Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 61 of 117
Found at i:13463601 original size:16 final size:16
Alignment explanation
Indices: 13463562--13463632 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 16
13463552 AATTTAATTT
13463562 TTTAAATTA-TTTAAA
1 TTTAAATTATTTTAAA
* *
13463577 TTCATATTATTTTAAA
1 TTTAAATTATTTTAAA
* **
13463593 TTTAAATTAATTTGGA
1 TTTAAATTATTTTAAA
* *
13463609 TATAAATTATTTTAGA
1 TTTAAATTATTTTAAA
13463625 TTTAAATT
1 TTTAAATT
13463633 GAACGGCTTC
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
15 7 0.16
16 37 0.84
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:13474488 original size:19 final size:19
Alignment explanation
Indices: 13474466--13474503 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13474456 ATCATATAAC
*
13474466 TATGAAAAACTCATAATTA
1 TATGAAAAACTCACAATTA
13474485 TATGAAAAACTCACAATTA
1 TATGAAAAACTCACAATTA
13474504 GATCCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (19 bp):
TATGAAAAACTCACAATTA
Found at i:13474922 original size:13 final size:13
Alignment explanation
Indices: 13474906--13474953 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
13474896 AAAATTATTT
13474906 ATTTAAAAAAGT-A
1 ATTTAAAAAA-TAA
13474919 ATTTAAAAAATCAA
1 ATTTAAAAAAT-AA
13474933 ATTTAAAAAAAATAA
1 ATTT--AAAAAATAA
13474948 ATTTAA
1 ATTTAA
13474954 CTCTTAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 12 0.39
14 5 0.16
15 6 0.19
16 7 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
ATTTAAAAAATAA
Found at i:13474944 original size:16 final size:15
Alignment explanation
Indices: 13474923--13474953 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
13474913 AAAGTAATTT
13474923 AAAAAATCAAATTTAA
1 AAAAAAT-AAATTTAA
13474939 AAAAAATAAATTTAA
1 AAAAAATAAATTTAA
13474954 CTCTTAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAATAAATTTAA
Found at i:13476061 original size:30 final size:30
Alignment explanation
Indices: 13476025--13476128 Score: 76
Period size: 30 Copynumber: 3.5 Consensus size: 30
13476015 ATAAAAAAAT
13476025 AAAAAATATAAAAAATGTAACATTTTATAC
1 AAAAAATATAAAAAATGTAACATTTTATAC
* *
13476055 AAAAAAT-TCAAAAAATAT-ACACTTTGA-A-
1 AAAAAATAT-AAAAAATGTAACA-TTTTATAC
* *
13476083 AAAAAGATTTAAAAAATGTTAAAATTTT-T-C
1 AAAAA-ATATAAAAAATG-TAACATTTTATAC
*
13476113 AAAAAAATACAAAAAA
1 -AAAAAATATAAAAAA
13476129 GGAAAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
28 5 0.09
29 14 0.24
30 32 0.55
31 7 0.12
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (30 bp):
AAAAAATATAAAAAATGTAACATTTTATAC
Found at i:13476620 original size:34 final size:35
Alignment explanation
Indices: 13476561--13476626 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
13476551 TTAAATATTT
* *
13476561 TTTAAATATTTTAAAATTTTATAAAAAATAAAGTA
1 TTTAAATATTTAAAAAATTTATAAAAAATAAAGTA
13476596 TTTAAATATTTAAAAAATTT-TAAAAAATAAA
1 TTTAAATATTTAAAAAATTTATAAAAAATAAA
13476627 AACTTAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (35 bp):
TTTAAATATTTAAAAAATTTATAAAAAATAAAGTA
Found at i:13476935 original size:27 final size:28
Alignment explanation
Indices: 13476879--13476955 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 28
13476869 AATCTTACAA
* * * *
13476879 TTTT-GATTTTTATATACTTTATGAAGT
1 TTTTAGATTTTTTTAAATTTTAAGAAGT
13476906 TTTTAGATTTTTTTAAATTTTAAGAA-T
1 TTTTAGATTTTTTTAAATTTTAAGAAGT
* * **
13476933 TTTAATAAATTTTTAAATTTTAA
1 TTTTAGATTTTTTTAAATTTTAA
13476956 AAAAATTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (28 bp):
TTTTAGATTTTTTTAAATTTTAAGAAGT
Found at i:13476951 original size:18 final size:18
Alignment explanation
Indices: 13476905--13476955 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
13476895 CTTTATGAAG
* **
13476905 TTTTTAGATTTTTTTAAA
1 TTTTTAAATTTTAATAAA
*
13476923 TTTTAAGAATTTTAATAAA
1 TTTTTA-AATTTTAATAAA
13476942 TTTTTAAATTTTAA
1 TTTTTAAATTTTAA
13476956 AAAAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTTTAAATTTTAATAAA
Found at i:13476962 original size:19 final size:19
Alignment explanation
Indices: 13476920--13476959 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
13476910 AGATTTTTTT
*
13476920 AAATTTTAAGAATTTTAAT
1 AAATTTTAAGAATTTTAAA
*
13476939 AAATTTTTA-AATTTTAAA
1 AAATTTTAAGAATTTTAAA
13476957 AAA
1 AAA
13476960 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AAATTTTAAGAATTTTAAA
Found at i:13477092 original size:20 final size:21
Alignment explanation
Indices: 13477047--13477095 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
13477037 TTTATTGTTG
* *
13477047 AATTTTTGA-ATTTTTATTAA
1 AATTTTTAAGATTTTTATGAA
13477067 AA-TTTTAAGATTTTT-TGAA
1 AATTTTTAAGATTTTTATGAA
13477086 AATTTTTAAG
1 AATTTTTAAG
13477096 TTTAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (21 bp):
AATTTTTAAGATTTTTATGAA
Found at i:13477186 original size:20 final size:20
Alignment explanation
Indices: 13477147--13477198 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
13477137 TATACTTTTT
13477147 AATTTTTTATAATTTAT-AAA
1 AATTTTTTA-AATTTATAAAA
*
13477167 AATTTTTTAAATTTTTTAAAA
1 AATTTTTTAAA-TTTATAAAA
*
13477188 AAATTTTTAAA
1 AATTTTTTAAA
13477199 AAGTTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 13 0.46
21 13 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTTTTAAATTTATAAAA
Found at i:13477205 original size:22 final size:22
Alignment explanation
Indices: 13477159--13477205 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13477149 TTTTTTATAA
* * **
13477159 TTTATAAAAATTTTTTAAATTT
1 TTTAAAAAAATTTTTAAAAAGT
13477181 TTTAAAAAAATTTTTAAAAAGT
1 TTTAAAAAAATTTTTAAAAAGT
13477203 TTT
1 TTT
13477206 TGAATCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAAAAAAATTTTTAAAAAGT
Found at i:13477243 original size:10 final size:10
Alignment explanation
Indices: 13477147--13477246 Score: 53
Period size: 10 Copynumber: 9.9 Consensus size: 10
13477137 TATACTTTTT
*
13477147 AATTTTTTAT
1 AATTTTTTAA
* *
13477157 AATTTATAAA
1 AATTTTTTAA
13477167 AATTTTTT-A
1 AATTTTTTAA
13477176 AATTTTTTAAAAA
1 AATTTTTT---AA
*
13477189 AATTTTTAAA
1 AATTTTTTAA
* *
13477199 AAGTTTTT-G
1 AATTTTTTAA
**
13477208 AATCTTTTTTG
1 AAT-TTTTTAA
*
13477219 AA-TTATTAA
1 AATTTTTTAA
*
13477228 AGTTTTTTAA
1 AATTTTTTAA
13477238 AATTTTTTA
1 AATTTTTTA
13477247 TTTAAACTAG
Statistics
Matches: 67, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
9 16 0.24
10 40 0.60
11 3 0.04
13 8 0.12
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:13479474 original size:24 final size:24
Alignment explanation
Indices: 13479429--13479474 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
13479419 AATACCATAT
* *
13479429 ATAATTTTTTTAACATATTAAAAA
1 ATAATTTTTTTAACAAAATAAAAA
13479453 ATAATTTTTTTTAA-AAAATAAA
1 ATAA-TTTTTTTAACAAAATAAA
13479475 TGTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAATTTTTTTAACAAAATAAAAA
Found at i:13480593 original size:18 final size:18
Alignment explanation
Indices: 13480572--13480607 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13480562 AATGTTTTAG
13480572 TGTAAGAATATGTCTTAA
1 TGTAAGAATATGTCTTAA
13480590 TGTAAGAATATGTCTTAA
1 TGTAAGAATATGTCTTAA
13480608 CATATAGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
TGTAAGAATATGTCTTAA
Found at i:13486149 original size:22 final size:23
Alignment explanation
Indices: 13486096--13486150 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
13486086 CATTACAGTG
13486096 ATATTATAATTTTTATATTAATAA
1 ATATTAT-ATTTTTATATTAATAA
*
13486120 A-ATAATA-TTTT-TATTATATAA
1 ATATTATATTTTTATATTA-ATAA
13486141 ATATTATATT
1 ATATTATATT
13486151 AATAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 6 0.23
23 5 0.19
24 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTATATTTTTATATTAATAA
Found at i:13486167 original size:23 final size:22
Alignment explanation
Indices: 13486141--13486215 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
13486131 TATTATATAA
13486141 ATATTATATTAATAAATATAATT
1 ATATTATATTAATAAATA-AATT
*
13486164 ATATT-TATT-AT--ATAAATA
1 ATATTATATTAATAAATAAATT
*
13486182 ATATTCTATTAATAAATAATATT
1 ATATTATATTAATAAATAA-ATT
13486205 ATATTATATTA
1 ATATTATATTA
13486216 TTATTAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 8 0.18
19 7 0.16
20 2 0.05
21 2 0.05
22 8 0.18
23 17 0.39
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTATATTAATAAATAAATT
Found at i:13486185 original size:18 final size:18
Alignment explanation
Indices: 13486119--13486213 Score: 93
Period size: 18 Copynumber: 5.0 Consensus size: 18
13486109 TATATTAATA
13486119 AAATAATATTTTTATTATAT
1 AAATAATA--TTTATTATAT
* * *
13486139 AAATATTATATTAATAAAT
1 AAATAATAT-TTATTATAT
*
13486158 ATAATTATATTTATTATAT
1 A-AATAATATTTATTATAT
13486177 AAATAATATTCTATTA-AT
1 AAATAATATT-TATTATAT
13486195 AAATAATATTATATTATAT
1 AAATAATATT-TATTATAT
13486214 TATTATTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
18 26 0.42
19 23 0.37
20 13 0.21
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAATATTTATTATAT
Found at i:13486196 original size:41 final size:40
Alignment explanation
Indices: 13486108--13486227 Score: 142
Period size: 41 Copynumber: 3.0 Consensus size: 40
13486098 ATTATAATTT
*
13486108 TTATATTAATAAA-ATAA-TATTTTTATTATAT-A-AATA
1 TTATATTAATAAATATAATTATATTTATTATATAATAATA
13486144 TTATATTAATAAATATAATTATATTTATTATATAAATAATA
1 TTATATTAATAAATATAATTATATTTATTATAT-AATAATA
*
13486185 TTCTATTAATAAATA-ATATTATATTATATTATTATTAATAATA
1 TTATATTAATAAATATA-ATTATATT-TATTA-TA-TAATAATA
13486228 AACGAAACCT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
36 13 0.18
37 4 0.05
38 13 0.18
40 2 0.03
41 26 0.36
42 5 0.07
43 9 0.12
44 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
TTATATTAATAAATATAATTATATTTATTATATAATAATA
Found at i:13487071 original size:28 final size:28
Alignment explanation
Indices: 13487038--13487116 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
