Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 33
Found at i:2669822 original size:29 final size:29
Alignment explanation
Indices: 2669786--2669851 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2669776 ATTATAAATA
*
2669786 TTGAAATTTAATTTTA-T-ATTGTATTTCAT
1 TTGAAATTT-ATTTTATTAATTG-ATTTAAT
2669815 TTGAAATTTATTTTATTAATTGATTTAAT
1 TTGAAATTTATTTTATTAATTGATTTAAT
2669844 TT-AAATTT
1 TTGAAATTT
2669852 TAAATTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 12 0.35
29 18 0.53
30 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (29 bp):
TTGAAATTTATTTTATTAATTGATTTAAT
Found at i:2675004 original size:138 final size:140
Alignment explanation
Indices: 2674727--2675017 Score: 342
Period size: 138 Copynumber: 2.1 Consensus size: 140
2674717 CTTGGCCGAG
* * * * * *
2674727 TCATTAGAAGCGGAAATTGAAAAGGAAAGGAGATTGTCAGAGCAAGTTTCTGCTAACTCAAATGA
1 TCATTAGAAGCAGAAATCGAAAAGGAAAGGACATTGTCAGAGCAAGTTTCAGCGAACACAAAT-A
* ***
2674792 GTCTAACTCGAAGCAACTTCTCGAGTCTCAACTCATTAGCATCAAGGCAGAGGCTTGGATGATGT
65 G--TAACTCGAAGCAACTTCTCGAGTCTCAACTCATTAGCATCAAAGCAGAGGCTCAAATGATGT
2674857 CTGCAAAGATCGAC
128 CTG-AAAGATCGAC
*
2674871 TCATTAGAAGCAGAAATCGAAAAGGAAAGGACCA-TGTCGGAGCAAGTTTCAGCGAACACAAAT-
1 TCATTAGAAGCAGAAATCGAAAAGGAAAGGA-CATTGTCAGAGCAAGTTTCAGCGAACACAAATA
*
2674934 G-AA-TCGAAGCAACTTCTCGAGTCTCAACTCATTAGCATCAAAG-ATGATGCTCAAATGATGTA
65 GTAACTCGAAGCAACTTCTCGAGTCTCAACTCATTAGCATCAAAGCA-GAGGCTCAAATGATGT-
*
2674996 CATG-AAGATCGAT
128 C-TGAAAGATCGAC
*
2675009 TCGTTAGAA
1 TCATTAGAA
2675018 ACGGAACGGA
Statistics
Matches: 129, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
137 1 0.01
138 67 0.52
139 3 0.02
140 2 0.02
142 1 0.01
144 54 0.42
145 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (140 bp):
TCATTAGAAGCAGAAATCGAAAAGGAAAGGACATTGTCAGAGCAAGTTTCAGCGAACACAAATAG
TAACTCGAAGCAACTTCTCGAGTCTCAACTCATTAGCATCAAAGCAGAGGCTCAAATGATGTCTG
AAAGATCGAC
Found at i:2675712 original size:25 final size:25
Alignment explanation
Indices: 2675678--2675839 Score: 202
Period size: 25 Copynumber: 6.4 Consensus size: 25
2675668 CTATTAAACA
2675678 TAGTGGGATAACCATCAAT-CAATAC
1 TAGTGGGATAACCA-CAATCCAATAC
* *
2675703 TAGTGGGATAACCACTATCTAATAC
1 TAGTGGGATAACCACAATCCAATAC
*
2675728 TAGTGGGATAACCACCATCCAATAC
1 TAGTGGGATAACCACAATCCAATAC
*
2675753 TAGTGGGATAATCA-ATATCCAATAC
1 TAGTGGGATAACCACA-ATCCAATAC
* *
2675778 TTAGTGGAATAACCACTATCCAATAC
1 -TAGTGGGATAACCACAATCCAATAC
* *
2675804 TAGTGGGATAACCACTATTCAATAC
1 TAGTGGGATAACCACAATCCAATAC
*
2675829 TAGTGGAATAA
1 TAGTGGGATAA
2675840 TAAGCATTAT
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
24 3 0.02
25 97 0.80
26 21 0.17
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (25 bp):
TAGTGGGATAACCACAATCCAATAC
Found at i:2675803 original size:76 final size:75
Alignment explanation
Indices: 2675697--2675840 Score: 234
Period size: 76 Copynumber: 1.9 Consensus size: 75
2675687 AACCATCAAT
* * *
2675697 CAATACTAGTGGGATAACCACTATCTAATACTAGTGGGATAACCACCATCCAATACTAGTGGGAT
1 CAATACTAGTGGAATAACCACTATCCAATACTAGTGGGATAACCACCATCCAATACTAGTGGAAT
2675762 AATCAATATC
66 AATCAATATC
* *
2675772 CAATACTTAGTGGAATAACCACTATCCAATACTAGTGGGATAACCACTATTCAATACTAGTGGAA
1 CAATAC-TAGTGGAATAACCACTATCCAATACTAGTGGGATAACCACCATCCAATACTAGTGGAA
2675837 TAAT
65 TAAT
2675841 AAGCATTATC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
75 6 0.10
76 57 0.90
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.26
Consensus pattern (75 bp):
CAATACTAGTGGAATAACCACTATCCAATACTAGTGGGATAACCACCATCCAATACTAGTGGAAT
AATCAATATC
Found at i:2681214 original size:25 final size:25
Alignment explanation
Indices: 2681169--2681328 Score: 214
Period size: 25 Copynumber: 6.4 Consensus size: 25
2681159 ATTAAACATT
*
2681169 GTGGGATAACCA-TCATTCAATACTA
1 GTGGGATAACCACT-ATCCAATACTA
* * *
2681194 GTGGGATAATCATTATCCAATGCTA
1 GTGGGATAACCACTATCCAATACTA
*
2681219 GTGGGATAACCACCATCCAATACTA
1 GTGGGATAACCACTATCCAATACTA
2681244 GTGGGATAACCACTATCCAATACTA
1 GTGGGATAACCACTATCCAATACTA
* *
2681269 GTGGGATAATCAATATCCAATACTTA
1 GTGGGATAACCACTATCCAATAC-TA
*
2681295 GTGGAATAACCACTATCCAATACTA
1 GTGGGATAACCACTATCCAATACTA
*
2681320 GTGGAATAA
1 GTGGGATAA
2681329 TGAGCATTAT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
25 97 0.81
26 23 0.19
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (25 bp):
GTGGGATAACCACTATCCAATACTA
Found at i:2681249 original size:75 final size:76
Alignment explanation
Indices: 2681169--2681328 Score: 243
Period size: 75 Copynumber: 2.1 Consensus size: 76
2681159 ATTAAACATT
* * * *
2681169 GTGGGATAACCA-TCATTCAATACTAGTGGGATAATCATTATCCAATGC-TAGTGGGATAACCAC
1 GTGGGATAACCACT-ATCCAATACTAGTGGGATAATCAATATCCAATACTTAGTGGAATAACCAC
2681232 CATCCAATACTA
65 CATCCAATACTA
*
2681244 GTGGGATAACCACTATCCAATACTAGTGGGATAATCAATATCCAATACTTAGTGGAATAACCACT
1 GTGGGATAACCACTATCCAATACTAGTGGGATAATCAATATCCAATACTTAGTGGAATAACCACC
2681309 ATCCAATACTA
66 ATCCAATACTA
*
2681320 GTGGAATAA
1 GTGGGATAA
2681329 TGAGCATTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
75 43 0.56
76 34 0.44
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (76 bp):
GTGGGATAACCACTATCCAATACTAGTGGGATAATCAATATCCAATACTTAGTGGAATAACCACC
ATCCAATACTA
Found at i:2682363 original size:16 final size:19
Alignment explanation
Indices: 2682328--2682370 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2682318 AATTTAAATT
2682328 TATTTTCAAAGAATAATAA
1 TATTTTCAAAGAATAATAA
* *
2682347 TATTTTCAAAAAATAATTA
1 TATTTTCAAAGAATAATAA
2682366 TATTT
1 TATTT
2682371 AATTAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (19 bp):
TATTTTCAAAGAATAATAA
Found at i:2683291 original size:2 final size:2
Alignment explanation
Indices: 2683284--2683322 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2683274 GTTAGTCCCT
*
2683284 TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2683323 GCTTCTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2683299 original size:10 final size:10
Alignment explanation
Indices: 2683279--2683321 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
2683269 TCTCCGTTAG
2683279 TCCCTTCTCTC
1 TCCC-TCTCTC
2683290 TCCCTCTCTC
1 TCCCTCTCTC
*
2683300 TCTCTCTCTC
1 TCCCTCTCTC
*
2683310 TCTCTCTCTC
1 TCCCTCTCTC
2683320 TC
1 TC
2683322 TGCTTCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 27 0.87
11 4 0.13
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (10 bp):
TCCCTCTCTC
Found at i:2691015 original size:26 final size:27
Alignment explanation
Indices: 2690961--2691015 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
2690951 TTTTTCGGAT
* * **
2690961 AAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAACCGATTTTTAATCCGGTTAAAA
2690988 AAAAACCGATTTTTAATCCGG-TAAAA
1 AAAAACCGATTTTTAATCCGGTTAAAA
2691014 AA
1 AA
2691016 CCGGTTGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (27 bp):
AAAAACCGATTTTTAATCCGGTTAAAA
Found at i:2693744 original size:140 final size:139
Alignment explanation
Indices: 2693492--2693744 Score: 300
Period size: 140 Copynumber: 1.8 Consensus size: 139
2693482 ATTTTATGAA
* * *
2693492 ATTGAAAAAACTTAGAGGCCTTAATTATATAGGTAGAAATTGAGATTGAAAAAAATAGGGGTCTA
1 ATTGAAAAAACTTAGAGGCCTTAATTATAAAGGTAAAAATAGAGATTGAAAAAAATAGGGGTCTA
* *
2693557 AATTATAAAGGTAAAAATTGAGCCTAAAAAACTTAAGAGGCCTCAATTGTACAGGTAGAAATAGC
66 AATTATAAAGGTAAAAAGTGAGACTAAAAAACTT-AGAGGCCTCAATTGTACAGGTAGAAATAGC
2693622 GGAAAGTGAG
130 GGAAAGTGAG
* *
2693632 ATTGAAAAAACTTA-AGGACCTTAATTATAAAGTTAAAAACTAG-GATT-AAAAAATTAGGGG-C
1 ATTGAAAAAACTTAGAGG-CCTTAATTATAAAGGTAAAAA-TAGAGATTGAAAAAAATAGGGGTC
* * * * *
2693693 ATCAATTATAATGGTAGAAAGTGAGATTGAAAAAAACTT-GAGGACTTCAATT
64 -TAAATTATAAAGGTAAAAAGTGAGACT--AAAAAACTTAGAGG-CCTCAATT
2693745 ATTAAGTTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
138 1 0.01
139 40 0.42
140 43 0.45
141 11 0.12
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (139 bp):
ATTGAAAAAACTTAGAGGCCTTAATTATAAAGGTAAAAATAGAGATTGAAAAAAATAGGGGTCTA
AATTATAAAGGTAAAAAGTGAGACTAAAAAACTTAGAGGCCTCAATTGTACAGGTAGAAATAGCG
GAAAGTGAG
Found at i:2693745 original size:87 final size:86
Alignment explanation
Indices: 2693623--2693832 Score: 243
Period size: 87 Copynumber: 2.5 Consensus size: 86
2693613 AGAAATAGCG
* *
2693623 GAAAGTGAGATTGAAAAAACTTAAGGACCTT-AATTATAAAGTTAAAAACT-AGGATTAAAAAAT
1 GAAAGTGAGATTGAAAAAACTTGAGGA-CTTCAATTATAAAGTTAAAAACTGA-GACTAAAAAAT
* *
2693686 TAGGGGCATCAATTATAATGGTA
64 TAGGGACATCAATTATAAAGGTA
* * *
2693709 GAAAGTGAGATTGAAAAAAACTTGAGGACTTCAATTATTAAGTTAAAAAGTGAGACTAAAAACTT
1 GAAAGTGAGATTG-AAAAAACTTGAGGACTTCAATTATAAAGTTAAAAACTGAGACTAAAAAATT
*
2693774 AGGGACCTCAATTATAAAGGTA
65 AGGGACATCAATTATAAAGGTA
* * *
2693796 -AAA-TGGGATTGGAAAAA-TTG-GAGATTTCAATTATAAA
1 GAAAGTGAGATTGAAAAAACTTGAG-GACTTCAATTATAAA
2693833 AATAAAAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
82 1 0.01
83 16 0.15
84 5 0.05
85 7 0.06
86 19 0.18
87 59 0.55
88 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (86 bp):
GAAAGTGAGATTGAAAAAACTTGAGGACTTCAATTATAAAGTTAAAAACTGAGACTAAAAAATTA
GGGACATCAATTATAAAGGTA
Found at i:2693812 original size:42 final size:43
Alignment explanation
Indices: 2693624--2693919 Score: 168
Period size: 42 Copynumber: 6.9 Consensus size: 43
2693614 GAAATAGCGG
