Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010008.1 Corchorus olitorius cultivar O-4 contig10040, 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: 13884
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:54 original size:15 final size:15
Alignment explanation
Indices: 21--63 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11 AACATACCAC
*
21 TAATAATAATTATTA
1 TAATAATAATAATTA
36 TAATAATAATAAGTT-
1 TAATAATAATAA-TTA
*
51 TAATAATTATAAT
1 TAATAATAATAAT
64 ATTAAGATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:63 original size:9 final size:9
Alignment explanation
Indices: 23--64 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
13 CATACCACTA
23 ATAATAATT
1 ATAATAATT
* *
32 ATTATAATA
1 ATAATAATT
41 ATAATAAGTT
1 ATAATAA-TT
51 -TAATAATT
1 ATAATAATT
59 ATAATA
1 ATAATA
65 TTAAGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:75 original size:24 final size:24
Alignment explanation
Indices: 27--77 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17 CCACTAATAA
* *
27 TAATTATTATAATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
51 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
75 TAA
1 TAA
78 CATAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:354 original size:2 final size:2
Alignment explanation
Indices: 349--416 Score: 50
Period size: 2 Copynumber: 33.5 Consensus size: 2
339 AGTTTAGACT
*
349 TA TA TA GTA TA T- TGA TA TA TA TA TA TA TT TA CTA -A TA TA TA
1 TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
390 TT TT TC TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
417 TTACAATCTC
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
1 2 0.04
2 47 0.87
3 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:377 original size:16 final size:16
Alignment explanation
Indices: 349--416 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
339 AGTTTAGACT
*
349 TATATAGTATATTGATA
1 TATATA-TATATTTATA
366 TATATATATATTTACTA
1 TATATATATATTTA-TA
* *
383 -ATATATATTTTTCTA
1 TATATATATATTTATA
* *
398 AATATATATATATATA
1 TATATATATATTTATA
414 TAT
1 TAT
417 TTACAATCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
15 2 0.05
16 32 0.76
17 8 0.19
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
TATATATATATTTATA
Found at i:386 original size:14 final size:14
Alignment explanation
Indices: 369--420 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
359 ATTGATATAT
369 ATATATATTTACTA
1 ATATATATTTACTA
*
383 ATATATATTTTTCTA
1 ATATATA-TTTACTA
*
398 A-ATATATATA-T-
1 ATATATATTTACTA
409 ATATATATTTAC
1 ATATATATTTAC
421 AATCTCCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 1 0.03
12 9 0.29
13 2 0.06
14 12 0.39
15 7 0.23
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATTTACTA
Found at i:988 original size:22 final size:22
Alignment explanation
Indices: 826--1011 Score: 75
Period size: 22 Copynumber: 8.4 Consensus size: 22
816 TAATAATAGG
*
826 ATTTCATAGTG-TGGCTATCAAA
1 ATTTCATAG-GATGGTTATCAAA
*
848 ATTTCATA--AT-GTAATAACAAAA
1 ATTTCATAGGATGGT--TATC-AAA
* *
870 ATTTCATA-GAAGGTAATCAAA
1 ATTTCATAGGATGGTTATCAAA
* * *
891 GTTTCATATTG-TGCTTATCAAA
1 ATTTCATA-GGATGGTTATCAAA
* *
913 ATTTCATAGTGA-GATTAACACAA
1 ATTTCATAG-GATGGTTATCA-AA
* * *
936 AATTCTATAGGGA-AGTTATCAAC
1 ATTTC-ATA-GGATGGTTATCAAA
* *
959 ATTCCATAGAGAT-GTTATTAAA
1 ATTTCATAG-GATGGTTATCAAA
* *
981 ATTTCATAGTATGGTTATCCAA
1 ATTTCATAGGATGGTTATCAAA
1003 ATTTCATAG
1 ATTTCATAG
1012 TGTACCAAAT
Statistics
Matches: 122, Mismatches: 26, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 16 0.13
22 79 0.65
23 12 0.10
24 12 0.10
25 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (22 bp):
ATTTCATAGGATGGTTATCAAA
