Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024701.1 Corchorus olitorius cultivar O-4 contig24734, 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: 67723
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2225 original size:16 final size:17
Alignment explanation
Indices: 2194--2226 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2184 TTCCTTTCAG
*
2194 AGTACCATAAGTTGCTT
1 AGTACCATAAGGTGCTT
2211 AGTACC-TAAGGTGCTT
1 AGTACCATAAGGTGCTT
2227 TACACTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (17 bp):
AGTACCATAAGGTGCTT
Found at i:4981 original size:15 final size:16
Alignment explanation
Indices: 4957--4993 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
4947 AGAGGTTGAA
*
4957 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
4972 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
4988 AGAAAA
1 AGAAAA
4994 TAAAGCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7378 original size:16 final size:16
Alignment explanation
Indices: 7357--7387 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7347 TCCTCTTGCA
*
7357 TGAAAACACTTTTTTT
1 TGAAAACAATTTTTTT
7373 TGAAAACAATTTTTT
1 TGAAAACAATTTTTT
7388 AACTACCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (16 bp):
TGAAAACAATTTTTTT
Found at i:8286 original size:21 final size:21
Alignment explanation
Indices: 8262--8335 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
8252 GGCTTGGAAT
*
8262 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATGGCC
* **
8283 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATGGCC
*
8304 GGTGGTGGCACGGTGAATGGCCC
1 GGTGGTGGCACGG-GCATGG-CC
*
8327 GGTTGTGGC
1 GGTGGTGGC
8336 TTGGTAGTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 30 0.71
22 2 0.05
23 10 0.24
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATGGCC
Found at i:10765 original size:30 final size:29
Alignment explanation
Indices: 10729--10791 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
10719 AATATATATA
* *
10729 TTTTTTTCTA-AAACCGCAGGAACAAGAATT
1 TTTTTTTCTAGAAAACGCA-AAACAA-AATT
*
10759 TTTTTTTTTAGAAAACGCAAAACAAAATT
1 TTTTTTTCTAGAAAACGCAAAACAAAATT
10788 TTTT
1 TTTT
10792 ATGATGCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 14 0.48
31 7 0.24
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTTTTTCTAGAAAACGCAAAACAAAATT
Found at i:10903 original size:30 final size:29
Alignment explanation
Indices: 10810--10904 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
10800 AAAACACTTT
* *
10810 TTTTTTTCAAAAACGCAACACAAAAC-AA
1 TTTTTTTAAAAAACGAAACACAAAACAAA
**
10838 TTTTTTTAAAAAA--AATTA-AAAACGCAAA
1 TTTTTTTAAAAAACGAAACACAAAA--CAAA
10866 CTTTTTTTTAAAAAACGAAACACAAAACAAA
1 --TTTTTTTAAAAAACGAAACACAAAACAAA
10897 TATTTTTT
1 T-TTTTTT
10905 TTAATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
25 4 0.08
26 2 0.04
27 1 0.02
28 14 0.27
29 1 0.02
30 19 0.37
31 4 0.08
32 3 0.06
33 4 0.08
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTTTTAAAAAACGAAACACAAAACAAA
Found at i:11283 original size:15 final size:16
Alignment explanation
Indices: 11259--11298 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
11249 AGAGGTTGAA
*
11259 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
