Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold256
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: 1244454
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 7 of 8
Found at i:1091664 original size:28 final size:30
Alignment explanation
Indices: 1091593--1091666 Score: 111
Period size: 28 Copynumber: 2.6 Consensus size: 30
1091583 ATAGAGTCGG
*
1091593 GGTTGGAGTATCCCC--TCGAAAATAACGG
1 GGTTGGAGTATCCCCGATCGAAAATAACGA
1091621 GGTTGGAGTATCCCCGAT-G-AAATAACGA
1 GGTTGGAGTATCCCCGATCGAAAATAACGA
1091649 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
1091667 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 41 0.95
29 1 0.02
30 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (30 bp):
GGTTGGAGTATCCCCGATCGAAAATAACGA
Found at i:1091760 original size:51 final size:51
Alignment explanation
Indices: 1091646--1091765 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
1091636 GATGAAATAA
*
1091646 CGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAAT
* * * *
1091697 CG-GAGTTAGAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAAT
1 CGAG-GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAAT
*
1091748 TGAGGTTGGAGTATCCCC
1 CGAGGTTGGAGTATCCCC
1091766 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.02
51 57 0.97
52 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAAAAATAAAAT
Found at i:1091788 original size:79 final size:79
Alignment explanation
Indices: 1091705--1091877 Score: 226
Period size: 79 Copynumber: 2.2 Consensus size: 79
1091695 ATCGGAGTTA
*
1091705 GAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATT-GAGGTTGGAGTATCCCCTC-
1 GAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAAT-AAATTCGAGGTTCGAGTATCCCCTCA
*
1091768 GAAAATAATGGGGTTG
65 G-AAATAACGGGGTTG
* * * * *
1091784 GAGTA-TCCCTAATTGTGAAAAATTGGTGTTTTGGGAATAAATTCGGGGTTCGAGTATCCCCTCA
1 GAGTATTCCC-GATTATGAAAAATTGGTGTTTTAGAAATAAATTCGAGGTTCGAGTATCCCCTCA
1091848 GAAATAACGGGGTTG
65 GAAATAACGGGGTTG
*
1091863 GAGTATCCCCGATTA
1 GAGTATTCCCGATTA
1091878 AATAACAGGG
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 9 0.11
79 67 0.84
80 4 0.05
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (79 bp):
GAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAATAAATTCGAGGTTCGAGTATCCCCTCAG
AAATAACGGGGTTG
Found at i:1091861 original size:28 final size:28
Alignment explanation
Indices: 1091827--1091899 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
1091817 GGAATAAATT
*
1091827 CGGGGTTCGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-CATGAAATAA
* *
1091855 CGGGGTTGGAGTATCCCCGATTAAATAA
1 CGGGGTTGGAGTATCCCCCATGAAATAA
*
1091883 CAGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
1091900 TGATTGTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATGAAATAA
Found at i:1091998 original size:51 final size:52
Alignment explanation
Indices: 1091883--1092003 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 52
1091873 GATTAAATAA
*
1091883 CAGGGTTGGAGTA-TCCCTGATTGTGAAAAATTGGTGTTTTGAAAATAAAAT
1 CAGGGTTGGAGTATTCCCTGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
** * *
1091934 CAAAGTTGAAGTATTCCC-GATTGTGGAAAATTGGTGTTTT-AGAAATAAAAC
1 CAGGGTTGGAGTATTCCCTGATTGTGAAAAATTGGTGTTTTGA-AAATAAAAC
* *
1091985 CGGGGTTGGAGTATCCCCT
1 CAGGGTTGGAGTATTCCCT
1092004 TAGAAATAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
50 1 0.02
51 52 0.91
52 4 0.07
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (52 bp):
CAGGGTTGGAGTATTCCCTGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
Found at i:1092027 original size:237 final size:237
Alignment explanation
Indices: 1091548--1092061 Score: 685
Period size: 237 Copynumber: 2.2 Consensus size: 237
1091538 CCGGGGTTGA
* * * ** * * *
1091548 AGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAGAGTCGGGGTTGGAGTATCCCCTCGAA
1 AGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAGTCGGGGTTCGAGTATCCCCTCGAA
1091613 AATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
66 AATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
**
1091678 AGTGTTTTAAAAATAAAATCGGAGTTAGAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAAT
131 AGTGTTTTAAAAATAAAATCAAAGTTAGAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAAT
** * * * * *
1091743 AAAATTGAGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGG
196 AAAACCGAGGTTGGAGTATCCCCTAGAAAATAACGAGATTAG
* * * * *
1091785 AGTATCCCTAATTGTGAAAAATTGGTGTTTTGGGAATAAATTCGGGGTTCGAGTATCCCCTC-AG
1 AGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAGTCGGGGTTCGAGTATCCCCTCGA-
* *
1091849 AAATAACGGGGTTGGAGTATCCCCGATTAAATAAC-AGGGTTGGAGTATCCCTGATTGTGAAAAA
65 AAATAACGGGGTTGGAGTATCCCCGATGAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAAAA
* * * *
1091913 TTGGTGTTTTGAAAATAAAATCAAAGTT-GAAGTATTCCCGATTGTGGAAAATTGGTGTTTTAGA
129 TTAGTGTTTTAAAAATAAAATCAAAGTTAG-AGTATTCCCGATTATGAAAAATTGGTGTTTTAGA
*
1091977 AATAAAACCGGGGTTGGAGTATCCCCTTAG-AAATAACGAGATTAG
193 AATAAAACCGAGGTTGGAGTATCCCC-TAGAAAATAACGAGATTAG
* *
1092022 AGTATCCCCGATTATGAAAAATTGATGCTTTGGAAATAAA
1 AGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAA
1092062 ACTGGGTTGG
Statistics
Matches: 240, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
236 3 0.01
237 235 0.98
238 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (237 bp):
AGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAGTCGGGGTTCGAGTATCCCCTCGAA
AATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
AGTGTTTTAAAAATAAAATCAAAGTTAGAGTATTCCCGATTATGAAAAATTGGTGTTTTAGAAAT
AAAACCGAGGTTGGAGTATCCCCTAGAAAATAACGAGATTAG
Found at i:1095295 original size:46 final size:45
Alignment explanation
Indices: 1095194--1095631 Score: 331
Period size: 45 Copynumber: 10.1 Consensus size: 45
1095184 AAACGAAATA
*
1095194 TGTCCTGCTCTTTGAGGAC-AAA-A-GAAAAG-AGAAAATA-AAG
1 TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
* *
1095234 TGCATCCCGCTCTTTGAGGACAAAAGAGGAAAATAAGGAAATAGAACG
1 TG--TCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAA-G
* * *
1095282 TGTCTTGCTCTTTGAGGACAAAGGA-GAAAAG--GAAAATA-AAG
1 TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
* *
1095323 TGT-GT-CT-TTTGAGGACAAAAG-GGAAAAGAAGGAAA-GGAAG
1 TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
* *
1095363 TGCGTCCTACTCTTTGAGGACAAAAG-GAGAAAAGAAGGAAATGGAACG
1 T--GTCCTGCTCTTTGAGGACAAAAGAG-GAAAAGAAGGAAATAGAA-G
* * *
1095411 TGTCTTGCTCTTTGAGGACAAAGGA-GAAAAG--GAAAATA-AAG
1 TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
* * * *
1095452 TGCATCATGCTCTTTAAAGATAAAAG-GGAAAAGAAGGAAAT-GAAG
1 TG--TCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
* * * * *
1095497 TGCATCCTACTCTTTTAGGACAAAAG-GAGAAAAGAAGGGAATGGACG
1 TG--TCCTGCTCTTTGAGGACAAAAGAG-GAAAAGAAGGAAATAGAAG
*
1095544 TGTCCTGCTCTTTGAGGACAAAAGA-GAAAAG--GAAAATA-AAGTG
1 TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAA--G
*
1095587 TGTCATGCTCTTTGAGGAC-AAA-AGGAAAAGAAGGAAAT-GAAG
1 TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
1095629 TGT
1 TGT
1095632 GTCTTGCCCT
Statistics
Matches: 323, Mismatches: 39, Indels: 70
0.75 0.09 0.16
Matches are distributed among these distances:
38 19 0.06
39 2 0.01
40 11 0.03
41 9 0.03
42 39 0.12
43 57 0.18
44 16 0.05
45 81 0.25
46 73 0.23
47 11 0.03
48 5 0.02
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.20
Consensus pattern (45 bp):
TGTCCTGCTCTTTGAGGACAAAAGAGGAAAAGAAGGAAATAGAAG
Found at i:1095401 original size:129 final size:129
Alignment explanation
Indices: 1095199--1095630 Score: 586
Period size: 129 Copynumber: 3.3 Consensus size: 129
1095189 AAATATGTCC
* * **
1095199 TGCTCTTTGAGGACAAAA-GAAAAG-AGAAAATAAAGTGCATCCCGCTCTTTGAGGACAAAA-GA
1 TGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTGCATCCTACTCTTTGAGGACAAAAGGA
*
1095261 GGAAAATAAGGAAATAGAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGT
66 -GAAAAGAAGGAAAT-GAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGT
1095326 G
129 G
* *
1095327 T-CT-TTTGAGGACAAAAGGGAAAAGAAGGAAAGGAAGTGCGTCCTACTCTTTGAGGACAAAAGG
1 TGCTCTTTGAGGACAAAA-GGAAAAGAAGGAAATGAAGTGCATCCTACTCTTTGAGGACAAAAGG
1095390 AGAAAAGAAGGAAATGGAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGC
65 AGAAAAGAAGGAAAT-GAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTG-
*
1095455 ATCA
128 -T-G
* * * *
1095459 TGCTCTTTAAAGATAAAAGGGAAAAGAAGGAAATGAAGTGCATCCTACTCTTTTAGGACAAAAGG
1 TGCTCTTTGAGGACAAAA-GGAAAAGAAGGAAATGAAGTGCATCCTACTCTTTGAGGACAAAAGG
* * * *
1095524 AGAAAAGAAGGGAATGGACGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAAATAAAGTGTG
65 AGAAAAGAAGGAAATGAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGTG
1095589 TCATGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTG
1 ---TGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTG
1095631 TGTCTTGCCC
Statistics
Matches: 269, Mismatches: 23, Indels: 20
0.86 0.07 0.06
Matches are distributed among these distances:
126 13 0.05
127 2 0.01
128 7 0.03
129 91 0.34
130 2 0.01
131 2 0.01
132 22 0.08
133 62 0.23
134 68 0.25
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.19
Consensus pattern (129 bp):
TGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTGCATCCTACTCTTTGAGGACAAAAGGA
GAAAAGAAGGAAATGAACGTGTCTTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGTG
Found at i:1095787 original size:46 final size:44
Alignment explanation
Indices: 1095708--1095868 Score: 118
Period size: 46 Copynumber: 3.6 Consensus size: 44
1095698 CTCTTTGAAA
*
1095708 ACAAAAGGGAAAAAAAGGAAATGAAGTACGTCCTACTTTTTAAGG
1 ACAAAAGGGAAAAAAAGGAAATGAAGTA-GTCCTACTCTTTAAGG
* *
1095753 ACAAAAGTGGAAAAGAAAGG-AATGGAATGT-GTCCTGCTCTTTGAGG
1 ACAAAAG-GGAAAA-AAAGGAAAT-GAA-GTAGTCCTACTCTTTAAGG
* * * *
1095799 AC-AAA-GG-AGAAAAGGAAAATAAAGTGTGTCCTGCTCTTTGAA-G
1 ACAAAAGGGAAAAAAAGG-AAATGAAGT-AGTCCTACTCTTT-AAGG
* * *
1095842 ACAAAAAGGAAATAAAGGAAATAAAGT
1 ACAAAAGGGAAAAAAAGGAAATGAAGT
1095869 GTGTCCTGCC
Statistics
Matches: 96, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
41 7 0.07
42 4 0.04
43 20 0.21
44 4 0.04
45 21 0.22
46 30 0.31
47 8 0.08
48 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (44 bp):
ACAAAAGGGAAAAAAAGGAAATGAAGTAGTCCTACTCTTTAAGG
Found at i:1095833 original size:43 final size:44
Alignment explanation
Indices: 1095696--1095888 Score: 169
Period size: 45 Copynumber: 4.3 Consensus size: 44
1095686 GAAGGCATCT
** * * **
1095696 TGCTCTTTGAAAACAAAAGGGAAAAAAAGGAAATGAAGTACGTCC
1 TGCTCTTTGAGGACAAAA-GGAAATAAAGGAAATAAAGTGTGTCC
* * * * *
1095741 TACTTTTTAAGGACAAAAGTGGAAAAGAAAGG-AATGGAA-TGTGTCC
1 TGCTCTTTGAGGACAAAA--GG-AAATAAAGGAAAT-AAAGTGTGTCC
*
1095787 TGCTCTTTGAGGAC-AAAGGAGA-AAAGGAAAATAAAGTGTGTCC
1 TGCTCTTTGAGGACAAAAGGAAATAAAGG-AAATAAAGTGTGTCC
*
1095830 TGCTCTTTGAAGACAAAAAGGAAATAAAGGAAATAAAGTGTGTCC
1 TGCTCTTTGAGGAC-AAAAGGAAATAAAGGAAATAAAGTGTGTCC
*
1095875 TGCCCTTTGAGGAC
1 TGCTCTTTGAGGAC
1095889 TAGGAGGTGC
Statistics
Matches: 121, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
41 5 0.04
42 4 0.03
43 25 0.21
45 50 0.41
46 26 0.21
47 11 0.09
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (44 bp):
TGCTCTTTGAGGACAAAAGGAAATAAAGGAAATAAAGTGTGTCC
Found at i:1095916 original size:239 final size:237
Alignment explanation
Indices: 1095453--1096218 Score: 1076
Period size: 239 Copynumber: 3.2 Consensus size: 237
1095443 AAAATAAAGT
* *
1095453 GCATCATGCTCTTT-AAAGATAAAAGGGAAAAGAAGGAAATGAAGTGCATCCTACTCTTTTAGGA
1 GCATCATGCTCTTTGAAA-ACAAAAGGGAAAAAAAGGAAATGAAGTGCATCCTACT-TTTTAGGA
* *
1095517 CAAAAGGAGAAAAGAAGGGAATGG-ACGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAAAT
64 CAAAAGGAGAAAAGAAGGGAATGGAATGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAT
* * * *
1095581 AAAGTGTGTCATGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTGTGTCTTGCCCTTTAA
129 AAAGTGTGTCCTGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATAAAGTGTGTCATGCCCTTTGA
*
1095646 AGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAG
194 GGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAG
* * *
1095690 GCATCTTGCTCTTTGAAAACAAAAGGGAAAAAAAGGAAATGAAGTACGTCCTACTTTTTAAGGAC
