Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1688
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: 28006
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:313 original size:7 final size:7
Alignment explanation
Indices: 298--699 Score: 116
Period size: 7 Copynumber: 54.6 Consensus size: 7
288 GGCCTTTTTA
298 GGGGAGG
1 GGGGAGG
*
305 GGGGCGG
1 GGGGAGG
312 GGGG-GG
1 GGGGAGG
318 GGGGAGG
1 GGGGAGG
*
325 GGGGAGTC
1 GGGGAG-G
* *
333 GTGGA-A
1 GGGGAGG
339 GGGGAGG
1 GGGGAGG
346 GGGGAGG
1 GGGGAGG
**
353 AGGTAAGG
1 -GGGGAGG
361 AGGGGAGG
1 -GGGGAGG
369 GGGG-GG
1 GGGGAGG
*
375 GGGGGGG
1 GGGGAGG
*
382 GGAGGAAG
1 GG-GGAGG
390 GGGGA-G
1 GGGGAGG
* *
396 GGAGAAG
1 GGGGAGG
403 GGGGA-G
1 GGGGAGG
*
409 GGGAAGAG
1 GGGGAG-G
*
417 GAGGAGG
1 GGGGAGG
424 GGGGAGG
1 GGGGAGG
431 AGAGGGCAAGG
1 -G-GGG--AGG
*
442 AAGGG-GG
1 -GGGGAGG
* *
449 GGAGAGA
1 GGGGAGG
456 GGGGAGG
1 GGGGAGG
**
463 GGGAGAAAA
1 GGG-G-AGG
472 GGGGAGG
1 GGGGAGG
*
479 GAGGGTAAAAG
1 G-GGG---AGG
490 GGGGAGG
1 GGGGAGG
497 GGGG-GG
1 GGGGAGG
*
503 GGGAAGAGA
1 GGG--GAGG
512 GGGG-GG
1 GGGGAGG
518 GGGGA-G
1 GGGGAGG
524 GGGGAGG
1 GGGGAGG
531 GGGGAGG
1 GGGGAGG
*
538 AGAAGGAGG
1 -G-GGGAGG
547 AAGGGGAGG
1 --GGGGAGG
*
556 GGGG-GA
1 GGGGAGG
562 GGGG-GG
1 GGGGAGG
568 GGGGAGG
1 GGGGAGG
*
575 GGAGAAGG
1 GG-GGAGG
583 GGAGG-GG
1 GG-GGAGG
*
590 GGGAAGG
1 GGGGAGG
*
597 GGGGGGG
1 GGGGAGG
604 GGGAAGAAAGG
1 GGG--G--AGG
615 GGGGAGGG
1 GGGGA-GG
623 GGGGAGG
1 GGGGAGG
** *
630 GGATTTAAGA
1 GG---GGAGG
640 GGGGAGG
1 GGGGAGG
647 TGGGG-GG
1 -GGGGAGG
654 GGGG-GG
1 GGGGAGG
660 GGGGAGGG
1 GGGGA-GG
668 GGGGAGG
1 GGGGAGG
675 AGGGG-GAG
1 -GGGGAG-G
*
683 AGGG-GG
1 GGGGAGG
689 GGGGAGG
1 GGGGAGG
696 GGGG
1 GGGG
700 GAAGGAGGGA
Statistics
Matches: 300, Mismatches: 50, Indels: 90
0.68 0.11 0.20
Matches are distributed among these distances:
6 69 0.23
7 120 0.40
8 64 0.21
9 23 0.08
10 12 0.04
11 12 0.04
ACGTcount: A:0.22, C:0.01, G:0.75, T:0.02
Consensus pattern (7 bp):
GGGGAGG
Found at i:319 original size:13 final size:13
Alignment explanation
Indices: 298--411 Score: 50
Period size: 13 Copynumber: 8.2 Consensus size: 13
288 GGCCTTTTTA
* *
298 GGGGAGGGGGGCG
1 GGGGGGGGGGGAG
311 GGGGGGGGGGGAG
1 GGGGGGGGGGGAG
* *
324 GGGGGAGTCGTGGAAG
1 GGGGG-G--GGGGGAG
340 GGGAGGGGGGAGGAG
1 GGG-GGGGGG-GGAG
*** *
355 GTAAGGAGGGGAG
1 GGGGGGGGGGGAG
368 GGGGGGGGGGG-G
1 GGGGGGGGGGGAG
380 GGGGAGGAAGGGGGAG
1 GGGG-GG--GGGGGAG
* **
396 GGAGAAGGGGGAG
1 GGGGGGGGGGGAG
409 GGG
1 GGG
412 AAGAGGAGGA
Statistics
Matches: 74, Mismatches: 18, Indels: 18
0.67 0.16 0.16
Matches are distributed among these distances:
12 5 0.07
13 38 0.51
14 7 0.09
15 9 0.12
16 13 0.18
17 2 0.03
ACGTcount: A:0.18, C:0.02, G:0.78, T:0.03
Consensus pattern (13 bp):
GGGGGGGGGGGAG
