Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 24
Found at i:2748652 original size:4 final size:4
Alignment explanation
Indices: 2748643--2748676 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2748633 AAGTATCACA
2748643 CACG CACG CACG CACG CACG CACG CACG CACG CA
1 CACG CACG CACG CACG CACG CACG CACG CACG CA
2748677 AATTATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.50, G:0.24, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:2750819 original size:2 final size:2
Alignment explanation
Indices: 2750812--2750846 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2750802 CTCCAGTGCA
2750812 TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2750847 CGTTTCTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2750834 original size:17 final size:17
Alignment explanation
Indices: 2750812--2750844 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2750802 CTCCAGTGCA
2750812 TCTCTCTCTCTCTCTCC
1 TCTCTCTCTCTCTCTCC
2750829 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTC
2750845 TCCGTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (17 bp):
TCTCTCTCTCTCTCTCC
Found at i:2762659 original size:23 final size:25
Alignment explanation
Indices: 2762630--2762676 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
2762620 CATGAAGGAG
*
2762630 ACAAAAACATG-T-TAAAAGAAGAT
1 ACAAAAACACGTTATAAAAGAAGAT
2762653 ACAAAAACACGTTATAAAAGAAGA
1 ACAAAAACACGTTATAAAAGAAGA
2762677 CAAAATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 10 0.48
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.15
Consensus pattern (25 bp):
ACAAAAACACGTTATAAAAGAAGAT
Found at i:2762679 original size:23 final size:21
Alignment explanation
Indices: 2762628--2762681 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
2762618 ATCATGAAGG
*
2762628 AGACAAAAACATGTTAAAAGA
1 AGACAAAAACACGTTAAAAGA
2762649 AGATACAAAAACACGTTATAAAAGA
1 AG--ACAAAAACACG-T-TAAAAGA
2762674 AGACAAAA
1 AGACAAAA
2762682 TTATCCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
23 16 0.57
24 1 0.04
25 9 0.32
ACGTcount: A:0.63, C:0.11, G:0.13, T:0.13
Consensus pattern (21 bp):
AGACAAAAACACGTTAAAAGA
Found at i:2763152 original size:17 final size:17
Alignment explanation
Indices: 2763130--2763162 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2763120 ATCCTATTCT
2763130 AATAAAA-ATACACATAA
1 AATAAAATATA-ACATAA
2763147 AATAAAATATAACATA
1 AATAAAATATAACATA
2763163 TTAGTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAATATAACATAA
Found at i:2773397 original size:16 final size:16
Alignment explanation
Indices: 2773360--2773407 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
2773350 TTAGTTTCTC
* *
2773360 TTCGAAATA-TTTGTA
1 TTCGACATATTTTGAA
*
2773375 TTTGACATATTTTGAA
1 TTCGACATATTTTGAA
2773391 TTCGACATATTTTGAA
1 TTCGACATATTTTGAA
2773407 T
1 T
2773408 ATGGATAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (16 bp):
TTCGACATATTTTGAA
Found at i:2778031 original size:20 final size:20
Alignment explanation
Indices: 2778006--2778069 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
2777996 TACACATTTA
2778006 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** *
2778026 TGCGATAGTTGAAATTCGCGT
1 TGCGAT-TTTCCATTTCGCGT
*
2778047 TGCGATTTTTCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
2778067 TGC
1 TGC
2778070 AATAGTCTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:2778091 original size:42 final size:41
Alignment explanation
Indices: 2778006--2778100 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
2777996 TACACATTTA
* *
2778006 TGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGT
1 TGCGATTTTCCATTTCGCGTTGCAATAGTTGAAACTCGCGT
* *
2778047 TGCGATTTTTCATTTCGCGTTGCAATAGTCT-ACAGCT-GTCGT
1 TGCGATTTTCCATTTCGCGTTGCAATAGT-TGA-AACTCG-CGT
2778089 TGCGATTTTCCA
1 TGCGATTTTCCA
2778101 AATTCGTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 29 0.63
42 17 0.37
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (41 bp):
TGCGATTTTCCATTTCGCGTTGCAATAGTTGAAACTCGCGT
Found at i:2778654 original size:6 final size:6
Alignment explanation
Indices: 2778643--2778668 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2778633 TCGTCTCGTC
2778643 TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TC
2778669 ATACGTGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.46, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2779716 original size:2 final size:2
Alignment explanation
Indices: 2779709--2779752 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2779699 GAAAGTAATA
2779709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2779751 AT
1 AT
2779753 TCAAAAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2783719 original size:20 final size:21
Alignment explanation
Indices: 2783694--2783738 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2783684 TATTTTTTAA
2783694 TATTTTTAATAAAAA-ATTAT
1 TATTTTTAATAAAAATATTAT
* *
2783714 TATTTTTACTAAAAATGTTAT
1 TATTTTTAATAAAAATATTAT
2783735 TATT
1 TATT
2783739 AAATACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTTTAATAAAAATATTAT
Found at i:2783786 original size:12 final size:12
Alignment explanation
Indices: 2783771--2783795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2783761 ACATATCCCG
2783771 TAAAATATTATT
1 TAAAATATTATT
2783783 TAAAATATTATT
1 TAAAATATTATT
2783795 T
1 T
2783796 TTTACCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:2791236 original size:299 final size:297
Alignment explanation
Indices: 2790559--2791327 Score: 1095
Period size: 299 Copynumber: 2.6 Consensus size: 297
2790549 GTGTGCGCAC
* * * * *
2790559 ACAGATTTTCAATGATATTCTAAAATTCTTTTCAGCAAATATTCACTGTTTAAACGTTGGAAGCT
1 ACAGATTTGCAATGATATTCTAAAA-TCCTTTCATCAAATATGCACTGTTTAAACTTTGGAAGCT
*
2790624 CAGAAGCCAAGCGTAACAA-CTACATTTCA-ATGAAGAATCCAACAAATAGATCCTTCTTACATG
65 CAGAAGCCAAGCGTAACAAGC-AAATTTCACA-GAAGAATCCAACAAATAGATCCTTCTTACATG
* * * *
2790687 TTATTGCTTCATCACTGCAACACAAATCTTCCAA-AAAAAAT-AATTTTGGATATGGACGGAAAC
128 TTATTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAAC
* * *
2790750 CACACCTCTAGACAAATTAAAAAGGGACATAATACAAGAGCAAGCATGACATAAGCTAGCTACAG
193 CACACCTCTAGAAAAATTAAAAAGGGACATAAAACAAGAACAAGCATGACATAAGCTAGCTACAG
* *
2790815 TAACTTTAGAGGGGGAAATTCCACATGCACACACACATAGT
258 TAACGTTAGAGGGGGAAATTCCACATG-ACACACACATAAT
* * *
2790856 ACAGATTTGCAATGATATTCTAAAATCCGTTTCATCAAATATGTATTGTTTAAACTATGGAAGCT
1 ACAGATTTGCAATGATATTCTAAAATCC-TTTCATCAAATATGCACTGTTTAAACTTTGGAAGCT
*
2790921 CAGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTTCATGTT
65 CAGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTACATGTT
*
2790986 ATTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAATCA
130 ATTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAACCA
* *
2791051 CACTTCTAGAAAAAATTAAAAAAGGGACATAAAACAAGAACTAGCATGACATAAGCTAGCTACA-
195 CACCTCTAG-AAAAATT-AAAAAGGGACATAAAACAAGAACAAGCATGACATAAGCTAGCTACAG
2791115 TAAACGTTAGA-GGGGAAATTTCCACATG-CACACACATAAT
258 T-AACGTTAGAGGGGGAAA-TTCCACATGACACACACATAAT
* * * *
2791155 GCAGATTTGCAATGATATTCTACAATCCTTCTCATCGAATATGCACTATTTAAACTTTGGAAGCT
1 ACAGATTTGCAATGATATTCTAAAATCCTT-TCATCAAATATGCACTGTTTAAACTTTGGAAGCT
* * * * *
2791220 CAGAAGCCAAGCGTAACAAGTATATTTCACATAAGAATCCAACAAATGGATCCTTCTTGCATGTT
65 CAGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTACATGTT
*
2791285 ATTGCTTCATCACTGCAAGACACAA-CTTCCAAGAAAAAATAAA
130 ATTGCTTCATCACTGCAACACA-AATCTTCCAAGAAAAAATAAA
2791328 TTTTAATATG
Statistics
Matches: 426, Mismatches: 35, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
296 2 0.00
297 145 0.34
298 11 0.03
299 192 0.45
300 16 0.04
301 60 0.14
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (297 bp):
ACAGATTTGCAATGATATTCTAAAATCCTTTCATCAAATATGCACTGTTTAAACTTTGGAAGCTC
AGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTACATGTTA
TTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAACCAC
ACCTCTAGAAAAATTAAAAAGGGACATAAAACAAGAACAAGCATGACATAAGCTAGCTACAGTAA
CGTTAGAGGGGGAAATTCCACATGACACACACATAAT
Found at i:2807552 original size:41 final size:43
Alignment explanation
Indices: 2807465--2807558 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 43
2807455 CATAAAACTC
* *
2807465 AAAATTTAAATATATAAATCTTAAAACATGAATCATTTATTCT
1 AAAATTTAAATATATAAATCTTAAAACATAAATCATTCATTCT
*
2807508 AAAATTTAAAT-TATAAA-CTT-AAACTATAAATC-TTACATTTT
1 AAAATTTAAATATATAAATCTTAAAAC-ATAAATCATT-CATTCT
*
2807549 AAAATCTAAA
1 AAAATTTAAA
2807559 CTCGTATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
40 6 0.13
41 22 0.49
42 6 0.13
43 11 0.24
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (43 bp):
AAAATTTAAATATATAAATCTTAAAACATAAATCATTCATTCT
