Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1258
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: 19762
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Found at i:4098 original size:40 final size:40
Alignment explanation
Indices: 4016--4309 Score: 413
Period size: 40 Copynumber: 7.5 Consensus size: 40
4006 AAGCCAAGTA
* * * *
4016 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
4054 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
4094 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
4134 CCTTC-GGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4173 CCTTC-GGACTTAGCCCGGATATAGTAACTCGC-CAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
4211 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
4251 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
4291 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
4310 TTATCATCCG
Statistics
Matches: 234, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
38 23 0.10
39 105 0.45
40 106 0.45
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:11180 original size:40 final size:40
Alignment explanation
Indices: 11105--11365 Score: 384
Period size: 40 Copynumber: 6.6 Consensus size: 40
11095 CTACTTGCTC
* *
11105 AATGCCTTCGGGACATAG-CCGGATATAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
11144 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * *
11184 AATGCCTTCGGAACTTAGCCCGGATGTAATAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
11224 AATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCCCA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
11263 AATGCCTTTGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * * *
11303 AATGCCTTCGGAACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA
11343 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
11366 TTATCATCCG
Statistics
Matches: 200, Mismatches: 19, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
39 52 0.26
40 148 0.74
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:11203 original size:79 final size:79
Alignment explanation
Indices: 11088--11365 Score: 375
Period size: 79 Copynumber: 3.5 Consensus size: 79
11078 GATTTAACCA
* * * *
11088 GATATAGCTACTTGCTC-AATGCCTTCGGGACATAG-CCGGATATAGTAACTCGCACCAATGCCT
1 GATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCT
11151 TCGGGACTTAGCCCG
65 TCGGGACTTAGCCCG
* * *
11166 GATATAGTAGCTCGCACAAATGCCTTCGGAACTTAGCCCGGATGTAATAACTCGCACAAATGCCT
1 GATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCT
11231 TC-GGACTTAGCCCG
65 TCGGGACTTAGCCCG
* *
11245 GATATAGTAACTCGCCCAAATGCCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCT
1 GATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCT
*
11310 TCGGAACTTAGCCCG
65 TCGGGACTTAGCCCG
* *
11325 GA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 GATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
11366 TTATCATCCG
Statistics
Matches: 177, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
77 2 0.01
78 12 0.07
79 89 0.50
80 74 0.42
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
GATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTT
CGGGACTTAGCCCG
Found at i:11316 original size:119 final size:120
Alignment explanation
Indices: 11105--11365 Score: 411
Period size: 119 Copynumber: 2.2 Consensus size: 120
11095 CTACTTGCTC
*
11105 AATGCCTTCGGGACATAG-CCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAT
* ** *
11169 ATAGTAGCTCGCACAAATGCCTTCGGAACTTAGCCCGGATGTAATAACTCGCACA
66 ATAGTAACTCGCACAAATGCCTTCGGAACTTAGCCCGGAACTAATAACTAGCACA
*
11224 AATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGC-CCAAATGCCTTTGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACC-AATGCCTTCGGGACTTAGCCCGGA
* * *
11287 TATAGTAACTCGCACAAATGCCTTCGGAACTTAGCCCGGAACTAGTCACTAGCGCA
65 TATAGTAACTCGCACAAATGCCTTCGGAACTTAGCCCGGAACTAATAACTAGCACA
11343 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
11366 TTATCATCCG
Statistics
Matches: 130, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
118 9 0.07
119 108 0.83
120 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (120 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTCGCACAAATGCCTTCGGAACTTAGCCCGGAACTAATAACTAGCACA
Found at i:18524 original size:40 final size:40
Alignment explanation
Indices: 18443--18737 Score: 377
Period size: 40 Copynumber: 7.5 Consensus size: 40
18433 AAACCAAGTA
* * * *
18443 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
18481 CCTTCGGGACATAGCCCGAATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
18521 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
18561 CCTTC-GGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
** *
18600 CCTTTAGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
18640 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
18680 CCTTCGGGACTTAG-CCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
18719 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
18738 TTATCATCCG
Statistics
Matches: 226, Mismatches: 25, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
38 13 0.06
39 83 0.37
40 130 0.58
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:18575 original size:79 final size:79
Alignment explanation
Indices: 18443--18737 Score: 375
Period size: 79 Copynumber: 3.7 Consensus size: 79
18433 AAACCAAGTA
* * * * * *
18443 CCTTCGGGATTTA-ACCGGATATAGCTACTTGCTC-AATGCCTTCGGGACATAGCCCGAATATAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
18506 TAACTCGCACCAATG
65 TAACTCGCACAAATG
* * *
18521 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGTACAAATGCCTTC-GGACTTAGCCCGGATGTAA
1 CCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
18585 TAACTCGCACAAATG
65 TAACTCGCACAAATG
** *
18600 CCTTTAGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
18665 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* *
18680 CCTTCGGGACTTAG-CCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
18738 TTATCATCCG
Statistics
Matches: 189, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
78 15 0.08
79 120 0.63
80 54 0.29
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGCACAAATG
Found at i:18698 original size:119 final size:119
Alignment explanation
Indices: 18477--18737 Score: 380
Period size: 119 Copynumber: 2.2 Consensus size: 119
18467 CTACTTGCTC
* * * *
18477 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGAT
* * ** *
18542 ATAGTAGCTCGTACAAATGCCTTCGGACTTAGCCCGGATGTAATAACTCGCACA
66 ATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGAACTAATAACTAGCACA
**
18596 AATGCCTTTAGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGAT
* * *
18661 ATAGTAACTCGCACAAATGCCTTCGGGACTTAG-CCGGAACTAGTCACTAGCGCA
66 ATAGTAACTCGCACAAATGCCTTC-GGACTTAGCCCGGAACTAATAACTAGCACA
18715 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
18738 TTATCATCCG
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
119 117 0.94
120 8 0.06
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGAACTAATAACTAGCACA
Done.