Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 40 of 198
Found at i:11967471 original size:20 final size:20
Alignment explanation
Indices: 11967417--11967471 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
11967407 CCTTATCAAA
* *
11967417 ATTTCTGAGACTTTACTAAT
1 ATTTCTGAAACTTTACCAAT
* *
11967437 ATATCT-AACAATTTACCAAT
1 ATTTCTGAA-ACTTTACCAAT
11967457 ATTTCTGAAACTTTA
1 ATTTCTGAAACTTTA
11967472 AGTGTCCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTTCTGAAACTTTACCAAT
Found at i:11967576 original size:40 final size:40
Alignment explanation
Indices: 11967532--11967653 Score: 181
Period size: 40 Copynumber: 3.0 Consensus size: 40
11967522 CTTCAACAAT
* *
11967532 ATATCTAATGATTTACCAATATTTTTAAGCATTTATCAAA
1 ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
* * *
11967572 ATATCTAACGATTTACCAAAATCTCTAAGAATTTATCAAA
1 ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
* *
11967612 ATATCTAAGGATTTACCAATATTTCTAAGCATTTACCAAA
1 ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
11967652 AT
1 AT
11967654 TTCTTAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.37
Consensus pattern (40 bp):
ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
Found at i:11967648 original size:195 final size:195
Alignment explanation
Indices: 11967298--11967657 Score: 433
Period size: 195 Copynumber: 1.8 Consensus size: 195
11967288 TCGATTGACA
* * *
11967298 CATCTAAGCCTTTACCAAAATTTTTGAGACTTTACCAACATTTCTAACAATTTACCAAAATTTCT
1 CATCTAAGCCTTTACCAAAATTTTTGAGACTTCAACAACATATCTAACAATTTACCAAAATTTCT
** * * * ** * *
11967363 AAGGTTTTACTAAAATATCAGAGGATTTACTAATATTCCCAAGCCCTTATCAAAATTTCTGAGAC
66 AAGCATTTACTAAAATATCAGACGATTTACCAAAATTCCCAAGAACTTATCAAAATATCTAAGAC
* *
11967428 TTTACTAATATATCTAACAATTTACCAATATTTCTGAAACTTTAAGTGTCCCATACTCATCAACG
131 TTTACCAATATATCTAACAATTTACCAAAATTTCTGAAACTTTAAGTGTCCCATACTCATCAACG
* * ** * *
11967493 CATCTAAGCCTTTACCAATATTTTTGAGACTTCAACAATATATCTAATGATTTACCAATATTTTT
1 CATCTAAGCCTTTACCAAAATTTTTGAGACTTCAACAACATATCTAACAATTTACCAAAATTTCT
* *
11967558 AAGCATTTA-TCAAAATATCTA-ACGATTTACCAAAA-TCTCTAAGAATTTATCAAAATATCTAA
66 AAGCATTTACT-AAAATATC-AGACGATTTACCAAAATTC-CCAAGAACTTATCAAAATATCTAA
*
11967620 GGA-TTTACCAATATTTCTAAGC-ATTTACCAAAATTTCT
128 -GACTTTACCAATATATCTAA-CAATTTACCAAAATTTCT
11967658 TAAAAAGTAA
Statistics
Matches: 137, Mismatches: 23, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
194 3 0.02
195 130 0.95
196 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (195 bp):
CATCTAAGCCTTTACCAAAATTTTTGAGACTTCAACAACATATCTAACAATTTACCAAAATTTCT
AAGCATTTACTAAAATATCAGACGATTTACCAAAATTCCCAAGAACTTATCAAAATATCTAAGAC
TTTACCAATATATCTAACAATTTACCAAAATTTCTGAAACTTTAAGTGTCCCATACTCATCAACG
Found at i:11967655 original size:20 final size:20
Alignment explanation
Indices: 11967542--11967657 Score: 126
Period size: 20 Copynumber: 5.8 Consensus size: 20
11967532 ATATCTAATG
* *
11967542 ATTTACCAATATTTTTAAGC
1 ATTTACCAAAATTTCTAAGC
* *
11967562 ATTTATCAAAATATCTAA-C
1 ATTTACCAAAATTTCTAAGC
* *
11967581 GATTTACCAAAATCTCTAAGA
1 -ATTTACCAAAATTTCTAAGC
* * *
11967602 ATTTATCAAAATATCTAAGG
1 ATTTACCAAAATTTCTAAGC
*
11967622 ATTTACCAATATTTCTAAGC
1 ATTTACCAAAATTTCTAAGC
11967642 ATTTACCAAAATTTCT
1 ATTTACCAAAATTTCT
11967658 TAAAAAGTAA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 78 0.99
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTACCAAAATTTCTAAGC
Found at i:11967748 original size:20 final size:21
Alignment explanation
Indices: 11967719--11967760 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11967709 TATTTATAAC
*
11967719 AATTTGTC-AAATTATTAAAG
1 AATTTATCAAAATTATTAAAG
*
11967739 AATTTATCAAAATTTTTAAAG
1 AATTTATCAAAATTATTAAAG
11967760 A
1 A
11967761 TTTGCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
AATTTATCAAAATTATTAAAG
Found at i:11967769 original size:20 final size:21
Alignment explanation
Indices: 11967727--11967771 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11967717 ACAATTTGTC
*
11967727 AAATTATTAAAGAATTTATCA
1 AAATTATTAAAGAATTTACCA
* *
11967748 AAATTTTTAAAG-ATTTGCCA
1 AAATTATTAAAGAATTTACCA
11967768 AAAT
1 AAAT
11967772 ATTTGAGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATTATTAAAGAATTTACCA
Found at i:11967960 original size:20 final size:20
Alignment explanation
Indices: 11967936--11968078 Score: 85
Period size: 20 Copynumber: 7.2 Consensus size: 20
11967926 TAATCTTTCT
11967936 CCAAAATTTCTAAGGATTTA
1 CCAAAATTTCTAAGGATTTA
* * * *
11967956 TCAAAATGTCTAAGTATTAA
1 CCAAAATTTCTAAGGATTTA
*
11967976 CCAATATTTCTAAGGATTTA
1 CCAAAATTTCTAAGGATTTA
* * * *
11967996 CCTAAATATCCAAGTA-TTA
1 CCAAAATTTCTAAGGATTTA
* * * * *
11968015 TCAGAA-TACCAAAGAGTTTA
1 CCAAAATTTCTAAGGA-TTTA
* *
11968035 CCAATATTTCTAAGTATTTA
1 CCAAAATTTCTAAGGATTTA
* *
11968055 TCAAAATATCTAA-GACTTTA
1 CCAAAATTTCTAAGGA-TTTA
11968075 CCAA
1 CCAA
11968079 TGTTTACCAA
Statistics
Matches: 86, Mismatches: 33, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
18 5 0.06
19 7 0.08
20 69 0.80
21 5 0.06
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.34
Consensus pattern (20 bp):
CCAAAATTTCTAAGGATTTA
Found at i:11968075 original size:40 final size:40
Alignment explanation
Indices: 11967937--11968079 Score: 114
Period size: 40 Copynumber: 3.6 Consensus size: 40
11967927 AATCTTTCTC
* * * * * *
11967937 CAAAATTTCTAAGGATTTATCAAAATGTCTAAGTATTAAC
1 CAAAATATCTAAGGATTTACCAATATATCTAAGTATTTAT
* * *
11967977 CAATATTTCTAAGGATTTACCTAA-ATATCCAAGTA-TTAT
1 CAAAATATCTAAGGATTTACC-AATATATCTAAGTATTTAT
* * * *
11968016 CAGAATA-CCAAAGAGTTTACCAATATTTCTAAGTATTTAT
1 CAAAATATCTAAGGA-TTTACCAATATATCTAAGTATTTAT
11968056 CAAAATATCTAA-GACTTTACCAAT
1 CAAAATATCTAAGGA-TTTACCAAT
11968080 GTTTACCAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
38 7 0.09
39 21 0.26
40 49 0.60
41 5 0.06
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (40 bp):
CAAAATATCTAAGGATTTACCAATATATCTAAGTATTTAT
Found at i:11968341 original size:20 final size:20
Alignment explanation
Indices: 11968295--11968356 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
11968285 GCATCTAGGT
11968295 TTTACCAAAATTTTAGAGAC
1 TTTACCAAAATTTTAGAGAC
* * *
11968315 TTCACCAATATTTATAGTGA-
1 TTTACCAAAATTT-TAGAGAC
* *
11968335 TTTACCATAATGTTTAAAGAC
1 TTTACCAAAAT-TTTAGAGAC
11968356 T
1 T
11968357 ATAAGGGTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTACCAAAATTTTAGAGAC
Found at i:11968416 original size:20 final size:22
Alignment explanation
Indices: 11968393--11968445 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 22
11968383 ATTTACCGAT
11968393 ATTTTTAATGATTTAT-C-AAA
1 ATTTTTAATGATTTATCCTAAA
* *
11968413 ATTTCTAAAGA--TATCCTAAA
1 ATTTTTAATGATTTATCCTAAA
11968433 ATTTTTAAT-ATTT
1 ATTTTTAATGATTT
11968446 TCATTTGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
18 3 0.12
19 2 0.08
20 19 0.76
21 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTTTAATGATTTATCCTAAA
Found at i:11970546 original size:119 final size:118
Alignment explanation
Indices: 11970332--11970567 Score: 319
Period size: 119 Copynumber: 2.0 Consensus size: 118
11970322 AGGGACCAAA
** * * * * * *
11970332 GGATGGAGAAGGTTGTCTCATCTGATATTATGTGATTTTGGGATTAAGTTTAAATGGTTCTGTAT
1 GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCAAGTCTAAATGATTCTGTAT
* * * *
11970397 TCATTGCTTATTAATAGATGACGGGTAGATTTATATATCTTCAGAACTGGAATG
66 TCATTGCTTATTAATAAATAACGAGAAGATTTATATATCTTCAGAA-TGGAATG
* *
11970451 GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCGAGTCTAACTGATTCTGTAT
1 GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCAAGTCTAAATGATTCTGTAT
* *
11970516 TCATTGCTTATTATTAAATAACGAGAAGATTTGTATATCTTCAGAATGGAAT
66 TCATTGCTTATTAATAAATAACGAGAAGATTTATATATCTTCAGAATGGAAT
11970568 TTATTCTGTC
Statistics
Matches: 101, Mismatches: 16, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
118 6 0.06
119 95 0.94
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (118 bp):
GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCAAGTCTAAATGATTCTGTAT
TCATTGCTTATTAATAAATAACGAGAAGATTTATATATCTTCAGAATGGAATG
Found at i:11975902 original size:35 final size:33
Alignment explanation
Indices: 11975826--11975927 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 33
11975816 AGATTTTTTT
*
11975826 AAAAATTAATTAAATTAGGTTTTAGGGGTTTT---
1 AAAAATTAATTAAATTAGGGTTTA--GGTTTTAAA
*
11975858 --AAATAAATTAAATTAGGGTTTAGGATTTTTAAA
1 AAAAATTAATTAAATTAGGGTTTAGG--TTTTAAA
*
11975891 AAAAATTAATTAAATTAGGGTTTATGTTTTAAA
1 AAAAATTAATTAAATTAGGGTTTAGGTTTTAAA
11975924 AAAA
1 AAAA
11975928 TAATTTTGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
28 2 0.03
30 24 0.41
33 11 0.19
35 22 0.37
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (33 bp):
AAAAATTAATTAAATTAGGGTTTAGGTTTTAAA
Found at i:11975920 original size:63 final size:61
Alignment explanation
Indices: 11975793--11975926 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 61
11975783 AGTTTAAAAA
** *
11975793 TTTTAAAAAA-TAAATCAAGGTTTAGATTTTTTTAAAAATTAATTAAATTAGGTTTTAGGGG
1 TTTTAAAAAATTAAATCAAGGTTTAGATTTTTAAAAAAATTAATTAAATTAGGGTTTA-GGG
* * *
11975854 TTTTAAATAAATTAAATTAGGGTTTAGGATTTTTAAAAAAAATTAATTAAATTAGGGTTTA-TG
1 TTTTAAA-AAATTAAATCAAGGTTTA-GATTTTT-AAAAAAATTAATTAAATTAGGGTTTAGGG
11975917 TTTTAAAAAA
1 TTTTAAAAAA
11975927 ATAATTTTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
61 7 0.11
62 6 0.10
63 20 0.32
64 7 0.11
65 23 0.37
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (61 bp):
