Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017785.1 Corchorus olitorius cultivar O-4 contig17818, 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: 31526
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5165 original size:41 final size:39
Alignment explanation
Indices: 5095--5194 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 39
5085 ACTTCAACGT
* * *
5095 GACAACTTCCAGTGTCAAATATTTATTTAATTTACTAGAG
1 GACAACTTCTAGTGTCAAATATATATTTAATTTACCA-AG
5135 CGACAACTTCTAGTGTCAAAGGTA-AT-TTTAATTTACCAAG
1 -GACAACTTCTAGTGTCAAA--TATATATTTAATTTACCAAG
5175 GTAACAACTTCTAGTGTCAA
1 G--ACAACTTCTAGTGTCAA
5195 TTAAATTTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
39 1 0.02
40 2 0.04
41 46 0.88
42 1 0.02
43 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (39 bp):
GACAACTTCTAGTGTCAAATATATATTTAATTTACCAAG
Found at i:5239 original size:47 final size:47
Alignment explanation
Indices: 5178--5301 Score: 194
Period size: 47 Copynumber: 2.6 Consensus size: 47
5168 TACCAAGGTA
*
5178 ACAACTTCTAGTGTCAATTAAATTTACTAAAATAAAATTTTAATTGG
1 ACAACTTCTGGTGTCAATTAAATTTACTAAAATAAAATTTTAATTGG
* * **
5225 ACAACTTTTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTT
1 ACAACTTCTGGTGTCAATTAAATTTACTAAAATAAAATTTTAATTGG
5272 ACAACTTCTGGTGTCAATTAAAATTTACTA
1 ACAACTTCTGGTGTCAATT-AAATTTACTA
5302 GAGCTCTTGT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 60 0.86
48 10 0.14
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (47 bp):
ACAACTTCTGGTGTCAATTAAATTTACTAAAATAAAATTTTAATTGG
Found at i:6641 original size:48 final size:48
Alignment explanation
Indices: 6478--6642 Score: 111
Period size: 48 Copynumber: 3.3 Consensus size: 48
6468 ATTAAAACTA
* * *
6478 ATATACTTATAATTTTTACCATTTTACTATTTTAATT-AAAAAACTTAT
1 ATATA-TTAGAATTTTTACCATTTTACAATTTTAATTAAAAAAATTTAT
* ** * * * **
6526 GTATATTAGAATTTTTTAAATATATTTTTACAGTTTTACTCAACTAAATCCTTAT
1 ATATATTAGAA-TTTTT--A-CCA-TTTTACAATTTTAATTAAAAAAAT--TTAT
** *
6581 ACCTATT--TATTTTTACCATTTTACAATTTTAATTAAAAAAATTTAT
1 ATATATTAGAATTTTTACCATTTTACAATTTTAATTAAAAAAATTTAT
6627 ATATATTAGAATTTTT
1 ATATATTAGAATTTTT
6643 TAAATATATT
Statistics
Matches: 82, Mismatches: 25, Indels: 20
0.65 0.20 0.16
Matches are distributed among these distances:
46 9 0.11
47 5 0.06
48 34 0.41
49 1 0.01
50 2 0.02
51 1 0.01
52 17 0.21
53 5 0.06
55 8 0.10
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (48 bp):
ATATATTAGAATTTTTACCATTTTACAATTTTAATTAAAAAAATTTAT
Found at i:10468 original size:30 final size:30
Alignment explanation
Indices: 10432--10493 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
10422 AAATCTCATA
10432 CTGTACAGTATGTTGGGAGAGGAACCCAGG
1 CTGTACAGTATGTTGGGAGAGGAACCCAGG
10462 CTGTACAGTATGTTGGGAGAGGAACCCAGG
1 CTGTACAGTATGTTGGGAGAGGAACCCAGG
10492 CT
1 CT
10494 CTGACTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (30 bp):
CTGTACAGTATGTTGGGAGAGGAACCCAGG
Found at i:12234 original size:42 final size:42
Alignment explanation
Indices: 12175--12256 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
12165 GTCACAAATA
*
12175 TCTTTTATTATATTTCTTGTAATATATAAATACATATTAATG
