Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019933.1 Corchorus olitorius cultivar O-4 contig19966, 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: 23207
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3345 original size:22 final size:21
Alignment explanation
Indices: 3320--3603 Score: 230
Period size: 22 Copynumber: 12.8 Consensus size: 21
3310 TATAAGATCT
3320 TGAAATTTTGATAACACTCCTA
1 TGAAATTTTGATAAC-CTCCTA
*
3342 TGAAATTTTAATAACCTGGTCCTA
1 TGAAATTTTGATAACC---TCCTA
* *
3366 TGAAATTTTAATAACCACTCTA
1 TGAAATTTTGATAACCTC-CTA
* *
3388 TGAGATTTTGGTAACCTAATTCCTA
1 TGAAATTTTGATAACC----TCCTA
* *
3413 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
3435 TGAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCT-CCTA
*
3457 TGCAATTTT-ATAACCTCCATA
1 TGAAATTTTGATAACCTCC-TA
* *
3478 TGAAATTTCGATAA-CTACACCA
1 TGAAATTTTGATAACCT-C-CTA
* *
3500 TGAAAATTTGAAAACCTCCATA
1 TGAAATTTTGATAACCTCC-TA
* *
3522 TGATATTTTGGTAACCTCACTA
1 TGAAATTTTGATAACCTC-CTA
3544 TGAAATTTTGATAACCTCCTCA
1 TGAAATTTTGATAACCTCCT-A
* * * *
3566 TGAAATTATAATAATCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
3588 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
3604 ACACAGAGAC
Statistics
Matches: 212, Mismatches: 31, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
20 2 0.01
21 24 0.11
22 140 0.66
23 6 0.03
24 21 0.10
25 18 0.08
26 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:3516 original size:65 final size:66
Alignment explanation
Indices: 3410--3559 Score: 189
Period size: 65 Copynumber: 2.3 Consensus size: 66
3400 AACCTAATTC
* * * * *
3410 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCCTATGCA-ATTTT-ATAACCT
1 CTATGAAATTTTGATAACCACACCATGAAAATTTGAAAACCTCCATATG-ATATTTTGATAACCT
3473 C-
65 CA
* * *
3474 CATATGAAATTTCGATAACTACACCATGAAAATTTGAAAACCTCCATATGATATTTTGGTAACCT
1 C-TATGAAATTTTGATAACCACACCATGAAAATTTGAAAACCTCCATATGATATTTTGATAACCT
3539 CA
65 CA
3541 CTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
3560 TCCTCATGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 2 0.03
65 46 0.64
66 23 0.32
67 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACACCATGAAAATTTGAAAACCTCCATATGATATTTTGATAACCTC
A
Found at i:4529 original size:29 final size:30
Alignment explanation
Indices: 4475--4548 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
4465 TACCCAGAAA
* *
4475 AATCCTTTATGTTTTGCTTTTGGGACAAAAT
1 AATCCCTTATGTTTT-CTTTCGGGACAAAAT
*
4506 AATCCCTTATGTTTT-TTTCGGGACAAATT
1 AATCCCTTATGTTTTCTTTCGGGACAAAAT
4535 AATCCCTTATGTTT
1 AATCCCTTATGTTT
4549 CAAAAATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.65
31 14 0.35
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (30 bp):
AATCCCTTATGTTTTCTTTCGGGACAAAAT
Found at i:4742 original size:31 final size:30
Alignment explanation
Indices: 4692--4784 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 30
4682 AAGGGACTAA
4692 TTTGTCCCAAAAAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAAAAAATATAAGGGATTTT
4722 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAA-AAAAATATAAGGGATTTT
4753 TTTGTCCCAAAAAAAACAT-T-AGGGATTTT
1 TTTGTCCCAAAAAAAA-ATATAAGGGATTTT
4782 TTT
1 TTT
4785 AGTATTTAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
29 12 0.20
30 17 0.28
31 32 0.52
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (30 bp):
TTTGTCCCAAAAAAAAATATAAGGGATTTT
Found at i:5209 original size:126 final size:123
Alignment explanation
Indices: 5011--5247 Score: 332
Period size: 126 Copynumber: 1.9 Consensus size: 123
5001 AATTCCCTAA
* * **
