Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021367.1 Corchorus olitorius cultivar O-4 contig21400, 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: 9784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5149 original size:43 final size:42
Alignment explanation
Indices: 5102--5186 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
5092 AAACAAAATA
*
5102 GGAGAAAGTGAAATGACAAAAAAATCCAATCCAACCCTCTTAT
1 GGAGAAAGTAAAATGACAAAAAAAT-CAATCCAACCCTCTTAT
*
5145 GGAGAAAGTAAAATGACAAAAAACTCAATCCAACCCTCTTAT
1 GGAGAAAGTAAAATGACAAAAAAATCAATCCAACCCTCTTAT
5187 CTCATGACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 17 0.43
43 23 0.57
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (42 bp):
GGAGAAAGTAAAATGACAAAAAAATCAATCCAACCCTCTTAT
Found at i:5166 original size:42 final size:43
Alignment explanation
Indices: 5102--5186 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
5092 AAACAAAATA
*
5102 GGAGAAAGTGAAATGACAAAAAAA-TCCAATCCAACCCTCTTAT
1 GGAGAAAGTAAAATGACAAAAAAACT-CAATCCAACCCTCTTAT
5145 GGAGAAAGTAAAATGAC-AAAAAACTCAATCCAACCCTCTTAT
1 GGAGAAAGTAAAATGACAAAAAAACTCAATCCAACCCTCTTAT
5187 CTCATGACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 23 0.57
43 17 0.43
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (43 bp):
GGAGAAAGTAAAATGACAAAAAAACTCAATCCAACCCTCTTAT
Found at i:6311 original size:437 final size:435
Alignment explanation
Indices: 5444--6312 Score: 1042
Period size: 435 Copynumber: 2.0 Consensus size: 435
5434 TTTGTATTTT
** * * * *
5444 TTTTTCTATTTGTCTGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAAT
1 TTTTTCTATTTGTCCAATGAAAGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCAACAAC
* ** * * * *
5509 TTTCATTTAAAACTCAAAAGTCAATTTTAATGTTTTGATTCTAAAAATTGCTTCTGAAATTTTGT
66 TTTCATTGAAAACTCAAAAGTCAATTTTAATG-TTCAACTCAAAAAAATGCTTCTGAAATTTGGT
* * * * *
5574 GGTTTTGATTGCCGGTTAATTTAATATCATATAATTTTTTGTCCACATCTCCGATTGAAGTTATT
130 CGTTTCGATTGCCGGTTAATTTAATACCATATAATTTTTTGTCCACATCTCCAATTCAAGTTATT
* * * * *
5639 GAAGTGTTGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACTCGAAAGCTAAATTT
195 CAAGTGTCGGTTAAAAGGTTATTGCATAATCTACGACTTTCATGAAGAACTCGAAAGCTAAATTT
* * * * *
5704 GATCTACGAGTTTCGTTAAGGGTTCAAAACGAAATTTTTATGTTTCAAGATCTCCATTAACAACA
260 AATCTACGAGTTTCATGAAGGATTCAAAACGAAATTTTTATGTTTCAAGATCTCCATTAAAAACA
* **
5769 TTTTCTTATTTGAATTATTTATCAAATGGCCATCATACTTTTCTACTTTATACTACTTAATTCTT
325 TTTTCTTATTTGAATTAGTTATCAAATCACCATCATACTTTTCTACTTTATACTACTTAATTCTT
* *
5834 TACAAATTCTATCTTAATCTAACGTTTAAGCTTTATTTTTTTATTCG
390 TACAAATTCTATCTTAATCT-ACGTTTAAACTTCATTTTTTTATTCG
* *
5881 TTTTTCTATTTGTCCAATGAAATTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCAACAAC
1 TTTTTCTATTTGTCCAATGAAAGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCAACAAC
*
5946 TTTCA-TGAAGAACTCAAAAG-CAAATTTTTATG-TCAACTCAAAAAAATGCTTCCT-AAATTTG
66 TTTCATTGAA-AACTCAAAAGTC-AATTTTAATGTTCAACTCAAAAAAATGCTT-CTGAAATTTG
** *
6007 GTCGTTTCGATTGTTGGTCT-ATTTAATACCATATAA-TTTTTGATCCACATGTCCAATTCAAGT
128 GTCGTTTCGATTGCCGGT-TAATTTAATACCATATAATTTTTTG-TCCACATCTCCAATTCAAGT
* *
6070 TATTCAAGTGTCGGTTAAAAGGTTATTGTATAATCTACGACTTTCATGAA-AACTCGAAAG-TTA
191 TATTCAAGTGTCGGTTAAAAGGTTATTGCATAATCTACGACTTTCATGAAGAACTCGAAAGCTAA
* * *
6133 ATTTAATCTACGAGTTTCATGAATGATTCAAAAGGGAATTTTTTATGTTTCAAGATCTCCATTAA
256 ATTTAATCTACGAGTTTCATGAAGGATTCAAAA-CGAAATTTTTATGTTTCAAGATCTCC----A
