Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1312
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: 28247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:15909 original size:20 final size:19
Alignment explanation
Indices: 15863--15915 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 19
15853 TATATATGTT
15863 TATT-AATTATTTA-TT-A
1 TATTAAATTATTTATTTAA
*
15879 TATTTAA-TATTTATTTAA
1 TATTAAATTATTTATTTAA
15897 TATTAAAATTATTT-TTTAA
1 TATT-AAATTATTTATTTAA
15916 ATCAATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 5 0.16
19 7 0.23
20 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTAAATTATTTATTTAA
Found at i:16406 original size:16 final size:16
Alignment explanation
Indices: 16368--16408 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
16358 CAATTGAATT
16368 ATTTAATTAAAAAAATA
1 ATTT-ATTAAAAAAATA
*
16385 A-ATATTAAAAAAATA
1 ATTTATTAAAAAAATA
16400 ATTTATTAA
1 ATTTATTAA
16409 TAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 13 0.62
16 7 0.33
17 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTTATTAAAAAAATA
Found at i:16422 original size:16 final size:15
Alignment explanation
Indices: 16373--16422 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
16363 GAATTATTTA
*
16373 ATTAAAAAAATAAAT
1 ATTAAAAAAATATAT
*
16388 ATTAAAAAAATAATTT
1 ATTAAAAAAAT-ATAT
*
16404 ATTAATAAATATATAT
1 ATTAA-AAAAATATAT
16420 ATT
1 ATT
16423 TAATTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 11 0.38
16 13 0.45
17 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAAAAATATAT
Found at i:16555 original size:20 final size:21
Alignment explanation
Indices: 16513--16566 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
16503 AAAAATAATC
16513 TTTTTATTAATTTAATCTGAT
1 TTTTTATTAATTTAATCTGAT
*
16534 TTTTTATTAA-TTCAT-TGAAT
1 TTTTTATTAATTTAATCTG-AT
16554 TTTTTATT-ATTTA
1 TTTTTATTAATTTA
16567 TTATATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 3 0.10
20 16 0.55
21 10 0.34
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTTATTAATTTAATCTGAT
Found at i:16840 original size:2 final size:2
Alignment explanation
Indices: 16833--16863 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16823 TTTAGCCCCT
16833 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16864 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16868 original size:2 final size:2
Alignment explanation
Indices: 16863--16898 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16853 TCTCTCTCTC
*
16863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16899 CACTTTCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17243 original size:30 final size:30
Alignment explanation
Indices: 17203--17364 Score: 207
Period size: 30 Copynumber: 5.4 Consensus size: 30
17193 TGTTGGTCTT
* * **
17203 GGTGCTGCTGCAGGTGGAGCAGGAGCTCTC
1 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
17233 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
1 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
***
17263 GGTGCCGCTGCTCACGGAGCAGCTGCTCTC
1 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
17293 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
1 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
* *** **
17323 CGTGCCGCTGCTCACGGAGCAGGAGCTCTC
1 GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
17353 GGTGCCGCTGCT
1 GGTGCCGCTGCT
17365 CTCGGTGCCG
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 115 1.00
ACGTcount: A:0.09, C:0.31, G:0.38, T:0.21
Consensus pattern (30 bp):
GGTGCCGCTGCTGGTGGAGCAGCTGCTCTC
Found at i:17296 original size:60 final size:60
Alignment explanation
Indices: 17218--17559 Score: 333
Period size: 60 Copynumber: 5.5 Consensus size: 60
17208 TGCTGCAGGT
*
17218 GGAGCAGGAGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCGGTGCCGCTGCTCAC
