Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018725.1 Corchorus olitorius cultivar O-4 contig18758, 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: 51426
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1288 original size:33 final size:33
Alignment explanation
Indices: 1242--1424 Score: 246
Period size: 33 Copynumber: 5.6 Consensus size: 33
1232 ATCTAGGCTT
* *
1242 TGCCATGGTGTGGCGCCCTCCGGGGGCGCCCAC
1 TGCCATGGCGTGGCGCCCTCCGGAGGCGCCCAC
1275 TGCCATGGCGTGGCGCCCTCCGGAGGCGCCCAC
1 TGCCATGGCGTGGCGCCCTCCGGAGGCGCCCAC
* *
1308 TGCCATGGCGTGGCGCCCTCCGGAGGCG-TCTC
1 TGCCATGGCGTGGCGCCCTCCGGAGGCGCCCAC
*
1340 TGCCATGGTGTGGCGCCCTCCGG-GGACGCCCAC
1 TGCCATGGCGTGGCGCCCTCCGGAGG-CGCCCAC
** * *
1373 TGCCATGGTATGGCGCCCTCCGGAGGTG-CCTC
1 TGCCATGGCGTGGCGCCCTCCGGAGGCGCCCAC
*
1405 TGCCATGGCTTGGCGCCCTC
1 TGCCATGGCGTGGCGCCCTC
1425 TGGGGGCGGT
Statistics
Matches: 135, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
31 2 0.01
32 47 0.35
33 84 0.62
34 2 0.01
ACGTcount: A:0.08, C:0.39, G:0.36, T:0.17
Consensus pattern (33 bp):
TGCCATGGCGTGGCGCCCTCCGGAGGCGCCCAC
Found at i:1291 original size:20 final size:20
Alignment explanation
Indices: 1266--1325 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
1256 GCCCTCCGGG
1266 GGCGCCCACTGCCATGGCGT
1 GGCGCCCACTGCCATGGCGT
*
1286 GGCG-CC-CT-CC---G-GA
1 GGCGCCCACTGCCATGGCGT
1299 GGCGCCCACTGCCATGGCGT
1 GGCGCCCACTGCCATGGCGT
1319 GGCGCCC
1 GGCGCCC
1326 TCCGGAGGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
13 5 0.16
14 3 0.10
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 3 0.10
20 12 0.39
ACGTcount: A:0.08, C:0.43, G:0.37, T:0.12
Consensus pattern (20 bp):
GGCGCCCACTGCCATGGCGT
Found at i:1361 original size:65 final size:65
Alignment explanation
Indices: 1242--1429 Score: 263
Period size: 65 Copynumber: 2.9 Consensus size: 65
1232 ATCTAGGCTT
* * *
1242 TGCCATGGTGTGGCGCCCTCCGGGGGCGCCCACTGCCATGGCGTGGCGCCCTCCGGAGG-CGCCC
1 TGCCATGGTGTGGCGCCCTCCGGAGGCG-CCTCTGCCATGGTGTGGCGCCCTCCGG-GGACGCCC
1306 AC
64 AC
* *
1308 TGCCATGGCGTGGCGCCCTCCGGAGGCGTCTCTGCCATGGTGTGGCGCCCTCCGGGGACGCCCAC
1 TGCCATGGTGTGGCGCCCTCCGGAGGCGCCTCTGCCATGGTGTGGCGCCCTCCGGGGACGCCCAC
* * *
1373 TGCCATGGTATGGCGCCCTCCGGAGGTGCCTCTGCCATGGCT-TGGCGCCCTCTGGGG
1 TGCCATGGTGTGGCGCCCTCCGGAGGCGCCTCTGCCATGG-TGTGGCGCCCTCCGGGG
1430 GCGGTGGCGC
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
64 2 0.02
65 81 0.74
66 27 0.25
ACGTcount: A:0.07, C:0.38, G:0.37, T:0.18
Consensus pattern (65 bp):
TGCCATGGTGTGGCGCCCTCCGGAGGCGCCTCTGCCATGGTGTGGCGCCCTCCGGGGACGCCCAC
Found at i:1486 original size:15 final size:16
Alignment explanation
Indices: 1462--1502 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1452 CCCCGAGTAT
*
1462 TTTTTCTATTTTGTT-A
1 TTTTT-TATTTTCTTGA
1478 TTTTTTATTTTCTTGA
1 TTTTTTATTTTCTTGA
1494 TTTTTTATT
1 TTTTTTATT
1503 ATTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTCTTGA
Found at i:1811 original size:3 final size:3
Alignment explanation
Indices: 1803--1847 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1793 CCTGCAAAAT
1803 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1848 ATAAATTACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2105 original size:20 final size:21
Alignment explanation
Indices: 2077--2116 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2067 CAAAAGTGTG
*
2077 AAAATGAGG-CGGTAGTTAGT
1 AAAAAGAGGACGGTAGTTAGT
*
2097 AAAAAGAGGACGGTATTTAG
1 AAAAAGAGGACGGTAGTTAG
2117 CAATTCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.23
Consensus pattern (21 bp):
AAAAAGAGGACGGTAGTTAGT
Found at i:21818 original size:1 final size:1
Alignment explanation
Indices: 21812--21842 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
21802 ATCATCGCGG
*
21812 TTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21843 CTACAGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:22454 original size:16 final size:17
Alignment explanation
Indices: 22433--22466 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22423 TTTTCTTTTG
*
22433 CTTTTAT-TATTTTTCA
1 CTTTTATATATGTTTCA
22449 CTTTTATATATGTTTCA
1 CTTTTATATATGTTTCA
22466 C
1 C
22467 ATGTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.62
Consensus pattern (17 bp):
CTTTTATATATGTTTCA
Found at i:28801 original size:21 final size:21
Alignment explanation
Indices: 28777--28816 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28767 CTGGAGCCTT
* *
28777 GAATGGCGTGGAAGAAGGCGC
1 GAATGACGCGGAAGAAGGCGC
*