Found at i:399 original size:55 final size:52
Alignment explanation
Indices: 339--464 Score: 128
Period size: 55 Copynumber: 2.3 Consensus size: 52
329 AGTCGTGGAA
* * * **
339 GGGGAGGGGGGAGGAGGTAAGGAGG-GGAGGGGGGGGGGGGGGGGGAGGAAGGGG
1 GGGGAGGGGGGAGG-GG-AA-GAGGAGGAGGGGGGAGGAGAGGGCAAGGAAGGGG
393 GAGGGAGAAGGGGGAGGGGAAGAGGAGGAGGGGGGAGGAGAGGGCAAGGAAGGGG
1 G-GGGAG--GGGGGAGGGGAAGAGGAGGAGGGGGGAGGAGAGGGCAAGGAAGGGG
*
448 GGGAGAGAGGGGAGGGG
1 GGG-GAGGGGGGAGGGG
465 GAGAAAAGGG
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
53 9 0.15
54 7 0.11
55 35 0.57
56 2 0.03
57 8 0.13
ACGTcount: A:0.25, C:0.01, G:0.74, T:0.01
Consensus pattern (52 bp):
GGGGAGGGGGGAGGGGAAGAGGAGGAGGGGGGAGGAGAGGGCAAGGAAGGGG
Found at i:405 original size:27 final size:27
Alignment explanation
Indices: 375--481 Score: 76
Period size: 27 Copynumber: 3.9 Consensus size: 27
365 GAGGGGGGGG
375 GGGGGGGGGAGGAAGGGGGAGGGAGAA
1 GGGGGGGGGAGGAAGGGGGAGGGAGAA
* * * *
402 GGGGGAGGGGAAG-AGGAGGAGGGGGGA
1 GGGGG-GGGGAGGAAGGGGGAGGGAGAA
* **
429 GGAGAGGGCAAGGAA-GGGG-GGGAGAGA
1 GG-GGGGGGGAGGAAGGGGGAGGGAGA-A
* *
456 GGGGAGGGGGAGAAAAGGGGAGGGAG
1 GGGG-GGGGGAGGAAGGGGGAGGGAG
482 GGTAAAAGGG
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
26 5 0.09
27 35 0.60
28 13 0.22
29 5 0.09
ACGTcount: A:0.29, C:0.01, G:0.70, T:0.00
Consensus pattern (27 bp):
GGGGGGGGGAGGAAGGGGGAGGGAGAA
Found at i:406 original size:34 final size:33
Alignment explanation
Indices: 359--430 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 33
349 GAGGAGGTAA
* * ** *
359 GGAGGGGAGGGGGGGGGGGGGGGGGAGGAAGGG
1 GGAGGGGAAGGGGGAGGGGAAGAGGAGGAAGGG
*
392 GGAGGGAGAAGGGGGAGGGGAAGAGGAGGAGGGG
1 GGAGGG-GAAGGGGGAGGGGAAGAGGAGGAAGGG
426 GGAGG
1 GGAGG
431 AGAGGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 6 0.19
34 26 0.81
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (33 bp):
GGAGGGGAAGGGGGAGGGGAAGAGGAGGAAGGG
Found at i:407 original size:64 final size:64
Alignment explanation
Indices: 297--420 Score: 164
Period size: 64 Copynumber: 1.9 Consensus size: 64
287 GGGCCTTTTT
* *
297 AGGGGAGGGGGGCGGGGGGGGGGGGAGGGGGGAGTCGTGGAAGGGGAGGGG-GGAGGAGGTAAGG
1 AGGGGAGGGGGGCGGGGGGGGGGGGAAGGGGGAG-CGTGGAAGGGGAGGGGAAGAGGAGGTAAGG
*
361 AGGGGAGGGGGGGGGGGGGGGGGAGGAAGGGGGAG-G-GAGAAGGGGGAGGGGAAGAGGAGG
1 AGGGGAGGGGGGCGGGGGGGGGG-GGAAGGGGGAGCGTG-GAA-GGGGAGGGGAAGAGGAGG
421 AGGGGGGAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
62 1 0.02
63 4 0.08
64 31 0.58
65 17 0.32
ACGTcount: A:0.20, C:0.02, G:0.76, T:0.02
Consensus pattern (64 bp):
AGGGGAGGGGGGCGGGGGGGGGGGGAAGGGGGAGCGTGGAAGGGGAGGGGAAGAGGAGGTAAGG
Found at i:478 original size:55 final size:53
Alignment explanation
Indices: 361--591 Score: 175
Period size: 55 Copynumber: 4.2 Consensus size: 53
351 GGAGGTAAGG
* * * * * *
