Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:298572 original size:20 final size:18
Alignment explanation
Indices: 298522--298590 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 18
298512 TTGAAGTTGA
298522 TTAT-TTAATAATTTATT
1 TTATATTAATAATTTATT
298539 TTATTATTTAAATAATTTTATTT
1 TTA-TA-TT-AATAA-TTTA-TT
298562 TTATATTAAT-ATTTA-T
1 TTATATTAATAATTTATT
*
298578 ATAT-TTAATAATT
1 TTATATTAATAATT
298591 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
15 5 0.11
16 7 0.16
17 3 0.07
18 5 0.11
19 1 0.02
20 5 0.11
21 7 0.16
22 6 0.14
23 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTAATAATTTATT
Found at i:298574 original size:14 final size:15
Alignment explanation
Indices: 298523--298587 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 15
298513 TGAAGTTGAT
*
298523 TATTTAATAATT-TA
1 TATTTAATATTTATA
* *
298537 T-TTTATTATTTAAA
1 TATTTAATATTTATA
*
298551 TAATTT--TATTTTTA
1 T-ATTTAATATTTATA
298565 TA-TTAATATTTATA
1 TATTTAATATTTATA
298579 TATTTAATA
1 TATTTAATA
298588 ATTAAAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
12 2 0.05
13 9 0.23
14 19 0.49
15 6 0.15
16 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTAATATTTATA
Found at i:298798 original size:13 final size:13
Alignment explanation
Indices: 298780--298806 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
298770 CTATACTCAA
298780 AAGATTATTTTAT
1 AAGATTATTTTAT
298793 AAGATTATTTTAT
1 AAGATTATTTTAT
298806 A
1 A
298807 TTTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
AAGATTATTTTAT
Found at i:299047 original size:6 final size:6
Alignment explanation
Indices: 299033--299135 Score: 62
Period size: 6 Copynumber: 17.8 Consensus size: 6
299023 TTAATATAAT
* *
299033 ATTTAA ATTTTA A-TTAA ATTT-A ACTT-A ATTT-A ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
299075 ATTTATA AATTAA A-TCATA ATTTAA A--TAA ATTTTAA ATTTTTAA ATTTAA
1 ATTTA-A ATTTAA ATTTA-A ATTTAA ATTTAA A-TTTAA A--TTTAA ATTTAA
299125 ATTTAA ATTTA
1 ATTTAA ATTTA
299136 GCTTGATCTG
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
4 8 0.10
5 19 0.24
6 35 0.44
7 10 0.13
8 7 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:299062 original size:10 final size:11
Alignment explanation
Indices: 299035--299075 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
299025 AATATAATAT
299035 TTAAATTTTAA-
1 TTAAA-TTTAAC
299046 TTAAATTTAAC
1 TTAAATTTAAC
*
299057 TT-AATTTAAT
1 TTAAATTTAAC
299067 TTAAATTTA
1 TTAAATTTA
299076 TTTATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAC
Found at i:299256 original size:19 final size:19
Alignment explanation
Indices: 299228--299272 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
299218 TATAATTAAA
*
299228 TTTAAATAAAATATATTAT
1 TTTAAATAAAAAATATTAT
* *
299247 TTTAATTAAAAAATCTTAT
1 TTTAAATAAAAAATATTAT
*
299266 TTCAAAT
1 TTTAAAT
299273 TAAATTATCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATAAAAAATATTAT
Found at i:300543 original size:20 final size:20
Alignment explanation
Indices: 300514--300565 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
300504 ACGGAGGGAA
300514 AAAG-GAGAAAAAAAAAAAG
1 AAAGAGAGAAAAAAAAAAAG
* **
300533 AAAGAGAGAAAGAAAAATTG
1 AAAGAGAGAAAAAAAAAAAG
300553 AAAGAGA-AAAAAA
1 AAAGAGAGAAAAAA
300566 TTGTGTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (20 bp):
AAAGAGAGAAAAAAAAAAAG
Found at i:306150 original size:8 final size:8
Alignment explanation
Indices: 306139--306202 Score: 58
Period size: 8 Copynumber: 8.1 Consensus size: 8
306129 TTTAAAATTT
306139 TAAAAAAA
1 TAAAAAAA
306147 T-AAAAAA
1 TAAAAAAA
306154 TAAAAAAA
1 TAAAAAAA
**
306162 TAAAAATT
1 TAAAAAAA
**
306170 TTTAAAAA
1 TAAAAAAA
*
306178 TAATAAAA
1 TAAAAAAA
*
306186 TAAATAAA
1 TAAAAAAA
*
306194 TAAATAAA
1 TAAAAAAA
306202 T
1 T
306203 TTTAAAAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 7 0.16
8 37 0.84
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
TAAAAAAA
Found at i:306165 original size:43 final size:44
Alignment explanation
Indices: 306101--306201 Score: 136
Period size: 43 Copynumber: 2.3 Consensus size: 44
306091 ATCTTTTGAT
* **
306101 AATAAATAATTAAAAAAATAAAAATAATTTT-AAAATTTTAAAA-A
1 AATAAATAAATAAAAAAATAAAAAT--TTTTAAAAATAATAAAATA
306145 AATAAA-AAATAAAAAAATAAAAATTTTTAAAAATAATAAAATA
1 AATAAATAAATAAAAAAATAAAAATTTTTAAAAATAATAAAATA
306188 AATAAATAAATAAA
1 AATAAATAAATAAA
306202 TTTTAAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
41 4 0.08
42 10 0.20
43 24 0.47
44 13 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (44 bp):
AATAAATAAATAAAAAAATAAAAATTTTTAAAAATAATAAAATA
Found at i:306177 original size:32 final size:32
Alignment explanation
Indices: 306113--306210 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 32
306103 TAAATAATTA
* *
306113 AAAAAATAAAAATAATTTTAAAATTTTAAAAAAAT
1 AAAAAATAAAAA-AA--TAAAAATTTTTAAAAAAT
306148 AAAAAATAAAAAAATAAAAATTTTT-AAAAAT
1 AAAAAATAAAAAAATAAAAATTTTTAAAAAAT
* *
306179 AATAAAATAAATAAATAAATAAATTTTAAAAA
1 AA-AAAATAAAAAAATAAA-AATTTTTAAAAA
306211 TTCTAAAGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
31 8 0.14
32 24 0.43
33 6 0.11
34 6 0.11
35 12 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (32 bp):
AAAAAATAAAAAAATAAAAATTTTTAAAAAAT
Found at i:306206 original size:33 final size:33
Alignment explanation
Indices: 306114--306211 Score: 110
Period size: 33 Copynumber: 2.9 Consensus size: 33
306104 AAATAATTAA
**
306114 AAAAATAAAAATAATTTTAAAATTTTAAAAA-AAT
1 AAAAATAAAAA-AA-TAAAAAATTTTAAAAATAAT
*
306148 AAAAAATAAAAAAATAAAAATTTTTAAAAATAAT
1 -AAAAATAAAAAAATAAAAAATTTTAAAAATAAT
*
306182 -AAAATAAATAAATAAATAAATTTTAAAAAT
1 AAAAATAAAAAAATAAA-AAATTTTAAAAAT
306212 TCTAAAGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
32 15 0.27
33 25 0.45
34 5 0.09
35 11 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (33 bp):
AAAAATAAAAAAATAAAAAATTTTAAAAATAAT
Found at i:310461 original size:17 final size:17
Alignment explanation
Indices: 310436--310497 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
310426 TACACTCATG
*
310436 TTATTTTTATAATATTA
1 TTATATTTATAATATTA
*
310453 TTATATTTAAAATATTA
1 TTATATTTATAATATTA
*
310470 -TAT-TTTATATAAATT-
1 TTATATTTATA-ATATTA
310485 TTA-ATTTATAATA
1 TTATATTTATAATA
310498 AAATTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 7 0.19
16 15 0.41
17 15 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTTATAATATTA
Found at i:310532 original size:11 final size:12
Alignment explanation
Indices: 310507--310552 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
310497 AAAATTTTTA
*
310507 ATATATTTATTTT
1 ATAT-TTTATATT
310520 ATATTTTA-ATT
1 ATATTTTATATT
*
310531 ATTTTTTATATT
1 ATATTTTATATT
310543 ATA-TTTATAT
1 ATATTTTATAT
310553 AAAAAATGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 9 0.31
13 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:310550 original size:18 final size:17
Alignment explanation
Indices: 310500--310550 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
310490 TTATAATAAA
310500 ATTTTTA-A-TATATTT
1 ATTTTTATATTATATTT
* *
310515 A-TTTTATATTTTAATT
1 ATTTTTATATTATATTT
310531 ATTTTTTATATTATATTT
1 A-TTTTTATATTATATTT
310549 AT
1 AT
310551 ATAAAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 2 0.07
16 6 0.21
17 1 0.04
18 14 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATATTATATTT
Found at i:311276 original size:14 final size:16
Alignment explanation
Indices: 311245--311276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
311235 CAAGATTGAT
311245 AAAATTATATTATTTA
1 AAAATTATATTATTTA
311261 AAAATTA-ATT-TTTA
1 AAAATTATATTATTTA
311275 AA
1 AA
311277 TGATAAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATTATATTATTTA
Found at i:314136 original size:12 final size:12
Alignment explanation
Indices: 314112--314207 Score: 61
Period size: 12 Copynumber: 7.8 Consensus size: 12
314102 TTTGTCATAA
314112 TTTATATTATTT
1 TTTATATTATTT
314124 TTTA-ATTATTT
1 TTTATATTATTT
*
314135 TTTATATTATATG
1 TTTATATTAT-TT
* * * *
314148 ATCATATCATAT
1 TTTATATTATTT
* * *
314160 TTAAAATTATTACAA
1 TTTATATTATT---T
*
314175 TCTATATTATTT
1 TTTATATTATTT
314187 TTTA-ATTATTT
1 TTTATATTATTT
314198 TTTATATTAT
1 TTTATATTAT
314208 ATAATCGTAT
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
11 22 0.36
12 23 0.38
13 8 0.13
15 8 0.13
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:315270 original size:4 final size:4
Alignment explanation
Indices: 315261--315294 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
315251 ACATGGATAA
*
315261 AAAC AAAC AAAC AAAC AAAC AAAA AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AA
315295 TTCTCCAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:319544 original size:7 final size:7
Alignment explanation
Indices: 319534--319559 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
319524 AAATATATTT
319534 TTATTAA
1 TTATTAA
319541 TTATTAA
1 TTATTAA
319548 TTATTAA
1 TTATTAA
319555 TTATT
1 TTATT
319560 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:319654 original size:22 final size:21
Alignment explanation
