Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016206.1 Corchorus olitorius cultivar O-4 contig16239, 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: 25191
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:453 original size:58 final size:57
Alignment explanation
Indices: 357--470 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 57
347 ATAACATCAT
*
357 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
* * * *
414 GCCTTGGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
471 TTTGATTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 17 0.33
58 34 0.67
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (57 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Found at i:5696 original size:21 final size:22
Alignment explanation
Indices: 5622--5698 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
5612 TATTTTTATG
* *
5622 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAATTACCATATA
* *
5644 AAATTTTGATAACTACCATATG
1 AAATTTTGATAATTACCATATA
*
5666 AAATTTTGATAATTA-CGTATA
1 AAATTTTGATAATTACCATATA
*
5687 AAATTGTGATAA
1 AAATTTTGATAA
5699 ACTCCATAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 15 0.31
22 33 0.69
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAATTACCATATA
Found at i:5706 original size:43 final size:44
Alignment explanation
Indices: 5618--5720 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 44
5608 TGAATATTTT
* *
5618 TATGAAATTTTGATAATTACCCTATTAAATTTTGATAACTACCA
1 TATGAAATTTTGATAATTACCCTATAAAATTGTGATAACTACCA
*
5662 TATGAAATTTTGATAATTA-CGTATAAAATTGTGATAAACT-CCA
1 TATGAAATTTTGATAATTACCCTATAAAATTGTGAT-AACTACCA
* *
5705 TAAGAAACTTTGATAA
1 TATGAAATTTTGATAA
5721 CCTAATCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 30 0.57
44 23 0.43
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAATTACCCTATAAAATTGTGATAACTACCA
Found at i:5771 original size:20 final size:21
Alignment explanation
Indices: 5732--5788 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
5722 CTAATCATGA
* *
5732 AATTTTAATAAACTTTCCTATG
1 AATTTTGATAATC-TTCCTATG
5754 AATTTTG-TAATCTTCCTATG
1 AATTTTGATAATCTTCCTATG
*
5774 ATTTTTGATAATCTT
1 AATTTTGATAATCTT
5789 TGTGTGAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.45
21 11 0.35
22 6 0.19
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (21 bp):
AATTTTGATAATCTTCCTATG
Found at i:8451 original size:27 final size:27
Alignment explanation
Indices: 8411--8471 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
8401 CTAAATTTCC
8411 ATTATTTTAATAATGGAATAATTA-AAAT
1 ATTA-TTTAATAATGGAA-AATTAGAAAT
* *
8439 ATTATTTAGTAATGGAAATTTAGAAAT
1 ATTATTTAATAATGGAAAATTAGAAAT
8466 A-TATTT
1 ATTATTT
8472 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.30
27 17 0.57
28 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (27 bp):
ATTATTTAATAATGGAAAATTAGAAAT
Found at i:8550 original size:4 final size:4
Alignment explanation
Indices: 8543--8579 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
8533 TATAGATATA
8543 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
8580 GTGAAGCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:9853 original size:36 final size:33
Alignment explanation
Indices: 9770--9853 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 33
9760 CCGGAAAGAG
9770 AAAAAAAAAGGAAAAATGGGCTAGGCCCAACTTT
1 AAAAAAAAA-GAAAAATGGGCTAGGCCCAACTTT
*
9804 AAGGAAAAGAAGAAATAATGGGCTAAGGCCCGAA-TTT
1 AA--AAAAAAAGAAA-AATGGGCT-AGGCCC-AACTTT
9841 AAAAATAAAAGAA
1 AAAAA-AAAAGAA
9854 GAGGGAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
34 2 0.05
35 7 0.17
36 20 0.48
