Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold340
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: 358576
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:376 original size:1 final size:1
Alignment explanation
Indices: 370--433 Score: 101
Period size: 1 Copynumber: 64.0 Consensus size: 1
360 AAAGTGTTTG
***
370 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
434 TTTAAATGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.03
Consensus pattern (1 bp):
A
Found at i:410 original size:30 final size:30
Alignment explanation
Indices: 374--430 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
364 TGTTTGAAAA
374 AAAAAAAAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAATTG
404 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
431 AAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.04
Consensus pattern (30 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAATTG
Found at i:410 original size:34 final size:34
Alignment explanation
Indices: 367--433 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
357 GATAAAGTGT
367 TTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
401 TTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
434 TTTAAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (34 bp):
TTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:411 original size:31 final size:31
Alignment explanation
Indices: 373--431 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
363 GTGTTTGAAA
373 AAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
404 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
432 AATTTAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.03
Consensus pattern (31 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
Found at i:413 original size:32 final size:32
Alignment explanation
Indices: 372--432 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
362 AGTGTTTGAA
372 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
433 ATTTAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.03
Consensus pattern (32 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
Found at i:413 original size:33 final size:33
Alignment explanation
Indices: 371--435 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
361 AAGTGTTTGA
371 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATT
436 TAAATGTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.02, T:0.06
Consensus pattern (33 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTG
Found at i:462 original size:21 final size:21
Alignment explanation
Indices: 438--494 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
428 AAAAAATTTA
438 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
459 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
480 AATGTATCGATACAT
1 AATGTATCGATACAT
495 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:574 original size:19 final size:19
Alignment explanation
Indices: 550--617 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
540 AATTCAACAA
550 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
569 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
584 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
601 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
618 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:589 original size:13 final size:13
Alignment explanation
Indices: 571--595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561 ACATAAGTTT
571 TGTATCGATACAA
1 TGTATCGATACAA
584 TGTATCGATACA
1 TGTATCGATACA
596 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:593 original size:32 final size:32
Alignment explanation
Indices: 552--614 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
542 TTCAACAATT
*
552 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
584 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
615 TAATTAGCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:675 original size:13 final size:13
Alignment explanation
Indices: 657--682 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
647 CATTTTTCTG
657 TGTATCGATACAT
1 TGTATCGATACAT
670 TGTATCGATACAT
1 TGTATCGATACAT
683 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:679 original size:33 final size:33
Alignment explanation
Indices: 637--703 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
627 GCCAAGGAAA
***
637 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
670 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
703 T
1 T
704 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3219 original size:28 final size:27
Alignment explanation
Indices: 3152--3224 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3142 CTTCACAATC
* *
3152 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
3179 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
3207 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3225 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3269 original size:51 final size:51
Alignment explanation
Indices: 3207--3377 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
3197 TTATTTCTGA
* * *
3207 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * **
3258 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCTTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-T-TCATAATC
** * *
3311 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3363 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3378 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3396 original size:28 final size:28
Alignment explanation
Indices: 3360--3441 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
3350 ATTTTTCACA
*
3360 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3388 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3416 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
3442 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:5042 original size:18 final size:18
Alignment explanation
Indices: 5021--5060 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5011 TTCAAAGCAG
5021 TTTATTTAAATCAAGCTT
1 TTTATTTAAATCAAGCTT
* *
5039 TTTATTTTAATTAAGCTT
1 TTTATTTAAATCAAGCTT
5057 TTTA
1 TTTA
5061 ATGCTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTATTTAAATCAAGCTT
Found at i:5233 original size:13 final size:13
Alignment explanation
Indices: 5211--5243 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5201 AAATATAGGC
5211 ACAAACATTTTAT
1 ACAAACATTTTAT
*
5224 ACAAATATTTTAT
1 ACAAACATTTTAT
5237 -CAAACAT
1 ACAAACAT
5244 GTAATACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (13 bp):
ACAAACATTTTAT
Found at i:10704 original size:15 final size:15
Alignment explanation
Indices: 10684--10720 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
10674 TAAAAATGTC
*
10684 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
10699 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
10714 CCAAATG
1 CAAAATG
10721 TAATTGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:12812 original size:13 final size:14
Alignment explanation
Indices: 12793--12830 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
12783 CATTTTTCTT
12793 TGTATCGATACAAC
1 TGTATCGATACAAC
12807 -GTATCGATAC-AC
1 TGTATCGATACAAC
12819 TGTATCGATACA
1 TGTATCGATACA
12831 GGGTGATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (14 bp):
TGTATCGATACAAC
Found at i:12994 original size:20 final size:20
Alignment explanation
Indices: 12951--12996 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
12941 AAATCTTTTG
12951 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
12972 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
12992 CAAAA
1 CAAAA
12997 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:15401 original size:13 final size:13
Alignment explanation
Indices: 15383--15408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15373 TACACTAAGT
15383 ATGTATCGATACA
1 ATGTATCGATACA
15396 ATGTATCGATACA
1 ATGTATCGATACA
15409 CAAAAAATTG
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:15406 original size:32 final size:33
Alignment explanation
Indices: 15365--15428 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
15355 TAGCCAAACT
* **
15365 TGTATCGATACACTAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
15397 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
15429 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:16719 original size:32 final size:33
Alignment explanation
Indices: 16658--16721 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
16648 CACCCAGATG
*
16658 TATCGATACATATTGCTTAGTATCGATACACTC
1 TATCGATACATATTGCTTAGTATCAATACACTC
* *
16691 TATCGATACATGTT-CTTTGTATCAATACACT
1 TATCGATACATATTGCTTAGTATCAATACACT
16722 ATAAAATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (33 bp):
TATCGATACATATTGCTTAGTATCAATACACTC
Found at i:17672 original size:19 final size:18
Alignment explanation
Indices: 17629--17742 Score: 108
Period size: 19 Copynumber: 6.8 Consensus size: 18
17619 AATTCAACGA
17629 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
17648 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
17664 TTTTGTATCGATAC--AA-
1 -TTTGTATCGATACATAAG
17680 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
17696 TTTTGTATCGATAC--AA-
1 -TTTGTATCGATACATAAG
17712 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
17728 TTTTGTATCGATACA
1 -TTTGTATCGATACA
17743 ATTTAAGCTA
Statistics
Matches: 80, Mismatches: 0, Indels: 30
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.28
15 4 0.05
16 3 0.04
17 17 0.21
19 34 0.43
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:17685 original size:13 final size:13
Alignment explanation
