Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016130.1 Corchorus olitorius cultivar O-4 contig16163, 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: 4508
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1329 original size:24 final size:24
Alignment explanation
Indices: 1300--1355 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1290 CTTTGAAGTA
* * *
1300 AATTGAGGCCTTGAATAATTGAAG
1 AATTGAAGCATTGAATAACTGAAG
*
1324 AATTGAAGCATTGAATAACTGAAC
1 AATTGAAGCATTGAATAACTGAAG
*
1348 ACTTGAAG
1 AATTGAAG
1356 AAAGACCACC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (24 bp):
AATTGAAGCATTGAATAACTGAAG
Found at i:1391 original size:36 final size:35
Alignment explanation
Indices: 1351--2307 Score: 768
Period size: 36 Copynumber: 26.9 Consensus size: 35
1341 ACTGAACACT
* **
1351 TGAAGAAAGACCACCCTGGGTCATTCTGAAATAAGT
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* *
1387 TGAAGCAAGACCACCCTGGGTC-ACTTGAAATAAAG
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* * * * * *
1422 TGAA-AAATGACCACCCTCGATCATTCCGACACAAAC
1 TGAAGAAA-GACCACCCTGGGTCA-ACTGAAATAAAC
* * * * *
1458 TAAAGAAAAACCACCCTGGGTCAAGTGAAGTAAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * *
1493 TGAA-AAATGACCACCCTCGATCATTCCGACACAAAC
1 TGAAGAAA-GACCACCCTGGGTCA-ACTGAAATAAAC
* * *
1529 TAAAGAAAGACCACCCTTGGTCAAGTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
1564 TGTAGAAAAGACCACCCTGGATCAACTGACATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
1600 TTAAGAAAGACCACCCTGGGTC-ACTTGAAACAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* *
1635 TGAAGAAAAGACCACCCTGGATCAACTGACATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
1671 TGAAGAAAGACCACCCTAGGT-TACTTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
*
1706 TGAAGGAAAGACCACCCTGGGTCAACTGACATAAAC
1 TGAA-GAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
1742 TGAAGAAAGATCGCCCTCGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * *
1777 TAAAGAATGATCGCCCTAGATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
* * **
1813 TGAAGAAAGACCGCCCTGGGTCAATTGAAATTTAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
1848 TGAATG-GAGACCGCCCTAGGTCAACTGAAAATAAAC
1 TGAA-GAAAGACCACCCTGGGTCAACTG-AAATAAAC
* * * *
1884 TGAAGAATGACCACCCTCGATCATTCT-AACATAAAC
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAA-ATAAAC
**
1920 TGAAGAAAAGACCACCCTGGGTCAACTTTAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
1956 TGAAGAAAGACCGCCCTAGGTCAACTGAAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTG-AAATAAAC
* * * *
1992 TGAAGAACA-ACCACCCTCGATCATTCTGACATAAAC
1 TGAAGAA-AGACCACCCTGGGTCA-ACTGAAATAAAC
**
2028 TGAAGAAAAGACCACCCTGGGTCAACTTTAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
2064 TGAAGAAAGACCGCCCTAGGTCAACTGAAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTG-AAATAAAC
* * * *
2100 TGAAGAACA-ACCACCCTCGATCATTCTGACATAAAC
