Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016306.1 Corchorus olitorius cultivar O-4 contig16339, 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: 46837
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2113 original size:16 final size:15
Alignment explanation
Indices: 2072--2113 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
2062 AACTAATCAG
2072 ATCATGACTCCACTA
1 ATCATGACTCCACTA
2087 A-CAAT-ACTCCACTAA
1 ATC-ATGACTCCACT-A
2102 ATCATGACTCCA
1 ATCATGACTCCA
2114 ATATCAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (15 bp):
ATCATGACTCCACTA
Found at i:7128 original size:18 final size:18
Alignment explanation
Indices: 7102--7167 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
7092 TACAAAATAT
*
7102 TGTTTCACTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
* * **
7120 TGTTCCACTACTGCAAAA
1 TGTTCCACTGCCGCAGGA
*
7138 TGTTCCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
*
7156 TGTTCCGCTGCC
1 TGTTCCACTGCC
7168 ACAAGAACCT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.29
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:13179 original size:53 final size:53
Alignment explanation
Indices: 13116--13221 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
13106 TGCACCCTTT
13116 CATCCGGTAGGATAAATGGATCTGTCACGGCGTCCAATGTGGCATGCCACGTG
1 CATCCGGTAGGATAAATGGATCTGTCACGGCGTCCAATGTGGCATGCCACGTG
13169 CATCCGGTAGGATAAATGGATCTGTCACGGCGTCCAATGTGGCATGCCACGTG
1 CATCCGGTAGGATAAATGGATCTGTCACGGCGTCCAATGTGGCATGCCACGTG
13222 GACAAAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (53 bp):
CATCCGGTAGGATAAATGGATCTGTCACGGCGTCCAATGTGGCATGCCACGTG
Found at i:14277 original size:15 final size:15
Alignment explanation
Indices: 14257--14295 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
14247 ATATTTCATT
14257 CATGTGCATGAATGA
1 CATGTGCATGAATGA
14272 CATGTGCATGAATGA
1 CATGTGCATGAATGA
14287 CATGTGCAT
1 CATGTGCAT
14296 ATAGACCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (15 bp):
CATGTGCATGAATGA
Found at i:14677 original size:18 final size:15
Alignment explanation
Indices: 14632--14677 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 15
14622 TCATTATTTA
14632 TTATTTAAAATATAT
1 TTATTTAAAATATAT
14647 TTATTTAATAATATAT
1 TTATTTAA-AATATAT
14663 ATTATATCTAAAATA
1 -TTAT-T-TAAAATA
14678 GTAAAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 4 0.15
18 5 0.19
19 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTAAAATATAT
Found at i:17762 original size:15 final size:15
Alignment explanation
Indices: 17728--17764 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
17718 TTTTTGTTTG
17728 AAAAAAA-AATAAAT
1 AAAAAAATAATAAAT
17742 AAAAAAATAATAAA-
1 AAAAAAATAATAAAT
17756 AATAAAAAT
1 AA-AAAAAT
17765 CAATCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAATAATAAAT
Found at i:28765 original size:13 final size:13
Alignment explanation
Indices: 28749--28774 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28739 AATCTTGAAA
28749 AATCATCTACTAT
1 AATCATCTACTAT
28762 AATCATCTACTAT
1 AATCATCTACTAT
28775 TCTGCTGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
AATCATCTACTAT
Found at i:28943 original size:233 final size:233
Alignment explanation
Indices: 28536--28999 Score: 919
Period size: 233 Copynumber: 2.0 Consensus size: 233
28526 CGTTCTACTA
28536 TACTATTCTGCTGTGGAGTATTAACACATGAAGTTTGGTGAATTATACCTGTTGATTAATGAAAT
1 TACTATTCTGCTGTGGAGTATTAACACATGAAGTTTGGTGAATTATACCTGTTGATTAATGAAAT
28601 TGAGAATCATTGAACTCTTGACCGTTATCAGACCTTATGCACTTGACAACAAGGTTAAACTGAGT
66 TGAGAATCATTGAACTCTTGACCGTTATCAGACCTTATGCACTTGACAACAAGGTTAAACTGAGT
28666 TTTGACCATAGTGACAAAGTCTTTCATAATCTGTCTAGCTTCTGACTTGTACTTCATGAGAAACA
131 TTTGACCATAGTGACAAAGTCTTTCATAATCTGTCTAGCTTCTGACTTGTACTTCATGAGAAACA
28731 CCCAAGTAAATCTTGAAAAATCATCTACTATAATCATC
196 CCCAAGTAAATCTTGAAAAATCATCTACTATAATCATC
*
28769 TACTATTCTGCTGTGGAGTATTAACACATGAAGTTTGGTGAATTATACTTGTTGATTAATGAAAT
1 TACTATTCTGCTGTGGAGTATTAACACATGAAGTTTGGTGAATTATACCTGTTGATTAATGAAAT
28834 TGAGAATCATTGAACTCTTGACCGTTATCAGACCTTATGCACTTGACAACAAGGTTAAACTGAGT
66 TGAGAATCATTGAACTCTTGACCGTTATCAGACCTTATGCACTTGACAACAAGGTTAAACTGAGT
28899 TTTGACCATAGTGACAAAGTCTTTCATAATCTGTCTAGCTTCTGACTTGTACTTCATGAGAAACA
131 TTTGACCATAGTGACAAAGTCTTTCATAATCTGTCTAGCTTCTGACTTGTACTTCATGAGAAACA
