Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 110 of 352
Found at i:35258788 original size:142 final size:139
Alignment explanation
Indices: 35258549--35258859 Score: 342
Period size: 142 Copynumber: 2.2 Consensus size: 139
35258539 TATGTGCGCC
* * *
35258549 AGTGTAAGACATGTCTGGGACATGCATCGGCTTTGAGACGAGAGCCAGTGTAAGATATGTCTAGG
1 AGTGTAAGACATGTCTGGGACACGCATCGGCCTTGAGACGAGAGCCAGTGTAAGACATGTCTAGG
* * *
35258614 ACATGCATCGGCCTCGAGATATGCATGTTAGTGTAAGACAATGTCTGAGACATGGCATCGGTATT
66 ACATGCATCGGACTCGACATATGCATGCTAGTGTAAGACAATGTCTGAGACATGGCATCGG-ATT
35258679 GAGTCGA-GTGCT
130 GA--C-ATGTGCT
* * * * * * *
35258691 AGTGTAAGACGTGTCTAGGACACGCATCGGCCTTGATGATGATAGTCAGTGTAAGACCATGTTTG
1 AGTGTAAGACATGTCTGGGACACGCATCGGCCTTGA-GACGAGAGCCAGTGTAAGA-CATGTCTA
* * * * *
35258756 GGACATGGCATC-GACTTGACATGTG-A-GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
64 GGACAT-GCATCGGACTCGACATATGCATGCTAGTGTAAGACAATGTCTGAGACATGGCATCGGA
*
35258818 TTGACATGTGTT
128 TTGACATGTGCT
*
35258830 AGTGTAAGACCTGTCTGGGACACGGCATCG
1 AGTGTAAGACATGTCTGGGACAC-GCATCG
35258860 ACACAGATGG
Statistics
Matches: 143, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
138 1 0.01
139 26 0.18
140 6 0.04
141 4 0.03
142 64 0.45
143 17 0.12
144 20 0.14
145 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (139 bp):
AGTGTAAGACATGTCTGGGACACGCATCGGCCTTGAGACGAGAGCCAGTGTAAGACATGTCTAGG
ACATGCATCGGACTCGACATATGCATGCTAGTGTAAGACAATGTCTGAGACATGGCATCGGATTG
ACATGTGCT
Found at i:35258789 original size:47 final size:45
Alignment explanation
Indices: 35258642--35258861 Score: 191
Period size: 47 Copynumber: 4.8 Consensus size: 45
35258632 ATATGCATGT
* *
35258642 TAGTGTAAGACAATGTCTGAGACATGGCATCGGTA-TTGAGTCGA-GTGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTGA--C-ATGTGC
* * * * *
35258690 TAGTGTAAGA-CGTGTCTAGGACA-CGCATCGGCCTTGATGATGATAG-
1 TAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA-CATG-T-GC
*
35258736 TCAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGACATGTGAGC
1 T-AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGACATGT--GC
* *
35258784 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGACATGTGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGACATGTGC
*
35258829 TAGTGTAAGACC-TGTCTGGGACACGGCATCGAC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGAC
35258862 ACAGATGGAT
Statistics
Matches: 145, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
44 20 0.14
45 15 0.10
46 14 0.10
47 64 0.44
48 27 0.19
49 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.26
Consensus pattern (45 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGACATGTGC
Found at i:35262143 original size:50 final size:50
Alignment explanation
Indices: 35262084--35262227 Score: 207
Period size: 50 Copynumber: 2.9 Consensus size: 50
35262074 AGTTTCGATA
* *
35262084 TGTGATCCCATGAAAGACCATGTCGGGGACATGGCATTGGCATCGATATG
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* *
35262134 TGTGATCCCATGTAAGACCATGTCTGGGACATGACATTGGAATCGATATG
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * ** *
35262184 TATGAACCCATGTAAGACCATACCTGGGATATGGCATTGGCATC
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
35262228 CCACTATGTG
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (50 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
Found at i:35264392 original size:39 final size:40
Alignment explanation
Indices: 35264347--35264514 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
35264337 CGGGGTTTAG
* * *
35264347 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
35264386 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
35264426 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
35264466 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
35264507 CCGGATAT
1 CCGGATAT
35264515 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:35264497 original size:41 final size:40
Alignment explanation
Indices: 35264370--35264514 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
35264360 CTCGCACAAG
* * * * *
35264370 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
35264410 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
35264450 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
35264491 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
35264515 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:35265742 original size:38 final size:38
Alignment explanation
Indices: 35265700--35265775 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
35265690 CAAGAACTCC
*
35265700 TTCCTCCTTCCTTAGAATTTTTGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
35265738 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
35265776 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:35272554 original size:41 final size:39
Alignment explanation
Indices: 35272391--35272570 Score: 175
Period size: 40 Copynumber: 4.5 Consensus size: 39
35272381 AATCAAGCAT
** ** * * *
35272391 CTTCGGGGTTTAGCCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCGGATATAGTCGCTAGCACAAATGC
* * * * *
35272429 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTT-AGCCGGATATAGTCGCTAGCACAAATGC
35272469 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAG-CCGGATATAGTCGCTAGCACAAATGC
* *
35272509 CTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGA-CTTAG-CCGGATATAGTCGC-TAGCACAAATGC
35272550 CTTCGGGACTTAGCCGGATAT
1 CTTCGGGACTTAGCCGGATAT
35272571 CATTCGAGTA
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 9 0.08
39 20 0.17
40 66 0.56
41 20 0.17
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (39 bp):
CTTCGGGACTTAGCCGGATATAGTCGCTAGCACAAATGC
Found at i:35273801 original size:38 final size:38
Alignment explanation
Indices: 35273759--35273834 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
35273749 CAAGAACTCC
*
35273759 TTCCTCCTTCCTTAGAATTTTTGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
*
35273797 TTCCTCCTTCCTTAGAATTTTCGTCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
35273835 AAAGGATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:35278263 original size:16 final size:16
Alignment explanation
Indices: 35278242--35278276 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
35278232 TTATACACAT
35278242 GTTCATGAGATTTATG
1 GTTCATGAGATTTATG
35278258 GTTCATGAGATTTATG
1 GTTCATGAGATTTATG
35278274 GTT
1 GTT
35278277 GGGTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.46
Consensus pattern (16 bp):
GTTCATGAGATTTATG
Found at i:35281305 original size:11 final size:11
Alignment explanation
Indices: 35281291--35281325 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
35281281 AATATTTAAT
*
35281291 AAATTTTAAAA
1 AAATTATAAAA
35281302 AAATTATAAAA
1 AAATTATAAAA
*
35281313 AAAGTATAAAA
1 AAATTATAAAA
35281324 AA
1 AA
35281326 GTATAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:35281312 original size:10 final size:10
Alignment explanation
Indices: 35281299--35281332 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
35281289 ATAAATTTTA
*
35281299 AAAAAATTAT
1 AAAAAAGTAT
35281309 AAAAAAAGTAT
1 -AAAAAAGTAT
35281320 AAAAAAGTAT
1 AAAAAAGTAT
35281330 AAA
1 AAA
35281333 CTTTAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAAAAAGTAT
Found at i:35281458 original size:24 final size:23
Alignment explanation
Indices: 35281416--35281460 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
35281406 AAAAGATAAA
* *
35281416 AATATTAGACATAATTTTTTTCC
1 AATATTAGAAATAACTTTTTTCC
35281439 AATATTAAGAAATAACTTTTTT
1 AATATT-AGAAATAACTTTTTT
35281461 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (23 bp):
AATATTAGAAATAACTTTTTTCC
Found at i:35282201 original size:16 final size:17
Alignment explanation
Indices: 35282157--35282195 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
35282147 TAAAATTAAT
35282157 AAAAAAGTGAAAGAAAG
1 AAAAAAGTGAAAGAAAG
* *
35282174 AAAAAATTGAAAGTAAG
1 AAAAAAGTGAAAGAAAG
35282191 AAAAA
1 AAAAA
35282196 GGGAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (17 bp):
AAAAAAGTGAAAGAAAG
Found at i:35286721 original size:13 final size:13
Alignment explanation
Indices: 35286705--35286730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35286695 ATATGTTTCA
35286705 TGATTGTTTTGGT
1 TGATTGTTTTGGT
35286718 TGATTGTTTTGGT
1 TGATTGTTTTGGT
35286731 ATGGATTCAA
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:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:35304042 original size:27 final size:27
Alignment explanation
Indices: 35304026--35304210 Score: 255
Period size: 27 Copynumber: 6.8 Consensus size: 27
35304016 CAATTTGTAG
* * * *
35304026 AATTACTATTTTACCCTCGATTAATAG
1 AATTACCATTTTACCCTCGATTTACAA
* *
35304053 AATTACCGTTTCACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAA
* * *
35304080 AATTACCTGTTTTACCCTCGATTTATAG
1 AATTACC-ATTTTACCCTCGATTTACAA
35304108 AATTACCATTTTACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAA
35304135 AATTACCATTTTACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAA
35304162 AATTACCATTTTACCCTC-AGTTTACAA
1 AATTACCATTTTACCCTCGA-TTTACAA
*
35304189 AATTACCGTTTTACCCTCGATT
1 AATTACCATTTTACCCTCGATT
35304211 GTGAAATTAC
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.01
27 116 0.82
28 25 0.18
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.38
Consensus pattern (27 bp):
AATTACCATTTTACCCTCGATTTACAA
Found at i:35304111 original size:82 final size:80
Alignment explanation
Indices: 35304012--35304210 Score: 263
Period size: 82 Copynumber: 2.4 Consensus size: 80
35304002 TACTGAAATG
* * * * *
35304012 CCCTCAATTTGTAGAATTACTATTTTACCCTCGATTAATAGAATTACCGTTTCACCCTCGATTTA
1 CCCTC-ATTTATAGAATTACCATTTTACCCTCGATTAACAAAATTACCATTTCACCCTCGATTTA
*
35304077 CAAAATTACCTGTTTTA
65 CAAAATTACC-ATTTTA
* *
35304094 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTA
