Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020071.1 Corchorus olitorius cultivar O-4 contig20104, 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: 20379
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:109 original size:23 final size:24
Alignment explanation
Indices: 64--110 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
54 GAAAAAGCTT
64 TTTAAAAAATCAAACAAAAATAAA
1 TTTAAAAAATCAAACAAAAATAAA
88 TTTAGAAAAAT-AAA-AAAAATAAA
1 TTTA-AAAAATCAAACAAAAATAAA
111 GGAACTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 7 0.32
25 6 0.27
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (24 bp):
TTTAAAAAATCAAACAAAAATAAA
Found at i:163 original size:9 final size:9
Alignment explanation
Indices: 149--181 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
139 AAGGATAAAC
149 AAAAAAAAG
1 AAAAAAAAG
158 AAAAAAAAG
1 AAAAAAAAG
167 AAAGAAAAAG
1 AAA-AAAAAG
177 AAAAA
1 AAAAA
182 TGTACAACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:164 original size:10 final size:10
Alignment explanation
Indices: 149--181 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
139 AAGGATAAAC
149 AAAAAAAAG-
1 AAAAAAAAGA
158 AAAAAAAAGA
1 AAAAAAAAGA
*
168 AAGAAAAAGA
1 AAAAAAAAGA
178 AAAA
1 AAAA
182 TGTACAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2787 original size:357 final size:356
Alignment explanation
Indices: 2108--2901 Score: 1365
Period size: 357 Copynumber: 2.2 Consensus size: 356
2098 GAAATTAATG
* ** * *
2108 GAAAGTGATTAATTATTGATTTACT-ATTGATTTAGTTAATTAATATATAAGTTAATTATAATTG
1 GAAAGTGAATAATTATTGATAGAATAATTGATTTAGTTAATTAATATGTAAGTTAATTATAATTG
*
2172 CTTTAATTTGACCAAGCTTCAAATAAGTTAATGGAAAGGTTTTTTTTTAAGTAATTTATATTTAG
66 CTTTAATTTGACCAAGCTTCAAATAAGTTAATGGAAAGGTTTTTTTTTAAGTAATTTATATGTAG
*
2237 GAAGTTAATTGAAGGAAATCATTATTAATGATTGTCTACCATGCTTACGATGTAAATTTACTTTT
131 GAAGTTAATTGAAAGAAATCATTATTAATGATTGTCTACCATGCTTACGATGTAAATTTACTTTT
* * *
2302 ATTAATTTAAATTCTATCTTTTAGGTGGGAAATAAATTTTGACCAAATTTATGTAGCATATTAAT
196 ATAAATTTAAATTCTATCTTTTAGGTGGAAAATAAATTTTGACCAAATTTATATAGCATATTAAT
2367 TGTTTGAAAGAATTAGTTAGTCACTATATATGTAAATTAATAAAAATTTATTACCGAAATTAAAG
261 TGTTTGAAAGAATTAGTTAGTCACTATATATGTAAATTAATAAAAATTTATTACCGAAATTAAAG
2432 TTTTAGAATTCAAATTTTACTACCATTTATA
326 TTTTAGAATTCAAATTTTACTACCATTTATA
2463 GAAAGTGAATAATTATTGATAGAATAATTGATTTAGTTAATTAATATGTAAGTTAATTATAATTG
1 GAAAGTGAATAATTATTGATAGAATAATTGATTTAGTTAATTAATATGTAAGTTAATTATAATTG
*
2528 CTTTAATTTGACCAAGCTTCAAATAAGTTGATGGAAAGGTTTTTTTTTAAAGTAATTTATATGTA
66 CTTTAATTTGACCAAGCTTCAAATAAGTTAATGGAAAGGTTTTTTTTT-AAGTAATTTATATGTA
* *
2593 TGAAGTTAATTGAAAGAAATCATTATTAATGATTGTTTACCATGCTTACGATGTAAATTTACTTT
130 GGAAGTTAATTGAAAGAAATCATTATTAATGATTGTCTACCATGCTTACGATGTAAATTTACTTT
*
2658 TATAAATTTAAATTCTATCTTTTAGGTGGAAAATTAATTTTGACCAAATTTATATAGCATATTAA
195 TATAAATTTAAATTCTATCTTTTAGGTGGAAAATAAATTTTGACCAAATTTATATAGCATATTAA
**
2723 TTGTTTGAAAGAATTAGTTAGTCACTATATATGTAAATTAATAATGATTTATTACCGAAATTAAA
260 TTGTTTGAAAGAATTAGTTAGTCACTATATATGTAAATTAATAAAAATTTATTACCGAAATTAAA
2788 GTTTTAGAATTCAAATTTTACTACCATTTATA
325 GTTTTAGAATTCAAATTTTACTACCATTTATA
* * * *
