Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024608.1 Corchorus olitorius cultivar O-4 contig24641, 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: 20079
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:653 original size:24 final size:23
Alignment explanation
Indices: 626--750 Score: 105
Period size: 24 Copynumber: 5.2 Consensus size: 23
616 CGCAGACACA
626 AAAAATTTTCTTTTTTTATGACGC
1 AAAAATTTT-TTTTTTTATGACGC
650 AAAAACTCTTTTTTTTTTA-GAAAAACGC
1 AAAAA-T-TTTTTTTTTTATG----ACGC
*
678 AAAAA-CTTTTTTTTTATGACGC
1 AAAAATTTTTTTTTTTATGACGC
*
700 AGAAACA-ATTTTTTTTTATGACGC
1 A-AAA-ATTTTTTTTTTTATGACGC
*
724 AAAAATATTTTTTTTTT-CGACGC
1 AAAAAT-TTTTTTTTTTATGACGC
747 AAAA
1 AAAA
751 CACAAAATAA
Statistics
Matches: 86, Mismatches: 4, Indels: 23
0.76 0.04 0.20
Matches are distributed among these distances:
22 6 0.07
23 15 0.17
24 33 0.38
25 19 0.22
26 4 0.05
28 9 0.10
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
AAAAATTTTTTTTTTTATGACGC
Found at i:662 original size:23 final size:23
Alignment explanation
Indices: 636--750 Score: 94
Period size: 23 Copynumber: 4.8 Consensus size: 23
626 AAAAATTTTC
*
636 TTTTTTTATGACGCAAAAACTCT
1 TTTTTTTATGACGCAAAAAATCT
* *
659 TTTTTTTTTAGAAAAACGCAAAAACT-T
1 TTTTTTTAT-G----ACGCAAAAAATCT
686 TTTTTTTATGACGCAGAAACAAT-T
1 TTTTTTTATGACGCA-AAA-AATCT
710 TTTTTTTATGACGCAAAAATAT-T
1 TTTTTTTATGACGCAAAAA-ATCT
733 TTTTTTT-TCGACGCAAAA
1 TTTTTTTAT-GACGCAAAA
751 CACAAAATAA
Statistics
Matches: 80, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.09
23 33 0.41
24 19 0.24
26 1 0.01
27 9 0.11
28 11 0.14
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (23 bp):
TTTTTTTATGACGCAAAAAATCT
Found at i:1133 original size:16 final size:16
Alignment explanation
Indices: 1112--1150 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1102 AGATTGACAC
1112 AAAACAATTAAACTAG
1 AAAACAATTAAACTAG
1128 AAAACAATTAAACTAG
1 AAAACAATTAAACTAG
1144 AAAACAA
1 AAAACAA
1151 AGCAAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.67, C:0.13, G:0.05, T:0.15
Consensus pattern (16 bp):
AAAACAATTAAACTAG
Found at i:1927 original size:11 final size:11
Alignment explanation
Indices: 1911--1936 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1901 TCTTTGCCTA
1911 AAAACTAGAAG
1 AAAACTAGAAG
1922 AAAACTAGAAG
1 AAAACTAGAAG
1933 AAAA
1 AAAA
1937 GAAATTATCT
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:5219 original size:32 final size:32
Alignment explanation
Indices: 5178--5274 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 32
5168 AAATTATATA
* * *
5178 TAGCGGCGTTTTGTTTAATAAACGCCGCTATT
1 TAGCAGCGTTTTCTTCAATAAACGCCGCTATT
* **
5210 TAGCAGCGTTTTCTTCAATAGACGCCGCTAAA
1 TAGCAGCGTTTTCTTCAATAAACGCCGCTATT
** *
5242 TAGGGGCGTTTTCTTCAATAGAA-GCTGCTATT
1 TAGCAGCGTTTTCTTCAATA-AACGCCGCTATT
5274 T
1 T
5275 TTCAGCAATT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 51 0.98
