Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022076.1 Corchorus olitorius cultivar O-4 contig22109, 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: 74505
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:359 original size:77 final size:79
Alignment explanation
Indices: 266--420 Score: 219
Period size: 77 Copynumber: 2.0 Consensus size: 79
256 AAAGATAATA
* **
266 CCAGGCCCAATCGGAAACTTTCTTGACCCAAAACACAAT-TTCAAAGCCCAATCAGACAT-AAAA
1 CCAGGCCCAATCGGAAACTTTCCTGACCCAAAACAC-ATGCCCAAAGCCCAATCAGAC-TCAAAA
329 GGG-AAAAGGAAGGGG
64 GGGAAAAAGGAAGGGG
**
344 CCAGGCCCAA-CGGAAACTTTCCTGACCCAAAACACATGCCCAAAGCCCAATTGGACTCAAAAGG
1 CCAGGCCCAATCGGAAACTTTCCTGACCCAAAACACATGCCCAAAGCCCAATCAGACTCAAAAGG
408 GAAAAAGGAAGGG
66 GAAAAAGGAAGGG
421 ACCAAACGCA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
76 3 0.04
77 45 0.65
78 21 0.30
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (79 bp):
CCAGGCCCAATCGGAAACTTTCCTGACCCAAAACACATGCCCAAAGCCCAATCAGACTCAAAAGG
GAAAAAGGAAGGGG
Found at i:16947 original size:33 final size:33
Alignment explanation
Indices: 16910--16978 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
16900 ATTAGCATCC
*
16910 AAAACAGAATTT-GTTTCATAAAAAACAACACCT
1 AAAACA-AATTTAGTGTCATAAAAAACAACACCT
* * *
16943 AAAACAAATTTAGTGTCATCACAAACAACACTT
1 AAAACAAATTTAGTGTCATAAAAAACAACACCT
16976 AAA
1 AAA
16979 TTAGGTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (33 bp):
AAAACAAATTTAGTGTCATAAAAAACAACACCT
Found at i:17657 original size:15 final size:15
Alignment explanation
Indices: 17637--17668 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17627 AAACTAAGTG
17637 GAGCTTGTCGATTTT
1 GAGCTTGTCGATTTT
*
17652 GAGCTTGTTGATTTT
1 GAGCTTGTCGATTTT
17667 GA
1 GA
17669 ACCCCCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47
Consensus pattern (15 bp):
GAGCTTGTCGATTTT
Found at i:20698 original size:29 final size:31
Alignment explanation
Indices: 20655--20728 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 31
20645 CACCAAATTG
20655 TAAGTAGAGGGACCAAATTGA-CAGTTTTTA
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
** *
20685 T-AGTAGAGGGACCAAATTGATCCTTTTTTG
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
20715 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
20729 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 19 0.49
30 8 0.21
31 12 0.31
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCAGTTTTTA
Found at i:20724 original size:31 final size:30
Alignment explanation
Indices: 20610--20728 Score: 116
Period size: 31 Copynumber: 3.9 Consensus size: 30
20600 ATATAATCAG
*
20610 TTGACAGATTTTGTCAAGTAGAGGGACTC-AA
1 TTGACAGTTTTTGT-AAGTAGAGGGAC-CAAA
****
20641 TTGACACCAAATTGTAAGTAGAGGGACCAAA
1 TTGACA-GTTTTTGTAAGTAGAGGGACCAAA
*
20672 TTGACAGTTTTTAT-AGTAGAGGGACCAAA
1 TTGACAGTTTTTGTAAGTAGAGGGACCAAA
**
20701 TTGATCCTTTTTTGTAAGTAGAGGGACC
1 TTGA-CAGTTTTTGTAAGTAGAGGGACC
20729 TGTACGGTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
29 19 0.26
30 11 0.15
31 38 0.52
32 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (30 bp):
TTGACAGTTTTTGTAAGTAGAGGGACCAAA
Found at i:26364 original size:17 final size:18
Alignment explanation
Indices: 26331--26366 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26321 CTCCTCTTGC
*
26331 ATGAAAGCACTTCTTTTT
1 ATGAAAGCAATTCTTTTT
26349 ATGAAAGCAATT-TTTTT
1 ATGAAAGCAATTCTTTTT
26366 A
1 A
26367 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
ATGAAAGCAATTCTTTTT
Found at i:26902 original size:14 final size:15
Alignment explanation
Indices: 26883--26912 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26873 CAATCAAAGC
26883 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
26897 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
26912 A
1 A
26913 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:32722 original size:21 final size:21
Alignment explanation
Indices: 32698--32761 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
32688 CTTTAGGCAA
32698 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
32719 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