1 GGAGCAGGAGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCCGTGCCGCTGCTCAC
**
17278 GGAGCAGCTGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCCGTGCCGCTGCTCAC
1 GGAGCAGGAGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCCGTGCCGCTGCTCAC
* * *
17338 GGAGCAGGAGCTCTCGGTGCCGCTGCTCTCGGTGCCGCAGCTCACGGAGCAGGAGCCCTCGGTGC
1 GGAGCAGGAGCTCTCGGTGCCGCTG--CT-GGTG--G-AG----C--AGC---TGCTCTCCGTGC
17403 CGCTGCTCAC
51 CGCTGCTCAC
* *** * * *
17413 GGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCCCTCGGTGCCGCTGCTCAC
1 GGAGCAGGAGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCCGTGCCGCTGCTCAC
* **** ** * *
17473 GGAGCAGGTGCTCTCGGTGCCGCTGCTCACAGAGCAGGAGCTCTCGGTGCCGCTGCTCAT
1 GGAGCAGGAGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCCGTGCCGCTGCTCAC
* *
17533 GGAGCAGGTGCTCTCGGTGCCACTGCT
1 GGAGCAGGAGCTCTCGGTGCCGCTGCT
17560 CATGGAGCTG
Statistics
Matches: 248, Mismatches: 19, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
60 183 0.74
62 2 0.01
63 6 0.02
65 2 0.01
66 2 0.01
69 2 0.01
70 2 0.01
72 4 0.02
73 2 0.01
75 43 0.17
ACGTcount: A:0.11, C:0.34, G:0.36, T:0.19
Consensus pattern (60 bp):
GGAGCAGGAGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGCTCTCCGTGCCGCTGCTCAC
Found at i:17332 original size:15 final size:15
Alignment explanation
Indices: 17227--17560 Score: 215
Period size: 15 Copynumber: 22.3 Consensus size: 15
17217 TGGAGCAGGA
17227 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * *
17242 GCTGGT-GGAGCAGCT
1 GCT-CTCGGTGCCGCT
17257 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * *
17272 GCTCACGGAGCAGCT
1 GCTCTCGGTGCCGCT
17287 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * *
17302 GCTGGT-GGAGCAGCT
1 GCT-CTCGGTGCCGCT
*
17317 GCTCTCCGTGCCGCT
1 GCTCTCGGTGCCGCT
* * * **
17332 GCTCACGGAGCAGGA
1 GCTCTCGGTGCCGCT
17347 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
*
17362 GCTCTCGGTGCCGCA
1 GCTCTCGGTGCCGCT
* * * **
17377 GCTCACGGAGCAGGA
1 GCTCTCGGTGCCGCT
*
17392 GCCCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * * *
17407 GCTCACGGAGCAGGT
1 GCTCTCGGTGCCGCT
17422 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * * *
17437 GCTCACGGAGCAGGT
1 GCTCTCGGTGCCGCT
*
17452 GCCCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * * *
17467 GCTCACGGAGCAGGT
1 GCTCTCGGTGCCGCT
17482 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * * * **
17497 GCTCACAGAGCAGGA
1 GCTCTCGGTGCCGCT
17512 GCTCTCGGTGCCGCT
1 GCTCTCGGTGCCGCT
* * *
17527 GCTCAT-GGAGCAGGT
1 GCTC-TCGGTGCCGCT
*
17542 GCTCTCGGTGCCACT
1 GCTCTCGGTGCCGCT
17557 GCTC
1 GCTC
17561 ATGGAGCTGG
Statistics
Matches: 226, Mismatches: 87, Indels: 12
0.70 0.27 0.04
Matches are distributed among these distances:
14 3 0.01
15 220 0.97
16 3 0.01
ACGTcount: A:0.10, C:0.34, G:0.36, T:0.20
Consensus pattern (15 bp):
GCTCTCGGTGCCGCT
Found at i:17380 original size:30 final size:30
Alignment explanation
Indices: 17347--17606 Score: 285
Period size: 30 Copynumber: 8.7 Consensus size: 30
17337 CGGAGCAGGA
* * * *
17347 GCTCTCGGTGCCGCTGCTCTCGGTGCCGCA
1 GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
* * *
17377 GCTCACGGAGCAGGAGCCCTCGGTGCCGCT
1 GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
*
17407 GCTCACGGAGCAGGTGCTCTCGGTGCCGCT
1 GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
* *
17437 GCTCACGGAGCAGGTGCCCTCGGTGCCGCT
1 GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
*
17467 GCTCACGGAGCAGGTGCTCTCGGTGCCGCT
1 GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
* * *
17497 GCTCACAGAGCAGGAGCTCTCGGTGCCGCT
1 GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
*
17527 GCTCAT-GGAGCAGGTGCTCTCGGTGCCACT
1 GCTC-TCGGAGCAGGTGCTCTCGGTGCCGCT
* * * *
17557 GCTCAT-GGAGCTGGTTCTATTGGTGCCAG-T