Indices: 319607--319661 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
319597 AATAAAAAAT
* * *
319607 TAATTAATCTTAAAATTATTTT
1 TAATTAATATT-AAATTAATTA
319629 TAATTAATATTAAATTAAATTA
1 TAATTAATATTAAATT-AATTA
319651 TAATTAA-ATTA
1 TAATTAATATTA
319662 TATTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTAATATTAAATTAATTA
Found at i:319671 original size:11 final size:11
Alignment explanation
Indices: 319629--319663 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
319619 AAATTATTTT
319629 TAATTAATATTA
1 TAATTAA-ATTA
319641 -AATTAAATTA
1 TAATTAAATTA
319651 TAATTAAATTA
1 TAATTAAATTA
319662 TA
1 TA
319664 TTTTAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATTAAATTA
Found at i:319683 original size:18 final size:16
Alignment explanation
Indices: 319637--319683 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
319627 TTTAATTAAT
* *
319637 ATTAAATTAAATTATA
1 ATTAAATTATATTTTA
319653 ATTAAATTATATTTTA
1 ATTAAATTATATTTTA
319669 ATTCAAATATATATT
1 ATT-AAAT-TATATT
319684 AAATATGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 17 0.63
17 4 0.15
18 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATTATATTTTA
Found at i:319818 original size:17 final size:17
Alignment explanation
Indices: 319773--319825 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
319763 ATTATTATTT
* *
319773 AAAAATTTAATAATAATA
1 AAAAAATTAA-AAAAATA
*
319791 AAATTAATTAAAAAAATA
1 AAA-AAATTAAAAAAATA
319809 AAAAAATTAAAAAAATA
1 AAAAAATTAAAAAAATA
319826 TCAAACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 13 0.43
18 12 0.40
19 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAATTAAAAAAATA
Found at i:319824 original size:9 final size:9
Alignment explanation
Indices: 319796--319824 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
319786 TAATAAAATT
319796 AATTAAAAA
1 AATTAAAAA
319805 AA-TAAAAA
1 AATTAAAAA
319813 AATTAAAAA
1 AATTAAAAA
319822 AAT
1 AAT
319825 ATCAAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTAAAAA
Found at i:319996 original size:30 final size:32
Alignment explanation
Indices: 319936--320010 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 32
319926 TTTTTTATTT
319936 TAATCAATTT-TTTATTTTTAAAATTTTAAAATAA
1 TAAT-AATTTATTTATTTTTAAAA--TTAAAATAA
319970 TAATAATTTATTTATTTTT-AAA-TAAAATAA
1 TAATAATTTATTTATTTTTAAAATTAAAATAA
*
320000 T-ATAATATATT
1 TAATAATTTATT
320011 AATATTAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 9 0.23
30 9 0.23
33 8 0.21
34 13 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
TAATAATTTATTTATTTTTAAAATTAAAATAA
Found at i:320010 original size:25 final size:25
Alignment explanation
Indices: 319958--320010 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
319948 TATTTTTAAA
* *
319958 ATTTTAAAATAATAATAATTTATTT
1 ATTTTAAAATAATAATAATTAATAT
*
319983 ATTTTTAAATAA-AATAATATAATAT
1 ATTTTAAAATAATAATAAT-TAATAT
320008 ATT
1 ATT
320011 AATATTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTTAAAATAATAATAATTAATAT
Found at i:320255 original size:18 final size:19
Alignment explanation
Indices: 320224--320261 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
320214 TAATTTTATG
* *
320224 ATTAAAATATTAAAA-AAA
1 ATTAAAAAAATAAAATAAA
320242 ATTAAAAAAATAAAATAAA
1 ATTAAAAAAATAAAATAAA
320261 A
1 A
320262 AATTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
ATTAAAAAAATAAAATAAA
Found at i:320417 original size:29 final size:30
Alignment explanation
Indices: 320348--320420 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
320338 ATTAAATTTT
*
320348 TAAAAAATATTATTTAAATTTTAAGAATAAA
1 TAAAATATATT-TTTAAATTTTAAGAATAAA
*
320379 TAAAAT-TATTTTTAAA-TTTAAGGAGT-AA
1 TAAAATATATTTTTAAATTTTAA-GAATAAA
*
320407 TAATATATATTTTT
1 TAAAATATATTTTT
320421 TAAAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 12 0.32
29 16 0.43
30 4 0.11
31 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (30 bp):
TAAAATATATTTTTAAATTTTAAGAATAAA
Found at i:323280 original size:24 final size:24
Alignment explanation
Indices: 323253--323299 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
323243 TTTTCATGCG
*
323253 ATAATTTTATCCTAATTTACAAAT
1 ATAATTTTATCCAAATTTACAAAT
323277 ATAATTTTATCCAAATTTACAAA
1 ATAATTTTATCCAAATTTACAAA
323300 AAAAGTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTTTATCCAAATTTACAAAT
Found at i:323652 original size:2 final size:2
Alignment explanation
Indices: 323645--323678 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
323635 TTTTATAAAT
323645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
323679 AGTTTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:324367 original size:22 final size:22
Alignment explanation
Indices: 324342--324385 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
324332 GAAAAACCCA
*
324342 AAAAAAAAAAAAAAGAAGAAAG
1 AAAAAAAAAAAAAAGAACAAAG
* *
324364 AAAAATAATAAAAAGAACAAAG
1 AAAAAAAAAAAAAAGAACAAAG
324386 CAATGCCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAAAAAAGAACAAAG
Found at i:325035 original size:2 final size:2
Alignment explanation
Indices: 325030--325086 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
325020 TCAAGACAAC
* * *
325030 AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325072 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
325087 GAGAGAGAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:325091 original size:2 final size:2
Alignment explanation
Indices: 325086--325111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325076 ATATATATAT
325086 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
325112 GTAATCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:327171 original size:2 final size:2
Alignment explanation
Indices: 327164--327198 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
327154 CATCAGATTG
327164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
327199 CCATAGTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:328821 original size:24 final size:24
Alignment explanation
Indices: 328794--328842 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
328784 ATTATATTAT
*
328794 ATTTATCATAATTCTAAATATATA
1 ATTTATCATAATTATAAATATATA
*
328818 ATTTATTATAATTATAAATATATA
1 ATTTATCATAATTATAAATATATA
328842 A
1 A
328843 ATATTATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTATCATAATTATAAATATATA
Found at i:328857 original size:23 final size:24
Alignment explanation
Indices: 328808--328861 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
328798 ATCATAATTC
* *
328808 TAAATATATAATTTATTATAATTA
1 TAAATATATAATATATTATAATAA
*
328832 TAAATATATAA-ATATTATGATAA
1 TAAATATATAATATATTATAATAA
328855 TAAATAT
1 TAAATAT
328862 TGACAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAATATATAATATATTATAATAA
Found at i:329920 original size:15 final size:17
Alignment explanation
Indices: 329875--329914 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
329865 TTTACATTTG
* *
329875 AAATAAATATTAAATAT
1 AAATATATATTTAATAT
329892 AAATATATATTTAATAT
1 AAATATATATTTAATAT
329909 AAATAT
1 AAATAT
329915 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATATTTAATAT
Found at i:338590 original size:13 final size:13
Alignment explanation
Indices: 338572--338596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338562 CAACATTCTC
338572 TGTATCGATACAT
1 TGTATCGATACAT
338585 TGTATCGATACA
1 TGTATCGATACA
338597 CTATATTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:338784 original size:22 final size:21
Alignment explanation
Indices: 338741--338781 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
338731 CAAATTTCTT
338741 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
338763 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
338782 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:339085 original size:20 final size:21
Alignment explanation
Indices: 339045--339096 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
339035 CCCCTAGGCA
*
339045 GCACCCACCAGGTCACGACC-G
1 GCACCC-CCAGGTCACAACCGG
*
339066 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCACAACCGG
339087 GCAACCCCCA
1 GC-ACCCCCA
339097 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 7 0.26
ACGTcount: A:0.23, C:0.50, G:0.23, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCACAACCGG
Found at i:341083 original size:13 final size:13
Alignment explanation
Indices: 341065--341089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
341055 ATGTTGCACA
341065 GTATCGATACATT
1 GTATCGATACATT
341078 GTATCGATACAT
1 GTATCGATACAT
341090 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:341102 original size:20 final size:21
Alignment explanation
Indices: 341077--341129 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
341067 ATCGATACAT
* *
341077 TGTATCGATACATGACCA-AA
1 TGTATCGATACACGACAAGAA
*
341097 TGTATCGATACACGAGAAGAA
1 TGTATCGATACACGACAAGAA
341118 TGTATCGATACA
1 TGTATCGATACA
341130 AGTCATTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (21 bp):
TGTATCGATACACGACAAGAA
Found at i:341199 original size:13 final size:13
Alignment explanation
Indices: 341181--341205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
