Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019275.1 Corchorus olitorius cultivar O-4 contig19308, 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: 43267
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2416 original size:2 final size:2
Alignment explanation
Indices: 2384--2525 Score: 54
Period size: 2 Copynumber: 75.0 Consensus size: 2
2374 TTAAAGTAAT
* *
2384 TA TA AA TA TA -A TA CTA TT TA T- TA TA TA -A TA TA T- TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
2423 TA TA TA TA AA TGA TT TA TG T- TT TC TGA TA TA TT TA TA AA T- TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* *
2465 TA -A TA TA TA TA TA AA TA TT TA TA -A TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2504 -A AA AA TA TT TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
2526 AAAATCCTAA
Statistics
Matches: 104, Mismatches: 22, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
1 11 0.11
2 88 0.85
3 5 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2485 original size:28 final size:30
Alignment explanation
Indices: 2451--2526 Score: 113
Period size: 28 Copynumber: 2.6 Consensus size: 30
2441 GTTTTCTGAT
*
2451 ATATTTATAAAT-TATAATATATAT-ATAA
1 ATATTTATAAATATATAATATATATAAAAA
2479 ATATTTAT-AATATATAATATATATAAAAA
1 ATATTTATAAATATATAATATATATAAAAA
2508 ATATTTATATAATATATAA
1 ATATTTATA-AATATATAA
2527 AAATCCTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 3 0.07
28 20 0.47
29 11 0.26
31 9 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATTTATAAATATATAATATATATAAAAA
Found at i:2498 original size:24 final size:24
Alignment explanation
Indices: 2451--2527 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 24
2441 GTTTTCTGAT
2451 ATATTTATAAATTATAATATATATATAA
1 ATATTTAT-AA-TAT-ATA-ATATATAA
2479 ATATTTATAATATATAATATATATA
1 ATATTTATAATATATAATATATA-A
* ** *
2504 AAAAATAT-TTATATAATATATAA
1 ATATTTATAATATATAATATATAA
2527 A
1 A
2528 AATCCTAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 2 0.05
24 20 0.45
25 9 0.20
26 3 0.07
27 2 0.05
28 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATTTATAATATATAATATATAA
Found at i:3272 original size:102 final size:104
Alignment explanation
Indices: 3052--3346 Score: 404
Period size: 106 Copynumber: 2.8 Consensus size: 104
3042 AATTTTTCTA
* * *
3052 ACCCATAAAATAAAATTTAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATATTTTA
1 ACCCTTAAAATAAAA-TAAAATTTAATTTGGGCTAAACTTAGTGAAATTAGTT-T-TATATTTTA
*
3116 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGGAATTT
63 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
* *
3156 ACCCTTAAAAT-AAA-AAAA-TTAATTTGAGCCTAAACTTAGTGAAATTAGTTTTTTATTTTATT
1 ACCCTTAAAATAAAATAAAATTTAATTTG-GGCTAAACTTAGTGAAATTAGTTTTATATTTTATT
*
3218 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
*
3258 ACCCTTAATATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTAT
1 ACCCTTAAAAT-AAAATAAAA-TTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTAT
* *
3323 TTCTAAAACTCTATAATAATAAAT
64 TTCTAAAACCCTATAACAATAAAT
3347 AATAAAAAAA
Statistics
Matches: 170, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
100 37 0.22
101 16 0.09
102 35 0.21
103 3 0.02
104 13 0.08
105 4 0.02
106 54 0.32
107 8 0.05
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (104 bp):
ACCCTTAAAATAAAATAAAATTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
CTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Found at i:4818 original size:98 final size:98
Alignment explanation
Indices: 4649--4844 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
4639 AAATTAATAT
4649 TTCATGAAAACGCTAGATAGCAAATATGTTAGGTGAATTACCATTTAGTAATACCATGGTTTAGA
1 TTCATGAAAACGCTAGATAGCAAATATGTTAGGTGAATTACCATTTAGTAATACCATGGTTTAGA