361 AGGGGAGGGGGGGGGGGGGGGGGAGGAAGGGGGAGG-GAGAAGGGGGAGGGGAAG
1 AGGGGAGGGGGGAGGAGAGGGGAAGGAAGGGGG-GGAGAG-AGGGGGGGGGGAAA
*
415 AGGAGGAGGGGGGAGGAGAGGGCAAGGAAGGGGGGGAGAGAGGGGAGGGGGAGAAA
1 AGG-GGAGGGGGGAGGAGAGGGGAAGGAAGGGGGGGAGAGAGGGG-GGGGG-GAAA
* * **
471 AGGGGAGGGAGGGTA--AAAGGGGGAGGGGGGGGGGGAAGAGAGGGGGGGGGG--A
1 AGGGGAGGG-GGG-AGGAGAGGGGAAGGAAGGGGGGG-AGAGAGGGGGGGGGGAAA
* * * * *
523 GGGGGAGGGGGGAGGAGAAGGAGGAAGGGGAGGGGGGGAGGGGGGGGGGAGGGGAGA
1 AGGGGAGGGGGGAGGAG-AGG-GGAA-GGAAGGGGGGGAGAGAGGGGGG-GGGGAAA
580 AGGGGAGGGGGG
1 AGGGGAGGGGGG
592 GAAGGGGGGG
Statistics
Matches: 143, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
50 1 0.01
51 3 0.02
52 10 0.07
53 3 0.02
54 23 0.16
55 72 0.50
56 18 0.13
57 13 0.09
ACGTcount: A:0.25, C:0.00, G:0.74, T:0.00
Consensus pattern (53 bp):
AGGGGAGGGGGGAGGAGAGGGGAAGGAAGGGGGGGAGAGAGGGGGGGGGGAAA
Found at i:493 original size:110 final size:106
Alignment explanation
Indices: 379--573 Score: 252
Period size: 107 Copynumber: 1.8 Consensus size: 106
369 GGGGGGGGGG
*
379 GGGGGAGGAAGGGGGAGGG-AGA-AGGGGGAGGGGAAGAGGAGGAGGGGGGAGGAGAGGGCAAGG
1 GGGGGAGG--GGGGGAGGGAAGAGAGGGGG-GGGG--GAGGAGGAGGGGGGAGGAGAAGG--AGG
442 AAGGGG-GGGAGAGAGGGGAGGGGGAGAAAAGGGGAGGGAGGGTAAAA
59 AAGGGGAGGGAGAGAGGGGAGGGGGAGAAAAGGGGAGGGAGGGTAAAA
* *
489 GGGGGAGGGGGGGGGGGAAGAGAGGGGGGGGGGAGGGGGAGGGGGGAGGAGAAGGAGGAAGGGGA
1 GGGGGAGGGGGGGAGGGAAGAGAGGGGGGGGGGAGGAGGAGGGGGGAGGAGAAGGAGGAAGGGGA
* * *
554 GGGGGGGAGGGGGGGGGGAG
66 GGGAGAGAGGGGAGGGGGAG
574 GGGAGAAGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
105 9 0.12
106 17 0.22
107 21 0.28
108 8 0.11
109 7 0.09
110 14 0.18
ACGTcount: A:0.27, C:0.01, G:0.72, T:0.01
Consensus pattern (106 bp):
GGGGGAGGGGGGGAGGGAAGAGAGGGGGGGGGGAGGAGGAGGGGGGAGGAGAAGGAGGAAGGGGA
GGGAGAGAGGGGAGGGGGAGAAAAGGGGAGGGAGGGTAAAA
Found at i:554 original size:73 final size:73
Alignment explanation
Indices: 368--607 Score: 196
Period size: 73 Copynumber: 3.3 Consensus size: 73
358 AGGAGGGGAG
* * * * *
368 GGGGGGGGGGGGGGGGAGGAAGGG-GGAG--GGAGAAGGGGGAGGGGAAGAGGAGGAGGGGGGAG
1 GGGGGGGGGGAGGGGGAGG-GGGGAGGAGAAGGAGGAAGGGGAGGGGAAGAGGGGGA-GGGGGAG
430 GAGAGGGCAAGGA
64 G-G-GGG-AAGGA
* * * * *
443 AGGGGGGGAGAGAGGGGA-GGGGGA-GAAAAGG-GG-A-GGGAGGGTAAAAGGGGGAGGGGG-GG
1 GGGGGGGGGGAG-GGGGAGGGGGGAGGAGAAGGAGGAAGGGGAGGGGAAGAGGGGGAGGGGGAGG
502 GGGGAAGAGA
65 GGGGAAG-GA
**
512 GGGGGGGGGGAGGGGGAGGGGGGAGGAGAAGGAGGAAGGGGAGGGGGGGAGGGGG-GGGGGAGGG
1 GGGGGGGGGGAGGGGGAGGGGGGAGGAGAAGGAGGAAGGGGAGGGGAAGAGGGGGAGGGGGAGGG
*
576 GAGAAGG-
66 GGGAAGGA
* *
583 GGAGGGGGGGAAGGGGGGGGGGGGA
1 GG-GGGGGGGGAGGGGGAGGGGGGA
608 AGAAAGGGGG
Statistics
Matches: 133, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
68 8 0.06
69 21 0.16
70 7 0.05
71 6 0.05
72 32 0.24
73 36 0.27
74 5 0.04
75 11 0.08
76 7 0.05
