Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008737.1 Hibiscus syriacus cultivar Beakdansim tig00111812_pilon, whole genome shotgun sequence
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: 2791265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1287893 original size:26 final size:25
Alignment explanation
Indices: 1287839--1287893 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
1287829 ATTTTTATTT
* *
1287839 CTTAAAATTTATAAATTTGTCCATT
1 CTTAAAATTTAGAAATTTGTCCATC
*
1287864 CTTAAAATTTTAGAAATTTGTCCCTC
1 CTTAAAA-TTTAGAAATTTGTCCATC
1287890 CTTA
1 CTTA
1287894 GATAAAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.45
Consensus pattern (25 bp):
CTTAAAATTTAGAAATTTGTCCATC
Found at i:1289168 original size:92 final size:92
Alignment explanation
Indices: 1289056--1289426 Score: 443
Period size: 91 Copynumber: 4.1 Consensus size: 92
1289046 GGTATGTTTG
* *
1289056 AAATTTTATGTTTCAGTGGAGGGAAATTGGAGGAAATGAGCAGGTAAGTAAAAAACCTCTAAATT
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCAGGTAATTAAAAAACCTCTAAATT
*
1289121 TTGTGACGAAACATATGAACCCGTCAC
66 TTGTGACGAAACATATGGACCCGTCAC
** * * *
1289148 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGTTGGTAATTGAAAAAAACT-AAAAA
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCAGGTAATT-AAAAAACCTCTAAAT
* *
1289212 ATTGTGACGGAACA-AGTGGA-CCGTCAC
65 TTTGTGACGAAACATA-TGGACCCGTCAC
* * *
1289239 AAATTTTATGTTTCAATGAATGGAAATTGGAGGAAATGAGCAGATAATT-AAAAACACTCTAAAT
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCAGGTAATTAAAAAAC-CTCTAAAT
*
1289303 TTTGTGAC-AGAACACATGGACCCGTCAC
65 TTTGTGACGA-AACATATGGACCCGTCAC
* * * *
1289331 AAATTTTATGTTTTAATAGA-GGAAATTGGAGGTAATGAGC-GGATAATTAAAAAA-CTATAAAT
1 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCAGG-TAATTAAAAAACCTCTAAAT
* * * *
1289393 TTTGTGGCGGAACATGTGGACTCGTCAC
65 TTTGTGACGAAACATATGGACCCGTCAC
1289421 AAATTT
1 AAATTT
1289427 GTGAGAGCCC
Statistics
Matches: 238, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
89 5 0.02
90 38 0.16
91 94 0.39
92 93 0.39
93 8 0.03
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (92 bp):
AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATGAGCAGGTAATTAAAAAACCTCTAAATT
TTGTGACGAAACATATGGACCCGTCAC
Found at i:1296181 original size:93 final size:93
Alignment explanation
Indices: 1296022--1296488 Score: 870
Period size: 93 Copynumber: 5.1 Consensus size: 93
1296012 TAGATTGCTT
*
1296022 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1296087 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1296115 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1296180 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1296208 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG--
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1296271 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1296298 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAATGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1296363 TTTGTCTTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1296392 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1296457 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1296484 AGTAA
1 AGTAA
1296489 TGCAATCCAT
Statistics
Matches: 366, Mismatches: 4, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
90 79 0.22
91 10 0.03
92 12 0.03
93 179 0.49
94 86 0.23
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1296343 original size:183 final size:186
Alignment explanation
Indices: 1296022--1296488 Score: 861
Period size: 184 Copynumber: 2.5 Consensus size: 186
1296012 TAGATTGCTT
*
1296022 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG-A
1296087 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
1296152 GTGTATTCTTTAACACTGTGAAATAGTATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACAATGTGAAATAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
1296208 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG-T
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGAT
1296272 TTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
1296336 TGTATTCTTTAACAATGTGAAATAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACAATGTGAAATAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
*
1296392 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAG-A
1296457 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
1296489 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
183 87 0.32
184 94 0.34
186 78 0.28
187 15 0.05
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACAATGTGAAATAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
Found at i:1296559 original size:21 final size:19
Alignment explanation
Indices: 1296535--1296666 Score: 97
Period size: 19 Copynumber: 7.3 Consensus size: 19
1296525 TAGTTTACTT
*
1296535 TCGCAACACGAAACTTAAAAA
1 TCGCAACGCGAAAC--AAAAA
*
1296556 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACAAAAA
1296575 TCGCAACGCGAAA-ACAAAA
1 TCGCAACGCGAAACA-AAAA
*
1296594 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACAAAAA
1296608 TCGCAACGCGAAAACCAAAAA
1 TCGCAACGCG-AAA-CAAAAA
*
1296629 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACAAAAA
*
1296643 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACAAAAA
1296662 TCGCA
1 TCGCA
1296667 TTGCAATTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 30
0.71 0.06 0.24
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 5 0.06
17 2 0.02
18 2 0.02
19 38 0.42
20 1 0.01
21 22 0.24
ACGTcount: A:0.48, C:0.29, G:0.16, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACAAAAA
Found at i:1296576 original size:19 final size:19
Alignment explanation
Indices: 1296552--1296666 Score: 115
Period size: 19 Copynumber: 6.5 Consensus size: 19
1296542 ACGAAACTTA
1296552 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
*
1296571 AAAATCGCAACGCGAAAAC
1 AAAATCGCAACGCGAAACC
1296590 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1296604 AGAATCGCAACGCGAAAACC
1 AAAATCGCAACGCG-AAACC
1296624 AAAAATCGCAA--CG--A-C
1 -AAAATCGCAACGCGAAACC
*
1296639 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1296658 AAAATCGCA
1 AAAATCGCA
1296667 TTGCAATTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
14 19 0.24
15 2 0.03
16 5 0.06
17 2 0.03
18 1 0.01
19 40 0.51
20 1 0.01
21 9 0.11
ACGTcount: A:0.49, C:0.29, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1296636 original size:35 final size:33
Alignment explanation
Indices: 1296572--1296666 Score: 149
Period size: 35 Copynumber: 2.8 Consensus size: 33
1296562 CGCGAAACCA
1296572 AAATCGCAACGCGAAAA-CAAAATCGCAACGAC
1 AAATCGCAACGCGAAAACCAAAATCGCAACGAC
1296604 AGAATCGCAACGCGAAAACCAAAAATCGCAACGAC
1 A-AATCGCAACGCGAAAACC-AAAATCGCAACGAC
1296639 AAGATCGCAACGCG-AAACCAAAATCGCA
1 AA-ATCGCAACGCGAAAACCAAAATCGCA
1296667 TTGCAATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
32 1 0.02
33 25 0.42
34 7 0.12
35 26 0.44
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.06
Consensus pattern (33 bp):
AAATCGCAACGCGAAAACCAAAATCGCAACGAC
Found at i:1296684 original size:19 final size:19
Alignment explanation
Indices: 1296662--1296780 Score: 105
Period size: 19 Copynumber: 6.8 Consensus size: 19
1296652 GAAACCAAAA
*
1296662 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1296681 TCGCGTTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
1296697 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1296714 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
1296730 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
1296747 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
*
1296766 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
1296781 AAGTTTCGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.14
16 15 0.18
17 15 0.18
19 42 0.50
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1296703 original size:14 final size:14
Alignment explanation
Indices: 1296684--1296740 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1296674 TTTCATTTCG
1296684 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1296698 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1296715 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1296731 CGTTGCGATT
1 CGTTGCGATT
1296741 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1296714 original size:33 final size:33
Alignment explanation
Indices: 1296667--1296759 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1296657 CAAAATCGCA
* *
1296667 TTGCAATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1296700 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1296733 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1296760 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1296788 original size:20 final size:19
Alignment explanation
Indices: 1296731--1296796 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
1296721 GCGATTCTGT
1296731 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1296750 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
1296769 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1296789 TGTTGCGA
1 CGTTGCGA
1296797 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:1298737 original size:14 final size:14
Alignment explanation
Indices: 1298718--1298749 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1298708 GTTTAATTGA
1298718 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
*
1298732 TTGTAAAAGTTGAT
1 TTGTAAAAGATGAT
1298746 TTGT
1 TTGT
1298750 GTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:1298884 original size:18 final size:18
Alignment explanation
Indices: 1298861--1298950 Score: 111
Period size: 18 Copynumber: 5.2 Consensus size: 18
1298851 GATTCTCTCG
1298861 TTGCGATTTTCATTCGCA
1 TTGCGATTTTCATTCGCA
1298879 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA-TTCGCA
*
1298898 TTGCGATTCT-A-TCG--
1 TTGCGATTTTCATTCGCA
1298912 -TGCGATTTTCATTCGCA
1 TTGCGATTTTCATTCGCA
1298929 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCA-TTCGCA
1298947 TTGC
1 TTGC
1298951 AATTCTTGCG
Statistics
Matches: 63, Mismatches: 2, Indels: 14
0.80 0.03 0.18
Matches are distributed among these distances:
13 8 0.13
14 1 0.02
15 3 0.05
16 3 0.05
17 5 0.08
18 28 0.44
19 15 0.24
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (18 bp):
TTGCGATTTTCATTCGCA
Found at i:1298925 original size:50 final size:48
Alignment explanation
Indices: 1298843--1298971 Score: 197
Period size: 50 Copynumber: 2.6 Consensus size: 48
1298833 ATGTTGAAGG
1298843 CGCATTGCGATTCTCTCGTTGCGATTTTCATTCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCT-TCG-TGCGATTTTCATTCGCATTGCGA-TTTCATTT
1298894 CGCATTGCGATTCTATCGTGCGATTTTCATTCGCATTGCGATTTCATTT
1 CGCATTGCGATTCT-TCGTGCGATTTTCATTCGCATTGCGATTTCATTT
* *
1298943 CGCATTGCAATTCTT-GCGCGATTTTCATT
1 CGCATTGCGATTCTTCGTGCGATTTTCATT
1298972 TCCGCAAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
47 13 0.17
48 1 0.01
49 21 0.28
50 23 0.31
51 17 0.23
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (48 bp):
CGCATTGCGATTCTTCGTGCGATTTTCATTCGCATTGCGATTTCATTT
Found at i:1301518 original size:24 final size:24
Alignment explanation
Indices: 1301484--1301530 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1301474 CTGAAACATC
1301484 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1301508 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1301531 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1302234 original size:20 final size:20
Alignment explanation
Indices: 1302206--1302396 Score: 215
Period size: 20 Copynumber: 9.6 Consensus size: 20
1302196 AAATTTCAGT
* * * *
1302206 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
1302226 GTTGCGATTTACAGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1302246 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1302266 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1302286 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1302306 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1302326 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1302346 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1302366 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1302386 GTTGCGATTTA