28964 CCCAAGTAAATCTTGAAAAATCATCTACTATAATCA
196 CCCAAGTAAATCTTGAAAAATCATCTACTATAATCA
29000 AGAAATAAAC
Statistics
Matches: 230, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 230 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (233 bp):
TACTATTCTGCTGTGGAGTATTAACACATGAAGTTTGGTGAATTATACCTGTTGATTAATGAAAT
TGAGAATCATTGAACTCTTGACCGTTATCAGACCTTATGCACTTGACAACAAGGTTAAACTGAGT
TTTGACCATAGTGACAAAGTCTTTCATAATCTGTCTAGCTTCTGACTTGTACTTCATGAGAAACA
CCCAAGTAAATCTTGAAAAATCATCTACTATAATCATC
Found at i:29862 original size:21 final size:21
Alignment explanation
Indices: 29838--29878 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29828 TTAGAAATAC
29838 CATAAGGATTGAATGTGGAAT
1 CATAAGGATTGAATGTGGAAT
*
29859 CATAAGGATTGGATGTGGAA
1 CATAAGGATTGAATGTGGAA
29879 GACTTTGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.27
Consensus pattern (21 bp):
CATAAGGATTGAATGTGGAAT
Found at i:34787 original size:84 final size:84
Alignment explanation
Indices: 34647--34810 Score: 285
Period size: 84 Copynumber: 2.0 Consensus size: 84
34637 TCAACGCAAT
*
34647 AGTTCAGGAGGCAAAAAAGCTAATAAACCATTTTAAAAATTATTTTACTCTTTGATGTCAAGAAT
1 AGTTCAGGAGGCAAAAAAGCTAATAAACCATTTTAAAAACTATTTTACTCTTTGATGTCAAGAAT
34712 GTT-AAAAAATACTAGCGA
66 GTTGAAAAAATACTAGCGA
34730 AGTTCAGGAGGCAAAAAAAGCTAATAAACCATTTTAAAAACTATTTTACTCTTTGATGTCAAGAA
1 AGTTCAGGAGGC-AAAAAAGCTAATAAACCATTTTAAAAACTATTTTACTCTTTGATGTCAAGAA
* *
34795 TTTTGAAAAAGTACTA
65 TGTTGAAAAAATACTA
34811 TGCTCTTCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 12 0.16
84 54 0.71
85 10 0.13
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (84 bp):
AGTTCAGGAGGCAAAAAAGCTAATAAACCATTTTAAAAACTATTTTACTCTTTGATGTCAAGAAT
GTTGAAAAAATACTAGCGA
Found at i:40330 original size:30 final size:30
Alignment explanation
Indices: 40296--40386 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
40286 TTTAGAAAGT
40296 AATGGGTCAAGTTGTCGCGATTTGAAGTTC
1 AATGGGTCAAGTTGTCGCGATTTGAAGTTC
** *** *
40326 AATGGG-CAAAATGTCTTAAATTTGGAAATT-
1 AATGGGTCAAGTTGTC-GCGATTT-GAAGTTC
*
40356 AATTGGTCAAGTTGTCGCGATTTGAAGTTC
1 AATGGGTCAAGTTGTCGCGATTTGAAGTTC
40386 A
1 A
40387 TAGGGCAAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
29 12 0.27
30 20 0.45
31 12 0.27
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (30 bp):
AATGGGTCAAGTTGTCGCGATTTGAAGTTC
Found at i:40340 original size:60 final size:60
Alignment explanation
Indices: 40273--40400 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
40263 GTTCAGGAGT
40273 AAAATGTCTTAAATTTAGAAAGTAATGGGTCAAGTTGTCGCGATTTGAAGTTCA-ATGGGC
1 AAAATGTCTTAAATTTAGAAAGTAATGGGTCAAGTTGTCGCGATTTGAAGTTCATA-GGGC
* * *
40333 AAAATGTCTTAAATTTGGAAATTAATTGGTCAAGTTGTCGCGATTTGAAGTTCATAGGGC
1 AAAATGTCTTAAATTTAGAAAGTAATGGGTCAAGTTGTCGCGATTTGAAGTTCATAGGGC
40393 AAAATGTC
1 AAAATGTC
40401 CTTTACGAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (60 bp):
AAAATGTCTTAAATTTAGAAAGTAATGGGTCAAGTTGTCGCGATTTGAAGTTCATAGGGC
Found at i:42285 original size:21 final size:23
Alignment explanation
Indices: 42244--42290 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
42234 CTTATTCTTC
42244 TTGCAAAGTATATATTCCAAGTCA
1 TTGCAAAG-ATATATTCCAAGTCA
42268 TTGCAAAG-TATA-TCCAAGTCA
1 TTGCAAAGATATATTCCAAGTCA
42289 TT
1 TT
42291 TGGAATGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
24 8 0.35
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (23 bp):
TTGCAAAGATATATTCCAAGTCA
Found at i:44520 original size:11 final size:11
Alignment explanation
Indices: 44504--44535 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
44494 AAATAGACGG
44504 ATCGCGACCGA
1 ATCGCGACCGA
44515 ATCGCGACCGA
1 ATCGCGACCGA
44526 ATCGCGACCG
1 ATCGCGACCG
44536 GACCATTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.38, G:0.28, T:0.09
Consensus pattern (11 bp):
ATCGCGACCGA
Found at i:45153 original size:21 final size:21
Alignment explanation
Indices: 45129--45181 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
45119 AGGAAATGAC
**
45129 ATGATAATAATTTCTGGATAG
1 ATGATAATAATTAATGGATAG
45150 ATGATAATACTAATTAATGGATAG
1 ATGAT-A-A-TAATTAATGGATAG
45174 ATGATAAT
1 ATGATAAT
45182 CAAATTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.22
22 2 0.07
23 2 0.07
24 17 0.63
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (21 bp):
ATGATAATAATTAATGGATAG
Done.