Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 92 of 125
Found at i:27819534 original size:41 final size:38
Alignment explanation
Indices: 27819445--27819536 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 38
27819435 ATTATATTTT
* *
27819445 AAATTATAAAAATTATAAAATTAATAAAACTTATTTAA
1 AAATTATAAAAATGATAAAATTAATAAAACTTATTAAA
** *
27819483 ATTTTAATAAAAATGATAAAAGTTGATAAAAACTTATTGAAA
1 AAATT-ATAAAAATGATAAAA-TTAAT-AAAACTTATT-AAA
27819525 AAATTATAAAAA
1 AAATTATAAAAA
27819537 ATAGTCGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
38 3 0.07
39 14 0.33
40 4 0.09
41 17 0.40
42 5 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (38 bp):
AAATTATAAAAATGATAAAATTAATAAAACTTATTAAA
Found at i:27821453 original size:33 final size:33
Alignment explanation
Indices: 27821416--27821484 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
27821406 TTGCAAACTA
*
27821416 CTTTGTTTTTGGAGTGGGTTTTGATAGTTCTTG
1 CTTTGTTTTTGGAGTGGGTTTTGATACTTCTTG
27821449 CTTTGTTTTTGGAGTGGGTTTTGATACTTCTTG
1 CTTTGTTTTTGGAGTGGGTTTTGATACTTCTTG
27821482 CTT
1 CTT
27821485 CTCCTTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.09, C:0.09, G:0.28, T:0.55
Consensus pattern (33 bp):
CTTTGTTTTTGGAGTGGGTTTTGATACTTCTTG
Found at i:27829373 original size:13 final size:12
Alignment explanation
Indices: 27829366--27829394 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27829356 CAAAAACTAG
27829366 AAAAAAAAGATA
1 AAAAAAAAGATA
27829378 AAAAAAAAGA-A
1 AAAAAAAAGATA
27829389 AAAAAA
1 AAAAAA
27829395 GCCAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGATA
Found at i:27829401 original size:21 final size:21
Alignment explanation
Indices: 27829364--27829406 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
27829354 AACAAAAACT
*
27829364 AGAAAAAAAAGATAAAAAAAA
1 AGAAAAAAAAGACAAAAAAAA
*
27829385 AGAAAAAAAAGCCAAAAAAAA
1 AGAAAAAAAAGACAAAAAAAA
27829406 A
1 A
27829407 AAAGAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (21 bp):
AGAAAAAAAAGACAAAAAAAA
Found at i:27835021 original size:18 final size:18
Alignment explanation
Indices: 27834998--27835032 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27834988 TTTTGAATTG
*
27834998 GGAGAATAACCTCATTAT
1 GGAGAAGAACCTCATTAT
27835016 GGAGAAGAACCTCATTA
1 GGAGAAGAACCTCATTA
27835033 GTTATCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (18 bp):
GGAGAAGAACCTCATTAT
Found at i:27837782 original size:3 final size:3
Alignment explanation
Indices: 27837765--27837809 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
27837755 GGAAAATTAG
27837765 AAT AA- AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27837810 AGTGAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27839124 original size:30 final size:29
Alignment explanation
Indices: 27839065--27839217 Score: 150
Period size: 30 Copynumber: 5.2 Consensus size: 29
27839055 AAATTAAAAC
* *
27839065 GGGGTCAAATTT-TATTTTTGAAAACTTTA
1 GGGGTTAAATTTGAATTTTTGAAAA-TTTA
*
27839094 GGGGTTAAACTTGAATTTTTAGAAAATTTA
1 GGGGTTAAATTTGAATTTTT-GAAAATTTA
* *
27839124 GGGGTCAAATTTGAAATTTTAGAAAATTT-
1 GGGGTTAAATTTG-AATTTTTGAAAATTTA
* * * *
27839153 GGAGTTGAAATTTAAAATTTTGGAAAATTCA
1 GGGGTT-AAATTT-GAATTTTTGAAAATTTA
27839184 GGGGTTAAATTTGAATTTTTGAAAACTTT-
1 GGGGTTAAATTTGAATTTTTGAAAA-TTTA
27839213 GGGGT
1 GGGGT
27839218 CAAAAAATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
29 30 0.29
30 56 0.55
31 16 0.16
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (29 bp):
GGGGTTAAATTTGAATTTTTGAAAATTTA
Found at i:27839561 original size:26 final size:28
Alignment explanation
Indices: 27839513--27839571 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 28
27839503 TATTTGATTA
* *
27839513 TTTCTATTAAAAAAGACATAACCCATTC
1 TTTCCATTAAAAAAGACAAAACCCATTC
27839541 TTTCCATT-AAAAA-ACAAAACCCATTC
1 TTTCCATTAAAAAAGACAAAACCCATTC
27839567 TTTCC
1 TTTCC
27839572 TTTTTCAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 17 0.59
27 5 0.17
28 7 0.24
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (28 bp):
TTTCCATTAAAAAAGACAAAACCCATTC
Found at i:27840842 original size:40 final size:40
Alignment explanation
Indices: 27840798--27840938 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 40
27840788 ATCTTTCTCA
*
27840798 TGATTGGGGTAAGAGATTGGAAGGTCTTCAATCTGCCCTC
1 TGATTAGGGTAAGAGATTGGAAGGTCTTCAATCTGCCCTC
* *
27840838 TGATTAGGGTAAAAGATTGGATA-GTTTTCAATCTGCCC-C
1 TGATTAGGGTAAGAGATTGGA-AGGTCTTCAATCTGCCCTC
** * *
27840877 ATGATCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTC
1 -TGATTAGGGTAAGAGATTGGAAGGTCTTCAATCTGCCCTC
* *
27840918 TGGTTAGGATAAGAGATTGGA
1 TGATTAGGGTAAGAGATTGGA
27840939 GGTTGTAACT
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 80 0.96
41 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (40 bp):
TGATTAGGGTAAGAGATTGGAAGGTCTTCAATCTGCCCTC
Found at i:27840880 original size:80 final size:79
Alignment explanation
Indices: 27840765--27840938 Score: 240
Period size: 80 Copynumber: 2.2 Consensus size: 79
27840755 ATAACTTTAG
* * ** * * *
27840765 GGGTAAAAGATTGAATTGTTTCAATCTTTCTCATGATTGGGGTAAGAGATTGGAAGGTCTTCAAT
1 GGGTAAAAGATTGGATAGTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGAAGGTCTTCAAT
27840830 CTGCCCTCTGATTA
66 CTGCCCTCTGATTA
*
27840844 GGGTAAAAGATTGGATAGTTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTGGATAG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGAAGGTCTTCAA
*
27840909 TCTGCCCTCTGGTTA
65 TCTGCCCTCTGATTA
* *
27840924 GGATAAGAGATTGGA
1 GGGTAAAAGATTGGA
27840939 GGTTGTAACT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 16 0.19
80 67 0.81
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (79 bp):
GGGTAAAAGATTGGATAGTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGAAGGTCTTCAAT
CTGCCCTCTGATTA
Found at i:27841118 original size:50 final size:50
Alignment explanation
Indices: 27840990--27841119 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 50
27840980 TCATCCTTAT
* *
27840990 GACTTCAATCCGC-CCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGC
1 GACTTCAATCTGCACCTTC-ACAGCTTTAGGTGAATGAGATTTGCCATTGC
* * ** * *
27841040 GGCTTCATTCTGTTCCTTTACAGCTTTAGGTGTATGAGATTTGCCATTGC
1 GACTTCAATCTGCACCTTCACAGCTTTAGGTGAATGAGATTTGCCATTGC
* *
27841090 GATTTCAATCTGCACCTTCACAGTTTTAGG
1 GACTTCAATCTGCACCTTCACAGCTTTAGG
27841120 GGTAAAAGAT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
50 62 0.95
51 3 0.05
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (50 bp):
GACTTCAATCTGCACCTTCACAGCTTTAGGTGAATGAGATTTGCCATTGC
Found at i:27852006 original size:20 final size:20
Alignment explanation
Indices: 27851981--27852021 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27851971 GTTCAAAGAA
27851981 AAAACCACAACCAGTGAATT
1 AAAACCACAACCAGTGAATT
*
27852001 AAAACCACATCCAGTGAATT
1 AAAACCACAACCAGTGAATT
27852021 A
1 A
27852022 GGGGATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.10, T:0.17
Consensus pattern (20 bp):
AAAACCACAACCAGTGAATT
Found at i:27852336 original size:29 final size:30
Alignment explanation
Indices: 27852229--27852385 Score: 178
Period size: 30 Copynumber: 5.3 Consensus size: 30
27852219 AGTTAAGACG
* *
27852229 GGGTCAAATTTTAATTTTT-GAAAACTTTAA
1 GGGTCAAATTTGAATTTTTGGAAAA-TTTGA
* *
27852259 GGGTTAAACTTT-AATTTTTGGAAAATTTAA
1 GGGTCAAA-TTTGAATTTTTGGAAAATTTGA
* * *
27852289 GGGTTAAATTTGAATTTTTGGAAATTTTGG
1 GGGTCAAATTTGAATTTTTGGAAAATTTGA
* *
27852319 GGGTGAAATTTGAATTTTTGGAAAATTCGA
1 GGGTCAAATTTGAATTTTTGGAAAATTTGA
27852349 GGGTCAAATTTGAA-TTTT-GAAAACTTTGA
1 GGGTCAAATTTGAATTTTTGGAAAA-TTTGA
27852378 GGGTCAAA
1 GGGTCAAA
27852386 AAATGATTTT
Statistics
Matches: 113, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
28 5 0.04
29 19 0.17
30 81 0.72
31 8 0.07
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTGA
Found at i:27856592 original size:29 final size:28
Alignment explanation
Indices: 27856559--27856619 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
27856549 TTCTTTAAAT
* *
27856559 ATGTATCAT-TGAATTAAAATTGAAATTTC
1 ATGTA-CATGTGAATCAAAA-TAAAATTTC
*
27856588 ATGTACATGTGAATCACAATAAAATTTC
1 ATGTACATGTGAATCAAAATAAAATTTC
27856616 ATGT
1 ATGT
27856620 GTATAATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (28 bp):
ATGTACATGTGAATCAAAATAAAATTTC
Found at i:27861950 original size:3 final size:3
Alignment explanation
Indices: 27861942--27861981 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
27861932 CATGACTCTG
27861942 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
27861982 GTGACTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:27863827 original size:21 final size:21
Alignment explanation
Indices: 27863803--27863847 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27863793 TAGCATAATT
* *
27863803 CAAATATAAAATTTAGAAATC
1 CAAACATAAAATTTAAAAATC
*
27863824 CAAACATAAAGTTTAAAAATC
1 CAAACATAAAATTTAAAAATC
27863845 CAA
1 CAA
27863848 TCGTCGACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.04, T:0.24
Consensus pattern (21 bp):
CAAACATAAAATTTAAAAATC
Found at i:27867678 original size:57 final size:55
Alignment explanation
Indices: 27867605--27867792 Score: 243
Period size: 57 Copynumber: 3.3 Consensus size: 55
27867595 ACCCGAGGGC
*
27867605 AAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGAAATATTTGAGAATTCGAGGT
1 AAAATGGTAATTTTGGTGAAATC-GGGTTAAAAATGGAAT-TTTGAGAATTCGAGGT
*
27867662 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTCGAGGGT
1 AAAATGGTAATTTTGGTGAAATC-GGGTTAAAAATGGAATTTT-GAGAATTCGA-GGT
* *
27867720 AAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTG-GAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCG-GGTTAAAAATGGAATTTTGAG-AA-TTC-GAGGT
27867779 AAAATGGTAATTTT
1 AAAATGGTAATTTT
27867793 TGAAAGTTTC
Statistics
Matches: 117, Mismatches: 7, Indels: 13
0.85 0.05 0.09
Matches are distributed among these distances:
56 3 0.03
57 47 0.40
58 20 0.17
59 46 0.39
60 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (55 bp):
AAAATGGTAATTTTGGTGAAATCGGGTTAAAAATGGAATTTTGAGAATTCGAGGT
Found at i:27867694 original size:29 final size:30
Alignment explanation
Indices: 27867605--27867792 Score: 157
Period size: 29 Copynumber: 6.5 Consensus size: 30
27867595 ACCCGAGGGC
*
27867605 AAAATGGTAATTTTGGTGAAATCAGGGTTA
1 AAAATGGTAATTTTGGTGAAATCGGGGTTA
* * * *
27867635 AAAAT-GAAATATTT-GAGAATTCGAGG-T-
1 AAAATGGTAAT-TTTGGTGAAATCGGGGTTA
27867662 AAAATGGTAATTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTGGTGAAATCGGGGTTA
*
27867692 AAAATGG-AATTTTGG-AAAATTCGAGGG-T-
1 AAAATGGTAATTTTGGTGAAA-TCG-GGGTTA
* *
27867720 AAAATAGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTA
*
27867751 AAAATGG-AATTTT-G-GAAAGTTCGGGGGT-
1 AAAATGGTAATTTTGGTGAAA--TCGGGGTTA
27867779 AAAATGGTAATTTT
1 AAAATGGTAATTTT
27867793 TGAAAGTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 31
0.73 0.09 0.18
Matches are distributed among these distances:
27 12 0.09
28 31 0.24
29 45 0.35
30 30 0.24
31 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTA
Found at i:27867752 original size:59 final size:58
Alignment explanation
Indices: 27867598--27867792 Score: 279
Period size: 59 Copynumber: 3.4 Consensus size: 58
27867588 TTTGGACACC
* * *
27867598 CGAGGGCAAAATGGTAATTTTGGTGAAATC-AGGGTTAAAAATGAAATATTT-GAGAATT
1 CGAGGGTAAAATGGTAATTTTGGTGAAATCGA-GGTTAAAAATGGAAT-TTTGGAAAATT
*
27867656 CGA-GGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATT
1 CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAATT
* *
27867713 CGAGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTT
1 CGAGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAATT
*
27867772 CGGGGGTAAAATGGTAATTTT
1 CGAGGGTAAAATGGTAATTTT
27867793 TGAAAGTTTC
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
56 3 0.02
57 48 0.39
58 19 0.15
59 54 0.44
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (58 bp):
CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAATT
Found at i:27867805 original size:59 final size:56
Alignment explanation
Indices: 27867605--27867820 Score: 235
Period size: 59 Copynumber: 3.7 Consensus size: 56
27867595 ACCCGAGGGC
* *
27867605 AAAATGGTAATTTTGGTGAAATC-AGGGTTAAAAATGAAATATTT-GAGAATTC-GAGGT
1 AAAATGGTAATTTT-GTGAAATCGA-GGTTAAAAATGGAAT-TTTGGA-AATTCGGGGGT
* *
27867662 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTCGAGGGT
1 AAAATGGTAATTTT-GTGAAATCGAGGTTAAAAATGGAATTTTGG-AAATTCGGGGGT
*
27867720 AAAATAGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAA-TTTT-GTGAAATCGAGGTTAAAAATGGAATTTTGGAAA-TTCGGGGGT
*
27867779 AAAATGGTAATTTT-TGAAAGTTTCGAGGTT-AAAATGTAATTT
1 AAAATGGTAATTTTGTGAAA---TCGAGGTTAAAAATGGAATTT
27867821 CCTAAAATTT
Statistics
Matches: 141, Mismatches: 9, Indels: 17
0.84 0.05 0.10
Matches are distributed among these distances:
56 8 0.06
57 43 0.30
58 31 0.22
59 59 0.42
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (56 bp):
AAAATGGTAATTTTGTGAAATCGAGGTTAAAAATGGAATTTTGGAAATTCGGGGGT
Found at i:27867812 original size:30 final size:28
Alignment explanation
Indices: 27867605--27867820 Score: 144
Period size: 29 Copynumber: 7.5 Consensus size: 28
27867595 ACCCGAGGGC
27867605 AAAATGGTAATTTTGGTGAAA-TC-AGGGTT
1 AAAATGGTAATTTT--TGAAATTCGA-GGTT
* *
27867634 AAAAAT-GAAATATTTGAGAATTCGAGG-T
1 -AAAATGGTAATTTTTGA-AATTCGAGGTT
