Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010801.1 Corchorus capsularis cultivar CVL-1 contig10822, 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: 54001
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10970 original size:13 final size:13
Alignment explanation
Indices: 10952--10978 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10942 GGTGACATCG
10952 GCATGGCATGGGT
1 GCATGGCATGGGT
10965 GCATGGCATGGGT
1 GCATGGCATGGGT
10978 G
1 G
10979 TTGTCAGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.48, T:0.22
Consensus pattern (13 bp):
GCATGGCATGGGT
Found at i:13328 original size:21 final size:20
Alignment explanation
Indices: 13295--13337 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
13285 AAGATTTGCA
**
13295 GCTTCTTGGAAATGGCTCTT
1 GCTTCTTGGAAATCCCTCTT
*
13315 GCTTCCTTTGAAATCCCTCTT
1 GCTT-CTTGGAAATCCCTCTT
13336 GC
1 GC
13338 ATCCCTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (20 bp):
GCTTCTTGGAAATCCCTCTT
Found at i:20611 original size:26 final size:26
Alignment explanation
Indices: 20575--20629 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
20565 TTAACTAGGG
20575 TTTGCATAAATTGGTTGTCTGTTTCT
1 TTTGCATAAATTGGTTGTCTGTTTCT
20601 TTTGCATAAATTGGTTGTCTGTTTCT
1 TTTGCATAAATTGGTTGTCTGTTTCT
20627 TTT
1 TTT
20630 TTTATTCCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (26 bp):
TTTGCATAAATTGGTTGTCTGTTTCT
Found at i:24255 original size:6 final size:6
Alignment explanation
Indices: 24245--24279 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
24235 GGCATTAGGT
* *
24245 AATAAT AATAAT AATAAG AATAAG AATAAG AATAA
1 AATAAG AATAAG AATAAG AATAAG AATAAG AATAA
24280 AGGAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (6 bp):
AATAAG
Found at i:24977 original size:17 final size:19
Alignment explanation
Indices: 24955--24998 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
24945 CCGGATAAAA
*
24955 AAAAAGAAGAGAAAAG-G-
1 AAAAAGAAGAAAAAAGAGT
*
24972 AAAAAGAGGAAAAAAGAGT
1 AAAAAGAAGAAAAAAGAGT
24991 AAAAAGAA
1 AAAAAGAA
24999 AAAGCACTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAAAAAAGAGT
Found at i:25096 original size:46 final size:45
Alignment explanation
Indices: 25030--25180 Score: 216
Period size: 45 Copynumber: 3.4 Consensus size: 45
25020 GGAGTCCAAC
* *
25030 AAAATGG-TTTTCAAAAAGAGTCATGGTTTTTAAAAGGCTTTGAT
1 AAAATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
*
25074 AAAATGGTTTTGTCAAAAAGAGTCATGATTTTCAAAAGGTTTTGAT
1 AAAATGGTTTT-TCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
* *
25120 AAAATGACTTTTT-AAAAAGAGTCATGGTTTTCAAAGGGTTTTGAT
1 AAAATG-GTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
*
25165 AAAATGGTTTTCCAAA
1 AAAATGGTTTTTCAAA
25181 GTTGTGTTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
44 11 0.12
45 42 0.44
46 38 0.40
47 4 0.04
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.36
Consensus pattern (45 bp):
AAAATGGTTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
Found at i:25929 original size:20 final size:19
Alignment explanation
Indices: 25902--25953 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
25892 AAAATGAAAG
25902 AAAA-AGAAAAAGAAA-AA
1 AAAAGAGAAAAAGAAAGAA
25919 AAGAGAGAGAAAAATGAAAGAA
1 AA-A-AGAGAAAAA-GAAAGAA
25941 AAAAGA-AAAAAGA
1 AAAAGAGAAAAAGA
25954 GAATAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.07
18 3 0.10
19 6 0.20
20 10 0.33
21 5 0.17
22 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAGAGAAAAAGAAAGAA
Found at i:25932 original size:27 final size:26
Alignment explanation
Indices: 25902--25965 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
25892 AAAATGAAAG
*
25902 AAAAAGAAAAAGAAAA-AAAGAGAGAGA
1 AAAAAGAAAAA-AAAAGAAA-AAAGAGA
*
25929 AAAATGAAAGAAAAAAGAAAAAAGAGA
1 AAAAAGAAA-AAAAAAGAAAAAAGAGA
*
25956 ATAAAGAAAA
1 AAAAAGAAAA
25966 GAGGCTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 1 0.03
27 25 0.81
28 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAAAAAAAGAAAAAAGAGA
Found at i:26278 original size:26 final size:26
Alignment explanation
Indices: 26249--26333 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
26239 ATAAGATTGC
26249 ATTCCATTTGTAAGTCCAATATCAAA
1 ATTCCATTTGTAAGTCCAATATCAAA
* * ***
26275 ATTCGATTT-TCAAGAT--AAGAT-TGC
1 ATTCCATTTGT-AAG-TCCAATATCAAA
26299 ATTCCATTTGTAAGTCCAATATCAAA
1 ATTCCATTTGTAAGTCCAATATCAAA
*
26325 ATTCGATTT
1 ATTCCATTT
26334 TCAAGATAAG
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
23 1 0.02
24 11 0.26
25 10 0.24
26 19 0.45
27 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (26 bp):
ATTCCATTTGTAAGTCCAATATCAAA
Found at i:26297 original size:50 final size:50
Alignment explanation
Indices: 26239--26387 Score: 262
Period size: 50 Copynumber: 3.0 Consensus size: 50
26229 AAGTTTTATA
26239 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