341171 ACACATAGTA
341181 TGTATCGATACAT
1 TGTATCGATACAT
341194 TGTATCGATACA
1 TGTATCGATACA
341206 CCAAATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:341202 original size:32 final size:33
Alignment explanation
Indices: 341161--341228 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
341151 GTAGCCAAAC
*
341161 TTGTATCGATACA-CATAGT-ATGTATCGATACA
1 TTGTATCGATACACCA-AATAATGTATCGATACA
341193 TTGTATCGATACACCAAATAATGTATCGATACA
1 TTGTATCGATACACCAAATAATGTATCGATACA
341226 TTG
1 TTG
341229 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.45
33 18 0.55
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCAAATAATGTATCGATACA
Found at i:342733 original size:17 final size:18
Alignment explanation
Indices: 342711--342750 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
342701 AAACATTGCC
*
342711 TTAATTTT-TTAAAAATT
1 TTAATTTTATTAAAAATA
342728 TTAATTTTATTAAAAATA
1 TTAATTTTATTAAAAATA
342746 TTAAT
1 TTAAT
342751 AAAATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTTATTAAAAATA
Found at i:343217 original size:154 final size:154
Alignment explanation
Indices: 343057--343440 Score: 375
Period size: 154 Copynumber: 2.5 Consensus size: 154
343047 AATTGAAAGC
* ** * * *
343057 ATCCCGATAACCCTAAAGGACTTGAATATAACTTA-AAAGGATGAATCTATCATAAATGCATACC
1 ATCCCGATAACCCTAAAGGACTTGAAAATAACCCAGAAAAG-TGAACCTATCATAAATGCACACC
** * *
343121 TTTGG-ATAAAAGCATTCC-GGTGATTGCTTAGGACTCGGTTCTAAAAAAATTACAAAAATGTTT
65 TTTGGCATAAAAGCA-TCCTAATGATTACTTAGGACTCGGTTCTAAAAAAATTACAAAAATGCTT
* * *
343184 CTAAGGGTATACCTTTAACATGAAAAT
129 CT-AGGGTACACATTCAACATGAAAAT
* * * * * *
343211 ATCCCGATAATCCTAAAAGACTTGAAAATAGCCCAGAAAAGTGGACCTATCCTAAATGCACATCT
1 ATCCCGATAACCCTAAAGGACTTGAAAATAACCCAGAAAAGTGAACCTATCATAAATGCACACCT
* * * * * *
343276 TTGGCATGAAAGTATCCTAATGATTACTTAGGATTTGGTTTTAAACAAATTACAAAAATGCTTCT
66 TTGGCATAAAAGCATCCTAATGATTACTTAGGACTCGGTTCTAAAAAAATTACAAAAATGCTTCT
* *
343341 AGGGTACACATTCGACATGAAAGT
131 AGGGTACACATTCAACATGAAAAT
* * * * * *
343365 ATTCC-AGTAACTCTAAAGGACTTGAAAATAGCCTA-AAAAGGTGAACTTAT-TTGAAATGCACA
1 ATCCCGA-TAACCCTAAAGGACTTGAAAATAACCCAGAAAA-GTGAACCTATCAT-AAATGCACA
343427 CCTTTGGCATAAAA
63 CCTTTGGCATAAAA
343441 CCAATATCGG
Statistics
Matches: 187, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
153 6 0.03
154 131 0.70
155 50 0.27
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (154 bp):
ATCCCGATAACCCTAAAGGACTTGAAAATAACCCAGAAAAGTGAACCTATCATAAATGCACACCT
TTGGCATAAAAGCATCCTAATGATTACTTAGGACTCGGTTCTAAAAAAATTACAAAAATGCTTCT
AGGGTACACATTCAACATGAAAAT
Found at i:345179 original size:16 final size:16
Alignment explanation
Indices: 345158--345188 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
345148 TTTCCATAAT
345158 TTTTATCATTTTTTTA
1 TTTTATCATTTTTTTA
*
345174 TTTTATGATTTTTTT
1 TTTTATCATTTTTTT
345189 GTAATTATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCATTTTTTTA
Found at i:347643 original size:72 final size:73
Alignment explanation
Indices: 347564--347740 Score: 203
Period size: 72 Copynumber: 2.4 Consensus size: 73
347554 TAGGTATACT
* * ** *** *
347564 TGTTGGACTTGAAAAATGACTAAACTACCCTTATGTGTTTTGGCCAATGACTAAAATGCC-TTTA
1 TGTTGGACTTGAAAAATGACCAAAATACCCTTACATGTTTCAACCAATAACTAAAATGCCTTTTA
* *
347628 AGAATGCA
66 AAAAAGCA
* * * *
347636 TGTTGGACTTGGAAAATAACCAAAATACCCCTACATGTTTCAACCATTAACTAAAATGCCTTTTA
1 TGTTGGACTTGAAAAATGACCAAAATACCCTTACATGTTTCAACCAATAACTAAAATGCCTTTTA
347701 AAAAAGCA
66 AAAAAGCA
* *
347709 TGTTGGATTTAAAAAATGACCAAAATACCCTT
1 TGTTGGACTTGAAAAATGACCAAAATACCCTT
347741 TCAATTAATA
Statistics
Matches: 85, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
72 48 0.56
73 37 0.44
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (73 bp):
TGTTGGACTTGAAAAATGACCAAAATACCCTTACATGTTTCAACCAATAACTAAAATGCCTTTTA
AAAAAGCA
Found at i:347785 original size:54 final size:56
Alignment explanation
Indices: 347718--347850 Score: 182
Period size: 54 Copynumber: 2.4 Consensus size: 56
347708 ATGTTGGATT
347718 TAAAAAATGACCAAAATACCCTTTCAATTAATAACTAAAATGCCCCTAAACATG-A
1 TAAAAAATGACCAAAATACCCTTTCAATTAATAACTAAAATGCCCCTAAACATGCA
* * * * *
347773 -ATAAAATAACCAAAATAACCC-TTCAATTAATGACTAAAATGCCTCTAGACATGCA
1 TAAAAAATGACCAAAAT-ACCCTTTCAATTAATAACTAAAATGCCCCTAAACATGCA
*
347828 TAAAAAATGACCCAAATACCCTT
1 TAAAAAATGACCAAAATACCCTT
347851 AAAGGTTTGG
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
54 43 0.65
55 9 0.14
56 14 0.21
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (56 bp):
TAAAAAATGACCAAAATACCCTTTCAATTAATAACTAAAATGCCCCTAAACATGCA
Found at i:348066 original size:29 final size:29
Alignment explanation
Indices: 348018--348082 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
348008 CGATATCAAG
*
348018 TAAATGAAATAATATCAACATAAAGTAAT
1 TAAATGAAATAAAATCAACATAAAGTAAT
*
348047 TAAAGTGAAATAAAAT-AACATAAAGTATAG
1 TAAA-TGAAATAAAATCAACATAAAGTA-AT
348077 TAAATG
1 TAAATG
348083 CAAGTAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (29 bp):
TAAATGAAATAAAATCAACATAAAGTAAT
Found at i:348151 original size:39 final size:39
Alignment explanation
Indices: 348086--348161 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
348076 GTAAATGCAA
*
348086 GTAAAGTAAATAACATACATTTAAATAACAAAAATAAAT
1 GTAAAGTAAATAACATACATTAAAATAACAAAAATAAAT
* *
348125 GTAAAGTAAATAACATGA-ATTAAAATAGCAATAATAA
1 GTAAAGTAAATAACAT-ACATTAAAATAACAAAAATAA
348162 CAATTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.25
Consensus pattern (39 bp):
GTAAAGTAAATAACATACATTAAAATAACAAAAATAAAT
Found at i:348710 original size:147 final size:144
Alignment explanation
Indices: 348405--348909 Score: 527
Period size: 147 Copynumber: 3.5 Consensus size: 144
348395 ATTTTAGGCA
* * * * * * *
348405 TAAAATTGGTTTTTGCACCTTTGGTTTAAACATGACCTAAGT-AAAGGCTT-GAGATCATCAAGC
1 TAAAATTGGTTTTTACACC-TTAGCTCAAACATTACTTAAGTAAAAAGCTTAG-GATCATCAAGC
* * * *
348468 TTTTATTAATACG-ATTTAAACATAATAAACTAAAAATAAATATGAACATAATTTAAATGACAAA
64 TTTAATTAA-AGGAATTT-AACATAATAAACAAAAAATAAATATGAACATAATTTAAATGACATA
*
348532 ATAGCTTAAAGTTTGTCCT
127 ATAGCTCAAAGTTTG-CCT
* * *
348551 TAAAATTGGTTTTTACACCTTAGCCTCAAATATTACTTGAGTAAAAAGC-TAGGATCATTAAGCT
1 TAAAATTGGTTTTTACACCTTAG-CTCAAACATTACTTAAGTAAAAAGCTTAGGATCATCAAGCT
*
348615 TTAATTAAAGGAATTTAGACAAAATAAACAAGAAAATAAATATGAACATAATTTAAATGACATAA
65 TTAATTAAAGGAATTTA-ACATAATAAACAA-AAAATAAATATGAACATAATTTAAATGACATAA
*
348680 TAGCTCAAAATTTAGCCT
128 TAGCTCAAAGTTT-GCCT
* * * * * * *
348698 CAAAATTGGTTTTTACACCTTAAGCTTAAACATCACCTAAGTAAAGA-CTTAGGATCATTAAGGT
1 TAAAATTGGTTTTTACACCTT-AGCTCAAACATTACTTAAGTAAAAAGCTTAGGATCATCAAGCT
* * * **
348762 TTAATTAATGTAATTTAAGCATAATAAACAATAAAATAAATATGAACATAATTTAAATAATGTAA
65 TTAATTAAAGGAATTTAA-CATAATAAACAA-AAAATAAATATGAACATAATTTAAATGACATAA
*
348827 TAGTTCAAAGTTTGGCCT
128 TAGCTCAAAGTTT-GCCT
* * * * *
348845 TAAAATTGATTTTTGCACCTTAGACTCAAACATTCCTTAAG-CAAATGCTTAGGATCATCAAGCT
1 TAAAATTGGTTTTTACACCTTAG-CTCAAACATTACTTAAGTAAAAAGCTTAGGATCATCAAGCT
348909 T
65 T
348910 GTATGTAAAA
Statistics
Matches: 300, Mismatches: 47, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
145 6 0.02
146 70 0.23
147 221 0.74
148 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (144 bp):
TAAAATTGGTTTTTACACCTTAGCTCAAACATTACTTAAGTAAAAAGCTTAGGATCATCAAGCTT
TAATTAAAGGAATTTAACATAATAAACAAAAAATAAATATGAACATAATTTAAATGACATAATAG
CTCAAAGTTTGCCT
Found at i:349939 original size:12 final size:13
Alignment explanation
Indices: 349909--349940 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
349899 ATTCTGCATG
349909 TAAAAACTATAAT
1 TAAAAACTATAAT
349922 TAAAAACTATAAT
1 TAAAAACTATAAT
349935 TAAAAA
1 TAAAAA
349941 TTCTATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAACTATAAT
Found at i:349966 original size:28 final size:27
Alignment explanation
Indices: 349935--350001 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
349925 AAACTATAAT
* *
349935 TAAAAATTCTATGAGTAAAGGGTTTAAC
1 TAAAAATTCTATGAGCAAA-AGTTTAAC
* *
349963 TAAAAAATCTATGAGCAAAAGTTTAAT
1 TAAAAATTCTATGAGCAAAAGTTTAAC
*
349990 TGAAAATTCTAT
1 TAAAAATTCTAT
350002 ATCTATGATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (27 bp):
TAAAAATTCTATGAGCAAAAGTTTAAC
Found at i:349995 original size:27 final size:27
Alignment explanation
Indices: 349931--350001 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
349921 TTAAAAACTA
* *
349931 TAATTAAAAATTCTATGAGTAAAGGGTT
1 TAATTAAAAA-TCTATGAGCAAAGAGTT
*
349959 TAACTAAAAAATCTATGAGCAAA-AGTT
1 TAA-TTAAAAATCTATGAGCAAAGAGTT
*
349986 TAATTGAAAATTCTAT
1 TAATT-AAAAATCTAT
350002 ATCTATGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 15 0.42
28 14 0.39
29 6 0.17
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (27 bp):
TAATTAAAAATCTATGAGCAAAGAGTT
Found at i:351385 original size:16 final size:16
Alignment explanation
Indices: 351364--351420 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
351354 AATTATTTGA
351364 CTTTTAATTAAATTAC
1 CTTTTAATTAAATTAC
* *
351380 CTTTTAATT-GATTAA
1 CTTTTAATTAAATTAC
* * *
351395 CTATTACTAAAATTAC
1 CTTTTAATTAAATTAC
351411 CTTTTAATTA
1 CTTTTAATTA
