Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009584.1 Hibiscus syriacus cultivar Beakdansim tig00116961_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2003061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:1150697 original size:28 final size:28
Alignment explanation
Indices: 1150661--1150732 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
1150651 AATCTAAAAT
* *
1150661 CAAGTACCTCTGTGCTTTTATAAACGAC
1 CAAGCACCTCTGTGCTTTTACAAACGAC
* *
1150689 CGAGCACCTCTGTGCTTTTACAAACGGC
1 CAAGCACCTCTGTGCTTTTACAAACGAC
1150717 CAAGCACCTCTGTGCT
1 CAAGCACCTCTGTGCT
1150733 AGGTTTAGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (28 bp):
CAAGCACCTCTGTGCTTTTACAAACGAC
Found at i:1151270 original size:21 final size:21
Alignment explanation
Indices: 1151244--1151290 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1151234 CAAAATAACA
*
1151244 GAAATGCTACCTATAGACGTT
1 GAAATGCTACCTATAAACGTT
1151265 GAAATGCTACCTATAAACGTT
1 GAAATGCTACCTATAAACGTT
1151286 GAAAT
1 GAAAT
1151291 TCTCAAACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
GAAATGCTACCTATAAACGTT
Found at i:1159511 original size:53 final size:53
Alignment explanation
Indices: 1159405--1159713 Score: 343
Period size: 53 Copynumber: 5.8 Consensus size: 53
1159395 ATGACATGTC
* * **** *
1159405 CGCTCCCTCTTG-TTCAGGGATTAAAGAACTCGAACAATCTTCTAAAAATGGGTT
1 CGCTCCCTCTTGCTTCAGAGAGT--AGAACTCGAACAATCTTCTGCCTACGGGTT
* * * * * *
1159459 CGCTCCCTGTTTCTTCAGATACTAGAACTCGAATAATCTTCTGCTTACGGGTT
1 CGCTCCCTCTTGCTTCAGAGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* * * * *
1159512 CGCTCCCTCTTGCTTCAGGGGGTAGAACTGGAACTATCTTCTGTCTACGGGTT
1 CGCTCCCTCTTGCTTCAGAGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* *
1159565 CACTCACTCTTGCTTCAGAGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
1 CGCTCCCTCTTGCTTCAGAGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* * * * *
1159618 CGCTCCCTCTTGCTTTAGGGAGTAAAAATCAAACAATCTTCTGCCTACGGGTT
1 CGCTCCCTCTTGCTTCAGAGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
*
1159671 CTCTCCCTCTTGCTTCA-AGGAGTAGAACTCGAACAATCTTCTG
1 CGCTCCCTCTTGCTTCAGA-GAGTAGAACTCGAACAATCTTCTG
1159714 GTGTGATTCT
Statistics
Matches: 211, Mismatches: 42, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
53 194 0.92
54 10 0.05
55 7 0.03
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (53 bp):
CGCTCCCTCTTGCTTCAGAGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
Found at i:1160162 original size:42 final size:41
Alignment explanation
Indices: 1160077--1160172 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
1160067 CAACACTCTT
* **
1160077 TCGAGAAGGCTTA-AAATGACCCGGAGGACTTATCATCTCGC
1 TCGA-AAGACTTATAAATGACCCAAAGGACTTATCATCTCGC
*
1160118 TCGAAAGACTTATAAATGACCCAAAGGATTTCATCATCAT-GC
1 TCGAAAGACTTATAAATGACCCAAAGGACTT-ATCATC-TCGC
1160160 TCGAAAGACTTAT
1 TCGAAAGACTTAT
1160173 TGATGAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 7 0.15
41 19 0.40
42 21 0.44
43 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (41 bp):
TCGAAAGACTTATAAATGACCCAAAGGACTTATCATCTCGC
Found at i:1160268 original size:42 final size:42
Alignment explanation
Indices: 1160221--1160300 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1160211 AAATTACCTG
1160221 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
* *
1160263 AAGGATTTCATCATCATGTTCGAAAGACTTACTGATGG
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1160301 AACTTACTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (42 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA
Found at i:1160307 original size:13 final size:13
Alignment explanation
Indices: 1160289--1160314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1160279 TGTTCGAAAG
1160289 ACTTACTGATGGA
1 ACTTACTGATGGA
1160302 ACTTACTGATGGA
1 ACTTACTGATGGA
1160315 TTTGCTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
ACTTACTGATGGA
Found at i:1160399 original size:42 final size:42
Alignment explanation
Indices: 1160352--1160436 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
1160342 TTACAAATTA
* * * *
1160352 CCCGAAGGATTTTATCATTATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGG
1160394 CCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGG
1 CCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGG
1160436 C
1 C
1160437 ACTTACTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (42 bp):
CCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGG
Found at i:1160409 original size:135 final size:135
Alignment explanation
Indices: 1160167--1160523 Score: 588
Period size: 135 Copynumber: 2.6 Consensus size: 135
1160157 TGCTCGAAAG
* * *
1160167 ACTTATTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCTGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
* *
1160232 CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATTTCATCATCATGTTCGAAAGACTTACTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATTTCATCATCATGCTCAAAAGACTTACTG
1160297 ATGGA
131 ATGGA
*
1160302 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTTAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
* * *
1160367 CATTATGCTCGAAAGACTTATTGATGGCCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATTTCATCATCATGCTCAAAAGACTTACTG
*
1160432 ATGGC
131 ATGGA
* * *
1160437 ACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAAGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
*
1160502 CATCATGCTTGAAAGACTTACT
66 CATCATGCTCGAAAGACTTACT
1160524 AATGACACTT
Statistics
Matches: 205, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 205 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (135 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCAAAGGATTTCATCATCATGCTCAAAAGACTTACTG
ATGGA
Found at i:1160442 original size:13 final size:13
Alignment explanation
Indices: 1160424--1160448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1160414 TGCTCAAAAG
1160424 ACTTACTGATGGC
1 ACTTACTGATGGC
1160437 ACTTACTGATGG
1 ACTTACTGATGG
1160449 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1160553 original size:93 final size:93
Alignment explanation
Indices: 1160394--1160609 Score: 344
Period size: 93 Copynumber: 2.3 Consensus size: 93
1160384 TTATTGATGG
* * * * *
1160394 CCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
1 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTAATGACACTTACTGATGGGTTTGCTTCA
1160459 CTACTCTTCCG-TGAAGGCTTACAAATTA
66 CTACTCTT-CGATGAAGGCTTACAAATTA
*
1160487 CCCGAAAGATTTAATCATCATGCTTGAAAGACTTACTAATGACACTTACTGATGGGTTTGCTTCA
1 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTAATGACACTTACTGATGGGTTTGCTTCA
1160552 CTACTCTTCGATGAAGGCTTACAAATTA
66 CTACTCTTCGATGAAGGCTTACAAATTA
* *
1160580 CCTGAAAGACTTAATCATCATGCTCGAAAG
1 CCCGAAAGATTTAATCATCATGCTCGAAAG
1160610 CCATACTGAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 2 0.02
93 111 0.98
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (93 bp):
CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTAATGACACTTACTGATGGGTTTGCTTCA
CTACTCTTCGATGAAGGCTTACAAATTA
Found at i:1169152 original size:17 final size:18
Alignment explanation
Indices: 1169124--1169160 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1169114 TATTACCATG
*
1169124 TAGAATAAATAAAACCCA
1 TAGAATAAATAAAACACA
1169142 TAGAA-AAATAAAACACA
1 TAGAATAAATAAAACACA
1169159 TA
1 TA
1169161 TGCTTAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.65, C:0.14, G:0.05, T:0.16
Consensus pattern (18 bp):
TAGAATAAATAAAACACA
Found at i:1172916 original size:17 final size:19
Alignment explanation
Indices: 1172880--1172917 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1172870 GAGAGAATGA
1172880 AGAAGAAAGAAAGATGAAG
1 AGAAGAAAGAAAGATGAAG
*
1172899 AGAA-AAAGAATGAT-AAG
1 AGAAGAAAGAAAGATGAAG
1172916 AG
1 AG
1172918 TTTGGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 9 0.50
19 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (19 bp):
AGAAGAAAGAAAGATGAAG
Found at i:1174689 original size:19 final size:19
Alignment explanation
Indices: 1174667--1174713 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1174657 GGAATGTAAC
1174667 ATTACTTTGGGAATATTGT
1 ATTACTTTGGGAATATTGT
1174686 ATTACTTTGGGAATATTGT
1 ATTACTTTGGGAATATTGT
1174705 ATTACTTTG
1 ATTACTTTG
1174714 TTTAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (19 bp):
ATTACTTTGGGAATATTGT
Found at i:1174750 original size:26 final size:28
Alignment explanation
Indices: 1174721--1174774 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1174711 TTGTTTAGTT
*
1174721 TTGTTTAG-T-AGGAATGTAAGATTACA
1 TTGTTTAGTTGAGGAATATAAGATTACA
1174747 TTGTTTAGTTGGAGGAATATAAGATTAC
1 TTGTTTAGTT-GAGGAATATAAGATTAC
1174775 TTGGATAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 1 0.04
29 15 0.62
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (28 bp):
TTGTTTAGTTGAGGAATATAAGATTACA
Found at i:1174784 original size:14 final size:14
Alignment explanation
Indices: 1174765--1174794 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1174755 TTGGAGGAAT
1174765 ATAAGATTACTTGG
1 ATAAGATTACTTGG
1174779 ATAAGATTACTTGG
1 ATAAGATTACTTGG
1174793 AT
1 AT
1174795 GCATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
ATAAGATTACTTGG
Found at i:1175824 original size:16 final size:17
Alignment explanation
Indices: 1175805--1175841 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1175795 TAAAATATTA
1175805 TTTTA-AATAATTAC-AT
1 TTTTATAATAA-TACTAT
1175821 TTTTATAATAATACTAT
1 TTTTATAATAATACTAT
1175838 TTTT
