 original size:40 final size:40
Alignment explanation
Indices: 64977--65056 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
64967 AAGCATGGAA
64977 GGTTTGTTTCAACTCTGATGCAGTGATGCTTAATGTCTTT
1 GGTTTGTTTCAACTCTGATGCAGTGATGCTTAATGTCTTT
65017 GGTTTGTTTCAACTCTGATGCAGTGATGCTTAATGTCTTT
1 GGTTTGTTTCAACTCTGATGCAGTGATGCTTAATGTCTTT
65057 TAATAACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (40 bp):
GGTTTGTTTCAACTCTGATGCAGTGATGCTTAATGTCTTT
Found at i:65118 original size:34 final size:34
Alignment explanation
Indices: 65080--65144 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
65070 ATAAGTACTG
*
65080 CTATTGGTTAATTGTCTTTTTCAGTTAAAAGTTA
1 CTATTGGTTAACTGTCTTTTTCAGTTAAAAGTTA
*
65114 CTATTGGTTAACTGTCTTTTTCAGTTTAAAG
1 CTATTGGTTAACTGTCTTTTTCAGTTAAAAG
65145 AATCAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (34 bp):
CTATTGGTTAACTGTCTTTTTCAGTTAAAAGTTA
Found at i:74352 original size:43 final size:43
Alignment explanation
Indices: 74304--74442 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 43
74294 AGATTTTGTT
74304 AATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGAC
1 AATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGAC
* ** * * * * * **
74347 AATCTCTCTATAA-AATTATATA-TA-ATTATCAGATTTTGTT
1 AATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGAC
74387 AATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGAC
1 AATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGAC
*
74430 AATCTCTCTATAA
1 AATCTCCCTATAA
74443 AATTATATAT
Statistics
Matches: 72, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
40 22 0.31
41 8 0.11
42 8 0.11
43 34 0.47
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.45
Consensus pattern (43 bp):
AATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGAC
Found at i:74404 original size:83 final size:83
Alignment explanation
Indices: 74294--74464 Score: 342
Period size: 83 Copynumber: 2.1 Consensus size: 83
74284 CTTCCCTATG
74294 AGATTTTGTTAATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGACAATCTCTCTATA
1 AGATTTTGTTAATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGACAATCTCTCTATA
74359 AAATTATATATAATTATC
66 AAATTATATATAATTATC
74377 AGATTTTGTTAATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGACAATCTCTCTATA
1 AGATTTTGTTAATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGACAATCTCTCTATA
74442 AAATTATATATAATTATC
66 AAATTATATATAATTATC
74460 AGATT
1 AGATT
74465 GAGCTCCTCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 88 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (83 bp):
AGATTTTGTTAATCTCCCTATAATTTTTTTATACTATAGTATGAAATTTCGACAATCTCTCTATA
AAATTATATATAATTATC
Done.