Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008007.1 Hibiscus syriacus cultivar Beakdansim tig00110469_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1953294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1512958 original size:37 final size:37
Alignment explanation
Indices: 1512885--1513076 Score: 234
Period size: 37 Copynumber: 5.2 Consensus size: 37
1512875 TTTTTGAAAC
* *
1512885 TATATAA-TTTCCAAAAATGTTTTAAAAATTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
1512921 TATATAAGTTTT-AAAAATGTTTTCAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATAT
1512958 TATATAAGTTTT-AAAAATGTTTTTTAAAAA-TCATATAT
1 TATATAAGTTTTCAAAAATG--TTTTAAAAACT-ATATAT
* *
1512996 TATATATA-TTTTCTAAAATATTTTAAAAACTATATAT
1 TATATA-AGTTTTCAAAAATGTTTTAAAAACTATATAT
*
1513033 TATAT-AGTTTTCAAAAATATTTTAGAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTT--AAAAACTATATAT
1513071 TATATA
1 TATATA
1513077 CGTATTTTTA
Statistics
Matches: 139, Mismatches: 5, Indels: 21
0.84 0.03 0.13
Matches are distributed among these distances:
35 1 0.01
36 33 0.24
37 55 0.40
38 40 0.29
39 10 0.07
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:1513116 original size:2 final size:2
Alignment explanation
Indices: 1513105--1513171 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
1513095 GTTTGCAAAC
1513105 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1513146 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1513172 CAATAATAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1513309 original size:58 final size:57
Alignment explanation
Indices: 1513208--1513694 Score: 403
Period size: 58 Copynumber: 8.4 Consensus size: 57
1513198 AGTGTCTACA
* * * * *
1513208 ATTCCCTTACCATTTTAGCACA-TAAAATGCCCTATCTGGAATCCATATTTTTAATATG
1 ATTCCCTTACCA-TTTAGCACACT-CAGTGCTCTATATGGAATCCATATTTTCAATATG
* * *** *
1513266 ATTCCCTTACCGTTTAGCACACTCAGTACTCTATATGGAAATCCATACACTCAGTATG
1 ATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGG-AATCCATATTTTCAATATG
* * * * * * *
1513324 ATTCCCTTACTATTTTAGCACA-TAAAATGCCCTATCTCGAATCCATCTTTTCAATATG
1 ATTCCCTTACCA-TTTAGCACACT-CAGTGCTCTATATGGAATCCATATTTTCAATATG
* *** * *
1513382 ATTCCTTTACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTACG
1 ATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGG-AATCCATATTTTCAATATG
* *
1513440 ATTCCCATACCATTTTAGCACA-TAACA-TG-TCCTATCTGGAATCCATATTTTCAATATG
1 ATTCCCTTACCA-TTTAGCACACT--CAGTGCT-CTATATGGAATCCATATTTTCAATATG
* *** *
1513498 ATTCCTTTACCATTTAGCACACTC-GATGCTCTATATGGAAATCCATACACTCAGTATG
1 ATTCCCTTACCATTTAGCACACTCAG-TGCTCTATATGG-AATCCATATTTTCAATATG
* * * * *
1513556 ATTCCCTTACCATTTTAGCATA-TAAAATGCCCTATCTGGAATCCATATTTTCAATATG
1 ATTCCCTTACCA-TTTAGCACACT-CAGTGCTCTATATGGAATCCATATTTTCAATATG
*** *
1513614 ATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATG
1 ATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGG-AATCCATATTTTCAATATG
* *
1513672 ATTTCCTTATCATTTTAGCACAC
1 ATTCCCTTACCA-TTTAGCACAC
1513695 AAAGTGCCAT
Statistics
Matches: 335, Mismatches: 73, Indels: 41
0.75 0.16 0.09
Matches are distributed among these distances:
56 1 0.00
57 75 0.22
58 193 0.58
59 64 0.19
60 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (57 bp):
ATTCCCTTACCATTTAGCACACTCAGTGCTCTATATGGAATCCATATTTTCAATATG
Found at i:1513414 original size:116 final size:116
Alignment explanation
Indices: 1513208--1513702 Score: 821
Period size: 116 Copynumber: 4.3 Consensus size: 116
1513198 AGTGTCTACA
*
1513208 ATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTTAATATGATTCCCT
1 ATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCT
* *
1513273 TACCGTTTAGCACACTCAGTACTCTATATGGAAATCCATACACTCAGTATG
66 TACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * *
1513324 ATTCCCTTACTATTTTAGCACATAAAATGCCCTATCTCGAATCCATCTTTTCAATATGATTCCTT
1 ATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCT
*
1513389 TACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTACG
66 TACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * *
1513440 ATTCCCATACCATTTTAGCACATAACATGTCCTATCTGGAATCCATATTTTCAATATGATTCCTT
1 ATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCT
1513505 TACCATTTAGCACACTC-GATGCTCTATATGGAAATCCATACACTCAGTATG
66 TACCATTTAGCACACTCAG-TGCTCTATATGGAAATCCATACACTCAGTATG
*
1513556 ATTCCCTTACCATTTTAGCATATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCT
1 ATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCT
1513621 TACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATG
66 TACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * *
1513672 ATTTCCTTATCATTTTAGCACACAAAGTGCC
1 ATTCCCTTACCATTTTAGCACATAAAATGCC
1513703 ATTTGGTAAT
Statistics
Matches: 352, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
115 1 0.00
116 350 0.99
117 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (116 bp):
ATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCT
TACCATTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATG
Found at i:1520138 original size:17 final size:18
Alignment explanation
Indices: 1520105--1520138 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1520095 TATTCTGATA
1520105 TTTAATCTCCAAGGAATC
1 TTTAATCTCCAAGGAATC
*
1520123 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAAGGAAT
1520139 GTACTACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTAATCTCCAAGGAATC
Found at i:1520587 original size:116 final size:116
Alignment explanation
Indices: 1520355--1521068 Score: 1142
Period size: 116 Copynumber: 6.1 Consensus size: 116
1520345 TATGATTTTG
* * * ** * * *
1520355 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATT-AGTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATCTG-GAATCCATA-TTTTCAATATGATTCCCTTACC
* * * * * *
1520419 TTTGTAGCACCCTTAATGCTTTATCTGGAAATCCATACACTCAGTATGATTCCC
64 ATT-TAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
1520473 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
* * * *
1520538 TTAGCACACTCAATTCTTTATATGGAAATCCATACACTCAGTATAATTCCC
66 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
* * * *
1520589 TTACCATTATAGCACATAAAATACCCTATATGGAATCCATATTTTCAATATGATTCTCTTACCAT
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
1520654 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
66 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
1520705 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
* *
1520770 TTAGCACACTCAGTGCTCTATATAGAAATCCATAAACTCAGTATGATTCCC
66 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
*
1520821 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCGCTTACCAT
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
1520886 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
66 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
*
1520937 TTACCATTTTAGCATATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
*
1521002 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTTCC
66 TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
*
1521053 TTATCATTTTAGCACA
1 TTACCATTTTAGCACA
1521069 CAAAGTGTCA
Statistics
Matches: 559, Mismatches: 36, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
116 505 0.90
117 24 0.04
118 30 0.05
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (116 bp):
TTACCATTTTAGCACATAAAATGCCCTATCTGGAATCCATATTTTCAATATGATTCCCTTACCAT
TTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGATTCCC
Found at i:1526232 original size:29 final size:29
Alignment explanation
Indices: 1526199--1526255 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1526189 TTTTTTTTGG
*
1526199 AACTTGAATTTTTAAAATTCTAAGGGACA
1 AACTTGAATTTATAAAATTCTAAGGGACA
* *
1526228 AACTTGAATTTATAAAATTTTATGGGAC
1 AACTTGAATTTATAAAATTCTAAGGGAC
1526256 GAAAACAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (29 bp):
AACTTGAATTTATAAAATTCTAAGGGACA
Found at i:1527961 original size:12 final size:12
Alignment explanation
Indices: 1527936--1528052 Score: 85
Period size: 12 Copynumber: 9.8 Consensus size: 12
1527926 ACGGAGATAT
* *
1527936 CAGAAATCAAAA
1 CAGAATTCAGAA
1527948 CAGAATTCAGAA
1 CAGAATTCAGAA
*
1527960 CA-AATATCATAA
1 CAGAAT-TCAGAA
* *
1527972 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
1527984 CATAAATCAGAA
1 CAGAATTCAGAA
**
1527996 CAGAATTCAGGT
1 CAGAATTCAGAA
*
1528008 CAGAAATCAGAA
1 CAGAATTCAGAA
**
1528020 CAGAATTCAGGT
1 CAGAATTCAGAA
*
1528032 CATGTA-TCAGAA
1 CA-GAATTCAGAA
1528044 CAGAATTCA
1 CAGAATTCA
1528053 AGTCAGAAAT
Statistics
Matches: 77, Mismatches: 24, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
11 5 0.06
12 67 0.87
13 5 0.06
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1527968 original size:24 final size:24
Alignment explanation
Indices: 1527934--1528066 Score: 146
Period size: 24 Copynumber: 5.5 Consensus size: 24
1527924 AAACGGAGAT
*
1527934 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1527958 AACA-AATATCATAACAGAATCCAG
1 ATCAGAA-ATCAGAACAGAATTCAG
*
1527982 ATCATAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
1528006 GTCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
1528030 GTCATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
1528053 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
1528067 TAAAATATTT
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
23 3 0.03
24 87 0.94
25 3 0.03
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1540896 original size:20 final size:19
Alignment explanation
Indices: 1540871--1540909 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1540861 AAACATTCTG
1540871 TTCTGGCCAGTTTCAAAACT
1 TTCTGG-CAGTTTCAAAACT
*
1540891 TTCTGGGAGTTTCAAAACT
1 TTCTGGCAGTTTCAAAACT
1540910 ATGACCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (19 bp):
TTCTGGCAGTTTCAAAACT
Found at i:1545594 original size:16 final size:16
Alignment explanation
Indices: 1545570--1545614 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1545560 TATCTAATTT
1545570 AACCTGAACCAAAAAC
1 AACCTGAACCAAAAAC
* *
1545586 AATCTGAACCGAAAAC
1 AACCTGAACCAAAAAC
*
1545602 AACCCGAACCAAA
1 AACCTGAACCAAA
1545615 TTTAATCTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.31, G:0.09, T:0.07
Consensus pattern (16 bp):
AACCTGAACCAAAAAC
Found at i:1545649 original size:32 final size:32
Alignment explanation
Indices: 1545586--1545685 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
1545576 AACCAAAAAC
* * *
1545586 AATCTGAACCGAAAACAACCCGAACCAAATTT
1 AATCTGAACCGAAAATAACCCAAACCGAATTT
* *
1545618 AATCTAAACCGAAAATAACCCAAACTGAATTT
1 AATCTGAACCGAAAATAACCCAAACCGAATTT
* *
1545650 AA-CTCGATCC-AAAAGTAACCCAAACCGAAATT
1 AATCT-GAACCGAAAA-TAACCCAAACCGAATTT
1545682 AATC
1 AATC
1545686 CGACCTGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
31 6 0.11
32 49 0.88
33 1 0.02
ACGTcount: A:0.48, C:0.26, G:0.08, T:0.18
Consensus pattern (32 bp):
AATCTGAACCGAAAATAACCCAAACCGAATTT
Found at i:1546265 original size:21 final size:20
Alignment explanation
Indices: 1546241--1546285 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
1546231 GATACTCAAT
1546241 TTAGATA-AATTGATTAATAAA
1 TTAGATATAA-TGATTAA-AAA
1546262 TTAGATATTAATGATTAAAAA
1 TTAGATA-TAATGATTAAAAA
1546283 TTA
1 TTA
1546286 AACAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 13 0.59
22 7 0.32
23 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
TTAGATATAATGATTAAAAA