1 TCTTTAATTATATTTCTTGTAATATATAAATACATATTAATG
12217 TCTTTAATTATATTTCTTGTAATATATAAATACATATTAA
1 TCTTTAATTATATTTCTTGTAATATATAAATACATATTAA
12257 AAAAGATGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (42 bp):
TCTTTAATTATATTTCTTGTAATATATAAATACATATTAATG
Found at i:12529 original size:79 final size:81
Alignment explanation
Indices: 12384--12544 Score: 290
Period size: 79 Copynumber: 2.0 Consensus size: 81
12374 TCACTGAAAT
12384 ATTAAAAGTATATATTGGCTGGGCCGGGGTCATATCCTGCTATATGTGGTATTAGGTTGATATTG
1 ATTAAAAG-ATATATTGGCTGGGCCGGGGTCATATCCTGCTATATGTGGTATTAGGTTGATATTG
12449 TATTCAAAGTGCAATGG
65 TATTCAAAGTGCAATGG
*
12466 ATTAAAAG-TATATTGGCTGGGCCGGGGTCATAT-TTGCTATATGTGGTATTAGGTTGATATTGT
1 ATTAAAAGATATATTGGCTGGGCCGGGGTCATATCCTGCTATATGTGGTATTAGGTTGATATTGT
12529 ATTCAAAGTGCAATGG
66 ATTCAAAGTGCAATGG
12545 CCATTGTGTT
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
79 45 0.58
80 25 0.32
82 8 0.10
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.36
Consensus pattern (81 bp):
ATTAAAAGATATATTGGCTGGGCCGGGGTCATATCCTGCTATATGTGGTATTAGGTTGATATTGT
ATTCAAAGTGCAATGG
Found at i:13038 original size:13 final size:15
Alignment explanation
Indices: 13009--13040 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12999 TACCATTTAG
13009 ATTTATATATTATTT
1 ATTTATATATTATTT
13024 ATTTATAT-TTA-TT
1 ATTTATATATTATTT
13037 ATTT
1 ATTT
13041 CAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTATATATTATTT
Found at i:13253 original size:120 final size:124
Alignment explanation
Indices: 13119--13452 Score: 435
Period size: 120 Copynumber: 2.6 Consensus size: 124
13109 TATTTAATTA
*
13119 AATCTAATATCCTTATAATTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATAT
1 AATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATAT
13184 ATATTAGAATTTTTCAAATATGCTTTTATAGTTTTACTAAACTAAAAACTC-TA-T-TT
66 ATATTAGAATTTTTCAAATATGCTTTTATAGTTTTACTAAACTAAAAACTCTTATTATT
*
13240 -ATCTAATATCCTTATAACTATCTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATAT
1 AATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATAT
* * * *
13304 ATTTTTGAATTTTTTTTAAATATGCTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTT
66 ATATTAGAA--TTTTTCAAATATGCTTTTATAGTTTTACTAAACTAAAAACTC------TTA-TT
13369 AATT
122 -ATT
* * * *
13373 AGATCTAATATCCTTATAGCTATTTTATTTTTACCATTTTACTAATTTAATTAAAAGAACTTAGT
1 A-ATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTA-T
13438 -TATATTAGAATTTTT
64 ATATATTAGAATTTTT
13453 AAAAATATTC
Statistics
Matches: 184, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
120 69 0.38
122 40 0.22
129 2 0.01
131 1 0.01
133 7 0.04
135 64 0.35
136 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (124 bp):
AATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATAT
ATATTAGAATTTTTCAAATATGCTTTTATAGTTTTACTAAACTAAAAACTCTTATTATT
Found at i:17101 original size:39 final size:39
Alignment explanation
Indices: 17057--17135 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
17047 TTGGAACATT
17057 ACCAATCAATCTTTGCTATGTTTGTGGTGATTCAAGTGA
1 ACCAATCAATCTTTGCTATGTTTGTGGTGATTCAAGTGA
17096 ACCAATCAATCTTTGCTATGTTTGTGGTGATTCAAGTGA
1 ACCAATCAATCTTTGCTATGTTTGTGGTGATTCAAGTGA