1 TTTT
1175842 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTATAATAATACTAT
Found at i:1177880 original size:23 final size:23
Alignment explanation
Indices: 1177836--1177881 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1177826 TTTTTAATAA
* *
1177836 TTATTTCTTTATGACACGTTTTC
1 TTATGTCTTTATGACACATTTTC
**
1177859 TTATGTCTTTATGGTACATTTTC
1 TTATGTCTTTATGACACATTTTC
1177882 GTCTGTCATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (23 bp):
TTATGTCTTTATGACACATTTTC
Found at i:1178604 original size:15 final size:14
Alignment explanation
Indices: 1178582--1178635 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
1178572 AATCATATAA
1178582 TTCATATTAAATAG
1 TTCATATTAAATAG
**
1178596 TTGCATATTTTATAG
1 TT-CATATTAAATAG
1178611 TTCATATTAAATAG
1 TTCATATTAAATAG
1178625 ATTACATATTA
1 -TT-CATATTA
1178636 TATTCCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 12 0.36
15 14 0.42
16 7 0.21
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (14 bp):
TTCATATTAAATAG
Found at i:1178658 original size:25 final size:25
Alignment explanation
Indices: 1178591--1178690 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 25
1178581 ATTCATATTA
* *
1178591 AATAGTTGCATATTTTATAGTTCATATT
1 AATAGTTGCATATTATATA--TC-CATT
*
1178619 AAATAGATTACATATTATAT-TCCATGT
1 -AATAG-TTGCATATTATATATCCAT-T
1178646 AATAGTTGCATATTATATAGTCCATT
1 AATAGTTGCATATTATATA-TCCATT
1178672 ATATAGTTAGCATATTATA
1 A-ATAGTT-GCATATTATA
1178691 AATAATAGCC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
25 12 0.20
26 9 0.15
27 14 0.23
28 10 0.16
29 5 0.08
30 11 0.18
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (25 bp):
AATAGTTGCATATTATATATCCATT
Found at i:1186206 original size:15 final size:15
Alignment explanation
Indices: 1186186--1186215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1186176 TATAATAGTC
*
1186186 CATGTGCGCTTGAGA
1 CATGTGCACTTGAGA
1186201 CATGTGCACTTGAGA
1 CATGTGCACTTGAGA
1186216 TCGAGATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (15 bp):
CATGTGCACTTGAGA
Found at i:1189974 original size:13 final size:13
Alignment explanation
Indices: 1189953--1189983 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1189943 TTAACCAGAG
*
1189953 TTGATCATTGACT
1 TTGACCATTGACT
1189966 TTGACCATTGACT
1 TTGACCATTGACT
1189979 TTGAC
1 TTGAC
1189984 AAAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:1199152 original size:40 final size:40
Alignment explanation
Indices: 1199080--1199203 Score: 187
Period size: 40 Copynumber: 3.1 Consensus size: 40
1199070 TATGCACCAT
** *
1199080 AGTGC-TTACACATAATATCTTGCCCACCATATGCACTGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACTGA
* *
1199119 AGTGCATTACACATAAGGTCGTGCGCACAATATGCACTGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACTGA
*
1199159 AGTGCATTACACATAAGGTTGTGCCCACCATATGCACTGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACTGA
1199199 AGTGC
1 AGTGC
1199204 TTAATCGATA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 5 0.07
40 71 0.93
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (40 bp):
AGTGCATTACACATAAGGTCGTGCCCACCATATGCACTGA
Found at i:1201493 original size:44 final size:43
Alignment explanation
Indices: 1201374--1201537 Score: 129
Period size: 43 Copynumber: 3.8 Consensus size: 43
1201364 GCGTTTTAGA
* * * *
1201374 ACAAAAAACGCCGCAATAGGTCAAT-ATCTATTA-CGGCATTTTT
1 ACAAAAAACGCCGCAAAAAGTC-ATGATCTA-TAGCGGCGTTTAT
** * * *
1201417 TGAACAAACGCCGCAAAAGGTCGAT-ATCTATAGCGGTGTTTATT
1 ACAAAAAACGCCGCAAAAAGTC-ATGATCTATAGCGGCGTTTA-T
* * * * *
1201461 TCCATAAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTAT
1 ACAAAAAACGCCGCAAAAAGTCATGATCTATAGCGGCGTTTAT
*
1201504 AGAAAAAACGCCGCAAAAAGTCA-GATCTATAGCG
1 ACAAAAAACGCCGCAAAAAGTCATGATCTATAGCG
1201538 ACGGTTTTGG
Statistics
Matches: 97, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
42 12 0.12
43 52 0.54
44 33 0.34
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (43 bp):
ACAAAAAACGCCGCAAAAAGTCATGATCTATAGCGGCGTTTAT
Found at i:1201669 original size:43 final size:42
Alignment explanation
Indices: 1201407--1201688 Score: 171
Period size: 43 Copynumber: 6.6 Consensus size: 42
1201397 ATATCTATTA
* * * *
1201407 CGGCATTTTTTGAACAAACGCCGCAAAAGG-TCGATATCTATAG
1 CGGCGTTTTTAGAACAAACGCCGCAAAAGGTTAGA-CT-TATAG
* *** * *
1201450 CGGTGTTTATTTCCATAAACGCCGCAAAAAGTTATGA-TATATAG
1 CGGCGTTT-TTAGAACAAACGCCGCAAAAGGTTA-GACT-TATAG
* * * *
1201494 CGGCGTTTATAGAAAAAACGCCGCAAAAAGTCAGA-TCTATAG
1 CGGCGTTTTTAGAACAAACGCCGCAAAAGGTTAGACT-TATAG
* * * * * *
1201536 CGACGGTTTTGGATACAAACGCCGCAAAAGATAAGACCTATA-
1 CGGCGTTTTTAGA-ACAAACGCCGCAAAAGGTTAGACTTATAG
* ** * *
1201578 CTGGCGTTTTTAGAACAAATGCCGTTATAGGTCTA-ACCTT-TTG
1 C-GGCGTTTTTAGAACAAACGCCGCAAAAGGT-TAGA-CTTATAG
*
1201621 CGGCGTTTTTAGACACAAACGCCGCAAAAGGTTAGACTTATAA
1 CGGCGTTTTTAGA-ACAAACGCCGCAAAAGGTTAGACTTATAG
*
1201664 CGGCGTTTTTGGATACAAACGCCGC
1 CGGCGTTTTTAGA-ACAAACGCCGC
1201689 TAATTACCTT
Statistics
Matches: 183, Mismatches: 44, Indels: 24
0.73 0.18 0.10
Matches are distributed among these distances:
42 50 0.27
43 99 0.54
44 31 0.17
45 1 0.01
46 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (42 bp):
CGGCGTTTTTAGAACAAACGCCGCAAAAGGTTAGACTTATAG
Found at i:1204921 original size:41 final size:41
Alignment explanation
Indices: 1204859--1205038 Score: 193
Period size: 41 Copynumber: 4.4 Consensus size: 41
1204849 GAGGATTGGC
* * *
1204859 AACGACACTATAGTACATGTGTATAACGGCGTTTGTATAAA
1 AACGCCACTAAAGTACATGTCTATAACGGCGTTTGTATAAA
* * * **
1204900 AATGCCACTATAGTACATGTGTATAACAACGTTTGTATAAA
1 AACGCCACTAAAGTACATGTCTATAACGGCGTTTGTATAAA
* *
1204941 AACGCCTCTAAAGTACAAT-TCTATAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTAC-ATGTCTATAACGGCGTTTGTATAAA
* * * * *
1204982 AATGCCACTAAATTATGA-GTCTTTAGCGGCGTTTGTATAAA
1 AACGCCACTAAAGTA-CATGTCTATAACGGCGTTTGTATAAA
1205023 AACGCCACTAAAGTAC
1 AACGCCACTAAAGTAC
1205039 TACTCTTTTG
Statistics
Matches: 117, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
41 115 0.98
42 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (41 bp):
AACGCCACTAAAGTACATGTCTATAACGGCGTTTGTATAAA
Found at i:1205015 original size:82 final size:82
Alignment explanation
Indices: 1204880--1205073 Score: 212
Period size: 82 Copynumber: 2.4 Consensus size: 82
1204870 AGTACATGTG
* * *
1204880 TATAACGGCGTTTGTATAAAAATGCCACTATAGTACATGTGTATAACAACGTTTGTATAAAAACG
1 TATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACATGTCTATAACAACGTTTGTATAAAAACG
* *
1204945 CCTCTAAAGTACAATTC
66 CCACTAAAGTACAACTC
* * * * **
1204962 TATAGCGGCGTTTGTATAAAAATGCCACTAAATTATGA-GTCTTTAGCGGCGTTTGTATAAAAAC
1 TATAGCGGCGTTTGTATAAAAATGCCACTAAAGTA-CATGTCTATAACAACGTTTGTATAAAAAC
*
1205026 GCCACTAAAGTACTACTC
65 GCCACTAAAGTACAACTC
* * * *
1205044 TTTTGCGACGTTTGT-TGAAAAACGCCACTA
1 TATAGCGGCGTTTGTAT-AAAAATGCCACTA
1205074 TCGATGAACC
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
81 1 0.01
82 92 0.98
83 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (82 bp):
TATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACATGTCTATAACAACGTTTGTATAAAAACG
CCACTAAAGTACAACTC
Found at i:1205046 original size:41 final size:40
Alignment explanation
Indices: 1204885--1205073 Score: 177
Period size: 41 Copynumber: 4.6 Consensus size: 40
1204875 ATGTGTATAA
* * * *
1204885 CGGCGTTTGTATAAAAATGCCACTATAGTAC-ATGTGTATAA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTATCT-T-TAG
** * * *
1204926 CAACGTTTGTATAAAAACGCCTCTAAAGTACAATTCTATAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTA-TCTTTAG
* *
1204967 CGGCGTTTGTATAAAAATGCCACTAAATTA-TGAGTCTTTAG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACT-A-TCTTTAG
*
1205008 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTG
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACTA-TCTTTAG
*
1205049 CGACGTTTGT-TGAAAAACGCCACTA
1 CGGCGTTTGTAT-AAAAACGCCACTA
1205074 TCGATGAACC
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
40 1 0.01
41 117 0.96
42 2 0.02
43 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (40 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACTATCTTTAG
Found at i:1209140 original size:61 final size:61
Alignment explanation
Indices: 1209049--1209168 Score: 240
Period size: 61 Copynumber: 2.0 Consensus size: 61
1209039 TTTTTCTTTA
1209049 TATATATTTTTTGTTCGATCAAATGTGATGACCGACAAAAGTCACAGTGGTCGGTGCTCTT
1 TATATATTTTTTGTTCGATCAAATGTGATGACCGACAAAAGTCACAGTGGTCGGTGCTCTT
1209110 TATATATTTTTTGTTCGATCAAATGTGATGACCGACAAAAGTCACAGTGGTCGGTGCTC
1 TATATATTTTTTGTTCGATCAAATGTGATGACCGACAAAAGTCACAGTGGTCGGTGCTC
1209169 GATGTTTGTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (61 bp):
TATATATTTTTTGTTCGATCAAATGTGATGACCGACAAAAGTCACAGTGGTCGGTGCTCTT
Found at i:1209994 original size:20 final size:21
Alignment explanation
Indices: 1209969--1210013 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1209959 CTAATATTAA
*
1209969 AATTAAACCTTTAG-CTTTTT
1 AATTAAAACTTTAGACTTTTT
*
1209989 AATTAAAACTTTAGATTTTTT
1 AATTAAAACTTTAGACTTTTT
1210010 AATT
1 AATT
1210014 CTTTAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (21 bp):
AATTAAAACTTTAGACTTTTT
Found at i:1213733 original size:35 final size:36
Alignment explanation
Indices: 1213654--1213745 Score: 116
Period size: 35 Copynumber: 2.6 Consensus size: 36
1213644 TTGAAAAGAT
* *
1213654 ATAATAAAATAAATAATTATAATTCAAAAAGAAAAA
1 ATAATAAAATAAATAATAATAAATCAAAAAGAAAAA
* **
1213690 ATAATAAAATAAATAATAATAAAT-ACAAAGGGAAA
1 ATAATAAAATAAATAATAATAAATCAAAAAGAAAAA
1213725 ATAATAAAAT-AATAAATAATA