Found at i:2810789 original size:23 final size:23
Alignment explanation
Indices: 2810761--2810874 Score: 167
Period size: 23 Copynumber: 5.0 Consensus size: 23
2810751 ATTATTATAT
2810761 GGCACTCTGGTGCAATTATACGC
1 GGCACTCTGGTGCAATTATACGC
2810784 GGCACTCTGGTGCAATTATACGC
1 GGCACTCTGGTGCAATTATACGC
* *
2810807 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCTGGTGCAATTATACGC
* * *
2810830 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCTGGTGCAATTATACGC
2810853 GGCACT-TCGGTGCAATTATACG
1 GGCACTCT-GGTGCAATTATACG
2810875 AGCTGTGGTG
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTATACGC
Found at i:2813443 original size:30 final size:30
Alignment explanation
Indices: 2813409--2813488 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
2813399 CAAAATGGTT
2813409 TTTGGACTTGAATTGAATTTACAAAACGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
*
2813439 TTTGGACTTGAATTGAATTTACAAAATGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
2813469 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
2813489 TTCAAAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 11 0.22
30 38 0.78
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACGTA
Found at i:2813699 original size:21 final size:21
Alignment explanation
Indices: 2813673--2813714 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2813663 ATTTGAATAT
*
2813673 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2813694 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2813715 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2813776 original size:21 final size:21
Alignment explanation
Indices: 2813743--2813782 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2813733 TTTTTGCAGA
*
2813743 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2813765 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2813783 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2815563 original size:23 final size:24
Alignment explanation
Indices: 2815519--2815567 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2815509 ATTTATCTTT
*
2815519 TAAATTTTATAAAAAAATTATATA
1 TAAATTTTATAAAAAAAGTATATA
*
2815543 TAAATTTTAT-TAAAAAGTATATA
1 TAAATTTTATAAAAAAAGTATATA
2815566 TA
1 TA
2815568 TATATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAATTTTATAAAAAAAGTATATA
Found at i:2815565 original size:25 final size:24
Alignment explanation
Indices: 2815519--2815569 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2815509 ATTTATCTTT
2815519 TAAATTTTATAAAAAAATTATATA
1 TAAATTTTATAAAAAAATTATATA
* *
2815543 TAAATTTTATTAAAAAGTATATATA
1 TAAATTTTATAAAAAAAT-TATATA
2815568 TA
1 TA
2815570 TATTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAATTTTATAAAAAAATTATATA
Found at i:2816898 original size:17 final size:18
Alignment explanation
Indices: 2816876--2816982 Score: 67
Period size: 17 Copynumber: 6.4 Consensus size: 18
2816866 CAAAGAGGTT
2816876 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTAATA
*
2816893 TTATATTTGATTTTAATA
1 TTATATTTAATTTTAATA
* *
2816911 TTAATTTTTAA--ATAA-A
1 TT-ATATTTAATTTTAATA
*
2816927 TTAAATATTAATTTTTAATA
1 TTATAT-TTAA-TTTTAATA
2816947 TTATA-TT-A--TT-ATA
1 TTATATTTAATTTTAATA
2816960 -TATA-TTAATTTTAATA
1 TTATATTTAATTTTAATA
2816976 TTA-ATTT
1 TTATATTT
2816983 TTAAATAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
12 6 0.09
13 4 0.06
14 2 0.03
15 4 0.06
16 11 0.16
17 21 0.30
18 7 0.10
19 9 0.13
20 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TTATATTTAATTTTAATA
Found at i:2816916 original size:29 final size:29
Alignment explanation
Indices: 2816874--2816983 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 29
2816864 TTCAAAGAGG
*
2816874 TTTT-ATATTTAATTTTATATTATATTTGA
1 TTTTAATA-TTAATTTTATATTATATTTAA
*
2816903 TTTTAATATTAATTTTTAAATAAATTAAATATTAA
1 TTTTAATATTAA-TTTT--AT--ATTATAT-TTAA
2816938 TTTTTAATATTATATTATTATA-TATA-TTAA
1 -TTTTAATATTA-ATT-TTATATTATATTTAA
2816968 TTTTAATATTAATTTT
1 TTTTAATATTAATTTT
2816984 TAAATAAATT
Statistics
Matches: 68, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
27 2 0.03
28 3 0.04
29 19 0.28
30 11 0.16
32 5 0.07
33 1 0.01
34 6 0.09
35 5 0.07
36 13 0.19
37 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTAATATTAATTTTATATTATATTTAA
Found at i:2816978 original size:65 final size:66
Alignment explanation
Indices: 2816888--2817036 Score: 232
Period size: 65 Copynumber: 2.3 Consensus size: 66
2816878 ATATTTAATT
*
2816888 TTATATTATATTTGATTTTAATATTAATTTTTAAATAAATTAAATATT-AATTTTTAATATTATA
1 TTATA-TATA-TTAATTTTAATATTAATTTTTAAATAAATTAAATATTCAATTTTTAATATTATA
2816952 TTA
64 TTA
*
2816955 TTATATATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTCATTTTTTAATATTATATT
1 TTATATATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTCAATTTTTAATATTATATT
2817020 A
66 A
*
2817021 -TAGATAT-TTAATTTTA
1 TTATATATATTAATTTTA
2817037 TATCATATAA
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
64 9 0.12
65 42 0.54
66 22 0.28
67 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (66 bp):
TTATATATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTCAATTTTTAATATTATATT
A
Found at i:2817091 original size:20 final size:19
Alignment explanation
Indices: 2817031--2817092 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2817021 TAGATATTTA
*
2817031 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
2817050 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
2817068 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
2817088 ATTTT
1 ATTTT
2817093 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:2818427 original size:137 final size:137
Alignment explanation
Indices: 2818181--2818454 Score: 494
Period size: 137 Copynumber: 2.0 Consensus size: 137
2818171 GGAGTATTAG
2818181 TATGTCGAACCTCTAAATGAATTTTCATTAATTTTGAATGATTTCGTGAACTACCAATCTAATGA
1 TATGTCGAACCTCTAAATGAATTTTCATTAATTTTGAATGATTTCGTGAACTACCAATCTAATGA
*
2818246 AAAGAAAGAGGAGTAAAATGTGAATATTTTGATATCAACGTTGTCGCCAATAACAATCGATGGTT
66 AAAGAAAGAGGAGTAAAATGTGAATATTTTGATATCAACGTTGTCGCAAATAACAATCGATGGTT
2818311 AGTTACT
131 AGTTACT
* * *
2818318 TATGTCGAACCTCTAAATGGATTTTCATTGATTTTGAATGATTTCGTGAACTACTAATCTAATGA
1 TATGTCGAACCTCTAAATGAATTTTCATTAATTTTGAATGATTTCGTGAACTACCAATCTAATGA
* *
2818383 AAAGAAAGAGGAGTAGAATGTGAATATTTTGATATCAACGTTGTCGCAAATAACGATCGATGGTT
66 AAAGAAAGAGGAGTAAAATGTGAATATTTTGATATCAACGTTGTCGCAAATAACAATCGATGGTT
2818448 AGTTACT
131 AGTTACT
2818455 AGTGACGATA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 131 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (137 bp):
TATGTCGAACCTCTAAATGAATTTTCATTAATTTTGAATGATTTCGTGAACTACCAATCTAATGA
AAAGAAAGAGGAGTAAAATGTGAATATTTTGATATCAACGTTGTCGCAAATAACAATCGATGGTT
AGTTACT
Found at i:2830257 original size:24 final size:24
Alignment explanation
Indices: 2830247--2830361 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
2830237 CATAATTCAC
* *
2830247 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAT
*
2830271 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
2830295 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
2830319 GTCATA-TATCATATCAGAATCCAT
1 GTCA-AGTATCATATCAGAATCCAT
*
2830343 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCATATCAGAA
2830362 ATCAAATCGA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:2833831 original size:105 final size:105
Alignment explanation
Indices: 2833649--2834098 Score: 685
Period size: 105 Copynumber: 4.3 Consensus size: 105
2833639 GCATTGTTCA
* * * ** *
2833649 GAGTCCAATATCCTCCGTCGTGATGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
2833709 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2833749 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
2833814 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2833854 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTGATTGGGAAGTTGTTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
2833919 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2833959 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
2834024 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2834064 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
2834099 CACGGATGAC
Statistics
Matches: 321, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
100 36 0.11
101 1 0.00
102 1 0.00
104 5 0.02
105 253 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2834835 original size:67 final size:67
Alignment explanation
Indices: 2834666--2835155 Score: 236
Period size: 73 Copynumber: 7.2 Consensus size: 67
2834656 AAAGAGATAG
* * * * * *
2834666 AATTCGTTTCAAGGGAAAT-GATCTCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGA
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGA
*