1 GCATCATGCTCTTTGAAAACAAAAGGGAAAAAAAGGAAATGAAGTGCATCCTACTTTTT-AGGAC
*
1095755 AAAAGTG-GAAAAGAAAGGAATGGAATGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAT
65 AAAAG-GAGAAAAGAAGGGAATGGAATGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAT
* *
1095819 AAAGTGTGTCCTGCTCTTTGAAGACAAAAAGGAAATA-AAGGAAATAAAGTGTGTCCTGCCCTTT
129 AAAGTGTGTCCTGCTCTTTGAGGAC-AAAAGGAAA-AGAAGGAAATAAAGTGTGTCATGCCCTTT
*
1095883 GAGGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAGAAG
192 GAGGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAG
* * ** * * * *
1095929 GCGTCTTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCATCCTGCTCTTTGAGGAT
1 GCATCATGCTCTTTGAAAACAAAAGGGAAAAAAAGGAAATGAAGTGCATCCTACT-TTTTAGGAC
*
1095994 AAAAGGAGAAAAGAAGGGAATGGAATGTGTCCTGCTCTTTGAGGACAAAGGGGAAAAGGAAAATA
65 AAAAGGAGAAAAGAAGGGAATGGAATGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATA
* * **
1096059 AAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAAGAAGGAAA-AGAAGTGCATCATGCCCTTTG
130 AAGTGTGTCCTGCTCTTTGAGGACAAAAG-GAAAAGAAGGAAATA-AAGTGTGTCATGCCCTTTG
* * * *
1096123 AGGACTAGGAGATGCCACCAACTTGTGTAGGCCTTG-AAGAAAAG
193 AGGACTAGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAG
** * *
1096167 GCATCATGCTCTTTGAGGACAAAAGAGAAAAAAAGGAAATGAAGTGCGTCCT
1 GCATCATGCTCTTTGAAAACAAAAGGGAAAAAAAGGAAATGAAGTGCATCCT
1096219 GCTCTTTGAG
Statistics
Matches: 476, Mismatches: 42, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
236 4 0.01
237 71 0.15
238 127 0.27
239 270 0.57
240 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (237 bp):
GCATCATGCTCTTTGAAAACAAAAGGGAAAAAAAGGAAATGAAGTGCATCCTACTTTTTAGGACA
AAAGGAGAAAAGAAGGGAATGGAATGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAA
AGTGTGTCCTGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATAAAGTGTGTCATGCCCTTTGAGG
ACTAGGAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAG
Found at i:1095999 original size:45 final size:45
Alignment explanation
Indices: 1095935--1096127 Score: 232
Period size: 45 Copynumber: 4.3 Consensus size: 45
1095925 GAAGGCGTCT
1095935 TGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCATCC
1 TGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCATCC
* *
1095980 TGCTCTTTGAGGATAAAAGGAGAAAAGAAGGGAATGGAATGTG--TCC
1 TGCTCTTTGAGGACAAAAGG-GAAAAGAAGGAAAT-GAA-GTGCATCC
* * * *
1096026 TGCTCTTTGAGGACAAAGGGGAAAAG--GAAAATAAAGTGCGTCC
1 TGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCATCC
** * *
1096069 TGCTCTTTGAGGACAAAAGAAAAAAGAAGGAAAAGAAGTGCATCA
1 TGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCATCC
*
1096114 TGCCCTTTGAGGAC
1 TGCTCTTTGAGGAC
1096128 TAGGAGATGC
Statistics
Matches: 125, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
41 3 0.02
42 2 0.02
43 30 0.24
45 50 0.40
46 34 0.27
47 3 0.02
48 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (45 bp):
TGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGCATCC
Found at i:1096027 original size:46 final size:44
Alignment explanation
Indices: 1095935--1096100 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 44
1095925 GAAGGCGTCT
1095935 TGCTCTTTGAGGACAAAAGG-GAAAAGAAGGAAATGAA-GTGCATCC
1 TGCTCTTTGAGGACAAAAGGAGAAAAGAAGG-AATGAATGTG--TCC
*
1095980 TGCTCTTTGAGGATAAAAGGAGAAAAGAAGGGAATGGAATGTGTCC
1 TGCTCTTTGAGGACAAAAGGAGAAAAGAA-GGAAT-GAATGTGTCC
* * *
1096026 TGCTCTTTGAGGAC-AAAGGGGAAAAGGAA--AATAAAGTGCGTCC
1 TGCTCTTTGAGGACAAAAGGAGAAAA-GAAGGAATGAA-TGTGTCC
*
1096069 TGCTCTTTGAGGACAAAA-GAAAAAAGAAGGAA
1 TGCTCTTTGAGGACAAAAGGAGAAAAGAAGGAA
1096101 AAGAAGTGCA
Statistics
Matches: 105, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
42 5 0.05
43 28 0.27
44 5 0.05
45 29 0.28
46 30 0.29
47 5 0.05
48 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.30, T:0.19
Consensus pattern (44 bp):
TGCTCTTTGAGGACAAAAGGAGAAAAGAAGGAATGAATGTGTCC
Found at i:1096203 original size:104 final size:105
Alignment explanation
Indices: 1096069--1096291 Score: 324
Period size: 104 Copynumber: 2.1 Consensus size: 105
1096059 AAGTGCGTCC
1096069 TGCTCTTTGAGGACAAAAGAAAAAAGAAGGAAAAGAAGTGCATCATGCCCTTTGAGGACTAGGAG
1 TGCTCTTTGAGGACAAAAGAAAAAAGAAGGAAAAGAAGTGCATCATGCCCTTTGAGGACTAGGAG
1096134 ATGCCACCAACTTGTGTAGGCCTTG-AAGAAAAGGCATCA
66 ATGCCACCAACTTGTGTAGGCCTTGAAAGAAAAGGCATCA
* * * *
1096173 TGCTCTTTGAGGACAAAAGAGAAAAA-AAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACTAGGA
1 TGCTCTTTGAGGACAAAAGA-AAAAAGAAGGAAAAGAAGTGCATCATGCCCTTTGAGGACTAGGA
* * * ** * *
1096237 GGTGCCACCAATTTGTGTGGGGTTTGAAAGAGAAGGCATCC
65 GATGCCACCAACTTGTGTAGGCCTTGAAAGAAAAGGCATCA
1096278 TGCTCTTTGAGGAC
1 TGCTCTTTGAGGAC
1096292 TAGAAGGTGC
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 75 0.71
105 31 0.29
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (105 bp):
TGCTCTTTGAGGACAAAAGAAAAAAGAAGGAAAAGAAGTGCATCATGCCCTTTGAGGACTAGGAG
ATGCCACCAACTTGTGTAGGCCTTGAAAGAAAAGGCATCA
Found at i:1096354 original size:62 final size:61
Alignment explanation
Indices: 1096213--1096976 Score: 788
Period size: 61 Copynumber: 12.4 Consensus size: 61
1096203 AAATGAAGTG
* * * * * **
1096213 CGTCCTGCTCTTTGAGGACTAGGAGGTGCCACCAATTTGTGTGGGGTTT-GAAAG-AGAAGG
1 CGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* *
1096273 CATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTCTGGGCTTTAAAAAGAAAAAAA
1 CGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * * *
1096335 CGTCTTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAAA
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * * * * **
1096396 TGTCCAGCTCTTTGAGGACTAAAGGGTACCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * * * * **
1096458 TGTCTTGCTCTTTGAGGATTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGGTA
1 CGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA-AAA
* * * **
1096521 --TCATGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * *
1096580 CGTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAA-TTCATGTGGGCTTTGAAAAGAAAAAAGA
1 CGTCCTGCTCTTTGAGGACT-AAA-GGTGCCACCAACTT-GTGTGGGCTTTAAAAAGAAAAAA-A
* *
1096644 CGTCCTGCTCTTTAAGGACTAAATGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * * * * **
1096706 CGTCTTACTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGAGCTTT-AAAAGAAGAAGG
1 CGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * * * * * *
1096767 CATCCTGCTTTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGTCTTT-AAAAGGAGAAAG
1 CGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* * * * *
1096828 CATCCTGCTCTTTGAGGATTGGAAGGTGGCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGG
1 CGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAA-A
* *
1096891 CGTCCTGCTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
* *
1096953 CATCCTACTCTTTGAGGACTAAAG
1 CGTCCTGCTCTTTGAGGACTAAAG
1096977 AGCTAAAAGG
Statistics
Matches: 597, Mismatches: 89, Indels: 35
0.83 0.12 0.05
Matches are distributed among these distances:
60 78 0.13
61 196 0.33
62 179 0.30
63 124 0.21
64 20 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
CGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAA
Found at i:1096418 original size:61 final size:61
Alignment explanation
Indices: 1096213--1096976 Score: 842
Period size: 62 Copynumber: 12.4 Consensus size: 61
1096203 AAATGAAGTG
* * * * * *
1096213 CGTCCTGCTCTTTGAGGACTAGGAGGTGCCACCAATTTGTGTGGGGTTT-GAAAG-AGAAGG
1 CGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * *
1096273 CATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTCTGGGCTTTAAAAAGAAAAAAA
1 CGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * * * *
1096335 CGTCTTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAAA
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * * * * *
1096396 TGTCCAGCTCTTTGAGGACTAAAGGGTACCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * * * * *
1096458 TGTCTTGCTCTTTGAGGATTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGGTA
1 CGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG-A
* * * *
1096521 --TCATGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * *
1096580 CGTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAA-TTCATGTGGGCTTTGAAAAGAAAAAAGA
1 CGTCCTGCTCTTTGAGGACT-AAA-GGTGCCACCAACTT-GTGTGGGCTTTAAAAAG-AAAAAGA
*
1096644 CGTCCTGCTCTTTAAGGACTAAATGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * * * * *
1096706 CGTCTTACTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGAGCTTT-AAAAGAAGAAGG
1 CGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * * * * *
1096767 CATCCTGCTTTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGTCTTTAAAAGGAGAAAG-
1 CGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* * * * *
1096828 CATCCTGCTCTTTGAGGATTGGAAGGTGGCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGG
1 CGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAAGA
*
1096891 CGTCCTGCTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
* *
1096953 CATCCTACTCTTTGAGGACTAAAG
1 CGTCCTGCTCTTTGAGGACTAAAG
1096977 AGCTAAAAGG
Statistics
Matches: 600, Mismatches: 85, Indels: 37
0.83 0.12 0.05
Matches are distributed among these distances:
60 79 0.13
61 191 0.32
62 196 0.33
63 108 0.18
64 26 0.04
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
CGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
Found at i:1096450 original size:123 final size:122
Alignment explanation
Indices: 1096213--1096976 Score: 874
Period size: 123 Copynumber: 6.2 Consensus size: 122
1096203 AAATGAAGTG
* * * * * * * *
1096213 CGTCCTGCTCTTTGAGGACT-AGGAGGTGCCACCAATTTGTGTGGGGTTTGAAAG-AGAAGGCAT
1 CGTCCTACTCTTTGAGGACTAAAG-GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCGT
* * *
1096276 CCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTCTGGGCTTTAAAAAGAAAAAAA
65 CCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
* * * **
1096335 CGTCTTACTCTTTAAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAAATGTC
1 CGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCGTC
* * * *
1096400 CAGCTCTTTGAGGACTAAAGGGTACCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGG
66 CTGCTCTTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
* * * * * * * * **
1096458 TGTCTTGCTCTTTGAGGATTAAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGGTATC
1 CGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCGTC
* * *
1096523 ATGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGG
66 CTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
*
1096580 CGTCCTACTCTTTGAGGACTAAAAGGGTGCCACCAA-TTCATGTGGGCTTTGAAAAGAAAAAAGA
1 CGTCCTACTCTTTGAGGACT-AAAGGGTGCCACCAACTT-GTGTGGGCTTT-AAAAGAAAAAAG-
* *
1096644 CGTCCTGCTCTTTAAGGACTAAATGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGA
62 CGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
* * * * * *
1096706 CGTCTTACTCTTTGAGGACTAGAA-GGTGCCACCAACTTATGTGAGCTTTAAAAGAAGAAGGCAT
1 CGTCCTACTCTTTGAGGACTA-AAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCGT
* * * * * *
1096770 CCTGCTTTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGTCTTTAAAAGGAGAAAG-
65 CCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
* * * * *
1096828 CATCCTGCTCTTTGAGGATTGGAA-GGTGGCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGC
1 CGTCCTACTCTTTGAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAA-GC
1096892 GTCCTGCTCTTTGAGGACTAAATGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
63 GTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
*
1096953 CATCCTACTCTTTGAGGACTAAAG
1 CGTCCTACTCTTTGAGGACTAAAG
1096977 AGCTAAAAGG
Statistics
Matches: 544, Mismatches: 81, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
122 140 0.26
123 211 0.39
124 76 0.14
125 59 0.11
126 58 0.11
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (122 bp):
CGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGCGTC
CTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGA
Found at i:1103291 original size:79 final size:78
Alignment explanation
Indices: 1103150--1103338 Score: 204
Period size: 79 Copynumber: 2.4 Consensus size: 78
1103140 GATAACAATG
* ** * * *
1103150 GGGTTGAAGTATCCCCAATTATGGAAAATCGATGTTCTGGAAATAAAATCAGGATTGCAGTATCC
