Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015024.1 Corchorus olitorius cultivar O-4 contig15057, 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: 15052
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:65 original size:2 final size:2
Alignment explanation
Indices: 7--48 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 GTAAAG
7 TA TA TA TA TA 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 TA TA TA TA TA
49 CTCCTATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:340 original size:18 final size:19
Alignment explanation
Indices: 317--355 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
307 GGTAAACTTG
*
317 TTTGTACCTGT-TATTTGT
1 TTTGTAACTGTATATTTGT
*
335 TTTGTAAGTGTATATTTGT
1 TTTGTAACTGTATATTTGT
354 TT
1 TT
356 CCACACATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.15, C:0.05, G:0.18, T:0.62
Consensus pattern (19 bp):
TTTGTAACTGTATATTTGT
Found at i:405 original size:15 final size:15
Alignment explanation
Indices: 387--431 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
377 ATATCATCAT
*
387 AATATATCCTTCAAA
1 AATATATCCTTAAAA
*
402 AATATATTCTTTAAAA
1 AATATA-TCCTTAAAA
*
418 AATACATCCTTAAA
1 AATATATCCTTAAA
432 TATCCTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATATCCTTAAAA
Found at i:1072 original size:2 final size:2
Alignment explanation
Indices: 1065--1092 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1055 AATGGGTAGG
1065 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
1093 TATTTACATT
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:1223 original size:13 final size:14
Alignment explanation
Indices: 1192--1232 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1182 TATTGAACTG
*
1192 TATAGTGTTTTTAT
1 TATAATGTTTTTAT
*
1206 AATAATGTTTTT-T
1 TATAATGTTTTTAT
1219 TATAAT-TTTTTAT
1 TATAATGTTTTTAT
1232 T
1 T
1233 TTGCATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 5 0.22
13 8 0.35
14 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TATAATGTTTTTAT
Found at i:1455 original size:16 final size:16
Alignment explanation
Indices: 1420--1461 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1410 GAAATGTGTC
*
1420 TTCCTTTCCCTTGCTGT
1 TTCCTTT-CCTTGCTAT
*
1437 TTCCTTTCCTTTCTAT
1 TTCCTTTCCTTGCTAT
1453 TT-CTTTCCT
1 TTCCTTTCCT
1462 CCCTACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.02, C:0.33, G:0.05, T:0.60
Consensus pattern (16 bp):
TTCCTTTCCTTGCTAT
Found at i:12400 original size:125 final size:125
Alignment explanation
Indices: 12202--12524 Score: 378
Period size: 125 Copynumber: 2.6 Consensus size: 125
12192 TTTGTATATA
* * * * *
12202 TCGGAACAAGTTTTTCACATCAATTGATCTCGACGTATTCCGACATTTGTAAGTGTTGTTTTAGA
1 TCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAGCGTTGGTATAGA
* * * *
12267 TATTATATAGGGACATTTAGTAAACGTCGCTACAAAATATTATACCGTCCCTTAT-AAATG
66 TATTATATAGGGACATTTAGTAAACATCGCTACAAAATAATATACCG-ACATTATCAAATG
* * *
12327 TCGGAATAAATTTTTCACATCATTTGATTTTGACGTATTCCGACATTTGTAAGCGTTGGTATAGA
1 TCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAGCGTTGGTATAGA
* ** * *
12392 TATTATATAGTGACATTTAGTAAGTATCGCTATAAAATAATATACCGACATTTTCAAATG
66 TATTATATAGGGACATTTAGTAAACATCGCTACAAAATAATATACCGACATTATCAAATG
* * * * * * * * * * *
12452 TCAGCACAGGTTATTCACATCATTTGAATTCAACATATTCCGACATTTATAAACATTGGTATAGC
1 TCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAGCGTTGGTATAGA
12517 TATTATAT
66 TATTATAT
12525 CGTGATATTA
Statistics
Matches: 166, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
124 4 0.02
125 162 0.98
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (125 bp):
TCGGAACAAGTTTTTCACATCATTTGATTTCGACGTATTCCGACATTTGTAAGCGTTGGTATAGA
TATTATATAGGGACATTTAGTAAACATCGCTACAAAATAATATACCGACATTATCAAATG
Found at i:12566 original size:125 final size:125
Alignment explanation
Indices: 12340--12584 Score: 292
Period size: 125 Copynumber: 2.0 Consensus size: 125
12330 GAATAAATTT
* ** * * * *
12340 TTCACATCATTTGATTTTGACGTATTCCGACATTTGTAAGCGTTGGTATAGATATTATATAGTGA
1 TTCACATCATTTGAATTCAACATATTCCGACATTTATAAACATTGGTATAGATATTATATAGTGA
* * * * *
12405 CATTTAGTAAGTATCGCTATAAAATAATATACCGACATTTTCAAATGTCAGCACAGGTTA
66 CATTAAGTAAATATCACTATAAAATAATATACCGACATTTACAAATATCAGCACAGGTTA
* *
12465 TTCACATCATTTGAATTCAACATATTCCGACATTTATAAACATTGGTATAGCTATTATATCGTGA
1 TTCACATCATTTGAATTCAACATATTCCGACATTTATAAACATTGGTATAGATATTATATAGTGA
* * * * * * * *
12530 TATTAATTAAATGTCACTTTAAATTACTATATCGACATTTACAAATATCGGCACA
66 CATTAAGTAAATATCACTATAAAATAATATACCGACATTTACAAATATCAGCACA
12585 AATATGCACA
Statistics
Matches: 98, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
125 98 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (125 bp):
TTCACATCATTTGAATTCAACATATTCCGACATTTATAAACATTGGTATAGATATTATATAGTGA
CATTAAGTAAATATCACTATAAAATAATATACCGACATTTACAAATATCAGCACAGGTTA
Found at i:14277 original size:125 final size:127
Alignment explanation
Indices: 14141--14395 Score: 401
Period size: 125 Copynumber: 2.0 Consensus size: 127
14131 TTGTTTAAAA
*
14141 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-TA-
1 TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTAT
14202 ATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTTAAATATAC
66 ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAA-TTTTTTAAATATAC
*
14266 TTTTACAGTTTTACTCAACTAAAAACTCTGTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-CTA
*
14331 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTATAATTTTTTAAATATA
65 ---TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATA
14396 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
125 52 0.44
126 3 0.03
127 2 0.02
129 2 0.02
131 13 0.11
132 21 0.18
133 26 0.22
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (127 bp):
TTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTAT
ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATAC
Found at i:14412 original size:14 final size:13
Alignment explanation
Indices: 14381--14419 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
14371 TATATATTAT
14381 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
14394 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
14408 AATTTTTTAAAT
1 AATTTTTTAAAT
14420 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.