Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 2 of 322
Found at i:269148 original size:10 final size:9
Alignment explanation
Indices: 269133--269177 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
269123 AGAGTGAATA
269133 ATAATACTAT
1 ATAATA-TAT
269143 ATAATATAT
1 ATAATATAT
269152 ATATATATAT
1 ATA-ATATAT
*
269162 ATATATGTAT
1 ATA-ATATAT
269172 ATAATA
1 ATAATA
269178 GAAATACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
9 8 0.25
10 24 0.75
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
ATAATATAT
Found at i:269151 original size:2 final size:2
Alignment explanation
Indices: 269140--269174 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
269130 ATAATAATAC
*
269140 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
269175 ATAGAAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:269398 original size:20 final size:21
Alignment explanation
Indices: 269335--269398 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
269325 TGTGTGCATA
*
269335 ATATATATTTAGATATTAAAAC
1 ATATATATATAG-TATTAAAAC
* * *
269357 ATATATACATAATGTATAAAAAG
1 ATATATATAT-A-GTATTAAAAC
269380 A-ATATATATAGTATTAAAA
1 ATATATATATAGTATTAAAA
269399 ATGGGAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.24
21 1 0.03
22 15 0.44
23 9 0.26
24 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (21 bp):
ATATATATATAGTATTAAAAC
Found at i:271078 original size:42 final size:42
Alignment explanation
Indices: 271030--271144 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
271020 CTAACTCTAT
* **
271030 TGAAACTTCAAGGAGATCTACTGTGGCTTCAATCAACTTCGTC
1 TGAAACTTCAAGGAGATCTGCTGTGGCTTCAATCAA-TTCCAC
* * *
271073 -GAAACTTCAAGGAGATCTGCTATAGCTTTAATCAATTCCAC
1 TGAAACTTCAAGGAGATCTGCTGTGGCTTCAATCAATTCCAC
271114 TGAAACTTCAAGGAGATCTGCTGTGGCTTCA
1 TGAAACTTCAAGGAGATCTGCTGTGGCTTCA
271145 GCCGCTACAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 4 0.06
42 58 0.94
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (42 bp):
TGAAACTTCAAGGAGATCTGCTGTGGCTTCAATCAATTCCAC
Found at i:271546 original size:43 final size:42
Alignment explanation
Indices: 271499--271829 Score: 171
Period size: 44 Copynumber: 7.6 Consensus size: 42
271489 TTTCAGCCTA
* *
271499 TTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATTTGGCTTC
1 TTACCCTACTGCTTAGGGGGTTAA-GCTTGTAAATTTAGCTTC
* * ** * * * *
271542 TTACCCTACTCCTTAGGGGCTTAAAGCTCAT-TATCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTT-AAGCTTGTAAAT-TTAGCT-TC
* * * * * *
271586 TTTCCCTACTGCTTAGGGTGATAAGATCTATAAACTTTAGCTTG
1 TTACCCTACTGCTTAGGGGGTTAAGCT-TGTAAA-TTTAGCTTC
* ** * * * *
271630 TTACCCTACTGCTTATGGGAGACAAGATCTGTAATTTTCAGCCTA
1 TTACCCTACTGCTTA-GGGGGTTAAGCT-TGTAAATTT-AGCTTC
* *
271675 TTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATTTGGCTTC
1 TTACCCTACTGCTTAGGGGGTTAA-GCTTGTAAATTTAGCTTC
** * * * *
271718 TTACCCTACTGCTTAGGGGGTTAAAGCTCAT-TATCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTT-AAGCTTGTAAAT-TTAGCT-TC
* * * * * *
271762 TTTCCCTACTGCTTAGGGTGATAAGATCTATAAACTTTAGCTTG
1 TTACCCTACTGCTTAGGGGGTTAAGCT-TGTAAA-TTTAGCTTC
*
271806 TTACCCTACTGCTTATGGGGTTAA
1 TTACCCTACTGCTTAGGGGGTTAA
271830 AGCTCGTTGC
Statistics
Matches: 220, Mismatches: 53, Indels: 29
0.73 0.18 0.10
Matches are distributed among these distances:
42 4 0.02
43 68 0.31
44 101 0.46
45 45 0.20
46 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (42 bp):
TTACCCTACTGCTTAGGGGGTTAAGCTTGTAAATTTAGCTTC
Found at i:271637 original size:44 final size:44
Alignment explanation
Indices: 271584--271825 Score: 197
Period size: 44 Copynumber: 5.5 Consensus size: 44
271574 ATCTTCGATC
* *
271584 TGTTTCCCTACTGCTTAGGGTGATAAGATCTATAAACTTTAGCT
1 TGTTACCCTACTGCTTAGGGGGATAAGATCTATAAACTTTAGCT
* * * * *
271628 TGTTACCCTACTGCTTATGGGAGACAAGATCTGT-AATTTTCAGCC
1 TGTTACCCTACTGCTTA-GGGGGATAAGATCTATAAACTTT-AGCT
* * * * * *
271673 TATTACCCTACTACTTAGGGGGTTAAG-GCTTGTAAA-TTTGGCT
1 TGTTACCCTACTGCTTAGGGGGATAAGATC-TATAAACTTTAGCT
* * * * * * *
271716 TCTTACCCTACTGCTTAGGGGGTTAA-AGCTCATTATC-TTCGAT
1 TGTTACCCTACTGCTTAGGGGGATAAGATCT-ATAAACTTTAGCT
* *
271759 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTATAAACTTTAGCT
1 -TGTTACCCTACTGCTTAGGGGGATAAGATCTATAAACTTTAGCT
*
271804 TGTTACCCTACTGCTTATGGGG
1 TGTTACCCTACTGCTTAGGGGG
271826 TTAAAGCTCG
Statistics
Matches: 155, Mismatches: 33, Indels: 20
0.75 0.16 0.10
Matches are distributed among these distances:
42 1 0.01
43 35 0.23
44 79 0.51
45 40 0.26
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (44 bp):
TGTTACCCTACTGCTTAGGGGGATAAGATCTATAAACTTTAGCT
Found at i:271664 original size:176 final size:176
Alignment explanation
Indices: 271470--271824 Score: 692
Period size: 176 Copynumber: 2.0 Consensus size: 176
271460 TGCAACTTCA
271470 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
1 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
271535 TGGCTTCTTACCCTACTCCTTAGGGGCTTAAAGCTCATTATCTTCGATCTGTTTCCCTACTGCTT
66 TGGCTTCTTACCCTACTCCTTAGGGGCTTAAAGCTCATTATCTTCGATCTGTTTCCCTACTGCTT
271600 AGGGTGATAAGATCTATAAACTTTAGCTTGTTACCCTACTGCTTAT
131 AGGGTGATAAGATCTATAAACTTTAGCTTGTTACCCTACTGCTTAT
271646 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
1 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
* *
271711 TGGCTTCTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTTCCCTACTGCTT
66 TGGCTTCTTACCCTACTCCTTAGGGGCTTAAAGCTCATTATCTTCGATCTGTTTCCCTACTGCTT
271776 AGGGTGATAAGATCTATAAACTTTAGCTTGTTACCCTACTGCTTAT
131 AGGGTGATAAGATCTATAAACTTTAGCTTGTTACCCTACTGCTTAT
271822 GGG
1 GGG
271825 GTTAAAGCTC
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (176 bp):
GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
TGGCTTCTTACCCTACTCCTTAGGGGCTTAAAGCTCATTATCTTCGATCTGTTTCCCTACTGCTT
AGGGTGATAAGATCTATAAACTTTAGCTTGTTACCCTACTGCTTAT
Found at i:271722 original size:88 final size:88
Alignment explanation
Indices: 271470--271736 Score: 310
Period size: 88 Copynumber: 3.0 Consensus size: 88
271460 TGCAACTTCA
271470 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
1 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
*
271535 TGGCTTCTTACCCTACTCCTTAG
66 TGGCTTCTTACCCTACTGCTTAG
** * * * * * * * * * *
271558 GGGCTTA-AAGCTCAT-T-ATCTTC-GATCTGTTTCCCTACTGCTTAGGGTGATAA-GATCTATA
1 GGG-AGACAAGATC-TGTAATTTTCAG-CCTATTACCCTACTACTTAGGGGGTTAAGGCT-TGTA
* * *
271618 AACTTTAGCTTGTTACCCTACTGCTTAT
62 AA-TTTGGCTTCTTACCCTACTGCTTAG
271646 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
1 GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
271711 TGGCTTCTTACCCTACTGCTTAG
66 TGGCTTCTTACCCTACTGCTTAG
271734 GGG
1 GGG
271737 GTTAAAGCTC
Statistics
Matches: 138, Mismatches: 31, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
86 3 0.02
87 34 0.25
88 64 0.46
89 34 0.25
90 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (88 bp):
GGGAGACAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGCTTGTAAATT
TGGCTTCTTACCCTACTGCTTAG
Found at i:271810 original size:88 final size:87
Alignment explanation
Indices: 271529--271877 Score: 379
Period size: 88 Copynumber: 4.0 Consensus size: 87
271519 TTAAGGCTTG
* * *
271529 TAAATTTGGCTTCTTACCCTACTCCTTAGGGGCTTAAAGCTCATTATCTTCGATCTGTTTCCCTA
1 TAAATTTAGCTTCTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTTCCCTA
271594 CTGCTTAGGGTGATAAGATCTA
66 CTGCTTAGGGTGATAAGATCTA
* * * * * *
271616 TAAACTTTAGCTTGTTACCCTACTGCTTATGGGAG--ACAAGATC-TGTAATTTTC-AGCCTATT
1 TAAA-TTTAGCTTCTTACCCTACTGCTTA-GGGGGTTA-AAGCTCAT-T-ATCTTCGA-TCTGTT
* * * * * *
271677 ACCCTACTACTTAGGGGGTTAAG-GCTTG
60 TCCCTACTGCTTAGGGTGATAAGATC-TA
*
271705 TAAATTTGGCTTCTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTTCCCTA
1 TAAATTTAGCTTCTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTTCCCTA
271770 CTGCTTAGGGTGATAAGATCTA
66 CTGCTTAGGGTGATAAGATCTA
* * * **
271792 TAAACTTTAGCTTGTTACCCTACTGCTTATGGGGTTAAAGCTCGTTGCCTTCGATCTGTTTCCCT
1 TAAA-TTTAGCTTCTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTTCCCT
271857 ACTGCTTATGGG-G-TAAGATCT
65 ACTGCTTA-GGGTGATAAGATCT
271878 GTGAATTCAC
Statistics
Matches: 214, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
87 51 0.24
88 122 0.57
89 41 0.19
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (87 bp):
TAAATTTAGCTTCTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTTCCCTA
CTGCTTAGGGTGATAAGATCTA
Found at i:271857 original size:44 final size:43
Alignment explanation
Indices: 271721--271870 Score: 144
Period size: 44 Copynumber: 3.4 Consensus size: 43
271711 TGGCTTCTTA
* *
271721 CCCTACTGCTTAGGGGGTTAAAGCTCATTATCTTCGATCTGTTT
1 CCCTACTGCTTATGGGGTTAAAGCTC-TTAACTTCGATCTGTTT
* * * * *
271765 CCCTACTGCTTA--GGGTGATAAGATCTATAAACTT-TAGCTTGTTA
1 CCCTACTGCTTATGGGGTTA-AAGCTCT-T-AACTTCGATC-TGTTT
**
271809 CCCTACTGCTTATGGGGTTAAAGCTCGTTGCCTTCGATCTGTTT
1 CCCTACTGCTTATGGGGTTAAAGCTC-TTAACTTCGATCTGTTT
271853 CCCTACTGCTTATGGGGT
1 CCCTACTGCTTATGGGGT
271871 AAGATCTGTG
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
42 6 0.07
43 8 0.09
44 57 0.67
45 8 0.09
46 6 0.07
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (43 bp):
CCCTACTGCTTATGGGGTTAAAGCTCTTAACTTCGATCTGTTT
Found at i:284330 original size:22 final size:21
Alignment explanation
Indices: 284264--284331 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 21
284254 GTGTGTGCAT
* *
284264 AATATATATTTAGATATTAAAA
1 AATATATATATA-TTATTAAAA
* * *
284286 CATATATACATAATGTATAAAAA
1 AATATATATAT-AT-TATTAAAA
284309 GAATATATATATATTATTAAAA
1 -AATATATATATATTATTAAAA
284331 A
1 A
284332 TGGGAAATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 15 0.43
23 10 0.29
24 9 0.26
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (21 bp):
AATATATATATATTATTAAAA
Found at i:285736 original size:24 final size:24
Alignment explanation