33 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (32 bp):
TAGCAGCGTTTTCTTCAATAAACGCCGCTATT
Found at i:10370 original size:161 final size:162
Alignment explanation
Indices: 10099--10445 Score: 511
Period size: 161 Copynumber: 2.1 Consensus size: 162
10089 AGGGAATTTT
* * * * *
10099 TCCCTCCATATATTACAATTGCGGTGTTTCCTTTCTTAGACGCCACTAATTAGTGGCGTCTGATG
1 TCCCTCCATATATTAAAATGGCGGCGTTTCCTTTCTTAGACGCCACTAATTAGCGGCGCCTGATG
* *
10164 AGAAAACACCGCTATATATTATAGACGTAGAGTTGGAAACTTTCTTTGTTTTAGAGGGAGGGAAG
66 ACAAAACACCCCTATATATTATAGACGTAGAGTTGGAAACTTTCTTTGTTTTAGAGGGAGGGAAG
10229 TTTTCCCTCTAAAAAA-AGGAAAAAAAA-TCTC
131 TTTTCCCTCTAAAAAAGA-GAAAAAAAATTCTC
*
10260 TCCCTTCATATATTAAAATGGCGGCGTTTCCTTT-TCTAGACGCCACTAATTAGCGGCGCCTGAT
1 TCCCTCCATATATTAAAATGGCGGCGTTTCCTTTCT-TAGACGCCACTAATTAGCGGCGCCTGAT
* * * * * *
10324 GTCAAAACGCCCCTATATATTATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTAGGGGGGGGGGA
65 GACAAAACACCCCTATATATTATAGACGTAGAGTTGGAAACTTTCTTTGTTTTAGAGGGAGGGAA
*
10389 TTTTTCCCTCTAAAAAAGAGAAAAAAAATTCTC
130 GTTTTCCCTCTAAAAAAGAGAAAAAAAATTCTC
*
10422 TCCCTCCATATATTAATATGGCGG
1 TCCCTCCATATATTAAAATGGCGG
10446 TGTCTTTCTA
Statistics
Matches: 166, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
160 1 0.01
161 138 0.83
162 27 0.16
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (162 bp):
TCCCTCCATATATTAAAATGGCGGCGTTTCCTTTCTTAGACGCCACTAATTAGCGGCGCCTGATG
ACAAAACACCCCTATATATTATAGACGTAGAGTTGGAAACTTTCTTTGTTTTAGAGGGAGGGAAG
TTTTCCCTCTAAAAAAGAGAAAAAAAATTCTC
Found at i:12673 original size:54 final size:54
Alignment explanation
Indices: 12573--12922 Score: 454
Period size: 54 Copynumber: 6.5 Consensus size: 54
12563 ACAGAAATTT
* * * * *
12573 TTCTAGGAACGACCGTACTAGATCAATTTGGACATCAACTTTGATCATCGAAAAC
1 TTCTTGGAACGACCGCACTGGATCAA-TTGGAGATCAACTCTGATCATCGAAAAC
*
12628 TTCTTGGAACGACCGCAATGGATCAATTGGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGGAACGACCGCACTGGATCAATTGGAGATCAACTCTGATCATCGAAAAC
*
12682 TTCTTGAAACGACCGCACTGGATCAATTGGAGATCAACTCTGATCATC-AAACAC
1 TTCTTGGAACGACCGCACTGGATCAATTGGAGATCAACTCTGATCATCGAAA-AC
* *
12736 TTCTTGGAACGACCGCACTGGATCAATTGGAGATAAACTTTGATCATCGAAAAC
1 TTCTTGGAACGACCGCACTGGATCAATTGGAGATCAACTCTGATCATCGAAAAC
* * * * *
12790 TTTTTGGAACGACCGCACTAGATC-ATCTAGG-GATTAACACTGATCATCAAAAAC
1 TTCTTGGAACGACCGCACTGGATCAAT-T-GGAGATCAACTCTGATCATCGAAAAC
* * *
12844 TTCTTGGAACGACCGCACCGAATCAATTGGAGATCAACTCTGATCATCGAAAAT
1 TTCTTGGAACGACCGCACTGGATCAATTGGAGATCAACTCTGATCATCGAAAAC
* * * *
12898 TTCTTGAAACAACCGTAATGGATCA
1 TTCTTGGAACGACCGCACTGGATCA
12923 TTTAAAACAT
Statistics
Matches: 258, Mismatches: 31, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
53 7 0.03
54 222 0.86
55 29 0.11
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (54 bp):
TTCTTGGAACGACCGCACTGGATCAATTGGAGATCAACTCTGATCATCGAAAAC
Found at i:15457 original size:6 final size:6
Alignment explanation
Indices: 15438--15496 Score: 84
