Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014204.1 Corchorus olitorius cultivar O-4 contig14237, 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: 52299
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:13128 original size:19 final size:18
Alignment explanation
Indices: 13095--13130 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13085 TTGAAATAAT
13095 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
13113 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
13131 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:14023 original size:4 final size:4
Alignment explanation
Indices: 14014--14122 Score: 84
Period size: 4 Copynumber: 27.5 Consensus size: 4
14004 AAAGGATAAT
* * *
14014 AATA AATA AATA GAT- AATA GATA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * *
14060 AGTA AATA AATA AATA TAGTTA AATT AATA AATA AA-A ATATA AAT- AGTA
1 AATA AATA AATA AATA -A-ATA AATA AATA AATA AATA A-ATA AATA AATA
14109 AATA AATA AATA AA
1 AATA AATA AATA AA
14123 AATCTTTTTG
Statistics
Matches: 82, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
3 10 0.12
4 64 0.78
5 6 0.07
6 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:14046 original size:27 final size:27
Alignment explanation
Indices: 14013--14124 Score: 100
Period size: 27 Copynumber: 4.5 Consensus size: 27
14003 AAAAGGATAA
*
14013 TAATAAATAAATAGAT-AATAGATAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
14040 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
14064 -AATAAAT--AAATAT-AGT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
14085 TAATAAATAAAAATATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
14112 AAATAAATAAAAA
1 TAATAAATAAAAA
14125 TCTTTTTGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.01
20 3 0.04
21 5 0.07
22 7 0.10
23 7 0.10
24 6 0.09
25 3 0.04
27 33 0.47
28 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:14086 original size:45 final size:45
Alignment explanation
Indices: 14002--14120 Score: 177
Period size: 45 Copynumber: 2.6 Consensus size: 45
13992 TAGGTAGGTA
* *
14002 AAAAAGGAT-AATAATAAATAAATAGATAATAGATAAATTAATAAAT
1 AAAAA-GATAAATAGTAAATAAATAAAT-ATAGATAAATTAATAAAT
*
14048 AAAAAGATAAATAGTAAATAAATAAATATAGTTAAATTAATAAAT
1 AAAAAGATAAATAGTAAATAAATAAATATAGATAAATTAATAAAT
*
14093 AAAAATATAAATAGTAAATAAATAAATA
1 AAAAAGATAAATAGTAAATAAATAAATA
14121 AAAATCTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
45 47 0.69
46 21 0.31
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (45 bp):
AAAAAGATAAATAGTAAATAAATAAATATAGATAAATTAATAAAT
Found at i:14112 original size:19 final size:19
Alignment explanation
Indices: 14043--14114 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 19
14033 GATAAATTAA
*
14043 TAAATAAAAAGATAAATAG
1 TAAATAAAAATATAAATAG
*
14062 TAAATAAATAAATATAGTTAAATTAA
1 TAAAT--A-AAA-ATA--TAAA-TAG
14088 TAAATAAAAATATAAATAG
1 TAAATAAAAATATAAATAG
14107 TAAATAAA
1 TAAATAAA
14115 TAAATAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
19 15 0.35
20 4 0.09
21 1 0.02
22 6 0.14
23 5 0.12
24 1 0.02
25 4 0.09
26 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (19 bp):
TAAATAAAAATATAAATAG
Found at i:14116 original size:23 final size:23
Alignment explanation
Indices: 14041--14118 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
14031 TAGATAAATT
*
14041 AATAAATAAAAAGATAAATAGTA
1 AATAAATAAAAATATAAATAGTA
*
14064 AATAAATAAATATAGTTAAAT--T-
1 AATAAATAAAAATA--TAAATAGTA
14086 AATAAATAAAAATATAAATAGTA
1 AATAAATAAAAATATAAATAGTA
14109 AATAAATAAA