Indices: 285706--285755 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
285696 GGGGCCGGGT
285706 AAATTTGGGTTCCCACAGTCTTCA
1 AAATTTGGGTTCCCACAGTCTTCA
*
285730 AAATTTGGGTTCTCACAGTCTTCA
1 AAATTTGGGTTCCCACAGTCTTCA
285754 AA
1 AA
285756 CTCTAACATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (24 bp):
AAATTTGGGTTCCCACAGTCTTCA
Found at i:292570 original size:27 final size:27
Alignment explanation
Indices: 292517--292571 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
292507 AATATTAAAG
* **
292517 ACATTTTCAAACCTACTCTGAGGATTC
1 ACATTTTCAAACCTACTCGGACAATTC
292544 ACATTTTCAAACCTACTCGGACAATTC
1 ACATTTTCAAACCTACTCGGACAATTC
292571 A
1 A
292572 ATATTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (27 bp):
ACATTTTCAAACCTACTCGGACAATTC
Found at i:293725 original size:21 final size:21
Alignment explanation
Indices: 293682--293723 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
293672 ACATGTAAAA
293682 AAATTATAAATAATATTATTT
1 AAATTATAAATAATATTATTT
*
293703 AAATTGTAATATAATATTATT
1 AAATTATAA-ATAATATTATT
293724 AATATTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATTATAAATAATATTATTT
Found at i:293772 original size:16 final size:16
Alignment explanation
Indices: 293750--293791 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
293740 TTTTTGTATT
293750 ATTTTAATATTAAATA
1 ATTTTAATATTAAATA
* *
293766 TTTTTAAAATTAAATA
1 ATTTTAATATTAAATA
*
293782 ACTTTAATAT
1 ATTTTAATAT
293792 AATTGATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAATATTAAATA
Found at i:300665 original size:45 final size:45
Alignment explanation
Indices: 300612--300737 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
300602 ACCTACTTAC
*
300612 CATGATGCCATAACATCTTTCAATTATGGTCTTACTTAAT-TATGT
1 CATGATGCCATAACATCTTTCAACTATGGTCTTACTTAATCT-TGT
* *
300657 CATGATGCCA-AAGCATCTTTCAACTATGGTCATAC-TCATCCTTGT
1 CATGATGCCATAA-CATCTTTCAACTATGGTCTTACTTAAT-CTTGT
* * * *
300702 CATGGTGCCATAGCATCTTTCAGCTATGATCTTACT
1 CATGATGCCATAACATCTTTCAACTATGGTCTTACT
300738 CATTTTAGGC
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
44 5 0.07
45 61 0.90
46 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.37
Consensus pattern (45 bp):
CATGATGCCATAACATCTTTCAACTATGGTCTTACTTAATCTTGT
Found at i:304862 original size:29 final size:30
Alignment explanation
Indices: 304827--304889 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
304817 ATTTATACCG
* *
304827 AAATCAAAGTTT-ATGTTTATAATTGCACA
1 AAATCAAAGTTTAAAGTTTAGAATTGCACA
304856 AAATCAAAGTTTAAAGTTTAGAATTGCACA
1 AAATCAAAGTTTAAAGTTTAGAATTGCACA
304886 AAAT
1 AAAT
304890 TAATATGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTTAAAGTTTAGAATTGCACA
Found at i:305147 original size:28 final size:30
Alignment explanation
Indices: 305083--305147 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
305073 TATTATTAAA
*
305083 ACATC-AT-TTTTTTAATTTTATAATTATC
1 ACATCAATATTTTTTAATTTTATAAATATC
* *
305111 AAATTAATATTTTTT-ATTTTA-AAATATC
1 ACATCAATATTTTTTAATTTTATAAATATC
305139 ACATCAATA
1 ACATCAATA
305148 AATAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 16 0.53
29 8 0.27
30 6 0.20
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (30 bp):
ACATCAATATTTTTTAATTTTATAAATATC
Found at i:314724 original size:15 final size:15
Alignment explanation
Indices: 314700--314731 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
314690 CAAGGCCACC
314700 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
*
314715 AAGAAGAAGAAAAAG
1 AAGAAAAAGAAAAAG
314730 AA
1 AA
314732 ACGTACTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:315555 original size:15 final size:15
Alignment explanation
Indices: 315535--315577 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
315525 AAAATGTTTA
*
315535 ATTAATTTAATTAAT
1 ATTAATTTAATTAAG
*
315550 ATTAATTTAATTCAG
1 ATTAATTTAATTAAG
315565 ATTAA-TTAATTAA
1 ATTAATTTAATTAA
315578 CCGTTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTAATTTAATTAAG
Found at i:315922 original size:23 final size:23
Alignment explanation
Indices: 315883--315932 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
315873 ACGCTTATTG
*
315883 TATTAATAAAATTTTTAATTTAT
1 TATTAATAAAATTTTTAATTTAA
*
315906 TATTGAATAAAA-TTTTATTTTAA
1 TATT-AATAAAATTTTTAATTTAA
315929 TATT
1 TATT
315933 TTTATACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTAATAAAATTTTTAATTTAA
Found at i:318822 original size:20 final size:19
Alignment explanation
Indices: 318793--318852 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
318783 ATATACATAG
*
318793 TAATATTATCTAAAAATATA
1 TAATAATATC-AAAAATATA
*
318813 TAATAATATCGAAAATATA
1 TAATAATATCAAAAATATA
* *
318832 TACATGATAT-AAAAAGATA
1 TA-ATAATATCAAAAATATA
318851 TA
1 TA
318853 GGGTTAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
TAATAATATCAAAAATATA
Found at i:324829 original size:12 final size:12
Alignment explanation
Indices: 324812--324854 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
324802 TACGTGGACA
324812 TTCAAGAAGACT
1 TTCAAGAAGACT
324824 TTCAAGAAGACT
1 TTCAAGAAGACT
*
324836 TTCAAGAAGATT
1 TTCAAGAAGACT
324848 TTCAAGA
1 TTCAAGA
324855 TTGGCAGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (12 bp):
TTCAAGAAGACT
Found at i:325084 original size:15 final size:17
Alignment explanation
Indices: 325046--325085 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
325036 TTTCAGTATT
*
325046 CTCTCTTTGTAAACACT
1 CTCTCTTTGTAAACACC
325063 CTCTCTTTGTAAA-ACC
1 CTCTCTTTGTAAACACC
325079 CT-TCTTT
1 CTCTCTTT
325086 TTACTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 4 0.18
17 13 0.59
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (17 bp):
CTCTCTTTGTAAACACC
Found at i:338359 original size:33 final size:33
Alignment explanation
Indices: 338317--338413 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
338307 TCTTCTTGAC
*
338317 ATTCCAGCTCCTGTCCAGCAACCAAACACTTCA
1 ATTCCAGCTCCTGTCCAGCAACCAAACACTCCA
* *
338350 ATTCCAGCTCCTGTCCAGCAACCAAATACTCCC
1 ATTCCAGCTCCTGTCCAGCAACCAAACACTCCA
* * *
338383 ATTCCAGCGCCTGTCCAGAAATCAAACACTC
1 ATTCCAGCTCCTGTCCAGCAACCAAACACTC
338414 TCACTCAGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.30, C:0.39, G:0.10, T:0.21
Consensus pattern (33 bp):
ATTCCAGCTCCTGTCCAGCAACCAAACACTCCA
Found at i:341247 original size:35 final size:35
Alignment explanation
Indices: 341175--341251 Score: 120
Period size: 34 Copynumber: 2.2 Consensus size: 35
341165 TAGGTTTAAT
* * *
341175 AAAAAAATGTAATAAAATTTGATCAAGAATTTGAA
1 AAAAAAAAGTAATAAAAGTTGAACAAGAATTTGAA
341210 AAAAAAAAG-AATAAAAGTTGAACAAGAATTTGAA
1 AAAAAAAAGTAATAAAAGTTGAACAAGAATTTGAA
341244 AAAAAAAA
1 AAAAAAAA
341252 AAGGTAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 31 0.79
35 8 0.21
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (35 bp):
AAAAAAAAGTAATAAAAGTTGAACAAGAATTTGAA
Found at i:341810 original size:330 final size:329
Alignment explanation
Indices: 341210--341854 Score: 1254
Period size: 330 Copynumber: 2.0 Consensus size: 329
341200 AGAATTTGAA
341210 AAAAAAAAGAATAAAAGTTGAACAAGAATTTGAAAAAAAAAAAAGGTAAAATAAAATCAAAGTCT
1 AAAAAAAAGAATAAAAGTTGAACAAGAATTTGAAAAAAAAAAAAGGTAAAATAAAATCAAAGTCT
341275 AGGAGAAGAACAATTGATATAGAAAAATGATGAAAAGGATCTTGACATACTTCAAAGAAGTGCTT
66 AGGAGAAGAACAATTGATATAGAAAAATGATGAAAAGGATCTTGACATACTTCAAAGAAGTGCTT
341340 GTGGGCCCTTGATACCAACTAGCATTAAGAAAAGCTTCAGGTGGACTATAATCATGAGTTTGCTC
131 GTGGGCCCTTGATACCAACTAGCATTAAGAAAAGCTTCAGGTGGACTATAATCATGAGTTTGCTC
341405 AGATCTGGAAAGATAAGAGTAGTTATCTGTCATAAGTTCTTTTTCTCTTGGAAGCCAAACTCATG
196 AGATCTGGAAAGATAAGAGTAGTTATCTGTCATAAGTTCTTTTTCTCTTGGAAGCCAAACTCATG
341470 GATAAGGAAAAACACAGAAATATCTTAAATAGAAACCCCACCTAGAAGGTCCAGCACTCTAGGTT
261 GATAAGGAAAAACACAGAAATATCTTAAATAGAAACCCCACCTAGAAGGTCCAGCACTCTAGGTT
341535 TAAT
326 TAAT
* * *
341539 AAAAAAATGTAATAAAATTTGATCAAGAATTTGAAAAAAAAAAAAGGTAAAATAAAATCAAAGTC
1 AAAAAAAAG-AATAAAAGTTGAACAAGAATTTGAAAAAAAAAAAAGGTAAAATAAAATCAAAGTC
341604 TAGGAGAAGAACAATTGATATAGAAAAATGATGAAAAGGATCTTGACATACTTCAAAGAAGTGCT
65 TAGGAGAAGAACAATTGATATAGAAAAATGATGAAAAGGATCTTGACATACTTCAAAGAAGTGCT
341669 TGTGGGCCCTTGATACCAACTAGCATTAAGAAAAGCTTCAGGTGGACTATAATCATGAGTTTGCT
130 TGTGGGCCCTTGATACCAACTAGCATTAAGAAAAGCTTCAGGTGGACTATAATCATGAGTTTGCT
341734 CAGATCTGGAAAGATAAGAGTAGTTATCTGTCATAAGTTCTTTTTCTCTTGGAAGCCAAACTCAT
195 CAGATCTGGAAAGATAAGAGTAGTTATCTGTCATAAGTTCTTTTTCTCTTGGAAGCCAAACTCAT
341799 GGATAAGGAAAAACACAGAAATATCTTAAATAGAAACCCCACCTAGAAGGTCCAGC
260 GGATAAGGAAAAACACAGAAATATCTTAAATAGAAACCCCACCTAGAAGGTCCAGC
341855 TGATCCATAT
Statistics
Matches: 312, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
329 8 0.03
330 304 0.97
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (329 bp):
AAAAAAAAGAATAAAAGTTGAACAAGAATTTGAAAAAAAAAAAAGGTAAAATAAAATCAAAGTCT
AGGAGAAGAACAATTGATATAGAAAAATGATGAAAAGGATCTTGACATACTTCAAAGAAGTGCTT
GTGGGCCCTTGATACCAACTAGCATTAAGAAAAGCTTCAGGTGGACTATAATCATGAGTTTGCTC
AGATCTGGAAAGATAAGAGTAGTTATCTGTCATAAGTTCTTTTTCTCTTGGAAGCCAAACTCATG
GATAAGGAAAAACACAGAAATATCTTAAATAGAAACCCCACCTAGAAGGTCCAGCACTCTAGGTT
TAAT
Found at i:356949 original size:70 final size:69
Alignment explanation
Indices: 356836--356965 Score: 224
Period size: 70 Copynumber: 1.9 Consensus size: 69
356826 GATAGTTTTT
*
356836 ATAAATTATGGAATAATATTTGATGTAATAACATAATAAATCATCATTAAATTAAACAAAAAAAT
1 ATAAATTATGAAATAATATTTGATGTAATAACATAATAAATCATCATTAAATTAAA-AAAAAAAT
356901 ATCTA
65 ATCTA
**
356906 ATAAATTATGAAATAATATTTTTTGTAATAACATAATAAATCATCATTAAATTAAAAAAA
1 ATAAATTATGAAATAATATTTGATGTAATAACATAATAAATCATCATTAAATTAAAAAAA
356966 TTGAAGAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
69 4 0.07
70 53 0.93
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.35
Consensus pattern (69 bp):
ATAAATTATGAAATAATATTTGATGTAATAACATAATAAATCATCATTAAATTAAAAAAAAAATA
TCTA