5011 AAAATGGTAAAGATAAAATAGTTATAAAAATTGAATTGAATTAAATAAAAATAGAATTTTTGGTA
1 AAAATAGTAAAAATAAAATAGTTATAAAAATTGAATTGAATTAAATAAAAATAGAATTTTTAATA
*
5076 AAATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAATTAAAATAGT
66 AAATAAAACTGTAAAAGTTTAAA-AATGGCATTTAAGAAATATATTTAATTAAAATAGT
* *
5135 AAAATAGTAAAAATAAAATAGTTATAAATATATTAGATTTG-ATTAAATAAAAATAGAGTTTTTA
1 AAAATAGTAAAAATAAAATAGTTATAAA-A-ATT-GAATTGAATTAAATAAAAATAGAATTTTTA
** * *
5199 ATTGAGTAAAATTGTAAAAGTTTAAAAATGGCATTTAAGAAATATATTT
63 ATAAAATAAAACTGTAAAAGTTTAAAAATGGCATTTAAGAAATATATTT
5248 GATAAATAAG
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
124 26 0.26
125 23 0.23
126 45 0.45
127 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (123 bp):
AAAATAGTAAAAATAAAATAGTTATAAAAATTGAATTGAATTAAATAAAAATAGAATTTTTAATA
AAATAAAACTGTAAAAGTTTAAAAATGGCATTTAAGAAATATATTTAATTAAAATAGT
Found at i:5893 original size:31 final size:31
Alignment explanation
Indices: 5857--5963 Score: 151
Period size: 31 Copynumber: 3.4 Consensus size: 31
5847 ACTAAATACT
* *
5857 AAAAAAATTCTCTTATATTTTTCTTTTGCGAC
1 AAAAAAA-TCCCTTATATTTTTCTTTTGGGAC
5889 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
* *
5920 AAAAAAATCCCTTATGTTGTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
**
5951 AAATCAATCCCTT
1 AAAAAAATCCCTT
5964 GCTTATGTGG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 62 0.90
32 7 0.10
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATATTTTTCTTTTGGGAC
Found at i:6114 original size:29 final size:30
Alignment explanation
Indices: 6077--6145 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
6067 CTCATTTTTG
* *
6077 AAACGTAAGGAATTAATTTGTCCCGAAA-A
1 AAACATAAGGAATTAATTTGTCCCAAAACA
*
6106 AAACATAAGGAATTATTTTGTCCCAAAAGCA
1 AAACATAAGGAATTAATTTGTCCCAAAA-CA
6137 AAACATAAG
1 AAACATAAG
6146 AGATCTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 25 0.71
31 10 0.29
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (30 bp):
AAACATAAGGAATTAATTTGTCCCAAAACA
Found at i:6499 original size:59 final size:59
Alignment explanation
Indices: 6407--6525 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
6397 CTAACATTCG
6407 TACTTTTATATATAATATGTATGTATATATATAGAGATAGATATATATATTGTTATAAT
1 TACTTTTATATATAATATGTATGTATATATATAGAGATAGATATATATATTGTTATAAT
6466 TACTTTTATATATAATATGTATGTATATATATAGAGATAGATATATATATTGTTATAAT
1 TACTTTTATATATAATATGTATGTATATATATAGAGATAGATATATATATTGTTATAAT
6525 T
1 T
6526 TATCTGCTCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (59 bp):
TACTTTTATATATAATATGTATGTATATATATAGAGATAGATATATATATTGTTATAAT
Found at i:14426 original size:17 final size:17
Alignment explanation
Indices: 14404--14436 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14394 CACCAGATGC
*
14404 AGATCACTGGTGATCTT
1 AGATCACTAGTGATCTT
14421 AGATCACTAGTGATCT
1 AGATCACTAGTGATCT
14437 GGGGGTGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (17 bp):
AGATCACTAGTGATCTT
Found at i:20408 original size:13 final size:13
Alignment explanation
Indices: 20390--20415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20380 TTTGGAATTC
20390 TAAATAATATTTA
1 TAAATAATATTTA
20403 TAAATAATATTTA
1 TAAATAATATTTA
20416 GAACATTGAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATAATATTTA
Found at i:21148 original size:13 final size:13
Alignment explanation
Indices: 21132--21156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21122 TTAATTATGC
21132 AATACTATTAATT
1 AATACTATTAATT
21145 AATACTATTAAT
1 AATACTATTAAT
21157 CATTTTATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATACTATTAATT
Done.