351421 TTTGCCCTTT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (16 bp):
CTTTTAATTAAATTAC
Found at i:353994 original size:7 final size:7
Alignment explanation
Indices: 353982--354078 Score: 69
Period size: 7 Copynumber: 14.1 Consensus size: 7
353972 GTTATCTTTG
353982 ATAAAAA
1 ATAAAAA
353989 AT--AAA
1 ATAAAAA
353994 ATAAAAA
1 ATAAAAA
354001 ATAAAAA
1 ATAAAAA
354008 ATAAAAAA
1 AT-AAAAA
*
354016 ATCAAATA
1 AT-AAAAA
*
354024 TTCAAAAA
1 AT-AAAAA
354032 ATAAAAA
1 ATAAAAA
*
354039 AT--AAT
1 ATAAAAA
354044 ATAAAAA
1 ATAAAAA
*
354051 TTAAAAA
1 ATAAAAA
*
354058 TTAAAAA
1 ATAAAAA
* *
354065 A-AATAT
1 ATAAAAA
354071 ATAAAAA
1 ATAAAAA
354078 A
1 A
354079 AGTCAGGGAC
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
5 9 0.13
6 4 0.06
7 40 0.56
8 18 0.25
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
ATAAAAA
Found at i:354065 original size:27 final size:27
Alignment explanation
Indices: 353984--354077 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
353974 TATCTTTGAT
* *
353984 AAAAAATAAAATAAAAAATAAAAAATA
1 AAAAAATAATATAAAAATTAAAAAATA
354011 AAAAAATCAA-AT----ATTCAAAAAAT-
1 AAAAAAT-AATATAAAAATT-AAAAAATA
*
354034 AAAAAATAATATAAAAATTAAAAATTA
1 AAAAAATAATATAAAAATTAAAAAATA
354061 AAAAAA-ATATATAAAAA
1 AAAAAATA-ATATAAAAA
354078 AAGTCAGGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
22 2 0.04
23 11 0.20
24 7 0.12
26 7 0.12
27 27 0.48
28 2 0.04
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (27 bp):
AAAAAATAATATAAAAATTAAAAAATA
Found at i:354065 original size:34 final size:31
Alignment explanation
Indices: 353996--354066 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 31
353986 AAAATAAAAT
* *
353996 AAAAAATAAAAAATAAAAAAATCAAATATTC
1 AAAAAATAAAAAATAAAAAAATCAAAAATTA
*
354027 AAAAAATAAAAAATAATATAAAAATTAAAAATTA
1 AAAAAATAAAAAAT-A-A-AAAAATCAAAAATTA
354061 AAAAAA
1 AAAAAA
354067 ATATATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 14 0.41
32 1 0.03
33 1 0.03
34 18 0.53
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (31 bp):
AAAAAATAAAAAATAAAAAAATCAAAAATTA
Found at i:354623 original size:80 final size:80
Alignment explanation
Indices: 354490--354743 Score: 298
Period size: 80 Copynumber: 3.2 Consensus size: 80
354480 AAAGCAAGAG
* * * ***
354490 GAAACATGCAGCATGTGAACAGCAAGAAAGGAGGATGGCAC-AAGCAGCAAACAACAAGCAAGCA
1 GAAACATGCAGCACGTGAAGAGCAAGGAAGGAGGACATCACGAA-CAGCAAACAACAAGCAAGCA
*
354554 ATATGCAAATGATGAA
65 ATGTGCAAATGATGAA
* * * * *
354570 GAAACATGCAGTACGTGAAGAGCAGGGAAGG-GTA-ATAGCACGAATAGCCAACAACAAGCAAGC
1 GAAACATGCAGCACGTGAAGAGCAAGGAAGGAGGACAT--CACGAACAGCAAACAACAAGCAAGC
354633 AATGTGCAAATGATGAA
64 AATGTGCAAATGATGAA
* * **
354650 GAAACATGTAACACGTGAAGAGCAAGGAAGGAGGACATCACGGGCAGCAAACAACAAGCAAGCAA
1 GAAACATGCAGCACGTGAAGAGCAAGGAAGGAGGACATCACGAACAGCAAACAACAAGCAAGCAA
* *
354715 CGTGGAAATGATGAA
66 TGTGCAAATGATGAA
354730 GAAACATGCAGCAC
1 GAAACATGCAGCAC
354744 ATCAAGAAGG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
79 2 0.01
80 137 0.94
81 4 0.03
82 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.27, T:0.10
Consensus pattern (80 bp):
GAAACATGCAGCACGTGAAGAGCAAGGAAGGAGGACATCACGAACAGCAAACAACAAGCAAGCAA
TGTGCAAATGATGAA
Found at i:357744 original size:38 final size:38
Alignment explanation
Indices: 357700--357787 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
357690 GTTTTTTCAA
* *
357700 TTTAAAATTTTAATTTA-AGT-TGTAATTATCTAATTATT
1 TTTAAAATTTAAATTTAGAGTAT-TAATCATCTAATTA-T
* *
357738 TTTAAAATTTAAATTTAGAGTATTGATCGTCTAATTAT
1 TTTAAAATTTAAATTTAGAGTATTAATCATCTAATTAT
357776 TTTAAAATTTAA
1 TTTAAAATTTAA
357788 GTTATAATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
38 29 0.66
39 14 0.32
40 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (38 bp):
TTTAAAATTTAAATTTAGAGTATTAATCATCTAATTAT
Found at i:357898 original size:37 final size:37
Alignment explanation
Indices: 357843--357913 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
357833 CCTAACTTTT
* * * * *
357843 AAATGATTAGATGGTTACAATCTTAATTTAAATTAAA
1 AAATAATTAGATGATTACAACCTAAATTAAAATTAAA
*
357880 AAATAATTTGATGATTACAACCTAAATTAAAATT
1 AAATAATTAGATGATTACAACCTAAATTAAAATT
357914 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (37 bp):
AAATAATTAGATGATTACAACCTAAATTAAAATTAAA
Found at i:357945 original size:14 final size:13
Alignment explanation
Indices: 357902--357946 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
357892 GATTACAACC
357902 TAAATTAAAATTT
1 TAAATTAAAATTT
**
357915 TAAATTAAAAAAAT
1 TAAATT-AAAATTT
357929 TAAATTAAATATTT
1 TAAATTAAA-ATTT
357943 TAAA
1 TAAA
357947 ATAATTGTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATTAAAATTT
Found at i:358080 original size:19 final size:18
Alignment explanation
Indices: 358035--358076 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
358025 TATTATTATA
358035 TTTATAATAATATTATCT
1 TTTATAATAATATTATCT
358053 TTTACTAATAATA-TAGTCT
1 TTTA-TAATAATATTA-TCT
358072 TTTAT
1 TTTAT
358077 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTATAATAATATTATCT
Found at i:358654 original size:18 final size:18
Alignment explanation
Indices: 358624--358709 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 18
358614 TAAAAAGATA
*
358624 CATTTGAATGAATGAATG
1 CATTTGGATGAATGAATG
*
358642 CAGTTGGATGAATGAATG
1 CATTTGGATGAATGAATG
* * *
358660 --TATGCATATAGATGAATG
1 CATTTGGAT-GA-ATGAATG
*
358678 CATTTGGATGAATGAATA
1 CATTTGGATGAATGAATG
*
358696 CATTTGAATGAATG
1 CATTTGGATGAATG
358710 CATTGGGTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
16 4 0.08
17 1 0.02
18 42 0.79
19 1 0.02
20 5 0.09
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (18 bp):
CATTTGGATGAATGAATG
Found at i:358673 original size:22 final size:22
Alignment explanation
Indices: 358628--358677 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
358618 AAGATACATT
*
358628 TGAATGAATGAATGCAGTTGGA
1 TGAATGAATGAATGCAGTTAGA
*
358650 TGAATGAATGTATGCA-TATAGA
1 TGAATGAATGAATGCAGT-TAGA
358672 TGAATG
1 TGAATG
358678 CATTTGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (22 bp):
TGAATGAATGAATGCAGTTAGA
Found at i:359845 original size:28 final size:28
Alignment explanation
Indices: 359789--359860 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
359779 GAAAAAATGT
** **
359789 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
359817 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
359845 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
359861 TCAATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:360006 original size:51 final size:50
Alignment explanation
Indices: 359848--360017 Score: 196
Period size: 52 Copynumber: 3.3 Consensus size: 50
359838 GAAATAACGA
* *
359848 GGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAATCG
** * * *
359899 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAGTCGG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATC-G
* * * *
359952 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTGGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-G
360003 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
360018 TCGGAGATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
51 38 0.38
52 48 0.48
53 13 0.13
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCG
Found at i:360043 original size:79 final size:80
Alignment explanation
Indices: 359949--360128 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 80
359939 AAAATAAAGT
* * *
359949 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA-TTTGGAAATAAAACC-AGGGTTGGAGT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTTTAGAAATAAAACCGAGGGTTGGAGT
* * *
360012 ATCCCCTCGGAGATAA
65 ATCCCCACGAAAATAA
* * * *
360028 CGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAGCCGGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGAGGGTTGGAGTA
*
360093 TCTCCACGAAAATAA
66 TCCCCACGAAAATAA
360108 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
360129 GATTAACGGG
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 1 0.01
79 44 0.50
80 43 0.49
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGAGGGTTGGAGTA
TCCCCACGAAAATAA
Found at i:360146 original size:27 final size:27
Alignment explanation
Indices: 360081--360157 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
360071 AATAAAGCCG
* *
360081 GGGGTTGGAGTATCTCCACGA-AAATAAC
1 GGGGTTGGAGTATC-CC-CGATGATTAAC
360109 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGATTAAC
*
360136 GGGGTTTGAGTATCCCCGATGA
1 GGGGTTGGAGTATCCCCGATGA
360158 AAAATTGATG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 28 0.62
28 14 0.31
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGATTAAC
Found at i:360221 original size:51 final size:51
Alignment explanation
Indices: 360158--360255 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
360148 TCCCCGATGA
360158 AAAATTGATGTTTT-AGAAATAAAATCGGAGTTGAAATATCCCCGATTATAG
1 AAAATTGATGTTTTGA-AAATAAAATCGGAGTTGAAATATCCCCGATTATAG
* **
360209 AAAATT-AGTGTTTTGAAAATGAAATCGGAGTTGGGATATCCCCGATT
1 AAAATTGA-TGTTTTGAAAATAAAATCGGAGTTGAAATATCCCCGATT
360256 GCAGAGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.02
51 40 0.95