2834730 AACAA
63 GACAA
** *
2834735 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGA
2834800 CAA
65 CAA
* * **
2834803 AATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGATAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
*
2834866 GA
66 AA
* * * ** * * *
2834868 AATTTGTTTCAAGAGAAACT--GTCTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTGTCTC
1 AATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-AG----ATTTTGTGTTTCAAGAGAAACTGTCTC
*
2834930 AAGGGAGACGA
57 AAGGGAGACAA
* * * * * * *
2834941 AATTTGTTTCAA-AGAAACATATTCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
2835003 AA
66 AA
* * * * * * *
2835005 AATTTATTTCAAGAGAAACT--GTCTCAAGAGAGACAAAATTT-TGTTTCAAGGGAAACTATCTC
1 AATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-AG----ATTTTGTGTTTCAAGAGAAACTGTCTC
* *
2835067 AAGAGAGACGA
57 AAGGGAGACAA
* * *** * * *
2835078 AATTTATTTCAAGGGAAATGTTTTCAATG--TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
2835141 -A
66 AA
2835142 AATCTTGTTTTAAG
1 AAT-TTGTTTTAAG
2835156 AAAAACAATC
Statistics
Matches: 340, Mismatches: 52, Indels: 62
0.75 0.11 0.14
Matches are distributed among these distances:
64 48 0.14
65 88 0.26
66 6 0.02
67 25 0.07
68 35 0.10
69 8 0.02
70 21 0.06
71 4 0.01
72 11 0.03
73 93 0.27
74 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
AA
Found at i:2834886 original size:36 final size:36
Alignment explanation
Indices: 2834834--2835095 Score: 272
Period size: 36 Copynumber: 7.4 Consensus size: 36
2834824 ATTCAAAGAT
* * *
2834834 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2834870 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2834906 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2834943 TTTGTTTCAA-AGAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAA
*
2834971 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
2835007 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2835043 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2835080 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
2835096 TGTTTTCAAT
Statistics
Matches: 189, Mismatches: 25, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
28 13 0.07
29 8 0.04
30 1 0.01
34 1 0.01
35 9 0.05
36 94 0.50
37 63 0.33
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2834975 original size:101 final size:101
Alignment explanation
Indices: 2834870--2835053 Score: 298
Period size: 101 Copynumber: 1.8 Consensus size: 101
2834860 ATAGACGAAA
*
2834870 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
*
2834935 AGACGAAA-TTTGTTTCAAAGAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAACATATTCAAATAT
* * * *
2834971 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
2835036 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
2835054 GGGAAACTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
100 28 0.37
101 48 0.63
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAACATATTCAAATAT
Found at i:2834989 original size:137 final size:136
Alignment explanation
Indices: 2834783--2835161 Score: 490
Period size: 137 Copynumber: 2.8 Consensus size: 136
2834773 TTTCAAGAGT
* * * * *
2834783 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCA-AGGAAATATATTCAAATATTTTGTTTCAAGGGA
*
2834848 AACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
65 AACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
2834913 CCAAAAGA
129 CCAAAAGA
* *
2834921 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAACATATTCAAATATTTTGTTTCAAGGGAA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAATATATTCAAATATTTTGTTTCAAGGGAA
* * * *
2834986 ACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTT
66 ACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTC
**
2835051 CAAGGGA
130 CAAAAGA
* * * * * * *
2835058 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AATGTTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAA-GGAAATATATTCAAATATTT-TGTTTCAAGGG
* *
2835122 AAACTGTCTCAAGAGAGACAAATCTTGTTTTAAGAAAAAC
64 AAACTGTCTCAAGAGAGACAAAT-TTGTTTCAAGAGAAAC
2835162 AATCATGAGT
Statistics
Matches: 211, Mismatches: 27, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
137 132 0.63
138 79 0.37
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (136 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAATATATTCAAATATTTTGTTTCAAGGGAA
ACTGTCTCAAGAGAGACAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
AAAAGA
Found at i:2836081 original size:22 final size:22
Alignment explanation
Indices: 2836056--2836099 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2836046 CATTTTTGTT
2836056 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
2836078 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
2836100 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:2836745 original size:9 final size:8
Alignment explanation
Indices: 2836697--2836734 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
2836687 TTTTTGTCCC
2836697 TTTTTC-T
1 TTTTTCTT
2836704 TTTTTCTT
1 TTTTTCTT
2836712 TTTGTTCTT
1 TTT-TTCTT
2836721 TTTTTGCTT
1 TTTTT-CTT
2836730 TTTTT
1 TTTTT
2836735 TTGCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 6 0.21
9 16 0.57
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2836746 original size:11 final size:11
Alignment explanation
Indices: 2836705--2836746 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
2836695 CCTTTTTCTT
2836705 TTTTCTTTTTG-
1 TTTT-TTTTTGC
2836716 TTCTTTTTTTGC
1 TT-TTTTTTTGC
2836728 TTTTTTTTTGC
1 TTTTTTTTTGC
2836739 TTTTTTTT
1 TTTTTTTT
2836747 CTTTTTGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTGC
Found at i:2836750 original size:9 final size:9
Alignment explanation
Indices: 2836703--2836752 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
2836693 TCCCTTTTTC
2836703 TTTTTTCTT
1 TTTTTTCTT
*
2836712 TTTGTTCTT
1 TTTTTTCTT
*
2836721 TTTTTGCTTT
1 TTTTTTC-TT
2836731 TTTTTTGCTT
1 TTTTTT-CTT
2836741 TTTTTTCTT
1 TTTTTTCTT
2836750 TTT
1 TTT
2836753 GCCCTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 19 0.54
10 15 0.43
11 1 0.03
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:2837952 original size:8 final size:8
Alignment explanation
Indices: 2837936--2837974 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2837926 AATGTAGATG
2837936 AAAATGCA
1 AAAATGCA
*
2837944 AAAAGGCA
1 AAAATGCA
2837952 AAAATGC-
1 AAAATGCA
2837959 AAAATGCA
1 AAAATGCA
*
2837967 AGAATGCA
1 AAAATGCA
2837975 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:2837962 original size:15 final size:15
Alignment explanation
Indices: 2837936--2837974 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2837926 AATGTAGATG
2837936 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
2837952 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
2837967 AGAATGCA
1 AAAATGCA
2837975 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:2840693 original size:16 final size:18
Alignment explanation
Indices: 2840661--2840695 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2840651 ATATAAAAAC
2840661 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
2840679 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
2840695 A
1 A
2840696 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:2840731 original size:20 final size:20
Alignment explanation
Indices: 2840706--2840743 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2840696 AATGAGTAAA
2840706 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
2840726 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
2840744 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:2841680 original size:21 final size:21
Alignment explanation
Indices: 2841654--2841698 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2841644 GATTTCTGGG
* *
2841654 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2841675 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2841696 CAA
1 CAA
2841699 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2842303 original size:18 final size:18
Alignment explanation
Indices: 2842280--2842314 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2842270 CTAGGAGATT
2842280 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2842298 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2842315 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2843392 original size:149 final size:149
Alignment explanation
Indices: 2843212--2843813 Score: 1177
Period size: 149 Copynumber: 4.0 Consensus size: 149
2843202 GAGTCGAGGG
