Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 50
Found at i:2649266 original size:15 final size:15
Alignment explanation
Indices: 2649246--2649279 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2649236 AAAAAAAGGC
*
2649246 AAAAAAAAGGAA-CA
1 AAAAAAAAAGAAGCA
2649260 AAAAAAAAAGAAGCA
1 AAAAAAAAAGAAGCA
2649275 AAAAA
1 AAAAA
2649280 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAGCA
Found at i:2656930 original size:15 final size:15
Alignment explanation
Indices: 2656910--2656942 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2656900 ATAAATTACA
2656910 TTTTTTGGAAAATAT
1 TTTTTTGGAAAATAT
2656925 TTTTTTGGAAAATAT
1 TTTTTTGGAAAATAT
2656940 TTT
1 TTT
2656943 ACAGTGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTTTTGGAAAATAT
Found at i:2657128 original size:32 final size:33
Alignment explanation
Indices: 2657092--2657154 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2657082 GTTTATTATT
* *
2657092 ATTAAAATATTAT-TAGCAATAAAAATATTAAG
1 ATTAAAACATTATATAGAAATAAAAATATTAAG
* *
2657124 ATTAATACATTATATTGAAATAAAAATATTA
1 ATTAAAACATTATATAGAAATAAAAATATTA
2657155 TAAATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (33 bp):
ATTAAAACATTATATAGAAATAAAAATATTAAG
Found at i:2657432 original size:19 final size:20
Alignment explanation
Indices: 2657391--2657450 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
2657381 ATCTTATATT
* *
2657391 TATATTATAATA-TAATGAG
1 TATATTATAATATTAATAAA
2657410 TATATTATAATATTAA-AAA
1 TATATTATAATATTAATAAA
* * *
2657429 TATATAATATTATTATTAAA
1 TATATTATAATATTAATAAA
2657449 TA
1 TA
2657451 ATAAATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 26 0.76
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATTATAATATTAATAAA
Found at i:2662752 original size:41 final size:41
Alignment explanation
Indices: 2662707--2662807 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 41
2662697 CTAGCTTTTA
* *
2662707 TTTAAATTAATTCAAT-ATTT-ATTTATT-TATTTAAAATACCT
1 TTTAAAATAATT-AATAATTTAATTTATTATAATT--AATACCT
*
2662748 TTTAAAATAATTTATAATTTAATTTATTATAATTAATACCT
1 TTTAAAATAATTAATAATTTAATTTATTATAATTAATACCT
*
2662789 TTTAAAAATAAATAATAAT
1 TTT-AAAATAATTAATAAT
2662808 AATTTAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 2 0.04
41 25 0.49
42 20 0.39
43 4 0.08
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.50
Consensus pattern (41 bp):
TTTAAAATAATTAATAATTTAATTTATTATAATTAATACCT
Found at i:2662807 original size:42 final size:37
Alignment explanation
Indices: 2662727--2662807 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 37
2662717 TTCAATATTT
* *
2662727 ATTTATTTATTTAAAATACCTTTTAAAATAATTTATA
1 ATTTATTTATTTAAAATACCTTTTAAAATAAATAATA
2662764 ATTTAATTTATTATAATTAATACCTTTTAAAAATAAATAATA
1 ATTT-ATTTATT-TAA--AATACCTTTT-AAAATAAATAATA
2662806 AT
1 AT
2662808 AATTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
37 4 0.11
38 7 0.19
39 3 0.08
41 10 0.27
42 13 0.35
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATTTATTTAAAATACCTTTTAAAATAAATAATA
Found at i:2665357 original size:21 final size:22
Alignment explanation
Indices: 2665319--2665371 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2665309 TCAAACAATT
* *
2665319 AAATATAAAATACT-AAAATAA
1 AAATATATATTACTAAAAATAA
*
2665340 AAAT-TATATTACTAAAAAATTA
1 AAATATATATTACT-AAAAATAA
2665362 AAATATATAT
1 AAATATATAT
2665372 ATATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.27
21 4 0.15
22 10 0.38
23 5 0.19
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATATATTACTAAAAATAA
Found at i:2665664 original size:14 final size:16
Alignment explanation
Indices: 2665634--2665665 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2665624 TATATGTTTA
2665634 TAATATATTTAATATT
1 TAATATATTTAATATT
2665650 TAATA-ATTT-ATATT
1 TAATATATTTAATATT
2665664 TA
1 TA
2665666 CCATTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATATATTTAATATT
Found at i:2665714 original size:23 final size:23
Alignment explanation
Indices: 2665669--2665714 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2665659 ATATTTACCA
*
2665669 TTTTATAGTTTGTTATGTATTTT
1 TTTTATAGTTTGTTATATATTTT
*
2665692 TTTTATAGTTTTTTA-ATATTTT
1 TTTTATAGTTTGTTATATATTTT
2665714 T
1 T
2665715 AATATGAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTATAGTTTGTTATATATTTT
Found at i:2670097 original size:13 final size:13
Alignment explanation
Indices: 2670079--2670109 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2670069 ACCTTGATCA
2670079 GATTGAATAGGAG
1 GATTGAATAGGAG
2670092 GATTGAATAGGAG
1 GATTGAATAGGAG
2670105 GATTG
1 GATTG
2670110 CAATTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (13 bp):
GATTGAATAGGAG
Found at i:2670666 original size:2 final size:2
Alignment explanation
Indices: 2670659--2670690 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2670649 CATTAATTCC
2670659 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
2670691 TACCTACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2671978 original size:24 final size:25
Alignment explanation
Indices: 2671928--2671994 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 25
2671918 TTACATTTAT
2671928 ATTT-ATATTTATATATATATATATA
1 ATTTCATATTTATAT-TATATATATA
2671953 ATATTACATATTTA-ATTAT-TA-ATA
1 AT-TT-CATATTTATATTATATATATA
2671977 ATTTCATATATTATATTA
1 ATTTCATAT-TTATATTA
2671995 AACTAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
22 5 0.14
23 5 0.14
24 9 0.24
25 4 0.11
26 5 0.14
27 2 0.05
28 7 0.19
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTCATATTTATATTATATATATA
Found at i:2680245 original size:18 final size:18
Alignment explanation
Indices: 2680218--2680254 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2680208 GCTATACAAG
* *
2680218 TGTGACTATTTCGAGACT
1 TGTGAATATTCCGAGACT
2680236 TGTGAATATTCCGAGACT
1 TGTGAATATTCCGAGACT
2680254 T
1 T
2680255 ATGCCAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
TGTGAATATTCCGAGACT
Found at i:2681407 original size:32 final size:31
Alignment explanation
Indices: 2681333--2681430 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 31
2681323 TTAATGTTAG
*
2681333 TTTTATTATTATAAGATTTATAAATAT-TTAA
1 TTTT-TTATTATAAGATTTATAAAAATATTAA
**
2681364 -TTAGTATTATAAGATTTATAATAAATATTAA
1 TTTTTTATTATAAGATTTATAA-AAATATTAA
* * *
2681395 TTTTTTAATATAAAATTTATGAAAAATAAT-A
1 TTTTTTATTATAAGATTTAT-AAAAATATTAA
2681426 TTTTT
1 TTTTT
2681431 GATAATAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 17 0.31
30 5 0.09
31 10 0.18
32 21 0.38
33 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (31 bp):
TTTTTTATTATAAGATTTATAAAAATATTAA
Found at i:2681931 original size:192 final size:185
Alignment explanation
Indices: 2681589--2681966 Score: 467
Period size: 192 Copynumber: 2.0 Consensus size: 185
2681579 TAACTAATTG
* *
2681589 TAACAAATTTATTTAGTAATAATATATTAAATTTAGTCAAAAAATAAATTATGCCAAATTTGTTT
1 TAACAAATTTATTTAGTAACAATATATTAAATTTAGTCAAAAAATAAATTATGCCAAATTTATTT
* * *
2681654 GTCACAATATTTTCTCAAAATAATAAATGATGAAAAATTATTTAGTCAAAATAACAATTGACAAT
66 GTCACAATATTTTCTCAAAATAATAAATGATGAAAAATTATTTAGTCAAAATAAAAAGTGACAAC
*
2681719 AAATATTAATTTCTCAATATAA-AATTTTATAAAAAATAATATTTTTTCACAATAAT
131 AAATATTAATTTCTCAATATAACAA--TTATAAAAAATAATATTCTTTCACAATAAT
* *
2681775 TAACAAATTTATTTAGTCACAATACCTTATTAAATTTAGTCAACATAAA-AAATTATGTCAAATT
1 TAACAAATTTATTTAGTAACAATA---TATTAAATTTAGTCAA-A-AAATAAATTATGCCAAATT
** * * *
2681839 TATTTCGTCACAATATTTTCTCAAAATAA-AAACTTTTGACAAATTTATTTATTCATAATAAAAA
61 TATTT-GTCACAATATTTTCTCAAAATAATAAA-TGATGA-AAAATTATTTAGTCAAAAT-AAAA
* * * *
2681903 AGT-ATAACAAATGTTAATTTCTCAATATAACGAATTATGAAAAATAATATTCTTTCATAATAAT
122 AGTGACAACAAATATTAATTTCTCAATATAAC-AATTATAAAAAATAATATTCTTTCACAATAAT
2681967 GAATTGTAAC
Statistics
Matches: 164, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
186 22 0.13
189 16 0.10
190 22 0.13
191 30 0.18
192 67 0.41
193 5 0.03
194 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (185 bp):
TAACAAATTTATTTAGTAACAATATATTAAATTTAGTCAAAAAATAAATTATGCCAAATTTATTT
GTCACAATATTTTCTCAAAATAATAAATGATGAAAAATTATTTAGTCAAAATAAAAAGTGACAAC
AAATATTAATTTCTCAATATAACAATTATAAAAAATAATATTCTTTCACAATAAT
Found at i:2687079 original size:19 final size:20
Alignment explanation
Indices: 2687042--2687089 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2687032 TCTAAATCCT
*
2687042 TTTTCAAAATTTCATTTTAG
1 TTTTCAAAATCTCATTTTAG
2687062 TTTTCAAAATCT-ATTTTAG
1 TTTTCAAAATCTCATTTTAG
*
2687081 CTTTCAAAA
1 TTTTCAAAA
2687090 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTAG
Found at i:2700361 original size:14 final size:16
Alignment explanation
Indices: 2700328--2700364 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
2700318 AACCTGAATC
2700328 GAGAGAGCAGAGATTA
1 GAGAGAGCAGAGATTA
*
2700344 GAGAGAG-ATAGATT-
1 GAGAGAGCAGAGATTA