1 TGAAGAA-AGACCACCCTGGGTCA-ACTGAAATAAAC
* **
2136 TGAAGAAAAGACCATCCTGGGTCAACTTTAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
** **
2172 TGAAGAAAGACCGTCCTGGGTCAACTGAAATCGAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * *
2207 TGACGAATGATCGCCCTGGATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
* * **
2243 TGAAGAAAGACCACCCTGGGTCGATTGAAATTTAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
2278 TGAATG-GAGACCGCCCTGGGTCAACTGAAA
1 TGAA-GAAAGACCACCCTGGGTCAACTGAAA
2308 CTTTGAACAT
Statistics
Matches: 730, Mismatches: 152, Indels: 79
0.76 0.16 0.08
Matches are distributed among these distances:
34 10 0.01
35 304 0.42
36 352 0.48
37 64 0.09
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (35 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
Found at i:2280 original size:71 final size:69
Alignment explanation
Indices: 1351--2306 Score: 744
Period size: 71 Copynumber: 13.4 Consensus size: 69
1341 ACTGAACACT
* * ** * *
1351 TGAAGAAAGACCACCCTGGGTCATTCTGAAATAAGTTGAAGCAAGACCACCCTGGGTCACTTGAA
1 TGAAGAAAGACCACCCTGGATCA-ACTG-AATAAACTGAAGAAAGACCACCCTGGGTCAATTGAA
*
1416 ATAAAG
64 ATAAAC
* * * * * * *
1422 TGAA-AAATGACCACCCTCGATCATTCCGACACAAACTAAAGAAAAACCACCCTGGGTCAAGTGA
1 TGAAGAAA-GACCACCCTGGATCA-ACTGA-ATAAACTGAAGAAAGACCACCCTGGGTCAATTGA
* *
1486 AGTAAAT
63 AATAAAC
* * * * * * *
1493 TGAA-AAATGACCACCCTCGATCATTCCGACACAAACTAAAGAAAGACCACCCTTGGTCAAGTGA
1 TGAAGAAA-GACCACCCTGGATCA-ACTGA-ATAAACTGAAGAAAGACCACCCTGGGTCAATTGA
1557 AATAAAC
63 AATAAAC
* * *
1564 TGTAGAAAAGACCACCCTGGATCAACTGACATAAACTTAAGAAAGACCACCCTGGGTCACTTGAA
1 TGAAG-AAAGACCACCCTGGATCAACTGA-ATAAACTGAAGAAAGACCACCCTGGGTCAATTGAA
*
1629 ACAAAC
64 ATAAAC
* * *
1635 TGAAGAAAAGACCACCCTGGATCAACTGACATAAACTGAAGAAAGACCACCCTAGGTTACTTGAA
1 TGAAG-AAAGACCACCCTGGATCAACTGA-ATAAACTGAAGAAAGACCACCCTGGGTCAATTGAA
1700 ATAAAC
64 ATAAAC
* * * * *
1706 TGAAGGAAAGACCACCCTGGGTCAACTGACATAAACTGAAGAAAGATCGCCCTCGGTCAACTGAA
1 TGAA-GAAAGACCACCCTGGATCAACTGA-ATAAACTGAAGAAAGACCACCCTGGGTCAATTGAA
1771 ATAAAC
64 ATAAAC
* * * * * * *
1777 TAAAGAATGATCGCCCTAGATCAACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCAATTGAA
1 TGAAGAAAGACCACCCTGGATCAAC-TGAATA-AACTGAAGAAAGACCACCCTGGGTCAATTGAA
**
1842 ATTTAC
64 ATAAAC
* * * * *
1848 TGAATG-GAGACCGCCCTAGG-TCAACTGAAAATAAACTGAAGAATGACCACCCTCGATC-ATTC
1 TGAA-GAAAGACCACCCT-GGATCAACTG--AATAAACTGAAGAAAGACCACCCTGGGTCAATT-
*
1910 TAACATAAAC
61 GAA-ATAAAC
* * * * *
1920 TGAAGAAAAGACCACCCTGGGTCAACTTTAATAAACTGAAGAAAGACCGCCCTAGGTCAACTGAA
1 TGAAG-AAAGACCACCCTGGATCAAC-TGAATAAACTGAAGAAAGACCACCCTGGGTCAATTG-A
1985 AATAAAC
63 AATAAAC
* *
1992 TGAAGAACA-ACCACCCTCGATCATTCTGACATAAACTGAAGAAAAGACCACCCTGGGTCAACTT
1 TGAAGAA-AGACCACCCTGGATCA-ACTGA-ATAAACTGAAG-AAAGACCACCCTGGGTCAA-TT
*
2056 -TAATAAAC
61 GAAATAAAC
* * * *
2064 TGAAGAAAGACCGCCCTAGG-TCAACTGAAAATAAACTGAAGAACA-ACCACCCTCGATCATTCT
1 TGAAGAAAGACCACCCT-GGATCAACTG--AATAAACTGAAGAA-AGACCACCCTGGGTCAAT-T