1 ATAATAAAATAAAT-AATAATA
1213746 GTAGTAAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 3 0.06
35 25 0.50
36 22 0.44
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (36 bp):
ATAATAAAATAAATAATAATAAATCAAAAAGAAAAA
Found at i:1214510 original size:12 final size:12
Alignment explanation
Indices: 1214493--1214520 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1214483 TCTAAAACAA
1214493 AAATAATATTTT
1 AAATAATATTTT
1214505 AAATAATATTTT
1 AAATAATATTTT
1214517 AAAT
1 AAAT
1214521 CCTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:1214563 original size:75 final size:75
Alignment explanation
Indices: 1214437--1214656 Score: 273
Period size: 76 Copynumber: 2.9 Consensus size: 75
1214427 AAGCTAAAAC
* * *
1214437 ATCTTAAATCTTAATTAAAATATTTAAAACTACTTAAACTAAAATATCTAAAACAAAAATAATAT
1 ATCTTAAATCTTAATTAAAATA-TTAAAACTATTTAAACTAAAATATCTAAAACAAAGATAAAAT
**
1214502 -TTTAAATAAT
65 ATAAAAATAAT
* * * * *
1214512 ATTTTAAATCCTAATTTAAATACTAAAACCTATTTAAACTAAAATATCTAAAATAAAGATAAAAT
1 ATCTTAAATCTTAATTAAAATATTAAAA-CTATTTAAACTAAAATATCTAAAACAAAGATAAAAT
1214577 ATAAAAATAAT
65 ATAAAAATAAT
* * *
1214588 ATCCTAAAACTTAATTAAAATATTAAAATCTATTTAAACTAACATA-CTTAAAACAAAGATAAAA
1 ATCTTAAATCTTAATTAAAATATTAAAA-CTATTTAAACTAAAATATC-TAAAACAAAGATAAAA
1214652 TATAA
64 TATAA
1214657 TGTTTAAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
74 5 0.04
75 52 0.42
76 66 0.54
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (75 bp):
ATCTTAAATCTTAATTAAAATATTAAAACTATTTAAACTAAAATATCTAAAACAAAGATAAAATA
TAAAAATAAT
Found at i:1214683 original size:16 final size:16
Alignment explanation
Indices: 1214662--1214694 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1214652 TATAATGTTT
1214662 AAAATATTATCCTAAA
1 AAAATATTATCCTAAA
1214678 AAAATATTATCCTAAA
1 AAAATATTATCCTAAA
1214694 A
1 A
1214695 CTTGAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATTATCCTAAA
Found at i:1215123 original size:22 final size:23
Alignment explanation
Indices: 1215095--1215137 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
1215085 ATTAAAAATA
1215095 CGGATGACAGGGTCTG-CTGAGC
1 CGGATGACAGGGTCTGACTGAGC
1215117 CGGATGACAGGGTCTGACTGA
1 CGGATGACAGGGTCTGACTGA
1215138 CAGCTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (23 bp):
CGGATGACAGGGTCTGACTGAGC
Found at i:1215182 original size:77 final size:77
Alignment explanation
Indices: 1215055--1215213 Score: 311
Period size: 77 Copynumber: 2.1 Consensus size: 77
1215045 AGCTGGTATC
1215055 GACTGACAGCTTTTGAGCATCGTACCTAATATTAAAAATACGGATGACAGGGTCTGCTGAGCCGG
1 GACTGACAGCTTTTGAGCATCGTACCTAATATTAAAAATACGGATGACAGGGTCTGCTGAGCCGG
1215120 ATGACAGGGTCT
66 ATGACAGGGTCT
1215132 GACTGACAGCTTTTGAGCATCGTACCTAATATTAAAAATACGGATGACAGGGTCTGCTGAGCCGG
1 GACTGACAGCTTTTGAGCATCGTACCTAATATTAAAAATACGGATGACAGGGTCTGCTGAGCCGG
1215197 ATGACAGGGTCT
66 ATGACAGGGTCT
1215209 G-CTGA
1 GACTGA
1215214 GCCAGATGAG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 4 0.05
77 78 0.95
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (77 bp):
GACTGACAGCTTTTGAGCATCGTACCTAATATTAAAAATACGGATGACAGGGTCTGCTGAGCCGG
ATGACAGGGTCT
Found at i:1215200 original size:22 final size:22
Alignment explanation
Indices: 1215172--1215222 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1215162 ATTAAAAATA
1215172 CGGATGACAGGGTCTGCTGAGC
1 CGGATGACAGGGTCTGCTGAGC
1215194 CGGATGACAGGGTCTGCTGAGC
1 CGGATGACAGGGTCTGCTGAGC
*
1215216 CAGATGA
1 CGGATGA
1215223 GAGGTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.18
Consensus pattern (22 bp):
CGGATGACAGGGTCTGCTGAGC
Found at i:1216729 original size:18 final size:18
Alignment explanation
Indices: 1216706--1216740 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1216696 CAACAGCCAC
1216706 CGCAGCCATATATGATGT
1 CGCAGCCATATATGATGT
1216724 CGCAGCCATATATGATG
1 CGCAGCCATATATGATG
1216741 CCGTCATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:1217308 original size:26 final size:24
Alignment explanation
Indices: 1217235--1217308 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
1217225 TTATATTTGT
1217235 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
** *
1217260 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1217284 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1217309 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1221020 original size:50 final size:51
Alignment explanation
Indices: 1220945--1221071 Score: 184
Period size: 51 Copynumber: 2.5 Consensus size: 51
1220935 CCTACGTGGT
* * * **
1220945 GTATAGCGCGCTGCAGGGGCCGCGCTATACC-CACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCACCAAATCACC
*
1220995 GTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCACCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCACCAAATCACC
*
1221046 GTATAGCACGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
1221072 TTACTGCTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 29 0.42
51 40 0.58
ACGTcount: A:0.18, C:0.31, G:0.35, T:0.16
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCACCAAATCACC
Found at i:1221676 original size:2 final size:2
Alignment explanation
Indices: 1221671--1221718 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1221661 GCAATTATGC
1221671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1221713 AT AT AT
1 AT AT AT
1221719 GAGAAAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1224119 original size:3 final size:3
Alignment explanation
Indices: 1224111--1224187 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
1224101 CTTTGGACAC
1224111 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1224159 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1224188 GAATTGTTTC
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1226637 original size:24 final size:24
Alignment explanation
Indices: 1226605--1226654 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1226595 ATCCTGTGAA
1226605 CGTGCAAGAGTTTGAGTGCGTGTC
1 CGTGCAAGAGTTTGAGTGCGTGTC
*
1226629 CGTGCAAGAGTTTGAGTGTGTGTC
1 CGTGCAAGAGTTTGAGTGCGTGTC
1226653 CG
1 CG
1226655 ATCGATGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (24 bp):
CGTGCAAGAGTTTGAGTGCGTGTC
Found at i:1227607 original size:21 final size:21
Alignment explanation
Indices: 1227545--1227608 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 21
1227535 TAAAATTTTA
* *
1227545 AAAAAATATTAAATTAAGAAAT
1 AAAAAATAATAAATTAA-AAAG
*
1227567 AAAAATAAAGATAAGA-TAAAAAG
1 AAAAA-ATA-ATAA-ATTAAAAAG
1227590 AAAAAATAATAAATTAAAA
1 AAAAAATAATAAATTAAAA
1227609 TAATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 7 0.21
23 10 0.29
24 6 0.18
25 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (21 bp):
AAAAAATAATAAATTAAAAAG
Found at i:1227645 original size:49 final size:50
Alignment explanation
Indices: 1227569--1227685 Score: 127
Period size: 53 Copynumber: 2.4 Consensus size: 50
1227559 TAAGAAATAA
1227569 AAATAAAG--ATAAGATAAAAAGAAAAAATAATAAA-TTAAAAT-AATATT
1 AAATAAAGAAATAA-ATAAAAAGAAAAAATAATAAATTTAAAATAAATATT
** *
1227616 AAA-AAAGAAATAAATAAAAATGAAGAAAATGTTAAATTTTAAAATAAATTTT
1 AAATAAAGAAATAAATAAAAA-GAA-AAAATAATAAA-TTTAAAATAAATATT
*
1227668 AAATAAATAAATAAATAA
1 AAATAAAGAAATAAATAA
1227686 GAAAATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
46 4 0.07
47 10 0.17
48 7 0.12
49 9 0.16
51 7 0.12
52 8 0.14
53 13 0.22
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (50 bp):
AAATAAAGAAATAAATAAAAAGAAAAAATAATAAATTTAAAATAAATATT
Found at i:1227651 original size:33 final size:32
Alignment explanation
Indices: 1227563--1227651 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 32
1227553 TTAAATTAAG
* *
1227563 AAATAAAAATAAAGATAA-GAT-AAAAAGAAA
1 AAATAAAAATAAAGAAAATGTTAAAAAAGAAA
* *
1227593 AAATAATAAATTAAA-ATAATATTAAAAAAGAAA
1 AAATAA-AAA-TAAAGAAAATGTTAAAAAAGAAA
*
1227626 TAAATAAAAATGAAGAAAATGTTAAA
1 -AAATAAAAATAAAGAAAATGTTAAA
1227652 TTTTAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
30 6 0.12
31 7 0.15
32 8 0.17
33 21 0.44
34 6 0.12
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (32 bp):
AAATAAAAATAAAGAAAATGTTAAAAAAGAAA
Found at i:1227717 original size:45 final size:45
Alignment explanation
Indices: 1227623--1227778 Score: 147
Period size: 46 Copynumber: 3.4 Consensus size: 45
1227613 ATTAAAAAAG
**
1227623 AAATAAAT-AA-AAATGAAGAAAATGTTAAATTTTAAAATAAATTTT
1 AAATAAATAAATAAAT-AAGAAAATGTTAAATTTTAAAATAAA-TAA
* *
1227668 AAATAAATAAATAAATAAGAAAATATTAATTTTTAAAATAAATAA
1 AAATAAATAAATAAATAAGAAAATGTTAAATTTTAAAATAAATAA
* * *
1227713 AAATAAAATAAAATAAAAAGAGAAAGAAATGTTAAATTTTAGAAGAAATAA
1 AAAT-AAAT-AAATAAATA-AG--A-AAATGTTAAATTTTAAAATAAATAA
*
1227764 AAAT-AATAAAAAAAT
1 AAATAAATAAATAAAT
1227779 TTAAAAAAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
45 13 0.14
46 30 0.33
47 12 0.13
48 8 0.09
49 3 0.03
50 1 0.01
51 25 0.27
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (45 bp):
AAATAAATAAATAAATAAGAAAATGTTAAATTTTAAAATAAATAA
Found at i:1227719 original size:15 final size:16
Alignment explanation
Indices: 1227701--1227731 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1227691 TATTAATTTT
1227701 TAAAAT-AAATAAAAA
1 TAAAATAAAATAAAAA
1227716 TAAAATAAAATAAAAA
1 TAAAATAAAATAAAAA
1227732 GAGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:1227722 original size:46 final size:46
Alignment explanation
Indices: 1227566--1227733 Score: 146
Period size: 46 Copynumber: 3.5 Consensus size: 46
1227556 AATTAAGAAA
* **
1227566 TAAAAATAAAGATAAGATAAAAAGAAAA-AATAATAAATTAAAATAATAT
