Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold295
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: 1524207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:406146 original size:28 final size:28
Alignment explanation
Indices: 406106--406177 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
406096 AAAAAAAAAT
* * *
406106 CGGGATTGGAGTATCCCC-TTGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
406134 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
406162 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
406178 TTGATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:406291 original size:13 final size:13
Alignment explanation
Indices: 406273--406298 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
406263 ACAAAGATCC
406273 ATGTATCGATACA
1 ATGTATCGATACA
406286 ATGTATCGATACA
1 ATGTATCGATACA
406299 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:406294 original size:33 final size:33
Alignment explanation
Indices: 406252--406318 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
406242 AAAATTTCCA
***
406252 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
406285 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
406318 A
1 A
406319 TTTTCTTGGC
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:406362 original size:19 final size:18
Alignment explanation
Indices: 406338--406405 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
406328 CAGTAGCTAA
406338 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
406357 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
406372 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
406389 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
406406 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:406378 original size:13 final size:13
Alignment explanation
Indices: 406360--406384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
406350 ACAATACTTA
406360 TGTATCGATACAT
1 TGTATCGATACAT
406373 TGTATCGATACA
1 TGTATCGATACA
406385 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:406382 original size:32 final size:32
Alignment explanation
Indices: 406341--406403 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
406331 TAGCTAATTA
*
406341 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
406373 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
406404 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:406485 original size:21 final size:21
Alignment explanation
Indices: 406461--406517 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
406451 CATTTGTAGG
406461 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
406482 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
406503 ATGTATCGATACATT
1 ATGTATCGATACATT
406518 TGGATAAATT
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:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:407323 original size:55 final size:55
Alignment explanation
Indices: 407239--408004 Score: 784
Period size: 55 Copynumber: 13.5 Consensus size: 55
407229 ATAAAGTGTA
* * * * *
407239 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
407294 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
407349 TCCTGCTCTTTAAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAGGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-GGCG
* * * *
407404 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCTACTTGTGTGGGCTTTAAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
407459 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG------AAAGGCG
*
407520 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * * *
407574 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAATTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
407629 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
407684 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
407745 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
*
407804 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* *
407863 TCCCGCTCTTTGAGGATTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * *
407922 TTC-ACTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
*
407980 TCCCGCTCTTTGAGGACTG-AAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTG
408005 GAAGGAGAAG
Statistics
Matches: 637, Mismatches: 47, Indels: 50
0.87 0.06 0.07
Matches are distributed among these distances:
53 2 0.00
54 30 0.05
55 299 0.47
56 15 0.02
58 54 0.08
59 138 0.22
60 52 0.08
61 41 0.06
64 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:407429 original size:26 final size:26
Alignment explanation
Indices: 407400--407484 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
407390 GGCTTTAAAG
407400 GGTGTCCTGCTCTTTGGGGACTGAAA
1 GGTGTCCTGCTCTTTGGGGACTGAAA
** *
407426 GGTG-CCACCTACTTGTGTGGG-CTTTAAAA
1 GGTGTCCTGCT-CTT-TG-GGGAC--TGAAA
*
407455 GGGGTCCTGCTCTTTGGGGACTGAAA
1 GGTGTCCTGCTCTTTGGGGACTGAAA
407481 GGTG
1 GGTG
407485 CCACCAACTT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 4 0.09
26 14 0.32
27 6 0.14
28 6 0.14
29 10 0.23
30 4 0.09
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.29
Consensus pattern (26 bp):
GGTGTCCTGCTCTTTGGGGACTGAAA
Found at i:407631 original size:225 final size:224
Alignment explanation
Indices: 407239--408004 Score: 989
Period size: 225 Copynumber: 3.4 Consensus size: 224
407229 ATAAAGTGTA
* * * * * *
407239 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAG-----GCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* *
407298 GCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTAAG
66 GCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAG
*
407363 GACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGGTGTCCTGCTCTTTGGGGACTGAAAG
130 GACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAA-GGTGTCCTGCTCTTTGAGGACTGAAAG
*
407427 GTGCCACCTACTTGTGTGGGCTTTAAAAGGGG
193 GTGCCACCAACTTGTGTGGGCTTTAAAAGGGG
* *
407459 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
407524 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGG
* *
407589 ACTGGAAAATGCCACCAATTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-A
131 ACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
* *
407653 TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
194 TGCCACCAACTTGTGTGGGCTTTAAAAGGGG
*
407684 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* * * *
407749 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCTT
** * *
407814 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
126 TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGA
*
407879 TTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
186 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG----GG-G
* * * *
407922 TTC-ACTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCATCCC
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
407984 GCTCTTTGAGGACTGAAGGTG
66 GCTCTTTGAGGACTGAAGGTG
408005 GAAGGAGAAG
Statistics
Matches: 482, Mismatches: 40, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
220 42 0.09
221 3 0.01
225 229 0.48
226 27 0.06
227 3 0.01
229 25 0.05
230 20 0.04
232 2 0.00
233 29 0.06
234 22 0.05
235 36 0.07
236 27 0.06
237 14 0.03
238 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (224 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGG
ACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTG
CCACCAACTTGTGTGGGCTTTAAAAGGGG
Found at i:408987 original size:12 final size:11
Alignment explanation
Indices: 408963--409021 Score: 59
Period size: 12 Copynumber: 5.4 Consensus size: 11
408953 CTTAAGTAGA
*
408963 TTTTTCTTTTT
1 TTTTTGTTTTT
408974 TTTTTG--TTT
1 TTTTTGTTTTT
*
408983 GTTTTGTTTGTT
1 TTTTTGTTT-TT
*
408995 TTGTTGTTTTT
1 TTTTTGTTTTT
409006 TTTTGTGTTTTT
1 TTTT-TGTTTTT
409018 TTTT
1 TTTT
409022 GAAAAAGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 8 0.21
11 11 0.28
12 20 0.51
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.85
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:409005 original size:9 final size:9
Alignment explanation
Indices: 408975--409004 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
408965 TTTCTTTTTT
408975 TTTTGTTTG
1 TTTTGTTTG
408984 TTTTGTTTG
1 TTTTGTTTG
408993 TTTTG-TTG
1 TTTTGTTTG
409001 TTTT
1 TTTT
409005 TTTTTGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (9 bp):
TTTTGTTTG
Found at i:418970 original size:13 final size:13
