Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012428.1 Corchorus olitorius cultivar O-4 contig12461, 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: 40368
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:232 original size:45 final size:45
Alignment explanation
Indices: 168--258 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
158 GCACATAATT
*
168 AACCTCACTCCAAGTAGCAATTCTAGCTAAATTATGAGCCAAAAA
1 AACCTCACTCCAAGTAGCAATTCTAACTAAATTATGAGCCAAAAA
213 AACCTCACTCCAAGTAGCAATTCTAACTAAATTATGAGCCAAAAA
1 AACCTCACTCCAAGTAGCAATTCTAACTAAATTATGAGCCAAAAA
258 A
1 A
259 TTAGCTTCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (45 bp):
AACCTCACTCCAAGTAGCAATTCTAACTAAATTATGAGCCAAAAA
Found at i:541 original size:6 final size:6
Alignment explanation
Indices: 530--580 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
520 ATTTAGCCTT
* * *
530 TTCAGC TTCAGC TTCAGC TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC
1 TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC
578 TTC
1 TTC
581 GAGCAAGCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.35
Consensus pattern (6 bp):
TTCAAC
Found at i:2871 original size:2 final size:2
Alignment explanation
Indices: 2864--2889 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2854 AGAAAAAGTT
2864 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2890 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2894 original size:2 final size:2
Alignment explanation
Indices: 2889--2924 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2879 GTGTGTGTGT
2889 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2925 CCTGAACTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7687 original size:15 final size:15
Alignment explanation
Indices: 7667--7698 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7657 CTATTTCCAC
7667 TTTTATATATGGTTA
1 TTTTATATATGGTTA
7682 TTTTATATATGGTTA
1 TTTTATATATGGTTA
7697 TT
1 TT
7699 ATACAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTTATATATGGTTA
Found at i:8117 original size:32 final size:33
Alignment explanation
Indices: 8066--8128 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
8056 GATATCAACT
*
8066 ACTTTTTTTATTTGATTTATTATTTTTTTCTCAA
1 ACTTTTTTTATTT-ATTTATTATTTTCTTCTCAA
*
8100 ACTTTTTTTATTT-TTTATTCTTTTCTTCT
1 ACTTTTTTTATTTATTTATTATTTTCTTCT
8129 TCGTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 14 0.52
34 13 0.48
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (33 bp):
ACTTTTTTTATTTATTTATTATTTTCTTCTCAA
Found at i:8887 original size:32 final size:33
Alignment explanation
Indices: 8840--8903 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
8830 TCAGAAAACG
8840 GAGAAGAAAAGAATAAA-AAATAAAAAAAGTTT
1 GAGAAGAAAAGAATAAACAAATAAAAAAAGTTT
*
8872 GAGAA-AAAAGTAATAAATCAAGTAAAAAAAGT
1 GAGAAGAAAAG-AATAAA-CAAATAAAAAAAGT
8904 AGTTGATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
34 12 0.43
ACGTcount: A:0.67, C:0.02, G:0.16, T:0.16
Consensus pattern (33 bp):
GAGAAGAAAAGAATAAACAAATAAAAAAAGTTT
Found at i:12391 original size:18 final size:18
Alignment explanation
Indices: 12365--12399 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12355 AGGCCGCCCT
12365 GCTTGTTATAATTATTTA
1 GCTTGTTATAATTATTTA
* *
12383 GCTTTTTATTATTATTT
1 GCTTGTTATAATTATTT
12400 CTACTTTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.63
Consensus pattern (18 bp):
GCTTGTTATAATTATTTA
Found at i:15776 original size:49 final size:47
Alignment explanation
Indices: 15682--15823 Score: 180
Period size: 49 Copynumber: 3.0 Consensus size: 47
15672 GAGCGTGCCA
* * *
15682 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
15729 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* *
15778 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA
15824 TGATTGCTTG
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
47 20 0.24
48 22 0.26
49 42 0.49
50 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:18611 original size:13 final size:13
Alignment explanation
Indices: 18593--18635 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
18583 TTTCACATTG
18593 CATTTGAATAAGT
1 CATTTGAATAAGT
* *
18606 CATTTGGAT-TG-
1 CATTTGAATAAGT
18617 CATTTGAATAAGT
1 CATTTGAATAAGT
18630 CATTTG
1 CATTTG
18636 TAGAAAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 14 0.58
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (13 bp):
