Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011821.1 Corchorus olitorius cultivar O-4 contig11854, 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: 24672
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Found at i:1355 original size:18 final size:18
Alignment explanation
Indices: 1332--1403 Score: 108
Period size: 18 Copynumber: 4.0 Consensus size: 18
1322 GTGTTAAGGA
* *
1332 TCATTCAAAGTTAATTTC
1 TCATTCAAAGTTAGTTCC
1350 TCATTCAAAGTTAGTTCC
1 TCATTCAAAGTTAGTTCC
*
1368 TCATTCAAAGTCAGTTCC
1 TCATTCAAAGTTAGTTCC
*
1386 GCATTCAAAGTTAGTTCC
1 TCATTCAAAGTTAGTTCC
1404 CTAGGATTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (18 bp):
TCATTCAAAGTTAGTTCC
Found at i:2690 original size:21 final size:21
Alignment explanation
Indices: 2664--2705 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2654 GCACCTTAGG
*
2664 CAACTCAGATGAGGTTGAAAC
1 CAACTCAGATGAGCTTGAAAC
*
2685 CAACTCCGATGAGCTTGAAAC
1 CAACTCAGATGAGCTTGAAAC
2706 TTCTTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
CAACTCAGATGAGCTTGAAAC
Found at i:9058 original size:21 final size:21
Alignment explanation
Indices: 9032--9073 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9022 GCACCTTAGG
9032 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
9053 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
9074 TTCTTTGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:10602 original size:16 final size:16
Alignment explanation
Indices: 10570--10614 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
10560 AATTTTGGGT
10570 ACCCGAACCCGAAAATG
1 ACCCGAACCC-AAAATG
*
10587 ACCCAAACCCAAAATG
1 ACCCGAACCCAAAATG
10603 ACCCGAACCCAA
1 ACCCGAACCCAA
10615 TCAACCTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.44, C:0.40, G:0.11, T:0.04
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:11602 original size:2 final size:2
Alignment explanation
Indices: 11591--11632 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
11581 GAAAGTCTAT
*
11591 TA TA -A TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
11633 AATCAGAGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16017 original size:33 final size:33
Alignment explanation
Indices: 15980--16474 Score: 147
Period size: 33 Copynumber: 15.6 Consensus size: 33
15970 GGTAATAATA
* *
15980 ATTTGGTAATTAAATTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
* * ** **
16013 ATTTGGCAATCAAAGTAAAAAGAAAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAG-AGTAAAATGGT
* *
16047 ATTGGGTAACTAAAGT--------T-AAATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
* * *
16071 ATTTGGTAATTAAAGTTAAAAGAGTAAATTGCT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
* ** **
16104 ATTTGGTAATCAAAGTAAAAAGAAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
** *
16137 ATTTGGTAATTAAAACAAAAAGAGTAATATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
*** ** **
16170 AAAAAGG-AA--AAAGTGAAATTTGGTAAGTAAAATGAA
1 -ATTTGGTAATTAAAGT-AAA--AAG--AGTAAAATGGT
* *
16206 ATTTGG----T-AACT--AAA-A-TTAAATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
* *
16230 ATTTGGTAATTAAAGTAGAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
* * **
16263 ATTTGGTAATCAAAGTAAAAA-AGAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAG-TAAAATGGT
* ** * **
16296 ATTTGGCAATTAAAACAAGAAGAGTAATAAAAG-
1 ATTTGGTAATTAAAGTAAAAAGAGTAA-AATGGT
16329 A----G--ATTAAAGTAAAAAGAGTAAAATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
** * ** * *
16356 AAAAT-GAAATT-CGGTAACTAA-AGTTAAATGGT
1 -ATTTGGTAATTAAAGTAA-AAAGAGTAAAATGGT
* * *
16388 ATTCGGTAATTAAAATAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
* * *
16421 ATTTGGTAAATATAGTAAAAAGTGTAAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAA-TGGT
*
16455 ATTTGATAATTAAAG-AAAAA
1 ATTTGGTAATTAAAGTAAAAA
16475 TTGGTAAAAA
Statistics
Matches: 322, Mismatches: 99, Indels: 82
0.64 0.20 0.16
Matches are distributed among these distances:
24 31 0.10
25 1 0.00
26 3 0.01
27 16 0.05
28 2 0.01
29 4 0.01
30 1 0.00
31 8 0.02
32 28 0.09
33 175 0.54
34 42 0.13
35 3 0.01
36 8 0.02
ACGTcount: A:0.51, C:0.03, G:0.19, T:0.28
Consensus pattern (33 bp):
ATTTGGTAATTAAAGTAAAAAGAGTAAAATGGT
Found at i:16067 original size:24 final size:24
Alignment explanation
Indices: 16040--16090 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
16030 AAAAGAAAAA
16040 AAATGAAATTGGGTAACTAAAGTT
1 AAATGAAATTGGGTAACTAAAGTT
** * *
16064 AAATGGTATTTGGTAATTAAAGTT
1 AAATGAAATTGGGTAACTAAAGTT
16088 AAA
1 AAA
16091 AGAGTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (24 bp):
AAATGAAATTGGGTAACTAAAGTT
Found at i:16081 original size:91 final size:90
Alignment explanation
Indices: 15980--16150 Score: 281
Period size: 91 Copynumber: 1.9 Consensus size: 90
15970 GGTAATAATA
*
15980 ATTTGGTAATTAAA-TTAAAAAGAGTAAATTGGTATTTGGCAATCAAAGTAAAAAGAAAAAAAAT
1 ATTTGGTAATTAAAGTT-AAAAGAGTAAATTGCTATTTGGCAATCAAAGTAAAAAG-AAAAAAAT
16044 GAAATTGGGTAACTAAAGTTAAATGGT
64 GAAATTGGGTAACTAAAGTTAAATGGT
*
16071 ATTTGGTAATTAAAGTTAAAAGAGTAAATTGCTATTTGGTAATCAAAGTAAAAAGAAAAAAATGA
1 ATTTGGTAATTAAAGTTAAAAGAGTAAATTGCTATTTGGCAATCAAAGTAAAAAGAAAAAAATGA
* *
16136 AATTTGGTAATTAAA
66 AATTGGGTAACTAAA
16151 ACAAAAAGAG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
90 23 0.31
91 50 0.67
92 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.30
Consensus pattern (90 bp):
ATTTGGTAATTAAAGTTAAAAGAGTAAATTGCTATTTGGCAATCAAAGTAAAAAGAAAAAAATGA
AATTGGGTAACTAAAGTTAAATGGT
Found at i:16145 original size:24 final size:24
Alignment explanation
Indices: 16118--16195 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
16108 GGTAATCAAA
16118 GTAAAAAGAAAAAAATGAAATTTG
1 GTAAAAAGAAAAAAATGAAATTTG
* *
16142 GTAATTAAA-ACAAAAAGA-GTAATATG
1 GTAA--AAAGA-AAAAA-ATGAAATTTG
* *
16168 GTAAAAAGGAAAAAGTGAAATTTG
1 GTAAAAAGAAAAAAATGAAATTTG
16192 GTAA
1 GTAA
16196 GTAAAATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
24 22 0.52
25 1 0.02
26 18 0.43
27 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.19, T:0.22
Consensus pattern (24 bp):
GTAAAAAGAAAAAAATGAAATTTG
Found at i:16207 original size:19 final size:19
Alignment explanation
Indices: 16178--16226 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
