Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 29
Found at i:5004073 original size:20 final size:20
Alignment explanation
Indices: 5004048--5004103 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5004038 GTGAAAGTTG
*
5004048 TCCCGAATGACCTATGTATA
1 TCCCGAAAGACCTATGTATA
* * * *
5004068 TCCCGAAGGATCTCTGTATG
1 TCCCGAAAGACCTATGTATA
*
5004088 TCTCGAAAGACCTATG
1 TCCCGAAAGACCTATG
5004104 AACCCTCGAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
TCCCGAAAGACCTATGTATA
Found at i:5015379 original size:20 final size:20
Alignment explanation
Indices: 5015343--5015380 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5015333 TCCATTTAAC
*
5015343 ACAACAAATCAAATATTTCA
1 ACAACAAATAAAATATTTCA
5015363 ACAACAAA-AAAATTATTT
1 ACAACAAATAAAA-TATTT
5015381 TTCCGTTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (20 bp):
ACAACAAATAAAATATTTCA
Found at i:5015928 original size:42 final size:42
Alignment explanation
Indices: 5015869--5015972 Score: 163
Period size: 42 Copynumber: 2.5 Consensus size: 42
5015859 ATAAACAAGT
* * * *
5015869 AAATAAATAATATCATAACACCATTAACTCTCAATAAGTCTA
1 AAATAAATAACACCATAACACCATTAAATCTCAATAAATCTA
5015911 AAATAAATAACACCATAACACCATTAAATCTCAATAAATCTA
1 AAATAAATAACACCATAACACCATTAAATCTCAATAAATCTA
*
5015953 AAATAAATAACACCGTAACA
1 AAATAAATAACACCATAACA
5015973 ATAGTAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (42 bp):
AAATAAATAACACCATAACACCATTAAATCTCAATAAATCTA
Found at i:5017659 original size:136 final size:136
Alignment explanation
Indices: 5017415--5017686 Score: 481
Period size: 136 Copynumber: 2.0 Consensus size: 136
5017405 GATTCTTCAA
* *
5017415 TTTTCCATGCCTGAGGGGGCTACTGATTTGATGGTCAGGGAAATTTCTGACAAGGAGATTAAAGA
1 TTTTCCATGCCTGAGGGGGCTACTAATTTGATGGTCAGGGAAATTTATGACAAGGAGATTAAAGA
*
5017480 TGCTATATTTTGTTAGGGAGATGATAAATCTCCTGGTTCGGATGGGTTCATTGTTTTCTTCTTTA
66 TGCTATATTTTGTTAGGGAGATGATAAATCTCCTGGTCCGGATGGGTTCATTGTTTTCTTCTTTA
5017545 AAGTTG
131 AAGTTG
* *
5017551 TTTTCCATGCCTGAGGGGGCTGCTAATTTGATGGTCAGGGAGATTTATGACAAGGAGATTAAAGA
1 TTTTCCATGCCTGAGGGGGCTACTAATTTGATGGTCAGGGAAATTTATGACAAGGAGATTAAAGA
* *
5017616 TGCTATATTTTGTTAGGGAGATGATAAATCTCCTGGTCCGGATGGGTTTATTTTTTTCTTCTTTA
66 TGCTATATTTTGTTAGGGAGATGATAAATCTCCTGGTCCGGATGGGTTCATTGTTTTCTTCTTTA
5017681 AAGTTG
131 AAGTTG
5017687 CAATGGAAGA
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 129 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (136 bp):
TTTTCCATGCCTGAGGGGGCTACTAATTTGATGGTCAGGGAAATTTATGACAAGGAGATTAAAGA
TGCTATATTTTGTTAGGGAGATGATAAATCTCCTGGTCCGGATGGGTTCATTGTTTTCTTCTTTA
AAGTTG
Found at i:5023488 original size:176 final size:176
Alignment explanation
Indices: 5023194--5023545 Score: 571
Period size: 176 Copynumber: 2.0 Consensus size: 176
5023184 GGGGTCGCTA
**
5023194 GGGAGCAGTTGGATGATATCCTTGGTTGCACGGGGTTTCATATTGACAGTCTGCCTGCCTGTTAT
1 GGGAGCAACTGGATGATATCCTTGGTTGCACGGGGTTTCATATTGACAGTCTGCCTGCCTGTTAT
* * * *
5023259 TTAGGGGTGTCTTTTGTAACTAGGAAACTCTCGGAGAAGGATTGTGCTCTGCTTATTGCTAAGAT
66 TTAGGGGTGCCTCTTGTAACTAGGAAACTCTCGGAGAAGGATTGTACTCTGCTTAGTGCTAAGAT
* *
5023324 TCGTGGTAGGCTAGGTTGTTGGGAGAACAAGCATTTGAGCTATGCT
131 TCGTGATAGGCTAGGTTGTTGGGAGAACAAGAATTTGAGCTATGCT
* **
5023370 GGGAGCAACTGGATGATATCCTTGGTTGCGCGGGGTTTCATATTGGTAGTCTGCCTGTCC-GTTA
1 GGGAGCAACTGGATGATATCCTTGGTTGCACGGGGTTTCATATTGACAGTCTGCCTG-CCTGTTA
*
5023434 TTTAGGGGTGCCTCTTGTAACTAGGAAACTCTCGGATAAGGATTGTACTCTGCTTAGTGCTAAGA
65 TTTAGGGGTGCCTCTTGTAACTAGGAAACTCTCGGAGAAGGATTGTACTCTGCTTAGTGCTAAGA
*
5023499 TTCGTGATAGGCTAGGTTGTTTGGAGAACAAGAATTTGAGCTATGCT
130 TTCGTGATAGGCTAGGTTGTTGGGAGAACAAGAATTTGAGCTATGCT
5023546 AGAAGGCTCC
Statistics
Matches: 162, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 160 0.99
177 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (176 bp):
GGGAGCAACTGGATGATATCCTTGGTTGCACGGGGTTTCATATTGACAGTCTGCCTGCCTGTTAT
TTAGGGGTGCCTCTTGTAACTAGGAAACTCTCGGAGAAGGATTGTACTCTGCTTAGTGCTAAGAT
TCGTGATAGGCTAGGTTGTTGGGAGAACAAGAATTTGAGCTATGCT
Found at i:5028496 original size:13 final size:13
Alignment explanation
Indices: 5028478--5028504 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5028468 ATAATTCCAT
5028478 CGACATACACCAA
1 CGACATACACCAA
5028491 CGACATACACCAA
1 CGACATACACCAA
5028504 C
1 C
5028505 ATACAGGGGG
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:0.41, G:0.07, T:0.07
Consensus pattern (13 bp):
CGACATACACCAA
Found at i:5029611 original size:22 final size:22
Alignment explanation
Indices: 5029581--5029646 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
5029571 TTCGCGAACA
*
5029581 TGTTCGTTTAGCGTTCATTTAT
1 TGTTTGTTTAGCGTTCATTTAT
** *
5029603 TGTTTGTTTAGCGTTGTTTTAG
1 TGTTTGTTTAGCGTTCATTTAT
* * *
5029625 TGTTTGTCTATCGTTCGTTTAT
1 TGTTTGTTTAGCGTTCATTTAT
5029647 ATATTCTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (22 bp):
TGTTTGTTTAGCGTTCATTTAT
Found at i:5031498 original size:23 final size:24
Alignment explanation
Indices: 5031467--5031513 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5031457 ATATTTATAT
5031467 ATTTATACATAATCAACTAAATAA
1 ATTTATACATAATCAACTAAATAA
* *
5031491 ATTT-TACATATTCAATTAAATAA
1 ATTTATACATAATCAACTAAATAA
5031514 TATCCAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTTATACATAATCAACTAAATAA
Found at i:5043373 original size:54 final size:54
Alignment explanation
Indices: 5043285--5043501 Score: 353
Period size: 54 Copynumber: 3.9 Consensus size: 54
5043275 GATTATGTTT
*
5043285 ATTTTAATTTATTAAAATTATGATCAAATTTATAAAACATATGAATAACATAGATATA
1 ATTTTAATTTATT--AA--ATGATCAAATTTATAAAACATATGAATAACATGGATATA
*
5043343 ATTTTAATTTATTAAATGATCAAATTTATAAAATATATGAATAACATGGATATA
1 ATTTTAATTTATTAAATGATCAAATTTATAAAACATATGAATAACATGGATATA
*
5043397 ATTTTAATTTATTAAATGATCAAATTTATAAAACACATGAATAACATGGATATA
1 ATTTTAATTTATTAAATGATCAAATTTATAAAACATATGAATAACATGGATATA
* *
5043451 ATTTTAATTTATTAAATGATCAAATTTATAAAATATATGAATAATATGGAT
1 ATTTTAATTTATTAAATGATCAAATTTATAAAACATATGAATAACATGGAT
5043502 TAAATGTAAA
Statistics
Matches: 152, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
54 137 0.90
56 2 0.01
58 13 0.09
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (54 bp):
ATTTTAATTTATTAAATGATCAAATTTATAAAACATATGAATAACATGGATATA
Found at i:5045170 original size:21 final size:20
Alignment explanation
Indices: 5045084--5045241 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
5045074 AAATGACCAA
**
5045084 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5045103 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5045123 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5045143 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5045164 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5045185 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5045205 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5045226 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5045242 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5045232 original size:20 final size:20
Alignment explanation
Indices: 5045208--5045457 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
5045198 CGATTTTCCA
** *
5045208 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
5045228 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
5045248 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
5045268 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
5045288 AAATCGCAACGC-ATATGGGT
1 AAATCGCAACGCGA-ATCCGT
* *
5045308 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5045328 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5045348 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
5045368 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5045388 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
5045408 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5045428 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
5045448 AAATCACAAC
1 AAATCGCAAC
5045458 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:5046179 original size:24 final size:24
Alignment explanation
Indices: 5046140--5046186 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5046130 AAATTTGGTC
5046140 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5046164 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5046187 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5048760 original size:19 final size:19
Alignment explanation
Indices: 5048720--5048817 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
5048710 GATTCTCTCG
5048720 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5048740 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5048759 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
5048773 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5048792 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5048811 TTGCGAT
1 TTGCGAT
5048818 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 40 0.56
20 15 0.21
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5048768 original size:53 final size:52