1 TAAAAATAAA-ATAA-ATAAAAAGAAAATATTAAT-TTTTAAAATAA-AT
* *
1227615 TAAAAA-AGAAATAAATAAAAATGAAGAAAATGTTAAATTTTAAAATAAAT
1 TAAAAATA-AAATAAAT--AAA--AAGAAAATATTAATTTTTAAAATAAAT
**
1227665 TTTAAAT-AAATAAATAAATAAGAAAATATTAATTTTTAAAATAAA-
1 TAAAAATAAAATAAATAAA-AAGAAAATATTAATTTTTAAAATAAAT
1227710 TAAAAATAAAATAAAATAAAAAGA
1 TAAAAATAAAAT-AAATAAAAAGA
1227734 GAAAGAAATG
Statistics
Matches: 98, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
45 5 0.05
46 32 0.33
47 12 0.12
48 5 0.05
49 19 0.19
50 6 0.06
51 16 0.16
52 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (46 bp):
TAAAAATAAAATAAATAAAAAGAAAATATTAATTTTTAAAATAAAT
Found at i:1227788 original size:97 final size:97
Alignment explanation
Indices: 1227603--1227788 Score: 213
Period size: 97 Copynumber: 1.9 Consensus size: 97
1227593 AAATAATAAA
* * **
1227603 TTAAAATAATATTAAAAAAGAAATAAATAAAAATGAAGAAAATGTTAAATTTTAAAATAAATTTT
1 TTAAAATAATATTAAAAAAGAAATAAATAAAAAAGAAGAAAATGTTAAATTTTAAAAGAAATTAA
* *
1227668 AAATAAATAAATAAATAAGAAAATATTAATTT
66 AAATAAATAAAAAAATAAAAAAATATTAATTT
*
1227700 TTAAAATAA-A-TAAAAATA-AAATAAAATAAAAAGAGAA-AGAAATGTTAAATTTTAGAAGAAA
1 TTAAAATAATATTAAAAA-AGAAAT-AAATAAAAA-AGAAGA-AAATGTTAAATTTTAAAAGAAA
1227761 -TAAAAAT-AATAAAAAAATTTAAAAAAAT
62 TTAAAAATAAATAAAAAAA--TAAAAAAAT
1227789 GAAGAAAGTG
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
95 19 0.25
96 17 0.22
97 40 0.53
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (97 bp):
TTAAAATAATATTAAAAAAGAAATAAATAAAAAAGAAGAAAATGTTAAATTTTAAAAGAAATTAA
AAATAAATAAAAAAATAAAAAAATATTAATTT
Found at i:1228877 original size:5 final size:4
Alignment explanation
Indices: 1228864--1228992 Score: 54
Period size: 4 Copynumber: 30.8 Consensus size: 4
1228854 CAAAAACAAA
*
1228864 AAAT -AAT AAGAT AAAT AAAT ATAT AATAT AAAT -AAT AAAT ATATAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT A-A-AT
* * *
1228910 AAAT ACAA- ATAAT -AAT AAAT AATAT TAAT ATAAT ATAT -AAT ATTAT
1 AAAT A-AAT A-AAT AAAT AAAT AA-AT AAAT A-AAT AAAT AAAT A-AAT
* *
1228956 AAAT -AAT AATAT ATAT AAAAT AAAT AATAT GAAT AAA
1 AAAT AAAT AA-AT AAAT -AAAT AAAT AA-AT AAAT AAA
1228993 ATATATAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
3 14 0.15
4 47 0.49
5 31 0.33
6 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (4 bp):
AAAT
Found at i:1228933 original size:33 final size:30
Alignment explanation
Indices: 1228864--1229004 Score: 137
Period size: 30 Copynumber: 4.6 Consensus size: 30
1228854 CAAAAACAAA
* * *
1228864 AAATAATAAGATAAATAAAT-ATATAATAT
1 AAATAATAATATATATAAATAAAATAATAT
1228893 AAATAATAAATATATATAAATACAAATAATAAT
1 AAATAAT-AATATATATAAATA-AAATAAT-AT
* * *
1228926 AAATAATATTA-ATATAATATATAATATTAT
1 AAATAATAATATATATAA-ATAAAATAATAT
1228956 AAATAATAATATATATAAA-ATAAATAATAT
1 AAATAATAATATATATAAATA-AAATAATAT
*
1228986 GAATAA-AATATATAATAAA
1 AAATAATAATATAT-ATAAA
1229005 AACTATATAA
Statistics
Matches: 94, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
29 15 0.16
30 41 0.44
31 17 0.18
32 12 0.13
33 9 0.10
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (30 bp):
AAATAATAATATATATAAATAAAATAATAT
Found at i:1228944 original size:18 final size:18
Alignment explanation
Indices: 1228917--1229002 Score: 90
Period size: 18 Copynumber: 4.9 Consensus size: 18
1228907 TATAAATACA
1228917 AATAATAATAAATAATATT
1 AATAA-AATAAATAATATT
* *
1228936 AATATAATATATAATATT
1 AATAAAATAAATAATATT
1228954 -AT-AAAT-AATAATA-T
1 AATAAAATAAATAATATT
*
1228968 ATATAAAATAAATAATATG
1 A-ATAAAATAAATAATATT
*
1228987 AATAAAATATATAATA
1 AATAAAATAAATAATA
1229003 AAAACTATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.02
15 6 0.11
16 5 0.09
17 6 0.11
18 33 0.59
19 5 0.09
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (18 bp):
AATAAAATAAATAATATT
Found at i:1228982 original size:51 final size:53
Alignment explanation
Indices: 1228868--1229013 Score: 155
Period size: 51 Copynumber: 2.8 Consensus size: 53
1228858 AACAAAAAAT
*
1228868 AATAAGATAAATAA-A-T-ATATAATATA-AATAATAAATATATATAAATACA
1 AATAAAATAAATAATATTAATATAATATATAATAATAAATATATATAAATACA
* *
1228917 AATAATAATAAATAATATTAATATAATATATAATATTATAA-ATA-AT-AATATA
1 AATAA-AATAAATAATATTAATATAATATATAATAATA-AATATATATAAATACA
* * *
1228969 TATAAAATAAATAATATGAATAAAATATATAATAA-AAACTATATA
1 AATAAAATAAATAATATTAATATAATATATAATAATAAA-TATATA
1229014 ATATTATATT
Statistics
Matches: 81, Mismatches: 7, Indels: 15
0.79 0.07 0.15
Matches are distributed among these distances:
49 7 0.09
50 9 0.11
51 31 0.38
52 11 0.14
53 12 0.15
54 9 0.11
55 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (53 bp):
AATAAAATAAATAATATTAATATAATATATAATAATAAATATATATAAATACA
Found at i:1229004 original size:46 final size:46
Alignment explanation
Indices: 1228864--1229004 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 46
1228854 CAAAAACAAA
* * *
1228864 AAATAATAAGATAAAT-AAATATATAATATAAATAATAA-ATATATAT
1 AAATAATAATATATATAAAATAAATAATAT-AATAATAATATATA-AT
1228910 AAATACA-AATA-ATA-ATAAATAATATTAATATAATATATAATAT-T-AT
1 AAATA-ATAATATATATA-AAATAA-A-TAATATAATA-ATAATATATAAT
1228956 AAATAATAATATATATAAAATAAATAATATGAATAA-AATATATAAT
1 AAATAATAATATATATAAAATAAATAATAT-AATAATAATATATAAT
1229002 AAA
1 AAA
1229005 AACTATATAA
Statistics
Matches: 79, Mismatches: 3, Indels: 26
0.73 0.03 0.24
Matches are distributed among these distances:
44 5 0.06
45 11 0.14
46 34 0.43
47 15 0.19
48 12 0.15
49 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (46 bp):
AAATAATAATATATATAAAATAAATAATATAATAATAATATATAAT
Found at i:1229011 original size:14 final size:13
Alignment explanation
Indices: 1228895--1229016 Score: 78
Period size: 12 Copynumber: 9.5 Consensus size: 13
1228885 TATAATATAA
*
1228895 ATAATAAATATAT
1 ATAATAAAAATAT
*
1228908 ATAAATACAAATA-
1 AT-AATAAAAATAT
1228921 ATAATAAATAATAT
1 ATAATAAA-AATAT
*
1228935 -TAAT-ATAATAT
1 ATAATAAAAATAT
** *
1228946 ATAAT-ATTATAA
1 ATAATAAAAATAT
*
1228958 ATAAT-AATATAT
1 ATAATAAAAATAT
1228970 ATAA-AATAAATAAT
1 ATAATAA-AAAT-AT
1228984 ATGAAT-AAAATAT
1 AT-AATAAAAATAT
1228997 ATAATAAAAACTAT
1 ATAATAAAAA-TAT
1229011 ATAATA
1 ATAATA
1229017 TTATATTTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
11 5 0.06
12 33 0.37
13 23 0.26
14 25 0.28
15 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:1229098 original size:2 final size:2
Alignment explanation
Indices: 1229091--1229143 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1229081 TTTGAAAAAC
1229091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1229133 TA TA TA TA TA T
1 TA TA TA TA TA T
1229144 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1229178 original size:24 final size:24
Alignment explanation
Indices: 1229131--1229176 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1229121 TATATATATA
*
1229131 TATATATATATATGTTTTCAAAAC
1 TATATATATATACGTTTTCAAAAC
1229155 TATAT-TATATACGTTTTCAAAA
1 TATATATATATACGTTTTCAAAA
1229177 ACGTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
TATATATATATACGTTTTCAAAAC
Found at i:1229184 original size:37 final size:36
Alignment explanation
Indices: 1229143--1229249 Score: 112
Period size: 37 Copynumber: 3.0 Consensus size: 36
1229133 TATATATATA
1229143 TGTTTTCAAAACTATATTATATACGTTTTCAAAAACG
1 TGTTTTCAAAACTATATTATATA-GTTTTCAAAAACG
* ** *
1229180 TGTTTTCAAAACTATATAATATATGTTTT-TGAAATG
1 TGTTTTCAAAACTATATTATATA-GTTTTCAAAAACG
* *
1229216 TATTTTTAAAA-TCATATTATATA-TTTTCAAAAAC
1 TGTTTTCAAAACT-ATATTATATAGTTTTCAAAAAC
1229250 CAATTTTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
34 4 0.07
35 4 0.07
36 22 0.39
37 27 0.47
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (36 bp):
TGTTTTCAAAACTATATTATATAGTTTTCAAAAACG
Found at i:1229345 original size:37 final size:36
Alignment explanation
Indices: 1229229--1229355 Score: 119
Period size: 39 Copynumber: 3.3 Consensus size: 36
1229219 TTTTAAAATC
*
1229229 ATATTATATATTTTCAAAAACCAATTTTTTAAAAACTAT
1 ATATTATATATTTT-AAAAA--AATTTTTCAAAAACTAT
* * * *
1229268 ATATTATATTTTTTTAAAAAAAGCGTCTTCTAAAACTAT
1 ATATTATA-TATTTTAAAAAAA--TTTTTCAAAAACTAT
* *
1229307 ATATTATATGTTTTAAAAAAATATTTTCAAAAATTAT
1 ATATTATATATTTTAAAAAAAT-TTTTCAAAAACTAT
1229344 ATTATTATATAT
1 A-TATTATATAT
1229356 ATACTAAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
37 14 0.19
38 21 0.29
39 32 0.44
40 5 0.07
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (36 bp):
ATATTATATATTTTAAAAAAATTTTTCAAAAACTAT
Found at i:1231060 original size:5 final size:5
Alignment explanation
Indices: 1231050--1231083 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1231040 ATATATTATT
*
1231050 TCGGG TCGGG TCAGG TCGGG TCGGG TCGGG TCGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGG
1231084 ATTGGGTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.21, G:0.56, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:1242524 original size:28 final size:28
Alignment explanation
Indices: 1242489--1242547 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1242479 TAAAAAAATC
* * *
1242489 AAATACTTTGGGTATTTATTTTGATCAA
1 AAATACTTTAGGTATATATTTTGACCAA
1242517 AAATACTTTAGGTATATATTTTGACCAA
1 AAATACTTTAGGTATATATTTTGACCAA
1242545 AAA
1 AAA
1242548 GATAAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (28 bp):
AAATACTTTAGGTATATATTTTGACCAA
Found at i:1242870 original size:18 final size:18
Alignment explanation
Indices: 1242844--1242878 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1242834 TATGTATTTA
*
1242844 TCTACTTAAATTGTTTTT
1 TCTACTTAAATTATTTTT
*
1242862 TCTATTTAAATTATTTT