Alignment explanation
Indices: 418952--418977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
418942 CAATTTTTTG
418952 TGTATCGATACAT
1 TGTATCGATACAT
418965 TGTATCGATACAT
1 TGTATCGATACAT
418978 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:419061 original size:20 final size:20
Alignment explanation
Indices: 419016--419088 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
419006 CTGCCAAGAA
***
419016 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
419037 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
419057 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
419077 ATGTATCGATAC
1 ATGTATCGATAC
419089 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:419089 original size:20 final size:20
Alignment explanation
Indices: 419036--419091 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
419026 ACATCTTTTT
*
419036 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
419056 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
419075 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
419092 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:419717 original size:21 final size:21
Alignment explanation
Indices: 419676--419719 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
419666 TTCCCCTTTA
* *
419676 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
419697 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
419718 TC
1 TC
419720 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:421542 original size:13 final size:13
Alignment explanation
Indices: 421524--421549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
421514 ATAATCACCC
421524 TGTATCGATACAA
1 TGTATCGATACAA
421537 TGTATCGATACAA
1 TGTATCGATACAA
421550 GGAAAAATGT
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):
TGTATCGATACAA
Found at i:423648 original size:15 final size:15
Alignment explanation
Indices: 423628--423658 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
423618 ATTTCGTTTG
*
423628 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
423643 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
423658 G
1 G
423659 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:425490 original size:21 final size:21
Alignment explanation
Indices: 425461--425505 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
425451 AAGTTTTCAT
*
425461 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
425481 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
425503 TTT
1 TTT
425506 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:427742 original size:13 final size:13
Alignment explanation
Indices: 427724--427749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
427714 CAATTTTTTG
427724 TGTATCGATACAT
1 TGTATCGATACAT
427737 TGTATCGATACAT
1 TGTATCGATACAT
427750 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:431420 original size:28 final size:28
Alignment explanation
Indices: 431380--431451 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
431370 AAAAAAAAAT
* *
431380 CGGGATTGGAGTATCCCCTCA-GAAGTAA
1 CGGGGTTGGAGTATCCCC-CATGAAATAA
*
431408 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCCATGAAATAA
*
431436 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
431452 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAATAA
Found at i:431509 original size:52 final size:52
Alignment explanation
Indices: 431440--431724 Score: 158
Period size: 52 Copynumber: 5.4 Consensus size: 52
431430 AAATAACGAG
*
431440 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* ** * ** *
431492 GTTAGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAATC-GA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* **** * * *
431543 GATTGGAGTATCCCC--TCG-GAAATAACGAGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 G-TTGGAGTATCCCCGATTGTG-AA-AA--A--TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
431599 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
431653 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
431704 GTTGGAATATCCCCAATTGTG
1 GTTGGAGTATCCCCGATTGTG
431725 GAGAATTGAG
Statistics
Matches: 171, Mismatches: 41, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 3 0.02
51 37 0.22
52 46 0.27
53 26 0.15
54 27 0.16
55 15 0.09
56 6 0.04
57 8 0.05
58 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:431553 original size:160 final size:159
Alignment explanation
Indices: 431369--431717 Score: 531
Period size: 160 Copynumber: 2.2 Consensus size: 159
431359 ATGATCAGAA
* * *
431369 GAAAAAAAAATCGGGATTGGAGTATCCCCTCAGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT
1 GAAAATAAAATC-GGATTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATG-AAT
*
431434 AACGAGGTTGGAGTATCCTCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAG
64 AACGAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAG
*
431497 AGTATCCCCGATTAAAGGAAAATTGGCGTTTT
129 AGTATCCCCGATTAAA-GAAAATTAGCGTTTT
* *
431529 GAAAATAAAATCGAGATTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATGATTA
1 GAAAATAAAATCG-GATTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATGAATA
* *
431594 ACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGA
65 ACGAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGA
* *
431659 GTATCCCCGATTATAGAAAATTAGTGTTTT
130 GTATCCCCGATTAAAGAAAATTAGCGTTTT
*
431689 GAAAATAAAATCGGAGTTGGAATATCCCC
1 GAAAATAAAATCGGA-TTGGAGTATCCCC
431718 AATTGTGGAG
Statistics
Matches: 173, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
159 32 0.18
160 101 0.58
161 40 0.23
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (159 bp):
GAAAATAAAATCGGATTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATGAATAA
CGAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAG
TATCCCCGATTAAAGAAAATTAGCGTTTT
Found at i:431576 original size:28 final size:27
Alignment explanation
Indices: 431540--431614 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
431530 AAAATAAAAT
* **
431540 CGAGATTGGAGTATCCCCTCGGAAATAA
1 CGAGGTTGGAGTATCCCCGAGG-AATAA
* *
431568 CGAGGTTGGAGTATCCCCGATGATTAA
1 CGAGGTTGGAGTATCCCCGAGGAATAA
*
431595 CGGGGTTGGAGTATCCCCGA
1 CGAGGTTGGAGTATCCCCGA
431615 TTGTGAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (27 bp):
CGAGGTTGGAGTATCCCCGAGGAATAA
Found at i:431699 original size:51 final size:53
Alignment explanation
Indices: 431603--431717 Score: 146
Period size: 51 Copynumber: 2.2 Consensus size: 53
431593 AACGGGGTTG
* * *
431603 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
431657 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
431708 GAATATCCCC
1 GAGTATCCCC
431718 AATTGTGGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
51 30 0.55
52 2 0.04
53 8 0.15
54 15 0.27
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:434092 original size:13 final size:13
Alignment explanation
Indices: 434074--434099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
434064 ACAAAGATCC
434074 ATGTATCGATACA
1 ATGTATCGATACA
434087 ATGTATCGATACA
1 ATGTATCGATACA
434100 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:434095 original size:33 final size:33
Alignment explanation
Indices: 434053--434119 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
434043 AAAATTTCCA
***
434053 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
434086 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
434119 A
1 A
434120 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:434163 original size:19 final size:19
Alignment explanation
Indices: 434139--434225 Score: 114
Period size: 19 Copynumber: 4.9 Consensus size: 19
434129 CAGTAGCTAA
*
434139 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
434158 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
434173 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
434190 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
*
434209 TTATGTATTGATACAAA
1 TTATGTATCGATACAAA
434226 TTGTTGAATT
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
13 11 0.18
14 1 0.02
16 2 0.03
18 1 0.02
19 46 0.75
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:434179 original size:13 final size:13
Alignment explanation
Indices: 434161--434185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
434151 ACAATACTTA
434161 TGTATCGATACAT
1 TGTATCGATACAT
434174 TGTATCGATACA
1 TGTATCGATACA
434186 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:434183 original size:32 final size:32
