Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022339.1 Corchorus olitorius cultivar O-4 contig22372, 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: 14750
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:327 original size:65 final size:65
Alignment explanation
Indices: 246--376 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
236 TATAACTGAC
*
246 AACTTTTTCAAGAAATTGCTTAACCAAAGAAGTTAAATATCTAAGGGGGTGTTTGGTTGGGGGTG
1 AACTTTTTCAAGAAATTGCTTAACCAAAGAAGTTAAATATCTAAGGGGGTGTTTGGTTGGAGGTG
311 AACTTTTTCAAGAAATTGCTTAACCAAAGAAGTTAAATATCTAAGGGGGTGTTTGGTTGGAGGTG
1 AACTTTTTCAAGAAATTGCTTAACCAAAGAAGTTAAATATCTAAGGGGGTGTTTGGTTGGAGGTG
376 A
1 A
377 TCACCTGTGG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (65 bp):
AACTTTTTCAAGAAATTGCTTAACCAAAGAAGTTAAATATCTAAGGGGGTGTTTGGTTGGAGGTG
Found at i:2170 original size:93 final size:94
Alignment explanation
Indices: 2033--2216 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 94
2023 CAACTAAGTA
2033 ACTTTAATTGGAATTATTATTTGAATGTAATGTATATATAACGGTGAGAAATTATTAAAAGGAT-
1 ACTTTAATTGGAATTATTATTTGAATGTAATGTATATATAACGGTGAGAAATTATTAAAAGGATA
*
2097 AAAAAGTATTAAAGACCCAATTGTAATTC
66 AAAAAGGATTAAAGACCCAATTGTAATTC
* *
2126 ACTTTAATTGGAATTATTATTTGAATGTAATGTATATATAACGGTGAGGAATTATTGAAAGGATA
1 ACTTTAATTGGAATTATTATTTGAATGTAATGTATATATAACGGTGAGAAATTATTAAAAGGATA
* *
2191 AAAAAGGGTTGAAGACCCAATTGTAA
66 AAAAAGGATTAAAGACCCAATTGTAA
2217 ATCATTATAT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
93 62 0.73
94 23 0.27
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (94 bp):
ACTTTAATTGGAATTATTATTTGAATGTAATGTATATATAACGGTGAGAAATTATTAAAAGGATA
AAAAAGGATTAAAGACCCAATTGTAATTC
Found at i:3824 original size:2 final size:2
Alignment explanation
Indices: 3817--3897 Score: 56
Period size: 2 Copynumber: 41.0 Consensus size: 2
3807 CCAAAAATAC
* * * * *
3817 AT AT AT AT AT AT AT AT GT AC AC AT AC AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
3859 AT AT GT AT GT AT -T AT GT AT AT AG AT AC AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3898 GACTATTTTT
Statistics
Matches: 58, Mismatches: 20, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4970 original size:29 final size:30
Alignment explanation
Indices: 4931--5008 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
4921 ACTTGTACGG
*
4931 TTTGGAC-TTTTATCCCTTAAACT-TTAAT
1 TTTGGACGTTTTATCCCTTAAACTCTCAAT
* *
4959 TTTGGACGTTTTGTCCCCTAAACTCTCAAT
1 TTTGGACGTTTTATCCCTTAAACTCTCAAT
4989 TTTGGACGTTTTAGTCCCTT
1 TTTGGACGTTTTA-TCCCTT
5009 TCGGATGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 7 0.17
29 14 0.33
30 16 0.38
31 5 0.12
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (30 bp):
TTTGGACGTTTTATCCCTTAAACTCTCAAT
Found at i:12590 original size:151 final size:150
Alignment explanation
Indices: 12285--12728 Score: 746
Period size: 151 Copynumber: 2.9 Consensus size: 150
12275 GAAGTTTCAC
* *
12285 CATTAAGGTATAAATTTTGTCTTGAAATAATGTTTGTTTTAAGTTGTGTTCAAATGGTGGATTTT
1 CATTAAGGTATACATTTTGTCTTGAAATAATGTTTGTTTTATGTTGTGTTCAAATGGTGGATTTT
*
12350 TTAGAGCATTATGTTGGG-CTTGACTCATTTAAATGATTTGGTATTAATTCTTTCAAATGAATGG
66 TTAGAGCATTATGATGGGTCTTGACTCATTT-AATGATTTGGTATTAATTCTTTCAAATGAATGG
12414 TAGTACGTTGGTGGATTCTTT
130 TAGTACGTTGGTGGATTCTTT
*
12435 CATTAAGGTATACATTTTGTCTTGAAATAATGTTTGTTTTATGTTGTGTTCAGATGGTGGATTTT
1 CATTAAGGTATACATTTTGTCTTGAAATAATGTTTGTTTTATGTTGTGTTCAAATGGTGGATTTT
* *
12500 TTAGAGCATTATGGTGGGTCTTGACTCATTTCAATGATTTGGTATCAATTCTTTCAAATGAATGG
66 TTAGAGCATTATGATGGGTCTTGACTCATTT-AATGATTTGGTATTAATTCTTTCAAATGAATGG
12565 TAGTACGTTGGTGGATTCTTT
130 TAGTACGTTGGTGGATTCTTT
* *
12586 CATTAAGGTATACATTTTGTCTTGAAATCATGTTTGTTTTATGTTTTGTTCAAATGGTGGATTTT
1 CATTAAGGTATACATTTTGTCTTGAAATAATGTTTGTTTTATGTTGTGTTCAAATGGTGGATTTT
*
12651 TTAGAGCATTATTATGATGGGTCTTCACTCATTTAAGTGATTTGGTATTAATTCTTTCAAATGAA
66 TTAGAGC---ATTATGATGGGTCTTGACTCATTTAA-TGATTTGGTATTAATTCTTTCAAATGAA
12716 TGGTAGTACGTTG
127 TGGTAGTACGTTG
12729 AAACATGGTA
Statistics
Matches: 277, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
150 79 0.29
151 134 0.48
153 2 0.01
154 62 0.22
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (150 bp):
CATTAAGGTATACATTTTGTCTTGAAATAATGTTTGTTTTATGTTGTGTTCAAATGGTGGATTTT
TTAGAGCATTATGATGGGTCTTGACTCATTTAATGATTTGGTATTAATTCTTTCAAATGAATGGT
AGTACGTTGGTGGATTCTTT
Done.