17135 A
1 A
17136 GATGGGTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (39 bp):
ACCAATCAATCTTTGCTATGTTTGTGGTGATTCAAGTGA
Found at i:17945 original size:2 final size:2
Alignment explanation
Indices: 17938--17962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17928 ACTAGATTTC
17938 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 A
17963 CTAGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22185 original size:22 final size:23
Alignment explanation
Indices: 22157--22211 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
22147 TCTCCCTAAG
*
22157 AATTTTGATAAACTTTTG-ATGA
1 AATTTTGATAAACTTCTGTATGA
*
22179 AATTTTGGT-AACTTCTGTATGA
1 AATTTTGATAAACTTCTGTATGA
22201 AATTTTGATAA
1 AATTTTGATAA
22212 TTATACTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.25
22 20 0.71
23 1 0.04
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (23 bp):
AATTTTGATAAACTTCTGTATGA
Found at i:28121 original size:30 final size:30
Alignment explanation
Indices: 28085--28144 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
28075 GTTAGTAAGA
28085 TATTAAAATTTGAGGGTATAAGAGGAAAGT
1 TATTAAAATTTGAGGGTATAAGAGGAAAGT
28115 TATTAAAATTTGAGGGTATAAGAGGAAAGT
1 TATTAAAATTTGAGGGTATAAGAGGAAAGT
28145 CAAGATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (30 bp):
TATTAAAATTTGAGGGTATAAGAGGAAAGT
Found at i:28518 original size:32 final size:32
Alignment explanation
Indices: 28477--28540 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28467 TGGAGAATAT
28477 TTCTTACTTGGGTATGCATCTTCCGGCAGTGG
1 TTCTTACTTGGGTATGCATCTTCCGGCAGTGG
28509 TTCTTACTTGGGTATGCATCTTCCGGCAGTGG
1 TTCTTACTTGGGTATGCATCTTCCGGCAGTGG
28541 CTTTACGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (32 bp):
TTCTTACTTGGGTATGCATCTTCCGGCAGTGG
Found at i:30857 original size:22 final size:22
Alignment explanation
Indices: 30824--31121 Score: 164
Period size: 22 Copynumber: 13.3 Consensus size: 22
30814 TCAATCAAAC
*
30824 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
30846 CAAATTTTCATAGTG-TGATTAT
1 CAAAATTTCATAG-GAAGGTTAT
*
30868 TAAAATTTCATATGG-AGGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
** *
30890 CAAAACGTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * * *
30912 CAAAATTCCATA-CAGACGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
* **
30934 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
30956 CAAAATTTCATA-GAGTGTCGTTAA
1 CAAAATTTCATAGGA-AG--GTTAT
* *
30980 CAAAATTTTATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
31002 CAAAATTT-ATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
*
31023 CAAAATTTCATAGGGAGGGAGGCTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* * * *
31049 CAAAGTTTCCTAGGGAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
31071 CAAAATTTCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
* *
31092 CAAAAATTTTAT-GGAGATGTTAT
1 C-AAAATTTCATAGGA-AGGTTAT
31115 CAAAATT
1 CAAAATT
31122 AAATAAAGAG
Statistics
Matches: 212, Mismatches: 43, Indels: 42
0.71 0.14 0.14
Matches are distributed among these distances:
21 24 0.11
22 147 0.69
23 6 0.03
24 16 0.08
25 4 0.02
26 15 0.07