11274 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
11290 AGAAAACAA
1 AGAAAACAA
11299 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:12734 original size:19 final size:18
Alignment explanation
Indices: 12683--12737 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
12673 CTTGAAATAT
12683 TCTTCAATAGTCTTCAAG
1 TCTTCAATAGTCTTCAAG
*
12701 TCTCCAAATTA-TCTTCAAG
1 TCTTC-AA-TAGTCTTCAAG
12720 TCTTCAATGAGTCTTCAA
1 TCTTCAAT-AGTCTTCAA
12738 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.23
19 21 0.68
20 2 0.06
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAG
Found at i:17511 original size:30 final size:30
Alignment explanation
Indices: 17475--17531 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17465 ATTCTTGCTC
*
17475 CTTGAAATAAATCTTCAAT-GATCTTCATGA
1 CTTGAAAT-AATCTTCAATAAATCTTCATGA
*
17505 CTTGAAATTATCTTCAATAAATCTTCA
1 CTTGAAATAATCTTCAATAAATCTTCA
17532 ATCACGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
CTTGAAATAATCTTCAATAAATCTTCATGA
Found at i:23501 original size:31 final size:31
Alignment explanation
Indices: 23416--23508 Score: 114
Period size: 33 Copynumber: 2.9 Consensus size: 31
23406 GTATGCAACG
* * *
23416 TGTCACTTTTTTGTACACGTGACGTGACACG
1 TGTCACTTTTTTGTACACGTGGCGTGCCACA
*
23447 TGTCACTTTTTTTTATACACGTGGCGTGCCACA
1 TGTCAC--TTTTTTGTACACGTGGCGTGCCACA
* *
23480 TGTCACTTTTTGGTACACGTGGCATGCCA
1 TGTCACTTTTTTGTACACGTGGCGTGCCA
23509 TGTCAAACAC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
31 26 0.49
33 27 0.51
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (31 bp):
TGTCACTTTTTTGTACACGTGGCGTGCCACA
Found at i:23586 original size:113 final size:113
Alignment explanation
Indices: 23456--23681 Score: 416
Period size: 113 Copynumber: 2.0 Consensus size: 113
23446 GTGTCACTTT
* *
23456 TTTTTATACACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCATGCCATGTCAAACACTG
1 TTTTTATACACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCATGCCACGTCAAACACCG
*
23521 TAATAGAGTTGTTTGTCTTACGGTGACGGAGGGTGCAAAGTAGCAAAA
66 TAATAGAGTTGTTTGTCCTACGGTGACGGAGGGTGCAAAGTAGCAAAA
23569 TTTTTATACACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCATGCCACGTCAAACACCG
1 TTTTTATACACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCATGCCACGTCAAACACCG
*
23634 TAATAGAGTTGTTTGTCCTACGGTGACGGAGGGTGCAAAGTAGTAAAA
66 TAATAGAGTTGTTTGTCCTACGGTGACGGAGGGTGCAAAGTAGCAAAA
23682 AATAAAATTT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (113 bp):
TTTTTATACACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCATGCCACGTCAAACACCG
TAATAGAGTTGTTTGTCCTACGGTGACGGAGGGTGCAAAGTAGCAAAA
Found at i:24041 original size:3 final size:3
Alignment explanation
Indices: 24033--24078 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
24023 GGACTTTGTT
24033 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
24079 TATTGCCCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26111 original size:6 final size:7
Alignment explanation
Indices: 26092--26119 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
26082 CAAGAGAACT
26092 GGAAAAA
1 GGAAAAA
26099 GGAAAAA
1 GGAAAAA
26106 GGAAAAA
1 GGAAAAA
26113 GGAAAAA
1 GGAAAAA
26120 AAAAAGATTA