* * *
2693624 AAAGTGAGATTGAAAAAACTTAAGGACCTTAATTATAAAGTTAA
1 AAAGTGAGATTG-AAAAACTTAGGGACCTCAATTATAAAGGTAA
* * * * * *
2693668 AAACT-AGGATT-AAAAAATTAGGGGCATCAATTATAATGGTAG
1 AAAGTGA-GATTGAAAAACTTAGGGACCTCAATTATAAAGGTAA
* * *
2693710 AAAGTGAGATTGAAAAAAACTT-GAGGACTTCAATTATTAAGTTAA
1 AAAGTGAGATTG--AAAAACTTAG-GGACCTCAATTATAAAGGTAA
*
2693755 AAAGTGAGACT-AAAAACTTAGGGACCTCAATTATAAAGGT-A
1 AAAGTGAGATTGAAAAACTTAGGGACCTCAATTATAAAGGTAA
* ** **
2693796 AAA-TGGGATTGGAAAAA-TT-GGAGATTTCAATTATAAAAATAAAA
1 AAAGTGAGATT-GAAAAACTTAGG-GACCTCAATTATAAAGGT--AA
* * * **
2693840 AAAGTGTGATTGAATAAAATTA-TGACCTCAATTATAAAAATAA
1 AAAGTGAGATTGAA-AAACTTAGGGACCTCAATTATAAAGGTAA
* *
2693883 AAAATGAGACTT-CAAAA-TTATGGG-CCT-AATTATAAAG
1 AAAGTGAGA-TTGAAAAACTTA-GGGACCTCAATTATAAAG
2693920 ATGAAAAAAT
Statistics
Matches: 196, Mismatches: 36, Indels: 43
0.71 0.13 0.16
Matches are distributed among these distances:
40 7 0.04
41 32 0.16
42 66 0.34
43 14 0.07
44 18 0.09
45 57 0.29
46 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.27
Consensus pattern (43 bp):
AAAGTGAGATTGAAAAACTTAGGGACCTCAATTATAAAGGTAA
Found at i:2696190 original size:24 final size:20
Alignment explanation
Indices: 2696141--2696180 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2696131 TCAGCATTAA
2696141 AAGCAAGTTAAATTTTCTTT
1 AAGCAAGTTAAATTTTCTTT
2696161 AAGCAAGTTAAATTTTCTTT
1 AAGCAAGTTAAATTTTCTTT
2696181 CTCCATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
AAGCAAGTTAAATTTTCTTT
Found at i:2699424 original size:29 final size:30
Alignment explanation
Indices: 2699357--2699429 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
2699347 GATTACCAAA
* * *
2699357 CCCGTCCCCGTTTAGCATACATGTTTTTTC
1 CCCGTCCCCGTTTAGCATAAACGTATTTTC
*
2699387 TCCGTCCCCGTTTAGCATAAACG-ATTTTC
1 CCCGTCCCCGTTTAGCATAAACGTATTTTC
2699416 CCCGTCCCCGTTTA
1 CCCGTCCCCGTTTA
2699430 ATTCGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.15, C:0.36, G:0.14, T:0.36
Consensus pattern (30 bp):
CCCGTCCCCGTTTAGCATAAACGTATTTTC
Found at i:2702758 original size:35 final size:35
Alignment explanation
Indices: 2702719--2702793 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2702709 TTCATGTTAA
*
2702719 AAATTCCAAAACAATTTAATTATATTCTAAACCCT
1 AAATTCCAAAACAATTTAATTATATTATAAACCCT
* * *
2702754 AAATTTCAAAATACTTTAATTATATTATAAACCCT
1 AAATTCCAAAACAATTTAATTATATTATAAACCCT
2702789 AAATT
1 AAATT
2702794 AATGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (35 bp):
AAATTCCAAAACAATTTAATTATATTATAAACCCT
Found at i:2704310 original size:31 final size:31
Alignment explanation
Indices: 2704272--2704396 Score: 162
Period size: 31 Copynumber: 4.0 Consensus size: 31
2704262 CCCGAAGGAC
** * *
2704272 CAGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CAGTCCATATATTCCGAAGAACATAGGTAAA
*
2704303 CAGTCCATATATTCTGAAGAACATAGGTAAA
1 CAGTCCATATATTCCGAAGAACATAGGTAAA
* *
2704334 CATTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATATTCCGAAGAACATAGGTAAA
*
2704365 CAGTCCATAT-GTCTCGAAGAACATAGGTAAA
1 CAGTCCATATATTC-CGAAGAACATAGGTAAA
2704396 C
1 C
2704397 CCTCGACCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 1 0.01
31 81 0.99
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (31 bp):
CAGTCCATATATTCCGAAGAACATAGGTAAA
Found at i:2706732 original size:15 final size:15
Alignment explanation
Indices: 2706712--2706756 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
2706702 ATCATAATTT
2706712 GGATATGTGTTATTC
1 GGATATGTGTTATTC
* *
2706727 GGATATATGTTATTT
1 GGATATGTGTTATTC
*
2706742 GAATATGTGTTATTC
1 GGATATGTGTTATTC
2706757 AGATCGAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.49
Consensus pattern (15 bp):
GGATATGTGTTATTC
Found at i:2711555 original size:18 final size:18
Alignment explanation
Indices: 2711528--2711592 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
2711518 ACCAAATTTT
2711528 GGTATCGATACTCAGTCC
1 GGTATCGATACTCAGTCC
*
2711546 GGTATTGATACTCAGTCC
1 GGTATCGATACTCAGTCC
** * *
2711564 AATATCGATACTCAATCT
1 GGTATCGATACTCAGTCC
*
2711582 AGTATCGATAC
1 GGTATCGATAC
2711593 CCCAACTCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (18 bp):
GGTATCGATACTCAGTCC
Found at i:2714127 original size:30 final size:31
Alignment explanation
Indices: 2714068--2714132 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2714058 GGGAAAGAAG
*
2714068 ATTATTTTTCACCCTTATGCATAAAAAACAA
1 ATTATTTTTCACCCTTAAGCATAAAAAACAA
*
2714099 ATTATTTTTCACCTTTAAGCAT-AAAAACAA
1 ATTATTTTTCACCCTTAAGCATAAAAAACAA
2714129 ATTA
1 ATTA
2714133 ATTCTTAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (31 bp):
ATTATTTTTCACCCTTAAGCATAAAAAACAA
Found at i:2721266 original size:60 final size:60
Alignment explanation
Indices: 2721193--2721315 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
2721183 ATATTGAACA
2721193 ACTAATAAAAACCTTCTATATGACATACATCATCTTCCCTTTTCAAAATAGCTAAAAACC
1 ACTAATAAAAACCTTCTATATGACATACATCATCTTCCCTTTTCAAAATAGCTAAAAACC
*
2721253 ACTAATAAAAACCTTCTATATGACATACATCATCTTCCCTTTTCAAAATGGCTAAAAACC
1 ACTAATAAAAACCTTCTATATGACATACATCATCTTCCCTTTTCAAAATAGCTAAAAACC
2721313 ACT
1 ACT
2721316 TCAAATTCCC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (60 bp):
ACTAATAAAAACCTTCTATATGACATACATCATCTTCCCTTTTCAAAATAGCTAAAAACC
Found at i:2723913 original size:37 final size:37
Alignment explanation
Indices: 2723871--2723947 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
2723861 CTGAATTCAT
*
2723871 TAAACTATCAAATATAAACAAAAAGTAAGGACCTTCG
1 TAAACTATCAAATATAAACAAAAAGAAAGGACCTTCG
* * *
2723908 TAAACTATCAAATGTAAACAAAAAGAAAGGATCTTTG
1 TAAACTATCAAATATAAACAAAAAGAAAGGACCTTCG
2723945 TAA
1 TAA
2723948 CCAAAATCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (37 bp):
TAAACTATCAAATATAAACAAAAAGAAAGGACCTTCG
Found at i:2725319 original size:75 final size:75
Alignment explanation
Indices: 2725196--2725348 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
2725186 GTCAACTGGA
2725196 TTAAAGGTGTTGTCATTTGTGAATACGGTTTTAAATTTAGAGATAATCAATTGATTTAAAGATAA
1 TTAAAGGTGTTGTCATTTGTGAATACGGTTTTAAATTTAGAGATAATCAATTGATTTAAAGATAA
2725261 TTTAATATTT
66 TTTAATATTT
2725271 TTAAAGGTGTTGTCATTTGTGAATACGGTTTTAAATTTAGAGATAATCAATTGATTTAAAGATAA
1 TTAAAGGTGTTGTCATTTGTGAATACGGTTTTAAATTTAGAGATAATCAATTGATTTAAAGATAA
2725336 TTTAATATTT
66 TTTAATATTT
2725346 TTA
1 TTA
2725349 TTATCATTTA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (75 bp):
TTAAAGGTGTTGTCATTTGTGAATACGGTTTTAAATTTAGAGATAATCAATTGATTTAAAGATAA
TTTAATATTT
Found at i:2725982 original size:18 final size:18
Alignment explanation
Indices: 2725948--2725985 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2725938 TTCCTCTCAA
*
2725948 ATTTAAAAATTGCTATAT
1 ATTTAAAAATTGATATAT
2725966 ATTTAAAAA-T-ATATAT
1 ATTTAAAAATTGATATAT
2725982 ATTT
1 ATTT
2725986 TTCTATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 9 0.47
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTAAAAATTGATATAT
Found at i:2726691 original size:22 final size:22
Alignment explanation
Indices: 2726665--2726708 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2726655 TTATAGTTTG
2726665 AGGAATTTGAACCTTAAACCCA
1 AGGAATTTGAACCTTAAACCCA
2726687 AGGAATTTGAACCTTAAACCCA
1 AGGAATTTGAACCTTAAACCCA
2726709 TGAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (22 bp):
AGGAATTTGAACCTTAAACCCA
Found at i:2727385 original size:22 final size:22
Alignment explanation
Indices: 2727358--2727402 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2727348 AGAAAAACCC
*
2727358 AATCAAGAAGAACAATACCCAA
1 AATCAAGAAGAACAACACCCAA
*
2727380 AATCAAGAAGAACGACACCCAA
1 AATCAAGAAGAACAACACCCAA
2727402 A
1 A
2727403 CGAAAATCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.24, G:0.11, T:0.07
Consensus pattern (22 bp):
AATCAAGAAGAACAACACCCAA
Found at i:2731402 original size:80 final size:77
Alignment explanation
Indices: 2731306--2731494 Score: 204
Period size: 76 Copynumber: 2.4 Consensus size: 77
2731296 AGGTTAAACG
* * * *
2731306 AGTT-TTATCATTATGAACTTCTTTTCTTGGGAATGTTGAGCTAACT-ACTTCTGTGATAGAATT
1 AGTTCTTATCATTATGAACTTC--TT-TTGGAAATGCTGAGCCAACTCA-TTCTGTGATAGAATC
* ** *
2731369 GAGCAAGTGTTGAGCA
62 AAGCAAAAGTTGAACA
* *
2731385 AGTTCTTATCATTATGAACTTC-TTTGGAAATGCTGATCCAACTCATTTTGTGATAGAATCAAGC
1 AGTTCTTATCATTATGAACTTCTTTTGGAAATGCTGAGCCAACTCATTCTGTGATAGAATCAAGC
2731449 AAAAGTTGAACA
66 AAAAGTTGAACA
* * *
2731461 AGTTCTTCTCATTATGAACTTCTCTTGGAGATGC
1 AGTTCTTATCATTATGAACTTCTTTTGGAAATGC
2731495 CAATCCAACT
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
76 62 0.66
77 11 0.12
79 4 0.04
80 17 0.18
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (77 bp):
AGTTCTTATCATTATGAACTTCTTTTGGAAATGCTGAGCCAACTCATTCTGTGATAGAATCAAGC
AAAAGTTGAACA
Found at i:2731457 original size:76 final size:77
Alignment explanation
Indices: 2731357--2731505 Score: 210
Period size: 76 Copynumber: 1.9 Consensus size: 77
2731347 TAACTACTTC
** ** * **
2731357 TGTGATAGAATTGAGCAAGTGTTGAGCAAGTTCTTATCATTATGAACTTCT-TTGGAAATGCTGA
1 TGTGATAGAATCAAGCAAAAGTTGAACAAGTTCTTATCATTATGAACTTCTCTTGGAAATGCCAA
2731421 TCCAACTCATTT
66 TCCAACTCATTT
* *
2731433 TGTGATAGAATCAAGCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTCTTGGAGATGCCAA
1 TGTGATAGAATCAAGCAAAAGTTGAACAAGTTCTTATCATTATGAACTTCTCTTGGAAATGCCAA
2731498 TCCAACTC
66 TCCAACTC
2731506 CCTTCTGTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
76 45 0.71
77 18 0.29
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (77 bp):
TGTGATAGAATCAAGCAAAAGTTGAACAAGTTCTTATCATTATGAACTTCTCTTGGAAATGCCAA
TCCAACTCATTT
Found at i:2731733 original size:79 final size:79
Alignment explanation
Indices: 2731593--2731739 Score: 231
Period size: 79 Copynumber: 1.9 Consensus size: 79
2731583 TGGTGATGCT
* * * * *
2731593 GATCCAACTCCTTATGTGATGGAATCGAGCAAAGGTCGAACATGTTCTTCTTATTATGAACTTCT
1 GATCCAACTCCTTATATGATGGAATCAAGCAAAGGTCGAACAAGTTCTTCTAATTAGGAACTTCT
2731658 TCTTTAGAAATGTC
66 TCTTTAGAAATGTC
* *
2731672 GATCCAACTCCTTCTATGATGGAATCAAGCAAAGGTTGAACAAGTTCTTCTAATTAGGAACTTCT
1 GATCCAACTCCTTATATGATGGAATCAAGCAAAGGTCGAACAAGTTCTTCTAATTAGGAACTTCT
2731737 TCT
66 TCT
2731740 CCTTCATCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (79 bp):
GATCCAACTCCTTATATGATGGAATCAAGCAAAGGTCGAACAAGTTCTTCTAATTAGGAACTTCT
TCTTTAGAAATGTC
Found at i:2732085 original size:17 final size:17
Alignment explanation
Indices: 2732063--2732106 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2732053 AATCTTTACT
*
2732063 TCTTTATCTTTGCTGAG
1 TCTTTATCTTTGCTGAA
*
2732080 TCTTTATCTTTGTTGAA
1 TCTTTATCTTTGCTGAA
*
2732097 TCTTCATCTT
1 TCTTTATCTT
2732107 GACAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (17 bp):
TCTTTATCTTTGCTGAA
Found at i:2733312 original size:23 final size:24
Alignment explanation
Indices: 2733228--2733329 Score: 120
Period size: 24 Copynumber: 4.3 Consensus size: 24
2733218 CACCACTGCT
*
2733228 CATATAATTTG-CACCGAAGTG-CCA
1 CATAGAATTTGTC-CCGAA-TGACCA
* * *
2733252 CATAGAATTTGTACCGAAGGACCG
1 CATAGAATTTGTCCCGAATGACCA
*
2733276 CGTAGAATTTGTCCCGAATGACCA
1 CATAGAATTTGTCCCGAATGACCA
2733300 CATAG-ATTTGTCCCGAATGACCA
1 CATAGAATTTGTCCCGAATGACCA
2733323 CATAGAA
1 CATAGAA
2733330 CCCTCGACTC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
23 24 0.36
24 42 0.64
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (24 bp):
CATAGAATTTGTCCCGAATGACCA
Found at i:2733956 original size:18 final size:18
Alignment explanation
Indices: 2733930--2733976 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2733920 TTCTTCTATG
*
2733930 GTATTGATACCCACTTCA
1 GTATCGATACCCACTTCA
*
2733948 GTATCGATACCGACTTCA
1 GTATCGATACCCACTTCA
2733966 GTATCGATACC
1 GTATCGATACC
2733977 ATTTTATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (18 bp):
GTATCGATACCCACTTCA
Found at i:2739952 original size:23 final size:24
Alignment explanation
Indices: 2739844--2739992 Score: 171
Period size: 24 Copynumber: 6.3 Consensus size: 24
2739834 CACCACTGCT
*
2739844 CATATAATTTG-CACCGAAGTG-CCA
1 CATAGAATTTGTC-CCGAAG-GACCA
*
2739868 CATAGAATTTGTCCCGAAGGACCG
1 CATAGAATTTGTCCCGAAGGACCA
* **
2739892 CGTAGAATTTGTCCCGAAGGACTG
1 CATAGAATTTGTCCCGAAGGACCA
* *
2739916 CGTAGAATTTGTCTCGAAGGACCA
1 CATAGAATTTGTCCCGAAGGACCA
*
2739940 CATAG-ATTTGTCTCGAAGGACCA
1 CATAGAATTTGTCCCGAAGGACCA
2739963 CATAG-ATTTGTCCCGAAGGACCA
1 CATAGAATTTGTCCCGAAGGACCA
*
2739986 CGTAGAA
1 CATAGAA
2739993 CTCATAACTC
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
23 45 0.40
24 66 0.59
25 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
CATAGAATTTGTCCCGAAGGACCA
Found at i:2740571 original size:20 final size:20
Alignment explanation
Indices: 2740542--2740597 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
2740532 TCAGACTGAG
*
2740542 TAGTATCGATACCCCTCCTA
1 TAGTACCGATACCCCTCCTA
* *
2740562 TAGTACCGATACTTCTCTTCTA
1 TAGTACCGATAC--CCCTCCTA
*
2740584 TGGTACCGATACCC
1 TAGTACCGATACCC
2740598 ACTTCAGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.41
22 17 0.59
ACGTcount: A:0.23, C:0.32, G:0.12, T:0.32
Consensus pattern (20 bp):
TAGTACCGATACCCCTCCTA
Found at i:2744762 original size:13 final size:13
Alignment explanation
Indices: 2744744--2744768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2744734 AGGATATGAA
2744744 TGCAAATGCAAAG
1 TGCAAATGCAAAG
2744757 TGCAAATGCAAA
1 TGCAAATGCAAA
2744769 ATGGTGTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (13 bp):
TGCAAATGCAAAG
Found at i:2745408 original size:132 final size:132
Alignment explanation
Indices: 2745171--2745431 Score: 441
Period size: 132 Copynumber: 2.0 Consensus size: 132
2745161 TTTTCACTTA
* *
2745171 GATATTCATATATGAATCAACATATTTGTATCATGTGATGATAATATGATGCAAAAAGGAAAAAA
1 GATATTCATATATGAATCAACACATTTATATCATGTGATGATAATATGATGCAAAAAGGAAAAAA
* *
2745236 TGACATAAGAACAAGAAATAAGTTAGTACAAATAAGATAATAAAAAAGATAAAAGGACAATTCAT
66 TGACATAAGAACAAGAAATAAGTTAGTACAAATAAGATAATAAAAAAAATAAAACGACAATTCAT
2745301 GT
131 GT
* * *
2745303 GATATTCATATATGAATCAACACATTTATATCATGTGATGATGATATTATGCAAAAAGGCAAAAA
1 GATATTCATATATGAATCAACACATTTATATCATGTGATGATAATATGATGCAAAAAGGAAAAAA
* *
2745368 TGGCATAAGAACAAGAAATAAGTTAGTACAAATACGATAATAAAAAAAATAAAACGACAATTCA
66 TGACATAAGAACAAGAAATAAGTTAGTACAAATAAGATAATAAAAAAAATAAAACGACAATTCA
2745432 AAGATGAATA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.25
Consensus pattern (132 bp):
GATATTCATATATGAATCAACACATTTATATCATGTGATGATAATATGATGCAAAAAGGAAAAAA
TGACATAAGAACAAGAAATAAGTTAGTACAAATAAGATAATAAAAAAAATAAAACGACAATTCAT
GT
Found at i:2750053 original size:20 final size:20
Alignment explanation
Indices: 2750028--2750067 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2750018 GATTGGATTA
2750028 AATTAATGCT-AGGATTAATT
1 AATTAAT-CTAAGGATTAATT
2750048 AATTAATCTAAGGATTAATT
1 AATTAATCTAAGGATTAATT
2750068 TGATTATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
AATTAATCTAAGGATTAATT
Found at i:2751511 original size:74 final size:76
Alignment explanation
Indices: 2751386--2751591 Score: 267
Period size: 74 Copynumber: 2.8 Consensus size: 76
2751376 CCGTTGTACA
* * * *
2751386 AGGGGGAATCGGTACC-CTT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 AGGGGGGATCGGTTCCTCTTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
**
2751448 CAAAACTGTTT
66 CAAAACCATTT
* *
2751459 AGGGGGGATCGGTTCCTCTTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 AGGGGGGATCGGTTCCTCTTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
2751523 CAAAACCATTT
66 CAAAACCATTT
* * * *
2751534 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGAAATT
1 AGGGGGG-ATCGGTTCCTCTTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
2751592 TTTTGGCTTT
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
73 14 0.12
74 40 0.35
75 17 0.15
76 14 0.12
77 30 0.26
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.25
Consensus pattern (76 bp):
AGGGGGGATCGGTTCCTCTTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
CAAAACCATTT
Found at i:2752201 original size:16 final size:15
Alignment explanation
Indices: 2752170--2752210 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
2752160 ACAATTCATA
*
2752170 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
2752185 AATCCACAAATCAAAC
1 AATCCA-AAATCAAAC
2752201 AATCCAAAAT
1 AATCCAAAAT
2752211 ATCCAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:2759931 original size:74 final size:76
Alignment explanation
Indices: 2759846--2760043 Score: 258
Period size: 74 Copynumber: 2.6 Consensus size: 76
2759836 CCGTTGTACA
* * *
2759846 AGGGGGAATCGGTACCTCCT-TGGGGGGGATCGGTTCCCTCCGAGTATACTGGAATTCTCGGAG-
1 AGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
**
2759909 CAAAACTGTTT
66 CAAAACCATTT
* * ** *
2759920 AGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGATTCCCTCCGAGCATTTTGGAAATCTCGGGGC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
2759984 CAAAACCATTT
66 CAAAACCATTT
*
2759995 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 A-GGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCA
2760044 ATCTGAAATT
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
74 53 0.50
75 11 0.10
76 21 0.20
77 5 0.05
78 16 0.15
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (76 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
CAAAACCATTT
Found at i:2762149 original size:14 final size:14
Alignment explanation
Indices: 2762130--2762169 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2762120 AAATTTATTA
*
2762130 AAAGAATATAAAAT
1 AAAGAATAAAAAAT
2762144 AAAGAATAAAAAAT
1 AAAGAATAAAAAAT
2762158 AAAGAATGAAAA
1 AAAGAAT-AAAA
2762170 TTGAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (14 bp):
AAAGAATAAAAAAT
Found at i:2769581 original size:23 final size:24
Alignment explanation
Indices: 2769550--2769608 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
2769540 AAAACCTAAT
* *
2769550 TGTTATTGGGTGTCAAG-TGGGCC
1 TGTTGTTGGGTGTCAAGTTGGGCA
*
2769573 TGTTGTTGGTTGTCAAGTTGGGCA
1 TGTTGTTGGGTGTCAAGTTGGGCA
2769597 TGTTGTTTGGGT
1 TGTTG-TTGGGT
2769609 TGTTGGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 15 0.50
24 10 0.33
25 5 0.17
ACGTcount: A:0.10, C:0.08, G:0.39, T:0.42
Consensus pattern (24 bp):
TGTTGTTGGGTGTCAAGTTGGGCA
Found at i:2769908 original size:20 final size:21
Alignment explanation
Indices: 2769883--2769934 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2769873 TTTTCCCAAT
*
2769883 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2769903 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2769924 TCGCAATGCGA
