Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021881.1 Corchorus olitorius cultivar O-4 contig21914, 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: 56576
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:5264 original size:8 final size:9
Alignment explanation
Indices: 5228--5265 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
5218 CCCAAATTAC
5228 TTATGGAAA
1 TTATGGAAA
*
5237 TTAAGGAAA
1 TTATGGAAA
5246 TTATGGAAA
1 TTATGGAAA
5255 TTAT-GAAA
1 TTATGGAAA
5263 TTA
1 TTA
5266 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:6616 original size:49 final size:47
Alignment explanation
Indices: 6541--6680 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 47
6531 CAAGCAACCC
*
6541 TTTACTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* * *
6588 TTTAATTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAACTGATCT
1 TTTAATTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
6637 TTTAATTTT-CATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
6681 TTGGCACGCT
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
47 19 0.24
48 20 0.25
49 40 0.50
50 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (47 bp):
TTTAATTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:7742 original size:23 final size:23
Alignment explanation
Indices: 7699--7742 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
7689 ATTCTAACTC
* *
7699 TCCCTCTCCCAATCGTATTTTTT
1 TCCCTCTCCCAAACATATTTTTT
7722 TCCCTCTCTCCAAACAT-TTTT
1 TCCCTCTC-CCAAACATATTTT
7743 CTCATCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.16, C:0.36, G:0.02, T:0.45
Consensus pattern (23 bp):
TCCCTCTCCCAAACATATTTTTT
Found at i:11612 original size:17 final size:17
Alignment explanation
Indices: 11590--11642 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
11580 ATTTTAGGAG
11590 TAATTATTGAATAATAA
1 TAATTATTGAATAATAA
*
11607 TAATTATTGAATAATTA
1 TAATTATTGAATAATAA
* *
11624 TTATTAGTTCAATAATAA
1 TAATTA-TTGAATAATAA
11642 T
1 T
11643 GGTTAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 21 0.68
18 10 0.32
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (17 bp):
TAATTATTGAATAATAA
Found at i:14194 original size:12 final size:12
Alignment explanation
Indices: 14177--14201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14167 CCACACATCA
14177 GAAATGGCAATG
1 GAAATGGCAATG
14189 GAAATGGCAATG
1 GAAATGGCAATG
14201 G
1 G
14202 CTTCAGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAATGGCAATG
Found at i:16216 original size:43 final size:43
Alignment explanation
Indices: 16070--16356 Score: 336
Period size: 41 Copynumber: 6.8 Consensus size: 43
16060 CCAATAACTA
*
16070 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGC-A-CCTCTATTCC
* * *
16115 AAAGTCCTCAAACACATTTATAACACAGAGGCACCTATA-T-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCC
16156 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCC
* * *
16199 AAAGTCCTCAAACACATTTATAACACAGAGGCACCTATA-T-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCC
* ** * *
16240 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCT-CTCTA
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTC-C
* * * *
16283 AAAGTCCTCAAACACATTTATAACACA-GAG-ACATCTATACC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCC
* *
16324 AAAGTCCCCAAACACAATTATAACACATGGGCA
1 AAAGTCCCCAAACACATTTATAACACAGGGGCA
16357 ATTCAATTTA
Statistics
Matches: 206, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
41 100 0.49
42 8 0.04
43 67 0.33
44 1 0.00
45 30 0.15
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCC
Found at i:16358 original size:84 final size:84
Alignment explanation
Indices: 16070--16360 Score: 458
Period size: 84 Copynumber: 3.4 Consensus size: 84
16060 CCAATAACTA
*
16070 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTATTCCAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTC--TTCCAAAGTCCTCAAACACATTTA
16135 TAACACAGAGGCACCTATATC
64 TAACACAGAGGCACCTATATC
* ** *
16156 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTCCAAAGTCCTCAAACACATTTATA
16221 ACACAGAGGCACCTATATC
66 ACACAGAGGCACCTATATC
*
16240 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTC-TCTAAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTC-CAAAGTCCTCAAACACATTTAT
* * *
16304 AACACAGAGACATCTATACC
65 AACACAGAGGCACCTATATC
*
16324 AAAGTCCCCAAACACAATTATAACACATGGGCAATTC