*
27867662 AAAATGGTAATTTTGGTGAAA-TCGGGGTT
1 AAAATGGTAATTTT--TGAAATTCGAGGTT
* *
27867691 AAAAATGG-AATTTTGGAAAATTCGAGGGT
1 -AAAATGGTAATTTTTG-AAATTCGAGGTT
*
27867720 AAAATAGTAATTTTTGGTGAAA-TCGAGGTT
1 AAAATGGTAA-TTTT--TGAAATTCGAGGTT
* * *
27867750 AAAAATGG-AATTTTGGAAAGTTCGGGGGT
1 -AAAATGGTAATTTTTGAAA-TTCGAGGTT
27867779 AAAATGGTAATTTTTGAAAGTTTCGAGGTT
1 AAAATGGTAATTTTTGAAA--TTCGAGGTT
27867809 AAAAT-GTAATTT
1 AAAATGGTAATTT
27867821 CCTAAAATTT
Statistics
Matches: 148, Mismatches: 19, Indels: 39
0.72 0.09 0.19
Matches are distributed among these distances:
27 13 0.09
28 30 0.20
29 54 0.36
30 41 0.28
31 9 0.06
32 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
AAAATGGTAATTTTTGAAATTCGAGGTT
Found at i:27868615 original size:15 final size:16
Alignment explanation
Indices: 27868595--27868625 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
27868585 TAAAACCGAA
27868595 CCAGATCTGG-GAAAT
1 CCAGATCTGGAGAAAT
27868610 CCAGATCTGGAGAAAT
1 CCAGATCTGGAGAAAT
27868626 TTCGAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (16 bp):
CCAGATCTGGAGAAAT
Found at i:27868907 original size:20 final size:20
Alignment explanation
Indices: 27868866--27868924 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
27868856 TTTCTTCCTT
* *
27868866 TTTATTTTTATTAAATAGTTA
1 TTTATTATTATT-AATATTTA
27868887 TTTATTATTATTAATATTTA
1 TTTATTATTATTAATATTTA
27868907 -TTATTAGTTATTAATATT
1 TTTATTA-TTATTAATATT
27868925 GAAAACTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 6 0.17
20 18 0.51
21 11 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTATTATTATTAATATTTA
Found at i:27869708 original size:6 final size:6
Alignment explanation
Indices: 27869692--27869811 Score: 108
Period size: 6 Copynumber: 20.0 Consensus size: 6
27869682 TAAATTTGTT
**
27869692 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
**
27869742 TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA TTTAAA TTTAAGA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAA-A TTTAAA
27869790 TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
27869812 ATCAATTTAA
Statistics
Matches: 94, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
4 5 0.05
5 9 0.10
6 63 0.67
7 5 0.05
8 12 0.13
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:27869729 original size:11 final size:11
Alignment explanation
Indices: 27869713--27869794 Score: 64
Period size: 11 Copynumber: 7.8 Consensus size: 11
27869703 AATTTAAATT
*
27869713 TAAATTTAAGG
1 TAAATTTAAGA
27869724 TAAATTTAA-A
1 TAAATTTAAGA
* **
27869734 T-AATTAAATT
1 TAAATTTAAGA
*
27869744 TAAATTTAAGG
1 TAAATTTAAGA
27869755 TAAATTTAA-A
1 TAAATTTAAGA
* **
27869765 T-AATTAAATT
1 TAAATTTAAGA
27869775 TAAATTTAAGA
1 TAAATTTAAGA
27869786 TAAATTTAA
1 TAAATTTAA
27869795 ATTTAAATAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
9 12 0.22
10 4 0.07
11 39 0.71
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:27869741 original size:31 final size:31
Alignment explanation
Indices: 27869697--27869811 Score: 180
Period size: 31 Copynumber: 3.7 Consensus size: 31
27869687 TTGTTTTTAT
27869697 AATTTAAAT--TTAAATTTAAATTTAAGGTA
1 AATTTAAATAATTAAATTTAAATTTAAGGTA
27869726 AATTTAAATAATTAAATTTAAATTTAAGGTA
1 AATTTAAATAATTAAATTTAAATTTAAGGTA
*
27869757 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAATAATTAAATTTAAATTTAAGGTA
*
27869788 AATTTAAATTTAAATAAATTTAAA
1 AATTTAAA--TAATTAAATTTAAA
27869812 ATCAATTTAA
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
29 9 0.11
31 58 0.73
33 13 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (31 bp):
AATTTAAATAATTAAATTTAAATTTAAGGTA
Found at i:27872876 original size:171 final size:167
Alignment explanation
Indices: 27872561--27872879 Score: 389
Period size: 168 Copynumber: 1.9 Consensus size: 167
27872551 CTCTAAATAA
* * * *
27872561 TTTTACTTTTCCCTTGAAACTTTTACTCACTCACTTTCCCCCAAAACTTTTACTTCCCTCTCATT
1 TTTTACTTTTCCCTTAAAACTTTTACTCACTCACTTTCCCCCAAAACATTTACTTCCCTCCCATC
*
27872626 CCACCCTCATCTACCCTAAACTCATCCCCCCCCTCATTTTTTTAATATTTTTCCTCCAAAATTTT
66 CCACCCTCATCTACCCTAAACTCATCCCCCCCCCCATTTTTTTAATATTTTTCCTCCAAAATTTT
* *
27872691 ATTTTCTCATTTACTTTCCCCAAAAACCCTCAAATTT
131 ATCTCCTCATTTACTTTCCCCAAAAACCCTCAAATTT
* * * *
27872728 TTTTA-TTTT-CCTTAAAACTTTTACTCCCTCCCCCTTTCCCCCTAAAACATTTACTTTCTTCCC
1 TTTTACTTTTCCCTTAAAACTTTTACTCACT--CACTTTCCCCC-AAAACATTTACTTCCCTCCC
*
27872791 ATCCCACTCC-CATTTATCCC-AAAC-CAATCCCCCCCCCCAATTTTTTTTGAATATTTTTCCTC
63 ATCCCAC-CCTCATCTA-CCCTAAACTC-ATCCCCCCCCCC-A-TTTTTTT-AATATTTTTCCTC
*
27872853 CAATATTTTACTCTCCT-ATTTACTTTC
122 CAAAATTTTA-TCTCCTCATTTACTTTC
27872880 TCTCAAATTT
Statistics
Matches: 129, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
165 18 0.14
166 4 0.03
167 16 0.12
168 42 0.33
169 6 0.05
170 7 0.05
171 32 0.25
172 4 0.03
ACGTcount: A:0.22, C:0.35, G:0.01, T:0.42
Consensus pattern (167 bp):
TTTTACTTTTCCCTTAAAACTTTTACTCACTCACTTTCCCCCAAAACATTTACTTCCCTCCCATC
CCACCCTCATCTACCCTAAACTCATCCCCCCCCCCATTTTTTTAATATTTTTCCTCCAAAATTTT
ATCTCCTCATTTACTTTCCCCAAAAACCCTCAAATTT
Found at i:27873381 original size:19 final size:19
Alignment explanation
Indices: 27873344--27873381 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
27873334 AAAAGTTAAT
*
27873344 AACAAATTTATTTATGGTG
1 AACAAATTTATTTACGGTG
27873363 AACAAATTTCA-TTACGGTG
1 AACAAATTT-ATTTACGGTG
27873382 GGTGACAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
AACAAATTTATTTACGGTG
Found at i:27875426 original size:25 final size:26
Alignment explanation
Indices: 27875377--27875426 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
27875367 GTCCAAATTC
* *
27875377 AAAAATTTCAAAAAAATTATAATTTT
1 AAAAACTTCAAAAAAAATATAATTTT
27875403 AAAAACTT-AAAAAAAATATAATTT
1 AAAAACTTCAAAAAAAATATAATTT
27875427 ATTATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAACTTCAAAAAAAATATAATTTT
Found at i:27876053 original size:24 final size:24
Alignment explanation
Indices: 27875996--27876056 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
27875986 GACTAATAAG
* * *
27875996 AGTTTGATTCAAACAAATAAACAG
1 AGTTTAATTGAAACAAATAAACAA
*
27876020 AGTTTAATTGAAACAAGTAAACAA
1 AGTTTAATTGAAACAAATAAACAA
27876044 AGTTTAATTGAAA
1 AGTTTAATTGAAA
27876057 GATTATTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (24 bp):
AGTTTAATTGAAACAAATAAACAA
Found at i:27880646 original size:2 final size:2
Alignment explanation
Indices: 27880639--27880710 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
27880629 AAGGCTGCTA
27880639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27880681 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
27880711 TTGTTAAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27883931 original size:21 final size:21
Alignment explanation
Indices: 27883895--27883941 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
27883885 AAATTTTGAA
*
27883895 TTTTAAAAATTATTTTA-AAT
1 TTTTGAAAATTATTTTATAAT
*
27883915 TTTTGAAAATTATTTTTATTAT
1 TTTTGAAAATTA-TTTTATAAT
27883937 TTTTG
1 TTTTG
27883942 TAATTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTGAAAATTATTTTATAAT
Found at i:27887040 original size:49 final size:49
Alignment explanation
Indices: 27886968--27887063 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
27886958 TATTATAATT
*
27886968 TGTAAATAAACAAATAGTACAAGTAGCATTAATAAAAGTGGGCCAAATA
1 TGTAAATAAACAAATAGTACAAGTACCATTAATAAAAGTGGGCCAAATA
27887017 TGTAAATAAACAAATAGTACAAGTACCATTAATAAAAGTGGGCCAAA
1 TGTAAATAAACAAATAGTACAAGTACCATTAATAAAAGTGGGCCAAA
27887064 ATAAAACAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (49 bp):
TGTAAATAAACAAATAGTACAAGTACCATTAATAAAAGTGGGCCAAATA
Found at i:27891152 original size:16 final size:15
Alignment explanation
Indices: 27891116--27891170 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 15
27891106 AACCATTTTA
*
27891116 AATTTACTTTGAAATT
1 AATTTA-TTTTAAATT
27891132 AAATTTATTTTAAATT
1 -AATTTATTTTAAATT
*
27891148 CAATTTTAATTTAAATT
1 -AA-TTTATTTTAAATT
27891165 AATTTA
1 AATTTA
27891171 ATATTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.12
16 12 0.35
17 18 0.53
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (15 bp):
AATTTATTTTAAATT
Found at i:27891161 original size:28 final size:28
Alignment explanation
Indices: 27891110--27891169 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
27891100 AGTCCAAACC
* * *
27891110 ATTTTAAATTTACTTTGAAATTAAATTT
1 ATTTTAAATTCAATTTGAAATTAAATTA
* *
27891138 ATTTTAAATTCAATTTTAATTTAAATTA
1 ATTTTAAATTCAATTTGAAATTAAATTA
27891166 ATTT
1 ATTT
27891170 AATATTATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTCAATTTGAAATTAAATTA
Found at i:27891168 original size:21 final size:21
Alignment explanation
Indices: 27891144--27891185 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27891134 ATTTATTTTA
*
27891144 AATTCAATTTTAATT-TAAATT
1 AATTCAATATT-ATTGTAAATT
*
27891165 AATTTAATATTATTGTAAATT
1 AATTCAATATTATTGTAAATT
27891186 TAATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTCAATATTATTGTAAATT
Found at i:27893162 original size:29 final size:29
Alignment explanation
Indices: 27893070--27893235 Score: 131
Period size: 29 Copynumber: 5.6 Consensus size: 29
27893060 CTCTGGAGGT
* *
27893070 CCCT-AAACTATCCTAAAATTATATTTTTA
1 CCCTAAAACT-TCCAAAAATTACATTTTTA
* ** **
27893099 ACCTCAAAACTTCTGGAAAATTACATTTTGG
1 CCCT-AAAACTTC-CAAAAATTACATTTTTA
*
27893130 CCCTAAAACTTCCAAAAATAACATTTTTA
1 CCCTAAAACTTCCAAAAATTACATTTTTA
*
27893159 CCCTCTAAAA-TT-CAATAAATTCCATTTTTAA
1 -CC-CTAAAACTTCCAA-AAATTACATTTTT-A
* *
27893190 CCCCAAAACTTCCAAAAATTACAATTTTA
1 CCCTAAAACTTCCAAAAATTACATTTTTA
**
27893219 CCCCCAAACTTCCAAAA
1 CCCTAAAACTTCCAAAA
27893236 TTCTATTTTT
Statistics
Matches: 110, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
29 40 0.36
30 40 0.36
31 30 0.27
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.32
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTACATTTTTA
Found at i:27893187 original size:30 final size:29
Alignment explanation
Indices: 27893074--27893281 Score: 147
Period size: 30 Copynumber: 7.0 Consensus size: 29
27893064 GGAGGTCCCT
* * *
27893074 AAACTATCCTAAAATTATATTTTTAACCTCA
1 AAACT-TCCAAAAATTACATTTTT-ACCCCA
** ** *
27893105 AAACTTCTGGAAAATTACATTTTGGCCCTA
1 AAACTTC-CAAAAATTACATTTTTACCCCA
*
27893135 AAACTTCCAAAAATAACATTTTTACCCTCTA
1 AAACTTCCAAAAATTACATTTTTACCC-C-A
*
27893166 AAA-TT-CAATAAATTCCATTTTTAACCCCA
1 AAACTTCCAA-AAATTACATTTTT-ACCCCA
* *
27893195 AAACTTCCAAAAATTACAATTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCA
*
27893224 AAACTTCC-AAAATT-CTATTTTTTGATCCCA
1 AAACTTCCAAAAATTAC-A-TTTTT-ACCCCA
**
27893254 AAACTTGTAAAAATTACCA-TTTTACCCC
1 AAACTTCCAAAAATTA-CATTTTTACCCC
27893282 TGAATGTCAA
Statistics
Matches: 140, Mismatches: 24, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 7 0.05
29 43 0.31
30 53 0.38
31 34 0.24
32 1 0.01
33 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCA
Found at i:27893295 original size:59 final size:59
Alignment explanation
Indices: 27893134--27893303 Score: 159
Period size: 59 Copynumber: 2.9 Consensus size: 59
27893124 TTTTGGCCCT
* * * * * *
27893134 AAAACTTCCAAAAATAACATTTTTACCCTCTAAAATTCAATAAAT-TCCA-TTTTTAACCCC
1 AAAACTTCCAAAAATTACAATTTTACCC-CCAAACTTCAA-AAATAT-CATTTTTTGATCCC
*
27893194 AAAACTTCCAAAAATTACAATTTTACCCCCAAACTTCCAAAAT-TCTATTTTTTGATCCC
1 AAAACTTCCAAAAATTACAATTTTACCCCCAAACTTCAAAAATATC-ATTTTTTGATCCC
** * **
27893253 AAAACTTGTAAAAATTACCATTTTACCCCTGAA-TGTCAAAAATATCATTTT
1 AAAACTTCCAAAAATTACAATTTTACCCCCAAACT-TCAAAAATATCATTTT
27893304 AACCCCTAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
57 1 0.01
58 7 0.08
59 57 0.61
60 28 0.30
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (59 bp):
AAAACTTCCAAAAATTACAATTTTACCCCCAAACTTCAAAAATATCATTTTTTGATCCC
Found at i:27900149 original size:49 final size:49
Alignment explanation
Indices: 27900086--27900257 Score: 138
Period size: 49 Copynumber: 3.5 Consensus size: 49
27900076 AAAGACACAA
* *
27900086 AAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAAAAGCATG
1 AAGGGAAAGATCTAAATCGCAACGGCGGACCGTGTACCTCAAAAGCATG
* * * * *
27900135 AAGGGAAAGATCTAAAACTGAAATGGCGGATCC-AGTACCGT--AAAGACA-A
1 AAGGGAAAGATCTAAATC-GCAACGGCGGA-CCGTGTACC-TCAAAAG-CATG
** * * *
27900184 AAGGGAAA-AGTCTAAATCGCAACGGCAAATCGTGCACCTCAGAAGCATG
1 AAGGGAAAGA-TCTAAATCGCAACGGCGGACCGTGTACCTCAAAAGCATG
*
27900233 AAGGGAAAGATCTAAGACCGCAACG
1 AAGGGAAAGATCTAA-ATCGCAACG
27900258 ACGAATCCAG
Statistics
Matches: 94, Mismatches: 18, Indels: 21
0.71 0.14 0.16
Matches are distributed among these distances:
47 2 0.02
48 14 0.15
49 50 0.53
50 25 0.27
51 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (49 bp):
AAGGGAAAGATCTAAATCGCAACGGCGGACCGTGTACCTCAAAAGCATG
Found at i:27900266 original size:98 final size:99
Alignment explanation
Indices: 27900037--27900278 Score: 290
Period size: 98 Copynumber: 2.4 Consensus size: 99
27900027 GAAATACAAC
* * *
27900037 GGGAAAGATCTAAGACTGCAACGGC-AGATACAATACCGCAAAGACACAAAAGGGAAAGGTCTAA
1 GGGAAAGATCTAAGACTGCAACGGCGA-ATCCAGTACCGCAAAGA-ACAAAAGGGAAAAGTCTAA
* ** *
27900101 GTCGCAACGGCGGACCGTGTACCTCAAAAGCATGAA
64 ATCGCAACGGCAAACCGTGCACCTCAAAAGCATGAA
* * * * *
27900137 GGGAAAGATCTAAAACTGAAATGGCGGATCCAGTACCGTAAAG-ACAAAAGGGAAAAGTCTAAAT