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:30986 original size:46 final size:45
Alignment explanation
Indices: 30907--31030 Score: 139
Period size: 46 Copynumber: 2.8 Consensus size: 45
30897 TCATAGTGTA
* * *
30907 GTTATCAAAATTCCATACA--GACGTTACCAAAATTTTATAAAAAG
1 GTTATCAAAATTTCATA-AGTGTCGTTAACAAAATTTTATAAAAAG
**
30951 GTTATCAAAATTTCATAGAGTGTCGTTAACAAAATTTTATACGAAG
1 GTTATCAAAATTTCATA-AGTGTCGTTAACAAAATTTTATAAAAAG
* *
30997 GTTATCAAAATTT-AT-AGTGTGGTTATCAAAATTT
1 GTTATCAAAATTTCATAAGTGTCGTTAACAAAATTT
31031 CATAGGGAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
43 17 0.24
44 17 0.24
45 2 0.03
46 34 0.49
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (45 bp):
GTTATCAAAATTTCATAAGTGTCGTTAACAAAATTTTATAAAAAG
Found at i:31237 original size:22 final size:22
Alignment explanation
Indices: 31166--31283 Score: 123
Period size: 22 Copynumber: 5.4 Consensus size: 22
31156 GAAGGGAAAC
*
31166 TTCATGGTGTGGTTATCAAAATT
1 TTCATAGTGTGGTTATCAAAA-T
* * *
31189 TTCATAATGCGGTTA-C-CAAT
1 TTCATAGTGTGGTTATCAAAAT
* *
31209 TTTATAGTGTGATTATCAAAAT
1 TTCATAGTGTGGTTATCAAAAT
* * *
31231 TTCATAGGGAGATTATCAAAAT
1 TTCATAGTGTGGTTATCAAAAT
31253 TTCATAGTGTGGTTATCAAAAT
1 TTCATAGTGTGGTTATCAAAAT
*
31275 TTCACAGTG
1 TTCATAGTG
31284 CGTGTATCAC
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
20 12 0.16
21 3 0.04
22 50 0.65
23 12 0.16
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
TTCATAGTGTGGTTATCAAAAT
Found at i:31292 original size:44 final size:44
Alignment explanation
Indices: 31166--31303 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 44
31156 GAAGGGAAAC
* *
31166 TTCATGGTGTGGTTATCAAAATTTTCATAATGCG-GT-T-ACCAAT
1 TTCATAGTGTGGTTATCAAAA-TTTCATAGTGCGTGTATCA-CAAT
* * * * *
31209 TTTATAGTGTGATTATCAAAATTTCATAGGGAGAT-TATCAAAAT
1 TTCATAGTGTGGTTATCAAAATTTCATAGTGCG-TGTATCACAAT
* *
31253 TTCATAGTGTGGTTATCAAAATTTCACAGTGCGTGTATCACATT
1 TTCATAGTGTGGTTATCAAAATTTCATAGTGCGTGTATCACAAT
31297 TTCATAG
1 TTCATAG
31304 CTTATCGAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
42 9 0.12
43 20 0.26
44 46 0.61
45 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (44 bp):
TTCATAGTGTGGTTATCAAAATTTCATAGTGCGTGTATCACAAT
Found at i:31339 original size:22 final size:21
Alignment explanation
Indices: 31166--31339 Score: 99
Period size: 22 Copynumber: 8.1 Consensus size: 21
31156 GAAGGGAAAC
*
31166 TTCATGGTGTGGTTATCAAAATT
1 TTCATAGTGT-GTTATC-AAATT
* * *
31189 TTCATAATGCGGTTA-CCAATT
1 TTCATAGTG-TGTTATCAAATT
*
31210 TT-ATAGTGTGATTATCAAAAT
1 TTCATAGTGTG-TTATCAAATT
* * *
31231 TTCATAGGGAGATTATCAAAAT
1 TTCATAGTGTG-TTATCAAATT
*
31253 TTCATAGTGTGGTTATCAAAAT
1 TTCATAGTGT-GTTATCAAATT
* * *
31275 TTCACAGTGCGTGTATCACATT
1 TTCATAGTGTGT-TATCAAATT
*
31297 TTCATA--G-CTTATCGAAA-T
1 TTCATAGTGTGTTATC-AAATT
*
31315 TTCATAATGATGTTATCAAATT
1 TTCATAGTG-TGTTATCAAATT
31337 TTC
1 TTC
31340 GCATCATTAT
Statistics
Matches: 119, Mismatches: 20, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
18 11 0.09
19 4 0.03
20 10 0.08
21 17 0.14
22 65 0.55
23 12 0.10
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (21 bp):
TTCATAGTGTGTTATCAAATT
Done.