Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009537.1 Corchorus olitorius cultivar O-4 contig09569, 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: 9146
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Found at i:1842 original size:43 final size:43
Alignment explanation
Indices: 1795--1893 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
1785 TAGTAATTCA
*
1795 GTAATAGTAGTCAATAA-AGAATAAAAGAGTAAACAGTAAAATG
1 GTAATAGTAATCAATAATAGAAT-AAAGAGTAAACAGTAAAATG
* * *
1838 GTAATGGTAATCAATAATAGAGTAAAGAGTAATCAGTAAAA-G
1 GTAATAGTAATCAATAATAGAATAAAGAGTAAACAGTAAAATG
*
1880 AGCAATAGTAATCA
1 -GTAATAGTAATCA
1894 GTTAAAGAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.02
43 43 0.90
44 4 0.08
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (43 bp):
GTAATAGTAATCAATAATAGAATAAAGAGTAAACAGTAAAATG
Found at i:1894 original size:21 final size:22
Alignment explanation
Indices: 1865--1912 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
1855 TAGAGTAAAG
1865 AGTAATCAGTAAAAGAGCAAT-
1 AGTAATCAGTAAAAGAGCAATC
*
1886 AGTAATCAGTTAAAGAGCAATC
1 AGTAATCAGTAAAAGAGCAATC
1908 AGTAA
1 AGTAA
1913 ATGGTAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (22 bp):
AGTAATCAGTAAAAGAGCAATC
Found at i:2007 original size:21 final size:21
Alignment explanation
Indices: 1980--2051 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1970 AAGAAAGAGG
1980 AATAGTAATCAGTAAAATGGT
1 AATAGTAATCAGTAAAATGGT
* *
2001 CATAGTAACCAGT-AAA-GAGT
1 AATAGTAATCAGTAAAATG-GT
*
2021 AAATAGTAATCA-AAAAATGGT
1 -AATAGTAATCAGTAAAATGGT
2042 AATAGTAATC
1 AATAGTAATC
2052 GTTAATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.02
20 15 0.36
21 25 0.60
22 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (21 bp):
AATAGTAATCAGTAAAATGGT
Found at i:2008 original size:41 final size:42
Alignment explanation
Indices: 1963--2051 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
1953 AATAGTAAAG
* * *
1963 AGTAATCAAG-AAAGAG-GAATAGTAATCAGTAAAATGGTCAT
1 AGTAATCAAGTAAAGAGTAAATAGTAATCA-AAAAATGGTAAT
*
2004 AGTAA-CCAGTAAAGAGTAAATAGTAATCAAAAAATGGTAAT
1 AGTAATCAAGTAAAGAGTAAATAGTAATCAAAAAATGGTAAT
2045 AGTAATC
1 AGTAATC
2052 GTTAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 3 0.07
41 26 0.63
42 12 0.29
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (42 bp):
AGTAATCAAGTAAAGAGTAAATAGTAATCAAAAAATGGTAAT
Found at i:2047 original size:20 final size:19
Alignment explanation
Indices: 1963--2051 Score: 63
Period size: 21 Copynumber: 4.4 Consensus size: 19
1953 AATAGTAAAG
1963 AGTAATCAAGAAAGAGG-AAT
1 AGTAATCAA-AAA-AGGTAAT
* *
1983 AGTAATCAGTAAAATGGTCAT
1 AGTAATCA--AAAAAGGTAAT
* **
2004 AGTAACCAGTAAAGAGTAAAT
1 AGTAATCAAAAAAG-GT-AAT
2025 AGTAATCAAAAAATGGTAAT
1 AGTAATCAAAAAA-GGTAAT
2045 AGTAATC
1 AGTAATC
2052 GTTAATTAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
19 3 0.06
20 22 0.42
21 26 0.49
22 2 0.04
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (19 bp):