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
GGAAAAA
Found at i:28959 original size:26 final size:26
Alignment explanation
Indices: 28923--28977 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
28913 TACCTCATGC
28923 GTGGCGTTGTAATTTGCTGACTTATG
1 GTGGCGTTGTAATTTGCTGACTTATG
28949 GTGGCGTTGTAATTTGCTGACTTATG
1 GTGGCGTTGTAATTTGCTGACTTATG
28975 GTG
1 GTG
28978 CTTTGCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.15, C:0.11, G:0.33, T:0.42
Consensus pattern (26 bp):
GTGGCGTTGTAATTTGCTGACTTATG
Found at i:31915 original size:30 final size:30
Alignment explanation
Indices: 31869--31932 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
31859 GGTATCAAGC
*
31869 CTGTGTCTTTTTTGTGTTCCGTCTATATTT
1 CTGTGTCTTTTCTGTGTTCCGTCTATATTT
* *
31899 CTGTGTGTTTTCTGTGTTCCGTGTATATTT
1 CTGTGTCTTTTCTGTGTTCCGTCTATATTT
31929 CTGT
1 CTGT
31933 TAGTTCATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.06, C:0.16, G:0.20, T:0.58
Consensus pattern (30 bp):
CTGTGTCTTTTCTGTGTTCCGTCTATATTT
Found at i:32396 original size:26 final size:26
Alignment explanation
Indices: 32359--32411 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
32349 AAAATATGTG
*
32359 TATGAATCATATGCCGTGTGAATTTT
1 TATGAATCATATACCGTGTGAATTTT
* * *
32385 TATGAATTATATATCGTGTGGATTTT
1 TATGAATCATATACCGTGTGAATTTT
32411 T
1 T
32412 CTTTGTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (26 bp):
TATGAATCATATACCGTGTGAATTTT
Found at i:38184 original size:18 final size:18
Alignment explanation
Indices: 38161--38197 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38151 TTCTTGGCTT
38161 TAACATCAAGAACCAAAA
1 TAACATCAAGAACCAAAA
38179 TAACATCAAGAACCAAAA
1 TAACATCAAGAACCAAAA
38197 T
1 T
38198 GCAGTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.22, G:0.05, T:0.14
Consensus pattern (18 bp):
TAACATCAAGAACCAAAA
Found at i:39723 original size:26 final size:26
Alignment explanation
Indices: 39686--39738 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39676 AAAATATGTG
*
39686 TATGAATCATATGCTGTGTGAATTTT
1 TATGAATCATATACTGTGTGAATTTT
* * *
39712 TATGAATTATATATTGTGTGGATTTT
1 TATGAATCATATACTGTGTGAATTTT
39738 T
1 T
39739 CTTTGTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (26 bp):
TATGAATCATATACTGTGTGAATTTT
Found at i:43697 original size:57 final size:57
Alignment explanation
Indices: 43609--43722 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
43599 GTACGTTGAA
43609 AAAAGATTTGCCTATGCTTTTTTAAAAAAATACAGATTTTTAGAAATTGAAGATGAT
1 AAAAGATTTGCCTATGCTTTTTTAAAAAAATACAGATTTTTAGAAATTGAAGATGAT
* * *
43666 AAAAGATTTGCTTATGTTTTTTTTAAAAAATACAGATTTTTAGAAATTGAAGATGAT
1 AAAAGATTTGCCTATGCTTTTTTAAAAAAATACAGATTTTTAGAAATTGAAGATGAT
43723 TTAACGCAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.39
Consensus pattern (57 bp):
AAAAGATTTGCCTATGCTTTTTTAAAAAAATACAGATTTTTAGAAATTGAAGATGAT
Found at i:44539 original size:292 final size:295
Alignment explanation
Indices: 43982--44563 Score: 904
Period size: 292 Copynumber: 2.0 Consensus size: 295
43972 TTTATACCAA
* **
43982 TTAACTCAGATTTTAGAAATTGGAATATGATATAATCCAGCTGGTCATTTTTCCTAGCTCATATT
1 TTAACTCAAATTTTAGAAATTGGAATATGATATAATCCAGCTACTCATTTTTCCTAGCTCATATT