Found at i:1118 original size:22 final size:22
Alignment explanation
Indices: 1080--1236 Score: 104
Period size: 22 Copynumber: 7.1 Consensus size: 22
1070 CATCAAAATT
* *
1080 AATTTCATA-TAGAGGTTATCAC
1 AATTTCATAGT-GTGGTTATCAA
*
1102 AATTTTATAGTGTGGTTAAT-AA
1 AATTTCATAGTGTGGTT-ATCAA
* *
1124 AATTTCATAGTGTGGTGACCAA
1 AATTTCATAGTGTGGTTATCAA
*
1146 AATTTCATTG-GATGGTTATCAA
1 AATTTCATAGTG-TGGTTATCAA
* *
1168 AATTTCATAATGTGGTTATTAA
1 AATTTCATAGTGTGGTTATCAA
* * * * * *
1190 AGTTCCACAGGGAGGTTATCAC
1 AATTTCATAGTGTGGTTATCAA
* * *
1212 AATTTCTTAGGGAGGTTATCTAA
1 AATTTCATAGTGTGGTTATC-AA
1235 AA
1 AA
1237 AATATATCGA
Statistics
Matches: 104, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
21 2 0.02
22 95 0.91
23 7 0.07
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:2134 original size:22 final size:21
Alignment explanation
Indices: 1975--2218 Score: 143
Period size: 22 Copynumber: 11.0 Consensus size: 21
1965 TTTTAATTTT
*
1975 GGAGGTTAT-TAAATTTTATA
1 GGAGGTTATCAAAATTTTATA
* *
1995 GTGTGGTTCTCAAAATTTTATA
1 G-GAGGTTATCAAAATTTTATA
* *
2017 GTGTGGTTATCAAAATTTTATT
1 G-GAGGTTATCAAAATTTTATA
* *
2039 GTGAGGTTACCAAAATTTCATA
1 G-GAGGTTATCAAAATTTTATA
* * *
2061 GGTAGGATAT-TAAATCTTATA
1 GG-AGGTTATCAAAATTTTATA
* * *
2082 GTGTA-GTTATCACAATTTAATG
1 G-G-AGGTTATCAAAATTTTATA
**
2104 GGATATTATCAAAATTTTATAA
1 GGAGGTTATCAAAATTTTAT-A
*
2126 GGAGGTTATTAAAATAAAATTTCATAA
1 GGAGGTTATCAAAAT----TTT-AT-A
* *
2153 GGATGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTTATA
*
2174 TGGAGGTTATCAAAATTTCATA
1 -GGAGGTTATCAAAATTTTATA
* *
2196 GGAAGATTATCAAAATTTCATA
1 GG-AGGTTATCAAAATTTTATA
2218 G
1 G
2219 TGTGCATATA
Statistics
Matches: 178, Mismatches: 32, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.01
21 37 0.21
22 117 0.66
23 2 0.01
26 3 0.02
27 17 0.10
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTTATA
Found at i:2233 original size:44 final size:43
Alignment explanation
Indices: 2141--2240 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 43
2131 TTATTAAAAT
* ** *
2141 AAAATTTCATAAGGATGTTATCAAAATTTCATATGGAGGTTATC
1 AAAATTTCAT-AGGAAGTTATCAAAATTTCATATGGAGCATATA
*
2185 AAAATTTCATAGGAAGATTATCAAAATTTCATA-GTGTGCATATA
1 AAAATTTCATAGGAAG-TTATCAAAATTTCATATG-GAGCATATA
*
2229 AAAATTACATAG
1 AAAATTTCATAG
2241 TGAGATAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 6 0.12
44 42 0.88
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (43 bp):
AAAATTTCATAGGAAGTTATCAAAATTTCATATGGAGCATATA
Found at i:4169 original size:2 final size:2
Alignment explanation
Indices: 4162--4190 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4152 AAATCACATG
4162 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4191 GTAATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4901 original size:22 final size:22
Alignment explanation
Indices: 4587--5194 Score: 307
Period size: 22 Copynumber: 27.4 Consensus size: 22
4577 GCAATCAAAC
* *
4587 CAAAATTACATA-AGAAAGTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* *
4609 CAAAATTTCATA-ATGCGGTTAC
1 CAAAATTTCATAGA-GAGGTTAT
*
4631 CAAAATTTCATATAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
4653 CAAAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* * *
4675 TAAAATTTCATATAGAGGTTAC
1 CAAAATTTCATAGAGAGGTTAT
* *
4697 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
4719 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGAGAGGTTAT
4741 CAAAATTTCATATGA-AGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
* * *
4763 CGAAATTTTATAGTGTA-GTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* * * *
4785 TAAAATTTCATAAAAAGGTTAA
1 CAAAATTTCATAGAGAGGTTAT
*
