Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold121
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: 1076282
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 28062 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:157092 original size:38 final size:41
Alignment explanation
Indices: 157000--157096 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 41
156990 TTTATTTTTA
* *
157000 ATATAAATA-AAATTTTAATATATATTTTATTATTTAGTAT
1 ATATATATATAAATTTTAATATATATTTAATTATTTAGTAT
* *
157040 A-A-ATATAT-TA-TTTAATA-AT-TTTAATT-TTTATTAT
1 ATATATATATAAATTTTAATATATATTTAATTATTTAGTAT
157074 ATATATATATAAATTTTAATATA
1 ATATATATATAAATTTTAATATA
157097 AATATTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
34 8 0.17
35 7 0.15
36 8 0.17
37 8 0.17
38 12 0.26
39 2 0.04
40 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (41 bp):
ATATATATATAAATTTTAATATATATTTAATTATTTAGTAT
Found at i:158586 original size:26 final size:27
Alignment explanation
Indices: 158554--158604 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
158544 TATATTTTAA
*
158554 TTTAAAATTTTAAAAAA-TAAATATTT
1 TTTAAAATATTAAAAAATTAAATATTT
158580 TTTAAAATATTAAAAAATTAAATAT
1 TTTAAAATATTAAAAAATTAAATAT
158605 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAAAATATTAAAAAATTAAATATTT
Found at i:158595 original size:27 final size:26
Alignment explanation
Indices: 158554--158604 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
158544 TATATTTTAA
*
158554 TTTAAAATTTTAAAAAATAAATATTT
1 TTTAAAATTTAAAAAAATAAATATTT
*
158580 TTTAAAATATTAAAAAATTAAATAT
1 TTTAAAAT-TTAAAAAAATAAATAT
158605 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAAAATTTAAAAAAATAAATATTT
Found at i:158618 original size:14 final size:15
Alignment explanation
Indices: 158584--158615 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
158574 ATATTTTTTA
*
158584 AAATATTAAAAAATT
1 AAATATAAAAAAATT
158599 AAATATAAAAAAATT
1 AAATATAAAAAAATT
158614 AA
1 AA
158616 TATCTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATATAAAAAAATT
Found at i:163985 original size:16 final size:16
Alignment explanation
Indices: 163964--163998 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
163954 TAAACAGATA
*
163964 AATTTAATTTAAATTT
1 AATTTAATTTAAATAT
163980 AATTTAATTTAAATAT
1 AATTTAATTTAAATAT
163996 AAT
1 AAT
163999 ATTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAATTTAAATAT
Found at i:163998 original size:11 final size:11
Alignment explanation
Indices: 163962--163991 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
163952 GTTAAACAGA
163962 TAAATTTAATT
1 TAAATTTAATT
163973 TAAATTTAATT
1 TAAATTTAATT
163984 T-AATTTAA
1 TAAATTTAA
163992 ATATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:165443 original size:14 final size:14
Alignment explanation
Indices: 165426--165455 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
165416 AATAAATTAA
165426 TTAAAAAATATTTT
1 TTAAAAAATATTTT
*
165440 TTAAAATATATTTT
1 TTAAAAAATATTTT
165454 TT
1 TT
165456 TCGGATTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAAAAATATTTT
Found at i:166237 original size:17 final size:18
Alignment explanation
Indices: 166199--166237 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
166189 CTATAAAAAG
*
166199 AAGAGGTAAGAGAAGCAA
1 AAGAGGTAAGAGAAGAAA
*
166217 AAGAGGTACGA-AAGAAA
1 AAGAGGTAAGAGAAGAAA
166234 AAGA
1 AAGA
166238 TAACTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.59, C:0.05, G:0.31, T:0.05
Consensus pattern (18 bp):
AAGAGGTAAGAGAAGAAA
Found at i:171523 original size:153 final size:155
Alignment explanation
Indices: 171297--171690 Score: 399
Period size: 155 Copynumber: 2.6 Consensus size: 155
171287 TTTTTAAAGG
* ** * * * * *
171297 GATGAATCTATCCTAAATATACATCTTCGGCATAAAAGC--ACCC-ATGGACGACTTAGGAGTTG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAAACCCGGT-GACAACCTAGGAATTG
** * *
171359 GTTCTGGAAAATTATGAAAATGCCGCTAGGGGATACTTTCGAT-TTAAA-AATGCCTGATA-CCC
65 GTTCTAAAAAATTATGAAAATGCCGCTAGGGGATACCTTCGATGTGAAATAAT-CCTGATATCCC
*
171421 ATAAAGGACTTAAAAAGGA-CATAGATGA
129 -TAAAGGACTTAAAAA-GATCACAGATGA
* * *
171449 GATGAACCTA-CTTAAATACCCACCTTTGGCATAAAAGCAAACCCGGTGAGAACCTAGGAATTGG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAAACCCGGTGACAACCTAGGAATTGG
* ** * * *
171513 TTCTAAAAAATTACGAAAATGCCTTTAGGGGATACCTTCGATGTGAAATTATCTTGGTATCCCTA
66 TTCTAAAAAATTATGAAAATGCCGCTAGGGGATACCTTCGATGTGAAATAATCCTGATATCCCTA
* *
171578 AAGGACTTAAAAAGATTACAGATGG
131 AAGGACTTAAAAAGATCACAGATGA
** * ** * * **
171603 GATGAACCTATCCTAAATATTCACCTTCGGCGTAAAAGCGGACTCGGTGACAACCTAGGATTTCT
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAAACCCGGTGACAACCTAGGAATTGG
171668 TTCTAAAAAATTATGAAAATGCC
66 TTCTAAAAAATTATGAAAATGCC
171691 CCTAAAAGAT
Statistics
Matches: 197, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
151 23 0.12
152 9 0.05
153 55 0.28
154 41 0.21
155 69 0.35
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (155 bp):
GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAAACCCGGTGACAACCTAGGAATTGG
TTCTAAAAAATTATGAAAATGCCGCTAGGGGATACCTTCGATGTGAAATAATCCTGATATCCCTA
AAGGACTTAAAAAGATCACAGATGA
Found at i:171703 original size:155 final size:154
Alignment explanation
Indices: 171417--171732 Score: 364
Period size: 155 Copynumber: 2.0 Consensus size: 154
171407 AATGCCTGAT
* * *
171417 ACCCATAAAGGACTTAAAAAGGACATAGATGAGATGAACCTACTTAAATACCCACCTTTGGCATA
1 ACCC-TAAAGGACTTAAAAAGGACACAGATGAGATGAACCTACCTAAATACCCACCTTCGGCATA
* * ** ***
171482 AAAGCAAACCCGGTGAGAACCTAGGAATTGGTTCTAAAAAATTACGAAAATGCCTTTAGGGGATA
65 AAAGCAAACCCGGTGACAACCTAGGAATTCGTTCTAAAAAATTACGAAAATGCCCCTAAAAGATA
* * * *
171547 CCTTCGATGTGAAATTATCTTGGTA
130 CCTTCAATATGAAAATATCATGGTA
* * * ** *
171572 TCCCTAAAGGACTTAAAAA-GATTACAGATGGGATGAACCTATCCTAAATATTCACCTTCGGCGT
1 ACCCTAAAGGACTTAAAAAGGA-CACAGATGAGATGAACCTA-CCTAAATACCCACCTTCGGCAT
** * * * *
171636 AAAAGCGGACTCGGTGACAACCTAGGATTTCTTTCTAAAAAATTATGAAAATGCCCCTAAAAGAT
64 AAAAGCAAACCCGGTGACAACCTAGGAATTCGTTCTAAAAAATTACGAAAATGCCCCTAAAAGAT
171701 ACCTTCAATATGAAAATATCATGGTA
129 ACCTTCAATATGAAAATATCATGGTA
171727 ACCCTA
1 ACCCTA
171733 GTGGACGTTA
Statistics
Matches: 132, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
153 2 0.02
154 31 0.23
155 99 0.75
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (154 bp):
ACCCTAAAGGACTTAAAAAGGACACAGATGAGATGAACCTACCTAAATACCCACCTTCGGCATAA
AAGCAAACCCGGTGACAACCTAGGAATTCGTTCTAAAAAATTACGAAAATGCCCCTAAAAGATAC
CTTCAATATGAAAATATCATGGTA
Found at i:173200 original size:61 final size:59
Alignment explanation
Indices: 173129--173248 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
173119 TCTCTCATTC
*
173129 TTCTTCATTTTGCCGTCTCTCCCTTGCTCTTTTTTTTTATGGAAGTTTGGCCAAGAAGATG
1 TTCTTCATTTTGCCGTCTCTCCCTTGCTC--TTTTTTTATGGAAGTTTGGCCAAAAAGATG
* *
173190 TTCTTCATTTTGTCGTTTCTCCCTTGCTCTTTTTTTATGGAAGTTTGGCCAAAAAGATG
1 TTCTTCATTTTGCCGTCTCTCCCTTGCTCTTTTTTTATGGAAGTTTGGCCAAAAAGATG
173249 ATGATGAAGC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 29 0.52
61 27 0.48
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (59 bp):
TTCTTCATTTTGCCGTCTCTCCCTTGCTCTTTTTTTATGGAAGTTTGGCCAAAAAGATG
Found at i:173956 original size:166 final size:164
Alignment explanation
Indices: 173664--174366 Score: 549
Period size: 165 Copynumber: 4.2 Consensus size: 164
173654 ATAAATTGAA
* * * *
173664 TTTTGAAAAACTGATTCA-ATGTATGTATAATAACAATATTAT-ATGAATTTTAAAAATTTTAAA
1 TTTTG-AAAACTGATTTACATGAAT-TA-AATAATAATATT-TGATGAATTTTAAAAATTTAAAA
* * * * * *
173727 CC--GAAAAATCC-C-CCTGAAAATATTTATGGAACAGAAAACT-TCGTTTTTTAGAAACAAGAG
62 CCAAGAAAAATCCTCTCC--AAAAAATTTACGAAATAGAAAACTCT-GTTTTTCA-AAAAAAGAG
* *
173787 AATTTCAAAGAAAAAATTCAAACCTCATGAAAATGAATGAAAT
123 AATTTCAAAGAAAAAATTAAAAACTCATGAAAATGAAT-AAAT
* * *
173830 TTTT-AAATCTGATTTACTATGAATTAAATAATAATATTTTATGAATTTTAAAAATTGAAAACCA
1 TTTTGAAAACTGATTTAC-ATGAATTAAATAATAATATTTGATGAATTTTAAAAATTTAAAACCA
* * *
173894 AGAAAAATCCT-TCCAAAAACATTTACGGAGTAGAAAACTCTGTTTTTCAAAAATAGGAGAATTT
65 AGAAAAATCCTCTCCAAAAA-ATTTACGAAATAGAAAACTCTGTTTTTCAAAAA-AAGAGAATTT
* * *
173958 C-AAGAAAAAAATGAAAAACTCATGAAGATGAGTAAAT
128 CAAAG-AAAAAATTAAAAACTCATGAAAATGAATAAAT
* * * * *
173995 TTTTGAAAACTG-TTTAAGATAAATTAAATAATAATATCTGATGAATTTTAAAAATTAAAAACTA
1 TTTTGAAAACTGATTT-ACATGAATTAAATAATAATATTTGATGAATTTTAAAAATTTAAAACCA
** * * * * * *
174059 AGAAAAATCCTCTCGTAAAAATTTATGAAATAGAAAATTTTGTATTTCAAAAAAAAAG-ATTTTA
65 AGAAAAATCCTCTCCAAAAAATTTACGAAATAGAAAACTCTGTTTTTCAAAAAAAGAGAATTTCA
* ** * * *
174123 AAGGAAAAATTGAAAATTTTATGAAAGTAAATAAAT
130 AAGAAAAAATT-AAAAACTCATGAAAATGAATAAAT
* * * *
174159 TTTTGAAAACGGATTTAACATGAATTAAATAATAATATTTGATGAATTTTAAAAATTTTAGATCA
1 TTTTGAAAACTGATTT-ACATGAATTAAATAATAATATTTGATGAATTTTAAAAATTTAAAACCA
* * * *
174224 A-ATGAAAATCCTCTCGAAAAAATTTACGAAGTAGAAAACTCTGGATTTTGAAAACAGAAG-GAA
65 AGA--AAAATCCTCTCCAAAAAATTTACGAAATAGAAAACTCT-GTTTTTCAAAA-A-AAGAGAA
* * * *
174287 TTTCAAA-AGAAAATTAACAAGTCAT-AAAAT-AAAACTAAT
125 TTTCAAAGAAAAAATTAAAAACTCATGAAAATGAATA--AAT
* * ***
174326 TTTTCAAAATTGATTTTTTTTGTAATTAAATAATAATATTT
1 TTTTGAAAACTGA-TTTACATG-AATTAAATAATAATATTT
174367 ATTAAATTTT
Statistics
Matches: 432, Mismatches: 78, Indels: 52
0.77 0.14 0.09
Matches are distributed among these distances:
163 11 0.03
164 77 0.18
165 150 0.35
166 124 0.29
167 32 0.07
168 29 0.07
169 9 0.02
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (164 bp):
TTTTGAAAACTGATTTACATGAATTAAATAATAATATTTGATGAATTTTAAAAATTTAAAACCAA
GAAAAATCCTCTCCAAAAAATTTACGAAATAGAAAACTCTGTTTTTCAAAAAAAGAGAATTTCAA
AGAAAAAATTAAAAACTCATGAAAATGAATAAAT
Found at i:176797 original size:87 final size:86
Alignment explanation
Indices: 176630--176800 Score: 195
Period size: 87 Copynumber: 2.0 Consensus size: 86
176620 TTGTTGTGCC
* * *
176630 ATTAGTCAAATATTTTTGTCATGTTAAAAGGAATTTGATACCATATGCATTTGTCATATCTTTCA
1 ATTAATCAAATATTTCTGTCATGTCAAAAGGAATTTGATACCATAT-CATTTGTCATATCTTTCA
*
176695 CGTTTTAAAAAATTTATTAAGT