2700358 GAGAGAG
1 GAGAGAG
2700365 GGAATGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 6 0.30
16 7 0.35
ACGTcount: A:0.43, C:0.03, G:0.41, T:0.14
Consensus pattern (16 bp):
GAGAGAGCAGAGATTA
Found at i:2700941 original size:14 final size:14
Alignment explanation
Indices: 2700922--2700949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2700912 GAGTTCAAAG
2700922 AAAGACATAGTAGT
1 AAAGACATAGTAGT
2700936 AAAGACATAGTAGT
1 AAAGACATAGTAGT
2700950 TGATTCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGACATAGTAGT
Found at i:2706362 original size:195 final size:190
Alignment explanation
Indices: 2706008--2706395 Score: 618
Period size: 195 Copynumber: 2.0 Consensus size: 190
2705998 ATTACAAATC
* * *
2706008 GACAATATCAGTGACCTAATTTTTACTTTTAAAATTTTAGTAGTTAAAAAACTTACTCAAACATC
1 GACAATATCAGTGACATAATTTTTACTTTTAAAACTTTAGTAGTAAAAAAACTTACTCAAACATC
2706073 AATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAAGC
66 AATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAAGC
* *
2706138 TAAAAACTTATGGTCAAAATGTTTTTTTTTTATAAAAAAAATTTGGGGATAAAGAATGTCATTA
131 TAAAAACTTAAGGTCAAAATGTATTTTTTTT-T---AAAAATTTGGGGATAAAGAATGTCATTA
*
2706202 GACAATATTAGTGACAT-ATTTGTTACTTTTAAAACTTTAGTAGGTAAAAAAACTTACTCAAACA
1 GACAATATCAGTGACATAATTT-TTACTTTTAAAACTTTAGTA-GTAAAAAAACTTACTCAAACA
*
2706266 TCAATGATTATTTTTGTAATTTACCCTAAAATATCATCATTTAGTTTAATTCGAGGTCAAAAGAA
64 TCAATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAA
* *
2706331 GCTAAAAAACTTAAGGTCAAAATG-ATTTTTTTTTTAAATTTTGGGGATAAAGAATGTCATTA
129 GCT-AAAAACTTAAGGTCAAAATGTATTTTTTTTTAAAAATTTGGGGATAAAGAATGTCATTA
2706393 GAC
1 GAC
2706396 CTATTTTTTC
Statistics
Matches: 182, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
191 29 0.16
193 4 0.02
194 35 0.19
195 95 0.52
196 19 0.10
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (190 bp):
GACAATATCAGTGACATAATTTTTACTTTTAAAACTTTAGTAGTAAAAAAACTTACTCAAACATC
AATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAAGC
TAAAAACTTAAGGTCAAAATGTATTTTTTTTTAAAAATTTGGGGATAAAGAATGTCATTA
Found at i:2706676 original size:40 final size:40
Alignment explanation
Indices: 2706632--2706754 Score: 194
Period size: 40 Copynumber: 3.1 Consensus size: 40
2706622 TTTAAGTTGA
2706632 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
1 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
* *
2706672 AATCGAAAATATTGTCTATTTCGTAATATTTTAGG-TTGA
1 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
* * *
2706711 AATCGAAAATATTGTATATTTCGTAATATTTCTGGTTTAT
1 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
2706751 AATC
1 AATC
2706755 TAATTATAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
39 35 0.47
40 40 0.53
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (40 bp):
AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
Found at i:2706731 original size:39 final size:39
Alignment explanation
Indices: 2706615--2706741 Score: 200
Period size: 39 Copynumber: 3.2 Consensus size: 39
2706605 GTTAGACATA
* *
2706615 GTAACATTTTAAGTTGAAATCGAAAATATTGTCTATTTC
1 GTAATATTTTAGGTTGAAATCGAAAATATTGTCTATTTC
* *
2706654 GTAATATTTTTGGTTTGTAATCGAAAATATTGTCTATTTC
1 GTAATATTTTAGG-TTGAAATCGAAAATATTGTCTATTTC
*
2706694 GTAATATTTTAGGTTGAAATCGAAAATATTGTATATTTC
1 GTAATATTTTAGGTTGAAATCGAAAATATTGTCTATTTC
2706733 GTAATATTT
1 GTAATATTT
2706742 CTGGTTTATA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 43 0.54
40 37 0.46
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (39 bp):
GTAATATTTTAGGTTGAAATCGAAAATATTGTCTATTTC
Found at i:2713050 original size:2 final size:2
Alignment explanation
Indices: 2713043--2713079 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2713033 GAACCTAGTG
2713043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2713080 ATTTAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2714836 original size:31 final size:31
Alignment explanation
Indices: 2714783--2714866 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
2714773 TCATTATAAT
* *
2714783 AAAT-TATGTT-TA-GATTTAAATATGTGAA
1 AAATATATGTTATATGATTTGAATATATGAA
2714811 AAATATATGTTATATGATTTGAATATATGAA
1 AAATATATGTTATATGATTTGAATATATGAA
* * *
2714842 CAATACATGTTATATGGTTTGAATA
1 AAATATATGTTATATGATTTGAATA
2714867 AAGTAAATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 4 0.08
29 6 0.12
30 2 0.04
31 36 0.75
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (31 bp):
AAATATATGTTATATGATTTGAATATATGAA
Found at i:2716965 original size:19 final size:19
Alignment explanation
Indices: 2716937--2716979 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2716927 GCCAGGAGTA
*
2716937 CATCGTTGCATGGTCAGTG
1 CATCGATGCATGGTCAGTG
*
2716956 CATCGATGCATGGTCTGTG
1 CATCGATGCATGGTCAGTG
2716975 CATCG
1 CATCG
2716980 GTACATAAAG
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:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (19 bp):
CATCGATGCATGGTCAGTG
Found at i:2718974 original size:44 final size:44
Alignment explanation
Indices: 2718869--2718975 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
2718859 CGATGCACTG
* * * * *
2718869 CATAGTGTATCGATGGACATTTAAGGCATGCATTGGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
* *
2718913 CATAGTGTATCGATGCATATTCAAGGGATGCATCGGTACACTTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
*
2718957 CATAGTGTATCAATGCATA
1 CATAGTGTATCGATGCATA
2718976 GTGTACAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (44 bp):
CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
Found at i:2722626 original size:20 final size:20
Alignment explanation
Indices: 2722588--2722626 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2722578 AAAGCTTTAA
*
2722588 GATCATCAATTTTCTTTGAT
1 GATCATCAATTTACTTTGAT
2722608 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACT-TTGA
2722627 AAGTAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (20 bp):
GATCATCAATTTACTTTGAT
Found at i:2727631 original size:23 final size:23
Alignment explanation
Indices: 2727574--2727641 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2727564 CATTTTATAT
* *
2727574 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTTGGTGCATTTCTACGC
**
2727597 GGCACTACGGTGCATTTCTACGC
1 GGCACTTTGGTGCATTTCTACGC
*
2727620 GGCACTTTGGTGCATTTATACG
1 GGCACTTTGGTGCATTTCTACG
2727642 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTTGGTGCATTTCTACGC
Found at i:2729405 original size:65 final size:65
Alignment explanation
Indices: 2729311--2729467 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
2729301 TACACTTGGG
* * * * *
2729311 GTGCATCGGTACACT-AATTACATTTGATGTTTCAA-AAGAGGCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACA-TAAAATACATTCGATGTTTCAATAA-AAGCACGAGTGCATCGATACATGGT
2729374 AT
64 AT
* * *
2729376 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAATCACGAGTGCATCGATACATGGTTT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAATAAAAGCACGAGTGCATCGATACATGGTAT
* *
2729441 GTGCACCGGTACACAAAATACATTCGA
1 GTGCATCGGTACATAAAATACATTCGA
2729468 ATTAGGATGT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 1 0.01
65 76 0.96
66 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAATAAAAGCACGAGTGCATCGATACATGGTAT
Found at i:2740695 original size:19 final size:19
Alignment explanation
Indices: 2740673--2740717 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2740663 TTTTCAGAAA
*
2740673 TTTTAATTATT-TTTATAAT
1 TTTTAATAATTATTTAT-AT
2740692 TTTTAATAATTCATTTATAT
1 TTTTAATAATT-ATTTATAT
2740712 TTTTAA
1 TTTTAA
2740718 AATAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
21 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAATAATTATTTATAT
Found at i:2740804 original size:16 final size:16
Alignment explanation
Indices: 2740783--2740836 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2740773 TACTTTCTTC
*
2740783 AAATTTTTATTAATTT
1 AAATTTTTATTATTTT
*
2740799 AAATTTAATATT-TTTT
1 AAATTT-TTATTATTTT
*
2740815 AAAATTTTATTTATTTT
1 AAATTTTTA-TTATTTT
2740832 AAATT
1 AAATT
2740837 AATATTTCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 12 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AAATTTTTATTATTTT
Found at i:2740819 original size:17 final size:18
Alignment explanation
Indices: 2740790--2740843 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 18
2740780 TTCAAATTTT
*
2740790 TATTAATTT-AAATTTAA
1 TATTTATTTAAAATTTAA
2740807 TATTT-TTTAAAATTT--
1 TATTTATTTAAAATTTAA
*
2740822 TATTTATTTTAAA-TTAA
1 TATTTATTTAAAATTTAA
2740839 TATTT
1 TATTT
2740844 CAGTCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 7 0.23
16 9 0.29
17 15 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTATTTAAAATTTAA
Found at i:2741561 original size:24 final size:23
Alignment explanation
Indices: 2741540--2741634 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 23