Alignment explanation
Indices: 434142--434204 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
434132 TAGCTAATTA
*
434142 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
434174 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
434205 AAACTTATGT
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:434305 original size:21 final size:21
Alignment explanation
Indices: 434281--434337 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
434271 CATTTGTAGG
434281 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
434302 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
434323 ATGTATCGATACATT
1 ATGTATCGATACATT
434338 TGGATAAATT
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:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:434710 original size:8 final size:8
Alignment explanation
Indices: 434692--434722 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
434682 TTTTCAACAT
434692 CAAACATCA
1 CAAA-ATCA
434701 CAAAATCA
1 CAAAATCA
434709 CAAAATCA
1 CAAAATCA
434717 CAAAAT
1 CAAAAT
434723 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:440684 original size:13 final size:13
Alignment explanation
Indices: 440666--440691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
440656 CAATTTGGGA
440666 TGTATCGATACAT
1 TGTATCGATACAT
440679 TGTATCGATACAT
1 TGTATCGATACAT
440692 CTTGTGTGTA
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:440688 original size:33 final size:32
Alignment explanation
Indices: 440646--440709 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
440636 TACAAGCCAA
440646 TGTATCGATACAAT-TTGGGATGTATCGATACAT
1 TGTATCGATAC-ATCTTGGG-TGTATCGATACAT
*
440679 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
440710 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:440815 original size:20 final size:19
Alignment explanation
Indices: 440792--440830 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
440782 CTGTGCATTA
440792 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
440812 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
440831 GTTTTAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:444406 original size:29 final size:28
Alignment explanation
Indices: 444374--444510 Score: 83
Period size: 29 Copynumber: 4.8 Consensus size: 28
444364 TAAATATCCC
444374 TAAAACATGACAAATTATTAAAATGATCT
1 TAAAACATGACAAATTA-TAAAATGATCT
* ** *
444403 TAAAATACATG--AAATTACATAAATGGCCC
1 T-AAA-ACATGACAAATTATA-AAATGATCT
444432 TAAAACATGAC--A-TACTAAAATGATCT
1 TAAAACATGACAAATTA-TAAAATGATCT
444458 TAAAATACATG--AAATTGCAT-AAATGATCT
1 T-AAA-ACATGACAAATT--ATAAAATGATCT
*
444487 TAAAACATGACAAATAACTAAAAT
1 TAAAACATGACAAATTA-TAAAAT
444511 AATATAAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 34
0.66 0.07 0.27
Matches are distributed among these distances:
26 9 0.11
27 16 0.20
28 14 0.17
29 33 0.40
30 4 0.05
31 6 0.07
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (28 bp):
TAAAACATGACAAATTATAAAATGATCT
Found at i:444479 original size:113 final size:113
Alignment explanation
Indices: 444332--444537 Score: 279
Period size: 113 Copynumber: 1.8 Consensus size: 113
444322 ATAAAAAACA
* ** * * *
444332 ACTAAAATGGTCCTAAAATGTATGATATTGCATAAAT-ATCCCTAAAACATGACAAATTATTAAA
1 ACTAAAATGATCCTAAAATACATGAAATTGCATAAATGAT-CCTAAAACATGACAAATAACTAAA
* * *
444396 ATGATCTTAAAATACATGAAATTACATAAATGGCCCTAAAACATGACAT
65 ATAATATAAAAATACATGAAATTACATAAATGGCCCTAAAACATGACAT
* *
444445 ACTAAAATGATCTTAAAATACATGAAATTGCATAAATGATCTTAAAACATGACAAATAACTAAAA
1 ACTAAAATGATCCTAAAATACATGAAATTGCATAAATGATCCTAAAACATGACAAATAACTAAAA
* *
444510 TAATATAAAAATGCATGAAATTATATAA
66 TAATATAAAAATACATGAAATTACATAA
444538 TAAACCCTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
113 77 0.97
114 2 0.03
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (113 bp):
ACTAAAATGATCCTAAAATACATGAAATTGCATAAATGATCCTAAAACATGACAAATAACTAAAA
TAATATAAAAATACATGAAATTACATAAATGGCCCTAAAACATGACAT
Found at i:444529 original size:58 final size:58
Alignment explanation
Indices: 444331--444588 Score: 249
Period size: 58 Copynumber: 4.5 Consensus size: 58
444321 CATAAAAAAC
** * * *
444331 AACTAAAATGGTCCTAAAATGTATGATATTGCATAAAT-ATCCCTAAAACATGACAAAT
1 AACTAAAATAATCTTAAAATGCATGAAATTGCATAAATGA-CCCTAAAACATGACAAAT
* * * * * *
444389 TATTAAAATGATCTTAAAATACATGAAATTACATAAATGGCCCTAAAACATGAC--AT
1 AACTAAAATAATCTTAAAATGCATGAAATTGCATAAATGACCCTAAAACATGACAAAT
* * * *
444445 -ACTAAAATGATCTTAAAATACATGAAATTGCATAAATGATCTTAAAACATGACAAAT
1 AACTAAAATAATCTTAAAATGCATGAAATTGCATAAATGACCCTAAAACATGACAAAT
* * * * *
444502 AACTAAAATAATATAAAAATGCATGAAATT--ATATAATAAACCCTAAATCATGAAAAAT
1 AACTAAAATAATCTTAAAATGCATGAAATTGCATA-AAT-GACCCTAAAACATGACAAAT
* *
444560 AACTAAAATAATGTTAAAATGTATGAAAT
1 AACTAAAATAATCTTAAAATGCATGAAAT
444589 GAAAAAAAAA
Statistics
Matches: 168, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
55 48 0.29
56 5 0.03
57 5 0.03
58 110 0.65
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.28
Consensus pattern (58 bp):
AACTAAAATAATCTTAAAATGCATGAAATTGCATAAATGACCCTAAAACATGACAAAT
Found at i:449468 original size:20 final size:19
Alignment explanation
Indices: 449420--449476 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
449410 CGAAAAAGGC
*
449420 AAAAAAT-AAAAAAATAAA
1 AAAAAATGAAGAAAATAAA
*
449438 AAAGAA-G-AGAAAATAAA
1 AAAAAATGAAGAAAATAAA
*
449455 AGAAAAATGAAGAATATAAA
1 A-AAAAATGAAGAAAATAAA
449475 AA
1 AA
449477 GTAAGAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 10 0.32
18 9 0.29
19 2 0.06
20 10 0.32
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAAATGAAGAAAATAAA
Found at i:450921 original size:11 final size:12
Alignment explanation
Indices: 450884--450924 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
450874 TTTTAAATAA
450884 AAATATAAAATT
1 AAATATAAAATT
* *
450896 AGATAAAAAATT
1 AAATATAAAATT
450908 AAATATAAAA-T
1 AAATATAAAATT
450919 AAATAT
1 AAATAT
450925 CAGATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:455396 original size:2 final size:2
Alignment explanation
Indices: 455346--455377 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
455336 CCACTTCTGA
455346 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
455378 ACGCTACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:457102 original size:22 final size:22
Alignment explanation
Indices: 457074--457146 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
457064 TATAGTGATA
457074 TATATATTGTTATATTAATATG
1 TATATATTGTTATATTAATATG
* *
457096 TATATATTATTATACTAATATG
1 TATATATTGTTATATTAATATG
* * *
457118 TACATATTGTTATATTGATATA
1 TATATATTGTTATATTAATATG
457140 TATATAT
1 TATATAT
457147 GGTATTATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (22 bp):
TATATATTGTTATATTAATATG
Found at i:457650 original size:22 final size:22
Alignment explanation
Indices: 457590--457651 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
457580 TGTTATTGTG
* * *
457590 ATATGTACATTTAATTATAATT
1 ATATATACATTTAGTTATAATC
457612 ATATATACATTTAGTTATAATC
1 ATATATACATTTAGTTATAATC
*
457634 ATATTTACATATT-GTTAT
1 ATATATACAT-TTAGTTAT
457652 TATGGTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (22 bp):
ATATATACATTTAGTTATAATC
Found at i:459591 original size:22 final size:22
Alignment explanation
Indices: 459582--459625 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
459572 CTATAATAGT
459582 ATGTATATATAGCTATAACTAA
1 ATGTATATATAGCTATAACTAA
**
459604 ATGTATATATAAATATAACTAA
1 ATGTATATATAGCTATAACTAA
459626 TACAAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
ATGTATATATAGCTATAACTAA
Found at i:459781 original size:30 final size:29
Alignment explanation
Indices: 459742--459823 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
459732 ACATATCAAT
459742 CACAAAATACAAATTAATATGAATATCCAC
1 CACAAAATACAAATTAATATGAATA-CCAC
* * * *
459772 CACATAATACTAATTATTATGAATACCAT
1 CACAAAATACAAATTAATATGAATACCAC
* *
459801 CACAAAATGCAAATTACTATGAA
1 CACAAAATACAAATTAATATGAA
459824 AACAAATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (29 bp):
CACAAAATACAAATTAATATGAATACCAC
Found at i:459816 original size:29 final size:30
Alignment explanation
Indices: 459734--459823 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
459724 AGATTAATAC
*
459734 ATATCAATCACAAAATACAAATTAATATGA
1 ATATCCATCACAAAATACAAATTAATATGA
* * * *
459764 ATATCCACCACATAATACTAATTATTATGA