1 TCTACTTAAATTATTTT
1242879 GTTTCACAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.63
Consensus pattern (18 bp):
TCTACTTAAATTATTTTT
Found at i:1243412 original size:2 final size:2
Alignment explanation
Indices: 1243405--1243458 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1243395 ATGAAAATTA
1243405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1243447 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1243459 TAAGCTATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1246580 original size:23 final size:24
Alignment explanation
Indices: 1246553--1246606 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1246543 AGGTTCAAAT
*
1246553 TCGAGTTTGAGT-TCGAGCTTCAA
1 TCGAGCTTGAGTCTCGAGCTTCAA
1246576 TCGAGCTTGAGTCTCGAGCTTCAA
1 TCGAGCTTGAGTCTCGAGCTTCAA
1246600 TCGAGCT
1 TCGAGCT
1246607 CCTTAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (24 bp):
TCGAGCTTGAGTCTCGAGCTTCAA
Found at i:1246712 original size:36 final size:35
Alignment explanation
Indices: 1246671--1246779 Score: 88
Period size: 36 Copynumber: 3.2 Consensus size: 35
1246661 ATATTTCAAG
1246671 TTCGAGCTGAGCTTGATAATTTTTATCTCGCGAGTT
1 TTCGAGCTGAG-TTGATAATTTTTATCTCGCGAGTT
* *
1246707 TTCGAG-TCGAGTT--TCAATATTATAT-T-TCGAG--
1 TTCGAGCT-GAGTTGAT-AAT-TTTTATCTCGCGAGTT
* *
1246738 TTCGAGCTGAGTTTGATAATTTTTAGCTCGCAAGTT
1 TTCGAGCTGAG-TTGATAATTTTTATCTCGCGAGTT
1246774 TTCGAG
1 TTCGAG
1246780 TCGAGTCGAG
Statistics
Matches: 56, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
31 9 0.16
32 7 0.12
33 9 0.16
34 8 0.14
35 8 0.14
36 15 0.27
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (35 bp):
TTCGAGCTGAGTTGATAATTTTTATCTCGCGAGTT
Found at i:1246720 original size:67 final size:67
Alignment explanation
Indices: 1246640--1246785 Score: 247
Period size: 67 Copynumber: 2.2 Consensus size: 67
1246630 CCTTTTCGAG
* * *
1246640 TTCGAGTCAAGTTTCAATATTATATTTCAAGTTCGAGCTGAGCTTGATAATTTTTATCTCGCGAG
1 TTCGAGTCGAGTTTCAATATTATATTTCAAGTTCGAGCTGAGCTTGATAATTTTTAGCTCGCAAG
1246705 TT
66 TT
* *
1246707 TTCGAGTCGAGTTTCAATATTATATTTCGAGTTCGAGCTGAGTTTGATAATTTTTAGCTCGCAAG
1 TTCGAGTCGAGTTTCAATATTATATTTCAAGTTCGAGCTGAGCTTGATAATTTTTAGCTCGCAAG
1246772 TT
66 TT
1246774 TTCGAGTCGAGT
1 TTCGAGTCGAGT
1246786 CGAGCCTAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (67 bp):
TTCGAGTCGAGTTTCAATATTATATTTCAAGTTCGAGCTGAGCTTGATAATTTTTAGCTCGCAAG
TT
Found at i:1246743 original size:31 final size:31
Alignment explanation
Indices: 1246633--1246751 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 31
1246623 GTTCGAGCCT
*
1246633 TTTCGAGTTCGAG-TCAAGTTTCAATATTATA
1 TTTCGAGTTCGAGCT-GAGTTTCAATATTATA
* *
1246664 TTTCAAGTTCGAGCTGAGCTTGAT-AAT-TTTTA
1 TTTCGAGTTCGAGCTGAG-TT--TCAATATTATA
*
1246696 TCTCGCGAGTTTTCGAG-TCGAGTTTCAATATTATA
1 T-T-TCGAG--TTCGAGCT-GAGTTTCAATATTATA
1246731 TTTCGAGTTCGAGCTGAGTTT
1 TTTCGAGTTCGAGCTGAGTTT
1246752 GATAATTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
31 26 0.38
32 9 0.13
33 9 0.13
34 8 0.12
35 8 0.12
36 9 0.13
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (31 bp):
TTTCGAGTTCGAGCTGAGTTTCAATATTATA
Found at i:1251114 original size:129 final size:128
Alignment explanation
Indices: 1250881--1251178 Score: 357
Period size: 129 Copynumber: 2.3 Consensus size: 128
1250871 TTTAGGAAAA
* * * *
1250881 GTGATAACTCAGTTCCTACGTGATGAGGACGGCTGGCTATCTAAGTTGACATAACCCCTACATCA
1 GTGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCAAAGTTGACATAACCCCTACATCA
* * *
1250946 TAAGGAGATTAGGTCGAGTGATGACACGATTCCTACGTGATGAGGACGACAT-GCCATCTAAAG
66 TAAGGAGATTAGGTCGAGTGATGACACGACTCATACGTGATGAAGA-GACATGGCCATCTAAAG
* ** * * * *
1251009 GTGATAACACAGTTCATACGTGATGAGGACGACTGGTTATCAAAGTTTGACATGGCTCTTACGTG
1 GTGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCAAAG-TTGACATAACCCCTACATC
* * * ***
1251074 ATGAGGAGATTAGGTCGTGTGATGACACGGCTCATACGTGATGAAGAGTTTTGGCCATCTAAAG
65 ATAAGGAGATTAGGTCGAGTGATGACACGACTCATACGTGATGAAGAGACATGGCCATCTAAAG
* *
1251138 GCGATAACACGGTTCCTACGTGATGAGGAC-AGCTGGTTATC
1 GTGATAACACAGTTCCTACGTGATGAGGACGA-CTGGTTATC
1251179 TGGATTAACA
Statistics
Matches: 144, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
128 43 0.30
129 101 0.70
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (128 bp):
GTGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCAAAGTTGACATAACCCCTACATCA
TAAGGAGATTAGGTCGAGTGATGACACGACTCATACGTGATGAAGAGACATGGCCATCTAAAG
Found at i:1259149 original size:30 final size:30
Alignment explanation
Indices: 1259084--1259156 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1259074 TTAATTTTTG
* * * *
1259084 AATGCATATTATTGGTGATGCTTTATAAAT
1 AATGCATTTTATTGGTAATGATTTACAAAT
*
1259114 GATGCATTTTATTGGTAAT-ATGTTACAAAT
1 AATGCATTTTATTGGTAATGAT-TTACAAAT
1259144 AATGCATTTTATT
1 AATGCATTTTATT
1259157 ATGCATGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
AATGCATTTTATTGGTAATGATTTACAAAT
Found at i:1259182 original size:6 final size:6
Alignment explanation
Indices: 1259171--1259208 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
1259161 ATGATGAATG
1259171 ATGCAA ATGCAAA ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCAA ATGC-AA ATGCAA ATGCAA ATGCAA ATGCAA A
1259209 AGGCATTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:1264360 original size:3 final size:3
Alignment explanation
Indices: 1264333--1264385 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
1264323 ACAAAATATA
* * *
1264333 AAT AA- AAT GAT ATT AAT ATT 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
1264380 AAT AAT
1 AAT AAT
1264386 CAAAACCCGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1266291 original size:55 final size:54
Alignment explanation
Indices: 1266127--1266299 Score: 211
Period size: 54 Copynumber: 3.2 Consensus size: 54
1266117 CTATGTGTAT
* * **
1266127 TTTCGGCACTATGTGTGCAACCCATAGAATTCATAATGAGTTTGTGAATTAATA
1 TTTCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCA
* * * *
1266181 TTTCGGCATTATGTGTGCAACCCATGGAGTTCATAATGAGTTTGTAAATTACCA
1 TTTCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCA
* ** * * *
1266235 TTTTGACACTATGTGTGCAAATTCATGGAATTCATAATAAGTTTATGAATTTCCA
1 TTTCGACACTATGTGTGC-AACCCATGGAATTCATAATGAGTTTGTGAATTACCA
1266290 TTTCGACACT
1 TTTCGACACT
1266300 TAGGTGCAAC
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 63 0.62
55 38 0.38
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (54 bp):
TTTCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCA
Found at i:1266960 original size:19 final size:19
Alignment explanation
Indices: 1266928--1266970 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1266918 CACCCAGGCA
* *
1266928 GCTCGGCTCGGTCCAAGCG
1 GCTCGACTCAGTCCAAGCG
*
1266947 GCTCGACTCAGTCCAAGTG
1 GCTCGACTCAGTCCAAGCG
1266966 GCTCG
1 GCTCG
1266971 GTCCAGACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.35, G:0.33, T:0.19
Consensus pattern (19 bp):
GCTCGACTCAGTCCAAGCG
Found at i:1268730 original size:13 final size:13
Alignment explanation
Indices: 1268679--1268741 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
1268669 ATATTTACGA
1268679 TAAAA-ATAAATT
1 TAAAATATAAATT
* *
1268691 TAAAATTTCTATATT
1 TAAAA--TATAAATT
*
1268706 TAATAT-TAAATT
1 TAAAATATAAATT
1268718 TAAAATATAAATT
1 TAAAATATAAATT
1268731 TAAAATATAAA
1 TAAAATATAAA
1268742 AAATGAGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 15 0.36
13 18 0.43
15 9 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAATATAAATT
Found at i:1268826 original size:21 final size:20
Alignment explanation
Indices: 1268755--1268826 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1268745 TGAGTTATAG
* *
1268755 AAATATTAAATTATAAAAGT
1 AAATATAAAAATATAAAAGT
**
1268775 AAATATAAAAATATAATTTGT
1 AAATATAAAAATATAA-AAGT
*
1268796 AAATTTTAAAAATATAAAAGT
1 AAA-TATAAAAATATAAAAGT
1268817 AAATACTAAA
1 AAATA-TAAA
1268827 TTAAACTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 15 0.37
21 14 0.34
22 12 0.29
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATATAAAAATATAAAAGT
Found at i:1270656 original size:273 final size:271
Alignment explanation
Indices: 1270011--1271021 Score: 1089
Period size: 273 Copynumber: 3.6 Consensus size: 271
1270001 CCAATTGCTG
* * * * * *
1270011 AAAAATATAATTTGAAGGACTAAATTAAACAAGCGTGAAATTACAAACTAAAATTTAAACAAATT
1 AAAAATATACTTTTAAGGACTAAATTAAACAAACGTGAAATTA-AAAGTGAAATTTAAATAAATT
** * *
1270076 AAACAACATGCAAGGATCAAATTGAAACAATTGTAAAATGTGAAGCTGAAATTAATATGTAAA-T
65 AAACAACACACAAGGATCAAATTGAAACAATTGTAAAATGTAAAGCTGAAATTAATAT-CAAATT
* * *
1270140 GGACTAAATTTCATTCA-TTTAAAA-TTGGTGAACAAAAGTTTATAGGGTTTAGAGACTATGATA
129 GGACTAAATTGCATTCATTTTAAAAGTTGGTGAACAAAA-TTTATAGGGTTTGGAGATTATGATA
* * * * * * *
1270203 TAATTTATAGGGTTTAAAATGAAGTTTATGATGTGATTTATAGGGTTTGAAGTAAATTAATAAAA
193 TAATTTATATGGTTTGAAATGAAATTTATGATGTAATTTATAGGATTTGAAATAAA--AATAATA
** *
1270268 TCAAGGGCTTATTTTAGAT
256 T--A-GGCCAATTTCAGAT
* *
1270287 AAAAAATATACTTTTAAGGACTAAAATAAACAAATGTGAAATTAAAAAGTGAAATTTAAATAAAT
1 -AAAAATATACTTTTAAGGACTAAATTAAACAAACGTGAAATT-AAAAGTGAAATTTAAATAAAT
* * * * * *
1270352 TAAACAACACATAGGGATCAAATTAAAACAATTATAAAATATAAAGTTGAAATTAATATCAAATT
64 TAAACAACACACAAGGATCAAATTGAAACAATTGTAAAATGTAAAGCTGAAATTAATATCAAATT
* * * *
1270417 GGACTAAATTTCATTGATTTTAAAAGTTGGTGAATAAGAATTTATAAGGTTTGGAGATTATGATA
129 GGACTAAATTGCATTCATTTTAAAAGTTGGTGAACAA-AATTTATAGGGTTTGGAGATTATGATA
* * *
1270482 TAATTTATATGATTTGAAATGAAACTTATGATGGT-ATTTATAGGATTTGAAATAGAAATAACTA
193 TAATTTATATGGTTTGAAATGAAATTTATGAT-GTAATTTATAGGATTTGAAATAAAAATAA-TA
* *
