Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023526.1 Corchorus olitorius cultivar O-4 contig23559, 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: 26646
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6883 original size:45 final size:42
Alignment explanation
Indices: 6819--6912 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
6809 AGCAACAATT
* * *
6819 AATATTAGCTTTATTTTGATGAATTATCTAGAGATAGAGGAGTAG
1 AATATTAGCTTTATTTTGATAAATAACCTAGAGAT---GGAGTAG
6864 AATATTAGCTTTATTTTGATAAATAACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATAAATAACCTAGAGATGGAGTAG
6906 AAT-TTAG
1 AATATTAG
6913 GTAATGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
45 32 0.70
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATAAATAACCTAGAGATGGAGTAG
Found at i:7828 original size:13 final size:14
Alignment explanation
Indices: 7810--7838 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7800 TATTATTATT
7810 ATAATAAT-AAATA
1 ATAATAATAAAATA
7823 ATAATAATAAAATA
1 ATAATAATAAAATA
7837 AT
1 AT
7839 TGAAGTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAATAATAAAATA
Found at i:8430 original size:13 final size:13
Alignment explanation
Indices: 8414--8485 Score: 65
Period size: 13 Copynumber: 5.3 Consensus size: 13
8404 GTAATTATTA
8414 TTGTATGTAATTT
1 TTGTATGTAATTT
* *
8427 TTGTAAGTAAATT
1 TTGTATGTAATTT
8440 TT-TATGTTAATTATT
1 TTGTATG-TAA-T-TT
8455 ATTGTATGTAATTT
1 -TTGTATGTAATTT
* *
8469 TTGTAAGTAATAT
1 TTGTATGTAATTT
8482 TTGT
1 TTGT
8486 TGTCCTCAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
12 3 0.06
13 31 0.65
14 2 0.04
15 3 0.06
16 5 0.10
17 4 0.08
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
TTGTATGTAATTT
Found at i:9428 original size:90 final size:90
Alignment explanation
Indices: 9327--9509 Score: 330
Period size: 90 Copynumber: 2.0 Consensus size: 90
9317 CTCTGATTCA
* * *
9327 AAATAAGTGTCACACTAAGAATATTACATATATTAAGACAATGATTAACTCATTTAATTAAATTT
1 AAATAAGTGTCACACTAAGAATATCACACATATTAAGACAATGATTAACTCATCTAATTAAATTT
9392 AGTAAAAAAATATTTGAAATAACCT
66 AGTAAAAAAATATTTGAAATAACCT
9417 AAATAAGTGTCACACTAAGAATATCACACATATTAAGACAATGATTAACTCATCTAATTAAATTT
1 AAATAAGTGTCACACTAAGAATATCACACATATTAAGACAATGATTAACTCATCTAATTAAATTT
*
9482 AGTAAAAAAATATTTGAAATGACCT
66 AGTAAAAAAATATTTGAAATAACCT
9507 AAA
1 AAA
9510 CACCCAAACC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.31
Consensus pattern (90 bp):
AAATAAGTGTCACACTAAGAATATCACACATATTAAGACAATGATTAACTCATCTAATTAAATTT
AGTAAAAAAATATTTGAAATAACCT
Found at i:10805 original size:15 final size:13
Alignment explanation
Indices: 10785--10884 Score: 74
Period size: 15 Copynumber: 6.8 Consensus size: 13
10775 AACACTTTCA
10785 GTGCCATCATCTTCG
1 GTGCCATCAT-TT-G
10800 GTGCCATCAGTTTTG
1 GTGCCATCA--TTTG
10815 GTGCCATCATTTTCG
1 GTGCCATCA-TTT-G
* *
10830 GTGACGTCGATGTTG
1 GTGCCATC-AT-TTG
10845 GTGCCATCAGTTTTG
1 GTGCCATCA--TTTG
10860 GTGCCATCGATGTTG
1 GTGCCATC-AT-TTG
10875 GTGCCATCAT
1 GTGCCATCAT
10885 CTTTTTCCAT
Statistics
Matches: 72, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.11
15 56 0.78
16 7 0.10
17 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (13 bp):