Found at i:357907 original size:5 final size:6
Alignment explanation
Indices: 357892--357928 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
357882 TAGGATTCGA
357892 AAAAAG AAAAAG AAAAAG AAAAAGG AAAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAA-G -AAAAAG AAAAA
357929 AAATTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.76
7 2 0.07
8 5 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:357921 original size:8 final size:7
Alignment explanation
Indices: 357890--357929 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
357880 TTTAGGATTC
357890 GAAAAAA
1 GAAAAAA
357897 G-AAAAA
1 GAAAAAA
357903 G-AAAAA
1 GAAAAAA
*
357909 GAAAAAG
1 GAAAAAA
357916 GAAAAAA
1 GAAAAAA
357923 GAAAAAA
1 GAAAAAA
357930 AATTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:383016 original size:8 final size:8
Alignment explanation
Indices: 382993--383027 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
382983 GGTTTCAACA
382993 ATATACAT
1 ATATACAT
*
383001 ATAGACAT
1 ATATACAT
*
383009 ACATACAT
1 ATATACAT
383017 ATATACAT
1 ATATACAT
383025 ATA
1 ATA
383028 CATATAGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (8 bp):
ATATACAT
Found at i:396499 original size:25 final size:25
Alignment explanation
Indices: 396463--396524 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
396453 ACAAATGTGC
*
396463 TAATC-GATGAGCACTGACATGCTAA
1 TAATCAGA-GAGCACTAACATGCTAA
*
396488 TAATTAGAGAGCACTAACATGCTAA
1 TAATCAGAGAGCACTAACATGCTAA
396513 TAATCAGAGAGC
1 TAATCAGAGAGC
396525 GTGCTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACATGCTAA
Found at i:406509 original size:39 final size:40
Alignment explanation
Indices: 406466--406633 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
406456 CTCGTTCAAG
* * * *
406466 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
406505 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
406545 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
406585 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
406625 TGCCTTCGG
1 TGCCTTCGG
406634 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:406617 original size:80 final size:80
Alignment explanation
Indices: 406501--406686 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
406491 AGTAACTCAT
* * *
406501 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
406565 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
406580 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
406644 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
406661 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
406687 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:406646 original size:40 final size:40
Alignment explanation
Indices: 406503--406686 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
406493 TAACTCATAC
* *
406503 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
406543 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
406583 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
406623 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
406664 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
406687 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:415313 original size:20 final size:21
Alignment explanation
Indices: 415257--415314 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
415247 TTTACATCCA
* *
415257 TTTTTCTTGTCGTTTTGCTATT
1 TTTTTCTTGT-ATTTTTCTATT
* *
415279 TGTTTCTTCTATTTTTC-ATT
1 TTTTTCTTGTATTTTTCTATT
*
415299 TTTTTCTTGTTTTTTT
1 TTTTTCTTGTATTTTT
415315 TACTGCTCGC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 16 0.55
21 5 0.17
22 8 0.28
ACGTcount: A:0.05, C:0.12, G:0.09, T:0.74
Consensus pattern (21 bp):
TTTTTCTTGTATTTTTCTATT
Found at i:418977 original size:16 final size:15
Alignment explanation
Indices: 418955--419007 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
418945 ATATATTTTT
418955 AAATTAAAATATAAA
1 AAATTAAAATATAAA
* **
418970 AAATTTAAATTATACT
1 AAA-TTAAAATATAAA
418986 AAATTAAAATAT-AA
1 AAATTAAAATATAAA
419000 AAATTAAA
1 AAATTAAA
419008 TTCTAAATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 8 0.26
15 11 0.35
16 12 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTAAAATATAAA
Found at i:419014 original size:14 final size:14
Alignment explanation
Indices: 418955--419007 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
418945 ATATATTTTT
418955 AAATTAAAATATAAA
1 AAATTAAAATAT-AA
* *
418970 AAATTTAAATTATACT
1 AAA-TTAAAATATA-A
418986 AAATTAAAATATAA
1 AAATTAAAATATAA
419000 AAATTAAA
1 AAATTAAA
419008 TTCTAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.25
15 13 0.41
16 11 0.34
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTAAAATATAA
Found at i:419145 original size:29 final size:31
Alignment explanation
Indices: 419099--419165 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
419089 AAATGATGAC
*
419099 TTGAATTTCTAAT-AAAAAAC-AACATTCAA
1 TTGAATTTCTAATAAAAAAACTAACAATCAA
*
419128 TTGAGTTT-TAATAAAAAAAACTAACAATCAA
1 TTGAATTTCTAAT-AAAAAAACTAACAATCAA
*
419159 TTAAATT
1 TTGAATT
419166 CTGAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.13
29 7 0.23
30 7 0.23
31 13 0.42
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (31 bp):
TTGAATTTCTAATAAAAAAACTAACAATCAA
Found at i:419766 original size:15 final size:16
Alignment explanation
Indices: 419748--419777 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
419738 TTTTTTATAA
419748 TTTTATA-ATTTTTAT
1 TTTTATATATTTTTAT
419763 TTTTATATATTTTTA
1 TTTTATATATTTTTA
419778 AATTCTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATATATTTTTAT
Found at i:419781 original size:24 final size:24
Alignment explanation
Indices: 419719--419804 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 24
419709 ACCTATATGA
* *
419719 TTTATAATTTTTTAA--GTTATTT
1 TTTATAATTTTATAATTTTTATTT
419741 TTTATAATTTTATAATTTTTATTT
1 TTTATAATTTTATAATTTTTATTT
*
419765 TTATATATTTTTA-AATTCTATTAGTTT
1 TT-TATAATTTTATAATT-T-TTA-TTT
419792 TTTAATAATTTTA
1 TTT-ATAATTTTA
419805 AAAAAAATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
22 14 0.26
24 12 0.23
25 10 0.19
26 4 0.08
27 13 0.25
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTATAATTTTATAATTTTTATTT
Found at i:420136 original size:29 final size:30
Alignment explanation
Indices: 420104--420161 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
420094 AAATGTTATA
*
420104 ATTTAA-TCACTGAACTATTAAAAATTTTC
1 ATTTAAGTCACTGAACCATTAAAAATTTTC
* *
420133 ATTTAAGTCATTGAACCATTAAAATTTTT
1 ATTTAAGTCACTGAACCATTAAAAATTTT
420162 TTATCTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (30 bp):
ATTTAAGTCACTGAACCATTAAAAATTTTC
Found at i:426732 original size:47 final size:47
Alignment explanation
Indices: 426658--426751 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
426648 ACATTACATG
*
426658 CAGACATATATTCGAGGACACTAGTTCACTTTCAATCCTACTGCCAT
1 CAGACATAAATTCGAGGACACTAGTTCACTTTCAATCCTACTGCCAT
*
426705 CAGACATAAATTCGAGGACACTGGTTCACTTTCAATCCTACTGCCAT
1 CAGACATAAATTCGAGGACACTAGTTCACTTTCAATCCTACTGCCAT
426752 TAGCAAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (47 bp):
CAGACATAAATTCGAGGACACTAGTTCACTTTCAATCCTACTGCCAT
Found at i:427438 original size:18 final size:18
Alignment explanation
Indices: 427417--427528 Score: 90
Period size: 17 Copynumber: 6.4 Consensus size: 18
427407 AAGTTTTTTT
*
427417 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
*
427435 AACACGAGAA--TTTGTA
1 AACACGAGAATTTTTGAA
* *
427451 AACACGAAAATTTTAG-A
1 AACACGAGAATTTTTGAA
* *
427468 AACATGAAAATTTTT-AA
1 AACACGAGAATTTTTGAA
* *
427485 AACACGACATTTTTTTTG-A
1 AACACGAGA--ATTTTTGAA
*
427504 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
427522 AACACGA
1 AACACGA
427529 ATTTTTTTAT
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
16 14 0.19
17 28 0.38
18 19 0.26
19 13 0.18
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
AACACGAGAATTTTTGAA
Found at i:427448 original size:16 final size:16
Alignment explanation
Indices: 427429--427491 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
427419 CACGGGAATT
*
427429 TTTGAAAACACGAGAA
1 TTTGAAAACACGAAAA
*
427445 TTTGTAAACACGAAAA
1 TTTGAAAACACGAAAA
* *
427461 TTTTAGAAACATGAAAA
1 TTTGA-AAACACGAAAA
*
427478 TTTTTAAAACACGA
1 -TTTGAAAACACGA
427492 CATTTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
16 17 0.44
17 17 0.44
18 5 0.13
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (16 bp):
TTTGAAAACACGAAAA
Found at i:427498 original size:16 final size:16
Alignment explanation
Indices: 427425--427534 Score: 71
Period size: 18 Copynumber: 6.4 Consensus size: 16
427415 TTAACACGGG
427425 AATTTTTGAAAACACGA
1 AATTTTT-AAAACACGA
*
427442 GAATTTGT-AAACACGA
1 -AATTTTTAAAACACGA
* *
427458 AAATTTTAGAAACATGAA
1 AATTTTTA-AAACACG-A
427476 AATTTTTAAAACACGA
1 AATTTTTAAAACACGA
* * *
427492 CATTTTTTTTGAAACACGGG
1 -A--ATTTTTAAAACAC-GA
427512 AATTTTTGAAAACACG-
1 AATTTTT-AAAACACGA
427528 AATTTTT
1 AATTTTT
427535 TTATTCACGA
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
15 5 0.07
16 16 0.22
17 19 0.26
18 20 0.27
19 12 0.16
20 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (16 bp):
AATTTTTAAAACACGA
Found at i:427506 original size:19 final size:18
Alignment explanation
Indices: 427478--427563 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
427468 AACATGAAAA
* *
427478 TTTTTAAAACACGACATTT
1 TTTTTGAAACACGAGA-TT
* *
427497 TTTTTGAAACACGGGA-A
1 TTTTTGAAACACGAGATT
427514 TTTTTGAAAACACGA-ATT
1 TTTTTG-AAACACGAGATT
**
427532 TTTTT-ATTCACGAGAATT
1 TTTTTGAAACACGAG-ATT
427550 TTTTTGAAACACGA
1 TTTTTGAAACACGA
427564 TTTTTCTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
16 6 0.12
17 7 0.13
18 20 0.38
19 19 0.37
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (18 bp):