1 GGGAAAGATCTAAGACTGCAACGGCGAATCCAGTACCGCAAAGAACAAAAGGGAAAAGTCTAAAT
* *
27900201 CGCAACGGCAAATCGTGCACCTCAGAAGCATGAA
66 CGCAACGGCAAACCGTGCACCTCAAAAGCATGAA
* * * *
27900235 GGGAAAGATCTAAGACCGCAACGACGAATCCAGTAACACAAAGA
1 GGGAAAGATCTAAGACTGCAACGGCGAATCCAGTACCGCAAAGA
27900279 TTTGAAGGGA
Statistics
Matches: 117, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
98 82 0.70
100 35 0.30
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (99 bp):
GGGAAAGATCTAAGACTGCAACGGCGAATCCAGTACCGCAAAGAACAAAAGGGAAAAGTCTAAAT
CGCAACGGCAAACCGTGCACCTCAAAAGCATGAA
Found at i:27900512 original size:40 final size:40
Alignment explanation
Indices: 27900458--27900608 Score: 108
Period size: 40 Copynumber: 3.5 Consensus size: 40
27900448 CAATTCATAT
27900458 CCTCT-TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTA
1 CCTCTCTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTA
* *** * *
27900497 CCTCTCTGAAGTTGTATTAAGAGCAAGATGAAGATTCAAACATCCATT-
1 CCTCTCTGAAGTTGTAGTAA-AGTTGGAT--AG---C-AA-GT-CTTTA
27900545 CCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTA
1 CC--T-CTC-TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTA
*
27900589 TCTCTCTGAAGTTGTAGTAA
1 CCTCTCTGAAGTTGTAGTAA
27900609 GACCAAGATG
Statistics
Matches: 84, Mismatches: 13, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
39 5 0.06
40 27 0.32
41 8 0.10
42 1 0.01
43 5 0.06
44 2 0.02
45 2 0.02
46 2 0.02
47 2 0.02
48 3 0.04
49 5 0.06
50 1 0.01
51 8 0.10
52 13 0.15
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (40 bp):
CCTCTCTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTA
Found at i:27900553 original size:92 final size:92
Alignment explanation
Indices: 27900391--27901298 Score: 1609
Period size: 92 Copynumber: 9.9 Consensus size: 92
27900381 TTAGATCAAA
* * * *
27900391 ATAGTAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCAT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27900456 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * * *
27900483 ATAGCAAGTCTTTACCTCTCTGAAGTTGTATTAAGAGCAAGATGAAGATTCAAACATCCATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27900548 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27900575 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGACCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27900640 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
27900667 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGTTTTAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27900732 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
27900759 ATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAATATGAAGCTTCAAACATCAATTTCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27900824 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
27900851 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
27900916 ATCCACTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27900943 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27901008 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27901035 ATAGCAAGTCTTTATCTCTATGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27901100 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
**
27901127 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAATTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27901192 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27901219 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27901284 ATCCTCTTGAAGTTG
66 ATCCTCTTGAAGTTG
27901299 GCAAGTCTTT
Statistics
Matches: 777, Mismatches: 39, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 777 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (92 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGTAGTAAAGTTGG
Found at i:27900705 original size:184 final size:184
Alignment explanation
Indices: 27900391--27901434 Score: 1767
Period size: 184 Copynumber: 5.8 Consensus size: 184
27900381 TTAGATCAAA
* * * *
27900391 ATAGTAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCAT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
* *
27900456 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTACCTCTCTGAAGTTGTATTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
* *
27900521 AAGATGAAGATTCAAACATCCATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
131 AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27900575 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGACCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27900640 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
* *
27900705 AAGATAAAGTTTTAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
131 AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
27900759 ATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAATATGAAGCTTCAAACATCAATTTCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
27900824 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
*
27900889 AAGATGAAGTTTCAAACATCAATTCCTATCCACTTGAAGTTGTAGTAAAGTTGG
131 AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27900943 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
27901008 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTATGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
*
27901073 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
131 AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
**
27901127 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAATTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27901192 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
27901257 AAGATGAAGTTTCAAACATCAATTCCTATCCTC-------T-T-G--AAGTT-G
131 AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
*
27901299 ---GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
* *
27901361 ATCCTCTTGAAGTTGTAGTAAAGTTGGGTAGCAAGTCTTTATCTCTCTGAAGTTGTAGCAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
27901426 AAGATGAAG
131 AAGATGAAG
27901435 CCTCGACATC
Statistics
Matches: 825, Mismatches: 35, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
169 133 0.16
172 1 0.00
173 5 0.01
175 1 0.00
176 1 0.00
177 1 0.00
184 683 0.83
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (184 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGG
Found at i:27900894 original size:276 final size:276
Alignment explanation
Indices: 27900391--27901435 Score: 1751
Period size: 276 Copynumber: 3.8 Consensus size: 276
27900381 TTAGATCAAA
* * * *
27900391 ATAGTAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCAT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
* *
27900456 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTACCTCTCTGAAGTTGTATTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
* *
27900521 AAGATGAAGATTCAAACATCCATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
131 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
*
27900586 TTATCTCTCTGAAGTTGTAGTAAGACCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAA
196 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAA
27900651 GTTGTAGTAAAGTTGG
261 GTTGTAGTAAAGTTGG
* * *
27900667 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGTTTTAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
27900732 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
* * *
27900797 AATATGAAGCTTCAAACATCAATTTCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGTAAGTCT
131 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
* *
27900862 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCACTTGAA
196 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAA
27900927 GTTGTAGTAAAGTTGG
261 GTTGTAGTAAAGTTGG
*
27900943 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
*
27901008 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTATGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
27901073 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
131 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
**
27901138 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAATTTCAAACATCAATTCCTATCCTCTTGAA
196 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAA
27901203 GTTGTAGTAAAGTTGG
261 GTTGTAGTAAAGTTGG
*
27901219 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
27901284 ATCCTC-------T-T-G--AAGTT-G---GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
66 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
* *
27901334 AAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGGTAGCAAGTCT
131 AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
*
27901399 TTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAGC
196 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
27901436 CTCGACATCA
Statistics
Matches: 732, Mismatches: 37, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
261 131 0.18
264 1 0.00
265 5 0.01
267 1 0.00
268 1 0.00
269 1 0.00
276 592 0.81
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (276 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGC
AAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCT
TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGAA
GTTGTAGTAAAGTTGG
Found at i:27900967 original size:40 final size:40
Alignment explanation
Indices: 27900923--27901252 Score: 162
Period size: 40 Copynumber: 7.3 Consensus size: 40
27900913 CCTATCCACT
27900923 TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
1 TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
*** *
27900963 TGAAGTTGTAGTAAGAGGAAGATGAAGCTTCAAACATCAATTCCTATC-CTC
1 TGAAGTTGTAGTAA-AGTTGGAT--AG---C-AA-GTC--TT--TATCTCTC
*
27901014 TTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTA
1 -TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
*** *
27901055 TGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC-CTC
1 TGAAGTTGTAGTAA-AGTTGGAT--AG---C-AA-GTC--TT--TATCTCTC
27901106 TTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
1 -TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
* * ** *
27901147 TGAAGTTGTAGTAAGAGCAAGATGAAATTTCAAACATCAATTCCTATC-CTC
1 TGAAGTTGTAGT---A--AAGTTG-GATAGC-AA-GTC--TT--TATCTCTC
27901198 TTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
1 -TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
27901239 TGAAGTTGTAGTAA
1 TGAAGTTGTAGTAA
27901253 GAGCAAGATG
Statistics
Matches: 220, Mismatches: 28, Indels: 84
0.66 0.08 0.25
Matches are distributed among these distances:
40 66 0.30
41 18 0.08
42 6 0.03
43 5 0.02
44 6 0.03
45 11 0.05
46 10 0.05
47 11 0.05
48 6 0.03
49 5 0.02
50 6 0.03
51 18 0.08
52 52 0.24
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (40 bp):
TGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTC
Found at i:27901349 original size:77 final size:77
Alignment explanation
Indices: 27901222--27901375 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
27901212 AAGTTGGATA
27901222 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATC
1 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATC
27901287 CTCTTGAAGTTG
66 CTCTTGAAGTTG
27901299 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATC
1 GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATC
27901364 CTCTTGAAGTTG
66 CTCTTGAAGTTG
27901376 TAGTAAAGTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (77 bp):
GCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATC
CTCTTGAAGTTG
Found at i:27901711 original size:17 final size:15
Alignment explanation
Indices: 27901689--27901747 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 15
27901679 CCAAACCATT
27901689 TTAAATTTACTTTGAAA
1 TTAAATTTA-TTT-AAA
27901706 TTAAATTTATTTTAAA
1 TTAAATTTA-TTTAAA
*
27901722 TTCAATTTTAATTTAAA
1 TT-AAATTT-ATTTAAA
27901739 TTAAATTTA
1 TTAAATTTA
27901748 ATGTTATTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.03
16 10 0.27
17 25 0.68
18 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (15 bp):
TTAAATTTATTTAAA
Found at i:27901737 original size:28 final size:28
Alignment explanation
Indices: 27901686--27901740 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
27901676 GGCCCAAACC
* *
27901686 ATTTTAAATTTACTTTGAAATTAAATTT
1 ATTTTAAATTCAATTTGAAATTAAATTT
* *
27901714 ATTTTAAATTCAATTTTAATTTAAATT
1 ATTTTAAATTCAATTTGAAATTAAATT
27901741 AAATTTAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTCAATTTGAAATTAAATTT
Found at i:27901748 original size:11 final size:11
Alignment explanation
Indices: 27901688--27901748 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
27901678 CCCAAACCAT
* *
27901688 TTTAAATTTAC
1 TTTAAATTAAA
27901699 TTTGAAATTAAA
1 TTT-AAATTAAA
**
27901711 TTTATTTTAAA
1 TTTAAATTAAA
* * *
27901722 TTCAATTTTAA
1 TTTAAATTAAA
27901733 TTTAAATTAAA
1 TTTAAATTAAA
27901744 TTTAA
1 TTTAA
27901749 TGTTATTGTA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 30 0.77
12 9 0.23
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:27901760 original size:22 final size:22
Alignment explanation
Indices: 27901717--27901762 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
27901707 TAAATTTATT
*
27901717 TTAAATTCAATTTTAATTTAAA
1 TTAAATTCAATGTTAATTTAAA
*
27901739 TTAAATTTAATGTT-ATTGTAAA
1 TTAAATTCAATGTTAATT-TAAA
27901761 TT
1 TT
27901763 TAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAAATTCAATGTTAATTTAAA
Found at i:27903749 original size:30 final size:29
Alignment explanation
Indices: 27903643--27903848 Score: 98
Period size: 30 Copynumber: 6.9 Consensus size: 29
27903633 CTCTAAACTA
* * *
27903643 TCCAAAAATTATATGTTTAACCCAAAAACT
1 TCCAAAAATTATATTTTTACCCCTAAAA-T
** * * *
27903673 TCTGGAAAATTACATTTTGATCCC-AAAACT
1 TC-CAAAAATTATATTTTTACCCCTAAAA-T
** * *
27903703 TTTAAAAATGACATTTTTACCCCTTAAAAT
1 TCCAAAAATTATATTTTTACCCC-TAAAAT
* *
27903733 TCCAAAAATTTTATTTTTGACACC-AAAACT
1 TCCAAAAATTATATTTTT-ACCCCTAAAA-T
* *
27903763 TCCAAAAATTACATTTTTACCCCCTAAACT
1 TCCAAAAATTATATTTTTA-CCCCTAAAAT
* * *
27903793 TCC-AAAATTCTATTTTTTGACCCCGAAACT
1 TCCAAAAATTATA-TTTTT-ACCCCTAAAAT
* *
27903823 TAC-AAAATTACCA-TTTTACCCCTAAA
1 TCCAAAAATTA-TATTTTTACCCCTAAA
27903849 TGTCAAAAAT
Statistics
Matches: 137, Mismatches: 29, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
28 8 0.06
29 32 0.23
30 69 0.50
31 28 0.20
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTATATTTTTACCCCTAAAAT
Found at i:27903838 original size:60 final size:60
Alignment explanation
Indices: 27903687--27903848 Score: 181
Period size: 60 Copynumber: 2.7 Consensus size: 60
27903677 GAAAATTACA
** * * *
27903687 TTTTGATC-CCAAAACTTTTAAAAATGACATTTTTACCCCTTAAAATTCCAAAAATTTTAT
1 TTTTGA-CACCAAAACTTACAAAAATTACATTTTTACCCCCTAAAATTCCAAAAATTCTAT
* *
27903747 TTTTGACACCAAAACTTCCAAAAATTACATTTTTACCCCCTAAACTTCC-AAAATTCTATT
1 TTTTGACACCAAAACTTACAAAAATTACATTTTTACCCCCTAAAATTCCAAAAATTCTA-T
* *
27903807 TTTTGACCCCGAAACTTAC-AAAATTACCA-TTTTA-CCCCTAAA
1 TTTTGACACCAAAACTTACAAAAATTA-CATTTTTACCCCCTAAA
27903849 TGTCAAAAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
58 8 0.09
59 21 0.23
60 61 0.68
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (60 bp):
TTTTGACACCAAAACTTACAAAAATTACATTTTTACCCCCTAAAATTCCAAAAATTCTAT
Found at i:27903857 original size:28 final size:30
Alignment explanation
Indices: 27903826--27903897 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
27903816 CGAAACTTAC
27903826 AAAATTACCATTTT-ACCCCTAAA-TGTCA
1 AAAATTACCATTTTAACCCCTAAATTGTCA
* *
27903854 AAAATGT--CATTTTAACCCCTAAATTTTTCC
1 AAAAT-TACCATTTTAACCCCTAAA-TTGTCA
27903884 AAAATTACCATTTT
1 AAAATTACCATTTT
27903898 TCCCTCGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 6 0.17
28 14 0.39
29 2 0.06
30 8 0.22
31 6 0.17
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCTAAATTGTCA
Found at i:27903918 original size:28 final size:28
Alignment explanation
Indices: 27903881--27903943 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
27903871 CCTAAATTTT
* *
27903881 TCCAAAATTACCATTTTTCCCTCGAGTG
1 TCCAAAATTACCATTTTGCCCCCGAGTG
* *
27903909 TCCAAAATTACTATTTTGCCCCCGGGTG
1 TCCAAAATTACCATTTTGCCCCCGAGTG
27903937 TCCAAAA
1 TCCAAAA
27903944 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.32
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCCCGAGTG
Found at i:27907074 original size:25 final size:25
Alignment explanation
Indices: 27907033--27907083 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
27907023 ATCTTTATAC
*
27907033 ATATTGAATTTTCATATCAATAAAT
1 ATATTGAATTTTAATATCAATAAAT
**
27907058 ATATTG-ATTTATAATATGTATAAAT
1 ATATTGAATTT-TAATATCAATAAAT
27907083 A
1 A
27907084 AATTTTACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
ATATTGAATTTTAATATCAATAAAT
Found at i:27911274 original size:59 final size:58
Alignment explanation
Indices: 27910926--27911448 Score: 668
Period size: 58 Copynumber: 8.9 Consensus size: 58
27910916 TAAGAAACGA
** * * *
27910926 TGAAATCGGGGTGGAAAATGGGACTTTTGGATA-CTCGGGGGCAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTTAAAAAT-GGAATTTTGGA-AGTTCGGGGGTAAAATGGTAATTTTTGG
* * *
27910984 TGAAATCGGGGTTAAAAATGGAATTTTTGAGGCTTCGAGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAG-TTCGGGGGTAAAATGGTAATTTTTGG
27911043 TGAAATC-GGGTTAAAAATGGAATTTTGGAAGTTCGAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCG-GGGGTAAAATGGTAATTTTTGG
* *
27911101 TGAAATCGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
*
27911159 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT-G
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * *
27911216 -GAAGTTTCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATTGTAATTTTTGG
1 TGAA--ATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGGGGGTAAAATGGTAATTTTTGG
27911276 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTT-G
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * *
27911333 -GAAGTTTTGGTGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTT-G
1 TGAA--ATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * *
27911392 -GAAGTTGTGGGGTTAAAAATGAAATTTTGGAATGTTTGGGGGTAAAATGGTAATTTT
1 TGAA-AT-CGGGGTTAAAAATGGAATTTTGGAA-GTTCGGGGGTAAAATGGTAATTTT
27911449 GGAAGTTTCG
Statistics
Matches: 418, Mismatches: 32, Indels: 29
0.87 0.07 0.06
Matches are distributed among these distances:
56 6 0.01
57 15 0.04
58 231 0.55
59 162 0.39
60 1 0.00
61 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (58 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
Found at i:27911454 original size:117 final size:116
Alignment explanation
Indices: 27910926--27911458 Score: 690
Period size: 117 Copynumber: 4.6 Consensus size: 116
27910916 TAAGAAACGA
** * * * *
27910926 TGAAATCGGGGTGGAAAATGGGACTTTTGGATA-CTCGGGGGCAAAATGGTAATTTTGGTGAA--
1 TGAAATCGGGGTTAAAAAT-GGAATTTTGGA-AGTTCGGGGGTAAAATGGTAATTTTTG-GAAGT
* * * * *
27910988 ATCGGGGTTAAAAATGGAATTTTTGAGGCTTCGAGGGTAAAATGGTAATTTTTGG
63 TTCGAGGTTAAAAATGGAATTTTGGAAG-TTCGGGGGTAAAATGGTAATTTTTGG
27911043 TGAAATC-GGGTTAAAAATGGAATTTTGGAAGTTCGAGGGGTAAAATGGTAATTTTTGGTGAA--
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCG-GGGGTAAAATGGTAATTTTT-G-GAAGT
* *
27911105 ATCGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTTGG
63 TTCGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
*
27911159 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTC
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTC
* *
27911224 GAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATTGTAATTTTTGG
66 GAGGTTAAAAATGGAATTTTGG-AAGTTCGGGGGTAAAATGGTAATTTTTGG
*
27911276 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTT
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTC
27911341 G-GTGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTT-G
66 GAG-GTTAAAAATGGAATTTTGG-AAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * *
27911392 -GAAGTTGTGGGGTTAAAAATGAAATTTTGGAATGTTTGGGGGTAAAATGGTAA-TTTTGGAAGT
1 TGAA-AT-CGGGGTTAAAAATGGAATTTTGGAA-GTTCGGGGGTAAAATGGTAATTTTTGGAAGT
27911455 TTCG
63 TTCG
27911459 GGGACCTATA
Statistics
Matches: 380, Mismatches: 25, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
114 4 0.01
115 17 0.04
116 104 0.27
117 236 0.62
118 19 0.05
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34
Consensus pattern (116 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTC
GAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG
Found at i:27911754 original size:161 final size:162
Alignment explanation
Indices: 27911520--27911860 Score: 508
Period size: 162 Copynumber: 2.1 Consensus size: 162
27911510 AGGCATGCAG
* * * *
27911520 CAGTCAAGGGATTAAATTGTAAACCTTGAAAAATTCTTGAGGCAATTTTATAATTAAATAAGAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGAGGCAATTTTATAATTAAATAAAAGT
*
27911585 TGATTT-GGGATTAAATTAAAATAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAA
66 TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAA
*
27911649 AGTGACACGTGGCAGCCCCTGGTGCAGTCAAA
131 AGTGACACGTGGCAGCACCTGGTGCAGTCAAA
* * *
27911681 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATTGTTG-GGCCAATTTTGTAATTAAATAAAAG
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGAGG-CAATTTTATAATTAAATAAAAG
27911745 TTGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAA
65 TTGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAA
* * * *
27911810 CAGTGACACGTGGCATCATCTGGTGCATTCAAA
130 AAGTGACACGTGGCAGCACCTGGTGCAGTCAAA
* *
27911843 -ATGTGAAAGGATTAAATT
1 CA-GTCAAAGGACTAAATT
27911861 GAAAAGCAAT
Statistics
Matches: 161, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
160 2 0.01
161 62 0.39
162 97 0.60
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (162 bp):
CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGAGGCAATTTTATAATTAAATAAAAGT
TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAA
AGTGACACGTGGCAGCACCTGGTGCAGTCAAA
Found at i:27913463 original size:17 final size:17
Alignment explanation
Indices: 27913442--27913522 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
27913432 AATATTAAAT
*
27913442 TTTAAATTAAATTCTAA
1 TTTAAATTAAATTATAA
* * *
27913459 CTTAAATAAAATTAAAA
1 TTTAAATTAAATTATAA
*
27913476 TTTAAATTAAATTAAAA
1 TTTAAATTAAATTATAA
*
27913493 TTTAAAATAAATT-TAA
1 TTTAAATTAAATTATAA
*
27913509 TTTCAAAGTAAATT
1 TTT-AAATTAAATT
27913523 CTAAAATGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
16 5 0.09
17 49 0.91
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTAAATTATAA
Found at i:27913470 original size:22 final size:23
Alignment explanation
Indices: 27913435--27913500 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 23
27913425 TACAAATAAT
*
27913435 ATTAAATTTTAAATT-AAATTCTAA
1 ATTAAA-TTAAAATTAAAATT-TAA
*
27913459 CTTAAA-TAAAATTAAAATTTAA
1 ATTAAATTAAAATTAAAATTTAA
27913481 ATTAAATTAAAATTTAAAAT
1 ATTAAATTAAAA-TTAAAAT
27913501 AAATTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 14 0.39
23 10 0.28
24 12 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTAAATTAAAATTAAAATTTAA
Found at i:27913473 original size:34 final size:34
Alignment explanation
Indices: 27913428--27913526 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 34
27913418 TTAAATTTAC
*
27913428 AAATAATATTAAATTTTAAATTAAATTCTAACTT
1 AAATAAAATTAAATTTTAAATTAAATTCTAACTT
* ** *
27913462 AAATAAAATTAAAATTTAAATTAAATTAAAATTT
1 AAATAAAATTAAATTTTAAATTAAATTCTAACTT
* * *
27913496 AAA-ATAAATTTAATTTCAAAGTAAATTCTAA
1 AAATA-AAATTAAATTTTAAATTAAATTCTAA
27913527 AATGGTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 1 0.02
34 52 0.98
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (34 bp):
AAATAAAATTAAATTTTAAATTAAATTCTAACTT
Found at i:27913497 original size:12 final size:11
Alignment explanation
Indices: 27913435--27913527 Score: 64
Period size: 12 Copynumber: 8.1 Consensus size: 11
27913425 TACAAATAAT
27913435 ATTAAATTTTAA
1 ATTAAA-TTTAA
27913447 ATTAAATTCTAA
1 ATTAAATT-TAA
* *
27913459 CTTAAA-TAAA
1 ATTAAATTTAA
27913469 ATTAAAATTTAA
1 ATT-AAATTTAA
*
27913481 ATTAAATTAAA
1 ATTAAATTTAA
*
27913492 ATTTAAA-ATAA
1 A-TTAAATTTAA
*
27913503 ATTTAATTTCAA
1 ATTAAATTT-AA
*
27913515 AGTAAATTCTAA
1 ATTAAATT-TAA
27913527 A
1 A
27913528 ATGGTTTGGG
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
10 8 0.13
11 18 0.29
12 36 0.57
13 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:27913884 original size:76 final size:76
Alignment explanation
Indices: 27913798--27914579 Score: 904
Period size: 76 Copynumber: 10.8 Consensus size: 76
27913788 TGCTCTTTAG
* * *
27913798 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
27913863 ACTTTAATTTC
66 ACTTCAATTTC
* *
27913874 AGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27913939 ACTTCAATTTC
66 ACTTCAATTTC
* * *
27913950 AGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--CTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
27914013 --TT--ACTTC
66 ACTTCAATTTC
* *
27914020 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914079 ACTTCAATTTC
66 ACTTCAATTTC
* * *
27914090 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGACGATAGGAAAAGATCTTG--CTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
27914153 --TT--ACTTC
66 ACTTCAATTTC
* * * *
27914160 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914219 ACTTCAATTTC
66 ACTTCAATTTC
* * *
27914230 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914295 ACTTCAATTTC
66 ACTTCAATTTC
* * * * * *
27914306 AGAGATAAAGACTTGTTATCCAACTTTACTCCCATTTCAAGAGGATAGGGAATGATGTTGTTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914371 ACTTCAATTTC
66 ACTTCAATTTC
** * * * *
27914382 AGAGATAGCGACTCTTTTATCCAACTCTACTTCAATTTCAAGCGGAT-------GACCTTGCTCT
1 AGAGATAAAGACT-TGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCT
27914440 TACTTCAATTTC
65 TACTTCAATTTC
* * *
27914452 AGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGAT-------GATGTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914509 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
27914520 AGAGATGAAGACATGTTATCTAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
1 AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
27914580 GTGTGGTTTG
Statistics
Matches: 617, Mismatches: 56, Indels: 66
0.83 0.08 0.09
Matches are distributed among these distances:
64 105 0.17
66 5 0.01
68 67 0.11
69 29 0.05
70 46 0.07
72 4 0.01
74 6 0.01
76 327 0.53
77 28 0.05
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:27914057 original size:64 final size:64
Alignment explanation
Indices: 27913956--27914225 Score: 378
Period size: 64 Copynumber: 4.0 Consensus size: 64
27913946 TTTCAGAGAT
*
27913956 AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTTACTTC
1 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTTACTTC
27914020 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCA
1 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--CTT--TT--
*
27914085 ATTTC
60 ACTTC
*
27914090 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGACGATAGGAAAAGATCTTGCTTTT
1 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTT
27914155 ACTTC
60 ACTTC
* **
27914160 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCATACTTC
1 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTTACTTC
27914224 AA
1 AA
27914226 TTTCAGAGAT
Statistics
Matches: 186, Mismatches: 8, Indels: 24
0.85 0.04 0.11
Matches are distributed among these distances:
64 115 0.62
66 3 0.02
68 2 0.01
70 8 0.04
72 2 0.01
74 3 0.02
76 53 0.28
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (64 bp):
AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTTACTTC
Found at i:27914137 original size:140 final size:141
Alignment explanation
Indices: 27913798--27914579 Score: 787
Period size: 140 Copynumber: 5.4 Consensus size: 141
27913788 TGCTCTTTAG
* * * *
27913798 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
1 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--C-T
* * *
27913863 ACTTTAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAG
63 --TTT-ACTTC----A-AAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
27913928 ATCTTGCTCTTACTTCAATTTC
120 ATCTTGCTCTTACTTCAATTTC
*
27913950 AGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTT
1 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTT
* *
27914015 ACTTC-AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
66 ACTTCAAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914079 ACTTCAATTTC
131 ACTTCAATTTC
* * *
27914090 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGACGATAGGAAAAGATCTTGCTTTT
1 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTT
* * * *
27914155 ACTTC-AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
66 ACTTCAAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
27914219 ACTTCAATTTC
131 ACTTCAATTTC
* * *
27914230 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--CTT
* * * * *
27914295 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTCCCATTTCAAGAGGATAGGGAATG
64 --TT--ACTTC----A-AAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
* *
27914360 ATGTTGTTCTTACTTCAATTTC
120 ATCTTGCTCTTACTTCAATTTC
** * * * * * *** * *
27914382 AGAGATAGCGACTCTTTTATCCAACTCTACTTCAATTTCAAGCGGAT--GACCTTGCTCTTACTT
1 AGAGATAAAGAC-GTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGA-AAAGATCTTGCTT
** * * * *
27914445 CAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGAT-------GATGT
64 TTACTTC----A-AAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCT
27914502 TGCTCTTACTTCAATTTC
124 TGCTCTTACTTCAATTTC
* * *
27914520 AGAGATGAAGACATGTTATCTAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
1 AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
27914580 GTGTGGTTTG
Statistics
Matches: 554, Mismatches: 60, Indels: 46
0.84 0.09 0.07
Matches are distributed among these distances:
137 28 0.05
138 36 0.06
139 2 0.00
140 256 0.46
142 3 0.01
144 2 0.00
145 21 0.04
146 33 0.06
147 3 0.01
149 1 0.00
150 4 0.01
151 2 0.00
152 132 0.24
153 31 0.06
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (141 bp):
AGAGATAAAGACGTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTT
ACTTCAAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:27914193 original size:32 final size:32
Alignment explanation
Indices: 27914096--27914193 Score: 76
Period size: 32 Copynumber: 3.1 Consensus size: 32
27914086 TTTCAGAGAT
27914096 AAAGACTTGATATCCAGCTTTACTTCAATTTC
1 AAAGACTTGATATCCAGCTTTACTTCAATTTC
*** * * ** *
27914128 -AAGAC--GATAGGAAAAGATCTTGCTTTTACTTC
1 AAAGACTTGATA--TCCAGCT-TTACTTCAATTTC
27914160 AAAGACTTGATATCCAGCTTTACTTCAATTTC
1 AAAGACTTGATATCCAGCTTTACTTCAATTTC
27914192 AA
1 AA
27914194 GAGGATAGGA
Statistics
Matches: 44, Mismatches: 16, Indels: 12
0.61 0.22 0.17
Matches are distributed among these distances:
29 4 0.09
31 8 0.18
32 20 0.45
33 8 0.18
35 4 0.09
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (32 bp):
AAAGACTTGATATCCAGCTTTACTTCAATTTC
Found at i:27914262 original size:216 final size:216
Alignment explanation
Indices: 27913798--27914579 Score: 782
Period size: 216 Copynumber: 3.6 Consensus size: 216
27913788 TGCTCTTTAG
* * * * *
27913798 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAACGATCTTGCTCAT
1 AGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGAT-GGAAAAGATCTTGCTCTT
* * * *
27913863 ACTTTAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
* * * * *
27913928 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGAC-GTGATATCCAGCTTTACTTCAATTTCAAGA
130 ATCTTG-TCTTA-TT-AACTTCA-AGAT-ACGACTCTGATATCCAACTCTACTTCAATTTCAAGA
*** * * * ** *
27913992 GGATAGGA-AAAGATCTTGCTTTTACTTC
190 GGAT--GACCTTGCTCATACTTCAATTTC
* * * *
27914020 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGAT-GGAAAAGATCTTGCTCTT
* *
27914079 ACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGACGATAGGAAAAG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
* *
27914144 ATCTTG-CTT-TT-ACTTC-A-A-A-GACT-TGATATCCAGCTTTACTTCAATTTCAAGAGGATA
130 ATCTTGTCTTATTAACTTCAAGATACGACTCTGATATCCAACTCTACTTCAATTTCAAGAGGAT-
27914201 GGAAACGATCTTGCTCATACTTCAATTTC
194 -G--AC---CTTGCTCATACTTCAATTTC
*
27914230 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGAT-GGAAAAGATCTTGCTCTT
* * * * *
27914295 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTCCCATTTCAAGAGGATAGGGAATG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
* * ** *
27914360 ATGTTGTTCTTACTTCAATTTCAGAGATAGCGACTCTTTTATCCAACTCTACTTCAATTTCAAGC
130 ATCTTG-TCTTA-TT-AACTTCA-AGATA-CGACTCTGATATCCAACTCTACTTCAATTTCAAGA
*
27914425 GGATGACCTTGCTCTTACTTCAATTTC
190 GGATGACCTTGCTCATACTTCAATTTC
*
27914452 AGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGAGGAT------GATGTTGCTCTTA
1 AGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGATGGAAAAGATCTTGCTCTTA
* * *
27914510 CTTCAATTTCAGAGATGAAGACATGTTATCTAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGA
66 CTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGA
27914575 TCTTG
131 TCTTG
27914580 GTGTGGTTTG
Statistics
Matches: 483, Mismatches: 51, Indels: 60
0.81 0.09 0.10
Matches are distributed among these distances:
204 39 0.08
205 1 0.00
206 1 0.00
207 1 0.00
208 1 0.00
210 15 0.03
212 2 0.00
214 76 0.16
216 237 0.49
218 3 0.01
220 2 0.00
221 24 0.05
222 43 0.09
224 1 0.00
225 3 0.01
226 1 0.00
227 1 0.00
228 4 0.01
229 28 0.06
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (216 bp):
AGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGATGGAAAAGATCTTGCTCTTA
CTTCAATTTCAGAGATAAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGA
TCTTGTCTTATTAACTTCAAGATACGACTCTGATATCCAACTCTACTTCAATTTCAAGAGGATGA
CCTTGCTCATACTTCAATTTC
Found at i:27914335 original size:38 final size:37
Alignment explanation
Indices: 27914218--27914558 Score: 114
Period size: 38 Copynumber: 9.4 Consensus size: 37
27914208 ATCTTGCTCA
* *
27914218 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTT
*
27914256 TACTTCAATTTCAAGAGGATGGGAAAAGATCTTG-----CTC-T
1 TACTTCAATTTC-AGA-GAT----AAAGA-CTTGTTATCCACTT
27914294 TACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTT
* * ** * * *
27914332 TACTCCCATTTCAAGAGGATAGGGAATGATGTTGT--TC-T
1 TACTTCAATTTC-AGA-GATAAAGACT--TGTTATCCACTT
** * *
27914370 TACTTCAATTTCAGAGATAGCGACTCTTTTATCCAACTC
1 TACTTCAATTTCAGAGATAAAGACT-TGTTATCC-ACTT
*** * *
27914409 TACTTCAATTTCA-AGCGGATGACCTTG-----CTC-T
1 TACTTCAATTTCAGAGATAAAGA-CTTGTTATCCACTT
* *
27914440 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCACTT
** * * *
27914477 TACTTCAATTTCA-AGAGGATGA--TG-T-TGCTC-T
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCACTT
* * *
27914508 TACTTCAATTTCAGAGATGAAGACATGTTATCTAGCTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTATCCA-CTT
27914546 TACTTCAATTTCA
1 TACTTCAATTTCA
27914559 AGAGGATAGG
Statistics
Matches: 220, Mismatches: 46, Indels: 74
0.65 0.14 0.22
Matches are distributed among these distances:
31 33 0.15
32 21 0.10
33 2 0.01
34 4 0.02
35 5 0.02
36 21 0.10
37 21 0.10
38 66 0.30
39 23 0.10
40 11 0.05
42 5 0.02
44 5 0.02
45 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (37 bp):
TACTTCAATTTCAGAGATAAAGACTTGTTATCCACTT
Found at i:27914497 original size:68 final size:68
Alignment explanation
Indices: 27914367--27914565 Score: 281
Period size: 68 Copynumber: 2.9 Consensus size: 68
27914357 ATGATGTTGT
** * * *
27914367 TCTTACTTCAATTTCAGAGATAGCGACTCTTTTATCCAACTCTACTTCAATTTCAAGCGGATGAC
1 TCTTACTTCAATTTCAGAGATAAAGAC-ATGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
27914432 CTTGC
64 CTTGC
**
27914437 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGATGT
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACCT
27914502 TGC
66 TGC
* * *
27914505 TCTTACTTCAATTTCAGAGATGAAGACATGTTATCTAGCTTTACTTCAATTTCAAGAGGAT
1 TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCA-CTCTACTTCAATTTCAAGAGGAT
27914566 AGGAAAAGAT
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
68 64 0.54
69 29 0.25
70 25 0.21
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (68 bp):
TCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATGACCT
TGC
Found at i:27914512 original size:31 final size:32
Alignment explanation
Indices: 27914409--27914565 Score: 102
Period size: 31 Copynumber: 4.6 Consensus size: 32
27914399 TATCCAACTC
* **
27914409 TACTTCAATTTCAAGCGGATG-ACCTTGCTCT
1 TACTTCAATTTCAAGAGGATGAATGTTGCTCT
** * * *
27914440 TACTTCAATTTCAGAGATAAAGACATGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGA-ATG-T-TGCTCT
27914476 CTACTTCAATTTCAAGAGGATG-ATGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGAATGTTGCTCT
* * *
27914508 TACTTCAATTTCAGAGATGAAGACATGTTATCTAGCTT
1 TACTTCAATTTCA-AGAGGATGA-ATGTT-GCT--C-T
27914546 TACTTCAATTTCAAGAGGAT
1 TACTTCAATTTCAAGAGGAT
27914566 AGGAAAAGAT
Statistics
Matches: 95, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
31 26 0.27
32 14 0.15
33 1 0.01
34 9 0.09
35 3 0.03
36 9 0.09
37 19 0.20
38 14 0.15
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (32 bp):
TACTTCAATTTCAAGAGGATGAATGTTGCTCT
Found at i:27926766 original size:58 final size:58
Alignment explanation
Indices: 27926686--27927219 Score: 629
Period size: 58 Copynumber: 9.2 Consensus size: 58
27926676 CCAGGGCAAT
* * *
27926686 ATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAGGCTTCGAGGGTAAA
1 ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAG-TTCGGGGGTAAA
* * *
27926743 ATGGTAATTTTTGGTGAATTCGGGATTAAAAATGAAATTTTGGAAGTTCGAGGGTAAA
1 ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAA
* ** *
27926801 ATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGAAAGTTCGAGGGGTAAA
1 ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAGTTCG-GGGGTAAA
* *
27926860 ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGCGTAAA
1 ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAA
* *
27926918 ATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAA
1 ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAA
* *
27926976 ATGGTAATTTTT-G-GAAGTTTCGGGGTTAAAAATGGATTTTTGGAAAGTTTGGGGGTAAA
1 ATGGTAATTTTTGGTGAA--TTCGGGGTTAAAAATGGAATTTTGG-AAGTTCGGGGGTAAA
** * * * * *
27927035 ATGGTAATTTTTGAAG-TTTTGGTGTTAAAAATGAAATTTTGGAAGTTTGGGGGTAAA
1 ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAA
*
27927092 ATGGTAA-TTTT-G-GAAGTTTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAA
1 ATGGTAATTTTTGGTGAA--TTCGGGGTTAAAAATGGAATTTTGG-AAGTTCGGGGGTAAA
** ** **
27927150 ATGGTAATTTTT-G-GAAGTTTTAGGGTTAAAAATGGAATTTTAAAAGGTTTAGGGGTAAA
1 ATGGTAATTTTTGGTGAA--TTCGGGGTTAAAAATGGAATTTTGGAA-GTTCGGGGGTAAA
27927209 ATGGTAATTTT
1 ATGGTAATTTT
27927220 GGAAGTTTCG
Statistics
Matches: 426, Mismatches: 37, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
54 1 0.00
56 7 0.02
57 52 0.12
58 228 0.54
59 137 0.32
61 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (58 bp):
ATGGTAATTTTTGGTGAATTCGGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTAAA
Found at i:27926899 original size:117 final size:117
Alignment explanation
Indices: 27926686--27927226 Score: 657
Period size: 117 Copynumber: 4.7 Consensus size: 117
27926676 CCAGGGCAAT
* *
27926686 ATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTG-AGGCTTCGA-GGGTAAAATGGT
1 ATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGAAAG-TTCGAGGGGTAAAATGGT
* * *
27926748 AATTTTTGGTGAA-TTCGGGATTAAAAATGAAATTTTGG-AAGTTCGAGGGTAAA
65 AATTTTT-G-GAAGTTCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAA
*
27926801 ATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGAAAGTTCGAGGGGTAAAATGGTA
1 ATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGAAAGTTCGAGGGGTAAAATGGTA
* *
27926866 ATTTTTGGTGAA-ATCGGGGTTAAAAATGGAATTTTGG-AAGTTCGGGCGTAAA
66 ATTTTT-G-GAAGTTCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAA
*
27926918 ATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAGTTCG-GGGGTAAAATGGTA
1 ATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGAAAGTTCGAGGGGTAAAATGGTA
* *
27926982 ATTTTTGGAAGTTTCGGGGTTAAAAATGGATTTTTGGAAAGTTTGGGGGTAAA