1 GGGTTGGAGTATCCCTGATTAT-GAAAATCGATATTCTGAAAATAAAATCAGGATTGAAGTATCC
*
1103215 CCTA-AGAAATAATA
65 CCTAGA-AAATAACA
* * *
1103229 GGGTTTGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAAATAAAATCGAGG-TTGAAGTATC
1 GGGTTGGAGTATCCCTGATTAT-GAAAATCGATATTCTGAAAATAAAATC-AGGATTGAAGTATC
* *
1103293 CCCTCGAAAATAACG
64 CCCTAGAAAATAACA
*
1103308 GGGTTGGAGT-TCCCTGATTGTGAAAATCGAT
1 GGGTTGGAGTATCCCTGATTATGAAAATCGAT
1103339 GCTTTAGAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
77 9 0.10
78 10 0.11
79 69 0.75
80 4 0.04
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCCTGATTATGAAAATCGATATTCTGAAAATAAAATCAGGATTGAAGTATCCC
CTAGAAAATAACA
Found at i:1103499 original size:50 final size:50
Alignment explanation
Indices: 1103437--1103552 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
1103427 GAAATAATGG
* *
1103437 GGTTGGAGTATCCCCGA-T-TAGAAAATTTGGTGTTTTGGAAATAAAATCA
1 GGTTGGAGTATCCCCGATTGTAGAAAA-TTGGTGTTTTAGAAATAAAACCA
* *
1103486 GAGTTGGAGTATCCCCGATTGTGGCAAATTGGTGTTTTAGAAATAAAACCA
1 G-GTTGGAGTATCCCCGATTGTAGAAAATTGGTGTTTTAGAAATAAAACCA
1103537 GGATTGGAGTATCCCC
1 GG-TTGGAGTATCCCC
1103553 TATGAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
49 1 0.02
50 17 0.29
51 36 0.61
52 5 0.08
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTAGAAAATTGGTGTTTTAGAAATAAAACCA
Found at i:1103623 original size:51 final size:51
Alignment explanation
Indices: 1103567--1103733 Score: 244
Period size: 51 Copynumber: 3.3 Consensus size: 51
1103557 AAATGACGGG
* * *
1103567 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGGAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
*
1103618 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * * *
1103669 GTTGAAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGCA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
*
1103720 GTTAGAGTATCCCC
1 GTTGGAGTATCCCC
1103734 TCGGAAATAA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:1103637 original size:130 final size:129
Alignment explanation
Indices: 1103396--1103682 Score: 380
Period size: 130 Copynumber: 2.2 Consensus size: 129
1103386 CAATATTCTG
* * * * * *
1103396 GAAATAAAACCGGGGTTGGAGAATCCACTCAGAAATAATGGGGTTGGAGTATCCCCGATTAGAAA
1 GAAATAAAACCAGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTAGAAA
* **
1103461 ATTTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTGTGGCAAATTGGTGTTTTA
66 AATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTA
* *
1103525 GAAATAAAACCAGGATTGGAGTATCCCCT-ATGAAATGACGGGGTTGGAGTATCCCCAATTGTGA
1 GAAATAAAACCAGGATTGGAGTATCCCCTCA-GAAATAACGGGGTTGGAGTATCCCCAATT-AGA
* * *
1103589 AAAATTGGTGTTTTGGGAATAAAATCGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTT
64 AAAATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTT
*
1103654 G
129 A
* *
1103655 GAAATAAAATCA-GAGTTGAAGTATCCCC
1 GAAATAAAACCAGGA-TTGGAGTATCCCC
1103683 GATTGTGGAA
Statistics
Matches: 138, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
128 1 0.01
129 53 0.38
130 84 0.61
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (129 bp):
GAAATAAAACCAGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCAATTAGAAA
AATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTA
Found at i:1103686 original size:181 final size:180
Alignment explanation
Indices: 1103435--1103793 Score: 531
Period size: 181 Copynumber: 2.0 Consensus size: 180
1103425 CAGAAATAAT
* *
1103435 GGGGTTGGAGTATCCCCGATTAGAAAATTTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCC
1 GGGGTTGGAGTATCCCCGATTAGAAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGAAGTATCC
* * * * *
1103500 CCGATTGTGGCAAATTGGTGTTTTAGAAATAAAACCAGGA-TTGGAGTATCCCCTATGAAATGAC
66 CCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACC-GCAGTTAGAGTATCCCCTAGGAAATAAC
* * ** * *
1103564 GGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGGAATAAAATC
130 AGGATTGGAGTATCCCCAATCATGAAAAATTGATGTTTTGGAAATAAAATC
*
1103615 GGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGAAGTATC
1 GGGGTTGGAGTATCCCCGATT-AGAAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGAAGTATC
*
1103680 CCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGCAGTTAGAGTATCCCCTCGGAAATAAC
65 CCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGCAGTTAGAGTATCCCCTAGGAAATAAC
* * *
1103745 AGGATTGGAGTATCCTCGATCATGAAAAGTTGATGTTTTGGAAATAAAA
130 AGGATTGGAGTATCCCCAATCATGAAAAATTGATGTTTTGGAAATAAAA
1103794 CCAAGGTTGG
Statistics
Matches: 159, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
180 23 0.14
181 136 0.86
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (180 bp):
GGGGTTGGAGTATCCCCGATTAGAAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGAAGTATCC
CCGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGCAGTTAGAGTATCCCCTAGGAAATAACA
GGATTGGAGTATCCCCAATCATGAAAAATTGATGTTTTGGAAATAAAATC
Found at i:1106214 original size:13 final size:13
Alignment explanation
Indices: 1106167--1106195 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1106157 GTAAACCCAG
1106167 AATGTATCGATAC
1 AATGTATCGATAC
1106180 AATGTATCGATAC
1 AATGTATCGATAC
1106193 AAT
1 AAT
1106196 AAACAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1108094 original size:23 final size:23
Alignment explanation
Indices: 1108060--1108110 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1108050 GAAATAAAAT
*
1108060 TGAAAAAAGGAGAGATTGTTTTA
1 TGAAAAAAGGAGAGATTATTTTA
*
1108083 TGAAAAAGGGAGAGATTATTTTA
1 TGAAAAAAGGAGAGATTATTTTA
1108106 T-AAAA
1 TGAAAA
1108111 GAGATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (23 bp):
TGAAAAAAGGAGAGATTATTTTA
Found at i:1108245 original size:116 final size:116
Alignment explanation
Indices: 1108041--1108272 Score: 367
Period size: 116 Copynumber: 2.0 Consensus size: 116
1108031 AAAAATGGGA
* * * *
1108041 GAAATTTTGGAAATAAAATTGAAAAAAGGAGAGATTGTTTTATGAAAAAGGGAGAGATTATTTTA
1 GAAATTTTGAAAATAAAATTGAAAAAAGGAAAGATTATTTTATGAAAAAAGGAGAGATTATTTTA
*
1108106 TAAAAGAGATTATTTTGGAAACAAAAAGGGGGAGAGATATTTTATTGAGGG
66 TAAAAGAGATTATTTTGGAAACAAAAAGGGGGAGAGATATTTTATTAAGGG
* * * *
1108157 GAAATTTTTAAAATAAATTTG-AAAATGAGAAAGATTATTTTATGAAAAAAGGAGTGATTATTTT
1 GAAATTTTGAAAATAAAATTGAAAAAAG-GAAAGATTATTTTATGAAAAAAGGAGAGATTATTTT
1108221 ATAAAAGAGATTATTTTGGAAACAAAAAGGGGGAGAGATATTTTATTAAGGG
65 ATAAAAGAGATTATTTTGGAAACAAAAAGGGGGAGAGATATTTTATTAAGGG
1108273 AGAGTTTTAT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
115 5 0.05
116 101 0.95
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.31
Consensus pattern (116 bp):
GAAATTTTGAAAATAAAATTGAAAAAAGGAAAGATTATTTTATGAAAAAAGGAGAGATTATTTTA
TAAAAGAGATTATTTTGGAAACAAAAAGGGGGAGAGATATTTTATTAAGGG
Found at i:1113048 original size:19 final size:19
Alignment explanation
Indices: 1113024--1113106 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
1113014 TTTCAGCGAT
1113024 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1113043 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1113062 TTGTATCGATAC---A---
1 TTGTATCGATACATAAGTG
* *
1113075 TTGTATAGATACATAAGTT
1 TTGTATCGATACATAAGTG
1113094 TTGTATCGATACA
1 TTGTATCGATACA
1113107 ATGTATCGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.20
16 2 0.04
19 43 0.77
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1113079 original size:32 final size:32
Alignment explanation
Indices: 1113043--1113114 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1113033 TACATAAGTG
1113043 TTGTATCGATACATAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCGATACA
* *
1113075 TTGTATAGATACATAAGTTTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCGATACA
*
1113107 ATGTATCG
1 TTGTATCG
1113115 CTAGGAAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (32 bp):
TTGTATCGATACATAAGTGTTGTATCGATACA
Found at i:1113202 original size:34 final size:33
Alignment explanation
Indices: 1113138--1113204 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1113128 GCCAAGGAAA
* *
1113138 TGTATCGATACATTTTTCTGTGTATTGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
1113171 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
1113205 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:1115651 original size:28 final size:27
Alignment explanation
Indices: 1115579--1115655 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
1115569 CATCAATTTT
1115579 TCATCGGGGATACTCCAACCCCGCTAA
1 TCATCGGGGATACTCCAACCCCGCTAA
*
1115606 TCATCGGGGATACTCCAACCCCG-TTA
1 TCATCGGGGATACTCCAACCCCGCTAA
**
1115632 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
1115656 CAGCTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.11
27 23 0.51
28 17 0.38
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGCTAA
Found at i:1115761 original size:80 final size:79
Alignment explanation
Indices: 1115608--1115787 Score: 238
Period size: 80 Copynumber: 2.3 Consensus size: 79
1115598 CCCGCTAATC
* *
1115608 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCAGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCAGCTTTATTTCTAAAA
* *
1115673 TATTATTTTCTCATA
66 TATGATTTTC-CACA
** * * *
1115688 ATCGGGGATACTCCAACCTTGTTATCTCCGAGGGGATACTCCAA-CCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCAGCTTTATTTCTAAAA
1115751 TCATCGATTTTCCACA
66 T-AT-GATTTTCCACA
1115767 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1115788 GCTTTATTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
78 4 0.05
79 37 0.43
80 46 0.53
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCAGCTTTATTTCTAAAA
TATGATTTTCCACA
Found at i:1115846 original size:52 final size:51
Alignment explanation
Indices: 1115719--1115888 Score: 196
Period size: 52 Copynumber: 3.3 Consensus size: 51
1115709 TTATCTCCGA
* * * *
1115719 GGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACAATC
* **
1115770 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCC-ACAATC
** * * * *
1115822 GGGGATACTCCAACTTCGATTTTATTTCTAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCCACAATC
*
1115874 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1115889 TCGTTATTTC
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
51 40 0.40
52 43 0.43
53 16 0.16
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCACAATC
Found at i:1116017 original size:290 final size:285
Alignment explanation
Indices: 1115505--1116076 Score: 808
Period size: 290 Copynumber: 2.0 Consensus size: 285
1115495 CAACTCCGAT
*
1115505 TTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAC
1 TTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAC
* * **
1115570 ATCAATTTTTCATCGGGGATACTCCAACCCCGCTAATCATCGGGGATACTCCAACCCCGTTATTT
66 ACCAATTTTTCATCGAGGATACTCCAACCCCGCTAATCATCGGGGATACTCCAACCCCGTTACCT
* * * *
1115635 TCGAGGGGATACTCCAACCCCCAGCTTTATTTCTAAAATATTATTTTCTCATAATCGGGGATACT
131 CCGAGGGGATACTCCAACCCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGATACT
** * *
1115700 CCAACCTTGTTATCTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTT-TCC
196 CCAACCCCGTTATCTCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAATCATCGATTTCT-C
*
1115764 ACAATCGGGGATACTCCAACCCCGGC
260 ACAACCGGGGATACTCCAACCCCGGC
* *
1115790 TTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTTCGATTTTATTTCTAAAA
1 TTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACTCCGATTTTATTTCT-AAA
* * * *
1115855 ACACCAATTTTTCACAATTGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCG
64 ACACCAATTTTT--C-ATCGAGGATACTCCAACCCCGCTA-ATCATCGGGGATACTCCAACCCCG
*
1115920 TTACCTCCGAGGGGATACTCCAA-CCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATTGGG
125 TTACCTCCGAGGGGATACTCCAACCCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATCGGG
* * * * *
1115984 GATACTTCAACCCCGTTAT-TCCCGAGAGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGA
190 GATACTCCAACCCCGTTATCT-CCGAGAGGATACTCCAACCCCGATTTTATTTCCAAATCATCGA
*
1116048 TTTCTCACAACCGGGGATACTCCAGCCCC
254 TTTCTCACAACCGGGGATACTCCAACCCC
1116077 ATTATTTTCA
Statistics
Matches: 252, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
285 22 0.09
286 35 0.14
287 14 0.06
289 2 0.01
290 135 0.54