1 GCTC-TCGGAGCAGGTGCTCTCGGTGCC-GCT
17587 GCTCAT-GGAGCAGGTGCTCT
1 GCTC-TCGGAGCAGGTGCTCT
17607 TAAAGGCGCT
Statistics
Matches: 203, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
30 203 1.00
ACGTcount: A:0.12, C:0.32, G:0.35, T:0.21
Consensus pattern (30 bp):
GCTCTCGGAGCAGGTGCTCTCGGTGCCGCT
Found at i:17399 original size:105 final size:105
Alignment explanation
Indices: 17254--17470 Score: 335
Period size: 105 Copynumber: 2.1 Consensus size: 105
17244 TGGTGGAGCA
* * * ***
17254 GCTGCTCTCGGTGCCGCTGCTCACGGAGCAGCTGCTCTCGGTGCCGCTGCTGGTGGAGCAGCTGC
1 GCTGCTCTCGGTGCCGCAGCTCACGGAGCAGCAGCCCTCGGTGCCGCTGCTCACGGAGCAGCTGC
*
17319 TCTCCGTGCCGCTGCTCACGGAGCAGGAGCTCTCGGTGCC
66 TCTCCGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCC
* *
17359 GCTGCTCTCGGTGCCGCAGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGGTGC
1 GCTGCTCTCGGTGCCGCAGCTCACGGAGCAGCAGCCCTCGGTGCCGCTGCTCACGGAGCAGCTGC
* *
17424 TCTCGGTGCCGCTGCTCACGGAGCAGGTGCCCTCGGTGCC
66 TCTCCGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCC
17464 GCTGCTC
1 GCTGCTC
17471 ACGGAGCAGG
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.09, C:0.36, G:0.35, T:0.19
Consensus pattern (105 bp):
GCTGCTCTCGGTGCCGCAGCTCACGGAGCAGCAGCCCTCGGTGCCGCTGCTCACGGAGCAGCTGC
TCTCCGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCC
Found at i:17501 original size:90 final size:90
Alignment explanation
Indices: 17365--17606 Score: 342
Period size: 90 Copynumber: 2.7 Consensus size: 90
17355 TGCCGCTGCT
* * *
17365 CTCGGTGCCGCAGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGG
1 CTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGG
17430 TGCCGCTGCTCACGGAGCAGGTGCC
66 TGCCGCTGCTCACGGAGCAGGTGCC
* *
17455 CTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACAGAGCAGGAGCTCTCGG
1 CTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGG
* *
17520 TGCCGCTGCTCATGGAGCAGGTGCT
66 TGCCGCTGCTCACGGAGCAGGTGCC
* * * * * * *
17545 CTCGGTGCCACTGCTCATGGAGCTGGTTCTATTGGTGCCAG-TGCTCATGGAGCAGGTGCTCT
1 CTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCC-GCTGCTCACGGAGCAGGTGCTCT
17607 TAAAGGCGCT
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
90 134 0.99
91 1 0.01
ACGTcount: A:0.12, C:0.32, G:0.35, T:0.21
Consensus pattern (90 bp):
CTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGG
TGCCGCTGCTCACGGAGCAGGTGCC
Found at i:17560 original size:60 final size:60
Alignment explanation
Indices: 17361--17567 Score: 351
Period size: 60 Copynumber: 3.5 Consensus size: 60
17351 TCGGTGCCGC
*
17361 TGCTCTCGGTGCCGCAGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGG
*
17421 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCCCTCGGTGCCGCTGCTCACGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGG
* * *
17481 TGCTCTCGGTGCCGCTGCTCACAGAGCAGGAGCTCTCGGTGCCGCTGCTCATGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGG
* *
17541 TGCTCTCGGTGCCACTGCTCATGGAGC
1 TGCTCTCGGTGCCGCTGCTCACGGAGC
17568 TGGTTCTATT
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 138 1.00
ACGTcount: A:0.12, C:0.34, G:0.35, T:0.19
Consensus pattern (60 bp):
TGCTCTCGGTGCCGCTGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGG
Found at i:17582 original size:60 final size:60
Alignment explanation
Indices: 17361--17606 Score: 350
Period size: 60 Copynumber: 4.1 Consensus size: 60
17351 TCGGTGCCGC
* * *
17361 TGCTCTCGGTGCCGCAGCTCACGGAGCAGGAGCCCTCGGTGCCGCTGCTCACGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGG
*
17421 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCCCTCGGTGCCGCTGCTCACGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGG
* * *
17481 TGCTCTCGGTGCCGCTGCTCACAGAGCAGGAGCTCTCGGTGCCGCTGCTCATGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGG
* * * * * * *
17541 TGCTCTCGGTGCCACTGCTCATGGAGCTGGTTCTATTGGTGCCAG-TGCTCATGGAGCAGG