28798 GAATGACGCGGAGGAAGGC
1 GAATGACGCGGAAGAAGGC
28817 ACGACTAGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.47, T:0.07
Consensus pattern (21 bp):
GAATGACGCGGAAGAAGGCGC
Found at i:31785 original size:26 final size:24
Alignment explanation
Indices: 31742--31802 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 24
31732 AAAGAAAAAT
31742 ATTTTTTTTTAGAAACGCAGAAACACA
1 ATTTTTTTTTAG-AACGC--AAACACA
*
31769 ATTTTTTTTTATG-ACGCAAACACT
1 ATTTTTTTTTA-GAACGCAAACACA
*
31793 TTTTTTTTTT
1 ATTTTTTTTT
31803 GCGCTAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 15 0.48
26 4 0.13
27 11 0.35
28 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTTTTTTTAGAACGCAAACACA
Found at i:31835 original size:24 final size:23
Alignment explanation
Indices: 31808--31852 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31798 TTTTTGCGCT
*
31808 AAAACCGAAAAACTTTTTTTTTTC
1 AAAAACGAAAAA-TTTTTTTTTTC
*
31832 AAAAACGCAAAATTTTTTTTT
1 AAAAACGAAAAATTTTTTTTT
31853 CTAGGACGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (23 bp):
AAAAACGAAAAATTTTTTTTTTC
Found at i:31840 original size:54 final size:58
Alignment explanation
Indices: 31782--31901 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 58
31772 TTTTTTTATG
*
31782 ACGCAAACACTTTTTTTTT-T-TG-CGCTAAAAC-CGAAA-A-ACTTTTTTTTTTC-AAAA
1 ACGCAAACACTTTTTTTTTCTAGGACGC-AAAACAC-AAACAGA-TTTTTTTTTTCAAAAA
31836 ACGCAAA-A-TTTTTTTTTCTAGGACGCAAAACACAAACAGATTTTTTTTTTCAAAAA
1 ACGCAAACACTTTTTTTTTCTAGGACGCAAAACACAAACAGATTTTTTTTTTCAAAAA
31892 ACGCAAACAC
1 ACGCAAACAC
31902 AAAAAATAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
52 9 0.16
53 2 0.04
54 16 0.29
55 16 0.29
56 12 0.21
57 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (58 bp):
ACGCAAACACTTTTTTTTTCTAGGACGCAAAACACAAACAGATTTTTTTTTTCAAAAA
Found at i:31956 original size:24 final size:26
Alignment explanation
Indices: 31929--31978 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
31919 AAAACAACAA
31929 TTTTTTTTTAGAA-A-AAACGCAGAG
1 TTTTTTTTTAGAACAGAAACGCAGAG
31953 TTTTTTTTTAGAACAGAAACGCAGAG
1 TTTTTTTTTAGAACAGAAACGCAGAG
31979 ACTTAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.54
25 1 0.04
26 10 0.42
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (26 bp):
TTTTTTTTTAGAACAGAAACGCAGAG
Found at i:33659 original size:29 final size:30
Alignment explanation
Indices: 33622--33681 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
33612 CAAATCTTGC
* *
33622 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
33651 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
33682 CACAAAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:42415 original size:31 final size:32
Alignment explanation
Indices: 42376--42457 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
42366 TTTTGTCAAC
* *
42376 TTAC-CAATTTGAACCTAAACCTTTC-AAAAA
1 TTACTCAATTTGAGCCTAAACATTTCAAAAAA
* *
42406 TTACTCAATTTGAGTCTAAATATTTCAAAAAA
1 TTACTCAATTTGAGCCTAAACATTTCAAAAAA
*
42438 TTGCTCAATTTGAGCCTAAA
1 TTACTCAATTTGAGCCTAAA
42458 AACTAAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 4 0.09
31 17 0.39
32 23 0.52
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.34
Consensus pattern (32 bp):
TTACTCAATTTGAGCCTAAACATTTCAAAAAA
Found at i:43209 original size:2 final size:2
Alignment explanation
Indices: 43202--43227 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43192 ATATGGGACA
43202 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
43228 TGAATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46011 original size:21 final size:21
Alignment explanation
Indices: 45985--46026 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45975 GAGGCAACAG
*
45985 AAGAGACATATACAGAAATGA
1 AAGAGACAGATACAGAAATGA
*
46006 AAGAGACAGATTCAGAAATGA
1 AAGAGACAGATACAGAAATGA
46027 CAGGGAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (21 bp):
AAGAGACAGATACAGAAATGA
Found at i:49052 original size:21 final size:21
Alignment explanation
Indices: 49028--49119 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
49018 CTTAGGCAAT
*
49028 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
49049 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
49070 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
49091 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
49112 TCCAATGA
1 TCCAATGA
49120 ACTTCTAGCA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
20 3 0.05
21 63 0.95
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.