Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013527.1 Corchorus capsularis cultivar CVL-1 contig13548, 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: 28870
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1968 original size:22 final size:22
Alignment explanation
Indices: 1931--1974 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1921 GAATTTCAGG
*
1931 ACAACTTCGGCCCAGAACTTGT
1 ACAACTTCGGCACAGAACTTGT
* *
1953 ACAACTTCGGGACAGAAGTTGT
1 ACAACTTCGGCACAGAACTTGT
1975 TACGGGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTTCGGCACAGAACTTGT
Found at i:5841 original size:6 final size:6
Alignment explanation
Indices: 5830--5860 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
5820 ATAATTGCTA
5830 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
5861 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:11650 original size:33 final size:32
Alignment explanation
Indices: 11613--11695 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 32
11603 CGCCTAGCAA
*
11613 TGGCCGGTTG-TGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGG-TGATGGCCGG-CATCTCCGA-GTCGCG
11646 TGGCCGGTGATGGCCAGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCC-GGCATCTCCGAGTCGCG
*
11679 TGGCCGGTGTTGGCCGG
1 TGGCCGGTGATGGCCGG
11696 GCTTCTCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 4 0.09
33 38 0.84
34 3 0.07
ACGTcount: A:0.08, C:0.28, G:0.42, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGATGGCCGGCATCTCCGAGTCGCG
Found at i:11709 original size:33 final size:33
Alignment explanation
Indices: 11640--11719 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
11630 ACATGTCCAT
**
11640 GTCGCGTGGCCGGTGATGGCCAGGCATCTCCGA
1 GTCGCGTGGCCGGTGATGGCCAGGCATCTCAAA
* * *
11673 GTCGCGTGGCCGGTGTTGGCCGGGCTTCTCAAA
1 GTCGCGTGGCCGGTGATGGCCAGGCATCTCAAA
* *
11706 GTCGCATGGTCGGT
1 GTCGCGTGGCCGGT
11720 CACTAGTGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.10, C:0.28, G:0.40, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTGATGGCCAGGCATCTCAAA
Found at i:17335 original size:28 final size:30
Alignment explanation
Indices: 17280--17358 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 30
17270 TTTCAATGCC
17280 ATCAACCAAAACAGGATTATTTGTAATGCTATG
1 ATCAACCAAAACA-GA--ATTTGTAATGCTATG
*
17313 ATCAATCAAAACA-AATTT-TAATGCTATG
1 ATCAACCAAAACAGAATTTGTAATGCTATG
*
17341 TTCAACCAAAACAGAATT
1 ATCAACCAAAACAGAATT
17359 GTTTTCATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 21 0.50
29 8 0.19
31 1 0.02
33 12 0.29
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.29
Consensus pattern (30 bp):
ATCAACCAAAACAGAATTTGTAATGCTATG
Found at i:25831 original size:30 final size:33
Alignment explanation
Indices: 25795--25871 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 33
25785 TTTTCGTCAC
*
25795 CCAAAACAGATTTATTTTCAATG-T-T-ATCTA
1 CCAAAACAGATTTATTTTCAATGCTATGATCAA
* *
25825 CCAAAACATGA-TTATTTTTAATGCTATGTTCAA
1 CCAAAACA-GATTTATTTTCAATGCTATGATCAA
25858 CCAAAACAGATTTA
1 CCAAAACAGATTTA
25872 GTATCATCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 19 0.49
31 3 0.08
32 3 0.08
33 14 0.36
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (33 bp):
CCAAAACAGATTTATTTTCAATGCTATGATCAA
Found at i:25897 original size:33 final size:33
Alignment explanation
Indices: 25860--25964 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 33
25850 ATGTTCAACC
*
25860 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* *
25893 AAAACAGATTTAGTGTCATTGCAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
25926 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
25959 AAAACA
1 AAAACA
25965 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:26493 original size:33 final size:33
Alignment explanation
Indices: 26456--26562 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
26446 AGCACTAGTG
* *
26456 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* *
26489 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* * *
26522 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
26554 AACCGGCCA
1 -ACCGGCCA
26563 TCGCTAGGCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 1 0.02
33 63 0.98
ACGTcount: A:0.22, C:0.40, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
Done.