TTTTTGAAACACGAGATT
Found at i:427516 original size:53 final size:53
Alignment explanation
Indices: 427425--427563 Score: 124
Period size: 53 Copynumber: 2.7 Consensus size: 53
427415 TTAACACGGG
* * *
427425 AATTTTTGAAAACACGAGAA--TTTGT-AAACACGAAAATTTTAG-AAACATGAA
1 AATTTTT-AAAACACGACAATTTTTTTGAAACACGAAAATTTTAGAAAACACG-A
* ** *
427476 AATTTTTAAAACACGACATTTTTTTTGAAACACGGGAATTTTTGAAAACACGA
1 AATTTTTAAAACACGACAATTTTTTTGAAACACGAAAATTTTAGAAAACACGA
* * ** *
427529 ATTTTTTTATTCACGAGAATTTTTTTGAAACACGA
1 AATTTTTAAAACACGACAATTTTTTTGAAACACGA
427564 TTTTTCTTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
50 10 0.14
51 7 0.10
52 4 0.06
53 43 0.61
54 6 0.09
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (53 bp):
AATTTTTAAAACACGACAATTTTTTTGAAACACGAAAATTTTAGAAAACACGA
Found at i:428160 original size:11 final size:11
Alignment explanation
Indices: 428144--428170 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
428134 GTTTTTATTT
428144 TTTTTAATTAC
1 TTTTTAATTAC
428155 TTTTTAATTAC
1 TTTTTAATTAC
428166 TTTTT
1 TTTTT
428171 TTCTTTCTTT
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:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTAATTAC
Found at i:428181 original size:10 final size:10
Alignment explanation
Indices: 428168--428210 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
428158 TTAATTACTT
428168 TTTTTCTTTC
1 TTTTTCTTTC
428178 TTTTTCTTTC
1 TTTTTCTTTC
428188 TCTTTT-TTTC
1 T-TTTTCTTTC
*
428198 TTTCTTTTTTC
1 TTT-TTCTTTC
428209 TT
1 TT
428211 CCTTCTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.07
10 18 0.60
11 10 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:428187 original size:14 final size:14
Alignment explanation
Indices: 428166--428219 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
428156 TTTTAATTAC
428166 TTTT-TTTCT-TTCT
1 TTTTCTTTCTCTT-T
428179 TTTTCTTTCTCTTT
1 TTTTCTTTCTCTTT
428193 TTTTCTTTCT-TTT
1 TTTTCTTTCTCTTT
*
428206 TTCTTCCTTCTCTT
1 TT-TTCTTTCTCTT
428220 CTTCTTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 9 0.25
14 23 0.64
15 4 0.11
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTCTCTTT
Found at i:428203 original size:28 final size:27
Alignment explanation
Indices: 428166--428219 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
428156 TTTTAATTAC
*
428166 TTTTTTTCTTTCTTT-TTCTTTCTCTTT
1 TTTTTTTCTTT-TTTCTTCCTTCTCTTT
428193 TTTTCTTTCTTTTTTCTTCCTTCTCTT
1 TTTT-TTTCTTTTTTCTTCCTTCTCTT
428220 CTTCTTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTTTCTTTTTTCTTCCTTCTCTTT
Found at i:428826 original size:30 final size:30
Alignment explanation
Indices: 428786--428857 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
428776 ATTTAGGATT
* *
428786 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
428816 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
428846 AAAATGAAATTT
1 AAAATGAAATTT
428858 TTATTTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.31
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:432634 original size:3 final size:3
Alignment explanation
Indices: 432626--432926 Score: 65
Period size: 3 Copynumber: 102.0 Consensus size: 3
432616 AAAACGATAG
* * * * * *
432626 TAA TAA TAA TAG TAG TAA AAA TAA AAA TAA T-A TAG TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
432673 AAA GAA -AA T-A TAA TAA TAA TAG TAA TAA TAA AAA GGT-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA
* * * * *
432716 TTA TAT TAGA TAG TAA -AA -AA CTAA AAA T-A TAA TAA TAA TAA TAG
1 TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * * *
432760 TAA TAA -AA AAA TGA TAA TAG TGA TAT TAG TAG TAA TAG TAA TAA -AG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * ** *
432806 TAA TAG TAA TAA AAA TAG TAC TAA TGT TAA TAG TAA TAA -AA TAA -AGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * ** * *
432853 AAA TAA AAA TTG TAA TAA TAA TAA TGA T-G TAAA TAA TAA TATA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TA-A
*
432900 TAA -AA TATA TATA TAA T-A TAA TGA TAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA
432927 CGATATGAAA
Statistics
Matches: 211, Mismatches: 65, Indels: 44
0.66 0.20 0.14
Matches are distributed among these distances:
2 26 0.12
3 165 0.78
4 20 0.09
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:432692 original size:28 final size:28
Alignment explanation
Indices: 432626--432768 Score: 110
Period size: 31 Copynumber: 4.8 Consensus size: 28
432616 AAAACGATAG
* *
432626 TAATAATAATAGTAGTAAAAATAAAA-A
1 TAATAATAATAGTAATAAAAAGAAAATA
432653 TAATATAGTAATAGTAATAAAAAGAAAATA
1 TAATA-A-TAATAGTAATAAAAAGAAAATA
*
432683 TAATAATAATAGTAATAATAAAAAGGTATAATA
1 TAATAATAATAG---TAATAAAAA-G-AAAATA
* * *
432716 TTATATTAGATAGTAA-AAAACTAAAAATATAA
1 TAATAATA-ATAGTAATAAAA--AGAAA-AT-A
432748 TAATAATAATAGTAATAAAAA
1 TAATAATAATAGTAATAAAAA
432769 AATGATAATA
Statistics
Matches: 93, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
27 5 0.05
28 7 0.08
29 19 0.20
30 13 0.14
31 21 0.23
32 13 0.14
33 11 0.12
34 4 0.04
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.29
Consensus pattern (28 bp):
TAATAATAATAGTAATAAAAAGAAAATA
Found at i:432750 original size:62 final size:63
Alignment explanation
Indices: 432677--432794 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 63
432667 TAATAAAAAG
* ** *
432677 AAAATATAATAATAATAGTAATAATAAAAAGGT-ATAATA-TTATATTAGATAGTAAAAAACTA
1 AAAATATAATAATAATAATAATAATAAAAAAATGATAATAGTGATATTAG-TAGTAAAAAACTA
*
432739 AAAATATAATAATAATAATAGTAATAAAAAAATGATAATAGTGATATTAGTAGTAA
1 AAAATATAATAATAATAATAATAATAAAAAAATGATAATAGTGATATTAGTAGTAA
432795 TAGTAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 29 0.59
63 12 0.24
64 8 0.16
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.31
Consensus pattern (63 bp):
AAAATATAATAATAATAATAATAATAAAAAAATGATAATAGTGATATTAGTAGTAAAAAACTA
Found at i:432823 original size:26 final size:27
Alignment explanation
Indices: 432737--432846 Score: 102
Period size: 26 Copynumber: 4.2 Consensus size: 27
432727 AGTAAAAAAC
*
432737 TAAAAATA-TAATAATAATAATAGTAA
1 TAAAAATAGTAATAATAGTAATAGTAA
* * * * *
432763 TAAAAA-AATGATAATAGTGATATTAG
1 TAAAAATAGTAATAATAGTAATAGTAA
**
432789 TAGTAATAGTAATAA-AGTAATAGTAA
1 TAAAAATAGTAATAATAGTAATAGTAA
*
432815 TAAAAATAGTACTAAT-GTTAATAGTAA
1 TAAAAATAGTAATAATAG-TAATAGTAA
432842 TAAAA
1 TAAAA
432847 TAAAGAAAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.02
26 44 0.68
27 20 0.31
ACGTcount: A:0.57, C:0.01, G:0.11, T:0.31
Consensus pattern (27 bp):
TAAAAATAGTAATAATAGTAATAGTAA
Found at i:432843 original size:41 final size:41
Alignment explanation
Indices: 432792--432871 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
432782 ATATTAGTAG
* * *
432792 TAATAGTAATAAAGTAATAG-TAATAAAAATAGTACTAATGT
1 TAATAGTAATAAAATAA-AGAAAATAAAAATAGTAATAATGT
*
432833 TAATAGTAATAAAATAAAGAAAATAAAAATTGTAATAAT
1 TAATAGTAATAAAATAAAGAAAATAAAAATAGTAATAAT
432872 AATAATGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.30
Consensus pattern (41 bp):
TAATAGTAATAAAATAAAGAAAATAAAAATAGTAATAATGT
Found at i:432908 original size:13 final size:14
Alignment explanation
Indices: 432870--432917 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
432860 AATTGTAATA
* *
432870 ATAATAATGATGTAA
1 ATAATAAT-ATATAC
432885 ATAATAATATATAC
1 ATAATAATATATAC
*
432899 ATAA-AATATATAT
1 ATAATAATATATAC
432912 ATAATA
1 ATAATA
432918 TAATGATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.41
14 9 0.31
15 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (14 bp):
ATAATAATATATAC
Found at i:433002 original size:3 final size:3
Alignment explanation
Indices: 432991--433068 Score: 54
Period size: 3 Copynumber: 26.7 Consensus size: 3
432981 AAAATGGTGG
* * * *
432991 TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TGA -AA TAA T-T TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
433037 TAG TAA TAA TGA CAA TAG TAGA -AA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA
433069 GTATTTGAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
2 3 0.05
3 54 0.95
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:433069 original size:15 final size:15
Alignment explanation
Indices: 432990--433071 Score: 67
Period size: 15 Copynumber: 5.2 Consensus size: 15
432980 AAAAATGGTG
*
432990 GTAATGATAATAATA
1 GTAATAATAATAATA
*
433005 ATAATAATAATAATGA
1 GTAATAATAATAAT-A
*
433021 TGAAATAATTTAATAATA
1 -GTAATAA--TAATAATA
* *
433039 GTAATAATGACAATA
1 GTAATAATAATAATA
433054 GTAGA-AATAATAATA
1 GTA-ATAATAATAATA
433069 GTA
1 GTA
433072 TTTGAATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 32 0.60
16 2 0.04
17 11 0.21
18 1 0.02
19 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.11, T:0.32
Consensus pattern (15 bp):
GTAATAATAATAATA
Found at i:434189 original size:68 final size:68
Alignment explanation
Indices: 433948--434755 Score: 1148
Period size: 68 Copynumber: 12.0 Consensus size: 68
433938 TCAATTTACT
* * *
433948 CGCTCAAACTTCAAGGAGATCTGCTGTGGCTTCTAA-CTGCT-CAATGCCATTTCAGGGAGAAGA
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTC-AAGCCGCTCCAACGCCATTTCAGGGAGAAGA
434011 GATC
65 GATC
* * *
434015 CACTGAAACTTCAAGAAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCA-GG-G-AGA-
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434076 A--
66 ATC
* * *
434077 CGCTGAAACTTCAAGGAGATCTACTGTGGCTTCTAGCCACTCCAACGCCATTTCAGGGAGAAGAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434142 ATC
66 ATC
* * * * * *
434145 CGTTGAAACTTTAAGGAGATCTACTGTGGCTTCAAGCCTCTCCAATGCCATTTCAGGGAGAAAAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434210 ATC
66 ATC
* * * * * *
434213 TGCTGAAACTTCAAGGAGATCTGTTGTGGCTTAAAGCCACTCCAACTCCATTTCAGGGAGAAGTG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434278 ATC