13487028 ATAAATTATA
*
13487038 ATAAAATATTTAATATGTTATTTTGATT
1 ATAAAATATTTAATATGTTATTTTAATT
* *
13487066 TTAAAA-ATTTTATCATGATT-TTTTAATT
1 ATAAAATATTTAAT-ATG-TTATTTTAATT
13487094 AT-AAATATATTAATAT-TTATTTT
1 ATAAAATAT-TTAATATGTTATTTT
13487117 TAATATTGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
26 2 0.05
27 13 0.32
28 20 0.49
29 6 0.15
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (28 bp):
ATAAAATATTTAATATGTTATTTTAATT
Found at i:13487219 original size:28 final size:28
Alignment explanation
Indices: 13487179--13487258 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
13487169 TATTATATTA
* *
13487179 ATTAATAAA-TTTATAATTTAAATTTTAT
1 ATTAA-AAATTTTATAATTTAAATATCAT
*
13487207 ATTAAAAATTTTA-AAATTAAGATATCAT
1 ATTAAAAATTTTATAATTTAA-ATATCAT
*
13487235 ATTAAATATTTATTATAATTTAAA
1 ATTAAA-AATT-TTATAATTTAAA
13487259 AATACAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 9 0.21
28 20 0.48
29 3 0.07
30 4 0.10
31 6 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTAAAAATTTTATAATTTAAATATCAT
Found at i:13491360 original size:26 final size:25
Alignment explanation
Indices: 13491330--13491386 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
13491320 AATTTGAGAC
*
13491330 AAATTTAGAT-AAAATTTCTCATTTA
1 AAATTT-GATAAAAATTTATCATTTA
*
13491355 AGAATTTTATAAAAATTTATCATTTA
1 A-AATTTGATAAAAATTTATCATTTA
13491381 AAATTT
1 AAATTT
13491387 TTATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (25 bp):
AAATTTGATAAAAATTTATCATTTA
Found at i:13491388 original size:26 final size:26
Alignment explanation
Indices: 13491340--13491398 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
13491330 AAATTTAGAT
*
13491340 AAAATTTCTCATTTAAGAATTTTATA
1 AAAATTTATCATTTAAGAATTTTATA
13491366 AAAATTTATCATTTAA-AATTTT-TA
1 AAAATTTATCATTTAAGAATTTTATA
*
13491390 TAAATTTAT
1 AAAATTTAT
13491399 TATTGGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 10 0.32
25 6 0.19
26 15 0.48
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (26 bp):
AAAATTTATCATTTAAGAATTTTATA
Found at i:13492493 original size:41 final size:41
Alignment explanation
Indices: 13492410--13492611 Score: 275
Period size: 41 Copynumber: 4.9 Consensus size: 41
13492400 AAAGCTCCTA
* *
13492410 TAAATAGAGGCTA--ACGACTTTGAGAAA-AAAATGCTCTTC
1 TAAATAGAGGC-ACCACAACTTTGAAAAATAAAATGCTCTTC
*
13492449 TAAATAGAGGCACCACAACTTTGAAAAATAAAAAGCTCTTC
1 TAAATAGAGGCACCACAACTTTGAAAAATAAAATGCTCTTC
* *
13492490 TAAATAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTC
1 TAAATAGAGGCACCACAACTTTGAAAAATAAAATGCTCTTC
*
13492531 TAAATAGAGGCACCACAACTTTGAAAAATAAATTGCTCTTC
1 TAAATAGAGGCACCACAACTTTGAAAAATAAAATGCTCTTC
* * *
13492572 TAAACAGATGCAACACAACTTTTGAAAAAATAAAATGCTC
1 TAAATAGAGGCACCACAAC-TTTG-AAAAATAAAATGCTC
13492612 ATCGACAATC
Statistics
Matches: 147, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 11 0.07
40 12 0.08
41 105 0.71
42 4 0.03
43 14 0.10
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (41 bp):
TAAATAGAGGCACCACAACTTTGAAAAATAAAATGCTCTTC
Found at i:13492541 original size:82 final size:80
Alignment explanation
Indices: 13492385--13492611 Score: 269
Period size: 82 Copynumber: 2.7 Consensus size: 80
13492375 TTTCTTTTTT
* * * *
13492385 TTTGAAAAAGTAAATAAAGCTCCTATAAATAGAGGCTA-ACGACTTTGAGAAAA-AAATGCTCTT
1 TTTGAAAAA-T-AA-AAAGCTCTTCTAAATAGAGGC-ACACAACTTTGA-AAAATAAATGCTCCT
13492448 CTAAATAGAGGCACCACAAC
61 CTAAATAGAGGCACCACAAC
13492468 TTTGAAAAATAAAAAGCTCTTCTAAATAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTCTA
1 TTTGAAAAATAAAAAGCTCTTCTAAATAGAGGCA-CACAACTTTGAAAAATAAA-TGCTCCTCTA
13492533 AATAGAGGCACCACAAC
64 AATAGAGGCACCACAAC
** * *
13492550 TTTGAAAAATAAATTGCTCTTCTAAACAGATGCAACACAACTTTTGAAAAAATAAAATGCTC
1 TTTGAAAAATAAAAAGCTCTTCTAAATAGAGGC-ACACAAC-TTTG-AAAAAT-AAATGCTC
13492612 ATCGACAATC
Statistics
Matches: 128, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
79 1 0.01
80 23 0.18
81 14 0.11
82 62 0.48
83 14 0.11
84 11 0.09
85 3 0.02
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (80 bp):
TTTGAAAAATAAAAAGCTCTTCTAAATAGAGGCACACAACTTTGAAAAATAAATGCTCCTCTAAA
TAGAGGCACCACAAC
Found at i:13493634 original size:21 final size:22
Alignment explanation
Indices: 13493610--13493652 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13493600 GACTTAAGTC
13493610 CTCTTTTTT-TTTTCT-TTTTTT
1 CTCTTTTTTATTTT-TATTTTTT
13493631 CTCTTTTTTATTTTTATTTTTT
1 CTCTTTTTTATTTTTATTTTTT
13493653 AAGTATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (22 bp):
CTCTTTTTTATTTTTATTTTTT
Found at i:13504572 original size:197 final size:192
Alignment explanation
Indices: 13504279--13504631 Score: 455
Period size: 198 Copynumber: 1.8 Consensus size: 192
13504269 ACAATTACTT
* * *
13504279 TTATTGAAACTTCATCTAAATTATTTCACAATTTGAGACAAATTTAGATAAAATTTCTCACTAAG
1 TTATTAAAACTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAATTTCTCACTAAG
* ** * **
13504344 AGATTTCTTAGGAATTTACTATTTGAAA-TTTTA-AGAATTTTATCATTGGGTAATTTGTATTTA
66 AGATTTCTTAGAAATTTACTATTTGAAATTTTTATA-AATTCCATCATTAGGTAATTAATATTTA
13504407 ATTCCAAAATTTTATATT-TTATATTTTTTTTTTTTTTTGTTTTGAAAATAAATATTGATTATTG
130 ATTCCAAAATTTT-T-TTATTATATTTTTTTTTTTTTTTGTTTTGAAAATAAATATTGATTATTG
* * *
13504471 TTATTAAAACTTTATCTAAATTATTCCACAATTAATTTGGGACAAATTTAGACAAAAATTTTTCA
1 TTATTAAAACTTCATCTAAATTATTCCAC----AATTTGAGACAAATTTAGA-AAAAATTTCTCA
13504536 CCTAAGA-ATTT-TATAGAAATTTACTATTTGAAATTTTTATAAATTCCATCATTAGGTAATTAA
61 -CTAAGAGATTTCT-TAGAAATTTACTATTTGAAATTTTTATAAATTCCATCATTAGGTAATTAA
* *
13504599 TATTTATTTTCAAAATTTTTTTATTATATTTTT
124 TATTTAATTCCAAAATTTTTTTATTATATTTTT
13504632 GATAAATTTA
Statistics
Matches: 137, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
192 26 0.19
196 21 0.15
197 44 0.32
198 45 0.33
199 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (192 bp):
TTATTAAAACTTCATCTAAATTATTCCACAATTTGAGACAAATTTAGAAAAAATTTCTCACTAAG
AGATTTCTTAGAAATTTACTATTTGAAATTTTTATAAATTCCATCATTAGGTAATTAATATTTAA
TTCCAAAATTTTTTTATTATATTTTTTTTTTTTTTTGTTTTGAAAATAAATATTGATTATTG
Found at i:13520306 original size:25 final size:24
Alignment explanation
Indices: 13520278--13520381 Score: 127
Period size: 25 Copynumber: 4.2 Consensus size: 24
13520268 AATATAAAAT
* *
13520278 AAATGACTTAATTTAAATATGCATG
1 AAATGACAT-ATTAAAATATGCATG
*
13520303 AAATGACATATTAAAATATGTATG
1 AAATGACATATTAAAATATGCATG
***
13520327 AAATGACATAATCCCAATATGCATG
1 AAATGACAT-ATTAAAATATGCATG
13520352 AAATGACATTATTAAAATATGCATG
1 AAATGACA-TATTAAAATATGCATG
13520377 AAATG
1 AAATG
13520382 TAAAAACACT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
24 22 0.33
25 44 0.66
26 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
AAATGACATATTAAAATATGCATG
Found at i:13520331 original size:49 final size:50
Alignment explanation
Indices: 13520278--13520381 Score: 156
Period size: 49 Copynumber: 2.1 Consensus size: 50
13520268 AATATAAAAT
* ** *
13520278 AAATGACTTAATTTAAATATGCATGAAATGACA-TATTAAAATATGTATG
1 AAATGACATAATCCAAATATGCATGAAATGACATTATTAAAATATGCATG
*
13520327 AAATGACATAATCCCAATATGCATGAAATGACATTATTAAAATATGCATG
1 AAATGACATAATCCAAATATGCATGAAATGACATTATTAAAATATGCATG
13520377 AAATG
1 AAATG
13520382 TAAAAACACT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 29 0.59
50 20 0.41
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (50 bp):
AAATGACATAATCCAAATATGCATGAAATGACATTATTAAAATATGCATG
Found at i:13521535 original size:13 final size:13
Alignment explanation
Indices: 13521498--13521650 Score: 111
Period size: 13 Copynumber: 11.5 Consensus size: 13
13521488 GGATCCATGC
*
13521498 TAGGGTTAGGGTTT
1 TAGGTTTAGGG-TT
13521512 TAGGATTTAGGGTT
1 TAGG-TTTAGGGTT
13521526 TAGGTTTAGGGTTT
1 TAGGTTTAGGG-TT
13521540 TAGG-TTAGGGTT
1 TAGGTTTAGGGTT
*
13521552 TGGAGTTTA-GGTT
1 TAG-GTTTAGGGTT
*
13521565 TAGCATTTAGGG-T
1 TAG-GTTTAGGGTT
13521578 TAGGTTTAGGGTT
1 TAGGTTTAGGGTT
* * * *
13521591 TGGGATTAAGATT
1 TAGGTTTAGGGTT
*
13521604 TTGAGTTTA-GGTT
1 TAG-GTTTAGGGTT
13521617 TAGAGTTTAGGG-T
1 TAG-GTTTAGGGTT
13521630 TAGGGTTTA-GGTT
1 TA-GGTTTAGGGTT
13521643 TAGAGTTT
1 TAG-GTTT
13521651 TGATTTGGAT
Statistics
Matches: 114, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
12 14 0.12
13 66 0.58
14 28 0.25
15 6 0.05
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (13 bp):
TAGGTTTAGGGTT
Found at i:13521617 original size:6 final size:6
Alignment explanation
Indices: 13521608--13521650 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
13521598 AAGATTTTGA
*
13521608 GTTTAG GTTTAG AGTTTAG GGTTAGG GTTTAG GTTTAG AGTTT
1 GTTTAG GTTTAG -GTTTAG GTTTA-G GTTTAG GTTTAG -GTTT
13521651 TGATTTGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 17 0.53
7 15 0.47
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (6 bp):
GTTTAG
Found at i:13521656 original size:52 final size:52
Alignment explanation
Indices: 13521510--13521640 Score: 165
Period size: 52 Copynumber: 2.5 Consensus size: 52
13521500 GGGTTAGGGT
* * * * * *
13521510 TTTAGGATTTAGGGTTTAGGTTTAGGGTTTTAGGTTAGGGTTTGGAGTTTAGG
1 TTTAGCATTTAGGG-TTAGGTTTAGGGTTTGAGATTAAGATTTTGAGTTTAGG
*
13521563 TTTAGCATTTAGGGTTAGGTTTAGGGTTTGGGATTAAGATTTTGAGTTTAGG
1 TTTAGCATTTAGGGTTAGGTTTAGGGTTTGAGATTAAGATTTTGAGTTTAGG
13521615 TTTAG-AGTTTAGGGTTAGGGTTTAGG
1 TTTAGCA-TTTAGGGTTA-GGTTTAGG
13521641 TTTAGAGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
51 1 0.01
52 47 0.68
53 21 0.30
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (52 bp):
TTTAGCATTTAGGGTTAGGTTTAGGGTTTGAGATTAAGATTTTGAGTTTAGG
Found at i:13521661 original size:6 final size:6
Alignment explanation
Indices: 13521652--13521676 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13521642 TTAGAGTTTT
13521652 GATTTG GATTTG GATTTG GATTTG G
1 GATTTG GATTTG GATTTG GATTTG G
13521677 TGTTTAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GATTTG
Found at i:13525436 original size:14 final size:15
Alignment explanation