4714 TACAATTAAAACTATCAAAACATGGTAACATAG
66 TACAATTAAAACTATCAAAACATGGTAACATAG
4747 TTCATGAAAACGCTAGATAGCAAATATGTTAGGTGAATTACCATTTAGTAATACCATGGTTTAGA
1 TTCATGAAAACGCTAGATAGCAAATATGTTAGGTGAATTACCATTTAGTAATACCATGGTTTAGA
4812 TACAATTAAAACTATCAAAACATGGTAACATAG
66 TACAATTAAAACTATCAAAACATGGTAACATAG
4845 GAGGTATAAC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (98 bp):
TTCATGAAAACGCTAGATAGCAAATATGTTAGGTGAATTACCATTTAGTAATACCATGGTTTAGA
TACAATTAAAACTATCAAAACATGGTAACATAG
Found at i:5781 original size:16 final size:16
Alignment explanation
Indices: 5739--5779 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
5729 AATTGGTAAG
5739 AATTATAAATATTCAA
1 AATTATAAATATTCAA
5755 AATTATAAATATTCAA
1 AATTATAAATATTCAA
5771 AATTCATAA
1 AATT-ATAA
5780 TAATCATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTATAAATATTCAA
Found at i:15157 original size:2 final size:2
Alignment explanation
Indices: 15150--15175 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15140 ACATCAGTCT
15150 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
15176 AAGATGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27634 original size:1 final size:1
Alignment explanation
Indices: 27630--27660 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
27620 AAAAATATAG
27630 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27661 GCAAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34657 original size:31 final size:31
Alignment explanation
Indices: 34619--34844 Score: 98
Period size: 31 Copynumber: 7.5 Consensus size: 31
34609 TATGGCTAAT
34619 TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
* * * **
34650 TGCTCAAATAAGGACTTGA--TCTT-TTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTGTTAAAA
** **
34679 TGGC-CAAATAAAAGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTTAAAA
* * **
34710 TGCTCAAATAAGGGTCTGA--TATT-TTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTGTTAAAA
** **
34739 TGGC-CAAATAAAAGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTTAAAA
* * **
34770 TGCTCAAATAAGGGTCTGA--TATT-TTAATT
1 TGCTCAAATAAGGGCCTAACGT-TTGTTAAAA
* **
34799 TGGC-CAAATAAGGGCATAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTTAAAA
34830 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
34845 TTGGCGTCAA
Statistics
Matches: 132, Mismatches: 45, Indels: 36
0.62 0.21 0.17
Matches are distributed among these distances:
29 47 0.36
30 24 0.18
31 61 0.46
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTTAAAA
Found at i:34749 original size:29 final size:29
Alignment explanation
Indices: 34714--34812 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
34704 CCAAAATGCT
34714 CAAATAAGGGTCTGATATTTTAATTTGGC
1 CAAATAAGGGTCTGATATTTTAATTTGGC
** * * ** * **
34743 CAAATAAAAGCCTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGTCTGATATTT--TAATTTGGC
34773 TCAAATAAGGGTCTGATATTTTAATTTGGC
1 -CAAATAAGGGTCTGATATTTTAATTTGGC
34803 CAAATAAGGG
1 CAAATAAGGG
34813 CATAACGTTT
Statistics
Matches: 48, Mismatches: 18, Indels: 8
0.65 0.24 0.11
Matches are distributed among these distances:
29 27 0.56
30 4 0.08
31 17 0.35
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGTCTGATATTTTAATTTGGC
Found at i:34843 original size:60 final size:60
Alignment explanation
Indices: 34623--34843 Score: 345
Period size: 60 Copynumber: 3.7 Consensus size: 60
34613 GCTAATTGCT
** ** * *
34623 CAAATAAGGGCCTAACGTTTGTTAAAATGCTCAAATAA-GGACTTGATCTTTTAATTTGGC
1 CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTC-TGATATTTTAATTTGGC
34683 CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGGC
1 CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGGC
34743 CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGGC
1 CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGGC
** *
34803 CAAATAAGGGCATAACGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
34844 CTTGGCGTCA
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
60 148 0.98
61 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (60 bp):
CAAATAAAAGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGGC
Found at i:34953 original size:29 final size:29
Alignment explanation
Indices: 34916--35017 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 29
34906 CGATGACGTT
*
34916 AGGCTCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
** * *
34945 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT
1 AGGCCCTTATTTG-GCCAAATT--A-AAAGATC
*
34976 AGGCCCTTATTTGACCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
35005 -GAGCCCTTATTTG
1 AG-GCCCTTATTTG
35018 AGCATTTTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
28 4 0.07
29 29 0.52
30 1 0.02
31 19 0.34
32 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:34965 original size:60 final size:60
Alignment explanation
Indices: 34888--35049 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 60
34878 TGACGCCAAA
* * * *
34888 CCCTTATTTGAGTATTTTCGATGACGTTAGGCTCTTATTTGGCCAAATTAAAAGATC-AGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGA-G
34948 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGAG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGAG
* *
35008 CCCTTATTTGAGCATTTT-GGTAAACGTTAAGCCCTTATTTGA
1 CCCTTATTTGAGCATTTTCGAT-AACGTTAGGCCCTTATTTGA
35050 GCAATTAGCA
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
59 2 0.02
60 91 0.97
61 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGAG
Found at i:34983 original size:31 final size:30
Alignment explanation
Indices: 34888--35052 Score: 106
Period size: 31 Copynumber: 5.5 Consensus size: 30
34878 TGACGCCAAA
* *
34888 CCCTTATTTGAGTATTTTCGATGACGTTAGG
1 CCCTTATTTGAGCATTTT-GATAACGTTAGG
* ** * *
34919 CTCTTATTTG-GCCAAATT-A-AAAGATCAGG
1 CCCTTATTTGAG-CATTTTGATAACG-TTAGG
34948 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTT-GATAACGTTAGG
* ** * * *
34979 CCCTTATTTGACCAAATT-A-AAAGATCGAG
1 CCCTTATTTGAGCATTTTGATAACGTTAG-G
* *
35008 CCCTTATTTGAGCATTTTGGTAAACGTTAAG
1 CCCTTATTTGAGCATTTTGAT-AACGTTAGG
35039 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
35053 ATTAGCATAT
Statistics
Matches: 98, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
28 7 0.07
29 35 0.36
30 2 0.02
31 47 0.48
32 7 0.07
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGATAACGTTAGG
Found at i:41871 original size:30 final size:30
Alignment explanation
Indices: 41835--41903 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
41825 ATCAAGCAAC
41835 CAAAGGTCCTACACAA-GCCACTGCACCAAG
1 CAAAGGTCCTACA-AACGCCACTGCACCAAG
* *
41865 CAAAGGTCCTGCAAACTCCACTGCACCAAG
1 CAAAGGTCCTACAAACGCCACTGCACCAAG
41895 CAAAGGTCC
1 CAAAGGTCC
41904 ACCAAGGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.35, C:0.36, G:0.17, T:0.12
Consensus pattern (30 bp):
CAAAGGTCCTACAAACGCCACTGCACCAAG
Found at i:42427 original size:33 final size:33
Alignment explanation
Indices: 42356--42445 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
42346 TTGGAAATGC
* * * *
42356 AGATTTCTACAAATGTAAAAATTAGGTGATAGT
1 AGATTTCTGCAAATGTTAACATTAGGTGATAGG
*
42389 AGATTTCTGGAAATGTTAACATTAGGTGAT-GG
1 AGATTTCTGCAAATGTTAACATTAGGTGATAGG
*
42421 AGGATTTCTGTAAATGTTAACATTA
1 A-GATTTCTGCAAATGTTAACATTA
42446 ACATTAGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 48 0.96
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.36
Consensus pattern (33 bp):
AGATTTCTGCAAATGTTAACATTAGGTGATAGG
Done.