1 CCCTC-ATTTATAGAATTACCATTTTACCCTCGATTAACAAAATTACCATTTCACCCTCGATTTA
35304159 CAAAATTACCATTTTA
65 CAAAATTACCATTTTA
* * *
35304175 CCCTCAGTTTACAAAATTACCGTTTTACCCTCGATT
1 CCCTCA-TTTATAGAATTACCATTTTACCCTCGATT
35304211 GTGAAATTAC
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 36 0.35
82 67 0.64
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (80 bp):
CCCTCATTTATAGAATTACCATTTTACCCTCGATTAACAAAATTACCATTTCACCCTCGATTTAC
AAAATTACCATTTTA
Found at i:35304272 original size:27 final size:27
Alignment explanation
Indices: 35304242--35304392 Score: 173
Period size: 27 Copynumber: 5.6 Consensus size: 27
35304232 TGTAGGATAG
35304242 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
35304269 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * ** *
35304296 AATTATCGAAATACCATTAGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
35304323 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
35304350 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
35304377 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
35304393 TTGACTTTCT
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.04
27 98 0.92
28 4 0.04
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:35304379 original size:81 final size:81
Alignment explanation
Indices: 35304242--35304391 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
35304232 TGTAGGATAG
* **
35304242 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTATC-GAA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTA-CAGAA
35304306 ATACCATTAGTTTGTGA
65 ATACCATTAGTTTGTGA
*
35304323 AATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTACAGA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAGA
35304386 AATACC
64 AATACC
35304392 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 6 0.10
81 56 0.90
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAA
TACCATTAGTTTGTGA
Found at i:35304454 original size:27 final size:27
Alignment explanation
Indices: 35304348--35304455 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
35304338 CTCAATTTGT
** * *
35304348 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
35304375 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
* *
35304402 TAAAAATTA-TAGAAATACCATCGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
35304431 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
35304456 GTAGATTTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
27 40 0.62
28 7 0.11
29 18 0.28
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:35304539 original size:27 final size:27
Alignment explanation
Indices: 35304496--35304569 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
35304486 AAATGACTAA
*
35304496 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
35304523 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
35304550 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
35304570 TGATGAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:35305306 original size:20 final size:20
Alignment explanation
Indices: 35305281--35305348 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
35305271 ATATGATATG
*
35305281 CATGAT-TGATATGATATGCA
1 CATGATATG-TATGAAATGCA
*
35305301 CATGATATGTATAAAATGCA
1 CATGATATGTATGAAATGCA
35305321 CATGATATGTATGAAATGCA
1 CATGATATGTATGAAATGCA
35305341 CATGATAT
1 CATGATAT
35305349 ATTCATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGATATGTATGAAATGCA
Found at i:35305474 original size:52 final size:51
Alignment explanation
Indices: 35305396--35305515 Score: 197
Period size: 52 Copynumber: 2.4 Consensus size: 51
35305386 GAGGAAGTGC
* * *
35305396 AAAAGGGCTTATGCCCCAGTTTATTGAAAATGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTT-TGCCCAAGTTTACCG
35305448 AAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTTTGCCCAAGTTTACCG
1 AAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTTTGCCCAAGTTTACCG
35305499 AAAAGGGCTT-TGCCCCA
1 AAAAGGGCTTATGCCCCA
35305516 GTTATTAAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 7 0.11
51 24 0.37
52 34 0.52
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTTTGCCCAAGTTTACCG
Found at i:35305495 original size:25 final size:26
Alignment explanation
Indices: 35305396--35305518 Score: 169
Period size: 26 Copynumber: 4.8 Consensus size: 26
35305386 GAGGAAGTGC
**
35305396 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
35305422 AAAATGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
35305448 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
35305474 AAAAGGGCTT-TGCCCAAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
35305499 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
35305519 ATTAAAGGAG
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 30 0.35
26 55 0.65
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:35305711 original size:42 final size:42
Alignment explanation
Indices: 35305664--35305755 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
35305654 TAGTCTCCCC
* ** *
35305664 AAATGGGCTCGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTCGCATACATCCATTGACATTACATATGATATTG
* *
35305706 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTCGCATACATCCATTGACATTACATATGATATTG
35305748 AAATGGGC
1 AAATGGGC
35305756 CTATGGTCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (42 bp):
AAATGGGCTCGCATACATCCATTGACATTACATATGATATTG
Found at i:35305833 original size:31 final size:31
Alignment explanation
Indices: 35305779--35305945 Score: 273
Period size: 31 Copynumber: 5.4 Consensus size: 31
35305769 CGTTTACAGT
* *
35305779 AAAGGCTTTGG-CCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
35305809 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * *
35305840 AAAGGCTTTGGCCTAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
35305871 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
35305902 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
35305933 AAAGGCTTCGGCC
1 AAAGGCTTCGGCC
35305946 TAGTAACCGT
Statistics
Matches: 127, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
30 10 0.08
31 117 0.92
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:35306009 original size:93 final size:93
Alignment explanation
Indices: 35305779--35305983 Score: 258
Period size: 93 Copynumber: 2.2 Consensus size: 93
35305769 CGTTTACAGT
* * ** *
35305779 AAAGGCTTTGG-CCAGTGAAATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTTATGAAAA
1 AAAGGCTTCGGCCCAGTGATATGATAGATGAAAAGGCTTCGGCCCAATGATATGATTTATGAAAA
* * * *
35305843 GGCTTTGGCCTAGTGAAATGATTTATGA
66 GGCTTCGGCCTAGTGAAACGATTAACGA
**
35305871 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAATGATATGATTTATGAAAA
1 AAAGGCTTCGGCCCAGTGATATGATAGATGAAAAGGCTTCGGCCCAATGATATGATTTATGAAAA
*
35305936 GGCTTCGGCCTAGT-AACCG-TTAAACG-
66 GGCTTCGGCCTAGTGAAACGATT-AACGA
35305962 AAAGGCTTCGGCCCAGTG-TATG
1 AAAGGCTTCGGCCCAGTGATATG
35305984 TCAAGACTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
90 4 0.04
91 20 0.19
92 15 0.15
93 64 0.62
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (93 bp):
AAAGGCTTCGGCCCAGTGATATGATAGATGAAAAGGCTTCGGCCCAATGATATGATTTATGAAAA
GGCTTCGGCCTAGTGAAACGATTAACGA
Found at i:35317315 original size:10 final size:8
Alignment explanation
Indices: 35317285--35317323 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
35317275 ATTTTAGAAA
35317285 AATAAAAT
1 AATAAAAT
35317293 AATAAAAT
1 AATAAAAT
35317301 AATAAAAGCT
1 AATAAAA--T
35317311 AATAAATAT
1 AATAAA-AT
35317320 AATA
1 AATA
35317324 TTAGACTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 15 0.54
9 5 0.18
10 7 0.25
11 1 0.04
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:35323069 original size:40 final size:40
Alignment explanation
Indices: 35323024--35323248 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
35323014 CTTGCACAAG
* * *
35323024 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
35323064 GCCTTCGGGACTTAACCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * * *
35323104 GCCTTCGGGTTTTAGCCCGGATACAATCGCTAACACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
35323144 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
35323184 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
35323225 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
35323249 CATTCGAATA
Statistics
Matches: 153, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 123 0.80
41 29 0.19
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:35334940 original size:40 final size:40
Alignment explanation
Indices: 35334887--35335165 Score: 414
Period size: 40 Copynumber: 7.0 Consensus size: 40
35334877 TTGAGAGTTA
*
35334887 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
* *
35334927 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
* *
35334967 TATATCCGGGCTAAGTCCCGAAAAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
* *
35335007 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGAGT
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
* *
35335047 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGAGT
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
* *
35335087 TATATCAGGGTTAAGTCTCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
* * * * *
35335127 TATATCCGAGCTAGGTCCCGAAGAGCAATCATGCTGGTG
1 TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTG
35335166 ATGTGTATTC
Statistics
Matches: 217, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
Found at i:35347037 original size:13 final size:13
Alignment explanation
Indices: 35347019--35347043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35347009 AATCACAAAT
35347019 AAATACACATATC
1 AAATACACATATC
35347032 AAATACACATAT
1 AAATACACATAT
35347044 ATTTTTTTTC
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:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATACACATATC
Found at i:35350909 original size:49 final size:49
Alignment explanation
Indices: 35350846--35351001 Score: 179
Period size: 49 Copynumber: 3.2 Consensus size: 49
35350836 GTCGATGTTG
*
35350846 TGTCCCAGACAGATCTTACACTGACTTCCATATATCGAGGCCGATGCCA
1 TGTCCCAGATAGATCTTACACTGACTTCCATATATCGAGGCCGATGCCA
* * * *
35350895 TGTTCTAGATAGATCTTACACTGACTTTCATATATCGAGGCTGATGCCA
1 TGTCCCAGATAGATCTTACACTGACTTCCATATATCGAGGCCGATGCCA
* * * * * * * *
35350944 TGTCCCAGATAGGTCTTAAACTGGCTCCCATCTATTG-GTGTCGGTGCCA
1 TGTCCCAGATAGATCTTACACTGACTTCCATATATCGAG-GCCGATGCCA
35350993 TGTCCCAGA
1 TGTCCCAGA
35351002 CTGGTCTCAC
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
48 1 0.01
49 88 0.99
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (49 bp):
TGTCCCAGATAGATCTTACACTGACTTCCATATATCGAGGCCGATGCCA
Found at i:35351101 original size:48 final size:46
Alignment explanation
Indices: 35351049--35351157 Score: 121
Period size: 46 Copynumber: 2.3 Consensus size: 46
35351039 TCCCAAATAG
* *
35351049 GTCTTACACTAGCT-TGTATATCACGAGGCCGATGCATGTCCCAGACAT
1 GTCTTACACTAGCTCT-TATATCA--AGGCCAATGCATGTCCCAGACAA
* * *
35351097 GTCTTACACTAGCTCTTGTCTCAATGCCAATGCATGTCCCAGACAA
1 GTCTTACACTAGCTCTTATATCAAGGCCAATGCATGTCCCAGACAA
* *
35351143 ATCTTACACTGGCTC
1 GTCTTACACTAGCTC
35351158 ACATACCACC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 33 0.62
48 19 0.36
49 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28
Consensus pattern (46 bp):
GTCTTACACTAGCTCTTATATCAAGGCCAATGCATGTCCCAGACAA
Found at i:35358266 original size:47 final size:47
Alignment explanation
Indices: 35358194--35358509 Score: 296
Period size: 47 Copynumber: 6.7 Consensus size: 47
35358184 AGGGTGTAAT
35358194 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCTAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-CATCTAG
* * *
35358242 G-TGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCGAAATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC---ATCTAG
* * * * *
35358290 GCTGATGCCATGTCCCATACATGGTCTTACAATGACACATC-TCGTA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATC-TAG
*
35358336 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATC-TCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCATCTAG
* *
35358382 GCCGATG-CATGTCCTAGACATGGTCTTACACTGGCTC-TCACATCTCTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT--CATCT-AG
* * *
35358430 TGCCGATGCCATGTCCCAGACATGGTCTTGCACTGGCTC-TCATAATGTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT-CT-AG
*
35358479 GCTGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
35358510 AGCACACAAA
Statistics
Matches: 229, Mismatches: 22, Indels: 36
0.80 0.08 0.13
Matches are distributed among these distances:
44 12 0.05
45 16 0.07
46 47 0.21
47 63 0.28
48 17 0.07
49 42 0.18
50 32 0.14
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTAG
Found at i:35361807 original size:46 final size:45
Alignment explanation
Indices: 35361699--35361860 Score: 148
Period size: 46 Copynumber: 3.5 Consensus size: 45
35361689 AAGCTGACGC
* * * * * *
35361699 CATGTCCCAGACAGGTCTTACATTAGCTTGTATATCCCAAGGTCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-T-TCTCAATGCCGATG
* *
35361747 CATGTCCCAAACATGTCTTACACTAGCTCTTGTCTCAATGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTT-TCTCAATGCCGATG
* *
35361793 CATGTCCCAGACATGTCTTACACT-G-GCTTTCATAATATGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTTTC-TCA-AT-GCCGATG
*
35361839 CATGTCCCAGACAAGTCTTACA
1 CATGTCCCAGACATGTCTTACA
35361861 GTGGCTCACA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 3 0.03
46 61 0.63
47 2 0.02
48 24 0.25
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTTTCTCAATGCCGATG
Found at i:35364200 original size:13 final size:13
Alignment explanation
Indices: 35364182--35364206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35364172 CGCACATTAT
35364182 TTTTTTATTTTTA
1 TTTTTTATTTTTA
35364195 TTTTTTATTTTT
1 TTTTTTATTTTT
35364207 CCTATATTTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:35366114 original size:93 final size:93
Alignment explanation
Indices: 35366003--35366173 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
35365993 GCCCCTAAGT
* * *
35366003 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
35366068 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
35366096 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
35366161 CGAGTTCGGATGC
66 CGAGTTCGGATGC
35366174 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:35366170 original size:46 final size:46
Alignment explanation
Indices: 35365998--35366170 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
35365988 AACCCGCCCC
* * * *
35365998 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
35366044 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
35366092 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
35366137 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
35366171 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:35373154 original size:46 final size:46
Alignment explanation
Indices: 35373087--35373257 Score: 215
Period size: 46 Copynumber: 3.7 Consensus size: 46
35373077 AACCCGCCCC
*
35373087 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
35373133 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
35373181 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
35373226 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
35373258 AATGCTCAAC
Statistics
Matches: 107, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.55
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:35373199 original size:93 final size:93
Alignment explanation
Indices: 35373092--35373262 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
35373082 GCCCCTAAGT
* *
35373092 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
35373157 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGAATGCCTAGTTACATCTCAC
*
35373185 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
35373250 CGAGTTCGAATGC
66 CGAGTTCGAATGC
35373263 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATCTCAC
Found at i:35375743 original size:21 final size:23
Alignment explanation
Indices: 35375717--35375763 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
35375707 CATGAAAAAT
*
35375717 ATAATTATATT-TATAAAT-TTA
1 ATAATTATATTATAAAAATATTA
35375738 ATAATTATATTATAAAAATATTA
1 ATAATTATATTATAAAAATATTA
35375761 ATA
1 ATA
35375764 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTATATTATAAAAATATTA
Found at i:35375762 original size:20 final size:20
Alignment explanation
Indices: 35375711--35375758 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
35375701 TACATACATG
35375711 AAAAATATAATTATATTTAT
1 AAAAATATAATTATATTTAT
**
35375731 AAATTTAATAATTATA-TTAT
1 AAAAAT-ATAATTATATTTAT
35375751 AAAAATAT
1 AAAAATAT
35375759 TAATATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 12 0.52
21 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATATAATTATATTTAT
Found at i:35379854 original size:29 final size:27
Alignment explanation
Indices: 35379821--35379912 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 27
35379811 TTTAAAAATA
35379821 ATTATATTAAGAATGTTATTAAATTATAT
1 ATTATATTAA-AAT-TTATTAAATTATAT
* * *
35379850 ATTATTTTATTAAATTATATTTAATAATA-
1 ATTATATTA--AAATT-TATTAAATTATAT
*
35379879 ATTATGTTAAAATATTATTAAATTATAT
1 ATTATATTAAAAT-TTATTAAATTATAT
35379907 AATTAT
1 -ATTAT
35379913 TTTTATTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
27 14 0.27
28 1 0.02
29 22 0.43
30 13 0.25
31 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
ATTATATTAAAATTTATTAAATTATAT
Found at i:35379948 original size:59 final size:58
Alignment explanation
Indices: 35379793--35379950 Score: 221
Period size: 59 Copynumber: 2.7 Consensus size: 58
35379783 ACATATTATG
* * *
35379793 ATTTTTATTAATTTATATTTTAAAAATAATTATATTAAGAATGTTATTAAATTATATATT
1 ATTTTTATTAAATTATA-TTTAATAATAATTATATTAA-AATATTATTAAATTATATATT
*
35379853 A-TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATTATTAAATTATATAATT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATTATTAAATTATAT-ATT
*
35379911 ATTTTTATTAAATTATATTTAGTAATAATCT-TATTAAAAT
1 ATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
35379951 TTAATAATAA
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
57 17 0.19
58 22 0.25
59 48 0.54
60 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATTATTAAATTATATATT
Found at i:35380090 original size:44 final size:46
Alignment explanation
Indices: 35380040--35380135 Score: 135
Period size: 44 Copynumber: 2.1 Consensus size: 46
35380030 GATTACAACA
35380040 TCCATTCCATTCAACCAAACACA-AGAA-TACTA-TTACAGCTTTAT
1 TCCATTCCATTCAACCAAACA-ATAGAATTACTAGTTACAGCTTTAT
* * *
35380084 TCCATTCCATTTAACCTAACAATTGAATTACTAGTTACAGCTTTAT
1 TCCATTCCATTCAACCAAACAATAGAATTACTAGTTACAGCTTTAT
35380130 TCCATT
1 TCCATT
35380136 ACAGCTATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 5 0.11
46 18 0.39
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.35
Consensus pattern (46 bp):
TCCATTCCATTCAACCAAACAATAGAATTACTAGTTACAGCTTTAT
Found at i:35380139 original size:16 final size:16
Alignment explanation
Indices: 35380118--35380183 Score: 96
Period size: 16 Copynumber: 4.1 Consensus size: 16
35380108 GAATTACTAG
35380118 TTACAGCTTTATTCCA
1 TTACAGCTTTATTCCA
*
35380134 TTACAGCTATATTCCA
1 TTACAGCTTTATTCCA
*
35380150 TTACATCTTTATTCCA
1 TTACAGCTTTATTCCA
**
35380166 TTACAGCCCTATTCCA
1 TTACAGCTTTATTCCA
35380182 TT
1 TT
35380184 CACCCCAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.26, C:0.27, G:0.05, T:0.42
Consensus pattern (16 bp):
TTACAGCTTTATTCCA
Found at i:35380634 original size:18 final size:18
Alignment explanation
Indices: 35380607--35380643 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35380597 GATTTTACCA
