Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015722.1 Corchorus olitorius cultivar O-4 contig15755, 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: 36262
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2267 original size:38 final size:38
Alignment explanation
Indices: 2216--2404 Score: 299
Period size: 38 Copynumber: 5.0 Consensus size: 38
2206 GAAATTTATT
2216 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
1 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
2254 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
1 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
2292 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
1 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
* * *
2330 GGTCTTGGTCCCAAGCGAATGATGAAATTGATCGCTTG
1 GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
* ** *
2368 GGTCTTGATCAAAAACGAATAAT-AAATTTGATCGCTT
1 GGTCTTGGTCCTAAGCGAATAATGAAA-TTGATCGCTT
2405 TGCTGAAAGT
Statistics
Matches: 142, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
37 3 0.02
38 139 0.98
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (38 bp):
GGTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTA
Found at i:4942 original size:30 final size:30
Alignment explanation
Indices: 4908--4967 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
4898 TTCAAACAAA
* *
4908 TTCTTTT-ATTTGATATTGTCAAGGATTTTT
1 TTCTTTTCATGTGATATTATCAAGG-TTTTT
4938 TTCTTTTGCATGTGATATTATCAAGGTTTT
1 TTCTTTT-CATGTGATATTATCAAGGTTTT
4968 CAATCTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 4 0.15
32 15 0.58
ACGTcount: A:0.20, C:0.08, G:0.15, T:0.57
Consensus pattern (30 bp):
TTCTTTTCATGTGATATTATCAAGGTTTTT
Found at i:5225 original size:105 final size:99
Alignment explanation
Indices: 5107--5305 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 99
5097 TAAATTTTTA
* * **
5107 TTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATAAGTGTT
1 TTATAGTTTTACTC-ACTAAAAACTCTA-TTTT-TTTAATTAAATATAATATCCTTAT-A--CCT
*
5172 CTTTTATTTTTACCATTTTACT-ATTTTAATTAAAATACTT
60 ATTTTATTTTTACCATTTTACTAATTTT-ATTAAAATACTT
*
5212 TTATAGTTTTACTCATTAAAAACTCTATTTTTTTAATTAAATATAATATCCTTATACCTATTTTA
1 TTATAGTTTTACTCACTAAAAACTCTATTTTTTTAATTAAATATAATATCCTTATACCTATTTTA
*
5277 TTTTTATCATTTTACTAATTTTATTAAAA
66 TTTTTACCATTTTACTAATTTTATTAAAA
5306 AAACTTATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
99 28 0.33
100 5 0.06
101 1 0.01
102 22 0.26
103 4 0.05
104 12 0.14
105 14 0.16
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.52
Consensus pattern (99 bp):
TTATAGTTTTACTCACTAAAAACTCTATTTTTTTAATTAAATATAATATCCTTATACCTATTTTA
TTTTTACCATTTTACTAATTTTATTAAAATACTT
Found at i:14187 original size:76 final size:76
Alignment explanation
Indices: 14102--14254 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
14092 AGTAATTGCA
14102 CACTGTAGATTGTTAAAGTTATGGGCAATCAGCTTGATGCAGCTTAAGTTCAATAATCTATTTGT
1 CACTGTAGATTGTTAAAGTTATGGGCAATCAGCTTGATGCAGCTTAAGTTCAATAATCTATTTGT
14167 GTTTCTTAGTT
66 GTTTCTTAGTT
14178 CACTGTAGATTGTTAAAGTTATGGGCAATCAGCTTGATGCAGCTTAAGTTCAATAATCTATTTGT
1 CACTGTAGATTGTTAAAGTTATGGGCAATCAGCTTGATGCAGCTTAAGTTCAATAATCTATTTGT
14243 GTTTCTTAGTT
66 GTTTCTTAGTT
14254 C
1 C
14255 TAATCTAATC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (76 bp):