Alignment explanation
Indices: 5048701--5048817 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 52
5048691 GAAATGAAAA
*
5048701 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCATTGCGATTTTCATTT-CGCATTGCGATTTTCATT
5048754 TCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
5048806 TCGCATTGCGAT
1 TCGCATTGCGAT
5048818 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:5050921 original size:19 final size:19
Alignment explanation
Indices: 5050881--5050979 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
5050871 TAGTTTACTT
* *
5050881 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
5050901 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
5050920 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
5050939 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
5050953 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
5050972 TCGCAACG
1 TCGCAACG
5050980 AAAGAATTGC
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.58
20 13 0.19
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:5050960 original size:33 final size:33
Alignment explanation
Indices: 5050918--5051010 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5050908 GCGAAACCAA
*
5050918 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
5050951 AATCGCAACGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5050984 AATTGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5051011 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5051007 original size:52 final size:50
Alignment explanation
Indices: 5050883--5051015 Score: 133
Period size: 52 Copynumber: 2.6 Consensus size: 50
5050873 GTTTACTTTC
* *
5050883 GCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAAT
1 GCAACACGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAAT
* * * *
5050934 G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAAAGAATT
1 GCAACA-CGAAATGA-A-AATCGCAACGCGAAACCAAAATCGCAACG--AGAAAT
* *
5050988 GCAACGCGAAATGAAAATCGCAATGCGA
1 GCAACACGAAATGAAAATCGCAACGCGA
5051016 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
50 4 0.06
51 6 0.09
52 41 0.63
53 1 0.02
54 11 0.17
55 2 0.03
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.10
Consensus pattern (50 bp):
GCAACACGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAAT
Found at i:5051015 original size:19 final size:18
Alignment explanation
Indices: 5050897--5051015 Score: 101
Period size: 19 Copynumber: 6.8 Consensus size: 18
5050887 CACGAAACTT
*
5050897 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-G
5050916 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-G
*
5050935 AAAATCGCAA--CGACAG
1 AAAATCGCAACGCGAAAG
*
5050951 --AATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-G
5050968 AAAATCGCAA--CGAAAG
1 AAAATCGCAACGCGAAAG
*
5050984 --AATTGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-G
*
5051001 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
5051016 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
14 15 0.19
16 10 0.12
17 10 0.12
19 46 0.57
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAG
Found at i:5051033 original size:19 final size:19
Alignment explanation
Indices: 5051011--5051140 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
5051001 AAAATCGCAA
5051011 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5051030 TGCGATTCTT-G--T--CGT
1 TGCGATT-TTGGTTTCGCGT
5051045 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5051064 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5051078 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5051097 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5051116 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5051136 TGCGA
1 TGCGA
5051141 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
14 13 0.14
15 11 0.12
16 1 0.01
17 3 0.03
18 1 0.01
19 48 0.52
20 15 0.16
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5051080 original size:14 final size:14
Alignment explanation
Indices: 5051027--5051084 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
5051017 TTTGGTTTCG
5051027 CGTTGCGATTCTTGT
1 CGTTGCGATTC-TGT
*
5051042 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
5051059 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
5051075 CGTTGCGATT
1 CGTTGCGATT
5051085 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.31
15 11 0.31
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.19, G:0.29, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:5051081 original size:33 final size:34
Alignment explanation
Indices: 5051011--5051103 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 34
5051001 AAAATCGCAA
5051011 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
5051045 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
5051078 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5051104 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:5051345 original size:93 final size:93
Alignment explanation
Indices: 5051184--5051656 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
5051174 TTGAATGGAT
5051184 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT-CTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5051248 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5051276 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5051341 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5051369 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5051434 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5051462 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5051527 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5051555 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5051620 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5051648 AAATTTACT
1 AAATTTACT
5051657 AAGCAATCTA
Statistics
Matches: 377, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 38 0.10
93 339 0.90
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5053398 original size:33 final size:33
Alignment explanation
Indices: 5053353--5053466 Score: 201
Period size: 33 Copynumber: 3.5 Consensus size: 33
5053343 TCTTTTGGTT
5053353 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5053386 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5053419 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5053452 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
5053467 TTGTTTCGCG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5053399 original size:19 final size:18
Alignment explanation
Indices: 5053360--5053466 Score: 85
Period size: 14 Copynumber: 6.4 Consensus size: 18
5053350 GTTGAAATGA
5053360 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5053375 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5053392 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5053408 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5053425 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5053441 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5053458 AAAATCGCA
1 -AAATCGCA
5053467 TTGTTTCGCG
Statistics
Matches: 74, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
14 24 0.32
16 15 0.20
17 12 0.16
19 23 0.31
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:5053494 original size:14 final size:14
Alignment explanation
Indices: 5053475--5053531 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5053465 CATTGTTTCG
5053475 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5053489 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5053508 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5053522 CGTTGCGATT
1 CGTTGCGATT
5053532 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5053507 original size:33 final size:33
Alignment explanation
Indices: 5053470--5053539 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
5053460 AATCGCATTG
*
5053470 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
5053503 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
5053536 TTTC
1 TTTC
5053540 TCTCGTTGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
Found at i:5053542 original size:21 final size:21
Alignment explanation
Indices: 5053516--5053591 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5053506 CGCGTTGCGA
5053516 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
5053537 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
5053557 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
5053578 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
5053592 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:5053572 original size:41 final size:41
Alignment explanation
Indices: 5053515--5053592 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5053505 TCGCGTTGCG
*
5053515 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
5053556 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
5053593 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:5053718 original size:33 final size:33
