Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011777.1 Corchorus capsularis cultivar CVL-1 contig11798, 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: 96546
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:64 original size:21 final size:21
Alignment explanation
Indices: 20--64 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10 TTTATTGGGA
*
20 TTTGCTAAACACCGCCCCCCT
1 TTTGCTAAACACCACCCCCCT
* * *
41 TTTGCTAAATACCACTCCCTT
1 TTTGCTAAACACCACCCCCCT
62 TTT
1 TTT
65 ATAATTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.38, G:0.07, T:0.36
Consensus pattern (21 bp):
TTTGCTAAACACCACCCCCCT
Found at i:261 original size:24 final size:21
Alignment explanation
Indices: 216--262 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
206 CGGCTAGGCC
*
216 ATTTTTTTTATTTATTTATTT
1 ATTTTTTTTATTTAATTATTT
237 ATTTTTTTTAATATTAATTAGTTT
1 ATTTTTTTT-AT-TTAATTA-TTT
261 AT
1 AT
263 GATTAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 6 0.27
24 5 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTTTTTTATTTAATTATTT
Found at i:325 original size:20 final size:20
Alignment explanation
Indices: 300--337 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
290 TACTAAGTTT
* *
300 ATTAGTTTTTGTTTAATTTA
1 ATTAGTTTATGATTAATTTA
320 ATTAGTTTATGATTAATT
1 ATTAGTTTATGATTAATT
338 AGTATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (20 bp):
ATTAGTTTATGATTAATTTA
Found at i:337 original size:15 final size:15
Alignment explanation
Indices: 317--361 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
307 TTTGTTTAAT
317 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
332 TTAATTAG--TAT--
1 TTAATTAGTTTATGA
343 TTAATTAGTTTATGA
1 TTAATTAGTTTATGA
358 TTAA
1 TTAA
362 AATGAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.31
13 6 0.23
15 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
TTAATTAGTTTATGA
Found at i:403 original size:24 final size:25
Alignment explanation
Indices: 371--425 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
361 AAATGAAGGA
*
371 AAATG-AATTTGAAG-ATTTGTTAG
1 AAATGAAATTTGAAGAAGTTGTTAG
394 AAATGAAATTTGAAGAAGTTGTTAG
1 AAATGAAATTTGAAGAAGTTGTTAG
419 AAATGAA
1 AAATGAA
426 GTTTAGGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 5 0.17
24 9 0.31
25 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (25 bp):
AAATGAAATTTGAAGAAGTTGTTAG
Found at i:525 original size:21 final size:21
Alignment explanation
Indices: 496--539 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
486 GCAAAAGTGT
*
496 AAAAAGGGGGTGGTATTTAGC
1 AAAAAGGGGGCGGTATTTAGC
* *
517 AAAAGGGGGGCGGTGTTTAGC
1 AAAAAGGGGGCGGTATTTAGC
538 AA
1 AA
540 TCCAGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (21 bp):
AAAAAGGGGGCGGTATTTAGC
Found at i:10400 original size:12 final size:12
Alignment explanation
Indices: 10383--10408 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10373 TTTAGTATGG
10383 CTAAGCATTACT
1 CTAAGCATTACT
10395 CTAAGCATTACT
1 CTAAGCATTACT
10407 CT
1 CT
10409 GATTCAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
CTAAGCATTACT
Found at i:18876 original size:11 final size:11
Alignment explanation
Indices: 18860--18888 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
18850 CTGCTTTTTA
18860 AATAAATTGTG
1 AATAAATTGTG
18871 AATAAATTGTG
1 AATAAATTGTG
18882 AATAAAT
1 AATAAAT
18889 GTCCTCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (11 bp):
AATAAATTGTG
Found at i:26237 original size:25 final size:25
Alignment explanation
Indices: 26203--26250 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
26193 CTGTATCTTG
26203 AATCTCAAATAACCTTGCCAAAAAA
1 AATCTCAAATAACCTTGCCAAAAAA
26228 AATCTCAAATAACCTTGCCAAAA
1 AATCTCAAATAACCTTGCCAAAA
26251 TGATTAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.21
Consensus pattern (25 bp):
AATCTCAAATAACCTTGCCAAAAAA
Found at i:31168 original size:2 final size:2
Alignment explanation
Indices: 31161--31188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31151 ACAAAGATGC
31161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31189 CTGTGCGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45987 original size:2 final size:2
Alignment explanation
Indices: 45980--46009 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45970 GCCAAATGTG
*
