Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2629
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: 6752
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Found at i:372 original size:27 final size:28
Alignment explanation
Indices: 342--403 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
332 TCGAGGACAC
**
342 CCAACCCCGTTA-ATCATCGGGGATACT
1 CCAACCCCGTTACATCAGAGGGGATACT
* *
369 CCAACCCCGTTACTTCCGAGGGGATACT
1 CCAACCCCGTTACATCAGAGGGGATACT
397 CCAACCC
1 CCAACCC
404 TGACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.19
Consensus pattern (28 bp):
CCAACCCCGTTACATCAGAGGGGATACT
Found at i:545 original size:51 final size:49
Alignment explanation
Indices: 390--553 Score: 188
Period size: 51 Copynumber: 3.3 Consensus size: 49
380 ACTTCCGAGG
*
390 GGATACTCCAACCCTGACTTTTATTTCCAAAATA--ACTTTTTCATATCGA
1 GGATACTCCAACCC-GA-TTTTATTTCCAAAATACCAATTTTTCATATCGA
* * * * * *
439 GGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGG
1 GGATACTCCAACCCGATTTTATTTCCAAAATACCAATTTTTC-AT-ATCGA
*
490 GGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAGTCGA
1 GGATACTCCAAC-CCGATTTTATTTCCAAAATACCAATTTTTCATA-TCGA
541 GGATACTCCAACC
1 GGATACTCCAACC
554 TCGTTATTCA
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
47 14 0.15
48 1 0.01
49 20 0.21
50 3 0.03
51 31 0.33
52 26 0.27
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (49 bp):
GGATACTCCAACCCGATTTTATTTCCAAAATACCAATTTTTCATATCGA
Found at i:571 original size:27 final size:28
Alignment explanation
Indices: 541--611 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
531 TCACAGTCGA
* **
541 GGATACTCCAACCTCGTTA-TTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
568 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
596 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
612 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:603 original size:206 final size:204
Alignment explanation
Indices: 228--628 Score: 619
Period size: 206 Copynumber: 2.0 Consensus size: 204
218 ATTCTCCACA
* *
228 ATCGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTCTATAATCGGGGATACTCCAA
1 ATCGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTATAATCGGGGATACTCCAA
293 CTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACCCAACCCCGTTAATCA
66 CTCCGATTTTATTTCC-AAAAACACCAATTTCTTCACAATCGAGGACACCCAACCCCGTTAATCA
* *
358 TCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCTGACTTTTATTTCCAAAAT
130 TCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGAC-TTTATTCCCAAAAT
423 AACTTTTTCAT
194 AACTTTTTCAT
* *
434 ATCGAGGATACTCCAAC-CCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTC
1 ATCG-GGATACTCCAACTCCGATTTTATTTTCAAAACACCAA-TTT-CTATAATCGGGGATACTC
* * * * *
498 CAACTCCGATTTTATTTCC-AAAATACCAATTT-TTCACAGTCGAGGATACTCCAACCTCGTTAT
63 CAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCACAATCGAGGACAC-CCAACCCCGTTAA
*
561 TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAA
127 TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAA
626 ATA
192 ATA
629 TTGATTTCTC
Statistics
Matches: 179, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
205 29 0.16
206 100 0.56
207 14 0.08
208 36 0.20
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (204 bp):
ATCGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTATAATCGGGGATACTCCAA
CTCCGATTTTATTTCCAAAAACACCAATTTCTTCACAATCGAGGACACCCAACCCCGTTAATCAT
CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAA
CTTTTTCAT
Found at i:605 original size:106 final size:105
Alignment explanation
Indices: 280--689 Score: 372
Period size: 106 Copynumber: 3.9 Consensus size: 105
270 TTCTATAATC
* *
280 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACAC-CC
1 GGGGATACTCCAACTCCGATTTTATTTCC--AAAATACCAATTT-TTCACAATCGAGGATACTCC
*
344 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGA
63 AACCCCGTT-ATTATCGGGGATACTCCAACCCCGTTACTTCCGA
* *
388 GGGGATACTCCAAC-CCTGACTTTTATTTCCAAAATA--ACTTTTTCA-TATCGAGGATACTCCA
1 GGGGATACTCCAACTCC-GA-TTTTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCA
* ***** * * ** * *
449 ACCCGGTT-TTATTTTCAAAACACCAATTTTCCTTTA-AT-C--
64 ACCCCGTTATTATCGGGGATACTCCAA--CCCCGTTACTTCCGA
*
488 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAGTCGAGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
*
553 CTCGTTATTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCGTTATT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* ** * *** * * * *
594 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
* *
659 CCCGTTATTTTCGAGGGATACTCCAATCCCG
66 CCCGTTATTATCG-GGGATACTCCAACCCCG
690 ATTTTTTTTC
Statistics
Matches: 238, Mismatches: 48, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
99 16 0.07
100 16 0.07
101 10 0.04
102 36 0.15
103 14 0.06
104 29 0.12
105 7 0.03
106 77 0.32
107 7 0.03
108 16 0.07
109 10 0.04
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
CCCGTTATTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:740 original size:77 final size:77
Alignment explanation
Indices: 565--767 Score: 228
Period size: 77 Copynumber: 2.6 Consensus size: 77
555 CGTTATTCAT
* * *
565 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGA-GGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
630 TGATTTCTCATAAT
64 CGATTTCTCACAAC
* * * ** *
644 TGGGGATACTCCAACCCCGTTATTTTCGAGGGATACTCCAATCCCGATTTTTTTTC-TAATCATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGATACTCCAACCCCGATTTATTCCCAAAAT-ATC
708 GATTTCTCACAAC
65 GATTTCTCACAAC
* * *
721 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGG-ATACTCCAACCCCG
768 TTATTATCTC
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
76 3 0.03
77 49 0.47
78 27 0.26
79 26 0.25
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (77 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGATACTCCAACCCCGATTTATTCCCAAAATATCG
ATTTCTCACAAC
Done.