Indices: 17667--17723 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
17657 ACATAAGTTT
17667 TGTATCGATACAA
1 TGTATCGATACAA
17680 TGTATCGATACATAA
1 TGTATCGATAC--AA
17695 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
17712 TGTATCGATACA
1 TGTATCGATACA
17724 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:17689 original size:32 final size:32
Alignment explanation
Indices: 17629--17744 Score: 196
Period size: 32 Copynumber: 3.5 Consensus size: 32
17619 AATTCAACGA
17629 TTTGTATCGATACATAAAGTGTATCGATACATAAGT
1 TTTGTATCGATAC---AA-TGTATCGATACATAAGT
17665 TTTGTATCGATACAATGTATCGATACATAAGT
1 TTTGTATCGATACAATGTATCGATACATAAGT
17697 TTTGTATCGATACAATGTATCGATACATAAGT
1 TTTGTATCGATACAATGTATCGATACATAAGT
17729 TTTGTATCGATACAAT
1 TTTGTATCGATACAAT
17745 TTAAGCTACT
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
32 65 0.81
33 2 0.03
36 13 0.16
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
TTTGTATCGATACAATGTATCGATACATAAGT
Found at i:17782 original size:13 final size:13
Alignment explanation
Indices: 17764--17788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17754 TACCAAAAAA
17764 TGTATCGATACAT
1 TGTATCGATACAT
17777 TGTATCGATACA
1 TGTATCGATACA
17789 CTGATCTTTG
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:18211 original size:20 final size:20
Alignment explanation
Indices: 18188--18261 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
18178 ACAATTCAAA
18188 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
18208 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
18229 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
18249 GTATCGATACATG
1 GTATCGATACATG
18262 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:18232 original size:21 final size:21
Alignment explanation
Indices: 18206--18281 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
18196 ACATGTTGCA
18206 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
18227 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
18247 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
18268 ATGTATCGATACAT
1 ATGTATCGATACAT
18282 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:18239 original size:41 final size:41
Alignment explanation
Indices: 18188--18281 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
18178 ACAATTCAAA
18188 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
18229 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
18270 GTATCGATACAT
1 GTATCGATACAT
18282 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:18338 original size:13 final size:13
Alignment explanation
Indices: 18320--18345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18310 TACAGCAAGT
18320 ATGTATCGATACA
1 ATGTATCGATACA
18333 ATGTATCGATACA
1 ATGTATCGATACA
18346 CAAAAAATTG
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:20597 original size:21 final size:21
Alignment explanation
Indices: 20564--20608 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20554 TTGCAAGTTG
*
20564 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
20586 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
20606 AAA
1 AAA
20609 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:22431 original size:15 final size:15
Alignment explanation
Indices: 22411--22441 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22401 TAAAAATGTC
*
22411 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
22426 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
22441 C
1 C
22442 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:24537 original size:13 final size:13
Alignment explanation
Indices: 24519--24544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24509 ACATTTTTCT
24519 TTGTATCGATACA
1 TTGTATCGATACA
24532 TTGTATCGATACA
1 TTGTATCGATACA
24545 AGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:27109 original size:13 final size:13
Alignment explanation
Indices: 27091--27116 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27081 TACAGCAAGT
27091 ATGTATCGATACA
1 ATGTATCGATACA
27104 ATGTATCGATACA
1 ATGTATCGATACA
27117 CAAAAAATTG
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:32581 original size:21 final size:21
Alignment explanation
Indices: 32541--32582 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
32531 TGATGTGCTT
*
32541 GAAAAGAAAATAATTAAATTA
1 GAAAAGAAAATAAATAAATTA
*
32562 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATAAATTA
32583 CAAGATGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (21 bp):
GAAAAGAAAATAAATAAATTA
Found at i:44535 original size:21 final size:21
Alignment explanation
Indices: 44509--44568 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
44499 AATTTTATTT
* *
44509 ACTTGTCTATTGGC-TAGAGTA
1 ACTTGTCTATTAGCATA-AATA
*
44530 ACTTGTCAATTAGCATAAATA
1 ACTTGTCTATTAGCATAAATA
44551 ACTTGTCTATTAGCATAA
1 ACTTGTCTATTAGCATAA
44569 GTAATTTTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
ACTTGTCTATTAGCATAAATA
Found at i:46023 original size:31 final size:29
Alignment explanation
Indices: 45970--46064 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
45960 ACATCACTGA
* *
45970 CTAAAACTATTATAAAAGCATTTAATTAAG
1 CTAAAACTATTA-AAAAACATTTACTTAAG
*
46000 CTAATAACTATCTAAAAAACATTTACGTAAG
1 CTAA-AACTAT-TAAAAAACATTTACTTAAG
* *
46031 CAAACAACTATTTAAACAACATTTACTTAAG
1 CTAA-AACTA-TTAAAAAACATTTACTTAAG
46062 CTA
1 CTA
46065 GTTGATACCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.07
31 47 0.87
32 3 0.06
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (29 bp):
CTAAAACTATTAAAAAACATTTACTTAAG
Found at i:51069 original size:100 final size:99
Alignment explanation
Indices: 50896--51096 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 99
50886 CTCAAAACCC
50896 TTTTTGGACCTCCCTTAGGTCATGTCAAAGCACAAATACTTTTATATCTTTATCGTCCTTATTCA
1 TTTTTGGACCTCCCTTAGGTCATGTCAAAGCACAAATACTTTTATATCTTTATCGTCCTTATTCA
50961 CATCAATTTTCTCTATAAAAAAAATCAAAATTTTA
66 CATCAATTTTCTCTAT-AAAAAAATCAAAATTTTA
50996 TTTTTGGACCTCCCTTAGGTCATGTCAAAGCACAAATACTTTTATATCTTTATCGTCCTTATTCA
1 TTTTTGGACCTCCCTTAGGTCATGTCAAAGCACAAATACTTTTATATCTTTATCGTCCTTATTCA
* *
51061 CATCAATTTTCTTTATAAAAAAATTAAAATTTTA
66 CATCAATTTTCTCTATAAAAAAATCAAAATTTTA
51095 TT
1 TT
51097 CATCGAGGAT
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 19 0.19
100 80 0.81
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (99 bp):
TTTTTGGACCTCCCTTAGGTCATGTCAAAGCACAAATACTTTTATATCTTTATCGTCCTTATTCA
CATCAATTTTCTCTATAAAAAAATCAAAATTTTA
Found at i:52957 original size:27 final size:28
Alignment explanation
Indices: 52899--52960 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
52889 TATATTAAAG
*
52899 ATTACTATGTCTCATTTCAAAAAAAAAT
1 ATTACTACGTCTCATTTCAAAAAAAAAT
52927 ATTACTACGTCTCATTTCAAAAAAAAA-
1 ATTACTACGTCTCATTTCAAAAAAAAAT
52954 ATTACTA
1 ATTACTA
52961 AGTCATTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.21
28 26 0.79
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (28 bp):
ATTACTACGTCTCATTTCAAAAAAAAAT
Found at i:53052 original size:29 final size:27
Alignment explanation
Indices: 52960--53067 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 27
52950 AAAAATTACT
* * *
52960 AAGTCATTTCATGCATTTAGATACATTT
1 AAGTCATTTCATG-ATTTAGAAATATTG
*
52988 AAGTCATTTTCTATGATTTAGAAATTGTTG
1 AAGTCA-TTTC-ATGATTTAGAAA-TATTG
* *
53018 TA-TCATTTCATGTATTTTAGAGATATTG
1 AAGTCATTTCATG-A-TTTAGAAATATTG
*
53046 AAGTCATTTCTATGATATAGAA
1 AAGTCATTTC-ATGATTTAGAA
53068 GTCTTTTTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
27 3 0.05
28 21 0.33
29 30 0.48
30 9 0.14
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (27 bp):
AAGTCATTTCATGATTTAGAAATATTG
Found at i:53092 original size:57 final size:58
Alignment explanation
Indices: 52962--53092 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 58
52952 AAATTACTAA
* * *
52962 GTCATTTCATGCA-TTTAGATACATTTAAGTCATTTTCTATGATTTAGAAATTGTTGT
1 GTCATTTCATGCATTTTAGAGACATTGAAGTCATTTTCTATGATATAGAAATTGTTGT
* * * * *
53019 ATCATTTCATGTATTTTAGAGATATTGAAGTCA-TTTCTATGATATAGAAGTCT-TTTT
1 GTCATTTCATGCATTTTAGAGACATTGAAGTCATTTTCTATGATATAGAAAT-TGTTGT
53076 GTCATTTCATGCATTTT
1 GTCATTTCATGCATTTT
53093 TAAGGATTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 45 0.73
58 17 0.27
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (58 bp):
GTCATTTCATGCATTTTAGAGACATTGAAGTCATTTTCTATGATATAGAAATTGTTGT
Found at i:53983 original size:17 final size:17
Alignment explanation
Indices: 53961--53993 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53951 TCATGTAAGA
53961 ACTTTTATATCAATACT
1 ACTTTTATATCAATACT
*
53978 ACTTTTATGTCAATAC
1 ACTTTTATATCAATAC
53994 ATGTCTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.45
Consensus pattern (17 bp):
ACTTTTATATCAATACT
Found at i:55878 original size:21 final size:22
Alignment explanation
Indices: 55835--55878 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55825 CATGATGCCT
* *
55835 AAACTTTGTCGAGCATTGGATA
1 AAACTTTGTCAAGCATTGAATA
*
55857 AAACTTTGTTAAGCATT-AATA
1 AAACTTTGTCAAGCATTGAATA
55878 A
1 A
55879 GAAAATGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
AAACTTTGTCAAGCATTGAATA
Found at i:58839 original size:76 final size:76
Alignment explanation
Indices: 58713--58859 Score: 233
Period size: 76 Copynumber: 1.9 Consensus size: 76
58703 CCCTGCCGCT
* * * *
58713 GCCAGTTACGGTGCTGCGGAGGTCACTCCTCAGTGCTGGCCGAGAATAGGGAAGATTGAAAAGTG
1 GCCAGTTACGCTCCTGCGGAGGTCAATCCTCAGTGCTGACCGAGAATAGGGAAGATTGAAAAGTG
58778 AAGATGTCGCC
66 AAGATGTCGCC
*
58789 GCCAGTTACGCTCCTGCGGAGGTCAATGCTCAGTGCTGACC-ACGAATAGGGAAGATTGAAAAGT
1 GCCAGTTACGCTCCTGCGGAGGTCAATCCTCAGTGCTGACCGA-GAATAGGGAAGATTGAAAAGT
58853 GAAGATG
65 GAAGATG
58860 AGAGAGCTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 1 0.02