TTTTAAAAAATTAAATCAAGGTTTAGATTTTTAAAAAAATTAATTAAATTAGGGTTTAGGG
Found at i:11976242 original size:126 final size:125
Alignment explanation
Indices: 11976017--11976414 Score: 554
Period size: 126 Copynumber: 3.2 Consensus size: 125
11976007 ATTTTGTTTT
* * *
11976017 TTTTTCTACAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGGTTC-TAAAAAGAT-GATGTCAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTTAAAAA-ATAG-TGTCAA
* *
11976080 AAACGA-TTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAATGCTCCCACGTGGACGCTC
64 AAAC-ACTTCAAGCAGAATGCACTGTCAGCAAAATTACTGAAAAA-GCTCCCACGTGGACGCTC
* *
11976143 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTTAGAAGACGGTTCTTAAAAAATAGTGCCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTTAAAAAATAGTGTCAAAA
*
11976208 ACACTTCAAGCAGAATGCATTGTCAGCAAAATTACTGTAAAAAGCTCCCACGTGGACGCTC
66 ACACTTCAAGCAGAATGCACTGTCAGCAAAATTACTG-AAAAAGCTCCCACGTGGACGCTC
* * * * *
11976269 TTTATCTACAGTAGTTCCT-AGAAAAATAAATTTGAGAAGATGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCCTGA-AAAAATAATTTTGAGAAGACGGTTCTTAAAAAATAGTGTCAAA
* *
11976333 AACGCTTCAAGCA-AGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
65 AACACTTCAAGCAGA-ATGCACTGTCAGCAAAATTACTG-AAAAAGCTCCCACGTGGACGCTC
11976395 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
11976415 CTTGGCCTTA
Statistics
Matches: 245, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
125 3 0.01
126 230 0.94
127 12 0.05
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTTAAAAAATAGTGTCAAAA
ACACTTCAAGCAGAATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCACGTGGACGCTC
Found at i:11979765 original size:18 final size:18
Alignment explanation
Indices: 11979742--11979779 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11979732 GGAAAAGAAA
*
11979742 ACATATAAGGGTTAGGAT
1 ACATATAAGGGATAGGAT
11979760 ACATATAAGGGATAGGAT
1 ACATATAAGGGATAGGAT
11979778 AC
1 AC
11979780 GCACTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGATAGGAT
Found at i:11982801 original size:31 final size:31
Alignment explanation
Indices: 11982763--11982828 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
11982753 GTCATGAATC
11982763 CTAAACCATGGCATGTAATCCGACGCACACG
1 CTAAACCATGGCATGTAATCCGACGCACACG
11982794 CTAAACCATGGCATGTAATCCGACGCACACG
1 CTAAACCATGGCATGTAATCCGACGCACACG
11982825 CTAA
1 CTAA
11982829 CTATGGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.17
Consensus pattern (31 bp):
CTAAACCATGGCATGTAATCCGACGCACACG
Found at i:11985595 original size:31 final size:31
Alignment explanation
Indices: 11985560--11985625 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
11985550 TACATTTATC
* **
11985560 ATTATGTTAAATTATTTAAACCTTATGTATT
1 ATTATATTAAATTATTTAAAAATTATGTATT
* * *
11985591 ATTATATTTAATTTTTTAAAAATTTTGTATT
1 ATTATATTAAATTATTTAAAAATTATGTATT
11985622 ATTA
1 ATTA
11985626 GTTTTACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAAAATTATGTATT
Found at i:11985726 original size:24 final size:24
Alignment explanation
Indices: 11985682--11985728 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11985672 TATATTTCAT
* *
11985682 ATATCATTATATTAAATTATTTAA
1 ATATCATTAAATTAAACTATTTAA
11985706 ATATCATATAAATT-AACTATTTA
1 ATATCAT-TAAATTAAACTATTTA
11985729 TTTTACTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATCATTAAATTAAACTATTTAA
Found at i:11993249 original size:19 final size:19
Alignment explanation
Indices: 11993213--11993265 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
11993203 TGCCTCTTTT
11993213 TGCATT-CATTTCATTCATCA
1 TGCATTACATTTCA-TCAT-A
11993233 -GCATTACATTTCATCATA
1 TGCATTACATTTCATCATA
*
11993251 TGCATTAAATTTCAT
1 TGCATTACATTTCAT
11993266 AAAAATACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 22 0.73
20 7 0.23
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (19 bp):
TGCATTACATTTCATCATA
Found at i:11996448 original size:26 final size:27
Alignment explanation
Indices: 11996400--11996457 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
11996390 CTTTGCTTGA
11996400 AAGAGGACTCGAAAAATACCTTCAAGG
1 AAGAGGACTCGAAAAATACCTTCAAGG
*
11996427 AAGAGGACTCG-AAAATACCTTCACGG
1 AAGAGGACTCGAAAAATACCTTCAAGG
11996453 AAGAG
1 AAGAG
11996458 TCAAGACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (27 bp):
AAGAGGACTCGAAAAATACCTTCAAGG
Found at i:12001098 original size:44 final size:44
Alignment explanation
Indices: 12001047--12001286 Score: 259
Period size: 44 Copynumber: 5.5 Consensus size: 44
12001037 TAAAGCGAAC
* *
12001047 CTTATCTCCTTGAAGTTGCAGTGGAGCATATTAAAGCTGCAAAT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
*
12001091 CTTATCT-CTCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAAT
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
* * *
12001135 CTAATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAAT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
** * * * * *
12001179 CTTATCTCCCAGAAGTTGCAGTGGAACAAATTGAAGCTATAAGT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
* * * * *
12001223 CTTATTTCCCTGAAGTTGTAGTGGAGTAGATTGAAA-CTACAATT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAAT
* * *
12001267 CCTATATCCCTGAAGTTGCA
1 CTTATCTCCTTGAAGTTGCA
12001287 ATGGGTTAGA
Statistics
Matches: 166, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.01
44 160 0.96
45 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
Found at i:12001199 original size:88 final size:88
Alignment explanation
Indices: 12001050--12001286 Score: 285
Period size: 88 Copynumber: 2.7 Consensus size: 88
12001040 AGCGAACCTT
* * * *
12001050 ATCTCCTTGAAGTTGCAGTGGAGCATATTAAAGCTGCAAATCTTATCTCTCTGAAGTTGCAGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGG
* *
12001115 AGCAGATTAAAGCCACAAATCTA
66 AACAAATTAAAGCCACAAATCTA
* *
12001138 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCAGAAGTTGCAGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
12001203 AACAAATTGAAGCTATAAGTCTT
66 AACAAATTAAAGCCACAAATCTA
* * * * * * * *
12001226 ATTTCCCTGAAGTTGTAGTGGAGTAGATTGAAACTACAATTCCTATATCCCTGAAGTTGCA
1 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
12001287 ATGGGTTAGA
Statistics
Matches: 126, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 126 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (88 bp):
ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGG
AACAAATTAAAGCCACAAATCTA
Found at i:12002772 original size:22 final size:21
Alignment explanation
Indices: 12002724--12002772 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
12002714 TAGTGCGTTA
**
12002724 TATTTCAATCATTTATTTATT
1 TATTTCAATCATTTATGAATT
*
12002745 TAATTTCAATCTTTTATGAACTT
1 T-ATTTCAATCATTTATGAA-TT
12002768 TATTT
1 TATTT
12002773 ATTTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTCAATCATTTATGAATT
Found at i:12002837 original size:35 final size:34
Alignment explanation
Indices: 12002765--12002843 Score: 81
Period size: 35 Copynumber: 2.2 Consensus size: 34
12002755 CTTTTATGAA
*
12002765 CTTTATTTATTTATTTTATTTATTATTTCTTTATC
1 CTTTATTTATTTATTTTA-TTATTATTTCATTATC
*
12002800 CTTTATTATATTTAAATTTTA-TATTA-TTCATTGTC
1 CTTTATT-TATTT--ATTTTATTATTATTTCATTATC
12002835 CTTTTATTT
1 C-TTTATTT
12002844 GCATATTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
35 16 0.42
36 16 0.42
38 6 0.16
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (34 bp):
CTTTATTTATTTATTTTATTATTATTTCATTATC
Found at i:12004788 original size:21 final size:21
Alignment explanation
Indices: 12004746--12004789 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12004736 GTAAAAAAAA
* *
12004746 TTACAATTTTTTTTATAATTT
1 TTACAATTTTTGTTACAATTT
*
12004767 TTACAATTTTTGTTACATTTT
1 TTACAATTTTTGTTACAATTT
12004788 TT
1 TT
12004790 TGTAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
TTACAATTTTTGTTACAATTT
Found at i:12004885 original size:19 final size:21
Alignment explanation
Indices: 12004858--12004904 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12004848 ATTTTACTTT
12004858 TATA-ATTTTT-TATA-ATT-
1 TATATATTTTTCTATAGATTA
*
12004875 TATATATTTTTCTCTAGATTA
1 TATATATTTTTCTATAGATTA
12004896 TATATATTT
1 TATATATTT
12004905 AAATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 6 0.24
19 3 0.12
20 3 0.12
21 9 0.36
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TATATATTTTTCTATAGATTA
Found at i:12004916 original size:15 final size:15
Alignment explanation
Indices: 12004896--12004926 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12004886 CTCTAGATTA
12004896 TATATATTTAAATTT
1 TATATATTTAAATTT
12004911 TATATATTTAAATTT
1 TATATATTTAAATTT
12004926 T
1 T
12004927 TAATGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATATTTAAATTT
Found at i:12024120 original size:38 final size:38
Alignment explanation
Indices: 12024078--12024154 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
12024068 ATGACACCAG
12024078 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
1 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
12024116 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
1 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
12024154 T
1 T
12024155 CACAAACCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (38 bp):
TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
Found at i:12025077 original size:22 final size:22
Alignment explanation
Indices: 12025052--12025121 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
12025042 CTTTGAAAGG
12025052 TCCAGTGATAGATTTTGAAGAA
1 TCCAGTGATAGATTTTGAAGAA