37 11 0.26
38 2 0.05
ACGTcount: A:0.54, C:0.11, G:0.21, T:0.14
Consensus pattern (33 bp):
AAAAAAAAAGAAAAATGGGCTAGGCCCAACTTT
Found at i:10938 original size:15 final size:13
Alignment explanation
Indices: 10902--10940 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
10892 TTTACTCTGG
*
10902 TTTATGACTTTGA
1 TTTATGATTTTGA
10915 TTTATGATTTTGA
1 TTTATGATTTTGA
10928 TTTTAATGATTTT
1 -TTT-ATGATTTT
10941 CTTGTGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.62
Consensus pattern (13 bp):
TTTATGATTTTGA
Found at i:13207 original size:351 final size:351
Alignment explanation
Indices: 12534--13236 Score: 919
Period size: 351 Copynumber: 2.0 Consensus size: 351
12524 TTTAAAACAG
* *
12534 TCTCCAAGTCGGTTTAGGAGAAGATCAATTCTGTCCAGAAATTTCAAGGGCAAAATCATACACCA
1 TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCATACACCA
* * *
12599 GAACTACAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAACG
66 GAACTACAGAATTAGGTCTCGAGGTAAACATAAAAATTGTAGATCTTGGAATCATCTTTCCAACA
* * * *
12664 GTAGCTTATTTGAATTTTTCTGAGCTCTAGACCAAAAGTTATGAATTTTCTTCCAAAACTGCTCT
131 GTACCTCATTTCAATTTTTCTGAGCTCTAGACCAAAAGTTATGAATTTTCTTCAAAAACTGCTCT
* ** * * * * *
12729 TGTGAAATCCTCTTTTGAATAGGATTTAACAATGCTGCATTAGTGGTGAATCATTACTACCTCAT
196 TGTGAAATCCTCCTCCGAATAGGATTTAACAATGCTGCATCAGAGGTGAATCATAAATACATCAT
* * * * * *
12794 AATTACTTATTGGACTTGGACTCCTTCTTTTGACCTCCATATTAACGAATTGGGTTTAAGAATAT
261 AATTACTGATTGGACTTGGACTCCTTCTTTAGACCTCCACATTAACAAATCGGGTCTAAGAATAT
* *
12859 CAGATTCATACTTCAAGACATCTGGC
326 CAGATTCAGACTACAAGACATCTGGC
* * **
12885 TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCGTCCACTG
1 TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCATACACCA
* **
12950 GAATTGTAGAATTAGGTCTCGAGGTAAACATAAAAATTGTAGATCTTGGAATCATCTTTCCAACA
66 GAACTACAGAATTAGGTCTCGAGGTAAACATAAAAATTGTAGATCTTGGAATCATCTTTCCAACA
* * *
13015 GTACCTCATTTTCAA-TTTTCTGA-CTTTCGGATCACAAA-TTATGAATTTTCTTCAAAAACTGC
131 GTACCTCA-TTTCAATTTTTCTGAGCTCT-AGACCA-AAAGTTATGAATTTTCTTCAAAAACTGC
* * *** * *
13077 TCTTTTGAAGTCCTCCTCCGAATATTTTTTAACAATGCTGCATCAGAGTTGAATCATAAATGCAT
193 TCTTGTGAAATCCTCCTCCGAATAGGATTTAACAATGCTGCATCAGAGGTGAATCATAAATACAT
* *
13142 CATAATTACTGATTGGACTTGGACTCCTTCTTTAGGCTTCCACAGTT-ACAAATCGGGTCTAAGA
258 CATAATTACTGATTGGACTTGGACTCCTTCTTTAGACCTCCACA-TTAACAAATCGGGTCTAAGA
* * *
13206 ATATTATATTTAGACTACAAGACATCTGGC
322 ATATCAGATTCAGACTACAAGACATCTGGC
13236 T
1 T
13237 TGGCAATTTG
Statistics
Matches: 301, Mismatches: 47, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
350 3 0.01
351 288 0.96
352 10 0.03
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (351 bp):
TCTCCAAGCCGGTTTAGGAGAAGATCAATTCTATCCAGAAATTTCAAGGGCAAAATCATACACCA
GAACTACAGAATTAGGTCTCGAGGTAAACATAAAAATTGTAGATCTTGGAATCATCTTTCCAACA
GTACCTCATTTCAATTTTTCTGAGCTCTAGACCAAAAGTTATGAATTTTCTTCAAAAACTGCTCT
TGTGAAATCCTCCTCCGAATAGGATTTAACAATGCTGCATCAGAGGTGAATCATAAATACATCAT
AATTACTGATTGGACTTGGACTCCTTCTTTAGACCTCCACATTAACAAATCGGGTCTAAGAATAT
CAGATTCAGACTACAAGACATCTGGC
Found at i:17256 original size:15 final size:15
Alignment explanation
Indices: 17217--17258 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
17207 AAAAGTACCT
*
17217 TATAACTAATTAAAG
1 TATAACTAATTAAAA
*
17232 TATAATTAATTAATAA
1 TATAACTAATTAA-AA
17248 T-TAACTAATTA
1 TATAACTAATTA
17259 GAATTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (15 bp):
TATAACTAATTAAAA
Found at i:17828 original size:13 final size:12
Alignment explanation
Indices: 17792--17838 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
17782 TCAATCTTTA
*
17792 TATATATTGATAA
1 TATATATT-ATAT
*
17805 TA-ATGTTATAT