1 GTTGCGATTTA
1302397 TGTATTATCG
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.02
20 146 0.97
21 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1302426 original size:21 final size:22
Alignment explanation
Indices: 1302388--1302435 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1302378 GGATACGCGT
* *
1302388 TGCGATTTATGTATTATCGCAA
1 TGCGAATTATGTACTATCGCAA
*
1302410 TGCGAATT-TGTACTATCGCAT
1 TGCGAATTATGTACTATCGCAA
1302431 TGCGA
1 TGCGA
1302436 TTTTCAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (22 bp):
TGCGAATTATGTACTATCGCAA
Found at i:1305331 original size:58 final size:58
Alignment explanation
Indices: 1305269--1305379 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
1305259 TGGTCACCTG
*
1305269 ATTATAGA-GCATTGCTTTATTGAAT-TCCTGACTAATAAAAGTTACAAAATGATCCCCA
1 ATTATA-ATGCATTGCTTTATTGAATCTAC-GACTAATAAAAGTTACAAAATGATCCCCA
* * * *
1305327 ATTATAATGCATTGCTTTGTTGAGTCTACGATTATTAAAAGTTACAAAATGAT
1 ATTATAATGCATTGCTTTATTGAATCTACGACTAATAAAAGTTACAAAATGAT
1305380 TCTCACATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.02
58 43 0.93
59 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (58 bp):
ATTATAATGCATTGCTTTATTGAATCTACGACTAATAAAAGTTACAAAATGATCCCCA
Found at i:1312264 original size:26 final size:27
Alignment explanation
Indices: 1312204--1312286 Score: 97
Period size: 26 Copynumber: 3.3 Consensus size: 27
1312194 TATATTATAG
*
1312204 ATATT-AATTTTAATATTAATTTTTTA
1 ATATTAAATTATAATATTAATTTTTTA
1312230 A-A-TAAATTA-AATATTAATTTTTTA
1 ATATTAAATTATAATATTAATTTTTTA
*
1312254 ATATTATATTATAGATATTAA--TTTTA
1 ATATTAAATTATA-ATATTAATTTTTTA
1312280 ATATTAA
1 ATATTAA
1312287 TTTTTTAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 17 0.35
25 6 0.12
26 18 0.37
27 1 0.02
28 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATATTAAATTATAATATTAATTTTTTA
Found at i:1312287 original size:64 final size:64
Alignment explanation
Indices: 1312186--1312344 Score: 300
Period size: 64 Copynumber: 2.5 Consensus size: 64
1312176 AGGTTTTATA
*
1312186 TTTAATTTTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1312250 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
1312314 TTTAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATAGATA-TTAATTTTA
1312345 TATCATATAA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
64 84 0.90
65 9 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (64 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTT
Found at i:1312289 original size:40 final size:37
Alignment explanation
Indices: 1312239--1312323 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 37
1312229 AAATAAATTA
*
1312239 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAATTTTTTAA-A-TAAATTA-A-ATATTAATTTTT
1312279 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAA-TTTTT
1312317 AATATTA
1 AATATTA
1312324 TATTATAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 17 0.40
39 1 0.02
40 16 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
Found at i:1312399 original size:20 final size:19
Alignment explanation
Indices: 1312339--1312400 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1312329 TAGATATTTA
*
1312339 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1312358 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1312376 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1312396 ATTTT
1 ATTTT
1312401 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1313052 original size:31 final size:31
Alignment explanation
Indices: 1313015--1313074 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1313005 TAGTTGTATG
* *
1313015 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGAATTGTAAAACTAA
1313046 AATTATTTAAATCTCAGAATTGTAAAACT
1 AATTATTTAAATCTCAGAATTGTAAAACT
1313075 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGAATTGTAAAACTAA
Found at i:1314100 original size:36 final size:36
Alignment explanation
Indices: 1313973--1314384 Score: 343
Period size: 36 Copynumber: 11.6 Consensus size: 36
1313963 ATACATACAT
* * *
1313973 ATATATTATATAG-TTTGAAAACATTTTTAAAATATA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATA-A
* **
1314009 CATATAATATATAGTTTTGAAAACATGTTTGAAAACGTTT
1 -ATATAATATATAGTTTTTAAAACAT-TTTGAAAA--TAA
* *
1314049 ATATATTATATAGTTTTTAAAATATTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* * *
1314085 ATATAATATACAGTTTTTAAATCTTTTTTGAAAAT--
1 ATATAATATATAGTTTTTAAAAC-ATTTTGAAAATAA
* *
1314120 ATATATTATATAGTTTTTAAAACATATTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* * *
1314156 ATATAATATATAATTTTTAAAACGTTTTTGAAAA-AT
1 ATATAATATATAGTTTTTAAAAC-ATTTTGAAAATAA
*
1314192 ATATATTATATAGTTTTTAAAACATTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* *
1314228 ATATAATATATAATTTTTAAAATATTTTTGAAAAT--
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAATAA
*
1314263 ATAT-AT-TGTAGTTTTTAAAACATTTTGAAAAT--
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* ** * *
1314295 ATAT-A-GT-T--TTTAAAAAACATTTTTGAAAACAT
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAATAA
* * * *
1314327 ATATACTATATAGTTTTGAAATCATTTTGAAAACT-T
1 ATATAATATATAGTTTTTAAAACATTTTGAAAA-TAA
* *
1314363 ATATAGTATATAGTTTTAAAAA
1 ATATAATATATAGTTTTTAAAA
1314385 AAAATTGAAA
Statistics
Matches: 309, Mismatches: 46, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
29 9 0.03
30 9 0.03
31 1 0.00
32 20 0.06
33 13 0.04
34 12 0.04
35 34 0.11
36 114 0.37
37 48 0.16
38 19 0.06
39 29 0.09
41 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:1314150 original size:71 final size:71
Alignment explanation
Indices: 1313971--1314483 Score: 461
Period size: 72 Copynumber: 7.3 Consensus size: 71
1313961 ATATACATAC
* * * *
1313971 ATATATATTATATAG-TTTGAAAACATTTTTAAAATATACATATAATATATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATA-A-ATATAATATATAATTTTTAAAACAT
*
1314035 GTTTGAAA
64 TTTTGAAA
* * * *
1314043 ACGTTTATATATTATATAGTTTTTAAAATATTTTGAAAATAAATATAATATACAGTTTTTAAATC
1 A----TATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAAC
*
1314108 TTTTTTGAAA
62 ATTTTTGAAA
* *
1314118 ATATATATTATATAGTTTTTAAAACATATTGAAAATAAATATAATATATAATTTTTAAAACGTTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
1314183 TTGAAAA
66 TTG-AAA
*
1314190 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAATATTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
1314255 TTGAAA
66 TTGAAA
* * **
1314261 ATATATA-T-TGTAGTTTTTAAAACATTTTGAAAAT--ATAT-A-GT-T--TTTAAAAAACATTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
1314317 TTGAAAA
66 TTG-AAA
* * * * * * * *
1314324 CATATATACTATATAGTTTTGAAATCATTTTGAAAACT-TATATAGTATAT-AGTTTTAAAAAAA
1 -ATATATATTATATAGTTTTTAAAACATTTTGAAAA-TAAATATAATATATAATTTTTAAAACAT
**
1314387 AATTG---
64 TTTTGAAA
* * * * *
1314392 A-A-A-ACTATATAGTTTTCAAAACATTTTTCAAAACAATATATAATATATAA-TTTTAAAATAT
1 ATATATATTATATAGTTTTTAAAACA-TTTTGAAAATAA-ATATAATATATAATTTTTAAAACA-
1314453 TTTTTTGAAA
63 -TTTTTGAAA
*
1314463 ATATATATTGTATAGATTTTT
1 ATATATATTATATAG-TTTTT
1314484 GGAAAATATT
Statistics
Matches: 365, Mismatches: 47, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
62 14 0.04
63 3 0.01
64 26 0.07
65 11 0.03
66 43 0.12
67 7 0.02
68 7 0.02
69 25 0.07
70 2 0.01
71 73 0.20
72 80 0.22
73 1 0.00
74 7 0.02
75 33 0.09
76 15 0.04
77 18 0.05
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (71 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
TTGAAA
Found at i:1314329 original size:30 final size:27
Alignment explanation
Indices: 1314271--1314329 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 27
1314261 ATATATATTG
*
1314271 TAGTTTTTAAAACATTTTGAAAATATA
1 TAGTTTTTAAAACATTTTGAAAACATA
1314298 TAGTTTTTAAAAAACATTTTTGAAAACATA
1 TAGTTTTT--AAAACA-TTTTGAAAACATA
1314328 TA
1 TA
1314330 TACTATATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 8 0.29
29 6 0.21
30 14 0.50
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (27 bp):
TAGTTTTTAAAACATTTTGAAAACATA
Found at i:1314393 original size:36 final size:35
Alignment explanation
Indices: 1314294--1314404 Score: 123
Period size: 36 Copynumber: 3.0 Consensus size: 35
1314284 ATTTTGAAAA
*
1314294 TATATAGTTTTTAAAAAACATTTTTGAAAACATATATAC
1 TATATAG-TTTTAAAAAA-A-TTTTGAAAAC-TATATAG
* **
1314333 TATATAGTTTTGAAATCATTTTGAAAACTTATATAG
1 TATATAGTTTTAAAAAAATTTTGAAAAC-TATATAG
**
1314369 TATATAGTTTTAAAAAAAAATTGAAAACTATATAG
1 TATATAGTTTTAAAAAAATTTTGAAAACTATATAG
1314404 T
1 T
1314405 TTTCAAAACA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 8 0.13
36 39 0.63
37 1 0.02
38 7 0.11
39 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (35 bp):
TATATAGTTTTAAAAAAATTTTGAAAACTATATAG
Found at i:1314401 original size:135 final size:132
Alignment explanation
Indices: 1314160--1314402 Score: 319
Period size: 135 Copynumber: 1.8 Consensus size: 132
1314150 AAATAAATAT
* * *
1314160 AATATATAATTTTTAAAACGTTTTTGAAAAATATATATTATATAGTTTTTAAAACATTTTGAAAA
1 AATATATAATTTTTAAAACATTTTTGAAAAATATATACTATATAGTTTTGAAAACATTTTGAAAA
* * ***
1314225 TAAATATAATATATAATTTTTAAAATATTTTTGAAAATATATATTGTAGTTTTTAAAACATTTTG
66 TAAATATAATATATAAGTTTTAAAAAAAAATTGAAAATATATATTGTAGTTTTTAAAACATTTTG
1314290 AA
131 AA
* *
1314292 AATATATAGTTTTTAAAAAACATTTTTGAAAACATATATACTATATAGTTTTGAAATCATTTTGA
1 AATATATAATTTTT--AAAACATTTTTGAAAA-ATATATACTATATAGTTTTGAAAACATTTTGA
* *
1314357 AAACT-TATATAGTATAT-AGTTTTAAAAAAAAATTGAAAACTATATA
63 AAA-TAAATATAATATATAAGTTTTAAAAAAAAATTGAAAA-TATATA
1314403 GTTTTCAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
132 13 0.14
134 32 0.34
135 48 0.51
136 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (132 bp):
AATATATAATTTTTAAAACATTTTTGAAAAATATATACTATATAGTTTTGAAAACATTTTGAAAA
TAAATATAATATATAAGTTTTAAAAAAAAATTGAAAATATATATTGTAGTTTTTAAAACATTTTG
AA
Found at i:1314500 original size:5 final size:5
Alignment explanation
Indices: 1314490--1314567 Score: 79
Period size: 5 Copynumber: 15.2 Consensus size: 5
1314480 TTTTGGAAAA
*
1314490 TATTT TATTT TATTT TATTT TATTTT TATTAT TATGTT TATTT T-TAT
1 TATTT TATTT TATTT TATTT TA-TTT TATT-T TAT-TT TATTT TATTT
* *
1314537 TATTT TA-TT AATTT CATTTT TATTT TATTT T
1 TATTT TATTT TATTT TA-TTT TATTT TATTT T
1314568 TTCTTTCCAG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
4 6 0.10
5 38 0.61
6 17 0.27
7 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:1314518 original size:6 final size:6
Alignment explanation
Indices: 1314492--1314568 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
1314482 TTGGAAAATA
* *
1314492 TTTTA- TTTTA- TTTTA- TTTTAT TTTTAT TATTAT GTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * * *
1314537 TATT-T TATTAA TTTCAT TTTTA- TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1314569 TCTTTCCAGG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
5 25 0.42
6 34 0.58
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:1314531 original size:18 final size:17
Alignment explanation
Indices: 1314490--1314568 Score: 92
Period size: 17 Copynumber: 4.7 Consensus size: 17
1314480 TTTTGGAAAA
1314490 TATTTTA-TTTTATT-T
1 TATTTTATTTTTATTAT
1314505 TATTTTATTTTTATTAT
1 TATTTTATTTTTATTAT
1314522 TATGTTTATTTTTATTAT
1 TAT-TTTATTTTTATTAT
* * *
1314540 T-TTATTAATTTCATTTT
1 TATT-TTATTTTTATTAT
1314557 TATTTTATTTTT
1 TATTTTATTTTT
1314569 TCTTTCCAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
15 7 0.13
16 8 0.15
17 22 0.41
18 17 0.31
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (17 bp):
TATTTTATTTTTATTAT
Found at i:1314532 original size:23 final size:22
Alignment explanation
Indices: 1314492--1314568 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 22
1314482 TTGGAAAATA
1314492 TTTTATT-TTATTTTATTTTAT
1 TTTTATTATTATTTTATTTTAT
1314513 TTTTATTATTATGTTTATTTTTATT
1 TTTTATTATTAT-TTTA-TTTTA-T
1314538 ATTTTATTAATTTCATTTTTATTTTAT