* * *
12025074 TCCAAGGGTGACA-A-GTTG-AG-G
1 TCC-A--GTGATAGATTTTGAAGAA
12025095 TCCAGTGATAGATTTTGAAGAA
1 TCCAGTGATAGATTTTGAAGAA
12025117 TCCAG
1 TCCAG
12025122 GAAACAGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 4 0.11
21 5 0.14
22 10 0.29
23 4 0.11
24 1 0.03
25 5 0.14
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (22 bp):
TCCAGTGATAGATTTTGAAGAA
Found at i:12032393 original size:25 final size:25
Alignment explanation
Indices: 12032354--12032448 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
12032344 TCATGTACAT
*
12032354 GTATGCTCATACGAGCTGTGAATCA
1 GTATGCTCACACGAGCTGTGAATCA
* *
12032379 GTATGCTCACTCGAGTTGT-AGATCA
1 GTATGCTCACACGAGCTGTGA-ATCA
* * * * *
12032404 ATATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTGAATCA
*
12032429 GTATGCTCTCACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
12032449 GAGTATCCGT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
24 1 0.02
25 54 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCA
Found at i:12034601 original size:22 final size:23
Alignment explanation
Indices: 12034548--12034603 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
12034538 CCCGTTTTTA
* * *
12034548 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
12034571 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
12034593 ATTAAAATTAA
1 ATTAAAATTAA
12034604 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:12034616 original size:16 final size:16
Alignment explanation
Indices: 12034579--12034618 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12034569 TTAATAAAAT
* *
12034579 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
12034595 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
12034611 TAAAATTA
1 TAAAATTA
12034619 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:12034724 original size:9 final size:9
Alignment explanation
Indices: 12034691--12034718 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12034681 TTTATCAAAT
12034691 TATTAATTG
1 TATTAATTG
12034700 TATTAATTG
1 TATTAATTG
12034709 TATTAATTG
1 TATTAATTG
12034718 T
1 T
12034719 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:12034728 original size:68 final size:68
Alignment explanation
Indices: 12034607--12034816 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
12034597 AAATTAATTG
*
12034607 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
12034670 TGA
66 TGA
12034673 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
12034738 TGA
66 TGA
*
12034741 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
12034806 TGA
66 TGA
*
12034809 TTAATAAA
1 TTAGTAAA
12034817 ACAAACTTGA
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 26 0.19
68 113 0.81
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:12034771 original size:9 final size:9
Alignment explanation
Indices: 12034759--12034786 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12034749 TTTATCAAAT
12034759 TATTAATTG
1 TATTAATTG
12034768 TATTAATTG
1 TATTAATTG
12034777 TATTAATTG
1 TATTAATTG
12034786 T
1 T
12034787 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:12037036 original size:2 final size:2
Alignment explanation
Indices: 12037029--12037053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12037019 TAGTGAGGTT
12037029 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12037054 GTTGCATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12037807 original size:17 final size:17
Alignment explanation
Indices: 12037785--12037823 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
12037775 TCTTTTTTTA
12037785 TTATTGAAATTGTATTT
1 TTATTGAAATTGTATTT
12037802 TTATTGAAATTGTATTT
1 TTATTGAAATTGTATTT
12037819 TTATT
1 TTATT
12037824 TTCACCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (17 bp):
TTATTGAAATTGTATTT
Found at i:12038465 original size:97 final size:97
Alignment explanation
Indices: 12038355--12038689 Score: 661
Period size: 97 Copynumber: 3.5 Consensus size: 97
12038345 TTTTAAATTA
12038355 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
1 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
*
12038420 TGCATATTTTAATTAAAATATAATTCGGTACT
66 TTCATATTTTAATTAAAATATAATTCGGTACT
12038452 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
1 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
12038517 TTCATATTTTAATTAAAATATAATTCGGTACT
66 TTCATATTTTAATTAAAATATAATTCGGTACT
12038549 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
1 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
12038614 TTCATATTTTAATTAAAATATAATTCGGTACT
66 TTCATATTTTAATTAAAATATAATTCGGTACT
12038646 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
1 TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
12038690 TGTTATTAAA
Statistics
Matches: 237, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 237 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (97 bp):
TATATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATC
TTCATATTTTAATTAAAATATAATTCGGTACT
Found at i:12038762 original size:23 final size:23
Alignment explanation
Indices: 12038727--12038771 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12038717 CCTTATTTAA
**
12038727 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
12038750 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
12038772 AAAATGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:12038794 original size:11 final size:11
Alignment explanation
Indices: 12038778--12038804 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12038768 TTATAAAATG
12038778 ACAATATCTCA
1 ACAATATCTCA
12038789 ACAATATCTCA
1 ACAATATCTCA
12038800 ACAAT
1 ACAAT
12038805 TGATAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAATATCTCA
Found at i:12041324 original size:92 final size:91
Alignment explanation
Indices: 12041167--12041375 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
12041157 TTGATTTTAG
* * * *
12041167 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
12041232 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
12041259 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
12041323 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
12041351 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
12041376 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:12041338 original size:24 final size:25
Alignment explanation
Indices: 12041303--12041350 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
12041293 TTATGAAATT
12041303 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
12041327 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
12041351 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:12041551 original size:15 final size:15
Alignment explanation
Indices: 12041527--12041567 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12041517 ATTAAATTAC
12041527 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
12041541 ATATATTTAATAATA
1 ATATATTTAATTATA
12041556 AT-TATGTTAATT
1 ATATAT-TTAATT
12041568 TATATTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:12042018 original size:153 final size:156
Alignment explanation
Indices: 12041740--12042052 Score: 515
Period size: 153 Copynumber: 2.0 Consensus size: 156
12041730 NNNNNNNNAT
* * * *
12041740 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
* *
12041805 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
12041870 T-A-A-TTACCAAAACAAATTTCTGC
131 TAACATTTACCAAAACAAATTTATGC
* *
12041893 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
12041958 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
12042023 TAATCATTTACCAAAACAAATTTATGC
131 TAA-CATTTACCAAAACAAATTTATGC
12042050 TAA
1 TAA
12042053 GGGTATTCTA
Statistics
Matches: 147, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
153 123 0.84
154 1 0.01
156 1 0.01
157 22 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAACATTTACCAAAACAAATTTATGC
Found at i:12042218 original size:15 final size:15
Alignment explanation
Indices: 12042198--12042236 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
12042188 CAATACAACG
12042198 AAATAAACTTAAAAT
1 AAATAAACTTAAAAT
12042213 AAATAAACTTAAAAT
1 AAATAAACTTAAAAT
*
12042228 AAAAAAACT
1 AAATAAACT
12042237 ATTACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAACTTAAAAT
Found at i:12047537 original size:25 final size:25
Alignment explanation
Indices: 12047509--12047616 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 25
12047499 ATGCTCATAT
* *
12047509 GAGCTGTGAATCGGTATGCTCACTC
1 GAGCTGTGAATCGGTATGCTCTCAC
* * *
12047534 GAGCTGTAGAAT-AGTATACTCTCAG
1 GAGCTGT-GAATCGGTATGCTCTCAC
* * * *
12047559 GAGCTATAAATTGGTATGTTCTCAC
1 GAGCTGTGAATCGGTATGCTCTCAC
* *
12047584 GAGCTATAAATCGGTATGCTCTCAC
1 GAGCTGTGAATCGGTATGCTCTCAC
12047609 GAGCTGTG
1 GAGCTGTG
12047617 GAGTATCCAC
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
24 3 0.05
25 59 0.89
26 4 0.06
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (25 bp):
GAGCTGTGAATCGGTATGCTCTCAC
Found at i:12049009 original size:24 final size:24
Alignment explanation
Indices: 12048963--12049020 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
12048953 AAATATATAT
* *
12048963 TATATATAATAAGACCTATGCATC
1 TATATATAATAAGACCTACGCATA
12048987 TATATATAATAAGATCC-ACGCATA
1 TATATATAATAAGA-CCTACGCATA
12049011 TA-ATATAATA
1 TATATATAATA
12049021 TATGTATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 8 0.26
24 21 0.68
25 2 0.06