Indices: 13525413--13525454 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
13525403 GTATTTGTAC
*
13525413 ACTATTTACACTAA-
1 ACTATATACACTAAG
13525427 ACTATATACACTAAG
1 ACTATATACACTAAG
* *
13525442 GCTATGTACACTA
1 ACTATATACACTA
13525455 GAGGGTGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
ACTATATACACTAAG
Found at i:13528691 original size:17 final size:17
Alignment explanation
Indices: 13528658--13528695 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13528648 ACTAAGACTG
**
13528658 CAAAAGCAAAAGTAAAA
1 CAAAAGCAAAAAAAAAA
13528675 CAAAAGCAAAAAAAAAA
1 CAAAAGCAAAAAAAAAA
13528692 -AAAA
1 CAAAA
13528696 AAACTCGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.79, C:0.11, G:0.08, T:0.03
Consensus pattern (17 bp):
CAAAAGCAAAAAAAAAA
Found at i:13532248 original size:6 final size:6
Alignment explanation
Indices: 13532225--13532289 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
13532215 TGAATATAAG
* * * * *
13532225 TATAAA TATATA CATATA TGTATA TATATA TATATT TATACA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
13532273 CATATA TATATA TATAT
1 TATATA TATATA TATAT
13532290 CCTGGTGTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (6 bp):
TATATA
Found at i:13532254 original size:4 final size:4
Alignment explanation
Indices: 13532225--13532289 Score: 76
Period size: 4 Copynumber: 16.2 Consensus size: 4
13532215 TGAATATAAG
* * * * *
13532225 TATA AATA TATA CATA TATG TATA TATA TATA TATT TATA CATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
13532273 CATA TATA TATA TATA T
1 TATA TATA TATA TATA T
13532290 CCTGGTGTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:13534580 original size:37 final size:40
Alignment explanation
Indices: 13534501--13534581 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 40
13534491 TTGTTTTTGT
13534501 TTATTTAAATATGTATAAAAATATAAATTAATATTATTTAA
1 TTATTTAAATATGTATAAAAATATAAATTAATATTA-TTAA
* *
13534542 TTATTTATATATTTA-AAAAATATATAA-T-ATATTA-TAA
1 TTATTTAAATATGTATAAAAATATA-AATTAATATTATTAA
13534579 TTA
1 TTA
13534582 AAACATCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 6 0.16
39 6 0.16
40 10 0.27
41 15 0.41
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (40 bp):
TTATTTAAATATGTATAAAAATATAAATTAATATTATTAA
Found at i:13534845 original size:15 final size:16
Alignment explanation
Indices: 13534825--13534857 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13534815 TAAATTGGAT
*
13534825 AAAATTTT-ATTTTTA
1 AAAATTTTGATATTTA
13534840 AAAATTTTGATATTTA
1 AAAATTTTGATATTTA
13534856 AA
1 AA
13534858 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AAAATTTTGATATTTA
Found at i:13535213 original size:17 final size:18
Alignment explanation
Indices: 13535193--13535231 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
13535183 TGAAATTAAA
* *
13535193 AAAATCTTCAAATATTT-
1 AAAATCTTAAAAAATTTC
13535210 AAAATCTTAAAAAATTTC
1 AAAATCTTAAAAAATTTC
13535228 AAAA
1 AAAA
13535232 ATACAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATCTTAAAAAATTTC
Found at i:13539331 original size:25 final size:25
Alignment explanation
Indices: 13539303--13539354 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
13539293 AAAAGGTAAT
13539303 TTGAGTGTTAAATTAATTGCTTACC
1 TTGAGTGTTAAATTAATTGCTTACC
*
13539328 TTGAGTGTTCAATTAATTGCTTACC
1 TTGAGTGTTAAATTAATTGCTTACC
13539353 TT
1 TT
13539355 AAATTGGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (25 bp):
TTGAGTGTTAAATTAATTGCTTACC
Found at i:13539722 original size:17 final size:17
Alignment explanation
Indices: 13539700--13539736 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
13539690 GCGGCCGCTA
13539700 TATAGCTATCCGATCGC
1 TATAGCTATCCGATCGC
13539717 TATAGCTATCCGATCGC
1 TATAGCTATCCGATCGC
13539734 TAT
1 TAT
13539737 TTAAATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (17 bp):
TATAGCTATCCGATCGC
Found at i:13542076 original size:20 final size:22
Alignment explanation
Indices: 13542034--13542077 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
13542024 AAATTAAACT
*
13542034 TAATAGTATGAAAAAATATATA
1 TAATAGTATGAAAAAATAAATA
*
13542056 TAATA-TAT-AAAAGATAAATA
1 TAATAGTATGAAAAAATAAATA
13542076 TA
1 TA
13542078 CTGTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 3 0.15
22 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
TAATAGTATGAAAAAATAAATA
Found at i:13542266 original size:14 final size:15
Alignment explanation
Indices: 13542247--13542275 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13542237 AGCTTTGTTT
13542247 CTTTCTTTA-TATGG
1 CTTTCTTTACTATGG
13542261 CTTTCTTTACTATGG
1 CTTTCTTTACTATGG
13542276 GATTCTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (15 bp):
CTTTCTTTACTATGG
Found at i:13542305 original size:2 final size:2
Alignment explanation
Indices: 13542298--13542324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13542288 CCTGTAAGCA
13542298 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 A
13542325 AACATCCTGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13544660 original size:12 final size:11
Alignment explanation
Indices: 13544643--13544714 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 11
13544633 CCTTTCTTTC
13544643 TTTTTTTTGTTG
1 TTTTTTTT-TTG
13544655 TTTTTTGTTTTG
1 TTTTTT-TTTTG
13544667 TTTTTGTTTTTG
1 TTTTT-TTTTTG
* *
13544679 TTCTTGTTTTG
1 TTTTTTTTTTG
*
13544690 -TTTTGTTTTG
1 TTTTTTTTTTG
* *
13544700 TTTTGTTTTTC
1 TTTTTTTTTTG
13544711 TTTT
1 TTTT
13544715 AAATTAAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
10 9 0.18
11 16 0.31
12 23 0.45
13 3 0.06
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:13544667 original size:5 final size:5
Alignment explanation
Indices: 13544643--13544708 Score: 82
Period size: 5 Copynumber: 12.8 Consensus size: 5
13544633 CCTTTCTTTC
13544643 TTTT- TTTTG TTGTT- TTTTG TTTTG TTTTTG TTTTTG TTCTTG TTTTG
1 TTTTG TTTTG TT-TTG TTTTG TTTTG -TTTTG -TTTTG TT-TTG TTTTG
13544690 TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTT
13544709 TCTTTTAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.11
5 33 0.58
6 18 0.32
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:13544678 original size:27 final size:27
Alignment explanation
Indices: 13544646--13544703 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
13544636 TTCTTTCTTT
*
13544646 TTTTTGTTGTT-TTTTGTTTTGTTTTTG
1 TTTTTGTTCTTGTTTTGTTTTG-TTTTG
13544673 TTTTTGTTCTTGTTTTGTTTTGTTTTG
1 TTTTTGTTCTTGTTTTGTTTTGTTTTG
13544700 TTTT
1 TTTT
13544704 GTTTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (27 bp):
TTTTTGTTCTTGTTTTGTTTTGTTTTG
Found at i:13544862 original size:35 final size:35
Alignment explanation
Indices: 13544770--13544952 Score: 102
Period size: 35 Copynumber: 5.1 Consensus size: 35
13544760 AGATGACTGG
* * *
13544770 AACAACATCACAGGTCGAAAAAATAAATATGACCAA
1 AACAACATCGCAGGTC-AAAAAATAAAAATGATCAA
* * * *
13544806 GACAATATTACG-A-ATCGAAAAATAAAAATGATCAA
1 AACAACA-T-CGCAGGTCAAAAAATAAAAATGATCAA
*
13544841 AACAACATCGCAGGTCAAAAAATAAAAATGATTAA
1 AACAACATCGCAGGTCAAAAAATAAAAATGATCAA
* * * * * * *
13544876 GACAATACTAGC-GGTAAGAAAAACAAATATGATCGA
1 AACAACA-TCGCAGGTCA-AAAAATAAAAATGATCAA
* * * * * *
13544912 GATAACATCGTAAGTTGAAAAAATAAAAATGATCGA
1 AACAACATCG-CAGGTCAAAAAATAAAAATGATCAA
13544948 AACAA
1 AACAA
13544953 TATTATAAGT
Statistics
Matches: 109, Mismatches: 30, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
33 2 0.02
34 2 0.02
35 51 0.47
36 48 0.44
37 5 0.05
38 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (35 bp):
AACAACATCGCAGGTCAAAAAATAAAAATGATCAA
Found at i:13544897 original size:71 final size:69
Alignment explanation
Indices: 13544770--13544954 Score: 176
Period size: 71 Copynumber: 2.6 Consensus size: 69
13544760 AGATGACTGG
* * * * *
13544770 AACAACATCACAGGTCGAAAAAATAAATATGACCAAGACAATATTACGAATCGAAAAATAAAAAT
1 AACAACATCGCAGGTC-AAAAAATAAAAATGATCAAGACAATACTACGAA-CGAAAAACAAAAAT
13544835 GATCAA
64 GATCAA
* *
13544841 AACAACATCGCAGGTCAAAAAATAAAAATGATTAAGACAATACTAGCGGTAA-GAAAAACAAATA
1 AACAACATCGCAGGTCAAAAAATAAAAATGATCAAGACAATACTA-C-G-AACGAAAAACAAAAA
*
13544905 TGATCGA
63 TGATCAA
* * * * *
13544912 GATAACATCGTAAGTTGAAAAAATAAAAATGATCGAA-ACAATA
1 AACAACATCG-CAGGTCAAAAAATAAAAATGATC-AAGACAATA
13544955 TTATAAGTCA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
70 25 0.26
71 40 0.42
72 26 0.27
73 4 0.04
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (69 bp):
AACAACATCGCAGGTCAAAAAATAAAAATGATCAAGACAATACTACGAACGAAAAACAAAAATGA
TCAA
Found at i:13545007 original size:72 final size:71
Alignment explanation
Indices: 13544926--13545199 Score: 169
Period size: 71 Copynumber: 3.9 Consensus size: 71
13544916 ACATCGTAAG
* * * *
13544926 TTGAAAAAATAAAAATGA-TCGAAACAATATTATAAGTCAAAAAAATAAAGATGATCAGGACAAC
1 TTGAAAAAATAAAAATGACT-GAAACAACATCACAAGTC-AAAAAATAAAGATGACCAGGACAAC
13544990 ACCAATGA
64 ACCAATGA
* * ** *
13544998 TTGAGAAAATAAATATGACTGGGACAACATCACAAGTCAAAAAATAAAGATGACCAGGATAACAT
1 TTGAAAAAATAAAAATGACTGAAACAACATCACAAGTCAAAAAATAAAGATGACCAGGACAACA-
13545063 CACAA-G-
65 C-CAATGA
* * ** * **
13545069 TT-AAAAAAT-AATATGAC-CAAGACAACA-CTGTAAGTAAAAAAAATAAAGAT-----GGTTAA
1 TTGAAAAAATAAAAATGACTGAA-ACAACATC-ACAAGT-CAAAAAATAAAGATGACCAGGACAA
*
13545125 CACCAATGG
63 CACCAATGA
* * * * * * *
13545134 TTGAAAAAATAAATATGA-TCAAGATAACATCACAGGTCAAAAAATAAAAATGATCAAGACAACA
1 TTGAAAAAATAAAAATGACTGAA-ACAACATCACAAGTCAAAAAATAAAGATGACCAGGACAACA
13545198 CC
65 CC
13545200 GTAGGTCAAA
Statistics
Matches: 159, Mismatches: 26, Indels: 35
0.72 0.12 0.16
Matches are distributed among these distances:
63 3 0.02
64 2 0.01
65 9 0.06
66 19 0.12
67 19 0.12
68 2 0.01
69 18 0.11
70 19 0.12
71 33 0.21
72 31 0.19
73 4 0.03
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.19
Consensus pattern (71 bp):
TTGAAAAAATAAAAATGACTGAAACAACATCACAAGTCAAAAAATAAAGATGACCAGGACAACAC
CAATGA
Found at i:13545051 original size:35 final size:35