291 44 0.17
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (285 bp):
TTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAC
ACCAATTTTTCATCGAGGATACTCCAACCCCGCTAATCATCGGGGATACTCCAACCCCGTTACCT
CCGAGGGGATACTCCAACCCCCAGCTTTATTCCCAAAATATTAATTTCTCATAATCGGGGATACT
CCAACCCCGTTATCTCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAATCATCGATTTCTCA
CAACCGGGGATACTCCAACCCCGGC
Found at i:1119720 original size:20 final size:19
Alignment explanation
Indices: 1119697--1119789 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 19
1119687 CACACCCAGA
*
1119697 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1119717 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1119736 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
**
1119756 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
*
1119776 TGTATCGACACATG
1 TGTATCGATACATG
1119790 AAACTGGCAG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.25
20 49 0.73
21 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1122022 original size:13 final size:13
Alignment explanation
Indices: 1122004--1122030 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1121994 ACATTATGCT
1122004 TTGTATCGATACA
1 TTGTATCGATACA
1122017 TTGTATCGATACA
1 TTGTATCGATACA
1122030 T
1 T
1122031 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1122039 original size:19 final size:19
Alignment explanation
Indices: 1122014--1122070 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1122004 TTGTATCGAT
*
1122014 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1122033 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
1122052 ACAATTCTATCGATACATG
1 AC-ATTGTATCGATACATG
1122071 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1122141 original size:33 final size:33
Alignment explanation
Indices: 1122099--1122167 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1122089 CTACCACTGT
*
1122099 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
* *
1122132 TTGTATCGATGCATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
1122165 TTG
1 TTG
1122168 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:1129284 original size:13 final size:13
Alignment explanation
Indices: 1129266--1129291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1129256 TACAGCAAGT
1129266 ATGTATCGATACA
1 ATGTATCGATACA
1129279 ATGTATCGATACA
1 ATGTATCGATACA
1129292 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1131543 original size:21 final size:21
Alignment explanation
Indices: 1131510--1131554 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1131500 TTGCAAGTTG
*
1131510 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1131532 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1131552 AAA
1 AAA
1131555 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1133379 original size:15 final size:15
Alignment explanation
Indices: 1133359--1133389 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1133349 TAAAAATGTC
*
1133359 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1133374 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1133389 C
1 C
1133390 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1134931 original size:13 final size:13
Alignment explanation
Indices: 1134913--1134938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1134903 CAATTTTTTG
1134913 TGTATCGATACAT
1 TGTATCGATACAT
1134926 TGTATCGATACAT
1 TGTATCGATACAT
1134939 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1137499 original size:13 final size:13
Alignment explanation
Indices: 1137481--1137519 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1137471 ATAATCACCC
*
1137481 TGTATCGATACAG
1 TGTATCGATACAA
1137494 TGTATCGATACAA
1 TGTATCGATACAA
1137507 TGTATCGATACAA
1 TGTATCGATACAA
1137520 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1137530 original size:20 final size:20
Alignment explanation
Indices: 1137505--1137583 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1137495 GTATCGATAC
1137505 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1137525 AATGTATCGATACATAGAATTTTCA
1 AATGTATCGATACAAAGAA-----A
* *
1137550 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1137570 CATGTATCGATACA
1 AATGTATCGATACA
1137584 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1139617 original size:15 final size:15
Alignment explanation
Indices: 1139597--1139627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1139587 ATTTCGTTTG
*
1139597 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1139612 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1139627 G
1 G
1139628 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1141460 original size:21 final size:21
Alignment explanation
Indices: 1141431--1141475 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1141421 AAGTTTTCAT
*
1141431 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1141451 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1141473 TTT
1 TTT
1141476 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1143707 original size:13 final size:13
Alignment explanation
Indices: 1143689--1143714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1143679 CAATTTTTTG
1143689 TGTATCGATACAT
1 TGTATCGATACAT
1143702 TGTATCGATACAT
1 TGTATCGATACAT
1143715 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1145420 original size:13 final size:13
Alignment explanation
Indices: 1145402--1145427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1145392 ACATTTTTCT
1145402 TTGTATCGATACA
1 TTGTATCGATACA
1145415 TTGTATCGATACA
1 TTGTATCGATACA
1145428 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1145591 original size:20 final size:20
Alignment explanation
Indices: 1145548--1145594 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1145538 AAATCTTTTG
1145548 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1145569 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1145589 CAAAAT
1 CAAAAT
1145595 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1148011 original size:13 final size:13
Alignment explanation
Indices: 1147993--1148018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1147983 TACAGCAAGT
1147993 ATGTATCGATACA
1 ATGTATCGATACA
1148006 ATGTATCGATACA
1 ATGTATCGATACA
1148019 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1150119 original size:22 final size:22
Alignment explanation
Indices: 1150093--1150155 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
1150083 TTTTTTAATT
*
1150093 TTTGACAAAGGGGGAGAAATGC
1 TTTGATAAAGGGGGAGAAATGC
*
1150115 TTTGATTAAA-GGGGAGAAATTC
1 TTTGA-TAAAGGGGGAGAAATGC
* *
1150137 TTTAATTAAGGGGGAGAAA
1 TTTGATAAAGGGGGAGAAA
1150156 AATGAAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.09
22 29 0.83
23 3 0.09
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.25
Consensus pattern (22 bp):
TTTGATAAAGGGGGAGAAATGC
Found at i:1150705 original size:19 final size:20
Alignment explanation
Indices: 1150681--1150734 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1150671 GATGTATGCT
**
1150681 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
1150700 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
1150720 TTGTATCGATACATG
1 TTGTATCGATACATG
1150735 AAATTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:1150800 original size:33 final size:33
Alignment explanation
Indices: 1150763--1150831 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1150753 CTACCACTAT
* *
1150763 TTGTATCGATTCATGGTATAA-TGTATCGAAACA
1 TTGTATCGATACATGATA-AATTGTATCGAAACA
*
1150796 TTGTATCGATACATGATAAATTGTATCGATACA
1 TTGTATCGATACATGATAAATTGTATCGAAACA
1150829 TTG
1 TTG
1150832 CTTGAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATAAATTGTATCGAAACA
Found at i:1159491 original size:181 final size:181
Alignment explanation
Indices: 1159187--1159553 Score: 626
Period size: 181 Copynumber: 2.0 Consensus size: 181
1159177 CTCATTCTCA
* * *
1159187 ACTTGAATCCTCTTTAAACCCTAAATTTAAGCTTCTTACCATCGGTTCTGCCTTCGATAAGTTGA
1 ACTTGAATCCCCTTTAAACCCTAAATTTAAGCTTCTTACCATCGATTCTACCTTCGATAAGTTGA
* *
1159252 CACAAGAGCTTGGATTCAAACAAGTTTTTCCTTATTGACCTTAGCTTCTTCTTCATATTGATGTA
66 CACAAAAGCTTGGATTCAAACAAGTTTTTCCTTATTGACCTTAGCTTCTTCTTCATATTGATGCA
1159317 GTTTCCTCTTGAGTGCTGCCATTTTTGTTTCCCCCTTACCACGATGCTGAG
131 GTTTCCTCTTGAGTGCTGCCATTTTTGTTTCCCCCTTACCACGATGCTGAG
*
1159368 ACTTGAATCCCCTTTAAACCCTAAATTTAAGCTTTTTACCATCGATTCTACCTTCGATAAGTTGA
1 ACTTGAATCCCCTTTAAACCCTAAATTTAAGCTTCTTACCATCGATTCTACCTTCGATAAGTTGA
* ** * *
1159433 CACAAAAGCTTGGGTTTGAACAAGTTTTTCCTTATTTACCTTGGCTTCTTCTTCATATTGATGCA
66 CACAAAAGCTTGGATTCAAACAAGTTTTTCCTTATTGACCTTAGCTTCTTCTTCATATTGATGCA
*
1159498 GTTTCCTCTTGAGTGCTTCCATTTTTGTTTCCCCCTTACCACGATGCTGAG
131 GTTTCCTCTTGAGTGCTGCCATTTTTGTTTCCCCCTTACCACGATGCTGAG
1159549 ACTTG
1 ACTTG
1159554 TTTTCCTTAA
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
181 174 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (181 bp):
ACTTGAATCCCCTTTAAACCCTAAATTTAAGCTTCTTACCATCGATTCTACCTTCGATAAGTTGA
CACAAAAGCTTGGATTCAAACAAGTTTTTCCTTATTGACCTTAGCTTCTTCTTCATATTGATGCA
GTTTCCTCTTGAGTGCTGCCATTTTTGTTTCCCCCTTACCACGATGCTGAG
Found at i:1163346 original size:27 final size:28
Alignment explanation
Indices: 1163267--1163337 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1163257 ATAAAAACGA
* * ** *
1163267 GGTTGGAGTATCCCTTCGAAAACAATGG
1 GGTTGGAGTATCCCCTAGAAAATGACGG
1163295 GGTTGGAGTATCCCCTAGAAAATGACGG
1 GGTTGGAGTATCCCCTAGAAAATGACGG
1163323 GGTTGGAGTA-CCCCT
1 GGTTGGAGTATCCCCT
1163338 CGATGATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 5 0.13
28 33 0.87
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTAGAAAATGACGG
Found at i:1163497 original size:79 final size:79
Alignment explanation
Indices: 1163377--1163816 Score: 503
Period size: 79 Copynumber: 5.6 Consensus size: 79
1163367 AAAAATGGGG
** ** *
1163377 TTGGAGTATCCTTGATGGT-GAAAAGTTTATATTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATGGTGGAAAA-TCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
1163441 TCAAAAATAACGGGA
65 TCAAAAATAACGGGA
* * * * *
1163456 TTGGAGTATCCCCAATGATGGAAAATCGATGTTTTAAAAATAAAATC-GAGGTTAGAGTATTCCC
1 TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAG-GGTTGGAGTATCCCC
1163520 TCAAAAATAACGGGA
65 TCAAAAATAACGGGA
** * ** * * *
1163535 TTGGAGTATCTTCGATGATGGAAAATTAATGCTTTAAAAATAAAATCGGGGTTGGAGTATCCCCT
1 TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCCT
*
1163600 CAAAAATAGCAGGG-
66 CAAAAATAAC-GGGA
* * * *
1163614 TTGGAGTATCCTCGATGGTGGAAAATCGGTGTTTTAGAAATAAAA-CAGGGACTGGAGTATCCTC
1 TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAGGG-TTGGAGTATCCCC
* *
1163678 TCAGAAATAACGGGG
65 TCAAAAATAACGGGA
* * * *
1163693 TTGGAGTATCCCTGATGGTGGAAAATCAATGTTTTGGAAATAAAA-CCGAGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAG-GGTTGGAGTATCCCC
* *
1163757 TCAGAAATAACGGGG
65 TCAAAAATAACGGGA
* *
1163772 TTGGAGTATCCCCGATGGTGGAAAATTGATATTTTAGAAATAAAA
1 TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAA
1163817 ACATCAATGA
Statistics
Matches: 310, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
78 8 0.03
79 291 0.94
80 11 0.04
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (79 bp):
TTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCCT
CAAAAATAACGGGA
Found at i:1163672 original size:237 final size:237
Alignment explanation
Indices: 1163374--1163816 Score: 611
Period size: 237 Copynumber: 1.9 Consensus size: 237
1163364 AATAAAAATG
* ** *
1163374 GGGTTGGAGTATCCTTGATGGTGAAAAGTTTATATTTTAGAAATAAAATCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCTCGATGGTGAAAAGTCGATATTTTAGAAATAAAATCAGGGCTGGAGTATCC
* *
1163439 CCTCAAAAATAACGGGATTGGAGTATCCCCAATGATGGAAAATCGATGTTTTAAAAATAAAATCG
66 CCTCAAAAATAACGGGATTGGAGTATCCCCAATGATGGAAAATCAATGTTTTAAAAATAAAACCG
* ** *
1163504 AGGTTAGAGTATTCCCTCAAAAATAACGGGATTGGAGTATCTTCGATGATGGAAAATTAATGCTT
131 AGGTTAGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGATGGAAAATTAATACTT
1163569 TAAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAGCA
196 TAAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAGCA
* *
1163611 GGGTTGGAGTATCCTCGATGGTGGAAAA-TCGGTGTTTTAGAAATAAAA-CAGGGACTGGAGTAT
1 GGGTTGGAGTATCCTCGATGGT-GAAAAGTCGATATTTTAGAAATAAAATCAGGG-CTGGAGTAT
* * * ** * **
1163674 CCTCTCAGAAATAACGGGGTTGGAGTATCCCTGATGGTGGAAAATCAATGTTTTGGAAATAAAAC
64 CCCCTCAAAAATAACGGGATTGGAGTATCCCCAATGATGGAAAATCAATGTTTTAAAAATAAAAC
* * * * * *
1163739 CGAGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATTGATAT
129 CGAGGTTAGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGATGGAAAATTAATAC
*
1163804 TTTAGAAATAAAA
194 TTTAAAAATAAAA
1163817 ACATCAATGA
Statistics
Matches: 177, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
236 5 0.03
237 167 0.94
238 5 0.03
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (237 bp):
GGGTTGGAGTATCCTCGATGGTGAAAAGTCGATATTTTAGAAATAAAATCAGGGCTGGAGTATCC
CCTCAAAAATAACGGGATTGGAGTATCCCCAATGATGGAAAATCAATGTTTTAAAAATAAAACCG
AGGTTAGAGTATCCCCTCAAAAATAACGGGATTGGAGTATCCCCGATGATGGAAAATTAATACTT
TAAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAGCA
Found at i:1167028 original size:52 final size:52
Alignment explanation
Indices: 1166950--1167077 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1166940 CGAAATATGA
*
1166950 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1167002 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1167054 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1167078 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:1167104 original size:13 final size:13
Alignment explanation
Indices: 1167086--1167110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1167076 CAAAGATCAG
1167086 TGTATCGATACAA
1 TGTATCGATACAA
1167099 TGTATCGATACA
1 TGTATCGATACA
1167111 TTTAAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1167188 original size:33 final size:33
Alignment explanation
Indices: 1167151--1167217 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1167141 AGTAGCTTAA
1167151 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1167184 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1167217 A
1 A
1167218 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1167191 original size:13 final size:13
Alignment explanation
Indices: 1167173--1167197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1167163 CAAAAAAATA
1167173 TGTATCGATACAT
1 TGTATCGATACAT
1167186 TGTATCGATACA
1 TGTATCGATACA
1167198 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1168215 original size:171 final size:172
Alignment explanation
Indices: 1168023--1168418 Score: 668
Period size: 171 Copynumber: 2.3 Consensus size: 172
1168013 TTTTAGAGAT
1168023 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1168088 GTGATAAAGAGGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGAGGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
1168153 TGTC-AACGTGCTGATTCAAAGCCAGCTACATTGAACTTAAA
131 TGTCAAACGTGCTGATTCAAAGCCAGCTACATTGAACTTAAA
* * * *
1168194 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
* *
1168259 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGAGGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
* *
1168324 TGTCAAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAAACGTGCTGATTCAAAGCCAGCTACATTGAACTTAAA
* *
1168366 GATGGAAAAGGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAG
1 GAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1168419 GTGTCAATGT
Statistics
Matches: 209, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
171 128 0.61
172 38 0.18
173 1 0.00
175 42 0.20
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (172 bp):
GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGAGGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAAACGTGCTGATTCAAAGCCAGCTACATTGAACTTAAA
Found at i:1168400 original size:52 final size:52
Alignment explanation
Indices: 1168264--1168558 Score: 301
Period size: 52 Copynumber: 5.8 Consensus size: 52
1168254 GAAAAGTGAT
* * * * * * * *
1168264 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* *
1168318 AAAGGATGTCAAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TG-CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
1168372 AAAGGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
1168415 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
1168465 --AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
1168515 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1168559 GAGGGGTTGC
Statistics
Matches: 204, Mismatches: 24, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
43 37 0.18
44 1 0.00
46 1 0.00
48 46 0.23
49 1 0.00
51 1 0.00
52 68 0.33
53 2 0.01
54 10 0.05
55 3 0.01
56 34 0.17
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:1168433 original size:43 final size:43
Alignment explanation
Indices: 1168372--1168509 Score: 195
Period size: 43 Copynumber: 3.1 Consensus size: 43
1168362 TAAAGATGGA
* * *
1168372 AAAGGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
1168415 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1168458 AAAGATGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 --A-A--AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1168506 AAAG
1 AAAG
1168510 ATGAAAAAGG
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
43 41 0.48
45 2 0.02
46 2 0.02
48 40 0.47
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1168507 original size:91 final size:95
Alignment explanation
Indices: 1168318--1168509 Score: 302
Period size: 91 Copynumber: 2.0 Consensus size: 95
1168308 AAGATGAGAA
1168318 AAAGGATGTCAAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAA
1 AAAGGATGTCAAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG--AAGGTGCCAA
* *
1168383 TATGCTGATTTAAGGCCAGCTATATTGGACTT
64 TATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
1168415 AAAGG-TGTC-AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AGGTGCCAATG
1 AAAGGATGTCAAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAGGTGCCAATA
1168476 TGCTGATTCAAGGCCAGCTACATTGGACTT
66 TGCTGATTCAAGGCCAGCTACATTGGACTT
1168506 AAAG
1 AAAG
1168510 ATGAAAAAGG
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.46
94 1 0.01
95 39 0.43
96 4 0.04
97 5 0.05
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (95 bp):
AAAGGATGTCAAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAGGTGCCAATA
TGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1168659 original size:32 final size:33
Alignment explanation
Indices: 1168563--1168655 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
1168553 GGCTTAGAGG
1168563 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1168596 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1168629 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
1168656 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:1168708 original size:35 final size:34
Alignment explanation
Indices: 1168662--1168898 Score: 322
Period size: 34 Copynumber: 6.9 Consensus size: 34
1168652 TTGGGAAGGA
*
1168662 AAAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
1168696 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1168730 AAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
1168766 AAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAG
1 -AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
1168802 AAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
*
1168836 AAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAG
1 AA-AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
1168871 AAGAAG-GTGCCACGGAGTTGTGGACTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT
1168899 GAGACAAAAT
Statistics
Matches: 187, Mismatches: 5, Indels: 23
0.87 0.02 0.11
Matches are distributed among these distances:
33 43 0.23
34 46 0.25
35 37 0.20
36 29 0.16
37 8 0.04
38 24 0.13
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (34 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:1168744 original size:33 final size:33
Alignment explanation
Indices: 1168660--1168936 Score: 301
Period size: 33 Copynumber: 8.1 Consensus size: 33
1168650 CTTTGGGAAG
*
1168660 GAAAAAAGATGCCACGGAGTTGTGGAC-TTAAAA
1 GAAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA
1168693 GGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 --GAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAA
1168729 GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAA
1168763 GGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACA
1 --G-AAAAA-AGTGCCACGGAGTTGTGGGCTTTAAA-A
*
1168801 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAA
*
1168835 GAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAA
1 GAA-AAA-AGTGCCACGGAGTTGTGGGCTTTAAAA
* * * *
1168870 GAAGAAGGTGCCACGGAGTTGTGGACTTT--GA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
* * * *
1168901 GACAAAA-TGCCACTGAGTCGTGGACTTTAAAGA
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA-A
1168934 GAA
1 GAA
1168937 GGATGCCACT
Statistics
Matches: 212, Mismatches: 16, Indels: 30
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.09
31 5 0.02
33 46 0.22
34 38 0.18
35 41 0.19
36 31 0.15
37 8 0.04
38 24 0.11
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (33 bp):
GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
Found at i:1168956 original size:62 final size:63
Alignment explanation
Indices: 1168857--1169022 Score: 200
Period size: 62 Copynumber: 2.7 Consensus size: 63
1168847 CCACGAAGTT
* * *
1168857 GTGGGCTTTAAAAGAAGAAGG-TGCCACGGAGTTGTGGACTTTGAGACA-A-AATGCCACTGAGT
1 GTGGACTTT-AAAG-AGAAGGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAATGCCACTGAGT
1168919 C
63 C
* *
1168920 GTGGACTTTAAAGAGAAGGATGCCACTGCGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTC
1 GTGGACTTTAAAGAGAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAATGCCACTGAGTC
1168983 GTGGACTTT---GAGAAGAGATTGCCACTGAGTCGTGGACTTT
1 GTGGACTTTAAAGAGAAG-GA-TGCCACTGAGTCGTGGACTTT
1169023 TTTTTTTTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
60 6 0.07
61 10 0.11
62 46 0.50
63 30 0.33
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.25
Consensus pattern (63 bp):
GTGGACTTTAAAGAGAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAATGCCACTGAGTC
Found at i:1168978 original size:31 final size:31
Alignment explanation
Indices: 1168878--1169022 Score: 172
Period size: 31 Copynumber: 4.7 Consensus size: 31
1168868 AAGAAGAAGG
* * *
1168878 TGCCACGGAGTTGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
*
1168908 TGCCACTGAGTCGTGGACTTTAAAG-AGAAGGA-
1 TGCCACTGAGTCGTGGACTTT-GAGCAG-A-GAT
*
1168940 TGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
*
1168971 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1169002 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1169023 TTTTTTTTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.01
30 21 0.21
31 56 0.55
32 22 0.22
33 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
Found at i:1169026 original size:1 final size:1
Alignment explanation
Indices: 1169020--1169082 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
1169010 AGTCGTGGAC
*** * * * *
1169020 TTTTTTTTTTTTTTTTGACTTTTTTCTTTTTTTTTCTTTTTTTTTTATTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1169083 AAAAAAAGGT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.05, C:0.05, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:1169041 original size:19 final size:19
Alignment explanation
Indices: 1169017--1169072 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
1169007 CTGAGTCGTG
1169017 GACTTTTTTTTTTTTTTTT
1 GACTTTTTTTTTTTTTTTT
*
1169036 GACTTTTTTCTTTTTTTTT
1 GACTTTTTTTTTTTTTTTT
1169055 --CTTTTTTTTTTATTTTTT
1 GACTTTTTTTTTT-TTTTTT
1169073 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 10 0.29
18 6 0.18
19 18 0.53
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.84
Consensus pattern (19 bp):
GACTTTTTTTTTTTTTTTT
Found at i:1177316 original size:52 final size:52
Alignment explanation
Indices: 1177238--1177365 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