2741530 ATTGAACCTT
*
2741540 AAACCATGCCCCAAACTAAACCC
1 AAACCAGGCCCCAAACTAAACCC
* *
2741563 TAAACCAAGCCCCAAATCAAAACCC
1 -AAACCAGGCCCCAAA-CTAAACCC
*
2741588 AAACCAGGCCCCAAATTAAAACCC
1 AAACCAGGCCCCAAACT-AAACCC
*
2741612 AAACCAGGCCCCAAACCAAACCC
1 AAACCAGGCCCCAAACTAAACCC
2741635 GACCAAGGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
23 6 0.10
24 49 0.79
25 7 0.11
ACGTcount: A:0.45, C:0.42, G:0.06, T:0.06
Consensus pattern (23 bp):
AAACCAGGCCCCAAACTAAACCC
Found at i:2741599 original size:48 final size:48
Alignment explanation
Indices: 2741540--2741631 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
2741530 ATTGAACCTT
* *
2741540 AAACCATGCCCCAAACT-AAACCCTAAACCAAGCCCCAAATCAAAACCC
1 AAACCAGGCCCCAAACTAAAACCC-AAACCAAGCCCCAAACCAAAACCC
* *
2741588 AAACCAGGCCCCAAATTAAAACCCAAACCAGGCCCCAAACCAAA
1 AAACCAGGCCCCAAACTAAAACCCAAACCAAGCCCCAAACCAAA
2741632 CCCGACCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 33 0.85
49 6 0.15
ACGTcount: A:0.47, C:0.40, G:0.07, T:0.07
Consensus pattern (48 bp):
AAACCAGGCCCCAAACTAAAACCCAAACCAAGCCCCAAACCAAAACCC
Found at i:2744428 original size:19 final size:19
Alignment explanation
Indices: 2744404--2744441 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2744394 TTTTTATTTT
2744404 ATAATTTTTCAAT-TTTTAA
1 ATAATTTTT-AATATTTTAA
2744423 ATAATTTTTAATATTTTAA
1 ATAATTTTTAATATTTTAA
2744442 TTGTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
ATAATTTTTAATATTTTAA
Found at i:2745478 original size:19 final size:20
Alignment explanation
Indices: 2745456--2745493 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2745446 CTTTTTTTTT
*
2745456 ATAATTTTTAAT-TTTTAAA
1 ATAATTTGTAATATTTTAAA
2745475 ATAATTTGTAATATTTTAA
1 ATAATTTGTAATATTTTAA
2745494 TTATTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATAATTTGTAATATTTTAAA
Found at i:2745872 original size:21 final size:21
Alignment explanation
Indices: 2745846--2745892 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2745836 TCAGAAATTT
* *
2745846 TAATTATTTTATAGATTTT-AA
1 TAATTAATTTA-AAATTTTAAA
2745867 TAATTAATTTAAAATTTTAAA
1 TAATTAATTTAAAATTTTAAA
2745888 TAATT
1 TAATT
2745893 TTAGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAATTAATTTAAAATTTTAAA
Found at i:2745904 original size:21 final size:19
Alignment explanation
Indices: 2745880--2745947 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 19
2745870 TTAATTTAAA
2745880 ATTTTAAATAATTTTAGTATT
1 ATTTTAAATAATTTT--TATT
**
2745901 ATTTTTTATAATTTTTATT
1 ATTTTAAATAATTTTTATT
* * *
2745920 TTTTTAAAAATAATTTGTAAT
1 ATTTT--AAATAATTTTTATT
2745941 ATTTTAA
1 ATTTTAA
2745948 TTATTTTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 10 0.27
21 27 0.73
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTTAAATAATTTTTATT
Found at i:2746490 original size:34 final size:36
Alignment explanation
Indices: 2746409--2746498 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 36
2746399 TTTTTTTAAA
*
2746409 TAATTTTAATATTTTAAT-TATTTTCTTAAAATGCTTGT
1 TAATTTTAA-A-TTTAATAT-TTTTCTTAAAATGCTTAT
* *
2746447 TAA-TCTAAATTTAATATTTTTC-TAAAAT-TTTAT
1 TAATTTTAAATTTAATATTTTTCTTAAAATGCTTAT
2746480 TAATTTTAAA-TTAATATTT
1 TAATTTTAAATTTAATATTT
2746499 GAAAATTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
33 15 0.33
34 11 0.24
35 11 0.24
36 2 0.04
37 4 0.09
38 3 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (36 bp):
TAATTTTAAATTTAATATTTTTCTTAAAATGCTTAT
Found at i:2747305 original size:20 final size:20
Alignment explanation
Indices: 2747259--2747305 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2747249 ATTTTTTTTC
*
2747259 AAATTTATTATTTTAATATT
1 AAATTTATTATTTTAATAAT
* *
2747279 AAGTTTATTCTATTTAA-AAT
1 AAATTTATTAT-TTTAATAAT
2747299 AAATTTA
1 AAATTTA
2747306 GAGAATGCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATTTATTATTTTAATAAT
Found at i:2756807 original size:21 final size:21
Alignment explanation
Indices: 2756747--2756818 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 21
2756737 TGAATATAAT
*
2756747 AATAATAATAATATTTTTTTAAA
1 AATAATAA-AATAATTTTTT-AA
** *
2756770 AATTAATATTATCATTTTTTAA
1 AA-TAATAAAATAATTTTTTAA
2756792 AATAATAAAATAATTTATTTAA
1 AATAATAAAATAATTT-TTTAA
2756814 TAATA
1 -AATA
2756819 TTTATGTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 11 0.28
22 9 0.23
23 14 0.36
24 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAATAAAATAATTTTTTAA
Found at i:2756940 original size:21 final size:21
Alignment explanation
Indices: 2756916--2756963 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
2756906 AATTATATTA
* * *
2756916 ATTATTTAATAAATTAATAGT
1 ATTATTTAATAAAATAAGAAT
* *
2756937 ATTAATTATTAAAATAAGAAT
1 ATTATTTAATAAAATAAGAAT
2756958 ATTATT
1 ATTATT
2756964 ATAACATAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTATTTAATAAAATAAGAAT
Found at i:2760492 original size:11 final size:12
Alignment explanation
Indices: 2760476--2760514 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
2760466 TATGAAATAT
2760476 TTTTAT-AATGA
1 TTTTATGAATGA
2760487 TTTTATGAAATGA
1 TTTTATG-AATGA
2760500 -TTTATGAATGA
1 TTTTATGAATGA
2760511 TTTT
1 TTTT
2760515 GGGTATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.44
12 9 0.36
13 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (12 bp):
TTTTATGAATGA
Found at i:2760503 original size:12 final size:12
Alignment explanation
Indices: 2760465--2760513 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2760455 TTGAATCATA
2760465 TTATGAAAT-AT
1 TTATGAAATGAT
*
2760476 TT-TTATAATGATT
1 TTATGA-AATGA-T
2760489 TTATGAAATGAT
1 TTATGAAATGAT
2760501 TTATG-AATGAT
1 TTATGAAATGAT
2760512 TT
1 TT
2760514 TGGGTATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 13 0.41
12 7 0.22
13 8 0.25
14 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (12 bp):
TTATGAAATGAT
Found at i:2762755 original size:13 final size:13
Alignment explanation
Indices: 2762737--2762763 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2762727 TTTTACCCTT
2762737 GTTCAAAATTAAG
1 GTTCAAAATTAAG
2762750 GTTCAAAATTAAG
1 GTTCAAAATTAAG
2762763 G
1 G
2762764 CTAAAATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (13 bp):
GTTCAAAATTAAG
Found at i:2779509 original size:3 final size:3
Alignment explanation
Indices: 2779503--2779573 Score: 81
Period size: 3 Copynumber: 23.0 Consensus size: 3
2779493 TTTTTTCAGT
* * *
2779503 TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA ATA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2779550 TATA TATA TATA TTA TTA TTA TTA
1 T-TA T-TA T-TA TTA TTA TTA TTA
2779574 AACAAAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 47 0.78
4 11 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2781329 original size:135 final size:137
Alignment explanation
Indices: 2781037--2781335 Score: 360
Period size: 135 Copynumber: 2.2 Consensus size: 137
2781027 TATAATTCGA
* * *
2781037 TTAGATAACAATGTTTATTTATTTTTAAATATTAAGAAAGGACAGTCTTAAAGCAACTGGATGTC
1 TTAGA-AA-AATGTTTATTTATTTTTTAATACTAAGAAAGGACAGTCTTAAAACAACTGGATGTC
* * * * *
2781102 CATTTTCTGATATTTTTAATTAAATAAACATCTTATTTTTATAAATTATATATATATATATATAT
64 AATTTTCTAATATTTTTAAATAAATAAACATCCTACTTTTATAAATTATATATATATATATATAT
2781167 TTAAATGTT
129 TTAAATGTT
** *
2781176 TT--ATTAATATTTATTTATTTTTTAATACTAAGAAAGGACAGTCTTAAAACAACTGGATGTCAA
1 TTAGAAAAATGTTTATTTATTTTTTAATACTAAGAAAGGACAGTCTTAAAACAACTGGATGTCAA
* *
2781239 TTTTCTAATATTTTTAAATAAATAAATATCCTACTTTTA-AAATTATATAT-TA-ATCTAT-TAT
66 TTTTCTAATATTTTTAAATAAATAAACATCCTACTTTTATAAATTATATATATATATATATAT-T
*
2781300 TATTAT-TT
130 TA-AATGTT
*
2781308 TTAGAAAAATGTCTTAATTATTTATTTA
1 TTAGAAAAATGT-TTATTTATTT-TTTA
2781336 TTTTTTAATA
Statistics
Matches: 136, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
131 1 0.01
132 12 0.09
133 4 0.03
134 16 0.12
135 96 0.71
136 4 0.03
137 1 0.01
139 2 0.01
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (137 bp):
TTAGAAAAATGTTTATTTATTTTTTAATACTAAGAAAGGACAGTCTTAAAACAACTGGATGTCAA
TTTTCTAATATTTTTAAATAAATAAACATCCTACTTTTATAAATTATATATATATATATATATTT
AAATGTT
Found at i:2786266 original size:10 final size:9
Alignment explanation
Indices: 2786250--2786300 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
2786240 TATTATACTT
2786250 GAAAAAAAA
1 GAAAAAAAA
2786259 GAAAAAAAA
1 GAAAAAAAA
*
2786268 GAAAAAAAG
1 GAAAAAAAA
2786277 GAAGGAAAAAA
1 GAA--AAAAAA
*
2786288 GGAAAAAAA
1 GAAAAAAAA
2786297 GAAA
1 GAAA
2786301 GAATTGAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 29 0.81
11 7 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2791046 original size:22 final size:22
Alignment explanation
Indices: 2791020--2791096 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
2791010 ATCTACACTC