Alignment explanation
Indices: 5053671--5053741 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
5053661 AATACTAACT
* *
5053671 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5053704 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5053737 TGAAA
1 TGAAA
5053742 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5053973 original size:22 final size:22
Alignment explanation
Indices: 5053921--5053975 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5053911 TGGTTGTGAG
**
5053921 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5053943 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5053965 GGATTTCTTCG
1 GGATTTCTTCG
5053976 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5054141 original size:39 final size:40
Alignment explanation
Indices: 5054098--5054179 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
5054088 TACGCGTAGC
*
5054098 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
5054137 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
5054177 GAT
1 GAT
5054180 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:5054148 original size:20 final size:20
Alignment explanation
Indices: 5054121--5054313 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
5054111 CTTTAAATAT
5054121 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
5054142 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
5054161 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5054181 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5054201 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5054221 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5054241 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5054261 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5054281 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5054301 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5054314 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5054307 original size:60 final size:60
Alignment explanation
Indices: 5054120--5054435 Score: 200
Period size: 60 Copynumber: 5.2 Consensus size: 60
5054110 GCTTTAAATA
* * * **
5054120 TCGCGTTGCGATTTACGGATTATCG--TTGCGATTTACAG-ATTCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGA-TA-CGCATTGCGATTTA-TGTATTCGCGTTGCGATTTTCATAT
* * *** * * **
5054180 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * *
5054240 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * * * *
5054300 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TGTACTATCGCATTGCGATTTTCAATAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-ATAT
* * ** * *
5054363 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTAT-T
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCATAT
5054422 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
5054436 TGTTGGTCAT
Statistics
Matches: 210, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
58 2 0.01
59 18 0.09
60 115 0.55
61 27 0.13
62 25 0.12
63 21 0.10
64 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
Found at i:5054330 original size:21 final size:21
Alignment explanation
Indices: 5054300--5054382 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
5054290 ATTTTCATAT
*
5054300 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
5054321 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
5054342 TCGCATTGCGATTTT-CAATAA
1 TCGCATTGCGATTTTGGAA-AA
*
5054363 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
5054383 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:5054373 original size:42 final size:43
Alignment explanation
Indices: 5054280--5054378 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
5054270 ATTTATGTGT
* *
5054280 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
5054321 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAATAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
5054363 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5054379 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:5060608 original size:21 final size:22
Alignment explanation
Indices: 5060572--5060612 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5060562 TTAAAAATTA
*
5060572 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
5060594 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
5060613 CCTGTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:5062412 original size:19 final size:20
Alignment explanation
Indices: 5062388--5062425 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5062378 TGAAAATGAT
5062388 TTGATTTTG-AAAACAAAAG
1 TTGATTTTGAAAAACAAAAG
5062407 TTGATTTTGAAAAACAAAA
1 TTGATTTTGAAAAACAAAA
5062426 TAAAACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (20 bp):
TTGATTTTGAAAAACAAAAG
Found at i:5069243 original size:14 final size:14
Alignment explanation
Indices: 5069206--5069244 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5069196 TTTGATAATC
5069206 CATTCGTTTATGTT
1 CATTCGTTTATGTT
* **
5069220 TATTTATTTATGTT
1 CATTCGTTTATGTT
5069234 CATTCGTTTAT
1 CATTCGTTTAT
5069245 ATTTAGTTCA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (14 bp):
CATTCGTTTATGTT
Found at i:5069551 original size:74 final size:74
Alignment explanation
Indices: 5069430--5069647 Score: 336
Period size: 74 Copynumber: 3.0 Consensus size: 74
5069420 TTGTTCATTT
* *
5069430 GTGTTCATTTATCATTTTAAGAATCAATGTGTAAGTTTATTATTTTAAAAAACGAACACGAACAA
1 GTGTTCATTTATCATTTTAAGAATCGATGTGTACGTTTATTATTTTAAAAAACGAACACGAACAA
5069495 ACAAAAAAC
66 ACAAAAAAC
* *
5069504 GTGTTCATTTATTATTTTAAGAATCGATGTGTACGTTTATTATTTTAAAAAACGAACGCGAACAA
1 GTGTTCATTTATCATTTTAAGAATCGATGTGTACGTTTATTATTTTAAAAAACGAACACGAACAA
5069569 ACAAAAAAC
66 ACAAAAAAC
* * * *
5069578 GTGTTCATTTATCATTTTAAGAATCGATGAGTACGTTTA-TA---AAAAAAACGAAAACGAACTA
1 GTGTTCATTTATCATTTTAAGAATCGATGTGTACGTTTATTATTTTAAAAAACGAACACGAACAA
5069639 ACAAAAAAC
66 ACAAAAAAC
5069648 AAATTGCATT
Statistics
Matches: 134, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
70 25 0.19
73 2 0.01
74 107 0.80
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (74 bp):
GTGTTCATTTATCATTTTAAGAATCGATGTGTACGTTTATTATTTTAAAAAACGAACACGAACAA
ACAAAAAAC
Found at i:5073336 original size:29 final size:29
Alignment explanation
Indices: 5073303--5073366 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
5073293 TAATTAAAAG
*
5073303 AAAGTTGAGGACTAAATTGCAAATTTTCA
1 AAAGTTGAAGACTAAATTGCAAATTTTCA
5073332 AAAGTTGAAGACTAAATTGCAAATTTTCA
1 AAAGTTGAAGACTAAATTGCAAATTTTCA
5073361 AAAGTT
1 AAAGTT
5073367 TGTAGTTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (29 bp):
AAAGTTGAAGACTAAATTGCAAATTTTCA
Found at i:5077945 original size:57 final size:57
Alignment explanation
Indices: 5077839--5077953 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 57
5077829 ATGTCCCTCA
* * *
5077839 TTCTAAATTAGTCCTTAAACTTTTAAATATTTTAATTTTATTCTTAAACTATGATCT
1 TTCTAAATTAGTCCTTAAACTTTTAAACATTTTAATTTCATTCTCAAACTATGATCT
* * *
5077896 TTCTAAATTATTCCTTAAACTTTTGAACA-TTTAATTCTCA-TCTCCAAACTGTGATCT
1 TTCTAAATTAGTCCTTAAACTTTTAAACATTTTAATT-TCATTCT-CAAACTATGATCT
5077953 T
1 T
5077954 CATTTTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 10 0.20
57 40 0.80
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (57 bp):
TTCTAAATTAGTCCTTAAACTTTTAAACATTTTAATTTCATTCTCAAACTATGATCT
Found at i:5084467 original size:16 final size:16
Alignment explanation
Indices: 5084436--5084465 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5084426 CTCCTGCAAA
5084436 GAAGAGTTATTATTTC
1 GAAGAGTTATTATTTC
5084452 GAAGA-TTATTATTT
1 GAAGAGTTATTATTT
5084466 TCCCAGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (16 bp):
GAAGAGTTATTATTTC
Found at i:5091638 original size:15 final size:15
Alignment explanation
Indices: 5091609--5091650 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
5091599 TACACTCATG
5091609 AAATAATAT-TTTAT
1 AAATAATATATTTAT
5091623 ATAA-AATATATTTAT
1 A-AATAATATATTTAT
5091638 AAATAAT-TATTTA
1 AAATAATATATTTA
5091651 ATGCATGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATAATATATTTAT
Found at i:5094324 original size:16 final size:16
Alignment explanation
Indices: 5094303--5094333 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5094293 AAGAGAAAGG
5094303 GGATGAATGTGGACAA
1 GGATGAATGTGGACAA
*
5094319 GGATGAGTGTGGACA
1 GGATGAATGTGGACA
5094334 TTCTACATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.19
Consensus pattern (16 bp):
GGATGAATGTGGACAA
Found at i:5094979 original size:17 final size:17
Alignment explanation
Indices: 5094957--5095028 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
5094947 AATTAATCTT
5094957 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
** * *
5094974 TAGTTTGGTGAATGGAC
1 TAGTTTAATAAATGAAC
*
5094991 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
5095008 TAACTTTACTAAATGAAC
1 T-AGTTTAATAAATGAAC
5095026 TAG
1 TAG
5095029 ATGCATGAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:5095056 original size:34 final size:33