1 -TTTTATT-A-TT-A-TTTTATTTTAT
1314565 TTTT
1 TTTT
1314569 TCTTTCCAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
21 7 0.15
22 4 0.09
23 4 0.09
24 5 0.11
25 1 0.02
26 11 0.23
27 2 0.04
28 7 0.15
29 5 0.11
30 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (22 bp):
TTTTATTATTATTTTATTTTAT
Found at i:1314550 original size:9 final size:8
Alignment explanation
Indices: 1314490--1314546 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
1314480 TTTTGGAAAA
1314490 TATTTTAT
1 TATTTTAT
1314498 T-TTATT-T
1 TATT-TTAT
1314505 TATTTTAT
1 TATTTTAT
*
1314513 TTTTATTAT
1 TATT-TTAT
1314522 TATGTTTA-
1 TAT-TTTAT
1314530 T-TTTTAT
1 TATTTTAT
1314537 TATTTTAT
1 TATTTTAT
1314545 TA
1 TA
1314547 ATTTCATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
6 4 0.10
7 8 0.20
8 18 0.45
9 9 0.22
10 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:1314574 original size:23 final size:21
Alignment explanation
Indices: 1314492--1314567 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1314482 TTGGAAAATA
1314492 TTTTATTTTATTTTATTTTAT
1 TTTTATTTTATTTTATTTTAT
1314513 TTTTATTATTATGTTTA-TTT-T
1 TTTTATT-TTAT-TTTATTTTAT
* * *
1314534 TATTATTTTA-TTAATTTCAT
1 TTTTATTTTATTTTATTTTAT
1314554 TTTTATTTTATTTT
1 TTTTATTTTATTTT
1314568 TTCTTTCCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.07
19 2 0.04
20 13 0.29
21 16 0.36
22 7 0.16
23 4 0.09
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTTATTTTATTTTATTTTAT
Found at i:1316106 original size:4 final size:4
Alignment explanation
Indices: 1316083--1316122 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
1316073 TTCCCCTTTG
*
1316083 ATTT A-TT ATTT TTCTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
1316123 TCCCTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1316237 original size:13 final size:13
Alignment explanation
Indices: 1316219--1316248 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1316209 TGAATCAGGT
1316219 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
1316232 TTTTAATTTTTAA
1 TTTTAAATTTTAA
1316245 TTTT
1 TTTT
1316249 CACGATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1319939 original size:67 final size:67
Alignment explanation
Indices: 1319829--1319973 Score: 245
Period size: 67 Copynumber: 2.2 Consensus size: 67
1319819 TGGTAGTAGC
* * *
1319829 TCAACTTCACAGCGAAGGGGCGACTGACTGTTAATAAATAACTTTTCAGTTTCATTCAAAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAA
1319894 TT
66 TT
* *
1319896 TCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAA
1319961 TT
66 TT
1319963 TCAACTTCACA
1 TCAACTTCACA
1319974 ATGAAGAATA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 73 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (67 bp):
TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAA
TT
Found at i:1320095 original size:110 final size:110
Alignment explanation
Indices: 1319896--1320169 Score: 431
Period size: 110 Copynumber: 2.5 Consensus size: 110
1319886 AAAGTCAATT
* *
1319896 TCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGGCAA
* *
1319961 TTTCAACTTCACAATGAAGAATATTGGACTCGAGACAACACAAGC
66 TTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACACAAGC
* *
1320006 TCAACTTCACAGCGAAGGAGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGGCAA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGGCAA
* * *
1320071 TTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACACAAGC
66 TTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACACAAGC
* * * *
1320116 TCAACTTCACAGCGAAGGGGCAACTGCCTGTCAACAAACAGCTTTCCAGTTTCA
1 TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
1320170 GAGTCAATTT
Statistics
Matches: 149, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 149 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (110 bp):
TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGGCAA
TTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACACAAGC
Found at i:1320481 original size:84 final size:84
Alignment explanation
Indices: 1320269--1320632 Score: 475
Period size: 84 Copynumber: 4.3 Consensus size: 84
1320259 AAGGGATTTT
* * * * * * *
1320269 TGCCCACC-AAAGACCTTCGAGTTCGACTACGCTTAGCTCAAAGGCACAATATTTACAGCATAGC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-TATATTTGCAACATAAC
1320333 TTAAGTCGAGAAGGGCTATC
65 TTAAGTCGAGAAGGGCTATC
1320353 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT-ATTTGCAACATAAC
*
1320418 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGCTATC
* * *
1320438 TGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCAACTTCAAGGCATATAGTTTGCAGCATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATA-TTTGCAACATAAC
* * *
1320502 TTAAGTCGATAAGGGTTATA
65 TTAAGTCGAGAAGGGCTATC
* * * *
1320522 TGCCAACC-AAATACCGTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAACATAAC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT-ATTTGCAACATAAC
*
1320586 TTAAGTTGAGAAGGGCTATC
65 TTAAGTCGAGAAGGGCTATC
*
1320606 TGCCAACCGAAA-ACCTTTCGAGTTCGA
1 TGCCAACCAAAAGACC-TTCGAGTTCGA
1320633 TTCAATTCAG
Statistics
Matches: 248, Mismatches: 25, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
83 1 0.00
84 160 0.65
85 87 0.35
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATATTTGCAACATAACT
TAAGTCGAGAAGGGCTATC
Found at i:1320599 original size:168 final size:170
Alignment explanation
Indices: 1320269--1320632 Score: 515
Period size: 169 Copynumber: 2.2 Consensus size: 170
1320259 AAGGGATTTT
* * * *
1320269 TGCCCACC-AAAGACCTTCGAGTTCGACTACGCTTAGCTCAAAGGCACAATATTTACAGCATAGC
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACAATATTTACAGCATAAC
* *
1320333 TTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
66 TTAAGTCGAGAAGGGCTATATGCCAACCAAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAAGG
* * *
1320398 CATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATC
131 AACATCATTTGCAACATAACTTAAGTCGAGAAGGGCTATC
* *
1320438 TGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCAACTTC-AAGGCA-TATAGTTTGCAGCATA
1 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAAC-TCAAAGGCACAATA-TTTACAGCATA
* * *
1320500 ACTTAAGTCGATAAGGGTTATATGCCAACC-AAATACCGTCGAGTTCGACTACGCTCAGCTCCAA
64 ACTTAAGTCGAGAAGGGCTATATGCCAACCAAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAA
*
1320564 GGAACATCATTTGCAACATAACTTAAGTTGAGAAGGGCTATC
129 GGAACATCATTTGCAACATAACTTAAGTCGAGAAGGGCTATC
*
1320606 TGCCAACCGAAA-ACCTTTCGAGTTCGA
1 TGCCAACCAAAAGACC-TTCGAGTTCGA
1320633 TTCAATTCAG
Statistics
Matches: 174, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
168 83 0.48
169 89 0.51
170 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (170 bp):
TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCAAAGGCACAATATTTACAGCATAAC
TTAAGTCGAGAAGGGCTATATGCCAACCAAAAGACCGTCGAGTTCGACTACGCTCAGCTCCAAGG
AACATCATTTGCAACATAACTTAAGTCGAGAAGGGCTATC
Found at i:1321367 original size:71 final size:71
Alignment explanation
Indices: 1321185--1321516 Score: 477
Period size: 71 Copynumber: 4.6 Consensus size: 71
1321175 ATATACATAC
* * * *
1321185 ATATATATTATATAG-TTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATA-A-ATATAATATATAATTTTTAAAACAT
*
1321249 GTTTGAAAA
64 TTTTG-AAA
* * *
1321258 CATTTATATATTATATAGTTTTTAAAACATTTTCAAAATAAATATAATATATAGTTTTTAAAACG
1 -A--TATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACA
1321323 TTTTTGAAA
63 TTTTTGAAA
*
1321332 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACGTTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
1321397 TTGAAA
66 TTGAAA
* * * *
1321403 ATATATATTTTATATTTTTTAAAACATTTTGAAAATAAATATAATATATAAATTTTAAAATATTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
1321468 TTGAAA
66 TTGAAA
*
1321474 ATATATATTATATAGTTTTTAAAACATTTTGAAAATATATATA
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATA
1321517 GTTTTTTAAA
Statistics
Matches: 240, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
71 174 0.73
73 1 0.00
74 4 0.02
75 27 0.11
76 15 0.06
77 19 0.08
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (71 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACATTT
TTGAAA
Found at i:1321620 original size:142 final size:141
Alignment explanation
Indices: 1321185--1321620 Score: 458
Period size: 142 Copynumber: 3.0 Consensus size: 141
1321175 ATATACATAC
* * * * *
1321185 ATATATATTATATAG-TTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTGAAAACAT
1 ATATATATTATATAGTTTTTAAAACA-TTTTGAAA-ATA-ATATAATATATA-TTTTAAAAAAAA
**
1321249 GTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTCAAAATAAATATAATATATAGTT
62 AATTGAAAACA--TATATATTATATAGTTTTTAAAACATTTTCAAAATAAATATAATATATAG-T
**
1321314 TTTAAAACGTTTTTGAAA
124 TTTAAAATATTTTTGAAA
* *****
1321332 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAACGTTT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAAT-AATATAATATAT-ATTTTAAAAAAAAAA
* * * *
1321397 TTG-AAA-ATATATATTTTATATTTTTTAAAACATTTTGAAAATAAATATAATATATAAATTTTA
64 TTGAAAACATATATATTATATAGTTTTTAAAACATTTTCAAAATAAATATAATATAT-AGTTTTA
1321460 AAATATTTTTGAAA
128 AAATATTTTTGAAA
1321474 ATATATATTATATAGTTTTTAAAACATTTTGAAAAT-ATAT-ATAGT-T-TTTTAAAAAAAAAAT
1 ATATATATTATATAGTTTTTAAAACATTTTGAAAATAATATAATA-TATATTTTAAAAAAAAAAT
* ** * *
1321535 TGAAAACATATATATTATATAGTTTTGAACTCAATTTT-AAAACT-TATATAGTATATAGTTTTA
65 TGAAAACATATATATTATATAGTTTTTAAAAC-ATTTTCAAAA-TAAATATAATATATAGTTTT-
1321598 AAAATATTTTTGAAA
127 AAAATATTTTTGAAA
1321613 ACTATATA
1 A-TATATA
1321621 GTTTTGAAAA
Statistics
Matches: 253, Mismatches: 25, Indels: 29
0.82 0.08 0.09
Matches are distributed among these distances:
137 11 0.04
138 8 0.03
139 54 0.21
140 17 0.07
142 98 0.39
143 1 0.00
144 1 0.00
145 3 0.01
146 27 0.11
147 24 0.09
148 9 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (141 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAATAATATAATATATATTTTAAAAAAAAAATT
GAAAACATATATATTATATAGTTTTTAAAACATTTTCAAAATAAATATAATATATAGTTTTAAAA
TATTTTTGAAA
Found at i:1321622 original size:36 final size:35
Alignment explanation
Indices: 1321185--1321620 Score: 379
Period size: 36 Copynumber: 12.2 Consensus size: 35
1321175 ATATACATAC
* *
1321185 ATATATATTATATAG-TTTGAAAACATTTTTAAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
1321219 TATATATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 -ATATATAT--TATATAGTTTTTAAAACATTTTTG-AAA
*
1321258 CATTTATATATTATATAGTTTTTAAAACA-TTTTCAAA
1 -A--TATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
1321295 ATAAATATAATATATAGTTTTTAAAACGTTTTTGAAA
1 AT--ATATATTATATAGTTTTTAAAACATTTTTGAAA
1321332 ATATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
1321366 ATAAATATAATATATAATTTTTAAAACGTTTTTGAAA
1 AT--ATATATTATATAGTTTTTAAAACATTTTTGAAA
* *
1321403 ATATATATTTTATATTTTTTAAAACA-TTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* ** *
1321437 ATAAATATAATATATAAATTTTAAAATATTTTTGAAA
1 AT--ATATATTATATAGTTTTTAAAACATTTTTGAAA
1321474 ATATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * ***
1321508 ATATATA-TAGT-T--TTTTAAAAAAAAAATTGAAAA
1 ATATATATTA-TATAGTTTTTAAAACATTTTTG-AAA
* ** *
1321541 CATATATATTATATAGTTTTGAACTCAATTTT-AAA
1 -ATATATATTATATAGTTTTTAAAACATTTTTGAAA
* * *
1321576 ACTTATATAGTATATAGTTTTAAAAATATTTTTGAAA
1 A--TATATATTATATAGTTTTTAAAACATTTTTGAAA
1321613 ACTATATA
1 A-TATATA
1321621 GTTTTGAAAA
Statistics
Matches: 331, Mismatches: 44, Indels: 51
0.78 0.10 0.12
Matches are distributed among these distances:
31 9 0.03
32 3 0.01
33 6 0.02
34 46 0.14
35 76 0.23
36 93 0.28
37 53 0.16
38 17 0.05
39 21 0.06
41 7 0.02
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (35 bp):
ATATATATTATATAGTTTTTAAAACATTTTTGAAA
Found at i:1321639 original size:19 final size:17
Alignment explanation
Indices: 1321586--1321637 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1321576 ACTTATATAG
1321586 TATATAGTTTT-AAAA-
1 TATATAGTTTTGAAAAC
1321601 -ATAT--TTTTGAAAAC
1 TATATAGTTTTGAAAAC
1321615 TATATAGTTTTGAAAAC
1 TATATAGTTTTGAAAAC
*
1321632 AATATA
1 TATATA
1321638 TAATATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 4 0.13