1 ATATCCATCACAAAATACAAATTAATATGA
* *
459794 ATA-CCATCACAAAATGCAAATTACTATGA
1 ATATCCATCACAAAATACAAATTAATATGA
459823 A
1 A
459824 AACAAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 22 0.44
30 28 0.56
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (30 bp):
ATATCCATCACAAAATACAAATTAATATGA
Found at i:460708 original size:22 final size:22
Alignment explanation
Indices: 460683--460759 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
460673 TACCAAAAAA
* * *
460683 ATCACTATAATATTATGTATAT
1 ATCAATATAATAATATGTACAT
460705 ATCAATATAATAATATGTACAT
1 ATCAATATAATAATATGTACAT
* * *
460727 GTTAATATAATAATATATACAT
1 ATCAATATAATAATATGTACAT
*
460749 ATCACTATAAT
1 ATCAATATAAT
460760 TAAGAGTGCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (22 bp):
ATCAATATAATAATATGTACAT
Found at i:462041 original size:10 final size:10
Alignment explanation
Indices: 462022--462062 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
462012 AAATAATTAG
*
462022 ATTTAGATTT
1 ATTTAAATTT
462032 ATTTAAATTT
1 ATTTAAATTT
462042 AATTT-AATTT
1 -ATTTAAATTT
462052 ATTTAAATTT
1 ATTTAAATTT
462062 A
1 A
462063 AGTTCAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.14
10 20 0.71
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:462053 original size:20 final size:21
Alignment explanation
Indices: 462022--462074 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
462012 AAATAATTAG
462022 ATTTAGATTTATTTAAATTTA
1 ATTTAGATTTATTTAAATTTA
462043 ATTTA-ATTTATTTAAATTTA
1 ATTTAGATTTATTTAAATTTA
*
462063 AGTTCAGATTTA
1 A-TTTAGATTTA
462075 AATTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.55
21 8 0.28
22 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTTAGATTTATTTAAATTTA
Found at i:463284 original size:21 final size:21
Alignment explanation
Indices: 463239--463299 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
463229 TTAACTTTCA
* * *
463239 TTAAAAAATTATCATAATTA-
1 TTAAAATATTATTATATTTAT
463259 TTAAAATATT-TTATTATTTAT
1 TTAAAATATTATTA-TATTTAT
463280 TTAAAATATTATTATATTTA
1 TTAAAATATTATTATATTTA
463300 AAGGGCTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 2 0.06
20 14 0.40
21 16 0.46
22 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAAATATTATTATATTTAT
Found at i:463289 original size:16 final size:17
Alignment explanation
Indices: 463270--463301 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
463260 TAAAATATTT
463270 TATTATT-TATTTAAAA
1 TATTATTATATTTAAAA
463286 TATTATTATATTTAAA
1 TATTATTATATTTAAA
463302 GGGCTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATTATATTTAAAA
Found at i:463679 original size:10 final size:10
Alignment explanation
Indices: 463664--463738 Score: 60
Period size: 10 Copynumber: 7.0 Consensus size: 10
463654 ACTTTATCTA
463664 AATTTAAATT
1 AATTTAAATT
* *
463674 ATTTTATATT
1 AATTTAAATT
463684 AATTATTTAAATT
1 -A--ATTTAAATT
463697 AATTTAAATTT
1 AATTTAAA-TT
* *
463708 AAATTAATTT
1 AATTTAAATT
*
463718 ATATTTAAATC
1 A-ATTTAAATT
463729 AATTTAAATT
1 AATTTAAATT
463739 CAAATAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
10 26 0.52
11 16 0.32
12 1 0.02
13 7 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTTAAATT
Found at i:463709 original size:16 final size:16
Alignment explanation
Indices: 463688--463748 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
463678 TATATTAATT
463688 ATTTAAATTAATTTAA
1 ATTTAAATTAATTTAA
*
463704 ATTTAAATTAATTTAT
1 ATTTAAATTAATTTAA
*
463720 ATTTAAATCAATTTAA
1 ATTTAAATTAATTTAA
*
463736 ATTCAAA-TAATTT
1 ATTTAAATTAATTT
463749 TATTTCGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
15 5 0.12
16 35 0.88
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAATTAATTTAA
Found at i:463733 original size:32 final size:30
Alignment explanation
Indices: 463686--463753 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 30
463676 TTTATATTAA
* *
463686 TTATTTAAATTAATTTAAATTTAAATTAATT
1 TTATTTAAATCAATTTAAATTCAAA-TAATT
463717 TATATTTAAATCAATTTAAATTCAAATAATT
1 T-TATTTAAATCAATTTAAATTCAAATAATT
463748 TTATTT
1 TTATTT
463754 CGAACATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 5 0.15
31 7 0.21
32 22 0.65
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
TTATTTAAATCAATTTAAATTCAAATAATT
Found at i:465368 original size:20 final size:20
Alignment explanation
Indices: 465339--465379 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
465329 TCTATTTGAA
465339 TGTTTAAATAATTATATTAT
1 TGTTTAAATAATTATATTAT
*
465359 TGTTTGAATAATTATATTAT
1 TGTTTAAATAATTATATTAT
465379 T
1 T
465380 TGAGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TGTTTAAATAATTATATTAT
Found at i:465441 original size:20 final size:19
Alignment explanation
Indices: 465394--465449 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
465384 TATTATCATA
*
465394 AATGTAATCATATTAAATT
1 AATGTAATTATATTAAATT
*
465413 AGATATAATTATATTAAATT
1 A-ATGTAATTATATTAAATT
465433 GAATGTAATTATATTAA
1 -AATGTAATTATATTAA
465450 GTAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
AATGTAATTATATTAAATT
Found at i:465577 original size:20 final size:20
Alignment explanation
Indices: 465536--465592 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
465526 AATAATTATG
* *
465536 AATATTATTATA-TAATTTA
1 AATATAATTATATTAAATTA
465555 AATATAATTATATTAAATTA
1 AATATAATTATATTAAATTA
*
465575 AATATGAA-CATATTAAAT
1 AATAT-AATTATATTAAAT
465593 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.33
20 20 0.61
21 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AATATAATTATATTAAATTA
Found at i:473753 original size:16 final size:16
Alignment explanation
Indices: 473734--473789 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
473724 AATTTTTAAA
473734 TAATTAAATTAAATTT
1 TAATTAAATTAAATTT
* *
473750 TAATT-ATTTAAAAATT
1 TAATTAAATT-AAATTT
*
473766 AAATTAAATTAAATTT
1 TAATTAAATTAAATTT
*
473782 TAAATAAA
1 TAATTAAA
473790 AACTTTTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTAAATTAAATTT
Found at i:473765 original size:27 final size:27
Alignment explanation
Indices: 473719--473788 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
473709 TTTTCCTTTT
473719 ATTTAAATTTTTAAATAATTAAATTAA
1 ATTTAAATTTTTAAATAATTAAATTAA
*
473746 ATTTTAATTATTTAAA-AATTAAATTAA
1 ATTTAAATT-TTTAAATAATTAAATTAA
473773 A-TTAAA-TTTTAAATAA
1 ATTTAAATTTTTAAATAA
473789 AAACTTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 6 0.15
25 3 0.08
26 4 0.10
27 20 0.51
28 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTAAATTTTTAAATAATTAAATTAA
Found at i:476239 original size:3 final size:3
Alignment explanation
Indices: 476231--476283 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
476221 AACTAAAACG
476231 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
476279 TAT TA
1 TAT TA
476284 AAGAATATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:476384 original size:8 final size:8
Alignment explanation
Indices: 476373--476436 Score: 74
Period size: 8 Copynumber: 8.0 Consensus size: 8
476363 AAAGACAGGT
*
476373 TATATATA
1 TATATATG
476381 TATATATG
1 TATATATG
*
476389 TATGTATG
1 TATATATG
*
476397 TATGTATG
1 TATATATG
*
476405 TATATATA
1 TATATATG
476413 TATATATG
1 TATATATG
*
476421 TATGTATG
1 TATATATG
*
476429 TATGTATG
1 TATATATG
476437 AATGTTTGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:476414 original size:32 final size:32
Alignment explanation
Indices: 476373--476436 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
476363 AAAGACAGGT
476373 TATATATATATATATGTATGTATGTATGTATG
1 TATATATATATATATGTATGTATGTATGTATG
476405 TATATATATATATATGTATGTATGTATGTATG
1 TATATATATATATATGTATGTATGTATGTATG
476437 AATGTTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (32 bp):
TATATATATATATATGTATGTATGTATGTATG
Found at i:476420 original size:28 final size:28
Alignment explanation
Indices: 476377--476435 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
476367 ACAGGTTATA
*
476377 TATATATATATGTATGTATGTATGTATG
1 TATATATATATATATGTATGTATGTATG
476405 TATATATATATATATGTATGTATGTATG
1 TATATATATATATATGTATGTATGTATG
476433 TAT
1 TAT
476436 GAATGTTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (28 bp):
TATATATATATATATGTATGTATGTATG
Found at i:476424 original size:4 final size:4
Alignment explanation
Indices: 476385--476441 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
476375 TATATATATA
* * *
476385 TATG TATG TATG TATG TATG TATA TATA TATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