1 TCGCAATGCGA
2769935 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2769948 original size:20 final size:20
Alignment explanation
Indices: 2769923--2770034 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
2769913 AATTGGGAAA
2769923 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2769943 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2769963 ATCGCAATGCGATAAT-ACAA
1 ATCGCAATGCGATACTGAC-T
* *
2769983 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2770003 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
2770023 TTCGCAA-GCGAT
1 ATCGCAATGCGAT
2770035 TTACATAGCG
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.09
20 71 0.89
21 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2770001 original size:60 final size:59
Alignment explanation
Indices: 2769921--2770034 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
2769911 CGAATTGGGA
* * * *
2769921 AAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAA-GCGATAATAC
* * *
2769981 AAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAAGCGAT
1 AAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAAGCGAT
2770035 TTACATAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 5 0.11
60 42 0.89
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (59 bp):
AAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAAGCGATAATAC
Found at i:2770571 original size:19 final size:19
Alignment explanation
Indices: 2770534--2770599 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
2770524 TTCGAGAATG
2770534 AAATCGCAACGCGGAAATAA
1 AAATCGCAACGC-GAAATAA
**
2770554 CTATCGCAACGCGAAATAA
1 AAATCGCAACGCGAAATAA
**
2770573 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAATAA
2770592 AAATCGCA
1 AAATCGCA
2770600 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
AAATCGCAACGCGAAATAA
Found at i:2770643 original size:19 final size:19
Alignment explanation
Indices: 2770595--2770759 Score: 120
Period size: 19 Copynumber: 9.1 Consensus size: 19
2770585 GAAACCAAAA
*
2770595 TCGCATTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
2770615 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2770635 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2770654 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2770668 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2770687 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
2770701 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2770718 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2770738 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2770758 TC
1 TC
2770760 AACCAAAACA
Statistics
Matches: 116, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
12 8 0.07
14 12 0.10
16 2 0.02
17 6 0.05
19 40 0.34
20 32 0.28
21 16 0.14
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2770686 original size:33 final size:33
Alignment explanation
Indices: 2770638--2770734 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2770628 TTTCATTTCG
** *
2770638 CGTTGCGATTTTCATTTCGTGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
2770671 CGTTGCGATAGTCATTTCGCGTTGCGA-T-TCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
2770702 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
2770735 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
31 20 0.34
32 11 0.19
33 25 0.43
34 2 0.03
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:2770736 original size:20 final size:20
Alignment explanation
Indices: 2770702--2770759 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2770692 TTGCGATTCT
**
2770702 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
2770722 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
2770742 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
2770760 AACCAAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:2772541 original size:90 final size:87
Alignment explanation
Indices: 2772386--2772556 Score: 256
Period size: 90 Copynumber: 1.9 Consensus size: 87
2772376 TAGATTGCTT
2772386 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATAACACTGTGAAGTTAGTATTTG
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATAACACTGTGAAGTTAGTATTTG
2772451 TCTTTTGTTTTGTCTTTTGGTGA
66 TC-TTTGTTTTGTCTTTTGGTGA
* * *
2772474 AGTAAA-TTATTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTTTACACTGTGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATAACACTGTGAAGTTAGTA
2772537 TTTGTCTTTGTTTTGTCTTT
62 TTTGTCTTTGTTTTGTCTTT
2772557 GGTAGAAAGT
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
86 19 0.25
87 8 0.11
88 9 0.12
89 16 0.21
90 24 0.32
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (87 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATAACACTGTGAAGTTAGTATTTG
TCTTTGTTTTGTCTTTTGGTGA
Found at i:2772855 original size:41 final size:40
Alignment explanation
Indices: 2772808--2772928 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 40
2772798 CTATCGTTGA
2772808 AGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AGAGGCCCCTATCATTCCTCGAGAGT-CCCTCCCACCGTTC
* * * * * * * * *
2772849 AGAGGCCACTGTCATCCCTCAAGAGTCCATCCTATCATTGA
1 AGAGGCCCCTATCATTCCTCGAGAGTCCCTCCCACCGTT-C
2772890 AGAGG-CCCTATCATTCCTCGAGAG-CCCTCCCACCGTTC
1 AGAGGCCCCTATCATTCCTCGAGAGTCCCTCCCACCGTTC
2772928 A
1 A
2772929 AGAGACCACT
Statistics
Matches: 61, Mismatches: 18, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
38 1 0.02
39 9 0.15
40 24 0.39
41 27 0.44
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.22
Consensus pattern (40 bp):
AGAGGCCCCTATCATTCCTCGAGAGTCCCTCCCACCGTTC
Found at i:2772932 original size:19 final size:20
Alignment explanation
Indices: 2772909--2772974 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
2772899 ATCATTCCTC
2772909 GAGAGCCCTCCCACCGTTCAA
1 GAGA-CCCTCCCACCGTTCAA
** * *
2772930 GAGACCACTGTCATCGTTGAA
1 GAGACC-CTCCCACCGTTCAA
* *
2772951 GAGGTCCCTCCCACCATTCAA
1 GA-GACCCTCCCACCGTTCAA
2772972 GAG
1 GAG
2772975 CCGATTCACA
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.18
Consensus pattern (20 bp):
GAGACCCTCCCACCGTTCAA
Found at i:2772974 original size:81 final size:81
Alignment explanation
Indices: 2772774--2772974 Score: 244
Period size: 81 Copynumber: 2.5 Consensus size: 81
2772764 CCCGACTCGC
* * * *
2772774 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCA-TCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAG-CCCCT
*
2772839 CCCACCGTTCAGAGGCCA
64 CCCACCGTTCAGAGACCA
* * *
2772857 CTGTCATCCCTCAAGAGTCCATCCTATCATTGAAGAGG-CCCTATCATTCCTCGAGAG-CCCTCC
1 CTGTCATCCCTCAAGAGTCCATCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGCCCCTCC
2772920 CACCGTTCAAGAGACCA
66 CACCGTTC-AGAGACCA
** * *
2772937 CTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCATCCCACCATTCAAGAG
2772975 CCGATTCACA
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
79 14 0.13
80 20 0.19
81 36 0.34
82 16 0.15
83 21 0.20
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (81 bp):
CTGTCATCCCTCAAGAGTCCATCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGCCCCTCC
CACCGTTCAGAGACCA
Found at i:2774311 original size:14 final size:14
Alignment explanation
Indices: 2774292--2774323 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2774282 TGTTTAATGA
2774292 TTGTAAAAGGTGAT
1 TTGTAAAAGGTGAT
*
2774306 TTGTAAAAGTTGAT
1 TTGTAAAAGGTGAT
2774320 TTGT
1 TTGT
2774324 TTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGGTGAT
Found at i:2774550 original size:32 final size:33
Alignment explanation
Indices: 2774463--2774591 Score: 169
Period size: 32 Copynumber: 4.0 Consensus size: 33
2774453 ACGCGAAATT
2774463 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
2774496 --ATTC-CCTCGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
2774526 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
2774558 -ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTGCG
2774591 A
1 A
2774592 TAGTAATTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
30 24 0.29
31 6 0.07
32 29 0.35
33 23 0.28
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (33 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:2774561 original size:62 final size:66
Alignment explanation
Indices: 2774463--2774591 Score: 212
Period size: 65 Copynumber: 2.0 Consensus size: 66
2774453 ACGCGAAATT
*
2774463 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTC-C-C-TCGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTCGCGATTTTCATTTCGCATTGC
2774525 G
66 G
*
2774526 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTCGCGATTTTCATTTCGCATTGC
2774590 G
66 G
2774591 A
1 A
2774592 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
62 21 0.34
63 15 0.25
64 1 0.02
65 24 0.39
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTCGCGATTTTCATTTCGCATTGC
G
Found at i:2776873 original size:12 final size:12
Alignment explanation
Indices: 2776856--2776880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2776846 TCTTCGGGGA
2776856 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2776868 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2776880 C
1 C
2776881 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2777089 original size:24 final size:24