Alignment explanation
Indices: 13544959--13545095 Score: 127
Period size: 35 Copynumber: 3.9 Consensus size: 35
13544949 ACAATATTAT
*
13544959 AAGTCAAAAAAATAAAGATGATCAGGACAACA-C-C
1 AAGTC-AAAAAATAAAGATGACCAGGACAACATCAC
* * * **
13544993 AATGATTGAGAAAATAAATATGACTGGGACAACATCAC
1 AA-G--TCAAAAAATAAAGATGACCAGGACAACATCAC
*
13545031 AAGTCAAAAAATAAAGATGACCAGGATAACATCAC
1 AAGTCAAAAAATAAAGATGACCAGGACAACATCAC
* * *
13545066 AAGTTAAAAAAT-AATATGACCAAGACAACA
1 AAGTCAAAAAATAAAGATGACCAGGACAACA
13545096 CTGTAAGTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
34 17 0.21
35 38 0.46
36 21 0.26
37 3 0.04
38 3 0.04
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.16
Consensus pattern (35 bp):
AAGTCAAAAAATAAAGATGACCAGGACAACATCAC
Found at i:13545166 original size:101 final size:102
Alignment explanation
Indices: 13545036--13545221 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
13545026 ATCACAAGTC
* * * *
13545036 AAAAAATAAAGATGACCAGGATAACATCACAAGTTAAAAAAT-AATATGACCAAGACAACACTGT
1 AAAAAATAAAGATGACCAAGATAACATCACAAGTCAAAAAATAAAAATGACCAAGACAACACCGT
13545100 AAGTAAAAAAAATAAAGATGGTTAACACCAATGGTTG
66 AAGTAAAAAAAATAAAGATGGTTAACACCAATGGTTG
* * * *
13545137 AAAAAATAAATATGATCAAGATAACATCACAGGTCAAAAAATAAAAATGATCAAGACAACACCGT
1 AAAAAATAAAGATGACCAAGATAACATCACAAGTCAAAAAATAAAAATGACCAAGACAACACCGT
* *
13545202 AGGTCAAAAAAATAAAGATG
66 AAGTAAAAAAAATAAAGATG
13545222 ATCGAGATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 37 0.50
102 37 0.50
ACGTcount: A:0.55, C:0.13, G:0.14, T:0.18
Consensus pattern (102 bp):
AAAAAATAAAGATGACCAAGATAACATCACAAGTCAAAAAATAAAAATGACCAAGACAACACCGT
AAGTAAAAAAAATAAAGATGGTTAACACCAATGGTTG
Found at i:13545176 original size:35 final size:35
Alignment explanation
Indices: 13545137--13545261 Score: 124
Period size: 35 Copynumber: 3.5 Consensus size: 35
13545127 CCAATGGTTG
*
13545137 AAAAAATAAATATGATCAAGATAACATCACAGGTC
1 AAAAAATAAATATGATCAAGACAACATCACAGGTC
* * **
13545172 AAAAAATAAAAATGATCAAGACAACACCGTAGGTC
1 AAAAAATAAATATGATCAAGACAACATCACAGGTC
* * * * *
13545207 AAAAAAATAAAGATGATCGAGATAACACCACAGGTTGA
1 -AAAAAATAAATATGATCAAGACAACATCACAGG-T-C
*
13545245 AAAAAATAAAGATGATC
1 AAAAAATAAATATGATC
13545262 GGACAATACT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 30 0.39
36 28 0.37
37 18 0.24
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (35 bp):
AAAAAATAAATATGATCAAGACAACATCACAGGTC
Found at i:13545177 original size:36 final size:36
Alignment explanation
Indices: 13544771--13545261 Score: 196
Period size: 36 Copynumber: 13.9 Consensus size: 36
13544761 GATGACTGGA
* *
13544771 ACAACATCACAGGTCGAAAAAATAAATATGACCAAG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* * * * * *
13544807 ACAATATTAC-GAATC-GAAAAATAAAAATGATCAAA
1 ACAACATCACAG-GTCAAAAAAATAAATATGATCAAG
* * *
13544842 ACAACATCGCAGGTC-AAAAAATAAAAATGATTAAG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* * *
13544877 ACAATA-CTAGC-GGT-AAGAAAAACAAATATGATCGAG
1 ACAACATC-A-CAGGTCAA-AAAAATAAATATGATCAAG
* ** * ** *
13544913 ATAACATCGTAAGTTGAAAAAATAAAAATGATCGAA-
1 ACAACATCACAGGTCAAAAAAATAAATATGATC-AAG
* * * * * *
13544949 ACAATATTATAAGTCAAAAAAATAAAGATGATCAGG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* * ** * **
13544985 ACAACACCA-ATGATTGAGAAAATAAATATGA-CTGGG
1 ACAACATCACA-GGTCAAAAAAATAAATATGATC-AAG
* * * *
13545021 ACAACATCACAAGTC-AAAAAATAAAGATGACCAGG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* * * *
13545056 ATAACATCACAAGT-TAAAAAAT-AATATGACCAAG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* * * * *
13545090 ACAACACTGTA-A-GTAAAAAAAATAAAGATGGT-TA-
1 ACAACA-T-CACAGGTCAAAAAAATAAATATGATCAAG
**
13545124 AC-AC--CA-ATGGTTGAAAAAATAAATATGATCAAG
1 ACAACATCACA-GGTCAAAAAAATAAATATGATCAAG
* *
13545157 ATAACATCACAGGTC-AAAAAATAAAAATGATCAAG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* ** * *
13545192 ACAACACCGTAGGTCAAAAAAATAAAGATGATCGAG
1 ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
* * * *
13545228 ATAACACCACAGGTTGAAAAAAATAAAGATGATC
1 ACAACATCACAGG-TCAAAAAAATAAATATGATC
13545262 GGACAATACT
Statistics
Matches: 342, Mismatches: 83, Indels: 59
0.71 0.17 0.12
Matches are distributed among these distances:
29 2 0.01
31 16 0.05
32 1 0.00
33 3 0.01
34 22 0.06
35 130 0.38
36 144 0.42
37 24 0.07
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (36 bp):
ACAACATCACAGGTCAAAAAAATAAATATGATCAAG
Found at i:13545278 original size:36 final size:35
Alignment explanation
Indices: 13545172--13545305 Score: 135
Period size: 36 Copynumber: 3.7 Consensus size: 35
13545162 ATCACAGGTC
* * *
13545172 AAAAAATAAAAATGATCAAGACAACACCGTAGGTCA
1 AAAAAATAAAGATGATC-GGACAACACCGTAGGTTA
* **
13545208 AAAAAATAAAGATGATCGAGATAACACCACAGGTTGA
1 AAAAAATAAAGATGATCG-GACAACACCGTAGGTT-A
* *
13545245 AAAAAATAAAGATGATCGGACAATACTGTAGGTT-
1 AAAAAATAAAGATGATCGGACAACACCGTAGGTTA
* *
13545279 AAAAAATAAAGATAATCGAAACAACAC
1 AAAAAATAAAGATGATCG-GACAACAC
13545306 TAATGATCAG
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
34 17 0.21
35 6 0.07
36 39 0.48
37 19 0.23
ACGTcount: A:0.54, C:0.13, G:0.16, T:0.16
Consensus pattern (35 bp):
AAAAAATAAAGATGATCGGACAACACCGTAGGTTA
Found at i:13545288 original size:107 final size:102
Alignment explanation
Indices: 13545036--13545261 Score: 258
Period size: 101 Copynumber: 2.2 Consensus size: 102
13545026 ATCACAAGTC
* * * * * * *
13545036 AAAAAATAAAGATGACCAGGATAACATCACAAGTTAAAAAAT-AATATGACCAAGACAACACTGT
1 AAAAAATAAAGATGATCAAGACAACATCACAGGTTAAAAAATAAAAATGATCAAGACAACACCGT
*
13545100 AAGTAAAAAAAATAAAGATGGTTAACACCAATGGTTG
66 AAGTAAAAAAAATAAAGATGGATAACACCAATGGTTG
* * *
13545137 AAAAAATAAATATGATCAAGATAACATCACAGGTCAAAAAATAAAAATGATCAAGACAACACCGT
1 AAAAAATAAAGATGATCAAGACAACATCACAGGTTAAAAAATAAAAATGATCAAGACAACACCGT
* *
13545202 AGGTCAAAAAAATAAAGATGATCGAGATAACACCACA-GGTTG
66 AAGTAAAAAAAAT-AA-A-GAT-G-GATAACACCA-ATGGTTG
13545244 AAAAAAATAAAGATGATC
1 -AAAAAATAAAGATGATC
13545262 GGACAATACT
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
101 37 0.35
102 30 0.29
103 2 0.02
104 1 0.01
105 3 0.03
106 1 0.01
107 14 0.13
108 17 0.16
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (102 bp):
AAAAAATAAAGATGATCAAGACAACATCACAGGTTAAAAAATAAAAATGATCAAGACAACACCGT
AAGTAAAAAAAATAAAGATGGATAACACCAATGGTTG
Found at i:13545297 original size:71 final size:70
Alignment explanation
Indices: 13545132--13545297 Score: 199
Period size: 71 Copynumber: 2.3 Consensus size: 70
13545122 TAACACCAAT
* * * *
13545132 GGTTGAAAAAATAAATATGATCAAGATAACATCACAGGTCAAAAAATAAAAATGATCAAGACAAC
1 GGTT-AAAAAATAAAGATGATCGAGATAACACCACAGGTAAAAAAATAAAAATGATCAAGACAAC
13545197 ACCGTA
65 ACCGTA
* * *
13545203 GGTCAAAAAAATAAAGATGATCGAGATAACACCACAGGTTGAAAAAAATAAAGATGATC-GGACA
1 GGT-TAAAAAATAAAGATGATCGAGATAACACCACAGG-T-AAAAAAATAAAAATGATCAAGACA
* *
13545267 ATACTGTA
63 ACACCGTA
*
13545275 GGTTAAAAAATAAAGATAATCGA
1 GGTTAAAAAATAAAGATGATCGA
13545298 AACAACACTA
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
71 51 0.63
72 14 0.17
73 16 0.20
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (70 bp):
GGTTAAAAAATAAAGATGATCGAGATAACACCACAGGTAAAAAAATAAAAATGATCAAGACAACA
CCGTA
Found at i:13545320 original size:71 final size:72
Alignment explanation
Indices: 13545137--13545334 Score: 172
Period size: 71 Copynumber: 2.8 Consensus size: 72
13545127 CCAATGGTTG
* * * * *
13545137 AAAAAATAAATATGATC-AAGATAACATCACAGG-TC-AAAAAATAAAAATGATCAAGACAACAC
1 AAAAAATAAAGATAATCGAA-ACAACACCACAGGATCAAAAAAATAAAAATGATC-GGACAACAC
13545199 CGTAGGTCA
64 CGTAGGTCA
* * * * * * * *
13545208 AAAAAATAAAGATGATCGAGATAACACCACAGGTTGAAAAAAATAAAGATGATCGGACAATACTG
1 AAAAAATAAAGATAATCGAAACAACACCACAGGATCAAAAAAATAAAAATGATCGGACAACACCG
*
13545273 TAGGT-T
66 TAGGTCA
* * * * *
13545279 AAAAAATAAAGATAATCGAAACAACACTA-ATGATCAGAAAAACAAATATGATCGGA
1 AAAAAATAAAGATAATCGAAACAACACCACAGGATCAAAAAAATAAAAATGATCGGA
13545335 ATAATATTAT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
70 21 0.20
71 53 0.50
72 15 0.14
73 16 0.15
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (72 bp):
AAAAAATAAAGATAATCGAAACAACACCACAGGATCAAAAAAATAAAAATGATCGGACAACACCG
TAGGTCA
Found at i:13545806 original size:36 final size:36
Alignment explanation
Indices: 13545548--13545811 Score: 144
Period size: 36 Copynumber: 7.3 Consensus size: 36
13545538 AATATAACCA
* * * *
13545548 GGACAACACCGGAGGTC-AAAAAATAAAAATGACTA
1 GGACAACACCGCAAGTCAAAAAAATAAAGATGACTG
* * * ** *
13545583 AGATAACACCGCTAGTTGAAAAAATAAATATGACTG
1 GGACAACACCGCAAGTCAAAAAAATAAAGATGACTG
* * * *
13545619 GGACAATA-C-CAATGGCCAAAAAAATAAATATGATTG
1 GGACAACACCGCAA--GTCAAAAAAATAAAGATGACTG
* * * * *
13545655 GAACAACATCACAAGTGAAAAAAATAAAGATGACCG
1 GGACAACACCGCAAGTCAAAAAAATAAAGATGACTG
* * * * * *
13545691 AGATAATACCACAAGTTAAAAAAAAAAAAAAGATGACTG
1 GGACAACACCGCAAG-T--CAAAAAAATAAAGATGACTG
* * * *
13545730 GGACAACACC-AAATGATC-AAAAAATAAATAT-AATCA
1 GGACAACACCGCAA-G-TCAAAAAAATAAAGATGACT-G
*
13545766 GGACAACACTGCAAGTCAAAAAAATAAAGATGACTG
1 GGACAACACCGCAAGTCAAAAAAATAAAGATGACTG
13545802 GGACAACACC
1 GGACAACACC
13545812 AAAGGTCAAG
Statistics
Matches: 169, Mismatches: 47, Indels: 25
0.70 0.20 0.10
Matches are distributed among these distances:
34 2 0.01
35 16 0.09
36 114 0.67
37 6 0.04
38 5 0.03
39 26 0.15
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.15
Consensus pattern (36 bp):
GGACAACACCGCAAGTCAAAAAAATAAAGATGACTG
Found at i:13545820 original size:36 final size:36
Alignment explanation
Indices: 13545601--13545831 Score: 157
Period size: 36 Copynumber: 6.3 Consensus size: 36
13545591 CCGCTAGTTG
* * * *
13545601 AAAAAATAAATATGACTGGGACAATACCAATGGCCA
1 AAAAAATAAAGATGACTGGGACAACACCAAAGGTCA
* * * * *
13545637 AAAAAATAAATATGATTGGAACAACATCACAA-GTGA
1 AAAAAATAAAGATGACTGGGACAACACCA-AAGGTCA
* * * * * *
13545673 AAAAAATAAAGATGACCGAGATAATACCACAAGTTAAAA
1 AAAAAATAAAGATGACTGGGACAACACCA-AAGGT--CA
* *