Alignment explanation
Indices: 5095013--5095100 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
5095003 TGAACTAACT
* *
5095013 TTACTAAATGAACTAGATGCATGAATGAAGTATC
1 TTACTAAATGAACTAGATGCATAAATAAAGTA-C
* * *
5095047 TTACTAAATGATCTAAATGCATAAATAAATTAC
1 TTACTAAATGAACTAGATGCATAAATAAAGTAC
*
5095080 TTCCCTAAATGAACTAGATGC
1 TT-ACTAAATGAACTAGATGC
5095101 TTTAAATGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 3 0.07
34 42 0.93
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (33 bp):
TTACTAAATGAACTAGATGCATAAATAAAGTAC
Found at i:5095108 original size:18 final size:17
Alignment explanation
Indices: 5095085--5095128 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5095075 ATTACTTCCC
*
5095085 TAAATGAACTAGATGCTT
1 TAAATGAACTACATGC-T
* *
5095103 TAAATGAAATTCATGCT
1 TAAATGAACTACATGCT
5095120 TAAATGAAC
1 TAAATGAAC
5095129 ATCACACTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (17 bp):
TAAATGAACTACATGCT
Found at i:5098359 original size:17 final size:17
Alignment explanation
Indices: 5098337--5098408 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
5098327 AATTAAGATT
5098337 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
5098354 TAGTTTGATGAATGGAC
1 TAGTTTAATAAATGAAC
*
5098371 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
5098388 TAACTTTACTAAATGAAC
1 T-AGTTTAATAAATGAAC
5098406 TAG
1 TAG
5098409 ATGTATGCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:5099272 original size:27 final size:27
Alignment explanation
Indices: 5099200--5099268 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
5099190 CCACATGGAG
5099200 GATGCTTGATGATCTTGATTGGTGGTT
1 GATGCTTGATGATCTTGATTGGTGGTT
5099227 GATGCTTGATGATCTTGATTGGTGGTT
1 GATGCTTGATGATCTTGATTGGTGGTT
**
5099254 TCTGCTTGATG-TCTT
1 GATGCTTGATGATCTT
5099269 TGATGATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.13, C:0.10, G:0.30, T:0.46
Consensus pattern (27 bp):
GATGCTTGATGATCTTGATTGGTGGTT
Found at i:5101642 original size:15 final size:15
Alignment explanation
Indices: 5101622--5101659 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5101612 TTCCTTGTAT
* *
5101622 AAAATTCTCGTAATG
1 AAAATTCCCGTAATA
5101637 AAAATTCCCGTAATA
1 AAAATTCCCGTAATA
5101652 AAAATTCC
1 AAAATTCC
5101660 AGCCAGCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (15 bp):
AAAATTCCCGTAATA
Found at i:5101978 original size:17 final size:17
Alignment explanation
Indices: 5101931--5102002 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
5101921 AATTAAGATT
*
5101931 TAGTTTAATGAATGAAA
1 TAGTTTAATGAATGAAC
* *
5101948 TATTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
5101965 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
5101982 TAACTTTACTAAATGAAC
1 T-AGTTTAATGAATGAAC
5102000 TAG
1 TAG
5102003 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:5102030 original size:34 final size:33
Alignment explanation
Indices: 5101987--5102074 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
5101977 TGAACTAACT
* * *
5101987 TTACTAAATGAACTAGATGCATGAATGAAGTATC
1 TTACTAAATGAACTAGATGCATAAATAAACTA-C
* *
5102021 TTACTAAATGATCTAAATGCATAAATAAACTAC
1 TTACTAAATGAACTAGATGCATAAATAAACTAC
*
5102054 TTCCCTAAATGAACTAGATGC
1 TT-ACTAAATGAACTAGATGC
5102075 TTTAAATGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 3 0.07
34 42 0.93
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (33 bp):
TTACTAAATGAACTAGATGCATAAATAAACTAC
Found at i:5102098 original size:17 final size:17
Alignment explanation
Indices: 5102059--5102103 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
5102049 ACTACTTCCC
*
5102059 TAAATGAACTAGATGCTT
1 TAAATGAAC-ACATGCTT
5102077 TAAATGCAACACATGC-T
1 TAAATG-AACACATGCTT
5102094 TAAATGAACA
1 TAAATGAACA
5102104 TCACACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 11 0.44
19 3 0.12
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (17 bp):
TAAATGAACACATGCTT
Found at i:5108740 original size:22 final size:21
Alignment explanation
Indices: 5108689--5108744 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
5108679 GAATGTTTTG
*
5108689 GAGTATCGATACCTCTAGTTA
1 GAGTATCGATACCTCTAGCTA
5108710 GAGTATCGATACTTCTCTA-CTA
1 GAGTATCGATAC--CTCTAGCTA
*
5108732 GGGTATCGATACC
1 GAGTATCGATACC
5108745 ATTTTGGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 13 0.42
23 5 0.16
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (21 bp):
GAGTATCGATACCTCTAGCTA
Found at i:5109564 original size:21 final size:21
Alignment explanation
Indices: 5109497--5109573 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
5109487 ATCGAGCCTT
* *
5109497 CGGTATGGATACTAGTTTGTC
1 CGGTATGGATACCAGTTTATC
** * *
5109518 CGGTATGGATACCAACTCATA
1 CGGTATGGATACCAGTTTATC
*
5109539 TGGTATGGATACCAGTTTATC
1 CGGTATGGATACCAGTTTATC
*
5109560 CGGTATGGTTACCA
1 CGGTATGGATACCA
5109574 ACATTATCGA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (21 bp):
CGGTATGGATACCAGTTTATC
Found at i:5113916 original size:35 final size:35
Alignment explanation
Indices: 5113877--5114072 Score: 134
Period size: 35 Copynumber: 5.8 Consensus size: 35
5113867 AGATTTACTC
*
5113877 ATAATAGATATATTTTAATATTCAAATTTAAATAG
1 ATAATAGATATCTTTTAATATTCAAATTTAAATAG
* *
5113912 ATAATAAATAT-TTTTAAT-TTGAAATATTCAAA-AG
1 ATAATAGATATCTTTTAATATTCAAAT-TT-AAATAG
*
5113946 AT-ATAGGT-TCCTTTTAATATTCAAATTTAAATAG
1 ATAATAGATAT-CTTTTAATATTCAAATTTAAATAG
* *
5113980 ---AT-G-T-TATTTTAAT-TTAAAATATTCAAA-A-
1 ATAATAGATATCTTTTAATATTCAAAT-TT-AAATAG
*
5114008 ATATATA-ATTATCTTTTAATATTCAAAGTTAAATAG
1 ATA-ATAGA-TATCTTTTAATATTCAAATTTAAATAG
* * *
5114044 ATAATAAATATCTTTTAATTTTAAAATTT
1 ATAATAGATATCTTTTAATATTCAAATTT
5114073 TAAAAAATAA
Statistics
Matches: 128, Mismatches: 13, Indels: 40
0.71 0.07 0.22
Matches are distributed among these distances:
28 6 0.05
29 10 0.08
30 5 0.04
31 1 0.01
32 5 0.04
33 13 0.10
34 28 0.22
35 51 0.40
36 9 0.07
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (35 bp):
ATAATAGATATCTTTTAATATTCAAATTTAAATAG
Found at i:5114029 original size:64 final size:63
Alignment explanation
Indices: 5113923--5114045 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 63
5113913 TAATAAATAT
* ** *
5113923 TTTTAATTTGAAATATTCAAAAGATATAGGTTCCTTTTAATATTCAAATTTAAATAGATGTTA
1 TTTTAATTTAAAATATTCAAAAGATATAAATTCCTTTTAATATTCAAAGTTAAATAGATGTTA
*
5113986 TTTTAATTTAAAATATTCAAAA-ATATATAATTATCTTTTAATATTCAAAGTTAAATAGAT
1 TTTTAATTTAAAATATTCAAAAGATATA-AATT-CCTTTTAATATTCAAAGTTAAATAGAT
5114046 AATAAATATC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 5 0.09
63 23 0.43
64 25 0.47
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.45
Consensus pattern (63 bp):
TTTTAATTTAAAATATTCAAAAGATATAAATTCCTTTTAATATTCAAAGTTAAATAGATGTTA
Found at i:5114083 original size:35 final size:35
Alignment explanation
Indices: 5113986--5114083 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
5113976 ATAGATGTTA
* *
5113986 TTTTAA-TTTAAAATATTCAAAAATATATAATTATC
1 TTTTAATTTTAAAATATTAAAAAATA-ATAAATATC
* * * *
5114021 TTTTAATATTCAAA-GTTAAATAGATAATAAATATC
1 TTTTAATTTTAAAATATTAAA-AAATAATAAATATC
*
5114056 TTTTAATTTTAAAATTTTAAAAAATAAT
1 TTTTAATTTTAAAATATTAAAAAATAAT
5114084 TATCCTAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
35 36 0.72
36 14 0.28
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (35 bp):
TTTTAATTTTAAAATATTAAAAAATAATAAATATC
Found at i:5114462 original size:15 final size:16
Alignment explanation
Indices: 5114442--5114514 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
5114432 GTTTACTTCA
*
5114442 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
5114457 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
* *
5114473 GAATGATTCAAATGTT
1 GAATGATTCAAACGCT
* *
5114489 GAATGATTCAAATGTT
1 GAATGATTCAAACGCT
5114505 GAATGATTCA
1 GAATGATTCA
5114515 GAGGCTCTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 8 0.15
16 46 0.85
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:5114475 original size:16 final size:16
Alignment explanation
Indices: 5114454--5114514 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
5114444 ATGATTAAGC
5114454 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
5114470 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
*
5114486 GTTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
*
5114502 GTTGAATGATTCA
1 GCTGAATGATTCA
5114515 GAGGCTCTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:5114636 original size:15 final size:15
Alignment explanation
Indices: 5114616--5114658 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
5114606 CATTGTTTTG
*
5114616 CTGAATCAGTCAGCA
1 CTGAATCATTCAGCA
*
5114631 CTGAATCATTCAACA
1 CTGAATCATTCAGCA
5114646 CTGAATCATTCAG
1 CTGAATCATTCAG
5114659 AGGTGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (15 bp):
CTGAATCATTCAGCA
Found at i:5114722 original size:20 final size:22
Alignment explanation
Indices: 5114683--5114722 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5114673 CAGTCTGAAT