*
2127 GACATAAAC
61 GAAATAAAC
* * * ** *
2136 TGAAGAAAAGACCATCCTGGGTCAACTTTAATAAACTGAAGAAAGACCGTCCTGGGTCAACTGAA
1 TGAAG-AAAGACCACCCTGGATCAAC-TGAATAAACTGAAGAAAGACCACCCTGGGTCAATTGAA
**
2201 ATCGAC
64 ATAAAC
* * * * * *
2207 TGACGAATGATCGCCCTGGATCAACTTGAAAACAACTGAAGAAAGACCACCCTGGGTCGATTGAA
1 TGAAGAAAGACCACCCTGGATCAAC-TGAATA-AACTGAAGAAAGACCACCCTGGGTCAATTGAA
**
2272 ATTTAC
64 ATAAAC
* * *
2278 TGAATG-GAGACCGCCCTGGGTCAACTGAA
1 TGAA-GAAAGACCACCCTGGATCAACTGAA
2307 ACTTTGAACA
Statistics
Matches: 728, Mismatches: 120, Indels: 75
0.79 0.13 0.08
Matches are distributed among these distances:
70 52 0.07
71 465 0.64
72 153 0.21
73 55 0.08
74 3 0.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (69 bp):
TGAAGAAAGACCACCCTGGATCAACTGAATAAACTGAAGAAAGACCACCCTGGGTCAATTGAAAT
AAAC
Found at i:3292 original size:35 final size:35
Alignment explanation
Indices: 3253--3320 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
3243 CGCCCTAGAG
3253 TTTC-TTTTCTTCATCATTTCATTTTCATTTTTTCA
1 TTTCTTTTTCTTCAT-ATTTCATTTTCATTTTTTCA
* *
3288 TTTCTTTTTTTTCATTTTTCATTTTCATTTTTT
1 TTTCTTTTTCTTCATATTTCATTTTCATTTTTT
3321 TTGTATGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 21 0.70
36 9 0.30
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (35 bp):
TTTCTTTTTCTTCATATTTCATTTTCATTTTTTCA
Found at i:3305 original size:21 final size:24
Alignment explanation
Indices: 3274--3322 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
3264 CATCATTTCA
3274 TTTTCATTTTTTCA-TTTC-TTTT
1 TTTTCATTTTTTCATTTTCATTTT
3296 TTTTCA-TTTTTCATTTTCATTTT
1 TTTTCATTTTTTCATTTTCATTTT
3319 TTTT
1 TTTT
3323 GTATGCACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 8 0.32
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCATTTTTTCATTTTCATTTT
Found at i:3320 original size:14 final size:13
Alignment explanation
Indices: 3269--3319 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3259 TTCTTCATCA
3269 TTTCATTTTCATTT
1 TTTCATTTTCA-TT
3283 TTTCA-TTTC--T
1 TTTCATTTTCATT
3293 TTT--TTTTCATT
1 TTTCATTTTCATT
3304 TTTCATTTTCATT
1 TTTCATTTTCATT
3317 TTT
1 TTT
3320 TTTGTATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.12
10 4 0.12
11 4 0.12
13 15 0.47
14 5 0.16
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTCATTTTCATT
Found at i:3672 original size:7 final size:7
Alignment explanation
Indices: 3658--3693 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3648 CAATTTTCAC
3658 TTCTTTT
1 TTCTTTT
*
3665 TT-TGTT
1 TTCTTTT
3671 TTCTTTT
1 TTCTTTT
3678 TTCTTTT
1 TTCTTTT
3685 TTCTTTT
1 TTCTTTT
3692 TT
1 TT
3694 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:4467 original size:2 final size:2
Alignment explanation
Indices: 4460--4490 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4450 GAGCAGTAGA
4460 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 A
4491 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.