52 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (51 bp):
AAAATTGATGTTTTGAAAATAAAATCGGAGTTGAAATATCCCCGATTATAG
Found at i:362640 original size:13 final size:13
Alignment explanation
Indices: 362622--362647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
362612 ACAAAGATCC
362622 ATGTATCGATACA
1 ATGTATCGATACA
362635 ATGTATCGATACA
1 ATGTATCGATACA
362648 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:362643 original size:33 final size:33
Alignment explanation
Indices: 362601--362667 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
362591 AAAATTTCCA
***
362601 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
362634 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
362667 A
1 A
362668 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:362711 original size:19 final size:18
Alignment explanation
Indices: 362687--362754 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
362677 CAGTAGCTAA
362687 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
362706 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
362721 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
362738 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
362755 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:362727 original size:13 final size:13
Alignment explanation
Indices: 362709--362733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362699 ACAATACTTA
362709 TGTATCGATACAT
1 TGTATCGATACAT
362722 TGTATCGATACA
1 TGTATCGATACA
362734 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:362731 original size:32 final size:32
Alignment explanation
Indices: 362690--362752 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
362680 TAGCTAATTA
*
362690 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
362722 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
362753 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:363862 original size:47 final size:47
Alignment explanation
Indices: 363793--363996 Score: 158
Period size: 55 Copynumber: 4.0 Consensus size: 47
363783 GACTGAAAGG
* *
363793 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCTTGCTCTTTGAGGA
1 TGCCACCAACTTGTGTGAGCTTTGAA-AGGTGTCCTGCTCTTTGAGGA
363840 TGCCACCAACTTGTGTGAGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGAGCTTTGAAAGGTGTCCTGCTCTTT---GA--GG---A
** * * * *
363895 TGTTACCAACTTGTGTGGGCTTCGAAAGGGGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGAGCTTTGAAAGGTGTCCTGCTCTTT---GA--G---GA
* *
363950 TGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGA
1 TGCCACCAACTTGTGTGAGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
363997 CTGGAAAATG
Statistics
Matches: 130, Mismatches: 15, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
47 38 0.29
48 2 0.02
50 3 0.02
52 4 0.03
55 82 0.63
58 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.31
Consensus pattern (47 bp):
TGCCACCAACTTGTGTGAGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
Found at i:364011 original size:212 final size:217
Alignment explanation
Indices: 363625--364713 Score: 984
Period size: 237 Copynumber: 4.8 Consensus size: 217
363615 GAGGACTAAA
* *
363625 AAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACC
1 AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAA-GTGCCACC
* *
363690 AACTTGTGTGGGCTTTA-AAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTG
65 AACTTGTGTGGGC-TTAGAAAGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTG
*
363753 TGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA
128 TGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA
* * *
363818 -G-AGGTGTCTTGCTCT-T-TGA-GG
192 GGAAGGCGTCCTGCTCTCTAGGACGG
* * **
363839 -A-TGCCACCAACTTGTGTGAGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGTTACC
1 AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACC
* * *
363902 AACTTGTGTGGGCTTCGAAAGGGGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTG
65 AACTTGTGTGGGCTTAGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTG
* *
363967 GGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA
130 GGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT--AA
364032 GGTGAAGGCGTCCTGCTCTCTGAGGACTGGG
192 -G-GAAGGCGTCCTGCTCTCT-AGGAC--GG
* *
364063 AAGTGCCACTAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACC
1 AAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACC
*
364127 AACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTT
65 AACTTGTGTGGGC-TT---AG-AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTT
* *
364191 GTGTGGGCTTTAAAAGAAAAGGCGT-CTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTG
125 GTGTGGGCTTT----G-AAAGGTGTCCT-GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTG
* * * * *
364255 GGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGAA
184 GGCTTT--AAG-GAAGGCGTCCTGCTCTCT-AGGAC-G-G
* * * *
364295 AAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGC
1 AAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGC
*
364360 CACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCA
61 CACCAACTTGTGTGGGC-TT---AG-AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCA
* * * * **
364424 ACTTGTGTGGGCTTTAAAAAAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGAGACCAACTTGT
121 ACTTGTGTGGGCTTT-----GAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGT
* * * *
364489 GTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGG
181 GTGGGCTTT--AAG-GAAGGCGTCCTGCTCTCT-AGGAC-GG
* * ** **
364531 AAAATGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCATCCCACTCTTTGAGGACTG-AAGAT
1 -AAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGAAAG-T
* *
364595 GCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAAA-ATGCCA
59 GCCACCAACTTGTGTGGGC-TT---AG-AAAGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCA
*
364659 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAG
118 CCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAG
364714 CGGAAGGAGA
Statistics
Matches: 775, Mismatches: 55, Indels: 65
0.87 0.06 0.07
Matches are distributed among these distances:
211 6 0.01
212 157 0.20
213 9 0.01
214 2 0.00
217 1 0.00
218 12 0.02
219 1 0.00
221 2 0.00
224 2 0.00
225 24 0.03
226 46 0.06
229 28 0.04
230 23 0.03
231 1 0.00
232 45 0.06
233 32 0.04
234 20 0.03
236 2 0.00
237 301 0.39
238 55 0.07
239 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (217 bp):
AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCA
ACTTGTGTGGGCTTAGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGG
GCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAGGAA
GGCGTCCTGCTCTCTAGGACGG
Found at i:364179 original size:59 final size:59
Alignment explanation
Indices: 363840--364708 Score: 1141
Period size: 59 Copynumber: 14.9 Consensus size: 59
363830 TCTTTGAGGA
* * * **
363840 TGCCACCAACTTGTGTGAGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGG
** * * * *
363895 TGTTACCAACTTGTGTGGGC-TT---CG-AAAGGGGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAGG
* * * **
363950 TGCCACCAACTTGTGTGGGCTTT----G-AGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGG
* ** * *
364005 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGGCGTCCTGCTCTCTGAGGACTGGGAA-G
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACT--GAAGG
* * *
364066 TGCCACTAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCTTTGAGGACTGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
364120 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
*
364179 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTCGCTCTTTGAGGACTGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
* **
364238 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAGG
364298 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
364357 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
*
364416 TGCCACCAACTTGTGTGGGCTTTAAAAAAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
** * **
364475 TGAGACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGG
* * * *
364535 TGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCATCCCACTCTTTGAGGACTGAAGA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
**
364594 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGG
*
364654 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
364709 GAAAGCGGAA
Statistics
Matches: 741, Mismatches: 53, Indels: 36
0.89 0.06 0.04
Matches are distributed among these distances:
53 3 0.00
54 26 0.04
55 130 0.18
56 6 0.01
58 2 0.00
59 362 0.49
60 165 0.22
61 43 0.06
62 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (59 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
Found at i:364322 original size:178 final size:177
Alignment explanation
Indices: 363839--364708 Score: 1118
Period size: 178 Copynumber: 5.0 Consensus size: 177
363829 CTCTTTGAGG
* * * ** **
363839 ATGCCACCAACTTGTGTGAGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGTT
1 ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCC
* * * * *
363899 ACCAACTTGTGTGGGC-TT---CG-AAAGGGGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAA
65 ACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAA
* * *
363959 CTTGTGTGGGCTTT----G-AGAGGTGTCCTGCTCTTTGAGGACTGGAAA
129 CTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAA
* ** * *
364004 ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGGCGTCCTGCTCTCTGAGGACTGGGAA-GTG
1 ATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACT--GAAGGTG
* * * *
364068 CCACTAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCA
63 CCACCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCA
*
364128 ACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
128 ACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAA
* *
364178 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTCGCTCTTTGAGGACTGAAGGTGCCA
1 ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
**
364243 CCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGAAAAATGCCACCAAC
66 CCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAAC
*
364308 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
130 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAA
*
364356 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
1 ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
**
364421 CCAACTTGTGTGGGCTTTAAAA-AAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGAGACCAAC
66 CCAACTTGTGTGGGCTTTAAAAGAAAAA-GCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAAC
*
364485 TTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAA
130 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAA
* * * *
364534 ATGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCATCCCACTCTTTGAGGACTGAAGATGCCA
1 ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
* **
364599 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAAC
66 CCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAAC
*
364664 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG
130 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
364709 GAAAGCGGAA
Statistics
Matches: 633, Mismatches: 47, Indels: 37
0.88 0.07 0.05
Matches are distributed among these distances:
165 23 0.04
170 28 0.04
171 64 0.10
172 29 0.05
173 26 0.04
174 30 0.05
175 22 0.03
177 79 0.12
178 275 0.43
179 57 0.09
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (177 bp):
ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
CCAACTTGTGTGGGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACT
TGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAA
Found at i:364364 original size:237 final size:234
Alignment explanation
Indices: 363839--364708 Score: 1194
Period size: 237 Copynumber: 3.7 Consensus size: 234
363829 CTCTTTGAGG
* * * * **
363839 ATGCCACCAACTTGTGTGAGCTTT--GAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGTTACC
1 ATGCCACCAACTTGTGTGGGCTTTAAGAAAGGCGTCCCGCTCTTTGAGGACT-GAAGATGCCACC
* * * *
363902 AACTTGTGTGGGC-TT---CG-AAAGGGGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTT
65 AACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTT
* * **
363962 GTGTGGGCTTT----G-AGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTG
129 GTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTG
* ** * * * *
364022 GGCTTTGAAAGGTGAAGGCGTCCTGCTCTCTGAGGACTGGGAA
193 GGCTTT-AAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAA
* * * * *
364065 GTGCCACTAACTTGTGTGGGCTTTAAG--AGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCA
1 ATGCCACCAACTTGTGTGGGCTTTAAGAAAGGCGTCCCGCTCTTTGAGGACTGAAGATGCCACCA
364128 ACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGT
66 ACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGT
364193 GTGGGCTTTAAAAGAAAAGGCGT-CTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGG
131 GTGGGCTTTAAAAGAAAAGGCGTCCT-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGG
*
364257 CTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGAAAA
195 CTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAA
*
364297 ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
1 ATGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGCGTCCCGCTCTTTGAGGACTGAAGATGCCA
364362 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACT
63 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACT
* * **
364427 TGTGTGGGCTTTAAAAAAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGAGACCAACTTGTGTG
128 TGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTG
364492 GGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAA
193 GGCTTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAA
* * *
364534 ATGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCATCCCACTCTTTGAGGACTGAAGATGCCA
1 ATGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGCGTCCCGCTCTTTGAGGACTGAAGATGCCA
**
364599 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAAC
63 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAAC
364664 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG
127 TTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG
364709 GAAAGCGGAA
Statistics
Matches: 584, Mismatches: 40, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
225 21 0.04
226 46 0.08
228 1 0.00
229 28 0.05
230 23 0.04
232 50 0.09
233 29 0.05
234 23 0.04
237 306 0.52
238 57 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (234 bp):
ATGCCACCAACTTGTGTGGGCTTTAAGAAAGGCGTCCCGCTCTTTGAGGACTGAAGATGCCACCA
ACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGT
GTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGC
TTTAAAAGAAAAAGCGTCCCGCTCTTTGAGGACTGGAAA
Found at i:365720 original size:25 final size:25
Alignment explanation
Indices: 365692--365739 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
365682 TTTTCTCTCT
*
365692 TTTTCTTTGTTTTGTTTTTTTTTTG
1 TTTTCTTTGTTTTCTTTTTTTTTTG
* *
365717 TTTTGTTTTTTTTCTTTTTTTTT
1 TTTTCTTTGTTTTCTTTTTTTTT
365740 GAAGAGAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (25 bp):
TTTTCTTTGTTTTCTTTTTTTTTTG
Found at i:365736 original size:16 final size:17
Alignment explanation
Indices: 365691--365736 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
365681 CTTTTCTCTC
365691 TTTTTCTTTGTTTTGTTT
1 TTTTTC-TTGTTTTGTTT
365709 TTTTT-TTGTTTTGTTT
1 TTTTTCTTGTTTTGTTT
365725 TTTTTCTT-TTTT
1 TTTTTCTTGTTTT
365737 TTTGAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 20 0.74
17 2 0.07
18 5 0.19
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (17 bp):
TTTTTCTTGTTTTGTTT
Found at i:374519 original size:4 final size:4
Alignment explanation
Indices: 374512--374536 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
374502 AAACAGATAT
374512 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
374537 CACCTCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:376874 original size:51 final size:51
Alignment explanation
Indices: 376719--376888 Score: 223
Period size: 52 Copynumber: 3.3 Consensus size: 51
376709 GAAATAACGA
* * * *
376719 GGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTTGGAAATAAAACCAG
* ** * *
376771 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAGCCAG
1 GGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTGGAAATAAAACCAG
* *
376823 GGTTGGAGTATCCCCGATTGTGGAAAATTGATGATTTGGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAACCAG
376874 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
376889 TCGAAAATAA
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
51 41 0.41
52 49 0.49
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAACCAG
Found at i:379448 original size:33 final size:33
Alignment explanation
Indices: 379390--379454 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
379380 AAAATTTTCA
*** *
379390 AATGTATCGATACAAAGATCCATGTATTGATAT
1 AATGTATCGATACAAAGAAAAATGTATCGATAT
*
379423 AATGTATCGATACACAGAAAAATGTATCGATA
1 AATGTATCGATACAAAGAAAAATGTATCGATA
379455 CATTTCCTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAT
Found at i:379500 original size:19 final size:18
Alignment explanation
Indices: 379476--379543 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
379466 CAATAGCTAA
379476 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
379495 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
379510 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
379527 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
379544 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:379516 original size:13 final size:13
Alignment explanation
Indices: 379498--379522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379488 ACAATACTTA
379498 TGTATCGATACAT
1 TGTATCGATACAT
379511 TGTATCGATACA
1 TGTATCGATACA
379523 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:379520 original size:32 final size:32
Alignment explanation
Indices: 379479--379541 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
379469 TAGCTAATTA
*
379479 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
379511 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
379542 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:379626 original size:21 final size:21
Alignment explanation
Indices: 379602--379655 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