1 TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCC-GCTGCTCACGGAGCAGG
17601 TGCTCT
1 TGCTCT
17607 TAAAGGCGCT
Statistics
Matches: 171, Mismatches: 14, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
60 170 0.99
61 1 0.01
ACGTcount: A:0.12, C:0.32, G:0.35, T:0.21
Consensus pattern (60 bp):
TGCTCTCGGTGCCGCTGCTCACGGAGCAGGTGCTCTCGGTGCCGCTGCTCACGGAGCAGG
Found at i:17689 original size:30 final size:30
Alignment explanation
Indices: 17648--17713 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
17638 GCTGCTGTTA
*
17648 CTCGTGGAGCA-GCTACTCTTGGTGCCGCTG
1 CTCGTGAAGCAGGC-ACTCTTGGTGCCGCTG
*
17678 CTCGTGAAGCAGGCGCTCTTGGTGCCGCTG
1 CTCGTGAAGCAGGCACTCTTGGTGCCGCTG
17708 CTCGTG
1 CTCGTG
17714 GAGGTTTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.09, C:0.30, G:0.35, T:0.26
Consensus pattern (30 bp):
CTCGTGAAGCAGGCACTCTTGGTGCCGCTG
Found at i:18471 original size:21 final size:22
Alignment explanation
Indices: 18434--18476 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
18424 TGATAAAATA
18434 TTAAATTAATTAGATAT-TCTT
1 TTAAATTAATTAGATATATCTT
*
18455 TTAAA-TAATATATATATATCTT
1 TTAAATTAAT-TAGATATATCTT
18477 CCTACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTAATTAGATATATCTT
Found at i:19841 original size:79 final size:79
Alignment explanation
Indices: 19750--19903 Score: 238
Period size: 80 Copynumber: 1.9 Consensus size: 79
19740 TTTGACAAAT
* * * *
19750 ATTATTATATTAATATGT-AAAAAATATAAGTAATTTTTTTAAAAATGAAATTAATAGGTAGTTC
1 ATTATTAGATTAATATGTAAAAAAATATAAGCAATCTTTTTAAAAATGAAATTAATAGGCAGTT-
19814 TTTTAAAAGTGCAAG
65 TTTTAAAAGTGCAAG
* *
19829 ATTATTAGATTAATATGTAAAAAAATATAAGCAATCTTTTTAAAAGTGAAATTAATGGGCAGTTT
1 ATTATTAGATTAATATGTAAAAAAATATAAGCAATCTTTTTAAAAATGAAATTAATAGGCAGTTT
19894 TTTAAAAGTG
66 TTTAAAAGTG
19904 AAATTAATAG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 28 0.41
80 40 0.59
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (79 bp):
ATTATTAGATTAATATGTAAAAAAATATAAGCAATCTTTTTAAAAATGAAATTAATAGGCAGTTT
TTTAAAAGTGCAAG
Found at i:19932 original size:27 final size:27
Alignment explanation
Indices: 19865--19923 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
19855 ATAAGCAATC
*
19865 TTTTTAAAAGTGAAATTAATGGGCAGT
1 TTTTTAAAAGTGAAATTAATAGGCAGT
*
19892 TTTTTAAAAGTGAAATTAATAGGTAGT
1 TTTTTAAAAGTGAAATTAATAGGCAGT
19919 TTTTT
1 TTTTT
19924 TTATGTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.44
Consensus pattern (27 bp):
TTTTTAAAAGTGAAATTAATAGGCAGT
Found at i:21493 original size:13 final size:13
Alignment explanation
Indices: 21475--21500 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21465 AATTTTTTTG
21475 TGTATCGATACAT
1 TGTATCGATACAT
21488 TGTATCGATACAT
1 TGTATCGATACAT
21501 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:24515 original size:34 final size:35
Alignment explanation
Indices: 24477--24543 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
24467 CCTTACAACA
24477 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
24511 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
24544 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:25020 original size:13 final size:13
Alignment explanation
Indices: 25002--25027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24992 CAATTTTTTG
25002 TGTATCGATACAT
1 TGTATCGATACAT
25015 TGTATCGATACAT
1 TGTATCGATACAT
25028 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:27358 original size:23 final size:24
Alignment explanation
Indices: 27313--27359 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
27303 CAAAGAATTG
*
27313 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
27337 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
27360 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Done.