AGTAATCAAAAAAGGTAAT
Found at i:2139 original size:34 final size:34
Alignment explanation
Indices: 2079--2164 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
2069 AAGAAAAGGT
*
2079 AGTAATTAAAGTGAAAAAAAATTAAAAATGGAATTC
1 AGTAATTAAAGT--AAAAAAAGTAAAAATGGAATTC
*
2115 AGTAATTAAAGTAAAAAAAGTAAAAATGGTATTC
1 AGTAATTAAAGTAAAAAAAGTAAAAATGGAATTC
2149 AGTAATTAAAGTAAAA
1 AGTAATTAAAGTAAAA
2165 CAGGAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 36 0.75
36 12 0.25
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.26
Consensus pattern (34 bp):
AGTAATTAAAGTAAAAAAAGTAAAAATGGAATTC
Found at i:2174 original size:34 final size:34
Alignment explanation
Indices: 2079--2180 Score: 125
Period size: 34 Copynumber: 2.9 Consensus size: 34
2069 AAGAAAAGGT
2079 AGTAATTAAAGTGAAAAAAA-ATTAAAAATGGAATTC
1 AGTAATTAAAGT-AAAAAAAGA--AAAAATGGAATTC
* *
2115 AGTAATTAAAGTAAAAAAAGTAAAAATGGTATTC
1 AGTAATTAAAGTAAAAAAAGAAAAAATGGAATTC
* *
2149 AGTAATTAAAGTAAAACAGGAAAAAAATGGAA
1 AGTAATTAAAGTAAAAAAAG-AAAAAATGGAA
2181 ACAAAATAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
34 30 0.52
35 16 0.28
36 12 0.21
ACGTcount: A:0.59, C:0.03, G:0.16, T:0.23
Consensus pattern (34 bp):
AGTAATTAAAGTAAAAAAAGAAAAAATGGAATTC
Found at i:2244 original size:27 final size:27
Alignment explanation
Indices: 2157--2251 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
2147 TCAGTAATTA
* *
2157 AAGTAAAACAG-G-AAAAAAATGGAAACA
1 AAGTAAAA-AGAGTAAAAAAATGGTAA-T
* *
2184 AAATAAAAAG-GTAAGAAAATGGTAAT
1 AAGTAAAAAGAGTAAAAAAATGGTAAT
* *
2210 AAGCAAAAAGAGTAAAAAAATGGTGAT
1 AAGTAAAAAGAGTAAAAAAATGGTAAT
*
2237 CAGTAAAAAGAGTAA
1 AAGTAAAAAGAGTAA
2252 GGTTAATCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 11 0.20
27 45 0.80
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.14
Consensus pattern (27 bp):
AAGTAAAAAGAGTAAAAAAATGGTAAT
Found at i:2335 original size:32 final size:36
Alignment explanation
Indices: 2272--2338 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 36
2262 TAATTTAGTT
*
2272 AAAAAAAGAGATGAGTAAACAATGGTAATCAGTAAA
1 AAAAAAAGAGATAAGTAAACAATGGTAATCAGTAAA
*
2308 AAAAAAAGAG-TAAG-AAA-AAT-GTGATCAGTAA
1 AAAAAAAGAGATAAGTAAACAATGGTAATCAGTAA
2339 TTTAATTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.34
33 3 0.10
34 3 0.10
35 3 0.10
36 10 0.34
ACGTcount: A:0.60, C:0.04, G:0.19, T:0.16
Consensus pattern (36 bp):
AAAAAAAGAGATAAGTAAACAATGGTAATCAGTAAA
Found at i:3616 original size:36 final size:36
Alignment explanation
Indices: 3576--3651 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3566 TAATCGCTTT
*
3576 TTTTCTTTTTGCAGAAGCATTTGTATAACCCTTTTG
1 TTTTCTCTTTGCAGAAGCATTTGTATAACCCTTTTG
3612 TTTTCTCTTTGCAGAAGCATTTGTATAACCCTTTTG
1 TTTTCTCTTTGCAGAAGCATTTGTATAACCCTTTTG
3648 TTTT
1 TTTT
3652 GCAGGTTGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.18, C:0.17, G:0.13, T:0.51
Consensus pattern (36 bp):
TTTTCTCTTTGCAGAAGCATTTGTATAACCCTTTTG