13545712 AAAAAAAAAAGATGACTGGGACAACACCAAATGATC-
1 AAAAAATAAAGATGACTGGGACAACACCAAA-GGTCA
* * *
13545748 AAAAAATAAATAT-AATCAGGACAACACTGC-AA-GTCA
1 AAAAAATAAAGATGACT-GGGACAACAC--CAAAGGTCA
13545784 AAAAAATAAAGATGACTGGGACAACACCAAAGGTCA
1 AAAAAATAAAGATGACTGGGACAACACCAAAGGTCA
* *
13545820 AGAAGATAAAGA
1 AAAAAATAAAGA
13545832 ATAAAGTTTC
Statistics
Matches: 149, Mismatches: 34, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
34 1 0.01
35 6 0.04
36 106 0.71
37 6 0.04
38 3 0.02
39 27 0.18
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.15
Consensus pattern (36 bp):
AAAAAATAAAGATGACTGGGACAACACCAAAGGTCA
Found at i:13546833 original size:7 final size:7
Alignment explanation
Indices: 13546821--13546925 Score: 90
Period size: 7 Copynumber: 14.9 Consensus size: 7
13546811 CCTAAATTAT
*
13546821 TTTTTTC
1 TTTTTTA
13546828 TTTTTTA
1 TTTTTTA
* *
13546835 TTTCTTC
1 TTTTTTA
13546842 TTTTCTT-
1 TTTT-TTA
*
13546849 TTGATTTA
1 TT-TTTTA
13546857 TTTTTTA
1 TTTTTTA
13546864 TTTTTTA
1 TTTTTTA
13546871 -TTTTTA
1 TTTTTTA
13546877 TTTTTTTA
1 -TTTTTTA
13546885 TTTTTTA
1 TTTTTTA
13546892 TTTTTTGA
1 TTTTTT-A
*
13546900 -TTTTGA
1 TTTTTTA
13546906 TTTTTTA
1 TTTTTTA
* *
13546913 CTTTTGA
1 TTTTTTA
13546920 TTTTTT
1 TTTTTT
13546926 TGCTTTAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
6 7 0.09
7 60 0.76
8 12 0.15
ACGTcount: A:0.11, C:0.05, G:0.04, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:13546884 original size:28 final size:28
Alignment explanation
Indices: 13546817--13546925 Score: 114
Period size: 28 Copynumber: 3.9 Consensus size: 28
13546807 TTAGCCTAAA
* * *
13546817 TTATTTTTTTCTTTTTTATTTCTTCTTT
1 TTATTTTTTTATTTTTTATTTTTTATTT
*
13546845 TCT-TTTGATTTATTTTTTATTTTTTATTT
1 T-TATTT-TTTTATTTTTTATTTTTTATTT
13546874 TTATTTTTTTATTTTTTATTTTTTGATTT
1 TTATTTTTTTATTTTTTATTTTTT-ATTT
* * *
13546903 TGA-TTTTTTACTTTTGATTTTTT
1 TTATTTTTTTATTTTTTATTTTTT
13546926 TGCTTTAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
28 40 0.58
29 29 0.42
ACGTcount: A:0.12, C:0.05, G:0.04, T:0.80
Consensus pattern (28 bp):
TTATTTTTTTATTTTTTATTTTTTATTT
Found at i:13546932 original size:20 final size:19
Alignment explanation
Indices: 13546919--13546963 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13546909 TTTACTTTTG
13546919 ATTTTTTTGCTTTAATTTA
1 ATTTTTTTGCTTTAATTTA
*
13546938 ATTTTTTTGATTT--TTTA
1 ATTTTTTTGCTTTAATTTA
13546955 CATTTTTTT
1 -ATTTTTTT
13546964 TACTAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
19 12 0.50
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (19 bp):
ATTTTTTTGCTTTAATTTA
Found at i:13546936 original size:28 final size:28
Alignment explanation
Indices: 13546873--13546953 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
13546863 ATTTTTTATT
* * *
13546873 TTTATTTTTTTATTTT-TTATTTTTTGAT
1 TTTAATTTTTTATTTTGAT-TTTTTTGAC
*
13546901 TTTGATTTTTTACTTTTGATTTTTTTG-C
1 TTTAATTTTTTA-TTTTGATTTTTTTGAC
13546929 TTTAATTTAATTT-TTTTGATTTTTT
1 TTTAATTT--TTTATTTTGATTTTTT
13546954 ACATTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 29 0.66
29 11 0.25
30 4 0.09
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (28 bp):
TTTAATTTTTTATTTTGATTTTTTTGAC
Found at i:13557202 original size:111 final size:110
Alignment explanation
Indices: 13557009--13557233 Score: 387
Period size: 111 Copynumber: 2.0 Consensus size: 110
13556999 ATATGCAAAA
*
13557009 ATATGCAAAGTGATGTATTAATTAAAATAACATAAAAAAATCATAAACACCAAATCAAAACAAAG
1 ATATGCAAAGTGATGTATTAATCAAAATAACATAAAAAAATCATAAACACCAAATCAAAACAAAG
* *
13557074 AAATAACTAATATAAAATTTATTTTATTTATTAACTTATGTGTAC
66 AAATAACTAACATAAAATTTATTTTATTTATTAACTTATGCGTAC
* *
13557119 ATATGCAAAGTGATGTATTAATCAAAATAACATAAAAAAAATCATAATCACCAAATCAAGACAAA
1 ATATGCAAAGTGATGTATTAATCAAAATAACAT-AAAAAAATCATAAACACCAAATCAAAACAAA
*
13557184 GAAATAACTAACATAAAATTTATTTTATTTATTAACTTATGCGTAT
65 GAAATAACTAACATAAAATTTATTTTATTTATTAACTTATGCGTAC
13557230 ATAT
1 ATAT
13557234 ATAATTTTTT
Statistics
Matches: 108, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 32 0.30
111 76 0.70
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.32
Consensus pattern (110 bp):
ATATGCAAAGTGATGTATTAATCAAAATAACATAAAAAAATCATAAACACCAAATCAAAACAAAG
AAATAACTAACATAAAATTTATTTTATTTATTAACTTATGCGTAC
Found at i:13558131 original size:3 final size:3
Alignment explanation
Indices: 13558125--13558202 Score: 79
Period size: 3 Copynumber: 24.3 Consensus size: 3
13558115 ACTATAAGTC
13558125 ACT ACT ACT ACT AGCTT AAGCT ACT ACCT ACT A-T ACT ACT GACT ACT
1 ACT ACT ACT ACT A-C-T -A-CT ACT A-CT ACT ACT ACT ACT -ACT ACT
13558172 ACT ACT A-T ACT ACT ACT AGCT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT A-CT ACT ACT ACT A
13558203 ACTATAAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.06
3 47 0.70
4 11 0.16
5 2 0.03
6 3 0.04
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:13558178 original size:21 final size:20
Alignment explanation
Indices: 13558036--13558199 Score: 94
Period size: 19 Copynumber: 8.0 Consensus size: 20
13558026 AACATTAATA
13558036 ACTACTACTACTACAATACCTAT
1 ACTACTACTACTAC--TA-CTAT
* *
13558059 AGGTTCTACTACTTACTAGCTA-
1 A-CTACTACTAC-TACTA-CTAT
13558081 ACATACTA-TA-TACTATCTAT
1 AC-TACTACTACTACTA-CTAT
**
13558101 ACTA-TACTAAAACTACTAT
1 ACTACTACTACTACTACTAT
*
13558120 AAGTCACTACTACTACTAGCT-T
1 -ACT-ACTACTACTACTA-CTAT
13558142 A--AGCTACTAC--CTACTAT
1 ACTA-CTACTACTACTACTAT
13558159 ACTACTGACTACTACTACTAT
1 ACTACT-ACTACTACTACTAT
13558180 ACTACTACTAGCTACTACTA
1 ACTACTACTA-CTACTACTA
13558200 CTAACTATAA
Statistics
Matches: 113, Mismatches: 10, Indels: 38
0.70 0.06 0.24
Matches are distributed among these distances:
16 2 0.02
17 5 0.04
18 5 0.04
19 29 0.26
20 12 0.11
21 26 0.23
22 15 0.13
23 8 0.07
24 8 0.07
25 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (20 bp):
ACTACTACTACTACTACTAT
Found at i:13562728 original size:21 final size:22
Alignment explanation
Indices: 13562676--13562733 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
13562666 ATAAAAAACT
13562676 AAAAATAAAATAAA-AACTTAA
1 AAAAATAAAATAAATAACTTAA
* *
13562697 GATAATAAAATAAATAA-TTAA
1 AAAAATAAAATAAATAACTTAA
*
13562718 AAAAATGAAATGAAAT
1 AAAAATAAAAT-AAAT
13562734 CGAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (22 bp):
AAAAATAAAATAAATAACTTAA
Found at i:13562741 original size:18 final size:19
Alignment explanation
Indices: 13562718--13562764 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
13562708 AAATAATTAA
13562718 AAAAATGAAATG-AAATCG
1 AAAAATGAAATGAAAATCG
* *
13562736 AAAAATAAAATGAAAATGG
1 AAAAATGAAATGAAAATCG
*
13562755 AAAAAAGAAA
1 AAAAATGAAA
13562765 ACCTATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAAATGAAATGAAAATCG
Found at i:13564045 original size:239 final size:238
Alignment explanation
Indices: 13563615--13564049 Score: 522
Period size: 239 Copynumber: 1.8 Consensus size: 238
13563605 GACTGAGTTA
* * *
13563615 AGATCAAATGACCGAAATAAAATCGCGAGTCTAAAGATGAAGTGACCAAGATCAAGTCAAGTTCA
1 AGATCAAATGACCGAAATAAAATCACGAGTCGAAAGATGAAGTGACCAAGATCAAGTCAAGGTCA
* * ** * *
13563680 AAGATGAATGACCAGGATAAATTCGTAAGTCAGGAAAATGATTTGGATTAAGCCGAAATCGAATG
66 AAGATGAATGACCAAGATAAATTCATAAGTCAAAAAAATGATATGGACTAAGCCGAAATCGAATG
* * * *
13563745 ACCAGGATAAAATCACTAGTCTAAAGATAAAGCAACCGGGACTAAGTTGAGATCTAAGATGAATG
131 ACCAGGATAAAATCACGAGTCTAAAGATAAAG-AACCAGGACTAAGTCGAGATCAAAGATGAATG
13563810 ATCAACATGAAGCTATGAATCAAAAAAAAAATTGGATTGAGTCG
195 ATCAACATGAAGCTATGAATCAAAAAAAAAATTGGATTGAGTCG
* * * * *
13563854 AGATCAAATGACTGAGATGAAATCACGAGTCGAAAGATGAAG-GAACTAGGATCAAGTCAAGGTC
1 AGATCAAATGACCGAAATAAAATCACGAGTCGAAAGATGAAGTG-ACCAAGATCAAGTCAAGGTC
* * * * *
13563918 GAAGATGAATGACTAAGATGAAA-TCATGAGTTAAAAAAATGATATGGACTAAG-CTAAGATCGA
65 AAAGATGAATGACCAAGAT-AAATTCATAAGTCAAAAAAATGATATGGACTAAGCCGAA-ATCGA
* * *
13563981 ATGACCAGGATGAAATCACGAGTCTAAAGATGAAATG-ACCAAGG-TTGAGTCGA-AGTCAAAGA
128 ATGACCAGGATAAAATCACGAGTCTAAAGAT-AAA-GAACC-AGGACTAAGTCGAGA-TCAAAGA
13564043 TGAATGA
189 TGAATGA
13564050 CCGAAATAAA
Statistics
Matches: 163, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
238 5 0.03
239 149 0.91
240 8 0.05
241 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (238 bp):
AGATCAAATGACCGAAATAAAATCACGAGTCGAAAGATGAAGTGACCAAGATCAAGTCAAGGTCA
AAGATGAATGACCAAGATAAATTCATAAGTCAAAAAAATGATATGGACTAAGCCGAAATCGAATG
ACCAGGATAAAATCACGAGTCTAAAGATAAAGAACCAGGACTAAGTCGAGATCAAAGATGAATGA
TCAACATGAAGCTATGAATCAAAAAAAAAATTGGATTGAGTCG
Found at i:13564098 original size:120 final size:121
Alignment explanation
Indices: 13563634--13564090 Score: 360
Period size: 120 Copynumber: 3.8 Consensus size: 121
13563624 GACCGAAATA
* * * **
13563634 AAATCGCGAGTCTAAAGATGAAGTGACCAA-GATCAAGTCAAGTTCAAAGATGAATGACCAGGAT
1 AAATCACGAGTCTAAAGATGAAATGACCAAGGATCAAGTCAAGATCAAAGATGAATGACCAACAT
** * * ** * *
13563698 AAATTCGTAAGTCAGGAAAATGATTTGGATTAAGCCGAAATCGAATGACCAGGATA
66 AAAACCATGAGTCAAAAAAATGATTTGGATTAAGCCGAGATCGAATGACCAGGATG
* * ** * *
13563754 AAATCACTAGTCTAAAGAT-AAA-GCAACC-GGGA-CTAAGTTGAGATCTAAGATGAATGATCAA
1 AAATCACGAGTCTAAAGATGAAATG--ACCAAGGATC-AAGTCAAGATCAAAGATGAATGACCAA
* * * * * * * * * *
13563815 CATGAAGCTATGAATCAAAAAAA-AAATTGGATTGAGTCGAGATCAAATGA-CTGAGATG
63 CATAAAACCATGAGTCAAAAAAATGATTTGGATTAAGCCGAGATCGAATGACCAG-GATG
* * * * * * * *
13563873 AAATCACGAGTCGAAAGATG-AAGGAACTAGGATCAAGTCAAGGTCGAAGATGAATGACTAAGAT
1 AAATCACGAGTCTAAAGATGAAATGACCAAGGATCAAGTCAAGATCAAAGATGAATGACCAACAT
* * * * * **
13563937 GAAATCATGAGTTAAAAAAATGATATGGACTAAGCTAAGATCGAATGACCAGGATG
66 AAAACCATGAGTCAAAAAAATGATTTGGATTAAGCCGAGATCGAATGACCAGGATG
**
13563993 AAATCACGAGTCTAAAGATGAAATGACCAAGG-TTGAGTCGAAG-TCAAAGATGAATGACCGAA-
1 AAATCACGAGTCTAAAGATGAAATGACCAAGGATCAAGTC-AAGATCAAAGATGAATGACC-AAC
*
13564055 ATAAAACCATGAGTCAAAAAAATGATTTGAATTAAG
64 ATAAAACCATGAGTCAAAAAAATGATTTGGATTAAG
13564091 TTGAGATCAA
Statistics
Matches: 255, Mismatches: 68, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