379592 TTGTAGAATA
379602 TATCGATACATTCCACAAATG
1 TATCGATACATTCCACAAATG
*
379623 TATCGATACATTCTACAAATG
1 TATCGATACATTCCACAAATG
379644 TATCGATACATT
1 TATCGATACATT
379656 TGGGTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.33
Consensus pattern (21 bp):
TATCGATACATTCCACAAATG
Found at i:381917 original size:14 final size:14
Alignment explanation
Indices: 381881--381919 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
381871 TGCCTTCAGA
* *
381881 TGAATGAACGTATT
1 TGAATGAATGTGTT
381895 TGAATGAATGTGTT
1 TGAATGAATGTGTT
*
381909 TGGATGAATGT
1 TGAATGAATGT
381920 TATGCACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (14 bp):
TGAATGAATGTGTT
Found at i:381951 original size:18 final size:18
Alignment explanation
Indices: 381930--381993 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
381920 TATGCACATT
*
381930 GATGAATGAATGCATTTA
1 GATGAATGAATACATTTA
* **
381948 GATGAATGAATATATGCA
1 GATGAATGAATACATTTA
* * *
381966 TATGGATGAATACATTTG
1 GATGAATGAATACATTTA
381984 GATGAATGAA
1 GATGAATGAA
381994 AGCATTTGAA
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (18 bp):
GATGAATGAATACATTTA
Found at i:381964 original size:22 final size:22
Alignment explanation
Indices: 381931--381976 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
381921 ATGCACATTG
*
381931 ATGAATGAATGCATTTAGATGA
1 ATGAATGAATGCATATAGATGA
*
381953 ATGAAT-ATATGCATATGGATGA
1 ATGAATGA-ATGCATATAGATGA
381975 AT
1 AT
381977 ACATTTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (22 bp):
ATGAATGAATGCATATAGATGA
Found at i:381999 original size:18 final size:18
Alignment explanation
Indices: 381930--382008 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
381920 TATGCACATT
* *
381930 GATGAATGAATGCATTTA
1 GATGAATGAAAGCATTTG
*
381948 GATGAATGAATATATGCATATG
1 GATGAATG-A-A-A-GCATTTG
381970 GATGAAT---A-CATTTG
1 GATGAATGAAAGCATTTG
381984 GATGAATGAAAGCATTTG
1 GATGAATGAAAGCATTTG
*
382002 AATGAAT
1 GATGAAT
382009 ACATTTGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
14 12 0.25
16 1 0.02
17 1 0.02
18 20 0.42
19 1 0.02
20 1 0.02
22 12 0.25
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (18 bp):
GATGAATGAAAGCATTTG
Found at i:382007 original size:32 final size:36
Alignment explanation
Indices: 381931--382015 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
381921 ATGCACATTG
* *
381931 ATGAATGAATGCATTTAGATGAATGAATATATGCAT
1 ATGAATGAATACATTTGGATGAATGAATATATGCAT
*
381967 ATGGATGAATACATTTGGATGAATG-A-A-A-GCAT
1 ATGAATGAATACATTTGGATGAATGAATATATGCAT
*
381999 TTGAATGAATACATTTG
1 ATGAATGAATACATTTG
382016 AATGCATCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 19 0.43
33 1 0.02
34 1 0.02
35 1 0.02
36 22 0.50
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (36 bp):
ATGAATGAATACATTTGGATGAATGAATATATGCAT
Found at i:382016 original size:14 final size:14
Alignment explanation
Indices: 381971--382019 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
381961 ATGCATATGG
*
381971 ATGAATACATTTGG
1 ATGAATACATTTGA
381985 ATGAATGAAAGCATTTGA
1 ATGAAT---A-CATTTGA
382003 ATGAATACATTTGA
1 ATGAATACATTTGA
382017 ATG
1 ATG
382020 CATCAGAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 16 0.53
15 1 0.03
17 1 0.03
18 12 0.40
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (14 bp):
ATGAATACATTTGA
Found at i:391224 original size:59 final size:59
Alignment explanation
Indices: 391104--391235 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
391094 ATAAGAGGAC
* * *
391104 GAGATGACCAATTTTGAACCTTTCAGAAGGCATGGTAACATTGTCGTACCTTAAAAGGT
1 GAGATGATCAATTTTGAACCTTTCAGAAGGCATAGTAACATTGTCATACCTTAAAAGGT
** * * *
391163 GAGATGATCAATTTTGAACCTTTGGGAAGGCATAGTAGCA-T-TCATGCGCTTGAAAATGT
1 GAGATGATCAATTTTGAACCTTTCAGAAGGCATAGTAACATTGTCATAC-CTT-AAAAGGT
391222 GAGATGATCAATTT
1 GAGATGATCAATTT
391236 ATACCTTTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 4 0.06
58 4 0.06
59 55 0.87
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (59 bp):
GAGATGATCAATTTTGAACCTTTCAGAAGGCATAGTAACATTGTCATACCTTAAAAGGT
Found at i:396881 original size:16 final size:15
Alignment explanation
Indices: 396845--396887 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
396835 ACAAATACTA
*
396845 ACATTTTAAATTGAT
1 ACATTTTAAAATGAT
*
396860 AAATTTTAAAATGAT
1 ACATTTTAAAATGAT
396875 AGCATTTTAAAAT
1 A-CATTTTAAAAT
396888 TTTTGTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (15 bp):
ACATTTTAAAATGAT
Found at i:399274 original size:24 final size:23
Alignment explanation
Indices: 399210--399267 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
399200 TTCTAATAGG
399210 GAAAACATTTGAATAGATGATTA
1 GAAAACATTTGAATAGATGATTA
399233 GAAAACATTTGAATAGATGATTA
1 GAAAACATTTGAATAGATGATTA
399256 GAAAAACATTTG
1 G-AAAACATTTG
399268 GACAGATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.29
Consensus pattern (23 bp):
GAAAACATTTGAATAGATGATTA
Found at i:400168 original size:2 final size:2
Alignment explanation
Indices: 400161--400198 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
400151 TTATTGCTGC
400161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400199 TTACAAGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403969 original size:6 final size:5
Alignment explanation
Indices: 403960--404120 Score: 53
Period size: 5 Copynumber: 31.2 Consensus size: 5
403950 AAATTTAATT
* *
403960 ATATGA ATATA ATATA A-ATA AAATA ATTAAA ATATA ATATA ATATAA
1 ATAT-A ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATAT-A
* * * * * * * * *
404007 ATATA TTTTAA ATTTT ATATA ATATA A-ATT AT-TA ATATT TTAAA AT-TT
1 ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * *
404055 ATATAA ATATA AAAT- ATTTAA ATATA ATTATA ATAAA AAATA TATATA
1 ATAT-A ATATA ATATA ATAT-A ATATA A-TATA ATATA ATATA -ATATA
*
404103 TATAAA ATATAA ATATA A
1 -ATATA ATAT-A ATATA A
404121 AAAATAATAG
Statistics
Matches: 113, Mismatches: 29, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
4 14 0.12
5 57 0.50
6 42 0.37
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:403979 original size:11 final size:11
Alignment explanation
Indices: 403960--404120 Score: 77
Period size: 11 Copynumber: 15.1 Consensus size: 11
403950 AAATTTAATT
*
403960 ATATGAATATA
1 ATATAAATATA
403971 ATATAAATA-A
1 ATATAAATATA
* *
403981 A-ATAATTAAA
1 ATATAAATATA
403991 ATAT-AATATA
1 ATATAAATATA
404001 ATATAAATATA
1 ATATAAATATA
* * * *
404012 TTTTAAATTTT
1 ATATAAATATA
404023 ATAT-AATATAA
1 ATATAAATAT-A
* *
404034 ATTATTAATATT
1 A-TATAAATATA
* *
404046 TTA-AAAT-TT
1 ATATAAATATA
404055 ATATAAATATA
1 ATATAAATATA
* **
404066 AAATATTTA-A
1 ATATAAATATA
*
404076 ATATAATTATA
1 ATATAAATATA
*
404087 ATA-AAAAATA
1 ATATAAATATA
* *
404097 TATATATATAAA
1 -ATATAAATATA
404109 ATATAAATATA
1 ATATAAATATA
404120 A
1 A
404121 AAAATAATAG
Statistics
Matches: 110, Mismatches: 29, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
9 10 0.09
10 36 0.33
11 52 0.47
12 7 0.06
13 5 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
ATATAAATATA
Found at i:404026 original size:16 final size:16
Alignment explanation
Indices: 404007--404059 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
403997 TATAATATAA
404007 ATATATTTTAAATTTT
1 ATATATTTTAAATTTT
* *
404023 ATATAATATAAATTATT
1 ATATATTTTAAATT-TT
*
404040 A-ATATTTTAAAATTT
1 ATATATTTTAAATTTT
404055 ATATA
1 ATATA
404060 AATATAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTTAAATTTT
Found at i:404027 original size:27 final size:26
Alignment explanation
Indices: 403971--404097 Score: 87
Period size: 27 Copynumber: 4.6 Consensus size: 26
403961 TATGAATATA
* * * *
403971 ATATAA-ATAAAATAATTAAAATATA
1 ATATAATATAAAATATTTTAAATTTT
403996 ATATAATATAAATATATTTTAAATTTT
1 ATATAATATAAA-ATATTTTAAATTTT
*
404023 ATATAATATAAATTATTAATATTTTAAAATTT
1 ATATAATAT--A--A--AATATTTTAAATTTT
* *
404055 ATATAAATATAAAATA-TTTAAATATA
1 ATAT-AATATAAAATATTTTAAATTTT
*
404081 ATTATAATAAAAAATAT
1 A-TATAATATAAAATAT
404098 ATATATATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
25 6 0.07
26 23 0.28
27 26 0.32
29 2 0.02
31 2 0.02
32 17 0.21
33 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATAATATAAAATATTTTAAATTTT
Found at i:404064 original size:33 final size:32
Alignment explanation
Indices: 403991--404072 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
403981 AATAATTAAA
* * *
403991 ATATAATATAATATA-AATATATTTTAAATTTT
1 ATATAATATAAAATATTA-ATATTTTAAAATTT
*
404023 ATATAATATAAATTATTAATATTTTAAAATTT
1 ATATAATATAAAATATTAATATTTTAAAATTT
404055 ATATAAATATAAAATATT
1 ATAT-AATATAAAATATT
404073 TAAATATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 30 0.70
33 13 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATATAATATAAAATATTAATATTTTAAAATTT
Found at i:404078 original size:15 final size:15
Alignment explanation
Indices: 404054--404122 Score: 69
Period size: 13 Copynumber: 5.0 Consensus size: 15
404044 TTTTAAAATT
404054 TATATAAATATAAAA
1 TATATAAATATAAAA
*
404069 TATTTAAATAT--AA
1 TATATAAATATAAAA
*
404082 T-TAT-AATAAAAAA
1 TATATAAATATAAAA
*
404095 TATATATATAT-AAA
1 TATATAAATATAAAA
404109 -ATATAAATATAAAA