65 CGTTTCAAAAAATTTATTAAGT
* * *
176717 ATTAATCAAATATTTCTGTCATGTCAGACA-GAATTTGATACCCCATAT-ATTTGTTATATTTTT
1 ATTAATCAAATATTTCTGTCATGTCA-AAAGGAATTTGATA--CCATATCATTTGTCATATCTTT
* *
176780 CA-GATTTCAAGAGATTTATTA
63 CACG-TTTCAAAAAATTTATTA
176801 TGCATTTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
86 1 0.01
87 62 0.87
88 2 0.03
89 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (86 bp):
ATTAATCAAATATTTCTGTCATGTCAAAAGGAATTTGATACCATATCATTTGTCATATCTTTCAC
GTTTCAAAAAATTTATTAAGT
Found at i:177159 original size:15 final size:15
Alignment explanation
Indices: 177139--177186 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
177129 TGCTGGTGCT
*
177139 TTTTTCGTGAATGGC
1 TTTTTCTTGAATGGC
*
177154 TTTTTCTTGAGTGG-
1 TTTTTCTTGAATGGC
177168 TTTCTTCTTGAATGGC
1 TTT-TTCTTGAATGGC
177184 TTT
1 TTT
177187 ATTTGAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.10, C:0.12, G:0.23, T:0.54
Consensus pattern (15 bp):
TTTTTCTTGAATGGC
Found at i:180247 original size:11 final size:11
Alignment explanation
Indices: 180231--180257 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
180221 GCATATTTTG
180231 AAAATTAATTT
1 AAAATTAATTT
180242 AAAATTAATTT
1 AAAATTAATTT
180253 AAAAT
1 AAAAT
180258 AAAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATTAATTT
Found at i:180882 original size:34 final size:34
Alignment explanation
Indices: 180837--181019 Score: 173
Period size: 34 Copynumber: 5.5 Consensus size: 34
180827 TATGTAATAA
*
180837 ATAATTAAAAATTTTATTTATGTTAAATAATAAAT
1 ATAATT-AAAATTATATTTATGTTAAATAATAAAT
* *
180872 ATAAATAAAATTACATTTATGTTAAATAAT--A-
1 ATAATTAAAATTATATTTATGTTAAATAATAAAT
** * *
180903 ATAA--AATGTTATTTTTATGTTAAATAATAAAA
1 ATAATTAAAATTATATTTATGTTAAATAATAAAT
* * * *
180935 ATTATTAAAATTATATTTATATTAAAAAATAAGT
1 ATAATTAAAATTATATTTATGTTAAATAATAAAT
* *
180969 -T-ATTAAAATTATATTTTTATTAAATAATAAAAT
1 ATAATTAAAATTATATTTATGTTAAATAAT-AAAT
181002 ATATATTAAAATTATATT
1 ATA-ATTAAAATTATATT
181020 ACATTAAATG
Statistics
Matches: 121, Mismatches: 18, Indels: 17
0.78 0.12 0.11
Matches are distributed among these distances:
29 20 0.17
31 5 0.04
32 29 0.24
33 4 0.03
34 44 0.36
35 5 0.04
36 14 0.12
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (34 bp):
ATAATTAAAATTATATTTATGTTAAATAATAAAT
Found at i:180898 original size:27 final size:28
Alignment explanation
Indices: 180867--180933 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
180857 TGTTAAATAA
180867 TAAATATAAATAAAA-TTACATTTATGT
1 TAAATATAAATAAAAGTTACATTTATGT
**
180894 TAAATA-ATAATAAAATGTTATTTTTATGT
1 TAAATATA-AATAAAA-GTTACATTTATGT
180923 TAAATAATAAA
1 TAAAT-ATAAA
180934 AATTATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 1 0.03
27 13 0.39
29 15 0.45
30 3 0.09
31 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (28 bp):
TAAATATAAATAAAAGTTACATTTATGT
Found at i:180957 original size:17 final size:17
Alignment explanation
Indices: 180937--181019 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
180927 TAATAAAAAT
180937 TATTAAAATTATATTTA
1 TATTAAAATTATATTTA
* **
180954 TATTAAAA-AATAAGT-
1 TATTAAAATTATATTTA
*
180969 TATTAAAATTATATTTT
1 TATTAAAATTATATTTA
* * *
180986 TATTAAATAATAAAATATA
1 TATT-AA-AATTATATTTA
181005 TATTAAAATTATATT
1 TATTAAAATTATATT
181020 ACATTAAATG
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
15 8 0.16
16 8 0.16
17 18 0.37
18 4 0.08
19 11 0.22
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (17 bp):
TATTAAAATTATATTTA
Found at i:181060 original size:66 final size:65
Alignment explanation
Indices: 180924--181062 Score: 149
Period size: 66 Copynumber: 2.1 Consensus size: 65
180914 TTTTTATGTT
* * * *
180924 AAATAATAAAAATTATTAAAATTATATTTATATTAAAAAATAAGTTATTAAAATTATATTTTTAT
1 AAATAATAAAAATTATTAAAATTATATTTACATTAAAAAATAAGCTA-TAAAATTATATTTTAAC
*
180989 T
65 A
**
180990 AAATAATAAAATATATATTAAAATTATA-TTACATTAAATGATAA-CTA-AAAATTATATATATT
1 AAATAATAAAA-AT-TATTAAAATTATATTTACATTAAAAAATAAGCTATAAAATTATAT-T-TT
181052 AACA
62 AACA
181056 AAATAAT
1 AAATAAT
181063 TATAGAAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
64 10 0.16
65 1 0.02
66 23 0.37
67 15 0.24
68 13 0.21
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (65 bp):
AAATAATAAAAATTATTAAAATTATATTTACATTAAAAAATAAGCTATAAAATTATATTTTAACA
Found at i:181221 original size:21 final size:21
Alignment explanation
Indices: 181188--181230 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
181178 AATTTAGCGT
181188 CACTAGAAAGTGGATCCGAATG
1 CACTAGAAAGTGGATCC-AATG
181210 CACTAG-AAGTGGATCCAATG
1 CACTAGAAAGTGGATCCAATG
181230 C
1 C
181231 GCCCCAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (21 bp):
CACTAGAAAGTGGATCCAATG
Found at i:181851 original size:20 final size:21
Alignment explanation
Indices: 181823--181863 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
181813 ATTTTAAATC
*
181823 AATTTAAAAT-TTATTATTTT
1 AATTAAAAATATTATTATTTT
181843 AATTAAAAATATTATTATTTT
1 AATTAAAAATATTATTATTTT
181864 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTAAAAATATTATTATTTT
Found at i:181874 original size:29 final size:29
Alignment explanation
Indices: 181842--181904 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
181832 TTTATTATTT
**
181842 TAATTAAAAATATTATTATT-TTTAATAAA
1 TAATTAAAAAT-TTATTATTATCAAATAAA
*
181871 TAATTAAAACTTTATTATTATCAAATAAA
1 TAATTAAAAATTTATTATTATCAAATAAA
181900 TAATT
1 TAATT
181905 TAGTATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
TAATTAAAAATTTATTATTATCAAATAAA
Found at i:181913 original size:50 final size:50
Alignment explanation
Indices: 181817--181917 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 50
181807 CGTAAAATTT
* * *
181817 TAAATCAATTTAAAATTTATTATTTTAATTAAAAATATTATTATTTTTAA
1 TAAATCAATTTAAAATTTATTATTTCAAATAAAAATATTAGTATTTTTAA
181867 TAAAT-AA-TTAAAACTTTATTATTATCAAATAAATAAT-TTAGTATTTTTAA
1 TAAATCAATTTAAAA-TTTATTATT-TCAAATAAA-AATATTAGTATTTTTAA
181917 T
1 T
181918 TATCTTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
48 6 0.13
49 11 0.24
50 25 0.56
51 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.50
Consensus pattern (50 bp):
TAAATCAATTTAAAATTTATTATTTCAAATAAAAATATTAGTATTTTTAA
Found at i:182010 original size:16 final size:18
Alignment explanation
Indices: 181989--182028 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
181979 TTGAATTAAC
*
181989 AAAATATAA-ATA-TATA
1 AAAATATAAGATAGAATA
182005 AAAATATAAGATAGAATA
1 AAAATATAAGATAGAATA
182023 AAAATA
1 AAAATA
182029 AAAAAGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATATAAGATAGAATA
Found at i:182237 original size:30 final size:30
Alignment explanation
Indices: 182196--182273 Score: 77
Period size: 33 Copynumber: 2.5 Consensus size: 30
182186 TTTAATTTTA
*
182196 AAAAATATATTTAAA-TACAAATAAAAAAAT
1 AAAAATTTATTTAAAGTA-AAATAAAAAAAT
* * *
182226 AATAATTTATTTATTTAAGTATAATAAAAATAT
1 AAAAATTTATTTA---AAGTAAAATAAAAAAAT
182259 AAAAATTTATTTAAA
1 AAAAATTTATTTAAA
182274 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
30 13 0.33
33 24 0.62
34 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAAATTTATTTAAAGTAAAATAAAAAAAT
Found at i:183263 original size:20 final size:21
Alignment explanation
Indices: 183212--183272 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
183202 TTATATCATA
* *
183212 TTTATATATTATATTTAAAATAT
1 TTTATAT-TTATTTTTATAA-AT
183235 TTTATATTT-TTTTATATAAAT
1 TTTATATTTATTTT-TATAAAT
183256 TTTA-ATTTATTTTTATA
1 TTTATATTTATTTTTATA
183273 TTTAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.24
21 13 0.38
22 6 0.18
23 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATATTTATTTTTATAAAT
Found at i:184012 original size:14 final size:14
Alignment explanation
Indices: 183993--184047 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
183983 TTCTTTCACC
183993 TTCTCTCTCTCAGG
1 TTCTCTCTCTCAGG
**
184007 TTCTCTCTCTC-TC
1 TTCTCTCTCTCAGG
184020 TCTCACTCTCTCTCAGG
1 T-T--CTCTCTCTCAGG
184037 TTCTCTCTCTC
1 TTCTCTCTCTC
184048 TCACTCTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.03
14 21 0.64
16 10 0.30
17 1 0.03
ACGTcount: A:0.05, C:0.42, G:0.07, T:0.45
Consensus pattern (14 bp):
TTCTCTCTCTCAGG
Found at i:184013 original size:2 final size:2
Alignment explanation
Indices: 184008--184059 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
183998 TCTCTCAGGT
* **
184008 TC TC TC TC TC TC TC TC AC TC TC TC TC AGG T- TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC
*
184050 AC TC TC TC TC
1 TC TC TC TC TC
184060 CAAATACAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.06, C:0.46, G:0.04, T:0.44
Consensus pattern (2 bp):
TC
Found at i:184015 original size:16 final size:16
Alignment explanation
Indices: 183994--184050 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
183984 TCTTTCACCT
183994 TCTCTCTCTCAGGTTC
1 TCTCTCTCTCAGGTTC
184010 TCTCTCTCTC---TCTC
1 TCTCTCTCTCAGGT-TC
*
184024 ACTCTCTCTCAGGTTC
1 TCTCTCTCTCAGGTTC
184040 TCTCTCTCTCA
1 TCTCTCTCTCA
184051 CTCTCTCTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 11 0.31
16 22 0.63
17 1 0.03
ACGTcount: A:0.07, C:0.42, G:0.07, T:0.44
Consensus pattern (16 bp):
TCTCTCTCTCAGGTTC
Found at i:184031 original size:30 final size:30
Alignment explanation
Indices: 183995--184059 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
183985 CTTTCACCTT
*
183995 CTCTCTCTCAGGTTCTCTCTCTCTCTCTCA
1 CTCTCTCTCAGGTTCTCTCTCTCTCACTCA
*
184025 CTCTCTCTCAGGTTCTCTCTCTCTCACTCT
1 CTCTCTCTCAGGTTCTCTCTCTCTCACTCA
184055 CTCTC
1 CTCTC
184060 CAAATACAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.06, C:0.45, G:0.06, T:0.43
Consensus pattern (30 bp):
CTCTCTCTCAGGTTCTCTCTCTCTCACTCA
Found at i:184055 original size:14 final size:15
Alignment explanation
Indices: 183994--184059 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 15
183984 TCTTTCACCT
*
183994 TCTCTCTCTCAGGTTC
1 TCTCTCTCTCA-GCTC
*
184010 TCTCTCTCTC-TCTC
1 TCTCTCTCTCAGCTC
* *
184024 ACTCTCTCTCAGGTTC