Alignment explanation
Indices: 2777055--2777108 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2777045 CTGAAACATC
*
2777055 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2777079 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2777103 ATCAAA
1 ATCAAA
2777109 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2777901 original size:20 final size:21
Alignment explanation
Indices: 2777876--2777927 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2777866 TTTTCCTAAT
*
2777876 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2777896 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2777917 TCGCAATGCGA
1 TCGCAATGCGA
2777928 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2778000 original size:20 final size:20
Alignment explanation
Indices: 2777954--2778003 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2777944 GAGATAATAC
*
2777954 AAATCGCAACGAGATTCTGA
1 AAATCGCAATGAGATTCTGA
***
2777974 CTTTCGCAATGAGATTCTGA
1 AAATCGCAATGAGATTCTGA
2777994 AAATCGCAAT
1 AAATCGCAAT
2778004 CATCTTCAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (20 bp):
AAATCGCAATGAGATTCTGA
Found at i:2778308 original size:20 final size:20
Alignment explanation
Indices: 2778213--2778300 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
2778203 CAACGGGGAA
2778213 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2778233 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
2778253 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
2778273 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2778293 ATCGCAAC
1 ATCGCAAC
2778301 TAGAAAATCG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 5 0.09
20 46 0.82
21 5 0.09
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:2778350 original size:14 final size:14
Alignment explanation
Indices: 2778331--2778384 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
2778321 TGAAATCGCA
2778331 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
2778345 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
2778362 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
2778378 TTGCGAT
1 TTGCGAT
2778385 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:2778530 original size:14 final size:14
Alignment explanation
Indices: 2778511--2778547 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2778501 CATCAATTAA
2778511 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2778525 ACAAATCATCTTTT
1 ACAAATCAACATTT
2778539 ACAAATCAA
1 ACAAATCAA
2778548 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2780416 original size:19 final size:19
Alignment explanation
Indices: 2780362--2780417 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2780352 CAAACTTAAA
2780362 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* * *
2780382 ATCACAACGCGGAATGGCT
1 ATCGCAACGCGAAATGACT
*
2780401 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
2780418 AAATCGTAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2780469 original size:14 final size:14
Alignment explanation
Indices: 2780417--2780539 Score: 93
Period size: 14 Copynumber: 7.9 Consensus size: 14
2780407 ATGCGAAATG
*
2780417 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
2780431 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2780450 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2780464 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2780480 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
2780496 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2780512 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2780528 AAAATCGCAACG
1 AAAATCGCAACG
2780540 CGAAACACAA
Statistics
Matches: 89, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
14 39 0.44
15 1 0.01
16 18 0.20
17 2 0.02
18 19 0.21
19 10 0.11
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2780492 original size:32 final size:33
Alignment explanation
Indices: 2780401--2780544 Score: 256
Period size: 32 Copynumber: 4.4 Consensus size: 33
2780391 CGGAATGGCT
*
2780401 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2780434 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2780467 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2780499 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2780531 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2780545 CACAAATCGC
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 61 0.56
33 48 0.44
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2780552 original size:65 final size:64
Alignment explanation
Indices: 2780401--2780555 Score: 231
Period size: 65 Copynumber: 2.4 Consensus size: 64
2780391 CGGAATGGCT
*
2780401 ATCGCAATGCGAAATGAAAATCGTAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAA--AAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
2780466 A
64 A
*
2780467 ATCGCAATGCGAAATGAAATCGCAACGACAAAATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAA-AAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2780531 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAA-A-AAATCGCA
2780556 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
64 29 0.35
65 39 0.48
66 14 0.17
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (64 bp):
ATCGCAATGCGAAAAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2780592 original size:14 final size:14
Alignment explanation
Indices: 2780573--2780630 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2780563 TTTCATTTAG
2780573 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2780587 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
2780603 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
2780619 CGTTGCGATTTT
1 CGTTGCGATTTT
2780631 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2780637 original size:33 final size:33
Alignment explanation
Indices: 2780556--2780643 Score: 142
Period size: 32 Copynumber: 2.7 Consensus size: 33
2780546 ACAAATCGCA
* * *
2780556 TTGCGATTTTCATTTAGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCAATTTTGTCG
2780589 TTGCGA-TTTCATTTCGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCAATTTTGTCG
2780621 TTGCGATTTTCATTTCGCATTGC
1 TTGCGATTTTCATTTCGCATTGC
2780644 GATAGCCATT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCAATTTTGTCG
Found at i:2780653 original size:19 final size:20
Alignment explanation
Indices: 2780631--2780674 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2780621 TTGCGATTTT
2780631 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
2780650 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
2780670 CATTT
1 CATTT
2780675 TCGTGTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:2782490 original size:20 final size:20
Alignment explanation
Indices: 2782465--2782505 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2782455 ATAGTTTCTG
2782465 AAATGAAAATCGCAACACGA
1 AAATGAAAATCGCAACACGA
**
2782485 AAATGACTATCGCAACACGA
1 AAATGAAAATCGCAACACGA
2782505 A
1 A
2782506 TTTGACTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (20 bp):
AAATGAAAATCGCAACACGA
Found at i:2782511 original size:20 final size:20
Alignment explanation
Indices: 2782473--2782520 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2782463 TGAAATGAAA
2782473 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
**
2782493 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
2782513 ATCGCAAC
1 ATCGCAAC
2782521 GATAGAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2783035 original size:39 final size:40
Alignment explanation
Indices: 2782980--2783055 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
2782970 GAAAATCGCA
*
2782980 TTGCGATTATGTATTATCGCTTTG-GAAAGTCAGTATCTCG
1 TTGCGATTATGTATTATCGCATTGCGAAAGTCA-TATCTCG
*
2783020 TTGCGATT-TGTATTATCGCATTGCGATAGTCATATC
1 TTGCGATTATGTATTATCGCATTGCGAAAGTCATATC
2783056 GCATGCGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 18 0.55
40 15 0.45
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (40 bp):
TTGCGATTATGTATTATCGCATTGCGAAAGTCATATCTCG
Found at i:2783043 original size:20 final size:20
Alignment explanation
Indices: 2782974--2783046 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
2782964 CGCTTTGAAA
2782974 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATT-TGTATT
* ** *
2782995 ATCGCTTTG-GA-AAGTCAGT
1 ATCGCATTGCGATTTGT-ATT
* *
2783014 ATCTCGTTGCGATTTGTATT
1 ATCGCATTGCGATTTGTATT
2783034 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2783047 AGTCATATCG
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
18 2 0.05
19 9 0.24
20 17 0.45
21 10 0.26
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
ATCGCATTGCGATTTGTATT
Found at i:2783169 original size:21 final size:21
Alignment explanation
Indices: 2783129--2783169 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2783119 CACTGTAGAC
** *
2783129 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
2783150 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
2783170 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:2784265 original size:59 final size:60
Alignment explanation
Indices: 2784131--2784281 Score: 241
