Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015459.1 Corchorus olitorius cultivar O-4 contig15492, 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: 20504
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:786 original size:337 final size:331
Alignment explanation
Indices: 51--835 Score: 969
Period size: 332 Copynumber: 2.4 Consensus size: 331
41 ATATATATAT
* * * * * *
51 ATATATAATTTAACGTCAAAAAGATTGGAGGACTTTACACGCTTTTAATATCGTTTT-TCATATT
1 ATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCTTATTTT
* * * *
115 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGAGTCAGATGCTTGTAAAAACAAATTCTTAAA
66 TTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* * * * *
180 TCCAATGTGGATGAGATTTGATTATATGAATATGGATATCTCAAGGAGTCTTGGCGTCAAAAATC
131 TCCAATGTGGATGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATC
* ** *
245 ATGCAAAACTGAGCCGGGATGAGAATGCTTTTTTTAGCCAAAAACTGTGATGGTTGTTACACGAT
196 ATACAAAACTGAGCCGGGATGAGAACACTATTTTTAGCCAAAAACTGTGATGGTTGTTACACGAT
* * *
310 TTCGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTACCTCAATTTATGGCTAAAATACTCA
261 TTCGGCTAAAATTTTGCAAAAATTGATCACAAAAATATTACCTCAATTTATGGCTAAAATACTCA
375 TAAAAA
326 TAAAAA
* * * * * *
381 ATATATAATTCAACT-CCAAAAAGATTGAAGGGCCTTTGACG-TTTCTAATATCATTTTTCCTA-
1 ATATATAATTCAA-TGCCAAAAAGATTGGAGGACTTTTCACGCTTT-TAATATC-GTTTTCTTAT
* *
443 TTTTTTCCAAATTAATTTTTAATTAAATCGAAACCAAGATTCAGATGCTCGTAAAAACAAATCCT
63 TTTTTTCTAAATTAATTTCTAATTAAATCGAAA-CAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * *
508 TAGATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGCCAAA
127 TAAATCCAATGTGGATGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAA
* * * *
573 AATCATACAAAATTGAGTCGGGTCCCTGA-AACAC-ATTTTTAGCCTAAAACTGTGATGGTTTGT
192 AATCATACAAAACTGAGCCGGG---ATGAGAACACTATTTTTAGCCAAAAACTGTGATGG-TTG-
*
636 TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CACAAAAGAT-TT-CTTCTCAATTTTT
252 T--TACACGATTTCGGCTAAAATTTTGCAAAAATTGATCACAAAA-ATATTAC--CTCAATTTAT
*
698 GGCTAAAATATTCAT-AAAA
312 GGCTAAAATACTCATAAAAA
* * *
717 ATATATAATTCAATGCCAAAAAGAGTGGAGGTCTTTTTACGCTTTTAATATCGTATTTCTTATTT
1 ATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGT-TTTCTTATTT
*
782 TTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
65 TTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
836 AAAAATTTTA
Statistics
Matches: 386, Mismatches: 50, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
329 3 0.01
330 39 0.10
331 33 0.09
332 104 0.27
333 22 0.06
334 6 0.02
335 7 0.02
336 80 0.21
337 92 0.24
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (331 bp):
ATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCTTATTTT
TTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
TCCAATGTGGATGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATC
ATACAAAACTGAGCCGGGATGAGAACACTATTTTTAGCCAAAAACTGTGATGGTTGTTACACGAT
TTCGGCTAAAATTTTGCAAAAATTGATCACAAAAATATTACCTCAATTTATGGCTAAAATACTCA
TAAAAA
Found at i:1240 original size:15 final size:16
Alignment explanation
Indices: 1222--1251 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1212 ATAAATAATA
1222 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
1237 ATATTATAATCTAAA
1 ATATTATAATCTAAA
1252 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:3059 original size:201 final size:200
Alignment explanation
Indices: 2690--3069 Score: 569
Period size: 201 Copynumber: 1.9 Consensus size: 200
2680 TAATTGCATG
