Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014021.1 Corchorus olitorius cultivar O-4 contig14054, 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: 22436
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6140 original size:216 final size:216
Alignment explanation
Indices: 5725--6152 Score: 543
Period size: 216 Copynumber: 2.0 Consensus size: 216
5715 AGTTAAGCAA
* * * * * *
5725 ATTTCCAATTCCATGAGGAATACTACCAGTGAGGCTATTTTGTGACAGGTAAAGCGTTTGAACTG
1 ATTTCCAATTCCATGAGGAATACTACCAATGAGACTATTTTGTGAAAGCTAAAGCGTTTCAACAG
* * ** * *
5790 ATCTTAACAACCCAATCTCCTCAGGAATGGGACCTGAGAGTTTGTTGGTATCAAGATAAAGAACA
66 ATCTCAACAACCCAATCTCCTCAGGAATGGGACCAGAGAGTTTGTTCCTATCAAAATAAAGAAAA
* * *
5855 AGCACATTGCTCAAGTTTCCAATAGAAGTTGGGATTGAACCTGTGAAACTGTTTTCATACAAGTA
131 AGCACATTGCTCAAGTTTCCAATAGAAGTTGGGATTGAACCTGTGAAACTGTTATCAGACAAATA
* *
5920 AAGCTTGGAAAGAGCAGAAAG
196 AAGCTCGAAAAGAGCAGAAAG
* * * * *
5941 ATTTCCTATTGCATGAGGAATACTGCCAATGAGACTATTTTGTGAGAAGCT-AAGCTTTTCAAGA
1 ATTTCCAATTCCATGAGGAATACTACCAATGAGACTATTTTGTGA-AAGCTAAAGCGTTTCAACA
** * * *
6005 GATCTCAACATGCCAATCTCTTGAGGAATGGGACCAGAGAGTTTGTTCCTATCAAAATAGAGAAA
65 GATCTCAACAACCCAATCTCCTCAGGAATGGGACCAGAGAGTTTGTTCCTATCAAAATAAAGAAA
* ** * * *
6070 AAGTATGTTGCTCAAGTTTCCAATAGAAGTTGGGATTGGACCTGTTAAATTGTTATCAGACAAAT
130 AAGCACATTGCTCAAGTTTCCAATAGAAGTTGGGATTGAACCTGTGAAACTGTTATCAGACAAAT
6135 AAAGCTCGAAAAGAGCAG
195 AAAGCTCGAAAAGAGCAG
6153 GTAGAAATCC
Statistics
Matches: 178, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
216 175 0.98
217 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (216 bp):
ATTTCCAATTCCATGAGGAATACTACCAATGAGACTATTTTGTGAAAGCTAAAGCGTTTCAACAG
ATCTCAACAACCCAATCTCCTCAGGAATGGGACCAGAGAGTTTGTTCCTATCAAAATAAAGAAAA
AGCACATTGCTCAAGTTTCCAATAGAAGTTGGGATTGAACCTGTGAAACTGTTATCAGACAAATA
AAGCTCGAAAAGAGCAGAAAG
Found at i:11035 original size:16 final size:15
Alignment explanation
Indices: 11002--11043 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
10992 CATAATTTTA
11002 ATATAT-ATTATAAT
1 ATATATAATTATAAT
*
11016 ATATTTAATTATATAT
1 ATATATAATTATA-AT
11032 ATATATAATTAT
1 ATATATAATTAT
11044 GATTAGGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 6 0.25
16 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATAATTATAAT
Found at i:11810 original size:28 final size:29
Alignment explanation
Indices: 11757--11811 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
11747 CAGTTAACTC
*
11757 CACTTTAGGGACTCAATTGCTCAATTTTT
1 CACTTGAGGGACTCAATTGCTCAATTTTT
11786 CACTTGAGGGAC-CAATTTGCT-AATTT
1 CACTTGAGGGACTCAA-TTGCTCAATTT
11812 CGCTCCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (29 bp):
CACTTGAGGGACTCAATTGCTCAATTTTT
Found at i:18359 original size:2 final size:2
Alignment explanation
Indices: 18352--18390 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18342 TTGACTTGAA
18352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18391 CTAGTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18478 original size:22 final size:21
Alignment explanation
Indices: 18453--18573 Score: 84
Period size: 22 Copynumber: 5.6 Consensus size: 21
18443 TATTTTTATG
*
18453 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAATTA-CCTATA
** * *
18475 AAATTTTGATAACCATCATATG
1 AAATTTTGATAATTA-CCTATA
18497 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATTACCTATA
* *
18518 AAATTGTGATAA--ACTCCATAA
1 AAATTTTGATAATTAC-CTAT-A
* *
18539 GAAATTTTGATAACCTAACTATA
1 -AAATTTTGATAA-TTACCTATA
*
18562 AAATTTTAATAA
1 AAATTTTGATAA
18574 ACTTTCCTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 16 0.21
22 52 0.67
23 1 0.01
24 3 0.04
25 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATA
Found at i:18574 original size:44 final size:42
Alignment explanation
Indices: 18452--18576 Score: 151
Period size: 44 Copynumber: 2.9 Consensus size: 42
18442 ATATTTTTAT
* * *
18452 GAAATTTTGATAATTACCCTATTAAATTTTGATAACCATCATAT
1 GAAATTTTGATAATTA-CCTATAAAATTTTGATAAAC-TCATAA
*
18496 GAAATTTTGATAATTACCTATAAAATTGTGATAAACTCCATAA
1 GAAATTTTGATAATTACCTATAAAATTTTGATAAACT-CATAA
* * *
18539 GAAATTTTGATAACCTAACTATAAAATTTTAATAAACT
1 GAAATTTTGATAA-TTACCTATAAAATTTTGATAAACT
18577 TTCCTATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 34 0.48
44 36 0.51
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (42 bp):
GAAATTTTGATAATTACCTATAAAATTTTGATAAACTCATAA
Found at i:18602 original size:20 final size:21
Alignment explanation
Indices: 18449--18619 Score: 80