2820 GACAGTGAAATAATTATTGATAGAATAATTGATCTAGTTAATTAATATGAAAATTAATTATAATT
1 GAAAGTG-AATAATTATTGATAGAATAATTGATTTAGTTAATTAATATGTAAGTTAATTATAATT
*
2885 GCTCTAAATTTGACCAA
65 GCT-TTAATTTGACCAA
2902 TACAAAAAAG
Statistics
Matches: 414, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
355 21 0.05
356 85 0.21
357 239 0.58
358 57 0.14
359 12 0.03
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (356 bp):
GAAAGTGAATAATTATTGATAGAATAATTGATTTAGTTAATTAATATGTAAGTTAATTATAATTG
CTTTAATTTGACCAAGCTTCAAATAAGTTAATGGAAAGGTTTTTTTTTAAGTAATTTATATGTAG
GAAGTTAATTGAAAGAAATCATTATTAATGATTGTCTACCATGCTTACGATGTAAATTTACTTTT
ATAAATTTAAATTCTATCTTTTAGGTGGAAAATAAATTTTGACCAAATTTATATAGCATATTAAT
TGTTTGAAAGAATTAGTTAGTCACTATATATGTAAATTAATAAAAATTTATTACCGAAATTAAAG
TTTTAGAATTCAAATTTTACTACCATTTATA
Found at i:3657 original size:191 final size:191
Alignment explanation
Indices: 3333--3709 Score: 736
Period size: 191 Copynumber: 2.0 Consensus size: 191
3323 AAGAAAAGAC
3333 TTTGTAGAGATAGAAAAATTTGACCAATTAACTATTGGTTAAGTTGGTTAAATAAATATTTGGAT
1 TTTGTAGAGATAGAAAAATTTGACCAATTAACTATTGGTTAAGTTGGTTAAATAAATATTTGGAT
3398 TTAGTCCATAAGAAAATTCATTTGGATTAAATCCTAATTTGAGCCCAATTAAAAATGTAGTTAAG
66 TTAGTCCATAAGAAAATTCATTTGGATTAAATCCTAATTTGAGCCCAATTAAAAATGTAGTTAAG
3463 TTGGCCCACTAAAATTGGCCCAATACTACTTTACAAGGGTTACTAAATTAACCCTGACTTT
131 TTGGCCCACTAAAATTGGCCCAATACTACTTTACAAGGGTTACTAAATTAACCCTGACTTT
3524 TTTGTAGAGATAGAAAAATTTGACCAATTAACTATTGGTTAAGTTGGTTAAATAAATATTTGGAT
1 TTTGTAGAGATAGAAAAATTTGACCAATTAACTATTGGTTAAGTTGGTTAAATAAATATTTGGAT
*
3589 TTAGTCCATAAGAAAATTCATTTGGATTAAATCCTAATTTGAGCCCGATTAAAAATGTAGTTAAG
66 TTAGTCCATAAGAAAATTCATTTGGATTAAATCCTAATTTGAGCCCAATTAAAAATGTAGTTAAG
*
3654 TTGGCCCACTAAAATTGGCCCAATACTACTTTACAAGGGTTACTAAATTAATCCTG
131 TTGGCCCACTAAAATTGGCCCAATACTACTTTACAAGGGTTACTAAATTAACCCTG
3710 GCTTCCTCTA
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 184 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (191 bp):
TTTGTAGAGATAGAAAAATTTGACCAATTAACTATTGGTTAAGTTGGTTAAATAAATATTTGGAT
TTAGTCCATAAGAAAATTCATTTGGATTAAATCCTAATTTGAGCCCAATTAAAAATGTAGTTAAG
TTGGCCCACTAAAATTGGCCCAATACTACTTTACAAGGGTTACTAAATTAACCCTGACTTT
Found at i:4108 original size:42 final size:42
Alignment explanation
Indices: 4052--4144 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
4042 CTCAATCTAG
*
4052 CAAATCCGACAACGAGGAATAACAAGCCTTCGGCCATTCCTCT
1 CAAATCC-ACAACGAGAAATAACAAGCCTTCGGCCATTCCTCT
*
4095 CAAATCCACAACGAGAAATAACAAGCCTTTGGCCATTCCTCT
1 CAAATCCACAACGAGAAATAACAAGCCTTCGGCCATTCCTCT
*
4137 CATATCCA
1 CAAATCCA
4145 TTTCATCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 40 0.85
43 7 0.15
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.20
Consensus pattern (42 bp):
CAAATCCACAACGAGAAATAACAAGCCTTCGGCCATTCCTCT
Found at i:7027 original size:11 final size:11
Alignment explanation
Indices: 7011--7037 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7001 CTGCAAAAAA
7011 AAAAAAAATCC
1 AAAAAAAATCC
7022 AAAAAAAATCC
1 AAAAAAAATCC
7033 AAAAA
1 AAAAA
7038 GTCAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.15, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAATCC
Found at i:7055 original size:19 final size:18
Alignment explanation
Indices: 7004--7056 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
6994 GCCTAAACTG
7004 CAAAAAAAA-AAAAAATC
1 CAAAAAAAATAAAAAATC
*
7021 CAAAAAAAATCCAAAAAGT-
1 CAAAAAAAAT--AAAAAATC
*
7040 CAAAAAAAATGAAAAAT
1 CAAAAAAAATAAAAAAT
7057 GAAAAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.47
19 10 0.33
20 6 0.20
ACGTcount: A:0.75, C:0.11, G:0.04, T:0.09
Consensus pattern (18 bp):
CAAAAAAAATAAAAAATC
Found at i:7403 original size:47 final size:47
Alignment explanation
Indices: 7274--7439 Score: 203
Period size: 47 Copynumber: 3.6 Consensus size: 47
7264 ACTCAAGGAA
* * * * * *
7274 AGGTAGAGGGTGATCACA-AATGATACTCCGCCAAGAAGTTGATGTAG
1 AGGTAGAGGGTGATTAAATAATCA-ACCCCGCCAAGAAGTCGATGCAG
* *
7321 TGGTAGAGGGTGATT-AATAATCAACCCCGCCAAGAAGCCGATGCAG
1 AGGTAGAGGGTGATTAAATAATCAACCCCGCCAAGAAGTCGATGCAG
* * *
7367 AGGTAGAGGGCGATTAAAAAATCAACCCCGCCAAGAAGTCAATGCAG
1 AGGTAGAGGGTGATTAAATAATCAACCCCGCCAAGAAGTCGATGCAG
7414 AGGTAGAGGGTGA-TAAATAATCAACC
1 AGGTAGAGGGTGATTAAATAATCAACC
7440 TGGAGGTAGA
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
46 45 0.44
47 57 0.56
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (47 bp):
AGGTAGAGGGTGATTAAATAATCAACCCCGCCAAGAAGTCGATGCAG
Found at i:7447 original size:29 final size:30
Alignment explanation
Indices: 7413--7469 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
7403 AGTCAATGCA
*
7413 GAGGTAGAGGGTGAT-AAATAATCAACCTG
1 GAGGTAGAGGGCGATAAAATAATCAACCTG
7442 GAGGTAGAGGGCGATAAAATAATCAACC
1 GAGGTAGAGGGCGATAAAATAATCAACC
7470 CCGCCAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.18
Consensus pattern (30 bp):
GAGGTAGAGGGCGATAAAATAATCAACCTG
Found at i:7506 original size:76 final size:76
Alignment explanation
Indices: 7366--7515 Score: 221
Period size: 76 Copynumber: 2.0 Consensus size: 76
7356 AGCCGATGCA
** **
7366 GAGGTAGAGGGCGATTAAAAAATCAACCCCGCCAAGAAGTCAATGCAGAGGTAGAGGGTGATAAA
1 GAGGTAGAGGGCGATTAAAAAATCAACCCCGCCAAGAACCCAATGCAGAGGTAGAGGGCAATAAA
*
7431 TAATCAACCTG
66 AAATCAACCTG
*
7442 GAGGTAGAGGGCGA-TAAAATAATCAACCCCGCCAAGAACCCGATGCAGAGGTAGAGGGCAATAA
1 GAGGTAGAGGGCGATTAAAA-AATCAACCCCGCCAAGAACCCAATGCAGAGGTAGAGGGCAATAA
*
7506 AAAATTAACC
65 AAAATCAACC
7516 CCGCCAAGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 5 0.08
76 61 0.92
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (76 bp):
GAGGTAGAGGGCGATTAAAAAATCAACCCCGCCAAGAACCCAATGCAGAGGTAGAGGGCAATAAA
AAATCAACCTG
Found at i:7700 original size:56 final size:56
Alignment explanation
Indices: 7593--7753 Score: 249
Period size: 56 Copynumber: 2.9 Consensus size: 56
7583 TAGGGGGTCC
*
7593 ATTCCACAAAGCTGAAG---TA-GTAGAGGGTGATCAAAAAAATGAAACACCCCGCA
1 ATTCCACAAAGCTGAAGCAAAAGGTAGAGGGTGATC-AAAAAATGAAACACCCCGCA
* *
7646 ATTCCATAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCC
1 ATTCCACAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCA
*
7702 ATTTCACAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCC
1 ATTCCACAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCC
7754 GTCCATCAAG
Statistics
