Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020287.1 Corchorus olitorius cultivar O-4 contig20320, 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: 26542
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:6651 original size:220 final size:220
Alignment explanation
Indices: 6269--6704 Score: 863
Period size: 220 Copynumber: 2.0 Consensus size: 220
6259 TCAAATAGGA
6269 GCAAACCGTCAAATTGGGGCAAAACCTTTTAGAGAGTGGGAAGAAGGCGCCGTGAGCACTAACGG
1 GCAAACCGTCAAATTGGGGCAAAACCTTTTAGAGAGTGGGAAGAAGGCGCCGTGAGCACTAACGG
6334 CAGCTAACGTTTACTAAAAGATTCTACCCTTATTTGTAAAATACGAAAACGTTTGACCATTATTT
66 CAGCTAACGTTTACTAAAAGATTCTACCCTTATTTGTAAAATACGAAAACGTTTGACCATTATTT
6399 GGTTATCCCTTTCATTTGTACATAATTTTTTTATTCAAATTATTTTGATTTTATTTTGTTTTCTT
131 GGTTATCCCTTTCATTTGTACATAATTTTTTTATTCAAATTATTTTGATTTTATTTTGTTTTCTT
6464 TTCAAAGAAAAAAATTAAAATTGGG
196 TTCAAAGAAAAAAATTAAAATTGGG
6489 GCAAACCGTCAAATTGGGGCAAAACCTTTTAGAGAGTGGGAAGAAGGCGCCGTGAGCACTAACGG
1 GCAAACCGTCAAATTGGGGCAAAACCTTTTAGAGAGTGGGAAGAAGGCGCCGTGAGCACTAACGG
6554 CAGCTAACGTTTACTAAAAGATTCTACCCTTATTTGTAAAATACGAAAACGTTTGACCATTATTT
66 CAGCTAACGTTTACTAAAAGATTCTACCCTTATTTGTAAAATACGAAAACGTTTGACCATTATTT
*
6619 GGTTATCCCTTTCATTTGTACATAATTTTTTTATTCAAATTCTTTTGATTTTATTTTGTTTTCTT
131 GGTTATCCCTTTCATTTGTACATAATTTTTTTATTCAAATTATTTTGATTTTATTTTGTTTTCTT
6684 TTCAAAGAAAAAAATTAAAAT
196 TTCAAAGAAAAAAATTAAAAT
6705 CACTTAAGAA
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 215 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (220 bp):
GCAAACCGTCAAATTGGGGCAAAACCTTTTAGAGAGTGGGAAGAAGGCGCCGTGAGCACTAACGG
CAGCTAACGTTTACTAAAAGATTCTACCCTTATTTGTAAAATACGAAAACGTTTGACCATTATTT
GGTTATCCCTTTCATTTGTACATAATTTTTTTATTCAAATTATTTTGATTTTATTTTGTTTTCTT
TTCAAAGAAAAAAATTAAAATTGGG
Found at i:9872 original size:46 final size:46
Alignment explanation
Indices: 9803--9892 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
9793 GGATTTCAAG
*
9803 TTCCATCAATTAAAATCCCTTAATGATAAGGAAAACCCA-AAAGTCA
1 TTCCATCAATTAAAATCCCTTAATGACAA-GAAAACCCAGAAAGTCA
* * * * *
9849 TTCCATCCATTAATATTCTTTAATGACAAGAAAAGCCAGAAAGT
1 TTCCATCAATTAAAATCCCTTAATGACAAGAAAACCCAGAAAGT
9893 TATATGGGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 8 0.22
46 29 0.78
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (46 bp):
TTCCATCAATTAAAATCCCTTAATGACAAGAAAACCCAGAAAGTCA
Found at i:15119 original size:18 final size:18
Alignment explanation
Indices: 15096--15135 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
15086 TCATGATTTC
15096 AAAACAATGCAGCGCATA
1 AAAACAATGCAGCGCATA
*
15114 AAAACAATGCAGGGCATA
1 AAAACAATGCAGCGCATA
15132 AAAA
1 AAAA
15136 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAACAATGCAGCGCATA
Found at i:17485 original size:15 final size:16
Alignment explanation
Indices: 17452--17491 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
17442 TTGCTTCGCT
17452 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
17468 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
17483 TTGCTTTCT
1 TTGTTTTCT
17492 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:23503 original size:18 final size:20
Alignment explanation
Indices: 23467--23503 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
23457 TGTACAGACT
23467 AATTAGTAGGGATTTGACAG
1 AATTAGTAGGGATTTGACAG
23487 AATTAG-AGGGA-TTGACA
1 AATTAGTAGGGATTTGACA
23504 ACCTAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (20 bp):
AATTAGTAGGGATTTGACAG
Found at i:24168 original size:32 final size:32
Alignment explanation
Indices: 24128--24412 Score: 419
Period size: 32 Copynumber: 8.9 Consensus size: 32
24118 ATTAAAGACA
* * *
24128 AACGCCACAGATTGGTGGCGTTTTCATCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* *
24160 TACGCCACAAATTAGTGGCGTTTTTTTC-AAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
24191 AACGCCACAAATTAGTGGCTTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
24223 TACGCCACAAATTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * *
24255 TACGCCACAAATTAGTGGCATTTTCTTTAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
24287 AACGCCACAAATTAGTGGCGTTTTCTTTAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
24319 AACGCCACAAATTAGTGGCGTTTTCTTTAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
24351 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
** * *
24383 AACGCCACTGATTTGTGGCGTTTTATTCAA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAA
24413 TAAACACCAT
Statistics
Matches: 233, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
31 28 0.12
32 205 0.88
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (32 bp):
AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
Found at i:25222 original size:33 final size:33
Alignment explanation
Indices: 25106--25222 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 33
25096 CAATCTCATT
* * *
25106 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATGCGAGCCAGCTC-TTG
* *
25139 TCTTCTCTCTTCTTCAACT-CGAGCCAGCTCCTG
1 TCTTCTATCTTCTTCAA-TGCGAGCCAGCTCTTG
*
25172 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATGCGAGCCAGCTCTTG
*
25205 TCTTCTTTCTTCTTCAAT
1 TCTTCTATCTTCTTCAAT
25223 TCTTGCAAGC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.03
33 70 0.97
ACGTcount: A:0.14, C:0.32, G:0.14, T:0.41
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATGCGAGCCAGCTCTTG
Found at i:25234 original size:33 final size:33
Alignment explanation
Indices: 25106--25238 Score: 133
Period size: 33 Copynumber: 4.0 Consensus size: 33
25096 CAATCTCATT
* ** *
25106 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTC-TTG
* * *
25139 TCTTCTCTCTTCTTCAACTCGAGCCAGCTCCTG
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
* *
25172 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
* ** *
25205 TCTTCTTTCTTCTTCAATTCTTGCAAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
25238 T
1 T
25239 TGCCTTTCTA
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 1 0.01
33 82 0.99
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
Done.