1 TCTCTCTCTCA-GCTC
184040 TCTCTCTCTCA-CTC
1 TCTCTCTCTCAGCTC
184054 TCTCTC
1 TCTCTC
184060 CAAATACAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 19 0.46
16 22 0.54
ACGTcount: A:0.06, C:0.44, G:0.06, T:0.44
Consensus pattern (15 bp):
TCTCTCTCTCAGCTC
Found at i:185624 original size:20 final size:19
Alignment explanation
Indices: 185599--185637 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
185589 TTTTTATTTA
185599 AAATTT-ATGATAAAATATAT
1 AAATTTAAT-ATAAAA-ATAT
185619 AAATTTAATATAAAAATAT
1 AAATTTAATATAAAAATAT
185638 TTTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 12 0.67
21 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATTTAATATAAAAATAT
Found at i:186240 original size:18 final size:18
Alignment explanation
Indices: 186212--186246 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
186202 TTATATTATC
186212 TTTATATTTATATACAAAG
1 TTTATATTTATAT-CAAAG
186231 TTTA-ATTTATATCAAA
1 TTTATATTTATATCAAA
186247 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTATATTTATATCAAAG
Found at i:187007 original size:2 final size:2
Alignment explanation
Indices: 187000--187026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
186990 TTCTTTATTG
187000 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
187027 ATTATGATTT
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:187516 original size:21 final size:21
Alignment explanation
Indices: 187492--187531 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
187482 TTCGCTCGAG
187492 TTATATTA-ATCAATTTAATAA
1 TTAT-TTAGATCAATTTAATAA
*
187513 TTATTTAGATTAATTTAAT
1 TTATTTAGATCAATTTAAT
187532 TTAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
TTATTTAGATCAATTTAATAA
Found at i:187685 original size:20 final size:21
Alignment explanation
Indices: 187660--187708 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
187650 TTTATCATTC
*
187660 TTAAAATA-GATTGAT-TTCTT
1 TTAAAATATGATTAATCTT-TT
187680 TTAAAA-ATGATTAATCTTTT
1 TTAAAATATGATTAATCTTTT
187700 TTAAAATAT
1 TTAAAATAT
187709 AATCAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (21 bp):
TTAAAATATGATTAATCTTTT
Found at i:187861 original size:19 final size:20
Alignment explanation
Indices: 187837--187877 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
187827 TGTCTTCTTT
187837 ATCTAAAATTATT-TTTAAA
1 ATCTAAAATTATTATTTAAA
* *
187856 ATCTAATATTTTTATTTAAA
1 ATCTAAAATTATTATTTAAA
187876 AT
1 AT
187878 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
ATCTAAAATTATTATTTAAA
Found at i:188005 original size:2 final size:2
Alignment explanation
Indices: 188000--188029 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
187990 ATAATATGTT
188000 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
188030 TCAGTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:188534 original size:18 final size:18
Alignment explanation
Indices: 188511--188549 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
188501 TTTAGTTCTT
188511 TTTAATAGAATA-ATTGAA
1 TTTAATAGAATATATT-AA
*
188529 TTTAATATAATATATTAA
1 TTTAATAGAATATATTAA
188547 TTT
1 TTT
188550 TATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTAATAGAATATATTAA
Found at i:188538 original size:73 final size:72
Alignment explanation
Indices: 188450--188601 Score: 218
Period size: 73 Copynumber: 2.1 Consensus size: 72
188440 AACCTCATTT
*
188450 ATTGAATTGAATATAATATATTAATTTCATTAATTACTTTTTAAATCACATTTTAGTTCTTTTTA
1 ATTGAATTGAATATAATATATTAATTTCATTAATTACTTTTTAAATCACATTTTAATT-TTTTTA
188515 ATAGAATA
65 ATAGAATA
* * * * *
188523 ATTGAATTTAATATAATATATTAATTTTATTAATTATTTTTTAAATTACGTTTTAATTTTTTTAA
1 ATTGAATTGAATATAATATATTAATTTCATTAATTACTTTTTAAATCACATTTTAATTTTTTTAA
188588 TA-AA-A
66 TAGAATA
*
188593 TTTGAATTG
1 ATTGAATTG
188602 TTTAATTACT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
70 8 0.11
71 2 0.03
72 9 0.13
73 52 0.73
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (72 bp):
ATTGAATTGAATATAATATATTAATTTCATTAATTACTTTTTAAATCACATTTTAATTTTTTTAA
TAGAATA
Found at i:188696 original size:20 final size:23
Alignment explanation
Indices: 188663--188713 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
188653 TATTTAATAT
* *
188663 ATATAAATTTT-TATAAATTAAA
1 ATATTAATTTTATATATATTAAA
188685 A-ATTAATTTTATATATATTAAA
1 ATATTAATTTTATATATATTAAA
188707 ATATTAA
1 ATATTAA
188714 CTGTGCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 12 0.48
23 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTAATTTTATATATATTAAA
Found at i:190758 original size:2 final size:2
Alignment explanation
Indices: 190751--190780 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
190741 AAATCCTGAG
190751 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
190781 AAAACTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:201895 original size:14 final size:14
Alignment explanation
Indices: 201864--201897 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
201854 ATTTAATATT
*
201864 TTAAAAATTTTAAA
1 TTAAAAATATTAAA
201878 -TAAAAATATTAAA
1 TTAAAAATATTAAA
201891 TTAAAAA
1 TTAAAAA
201898 AATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAATATTAAA
Found at i:201910 original size:19 final size:19
Alignment explanation
Indices: 201881--201917 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
201871 TTTTAAATAA
201881 AAATATTAAATTAAAAAAAT
1 AAATATTAAA-TAAAAAAAT
201901 AAAT-TTAAATAAAAAAA
1 AAATATTAAATAAAAAAA
201918 GTTACCCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATATTAAATAAAAAAAT
Found at i:203660 original size:22 final size:24
Alignment explanation
Indices: 203635--203680 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
203625 TGAGTTCATC
* *
203635 AAATCAATTATTT-TAA-ATATTA
1 AAATAAATAATTTATAATATATTA
203657 AAATAAATAATTTATAATATATTA
1 AAATAAATAATTTATAATATATTA
203681 TTTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 3 0.15
24 6 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATAAATAATTTATAATATATTA
Found at i:203683 original size:14 final size:14
Alignment explanation
Indices: 203658--203700 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
203648 TAAATATTAA
*
203658 AATAAATAATTTAT
1 AATAAATTATTTAT
*
203672 AATATATTATTTTTAT
1 AATAAATTA--TTTAT
203688 AATAAATTATTTA
1 AATAAATTATTTA
203701 ACAAATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATAAATTATTTAT
Found at i:203688 original size:16 final size:16
Alignment explanation
Indices: 203667--203734 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
203657 AAATAAATAA
*
203667 TTTATAATATATTATT
1 TTTATAATAAATTATT
203683 TTTATAATAAATTA--
1 TTTATAATAAATTATT
*
203697 -TT-TAACAAATTAATT
1 TTTATAATAAATT-ATT
*
203712 TTCTATAATAAATTAAT
1 TT-TATAATAAATTATT
203729 TTTATA
1 TTTATA
203735 TATTTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 8 0.19
13 3 0.07
16 18 0.43
17 5 0.12
18 8 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATAATAAATTATT
Found at i:203694 original size:30 final size:31
Alignment explanation
Indices: 203658--203742 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 31
203648 TAAATATTAA
203658 AATAAATAATTTATAATATATTATTTT-TAT
1 AATAAATAATTTATAATATATTATTTTCTAT
*
203688 AATAAATTATTTA-ACA-A-ATTAATTTTCTAT
1 AATAAATAATTTATA-ATATATT-ATTTTCTAT
203718 AATAAATTAATTT-T-ATATATT-TTTT
1 AATAAA-TAATTTATAATATATTATTTT
203743 ATGCTACCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
28 3 0.07
29 12 0.26
30 23 0.50
31 8 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
AATAAATAATTTATAATATATTATTTTCTAT
Found at i:203947 original size:16 final size:16
Alignment explanation
Indices: 203934--203973 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
203924 AATGAACTTG
*
203934 AAATGATTTAAACTCA
1 AAATAATTTAAACTCA
* *
203950 AAATAATTTAAATTTA
1 AAATAATTTAAACTCA
203966 AAATAATT
1 AAATAATT
203974 CAAATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATAATTTAAACTCA
Found at i:203978 original size:16 final size:16
Alignment explanation
Indices: 203949--204001 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
203939 ATTTAAACTC
*
203949 AAAATAATTTAAATTT
1 AAAATAATTAAAATTT
*
203965 AAAATAATTCAAATTT
1 AAAATAATTAAAATTT
* *
203981 AAAACAATTAAAATCT
1 AAAATAATTAAAATTT
203997 AAAAT
1 AAAAT
204002 TGATCGTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAATTAAAATTT
Found at i:208149 original size:2 final size:2
Alignment explanation
Indices: 208142--208178 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
208132 GATTTTGGAA
208142 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
208179 GTTTTTATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:211139 original size:2 final size:2
Alignment explanation
Indices: 211132--211184 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
211122 CGTCAAAGAA
211132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
211173 -T AT TT AT AT AT A
1 AT AT AT AT AT AT A
211185 CGCAGCTGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:213064 original size:46 final size:46
Alignment explanation
Indices: 212997--213087 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
212987 AGAGCTTTGT
212997 CCAATGTCCAGCATTGTAATGAGTCTTGTTCCATTTATCAGACTTG
1 CCAATGTCCAGCATTGTAATGAGTCTTGTTCCATTTATCAGACTTG
213043 CCAATGTCCAGCATTGTAATGAGTCTTGTTCCATTTATCAGACTT
1 CCAATGTCCAGCATTGTAATGAGTCTTGTTCCATTTATCAGACTT
213088 ACTTGATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (46 bp):
CCAATGTCCAGCATTGTAATGAGTCTTGTTCCATTTATCAGACTTG
Found at i:216337 original size:16 final size:16
Alignment explanation
Indices: 216318--216368 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
216308 CTCGAAATTG
216318 AAATGATCTAAATTTA
1 AAATGATCTAAATTTA
*
216334 AAATGA-CTTAAAATTA
1 AAATGATC-TAAATTTA
* *
216350 AAATGATCTGAATATA
1 AAATGATCTAAATTTA
216366 AAA
1 AAA
216369 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (16 bp):
AAATGATCTAAATTTA
Found at i:219305 original size:31 final size:31
Alignment explanation