32740 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
32760 CT
1 CT
32762 TTGTGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:34810 original size:12 final size:13
Alignment explanation
Indices: 34795--34837 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
34785 CCCTAGCCCT
34795 AAAACTAGAAGA-
1 AAAACTAGAAGAG
34807 AAAACTAGAAGAG
1 AAAACTAGAAGAG
**
34820 AAAAAGAAGAAGAG
1 -AAAACTAGAAGAG
34834 AAAA
1 AAAA
34838 TTATCTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 12 0.44
13 4 0.15
14 11 0.41
ACGTcount: A:0.70, C:0.05, G:0.21, T:0.05
Consensus pattern (13 bp):
AAAACTAGAAGAG
Found at i:34823 original size:14 final size:14
Alignment explanation
Indices: 34795--34837 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
34785 CCCTAGCCCT
34795 AAAACTAG-A-AGA
1 AAAACTAGAAGAGA
34807 AAAACTAGAAGAGA
1 AAAACTAGAAGAGA
**
34821 AAAAGAAGAAGAGA
1 AAAACTAGAAGAGA
34835 AAA
1 AAA
34838 TTATCTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 8 0.30
13 1 0.04
14 18 0.67
ACGTcount: A:0.70, C:0.05, G:0.21, T:0.05
Consensus pattern (14 bp):
AAAACTAGAAGAGA
Found at i:39748 original size:25 final size:24
Alignment explanation
Indices: 39711--39757 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
39701 CTTGAAAATT
39711 TGAAAAACTTTGATGGATGAGATGTA
1 TGAAAAACTTTGAT-GAT-AGATGTA
39737 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
39758 GATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGTA
Found at i:40654 original size:21 final size:21
Alignment explanation
Indices: 40594--40655 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
40584 CCTTAGGCAA
* *
40594 CTCCAATGAGCATGAAACCTT
1 CTCCAATGAGCTTGAAACTTT
40615 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACTTT
40636 CTCCAATGAGCTTGAAACTT
1 CTCCAATGAGCTTGAAACTT
40656 CATTGTGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACTTT
Found at i:41396 original size:28 final size:28
Alignment explanation
Indices: 41356--41410 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
41346 CTCCTCATGG
41356 CATTTTGCATGTCTAGGGGCATTTTGGT
1 CATTTTGCATGTCTAGGGGCATTTTGGT
41384 CATTTTGCATGTCTAGGGGCATTTTGG
1 CATTTTGCATGTCTAGGGGCATTTTGG
41411 GTCACTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.42
Consensus pattern (28 bp):
CATTTTGCATGTCTAGGGGCATTTTGGT
Found at i:41680 original size:61 final size:61
Alignment explanation
Indices: 41551--41675 Score: 211
Period size: 61 Copynumber: 2.1 Consensus size: 61
41541 CAGTATAACA
*
41551 TATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGAAAATAGTAGATGGCT
1 TATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGAAAATAGGAGATGGCT
*
41612 TATTTAGTAATCCTCCATTTAATTAATG-TAATTGTCATGTGTAGGAAATAGGAGAT-G-T
1 TATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGAAAATAGGAGATGGCT
41670 TATTTA
1 TATTTA
41676 TTAGTTGCAA
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
58 7 0.11
59 1 0.02
60 26 0.42
61 28 0.45
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (61 bp):
TATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGAAAATAGGAGATGGCT
Found at i:42607 original size:22 final size:22
Alignment explanation
Indices: 42582--42664 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
42572 TCATTCTTTC
*
42582 CAAATCAGCAAGGTTCAAAGCT
1 CAAATCAACAAGGTTCAAAGCT
* *
42604 CAAATCAACAAGGGTCCAAGAACAT
1 CAAATCAACAA-GGTTCAA-AGC-T
* *
42629 CCAATTCAACAAGGTTTAAAGCT
1 -CAAATCAACAAGGTTCAAAGCT
* *
42652 CAAGTCAGCAAGG
1 CAAATCAACAAGG
42665 GTCCAAGAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
22 21 0.44
23 7 0.15
24 4 0.08
25 6 0.12
26 10 0.21
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (22 bp):
CAAATCAACAAGGTTCAAAGCT
Found at i:42651 original size:48 final size:48
Alignment explanation
Indices: 42580--42682 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 48
42570 TGTCATTCTT
* *
42580 TCCAAATCAGCAAGGTTCAAAGCTCAAATCAACAAGGGTCCAAGAACA
1 TCCAATTCAACAAGGTTCAAAGCTCAAATCAACAAGGGTCCAAGAACA
* * *
42628 TCCAATTCAACAAGGTTTAAAGCTCAAGTCAGCAAGGGTCCAAGAACA
1 TCCAATTCAACAAGGTTCAAAGCTCAAATCAACAAGGGTCCAAGAACA
42676 TCCAATT
1 TCCAATT
42683 AAGCATACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (48 bp):
