Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2545
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: 34977
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Found at i:4415 original size:40 final size:39
Alignment explanation
Indices: 4266--4416 Score: 203
Period size: 40 Copynumber: 3.8 Consensus size: 39
4256 GGATGATAAC
* * *
4266 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * * *
4305 CTGGGCTAACTCCTGAAGGCATTTGTGCAAGTTACTATAT
1 C-GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
4345 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAAT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
*
4386 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
4417 AGTTATATCC
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 93 0.95
41 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:4428 original size:80 final size:80
Alignment explanation
Indices: 4265--4412 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 80
4255 CGGATGATAA
* * *
4265 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAACTCCTGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAATCTGGGCTAACTCCCGAAGGCATTTG
*
4330 TGCAAGTTACTATAT
66 AGCAAGTTACTATAT
* *
4345 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAATC-GGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT-AAATCTGGGCTAACTCCCGAAGGCATTT
4409 GAGC
65 GAGC
4413 GAGTAGTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 57 0.93
81 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAATCTGGGCTAACTCCCGAAGGCATTTG
AGCAAGTTACTATAT
Found at i:12586 original size:40 final size:40
Alignment explanation
Indices: 12436--12587 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
12426 CGGATGATAA
* * *
12436 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* * * *
12476 CCGGGCTAACTTCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
12516 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
*
12557 -CGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
12588 AGTTATATCC
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 97 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:20234 original size:40 final size:40
Alignment explanation
Indices: 20134--20350 Score: 253
Period size: 40 Copynumber: 5.5 Consensus size: 40
20124 CGGATGATAA
* *
20134 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
20174 CCGGGCTAAG-CCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
20213 CCGGGCTAACTCCCGAAGGCATTTGTGAAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
20253 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
20293 CCGGGTTAAGTCCCAAAGGCATTTGAGCGAG-TAGTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
20333 CC-GGATAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20351 TACCGGGTTG
Statistics
Matches: 151, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
39 48 0.32
40 103 0.68
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:20346 original size:119 final size:119
Alignment explanation
Indices: 20134--20350 Score: 294
Period size: 119 Copynumber: 1.8 Consensus size: 119
20124 CGGATGATAA
* ** * *
20134 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATTCGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAAACCGGGCTAAGCCCAAAGGCATTCGA
* *
20199 GCGAGTTACTATATCCGGGCTAACTCCCGAAGGCATTTGTGAAAGTTACTATAT
66 GCGAGTTACTATATCCGGGATAAATCCCGAAGGCATTTGTGAAAGTTACTATAT
* * * *
20253 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAAACCGGGTTAAGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAAACCGGGCTAAG-CCCAAAGGCATTCG
*
20318 AGCGAG-TAGTTATATCC-GGATAAATCCCGAAGG
65 AGCGAGTTA-CTATATCCGGGATAAATCCCGAAGG
20351 TACCGGGTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
119 60 0.71
120 24 0.29
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAAACCGGGCTAAGCCCAAAGGCATTCGA
GCGAGTTACTATATCCGGGATAAATCCCGAAGGCATTTGTGAAAGTTACTATAT
Found at i:27603 original size:40 final size:40
Alignment explanation
Indices: 27559--27786 Score: 264
Period size: 40 Copynumber: 5.7 Consensus size: 40
27549 GCCACTAGCT
*
27559 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
27599 CAAATGCCTTCGGGACTTAGCCCGGTT-TAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
27638 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* ** * *
27678 CAAACGCCTTCGGGACTTAGCCCGAATATAGTAGCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * ** *
27718 CGAATGCCTTCGGAACTTAGCCCGG-AATTAGCCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
27758 CAAATG-CTCTCGGGACTTAGCCCGGTTAT
1 CAAATGCCT-TCGGGACTTAGCCCGGTTAT
27787 CATCCGAACA
Statistics
Matches: 161, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 39 0.24
40 121 0.75
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:27657 original size:79 final size:78
Alignment explanation
Indices: 27559--27784 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
27549 GCCACTAGCT
*
27559 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
*
27624 TTTAATAACTCGCA
65 TTTAATAACTCACA
* * * * *
27638 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGTACAAACGCCTTCGGGACTTAGCCCGA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG-
* * * *
27703 ATATAGTAGCTCACA
64 GTTTAATAACTCACA
* * * **
27718 CGAATGCCTTCGGAACTTAGCCCGGAATTAGCCACTAGCACAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTAGCACAAATGCCT-TCGGGACTTAGCCCG
27782 GTT
64 GTT
27785 ATCATCCGAA
Statistics
Matches: 121, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
79 62 0.51
80 59 0.49
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
TTAATAACTCACA
Done.