118 5 0.02
119 87 0.34
120 148 0.58
121 15 0.06
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (121 bp):
AAATCACGAGTCTAAAGATGAAATGACCAAGGATCAAGTCAAGATCAAAGATGAATGACCAACAT
AAAACCATGAGTCAAAAAAATGATTTGGATTAAGCCGAGATCGAATGACCAGGATG
Found at i:13564930 original size:17 final size:15
Alignment explanation
Indices: 13564897--13564943 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
13564887 CCTTTCCTCA
*
13564897 TTTTTCATTTTCTTT
1 TTTTTCTTTTTCTTT
13564912 TTTTTACTTTTTCCTTT
1 TTTTT-CTTTTT-CTTT
13564929 TTTTTCTTTTT-TTT
1 TTTTTCTTTTTCTTT
13564943 T
1 T
13564944 CATTACCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.14
15 5 0.17
16 11 0.38
17 9 0.31
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:13564953 original size:26 final size:26
Alignment explanation
Indices: 13564904--13564955 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
13564894 TCATTTTTCA
* **
13564904 TTTTCTTTTTTTTACTTTTTCCTTTT
1 TTTTCTTTTTTTTACATTACCCTTTT
*
13564930 TTTTCTTTTTTTTTCATTACCCTTTT
1 TTTTCTTTTTTTTACATTACCCTTTT
13564956 ATCCATTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTCTTTTTTTTACATTACCCTTTT
Found at i:13569497 original size:20 final size:20
Alignment explanation
Indices: 13569474--13569525 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
13569464 TTTCTTTGTC
13569474 TAAATAAAAACTAGT-AAAAT
1 TAAATAAAAACT-GTGAAAAT
* *
13569494 TAAATAAAAAATTTGAAAAT
1 TAAATAAAAACTGTGAAAAT
*
13569514 AAAATAAAAACT
1 TAAATAAAAACT
13569526 TAAGATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
TAAATAAAAACTGTGAAAAT
Found at i:13569535 original size:21 final size:21
Alignment explanation
Indices: 13569509--13569559 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
13569499 AAAAAATTTG
13569509 AAAATAAAATAAA-AACTTAA
1 AAAATAAAATAAATAACTTAA
* *
13569529 GATAATAAAATAAATAATTTAA
1 -AAAATAAAATAAATAACTTAA
13569551 AAAATAAAA
1 AAAATAAAA
13569560 ATGAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAAAATAAATAACTTAA
Found at i:13570419 original size:3 final size:3
Alignment explanation
Indices: 13570392--13570442 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
13570382 CAAAGAAAGA
* * *
13570392 AAT AAG AAT AAA AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13570440 AAT
1 AAT
13570443 CTAATATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:13570476 original size:16 final size:15
Alignment explanation
Indices: 13570448--13570479 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
13570438 ATAATCTAAT
13570448 ATAATATACCATATA
1 ATAATATACCATATA
13570463 ATAATATCACCATATA
1 ATAATAT-ACCATATA
13570479 A
1 A
13570480 CACAATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATATACCATATA
Found at i:13576031 original size:25 final size:25
Alignment explanation
Indices: 13576003--13576053 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
13575993 TCTAATTGTC
13576003 AGTATAGGTAAAAAAATTAAAACAT
1 AGTATAGGTAAAAAAATTAAAACAT
*
13576028 AGTATAGGTAAAAAAATTTAAACAT
1 AGTATAGGTAAAAAAATTAAAACAT
13576053 A
1 A
13576054 CATGTCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (25 bp):
AGTATAGGTAAAAAAATTAAAACAT
Found at i:13576204 original size:130 final size:130
Alignment explanation
Indices: 13575999--13576287 Score: 535
Period size: 130 Copynumber: 2.2 Consensus size: 130
13575989 AATCTCTAAT
* *
13575999 TGTCAGTATAGGTAA-AAAAATTAAAACATAGTATAGGTAAAAAAATTTAAACATACATGTCTAT
1 TGTCAGTTTAGGTAACAAAAATTAAAACATAGTATAGGTAAAAAAATTAAAACATACATGTCTAT
*
13576063 ACTAACAATCTCTAACCGTCAGTATAGGTATGAAAAATTATAAGTCTATACTAACAGGTATTAAC
66 ACTAACAATCTCTAACCGTCAGTATAGGTATGAAAAATTATAAGTCTATACTAACAAGTATTAAC
*
13576128 TGTCGGTTTAGGTAACAAAAATTAAAACATAGTATAGGTAAAAAAATTAAAACATACATGTCTAT
1 TGTCAGTTTAGGTAACAAAAATTAAAACATAGTATAGGTAAAAAAATTAAAACATACATGTCTAT
13576193 ACTAACAATCTCTAACCGTCAGTATAGGTATGAAAAATTATAAGTCTATACTAACAAGTATTAAC
66 ACTAACAATCTCTAACCGTCAGTATAGGTATGAAAAATTATAAGTCTATACTAACAAGTATTAAC
13576258 TGTCAGTTTAGGTAACAAAAATTAAAACAT
1 TGTCAGTTTAGGTAACAAAAATTAAAACAT
13576288 GTAAGTCTAT
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
129 13 0.08
130 141 0.92
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (130 bp):
TGTCAGTTTAGGTAACAAAAATTAAAACATAGTATAGGTAAAAAAATTAAAACATACATGTCTAT
ACTAACAATCTCTAACCGTCAGTATAGGTATGAAAAATTATAAGTCTATACTAACAAGTATTAAC
Found at i:13576263 original size:49 final size:49
Alignment explanation
Indices: 13576187--13576281 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
13576177 AAACATACAT
* **
13576187 GTCTATACTAACAATCTCTAACCGTCAGTATAGGTATGAAAAATTATAA
1 GTCTATACTAACAATATCTAACCGTCAGTATAGGTAACAAAAATTATAA
* *
13576236 GTCTATACTAACAAGTAT-TAACTGTCAGTTTAGGTAACAAAAATTA
1 GTCTATACTAACAA-TATCTAACCGTCAGTATAGGTAACAAAAATTA
13576282 AAACATGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 38 0.95
50 2 0.05
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (49 bp):
GTCTATACTAACAATATCTAACCGTCAGTATAGGTAACAAAAATTATAA
Found at i:13577542 original size:20 final size:20
Alignment explanation
Indices: 13577512--13577561 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
13577502 CATGGTTGTA
*
13577512 CAAGCTTGACCAAATTGACT
1 CAAGTTTGACCAAATTGACT
*
13577532 TAAGTTTGACCAAATTGACT
1 CAAGTTTGACCAAATTGACT
*
13577552 CAGGTTTGAC
1 CAAGTTTGAC
13577562 TAAAATTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (20 bp):
CAAGTTTGACCAAATTGACT
Found at i:13578306 original size:19 final size:19
Alignment explanation
Indices: 13578282--13578324 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
13578272 AACTATTAAT
*
13578282 AAAAAA-AATTAAGAAAAGG
1 AAAAAATAA-TAAAAAAAGG
13578301 AAAAAATAATAAAAAAAGG
1 AAAAAATAATAAAAAAAGG
13578320 AAAAA
1 AAAAA
13578325 CAAACAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (19 bp):
AAAAAATAATAAAAAAAGG
Found at i:13578333 original size:19 final size:19
Alignment explanation
Indices: 13578295--13578333 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13578285 AAAAATTAAG
*
13578295 AAAAGGAAAAAATAATAAA
1 AAAAGGAAAAAATAACAAA
13578314 AAAAGGAAAAACA-AACAAA
1 AAAAGGAAAAA-ATAACAAA
13578333 A
1 A
13578334 CACAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (19 bp):
AAAAGGAAAAAATAACAAA
Found at i:13579894 original size:20 final size:20
Alignment explanation
Indices: 13579864--13579931 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 20
13579854 CTTGCATATA
13579864 TATTATATTTAACATGTAAAT
1 TATT-TATTTAACATGTAAAT
*
13579885 TATTTATTTACTTAATATGTAAAT
1 TATTTA--T--TTAACATGTAAAT
13579909 TATTTATTTAACATGTAAAT
1 TATTTATTTAACATGTAAAT
13579929 TAT
1 TAT
13579932 AAAAATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 17 0.41
21 4 0.10
22 2 0.05
24 18 0.44
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
TATTTATTTAACATGTAAAT
Found at i:13579899 original size:24 final size:24
Alignment explanation
Indices: 13579872--13579918 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13579862 TATATTATAT
13579872 TTAACATGTAAATTATTTATTTAC
1 TTAACATGTAAATTATTTATTTAC
*
13579896 TTAATATGTAAATTATTTATTTA
1 TTAACATGTAAATTATTTATTTA
13579919 ACATGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TTAACATGTAAATTATTTATTTAC
Found at i:13583853 original size:18 final size:18
Alignment explanation
Indices: 13583830--13583864 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13583820 TGAGGTGGAT
*
13583830 AATAACCATATGGAGGTG
1 AATAACCATAAGGAGGTG
13583848 AATAACCATAAGGAGGT
1 AATAACCATAAGGAGGT
13583865 TGAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (18 bp):
AATAACCATAAGGAGGTG
Found at i:13587804 original size:27 final size:27
Alignment explanation
Indices: 13587749--13587800 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
13587739 TATCACAAAT
* *
13587749 AATTTTCAATAATTATATAATAAATAC
1 AATTTTCAATAATTACACAATAAATAC
13587776 AATTTTCAATAATTACACAA-AAATA
1 AATTTTCAATAATTACACAATAAATA
13587801 ACAAGAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (27 bp):
AATTTTCAATAATTACACAATAAATAC
Found at i:13587865 original size:19 final size:20
Alignment explanation
Indices: 13587831--13587870 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
13587821 AAAAGAATTG
*
13587831 ACAACAATATAAATATCAAA
1 ACAACAATAAAAATATCAAA
*
13587851 ACAACAA-AAAAATATTAAA
1 ACAACAATAAAAATATCAAA
13587870 A
1 A
13587871 TTCAGATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.17
Consensus pattern (20 bp):
ACAACAATAAAAATATCAAA
Found at i:13590272 original size:18 final size:18
Alignment explanation
Indices: 13590249--13590477 Score: 74
Period size: 18 Copynumber: 12.4 Consensus size: 18
13590239 TCGTTATTAA
13590249 TAATATAATAATATTTAT
1 TAATATAATAATATTTAT
13590267 TAATAT-AT--TATTT-T
1 TAATATAATAATATTTAT
* *
13590281 TAA-AT-ATTATATTAAT
1 TAATATAATAATATTTAT
*
13590297 AAATAAGTAATATATTATTTATT
1 TAAT-A-TAATA-A-TATTTA-T
* *
13590320 TATGTATAATTAATATAATAT
1 TA-ATATAA-TAATAT-TTAT
* *
13590341 ATGATATTGATAATATATTAT
1 -TAATA-TAATAATAT-TTAT
*
13590362 TAATATAAT-ATAATATAT
1 TAATATAATAAT-ATTTAT
13590380 T-A-ATAAT-ATATTATAT
1 TAATATAATAATATT-TAT
* *
13590396 TGATA-ATATATTATTTAT
1 TAATATA-ATAATATTTAT
*
13590414 TAATATAATATTATTTAT
1 TAATATAATAATATTTAT
13590432 ATAATA-AATATTTTAGTATTTAT
1 -TAATATAATA----A-TATTTAT
13590455 TAATAT-AT--TATTTAT
1 TAATATAATAATATTTAT
13590470 TAATATAA
1 TAATATAA
13590478 GAATTGTAGT
Statistics
Matches: 163, Mismatches: 18, Indels: 62
0.67 0.07 0.26
Matches are distributed among these distances:
13 4 0.02
14 4 0.02
15 24 0.15
16 15 0.09
17 5 0.03
18 38 0.23
19 16 0.10
20 6 0.04
21 17 0.10
22 21 0.13
23 12 0.07
24 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAATATAATAATATTTAT
Found at i:13590277 original size:11 final size:11
Alignment explanation
Indices: 13590242--13590466 Score: 82
Period size: 11 Copynumber: 20.5 Consensus size: 11
13590232 GGTCTATTCG
13590242 TTATTAATA-A