GTGCCATCATTTG
Found at i:10821 original size:30 final size:30
Alignment explanation
Indices: 10785--10887 Score: 129
Period size: 30 Copynumber: 3.4 Consensus size: 30
10775 AACACTTTCA
*
10785 GTGCCATCATCTTCGGTGCCATC-AGTTTTG
1 GTGCCATCATCTTCGGTGCCATCGA-TGTTG
* * *
10815 GTGCCATCATTTTCGGTGACGTCGATGTTG
1 GTGCCATCATCTTCGGTGCCATCGATGTTG
*
10845 GTGCCATCAGT-TTTGGTGCCATCGATGTTG
1 GTGCCATCA-TCTTCGGTGCCATCGATGTTG
10875 GTGCCATCATCTT
1 GTGCCATCATCTT
10888 TTTCCATGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 1 0.02
30 60 0.95
31 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (30 bp):
GTGCCATCATCTTCGGTGCCATCGATGTTG
Found at i:12139 original size:18 final size:18
Alignment explanation
Indices: 12116--12217 Score: 141
Period size: 18 Copynumber: 5.7 Consensus size: 18
12106 GTGTGGTAAT
*
12116 TTGGTGCGGAGCGAACAC
1 TTGGTGCGGTGCGAACAC
* * *
12134 TTGGTGCGTTGCGACCAT
1 TTGGTGCGGTGCGAACAC
12152 TTGGTGCGGTGCGAACAC
1 TTGGTGCGGTGCGAACAC
* *
12170 TTGGTGCGGTGCGACCAT
1 TTGGTGCGGTGCGAACAC
*
12188 TTGGTGCGGTGCGAATAC
1 TTGGTGCGGTGCGAACAC
12206 TTGGTGCGGTGC
1 TTGGTGCGGTGC
12218 AATTTGTTGT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.14, C:0.21, G:0.39, T:0.26
Consensus pattern (18 bp):
TTGGTGCGGTGCGAACAC
Found at i:12166 original size:36 final size:36
Alignment explanation
Indices: 12114--12217 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
12104 AAGTGTGGTA
* *
12114 ATTTGGTGCGGAGCGAACACTTGGTGCGTTGCGACC
1 ATTTGGTGCGGTGCGAACACTTGGTGCGGTGCGACC
12150 ATTTGGTGCGGTGCGAACACTTGGTGCGGTGCGACC
1 ATTTGGTGCGGTGCGAACACTTGGTGCGGTGCGACC
*
12186 ATTTGGTGCGGTGCGAATACTTGGTGCGGTGC
1 ATTTGGTGCGGTGCGAACACTTGGTGCGGTGC
12218 AATTTGTTGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.14, C:0.20, G:0.38, T:0.27
Consensus pattern (36 bp):
ATTTGGTGCGGTGCGAACACTTGGTGCGGTGCGACC
Found at i:12836 original size:49 final size:47
Alignment explanation
Indices: 12767--12895 Score: 152
Period size: 49 Copynumber: 2.7 Consensus size: 47
12757 AATTTTGTCA
* * *
12767 AAAAATTGATAAAAAGTGCAATGAAATTTAAAAGATCAATTTTG-ACTT
1 AAAAATTGAGAAAAAGTGCAATGAAA-ATAAAAGATCAATTTTGTA-GT
* *
12815 AAAAATTGAGATAAAGATGCAAGTGAAAATAAAAGTTCAATTTTGTAGT
1 AAAAATTGAGAAAAAG-TGCAA-TGAAAATAAAAGATCAATTTTGTAGT
*
12864 AAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 AAAAATTGAGAAAAAGTGCAATGAAAA-TAAA
12896 GGGTTGCTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
47 6 0.09
48 22 0.31
49 36 0.51
50 6 0.09
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (47 bp):
AAAAATTGAGAAAAAGTGCAATGAAAATAAAAGATCAATTTTGTAGT
Found at i:14189 original size:9 final size:9
Alignment explanation
Indices: 14169--14206 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
14159 TTAATTCATT
14169 TAATTTCC-
1 TAATTTCCA
*
14177 TAATCTCCA
1 TAATTTCCA
*
14186 TAATTTCCC
1 TAATTTCCA
14195 TAATTTCCA
1 TAATTTCCA
14204 TAA
1 TAA
14207 GTAATTTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATTTCCA
Found at i:14198 original size:18 final size:17
Alignment explanation
Indices: 14169--14206 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