5114683 GCTGAATGGTTCAGCATTCAGC
1 GCTGAATGGTTCAGCATTCAGC
5114705 GCTGAATGGTT-A-CATTCA
1 GCTGAATGGTTCAGCATTCA
5114723 TAGCCAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (22 bp):
GCTGAATGGTTCAGCATTCAGC
Found at i:5122639 original size:21 final size:21
Alignment explanation
Indices: 5122613--5122652 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5122603 CCCCCTTTGA
*
5122613 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
5122634 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
5122653 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:5127703 original size:58 final size:58
Alignment explanation
Indices: 5127609--5127727 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
5127599 GTAGATTTTC
*
5127609 GTTAGGCCTACGACTCTGTAGATTGGAATTGCTTTGATCTCATTATGGGATACATGGG
1 GTTAGGCCTACGACTCTGTAGATTGGAATTGATTTGATCTCATTATGGGATACATGGG
5127667 GTTAGGCCTACGACTCTGTAGATTGGAATTGATTTGATCTCATTATGGGATACATGGG
1 GTTAGGCCTACGACTCTGTAGATTGGAATTGATTTGATCTCATTATGGGATACATGGG
5127725 GTT
1 GTT
5127728 CAATGATAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (58 bp):
GTTAGGCCTACGACTCTGTAGATTGGAATTGATTTGATCTCATTATGGGATACATGGG
Found at i:5136798 original size:16 final size:16
Alignment explanation
Indices: 5136777--5137411 Score: 613
Period size: 16 Copynumber: 39.7 Consensus size: 16
5136767 TGCATTCTTT
5136777 ATACATACATACATAC
1 ATACATACATACATAC
5136793 ATACATACATACATAC
1 ATACATACATACATAC
5136809 ATACATACATACATAC
1 ATACATACATACATAC
5136825 ATACATACATACATAC
1 ATACATACATACATAC
5136841 ATACATACATACATAC
1 ATACATACATACATAC
5136857 ATACATACATACATAC
1 ATACATACATACATAC
* * * *
5136873 ATGCATGCATGCATGC
1 ATACATACATACATAC
*
5136889 ATACATACATGCATAC
1 ATACATACATACATAC
*
5136905 ATACATACATGCATAC
1 ATACATACATACATAC
5136921 ATACATACATACATAC
1 ATACATACATACATAC
* *
5136937 ATGCATACATGCATAC
1 ATACATACATACATAC
* *
5136953 ATGCATACATGCATAC
1 ATACATACATACATAC
* *
5136969 ATGCATACATGCATAC
1 ATACATACATACATAC
* *
5136985 ATGCATACATGCATAC
1 ATACATACATACATAC
* *
5137001 ATGCATACATGCATAC
1 ATACATACATACATAC
* *
5137017 ATGCATACATGCATAC
1 ATACATACATACATAC
5137033 ATACATACATACATAC
1 ATACATACATACATAC
*
5137049 ATACATACATGCATAC
1 ATACATACATACATAC
*
5137065 ATACATACATGCATAC
1 ATACATACATACATAC
*
5137081 ATACATACATGCATAC
1 ATACATACATACATAC
*
5137097 ATACATACATGCATAC
1 ATACATACATACATAC
*
5137113 ATACATACATGCATAC
1 ATACATACATACATAC
* *
5137129 ATACATGCATGCATAC
1 ATACATACATACATAC
* * * *
5137145 ATCCATGCATGCATGC
1 ATACATACATACATAC
* * *
5137161 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137177 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137193 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137209 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137225 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137241 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137257 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137273 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137289 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137305 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137321 ATCCATGCATACATGC
1 ATACATACATACATAC
* * *
5137337 ATCCATGCATACATGC
1 ATACATACATACATAC
* *
5137353 ATACATGCATACATGC
1 ATACATACATACATAC
* * *
5137369 ATCCATGCATACATGC
1 ATACATACATACATAC
* *
5137385 ATACATGCATACATGC
1 ATACATACATACATAC
*
5137401 ATACATGCATA
1 ATACATACATA
5137412 TTCGATCTAT
Statistics
Matches: 599, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 599 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (16 bp):
ATACATACATACATAC
Found at i:5140866 original size:94 final size:94
Alignment explanation
Indices: 5140760--5140937 Score: 313
Period size: 94 Copynumber: 1.9 Consensus size: 94
5140750 GTAACTAAGC
5140760 CCTCACACACACGCAATGCACTAT-GAACATTATTAACTAACATTCTCCCCGCTTTATTCTTCTC
1 CCTCACACACACGCAATGCACTATAGAA-ATTATTAACTAACATTCTCCCCGCTTTATTCTTCTC
5140824 ATCCTTTTAACACGGTTGAAACGTTATTAA
65 ATCCTTTTAACACGGTTGAAACGTTATTAA
* * *
5140854 CCTCACACACACGCAATGCACTATAGAAATTATTAACTAACATTCTCTCTGCTTTCTTCTTCTCA
1 CCTCACACACACGCAATGCACTATAGAAATTATTAACTAACATTCTCCCCGCTTTATTCTTCTCA
5140919 TCCTTTTAACACGGTTGAA
66 TCCTTTTAACACGGTTGAA
5140938 CATGAACCTT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 77 0.96
95 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (94 bp):
CCTCACACACACGCAATGCACTATAGAAATTATTAACTAACATTCTCCCCGCTTTATTCTTCTCA
TCCTTTTAACACGGTTGAAACGTTATTAA
Found at i:5143537 original size:14 final size:14
Alignment explanation
Indices: 5143514--5143551 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5143504 TTTGTCTATA
*
5143514 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
5143527 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
5143542 TGCAGGGATT
1 TGCAGGGATT
5143552 ACTGCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:5146674 original size:30 final size:30
Alignment explanation
Indices: 5146613--5146704 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 30
5146603 CTAAGGAACA
* * **
5146613 TATGGATAGTTAACCTAGGTTCTTTGGTACC
1 TATGGATAGTT-ACCGAGGATCTTTATTACC
*
5146644 TATGGACAGTTACCGAGGATCTTTATTACC
1 TATGGATAGTTACCGAGGATCTTTATTACC
* *
5146674 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATTACC
5146704 T
1 T
5146705 CTGAATAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 43 0.81
31 10 0.19
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATTACC
Found at i:5151094 original size:30 final size:30
Alignment explanation
Indices: 5151029--5151126 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
5151019 AAGGAACATA
* * ** *
5151029 TGGATAGTTAACCTAGGTTCTTTGGGACCTA
1 TGGATAGTT-ACCGAGGATCTTTATGACCTC
*
5151060 TGGATAGTTACCGAGGATCTTTATTACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
5151090 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
5151120 TGGATAG
1 TGGATAG
5151127 GTCCTGCGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 51 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:5152459 original size:45 final size:44
Alignment explanation
Indices: 5152379--5152474 Score: 102
Period size: 45 Copynumber: 2.2 Consensus size: 44
5152369 ATTCTCTGTA
* * ** **
5152379 ATGTGATATGATTTAGGTGATTAGGTGAACTTGTGACATAAGAT
1 ATGTGATATGAATTAGGTGAATACCTGAAAATGTGACATAAGAT
* *
5152423 ATGTGATATTGAATTAGGTGAATACCTGAAAATGTGATATAGGAT
1 ATGTGATA-TGAATTAGGTGAATACCTGAAAATGTGACATAAGAT
*
5152468 ATATGAT
1 ATGTGAT
5152475 CATAAGCTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (44 bp):
ATGTGATATGAATTAGGTGAATACCTGAAAATGTGACATAAGAT
Found at i:5152904 original size:8 final size:8
Alignment explanation
Indices: 5152891--5152919 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5152881 TGATGATTTG
5152891 TGTGACTA
1 TGTGACTA
5152899 TGTGACTA
1 TGTGACTA
5152907 TGTGACTA
1 TGTGACTA
5152915 TGTGA
1 TGTGA
5152920 ACATGTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (8 bp):
TGTGACTA
Found at i:5162633 original size:20 final size:20
Alignment explanation
Indices: 5162608--5162649 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5162598 ATCATTTTTA
5162608 TTCTGTTTTGATTACTTGTT
1 TTCTGTTTTGATTACTTGTT
5162628 TTCTGTTTTGATTACTTGTT
1 TTCTGTTTTGATTACTTGTT
5162648 TT
1 TT
5162650 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.14, T:0.67
Consensus pattern (20 bp):
TTCTGTTTTGATTACTTGTT
Found at i:5162895 original size:21 final size:21
Alignment explanation
Indices: 5162869--5162911 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5162859 AGTAGTCGTC
5162869 CTCGCCTCTACAATACTCGAT
1 CTCGCCTCTACAATACTCGAT
5162890 CTCGCCTCTACAATACTCGAT
1 CTCGCCTCTACAATACTCGAT
5162911 C
1 C
5162912 GGATAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.40, G:0.09, T:0.28
Consensus pattern (21 bp):
CTCGCCTCTACAATACTCGAT
Found at i:5164138 original size:34 final size:35
Alignment explanation
Indices: 5164071--5164140 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5164061 CATTAGAAAC
5164071 ACTATCATAGAATGGCTTCTAACAAAAAATTATTA
1 ACTATCATAGAATGGCTTCTAACAAAAAATTATTA
5164106 ACTATCATAGAATGGCTTCTAAC-AAAAATTATTA
1 ACTATCATAGAATGGCTTCTAACAAAAAATTATTA
5164140 A
1 A
5164141 ATGAACACGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 12 0.34
35 23 0.66
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (35 bp):
ACTATCATAGAATGGCTTCTAACAAAAAATTATTA
Found at i:5169752 original size:20 final size:20
Alignment explanation
Indices: 5169716--5169753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5169706 ATCCTATTCT
**
5169716 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
5169736 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5169754 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:5174625 original size:31 final size:32
Alignment explanation
Indices: 5174536--5174629 Score: 104
Period size: 31 Copynumber: 3.0 Consensus size: 32
5174526 GAGTCGAGGG
5174536 TTTACCTATG-TCTTTCGGGACATATGGACAGGA
1 TTTACCTATGTTC-TTCGGGACATATGGACA-GA