Indices: 219260--219379 Score: 125
Period size: 31 Copynumber: 3.9 Consensus size: 31
219250 TTTCAAACTA
* *
219260 TGCCACCGGTTAAGAATAGTAGTTTTTGCCG
1 TGCCACCAGATAAGAATAGTAGTTTTTGCCG
* * *
219291 TGCCATCATATAAGAATAGT-GATTTTTGACG
1 TGCCACCAGATAAGAATAGTAG-TTTTTGCCG
* * *
219322 TGCTACCGGATAAGAATAGTAGTTTTTACCG
1 TGCCACCAGATAAGAATAGTAGTTTTTGCCG
* * *
219353 TACCACCAGATAACAATAGTGGTTTTT
1 TGCCACCAGATAAGAATAGTAGTTTTT
219380 TTTCTAACTT
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
30 1 0.01
31 69 0.97
32 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (31 bp):
TGCCACCAGATAAGAATAGTAGTTTTTGCCG
Found at i:219511 original size:17 final size:17
Alignment explanation
Indices: 219489--219522 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
219479 GATAAATGTG
219489 ATTTTGTAAA-TAATATA
1 ATTTTG-AAAGTAATATA
219506 ATTTTGAAAGTAATATA
1 ATTTTGAAAGTAATATA
219523 TTTATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
ATTTTGAAAGTAATATA
Found at i:220202 original size:16 final size:17
Alignment explanation
Indices: 220160--220202 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
220150 TTTAATATTT
*
220160 ATAAAATTTCTAATCAC
1 ATAAAATTTATAATCAC
*
220177 ATAAAA-TTATAATTA-
1 ATAAAATTTATAATCAC
220192 ATAAAATTTAT
1 ATAAAATTTAT
220203 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAATTTATAATCAC
Found at i:220344 original size:27 final size:24
Alignment explanation
Indices: 220283--220346 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
220273 AAATTAAGAC
* *
220283 ATAATACAAATATAATATTAGAAA
1 ATAATATAAATATAATATTAAAAA
220307 ATAAT-TAAAATATAATATGATATAAAA
1 ATAATAT-AAATATAATAT--TA-AAAA
220334 ATAATATAAATAT
1 ATAATATAAATAT
220347 GACAGAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 16 0.48
26 2 0.06
27 14 0.42
28 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (24 bp):
ATAATATAAATATAATATTAAAAA
Found at i:221014 original size:18 final size:17
Alignment explanation
Indices: 220973--221016 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
220963 ATTAGCTATG
**
220973 CAAAATATAACATGAAT
1 CAAAATATAACACAAAT
*
220990 TAAAATATAACACAAACT
1 CAAAATATAACACAAA-T
221008 CAAAATATA
1 CAAAATATA
221017 TATATAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (17 bp):
CAAAATATAACACAAAT
Found at i:221216 original size:19 final size:21
Alignment explanation
Indices: 221172--221217 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
221162 AATATTTAAA
*
221172 ACATAACATGAAAATGATATGT
1 ACATAACAT-AAAATGATACGT
221194 ACATAACAT-AAAT-ATACGT
1 ACATAACATAAAATGATACGT
221213 ACATA
1 ACATA
221218 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
22 9 0.39
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (21 bp):
ACATAACATAAAATGATACGT
Found at i:221334 original size:10 final size:9
Alignment explanation
Indices: 221316--221370 Score: 56
Period size: 10 Copynumber: 5.6 Consensus size: 9
221306 AACACATAAA
221316 TTTTTTTCT
1 TTTTTTTCT
221325 TTTCTTTTCT
1 TTT-TTTTCT
221335 TTCCTTTTTCAT
1 TT--TTTTTC-T
221347 TTTTTTTCCT
1 TTTTTTT-CT
*
221357 TTTTTTCCT
1 TTTTTTTCT
221366 TTTTT
1 TTTTT
221371 CGCCCTATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 10 0.25
10 20 0.50
11 6 0.15
12 4 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:221354 original size:17 final size:16
Alignment explanation
Indices: 221316--221360 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
221306 AACACATAAA
221316 TTTTTTT-C-TTTTCT
1 TTTTTTTCCTTTTTCT
*
221330 TTTCTTTCCTTTTTCAT
1 TTTTTTTCCTTTTTC-T
221347 TTTTTTTCCTTTTT
1 TTTTTTTCCTTTTT
221361 TTCCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 1 0.04
16 5 0.19
17 14 0.54
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTCCTTTTTCT
Found at i:221363 original size:26 final size:28
Alignment explanation
Indices: 221318--221369 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
221308 CACATAAATT
*
221318 TTTTTCTTTTCTTTTCTTTCCTTTTTCA
1 TTTTTCTTTCCTTTTCTTTCCTTTTTCA
221346 TTTTT-TTTCCTTTT-TTTCCTTTTT
1 TTTTTCTTTCCTTTTCTTTCCTTTTT
221370 TCGCCCTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 8 0.35
28 5 0.22
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTTCTTTCCTTTTCTTTCCTTTTTCA
Found at i:221838 original size:8 final size:8
Alignment explanation
Indices: 221825--221867 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
221815 ATAATAAATT
221825 TTTTTCTC
1 TTTTTCTC
*
221833 TTTTTCTT
1 TTTTTCTC
221841 TTTTTCT-
1 TTTTTCTC
*
221848 TTTTTCTT
1 TTTTTCTC
221856 TTTTTCTAC
1 TTTTTCT-C
221865 TTT
1 TTT
221868 CTTTCTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 7 0.23
8 21 0.68
9 3 0.10
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTC
Found at i:221844 original size:15 final size:14
Alignment explanation
Indices: 221824--221892 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 14
221814 AATAATAAAT
221824 TTTTTTCTCTTTTTC
1 TTTTTT-TCTTTTTC
221839 TTTTTTTCTTTTTTC
1 TTTTTTTC-TTTTTC
*
221854 TTTTTTTCTACTTTC
1 TTTTTTTCT-TTTTC
*
221869 TTTCTTTCTTTCTTTC
1 TTTTTTTC-TT-TTTC
221885 TTTTTTTC
1 TTTTTTTC
221893 AGTCTTGTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
14 3 0.07
15 31 0.67
16 12 0.26
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:221854 original size:23 final size:22
Alignment explanation
Indices: 221824--221892 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
221814 AATAATAAAT
221824 TTTTTTCTCTTTTTCTTTTTTTC
1 TTTTTTCT-TTTTTCTTTTTTTC
**
221847 TTTTTTCTTTTTT-TCTACTTTC
1 TTTTTTCTTTTTTCT-TTTTTTC
221869 TTTCTTTCTTTCTTTCTTTTTTTC
1 TTT-TTTCTTT-TTTCTTTTTTTC
221893 AGTCTTGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.03
22 13 0.34
23 15 0.39
24 8 0.21
25 1 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTCTTTTTTCTTTTTTTC
Found at i:221861 original size:31 final size:31
Alignment explanation
Indices: 221835--221892 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
221825 TTTTTCTCTT
*
221835 TTTCTTTTTTTCTTT-TTTCTTTTTTTCTAC
1 TTTCTTTCTTTCTTTCTTTCTTTTTTTCTAC
221865 TTTCTTTCTTTCTTTCTTTCTTTTTTTC
1 TTTCTTTCTTTCTTTCTTTCTTTTTTTC
221893 AGTCTTGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (31 bp):
TTTCTTTCTTTCTTTCTTTCTTTTTTTCTAC
Found at i:221873 original size:4 final size:4
Alignment explanation
Indices: 221835--221892 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
221825 TTTTTCTCTT
* * *
221835 TTTC TTTT TTTC TTT- TTTC TTTT TTTC -TAC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
221881 TTTC TTTT TTTC
1 TTTC TTTC TTTC
221893 AGTCTTGTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 5 0.11
4 39 0.89
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:222371 original size:16 final size:16
Alignment explanation
Indices: 222350--222402 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
222340 ACATAAAATA
222350 TTTTCTCTTTTTCTTT
1 TTTTCTCTTTTTCTTT
222366 TTTTCTCCTTTCTATCTTT
1 TTTTCT-CTTT-T-TCTTT
*
222385 CTTTCT-TTCTTTCTTT
1 TTTTCTCTT-TTTCTTT
222401 TT
1 TT
222403 CAACTAACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 12 0.39
17 7 0.23
18 2 0.06
19 10 0.32
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCTCTTTTTCTTT
Found at i:222389 original size:4 final size:4
Alignment explanation
Indices: 222359--222400 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
222349 ATTTTCTCTT
* * *
222359 TTTC TTTT TTTC -TCC TTTC TATC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
222401 TTCAACTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
3 2 0.06
4 29 0.94
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:222399 original size:529 final size:506
Alignment explanation
Indices: 220953--222402 Score: 1588
Period size: 529 Copynumber: 2.8 Consensus size: 506
220943 TTAAAAACTA
** * * * *
220953 AATCACGATGATTAGCTATGCAAAATATAACATGAATTAAAATATAACACAAACTCAAA-ATATA
1 AATCACGACAATTAACTATGAAAAATATAACATGAATT-AGATATAATACAAACTCAAATATATA
* *
221017 TATATAATTAAAACACAATATGAAAAATAATATAAATACAGTACGAATACACGAATATGTCAAAA
65 TATAAAATTAAAACACAATATGAAAAATAATATAAACACAGTACGAATACACGAATATGTCAAAA
* * *
221082 TATAGATAAATGAATACTTAA-CGT----A--TAA-AAATTTATTTTATTTTAAATATAAAAAAA
130 TATAGATAAATGAATAATTAAGTGTAAAAATTTAATAAATTTATTTTATTTTAAACATAAAAAAA
** * * * **
221139 ACATAAACATGATGTTTACAAAAAATATTTAAAACATAACATGAAAATGATATGTACATAACATA
195 ACATAAACACAATGTTTATAAAAAATATTTAAAACATAACATGAAAATAATATGTACATAATACG
* *
221204 AATATACGTACATATAAAAATATACATGAAATAAAATGAATTATTAATATATAAAAAATAC-AAA
260 AATA-ACATACATATAAAAATATACATAAAATAAAATGAATTATTAATATATAAAAAATACAAAA
* * * * *
221268 AATATTATATTTTAAATATAAAAAATAATACAAATACGAACACAT-AAATTTTTTTC-TTTTCTT
324 AATATAATATTTT-AA-ATAAAAAATAACACAAATACAAATACATAAAATTTTTCTCTTTTTCTT
* * * *
221331 TTCTT-TCCTTTTTCATTTTT-TTTC---C--TTTTTTTCCTTTTTTCGCCCTATCTTACTTATC
387 TTTTTCTCCTTTTTCTTTTTTCTTTCTTTCTTTTTTTTTCCTTTTTTCGCCCTATCTTACTGAAC
* * * *
221389 GCCAAAAAAAATCACGTCTCAGTACCAAGTGAGTTTGTATAGTTGATTTTATATG
452 ACAAAAAAAAATCACGTCTCAGTACCAAGTGAGTTTATATAATTGATTTTATATG
* *
221444 AATCACGACAATTAGCTAT-ATAAAATATAACATAAATTATGATATAATACAAACTCAACATATA
1 AATCACGACAATTAACTATGA-AAAATATAACATGAATTA-GATATAATACAAACTCAA-ATATA
* * * * * *
221508 TATGTAAAATTAAAATACAATATGAAAAATAATATAAACATAATACGAATATACGAATATATCAA
63 TATATAAAATTAAAACACAATATGAAAAATAATATAAACACAGTACGAATACACGAATATGTCAA
*
221573 AATATAGATAAATGAATAACTAACGTGTAAAAATTTATATAAATTTATTTTATTTTAAACATAAA
128 AATATAGATAAATGAATAATTAA-GTGTAAAAATTTA-ATAAATTTATTTTATTTTAAACATAAA
* * * * *
221638 AAATAATATAAACACTATGTTTATAAAAAATATTTAAAACATAACTTGAAAATGATATATATATA
191 AAA-AACATAAACACAATGTTTATAAAAAATATTTAAAACATAACATGAAAAT-A-ATATGTACA
* * *
221703 TATATAACACGAAT-ATATACATATAAAAATATACATAAAATAAAACGAATTATTAATATGTAAA
253 TA-AT---ACGAATAACATACATATAAAAATATACATAAAATAAAATGAATTATTAATATATAAA
* *
221767 AATTATAC-AAAAATATAATATTTTATATAAAAAATAACACAAATA-AGAATA-ATAAATTTTTT
314 AA--ATACAAAAAATATAATATTTTAAATAAAAAATAACACAAATACA-AATACATAAA-ATTTT
*
