Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009350.1 Hibiscus syriacus cultivar Beakdansim tig00113145_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2139524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1245114 original size:109 final size:109
Alignment explanation
Indices: 1245001--1245212 Score: 415
Period size: 109 Copynumber: 1.9 Consensus size: 109
1244991 AAGATTTCAA
1245001 ATAAATAATATGGAAAAAATGATGACTAAATTAAAATAAAATGAAACAGTGAGCCGAAATCAAAA
1 ATAAATAATATGGAAAAAATGATGACTAAATTAAAATAAAATGAAACAGTGAGCCGAAATCAAAA
1245066 TAAACAAAAAAGTTTATGTGATCAATTTATGAATAAACAGAAAC
66 TAAACAAAAAAGTTTATGTGATCAATTTATGAATAAACAGAAAC
*
1245110 ATAAATAATATGTAAAAAATGATGACTAAATTAAAATAAAATGAAACAGTGAGCCGAAATCAAAA
1 ATAAATAATATGGAAAAAATGATGACTAAATTAAAATAAAATGAAACAGTGAGCCGAAATCAAAA
1245175 TAAACAAAAAAGTTTATGTGATCAATTTATGAATAAAC
66 TAAACAAAAAAGTTTATGTGATCAATTTATGAATAAAC
1245213 GACAAAGTTA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (109 bp):
ATAAATAATATGGAAAAAATGATGACTAAATTAAAATAAAATGAAACAGTGAGCCGAAATCAAAA
TAAACAAAAAAGTTTATGTGATCAATTTATGAATAAACAGAAAC
Found at i:1246631 original size:44 final size:44
Alignment explanation
Indices: 1246583--1246681 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
1246573 GTTTTAATTC
*
1246583 ACAAACACCACTATATATCATAACATTTAGCGGCATTTTTGGGA
1 ACAAACACCACTATATATCAGAACATTTAGCGGCATTTTTGGGA
* * ***
1246627 ACAAACACTACTATATGTCAGAACATTTAGCGGCATTTTTTTTA
1 ACAAACACCACTATATATCAGAACATTTAGCGGCATTTTTGGGA
1246671 ACAAACACCAC
1 ACAAACACCAC
1246682 AAAAGAAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.29
Consensus pattern (44 bp):
ACAAACACCACTATATATCAGAACATTTAGCGGCATTTTTGGGA
Found at i:1256773 original size:17 final size:17
Alignment explanation
Indices: 1256725--1256775 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
1256715 TATCAATTTA
1256725 AACTATAATAAAAATAT
1 AACTATAATAAAAATAT
1256742 AA--ATAA-AAAATATAT
1 AACTATAATAAAA-ATAT
1256757 AACTATAATAAAAATAT
1 AACTATAATAAAAATAT
1256774 AA
1 AA
1256776 TTTTATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.13
15 10 0.33
17 12 0.40
18 4 0.13
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (17 bp):
AACTATAATAAAAATAT
Found at i:1256776 original size:11 final size:11
Alignment explanation
Indices: 1256728--1256776 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1256718 CAATTTAAAC
1256728 TATAATAAAAA
1 TATAATAAAAA
1256739 TATAAATAAAAA
1 TAT-AATAAAAA
* *
1256751 -AT-ATATAAC
1 TATAATAAAAA
1256760 TATAATAAAAA
1 TATAATAAAAA
1256771 TATAAT
1 TATAAT
1256777 TTTATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
9 5 0.16
10 2 0.06
11 16 0.52
12 8 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:1258810 original size:26 final size:29
Alignment explanation
Indices: 1258774--1258828 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1258764 AAGACATATT
1258774 AGAAGTG-AA-AG-TGAAAGTGTGCAAAG
1 AGAAGTGAAAGAGATGAAAGTGTGCAAAG
1258800 AGAAGTGAAAGAGAATGAAAGTGTGCAAA
1 AGAAGTGAAAGAG-ATGAAAGTGTGCAAA
1258829 TCGAAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 2 0.08
30 14 0.56
ACGTcount: A:0.49, C:0.04, G:0.33, T:0.15
Consensus pattern (29 bp):
AGAAGTGAAAGAGATGAAAGTGTGCAAAG
Found at i:1258847 original size:30 final size:30
Alignment explanation
Indices: 1258785--1258848 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1258775 GAAGTGAAAG
**
1258785 TGAAAGTGTGCAAAGAGAAGTGAAAGAGAA
1 TGAAAGTGTGCAAAGAGAAGCCAAAGAGAA
** * *
1258815 TGAAAGTGTGCAAATCGAAGCCAATGATAA
1 TGAAAGTGTGCAAAGAGAAGCCAAAGAGAA
1258845 TGAA
1 TGAA
1258849 TTAAAGAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.08, G:0.28, T:0.17
Consensus pattern (30 bp):
TGAAAGTGTGCAAAGAGAAGCCAAAGAGAA
Found at i:1259078 original size:20 final size:20
Alignment explanation
Indices: 1259053--1259100 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1259043 ATATTTAATT
*
1259053 ATTAAGTGTTTGTGTCAAAG
1 ATTAAGTGTTTGTGTCAAAA
1259073 ATTAAGTGTTTGTGTCAAAA
1 ATTAAGTGTTTGTGTCAAAA
1259093 ATTAAGTG
1 ATTAAGTG
1259101 ATTGCCGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTAAGTGTTTGTGTCAAAA
Found at i:1263604 original size:131 final size:130
Alignment explanation
Indices: 1263360--1263728 Score: 397
Period size: 131 Copynumber: 2.8 Consensus size: 130
1263350 ATAATTTTAA
* * * * * * * *