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (24 bp):
TATATATAATAAGACCTACGCATA
Found at i:12053904 original size:13 final size:13
Alignment explanation
Indices: 12053888--12053917 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12053878 TTACACATTT
*
12053888 CCATTTCAAGTAA
1 CCATTTCAAATAA
12053901 CCATTTCAAATAA
1 CCATTTCAAATAA
12053914 CCAT
1 CCAT
12053918 ATCATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (13 bp):
CCATTTCAAATAA
Found at i:12055976 original size:2 final size:2
Alignment explanation
Indices: 12055969--12056021 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
12055959 AGGTTTTGGC
12055969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12056011 AT AT AT AT AT A
1 AT AT AT AT AT A
12056022 ATGTGTCTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12059000 original size:18 final size:18
Alignment explanation
Indices: 12058971--12059014 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
12058961 AACAACGCCA
12058971 TGTTAT-TTTGTGTATTG
1 TGTTATATTTGTGTATTG
12058988 TGTTATATTTGTGTATTG
1 TGTTATATTTGTGTATTG
12059006 TGTTATATT
1 TGTTATATT
12059015 GTGAACCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.16, C:0.00, G:0.20, T:0.64
Consensus pattern (18 bp):
TGTTATATTTGTGTATTG
Found at i:12062291 original size:17 final size:16
Alignment explanation
Indices: 12062265--12062353 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 16
12062255 TGGTATGAAC
*
12062265 GAATTGTTATACTTAAT
1 GAATTATTATA-TTAAT
12062282 GAATTATTATATTGAAT
1 GAATTATTATATT-AAT
*
12062299 GAATTATAATATTTAAT
1 GAATTATTATA-TTAAT
* *
12062316 GAATTGTTATATTGTAT
1 GAATTATTATATT-AAT
* *
12062333 GAACTGTTATATTGAAT
1 GAATTATTATATT-AAT
12062350 GAAT
1 GAAT
12062354 GTTATTATGC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
16 4 0.07
17 55 0.90
18 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (16 bp):
GAATTATTATATTAAT
Found at i:12062368 original size:33 final size:34
Alignment explanation
Indices: 12062269--12062375 Score: 112
Period size: 34 Copynumber: 3.2 Consensus size: 34
12062259 ATGAACGAAT
* * *
12062269 TGTTATACTT-AATGAATTATTATATTGAATGAAT
1 TGTTATA-TTGAATGAATTGTTATATTGCATGAAC
* * * *
12062303 TATAATATTTAATGAATTGTTATATTGTATGAAC
1 TGTTATATTGAATGAATTGTTATATTGCATGAAC
12062337 TGTTATATTGAATGAA-TGTTAT-TATGCATGAAC
1 TGTTATATTGAATGAATTGTTATAT-TGCATGAAC
12062370 TGTTAT
1 TGTTAT
12062376 TTCATATGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
32 1 0.02
33 22 0.35
34 39 0.63
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.47
Consensus pattern (34 bp):
TGTTATATTGAATGAATTGTTATATTGCATGAAC
Found at i:12062375 original size:17 final size:18
Alignment explanation
Indices: 12062291--12062376 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 18
12062281 TGAATTATTA
*
12062291 TATTGAATGAA-T-TATAA
1 TATTGAATGAACTGT-TAT
* *
12062308 TATTTAATGAATTGTTA-
1 TATTGAATGAACTGTTAT
*
12062325 TATTGTATGAACTGTTA-
1 TATTGAATGAACTGTTAT
12062342 TATTGAATGAA-TGTTAT
1 TATTGAATGAACTGTTAT
*
12062359 TA-TGCATGAACTGTTAT
1 TATTGAATGAACTGTTAT
12062376 T
1 T
12062377 TCATATGAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 12 0.20
17 43 0.73
18 3 0.05
19 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
TATTGAATGAACTGTTAT
Found at i:12062384 original size:17 final size:16
Alignment explanation
Indices: 12062308--12062405 Score: 69
Period size: 17 Copynumber: 5.9 Consensus size: 16
12062298 TGAATTATAA
*
12062308 TATTTA-ATGAATTGT
1 TATTTATATGAACTGT
*
12062323 TATATTGTATGAACTGT
1 TAT-TTATATGAACTGT
12062340 TATATTGA-ATGAA-TGT
1 TAT-TT-ATATGAACTGT
12062356 TA-TTATGCATGAACTGT
1 TATTTAT--ATGAACTGT
*
12062373 TATTTCATATGAACTAT
1 TATTT-ATATGAACTGT
*
12062390 TATTTTATGTGAACTG
1 TA-TTTATATGAACTG
12062406 CCTGTTCTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
13 1 0.01
14 2 0.03
15 3 0.04
16 12 0.18
17 42 0.63
18 5 0.07
19 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (16 bp):
TATTTATATGAACTGT
Found at i:12070327 original size:2 final size:2
Alignment explanation
Indices: 12070322--12070347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12070312 AAAATTTTAA
12070322 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12070348 TTTTTGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12077159 original size:26 final size:27
Alignment explanation
Indices: 12077124--12077174 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
12077114 TTCTAATTTT
*
12077124 TTTTGTAA-TTTGTCTCGGTTTAATTC
1 TTTTCTAATTTTGTCTCGGTTTAATTC
* *
12077150 TTTTCTAATTTTTTCTTGGTTTAAT
1 TTTTCTAATTTTGTCTCGGTTTAAT
12077175 AGAAGTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.16, C:0.10, G:0.12, T:0.63
Consensus pattern (27 bp):
TTTTCTAATTTTGTCTCGGTTTAATTC
Found at i:12083027 original size:45 final size:45
Alignment explanation
Indices: 12082967--12083055 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
12082957 AACAGATACT
* * *
12082967 CGGTGGATTCAGCACATAGCAATCACCTTATTAATCAATAATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
* * *
12083012 CGGTGGAATCCGCACATAGCAACCACCTTACTAATTAATGATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGT
12083056 TCAGCTCACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
Found at i:12083121 original size:51 final size:51
Alignment explanation
Indices: 12083066--12083252 Score: 168
Period size: 51 Copynumber: 3.7 Consensus size: 51
12083056 TCAGCTCACA
* * *
12083066 TAGTAGCTTGCACACAGTACTACACATGTGACAATTATCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACAATTATCATCCGATACACG
* * * ** *
12083117 TAGTAGTCTGCACATAATACTACACACGTGATCGAA--A-CTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-C-AATTATC-ATCCGATACACG
* * * * *
12083168 TAGTAGCCTGCACATAGTACTACACATGCGAC--CTATCATTCTAGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACAATTATCATCCGA-TACACG
*
12083218 TAGTAGCCTGCACATAGTACTACACACGTGGCAAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACAAT
12083253 CATTTTCACT
Statistics
Matches: 104, Mismatches: 23, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
49 4 0.04
50 35 0.34
51 62 0.60
52 1 0.01
53 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACAATTATCATCCGATACACG
Found at i:12083241 original size:101 final size:101
Alignment explanation
Indices: 12083064--12083247 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
12083054 GTTCAGCTCA
* * * *
12083064 CATAGTAGCTTGCACACAGTACTACACATGTGACAATTATCATCCGATACACGTAGTAGTCTGCA
1 CATAGTAGCCTGCACACAGTACTACACATGCGAC-ACTATCATCCGATACACGTAGTAGCCTGCA
12083129 CATAATACTACACACGTGATCGAAACTATCCGGTATG
65 CATAATACTACACACGTGATCGAAACTATCCGGTATG
* * *
12083166 CATAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCTAGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACACAGTACTACACATGCGACACTATCATCCGA-TACACGTAGTAGCCTGCA
*
12083230 CATAGTACTACACACGTG
65 CATAATACTACACACGTG
12083248 GCAATCATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 8 0.11
101 34 0.47
102 31 0.42
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACACAGTACTACACATGCGACACTATCATCCGATACACGTAGTAGCCTGCAC
ATAATACTACACACGTGATCGAAACTATCCGGTATG
Found at i:12084696 original size:15 final size:15
Alignment explanation
Indices: 12084676--12084706 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12084666 GGTTCCAGAA
12084676 GAAGATGATGCGTTG
1 GAAGATGATGCGTTG
12084691 GAAGATGATGCGTTG
1 GAAGATGATGCGTTG
12084706 G
1 G
12084707 TTGTCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.42, T:0.26
Consensus pattern (15 bp):
GAAGATGATGCGTTG
Found at i:12085778 original size:94 final size:94
Alignment explanation
Indices: 12085617--12085805 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
12085607 GTTTACCTTC
12085617 TTCTGTGTAATTGGAATGGGTGAGAAGATTTCTTGCTGACCATTAAAAATCATGATTGTGTTGGT
1 TTCTGTGTAATTGGAATGGGTGAGAAGATTTCTTGCTGACCATTAAAAATCATGATTGTGTTGGT
12085682 AATGTTTTGGTAACTTTTTGTGTTTGTAA
66 AATGTTTTGGTAACTTTTTGTGTTTGTAA
12085711 TTCTGTGTAATTGGAATGGGTGAGAAGATTTCTTGCTGACCATTAAAAATCATGATTGTGTTGGT
1 TTCTGTGTAATTGGAATGGGTGAGAAGATTTCTTGCTGACCATTAAAAATCATGATTGTGTTGGT
12085776 AATGTTTTGGTAACTTTTTGTGTTTGTAA
66 AATGTTTTGGTAACTTTTTGTGTTTGTAA
12085805 T
1 T
12085806 ATTTGGATAG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (94 bp):
TTCTGTGTAATTGGAATGGGTGAGAAGATTTCTTGCTGACCATTAAAAATCATGATTGTGTTGGT
AATGTTTTGGTAACTTTTTGTGTTTGTAA
Found at i:12086134 original size:25 final size:23
Alignment explanation
Indices: 12086082--12086124 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12086072 ATAAAGTAGA
12086082 TTATATATT-ATTTTTATAATAT
1 TTATATATTAATTTTTATAATAT
12086104 TATATATATTAATTTTT-TAAT
1 T-TATATATTAATTTTTATAAT
12086125 TCATGTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.05
23 12 0.63
24 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATATATTAATTTTTATAATAT
Found at i:12089912 original size:26 final size:26
Alignment explanation
Indices: 12089883--12089935 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12089873 AAAATGAGTT
12089883 AGTTTGACACTTTAGCTTCCGAAGGA
1 AGTTTGACACTTTAGCTTCCGAAGGA
12089909 AGTTTGACACTTTAGCTTCCGAAGGA
1 AGTTTGACACTTTAGCTTCCGAAGGA
12089935 A
1 A
12089936 CAGCACTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (26 bp):
AGTTTGACACTTTAGCTTCCGAAGGA
Found at i:12091405 original size:126 final size:127
Alignment explanation
Indices: 12091211--12091781 Score: 877
Period size: 127 Copynumber: 4.5 Consensus size: 127
12091201 GATAAAATCA