Period size: 59 Copynumber: 2.5 Consensus size: 60
2784121 TATAATTTTA
2784131 TAATATTTATAAATATTAAAGATGTAACAAATCTTAATTATATATATATATTTATTTGGG
1 TAATATTTATAAATATTAAAGATGTAACAAATCTTAATTATATATATATATTTATTTGGG
* * *
2784191 TAATATTTATAAATATTAAAGATGTAACACATTTTAATTAT-TATATATTTTTATTTGGG
1 TAATATTTATAAATATTAAAGATGTAACAAATCTTAATTATATATATATATTTATTTGGG
* * *
2784250 TAATATTTGTAAATATTAAAAATGTAAAAAAT
1 TAATATTTATAAATATTAAAGATGTAACAAAT
2784282 AATATTTATT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 45 0.54
60 39 0.46
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (60 bp):
TAATATTTATAAATATTAAAGATGTAACAAATCTTAATTATATATATATATTTATTTGGG
Found at i:2795646 original size:62 final size:60
Alignment explanation
Indices: 2795558--2795681 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 60
2795548 CCATCAACAG
*
2795558 TTTGGTTTTTTTTTAAGATTAGTGATTGAAACGGAATAAATACATAACATTAAATATAAT
1 TTTGGTTTTTTTTAAAGATTAGTGATTGAAACGGAATAAATACATAACATTAAATATAAT
* * * *
2795618 TTTGGTTTATTTTTAAAATATTAGTGATTGAAACGGAATCAATACGTAATATTAAATATAAT
1 TTTGGTTT-TTTTT-AAAGATTAGTGATTGAAACGGAATAAATACATAACATTAAATATAAT
2795680 TT
1 TT
2795682 AAAAAATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 8 0.14
61 5 0.09
62 44 0.77
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.43
Consensus pattern (60 bp):
TTTGGTTTTTTTTAAAGATTAGTGATTGAAACGGAATAAATACATAACATTAAATATAAT
Found at i:2798196 original size:14 final size:14
Alignment explanation
Indices: 2798167--2798210 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2798157 TACATTTCTG
* *
2798167 TTTATATGCAGAGA
1 TTTATTTGCAGGGA
2798181 TTT-TTTCGCAGGGA
1 TTTATTT-GCAGGGA
2798195 TTTATTTGCAGGGA
1 TTTATTTGCAGGGA
2798209 TT
1 TT
2798211 ACTTCCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 21 0.81
15 3 0.12
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (14 bp):
TTTATTTGCAGGGA
Found at i:2812368 original size:18 final size:18
Alignment explanation
Indices: 2812345--2812380 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2812335 TTTGTTAACC
2812345 AAAATTTCTAGATTTGTT
1 AAAATTTCTAGATTTGTT
2812363 AAAATTTCTAGATTTGTT
1 AAAATTTCTAGATTTGTT
2812381 CTTTCATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
AAAATTTCTAGATTTGTT
Found at i:2812583 original size:37 final size:37
Alignment explanation
Indices: 2812533--2812609 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
2812523 TCCTTAGTTT
2812533 TAGTAAGTTTGCTGCAAAGGAATTACTTACTTCTTTC
1 TAGTAAGTTTGCTGCAAAGGAATTACTTACTTCTTTC
2812570 TAGTAAGTTTGCTGCAAAGGAATTACTTACTTCTTTC
1 TAGTAAGTTTGCTGCAAAGGAATTACTTACTTCTTTC
2812607 TAG
1 TAG
2812610 ATCTATTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (37 bp):
TAGTAAGTTTGCTGCAAAGGAATTACTTACTTCTTTC
Found at i:2812971 original size:2 final size:2
Alignment explanation
Indices: 2812953--2813038 Score: 144
Period size: 2 Copynumber: 45.0 Consensus size: 2
2812943 ATTAATGAAA
2812953 AT AT AT A- AT AT -T A- AT AT AT AT -T 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
2812991 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
2813033 AT AT AT
1 AT AT AT
2813039 TAAGCTCATG
Statistics
Matches: 80, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
1 4 0.05
2 76 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2813859 original size:6 final size:7
Alignment explanation
Indices: 2813842--2813870 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2813832 CTATGAATAT
2813842 TTTTTTC
1 TTTTTTC
2813849 TTTTTTC
1 TTTTTTC
2813856 TTTTTTC
1 TTTTTTC
2813863 TTTTTTC
1 TTTTTTC
2813870 T
1 T
2813871 GTTAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:2815154 original size:2 final size:2
Alignment explanation
Indices: 2815147--2815176 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2815137 CCGTAAATTA
2815147 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
2815177 CAACAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2819394 original size:20 final size:20
Alignment explanation
Indices: 2819350--2819817 Score: 534
Period size: 20 Copynumber: 23.2 Consensus size: 20
2819340 AATGACCAAC
*
2819350 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
2819369 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
2819389 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
2819409 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
2819429 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
2819450 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
2819471 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
2819492 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
2819513 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
2819535 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2819553 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819573 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
2819593 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
2819613 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819633 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2819655 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819673 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2819695 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2819715 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819733 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
2819755 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819773 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819793 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
2819813 AAAAT
1 AAAAT
2819818 GAGTAAATTC
Statistics
Matches: 396, Mismatches: 26, Indels: 53
0.83 0.05 0.11
Matches are distributed among these distances:
18 12 0.03
19 15 0.04
20 315 0.80
21 14 0.04
22 40 0.10
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:2819921 original size:6 final size:6
Alignment explanation
Indices: 2819910--2819975 Score: 132
Period size: 6 Copynumber: 11.0 Consensus size: 6
2819900 GAAGACACGT
2819910 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
2819958 ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC
2819976 CGAGACGAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:2820484 original size:6 final size:6
Alignment explanation
Indices: 2820473--2820571 Score: 198
Period size: 6 Copynumber: 16.5 Consensus size: 6
2820463 TCTCGTCTCG
2820473 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2820521 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2820569 GGT
1 GGT
2820572 AATAGTGTCT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2820721 original size:40 final size:40
Alignment explanation
Indices: 2820666--2820876 Score: 325
Period size: 40 Copynumber: 5.2 Consensus size: 40
2820656 GAATTTACTC
2820666 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
2820706 ATTTTCTTAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
2820746 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
2820786 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * *
2820828 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
2820870 ATTTTCT
1 ATTTTCT
2820877 TTTGACCGTT
Statistics
Matches: 158, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
39 2 0.01
40 98 0.62
41 3 0.02
42 55 0.35
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:2820926 original size:20 final size:20
Alignment explanation
Indices: 2820666--2820953 Score: 272
Period size: 20 Copynumber: 14.2 Consensus size: 20
2820656 GAATTTACTC
2820666 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2820686 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
2820706 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
2820726 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
2820746 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2820766 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
2820786 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2820806 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
2820828 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2820848 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
2820870 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
2820890 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
2820910 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
2820930 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
2820949 ATTTT
1 ATTTT
2820954 GTTGGTCATT
Statistics
Matches: 226, Mismatches: 21, Indels: 43
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 20 0.09
20 158 0.70
21 16 0.07
22 28 0.12
25 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:2821221 original size:60 final size:60
Alignment explanation
Indices: 2821149--2821263 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
2821139 AAATAATCTA
* ** *
2821149 TCGATTATAGGGTGTTGTTTTATTAAGT-TCTCCGACTATTAAAAGTTATAAAATGATTTT
1 TCGATTATAGGGTATCATTTTATTAAGTCCCT-CGACTATTAAAAGTTATAAAATGATTTT
* * *
2821209 TCGATTGA-AGGGTATCATTTTGTTGAGTCCCTCGACTATTAAAATTTATAAAATG
1 TCGATT-ATAGGGTATCATTTTATTAAGTCCCTCGACTATTAAAAGTTATAAAATG
2821264 GTCACCGAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (60 bp):
TCGATTATAGGGTATCATTTTATTAAGTCCCTCGACTATTAAAAGTTATAAAATGATTTT