35380607 TCCTCTCTTCAACA-ACC
1 TCCTCTCTTCAACAGACC
35380624 TCCTCCTCTTCAACAGACC
1 TCCT-CTCTTCAACAGACC
35380643 T
1 T
35380644 TGCAACCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.22, C:0.46, G:0.03, T:0.30
Consensus pattern (18 bp):
TCCTCTCTTCAACAGACC
Found at i:35384252 original size:89 final size:89
Alignment explanation
Indices: 35384100--35384277 Score: 302
Period size: 89 Copynumber: 2.0 Consensus size: 89
35384090 CCACACCATG
* *
35384100 TAAGTCCCTGAAGCTTCTCCTTACCATACCATTCTATCCACTTCTTCCTCAATAGGGAAAGGAAT
1 TAAGTCCCTGAAGCTTCTCCTCACCATACCATTCTATCCACTTCTTCCTCAAGAGGGAAAGGAAT
35384165 GCATAGAATCCTCTTGTCATCATC
66 GCATAGAATCCTCTTGTCATCATC
* * *
35384189 TAAGTCCCTGAAGCTTTTCCTCACTATACCATTCTATCCACTTCTTCCTCAAGAGGGAGAGGAAT
1 TAAGTCCCTGAAGCTTCTCCTCACCATACCATTCTATCCACTTCTTCCTCAAGAGGGAAAGGAAT
*
35384254 GCATAGGATCCTCTTGTCATCATC
66 GCATAGAATCCTCTTGTCATCATC
35384278 CGGGTGAAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (89 bp):
TAAGTCCCTGAAGCTTCTCCTCACCATACCATTCTATCCACTTCTTCCTCAAGAGGGAAAGGAAT
GCATAGAATCCTCTTGTCATCATC
Found at i:35389069 original size:25 final size:25
Alignment explanation
Indices: 35389004--35389062 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
35388994 AGATATAAAT
*** * *
35389004 GGTAAGCTCATACAAGCTGAATATC
1 GGTAAGCTCATGTGAGCTAAATATA
35389029 GGTAAGCTCATGTGAGCTAAATATA
1 GGTAAGCTCATGTGAGCTAAATATA
35389054 GGTAAGCTC
1 GGTAAGCTC
35389063 TCTTGAGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (25 bp):
GGTAAGCTCATGTGAGCTAAATATA
Found at i:35389909 original size:45 final size:45
Alignment explanation
Indices: 35389845--35389935 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
35389835 AATCAGTTGA
*
35389845 AGAAAGAAGAAAAGATGATACTTGGCTTTTATTTTAATTAATTTT
1 AGAAAGAAGAAAAGATGATACTTGGCTTTTATTTCAATTAATTTT
35389890 AGAAAGAAGAAAAGATGATACTTGGCTTTTATTTCAATTAATTTT
1 AGAAAGAAGAAAAGATGATACTTGGCTTTTATTTCAATTAATTTT
35389935 A
1 A
35389936 ACTTTAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (45 bp):
AGAAAGAAGAAAAGATGATACTTGGCTTTTATTTCAATTAATTTT
Found at i:35391487 original size:69 final size:69
Alignment explanation
Indices: 35391276--35391489 Score: 194
Period size: 69 Copynumber: 3.1 Consensus size: 69
35391266 GGACCGTATT
*
35391276 CATTTATTCAAACAAAATTTAGCATCTTTCAAGCATTATCAAGCATGTGGTCAATCTCATATATT
1 CATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATATT
35391341 TATG
66 TATG
* * * ** ** *
35391345 CATTTATGCAATCCAAATGTTCA-CATTCAACTCAAGCA-TA--AA--AT-TAAAATCACATATC
1 CATTTATTCAAACAAAAT-TT-AGCA-T-ATTTCAAGCATTATCAAGCATGT--GGTCA-ATCT-
*
35391403 CAT-TAATTT-TT
58 CATAT-ATTTATG
35391414 CATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATATT
1 CATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATATT
35391479 TATG
66 TATG
35391483 CATTTAT
1 CATTTAT
35391490 GCAATCCAAA
Statistics
Matches: 108, Mismatches: 19, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
66 9 0.08
67 6 0.06
68 14 0.13
69 51 0.47
70 14 0.13
71 6 0.06
72 8 0.07
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (69 bp):
CATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATATT
TATG
Found at i:35391522 original size:138 final size:138
Alignment explanation
Indices: 35391274--35391532 Score: 509
Period size: 138 Copynumber: 1.9 Consensus size: 138
35391264 CAGGACCGTA
*
35391274 TTCATTTATTCAAACAAAATTTAGCATCTTTCAAGCATTATCAAGCATGTGGTCAATCTCATATA
1 TTCATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATA
35391339 TTTATGCATTTATGCAATCCAAATGTTCACATTCAACTCAAGCATAAAATTAAAATCACATATCC
66 TTTATGCATTTATGCAATCCAAATGTTCACATTCAACTCAAGCATAAAATTAAAATCACATATCC
35391404 ATTAATTT
131 ATTAATTT
35391412 TTCATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATA
1 TTCATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATA
35391477 TTTATGCATTTATGCAATCCAAATGTTCACATTCAACTCAAGCATAAAATTAAAAT
66 TTTATGCATTTATGCAATCCAAATGTTCACATTCAACTCAAGCATAAAATTAAAAT
35391533 TTTTATCATT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 120 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (138 bp):
TTCATTTATTCAAACAAAATTTAGCATATTTCAAGCATTATCAAGCATGTGGTCAATCTCATATA
TTTATGCATTTATGCAATCCAAATGTTCACATTCAACTCAAGCATAAAATTAAAATCACATATCC
ATTAATTT
Found at i:35412835 original size:43 final size:44
Alignment explanation
Indices: 35412788--35412902 Score: 150
Period size: 43 Copynumber: 2.7 Consensus size: 44
35412778 ATCACTTATC
*
35412788 GATGCCAATGTCCCAGACATGATCTTACACGA-AATCA-TATA-A
1 GATGCCAATGTCCCAGACATGATCTTACAC-ATAATCACAATACA
35412830 TGATGCCAATGTCCCAGACAT-AGTCTTACACATAATCACAATACA
1 -GATGCCAATGTCCCAGACATGA-TCTTACACATAATCACAATACA
*
35412875 -ATGCCAATGTCCCAGACATGGTCTTACA
1 GATGCCAATGTCCCAGACATGATCTTACA
35412903 TGTAAACACA
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
42 2 0.03
43 59 0.91
44 3 0.05
45 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (44 bp):
GATGCCAATGTCCCAGACATGATCTTACACATAATCACAATACA
Found at i:35416440 original size:18 final size:19
Alignment explanation
Indices: 35416404--35416442 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
35416394 CCTAGCAGCC
35416404 CACATTTATCAACTTTTCA
1 CACATTTATCAACTTTTCA
35416423 CACATTT-TC-ACATTTTCA
1 CACATTTATCAAC-TTTTCA
35416441 CA
1 CA
35416443 AATAAATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 10 0.53
19 7 0.37
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (19 bp):
CACATTTATCAACTTTTCA
Found at i:35420913 original size:21 final size:21
Alignment explanation
Indices: 35420871--35420913 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
35420861 TATAATATTT
*
35420871 ATCAAACATTCAATATCGCAA
1 ATCAAACATTCAATATCACAA
*
35420892 ATCAATCATTCACATA-CACAA
1 ATCAAACATTCA-ATATCACAA
35420913 A
1 A
35420914 GTCCCTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (21 bp):
ATCAAACATTCAATATCACAA
Found at i:35422239 original size:47 final size:47
Alignment explanation
Indices: 35422162--35422292 Score: 140
Period size: 47 Copynumber: 2.8 Consensus size: 47
35422152 CATAATCGAT
* * * *
35422162 AAGTACCTATACCAT-TGCCCGTTGCTAAATCTAGGTAACTTATTCT-A
1 AAGTACCTATACCATGT-CCCGTAGCCAAATCAAGGTAAC-TACTCTCA
* * *
35422209 GAGTACCTATACCATGTCTCGTAGCCAAATCAAGGTAACTCCTCTCA
1 AAGTACCTATACCATGTCCCGTAGCCAAATCAAGGTAACTACTCTCA
* * *
35422256 AAATATCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGTCCCGTAGCCAAATCAAGGTA
35422293 TTATTCGTAC
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 4 0.06
47 65 0.93
48 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (47 bp):
AAGTACCTATACCATGTCCCGTAGCCAAATCAAGGTAACTACTCTCA
Found at i:35425961 original size:27 final size:27
Alignment explanation
Indices: 35425928--35425988 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
35425918 CCATATTGAG
35425928 GGCCCATGTGGGCCTATACCTCCATAT
1 GGCCCATGTGGGCCTATACCTCCATAT
*
35425955 GGCCCATGTGGGCCTATACCTCTATAT
1 GGCCCATGTGGGCCTATACCTCCATAT
35425982 GGCCCAT
1 GGCCCAT
35425989 TTAGCCTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.33, G:0.23, T:0.26
Consensus pattern (27 bp):
GGCCCATGTGGGCCTATACCTCCATAT
Found at i:35426232 original size:8 final size:8
Alignment explanation
Indices: 35426219--35426259 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
35426209 CATCTACCCA
*
35426219 CTTTTCGG
1 CTTTTCAG
35426227 CTTTTCAG
1 CTTTTCAG
* *
35426235 CCTTTCTG
1 CTTTTCAG
35426243 CTTTTCAG
1 CTTTTCAG
35426251 CTTTTCAG
1 CTTTTCAG
35426259 C
1 C
35426260 CTTAGCAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.07, C:0.29, G:0.15, T:0.49
Consensus pattern (8 bp):
CTTTTCAG
Found at i:35426271 original size:24 final size:24
Alignment explanation
Indices: 35426219--35426271 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35426209 CATCTACCCA
* * *
35426219 CTTTTCGGCTTTTCAGCCTTTCTG
1 CTTTTCAGCTTTTCAGCCTTGCAG
35426243 CTTTTCAGCTTTTCAGCCTTAGCAG
1 CTTTTCAGCTTTTCAGCCTT-GCAG
35426268 -TTTT
1 CTTTT
35426272 ACATCCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.26, G:0.15, T:0.49
Consensus pattern (24 bp):
CTTTTCAGCTTTTCAGCCTTGCAG
Found at i:35433172 original size:19 final size:18
Alignment explanation
Indices: 35433135--35433178 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
35433125 ATACATACAG
35433135 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
35433152 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
35433171 TACTAATT
1 TAATAATT
35433179 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:35435644 original size:40 final size:40
Alignment explanation
Indices: 35435600--35435826 Score: 368
Period size: 40 Copynumber: 5.7 Consensus size: 40
35435590 GCTTCTCACT
35435600 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
35435640 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
35435680 CAATTGCCATCGGGACTTGGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
35435720 CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
35435760 CAAATGCCTTCGGG-CATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35435799 CAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
35435827 CAATCCGAAT
Statistics
Matches: 173, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 49 0.28
40 124 0.72
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:35438478 original size:13 final size:13
Alignment explanation
Indices: 35438460--35438487 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35438450 GAAATCATAG
35438460 GTCACATGCCCGT
1 GTCACATGCCCGT
35438473 GTCACATGCCCGT
1 GTCACATGCCCGT
35438486 GT
1 GT
35438488 AAACAGGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.36, G:0.25, T:0.25
Consensus pattern (13 bp):
GTCACATGCCCGT
Found at i:35439706 original size:47 final size:47
Alignment explanation
Indices: 35439634--35439764 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
35439624 CATAATTGAT
* ** * *