13 4 0.13
14 4 0.13
15 4 0.13
17 15 0.48
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (17 bp):
TATATAGTTTTGAAAAC
Found at i:1321749 original size:9 final size:8
Alignment explanation
Indices: 1321696--1321745 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1321686 TTTTGGAAAA
1321696 TATTTTAT
1 TATTTTAT
1321704 TATTATTAT
1 TATT-TTAT
*
1321713 TATTAT-T
1 TATTTTAT
1321720 TATTTCT-T
1 TATTT-TAT
*
1321728 TTTTTTAT
1 TATTTTAT
1321736 TATTTTAT
1 TATTTTAT
1321744 TA
1 TA
1321746 ATTTCATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 6 0.17
8 21 0.60
9 8 0.23
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTAT
Found at i:1321749 original size:25 final size:26
Alignment explanation
Indices: 1321703--1321766 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
1321693 AAATATTTTA
*
1321703 TTATTATTATTATTATTTATTTC-TTT
1 TTATTATTATT-TTATTAATTTCATTT
*
1321729 TTTTTATTATTTTATTAATTTCATTT
1 TTATTATTATTTTATTAATTTCATTT
1321755 TTATT-TTATTTT
1 TTATTATTATTTT
1321767 TTCTTTCCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (26 bp):
TTATTATTATTTTATTAATTTCATTT
Found at i:1321773 original size:23 final size:23
Alignment explanation
Indices: 1321706--1321773 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
1321696 TATTTTATTA
*
1321706 TTATTATTATTATTTATTTCTTT
1 TTATTATTATTTTTTATTTCTTT
*
1321729 TTTTTATTATTTTATTAATTTCATTT
1 TTATTATTATTTT-TT-ATTTC-TTT
*
1321755 TTATT-TTATTTTTTCTTTC
1 TTATTATTATTTTTTATTTC
1321774 CAGGTCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 15 0.39
24 4 0.11
25 12 0.32
26 7 0.18
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTATTATTTTTTATTTCTTT
Found at i:1322896 original size:34 final size:34
Alignment explanation
Indices: 1322858--1322927 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1322848 GCATGTTAAA
1322858 ATTTGGCCATTGTTTTTTT-TTCTCTTTTC-TTTTG
1 ATTTGGCCATTGTTTTTTTATT-T-TTTTCGTTTTG
1322892 ATTTGGCCATTGTTTTTTTATTTTTTTCGTTTTG
1 ATTTGGCCATTGTTTTTTTATTTTTTTCGTTTTG
1322926 AT
1 AT
1322928 CCTTTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 5 0.15
34 27 0.79
35 2 0.06
ACGTcount: A:0.09, C:0.11, G:0.13, T:0.67
Consensus pattern (34 bp):
ATTTGGCCATTGTTTTTTTATTTTTTTCGTTTTG
Found at i:1323039 original size:13 final size:13
Alignment explanation
Indices: 1323023--1323052 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1323013 ACTCTTCATT
*
1323023 TTTTATTATTTTG
1 TTTTATTATTTTA
1323036 TTTTATTATTTTA
1 TTTTATTATTTTA
1323049 TTTT
1 TTTT
1323053 TATCATTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:1323387 original size:7 final size:7
Alignment explanation
Indices: 1323365--1323407 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
1323355 TCAAATCAGG
1323365 TTTTTAA
1 TTTTTAA
*
1323372 ATTTT-A
1 TTTTTAA
1323378 TTTTTAA
1 TTTTTAA
1323385 TTTTTAA
1 TTTTTAA
1323392 -TTTTAA
1 TTTTTAA
1323398 TTTTTAA
1 TTTTTAA
1323405 TTT
1 TTT
1323408 CCTTGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:1323390 original size:20 final size:20
Alignment explanation
Indices: 1323365--1323407 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
1323355 TCAAATCAGG
1323365 TTTTTAAATTTT-ATTTTTAA
1 TTTTT-AATTTTAATTTTTAA
1323385 TTTTTAATTTTAATTTTTAA
1 TTTTTAATTTTAATTTTTAA
1323405 TTT
1 TTT
1323408 CCTTGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTAATTTTAATTTTTAA
Found at i:1323404 original size:13 final size:13
Alignment explanation
Indices: 1323366--1323407 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1323356 CAAATCAGGT
* *
1323366 TTTTAAATTTTAT
1 TTTTAATTTTTAA
1323379 TTTTAATTTTTAA
1 TTTTAATTTTTAA
1323392 TTTTAATTTTTAA
1 TTTTAATTTTTAA
1323405 TTT
1 TTT
1323408 CCTTGATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:1324020 original size:29 final size:30
Alignment explanation
Indices: 1323963--1324021 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1323953 CCCCTCCCAT
* * *
1323963 AAATTTTAAAAATTCTCATTAAGCCTCTAA
1 AAATTTCAAAAATTCTAATTAAGACTCTAA
*
1323993 AAATTTCAAAAATTTTAATT-AGACTCTAA
1 AAATTTCAAAAATTCTAATTAAGACTCTAA
1324022 TTTTTTGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTTCAAAAATTCTAATTAAGACTCTAA
Found at i:1327869 original size:4 final size:4
Alignment explanation
Indices: 1327860--1327884 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1327850 ACCCCCGATC
1327860 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
1327885 CTCTCTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:1329982 original size:14 final size:14
Alignment explanation
Indices: 1329963--1329992 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1329953 TCCCTGGCAC
1329963 GAGGACGGTACGGG
1 GAGGACGGTACGGG
1329977 GAGGACGGTACGGG
1 GAGGACGGTACGGG
1329991 GA
1 GA
1329993 CGGCCGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.57, T:0.07
Consensus pattern (14 bp):
GAGGACGGTACGGG
Found at i:1330002 original size:10 final size:10
Alignment explanation
Indices: 1329987--1330012 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1329977 GAGGACGGTA
1329987 CGGGGACGGC
1 CGGGGACGGC
1329997 CGGGGACGGC
1 CGGGGACGGC
1330007 CGGGGA
1 CGGGGA
1330013 ACGTACCAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.27, G:0.62, T:0.00
Consensus pattern (10 bp):
CGGGGACGGC
Found at i:1332961 original size:12 final size:12
Alignment explanation
Indices: 1332940--1332969 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1332930 GATTCTCTAA
1332940 ATAA-TTTTAAT
1 ATAATTTTTAAT
1332951 ATAATTTTTAAT
1 ATAATTTTTAAT
1332963 ATAATTT
1 ATAATTT
1332970 ATATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATAATTTTTAAT
Found at i:1332975 original size:23 final size:24
Alignment explanation
Indices: 1332940--1333014 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 24
1332930 GATTCTCTAA
1332940 ATAATTTTAATATAATT-TTTAAT
1 ATAATTTTAATATAATTATTTAAT
* *
1332963 ATAA-TTTATATATTATTATTTAGAAA
1 ATAATTTTA-ATATAATTATTT--AAT
* *
1332989 ATAATTTTAA-AAAATAATTTAA-
1 ATAATTTTAATATAATTATTTAAT
1333011 ATAA
1 ATAA
1333015 AAATATTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
22 8 0.19
23 13 0.31
24 3 0.07
25 7 0.17
26 7 0.17
27 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
ATAATTTTAATATAATTATTTAAT
Found at i:1333158 original size:120 final size:117
Alignment explanation
Indices: 1332904--1333158 Score: 327
Period size: 120 Copynumber: 2.2 Consensus size: 117
1332894 TTAATTTAAT
* * *
1332904 TTAAA-TTATTTTTATTTTATTATTTGGATTCTCTAAATAATTTTAATATAATTTTTAATATAAT
1 TTAAACTTATTTTTATTTTATGATTTGAATTCTCTAAATAAATTTAATATAATTTTTAATATAAT
*
1332968 TTATATATTATTATTTAGAAAATAATTTTAAAAAATAATTTAAATAAAAATA
66 TTATATATTATTATTTAGAAAATAATTCTAAAAAATAATTTAAATAAAAATA
* * * * *
1333020 TTAATCTCATTTTCATTTTGTGATTTGAATTCTCTAAA-AAATTTAATATAATTTTATTTTTATA
1 TTAAACTTATTTTTATTTTATGATTTGAATTCTCTAAATAAATTTAATATAA---T-TTTTAAT-
* * *
1333084 ATATTTTATATATTATTATTT-TAAAGTAATTCTAAAAAATAATTTAAATAAAAATA
61 ATAATTTATATATTATTATTTAGAAAATAATTCTAAAAAATAATTTAAATAAAAATA
*
1333140 TTAAACTTGTTTTTATTTT
1 TTAAACTTATTTTTATTTT
1333159 TAAGTTTTAC
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
116 16 0.14
117 27 0.23
119 1 0.01
120 53 0.45
121 20 0.17
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (117 bp):
TTAAACTTATTTTTATTTTATGATTTGAATTCTCTAAATAAATTTAATATAATTTTTAATATAAT
TTATATATTATTATTTAGAAAATAATTCTAAAAAATAATTTAAATAAAAATA
Found at i:1337503 original size:24 final size:24
Alignment explanation
Indices: 1337476--1337521 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1337466 AACAGCGACA
*
1337476 GTCAATGGTCAATAGTTTGGTTCG
1 GTCAATGGTCAATAGTTCGGTTCG
*
1337500 GTCAATGGTCAATGGTTCGGTT
1 GTCAATGGTCAATAGTTCGGTT
1337522 TGGTTAGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (24 bp):
GTCAATGGTCAATAGTTCGGTTCG
Found at i:1341202 original size:34 final size:30
Alignment explanation
Indices: 1341164--1341232 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 30
1341154 TTGATATAAC
*
1341164 AATTTAAGGCAAAATGGTGTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTGTTTGGAATT-AATTG
*
1341198 AATTT-ACAAAATGTTTTTGGAATTAATTG
1 AATTTAACAAAATGTGTTTGGAATTAATTG
1341227 AATTTA
1 AATTTA
1341233 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 10 0.31
30 10 0.31
31 6 0.19
33 1 0.03
34 5 0.16
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTGTTTGGAATTAATTG
Found at i:1341228 original size:29 final size:31
Alignment explanation
Indices: 1341173--1341232 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
1341163 CAATTTAAGG
*
1341173 CAAAATGGTGTTTGGACTTGAATTGAATTTA
1 CAAAATGGTGTTTGGAATTGAATTGAATTTA
*
1341204 CAAAAT-GTTTTTGGAATT-AATTGAATTTA
1 CAAAATGGTGTTTGGAATTGAATTGAATTTA
1341233 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (31 bp):
CAAAATGGTGTTTGGAATTGAATTGAATTTA
Found at i:1343328 original size:29 final size:31
Alignment explanation
Indices: 1343272--1343330 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
1343262 ACTTTAAGGA
1343272 AAAATGGTGTTTGGACTTGAATTGAATTTAC
1 AAAATGGTGTTTGGACTTGAATTGAATTTAC
*
1343303 AAAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAAATGGTGTTTGGACTTGAATTGAATTTA
1343331 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (31 bp):
AAAATGGTGTTTGGACTTGAATTGAATTTAC
Found at i:1343437 original size:21 final size:20
Alignment explanation
Indices: 1343410--1343508 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 20
1343400 AGGGTGTTAA
1343410 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
1343431 GGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1343452 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
*
1343473 TAGTGCATCCATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
1343494 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1343509 TAAAACACCG
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 15 0.21
21 34 0.49
22 14 0.20
23 3 0.04
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:1343592 original size:21 final size:21
Alignment explanation
Indices: 1343548--1343604 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1343538 TGCATCCTTC
1343548 TGTGCATCGATGCA-CAAGGA
1 TGTGCATCGATGCATCAAGGA
* *
1343568 TGTGCATCGATGCATTAAGGT
1 TGTGCATCGATGCATCAAGGA
1343589 TGTGCATCGATGCATC
1 TGTGCATCGATGCATC
1343605 CTGTTGTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
TGTGCATCGATGCATCAAGGA
Found at i:1343612 original size:20 final size:20
Alignment explanation
Indices: 1343529--1343622 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
1343519 AATGCAATTA
**
1343529 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAGGT-T
*
1343549 GTGCATCGATGCA-CAAGGAT
1 GTGCATCGATGCATC-AGGTT
*
1343569 GTGCATCGATGCATTAAGGTT
1 GTGCATCGATGCA-TCAGGTT
**
1343590 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCAGGTT
*
1343610 GTGCATCCATGCA
1 GTGCATCGATGCA
1343623 CGAAGGCTGC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.02
20 43 0.70
21 17 0.28
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGTT
Found at i:1345033 original size:39 final size:39
Alignment explanation
Indices: 1344979--1345056 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1344969 TTTTGAATTA
1344979 GATGAGTTTGAGGATACCTTTGAATCTTCTTGGATGGCC
1 GATGAGTTTGAGGATACCTTTGAATCTTCTTGGATGGCC
1345018 GATGAGTTTGAGGATACCTTTGAATCTTCTTGGATGGCC
1 GATGAGTTTGAGGATACCTTTGAATCTTCTTGGATGGCC
1345057 ATAAGGCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (39 bp):
GATGAGTTTGAGGATACCTTTGAATCTTCTTGGATGGCC
Found at i:1347903 original size:72 final size:70
Alignment explanation
Indices: 1347764--1347911 Score: 208
Period size: 72 Copynumber: 2.1 Consensus size: 70
1347754 TTACTTGGTC
* * * *
1347764 TAAACTGATGCGAAATAGAGCTTTCATCGACTCCAATGTATCATCATAAATCCATATAGGACATC
1 TAAACTAATGCGAAATAAAGCCTTCATCAACTCCAATGTATCATCATAAATCCATATAGGACATC
1347829 CTCGTA
66 CTC-TA
* *
1347835 TGAACTAATGCGAGAATAAAGCCTTCATCAACTCCAATGTCTCATCATAAATCTC-TATAGGACA
1 TAAACTAATGCGA-AATAAAGCCTTCATCAACTCCAATGTATCATCATAAATC-CATATAGGACA
1347899 TCCTCTA