66 ATTTTTGGAAG-TTCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAA
* ** * * *
27927035 ATGGTAA-TTTT--TGAAGTTTTGGTGTTAAAAATGAAATTTTGGAAGTTTG-GGGGTAAAATGG
1 ATGGTAATTTTTGGTGAA-ATCAGG-GTTAAAAATGGAATTTTGAAAGTTCGAGGGGTAAAATGG
*
27927096 TAA-TTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAA
64 TAATTTTTGGAAG-TTCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAA
* * * *
27927150 ATGGTAATTTTT-G-GAAGTTTTAGGGTTAAAAATGGAATTTTAAAAGGTT-TAGGGGTAAAATG
1 ATGGTAATTTTTGGTGAA--ATCAGGGTTAAAAATGGAATTTTGAAA-GTTCGAGGGGTAAAATG
27927212 GTAA-TTTTGGAAGTT
63 GTAATTTTTGGAAGTT
27927227 TCGAGGACCT
Statistics
Matches: 387, Mismatches: 26, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
114 7 0.02
115 68 0.18
116 150 0.39
117 162 0.42
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (117 bp):
ATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGAAAGTTCGAGGGGTAAAATGGTA
ATTTTTGGAAGTTCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAA
Found at i:27927019 original size:29 final size:29
Alignment explanation
Indices: 27926704--27927229 Score: 345
Period size: 29 Copynumber: 18.1 Consensus size: 29
27926694 TTTGGTGAAA
* *
27926704 TCGGGGTTAAAAATGG-AATTTT-GAGGCT
1 TCGGGGTT-AAAATGGTAATTTTGGAAGTT
27926732 TCGAGGG-TAAAATGGTAATTTTTGGTGAA--T
1 TCG-GGGTTAAAATGGTAA-TTTT-G-GAAGTT
* *
27926762 TCGGGATTAAAAAT-GAAATTTTGGAAG-T
1 TCGGGGTT-AAAATGGTAATTTTGGAAGTT
*
27926790 TCGAGGG-TAAAATGGTAATTTTTGGTGAA--A
1 TCG-GGGTTAAAATGGTAA-TTTT-G-GAAGTT
** *
27926820 TCAAGGTTAAAAATGG-AATTTTGAAAG-T
1 TCGGGGTT-AAAATGGTAATTTTGGAAGTT
* *
27926848 TCGAGGGGTAAAATGGTAATTTTTGGTGAA--A
1 TCG-GGGTTAAAATGGTAA-TTTT-G-GAAGTT
27926879 TCGGGGTTAAAAATGG-AATTTTGGAAG-T
1 TCGGGGTT-AAAATGGTAATTTTGGAAGTT
*
27926907 TCGGGCG-TAAAATGGTAATTTTTGGTGAA--A
1 TCGGG-GTTAAAATGGTAA-TTTT-G-GAAGTT
*
27926937 TCAGGGTTAAAAATGG-AATTTTGGAAG-T
1 TCGGGGTT-AAAATGGTAATTTTGGAAGTT
*
27926965 TCGGGGGTAAAATGGTAATTTTTGGAAGTT
1 TCGGGGTTAAAATGGTAA-TTTTGGAAGTT
*
27926995 TCGGGGTTAAAAATGG-ATTTTTGGAAAGTT
1 TCGGGGTT-AAAATGGTAATTTTGG-AAGTT
* *
27927025 T-GGGGGTAAAATGGTAATTTTTGAAGTT
1 TCGGGGTTAAAATGGTAATTTTGGAAGTT
* * *
27927053 TTGGTGTTAAAAAT-GAAATTTTGGAAGTT
1 TCGGGGTT-AAAATGGTAATTTTGGAAGTT
*
27927082 T-GGGGGTAAAATGGTAATTTTGGAAGTT
1 TCGGGGTTAAAATGGTAATTTTGGAAGTT
27927110 TCGGGGTTAAAAATGG-AATTTTGGAAAGTT
1 TCGGGGTT-AAAATGGTAATTTTGG-AAGTT
*
27927140 T-GGGGGTAAAATGGTAATTTTTGGAAGTT
1 TCGGGGTTAAAATGGTAA-TTTTGGAAGTT
** **
27927169 TTAGGGTTAAAAATGG-AATTTTAAAAGGTT
1 TCGGGGTT-AAAATGGTAATTTTGGAA-GTT
*
27927199 TAGGGG-TAAAATGGTAATTTTGGAAGTT
1 TCGGGGTTAAAATGGTAATTTTGGAAGTT
27927227 TCG
1 TCG
27927230 AGGACCTATA
Statistics
Matches: 403, Mismatches: 45, Indels: 100
0.74 0.08 0.18
Matches are distributed among these distances:
27 42 0.10
28 94 0.23
29 129 0.32
30 84 0.21
31 50 0.12
32 4 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
TCGGGGTTAAAATGGTAATTTTGGAAGTT
Found at i:27927649 original size:162 final size:162
Alignment explanation
Indices: 27927317--27927649 Score: 456
Period size: 162 Copynumber: 2.1 Consensus size: 162
27927307 TTGTAAACCT
* * *
27927317 TGAAAAATTCTTAGGGTAATTTTATAATTAAATAAGAGTTGATTTGGGGATTAAATTAAAATAAA
1 TGAAAAATTCTTAGGCTAATTTTATAATTAAATAAAAGTTGATTTGGGGATTAAATTAAAACAAA
* ** *
27927382 TTAAAAATAAAAAGGACTAAATGCATAAATAAGCTAAAAAGTGACACGTGGCAGCCCCTGGTGCA
66 TTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACACGTGGCAGAACCTAGTGCA
* * **
27927447 GTCAAACAGTTAAAGGACTAATTTATAAACCT
131 GTCAAACAGTGAAAGGACTAATTGATAAACAA
* *
27927479 TGAAAAATTGTTAGGCTAATTTTGTAATTAAATAAAAGTTGATTTGGGGATTAAATTAAAACAAA
1 TGAAAAATTCTTAGGCTAATTTTATAATTAAATAAAAGTTGATTTGGGGATTAAATTAAAACAAA
* * *
27927544 TTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAACAGTGACACGTGGCATAATCTAGTGCA
66 TTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACACGTGGCAGAACCTAGTGCA
* *
27927609 TTCAAA-ATGTGAAAGGATTAAATTGA-AAAGCAA
131 GTCAAACA-GTGAAAGGACT-AATTGATAAA-CAA
27927642 T-AAAAATT
1 TGAAAAATT
27927650 ATTGGGCAAA
Statistics
Matches: 150, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
161 1 0.01
162 142 0.95
163 7 0.05
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (162 bp):
TGAAAAATTCTTAGGCTAATTTTATAATTAAATAAAAGTTGATTTGGGGATTAAATTAAAACAAA
TTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACACGTGGCAGAACCTAGTGCA
GTCAAACAGTGAAAGGACTAATTGATAAACAA
Found at i:27936601 original size:25 final size:25
Alignment explanation
Indices: 27936560--27936610 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
27936550 ATCTTTATAC
*
27936560 ATATTGAATTTTCATATCAATAAAT
1 ATATTGAATTTTAATATCAATAAAT
**
27936585 ATATTG-ATTTATAATATGTATAAAT
1 ATATTGAATTT-TAATATCAATAAAT
27936610 A
1 A
27936611 AATTTTACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
ATATTGAATTTTAATATCAATAAAT
Found at i:27942766 original size:29 final size:29
Alignment explanation
Indices: 27942733--27942862 Score: 154
Period size: 30 Copynumber: 4.4 Consensus size: 29
27942723 AAAAATGTGA
*
27942733 TTTT-GAAAGTTTGGGAGTCAAAATATAAT
1 TTTTGGAAAGTTCGGG-GTCAAAATATAAT
* *
27942762 TTTTGAAAAGCTCGAGGGTCAAAATATAAT
1 TTTTGGAAAGTTCG-GGGTCAAAATATAAT
* *
27942792 TTTTGGAAAGCTTAGGGGTCAAAATGTAAT
1 TTTTGGAAAG-TTCGGGGTCAAAATATAAT
* *
27942822 TTTTGGAAAGTTCGTGGTCAATATATAAT
1 TTTTGGAAAGTTCGGGGTCAAAATATAAT
*
27942851 TTTTAGAAAGTT
1 TTTTGGAAAGTT
27942863 TATGGGTTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
29 30 0.35
30 52 0.60
31 4 0.05
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAGTTCGGGGTCAAAATATAAT
Found at i:27942851 original size:59 final size:58
Alignment explanation
Indices: 27942733--27942885 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 58
27942723 AAAAATGTGA
*
27942733 TTTTGAAAGTTTGGGAGTCAAAATATAATTTTTGAAAAGCTCGAGGGTCAAAATATAAT
1 TTTTGAAAGTTAGGG-GTCAAAATATAATTTTTGAAAAGCTCGAGGGTCAAAATATAAT
* * * * *
27942792 TTTTGGAAAGCTTAGGGGTCAAAATGTAATTTTTGGAAAGTTCG-TGGTCAATATATAAT
1 TTTT-GAAAG-TTAGGGGTCAAAATATAATTTTTGAAAAGCTCGAGGGTCAAAATATAAT
* * * *
27942851 TTTTAGAAAGTTTATGGGTTAAAACATGATTTTTG
1 TTTT-GAAAG-TTAGGGGTCAAAATATAATTTTTG
27942886 GATAATTCAG
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 45 0.57
60 29 0.37
61 5 0.06
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.38
Consensus pattern (58 bp):
TTTTGAAAGTTAGGGGTCAAAATATAATTTTTGAAAAGCTCGAGGGTCAAAATATAAT
Found at i:27943948 original size:3 final size:3
Alignment explanation
Indices: 27943933--27943993 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
27943923 TCTCCTTCTT
* * * *
27943933 TTA TTA TTG TTA TTA TTA TTTA TTA TTA ATA TTA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
27943979 -TA TTTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA
27943994 ATGTTATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.86
4 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:27943956 original size:19 final size:19
Alignment explanation
Indices: 27943932--27944006 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
27943922 TTCTCCTTCT
**
27943932 TTTATTATTGTTATTATTA
1 TTTATTATTAATATTATTA
27943951 TTTATTATTAATATTATTA
1 TTTATTATTAATATTATTA
27943970 -TTA--A-TAATA-TATT-
1 TTTATTATTAATATTATTA
*
27943983 TATTATTATTAATGTTATTTA
1 T-TTATTATTAATATTA-TTA
27944004 TTT
1 TTT
27944007 GATGCGTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.09
15 8 0.18
16 1 0.02
17 1 0.02
18 7 0.16
19 19 0.42
20 4 0.09
21 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATTATTAATATTATTA
Found at i:27943987 original size:18 final size:19
Alignment explanation
Indices: 27943964--27944005 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
27943954 ATTATTAATA
27943964 TTATTATTAATAAT-ATAT
1 TTATTATTAATAATGATAT
* *
27943982 TTATTATTATTAATGTTAT
1 TTATTATTAATAATGATAT
27944001 TTATT
1 TTATT
27944006 TGATGCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATTATTAATAATGATAT
Found at i:27944726 original size:17 final size:17
Alignment explanation
Indices: 27944704--27944743 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
27944694 AAATTTTAAT
27944704 TTTAAACTCAAAATAAA
1 TTTAAACTCAAAATAAA
* * *
27944721 TTTAAATTTAAAGTAAA
1 TTTAAACTCAAAATAAA
27944738 TTTAAA
1 TTTAAA
27944744 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTAAACTCAAAATAAA
Found at i:27944730 original size:23 final size:23
Alignment explanation
Indices: 27944693--27944754 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
27944683 TTTGGACATT
*
27944693 TAAATTTTAATTTTAAACTCAAA-A
1 TAAA-TTTAAATTTAAACT-AAATA
* *
27944717 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATTTAAACTAAATA
27944740 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
27944755 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.09
23 27 0.79
24 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAATTTAAATTTAAACTAAATA
Found at i:27944744 original size:17 final size:17
Alignment explanation
Indices: 27944717--27944767 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
27944707 AAACTCAAAA
27944717 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
27944734 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAG
*
27944751 TTAATTTAAAATTTAAA
1 TAAATTT-AAATTTAAA
27944768 ATTTAGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:27944765 original size:7 final size:6
Alignment explanation
Indices: 27944690--27944777 Score: 74
Period size: 6 Copynumber: 14.5 Consensus size: 6
27944680 CATTTTGGAC
* * * * *
27944690 ATTTAA ATTTTAA TTTTAA ACTCAA A-ATAA ATTTAA ATTTAA A-GTAA
1 ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
27944737 ATTTAA ATTTAA ATTT-A ATTTAAA ATTTAAA ATTTAGA ATT
1 ATTTAA ATTTAA ATTTAA ATTT-AA ATTT-AA ATTTA-A ATT
27944778 GGGTTTAATG
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
5 12 0.18
6 34 0.51
7 21 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:27945516 original size:208 final size:208
Alignment explanation
Indices: 27945200--27945864 Score: 1053
Period size: 208 Copynumber: 3.2 Consensus size: 208
27945190 ATTTTAATTC
** * * * * * * **
27945200 GCTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTTGCTCACATTAAGCTTTGTTTTATT
1 GCTTCTCAATATCTCATCAGGAAGCT-AGGTTCGAAGTTTCGCTCATATTGAGCTTTGTTCCATT
* *
27945265 GATTTGGTATACTTTTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTTCT
65 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTTCT
* *
27945330 CTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCA-TT
130 CTGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTT
27945394 TATTGCTTCGACCT
195 TATTGCTTCGACCT
* *
27945408 GCTTCTCAATATCTCATCATGAAGCTGGGATTCGAAGTTTCGCTCATATTGAGCTTTGTTCCATT
1 GCTTCTCAATATCTCATCAGGAAGCTAGG-TTCGAAGTTTCGCTCATATTGAGCTTTGTTCCATT
* *
27945473 GATTTGGTATACTTCTCTGTATCTCATCAAGAAGATAACCGCCTCACTTGTTTTAATCCACTTCT
65 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTTCT
* * ** *
27945538 TTGTATTTCATCAAGAAGACGGATTTGGTTAACTTCTCTGTATCTTATCAGGAAGCTGACCATTT
130 CTGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTT
27945603 TATTGCTTCGACCT
195 TATTGCTTCGACCT
*
27945617 GCTTCTCAATATCTCATCAGGAAGCTAGGTTCGAAGCTTCGCTCATATTGAGCTTTGTTCCATTG
1 GCTTCTCAATATCTCATCAGGAAGCTAGGTTCGAAGTTTCGCTCATATTGAGCTTTGTTCCATTG
*
27945682 ATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTTAATCCACTTCTC
66 ATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTTCTC
*
27945747 TGTATCACATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTTT
131 TGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTTT
*
27945812 ATTGCTTGGACCT
196 ATTGCTTCGACCT
*
27945825 GCTTCTCAGTATCTCATCAGGAAGCTAGGTTCGAAGTTTC
1 GCTTCTCAATATCTCATCAGGAAGCTAGGTTCGAAGTTTC
27945865 AAACTTCTCT
Statistics
Matches: 419, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
207 3 0.01
208 373 0.89
209 43 0.10
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (208 bp):
GCTTCTCAATATCTCATCAGGAAGCTAGGTTCGAAGTTTCGCTCATATTGAGCTTTGTTCCATTG
ATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTTCTC
TGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTTT
ATTGCTTCGACCT
Found at i:27947773 original size:15 final size:15
Alignment explanation
Indices: 27947753--27947786 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27947743 GGTCATCCCT
* *
27947753 TTCTTTTTCTTCTTC
1 TTCTTTTACTTATTC
27947768 TTCTTTTACTTATTC
1 TTCTTTTACTTATTC
27947783 TTCT
1 TTCT
27947787 GCTTCGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTTTACTTATTC
Found at i:27953153 original size:31 final size:31
Alignment explanation
Indices: 27953118--27953176 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
27953108 AATAAACTAC
*
27953118 TAAGTTTCAAAACTAATATAGTTAAAAATAT
1 TAAGTTTCAAAACTAACATAGTTAAAAATAT
* *
27953149 TAAGTTTCAAAACTCACATGGTTAAAAA
1 TAAGTTTCAAAACTAACATAGTTAAAAA
27953177 ACTATTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (31 bp):
TAAGTTTCAAAACTAACATAGTTAAAAATAT
Found at i:27953160 original size:15 final size:16
Alignment explanation
Indices: 27953111--27953162 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
27953101 TTTAAAAAAT
*
27953111 AAACTACTAAGTTTCA
1 AAACTAATAAGTTTCA
27953127 AAACTAATATAG-TT-A
1 AAACTAATA-AGTTTCA
* *
27953142 AAAATATTAAGTTTCA
1 AAACTAATAAGTTTCA
27953158 AAACT
1 AAACT