Matches: 99, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
53 16 0.16
56 70 0.71
57 13 0.13
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (56 bp):
ATTCCACAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCA
Found at i:7896 original size:152 final size:153
Alignment explanation
Indices: 7652--7956 Score: 549
Period size: 152 Copynumber: 2.0 Consensus size: 153
7642 CGCAATTCCA
*
7652 TAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCCATTTCACAAAGCTGA
1 TAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCCATTCCACAAAGCTGA
* *
7717 AGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCGTCCATCAA-GGGGAGAGGATGATCAAC
66 AGCAAAAGGTAGAAGGTGATAAAAAAATGAAACACCCGTCCATCAAGGGGGAGAGGATGATCAAC
7781 CTCGAAAAGTAGCACATTCCGCC
131 CTCGAAAAGTAGCACATTCCGCC
**
7804 TAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACATTCCGCCATTCCACAAAGCTGA
1 TAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCCATTCCACAAAGCTGA
7869 AGCAAAAGGTAGAAGGTGATAAAAAAATGAAACACCCGTCCATCAAGGGGGAGAGGATGATCAAC
66 AGCAAAAGGTAGAAGGTGATAAAAAAATGAAACACCCGTCCATCAAGGGGGAGAGGATGATCAAC
*
7934 CTCGAAAGGTAGCACATTCCGCC
131 CTCGAAAAGTAGCACATTCCGCC
7957 AAATTGTGAT
Statistics
Matches: 146, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
152 106 0.73
153 40 0.27
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (153 bp):
TAAAGCTGAAGCAAAAGGTAGAGGGTGATCAAAAAATGAAACACCCCGCCATTCCACAAAGCTGA
AGCAAAAGGTAGAAGGTGATAAAAAAATGAAACACCCGTCCATCAAGGGGGAGAGGATGATCAAC
CTCGAAAAGTAGCACATTCCGCC
Found at i:12068 original size:12 final size:13
Alignment explanation
Indices: 12038--12070 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12028 ATCAAAATAT
12038 TCAAATCAATCAA
1 TCAAATCAATCAA
12051 TC-AATCAATCAA
1 TCAAATCAATCAA
12063 -CAAATCAA
1 TCAAATCAA
12071 ATAGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 16 0.84
13 2 0.11
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (13 bp):
TCAAATCAATCAA
Found at i:12109 original size:4 final size:4
Alignment explanation
Indices: 12100--12145 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
12090 AAAATATTCA
* * * *
12100 AATC AATC AATC AATT AATC AATC AATC GATC GATC GATC AATC AA
1 AATC AATC AATC AATC AATC AATC AATC AATC AATC AATC AATC AA
12146 ATAGTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (4 bp):
AATC
Found at i:12121 original size:75 final size:76
Alignment explanation
Indices: 12041--12194 Score: 240
Period size: 75 Copynumber: 2.0 Consensus size: 76
12031 AAAATATTCA
*
12041 AATCAATCAATCAATCAATC-AACAAATCAAATAGTATTTTAATTTGATCAAAATATTCAAATCA
1 AATCAATCAATCAATCAATCGAAC-AATCAAATAGTATTTTAATTTGATCAAAAAATTCAAATCA
12105 ATCAATCAAT-T
65 ATCAATCAATCT
* * * *
12116 AATCAATCAATCGATCGATCGATCAATCAAATAGTATTTTAATTTGATCAAAAAATTTAAATCAA
1 AATCAATCAATCAATCAATCGAACAATCAAATAGTATTTTAATTTGATCAAAAAATTCAAATCAA
12181 TCAATCAATCT
66 TCAATCAATCT
12192 AAT
1 AAT
12195 ATCTATAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
75 66 0.92
76 6 0.08
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (76 bp):
AATCAATCAATCAATCAATCGAACAATCAAATAGTATTTTAATTTGATCAAAAAATTCAAATCAA
TCAATCAATCT
Done.