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (73 bp):
GGGGGGGGGGAGGGGGAGGGGGGAGGAGAAGGAGGAAGGGGAGGGGAAGAGGGGGAGGGGGAGGG
GGGAAGGA
Found at i:579 original size:39 final size:36
Alignment explanation
Indices: 368--700 Score: 131
Period size: 34 Copynumber: 9.7 Consensus size: 36
358 AGGAGGGGAG
* **
368 GGGGGGGGGGGGGGGGA-GGAAGGGGGAG-GGAGAA
1 GGGGAGGGGGGGGGGGAGGGGGGGGGGAGAGGAGAA
* * *
402 GGGGGAGGGGAAGAGGAGGA-GGGGGGAGGAGAGG-GCAA
1 -GGGGAGGGG--GGGGGGGAGGGGGGGGGGAGAGGAG-AA
* * * *
440 -GGAAGGGGGGGAGAGAGGGGAGGGGGAGA--A-AA
1 GGGGAGGGGGGGGGGGAGGGGGGGGGGAGAGGAGAA
* **** * *
472 GGGGAGGGAGGGTAAAAGGGGGAGGGGG-GGGGGGAA
1 GGGGAGGGGGGGGGGGAGGGGG-GGGGGAGAGGAGAA
*
508 -GAGA-GGGGGGGGGGAGGGGGAGGGGG-GAGGAGAA
1 GGGGAGGGGGGGGGGGAGGGGG-GGGGGAGAGGAGAA
*
542 GGAGGAAGGGGAGGGGGGGAGGGGGGGGGGAGGGGAGAA
1 GG-GG-AGGGG-GGGGGGGAGGGGGGGGGGAGAGGAGAA
**
581 GGGGAGGGGGGGAAGG-GGGGGGGGGGA-A-GA-AA
1 GGGGAGGGGGGGGGGGAGGGGGGGGGGAGAGGAGAA
* ***** *
613 -GGG-GGGAGGGGGGGA-GGGGATTTAAGAGG-GGA
1 GGGGAGGGGGGGGGGGAGGGGGGGGGGAGAGGAGAA
*
645 GGTGG-GGGGGGGGGGG-GGGAGGGGGG-GAGGAG--
1 GG-GGAGGGGGGGGGGGAGGGGGGGGGGAGAGGAGAA
*
677 GGGGAGAGGGGGGGGGAGGGGGGG
1 GGGGAGGGGGGGGGGGAGGGGGGG
701 AAGGAGGGAG
Statistics
Matches: 219, Mismatches: 52, Indels: 56
0.67 0.16 0.17
Matches are distributed among these distances:
30 13 0.06
31 6 0.03
32 18 0.08
33 29 0.13
34 48 0.22
35 33 0.15
36 15 0.07
37 21 0.10
38 14 0.06
39 22 0.10
ACGTcount: A:0.23, C:0.00, G:0.75, T:0.02
Consensus pattern (36 bp):
GGGGAGGGGGGGGGGGAGGGGGGGGGGAGAGGAGAA
Found at i:599 original size:66 final size:67
Alignment explanation
Indices: 489--631 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 67
479 GAGGGTAAAA
* * * *
489 GGGGGAGGGGGGGGGGGAAGAGAGGGGGGGGGGAGGGGGA-GGGGGGAGGAGAAG-GAGGAAGGG
1 GGGGGAGGGGGGGGGGGAAGAGAGAGGGGAGGGAGGGGAAGGGGGGGAGGAGAAGAAAGG--GGG
552 GAGG
64 GAGG
* * * *
556 GGGGGA-GGGGGGGGGGAGGGGAGAAGGGGAGGG-GGGGAAGGGGGGGGGGGGAAGAAAGGGGGG
1 GGGGGAGGGGGGGGGGGAAGAGAG-AGGGGAGGGAGGGGAAGGGGGGGAGGAGAAGAAAGGGGGG
619 AGG
65 AGG
622 GGGGGAGGGG
1 GGGGGAGGGG
632 ATTTAAGAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
66 33 0.52
67 28 0.44
68 3 0.05
ACGTcount: A:0.21, C:0.00, G:0.79, T:0.00
Consensus pattern (67 bp):
GGGGGAGGGGGGGGGGGAAGAGAGAGGGGAGGGAGGGGAAGGGGGGGAGGAGAAGAAAGGGGGGA
GG
Found at i:681 original size:37 final size:37
Alignment explanation
Indices: 549--710 Score: 102
Period size: 37 Copynumber: 4.4 Consensus size: 37
539 GAAGGAGGAA
* * * *
549 GGGGAGGGGGGGAGGGGGGGGGGAGGGGAGAAGGGGAGGG
1 GGGGAAGGAGGGAGGAGGGGGAGAGGGG-G--GGGGAGGG
**
589 GGGGAAGG-GGG-GG-GGGGGA-AGAAAGGGGGGAGGG
1 GGGGAAGGAGGGAGGAGGGGGAGAG-GGGGGGGGAGGG
* *** * *
623 GGGGAGGGGATTTAAGA-GGGGAG-GTGGGGGGGGGGGG
1 GGGGA-AGGAGGGAGGAGGGGGAGAG-GGGGGGGGAGGG
* *