35439634 AAGTACCTATTCCATGGCCAATAGCCAAATCAAGGTAACTTATCCCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAAATCATCCCA
* * **
35439681 GAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAAATCCTTTCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAAATCATCCCA
* *
35439728 AAATACCTATACCATGGCCCGTAGCTAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
35439765 CTATTCACAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAAATCATCCCA
Found at i:35443614 original size:41 final size:41
Alignment explanation
Indices: 35443557--35443650 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
35443547 ACTTGACATG
* * * *
35443557 GGTATCGATACCCAAGTTAATGTATCAACACCA-TTGGCAGA
1 GGTATCGATACCCAAGTCAATGCATCAACA-CAGTTAGCAAA
* *
35443598 GGTATCGATACCCAAGTCAATGCATCGATACAGTTAGCAAA
1 GGTATCGATACCCAAGTCAATGCATCAACACAGTTAGCAAA
35443639 GGTATCGATACC
1 GGTATCGATACC
35443651 TCTCATATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 2 0.04
41 44 0.96
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (41 bp):
GGTATCGATACCCAAGTCAATGCATCAACACAGTTAGCAAA
Found at i:35446792 original size:18 final size:17
Alignment explanation
Indices: 35446771--35446808 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
35446761 ATGACATAAA
35446771 AAATAAATAACGAAAAAT
1 AAATAAATAA-GAAAAAT
35446789 AAATAAATAAGAAAAAT
1 AAATAAATAAGAAAAAT
35446806 AAA
1 AAA
35446809 CAAACGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
AAATAAATAAGAAAAAT
Found at i:35448251 original size:28 final size:28
Alignment explanation
Indices: 35448214--35448269 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
35448204 CACACAGAGT
35448214 AAGCTTTCAAAAGCTTAGTAAGCTCGTA
1 AAGCTTTCAAAAGCTTAGTAAGCTCGTA
35448242 AAGCTTTCAAAAGCTTAGTAAGCTCGTA
1 AAGCTTTCAAAAGCTTAGTAAGCTCGTA
35448270 CTCAAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (28 bp):
AAGCTTTCAAAAGCTTAGTAAGCTCGTA
Found at i:35448660 original size:30 final size:29
Alignment explanation
Indices: 35448603--35448660 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
35448593 CAAATAACCG
*
35448603 AAGCTAGTTAAATCGCACATTTAGTGCCT
1 AAGCTAGTTAAATCGCACACTTAGTGCCT
* *
35448632 AAGCTAGTTTAAATCGCATACTTGGTGCC
1 AAGCTAG-TTAAATCGCACACTTAGTGCC
35448661 AAAACTTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCT
Found at i:35456629 original size:22 final size:22
Alignment explanation
Indices: 35456601--35456722 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
35456591 TTCCACATCC
35456601 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
35456623 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
35456647 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
35456670 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
35456694 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
35456717 ATCACA
1 ATCACA
35456723 CATACAAATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:35456636 original size:47 final size:47
Alignment explanation
Indices: 35456573--35456876 Score: 416
Period size: 47 Copynumber: 6.4 Consensus size: 47
35456563 CTCTTCGGGA
* * *
35456573 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
35456620 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35456667 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
35456714 CTTATCACACATACA-AATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
35456761 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
35456808 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
35456857 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
35456877 GTACATCAAT
Statistics
Matches: 237, Mismatches: 14, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.01
47 193 0.81
48 1 0.00
49 40 0.17
50 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:35460367 original size:29 final size:29
Alignment explanation
Indices: 35460308--35460365 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
35460298 CAAATAGCCG
35460308 AAGCTAGTTAAATCGCACACTTAGTGCCC
1 AAGCTAGTTAAATCGCACACTTAGTGCCC
35460337 AAGCTAGTTTAAATCGCACACTTAGTGCC
1 AAGCTAG-TTAAATCGCACACTTAGTGCC
35460366 AAAACTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCC
Found at i:35469469 original size:27 final size:27
Alignment explanation
Indices: 35469439--35469500 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
35469429 GTGATATTGT
35469439 CACCAGATACAGATA-TTGTGGCAGAGC
1 CACCAGA-ACAGATATTTGTGGCAGAGC
**
35469466 CACCAGAACAGATATTTGTGGCTTAGC
1 CACCAGAACAGATATTTGTGGCAGAGC
35469493 CACCAGAA
1 CACCAGAA
35469501 TGCTTCCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.22
27 25 0.78
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGAGC
Found at i:35476300 original size:28 final size:28
Alignment explanation
Indices: 35476201--35476327 Score: 137
Period size: 28 Copynumber: 4.5 Consensus size: 28
35476191 GCTACGTATA
* ** *
35476201 GCACATAGTGTGCAAGATATTGAATATG
1 GCACTTAGTGTGTGAGACATTGAATATG
* ** * *
35476229 ACACTTAGTGTGCAAGATATTGATTATG
1 GCACTTAGTGTGTGAGACATTGAATATG
35476257 GCACTTAGTGTGTGAGACATTGAATATG
1 GCACTTAGTGTGTGAGACATTGAATATG
* * **
35476285 GCACTTAGTGTATGAGGCATTGGGTATG
1 GCACTTAGTGTGTGAGACATTGAATATG
35476313 GCACTTAGTGTGTGA
1 GCACTTAGTGTGTGA
35476328 AATATCGAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTTAGTGTGTGAGACATTGAATATG
Found at i:35478197 original size:26 final size:26
Alignment explanation
Indices: 35478168--35478245 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
35478158 TTAGGTCACG
35478168 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
* * * *
35478194 TGTGTACG-A-GATAGT-TAGGTTGC-A
1 TGTGTA-GTACTA-AGTGCAGGCTACTA
35478218 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
35478244 TG
1 TG
35478246 CGTACCAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
23 1 0.03
24 11 0.29
25 12 0.32
26 13 0.34
27 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCTACTA
Found at i:35478229 original size:50 final size:51
Alignment explanation
Indices: 35478112--35478257 Score: 177
Period size: 50 Copynumber: 2.9 Consensus size: 51
35478102 ATTGTGAGAA
* * ** *
35478112 CACATGTGTAGTAATATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAG-TTTAGGT
* *
35478164 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACGAGATAG-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTTAGGT
** * *
35478214 TGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAG
35478258 CTTCAGTTAC
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
50 45 0.55
52 37 0.45
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTTAGGT
Found at i:35483199 original size:43 final size:42
Alignment explanation
Indices: 35483138--35483222 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 42
35483128 AGTGGGAGAT
35483138 AGAGTTTATTATCTCTTATTGTACAATATGCTAAGATAGTATA
1 AGAGTTTATTATCTCTTATTGTACAATAT-CTAAGATAGTATA
35483181 AGAGTTTATTATCTCTTATTGTACAATATCTAAGATAGTATA
1 AGAGTTTATTATCTCTTATTGTACAATATCTAAGATAGTATA
35483223 TTATCTTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 13 0.31
43 29 0.69
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.42
Consensus pattern (42 bp):
AGAGTTTATTATCTCTTATTGTACAATATCTAAGATAGTATA
Found at i:35487386 original size:16 final size:16
Alignment explanation
Indices: 35487361--35487391 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35487351 GAAAATTCAG
35487361 GATTTCGGGATTTTTA
1 GATTTCGGGATTTTTA
*
35487377 GATTTTGGGATTTTT
1 GATTTCGGGATTTTT
35487392 GAGGCGTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (16 bp):
GATTTCGGGATTTTTA
Found at i:35488137 original size:26 final size:26
Alignment explanation
Indices: 35488101--35488156 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
35488091 AACTTCACAT
35488101 GGCCTGGGCGCACGACCATGTCCTAA
1 GGCCTGGGCGCACGACCATGTCCTAA
* *
35488127 GGCCTGGGCGCACGGCCATGTCCTAG
1 GGCCTGGGCGCACGACCATGTCCTAA
35488153 GGCC
1 GGCC
35488157 ATGCCCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (26 bp):
GGCCTGGGCGCACGACCATGTCCTAA
Found at i:35494067 original size:39 final size:39
Alignment explanation
Indices: 35494037--35494192 Score: 164
Period size: 39 Copynumber: 4.1 Consensus size: 39
35494027 AGGAGTATCG
*
35494037 AAGTACAACAGGGGCACGTAAGTGTGATCAGGGGTACCA
1 AAGTACAACAGGGGCACGTAAGTGAGATCAGGGGTACCA
* *
35494076 AAGTACAGCAGGGGCATGTAAGTGCA-ATCAGGGGTACCA
1 AAGTACAACAGGGGCACGTAAGTG-AGATCAGGGGTACCA
* *
35494115 AAATACAACA-AGGCACGTAAGTGAGATCAGGGGTA-CA
1 AAGTACAACAGGGGCACGTAAGTGAGATCAGGGGTACCA
* * * *
35494152 GAACTAGAACA-GGGCATGTAAGT-A-CT-AGGGGTACCA
1 -AAGTACAACAGGGGCACGTAAGTGAGATCAGGGGTACCA
35494188 AAGTA
1 AAGTA
35494193 AAAAAGGGAA
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
35 11 0.11
36 3 0.03
37 4 0.04
38 39 0.39
39 43 0.43
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.15
Consensus pattern (39 bp):
AAGTACAACAGGGGCACGTAAGTGAGATCAGGGGTACCA
Found at i:35494165 original size:77 final size:74
Alignment explanation
Indices: 35494040--35494189 Score: 187
Period size: 77 Copynumber: 2.0 Consensus size: 74
35494030 AGTATCGAAG
* * * *
35494040 TACAACAGGGGCACGTAAGTGTGATCAGGGGTACCAAAGTACAGCAGGGGCATGTAAGTGCAATC
1 TACAACAGAGGCACGTAAGTGAGATCAGGGGTACCAAACTACAACA-GGGCATGTAAGT--AAT-
35494105 AGGGGTACCAAAA
62 AGGGGTACCAAAA
* *
35494118 TACAACA-AGGCACGTAAGTGAGATCAGGGGTA-CAGAACTAGAACAGGGCATGTAAGTACTAGG
1 TACAACAGAGGCACGTAAGTGAGATCAGGGGTACCA-AACTACAACAGGGCATGTAAGTAATAGG
35494181 GGTACCAAA
65 GGTACCAAA
35494190 GTAAAAAAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
73 12 0.18
74 2 0.03
76 14 0.22
77 30 0.46
78 7 0.11
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.15
Consensus pattern (74 bp):
TACAACAGAGGCACGTAAGTGAGATCAGGGGTACCAAACTACAACAGGGCATGTAAGTAATAGGG
GTACCAAAA
Found at i:35496682 original size:39 final size:39
Alignment explanation