Period size: 6 Copynumber: 9.8 Consensus size: 6
15428 ACACTATTGC
* *
15438 AAAA-A AAAACAA AAAAAA AAAAAA AAAACA AAAACA AAAACA AAAACA
1 AAAACA AAAAC-A AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
15486 AAAACA AAAAC
1 AAAACA AAAAC
15497 CAACAGTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
5 4 0.08
6 41 0.82
7 5 0.10
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:15515 original size:1 final size:1
Alignment explanation
Indices: 15438--15495 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
15428 ACACTATTGC
* * * * * *
15438 AAAAAAAAACAAAAAAAAAAAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15496 CCAACAGTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19347 original size:21 final size:21
Alignment explanation
Indices: 19318--19485 Score: 88
Period size: 21 Copynumber: 7.6 Consensus size: 21
19308 ATTGTACGGG
* *
19318 TGGTAGTGGTGGTGAGTAAAC
1 TGGTGGTGGTGGTGAGTAGAC
*
19339 TGGTGGTGGAGGTGGCGAGTAGAC
1 TGGTGGT---GGTGGTGAGTAGAC
* * *
19363 GGGTGGTGGAGGGGAGTAGAC
1 TGGTGGTGGTGGTGAGTAGAC
19384 TGGTGGTGGAGGTGGTG-GTGACTGGAC
1 TGGTGGT---GGTGGTGAGT-A---GAC
* * *
19411 AGGTGGTGGAGGTGAGTATAC
1 TGGTGGTGGTGGTGAGTAGAC
* *
19432 GGGTGGTGGTGGGGAGTAGAC
1 TGGTGGTGGTGGTGAGTAGAC
* * *
19453 TGGTGGAGGGGGTGAAG-AAAC
1 TGGTGGTGGTGGTG-AGTAGAC
*
19474 AGGTGGTGGTGG
1 TGGTGGTGGTGG
19486 CGAACTGACA
Statistics
Matches: 111, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
21 65 0.59
22 2 0.02
23 2 0.02
24 31 0.28
25 2 0.02
27 9 0.08
ACGTcount: A:0.18, C:0.05, G:0.55, T:0.21
Consensus pattern (21 bp):
TGGTGGTGGTGGTGAGTAGAC
Found at i:19390 original size:69 final size:66
Alignment explanation
Indices: 19316--19482 Score: 189
Period size: 69 Copynumber: 2.5 Consensus size: 66
19306 AGATTGTACG
*
19316 GGTGGTAGTGGTGGTGAGTAAACTGGTGGTGGAGGTGGCGAGTAGACGGGTGGTGGAGGGGAGTA
1 GGTGGTAGTGGTGGTGAGTAAACAGGTGGTGGAGGT---GAGTAGACGGGTGGTGGAGGGGAGTA
19381 GACT
63 GACT
* ** * *
19385 GGTGGTGGAGGTGGTGGTGACTGGACAGGTGGTGGAGGTGAGTATACGGGTGGTGGTGGGGAGTA
1 GGTGGT--A-GTGGTGGTGAGTAAACAGGTGGTGGAGGTGAGTAGACGGGTGGTGGAGGGGAGTA
19450 GACT
63 GACT
19454 GGTGG-AG-GG-GGTGAAG-AAACAGGTGGTGG
1 GGTGGTAGTGGTGGTG-AGTAAACAGGTGGTGG
19483 TGGCGAACTG
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
63 15 0.18
64 3 0.04
65 1 0.01
66 1 0.01
69 39 0.46
71 1 0.01
72 25 0.29
ACGTcount: A:0.19, C:0.05, G:0.55, T:0.21
Consensus pattern (66 bp):
GGTGGTAGTGGTGGTGAGTAAACAGGTGGTGGAGGTGAGTAGACGGGTGGTGGAGGGGAGTAGAC
T
Found at i:19397 original size:27 final size:27
Alignment explanation
Indices: 19367--19424 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
19357 GTAGACGGGT
* *
19367 GGTGGAGGGGAGTAGACTGGTGGTGGA
1 GGTGGAGGGGACTAGACAGGTGGTGGA
* * *
19394 GGTGGTGGTGACTGGACAGGTGGTGGA
1 GGTGGAGGGGACTAGACAGGTGGTGGA
19421 GGTG
1 GGTG
19425 AGTATACGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.59, T:0.21