660 GGGGAGGGGGGGAGGAGGGGGAGAGGGGGGGGGAGGG
1 GGGGAAGGAGGGAGGAGGGGGAGAGGGGGGGGGAGGG
697 GGGGAAGGAGGGAG
1 GGGGAAGGAGGGAG
711 ATGGGGGTAG
Statistics
Matches: 93, Mismatches: 21, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
34 13 0.14
35 2 0.02
36 9 0.10
37 56 0.60
38 3 0.03
39 3 0.03
40 7 0.08
ACGTcount: A:0.19, C:0.00, G:0.78, T:0.02
Consensus pattern (37 bp):
GGGGAAGGAGGGAGGAGGGGGAGAGGGGGGGGGAGGG
Found at i:716 original size:29 final size:28
Alignment explanation
Indices: 489--717 Score: 95
Period size: 29 Copynumber: 8.1 Consensus size: 28
479 GAGGGTAAAA
*
489 GGGGGAGGGGGGG-GG-GGAAGAGAGGGGG
1 GGGGGAGGGGGGGAGGAGG-GGAGA-GGGG
517 GGGGGAGGGGGAGG-GG-GGAGGAGAAGGAGG
1 GGGGGAGGGGG-GGAGGAGG-GGAG-AGG-GG
* * *
547 AAGGGGAGGGGGGGAGGGGGGGGGGAGGGG
1 -GGGGGAGGGGGGGA-GGAGGGGAGAGGGG
577 AGAAGGGGAGGGGGGGA--AGGGG-G-GGGG
1 -G--GGGGAGGGGGGGAGGAGGGGAGAGGGG
* *
604 GGGAAGAAAGGGGGGAGG-GGGG-GA-GGG
1 GGG--GGAGGGGGGGAGGAGGGGAGAGGGG
**** * * * * *
631 GATTTAAGAGGGGAGGTGGGGGGGGGGG
1 GGGGGAGGGGGGGAGGAGGGGAGAGGGG
659 GGGGGAGGGGGGGAGGAGGGGGAGAGGGG
1 GGGGGAGGGGGGGAGGA-GGGGAGAGGGG
*
688 GGGGGAGGGGGGGAAGGA-GGGAGATGGG
1 GGGGGAGGGGGGG-AGGAGGGGAGAGGGG
716 GG
1 GG
718 TAGGAAATAT
Statistics
Matches: 159, Mismatches: 23, Indels: 38
0.72 0.10 0.17
Matches are distributed among these distances:
24 2 0.01
25 10 0.06
26 14 0.09
27 14 0.09
28 36 0.23
29 38 0.24
30 12 0.08
31 13 0.08
32 18 0.11
33 2 0.01
ACGTcount: A:0.20, C:0.00, G:0.78, T:0.02
Consensus pattern (28 bp):
GGGGGAGGGGGGGAGGAGGGGAGAGGGG
Found at i:717 original size:1 final size:1
Alignment explanation
Indices: 648--700 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
638 GAGGGGAGGT
* * * * * *
648 GGGGGGGGGGGGGGGGAGGGGGGGAGGAGGGGGAGAGGGGGGGGGAGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
701 AAGGAGGGAG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.11, C:0.00, G:0.89, T:0.00
Consensus pattern (1 bp):
G
Found at i:733 original size:90 final size:89
Alignment explanation
Indices: 547--746 Score: 203
Period size: 92 Copynumber: 2.2 Consensus size: 89
537 GAGAAGGAGG
* *
547 AAGGGGAGGGGGGGAGGGGGGGGGGAGGGGAGAAGGGGAGGGGGGGAAGGGGGGGGGGGGAAGAA
1 AAGGGGAGGGGGGGGGGGGGGGGGGAGGGGAG-AGGGGAGGGGGAGAAGGGGGGGGGGGGAAGAA
** *
612 AGGGGGGAGGGGGGGAGGGGATTTA
65 AGGGGGGAGGGGGGGAGGAAATATA
**
637 AGAGGGGAGGTGGGGGGGGGGGGGGGGAGGGG-G-GGAGGAGGGGGAG-AGGGGGGGGGAGGGGG
1 A-AGGGGAGG-GGGGGGGGGGGGGGGGAGGGGAGAGG-GGAGGGGGAGAAGGGGGGGGG-GGGAA
* * *
699 GGAAGGAGGGAGATGGGGGTAGGAAATAT-
62 GAAAGG-GGG-GAGGGGGGGAGGAAATATA
*
728 AAGGGG-GGGAGGGGGGGGG
1 AAGGGGAGGGGGGGGGGGGG
747 TATCGGAGAA
Statistics
Matches: 93, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
88 10 0.11
89 14 0.15
90 23 0.25
91 13 0.14
92 33 0.35
ACGTcount: A:0.21, C:0.00, G:0.75, T:0.04