Found at i:5007 original size:14 final size:13
Alignment explanation
Indices: 4988--5039 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
4978 AACAAGAGGT
4988 TTTTCAAAAATATG
1 TTTTCAAAAATA-G
5002 TTTTCAAGAAA-AGG
1 TTTTCAA-AAATA-G
5016 TTTTCAAAAATGAG
1 TTTTCAAAAAT-AG
5030 TTTTCAAAAA
1 TTTTCAAAAA
5040 GGTTTAGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 3 0.09
14 27 0.79
15 4 0.12
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:5022 original size:28 final size:26
Alignment explanation
Indices: 4988--5044 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 26
4978 AACAAGAGGT
4988 TTTTCAAAAAT-ATGTTTTCAAGAAAAGG
1 TTTTCAAAAATGA-GTTTTC-A-AAAAGG
5016 TTTTCAAAAATGAGTTTTCAAAAAGG
1 TTTTCAAAAATGAGTTTTCAAAAAGG
5042 TTT
1 TTT
5045 AGGGTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.32
27 1 0.04
28 17 0.61
29 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (26 bp):
TTTTCAAAAATGAGTTTTCAAAAAGG
Found at i:7423 original size:53 final size:52
Alignment explanation
Indices: 7361--7461 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 52
7351 GGTGGCCTTT
* * *
7361 CTTCAATTTCAATTACTTGAATGCTTCAA-TTTCAATTCTTCAAAACTTTAAAA
1 CTTCAATTTCAA-TA-TTCAAAGCTTCAAGTTTCAATTATTCAAAACTTTAAAA
*
7414 CTTCAATTTCAATATTCAAAGCTTCAAGTTTTCAATTATTCAATACTT
1 CTTCAATTTCAATATTCAAAGCTTCAAG-TTTCAATTATTCAAAACTT
7462 CAAATTCTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 11 0.26
52 2 0.05
53 29 0.69
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (52 bp):
CTTCAATTTCAATATTCAAAGCTTCAAGTTTCAATTATTCAAAACTTTAAAA
Found at i:7456 original size:24 final size:24
Alignment explanation
Indices: 7391--7522 Score: 98
Period size: 24 Copynumber: 5.6 Consensus size: 24
7381 ATGCTTCAAT
* * *
7391 TTCAATTCTTCAA-AACTTTAAAAC
1 TTCAATTCTTCAATTA-TTCAAAGC
7415 TTCAA-T-TTCAA-TATTCAAAGC
1 TTCAATTCTTCAATTATTCAAAGC
7436 TTCAAGTT-TTCAATTATTCAATA-C
1 TTCAA-TTCTTCAATTATTCAA-AGC
* *
7460 TTCAAATTCTTCAAGTATTCAACGC
1 TTC-AATTCTTCAATTATTCAAAGC
* * *
7485 TCCAATTCTTCAATCT-TTCAATGT
1 TTCAATTCTTCAAT-TATTCAAAGC
7509 TTCAATTCTTCAAT
1 TTCAATTCTTCAAT
7523 GCTTCAATTT
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
21 11 0.12
22 6 0.07
23 7 0.08
24 47 0.52
25 19 0.21
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (24 bp):
TTCAATTCTTCAATTATTCAAAGC
Found at i:7481 original size:33 final size:31
Alignment explanation
Indices: 7421--7481 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
7411 AAACTTCAAT
*
7421 TTCAATATTCAAAGCTTCAAGTTTTCAATTA
1 TTCAATATTCAAAGCTTCAAGTATTCAATTA
*
7452 TTCAATACTTCAAATTCTTCAAGTATTCAA
1 TTCAATA-TTCAAA-GCTTCAAGTATTCAA
7482 CGCTCCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 7 0.27
32 6 0.23
33 13 0.50
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (31 bp):
TTCAATATTCAAAGCTTCAAGTATTCAATTA
Found at i:7498 original size:8 final size:8
Alignment explanation
Indices: 7359--7531 Score: 69
Period size: 8 Copynumber: 22.2 Consensus size: 8