221829 TCTCTTTTTCTTTTTTTCT--TTTTTCTTTTTTTCTACTTTCTTTCTTTCTTTCTTTCTTTTTTT
375 TCTCTTTTTCTTTTTTTCTCCTTTTTC--TTTTT-T-CTTTCTTTCTTT-TTT-TTTCCTTTTTT
* * * * * *
221892 CAGTCTTGTCTTGCTGAACACAAAAAAAAAAAAAAAATCACGTGTCAGTACTAAGTGAGTTTATA
434 C-GCCCTATCTTACTGAACAC-------AAAAAAAAATCACGTCTCAGTACCAAGTGAGTTTATA
221957 TAATTGATTTTATATG
491 TAATTGATTTTATATG
** * * *
221973 AATCACGGTAATTAATTATGAAAAATATAGCATGAATTGAGATATAATACAAACTCAATATATAA
1 AATCACGACAATTAACTATGAAAAATATAACATGAATT-AGATATAATACAAACTCAA-ATATAT
* * * * * *
222038 ATAAAAAATTAAAACATAACAAGAAAAATAATATAAACACAGTATGAATACATGAATATGTCAAA
64 ATATAAAATTAAAACACAATATGAAAAATAATATAAACACAGTACGAATACACGAATATGTCAAA
* *
222103 ATATAAATAAATAAATAATTAATGTGTAAAAATTTACATAAATTTATTTTATTTTAAACATAAAA
129 ATATAGATAAATGAATAATTAA-GTGTAAAAATTTA-ATAAATTTATTTTATTTTAAACATAAAA
* * *
222168 AAAACATAAACACAATATTTATAAAAAATATTTAAAATATAACATGAAAATAATATGCACATAAT
192 AAAACATAAACACAATGTTTATAAAAAATATTTAAAACATAACATGAAAATAATATGTACATAAT
* * * *
222233 ACGAATACACATATATATAAAAATATACATAAAATAAAATAAAATATTAATATTTAAAAAACTAC
257 ACGAATA-ACATACATATAAAAATATACATAAAATAAAATGAATTATTAATATATAAAAAA-TAC
222298 ATAAAAATATAATATTTTAAAT-AAAAA-AACACAAATACAAATACATAAAATATTTTCTCTTTT
320 A-AAAAATATAATATTTTAAATAAAAAATAACACAAATACAAATACATAAAAT-TTTTCTCTTTT
222361 TCTTTTTTTCTCCTTTCTATCTTTCTTTCTTTCTTTCTTTTT
383 TCTTTTTTTCTCCTTT-T-TCTTT-TTTCTTTCTTTCTTTTT
222403 CAACTAACCA
Statistics
Matches: 799, Mismatches: 97, Indels: 93
0.81 0.10 0.09
Matches are distributed among these distances:
490 1 0.00
491 49 0.06
492 1 0.00
493 81 0.10
495 2 0.00
499 1 0.00
501 2 0.00
502 1 0.00
503 27 0.03
504 44 0.06
506 9 0.01
507 3 0.00
508 70 0.09
509 14 0.02
510 34 0.04
511 5 0.01
512 1 0.00
514 4 0.01
517 1 0.00
519 1 0.00
520 3 0.00
521 11 0.01
522 19 0.02
523 18 0.02
524 81 0.10
525 33 0.04
526 15 0.02
527 4 0.01
528 46 0.06
529 216 0.27
530 2 0.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (506 bp):
AATCACGACAATTAACTATGAAAAATATAACATGAATTAGATATAATACAAACTCAAATATATAT
ATAAAATTAAAACACAATATGAAAAATAATATAAACACAGTACGAATACACGAATATGTCAAAAT
ATAGATAAATGAATAATTAAGTGTAAAAATTTAATAAATTTATTTTATTTTAAACATAAAAAAAA
CATAAACACAATGTTTATAAAAAATATTTAAAACATAACATGAAAATAATATGTACATAATACGA
ATAACATACATATAAAAATATACATAAAATAAAATGAATTATTAATATATAAAAAATACAAAAAA
TATAATATTTTAAATAAAAAATAACACAAATACAAATACATAAAATTTTTCTCTTTTTCTTTTTT
TCTCCTTTTTCTTTTTTCTTTCTTTCTTTTTTTTTCCTTTTTTCGCCCTATCTTACTGAACACAA
AAAAAAATCACGTCTCAGTACCAAGTGAGTTTATATAATTGATTTTATATG
Found at i:222841 original size:4 final size:4
Alignment explanation
Indices: 222832--222882 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
222822 ACACATATTA
* * *
222832 TTTC TTTC TTTC TTTC TTTCC TTTT TTTT TTTC -TTC TTTC TATC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC
222880 TTT
1 TTT
222883 TTCAACTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 34 0.83
5 4 0.10
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:223041 original size:481 final size:479
Alignment explanation
Indices: 222383--223301 Score: 1430
Period size: 481 Copynumber: 1.9 Consensus size: 479
222373 CTTTCTATCT
* *
222383 TTCTTTCTTTCTTTCTTTTTCAACTAACCAAAAAAAAAAGTACCACATGTTAGCACCAAAATGAT
1 TTCTTTCTATCTTTCTTTTTCAACTAACCAAAAAAAAAAGTACCACATGGTAGCACCAAAATGAT
222448 TTGTGTAACTAAAATTAGATATATGTATAAATTATGATAAAGTAATTTGAGAGAATACTTTTAAA
66 TTGTGTAACTAAAATTAGATATATGTATAAATTATGATAAAGTAATTTGAGAGAATACTTTTAAA
* *
222513 TATATCCTCGTTACGTGTTGGGAACTAGATTAAAAGTTTAAATAATAATTTAATTCTTAAATTAA
131 TATATCCTCGTTACGTGTTGAGAACTAAATTAAAAGTTTAAATAATAATTTAATTCTTAAATTAA
* * *
222578 TAAATTTAAAATTAAAATTAAATCACTATGATAAATAATATAAAAAATTAAAAA-ATAAAGAGAT
196 TAAATTTAAAATTAAAATTAAATAACTATGATAAATAATACAAAAAA-TAAAAAGA-AAAGAGAG
* * *
222642 AATATCTACAAAACATTAAAAAAATAATTAAAACATTAGAAAAAAATAAAATGTACATGATAAAA
259 AACATCTACAAAACATTAAAAAAATAATTAAAACATTACAAAAAAAT--AATATACATGATAAAA
222707 TA-CATGAACATATCAAATCTATATAAAACAAATTATGACTATGCCAAAATTTATATAAATTTAT
322 TATC-TGAACATATCAAATCTATATAAAACAAATTATGACTATGCCAAAATTTATATAAATTTAT
* * * *
222771 AATATTTTGAATATAATAATGATACAAAAACTAATACAAAAATAAAAATAAACACATATTATTTC
386 AATATTTTAAATACAATAATGACACAAAAACTAACACAAAAATAAAAATAAACACATATTATTTC
222836 TTTCTTTCTTTCTTTCCTTTTTTTTTTTC
451 TTTCTTTCTTTCTTTCCTTTTTTTTTTTC
* * *
222865 TTCTTTCTATCTTTCTTTTTCAACTAACCAAAAAAAAAAGTGCCACATGGTAGTACTAAAATGAT
1 TTCTTTCTATCTTTCTTTTTCAACTAACCAAAAAAAAAAGTACCACATGGTAGCACCAAAATGAT
** *
222930 TTGTGTAGTTAAAATTTGATATATGTAT-AATTATGATAAAGTAATTTGAGAGAATACTTTTAAA
66 TTGTGTAACTAAAATTAGATATATGTATAAATTATGATAAAGTAATTTGAGAGAATACTTTTAAA
* *
222994 TATATCCTCGTTACGTGTTGAGAATTAAATTAAAAGTTTAAATAATAATTTAATTTTTAAATTAA
131 TATATCCTCGTTACGTGTTGAGAACTAAATTAAAAGTTTAAATAATAATTTAATTCTTAAATTAA
** **
223059 TGGATTTAAAATTAAAATTAAATAACTATGATAAATAATACAAAAAATAAAAAGAATGGAGAGAA
196 TAAATTTAAAATTAAAATTAAATAACTATGATAAATAATACAAAAAATAAAAAGAAAAGAGAGAA
* * * *
223124 CATCTACAAAATATTGAAAAAATAATTAAAATATTACACAAAAATAATATACATGATAAAATATC
261 CATCTACAAAACATTAAAAAAATAATTAAAACATTACAAAAAAATAATATACATGATAAAATATC
* * * *
223189 TGAACATATTAAATTTATATAAAACACATTATGACTATGTCAAAATTTATATAAATTTATAATAT
326 TGAACATATCAAATCTATATAAAACAAATTATGACTATGCCAAAATTTATATAAATTTATAATAT
* * * *
223254 TTTAAATGCGATAATGACATAAAAACTAACATAAAAATAAAAATAAAC
391 TTTAAATACAATAATGACACAAAAACTAACACAAAAATAAAAATAAAC
223302 GCATTATAAA
Statistics
Matches: 397, Mismatches: 38, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
478 118 0.30
479 1 0.00
480 52 0.13
481 141 0.36
482 85 0.21
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (479 bp):
TTCTTTCTATCTTTCTTTTTCAACTAACCAAAAAAAAAAGTACCACATGGTAGCACCAAAATGAT
TTGTGTAACTAAAATTAGATATATGTATAAATTATGATAAAGTAATTTGAGAGAATACTTTTAAA
TATATCCTCGTTACGTGTTGAGAACTAAATTAAAAGTTTAAATAATAATTTAATTCTTAAATTAA
TAAATTTAAAATTAAAATTAAATAACTATGATAAATAATACAAAAAATAAAAAGAAAAGAGAGAA
CATCTACAAAACATTAAAAAAATAATTAAAACATTACAAAAAAATAATATACATGATAAAATATC
TGAACATATCAAATCTATATAAAACAAATTATGACTATGCCAAAATTTATATAAATTTATAATAT
TTTAAATACAATAATGACACAAAAACTAACACAAAAATAAAAATAAACACATATTATTTCTTTCT
TTCTTTCTTTCCTTTTTTTTTTTC
Found at i:224094 original size:21 final size:22
Alignment explanation
Indices: 224070--224124 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
224060 ATTTTTATTT
224070 AAATTAATTATAAATA-TATAA
1 AAATTAATTATAAATATTATAA
* * *
224091 AAA-TAATTTTTAATATTTTAA
1 AAATTAATTATAAATATTATAA
*
224112 ATATT-ATTATAAA
1 AAATTAATTATAAA
224125 ATACATAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 10 0.38
21 15 0.58
22 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTAATTATAAATATTATAA
Found at i:225923 original size:20 final size:20
Alignment explanation
Indices: 225868--225910 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
225858 ATGTCTAAGA
* *
225868 TAATAAAATAAAATTTAAAT
1 TAATTAAATTAAATTTAAAT
225888 TAATTAAATTAAATTTAAAT
1 TAATTAAATTAAATTTAAAT
225908 TAA
1 TAA
225911 AATTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATTAAATTAAATTTAAAT
Found at i:226286 original size:20 final size:20
Alignment explanation
Indices: 226235--226288 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
226225 AATTTAAGTG
* *
226235 AGAA-AAGGGAGGAAAAGAG
1 AGAAGAAGGAAGGAAAAGAA
*
226254 AG-AGAAAGAAAGGAAAAGAA
1 AGAAG-AAGGAAGGAAAAGAA
226274 AGAAGAAGGAAGGAA
1 AGAAGAAGGAAGGAA
226289 GAAAAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 1 0.04
19 2 0.07
20 23 0.82
21 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
AGAAGAAGGAAGGAAAAGAA
Found at i:226330 original size:23 final size:23
Alignment explanation
Indices: 226248--226330 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 23
226238 AAAGGGAGGA
* * *
226248 AAAGAGAGAGAAAGAAAGGAAAAG
1 AAAGAG-GAAAAAGGAAGAAAAAG
* * *
226272 AAAGAAGAAGGAAGGAAGAAAAAACT
1 AAAGAGGAA-AAAGGAAG-AAAAA-G
226298 AAAGA-G-AAAAGGAAGAAAAAG
1 AAAGAGGAAAAAGGAAGAAAAAG
226319 AAAGAGGAAAAA
1 AAAGAGGAAAAA
226331 ATTATGTAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
21 5 0.11
22 6 0.13
23 13 0.28
24 12 0.26
25 5 0.11
26 5 0.11
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (23 bp):
AAAGAGGAAAAAGGAAGAAAAAG
Found at i:226400 original size:12 final size:11
Alignment explanation
Indices: 226383--226481 Score: 50
Period size: 11 Copynumber: 9.4 Consensus size: 11
226373 AAGTATTAAA
226383 ATTTTATTTATT
1 ATTTTATTT-TT
226395 ATTTTATTTTT
1 ATTTTATTTTT
**
226406 A---TATGATT
1 ATTTTATTTTT
226414 ATTTT-TTTGTT
1 ATTTTATTT-TT
226425 ATTTTATGTTTT
1 ATTTTAT-TTTT
*
226437 A-ATTATTTTT
1 ATTTTATTTTT
**
226447 ATAAT-TTTTT
1 ATTTTATTTTT
* *
226457 ATTATATTTTA
1 ATTTTATTTTT
*
226468 ATTTT-TTATT
1 ATTTTATTTTT
226478 ATTT
1 ATTT
226482 GTTATATTGA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
8 6 0.09
10 22 0.32
11 25 0.37
12 13 0.19
13 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:226454 original size:18 final size:19
Alignment explanation
Indices: 226433--226487 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
226423 TTATTTTATG
*
226433 TTTTAATTATTTTTATAAT
1 TTTTTATTATTTTTATAAT
*
226452 TTTTTATTATATTT-TAAT
1 TTTTTATTATTTTTATAAT
226470 TTTTTATTATTTGTTATA
1 TTTTTATTATTT-TTATA
226488 TTGATTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.48
19 14 0.45
20 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTTTATAAT
Found at i:226480 original size:16 final size:16
Alignment explanation
Indices: 226389--226481 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 16
226379 TAAAATTTTA
226389 TTTATTATTTT-A-TT
1 TTTATTATTTTAATTT
* *
226403 TTTA-TATGATTATTTT
1 TTTATTAT-TTTAATTT
*
226419 TTTGTTATTTT-ATGTT
1 TTTATTATTTTAAT-TT
*
226435 TTAATTATTTTTATAATTT
1 TTTATTA--TTT-TAATTT
226454 TTTATTATATTTTAATTT
1 TTTA-T-TATTTTAATTT
226472 TTTATTATTT
1 TTTATTATTT
226482 GTTATATTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
13 3 0.05
14 6 0.10
15 1 0.02
16 19 0.32
17 4 0.07
18 13 0.22
19 9 0.15
20 3 0.05
21 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTATTATTTTAATTT
Found at i:226481 original size:10 final size:10
