Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019878.1 Corchorus olitorius cultivar O-4 contig19911, 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: 3778
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Found at i:284 original size:153 final size:154
Alignment explanation
Indices: 4--574 Score: 700
Period size: 153 Copynumber: 3.7 Consensus size: 154
1 GGC
* * * *
4 CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA-CCTCAAAGCTTTTCATTCCATTGTTT
1 CCATTAGTGACGTTTCGAATCGTCTTCGATTTGGAAAACCCTCAATGCTTTTCTTTCCATTGTTT
* *
68 ATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
66 AAGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
*
133 CTTGTTATTTTGTG-CTTTCGGGG
131 CTTGTTATTTTGTGCCTATCGGGG
* *
156 CCAATTAGT-TCTGTTTCGAATCGTCTTCGATTTGG-AAACCCTCGATGAC-TTTCTTTCCATTG
1 CC-ATTAGTGAC-GTTTCGAATCGTCTTCGATTTGGAAAACCCTCAATG-CTTTTCTTTCCATTG
*
218 TTTAAGGCCTAACTATAATCATTTT-GTTGAGATTAGTCCACTGTGAAGTTTTTAGCACATTTGG
63 TTTAAGGCCTAACTATAATCATTTTAG-TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG
**
282 AACACTTGTTATTTTGTGCCTATCAGGAT
127 AACACTTGTTATTTTGTGCCTATC-GGGG
* *
311 CCATTAGTGACGTTTTTGAATCGTCTTCGATATGGAAAAAATCCCTCAATGCTTTTCTTTCCATT
1 CCATTAGTGACG-TTTCGAATCGTCTTCGATTTGG--AAAA-CCCTCAATGCTTTTCTTTCCATT
** * * * * *
376 GTTTTTGGGGCTAACTATATTTATTTTAGAGAGA--AGTCCACTGTGAAGGTTTTAGCTCATTTG
62 G-TTTAAGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
* *
439 GAACACCTGTTATTTT-TGGCCTATCAGGGC
126 GAACACTTGTTATTTTGT-GCCTATC-GGGG
*
469 CCATTAGTGACGTTTCGAATCGTCTTCGATTTGG-AAACCCT-AGATGCATTTCTTTCCATTGTT
1 CCATTAGTGACGTTTCGAATCGTCTTCGATTTGGAAAACCCTCA-ATGCTTTTCTTTCCATTGTT
*
532 AAAGGCCTAACTATAATCA-TTT-GTTGAGATTAGTCCACTGTGA
65 TAAGGCCTAACTATAATCATTTTAG-TGAGATTAGTCCACTGTGA
575 TACGAATCTA
Statistics
Matches: 362, Mismatches: 36, Indels: 41
0.82 0.08 0.09
Matches are distributed among these distances:
150 1 0.00
151 7 0.02
152 23 0.06
153 156 0.43
154 15 0.04
155 25 0.07
157 21 0.06
158 68 0.19
159 21 0.06
160 24 0.07
161 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
CCATTAGTGACGTTTCGAATCGTCTTCGATTTGGAAAACCCTCAATGCTTTTCTTTCCATTGTTT
AAGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
CTTGTTATTTTGTGCCTATCGGGG
Found at i:1397 original size:21 final size:22
Alignment explanation
Indices: 1373--1464 Score: 129
Period size: 21 Copynumber: 4.4 Consensus size: 22
1363 CTTAGGCATT
*
1373 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAACCTTGC
*
1394 TCCAATGATCTTGGAACCTT-C
1 TCCAATGAGCTTGGAACCTTGC
*
1415 TCCAATGAGCTTGG-AGCTTGC
1 TCCAATGAGCTTGGAACCTTGC
1436 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTTGC
1457 TCCAATGA
1 TCCAATGA
1465 ACTTCTAGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.06
21 60 0.92
22 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (22 bp):
TCCAATGAGCTTGGAACCTTGC
Found at i:3341 original size:33 final size:31
Alignment explanation
Indices: 3268--3413 Score: 123
Period size: 33 Copynumber: 4.5 Consensus size: 31
3258 GCTATGATCA
** *
3268 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
3300 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
3333 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * *
3366 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC
*
3399 ATCTAAAACAGATTT
1 A-CCAAAACAGATTT
3414 AGAATTACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
32 7 0.07
33 79 0.84
34 8 0.09
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Done.