Indices: 35496478--35496700 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
35496468 TTGAATGCTG
* * * * * *
35496478 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
35496518 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
35496558 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
35496598 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
35496638 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
35496677 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35496701 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:35496720 original size:79 final size:80
Alignment explanation
Indices: 35496558--35496735 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
35496548 AGATACAAGT
* * * *
35496558 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35496623 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
35496638 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35496702 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35496717 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35496736 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35504175 original size:39 final size:39
Alignment explanation
Indices: 35503971--35504193 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
35503961 TTGAATGCTG
* * * * * *
35503971 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
35504011 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
35504051 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
35504091 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
35504131 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
35504170 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35504194 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:35504213 original size:79 final size:80
Alignment explanation
Indices: 35504051--35504228 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
35504041 AGATACAAGT
* * * *
35504051 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35504116 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
35504131 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35504195 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35504210 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35504229 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35519006 original size:44 final size:44
Alignment explanation
Indices: 35518943--35519035 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
35518933 AAATTTGACG
*
35518943 AGTAAATTTTTATTTTATTATTATTTTAATTTCTATGGGATGTT
1 AGTAAATTTTTATTTTATTATTATTTTAATTTCTACGGGATGTT
35518987 AGTAAATTTTTATTTTATTATTATTTTAATTTCTACGGGATGTT
1 AGTAAATTTTTATTTTATTATTATTTTAATTTCTACGGGATGTT
35519031 AGTAA
1 AGTAA
35519036 GGTCATAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (44 bp):
AGTAAATTTTTATTTTATTATTATTTTAATTTCTACGGGATGTT
Found at i:35523317 original size:23 final size:23
Alignment explanation
Indices: 35523231--35523317 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
35523221 TTAGCTTAGA
*
35523231 AAAGCTTACTGCTTTCAGCTCGATT
1 AAAGCTTACCG-TTTCAGCTCGA-T
* * *
35523256 GAA-CTTACCATTTCAGCTTG-T
1 AAAGCTTACCGTTTCAGCTCGAT
** *
35523277 ATGGCCTTACTG-TTCAGCTCGAT
1 AAAG-CTTACCGTTTCAGCTCGAT
35523300 AAAGCTTACCGTTTCAGC
1 AAAGCTTACCGTTTCAGC
35523318 CTAATAGAGC
Statistics
Matches: 45, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
21 1 0.02
22 14 0.31
23 23 0.51
24 5 0.11
25 2 0.04
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (23 bp):
AAAGCTTACCGTTTCAGCTCGAT
Found at i:35527829 original size:50 final size:50
Alignment explanation
Indices: 35527712--35528002 Score: 327
Period size: 50 Copynumber: 5.8 Consensus size: 50
35527702 TGTGAGCATA
* * *** * * *
35527712 CATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAAGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG--TTAGGTCG
* *
35527764 CGTGTGTAGTACTAATTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
*
35527814 CATGTGTAGTACTAATTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
* * * *
35527864 CA--TGTATTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
* * * * *
35527912 CGTGTGTAGTACTAAGTGCAAGCTACTACATGTACCGGATTGTT-GGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
* * * *
35527961 CATGTGGAGTACTAAGTGCAGCCTACTATGCGTACCAGATAG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
35528003 CTTCGGTTAC
Statistics
Matches: 204, Mismatches: 33, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
48 42 0.21
49 37 0.18
50 91 0.45
52 34 0.17
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
Found at i:35527901 original size:98 final size:97
Alignment explanation
Indices: 35527768--35528002 Score: 317
Period size: 98 Copynumber: 2.4 Consensus size: 97
35527758 AAGTCACGTG
* * *
35527768 TGTAGTACTAATTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAATTGC
1 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGC
* *
35527833 AGGCTACTACGTGTACCAGATAGTTAGGTCGCA
66 AAGCTACTACATGTACCAGATAGTT-GGTCGCA
* * * *
35527866 TGTATTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGC
1 TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGC
* *
35527931 AAGCTACTACATGTACCGGATTGTTGGTCGCA
66 AAGCTACTACATGTACCAGATAGTTGGTCGCA
* * *
35527963 TGTGGAGTACTAAGTGCAGCCTACTATGCGTACCAGATAG
1 TGT--AGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
35528003 CTTCGGTTAC
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
97 10 0.08
98 79 0.67
99 29 0.25
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (97 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTACTAAGTGC
AAGCTACTACATGTACCAGATAGTTGGTCGCA
Found at i:35527996 original size:147 final size:149
Alignment explanation
Indices: 35527716--35528002 Score: 407
Period size: 148 Copynumber: 1.9 Consensus size: 149
35527706 AGCATACATG
* * * *
35527716 TGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAAGTCACGTGTGTAGTACTAATT
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATAAGATGG-TTTAAGTCACGTGTGTAGTACTAAGT
* * * * * *
35527781 GCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAATTGCAGGCTACTACGTG
65 GCAAGCTACTACATGTACCAGATAGTTAGGTCGCATGTGGAGTACTAAGTGCAGCCTACTACGCG
35527846 TACCAGATAGTTAGGTCGCA
130 TACCAGATAGTTAGGTCGCA
* * *
35527866 TGTATTACTAAGTGCAGGCTACTACGTGTATCAGATGG-TTAGGTCACGTGTGTAGTACTAAGTG
1 TGTAGTACTAAGTGCAGGCTACTACGTGTATAAGATGGTTTAAGTCACGTGTGTAGTACTAAGTG
* * *
35527930 CAAGCTACTACATGTACCGGATTGTT-GGTCGCATGTGGAGTACTAAGTGCAGCCTACTATGCGT
66 CAAGCTACTACATGTACCAGATAGTTAGGTCGCATGTGGAGTACTAAGTGCAGCCTACTACGCGT
35527994 ACCAGATAG
131 ACCAGATAG
35528003 CTTCGGTTAC
Statistics
Matches: 121, Mismatches: 16, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
147 42 0.35
148 46 0.38
150 33 0.27
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (149 bp):
TGTAGTACTAAGTGCAGGCTACTACGTGTATAAGATGGTTTAAGTCACGTGTGTAGTACTAAGTG
CAAGCTACTACATGTACCAGATAGTTAGGTCGCATGTGGAGTACTAAGTGCAGCCTACTACGCGT
ACCAGATAGTTAGGTCGCA
Found at i:35530902 original size:40 final size:40
Alignment explanation
Indices: 35530858--35530955 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 40
35530848 GGCTTGACCA
* *
35530858 CATTACTGGCAGTTTATCAACAATACTGGAAGCTTGTTTG
1 CATTACTGGCAGTTTATCAACAATACTGGAAGCTTATCTG
* * * *
35530898 CATTACTGGCATTTTATCTACAATATTGGTAGCTTATCTG
1 CATTACTGGCAGTTTATCAACAATACTGGAAGCTTATCTG
* *
35530938 TACTACTGGCAGTTTATC
1 CATTACTGGCAGTTTATC
35530956 TGCATTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (40 bp):
CATTACTGGCAGTTTATCAACAATACTGGAAGCTTATCTG
Found at i:35530956 original size:40 final size:40
Alignment explanation
Indices: 35530861--35530966 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
35530851 TTGACCACAT
* * * *
35530861 TACTGGCAGTTTATCAACAATACTGGAAGCTTGTTTGCAT
1 TACTGGCAGTTTATCTACAATACTGGAAGCTTATCTGCAC
* * * *
35530901 TACTGGCATTTTATCTACAATATTGGTAGCTTATCTGTAC
1 TACTGGCAGTTTATCTACAATACTGGAAGCTTATCTGCAC
* *
35530941 TACTGGCAGTTTATCTGCATTACTGG
1 TACTGGCAGTTTATCTACAATACTGG
35530967 TGGCTTCACC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (40 bp):
TACTGGCAGTTTATCTACAATACTGGAAGCTTATCTGCAC
Found at i:35530964 original size:20 final size:20
Alignment explanation
Indices: 35530858--35530966 Score: 83
Period size: 20 Copynumber: 5.5 Consensus size: 20
35530848 GGCTTGACCA
**
35530858 CATTACTGGCAGTTTATCAA
1 CATTACTGGCAGTTTATCTG
* * * * *
35530878 CAATACTGGAAGCTTGTTTG
1 CATTACTGGCAGTTTATCTG
* *
35530898 CATTACTGGCATTTTATCTA
1 CATTACTGGCAGTTTATCTG
* * * *
35530918 CAATATTGGTAGCTTATCTG
1 CATTACTGGCAGTTTATCTG
* *
35530938 TACTACTGGCAGTTTATCTG
1 CATTACTGGCAGTTTATCTG
35530958 CATTACTGG
1 CATTACTGG
35530967 TGGCTTCACC
Statistics
Matches: 62, Mismatches: 27, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTACTGGCAGTTTATCTG
Found at i:35531001 original size:20 final size:20
Alignment explanation
Indices: 35530928--35531006 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
35530918 CAATATTGGT
* * *
35530928 AGCTTATCTGTACTACTGGC
1 AGCTTATCTGCATTACTAGC
* * *
35530948 AGTTTATCTGCATTACTGGT
1 AGCTTATCTGCATTACTAGC
* **
35530968 GGCTTCA-CCACATTACTAGC
1 AGCTT-ATCTGCATTACTAGC
35530988 AGCTTATCTGCATTACTAG
1 AGCTTATCTGCATTACTAG
35531007 TGGCTTGTCC
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (20 bp):
AGCTTATCTGCATTACTAGC
Found at i:35531012 original size:20 final size:20
Alignment explanation
Indices: 35530951--35531012 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
35530941 TACTGGCAGT
*
35530951 TTATCTGCATTACTGGTGGC
1 TTATCTGCATTACTAGTGGC
** **
35530971 TTCA-CCACATTACTAGCAGC
1 TT-ATCTGCATTACTAGTGGC
35530991 TTATCTGCATTACTAGTGGC
1 TTATCTGCATTACTAGTGGC
35531011 TT
1 TT
35531013 GTCCACGAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (20 bp):
TTATCTGCATTACTAGTGGC
Found at i:35536008 original size:46 final size:44
Alignment explanation