Alignment explanation
Indices: 226428--226486 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
226418 TTTTGTTATT
*
226428 TTATGTTTTAA
1 TTAT-TTTTTA
226439 TTA-TTTTTA
1 TTATTTTTTA
*
226448 TAATTTTTTA
1 TTATTTTTTA
*
226458 TTATATTTTA
1 TTATTTTTTA
226468 --ATTTTTTA
1 TTATTTTTTA
*
226476 TTATTTGTTA
1 TTATTTTTTA
226486 T
1 T
226487 ATTGATTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
8 7 0.18
9 7 0.18
10 22 0.56
11 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:227626 original size:25 final size:23
Alignment explanation
Indices: 227598--227648 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
227588 TAATAAAATT
* *
227598 TAATTTAAATAATTTTATAAATAAA
1 TAATTTAAA-AA-ATTATAAAAAAA
227623 TAATTTAAAAAATTATAAAAAAA
1 TAATTTAAAAAATTATAAAAAAA
227646 TAA
1 TAA
227649 AACCCTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.54
24 2 0.08
25 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAATTTAAAAAATTATAAAAAAA
Found at i:227719 original size:18 final size:20
Alignment explanation
Indices: 227676--227720 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
227666 AAAGTTAAAT
*
227676 TTTAATATGAGTATTGATTA
1 TTTAATATGAGTATTCATTA
227696 -TTAATAT-AGT-TTCATTA
1 TTTAATATGAGTATTCATTA
227713 TTTAATAT
1 TTTAATAT
227721 TGGTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 10 0.43
19 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTAATATGAGTATTCATTA
Found at i:229130 original size:2 final size:2
Alignment explanation
Indices: 229118--229147 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
229108 TATGAATTTA
*
229118 AT AT GT 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
229148 TACATGGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229293 original size:24 final size:24
Alignment explanation
Indices: 229247--229292 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
229237 TTCTAATCAT
*
229247 GTATTTGATTTAAAATATGAAAAG
1 GTATTTGATTTAAAATATAAAAAG
229271 GTATTTGATTTAAAAT-TAAAAA
1 GTATTTGATTTAAAATATAAAAA
229293 AAAAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (24 bp):
GTATTTGATTTAAAATATAAAAAG
Found at i:230556 original size:3 final size:3
Alignment explanation
Indices: 230548--230575 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
230538 TATAAGTTTA
230548 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
230576 GCTATTTATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:237080 original size:19 final size:18
Alignment explanation
Indices: 237046--237084 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
237036 TGATTAAAAA
237046 AATATTAAAATTGATATGC
1 AATATTAAAATTGATA-GC
237065 AATATT-AAATTCGATAGC
1 AATATTAAAATT-GATAGC
237083 AA
1 AA
237085 ACCTCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (18 bp):
AATATTAAAATTGATAGC
Found at i:237118 original size:25 final size:25
Alignment explanation
Indices: 237096--237142 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
237086 CCTCTAATTT
237096 ATAA-AAAAAAAAAAAATAATAATA
1 ATAATAAAAAAAAAAAATAATAATA
* *
237120 ATAATTAAAAAATAAAATAATAA
1 ATAATAAAAAAAAAAAATAATAA
237143 AAAGTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (25 bp):
ATAATAAAAAAAAAAAATAATAATA
Found at i:246422 original size:20 final size:20
Alignment explanation
Indices: 246373--246429 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
246363 GTAAAAAGAC
*
246373 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTCA
*
246393 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTCA
*
246413 TA-CATGTATCGATACAT
1 -AGAATGTATCGATACAT
246430 GGTAAAATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:257013 original size:9 final size:9
Alignment explanation
Indices: 256999--257034 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
256989 TTACACCAAA
256999 AAAAAAAAC
1 AAAAAAAAC
257008 AAAAAAAAAC
1 -AAAAAAAAC
*
257018 AAAGAAAAC
1 AAAAAAAAC
257027 AAAAAAAA
1 AAAAAAAA
257035 AAACAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:257025 original size:21 final size:20
Alignment explanation
Indices: 257001--257057 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 20
256991 ACACCAAAAA
257001 AAAAAACAAAAAAAAACAAAG
1 AAAAAACAAAAAAAAAC-AAG
257022 AAAACAA-AAAAAAAAACAAG
1 AAAA-AACAAAAAAAAACAAG
257042 AAAAATAGCAAAAAAA
1 AAAAA-A-CAAAAAAA
257058 GAAAAGGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 8 0.25
21 14 0.44
22 9 0.28
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAACAAAAAAAAACAAG
Found at i:257027 original size:19 final size:20
Alignment explanation
Indices: 257003--257045 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
256993 ACCAAAAAAA
*
257003 AAAACAAAAAAAAACA-AAG
1 AAAACAAAAAAAAAAACAAG
257022 AAAACAAAAAAAAAAACAAG
1 AAAACAAAAAAAAAAACAAG
257042 AAAA
1 AAAA
257046 ATAGCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAACAAAAAAAAAAACAAG
Found at i:258316 original size:28 final size:28
Alignment explanation
Indices: 258278--258509 Score: 288
Period size: 28 Copynumber: 8.2 Consensus size: 28
258268 CATCCTTTTT
258278 AAGCCCACAAGTCAGTGGCACTCTTTCA
1 AAGCCCACAAGTCAGTGGCACTCTTTCA
* * * *
258306 AAGCCCCCAAGTTAGTGGTACCCTTTCA
1 AAGCCCACAAGTCAGTGGCACTCTTTCA
* * *
258334 AAGTCCACAAGTCAGTGGCACCCTTTTA
1 AAGCCCACAAGTCAGTGGCACTCTTTCA
*
258362 GAGCCCACAAGTCAGTGGCA-TCCTTTCA
1 AAGCCCACAAGTCAGTGGCACT-CTTTCA
* * **
258390 AAGCCCACGAGTCGGTGGCAACAATTTCA
1 AAGCCCACAAGTCAGTGGC-ACTCTTTCA
258419 AAGCCCACAAGTCAGTGGCA-TCCTTTCA
1 AAGCCCACAAGTCAGTGGCACT-CTTTCA
*
258447 AAGCCCACAAGTCAGTGGCACCCTTTCA
1 AAGCCCACAAGTCAGTGGCACTCTTTCA
*
258475 AAGCCCACAAGTCAGTGGCACTTTTTTCA
1 AAGCCCACAAGTCAGTGGCAC-TCTTTCA
258504 AAGCCC
1 AAGCCC
258510 CCACGAGTTG
Statistics
Matches: 173, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
28 139 0.80
29 34 0.20
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCACTCTTTCA
Found at i:258367 original size:56 final size:56
Alignment explanation
Indices: 258268--258509 Score: 322
Period size: 56 Copynumber: 4.3 Consensus size: 56
258258 TTAGAATGTT
** * * *
258268 CATCCTTTTTAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCCCAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
* * * * *
258324 TACCCTTTCAAAGTCCACAAGTCAGTGGCACCCTTTTAGAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
* * **
258380 CATCCTTTCAAAGCCCACGAGTCGGTGGCAACAATTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTCAGTGG
258437 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
**
258493 CACTTTTTTCAAAGCCC
1 CA-TCCTTTCAAAGCCC
258510 CCACGAGTTG
Statistics
Matches: 159, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
56 97 0.61
57 62 0.39
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (56 bp):
CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:258503 original size:85 final size:84
Alignment explanation
Indices: 258268--258509 Score: 322
Period size: 85 Copynumber: 2.9 Consensus size: 84
258258 TTAGAATGTT
* * * * * **
258268 CATCCTTTTTAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCCCAAGTTAGTGGTACCCTTTC
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACAATTTC
*
258333 AAAGTCCACAAGTCAGTGG
66 AAAGCCCACAAGTCAGTGG
* * * * *
258352 CACCCTTTTAGAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCGGTGGCAACAATTT
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-ACAATTT
258417 CAAAGCCCACAAGTCAGTGG
65 CAAAGCCCACAAGTCAGTGG
* **
258437 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTT
1 CATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-AATTT
258502 CAAAGCCC
65 CAAAGCCC
258510 CCACGAGTTG
Statistics
Matches: 135, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
84 49 0.36
85 86 0.64
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (84 bp):
CATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACAATTTC
AAAGCCCACAAGTCAGTGG
Found at i:259097 original size:20 final size:20
Alignment explanation
Indices: 259069--259143 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
259059 TTTTACCTAG
259069 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
259089 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
259109 ATGTATCGAT-CTATTCTTCA
1 ATGTATCGATAC-ATTTTTCA
259129 ATGTATCGATACATT
1 ATGTATCGATACATT
259144 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:259129 original size:40 final size:39
Alignment explanation
Indices: 259069--259146 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
259059 TTTTACCTAG
*
259069 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
*
259109 ATGTATCGAT-CTATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATAC-ATTCTTCAATATATCGATACATTATG
259147 TCTTTTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 5 0.14
40 30 0.86
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:262719 original size:22 final size:22
Alignment explanation
Indices: 262688--262756 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
262678 GAAGGCACTA
* *
262688 CCATTGGAACATAGGAGGTGTT
1 CCATTAGAACGTAGGAGGTGTT
*
262710 TCATTAGAACGTAGGAGGTGTT
1 CCATTAGAACGTAGGAGGTGTT
*
262732 CCATTAGAAGGTAGGAGGTGTT
1 CCATTAGAACGTAGGAGGTGTT
262754 CCA
1 CCA
262757 AATTGAGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.28
Consensus pattern (22 bp):
CCATTAGAACGTAGGAGGTGTT
Found at i:263740 original size:20 final size:20
Alignment explanation
Indices: 263712--263786 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
263702 TTTTACCTTG
*
263712 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* * * *
263732 ATATATCGATACATGCATGA
1 ATGTATCGATACATTCTTCA
* *
263752 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTCTTCA
263772 ATGTATCGATACATT
1 ATGTATCGATACATT
263787 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:264734 original size:23 final size:23
Alignment explanation
Indices: 264698--264753 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
264688 AGCCTTTGAC
264698 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
