Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012882.1 Corchorus olitorius cultivar O-4 contig12915, 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: 25159
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:848 original size:22 final size:22
Alignment explanation
Indices: 820--862 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
810 GTTATACCAA
820 TCTTCTTATTCAAGGTTACTAT
1 TCTTCTTATTCAAGGTTACTAT
842 TCTTCTTATTCAAGGTTACTA
1 TCTTCTTATTCAAGGTTACTA
863 AAAGAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (22 bp):
TCTTCTTATTCAAGGTTACTAT
Found at i:1093 original size:161 final size:161
Alignment explanation
Indices: 913--1236 Score: 630
Period size: 161 Copynumber: 2.0 Consensus size: 161
903 TACTAGCTAT
913 TAGCTAATTTAATTTGTAACCTTACTTTAGTTACAAATTTTCTTATATAAGATTTTAAAAAACTG
1 TAGCTAATTTAATTTGTAACCTTACTTTAGTTACAAATTTTCTTATATAAGATTTTAAAAAACTG
*
978 TAGAGGTTATCAAAAAATTAAGATGCTATCAACAAATTTAATAATGATATGAATCCTTAATTAAT
66 TAGAGGTTATCAAAAAATTAAGATGCTATCAAAAAATTTAATAATGATATGAATCCTTAATTAAT
*
1043 AAAATTATGTACATTTCATCAATGAAGAGGC
131 AAAATTATGTACATTTCATCAATAAAGAGGC
1074 TAGCTAATTTAATTTGTAACCTTACTTTAGTTACAAATTTTCTTATATAAGATTTTAAAAAACTG
1 TAGCTAATTTAATTTGTAACCTTACTTTAGTTACAAATTTTCTTATATAAGATTTTAAAAAACTG
1139 TAGAGGTTATCAAAAAATTAAGATGCTATCAAAAAATTTAATAATGATATGAATCCTTAATTAAT
66 TAGAGGTTATCAAAAAATTAAGATGCTATCAAAAAATTTAATAATGATATGAATCCTTAATTAAT
1204 AAAATTATGTACATTTCATCAATAAAGAGGC
131 AAAATTATGTACATTTCATCAATAAAGAGGC
1235 TA
1 TA
1237 TTGGTTTTCT
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (161 bp):
TAGCTAATTTAATTTGTAACCTTACTTTAGTTACAAATTTTCTTATATAAGATTTTAAAAAACTG
TAGAGGTTATCAAAAAATTAAGATGCTATCAAAAAATTTAATAATGATATGAATCCTTAATTAAT
AAAATTATGTACATTTCATCAATAAAGAGGC
Found at i:3955 original size:20 final size:20
Alignment explanation
Indices: 3917--3955 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3907 GCGTTTGGCA
**
3917 TTGTTGCCATTTTTGTTTTC
1 TTGTTGCCATTTTCATTTTC
*
3937 TTGTTGTCATTTTCATTTT
1 TTGTTGCCATTTTCATTTT
3956 TTGAAAACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.13, G:0.13, T:0.67
Consensus pattern (20 bp):
TTGTTGCCATTTTCATTTTC
Found at i:5680 original size:20 final size:20
Alignment explanation
Indices: 5655--5697 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
5645 ATTGCAACTC
5655 AATTGTGGGAAA-ATTGTCAA
1 AATTGT-GGAAAGATTGTCAA
5675 AATTGTGGAAAGATTGTCAA
1 AATTGTGGAAAGATTGTCAA
5695 AAT
1 AAT
5698 GTATAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (20 bp):
AATTGTGGAAAGATTGTCAA
Found at i:6897 original size:17 final size:17
Alignment explanation
Indices: 6877--6909 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6867 TTAGACTTAT
6877 ATAATATATAGATATAG
1 ATAATATATAGATATAG
6894 ATAATATATAGATATA
1 ATAATATATAGATATA
6910 TAATCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (17 bp):
ATAATATATAGATATAG
Found at i:6912 original size:15 final size:15
Alignment explanation
Indices: 6874--6913 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 15
6864 AGTTTAGACT
6874 TATATAATATATAGA
1 TATATAATATATAGA
6889 TATAGATAATATATAGA
1 TAT--ATAATATATAGA
6906 TATATAAT
1 TATATAAT
6914 CAAATAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.35
17 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
TATATAATATATAGA