* * * * * * *
12091211 AAGCAGGATGCT-TTATCAGAAGGATTTCTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAA
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
12091275 TAGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
65 TAGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
*
12091337 AAGTAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
12091401 TAGGTCCTGGAAGAAATAATTTTGAGTTAACGTTTCTGAGCAAATAGT-TAAAAAAAACGATTC
65 TAGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAT-AAAAAAACGCTTC
* *
12091464 AAGTAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * *
12091529 AGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTTTTAAAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
* * *
12091591 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCACTCCCTCGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
12091656 AGGTCCTGGAA-AAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAT--AAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
*
12091715 TAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
12091780 AG
66 AG
12091782 CATGTTTGGG
Statistics
Matches: 412, Mismatches: 29, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
124 74 0.18
126 103 0.25
127 232 0.56
128 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (127 bp):
AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTATAAAAAAACGCTTC
Found at i:12094982 original size:21 final size:21
Alignment explanation
Indices: 12094954--12095107 Score: 191
Period size: 21 Copynumber: 7.2 Consensus size: 21
12094944 TCAAATTATA
12094954 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
12094975 TTAAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
** *
12094996 TTTAAGTTAAGGGACAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
12095017 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
12095039 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
12095061 TTAAAGTTAAAGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
12095082 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
12095104 TTTA
1 TTTA
12095108 GGTAGGTTAT
Statistics
Matches: 112, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
21 67 0.60
22 45 0.40
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.42
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:12095035 original size:43 final size:42
Alignment explanation
Indices: 12094954--12095105 Score: 205
Period size: 43 Copynumber: 3.5 Consensus size: 42
12094944 TCAAATTATA
12094954 TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAAGGTT
** * *
12094996 TTTAAGTTAAGGGACAGAGTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGG-TTAAGGTT
* * *
12095039 TTTAGGTTAAGGGTTTAGGGTTTTAAAGTTAAAGGTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTAAAGTTAAGGGTTAAGGTT
*
12095082 TTTAAGTTAAGGGTTTAAGGTTTT
1 TTTAAGTTAAGGG-TTAGGGTTTT
12095106 TAGGTAGGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
42 30 0.32
43 49 0.52
44 16 0.17
ACGTcount: A:0.28, C:0.01, G:0.30, T:0.42
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAAGGTT
Found at i:12095083 original size:65 final size:64
Alignment explanation
Indices: 12094954--12095110 Score: 217
Period size: 65 Copynumber: 2.5 Consensus size: 64
12094944 TCAAATTATA
* * * * *
12094954 TTTAAGTTAAGGG-TTAGGGTTTTAAAGTTAAGGGTTAAGGTTTTTAAGTTAAGGGACAGAGTT
1 TTTAAGTTAAGGGTTTAAGGTTTTTAGGTTAAGGGTTAAGGTTTTAAAGTTAAAGGACAGAGTT
* ** *
12095017 TTTAAGTTAAGGGTTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTAAAGTTAAAGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAAGGTTTTTAGGTTAAGGG-TTAAGGTTTTAAAGTTAAAGGACAGAGTT
12095082 TTTAAGTTAAGGGTTTAAGGTTTTTAGGT
1 TTTAAGTTAAGGGTTTAAGGTTTTTAGGT
12095111 AGGTTATGNN
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 13 0.16
64 18 0.22
65 52 0.63
ACGTcount: A:0.27, C:0.01, G:0.30, T:0.42
Consensus pattern (64 bp):
TTTAAGTTAAGGGTTTAAGGTTTTTAGGTTAAGGGTTAAGGTTTTAAAGTTAAAGGACAGAGTT
Found at i:12096175 original size:43 final size:44
Alignment explanation
Indices: 12096072--12096182 Score: 145
Period size: 43 Copynumber: 2.5 Consensus size: 44
12096062 NNNNNNNNNN
** * *
12096072 TTTTAAGTTAAGGGTTTACAGCTTTTAAGTTAATGGTTTATGGT
1 TTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAATGGGTTATGGT
*
12096116 TTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAA-GGGTTA-GAGT
1 TTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAATGGGTTATG-GT
*
12096159 TTTTAAGTTAAGGGTTTTGGGTTT
1 TTTTAAGTTAAGGGTTTAGGGTTT
12096183 GTCAATTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 30 0.50
44 29 0.48
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (44 bp):
TTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAATGGGTTATGGT
Found at i:12096191 original size:22 final size:22
Alignment explanation
Indices: 12096072--12096182 Score: 143
Period size: 22 Copynumber: 5.1 Consensus size: 22
12096062 NNNNNNNNNN
** *
12096072 TTTTAAGTTAAGGGTTTACAGC
1 TTTTAAGTTAAGGGTTTAGGGT
* *
12096094 TTTTAAGTTAATGGTTTATGGT
1 TTTTAAGTTAAGGGTTTAGGGT
12096116 TTTTAAGTTAAGGGTTTAGGGT
1 TTTTAAGTTAAGGGTTTAGGGT
* *
12096138 TTTTAATTTAAGGG-TTAGAGT
1 TTTTAAGTTAAGGGTTTAGGGT
*
12096159 TTTTAAGTTAAGGGTTTTGGGT
1 TTTTAAGTTAAGGGTTTAGGGT
12096181 TT
1 TT
12096183 GTCAATTAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
21 19 0.25
22 58 0.75
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (22 bp):
TTTTAAGTTAAGGGTTTAGGGT
Found at i:12096762 original size:18 final size:18
Alignment explanation
Indices: 12096723--12096765 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12096713 GACCCAAAAA
*
12096723 AGGAAACATATAAGGGTC
1 AGGAAACATAAAAGGGTC
*
12096741 AGGATACATAAAAGGG-C
1 AGGAAACATAAAAGGGTC
12096758 TAGGAAAC
1 -AGGAAAC
12096766 GCACCTGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14
Consensus pattern (18 bp):
AGGAAACATAAAAGGGTC
Found at i:12098563 original size:19 final size:19
Alignment explanation
Indices: 12098517--12098566 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
12098507 AATTTTTACG
12098517 ATTTAAAAAATTTTAAAAAA
1 ATTT-AAAAATTTTAAAAAA
** **
12098537 ATAAAAAAATTTTAAAATT
1 ATTTAAAAATTTTAAAAAA
12098556 ATTTAAAAATT
1 ATTTAAAAATT
12098567 GGGATTTAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAAAAATTTTAAAAAA
Found at i:12098634 original size:11 final size:11
Alignment explanation
Indices: 12098620--12098694 Score: 66
Period size: 11 Copynumber: 6.7 Consensus size: 11
12098610 ATTAAATATG
*
12098620 AATTTCAGAGA
1 AATTTGAGAGA
*
12098631 AATTTG-GAAGG
1 AATTTGAG-AGA
12098642 AATTTGAGAGCA
1 AATTTGAGAG-A
12098654 AA-TTGAGAGGA
1 AATTTGAGA-GA
12098665 AATTT-AGAGA
1 AATTTGAGAGA
*
12098675 AAATTGAGAGGA
1 AATTTGAGA-GA
12098687 AATTTGAG
1 AATTTGAG
12098695 GGAGGATTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 30 0.58
12 15 0.29
ACGTcount: A:0.44, C:0.03, G:0.28, T:0.25
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:12098664 original size:22 final size:23
Alignment explanation
Indices: 12098620--12098694 Score: 93
Period size: 22 Copynumber: 3.3 Consensus size: 23
12098610 ATTAAATATG
* *
12098620 AATTTCAGAGAAATTTG-GAAGG-
1 AATTTGAGAGAAAATTGAG-AGGA
*
12098642 AATTTGAGAGCAAATTGAGAGGA
1 AATTTGAGAGAAAATTGAGAGGA
12098665 AATTT-AGAGAAAATTGAGAGGA
1 AATTTGAGAGAAAATTGAGAGGA
12098687 AATTTGAG
1 AATTTGAG
12098695 GGAGGATTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 38 0.83
23 8 0.17
ACGTcount: A:0.44, C:0.03, G:0.28, T:0.25
Consensus pattern (23 bp):
AATTTGAGAGAAAATTGAGAGGA
Found at i:12107275 original size:14 final size:15
Alignment explanation
Indices: 12107250--12107278 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12107240 CCATTCAATT
12107250 AATCAGTTCATAACA
1 AATCAGTTCATAACA
12107265 AATCA-TTCATAACA
1 AATCAGTTCATAACA
12107279 TATTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
AATCAGTTCATAACA
Found at i:12107559 original size:37 final size:39
Alignment explanation
Indices: 12107469--12107602 Score: 155
Period size: 40 Copynumber: 3.4 Consensus size: 39
12107459 CCAGTTTGGT
* *
12107469 ACCCAGTACCTCATCGGATAATTCGAAGTAATAAGTTGAC
1 ACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGAC
* * *
12107509 ACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AATTGAC
1 ACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGAC
* *
12107546 ACCCAATGCCTCATCGAATTAATCCGAAGTAATAGATTGAC
1 ACCCAGTGCCTCATCGGA-TAATCCGAAGTAATA-ATTGAC
*
12107587 ACCCAGTGTCTCATCG
1 ACCCAGTGCCTCATCG
12107603 ACTCATAGTC
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
37 19 0.24
38 12 0.15
39 2 0.03
40 25 0.32
41 20 0.26
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (39 bp):
ACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGAC
Found at i:12114338 original size:5 final size:5
Alignment explanation
Indices: 12114330--12114405 Score: 152
Period size: 5 Copynumber: 15.2 Consensus size: 5
12114320 ACTACAAAAG
12114330 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
12114380 TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA T
12114406 TAAGTAATAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:12115020 original size:17 final size:17
Alignment explanation
Indices: 12114991--12115023 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12114981 ATTTGATGTA
12114991 TTATATTTTTTTAAAAT
1 TTATATTTTTTTAAAAT
12115008 TTAT-TTTTATTTAAAA
1 TTATATTTT-TTTAAAA
12115024 ATAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTTTTTTAAAAT
Found at i:12117629 original size:20 final size:20
Alignment explanation
Indices: 12117604--12117647 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12117594 AAATAAACAT
* *
12117604 AAAAAAAT-TTCGAAAATTA
1 AAAAAAATATTTGAAAAATA
*
12117623 AAAAAAATATTTTAAAAATA
1 AAAAAAATATTTGAAAAATA
12117643 AAAAA
1 AAAAA
12117648 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAATATTTGAAAAATA
Found at i:12117645 original size:16 final size:15
Alignment explanation
Indices: 12117622--12117655 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12117612 TTCGAAAATT
*
12117622 AAAAAAAATATTTTA
1 AAAAAAAAAATTTTA
12117637 AAAATAAAAAATTTTA
1 AAAA-AAAAAATTTTA
12117653 AAA
1 AAA
12117656 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAAAAAAATTTTA
Found at i:12117656 original size:15 final size:15
Alignment explanation
Indices: 12117620--12117657 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12117610 ATTTCGAAAA
*
12117620 TTAAAA-AAAATATT
1 TTAAAATAAAAAATT
12117634 TTAAAAATAAAAAATT
1 TT-AAAATAAAAAATT
12117650 TTAAAATA
1 TTAAAATA
12117658 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 10 0.48
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAATAAAAAATT
Found at i:12117686 original size:27 final size:27
Alignment explanation
Indices: 12117616--12117680 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
12117606 AAAAATTTCG
* *
12117616 AAAATTAAAAAAAATATTTTAAAAATAA
1 AAAATTATAAAATAT-TTTTAAAAATAA
*
12117644 AAAATTTTAAAATATTTTTAAAAATAA
1 AAAATTATAAAATATTTTTAAAAATAA
12117671 AAAATATATA
1 AAAAT-TATA
12117681 TTTATTATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATTATAAAATATTTTTAAAAATAA
Found at i:12118350 original size:27 final size:27
Alignment explanation
Indices: 12118308--12118436 Score: 152
Period size: 27 Copynumber: 4.7 Consensus size: 27
12118298 AACACATTAG
* *
12118308 GAAAGAATAACCTTTGTGGCAAACTAT
1 GAAAGAATAGCTTTTGTGGCAAACTAT
*
12118335 GAAAGAATAGCTTTTGTGACAAACTAT
1 GAAAGAATAGCTTTTGTGGCAAACTAT
* *
12118362 GAAATAATAG-TCTTTGTGGCAAATTAT
1 GAAAGAATAGCT-TTTGTGGCAAACTAT
** *
12118389 GAAAGAATAGCCATTGTGGCAAATTAT
1 GAAAGAATAGCTTTTGTGGCAAACTAT
*
12118416 GAAGGAATAGCTTTTGGTGGC
1 GAAAGAATAGCTTTT-GTGGC
12118437 GCACTCTAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
26 1 0.01
27 81 0.93
28 5 0.06
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (27 bp):
GAAAGAATAGCTTTTGTGGCAAACTAT
Found at i:12127248 original size:2 final size:2
Alignment explanation
Indices: 12127241--12127270 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12127231 TCAATTCAAG
12127241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12127271 TACTTAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12129579 original size:105 final size:105
Alignment explanation
Indices: 12129386--12129580 Score: 239
Period size: 105 Copynumber: 1.9 Consensus size: 105
12129376 AATGTTTAAA
** * * * **
12129386 TGTAAGACCATATTTAGGCTATGAAATTTTAATGAAAAGACCATAACTGGGTTATGGTACCTTGA
1 TGTAAGACCATAGCTAGGCTATGAAATTCTAATGAAAAGACCATAACTGAGTTATGGCACCTCAA
**
12129451 ACGTAAGACCATGGTTGGACCATGGTAGTATATATACATG
66 ACGTAAGACCATGGCAGGACCATGGTAGTATATATACATG
* * * *
12129491 TGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAACTGAGTTATGGCA-CTACA
1 TGTAAGACCATAGCTAGGCTATGAAATTCTAATGAAAAGACCATAACTGAGTTATGGCACCT-CA
* *
12129555 AATGTAAGACCATGGCAGGGCCATGG
65 AACGTAAGACCATGGCAGGACCATGG
12129581 CAATGCATGT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
104 2 0.03
105 72 0.97
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAGCTAGGCTATGAAATTCTAATGAAAAGACCATAACTGAGTTATGGCACCTCAA
ACGTAAGACCATGGCAGGACCATGGTAGTATATATACATG
Found at i:12131788 original size:48 final size:48
Alignment explanation
Indices: 12131717--12131819 Score: 179
Period size: 48 Copynumber: 2.1 Consensus size: 48
12131707 GAGTCCAAAA
* *
12131717 GTTAATTAGCAACACAGAAGTTAACCAACCGCTGTCTGTTATTAATTT
1 GTTAATTAGCAACACAGAAGTTAACCAACCACTATCTGTTATTAATTT
*
12131765 GTTAATTAGCAACACAGAAGTTAACCAACTACTATCTGTTATTAATTT
1 GTTAATTAGCAACACAGAAGTTAACCAACCACTATCTGTTATTAATTT
12131813 GTTAATT
1 GTTAATT
12131820 TCATAAGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (48 bp):
GTTAATTAGCAACACAGAAGTTAACCAACCACTATCTGTTATTAATTT
Found at i:12133040 original size:2 final size:2
Alignment explanation
Indices: 12133027--12133070 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
12133017 GACTCCGAGT
* *
12133027 GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12133069 GA
1 GA
12133071 AGTGAAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.05
Consensus pattern (2 bp):
GA
Found at i:12137982 original size:11 final size:12
Alignment explanation
Indices: 12137940--12137989 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
12137930 ATATAAGTTA
12137940 AATTATTTTTGTAT
1 AATTA-TTTT-TAT
* *
12137954 TATTATTTTAAT
1 AATTATTTTTAT
12137966 AATTATTTTTA-
1 AATTATTTTTAT
12137977 AATTATTTTTAT
1 AATTATTTTTAT
12137989 A
1 A
12137990 CAACATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 11 0.35
12 12 0.39
13 4 0.13
14 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
AATTATTTTTAT
Found at i:12140648 original size:50 final size:50
Alignment explanation
Indices: 12140581--12140676 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
12140571 ATACTTCTTT
12140581 TTCAATAATTTGATATCATGGCATGCATTTCATAACAAATATATTTATTC
1 TTCAATAATTTGATATCATGGCATGCATTTCATAACAAATATATTTATTC
* *
12140631 TTCAATATTTTGGTATCATGGCATGCATTTCATAACAAATATATTT
1 TTCAATAATTTGATATCATGGCATGCATTTCATAACAAATATATTT
12140677 GGCATTTGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (50 bp):
TTCAATAATTTGATATCATGGCATGCATTTCATAACAAATATATTTATTC
Found at i:12149369 original size:37 final size:37
Alignment explanation
Indices: 12149319--12149394 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
12149309 TTTTAAAAAT
*
12149319 AATATTATTTTAATAGT-TTAATATTAAATTAA-ATTA
1 AATATTATCTTAATAGTATT-ATATTAAATTAATATTA
* *
12149355 AATACTTATCTTAATAGTATTTTATTAATTTAATATTA
1 AATA-TTATCTTAATAGTATTATATTAAATTAATATTA
12149393 AA
1 AA
12149395 GTGTCTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.12
37 22 0.65
38 8 0.24
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (37 bp):
AATATTATCTTAATAGTATTATATTAAATTAATATTA
Found at i:12149534 original size:124 final size:123
Alignment explanation
Indices: 12149312--12149543 Score: 294
Period size: 124 Copynumber: 1.9 Consensus size: 123
12149302 TTAACTATTT
*
12149312 TAAAAATAATATTATTTTAATAGTTTAATATTAAATTAAATTAAATACTTATCTTAATAGTATTT
1 TAAAAATAATATTATTTTAATAGTTTAATATTAAATTAAATTAAATACTTATCTTAATAATATTT
* *
12149377 TATTAATTTAATATTAAAGTGTCTTAATATTAAATTTAATTTAATGTTTATCTTGTAGA
66 TATTAATTT-ATAATAAAGTATCTTAATATTAAATTTAATTTAATGTTTATCTTGTAGA
** * **
12149436 TAAAAATTCTATTATTTTAATAAGATTTAATATTAAATTAAATTTAATGTTTATCTTGCAGATAA
1 TAAAAATAATATTATTTTAAT-AG-TTTAATATTAAATTAAATTAAATACTTATCTT--A-AT-A
12149501 ATATTTTATT-ATTT-TAAT-AAG-AT-TTAATATTAAATTTAATTTA
60 ATATTTTATTAATTTATAATAAAGTATCTTAATATTAAATTTAATTTA
12149544 GTATTTGTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
124 39 0.41
125 3 0.03
126 32 0.34
127 3 0.03
128 1 0.01
129 6 0.06
130 10 0.11
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (123 bp):
TAAAAATAATATTATTTTAATAGTTTAATATTAAATTAAATTAAATACTTATCTTAATAATATTT
TATTAATTTATAATAAAGTATCTTAATATTAAATTTAATTTAATGTTTATCTTGTAGA
Found at i:12149555 original size:62 final size:62
Alignment explanation
Indices: 12149400--12149543 Score: 252
Period size: 62 Copynumber: 2.3 Consensus size: 62
12149390 TTAAAGTGTC
*
12149400 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAAAATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATTTAATGTTTATCTTGCAGATAAAAATTCTATTATTTTAATAAGAT
* * *
12149462 TTAATATTAAATTAAATTTAATGTTTATCTTGCAGATAAATATTTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATTTAATGTTTATCTTGCAGATAAAAATTCTATTATTTTAATAAGAT
12149524 TTAATATTAAATTTAATTTA
1 TTAATATTAAATTTAATTTA
12149544 GTATTTGTCT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (62 bp):
TTAATATTAAATTTAATTTAATGTTTATCTTGCAGATAAAAATTCTATTATTTTAATAAGAT
Found at i:12150783 original size:14 final size:14
Alignment explanation
Indices: 12150766--12150796 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12150756 AGTAAAATAT
12150766 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
12150780 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
12150794 TTT
1 TTT
12150797 ACTTTTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (14 bp):
TTTCTGGAAAATGA
Found at i:12152944 original size:15 final size:15
Alignment explanation
Indices: 12152924--12152954 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12152914 AAAACAACAT
12152924 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
12152939 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
12152954 A
1 A
12152955 CTTACATAAC
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:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:12156892 original size:15 final size:15
Alignment explanation
Indices: 12156872--12156902 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12156862 AAAACAACAT
12156872 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
12156887 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
12156902 A
1 A
12156903 CTTACATAAC
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:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:12157112 original size:47 final size:45
