Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022403.1 Corchorus olitorius cultivar O-4 contig22436, 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: 45201
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1078 original size:58 final size:58
Alignment explanation
Indices: 982--1096 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
972 ATTAATCAAA
* *
982 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGGACCAAGACT
* * * *
1040 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACATTTTAGGACCGAGAC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACATTTTAGGACCAAGAC
1097 ATGATGCTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 35 0.70
59 15 0.30
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGGACCAAGACT
Found at i:1994 original size:281 final size:280
Alignment explanation
Indices: 1491--2187 Score: 1304
Period size: 281 Copynumber: 2.5 Consensus size: 280
1481 GATTCAAATA
1491 ATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATAATGAAAGTTACCAATTTAATTA
1 ATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATAATGAAAGTTACCAATTTAATTA
*
1556 CTTAAGTAATCTACTAAAAAGGCTAAAAAAAGTTATTAAAATTGTATTTACCAATCCTTACATTC
66 CTTGAGTAATCTACTAAAAAGGCT-AAAAAAGTTATTAAAATTGTATTTACCAATCCTTACATTC
*
1621 TTAATATTTTTTTGGCCTAAAAACATTATAGTACTATCTAGATTCAAGTCATCTTACATCCTTAT
130 TTAATATTTTTTTGGCCGAAAAACATTATAGTACTATCTAGATTCAAGTCATCTTACATCCTTAT
*
1686 TGAAGACCGGATTGGGGTTGGCATCCTGAGGCTGTAGTTACTGCCATCTCTTTTACTTTCTGGTA
195 TGAAGACCGGATTGGGGTTGGCATCCTGAGGCTGTAGTTACTGCCATCTCTTTTACTTTATGGTA
1751 CTTTTGTAGCAAAAATAAGTC
260 CTTTTGTAGCAAAAATAAGTC
*
1772 ATCTTACATCCTTATTAATTTTAGTAACTTCTTATGATCAATAATGAAAGTTACCAATTTAATTA
1 ATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATAATGAAAGTTACCAATTTAATTA
1837 CTTGAGTAATCTACTAAAAAGGCTAAAAAAGTTATTAAAATTGTATTTACCAATCCTTACATTCT
66 CTTGAGTAATCTACTAAAAAGGCTAAAAAAGTTATTAAAATTGTATTTACCAATCCTTACATTCT
1902 TAATATTTTTTTTGGCCGAAAAACATTATAGTACTATCTAGATTCAAGTCATCTTACATCCTTAT
131 TAATA-TTTTTTTGGCCGAAAAACATTATAGTACTATCTAGATTCAAGTCATCTTACATCCTTAT
1967 TGAAGACCGGATTGGGGTTGGCATCCTGAGGCTGTAGTTACTGCCATCTCTTTTACTTTATGGTA
195 TGAAGACCGGATTGGGGTTGGCATCCTGAGGCTGTAGTTACTGCCATCTCTTTTACTTTATGGTA
2032 CTTTTGTAGCAAAAATAAGTC
260 CTTTTGTAGCAAAAATAAGTC
2053 ATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATAATGAAAGTTACCAATTTAATTA
1 ATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATAATGAAAGTTACCAATTTAATTA
* * * *
2118 CTTGAGTAATCTACTAAAAAAGCTATAAAAGTTTTTAAAATTGTATTTATCAATCCTTACATTCT
66 CTTGAGTAATCTACTAAAAAGGCTAAAAAAGTTATTAAAATTGTATTTACCAATCCTTACATTCT
2183 TAATA
131 TAATA
2188 ACATTAGTAA
Statistics
Matches: 406, Mismatches: 9, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
280 46 0.11
281 360 0.89
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (280 bp):
ATCTTACATCCTTATTAATTTTAGTAACTTTTTATGATCAATAATGAAAGTTACCAATTTAATTA
CTTGAGTAATCTACTAAAAAGGCTAAAAAAGTTATTAAAATTGTATTTACCAATCCTTACATTCT
TAATATTTTTTTGGCCGAAAAACATTATAGTACTATCTAGATTCAAGTCATCTTACATCCTTATT
GAAGACCGGATTGGGGTTGGCATCCTGAGGCTGTAGTTACTGCCATCTCTTTTACTTTATGGTAC
TTTTGTAGCAAAAATAAGTC
Found at i:3566 original size:205 final size:204
Alignment explanation
Indices: 3207--3624 Score: 655
Period size: 205 Copynumber: 2.0 Consensus size: 204
3197 GCTTAATAAC
* *
3207 TTTATGAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTATTAACAAAGTTGTAGTAAATAA
1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
*
3272 GATACCACAACACATTATTATTATTATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTG
66 GAT--CACAACACATTACTATTATTATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTG
*
3337 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-A-AAAGATATTA
129 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAA-TTCAAAATTATAATAAAAATATT-
3400 AAGATCCGATTTA
192 AAGATCCGATTTA
*
3413 TTTATCAATGGTGAATGTTATTAATTT-TTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
* **
3477 GAT-ACAACACATTACTATTATATATATATAGAACTATACCAAAAAAATTTAGTTGAACATTAGT