Consensus pattern (89 bp):
AAGGGGAGGGGGGGGGGGGGGGGGGAGGGGAGAGGGGAGGGGGAGAAGGGGGGGGGGGGAAGAAA
GGGGGGAGGGGGGGAGGAAATATA
Found at i:783 original size:5 final size:5
Alignment explanation
Indices: 775--852 Score: 52
Period size: 5 Copynumber: 14.8 Consensus size: 5
765 GGGGGGGGGA
* * *
775 GGAGG GGAGG GGAGG GG-GG GAGAAAGAG GGAGGG GGAAG AGAGA GGAGG
1 GGAGG GGAGG GGAGG GGAGG G-G--AG-G GGA-GG GGAGG GGAGG GGAGG
*
824 GGGGG GGAGG GGAGGG GGAGG GG-GG GGAG
1 GGAGG GGAGG GGA-GG GGAGG GGAGG GGAG
853 ATGAGTCGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
4 7 0.12
5 35 0.61
6 10 0.18
7 1 0.02
8 2 0.04
9 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:793 original size:20 final size:20
Alignment explanation
Indices: 768--852 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 20
758 TACAGAAGGG
768 GGGGGGAGGAGGGGAGGGGA
1 GGGGGGAGGAGGGGAGGGGA
*
788 GGGGGGGAGAAAGAGGGAGGGGGA
1 -GGGGGGAG-GAG-GGGA-GGGGA
* * * *
812 AGAGAGAGGAGGGGGGGGGA
1 GGGGGGAGGAGGGGAGGGGA
*
832 GGGGAGGGGGAGGGG-GGGGA
1 GGGG-GGAGGAGGGGAGGGGA
852 G
1 G
853 ATGAGTCGTG
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
20 13 0.26
21 19 0.38
22 4 0.08
23 9 0.18
24 5 0.10
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (20 bp):
GGGGGGAGGAGGGGAGGGGA
Found at i:803 original size:19 final size:19
Alignment explanation
Indices: 781--832 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
771 GGGAGGAGGG
781 GAGGGGAGGGGGGGAGAAA
1 GAGGGGAGGGGGGGAGAAA
* *
800 GA-GGGA-GGGGGAAGAGA
1 GAGGGGAGGGGGGGAGAAA
817 GAGGAGG-GGGGGGGAG
1 GAGG-GGAGGGGGGGAG
833 GGGAGGGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.41
18 5 0.19
19 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (19 bp):
GAGGGGAGGGGGGGAGAAA
Found at i:811 original size:16 final size:16
Alignment explanation
Indices: 786--826 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
776 GAGGGGAGGG
786 GAGG-GGGGGAGAAAGA
1 GAGGAGGGGGA-AAAGA
*
802 G-GGAGGGGGAAGAGA
1 GAGGAGGGGGAAAAGA
817 GAGGAGGGGG
1 GAGGAGGGGG
827 GGGGAGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (16 bp):
GAGGAGGGGGAAAAGA
Found at i:837 original size:15 final size:16
Alignment explanation
Indices: 775--852 Score: 72
Period size: 15 Copynumber: 4.9 Consensus size: 16
765 GGGGGGGGGA
775 GGAGGGGAGGGGAGGG
1 GGAGGGGAGGGGAGGG
*
791 GG-GGAGAAAGAGGGAGGG
1 GGAGG-G-GAG-GGGAGGG
* * *
809 GGAAGAGAGAGGAGGG
1 GGAGGGGAGGGGAGGG
825 GG-GGGGAGGGGAGGG
1 GGAGGGGAGGGGAGGG
840 GGAGGGG-GGGGAG
1 GGAGGGGAGGGGAG
853 ATGAGTCGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 20 0.41
16 15 0.31
17 4 0.08
18 9 0.18
19 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (16 bp):
GGAGGGGAGGGGAGGG
Found at i:3322 original size:79 final size:81
Alignment explanation