45980 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46010 GTTATTGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:51402 original size:77 final size:77
Alignment explanation
Indices: 51275--51428 Score: 274
Period size: 77 Copynumber: 2.0 Consensus size: 77
51265 GGATTAGAAG
51275 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTGGTTGCTTTTTATGTGC-ATC
1 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTGGTTGCTTTTTATGTGCTA-C
51339 TTGATCATTTGTT
65 TTGATCATTTGTT
* *
51352 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAGTATTGTTGGTTGCTTTTTCTGTGCTACT
1 GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTGGTTGCTTTTTATGTGCTACT
51417 TGATCATTTGTT
66 TGATCATTTGTT
51429 CCTTTGGCTT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 73 0.99
78 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (77 bp):
GTCTGCTAAACCAATCTCGTTCTCCATATATCTTAAATATTGTTGGTTGCTTTTTATGTGCTACT
TGATCATTTGTT
Found at i:59800 original size:64 final size:64
Alignment explanation
Indices: 59722--59883 Score: 315
Period size: 64 Copynumber: 2.5 Consensus size: 64
59712 GCCATGTGAC
59722 AATATCTTTGGTATTGATCCGTTTTACATTGAAACAGGTATTAATTTATCCAATGTAAATATAA
1 AATATCTTTGGTATTGATCCGTTTTACATTGAAACAGGTATTAATTTATCCAATGTAAATATAA
59786 AATATCTTTGGTATTGATCCGTTTTACATTGAAACAGGTATTAATTTATCCAATGTAAATATAA
1 AATATCTTTGGTATTGATCCGTTTTACATTGAAACAGGTATTAATTTATCCAATGTAAATATAA
*
59850 AATATCTTTGGTATTGATCCGTTTTACAATGAAA
1 AATATCTTTGGTATTGATCCGTTTTACATTGAAA
59884 GTCCACTATG
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 97 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (64 bp):
AATATCTTTGGTATTGATCCGTTTTACATTGAAACAGGTATTAATTTATCCAATGTAAATATAA
Found at i:67621 original size:2 final size:2
Alignment explanation
Indices: 67614--67640 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67604 CAATAATGGG
67614 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
67641 GACAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88057 original size:2 final size:2
Alignment explanation
Indices: 88050--88109 Score: 59
Period size: 2 Copynumber: 30.0 Consensus size: 2
88040 TAGTCTTCTG
* * * *
88050 AT AT AT AT CCT AT AT A- AT AT AT AC AT AT AC AT AC AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
88092 AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
88110 TAGATTGATG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:88085 original size:10 final size:10
Alignment explanation
Indices: 88066--88109 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
88056 ATCCTATATA
88066 ATATATACAT
1 ATATATACAT
*
88076 ATACATACAT
1 ATATATACAT
88086 ATATATACAT
1 ATATATACAT
*
88096 ATATATATAT
1 ATATATACAT
88106 ATAT
1 ATAT
88110 TAGATTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATACAT
Found at i:90218 original size:21 final size:23
Alignment explanation
Indices: 90181--90222 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
90171 ATATTGTTAT
90181 TCAATTCATTCTTTTTAACTAAA
1 TCAATTCATTCTTTTTAACTAAA
90204 TCAATTCA-T-TTTTTAACTA
1 TCAATTCATTCTTTTTAACTA
90223 TACTATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (23 bp):
TCAATTCATTCTTTTTAACTAAA
Found at i:95993 original size:2 final size:2
Alignment explanation
Indices: 95988--96032 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
95978 TTTGTGTGTG
* *
95988 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
96031 TA
1 TA
96033 CGAGTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:96327 original size:108 final size:108
Alignment explanation
Indices: 96118--96391 Score: 428
Period size: 108 Copynumber: 2.5 Consensus size: 108
96108 ACTATTATAG
*
96118 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
96183 TATTTTTACCAAAAAATATGGATATACTAAAATTTTTCTAATATACAA
61 TATTTTTACCAAAAAATATGGATATACTAAAATTTTTCTAATATACAA
96231 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTA-TT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
96295 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATATGGATATACTAAAA-TTTTTCTAATATACAA
96339 TTTTATTCTACTAAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACT-AAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
96392 TAGTTTTTTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
107 27 0.17
108 69 0.45
109 35 0.23
110 2 0.01
113 22 0.14
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATATGGATATACTAAAATTTTTCTAATATACAA
Done.