2791020 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2791042 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2791064 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2791086 TTCAAAGATGA
1 TTCAAAGATGA
2791097 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2791892 original size:76 final size:76
Alignment explanation
Indices: 2791766--2792951 Score: 2129
Period size: 76 Copynumber: 15.6 Consensus size: 76
2791756 CTATTTCCCA
*
2791766 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2791831 AGCCTTAGGGT
66 AGCCTTAGGGT
2791842 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2791907 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2791918 CATCTGTAAGTCATACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2791983 AGCCTTAGGGT
66 AGCCTTAGGGT
2791994 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792059 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2792070 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792135 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
2792146 CATCTGTAAGTCATATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792211 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2792222 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792287 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2792298 CATCTGTAAGTCATACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792363 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2792374 CATCTGTAAGTCATACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2792439 AGCCTTAAGGT
66 AGCCTTAGGGT
*
2792450 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792515 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2792526 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTGTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2792591 AACCTTAGGGT
66 AGCCTTAGGGT
* * *
2792602 TATCTGTAAGTCATACAGTGCTTGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792667 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2792678 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792743 AGCCTTAGGGT
66 AGCCTTAGGGT
2792754 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2792819 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2792830 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTATGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
2792895 AACCTTCGGGT
66 AGCCTTAGGGT
* * * *
2792906 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
2792952 TCATCTGTAA
Statistics
Matches: 1066, Mismatches: 44, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 1066 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2792954 original size:47 final size:47
Alignment explanation
Indices: 2792882--2792987 Score: 180
Period size: 47 Copynumber: 2.3 Consensus size: 47
2792872 CGGGAGCTTT
*
2792882 ATGATGTTTTC--AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTAC
*
2792927 ATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTAC
1 ATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTAC
2792974 ATGATGTTTTCAAA
1 ATGATGTTTTCAAA
2792988 CATTTTCATC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
45 11 0.19
47 46 0.81
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (47 bp):
ATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTAC
Found at i:2793117 original size:3 final size:3
Alignment explanation
Indices: 2793111--2793180 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
2793101 TTTTTTCAGT
* * *
2793111 TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA ATA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
2793157 TAA ATA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA
2793181 AACAAAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2793135 original size:15 final size:15
Alignment explanation
Indices: 2793115--2793172 Score: 82
Period size: 15 Copynumber: 3.8 Consensus size: 15
2793105 TTCAGTTTAT
2793115 TATTATTATTATAAA
1 TATTATTATTATAAA
*
2793130 TATTATTATTATTAA
1 TATTATTATTATAAA
2793145 TATTATTATATATAAA
1 TATTATTAT-TATAAA
2793161 TA-TATATATTAT
1 TATTAT-TATTAT
2793173 TATTATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 29 0.74
16 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTATTATAAA
Found at i:2803423 original size:50 final size:50
Alignment explanation
Indices: 2803348--2803445 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 50
2803338 TTGAAACCAC
* * * *
2803348 TGCTGTTGAAACCACTCATCTAACCGACTTGTTGGATTCTACCGATAAAT
1 TGCTGTTAAAACCACTAATCCAACCGACTTGTTGGATTATACCGATAAAT
* *
2803398 TGCTGTTAAAACCACTAATCCAACCGGCTTGTTGGATTATACTGATAA
1 TGCTGTTAAAACCACTAATCCAACCGACTTGTTGGATTATACCGATAA
2803446 TGATATGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (50 bp):
TGCTGTTAAAACCACTAATCCAACCGACTTGTTGGATTATACCGATAAAT
Found at i:2804019 original size:29 final size:29
Alignment explanation
Indices: 2803985--2804043 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2803975 CCTAAATTAA
2803985 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2804014 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2804043 T
1 T
2804044 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2808691 original size:28 final size:27
Alignment explanation
Indices: 2808658--2808713 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 27
2808648 CCTAAATTAA
2808658 TTTGATGTCATTGCTTACATCAATTAGT
1 TTTGATGTCATTGCTTACATC-ATTAGT
2808686 TTTGATGTCATTGCTTACATCATTAGT
1 TTTGATGTCATTGCTTACATCATTAGT
2808713 T
1 T
2808714 AGGTGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.48
Consensus pattern (27 bp):
TTTGATGTCATTGCTTACATCATTAGT
Found at i:2813407 original size:21 final size:19
Alignment explanation
Indices: 2813369--2813414 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2813359 AATTAATCCT
2813369 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
2813389 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
2813410 A-TAAT
1 ACTAAT
2813415 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:2823779 original size:21 final size:19
Alignment explanation
Indices: 2823741--2823786 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2823731 AATTAATCCT
2823741 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
2823761 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
2823782 A-TAAT
1 ACTAAT
2823787 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:2825282 original size:55 final size:55
Alignment explanation
Indices: 2825224--2825522 Score: 476
Period size: 55 Copynumber: 5.5 Consensus size: 55
2825214 GGAGTTATCA
* * *
2825224 CACACATGGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTGGGGTTA
1 CACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
*
2825279 CACACATAGTGCTAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
1 CACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
* * *
2825334 CGCACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCATGGGGTTG
1 CACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
* *
2825389 CACACATAGTGCCAATACGAAAATTTATAAACTCATTATGAATTTCGTGAGGTTG
1 CACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
* *
2825444 CACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGGTTG
1 CACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
*
2825499 CACAC--AGTGCCAATACGGAAATTC
1 CACACATAGTGCCAATACGAAAATTC
2825523 CAACATATAC
Statistics
Matches: 229, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
53 19 0.08
55 210 0.92
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (55 bp):
CACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTG
Found at i:2831060 original size:54 final size:55
Alignment explanation
Indices: 2830966--2831125 Score: 162
Period size: 55 Copynumber: 2.9 Consensus size: 55
2830956 TATATGTTGG
* * * *
2830966 AATTTCAGTTTTGGCACTATGTGTGCAACCTCATGA-AATTCA-AATGAGTTTATA
1 AATTTCTGTATTGGCACTATGTGTGCAACCCCA-CATAATTCATAATGAGTTTATA
* * * *
2831020 AATTTCTGTATTGGCATTATGTGTGCAACCCCACATAATTCATAATGAGCTTGTG
1 AATTTCTGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTTTATA
* * * * ** *
2831075 AATTACTGTATCGCCACTAGGTGTGCAAAACCACATAATTTATAATGAGTT
1 AATTTCTGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTT
2831126 GAAATATTCA
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.01
54 35 0.40
55 51 0.59
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (55 bp):
AATTTCTGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTTTATA
Found at i:2850589 original size:22 final size:23
Alignment explanation
Indices: 2850561--2850606 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2850551 AAGATTTTTT
*
2850561 ATGAACAGTA-CTGTGAACAGTG
1 ATGAACAGTACCCGTGAACAGTG
*
2850583 ATGAACATTACCCGTGAACAGTG
1 ATGAACAGTACCCGTGAACAGTG
2850606 A
1 A
2850607 CTGTACCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (23 bp):
ATGAACAGTACCCGTGAACAGTG