66 ATC
** * * *
434281 AACTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGTTCCAACGCCATTTTAAGGAGAAGAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
*
434346 GTC
66 ATC
* *
434349 CGCTAAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434414 ATC
66 ATC
** * * *
434417 TACTGAAACTTCAAGGAGATCTGCTGTAGCTTCTAGTCGCTCCAACGCCATTTCAGGGAGAAGAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
*
434482 ATT
66 ATC
*
434485 CGCTGAAACTTCAAGGAGATCTGCTGTGGC-TCAAAGCCGCTCCAACGCCATTTTAGGGAGAAGA
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTC-AAGCCGCTCCAACGCCATTTCAGGGAGAAGA
434549 GATC
65 GATC
* *
434553 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCTATTTTAGGGAGAAGAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434618 ATC
66 ATC
* * * *
434621 CGCTGAAACTTCAAGAAGATCTACTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAGAA
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434686 ATC
66 ATC
*
434689 CGCTGAAACTTCAAAGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
1 CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
434754 AT
66 AT
434756 TTGTAATTCC
Statistics
Matches: 660, Mismatches: 71, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
62 51 0.08
63 2 0.00
64 2 0.00
65 6 0.01
66 3 0.00
67 38 0.06
68 556 0.84
69 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (68 bp):
CGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAG
ATC
Found at i:434920 original size:88 final size:88
Alignment explanation
Indices: 434743--435239 Score: 692
Period size: 88 Copynumber: 5.6 Consensus size: 88
434733 ACGCCATTTC
* ** ** *
434743 AGGGAGA-AGAGATTTGTAATTCCCAGCCTGTTACCCTA-TCGCTTAGGGGGTTAAGGCTTACCG
1 AGGGAGACA-AGATCTGTAATTTTCAGCCTGTTACCCTACT-GCTTAGGGGGTTAAGGCCCATCG
* * * * *
434806 TATTTGATCTACTCCACTATTACTT
64 TCTTCGATCTGCTCCACTACTGCTT
* ** * * * *
434831 AGAGAGGTAAGATCTGAAATTTTCAGCTTGTTACCCTACTACTTAGGGGGTTAAGGCTCATCGTC
1 AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGTC
*
434896 TTTGATCTGCTCCACTACTGCTT
66 TTCGATCTGCTCCACTACTGCTT
* * *
434919 AGGGAGACGAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGAGGGTTAAAGCCCATCGTC
1 AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGTC
*
434984 TTCGATCTTCTCCACTACTGCTT
66 TTCGATCTGCTCCACTACTGCTT
* * *
435007 AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTC
1 AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGTC
435072 TTCGATCTGCTCCACTACTGCTT
66 TTCGATCTGCTCCACTACTGCTT
* *
435095 AGGGAGACAAGATATGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTC
1 AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGTC
*
435160 TTCGATCTGTTCCACTACTGCTT
66 TTCGATCTGCTCCACTACTGCTT
*
435183 AGGGAGACAAGATCTGTAATTTTCAGTCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
435240 TTACGAATTC
Statistics
Matches: 368, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
88 366 0.99
89 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (88 bp):
AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGTC
TTCGATCTGCTCCACTACTGCTT
Found at i:434958 original size:44 final size:44
Alignment explanation
Indices: 434910--435230 Score: 182
Period size: 44 Copynumber: 7.3 Consensus size: 44
434900 ATCTGCTCCA
* *
434910 CTACTGCTTAGGGAGACGAGATCTGTAATTTTCAGCCTGTTACC
1 CTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGTCTGTTACC
* ** ** *
434954 CTACTGCTTAGAGG-GTTA-AAG-CCCATCGTCTTC-GATCT-TCT-CC
1 CTACTGCTTAG-GGAG--ACAAGATCTGTAATTTTCAG-TCTGT-TACC
*
434997 ACTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGTCTGTTACC
* ** ** ** * *
435042 CTACTACTTAAGGG-GTTAAGGCCCT-TCGTCTTC-GATCTGCT-CC
1 CTACTGCTT-AGGGAGACAA-GATCTGTAATTTTCAG-TCTGTTACC
* *
435085 ACTACTGCTTAGGGAGACAAGATATGTAATTTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGTCTGTTACC
* ** ** ** *
435130 CTACTGCTTAGGGGGTTAAGGCCCT-TCGTCTTC-GATCTGTT-CC
1 CTACTGCTTAGGGAGACAA-GATCTGTAATTTTCAG-TCTGTTACC
435173 ACTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGTCTGTTACC
1 -CTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGTCTGTTACC
435218 CTACTGCTTAGGG
1 CTACTGCTTAGGG
435231 GGTTAAGGCT
Statistics
Matches: 197, Mismatches: 54, Indels: 52
0.65 0.18 0.17
Matches are distributed among these distances:
42 1 0.01
43 24 0.12
44 148 0.75
45 23 0.12
46 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (44 bp):
CTACTGCTTAGGGAGACAAGATCTGTAATTTTCAGTCTGTTACC
Found at i:438988 original size:22 final size:22
Alignment explanation
Indices: 438945--438988 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
438935 GCAGCACTAC
* *
438945 TTTAAGTTCTTCTATCTTCTCT
1 TTTAAGTTCTTCAATCTGCTCT
438967 TTTAA-TTCTTCAATTCTGCTCT
1 TTTAAGTTCTTCAA-TCTGCTCT
438989 GACTAGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTAAGTTCTTCAATCTGCTCT
Found at i:442316 original size:18 final size:18
Alignment explanation
Indices: 442295--442329 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
442285 GCGACAATAT
*
442295 CAATAACAATAATATGAG
1 CAATAACAAAAATATGAG
*
442313 CAATAATAAAAATATGA
1 CAATAACAAAAATATGA
442330 AAAAAGCAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (18 bp):
CAATAACAAAAATATGAG
Found at i:442485 original size:3 final size:3
Alignment explanation
Indices: 442462--442764 Score: 78
Period size: 3 Copynumber: 103.3 Consensus size: 3
442452 AACGATAGTG
* * * * * * *
442462 ATA ATG ATA ATA TTG ATA ATA ATA ATA GTA GTA AAA ATA AAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
442509 ATA GTA ATA GTA ATA A-A A-A AGA A-A AT- ATA ATA ATA ATA ATA AGGT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA
* * * * *
442554 ATA ATA AT- ATA TTA GATA GTA AAA AAA ATA ATA A-A ATA ATA AAA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * *
442598 ATA ATA ATA A-A AAA ATG ATA ATA GTG ATG TTA GTA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
442645 A-A GTA ATA GTA ATA AAA ATA GTA CTA ATG TTA ATA GTA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
442691 A-A GAAA ATA AAA ATT GTA ATA ATA ATA ATG ATGC A-A ATA ATA ATA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
*
442736 TATA CATA AT- ATA TATA AT- ATA ATG ATA A
1 -ATA -ATA ATA ATA -ATA ATA ATA ATA ATA A
442765 CGATATGAAA
Statistics
Matches: 215, Mismatches: 64, Indels: 42
0.67 0.20 0.13
Matches are distributed among these distances:
2 26 0.12
3 174 0.81
4 14 0.07
5 1 0.00
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:442516 original size:29 final size:29
Alignment explanation
Indices: 442479--442546 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
442469 TAATATTGAT
*
442479 AATAATAATAGTAGTAAAAATA-AAAATAA
1 AATAATAATAGTAATAAAAA-AGAAAATAA
* *
442508 AATAGTAATAGTAATAAAAAAGAAAATAT
1 AATAATAATAGTAATAAAAAAGAAAATAA
442537 AATAATAATA
1 AATAATAATA
442547 ATAAGGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (29 bp):
AATAATAATAGTAATAAAAAAGAAAATAA
Found at i:442523 original size:23 final size:23
Alignment explanation
Indices: 442479--442606 Score: 77
Period size: 23 Copynumber: 5.4 Consensus size: 23
442469 TAATATTGAT
* *
442479 AATAATAATAGTAGTAAAAATAAA
1 AATAA-AATAGTAATAATAATAAA
*
442503 AATAAAATAGTAATAGTAATAAAA
1 AATAAAATAGTAATAATAAT-AAA
*
442527 AAGAAAATA-TAATAATAATAATA
1 AATAAAATAGTAATAATAATAA-A
* *
442550 AGGTATAATAATA-TATTAGATAGT-AA
1 A---ATAA-AATAGTAATA-ATAATAAA
*
442576 AA-AAAATAATAA-AATAATAAA
1 AATAAAATAGTAATAATAATAAA
442597 AATAATAATA
1 AATAA-AATA
442607 AAAAAATGAT
Statistics
Matches: 83, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
20 4 0.05
21 9 0.11
22 8 0.10
23 28 0.34
24 16 0.19
26 5 0.06
27 9 0.11
28 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (23 bp):
AATAAAATAGTAATAATAATAAA
Found at i:442620 original size:20 final size:20
Alignment explanation
Indices: 442573--442613 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
442563 TATTAGATAG
* *
442573 TAAAAAAAATAATAAAATAA
1 TAAAAATAATAATAAAAAAA
442593 TAAAAATAATAATAAAAAAA
1 TAAAAATAATAATAAAAAAA
442613 T
1 T
442614 GATAATAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAAATAATAATAAAAAAA
Found at i:442679 original size:41 final size:41
Alignment explanation
Indices: 442634--442713 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
442624 ATGTTAGTAG
* * *
442634 TAATAGTAATAAAGTAATAG-TAATAAAAATAGTACTAATGT
1 TAATAGTAATAAAATAA-AGAAAATAAAAATAGTAATAATGT
*
442675 TAATAGTAATAAAATAAAGAAAATAAAAATTGTAATAAT
1 TAATAGTAATAAAATAAAGAAAATAAAAATAGTAATAAT
442714 AATAATGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.30
Consensus pattern (41 bp):
TAATAGTAATAAAATAAAGAAAATAAAAATAGTAATAATGT
Found at i:442891 original size:18 final size:17
Alignment explanation
Indices: 442851--442894 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
442841 TGATGATGAT
*
442851 GAAATAATTCAATAATA
1 GAAATAATACAATAATA
* *
442868 GTAATAATGACAATAGTA
1 GAAATAAT-ACAATAATA
442886 GAAATAATA
1 GAAATAATA
442895 ATAGTATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (17 bp):
GAAATAATACAATAATA
Found at i:447120 original size:12 final size:12
Alignment explanation
Indices: 447100--447130 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
447090 AAACAGAAAC
447100 GAAATGGATATG
1 GAAATGGATATG
*
447112 GATATGGATATG
1 GAAATGGATATG
447124 GAAATGG
1 GAAATGG
447131 TTTTGCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (12 bp):
GAAATGGATATG
Found at i:447479 original size:5 final size:5
Alignment explanation
Indices: 447445--447472 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
447435 CCATAAGGTA
447445 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
447473 TTATTTTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:456289 original size:17 final size:17
Alignment explanation
Indices: 456264--456300 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