1270546 TAGGTCAATTTCGGAT
256 TAGGCCAATTTCAGAT
* * * * *
1270562 AAAAATAT-GTTTTAAGGACTAAATTGAACAAACATTAAATTAAATAGTGAAATTTTAATAAATT
1 AAAAATATACTTTTAAGGACTAAATTAAACAAACGTGAAATTAAA-AGTGAAATTTAAATAAATT
** * *
1270626 AAACAACACACTTGGATCGAACTGAAACAATTGTAAAATGTAAAGCTGAAATTAATATCAAATTG
65 AAACAACACACAAGGATCAAATTGAAACAATTGTAAAATGTAAAGCTGAAATTAATATCAAATTG
* * * *
1270691 GACGAAATTGCATTCATTTTAAAAGTTAGTGAACAAAAATTTGTAGGGTTTGAAGATTATGATAT
130 GACTAAATTGCATTCATTTTAAAAGTTGGTGAAC-AAAATTTATAGGGTTTGGAGATTATGATAT
* * * *
1270756 AATTTATATGGTTAGAAATAAAATTTATGATGTAATTTATTGGGCTTGGAGTAAATTACAAAAAA
194 AATTTATATGGTTTGAAATGAAATTTATGATGTAATTTA------TAGGA-T---TT----GAAA
*
1270821 TAAAAATAAATATAGGCCAATTTCAAAT
245 TAAAAAT-AATATAGGCCAATTTCAGAT
* * *
1270849 AAAAATATACTTTTGAGGACTAAATTAAACAAACGTAAAATTGAAAAATGAAATTTAAATAAATT
1 AAAAATATACTTTTAAGGACTAAATTAAACAAACGTGAAATT-AAAAGTGAAATTTAAATAAATT
** *
1270914 AAACAACGTACAAGGATCAAATTGAAACAATTGTAAAATGTAAAGCT-AAATTATTATCAAATTG
65 AAACAACACACAAGGATCAAATTGAAACAATTGTAAAATGTAAAGCTGAAATTAATATCAAATTG
* * * *
1270978 GACTAAGTTGCATTCATTTTAATAGTTGGCGAACAAAAGTTATA
130 GACTAAATTGCATTCATTTTAAAAGTTGGTGAACAAAATTTATA
1271022 TTATTGGAGA
Statistics
Matches: 615, Mismatches: 92, Indels: 45
0.82 0.12 0.06
Matches are distributed among these distances:
272 5 0.01
273 187 0.30
274 10 0.02
275 9 0.01
276 4 0.01
277 126 0.20
278 10 0.02
279 81 0.13
280 5 0.01
283 2 0.00
286 8 0.01
287 77 0.13
288 88 0.14
289 3 0.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (271 bp):
AAAAATATACTTTTAAGGACTAAATTAAACAAACGTGAAATTAAAAGTGAAATTTAAATAAATTA
AACAACACACAAGGATCAAATTGAAACAATTGTAAAATGTAAAGCTGAAATTAATATCAAATTGG
ACTAAATTGCATTCATTTTAAAAGTTGGTGAACAAAATTTATAGGGTTTGGAGATTATGATATAA
TTTATATGGTTTGAAATGAAATTTATGATGTAATTTATAGGATTTGAAATAAAAATAATATAGGC
CAATTTCAGAT
Found at i:1271161 original size:31 final size:31
Alignment explanation
Indices: 1271126--1271190 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1271116 AAAATAGGTT
1271126 CTAACGTTTTCTCTGTTACATTTTTAGGTGC
1 CTAACGTTTTCTCTGTTACATTTTTAGGTGC
* *
1271157 CTAACTTTTTCTTTGTTACATTTTTAGGTGC
1 CTAACGTTTTCTCTGTTACATTTTTAGGTGC
1271188 CTA
1 CTA
1271191 CACAGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.17, C:0.18, G:0.14, T:0.51
Consensus pattern (31 bp):
CTAACGTTTTCTCTGTTACATTTTTAGGTGC
Found at i:1273314 original size:55 final size:55
Alignment explanation
Indices: 1273086--1273388 Score: 353
Period size: 55 Copynumber: 5.5 Consensus size: 55
1273076 TTTTGTGGTT
* * * * * *
1273086 TTGCACACATATTGCCGATACGATAATTTACAAACTCATTATGAATTACGTGGGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGG
* * * *
1273141 ATGTG-A-ACATAGTGCTAGTACGGAAATTCATAAACGCATTATGAATTTCGTGGGG
1 -T-TGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGG
* * * *
1273196 TTGCACACATAGTTCCAATACGGAAATTCATAAACTCGA-TATGAATTTCGTGAGT
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTC-ATTATGAATTTCGTGGGG
* *
1273251 TTGTACACATAGTGCCAATACGAAAATTCATAAACTCATTTTGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGG
* * *
1273306 TTGCACACATAGTGCCAATAC-ATAAATTCATAAACTTAATATGAATTTCATGGGG
1 TTGCACACATAGTGCCAATACGA-AAATTCATAAACTCATTATGAATTTCGTGGGG
* *
1273361 TTGCACACATAGTGTCAATACAAAAATT
1 TTGCACACATAGTGCCAATACGAAAATT
1273389 GCAACATATA
Statistics
Matches: 212, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
53 2 0.01
54 4 0.02
55 200 0.94
56 4 0.02
57 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGG
Found at i:1273335 original size:165 final size:165
Alignment explanation
Indices: 1273085--1273381 Score: 402
Period size: 165 Copynumber: 1.8 Consensus size: 165
1273075 ATTTTGTGGT
* * * *
1273085 TTTGCACACATATTGCCGATACGATAATTTACAAACTCATTATGAATTACGTGGGGATGTGAACA
1 TTTGCACACATAGTGCCAATACGAAAATTCACAAACTCATTATGAATTACGTGGGGATGTGAACA
* * * * *
1273150 TAGTGCTAGTACGGAAATTCATAAACGCATTATGAATTTCGTGGGGTTGCACACATAGT-TCCAA
66 TAGTGCCAATACAGAAATTCATAAACGCAATATGAATTTCATGGGGTTGCACACATAGTGT-CAA
1273214 TACGGAAATTCATAAACTCGATATGAATTTCGTGAG
130 TACGGAAATTCATAAACTCGATATGAATTTCGTGAG
* * * *
1273250 TTTGTACACATAGTGCCAATACGAAAATTCATAAACTCATTTTGAATTTCGTGGGG-T-TGCACA
1 TTTGCACACATAGTGCCAATACGAAAATTCACAAACTCATTATGAATTACGTGGGGATGTG-A-A
* **
1273313 CATAGTGCCAATACATAAATTCATAAACTTAATATGAATTTCATGGGGTTGCACACATAGTGTCA
64 CATAGTGCCAATACAGAAATTCATAAACGCAATATGAATTTCATGGGGTTGCACACATAGTGTCA
1273378 ATAC
129 ATAC
1273382 AAAAATTGCA
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
163 2 0.02
164 2 0.02
165 108 0.96
166 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (165 bp):
TTTGCACACATAGTGCCAATACGAAAATTCACAAACTCATTATGAATTACGTGGGGATGTGAACA
TAGTGCCAATACAGAAATTCATAAACGCAATATGAATTTCATGGGGTTGCACACATAGTGTCAAT
ACGGAAATTCATAAACTCGATATGAATTTCGTGAG
Found at i:1286296 original size:55 final size:55
Alignment explanation
Indices: 1286200--1286522 Score: 396
Period size: 55 Copynumber: 5.9 Consensus size: 55
1286190 ATATTATAAT
* * ** * * * * *
1286200 TCATTATAAATTCCGTGGTTTTGTACACATATTGTCGATACGGTAATTCATAAAC
1 TCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
* *
1286255 TCATTATGAATTACGTGGGGTTGCACACAAAGTGCCAATACGGAAATTCATAAAC
1 TCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
* *
1286310 TCATTATGAATTTCATGGGGTTGCACA-AGTAGTGCCAATACGAAAATTCATAAAC
1 TCATTATGAATTTCGTGGGGTTGCACACA-TAGTGCCAATACGGAAATTCATAAAC
* * * * * * *
1286365 TCACTATGAATTTTGAGAGGTTGCACACATAATGGCAATACGAAAATTCATAAAC
1 TCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
* * *
1286420 TCATTATGAATTTCGTGGGGTTGCACACATTGTGCCAATACGTAAATTCATAAAA
1 TCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
** *
1286475 TCATTATGAATTTCGTGGGGTTGCACACATAGTGTAAATACAGAAATT
1 TCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATT
1286523 GCAACATATA
Statistics
Matches: 231, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
54 1 0.00
55 229 0.99
56 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (55 bp):
TCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATAAAC
Found at i:1291300 original size:149 final size:148
Alignment explanation
Indices: 1291029--1291473 Score: 649
Period size: 149 Copynumber: 3.0 Consensus size: 148
1291019 TCTTTTGAAA
** *
1291029 TTTTCCAATGTATTTAGAGGGTCAGCCTGGAAGGTCATACTCCAGTATTCATATTCGAATACTGG
1 TTTTCCAATGTATTTAGAGGGTCAGCCTGGAAGGTCATACTCCAGTAGCCATATTCGAATACGGG
* * *
1291094 GAAAATATGAGTACTTTTTACAAAAATGAAGAGCTAGTGCAACATAGGATGTCACTAGTTATTGT
66 GCAAACATGAGTAC-TTTTACAAAAATGAAGAGCTAGTGCAACATAGGATGTTACTAGTTATTGT
*
1291159 GCTCCAATGTAAAAGTAAT
130 GCTCCAATGTAAAAGTAAG
* * * *
1291178 TTTTCCGATGTATTTAGAGGGTCAGCCGGGAAGTTCATACTCCAGTAGCCATATTTGAATACGGG
1 TTTTCCAATGTATTTAGAGGGTCAGCCTGGAAGGTCATACTCCAGTAGCCATATTCGAATACGGG
* * *
1291243 GCAAACATGAGTACTATTTACAAAAATGAAGAGCTAGTGCAACATAGGACGTTACTAG-AAATGT
66 GCAAACATGAGTACT-TTTACAAAAATGAAGAGCTAGTGCAACATAGGATGTTACTAGTTATTG-
*
1291307 TGCTCCAATGTAAAATTAAG
129 TGCTCCAATGTAAAAGTAAG
* *
1291327 TTTTCCAATGTATTTACAGGGTCAGCCTGGAAGGTCATACTTCAGTAGCCATATTCGAATACGGG
1 TTTTCCAATGTATTTAGAGGGTCAGCCTGGAAGGTCATACTCCAGTAGCCATATTCGAATACGGG
* * * * *
1291392 GCAAACATGTGTACGTTTTACAGAAATGAAGAGCTGGTGCAACATAGGATGTTCCTAGTTATGGT
66 GCAAACATGAGTAC-TTTTACAAAAATGAAGAGCTAGTGCAACATAGGATGTTACTAGTTATTGT
1291457 GCTCCAATGTAAAAGTA
130 GCTCCAATGTAAAAGTA
1291474 TAACTACATG
Statistics
Matches: 262, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
148 4 0.02
149 255 0.97
150 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (148 bp):
TTTTCCAATGTATTTAGAGGGTCAGCCTGGAAGGTCATACTCCAGTAGCCATATTCGAATACGGG
GCAAACATGAGTACTTTTACAAAAATGAAGAGCTAGTGCAACATAGGATGTTACTAGTTATTGTG
CTCCAATGTAAAAGTAAG
Found at i:1293947 original size:20 final size:20
Alignment explanation
Indices: 1293924--1293975 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1293914 AACGCGATCC
1293924 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1293944 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1293964 CCAAAATCGCAA
1 CCAGAATCGCAA
1293976 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1293992 original size:21 final size:20
Alignment explanation
Indices: 1293965--1294063 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1293955 AATCAGTTTC
1293965 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1293986 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1294007 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1294027 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1294048 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1294064 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1294092 original size:20 final size:20
Alignment explanation
Indices: 1294030--1294223 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1294020 CGATTTTCCA
* ** *
1294030 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1294050 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1294070 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1294090 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1294110 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1294130 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1294150 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
1294170 AAATCGCAATG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1294190 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1294211 AAATCGCAACGCG
1 AAATCGCAACGCG
1294224 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1294114 original size:60 final size:60
Alignment explanation