16168 GTAAAAAGGA
*
16178 AAAAGTGAAATTTGGTAAGT
1 AAAA-TGAAATTTGGTAACT
16198 AAAATGAAATTTGGTAACT
1 AAAATGAAATTTGGTAACT
*
16217 AAAATTAAAT
1 AAAATGAAAT
16227 GGTATTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (19 bp):
AAAATGAAATTTGGTAACT
Found at i:16419 original size:158 final size:157
Alignment explanation
Indices: 16039--16442 Score: 541
Period size: 159 Copynumber: 2.6 Consensus size: 157
16029 AAAAAGAAAA
* * *
16039 AAAATGAAATTGGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTTAAAAGAGTAAATTGCT
1 AAAATGAAATTCGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* *
16104 ATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGTAATTAAAACAAAAAGAGTAATATGG
66 ATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATAAGG
* *
16169 TAAAAAGGAAAAAGTGAAATTTGGTAAGT
131 TAAAAAGGAAAAAGAGAAATATGG--AGT
* * *
16198 AAAATGAAATTTGGTAACTAAAATTAAATGGTATTTGGTAATTAAAGTAGAAAGAGTAAATTGGT
1 AAAATGAAATTCGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
*
16263 ATTTGGTAATCAAAGTAAAAA-AGAAAAAATGAAATTTGGCAATTAAAACAAGAAGAGTAATAAA
66 ATTTGGTAATCAAAGTAAAAAGA-AAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAAT--A
* *
16327 AGAG-ATTAAAGTAAAAAGAGTAAA-AT-G-GT
128 AG-GTA-AAAAGGAAAAAGAG-AAATATGGAGT
* *
16356 AAAATGAAATTCGGTAACTAAAGTTAAATGGTATTCGGTAATTAAAATAAAAAGAGTAAATTGGT
1 AAAATGAAATTCGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
*
16421 ATTTGGTAAAT-ATAGTAAAAAG
66 ATTTGGT-AATCAAAGTAAAAAG
16443 TGTAAAATTG
Statistics
Matches: 219, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
158 79 0.36
159 120 0.55
161 4 0.02
162 13 0.06
163 3 0.01
ACGTcount: A:0.51, C:0.03, G:0.19, T:0.27
Consensus pattern (157 bp):
AAAATGAAATTCGGTAACTAAAGTTAAATGGTATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
ATTTGGTAATCAAAGTAAAAAGAAAAAAATGAAATTTGGCAATTAAAACAAAAAGAGTAATAAGG
TAAAAAGGAAAAAGAGAAATATGGAGT
Found at i:16482 original size:34 final size:33
Alignment explanation
Indices: 16413--16529 Score: 94
Period size: 34 Copynumber: 3.3 Consensus size: 33
16403 TAAAAAGAGT
* * *
16413 AAATTGGTATTTGGTAAATATAGTAAAAA-GTGTA
1 AAATTGGTATTTGATAATTAAAG-AAAAATG-GTA
16447 AAATTGGTATTTGATAATTAAAGAAAAATTGGTAAA
1 AAATTGGTATTTGATAATTAAAGAAAAA-TGGT--A
*
16483 AAGATATGGTATTT-AGTAATTAAAGGAAAAAGGGTA
1 AA-AT-TGGTATTTGA-TAATTAAA-GAAAAATGGTA
*
16519 AAATTGATATT
1 AAATTGGTATT
16530 CAGTAATCAG
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
33 5 0.07
34 28 0.40
35 3 0.04
36 6 0.09
37 3 0.04
38 19 0.27
39 6 0.09
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (33 bp):
AAATTGGTATTTGATAATTAAAGAAAAATGGTA
Found at i:17434 original size:23 final size:23
Alignment explanation
Indices: 17404--17468 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
17394 AACTTGAATG
17404 ACTCGACTATTCAACCCGAAATC
1 ACTCGACTATTCAACCCGAAATC
17427 ACTCGACTATTCAACCCGAAATC
1 ACTCGACTATTCAACCCGAAATC
*
17450 AC-CTGACTATTAAACCCGA
1 ACTC-GACTATTCAACCCGA
17469 GGTTCAAACC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.35, C:0.34, G:0.09, T:0.22
Consensus pattern (23 bp):
ACTCGACTATTCAACCCGAAATC
Done.