2843212 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2843277 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2843342 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2843361 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2843426 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2843491 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
2843510 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGGAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2843575 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2843640 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2843659 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2843724 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
*
2843789 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
2843808 TCTACG
1 TCTACG
2843814 TGGCACTTCA
Statistics
Matches: 449, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 449 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:2843831 original size:23 final size:23
Alignment explanation
Indices: 2843791--2843836 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2843781 CATCATTATA
* * *
2843791 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACAGTGCAATTATACG
*
2843814 TGGCACTTCAGTGCAATTATACG
1 TGGCACTACAGTGCAATTATACG
2843837 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTATACG
Found at i:2846931 original size:21 final size:21
Alignment explanation
Indices: 2846905--2846949 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2846895 GATTTCTGGG
* *
2846905 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2846926 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2846947 CAA
1 CAA
2846950 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2847557 original size:18 final size:18
Alignment explanation
Indices: 2847534--2847568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2847524 CTAGGAGATT
2847534 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2847552 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2847569 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2848642 original size:149 final size:149
Alignment explanation
Indices: 2848462--2849063 Score: 1195
Period size: 149 Copynumber: 4.0 Consensus size: 149
2848452 GAGTCGAGGG
2848462 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2848527 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2848592 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2848611 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2848676 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2848741 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2848760 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2848825 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2848890 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2848909 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2848974 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
2849039 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2849058 TCTACG
1 TCTACG
2849064 TGGCACTTCG
Statistics
Matches: 452, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 452 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:2849075 original size:23 final size:23
Alignment explanation
Indices: 2849041--2849086 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2849031 CATCATTATA
*
2849041 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
2849064 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
2849087 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:2854608 original size:6 final size:6
Alignment explanation
Indices: 2854594--2854648 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
2854584 AGGTTTTATA
* *
2854594 TTTAA- TTTAAT TTT-AT ATT-AT ATTTGAT TTTAAT TTTAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT TTTAAT
*
2854640 ATTAAT TTT
1 TTTAAT TTT
2854649 TAAATAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
5 11 0.26
6 29 0.69
7 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (6 bp):
TTTAAT
Found at i:2854609 original size:17 final size:17
Alignment explanation
Indices: 2854587--2854635 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2854577 TTCAAAGAGG
2854587 TTTTATATTTAATTTAA
1 TTTTATATTTAATTTAA
*
2854604 TTTTATA-TTATATTTGA
1 TTTTATATTTA-ATTTAA
2854621 TTTTA-ATTTTAATTT
1 TTTTATA-TTTAATTT
2854636 TAATATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 21 0.75
18 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATATTTAATTTAA
Found at i:2854617 original size:22 final size:23
Alignment explanation
Indices: 2854589--2854631 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2854579 CAAAGAGGTT
2854589 TTATATTT-AATTTAATTTTATA
1 TTATATTTGAATTTAATTTTATA
*
2854611 TTATATTTGATTTTAATTTTA
1 TTATATTTGAATTTAATTTTA
2854632 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTATATTTGAATTTAATTTTATA
Found at i:2854701 original size:63 final size:65
Alignment explanation
Indices: 2854629--2854765 Score: 226
Period size: 64 Copynumber: 2.1 Consensus size: 65
2854619 GATTTTAATT
*
2854629 TTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAATTTTTT-AATATTATATTATAGAT-
1 TTAATTTTAATATTAATTTTTTAAATAAATTAAATAAT-ATTTTTTAAATATTATATTATAGATG
2854691 A
65 A
*
2854692 TTAATTTTAATATTAATTTTTTAAATAAATTAAATAATATTTTTTAAATATTATATTATAGATGT
1 TTAATTTTAATATTAATTTTTTAAATAAATTAAATAATATTTTTTAAATATTATATTATAGATGA
2854757 TTAATTTTA
1 TTAATTTTA
2854766 TATCATATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
63 23 0.33
64 37 0.54
65 9 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (65 bp):
TTAATTTTAATATTAATTTTTTAAATAAATTAAATAATATTTTTTAAATATTATATTATAGATGA
Found at i:2855323 original size:31 final size:31
Alignment explanation
Indices: 2855286--2855345 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2855276 TAGTTGTATG
* *
2855286 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
*
2855317 AATTATTTAAATCTCGGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
2855346 CTTTTAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:2864836 original size:10 final size:10
Alignment explanation
Indices: 2864821--2864845 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2864811 GAATTTGTTC
2864821 AAAATTTTCA
1 AAAATTTTCA
2864831 AAAATTTTCA
1 AAAATTTTCA
2864841 AAAAT
1 AAAAT
2864846 AATTATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTTCA
Found at i:2865269 original size:17 final size:17
Alignment explanation
Indices: 2865235--2865274 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2865225 ATTGTTTGAA
2865235 TAAATTATTATAATATT
1 TAAATTATTATAATATT
*
2865252 TGAATTATT-TAATAATT
1 TAAATTATTATAAT-ATT
2865269 TAAATT
1 TAAATT
2865275 TAACTCGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAATTATTATAATATT
Found at i:2875973 original size:22 final size:22
Alignment explanation
Indices: 2875935--2876005 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 22
2875925 CATTTTAAAT
*
2875935 TTATAATATTCTATTTTATACA
1 TTATAATATTATATTTTATACA
*
2875957 TTAT-ATATTATATTTT-TATA
1 TTATAATATTATATTTTATACA
2875977 TTATAATTAATTA-ATTTTATACA
1 TTATAA-T-ATTATATTTTATACA
*
2876000 ATATAA
1 TTATAA
2876006 CAAGACAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.17
21 12 0.29
22 10 0.24
23 12 0.29
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAATATTATATTTTATACA
Found at i:2879543 original size:16 final size:16
Alignment explanation
Indices: 2879522--2879554 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2879512 CTTTTATTAC
2879522 TCATTGTTTATATATA
1 TCATTGTTTATATATA
*
2879538 TCATTGTTTTTATATA
1 TCATTGTTTATATATA
2879554 T
1 T
2879555 ATATAGTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TCATTGTTTATATATA
Found at i:2885438 original size:8 final size:8
Alignment explanation
Indices: 2885425--2885508 Score: 80
Period size: 8 Copynumber: 10.2 Consensus size: 8
2885415 TAATTGCATG
2885425 AACTCTCA
1 AACTCTCA
2885433 AACTCTCTTA
1 AACTCTC--A
*
2885443 AA-TGATCA
1 AACT-CTCA
*
2885451 AACTCTCT
1 AACTCTCA
*
2885459 AACTCTGA
1 AACTCTCA
* *
2885467 AATTATCA
1 AACTCTCA
2885475 AACTCTCA
1 AACTCTCA
*
2885483 AACTTTCA
1 AACTCTCA
2885491 AACTCTCA
1 AACTCTCA
2885499 AACTCTCA
1 AACTCTCA
2885507 AA
1 AA
2885509 ATGACTTCTA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
8 53 0.88
9 2 0.03
10 5 0.08
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.30
Consensus pattern (8 bp):
AACTCTCA
Found at i:2902500 original size:29 final size:29
Alignment explanation
Indices: 2902454--2902510 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2902444 TGTTGACGGT
* *
2902454 AGGTCGTCATGCATTCCGGGCGACCTACA
1 AGGTCGCCATGCACTCCGGGCGACCTACA
2902483 AGGTCGCCATGCACTCCGGGCGACCTAC
1 AGGTCGCCATGCACTCCGGGCGACCTAC
2902511 CCTTGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.35, G:0.28, T:0.18
