Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015927.1 Corchorus olitorius cultivar O-4 contig15960, 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: 31248
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2008 original size:15 final size:15
Alignment explanation
Indices: 1985--2014 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1975 GAAATCTGCC
1985 TCCAATCTGATTCAA
1 TCCAATCTGATTCAA
*
2000 TCCAGTCTGATTCAA
1 TCCAATCTGATTCAA
2015 GTCCTGATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (15 bp):
TCCAATCTGATTCAA
Found at i:7405 original size:36 final size:35
Alignment explanation
Indices: 7291--7561 Score: 375
Period size: 36 Copynumber: 7.6 Consensus size: 35
7281 AAAATGACGT
* *
7291 GAACTTTCCCTAAATTGAAAAC-TAAAACCTGATGG
1 GAACTTTCCC-AATTTGAAAACTTAAAACTTGATGG
* *
7326 GAACTTTCCCAATTTGAAAACTTTGAAATCTGGATGG
1 GAACTTTCCCAATTTGAAAAC-TT-AAAACTTGATGG
*
7363 GAACTTTCCCAATTTGAAAACTCAAAAGCTTGATGG
1 GAACTTTCCCAATTTGAAAACTTAAAA-CTTGATGG
*
7399 GAACTTTCCCAATTTGAAAACTTAAGAACTTAATGG
1 GAACTTTCCCAATTTGAAAACTTAA-AACTTGATGG
7435 GAACTTTCCCAATTTGAAAAC-TAAAACTTGATGG
1 GAACTTTCCCAATTTGAAAACTTAAAACTTGATGG
*
7469 GAACTTTCCCAATTTGATAACTTAAAAACTTGATGG
1 GAACTTTCCCAATTTGAAAACTT-AAAACTTGATGG
7505 GAACTTTCCCAATTTGAAAACTTTGAAAACTTGATGG
1 GAACTTTCCCAATTTGAAAAC-TT-AAAACTTGATGG
* *
7542 GAATTTTTCCAATTTGAAAA
1 GAACTTTCCCAATTTGAAAA
7562 GAGCTAAATT
Statistics
Matches: 213, Mismatches: 15, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
34 39 0.18
35 17 0.08
36 93 0.44
37 64 0.30
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (35 bp):
GAACTTTCCCAATTTGAAAACTTAAAACTTGATGG
Found at i:7474 original size:143 final size:145
Alignment explanation
Indices: 7247--7561 Score: 426
Period size: 143 Copynumber: 2.2 Consensus size: 145
7237 AATGCTGTTA
*
7247 GATGGGAACTTTCCCATTTTGAAAACTAAAACCGAAAATGACGTGAACTTTCCCTAAATTGAAAA
1 GATGGGAACTTTCCCAATTTGAAAACTAAAACCGAAAATGA-GTGAACTTTCCCTAAATTGAAAA
* *
7312 CTAAAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAATCTGGATGGGAACTTTCCCAATT
65 CTAAAACCTGATGGGAACTTTCCCAATTTGAAAAC-TTAAAAACTGGATGGGAACTTTCCCAATT
7377 TGAAAAC-TCAAAAGCTT
129 TGAAAACTTCAAAA-CTT
** *
7394 GATGGGAACTTTCCCAATTTGAAAACTTAAGAA-C-TTAATG-G-GAACTTTCCC-AATTTGAAA
1 GATGGGAACTTTCCCAATTTGAAAAC-TAA-AACCGAAAATGAGTGAACTTTCCCTAAATTGAAA
* * *
7454 ACTAAAACTTGATGGGAACTTTCCCAATTTGATAACTTAAAAACTTGATGGGAACTTTCCCAATT
64 ACTAAAACCTGATGGGAACTTTCCCAATTTGAAAACTTAAAAACTGGATGGGAACTTTCCCAATT
*
7519 TGAAAACTTTGAAAACTT
129 TGAAAAC-TTCAAAACTT
* *
7537 GATGGGAATTTTTCCAATTTGAAAA
1 GATGGGAACTTTCCCAATTTGAAAA
7562 GAGCTAAATT
Statistics
Matches: 152, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
142 33 0.22
143 68 0.45
144 15 0.10
145 1 0.01
147 29 0.19
148 4 0.03
149 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (145 bp):
GATGGGAACTTTCCCAATTTGAAAACTAAAACCGAAAATGAGTGAACTTTCCCTAAATTGAAAAC
TAAAACCTGATGGGAACTTTCCCAATTTGAAAACTTAAAAACTGGATGGGAACTTTCCCAATTTG
AAAACTTCAAAACTT
Found at i:7501 original size:106 final size:107
Alignment explanation
Indices: 7247--7561 Score: 393
Period size: 106 Copynumber: 2.9 Consensus size: 107
7237 AATGCTGTTA
* * ** * * *
7247 GATGGGAACTTTCCCATTTTGAAAACTAAAACCGAAAATGACGTGAACTTTCCCTAAATTGAAAA