Indices: 35535941--35536116 Score: 192
Period size: 46 Copynumber: 3.9 Consensus size: 44
35535931 TGTAACCCGC
35535941 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGAGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGA-TTCACAT
* * *
35535987 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCCAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATTCACA--T
* *** * *
35536033 ACATCTCTCGAACTCGGA-TCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG--ATTCACAT
*
35536079 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAT
35536117 GCCCAAACAT
Statistics
Matches: 109, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
44 6 0.06
45 12 0.11
46 78 0.72
47 8 0.07
48 5 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATTCACAT
Found at i:35536063 original size:92 final size:93
Alignment explanation
Indices: 35535949--35536121 Score: 278
Period size: 92 Copynumber: 1.9 Consensus size: 93
35535939 GCCCATAAGT
*
35535949 GAACTCGGACTCAACTCAACGAGCTCGGGA-GTTCACATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
35536013 ACGAGCTCGGATGCCCAGTTACATCTCTC
65 ACGAGCTCGGATGCCCAGTTACATCTCTC
* * *
35536042 GAACTCGGA-TCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
*
35536106 CGAGTTCGGATGCCCA
66 CGAGCTCGGATGCCCA
35536122 AACATCCTAG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 3 0.04
92 62 0.84
93 9 0.12
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCCAGTTACATCTCTC
Found at i:35539443 original size:54 final size:54
Alignment explanation
Indices: 35539361--35539468 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
35539351 TTCCAAGCCT
35539361 TCGCTATTTCCTTTACTAAGGCTATGGCTCCTTAAATTACGTATAAGGAGACCA
1 TCGCTATTTCCTTTACTAAGGCTATGGCTCCTTAAATTACGTATAAGGAGACCA
*
35539415 TCGCTATTTCCTTTACTAAGGCTATGGCTCCTTAAATTGCGTATAAGGAGACCA
1 TCGCTATTTCCTTTACTAAGGCTATGGCTCCTTAAATTACGTATAAGGAGACCA
35539469 CCATACCTAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (54 bp):
TCGCTATTTCCTTTACTAAGGCTATGGCTCCTTAAATTACGTATAAGGAGACCA
Found at i:35543796 original size:46 final size:46
Alignment explanation
Indices: 35543617--35543915 Score: 171
Period size: 46 Copynumber: 6.5 Consensus size: 46
35543607 GTCGATATCG
* **
35543617 TGTCCCAGACA-GGTCTTACACTAACACAT-ATCAAGCCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGACACATCATGTAGCCGATGCCA
* * **
35543661 TGTCCCAGACATGGTCTTACACT-AGCTTTCA-CGATGTGGCTAATG-CA
1 TGTCCCAGACATGGTCTTACACTGA-C--ACATC-ATGTAGCCGATGCCA
*
35543708 TGTTCCAGACAT-GTCTTACACTAGCACACAT-ATCCGTA-CCGATGCCA
1 TGTCCCAGACATGGTCTTACACT-G-ACACATCAT--GTAGCCGATGCCA
* *
35543755 TGTCCCAAACATGGTCTTACACTGACACATCTTGTAGCCGAT-CCA
1 TGTCCCAGACATGGTCTTACACTGACACATCATGTAGCCGATGCCA
* * * * ** *
35543800 TGTCCCAAACAT-GTCTTACATTGGCTTATATCCCG-AGACTGATG-CA
1 TGTCCCAGACATGGTCTTACACTGAC--ACATCATGTAG-CCGATGCCA
* *
35543846 TGTCCCAGACAT-GTCTTACACT-AGCATTCGTC-TCAATA-CCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGA-CA--CATCAT--GTAGCCGATGCCA
35543893 TGTCCCAGACATGGTCTTACACT
1 TGTCCCAGACATGGTCTTACACT
35543916 AGCTCTCATA
Statistics
Matches: 199, Mismatches: 28, Indels: 52
0.71 0.10 0.19
Matches are distributed among these distances:
44 24 0.12
45 34 0.17
46 66 0.33
47 45 0.23
48 29 0.15
49 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (46 bp):
TGTCCCAGACATGGTCTTACACTGACACATCATGTAGCCGATGCCA
Found at i:35546374 original size:24 final size:25
Alignment explanation
Indices: 35546347--35546423 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
35546337 GCCTAGCCTC
* *
35546347 TTTTAAT-AACTGGGGTAAAGCCCT
1 TTTTAATAAAATGGGGCAAAGCCCT
*
35546371 TTTTGATAAAATGGGGCAAAGCCCT
1 TTTTAATAAAATGGGGCAAAGCCCT
** * * *
35546396 TTTCGATAAACTGGGGCATAGCGCT
1 TTTTAATAAAATGGGGCAAAGCCCT
35546421 TTT
1 TTT
35546424 GCACTTCCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (25 bp):
TTTTAATAAAATGGGGCAAAGCCCT
Found at i:35546391 original size:25 final size:25
Alignment explanation
Indices: 35546357--35546423 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
35546347 TTTTAATAAC
* *
35546357 TGGGGTAAAGCCCTTTTTGATAAAA
1 TGGGGCAAAGCCCTTTTCGATAAAA
*
35546382 TGGGGCAAAGCCCTTTTCGATAAAC
1 TGGGGCAAAGCCCTTTTCGATAAAA
* *
35546407 TGGGGCATAGCGCTTTT
1 TGGGGCAAAGCCCTTTT
35546424 GCACTTCCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (25 bp):
TGGGGCAAAGCCCTTTTCGATAAAA
Found at i:35546502 original size:11 final size:11
Alignment explanation
Indices: 35546471--35546518 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
35546461 ATATGGATAC
35546471 ATCATGTGCAT
1 ATCATGTGCAT
*
35546482 ATCA--TACAT
1 ATCATGTGCAT
35546491 ATCATGTGCAT
1 ATCATGTGCAT
*
35546502 ATCATGT-CAA
1 ATCATGTGCAT
35546512 ATCATGT
1 ATCATGT
35546519 ATATCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:35554226 original size:24 final size:25
Alignment explanation
Indices: 35554199--35554250 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
35554189 GCCTAGCCTC
*
35554199 TTTTAAT-AACTGGGGCA-AAGCCCT
1 TTTTAATAAAATGGGGCACAA-CCCT
*
35554223 TTTTGATAAAATGGGGCACAACCCT
1 TTTTAATAAAATGGGGCACAACCCT
35554248 TTT
1 TTT
35554251 CGGTAAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 16 0.67
26 2 0.08
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (25 bp):
TTTTAATAAAATGGGGCACAACCCT
Found at i:35554247 original size:25 final size:25
Alignment explanation
Indices: 35554209--35554275 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
35554199 TTTTAATAAC
*
35554209 TGGGGCAAAGCCCTTTTTGATAAAA
1 TGGGGCAAAGCCCTTTTCGATAAAA
* *
35554234 TGGGGCACAA-CCCTTTTCGGTAAAC
1 TGGGGCA-AAGCCCTTTTCGATAAAA
* *
35554259 TGGGGCATAGCGCTTTT
1 TGGGGCAAAGCCCTTTT
35554276 GCCCTTCCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.91
26 2 0.06
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (25 bp):
TGGGGCAAAGCCCTTTTCGATAAAA
Found at i:35554354 original size:11 final size:11
Alignment explanation
Indices: 35554323--35554370 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
35554313 ATATGGATAC
35554323 ATCATGTGCAT
1 ATCATGTGCAT
*
35554334 ATCA--TACAT
1 ATCATGTGCAT
35554343 ATCATGTGCAT
1 ATCATGTGCAT
*
35554354 ATCATGT-CAA
1 ATCATGTGCAT
35554364 ATCATGT
1 ATCATGT
35554371 ATATCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:35559789 original size:40 final size:40
Alignment explanation
Indices: 35559661--35559791 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 40
35559651 AAGAAGTGCT
* * **
35559661 CTTGTTTGCACAACTATGCCTCTGAATACAAC-TCGGTGTC
1 CTTGTTTGCACAACTGTGCCACTGAATAC-ACTTTAGTGTC
* * *
35559701 CTTGTTTGCACAATTGTGCCCCCT-AATACAATTTAGTGTC
1 CTTGTTTGCACAACTGTG-CCACTGAATACACTTTAGTGTC
*
35559741 CCTGTTTGCACAACTGTGCCACTGAATACACTTTAGTGTC
1 CTTGTTTGCACAACTGTGCCACTGAATACACTTTAGTGTC
* *
35559781 TTTATTTGCAC
1 CTTGTTTGCAC
35559792 TTCGGCACCC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 5 0.07
40 66 0.88
41 4 0.05
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (40 bp):
CTTGTTTGCACAACTGTGCCACTGAATACACTTTAGTGTC
Found at i:35562784 original size:42 final size:42
Alignment explanation
Indices: 35562736--35562837 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
35562726 CGACATGTGG
*
35562736 TTTCGTGTAAAACCATGTCTGAGACA-TAGGCATCG-TATATGA
1 TTTCGTGTAAGACCATGTCTGAGACAGT-GGCAT-GATATATGA
* * *
35562778 TTTCGTGTAAGACCCTGTCTGGGACAGTGGCATGATATTTGA
1 TTTCGTGTAAGACCATGTCTGAGACAGTGGCATGATATATGA
* *
35562820 TTACATGTAAGACCATGT
1 TTTCGTGTAAGACCATGT
35562838 TTGGGATGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
41 1 0.02
42 49 0.96
43 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
TTTCGTGTAAGACCATGTCTGAGACAGTGGCATGATATATGA
Found at i:35564302 original size:34 final size:35
Alignment explanation
Indices: 35564264--35564331 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
35564254 AAGCCCATAT
*
35564264 CAGTAGCAATATCAATGTGGGCCTTAG-CCAATTA
1 CAGTAGCAATAACAATGTGGGCCTTAGCCCAATTA
* *
35564298 CAGTAGCAGTAACAGTGTGGGCCTTAGCCCAATT
1 CAGTAGCAATAACAATGTGGGCCTTAGCCCAATT
35564332 TAGTACCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (35 bp):
CAGTAGCAATAACAATGTGGGCCTTAGCCCAATTA
Found at i:35570153 original size:38 final size:38
Alignment explanation
Indices: 35570110--35570240 Score: 145
Period size: 38 Copynumber: 3.2 Consensus size: 38
35570100 TTTCAAATTA
35570110 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
35570148 ACATGTTTAATCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
*
35570189 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
35570233 ACATGTAT
1 ACATGTAT
35570241 CAATATGTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
38 34 0.45
39 1 0.01
40 4 0.05
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 27 0.36
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:35570264 original size:48 final size:47
Alignment explanation
Indices: 35570150--35570274 Score: 187
Period size: 48 Copynumber: 2.6 Consensus size: 47
35570140 ACCACGTTAC
*
35570150 ATGTTTAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
* * * *
35570197 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAAT
*
35570245 ATGTGTAATTGTGGTATATCCACTTAGCAC
1 ATGTGTAATCGTGGTATATCCACTTAGCAC
35570275 TAACAGATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 33 0.49
48 35 0.51
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (47 bp):
ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAAT
Found at i:35571288 original size:17 final size:19
Alignment explanation
Indices: 35571246--35571289 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35571236 ATGAAATTTT
*
35571246 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
35571265 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
35571283 AA-TATTA
1 AATTATTA
35571290 CTGTAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:35573315 original size:20 final size:20