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTC
16361 AATTTATGGC
Statistics
Matches: 192, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
83 2 0.01
84 154 0.80
86 36 0.19
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTCCAAAGTCCTCAAACACATTTATA
ACACAGAGGCACCTATATC
Found at i:21352 original size:28 final size:26
Alignment explanation
Indices: 21297--21346 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
21287 ATGATTTAGG
*
21297 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
* *
21323 GGTTACTAACGCTCTTTTTTTTTT
1 GGTTACTAACGCCCTTTTTCTTTT
21347 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Found at i:28093 original size:22 final size:22
Alignment explanation
Indices: 28068--28119 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
28058 AATTTAGAGG
*
28068 ATTAATTTGGATCTTA-ATCCAA
1 ATTAATTTGGAT-TAAGATCCAA
28090 ATTAATTTGGATTAAGATCCAA
1 ATTAATTTGGATTAAGATCCAA
28112 ATTAATTT
1 ATTAATTT
28120 AGTGAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (22 bp):
ATTAATTTGGATTAAGATCCAA
Found at i:35284 original size:17 final size:17
Alignment explanation
Indices: 35245--35297 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
35235 ATTTTAGGAG
*
35245 TAATTACTGAATAATAA
1 TAATTACTTAATAATAA
*
35262 TAATTACTTAATAATTA
1 TAATTACTTAATAATAA
* *
35279 TTATTAGTTCAATAATAA
1 TAATTACTT-AATAATAA
35297 T
1 T
35298 GGTCAGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (17 bp):
TAATTACTTAATAATAA
Found at i:36522 original size:20 final size:21
Alignment explanation
Indices: 36483--36522 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36473 GCAAAAACCT
* *
36483 AAGCTTCGCGCTTATTTTCTC
1 AAGCTCCGCGCCTATTTTCTC
36504 AAGCTCCGCGCCT-TTTTCT
1 AAGCTCCGCGCCTATTTTCT
36523 GCAGCAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.33, G:0.15, T:0.40
Consensus pattern (21 bp):
AAGCTCCGCGCCTATTTTCTC
Found at i:41583 original size:25 final size:24
Alignment explanation
Indices: 41546--41592 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
41536 TTGAAAATTT
41546 TGAAAAACTTTGATGGATGAGATGTA
1 TGAAAAACTTTGAT-GAT-AGATGTA
41572 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
41593 AATAGAAGGA
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:45970 original size:15 final size:15
Alignment explanation
Indices: 45947--45979 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
45937 CTAAATATGA
45947 AGTCCAGGATGTTTT
1 AGTCCAGGATGTTTT
*
45962 AGTCGAGGATGTTTT
1 AGTCCAGGATGTTTT
45977 AGT
1 AGT
45980 GCAGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.30, T:0.39
Consensus pattern (15 bp):
AGTCCAGGATGTTTT
Found at i:50466 original size:23 final size:22
Alignment explanation
Indices: 50392--50483 Score: 123
Period size: 22 Copynumber: 4.2 Consensus size: 22
50382 GTCGACTAAG
50392 AATTGTCGACTTCAAGGAGAGA
1 AATTGTCGACTTCAAGGAGAGA
*
50414 AATTGTTGACTTCAAGGAGAGA
1 AATTGTCGACTTCAAGGAGAGA
*
50436 AATTGTCGACTTCAAGGAAGAGC
1 AATTGTCGACTTCAAGG-AGAGA
* **
50459 AATAGTCGACTAAAAGGAG-GA
1 AATTGTCGACTTCAAGGAGAGA
50480 AATT
1 AATT
50484 TTTGACTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.07
22 39 0.64
23 18 0.30
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (22 bp):
AATTGTCGACTTCAAGGAGAGA
Found at i:52186 original size:17 final size:18
Alignment explanation
Indices: 52164--52199 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52154 AAAGGGTAAT
*
52164 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
52181 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
52199 T
1 T
52200 GATAGAGGAG
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:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:53010 original size:11 final size:12
Alignment explanation
Indices: 52994--53025 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
52984 AAAGTTCGTG
52994 TTTGAAGACT-A
1 TTTGAAGACTAA
53005 TTTGAAGA-TAA
1 TTTGAAGACTAA
53016 TTTGAAGACT
1 TTTGAAGACT
53026 TGAAGATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:53030 original size:19 final size:18
Alignment explanation
Indices: 53006--53041 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52996 TGAAGACTAT
53006 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
53025 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
53042 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Done.