Period size: 22 Copynumber: 7.9 Consensus size: 21
18439 TGAATATTTT
*
18449 TATGAAATTTTGATAAT-TACCC
1 TATG-AATTTTGATAATCT-TCC
* * * *
18471 TATTAAATTTTGATAACCATCA
1 TA-TGAATTTTGATAATCTTCC
*
18493 TATGAAATTTTGATAAT-TACC
1 TATG-AATTTTGATAATCTTCC
* * *
18514 TATAAAATTGTGATAAAC-TCC
1 TAT-GAATTTTGATAATCTTCC
* * **
18535 ATAAGAAATTTTGATAACCTAAC
1 -TATG-AATTTTGATAATCTTCC
* * *
18558 TATAAAATTTTAATAAACTTTCC
1 TAT-GAATTTTGATAATC-TTCC
18581 TATGAATTTTG-TAATCTTCC
1 TATGAATTTTGATAATCTTCC
*
18601 TATGATTTTTGATAATCTT
1 TATGAATTTTGATAATCTT
18620 TGTGTGAGAT
Statistics
Matches: 108, Mismatches: 30, Indels: 23
0.67 0.19 0.14
Matches are distributed among these distances:
20 14 0.13
21 28 0.26
22 59 0.55
23 7 0.06
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (21 bp):
TATGAATTTTGATAATCTTCC
Found at i:18618 original size:21 final size:20
Alignment explanation
Indices: 18577--18619 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18567 TTAATAAACT
18577 TTCCTATGAATTTTGTAATC
1 TTCCTATGAATTTTGTAATC
*
18597 TTCCTATGATTTTTGATAATC
1 TTCCTATGAATTTTG-TAATC
18618 TT
1 TT
18620 TGTGTGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (20 bp):
TTCCTATGAATTTTGTAATC
Found at i:21062 original size:2 final size:2
Alignment explanation
Indices: 21055--21104 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
21045 TTCGTACTTT
21055 TA TA TA TA GTA TA TA TA 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 TA TA TA TA TA TA TA TA
21098 TA TA TA T
1 TA TA TA T
21105 GCATGATTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21876 original size:13 final size:13
Alignment explanation
Indices: 21858--21883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21848 TTGTTGGCTC
21858 ATAGATTAGCATT
1 ATAGATTAGCATT
21871 ATAGATTAGCATT
1 ATAGATTAGCATT
21884 TCTGGGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATAGATTAGCATT
Found at i:21892 original size:43 final size:43
Alignment explanation
Indices: 21844--21930 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
21834 GTTGGGGAAG
21844 GGGTTTGTTGGCTCATAGATTAGCATTATAGATTAGCATTTCT
1 GGGTTTGTTGGCTCATAGATTAGCATTATAGATTAGCATTTCT
21887 GGGTTTGTTGGCTCATAGATTAGCATTATAGATTAGCATTTCT
1 GGGTTTGTTGGCTCATAGATTAGCATTATAGATTAGCATTTCT
21930 G
1 G
21931 TATTGTAGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.41
Consensus pattern (43 bp):
GGGTTTGTTGGCTCATAGATTAGCATTATAGATTAGCATTTCT
Found at i:21919 original size:13 final size:13
Alignment explanation
Indices: 21901--21926 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21891 TTGTTGGCTC
21901 ATAGATTAGCATT
1 ATAGATTAGCATT
21914 ATAGATTAGCATT
1 ATAGATTAGCATT
21927 TCTGTATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATAGATTAGCATT
Found at i:22070 original size:13 final size:13
Alignment explanation
Indices: 22052--22077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22042 TTGTTGGCTC
22052 ATAGATTAGCATT
1 ATAGATTAGCATT
22065 ATAGATTAGCATT
1 ATAGATTAGCATT
22078 TCTGTATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATAGATTAGCATT
Found at i:22215 original size:58 final size:57
Alignment explanation
Indices: 22126--22252 Score: 193
Period size: 58 Copynumber: 2.2 Consensus size: 57
22116 TCCTGTGTGT
* *
22126 TTGTAATCCCAA-TCTCTTTAAAAAATGAAAATGATTTTTATCTAAAAAAAGTAGTAG
1 TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAA-TAGTAG
* * *
22183 TTGTAATTCCAATTCTCTTTAAGAAATGAAAATTATTCTTATCTAAAAAAATAGTGG
1 TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAATAGTAG
22240 TTGTAATTCCAAT
1 TTGTAATTCCAAT
22253 ATCTAAATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 29 0.45
58 35 0.55
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (57 bp):
TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAATAGTAG
Found at i:22232 original size:57 final size:58
Alignment explanation
Indices: 22126--22252 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 58
22116 TCCTGTGTGT
* * *
22126 TTGTAATCCCAA-TCTCTTTAAAAAATGAAAATGATTTTTATCTAAAAAAAGTAGTAG
1 TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAAATAGTAG
* * *
22183 TTGTAATTCCAATTCTCTTTAAGAAATGAAAATTATTCTTATCT-AAAAAAATAGTGG
1 TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAAATAGTAG
22240 TTGTAATTCCAAT
1 TTGTAATTCCAAT
22253 ATCTAAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 35 0.56
58 28 0.44
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (58 bp):
TTGTAATTCCAATTCTCTTTAAAAAATGAAAATGATTCTTATCTAAAAAAAATAGTAG
Done.