2690 TGCTAAATTGCTAAAACACTTGGCAAGAAGAACATAACAATGTGGCATTCATGCATACATATTTG
1 TGCTAAATTGCTAAAACACTTGGCAAGAAGAACATAACAATGTGGCATTCAT-CATACATATTTG
2755 AAGAACACTTGACAAGTGAAATATTCATGTGATGAAATCCCAAATATGATTCATGTGAGGCTTGG
65 AAGAACACTTGACAAGTGAAATATTCATGTGATGAAATCCCAAATATGATTCATGTGAGGCTTGG
2820 CAAAAAGCCAACAAGAACAAAAATGATGTTAAAGTAACCTCAAAACCTAGTTTGGCTGAGTTGCA
130 CAAAAAGCCAACAAGAACAAAAA-GATG-T-AAGTAACCTCAAAACCTAGTTTGGCTGAGTTGCA
2885 GCCATTGCA
192 GCCATTGCA
* *
2894 TGCT-AATTGCTAATAACACTTGGCAAGAAGAACA-AAGCAATGTGGCATTCAT-ATGCA-CTTT
1 TGCTAAATTGCTAA-AACACTTGGCAAGAAGAACATAA-CAATGTGGCATTCATCATACATATTT
2955 GAAGATA-ACTTGACAAGTGAAATATTCATGTGATGAAAAATCCCAAATATGTATGATTCATGTG
64 GAAGA-ACACTTGACAAGTGAAATATTCATGTGATG--AAATCCC-AA-A--TATGATTCATGTG
3019 AGGCTTGGCAAAAAGCCAACAAGAAC-AAAA-ATG-AAGTAACCTCAAAACCTA
122 AGGCTTGGCAAAAAGCCAACAAGAACAAAAAGATGTAAGTAACCTCAAAACCTA
3070 AAGCATGCAA
Statistics
Matches: 165, Mismatches: 2, Indels: 21
0.88 0.01 0.11
Matches are distributed among these distances:
201 54 0.33
202 5 0.03
203 18 0.11
204 44 0.27
205 1 0.01
206 4 0.02
207 39 0.24
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (200 bp):
TGCTAAATTGCTAAAACACTTGGCAAGAAGAACATAACAATGTGGCATTCATCATACATATTTGA
AGAACACTTGACAAGTGAAATATTCATGTGATGAAATCCCAAATATGATTCATGTGAGGCTTGGC
AAAAAGCCAACAAGAACAAAAAGATGTAAGTAACCTCAAAACCTAGTTTGGCTGAGTTGCAGCCA
TTGCA
Found at i:7000 original size:10 final size:10
Alignment explanation
Indices: 6976--7011 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
6966 ATTGCCATCT
6976 CTCTG-TTTC
1 CTCTGTTTTC
6985 CTCTGTTTTC
1 CTCTGTTTTC
*
6995 CCCTGTTTTC
1 CTCTGTTTTC
7005 CTCTGTT
1 CTCTGTT
7012 CCTTAGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.00, C:0.33, G:0.11, T:0.56
Consensus pattern (10 bp):
CTCTGTTTTC
Found at i:8446 original size:15 final size:16
Alignment explanation
Indices: 8411--8448 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
8401 GCCTAAGGGT
8411 ATTTCTTCTATTTACC
1 ATTTCTTCTATTTACC
* *
8427 TTTTCTT-TATTTTCC
1 ATTTCTTCTATTTACC
8442 ATTTCTT
1 ATTTCTT
8449 AAAACATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTCTTCTATTTACC
Found at i:15634 original size:29 final size:29
Alignment explanation
Indices: 15600--15698 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
15590 AGAAAGCATA
15600 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
* ** * **
15629 TCCTTATTTAGG-CATTTTGGTAAACG-TTAGG
1 CCCTTATTT-GGCCA-AAT--TAAAAGATCGGG
15660 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
15689 CCCTTATTTG
1 CCCTTATTTG
15699 AGATTTTGGT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 5 0.10
29 23 0.44
30 6 0.12
31 13 0.25
32 5 0.10
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:15694 original size:60 final size:59
Alignment explanation
Indices: 15600--15728 Score: 224
Period size: 60 Copynumber: 2.2 Consensus size: 59
15590 AGAAAGCATA
*
15600 CCCTTATTTGGCCAAATTAAAAGATCGGGTCCTTATTT-AGGCATTTTGGTAAACGTTAGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGA-G-ATTTTGGTAAACGTTAGG
15660 CCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGATTTTGGTAAACGTTAGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGATTTTGGTAAACGTTAGG
15719 CCCTTATTTG
1 CCCTTATTTG
15729 AGCAATTAGC
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
59 28 0.42
60 38 0.57
61 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (59 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGATTTTGGTAAACGTTAGG
Done.