1 TATATAAATATAAAA
404123 AATAATAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
11 4 0.09
12 2 0.05
13 15 0.35
14 9 0.21
15 13 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:404096 original size:33 final size:32
Alignment explanation
Indices: 404059--404129 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
404049 AAATTTATAT
* *
404059 AAATATAAA-ATATTTAAATATAATTATAATAAA
1 AAATATAAATATA-TAAAATATAAATATAA-AAA
*
404092 AAATATATATATATAAAATATAAATATAAAAA
1 AAATATAAATATATAAAATATAAATATAAAAA
404124 ATAATA
1 A-AATA
404130 GATCTACCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.12
33 26 0.79
34 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (32 bp):
AAATATAAATATATAAAATATAAATATAAAAA
Found at i:404121 original size:6 final size:6
Alignment explanation
Indices: 404055--404121 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
404045 TTTAAAATTT
* * * *
404055 ATATAA ATATAAA ATATTTAA ATATAA TTAT-A ATA-AA AAATAT ATATAT
1 ATATAA ATAT-AA ATA--TAA ATATAA ATATAA ATATAA ATATAA ATATAA
404104 ATA-AA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA A
404122 AAATAATAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 10 0.20
6 28 0.57
7 5 0.10
8 5 0.10
9 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:404124 original size:15 final size:15
Alignment explanation
Indices: 404087--404126 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
404077 TATAATTATA
*
404087 ATAAAAAATATATAT
1 ATAAAAAATATAAAT
*
404102 ATATAAAATATAAAT
1 ATAAAAAATATAAAT
404117 ATAAAAAATA
1 ATAAAAAATA
404127 ATAGATCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAAATATAAAT
Found at i:405059 original size:21 final size:21
Alignment explanation
Indices: 405029--405099 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
405019 ATAATAATAA
405029 TAATATTTAAAATATTA-TATAT
1 TAAT-TTTAAAATATTATTA-AT
*
405051 TAATTTTAATATATTATTAAT
1 TAATTTTAAAATATTATTAAT
* *
405072 TAATATTAAATAAATT-TTAA-
1 TAATTTTAAA-ATATTATTAAT
405092 TAATTTTA
1 TAATTTTA
405100 TATATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 7 0.17
21 25 0.60
22 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTTTAAAATATTATTAAT
Found at i:405110 original size:46 final size:45
Alignment explanation
Indices: 405060--405161 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 45
405050 TTAATTTTAA
405060 TATATTAT-TAATTAATATTAAAT-AAATTTTAATAATTTTATATATT
1 TATATTATATAA-TAATATTAAATCAAA-TTTAATAATTTTATATA-T
* * * * *
405106 TATATTATATAATATTTTTAAATCACATTTAATTATTTTTTATAT
1 TATATTATATAATAATATTAAATCAAATTTAATAATTTTATATAT
405151 TATATT-TATAA
1 TATATTATATAA
405162 CATTTAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
44 5 0.10
45 7 0.14
46 32 0.65
47 5 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (45 bp):
TATATTATATAATAATATTAAATCAAATTTAATAATTTTATATAT
Found at i:405626 original size:3 final size:3
Alignment explanation
Indices: 405618--405650 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
405608 AATAAAAAAC
405618 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
405651 TGAAGCAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:407295 original size:6 final size:6
Alignment explanation
Indices: 407284--407376 Score: 60
Period size: 6 Copynumber: 16.3 Consensus size: 6
407274 CGATGACATG
*
407284 ATATAA ATAT-A ATATAA AAAT-A AT-TAA ATATAA A-ATATA ATATTAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA-A ATA-TAA
* *
407330 AT-T-- ATATAA AAAT-A TTATAA ATATAA ATATATGA ATATAA ATA-AA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA--A ATATAA ATATAA
407375 AT
1 AT
407377 TTATATAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 25
0.69 0.06 0.25
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 21 0.30
6 32 0.46
7 4 0.06
8 8 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:407335 original size:20 final size:20
Alignment explanation
Indices: 407306--407371 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
407296 TATAAAAATA
407306 ATTAAA-TATAAAATATAAT
1 ATTAAATTATAAAATATAAT
*
407325 ATTAAATTATATAA-A-AAT
1 ATTAAATTATAAAATATAAT
*
407343 ATTATAAATATAAATATATGAAT
1 ATTA-AATTATAAA-ATAT-AAT
407366 A-TAAAT
1 ATTAAAT
407372 AAAATTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 7 0.19
19 14 0.38
20 7 0.19
21 3 0.08
22 2 0.05
23 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTAAATTATAAAATATAAT
Found at i:407338 original size:38 final size:40
Alignment explanation
Indices: 407284--407371 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
407274 CGATGACATG
407284 ATATAAATATAATATAAAAATAAT-TAAATATAAA-ATAT-A
1 ATATAAAT-T-ATATAAAAATAATATAAATATAAATATATGA
*
407323 ATATTAAATTATATAAAAATATTATAAATATAAATATATGA
1 ATA-TAAATTATATAAAAATAATATAAATATAAATATATGA
407364 ATATAAAT
1 ATATAAAT
407372 AAAATTTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
38 12 0.27
39 14 0.32
40 14 0.32
41 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (40 bp):
ATATAAATTATATAAAAATAATATAAATATAAATATATGA
Found at i:407386 original size:20 final size:20
Alignment explanation
Indices: 407284--407376 Score: 63
Period size: 20 Copynumber: 4.7 Consensus size: 20
407274 CGATGACATG
**
407284 ATATAAATAT-AATATAAAA
1 ATATAAATATAAATATATGA
407303 ATAATTAAATATAAA-ATAT-A
1 AT-A-TAAATATAAATATATGA
*
407323 ATATTAAATTATATAA-AAAT-A
1 ATA-TAAA-TATA-AATATATGA
*
407344 TTATAAATATAAATATATGA
1 ATATAAATATAAATATATGA
407364 ATATAAATA-AAAT
1 ATATAAATATAAAT
407377 TTATATAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.03
19 19 0.31
20 21 0.34
21 18 0.29
22 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
ATATAAATATAAATATATGA
Found at i:407387 original size:18 final size:18
Alignment explanation
Indices: 407290--407408 Score: 77
Period size: 18 Copynumber: 6.7 Consensus size: 18
407280 CATGATATAA
*
407290 ATATAATATAAAAATAATT
1 ATATAATAAAAAAAT-ATT
*
407309 AAAT-ATAAAATATAATATT
1 ATATAATAAAA-A-AATATT
* * *
407328 AAATTATATAAAAATATT
1 ATATAATAAAAAAATATT
* * *
407346 ATA-AATATAAATATATG
1 ATATAATAAAAAAATATT
407363 A-AT-ATAAATAAAAT-TT
1 ATATAATAAA-AAAATATT
*
407379 ATATAATAAAAAATTATT
1 ATATAATAAAAAAATATT
*
407397 ATATCATAAAAA
1 ATATAATAAAAA
407409 TTAAAAAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.09
17 22 0.28
18 31 0.39
19 12 0.15
20 8 0.10
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (18 bp):
ATATAATAAAAAAATATT
Found at i:407442 original size:15 final size:15
Alignment explanation
Indices: 407335--407433 Score: 58
Period size: 16 Copynumber: 6.2 Consensus size: 15
407325 ATTAAATTAT
407335 ATAAAAATATTATAAA
1 ATAAAAATA-TATAAA
*
407351 TATAAATATATGAATATAA
1 -ATAAAAATAT--ATA-AA
*
407370 ATAAAATTTATATAATA
1 ATAAAA-ATATATAA-A
* **
407387 A-AAAATTATTATATC
1 ATAAAAATA-TATAAA
*
407402 ATAAAAAT-TAAAAA
1 ATAAAAATATATAAA
407416 ATAAAAATATATAAA
1 ATAAAAATATATAAA
407431 ATA
1 ATA
407434 CAATTATATC
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
14 11 0.17
15 12 0.19
16 15 0.23
17 13 0.20
18 8 0.12
19 5 0.08
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (15 bp):
ATAAAAATATATAAA
Found at i:408154 original size:21 final size:22
Alignment explanation
Indices: 408121--408188 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 22
408111 ACTCATTTCA
*
408121 ATATTTATTATATTATTA-AAAT
1 ATATTT-TTATATTAATATAAAT
*
408143 TTATTTTTATATTAATATAAAT
1 ATATTTTTATATTAATATAAAT
*
408165 AT-TTTTTATAATTAAATTTAAAT
1 ATATTTTTAT-ATT-AATATAAAT
408188 A
1 A
408189 AAAAATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 17 0.44
22 13 0.33
23 9 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTTATATTAATATAAAT
Found at i:408796 original size:34 final size:33
Alignment explanation
Indices: 408748--408966 Score: 262
Period size: 34 Copynumber: 6.5 Consensus size: 33
408738 TGGTAAAAAC
*
408748 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
408781 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
408815 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
408849 TTCTTATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* *
408883 CTCCCATTTAATCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
408917 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
408951 CACCATTTAATCAACA
1 CACCATTTAATCAACA
408967 GTTCTCCCAC
Statistics
Matches: 160, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 21 0.13
34 133 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:408864 original size:68 final size:67
Alignment explanation
Indices: 408750--408966 Score: 292
Period size: 68 Copynumber: 3.2 Consensus size: 67
408740 GTAAAAACCA
* * *
408750 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
408815 CAC
65 CAC
* * * * *
408818 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTTATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
408883 CTC
65 CAC
* * *
408886 CCATTTAATCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
408951 CA-
65 CAC
408953 CCATTTAATCAACA
1 CCATTTAATCAACA
408967 GTTCTCCCAC
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 16 0.12
68 113 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Done.