1263360 GAGAGAAAATGATAATATCTAATTATTTCTAATCAATAATAAATGACCTTTCATTCTTTAAA-AT
1 GAGAGAAAATTATAATAT-TAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGA-
* * ***
1263424 AATCATTTATTACTCCAATCGGAAT-ATAGAGATATTACAATTTGGTCTT-AAAATACAATATCG
64 AATCATTTATTACTCCAATCGAAATGA-AGAGATATTACTATTCCATCTTAAAAAT-CAATATCG
*
1263487 ATTT
127 ATTC
* * *
1263491 GAGTGAAAATTATAATATGTAATGATTTCCAATCGAGAATAAACGATCTCTCATACCTTAAAGAA
1 GAGAGAAAATTATAATAT-TAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGAA
* *
1263556 ATCATTTATTACTCCAATCCAAATGAAGAGATATTACTATTCCATCTTAAAAATCAATATTGATT
65 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCCATCTTAAAAATCAATATCGATT
1263621 C
130 C
* * * *
1263622 GAGAGAAAA-TAGTAATATTGAATTATTTCCAATCGAGAATATATAATCTCTCATGCCTTAAAGC
1 GAGAGAAAATTA-TAATATT-AATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGA
* * *
1263686 AATCATTTAATACTCCAA-CTGAAATGAAAATATATTACTATTC
64 AATCATTTATTACTCCAATC-GAAATGAAGAGATATTACTATTC
1263729 TCAATATCGA
Statistics
Matches: 201, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
130 4 0.02
131 190 0.95
132 7 0.03
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (130 bp):
GAGAGAAAATTATAATATTAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGAAA
TCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCCATCTTAAAAATCAATATCGATTC
Found at i:1265930 original size:17 final size:16
Alignment explanation
Indices: 1265908--1265978 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
1265898 ACACAAAGAA
1265908 ATAATACAATTATTAAT
1 ATAATA-AATTATTAAT
*
1265925 ATAATAATATTAATAAT
1 ATAATAA-ATTATTAAT
*
1265942 ATTAATAAATTA-TACT
1 A-TAATAAATTATTAAT
1265958 AATAAT-AA-TATTAAT
1 -ATAATAAATTATTAAT
1265973 A-AATAA
1 ATAATAA
1265979 TATAATAGCG
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.07
14 4 0.09
15 5 0.11
16 8 0.17
17 20 0.43
18 6 0.13
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATAAATTATTAAT
Found at i:1265931 original size:3 final size:3
Alignment explanation
Indices: 1265921--1265985 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
1265911 ATACAATTAT
* * * *
1265921 TAA T-A TAA TAA TAT TAA TAA TAT TAA TAAA TTA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
1265966 TAT TAA TAAA TAA T-A TAA TA
1 TAA TAA T-AA TAA TAA TAA TA
1265986 GCGGGATGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1265953 original size:34 final size:35
Alignment explanation
Indices: 1265909--1265974 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1265899 CACAAAGAAA
1265909 TAATACAATTATTAAT-ATAATAATATTAATAATAT
1 TAATACAATTA-TAATAATAATAATATTAATAATAT
*
1265944 TAATA-AATTATACTAATAATAATATTAATAA
1 TAATACAATTATAATAATAATAATATTAATAA
1265975 ATAATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.10
34 21 0.72
35 5 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (35 bp):
TAATACAATTATAATAATAATAATATTAATAATAT
Found at i:1265969 original size:25 final size:24
Alignment explanation
Indices: 1265918--1265985 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
1265908 ATAATACAAT
1265918 TATTAATATAATAATAT--TAATAA
1 TATTAATA-AATAATATAATAATAA
*
1265941 TATTAATAAATTATACTAATAATAA
1 TATTAATAAATAATA-TAATAATAA
1265966 TATTAATAAATAATATAATA
1 TATTAATAAATAATATAATA
1265986 GCGGGATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.15
23 9 0.22
24 5 0.12
25 20 0.50
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
TATTAATAAATAATATAATAATAA
Found at i:1265983 original size:9 final size:9
Alignment explanation
Indices: 1265916--1265974 Score: 70
Period size: 9 Copynumber: 6.9 Consensus size: 9
1265906 AAATAATACA
*
1265916 ATTATTAAT
1 ATTAATAAT
1265925 A-TAATAAT
1 ATTAATAAT
1265933 ATTAATAAT
1 ATTAATAAT
1265942 ATTAATAA-
1 ATTAATAAT
*
1265950 ATT-ATACT
1 ATTAATAAT
*
1265958 AATAATAAT
1 ATTAATAAT
1265967 ATTAATAA
1 ATTAATAA
1265975 ATAATATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
7 3 0.07
8 12 0.29
9 27 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTAATAAT
Found at i:1266457 original size:135 final size:133
Alignment explanation
Indices: 1266161--1266509 Score: 382
Period size: 135 Copynumber: 2.6 Consensus size: 133
1266151 AAACGTTGGC
* * * * * * *
1266161 TCATTCCATTATTCTTTA-GAGAAGATTGAAT-AGAGGCATATTTGTTCCATTATTACTCAAGGA
1 TCATTCCACTATTCTTCACG-GAAGATTGAATCA-AGGAAGATTTGTTCCACTGTTCCTCAAGGA
* * * *