* * * * * * *
6198 TTAATAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTTATATTTTTTTATTTTATGCTA
316 TTAA-AAACATTTTCTTATTTGAATTAGTTATCAAATCACCATCATACTTTTCTACTTTATACTA
*
6263 CTT-AGTCTTTTACAAATTCTATCTT-A-CT-CGATTTAACACTTCATTTTTTT
380 CTTAATTC-TTTACAAATTCTATCTTAATCTACG-TTTAA-ACTTCATTTTTTT
6313 GAAATGTAAT
Statistics
Matches: 366, Mismatches: 52, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
433 30 0.08
434 39 0.11
435 113 0.31
436 12 0.03
437 94 0.26
438 9 0.02
439 69 0.19
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (435 bp):
TTTTTCTATTTGTCCAATGAAAGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCAACAAC
TTTCATTGAAAACTCAAAAGTCAATTTTAATGTTCAACTCAAAAAAATGCTTCTGAAATTTGGTC
GTTTCGATTGCCGGTTAATTTAATACCATATAATTTTTTGTCCACATCTCCAATTCAAGTTATTC
AAGTGTCGGTTAAAAGGTTATTGCATAATCTACGACTTTCATGAAGAACTCGAAAGCTAAATTTA
ATCTACGAGTTTCATGAAGGATTCAAAACGAAATTTTTATGTTTCAAGATCTCCATTAAAAACAT
TTTCTTATTTGAATTAGTTATCAAATCACCATCATACTTTTCTACTTTATACTACTTAATTCTTT
ACAAATTCTATCTTAATCTACGTTTAAACTTCATTTTTTTATTCG
Found at i:6834 original size:21 final size:21
Alignment explanation
Indices: 6805--6879 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
6795 TGAGTATAGA
* *
6805 TTTGGAGATTCGAAGTTCATG
1 TTTGAAGATTTGAAGTTCATG
* *
6826 TTTGAAGATTTATTGAAG-ACA-A
1 TTTGAAGA--T-TTGAAGTTCATG
*
6848 ATTGAAGATTTGAAGTTCATG
1 TTTGAAGATTTGAAGTTCATG
6869 TTTGAAGATTT
1 TTTGAAGATTT
6880 ATTGAAGACA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 6 0.15
20 3 0.07
21 17 0.41
22 7 0.17
23 3 0.07
24 5 0.12
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (21 bp):
TTTGAAGATTTGAAGTTCATG
Found at i:6853 original size:22 final size:22
Alignment explanation
Indices: 6827--6901 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
6817 AAGTTCATGT
6827 TTGAAGATTTATTGAAGACAAA
1 TTGAAGATTTATTGAAGACAAA
* **
6849 TTGAAGA--T-TTGAAGTTCATGT
1 TTGAAGATTTATTGAAG-ACA-AA
6870 TTGAAGATTTATTGAAGACAAA
1 TTGAAGATTTATTGAAGACAAA
6892 TTGAAGATTT
1 TTGAAGATTT
6902 GAAGACCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 6 0.14
20 3 0.07
21 7 0.17
22 17 0.40
23 3 0.07
24 6 0.14
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (22 bp):
TTGAAGATTTATTGAAGACAAA
Found at i:6871 original size:43 final size:43
Alignment explanation
Indices: 6810--6905 Score: 183
Period size: 43 Copynumber: 2.2 Consensus size: 43
6800 ATAGATTTGG
*
6810 AGATTCGAAGTTCATGTTTGAAGATTTATTGAAGACAAATTGA
1 AGATTTGAAGTTCATGTTTGAAGATTTATTGAAGACAAATTGA
6853 AGATTTGAAGTTCATGTTTGAAGATTTATTGAAGACAAATTGA
1 AGATTTGAAGTTCATGTTTGAAGATTTATTGAAGACAAATTGA
6896 AGATTTGAAG
1 AGATTTGAAG
6906 ACCATTGAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (43 bp):
AGATTTGAAGTTCATGTTTGAAGATTTATTGAAGACAAATTGA
Found at i:6914 original size:18 final size:19
Alignment explanation
Indices: 6838--6916 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 19
6828 TGAAGATTTA
6838 TTGAAGACAAATTGAAGAT
1 TTGAAGACAAATTGAAGAT
* **
6857 TTGAAGTTCATGTTTGAAGATTT
1 TTGAAG-ACA-AATTGAAGA--T
6880 ATTGAAGACAAATTGAAGAT
1 -TTGAAGACAAATTGAAGAT
*
6900 TTGAAGAC-CATTGAAGA
1 TTGAAGACAAATTGAAGA
6917 ATAATTTCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
18 8 0.17
19 14 0.29
20 3 0.06
21 7 0.15
22 7 0.15
23 3 0.06
24 6 0.12
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (19 bp):
TTGAAGACAAATTGAAGAT
Done.