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCGGGCGACCTACA
Found at i:2902543 original size:12 final size:12
Alignment explanation
Indices: 2902526--2902550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2902516 TTCAAACAGA
2902526 GAGAATGAACGT
1 GAGAATGAACGT
2902538 GAGAATGAACGT
1 GAGAATGAACGT
2902550 G
1 G
2902551 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:2902612 original size:29 final size:29
Alignment explanation
Indices: 2902579--2902634 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2902569 TCCCAACACA
* *
2902579 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
2902608 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
2902635 ACACTCGCTC
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:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:2902710 original size:23 final size:23
Alignment explanation
Indices: 2902661--2902711 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2902651 CCTCGGATTT
* *
2902661 CCTCGCGTAGCTCGCCCGGTTGC
1 CCTCGCATAGCTCGCCCGGATGC
** *
2902684 CCTCGCATAGCTCGTTCGGATGG
1 CCTCGCATAGCTCGCCCGGATGC
2902707 CCTCG
1 CCTCG
2902712 GTCGGATGGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.08, C:0.39, G:0.29, T:0.24
Consensus pattern (23 bp):
CCTCGCATAGCTCGCCCGGATGC
Found at i:2907775 original size:16 final size:16
Alignment explanation
Indices: 2907754--2907784 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2907744 CCTGCCCCTG
*
2907754 TAGGATCTAAGAGTCT
1 TAGGATCCAAGAGTCT
2907770 TAGGATCCAAGAGTC
1 TAGGATCCAAGAGTC
2907785 ATCGAGCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (16 bp):
TAGGATCCAAGAGTCT
Found at i:2912327 original size:11 final size:12
Alignment explanation
Indices: 2912285--2912335 Score: 86
Period size: 12 Copynumber: 4.3 Consensus size: 12
2912275 GTTATTTAAA
2912285 CGGGTATTGGGT
1 CGGGTATTGGGT
2912297 CGGGTATTGGGT
1 CGGGTATTGGGT
2912309 CGGGTATTGGGT
1 CGGGTATTGGGT
*
2912321 C-GGTATTGGGC
1 CGGGTATTGGGT
2912332 CGGG
1 CGGG
2912336 AATCGGGCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
11 10 0.27
12 27 0.73
ACGTcount: A:0.08, C:0.12, G:0.51, T:0.29
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:2912329 original size:23 final size:24
Alignment explanation
Indices: 2912285--2912335 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
2912275 GTTATTTAAA
*
2912285 CGGGTATTGGGTCGGGTATTGGGT
1 CGGGTATTGGGTCGGGTATTGGGC
2912309 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGTCGGGTATTGGGC
2912332 CGGG
1 CGGG
2912336 AATCGGGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.08, C:0.12, G:0.51, T:0.29
Consensus pattern (24 bp):
CGGGTATTGGGTCGGGTATTGGGC
Found at i:2912412 original size:24 final size:24
Alignment explanation
Indices: 2912349--2912412 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
2912339 CGGGCCCGGT
2912349 ATATATATATATATATTTAAATTAA
1 ATATATATATAT-TATTTAAATTAA
*
2912374 ATATATATATTTTATTTAAATTAA
1 ATATATATATATTATTTAAATTAA
*
2912398 ATTTAT-TAATATTAT
1 ATATATAT-ATATTAT
2912413 ATATATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 23 0.66
25 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATATATATATTATTTAAATTAA
Found at i:2912500 original size:13 final size:13
Alignment explanation
Indices: 2912444--2912487 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2912434 TTTAATATTT
*
2912444 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
* *
2912456 ATCGAGGTGGGTA
1 ATCGGGGCGGGTA
2912469 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
2912482 ATCGGG
1 ATCGGG
2912488 TAATCGGGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.16, C:0.14, G:0.50, T:0.20
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:2912562 original size:6 final size:6
Alignment explanation
Indices: 2912551--2912575 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2912541 AAATAAATTT
2912551 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
2912576 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:2917484 original size:20 final size:20
Alignment explanation
Indices: 2917456--2917506 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2917446 AGAAAGATGT
*
2917456 TCGCCACAAGGCACAGTTGG
1 TCGCTACAAGGCACAGTTGG
*
2917476 TCGCTACAAGACACAGTTGG
1 TCGCTACAAGGCACAGTTGG
*
2917496 TAGCTA-AAGGC
1 TCGCTACAAGGC
2917507 TATGCTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.18
Consensus pattern (20 bp):
TCGCTACAAGGCACAGTTGG
Found at i:2920753 original size:13 final size:13
Alignment explanation
Indices: 2920735--2920760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2920725 AATCTAGATT
2920735 GTTTTTTGTTTTA
1 GTTTTTTGTTTTA
2920748 GTTTTTTGTTTTA
1 GTTTTTTGTTTTA
2920761 AAATTCCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (13 bp):
GTTTTTTGTTTTA
Found at i:2926952 original size:30 final size:30
Alignment explanation
Indices: 2926904--2927152 Score: 155
Period size: 30 Copynumber: 8.0 Consensus size: 30
2926894 GCTTACCATA
* * *
2926904 TGCACTGAGTGTCTTTACACACCAAAGTGT
1 TGCACTAAGTGTCCTTACACACTAAAGTGT
* *
2926934 TGCACTAAG-GATCCTTACACACTACATTGT
1 TGCACTAAGTG-TCCTTACACACTAAAGTGT
** * *
2926964 TATACTAAGTGTCCTTACACACTATAGTACCAT
1 TGCACTAAGTGTCCTTACACACTAAAGT---GT
* * *
2926997 ATGCACCAAGTGTCCTTACACACCATAGTGT
1 -TGCACTAAGTGTCCTTACACACTAAAGTGT
* * *
2927028 TGCACTGAGAGTCCTTACACAATACAA-TGT
1 TGCACTAAGTGTCCTTACACACTA-AAGTGT
* * *
2927058 TGTACTAAGTGTCCTTACACACTATAGTACCAT
1 TGCACTAAGTGTCCTTACACACTAAAGT---GT
* *
2927091 ATG-ACCTAAGTGTCCTTACACACCATAA-TGC
1 -TGCA-CTAAGTGTCCTTACACACTA-AAGTGT
* * *
2927122 TACACTAAGTGTCCTTACACATTATAGTGT
1 TGCACTAAGTGTCCTTACACACTAAAGTGT
2927152 T
1 T
2927153 AATCCGATTA
Statistics
Matches: 167, Mismatches: 36, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
29 3 0.02
30 110 0.66
31 4 0.02
33 3 0.02
34 46 0.28
35 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (30 bp):
TGCACTAAGTGTCCTTACACACTAAAGTGT
Found at i:2927013 original size:34 final size:34
Alignment explanation
Indices: 2926970--2927113 Score: 119
Period size: 34 Copynumber: 4.5 Consensus size: 34
2926960 TTGTTATACT
2926970 AAGTGTCCTTACACACTATAGTACCATATGCACC
1 AAGTGTCCTTACACACTATAGTACCATATGCACC
* * *
2927004 AAGTGTCCTTACACACCATAGT---GT-TGCACT
1 AAGTGTCCTTACACACTATAGTACCATATGCACC
* * * * * *
2927034 GAGAGTCCTT--ACAC-A-A-TACAATGTTGTACT
1 AAGTGTCCTTACACACTATAGTACCAT-ATGCACC
2927064 AAGTGTCCTTACACACTATAGTACCATATG-ACC
1 AAGTGTCCTTACACACTATAGTACCATATGCACC
2927097 TAAGTGTCCTTACACAC
1 -AAGTGTCCTTACACAC
2927114 CATAATGCTA
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 1 0.01
28 5 0.06
30 26 0.30
31 1 0.01
32 4 0.05
33 3 0.03
34 40 0.46
35 5 0.06
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (34 bp):
AAGTGTCCTTACACACTATAGTACCATATGCACC
Found at i:2927064 original size:94 final size:93
Alignment explanation
Indices: 2926897--2927142 Score: 350
Period size: 94 Copynumber: 2.6 Consensus size: 93
2926887 CCGAAGTGCT
** * * * *
2926897 TACCATATGCACTGAGTGTCTTTACACACCAAAGTGTTGCACTAAGGATCCTTACACACTACATT
1 TACCATATGCACCAAGTGTCCTTACACACCATAGTGTTGCACTAAGG-TCCTTACACAATACAAT
2926962 GTTATACTAAGTGTCCTTACACACTATAG
65 GTTATACTAAGTGTCCTTACACACTATAG
*
2926991 TACCATATGCACCAAGTGTCCTTACACACCATAGTGTTGCACTGAGAGTCCTTACACAATACAAT
1 TACCATATGCACCAAGTGTCCTTACACACCATAGTGTTGCACTAAG-GTCCTTACACAATACAAT
*
2927056 GTTGTACTAAGTGTCCTTACACACTATAG
65 GTTATACTAAGTGTCCTTACACACTATAG
* * *
2927085 TACCATATG-ACCTAAGTGTCCTTACACACCATAATGCTACACTAAGTGTCCTTACACA
1 TACCATATGCACC-AAGTGTCCTTACACACCATAGTGTTGCACTAAG-GTCCTTACACA
2927143 TTATAGTGTT
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
93 3 0.02
94 133 0.97
95 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (93 bp):
TACCATATGCACCAAGTGTCCTTACACACCATAGTGTTGCACTAAGGTCCTTACACAATACAATG
TTATACTAAGTGTCCTTACACACTATAG
Found at i:2930261 original size:367 final size:358
Alignment explanation
Indices: 2929597--2930328 Score: 1173
Period size: 367 Copynumber: 2.0 Consensus size: 358
2929587 CAAGAATCTG
** * *
2929597 ATTTCAATAAAACCTCTTCCTCAATAGTAAATTATTCATTTATGGAATAATTTTTTTGGGAAAAT
1 ATTTCAATAAAACCTCACCCTCAAGAGTAAATTATCCATTTATGGAATAATTTTTTTGGGAAAAT
* *
2929662 TACCACTTAACTCCCTAAACTTTTCCTAATTTTTTACTTTGGCCACTAAACTTTCAAAATTTACA
66 TACCACTTAACTCCCTAAACTTTTCCTAATTTTATACTTTAGCCACTAAACTTTCAAAATTTACA
* *
2929727 TTTTAGTCACTAACCAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCATGGAAGGTTAAG
131 TTTTAGCCACTAACCAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGGTTAAG
*
2929792 AATGAAGCATCTCCATGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAGCATCTCATCGT
196 AATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAGCATCTCATCGT
2929857 CCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCATGAGAATTGTGG
261 CCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCATGAGAATTGTGG
2929922 GCATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
326 GCATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
*
2929955 ATTTCAATAAAACTTCACCCTCAAGAGTAAATTATCCATTTATGGAATAAAAATTCTTTTTGGGA
1 ATTTCAATAAAACCTCACCCTCAAGAGTAAATTATCCATTTATGGAAT---AATT-TTTTTGGGA
* ** **
2930020 AACTTATTACTTAGTTCCCTAAACGTTTTCC-AATTTTATACTTTAGCCACTAAACTTT-AAAAT
62 AAATTACCACTTAACTCCCTAAAC-TTTTCCTAATTTTATACTTTAGCCACTAAACTTTCAAAAT
2930083 TTACATTTTAGCCACTAA-CAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGG
126 TTACATTTTAGCCACTAACCAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGG
* *
2930147 TTAAGAATGAAGCATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTGCGTGCAGCCTGAA
191 TT---AA-G-A--ATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAA
2930212 GCATCTCATCGTCCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCA
249 GCATCTCATCGTCCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCA
*
2930277 TGAGAATTGTGGGCATTGAAGTGAGCTTGCGCAAGCTTTAGAGTC
314 TGAGAATTGTGGGCATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
2930322 ATTTCAA
1 ATTTCAA
2930329 CCAGCACAAC
Statistics
Matches: 344, Mismatches: 18, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
358 43 0.12
360 47 0.14
361 26 0.08
362 53 0.15
363 8 0.02
364 1 0.00
365 1 0.00
367 165 0.48
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (358 bp):
ATTTCAATAAAACCTCACCCTCAAGAGTAAATTATCCATTTATGGAATAATTTTTTTGGGAAAAT
TACCACTTAACTCCCTAAACTTTTCCTAATTTTATACTTTAGCCACTAAACTTTCAAAATTTACA
TTTTAGCCACTAACCAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGGTTAAG
AATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAGCATCTCATCGT
CCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCATGAGAATTGTGG
GCATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
Found at i:2932346 original size:27 final size:27
Alignment explanation
Indices: 2932314--2932378 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
2932304 TTTAATTTTT
2932314 TAAAATTTTATAAATTTACTCATAACG
1 TAAAATTTTATAAATTTACTCATAACG
2932341 TAAAATTTTATAAATTTACTCATAACG
1 TAAAATTTTATAAATTTACTCATAACG
2932368 TAAAATTTTAT
1 TAAAATTTTAT
2932379 GTACGTGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (27 bp):
TAAAATTTTATAAATTTACTCATAACG
Found at i:2933159 original size:16 final size:15
Alignment explanation
Indices: 2933138--2933168 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2933128 TGTATATAAA
2933138 ATTTTTAAAATAATAT
1 ATTTTTAAAA-AATAT
2933154 ATTTTTAAAAAATAT
1 ATTTTTAAAAAATAT
2933169 TGATGGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTAAAAAATAT
Found at i:2934533 original size:2 final size:2
Alignment explanation
Indices: 2934526--2934553 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2934516 TCTATTATCT
2934526 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
2934554 ACATGCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2937340 original size:29 final size:29
Alignment explanation
Indices: 2937298--2937356 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2937288 TAACTCTTTG
*
2937298 ACGTAATCATAAACAGATTCATATTATCT
1 ACGTAATCATAAACAAATTCATATTATCT
2937327 ACGTAATCATAAACAAATTCATATTATCT
1 ACGTAATCATAAACAAATTCATATTATCT
2937356 A
1 A
2937357 TAAAATAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (29 bp):
ACGTAATCATAAACAAATTCATATTATCT
Found at i:2941400 original size:23 final size:24
Alignment explanation
Indices: 2941346--2941400 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
2941336 TTTAATATTT
* *
2941346 TATTAATTTAATATTATAAATAAAA
1 TATTAA-TTAAAATTATAAAAAAAA
2941371 T-TATAATTAAAATT-TAAAAAAAA
1 TAT-TAATTAAAATTATAAAAAAAA
2941394 TATTAAT
1 TATTAAT
2941401 CTATTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 13 0.50
24 9 0.35
25 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TATTAATTAAAATTATAAAAAAAA
Found at i:2950094 original size:17 final size:18
Alignment explanation
Indices: 2950054--2950094 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2950044 TGATATGAAT
2950054 TATATGATATGATATGTG
1 TATATGATATGATATGTG
*
2950072 TGTATGA-ATGATTAT-TG
1 TATATGATATGA-TATGTG
2950089 TATATG
1 TATATG
2950095 TTATAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (18 bp):
TATATGATATGATATGTG
Found at i:2952519 original size:18 final size:18
Alignment explanation
Indices: 2952496--2952546 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2952486 AATCAAAACC
2952496 ACATACATATACATACAT
1 ACATACATATACATACAT
* * *
2952514 ACATACATACATATATAT
1 ACATACATATACATACAT
**
2952532 GTATACATATACATA
1 ACATACATATACATA
2952547 AAATAGTTGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (18 bp):
ACATACATATACATACAT
Found at i:2955880 original size:22 final size:23
Alignment explanation
Indices: 2955850--2955906 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2955840 ATTTGGTATT
* *
2955850 AAAAA-AATATTTAGTT-TTTTA
1 AAAAATAATATTTAATTATTCTA
*
2955871 AAAAATAATATTAAATTATTCTA
1 AAAAATAATATTTAATTATTCTA
2955894 AAAAATAA-ATTTA
1 AAAAATAATATTTA
2955907 TAATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 13 0.43
23 12 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAATAATATTTAATTATTCTA
Found at i:2956140 original size:2 final size:2
Alignment explanation
Indices: 2956133--2956245 Score: 226
Period size: 2 Copynumber: 56.5 Consensus size: 2
2956123 TATGTTTGGT
2956133 TA TA TA 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
2956175 TA TA TA 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
2956217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2956246 GTTCATATTT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 111 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2956851 original size:25 final size:25
Alignment explanation
Indices: 2956817--2956870 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
2956807 CAGCTGCAGG
**
2956817 TGCTCGAGTCAATTGGGATTTTATT
1 TGCTCGAGTCAATTCAGATTTTATT
2956842 TGCTCGAGTCAATTCAGATTTTATT
1 TGCTCGAGTCAATTCAGATTTTATT
2956867 TGCT
1 TGCT
2956871 TTTCTAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (25 bp):
TGCTCGAGTCAATTCAGATTTTATT
Found at i:2980862 original size:2 final size:2
Alignment explanation
Indices: 2980855--2980885 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2980845 AAGTTTAAGA
2980855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2980886 AAATAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2981054 original size:21 final size:21
Alignment explanation
Indices: 2981028--2981085 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
2981018 AATTTCTTTC
2981028 TCGCAACGT-GATTT-TCGAAAT
1 TCGCAACGTCGATTTCT-G-AAT
2981049 TCGCAAC-TCGATTTCTGAAT
1 TCGCAACGTCGATTTCTGAAT
2981069 TCGCAACG-CGAATTTCT
1 TCGCAACGTCG-ATTTCT
2981086 TTTTCGCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 13 0.39
21 19 0.58
22 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
TCGCAACGTCGATTTCTGAAT
Found at i:2981069 original size:20 final size:21
Alignment explanation
Indices: 2980999--2981085 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 21
2980989 CGCAACTCAG
*
2980999 TTTCTGCAA-TCGAAACGCGAA
1 TTTCTG-AATTCGCAACGCGAA
* * *
2981020 TTTCT--TTCTCGCAACGTGAT
1 TTTCTGAAT-TCGCAACGCGAA
*
2981040 TTTC-GAAATTCGCAACTCG-A
1 TTTCTG-AATTCGCAACGCGAA
2981060 TTTCTGAATTCGCAACGCGAA
1 TTTCTGAATTCGCAACGCGAA
2981081 TTTCT
1 TTTCT
2981086 TTTTCGCAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
20 29 0.58
21 20 0.40
22 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (21 bp):
TTTCTGAATTCGCAACGCGAA
Found at i:2981091 original size:20 final size:20
Alignment explanation
Indices: 2981012--2981095 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
2981002 CTGCAATCGA
*
2981012 AACGCGAATTTCT-TTCTCGC
1 AACGCGAATTTCTAAT-TCGC
* * *
2981032 AACGTGATTTTCGAAATTCGC
1 AACGCGAATTTC-TAATTCGC
*
2981053 AACTCG-ATTTCTGAATTCGC
1 AACGCGAATTTCT-AATTCGC
**
2981073 AACGCGAATTTCTTTTTCGC
1 AACGCGAATTTCTAATTCGC
2981093 AAC
1 AAC
2981096 CCAAGTTTTC
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 34 0.69
21 14 0.29
22 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
AACGCGAATTTCTAATTCGC
Found at i:2981125 original size:19 final size:20
Alignment explanation
Indices: 2981081--2981125 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2981071 GCAACGCGAA
* *
2981081 TTTCTTTTTCGCAACCCAAGT
1 TTTC-TTTTCGCAACCAAAAT
2981102 TTTCTTTTCGCAA-CAAAAT
1 TTTCTTTTCGCAACCAAAAT
2981121 TTTCT
1 TTTCT