4807 CAAAATTTCATAGGGAGAGAGGTTAC
1 CAAAATTTCAT----AGAGAGGTTAT
*
4833 CAAAA-TT--T-GTGA--TTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
4849 CAAAATTTCCTAGGGAGGTTAA
1 CAAAATTTCATAGAGAGGTTAT
4871 CAAAAATTTCATAGAGAGGTTAT
1 C-AAAATTTCATAGAGAGGTTAT
* * *
4894 GAAAATTTTATGGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
4916 CAAAATTACATAGAGAGGATATT
1 CAAAATTTCATAGAGAGGTTA-T
** *
4939 ACAGTTTCATTCTCATAGGGAGGTTAT
1 -CA---AAATT-TCATAGAGAGGTTAT
** * * *
4966 TGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
*
4988 CAAAATTTTAT-GAGGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
* *
5010 CAAAATTTTCATAGTGCGGTTGA-
1 CAAAA-TTTCATAGAGAGGTT-AT
* * * *
5033 C--AATTTTATAGTGTGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
5053 CAAAATTTCATAGGGAGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* * ***
5075 CAAAATTCCACACTTAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * * *
5097 TAAAATTTAATTGTGTA-GTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* ***
5119 CAAAATTTTCACAGTTTGGTTAT
1 CAAAA-TTTCATAGAGAGGTTAT
*
5142 CAAATTTTCATA-AGGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
5164 CAAAATTTCATA-ATGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
*
5186 CAAATTTTC
1 CAAAATTTC
5195 GCAACGTGGT
Statistics
Matches: 442, Mismatches: 108, Indels: 72
0.71 0.17 0.12
Matches are distributed among these distances:
16 8 0.02
17 2 0.00
18 3 0.01
19 2 0.00
20 16 0.04
21 6 0.01
22 316 0.71
23 55 0.12
24 4 0.01
25 2 0.00
26 13 0.03
27 4 0.01
28 11 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:5205 original size:22 final size:22
Alignment explanation
Indices: 5136--5215 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
5126 TTCACAGTTT
*
5136 GGTTATCAAATTTTCATAAGGA
1 GGTTATCAAATTTTCATAACGA
* *
5158 GGTTATCAAAATTTCATAATGA
1 GGTTATCAAATTTTCATAACGA
** *
5180 GGTTATCAAATTTTCGCAACGT
1 GGTTATCAAATTTTCATAACGA
5202 GGTTATCAATATTT
1 GGTTATCAA-ATTT
5216 CTATGTTGGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 46 0.92
23 4 0.08
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAACGA
Found at i:6003 original size:2 final size:2
Alignment explanation
Indices: 5996--6032 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5986 AAATACTAGG
5996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6033 AAAGGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12959 original size:176 final size:176
Alignment explanation
Indices: 12656--12990 Score: 544
Period size: 176 Copynumber: 1.9 Consensus size: 176
12646 TTTGTACGTA
* * *
12656 ATTATTTTCTTTCTCGCAATTATTGCAACTCACATTTACCTAAACCACAAAACATGGAATCTCCT
1 ATTATTTTATTTCTCGCAATTACTACAACTCACATTTACCTAAACCACAAAACATGGAATCTCCT
* * *
12721 ATACAAAGCTTTCATCGATTATACTAATTTTTGTAATATGAGTTTATTTGGACCAAAGTTATAAA
66 ATACAAAGATTTCATAGATTATACTAATTTTTGTAATATAAGTTTATTTGGACCAAAGTTATAAA
*
12786 GTTGGGTTGGGAGAAGAAAACAATACTATACAATAAGGGGTACATG
131 GTTGGGTTGCGAGAAGAAAACAATACTATACAATAAGGGGTACATG
* *
12832 ATTATTTTATTTCTCGCAATTACTACAACTCACATTTACCTAAACCTCAAAACATGGAATCTCTT
1 ATTATTTTATTTCTCGCAATTACTACAACTCACATTTACCTAAACCACAAAACATGGAATCTCCT
* * * *
12897 ATACAAAGATTTCATATATTATACTAATTTTTGTGATATAAGTTTATTTGGGCCAGAGTTATAAA
66 ATACAAAGATTTCATAGATTATACTAATTTTTGTAATATAAGTTTATTTGGACCAAAGTTATAAA
*
12962 GTTGGGTTGCGAGAAGAAAATAATACTAT
131 GTTGGGTTGCGAGAAGAAAACAATACTAT
12991 GTAATAATGG
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
176 145 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (176 bp):
ATTATTTTATTTCTCGCAATTACTACAACTCACATTTACCTAAACCACAAAACATGGAATCTCCT
ATACAAAGATTTCATAGATTATACTAATTTTTGTAATATAAGTTTATTTGGACCAAAGTTATAAA
GTTGGGTTGCGAGAAGAAAACAATACTATACAATAAGGGGTACATG
Done.