Found at i:2853245 original size:24 final size:24
Alignment explanation
Indices: 2853190--2853294 Score: 88
Period size: 24 Copynumber: 4.4 Consensus size: 24
2853180 GGTTTATCTT
* *
2853190 ATTTCTGATTTGAATTCTGTTCTG
1 ATTTCTGATCTGAATTATGTTCTG
** *
2853214 ATACCTGATCTGAATTATGTTATG
1 ATTTCTGATCTGAATTATGTTCTG
*
2853238 ATTTCTGACCT-AGATTATGTTCTG
1 ATTTCTGATCTGA-ATTATGTTCTG
* * *
2853262 ATATT-TGATATGAATTCTGTTTTG
1 AT-TTCTGATCTGAATTATGTTCTG
*
2853286 ATTTATGAT
1 ATTTCTGAT
2853295 ATCTCTGTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
23 3 0.05
24 58 0.91
25 3 0.05
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (24 bp):
ATTTCTGATCTGAATTATGTTCTG
Found at i:2854927 original size:24 final size:24
Alignment explanation
Indices: 2854900--2854984 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
2854890 ATTTTCAATT
* *
2854900 TGAATTCTATTCTGATATCTTATC
1 TGAATTATGTTCTGATATCTTATC
* * * *
2854924 TGAATTATGTTATGATTTCTGACC
1 TGAATTATGTTCTGATATCTTATC
*
2854948 TGGATTATGTTCTGATATCTTATC
1 TGAATTATGTTCTGATATCTTATC
* *
2854972 TGGATTCTGTTCT
1 TGAATTATGTTCT
2854985 TATTTTTGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.49
Consensus pattern (24 bp):
TGAATTATGTTCTGATATCTTATC
Found at i:2856925 original size:16 final size:17
Alignment explanation
Indices: 2856906--2856939 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2856896 TTAAGTGTGT
2856906 TATA-TAAAAACTAATG
1 TATACTAAAAACTAATG
2856922 TATACTTAAAAACTAATG
1 TATAC-TAAAAACTAATG
2856940 ATGCATCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (17 bp):
TATACTAAAAACTAATG
Found at i:2858757 original size:47 final size:47
Alignment explanation
Indices: 2858703--2858875 Score: 253
Period size: 47 Copynumber: 3.7 Consensus size: 47
2858693 TTAAGAGTTT
*
2858703 CTAGGGATTTGAAGAAAAGAAGGACAAAGGACTTTGTTTTAGGGCTG
1 CTAGGGATTTCAAGAAAAGAAGGACAAAGGACTTTGTTTTAGGGCTG
* * * * *
2858750 CTAGGGATTTGAAG--AA-AAGGTCAAATGATTTTGATTTAGGGCTG
1 CTAGGGATTTCAAGAAAAGAAGGACAAAGGACTTTGTTTTAGGGCTG
* *
2858794 CTAGGGATTTCAAGAAAAGAAGGACAAATGATTTTGTTTTAGGGCTG
1 CTAGGGATTTCAAGAAAAGAAGGACAAAGGACTTTGTTTTAGGGCTG
2858841 CTAGGGATTTCAAGAAAAGAAGGACAAAGGACTTT
1 CTAGGGATTTCAAGAAAAGAAGGACAAAGGACTTT
2858876 TAGCCCCATG
Statistics
Matches: 114, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
44 37 0.32
45 2 0.02
46 2 0.02
47 73 0.64
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (47 bp):
CTAGGGATTTCAAGAAAAGAAGGACAAAGGACTTTGTTTTAGGGCTG
Found at i:2859149 original size:29 final size:28
Alignment explanation
Indices: 2859111--2859180 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2859101 TTTGTTGATG
* *
2859111 TTTTATATTTTATTTTTATATTTTGTGAATA
1 TTTTA-ATTTTATTTAT-TATTTT-TCAATA
*
2859142 -TTTAATTTTCTTTATTATTTTTCAATA
1 TTTTAATTTTATTTATTATTTTTCAATA
2859169 TTTTGAATTTTA
1 TTTT-AATTTTA
2859181 AATAATTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 5 0.15
28 9 0.27
29 15 0.45
30 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTAATTTTATTTATTATTTTTCAATA
Found at i:2859257 original size:28 final size:28
Alignment explanation
Indices: 2859216--2859270 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2859206 ATTAAATAAG
2859216 CCCTCAAACATTCTAAAAATCAATTAAA
1 CCCTCAAACATTCTAAAAATCAATTAAA
* *
2859244 CCCTCAAACTTTCTAAAAATCTATTAA
1 CCCTCAAACATTCTAAAAATCAATTAA
2859271 GTTCCTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (28 bp):
CCCTCAAACATTCTAAAAATCAATTAAA
Found at i:2866493 original size:16 final size:18
Alignment explanation
Indices: 2866472--2866508 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2866462 AATATGATGC
2866472 ATATTTTAA-ATATAT-T
1 ATATTTTAATATATATAT
2866488 ATA-TTTAATATATATAT
1 ATATTTTAATATATATAT
2866505 ATAT
1 ATAT
2866509 GTACATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTTAATATATATAT
Found at i:2889970 original size:72 final size:73
Alignment explanation
Indices: 2889890--2890038 Score: 214
Period size: 73 Copynumber: 2.1 Consensus size: 73
2889880 GAAAAATATT
*
2889890 GATATTGTTCATAGTAAATGCACAAAATATGG-TGA-TTTTTAGGGGAATATCGATACTTA-TTT
1 GATATTGTTCATAGTAAAAGCACAAAATA-GGTTGATTTTTTAGGGGAATATCGATACTTATTTT
2889952 AAAGGGTATC
65 AAA-GGTATC
* * * *
2889962 GATATTGTTCATAGTAAAAGTACAAAATAGGTTGATTTTTTAGGTGAGTATCGATATTTATTTTA
1 GATATTGTTCATAGTAAAAGCACAAAATAGGTTGATTTTTTAGGGGAATATCGATACTTATTTTA
2890027 AAGGTATC
66 AAGGTATC
2890035 GATA
1 GATA
2890039 CTCAGGGTCA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
71 2 0.03
72 30 0.43
73 31 0.45
74 6 0.09
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (73 bp):
GATATTGTTCATAGTAAAAGCACAAAATAGGTTGATTTTTTAGGGGAATATCGATACTTATTTTA
AAGGTATC
Found at i:2890126 original size:19 final size:20
Alignment explanation
Indices: 2890101--2890153 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
2890091 TTATACATTT
2890101 TTTGTATCAATACTCTAGGG
1 TTTGTATCAATACTCTAGGG
***
2890121 -TTGTATTGGTAC-CTAGGG
1 TTTGTATCAATACTCTAGGG
2890139 TTATGTATCAATACT
1 TT-TGTATCAATACT
2890154 TCCCATAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
18 6 0.25
19 10 0.42
20 8 0.33
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGTATCAATACTCTAGGG
Found at i:2890263 original size:21 final size:19
Alignment explanation
Indices: 2890228--2890277 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
2890218 CCTTATGAGT
*
2890228 GTATCGATACAAAAGGTATG
1 GTATCGATACAAAAGGT-TA
*
2890248 GTATCGATGCCAAAAGGTTA
1 GTATCGAT-ACAAAAGGTTA
2890268 GTATCGATAC
1 GTATCGATAC
2890278 TATAGTATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 17 0.65
21 8 0.31
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (19 bp):
GTATCGATACAAAAGGTTA
Found at i:2895096 original size:69 final size:69
Alignment explanation
Indices: 2895013--2895145 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 69
2895003 CCTAGCCAAG
* * * *
2895013 GAGGTGAATTAGTTGAGTAACATAATGATTACTCTAGTGAAGGTTCTATGGAGGGACCATGGGGT
1 GAGGTGAATGAGTTGAGGAACATAATGATTACTCTAGTGAAGGTTCTATAGAGGAACCATGGGGT
2895078 CGAT
66 CGAT
*
2895082 GAGGTGAATGAGTTGAGGAACATAATGATTACTCTAGTTAAGGTTCTATAGAGGAACCATGGGG
1 GAGGTGAATGAGTTGAGGAACATAATGATTACTCTAGTGAAGGTTCTATAGAGGAACCATGGGG
2895146 ATGAAGCTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.31, C:0.10, G:0.32, T:0.28
Consensus pattern (69 bp):
GAGGTGAATGAGTTGAGGAACATAATGATTACTCTAGTGAAGGTTCTATAGAGGAACCATGGGGT
CGAT
Found at i:2897300 original size:30 final size:30
Alignment explanation
Indices: 2897245--2897301 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2897235 TTCATCTATA
*
2897245 TTTTATGAATGGATTTTCTTATTAAAATGG
1 TTTTATGAATGGATTTTCATATTAAAATGG
*
2897275 TTTT-TGAATGGTTATTTCATATTAAAA
1 TTTTATGAATGGAT-TTTCATATTAAAA
2897302 ATGAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.51
Consensus pattern (30 bp):
TTTTATGAATGGATTTTCATATTAAAATGG
Found at i:2898561 original size:23 final size:23
Alignment explanation
Indices: 2898531--2898584 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2898521 CCAATATTAC
* *
2898531 TGAAGTGATCGAGCGAATGGGTA
1 TGAAGTGATCAAACGAATGGGTA
2898554 TGAAGTGATCAAACGAATGGGTA
1 TGAAGTGATCAAACGAATGGGTA
*
2898577 TGGAGTGA
1 TGAAGTGA
2898585 AAGAGAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.22
Consensus pattern (23 bp):
TGAAGTGATCAAACGAATGGGTA
Found at i:2913304 original size:16 final size:17
Alignment explanation
Indices: 2913277--2913311 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2913267 TATCGCCAAC
2913277 CAAAATTTTACTATTCA
1 CAAAATTTTACTATTCA
2913294 CAAAA-TTTACTATTCA
1 CAAAATTTTACTATTCA
2913310 CA
1 CA
2913312 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (17 bp):
CAAAATTTTACTATTCA
Found at i:2913822 original size:14 final size:14
Alignment explanation
Indices: 2913803--2913830 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2913793 TTGGCCTACT
2913803 TGCTTGACTTTTCA
1 TGCTTGACTTTTCA
2913817 TGCTTGACTTTTCA
1 TGCTTGACTTTTCA
2913831 ACAGGTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
TGCTTGACTTTTCA
Found at i:2915713 original size:21 final size:22
Alignment explanation
Indices: 2915689--2915732 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2915679 CATTGTTCAT
*
2915689 TACACATGATG-TTATTATGAA
1 TACACATGATGTTTATCATGAA
*
2915710 TACATATGATGTTTATCATGAA
1 TACACATGATGTTTATCATGAA
2915732 T
1 T
2915733 GTTATTTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
TACACATGATGTTTATCATGAA
Found at i:2917969 original size:13 final size:13
Alignment explanation
Indices: 2917943--2917979 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2917933 GTTTAAACCC
2917943 AAATAACAATAATA
1 AAATAAC-ATAATA
2917957 AAATAACATAATA
1 AAATAACATAATA
2917970 AAATAACATA
1 AAATAACATA
2917980 TTCAACTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAACATAATA
Found at i:2921799 original size:21 final size:21
Alignment explanation
Indices: 2921748--2921800 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2921738 ATTATGACTA
2921748 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2921769 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2921790 TCGCAATGCGA
1 TCGCAATGCGA
2921801 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2921881 original size:21 final size:21
Alignment explanation
Indices: 2921851--2921926 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
2921841 ATACTGACTA
*
2921851 TCGCAATGCAATTTTCTTAAT
1 TCGCAATGCAATTTTCATAAT
* * *
2921872 TCGCATTGCAATTTACGT-AT
1 TCGCAATGCAATTTTCATAAT
** *
2921892 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCAATTTTCATAAT
2921913 TCGCAATGCGAATT
1 TCGCAATGC-AATT
2921927 CGTAAATCGC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 16 0.37
21 24 0.56
22 3 0.07
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCAATGCAATTTTCATAAT
Found at i:2921938 original size:20 final size:20
Alignment explanation
Indices: 2921913--2921959 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2921903 TTTTCATAAT
* **
2921913 TCGCAATGCGAATTCGTAAA
1 TCGCAACGCGAATAAGTAAA
*
2921933 TCGCAACGCGAGTAAGTAAA
1 TCGCAACGCGAATAAGTAAA
2921953 TCGCAAC
1 TCGCAAC
2921960 ACGATGGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:2922244 original size:21 final size:21
Alignment explanation
Indices: 2922193--2922245 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2922183 ATTATGACTA
*
2922193 TCGCAATGCAATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2922214 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2922235 TCGCAATGCGA
1 TCGCAATGCGA
2922246 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2922265 original size:41 final size:41
Alignment explanation
Indices: 2922220--2922428 Score: 106
Period size: 41 Copynumber: 5.1 Consensus size: 41
2922210 AATTTCGCGT
**
2922220 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
** * * * *
2922261 TGCGAATTTGGA-AAATCACAATGCG-AT-ACTGACTATCGCAA
1 TGCG-ATTTTCATAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
2922302 TGCAATTTTCTTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCATAATTCGCAATGCGA-ATAAGTAAATCGCAA
* **
2922343 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCATAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
* * * * * *
2922384 CGTGA--TTAAGTAAATCGCAACGCGATTAAGTAAATCGCAA
1 TGCGATTTTCA-TAATTCGCAATGCGAATAAGTAAATCGCAA
2922424 TGCGA
1 TGCGA
2922429 ATTAGGAAAA
Statistics
Matches: 118, Mismatches: 41, Indels: 19
0.66 0.23 0.11
Matches are distributed among these distances:
39 5 0.04
40 39 0.33
41 68 0.58
42 4 0.03
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:2922330 original size:21 final size:21
Alignment explanation
Indices: 2922296--2922368 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
2922286 ATACTGACTA
* *
2922296 TCGCAATGCAATTTTCTTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
2922317 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
2922337 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
2922358 TCGCAATGCGA
1 TCGCAATGCGA
2922369 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:2922349 original size:445 final size:445
Alignment explanation
Indices: 2921520--2922409 Score: 1699
Period size: 445 Copynumber: 2.0 Consensus size: 445
2921510 GATGTCGTTG
2921520 GGGTGATCACAAAATTTCTCCTATCCTCGCTTTGTGATCATTTTGGAGATGTAATAAAAAATAGA
1 GGGTGATCACAAAATTTCTCCTATCCTCGCTTTGTGATCATTTTGGAGATGTAATAAAAAATAGA
2921585 GAAAATAACCTCAGTGACCAAAAATCCCATATAATATACGATTTTAACCAACTTTTTTCGGATTT
66 GAAAATAACCTCAGTGACCAAAAATCCCATATAATATACGATTTTAACCAACTTTTTTCGGATTT
*
2921650 GCCAAAATGACCAACAAAATCTCAATGCGATCGCTAATTCGCAACGCGATCTCCATTTTCGCAAA
131 GCCAAAATGACCAACAAAATCTCAATGCGATCGCTAATTCGCAACGCGATCTCCATTATCGCAAA
*
2921715 TCAATTTCCAGATTCGCAACGCGATTATGACTATCGCAATGCGATTTTCCAATTTCGCGTTGCGA
196 TCAATTTCCAGATTCGCAACGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCGTTGCGA
2921780 TTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCACAATGCGATAC
261 TTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCACAATGCGATAC
2921845 TGACTATCGCAATGCAATTTTCTTAATTCGCATTGCAATTTACGTATTCGCGTTGCGATTTTCAT
326 TGACTATCGCAATGCAATTTTCTTAATTCGCATTGCAATTTACGTATTCGCGTTGCGATTTTCAT
* *
2921910 AATTCGCAATGCGAATTCGTAAATCGCAACGCGAGTAAGTAAATCGCAACACGAT
391 AATTCGCAATGCGAATACGTAAATCACAACGCGAGTAAGTAAATCGCAACACGAT
2921965 GGGTGATCACAAAATTTCTCCTATCCTCGCTTTGTGATCATTTTGGAGATGTAATAAAAAATAGA
1 GGGTGATCACAAAATTTCTCCTATCCTCGCTTTGTGATCATTTTGGAGATGTAATAAAAAATAGA
2922030 GAAAATAACCTCAGTGACCAAAAATCCCATATAATATACGATTTTAACCAACTTTTTTCGGATTT
66 GAAAATAACCTCAGTGACCAAAAATCCCATATAATATACGATTTTAACCAACTTTTTTCGGATTT
2922095 GCCAAAATGACCAACAAAATCTCAATGCGATCGCTAATTCGCAACGCGATCTCCATTATCGCAAA
131 GCCAAAATGACCAACAAAATCTCAATGCGATCGCTAATTCGCAACGCGATCTCCATTATCGCAAA
2922160 TCAATTTCCAGATTCGCAACGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCGTTGCGA
196 TCAATTTCCAGATTCGCAACGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCGTTGCGA
2922225 TTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCACAATGCGATAC
261 TTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCACAATGCGATAC
*
2922290 TGACTATCGCAATGCAATTTTCTTAATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCAT
326 TGACTATCGCAATGCAATTTTCTTAATTCGCATTGCAATTTACGTATTCGCGTTGCGATTTTCAT
* * * *
2922355 AATTCGCAATGCGAATACGTAAATCATAACGTGATTAAGTAAATCGCAACGCGAT
391 AATTCGCAATGCGAATACGTAAATCACAACGCGAGTAAGTAAATCGCAACACGAT
2922410 TAAGTAAATC
Statistics
Matches: 436, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
445 436 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (445 bp):
GGGTGATCACAAAATTTCTCCTATCCTCGCTTTGTGATCATTTTGGAGATGTAATAAAAAATAGA
GAAAATAACCTCAGTGACCAAAAATCCCATATAATATACGATTTTAACCAACTTTTTTCGGATTT
GCCAAAATGACCAACAAAATCTCAATGCGATCGCTAATTCGCAACGCGATCTCCATTATCGCAAA
TCAATTTCCAGATTCGCAACGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCGTTGCGA
TTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCACAATGCGATAC
TGACTATCGCAATGCAATTTTCTTAATTCGCATTGCAATTTACGTATTCGCGTTGCGATTTTCAT
AATTCGCAATGCGAATACGTAAATCACAACGCGAGTAAGTAAATCGCAACACGAT
Found at i:2922420 original size:20 final size:20
Alignment explanation
Indices: 2922358--2922449 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
2922348 TTTTCATAAT
* *
2922358 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTAAGTAAA
** * *
2922378 TCATAACGTGATTAAGTAAA
1 TCGCAATGCGATTAAGTAAA
*
2922398 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGATTAAGTAAA
* *
2922418 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTAAGTAAA
2922439 TCGCAATGCGA
1 TCGCAATGCGA
2922450 ATCTTACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 41 0.69
21 18 0.31
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGATTAAGTAAA
Found at i:2922439 original size:21 final size:21
Alignment explanation
Indices: 2922388--2922451 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
2922378 TCATAACGTG
* *
2922388 ATTAAGTAAATCGCAACGCG-
1 ATTAAGAAAATCGCAATGCGA
*
2922408 ATTAAGTAAATCGCAATGCGA
1 ATTAAGAAAATCGCAATGCGA
*
2922429 ATTAGGAAAATCGCAATGCGA
1 ATTAAGAAAATCGCAATGCGA
2922450 AT
1 AT
2922452 CTTACTATCG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (21 bp):
ATTAAGAAAATCGCAATGCGA
Found at i:2923064 original size:19 final size:19
Alignment explanation
Indices: 2923042--2923197 Score: 125
Period size: 19 Copynumber: 8.6 Consensus size: 19
2923032 ATCGCATTGT
*
2923042 GATTTTTATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
2923061 GATTCTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
2923080 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
2923094 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
** *
2923113 GATAGTCACTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
2923132 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
**
2923146 GATAGTCATTTCTGCGTTGC
1 GATTTTCATTTC-GCGTTGC
* *
2923166 GATTCTCATTATCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
2923186 GATTTTCATTTC
1 GATTTTCATTTC
2923198 AACCAAAGAC
Statistics
Matches: 109, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
14 20 0.18
16 5 0.05
17 4 0.04
19 49 0.45
20 29 0.27
21 2 0.02
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:2923126 original size:52 final size:52
Alignment explanation
Indices: 2923042--2923189 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 52
2923032 ATCGCATTGT
* * *
2923042 GATTTTTATTTCGCGTTGCGATTCTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATACTCACTTCGCGTTGCGATTCTCTCGTTGC
*
2923094 GATTTTCATTTCGCGTTGCGATAGTCACTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATACTCACTTCGCGTTGCGATTCTCTCGTTGC
** * * *
2923146 GATAGTCATTTCTGCGTTGCGATTCTCATTATCTCGTTGCGATT