Found at i:1547078 original size:14 final size:15
Alignment explanation
Indices: 1547061--1547092 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1547051 ATAATAAATA
1547061 ATTAT-AAATATATT
1 ATTATAAAATATATT
1547075 ATTATAAAATATATT
1 ATTATAAAATATATT
1547090 ATT
1 ATT
1547093 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:1547693 original size:55 final size:52
Alignment explanation
Indices: 1547578--1547690 Score: 217
Period size: 52 Copynumber: 2.2 Consensus size: 52
1547568 CTCCGTTAAC
*
1547578 CTTCTTTTTTTGCTGACGAGGCAGTTCTTTCTTCTTCTTCAACTCCCGTTGA
1 CTTCTTCTTTTGCTGACGAGGCAGTTCTTTCTTCTTCTTCAACTCCCGTTGA
1547630 CTTCTTCTTTTGCTGACGAGGCAGTTCTTTCTTCTTCTTCAACTCCCGTTGA
1 CTTCTTCTTTTGCTGACGAGGCAGTTCTTTCTTCTTCTTCAACTCCCGTTGA
1547682 CTTCTTCTT
1 CTTCTTCTT
1547691 CTTCTTCTTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.11, C:0.28, G:0.14, T:0.47
Consensus pattern (52 bp):
CTTCTTCTTTTGCTGACGAGGCAGTTCTTTCTTCTTCTTCAACTCCCGTTGA
Found at i:1548474 original size:16 final size:16
Alignment explanation
Indices: 1548453--1548484 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1548443 ATTTTTTGAA
*
1548453 AAATGACTTACGGTCT
1 AAATGACTTACAGTCT
1548469 AAATGACTTACAGTCT
1 AAATGACTTACAGTCT
1548485 GATTTTCCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (16 bp):
AAATGACTTACAGTCT
Found at i:1548657 original size:21 final size:21
Alignment explanation
Indices: 1548611--1548663 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1548601 TAATTATTAA
*
1548611 AATATTTAAAATATATTTATT
1 AATATTTAAAATATATATATT
*
1548632 AATATTTATAATATATAATATT
1 AATATTTAAAATATAT-ATATT
*
1548654 ATATCTTTAA
1 A-ATATTTAA
1548664 TGTTATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 15 0.58
22 5 0.19
23 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTTAAAATATATATATT
Found at i:1548754 original size:55 final size:55
Alignment explanation
Indices: 1548639--1548745 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 55
1548629 ATTAATATTT
* *
1548639 ATAATATATAATATTATATCTTTAATGTTATAATAATATACTCAATTATATTATA
1 ATAATATATAATATTATATCTTTAATGTTATAATAATATAATAAATTATATTATA
* *
1548694 ATAATATA-AGATATTATAT-TTTTATTTTAATAAT-ATATAATAAATTAT-TTAT
1 ATAATATATA-ATATTATATCTTTAATGTT-ATAATAATATAATAAATTATATTAT
1548746 TATTTAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 4 0.09
54 20 0.43
55 22 0.48
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (55 bp):
ATAATATATAATATTATATCTTTAATGTTATAATAATATAATAAATTATATTATA
Found at i:1548822 original size:27 final size:26
Alignment explanation
Indices: 1548743--1548846 Score: 84
Period size: 27 Copynumber: 3.7 Consensus size: 26
1548733 ATAAATTATT
* *
1548743 TATTATTTAATAATTTCATAGAAATAA
1 TATTATTTAAT-ATTTAATATAAATAA
* *
1548770 TATTATTAAAT-TATTAATAATGAATAA
1 TATTATTTAATAT-TTAAT-ATAAATAA
1548797 TATTATTTATATATTTAATATTAATATAA
1 TATTATTTA-ATATTTAATA-TAA-ATAA
*
1548826 TAATATTTTAATATTTTAATA
1 TATTA-TTTAATA-TTTAATA
1548847 AAAACATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
25 1 0.02
26 4 0.06
27 25 0.40
28 9 0.15
29 12 0.19
30 11 0.18
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (26 bp):
TATTATTTAATATTTAATATAAATAA
Found at i:1552634 original size:3 final size:3
Alignment explanation
Indices: 1552628--1553086 Score: 348
Period size: 3 Copynumber: 152.7 Consensus size: 3
1552618 CATCACCACG
* * * * * * * * *
1552628 ATT ATT ATT ATG ATT ATT ATG ATC ATC ATC ATC ATC ATT ATC ATG ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
1552676 ATT ATT ATG ATC ATC ATC ATC ATT ATT ATC ATG ATT ATT ATT ATG ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
1552724 ATT ATT ATT ATG ATC ATC ATC ATC ATT ATT ATC ATT ATT A-G ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
1552770 GATT ATT ATG ATC ATC ATC ATC ATT ATT ATC ATT ATT ATG ATT -TT
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
1552815 GATT ATT ATG ATC ATC ATC ATT ATT ATC ATG ATT ATT ATT ATG ATT
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
1552861 ATT ATT ATT ATG ATC ATC ATC ATC ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
1552909 ATC ATT ATT ATT ATT ATC ATT ATT ATT ATT ATA ATT ATC ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1552957 ATT ATT ATC ATT ATC ATT ATT ATT ATT ATT CATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
* * *
1553003 CATT ATT ATT ATT ATC ATT ATT ATT ATT ATC ATT ATT ATT ATT ATC
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
1553049 ATT ATT ATC ATT ATC ATT ATC ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1553087 CATCTTCTTC
Statistics
Matches: 380, Mismatches: 69, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
2 5 0.01
3 365 0.96
4 10 0.03
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:1553331 original size:18 final size:18
Alignment explanation
Indices: 1553308--1553349 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1553298 CCTTAATATC
*
1553308 ATATTTCAA-AAATTTTAA
1 ATATTT-AATAAAATTTAA
1553326 ATATTTAATAAAATTTAA
1 ATATTTAATAAAATTTAA
1553344 AT-TTTA
1 ATATTTA
1553350 GGGTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATTTAATAAAATTTAA
Found at i:1559024 original size:21 final size:20
Alignment explanation
Indices: 1558999--1559050 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1558989 ACACAGTTTC
1558999 CGAATTCGCAACACAGAATAT
1 CGAATTCGCAACACAGAA-AT
* *
1559020 GGAATTCGC-ACACAGAAGT
1 CGAATTCGCAACACAGAAAT
1559039 CGAATTCGCAAC
1 CGAATTCGCAAC
1559051 TCGAATTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
CGAATTCGCAACACAGAAAT
Found at i:1559045 original size:19 final size:20
Alignment explanation
Indices: 1558999--1559048 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1558989 ACACAGTTTC
1558999 CGAATTCGCAACACAGAATAT
1 CGAATTCGC-ACACAGAATAT
* *
1559020 GGAATTCGCACACAGAA-GT
1 CGAATTCGCACACAGAATAT
1559039 CGAATTCGCA
1 CGAATTCGCA
1559049 ACTCGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 8 0.31
21 8 0.31
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
CGAATTCGCACACAGAATAT
Found at i:1559108 original size:20 final size:20
Alignment explanation
Indices: 1559085--1559213 Score: 79
Period size: 20 Copynumber: 6.5 Consensus size: 20
1559075 AAATTTCTTT
1559085 TTCGCAAATCGATTTTTAAA
1 TTCGCAAATCGATTTTTAAA
*
1559105 TTCGCAACA-CGAGTTTCTT--T
1 TTCGCAA-ATCGA-TTT-TTAAA
* * *
1559125 TTCTCAACTCGATTTTTTAA
1 TTCGCAAATCGATTTTTAAA
* * *
1559145 TTCGCAAAGCGAGTTTTAAT
1 TTCGCAAATCGATTTTTAAA
*
1559165 TTCGCAACTCGA-TTTTAGAA
1 TTCGCAAATCGATTTTTA-AA
* * *
1559185 TTCGTAAAACGA-ATTTAAA
1 TTCGCAAATCGATTTTTAAA
1559204 TTTCGCAAAT
1 -TTCGCAAAT
1559214 AAGCTTTTAA
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
18 2 0.02
19 10 0.12
20 64 0.78
21 4 0.05
22 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
TTCGCAAATCGATTTTTAAA
Found at i:1559158 original size:40 final size:40
Alignment explanation
Indices: 1559043--1559188 Score: 154
Period size: 40 Copynumber: 3.6 Consensus size: 40
1559033 AGAAGTCGAA
** * *
1559043 TTCGCAACTCGAATTTGACAAATTCGCAACACAAATTTCTTT
1 TTCGCAACTCG-ATTT-TTAAATTCGCAACACGAGTTTCTTT
*
1559085 TTCGCAAATCGATTTTTAAATTCGCAACACGAGTTTCTTT
1 TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCTTT
* * *
1559125 TTCTCAACTCGATTTTTTAATTCGCAA-AGCGAGTTT-TAAT
1 TTCGCAACTCGATTTTTAAATTCGCAACA-CGAGTTTCT-TT
1559165 TTCGCAACTCGA-TTTTAGAATTCG
1 TTCGCAACTCGATTTTTA-AATTCG
1559189 TAAAACGAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 6 0.07
40 70 0.78
41 4 0.04
42 10 0.11
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (40 bp):
TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCTTT
Found at i:1559206 original size:40 final size:39
Alignment explanation
Indices: 1559084--1559211 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 39
1559074 CAAATTTCTT
* * ***
1559084 TTTCGCAAATCGATTTTTAAATTCGCAACACGAGTTTCTT
1 TTTCGCAACTCGA-TTTTAAATTCGCAAAACGAGTTTAAA
* * * *
1559124 TTTCTCAACTCGATTTTTTAATTCGCAAAGCGAGTTTTAA
1 TTTCGCAACTCGA-TTTTAAATTCGCAAAACGAGTTTAAA
* *
1559164 TTTCGCAACTCGATTTTAGAATTCGTAAAACGAATTTAAA
1 TTTCGCAACTCGATTTTA-AATTCGCAAAACGAGTTTAAA
1559204 TTTCGCAA
1 TTTCGCAA
1559212 ATAAGCTTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 4 0.05
40 69 0.95
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (39 bp):
TTTCGCAACTCGATTTTAAATTCGCAAAACGAGTTTAAA
Found at i:1559344 original size:22 final size:22
Alignment explanation
Indices: 1559326--1559373 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1559316 CTCTCTCCAG
1559326 CGACATCCGTCCCCATCTCCGA
1 CGACATCCGTCCCCATCTCCGA
1559348 CGACATCCGTCCCCATCTCCGA
1 CGACATCCGTCCCCATCTCCGA
1559370 CGAC
1 CGAC
1559374 CCCCCTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.15, T:0.17
Consensus pattern (22 bp):
CGACATCCGTCCCCATCTCCGA
Found at i:1559385 original size:20 final size:21
Alignment explanation
Indices: 1559326--1559387 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
1559316 CTCTCTCCAG
*
1559326 CGACATCCGTCCCCATCTCCGA
1 CGACA-CCGCCCCCATCTCCGA
*
1559348 CGACATCCGTCCCCATCTCCGA
1 CGACA-CCGCCCCCATCTCCGA
1559370 CGAC-CC-CCCTCCATCTCC
1 CGACACCGCCC-CCATCTCC
1559388 ATCTCTCACA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 2 0.05
20 10 0.26
22 26 0.68
ACGTcount: A:0.16, C:0.55, G:0.11, T:0.18
Consensus pattern (21 bp):
CGACACCGCCCCCATCTCCGA
Found at i:1559743 original size:20 final size:20
Alignment explanation
Indices: 1559720--1559787 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1559710 CAAGAAACTT
*
1559720 AAATTCACAACACGAAAATG
1 AAATTCGCAACACGAAAATG
* *
1559740 AAATTCGTAATACGAAAATCG
1 AAATTCGCAACACGAAAAT-G
* *
1559761 AAAATT-GCAACTCGAAAATA
1 -AAATTCGCAACACGAAAATG
1559781 AAATTCG
1 AAATTCG
1559788 AAAATAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 5 0.13
20 17 0.45
21 11 0.29
22 5 0.13
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:1559790 original size:13 final size:13
Alignment explanation
Indices: 1559772--1559801 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1559762 AAATTGCAAC
1559772 TCGAAAATAAAAT
1 TCGAAAATAAAAT
1559785 TCGAAAATAAAAT
1 TCGAAAATAAAAT
1559798 TCGA
1 TCGA
1559802 GTTGCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (13 bp):
TCGAAAATAAAAT
Found at i:1561265 original size:42 final size:42
Alignment explanation
Indices: 1561206--1561371 Score: 248
Period size: 42 Copynumber: 4.0 Consensus size: 42
1561196 CCCCACTTTT
*
1561206 TCATCAAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
*
1561248 TCATCGAGTCGATTCTCCACTTCGACACCAAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
*
1561290 TCATCGAGTCGATTCTCCACTTCAACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
* * * *
1561332 TC-T--AGCCGACTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1561371 T
1 T
1561372 ATTCCATCAC
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 32 0.28
41 1 0.01
42 82 0.71
ACGTcount: A:0.26, C:0.39, G:0.12, T:0.23
Consensus pattern (42 bp):
TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
Found at i:1561505 original size:21 final size:21
Alignment explanation
Indices: 1561471--1561766 Score: 290
Period size: 21 Copynumber: 14.1 Consensus size: 21
1561461 ACCTCCACGG
* * *
1561471 GATGAGTTAGGTGCTTTACAT
1 GATGAGGTCGGTGCTTTACGT
* *
1561492 GACGAGGTCAGTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