27953163 CACATGGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 15 0.52
17 2 0.07
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (16 bp):
AAACTAATAAGTTTCA
Found at i:27954522 original size:38 final size:37
Alignment explanation
Indices: 27954480--27954553 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
27954470 AATGGTGATT
* *
27954480 TTTGGTAAAA-CTGAGGTTAAAAATGGAATTTTGGAAAC
1 TTTGGTAAAATCAG-GGCTAAAAATGGAA-TTTGGAAAC
*
27954518 TTTGGTGAAATCAGGGCTAAAAATGGAATTTGGAAA
1 TTTGGTAAAATCAGGGCTAAAAATGGAATTTGGAAA
27954554 GTTCGGGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 8 0.25
38 22 0.69
39 2 0.06
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (37 bp):
TTTGGTAAAATCAGGGCTAAAAATGGAATTTGGAAAC
Found at i:27954550 original size:28 final size:28
Alignment explanation
Indices: 27954518--27954606 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
27954508 TTTTGGAAAC
27954518 TTTGGTGAAATCAGGGCTAAAAATGGAA
1 TTTGGTGAAATCAGGGCTAAAAATGGAA
* *
27954546 TTT-G-GAAAGTTCGGGGGT-AAAATGGTAA
1 TTTGGTGAAA--TCAGGGCTAAAAATGG-AA
* *
27954574 TTTTTGGTAAAATCAGGGTTAAAAATGGAA
1 --TTTGGTGAAATCAGGGCTAAAAATGGAA
27954604 TTT
1 TTT
27954607 TGGAAAGTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
26 4 0.08
27 8 0.17
28 14 0.29
30 11 0.23
31 8 0.17
32 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.31
Consensus pattern (28 bp):
TTTGGTGAAATCAGGGCTAAAAATGGAA
Found at i:27954657 original size:58 final size:59
Alignment explanation
Indices: 27954518--27954816 Score: 406
Period size: 59 Copynumber: 5.1 Consensus size: 59
27954508 TTTTGGAAAC
* * *
27954518 TTTGGTGAAATCAGGGCTAAAAATGGAA-TTTGGAAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
* *
27954576 TTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGCAAAATGGTAATT
1 TTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
* * **
27954635 TTTGGTAAAATTGGGGTT-AAAATGGAATTTTGGAGAGTTTAGGGGTAAAATGGTAATT
1 TTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
* * **
27954693 TTTGGTAAAAATTGGGGTT-AAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
1 TTTGGT-AAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
* * * *
27954752 TTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGGTAAAATGGTAATT
1 TTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGGTAAAATGGTAATT
27954812 TTTGG
1 TTTGG
27954817 ACAGCCCAAG
Statistics
Matches: 218, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
58 78 0.36
59 117 0.54
60 23 0.11
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.33
Consensus pattern (59 bp):
TTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
Found at i:27954667 original size:117 final size:118
Alignment explanation
Indices: 27954525--27954816 Score: 403
Period size: 117 Copynumber: 2.5 Consensus size: 118
27954515 AACTTTGGTG
* * *
27954525 AAATCAGGGCTAAAAATGGAA-TTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGT-AAAATC
1 AAATCGGGGTTAAAAATGGAATTTTGGAAAGTTAGGGGGTAAAATGGTAATTTTTGGTAAAAATC
* * *
27954588 AGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGCAAAATGGTAATTTTTGGTA
66 AGGGTT-AAAATAGAATTTTGGAAAGTTCAGGGGCAAAATGGTAATTTTTGATA
* *
27954642 AAATTGGGGTT-AAAATGGAATTTTGGAGAGTTTA-GGGGTAAAATGGTAATTTTTGGTAAAAAT
1 AAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTAGGGGGTAAAATGGTAATTTTTGGTAAAAAT
** * * *
27954705 TGGGGTTAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATG
65 CAGGGTTAAAATAGAATTTTGGAAAGTTCAGGGGCAAAATGGTAATTTTTGATA
*
27954759 AAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGGTAAAATGGTAATTTTTGG
1 AAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTAGGGGGTAAAATGGTAATTTTTGG
27954817 ACAGCCCAAG
Statistics
Matches: 154, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
116 9 0.06
117 90 0.58
118 33 0.21
119 22 0.14
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (118 bp):
AAATCGGGGTTAAAAATGGAATTTTGGAAAGTTAGGGGGTAAAATGGTAATTTTTGGTAAAAATC
AGGGTTAAAATAGAATTTTGGAAAGTTCAGGGGCAAAATGGTAATTTTTGATA
Found at i:27956709 original size:18 final size:17
Alignment explanation
Indices: 27956671--27956711 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
27956661 TTCAAATATT
27956671 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
27956688 TTTAAATTTAATAATGAA
1 TTTAAATTTAA-AATAAA
27956706 TTTAAA
1 TTTAAA
27956712 CCTAAAGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:27957515 original size:15 final size:15
Alignment explanation
Indices: 27957497--27957528 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27957487 AAGTGTTAAA
27957497 AAAATTTAAGTAGTG
1 AAAATTTAAGTAGTG
*
27957512 AAAATTTAATTAGTG
1 AAAATTTAAGTAGTG
27957527 AA
1 AA
27957529 TTTAAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (15 bp):
AAAATTTAAGTAGTG
Found at i:27957532 original size:13 final size:14
Alignment explanation
Indices: 27957498--27957535 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
27957488 AGTGTTAAAA
27957498 AAATTTAAGTAGTG
1 AAATTTAAGTAGTG
*
27957512 AAAATTTAATTAGTG
1 -AAATTTAAGTAGTG
27957527 -AATTTAAGT
1 AAATTTAAGT
27957536 TATAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (14 bp):
AAATTTAAGTAGTG
Found at i:27962807 original size:19 final size:18
Alignment explanation
Indices: 27962773--27962818 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
27962763 AACCGCTTCT
27962773 TTATA-ACAAAAAAATC-
1 TTATAGACAAAAAAATCA
27962789 TTAGTAGACAAATAAAATCA
1 TTA-TAGACAAA-AAAATCA
27962809 TTATAGACAA
1 TTATAGACAA
27962819 GGTTGAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.12
17 2 0.08
18 5 0.19
19 13 0.50
20 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (18 bp):
TTATAGACAAAAAAATCA
Found at i:27965383 original size:23 final size:23
Alignment explanation
Indices: 27965332--27965522 Score: 164
Period size: 23 Copynumber: 8.4 Consensus size: 23
27965322 CGAAGTACTG
*
27965332 AACAGAGAGCACA-TAAGTGCTGA
1 AACAGAGAGCACACAAAGTGCT-A
*
27965355 GTAACAGAGGGCACACAAAGTGCTA
1 --AACAGAGAGCACACAAAGTGCTA
*
27965380 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
27965399 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
27965419 ATCAGAGAGCACACGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* * *
27965443 TAACAGAGAGCACATACAGTACTA
1 -AACAGAGAGCACACAAAGTGCTA
*
27965467 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
27965490 ATCAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
27965513 ATCAGAGAGC
1 AACAGAGAGC
27965523 GCGCTAGTGT
Statistics
Matches: 137, Mismatches: 19, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
23 81 0.59
24 2 0.01
25 30 0.22
26 7 0.05
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:27965473 original size:48 final size:46
Alignment explanation
Indices: 27965402--27965522 Score: 188
Period size: 48 Copynumber: 2.6 Consensus size: 46
27965392 ACAAAGTACT
* *
27965402 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTAAT--CAGA
* *
27965450 GAGCACATACAGTACTAATCAGAGAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGA
27965496 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
27965523 GCGCTAGTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 29 0.43
48 38 0.57
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.13
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGA
Found at i:27972802 original size:17 final size:17
Alignment explanation
Indices: 27972780--27972818 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
27972770 AATGTTGATG
**
27972780 TATTTTAATATTTTAAA
1 TATTTTAATATTAAAAA
*
27972797 TATTTTATTATTAAAAA
1 TATTTTAATATTAAAAA
27972814 TATTT
1 TATTT
27972819 CCATTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTAATATTAAAAA
Found at i:27975360 original size:34 final size:34
Alignment explanation
Indices: 27975316--27975380 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
27975306 AGAATATGAA
* *
27975316 AGGTTGAGGAAGATGGAAGGTTAAACGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
27975350 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAA
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAA
27975381 TGAAGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.18
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
Found at i:27975370 original size:17 final size:17
Alignment explanation
Indices: 27975315--27975373 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
27975305 AAGAATATGA
*
27975315 AAGGTTGAGGAAGATGG
1 AAGGTTAAGGAAGATGG
*
27975332 AAGGTTAAACGTCAAG--GG
1 AAGGTT-AA-G-GAAGATGG
27975350 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
27975366 AAGGTTAA
1 AAGGTTAA
27975374 AAGTCAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 4 0.12
17 18 0.55
18 3 0.09
19 1 0.03
20 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.19
Consensus pattern (17 bp):
AAGGTTAAGGAAGATGG
Found at i:27977527 original size:405 final size:405
Alignment explanation
Indices: 27976776--27977591 Score: 1465
Period size: 405 Copynumber: 2.0 Consensus size: 405
27976766 TTTCATAAGT
* *
27976776 TATAATAGAAACACTTATTTATTTTTGATGACTTGTTCTCATCTCAATGCTTTCAAGTATATTTT
1 TATAATAGAAACACTTATTTATTTTTGATAACTTATTCTCATCTCAATGCTTTCAAGTATATTTT
* *
27976841 CATTCAAGATCCTCACTTTTCCATAATATTGAAGTGTTCTACGTATATTATCGTTATTGACAACA
66 CATTCAAGATCCTCACTTTTCCATAATATTGAAGTGTTCTACGTACATTATCGTTATCGACAACA
27976906 ATTTCATTTTTTTTTCAACTCCATCATATTTAGTTATGACATAACTAATTGAGATATCTCATTAT
131 ATTTCATTTTTTTTTCAACTCCATCATATTTAGTTATGACATAACTAATTGAGATATCTCATTAT
*
27976971 ATTCATAATTTCAGGTACCTGAACCTCTTCTAGGGTTTTATCAAAAGTTATGCCTTGGGCCTCTT
196 ATTCATAATTTCAAGTACCTGAACCTCTTCTAGGGTTTTATCAAAAGTTATGCCTTGGGCCTCTT
*
27977036 CAGGAGTACCCGCCTCCTTTTAGTATGTGACCATCATTTTTTTTTCTCCTTTCTTTCAATAATTT
261 CAGGAGTACCCGCCTCCTTTTAGTATGTGACCATCATTTTTCTTTCTCCTTTCTTTCAATAATTT
* *
27977101 TTTGTTTTATGGAGTCGACTAGCTTGTCATGCTTTTAGCATGCTCAAGACTTATTTTTATCACAT
326 TTCGTTTTATGGAGTCGACTAGCTTGTCATGCTTCTAGCATGCTCAAGACTTATTTTTATCACAT
27977166 TGTCCTTCTGGGACA
391 TGTCCTTCTGGGACA
*
27977181 TATAATAGAAACACTTATTTATTTTTGATAACTTATTCTCATCTCAATGCTTTCAATTATATTTT
1 TATAATAGAAACACTTATTTATTTTTGATAACTTATTCTCATCTCAATGCTTTCAAGTATATTTT
27977246 CATTCAAGATCCTCACTTTTCCATAATATTGAAGTGTTCTACGTACATTATCGTTATCGACAACA
66 CATTCAAGATCCTCACTTTTCCATAATATTGAAGTGTTCTACGTACATTATCGTTATCGACAACA
*
27977311 ATTTCA-TTTTTTTTCAACTCCATCATGTTTAGTTATGACATAACTAATTGAGATATCTCATTAT
131 ATTTCATTTTTTTTTCAACTCCATCATATTTAGTTATGACATAACTAATTGAGATATCTCATTAT
*
27977375 ATTCATAATTTCAAGTACCTGAACCTCTTTTAGGGTTTTATCAAAAGTTATGCCTTGGGCCTCTT
196 ATTCATAATTTCAAGTACCTGAACCTCTTCTAGGGTTTTATCAAAAGTTATGCCTTGGGCCTCTT
*
27977440 TAGGAGTACCCGCCTCCTTTTAGTATGTGACCATC-TTCATTTCTTTCTCCTTTCTTTCAATAAT
261 CAGGAGTACCCGCCTCCTTTTAGTATGTGACCATCATT--TTTCTTTCTCCTTTCTTTCAATAAT
* *
27977504 TTTTCGTTTTATGGAGTCGACTAGCTTGTCATGCTTCTAGCATGCTTAAGACTTGTTTTTATCAC
324 TTTTCGTTTTATGGAGTCGACTAGCTTGTCATGCTTCTAGCATGCTCAAGACTTATTTTTATCAC
*
27977569 ATTGTCCTTTTGGGACA
389 ATTGTCCTTCTGGGACA
27977586 TATAAT
1 TATAAT
27977592 TATTTGGAGC
Statistics
Matches: 394, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
403 2 0.01
404 154 0.39
405 238 0.60
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (405 bp):
TATAATAGAAACACTTATTTATTTTTGATAACTTATTCTCATCTCAATGCTTTCAAGTATATTTT
CATTCAAGATCCTCACTTTTCCATAATATTGAAGTGTTCTACGTACATTATCGTTATCGACAACA
ATTTCATTTTTTTTTCAACTCCATCATATTTAGTTATGACATAACTAATTGAGATATCTCATTAT
ATTCATAATTTCAAGTACCTGAACCTCTTCTAGGGTTTTATCAAAAGTTATGCCTTGGGCCTCTT
CAGGAGTACCCGCCTCCTTTTAGTATGTGACCATCATTTTTCTTTCTCCTTTCTTTCAATAATTT
TTCGTTTTATGGAGTCGACTAGCTTGTCATGCTTCTAGCATGCTCAAGACTTATTTTTATCACAT
TGTCCTTCTGGGACA
Found at i:27980133 original size:98 final size:98
Alignment explanation
Indices: 27979941--27980130 Score: 235
Period size: 97 Copynumber: 1.9 Consensus size: 98
27979931 TGGAAAATGA
* * *
27979941 TATTCGATTACCTTGATTTAAAGAAAAATTGCACCTAGTAAATTTAAGGCACAAATTTTCAGAAT
1 TATTCGATTACCTTGATTTAAAGAAAAATCGCACCTAGTAAAGTTAAGGCACAAATTTTCAGAAA
* *
27980006 CAGAGATAAAGAAACATTGCCTTGATTTAAGGG
66 CAGAAATAAAGAAACATTGCCTCGATTTAAGGG
* * *
27980039 TATTCGATTA-TTTCGATTTGAAGAAAAATCGCGCCTAGT-AAGTTAAGGCACAAATTTTC-GAA
1 TATTCGATTACCTT-GATTTAAAGAAAAATCGCACCTAGTAAAGTTAAGGCACAAATTTTCAGAA
* *
27980101 ACTTGAAATAAA-AGAATATTGCCTCGATTT
65 AC-AGAAATAAAGA-AACATTGCCTCGATTT
27980131 TAAAGGTTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
96 5 0.06
97 42 0.53
98 32 0.41
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (98 bp):
TATTCGATTACCTTGATTTAAAGAAAAATCGCACCTAGTAAAGTTAAGGCACAAATTTTCAGAAA
CAGAAATAAAGAAACATTGCCTCGATTTAAGGG
Found at i:27980432 original size:29 final size:30
Alignment explanation
Indices: 27980400--27980656 Score: 168
Period size: 30 Copynumber: 8.8 Consensus size: 30
27980390 ACTCAAGGGC
* *
27980400 AAAATGGTAATTTTTGGAAATTTTGGGATA
1 AAAATGGTAATTTTTGGAAATTTCGGGGTA
*
27980430 AAAATGG-GATTTTTGG-AA-TTCGAGGGT-
1 AAAATGGTAATTTTTGGAAATTTCG-GGGTA
* *
27980457 AAAATGGTAACTTTTGGAAGA-ATCGGGGTCA
1 AAAATGGTAATTTTTGGAA-ATTTCGGGGT-A
** *
27980488 AATTTGG-AATTTTT-GAAAGTTCGGGGGT-
1 AAAATGGTAATTTTTGGAAATTTC-GGGGTA
* **
27980516 -AAATGGTAATTTTTGGAAGA-GTCAAGGTCA
1 AAAATGGTAATTTTTGGAA-ATTTCGGGGT-A
* *
27980546 AAAATGG-AATTTTTGG-AAGTTCGAGAGT-
1 AAAATGGTAATTTTTGGAAATTTCG-GGGTA
*