76 64 0.98
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (76 bp):
GCCAGTTACGCTCCTGCGGAGGTCAATCCTCAGTGCTGACCGAGAATAGGGAAGATTGAAAAGTG
AAGATGTCGCC
Found at i:59438 original size:19 final size:18
Alignment explanation
Indices: 59411--59449 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
59401 AGTAATTTTA
*
59411 TTTAATTTTTTTATTAAT
1 TTTAAATTTTTTATTAAT
59429 TTTAAATTTTTTATTAAT
1 TTTAAATTTTTTATTAAT
59447 TTT
1 TTT
59450 TTAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTAAATTTTTTATTAAT
Found at i:60710 original size:11 final size:12
Alignment explanation
Indices: 60684--60739 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
60674 CTTATGATTA
60684 TTAATTTTAATT
1 TTAATTTTAATT
*
60696 TTAATTTT-CTT
1 TTAATTTTAATT
*
60707 TTAATTTTGGATT
1 TTAATTTT-AATT
60720 TT-ATTTT-ATT
1 TTAATTTTAATT
*
60730 TTATTTTTAA
1 TTAATTTTAA
60740 CCTAGTTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 5 0.14
11 14 0.38
12 14 0.38
13 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (12 bp):
TTAATTTTAATT
Found at i:60710 original size:17 final size:16
Alignment explanation
Indices: 60687--60736 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
60677 ATGATTATTA
60687 ATTTTAATTTTAATTTT
1 ATTTTAATTTT-ATTTT
*
60704 CTTTTAATTTTGGATTTT
1 ATTTTAATTTT--ATTTT
60722 ATTTT-ATTTTATTTT
1 ATTTTAATTTTATTTT
60737 TAACCTAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 5 0.17
17 15 0.52
18 9 0.31
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (16 bp):
ATTTTAATTTTATTTT
Found at i:60712 original size:23 final size:22
Alignment explanation
Indices: 60684--60739 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
60674 CTTATGATTA
*
60684 TTAATTTTAATTTTAATTTTCTT
1 TTAATTTTAATTTT-ATTTTATT
*
60707 TTAATTTTGGATTTTATTTTATT
1 TTAATTTT-AATTTTATTTTATT
*
60730 TTATTTTTAA
1 TTAATTTTAA
60740 CCTAGTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.79
24 5 0.18
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TTAATTTTAATTTTATTTTATT
Found at i:60725 original size:5 final size:6
Alignment explanation
Indices: 60684--60739 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
60674 CTTATGATTA
* *
60684 TTAATT TTAATT TTAATT TT-CTT TTAATT TTGGATT TT-ATT TT-ATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TT-AATT TTAATT TTAATT
*
60730 TTATTT TTAA
1 TTAATT TTAA
60740 CCTAGTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 14 0.33
6 23 0.55
7 5 0.12
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (6 bp):
TTAATT
Found at i:61827 original size:52 final size:52
Alignment explanation
Indices: 61764--61868 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
61754 ATCTCATTTT
* * *
61764 TCACTGTTCATCACTATTCTTATATCGATATATTGTGAATAGTATTGATACA
1 TCACTGTTCATCACTATTCATATATCGATATATTATGAATAGTATCGATACA
* * *
61816 TCACTGTTCATCACTGTTCATGTATTGATATATTATGAATAGTATCGATACA
1 TCACTGTTCATCACTATTCATATATCGATATATTATGAATAGTATCGATACA
61868 T
1 T
61869 TGAGTTCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (52 bp):
TCACTGTTCATCACTATTCATATATCGATATATTATGAATAGTATCGATACA
Found at i:62946 original size:13 final size:13
Alignment explanation
Indices: 62930--62954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62920 ATGTTTGATG
62930 TTTAATTTTGTAT
1 TTTAATTTTGTAT
62943 TTTAATTTTGTA
1 TTTAATTTTGTA
62955 AGGACCAATT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTAATTTTGTAT
Found at i:63975 original size:14 final size:15
Alignment explanation
Indices: 63942--63972 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63932 ATAAAAATTT
*
63942 AATTATTTTTTAAAA
1 AATTACTTTTTAAAA
63957 AATTACTTTTTAAAA
1 AATTACTTTTTAAAA
63972 A
1 A
63973 TTATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTACTTTTTAAAA
Found at i:64212 original size:18 final size:17
Alignment explanation
Indices: 64185--64221 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
64175 AATTTTATTT
64185 AATTTTTATTAATTCTA
1 AATTTTTATTAATTCTA
*
64202 AATTCTTTATTAATTTTA
1 AATT-TTTATTAATTCTA
64220 AA
1 AA
64222 ACATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTTATTAATTCTA
Found at i:72615 original size:31 final size:31
Alignment explanation
Indices: 72569--72937 Score: 239
Period size: 31 Copynumber: 11.8 Consensus size: 31
72559 CTGACTAACC
*
72569 TTTT-TTTCTTTGTCCTCAAAGAGCAAGATG
1 TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
* ** * *
72599 TTTTCTTTTTTTGTCCTTGAAGAGCAGGACA
1 TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
* * *
72630 TTTTCTTTCTTTGTCCTCAAATGA-CAGGGCA
1 TTTTCTTTCTTTGTCCTCAAA-GAGCAAGACG
*
72661 TTTT-TTTCTTTTGTCCAT-AAAGAGCATGACG
1 TTTTCTTTC-TTTGTCC-TCAAAGAGCAAGACG
* *
72692 TTTTCTTTCTTTGTCTTCAAAGAGTAAGACG
1 TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
* * * * * *
72723 TTTTCTTCCTTTGTCCTAAAAAAACATGATG
1 TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
* * * *
72754 TTTT-TTTCCTTTGTCCTTAAAAAG-AGGACA
1 TTTTCTTT-CTTTGTCCTCAAAGAGCAAGACG
* ** * *
72784 TTTTCTTCCTTTACCCTTAAAGAGCAAGATG
1 TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
* * *
72815 TTTTCCCTT-TTTATCCTCAAAGAGCAAGACATT
1 TTTT-CTTTCTTTGTCCTCAAAGAGCAAGAC--G
* * * *
72848 TTCTTCCTTTCTTTGTCCTCAAAAAGTAGGACA
1 TT-TT-CTTTCTTTGTCCTCAAAGAGCAAGACG
* * * *
72881 TTTCCTTTATTTGTCCTTAAAGAGTAAGACG
1 TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
* * *
72912 TTTCCCTTCTTTTTCCTCAAAGAGCA
1 TTTTCTTTCTTTGTCCTCAAAGAGCA
72938 GGACATCTCT
Statistics
Matches: 264, Mismatches: 60, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
30 33 0.12
31 194 0.73
32 10 0.04
33 4 0.02
34 6 0.02
35 17 0.06
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (31 bp):
TTTTCTTTCTTTGTCCTCAAAGAGCAAGACG
Found at i:72815 original size:61 final size:62
Alignment explanation
Indices: 72678--72857 Score: 170
Period size: 61 Copynumber: 2.9 Consensus size: 62
72668 CTTTTGTCCA
* * * **
72678 TAAAGAGCATGACGTTTTCTTTCTTTGTCTTCAAAGAGTAAGACGTTTTCTTCCTTTGTCCT
1 TAAAGAGCATGATGTTTTCTTTCTTTGTCTTCAAAAAGTAAGACATTTTCTTCCTTTACCCT
* * * *
72740 AAAAAAACATGATGTTTT-TTTCCTTTGTCCTT-AAAAAG-AGGACATTTTCTTCCTTTACCCT
1 TAAAGAGCATGATGTTTTCTTT-CTTTGT-CTTCAAAAAGTAAGACATTTTCTTCCTTTACCCT
* * * * * *
72801 TAAAGAGCAAGATGTTTTCCCTT-TTTATCCTCAAAGAGCAAGACATTTTCTTCCTTT
1 TAAAGAGCATGATGTTTT-CTTTCTTTGTCTTCAAAAAGTAAGACATTTTCTTCCTTT
72858 CTTTGTCCTC
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
60 2 0.02
61 45 0.48
62 42 0.45
63 5 0.05
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (62 bp):
TAAAGAGCATGATGTTTTCTTTCTTTGTCTTCAAAAAGTAAGACATTTTCTTCCTTTACCCT
Found at i:72900 original size:97 final size:96
Alignment explanation
Indices: 72762--72943 Score: 249
Period size: 97 Copynumber: 1.9 Consensus size: 96
72752 TGTTTTTTTC
* * * *
72762 CTTTGTCCTTAAAAAGAGGACATTTTCTTCCTTTACCCTTAAAGAGCAAGATGTTTTCCCTT-TT
1 CTTTGTCCTCAAAAAGAGGACATTTCCTTCATTTACCCTTAAAGAGCAAGACG-TTTCCCTTCTT
72826 TATCCTCAAAGAGCAAGACATTTTCTTCCTTT
65 TATCCTCAAAGAGCAAGACATTTTCTTCCTTT
* ** *
72858 CTTTGTCCTCAAAAAGTAGGACATTTCCTTTATTTGTCCTTAAAGAGTAAGACGTTTCCCTTCTT
1 CTTTGTCCTCAAAAAG-AGGACATTTCCTTCATTTACCCTTAAAGAGCAAGACGTTTCCCTTCTT
* *
72923 TTTCCTCAAAGAGCAGGACAT
65 TATCCTCAAAGAGCAAGACAT
72944 CTCTTTCTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
96 23 0.31
97 51 0.69
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (96 bp):
CTTTGTCCTCAAAAAGAGGACATTTCCTTCATTTACCCTTAAAGAGCAAGACGTTTCCCTTCTTT
ATCCTCAAAGAGCAAGACATTTTCTTCCTTT
Found at i:76283 original size:172 final size:172
Alignment explanation
Indices: 75936--76356 Score: 514
Period size: 172 Copynumber: 2.4 Consensus size: 172
75926 AACATTAAAA
* **
75936 GGGATACTCTAA-CTCCATTTTTACTTCCAAAACACCGAATTTTTCATCTCCAGGGATACTT-CA
1 GGGATACTCTAACCT-CTTTTTTACTTCCAAAACACTAAATTTTTCATCTCCA-GGATA-TTCCA
* * * *
75999 ACCCCACCATCTCTGAGGTGATACTCTAACCCCATTTTTTCACTAAAATTTGATTTATGAAAATC
63 ACCCCACCATCTCTGAGGTGATACTCTAACCCCACTTTTACACTAAAATTCGATTTATGAAAATA
*
76064 TTAAATTGTCACCTTCGAGGATACTCCAACCCTACCATCTCTAAG
128 TCAAATTGTCACCTTCGAGGATACTCCAACCCTACCATCTCTAAG
* **
76109 GGGATACTCCAACCTCTTTTTTACTTCCAAAACACTAAATTTTTCATCTTTAGGATATTCCAACC
1 GGGATACTCTAACCTCTTTTTTACTTCCAAAACACTAAATTTTTCATCTCCAGGATATTCCAACC
* * ** *
76174 CCACTATCTCTGAAGG-GATACTCTAAGCCTGCTTTTAGACTAAAATTCGA-TTATGAAAATATC
66 CCACCATCTCTG-AGGTGATACTCTAACCCCACTTTTACACTAAAATTCGATTTATGAAAATATC
* * * * *
76237 AAATTGTCATCTTC-AGGGATATTCCAACCCCTGCTATCTTTAAG
130 AAATTGTCACCTTCGA-GGATACTCCAA-CCCTACCATCTCTAAG
*
76281 GGGATACTCTAACC-CTGTTTTTACTTCCAAAACA-TCAAATTTTTCATCTCCAGAGATACTCCA
1 GGGATACTCTAACCTCT-TTTTTACTTCCAAAACACT-AAATTTTTCATCTCCAG-GATATTCCA
76344 ACCCCACCATCTC
63 ACCCCACCATCTC
76357 CGAGAGGACA
Statistics
Matches: 214, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
170 1 0.00
171 39 0.18
172 106 0.50
173 66 0.31
174 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (172 bp):
GGGATACTCTAACCTCTTTTTTACTTCCAAAACACTAAATTTTTCATCTCCAGGATATTCCAACC
CCACCATCTCTGAGGTGATACTCTAACCCCACTTTTACACTAAAATTCGATTTATGAAAATATCA
AATTGTCACCTTCGAGGATACTCCAACCCTACCATCTCTAAG
Found at i:76817 original size:13 final size:13
Alignment explanation
Indices: 76799--76825 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
76789 ACATTATGCT
76799 TTGTATCGATACA
1 TTGTATCGATACA
76812 TTGTATCGATACA
1 TTGTATCGATACA
76825 T
1 T
76826 ATTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:76840 original size:32 final size:33
Alignment explanation
Indices: 76780--76844 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
76770 CACACCCAGA
*
76780 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCATTGTATCGATACAT
*
76813 TGTATCGATACA-TATTCATTGTATCGATACAT
1 TGTATCGATACATTATGCATTGTATCGATACAT