*
1561513 GATAAGGTCGGTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
1561534 GATGAGGTCGGTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
1561555 GATGAGGTCGGTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
* *
1561576 GATGAGGTCGGTACTTTATGT
1 GATGAGGTCGGTGCTTTACGT
** *
1561597 GATGATAAT-GGTACTTTACGT
1 GATGA-GGTCGGTGCTTTACGT
* *
1561618 GATAAGGTAGGTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
* * *
1561639 GGTGAGGTAGCTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
* * *
1561660 GGTGAGGTAGCTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
** *
1561681 GATGACAAT-GGTGTTTTACGT
1 GATGA-GGTCGGTGCTTTACGT
* * *
1561702 GATGAGGTAGGTGTTTTACAT
1 GATGAGGTCGGTGCTTTACGT
* * *
1561723 GGTGAGGTAGCTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
* *
1561744 TATGAGGTAGGTGCTTTACGT
1 GATGAGGTCGGTGCTTTACGT
1561765 GA
1 GA
1561767 GATTGTTTCA
Statistics
Matches: 234, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
20 2 0.01
21 230 0.98
22 2 0.01
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.35
Consensus pattern (21 bp):
GATGAGGTCGGTGCTTTACGT
Found at i:1561614 original size:84 final size:84
Alignment explanation
Indices: 1561473--1561766 Score: 342
Period size: 84 Copynumber: 3.5 Consensus size: 84
1561463 CTCCACGGGA
* * * * * *
1561473 TGAGTTAGGTGCTTTACATGACGAGGTCA-GTGCTTTACGTGAT-A-AGGTCGGTGCTTTACGTG
1 TGAGGTAGCTGCTTTACGTGATGAGGT-AGGTGCTTTACGTGATGACA-AT-GGTACTTTACGTG
* *
1561535 ATGAGGTCGGTGCTTTACGTGA
63 ATGAGGTAGGTGCTTTACGTGG
* * * * * * *
1561557 TGAGGTCGGTGCTTTACGTGATGAGGTCGGTACTTTATGTGATGATAATGGTACTTTACGTGATA
1 TGAGGTAGCTGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAATGGTACTTTACGTGATG
1561622 AGGTAGGTGCTTTACGTGG
66 AGGTAGGTGCTTTACGTGG
* * **
1561641 TGAGGTAGCTGCTTTACGTGGTGAGGTAGCTGCTTTACGTGATGACAATGGTGTTTTACGTGATG
1 TGAGGTAGCTGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAATGGTACTTTACGTGATG
* *
1561706 AGGTAGGTGTTTTACATGG
66 AGGTAGGTGCTTTACGTGG
*
1561725 TGAGGTAGCTGCTTTACGTTATGAGGTAGGTGCTTTACGTGA
1 TGAGGTAGCTGCTTTACGTGATGAGGTAGGTGCTTTACGTGA
1561767 GATTGTTTCA
Statistics
Matches: 179, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
84 176 0.98
85 2 0.01
86 1 0.01
ACGTcount: A:0.19, C:0.12, G:0.34, T:0.35
Consensus pattern (84 bp):
TGAGGTAGCTGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAATGGTACTTTACGTGATG
AGGTAGGTGCTTTACGTGG
Found at i:1562128 original size:21 final size:21
Alignment explanation
Indices: 1562068--1562197 Score: 111
Period size: 21 Copynumber: 6.2 Consensus size: 21
1562058 GAAAAAGCCT
** *
1562068 GATCCACCTATCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * *
1562089 GGTCCACATCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * *
1562110 GATTCACCTCTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
1562131 GAGGCC-CCTCCCATCATTCAG
1 GA-TCCACCTCCCATCGTTCAG
*
1562152 GATCCACCTCCCATCATTCAG
1 GATCCACCTCCCATCGTTCAG
*
1562173 GATCCACC-CCACATCGTTTAG
1 GATCCACCTCC-CATCGTTCAG
1562194 GATC
1 GATC
1562198 TACATTCCAT
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
20 4 0.05
21 83 0.94
22 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:1564439 original size:20 final size:20
Alignment explanation
Indices: 1564325--1564439 Score: 142
Period size: 20 Copynumber: 5.8 Consensus size: 20
1564315 ATCAAATTCG
*
1564325 TCGAGTTGCGAATTCGATTT
1 TCGAGTTGCGAATTTGATTT
* *
1564345 TCGAGTT-CGAATTTGAATA
1 TCGAGTTGCGAATTTGATTT
* *
1564364 TCGAGTTGCGATTTTCATGTT
1 TCGAGTTGCGAATTTGAT-TT
* **
1564385 TCGAATTGCGAATTCAATTT
1 TCGAGTTGCGAATTTGATTT
1564405 TCGAGTTGCGAATTTGATTT
1 TCGAGTTGCGAATTTGATTT
1564425 TCGAGTTGCGAATTT
1 TCGAGTTGCGAATTT
1564440 AAGCTGCGAA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
19 16 0.20
20 48 0.61
21 15 0.19
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGAGTTGCGAATTTGATTT
Found at i:1564989 original size:18 final size:18
Alignment explanation
Indices: 1564963--1565003 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1564953 AGGTGAAGGC
*
1564963 GATTGTGATTGAGATTTT
1 GATTTTGATTGAGATTTT
*
1564981 GATTTTGATTGCGATTTT
1 GATTTTGATTGAGATTTT
1564999 GATTT
1 GATTT
1565004 CCCTTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGAGATTTT
Found at i:1567333 original size:24 final size:24
Alignment explanation
Indices: 1567304--1567363 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1567294 CTGAAACATC
1567304 ATCAAAA-TCTGAGTATTGACCAAG
1 ATCAAAATTC-GAGTATTGACCAAG
* *
1567328 ATCAAAGTTCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
1567352 ATCAAATTTCGA
1 ATCAAAATTCGA
1567364 ATACTTACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:1568429 original size:20 final size:19
Alignment explanation
Indices: 1568347--1568430 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 19
1568337 GAAAAATCAA
* * *
1568347 GTTGCAAAAACGAAATTCAT
1 GTTGCGAAAA-GAAACTCGT
*
1568367 GTTGCGAAAATGAAACTCGC
1 GTTGCGAAAA-GAAACTCGT
* * * *
1568387 GTTACGAATTAGAAAATCTT
1 GTTGCGAA-AAGAAACTCGT
1568407 GTTGCGAAAAGGAAACTCGT
1 GTTGCGAAAA-GAAACTCGT
1568427 GTTG
1 GTTG
1568431 TGAATTTAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (19 bp):
GTTGCGAAAAGAAACTCGT
Found at i:1568436 original size:40 final size:40
Alignment explanation
Indices: 1568366--1568444 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1568356 ACGAAATTCA
*
1568366 TGTTGCGAAAATGAAACTCGCGTTACGAA-TTAGAAAATCT
1 TGTTGCGAAAAGGAAACTCGCGTTACGAATTTA-AAAATCT
* **
1568406 TGTTGCGAAAAGGAAACTCGTGTTGTGAATTTAAAAATC
1 TGTTGCGAAAAGGAAACTCGCGTTACGAATTTAAAAATC
1568445 AAGTTTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (40 bp):
TGTTGCGAAAAGGAAACTCGCGTTACGAATTTAAAAATCT
Found at i:1569043 original size:34 final size:35
Alignment explanation
Indices: 1568975--1569070 Score: 86
Period size: 37 Copynumber: 2.6 Consensus size: 35
1568965 TAAAATATTA
** * *
1568975 AAAAAATAAATAAATATTAAAAAGTATTTTAAAAA-TT
1 AAAAAATAAA-AAATA--AAAAATAATTTAAAAAAGAT
*
1569012 AAGAAATAAAAAATAAAAAATAATTTAAAAAAGAT
1 AAAAAATAAAAAATAAAAAATAATTTAAAAAAGAT
*
1569047 AAAAATATAAAAAATGATAAAATA
1 AAAAA-ATAAAAAAT-AAAAAATA
1569071 TAAATTATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
34 14 0.29
35 5 0.10
36 14 0.29
37 16 0.33
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (35 bp):
AAAAAATAAAAAATAAAAAATAATTTAAAAAAGAT
Found at i:1569057 original size:17 final size:17
Alignment explanation
Indices: 1569037--1569074 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1569027 AAAAATAATT
1569037 TAAAAAA-GATAAAAATA
1 TAAAAAATGAT-AAAATA
1569054 TAAAAAATGATAAAATA
1 TAAAAAATGATAAAATA
1569071 TAAA
1 TAAA
1569075 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAAAAATGATAAAATA
Found at i:1569261 original size:49 final size:48
Alignment explanation
Indices: 1569174--1569268 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 48
1569164 TATAGTTTTA
***
1569174 ATAAAAATATAAAAATAAATTTTATTTTTTAATATTTT-AATAAAAAT
1 ATAAAAATATAAAAATAAATTTTATTGAATAATATTTTAAATAAAAAT
*
1569221 ATAAAAATATAGTAAATTAAATTTTATTGAAT-ATAGTTTTAAATAAAA
1 ATAAAAATATA--AAAATAAATTTTATTGAATAATA-TTTTAAATAAAA
1569269 TGAAAACGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 11 0.28
48 3 0.08
49 19 0.47
50 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (48 bp):
ATAAAAATATAAAAATAAATTTTATTGAATAATATTTTAAATAAAAAT
Found at i:1569895 original size:22 final size:22
Alignment explanation
Indices: 1569870--1569912 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1569860 GATCTTAAGT
1569870 TACTAATTTTGTTTTAATGATC
1 TACTAATTTTGTTTTAATGATC
*
1569892 TACTACTTTTGTTTTAATGAT
1 TACTAATTTTGTTTTAATGAT
1569913 TATAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (22 bp):
TACTAATTTTGTTTTAATGATC
Found at i:1570833 original size:26 final size:27
Alignment explanation
Indices: 1570775--1570834 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 27
1570765 TTTAAAGTTT
*
1570775 TCGAGTTCGAGTCGAGCTCAGCAATAC
1 TCGAGTTCGACTCGAGCTCAGCAATAC
1570802 TC-AGTTCGACTCG-GCTCAGCAATAC
1 TCGAGTTCGACTCGAGCTCAGCAATAC
1570827 TCGAGTTC
1 TCGAGTTC
1570835 TCATCCGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 14 0.45
26 15 0.48
27 2 0.06
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (27 bp):
TCGAGTTCGACTCGAGCTCAGCAATAC
Found at i:1573418 original size:26 final size:24
Alignment explanation
Indices: 1573352--1573432 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
1573342 TTTCATATAA
* * *
1573352 TATTTTTTACATT-TTTTACATTT
1 TATTTTTTACATTAATATATATTT
* *
1573375 TCTTTTTTACTTTAATATATATTTT
1 TATTTTTTACATTAATATATA-TTT
* *
1573400 TATTTTTTAGATTATATATATATAT
1 TATTTTTTACATTA-ATATATATTT
1573425 TATTTTTT
1 TATTTTTT
1573433 TATTATCAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 11 0.24
24 4 0.09
25 24 0.52
26 7 0.15
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (24 bp):
TATTTTTTACATTAATATATATTT
Found at i:1573435 original size:33 final size:33
Alignment explanation
Indices: 1573389--1573520 Score: 106
Period size: 35 Copynumber: 3.8 Consensus size: 33
1573379 TTTTACTTTA
*
1573389 ATATATATTTTTATTTTTTAGATTATATATATAT
1 ATATATTTTTTTATTTTTTA-ATTATATATATAT
* *
1573423 AT-TATTTTTTTATTATCAATTTTATTAATTTATATAT
1 ATATATTTTTTTATT-T---TTTAATT-ATATATATAT
** *
1573460 ATATATATTTACTATTTTTTATTATATATATATAT
1 ATATAT-TTTTTTATTTTTTAAT-TATATATATAT
1573495 ATATATTATTTTTACTTTTTT-ATTAT
1 ATATATT-TTTTTA-TTTTTTAATTAT
1573521 TTTATTTATT
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
33 11 0.14
34 7 0.09
35 24 0.31
36 10 0.13
37 14 0.18
38 4 0.05
39 7 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (33 bp):
ATATATTTTTTTATTTTTTAATTATATATATAT
Found at i:1573494 original size:29 final size:29
Alignment explanation
Indices: 1573452--1573507 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1573442 TTTTATTAAT
*
1573452 TTATATATATATATATTTACTATTTTTTA
1 TTATATATATATATATATACTATTTTTTA
*
1573481 TTATATATATATATATATATTATTTTT
1 TTATATATATATATATATACTATTTTT
1573508 ACTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TTATATATATATATATATACTATTTTTTA
Found at i:1573522 original size:46 final size:44
Alignment explanation
Indices: 1573467--1573571 Score: 106
Period size: 48 Copynumber: 2.3 Consensus size: 44
1573457 TATATATATA
*
1573467 TTTACTATTTTTTATTAT-ATATATATATATATATTATTTTTACTTT
1 TTTATTATTTTTTATT-TGATATATATATATATATT-TTTTT-CTTT
* * *
1573513 TTTATTATTTTATTTATTTGTTTTATTTATATATATTTTTTTCTTT
1 TTTATTA-TTT-TTTATTTGATATATATATATATATTTTTTTCTTT
1573559 TTCT-TTATTTTTT
1 TT-TATTATTTTTT
1573572 TATATTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
44 3 0.06
45 3 0.06
46 15 0.29
47 10 0.20
48 20 0.39
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (44 bp):
TTTATTATTTTTTATTTGATATATATATATATATTTTTTTCTTT
Found at i:1573540 original size:18 final size:17
Alignment explanation
Indices: 1573511--1573582 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
1573501 TATTTTTACT
1573511 TTTTTATTATTTTATTTA
1 TTTTT-TTATTTTATTTA
*
1573529 TTTGTTTTATTTATATATA
1 TTT-TTTTATTT-TATTTA
* *
1573548 TTTTTTTCTTTTTCTTTA
1 TTTTTTT-ATTTTATTTA
1573566 TTTTTTTATATTTATTT
1 TTTTTTTAT-TTTATTT
1573583 TACTTACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.02
18 30 0.68
19 13 0.30
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTTTTTATTTTATTTA
Found at i:1573545 original size:48 final size:47