27980574 AAAATGGTAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGTAATTTTTGGAAATTTCGGGGT-A
* *
27980605 AAAATGG-AATTTTT-GAAAGTTCAAGGGT-
1 AAAATGGTAATTTTTGGAAATTTC-GGGGTA
27980633 AAAATGGTAATTTTTGGACAATTT
1 AAAATGGTAATTTTTGGA-AATTT
27980657 AGGGACCTCC
Statistics
Matches: 177, Mismatches: 26, Indels: 47
0.71 0.10 0.19
Matches are distributed among these distances:
27 14 0.08
28 38 0.21
29 51 0.29
30 52 0.29
31 22 0.12
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAATTTCGGGGTA
Found at i:27980590 original size:117 final size:117
Alignment explanation
Indices: 27980392--27980650 Score: 353
Period size: 117 Copynumber: 2.2 Consensus size: 117
27980382 TTTTGGACAC
* * *** * *
27980392 TCAAGGGCAAAATGGTAATTTTTGGAA-ATTTTGGGAT-AAAAATGGGATTTTTGGAATTCGAGG
1 TCAAGGGTAAAATGGTAATTTTTGGAAGAGTCAAGG-TCAAAAATGGAATTTTTGGAATTCGAGA
**
27980455 GTAAAATGGTAACTTTTGGAAGAATCGGGGTCAAATTTGGAATTTTTGAAAGT
65 GTAAAATGGTAACTTTTGGAAGAATCGGGGTCAAAAATGGAATTTTTGAAAGT
**
27980508 TCGGGGGT-AAATGGTAATTTTTGGAAGAGTCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGA
1 TCAAGGGTAAAATGGTAATTTTTGGAAGAGTCAAGGTCAAAAATGGAATTTTTGGAA-TTCGAGA
* **
27980572 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGAAAGT
65 GTAAAATGGTAACTTTTGGAAGAATCGGGGTCAAAAATGGAATTTTTGAAAGT
27980625 TCAAGGGTAAAATGGTAATTTTTGGA
1 TCAAGGGTAAAATGGTAATTTTTGGA
27980651 CAATTTAGGG
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
115 19 0.15
116 27 0.22
117 60 0.49
118 17 0.14
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (117 bp):
TCAAGGGTAAAATGGTAATTTTTGGAAGAGTCAAGGTCAAAAATGGAATTTTTGGAATTCGAGAG
TAAAATGGTAACTTTTGGAAGAATCGGGGTCAAAAATGGAATTTTTGAAAGT
Found at i:27980605 original size:59 final size:59
Alignment explanation
Indices: 27980395--27980650 Score: 322
Period size: 59 Copynumber: 4.4 Consensus size: 59
27980385 TGGACACTCA
* * * * *
27980395 AGGGCAAAATGGTAATTTTTGGAA-ATTTTGGGAT-AAAAATGGGATTTTTGGAA-TTCG
1 AGGGTAAAATGGTAATTTTTGGAAGA-TTCGGGGTCAAAAATGGAATTTTTGAAAGTTCG
* * **
27980452 AGGGTAAAATGGTAACTTTTGGAAGAATCGGGGTCAAATTTGGAATTTTTGAAAGTTCG
1 AGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGAAAGTTCG
* * ** *
27980511 GGGGT-AAATGGTAATTTTTGGAAGAGTCAAGGTCAAAAATGGAATTTTTGGAAGTTCG
1 AGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGAAAGTTCG
* * *
27980569 AGAGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGAAAGTTCA
1 AGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGAAAGTTCG
27980628 AGGGTAAAATGGTAATTTTTGGA
1 AGGGTAAAATGGTAATTTTTGGA
27980651 CAATTTAGGG
Statistics
Matches: 169, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
57 27 0.16
58 65 0.38
59 77 0.46
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTTGGAAGATTCGGGGTCAAAAATGGAATTTTTGAAAGTTCG
Found at i:27980660 original size:29 final size:28
Alignment explanation
Indices: 27980368--27980660 Score: 149
Period size: 29 Copynumber: 10.1 Consensus size: 28
27980358 GGATGCCTGG
* **
27980368 GGGTAAAATGGTAA-TTTTGGACACTCAA
1 GGGTAAAATGGTAATTTTTGGA-AATTGA
* **
27980396 GGGCAAAATGGTAATTTTTGGAAATTTT
1 GGGTAAAATGGTAATTTTTGGAAATTGA
*
27980424 GGGATAAAAATGG-GATTTTTGG-AATTCGA
1 GGG-T-AAAATGGTAATTTTTGGAAATT-GA
* *
27980453 GGGTAAAATGGTAACTTTTGGAAGAATCG-
1 GGGTAAAATGGTAATTTTTGG-A-AATTGA
* *
27980482 GGGTCAAATTTGG-AATTTTT-GAAAGTTCGG
1 GGGT-AAA-ATGGTAATTTTTGGAAA-TT-GA
* *
27980512 GGGT-AAATGGTAATTTTTGGAAGAGTCA
1 GGGTAAAATGGTAATTTTTGGAA-ATTGA
* *
27980540 AGGTCAAAAATGG-AATTTTTGGAAGTTCGA
1 GGGT--AAAATGGTAATTTTTGGAAATT-GA
* *
27980570 GAGTAAAATGGTAATTTTTGGAAGTTTCG-
1 GGGTAAAATGGTAATTTTTGGAA-ATT-GA
*
27980599 GGGTCAAAAATGG-AATTTTT-GAAAGTTCAA
1 GGGT--AAAATGGTAATTTTTGGAAA-TT-GA
*
27980629 GGGTAAAATGGTAATTTTTGGACAATTTA
1 GGGTAAAATGGTAATTTTTGGA-AATTGA
27980658 GGG
1 GGG
27980661 ACCTCCAGGG
Statistics
Matches: 206, Mismatches: 30, Indels: 57
0.70 0.10 0.19
Matches are distributed among these distances:
27 12 0.06
28 58 0.28
29 60 0.29
30 55 0.27
31 21 0.10
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGAAATTGA
Found at i:27981879 original size:21 final size:21
Alignment explanation
Indices: 27981855--27981903 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
27981845 ATTTCTTTTT
*
27981855 TTTATTATAAATAAATTA-ATA
1 TTTATTATAAA-AAATTATAAA
*
27981876 TTTATT-TAAAATATTATAAA
1 TTTATTATAAAAAATTATAAA
27981896 TTTATTAT
1 TTTATTAT
27981904 TTATTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATTATAAAAAATTATAAA
Found at i:27982620 original size:6 final size:6
Alignment explanation
Indices: 27982609--27982691 Score: 82
Period size: 6 Copynumber: 14.2 Consensus size: 6
27982599 GTTTAAAACC
* ** *
27982609 ATTTAA ATTTAA A-GTAA ATTTAA ATTTAA AAATAG ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
27982656 ATTTAA GA--TAA ATTTAA ATTTAA AAATAA ATTTAA A
1 ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
27982692 AGCAATTTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 52 0.85
7 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:27982631 original size:17 final size:17
Alignment explanation
Indices: 27982609--27982691 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
27982599 GTTTAAAACC
*
27982609 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
27982626 ATTTAAATTTAAAAATAGATTTAA
1 ATTTAAATTT---AA-A-A--TAA
*
27982650 ATTTAAATTTAAGATAA
1 ATTTAAATTTAAAATAA
27982667 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
27982685 ATTTAAA
1 ATTTAAA
27982692 AGCAATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
17 23 0.42
18 13 0.24
19 1 0.02
20 2 0.04
21 3 0.05
24 13 0.24
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:27982661 original size:41 final size:41
Alignment explanation
Indices: 27982609--27982691 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
27982599 GTTTAAAACC
*
27982609 ATTTAAATTTAA-AGTAAATTTAAATTTAAAAATAGATTTAA
1 ATTTAAATTTAAGA-TAAATTTAAATTTAAAAATAAATTTAA
27982650 ATTTAAATTTAAGATAAATTTAAATTTAAAAATAAATTTAA
1 ATTTAAATTTAAGATAAATTTAAATTTAAAAATAAATTTAA
27982691 A
1 A
27982692 AGCAATTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 39 0.98
42 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (41 bp):
ATTTAAATTTAAGATAAATTTAAATTTAAAAATAAATTTAA
Found at i:27982667 original size:29 final size:29
Alignment explanation
Indices: 27982612--27982690 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
27982602 TAAAACCATT
*
27982612 TAAATTT-AAAGTAAATTTAA-ATTTAAAAA
1 TAAATTTAAAAATAAATTTAAGA--TAAAAA
* ** **
27982641 TAGATTTAAATTTAAATTTAAGATAAATT
1 TAAATTTAAAAATAAATTTAAGATAAAAA
27982670 TAAATTTAAAAATAAATTTAA
1 TAAATTTAAAAATAAATTTAA
27982691 AAGCAATTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 28 0.70
30 11 0.28
31 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
TAAATTTAAAAATAAATTTAAGATAAAAA
Found at i:27982674 original size:23 final size:24
Alignment explanation
Indices: 27982623--27982679 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
27982613 AAATTTAAAG
*
27982623 TAAATTTAAATTTAAAAATAGATT
1 TAAATTTAAATTTAAAAATAAATT
*
27982647 TAAATTTAAATTT-AAGATAAATT
1 TAAATTTAAATTTAAAAATAAATT
27982670 TAAATTTAAA
1 TAAATTTAAA
27982680 AATAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAATTTAAATTTAAAAATAAATT
Found at i:27983259 original size:49 final size:49
Alignment explanation
Indices: 27983139--27983777 Score: 393
Period size: 49 Copynumber: 13.0 Consensus size: 49
27983129 CTTCAATCTG
** * * *
27983139 CATGGTACTAAATTCGCCGTCGTGGCTTAAAT-TTTCCTTTCATG-CTT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
* * *
27983186 C-TGAGGTA-TAAGG-TTCGCCATTGCGGCTTAAACCTTTCCCTTCGTGTCTT
1 CAT--GGTACT--GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
* * *
27983236 CATGGTATTGGATTCGTCGTTGCGGCTTAAATATTTCCCTTCATGTCTCT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCT-T
* ** * * * *
27983286 GA-GGTA-TAAGG-TTTTCCGTTGTGACTTAAATCTTTCCCTCCATATCTT
1 CATGGTACT--GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
*
27983334 CATCGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
* * * * * *
27983382 C-TGAGGTACAAGG-TTCACCGTTGTGACTTAAACCTTTCCC-TCTATATCTT
1 CAT--GGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTC-ATGTCTT
*
27983432 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TT
* * * * **
27983482 GA-GGTA-TAAGG-TTCGCCGTTGCGACTTAAACCTTTTCCCTCCAAATCTT
1 CATGGTACT--GGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCATGTCTT
* * *
27983531 CGTGATACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATG-CTT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
* * * * * * * **
27983579 CTAAGGTACAAGG-TTCGCCATTGCGACTTAAACCTTTTTCCTCCAAATCTT
1 C-ATGGTAC-TGGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCATGTCTT
* *
27983630 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATATTTCCCTTCATG-CTT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
* * * * * * * **
27983678 C-TGAGGTACAAGG-TTTGCCGTTACGACTTAAACCTTTTTCCTCCAAATCTT
1 CAT--GGTAC-TGGATTCGCCGTTGCGGCTTAAATC-TTTCCCTTCATGTCTT
* * * * *
27983729 CGTGATACTGGATTCGTCGTTACGGCTTAAATCTTTTCCTTCATG-CTT
1 CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
27983777 C
1 C
27983778 TGCGGTACTG
Statistics
Matches: 449, Mismatches: 101, Indels: 83
0.71 0.16 0.13
Matches are distributed among these distances:
46 1 0.00
47 4 0.01
48 48 0.11
49 267 0.59
50 117 0.26
51 11 0.02
52 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (49 bp):
CATGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT
Found at i:27983314 original size:98 final size:99
Alignment explanation
Indices: 27983141--27983785 Score: 843
Period size: 99 Copynumber: 6.6 Consensus size: 99
27983131 TCAATCTGCA
** * * * *
27983141 TGGTACTAAATTCGCCGTCGTGGCTTAAAT-TTTCCTTTCATGCTTCTGAGGTATAAGGTTCGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
* * * *** *
27983205 ATTGCGGCTTAAACC-TTTCCCTTCGTGTCTTCA
66 GTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
* * * * **
27983238 TGGTATTGGATTCGTCGTTGCGGCTTAAATATTTCCCTTCATG-TCTCTGAGGTATAAGGTTTTC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTCGC
* * * *
27983302 CGTTGTGACTTAAATC-TTTCCCTCCATATCTTCA
65 CGTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
* *
27983336 TCGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
* * *
27983401 GTTGTGACTTAAACC-TTTCCCTCTATATCTTCG
66 GTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
*
27983434 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTCGC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGGTTCGC
27983498 CGTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
65 CGTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
* * *
27983533 TGATACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
* *
27983598 ATTGCGACTTAAACCTTTTTCCTCCAAATCTTCG
66 GTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
* *
27983632 TGGTACTGGATTCGCCGTTGCGGCTTAAATATTTCCCTTCATGCTTCTGAGGTACAAGGTTTGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
* *
27983697 GTTACGACTTAAACCTTTTTCCTCCAAATCTTCG
66 GTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
* * * * *
27983731 TGATACTGGATTCGTCGTTACGGCTTAAATCTTTTCCTTCATGCTTCTGCGGTAC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTAC
27983786 TGAGACTTGT
Statistics
Matches: 491, Mismatches: 51, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
97 25 0.05
98 216 0.44
99 250 0.51
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (99 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
GTTGCGACTTAAACCTTTTCCCTCCAAATCTTCG
Found at i:27984230 original size:18 final size:18
Alignment explanation
Indices: 27984204--27984238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27984194 AAAATTGCTG
*
27984204 AATATTTACAAGAAACAA
1 AATAATTACAAGAAACAA
*
27984222 AATAATTACAAGGAACA
1 AATAATTACAAGAAACA
27984239 GTATTAGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGAAACAA
Found at i:27989138 original size:17 final size:18
Alignment explanation
Indices: 27989118--27989159 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27989108 GTTTAAAACC
27989118 ATTTCAAATTT-AAT-TAA
1 ATTT-AAATTTAAATATAA
27989135 ATTTAAATTTAAATATAA
1 ATTTAAATTTAAATATAA
27989153 ATTTAAA
1 ATTTAAA
27989160 ACCAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 7 0.30
18 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTAAATTTAAATATAA
Found at i:27989142 original size:6 final size:6
Alignment explanation
Indices: 27989118--27989159 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
27989108 GTTTAAAACC
*
27989118 ATTTCAA ATTT-A A-TTAA ATTTAA ATTTAA ATATAA ATTTAA A
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
27989160 ACCAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 2 0.06
5 4 0.13
6 21 0.68
7 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:27989509 original size:25 final size:25
Alignment explanation
Indices: 27989468--27989518 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
27989458 ATCTTTATAC
*
27989468 ATATTGAATTTTCATAT-TAATAAAT
1 ATATTGAATTTTAATATGT-ATAAAT
27989493 ATATTG-ATTTATAATATGTATAAAT
1 ATATTGAATTT-TAATATGTATAAAT
27989518 A
1 A
27989519 AATTTTACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 18 0.78
26 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
ATATTGAATTTTAATATGTATAAAT
Done.