44047 TCATCTTTTCCTTTCTTTAATTATATACGTGTCCATATGTGGATATTTGGTGCCTACATTTGTTG
66 TCATCTTTTCCTTTCTTTAATTATATACGTGTCCATATGTGGATATTTGGTGCCTACATTTGTTG
* * * *
44112 GATTTATGGATTTGATTCGATTGTGTGTGCGTTTTTGTTGTGGCCATCATCTATGCAGATTTTTA
131 GATTTATGGATGTGATTCAATTGTGTGCGCG--TCTGTTGTGGCCATCATCTATGCAGATTTTTA
* * * *
44177 TTTGTTATTACCTATCTCTATATCTCTCCGTAGTATAGCAAAGCAAGGTAATTTTATATAGATAT
194 TTTGTTATTACCTATCTCGATATCTCTCCATAGCATAGCAAAGCAAGATAATTTTATATAGATAT
44242 CACAGCAGAATCAGTTTGATTAGAATTAACTCAGATT
259 CACAGCAGAATCAGTTTGATTAGAATTAACTCAGATT
*
44279 TTAATTCAAATTTTAGAAATTGGAATATGATATAATCCAGCTACTCA-TTTTCCGTAGCTCATAT
1 TTAACTCAAATTTTAGAAATTGGAATATGATATAATCCAGCTACTCATTTTTCC-TAGCTCATAT
* * *
44343 TT-TTCTTTTCCTTTCTTTAATTATATGCGTGTCCATATGTGGATATTTGGTTCCTACATTT-TC
65 TTCATCTTTTCCTTTCTTTAATTATATACGTGTCCATATGTGGATATTTGGTGCCTACATTTGT-
44406 TGGATTTATGGATGTGATTCAATTGTGTGCGCG-CT-TTGTGGCCATCATCTATGCAGATTTTTA
129 TGGATTTATGGATGTGATTCAATTGTGTGCGCGTCTGTTGTGGCCATCATCTATGCAGATTTTTA
* * * *
44469 TTTGTTATTATCTATCTCGATATCTCTCCATAGCATAGCAAATCAAGATAGTTTTATATAGATGT
194 TTTGTTATTACCTATCTCGATATCTCTCCATAGCATAGCAAAGCAAGATAATTTTATATAGATAT
* *
44534 CACAGCAGGATCAGTTTGGTTAGAATTAAC
259 CACAGCAGAATCAGTTTGATTAGAATTAAC
44564 CATGTGCATT
Statistics
Matches: 262, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
292 113 0.43
293 1 0.00
295 1 0.00
296 92 0.35
297 55 0.21
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (295 bp):
TTAACTCAAATTTTAGAAATTGGAATATGATATAATCCAGCTACTCATTTTTCCTAGCTCATATT
TCATCTTTTCCTTTCTTTAATTATATACGTGTCCATATGTGGATATTTGGTGCCTACATTTGTTG
GATTTATGGATGTGATTCAATTGTGTGCGCGTCTGTTGTGGCCATCATCTATGCAGATTTTTATT
TGTTATTACCTATCTCGATATCTCTCCATAGCATAGCAAAGCAAGATAATTTTATATAGATATCA
CAGCAGAATCAGTTTGATTAGAATTAACTCAGATT
Found at i:61794 original size:21 final size:19
Alignment explanation
Indices: 61769--61826 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
61759 GCTGCTCTAA
*
61769 TAATCTCATATGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
61790 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
61809 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
61827 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:63581 original size:16 final size:17
Alignment explanation
Indices: 63560--63591 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
63550 GTCTAACGTG
63560 TCGTGTAA-CGTGTTAT
1 TCGTGTAACCGTGTTAT
63576 TCGTGTAACCGTGTTA
1 TCGTGTAACCGTGTTA
63592 ACCCGGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (17 bp):
TCGTGTAACCGTGTTAT
Found at i:66541 original size:11 final size:11
Alignment explanation
Indices: 66525--66550 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66515 AGATAATTTC
66525 TTTTCTTCTAG
1 TTTTCTTCTAG
66536 TTTTCTTCTAG
1 TTTTCTTCTAG
66547 TTTT
1 TTTT
66551 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:67339 original size:15 final size:15
Alignment explanation
Indices: 67309--67350 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
67299 TTACTTTGCT
67309 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
67325 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
67340 TTGCTTTCTGT
1 TTGTTTTCTGT
67351 CAATCTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.