Alignment explanation
Indices: 1573492--1573636 Score: 127
Period size: 47 Copynumber: 2.9 Consensus size: 47
1573482 TATATATATA
*
1573492 TATATATATTATTTTTACTTTTTTATTATTTTATTTATTTGTTTTATT
1 TATATATATTATTTTT-CTTTTTTATTATTTTATTTATTTGTTTTACT
* *
1573540 TATATATATT-TTTTTCTTTTTCT-TTATTTTTTTATATTTATTTTACT
1 TATATATATTATTTTTCTTTTT-TATTATTTTATT-TATTTGTTTTACT
*
1573587 TACTAT-T-TTATATTTGCTTTCTTTATCTTATCTTTTATTTAATTTGTTTT
1 TA-TATATATTAT-TTTTCTTT-TTTA--TTA--TTTTATTT-ATTTGTTTT
1573637 TTTCTTCATT
Statistics
Matches: 79, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
46 17 0.22
47 21 0.27
48 21 0.27
49 2 0.03
51 3 0.04
52 1 0.01
53 14 0.18
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (47 bp):
TATATATATTATTTTTCTTTTTTATTATTTTATTTATTTGTTTTACT
Found at i:1573583 original size:11 final size:10
Alignment explanation
Indices: 1573496--1573584 Score: 53
Period size: 9 Copynumber: 9.2 Consensus size: 10
1573486 TATATATATA
*
1573496 TATATTATTT
1 TATATTTTTT
*
1573506 T-TACTTTTT
1 TATATTTTTT
*
1573515 TATTATTTTAT
1 TA-TATTTTTT
*
1573526 T-TATTTGTT
1 TATATTTTTT
* *
1573535 T-TATTTATA
1 TATATTTTTT
1573544 TATATTTTTT
1 TATATTTTTT
* *
1573554 TCT-TTTTCT
1 TATATTTTTT
1573563 T-TATTTTTT
1 TATATTTTTT
1573572 TATATTTATTT
1 TATATTT-TTT
1573583 TA
1 TA
1573585 CTTACTATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
8 1 0.02
9 33 0.55
10 14 0.23
11 12 0.20
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (10 bp):
TATATTTTTT
Found at i:1576864 original size:68 final size:69
Alignment explanation
Indices: 1576748--1576881 Score: 243
Period size: 68 Copynumber: 2.0 Consensus size: 69
1576738 GATTCAAACT
*
1576748 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
1576813 TTAA
66 TTAA
*
1576817 ATGAGATTGATCAAGCATAATCA-TTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
1576881 T
66 T
1576882 CAAGAGAGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
68 41 0.65
69 22 0.35
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCAAAGATCATAGAGCA
TTAA
Found at i:1577856 original size:32 final size:31
Alignment explanation
Indices: 1577810--1577894 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
1577800 ACAATGAGGA
*
1577810 CATCTTTGAAGATTCAACATCAAATGTTGGGG
1 CATCTTTG-AGATTCAACATCAAATATTGGGG
* * **
1577842 CATTTTTTGAGATTCAATATTGAATATTGGGG
1 CA-TCTTTGAGATTCAACATCAAATATTGGGG
*
1577874 CATCTTTGGGAATTCAACATC
1 CATCTTTGAG-ATTCAACATC
1577895 CTGATGCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
31 6 0.14
32 31 0.74
33 5 0.12
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
CATCTTTGAGATTCAACATCAAATATTGGGG
Found at i:1578580 original size:94 final size:96
Alignment explanation
Indices: 1578471--1578733 Score: 323
Period size: 106 Copynumber: 2.7 Consensus size: 96
1578461 ATATCGTGCC
*
1578471 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC-
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
1578535 T-AATTTCAACTTCACAGCGAAGGATATTGG
66 TCAATTTCAACTTCACAGCGAAGGATATTGG
*
1578565 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
*
1578630 AATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
65 -A--T------CAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * * *
1578671 ACTCGAGACAGGACAAGCTCAATTTCACAGCAAAGGGGCGGCTGGCTGTCAACAAACAATTTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTC
1578734 TTAGTTCCAT
Statistics
Matches: 145, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
94 60 0.41
95 2 0.01
99 1 0.01
105 1 0.01
106 81 0.56
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (96 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
TCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1578721 original size:106 final size:106
Alignment explanation
Indices: 1578536--1578781 Score: 321
Period size: 106 Copynumber: 2.3 Consensus size: 106
1578526 ACAATTTCCT
* *
1578536 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACAAAGG
* * * *
1578601 GACGGTTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCC
66 GACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAGCC
* ** * *
1578642 AATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAGGACAAGCTCAATTTCACAGCAAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACAAAGG
* ** * *
1578707 GGCGGCTGGCTGTCAACAAACAATTTCTTAGTTCCATAGCC
66 GACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAGCC
* * *
1578748 AATTTTAACTTCACGGCGGAGGATATTGGACTCG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCG
1578782 GAACAATAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 120 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (106 bp):
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACAAAGG
GACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAGCC
Found at i:1579133 original size:65 final size:65
Alignment explanation
Indices: 1579013--1579169 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
1579003 TTTGGAACTA
*
1579013 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
* * * * *
1579078 AATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATCTGTTTCCCTTGAAA
1 AATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC-ATTTCCCTTGAAA
**
1579141 CA
64 TG
* * *
1579143 AATTTCGTCTCCCTTGAGACATTTTCT
1 AATTTTGTCTCCCTTAAGACAGTTTCT
1579170 TTTGGAACTA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 6 0.08
65 71 0.92
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.39
Consensus pattern (65 bp):
AATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:1579214 original size:167 final size:167
Alignment explanation
Indices: 1578931--1579455 Score: 836
Period size: 167 Copynumber: 3.1 Consensus size: 167
1578921 ACAGTTTCCA
* * * * * * * *
1578931 AGTTTCCCTTGAAACAAAATATTTAAATTTGTTTTCATTGAAACTAATTTCGTCTCCCTTGATAT
1 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
* * *
1578996 ATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
66 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
*
1579061 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTAAGAT
131 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
* *
1579098 AGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
1 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
*
1579163 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTGAAA
66 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
*
1579228 ACATTTCCATTGAAATGAATTTTGTCTCTCTTGAGAT
131 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
*
1579265 AGTTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
1 AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
*
1579330 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGGAACATAAACATTGAAA
66 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
* * *
1579395 ACATTTCCCTTGAGATGAATTTTTTTTCTCTTGAGAT
131 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
* *
1579432 AGGTTCCCTTAAAACAAAAT-TTTG
1 AGTTTCCCTTGAAACAAAATCTTTG
1579456 TCTCCCTTGA
Statistics
Matches: 333, Mismatches: 25, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
166 4 0.01
167 329 0.99
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (167 bp):
AGTTTCCCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
Found at i:1579261 original size:102 final size:102
Alignment explanation
Indices: 1579080--1579263 Score: 246
Period size: 102 Copynumber: 1.8 Consensus size: 102
1579070 TTGAAATGAA
* * * * *
1579080 TTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTAAGATAATTTCTCTTGAAACAAAATCATTGAAACTATTTCCATTGAAACAAA
1579145 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
66 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
* **
1579182 TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAA-CATTGAAAAC-ATTTCCATTGAAATG
1 TTTTGTCTCTCTTAAGATAATTTCTCTTGAAACA-AAATCATTG-AAACTATTTCCATTGAAACA
* *
1579245 AATTTTGTCTCTCTTGAGA
64 AATTTCGTCTCCCTTGAGA
1579264 TAGTTTCTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
102 64 0.91
103 6 0.09
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (102 bp):
TTTTGTCTCTCTTAAGATAATTTCTCTTGAAACAAAATCATTGAAACTATTTCCATTGAAACAAA
TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
Found at i:1579291 original size:65 final size:65
Alignment explanation
Indices: 1579182--1579328 Score: 188
Period size: 65 Copynumber: 2.3 Consensus size: 65
1579172 TGGAACTAAG
**
1579182 TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAATGAA
1 TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAACAAA
* * * ** *
1579247 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATATGTTTCCCTTGAAACAA
1 TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAA-CATTGAAAACATTTCCATTGAAACAA
1579311 A
65 A
* *
1579312 TTTCGTCTCCCTTGAGA
1 TTTTGTCTCTCTTGAGA
1579329 CATTTTCTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 3 0.04
65 68 0.96
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTGAAAACATTTCCATTGAAACAAA
Found at i:1579361 original size:102 final size:101
Alignment explanation
Indices: 1579231--1579617 Score: 425
Period size: 102 Copynumber: 3.8 Consensus size: 101
1579221 ATTGAAAACA
** * * * * *
1579231 TTTCCATTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATAT
1 TTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
* * * * *
1579295 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
** * * * * *
1579332 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGGAACATAAACATTGAAAAC
1 TTTCCATTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* ** * *
1579397 ATTTCCCTTGAGATGAATTTTTTTTCTCTTGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* * *
1579434 GTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCATTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
** * *
1579499 ATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* *
1579536 TTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAACA
1 TTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1579601 GTTTCCTTTGAAACAAA
66 -TTTCCCTTGAAACAAA
1579618 ATATTTGAAT
Statistics
Matches: 240, Mismatches: 43, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
101 59 0.25
102 178 0.74
103 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
Found at i:1579568 original size:36 final size:36
Alignment explanation
Indices: 1579500--1579575 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
1579490 ATTGAAAACA
* ** * *
1579500 TTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
1 TTTCCATTGAAACAAATTTTGTCACCCATGAGACAG
* *
1579536 TTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCATTGAAACAAATTTTGTCACCCATGAGACAG
1579572 TTTC
1 TTTC
1579576 TCTTGAAGCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTCCATTGAAACAAATTTTGTCACCCATGAGACAG
Found at i:1579702 original size:21 final size:21
Alignment explanation
Indices: 1579681--1579757 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
1579671 TTTTGGAAGT
*
1579681 TTTTGTCTCTCTTGAGACAG-
1 TTTTGTCTCTCTTGAAACAGA
*
1579701 --TT-TCTCT-TT-AAACAAA
1 TTTTGTCTCTCTTGAAACAGA
*
1579717 TTTTGTCTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAAACAGA
*
1579738 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAAACAG
1579758 TTTCCCTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.09
16 2 0.04
17 5 0.11
18 4 0.09
19 5 0.11
20 2 0.04
21 25 0.53
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.44