CATTTGAATAAGT
Found at i:18616 original size:24 final size:24
Alignment explanation
Indices: 18589--18635 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
18579 AGAATTTCAC
18589 ATTGCATTTGAATAAGTCATTTGG
1 ATTGCATTTGAATAAGTCATTTGG
18613 ATTGCATTTGAATAAGTCATTTG
1 ATTGCATTTGAATAAGTCATTTG
18636 TAGAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (24 bp):
ATTGCATTTGAATAAGTCATTTGG
Found at i:20164 original size:36 final size:35
Alignment explanation
Indices: 20065--20313 Score: 164
Period size: 36 Copynumber: 7.1 Consensus size: 35
20055 CAGGGTCTTA
*
20065 TCATATCAAACCTGCTTAGGTCTATGTTTAGAATT
1 TCATAGCAAACCTGCTTAGGTCTATGTTTAGAATT
* *
20100 TC--AGTAAACCTGCTTAGGTCCT-TATTTAGAATT
1 TCATAGCAAACCTGCTTAGGT-CTATGTTTAGAATT
* *
20133 ATCATAGCAAACTTGTTTAGGTCTATGTTTAGAATT
1 -TCATAGCAAACCTGCTTAGGTCTATGTTTAGAATT
* * * * *
20169 TCATTTAATCAAGCCTGCTTAGGATCTTTGCTTAGAGTT
1 TCA--T-AGCAAACCTGCTTAGG-TCTATGTTTAGAATT
* * *
20208 TCGATCAAGTAAACCTGCTTAGGCCCCCAT-TTT-G-A--
1 TC-AT--AGCAAACCTGCTTAGG--TCTATGTTTAGAATT
*
20243 --ATA--AAACCTGCTTAGGTCCT-TATTTAGAATT
1 TCATAGCAAACCTGCTTAGGT-CTATGTTTAGAATT
20274 ATCATAGCAAACCTGCTTAGGTCTATGTTTAGAATT
1 -TCATAGCAAACCTGCTTAGGTCTATGTTTAGAATT
20310 TCAT
1 TCAT
20314 TTAATCAAGC
Statistics
Matches: 164, Mismatches: 26, Indels: 48
0.69 0.11 0.20
Matches are distributed among these distances:
26 1 0.01
27 4 0.02
28 14 0.09
29 1 0.01
30 1 0.01
32 2 0.01
33 25 0.15
34 7 0.04
35 13 0.08
36 48 0.29
37 1 0.01
38 14 0.09
39 30 0.18
40 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (35 bp):
TCATAGCAAACCTGCTTAGGTCTATGTTTAGAATT
Found at i:20267 original size:28 final size:28
Alignment explanation
Indices: 20218--20272 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
20208 TCGATCAAGT
*
20218 AAACCTGCTTAGGCCCCCATTTTGAATA
1 AAACCTGCTTAGGCCCCCATTTAGAATA
* **
20246 AAACCTGCTTAGGTCCTTATTTAGAAT
1 AAACCTGCTTAGGCCCCCATTTAGAAT
20273 TATCATAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (28 bp):
AAACCTGCTTAGGCCCCCATTTAGAATA
Found at i:20270 original size:141 final size:141
Alignment explanation
Indices: 20105--20386 Score: 537
Period size: 141 Copynumber: 2.0 Consensus size: 141
20095 GAATTTCAGT
* *
20105 AAACCTGCTTAGGTCCTTATTTAGAATTATCATAGCAAACTTGTTTAGGTCTATGTTTAGAATTT
1 AAACCTGCTTAGGTCCTTATTTAGAATTATCATAGCAAACCTGCTTAGGTCTATGTTTAGAATTT
*
20170 CATTTAATCAAGCCTGCTTAGGATCTTTGCTTAGAGTTTCGATCAAGTAAACCTGCTTAGGCCCC
66 CATTTAATCAAGCCTGCTTAGGATCTCTGCTTAGAGTTTCGATCAAGTAAACCTGCTTAGGCCCC
20235 CATTTTGAATA
131 CATTTTGAATA
20246 AAACCTGCTTAGGTCCTTATTTAGAATTATCATAGCAAACCTGCTTAGGTCTATGTTTAGAATTT
1 AAACCTGCTTAGGTCCTTATTTAGAATTATCATAGCAAACCTGCTTAGGTCTATGTTTAGAATTT
20311 CATTTAATCAAGCCTGCTTAGGATCTCTGCTTAGAGTTTCGATCAAGTAAACCTGCTTAGGCCCC
66 CATTTAATCAAGCCTGCTTAGGATCTCTGCTTAGAGTTTCGATCAAGTAAACCTGCTTAGGCCCC
20376 CATTTTGAATA
131 CATTTTGAATA
20387 GAGACTACTT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (141 bp):
AAACCTGCTTAGGTCCTTATTTAGAATTATCATAGCAAACCTGCTTAGGTCTATGTTTAGAATTT
CATTTAATCAAGCCTGCTTAGGATCTCTGCTTAGAGTTTCGATCAAGTAAACCTGCTTAGGCCCC
CATTTTGAATA
Found at i:23371 original size:17 final size:17
Alignment explanation
Indices: 23349--23391 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
23339 ACCAAAAGAA
23349 ACAGATCCCAAACACAT
1 ACAGATCCCAAACACAT
*
23366 ACAGATCCCATACACAT
1 ACAGATCCCAAACACAT
*
23383 ATAGATCCC
1 ACAGATCCC
23392 TAGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.35, G:0.07, T:0.16
Consensus pattern (17 bp):
ACAGATCCCAAACACAT
Found at i:28933 original size:18 final size:18
Alignment explanation
Indices: 28912--28962 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
28902 ATGAAGGTTA
*
28912 AAATGAAATATGTCAAAT
1 AAATCAAATATGTCAAAT
*
28930 AAATCAGAT-TAGTCAAAT
1 AAATCAAATAT-GTCAAAT
28948 AAATCAAATATGTCA
1 AAATCAAATATGTCA
28963 GAGAGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (18 bp):
AAATCAAATATGTCAAAT
Found at i:39080 original size:27 final size:27
Alignment explanation
Indices: 39050--39122 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
39040 TAGGTCACCT
* *
39050 AGGGGCATTTTGGTCATTTTTACACTG
1 AGGGGCATTTTGGTCATTTTCACACTC
* * *
39077 A-GGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTTCACACTC
*
39103 AGGGGCATGTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
39123 GAGTCCACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACACTC
Done.