1 AATAAATAAA
14119 TAAAAATCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 5 0.11
22 14 0.30
23 23 0.49
25 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (23 bp):
AATAAATAAAAATATAAATAGTA
Found at i:15699 original size:54 final size:54
Alignment explanation
Indices: 15564--15916 Score: 398
Period size: 54 Copynumber: 6.5 Consensus size: 54
15554 TTAAAACTTG
* * ** *
15564 AACTTCTT-AAATAACCACACTGGATCAT-TTAAGATGCAAC-CTTGATCAT-GGA
1 AACTTCTTCGAATGACCACACTGGATCATCTGGAGAT-CAACTC-TGATCATCGAA
* * *
15616 AACTTTTCTTGGAGTGACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATCGAA
1 AAC--TTCTTCGAATGACCACACTGGATC--ATCTGGAGATCAACTCTGATCATCGAA
* *
15673 AACTTCTT-GAATGACCACACTGGATCATCTGAAGATCAACTCTGATCATCAAA
1 AACTTCTTCGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAA
* *
15726 AACTTCTTCGAATGACCACACTGGATCATCTAGAGATCAACTCTGATCTTCGAA
1 AACTTCTTCGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAA
* * *
15780 AACTTCTT-GAAACGACCGCACTGGATCATCTGGAGATCAACTCTGATCATCAAA
1 AACTTCTTCG-AATGACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAA
* *
15834 AACTTCTTCGAATGACCGCACTGGATCATCT-GAGGATCAACTCTGATCATTGAA
1 AACTTCTTCGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATCATCGAA
* **
15888 AACTTCTTGGAATGACTGCACTGGATCAT
1 AACTTCTTCGAATGACCACACTGGATCAT
15917 TTGAACACCT
Statistics
Matches: 264, Mismatches: 25, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
52 5 0.02
53 33 0.12
54 182 0.69
55 20 0.08
56 11 0.04
57 13 0.05
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (54 bp):
AACTTCTTCGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCATCGAA
Found at i:20325 original size:4 final size:4
Alignment explanation
Indices: 20318--20343 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
20308 TACCAAAGGA
20318 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
20344 GTGAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:28190 original size:24 final size:24
Alignment explanation
Indices: 28162--28218 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
28152 AAAAAAAAAT
*
28162 AAATAGGTATAGAG-ATAAATAGAA
1 AAATAGGTACAGAGAAT-AATAGAA
* *
28186 AAATAGATACAGAGAATAATAGAT
1 AAATAGGTACAGAGAATAATAGAA
28210 AAATAGGTA
1 AAATAGGTA
28219 GGTAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.21
Consensus pattern (24 bp):
AAATAGGTACAGAGAATAATAGAA
Found at i:28193 original size:16 final size:16
Alignment explanation
Indices: 28174--28215 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28164 ATAGGTATAG
28174 AGATAAATAGAAAAAT
1 AGATAAATAGAAAAAT
* * *
28190 AGATACAGAGAATAAT
1 AGATAAATAGAAAAAT
28206 AGATAAATAG
1 AGATAAATAG
28216 GTAGGTAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.19
Consensus pattern (16 bp):
AGATAAATAGAAAAAT
Found at i:28278 original size:27 final size:27
Alignment explanation
Indices: 28236--28348 Score: 111
Period size: 27 Copynumber: 4.5 Consensus size: 27
28226 AAAAGGATAA
*
28236 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
28263 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
28287 -AATAAAT---AA-AT-AATAGTTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
*
28309 TAATAAATAAAAATATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
28336 AAATAAATAAAAA
1 TAATAAATAAAAA
28349 TCATTTTGGT
Statistics
Matches: 73, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
18 5 0.07
19 3 0.04
20 2 0.03
21 1 0.01
23 14 0.19
25 1 0.01
26 2 0.03
27 35 0.48
28 10 0.14
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:28292 original size:46 final size:46