476433 TATG AATG T
1 TATG TATG T
476442 TTGCAGATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:476944 original size:2 final size:2
Alignment explanation
Indices: 476937--476981 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
476927 CCAAATACGT
* * *
476937 TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
476979 TA T
1 TA T
476982 TTATTATGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:476958 original size:12 final size:12
Alignment explanation
Indices: 476936--476981 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
476926 TCCAAATACG
476936 TTATATATATAT
1 TTATATATATAT
* *
476948 ATATATTTATAT
1 TTATATATATAT
476960 TTATATATATAT
1 TTATATATATAT
476972 TTATATATAT
1 TTATATATAT
476982 TTATTATGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATATATATAT
Found at i:482949 original size:13 final size:13
Alignment explanation
Indices: 482931--482959 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
482921 CAATTCTTCA
482931 TGTATCGATACAT
1 TGTATCGATACAT
482944 TGTATCGATACAT
1 TGTATCGATACAT
482957 TGT
1 TGT
482960 TCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:484990 original size:21 final size:21
Alignment explanation
Indices: 484964--485004 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
484954 CGAAGAAAAA
484964 GCACGTTGAGTGCGT-TTTTGT
1 GCACGTTGAGTG-GTGTTTTGT
484985 GCACGTTGAGTGGTGTTTTG
1 GCACGTTGAGTGGTGTTTTG
485005 GTGTTAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.10, C:0.12, G:0.37, T:0.41
Consensus pattern (21 bp):
GCACGTTGAGTGGTGTTTTGT
Found at i:490286 original size:169 final size:169
Alignment explanation
Indices: 490007--490333 Score: 600
Period size: 169 Copynumber: 1.9 Consensus size: 169
489997 CTTGAATGCA
* * *
490007 TGAATTTTTCAAAAATTAATCCAGGTTTTGATAAAAATTTTAATCTCATATGCGCCCTAGAAAGA
1 TGAATTTTCCAAAAATTAATCCAGGTTTTGATAAAAAATTTAATCTCATATGCACCCTAGAAAGA
490072 TGGGGAACATAGAAACATAAAATGACCTCTGGATTTTACTTTGAAAATTGAGTATTCTGTGTCAA
66 TGGGGAACATAGAAACATAAAATGACCTCTGGATTTTACTTTGAAAATTGAGTATTCTGTGTCAA
490137 GCACTGGAGAGATACCGGCACGGAACATAAAATGACCTC
131 GCACTGGAGAGATACCGGCACGGAACATAAAATGACCTC
*
490176 TGAATTTTCCAAAAATTAATCCAGGTTTTGATAAAAAATTTAATCTCATATGCATCCTAGAAAGA
1 TGAATTTTCCAAAAATTAATCCAGGTTTTGATAAAAAATTTAATCTCATATGCACCCTAGAAAGA
*
490241 TGGGGAACATAGAGACATAAAATGACCTCTGGATTTTACTTTGAAAATTGAGTATTCTGTGTCAA
66 TGGGGAACATAGAAACATAAAATGACCTCTGGATTTTACTTTGAAAATTGAGTATTCTGTGTCAA
*
490306 GCACTGGAGTGATACCGGCACGGAACAT
131 GCACTGGAGAGATACCGGCACGGAACAT
490334 TGCCTTTACA
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 152 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (169 bp):
TGAATTTTCCAAAAATTAATCCAGGTTTTGATAAAAAATTTAATCTCATATGCACCCTAGAAAGA
TGGGGAACATAGAAACATAAAATGACCTCTGGATTTTACTTTGAAAATTGAGTATTCTGTGTCAA
GCACTGGAGAGATACCGGCACGGAACATAAAATGACCTC
Found at i:492936 original size:20 final size:20
Alignment explanation
Indices: 492905--493036 Score: 102
Period size: 20 Copynumber: 6.0 Consensus size: 20
492895 ATGCTTAATT
492905 TTAAATAAATGTATCGATACA
1 TTAAA-AAATGTATCGATACA
492926 TTAAAAAATGTATCGATACA
1 TTAAAAAATGTATCGATACA
492946 TCAGCGTAAAAATATAAATGTATCGATACA
1 T-----T---AA-A-AAATGTATCGATACA
* * *
492976 CTGAAGAATGTATCGATACA
1 TTAAAAAATGTATCGATACA
* * *
492996 TTCATACATGTATCGATACA
1 TTAAAAAATGTATCGATACA
*
493016 TTGAAAAATGTATCGATACA
1 TTAAAAAATGTATCGATACA
493036 T
1 T
493037 CTGGTAAAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
20 63 0.70
21 6 0.07
22 1 0.01
25 2 0.02
28 2 0.02
29 1 0.01
30 15 0.17
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
TTAAAAAATGTATCGATACA
Found at i:492969 original size:50 final size:48
Alignment explanation
Indices: 492909--493065 Score: 170
Period size: 50 Copynumber: 3.4 Consensus size: 48
492899 TTAATTTTAA
* *
492909 ATAAATGTATCGATACATTAAAAAATGTATCGATACATCAGCGTAAAAAT
1 ATAAATGTATCGATACATTGAAAAATGTATCGATACATC-G-GTAAAAAC
* *
492959 ATAAATGTATCGATACACTGAAGAATGTATCGATACAT---T-----C
1 ATAAATGTATCGATACATTGAAAAATGTATCGATACATCGGTAAAAAC
*
492999 ATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGTAAAAGAC
1 ATAAATGTATCGATACATTGAAAAATGTATCGATACATC-GGTAAAA-AC
493049 A-AAATGTATCGATACAT
1 ATAAATGTATCGATACAT
493066 CTGGGTAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
40 35 0.39
44 1 0.01
45 1 0.01
49 15 0.17
50 37 0.42
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (48 bp):
ATAAATGTATCGATACATTGAAAAATGTATCGATACATCGGTAAAAAC
Found at i:493885 original size:30 final size:28
Alignment explanation
Indices: 493747--494209 Score: 446
Period size: 30 Copynumber: 15.5 Consensus size: 28
493737 CACCAACTTG
*
493747 TGTGGGCTTTAGAGAAGGTTGCCACTAACTT
1 TGTGGGCTTT-GA-AAGGTTGCCACTGAC-T
* *
493778 GTGTGGGCTTTAGAAGGGTTACCACTGACT
1 -TGTGGGCTTT-GAAAGGTTGCCACTGACT
*
493808 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACT
493836 TGTGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACT
* *
493864 TGTGGGTTTTGAGAGAGGTTGCCACCGACT
1 TGTGGGCTTTGA-A-AGGTTGCCACTGACT
* *
493894 TGTATGGGCTTT-AAGGGGTTGCCACCGACT
1 TG--TGGGCTTTGAA-AGGTTGCCACTGACT
493924 TGTGGGCTTTGAGAGAGGTTGCCA-TCGACTT
1 TGTGGGCTTTGA-A-AGGTTGCCACT-GAC-T
* *
493955 GTGTGGGCTTTGAAAAGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGTTGCCACTGACT
*
493984 TGTGAGCTTTGATAGAGGTTGCCACTGACTT
1 TGTGGGCTTTGA-A-AGGTTGCCACTGAC-T
* * *
494015 GTGTGGGCTTTGAAATGATGCTACTGACT
1 -TGTGGGCTTTGAAAGGTTGCCACTGACT
* *
494044 TATGGGCTTTGAGAGAGGTTGCCACCGACTT
1 TGTGGGCTTTGA-A-AGGTTGCCACTGAC-T
*
494075 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGTTGCCACTGACT
*
494104 TGTGGGCTTTGAGAGAGGTTGCCACCGACT
1 TGTGGGCTTTGA-A-AGGTTGCCACTGACT
*
494134 TGTGTGGACTTTGAAAGGATGCCACTGACT
1 TGTG-GG-CTTTGAAAGGTTGCCACTGACT
494164 TGTGGGCTTTGAGAAAGGTTGCCA-TCGACTT
1 TGTGGGCTTT--GAAAGGTTGCCACT-GAC-T
494195 GTGTGGGCTTTGAAA
1 -TGTGGGCTTTGAAA
494210 AGGGTCGTAT
Statistics
Matches: 369, Mismatches: 35, Indels: 56
0.80 0.08 0.12
Matches are distributed among these distances:
28 99 0.27
29 21 0.06
30 155 0.42
31 24 0.07
32 70 0.19
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGTTGCCACTGACT
Found at i:493924 original size:60 final size:60
Alignment explanation
Indices: 493747--494209 Score: 641
Period size: 60 Copynumber: 7.8 Consensus size: 60
493737 CACCAACTTG
** * * *
493747 TGTGGGCTTT-AGAGAAGGTTGCCACTAACTTGTGTGGGCTTTAGAAGGGTTACCACTGACT
1 TGTGGGCTTTGAGAG-AGGTTGCCACCGACTTGTGTGGGCTTT-GAAAGGATGCCACTGACT
* * *
493808 TGTGGGCTTTGA-A-AGGGTGCCACTGAC-T-TGTGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
493864 TGTGGGTTTTGAGAGAGGTTGCCACCGACTTGTATGGGCTTT-AAGGGGTTGCCACCGACT
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAA-AGGATGCCACTGACT
* *
493924 TGTGGGCTTTGAGAGAGGTTGCCATCGACTTGTGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
493984 TGTGAGCTTTGATAGAGGTTGCCACTGACTTGTGTGGGCTTTGAAATGATGCTACTGACT
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
*
494044 TATGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
*
494104 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
* *
494164 TGTGGGCTTTGAGAAAGGTTGCCATCGACTTGTGTGGGCTTTGAAA
1 TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAA
494210 AGGGTCGTAT
Statistics
Matches: 361, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
56 27 0.07
57 11 0.03
58 13 0.04
59 15 0.04
60 281 0.78
61 13 0.04
62 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (60 bp):
TGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:509497 original size:13 final size:13
Alignment explanation
Indices: 509479--509516 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
509469 ATAATCCCCC
509479 TGTATCGATACAG
1 TGTATCGATACAG
*
509492 TGTATCGATACAT
1 TGTATCGATACAG
509505 TGTATCGATACA
1 TGTATCGATACA
509517 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:511617 original size:15 final size:15
Alignment explanation
Indices: 511597--511627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
511587 ATTTCGTTTG
*
511597 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
511612 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
511627 G
1 G
511628 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:513452 original size:21 final size:21
Alignment explanation
Indices: 513423--513467 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
513413 AAGTTTTTAT
*
513423 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAAGTTCATTA
*
513443 TTTTCATTAGCCAAGTTCTTTA
1 TTTTC-TTAGCCAAGTTCATTA
513465 TTT
1 TTT
513468 CAACTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAAGTTCATTA
Found at i:513467 original size:22 final size:21
Alignment explanation
Indices: 513412--513467 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
513402 ATGAATCATG
513412 CAAGTT-TTTATTTTTCTTAGC
1 CAAGTTCTTTA-TTTTCTTAGC
* *
513433 TAA-TTCATTATTTTCATTAGC
1 CAAGTTCTTTATTTTC-TTAGC
513454 CAAGTTCTTTATTT
1 CAAGTTCTTTATTT
513468 CAACTTGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 7 0.25
21 12 0.43
22 9 0.32
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.55
Consensus pattern (21 bp):
CAAGTTCTTTATTTTCTTAGC
Found at i:515696 original size:13 final size:13
Alignment explanation
Indices: 515678--515703 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
515668 CAATTTTTTG
515678 TGTATCGATACAT
1 TGTATCGATACAT
515691 TGTATCGATACAT
1 TGTATCGATACAT
515704 ACTTGGTGTA
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:515718 original size:32 final size:33
Alignment explanation
Indices: 515658--515722 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
515648 TACAAGCCAA
** *
515658 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
515691 TGTATCGATAC-ATACTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
515723 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:519322 original size:51 final size:51
Alignment explanation
Indices: 519265--519410 Score: 215
Period size: 50 Copynumber: 2.9 Consensus size: 51
519255 TTTTAACTAG
* *
519265 ATATATCAATACATTGAAAAATGTATCGATACATCTGAGTAAAAAGACAGA
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGAGTAAAAAGACAAA
* *
519316 ATATATCGATATATTGAAGAATGTATCGATACATCT-AGGT-AAAAGACAAA
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGA-GTAAAAAGACAAA
* *
519366 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGAGTAAAAA
519411 TGTGACTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
50 45 0.54
51 39 0.46
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (51 bp):
ATATATCGATACATTGAAAAATGTATCGATACATCTGAGTAAAAAGACAAA
Found at i:520517 original size:20 final size:20
Alignment explanation
Indices: 520483--520539 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
520473 GTCAAAACCC
* *
520483 TGAAAAGTATTGATACACAT
1 TGAAATGTATCGATACACAT
* *
520503 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
520523 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
520540 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:520543 original size:13 final size:13
Alignment explanation
Indices: 520525--520553 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
520515 ATACAGATTG
520525 CATTGTATCGATA
1 CATTGTATCGATA
520538 CATTGTATCGATA
1 CATTGTATCGATA
520551 CAT
1 CAT
520554 GATCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:520566 original size:20 final size:21
Alignment explanation
Indices: 520541--520593 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
520531 ATCGATACAT
**
520541 TGTATCGATACATGATCAA-A
1 TGTATCGATACATGAAAAAGA
*
520561 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
520582 TGTATCGATACA
1 TGTATCGATACA
520594 GGTCATTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:520689 original size:33 final size:32
Alignment explanation
Indices: 520628--520691 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
520618 GCTAAATTTG
*
520628 TATCGATACACACAATATGTATCAATACATTA
1 TATCGATACACACAAAATGTATCAATACATTA
* *
520660 TATCGATACACCATAAAATGTATCGATACATT
1 TATCGATACA-CACAAAATGTATCAATACATT
520692 GGCTTGTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (32 bp):
TATCGATACACACAAAATGTATCAATACATTA
Found at i:524475 original size:32 final size:32
Alignment explanation
Indices: 524439--524503 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
524429 TTCAACGATT
524439 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
** *
524471 TGTATCGATACATATTTTTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
524503 T
1 T
524504 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:524476 original size:13 final size:13
Alignment explanation
Indices: 524458--524482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524448 ACATAAATGT
524458 TGTATCGATACAA
1 TGTATCGATACAA
524471 TGTATCGATACA
1 TGTATCGATACA
524483 TATTTTTTGT
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:524563 original size:13 final size:13
Alignment explanation
Indices: 524545--524569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524535 ATTACTCACA
524545 TGTATCGATACAT
1 TGTATCGATACAT
524558 TGTATCGATACA
1 TGTATCGATACA
524570 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:524634 original size:52 final size:51
Alignment explanation
Indices: 524578--524754 Score: 282
Period size: 52 Copynumber: 3.4 Consensus size: 51
524568 CACTGATCTT
524578 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTATAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTA-AA
* * *
524630 TGTATCGATACATGCAGGAAAATTTACCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATT-TTAAA
*
524682 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA-TTTTAAA
*
524734 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
524755 CTTTTCATAT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
52 112 0.97
53 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTAAA
Found at i:528022 original size:21 final size:21
Alignment explanation
Indices: 527997--528039 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
527987 CATGTCAGGA
527997 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
528018 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
528039 G
1 G
528040 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:531706 original size:16 final size:16
Alignment explanation
Indices: 531687--531719 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
531677 AGCCAAAAGT
531687 AAACACAAA-AAAAAAA
1 AAACA-AAACAAAAAAA
531703 AAACAAAACAAAAAAA
1 AAACAAAACAAAAAAA
531719 A
1 A
531720 GTGCAAAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAACAAAACAAAAAAA
Found at i:531708 original size:14 final size:15
Alignment explanation
Indices: 531691--531719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
531681 AAAAGTAAAC
531691 ACAAAA-AAAAAAAA
1 ACAAAACAAAAAAAA
531705 ACAAAACAAAAAAAA
1 ACAAAACAAAAAAAA
531720 GTGCAAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAACAAAAAAAA
Found at i:531988 original size:16 final size:16
Alignment explanation
Indices: 531957--532002 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
531947 TTTCTTTTCC
531957 AAACACAAAAA-AAAAA
1 AAACA-AAAAAGAAAAA
*
531973 AGA-AAAAAAGAAAAA
1 AAACAAAAAAGAAAAA
*
531988 AAACAAAATAGAAAA
1 AAACAAAAAAGAAAA
532003 TCTCGGTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 12 0.48
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.02
Consensus pattern (16 bp):
AAACAAAAAAGAAAAA
Found at i:532090 original size:1 final size:1
Alignment explanation
Indices: 532044--532082 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
532034 TAATCTTCAC
* *
532044 AAAAAAAAAAAAAAAAAAAAAAACAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
532083 GGGAAAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:533164 original size:34 final size:34
Alignment explanation
Indices: 533098--533260 Score: 197
Period size: 33 Copynumber: 4.8 Consensus size: 34
533088 TTTTTCTTTA
*
533098 AAGCCCACAACTACGTGGCACTC-TTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
533131 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
533165 AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACTC--TTTTTCC-TTCT
* * * *
533202 AAAGCCCACAACTCTGTGGCAC-CTTGTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
533236 AAGTCCACAACTTCGTGGCA-TCTTT
1 AAGCCCACAACTCCGTGGCACTCTTT
533261 CACCCTTTCT
Statistics
Matches: 115, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
33 42 0.37
34 37 0.32
35 5 0.04
36 7 0.06
37 4 0.03
38 20 0.17
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
Found at i:533293 original size:71 final size:72
Alignment explanation
Indices: 533098--533280 Score: 211
Period size: 71 Copynumber: 2.7 Consensus size: 72
533088 TTTTTCTTTA
* *
533098 AAGCCCACAACTACGTGGCACTCTTTT---CC-TTCT-AAGCCCACAACTCCGTGGCACTCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTCACCCTTTCTAAAGCCCACAACTCCGTGGCACTCTTGT