1 GATGGGAACTTTCCCAATTTGAAAACTCAAA---AACTTGATGGGAACTTTCCC-AATTTGAAAA
* *
7312 C-TAAAACCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAATCTG
62 CTTAAAACTTGATGGGAACTTTCCCAATTTGAAAAC-TTGAAAACTG
*
7358 GATGGGAACTTTCCCAATTTGAAAACTCAAAAGCTTGATGGGAACTTTCCCAATTTGAAAACTTA
1 GATGGGAACTTTCCCAATTTGAAAACTCAAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTA
* *
7423 AGAACTTAATGGGAACTTTCCCAATTTGAAAAC-T-AAAACTT
66 A-AACTTGATGGGAACTTTCCCAATTTGAAAACTTGAAAACTG
* *
7464 GATGGGAACTTTCCCAATTTGATAACTTAAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTT
1 GATGGGAACTTTCCCAATTTGAAAACTCAAAAACTTGATGGGAACTTTCCCAATTTGAAAAC-TT
* *
7529 GAAAACTTGATGGGAATTTTTCCAATTTGAAAA
65 -AAAACTTGATGGGAACTTTCCCAATTTGAAAA
7562 GAGCTAAATT
Statistics
Matches: 182, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
106 64 0.35
107 40 0.22
108 20 0.11
109 29 0.16
111 29 0.16
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (107 bp):
GATGGGAACTTTCCCAATTTGAAAACTCAAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTA
AAACTTGATGGGAACTTTCCCAATTTGAAAACTTGAAAACTG
Found at i:7586 original size:52 final size:52
Alignment explanation
Indices: 7518--7640 Score: 201
Period size: 52 Copynumber: 2.4 Consensus size: 52
7508 CTTTCCCAAT
* * *
7518 TTGAAAACTTTGAAAACTTGATGGGAATTTTTCCAATTTGAAAAGAGCTAAA
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
* *
7570 TTGAATACTTAGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGATCTAAA
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
7622 TTGAATACTTTGAAAACTT
1 TTGAATACTTTGAAAACTT
7641 TGAAGGAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (52 bp):
TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
Found at i:10869 original size:31 final size:31
Alignment explanation
Indices: 10831--10892 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
10821 GAGATATCAT
10831 TTGATGGTGCAATACGAGATCAAATTGTACA
1 TTGATGGTGCAATACGAGATCAAATTGTACA
10862 TTGATGGTGCAATACGAGATCAAATTGTACA
1 TTGATGGTGCAATACGAGATCAAATTGTACA
10893 ATTTTCAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (31 bp):
TTGATGGTGCAATACGAGATCAAATTGTACA
Found at i:17293 original size:15 final size:15
Alignment explanation
Indices: 17273--17310 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
17263 AAGACCCTGC
17273 AAAAAGA-GAGAAAAT
1 AAAAAGAGGA-AAAAT
17288 AAAAAGAGGTAAAAAT
1 AAAAAGAGG-AAAAAT
17304 AAAAAGA
1 AAAAAGA
17311 AAACCTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
AAAAAGAGGAAAAAT
Found at i:20404 original size:17 final size:16
Alignment explanation
Indices: 20378--20411 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
20368 AAGAAACAAT
20378 ATTAATTTGTTTTACA
1 ATTAATTTGTTTTACA
20394 ATTAGATTTGTTTTACA
1 ATTA-ATTTGTTTTACA
20411 A
1 A
20412 CTTTTACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (16 bp):
ATTAATTTGTTTTACA
Found at i:24092 original size:30 final size:30
Alignment explanation
Indices: 24056--24553 Score: 652
Period size: 30 Copynumber: 16.6 Consensus size: 30
24046 TCACAAAGAA
24056 TTTGAGGATCATTGCTTTATTTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
*
24086 TTTGAGGATCATTGCTTTATTTTAATCTTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
*
24116 TTTGAGGATCATTGCTTTATGTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