*
264720 CATGTATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
264743 CATGCATTTTT
1 CATGCATTTTT
264754 AACATGTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:279194 original size:28 final size:29
Alignment explanation
Indices: 279085--280324 Score: 1390
Period size: 28 Copynumber: 42.9 Consensus size: 29
279075 TGTTCATCCC
279085 TTTCAAAGCCCACAAGTCAGTGGCACTCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CT
279115 TTT-AAAGCCCACGCAAGTCAGTGGCACTCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* *
279145 TTTCAAAGCCCACAAATAAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279174 TTTC-AAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279201 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279230 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279258 TTTCAAAGCCCACATGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
279287 TTTCAGAGCCCACAAGTGAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
279315 TTTCAGAGCCCACAAGTGAGTGGC-CCCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
279343 TTTCGAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
279371 TTACGAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
279399 TTTCAAAGCCAACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279427 TTTCAAAGCCCACACAAGTTAGTGGCACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
* *
279458 TTTCAAAGCCCACAAATTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
279487 TTTCAAAGCCTACAAATTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
279516 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279544 TTTCAGAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
279573 TTTCGAAGCCTACAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
279602 TTT-AAAGCCCACACAAGTCAGTGGCACTCCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCACT-CT
279633 TTT-AAAGCCCACGCAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* *
279662 TTTTAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279690 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
279718 TTTC-AAGCCCACGAGTCAGTGGTAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279745 TTTCAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
279773 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
279802 TTTCAAAGCCCACAAATCATTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
279831 TTTCAAAGCCTACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
279860 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
279889 TTTCGAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
279917 TTTCAAAGCCCACACAAGTCAGTGGCACTCCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCACT-CT
279949 TTT-AAAGCCCACGCAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
279978 TTTCAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
280006 TTTCAAAGCCCACAAGTCAGTGGACAC-CC
1 TTTCAAAGCCCACAAGTCAGTGG-CACTCT
*
280035 TTTC-AAGCCCACAAGTCAGTGGTAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
280062 TTTCAAAGCCCACGAGTTAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
280090 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
280118 TTTCAAAGCCCACGAGCCAATGGCATTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
280146 TTTCAAATCCCACACAAGTCAGTGGCA-TCC
1 TTTCAAA-GCC-CACAAGTCAGTGGCACTCT
* * * *
280176 TTTCAAAGCCCACGAGCCAATGGCATTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
280204 TTTCAAATCCCACACAAGTCAGTGGCACCCT
1 TTTCAAA-GCC-CACAAGTCAGTGGCACTCT
* **
280235 TTT-AAAGCCTACGCAAGTCAGTAACACTCT
1 TTTCAAAGCC--CACAAGTCAGTGGCACTCT
* * * *
280265 TTTCAAAGCCCACATGTGTTAGTGGTAACTTT
1 TTTCAAAGCCCACA--AGTCAGTGG-CACTCT
*
280297 TTTCAAAGCCTACACAAGTTAGTGGCAC
1 TTTCAAAGCC--CACAAGTCAGTGGCAC
280325 ATTTTTTTAA
Statistics
Matches: 1057, Mismatches: 100, Indels: 105
0.84 0.08 0.08
Matches are distributed among these distances:
27 41 0.04
28 441 0.42
29 329 0.31
30 127 0.12
31 89 0.08
32 26 0.02
34 4 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:279906 original size:316 final size:318
Alignment explanation
Indices: 279082--280277 Score: 1602
Period size: 316 Copynumber: 3.8 Consensus size: 318
279072 GAATGTTCAT
279082 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTT-AAAGCCCACGCAAGTCAGTGGCACTCTT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTTCAAAGCCCACG--AGTCAGTGGCACTCTT
* * *
279146 TTCAAAGCCCACAAATAAGTGGCACTCTTTTC-AAGCCCACAAGTCAGTGGCAC-CCTTTCAAAG
62 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAG
*
279209 CCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAT
127 CCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAA
* * * * * *
279273 GTCAGTGGCACTCTTTTCAGAG-CC-CACAAGTGAGTGGCAC-CCTTTCAGAGCCCA--CAAGTG
192 GTCAGTGGCACCCTTTT-AAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTC
* * * * * * *
279333 AGTGGCCCCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTACGAAGCCCACAAGTCAGTGGCA
256 AGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
279396 CTCTTTCAAAGCCAACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTTAGTGGCACTCTTTT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG-CC-CACGAGTCAGTGGCACTCTTTT
* * *
279461 CAAAGCCCACAAATTAGTGGCACTCTTTTCAAAGCCTACAAATTAGTGGCACTCTTTTCAAAGCC
64 CAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCC
* * * * *
279526 CACAAGTCAGTGGCAC-CTTTTCAGAGCCCACAAGTCAGTGGCACTCTTTTCGAAGCCTACAAGT
129 CACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGT
*
279590 TAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGT
194 CAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGT
*
279655 GGCACCTTTTTAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
259 GGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* *
279715 CCCTTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTTCA
* * *
279778 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCATTGGCACTCTTTTCAAAGCCTA
66 AAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCA
* *
279843 CAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCGAAGCCCACAAGTTA
131 CAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
*
279908 GTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGG
196 GTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGG
279973 CACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGACA
261 CACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGG-CA
* *
280032 CCCTTTC-AAGCCCACAAGTCAGTGGTACCTTTTCAAAGCCCACGAGTTAGTGGCACTC-TTTCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTTCA
* * * ** * * *
280095 AAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGCCAATGGCATTC-TTTCAAATCCCA
66 AAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCA
* * * * * *
280158 CACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGCCAATGGCA-TTCTTTCAAATCCCACACAA
131 CA-AA-TCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA-GCC-CACAA
* * **
280221 GTCAGTGGCACCCTTTTAAAGCCTACGCAAGTCAGTAACACT-CTTTTCAAAGCCCAC
192 GTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTT-AAAGCCCAC
280278 ATGTGTTAGT
Statistics
Matches: 791, Mismatches: 73, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
312 5 0.01
313 50 0.06
314 76 0.10
315 156 0.20
316 255 0.32
317 156 0.20
318 27 0.03
319 66 0.08
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (318 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTTCA
AAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCA
CAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
GTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGG
CACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:280914 original size:20 final size:20
Alignment explanation
Indices: 280886--280960 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
280876 TTTTACCTTG
280886 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
280906 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
280926 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
280946 ATGTATCGATACATT
1 ATGTATCGATACATT
280961 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:280953 original size:40 final size:39
Alignment explanation
Indices: 280886--280963 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
280876 TTTTACCTTG
* *
280886 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
280926 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
280964 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:281899 original size:22 final size:22
Alignment explanation
Indices: 281873--281929 Score: 87
Period size: 24 Copynumber: 2.5 Consensus size: 22
281863 AGCCTTTGAC
281873 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
281895 CATGCATTTTTTTTTATTATGTTT
1 CATGCA--TTTTTTTATTATGTTT
*
281919 TATGCATTTTT
1 CATGCATTTTT
281930 AACATGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.34
24 21 0.66
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:281911 original size:24 final size:24
Alignment explanation
Indices: 281879--281929 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
281869 TGACCATGCA
281879 TTTTTTTATTATGTTTCATGCATT
1 TTTTTTTATTATGTTTCATGCATT
*
281903 TTTTTTTATTATGTTTTATGCATT
1 TTTTTTTATTATGTTTCATGCATT
281927 TTT
1 TTT
281930 AACATGTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.71
Consensus pattern (24 bp):
TTTTTTTATTATGTTTCATGCATT
Found at i:286191 original size:22 final size:22
Alignment explanation
Indices: 286149--286203 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
286139 AAATAAAATT
* *
286149 AAAATAAAATAATTATTTTATA
1 AAAATAAAATAAATATATTATA
286171 AAAATAAAATTAAATA-ATTATA
1 AAAATAAAA-TAAATATATTATA
* *
286193 GAAATAGAATA
1 AAAATAAAATA
286204 GTTATCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 21 0.75
23 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATAAAATAAATATATTATA
Found at i:286434 original size:28 final size:28
Alignment explanation
Indices: 286351--286436 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