Indices: 1294030--1294223 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1294020 CGATTTTCCA
* ** * *
1294030 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1294090 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
1294150 ATATCGCAACGCGTATCCGTAAATCGCAATGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1294211 AAATCGCAACGCG
1 AAATCGCAACGCG
1294224 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1294643 original size:33 final size:34
Alignment explanation
Indices: 1294604--1294675 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
1294594 TTCACTTAGA
1294604 TTTCATTTCGCGTTACGATTCT-GTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCGTCGTTGCGAT
* *
1294637 TTTCATTTCGCGTTGCTATTCTCGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCGTCGTTGCGAT
1294671 TTTCA
1 TTTCA
1294676 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.47
Consensus pattern (34 bp):
TTTCATTTCGCGTTACGATTCTCGTCGTTGCGAT
Found at i:1294815 original size:14 final size:14
Alignment explanation
Indices: 1294796--1294850 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1294786 AGAATGACTG
1294796 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1294810 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
1294829 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1294843 TCGCAACG
1 TCGCAACG
1294851 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1294863 original size:33 final size:33
Alignment explanation
Indices: 1294796--1294866 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1294786 AGAATGACTG
***
1294796 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1294829 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1294862 TCGCA
1 TCGCA
1294867 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1294884 original size:19 final size:19
Alignment explanation
Indices: 1294862--1294959 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1294852 GAAACCAAAA
*
1294862 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1294881 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1294895 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1294914 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1294928 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1294947 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1294960 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1294903 original size:14 final size:14
Alignment explanation
Indices: 1294884--1294973 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1294874 TTTCATTTCG
1294884 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1294898 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1294917 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1294931 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1294948 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1294964 CGTTGCGATT
1 CGTTGCGATT
1294974 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1294909 original size:33 final size:33
Alignment explanation
Indices: 1294867--1294981 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1294857 CAAAATCGCA
1294867 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1294900 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1294933 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1294966 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1294982 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1296087 original size:20 final size:20
Alignment explanation
Indices: 1296059--1296427 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1296049 AAATTTCAGT
* * * *
1296059 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1296079 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1296099 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1296119 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1296139 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1296159 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1296179 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1296199 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1296219 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1296239 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1296259 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1296279 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1296299 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1296319 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1296339 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1296359 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1296379 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1296399 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1296419 GTTGCGATT
1 GTTGCGATT
1296428 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1297527 original size:10 final size:10
Alignment explanation
Indices: 1297488--1297527 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1297478 TTCATCACAC
1297488 CAAATTCTCT
1 CAAATTCTCT
*
1297498 CAATTTCTCT
1 CAAATTCTCT
*
1297508 CAACTTCTCT
1 CAAATTCTCT
*
1297518 CAAATACTCT
1 CAAATTCTCT
1297528 TATATTCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1297586 original size:9 final size:9
Alignment explanation
Indices: 1297574--1297607 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1297564 TGATATTCTG
1297574 TATTTAATT
1 TATTTAATT
*
1297583 TATTTAA-G
1 TATTTAATT
1297591 TATTTAATT
1 TATTTAATT
1297600 TATTTAAT
1 TATTTAAT
1297608 ATTTTACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1297613 original size:17 final size:17
Alignment explanation
Indices: 1297573--1297611 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1297563 TTGATATTCT
1297573 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1297590 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1297607 -TATTT
1 GTATTT
1297612 TACTTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1299535 original size:3 final size:3
Alignment explanation
Indices: 1299512--1299556 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
1299502 AGCTGCTCAG
* * * *
1299512 GAC GAC AAC GAA GAT GAC GAC GAC GAC GAC GAC GAT GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
1299557 AAGATGATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.27, G:0.31, T:0.04
Consensus pattern (3 bp):
GAC
Found at i:1299745 original size:13 final size:13
Alignment explanation
Indices: 1299711--1299760 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
1299701 TGTATTTAGT
*
1299711 ACTTTTTTATTGT
1 ACTTTTTTATTGG
* *
1299724 AGTTGTTTATTGG
1 ACTTTTTTATTGG
1299737 ACTTTTTTATTGG
1 ACTTTTTTATTGG
1299750 ACTTTTTTATT
1 ACTTTTTTATT
1299761 ATTTATCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.16, C:0.06, G:0.14, T:0.64
Consensus pattern (13 bp):
ACTTTTTTATTGG
Found at i:1304129 original size:21 final size:20
Alignment explanation
Indices: 1304105--1304146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1304095 TTTTTTGTAA
1304105 TTTTAAAAAAATTAAGATTTT
1 TTTTAAAAAAA-TAAGATTTT
* *
1304126 TTTTAAAATAATAATATTTT
1 TTTTAAAAAAATAAGATTTT
1304146 T
1 T
1304147 AAGTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTAAAAAAATAAGATTTT
Found at i:1304133 original size:20 final size:20
Alignment explanation
Indices: 1304105--1304146 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1304095 TTTTTTGTAA
1304105 TTTTAAAAA-AATTAAGATTT
1 TTTTAAAAATAA-TAAGATTT
* *
1304125 TTTTTAAAATAATAATATTT
1 TTTTAAAAATAATAAGATTT
1304145 TT
1 TT
1304147 AAGTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTAAAAATAATAAGATTT
Found at i:1305174 original size:2 final size:2
Alignment explanation
Indices: 1305167--1305193 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1305157 TGTATTACCA
1305167 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
1305194 ACTTTGATTA
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:1308132 original size:41 final size:41
Alignment explanation
Indices: 1308087--1308169 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
1308077 AGGAACCAAA
1308087 TCTAAGCCTTAGCCATTTAGGCTAGGATACTGTAGCTGATG
1 TCTAAGCCTTAGCCATTTAGGCTAGGATACTGTAGCTGATG
1308128 TCTAAGCCTTAGCCATTTAGGCTAGGATACTGTAGCTGATG
1 TCTAAGCCTTAGCCATTTAGGCTAGGATACTGTAGCTGATG
1308169 T
1 T
1308170 GAGATAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
TCTAAGCCTTAGCCATTTAGGCTAGGATACTGTAGCTGATG
Found at i:1313132 original size:19 final size:19
Alignment explanation
Indices: 1313105--1313149 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1313095 GAGCCTTCTG
* * *
1313105 GAACTGGTCCTGTCTGACC
1 GAACCGGTCCAGTCAGACC
1313124 GAACCGGTCCAGTCAGACC
1 GAACCGGTCCAGTCAGACC
1313143 GAACCGG
1 GAACCGG
1313150 GTCGAGCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (19 bp):
GAACCGGTCCAGTCAGACC
Found at i:1313231 original size:16 final size:16
Alignment explanation
Indices: 1313210--1313252 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1313200 AGACCTGACC
1313210 GTTGACTTTGATCAGA
1 GTTGACTTTGATCAGA
*
1313226 GTTGACTTTGATCAGC
1 GTTGACTTTGATCAGA
1313242 GTTGACTTTGA
1 GTTGACTTTGA
1313253 CCAAAAAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.40
Consensus pattern (16 bp):
GTTGACTTTGATCAGA
Found at i:1314042 original size:27 final size:28
Alignment explanation
Indices: 1314012--1314075 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1314002 AAAAAAACTG
* * *
1314012 AAATACCCTTGAACTGTAAAATGATC-A
1 AAATACCCCTGAACTGTAAAATAACCTA
* *