Indices: 3220--3404 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
3210 GCTCCTCGTT
* *
3220 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
3283 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
3300 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
3364 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
3380 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3405 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:3404 original size:40 final size:40
Alignment explanation
Indices: 3220--3404 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
3210 GCTCCTCGTT
* *
3220 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
3260 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
3300 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
3339 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
3380 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3405 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:9217 original size:22 final size:22
Alignment explanation
Indices: 9192--9238 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
9182 ATAAGAGAGT
9192 TGAGAGAGGAGA-GAATGA-TGAA
1 TGAGAGAGG-GATG-ATGAGTGAA
*
9214 TGAGTGAGGGATGATGAGTGAA
1 TGAGAGAGGGATGATGAGTGAA
9236 TGA
1 TGA
9239 TGGATGGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.19
Consensus pattern (22 bp):
TGAGAGAGGGATGATGAGTGAA
Found at i:9229 original size:18 final size:18
Alignment explanation
Indices: 9206--9244 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9196 AGAGGAGAGA
*
9206 ATGATGAATGAGTGAGGG
1 ATGATGAATGAATGAGGG
* *
9224 ATGATGAGTGAATGATGG
1 ATGATGAATGAATGAGGG
9242 ATG
1 ATG
9245 GGGTCTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (18 bp):
ATGATGAATGAATGAGGG
Found at i:10867 original size:40 final size:40
Alignment explanation
Indices: 10823--11043 Score: 247
Period size: 40 Copynumber: 5.5 Consensus size: 40
10813 GCTCCTCGTT
*
10823 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
10863 CAAATGCCTTCAGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
*
10903 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
10943 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
10982 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
11023 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
11044 TGGACATCAT
Statistics
Matches: 157, Mismatches: 16, Indels: 16
0.83 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 111 0.71
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:11007 original size:79 final size:79
Alignment explanation
Indices: 10823--11043 Score: 259
Period size: 79 Copynumber: 2.8 Consensus size: 79
10813 GCTCCTCGTT
* * * *
10823 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACCAATGCCTTC-GGGCTTAGCCCG
*