1 TTATTAATATA
*
13590252 TATAATAATAT-
1 T-TATTAATATA
13590263 TTATTAATATA
1 TTATTAATATA
13590274 TTATTTTTAA-ATA
1 TTA---TTAATATA
*
13590287 TTATATTAATAAA
1 -T-TATTAATATA
* *
13590300 TAAGTAATATA
1 TTATTAATATA
* *
13590311 TTATTTATTTA
1 TTATTAATATA
13590322 TGTA-TAAT-TA
1 T-TATTAATATA
*
13590332 ATA-TAATATA
1 TTATTAATATA
13590342 TGATATTGATAATATA
1 T--TA-T--TAATATA
13590358 TTATTAATATA
1 TTATTAATATA
*
13590369 ATA-TAATATA
1 TTATTAATATA
*
13590379 TTAATAATATA
1 TTATTAATATA
*
13590390 TTA-TATTGATA
1 TTATTAAT-ATA
* *
13590401 ATA-TATTAT-
1 TTATTAATATA
13590410 TTATTAATATA
1 TTATTAATATA
* *
13590421 ATATT-ATTTA
1 TTATTAATATA
*
13590431 TATAATAA-ATA
1 T-TATTAATATA
*
13590442 TT-TTAGTAT-
1 TTATTAATATA
13590451 TTATTAATATA
1 TTATTAATATA
13590462 TTATT
1 TTATT
13590467 TATTAATATA
Statistics
Matches: 162, Mismatches: 27, Indels: 51
0.68 0.11 0.21
Matches are distributed among these distances:
9 12 0.07
10 45 0.28
11 72 0.44
12 10 0.06
13 6 0.04
14 7 0.04
15 2 0.01
16 8 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
TTATTAATATA
Found at i:13590278 original size:32 final size:32
Alignment explanation
Indices: 13590242--13590437 Score: 100
Period size: 32 Copynumber: 5.9 Consensus size: 32
13590232 GGTCTATTCG
*
13590242 TTATTAATAATATAATAATATTTAT-TAATATA
1 TTATTAATAATAT-ATAATATTAATATAATATA
** *
13590274 TTATTTTTAA-ATATTATATTAATA-AATAAGTAA
1 TTATTAATAATATATAATATTAATATAAT-A-T-A
* * * *
13590307 TATATTATTTATTTATGTATAATTAATATAATATA
1 T-TATTAATAATATAT-AAT-ATTAATATAATATA
*
13590342 TGATATTGATAATATAT--TATTAATATAATATAA
1 T--TATTAATAATATATAATATTAATATAATAT-A
* *
13590375 TATATTAATAATATATTATATT--GATAATATA
1 T-TATTAATAATATATAATATTAATATAATATA
* * *
13590406 TTATTTATTAATATAATATTATTTATATAATA
1 TTA-TTAATAATAT-ATAATATTAATATAATA
13590438 AATATTTTAG
Statistics
Matches: 130, Mismatches: 17, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
30 14 0.11
31 14 0.11
32 49 0.38
33 5 0.04
34 17 0.13
35 5 0.04
36 15 0.12
37 8 0.06
38 3 0.02
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TTATTAATAATATATAATATTAATATAATATA
Found at i:13590287 original size:13 final size:14
Alignment explanation
Indices: 13590255--13590301 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
13590245 TTAATAATAT
*
13590255 AATAATATTTATTA
1 AATATTATTTATTA
13590269 ATATATTATTT-TTA
1 A-ATATTATTTATTA
*
13590283 AATATTATATTAATA
1 AATATTAT-TTATTA
13590298 AATA
1 AATA
13590302 AGTAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.25
14 7 0.25
15 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTATTTATTA
Found at i:13590332 original size:37 final size:36
Alignment explanation
Indices: 13590267--13590339 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 36
13590257 TAATATTTAT
13590267 TAATATATTATTTTTAAATATTATATTAATA-AATAAG
1 TAATATATTATTTTT--ATATTATATTAATATAATAAG
13590304 TAATATATTATTTATT-TATGTATAATTAATATAATA
1 TAATATATTATTT-TTATAT-TAT-ATTAATATAATA
13590340 TATGATATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
35 3 0.09
36 3 0.09
37 20 0.62
38 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (36 bp):
TAATATATTATTTTTATATTATATTAATATAATAAG
Found at i:13590333 original size:4 final size:5
Alignment explanation
Indices: 13590324--13590442 Score: 68
Period size: 5 Copynumber: 23.6 Consensus size: 5
13590314 TTTATTTATG
* *
13590324 TATAA T-TAA TATAA TAT-A TGATAT TGATAA TATAT TATTAA TATAA
1 TATAA TATAA TATAA TATAA T-ATAA T-ATAA TATAA TA-TAA TATAA
* * * * *
13590370 TATAA TATAT TAATAA TATAT TATAT TGATAA TATAT TAT-T TATTAA
1 TATAA TATAA T-ATAA TATAA TATAA T-ATAA TATAA TATAA TA-TAA
* *
13590417 TATAA TATTA T-TTA TATAA TA-AA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
13590443 TTTAGTATTT
Statistics
Matches: 92, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
4 17 0.18
5 55 0.60
6 20 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (5 bp):
TATAA
Found at i:13590355 original size:16 final size:16
Alignment explanation
Indices: 13590334--13590409 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
13590324 TATAATTAAT
*
13590334 ATAATATATGATATTG
1 ATAATATATTATATTG
*
13590350 ATAATATATTATTAAT-
1 ATAATATATTA-TATTG
* *
13590366 ATAATATAATATATTA
1 ATAATATATTATATTG
13590382 ATAATATATTATATTG
1 ATAATATATTATATTG
13590398 ATAATATATTAT
1 ATAATATATTAT
13590410 TTATTAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
15 3 0.06
16 46 0.88
17 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
ATAATATATTATATTG
Found at i:13590396 original size:48 final size:47
Alignment explanation
Indices: 13590304--13590477 Score: 181
Period size: 48 Copynumber: 3.5 Consensus size: 47
13590294 AATAAATAAG
* * *
13590304 TAATATATTATTTATTTATGT-ATA-ATTAATATAATATATGATATTGA
1 TAATATATTATTTATTAATATAATATATT-A-ATAATATATTATATTGA
*
13590351 TAATATATTATTAATATAATATAATATATTAATAATATATTATATTGA
1 TAATATATTATTTAT-TAATATAATATATTAATAATATATTATATTGA
*
13590399 TAATATATTATTTATTAATATAATATTATTTATATAATAAATATTTTAGTATTTA
1 TAATATATTATTTATTAATATAATA-TA-TTA-ATAAT--ATA--TTA-TATTGA
13590454 TTAATATATTATTTATTAATATAA
1 -TAATATATTATTTATTAATATAA
13590478 GAATTGTAGT
Statistics
Matches: 109, Mismatches: 6, Indels: 15
0.84 0.05 0.12
Matches are distributed among these distances:
47 24 0.22
48 36 0.33
49 7 0.06
50 8 0.07
52 3 0.03
54 3 0.03
55 5 0.05
56 23 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (47 bp):
TAATATATTATTTATTAATATAATATATTAATAATATATTATATTGA
Found at i:13590466 original size:56 final size:52
Alignment explanation
Indices: 13590304--13590477 Score: 186
Period size: 56 Copynumber: 3.4 Consensus size: 52
13590294 AATAAATAAG
* * *
13590304 TAATATATTATTTATT--TAT-GTATAAT-TAAT-ATAATATATGATATTGA
1 TAATATATTATTTATTAATATAATATAATATATTAATAATATATTATATTGA
13590351 T-A-ATA-TA-TTATTAATATAATATAATATATTAATAATATATTATATTGA
1 TAATATATTATTTATTAATATAATATAATATATTAATAATATATTATATTGA
* * * *
13590399 TAATATATTATTTATTAATATAATATTATTTATATAATAAATATTTTAGTATTTA
1 TAATATATTATTTATTAATATAATATAATATAT-TAAT-AATATATTA-TATTGA
13590454 TTAATATATTATTTATTAATATAA
1 -TAATATATTATTTATTAATATAA
13590478 GAATTGTAGT
Statistics
Matches: 107, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 6 0.06
46 7 0.07
47 4 0.04
48 17 0.16
49 1 0.01
50 3 0.03
51 2 0.02
52 20 0.19
53 4 0.04
54 8 0.07
55 5 0.05
56 23 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (52 bp):
TAATATATTATTTATTAATATAATATAATATATTAATAATATATTATATTGA
Found at i:13594123 original size:10 final size:10
Alignment explanation
Indices: 13594108--13594166 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
13594098 ACACAGCATT
13594108 GAAAGAGAGA
1 GAAAGAGAGA
13594118 GAAAGAGAGAA
1 GAAAGAGAG-A
*
13594129 AAAAGAGAGA
1 GAAAGAGAGA
* *
13594139 GAAAAAGAAA
1 GAAAGAGAGA
*
13594149 GAAAGGGA-A
1 GAAAGAGAGA
13594158 G-AAGAGAGA
1 GAAAGAGAGA
13594167 AGGTTCAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
8 5 0.12
9 3 0.08
10 23 0.57
11 9 0.22
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
GAAAGAGAGA
Found at i:13594133 original size:21 final size:22
Alignment explanation
Indices: 13594108--13594167 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
13594098 ACACAGCATT
13594108 GAAAGAGAGAGAAAGAGAGAAA
1 GAAAGAGAGAGAAAGAGAGAAA
13594130 -AAAGAGAGAGAAA-A-AGAAA
1 GAAAGAGAGAGAAAGAGAGAAA
*
13594149 GAAAGGGA-AG-AAGAGAGAA
1 GAAAGAGAGAGAAAGAGAGAA
13594168 GGTTCAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 8 0.24
20 11 0.32
21 13 0.38
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAAGAGAGAGAAAGAGAGAAA
Found at i:13600689 original size:21 final size:21
Alignment explanation
Indices: 13600663--13600704 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13600653 AGAAAAATAG
*
13600663 CATGAATAAAGTTTCATATGC
1 CATGAATAAAGTTCCATATGC
*
13600684 CATGAATAAGGTTCCATATGC
1 CATGAATAAAGTTCCATATGC
13600705 TTTGGCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
CATGAATAAAGTTCCATATGC
Found at i:13607702 original size:35 final size:35
Alignment explanation
Indices: 13607654--13607722 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
13607644 ATTATGATGA
* * *
13607654 AACTAATCTTGAAGAAACCCTTAGTCTTTGAAACT
1 AACTAATCGTGAAGAAACACTTAGTCTATGAAACT
*
13607689 AACTAATCGTGAAGGAACACTTAGTCTATGAAAC
1 AACTAATCGTGAAGAAACACTTAGTCTATGAAAC
13607723 CAACCCTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (35 bp):
AACTAATCGTGAAGAAACACTTAGTCTATGAAACT
Found at i:13612276 original size:16 final size:17
Alignment explanation
Indices: 13612255--13612288 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13612245 TTCTTTTCTC
13612255 TCTTTTAGTTC-TTAGT
1 TCTTTTAGTTCTTTAGT
*
13612271 TCTTTTATTTCTTTAGT
1 TCTTTTAGTTCTTTAGT
13612288 T
1 T
13612289 GAGTTATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (17 bp):
TCTTTTAGTTCTTTAGT
Found at i:13620940 original size:42 final size:42
Alignment explanation
Indices: 13620893--13620978 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
13620883 AATGTTGTAA
13620893 ATAATATTTGAAAAGAGTAAATTTTGAAATAAATTTTATCTT
1 ATAATATTTGAAAAGAGTAAATTTTGAAATAAATTTTATCTT
* *
13620935 ATAATATTTGAAAAGAGTTAATTTTGAAATCAATTTTATCTT
1 ATAATATTTGAAAAGAGTAAATTTTGAAATAAATTTTATCTT
13620977 AT
1 AT
13620979 TTAAATTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (42 bp):
ATAATATTTGAAAAGAGTAAATTTTGAAATAAATTTTATCTT
Found at i:13622056 original size:55 final size:55
Alignment explanation
Indices: 13621997--13622138 Score: 146
Period size: 55 Copynumber: 2.6 Consensus size: 55
13621987 TGCTTAGCAT
*
13621997 CTGTCAGTATAAACTTATATTTTTTAATTTTCT-TACCTATAAT-GACAGTTAGAGA
1 CTGTCAGTATAAACTTATATATTTTAATTTT-TGTACCT-TAATCGACAGTTAGAGA
* * * * * *
13622052 CTGTCAGTATAGAA-TTGTGTACTTTAATTTTTGTACCTTTATCGATAGTTATAGA
1 CTGTCAGTATA-AACTTATATATTTTAATTTTTGTACCTTAATCGACAGTTAGAGA
* * *
13622107 TTATCAGTATAGACTTATATATTTTAATTTTT
1 CTGTCAGTATAAACTTATATATTTTAATTTTT