* *
24146 GTTGAGGATCGTTGC-----TTT-ATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
*
24170 TTTGAGGATCAATGCTTTATATTTATTTTAATCCTG
1 TTTGAGGATCATTGC------TTTATTTTAATCCTG
* *
24206 TTTGAGGATCATTTCTTCATTTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
24236 TTTGAGGATCATTGCTTTATTTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
*
24266 TTTGAGGATCATTGCTTTATTTTAGTCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
* * *
24296 GTTAAGGATCATCGCTTTATTTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
*
24326 TTTGAGGATCATTGCTATATTTTTAATCCTG
1 TTTGAGGATCATTGCTTTA-TTTTAATCCTG
24357 TTTGAGGATCATTGCTTTATTTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
* *
24387 GTTAAGGATCATTGCTTTATTTTAATCCTAG
1 TTTGAGGATCATTGCTTTATTTTAATCCT-G
* *
24418 -TTGAGGATCATTGCTTCATTTCAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
*
24447 GTTGAGGATCATTGCTTTATTTTAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
* * *
24477 GTTGAGGATCATTGCTTCATTTCAATCCTG
1 TTTGAGGATCATTGCTTTATTTTAATCCTG
* * *
24507 GTTGAGGGTCGTTGCTTTATTTTAATCCTGG
1 TTTGAGGATCATTGCTTTATTTTAATCCT-G
24538 TTT-AGGATCATTGCTT
1 TTTGAGGATCATTGCTT
24554 CAGTTTATTT
Statistics
Matches: 412, Mismatches: 40, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
24 18 0.04
25 2 0.00
29 1 0.00
30 336 0.82
31 33 0.08
35 3 0.01
36 19 0.05
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.47
Consensus pattern (30 bp):
TTTGAGGATCATTGCTTTATTTTAATCCTG
Found at i:24174 original size:24 final size:24
Alignment explanation
Indices: 24140--24189 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
24130 CTTTATGTTA
**
24140 ATCCTGGTTGAGGATCGTTGCTTT
1 ATCCTGGTTGAGGATCAATGCTTT
*
24164 ATCCTGTTTGAGGATCAATGCTTT
1 ATCCTGGTTGAGGATCAATGCTTT
24188 AT
1 AT
24190 ATTTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (24 bp):
ATCCTGGTTGAGGATCAATGCTTT
Found at i:25027 original size:28 final size:27
Alignment explanation
Indices: 24995--25071 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
24985 TTAGGTCATT
* *
24995 TAGGGGGGATTTTGGTCATTTTTGCACC
1 TAGGGGAGATTTTGGTCATTTTTACA-C
* *
25023 TA-GGGAAATTTTGGGTCATTTTTACAT
1 TAGGGGAGATTTT-GGTCATTTTTACAC
*
25050 TCAGGGGTG-TTTTGGTCATTTT
1 T-AGGGGAGATTTTGGTCATTTT
25072 AAGTTTACTG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
27 18 0.45
28 19 0.47
29 3 0.08
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.44
Consensus pattern (27 bp):
TAGGGGAGATTTTGGTCATTTTTACAC
Found at i:29757 original size:35 final size:35
Alignment explanation
Indices: 29705--29875 Score: 150
Period size: 35 Copynumber: 4.8 Consensus size: 35
29695 GAGTCAAGTA
*
29705 AACTGAAGAAAAGATCGCCCTGGATCAACTAAAAT-
1 AACTGAAG-TAAGATCGCCCTGGATCAACTAAAATG
* * *
29740 AACTTGAAGTAAGATCGCCCTGAATCAATTGAAATG
1 AAC-TGAAGTAAGATCGCCCTGGATCAACTAAAATG
* * * * *
29776 AATTGAAG-AAGGACCGCCCTGGGTCAACTGAAATA
1 AACTGAAGTAA-GATCGCCCTGGATCAACTAAAATG
* *
29811 AACTGAA-TAAAAGATCACCCTGGATCAATTAAAATG
1 AACTGAAGT--AAGATCGCCCTGGATCAACTAAAATG
* * *
29847 AACTAAAGAAAGATCGCCCTGGGTCAACT
1 AACTGAAGTAAGATCGCCCTGGATCAACT
29876 GAAACAAACT
Statistics
Matches: 107, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
34 2 0.02
35 72 0.67
36 31 0.29