1177228 CGAAATATGA
* *
1177238 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACCTCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1177290 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1177342 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1177366 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:1177378 original size:51 final size:50
Alignment explanation
Indices: 1177238--1177385 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 50
1177228 CGAAATATGA
* *
1177238 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACCTCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGC
1177290 AAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGC
1177342 AAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1177386 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.38
52 46 0.52
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGC
Found at i:1177392 original size:13 final size:13
Alignment explanation
Indices: 1177374--1177398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1177364 CAAAGATCAG
1177374 TGTATCGATACAA
1 TGTATCGATACAA
1177387 TGTATCGATACA
1 TGTATCGATACA
1177399 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1177476 original size:33 final size:33
Alignment explanation
Indices: 1177439--1177505 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1177429 AGTAGCTTAA
1177439 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1177472 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1177505 A
1 A
1177506 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1177479 original size:13 final size:13
Alignment explanation
Indices: 1177461--1177485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1177451 CAAAAAAATA
1177461 TGTATCGATACAT
1 TGTATCGATACAT
1177474 TGTATCGATACA
1 TGTATCGATACA
1177486 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1180184 original size:22 final size:20
Alignment explanation
Indices: 1180135--1180188 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
1180125 AAAAACCCAG
1180135 AATGTATCGATATAATTATA
1 AATGTATCGATATAATTATA
1180155 AATGTATCGATATAATTATA
1 AATGTATCGATATAATTATA
1180175 AGTATGTATCGATA
1 A--ATGTATCGATA
1180189 CATTTCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 21 0.66
22 11 0.34
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATATAATTATA
Found at i:1180285 original size:21 final size:20
Alignment explanation
Indices: 1180237--1180291 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1180227 ATATTTTAGG
1180237 CATGTATCGATACATTCACT
1 CATGTATCGATACATTCACT
*
1180257 CATGTATCGATACATTTACT
1 CATGTATCGATACATTCACT
1180277 -ATTTGTATCGATACA
1 CA--TGTATCGATACA
1180292 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 19 0.59
21 12 0.38
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACATTCACT
Found at i:1181603 original size:20 final size:20
Alignment explanation
Indices: 1181579--1181622 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1181569 AAAATTTAAA
*
1181579 AAAAAAGGAA-AAGAAAAAGAG
1 AAAAAA-GAATAA-AAAAAAAG
1181600 AAAAAAGAATAAAAAAAAAG
1 AAAAAAGAATAAAAAAAAAG
1181620 AAA
1 AAA
1181623 GCTTTCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAGAATAAAAAAAAAG
Found at i:1181617 original size:22 final size:21
Alignment explanation
Indices: 1181579--1181620 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1181569 AAAATTTAAA
* *
1181579 AAAAAAGGAAAAGAAAAAGAG
1 AAAAAAGAAAAAAAAAAAGAG
1181600 AAAAAAGAATAAAAAAAAAGA
1 AAAAAAGAA-AAAAAAAAAGA
1181621 AAGCTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAAAGAG
Found at i:1182185 original size:39 final size:39
Alignment explanation
Indices: 1182142--1182271 Score: 187
Period size: 39 Copynumber: 3.4 Consensus size: 39
1182132 TTATTTTGGG
* * *
1182142 AATTTCGAGTCAAAATTGGGTTTTTAGGGTTATTTTGAT
1 AATTTTGAGTCAAAATTGGGTTTTTAGGGATATTTTAAT
1182181 AATTTTGAGTCAAAATTGGGTTTTTAGGGATATTTTAAT
1 AATTTTGAGTCAAAATTGGGTTTTTAGGGATATTTTAAT
*
1182220 GATTTTGAGTC---A-TGGGTTTTTAGGGATATTTTAAT
1 AATTTTGAGTCAAAATTGGGTTTTTAGGGATATTTTAAT
*
1182255 GATTTTGAGTCAAAATT
1 AATTTTGAGTCAAAATT
1182272 AAATTTTTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
35 34 0.41
36 1 0.01
38 1 0.01
39 47 0.57
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (39 bp):
AATTTTGAGTCAAAATTGGGTTTTTAGGGATATTTTAAT
Found at i:1182243 original size:35 final size:36
Alignment explanation
Indices: 1182156--1182266 Score: 161
Period size: 35 Copynumber: 3.0 Consensus size: 36
1182146 TCGAGTCAAA
* * *
1182156 ATTGGGTTTTTAGGGTTATTTTGATAATTTTGAGTC
1 ATTGGGTTTTTAGGGATATTTTAATGATTTTGAGTC
1182192 AAAATTGGGTTTTTAGGGATATTTTAATGATTTTGAGTC
1 ---ATTGGGTTTTTAGGGATATTTTAATGATTTTGAGTC
1182231 A-TGGGTTTTTAGGGATATTTTAATGATTTTGAGTC
1 ATTGGGTTTTTAGGGATATTTTAATGATTTTGAGTC
1182266 A
1 A
1182267 AAATTAAATT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 35 0.51
36 1 0.01
39 33 0.48
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (36 bp):
ATTGGGTTTTTAGGGATATTTTAATGATTTTGAGTC
Found at i:1182781 original size:15 final size:15
Alignment explanation
Indices: 1182761--1182790 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1182751 TAAATACTTA
1182761 TTAATTTTTAATTTT
1 TTAATTTTTAATTTT
1182776 TTAATTTTTAATTTT
1 TTAATTTTTAATTTT
1182791 AGTATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTAATTTTTAATTTT
Found at i:1182791 original size:6 final size:7
Alignment explanation
Indices: 1182761--1182790 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1182751 TAAATACTTA
1182761 TTAATTT
1 TTAATTT
1182768 TTAATTTT
1 TTAA-TTT
1182776 TTAATTT
1 TTAATTT
1182783 TTAATTT
1 TTAATTT
1182790 T
1 T
1182791 AGTATTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTAATTT
Found at i:1182797 original size:15 final size:15
Alignment explanation
Indices: 1182762--1182799 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1182752 AAATACTTAT
*
1182762 TAATTTTTAATTTTT
1 TAATTTTTAATTTTG
1182777 TAATTTTTAATTTTAG
1 TAATTTTTAATTTT-G
1182793 T-ATTTTT
1 TAATTTTT
1182800 GTCACTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TAATTTTTAATTTTG
Found at i:1190183 original size:21 final size:21
Alignment explanation
Indices: 1190159--1190199 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1190149 CCACATAGCC
1190159 TCTGCTGTAAATTCTCCCTAT
1 TCTGCTGTAAATTCTCCCTAT
1190180 TCTGCTGTAAATTCTCCCTA
1 TCTGCTGTAAATTCTCCCTA
1190200 CCCCCAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (21 bp):
TCTGCTGTAAATTCTCCCTAT
Found at i:1191805 original size:14 final size:15
Alignment explanation
Indices: 1191788--1191820 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1191778 TTTAAATATA
*
1191788 TTATTTAATAATT-T
1 TTATTGAATAATTAT
1191802 TTATTGAATAATTAT
1 TTATTGAATAATTAT
1191817 TTAT
1 TTAT
1191821 ATATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTGAATAATTAT
Found at i:1193548 original size:12 final size:12
Alignment explanation
Indices: 1193531--1193563 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1193521 TATCATATTC
1193531 ATATTATTTTTT
1 ATATTATTTTTT
*
1193543 ATATTATGTTTT
1 ATATTATTTTTT
1193555 A-ATTATTTT
1 ATATTATTTT
1193564 CTATGTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1193915 original size:28 final size:27
Alignment explanation
Indices: 1193883--1193972 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
1193873 TTTATCTTAT
1193883 ATTTTATATAAATTTTTTATATAATTAA
1 ATTTTATATAAATTTTTTAT-TAATTAA
* *
1193911 ATTTTAACTTTAAATTTATTTATTAAAT-A
1 ATTTT-A-TATAAATTT-TTTATTAATTAA
* *
1193940 TTTTTAAATAAA--TTTTATTAATTATA
1 ATTTTATATAAATTTTTTATTAATTA-A
1193966 ATTTTAT
1 ATTTTAT
1193973 TTAATTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 9 0.18
25 1 0.02
26 6 0.12
27 4 0.08
28 6 0.12
29 6 0.12
30 12 0.24
31 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATAAATTTTTTATTAATTAA
Found at i:1195724 original size:20 final size:20
Alignment explanation
Indices: 1195701--1195825 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1195691 AAGTACCCAG
1195701 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*** *
1195721 ATGTATCGATACATGCATAA
1 ATGTATCGATACATTTTTCA
1195741 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
1195761 ATGTATTGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
1195791 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1195812 ATGTATCGATACAT
1 ATGTATCGATACAT
1195826 CTAAATGTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 58 0.69
21 2 0.02
24 5 0.06
27 5 0.06
30 2 0.02
31 12 0.14
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1203034 original size:8 final size:8
Alignment explanation
Indices: 1203021--1203046 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1203011 ATTTGATTAA
1203021 ATTTTGTG
1 ATTTTGTG
1203029 ATTTTGTG
1 ATTTTGTG
1203037 ATTTTGTG
1 ATTTTGTG
1203045 AT
1 AT
1203047 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1203738 original size:21 final size:21
Alignment explanation
Indices: 1203703--1203743 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1203693 AGCACTCACC
1203703 AGGTCGCAACCGGCA-CCCCT
1 AGGTCGCAACCGGCAGCCCCT
1203723 AGGTCGCAACCGGGCAGCCCC
1 AGGTCGCAACC-GGCAGCCCC
1203744 CACACTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.20, C:0.44, G:0.29, T:0.07
Consensus pattern (21 bp):
AGGTCGCAACCGGCAGCCCCT
Found at i:1205707 original size:13 final size:13
Alignment explanation
Indices: 1205689--1205713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205679 AGATTGCACA
1205689 GTATCGATACATT
1 GTATCGATACATT
1205702 GTATCGATACAT
1 GTATCGATACAT
1205714 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1205726 original size:20 final size:21
Alignment explanation
Indices: 1205701--1205753 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1205691 ATCGATACAT
**
1205701 TGTATCGATACATG-ACCAAA
1 TGTATCGATACATGTAAAAAA
*
1205721 TGTATCGATACTTGTAAAAAA
1 TGTATCGATACATGTAAAAAA
1205742 TGTATCGATACA
1 TGTATCGATACA
1205754 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAAAA
Found at i:1205838 original size:20 final size:20
Alignment explanation
Indices: 1205795--1205846 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1205785 CTTAACTGTT
*
1205795 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
1205814 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1205834 TGTATCGATACAT
1 TGTATCGATACAT
1205847 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1207563 original size:13 final size:13
Alignment explanation
Indices: 1207545--1207572 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1207535 TTTTTACAAT
1207545 TTGTATCGATACA
1 TTGTATCGATACA
1207558 TTGTATCGATACA
1 TTGTATCGATACA
1207571 TT
1 TT
1207573 TTGGGTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1209167 original size:306 final size:306
Alignment explanation
Indices: 1208614--1209225 Score: 1206
Period size: 306 Copynumber: 2.0 Consensus size: 306
1208604 GTCCATGCAT
1208614 GGTTAATAGCTTGATAGGTTCCATGAAATAAAAATGTTTTTTTAACATGTTTATCTTGATGATAT
1 GGTTAATAGCTTGATAGGTTCCATGAAATAAAAATGTTTTTTTAACATGTTTATCTTGATGATAT
1208679 CTTGCCATCACCATGCATTTGTGTCGTAACGTGCGCTCGATATTGGTTGCATTGTTTTCGATTTA
66 CTTGCCATCACCATGCATTTGTGTCGTAACGTGCGCTCGATATTGGTTGCATTGTTTTCGATTTA
*
1208744 TCATTATTTTGATATGATCCCTTTTGAATGTATGAATTGTGTTGAAAATAAATCCAGGTTTTGAT
131 TCATTATTTTGATATGATCCCCTTTGAATGTATGAATTGTGTTGAAAATAAATCCAGGTTTTGAT
1208809 AAAAGTTTTCATCTCATATGCGCCCCAGAGAGATGGAAAATATAGAGACATAAAAGCTGTCAAGA
196 AAAAGTTTTCATCTCATATGCGCCCCAGAGAGATGGAAAATATAGAGACATAAAAGCTGTCAAGA
1208874 TTAATAAGGAGGAAGCATGCTGATAGAGCAATAGAGGCATATGATA
261 TTAATAAGGAGGAAGCATGCTGATAGAGCAATAGAGGCATATGATA
1208920 GGTTAATAGCTTGATAGGTTCCATGAAATAAAAATGTTTTTTTAACATGTTTATCTTGATGATAT
1 GGTTAATAGCTTGATAGGTTCCATGAAATAAAAATGTTTTTTTAACATGTTTATCTTGATGATAT
1208985 CTTGCCATCACCATGCATTTGTGTCGTAACGTGCGCTCGATATTGGTTGCATTGTTTTCGATTTA
66 CTTGCCATCACCATGCATTTGTGTCGTAACGTGCGCTCGATATTGGTTGCATTGTTTTCGATTTA
1209050 TCATTATTTTGATATGATCCCCTTTGAATGTATGAATTGTGTTGAAAATAAATCCAGGTTTTGAT