13622139 TATTATATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
54 5 0.07
55 63 0.90
56 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (55 bp):
CTGTCAGTATAAACTTATATATTTTAATTTTTGTACCTTAATCGACAGTTAGAGA
Found at i:13629390 original size:24 final size:24
Alignment explanation
Indices: 13629260--13629392 Score: 66
Period size: 24 Copynumber: 5.7 Consensus size: 24
13629250 ATAAGAAACT
*
13629260 TTTAAA-T-TTAAAAAGATGTATA
1 TTTAAATTATTAAAAAGATATATA
**
13629282 TTTAAATTATTAAAAA-ATCCAT-
1 TTTAAATTATTAAAAAGATATATA
** * * *
13629304 TTTAAAAGA-T-AATATATCATTATT
1 TTTAAATTATTAAAAAGAT-A-TATA
*
13629328 TTTAAATT-TT-AAAACATATATA
1 TTTAAATTATTAAAAAGATATATA
* *
13629350 TCTAGATTATTAATAAAAAGATATATA
1 TTTA-A--ATTATTAAAAAGATATATA
13629377 TTTAAATTATTAAAAA
1 TTTAAATTATTAAAAA
13629393 ATTCATTTTA
Statistics
Matches: 82, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
20 3 0.04
21 3 0.04
22 19 0.23
23 9 0.11
24 29 0.35
25 3 0.04
26 2 0.02
27 14 0.17
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
TTTAAATTATTAAAAAGATATATA
Found at i:13629392 original size:25 final size:27
Alignment explanation
Indices: 13629338--13629393 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
13629328 TTTAAATTTT
*
13629338 AAAACATATATATCTAGATTATTAATA
1 AAAACATATATATCTAAATTATTAATA
* *
13629365 AAAAGATATATATTTAAATTATTAA-A
1 AAAACATATATATCTAAATTATTAATA
13629391 AAA
1 AAA
13629394 TTCATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (27 bp):
AAAACATATATATCTAAATTATTAATA
Found at i:13630730 original size:18 final size:18
Alignment explanation
Indices: 13630709--13630779 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
13630699 AAAGTTAAAA
13630709 ATATAAAAAAGAAAAATT
1 ATATAAAAAAGAAAAATT
*
13630727 ATATAAAAAAAGAAAAA-A
1 ATAT-AAAAAAGAAAAATT
* *
13630745 ATCATAAAAAATATAAATT
1 AT-ATAAAAAAGAAAAATT
* *
13630764 -TAAAAAAAATAAAAAT
1 ATATAAAAAAGAAAAAT
13630780 ACTTTCAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 13 0.30
18 17 0.39
19 14 0.32
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (18 bp):
ATATAAAAAAGAAAAATT
Found at i:13630738 original size:36 final size:33
Alignment explanation
Indices: 13630698--13630780 Score: 87
Period size: 37 Copynumber: 2.4 Consensus size: 33
13630688 TAAATATCCT
13630698 AAAAGTTAAAAATATAAAAAAGAAAAATTATATAAA
1 AAAAG-TAAAAATATAAAAAAGAAAAATT-TA-AAA
* * *
13630734 AAAAGAAAAAAATCATAAAAAATATAAATTTAAAA
1 AAAAG-TAAAAAT-ATAAAAAAGAAAAATTTAAAA
13630769 AAAA-TAAAAATA
1 AAAAGTAAAAATA
13630781 CTTTCAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
32 1 0.02
33 6 0.15
35 7 0.17
36 13 0.32
37 14 0.34
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (33 bp):
AAAAGTAAAAATATAAAAAAGAAAAATTTAAAA
Found at i:13630751 original size:19 final size:18
Alignment explanation
Indices: 13630705--13630755 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
13630695 CCTAAAAGTT
13630705 AAAAATAT-AAAAAAGAA
1 AAAAATATAAAAAAAGAA
*
13630722 AAATTATATAAAAAAAGAA
1 AAA-AATATAAAAAAAGAA
13630741 AAAAATCATAAAAAA
1 AAAAAT-ATAAAAAA
13630756 TATAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 6 0.21
19 20 0.69
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAAATATAAAAAAAGAA
Found at i:13633107 original size:54 final size:55
Alignment explanation
Indices: 13633011--13633127 Score: 148
Period size: 54 Copynumber: 2.2 Consensus size: 55
13633001 TTATATTTTT
13633011 TTTAA-TTTCTTACCTATACTAACAGTTAAAAATGTTCAGTATAAAATTATATGC
1 TTTAATTTTCTTACCTATACTAACAGTTAAAAATGTTCAGTATAAAATTATATGC
* * * * * * * *
13633065 TTTAATTTTCTTACCTTTATTGACGGTTAAAAGTG-TCAGTATAGATTTATATGT
1 TTTAATTTTCTTACCTATACTAACAGTTAAAAATGTTCAGTATAAAATTATATGC
13633119 TTTAATTTT
1 TTTAATTTT
13633128 TTTATTATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 30 0.56
55 24 0.44
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (55 bp):
TTTAATTTTCTTACCTATACTAACAGTTAAAAATGTTCAGTATAAAATTATATGC
Found at i:13642295 original size:293 final size:294
Alignment explanation
Indices: 13641765--13642328 Score: 712
Period size: 293 Copynumber: 1.9 Consensus size: 294
13641755 TCCTAGATTA
* * *
13641765 TTGGCCAAAAACATATTTAATAATCCCCTCCAATATTTTGGAGGGGATTATTCGAGGCAATTTCT
1 TTGGCCAAAAACACATTTAATAATCCCCTCCAATATTTTGAAGGAGATTATTCGAGGCAATTTCT
** * *
13641830 TTCAAAAACGTCTTCAATAATCTCTTTTCATTTTTTTTGGGATCATTCAAGGTATTTTTATAATA
66 ACCAAAAACGTCTTCAATAATCCCTTTCCATTTTTTTTGGGATCATTCAAGGTATTTTTATAATA
* ** ** * *
13641895 AAACACCTTAAATAATCCCCTTTAGGTGTTTACGAAGAGATTATTGAAAGTATTTTTTGTCAGAA
131 AAACACCTTAAATAATCCCCTTTAAGCATTTACGAAGAGATTATTGAAAGTAGCTTTTGCCAAAA
** * **
13641960 AATACCTTGAATAATTTCTAAAAAAATATTAAATAGGGTTATTGAAA-GTATTTCTGGTTAAAAA
196 AATACCTTGAATAATCCCTAAAAAAATATTAAATAGGGTTATT-AAAGGTATTTCTAGCCAAAAA
13642024 TGCCTTGAATAAATCTTGGATTATTGAAGGCTTTT
260 TGCCTTGAATAAATCTTGGATTATTGAAGGCTTTT
* * * *
13642059 TTGGCCAAAAACGCCTTTAATAATCCCCTCCAAT-TTTTAGAAGGAGATTATTTGAGGCATTTTC
1 TTGGCCAAAAACACATTTAATAATCCCCTCCAATATTTT-GAAGGAGATTATTCGAGGCAATTTC
* *
13642123 TACCAAAAACG-CTTTCAATAATCCCTTTCCA-TTTTTTTGGGATTATTCAAGGTATTTTTATGA
65 TACCAAAAACGTC-TTCAATAATCCCTTTCCATTTTTTTTGGGATCATTCAAGGTATTTTTATAA
** * * *
13642186 TAAAATGCCTTGAATAAT-CCCTTTCAAGCATTTATGACA-AGATTATTGAAGGT-GCTTTTGCC
129 TAAAACACCTTAAATAATCCCCTTT-AAGCATTTACGA-AGAGATTATTGAAAGTAGCTTTTG-C
* * *
13642248 CAAAAAATATCTTGAATAATCCCTAACAAAATATTAAAT-GAGGTTATTAAAGGTGTTTCTAGCC
191 CAAAAAATACCTTGAATAATCCCTAAAAAAATATTAAATAG-GGTTATTAAAGGTATTTCTAGCC
13642312 AAAAATGCCTTGAATAA
255 AAAAATGCCTTGAATAA
13642329 TCTCCTCTAA
Statistics
Matches: 230, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
292 15 0.07
293 137 0.60
294 78 0.34
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (294 bp):
TTGGCCAAAAACACATTTAATAATCCCCTCCAATATTTTGAAGGAGATTATTCGAGGCAATTTCT
ACCAAAAACGTCTTCAATAATCCCTTTCCATTTTTTTTGGGATCATTCAAGGTATTTTTATAATA
AAACACCTTAAATAATCCCCTTTAAGCATTTACGAAGAGATTATTGAAAGTAGCTTTTGCCAAAA
AATACCTTGAATAATCCCTAAAAAAATATTAAATAGGGTTATTAAAGGTATTTCTAGCCAAAAAT
GCCTTGAATAAATCTTGGATTATTGAAGGCTTTT
Found at i:13645945 original size:24 final size:25
Alignment explanation
Indices: 13645917--13645964 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
13645907 CTAGATTAGG
*
13645917 ATATTGGTTTAATAT-TATTGGCAT
1 ATATTGGTTTAATATCAATTGGCAT
* *
13645941 ATATTTGTTTTATATCAATTGGCA
1 ATATTGGTTTAATATCAATTGGCA
13645965 GCTTATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (25 bp):
ATATTGGTTTAATATCAATTGGCAT
Found at i:13646176 original size:3 final size:3
Alignment explanation
Indices: 13646148--13646308 Score: 164
Period size: 3 Copynumber: 57.0 Consensus size: 3
13646138 ACCAAGTTTA
* * *
13646148 ATT ATT TTT ATT A-T ATT A-T ATT -TT ATT A-T AGT ATT ATT A-T ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
13646191 A-T ATC ATT ATT ATT ATT AGT A-T ATT ATAT AAT ATT A-T ATC A-C
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
13646233 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13646281 ATT -TT ATT ATT ATT -TT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13646309 TTTCCCTTTT
Statistics
Matches: 134, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
2 21 0.16
3 111 0.83
4 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:13647190 original size:13 final size:13
Alignment explanation
Indices: 13647162--13647203 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
13647152 GAATCGCAGG
13647162 TTTT-TTTTATTAT
1 TTTTATTTTATT-T
13647175 TTTTATTTTATTT
1 TTTTATTTTATTT
*
13647188 TTTGATTTTATTT
1 TTTTATTTTATTT
13647201 TTT
1 TTT
13647204 AATCTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:13652342 original size:21 final size:21
Alignment explanation
Indices: 13652316--13652355 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13652306 ATTATTTAAT
13652316 GATATAATAATTGATTATATA
1 GATATAATAATTGATTATATA
*
13652337 GATATAATATTTGATTATA
1 GATATAATAATTGATTATA
13652356 AGTACAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (21 bp):
GATATAATAATTGATTATATA
Found at i:13652828 original size:19 final size:19
Alignment explanation
Indices: 13652806--13652848 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
13652796 TTTATTTATT
*
13652806 TATTTATTTATTGTTTA-AA
1 TATTTATATATT-TTTATAA
13652825 TATTTATATATTTTTATAA
1 TATTTATATATTTTTATAA
13652844 TATTT
1 TATTT
13652849 TACCTTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTATATATTTTTATAA
Found at i:13655439 original size:10 final size:10
Alignment explanation
Indices: 13655389--13655448 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
13655379 TATTTTTCAT
13655389 AAATACTTTAA
1 AAATA-TTTAA
*
13655400 AAACATTT-A
1 AAATATTTAA
13655409 AAATA-TTACA
1 AAATATTTA-A
13655419 AAATTATTTTAA
1 AAA-TA-TTTAA
*
13655431 AAATATTTAG
1 AAATATTTAA
13655441 AAATATTT
1 AAATATTT
13655449 TATTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 19 0.46
11 8 0.20
12 4 0.10
13 3 0.07
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (10 bp):
AAATATTTAA
Found at i:13659429 original size:25 final size:25
Alignment explanation
Indices: 13659401--13659482 Score: 137
Period size: 25 Copynumber: 3.3 Consensus size: 25
13659391 CTAAAAGAAT
13659401 AGGTTCGGGTCTGTTAACCAGAACA
1 AGGTTCGGGTCTGTTAACCAGAACA
13659426 AGGTTCGGGTCTGTTAACCAGAACA
1 AGGTTCGGGTCTGTTAACCAGAACA
* *
13659451 AGGTTCGGGTTTGTTAATCAGAACA
1 AGGTTCGGGTCTGTTAACCAGAACA
*
13659476 GGGTTCG
1 AGGTTCG
13659483 AGAGTACGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (25 bp):
AGGTTCGGGTCTGTTAACCAGAACA
Found at i:13659989 original size:16 final size:17
Alignment explanation
Indices: 13659970--13660002 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13659960 TTCTCAAAAA
*
13659970 TATTTTTTA-AAAAATT
1 TATTTTTAAGAAAAATT
13659986 TATTTTTAAGAAAAATT
1 TATTTTTAAGAAAAATT
13660003 GATACTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TATTTTTAAGAAAAATT
Done.