456254 TAACTACATG
456264 ATATATAAAAATTTAAA
1 ATATATAAAAATTTAAA
* *
456281 ATATGTAAAACTTTAAA
1 ATATATAAAAATTTAAA
456298 ATA
1 ATA
456301 CATGGTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
ATATATAAAAATTTAAA
Found at i:462758 original size:3 final size:3
Alignment explanation
Indices: 462744--462829 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
462734 GAGCTTTGTT
* *
462744 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
462788 TT- TCTCA TGTA TATA TTA TT- TT- TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
462830 ATATGCCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 12 0.18
3 48 0.71
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:462786 original size:18 final size:18
Alignment explanation
Indices: 462744--462833 Score: 83
Period size: 18 Copynumber: 4.7 Consensus size: 18
462734 GAGCTTTGTT
*
462744 TTATTATTTTATTATTTTTA
1 TTATTA-TTTA-TATTATTA
*
462764 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
462782 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
*
462803 TTATTTTTTATATTATTA
1 TTATTATTTATATTATTA
462821 TTA-TATTATATAT
1 TTATTATT-TATAT
462834 GCCCTCTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 3 0.05
18 26 0.44
19 9 0.15
20 10 0.17
21 11 0.19
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:463071 original size:18 final size:19
Alignment explanation
Indices: 463035--463091 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
463025 ACTATTACTA
*
463035 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
463055 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
463072 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
463090 TT
1 TT
463092 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:463190 original size:12 final size:12
Alignment explanation
Indices: 463173--463202 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
463163 GTATTTCTAT
463173 TATATACATATA
1 TATATACATATA
*
463185 TATATACATTTA
1 TATATACATATA
463197 TATATA
1 TATATA
463203 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:475523 original size:44 final size:44
Alignment explanation
Indices: 475346--475659 Score: 231
Period size: 44 Copynumber: 7.1 Consensus size: 44
475336 TCATTAAAGT
* * *
475346 AGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
* * * ** * * *
475390 AGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAGGAT-GC
1 AGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAGATAGC
* * * * *
475433 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* *
475478 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
* * * ** * *
475522 AGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGAT-GC
1 AGATCTTGTCTTCCTATATTG-GCGTGAAGTAGATCGAAGATAGC
* * * * *
475565 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGATTGC
1 AGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCGAAGATAGC
* * * * *
475610 AGATCTTGTCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGC
1 AGATCTTGTCTTCCTATA-TTGGC-GTGAAGTAGATCGAAGATAGC
475656 AGAT
1 AGAT
475660 TTTACCTCCC
Statistics
Matches: 203, Mismatches: 57, Indels: 18
0.73 0.21 0.06
Matches are distributed among these distances:
43 39 0.19
44 100 0.49
45 41 0.20
46 23 0.11
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (44 bp):
AGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCGAAGATAGC
Found at i:475588 original size:132 final size:132
Alignment explanation
Indices: 475341--475657 Score: 499
Period size: 132 Copynumber: 2.4 Consensus size: 132
475331 TGAAGTCATT
*
475341 AAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * *
475406 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
475471 AG
131 AG
*
475473 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
475538 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
475603 AG
131 AG
** * * * *
475605 ATTGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAG
1 AAAGCAGATCTTGTCTTCATGTA-TTGGC-GTGAAGCAGATCGAAGATAGCAG
475658 ATTTTACCTC
Statistics
Matches: 169, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 145 0.86
133 5 0.03
134 19 0.11
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
AG
Found at i:475739 original size:134 final size:135
Alignment explanation
Indices: 475595--475899 Score: 531
Period size: 136 Copynumber: 2.3 Consensus size: 135
475585 GGTGGTGAAG
* *
475595 TAGATTGAAGATTGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
475660 TTTACCTCCC-TGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
66 TTTACCTCCCGTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
475724 TGGAA
131 TGGAA
*
475729 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
* *
475794 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
66 TTTACCTCCC-GTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
475859 GTGGAA
130 GTGGAA
* *
475865 TAGATTGAAGATTGCAGATCCTGCCTTCCTATATT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATT
475900 GGTAGGAAGT
Statistics
Matches: 162, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
134 72 0.44
136 90 0.56
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (135 bp):
TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
TTTACCTCCCGTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
TGGAA
Found at i:476085 original size:43 final size:40
Alignment explanation
Indices: 476038--476208 Score: 128
Period size: 40 Copynumber: 4.2 Consensus size: 40
476028 CTTGGGCAAC
*
476038 AGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCG--CATTA-AATCTTATCTCCCTAAGCAGT
* *
476081 AGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
** *** ** * *
476121 AGTGGAGCAGATAAAACCACAGATCTTATTTCCCTAAGCAAT
1 AGTGGAATAGATCGCATTA-A-ATCTTATCTCCCTAAGCAGT
* * * * *
476163 AGT-AAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGT
1 AGTGGAA-TAGATCGCATTAAATCTTATCTCCCTAAGCAGT
476203 AGTGGA
1 AGTGGA
476209 GCAGACTAAA
Statistics
Matches: 101, Mismatches: 23, Indels: 10
0.75 0.17 0.07
Matches are distributed among these distances:
40 52 0.51
41 8 0.08
42 28 0.28
43 13 0.13
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
Found at i:476114 original size:40 final size:40
Alignment explanation
Indices: 476062--476213 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
476052 AAGATTACAA
* *
476062 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*** *
476102 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCA-AG
* * **
476143 ATCTTATTTCCCTAAGCAATAGTAAAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
476184 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
476214 CTAAAAACAC
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
40 57 0.63
41 4 0.04
42 30 0.33
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:476156 original size:82 final size:83
Alignment explanation
Indices: 476060--476229 Score: 252
Period size: 82 Copynumber: 2.1 Consensus size: 83
476050 CGAAGATTAC
* ** * *
476060 AATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTAAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
*
476125 GAGCAGA-TAAAACCACA
66 GAGCAGACTAAAAACACA
* * *
476142 GATCTTATTTCCCTAAGCAATAGTAAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTAAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
476207 GAGCAGACTAAAAACACA
66 GAGCAGACTAAAAACACA
476225 AATCT
1 AATCT
476230 CATCCCCATG
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 64 0.83
83 13 0.17
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (83 bp):
AATCTTATCTCCCTAAGCAATAGTAAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
GAGCAGACTAAAAACACA
Found at i:476518 original size:37 final size:38
Alignment explanation
Indices: 476455--476529 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
476445 GCTGTAAAGG
* *
476455 CCCAATTTTGGCCCAACTTAAACCAACCCTAAC-CAAA
1 CCCAATTTTGGCCCAACCTAAACCAACCCAAACACAAA
*
476492 CCCAA-TTTGGCCCAACCTAATCCCAACCCAAACACAAA
1 CCCAATTTTGGCCCAACCTAA-ACCAACCCAAACACAAA
476530 AAATAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 14 0.42
37 15 0.45
38 4 0.12
ACGTcount: A:0.39, C:0.40, G:0.05, T:0.16
Consensus pattern (38 bp):
CCCAATTTTGGCCCAACCTAAACCAACCCAAACACAAA
Found at i:476753 original size:21 final size:21
Alignment explanation
Indices: 476708--476773 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
476698 GTTTTTGGTT
* *
476708 TTTTGGAGAAGGATTGTTCTTTG
1 TTTTGGAGGAGG-TT-TTTTTTG
476731 TTTTGGAGGAGGTTTTTTTTG
1 TTTTGGAGGAGGTTTTTTTTG
**
476752 TTTT-TTGGAGGTGTTTTTTTG
1 TTTTGGAGGAGGT-TTTTTTTG
476773 T
1 T
476774 AAAAAAGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 19 0.50
22 2 0.05
23 11 0.29
ACGTcount: A:0.11, C:0.02, G:0.30, T:0.58
Consensus pattern (21 bp):
TTTTGGAGGAGGTTTTTTTTG
Found at i:476757 original size:23 final size:23
Alignment explanation
Indices: 476699--476771 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
476689 TAGGGGTGGG
* *
476699 TTTTTGGTTTTTTGGAGAAGGATT
1 TTTTTTGTTTTTTGGAGGAGG-TT
*
476723 GTTCTTTG--TTTTGGAGGAGGTT
1 -TTTTTTGTTTTTTGGAGGAGGTT
*
476745 TTTTTTGTTTTTTGGAGG-TGTT
1 TTTTTTGTTTTTTGGAGGAGGTT
476767 TTTTT
1 TTTTT
476772 GTAAAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 6 0.15
22 10 0.24
23 20 0.49
25 5 0.12
ACGTcount: A:0.10, C:0.01, G:0.29, T:0.60
Consensus pattern (23 bp):
TTTTTTGTTTTTTGGAGGAGGTT
Found at i:477116 original size:3 final size:3
Alignment explanation
Indices: 477102--477187 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
477092 GAGCTTTGTT
* *
477102 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
477146 TT- TCTCA TGTA TATA TTA TT- TT- TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
477188 ATATGCCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 12 0.18
3 48 0.71
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:477144 original size:18 final size:18