131 TCATTATTTTGATATGATCCCCTTTGAATGTATGAATTGTGTTGAAAATAAATCCAGGTTTTGAT
*
1209115 AAAAGTTTTCATCTCATATGCGCCCCGGAGAGATGGAAAATATAGAGACATAAAAGCTGTCAAGA
196 AAAAGTTTTCATCTCATATGCGCCCCAGAGAGATGGAAAATATAGAGACATAAAAGCTGTCAAGA
1209180 TTAATAAGGAGGAAGCATGCTGATAGAGCAATAGAGGCATATGATA
261 TTAATAAGGAGGAAGCATGCTGATAGAGCAATAGAGGCATATGATA
1209226 TTTCATGTAG
Statistics
Matches: 304, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
306 304 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (306 bp):
GGTTAATAGCTTGATAGGTTCCATGAAATAAAAATGTTTTTTTAACATGTTTATCTTGATGATAT
CTTGCCATCACCATGCATTTGTGTCGTAACGTGCGCTCGATATTGGTTGCATTGTTTTCGATTTA
TCATTATTTTGATATGATCCCCTTTGAATGTATGAATTGTGTTGAAAATAAATCCAGGTTTTGAT
AAAAGTTTTCATCTCATATGCGCCCCAGAGAGATGGAAAATATAGAGACATAAAAGCTGTCAAGA
TTAATAAGGAGGAAGCATGCTGATAGAGCAATAGAGGCATATGATA
Found at i:1211669 original size:52 final size:52
Alignment explanation
Indices: 1211591--1211739 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 52
1211581 CGAAATATGA
*
1211591 AAATTTACCTGCATGCATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
* * *
1211643 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
* *** *
1211695 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACA
1211740 ATGCATCGAT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
Found at i:1211733 original size:20 final size:20
Alignment explanation
Indices: 1211708--1211773 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1211698 TTTGCCTGCA
1211708 TGTATCGATACAAAGATTAG
1 TGTATCGATACAAAGATTAG
1211728 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATTAG
*
1211741 TGCATCGATACAAAGATTAG
1 TGTATCGATACAAAGATTAG
1211761 TGTATCGATACAA
1 TGTATCGATACAA
1211774 TGTATCGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 23 0.62
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAGATTAG
Found at i:1211751 original size:33 final size:33
Alignment explanation
Indices: 1211711--1211785 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
1211701 GCCTGCATGT
1211711 ATCGATACAAAGATTAGTGTATCGATACAATGC
1 ATCGATACAAAGATTAGTGTATCGATACAATGC
*
1211744 ATCGATACAAAGATTAGTGTATCGATACAATGT
1 ATCGATACAAAGATTAGTGTATCGATACAATGC
1211777 ATCGATACA
1 ATCGATACA
1211786 TTTGAGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (33 bp):
ATCGATACAAAGATTAGTGTATCGATACAATGC
Found at i:1211779 original size:13 final size:13
Alignment explanation
Indices: 1211761--1211785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1211751 CAAAGATTAG
1211761 TGTATCGATACAA
1 TGTATCGATACAA
1211774 TGTATCGATACA
1 TGTATCGATACA
1211786 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1212694 original size:49 final size:49
Alignment explanation
Indices: 1212575--1212697 Score: 228
Period size: 49 Copynumber: 2.5 Consensus size: 49
1212565 ATATGCGGCT
* *
1212575 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1212624 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1212673 AGCGACATTGGACTTAAAGATGAAG
1 AGCGACATTGGACTTAAAGATGAAG
1212698 ATGAGAAAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 72 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:1212884 original size:43 final size:43
Alignment explanation
Indices: 1212818--1213230 Score: 439
Period size: 43 Copynumber: 9.0 Consensus size: 43
1212808 TTAAAGATGG
1212818 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAA-GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1212862 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1212905 AAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
1 ----AA-AAG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1212954 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1212997 AAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A-AAA-GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
** * * *
1213046 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1213089 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ----AA-AA-GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1213138 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1213181 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 --A-A--AA-GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1213230 A
1 A
1213231 GAAGGGTTGC
Statistics
Matches: 310, Mismatches: 35, Indels: 45
0.79 0.09 0.12
Matches are distributed among these distances:
43 143 0.46
44 8 0.03
45 5 0.02
46 1 0.00
47 4 0.01
48 7 0.02
49 142 0.46
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:1212904 original size:217 final size:217
Alignment explanation
Indices: 1212430--1212917 Score: 555
Period size: 218 Copynumber: 2.2 Consensus size: 217
1212420 GTTTTGTAAT
* * * * * *
1212430 GTGCCACTGTGCAGATTCAAGGCCTGCCACACTGGACTTAAAGAT-AATGAGGATGAAGAGCGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCCACATTGGACTTAAAGATGAA-GATGATGAAAAGCGAT
* *
1212494 AAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGCTTTAAAGATGAGAAAAAGGATAAAA
65 AAAAGGACCAATACGTTGACTCACGGCCAACGATATTGGCTTTAAAGATGAGAAAAAAGATAAAA
* * * *
1212559 GAGCCAATATGCGGCTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
130 GAGCCAATATGCGGCCAGCGACATTGAACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
1212624 AGCGACATTGGACTTAAAGATGAAG
195 AGCGACATTGGACTT-AAGA-GAAG
* *
1212649 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGA-GAAAAGTGATA
1 GTGCCAATGTGCTGATTCAAGGCCAGCCACATTGGACTTAAAGATGAAGATGATGAAAAGCGATA
* * *
1212713 AAGATG-CCAATATGTTGACTCACGGCCAACGATATTGGGC-TTAAAGATGAGAAAAAAGATGTC
66 AA-AGGACCAATACGTTGACTCACGGCCAACGATATT-GGCTTTAAAGATGAGAAAAAAGA--TA
* * ** * *
1212776 AATGTGCTGAT-T-CAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGAT
127 AAAGAGCCAATATGC--GGCCAGCGACATTGAACTTAAAGAT---AAAGGTGCCAATATGCTGAT
* *
1212839 TCAAGGCCAGCTATATTGGACTT-A-A-AA-
187 TCAAGGCCAGCGACATTGGACTTAAGAGAAG
* *
1212866 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGATG
1 GTGCCAATGTGCTGATTCAAGGCCAGCCACATTGGACTTAAAGATGAAGATG
1212918 CCAATATGCT
Statistics
Matches: 232, Mismatches: 27, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
217 50 0.22
218 60 0.26
219 50 0.22
220 32 0.14
221 1 0.00
223 39 0.17
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (217 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCCACATTGGACTTAAAGATGAAGATGATGAAAAGCGATA
AAAGGACCAATACGTTGACTCACGGCCAACGATATTGGCTTTAAAGATGAGAAAAAAGATAAAAG
AGCCAATATGCGGCCAGCGACATTGAACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCA
GCGACATTGGACTTAAGAGAAG
Found at i:1212955 original size:92 final size:92
Alignment explanation
Indices: 1212775--1213235 Score: 753
Period size: 92 Copynumber: 5.0 Consensus size: 92
1212765 AAAAAGATGT
* * *
1212775 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATT
*
1212840 CAAGGCCAGCTATATTGGACTTAAAAGTGC
63 CAAGGCCAGCTATATTGGACTTAAAGGTGC
*
1212870 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGATGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
1212935 GGCCAACTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
1212962 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
* **
1213026 AGGCCAGCGATATTGGACTTGGAGGTGC
65 AGGCCAGCTATATTGGACTTAAAGGTGC
1213054 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* *
1213119 GGCCAGCGATATTGGGCTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
*
1213146 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
1213211 GGCCAGCTATATTGGGCTTAGAAGG
66 GGCCAGCTATATTGGACTTA-AAGG
1213236 GTTGCCACCG
Statistics
Matches: 347, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
91 1 0.00
92 302 0.87
93 5 0.01
95 39 0.11
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGC
Found at i:1213309 original size:32 final size:33
Alignment explanation
Indices: 1213230--1213466 Score: 392
Period size: 33 Copynumber: 7.2 Consensus size: 33
1213220 TATTGGGCTT
*
1213230 AGAAGGGTTGCCACCGACTTGTGTAGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1213263 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1213296 AG-AGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1213327 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1213360 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1213393 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
*
1213427 AGAAGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1213460 A-AAGGGT
1 AGAAGGGT
1213467 GAAAGATGCC
Statistics
Matches: 192, Mismatches: 7, Indels: 11
0.91 0.03 0.05
Matches are distributed among these distances:
31 3 0.02
32 63 0.33
33 90 0.47
34 36 0.19
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1213596 original size:67 final size:65
Alignment explanation
Indices: 1213502--1213766 Score: 318
Period size: 67 Copynumber: 4.0 Consensus size: 65
1213492 TAAAAAGAAC
* *
1213502 AAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAA
1 AAGGTGCCACGGAGTCGTGGACTTTAAAA-GGAAAAAG-GTGCCACAGAGTTGTGGGCTTTGAAA
1213567 AG
64 AG
* * *
1213569 AAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAGGTGCCACGGAGTCGTGGACTTTAAAA-GG-AAAAAGGTGCCACAGAGTTGTGGGCTTTGAAA
1213634 AG
64 AG
* * * * * *
1213636 AAAAAGGTGCCACGGAGTTGTGGACCTGAAAAAGAAAAAGGTACCACAGAGTTGTGAGCTTTGAA
1 ---AAGGTGCCACGGAGTCGTGGACTTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAA
1213701 AAG
63 AAG
* * * *
1213704 AAGGTGCCACGGAGTCATGGAC-TTAAAAGGAACAAGGTGCCATAGAGTTGTGGACTTT-AAAAG
1 AAGGTGCCACGGAGTCGTGGACTTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAG
1213767 GGAAAAAGAG
Statistics
Matches: 171, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
63 5 0.03
64 29 0.17
65 20 0.12
67 56 0.33
68 34 0.20
69 1 0.01
70 26 0.15
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (65 bp):
AAGGTGCCACGGAGTCGTGGACTTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAG
Found at i:1213760 original size:168 final size:168
Alignment explanation
Indices: 1213569--1213936 Score: 494
Period size: 168 Copynumber: 2.2 Consensus size: 168
1213559 CTTTGAAAAG
* *
1213569 AAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAGGTGCCATGGAGTTGTGGACTTTAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
*
1213634 AGAAAAAGGTGCCACGGAGTTGTGGACCTGAA-AAAGAAAAAG-GTACCACAGAGTTGTGAGCTT
66 AG---AAGGTGCCACGGAGTCGTGGACCTGAAGAAAGAAAAAGAGTACCACAGAGTTGTGAGCTT
* * *
1213697 TGAAAAGAAGGTGCCACGGAGTCATG-GAC-TTAAAAGGAAC
128 TGAAAAGAAGGTGCCACAGAGTCATGAG-CTTTAAAAAGAAA
* * *
1213737 AAGGTGCCATAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAGGTGCCATGGAGTTGTGGACTTTAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
* * * * * * *
1213802 AGAAGGTGCGACGGAGTCGTGGACTTTAAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
66 AGAAGGTGCCACGGAGTCGTGGACCTGAAGAAAGAAAAAGAGTACCACAGAGTTGTGAGCTTTGA
*
1213867 AAAGAAGGTGCCACAGAGTTATGAGCTTTAAAAAGAAA
131 AAAGAAGGTGCCACAGAGTCATGAGCTTTAAAAAGAAA
*
1213905 AAGAGTGCCATGGAGTTGTGGGC-TTAAAAGGG
1 AAG-GTGCCATGGAGTTGTGGACTTTAAAAGGG
1213937 TGCCATAGAG
Statistics
Matches: 176, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
165 23 0.13
166 9 0.05
167 43 0.24
168 84 0.48
169 17 0.10
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (168 bp):
AAGGTGCCATGGAGTTGTGGACTTTAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
AGAAGGTGCCACGGAGTCGTGGACCTGAAGAAAGAAAAAGAGTACCACAGAGTTGTGAGCTTTGA
AAAGAAGGTGCCACAGAGTCATGAGCTTTAAAAAGAAA
Found at i:1213824 original size:67 final size:64
Alignment explanation
Indices: 1213473--1214112 Score: 520
Period size: 61 Copynumber: 9.9 Consensus size: 64
1213463 GGGTGAAAGA
* *
1213473 TGCCAC-GAAGTTGTGGAC-TTAAAAAGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGA
1 TGCCACAG-AGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA--G-
1213535 AAAAGAG
61 --AAG-G
* * *
1213542 TGCCACAGAGTTGTGGGCTTTGAAAA-G---AAG-GTGCCACGGAGTCGTGGACTTTAAAAGGGA
1 TGCCACAGAGTTGTGGACTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAA--G-
*
1213602 AAAAAAG
61 ---AAGG
* * * * *
1213609 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGACCTGAAAAAGAAA
1 TGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGG-GCT-TAAAAG---
1213673 AAGG
61 AAGG
* ** *