Consensus pattern (27 bp):
GGTGGAGGGGACTAGACAGGTGGTGGA
Found at i:19401 original size:48 final size:45
Alignment explanation
Indices: 19331--19440 Score: 121
Period size: 48 Copynumber: 2.4 Consensus size: 45
19321 TAGTGGTGGT
* *
19331 GAGTAAACTGGTGGTGGAGGTGGCGAGTAGACGGGTGGTGGAGGG
1 GAGTAAACTGGTGGTGGAGGTGGCGACTAGACAGGTGGTGGAGGG
* * * *
19376 GAGTAGACTGGTGGTGGAGGTGGTGGTGACTGGACAGGTGGTGGAGGT
1 GAGTAAACTGGTGGTGGA---GGTGGCGACTAGACAGGTGGTGGAGGG
* *
19424 GAGTATACGGGTGGTGG
1 GAGTAAACTGGTGGTGG
19441 TGGGGAGTAG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 17 0.31
48 37 0.69
ACGTcount: A:0.18, C:0.06, G:0.55, T:0.21
Consensus pattern (45 bp):
GAGTAAACTGGTGGTGGAGGTGGCGACTAGACAGGTGGTGGAGGG
Found at i:19439 original size:24 final size:24
Alignment explanation
Indices: 19313--19458 Score: 101
Period size: 24 Copynumber: 6.3 Consensus size: 24
19303 TTGAGATTGT
* *
19313 ACGGGTGGTAGTGGTGGTGAGTAA
1 ACGGGTGGTGGTGGTGGTGAGTAG
* * *
19337 ACTGGTGGTGGAGGTGGCGAGTAG
1 ACGGGTGGTGGTGGTGGTGAGTAG
*
19361 ACGGGTGGTGG-AG-GG-GAGTAG
1 ACGGGTGGTGGTGGTGGTGAGTAG
* *
19382 ACTGGTGGTGGAGGTGGTG-GT-G
1 ACGGGTGGTGGTGGTGGTGAGTAG
** * *
19404 ACTGGACAGGTGGTGGAGGTGAGTAT
1 AC-GG-GTGGTGGTGGTGGTGAGTAG
19430 ACGGGTGGTGGT-G-GG-GAGTAG
1 ACGGGTGGTGGTGGTGGTGAGTAG
*
19451 ACTGGTGG
1 ACGGGTGG
19459 AGGGGGTGAA
Statistics
Matches: 96, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
21 28 0.29
22 8 0.08
23 7 0.07
24 47 0.49
25 4 0.04
26 2 0.02
ACGTcount: A:0.17, C:0.06, G:0.55, T:0.22
Consensus pattern (24 bp):
ACGGGTGGTGGTGGTGGTGAGTAG
Found at i:19904 original size:21 final size:20
Alignment explanation
Indices: 19880--19928 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
19870 GTAGACGAGA
*
19880 GGTGGTGGGGAGGAGTAGACC
1 GGTGGAGGGG-GGAGTAGACC
* **
19901 GGTGGAGGGGTGAGTAGATT
1 GGTGGAGGGGGGAGTAGACC
19921 GGTGGAGG
1 GGTGGAGG
19929 TGGTGAATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.18, C:0.04, G:0.59, T:0.18
Consensus pattern (20 bp):
GGTGGAGGGGGGAGTAGACC
Found at i:19917 original size:20 final size:21
Alignment explanation
Indices: 19892--19951 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
19882 TGGTGGGGAG
*
19892 GAGTAGACCGGTGGAGG-GGT
1 GAGTAGACAGGTGGAGGTGGT
**
19912 GAGTAGATTGGTGGAGGTGGT
1 GAGTAGACAGGTGGAGGTGGT
* *
19933 GAATAGACAGGTGGTGGTG
1 GAGTAGACAGGTGGAGGTG
19952 ATTGCTTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.22, C:0.05, G:0.52, T:0.22
Consensus pattern (21 bp):
GAGTAGACAGGTGGAGGTGGT
Found at i:20055 original size:21 final size:21
Alignment explanation
Indices: 20029--20069 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20019 TTCTTGGACA
20029 GGTGGTGGAGGAGAGTAGACG
1 GGTGGTGGAGGAGAGTAGACG
* *
20050 GGTGGTGGTGGGGAGTAGAC
1 GGTGGTGGAGGAGAGTAGAC
20070 AGGGGGAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.59, T:0.17
Consensus pattern (21 bp):
GGTGGTGGAGGAGAGTAGACG
Done.