Found at i:2831487 original size:18 final size:21
Alignment explanation
Indices: 2831466--2831504 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2831456 GTGTAAGGTA
2831466 ATTT-TTTTA-ATAT-ATTAT
1 ATTTATTTTATATATGATTAT
2831484 ATTTATTTTATATATGATTAT
1 ATTTATTTTATATATGATTAT
2831505 TTGAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTATTTTATATATGATTAT
Found at i:2835011 original size:46 final size:46
Alignment explanation
Indices: 2834968--2835276 Score: 429
Period size: 46 Copynumber: 6.7 Consensus size: 46
2834958 TTATTCATTA
* * * * * * *
2834968 ATTTCAGTTTTGGCCTCTTTTCATGCCTTAATACACCCGTTCATAC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
* * * *
2835014 ATTTTAGTTATGACATCCTTTCATGCATTAATGCATTCATTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
*
2835060 ATTTTAGTTATGGCATCATTTCATGCCTTAATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
* * *
2835106 ATTTTAGTTATGGCATCATTTCTTGCCTTAATGCATTCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
* * *
2835152 ATTTTAGTTATGGCATCCTTTCATTCCTTAATGCATCCATTCATCC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
*
2835198 ATTTTAGTTATGTCATCCTTTCATGCCTTAATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
* *
2835244 ATTTTAGGTATGTCATCCTTTCATGCCTTAATG
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATG
2835277 ATAACATAGT
Statistics
Matches: 234, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 234 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
Found at i:2835102 original size:20 final size:20
Alignment explanation
Indices: 2835079--2835243 Score: 62
Period size: 20 Copynumber: 7.3 Consensus size: 20
2835069 ATGGCATCAT
2835079 TTCATGCCTTAATGCATCCG
1 TTCATGCCTTAATGCATCCG
* **
2835099 TTCATGCATTTTAGTTATGGCATCAT
1 TTCATGC--CTTA---AT-GCATCCG
* *
2835125 TTCTTGCCTTAATGCATTCG
1 TTCATGCCTTAATGCATCCG
* *
2835145 TTCATGCATTTTAGTTATGGCATCCT
1 TTCATGC--CTTA---AT-GCATCCG
* *
2835171 TTCATTCCTTAATGCATCCA
1 TTCATGCCTTAATGCATCCG
*
2835191 TTCAT-CCATTTTAGTTATGTCATCCT
1 TTCATGCC---TTA---ATG-CATCCG
2835217 TTCATGCCTTAATGCATCCG
1 TTCATGCCTTAATGCATCCG
2835237 TTCATGC
1 TTCATGC
2835244 ATTTTAGGTA
Statistics
Matches: 108, Mismatches: 17, Indels: 40
0.65 0.10 0.24
Matches are distributed among these distances:
19 2 0.02
20 40 0.37
21 7 0.06
22 9 0.08
24 9 0.08
25 7 0.06
26 32 0.30
27 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (20 bp):
TTCATGCCTTAATGCATCCG
Found at i:2835260 original size:26 final size:25
Alignment explanation
Indices: 2835007--2835269 Score: 108
Period size: 26 Copynumber: 11.3 Consensus size: 25
2834997 AATACACCCG
* *
2835007 TTCATACATTTTAGTTATGACATCCT
1 TTCATGCATTTTAG-TATGTCATCCT
* *
2835033 TTCATGCA--TTA--ATG-CATTCA
1 TTCATGCATTTTAGTATGTCATCCT
* *
2835053 TTCATGCATTTTAGTTATGGCATCAT
1 TTCATGCATTTTAG-TATGTCATCCT
* *
2835079 TTCATGC--CTTA--ATG-CATCCG
1 TTCATGCATTTTAGTATGTCATCCT
* *
2835099 TTCATGCATTTTAGTTATGGCATCAT
1 TTCATGCATTTTAG-TATGTCATCCT
* * * *
2835125 TTCTTGC--CTTA--ATG-CATTCG
1 TTCATGCATTTTAGTATGTCATCCT
*
2835145 TTCATGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAG-TATGTCATCCT
* * *
2835171 TTCATTC--CTTA--ATG-CATCCA
1 TTCATGCATTTTAGTATGTCATCCT
*
2835191 TTCATCCATTTTAGTTATGTCATCCT
1 TTCATGCATTTTAG-TATGTCATCCT
* *
2835217 TTCATGC--CTTA--ATG-CATCCG
1 TTCATGCATTTTAGTATGTCATCCT
2835237 TTCATGCATTTTAGGTATGTCATCCT
1 TTCATGCATTTTA-GTATGTCATCCT
2835263 TTCATGC
1 TTCATGC
2835270 CTTAATGATA
Statistics
Matches: 175, Mismatches: 32, Indels: 60
0.66 0.12 0.22
Matches are distributed among these distances:
20 55 0.31
21 15 0.09
22 15 0.09
24 15 0.09
25 15 0.09
26 60 0.34
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (25 bp):
TTCATGCATTTTAGTATGTCATCCT
Found at i:2840741 original size:23 final size:23
Alignment explanation
Indices: 2840680--2840744 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 23
2840670 CAGCTTGTAT
* *
2840680 AAATGCACCGAAGTGTCACGTAG
1 AAATGCACCGAAGTGCCAAGTAG
**
2840703 AGTTTGCACCGAAGTGCCAAGTAG
1 A-AATGCACCGAAGTGCCAAGTAG
*
2840727 AAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
2840745 TATAAGATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCAAGTAG
Found at i:2840884 original size:23 final size:23
Alignment explanation
Indices: 2840857--2840900 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2840847 AATACATATA
2840857 TGTCCCGAAGAACCACGTAGAAT
1 TGTCCCGAAGAACCACGTAGAAT
* *
2840880 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGAACCACGTAGA
2840901 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAGAACCACGTAGAAT
Found at i:2852939 original size:23 final size:23
Alignment explanation
Indices: 2852880--2852940 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2852870 ACATCTTATA
* *
2852880 TGGCACTTCGATGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * **
2852903 CGGCATTTAAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
2852926 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
2852941 TTTATATGAG
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2854106 original size:26 final size:27
Alignment explanation
Indices: 2854047--2854106 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
2854037 TCATATGTTC
2854047 ATATT-TA-TTATAAAACACATAACTT
1 ATATTATATTTATAAAACACATAACTT
* * * *
2854072 ATGTCATATTTAT-AAACATATATCTT
1 ATATTATATTTATAAAACACATAACTT
2854098 ATATTATAT
1 ATATTATAT
2854107 GTGCATATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 3 0.11
26 20 0.74
27 4 0.15
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATTATATTTATAAAACACATAACTT
Found at i:2855585 original size:16 final size:17
Alignment explanation
Indices: 2855558--2855589 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2855548 TGCTTCCTCG
2855558 GGGAGAAGGAAGAAGAA
1 GGGAGAAGGAAGAAGAA
2855575 GGGAG-AGGAAGAAGA
1 GGGAGAAGGAAGAAGA
2855590 GGGTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (17 bp):
GGGAGAAGGAAGAAGAA
Found at i:2857510 original size:46 final size:46
Alignment explanation
Indices: 2857467--2857682 Score: 317
Period size: 46 Copynumber: 4.7 Consensus size: 46
2857457 TTATTCATTA
* * * *
2857467 ATTTCAGTTATGGCCTCTTTTCATGCCTTAATACATTCGTTCATAC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATTCGTTCATGC
*
2857513 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATAT-GTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACAT-TCGTTCATGC
** * **
2857559 ATTTTAGTTATAACATCCTTTCATGCCTTAATGCAACCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATTCGTTCATGC
*
2857605 ATTTTAGTTATGGCTTCCTTTCATGCCTTAATACATTCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATTCGTTCATGC
2857651 ATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAAT
2857683 GCATCCGTAC
Statistics
Matches: 152, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
46 151 0.99
47 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATACATTCGTTCATGC
Found at i:2857688 original size:20 final size:20
Alignment explanation
Indices: 2857572--2857688 Score: 54
Period size: 20 Copynumber: 5.2 Consensus size: 20
2857562 TTAGTTATAA
2857572 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* * *
2857592 CAACCGTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
* *
2857618 CTTCCTTTCATGCCTTAATA
1 CATCCTTTCATGCCTTAATG
* * *
2857638 CATTCGTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
2857664 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
2857684 CATCC
1 CATCC
2857689 GTACTGTTCT
Statistics
Matches: 69, Mismatches: 16, Indels: 24
0.63 0.15 0.22
Matches are distributed among these distances:
20 27 0.39
21 4 0.06
22 6 0.09
24 6 0.09
25 4 0.06
26 22 0.32
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:2858621 original size:3 final size:3
Alignment explanation
Indices: 2858613--2858642 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2858603 CTCCTCACTC
*
2858613 TCA TCA TCA TCA TCA TCA TCA CCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2858643 GGAGCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
TCA
Found at i:2861274 original size:32 final size:32
Alignment explanation
Indices: 2861233--2861306 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
2861223 CCATACTAAC
2861233 TAATTTAATGCTTAATTATAATGTAAAAAAGG
1 TAATTTAATGCTTAATTATAATGTAAAAAAGG
2861265 TAATTTAATGCTTAATTATAATGTAAAAAAGG
1 TAATTTAATGCTTAATTATAATGTAAAAAAGG
2861297 TAATTTAATG
1 TAATTTAATG
2861307 TTTATGTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (32 bp):
TAATTTAATGCTTAATTATAATGTAAAAAAGG
Found at i:2861518 original size:18 final size:18
Alignment explanation
Indices: 2861475--2861532 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
2861465 GGAGTAAAAA
* *
2861475 TAAATTATATATATA-TA
1 TAAAATATATATATATTT
*
2861492 TATATATATATATATATTT
1 TA-AAATATATATATATTT
2861511 TAAAATATATA-ATAATTT
1 TAAAATATATATAT-ATTT
2861529 TAAA
1 TAAA
2861533 TTTGTAAGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.12
18 27 0.79
19 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAATATATATATATTT
Found at i:2861518 original size:20 final size:18
Alignment explanation
Indices: 2861495--2861532 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