1266224 AGATCAAATCTGGAAGAGAGGGATCTGTTCCACTACTTCTTGATGGAAAATCAGATATGGAATCG
64 AGATCAAATCTGGAAAAGAAGGATCTGTTCCACTACTTCTTGAGGGAAAATCAGATATGAAATCG
1266289 TTGAT
129 TTGAT
* * *
1266294 TCATTCTACTATTCTTCACGGAAGATTGAATCAA-TATAGATTTGTTCCACTGTTCCACAAGGAA
1 TCATTCCACTATTCTTCACGGAAGATTGAATCAAGGA-AGATTTGTTCCACTGTTCCTCAAGGAA
* * * * * *
1266358 GATCAAATCTGGAAAATGAAGGATTTGTTCCGCTGCTTCTTGGGGGGAAATCAGATCTGAAAAAT
65 GATCAAATCTGGAAAA-GAAGGATCTGTTCCACTACTTCTTGAGGGAAAATCAGATATG--AAAT
1266423 -GTTGAT
127 CGTTGAT
* * * * * *
1266429 TCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGAAGACTTGTTCAACTGTTCGTCAGGGAAG
1 TCATTCCACTATTCTTCACGGAAGATTGAATCAAGGAAGATTTGTTCCACTGTTCCTCAAGGAAG
1266494 ATCAAATCTGGAAAAG
66 ATCAAATCTGGAAAAG
1266510 GAGGGGATAT
Statistics
Matches: 180, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
133 64 0.36
134 37 0.21
135 75 0.42
136 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (133 bp):
TCATTCCACTATTCTTCACGGAAGATTGAATCAAGGAAGATTTGTTCCACTGTTCCTCAAGGAAG
ATCAAATCTGGAAAAGAAGGATCTGTTCCACTACTTCTTGAGGGAAAATCAGATATGAAATCGTT
GAT
Found at i:1266544 original size:135 final size:130
Alignment explanation
Indices: 1266218--1266594 Score: 387
Period size: 135 Copynumber: 2.8 Consensus size: 130
1266208 CATTATTACT
* * * *
1266218 CAAGGAAGATCAAATCTGGAAGAGAGGGATCTGTTCCACTACTTCTTGATGGAAAATCAGATATG
1 CAAGGAAGATCAAATCTGGAAAAGAGGGATATGTTCCA-TGCTTCTTGA-GGAAAATCAGATCTG
* * * * * *
1266283 GAATCGTTGATTCATTCTACTATTCTTCACGGAAGATTGAATCAATATAGATTTGTTCCACTGTT
64 GAAT-GTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCAAGATAGACTTGTTCAACTGTT
1266348 CCA
128 CCA
* * * * *
1266351 CAAGGAAGATCAAATCTGGAAAATGAAGGATTTGTTCCGCTGCTTCTTGGGGGGAAATCAGATCT
1 CAAGGAAGATCAAATCTGGAAAA-GAGGGATATGTTCC-ATGCTTCTT-GAGGAAAATCAGATCT
* *
1266416 GAAAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGA-AGACTTGTTCAACT
63 G--GAATGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCAA-GATAGACTTGTTCAACT
**
1266480 GTTCGT
125 GTTCCA
* * *
1266486 CAGGGAAGATCAAATCTGGAAAAGGAGGGGATATGTTCTCATGTTTCTTCAGGAAAATCAGATCC
1 CAAGGAAGATCAAATCTGGAAAA-GA-GGGATATGTTC-CATGCTTCTTGAGGAAAATCAGAT-C
* * ** *
1266551 GGGGACCTTGATTTATTCCACTGTTCTTCAAGGAAGATTGAATC
62 TGGAATGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATC
1266595 GGGTTCGATT
Statistics
Matches: 202, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
133 22 0.11
134 68 0.34
135 89 0.44
136 22 0.11
137 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (130 bp):
CAAGGAAGATCAAATCTGGAAAAGAGGGATATGTTCCATGCTTCTTGAGGAAAATCAGATCTGGA
ATGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAATCAAGATAGACTTGTTCAACTGTTCCA
Found at i:1267838 original size:14 final size:15
Alignment explanation
Indices: 1267821--1267854 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1267811 CCCCCTTTTA
1267821 TTTTTTC-TCTTTCT
1 TTTTTTCTTCTTTCT
*
1267835 TTTTTTCTTTTTTCT
1 TTTTTTCTTCTTTCT
1267850 TTTTT
1 TTTTT
1267855 CATTTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTCTTTCT
Found at i:1267845 original size:7 final size:7
Alignment explanation
Indices: 1267816--1267872 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
1267806 TTGAACCCCC
*
1267816 TTTTATT
1 TTTTCTT
1267823 TTTTC-T
1 TTTTCTT
*
1267829 CTTTCTTT
1 TTTTC-TT
1267837 TTTTCTT
1 TTTTCTT
1267844 TTTTCTT
1 TTTTCTT
*
1267851 TTTTCAT
1 TTTTCTT
* *
1267858 TTCTCAT
1 TTTTCTT
1267865 TTTTCTT
1 TTTTCTT
1267872 T
1 T
1267873 CTTCAGGCGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 5 0.12
7 31 0.76
8 5 0.12
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:1274291 original size:2 final size:2
Alignment explanation
Indices: 1274286--1274317 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1274276 AATTTTTTTG
1274286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1274318 CTCTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1283148 original size:195 final size:196
Alignment explanation
Indices: 1282823--1283545 Score: 829
Period size: 199 Copynumber: 3.7 Consensus size: 196
1282813 ATTTTCATTT
* * * * * * * ** *
1282823 TTTCATTTATTTTCAATTCTTAAAGTATCGATACTATGGTACATATACTTATAGCAGTATTGATA
1 TTTCAATTCTTTTAAATTCCTAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATA
* * *
1282888 C-CA--TCAA-CATATCTGATAG-TGCTTTACCGGTTTTGTCAAATTGAAA-CTGGATTTT-TCA