64 TCCTCTA
1347906 TAAACT
1 TAAACT
1347912 CAGTCCAACT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
71 18 0.26
72 49 0.72
73 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (70 bp):
TAAACTAATGCGAAATAAAGCCTTCATCAACTCCAATGTATCATCATAAATCCATATAGGACATC
CTCTA
Found at i:1353399 original size:18 final size:17
Alignment explanation
Indices: 1353376--1353417 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
1353366 TATTTAATAT
1353376 TAAATAATAAATTATTAA
1 TAAATAATAAATT-TTAA
1353394 TAAAT-ATAAATTTTAA
1 TAAATAATAAATTTTAA
1353410 T-AATAATA
1 TAAATAATA
1353418 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 8 0.35
17 7 0.30
18 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATAATAAATTTTAA
Found at i:1353430 original size:17 final size:17
Alignment explanation
Indices: 1353374--1353432 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
1353364 TTTATTTAAT
1353374 ATTAAATAATAAATTATTA
1 ATTAAATAAT-AA-TATTA
1353393 A-TAAAT-ATAA-ATT-
1 ATTAAATAATAATATTA
1353406 -TT-AATAATAATATTA
1 ATTAAATAATAATATTA
1353421 ATTAAATAATAA
1 ATTAAATAATAA
1353433 ACCAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 6 0.18
16 4 0.12
17 10 0.29
18 5 0.15
19 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATAATAATATTA
Found at i:1357852 original size:14 final size:14
Alignment explanation
Indices: 1357833--1357868 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1357823 TGAAAACGAA
1357833 AAATTAAAATAATG
1 AAATTAAAATAATG
* *
1357847 AAATTAAAGTACTG
1 AAATTAAAATAATG
1357861 AAATTAAA
1 AAATTAAA
1357869 TAAATAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (14 bp):
AAATTAAAATAATG
Found at i:1357926 original size:29 final size:31
Alignment explanation
Indices: 1357885--1357944 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 31
1357875 AAAGTAAAGG
* * *
1357885 ACAAAAATTTAAATGTGC-ATAAAATTAAATA
1 ACAAAAA-TTAAAAGAGCAATAAAATAAAATA
1357916 ACAAAAA-TAAAAGAGCAATAAAATAAAAT
1 ACAAAAATTAAAAGAGCAATAAAATAAAAT
1357945 GTTAGCGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 7 0.28
30 11 0.44
31 7 0.28
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (31 bp):
ACAAAAATTAAAAGAGCAATAAAATAAAATA
Found at i:1359718 original size:163 final size:163
Alignment explanation
Indices: 1359506--1359913 Score: 563
Period size: 163 Copynumber: 2.5 Consensus size: 163
1359496 TATGAAGTCA
* * *
1359506 TTCTCACTCTTCAGACGAGTTCTTCTCATTATGAATCATTCCATTGGAAATGATGATCCACCTCA
1 TTCTCACTCTTTAGATGAGTTCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACCTCA
* *
1359571 TTCTGTGATGGATTCGATCAAAATGATGATGCTGGTATATCTCCTTCAGCGATAGAGT-TGAGCA
66 TTCTGTGATGGATTCGATCAAAATGATGATGCTGATATATCTCCTTCAGCGATAGAATCT-AGCA
* *
1359635 AAAGGGTGAGCAAGTTCTTCTCATTATGAACTTC
130 AAAGAGTGAACAAGTTCTTCTCATTATGAACTTC
* *
1359669 TTCTCACTCTTTAGATGAGTTCTTCTCATTATGAACCATTCAATTGGAAATGAAGATCCACCTCA
1 TTCTCACTCTTTAGATGAGTTCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACCTCA
* * * * *
1359734 TTCTATGATGGATTCGATCAAAATGTTGATGTTGATTTATCTCCTTCTGCGATAGAATCTAGCAA
66 TTCTGTGATGGATTCGATCAAAATGATGATGCTGATATATCTCCTTCAGCGATAGAATCTAGCAA
1359799 AAGAGTGAACAAGTTCTTCTCATTATGAACTTC
131 AAGAGTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1359832 TTCT--CTTTTTATGGATGAGTTCTTCTCATTATGAACTC-TTCCATTGCAAATGTTGAGCCACC
1 TTCTCACTCTTTA--GATGAGTTCTTCTCATTATGAAC-CATTCCATTGGAAATGATGATCCACC
* * *
1359894 TCCTACTGTGATGGAATCGA
63 TCATTCTGTGATGGATTCGA
1359914 GAAAAATGGT
Statistics
Matches: 217, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
161 6 0.03
163 209 0.96
164 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (163 bp):
TTCTCACTCTTTAGATGAGTTCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACCTCA
TTCTGTGATGGATTCGATCAAAATGATGATGCTGATATATCTCCTTCAGCGATAGAATCTAGCAA
AAGAGTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:1360125 original size:117 final size:116
Alignment explanation
Indices: 1359794--1360148 Score: 471
Period size: 118 Copynumber: 3.0 Consensus size: 116
1359784 GATAGAATCT
* * *
1359794 AGCAAAAGAGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTTTTATGGATGAGTTCTTCTC
1 AGCAAAAGA-TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTCA--GACGAGTTCTTCTC
* * * * *
1359859 ATTATGAACTCTTCCATTGCAAATGTTGAGCCACCTCCTACTGTGATGGAATCG
63 ATTATGAACTCTTCCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTTG
* * * *
1359913 AGAAAAATGGTGAACAAGTTCTTCTCATTATGAACTT-TTTTCCTTTTTCGGACGAGTTCTTCTC
1 AGCAAAA-GATGAACAAGTTCTTCTCATTATGAACTTCTTCTCC--TTTCAGACGAGTTCTTCTC
* *
1359977 ATTATGAACTCTTCCATTGGAAATATTGATCCACCTCATTCTGTGATGGATTTG
63 ATTATGAACTCTTCCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTTG
*
1360031 AGCAAAAGATCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCAGACGAGTTCTTCTCAT
1 AGCAAAAGAT-GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTCAGACGAGTTCTTCTCAT
* *
1360096 TATGAAC-CATTCCATTGGAAATGTTGATCCACCTCCTTATATGATGGATTTG
65 TATGAACTC-TTCCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTTG
1360148 A
1 A
1360149 ATTTTTTTTT
Statistics
Matches: 207, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
116 1 0.00
117 68 0.33
118 96 0.46
119 38 0.18
120 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (116 bp):
AGCAAAAGATGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTCAGACGAGTTCTTCTCATT
ATGAACTCTTCCATTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTTG
Found at i:1360575 original size:101 final size:101
Alignment explanation
Indices: 1360350--1360611 Score: 373
Period size: 101 Copynumber: 2.6 Consensus size: 101
1360340 CTCGAGCGAA
* * *
1360350 AAACTGTCTCAAGTGAGACGAAGTTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTTT
1 AAACTGTCTCAAGTGAGACGAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAA-TCTTGT
** * *
1360415 TTCTGGTGAAACAATTTCAAAATTTGTACTTCAAGGG
65 TTCAAGTGAAACAATTCCAAAACTTGTACTTCAAGGG
* * *
1360452 AAACGGTCTCAAGTGAGACGAAATTGATTTTAAGAAAAAGAATCTCCAGTGAGATAAATCTTGTT
1 AAACTGTCTCAAGTGAGACGAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTGTT
*
1360517 TCAAGT-AAAGCAATTCCAAAACTTGTGCTTCAAGGG
66 TCAAGTGAAA-CAATTCCAAAACTTGTACTTCAAGGG
* * *
1360553 AAACTGTCTCAAGTGAGACGAAATTGCTTTTAATAAAAACAATCTCAAGTGATATAAAT
1 AAACTGTCTCAAGTGAGACGAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAAT
1360612 TTATTCGTAT
Statistics
Matches: 142, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
100 3 0.02
101 85 0.60
102 54 0.38
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (101 bp):
AAACTGTCTCAAGTGAGACGAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTGTT
TCAAGTGAAACAATTCCAAAACTTGTACTTCAAGGG
Found at i:1368627 original size:16 final size:18
Alignment explanation
Indices: 1368592--1368629 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1368582 AATCCCCTCT
1368592 ATAAAAACCACGTGTCAA
1 ATAAAAACCACGTGTCAA
*
1368610 ATAAATACCAC-T-TCAA
1 ATAAAAACCACGTGTCAA
1368626 ATAA
1 ATAA
1368630 CCAAAACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (18 bp):
ATAAAAACCACGTGTCAA
Found at i:1377272 original size:18 final size:17
Alignment explanation
Indices: 1377249--1377291 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1377239 ATATATACGT
1377249 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1377267 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1377284 ATAA-AATA
1 ATAATAATA
1377292 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1377703 original size:35 final size:35
Alignment explanation
Indices: 1377664--1377735 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1377654 ACTAAAAACC
1377664 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1377699 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1377734 CT
1 CT
1377736 TCTTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:1378411 original size:106 final size:106
Alignment explanation
Indices: 1378219--1378975 Score: 902
Period size: 106 Copynumber: 7.4 Consensus size: 106
1378209 TGTATTGTTC
* ** * * * *
1378219 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
1378284 GCCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * *
1378325 TAAGTCTAATATCATTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
1378390 ACCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
1378431 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTATTTGTTAACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
1378496 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATG--GTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
1378535 CGAGCCCAATATCCTTCGATGTGAAGTTAAAATTGACCCTGAAATTTGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
1378600 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1378641 CGAGTCCAATATCCTTC--------GCT---ATTGACTCTGAAATTGGGAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
** * *
1378695 ACCAGCCGTCCCTTTATTGTGAAGTTAAACTTGTATTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
1378736 TGAGTCCAATATCCTTC-ACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGAC
1378800 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1378842 CGTGTCCAACATCCTTCGATGTGAAGTTG-AA---A-T-T---A---GGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
*
1378895 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1378936 TGAGTCCAATATCCTT-TACTGTGAAGTTGAAATTGACTCT
1 CGAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGACTCT
1378976 AGCTAAAATC
Statistics
Matches: 566, Mismatches: 64, Indels: 48
0.83 0.09 0.07
Matches are distributed among these distances:
93 1 0.00
94 81 0.14
95 84 0.15
97 1 0.00
98 3 0.01
99 1 0.00
100 2 0.00
101 1 0.00
102 1 0.00
103 2 0.00
104 97 0.17
105 2 0.00
106 289 0.51
107 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1378789 original size:305 final size:294
Alignment explanation
Indices: 1378356--1378951 Score: 843
Period size: 305 Copynumber: 2.0 Consensus size: 294
1378346 TGAAGTTGAA
* *
1378356 ATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAACCATCCCTTCGTTGTGAAGTTGAACT
1 ATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAACCATCCCTTCATTGTGAAGTTAAACT
* * * *
1378421 TGTGTCGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTA
66 TGTATCGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTA
*
1378486 TTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATG-GTCTCGAGCCCAATATCCT
131 TTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTGTCTCGAGCCCAACATCCT
*
1378550 TCGATGTGAAGTTAAAATTGACCCTGAAATTTGGAAATTATTTGTTGACAACCAGCCGTCCCTTC
196 TCGATGTGAAG-------T-----TGAAATTAGGAAATTATTTGTTGACAACCAGCCGTCCCTTC
*
1378615 GTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAATATCCTTCGCT
249 GTTGTGAAGTTGAACTTGTGTCATCTCGAGTCCAATATCCTTCGCT
* * * * * *
1378661 ATTGACTCTGAAATTGGGAGATTGTTTGTTGACAACCAGCCGTCCCTTTATTGTGAAGTTAAACT
1 ATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAACCATCCCTTCATTGTGAAGTTAAACT
* * *
1378726 TGTATTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTG
66 TGTATCGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTA
* * * *
1378791 TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGTGTCCAACATCC
131 TTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATG-TGTCTCGAGCCCAACATCC
*
1378856 TTCGATGTGAAGTTGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
195 TTCGATGTGAAGTTGAAATTAGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
* *
1378921 GAACTTGTGTTATCTTGAGTCCAATATCCTT
260 GAACTTGTGTCATCTCGAGTCCAATATCCTT
1378952 TACTGTGAAG
Statistics
Matches: 264, Mismatches: 25, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
295 78 0.30
300 1 0.00
305 158 0.60
307 27 0.10
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (294 bp):
ATTGACCCTGAAATTGGGAAATTATTTGTTGACAACCAACCATCCCTTCATTGTGAAGTTAAACT
TGTATCGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTA
TTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTGTCTCGAGCCCAACATCCT
TCGATGTGAAGTTGAAATTAGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
AACTTGTGTCATCTCGAGTCCAATATCCTTCGCT
Found at i:1378813 original size:201 final size:199