Alignment explanation
Indices: 12157059--12157153 Score: 172
Period size: 47 Copynumber: 2.1 Consensus size: 45
12157049 AAGAAGCTAG
12157059 AGATAAATTATACATGCATAATACAGAAAAAAAAGATATATATATAT
1 AGATAAATTATACATGCATAATACAG--AAAAAAGATATATATATAT
12157106 AGATAAATTATACATGCATAATACAGAAAAAAGATATATATATAT
1 AGATAAATTATACATGCATAATACAGAAAAAAGATATATATATAT
12157151 AGA
1 AGA
12157154 GAGAGAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 22 0.46
47 26 0.54
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.27
Consensus pattern (45 bp):
AGATAAATTATACATGCATAATACAGAAAAAAGATATATATATAT
Found at i:12168796 original size:20 final size:20
Alignment explanation
Indices: 12168771--12168809 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12168761 TTGATGATAA
*
12168771 TTGAGATGCGAGTGAAGTAC
1 TTGAGATGCGAGTAAAGTAC
12168791 TTGAGATGCGAGTAAAGTA
1 TTGAGATGCGAGTAAAGTA
12168810 AGAGCGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.26
Consensus pattern (20 bp):
TTGAGATGCGAGTAAAGTAC
Found at i:12174089 original size:105 final size:105
Alignment explanation
Indices: 12173912--12174111 Score: 267
Period size: 105 Copynumber: 1.9 Consensus size: 105
12173902 AATGTTTAAA
* * * **
12173912 TGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAATACCATAACTGGGTTATGGCACCTTGA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
* * *
12173977 ACGTAAGACCATGTTTGGACCATGGCAATATAAATACATG
66 ACATAAGACCATGGTAGGACCATGGCAATATAAATACATG
* * *
12174017 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAATTGGGTTATGACA-CTACA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCT-CA
* *
12174081 AATATAAGACCATGGTAGGGCCATGGCAATA
65 AACATAAGACCATGGTAGGACCATGGCAATA
12174112 CATGCGTAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 2 0.02
105 79 0.98
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTCAA
ACATAAGACCATGGTAGGACCATGGCAATATAAATACATG
Found at i:12176238 original size:41 final size:43
Alignment explanation
Indices: 12176166--12176248 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 43
12176156 GACCTACAGC
* *
12176166 TAGTGTGGGTAGTGTGCAAAATGTTCCTAAGCCCAAATGTAAA
1 TAGTGTAGGTAGTGTGCAAAATGTTCCTAAGCCCAAAGGTAAA
*
12176209 TAGTGTAGGTAG-GTG-AAAGTGTTCCTAAGCCCAAAGGTAA
1 TAGTGTAGGTAGTGTGCAAAATGTTCCTAAGCCCAAAGGTAA
12176249 GGCAGGAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 23 0.62
42 3 0.08
43 11 0.30
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (43 bp):
TAGTGTAGGTAGTGTGCAAAATGTTCCTAAGCCCAAAGGTAAA
Found at i:12189440 original size:33 final size:32
Alignment explanation
Indices: 12189368--12189444 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
12189358 TAGATACATG
* * **
12189368 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
*
12189400 TGATAAGACCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
12189434 TGTAAGACCAT
1 TGTAAGACCAT
12189445 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 31 0.82
34 5 0.13
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:12189456 original size:105 final size:99
Alignment explanation
Indices: 12189263--12189492 Score: 255
Period size: 105 Copynumber: 2.3 Consensus size: 99
12189253 AATGTTTAAA
* * * **
12189263 TGTAAGACCATAGCTGGGCTATGACATTTTAATGAAAATACCATAACTGCGTTATGGCACCTTGA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGCGTTATGGCACCTCAA
**
12189328 ACGTAAGACCATGGTTGGACCATGACAGTATAGATACATG
66 ACGTAAGACCATGGCAGGACCATGACA--AT-G--A-ATG
* * *
12189368 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCA-CTACA
1 TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGCGTTATGGCACCT-CA
* * *
12189432 AATGTAAGACCATGGCAGGGCCATGGCAATGAATG
65 AACGTAAGACCATGGCAGGACCATGACAATGAATG
* *
12189467 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGCTGGGCTATGGCA
12189493 CAAAAAGAAC
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
99 27 0.25
100 1 0.01
102 1 0.01
103 2 0.02
104 2 0.02
105 76 0.70
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (99 bp):
TGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGCGTTATGGCACCTCAA
ACGTAAGACCATGGCAGGACCATGACAATGAATG
Found at i:12198347 original size:72 final size:71
Alignment explanation
Indices: 12198263--12198527 Score: 228
Period size: 72 Copynumber: 3.7 Consensus size: 71
12198253 TATTCAGCAA
* * * * *
12198263 AAAATTACGCTAGTTATGCAACAAAAACTTATGCGAACTCTACAGTAGAAAATTATGCGAGCTAT
1 AAAATTATGCTAGCTATGCAACAAAAA-TTATGCGAACTGTACAGCAGAAAATTATGTGAGCTAT
12198328 GCAACGG
65 GCAACGG
* ** * ** * * *
12198335 AAAATTATGCTAGCTGTGCAGTGAAAAATTATGCTAGTTGTGCAGCAGAAAATTATGTGAACTGT
1 AAAATTATGCTAGCTATGCA-ACAAAAATTATGCGAACTGTACAGCAGAAAATTATGTGAGCTAT
*
12198400 GCAACGA
65 GCAACGG
* * * * * *
12198407 AAAATTTTGCTATCTATGCAGCAAAAAGATTTATGCGAACTGTGCAGCAAAAAATTATGTTAGC-
1 AAAATTATGCTAGCTATGCAAC-AAAA-A-TTATGCGAACTGTACAGCAGAAAATTATGTGAGCT
*
12198471 A-GCAACAG
63 ATGCAACGG
* * * *
12198479 AAAATTATGCTAGCTGTGCCACATAAAATTATGTGAACTGTACAACAGA
1 AAAATTATGCTAGCTATGCAACA-AAAATTATGCGAACTGTACAGCAGA
12198528 TATTATGCTA
Statistics
Matches: 150, Mismatches: 38, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
70 17 0.11
71 2 0.01
72 97 0.65
73 6 0.04
74 28 0.19
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (71 bp):
AAAATTATGCTAGCTATGCAACAAAAATTATGCGAACTGTACAGCAGAAAATTATGTGAGCTATG
CAACGG
Found at i:12198460 original size:50 final size:48
Alignment explanation
Indices: 12198257--12198465 Score: 179
Period size: 48 Copynumber: 4.3 Consensus size: 48
12198247 GTGAGCTATT
* * * * * *
12198257 CAGCAAAAAATTACGCTAGTTATGCAACAAAAACTTATGCGAACTCTA
1 CAGCGAAAAATTATGCTAGTTATGCAGCAAAAAATTATGCGAACTGTG
* * * * ** * *
12198305 CAG-TAGAAAATTATGCGAGCTATGCAACGGAAAATTATGCTAGCTGTG
1 CAGCGA-AAAATTATGCTAGTTATGCAGCAAAAAATTATGCGAACTGTG
* * * *
12198353 CAGTGAAAAATTATGCTAGTTGTGCAGCAGAAAATTATGTGAACTGTG
1 CAGCGAAAAATTATGCTAGTTATGCAGCAAAAAATTATGCGAACTGTG
* *
12198401 CAACGAAAAATTTTGCTA-TCTATGCAGCAAAAAGATTTATGCGAACTGTG
1 CAGCGAAAAATTATGCTAGT-TATGCAGCAAAAA-A-TTATGCGAACTGTG
*
12198451 CAGCAAAAAATTATG
1 CAGCGAAAAATTATG
12198466 TTAGCAGCAA
Statistics
Matches: 127, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
47 2 0.02
48 98 0.77
49 2 0.02
50 25 0.20
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (48 bp):
CAGCGAAAAATTATGCTAGTTATGCAGCAAAAAATTATGCGAACTGTG
Found at i:12198553 original size:46 final size:46
Alignment explanation
Indices: 12198433--12198570 Score: 131
Period size: 47 Copynumber: 3.0 Consensus size: 46
12198423 TGCAGCAAAA
* * * * *
12198433 AGAT-TTATGCGAACTGTGCAGCAAAAAATTATGTTAGCAG--CAAC
1 AGATATTATGCTAGCTGTGCAGC-AAAAATTATGTGAACTGTACAAC
*
12198477 AGAAAATTATGCTAGCTGTGCCA-CATAAAATTATGTGAACTGTACAAC
1 AG-ATATTATGCTAGCTGTG-CAGCA-AAAATTATGTGAACTGTACAAC
* *
12198525 AGATATTATGCTAGCTGTGCAGCAAAAATTTATGCGAACTATACAA
1 AGATATTATGCTAGCTGTGCAGCAAAAA-TTATGTGAACTGTACAA
12198571 TAGAAATTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 32 0.42
47 35 0.45
48 6 0.08
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (46 bp):
AGATATTATGCTAGCTGTGCAGCAAAAATTATGTGAACTGTACAAC
Found at i:12198557 original size:24 final size:23
Alignment explanation
Indices: 12198257--12198559 Score: 148
Period size: 24 Copynumber: 12.7 Consensus size: 23
12198247 GTGAGCTATT
* * *
12198257 CAGCAAAAAATTACGCTAGTTATG
1 CAGC-AAAAATTATGCTAGCTGTG
* * * * *
12198281 CAACAAAAACTTATGCGAACTCTA
1 CAGCAAAAA-TTATGCTAGCTGTG
* * *
12198305 CAGTAGAAAATTATGCGAGCTATG
1 CAGCA-AAAATTATGCTAGCTGTG
* *
12198329 CAACGGAAAATTATGCTAGCTGTG
1 CAGC-AAAAATTATGCTAGCTGTG
* *
12198353 CAGTGAAAAATTATGCTAGTTGTG
1 CAG-CAAAAATTATGCTAGCTGTG
*
12198377 CAGCAGAAAATTATG-TGAACTGTG
1 CAGCA-AAAATTATGCT-AGCTGTG
* * * *
12198401 CAACGAAAAATTTTGCTATCTATG
1 CAGC-AAAAATTATGCTAGCTGTG
* *
12198425 CAGCAAAAAGATTTATGCGAACTGTG
1 CAGC-AAAA-A-TTATGCTAGCTGTG
* *
12198451 CAGCAAAAAATTATGTTAGC--AG
1 CAGC-AAAAATTATGCTAGCTGTG
*
12198473 CAACAGAAAATTATGCTAGCTGTG
1 CAGCA-AAAATTATGCTAGCTGTG
* *
12198497 CCA-CATAAAATTATG-TGAACTGTA
1 -CAGCA-AAAATTATGCT-AGCTGTG
* * *
12198521 CAACAGATATTATGCTAGCTGTG
1 CAGCAAAAATTATGCTAGCTGTG
12198544 CAGCAAAAATTTATGC
1 CAGCAAAAA-TTATGC
12198560 GAACTATACA
Statistics
Matches: 210, Mismatches: 51, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
21 1 0.00
22 17 0.08
23 28 0.13
24 135 0.64
25 10 0.05
26 19 0.09
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (23 bp):
CAGCAAAAATTATGCTAGCTGTG
Found at i:12199934 original size:43 final size:44
Alignment explanation
Indices: 12199878--12200047 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 44
12199868 TTACTGAGAG
*
12199878 GTGATAACATGTAAGACCATGTCTAAGACATTGGCATTGTAT-T
1 GTGATAACATGTAAGACCATGTCTAAGACATTGGCATCGTATAT
* * **
12199921 GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGT-TAT
1 GTGATAACATGTAAGACCATGTCTAAGACATTGGCATCGTATAT
* ** * * * * ** *
12199964 ATGATTTCGTATAAGACCCTCTCTGGGACAGTGGCATCG-ATAT
1 GTGATAACATGTAAGACCATGTCTAAGACATTGGCATCGTATAT
* * *
12200007 GTGATAACATGTAAGACCATATCTAAGATA-TGGCATTGTAT
1 GTGATAACATGTAAGACCATGTCTAAGACATTGGCATCGTAT
12200048 GAGCTATTAT
Statistics
Matches: 102, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
42 8 0.08
43 94 0.92
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (44 bp):
GTGATAACATGTAAGACCATGTCTAAGACATTGGCATCGTATAT
Found at i:12201962 original size:59 final size:59
Alignment explanation
Indices: 12201895--12202198 Score: 226
Period size: 59 Copynumber: 5.2 Consensus size: 59