CACTGTAGATTGTTAAAGTTATGGGCAATCAGCTTGATGCAGCTTAAGTTCAATAATCTATTTGT
GTTTCTTAGTT
Found at i:18119 original size:23 final size:24
Alignment explanation
Indices: 18064--18114 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
18054 AATAAAAAAT
*
18064 AAAAAA-AATTTAAAAAAAAGACA
1 AAAAAAGAAATTAAAAAAAAGACA
*
18087 AAAAAAGAAATTAAAACAAAGACA
1 AAAAAAGAAATTAAAAAAAAGACA
18111 AAAA
1 AAAA
18115 GGAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (24 bp):
AAAAAAGAAATTAAAAAAAAGACA
Found at i:18123 original size:28 final size:28
Alignment explanation
Indices: 18089--18145 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
18079 AAAAGACAAA
18089 AAAAGAAATTAAAACAAAGACA-AAAAGG
1 AAAAGAAATTAAAACAAAGA-AGAAAAGG
* *
18117 AAAAGAAATTACAACGAAGAAGAAAAGG
1 AAAAGAAATTAAAACAAAGAAGAAAAGG
18145 A
1 A
18146 GAATTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.68, C:0.07, G:0.18, T:0.07
Consensus pattern (28 bp):
AAAAGAAATTAAAACAAAGAAGAAAAGG
Found at i:19080 original size:16 final size:17
Alignment explanation
Indices: 19058--19098 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
19048 GATTAAATGA
*
19058 ATTTTTTTC-GTTTTCT
1 ATTTTTTTCAATTTTCT
*
19074 TTTTTTTTCAATTTTCT
1 ATTTTTTTCAATTTTCT
19091 ATTTTTTT
1 ATTTTTTT
19099 ATTCCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (17 bp):
ATTTTTTTCAATTTTCT
Found at i:19088 original size:17 final size:17
Alignment explanation
Indices: 19059--19098 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
19049 ATTAAATGAA
*
19059 TTTTTTTCGTTTTCT-T
1 TTTTTTTCATTTTCTAT
19075 TTTTTTTCAATTTTCTAT
1 TTTTTTTC-ATTTTCTAT
19093 TTTTTT
1 TTTTTT
19099 ATTCCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 6 0.29
18 7 0.33
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTTTCATTTTCTAT
Found at i:19292 original size:31 final size:30
Alignment explanation
Indices: 19217--19295 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
19207 TACCCGGTTA
* *
19217 ACTCCACTTAAGGGACCAAATTACATATTT
1 ACTCCACTTGAGGGACCAAAATACATATTT
* * *
19247 -TTTCACTTGGGGGACCAAAATAC-TAGTTT
1 ACTCCACTTGAGGGACCAAAATACATA-TTT
19276 CACTCCACTTGAGGGACCAA
1 -ACTCCACTTGAGGGACCAA
19296 TTCTGTACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 2 0.05
29 21 0.55
31 15 0.39
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (30 bp):
ACTCCACTTGAGGGACCAAAATACATATTT
Found at i:21878 original size:2 final size:2
Alignment explanation
Indices: 21871--21902 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21861 CTACCCTCAA
21871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21903 TCTCCCTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28106 original size:36 final size:36
Alignment explanation
Indices: 28039--28123 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
28029 CTCAACTTGT
* *
28039 AAAGGCGTGAT---GAAGGCCTGTAAACTTCATTGA
1 AAAGGCGTGATGAAGAAGGCCCGTAAACTCCATTGA
*
28072 AAAGGCGTGATGAAGAAGGCCCGTGAACTCCATTGA
1 AAAGGCGTGATGAAGAAGGCCCGTAAACTCCATTGA
*
28108 AACGGCGTGATGAAGA
1 AAAGGCGTGATGAAGA
28124 CCCGCAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 11 0.24
36 34 0.76
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (36 bp):
AAAGGCGTGATGAAGAAGGCCCGTAAACTCCATTGA
Done.