533158 TCCTTCT
66 TCCTTCT
*** * *
533165 AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCAC-CTTGT
1 AAGCCCACAACTCCGTGGCACTCTTTTCACCCTTTCTAAAGCCCACAACTCCGTGGCACTCTTGT
* *
533229 TCTTTTT
66 TCCTTCT
* *
533236 AAGTCCACAACTTCGTGGCA-TC-TTTCACCCTTTCTAAAGCCCACA
1 AAGCCCACAACTCCGTGGCACTCTTTTCACCCTTTCTAAAGCCCACA
533281 CAAGTCGGTG
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
67 26 0.26
69 19 0.19
70 4 0.04
71 30 0.30
72 20 0.20
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (72 bp):
AAGCCCACAACTCCGTGGCACTCTTTTCACCCTTTCTAAAGCCCACAACTCCGTGGCACTCTTGT
TCCTTCT
Found at i:533365 original size:49 final size:48
Alignment explanation
Indices: 533301--533966 Score: 846
Period size: 49 Copynumber: 14.2 Consensus size: 48
533291 GCAACCCTTC
* *
533301 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTATCTT
* * *
533350 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
*
533399 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTATCTT
* *
533448 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* *
533491 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATATT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTATCTT
* *
533540 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTATCTT
*
533589 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C---T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* *
533632 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
* *
533681 T--GTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCA-C---T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* *
533722 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
*
533771 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C---T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* *
533814 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
*
533863 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C---T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
*
533906 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTATCTT
533955 TAAGTCCAATAT
1 TAAGTCCAATAT
533967 CGCTAGCCGC
Statistics
Matches: 541, Mismatches: 42, Indels: 68
0.83 0.06 0.10
Matches are distributed among these distances:
41 3 0.01
42 1 0.00
43 186 0.34
44 8 0.01
46 1 0.00
47 32 0.06
48 10 0.02
49 298 0.55
50 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (48 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
Found at i:533506 original size:43 final size:43
Alignment explanation
Indices: 533445--533950 Score: 562
Period size: 43 Copynumber: 11.1 Consensus size: 43
533435 GCACCTTTAT
*
533445 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
533488 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
533531 CTTTATATTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC
1 C------TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
533581 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 -----CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
533629 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
** *
533672 CTTCATCTTTGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 C-T--T-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
533719 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C
533766 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
533811 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C
533858 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
533903 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
533946 CTTTA
1 CTTTA
533951 TCTTTAAGTC
Statistics
Matches: 394, Mismatches: 41, Indels: 56
0.80 0.08 0.11
Matches are distributed among these distances:
43 195 0.49
44 2 0.01
45 2 0.01
46 2 0.01
47 36 0.09
48 1 0.00
49 154 0.39
50 1 0.00
55 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:533569 original size:141 final size:141
Alignment explanation
Indices: 533301--533966 Score: 874
Period size: 141 Copynumber: 4.7 Consensus size: 141
533291 GCAACCCTTC
* * * * *
533301 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATAGCT
* *
533366 GGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
60 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAC
533431 ATTGGCACCTTTATCTT
125 ATTGGCACCTTTATCTT
*
533448 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
* * * * *
533513 GAATCAGCATATTGGCACCTTTATATTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC
533578 ACCTTTATCTT
131 ACCTTTATCTT
* *
533589 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
* * *
533654 GAATCAGCATATTGGCACCTTCATCTTT--GTCCAATGTAGCTGGCCTTGAATCAGCACATTAGC
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC
533717 A-C----T-TT
131 ACCTTTATCTT
* * * *
533722 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
* *
533787 GGCCTTGAATCAGCACATTGGCA----C-T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
60 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAC
*
533846 ATTGGCACCTTCATCTT
125 ATTGGCACCTTTATCTT
* *
533863 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
*
533928 GAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATAT
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
533967 CGCTAGCCGC
Statistics
Matches: 461, Mismatches: 38, Indels: 46
0.85 0.07 0.08
Matches are distributed among these distances:
133 41 0.09
134 2 0.00
135 72 0.16
136 1 0.00
137 2 0.00
138 1 0.00
139 72 0.16
140 2 0.00
141 232 0.50
146 1 0.00
147 35 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (141 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC
ACCTTTATCTT
Found at i:533998 original size:92 final size:91
Alignment explanation
Indices: 533348--533964 Score: 791
Period size: 92 Copynumber: 6.7 Consensus size: 91
533338 CACCTTTATC
* * * * * *
533348 TTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
533413 CTGGCCTTGAATCAGCATATTGGCACCTTTAT
66 CTGGCC-TGAATCAGCACATTAGCA-C----T
* * * * *
533445 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTTTAAGTCCAATATA
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
533504 GCTGGCCTTGAATCAGCATATTGGCACCTTTAT
65 GCTGGCC-TGAATCAGCACATTAGCA-C----T
* * * * *
533537 ATTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTA
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
533602 GCTGGCCTTGAATCAGCACATTGGCACT
65 GCTGGCC-TGAATCAGCACATTAGCACT
533630 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTT--GTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
533693 CTGGCCTTGAATCAGCACATTAGCACT
66 CTGGCC-TGAATCAGCACATTAGCACT
533720 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
533785 CTGGCCTTGAATCAGCACATTGGCACT
66 CTGGCC-TGAATCAGCACATTAGCACT
533812 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
533877 CTGGCCTTGAATCAGCACATTGGCACT
66 CTGGCC-TGAATCAGCACATTAGCACT
* *
533904 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
533965 ATCGCTAGCC
Statistics
Matches: 497, Mismatches: 14, Indels: 22
0.93 0.03 0.04
Matches are distributed among these distances:
90 89 0.18
92 325 0.65
93 1 0.00
94 1 0.00
97 1 0.00
98 80 0.16
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (91 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTGAATCAGCACATTAGCACT
Found at i:534709 original size:13 final size:13
Alignment explanation
Indices: 534691--534715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534681 CATAAAATGT
534691 TGTATCGATACAA
1 TGTATCGATACAA
534704 TGTATCGATACA
1 TGTATCGATACA
534716 TATTTTTTTG
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:534713 original size:33 final size:33
Alignment explanation
Indices: 534671--534737 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
534661 TTCAACGATT
534671 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
534704 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
534737 T
1 T
534738 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:534797 original size:13 final size:13
Alignment explanation
Indices: 534779--534803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534769 ATTACTCACA
534779 TGTATCGATACAT
1 TGTATCGATACAT
534792 TGTATCGATACA
1 TGTATCGATACA
534804 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:534868 original size:52 final size:51
Alignment explanation
Indices: 534812--534988 Score: 300
Period size: 52 Copynumber: 3.4 Consensus size: 51
534802 CACTGATCTT