2981126 AAATCGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 9 0.41
21 4 0.18
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTCTTTTCGCAACCAAAAT
Found at i:2981150 original size:40 final size:40
Alignment explanation
Indices: 2981101--2981196 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 40
2981091 GCAACCCAAG
* * *
2981101 TTTTCTTTTCGCAACAAAATTTTCTAAATCGCAATACGAA
1 TTTTATTTTCGCAACAAAATTTTCGAAATCGCAACACGAA
* ** *** *
2981141 TTTTGTTTTCTTAACTCGATTTTCGAATTCGCAACACGAA
1 TTTTATTTTCGCAACAAAATTTTCGAAATCGCAACACGAA
*
2981181 TTTTAATTTCGCAACA
1 TTTTATTTTCGCAACA
2981197 GCTTTTATTT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTATTTTCGCAACAAAATTTTCGAAATCGCAACACGAA
Found at i:2981193 original size:20 final size:20
Alignment explanation
Indices: 2981168--2981222 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
2981158 GATTTTCGAA
2981168 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* *
2981188 TTCGCAACA-G-CTTTTATT
1 TTCGCAACACGAATTTTAAT
*
2981206 TTCGCAACACAAATTTT
1 TTCGCAACACGAATTTT
2981223 TTGGGTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.52
19 1 0.03
20 13 0.45
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:2981369 original size:14 final size:15
Alignment explanation
Indices: 2981350--2981387 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2981340 TCCCCATCTC
2981350 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
2981364 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2981380 TAATTTTT
1 TAATTTTT
2981388 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2982180 original size:24 final size:24
Alignment explanation
Indices: 2982148--2982201 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2982138 GTATTCGAAA
*
2982148 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTAAATACCCGGAC
* * *
2982172 TTTGATCTTGTTAAATACTCGGAT
1 TTTGATCTTGGTAAATACCCGGAC
2982196 TTTGAT
1 TTTGAT
2982202 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCGGAC
Found at i:2982207 original size:24 final size:24
Alignment explanation
Indices: 2982161--2982207 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2982151 GATCTTGGTC
*
2982161 AATACCCGGACTTTGATCTTGTTA
1 AATACCCGGACTTTGATCATGTTA
* * *
2982185 AATACTCGGATTTTGATGATGTT
1 AATACCCGGACTTTGATCATGTT
2982208 TCAGAAGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
AATACCCGGACTTTGATCATGTTA
Found at i:2984802 original size:16 final size:15
Alignment explanation
Indices: 2984781--2984815 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2984771 TATAGATTGA
*
2984781 AATTAAACAACAAATC
1 AATTAAACAA-AAAAC
2984797 AATTAAACAAAAAAC
1 AATTAAACAAAAAAC
2984812 AATT
1 AATT
2984816 CTTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTAAACAAAAAAC
Found at i:2986233 original size:21 final size:21
Alignment explanation
Indices: 2986207--2986303 Score: 151
Period size: 21 Copynumber: 4.6 Consensus size: 21
2986197 GTGAATCGAG
2986207 CTCTTGAAC-AGTGGGAGGGGC
1 CTCTTGAACGA-TGGGAGGGGC
*
2986228 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
2986249 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
2986270 CTCTTGAACGATAGGAGTGGC
1 CTCTTGAACGATGGGAGGGGC
2986291 CTCTTGAACGATG
1 CTCTTGAACGATG
2986304 ACAGATGAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
21 69 0.99
22 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:2986615 original size:21 final size:21
Alignment explanation
Indices: 2986585--2986639 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2986575 ATAAAACAAT
* * *
2986585 ATCACTTAAAGCGGCTACCTC
1 ATCACGTAAAGCAGATACCTC
*
2986606 ATCACGTAAAGTAGATACCTC
1 ATCACGTAAAGCAGATACCTC
* *
2986627 ACCACGTAGAGCA
1 ATCACGTAAAGCA
2986640 TCATTGTCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (21 bp):
ATCACGTAAAGCAGATACCTC
Found at i:2986737 original size:21 final size:21
Alignment explanation
Indices: 2986709--2986761 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2986699 TGCACCATTG
* *
2986709 TCATCACGTAAAGTACCGACC
1 TCATCACGTAAAGCACCAACC
* * *
2986730 TCGTCACGCAAAGCACTAACC
1 TCATCACGTAAAGCACCAACC
2986751 TCATCACGTAA
1 TCATCACGTAA
2986762 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.19
Consensus pattern (21 bp):
TCATCACGTAAAGCACCAACC
Found at i:2986951 original size:42 final size:42
Alignment explanation
Indices: 2986876--2986973 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
2986866 GTGATGGAAT
** * * *
2986876 AGGTGATGGCTCTCGGTGTGGAGGTGTATAATCGACCCGATC
1 AGGTGATGGCTCTCAATGTCGAGCTGTAGAATCGACCCGATC
* * *
2986918 AGGTGATGGCTCTCAATTTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCAATGTCGAGCTGTAGAATCGACCCGATC
2986960 AGGTGATGGCTCTC
1 AGGTGATGGCTCTC
2986974 GAAGTAGGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCAATGTCGAGCTGTAGAATCGACCCGATC
Found at i:2988887 original size:22 final size:22
Alignment explanation
Indices: 2988844--2988891 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2988834 ATAGAGGGGG
* *
2988844 GTCGTCGGATATATGGACGGAT
1 GTCGTCGGAGATAGGGACGGAT
* *
2988866 GTCGTCGGAGATGGGGATGGAT
1 GTCGTCGGAGATAGGGACGGAT
2988888 GTCG
1 GTCG
2988892 CTGTAGAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.25
Consensus pattern (22 bp):
GTCGTCGGAGATAGGGACGGAT
Found at i:2989098 original size:20 final size:20
Alignment explanation
Indices: 2989059--2989099 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2989049 TTTGACTTCT
*
2989059 GCGTTGCGAATTATAAATTC
1 GCGTTGCGAATTACAAATTC
* *
2989079 GCGTTGCGATTTACATATTC
1 GCGTTGCGAATTACAAATTC
2989099 G
1 G
2989100 TATTGCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
GCGTTGCGAATTACAAATTC
Found at i:2989261 original size:2 final size:2
Alignment explanation
Indices: 2989254--2989312 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2989244 TATTTTCTTT
2989254 TA TA TA 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
2989296 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2989313 TATTGTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2994157 original size:36 final size:36
Alignment explanation
Indices: 2994106--2994187 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
2994096 TTGTTTGTCT
*
2994106 GGACATTCATCTCGTATTGCTTGTCTCGTATGTTGA
1 GGACATTCAACTCGTATTGCTTGTCTCGTATGTTGA
* *
2994142 GGATATTCAACTCGTATTGTTTGTCTCGTATGTTGA
1 GGACATTCAACTCGTATTGCTTGTCTCGTATGTTGA
2994178 GGACATTCAA
1 GGACATTCAA
2994188 TGTGAAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (36 bp):
GGACATTCAACTCGTATTGCTTGTCTCGTATGTTGA
Found at i:2994732 original size:36 final size:36
Alignment explanation
Indices: 2994691--2994769 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
2994681 TTAAAAAAAT
2994691 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
1 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
2994727 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
1 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
2994763 TATAATT
1 TATAATT
2994770 ATATTTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (36 bp):
TATAATTTAAATATTTATTATTCCGTTAAACTAACG
Found at i:2995663 original size:19 final size:18
Alignment explanation
Indices: 2995635--2995671 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
2995625 TTTATTTGTA
2995635 AATATAATAGTAAAATAT
1 AATATAATAGTAAAATAT
2995653 AATATTAATAGTAAAATAT
1 AATA-TAATAGTAAAATAT
2995672 TTTAATGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AATATAATAGTAAAATAT
Found at i:3007329 original size:2 final size:2
Alignment explanation
Indices: 3007322--3007350 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3007312 ATTAGATTAC
3007322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3007351 CTTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3015979 original size:20 final size:20
Alignment explanation
Indices: 3015954--3015994 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3015944 ATGGACTGCA
3015954 TGGTAATCAGGGTTTTCATG
1 TGGTAATCAGGGTTTTCATG
3015974 TGGTAATCAGGGTTTTCATG
1 TGGTAATCAGGGTTTTCATG
3015994 T
1 T
3015995 AGATGCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (20 bp):
TGGTAATCAGGGTTTTCATG
Found at i:3027350 original size:16 final size:17
Alignment explanation
Indices: 3027329--3027361 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3027319 AAGAAGTTGT
*
3027329 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
3027345 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
3027362 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Found at i:3044191 original size:11 final size:11
Alignment explanation
Indices: 3044168--3044203 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3044158 TTTTATTCAC
3044168 TTTTTATT-T-