76845 GAAACTGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATGCATTGTATCGATACAT
Found at i:76930 original size:33 final size:33
Alignment explanation
Indices: 76877--76941 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
76867 CCATTATTTG
*
76877 TATCGATACATGGCACATTGTATTGATACATTA
1 TATCGATACATGGCACATTGTATCGATACATTA
76910 TATCGATACATGATG-A-ATTGTATCGATACATT
1 TATCGATACATG--GCACATTGTATCGATACATT
76942 GCTTGTAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (33 bp):
TATCGATACATGGCACATTGTATCGATACATTA
Found at i:83121 original size:13 final size:13
Alignment explanation
Indices: 83103--83138 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
83093 CATTCCTTGT
83103 ATCGATACATTGC
1 ATCGATACATTGC
*
83116 ATCGATACATTGT
1 ATCGATACATTGC
83129 ATCGATACAT
1 ATCGATACAT
83139 GAGTTACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
ATCGATACATTGC
Found at i:85660 original size:20 final size:19
Alignment explanation
Indices: 85595--85667 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
85585 AAAACCCTTG
* *
85595 AATGTATCGATACACACCC
1 AATGTATCGATACATACAC
**
85614 AAATGTATCGATACATATTC
1 -AATGTATCGATACATACAC
*
85634 -ATGTATCGATACATAGAC
1 AATGTATCGATACATACAC
85652 AATTGTATCGATACAT
1 AA-TGTATCGATACAT
85668 GAAACTGGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 16 0.35
19 1 0.02
20 29 0.63
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACATACAC
Found at i:91112 original size:20 final size:18
Alignment explanation
Indices: 91086--91158 Score: 56
Period size: 20 Copynumber: 3.8 Consensus size: 18
91076 CTATTAGTTT
**
91086 CATGTATCGATACAATTCA
1 CATGTATCGATACAA-GAA
*
91105 CTATGTATCAATATCAAGAA
1 C-ATGTATCGATA-CAAGAA
91125 CATGTATCGATACAAAGTAA
1 CATGTATCGATAC-AAG-AA
* *
91145 TATGTATCAATACA
1 CATGTATCGATACA
91159 TCTAGGTGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 15 0.34
20 25 0.57
21 3 0.07
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.30
Consensus pattern (18 bp):
CATGTATCGATACAAGAA
Found at i:91131 original size:19 final size:20
Alignment explanation
Indices: 91107--91158 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
91097 ACAATTCACT
91107 ATGTATCAATATC-AAG-AAC
1 ATGTATCAATA-CAAAGTAAC
* *
91126 ATGTATCGATACAAAGTAAT
1 ATGTATCAATACAAAGTAAC
91146 ATGTATCAATACA
1 ATGTATCAATACA
91159 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 13 0.46
20 14 0.50
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (20 bp):
ATGTATCAATACAAAGTAAC
Found at i:110221 original size:16 final size:15
Alignment explanation
Indices: 110191--110228 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
110181 GAGTTTCAGA
*
110191 TTTTATTTTATTTTT
1 TTTTATTTGATTTTT
110206 TTTTAGTTTGATTTTT
1 TTTTA-TTTGATTTTT
110222 TTTTATT
1 TTTTATT
110229 CCAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTATTTGATTTTT
Found at i:112698 original size:26 final size:27
Alignment explanation
Indices: 112660--112723 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
112650 ATTTTTTATC
*
112660 ATTTTAATT-AATTTTT-ATAATTAAT
1 ATTTTAATTAAATTTTTAAAAATTAAT
*
112685 ATTTTTATTAAATTTTTAAAAATTAAT
1 ATTTTAATTAAATTTTTAAAAATTAAT
*
112712 GTTTTAATTAAA
1 ATTTTAATTAAA
112724 AAGTTTTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 8 0.24
26 7 0.21
27 18 0.55
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTTTAATTAAATTTTTAAAAATTAAT
Found at i:118245 original size:16 final size:16
Alignment explanation
Indices: 118224--118254 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
118214 TTTATTTTTT
118224 AAAATTATAATTATAC
1 AAAATTATAATTATAC
118240 AAAATTATAATTATA
1 AAAATTATAATTATA
118255 ATCAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATTATAATTATAC
Found at i:118798 original size:32 final size:34
Alignment explanation
Indices: 118754--118824 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 34
118744 TTAATATAAA
* *
118754 AAATT-TTAATTTAAATTAGT-A-TATTTTAATTT
1 AAATTATTAATTT-AATTAATAATTATTTAAATTT
118786 AAATTATT-ATTTAATTAATAATTATTTAAATTT
1 AAATTATTAATTTAATTAATAATTATTTAAATTT
118819 -AATTAT
1 AAATTAT
118825 AAAATACAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 6 0.18
32 16 0.47
33 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
AAATTATTAATTTAATTAATAATTATTTAAATTT
Found at i:118808 original size:18 final size:17
Alignment explanation
Indices: 118758--118811 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
118748 TATAAAAAAT
*
118758 TTTAATTTAAATTAGTATA
1 TTTAATTAAAATTA-T-TA
*
118777 TTTTAATTTAAATTATTA
1 -TTTAATTAAAATTATTA
118795 TTTAATTAATAATTATT
1 TTTAATTAA-AATTATT
118812 TAAATTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.25
18 9 0.28
19 1 0.03
20 14 0.44
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAATTAAAATTATTA
Found at i:118868 original size:21 final size:19
Alignment explanation
Indices: 118839--118879 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
118829 TACAACAATA
*
118839 TTAATATAAAAATAAAATTT
1 TTAATAT-AAAACAAAATTT
118859 TTAATAATAAAACAAAATTT
1 TTAAT-ATAAAACAAAATTT
118879 T
1 T
118880 AACTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATATAAAACAAAATTT
Found at i:119052 original size:2 final size:2
Alignment explanation
Indices: 119045--119108 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
119035 ACAACAAATA
* * *
119045 AT AT AT AT AT GT AT AT AT AT AT AT AT GT AT GT 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 AT AT
*
119087 AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
119109 GCGCGAAGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121566 original size:15 final size:15
Alignment explanation
Indices: 121546--121575 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
121536 ATTTATCCCA
121546 AGTTTATGATGTTCG
1 AGTTTATGATGTTCG
121561 AGTTTATGATGTTCG
1 AGTTTATGATGTTCG
121576 CTTGATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (15 bp):
AGTTTATGATGTTCG
Found at i:123779 original size:29 final size:30
Alignment explanation
Indices: 123703--123810 Score: 114
Period size: 32 Copynumber: 3.6 Consensus size: 30
123693 AAAAAAAGAA
** *
123703 GGTGCCACTAACTTGTATAGGCTTTGAAAAG
1 GGTGCCACCGACTTGTGTAGGCTTTG-AAAG
*
123734 AGTTGCCACCGACTTGTGTAGGCTTT-AAAG
1 -GGTGCCACCGACTTGTGTAGGCTTTGAAAG
123764 GGTGCCACCGACTTGTG--GGCTTTGAAAG
1 GGTGCCACCGACTTGTGTAGGCTTTGAAAG
*
123792 GGTATGCCACTGACTTGTG
1 GG--TGCCACCGACTTGTG
123811 GACTTAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.09
28 6 0.09
29 16 0.24
30 18 0.27
32 21 0.31
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (30 bp):
GGTGCCACCGACTTGTGTAGGCTTTGAAAG
Found at i:123807 original size:30 final size:29
Alignment explanation
Indices: 123722--123811 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 29
123712 AACTTGTATA
*
123722 GGCTTTGAAAAGAGTTGCCACCGACTTGTG
1 GGCTTTG-AAAGGGTTGCCACCGACTTGTG
123752 TAGGCTTT-AAAGGG-TGCCACCGACTTGTG
1 --GGCTTTGAAAGGGTTGCCACCGACTTGTG
*
123781 GGCTTTGAAAGGGTATGCCACTGACTTGTG
1 GGCTTTGAAAGGGT-TGCCACCGACTTGTG
123811 G
1 G
123812 ACTTAAAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.11
28 6 0.11
29 15 0.28
30 20 0.38
32 6 0.11
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (29 bp):
GGCTTTGAAAGGGTTGCCACCGACTTGTG
Found at i:123842 original size:27 final size:28
Alignment explanation
Indices: 123760--124126 Score: 404
Period size: 28 Copynumber: 13.2 Consensus size: 28
123750 TGTAGGCTTT
* * * * *
123760 AAAGGGTGCCACCGACTTGTGGGCTTTGA
1 AAAGGTTGCCACGGAGTTGTGGAC-TTAA
* * *
123789 AAGGGTATGCCACTGACTTGTGGACTTAA
1 AAAGGT-TGCCACGGAGTTGTGGACTTAA
* * *
123818 AAAGG-TGCCACGGAGTTATGAACTTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
* * *
123845 AAAGGATGCCACGGAGTTGTGAACTTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
* * *
123873 AAAGGGTGCCATGGAGTTGTGGACTTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
*
123901 AAAGGGTGCCACGGAGTTGTGGAC-TAA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
123928 AAAGAG-TGCCACGGAGTTGTGGACTT-A
1 AAAG-GTTGCCACGGAGTTGTGGACTTAA
* *
123955 AAAGGATGCCACAGAGTTGTGGACTT-A
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
**
123982 AAAGGTTGCCATAGAGTTGTGGACTTAA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
*
124010 AAAGGGTGCCACGGAGTTGTGGACTTAA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
* * *
124038 AAAGGGTTGCCACGAAGTTGAGGACTTTA
1 AAA-GGTTGCCACGGAGTTGTGGACTTAA
* *
124067 GAAGGTTGCCACAGAGTTGTGGACTT-A
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
124094 AAAGGTTGCCACGGAGTTGTGGACTTAA
1 AAAGGTTGCCACGGAGTTGTGGACTTAA
124122 AAAGG
1 AAAGG
124127 AATGCCACTA
Statistics
Matches: 297, Mismatches: 33, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
26 1 0.00
27 120 0.40
28 126 0.42
29 34 0.11
30 16 0.05
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.24
Consensus pattern (28 bp):
AAAGGTTGCCACGGAGTTGTGGACTTAA
Found at i:123876 original size:55 final size:55
Alignment explanation
Indices: 123760--124134 Score: 414
Period size: 55 Copynumber: 6.7 Consensus size: 55
123750 TGTAGGCTTT
* * * * * * *
123760 AAAGGGTGCCACCGACTTGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGACTTAA
1 AAAGGTTGCCACGGAGTTGTGGACTTT-AAAAGG-ATGCCACGGAGTTGTGGAC-TAA
* * * *
123818 AAAGG-TGCCACGGAGTTATGAACTTTAAAAGGATGCCACGGAGTTGTGAACTTTA
1 AAAGGTTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TAA
* * *
123873 AAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTAA
1 AAAGGTTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTAA
* *
123928 AAAGAG-TGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTA
1 AAAG-GTTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTAA
** * *
123982 AAAGGTTGCCATAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTAA
1 AAAGGTTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TAA
* * * * * *
124038 AAAGGGTTGCCACGAAGTTGAGGACTTTAGAAGGTTGCCACAGAGTTGTGGACTTA
1 AAA-GGTTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTAA
*
124094 AAAGGTTGCCACGGAGTTGTGGACTTAAAAAGGAATGCCAC
1 AAAGGTTGCCACGGAGTTGTGGACTTTAAAAGG-ATGCCAC
124135 TAAATCATGG
Statistics
Matches: 270, Mismatches: 40, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.00
54 47 0.17
55 97 0.36
56 63 0.23
57 57 0.21
58 5 0.02
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (55 bp):
AAAGGTTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTAA
Found at i:125561 original size:22 final size:24
Alignment explanation
Indices: 125536--125597 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 24
125526 CCTTTCCTTA
*
125536 TTTTACTTTTGCACTTTTT-TTGT
1 TTTTACTTTTGCACTTTTTGTTCT
*
125559 TTTTA-TTTT-CATTTTTTGTTC-
1 TTTTACTTTTGCACTTTTTGTTCT
*
125580 TTTTGCTTTTG-ACTTTTT
1 TTTTACTTTTGCACTTTTT
125598 CGTAATTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 11 0.34
22 16 0.50
23 5 0.16
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.73
Consensus pattern (24 bp):
TTTTACTTTTGCACTTTTTGTTCT
Found at i:142024 original size:79 final size:78
Alignment explanation
Indices: 141924--142344 Score: 423
Period size: 79 Copynumber: 5.3 Consensus size: 78
141914 ATTCATGTTT
** * *
141924 TTATTTCTAAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACAATTAGGA
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAATTAGGA
*
141989 TACTCTAACCCCA
66 TACTCTAACCCCG
** ** * * * *
142002 TT-TTTTTGAGGGGATACCCTCCAACCCTGGTTTTATTTCCAAAACACTAATTTT-TATAATCGA
1 TTATTTCCGAGGGGATA--CTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAAT-TA
*
142065 GGATACTCCAACCCCG
63 GGATACTCTAACCCCG
* * * * * * **
142081 TTATTTCCGAGTGGATACTCTAACCCTAGTTTTACTTCCAAAACATCAATTTTTCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAAT-TAGG
* *
142146 ATACTCTAATCACG
65 ATACTCTAACCCCG
* ** *
142160 TTATTTCCGAGAGGATACTCCAACTTCAGTTTTATTTCCAAAACACCAATTTTCCACAATTGGGG
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAATT-AGG
* *
142225 ATACTCCAATCCCG
65 ATACTCTAACCCCG
* * * * *
142239 TTATTTCCGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACATCGATCTTCCACCATTAGCG
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAATTAG-G
142304 ATACTCTAACCCCG
65 ATACTCTAACCCCG
* * * *
142318 TTATTTCTGGGGGGGTACTCCGACCCC
1 TTATTTCCGAGGGGATACTCCAACCCC
142345 TTTTTTTCTC
Statistics
Matches: 286, Mismatches: 50, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
77 12 0.04
78 38 0.13
79 225 0.79
80 11 0.04
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (78 bp):
TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAATTAGGA
TACTCTAACCCCG
Found at i:142337 original size:158 final size:156
Alignment explanation
Indices: 141924--142343 Score: 475
Period size: 158 Copynumber: 2.7 Consensus size: 156
141914 ATTCATGTTT
** * * *
141924 TTATTTCTAAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACAATTAGGA
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTCCACAATTAGGA
* * * *
141989 TACTCTAACCCCATT-TTTTTGAGGGGATACCCTCCAACCCTGGTTTTATTTCCAAAACACTAAT
66 TACTCTAACCCCGTTATTTCTGAGGGGATA--CTCCAACCCTAGTTTTATTTCCAAAACACCAAT
* *
142053 TTTTATAATCGAGGATACTCCAACCCCG
129 TTTCACAATCGAGGATACTCCAACCCCG
* * * * * **
142081 TTATTTCCGAGTGGATACTCTAACCCTAGTTTTACTTCCAAAACATCAATTTTTCACAATCGGGG
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTCCACAAT-TAGG
* * * * *
142146 ATACTCTAATCACGTTATTTCCGAGAGGATACTCCAA-CTTCAGTTTTATTTCCAAAACACCAAT
65 ATACTCTAACCCCGTTATTTCTGAGGGGATACTCCAACCCT-AGTTTTATTTCCAAAACACCAAT
* * *
142210 TTTCCACAATTGGGGATACTCCAATCCCG
129 TTT-CACAATCGAGGATACTCCAACCCCG
* * * *
142239 TTATTTCCGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACATCGATCTTCCACCATTAGCG
1 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTCCACAATTAG-G
* * *
142304 ATACTCTAACCCCGTTATTTCTGGGGGGGTACTCCGACCC
65 ATACTCTAACCCCGTTATTTCTGAGGGGATACTCCAACCC
142344 CTTTTTTTCT
Statistics
Matches: 212, Mismatches: 45, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
156 2 0.01
157 81 0.38
158 117 0.55
159 12 0.06
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (156 bp):
TTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTCCACAATTAGGA
TACTCTAACCCCGTTATTTCTGAGGGGATACTCCAACCCTAGTTTTATTTCCAAAACACCAATTT
TCACAATCGAGGATACTCCAACCCCG
Found at i:146497 original size:79 final size:79
Alignment explanation
Indices: 146307--146498 Score: 206
Period size: 79 Copynumber: 2.4 Consensus size: 79
146297 TGGAGATAAC
* * * *
146307 AACGGGGCTGGAGTATCCCCGATTATGGAAAATCAGTGTTCTGGAAATAAAATCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTATTCTGAAAATAAAATCGAGGTTGGAGT
**
146372 ACCCCCTCGGAAAT
66 ACCCCCTCAAAAAT
* * ** ** * * *
146386 AACAGAGTTGGAGTATCCTTGATTAT-AGAAAATTGGTATTTTGAAAATAAAATTGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATCAGTATTCTGAAAATAAAATCGAGGTTGGAG
* *
146450 TATCCCTTCAAAAAT
65 TACCCCCTCAAAAAT
*
146465 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATC
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATC
146499 GATGCTTTAG
Statistics
Matches: 88, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
79 87 0.99
80 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCAGTATTCTGAAAATAAAATCGAGGTTGGAGT
ACCCCCTCAAAAAT
Found at i:146547 original size:49 final size:50
Alignment explanation
Indices: 146467--146573 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 50
146457 TCAAAAATAA
* * *
146467 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGC
1 CGGGGTTGGAG-ATCCCCGATTGTGAAAAATCAATACTTTAGAAATAAAGC
* * *
146518 CGGGGTTGGAG-TCCTCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
1 CGGGGTTGGAGATCCCCGATTGTGAAAAATCAATACTTTAGAAATAAAGC
146567 CGGGGTT
1 CGGGGTT
146574 AGAGCATCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 39 0.78
51 11 0.22
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (50 bp):
CGGGGTTGGAGATCCCCGATTGTGAAAAATCAATACTTTAGAAATAAAGC
Found at i:146688 original size:51 final size:49
Alignment explanation
Indices: 146625--146792 Score: 212
Period size: 51 Copynumber: 3.3 Consensus size: 49
146615 TGAAATAACG
* *
146625 GGGTTGGAGTATCCCCAATTGTGAAAGATTGGTGTTTTGAAAATAAAATC
1 GGGTTGGAGTATCCCCGATTGTGAAA-ATTGGTGTTTTGAAAATAAAACC
* *
146675 GGAGTTGAAGTATCCTCGATTGTGGAAAATTGGTGTTTT-AGAAATAAAACC
1 GG-GTTGGAGTATCCCCGATTGT-GAAAATTGGTGTTTTGA-AAATAAAACC
* *
146726 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAACC
1 -GGGTTGGAGTATCCCCGATTGTG-AAAATTGGTGTTTTGAAAATAAAACC
146777 TGGGTTGGAGTATCCC
1 -GGGTTGGAGTATCCC
146793 TGAGATGAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
50 4 0.04
51 92 0.89
52 7 0.07
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (49 bp):
GGGTTGGAGTATCCCCGATTGTGAAAATTGGTGTTTTGAAAATAAAACC
Found at i:149208 original size:21 final size:21
Alignment explanation
Indices: 149182--149238 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
149172 ACAATGAACA
149182 ATGTATCGATACATTAAGGGC
1 ATGTATCGATACATTAAGGGC
149203 ATGTATCGATACATTAAGGGC
1 ATGTATCGATACATTAAGGGC
149224 ATGTATCGATACATT
1 ATGTATCGATACATT
149239 TTAGCAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTAAGGGC
Found at i:149786 original size:40 final size:41
Alignment explanation
Indices: 149742--149844 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 41
149732 GTCCCACTTT
* *
149742 TTGAGGACAAA-GAAAAAGAGAATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGGAAAAAGAGAAAGAAA-AGTGTCCTGCTCC
* *
149782 TTGAGGACAAAGGAAGAAAGA-AAAGGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGGAA-AAAGAGAAAGAAAAGTGTCCTGCTCC
149823 TTGAGGACAAAGTGAAAAAGAG
1 TTGAGGACAAAG-GAAAAAGAG
149845 TACGTCCTGC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
40 13 0.24
41 33 0.61
42 8 0.15
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (41 bp):
TTGAGGACAAAGGAAAAAGAGAAAGAAAAGTGTCCTGCTCC
Found at i:150001 original size:43 final size:41
Alignment explanation
Indices: 149741--150033 Score: 152
Period size: 43 Copynumber: 7.2 Consensus size: 41
149731 TGTCCCACTT
* * *
149741 TTTGAGGACAAA-GAAAAAGAGAATGAAATAG-GTCTTGCTC
1 TTTGAGGACAAAGGAAAAAGGGAATGAAGT-GCGTCCTGCTC
* ** *
149781 CTTGAGGACAAAGGAAGAAAGAAAAGGAAAGT--GTCCTGCT-
1 TTTGAGGACAAAGGAA-AAAGGGAATG-AAGTGCGTCCTGCTC
*
149821 TCTTGAGGACAAAGTG--AAA---AA-G-AGTACGTCCTGCT-
1 T-TTGAGGACAAAG-GAAAAAGGGAATGAAGTGCGTCCTGCTC
* * *
149856 TTTCGAGGACAAAGGAAAAAGGGAAAACGAAATGCGTCATGCTC
1 TTT-GAGGACAAAGGAAAAAGGG--AATGAAGTGCGTCCTGCTC
* * * * * *
149900 TTTGAGGGCAAAAGAAAAAGGAAAATAAAGTGCGTCCTACTT
1 TTTGAGGACAAAGGAAAAAGG-GAATGAAGTGCGTCCTGCTC
* *
149942 TTTAAGGACAAAAAGGAAAAGAAGGGAATGAAGTGTGTCCTGCTC
1 TTTGAGGAC--AAAGG-AAA-AAGGGAATGAAGTGCGTCCTGCTC
* *
149987 TTTGAGGACAAAGGAGAAAA-GGAA--AAG-ACGTCCTACTC
1 TTTGAGGACAAAGGA-AAAAGGGAATGAAGTGCGTCCTGCTC
150025 TTTGAGGAC
1 TTTGAGGAC
150034 TAAAAAGTGC
Statistics
Matches: 199, Mismatches: 30, Indels: 50
0.71 0.11 0.18
Matches are distributed among these distances:
33 3 0.02
34 3 0.02
35 20 0.10
36 5 0.03
38 17 0.09
39 6 0.03
40 11 0.06
41 28 0.14
42 33 0.17
43 36 0.18
44 7 0.04
45 26 0.13
46 4 0.02
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.19
Consensus pattern (41 bp):
TTTGAGGACAAAGGAAAAAGGGAATGAAGTGCGTCCTGCTC
Found at i:150006 original size:45 final size:45
Alignment explanation
Indices: 149847--150007 Score: 138
Period size: 45 Copynumber: 3.7 Consensus size: 45
149837 AAAAAGAGTA
* * *
149847 CGTCCTGCT-TTTCGAGGACAAAG-GAAAA-AGGGAAAACGAAATG
1 CGTCCTGCTCTTT-GAGGACAAAGAGAAAAGAAGGAAAATGAAGTG
* * *
149890 CGTCATGCTCTTTGAGGGCAAA-AG-AAA-AAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAAATGAAGTG
* * * * *
149932 CGTCCTACTTTTTAAGGACAAAAAGGAAAAGAAGG-GAATGAAGTG
1 CGTCCTGCTCTTTGAGGACAAAGA-GAAAAGAAGGAAAATGAAGTG
*
149977 TGTCCTGCTCTTTGAGGACAAAGGAGAAAAG
1 CGTCCTGCTCTTTGAGGACAAA-GAGAAAAG
150008 GAAAAGACGT
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
42 31 0.33
43 18 0.19
44 4 0.04
45 35 0.38
46 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (45 bp):
CGTCCTGCTCTTTGAGGACAAAGAGAAAAGAAGGAAAATGAAGTG
Found at i:150080 original size:61 final size:60
Alignment explanation
Indices: 150003--150392 Score: 342
Period size: 61 Copynumber: 6.6 Consensus size: 60
149993 GACAAAGGAG
* * *
150003 AAAAGGAAAAGACGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
1 AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
150064 GAAAATAAAAGGCGTCCTGCTCTTTGACGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * ** * * * * *
150125 CCAAAGAGAAAA--CATCCTGCTCTTTGAGGAATGGAAGGTGCCACAAACTCGAGTGGTCTTT
1 --AAA-AGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
150186 AAAAGGAGAAA-GCATCTTGCTCTTTGAGGACTGGAAAA-TGCCACTAACTTGTGTGGGCTTT
1 AAAA-GA-AAAGGCGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
150247 ----G-AAAGGTGTCATGCCCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
150302 AAAAGGAAAAGACGTCCTGCTCTTTGAGGACTAGAAATGTGCCACCAACTTGTGTGGGCTTT
1 AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
150364 -----AAAAGGCGTCCTGCTCTTTGAGGACTAAA
1 AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAA
150393 GGGCAAAAGG
Statistics
Matches: 276, Mismatches: 37, Indels: 37
0.79 0.11 0.11
Matches are distributed among these distances:
54 3 0.01
55 47 0.17
56 27 0.10
58 1 0.00
59 5 0.02
60 4 0.01
61 151 0.55
62 33 0.12
63 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (60 bp):
AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:150276 original size:55 final size:55
Alignment explanation
Indices: 150203--150389 Score: 239
Period size: 55 Copynumber: 3.3 Consensus size: 55
150193 GAAAGCATCT
* * *
150203 TGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGTGTCA
1 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* *
150258 TGCCCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCC
1 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
* * *
150319 TGCTCTTTGAGGACTAGAAATGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCC
1 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
150375 TGCTCTTTGAGGACT
1 TGCTCTTTGAGGACT
150390 AAAGGGCAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
55 42 0.37
56 24 0.21
60 1 0.01
61 25 0.22
62 23 0.20
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (55 bp):
TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
Found at i:150616 original size:55 final size:55
Alignment explanation
Indices: 150408--150824 Score: 457
Period size: 55 Copynumber: 7.4 Consensus size: 55
150398 AAAGGAGAGA
* *
150408 GCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---A--A-AAG
* * *
150469 GCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACAAACTTATGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---A--A-AAG
* * *
150530 GTGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
150585 GTGTCCTGC-CTTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-
1 GCGTCCTGCTC-TTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG
** * *
150640 GCG-CCTCGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTT-GAAG
1 GCGTCCT-GCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
* * *
150694 GCATCCTGTTCTTTGAGGACT-GAAAGGTGCCATCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
* * * *
150749 GCGTCTTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
150804 GCGTCCTGCTCTTTGAGGACT
1 GCGTCCTGCTCTTTGAGGACT
150825 AAAGGGTGAA
Statistics
Matches: 316, Mismatches: 31, Indels: 24
0.85 0.08 0.06
Matches are distributed among these distances:
53 5 0.02
54 41 0.13
55 155 0.49
56 9 0.03
58 1 0.00
61 105 0.33
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
Found at i:150760 original size:109 final size:109
Alignment explanation
Indices: 150416--150824 Score: 439
Period size: 109 Copynumber: 3.6 Consensus size: 109
150406 GAGCGTCCTA
* *
150416 CTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCT
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-------GAAGGCGTCCTGCTCT
* * * *
150481 TTGAGGACTGGGAAGTGCCACAAACTTATGTGGGCTTTAAAAGGAGAAGGTGTCCTG
59 TTGAGGACTGGAAAGTGCCAC-AACTTGTGTGGGCTTT--AA--A-AAGGCGTCTTG
* * * *
150538 CTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGC-CTTTTGAG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGA-AGGCGTCCTGCTC-TTTGAG
* * * * *
150602 GATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA-GCGCCTCG
64 GACTGGAAAGTGCCA-CAACTTGTGTGGGCTTTAAAAAGGCGTCTTG
** * *
150648 CTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAGGCATCCTGTTCTTTGAGGA
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAGGCGTCCTGCTCTTTGAGGA
150713 CT-GAAAGGTGCCATCAACTTGTGTGGGCTTT-AAAAGGCGTCTTG
66 CTGGAAA-GTGCCA-CAACTTGTGTGGGCTTTAAAAAGGCGTCTTG
*
150757 CTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAGGCGTCCTGCTCTTTGAGG
150822 ACT
65 ACT
150825 AAAGGGTGAA
Statistics
Matches: 251, Mismatches: 29, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
108 8 0.03
109 85 0.34
110 66 0.26
111 2 0.01
112 1 0.00
114 1 0.00
115 2 0.01
116 43 0.17
117 1 0.00
122 42 0.17
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (109 bp):
CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAGGCGTCCTGCTCTTTGAGGA
CTGGAAAGTGCCACAACTTGTGTGGGCTTTAAAAAGGCGTCTTG
Found at i:164295 original size:79 final size:79
Alignment explanation
Indices: 164145--164319 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 79
164135 ACAACGGGGC
* * * *
164145 TGGAGTATCCCCGATTATGGAAAATCGGTGTTCTGTAAATAAAATTGGAGTTGGAGTATTGCCTC
1 TGGAGTATCCCCGATTATAGAAAATCGGTATTCTGAAAATAAAATAGGAGTTGGAGTATTGCCTC
**
164210 GGAAATAATAG-GGT
66 AAAAATAA-AGAGGT
* *
164224 TGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAAATAAAATCAGG-GTTGGAGTATCT-CC
1 TGGAGTATCCCCGATTATAGAAAATCGGTATTCTGAAAATAAAAT-AGGAGTTGGAGTAT-TGCC
*
164287 TCAAAAATAACGAGGT
64 TCAAAAATAAAGAGGT
*
164303 TAGAGTATCCCCGATTA
1 TGGAGTATCCCCGATTA
164320 GTGAAAAATC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 78 0.95
80 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATAGAAAATCGGTATTCTGAAAATAAAATAGGAGTTGGAGTATTGCCTC
AAAAATAAAGAGGT
Found at i:164403 original size:51 final size:52
Alignment explanation
Indices: 164300--164417 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 52
164290 AAAATAACGA
* * * **
164300 GGTTAGAGTATCCCCGATTAGTGAAAAATCGATGCTTTAGAAATAAGGCTGG
1 GGTTGGAGTATCCCCGATTAGTGAAAAATCAATACTTTAGAAATAAACCTGG
* * *
164352 GGTTGGAGTATCCCCGATTA-TGAGAAATCAATATTTTGGAAATAAACCTGG
1 GGTTGGAGTATCCCCGATTAGTGAAAAATCAATACTTTAGAAATAAACCTGG
164403 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
164418 TTTGAAATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 39 0.67
52 19 0.33
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTAGTGAAAAATCAATACTTTAGAAATAAACCTGG
Found at i:164436 original size:28 final size:28
Alignment explanation
Indices: 164402--164472 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
164392 AATAAACCTG
** *
164402 GGGTTGGAGTATCCCCTTTGAAATAATA
1 GGGTTGGAGTATCCCCGATGAAATAACA
*
164430 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGATGAAATAACA
164458 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
164473 TGATTGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACA
Found at i:164530 original size:51 final size:50
Alignment explanation
Indices: 164458--164629 Score: 193
Period size: 51 Copynumber: 3.4 Consensus size: 50
164448 TGAAATAACG
* *
164458 GGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGAAAATAAAATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACC
* * ***
164508 GGAGTTTGAGTATCCCCAATTGTGCAAAAATTGGCACTTT-AGAAATAAAACC
1 GG-GTTGGAGTATCCCCGATTGTG-AAAAATTGGTGTTTTGA-AAATAAAACC
* * * *
164560 AGTGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTGAAAATAAAACC
1 -GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACC
164611 AGGGTTGGAGTATCCCCGA
1 -GGGTTGGAGTATCCCCGA
164630 GATGAAAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
50 2 0.02
51 57 0.58
52 39 0.39
53 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACC
Found at i:166957 original size:13 final size:13
Alignment explanation
Indices: 166939--166963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
166929 AACCCAGAAT
166939 GTATCGATACAAC
1 GTATCGATACAAC
166952 GTATCGATACAA
1 GTATCGATACAA
166964 TGAATAATGT
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:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:169500 original size:40 final size:40
Alignment explanation
Indices: 169456--169536 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
169446 ATAGGGAAAA
169456 AAACTATAATAAGTGAAAAAATTAGTTTTTATATATAAAT
1 AAACTATAATAAGTGAAAAAATTAGTTTTTATATATAAAT
169496 AAACTATAATAAGTGAAAAAATTAGTTTTTATATATAAAT
1 AAACTATAATAAGTGAAAAAATTAGTTTTTATATATAAAT
169536 A
1 A
169537 TTTTGAAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (40 bp):
AAACTATAATAAGTGAAAAAATTAGTTTTTATATATAAAT
Found at i:169698 original size:18 final size:17
Alignment explanation
Indices: 169652--169705 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
169642 ATAAATAATT
169652 TTTTAAATATTATTTATTA
1 TTTTAAA-ATT-TTTATTA
169671 -TTTAATAATTTGTTATTA
1 TTTTAA-AATTT-TTATTA
169689 TTTTAAAA-TTTTATTA
1 TTTTAAAATTTTTATTA
169705 T
1 T
169706 AGCAATTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 16 0.50
19 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTAAAATTTTTATTA
Found at i:171885 original size:156 final size:150
Alignment explanation
Indices: 171431--171928 Score: 459
Period size: 152 Copynumber: 3.2 Consensus size: 150
171421 TAAAGGAGGG
* ** * *
171431 TGAACTATCCTAAAAGCATACTTTTGGCATAAAA-CCAGCCTGGTGATTATTTAGGATTCGGTTC
1 TGAACTATCCTAAAAGCATACCTTTGGCATAAAAGTGA-CCAGGTGATTA-TTAGGATTCAGTT-
* * * * ** *
171495 AAAAAAGAATTATCAAAATGCCCTTA-AAGTATACCTTCAATGTGAAAGTATCCTAGTAACCCTA
63 TAAGAA-AATTACCAAAATGCCCTTAGGA-TATACCTTTGACGTGAAAGTAT-CTAGTAACCCTA
* *
171559 AAGAACACAAAAATGATATAAAAGGA
125 AAGGACACAAAAATGATATAAAAAGA
* * * * * * *
171585 TGAACCTATCCTAAAAGCATTGCCTTTAGTATAAAAGTGGCTAGGTGATTATCGAGGACT-AGGT
1 TGAA-CTATCCTAAAAGCA-TACCTTTGGCATAAAAGTGACCAGGTGATTAT-TAGGATTCA-GT
* * * * *
171649 TTAAGAGAA--ACCAAAATGCCCCTAAGG-TATATCTTTGACGTGAAAGTATCTCAATAACCTTA
62 TTAAGAAAATTACCAAAATG-CCCTTAGGATATACCTTTGACGTGAAAGTATCT-AGTAACCCTA
* * *
171711 AAAGACACGAAATTGATATAAAAAGA
125 AAGGACACAAAAATGATATAAAAAGA
* *
171737 TGAACTTATTCTAAAAGCATACCTTTTGGCATAAAAGTGACCCGGTGATTACTTAGGATTCAGTT
1 TGAAC-TATCCTAAAAGCATACC-TTTGGCATAAAAGTGACCAGGTGATTA-TTAGGATTCAGTT
* * *
171802 TAAGGGAAAATTACCAAAATGCCCTTAGGATATACCTTTGACATAAAAGTATCATGGTAACCCTA
63 TAA--GAAAATTACCAAAATGCCCTTAGGATATACCTTTGACGTGAAAGTATC-TAGTAACCCTA
171867 AAGGACACAAAAATGATATAAAAAGA
125 AAGGACACAAAAATGATATAAAAAGA
* *
171893 TGAAACTATCCTAAAAGTATGCCTTTGGCATAAAAG
1 TG-AACTATCCTAAAAGCATACCTTTGGCATAAAAG
171929 CGACTTAATG
Statistics
Matches: 273, Mismatches: 52, Indels: 37
0.75 0.14 0.10
Matches are distributed among these distances:
151 6 0.02
152 104 0.38
153 7 0.03
154 10 0.04
155 38 0.14
156 104 0.38
157 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (150 bp):
TGAACTATCCTAAAAGCATACCTTTGGCATAAAAGTGACCAGGTGATTATTAGGATTCAGTTTAA
GAAAATTACCAAAATGCCCTTAGGATATACCTTTGACGTGAAAGTATCTAGTAACCCTAAAGGAC
ACAAAAATGATATAAAAAGA
Found at i:175016 original size:13 final size:13
Alignment explanation
Indices: 174998--175025 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
174988 ATACAAAGGT
174998 CAATGTATCGATA
1 CAATGTATCGATA
175011 CAATGTATCGATA
1 CAATGTATCGATA
175024 CA
1 CA
175026 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:175102 original size:19 final size:19
Alignment explanation
Indices: 175078--175128 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
175068 AGCGATACAT
175078 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
175097 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
175116 TGTATCGATACAA
1 TGTATCGATACAA
175129 TTTCTATCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:176021 original size:49 final size:49
Alignment explanation
Indices: 175906--176301 Score: 459
Period size: 49 Copynumber: 7.9 Consensus size: 49
175896 TGAAGAAAAA
* ** * * * * *
175906 TGCCAATGTGCTGAGCCAAGGCCAGCGACATTGGGCTTAGGAATATTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA--AAGA-TGAAGG
* * *
175958 TGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
176007 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* ** *
176056 TGCCAATATGCTGATTCAAGGCTAGCGATACCGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
176105 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* *
176157 CGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
176206 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* *
176258 CGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
176302 AGATGCCACC
Statistics
Matches: 294, Mismatches: 43, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
49 173 0.59
50 2 0.01
52 115 0.39
53 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:176027 original size:101 final size:100
Alignment explanation
Indices: 175906--176301 Score: 530
Period size: 101 Copynumber: 3.9 Consensus size: 100
175896 TGAAGAAAAA
** * * * *
175906 TGCCAATGTGCTGAGCCAAGGCCAGCGACATTGGGCTT-AGGAATATTAAAGATGCCAATATGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG-ATA-CAAAGACGCCAATATGCT
* * *
175970 GATTCAAGGCCAACGATATTAGACTTAAGGATGAAGG
64 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* **
176007 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAC---GGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-ACAAAGACGCCAATATGCTG
* ** *
176069 ATTCAAGGCTAGCGATACCGGACTTAAAGATGAAGA
65 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
176105 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-ACAAAGACGCCAATATGCTG
*
176170 ATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGG
65 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
176206 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-ACAAAGACGCCAATATGCTG
*
176271 ATTCAAGGCCAGCAATATTGGACTTAGAAGA
65 ATTCAAGGCCAGCGATATTGGACTTA-AAGA
176302 AGATGCCACC
Statistics
Matches: 266, Mismatches: 23, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
98 88 0.33
101 171 0.64
102 7 0.03
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (100 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATACAAAGACGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:176164 original size:199 final size:198
Alignment explanation
Indices: 175905--176309 Score: 555
Period size: 199 Copynumber: 2.0 Consensus size: 198
175895 TTGAAGAAAA
* * * * *
175905 ATGCCAATGTGCTGAGCCAAGGCCAGCGACATTGGGCTTAGGAATATTAAAGATGCCAATATGCT
1 ATGCCAATATGCTGAGCCAAGGCCAGCGACATTGGACTTAAGAATATCAAAGACGCCAATATGCT
*
175970 GATTCAAGGCCAACGATATTAGACTTAAGGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
66 GATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
* ** * *
176035 CATTGGTCTTAAAGATGAC-GGTGCCAATATGCTGATTCAAGGCTAGCGATACCGGACTTAAAGA
131 CATTGGACTTAAAGATGACAGACGCCAATATGCTGATTCAAGGCCAGCAATACCGGACTT--AGA
*
176099 TGAAG
194 AGAAG
** *
176104 ATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAA-AGATGA-CAAAGGCGCCAATATG
1 ATGCCAATATGCTGAGCCAAGGCCAGCGACATTGGACTTAAGA-AT-ATCAAAGACGCCAATATG
* * *
176167 CTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGC
64 CTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGC
**
176232 GACATTGGACTTAAAGATGACAAAGACGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTA
129 GACATTGGACTTAAAGATGAC--AGACGCCAATATGCTGATTCAAGGCCAGCAATACCGGACTTA
176297 GAAGAAG
192 GAAGAAG
176304 ATGCCA
1 ATGCCA
176310 CCAACTTGTG
Statistics
Matches: 181, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
198 1 0.01
199 132 0.73
200 14 0.08
202 34 0.19
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (198 bp):
ATGCCAATATGCTGAGCCAAGGCCAGCGACATTGGACTTAAGAATATCAAAGACGCCAATATGCT
GATTCAAGGCCAACGATATTAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
CATTGGACTTAAAGATGACAGACGCCAATATGCTGATTCAAGGCCAGCAATACCGGACTTAGAAG
AAG
Found at i:176383 original size:28 final size:28
Alignment explanation
Indices: 176318--176871 Score: 684
Period size: 28 Copynumber: 19.4 Consensus size: 28
176308 CACCAACTTG
**
176318 TGTGGGCTTTTGATAGGGTTG-CACCAACT
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACT
*
176347 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
176375 TGTGGGCTTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
176404 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
176432 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
176462 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
176490 TGTGGGC-TTCGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
*
176518 TGTGGGC-TTCGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* *
176546 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
* *
176576 TATGAGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
176604 TGTGGGCTTTGGAAAGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
176632 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
176662 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
176690 TGTGGGCTTTGGAAAAGATGCCA-TGGACT
1 TGTGGGCTTTTG-AAGGTTGCCACT-GACT
176719 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
176747 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
176777 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * * *
176805 TATGGGCTTTGGAAAAGATGCCACAGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
176834 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
176862 TGTGGGCTTT
1 TGTGGGCTTT
176872 GGAAAAGGTG
Statistics
Matches: 461, Mismatches: 49, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.02
28 264 0.57
29 87 0.19
30 102 0.22
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:176485 original size:58 final size:58
Alignment explanation
Indices: 176318--176876 Score: 721
Period size: 58 Copynumber: 9.8 Consensus size: 58
176308 CACCAACTTG
* ** * *
176318 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGA-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
* * * *
176375 TGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
* * *
176432 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
* *
176490 TGTGGGC-TTCGAAAGGTTGCCACTGACTTGTGGGC-TTCGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
* * * * *
176546 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTATGAGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
* *
176604 TGTGGGCTTTGGAAA-GTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGGTTGCCACTGACT
* *
176662 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCA-TGGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACT-GACT
*
176719 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGGTTGCCACTGACT
* * * *
176777 TGTGGGCTTTTG-AAGGTTGCCACTGACTTATGGGCTTTGGAAAAGATGCCACAGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
176834 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAA
1 TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGGAAA
176877 AGGTGAGGAA
Statistics
Matches: 456, Mismatches: 34, Indels: 24
0.89 0.07 0.05
Matches are distributed among these distances:
55 3 0.01
56 71 0.16
57 177 0.39
58 201 0.44
59 4 0.01
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (58 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGTTGCCACTGACT
Found at i:176753 original size:115 final size:114
Alignment explanation
Indices: 176318--176879 Score: 733
Period size: 115 Copynumber: 4.9 Consensus size: 114
176308 CACCAACTTG
** *
176318 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
* * * * *
176382 TTTTGAAAAGATACCACTGACTTGTGGGCTTTTG--AAGGTTGCCACTGACT
64 TTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
* *
176432 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
* * *
176497 -TTCGAAAGGTTGCCACTGACTTGTGGGC-TTCG-AAAGGTTGCCACTGACT
64 TTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
* * * *
176546 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTATGAGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
* *
176611 TTTGGAAAGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
64 TTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
* * *
176662 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCA-TGGACTTGTGGGC
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACT-GACTTGTGGGC
176726 TTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
64 TTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
* * * * *
176777 TGTGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGGAAAAGATGCCACAGACTTGTGGGCT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCT
176842 TTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGG
65 TTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGG
176880 TGAGGAATGC
Statistics
Matches: 411, Mismatches: 27, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
113 3 0.01
114 165 0.40
115 215 0.52
116 28 0.07
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.31
Consensus pattern (114 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
TTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACT
Found at i:178314 original size:1 final size:1
Alignment explanation
Indices: 178310--178413 Score: 82
Period size: 1 Copynumber: 104.0 Consensus size: 1
178300 TTTGTTGTTG
* * * * * * *
178310 TTTTTTTGTTTGTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
178375 GTTTTGTTGTTGTTTTTTTTTTGTTTGTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
178414 GTGGAGGACG
Statistics
Matches: 75, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:178364 original size:38 final size:40
Alignment explanation
Indices: 178299--178413 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 40
178289 TCCGGACCCT
*
178299 TTTTGTTGTTG-TTTTTTTG-TTTGTTTGTTTTTTTTTTG
1 TTTTGTTGTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTTG
178337 TTTT-TT-TTGTTTTTTTTGTTTTTTTTGTTTTTTTTTTTG
1 TTTTGTTGTTGTTTTTTTTGTTTTTTTTG-TTTTTTTTTTG
178376 TTTTGTTGTTGTTTTTTTT-TTGTTTGTTTGTTTTTTTT
1 TTTTGTTGTTGTTTTTTTTGTT-TTT-TTTGTTTTTTTT
178414 GTGGAGGACG
Statistics
Matches: 69, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
36 3 0.04
37 10 0.14
38 11 0.16
39 15 0.22
40 4 0.06
41 22 0.32
42 4 0.06
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (40 bp):
TTTTGTTGTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTTG
Found at i:178413 original size:18 final size:19
Alignment explanation
Indices: 178300--178413 Score: 135
Period size: 19 Copynumber: 5.8 Consensus size: 19
178290 CCGGACCCTT
*
178300 TTTG-TTGTTGTTTTTTTG
1 TTTGTTTGTTTTTTTTTTG
178318 TTTGTTTGTTTTTTTTTTG
1 TTTGTTTGTTTTTTTTTTG
178337 TTT-TTT-TTGTTTTTTTTG
1 TTTGTTTGTT-TTTTTTTTG
*
178355 TTTTTTTTGTTTTTTTTTTTG
1 -TTTGTTTG-TTTTTTTTTTG
178376 TTTTGTTGTTGTTTTTTTTTTG
1 -TTTG-T-TTGTTTTTTTTTTG
178398 TTTGTTTGTTTTTTTT
1 TTTGTTTGTTTTTTTT
178414 GTGGAGGACG
Statistics
Matches: 86, Mismatches: 2, Indels: 15
0.83 0.02 0.15
Matches are distributed among these distances:
17 2 0.02
18 16 0.19
19 30 0.35
20 4 0.05
21 17 0.20
22 14 0.16
23 3 0.03
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (19 bp):
TTTGTTTGTTTTTTTTTTG
Found at i:192424 original size:19 final size:19
Alignment explanation
Indices: 192400--192464 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
192390 AGCAATACAT
192400 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
192419 TGTATCGAT---AGA--T-
1 TGTATCGATACAAAACTTA
*
192432 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
192451 TGTATCGATACAAA
1 TGTATCGATACAAA
192465 TCGTTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 4 0.11
18 1 0.03
19 22 0.59
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:192439 original size:32 final size:32
Alignment explanation
Indices: 192398--192460 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
192388 GTAGCAATAC
192398 ATTGTATCGATACAAAACTTATGTATCGATAG
1 ATTGTATCGATACAAAACTTATGTATCGATAG
*
192430 ATTGTATCGATACAACACTTATGTATCGATA
1 ATTGTATCGATACAAAACTTATGTATCGATA
192461 CAAATCGTTG
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:0.14, G:0.14, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAG
Found at i:193074 original size:152 final size:153
Alignment explanation
Indices: 192782--193197 Score: 430
Period size: 152 Copynumber: 2.7 Consensus size: 153
192772 TAAGGCTTGG
* * * * * *
192782 TTCAAAAGAAAATTA-CTAAAATGCCTCTAAGGTATATCTTCAACATGAAAATATCCCAATAACC
1 TTCAAAAGAAAATTATC-AAAATACCCCTGAGGTATATCTTCGACAT--AAATATCTCGATAA-C
* * * * *
192846 CTAAAGGACACGAAAATGATGCAAAAAGATGAACCTATCCTAAAAGCATACCTTTGACATAAAAA
62 CTAAAGGACACAAAAATGATGTAAAAGGATGAA-CTATCTTAAAAGCATACCTTTGACAGAAAAA
*
192911 TGACCTAGTGATTACCTAGGACTCA-AT
126 TGACCCAGTGATTACCTAGGACTCAGAT
** * * *
192938 TT-AAGGGAAAATTATCAAAATGCTCCT-AGGGTATATCTTCGACGT-AATATCTCGATAACCTT
1 TTCAAAAGAAAATTATCAAAATACCCCTGA-GGTATATCTTCGACATAAATATCTCGATAACC-T
* * * * * *
193000 AAAAGATACAAAAATGATGTAAAAGGATAAACTTATCTTAAAAGCATA-TTTTCGGCAGAAAAGT
64 AAAGGACACAAAAATGATGTAAAAGGATGAAC-TATCTTAAAAGCATACCTTT-GACAGAAAAAT
* * *
193064 GACCCGGTGATTACCTAGGAGTCAGTT
127 GACCCAGTGATTACCTAGGACTCAGAT
*
193091 TTCAAAAGAAAATTATCAAAATACCCCTGAGGTATATCTTCGACATAAATGTATCTCGGTAAACC
1 TTCAAAAGAAAATTATCAAAATACCCCTGAGGTATATCTTCGACATAAA--TATCTCGAT-AACC
*
193156 TAAAGGACACAAAAATGATGTGAAAGGATGAACTATCTTAAA
63 TAAAGGACACAAAAATGATGTAAAAGGATGAACTATCTTAAA
193198 TAGGTAATTT
Statistics
Matches: 215, Mismatches: 33, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
151 6 0.03
152 80 0.37
153 3 0.01
154 37 0.17
155 36 0.17
156 12 0.06
157 37 0.17
158 4 0.02
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (153 bp):
TTCAAAAGAAAATTATCAAAATACCCCTGAGGTATATCTTCGACATAAATATCTCGATAACCTAA
AGGACACAAAAATGATGTAAAAGGATGAACTATCTTAAAAGCATACCTTTGACAGAAAAATGACC
CAGTGATTACCTAGGACTCAGAT
Found at i:196776 original size:17 final size:17
Alignment explanation
Indices: 196749--196789 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
196739 TATATACTTA
196749 ATGATATTATGTACA-TTC
1 ATGA-ATTATGT-CATTTC
196767 ATGAATTATGTCATTTC
1 ATGAATTATGTCATTTC
196784 ATGAAT
1 ATGAAT
196790 GTGGATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 16 0.73
18 4 0.18
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (17 bp):
ATGAATTATGTCATTTC
Found at i:196800 original size:16 final size:16
Alignment explanation
Indices: 196781--196823 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
196771 ATTATGTCAT
*
196781 TTCATGAATGTGGATA
1 TTCATGAATGTGAATA
*
196797 TTCATGAACTATGAATA
1 TTCATGAA-TGTGAATA
*
196814 TACATGAATG
1 TTCATGAATG
196824 GCATTAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (16 bp):
TTCATGAATGTGAATA
Found at i:197777 original size:19 final size:19
Alignment explanation
Indices: 197734--197787 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
197724 GCCAGTTTCG
* **
197734 TGTATCGATATAATTGAGTA
1 TGTATCGATACAA-TGAACA
197754 TGTATCGATACAATGAACA
1 TGTATCGATACAATGAACA
*
197773 TGTATCGATGCAATG
1 TGTATCGATACAATG
197788 TATCGATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAATGAACA
Found at i:200252 original size:13 final size:13
Alignment explanation
Indices: 200233--200269 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
200223 ATAGTAACCC
*
200233 ATGTATCGATATA
1 ATGTATCGATACA
*
200246 TTGTATCGATACA
1 ATGTATCGATACA
200259 ATGTATCGATA
1 ATGTATCGATA
200270 GAAAGAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:205403 original size:14 final size:14
Alignment explanation
Indices: 205384--205411 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
205374 CAAACATGCC
205384 TTGTGACGATACAA
1 TTGTGACGATACAA
205398 TTGTGACGATACAA
1 TTGTGACGATACAA
205412 GCCATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
TTGTGACGATACAA
Found at i:206119 original size:10 final size:10
Alignment explanation
Indices: 206106--206153 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
206096 AAAACTACCA
206106 AAAAAAGAAG
1 AAAAAAGAAG
*
206116 -AAAAAGAAAA
1 AAAAAAG-AAG
206126 AGAAAAAGAGAG
1 A-AAAAAGA-AG
206138 AAAAAAGAAG
1 AAAAAAGAAG
206148 AAAAAA
1 AAAAAA
206154 AGGAGAGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 6 0.19
10 10 0.31
11 8 0.25
12 8 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:206120 original size:12 final size:12
Alignment explanation
Indices: 206105--206154 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
206095 AAAAACTACC
*
206105 AAAAA-AAGAAG
1 AAAAAGAAGAAA
206116 AAAAAGAA-AAA
1 AAAAAGAAGAAA
*
206127 GAAAAAG-AGAGA
1 -AAAAAGAAGAAA
206139 AAAAAGAAGAAA
1 AAAAAGAAGAAA
206151 AAAA
1 AAAA
206155 GGAGAGCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 14 0.44
12 18 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAA
Done.