Alignment explanation
Indices: 477102--477191 Score: 83
Period size: 18 Copynumber: 4.7 Consensus size: 18
477092 GAGCTTTGTT
*
477102 TTATTATTTTATTATTTTTA
1 TTATTA-TTTA-TATTATTA
*
477122 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
477140 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
*
477161 TTATTTTTTATATTATTA
1 TTATTATTTATATTATTA
477179 TTA-TATTATATAT
1 TTATTATT-TATAT
477192 GCCCTCTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 3 0.05
18 26 0.44
19 9 0.15
20 10 0.17
21 11 0.19
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:477429 original size:18 final size:19
Alignment explanation
Indices: 477393--477449 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
477383 ACTATTACTA
*
477393 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
477413 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
477430 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
477448 TT
1 TT
477450 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:497469 original size:3 final size:3
Alignment explanation
Indices: 497461--497608 Score: 71
Period size: 3 Copynumber: 48.0 Consensus size: 3
497451 ATAATTGTAA
* * * * * *
497461 AAT AAT AAT AGT GAAA AAT AAT AGT AAT AAT GAT GTAT AAA AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * * * * *
497508 AGT AAT AAA AAT AGT AAC GAT AAT AAT AAT AAC ATAT AAT AGT AAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * * *
497554 AAT AAT AAC AAT TAT ATAT AAT AGT AAG AAT AAT AAT AAC AAT GAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
497600 AAT ATT AAT
1 AAT AAT AAT
497609 TAGTAATCCA
Statistics
Matches: 100, Mismatches: 41, Indels: 8
0.67 0.28 0.05
Matches are distributed among these distances:
3 92 0.92
4 8 0.08
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:497491 original size:22 final size:25
Alignment explanation
Indices: 497447--497515 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
497437 TATGGTATAT
* *
497447 AAAAATAATTGTAAAATAATAATAGT-G
1 AAAAATAATAGT--AATAATGAT-GTAG
*
497474 AAAAATAATAGTAATAATGATGTAT
1 AAAAATAATAGTAATAATGATGTAG
497499 AAAAATAATAGTAATAA
1 AAAAATAATAGTAATAA
497516 AAATAGTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 2 0.05
25 25 0.66
27 11 0.29
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (25 bp):
AAAAATAATAGTAATAATGATGTAG
Found at i:497551 original size:28 final size:28
Alignment explanation
Indices: 497517--497592 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
497507 TAGTAATAAA
497517 AATAGTAACG-ATAATAATAATAACATAT
1 AATAGTAA-GAATAATAATAATAACATAT
* * *
497545 AATAGTAAGAATAATAACAATTATATAT
1 AATAGTAAGAATAATAATAATAACATAT
497573 AATAGTAAGAATAATAATAA
1 AATAGTAAGAATAATAATAA
497593 CAATGATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (28 bp):
AATAGTAAGAATAATAATAATAACATAT
Found at i:499244 original size:133 final size:133
Alignment explanation
Indices: 499071--499346 Score: 385
Period size: 133 Copynumber: 2.1 Consensus size: 133
499061 TACTGCTTAG
* *
499071 GGAGATAAGATCTAAAATTTTCAGTCTGCTTCCTTGCTACCTCAAGAAGATAAGACTTGTATCTT
1 GGAGATAAGATCTAAAATTTTCAGTCTGCTTCCTTCCTACCTCAAGAAAATAAGACTTGTATCTT
* * * * *
499136 CGACCTGCTCTCTTGCTACCTCAGAA-AGACAAGGCCGGTGGCTAAAATCTGC-TCTATAGCCGA
66 CAACCTGCTCTCTTGCTACCTCA-AAGAGACAAGGCCGATAGCTAAAATCTACTTC-ATAACCGA
499199 TACAT
129 TACAT
** * *
499204 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTACCTCAGGAAAATGAGACTTGTATCTT
1 GGAGATAAGATCTAAAATTTTCAGTCTGCTTCCTTCCTACCTCAAGAAAATAAGACTTGTATCTT
* * *
499269 CAACCTGCTCTCTTGCTACCTCAAAGGGATAAGGCTGATAGCTAAAATCTACTTCATAACCGATA
66 CAACCTGCTCTCTTGCTACCTCAAAGAGACAAGGCCGATAGCTAAAATCTACTTCATAACCGATA
499334 CAT
131 CAT
*
499337 AGAGATAAGA
1 GGAGATAAGA
499347 CTCACCATTT
Statistics
Matches: 126, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
132 2 0.02
133 122 0.97
134 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (133 bp):
GGAGATAAGATCTAAAATTTTCAGTCTGCTTCCTTCCTACCTCAAGAAAATAAGACTTGTATCTT
CAACCTGCTCTCTTGCTACCTCAAAGAGACAAGGCCGATAGCTAAAATCTACTTCATAACCGATA
CAT
Found at i:499402 original size:45 final size:44
Alignment explanation
Indices: 499314--499408 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
499304 TGATAGCTAA
*
499314 AATCTACTTCATAACCGATACATAGAGATAAGACTCACCATTTTC
1 AATCTACTCCATAACCGATACATAGAGATAAGACTCA-CATTTTC
* * * *
499359 GATCTACTCCATAGCCGATACATGGAGATAAGATCTGTA-ATTTTC
1 AATCTACTCCATAACCGATACATAGAGATAAGA-CT-CACATTTTC
499404 AATCT
1 AATCT
499409 GCTTCCTTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
45 39 0.93
46 2 0.05
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (44 bp):
AATCTACTCCATAACCGATACATAGAGATAAGACTCACATTTTC
Found at i:499404 original size:178 final size:178
Alignment explanation
Indices: 499182--499943 Score: 998
Period size: 178 Copynumber: 4.3 Consensus size: 178
499172 GGTGGCTAAA
*
499182 ATCTGCTCTATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTACCTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTACCTC
* * * * *
499247 AGGAAAATGAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAAAGGGATAAGGCTGATAGCT
66 AGGAAGATGAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCT
*
499312 AAAATCTACTT-CATAACCGATACATAGAGATAAGACTCACCATTTTCG
131 AAAATCT-CTTCCATAGCCGATACATAGAGATAAGACTCACCATTTTCG
* * *
499360 ATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAATCTGCTTCCTTGCTACCTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTACCTC
499425 AGGAAGATGAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCT
66 AGGAAGATGAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCT
* *
499490 AAAATCTGC-TCCATAGCCAATACATGGAGATAAGACTCACCA-TTTCTG
131 AAAATCT-CTTCCATAGCCGATACATAGAGATAAGACTCACCATTTTC-G
*
499538 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTACTACCTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTACCTC
* * * *
499603 AGGAATAT-AGGACTTGTATCTTCAACTTGCTCTCTTGCTACCTTAGAGAAATAAGGCTGGTGGC
66 AGGAAGATGA-GACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGC
* * ** **
499667 TAAAATCTGTTCCATAGCCGATACATGGAGATAAGACTCGTCATTTTTT
130 TAAAATCTCTTCCATAGCCGATACATAGAGATAAGACTCACCATTTTCG
* * * * * * *
499716 ATCTACTCTATAGCCAATACATGGAGATAAGATATGTAATTTTTAGCCTG-TTAC--CCTACTGC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTAC--C
* * * * ** * * *
499778 TTAGGTAGATAAGGCTCATCGTCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCCGGTG
64 TCAGGAAGATGAGACTTGT-ATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTG
* * * * *
499843 GCTAAAATCTGTTCCATAGTCGATATATAGAGATAAGACTCGCCATTTCCG
128 GCTAAAATCTCTTCCATAGCCGATACATAGAGATAAGACTCACCATTTTCG
* *
499894 ATCTGCTCAATAGCCGATACATGGAGATAAGATCTATAATTTTCAGTCTG
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTG
499944 TTATCCTACT
Statistics
Matches: 515, Mismatches: 60, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
175 4 0.01
177 21 0.04
178 487 0.95
179 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (178 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTCCTACCTC
AGGAAGATGAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCT
AAAATCTCTTCCATAGCCGATACATAGAGATAAGACTCACCATTTTCG
Found at i:500081 original size:12 final size:12
Alignment explanation
Indices: 500066--500090 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
500056 TTATGCCTAA
500066 TGATTAGGATGC
1 TGATTAGGATGC
500078 TGATTAGGATGC
1 TGATTAGGATGC
500090 T
1 T
500091 ATGATCAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TGATTAGGATGC
Found at i:511811 original size:3 final size:3
Alignment explanation
Indices: 511787--511922 Score: 67
Period size: 3 Copynumber: 44.7 Consensus size: 3
511777 ACTATGGTAT
* * * * *
511787 ATA AAA ATA ATT ATA A-A ATA ATA ATA GTGA AAA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * * * * **
511832 ATG ATGT ATA AAA ATA ATA GTA ATA AAA ATA GTA ACG ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
511878 ATA ACA TATA ATA GTA AGA ATA ATA ATA ACA ATG ATA ATA TTA AT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
511923 TAGCAATCCA
Statistics
Matches: 92, Mismatches: 37, Indels: 8
0.67 0.27 0.06
Matches are distributed among these distances:
2 2 0.02
3 85 0.92
4 5 0.05
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:511824 original size:13 final size:12
Alignment explanation
Indices: 511788--511902 Score: 65
Period size: 13 Copynumber: 8.9 Consensus size: 12
511778 CTATGGTATA
511788 TAAAAATAATTA-
1 TAAAAATAA-TAG
511800 TAAAATAATAATAG
1 T-AAA-AATAATAG
511814 TGAAAAATAATAG
1 T-AAAAATAATAG
* *
511827 TAATAATGAT-G
1 TAAAAATAATAG
511838 TATAAAAATAATAG
1 --TAAAAATAATAG
511852 TAATAAA-AATAG
1 TAA-AAATAATAG
*
511864 TAACGATAATAATAA
1 TAA--A-AATAATAG
*
511879 TAACATATAATAG
1 TAA-AAATAATAG
*
511892 TAAGAATAATA
1 TAAAAATAATA
511903 ATAACAATGA
Statistics
Matches: 81, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
11 1 0.01
12 25 0.31
13 35 0.43
14 13 0.16
15 7 0.09
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.29
Consensus pattern (12 bp):
TAAAAATAATAG
Found at i:517150 original size:50 final size:50
Alignment explanation
Indices: 517071--517169 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
517061 GCCTTATTCT
* * * *
517071 AATCAATGTCAAATAGAAGGAGAGAAGTTCTATATGGATTCTACTTGTAC
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTAC
*
517121 AATCAATATCAAATAGAAGAAGAGTAGTTCTATACGAATTCTACTTGTA
1 AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTA
517170 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (50 bp):
AATCAATATCAAATAGAAGAAGAGAAGTTCTATACGAATTCTACTTGTAC
Found at i:522429 original size:13 final size:14
Alignment explanation
Indices: 522387--522431 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
522377 TACTAATGAT