Consensus pattern (21 bp):
TTTTGTCTCTCTTGAAACAGA
Found at i:1579721 original size:36 final size:35
Alignment explanation
Indices: 1579638--1579731 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 35
1579628 ATATTTTACG
* * *
1579638 TTAAACAAATCTCGTCTCCCTTGAGACAGTTTCTT
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
** **
1579673 TTGGA-AGTTTTTGTCTCTCTTGAGACAGTTTCTCT
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCT-T
1579708 TTAAACAAATTTTGTCTCTCTTGA
1 TTAAACAAATTTTGTCTCTCTTGA
1579732 AACAAATTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
34 23 0.50
35 7 0.15
36 16 0.35
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (35 bp):
TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:1579859 original size:35 final size:34
Alignment explanation
Indices: 1579788--1579870 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 34
1579778 TTTGAATACA
* * *
1579788 GTTTCTCTTGAAAC-ACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACAAAAAAAAACCTTTAAAAAT
1579821 GTTTCTCTTGAAACAAAAAAAAAACCTTTAAAAAT
1 GTTTCTCTTGAAAC-AAAAAAAAACCTTTAAAAAT
1579856 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1579871 CTAAACCCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.31
34 1 0.02
35 30 0.67
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (34 bp):
GTTTCTCTTGAAACAAAAAAAAACCTTTAAAAAT
Found at i:1581065 original size:2 final size:2
Alignment explanation
Indices: 1581058--1581118 Score: 70
Period size: 2 Copynumber: 30.5 Consensus size: 2
1581048 TTTATTAATT
* * * *
1581058 TA TA TA TA TA TA TA TA TA TT TA CTA TT TA TT TA TT TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
1581100 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1581119 TATTTTTACT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1581113 original size:40 final size:41
Alignment explanation
Indices: 1581048--1581138 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 41
1581038 TATTATCAGT
*
1581048 TTTATTAATT-TATATATATATATATATAT-TTACTATTTA-
1 TTTATTTATTATATATATATATATATATATATTA-TATTTAC
*
1581087 TTTATTTATTATATATATATATATATATATATTATTTTTAC
1 TTTATTTATTATATATATATATATATATATATTATATTTAC
1581128 TTT-TTTATTAT
1 TTTATTTATTAT
1581139 TATTTTATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 9 0.19
40 32 0.68
41 6 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (41 bp):
TTTATTTATTATATATATATATATATATATATTATATTTAC
Found at i:1581148 original size:5 final size:5
Alignment explanation
Indices: 1581130--1581284 Score: 64
Period size: 5 Copynumber: 31.6 Consensus size: 5
1581120 ATTTTTACTT
* *
1581130 TTTTA TTATTA TTTTA -TTTA -TTTG TTTTA TTTATA TATTT- TTTTC
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTT-TA T-TTTA TTTTA
* *
1581175 TTTT- TTTT- CTTT- TTTTA TATTTA TTTTAA TTACTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTT-A TT-TTA TTTTA T-TTTA
* * * *
1581221 TTTT- CTTTA TCTTA TCTTT- TATTTA ATTTA -TTT- TTTTA TTTTA ATTTA
1 TTTTA TTTTA TTTTA T-TTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
1581269 ATTTA -TTTA -TTTA TTT
1 TTTTA TTTTA TTTTA TTT
1581285 CTTACCTTTT
Statistics
Matches: 121, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
4 37 0.31
5 54 0.45
6 27 0.22
7 3 0.02
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:1581150 original size:9 final size:9
Alignment explanation
Indices: 1581138--1581284 Score: 75
Period size: 9 Copynumber: 15.2 Consensus size: 9
1581128 TTTTTTATTA
1581138 TTATTTTAT
1 TTATTTTAT
1581147 TTATTTGT-T
1 TTATTT-TAT
1581156 TTATTTATAT
1 TTATTT-TAT
* *
1581166 ATTTTTTTCT
1 -TTATTTTAT
* *
1581176 TTTTTTTCT
1 TTATTTTAT
*
1581185 TTTTTTATAT
1 TTATTT-TAT
1581195 TTATTTTAAT
1 TTATTTT-AT
1581205 TACTATTTTATCT
1 T--TATTTTA--T
*
1581218 TTATTTTCT
1 TTATTTTAT
*
1581227 TTATCTTATCTT
1 TTAT-TT-T-AT
*
1581239 TTATTTAAT
1 TTATTTTAT
1581248 TTATTTT-T
1 TTATTTTAT
1581256 TTATTTTAAT
1 TTATTTT-AT
*
1581266 TTAATTTAT
1 TTATTTTAT
1581275 TTA-TTTAT
1 TTATTTTAT
1581283 TT
1 TT
1581285 CTTACCTTTT
Statistics
Matches: 113, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
8 15 0.13
9 47 0.42
10 23 0.20
11 15 0.13
12 11 0.10
13 2 0.02
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:1581151 original size:4 final size:4
Alignment explanation
Indices: 1581048--1581284 Score: 66
Period size: 4 Copynumber: 58.8 Consensus size: 4
1581038 TATTATCAGT
* * * * * *
1581048 TTTA TTAA TTTA TATA TATA TATA TATA TTTA -CTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
1581095 TTATA TATA TATA TATA TATA TATTA -TT- TTTA CTTT- TTTA -TTA -TTA
1 TT-TA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA TTTA TTTA
* * * * *
1581141 TTTTA TTTA TTTGT TTTA TTTA TATA TTTT TTTC TTT- TTT- TTCT- TTTT
1 -TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA
* * * * *
1581189 TTATA TTTA TTTTA ATTA -CTA TTT- TATC TTTA TTTTC TTTA TCTTA
1 TT-TA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA
* *
1581235 TCT- TTTA TTTAA TTTA TTTT TTTA TTTTAA TTTAA TTTA TTTA TTTA
1 TTTA TTTA TTT-A TTTA TTTA TTTA -TTT-A TTT-A TTTA TTTA TTTA
1581282 TTT
1 TTT
1581285 CTTACCTTTT
Statistics
Matches: 184, Mismatches: 27, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
3 27 0.15
4 113 0.61
5 43 0.23
6 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:1581152 original size:29 final size:29
Alignment explanation
Indices: 1581100--1581202 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 29
1581090 ATTTATTATA
*
1581100 TATATATATATATATATATTATTTTTACTTTTT
1 TATATAT-TAT-TTTAT-TTATTTTT-CTTTTT
*
1581133 TAT-TATTATTTTATTTATTTGTT-TTATT
1 TATATATTATTTTATTTATTT-TTCTTTTT
* *
1581161 TATATATTTTTTTCTTT-TTTTTCTTTTT
1 TATATATTATTTTATTTATTTTTCTTTTT
1581189 T-TATATTTATTTTA
1 TATATA-TTATTTTA
1581203 ATTACTATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
27 6 0.10
28 21 0.36
29 17 0.29
30 6 0.10
31 3 0.05
32 3 0.05
33 3 0.05
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (29 bp):
TATATATTATTTTATTTATTTTTCTTTTT
Found at i:1581196 original size:48 final size:47
Alignment explanation
Indices: 1581112--1581261 Score: 128
Period size: 53 Copynumber: 3.0 Consensus size: 47
1581102 TATATATATA
* *
1581112 TATATATTATTTTTACTTTTTTATT-ATTATTT-TATTTATTTGTTTTATT
1 TATATATT-TTTTT-CTTTTTT-TTCTTTTTTTATATTTATTT-TTTTATT
1581161 TATATATTTTTTTCTTTTTTTTCTTTTTTTATATTTATTTTAATTACTATT
1 TATATATTTTTTTCTTTTTTTTCTTTTTTTATATTTATTTT--TT--TATT
* *
1581212 T-TATCTTTATTTTCTTTATCTTATCTTTTATTTA-ATTTATTTTTTTATT
1 TATATATTT-TTTTCTTT-T-TTTTCTTTT-TTTATATTTATTTTTTTATT
1581261 T
1 T
1581262 TAATTTAATT
Statistics
Matches: 87, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
46 2 0.02
47 13 0.15
48 14 0.16
49 15 0.17
50 6 0.07
51 15 0.17
52 1 0.01
53 17 0.20
54 4 0.05
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (47 bp):
TATATATTTTTTTCTTTTTTTTCTTTTTTTATATTTATTTTTTTATT
Found at i:1581268 original size:23 final size:22
Alignment explanation
Indices: 1581237--1581284 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
1581227 TTATCTTATC
*
1581237 TTTTATTTAATTTATTTTTTTA
1 TTTTATTTAATTTATTTATTTA
1581259 TTTTAATTTAATTTATTTATTTA
1 TTTT-ATTTAATTTATTTATTTA
1581282 TTT
1 TTT
1581285 CTTACCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTATTTAATTTATTTATTTA
Found at i:1582501 original size:31 final size:31
Alignment explanation
Indices: 1582456--1582523 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1582446 TCAAAATACA
* *
1582456 TAAGATATGGTCACTTTCG-TATTTATTTAAT
1 TAAGATACGATCACTTTCGCT-TTTATTTAAT
* *
1582487 TAAGATACGATCACTTTTGCTTTTATTTATT
1 TAAGATACGATCACTTTCGCTTTTATTTAAT
1582518 TAAGAT
1 TAAGAT
1582524 GTGGTCATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (31 bp):
TAAGATACGATCACTTTCGCTTTTATTTAAT
Found at i:1582793 original size:15 final size:15
Alignment explanation
Indices: 1582764--1582802 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1582754 AATTGGTGGA
*
1582764 AAAAT-AAATATATT
1 AAAATAAAATAAATT
*
1582778 AAATTAAAATAAATT
1 AAAATAAAATAAATT
1582793 AAAATAAAAT
1 AAAATAAAAT
1582803 TAGTCCTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAAAATAAATT
Found at i:1583990 original size:98 final size:98
Alignment explanation
Indices: 1583816--1584017 Score: 395
Period size: 98 Copynumber: 2.1 Consensus size: 98
1583806 GTGTGCTTAA
*
1583816 TTTTTAATCACCCCACCTAACAGTTAAGGGTCTATCTTTGGTTCTTTGCCAAAAGGAAAATGGTT
1 TTTTGAATCACCCCACCTAACAGTTAAGGGTCTATCTTTGGTTCTTTGCCAAAAGGAAAATGGTT
1583881 GAAAGGTGACATAATAGTTTCATGCTTCTGTGC
66 GAAAGGTGACATAATAGTTTCATGCTTCTGTGC
1583914 TTTTGAATCACCCCACCTAACAGTTAAGGGTCTATCTTTGGTTCTTTGCCAAAAGGAAAATGGTT
1 TTTTGAATCACCCCACCTAACAGTTAAGGGTCTATCTTTGGTTCTTTGCCAAAAGGAAAATGGTT
1583979 GAAAGGTGACATAATAGTTTCATGCTTCTGTGC
66 GAAAGGTGACATAATAGTTTCATGCTTCTGTGC
1584012 TTTTGA
1 TTTTGA
1584018 TTTTCTATTT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 103 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (98 bp):
TTTTGAATCACCCCACCTAACAGTTAAGGGTCTATCTTTGGTTCTTTGCCAAAAGGAAAATGGTT
GAAAGGTGACATAATAGTTTCATGCTTCTGTGC
Found at i:1585464 original size:32 final size:31
Alignment explanation
Indices: 1585383--1585467 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
1585373 AGTGATGACA
* * *
1585383 TGATATATATTATATCATCATTTATACACATG
1 TGATA-ATATCATATCGTCACTTATACACATG
*
1585415 TGATAATATCATATCGTCACTTATATACATG
1 TGATAATATCATATCGTCACTTATACACATG
*
1585446 TGATAAGTATCATGTCGTCACT
1 TGATAA-TATCATATCGTCACT
1585468 GTAACCCCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 28 0.60
32 19 0.40
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (31 bp):
TGATAATATCATATCGTCACTTATACACATG
Found at i:1587019 original size:22 final size:22
Alignment explanation
Indices: 1586994--1587053 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
1586984 AAGTCAATGA
*
1586994 TCAACGGTCCGGTCGGGTCGGG
1 TCAACGGTCAGGTCGGGTCGGG
*
1587016 TCAACGGTCGGGTCGGGTCGGG
1 TCAACGGTCAGGTCGGGTCGGG
1587038 TCAACGGTCAGGTCGG
1 TCAACGGTCAGGTCGG
1587054 TTCAGATCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.12, C:0.25, G:0.45, T:0.18
Consensus pattern (22 bp):
TCAACGGTCAGGTCGGGTCGGG
Found at i:1594305 original size:9 final size:9
Alignment explanation
Indices: 1594287--1594365 Score: 77
Period size: 9 Copynumber: 8.3 Consensus size: 9
1594277 GGTCGGGTCG
*
1594287 GGTCAGACC
1 GGTCAAACC
1594296 GGTCAAACC
1 GGTCAAACC
*
1594305 GGTTCAGACC
1 GG-TCAAACC
1594315 GGTCAAACC
1 GGTCAAACC
* *
1594324 GGTTCGAACT
1 GG-TCAAACC
*
1594334 GGTTGAAACC
1 GG-TCAAACC
1594344 GGTCAAACC
1 GGTCAAACC
1594353 GGTCAGAACC
1 GGTCA-AACC
1594363 GGT
1 GGT
1594366 TGAAAACCGG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
9 29 0.50
10 29 0.50
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1594311 original size:19 final size:19
Alignment explanation
Indices: 1594289--1594366 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
1594279 TCGGGTCGGG
1594289 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1594308 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
1594327 TC-GAACTGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
1594346 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
1594366 T
1 T
1594367 GAAAACCGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.06
19 37 0.76
20 9 0.18
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1603794 original size:35 final size:35