7349 GGGGTGGCCT
7359 TTCTTCAA
1 TTCTTCAA
7367 -T-TTCAA
1 TTCTTCAA
*
7373 TTACTTGAA
1 TT-CTTCAA
*
7382 TGCTTCAA
1 TTCTTCAA
7390 -T-TTCAA
1 TTCTTCAA
7396 TTCTTCAA
1 TTCTTCAA
** *
7404 AACTTTAA
1 TTCTTCAA
**
7412 AACTTCAA
1 TTCTTCAA
7420 -T-TTCAA
1 TTCTTCAA
*
7426 -TATTCAA
1 TTCTTCAA
**
7433 AGCTTCAA
1 TTCTTCAA
7441 GTT-TTCAA
1 -TTCTTCAA
*
7449 TTATTCAA
1 TTCTTCAA
*
7457 TACTTCAAA
1 TTCTTC-AA
7466 TTCTTCAA
1 TTCTTCAA
* *
7474 GTATTCAA
1 TTCTTCAA
** *
7482 CGCTCCAA
1 TTCTTCAA
7490 TTCTTCAA
1 TTCTTCAA
7498 -TCTTTCAA
1 TTC-TTCAA
7506 TGT-TTCAA
1 T-TCTTCAA
7514 TTCTTCAA
1 TTCTTCAA
*
7522 TGCTTCAA
1 TTCTTCAA
7530 TT
1 TT
7532 TATTTCAAGT
Statistics
Matches: 124, Mismatches: 27, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
6 16 0.13
7 13 0.10
8 82 0.66
9 12 0.10
10 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (8 bp):
TTCTTCAA
Found at i:7602 original size:55 final size:55
Alignment explanation
Indices: 7530--7694 Score: 253
Period size: 55 Copynumber: 3.0 Consensus size: 55
7520 AATGCTTCAA
* * *
7530 TTTAT-TTC-AAGTGATCCAGTACGGTCAATCAAGAAAGTTTACAATGGTTTATG
1 TTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAG
*
7583 TTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTCAAG
1 TTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAG
* *
7638 TTTATCTTCAAAGTGGTCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTCAAG
1 TTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTT-AAG
7694 T
1 T
7695 GATCTAGTGC
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
53 5 0.05
54 3 0.03
55 90 0.88
56 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (55 bp):
TTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAG
Found at i:7950 original size:62 final size:60
Alignment explanation
Indices: 7735--8041 Score: 337
Period size: 58 Copynumber: 5.2 Consensus size: 60
7725 AAGAGTGAGG
* * * *
7735 CTGAAGATAGCTCATAA-ATGGTTCTGAAGACATTTCCTTAAAGAT-TTTAAGATTGAGA-
1 CTGAAGACAGCTCACAAGATGGTTCTGAAGACAGTTCCTAAAAGATATTTAAGATTGA-AT
* *
7793 CTGAAGACAGCTCAC-AGATGGATCTGAAGACAGTTCCTTAAAGAT-TTTAAGATTGAGA-
1 CTGAAGACAGCTCACAAGATGGTTCTGAAGACAGTTCCTAAAAGATATTTAAGATTGA-AT
* *
7851 CTGAAGACAGCTCACAA-ATGGATT-TGAAGACAGTTCCTAAAAGGTATTTAAGAGTGAAT
1 CTGAAGACAGCTCACAAGATGG-TTCTGAAGACAGTTCCTAAAAGATATTTAAGATTGAAT
* * * *
7910 CTGAAGATAGTTCACGAAGATGGGTTCTGAAGACAGTTCCTAAAAGGTATTTAGGATTGAAT
1 CTGAAGACAGCTCAC-AAGAT-GGTTCTGAAGACAGTTCCTAAAAGATATTTAAGATTGAAT
* * * *
7972 CTGAAGACAGTTCACGAAGATGGATCTGAAGACA-TTCCTAAATGATATTT-AGAAATGAAT
1 CTGAAGACAGCTCAC-AAGATGGTTCTGAAGACAGTTCCTAAAAGATATTTAAG-ATTGAAT
8032 CTGAAGACAG
1 CTGAAGACAG
8042 TTCATGAAAG
Statistics
Matches: 221, Mismatches: 18, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.00
58 91 0.41
59 26 0.12
60 32 0.14
61 16 0.07
62 55 0.25
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (60 bp):
CTGAAGACAGCTCACAAGATGGTTCTGAAGACAGTTCCTAAAAGATATTTAAGATTGAAT
Done.