Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006824.1 Corchorus capsularis cultivar CVL-1 contig06845, 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: 34627
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9141 original size:21 final size:21
Alignment explanation
Indices: 9115--9163 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
9105 GCGCTGGGGG
* *
9115 CCCATGTGGTATGCTTGGCGA
1 CCCATGTGGTATGCCTCGCGA
*
9136 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
9157 CCCATGT
1 CCCATGT
9164 ACTCCAGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:10964 original size:193 final size:192
Alignment explanation
Indices: 10606--10966 Score: 533
Period size: 193 Copynumber: 1.9 Consensus size: 192
10596 CATTTTATGC
* * * * *
10606 ATTCATTTCTGGTGTGTGTTCGACTTTATGATTTAGCCTCTCTGATTAGCTATTATGGCATGTAG
1 ATTCATTTCTGCTGGGTGTTCGACTTTATGATTTAGCCTCTCTAATTACCCATTATGGCATGTAG
* * * * *
10671 TTGCATTTCCATTATGGTTCTTTGTAGGGTAATAGGGGTCATCGGCATAATCAAATGGTTAAGTT
66 TTGCATTTCCATTATGGTTATTTGTAGGGTAATAGGGGGCATAGACATAATCAAATGATTAAGTT
*
10736 GAAAATTTAGGCCAAGCTGATAGTGCATCTTTCTGGAAAGAACTAGAAAAAAAATTGACTTT
131 GAAAAGTTAGGCCAAGCTGATAGTGCATCTTTCTGGAAAGAACTAGAAAAAAAATTGACTTT
* * *
10798 ATTCATTTCTTCTGGGTGTTCCGAGTTTATGATTTAGGCTCTCTAATTACCCATTATGGCATGTA
1 ATTCATTTCTGCTGGGTGTT-CGACTTTATGATTTAGCCTCTCTAATTACCCATTATGGCATGTA
*
10863 GTTGCATTTCCATTATGGTTATTTGTAGGGTAATAGGGGGCATAGACATAATCAAATGATTGAGT
65 GTTGCATTTCCATTATGGTTATTTGTAGGGTAATAGGGGGCATAGACATAATCAAATGATTAAGT
* * * * *
10928 TGAAGAGTTAGGCCAAGTTGATGGTTCATGTTTCTGGAA
130 TGAAAAGTTAGGCCAAGCTGATAGTGCATCTTTCTGGAA
10967 TGATAGTACA
Statistics
Matches: 148, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
192 17 0.11
193 131 0.89
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (192 bp):
ATTCATTTCTGCTGGGTGTTCGACTTTATGATTTAGCCTCTCTAATTACCCATTATGGCATGTAG
TTGCATTTCCATTATGGTTATTTGTAGGGTAATAGGGGGCATAGACATAATCAAATGATTAAGTT
GAAAAGTTAGGCCAAGCTGATAGTGCATCTTTCTGGAAAGAACTAGAAAAAAAATTGACTTT
Found at i:13372 original size:7 final size:7
Alignment explanation
Indices: 13350--13392 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
13340 TATTACACAC
13350 ATATATAT
1 ATATAT-T
13358 ATATATT
1 ATATATT
*
13365 ACATATT
1 ATATATT
*
13372 A-ATAAT
1 ATATATT
13378 ATATATT
1 ATATATT
13385 ATATATT
1 ATATATT
13392 A
1 A
13393 AAATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 6 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (7 bp):
ATATATT
Found at i:13381 original size:20 final size:20
Alignment explanation
Indices: 13356--13479 Score: 71
Period size: 20 Copynumber: 6.2 Consensus size: 20
13346 ACACATATAT
13356 ATATATATTACATATTAATA
1 ATATATATTACATATTAATA
*
13376 ATATATATTATATATTAA-A
1 ATATATATTACATATTAATA
* *
13395 ATAAAATTTTTACATATATATATA
1 AT-ATA-TATTACATAT-TA-ATA
* *
13419 TTCT-TATTTACATA-T-ATA
1 ATATATA-TTACATATTAATA
*
13437 TATATATATT-CTTATTTAATA
1 -ATATATATTACATA-TTAATA
* *
13458 AAATATTTTACATATTAA-A
1 ATATATATTACATATTAATA
13477 ATA
1 ATA
13480 AAAATGATTT
Statistics
Matches: 77, Mismatches: 15, Indels: 25
0.66 0.13 0.21
Matches are distributed among these distances:
18 6 0.08
19 10 0.13
20 34 0.44
21 15 0.19
22 9 0.12
23 1 0.01
24 2 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATATTACATATTAATA
Found at i:13463 original size:26 final size:26
Alignment explanation
Indices: 13408--13463 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
13398 AAATTTTTAC
*
13408 ATATATATATATTCTTATTTACATAT
1 ATATATATATATTCTTATTTACATAA
13434 ATATATATATATTCTTATTTA-ATAA
1 ATATATATATATTCTTATTTACATAA
13459 A-ATAT
1 ATATAT
13464 TTTACATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 4 0.14
25 4 0.14
26 21 0.72
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATATATATATTCTTATTTACATAA
Found at i:22941 original size:15 final size:15
Alignment explanation
Indices: 22903--22950 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
22893 TAGAGAAAGG
* *
22903 AGAAGAAAAAGAAAAT
1 AGAA-AAAAATAAAAA
*
22919 AGAGAAAAATAAAAA
1 AGAAAAAAATAAAAA
22934 AGAAAAAAATAATAAA
1 AGAAAAAAATAA-AAA
22950 A
1 A
22951 CATTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.08
Consensus pattern (15 bp):
AGAAAAAAATAAAAA
Found at i:26082 original size:120 final size:120
Alignment explanation
Indices: 25856--26096 Score: 457
Period size: 120 Copynumber: 2.0 Consensus size: 120
25846 TTAGCTTACT
*
25856 TTTCTTCCTTTTATTTTATTAAGCTGTACAAAAGAATTAAAAAAAAAGTTGAATTTTTCTTTTTT
1 TTTCTTCCTTTTATTTTATTAAGCTATACAAAAGAATTAAAAAAAAAGTTGAATTTTTCTTTTTT
25921 TTTAATTGTTTTTGGCTTATGGGACCAAATGAAGAATTTTTTTTTTTCCTTTTGC
66 TTTAATTGTTTTTGGCTTATGGGACCAAATGAAGAATTTTTTTTTTTCCTTTTGC
25976 TTTCTTCCTTTTATTTTATTAAGCTATACAAAAGAATTAAAAAAAAAGTTGAATTTTTCTTCTTT
1 TTTCTTCCTTTTATTTTATTAAGCTATACAAAAGAATTAAAAAAAAAGTTGAATTTTTCTT-TTT
26041 TTTTAATTGTTTTTGGCTTATGGGACCAAATGAAGAA-TTTTTTTTTTCCTTTTGC
65 TTTTAATTGTTTTTGGCTTATGGGACCAAATGAAGAATTTTTTTTTTTCCTTTTGC
26096 T
1 T
26097 CAGGGTTTGT
Statistics
Matches: 119, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
120 79 0.66
121 40 0.34
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (120 bp):
TTTCTTCCTTTTATTTTATTAAGCTATACAAAAGAATTAAAAAAAAAGTTGAATTTTTCTTTTTT
TTTAATTGTTTTTGGCTTATGGGACCAAATGAAGAATTTTTTTTTTTCCTTTTGC
Found at i:26350 original size:210 final size:212
Alignment explanation
Indices: 26012--26432 Score: 740
Period size: 210 Copynumber: 2.0 Consensus size: 212
26002 TACAAAAGAA
*
26012 TTAAAAAAAAAGTTGAATTTTTCTTCTTTTTTTAATTGTTTTTGGCTTATGGGACCAAATGAAGA
1 TTAAAAAAAAAGTTGAATTTTTCTTCTTTTTTTAATTGTTTTTGGCTTATGGGAACAAATGAAGA
* *
26077 ATTTTTTTTTTCCTTTTGCTCAGGGTTTGTTTCTCCTATTGTGTTGAAGGAATAATGAAATTGAA
66 AGTTTTTTTTCCCTTTTGCTCAGGGTTTGTTTCTCCTATTGTGTTGAAGGAATAATGAAATTGAA
26142 AGGCACTTCTCTTTTTGTTCTTTTGTTTCTTAGAAGAAAGGAAAATAAAATTAGAGTATTTTAGA
131 AGGCACTTCTCTTTTTGTTCTTTTGTTTCTTAGAAGAAAGGAAAATAAAATTAGAGTATTTTAGA
* *
26207 AAAAAAGAAAATAAAAT
196 AAAAAAAAAAAGAAAAT
*
26224 TTAAAATAAAA-TTGAATTTTTCTT-TTTTTTT-ATTGTTTTTGGCTTATGGGAACAAATGAAGA
1 TTAAAAAAAAAGTTGAATTTTTCTTCTTTTTTTAATTGTTTTTGGCTTATGGGAACAAATGAAG-
26286 AAGTTTTTTTTCCCTTTTGCTCAGGGTTTGTTTCTCCTATTGTGTTGAAGGAATAATGAAATTGA
65 AAGTTTTTTTTCCCTTTTGCTCAGGGTTTGTTTCTCCTATTGTGTTGAAGGAATAATGAAATTGA
* *
26351 AAGGTACTTCTCTTTTTGTTCTTTTGTTTTTTAGAAGAAAGGAAAATAAAATTAGAGTATTTTAG
130 AAGGCACTTCTCTTTTTGTTCTTTTGTTTCTTAGAAGAAAGGAAAATAAAATTAGAGTATTTTAG
26416 AAAAAAAAAAAAGAAAA
195 AAAAAAAAAAAAGAAAA
26433 CAAAATTCAT
Statistics
Matches: 200, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
209 29 0.14
210 148 0.74
211 13 0.06
212 10 0.05
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (212 bp):
TTAAAAAAAAAGTTGAATTTTTCTTCTTTTTTTAATTGTTTTTGGCTTATGGGAACAAATGAAGA
AGTTTTTTTTCCCTTTTGCTCAGGGTTTGTTTCTCCTATTGTGTTGAAGGAATAATGAAATTGAA
AGGCACTTCTCTTTTTGTTCTTTTGTTTCTTAGAAGAAAGGAAAATAAAATTAGAGTATTTTAGA
AAAAAAAAAAAGAAAAT
Found at i:27668 original size:6 final size:6
Alignment explanation
Indices: 27659--27691 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
27649 TTCTCTCTCT
27659 CACTCA CACTCA CACTCA CACTC- CACT-A CACTC
1 CACTCA CACTCA CACTCA CACTCA CACTCA CACTC
27692 TCTATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.32
6 17 0.68
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.18
Consensus pattern (6 bp):
CACTCA
Found at i:29591 original size:2 final size:2
Alignment explanation
Indices: 29584--29615 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29574 AAAGTTGGTG
29584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29616 GTACTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.