522387 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
522402 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
522415 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
522428 TAAA
1 TAAA
522432 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:534145 original size:29 final size:29
Alignment explanation
Indices: 534081--534142 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
534071 TAAATGGTAC
* *
534081 TAAAGTTTCACAATTATTATTATTTAAAA
1 TAAAATTTCAAAATTATTATTATTTAAAA
534110 TAAAATTTCAAAATTATTA-TATTTAAAA
1 TAAAATTTCAAAATTATTATTATTTAAAA
534138 TAAAA
1 TAAAA
534143 ATTATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (29 bp):
TAAAATTTCAAAATTATTATTATTTAAAA
Found at i:556466 original size:20 final size:18
Alignment explanation
Indices: 556420--556471 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
556410 ATAATATAAT
*
556420 AAAAGAAATAATAAAAGA
1 AAAAGAAATAAAAAAAGA
556438 ATAAAGAAATAAAATAAAGA
1 A-AAAGAAATAAAA-AAAGA
556458 AAAAGGAAA-AAAAA
1 AAAA-GAAATAAAAA
556472 GAAGGACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.07
19 18 0.60
20 10 0.33
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAGAAATAAAAAAAGA
Found at i:557382 original size:6 final size:6
Alignment explanation
Indices: 557371--557407 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
557361 CCTGACTATA
* *
557371 ACTGTT ACTGTT ACTGTC ATTGTT ACTGTT ACTGTT A
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT A
557408 TCCTACGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
ACTGTT
Found at i:558722 original size:13 final size:13
Alignment explanation
Indices: 558704--558736 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
558694 GCTACACTAG
558704 TTTAGTTTTTTGC
1 TTTAGTTTTTTGC
558717 TTTAG--TTTTGC
1 TTTAGTTTTTTGC
558728 TTTAGTTTT
1 TTTAGTTTT
558737 CTCTTAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (13 bp):
TTTAGTTTTTTGC
Found at i:562403 original size:20 final size:18
Alignment explanation
Indices: 562369--562405 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
562359 GCAACTCATA
562369 ATTTCAACTATTTTACAC
1 ATTTCAACTATTTTACAC
562387 ATTTACAACTCATTTTACA
1 ATTT-CAACT-ATTTTACA
562406 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCAACTATTTTACAC
Found at i:564983 original size:39 final size:39
Alignment explanation
Indices: 564924--565020 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
564914 TGATCTGAAA
* * * *
564924 CCCGAAGTCTAGCTGCAGCACATAAGTGCTAAACGGAAG
1 CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
564963 CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
1 CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
565002 CCCGAAGGCTAACTGAAGC
1 CCCGAAGGCTAACTGAAGC
565021 TCATCAGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.35, C:0.27, G:0.26, T:0.12
Consensus pattern (39 bp):
CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
Found at i:573470 original size:2 final size:2
Alignment explanation
Indices: 573458--573487 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
573448 ACCAAAATTT
573458 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
573488 TCATGTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:573960 original size:90 final size:90
Alignment explanation
Indices: 573810--574030 Score: 275
Period size: 90 Copynumber: 2.4 Consensus size: 90
573800 GTTTTTCAAG
* * * **
573810 AAAAGCAATTAAGCCCCTATTTTATTTTTTACACTCAATTGAGTACTTAAACTTTTAAAATGTA-
1 AAAAGCAATTAAGCCCCTGTTTT-TTTTTTACACTCAATTGAGTACTTAAACTATCAAAATACAC
** **
573874 TTAAAAAGACCCTCAAACTTTAAAAAA
65 CAAAAAAG-CCCTCAAAAATTAAAAAA
* * * *
573901 AAAAGTAATTAAGCCCCTGCTTTTTTTTTGCACTCAATTG-GATACTTGAACTATCAAAATACAC
1 AAAAGCAATTAAGCCCCTGTTTTTTTTTTACACTCAATTGAG-TACTTAAACTATCAAAATACAC
573965 CAAAAAAGCCCTCAAAAATTAAAAAA
65 CAAAAAAGCCCTCAAAAATTAAAAAA
573991 AAAAGCAATTAAGCCCCTGTTTTTTTTTTTACACTCAATT
1 AAAAGCAATTAAGCCCCTG-TTTTTTTTTTACACTCAATT
574031 TTCAAAATGC
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
89 1 0.01
90 66 0.59
91 44 0.40
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.33
Consensus pattern (90 bp):
AAAAGCAATTAAGCCCCTGTTTTTTTTTTACACTCAATTGAGTACTTAAACTATCAAAATACACC
AAAAAAGCCCTCAAAAATTAAAAAA
Found at i:574265 original size:27 final size:30
Alignment explanation
Indices: 574229--574293 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
574219 TTTATTTTTT
* *
574229 ATTAAAAATTAGA-A-AAAAATA-TAAAAA
1 ATTATAAATTAGATAGAAAAATAGGAAAAA
* *
574256 ATTATAAATTATATAGAAATATAGGAAAAA
1 ATTATAAATTAGATAGAAAAATAGGAAAAA
574286 ATTATAAA
1 ATTATAAA
574294 ATTTTATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 11 0.35
28 1 0.03
29 6 0.19
30 13 0.42
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (30 bp):
ATTATAAATTAGATAGAAAAATAGGAAAAA
Found at i:574333 original size:21 final size:22
Alignment explanation
Indices: 574291--574363 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
574281 AAAAAATTAT
* * *
574291 AAAATTTTATAAAGTCGT-AAG
1 AAAATTATAAAAAATCGTAAAG
574312 AAAATTATAAAAAAT-GTAAAG
1 AAAATTATAAAAAATCGTAAAG
* *
574333 AAAA--AT-AAAATTCGTAAAA
1 AAAATTATAAAAAATCGTAAAG
574352 AAAATTATAAAA
1 AAAATTATAAAA
574364 GTTATCGTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 5 0.12
19 11 0.26
20 2 0.05
21 21 0.50
22 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (22 bp):
AAAATTATAAAAAATCGTAAAG
Found at i:574551 original size:22 final size:22
Alignment explanation
Indices: 574523--574570 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
574513 TTAAAGGGCC
*
574523 TTTTTTTATGCA-TTTTATAAAT
1 TTTTTTTATG-ATTTTTATAAAA
574545 TTTTTTTATGATTTTTATAAAA
1 TTTTTTTATGATTTTTATAAAA
574567 TTTT
1 TTTT
574571 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTTTATGATTTTTATAAAA
Found at i:574579 original size:30 final size:29
Alignment explanation
Indices: 574543--574635 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
574533 CATTTTATAA
*
574543 ATTTTTTTTATGATTTTTATAAAATTTTAT
1 ATTTTTTTTAT-ATTTTTATAAAATTTAAT
* *
574573 ATTTTTTTCTA-ATATTTAATAAAATTAAAT
1 ATTTTTTT-TATAT-TTTTATAAAATTTAAT
* *
574603 A-TTTTTATATATTTTT-TAATATTTAAT
1 ATTTTTTTTATATTTTTATAAAATTTAAT
574630 ATTTTT
1 ATTTTT
574636 ATGTTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
27 10 0.19
28 9 0.17
29 9 0.17
30 22 0.42
31 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTTTTTTATATTTTTATAAAATTTAAT
Found at i:574615 original size:27 final size:27
Alignment explanation
Indices: 574584--574637 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
574574 TTTTTTTCTA
574584 ATATTTAATAAAATTAAATATTTTTAT
1 ATATTTAATAAAATTAAATATTTTTAT
** * *
574611 ATATTTTTTAATATTTAATATTTTTAT
1 ATATTTAATAAAATTAAATATTTTTAT
574638 GTTTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATATTTAATAAAATTAAATATTTTTAT
Found at i:574659 original size:25 final size:25
Alignment explanation
Indices: 574603--574659 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
574593 AAAATTAAAT
*
574603 ATTTTTATATATTTTTTAATATTTA
1 ATTTTTTTATATTTTTTAATATTTA
* * *
574628 ATATTTTTATGTTTTTTATTATTT-
1 ATTTTTTTATATTTTTTAATATTTA
574652 ATTTTTTT
1 ATTTTTTT
574660 GGCACATGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (25 bp):
ATTTTTTTATATTTTTTAATATTTA
Found at i:576395 original size:10 final size:11
Alignment explanation
Indices: 576377--576401 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
576367 ACTCTTTCAC
576377 TTTCTTTTTTT
1 TTTCTTTTTTT
576388 TTTCTTTTTTT
1 TTTCTTTTTTT
576399 TTT
1 TTT
576402 GTAAATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:576960 original size:12 final size:13
Alignment explanation
Indices: 576941--576978 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
576931 TTGGTCAATA
576941 ATTAGTTTTAATT
1 ATTAGTTTTAATT
* *
576954 ATT-GTTTGATTT
1 ATTAGTTTTAATT
576966 ATTAGTTTTAATT
1 ATTAGTTTTAATT
576979 CTTTTTCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (13 bp):
ATTAGTTTTAATT
Found at i:579469 original size:46 final size:46
Alignment explanation
Indices: 579382--579556 Score: 271
Period size: 46 Copynumber: 3.8 Consensus size: 46
579372 TGATGTCATA
* * * * * *
579382 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGTTGCCATG
579428 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
579474 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
*
579520 GTATCTTTCAACCATGGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
579557 AGAGCACACT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.03
46 117 0.97
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
Found at i:580712 original size:147 final size:147
Alignment explanation
Indices: 580435--580731 Score: 486
Period size: 147 Copynumber: 2.0 Consensus size: 147
580425 TTAAGATCCG
*
580435 ATAATTTTCCCTGAAACTAGACTCATATATCTTCTTACCATAAAATTTTCAGAATTTTTGGTTTA
1 ATAATTTTCCCTAAAACTAGACTCATATATCTTCTTACCATAAAATTTTCAGAATTTTTGGTTTA
* * *
580500 GCCAATAAGTATAGTTTATTCTTTAAAGTTACCCCTATTCTGCGGTCTGACAGTTTCGACCCTTC
66 GCCAATAAGTACAGTTTATTCTTTAAAGTTACCCCTATTCTGCGGTCTAACAGTTCCGACCCTTC
*
580565 TTCACTAAGAATTAATT
131 TTCACTAAAAATTAATT
* *
580582 ATAATTTTCCCTAAAACTATACTCATATATCTTCTTACCATAAAATTTTCAGAATTTTTTGTTTA
1 ATAATTTTCCCTAAAACTAGACTCATATATCTTCTTACCATAAAATTTTCAGAATTTTTGGTTTA
* * * * *
580647 TCCAATAAGTACAGTTTATTCTTTAAAGTTACCCCTGTTTTGCTGTCTAACAGTTCCGACTCTTC
66 GCCAATAAGTACAGTTTATTCTTTAAAGTTACCCCTATTCTGCGGTCTAACAGTTCCGACCCTTC
580712 TTCACTAAAAATTAATT
131 TTCACTAAAAATTAATT
580729 ATA
1 ATA
580732 TCCTCGTACA
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
147 138 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (147 bp):
ATAATTTTCCCTAAAACTAGACTCATATATCTTCTTACCATAAAATTTTCAGAATTTTTGGTTTA
GCCAATAAGTACAGTTTATTCTTTAAAGTTACCCCTATTCTGCGGTCTAACAGTTCCGACCCTTC
TTCACTAAAAATTAATT
Done.