66 CAAATGTCAACCATTTC-GGTAGCT-CTTTACCGGTTTTGTCAAATTGAAATC-GG-TTTTGTCA
* * *
1282946 AATTTCAACCTGTTACATTGTCATGTATCGATACATGTGCCTAAGGTATCAATACTTTATAGCTC
127 AATTTCAACCTGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGCTC
1283011 TATTA
192 TATTA
* * *
1283016 TTGCAATTCTTTTAAATTCCTAAAGTACCAATACTCTGGTACATATACTTATAAAAGTATCAATA
1 TTTCAATTCTTTTAAATTCCTAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATA
** *
1283081 CAAATGTCAACCA-TTCTGGTAGCTCTTTATTGG-TTTGTCAAATTGAAATCGGTTTTGTTAAAT
66 CAAATGTCAACCATTTC-GGTAGCTCTTTACCGGTTTTGTCAAATTGAAATCGGTTTTGTCAAAT
* **
1283144 TTCAACCTGTTATATTGTCATGTATCTATACATGTGTCTAAGGTATCGATACTTTATAGGAGCTA
130 TTCAACCTGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATA-GCTCTA
1283209 TTA
194 TTA
* * * * *
1283212 TTTTAATTCTTTTAAATTCATAAAGTACCGATACTTTGGTACATATACTTATAAAGGTATTGATA
1 TTTCAATTCTTTTAAATTCCTAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATA
* **
1283277 CAAATGTCAACCATTTCGGTAGCTCTTTACCGGTTTTATCAAATTGAAATCAATTTTGTCAAATT
66 CAAATGTCAACCATTTCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAATCGGTTTTGTCAAATT
* * ** *
1283342 TCAACCTGTTATATTGTCATGTATCGATACATGTGTGTAAGGTATTGATACTTTCGAGACGT-TT
131 TCAACCTGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAG-C-TCTA
*
1283406 TCCTT
194 T--TA
* * *
1283411 TTTCATTTCTTTTAAATTCCTATAGTACCAATACTTTGGTACATATACTTATAAATGTATCGATA
1 TTTCAATTCTTTTAAATTCCTAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATA
* * * * * * *
1283476 CAAATTTCAACAATTTCGATAGCTCTTTACCAGTTTTCTCAAATTGAAACTAGG-TTTATCAAAT
66 CAAATGTCAACCATTTCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAA-TCGGTTTTGTCAAAT
1283540 TTCAAC
130 TTCAAC
1283546 TGGTTTTGCC
Statistics
Matches: 452, Mismatches: 63, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
193 54 0.12
194 5 0.01
195 76 0.17
196 111 0.25
197 87 0.19
199 118 0.26
200 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.41
Consensus pattern (196 bp):
TTTCAATTCTTTTAAATTCCTAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATA
CAAATGTCAACCATTTCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAATCGGTTTTGTCAAATT
TCAACCTGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTATAGCTCTATT
A
Found at i:1283523 original size:199 final size:197
Alignment explanation
Indices: 1282790--1283524 Score: 823
Period size: 197 Copynumber: 3.7 Consensus size: 197
1282780 TACTTTCGTG
* * * * * * * *
1282790 TAAGGTATCGATACTTTTGAGACATTTTCATTTTTTCATTTATTTTCAATTCTTAAAGTATCGAT
1 TAAGGTATCGATACTTTAGAGAC-GTTT--TTTTTTCAATTCTTTTAAATTCCTAAAGTACCAAT
* * * * *
1282855 ACTATGGTACATATACTTATAGCAGTATTGATAC-CA--TCAA-CATATCTGATAG-TGCTTTAC
63 ACTTTGGTACATATACTTATA-AAGTATCGATACAAATGTCAACCATTTCTGATAGCT-CTTTAC
* *
1282915 CGGTTTTGTCAAATTGAAACTGGATTTT-TCAAATTTCAACCTGTTACATTGTCATGTATCGATA
126 CGGTTTTGTCAAATTGAAA-TCGATTTTGTCAAATTTCAACCTGTTATATTGTCATGTATCGATA
*
1282979 CATGTGCC
190 CATGTGTC
* * * * *
1282987 TAAGGTATCAATACTTTATAG-C-TCTATTATTGCAATTCTTTTAAATTCCTAAAGTACCAATAC
1 TAAGGTATCGATACTTTAGAGACGT-TTTTTTTTCAATTCTTTTAAATTCCTAAAGTACCAATAC
* * * **
1283050 TCTGGTACATATACTTATAAAAGTATCAATACAAATGTCAACCA-TTCTGGTAGCTCTTTATTGG
65 TTTGGTACATATACTTAT-AAAGTATCGATACAAATGTCAACCATTTCTGATAGCTCTTTACCGG
* * *
1283114 -TTTGTCAAATTGAAATCGGTTTTGTTAAATTTCAACCTGTTATATTGTCATGTATCTATACATG
129 TTTTGTCAAATTGAAATCGATTTTGTCAAATTTCAACCTGTTATATTGTCATGTATCGATACATG
1283178 TGTC
194 TGTC
* * * * *
1283182 TAAGGTATCGATACTTTATAGGA-GCTATTATTTT-AATTCTTTTAAATTCATAAAGTACCGATA
1 TAAGGTATCGATACTTTAGA-GACG-TTTTTTTTTCAATTCTTTTAAATTCCTAAAGTACCAATA
* *
1283245 CTTTGGTACATATACTTATAAAGGTATTGATACAAATGTCAACCATTTC-GGTAGCTCTTTACCG
64 CTTTGGTACATATACTTATAAA-GTATCGATACAAATGTCAACCATTTCTGATAGCTCTTTACCG
* *
1283309 GTTTTATCAAATTGAAATCAATTTTGTCAAATTTCAACCTGTTATATTGTCATGTATCGATACAT
128 GTTTTGTCAAATTGAAATCGATTTTGTCAAATTTCAACCTGTTATATTGTCATGTATCGATACAT
*
1283374 GTGTG
193 GTGTC
* * * *
1283379 TAAGGTATTGATACTTTCGAGACGTTTTCCTTTTTCATTTCTTTTAAATTCCTATAGTACCAATA
1 TAAGGTATCGATACTTTAGAGACGTTTT--TTTTTCAATTCTTTTAAATTCCTAAAGTACCAATA
* * *
1283444 CTTTGGTACATATACTTATAAATGTATCGATACAAATTTCAACAATTTC-GATAGCTCTTTACCA
64 CTTTGGTACATATACTTATAAA-GTATCGATACAAATGTCAACCATTTCTGATAGCTCTTTACCG
*
1283508 GTTTTCTCAAATTGAAA
128 GTTTTGTCAAATTGAAA
1283525 CTAGGTTTAT
Statistics
Matches: 457, Mismatches: 62, Indels: 36
0.82 0.11 0.06
Matches are distributed among these distances:
193 55 0.12
194 9 0.02
195 78 0.17
196 104 0.23
197 107 0.23
198 5 0.01
199 99 0.22
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.41
Consensus pattern (197 bp):
TAAGGTATCGATACTTTAGAGACGTTTTTTTTTCAATTCTTTTAAATTCCTAAAGTACCAATACT
TTGGTACATATACTTATAAAGTATCGATACAAATGTCAACCATTTCTGATAGCTCTTTACCGGTT
TTGTCAAATTGAAATCGATTTTGTCAAATTTCAACCTGTTATATTGTCATGTATCGATACATGTG
TC
Found at i:1283546 original size:20 final size:19
Alignment explanation
Indices: 1283523--1283582 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 19
1283513 CTCAAATTGA
1283523 AACTAGGTTTATCAAATTTC
1 AACT-GGTTTATCAAATTTC
*
1283543 AACTGGTTT-TGCCAATTTCC
1 AACTGGTTTAT-CAAATTT-C
1283563 AA-TCGGTTTAGTCAAATTTC
1 AACT-GGTTTA-TCAAATTTC
1283583 GTTACCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 1 0.03
19 12 0.36
20 13 0.39
21 6 0.18
22 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (19 bp):
AACTGGTTTATCAAATTTC
Found at i:1283668 original size:21 final size:18
Alignment explanation
Indices: 1283632--1283672 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
1283622 TTCACCATGT
1283632 TATATTGTTAAGTATCGA
1 TATATTGTTAAGTATCGA
1283650 TATATGTGTGTAAGGTATCGA
1 TATAT-TGT-TAA-GTATCGA
1283671 TA
1 TA
1283673 CTTCGTAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 3 0.15
21 9 0.45
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (18 bp):
TATATTGTTAAGTATCGA
Found at i:1297313 original size:12 final size:12
Alignment explanation
Indices: 1297296--1297323 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1297286 CCTAATTTGG
1297296 ATCATCCTCTTC
1 ATCATCCTCTTC
1297308 ATCATCCTCTTC
1 ATCATCCTCTTC
1297320 ATCA
1 ATCA
1297324 CTATGTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (12 bp):
ATCATCCTCTTC
Found at i:1298256 original size:59 final size:59
Alignment explanation
Indices: 1298164--1298284 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 59
1298154 TGAGGGTTGG
* * * ** * **
1298164 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTGCGACTAGGAGGTTTTGATAGGACAC
1 TTAGAGCCATATTATCAAGTTTGCATTTTCATTGAAACTAGGAGGGTTCAATAGGACAC
*
1298223 TTAGAGCCATATTATCAAGTTTGCATTTTCATTGAAACTAGGTGGGTTCAATAGGACAC
1 TTAGAGCCATATTATCAAGTTTGCATTTTCATTGAAACTAGGAGGGTTCAATAGGACAC
1298282 TTA
1 TTA
1298285 TCCATCTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCAAGTTTGCATTTTCATTGAAACTAGGAGGGTTCAATAGGACAC
Found at i:1300564 original size:17 final size:17
Alignment explanation
Indices: 1300542--1300575 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1300532 TCATCATGTT
* *
1300542 AATTTTGAATTTGAATA
1 AATTTTAAATTTAAATA
1300559 AATTTTAAATTTAAATA
1 AATTTTAAATTTAAATA
1300576 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AATTTTAAATTTAAATA
Found at i:1303013 original size:16 final size:16
Alignment explanation
Indices: 1302992--1303023 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1302982 AACATAGATT
*
1302992 AAGACAATAAAAAATA
1 AAGACAAGAAAAAATA
1303008 AAGACAAGAAAAAATA
1 AAGACAAGAAAAAATA
1303024 TGGATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.06, G:0.09, T:0.09
Consensus pattern (16 bp):
AAGACAAGAAAAAATA
Found at i:1309322 original size:12 final size:11
Alignment explanation
Indices: 1309289--1309336 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
1309279 TATATAACAT
1309289 TTTTTTATTTGA
1 TTTTTTATTT-A
1309301 TTTATTTATTTA
1 TTT-TTTATTTA
*
1309313 CTTTTTTATTTT
1 -TTTTTTATTTA
1309325 TATTTTTATTTA
1 T-TTTTTATTTA
1309337 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 20 0.65
13 10 0.32
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:1314181 original size:27 final size:27
Alignment explanation
Indices: 1314139--1314200 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
1314129 TGATTACACT
* *
1314139 TAGCTCAAAGGTACATCATTTGTAGCA
1 TAGCTCAAAGGCACATCATTTGCAGCA
1314166 TAGCTCAAAGGCACATCATTTGCAGCA
1 TAGCTCAAAGGCACATCATTTGCAGCA
1314193 TAGCTCAA
1 TAGCTCAA
1314201 GGCGAGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (27 bp):
TAGCTCAAAGGCACATCATTTGCAGCA
Found at i:1314250 original size:111 final size:111
Alignment explanation
Indices: 1314056--1314284 Score: 404
Period size: 111 Copynumber: 2.1 Consensus size: 111
1314046 GATTACAGTC
* * *
1314056 AGCTCAAAGGCACATCATTTGCAGCATAATTCAAGGCGAGAAGGGTTATCTACCAATAAAAGACC