Alignment explanation
Indices: 1603755--1603846 Score: 96
Period size: 39 Copynumber: 2.5 Consensus size: 35
1603745 TAGATGTATA
*
1603755 ATATATAGTTTTTAAAAAAAAGCATATTGGAAA-AC
1 ATATATAATTTTTAAAAAAAA-CATATTGGAAATAC
* *
1603790 ATATATATTATATATTTAAAAAAAACATTTTGGAAATAT
1 ATATATA--AT-T-TTTAAAAAAAACATATTGGAAATAC
*
1603829 ATATATAATTTTTGAAAA
1 ATATATAATTTTTAAAAA
1603847 CATTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
35 14 0.29
36 1 0.02
37 3 0.06
38 11 0.23
39 19 0.40
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (35 bp):
ATATATAATTTTTAAAAAAAACATATTGGAAATAC
Found at i:1603796 original size:37 final size:34
Alignment explanation
Indices: 1603755--1603846 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 34
1603745 TAGATGTATA
1603755 ATATATAGTTTTTAAAAAAAAGCATATTGGAAAACAT
1 ATATATA-TTTTTAAAAAAAA-CATATTGG-AAACAT
* *
1603792 ATATATTATATATTTAAAAAAAACATTTTGGAAATAT
1 ATATA-TAT-T-TTTAAAAAAAACATATTGGAAACAT
*
1603829 ATATATAATTTTTGAAAA
1 ATATAT-ATTTTTAAAAA
1603847 CATTTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
35 7 0.15
36 2 0.04
37 18 0.38
38 10 0.21
39 11 0.23
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (34 bp):
ATATATATTTTTAAAAAAAACATATTGGAAACAT
Found at i:1603960 original size:35 final size:34
Alignment explanation
Indices: 1603917--1604066 Score: 101
Period size: 35 Copynumber: 4.1 Consensus size: 34
1603907 AAGATATAGT
1603917 TTTTAAAACATTTTAAAAACTATATATTATATGA
1 TTTTAAAACATTTTAAAAACTATATATTATATGA
* * *
1603951 TTTTGAAAACATTTTTTTTAGAAAGTATGTATATAATATATAA
1 TTTT-AAAACA----TTTTA-AAA--A-CTATATATTATATGA
* *
1603994 TTTTAAAATATTATTCGAAAA-TATATATTATATGA
1 TTTTAAAACATT-TT-AAAAACTATATATTATATGA
1604029 TTTTAAAAATACATTTT-AAAAC-ATATATTATAT-A
1 TTTT--AAA-ACATTTTAAAAACTATATATTATATGA
1604063 TTTT
1 TTTT
1604067 TTTTAAATGT
Statistics
Matches: 93, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
34 9 0.10
35 37 0.40
37 6 0.06
38 6 0.06
39 10 0.11
40 3 0.03
42 6 0.06
43 16 0.17
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (34 bp):
TTTTAAAACATTTTAAAAACTATATATTATATGA
Found at i:1604103 original size:14 final size:13
Alignment explanation
Indices: 1604080--1604123 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1604070 TAAATGTTCC
1604080 TTTTTA-TTTTAT
1 TTTTTATTTTTAT
1604092 TTATTTATTTTTAT
1 TT-TTTATTTTTAT
*
1604106 TTTTTAATTTTTCT
1 TTTTT-ATTTTTAT
1604120 TTTT
1 TTTT
1604124 CAGGACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 7 0.25
14 19 0.68
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:1604122 original size:19 final size:19
Alignment explanation
Indices: 1604080--1604115 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1604070 TAAATGTTCC
*
1604080 TTTTTATTTTATTTATTTA
1 TTTTTATTTTATTAATTTA
1604099 TTTTTATTTT-TTAATTT
1 TTTTTATTTTATTAATTT
1604116 TTCTTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTATTAATTTA
Found at i:1605419 original size:12 final size:11
Alignment explanation
Indices: 1605388--1605428 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1605378 AATCTGATCC
1605388 TTTTATTTT--
1 TTTTATTTTCA
1605397 TTATTATTTTCA
1 TT-TTATTTTCA
1605409 TTTTCATTTTCA
1 TTTT-ATTTTCA
1605421 TTTTATTT
1 TTTTATTT
1605429 GTTATGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.25
11 6 0.21
12 13 0.46
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:1605601 original size:18 final size:20
Alignment explanation
Indices: 1605565--1605602 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1605555 TTTACATGTA
1605565 TATATATATATATTCTTATT
1 TATATATATATATTCTTATT
*
1605585 TATAT-TATA-ATTGTTATT
1 TATATATATATATTCTTATT
1605603 ATTATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TATATATATATATTCTTATT
Found at i:1606729 original size:17 final size:17
Alignment explanation
Indices: 1606709--1606741 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1606699 CTCACTAACC
*
1606709 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
1606726 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
1606742 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:1607375 original size:18 final size:19
Alignment explanation
Indices: 1607354--1607395 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1607344 TAGACATTTT
1607354 GCATTTT-TTATTTTCTTC
1 GCATTTTGTTATTTTCTTC
*
1607372 GCATTTTGTTATTTTCTTT
1 GCATTTTGTTATTTTCTTC
1607391 GCATT
1 GCATT
1607396 CACATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.12, C:0.14, G:0.10, T:0.64
Consensus pattern (19 bp):
GCATTTTGTTATTTTCTTC
Found at i:1610968 original size:84 final size:81
Alignment explanation
Indices: 1610803--1611580 Score: 688
Period size: 84 Copynumber: 9.4 Consensus size: 81
1610793 AAAAGATAGT
* * * * **
1610803 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAGCAAAGACCTTCGAGTTCGACCACGC
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCA-CAAAGACCTTCGAGTTCGATTACGC
1610868 TCAGCTCCAAGGCACATC
65 TCAGCT-CAAGGCACATC
** * * * * *
1610886 ATTTGCAATATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCC-AC-AAAGACCTTCGAGTTCGATTACG
* *
1610951 CTCAACTCAACGACACATC
64 CTCAGCTCAA-GGCACATC
* * * *
1610970 GTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACC-CCTGAGTTCGATTAC
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCC-A-CAAAGACCTTC-GAGTTCGATTAC
* * *
1611034 ACTCAGCTTCGAGGGCATATC
63 GCTCAGC-TC-AAGGCACATC
* * * * * * *
1611055 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAATACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCA-CAAAGACCTTCGAGTTCGATTACGC
1611120 TCAGCTCCAAGGCACATC
65 TCAGCT-CAAGGCACATC
* * * * ** *
1611138 ATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCA-AAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGATTACGCT
*
1611202 CAGCTTCGAGGGCACATC
66 CAGC-TC-AAGGCACATC
* * * * * * * *
1611220 ATTTGCGGCATAACTTAAGTCGATAAGGGTTATCCGCCAACCAAAGACCTTTGAGTTCGATTACG
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCC-A-CAAAGACCTTCGAGTTCGATTACG
*
1611285 CTCAGCTCCAAGGCATATC
64 CTCAGCT-CAAGGCACATC
* * * * *
1611304 ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACCCTT-AAGTTCGATTACAC
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCACAAAGA-CCTTCGAGTTCGATTACGC
*
1611366 TCAGCTTCAAGGGCATATC
65 TCAGC-TCAA-GGCACATC
* * * * *
1611385 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGATTACGCT
1611450 CAGCTCCAAGGCACATC
66 CAGCT-CAAGGCACATC
* * ** *
1611467 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGATTACGCT
* * *
1611530 CAACTTCGAGGTCATATC
66 CAGC-TCAAGG-CACATC
* * *
1611548 ATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
1 ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTAT
1611581 TTTTCAATAA
Statistics
Matches: 573, Mismatches: 98, Indels: 50
0.79 0.14 0.07
Matches are distributed among these distances:
80 55 0.10
81 104 0.18
82 86 0.15
83 105 0.18
84 156 0.27
85 66 0.12
86 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGATTACGCT
CAGCTCAAGGCACATC
Found at i:1611250 original size:165 final size:166
Alignment explanation
Indices: 1610803--1611576 Score: 986
Period size: 163 Copynumber: 4.7 Consensus size: 166
1610793 AAAAGATAGT
* * * * * * ** ** *
1610803 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAGCAAAGACCTTCGAGTTCGACCACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAAGACCCCCGAGTTCGATTACAC
* * * * ** * * * *
1610868 TCAGC-TCCAAGGCACATCATTTGCAATATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAG
64 TCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAG
* * *
1610932 ACCTTTGAGTTCGACTACGCTCAACT-CAACGACACATC
129 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
* *
1610970 GTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCCCTGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A--AAAGACCCCCGAGTTCGATTACA
*
1611035 CTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAA
63 CTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAA
*
1611099 TACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
128 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
1611138 ATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACTC
* * * * * * * *
1611203 AGCTTCGAGGGCACATCATTTGCGGCATAACTTAAGTCGATAAGGGTTATCCGCCAACCAAAGAC
66 AGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGAC
* * *
1611268 CTTTGAGTTCGATTACGCTCAGCTCCAAGGCATATC
131 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* ***
1611304 ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCTTAAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACTC
*
1611368 AGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-A-CAAAGAC
66 AGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGAC
1611431 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
1611467 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACTC
* * * * *
1611531 AACTTCGAGGTCATATCATTTACAACATAGCTCAAGGCAAGAAGGG
66 AGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGG
1611577 CTATTTTTCA
Statistics
Matches: 529, Mismatches: 74, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
163 140 0.26
164 1 0.00
165 140 0.26
166 76 0.14
167 32 0.06
168 96 0.18
169 44 0.08
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (166 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACTC
AGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGAC
CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1611607 original size:163 final size:164
Alignment explanation
Indices: 1610899--1611576 Score: 941
Period size: 165 Copynumber: 4.1 Consensus size: 164
1610889 TGCAATATAG
* *
1610899 CTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTT-GAGTTCGACTACGCTCAACT-CAAC
1 CTCAAGGCAAGAAGGGTTATCTGCCAAC-AAAGA-CTTTCGAGTTCGACTACGCTCAGCTCCAA-
* * *
1610962 GACACATCGTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCCCTGAGTT
63 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTT
1611027 CGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAA
124 CGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* * * * *
1611068 CTCAAGGCTAGAAGGGTTATCTGTCACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACTTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* *
1611133 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTA
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCCCGAGTTCGATTA
* * *
1611198 CACTCAGCTTCGAGGGCACATCATTTGCGGCATAA
130 CACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* * * * * *
1611233 CTTAAGTCGATAAGGGTTATCCGCCAACCAAAGACCTTT-GAGTTCGATTACGCTCAGCTCCAAG
1 CTCAAGGCAAGAAGGGTTATCTGCCAA-CAAAGA-CTTTCGAGTTCGACTACGCTCAGCTCCAAG
* * ***
1611297 GCATATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATT
64 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
*
1611362 ACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
129 ACACTCAGCTTCGAGGGCATATCATTTACAGCATAA
* *
1611398 CTCAAGGCTAGAAGGGTTATCTGCC-ACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACTTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1611462 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
* * * *
1611527 ACTCAACTTCGAGGTCATATCATTTACAACATAG
131 ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
1611561 CTCAAGGCAAGAAGGG
1 CTCAAGGCAAGAAGGG
1611577 CTATTTTTCA
Statistics
Matches: 449, Mismatches: 54, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