** *
5174569 -TTACCTATGTTCTAAGGAACATATGGACA-A
1 TTTACCTATGTTCTTCGGGACATATGGACAGA
* *
5174599 TTTACCTAGGTTCTTCGGGACCTATGGACAG
1 TTTACCTATGTTCTTCGGGACATATGGACAG
5174630 TTGTCGAGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
30 1 0.02
31 24 0.48
32 23 0.46
33 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (32 bp):
TTTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:5175244 original size:21 final size:22
Alignment explanation
Indices: 5175209--5175253 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
5175199 TGTAGTAGTA
5175209 CTATAGCAGGGGAATCGGTACC
1 CTATAGCAGGGGAATCGGTACC
*
5175231 CTATAGCA-GGGAATCGGTTCC
1 CTATAGCAGGGGAATCGGTACC
5175252 CT
1 CT
5175254 GTTTGCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (22 bp):
CTATAGCAGGGGAATCGGTACC
Found at i:5175352 original size:18 final size:18
Alignment explanation
Indices: 5175306--5175356 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 18
5175296 GAATTGTTCA
*
5175306 TTACTGTTCATATAGTAT
1 TTACTGTTCATACAGTAT
*
5175324 TGATCACTGTTCATACCGTAT
1 T--T-ACTGTTCATACAGTAT
5175345 TTACTGTTCATA
1 TTACTGTTCATA
5175357 AATACGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 11 0.39
19 1 0.04
20 1 0.04
21 15 0.54
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (18 bp):
TTACTGTTCATACAGTAT
Found at i:5176697 original size:22 final size:22
Alignment explanation
Indices: 5176661--5176711 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5176651 CTGAGTGGCA
* *
5176661 TATGAAATTTGTCCCTAAGAACC
1 TATG-AATATGTCCCGAAGAACC
*
5176684 TATGAATATGTCCCGAAGGACC
1 TATGAATATGTCCCGAAGAACC
5176706 TATGAA
1 TATGAA
5176712 ACCCTCGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (22 bp):
TATGAATATGTCCCGAAGAACC
Found at i:5179037 original size:20 final size:20
Alignment explanation
Indices: 5179014--5179078 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
5179004 CTTTGCAACT
5179014 ATATATTCAAAATTATAATC
1 ATATATTCAAAATTATAATC
* ** * *
5179034 ATATA-AC-ATGTTTTGGAATT
1 ATATATTCAAAATTAT--AATC
5179054 ATATATTCAAAATTATAATC
1 ATATATTCAAAATTATAATC
5179074 ATATA
1 ATATA
5179079 ACATGTTTTG
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
18 4 0.13
19 1 0.03
20 21 0.68
21 1 0.03
22 4 0.13
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
ATATATTCAAAATTATAATC
Found at i:5179039 original size:40 final size:41
Alignment explanation
Indices: 5178981--5179142 Score: 256
Period size: 40 Copynumber: 4.0 Consensus size: 41
5178971 CATATCATAT
*
5178981 AAAATTATAAATCATATAACATACTTTGCAACTATATATTC
1 AAAATTATAAATCATATAACATGCTTTGCAACTATATATTC
* * *
5179022 AAAATTAT-AATCATATAACATGTTTTGGAATTATATATTC
1 AAAATTATAAATCATATAACATGCTTTGCAACTATATATTC
*
5179062 AAAATTAT-AATCATATAACATGTTTTGCAACTATATATTC
1 AAAATTATAAATCATATAACATGCTTTGCAACTATATATTC
*
5179102 AAAATTGTAAATCATATAACATGCTTTGCAACTATATATTC
1 AAAATTATAAATCATATAACATGCTTTGCAACTATATATTC
5179143 GTACCAAACA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 73 0.65
41 39 0.35
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (41 bp):
AAAATTATAAATCATATAACATGCTTTGCAACTATATATTC
Found at i:5182798 original size:25 final size:25
Alignment explanation
Indices: 5182765--5182813 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5182755 TTATTTTGTA
*
5182765 TTTATTTAA-ATTTTTTAATATTATT
1 TTTACTTAATATTTTTTAA-ATTATT
5182790 TTTACTTAATATTTTTTAAATTAT
1 TTTACTTAATATTTTTTAAATTAT
5182814 ATCTGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTACTTAATATTTTTTAAATTATT
Found at i:5182950 original size:28 final size:27
Alignment explanation
Indices: 5182909--5182978 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 27
5182899 TTGTAGGTTT
5182909 TAAAAAAATTAAATTATTGAATGAATA
1 TAAAAAAATTAAATTATTGAATGAATA
5182936 TAAAAAAATTTAAATTATTGAATGAATA
1 TAAAAAAA-TTAAATTATTGAATGAATA
5182964 TAAAAAAAATTAAAT
1 T-AAAAAAATTAAAT
5182979 AAATTCTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 8 0.20
28 26 0.63
29 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (27 bp):
TAAAAAAATTAAATTATTGAATGAATA
Found at i:5183610 original size:32 final size:32
Alignment explanation
Indices: 5183578--5183657 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 32
5183568 GGATTTTTTA
*
5183578 AATAATTTAATATTATACTA-TTTTTATATTT
1 AATAATTTAATATTATAATATTTTTTATATTT
* *
5183609 AATGTATTAAATATCT-TAATATTTTTTATATTTT
1 AAT-AATTTAATAT-TATAATATTTTTTATA-TTT
5183643 AA-AATTTAA-ATTATA
1 AATAATTTAATATTATA
5183658 TCTTAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
30 1 0.03
31 7 0.18
32 17 0.44
33 9 0.23
34 5 0.13
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
AATAATTTAATATTATAATATTTTTTATATTT
Found at i:5200284 original size:22 final size:23
Alignment explanation
Indices: 5200249--5200310 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
5200239 CAGCTCATAT
*
5200249 ATTGCACCTAAGTGCCACGTA-A
1 ATTGCACCGAAGTGCCACGTAGA
* **
5200271 ATTGCACCGGAGTGCCGTGTAGA
1 ATTGCACCGAAGTGCCACGTAGA
* *
5200294 ATTGCAACGTAGTGCCA
1 ATTGCACCGAAGTGCCA
5200311 TATAATGTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
ATTGCACCGAAGTGCCACGTAGA
Found at i:5200512 original size:99 final size:101
Alignment explanation
Indices: 5200309--5200631 Score: 484
Period size: 99 Copynumber: 3.2 Consensus size: 101
5200299 AACGTAGTGC
** * *
5200309 CATATAATGTCCATAAGGACCACATATCATTCCTTAAGAACCATACATATGCCAAGGATCAAGTA
1 CATAT-ATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATACATGCCAAGGATCAAGTA
*
5200374 TGTGTCTCACCAGACTT--CACATGTTCCAAAGAATA
65 TGTGTCTCACTAGACTTCACACATGTTCCAAAGAATA
5200409 CATATATGTCCCGAAGGACC-CATATCATTCCTTAAGAACCATATACATGCCAAGGATC-AGTAT
1 CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATACATGCCAAGGATCAAGTAT
5200472 GTGTCTCACTAGACTTCACACATGTTCCAAAGAATA
66 GTGTCTCACTAGACTTCACACATGTTCCAAAGAATA
* *
5200508 CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGT
1 CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATAC--ATGCCAAGGATCAAGT
5200573 ATGTGTCTCA-TCAGACTTCACACATGTTCC-AAGAATA
64 ATGTGTCTCACT-AGACTTCACACATGTTCCAAAGAATA
5200610 C--ATATGTCCC-AAGGACCACATA
1 CATATATGTCCCGAAGGACCACATA
5200632 GACCCTCTAC
Statistics
Matches: 209, Mismatches: 7, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
97 20 0.10
98 36 0.17
99 63 0.30
100 39 0.19
102 20 0.10
103 31 0.15
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (101 bp):
CATATATGTCCCGAAGGACCACATATCATTCCTTAAGAACCATATACATGCCAAGGATCAAGTAT
GTGTCTCACTAGACTTCACACATGTTCCAAAGAATA
Found at i:5201198 original size:16 final size:17
Alignment explanation
Indices: 5201172--5201204 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5201162 TTCATATTCG
5201172 TTGAGGGGGTATCGATT
1 TTGAGGGGGTATCGATT
5201189 TTGA-GGGGTATCGATT
1 TTGAGGGGGTATCGATT
5201205 CCCTTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.06, G:0.39, T:0.36
Consensus pattern (17 bp):
TTGAGGGGGTATCGATT
Found at i:5202818 original size:89 final size:90
Alignment explanation
Indices: 5202684--5202863 Score: 328
Period size: 89 Copynumber: 2.0 Consensus size: 90
5202674 TTTAAATTCC
*
5202684 ATTACGCATGCTCTCAACAATCTTCCAATATCTGACTAGTTTCTCTCTGATTGCCCATTAGTCTG
1 ATTACGCATGCTCTCAACAATCTTCCAATATCTGAATAGTTTCTCTCTGATTGCCCATTAGTCTG
5202749 AGGATG-AAAGCCGTACTAAAGTTT
66 AGGATGAAAAGCCGTACTAAAGTTT
5202773 ATTACGCATGCTCTCAACATATCTTCCAATATCTGAATAG-TTCTCTCTGATTGCCCATTAGTCT
1 ATTACGCATGCTCTCAACA-ATCTTCCAATATCTGAATAGTTTCTCTCTGATTGCCCATTAGTCT
5202837 GAGGATGAAAAGCCGTACTAAAGTTT
65 GAGGATGAAAAGCCGTACTAAAGTTT
5202863 A
1 A
5202864 AACGAGTCCC
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
89 50 0.57
90 38 0.43
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (90 bp):
ATTACGCATGCTCTCAACAATCTTCCAATATCTGAATAGTTTCTCTCTGATTGCCCATTAGTCTG
AGGATGAAAAGCCGTACTAAAGTTT
Found at i:5207105 original size:23 final size:23
Alignment explanation
Indices: 5207079--5207131 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5207069 ACTGCACCTA
5207079 AGTGCCACGTAGAATTGCACCGG
1 AGTGCCACGTAGAATTGCACCGG
** *
5207102 AGTGCCGTGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGG
5207125 AGTGCCA
1 AGTGCCA
5207132 TATAATAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGG
Found at i:5207267 original size:103 final size:103
Alignment explanation
Indices: 5207147--5207467 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
5207137 TAATGTCCAT
5207147 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
5207212 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
5207250 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
5207315 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
5207353 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
5207418 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5207456 AAGGACCACATA
1 AAGGACCACATA
5207468 GACCCTCTAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:5208036 original size:21 final size:21
Alignment explanation
Indices: 5208012--5208054 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5208002 TTCATATTCG