1213677 TACCACAGAGTTGT-GAGCTTTGAAAA-G---AAG-GTGCCACGGAGTCATGGACTTAAAAGGAA
1 TGCCACAGAGTTGTGGA-CTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-G--
1213736 CAAGG
61 -AAGG
*
1213741 TGCCATAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 TGCCACAGAGTTGTGGACTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGAA
1213806 GG
63 GG
* * *
1213808 TGCGACGGAGTCGTGGACTTTAAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 TGCCACAGAGTTGTGGACTTTAA-AAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGAA
1213873 GG
63 GG
* * *
1213875 TGCCACAGAGTTAT-GAGCTTTAAAAAGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAG--GG
1 TGCCACAGAGTTGTGGA-CTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGG
* * * *
1213937 TGCCATAGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT-AAA-ATGG
1 TGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGG
* * *
1213998 TGCCACAGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT-AAA-ATGG
1 TGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGG
* *
1214059 TGCCATAGAGTTGTGGACTTT-GAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 TGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1214113 TGAGACAAAA
Statistics
Matches: 502, Mismatches: 41, Indels: 64
0.83 0.07 0.11
Matches are distributed among these distances:
60 3 0.01
61 143 0.28
62 17 0.03
63 10 0.02
64 30 0.06
65 23 0.05
66 34 0.07
67 133 0.26
68 33 0.07
69 36 0.07
70 27 0.05
71 13 0.03
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (64 bp):
TGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGG
Found at i:1213934 original size:27 final size:27
Alignment explanation
Indices: 1213903--1214074 Score: 123
Period size: 27 Copynumber: 5.9 Consensus size: 27
1213893 TTTAAAAAGA
**
1213903 AAAAGAGTGCCATGGAGTTGTGGGCTT
1 AAAAGAGTGCCACAGAGTTGTGGGCTT
* * *
1213930 AAAAGGGTGCCATAGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTGTGGGCTT
1213957 AGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACAGAGTTGTGGGCTT
*
1213991 AAAATG-GTGCCACAGAGTTGTGGACTT
1 AAAA-GAGTGCCACAGAGTTGTGGGCTT
1214018 AGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACAGAGTTGTGGGCTT
*
1214052 AAAATG-GTGCCATAGAGTTGTGG
1 AAAA-GAGTGCCACAGAGTTGTGG
1214075 ACTTTGAAGG
Statistics
Matches: 119, Mismatches: 9, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
27 68 0.57
28 2 0.02
33 1 0.01
34 48 0.40
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.23
Consensus pattern (27 bp):
AAAAGAGTGCCACAGAGTTGTGGGCTT
Found at i:1214134 original size:30 final size:30
Alignment explanation
Indices: 1214066--1214331 Score: 200
Period size: 30 Copynumber: 8.5 Consensus size: 30
1214056 TGGTGCCATA
* * *
1214066 GAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACG
1 GAGTCGTGGACTTTG-A-GACAAA-A-TGCCACT
* * *
1214100 GAGTTGTGGGCTTTGAGACAAAACGCCACT
1 GAGTCGTGGACTTTGAGACAAAATGCCACT
*
1214130 GAGTTGTGGACTTTGAAGA-AAATGATGCCACT
1 GAGTCGTGGACTTTG-AGACAAA--ATGCCACT
*
1214162 GAGTCGTGGACTTTG-GAAAAAGATGCCACT
1 GAGTCGTGGACTTTGAGACAAA-ATGCCACT
* * *
1214192 GAATTGTGGACTTTTAGGACAAAATGCCACT
1 GAGTCGTGGACTTTGA-GACAAAATGCCACT
* *
1214223 GAGTCGTGGGA-TTTGAGAAGAAAAAGGTGCCACA
1 GAGTCGT-GGACTTTGAG-A-CAAAA--TGCCACT
1214257 GAGTCGTGGACTTT-AGGACAAAATGCCACT
1 GAGTCGTGGACTTTGA-GACAAAATGCCACT
* * *
1214287 GAATCGTGGGCTTTGAGA-AGAGATTGCCACT
1 GAGTCGTGGACTTTGAGACA-A-AATGCCACT
1214318 GAGTCGTGGACTTT
1 GAGTCGTGGACTTT
1214332 TAGAAGGTAT
Statistics
Matches: 193, Mismatches: 23, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.01
30 67 0.35
31 46 0.24
32 42 0.22
33 6 0.03
34 31 0.16
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (30 bp):
GAGTCGTGGACTTTGAGACAAAATGCCACT
Found at i:1214171 original size:157 final size:154
Alignment explanation
Indices: 1213991--1214330 Score: 336
Period size: 157 Copynumber: 2.2 Consensus size: 154
1213981 TTGTGGGCTT
* * * * *
1213991 AAAATGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TTA-A
1 AAAATGATGCCACTGAGTCGTGGACTT---AGGAAAAAGA-TGCCACAGAATTGTGGACTTTAGA
** * * * * *
1214054 -AATGGTGCCA-TAGAGTTGT-GGACTTTGA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
62 CAA-AATGCCACT-GAGTCGTGGGA-TTTGAGAAGAAAAAG-GTGCCACAGAGTCGTGGACTTTA
* *
1214114 GAGACAAAACGCCACTGAGTTGTGGACTTTGAAG
123 G-GACAAAACGCCACTGAATCGTGGACTTTG-AG
* *
1214148 AAAATGATGCCACTGAGTCGTGGACTTTGGAAAAAGATGCCACTGAATTGTGGACTTTTAGGACA
1 AAAATGATGCCACTGAGTCGTGGACTTAGGAAAAAGATGCCACAGAATTGTGGAC-TTTA-GACA
1214213 AAATGCCACTGAGTCGTGGGATTTGAGAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAGGACAA
64 AAATGCCACTGAGTCGTGGGATTTGAGAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAGGACAA
* *
1214278 AATGCCACTGAATCGTGGGCTTTGAG
129 AACGCCACTGAATCGTGGACTTTGAG
*
1214304 AAGA-GATTGCCACTGAGTCGTGGACTT
1 AAAATGA-TGCCACTGAGTCGTGGACTT
1214331 TTAGAAGGTA
Statistics
Matches: 154, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
153 15 0.10
154 9 0.06
155 5 0.03
156 25 0.16
157 85 0.55
158 15 0.10
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.24
Consensus pattern (154 bp):
AAAATGATGCCACTGAGTCGTGGACTTAGGAAAAAGATGCCACAGAATTGTGGACTTTAGACAAA
ATGCCACTGAGTCGTGGGATTTGAGAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAGGACAAAA
CGCCACTGAATCGTGGACTTTGAG
Found at i:1214294 original size:64 final size:64
Alignment explanation
Indices: 1214124--1214331 Score: 211
Period size: 61 Copynumber: 3.3 Consensus size: 64
1214114 GAGACAAAAC
* * *
1214124 GCCACTGAGTTGTGGACTTTGAAGA-AAATGATGCCACTGAGTCGT-GGACTTT--G--GAAAAA
1 GCCACTGAGTCGTGGACTTT-AGGACAAA--ATGCCACTGAATCGTGGGA-TTTGAGAAGAAAAA
1214183 GAT
62 GAT
* * * *
1214186 GCCACTGAATTGTGGACTTTTAGGACAAAATGCCACTGAGTCGTGGGATTTGAGAAGAAAAAGGT
1 GCCACTGAGTCGTGGAC-TTTAGGACAAAATGCCACTGAATCGTGGGATTTGAGAAGAAAAAGAT
* *
1214251 GCCACAGAGTCGTGGACTTTAGGACAAAATGCCACTGAATCGTGGGCTTTGAGAAG----AGATT
1 GCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAATCGTGGGATTTGAGAAGAAAAAGA-T
1214312 GCCACTGAGTCGTGGACTTT
1 GCCACTGAGTCGTGGACTTT
1214332 TAGAAGGTAT
Statistics
Matches: 128, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
60 2 0.02
61 38 0.30
62 22 0.17
63 7 0.05
64 37 0.29
65 22 0.17
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (64 bp):
GCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAATCGTGGGATTTGAGAAGAAAAAGAT
Found at i:1214337 original size:95 final size:94
Alignment explanation
Indices: 1214052--1214337 Score: 321
Period size: 95 Copynumber: 3.0 Consensus size: 94
1214042 TTGTGGGCTT
* * * *
1214052 AAAATGGTGCCATAGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAG
1 AAAATGGTGCCACAGAGTCGTGGACTTT--AGGAAAAAGA-TGCCACTGAATTGTGGGCTTTGAG
* *
1214117 ACAAAACGCCACTGAGTTGTGGAC-TTT-GAAG
63 A-AAAATGCCACTGAGTCGTGGACTTTTAGAAG
* * * *
1214148 AAAATGATGCCACTGAGTCGTGGACTTT-GGAAAAAGATGCCACTGAATTGTGGACTTTTAGGAC
1 AAAATGGTGCCACAGAGTCGTGGACTTTAGGAAAAAGATGCCACTGAATTGTGGGCTTTGA-GA-
*
1214212 AAAATGCCACTGAGTCGTGGGA-TTTGAGAAG
64 AAAATGCCACTGAGTCGT-GGACTTTTAGAAG
* * *
1214243 AAAAAGGTGCCACAGAGTCGTGGACTTTAGGACAAA-ATGCCACTGAATCGTGGGCTTTGAGAAG
1 AAAATGGTGCCACAGAGTCGTGGACTTTAGGAAAAAGATGCCACTGAATTGTGGGCTTTGAGAA-
*
1214307 AGATTGCCACTGAGTCGTGGACTTTTAGAAG
65 A-AATGCCACTGAGTCGTGGACTTTTAGAAG
1214338 GTATTTGAAG
Statistics
Matches: 162, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
92 19 0.12
93 29 0.18
94 11 0.07
95 73 0.45
96 30 0.19
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (94 bp):
AAAATGGTGCCACAGAGTCGTGGACTTTAGGAAAAAGATGCCACTGAATTGTGGGCTTTGAGAAA
AATGCCACTGAGTCGTGGACTTTTAGAAG
Found at i:1215328 original size:17 final size:17
Alignment explanation
Indices: 1215308--1215341 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1215298 TTGTTTCTTC
*
1215308 TTTTTTTTCCTTTTTTG
1 TTTTGTTTCCTTTTTTG
*
1215325 TTTTGTTTCTTTTTTTG
1 TTTTGTTTCCTTTTTTG
1215342 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTGTTTCCTTTTTTG
Found at i:1215631 original size:17 final size:16
Alignment explanation
Indices: 1215595--1215632 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1215585 TTTTACTCTC
1215595 TTTTTTTTGTTTGTTG
1 TTTTTTTTGTTTGTTG
1215611 TTTTGTTTTGTTT-TT-
1 TTTT-TTTTGTTTGTTG
1215626 TTTTTTT
1 TTTTTTT
1215633 GACTTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 4 0.19
16 6 0.29
17 8 0.38
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTTTGTTTGTTG
Found at i:1222205 original size:13 final size:13
Alignment explanation
Indices: 1222187--1222211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1222177 CAAAGATCAG
1222187 TGTATCGATACAA
1 TGTATCGATACAA
1222200 TGTATCGATACA
1 TGTATCGATACA
1222212 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1222292 original size:13 final size:13
Alignment explanation
Indices: 1222274--1222298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1222264 CAAAAAAATG
1222274 TGTATCGATACAT
1 TGTATCGATACAT
1222287 TGTATCGATACA
1 TGTATCGATACA
1222299 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1223077 original size:49 final size:49
Alignment explanation
Indices: 1223014--1223132 Score: 229
Period size: 49 Copynumber: 2.4 Consensus size: 49
1223004 ATATGCGGCT
*
1223014 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1223063 AGCGACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1223112 AGCGACATTGGACTTAAAGAT
1 AGCGACATTGGACTTAAAGAT
1223133 GAAGATGAGA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:1223250 original size:55 final size:52
Alignment explanation
Indices: 1223191--1223662 Score: 205
Period size: 49 Copynumber: 10.0 Consensus size: 52
1223181 TGATATTGGG
* *
1223191 CTTAAAGATGAGAAAAAAGATGTCAATGTGCTAATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAAG-TGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * * *
1223246 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * *
1223298 C-T-----T---AAAAGTG-CAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * * * * *
1223340 CTTAAAGA-AG-AAGA-TGCCAATATGCTGATTCAAGGCCAACTATATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * *
1223389 CTT-AA-A--G-----GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * * * *
1223432 CTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * * *
1223481 C-T-----TGG---AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * * * * * **
1223524 CTTAAAGA---AGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGG
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * *
1223573 CTT-AA-A--G-----GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
* * *
1223616 CTTAAAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTG
1223663 GGCTTAGAAG
Statistics
Matches: 348, Mismatches: 34, Indels: 76
0.76 0.07 0.17
Matches are distributed among these distances:
42 31 0.09
43 113 0.32
44 5 0.01
45 2 0.01
46 3 0.01
47 2 0.01
48 7 0.02
49 137 0.39
51 1 0.00
52 31 0.09
53 5 0.01
54 1 0.00
55 10 0.03
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAAGTGCCAATATGCTAATTCAAGGCCAGCTACATTGAA
Found at i:1223387 original size:49 final size:49
Alignment explanation
Indices: 1223308--1223668 Score: 436
Period size: 49 Copynumber: 7.7 Consensus size: 49
1223298 CTTAAAAGTG
* *
1223308 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
1223357 CAATATGCTGATTCAAGGCCAACTATATTGGACTT-----A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
1223400 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGC
* *
1223449 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT---G--G-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
1223492 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * *
1223541 CAATATGCTGATTCAAGGCCAACGATATTGGGCTT-----A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
1223584 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
1223633 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
1223669 GAAGGGTTGC
Statistics
Matches: 266, Mismatches: 27, Indels: 38
0.80 0.08 0.11
Matches are distributed among these distances:
43 113 0.42
44 2 0.01
46 2 0.01
48 1 0.00
49 148 0.56
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
Done.