1 GATTTTCATTTC-GCGTTGCGATACTCACT-TCGCGTTGCGATT
2923190 TTCATTTCAA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 58 0.69
53 14 0.17
54 12 0.14
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (52 bp):
GATTTTCATTTCGCGTTGCGATACTCACTTCGCGTTGCGATTCTCTCGTTGC
Found at i:2923144 original size:33 final size:34
Alignment explanation
Indices: 2923107--2923172 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
2923097 TTTCATTTCG
2923107 CGTTGCGATAGTCACTTC-GCGTTGCGATTCTCT
1 CGTTGCGATAGTCACTTCTGCGTTGCGATTCTCT
*
2923140 CGTTGCGATAGTCATTTCTGCGTTGCGATTCTC
1 CGTTGCGATAGTCACTTCTGCGTTGCGATTCTC
2923173 ATTATCTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCACTTCTGCGTTGCGATTCTCT
Found at i:2926887 original size:19 final size:19
Alignment explanation
Indices: 2926863--2926927 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
2926853 AAAAAGTACT
2926863 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2926882 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2926896 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2926915 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2926928 TTTCATTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2926945 original size:19 final size:19
Alignment explanation
Indices: 2926923--2926976 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
2926913 AAATCGCAAC
2926923 GCGAATTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
2926942 GCG-A-TTC---TCG--TT
1 GCGAATTTCATTTCGCATT
*
2926954 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
2926973 GCGA
1 GCGA
2926977 TAGTAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 14
0.64 0.02 0.33
Matches are distributed among these distances:
12 5 0.19
14 6 0.22
17 6 0.22
18 1 0.04
19 9 0.33
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:2929260 original size:12 final size:12
Alignment explanation
Indices: 2929243--2929267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2929233 TCTTCGGGGA
2929243 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2929255 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2929267 C
1 C
2929268 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:2929494 original size:24 final size:22
Alignment explanation
Indices: 2929451--2929503 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
2929441 AAAATCCGAG
*
2929451 TATTGACCAATCAAAGTTCGGA
1 TATTGACCAATCAAAGTTCGAA
*
2929473 TATTGACCAAGATCAAATTTCGAA
1 TATTGACC-A-ATCAAAGTTCGAA
*
2929497 TACTGAC
1 TATTGAC
2929504 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 1 0.04
24 17 0.65
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (22 bp):
TATTGACCAATCAAAGTTCGAA
Found at i:2930318 original size:20 final size:20
Alignment explanation
Indices: 2930271--2930320 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2930261 GAGATAATAC
*
2930271 AAAATCACAACAAGATTCTG
1 AAAATCGCAACAAGATTCTG
*** *
2930291 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACAAGATTCTG
2930311 AAAATCGCAA
1 AAAATCGCAA
2930321 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACAAGATTCTG
Found at i:2932097 original size:40 final size:42
Alignment explanation
Indices: 2932053--2932142 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 42
2932043 CCTCTTCAAC
*
2932053 GATGACAGCGGCCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGACAGCGGCCTCTTGAACGAGTGGAGGAGACTCTTGAGG
* * * *
2932093 GATGATAGGGGCCTCTTGAACGATTGGAGGATACTCTTGAGG
1 GATGACAGCGGCCTCTTGAACGAGTGGAGGAGACTCTTGAGG
*
2932135 AATGACAG
1 GATGACAG
2932143 GTGAGTCGGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 20 0.49
41 3 0.07
42 18 0.44
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGCGGCCTCTTGAACGAGTGGAGGAGACTCTTGAGG
Found at i:2932496 original size:20 final size:20
Alignment explanation
Indices: 2932471--2932523 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2932461 GAAGAATAGT
*
2932471 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
2932491 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
2932511 TGACTATCGCAAC
1 TTACTTTCGCAAC
2932524 GGAAATGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:2932531 original size:18 final size:19
Alignment explanation
Indices: 2932477--2932566 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 19
2932467 TAGTTTACTT
* * *
2932477 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAA-TGACTA
2932497 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
2932517 TCGCAACG-GAAATGACT-
1 TCGCAACGCGAAATGACTA
*
2932534 T-GCAACGC-AAATGGCTA
1 TCGCAACGCGAAATGACTA
*
2932551 TCGCAATGCGAAATGA
1 TCGCAACGCGAAATGA
2932567 AAATCGCAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
16 13 0.22
17 2 0.03
18 14 0.24
19 6 0.10
20 21 0.36
21 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:2932540 original size:16 final size:18
Alignment explanation
Indices: 2932497--2932566 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
2932487 AAACTTACTT
2932497 TCGCAACGCGAAAATGACTA
1 TCGCAACGC--AAATGACTA
*
2932517 TCGCAACGGAAATGACT-
1 TCGCAACGCAAATGACTA
*
2932534 T-GCAACGCAAATGGCTA
1 TCGCAACGCAAATGACTA
*
2932551 TCGCAATGCGAAATGA
1 TCGCAACGC-AAATGA
2932567 AAATCGCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 13 0.31
17 2 0.05
18 14 0.33
19 5 0.12
20 8 0.19
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (18 bp):
TCGCAACGCAAATGACTA
Found at i:2932552 original size:34 final size:36
Alignment explanation
Indices: 2932499--2932566 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 36
2932489 ACTTACTTTC
2932499 GCAACGCGAAAATGACTATCGCAACG-GAAATGACTT
1 GCAACGC-AAAATGACTATCGCAACGCGAAATGACTT
* *
2932535 GCAACGC-AAATGGCTATCGCAATGCGAAATGA
1 GCAACGCAAAATGACTATCGCAACGCGAAATGA
2932567 AAATCGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 15 0.52
35 7 0.24
36 7 0.24
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (36 bp):
GCAACGCAAAATGACTATCGCAACGCGAAATGACTT
Found at i:2932572 original size:19 final size:19
Alignment explanation
Indices: 2932550--2932608 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
2932540 GCAAATGGCT
2932550 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2932569 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
2932583 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2932602 ATCGCAA
1 ATCGCAA
2932609 CGACAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2932590 original size:33 final size:33
Alignment explanation
Indices: 2932550--2932628 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
2932540 GCAAATGGCT
*
2932550 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2932583 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
2932616 AACGCAACGCGAA
1 ATCGCAATGCGAA
2932629 CACAATCGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2932661 original size:19 final size:19
Alignment explanation
Indices: 2932634--2932713 Score: 107
Period size: 19 Copynumber: 4.5 Consensus size: 19
2932624 GCGAACACAA
2932634 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2932653 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2932672 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2932688 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2932705 TCGCATTGC
1 TCGCATTGC
2932714 AATAGCCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 32 0.62
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2933300 original size:18 final size:18
Alignment explanation
Indices: 2933279--2933326 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2933269 AGGGTCGATC
*
2933279 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
*
2933297 AGGTGATAGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
2933315 AGGTGATGGCTC
1 AGGTGATGGCTC
2933327 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:2934679 original size:20 final size:20
Alignment explanation
Indices: 2934631--2934689 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2934621 AATAGTTTCT
* *
2934631 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
2934651 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
2934671 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
2934690 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:2934979 original size:22 final size:22
Alignment explanation
Indices: 2934952--2934995 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2934942 GATGGAGATA
2934952 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
2934974 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
2934996 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.45, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:2935160 original size:20 final size:20
Alignment explanation
Indices: 2935135--2935212 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
