Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017391.1 Corchorus olitorius cultivar O-4 contig17424, 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: 19246
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1662 original size:193 final size:193
Alignment explanation
Indices: 1329--1710 Score: 611
Period size: 193 Copynumber: 2.0 Consensus size: 193
1319 CTTAAAATCA
* * ** *
1329 CTTTGCTCATATCTGTGTAAAAAGACATCAAAATAGCTCCAAAAGTAGTGAAAATTATCAAATTA
1 CTTTGCTCAAATCTGTGTAAAAAGACATCAAAATAGCTCCAAAAATAGTGAAAAACAACAAATTA
* *
1394 TCAATTTCACATCTCATAAAGACTCAAATCACAAATATTAACAAAATAACATATATTTAAGCATA
66 TCAATTTCACATCACATAAAGACTCAAAACACAAATATTAACAAAATAACATATATTTAAGCATA
* * * *
1459 AATTGATCCAAAAACATAATAAAATAGCCATAAAAATAGGGTTGTTTTTGGCTCGATCAATTG
131 AATGGATCCAAAAACATAACAAAATAGCCATAAAAATAGGGTTGTTTTTAGCTCAATCAATTG
* * *
1522 CTTTGCTCAAATTTGTGTAAAAAGTCATCAAAATAGCTCCAAAAATAGTGAAAAACAACAAATTC
1 CTTTGCTCAAATCTGTGTAAAAAGACATCAAAATAGCTCCAAAAATAGTGAAAAACAACAAATTA
* *
1587 TCAATTTCACATCACTTAAAGACTCAAAACACAAATATTATCAAAATAACATATATTTAAGCATA
66 TCAATTTCACATCACATAAAGACTCAAAACACAAATATTAACAAAATAACATATATTTAAGCATA
*
1652 AATGGATCCAAAAACATAGCAAAATAGCCATAAAAATAGGGTTGTTTTTAGCTCAATCA
131 AATGGATCCAAAAACATAACAAAATAGCCATAAAAATAGGGTTGTTTTTAGCTCAATCA
1711 TAATTCCCCC
Statistics
Matches: 172, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
193 172 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (193 bp):
CTTTGCTCAAATCTGTGTAAAAAGACATCAAAATAGCTCCAAAAATAGTGAAAAACAACAAATTA
TCAATTTCACATCACATAAAGACTCAAAACACAAATATTAACAAAATAACATATATTTAAGCATA
AATGGATCCAAAAACATAACAAAATAGCCATAAAAATAGGGTTGTTTTTAGCTCAATCAATTG
Found at i:3310 original size:21 final size:21
Alignment explanation
Indices: 3286--3353 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3276 GGAATGGTAA
3286 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATGGCCGGTGG
* ** *
3307 TGGCACGGGCTTAACCGATGG
1 TGGCACGGGCATGGCCGGTGG
* * *
3328 TGCCACGGTGAATGGCCGGTTG
1 TGGCACGG-GCATGGCCGGTGG
3350 TGGC
1 TGGC
3354 TTGGTAGTGG
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
21 24 0.71
22 10 0.29
ACGTcount: A:0.13, C:0.24, G:0.44, T:0.19
Consensus pattern (21 bp):
TGGCACGGGCATGGCCGGTGG
Found at i:3524 original size:21 final size:21
Alignment explanation
Indices: 3500--3557 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
3490 AGCTTGGAAT
3500 GGCGCGGATGACCGGGCAGGC
1 GGCGCGGATGACCGGGCAGGC
3521 GGCGCGGATGACCGGGCAGGC
1 GGCGCGGATGACCGGGCAGGC
*
3542 GGCGCGGATGGCCGGG
1 GGCGCGGATGACCGGG
3558 TAGAAGACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.12, C:0.28, G:0.55, T:0.05
Consensus pattern (21 bp):
GGCGCGGATGACCGGGCAGGC
Found at i:6537 original size:20 final size:21
Alignment explanation
Indices: 6513--6552 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6503 CACAAAATTT
*
6513 TTTTTTATAATGCAAAAACTC
1 TTTTCTATAATGCAAAAACTC
* *
6534 TTTTCTTTATTGCAAAAAC
1 TTTTCTATAATGCAAAAAC
6553 CGAATTTTTT
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:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTTCTATAATGCAAAAACTC
Found at i:9627 original size:19 final size:18
Alignment explanation
Indices: 9590--9629 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
9580 TTCTTGAAAT
*
9590 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
9608 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
9627 AAT
1 AAT
9630 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:12568 original size:54 final size:53
Alignment explanation
Indices: 12521--12923 Score: 385
Period size: 54 Copynumber: 7.6 Consensus size: 53
12511 TGGATCAAAT
** *
12521 TGGAGATCAACTCTGATCATCTTAAACTTCTTGAACGACCACACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAACGACCGCACTGGATCATC
* * * *
12574 TGGAGATCAACTCTGATCTTCGAAAACTTCTTAAAACGACTGCACCGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTT-GAACGACCGCACTGGATCATC
* *
12628 TGAAGATCAA--CT--T--T-GAAAACTTCTCGGAA-GAACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCT-TGAACG-ACCGCACTGGATCATC
* * * * *
12675 TGGACATCAACTCTGAACTTCGAAAACTTCTTGTAAGGACCACACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTG-AACGACCGCACTGGATCATC
* * * * *
12729 TGGACATCAACTCTGAACTTCGAAAACTTCTTGTAAGGACCGTACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTG-AACGACCGCACTGGATCATC
* * *
12783 TGGAGATCAACTCTGATCATCAAAAACTTCTTCGAATGACCGCACTAGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTT-GAACGACCGCACTGGATCATC
* * * *
12837 T-GAGGATCAACTCTGATCATTGAATACTTCTTGGAATGACCGCACCGGATCATC
1 TGGA-GATCAACTCTGATCATCGAAAACTTCTT-GAACGACCGCACTGGATCATC
* * * *
12891 T-TAGGATCAACTCTGACCATTGAAGACTTCTTG
1 TGGA-GATCAACTCTGATCATCGAAAACTTCTTG
12924 GAATGAGATC
Statistics
Matches: 301, Mismatches: 35, Indels: 28
0.83 0.10 0.08
Matches are distributed among these distances:
46 1 0.00
47 34 0.11
48 1 0.00
49 2 0.01
50 1 0.00
52 2 0.01
53 34 0.11
54 224 0.74
55 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (53 bp):
TGGAGATCAACTCTGATCATCGAAAACTTCTTGAACGACCGCACTGGATCATC
Found at i:12934 original size:35 final size:35
Alignment explanation
Indices: 12895--13339 Score: 574
Period size: 35 Copynumber: 12.8 Consensus size: 35
12885 ATCATCTTAG
* * * *
12895 GATCAACTCTGACCATTGAAGACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
12930 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
12965 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
13000 GATCAACTCTGACCAT-AAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
13034 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* ** *
13069 GATCAACTCTAATCATAAAAAACTTTTTGAAA-GTA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATG-A
* *
13104 GATCAACTTTGATCATCGAAAACTTCTTAAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
** *
13139 GATCAACTCTGATCATAAAAAACTTTTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
13174 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
13209 GATCAGCTCTAATCAT--AAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
13242 GATCAATTCTGATCATAGAAAGCTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
13277 GATCAACTCTGATCATAGAAAGCTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
*
13312 GAACAACTCTGATCATCGAAAACTTCTT
1 GATCAACTCTGATCATCGAAAACTTCTT
13340 ATGAAAGACT
Statistics
Matches: 358, Mismatches: 47, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
33 29 0.08
34 31 0.09
35 297 0.83
36 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
Found at i:13148 original size:209 final size:208
Alignment explanation
Indices: 12895--13340 Score: 671
Period size: 209 Copynumber: 2.1 Consensus size: 208
12885 ATCATCTTAG
* * * ** *
12895 GATCAACTCTGACCATTGAAGACTTCTTGGAATGAGATCAACTCTGATCATCAAAAACTTCTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATAAAAAACTTCTTGA
*
12960 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGACCATAAAAACTTC
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTAACCAT-AAAACTTC
13025 TTGAAACGAGATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGAGATCAACTCTAATCATAAAA
130 TTGAAACGAGATCAACTCTGATCATA-GAAAACTTCTTGAAAGGAGATCAACTCTAATCATAAAA
*
13089 AACTTTTTGAAA-GTA
194 AACTTCTTGAAATG-A
* *
13104 GATCAACTTTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATAAAAAACTTTTTGA
1 GATCAACTCTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATAAAAAACTTCTTGA
* * *
13169 AATGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAGCTCTAATCATAAAACTTCT
66 AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTAACCATAAAACTTCT
* * * * * *
13234 TGAAACGAGATCAATTCTGATCATAGAAAGCTTCTTGAAATGAGATCAACTCTGATCATAGAAAG
131 TGAAACGAGATCAACTCTGATCATAGAAAACTTCTTGAAAGGAGATCAACTCTAATCATAAAAAA
13299 CTTCTTGAAATGA
196 CTTCTTGAAATGA
*
13312 GAACAACTCTGATCATCGAAAACTTCTTA
1 GATCAACTCTGATCATCGAAAACTTCTTA
13341 TGAAAGACTG
Statistics
Matches: 214, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
208 103 0.48
209 111 0.52
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (208 bp):
GATCAACTCTGATCATCGAAAACTTCTTAAAATGAGATCAACTCTGATCATAAAAAACTTCTTGA
AACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTAACCATAAAACTTCT
TGAAACGAGATCAACTCTGATCATAGAAAACTTCTTGAAAGGAGATCAACTCTAATCATAAAAAA
CTTCTTGAAATGA
Found at i:13414 original size:54 final size:54
Alignment explanation
Indices: 13329--13528 Score: 283
Period size: 54 Copynumber: 3.7 Consensus size: 54
13319 TCTGATCATC
** ** * * * *
13329 GAAAACTTCTTATGAAAGACTGCACAAGGTCATCTGAAGATCAACTTAGATTTCT
1 GAAAACTTC-TATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCT
*
13384 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCT
13438 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCT
* * *
13492 GAAAACTTCTATGAAAGACCATATTGGGTCATTTTAA
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
13529 ACACATGTAC
Statistics
Matches: 132, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 123 0.93
55 9 0.07
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (54 bp):
GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATCTCT
Found at i:14638 original size:40 final size:42
Alignment explanation
Indices: 14580--14663 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 42
14570 AATCTTTTTG
** *
14580 AAAAACATTTTTTCTCTTTTGAAAAGATTGCACTTTGAGGAAA
1 AAAAACA-TTTTTCTCTTTTGAAAAGATCACACTTTGAAGAAA
14623 AAAAACA-TTTT-TCTTTTGAAAAGATCACACTTTGAAGAAA
1 AAAAACATTTTTCTCTTTTGAAAAGATCACACTTTGAAGAAA
14663 A
1 A
14664 TATTTTTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 27 0.71
41 4 0.11
43 7 0.18
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (42 bp):
AAAAACATTTTTCTCTTTTGAAAAGATCACACTTTGAAGAAA
Found at i:14884 original size:16 final size:16
Alignment explanation
Indices: 14865--14916 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
14855 TTTCAACTTC
14865 TTTC-TTTTCTTTTCTT
1 TTTCATTTT-TTTTCTT
*
14881 TTTCAATTCTTTTTTTCAT
1 TTTC-A-T-TTTTTTTCTT
14900 TTTCATTTTTTTTCTT
1 TTTCATTTTTTTTCTT
14916 T
1 T
14917 CCCTCTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
18 1 0.03
19 11 0.37
20 3 0.10
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCATTTTTTTTCTT
Found at i:14902 original size:19 final size:17
Alignment explanation
Indices: 14865--14912 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
14855 TTTCAACTTC
* *
14865 TTTC-TTTTCTTTTCTT
1 TTTCATTTTTTTTTCAT
14881 TTTCAATTCTTTTTTTCAT
1 TTTC-ATT-TTTTTTTCAT
14900 TTTCATTTTTTTT
1 TTTCATTTTTTTT
14913 CTTTCCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 5 0.19
19 12 0.44
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCATTTTTTTTTCAT
Found at i:14908 original size:26 final size:26
Alignment explanation
Indices: 14845--14909 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
14835 ATTATCTCCA
14845 TCTTTTGCTTTTTCAACTTCTTTCTTT
1 TCTTTT-CTTTTTCAACTTCTTTCTTT
14872 TCTTTTCTTTTTCAA-TTCTTT-TTT
1 TCTTTTCTTTTTCAACTTCTTTCTTT
14896 TCATTTTCATTTTT
1 TC-TTTTC-TTTTT
14910 TTTCTTTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.14
25 11 0.31
26 14 0.39
27 6 0.17
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (26 bp):
TCTTTTCTTTTTCAACTTCTTTCTTT
Done.