Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018410.1 Corchorus olitorius cultivar O-4 contig18443, 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: 25705
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1106 original size:36 final size:36
Alignment explanation
Indices: 1059--1128 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1049 TTCAATAACC
* *
1059 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1095 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1129 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3684 original size:22 final size:22
Alignment explanation
Indices: 3626--3686 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 22
3616 AATACCTAAG
*
3626 AATTTAATTAATGTAAGTATTT
1 AATTTAATTAATGTAAGTATTA
* *
3648 CAGTT-ATT-AT-T-AGTATTA
1 AATTTAATTAATGTAAGTATTA
3666 AATTTAATTAATGTAAGTATT
1 AATTTAATTAATGTAAGTATT
3687 TTAGTTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
18 9 0.30
19 4 0.13
20 4 0.13
21 4 0.13
22 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (22 bp):
AATTTAATTAATGTAAGTATTA
Found at i:3935 original size:2 final size:2
Alignment explanation
Indices: 3924--3967 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
3914 AGTTTAGACT
* *
3924 TA TA TA -A TA TA TA TA TA TA TA TA GTA TA TA GA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
3966 TA
1 TA
3968 AAAGACGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3946 original size:17 final size:17
Alignment explanation
Indices: 3924--3959 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3914 AGTTTAGACT
*
3924 TATATAATATATATATA
1 TATATAATATATAGATA
*
3941 TATATAGTATATAGATA
1 TATATAATATATAGATA
3958 TA
1 TA
3960 GATATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATAATATATAGATA
Found at i:6995 original size:26 final size:26
Alignment explanation
Indices: 6943--6991 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
6933 GTCCATATTT
6943 ATTTTTTAAAATAAAATAATAATTAA
1 ATTTTTTAAAATAAAATAATAATTAA
6969 ATTTTTTAATAA-AAAATAA-AATT
1 ATTTTTTAA-AATAAAATAATAATT
6992 TAAACATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATAATAATTAA
Found at i:9469 original size:20 final size:19
Alignment explanation
Indices: 9446--9484 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
9436 GGCGTCTAGG
*
9446 GTTTAGAGGAAGAAGAAGAA
1 GTTTAGAGAAAGAA-AAGAA
*
9466 GTTTTGAGAAAGAAAAGAA
1 GTTTAGAGAAAGAAAAGAA
9485 AGGAAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (19 bp):
GTTTAGAGAAAGAAAAGAA
Found at i:10944 original size:16 final size:15
Alignment explanation
Indices: 10919--10961 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
10909 GTCAAATTTG
10919 AAGAAAAAAACGAAAA
1 AAGAAAAAAA-GAAAA
*
10935 AAGAAGAAAAGAAAA
1 AAGAAAAAAAGAAAA
10950 AATGGAAAAAAA
1 AA--GAAAAAAA
10962 TCAGAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (15 bp):
AAGAAAAAAAGAAAA
Found at i:13631 original size:23 final size:23
Alignment explanation
Indices: 13601--13654 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
13591 GAAAGTTGTA
13601 GCTCTTGGAGTTAGCTTTCCAAC
1 GCTCTTGGAGTTAGCTTTCCAAC
13624 GCTCTTGGAGTTAGCTTTCCAAC
1 GCTCTTGGAGTTAGCTTTCCAAC
13647 GCATCTTG
1 GC-TCTTG
13655 ATTCACTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (23 bp):
GCTCTTGGAGTTAGCTTTCCAAC
Found at i:20153 original size:16 final size:16
Alignment explanation
Indices: 20132--20162 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20122 TGAGACGCAG
*
20132 AGAAGAAGGAAGAAGA
1 AGAAGAAGAAAGAAGA
20148 AGAAGAAGAAAGAAG
1 AGAAGAAGAAAGAAG
20163 CGTTGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
AGAAGAAGAAAGAAGA
Found at i:21815 original size:50 final size:50
Alignment explanation
Indices: 21735--22361 Score: 1007
Period size: 50 Copynumber: 12.7 Consensus size: 50
21725 AGTTTTCTTC
21735 TTATTCCAAAAATG-CCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
*
21784 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
*
21834 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCATTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
* *
21884 TTATTCCAAAAATGCCCCTACCTGGTTGGAAGGTTCCCGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
* *
21934 TTATTCCAAAAATACCCCTTCCTGGTTGGAAGATCCCCGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
*
21984 TTATTCCAAAAATGCCCCTTCTTGGTTGGAAGGTCCCCGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
*
22034 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCATTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
* * * * *
22084 TTATTCCAAAAATGCACATTCCTAGTTGGAAGGTTCCTGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
*
22134 TTATTCCAAAAATGCCCTTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
22184 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
*
22234 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTCA--
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
* *** *
22282 -T-TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAATTTTCGTTA-T
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
* *
22329 TTATTCCAAAAATGCTCTTTCC-GGTTGGAAGGT
1 TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGT
22362 GTATGATTTG
Statistics
Matches: 537, Mismatches: 37, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
46 39 0.07
47 1 0.00
48 11 0.02
49 31 0.06
50 455 0.85
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (50 bp):
TTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTTTATT
Found at i:24316 original size:21 final size:21
Alignment explanation
Indices: 24289--24484 Score: 248
Period size: 21 Copynumber: 9.3 Consensus size: 21
24279 TATATGAAAC
*
24289 TTTGGGGTTTGACTATTAAAA
1 TTTGGGGTTTGACTATCAAAA
* * * *
24310 TTCGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
24331 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
24352 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
*
24373 TTTGGGGTTTGACTATTAAAA
1 TTTGGGGTTTGACTATCAAAA
* * * *
24394 TTCGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
24415 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
24436 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
24457 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
24478 TTTGGGG
1 TTTGGGG
24485 GTTCACCATC
Statistics
Matches: 144, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 144 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAAAA
Found at i:24331 original size:42 final size:42
Alignment explanation
Indices: 24285--24496 Score: 379
Period size: 42 Copynumber: 5.0 Consensus size: 42
24275 GAAATATATG
* *
24285 AAACTTTGGGGTTTGACTATTAAAATTCGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
24327 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* *
24369 AAACTTTGGGGTTTGACTATTAAAATTCGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
24411 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
*
24453 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTCACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
24495 AA
1 AA
24497 TGGGATTTGA
Statistics
Matches: 163, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 163 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (42 bp):
AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
Found at i:24635 original size:21 final size:21
Alignment explanation
Indices: 24611--24663 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
24601 TCAAACCCTA
*
24611 TTGATGGTCAAACCCCAAATT
1 TTGATGGTCAAACCCCAAAGT
24632 TTGA-GAGTCAAACCCCAAAGT
1 TTGATG-GTCAAACCCCAAAGT
*
24653 TTGATAGTCAA
1 TTGATGGTCAA
24664 CACGTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (21 bp):
TTGATGGTCAAACCCCAAAGT
Done.