Found at i:9269 original size:111 final size:113
Alignment explanation
Indices: 9087--9405 Score: 385
Period size: 120 Copynumber: 2.8 Consensus size: 113
9077 AAAATGATGA
* * * * *
9087 AAGAAACTGAATATTGGGTTAGGAGAGGACCAAGATGGAATGGTGTGGAAAGTGATCCAAACTTG
1 AAGAAACTAAATATTGGGTTAGGAAAGGACCAAGATTG-ATGGTGTGGGAAGAGATCCAAACTTG
* *
9152 CTAGAGAAAAAGTCCTTAGATGAAAT-A-C-GCCAGATGAAATTCGGTG
65 CTAGAGAAAAAGTCCTTGGATGAAATCACCAGCCAGATGAAATTCAGTG
* * * *
9198 AAGAAACTAAACATTGGGTTAGGAAAGGACCAAGATATGATCGTGTGGGAAGAGATTCGAACTTG
1 AAGAAACTAAATATTGGGTTAGGAAAGGACCAAGAT-TGATGGTGTGGGAAGAGATCCAAACTTG
* *
9263 CAAGAGAAAAAGTCCTTGGATGAAATCATGCCAGAATGTCAGATGAAATTCAGTG
65 CTAGAGAAAAAGTCCTTGGATGAAATCA--CC---A-GCCAGATGAAATTCAGTG
* *
9318 AAGAAACTAAATGTTGGGTTAGGAAAGGACCAAAATGTGATGGTGTGGGAAGAGATCCAAACTTG
1 AAGAAACTAAATATTGGGTTAGGAAAGGACCAAGAT-TGATGGTGTGGGAAGAGATCCAAACTTG
9383 CTAGAGAAGAAA-TCCTTGGATGA
65 CTAGAGAA-AAAGTCCTTGGATGA
9406 GCAGAAGTTG
Statistics
Matches: 176, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
111 78 0.44
112 2 0.01
115 1 0.01
120 92 0.52
121 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.22
Consensus pattern (113 bp):
AAGAAACTAAATATTGGGTTAGGAAAGGACCAAGATTGATGGTGTGGGAAGAGATCCAAACTTGC
TAGAGAAAAAGTCCTTGGATGAAATCACCAGCCAGATGAAATTCAGTG
Found at i:20514 original size:48 final size:47
Alignment explanation
Indices: 20439--20582 Score: 168
Period size: 49 Copynumber: 3.0 Consensus size: 47
20429 GAGCGTGCCA
* * *
20439 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGATAAAAAGTGCAAGT-AAAAATAAAAG
*
20486 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGATAAAAAG-TGCAAGTAAAAATAAAAG
* * *
20535 TTCAATTTTGTAGTAAAAATTGATAAAAAGTGC-AGT-AAAGTAAAAG
1 ATCAATTTTGT-CTAAAAATTGATAAAAAGTGCAAGTAAAAATAAAAG
20581 AT
1 AT
20583 TGCTTTAACT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
46 10 0.12
47 15 0.18
48 18 0.21
49 40 0.48
50 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGATAAAAAGTGCAAGTAAAAATAAAAG
Found at i:23520 original size:49 final size:47
Alignment explanation
Indices: 23431--23559 Score: 179
Period size: 49 Copynumber: 2.7 Consensus size: 47
23421 GAGCGTGCCA
* *
23431 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAATTAAAAG
23478 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAATTAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAATTAAAAG
* *
23527 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGC
23560 GGGAAAAGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
47 12 0.16
48 19 0.26
49 43 0.58
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAATTAAAAG
Found at i:24864 original size:9 final size:9
Alignment explanation
Indices: 24844--24881 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
24834 TTAATTCATT
24844 TAATTTCC-
1 TAATTTCCA
24852 TAATTTCCA
1 TAATTTCCA
*
24861 TAATTTCCT
1 TAATTTCCA
24870 TAATTTCCA
1 TAATTTCCA
24879 TAA
1 TAA
24882 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTTCCA
Found at i:24864 original size:17 final size:18
Alignment explanation
Indices: 24844--24881 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
24834 TTAATTCATT
24844 TAATTTCC-TAATTTCCA
1 TAATTTCCTTAATTTCCA
24861 TAATTTCCTTAATTTCCA
1 TAATTTCCTTAATTTCCA
24879 TAA
1 TAA
24882 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTCCTTAATTTCCA
Done.