2935125 TATTATCTCA
*
2935135 TTGCGAAAGTCAGTATTGAG
1 TTGCGAAAGTCAGTATCGAG
* *
2935155 TTGCGAAATTAAGTATCGAG
1 TTGCGAAAGTCAGTATCGAG
2935175 TTGCGAAAGTCAGTATCGAG
1 TTGCGAAAGTCAGTATCGAG
2935195 TTGCGAAAGTCAGTATCG
1 TTGCGAAAGTCAGTATCG
2935213 CATTGCGATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGAG
Found at i:2935180 original size:40 final size:40
Alignment explanation
Indices: 2935128--2935220 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
2935118 GATTATGTAT
* * *
2935128 TATCTCATTGCGAAAGTCAGTATTGAGTTGCGAAATTAAG
1 TATCGCATTGCGAAAGTCAGTATCGAGTTGCGAAAGTAAG
*
2935168 TATCG-AGTTGCGAAAGTCAGTATCGAGTTGCGAAAGTCAG
1 TATCGCA-TTGCGAAAGTCAGTATCGAGTTGCGAAAGTAAG
2935208 TATCGCATTGCGA
1 TATCGCATTGCGA
2935221 TTTTGTATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 45 0.96
41 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (40 bp):
TATCGCATTGCGAAAGTCAGTATCGAGTTGCGAAAGTAAG
Found at i:2935247 original size:41 final size:40
Alignment explanation
Indices: 2935188--2935324 Score: 157
Period size: 41 Copynumber: 3.4 Consensus size: 40
2935178 CGAAAGTCAG
* * **
2935188 TATCGAGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCA
* *
2935228 TTATCGCGTTGCGATAGTCAGTACCGCGTTGCGATTTTCCA
1 -TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCA
* *
2935269 AATTCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCA
1 TA-TCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCA
* *
2935310 AATTCGCATTGCGAT
1 TA-TCGCGTTGCGAT
2935325 TTACTTATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 84 0.99
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (40 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCA
Found at i:2935282 original size:21 final size:21
Alignment explanation
Indices: 2935256--2935326 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
2935246 CAGTACCGCG
2935256 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
** *
2935277 TTGCGATAGT-C-AGTATCGCA
1 TTGCGATTTTCCAAAT-TCGCA
2935297 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
2935318 TTGCGATTT
1 TTGCGATTT
2935327 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.34
21 23 0.56
22 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:2935303 original size:20 final size:20
Alignment explanation
Indices: 2935128--2935303 Score: 110
Period size: 20 Copynumber: 8.7 Consensus size: 20
2935118 GATTATGTAT
* *
2935128 TATCTCATTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * * *
2935148 TATTG-AGTTGCGAAATTAAG
1 TATCGCA-TTGCGATAGTCAG
*
2935168 TATCG-AGTTGCGAAAGTCAG
1 TATCGCA-TTGCGATAGTCAG
*
2935188 TATCG-AGTTGCGAAAGTCAG
1 TATCGCA-TTGCGATAGTCAG
* *
2935208 TATCGCATTGCGATTTTGT-AT
1 TATCGCATTGCGA--TAGTCAG
*
2935229 TATCGCGTTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
* * **
2935249 TACCGCGTTGCGATTTTCCA-
1 TATCGCATTGCGATAGT-CAG
*
2935269 AATTCGCATTGCGATAGTCAG
1 TA-TCGCATTGCGATAGTCAG
2935290 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2935304 TTTCCAAATT
Statistics
Matches: 126, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.03
20 92 0.73
21 28 0.22
22 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:2935336 original size:20 final size:21
Alignment explanation
Indices: 2935256--2935340 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 21
2935246 CAGTACCGCG
*
2935256 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTACAAATTCGCA
** *
2935277 TTGCGATAGT-C-AGTATCGCA
1 TTGCGATTTTACAAAT-TCGCA
*
2935297 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTACAAATTCGCA
**
2935318 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTACAAATTCGCA
2935338 TTG
1 TTG
2935341 TGAATTGGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 28 0.54
21 20 0.38
22 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTACAAATTCGCA
Found at i:2949754 original size:23 final size:23
Alignment explanation
Indices: 2949676--2949756 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
2949666 CGTATAAATA
* * *
2949676 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCGCATAGAATTC
* * * *
2949699 TACCAAAATGCCGCATAGAATTG
1 CACCGAAGTGCCGCATAGAATTC
* *
2949722 CACTGAAGTGCCGCGTAGAATTC
1 CACCGAAGTGCCGCATAGAATTC
*
2949745 CACCGTAGTGCC
1 CACCGAAGTGCC
2949757 ATATAAGATG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCGCATAGAATTC
Found at i:2950492 original size:66 final size:66
Alignment explanation
Indices: 2950363--2950492 Score: 145
Period size: 66 Copynumber: 2.0 Consensus size: 66
2950353 TTTTTCCTTT
* * * * * *
2950363 AGGGGGTATCGATACCCTACTTAAGCTATCGATACCCTCATGGCATTTTGAAATTTTTTTCGTTC
1 AGGGGGTATCGATACCCAACTTAAGCTATCGACACCCTCATGACATTATGAAATTCTTCTCGTTC
2950428 A
66 A
* * * * *
2950429 AGGGGGTATCGGTACCCAAC-TAGGGGTATCGACACCCTTATGACATTATGCAATTCTTCTCGTT
1 AGGGGGTATCGATACCCAACTTA-AGCTATCGACACCCTCATGACATTATGAAATTCTTCTCGTT
2950493 TGAGAAGGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
65 2 0.04
66 50 0.96
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (66 bp):
AGGGGGTATCGATACCCAACTTAAGCTATCGACACCCTCATGACATTATGAAATTCTTCTCGTTC
A
Found at i:2950683 original size:20 final size:21
Alignment explanation
Indices: 2950646--2950684 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2950636 ACTCATTCCT
2950646 ACTCAATAATCACTTCCTTAA
1 ACTCAATAATCACTTCCTTAA
2950667 ACTCAA-AATC-CTATCCTT
1 ACTCAATAATCACT-TCCTT
2950685 TATATGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (21 bp):
ACTCAATAATCACTTCCTTAA
Found at i:2952780 original size:14 final size:14
Alignment explanation
Indices: 2952761--2952800 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2952751 TGATAAAATC
*
2952761 TAAAAAAATAAACA
1 TAAAAAAATAAAAA
2952775 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
*
2952789 TAAATAAATAAA
1 TAAAAAAATAAA
2952801 GTATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:2955709 original size:2 final size:2
Alignment explanation
Indices: 2955702--2955734 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2955692 ATTCAATTGA
2955702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2955735 ACATCAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2958347 original size:55 final size:55
Alignment explanation
Indices: 2958188--2958495 Score: 492
Period size: 55 Copynumber: 5.6 Consensus size: 55
2958178 AGTTCACCTC
* * * * * *
2958188 CTTATTATGAATGTCTT-ATGTTTACACATATAGTTCTCATACGGAAATTCATACA
1 CTTAGTATGAATTTCTTAAT-TTTGCACACATAGTGCCCATACGGAAATTCATACA
*
2958243 CTTAGTATAAATTTCTTAATTTTTGCACACATAGTGCCCATACGGAAATTCATACA
1 CTTAGTATGAATTTCTTAA-TTTTGCACACATAGTGCCCATACGGAAATTCATACA
* *
2958299 CTTAGTATGAATTTCTTAATTTTGCACAAATAGTGCCAATACGGAAATTCATACA
1 CTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACA
* *
2958354 CTTAGTATGAATTTCTTAATTTTTCACACATAGTGCCCATACGGAAATTTATACA
1 CTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACA
2958409 CTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACA
1 CTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACA
2958464 CTTAGTATGAATTTCTTAATTTTGCACACATA
1 CTTAGTATGAATTTCTTAATTTTGCACACATA
2958496 CTACCATTCG
Statistics
Matches: 235, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
55 184 0.78
56 50 0.21
57 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.37
Consensus pattern (55 bp):
CTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCCATACGGAAATTCATACA
Found at i:2958881 original size:19 final size:21
Alignment explanation
Indices: 2958839--2958891 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
2958829 ACCCCTACCG
2958839 TGGTATCGATACTACTATACTA
1 TGGTATCGATACTACTATA-TA
2958861 TGGTATCGATACT-CTAT-TA
1 TGGTATCGATACTACTATATA
*
2958880 TGGTATTGATAC
1 TGGTATCGATAC
2958892 CATTTTTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGGTATCGATACTACTATATA
Found at i:2961821 original size:46 final size:45
Alignment explanation
Indices: 2961765--2961851 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 45
2961755 TGCACATATC
*
2961765 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTG
* * *
2961811 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCA
1 ATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCA
2961852 CAATGGGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 14 0.39
46 19 0.53
47 3 0.08
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (45 bp):
ATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTG
Found at i:2969149 original size:21 final size:21
Alignment explanation
Indices: 2969107--2969150 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2969097 ACTCCGGGAG
* *
2969107 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
2969128 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
2969149 CT
1 CT
2969151 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Done.