37 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (35 bp):
AACTGAAGTAAGATCGCCCTGGATCAACTAAAATG
Found at i:29838 original size:71 final size:68
Alignment explanation
Indices: 29667--29885 Score: 216
Period size: 71 Copynumber: 3.2 Consensus size: 68
29657 CTGGATCCAT
* * * *
29667 TGAAATAAATTGAAGAAAAGATCGCCCT-GAGTCAAGTAAACTGAA-GAA-AAGATCGCCCTGGA
1 TGAAATAAACTGAATAAAAGATCGCCCTGGA-TCAATTAAA-TGAATGAAGAAGATCGCCCTGGG
29729 TCAAC
64 TCAAC
* * *
29734 TAAAAT-AACTTGAAGT--AAGATCGCCCTGAATCAATTGAAATGAATTGAAGAAGGACCGCCCT
1 TGAAATAAAC-TGAA-TAAAAGATCGCCCTGGATCAATT-AAATGAA-TGAAGAA-GATCGCCCT
29796 GGGTCAAC
61 GGGTCAAC
* *
29804 TGAAATAAACTGAATAAAAGATCACCCTGGATCAATTAAAATGAACTAAAGAAAGATCGCCCTGG
1 TGAAATAAACTGAATAAAAGATCGCCCTGGATCAATT-AAATGAA-TGAAG-AAGATCGCCCTGG
29869 GTCAAC
63 GTCAAC
*
29875 TGAAACAAACT
1 TGAAATAAACT
29886 TAGTGGATCT
Statistics
Matches: 125, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
66 22 0.18
67 13 0.10
68 3 0.02
69 3 0.02
70 24 0.19
71 58 0.46
72 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (68 bp):
TGAAATAAACTGAATAAAAGATCGCCCTGGATCAATTAAATGAATGAAGAAGATCGCCCTGGGTC
AAC
Found at i:30020 original size:37 final size:37
Alignment explanation
Indices: 29896--30119 Score: 150
Period size: 37 Copynumber: 6.4 Consensus size: 37
29886 TAGTGGATCT
* * * *
29896 ATTGAAACAAACTG-AGTAATGACCGCCCTGGATC-A
1 ATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAA
* *
29931 ATTGAAATAAATTGAAGAAAAGATCGCCCTGGATTTAA
1 ATTGAAATAAACTGAAGAAAAGATCGCCCTGGA-TCAA
* *
29969 A-TGAAAGAAACTGAATAAAA-ATCGCCCTGGATCAA
1 ATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAA
* * * * * *
30004 ACTTGAAATAGACTGAAG-AAGGACCACCCTGGGTC-C
1 A-TTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAA
* * * *
30040 ACTGAAATAAACTGAAG-AAAGACCGCCATGGGTC--
1 ATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAA
*
30074 ----AAATAAACTGAAGCAAAGATCGCCCTGGATCAA
1 ATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAA
* *
30107 CTTGAAATTAACT
1 ATTGAAATAAACT
30120 TTAGCATCTG
Statistics
Matches: 149, Mismatches: 27, Indels: 24
0.75 0.14 0.12
Matches are distributed among these distances:
30 13 0.09
31 14 0.09
35 44 0.30
36 29 0.19
37 47 0.32
38 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.20
Consensus pattern (37 bp):
ATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAA
Found at i:30054 original size:35 final size:35
Alignment explanation
Indices: 30007--30073 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
29997 GGATCAAACT
* * *
30007 TGAAATAGACTGAAGAAGGACCACCCTGGGTCCAC
1 TGAAATAAACTGAAGAAAGACCACCATGGGTCCAC
*
30042 TGAAATAAACTGAAGAAAGACCGCCATGGGTC
1 TGAAATAAACTGAAGAAAGACCACCATGGGTC
30074 AAATAAACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (35 bp):
TGAAATAAACTGAAGAAAGACCACCATGGGTCCAC
Found at i:30080 original size:30 final size:31
Alignment explanation
Indices: 30044--30106 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
30034 GGGTCCACTG
*
30044 AAATAAACTGAAG-AAAGACCGCCATGGGTC
1 AAATAAACTGAAGCAAAGACCGCCATGGATC
* *
30074 AAATAAACTGAAGCAAAGATCGCCCTGGATC
1 AAATAAACTGAAGCAAAGACCGCCATGGATC
30105 AA
1 AA
30107 CTTGAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (31 bp):
AAATAAACTGAAGCAAAGACCGCCATGGATC
Done.