26289 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
* * * *
26339 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCTTTTCAA
1 ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAA
26388 AGGGCATTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (50 bp):
ATAAGATTGCATTCCATTTGTAAGTCCAATATCAAAATTCGATTTTCAAG
Found at i:26307 original size:24 final size:24
Alignment explanation
Indices: 26275--26357 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 24
26265 CAATATCAAA
*
26275 ATTCGATTTTCAAGATAAGATTGC
1 ATTCCATTTTCAAGATAAGATTGC
* ***
26299 ATTCCATTTGT-AAG-TCCAATATCAAA
1 ATTCCATTT-TCAAGAT--AAGAT-TGC
*
26325 ATTCGATTTTCAAGATAAGATTGC
1 ATTCCATTTTCAAGATAAGATTGC
26349 ATTCCATTT
1 ATTCCATTT
26358 GTGAGTCCAA
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
23 1 0.02
24 19 0.45
25 10 0.24
26 11 0.26
27 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (24 bp):
ATTCCATTTTCAAGATAAGATTGC
Found at i:27260 original size:69 final size:70
Alignment explanation
Indices: 27091--27439 Score: 494
Period size: 69 Copynumber: 5.0 Consensus size: 70
27081 TTTCATAAGT
* * * *
27091 CAAACTCGTTTACACACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGCATGGGCTTTTTCA
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGCTTTTCCA
27156 CAAGC
66 CAAGC
27161 CAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGC-TTTCC
1 CAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGCTTTTCC
27224 ACAAGC
65 ACAAGC
*
27230 CAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCAAAGCATGCAGGGGCTTTTCC
1 CAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGCTTTTCC
27294 ACAAGC
65 ACAAGC
* * * * * *
27300 CAAACTCGTTTCCATTCGAGTCACTT-TAGCCTTGGTTCCATCCAAGCA-ACAGAGGCTTTTCCA
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGCTTTTCCA
27363 CAAGC
66 CAAGC
* * * *
27368 CAAACTCGTTTCCATACGAGTCAGTTTAAACTTTGGTTCCATCCAAGCA-ACATGGGCTTTTCCA
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGCTTTTCCA
*
27432 TAAGC
66 CAAGC
27437 CAA
1 CAA
27440 GTTCAATGAT
Statistics
Matches: 255, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
68 42 0.16
69 126 0.49
70 86 0.34
71 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (70 bp):
CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGCAGGGGCTTTTCCA
CAAGC
Found at i:27658 original size:3 final size:3
Alignment explanation
Indices: 27652--27681 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
27642 AAGAGAGAGA
27652 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
27682 GAAAAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30449 original size:21 final size:21
Alignment explanation
Indices: 30384--30455 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
30374 AACTCTGCTG
30384 TTGGGCCTTTAATTAGTTTAA
1 TTGGGCCTTTAATTAGTTTAA
* *
30405 TTGGG-TTTAGCTAACTA-TTT--
1 TTGGGCCTT---TAATTAGTTTAA
30425 TTGGGCCTTTAATTAGTTTAA
1 TTGGGCCTTTAATTAGTTTAA
*
30446 TTGGGTCTTT
1 TTGGGCCTTT
30456 CTAATTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
18 5 0.13
19 3 0.08
20 7 0.18
21 16 0.41
22 3 0.08
23 5 0.13
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (21 bp):
TTGGGCCTTTAATTAGTTTAA
Found at i:36509 original size:33 final size:32
Alignment explanation
Indices: 36412--36516 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 32
36402 TTGCAAAGAG
*
36412 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * *
36445 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
36478 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
*
36511 AGTTTT
1 TGTTTT
36517 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 3 0.05
33 51 0.86
34 5 0.08
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:36572 original size:33 final size:33
Alignment explanation
Indices: 36535--36683 Score: 244
Period size: 33 Copynumber: 4.5 Consensus size: 33
36525 ATTGTGATGA
* *
36535 AAATAAATCTGTTTTGGTTGATCATAACATTGC
1 AAATAATTCTGTTTTGGTTGATCATAGCATTGC
36568 AAATAATTCTGTTTTGGTTGATCATAGCATTGC
1 AAATAATTCTGTTTTGGTTGATCATAGCATTGC
*
36601 AAACAATTCTGTTTTGGTTGATCATAGCATTGC
1 AAATAATTCTGTTTTGGTTGATCATAGCATTGC
* **
36634 AAATAATTCTGTTTTGGTTGATTATAGCATTAA
1 AAATAATTCTGTTTTGGTTGATCATAGCATTGC
36667 AAATAATTCTGTTTTGG
1 AAATAATTCTGTTTTGG
36684 GTGAAAAGAA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 109 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (33 bp):
AAATAATTCTGTTTTGGTTGATCATAGCATTGC
Found at i:50034 original size:26 final size:26
Alignment explanation
Indices: 49971--50034 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
49961 TTTGCATAAA
* * *
49971 TTTAATAACCTCATATTCTTGAAATT
1 TTTAGTAACCTTACATTCTTGAAATT
*
49997 TTTAGTGACCTTACATTCTTAGAAA-T
1 TTTAGTAACCTTACATTCTT-GAAATT
50023 TTTAGTAACCTT
1 TTTAGTAACCTT
50035 TCATCAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (26 bp):
TTTAGTAACCTTACATTCTTGAAATT
Done.