286341 ATTATTTTGA
286351 TATTTTATGAAATAAAATCATAAT-AAGT
1 TATTTTATGAAATAAAATCATAATGAA-T
* *
286379 TATTTTATAAAATAAAATCATAACGAAT
1 TATTTTATGAAATAAAATCATAATGAAT
* *
286407 TATTTTACGAAATAAATAT-TTAATGAAT
1 TATTTTATGAAATAAA-ATCATAATGAAT
286435 TA
1 TA
286437 AATAATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 46 0.92
29 4 0.08
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.40
Consensus pattern (28 bp):
TATTTTATGAAATAAAATCATAATGAAT
Found at i:286683 original size:3 final size:3
Alignment explanation
Indices: 286631--286669 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
286621 CTACTACTAC
*
286631 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
286670 CAGTTGCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:286907 original size:20 final size:21
Alignment explanation
Indices: 286879--286919 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
286869 ATTAATAGTT
*
286879 AATTGAAAAT-AAAACAAAAA
1 AATTAAAAATGAAAACAAAAA
*
286899 AATTAAAAATGAAAATAAAAA
1 AATTAAAAATGAAAACAAAAA
286920 GGTTCCATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (21 bp):
AATTAAAAATGAAAACAAAAA
Found at i:287407 original size:19 final size:18
Alignment explanation
Indices: 287385--287431 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
287375 ATAAAAGAAA
287385 ATAAAATAAATTCA-AATAG
1 ATAAAATAAATT-ATAAT-G
*
287404 ATAAATAAAAATTATAATG
1 ATAAA-ATAAATTATAATG
287423 ATAAAATAA
1 ATAAAATAA
287432 TACTATCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAAAATAAATTATAATG
Found at i:287414 original size:29 final size:29
Alignment explanation
Indices: 287350--287415 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
287340 AACTAATGGG
* * *
287350 ATAATAATAAAATAATTTAAAATATATAA
1 ATAAAAATAAAATAAATTAAAATAGATAA
*
287379 A-AGAAAATAAAATAAATTCAAATAGATAA
1 ATA-AAAATAAAATAAATTAAAATAGATAA
287408 ATAAAAAT
1 ATAAAAAT
287416 TATAATGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (29 bp):
ATAAAAATAAAATAAATTAAAATAGATAA
Found at i:287514 original size:3 final size:3
Alignment explanation
Indices: 287506--287551 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
287496 GTTAAAAAAT
287506 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
287552 TTTCATAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:288393 original size:30 final size:30
Alignment explanation
Indices: 288359--288423 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
288349 TATAACTATG
288359 TTTTTAACTTTT-AATTTATATTTAAATAAA
1 TTTTTAA-TTTTAAATTTATATTTAAATAAA
288389 TTTTTAATTTTAAATTTATATTTAAATAAA
1 TTTTTAATTTTAAATTTATATTTAAATAAA
288419 TTTTT
1 TTTTT
288424 TATACAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTAATTTTAAATTTATATTTAAATAAA
Found at i:288394 original size:18 final size:18
Alignment explanation
Indices: 288373--288423 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
288363 TAACTTTTAA
288373 TTTATATTTAAATAAATT
1 TTTATATTTAAATAAATT
288391 TTTA-ATTT---TAAA--
1 TTTATATTTAAATAAATT
288403 TTTATATTTAAATAAATT
1 TTTATATTTAAATAAATT
288421 TTT
1 TTT
288424 TATACAGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 4 0.15
16 4 0.15
17 4 0.15
18 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATATTTAAATAAATT
Found at i:290477 original size:42 final size:42
Alignment explanation
Indices: 290417--290574 Score: 151
Period size: 42 Copynumber: 3.7 Consensus size: 42
290407 CTCAACCTCA
290417 AGTCTGCCTATC-GACTTTGACCCTGGAGA-TTTTCTTACTTTC
1 AGTCTGCCTATCAG-CTTTGACCCTGGAGACTTTT-TTACTTTC
* * ** * *
290459 AGTCTGCTTATCAGCTTTGACCTTAAAGACTACTTTAAC-TTC
1 AGTCTGCCTATCAGCTTTGACCCTGGAGACT-TTTTTACTTTC
* * *
290501 AAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTATTTTC
1 -AGTCTGCCTATCAGCTTTGACCCTGGAGACTTTTTTACTTTC
** *
290544 AGTCTATCTATCAGCTTTGACTCTGGAGACT
1 AGTCTGCCTATCAGCTTTGACCCTGGAGACT
290575 GACTCAACCT
Statistics
Matches: 93, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 56 0.60
43 35 0.38
44 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.40
Consensus pattern (42 bp):
AGTCTGCCTATCAGCTTTGACCCTGGAGACTTTTTTACTTTC
Found at i:290532 original size:43 final size:43
Alignment explanation
Indices: 290392--290606 Score: 145
Period size: 43 Copynumber: 5.0 Consensus size: 43
290382 TAACTACTGA
* * * * *
290392 GACCCTGGAGACTACCTCAACCTCAAGTCTGCCTATCGACTTT
1 GACCTTGGAGACTACTTTAACTTCAAGTCTGCCTATCGGCTTT
* * * * *
290435 GACCCTGGAGA-T-TTTCTTACTTTC-AGTCTGCTTATCAGCTTT
1 GACCTTGGAGACTACTT-TAAC-TTCAAGTCTGCCTATCGGCTTT
**
290477 GACCTTAAAGACTACTTTAACTTCAAGTCTGCCTATCGGCTTT
1 GACCTTGGAGACTACTTTAACTTCAAGTCTGCCTATCGGCTTT
** ** ** *
290520 GACCTTGGAGACTTTTTTATTTTC-AGTCTATCTATCAGCTTT
1 GACCTTGGAGACTACTTTAACTTCAAGTCTGCCTATCGGCTTT
* * * *
290562 GA-CTCTGGAGACTGAC-TCAACCTCAAGTCTGCCTGTCGGTTTT
1 GACCT-TGGAGACT-ACTTTAACTTCAAGTCTGCCTATCGGCTTT
290605 GA
1 GA
290607 TCCTGAAGAC
Statistics
Matches: 129, Mismatches: 35, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
41 3 0.02
42 58 0.45
43 66 0.51
44 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (43 bp):
GACCTTGGAGACTACTTTAACTTCAAGTCTGCCTATCGGCTTT
Found at i:290544 original size:85 final size:85
Alignment explanation
Indices: 290400--290963 Score: 362
Period size: 85 Copynumber: 6.7 Consensus size: 85
290390 GAGACCCTGG
* * *
290400 AGACTACCTCAACCTCAAGTCTGCCTATCGACTTTGACCCTGGAGA-TTTTCTTACTTTCAGTCT
1 AGACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTT-TTACCTTCAGTCT
290464 GCTTATCAGCTTTGAC-CTTAA
65 GCTTATCAGCTTTGACTC-TAA
* * * **
290485 AGACTACTTTAACTTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTATTTTCAGTCT-
1 AGACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTACCTTCAGTCTG
* **
290549 ATCTATCAGCTTTGACTCTGG
66 CT-TATCAGCTTTGACTCTAA
* * * * * * *
290570 AGACTGA-CTCAACCTCAAGTCTGCCTGTCGGTTTTGATCC-TGAAGACTTTCTTATCTTAAGTT
1 AGACT-ACCTCAACCTCAAGTCTGCCTATCGGCTTTGA-CCTTGGAGACTTTTTTACCTTCAGTC
* * *
290633 TGTTTGTCGGCTTTGACTCTAA
64 TGCTTATCAGCTTTGACTCTAA
* * * * * * *
290655 ACG-CTGCCTTACCCTCAAGTTTGCCTGTCGGCTTTAACTTTGGAGACTTTTTTACCTTCAGTCT
1 A-GACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTACCTTCAGTCT
* * ** * *
290719 GCCTGTCAATTTTGACCCTAG
65 GCTTATCAGCTTTGACTCTAA
* * *** * ** * *
290740 AGACTGCCTC-ATCTCAAGTCTATTTATCGGCTTTGATCC-TAGAGACTTTCATACCCTCAGTTT
1 AGACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGA-CCTTGGAGACTTTTTTACCTTCAGTCT
** **
290803 GCTGGTC-GACTTTGAC-CTTGG
65 GCTTATCAG-CTTTGACTC-TAA
* * * *
290824 AGACTACC-CCACCTCAAGTCTACCTATCGGCTTTGACCTTGGAGACTTTCTTACC-TCTAGTTT
1 AGACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTACCTTC-AGTCT
* * * **
290887 GCCTATCGGCTTTGACCCTGG
65 GCTTATCAGCTTTGACTCTAA
* * * * * ***
290908 AGATTACCTC-ACCTCAAGTCTACTTGTCGACTTTGACCCAAGAGACTTTTTTACCT
1 AGACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTACCT
290964 CTTGTCTACC
Statistics
Matches: 379, Mismatches: 80, Indels: 40
0.76 0.16 0.08
Matches are distributed among these distances:
83 6 0.02
84 161 0.42
85 202 0.53
86 10 0.03
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (85 bp):
AGACTACCTCAACCTCAAGTCTGCCTATCGGCTTTGACCTTGGAGACTTTTTTACCTTCAGTCTG
CTTATCAGCTTTGACTCTAA
Found at i:290688 original size:170 final size:170
Alignment explanation
Indices: 290396--290946 Score: 447
Period size: 170 Copynumber: 3.3 Consensus size: 170
290386 TACTGAGACC
* * *
290396 CTGGAGACTACCTCAACCTCAAGTCTGCCTATCGACTTTGACCCTGGAGATTTTCTTACTTTCAG
1 CTGGAGACTACCTCAACCTCAAGTCTGCCTATCGACTTTGACCCTGAAGACTTTCTTACTTTAAG
* * *
290461 TCTGCTTATCAGCTTTGACCTTAAAGACTACTTTAACTTCAAGTCTGCCTATCGGCTTTGACCTT
66 TCTGCTTATCAGCTTTGACCTTAAAGACTACCTTAACCTCAAGTCTGCCTATCGGCTTTAACCTT
**
290526 GGAGACTTTTTTATTTTCAGTCTATCTATCAGCTTTGACT
131 GGAGACTTTTTTACCTTCAGTCTATCTATCAGCTTTGACT
* ** *
290566 CTGGAGACTGA-CTCAACCTCAAGTCTGCCTGTCGGTTTTGATCCTGAAGACTTTCTTA-TCTTA
1 CTGGAGACT-ACCTCAACCTCAAGTCTGCCTATCGACTTTGACCCTGAAGACTTTCTTACT-TTA
* * * * * * * *
290629 AGTTTGTTTGTCGGCTTTGA-CTCTAAACG-CTGCCTTACCCTCAAGTTTGCCTGTCGGCTTTAA
64 AGTCTGCTTATCAGCTTTGACCT-TAAA-GACTACCTTAACCTCAAGTCTGCCTATCGGCTTTAA
* ** * ** *
290692 CTTTGGAGACTTTTTTACCTTCAGTCTGCCTGTCAATTTTGACC
127 CCTTGGAGACTTTTTTACCTTCAGTCTATCTATCAGCTTTGACT
* * * *** * * * ** *
290736 CTAGAGACTGCCTC-ATCTCAAGTCTATTTATCGGCTTTGATCCT-AGAGACTTTCATACCCTCA
1 CTGGAGACTACCTCAACCTCAAGTCTGCCTATCGACTTTGACCCTGA-AGACTTTCTTACTTTAA
* ** ** ** * *
290799 GTTTGCTGGTC-GACTTTGACCTTGGAGACTACC-CCACCTCAAGTCTACCTATCGGCTTTGACC
65 GTCTGCTTATCAG-CTTTGACCTTAAAGACTACCTTAACCTCAAGTCTGCCTATCGGCTTTAACC
* * ** * *
290862 TTGGAGACTTTCTTACC-TCTAGTTTGCCTATCGGCTTTGACC
129 TTGGAGACTTTTTTACCTTC-AGTCTATCTATCAGCTTTGACT
* * * *
290904 CTGGAGATTACCTC-ACCTCAAGTCTACTTGTCGACTTTGACCC
1 CTGGAGACTACCTCAACCTCAAGTCTGCCTATCGACTTTGACCC
290947 AAGAGACTTT
Statistics
Matches: 304, Mismatches: 66, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
167 2 0.01
168 93 0.31
169 60 0.20
170 147 0.48
171 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.36
Consensus pattern (170 bp):
CTGGAGACTACCTCAACCTCAAGTCTGCCTATCGACTTTGACCCTGAAGACTTTCTTACTTTAAG
TCTGCTTATCAGCTTTGACCTTAAAGACTACCTTAACCTCAAGTCTGCCTATCGGCTTTAACCTT
GGAGACTTTTTTACCTTCAGTCTATCTATCAGCTTTGACT
Found at i:290858 original size:42 final size:42
Alignment explanation
Indices: 290812--290945 Score: 160
Period size: 42 Copynumber: 3.2 Consensus size: 42
290802 TGCTGGTCGA
*
290812 CTTTGACCTTGGAGACTACCCCACCTCAAGTCTACCTATCGG
1 CTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTATCGG
** * * * *
290854 CTTTGACCTTGGAGACTTTCTTACCTCTAGTTTGCCTATCGG
1 CTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTATCGG
* * * * *
290896 CTTTGACCCTGGAGATTACCTCACCTCAAGTCTACTTGTCGA
1 CTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTATCGG
290938 CTTTGACC
1 CTTTGACC
290946 CAAGAGACTT
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (42 bp):
CTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTATCGG
Done.