Alignment explanation
Indices: 1378462--1378975 Score: 748
Period size: 201 Copynumber: 2.6 Consensus size: 199
1378452 TGAAGTTGAA
* * * *
1378462 ATTGGCTCTGAAATTTGGAAATTATTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC-
1 ATTGACTCTGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACT
* * * * * *
1378526 T-TATGGTCTCGAGCCCAATATCCTTCGA-TGTGAAGTTAAAATTGACCCTGAAATTTGGAAATT
66 TGTATTGTCTTGAGTCCAATATCCTTC-ACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATT
*
1378589 ATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAATATC
130 ATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAACATC
1378654 CTTCG
195 CTTCG
* * ** *
1378659 CTATTGACTCTGAAATTGGGAGATTGTTTGTTGACAACCAGCCGTCCCTTTATTGTGAAGTTAAA
1 --ATTGACTCTGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
1378724 CTTGTATTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAAT
64 CTTGTATTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAAT
* * *
1378789 TGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGTGTCCAACAT
129 TATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAACAT
1378854 CCTTCG
194 CCTTCG
*
1378860 ATGTGAAGT-TGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
1 AT-TG-ACTCTGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
* * *
1378924 CTTGTGTTATCTTGAGTCCAATATCCTTTACTGTGAAGTTGAAATTGACTCT
64 CTTGTATTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCT
1378976 AGCTAAAATC
Statistics
Matches: 283, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
199 58 0.20
200 103 0.36
201 122 0.43
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (199 bp):
ATTGACTCTGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACT
TGTATTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTA
TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAACATCC
TTCG
Found at i:1378943 original size:94 final size:95
Alignment explanation
Indices: 1378574--1378969 Score: 478
Period size: 94 Copynumber: 4.1 Consensus size: 95
1378564 AAATTGACCC
* * *
1378574 TGAAATTTGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGT
1 TGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
* *
1378639 CTCGAGTCCAATATCCTTCG-CTATTG-ACT
66 CTCGAGTCCAATATCCTTCGACT-GTGAAGT
* * ** * *
1378668 CTGAAATTGGGAGATTGTTTGTTGACAACCAGCCGTCCCTTTATTGTGAAGTTAAACTTGTATTG
1 -TGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
*
1378733 TCTTGAGTCCAATATCCTTC-ACTGTGAAGT
65 TCTCGAGTCCAATATCCTTCGACTGTGAAGT
1378763 TGAAATTGACTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
1 TG-AA---A-T-T---A---GGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
* *
1378828 AACTTGTGTTGTCTCGTGTCCAACATCCTTCGA-TGTGAAGT
54 AACTTGTGTTGTCTCGAGTCCAATATCCTTCGACTGTGAAGT
*
1378869 TGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTAT
1 TGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
* *
1378934 CTTGAGTCCAATATCCTT-TACTGTGAAGT
66 CTCGAGTCCAATATCCTTCGACTGTGAAGT
1378963 TGAAATT
1 TGAAATT
1378970 GACTCTAGCT
Statistics
Matches: 260, Mismatches: 25, Indels: 33
0.82 0.08 0.10
Matches are distributed among these distances:
93 1 0.00
94 90 0.35
95 81 0.31
97 1 0.00
98 1 0.00
99 1 0.00
100 2 0.01
101 1 0.00
102 1 0.00
105 2 0.01
106 78 0.30
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (95 bp):
TGAAATTAGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
CTCGAGTCCAATATCCTTCGACTGTGAAGT
Found at i:1387629 original size:38 final size:40
Alignment explanation
Indices: 1387561--1387639 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
1387551 AATGAAAAAA
*
1387561 ATATATATATACATCAAATTATTAATAAAATA-AATAAGCT
1 ATATATATATACAACAAATTATTAATAAAATAGAA-AAGCT
*
1387601 ATATATATATACAACAAA-TATTTA-AAAATAGAAAAGCT
1 ATATATATATACAACAAATTATTAATAAAATAGAAAAGCT
1387639 A
1 A
1387640 CCCTCTCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.32
Consensus pattern (40 bp):
ATATATATATACAACAAATTATTAATAAAATAGAAAAGCT
Found at i:1388079 original size:49 final size:52
Alignment explanation
Indices: 1388000--1388116 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 52
1387990 GATAATTACA
** * *
1388000 ATATATATA-ATA-ATAATAGACTTATAAGTAAAATATTAAA-GAAACAT-AT
1 ATATATATATATATATAATAGAAATATAAGTAAAAAATCAAATGAAA-ATAAT
1388049 ATATATATATATATATAATA-AAATAT-AGTAAAAAATCAAATGAAAATAAT
1 ATATATATATATATATAATAGAAATATAAGTAAAAAATCAAATGAAAATAAT
*
1388099 TTAATATATATATATATA
1 AT-ATATATATATATATA
1388117 TATATACACG
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
49 23 0.40
50 14 0.24
51 21 0.36
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (52 bp):
ATATATATATATATATAATAGAAATATAAGTAAAAAATCAAATGAAAATAAT
Found at i:1388149 original size:18 final size:17
Alignment explanation
Indices: 1388128--1388170 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1388118 ATATACACGT
1388128 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
1388146 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
1388163 ATAA-AATA
1 ATAATAATA
1388171 TTCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:1388156 original size:61 final size:56
Alignment explanation
Indices: 1388045--1388158 Score: 131
Period size: 57 Copynumber: 1.9 Consensus size: 56
1388035 TTAAAGAAAC
* *
1388045 ATATATATATATATATATATAATAAAATATAGTAAAAAATCAAATGAAAATAATTTA
1 ATATATATATATATATATATAATAAAATATAATAAAAAAT-AAATAAAAATAATTTA
*
1388102 ATATATATATATATATATATACACGTATAATAATAATAACATAAAT-AATAAAAATAA
1 ATATATATATATATATATATA-A--TAAAAT-ATAATAA-A-AAATAAATAAAAATAA
1388159 ATGAATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
57 21 0.44
58 1 0.02
60 5 0.10
61 16 0.33
62 1 0.02
63 4 0.08
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (56 bp):
ATATATATATATATATATATAATAAAATATAATAAAAAATAAATAAAAATAATTTA
Found at i:1388167 original size:14 final size:13
Alignment explanation
Indices: 1388130--1388168 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1388120 ATACACGTAT
1388130 AATAATAATAACATA
1 AATAATAA-AA-ATA
1388145 AATAATAAAAATA
1 AATAATAAAAATA
1388158 AATGAATAAAA
1 AAT-AATAAAA
1388169 TATTCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:1388597 original size:34 final size:35
Alignment explanation
Indices: 1388545--1388615 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 35
1388535 CTAAAAAACC
*
1388545 CTATTTTAGACTAGTATTTAAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
*
1388580 CTATTTTA-ACTAGTATTTGAGTCATAATCCAACT
1 CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
1388614 CT
1 CT
1388616 TCTTTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 26 0.76
35 8 0.24
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTAAGTCATAATCCAACT
Found at i:1397612 original size:2 final size:2
Alignment explanation
Indices: 1397605--1397637 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1397595 ACGAAAAGGA
1397605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1397638 ATGATACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1399092 original size:73 final size:71
Alignment explanation
Indices: 1398942--1399440 Score: 496
Period size: 73 Copynumber: 6.8 Consensus size: 71
1398932 TTTTTTTAAA
* * * **
1398942 AAAAACCATATA-ATATATAGTTTTAAAAAATTATTTTTTAAAAACTATATAT-TATACGTATTT
1 AAAAACTATATATATATATA-TTTT-CAAAA--ATGTTTTAAAAACTATATATATATAAAT-TTT
*
1399005 CAAAAACGTTTT
61 C-AAAATGTTTT
1399017 AAAAACTATATA-ATATATATTTTCAAAAATG-TTTAAAAACTATATTATATATAAATGTTTTCA
1 AAAAACTATATATATATATATTTTCAAAAATGTTTTAAAAACTATA-TATATATAAA--TTTTCA
1399080 AAATGATTTT
63 AAATG-TTTT
* * *
1399090 AAAAATTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATAT-TATATAGTTTTCAA
1 AAAAACTATATA-TATATATATTTTCAAAAATGTTTTAAAAACTATATATATATA-AATTTTCAA
1399154 AAGTGTTTT
64 AA-TGTTTT
* * *
1399163 AAAAACTATATATTATATACATTTTC-AAAATGTTTTCAAAATTATATATGATATAAATTTTCAA
1 AAAAACTATATA-TATATATATTTTCAAAAATGTTTTAAAAACTATATAT-ATATAAATTTTC-A
1399227 AAATGTTTT
63 AAATGTTTT
* * *
1399236 CAAAACTATATAT-TATAAACGTTTTC-AAAATGATTTTAAAAACTATATATTATATATATTTTC
1 AAAAACTATATATATATATA--TTTTCAAAAATG-TTTTAAAAACTATATA-TATATAAATTTTC
1399299 TAAAATGTTTT
62 -AAAATGTTTT
* *
1399310 AAAAACTATATAT-TATATAGTTTTCAAAAGTGTTTTAAAAACTATATATTATATACATTTTCAA
1 AAAAACTATATATATATATA-TTTTCAAAAATGTTTTAAAAACTATATA-TATATAAATTTTCAA
1399374 AATGTTTTT
64 AATG-TTTT
**
1399383 AAAAACTATATATTATATACATATTTTCAAAAATCG-TTTGCAAACTATATAATATATA
1 AAAAACTATATA-TATAT--ATATTTTCAAAAAT-GTTTTAAAAACTATAT-ATATATA
1399441 TATATAGATA
Statistics
Matches: 372, Mismatches: 27, Indels: 49
0.83 0.06 0.11
Matches are distributed among these distances:
70 13 0.03
71 10 0.03
72 37 0.10
73 145 0.39
74 77 0.21
75 44 0.12
76 41 0.11
77 5 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (71 bp):
AAAAACTATATATATATATATTTTCAAAAATGTTTTAAAAACTATATATATATAAATTTTCAAAA
TGTTTT
Found at i:1399115 original size:37 final size:36
Alignment explanation
Indices: 1398977--1399443 Score: 552
Period size: 37 Copynumber: 12.7 Consensus size: 36
1398967 AAAAATTATT
** *
1398977 TTTTAAAAACTATATATTATACGTA-TTTCAAAAACG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAATG
1399013 TTTTAAAAACTATATA--ATATATATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAATG
* *
1399048 -TTTAAAAACTATATTATATATAAATGTTTTCAAAATG
1 TTTTAAAAACTATA-TAT-TATATATATTTTCAAAATG
*
1399085 ATTTTAAAAATTATATATTATATATATTTTCTAAAATG
1 -TTTTAAAAACTATATATTATATATATTTTC-AAAATG
*
1399123 TTTTAAAAACTATATATTATATA-GTTTTCAAAAGTG
1 TTTTAAAAACTATATATTATATATATTTTCAAAA-TG
*
1399159 TTTTAAAAACTATATATTATATACATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
* * * *
1399195 TTTTCAAAATTATATATGATATAAATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAATG
* * **
1399232 TTTTCAAAACTATATATTATAAACGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
1399268 ATTTTAAAAACTATATATTATATATATTTTCTAAAATG
1 -TTTTAAAAACTATATATTATATATATTTTC-AAAATG
*
1399306 TTTTAAAAACTATATATTATATA-GTTTTCAAAAGTG
1 TTTTAAAAACTATATATTATATATATTTTCAAAA-TG
*
1399342 TTTTAAAAACTATATATTATATACATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
1399378 TTTTTAAAAACTATATATTATATACATATTTTCAAAAATCG
1 -TTTTAAAAACTATATATTATAT--ATATTTTC-AAAAT-G
** *
1399419 -TTTGCAAACTATATAATATATATAT
1 TTTTAAAAACTATATATTATATATAT
1399444 ATAGATATAT
Statistics
Matches: 381, Mismatches: 30, Indels: 39
0.85 0.07 0.09
Matches are distributed among these distances:
34 18 0.05
35 20 0.05
36 112 0.29
37 163 0.43
38 25 0.07
39 37 0.10
40 5 0.01
41 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATG
Found at i:1399190 original size:110 final size:110
Alignment explanation
Indices: 1398977--1399443 Score: 576
Period size: 110 Copynumber: 4.2 Consensus size: 110
1398967 AAAAATTATT
** * *
1398977 TTTTAAAAACTATATATTATACGTA-TTTCAAAAACGTTTTAAAAACTATATAATATATA--TTT
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATACGTTT
*
1399039 TCAAAA--ATGTTTAAAAACTATAT-TATATATAAATGTTTTCAAAATG
66 TCAAAATGAT-TTTAAAAACTATATAT-TATATACA--TTTTCAAAATG
* *
1399085 ATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATATTATATA-GTT
1 -TTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATACGTT
1399149 TTCAAAAGTG-TTTTAAAAACTATATATTATATACATTTTCAAAATG
65 TTCAAAA-TGATTTTAAAAACTATATATTATATACATTTTCAAAATG
* * * * * *
1399195 TTTTCAAAATTATATATGATATAAATTTTCAAAAATGTTTTCAAAACTATATATTATAAACGTTT
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATACGTTT
*
1399260 TCAAAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATG
66 TCAAAATGATTTTAAAAACTATATATTATATACATTTTC-AAAATG
* * *
1399306 TTTTAAAAACTATATATTATATA-GTTTTCAAAAGTGTTTTAAAAACTATATATTATATACATTT
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATACGTTT
*
1399370 TCAAAATGTTTTTAAAAACTATATATTATATACATATTTTCAAAAATCG
66 TCAAAATGATTTTAAAAACTATATATTATATAC--ATTTTC-AAAAT-G
** *
1399419 -TTTGCAAACTATATAATATATATAT
1 TTTTAAAAACTATATATTATATATAT
1399444 ATAGATATAT
Statistics
Matches: 316, Mismatches: 29, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
109 78 0.25
110 148 0.47
111 35 0.11
112 51 0.16
113 4 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (110 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATACGTTT
TCAAAATGATTTTAAAAACTATATATTATATACATTTTCAAAATG
Found at i:1400142 original size:84 final size:81
Alignment explanation
Indices: 1400020--1400698 Score: 561
Period size: 84 Copynumber: 8.2 Consensus size: 81
1400010 ATTTTTTTGA
* * * * *
1400020 CAGATAACCCTTCT-TCCTTGAGCTATGCTGTAAATGATGTGCGTTTGAGCTGAGTATAATCGAA
1 CAGATAACCCTTCTAGCCTTGAACTATGCTGCAAATGATGTGC-TTGGAGCTGAGTGTAATCGAA
*
1400084 CTCGCAGGTCTTTTGTTAG
65 CTCGAAGGTC-TTTGTT-G
* * * * *
1400103 CATATAACCCTTCTAGCCTTGAATTATACTGCAAATGATGTGCATTTGAGCTGAATGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAACTATGCTGCAAATGATGTGC-TTGGAGCTGAGTGTAATCGAA
*
1400168 CTCGAAGGTCTTTGATG
65 CTCGAAGGTCTTTGTTG
* * * * * * *
1400185 AAAGATAGCCCTTCTCGACTT-AAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
1 -CAGATAACCCTTCTAGCCTTGAA-CTATGCTGCAAATGATGTG-CTTGGAGCTGAGTGTAATCG
*
1400249 AACTCGAAAGTCTTTTGTTGG
63 AACTCGAAGGTC-TTTGTT-G
* * ** * * * * * * *
1400270 CAAATAACCCTTATAGCCTTGAGTTATGCAGTAAATTATGTGTCTTGGAGTTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAACTATGCTGCAAATGATGTG-CTTGGAGCTGAGTGTAATCGAA
*
1400335 CTCGAAGGTCTTTGGCTAG
65 CTCGAAGGTCTTT-G-TTG
* * * * * *
1400354 TAGATAACCCTTCTCGACTT-AAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGCCTTGAA-CTATGCTGCAAATGATGTG-CTTGGAGCTGAGTGTAATCGA
1400418 ACTCGAAGGTCTTTGTTG
64 ACTCGAAGGTCTTTGTTG
* * ** * * * *
1400436 ACAGGTAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGTTGAGTATAGTCGA
1 -CAGATAACCCTTCTAGCCTTGAACTATGCTGCAAATGATGTG-CTTGGAGCTGAGTGTAATCGA
*
1400501 ACTCGAATGTC-TT-TT-
64 ACTCGAAGGTCTTTGTTG
** * * * *
1400516 --G-T-ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAACTATGCTGCAAATGATGTG-CTTGGAGCTGAGTGTAATCGAA
1400577 CTCGAAGGTCTTTGGTTGG
65 CTCGAAGGTCTTT-GTT-G
* * * **
1400596 CAGATAGCCCTTCTAGACTT-AAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATAAA
1 CAGATAACCCTTCTAGCCTTGAA-CTATGCTGCAAATGATGTG-CTTGGAGCTGAGTGTAATCGA
1400660 ACTCGAAGGTCTTTGTTG
64 ACTCGAAGGTCTTTGTTG
1400678 ACAGATAACCCTTCTAGCCTT
1 -CAGATAACCCTTCTAGCCTT
1400699 CAGTTATGCT
Statistics
Matches: 477, Mismatches: 96, Indels: 46
0.77 0.16 0.07
Matches are distributed among these distances:
75 63 0.13
76 3 0.01
77 1 0.00
78 2 0.00
81 2 0.00
82 9 0.02
83 160 0.34
84 234 0.49
85 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (81 bp):
CAGATAACCCTTCTAGCCTTGAACTATGCTGCAAATGATGTGCTTGGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTTGTTG
Found at i:1400252 original size:167 final size:164
Alignment explanation
Indices: 1400021--1400692 Score: 662
Period size: 167 Copynumber: 4.1 Consensus size: 164
1400011 TTTTTTTGAC
* * * * **
1400021 AGATAACCCTTCTTC--CTTGAGCTATGCTGTAAATGATGTGCGTTTGAGCTGAGTATAATCGAA
1 AGATAACCCTTC-TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
* * * *
1400084 CTCGCAGGTCTTTTGTTAGCATATAACCCTTCTAGCCTTGAATTATACTGCAAATGATGTG-CAT
65 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAATTATGCTGCAAATGATGTGTC-T
* *
1400148 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGAA
129 TGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-T--A
* * *
1400187 AGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAAC
* * * * * * *
1400252 TCGAAAGTCTTTTGTTGGCAAATAACCCTTATAGCCTTGAGTTATGCAGTAAATTATGTGTCTTG
66 TCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAATTATGCTGCAAATGATGTGTCTTG
* * * *
1400317 GAGTTGAGCGTAGTTGAACTCGAAGGTCTTTGGCTA
131 GAGCTGAGTGTAATCGAACTCGAAGGTCTTT-G-TA
* * * *
1400353 GTAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
1 --AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGA
* * * * *
1400418 ACTCGAAGGTC-TTTGTTGACAGGTAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCT
64 ACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAATTATGCTGCAAATGATGTGTCT
* * * *
1400482 TGGAGTTGAGTATAGTCGAACTCGAATGTCTTT-T-
129 TGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTA
* * * * * * * *
1400516 -G-T-ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGAAC
1 AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAAC
* * * * *
1400578 TCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTT-AAGCTATGCTGCAAATGATGTGCCTT
66 TCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAA-TTATGCTGCAAATGATGTGTCTT
* **
1400642 TGAGCTGAGTGTAATAAAACTCGAAGGTCTTTGTTGA
130 GGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-T-A
1400679 CAGATAACCCTTCT
1 -AGATAACCCTTCT
1400693 AGCCTTCAGT
Statistics
Matches: 416, Mismatches: 74, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
158 58 0.14
159 68 0.16
160 1 0.00
161 1 0.00
164 1 0.00
165 3 0.01
166 13 0.03
167 202 0.49
168 69 0.17
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (164 bp):
AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAAC
TCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAATTATGCTGCAAATGATGTGTCTTG
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTA
Found at i:1400578 original size:75 final size:75
Alignment explanation
Indices: 1400446--1400589 Score: 243
Period size: 75 Copynumber: 1.9 Consensus size: 75
1400436 ACAGGTAACT
* * *
1400446 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGTTGAGTATAGTCGAACTCGAATGT
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGT
1400511 CTTTTGTACC
66 CTTTTGTACC
* *
1400521 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGAACTCGAAGGT
1 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGT
1400586 CTTT
66 CTTT
1400590 GGTTGGCAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (75 bp):
CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGT
CTTTTGTACC
Found at i:1400638 original size:242 final size:247
Alignment explanation
Indices: 1400022--1400714 Score: 889
Period size: 251 Copynumber: 2.8 Consensus size: 247
1400012 TTTTTTGACA
* * * ** * *
1400022 GATAACCCTTCT-TCCTTGAGCTATGCTGTAAATGATGTG-CGTTTGAGCTGAGTATAATCGAAC
1 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTC-TTGGAGCTGAGCGTAGTTGAAC
* * * * * *
1400085 TCGCAGGTCTTTTGTTAGCATATAACCCTTCTAGCCTTGAA-TTATACTGCAAATGATGTGCATT
65 TCGAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTT-AAGCTATACTGCAAATGATGTGCCTT
* * * * * * * *
1400149 TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGATGAAAGATAGCCCTTCTCGACTTAAGCTATG
129 TGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATG
* *
1400214 CTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTGTTG
194 CTATAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAAGTC-TTTGTTG
* * * *
1400269 GCAAATAACCCTTATAGCCTTGAGTTATGCAGTAAATTATGTGTCTTGGAGTTGAGCGTAGTTGA
1 G---ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGA
* * *
1400334 ACTCGAAGGTCTTTGGCTAGTAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCT
63 ACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCT
* * *
1400399 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGGTAACTCTTCTAGCCTTGAGTTAT
128 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTAT
* * * * *
1400464 GCTGTAAATGATGTGTCTTGGAGTTGAGTATAGTCGAACTCGAATGTC-TT-TT-
193 GCTATAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAAGTCTTTGTTG
1400516 G-T-ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGAACT
1 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGAACT
* * *
1400579 CGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTTG
66 CGAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTTG
* *
1400644 AGCTGAGTGTAATAAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTCAGTTATGCT
131 AGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATGCT
1400709 ATAAAT
196 ATAAAT
1400715 AGGCTAGGGA
Statistics
Matches: 387, Mismatches: 53, Indels: 17
0.85 0.12 0.04
Matches are distributed among these distances:
242 182 0.47
243 1 0.00
247 2 0.01
248 2 0.01
249 2 0.01
250 12 0.03
251 185 0.48
252 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (247 bp):
GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTTGAACT
CGAAGGTCTTTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTTG
AGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATGCT
ATAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAAGTCTTTGTTG
Found at i:1401076 original size:123 final size:122
Alignment explanation
Indices: 1400859--1401132 Score: 446
Period size: 123 Copynumber: 2.2 Consensus size: 122
1400849 TTGGATATCC
* *
1400859 TTGAAATCC-ATCTAAAGATGAATGTTACTGGTGAGCACGATTCTTCGTCGTGAAGTTGAAACCG
1 TTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATCCTTCGTCGTGAAGTTGAAACCG
* * *
1400923 TGGATGGCCCCTTTGTTGTGAAGTTGAGCCTTGAATTCG-ATATCTTTCGTCGTGAAG
66 TGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATT-GAATATCCTTCGTCGTGAAG
1400980 TTGAAATCCAATCTAAA-ATGAATGTTGCTGGTGAGCACGAGTCCCTTCGTCGTGAAGTTGAAAC
1 TTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGA-T-CCTTCGTCGTGAAGTTGAAAC
1401044 CGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAG
64 CGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAG
*
1401103 ATGAAATCCAATCTAAAGATGAATGTTGCT
1 TTGAAATCCAATCTAAAGATGAATGTTGCT
1401133 TCGAGTCCAA
Statistics
Matches: 142, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
121 31 0.22
122 9 0.06
123 90 0.63
124 12 0.08
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (122 bp):
TTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATCCTTCGTCGTGAAGTTGAAACCG
TGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGAATATCCTTCGTCGTGAAG
Found at i:1402847 original size:95 final size:95
Alignment explanation
Indices: 1402656--1402907 Score: 380
Period size: 95 Copynumber: 2.6 Consensus size: 95
1402646 AGCTGAATCT
* * * * *
1402656 ATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGTCAGCTTAA-TTTTATTGTACAGATATTA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGT----ATATTA
1402720 TAATCACCTTTATCAGGCTAGCTGAATATTATCC
62 TAATCACCTTTATCAGGCTAGCTGAATATTATCC
*
1402754 ATAAAGCCGGGGCGTTTAACCAATTGGTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
* *
1402819 CACCTTTATCAGGCTAGTTGAATCTTATCC
66 CACCTTTATCAGGCTAGCTGAATATTATCC
*
1402849 ATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAT
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT
1402908 ACATAATATT
Statistics
Matches: 143, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
95 95 0.66
98 40 0.28
99 8 0.06
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (95 bp):
ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
CACCTTTATCAGGCTAGCTGAATATTATCC
Found at i:1405554 original size:18 final size:18
Alignment explanation
Indices: 1405539--1405578 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1405529 ATAAAAAAAG
1405539 TAAAGATAAAAGAAAATAA
1 TAAA-ATAAAAGAAAATAA
1405558 TAAAATAAAA-AATAATAA
1 TAAAATAAAAGAA-AATAA
1405576 TAA
1 TAA
1405579 TAAAGAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 14 0.70
19 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
TAAAATAAAAGAAAATAA
Found at i:1405571 original size:15 final size:16
Alignment explanation
Indices: 1405551--1405582 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1405541 AAGATAAAAG
1405551 AAAATAATAA-AATAA
1 AAAATAATAATAATAA
1405566 AAAATAATAATAATAA
1 AAAATAATAATAATAA
1405582 A
1 A
1405583 GAAGGGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAATAATAATAA
Found at i:1406768 original size:18 final size:18
Alignment explanation
Indices: 1406747--1406788 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1406737 AACCATAAAT
1406747 AATAAA-AAAATAAAATAA
1 AATAAAGAAAA-AAAATAA
**
1406765 AATAAAGTTAAAAAATAA
1 AATAAAGAAAAAAAATAA
1406783 AATAAA
1 AATAAA
1406789 TATTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAAGAAAAAAAATAA
Found at i:1406799 original size:18 final size:18
Alignment explanation
Indices: 1406758--1406809 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1406748 ATAAAAAAAT
1406758 AAAATAAAATAAAGT-TAA
1 AAAATAAAATAAA-TATAA
*
1406776 AAAATAAAATAAATATTA
1 AAAATAAAATAAATATAA
*
1406794 ATAATAATAATAAATA
1 AAAATAA-AATAAATA