Alignment explanation
Indices: 28221--28345 Score: 191
Period size: 46 Copynumber: 2.7 Consensus size: 46
28211 AATAGGTAGG
* *
28221 TAAA-AAAAAGGAT-AATAATAAATAAATAGATAATAGCTAAATTAA
1 TAAATAAAAA-GATAAATAGTAAATAAATAAATAATAGCTAAATTAA
*
28266 TAAATAAAAAGATAAATAGTAAATAAATAAATAATAGTTAAATTAA
1 TAAATAAAAAGATAAATAGTAAATAAATAAATAATAGCTAAATTAA
*
28312 TAAATAAAAATATAAATAGTAAATAAATAAATAA
1 TAAATAAAAAGATAAATAGTAAATAAATAAATAA
28346 AAATCATTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
45 7 0.09
46 67 0.91
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.26
Consensus pattern (46 bp):
TAAATAAAAAGATAAATAGTAAATAAATAAATAATAGCTAAATTAA
Found at i:28346 original size:19 final size:19
Alignment explanation
Indices: 28234--28346 Score: 69
Period size: 19 Copynumber: 6.1 Consensus size: 19
28224 AAAAAAGGAT
* *
28234 AATAATAAATAAATAGAT-
1 AATAGTAAATAAATAAATA
*
28252 AATAGCTAAATTAATAAATA
1 AATAG-TAAATAAATAAATA
* *
28272 AAAAGATAAAT-AGTAAAT-
1 AATAG-TAAATAAATAAATA
**
28290 AA-A-TAAAT-AATAGTTA
1 AATAGTAAATAAATAAATA
*
28306 AATTAATAAATAAA-AATATA
1 AA-TAGTAAATAAATAA-ATA
28326 AATAGTAAATAAATAAATA
1 AATAGTAAATAAATAAATA
28345 AA
1 AA
28347 AATCATTTTG
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
15 9 0.12
16 2 0.03
17 1 0.01
18 7 0.09
19 38 0.51
20 17 0.23
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (19 bp):
AATAGTAAATAAATAAATA
Found at i:39521 original size:3 final size:3
Alignment explanation
Indices: 39509--39538 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
39499 AGGGACGGGG
39509 GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
39539 GAAGCGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43559 original size:18 final size:18
Alignment explanation
Indices: 43536--43602 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
43526 TACAAAATAT
*
43536 TGTTCCACTGCCACAGGA
1 TGTTCCACTGCCGCAGGA
* * *
43554 TGTTCCACTACTGCAGAA
1 TGTTCCACTGCCGCAGGA
* *
43572 TGTTGCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
43590 TGTTCCACTGCCG
1 TGTTCCACTGCCG
43603 TAAGAACCTT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:45932 original size:97 final size:97
Alignment explanation
Indices: 45766--45961 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 97
45756 AGGCTCTTTT
*
45766 CCTTCTTTTGTACTCGGTGAGGGGTGAGTGTACTCTTTTTCCTTCTTGAGGATTTTTCCCACTAG
1 CCTTCTTTTGTACTCGGTGAGGGGTGAGTGTACTCTTTTTCCTTCTTAAGGATTTTTCCCACTAG
45831 ATTTTTCCTCTTGAAGGTTTTAACGAGACACC
66 ATTTTTCCTCTTGAAGGTTTTAACGAGACACC
45863 CCTTCTTTTGTACTCGGTGAGGGGTGAGTGTACTCTTTTTCCTTCTTAAGGATTTTTCCCACTAG
1 CCTTCTTTTGTACTCGGTGAGGGGTGAGTGTACTCTTTTTCCTTCTTAAGGATTTTTCCCACTAG
45928 ATTTTTCCTCTTGAAGGTTTTAACGAGACACC
66 ATTTTTCCTCTTGAAGGTTTTAACGAGACACC
45960 CC
1 CC
45962 CATATACCCC
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (97 bp):
CCTTCTTTTGTACTCGGTGAGGGGTGAGTGTACTCTTTTTCCTTCTTAAGGATTTTTCCCACTAG
ATTTTTCCTCTTGAAGGTTTTAACGAGACACC
Found at i:47127 original size:51 final size:51
Alignment explanation
Indices: 47046--47147 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
47036 TCTTGGGCCT
*
47046 ACAATTGGTGGTCGTTCCTGCAGGCTTGGGAGTGGGAGAGACGAGACTAGC
1 ACAATTGGTGGTCGTTCCTGCAGGCGTGGGAGTGGGAGAGACGAGACTAGC
*
47097 ACAATTGGTGGTCGTTCCTGCAGGCGTGGGAGTGGGAGAGACGAGAGTAGC
1 ACAATTGGTGGTCGTTCCTGCAGGCGTGGGAGTGGGAGAGACGAGACTAGC
47148 GATACAGACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.21
Consensus pattern (51 bp):
ACAATTGGTGGTCGTTCCTGCAGGCGTGGGAGTGGGAGAGACGAGACTAGC
Done.