Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014952.1 Corchorus capsularis cultivar CVL-1 contig14973, 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: 7842
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1997 original size:44 final size:44
Alignment explanation
Indices: 1934--2045 Score: 224
Period size: 44 Copynumber: 2.5 Consensus size: 44
1924 AGAAATTTTA
1934 TGCTAACCTTAAGAAGTGCACCTTTTGCACAAACAAGCTTGGTT
1 TGCTAACCTTAAGAAGTGCACCTTTTGCACAAACAAGCTTGGTT
1978 TGCTAACCTTAAGAAGTGCACCTTTTGCACAAACAAGCTTGGTT
1 TGCTAACCTTAAGAAGTGCACCTTTTGCACAAACAAGCTTGGTT
2022 TGCTAACCTTAAGAAGTGCACCTT
1 TGCTAACCTTAAGAAGTGCACCTT
2046 CTTGGTTTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
TGCTAACCTTAAGAAGTGCACCTTTTGCACAAACAAGCTTGGTT
Found at i:5916 original size:33 final size:32
Alignment explanation
Indices: 5819--5959 Score: 122
Period size: 33 Copynumber: 4.3 Consensus size: 32
5809 TTGCAAAGAG
* * *
5819 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTT-GGTGTTGTTTGCGATGAAACTAAATC
** * *
5852 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTG-GTGTTGTTTGCGATGAAACTAAATC
*
5885 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTT-GGTGTTGTTTGCGATGAAACTAAATC
* ** *
5918 TGTTTTGGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTGG-TGTTGTTTGCGATG-AAACTAAATC
5951 TGTTTTGGT
1 TGTTTTGGT
5960 TGAGCATAGC
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
32 4 0.04
33 81 0.90
34 5 0.06
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (32 bp):
TGTTTTGGTGTTGTTTGCGATGAAACTAAATC
Found at i:6405 original size:30 final size:30
Alignment explanation
Indices: 6369--6427 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6359 CAAGGGGGAG
*
6369 GGAATGATGCGTCTAAGG-CTTATTATGGAA
1 GGAATGATGCG-CCAAGGACTTATTATGGAA
6399 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATTATGGA
6428 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATTATGGAA
Found at i:7679 original size:345 final size:341
Alignment explanation
Indices: 6994--7681 Score: 818
Period size: 345 Copynumber: 2.0 Consensus size: 341
6984 ATATAAAGGG
*** *
6994 ACCAACCCCCTCTTGTAAAGTTGAGTTGAGTTGATTAATAAAGTTGAGGTTTTACACCCAAATTG
1 ACCAACCCCCTCTTGTAAAGACAAGTTAAGTT-ATTAATAAAGTTGAGGTTTTACACCCAAATTG
* * *
7059 ATTATCATAGCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGCGTCCTAG
65 ATTATCATAGCTTCATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTCCTAC
* * * * * *
7124 CAAACAATTAGGTTGTGATTGCTTAGTTGTTTCTTAATCTTATGATCTTAGGTGTTCAATTGCAG
130 CAAACAATTAGGTTGTGATTGCTTAATTGCTTCTGAATCTTATGATCTTAGGTCTACAATTGCAA
* * * * *
7189 GTCTAATTGGAGACTTAAGGCCAACGAGAGAAGAAGTAAACTTTGTGAAGATCATCGATTTACTC
195 GTCTAATTGCAGACTTAAGGCCAACGAAAGAAGAAGTAAACTTTGTGAAGATCATCAACTTACAC
** ** *
7254 ATCTAGAAGAGTTGGTGTTTCAAGTCGACTTTGGTGGCTATTCAAAGGGTAGATTTGAATCTAAC
260 ATCTAGAAGAGTTGAAGTTTCAAGTCGACTTTGGAAGCTATTCAAAGGATAGATTTGAATCTAAC
7319 ACAACTAGATTCGTATC
325 ACAACTAGATTCGTATC
*
7336 ACCAACCCCCTCTTGTAAAGACAAGTTAAGTT-TTCAATAAAGATTCTGAGGTTTATTCACCCAA
1 ACCAACCCCCTCTTGTAAAGACAAGTTAAGTTATT-AATAAAG--T-TGAGGTTT-TACACCCAA
* * * *
7400 ATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGCATACATAGGTTTCTTCAATGTTGTAGAGTC
61 ATTGATTATCATAGCTTCATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTC
* * *
7465 CTACCAAACAATTAGGTTGTGATTGCTTAATTGCTTGTGAATATTTGTGATCTTA-GTCTAACAA
126 CTACCAAACAATTAGGTTGTGATTGCTTAATTGCTTCTGAAT-CTTATGATCTTAGGTCT-ACAA
* ** * **
7529 TTGCAAGTCTAATTGTCA-AC-TAAGG-CAGACGAAATAAGAGGAGT-TGCTTTGTGAAGGTTGT
189 TTGCAAGTCTAATTG-CAGACTTAAGGCCA-ACGAAAGAAGA--AGTAAACTTTGTGAAGATCAT
* * *
7590 CAACTTACACATCTAG-A-AGTTGAAGTTGTCAAGTTGGTCTTTGGAAGCTTTTC-AAGGATAGA
250 CAACTTACACATCTAGAAGAGTTGAAGTT-TCAAG-TCGACTTTGGAAGCTATTCAAAGGATAGA
*
7652 TTTGAATCTAACATAACTAGATTCGTATC
313 TTTGAATCTAACACAACTAGATTCGTATC
7681 A
1 A
7682 TTTTTAGACA
Statistics
Matches: 292, Mismatches: 41, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
340 2 0.01
341 7 0.02
342 28 0.10
343 1 0.00
344 18 0.06
345 164 0.56
346 68 0.23
347 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (341 bp):
ACCAACCCCCTCTTGTAAAGACAAGTTAAGTTATTAATAAAGTTGAGGTTTTACACCCAAATTGA
TTATCATAGCTTCATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTCCTACC
AAACAATTAGGTTGTGATTGCTTAATTGCTTCTGAATCTTATGATCTTAGGTCTACAATTGCAAG
TCTAATTGCAGACTTAAGGCCAACGAAAGAAGAAGTAAACTTTGTGAAGATCATCAACTTACACA
TCTAGAAGAGTTGAAGTTTCAAGTCGACTTTGGAAGCTATTCAAAGGATAGATTTGAATCTAACA
CAACTAGATTCGTATC
Done.