1314039 AAATACCCCTGAAGTGTGAAATAACCTA
1 AAATACCCCTGAACTGTAAAATAACCTA
1314067 AAATACCCC
1 AAATACCCC
1314076 AAGCCCTGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (28 bp):
AAATACCCCTGAACTGTAAAATAACCTA
Found at i:1321504 original size:36 final size:36
Alignment explanation
Indices: 1321457--1321528 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1321447 AACCTCCAAA
1321457 CAGGAGAATAGTTTGTTGAATATTTTGTCACAGCAC
1 CAGGAGAATAGTTTGTTGAATATTTTGTCACAGCAC
1321493 CAGGAGAATAGTTTGTTGAATATTTTGTCACAGCAC
1 CAGGAGAATAGTTTGTTGAATATTTTGTCACAGCAC
1321529 AAAAAGGCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (36 bp):
CAGGAGAATAGTTTGTTGAATATTTTGTCACAGCAC
Found at i:1327387 original size:101 final size:101
Alignment explanation
Indices: 1327212--1327413 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
1327202 CCATTTTAAT
1327212 TTTTTTTCTAGATATTGTACATTGCTTGAGGACAAGCAATAGCTTAAGTTTGGGGGTGTGATAAC
1 TTTTTTTCTAGATATTGTACATTGCTTGAGGACAAGCAATAGCTTAAGTTTGGGGGTGTGATAAC
1327277 TCCGTAAAAAGACTCAATTTCTAGTCTTTTCACTTA
66 TCCGTAAAAAGACTCAATTTCTAGTCTTTTCACTTA
1327313 TTTTTTTCTAGATATTGTACATTGCTTGAGGACAAGCAATAGCTTAAGTTTGGGGGTGTGATAAC
1 TTTTTTTCTAGATATTGTACATTGCTTGAGGACAAGCAATAGCTTAAGTTTGGGGGTGTGATAAC
1327378 TCCGTAAAAAGACTCAATTTCTAGTCTTTTCACTTA
66 TCCGTAAAAAGACTCAATTTCTAGTCTTTTCACTTA
1327414 AGTTATTACT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.39
Consensus pattern (101 bp):
TTTTTTTCTAGATATTGTACATTGCTTGAGGACAAGCAATAGCTTAAGTTTGGGGGTGTGATAAC
TCCGTAAAAAGACTCAATTTCTAGTCTTTTCACTTA
Found at i:1328073 original size:45 final size:45
Alignment explanation
Indices: 1328009--1328109 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
1327999 CTGTAGTAGA
***
1328009 GCGGTGATCAGGTCTGGAGAGAGGTTGATCACCAAGGCAGGCACG
1 GCGGTGATCAGGTCTGGAGAGAAACTGATCACCAAGGCAGGCACG
1328054 GCGGTGATCAGGTCTGGAGAGAAACTGATCACCAAGGCAGGCACG
1 GCGGTGATCAGGTCTGGAGAGAAACTGATCACCAAGGCAGGCACG
* *
1328099 ACGCTGATCAG
1 GCGGTGATCAG
1328110 AATTGTCATG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.27, C:0.22, G:0.37, T:0.15
Consensus pattern (45 bp):
GCGGTGATCAGGTCTGGAGAGAAACTGATCACCAAGGCAGGCACG
Found at i:1335578 original size:23 final size:23
Alignment explanation
Indices: 1335552--1335623 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
1335542 TATAGCTTAA
1335552 ACATTTCGTTAAGCCATCAAACC
1 ACATTTCGTTAAGCCATCAAACC
* *
1335575 ACATTT--TTAAACTC-TCTGAA--
1 ACATTTCGTTAAGC-CATC-AAACC
1335595 ACATTTCGTTAAGCCATCAAACC
1 ACATTTCGTTAAGCCATCAAACC
1335618 ACATTT
1 ACATTT
1335624 TTAAACTCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 6 0.16
21 10 0.26
22 10 0.26
23 12 0.32
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (23 bp):
ACATTTCGTTAAGCCATCAAACC
Found at i:1335611 original size:43 final size:43
Alignment explanation
Indices: 1335550--1335636 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
1335540 ATTATAGCTT
1335550 AAACATTTCGTTAAGCCATCAAACCACATTTTTAAACTCTCTG
1 AAACATTTCGTTAAGCCATCAAACCACATTTTTAAACTCTCTG
1335593 AAACATTTCGTTAAGCCATCAAACCACATTTTTAAACTCTCTG
1 AAACATTTCGTTAAGCCATCAAACCACATTTTTAAACTCTCTG
1335636 A
1 A
1335637 CTGATTCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (43 bp):
AAACATTTCGTTAAGCCATCAAACCACATTTTTAAACTCTCTG
Found at i:1335616 original size:20 final size:21
Alignment explanation
Indices: 1335550--1335615 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1335540 ATTATAGCTT
1335550 AAACATTTCGTTAAGCCATCA
1 AAACATTTCGTTAAGCCATCA
* *
1335571 AACCACATTT--TTAAACTC-TCTG
1 AA--ACATTTCGTTAAGC-CATC-A
1335593 AAACATTTCGTTAAGCCATCA
1 AAACATTTCGTTAAGCCATCA
1335614 AA
1 AA
1335616 CCACATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
20 6 0.18
21 12 0.35
22 10 0.29
23 6 0.18
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (21 bp):
AAACATTTCGTTAAGCCATCA
Found at i:1336529 original size:123 final size:123
Alignment explanation
Indices: 1336375--1336600 Score: 371
Period size: 123 Copynumber: 1.8 Consensus size: 123
1336365 CAAACTTATA
* *
1336375 TTATCGGTAAGTATCGATACATATATACAAGTATCGATACATAAGAAGACAACATGTTGGAATTT
1 TTATCGGTAAGTATCGATACATATATACAAGTATCGATACATAAGAAGACAACAGGTTGGAACTT
* *
1336440 AAACAAATCGGTTAAAACTTAACATTAGAGGTAGGTTGGATCGGATAACATTTAAATT
66 AAACAAACCAGTTAAAACTTAACATTAGAGGTAGGTTGGATCGGATAACATTTAAATT
* *
1336498 TTATCGGTAGGTATCGATACATGTATACAAGTATCGATACATAAGAAGACAACAGGTTGGAACTT
1 TTATCGGTAAGTATCGATACATATATACAAGTATCGATACATAAGAAGACAACAGGTTGGAACTT
* * *
1336563 AAACAAACCAGTTGAAACTTATCATTTGAGGTAGGTTG
66 AAACAAACCAGTTAAAACTTAACATTAGAGGTAGGTTG
1336601 TTGGACCGGA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 94 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (123 bp):
TTATCGGTAAGTATCGATACATATATACAAGTATCGATACATAAGAAGACAACAGGTTGGAACTT
AAACAAACCAGTTAAAACTTAACATTAGAGGTAGGTTGGATCGGATAACATTTAAATT
Found at i:1336654 original size:20 final size:20
Alignment explanation
Indices: 1336626--1336667 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1336616 TTTGAGACTA
* * *
1336626 TAAAGAAGTTTCGATACGTG
1 TAAACAAGTATCGATACATG
1336646 TAAACAAGTATCGATACATG
1 TAAACAAGTATCGATACATG
1336666 TA
1 TA
1336668 GTAAACTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (20 bp):
TAAACAAGTATCGATACATG
Found at i:1337066 original size:31 final size:32
Alignment explanation
Indices: 1337021--1337086 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
1337011 GATATAAGAA
* * * *
1337021 TTTTAGATAGAATATTAATTTAACC-CTTAAT
1 TTTTAAATAAAATATCAATTTAACCTCTAAAT
1337052 TTTTAAATAAAATATCAATTTAACCTCTAAAT
1 TTTTAAATAAAATATCAATTTAACCTCTAAAT
1337084 TTT
1 TTT
1337087 AGGGGTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (32 bp):
TTTTAAATAAAATATCAATTTAACCTCTAAAT
Found at i:1338270 original size:37 final size:39
Alignment explanation
Indices: 1338216--1338295 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 39
1338206 TGTTTCGCTC
*
1338216 GAAACAAATTTTTTATCTCACTTGAGA-TTATTTCTCTA
1 GAAACAAATATTTTATCTCACTTGAGATTTATTTCTCTA
* * *
1338254 GAAACAAA-ATTTTATCTCGCTTGAGATTTCTTTCTCTT
1 GAAACAAATATTTTATCTCACTTGAGATTTATTTCTCTA
1338292 GAAA
1 GAAA
1338296 ATACAACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 16 0.43
38 21 0.57
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (39 bp):
GAAACAAATATTTTATCTCACTTGAGATTTATTTCTCTA
Found at i:1339703 original size:54 final size:55
Alignment explanation
Indices: 1339584--1339708 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 55
1339574 AACATTAATG
* *
1339584 ACTCATACTTATAAGGTAACCGATAAAAAATAAAATAAGGCACAACCGATTATGTT
1 ACTCATACTTATAAGGTAACCGATAAAAAAT-AAACAAGGCACAACCGATTACGTT
* * **
1339640 ACTCATACTTATAAGGTAACCGATTACAAAT-AACAAGGCGTAACCG-TTAACGTT
1 ACTCATACTTATAAGGTAACCGATAAAAAATAAACAAGGCACAACCGATT-ACGTT
*
1339694 ACTCTTACTTATAAG
1 ACTCATACTTATAAG
1339709 ATATACAGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 30 0.49
56 29 0.48
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (55 bp):
ACTCATACTTATAAGGTAACCGATAAAAAATAAACAAGGCACAACCGATTACGTT
Found at i:1343061 original size:30 final size:31
Alignment explanation
Indices: 1343020--1343079 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
1343010 AAGTTTTAAA
1343020 TAAATTATCATTTTAACCAT-TAAATTTTAGT
1 TAAATTATCATTTTAACC-TCTAAATTTTAGT
1343051 TAAA-TATCATTTTAACCTCTAAATTTTAG
1 TAAATTATCATTTTAACCTCTAAATTTTAG
1343080 GGTTCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 1 0.04
30 23 0.82
31 4 0.14
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (31 bp):
TAAATTATCATTTTAACCTCTAAATTTTAGT
Found at i:1344117 original size:24 final size:24
Alignment explanation
Indices: 1344085--1344172 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
1344075 GATATCAGAA
*
1344085 ATCAAAACAGAATTCAGATAAGAT
1 ATCAGAACAGAATTCAGATAAGAT
* * * *
1344109 ATCAGAACAGAATCCATATCAGAA
1 ATCAGAACAGAATTCAGATAAGAT
* *
1344133 ATCAGAACATAATTCAGGTAATG-T
1 ATCAGAACAGAATTCAGATAA-GAT
1344157 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
1344173 AGTTGGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 50 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATAAGAT
Found at i:1344186 original size:48 final size:48
Alignment explanation
Indices: 1344076--1344169 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
1344066 GTAAATAGAG
*
1344076 ATATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCC
* *
1344124 ATATCAGAAATCAGAACATAATTCAGGTAATG-TATCAGAACAGAAT
1 ATATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAAT
1344170 TCAAGTTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCC
Found at i:1346706 original size:23 final size:22
Alignment explanation
Indices: 1346680--1346728 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1346670 CCACCTTCTG
1346680 CAAATATTA-ACGAAACTAACACC
1 CAAATATTACAC-AAA-TAACACC
* *
1346703 CAAATTTTACACAAATAGCACC
1 CAAATATTACACAAATAACACC
1346725 CAAA
1 CAAA
1346729 AAGAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
23 11 0.48
24 2 0.09
ACGTcount: A:0.51, C:0.27, G:0.04, T:0.18
Consensus pattern (22 bp):
CAAATATTACACAAATAACACC
Found at i:1347644 original size:30 final size:30
Alignment explanation
Indices: 1347608--1347664 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1347598 CGGATCGGAT
*
1347608 ATTTTTTAAAAAAATTTCGGGATCGGTCGG
1 ATTTTTTAAAAAAATTTCAGGATCGGTCGG
* *
1347638 ATTTTTTTAAAAAATTTCAGGTTCGGT
1 ATTTTTTAAAAAAATTTCAGGATCGGT
1347665 TCGGGTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (30 bp):
ATTTTTTAAAAAAATTTCAGGATCGGTCGG
Done.