534812 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTATAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTA-AA
*
534864 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATT-TTAAA
*
534916 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA-TTTTAAA
*
534968 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
534989 CTTTTCATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
52 116 0.97
53 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTTAAA
Found at i:540800 original size:13 final size:13
Alignment explanation
Indices: 540781--540819 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
540771 ACAGCATTCT
540781 CTGTATCGATACA
1 CTGTATCGATACA
*
540794 TTGTATCGATACA
1 CTGTATCGATACA
*
540807 CAGTATCGATACA
1 CTGTATCGATACA
540820 AGGAGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:540986 original size:20 final size:20
Alignment explanation
Indices: 540951--540991 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
540941 CAAAATTCTT
540951 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
540973 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
540992 AACAAAAACA
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 (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:543303 original size:20 final size:20
Alignment explanation
Indices: 543254--543311 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
543244 GGTCAAAACC
*
543254 TTGAAAAGTATCGATACACA
1 TTGAAATGTATCGATACACA
* *
543274 TTTAAATGTATCGATACAGA
1 TTGAAATGTATCGATACACA
* * *
543294 TTGCATTGTATCAATACA
1 TTGAAATGTATCGATACA
543312 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
TTGAAATGTATCGATACACA
Found at i:543338 original size:20 final size:21
Alignment explanation
Indices: 543313--543363 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
543303 ATCAATACAT
**
543313 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
543333 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
543354 TGTATCGATA
1 TGTATCGATA
543364 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:543435 original size:13 final size:13
Alignment explanation
Indices: 543417--543441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
543407 ACACACAATA
543417 TGTATCGATACAT
1 TGTATCGATACAT
543430 TGTATCGATACA
1 TGTATCGATACA
543442 CCACAAAATG
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:543438 original size:32 final size:33
Alignment explanation
Indices: 543397--543464 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
543387 ATAGCTAAAT
*
543397 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
543429 TTGTATCGATACACCACAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
543462 TTG
1 TTG
543465 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:546046 original size:33 final size:33
Alignment explanation
Indices: 546003--546069 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
545993 TTAGGCATAC
*
546003 TGTATCGATACAATTCT-TCATGTATCGATACAT
1 TGTATCGATAC-ATTCTCCCATGTATCGATACAT
* *
546036 TGTATGGATACATTGTCCCATGTATCGATACAT
1 TGTATCGATACATTCTCCCATGTATCGATACAT
546069 T
1 T
546070 TGACTTAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTCTCCCATGTATCGATACAT
Found at i:546141 original size:19 final size:20
Alignment explanation
Indices: 546097--546149 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
546087 TACCACTTTT
* **
546097 ATGTATCTATACAATTGAGT
1 ATGTATCAATACAATTGAAC
*
546117 ATGTATCGATACAA-TGAAC
1 ATGTATCAATACAATTGAAC
546136 ATGTATCAATACAA
1 ATGTATCAATACAA
546150 CGTATCGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGTATCAATACAATTGAAC
Found at i:550364 original size:20 final size:19
Alignment explanation
Indices: 550339--550378 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
550329 AGTTTGCATT
550339 AAAATAATTATAAATGTTAA
1 AAAAT-ATTATAAATGTTAA
* *
550359 AAAATATTTTTAATGTTAA
1 AAAATATTATAAATGTTAA
550378 A
1 A
550379 TAAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAATATTATAAATGTTAA
Found at i:550791 original size:13 final size:12
Alignment explanation
Indices: 550737--550827 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
550727 TCTTATTTCA
550737 TTTTATTTTATT
1 TTTTATTTTATT
* *
550749 TTTT-CTTTACT
1 TTTTATTTTATT
*
550760 TTTTA--CTACTT
1 TTTTATTTTA-TT
*
550771 ATTTATTTTATT
1 TTTTATTTTATT
550783 TTCTTA-TTTATT
1 TT-TTATTTTATT
*
550795 TTTTGTTTTCATT
1 TTTTATTTT-ATT
*
550808 TTTT-TTATATT
1 TTTTATTTTATT
*
550819 TATTATTTT
1 TTTTATTTT
550828 TGTTTAATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
10 2 0.03
11 22 0.37
12 24 0.40
13 12 0.20
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:550812 original size:28 final size:29
Alignment explanation
Indices: 550787--550841 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
550777 TTTATTTTCT
*
550787 TATTTA-T-TTTTTGTTTTCATTTTTTTTA
1 TATTTATTATTTTTG-TTTAATTTTTTTTA
550815 TATTTATTATTTTTGTTTAATTTTTTT
1 TATTTATTATTTTTGTTTAATTTTTTT
550842 AATAATTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 12 0.50
30 6 0.25
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (29 bp):
TATTTATTATTTTTGTTTAATTTTTTTTA
Found at i:550814 original size:34 final size:35
Alignment explanation
Indices: 550730--550826 Score: 92
Period size: 34 Copynumber: 2.7 Consensus size: 35
550720 TAAGTTTTCT
*
550730 TATTTCATTTTATTTTATTTTTTCTTTACTTTTTAC
1 TATTTCATTTT-TTTTATTTTTTATTTACTTTTTAC
* * **
550766 TACTT-ATTTATTTTATTTTCTTATTTA-TTTTTTG
1 TATTTCATTTTTTTTATTTT-TTATTTACTTTTTAC
550800 T-TTTCATTTTTTTTATATTTATTATTT
1 TATTTCATTTTTTTTAT-TTT-TTATTT
550827 TTGTTTAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
33 2 0.04
34 25 0.50
35 19 0.38
36 4 0.08
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (35 bp):
TATTTCATTTTTTTTATTTTTTATTTACTTTTTAC
Found at i:559259 original size:16 final size:16
Alignment explanation
Indices: 559238--559271 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
559228 TATTGAATCA
559238 TAATTAAATTCTATTT
1 TAATTAAATTCTATTT
* *
559254 TAATTAATTTTTATTT
1 TAATTAAATTCTATTT
559270 TA
1 TA
559272 TAATATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTAAATTCTATTT
Found at i:572223 original size:53 final size:53
Alignment explanation
Indices: 572152--572257 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
572142 AACTAGTAAA
572152 AAGGTTAACAATCAATGTCTTCAACTTGATTATAACCTTTCGCCACTAGTCTG
1 AAGGTTAACAATCAATGTCTTCAACTTGATTATAACCTTTCGCCACTAGTCTG
* * * * *
572205 AAGGTTAATAATTAATGTCTTCAATTTGATTATAACCTTTTGCTACTAGTCTG
1 AAGGTTAACAATCAATGTCTTCAACTTGATTATAACCTTTCGCCACTAGTCTG
572258 GCCTTATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (53 bp):
AAGGTTAACAATCAATGTCTTCAACTTGATTATAACCTTTCGCCACTAGTCTG
Found at i:573934 original size:20 final size:20
Alignment explanation
Indices: 573892--573945 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
573882 GTTTGGGACA
* **
573892 ATGTATCGATACAATTTTTC
1 ATGTATCGATACAATGTACC
573912 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
* *
573932 ATGCACCGATACAA
1 ATGTATCGATACAA
573946 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:574763 original size:106 final size:106
Alignment explanation
Indices: 574577--574772 Score: 313
Period size: 106 Copynumber: 1.8 Consensus size: 106
574567 TTAAAGCCTT
* * * *
574577 GCCTAAAAATTTCTCCCTCTTTATAAACTAGTTAAGGCTTTCATTTTTTAAAAAGATCTTCAAGA
1 GCCTAAAAATTTCTCCCTCTTGATAAAATAATTAAGGCTCTCATTTTTTAAAAAGATCTTCAAGA
574642 TTTTCTCCCCCTTATTGTTATAAAAGGATTTTCTCCCCCTA
66 TTTTCTCCCCCTTATTGTTATAAAAGGATTTTCTCCCCCTA
* *
574683 GCCTAAAAATTTCTCCC-CATTGATAAAATAATTAAGGCTCTCCTTTTTTAAAAAGATTTTCAAG
1 GCCTAAAAATTTCTCCCTC-TTGATAAAATAATTAAGGCTCTCATTTTTTAAAAAGATCTTCAAG
*
574747 ATTTTCTCCCCTTTATTGTTATAAAA
65 ATTTTCTCCCCCTTATTGTTATAAAA
574773 ATTCTTTTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 1 0.01
106 81 0.99
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (106 bp):
GCCTAAAAATTTCTCCCTCTTGATAAAATAATTAAGGCTCTCATTTTTTAAAAAGATCTTCAAGA
TTTTCTCCCCCTTATTGTTATAAAAGGATTTTCTCCCCCTA
Found at i:575539 original size:16 final size:16
Alignment explanation
Indices: 575518--575548 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
575508 CAACATTTCC
*
575518 TCTATTAAAACTTTTT
1 TCTATTAAAAATTTTT
575534 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
575549 GAAAACCTTT
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:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTATTAAAAATTTTT
Done.