66 GATCACAACACATTACTATTAT-TATATAT--AACTATAACAAAAAAAAGTAGTTGAACATTAGT
3541 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCAAAATTATAAATTAAAAATAT
128 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCAAAATTAT-AA-TAAAAATAT
3606 TAAGATCCGATTTA
191 TAAGATCCGATTTA
3620 TTTAT
1 TTTAT
3625 TATTAAGCAA
Statistics
Matches: 197, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
202 17 0.09
203 7 0.04
204 11 0.06
205 109 0.55
206 27 0.14
207 18 0.09
208 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (204 bp):
TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
GATCACAACACATTACTATTATTATATATAACTATAACAAAAAAAAGTAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTCAAAATTATAATAAAAATATTAAGA
TCCGATTTA
Found at i:3805 original size:21 final size:21
Alignment explanation
Indices: 3739--3805 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3729 TAAGAATTTA
*
3739 ATTAATGTAAGTGTTTTAGTT
1 ATTAATGTAAGTATTTTAGTT
* ** *
3760 ATT-ATAGT-ATTATTACATTT
1 ATTAAT-GTAAGTATTTTAGTT
3780 AATTAATGTAAGTATTTTAGTT
1 -ATTAATGTAAGTATTTTAGTT
3802 ATTA
1 ATTA
3806 TTTATATTAC
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 9 0.27
21 14 0.42
22 10 0.30
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (21 bp):
ATTAATGTAAGTATTTTAGTT
Found at i:4052 original size:6 final size:6
Alignment explanation
Indices: 4034--4069 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
4024 GTTTAGACTT
4034 ATATAG TATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATA
4070 TACACAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:19268 original size:6 final size:6
Alignment explanation
Indices: 19257--19282 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19247 TGCTTATACC
19257 TCAAAA TCAAAA TCAAAA TCAAAA TC
1 TCAAAA TCAAAA TCAAAA TCAAAA TC
19283 CTGTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (6 bp):
TCAAAA
Found at i:20627 original size:28 final size:27
Alignment explanation
Indices: 20572--20638 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
20562 ACTATCATTT
*
20572 AATCCTTGAA--TATTTTTTGGCCCAA
1 AATCCTTGAATCTTTTTTTTGGCCCAA
20597 AATCCTTGAATCTTTTTTTTGG-CCATCA
1 AATCCTTGAATCTTTTTTTTGGCCCA--A
20625 AATCCTTGAATCTT
1 AATCCTTGAATCTT
20639 GATTCTTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 10 0.27
26 3 0.08
27 9 0.24
28 15 0.41
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.43
Consensus pattern (27 bp):
AATCCTTGAATCTTTTTTTTGGCCCAA
Found at i:37826 original size:5 final size:5
Alignment explanation
Indices: 37818--37842 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
37808 AAAGAAATAC
37818 ATCAT ATCAT ATCAT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT
37843 GGCTTCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATCAT
Found at i:38826 original size:120 final size:120
Alignment explanation
Indices: 38638--38946 Score: 537
Period size: 120 Copynumber: 2.6 Consensus size: 120
38628 GCGGAGACGG
* * *
38638 AGGAGAAAGCCAAACAAGGCTATGAGGCAGCCAAAAGCAAAGGTGAAGAGACTTTAGAATCTGTC
1 AGGACAAAGCCAAACAAGGCTATGACGCAGCCAAAAGCAAAGGTGAAGAGACTTTAGAATCTGCC
38703 AAGGATGAAACAAAGAAGAAGACAGCGGAAACAGACGAGAACCTGAGGTGGGCCA
66 AAGGATGAAACAAAGAAGAAGACAGCGGAAACAGACGAGAACCTGAGGTGGGCCA
* *
38758 AGGACAAAGCCAAACAAGGCTATGACGCAGCCAAAGGAAAAGGTGAAGAGACTTTAGAATCTGCC
1 AGGACAAAGCCAAACAAGGCTATGACGCAGCCAAAAGCAAAGGTGAAGAGACTTTAGAATCTGCC
* * *
38823 AAGGATGAAACAAAGAAGAAGACAGCGGAAGCAGAGGAGAACCTTAGGTGGGCCA
66 AAGGATGAAACAAAGAAGAAGACAGCGGAAACAGACGAGAACCTGAGGTGGGCCA
*
38878 AGGACAAAGCCAAACAAGGCTTTGACGCAGCCAAAAGCAAAGGTGAAGAGACTTTAGAATCTGCC
1 AGGACAAAGCCAAACAAGGCTATGACGCAGCCAAAAGCAAAGGTGAAGAGACTTTAGAATCTGCC
38943 AAGG
66 AAGG
38947 GGACTTATGA
Statistics
Matches: 178, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 178 1.00
ACGTcount: A:0.42, C:0.18, G:0.29, T:0.11
Consensus pattern (120 bp):
AGGACAAAGCCAAACAAGGCTATGACGCAGCCAAAAGCAAAGGTGAAGAGACTTTAGAATCTGCC
AAGGATGAAACAAAGAAGAAGACAGCGGAAACAGACGAGAACCTGAGGTGGGCCA
Done.