1 TATATATTATAT
17816 TATATTATTATAT
1 TATA-TATTATAT
17829 TATATATTAT
1 TATATATTAT
17839 CAATAGACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:17987 original size:17 final size:17
Alignment explanation
Indices: 17965--18009 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
17955 CGAAATCAAA
*
17965 CCCGAACCCGATCCGAG
1 CCCGAACCCGACCCGAG
*
17982 CCCGAACCCTACCCGAG
1 CCCGAACCCGACCCGAG
*
17999 ACCGAACCCGA
1 CCCGAACCCGA
18010 AAATACCCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.27, C:0.49, G:0.20, T:0.04
Consensus pattern (17 bp):
CCCGAACCCGACCCGAG
Found at i:18042 original size:16 final size:16
Alignment explanation
Indices: 18000--18057 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
17990 CTACCCGAGA
18000 CCGAACCCGAA-AATAC
1 CCGAACCCGAAGAAT-C
**
18016 CCGAATTCGAAGAATC
1 CCGAACCCGAAGAATC
*
18032 CCGAACCCGAAGTA-C
1 CCGAACCCGAAGAATC
*
18047 ACGAACCCGAA
1 CCGAACCCGAA
18058 CCTGCCCGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 11 0.31
16 21 0.60
17 3 0.09
ACGTcount: A:0.40, C:0.34, G:0.17, T:0.09
Consensus pattern (16 bp):
CCGAACCCGAAGAATC
Found at i:19327 original size:11 final size:10
Alignment explanation
Indices: 19296--19333 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
19286 TTCTTTTTGG
19296 TTTTTATG-T
1 TTTTTATGTT
* *
19305 TTTCTCTGTT
1 TTTTTATGTT
19315 TTTTTATGTT
1 TTTTTATGTT
19325 TTTTTATGT
1 TTTTTATGT
19334 CTATGTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.08, C:0.05, G:0.11, T:0.76
Consensus pattern (10 bp):
TTTTTATGTT
Found at i:19785 original size:68 final size:68
Alignment explanation
Indices: 19695--19830 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
19685 TGGTTGTGAA
* * *
19695 TCTGTGAATTGCATGCTTTGCTTATGTGTTGAATGGATGTGATTTTGCACACTGATTGTAATGAG
1 TCTGAGAATTGCATGCTCTGCTTATGTGGTGAATGGATGTGATTTTGCACACTGATTGTAATGAG
19760 TGT
66 TGT
*
19763 TCTGAGAATTGCATGCTCTGCTTATGTGGTGAATGGTTGTGATTTTGCACACTGATTGTAATGAG
1 TCTGAGAATTGCATGCTCTGCTTATGTGGTGAATGGATGTGATTTTGCACACTGATTGTAATGAG
19828 TGT
66 TGT
19831 GCTATCAAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (68 bp):
TCTGAGAATTGCATGCTCTGCTTATGTGGTGAATGGATGTGATTTTGCACACTGATTGTAATGAG
TGT
Found at i:20237 original size:18 final size:18
Alignment explanation
Indices: 20214--20258 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
20204 TGTTTCAATT
20214 AACTAATAGATCAAACTA
1 AACTAATAGATCAAACTA
*
20232 AACTAACTA-ATTAAACTA
1 AACTAA-TAGATCAAACTA
*
20250 AATTAATAG
1 AACTAATAG
20259 GACAATTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (18 bp):
AACTAATAGATCAAACTA
Found at i:24923 original size:42 final size:40
Alignment explanation
Indices: 24864--24947 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 40
24854 TTTAATTCCG
*
24864 ATGTAATATATATAATAATTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
24904 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
24946 AT
1 AT
24948 TCTTAGGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 7 0.17
41 3 0.08
42 30 0.75
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:24942 original size:21 final size:21
Alignment explanation
Indices: 24876--24947 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
24866 GTAATATATA
* *
24876 TAATAATTAAAATACTTACAT
1 TAATAAATGAAATACTTACAT
* *
24897 TAATTAAATGTAATA-ATAC-T
1 TAA-TAAATGAAATACTTACAT
*
24917 ATAATAACTGAAATACTTACAT
1 -TAATAAATGAAATACTTACAT
24939 TAATTAAAT
1 TAA-TAAAT
24948 TCTTAGGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 10 0.26
21 15 0.39
22 13 0.34
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAAATGAAATACTTACAT
Done.