*
5208012 TTGAGGGGGTA-TCGATTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
5208033 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
5208054 T
1 T
5208055 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:5208347 original size:145 final size:145
Alignment explanation
Indices: 5208084--5208353 Score: 540
Period size: 145 Copynumber: 1.9 Consensus size: 145
5208074 GAGCTCGAAA
5208084 ATCATCTCATTTCAGCTCAAACATTCATATTTCACTCCCTTTAATACTCTTAACTTTCATACACT
1 ATCATCTCATTTCAGCTCAAACATTCATATTTCACTCCCTTTAATACTCTTAACTTTCATACACT
5208149 TACTTAAACTAATTATTATCCATTCAATACCTCTAAAACTAAAAAAAAGTAATCCTCCATTCAAT
66 TACTTAAACTAATTATTATCCATTCAATACCTCTAAAACTAAAAAAAAGTAATCCTCCATTCAAT
5208214 ACTCTTAAACTAATT
131 ACTCTTAAACTAATT
5208229 ATCATCTCATTTCAGCTCAAACATTCATATTTCACTCCCTTTAATACTCTTAACTTTCATACACT
1 ATCATCTCATTTCAGCTCAAACATTCATATTTCACTCCCTTTAATACTCTTAACTTTCATACACT
5208294 TACTTAAACTAATTATTATCCATTCAATACCTCTAAAACTAAAAAAAAGTAATCCTCCAT
66 TACTTAAACTAATTATTATCCATTCAATACCTCTAAAACTAAAAAAAAGTAATCCTCCAT
5208354 ATAGAATTTA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 125 1.00
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.36
Consensus pattern (145 bp):
ATCATCTCATTTCAGCTCAAACATTCATATTTCACTCCCTTTAATACTCTTAACTTTCATACACT
TACTTAAACTAATTATTATCCATTCAATACCTCTAAAACTAAAAAAAAGTAATCCTCCATTCAAT
ACTCTTAAACTAATT
Found at i:5209220 original size:16 final size:15
Alignment explanation
Indices: 5209199--5209228 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5209189 AATAAATAAC
5209199 TAAAATGAAGTATGAT
1 TAAAATGAA-TATGAT
5209215 TAAAATGAATATGA
1 TAAAATGAATATGA
5209229 AATAATGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (15 bp):
TAAAATGAATATGAT
Found at i:5210314 original size:3 final size:3
Alignment explanation
Indices: 5210306--5210333 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5210296 ATAAAATTTT
5210306 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5210334 ATTATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5212156 original size:43 final size:43
Alignment explanation
Indices: 5212049--5212334 Score: 312
Period size: 42 Copynumber: 6.7 Consensus size: 43
5212039 ATAGGTTGAT
* * * *
5212049 ATCTATAGCGACGTTTTTGGAAC-AACATCGCAAAAGGTTGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCGAG
*
5212091 ATATATAGCGGCG-TTTTGGAACAAACACCGCAAAAGGTCGAG
1 ATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCGAG
* * *
5212133 ATCTATAACGGCATTTTTGGAACAAACACGGCAAAAGGTCGAG
1 ATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCGAG
* *
5212176 ATCTATAGCGACGTTTGTT-GAACAAACACCGCAAAAGGTCAAG
1 ATCTATAGCGGCGTTT-TTGGAACAAACACCGCAAAAGGTCGAG
* * ** * *
5212219 ATATATAGCGGCGTTTTTGGGACAAACGTCGTAAAAGGT-TAG
1 ATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCGAG
* ** *
5212261 ATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAGGTC-AT
1 ATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCGAG
* ** *
5212303 ATCTATAGCTGTATTTTTGGAACAAACGCCGC
1 ATCTATAGCGGCGTTTTTGGAACAAACACCGC
5212335 TAATTACCTT
Statistics
Matches: 208, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
41 9 0.04
42 104 0.50
43 93 0.45
44 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAGGTCGAG
Found at i:5212263 original size:128 final size:127
Alignment explanation
Indices: 5212049--5212287 Score: 338
Period size: 128 Copynumber: 1.9 Consensus size: 127
5212039 ATAGGTTGAT
* ** *
5212049 ATCTATAGCGACGTTTTTGGAACAACATCGCAAAAGGTTGATATATATAGCGGCGTTTTGGAACA
1 ATCTATAGCGACGTTTTTGGAACAACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTGGAACA
5212114 AACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACGGCAAAAGGTCGAG
66 AACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACGGCAAAAGGTCGAG
*
5212176 ATCTATAGCGACGTTTGTT-GAACAAACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGG
1 ATCTATAGCGACGTTT-TTGGAAC-AACACCGCAAAAGGTCAAGATATATAGCGGCG-TTTTGGA
** * * * *
5212240 ACAAACGTCGTAAAAGGT-TAGATCTATAGCGGCGTTTTTGGAACAAAC
63 ACAAACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAAC
5212288 GCCATAAAAG
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
127 20 0.20
128 57 0.58
129 21 0.21
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (127 bp):
ATCTATAGCGACGTTTTTGGAACAACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTGGAACA
AACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACGGCAAAAGGTCGAG
Found at i:5212297 original size:128 final size:126
Alignment explanation
Indices: 5212049--5212327 Score: 332
Period size: 128 Copynumber: 2.2 Consensus size: 126
5212039 ATAGGTTGAT
* ** *
5212049 ATCTATAGCGACGTTTTTGGAACAACATCGCAAAAGGTTGATATATATAGCGGCGTTTTGGAACA
1 ATCTATAGCGACGTTTTTGGAACAACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTGGAACA
**
5212114 AACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACGGCAAAAGGTCGAG
66 AACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACCACAAAAGGTC-AG
*
5212176 ATCTATAGCGACGTTTGTT-GAACAAACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGGG
1 ATCTATAGCGACGTTT-TTGGAAC-AACACCGCAAAAGGTCAAGATATATAGCGGCG-TTTTGGA
** * * * * * * *
5212240 ACAAACGTCGTAAAAGGT-TAGATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAGGTCAT
63 ACAAACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACCACAAAAGGTCAG
5212303 ATCTATAGCTGTA--TTTTTGGAACAA
1 ATCTATAGC-G-ACGTTTTTGGAACAA
5212328 ACGCCGCTAA
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
126 4 0.03
127 37 0.28
128 67 0.52
129 22 0.17
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (126 bp):
ATCTATAGCGACGTTTTTGGAACAACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTGGAACA
AACACCGCAAAAGGTCGAGATCTATAACGGCATTTTTGGAACAAACACCACAAAAGGTCAG
Found at i:5219178 original size:2 final size:2
Alignment explanation
Indices: 5219171--5219220 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5219161 AAATAATAAA
5219171 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
5219213 AT AT AT AT
1 AT AT AT AT
5219221 CGGGTCGGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5224226 original size:15 final size:16
Alignment explanation
Indices: 5224198--5224229 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5224188 AAAATCTTTC
5224198 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
5224214 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
5224229 T
1 T
5224230 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:5225396 original size:12 final size:12
Alignment explanation
Indices: 5225379--5225418 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
5225369 TACAGCAGCC
5225379 CCCCCTTAGCAG
1 CCCCCTTAGCAG
5225391 CCCCCTTAGCAG
1 CCCCCTTAGCAG
5225403 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
5225416 CCC
1 CCC
5225419 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:5225407 original size:13 final size:13
Alignment explanation
Indices: 5225372--5225418 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
5225362 AAAAAATTAC
5225372 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
5225386 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
5225398 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
5225411 AGCAGCCC
1 AGCAGCCC
5225419 ATGTGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.38
13 15 0.47
14 5 0.16
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:5226337 original size:17 final size:17
Alignment explanation
Indices: 5226315--5226355 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
5226305 AAAGTGATAG
5226315 ATGATGTTGTTGGGAAA
1 ATGATGTTGTTGGGAAA
5226332 ATGATGTTGTTGGGAAA
1 ATGATGTTGTTGGGAAA
5226349 ATGATGT
1 ATGATGT
5226356 ATATAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (17 bp):
ATGATGTTGTTGGGAAA
Found at i:5226366 original size:18 final size:17
Alignment explanation
Indices: 5226315--5226366 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
5226305 AAAGTGATAG
* *
5226315 ATGATGTTGTTGGGAAA
1 ATGATGTTATAGGGAAA
* *
5226332 ATGATGTTGTTGGGAAA
1 ATGATGTTATAGGGAAA
5226349 ATGATGTATATAGGGAAA
1 ATGATGT-TATAGGGAAA
5226367 TCAAGGGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (17 bp):
ATGATGTTATAGGGAAA
Found at i:5226554 original size:23 final size:25
Alignment explanation
Indices: 5226516--5226575 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
5226506 TATAAAAAAC
* *
5226516 AAATTATATAAATTTAAAATAT-TT
1 AAATTAAATAAATTTAAAATATATA
*
5226540 AAA-TAAATAATTTTAAAATATATA
1 AAATTAAATAAATTTAAAATATATA
5226564 AAATTAAATAAA
1 AAATTAAATAAA
5226576 AAAAATCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 16 0.53
24 7 0.23
25 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTAAATAAATTTAAAATATATA
Found at i:5230640 original size:2 final size:2
Alignment explanation
Indices: 5230633--5230659 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5230623 TTACTTTACC
5230633 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 T
5230660 GAATATGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5231757 original size:2 final size:2