162 3 0.01
163 136 0.30
164 3 0.01
165 141 0.31
166 70 0.16
167 6 0.01
168 63 0.14
169 27 0.06
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (164 bp):
CTCAAGGCAAGAAGGGTTATCTGCCAACAAAGACTTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
ACTCAGCTTCGAGGGCATATCATTTACAGCATAA
Found at i:1612243 original size:40 final size:43
Alignment explanation
Indices: 1612154--1612255 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 43
1612144 ATGCTAATGG
* * *
1612154 TTTTTGAAATAGATGTATAATATATAGTTTTTAAAAAAAAACA
1 TTTTGGAAATACATATATAATATATAGTTTTTAAAAAAAAACA
* * *
1612197 TTTTGGAAA-ACATATATATTATATA-TTTTT-TAAAAATACA
1 TTTTGGAAATACATATATAATATATAGTTTTTAAAAAAAAACA
*
1612237 TTTTGGAAATATATATATA
1 TTTTGGAAATACATATATA
1612256 GTTTTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
40 17 0.33
41 13 0.25
42 13 0.25
43 8 0.16
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (43 bp):
TTTTGGAAATACATATATAATATATAGTTTTTAAAAAAAAACA
Found at i:1612270 original size:32 final size:34
Alignment explanation
Indices: 1612210--1612285 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
1612200 TGGAAAACAT
* **
1612210 ATATATTATATATTTTTTAAAAATACATTTTGGAA
1 ATATA-TATATAGTTTTTAAAAATACATTTTAAAA
*
1612245 ATATATATATAGTTTTT-GAAA-ACATTTTAAAA
1 ATATATATATAGTTTTTAAAAATACATTTTAAAA
1612277 ATATATATA
1 ATATATATA
1612286 ATATATGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 18 0.49
33 3 0.08
34 11 0.30
35 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (34 bp):
ATATATATATAGTTTTTAAAAATACATTTTAAAA
Found at i:1612289 original size:41 final size:40
Alignment explanation
Indices: 1612244--1612367 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 40
1612234 ACATTTTGGA
1612244 AATATATATATAGTTTTTGAAAACATTTTAAAAATATATAT
1 AATATATATATAGTTTTT-AAAACATTTTAAAAATATATAT
* * *
1612285 AATATATGAT-T-TTTTTTAAAAACGGTTTGAAAAATAT-T-T
1 AATATAT-ATATAGTTTTT-AAAAC-ATTTTAAAAATATATAT
*
1612324 -ATA-AGATATAGTTTTTAAAACATTTTAAAAACTATATAT
1 AATATATATATAGTTTTTAAAACATTTTAAAAA-TATATAT
*
1612363 TATAT
1 AATAT
1612368 GATTTTGAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
36 10 0.15
37 10 0.15
38 9 0.14
39 2 0.03
40 14 0.21
41 19 0.29
42 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (40 bp):
AATATATATATAGTTTTTAAAACATTTTAAAAATATATAT
Found at i:1612410 original size:77 final size:75
Alignment explanation
Indices: 1612245--1612419 Score: 180
Period size: 77 Copynumber: 2.3 Consensus size: 75
1612235 CATTTTGGAA
*
1612245 ATAT-ATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATGATTTTTTTTAAAAACG
1 ATATAATATATAGTTTTT-AAAACATTTTAAAAATATATAT-ATATATGA--TTTTTGAAAAACG
1612309 GTTTGAAAAATATT
62 GTTTGAAAAATATT
* **
1612323 -TATAAGATATAGTTTTTAAAACATTTTAAAAACTATATAT-TATATGA-TTTTGAAAACATTGT
1 ATATAATATATAGTTTTTAAAACATTTTAAAAA-TATATATATATATGATTTTTGAAAA-ACGGT
* *
1612385 TTTAGAAAGTATGT
64 TTGA-AAAATAT-T
*
1612399 ATATAATATATA-ATTTTAAAA
1 ATATAATATATAGTTTTTAAAA
1612420 TATATATTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
73 8 0.10
74 6 0.07
75 6 0.07
76 16 0.19
77 28 0.34
78 19 0.23
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (75 bp):
ATATAATATATAGTTTTTAAAACATTTTAAAAATATATATATATATGATTTTTGAAAAACGGTTT
GAAAAATATT
Found at i:1612425 original size:22 final size:22
Alignment explanation
Indices: 1612398--1612441 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1612388 AGAAAGTATG
1612398 TATATAATATATAATTTTAAAA
1 TATATAATATATAATTTTAAAA
* *
1612420 TATATATTATATGATTTTAAAA
1 TATATAATATATAATTTTAAAA
1612442 ATACATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATAATATATAATTTTAAAA
Found at i:1612484 original size:64 final size:64
Alignment explanation
Indices: 1612345--1612477 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
1612335 TTTTTAAAAC
* ** * *
1612345 ATTTTAAAAACTATATATTATATGATTTTGAAAACATTGTTTTAGAAAGTATGTATATAATATAT
1 ATTTTTAAAA-TATATATTATATGATTTTGAAAACATCATTTTAGAAAGCATATATATAATATAT
*
1612410 AATTTTAAAATATATATTATATGATTTT-AAAA-ATACATTTTA-AAA-CATATATATAATATAT
1 ATTTTTAAAATATATATTATATGATTTTGAAAACAT-CATTTTAGAAAGCATATATATAATATA-
1612471 T
64 T
1612472 ATTTTT
1 ATTTTT
1612478 TTAAAATGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
61 13 0.22
62 11 0.19
63 9 0.15
64 18 0.31
65 8 0.14
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (64 bp):
ATTTTTAAAATATATATTATATGATTTTGAAAACATCATTTTAGAAAGCATATATATAATATAT
Found at i:1612528 original size:14 final size:13
Alignment explanation
Indices: 1612490--1612527 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
1612480 AAAATGTTCC
1612490 TTTTTATTTTTAT
1 TTTTTATTTTTAT
1612503 TTATTTATTTTTAT
1 TT-TTTATTTTTAT
*
1612517 TTTTTCTTTTT
1 TTTTTATTTTT
1612528 TCTTTTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:1612533 original size:20 final size:20
Alignment explanation
Indices: 1612489--1612534 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1612479 TAAAATGTTC
1612489 CTTTTTATTTTTATTTATTT
1 CTTTTTATTTTTATTTATTT
* *
1612509 ATTTTTATTTTT-TCTTTTTT
1 CTTTTTATTTTTAT-TTATTT
1612529 CTTTTT
1 CTTTTT
1612535 CAGGACCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.83
Consensus pattern (20 bp):
CTTTTTATTTTTATTTATTT
Found at i:1613833 original size:12 final size:11
Alignment explanation
Indices: 1613798--1613896 Score: 51
Period size: 11 Copynumber: 8.8 Consensus size: 11
1613788 AATCTGATCC
1613798 TTTTATTTTT-
1 TTTTATTTTTA
* *
1613808 TATTATTTTCA
1 TTTTATTTTTA
1613819 TTTTCATTTTTA
1 TTTT-ATTTTTA
1613831 TTTTATTTGTTA
1 TTTTATTT-TTA
*
1613843 TGTTTTTTGTTTA
1 T-TTTATT-TTTA
*** *
1613856 TACGA-TATTA
1 TTTTATTTTTA
*
1613866 -TATATATTTTA
1 TTTTAT-TTTTA
*
1613877 TTTTATCTTTA
1 TTTTATTTTTA
1613888 TTTTATTTT
1 TTTTATTTT
1613897 AATCCTTTCG
Statistics
Matches: 64, Mismatches: 17, Indels: 15
0.67 0.18 0.16
Matches are distributed among these distances:
9 1 0.02
10 11 0.17
11 24 0.38
12 18 0.28
13 9 0.14
14 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1614229 original size:6 final size:6
Alignment explanation
Indices: 1614199--1614228 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1614189 CGAGTTTCTA
*
1614199 AATTTT AATTTT AATTTT AATTTT TATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
1614229 TTCGTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
AATTTT
Found at i:1616980 original size:41 final size:40
Alignment explanation
Indices: 1616905--1617041 Score: 143
Period size: 42 Copynumber: 3.3 Consensus size: 40
1616895 AGGTTAAACA
1616905 ATAGCGGCGTTTATAG-TAAAAACGCCGCAATATAGTAGACAT
1 ATAGCGGCGTTTATAGCT-AAAACGCCGCAATATAGT-GA-AT
1616947 ATAGCGGCGTTT-TAGCTAAAACGCCGCAATATAGTGTTAAT
1 ATAGCGGCGTTTATAGCTAAAACGCCGCAATATAGTG--AAT
* * * * * *
1616988 TTAGCGGCGTTTATACCAAAAACGCCGTAATAGAGTGATAA
1 ATAGCGGCGTTTATAGCTAAAACGCCGCAATATAGTGA-AT
1617029 ATTAGCGGCGTTT
1 A-TAGCGGCGTTT
1617042 TTTGTATAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.02
41 35 0.43
42 45 0.55
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (40 bp):
ATAGCGGCGTTTATAGCTAAAACGCCGCAATATAGTGAAT
Found at i:1618172 original size:52 final size:52
Alignment explanation
Indices: 1618107--1618265 Score: 309
Period size: 52 Copynumber: 3.1 Consensus size: 52
1618097 TATTGAACAA
1618107 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
1618159 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1618211 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1618263 TAT
1 TAT
1618266 TTTGTTGTTA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:1621376 original size:43 final size:43
Alignment explanation
Indices: 1621308--1621445 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 43
1621298 AAGGTAATTA
*
1621308 GCGACGTTTGTATCCAAAAATGCCACTATAGATCTGACCTTTT
1 GCGACGTTTGTATCCAAAAAAGCCACTATAGATCTGACCTTTT
*
1621351 GC-AGTGTTTGTATCCAAAAAAGCCACTATAGATCTGACCTTTT
1 GCGA-CGTTTGTATCCAAAAAAGCCACTATAGATCTGACCTTTT
* * **** *
1621394 GCGACGTTTGTTTCCAAAAACGATGTTATAGGTCTGACCTTTT
1 GCGACGTTTGTATCCAAAAAAGCCACTATAGATCTGACCTTTT
*
1621437 GCGGCGTTT
1 GCGACGTTT
1621446 TGCACTAGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 80 0.98
44 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (43 bp):
GCGACGTTTGTATCCAAAAAAGCCACTATAGATCTGACCTTTT
Found at i:1621658 original size:43 final size:43
Alignment explanation
Indices: 1621611--1621766 Score: 122
Period size: 43 Copynumber: 3.6 Consensus size: 43
1621601 AAACCATTTA
* * *
1621611 CGGCGTTTTTTCTAAAAACGCCGTTAAACATCAACGCCTATTG
1 CGGCGTTTTTTCTAAAAACGCCGCTAAACAACAAAGCCTATTG
* * *
1621654 CGGCG-TTTTTCTGACAAACGCCGCTAAATAACAAATCCTATTG
1 CGGCGTTTTTTCT-AAAAACGCCGCTAAACAACAAAGCCTATTG
* * ******
1621697 CGGCGTTTGTTC-AGAAAACGCCACTATATGTTGTAA-CCTATTG
1 CGGCGTTTTTTCTA-AAAACGCCGCTA-AACAACAAAGCCTATTG
1621740 CGGCGTTTTTT-TAAAAAACGCCGCTAA
1 CGGCGTTTTTTCT-AAAAACGCCGCTAA
1621767 CTTTAGCGGC
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 9 0.10
43 72 0.80
44 9 0.10
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
CGGCGTTTTTTCTAAAAACGCCGCTAAACAACAAAGCCTATTG
Found at i:1624627 original size:43 final size:41
Alignment explanation
Indices: 1624571--1624798 Score: 321
Period size: 43 Copynumber: 5.3 Consensus size: 41
1624561 GCGGCGTTGG
* *
1624571 ACAAACGCCGCAATAGGTGTTGATATTTGGCGGTATTTTTCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGT-TTTTTCC
*
1624613 AACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 -ACAAACGCCGCAATAGGTGTTGAGATTTAGC-G-GTTTTTTCC
1624657 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGC-G-GTTTTTTCC
1624700 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGC-G-GTTTTTTCC
*
1624743 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGT-TTTTT-CC
*
1624786 ACAAACACCGCAA
1 ACAAACGCCGCAA
1624799 AAGATCTGAT
Statistics
Matches: 175, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
41 2 0.01
42 6 0.03
43 158 0.90
44 7 0.04
45 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (41 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGTTTTTTCC
Found at i:1624739 original size:129 final size:129
Alignment explanation
Indices: 1624571--1624841 Score: 384
Period size: 129 Copynumber: 2.1 Consensus size: 129
1624561 GCGGCGTTGG
* * * *
1624571 ACAAACGCCGCAATAGGTGTTGATATTTGGCGGTA-TTTTTCCAACAAACGCCGCAATAGGTGTT
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTTCC-ACAAACGCCGCAATAGGTCTT
* * * * *
1624635 GAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTT-C
65 GAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGAT-CTGAGATATAGCGGCGTTTTTTAC
1624699 C
129 C
*
1624700 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTG
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTTCCACAAACGCCGCAATAGGTCTTG
* * **
1624765 AGATTTAGCGGTGTTTTTCCCACAAACACCGCAAAAGATCTGATATATAGCGGCGTTTTTTAGG
66 AGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTGAGATATAGCGGCGTTTTTTACC
1624829 ACAAACGCCGCAA
1 ACAAACGCCGCAA
1624842 AATGTCATAT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
128 19 0.15
129 100 0.79
130 7 0.06
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (129 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTTCCACAAACGCCGCAATAGGTCTTG
AGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTGAGATATAGCGGCGTTTTTTACC
Found at i:1624825 original size:86 final size:86
Alignment explanation
Indices: 1624571--1624841 Score: 373