12201885 AAAAGATTCA
* ** * *
12201895 AAAATCTTGTAAGTGGAGTAAATGGTTACGGTCGTAAATCGGTGAATCATAAGATTCTG
1 AAAATCTTGTAAGTGGAGTAAATGGTTACGATCGTAAATCGACGAACCATAAGATTTTG
* * * * * *
12201954 AAAATCTTGCAAATGG-G---A-GGTCATGATTGTAAATCGACAAACCATAAGATTTTG
1 AAAATCTTGTAAGTGGAGTAAATGGTTACGATCGTAAATCGACGAACCATAAGATTTTG
* * * * * * * *
12202008 AAAATCTTATAAGTGGTGTAAATAGTTGCAATCGTAAATC-AGTGAACCGTGAGATTTTG
1 AAAATCTTGTAAGTGGAGTAAATGGTTACGATCGTAAATCGA-CGAACCATAAGATTTTG
* * * * * **
12202067 AAAATCTTGTAATTTGAGTAAATAGTTACGATTGTCAATCGACGAACTGTAAGATTTTG
1 AAAATCTTGTAAGTGGAGTAAATGGTTACGATCGTAAATCGACGAACCATAAGATTTTG
* * * ** * *
12202126 AAAATCTTGTAATTGGAGTAAATGGTTGC-AGTCGTAAATTGAAAAAAATCGTAAGATTTTG
1 AAAATCTTGTAAGTGGAGTAAATGGTTACGA-TCGTAAATCG--ACGAACCATAAGATTTTG
12202187 AAAATCTTGTAA
1 AAAATCTTGTAA
12202199 ATGAGAGGTC
Statistics
Matches: 190, Mismatches: 45, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
54 40 0.21
55 2 0.01
58 4 0.02
59 117 0.62
60 1 0.01
61 26 0.14
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (59 bp):
AAAATCTTGTAAGTGGAGTAAATGGTTACGATCGTAAATCGACGAACCATAAGATTTTG
Found at i:12203690 original size:31 final size:31
Alignment explanation
Indices: 12203655--12203716 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
12203645 TCCGAACCAA
12203655 CTTGCGAAGAGGTCGAGCTCATCGGGACGAT
1 CTTGCGAAGAGGTCGAGCTCATCGGGACGAT
12203686 CTTGCGAAGAGGTCGAGCTCATCGGGACGAT
1 CTTGCGAAGAGGTCGAGCTCATCGGGACGAT
12203717 TACAAGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (31 bp):
CTTGCGAAGAGGTCGAGCTCATCGGGACGAT
Found at i:12205311 original size:30 final size:30
Alignment explanation
Indices: 12205270--12205327 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12205260 TTGGGCATTT
*
12205270 CCACACGGGCTGACCACACGCCCGTGTGAG
1 CCACACGGGCTGACCACACGCCCATGTGAG
* * *
12205300 CCACACTGGCTGGCCCCACGCCCATGTG
1 CCACACGGGCTGACCACACGCCCATGTG
12205328 CTAGTTCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.17, C:0.43, G:0.28, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGACCACACGCCCATGTGAG
Found at i:12208305 original size:5 final size:5
Alignment explanation
Indices: 12208295--12208349 Score: 69
Period size: 5 Copynumber: 11.0 Consensus size: 5
12208285 AAGCCACCCC
*
12208295 TTTTA TTTTA TTTTA TTTTA -TTTA TTATTA TTTTTA TATTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA
12208345 TTTTA
1 TTTTA
12208350 CTAATTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 7 0.16
5 29 0.66
6 6 0.14
7 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:12208320 original size:9 final size:9
Alignment explanation
Indices: 12208296--12208347 Score: 59
Period size: 9 Copynumber: 5.3 Consensus size: 9
12208286 AGCCACCCCT
12208296 TTTATTTTA
1 TTTATTTTA
12208305 TTTTATTTTA
1 -TTTATTTTA
12208315 TTTATTATTA
1 TTTATT-TTA
*
12208325 TTTTTATATTA
1 --TTTATTTTA
12208336 TTTATTTTA
1 TTTATTTTA
12208345 TTT
1 TTT
12208348 TACTAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
9 17 0.46
10 12 0.32
11 3 0.08
12 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:12208403 original size:45 final size:40
Alignment explanation
Indices: 12208296--12208406 Score: 98
Period size: 42 Copynumber: 2.6 Consensus size: 40
12208286 AGCCACCCCT
* * *
12208296 TTTATTTTATTTTATTTTATTTA-TTATTATTTTTATATTA
1 TTTAATTTATTTTAATTT-TTTATTTATTATTCTTATATTA
* *
12208336 TTTATTTTATTTTACTAATTTTTATTTATTATTCTTATACTTTGA
1 TTTAATTTATTTTA--ATTTTTTATTTATTATTCTTATA--TT-A
12208381 TTTTAAATTTATTTTAATTTTTTATT
1 -TTT-AATTTATTTTAATTTTTTATT
12208407 ATCTTTCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
40 14 0.24
41 4 0.07
42 15 0.26
44 2 0.03
45 10 0.17
46 3 0.05
47 10 0.17
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (40 bp):
TTTAATTTATTTTAATTTTTTATTTATTATTCTTATATTA
Found at i:12209405 original size:13 final size:13
Alignment explanation
Indices: 12209387--12209422 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
12209377 TTATTGTTCA
*
12209387 AAAAAAATCTAAG
1 AAAAAAATATAAG
*
12209400 AAAAAAATATAAT
1 AAAAAAATATAAG
12209413 AAAAAAATAT
1 AAAAAAATAT
12209423 TGATCATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAAAATATAAG
Found at i:12216370 original size:16 final size:16
Alignment explanation
Indices: 12216339--12216375 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12216329 ACGTGAATAA
12216339 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
12216355 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
12216371 TATTA
1 TATTA
12216376 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:12216435 original size:22 final size:20
Alignment explanation
Indices: 12216383--12216443 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
12216373 TTAAAATAAA
* * *
12216383 ATTAAAATATTAAATAATTT
1 ATTAAAATAATAATTTATTT
12216403 ATTAAAATAATCAATTATATTT
1 ATTAAAATAAT-AATT-TATTT
* *
12216425 ATTATATTAATAATTTATT
1 ATTAAAATAATAATTTATT
12216444 ATATGACTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 14 0.41
21 7 0.21
22 13 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAAATAATAATTTATTT
Found at i:12219290 original size:18 final size:19
Alignment explanation
Indices: 12219267--12219302 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12219257 AAACTTTAGC
*
12219267 TTTTTC-TTTATTTACAAG
1 TTTTTCATTAATTTACAAG
12219285 TTTTTCATTAATTTACAA
1 TTTTTCATTAATTTACAA
12219303 TGAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.11, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTTCATTAATTTACAAG
Found at i:12220890 original size:130 final size:131
Alignment explanation
Indices: 12220690--12221060 Score: 369
Period size: 130 Copynumber: 2.8 Consensus size: 131
12220680 ACTTATATTT
* * * * *
12220690 TTATTTCTTATTTCATGTTG-TT--GCTTTTTAAATTTTTAATTAATTTTTTTAACATGTTAGTT
1 TTATTTTTTATTTTATGTTGCTTAAGCTTTTTTAATTTTTAATTAATTTTTTTAACATATTAATT
* * * * * * * *
12220752 ATTTTGTTAGATGTTTTGATAGTTACAGTTACATTCTTGAGTCTTGAGTTCGATTTTTCTTTTA-
66 ACTTTGTTAGATGGTTCGATAGTTACAATTACATCCTTAAATCTTGAGTTCGATTTCTCTTTTAC
12220816 C
131 C
12220817 -TATTTTTTATTTTATGTTGCTTAAGCTTTTTTAATTTTTAATTAATTCTTTTTAACATATTAAT
1 TTATTTTTTATTTTATGTTGCTTAAGCTTTTTTAATTTTTAATTAATT-TTTTTAACATATTAAT
* *
12220881 TACTTTGTTAGATGGTTCGATAGTTGCAATTACATCCTTAAATCTTGAGTTTGATTTCTCTTTTA
65 TACTTTGTTAGATGGTTCGATAGTTACAATTACATCCTTAAATCTTGAGTTCGATTTCTCTTTTA
12220946 CTC
130 C-C
* *
12220949 ATATTTGTATTTTTTTAATTTTATGTTACTTCAAGCTTTTTT-ATTTTTAATTAATATTTTTAAC
1 -----T-TA-TTTTTT-ATTTTATGTTGCTT-AAGCTTTTTTAATTTTTAATTAATTTTTTTAAC
* * * * * *
12221013 ATATT-ATCTCATTTTGATAGATTGTTAGATAATTACGATTACATCCTT
57 ATATTAAT-T-ACTTTGTTAGATGGTTCGATAGTTACAATTACATCCTT
12221061 GAGTTTGAGG
Statistics
Matches: 202, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
126 17 0.08
127 2 0.01
129 22 0.11
130 69 0.34
132 1 0.00
139 4 0.02
140 20 0.10
141 57 0.28
142 10 0.05
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (131 bp):
TTATTTTTTATTTTATGTTGCTTAAGCTTTTTTAATTTTTAATTAATTTTTTTAACATATTAATT
ACTTTGTTAGATGGTTCGATAGTTACAATTACATCCTTAAATCTTGAGTTCGATTTCTCTTTTAC
C
Found at i:12221094 original size:141 final size:141
Alignment explanation
Indices: 12220819--12221077 Score: 321
Period size: 141 Copynumber: 1.8 Consensus size: 141
12220809 TCTTTTACTA
* *
12220819 TTTTTTATTTTATGTTGCTTAAGCTTTTTTAATTTTTAATTAATTCTTTTTAACATATTAATTAC
1 TTTTTTATTTTATGTTACTTAAGCTTTTTTAATTTTTAATTAATTATTTTTAACATATTAATTAC
* * * * * *
12220884 TTTGTTAGATGGTTCGATAGTTGCAATTACATCCTTAAATCTTGAGTTTGATTTCTCTTTTACTC
66 TTTGATAGATGGTTAGATAATTACAATTACATCCTTAAATCTTGAGCTTCATTTCTCTTTTACTC
12220949 ATATT-TGTAT
131 ATATTATGTAT
12220959 TTTTTTAATTTTATGTTACTTCAAGCTTTTTT-ATTTTTAATTAA-TATTTTTAACATATT-ATC
1 TTTTTT-ATTTTATGTTACTT-AAGCTTTTTTAATTTTTAATTAATTATTTTTAACATATTAAT-
* * * * *
12221021 TCATTTTGATAGATTGTTAGATAATTACGATTACATCCTTGAGT-TTGAGGCTTCATT
63 T-ACTTTGATAGATGGTTAGATAATTACAATTACATCCTTAAATCTTGA-GCTTCATT
12221078 GTTTTTATAA
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
139 2 0.02
140 25 0.25
141 64 0.63
142 10 0.10
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.54
Consensus pattern (141 bp):
TTTTTTATTTTATGTTACTTAAGCTTTTTTAATTTTTAATTAATTATTTTTAACATATTAATTAC
TTTGATAGATGGTTAGATAATTACAATTACATCCTTAAATCTTGAGCTTCATTTCTCTTTTACTC
ATATTATGTAT
Found at i:12221871 original size:13 final size:13
Alignment explanation
Indices: 12221853--12221878 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12221843 NNNNNNCGAA
12221853 TTATTCGAATTCG
1 TTATTCGAATTCG
12221866 TTATTCGAATTCG
1 TTATTCGAATTCG
12221879 AAAACTCAAC
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:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TTATTCGAATTCG
Found at i:12223908 original size:3 final size:3
Alignment explanation
Indices: 12223900--12223927 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12223890 TCATTTAACC
12223900 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12223928 AAACAACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12224826 original size:27 final size:27
Alignment explanation
Indices: 12224796--12224857 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
12224786 ACGTTCCTCT
* *
12224796 AACAGATACATTGCGGACTGTCCTGCG
1 AACAGATACATTACGGACTGTCCCGCG
*
12224823 AACA-ACTACATTACGGACTGTCCCGTG
1 AACAGA-TACATTACGGACTGTCCCGCG
12224850 AACAGATA
1 AACAGATA
12224858 AACTGCAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (27 bp):
AACAGATACATTACGGACTGTCCCGCG
Done.