Alignment explanation
Indices: 5231750--5231780 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5231740 AAATATTTTG
5231750 TA 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 TA T
5231781 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5234584 original size:16 final size:16
Alignment explanation
Indices: 5234563--5234593 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5234553 TACTATTCAT
5234563 GTGAATAGTGAATTTA
1 GTGAATAGTGAATTTA
5234579 GTGAATAGTGAATTT
1 GTGAATAGTGAATTT
5234594 TGGTCGACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (16 bp):
GTGAATAGTGAATTTA
Found at i:5238371 original size:29 final size:29
Alignment explanation
Indices: 5238329--5238399 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
5238319 ATTGCGACAA
*
5238329 TCAAAGTTTGGCACCGAATGGTGCATGAT
1 TCAAAGTTTGGCACCAAATGGTGCATGAT
*
5238358 TCAAAGTTTGGCACCAAATGGTGCATGGT
1 TCAAAGTTTGGCACCAAATGGTGCATGAT
5238387 TCAAAGTTTGGCA
1 TCAAAGTTTGGCA
5238400 GTTTTTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (29 bp):
TCAAAGTTTGGCACCAAATGGTGCATGAT
Found at i:5239339 original size:199 final size:203
Alignment explanation
Indices: 5238999--5239401 Score: 778
Period size: 199 Copynumber: 2.0 Consensus size: 203
5238989 ATATTATAAA
5238999 AATTCTTAAACGAAATAAGAATGACTTTAGATACAGCAAATTCGCCACCATCAGCCACCACAGCA
1 AATTCTTAAACGAAATAAGAATGACTTTAGATACAGCAAATTCGCCACCATCAGCCACCACAGCA
5239064 AGAGCCGCAAGCCGGAAGTGAACCTGAAAATACAGCAGTGGCAAATAAAAACCTAATTTGCCTGG
66 AGAGCCGCAAGCCGGAAGTGAACCTGAAAATACAGCAGTGGCAAATAAAAACCTAATTTGCCTGG
5239129 TGACAGACAACAGATAATTGGCAAGTTTTTCTGGCAATAAGGC-AA-CGC-TACTGT-AACAATT
131 TGACAGACAACAGATAATTGGCAAGTTTTTCTGGCAATAAGGCAAACCGCTTACTGTGAACAATT
5239190 CCTCCAAC
196 CCTCCAAC
5239198 AATTCTTAAACGAAATAAGAATGACTTTAGATACAGCAAATTCGCCACCATCAGCCACCACAGCA
1 AATTCTTAAACGAAATAAGAATGACTTTAGATACAGCAAATTCGCCACCATCAGCCACCACAGCA
5239263 AGAGCCGCAAGCCGGAAGTGAACCTGAAAATACAGCAGTGGCAAATAAAAACCTAATTTGCCTGG
66 AGAGCCGCAAGCCGGAAGTGAACCTGAAAATACAGCAGTGGCAAATAAAAACCTAATTTGCCTGG
5239328 TGACAGACAACAGATAATTGGCAAGTTTTTCTGGCAATAAGGCAAACCGCTTACTGTGAACAATT
131 TGACAGACAACAGATAATTGGCAAGTTTTTCTGGCAATAAGGCAAACCGCTTACTGTGAACAATT
5239393 CCTCCAAC
196 CCTCCAAC
5239401 A
1 A
5239402 TTTGTCTAGT
Statistics
Matches: 200, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
199 173 0.87
200 2 0.01
201 3 0.01
202 6 0.03
203 16 0.08
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (203 bp):
AATTCTTAAACGAAATAAGAATGACTTTAGATACAGCAAATTCGCCACCATCAGCCACCACAGCA
AGAGCCGCAAGCCGGAAGTGAACCTGAAAATACAGCAGTGGCAAATAAAAACCTAATTTGCCTGG
TGACAGACAACAGATAATTGGCAAGTTTTTCTGGCAATAAGGCAAACCGCTTACTGTGAACAATT
CCTCCAAC
Found at i:5241776 original size:2 final size:2
Alignment explanation
Indices: 5241769--5241803 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5241759 GTTATTATTG
5241769 TA TA TA 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 TA TA TA T
5241804 TAGTATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5241828 original size:15 final size:15
Alignment explanation
Indices: 5241808--5241845 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
5241798 ATATATTAGT
5241808 ATTTTGTTCTTTAAC
1 ATTTTGTTCTTTAAC
5241823 ATTTTGTTCTTTAAC
1 ATTTTGTTCTTTAAC
5241838 ATTTTGTT
1 ATTTTGTT
5241846 TTAAGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.63
Consensus pattern (15 bp):
ATTTTGTTCTTTAAC
Found at i:5255404 original size:12 final size:12
Alignment explanation
Indices: 5255374--5255418 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
5255364 GTTTATGTAG
*
5255374 ATGTATGTGTAT
1 ATGTATGTATAT
5255386 ATG--TGTATAT
1 ATGTATGTATAT
*
5255396 ATGTATGTATGT
1 ATGTATGTATAT
5255408 ATGTATGTATA
1 ATGTATGTATA
5255419 GTGTTCTGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (12 bp):
ATGTATGTATAT
Found at i:5258226 original size:3 final size:3
Alignment explanation
Indices: 5258218--5258307 Score: 153
Period size: 3 Copynumber: 30.0 Consensus size: 3
5258208 TAAATTTATT
* * *
5258218 TAA TAA TAA TAT TTA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5258266 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5258308 AAGGTTGGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:5262619 original size:41 final size:41
Alignment explanation
Indices: 5262485--5262641 Score: 151
Period size: 41 Copynumber: 3.8 Consensus size: 41
5262475 AAAATGATAC
* * *
5262485 TTTAGTGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGGAA
1 TTTAGCGGCG-TTTTTAAACAAAAGCCGCAATAGAGTGGTAA
* *
5262527 TTTAGCGGCGTTTAT-AGCTAAAACGCCGCAATAGAGAT-GT--
1 TTTAGCGGCGTTTTTAAAC-AAAA-GCCGCAATAGAG-TGGTAA
* *
5262567 TTATAGTGGCGTTTTTAAACAAAAACCGCAATAGAGTGGTAA
1 TT-TAGCGGCGTTTTTAAACAAAAGCCGCAATAGAGTGGTAA
* * *
5262609 TTTAGCGGCGTTTTTACACAAACGCCGCGATAG
1 TTTAGCGGCGTTTTTAAACAAAAGCCGCAATAG
5262642 TGTTGTTTAT
Statistics
Matches: 93, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
39 1 0.01
40 17 0.18
41 48 0.52
42 26 0.28
43 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAACAAAAGCCGCAATAGAGTGGTAA
Found at i:5262683 original size:82 final size:83
Alignment explanation
Indices: 5262487--5262826 Score: 300
Period size: 82 Copynumber: 4.1 Consensus size: 83
5262477 AATGATACTT
* * * * *
5262487 TAGTGGCGTTTTTTAAACAAACGCCGCAATAGAGTGGGAATTTAGCGGCGTTTATAGCTA-AAAC
1 TAGTGGCGTTTGTTAAACAAACGACGCAATAGAGTAGTAATTTAGCGGCGTTTTTA-CTACAAAC
* *
5262551 GCCGCAATAGAGATGTTTA
65 GCCGCAATAGTGTTGTTTA
* *
5262570 TAGTGGCGTTT-TTAAACAAA-AACCGCAATAGAGTGGTAATTTAGCGGCGTTTTTAC-ACAAAC
1 TAGTGGCGTTTGTTAAACAAACGA-CGCAATAGAGTAGTAATTTAGCGGCGTTTTTACTACAAAC
*
5262632 GCCGCGATAGTGTTGTTTA
65 GCCGCAATAGTGTTGTTTA
* * * * * * * *
5262651 TAGTGGCGTTTGTTCAACAAATGACGCTATAGAGAAGTAATTTCGCGATGC-TTATCA-AACAAA
1 TAGTGGCGTTTGTTAAACAAACGACGCAATAGAGTAGTAATTTAGCG--GCGTTTTTACTACAAA
* *
5262714 CGCCGTAATAGTATTGTTTA
64 CGCCGCAATAGTGTTGTTTA
* * * * * * * *
5262734 TAGTGGCGTTTGTGCAAA-AAACGCCGTAATAGAGTAATAATATAGCGGCATTTGTCCTACAAAC
1 TAGTGGCGTTTGT-TAAACAAACGACGCAATAGAGTAGTAATTTAGCGGCGTTTTTACTACAAAC
*
5262798 GACGCAATA-TGTTGTTTA
65 GCCGCAATAGTGTTGTTTA
* *
5262816 TCGTGGTGTTT
1 TAGTGGCGTTT
5262827 ATATAAAAAG
Statistics
Matches: 209, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
80 1 0.00
81 34 0.16
82 85 0.41
83 85 0.41
84 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (83 bp):
TAGTGGCGTTTGTTAAACAAACGACGCAATAGAGTAGTAATTTAGCGGCGTTTTTACTACAAACG
CCGCAATAGTGTTGTTTA
Found at i:5266233 original size:2 final size:2
Alignment explanation
Indices: 5266226--5266261 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5266216 GAGTTGTTCA
5266226 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
5266262 TTACAATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5272878 original size:20 final size:20
Alignment explanation
Indices: 5272862--5272912 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 20
5272852 GAGGGAATCT
5272862 ATTCCCCCTTTAGGGAACCG
1 ATTCCCCCTTTAGGGAACCG
*
5272882 ATTCCCCCTTTGAAGGGGAACTG
1 ATTCCCCCTTT--A-GGGAACCG
5272905 ATTCCCCC
1 ATTCCCCC
5272913 CACAGGGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
22 1 0.04
23 15 0.56
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTCCCCCTTTAGGGAACCG
Found at i:5272907 original size:23 final size:20
Alignment explanation
Indices: 5272853--5272912 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
5272843 TTTGGTGCAG
5272853 AGGGAATCT-ATTCCCCCTTT
1 AGGGAA-CTGATTCCCCCTTT
*
5272873 AGGGAACCGATTCCCCCTTT
1 AGGGAACTGATTCCCCCTTT
5272893 GAAGGGGAACTGATTCCCCC
1 --A-GGGAACTGATTCCCCC
5272913 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.03
20 17 0.50
22 1 0.03
23 15 0.44
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (20 bp):
AGGGAACTGATTCCCCCTTT
Found at i:5281961 original size:20 final size:21
Alignment explanation
Indices: 5281933--5281984 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
5281923 GGGTAGATGT
* *
5281933 TTTAAATTTACC-TGACTTTA
1 TTTATATTTACCATGACATTA
5281953 TTTATATTTGTACCATGACATTA
1 TTTATA-TT-TACCATGACATTA
5281976 TTTAT-TTTA
1 TTTATATTTA
5281985 ATGATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 4 0.15
23 12 0.44
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTATATTTACCATGACATTA
Found at i:5282729 original size:43 final size:44
Alignment explanation
Indices: 5282681--5282802 Score: 185
Period size: 44 Copynumber: 2.8 Consensus size: 44
5282671 TATTGCGGCG
5282681 TTTGTAT-C-AAAAGATGCCGCTATATACCAGACCTATCGCGACA
1 TTTGTATCCTAAAA-ATGCCGCTATATACCAGACCTATCGCGACA
* * *
5282724 TTTGTATCCTAAAAACGCCGCTATATAACAGACCTATCGCGACG
1 TTTGTATCCTAAAAATGCCGCTATATACCAGACCTATCGCGACA
*
5282768 TTTGTATCCTAAAAATGCCGCTAAATACCAGACCT
1 TTTGTATCCTAAAAATGCCGCTATATACCAGACCT
5282803 TAGCGGCGTT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
43 7 0.10
44 60 0.85
45 4 0.06
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (44 bp):
TTTGTATCCTAAAAATGCCGCTATATACCAGACCTATCGCGACA
Done.