2861485 ATATATATAT
2861495 ATATATATATATATTTTAAA
1 ATATATA-ATA-ATTTTAAA
2861515 ATATATAATAATTTTAAA
1 ATATATAATAATTTTAAA
2861533 TTTGTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATAATAATTTTAAA
Found at i:2861521 original size:2 final size:2
Alignment explanation
Indices: 2861480--2861508 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2861470 AAAAATAAAT
2861480 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
2861509 TTTAAAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2862275 original size:2 final size:2
Alignment explanation
Indices: 2862268--2862296 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2862258 CTCGATACAA
2862268 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2862297 TCTTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2865555 original size:59 final size:60
Alignment explanation
Indices: 2865481--2865613 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
2865471 AAAGTAGTCT
* * * ** *
2865481 TTAAACCTTTGAATATTTTAATTT-ATCCCTAAACTATGATTAT-TATTCTAAATTAATCC
1 TTAAACTTTTAAATATTATAATTTCATAACTAAACTATGAATATAT-TTCTAAATTAATCC
*
2865540 TTAAACTTTTAAATATTATAATTTCATAACTAAACTATGAATATATTTCTAAATTAGTCC
1 TTAAACTTTTAAATATTATAATTTCATAACTAAACTATGAATATATTTCTAAATTAATCC
** *
2865600 CCATACTTTTAAAT
1 TTAAACTTTTAAAT
2865614 CTTTCGATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 21 0.34
60 40 0.65
61 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.44
Consensus pattern (60 bp):
TTAAACTTTTAAATATTATAATTTCATAACTAAACTATGAATATATTTCTAAATTAATCC
Found at i:2866728 original size:29 final size:29
Alignment explanation
Indices: 2866664--2866728 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
2866654 TGACTTTTGT
* * * *
2866664 TTTGATGCAATTTGGGCTCTAAACTTTAG
1 TTTGATACAATTTGGCCCCTAAACTTTAC
*
2866693 TTAGATACAATTTGGCCCCT-AACTTTGAC
1 TTTGATACAATTTGGCCCCTAAACTTT-AC
2866722 TTTGATA
1 TTTGATA
2866729 TGCAATTGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (29 bp):
TTTGATACAATTTGGCCCCTAAACTTTAC
Found at i:2871769 original size:163 final size:163
Alignment explanation
Indices: 2871486--2871901 Score: 717
Period size: 163 Copynumber: 2.5 Consensus size: 163
2871476 ATCATGGAAT
* * * *
2871486 TTAGTAGGTGTGCAGGTGGGTGTAAGGTTCTGTGGAACCTACACATTATGGAGTGTTGGTTGGAG
1 TTAGTTGGTGTGTAGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAG
*
2871551 GGAATAATATGATTTTTGATAAATGTTTTATGGGAGGGTGTTGTTAGAGGAAGTTATCGTTACTG
66 GGAATAATATGATTTTTGATAAATGTTTTATGGGAGGGTATTGTTAGAGGAAGTTATCGTTACTG
*
2871616 CAGGCTCCTCTGCTTTGTGCTCAGGGTAAGTCC
131 CAGGCTCCTCTGCTTTGTGCTCAAGGTAAGTCC
2871649 TTAGTTGGTGTGTAGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAG
1 TTAGTTGGTGTGTAGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAG
*
2871714 GGAATAATATGATTTTTGATAAATGTTTTATGGGAGGGTATTGTTGGAGGAAGTTATCGTTACTG
66 GGAATAATATGATTTTTGATAAATGTTTTATGGGAGGGTATTGTTAGAGGAAGTTATCGTTACTG
2871779 CAGGCTCCTCTGCTTTGTGCTCAAGGTAAGTCC
131 CAGGCTCCTCTGCTTTGTGCTCAAGGTAAGTCC
2871812 TTAGTTGGTGTGTAGGTGGGTGTATGGTTCTGGGGAACCTACACATTATAGAGAGT-TTGGTTGG
1 TTAGTTGGTGTGTAGGTGGGTGTATGGTTCTGGGGAACCTACACATTAT-G-GAGTGTTGGTTGG
* *
2871876 AGGGATTAATATGGTTTTTGAATAAA
64 AGGGAATAATATGATTTTTG-ATAAA
2871902 AATATATTTT
Statistics
Matches: 241, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
163 205 0.85
164 27 0.11
165 9 0.04
ACGTcount: A:0.22, C:0.10, G:0.33, T:0.36
Consensus pattern (163 bp):
TTAGTTGGTGTGTAGGTGGGTGTATGGTTCTGGGGAACCTACACATTATGGAGTGTTGGTTGGAG
GGAATAATATGATTTTTGATAAATGTTTTATGGGAGGGTATTGTTAGAGGAAGTTATCGTTACTG
CAGGCTCCTCTGCTTTGTGCTCAAGGTAAGTCC
Found at i:2876751 original size:60 final size:59
Alignment explanation
Indices: 2876635--2876755 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 59
2876625 TCGGATAATC
* * * *
2876635 ATTTTGTAACTTTTAATAGTTGATAGACTTAACAAAGCAACGTCCTATAATCATGGAACT
1 ATTTTATAACTTTTAATAGTTCAAAGACTTAACAAAGCAACATCCTATAATCATGG-ACT
* * *
2876695 ATTTTATAACTTTTAATAG-TCAAAGACTTAACAAAGTAACATCTTATAGTCGATGGACT
1 ATTTTATAACTTTTAATAGTTCAAAGACTTAACAAAGCAACATCCTATAATC-ATGGACT
2876754 AT
1 AT
2876756 GTACTTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 31 0.58
60 22 0.42
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAGTTCAAAGACTTAACAAAGCAACATCCTATAATCATGGACT
Found at i:2877867 original size:15 final size:15
Alignment explanation
Indices: 2877847--2877928 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
2877837 TTCCAGAAAA
2877847 TGAATTACTGGAATT
1 TGAATTACTGGAATT
2877862 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2877877 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
2877892 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2877907 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
2877921 TGAATTAC
1 TGAATTAC
2877929 ATTTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:2877881 original size:30 final size:30
Alignment explanation
Indices: 2877847--2877928 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
2877837 TTCCAGAAAA
**
2877847 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2877877 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
2877907 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
2877929 ATTTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:2877906 original size:45 final size:44
Alignment explanation
Indices: 2877842--2877928 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
2877832 TGGTTTTCCA
**
2877842 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
2877887 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
2877929 ATTTCTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:2877934 original size:20 final size:20
Alignment explanation
Indices: 2877911--2877980 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
2877901 GGAATTTGAA
2877911 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2877931 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2877951 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2877971 TTCTGGAAAA
1 TTCTGGAAAA
2877981 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2878195 original size:30 final size:29
Alignment explanation
Indices: 2878138--2878240 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 29
2878128 CTTTACTAAA
*
2878138 ATATTATTGAAATATAT-AAATAATATTAT
1 ATATTATT-AAATATATAAAAAAATATTAT
2878167 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAAAAA-TATTAT
2878197 ATATTATTAAA-ATA-AAAATATAATATCT-T
1 ATATTATTAAATATATAAAA-A-AATAT-TAT
2878226 ATATTA-TATAATATA
1 ATATTATTA-AATATA
2878241 ATTGATTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
28 15 0.23
29 27 0.42
30 21 0.33
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATTATTAAATATATAAAAAAATATTAT
Found at i:2878272 original size:14 final size:14
Alignment explanation
Indices: 2878253--2878300 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2878243 TGATTATTTT
2878253 ATATAATATTAAAA
1 ATATAATATTAAAA
**
2878267 ATATAATATTATTA
1 ATATAATATTAAAA
*
2878281 TTATAAATATTAATAA
1 ATAT-AATATTAA-AA
2878297 ATAT
1 ATAT
2878301 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 15 0.58
15 7 0.27
16 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAATATTAAAA
Found at i:2878278 original size:29 final size:31
Alignment explanation
Indices: 2878226--2878300 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 31
2878216 ATAATATCTT
*
2878226 ATATTATATAATATAATTGATTATT-TTATATA
1 ATATTA-AAAATATAATTGATTATTATTATA-A
2878258 ATATTAAAAATATAA-T-ATTATTATTATAA
1 ATATTAAAAATATAATTGATTATTATTATAA
2878287 ATATTAATAAATAT
1 ATATTAA-AAATAT
2878301 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 14 0.35
30 12 0.30
31 8 0.20
32 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
ATATTAAAAATATAATTGATTATTATTATAA
Found at i:2878281 original size:32 final size:28
Alignment explanation
Indices: 2878226--2878300 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 28
2878216 ATAATATCTT
*
2878226 ATATTATATAATATAATTGATTATTTTATATA
1 ATATTA-AAAATATAATTGATTA--TTATA-A
*
2878258 ATATTAAAAATATAATATTATTATTATAA
1 ATATTAAAAATATAAT-TGATTATTATAA
2878287 ATATTAATAAATAT
1 ATATTAA-AAATAT
2878301 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 8 0.21
30 11 0.28
31 9 0.23
32 11 0.28
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
ATATTAAAAATATAATTGATTATTATAA
Found at i:2878559 original size:42 final size:42
Alignment explanation
Indices: 2878500--2878614 Score: 212
Period size: 42 Copynumber: 2.7 Consensus size: 42
2878490 ATGAATTACA
**
2878500 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2878542 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2878584 TTCCGGAAAACGAATTACGTGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
2878615 TGAAATTCGG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:2882230 original size:18 final size:18
Alignment explanation
Indices: 2882207--2882251 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2882197 ACTAGATAAA
*
2882207 GATAAGATTACCTAGTAT
1 GATAAGATTACATAGTAT
*
2882225 GATAAGATTACATAGTGT
1 GATAAGATTACATAGTAT
2882243 GATAAGATT
1 GATAAGATT
2882252 TAGATTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (18 bp):
GATAAGATTACATAGTAT
Done.