Alignment explanation
Indices: 35573292--35573349 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
35573282 TAAACATGGT
35573292 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
35573312 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
35573332 ATGTATGATATGCACATG
1 ATGTATGATATGCACATG
35573350 GTGTATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:35573332 original size:11 final size:11
Alignment explanation
Indices: 35573296--35573349 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
35573286 CATGGTATGT
35573296 ATGATATGCAC
1 ATGATATGCAC
* *
35573307 ATGACATG--T
1 ATGATATGCAC
35573316 ATGATATGCAC
1 ATGATATGCAC
*
35573327 ATGATATG--T
1 ATGATATGCAC
35573336 ATGATATGCAC
1 ATGATATGCAC
35573347 ATG
1 ATG
35573350 GTGTATTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.45
11 18 0.55
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:35573426 original size:24 final size:24
Alignment explanation
Indices: 35573399--35573543 Score: 204
Period size: 24 Copynumber: 6.0 Consensus size: 24
35573389 GGAGGAAGTG
35573399 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
35573423 CAAAAGGGCTTATGCCCTAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
35573446 CTAAAAGGGCTTATGCCCCAGTTAT
1 C-AAAAGGGCTTATGCCCCAGTTAT
35573471 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
35573495 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
35573519 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
35573544 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
23 1 0.01
24 98 0.88
25 12 0.11
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:35592526 original size:48 final size:50
Alignment explanation
Indices: 35592471--35592596 Score: 139
Period size: 50 Copynumber: 2.6 Consensus size: 50
35592461 CTGGTACGTA
* **
35592471 TAGTAGCCTGCACTTAGTACTAAACATGCGACC-AATTATC-CAGACACG
1 TAGTAGCCTGCACTTAGTACTAAACACGCGACCTAAACATCTCAGACACG
* * ** * * *
35592519 TAGTAGCCTACACTTAGTAATACGCACGTGACCTAAACATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTAAACACGCGACCTAAACATCTCAGACACG
*
35592569 TAGTAGCCTGCACTTAGTACTACACACG
1 TAGTAGCCTGCACTTAGTACTAAACACG
35592597 TGATCGAAGT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
48 27 0.43
49 5 0.08
50 31 0.49
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTAAACACGCGACCTAAACATCTCAGACACG
Found at i:35594320 original size:34 final size:34
Alignment explanation
Indices: 35594282--35594364 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
35594272 TGAAAAATGA
*
35594282 TTAATGTTAGTCAGGTGAGCAATGTATGAATTGG
1 TTAATGTTAGTCAAGTGAGCAATGTATGAATTGG
35594316 TTAATGTTAGTCAAGTGAGCAATGTATGAATTGG
1 TTAATGTTAGTCAAGTGAGCAATGTATGAATTGG
35594350 TT-ATGTT-G-CAAGTGA
1 TTAATGTTAGTCAAGTGA
35594365 AATTTGGTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 7 0.15
32 1 0.02
33 5 0.10
34 35 0.73
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.36
Consensus pattern (34 bp):
TTAATGTTAGTCAAGTGAGCAATGTATGAATTGG
Found at i:35597614 original size:24 final size:24
Alignment explanation
Indices: 35597587--35597632 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
35597577 GTATACGTAT
35597587 ATATATTAATATTAATAATAAAAC
1 ATATATTAATATTAATAATAAAAC
35597611 ATATATTAATATTAATAATAAA
1 ATATATTAATATTAATAATAAA
35597633 TATAGAGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATATTAATATTAATAATAAAAC
Found at i:35599930 original size:234 final size:234
Alignment explanation
Indices: 35599521--35599991 Score: 870
Period size: 234 Copynumber: 2.0 Consensus size: 234
35599511 TGAGAGTTAA
*
35599521 TGATAAGTAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTACTGATACAAATGAAGAATGTC
1 TGATAAGCAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTACTGATACAAATGAAGAATGTC
*
35599586 ACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGTAGAATTTTATCACAATAATTCT
66 ACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGAATTTTATCACAATAATTCT
* *
35599651 TATGATGATGTAGACTCATTTTAGTTAATTGAAGCAGAAATGATTGAAGAGCATGGTGAATTGAT
131 AATGATGATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTGAAGAGCATGGTGAATTGAT
35599716 GGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTT
196 GGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTT
35599755 TGATAAGCAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTACTGATACAAATGAAGAATGTC
1 TGATAAGCAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTACTGATACAAATGAAGAATGTC
* *
35599820 ACGTTGTTTAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGAATTTTATCATAATAATTCT
66 ACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGAATTTTATCACAATAATTCT
* *
35599885 AATGATGATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTGAAGAGCTTGGTGAATTTAT
131 AATGATGATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTGAAGAGCATGGTGAATTGAT
35599950 GGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTT
196 GGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTT
35599989 TGA
1 TGA
35599992 ATTATTAAAT
Statistics
Matches: 229, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
234 229 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (234 bp):
TGATAAGCAGATAACCTTTAATGTTTTCGATGCTATGAAGTGTACTGATACAAATGAAGAATGTC
ACGTTGTTGAGATTGTTAACACAATAGTTCAAGAAGAATTTGCAGAATTTTATCACAATAATTCT
AATGATGATGTAGACTCATTTGAGTTAATTGAAGCAGAAATGATTGAAGAGCATGGTGAATTGAT
GGAAGCTAAGCAAATTGAGAATGGATCAAGGAGAAGTTT
Found at i:35608476 original size:93 final size:93
Alignment explanation
Indices: 35608364--35608534 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
35608354 GCCCCTAAGT
* * *
35608364 GAACTCGGACTCAATTCAACGAGCTCAGG-CATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACAAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
35608428 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGAATGCCTAGTTACATCTCAC
* *
35608457 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATTCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
35608522 CGAGTTCGAATGC
66 CGAGTTCGAATGC
35608535 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATCTCAC
Found at i:35608529 original size:46 final size:45
Alignment explanation
Indices: 35608359--35608529 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 45
35608349 AACCCGCCCC
* * * *
35608359 TAAGTGAACTCGGACTCAATTCAACGAGCTCAGGCATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCATTCA
*
35608405 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A-TT-CA
* * *
35608451 TCTCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATTCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATTCA
35608498 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
35608530 AATGCTCAAC
Statistics
Matches: 104, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 5 0.05
46 57 0.55
47 29 0.28
48 4 0.04
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATTCA
Found at i:35608550 original size:46 final size:43
Alignment explanation
Indices: 35608407--35608550 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 43
35608397 TGCATCCATA
*
35608407 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCC-A---ACATCT
* * * * *
35608454 CA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATTCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTC-GA-ATGC-CA-ACATCT
35608500 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGC-CAA-CAT-CT
35608546 AGTGA
1 AGTGA
35608551 CATGTCACTT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
44 8 0.10
45 3 0.04
46 30 0.39
47 29 0.38
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCAACATCT
Found at i:35613742 original size:46 final size:49
Alignment explanation
Indices: 35613597--35613957 Score: 290
Period size: 46 Copynumber: 7.6 Consensus size: 49
35613587 TGTGTGCTAT
* *
35613597 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-ATTATG-AGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-GATGTAGAGCCAG
* ** * * * *
35613643 TGTAAGACCATGTATGGGACATGGCATCAACATTGAGACG-AGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGAGCCAG
35613691 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGAGCCAG
* *
35613737 TGTAAGA-TATGTCTGGGACAT-GCATCGG-CTGCGAGATGT---GTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGTAGAGCCAG
* * * *
35613781 TGTAAGACCATGTCTGGGACATGGCGTCGG-CACGAATATGTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCG-AGATGT-AGAGCCAG
* * * * ** * * **
35613831 TGTAAGACCATGTGTTGGACATGGCATCAGCCTTGATTTCTATAGTTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGAGCCAG
* * * *
35613880 TGTAAGACCATGTCTGGAACATGGCATC-GACT--TGATGGATGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA-GAGCCAG
35613927 TGTAAGACCATGTCTGGGACATGGCATCGGC
1 TGTAAGACCATGTCTGGGACATGGCATCGGC
35613958 ATTATACCCT
Statistics
Matches: 252, Mismatches: 48, Indels: 28
0.77 0.15 0.09
Matches are distributed among these distances:
44 11 0.04
45 17 0.07
46 73 0.29
47 58 0.23
48 26 0.10
49 32 0.13
50 33 0.13
51 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (49 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAGAGCCAG
Found at i:35613902 original size:49 final size:46
Alignment explanation
Indices: 35613824--35613955 Score: 149
Period size: 47 Copynumber: 2.8 Consensus size: 46
35613814 GAATATGTGA
* * *
35613824 GAGCTAGTGTAAGACCATGTGTTGGACATGGCATCAGCCTTGATTTCTAT
1 GAGCTAGTGTAAGACCATGT-CTGGACATGGCATC-GACTTGA--TCGAT
* *
35613874 -AGTTAGTGTAAGACCATGTCTGGAACATGGCATCGACTTGATGGAT
1 GAGCTAGTGTAAGACCATGTCTGG-ACATGGCATCGACTTGATCGAT
*
35613920 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCTAGTGTAAGACCATGTCT-GGACATGGCATCG
35613956 GCATTATACC
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
46 3 0.04
47 30 0.42
48 11 0.15
49 28 0.39
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (46 bp):
GAGCTAGTGTAAGACCATGTCTGGACATGGCATCGACTTGATCGAT
Done.