14159 TTAATTCATT
14169 TAATTTCCTAATCTCCA
1 TAATTTCCTAATCTCCA
*
14186 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATCTCCA
14204 TAA
1 TAA
14207 GTAATTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTTCCTAATCTCCA
Found at i:15055 original size:72 final size:70
Alignment explanation
Indices: 14955--15100 Score: 265
Period size: 72 Copynumber: 2.1 Consensus size: 70
14945 ATTTCTAGAG
*
14955 AAAAAAAAATTGGGAAAAAATAATTGGGTGCACAGATGGTGCAGGGTGTGGTTAAGTGTGAACAA
1 AAAAAAAAATTGGGAAAAAACAATTGGGTGCACAGATGGTGCAGGGTGTGGTTAAGTGTGAACAA
15020 GCCCGA
66 GCCC-A
15026 AAAAAAATAATTGGGAAAAAACAATTGGGTGCACAGATGGTGCAGGGTGTGGTTAAGTGTGAACA
1 AAAAAAA-AATTGGGAAAAAACAATTGGGTGCACAGATGGTGCAGGGTGTGGTTAAGTGTGAACA
15091 AGCCCA
65 AGCCCA
15097 AAAA
1 AAAA
15101 GAACGGGCCA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 12 0.16
72 61 0.84
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.19
Consensus pattern (70 bp):
AAAAAAAAATTGGGAAAAAACAATTGGGTGCACAGATGGTGCAGGGTGTGGTTAAGTGTGAACAA
GCCCA
Found at i:16001 original size:31 final size:29
Alignment explanation
Indices: 15937--16001 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
15927 TATGGGATTT
*
15937 ATTTGTCCCAAAAAAAAGTTAAGGGGCCG
1 ATTTGTCCCAAAAAAAAGTTAAGGGGCCA
* * *
15966 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAA--AAAAGTTAAGGGGCCA
15997 ATTTG
1 ATTTG
16002 GGTATCAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (29 bp):
ATTTGTCCCAAAAAAAAGTTAAGGGGCCA
Found at i:20825 original size:54 final size:54
Alignment explanation
Indices: 20743--20853 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
20733 CTTGATGATT
20743 TTTCGGATAAGATGCTTTTTGAATTAAATTAAACTTCAGAAAACTGTAAAACGG
1 TTTCGGATAAGATGCTTTTTGAATTAAATTAAACTTCAGAAAACTGTAAAACGG
20797 TTTCGGATAAGATGCTTTTTGAATTAAATTAAACTTCAGAAAACTGTAAAACGG
1 TTTCGGATAAGATGCTTTTTGAATTAAATTAAACTTCAGAAAACTGTAAAACGG
20851 TTT
1 TTT
20854 ATAGTTTTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (54 bp):
TTTCGGATAAGATGCTTTTTGAATTAAATTAAACTTCAGAAAACTGTAAAACGG
Found at i:21203 original size:41 final size:40
Alignment explanation
Indices: 21144--21231 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 40
21134 AGGTGGCAAA
*
21144 ATGAATCCTACCCGAGAAAAACCCGCATGAAAAATCTGAAC
1 ATGAA-CCTACCCCAGAAAAACCCGCATGAAAAATCTGAAC
*
21185 ATGAACCTGACCCCAGAAAAACCCGCCTGAAAAATCTGAAC
1 ATGAACCT-ACCCCAGAAAAACCCGCATGAAAAATCTGAAC
*
21226 ACGAAC
1 ATGAAC
21232 TTGATCACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 3 0.07
41 40 0.93
ACGTcount: A:0.43, C:0.30, G:0.15, T:0.12
Consensus pattern (40 bp):
ATGAACCTACCCCAGAAAAACCCGCATGAAAAATCTGAAC
Found at i:25207 original size:20 final size:20
Alignment explanation
Indices: 25181--25237 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
25171 TATTATAAGT
25181 ATTTTTAGTAACCTTATTAA
1 ATTTTTAGTAACCTTATTAA
* *
25201 GTTTTTAGTAA-CTTTTTAA
1 ATTTTTAGTAACCTTATTAA
*
25220 ATATTTTAGTATCCTTAT
1 AT-TTTTAGTAACCTTAT
25238 ATATTTTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 8 0.27
20 18 0.60
21 4 0.13
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTTTTAGTAACCTTATTAA
Done.