Period size: 86 Copynumber: 3.2 Consensus size: 86
1624561 GCGGCGTTGG
* * * *
1624571 ACAAACGCCGCAATAGGTGTTGATATTTGGCGGTATTTTTCCAACAAACGCCGCAATAGGTGTTG
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGTGTTTTTCCCACAAACGCCGCAATAGGTGTTG
*
1624636 AGATTTAGCGGCGTTTTTCCC
66 AGATTTAGCGGCGTTTTTACC
* *
1624657 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTG
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGTGTTTTTCCCACAAACGCCGCAATAGGTGTTG
*
1624722 AGATTTAGCGGCGTTTTTTCC
66 AGATTTAGCGGCGTTTTTACC
* * * * *
1624743 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCCACAAACACCGCAAAAGAT-CTG
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGTGTTTTTCCCACAAACGCCGCAATAGGTGTTG
* * **
1624807 ATATATAGCGGCGTTTTTTAGG
66 AGATTTAGCGGCG-TTTTTACC
1624829 ACAAACGCCGCAA
1 ACAAACGCCGCAA
1624842 AATGTCATAT
Statistics
Matches: 165, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
85 13 0.08
86 152 0.92
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (86 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGTGTTTTTCCCACAAACGCCGCAATAGGTGTTG
AGATTTAGCGGCGTTTTTACC
Found at i:1624843 original size:43 final size:42
Alignment explanation
Indices: 1624571--1624841 Score: 312
Period size: 43 Copynumber: 6.3 Consensus size: 42
1624561 GCGGCGTTGG
* * *
1624571 ACAAACGCCGCAATAGGTGTTGATATTTGGC-G-GTATTTTTCC
1 ACAAACGCCGCAATAGGT-CTGAGATTTAGCGGCGT-TTTTTCC
* *
1624613 AACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1 -ACAAACGCCGCAATAGGT-CTGAGATTTAGCGGCGTTTTTTCC
*
1624657 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
1 ACAAACGCCGCAATAGGT-CTGAGATTTAGCGGCGTTTTTTCC
*
1624700 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
1 ACAAACGCCGCAATAGGT-CTGAGATTTAGCGGCGTTTTTTCC
* *
1624743 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCC
1 ACAAACGCCGCAATAGGTC-TGAGATTTAGCGGCGTTTTTTCC
* * * * * **
1624786 ACAAACACCGCAAAAGATCTGATATATAGCGGCGTTTTTTAGG
1 ACAAACGCCGCAATAGGTCTGAGATTTAGCGGCGTTTTTT-CC
1624829 ACAAACGCCGCAA
1 ACAAACGCCGCAA
1624842 AATGTCATAT
Statistics
Matches: 207, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
42 17 0.08
43 181 0.87
44 7 0.03
45 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (42 bp):
ACAAACGCCGCAATAGGTCTGAGATTTAGCGGCGTTTTTTCC
Found at i:1624876 original size:129 final size:129
Alignment explanation
Indices: 1624614--1624882 Score: 312
Period size: 129 Copynumber: 2.1 Consensus size: 129
1624604 TATTTTTCCA
* * * * *
1624614 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTG
1 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATGCTG
* * * ***
1624679 AGATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
66 AGATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGATGTTCAGATTTAGCGGCGTTTTAGAC
*
1624743 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGTGTTTTTCCCACAAACACCGCAAAAGAT-CTG
1 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATGCTG
* ** *
1624807 ATATATAGCGGCGTTTTTTAGGACAAACGCCGCAA-A-ATG-TCATATCTATAGCGGCGTTTTAA
66 AGATATAGCGGCGTTTTTT-CCACAAACGCCGCAATAGATGTTCAGAT-T-TAGCGGCGTTTT-A
*
1624869 GAT
127 GAC
*
1624872 ACAAACACCGC
1 ACAAACGCCGC
1624883 TAATTACCTC
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
126 4 0.03
127 3 0.03
128 32 0.27
129 79 0.67
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (129 bp):
ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGATGCTG
AGATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGATGTTCAGATTTAGCGGCGTTTTAGAC
Found at i:1625019 original size:21 final size:21
Alignment explanation
Indices: 1624993--1625051 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1624983 ATTTTCCAAT
*
1624993 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1625014 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
1625035 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
1625052 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1627794 original size:41 final size:41
Alignment explanation
Indices: 1627728--1628212 Score: 476
Period size: 41 Copynumber: 11.6 Consensus size: 41
1627718 TTGTAAACTT
* * * *
1627728 GCGGCGTTTGTAAACACAAACGCCACTATAA-TACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTA-AAGTACGAGTCTTTA
* *
1627771 ACGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1627812 GCGGCGTTTGTATAAAAATGTCAATAAAGTAC-AGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
1627852 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * *
1627893 GCGACGTTTGTAAACACAAACGCCACTATAA-TACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTA-AAGTACGAGTCTTTA
* * * * *
1627936 ACGGTGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1627977 GCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTATTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1628018 GCGGCGTTTGTATAAAAACAAATGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATAAAAAC----GCCACTAAAGTACGA-GTCTTTA
* * * * *
1628063 ACGACGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
1628104 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
1628145 GCGGTGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
1628186 GCGGCGTTTGT-TGAAAAAACGCCACTA
1 GCGGCGTTTGTAT--AAAAACGCCACTA
1628213 TCGATGAACC
Statistics
Matches: 367, Mismatches: 61, Indels: 29
0.80 0.13 0.06
Matches are distributed among these distances:
40 42 0.11
41 233 0.63
42 17 0.05
43 39 0.11
44 3 0.01
45 33 0.09
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:1628093 original size:127 final size:126
Alignment explanation
Indices: 1627816--1628163 Score: 484
Period size: 127 Copynumber: 2.8 Consensus size: 126
1627806 TCTTTAGCGG
* *
1627816 CGTTTGTATAAAAATGTCAATAAAGTACAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAT
1 CGTTTGTATAAAAATGCCACTAAAGTACAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAT
* * *
1627881 TACGAGTCTTTAGCGACGTTTG--TAAACACAAACGCCACTATAATACAAGTGTATAACGG
66 TACGAGTCTTTAGCGGCGTTTGTATAAAAACAAACGCCACTATAATACAAGTGTATAACGA
* * * * *
1627940 TGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAA
1 CGTTTGTATAAAAATGCCACTAAAGTAC-AGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAA
* * * * * *
1628005 GTATGAGTATTTAGCGGCGTTTGTATAAAAACAAATGCCACTATAGTACATGTGTATAACGA
65 TTACGAGTCTTTAGCGGCGTTTGTATAAAAACAAACGCCACTATAATACAAGTGTATAACGA
* * *
1628067 CGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAA
1 CGTTTGTATAAAAATGCCACTAAAGTAC-AGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAA
*
1628132 TTACGAGTCTTTAGCGGTGTTTGTATAAAAAC
65 TTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
1628164 GCCACTAAAG
Statistics
Matches: 192, Mismatches: 29, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
124 24 0.12
125 52 0.27
127 116 0.60
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (126 bp):
CGTTTGTATAAAAATGCCACTAAAGTACAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAT
TACGAGTCTTTAGCGGCGTTTGTATAAAAACAAACGCCACTATAATACAAGTGTATAACGA
Found at i:1628192 original size:168 final size:166
Alignment explanation
Indices: 1627732--1628196 Score: 627
Period size: 165 Copynumber: 2.8 Consensus size: 166
1627722 AAACTTGCGG
*
1627732 CGTTTGTAAACACAAACGCCACTATAATACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAATACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
* * * *
1627797 AAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTAC-AGTCTTTAGCGGCGTTT
66 AAGTACGAGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTT
* * *
1627861 GTATAAAAATGCCACTAAATTACGAGTCTTTAGCGA
131 GTATAAAAATGCCACTAAAGTACGAGTCTATAACGA
*
1627897 CGTTTGTAAACACAAACGCCACTATAATACAAGTGTATAACGGTGTTTGAATAAAAATGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAATACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
* *
1627962 AAGTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTA-TGAGTATTTAGCGGCGTT
66 AAGTACGAGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACT-AGTCTTTAGCGGCGTT
* *
1628026 TGTATAAAAACAAATGCCACTATAGTAC-ATGTGTATAACGA
130 TGTAT---AA-AAATGCCACTAAAGTACGA-GTCTATAACGA
* * * * *
1628067 CGTTTGTATA-A-AAACGCCACTA-AAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACT
1 CGTTTGTAAACACAAACGCCACTATAA-TACAAGTGTATAACGGCGTTTGAATAAAAATGCCACT
* * * *
1628129 AAATTACGAGTCTTTAGCGGTGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTT
65 AAAGTACGAGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTT
1628194 TGT
130 TGT
1628197 TGAAAAAACG
Statistics
Matches: 266, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
165 104 0.39
166 20 0.08
167 2 0.01
168 103 0.39
169 5 0.02
170 32 0.12
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (166 bp):
CGTTTGTAAACACAAACGCCACTATAATACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
AAGTACGAGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACTAGTCTTTAGCGGCGTTT
GTATAAAAATGCCACTAAAGTACGAGTCTATAACGA
Found at i:1637866 original size:37 final size:37
Alignment explanation
Indices: 1637816--1637889 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1637806 CAGAGCAGAT
1637816 AGTACTACTGTACACCAACAATGCAAACAGCGATGCA
1 AGTACTACTGTACACCAACAATGCAAACAGCGATGCA
1637853 AGTACTACTGTACACCAACAATGCAAACAGCGATGCA
1 AGTACTACTGTACACCAACAATGCAAACAGCGATGCA
1637890 GACGAGAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (37 bp):
AGTACTACTGTACACCAACAATGCAAACAGCGATGCA
Found at i:1639449 original size:21 final size:23
Alignment explanation
Indices: 1639425--1639468 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1639415 ATATTATTAG
1639425 AAATA-TTAATAAAT-ATATTTT
1 AAATATTTAATAAATAATATTTT
*
1639446 AAATATTTAATAATTAATATTTT
1 AAATATTTAATAAATAATATTTT
1639469 GATTAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATTTAATAAATAATATTTT
Found at i:1654676 original size:16 final size:16
Alignment explanation
Indices: 1654655--1654688 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1654645 GAAAAATGTT
1654655 AAAAACTC-AACAACAA
1 AAAAACTCTAACAA-AA
1654671 AAAAACTCTAACAAAA
1 AAAAACTCTAACAAAA
1654687 AA
1 AA
1654689 TAGATGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.71, C:0.21, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAACTCTAACAAAA
Found at i:1655916 original size:13 final size:13
Alignment explanation
Indices: 1655898--1655925 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1655888 AGTTTAAAAA
1655898 ATTATTAATTATT
1 ATTATTAATTATT
1655911 ATTATTAATTATT
1 ATTATTAATTATT
1655924 AT
1 AT
1655926 CTATCACGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTAATTATT
Found at i:1656023 original size:33 final size:33
Alignment explanation
Indices: 1655986--1656058 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
1655976 CCACACTATT
*
1655986 CACTATCATAACTTAATCCAACCTACCACTACC
1 CACTATCATAACCTAATCCAACCTACCACTACC
1656019 CACTATCATAACCTAATCCAACCTACCACTACC
1 CACTATCATAACCTAATCCAACCTACCACTACC
1656052 CACTATC
1 CACTATC
1656059 TATCACTACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (33 bp):
CACTATCATAACCTAATCCAACCTACCACTACC
Found at i:1679404 original size:15 final size:16
Alignment explanation
Indices: 1679375--1679409 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1679365 TTAAAATATA
1679375 TAAATATAGAAAAAAC
1 TAAATATAGAAAAAAC
*
1679391 TAAATATA-AAAAAAT
1 TAAATATAGAAAAAAC
1679406 TAAA
1 TAAA
1679410 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAATATAGAAAAAAC
Done.