1406810 AATGTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 1 0.03
18 21 0.70
19 8 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATAAAATAAATATAA
Found at i:1406808 original size:28 final size:26
Alignment explanation
Indices: 1406741--1406811 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 26
1406731 CCTGAAAACC
1406741 ATAAATAATAAA-AAAATAAAATAAA
1 ATAAATAATAAATAAAATAAAATAAA
*
1406766 ATAAAGTTAAAAAATAAAATAAATATTAATA
1 ATAAA--TAATAAATAAAATAAA-A-TAA-A
1406797 AT-AATAATAAATAAA
1 ATAAATAATAAATAAA
1406812 TGTTTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 5 0.13
27 6 0.16
28 18 0.47
29 1 0.03
30 5 0.13
31 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.25
Consensus pattern (26 bp):
ATAAATAATAAATAAAATAAAATAAA
Found at i:1406825 original size:23 final size:22
Alignment explanation
Indices: 1406749--1406825 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
1406739 CCATAAATAA
1406749 TAAAAAAATAAAATAAAATAAA-GT
1 TAAAAAAAT--AAT-AAATAAATGT
*
1406773 T-AAAAAAT-A-AAATAAATAT
1 TAAAAAAATAATAAATAAATGT
*
1406792 TAATAATAATAATAAATAAATGTT
1 TAA-AAAAATAATAAATAAATG-T
1406816 TAAAAAAATA
1 TAAAAAAATA
1406826 TAATATATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
18 7 0.16
19 2 0.05
20 2 0.05
21 5 0.12
22 1 0.02
23 21 0.49
24 5 0.12
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (22 bp):
TAAAAAAATAATAAATAAATGT
Found at i:1406908 original size:2 final size:2
Alignment explanation
Indices: 1406903--1406932 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1406893 AAAACTATTA
1406903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1406933 TCCAAAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1407031 original size:37 final size:36
Alignment explanation
Indices: 1406914--1407338 Score: 487
Period size: 37 Copynumber: 11.4 Consensus size: 36
1406904 TATATATATA
* *
1406914 TATATATATATATATATATTCCAAAATGTTTAAAAAAC
1 TATATAT-TATATATAT-TTTCAAAATGTTTTAAAAAC
* *
1406952 TATATAATATATAAATGTTTTCAAAATGATTTTAAAAAC
1 TATAT-AT-TATATATATTTTCAAAATG-TTTTAAAAAC
*
1406991 TATATATTATATATATATTCTAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTC-AAAATGTTTTAAAAAC
*
1407028 TATATATTATATA-GTTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTAAAAAC
* *
1407063 TATATATTATAT-TCATTTTCAAAATGTTTTCAAAAT
1 TATATATTATATAT-ATTTTCAAAATGTTTTAAAAAC
* **
1407099 TATATATTATATAAATTTTCAAAAATGTTTTCGAAAC
1 TATATATTATATATATTTTC-AAAATGTTTTAAAAAC
* * *
1407136 TATATATTATATTTGTTTTCAAAATAATTTTAAAAAC
1 TATATATTATATATATTTTCAAAAT-GTTTTAAAAAC
1407173 TATATATTATATATATTTTCTAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTC-AAAATGTTTTAAAAAC
*
1407210 TATATATTATATA-GTTTTCAAAAGTGTTTTAAAAAC
1 TATATATTATATATATTTTCAAAA-TGTTTTAAAAAC
* *
1407246 TATATATTATATACATTTTCAAAATGTTTTTAAAAAG
1 TATATATTATATATATTTTCAAAATG-TTTTAAAAAC
* * **
1407283 TATATATTATATACGTATTTTTAAAAAACGTTTTGCAAAC
1 TATATATTATATA--TA-TTTT-CAAAATGTTTTAAAAAC
*
1407323 TATATAATATATATAT
1 TATATATTATATATAT
1407339 AAAGATATAT
Statistics
Matches: 337, Mismatches: 34, Indels: 33
0.83 0.08 0.08
Matches are distributed among these distances:
35 32 0.09
36 78 0.23
37 145 0.43
38 29 0.09
39 25 0.07
40 23 0.07
41 5 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAAAC
Found at i:1407110 original size:147 final size:145
Alignment explanation
Indices: 1406916--1407295 Score: 500
Period size: 147 Copynumber: 2.6 Consensus size: 145
1406906 TATATATATA
* * *
1406916 TATATATATATATA-TATTCCAAAATGTTTAAAAAACTATATAATATATAAATGTTTTCAAAATG
1 TATATAT-TATATAGT-TTTCAAAATGTTTTAAAAACTATATATTATATAAA--TTTTCAAAATG
* *
1406980 ATTTTAAAAACTATATATTATATATATATTCTAAAAT-GTTTTAAAAACTATATATTATATA-GT
62 -TTTTAAAAACTATATATTATATATATATTC-AAAATAATTTTAAAAACTATATATTATATATAT
1407043 TTTC-AAAATGTTTTAAAAAC
125 TTTCTAAAATGTTTTAAAAAC
* *
1407063 TATATATTATATTCA-TTTTCAAAATGTTTTCAAAATTATATATTATATAAATTTTCAAAAATGT
1 TATATATTATA-T-AGTTTTCAAAATGTTTTAAAAACTATATATTATATAAATTTTC-AAAATGT
** * * *
1407127 TTTCGAAACTATATATTATATTTGTTTTCAAAATAATTTTAAAAACTATATATTATATATATTTT
63 TTTAAAAACTATATATTATATATATATTCAAAATAATTTTAAAAACTATATATTATATATATTTT
1407192 CTAAAATGTTTTAAAAAC
128 CTAAAATGTTTTAAAAAC
*
1407210 TATATATTATATAGTTTTCAAAAGTGTTTTAAAAACTATATATTATATACATTTTCAAAATGTTT
1 TATATATTATATAGTTTTCAAAA-TGTTTTAAAAACTATATATTATATAAATTTTCAAAATG-TT
*
1407275 TTAAAAAGTATATATTATATA
64 TTAAAAACTATATATTATATA
1407296 CGTATTTTTA
Statistics
Matches: 205, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
144 5 0.02
145 54 0.26
146 31 0.15
147 113 0.55
148 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (145 bp):
TATATATTATATAGTTTTCAAAATGTTTTAAAAACTATATATTATATAAATTTTCAAAATGTTTT
AAAAACTATATATTATATATATATTCAAAATAATTTTAAAAACTATATATTATATATATTTTCTA
AAATGTTTTAAAAAC
Found at i:1407146 original size:73 final size:71
Alignment explanation
Indices: 1406914--1407294 Score: 478
Period size: 73 Copynumber: 5.2 Consensus size: 71
1406904 TATATATATA
* * *
1406914 TATATATATATATATATATTCCAAAATGTTTAAAAAACTATATAATATATAAATGTTTTCAAAAT
1 TATATAT-TATAT-TAT-TTTCAAAATGTTTTAAAAACTATATATTATATAAA--TTTTCAAAAT
1406979 GATTTTAAAAAC
61 G-TTTTAAAAAC
* *
1406991 TATATATTATATATATATTCTAAAATGTTTTAAAAACTATATATTATAT-AGTTTTCAAAATGTT
1 TATATATTATAT-TATTTTC-AAAATGTTTTAAAAACTATATATTATATAAATTTTCAAAATGTT
1407055 TTAAAAAC
64 TTAAAAAC
* *
1407063 TATATATTATATTCATTTTCAAAATGTTTTCAAAATTATATATTATATAAATTTTCAAAAATGTT
1 TATATATTATATT-ATTTTCAAAATGTTTTAAAAACTATATATTATATAAATTTTC-AAAATGTT
**
1407128 TTCGAAAC
64 TTAAAAAC
* * *
1407136 TATATATTATATTTGTTTTCAAAATAATTTTAAAAACTATATATTATATATATTTTCTAAAATGT
1 TATATATTATA-TTATTTTCAAAAT-GTTTTAAAAACTATATATTATATAAATTTTC-AAAATGT
1407201 TTTAAAAAC
63 TTTAAAAAC
*
1407210 TATATATTATA-TAGTTTTCAAAAGTGTTTTAAAAACTATATATTATATACATTTTCAAAATGTT
1 TATATATTATATTA-TTTTCAAAA-TGTTTTAAAAACTATATATTATATAAATTTTCAAAATG-T
*
1407274 TTTAAAAAG
63 TTTAAAAAC
1407283 TATATATTATAT
1 TATATATTATAT
1407295 ACGTATTTTT
Statistics
Matches: 271, Mismatches: 23, Indels: 23
0.85 0.07 0.07
Matches are distributed among these distances:
71 27 0.10
72 40 0.15
73 104 0.38
74 55 0.20
75 3 0.01
76 35 0.13
77 7 0.03
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (71 bp):
TATATATTATATTATTTTCAAAATGTTTTAAAAACTATATATTATATAAATTTTCAAAATGTTTT
AAAAAC
Found at i:1407352 original size:18 final size:19
Alignment explanation
Indices: 1407324--1407359 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1407314 TTTGCAAACT
1407324 ATATAATATATATATAAAG
1 ATATAATATATATATAAAG
*
1407343 ATAT-ATATATGTATAAA
1 ATATAATATATATATAAA
1407360 AAAATATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
ATATAATATATATATAAAG
Found at i:1419233 original size:17 final size:17
Alignment explanation
Indices: 1419211--1419264 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
1419201 AATTGAAATA
1419211 AAAGACTCTAAATAAAG
1 AAAGACTCTAAATAAAG
* *
1419228 AAAGACTCCTAAAGAAAT
1 AAAGACT-CTAAATAAAG
*
1419246 AAGATACTCATAAATAAAG
1 AA-AGACTC-TAAATAAAG
1419265 TCATATAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.24
18 11 0.38
19 11 0.38
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.19
Consensus pattern (17 bp):
AAAGACTCTAAATAAAG
Found at i:1421767 original size:17 final size:17
Alignment explanation
Indices: 1421732--1421789 Score: 82
Period size: 17 Copynumber: 3.3 Consensus size: 17
1421722 CATGCTCGAG
1421732 AAGAAAAACTGCATGGACA
1 AAGAAAAACT-C-TGGACA
1421751 AAGAAAAACTCTGGACA
1 AAGAAAAACTCTGGACA
1421768 AAGAAAAACTCT-GAGCA
1 AAGAAAAACTCTGGA-CA
1421785 AAGAA
1 AAGAA
1421790 GAATCGTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.05
17 25 0.66
18 1 0.03
19 10 0.26
ACGTcount: A:0.55, C:0.16, G:0.19, T:0.10
Consensus pattern (17 bp):
AAGAAAAACTCTGGACA
Found at i:1423244 original size:20 final size:19
Alignment explanation
Indices: 1423219--1423261 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1423209 ATACATGTTG
1423219 TTTTAAAGAATA-TTCATGAC
1 TTTTAAAGAA-AGTTCATG-C
*
1423239 TTTTAATGAAAGTTCATGC
1 TTTTAAAGAAAGTTCATGC
1423258 TTTT
1 TTTT
1423262 TTCTGAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (19 bp):
TTTTAAAGAAAGTTCATGC
Found at i:1423634 original size:21 final size:21
Alignment explanation
Indices: 1423609--1423659 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1423599 GTAGCTAGTG
1423609 ACACTCCAACTACCTTAGCTC
1 ACACTCCAACTACCTTAGCTC
1423630 ACACTCCAACTACCTTAGCTC
1 ACACTCCAACTACCTTAGCTC
*
1423651 ACACACCAA
1 ACACTCCAA
1423660 GTGCCTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.43, G:0.04, T:0.20
Consensus pattern (21 bp):
ACACTCCAACTACCTTAGCTC
Found at i:1428115 original size:75 final size:75
Alignment explanation
Indices: 1427978--1428123 Score: 222
Period size: 75 Copynumber: 1.9 Consensus size: 75
1427968 CTTCAATTCC
* * * *
1427978 CCTTTTGATCTCACTCACTCGATTTGCCTTTATTTTTACTCCTTTCTCTTGTTAACTTAGAGAGA
1 CCTTATGATCTCACTCACTCGATTTGCCTTTATTTTCACTCATTTCTCCTGTTAACTTAGAGAGA
1428043 GAGAGATCCT
66 GAGAGATCCT
* *
1428053 CCTTATGATCTCACTCACTCGATTTGCCTTT-TTTTCACTCATTTTTCCTGTTAAGTTCAGAGAG
1 CCTTATGATCTCACTCACTCGATTTGCCTTTATTTTCACTCATTTCTCCTGTTAACTT-AGAGAG
1428117 AGAGAGA
65 AGAGAGA
1428124 GAGAGAGAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 21 0.33
75 43 0.67
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (75 bp):
CCTTATGATCTCACTCACTCGATTTGCCTTTATTTTCACTCATTTCTCCTGTTAACTTAGAGAGA
GAGAGATCCT
Found at i:1428239 original size:33 final size:33
Alignment explanation
Indices: 1428189--1428256 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1428179 TTGAGAGAGA
1428189 GAGAGAGAGAGAATTCATGAACAAATATATATT
1 GAGAGAGAGAGAATTCATGAACAAATATATATT
* * *
1428222 GAGAGAGAGGGAGTTCATGAACGAATATATATT
1 GAGAGAGAGAGAATTCATGAACAAATATATATT
1428255 GA
1 GA
1428257 AAGATAGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (33 bp):
GAGAGAGAGAGAATTCATGAACAAATATATATT
Found at i:1433023 original size:39 final size:37
Alignment explanation
Indices: 1432938--1433023 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
1432928 AACAAATTGT
* * *
1432938 AAAATATTTATATATTTTTTTTAAAAAATTTAAATTC
1 AAAAAATTTATATAATTTTTTTAAAAAATTAAAATTC
* *
1432975 ATAAAATTTATATAATTTTTTTACAAAATTGAAAATAT-
1 AAAAAATTTATATAATTTTTTTAAAAAATT-AAAAT-TC
1433013 AAAAAGATTTA
1 AAAAA-ATTTA
1433024 ATGAAATTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 26 0.65
38 8 0.20
39 6 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (37 bp):
AAAAAATTTATATAATTTTTTTAAAAAATTAAAATTC
Found at i:1433488 original size:23 final size:24
Alignment explanation
Indices: 1433444--1433488 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1433434 AAAAATCCAG
*
1433444 ATTTCAACTTAAAAATTAAAAGAA
1 ATTTCAACTTAAAAATGAAAAGAA
* *
1433468 ATTTCAA-TTATAAATGCAAAG
1 ATTTCAACTTAAAAATGAAAAG
1433489 TGCTCGGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (24 bp):
ATTTCAACTTAAAAATGAAAAGAA
Found at i:1434093 original size:16 final size:17
Alignment explanation
Indices: 1434055--1434097 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1434045 CTAAAAATAA
1434055 TTAA-TTAATATTTACAT
1 TTAATTTAAT-TTTACAT
1434072 TT-ATTTAATTTTA-AT
1 TTAATTTAATTTTACAT
1434087 TTAATTTAATT
1 TTAATTTAATT
1434098 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATTTAATTTTACAT
Found at i:1434103 original size:20 final size:21
Alignment explanation
Indices: 1434064--1434105 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1434054 ATTAATTAAT
*
1434064 ATTTACATTTATTTAATTTTA
1 ATTTACATTTAATTAATTTTA
*
1434085 ATTTA-ATTTAATTATTTTTA
1 ATTTACATTTAATTAATTTTA
1434105 A
1 A
1434106 AAAAGTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTACATTTAATTAATTTTA
Found at i:1435006 original size:22 final size:22
Alignment explanation
Indices: 1434978--1435024 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1434968 TAGGTCGCTC
1434978 AATATTATTTCTAATTCCCTTG
1 AATATTATTTCTAATTCCCTTG
1435000 AATATTATTTCTAATTCCCTTG
1 AATATTATTTCTAATTCCCTTG
1435022 AAT
1 AAT
1435025 TTCTTGGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (22 bp):
AATATTATTTCTAATTCCCTTG
Done.