1 TTTTTATTGTA
3044177 TTTTTATTGTA
1 TTTTTATTGTA
3044188 TTTTTATTG-A
1 TTTTTATTGTA
3044198 TTTTTA
1 TTTTTA
3044204 AATATATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTATTGTA
Found at i:3045367 original size:20 final size:20
Alignment explanation
Indices: 3045324--3045417 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
3045314 TTTTCCTAAT
3045324 TCGCAATGCGAATACGTAAAA
1 TCGCAATGCGAATACGT-AAA
3045345 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3045365 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
3045385 TCTCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
3045405 TCGCAACGCGAAT
1 TCGCAATGCGAAT
3045418 CTGACTATCG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
20 52 0.75
21 17 0.25
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3045432 original size:40 final size:41
Alignment explanation
Indices: 3045324--3045435 Score: 140
Period size: 40 Copynumber: 2.8 Consensus size: 41
3045314 TTTTCCTAAT
* * *
3045324 TCGCAATGCGAATACGTAAAATCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTACAATCGCAATGCGAATATGTAAA
* *
3045365 TCGCAATGCGAATACGTA-AATCTCAATGCGAATATGTAAA
1 TCGCAACGCGAATACGTACAATCGCAATGCGAATATGTAAA
*
3045405 TCGCAACGCGAAT-C-TGACTATCGCAATGCGA
1 TCGCAACGCGAATACGT-ACAATCGCAATGCGA
3045436 TTTACATAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
38 1 0.02
39 2 0.03
40 43 0.67
41 18 0.28
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAACGCGAATACGTACAATCGCAATGCGAATATGTAAA
Found at i:3045640 original size:22 final size:22
Alignment explanation
Indices: 3045615--3045702 Score: 149
Period size: 22 Copynumber: 4.0 Consensus size: 22
3045605 GGCGACATCC
3045615 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3045637 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
3045659 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3045681 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3045703 TTCACGGTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3046063 original size:19 final size:19
Alignment explanation
Indices: 3046039--3046196 Score: 84
Period size: 20 Copynumber: 8.6 Consensus size: 19
3046029 GCGATTTTGT
*
3046039 CGTTGCGATTTTTAATTCG
1 CGTTGCGATTTTCAATTCG
*
3046058 CGTTGC-A-ATTC--TT-G
1 CGTTGCGATTTTCAATTCG
**
3046072 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTC-AATTCG
* *
3046092 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTTTCA-ATTCG
* *
3046112 TGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCAATTCG
3046131 CGTTGCGA--TTC--TT-G
1 CGTTGCGATTTTCAATTCG
** *
3046145 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-ATTCG
* *
3046165 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCA-ATTCG
*
3046185 TGTTGCGATTTT
1 CGTTGCGATTTT
3046197 AAGTTTTAGA
Statistics
Matches: 114, Mismatches: 12, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.14
15 5 0.04
16 5 0.04
17 5 0.04
18 1 0.01
19 23 0.20
20 59 0.52
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCAATTCG
Found at i:3046096 original size:20 final size:20
Alignment explanation
Indices: 3046071--3046194 Score: 100
Period size: 20 Copynumber: 6.5 Consensus size: 20
3046061 TGCAATTCTT
* *
3046071 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATTGTCAATTTC
*
3046091 GCGTTGCGATTGTCATTTTC
1 GCGTTGCGATTGTCAATTTC
* *
3046111 GTGTTGCGATTTTC-ATTTC
1 GCGTTGCGATTGTCAATTTC
3046130 GCGTTGCGA-T-TC---TT-
1 GCGTTGCGATTGTCAATTTC
* *
3046144 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATTGTCAATTTC
* * *
3046164 GTGTTGCGATTTTCATTTTC
1 GCGTTGCGATTGTCAATTTC
*
3046184 GTGTTGCGATT
1 GCGTTGCGATT
3046195 TTAAGTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.10
15 2 0.02
16 2 0.02
17 2 0.02
18 1 0.01
19 14 0.16
20 57 0.66
ACGTcount: A:0.13, C:0.18, G:0.25, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATTGTCAATTTC
Found at i:3046120 original size:73 final size:73
Alignment explanation
Indices: 3046032--3046196 Score: 251
Period size: 73 Copynumber: 2.3 Consensus size: 73
3046022 TCGTAATGCG
*
3046032 ATTTT-GTCGTTGCGATTTTTAATTCGCGTTGCAATTCTTGCGTTGCGATAGTCAAATTCGCGTT
1 ATTTTCGT-GTTGCGATTTTCAATTCGCGTTGCAATTCTTGCGTTGCGATAGTCAAATTCGCGTT
3046096 GCGATTGTC
65 GCGATTGTC
* * ** *
3046105 ATTTTCGTGTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCATTTTCGTGTTG
1 ATTTTCGTGTTGCGATTTTCAATTCGCGTTGCAATTCTTGCGTTGCGATAGTCAAATTCGCGTTG
*
3046170 CGATTTTC
66 CGATTGTC
3046178 ATTTTCGTGTTGCGATTTT
1 ATTTTCGTGTTGCGATTTT
3046197 AAGTTTTAGA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 82 0.98
74 2 0.02
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.47
Consensus pattern (73 bp):
ATTTTCGTGTTGCGATTTTCAATTCGCGTTGCAATTCTTGCGTTGCGATAGTCAAATTCGCGTTG
CGATTGTC
Found at i:3046148 original size:53 final size:54
Alignment explanation
Indices: 3046091--3046194 Score: 183
Period size: 53 Copynumber: 1.9 Consensus size: 54
3046081 AGTCAAATTC
*
3046091 GCGTTGCGATTGTCATTTTCGTGTTGCGATTTTCA-TTTCGCGTTGCGATTCTT
1 GCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTCTT
*
3046144 GCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGTTGCGATT
1 GCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATT
3046195 TTAAGTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 34 0.71
54 14 0.29
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (54 bp):
GCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTCTT
Found at i:3046195 original size:20 final size:20
Alignment explanation
Indices: 3046088--3046196 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
3046078 GATAGTCAAA
*
3046088 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTTTCATT
*
3046108 TTCGTGTTGCGATTTTCA-T
1 TTCGCGTTGCGATTTTCATT
3046127 TTCGCGTTGCGA--TTC---
1 TTCGCGTTGCGATTTTCATT
**
3046142 TT-GCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCATT
*
3046161 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
3046181 TTCGTGTTGCGATTTT
1 TTCGCGTTGCGATTTT
3046197 AAGTTTTAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.12
15 2 0.03
16 2 0.03
17 3 0.04
19 14 0.18
20 46 0.61
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:3046215 original size:73 final size:73
Alignment explanation
Indices: 3046065--3046216 Score: 189
Period size: 73 Copynumber: 2.1 Consensus size: 73
3046055 TCGCGTTGCA
*
3046065 ATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTGTCATTTTCGTGTTGCGATTTTCATTTC
1 ATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTGTCATTTTCGTGTTGCGATTTTAATTTC
* ***
3046130 GCGTTGCG
66 GAGAAACG
** * *
3046138 ATTCTTGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGTTGCGATTTTAAGTTT
1 ATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTGTCATTTTCGTGTTGCGATTTTAA-TTT
* *
3046203 -TAGAAACT
65 CGAGAAACG
3046211 ATTCTT
1 ATTCTT
3046217 CTTCTGCAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
73 64 0.96
74 3 0.04
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (73 bp):
ATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTGTCATTTTCGTGTTGCGATTTTAATTTC
GAGAAACG
Found at i:3048103 original size:20 final size:20
Alignment explanation
Indices: 3048078--3048220 Score: 138
Period size: 20 Copynumber: 7.5 Consensus size: 20
3048068 AGAATAGTTT
3048078 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
3048098 ACTATCGCAACACGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
3048118 ACTATAGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
3048134 A--ATCGCAATGCG-AAATA
1 ACTATCGCAATGCGAAAATG
** * *
3048151 AAAATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
3048171 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
3048191 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
3048211 ACTATCGCAA
1 ACTATCGCAA
3048221 CGAAAGAATC
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
14 6 0.06
16 6 0.06
17 3 0.03
18 2 0.02
19 9 0.09
20 75 0.74
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:3048237 original size:93 final size:93
Alignment explanation
Indices: 3048078--3048252 Score: 287
Period size: 93 Copynumber: 1.9 Consensus size: 93
3048068 AGAATAGTTT
*
3048078 ACTATCGCAATGCGAAAATGACTATCGCAACACGAAAATGACTATAGCAACGAGAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACACGAAAATGACTATAGCAACGAAAGAATCGCAAT
3048143 GCGAAATAAAAATCGCAACGTGAAAATG
66 GCGAAATAAAAATCGCAACGTGAAAATG
** ** *
3048171 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACACGAAAATGACTATAGCAACGAAAGAATCGCAAT
*
3048236 GCGAAATGAAAATCGCA
66 GCGAAATAAAAATCGCA
3048253 TTGCGATTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (93 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACACGAAAATGACTATAGCAACGAAAGAATCGCAAT
GCGAAATAAAAATCGCAACGTGAAAATG
Done.