1 AGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTACCAACAAAAGACC
*
1314121 TTCGAGTTTGATTACACTTAGCTCAAAGGTACATCATTTGTAGCAT
66 TTCGAGTTTGATTACACTTAGCTCAAAGGGACATCATTTGTAGCAT
* *
1314167 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
1 AGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTACCAACAAAAGACC
1314232 TTCGAGTTTGATTACACTTAGCTCAAAGGGACATCATTTGTAGCAT
66 TTCGAGTTTGATTACACTTAGCTCAAAGGGACATCATTTGTAGCAT
1314278 AGCTCAA
1 AGCTCAA
1314285 GCCGAGAAGG
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (111 bp):
AGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTACCAACAAAAGACC
TTCGAGTTTGATTACACTTAGCTCAAAGGGACATCATTTGTAGCAT
Found at i:1314401 original size:83 final size:84
Alignment explanation
Indices: 1314167--1314449 Score: 460
Period size: 84 Copynumber: 3.4 Consensus size: 84
1314157 TTTGTAGCAT
1314167 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
1 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
* *
1314232 TTCGAGTTTGATTACACTT
66 TTCGAGTTCGATTACACTC
* * * * *
1314251 AGCTCAAAGGGACATCATTTGTAGCATAGCTCAAGCCGAGAAGGGCTATCTGCCAACAACAGGCC
1 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
1314316 TTCGAGTTCGATTACACTC
66 TTCGAGTTCGATTACACTC
* * * *
1314335 AGCTTAAAGGCACA-CATTTGCAGCATAGCTCAAGGAGAGAATGACTATCTGCCAACAAAAGACC
1 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
1314399 TTCGAGTTCGATTACACTC
66 TTCGAGTTCGATTACACTC
1314418 AGCTCAAAGGCACATCATTTGCAGCATAGCTC
1 AGCTCAAAGGCACATCATTTGCAGCATAGCTC
1314450 TGCCGACAAA
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
83 75 0.41
84 106 0.59
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (84 bp):
AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
TTCGAGTTCGATTACACTC
Found at i:1314493 original size:66 final size:66
Alignment explanation
Indices: 1314382--1314515 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
1314372 AGAATGACTA
1314382 TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAG
1 TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAG
1314447 C
66 C
* * *
1314448 TCTGCCGACAAAAGACCTTCGAGTTTGATTACACTCAGCTTAAAGGCACATCATTTGCAGCATAG
1 TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAG
1314513 C
66 C
1314514 TC
1 TC
1314516 AAGGCGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (66 bp):
TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAG
C
Found at i:1314569 original size:150 final size:149
Alignment explanation
Indices: 1314299--1314580 Score: 467
Period size: 150 Copynumber: 1.9 Consensus size: 149
1314289 AGAAGGGCTA
* *
1314299 TCTGCCAACAACAGGCCTTCGAGTTCGATTACACTCAGCTTAAAGGCACACATTTGCAGCATAGC
1 TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACACATTTGCAGCATAGC
* *
1314364 TCAAGGAGAGAATGACTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
66 TCAAGGAGAAAAGGACTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
1314429 ACATCATTTGCAGCATAGC
131 ACATCATTTGCAGCATAGC
* *
1314448 TCTGCCGACAAAAGACCTTCGAGTTTGATTACACTCAGCTTAAAGGCACATCATTTGCAGCATAG
1 TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACA-CATTTGCAGCATAG
* *
1314513 CTCAAGGCGAAAAAGGA-TATCTGCCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAAG
65 CTCAAGGAG-AAAAGGACTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
1314577 GCAC
129 GCAC
1314581 GTCAAATTTA
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
149 46 0.37
150 72 0.59
151 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (149 bp):
TCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACACATTTGCAGCATAGC
TCAAGGAGAAAAGGACTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
ACATCATTTGCAGCATAGC
Found at i:1314657 original size:85 final size:85
Alignment explanation
Indices: 1314458--1315099 Score: 654
Period size: 85 Copynumber: 7.6 Consensus size: 85
1314448 TCTGCCGACA
* * *
1314458 AAAGACCTTCGAGTTTGATTACACTCAGCTTAAAGGCACATC--ATTTGCAGCATAGCTCAAGGC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGGC
* * * *
1314521 GAAAAAGGATATCTGCCAAC
66 GAGAAGGGTTATCTGTCAAC
* * *
1314541 AAAATACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGTATAGCTCAAGG
1 -AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGG
1314606 CGAGAAGGGTTATCTGTCAAC
65 CGAGAAGGGTTATCTGTCAAC
* ** *
1314627 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA--T---ATTTACAATATAACTCAAGGC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGGC
* *
1314687 AAGAAGGGTTATTTGTCAAC
66 GAGAAGGGTTATCTGTCAAC
* * *** *
1314707 CAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGATGCGTCCAATTTACAGCATAGCTCAAGGC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGGC
1314772 GAGAAGGGTTATCTGTCAAC
66 GAGAAGGGTTATCTGTCAAC
* * *
1314792 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCCAATTTATAGCATAGCTCAAGGC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGGC
*
1314857 GAGAAGGGCTATCTGTCAAC
66 GAGAAGGGTTATCTGTCAAC
* * * ** * * *
1314877 AAAAGACCTTCGAGTTTGGTTACACTTAGCTCTAAGGCATATCAAATGTACAACATAACTCAAGG
1 -AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGG
*
1314942 CGAGAAGGGTTATCTATCAAC
65 CGAGAAGGGTTATCTGTCAAC
* ** * * * * * ** ** *
1314963 AAATACCTTTAAGTTTGATTCCATTCAGTTC-AAGGGATGTCAAATTTACAGTTTAGCTTGAGTC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGGC
** * **
1315027 GAGAAAAGCTATCCATCAAC
66 GAGAAGGGTTATCTGTCAAC
* * * * * *
1315047 -AAGAAACTGTCGAGTTCGATTTCATTCAGCTCAAGGGCATGTCAAATTTACAG
1 AAAG-ACCT-TCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAG
1315100 TTTAGCCTGA
Statistics
Matches: 471, Mismatches: 76, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
80 69 0.15
82 1 0.00
83 3 0.01
84 80 0.17
85 191 0.41
86 127 0.27
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (85 bp):
AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACGTCAAATTTACAGCATAGCTCAAGGC
GAGAAGGGTTATCTGTCAAC
Found at i:1314767 original size:165 final size:166
Alignment explanation
Indices: 1314458--1314982 Score: 653
Period size: 165 Copynumber: 3.1 Consensus size: 166
1314448 TCTGCCGACA
* *
1314458 AAAGACCTTCGAGTTTGATTACACTCAGCTTAAAGGCACATCATTTGCAGCATAGCTCAAGGCGA
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGG-ACATCATTTACAGCATAGCTCAAGGC-A
* * * *
1314523 A-AAAGGATATCTGCCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCAAA
64 AGAAGGGATATCTGTCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGG--CGTCAAA
*
1314587 TTTACAGTATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC
127 TTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC
* ** *
1314627 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG-CAT-ATTTACAATATAACTCAAGGCAAG
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGACATCATTTACAGCATAGCTCAAGGCAAG
* * * * *
1314690 AAGGGTTATTTGTCAAC-CAAGACCTTTGAGTTTGATTACACTCAGCTCAAAGATGCGTCCAATT
66 AAGGGATATCTGTCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAG--GCGTCAAATT
1314754 TACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC
129 TACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC
*
1314792 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCCAATTTATAGCATAGCTCAAGGC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGG-ACAT-C-ATTTACAGCATAGCTCAAGGC
* * * * * *
1314857 GAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTTGGTTACACTTAGCTCTAAGGCATATCAA
63 AAGAAGGGATATCTGTCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGC--GTCAA
* * * *
1314922 ATGTACAACATAACTCAAGGCGAGAAGGGTTATCTATCAAC
126 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC
* **
1314963 AAATACCTTTAAGTTTGATT
1 AAAGACCTTCGAGTTTGATT
1314983 CCATTCAGTT
Statistics
Matches: 307, Mismatches: 38, Indels: 20
0.84 0.10 0.05
Matches are distributed among these distances:
165 113 0.37
166 30 0.10
167 7 0.02
169 36 0.12
170 34 0.11
171 87 0.28
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (166 bp):
AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGACATCATTTACAGCATAGCTCAAGGCAAG
AAGGGATATCTGTCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCGTCAAATTTA
CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC
Found at i:1315098 original size:86 final size:85
Alignment explanation
Indices: 1314974--1315164 Score: 283
Period size: 86 Copynumber: 2.2 Consensus size: 85
1314964 AATACCTTTA
* * * *
1314974 AGTTTGATTCCATTCAGTTCAAGGGATGTCAAATTTACAGTTTAGCTTGAGTCGAGAAAAGCTAT
1 AGTTCGATTCCATTCAGCTCAAGGGATGTCAAATTTACAGTTTAGCCTGAGTCGAGAAAAGATAT
*
1315039 CCATCAACAAGAAACTGTCG
66 CCATCAACAAGAAACTATCG
*
1315059 AGTTCGATTTCATTCAGCTCAAGGGCATGTCAAATTTACAGTTTAGCCTGAGTCGAGAAAAGATA
1 AGTTCGATTCCATTCAGCTCAAGGG-ATGTCAAATTTACAGTTTAGCCTGAGTCGAGAAAAGATA
* * *
1315124 TTCGTCAACAAGAAACTATTG
65 TCCATCAACAAGAAACTATCG
*
1315145 AGTTCGATTCCATTTAGCTC