TCCAATTCAACAAGGTTCAAAGCTCAAATCAACAAGGGTCCAAGAACA
Found at i:49301 original size:32 final size:32
Alignment explanation
Indices: 49264--49342 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
49254 ACTAATATAA
* **
49264 TAGTGGCGTTTTTAAACTAAAATGCCACTAAT
1 TAGTGGCGTTTCTAAACTAAAACACCACTAAT
* * *
49296 TAGTGGCATTTCTCAAGTAAAACACCACTAAT
1 TAGTGGCGTTTCTAAACTAAAACACCACTAAT
49328 TAGTGGCGTTTCTAA
1 TAGTGGCGTTTCTAA
49343 CAAAAAAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (32 bp):
TAGTGGCGTTTCTAAACTAAAACACCACTAAT
Found at i:62564 original size:23 final size:23
Alignment explanation
Indices: 62534--62612 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
62524 AGAGTGAATT
62534 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
* * **
62557 GGAAGACAGTCCTTTAAAGGGTGAATT
1 GGAAGACAG---TTCAAAGGAT-AAGC
*
62584 GGAAGACAATTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
62607 GGAAGA
1 GGAAGA
62613 TGATCCTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
23 17 0.40
24 8 0.19
26 8 0.19
27 10 0.23
ACGTcount: A:0.42, C:0.11, G:0.30, T:0.16
Consensus pattern (23 bp):
GGAAGACAGTTCAAAGGATAAGC
Found at i:62583 original size:50 final size:49
Alignment explanation
Indices: 62527--62691 Score: 231
Period size: 50 Copynumber: 3.3 Consensus size: 49
62517 ATCCAGAAGA
*
62527 GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTAAAGG
1 GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGA-AGTCCTTTTAAGG
* * *
62577 GTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGATGATCCTTTTAAGA
1 GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAAG-TCCTTTTAAGG
* * *
62627 TTAAATTGGAAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTTTTAAGG
1 GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGA-AGTCCTTTTAAGG
*
62677 GTGAATTAGAAGACA
1 GTGAATTGGAAGACA
62692 ATTCGAAGAA
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 99 0.98
51 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.23
Consensus pattern (49 bp):
GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAAGTCCTTTTAAGG
Found at i:62954 original size:28 final size:28
Alignment explanation
Indices: 62922--62987 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
62912 TACTCCTCAT
*
62922 GGCATTTTGGTTATTTTGCATGTCTAGC
1 GGCATTTTGGTCATTTTGCATGTCTAGC
*
62950 GGCATTTTGGTCATTTTGCATGTCTAGG
1 GGCATTTTGGTCATTTTGCATGTCTAGC
62978 GGCATTTTGG
1 GGCATTTTGG
62988 GTCACTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.44
Consensus pattern (28 bp):
GGCATTTTGGTCATTTTGCATGTCTAGC
Found at i:63200 original size:61 final size:61
Alignment explanation
Indices: 63125--63242 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
63115 CAGCAGTGTA
*
63125 GCTTATTTATTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGGAAATAGGAGATG
1 GCTTATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGGAAATAGGAGATG
63186 GCTTATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGGAAATAGGA
1 GCTTATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGGAAATAGGA
63243 TATGATGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (61 bp):
GCTTATTTAGTAATCCTCCATTTAATTAATGTTAATTGTCATGTGTAGGAAATAGGAGATG
Found at i:64435 original size:48 final size:48
Alignment explanation
Indices: 64365--64467 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 48
64355 TGTCATTCTT
* *
64365 TCCAAATCAGCAAGCTTCAAAGCTCAAATCAGCAAGGGTCCAAGAACA
1 TCCAATTCAACAAGCTTCAAAGCTCAAATCAGCAAGGGTCCAAGAACA
* * *
64413 TCCAATTCAACAAGGTTTAAAGCTCAAGTCAGCAAGGGTCCAAGAACA
1 TCCAATTCAACAAGCTTCAAAGCTCAAATCAGCAAGGGTCCAAGAACA
64461 TCCAATT
1 TCCAATT
64468 AAGCATACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (48 bp):
TCCAATTCAACAAGCTTCAAAGCTCAAATCAGCAAGGGTCCAAGAACA
Found at i:72671 original size:21 final size:21
Alignment explanation
Indices: 72638--72677 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72628 TCCTCGCAAT
72638 TCTGCTTGACCAGCTAGTAGC
1 TCTGCTTGACCAGCTAGTAGC
* *
72659 TCTGTTTGCCCAGCTAGTA
1 TCTGCTTGACCAGCTAGTA
72678 ATTAAGTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.33
Consensus pattern (21 bp):
TCTGCTTGACCAGCTAGTAGC
Done.