10887 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
*
10903 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGA
*
10968 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * * * *
10982 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGG-CTTAGCC
11044 TGGACATCAT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
78 3 0.02
79 62 0.50
80 56 0.46
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:11007 original size:119 final size:120
Alignment explanation
Indices: 10825--11040 Score: 296
Period size: 119 Copynumber: 1.8 Consensus size: 120
10815 TCCTCGTTCA
*
10825 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAT
* *
10890 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
10945 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCAGGA-CTTAACCCGG
* *
11007 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
11041 GCCTGGACAT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.05
119 60 0.71
120 20 0.24
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:17841 original size:68 final size:64
Alignment explanation
Indices: 17754--17975 Score: 223
Period size: 67 Copynumber: 3.4 Consensus size: 64
17744 TAATACGGGA
* *
17754 TGTATACCATGTGTACAAGAGAGCTACGAGACATTATGAGGTAGCTAGGTTGCATGGGTGATACT
1 TGTACACCATGTGTACAAGAGAGCTACGAG--A-TA-GAAGTAGCTAGGTTGCATGGGTGATACT
17819 ATG
62 ATG
* * * * * *
17822 TGTACACCATGTAG-ACAAGAGAGCTATGAGATAGACGTAGCTAGGTTGCATGTGTGGTTCCAGG
1 TGTACACCATGT-GTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTTGCATGGGTGATACTA--
17886 TG
63 TG
* * ** * **
17888 AAGGACACCATGTAAACAAGAGAGCTACGAGATA-AAGTGGCTAGGTCACATGGGTGATACTATG
1 -TGTACACCATGTGTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTTGCATGGGTGATACTATG
17952 TGTACACCATGTGTACAAGAGAGC
1 TGTACACCATGTGTACAAGAGAGC
17976 CAAAATTATG
Statistics
Matches: 126, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
63 20 0.16
64 26 0.21
65 2 0.02
66 23 0.18
67 28 0.22
68 26 0.21
69 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (64 bp):
TGTACACCATGTGTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTTGCATGGGTGATACTATG
Found at i:21418 original size:27 final size:27
Alignment explanation
Indices: 21378--21486 Score: 148
Period size: 27 Copynumber: 4.1 Consensus size: 27
21368 ACATCACATA
* *
21378 GGCAAAACAGTCATCTTACCATATAAG
1 GGCAAAACAATCATCTTACCACATAAG
21405 GGCAAAACAATCATCTTACCACATAAG
1 GGCAAAACAATCATCTTACCACATAAG
*
21432 GGCAAAACAATCATTTTACCACATAAG
1 GGCAAAACAATCATCTTACCACATAAG
* * * *
21459 GGAAAAATAGTCATTTTACCA-ATAAG
1 GGCAAAACAATCATCTTACCACATAAG
21485 GG
1 GG
21487 GTCCAGGCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
26 7 0.09
27 69 0.91
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (27 bp):
GGCAAAACAATCATCTTACCACATAAG
Done.