1 AGTTCGATTCCATTCAGCTC
1315165 GATGACACAT
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 22 0.23
86 72 0.77
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (85 bp):
AGTTCGATTCCATTCAGCTCAAGGGATGTCAAATTTACAGTTTAGCCTGAGTCGAGAAAAGATAT
CCATCAACAAGAAACTATCG
Found at i:1316636 original size:12 final size:12
Alignment explanation
Indices: 1316619--1316652 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1316609 TTTCTTTGAT
1316619 TTATTTATTTTC
1 TTATTTATTTTC
1316631 TTATTTATTTTTC
1 TTATTTA-TTTTC
1316644 TT-TTTATTT
1 TTATTTATTT
1316653 AATTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 11 0.52
13 7 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTATTTTC
Found at i:1316653 original size:32 final size:31
Alignment explanation
Indices: 1316601--1316683 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 31
1316591 TGTAACATTT
* *
1316601 TTTATTTTT-TTCTTTGATTTATTTATTTTCTTA
1 TTTATTTTTCTT-TTT-ATTTAATTAATTT-TTA
1316634 TTTATTTTTCTTTTTATTTAATTAATTTTTA
1 TTTATTTTTCTTTTTATTTAATTAATTTTTA
* *
1316665 TTCGATATTTC-TTTTATTT
1 TT-TATTTTTCTTTTTATTT
1316684 TTCCATCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 13 0.30
32 17 0.39
33 12 0.27
34 2 0.05
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.73
Consensus pattern (31 bp):
TTTATTTTTCTTTTTATTTAATTAATTTTTA
Found at i:1317169 original size:19 final size:19
Alignment explanation
Indices: 1317145--1317187 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1317135 ACATATACTA
* *
1317145 TATTATAATTACTCCAAAC
1 TATTATAATAACCCCAAAC
*
1317164 TATTATAGTAACCCCAAAC
1 TATTATAATAACCCCAAAC
1317183 TATTA
1 TATTA
1317188 AAAATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (19 bp):
TATTATAATAACCCCAAAC
Found at i:1318032 original size:25 final size:23
Alignment explanation
Indices: 1318004--1318052 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 23
1317994 ATAGTTGTGA
1318004 AATTTATTA-ATTAAATTATATCATT
1 AATTT-TTATATTAAA-TAT-TCATT
1318029 AATTTTTATATTAAATATTCATT
1 AATTTTTATATTAAATATTCATT
1318052 A
1 A
1318053 TAGATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
24 6 0.26
25 11 0.48
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTTTATATTAAATATTCATT
Found at i:1320911 original size:3 final size:3
Alignment explanation
Indices: 1320903--1320929 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1320893 GAGGTAAAGA
1320903 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1320930 TATGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1322734 original size:29 final size:29
Alignment explanation
Indices: 1322694--1322770 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
1322684 ATTATAGGTA
* *
1322694 TTATTGTAATTTATGAGA-AGTTTT-TTCT
1 TTATTGTAATTTAT-AAATAGTTTTGTTAT
1322722 TTGATTGTAATTTATAAATAGTTTTGTTAT
1 TT-ATTGTAATTTATAAATAGTTTTGTTAT
*
1322752 TTATTGTAATATTAAAAAT
1 TTATTGTAAT-TTATAAAT
1322771 TGACTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.10
29 26 0.62
30 12 0.29
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (29 bp):
TTATTGTAATTTATAAATAGTTTTGTTAT
Found at i:1322844 original size:15 final size:15
Alignment explanation
Indices: 1322815--1322849 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1322805 TTTTATCGTA
*
1322815 ATTTT-ATAATTTTT
1 ATTTTAATAATATTT
1322829 ATTTTAATAATATTT
1 ATTTTAATAATATTT
1322844 ATTTTA
1 ATTTTA
1322850 GAAATTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTAATAATATTT
Found at i:1323087 original size:19 final size:19
Alignment explanation
Indices: 1323059--1323102 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1323049 AATACAACGT
*
1323059 CACACTAGACATTTAGTGA
1 CACACCAGACATTTAGTGA
1323078 CACACCAGACATTTAGTGA
1 CACACCAGACATTTAGTGA
1323097 CACACC
1 CACACC
1323103 TAGGGTGACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (19 bp):
CACACCAGACATTTAGTGA
Found at i:1323961 original size:3 final size:3
Alignment explanation
Indices: 1323953--1323992 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1323943 TTGTCCAGGT
1323953 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1323993 TTATATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1324002 original size:3 final size:3
Alignment explanation
Indices: 1323996--1324077 Score: 155
Period size: 3 Copynumber: 27.3 Consensus size: 3
1323986 TAATAATTTA
*
1323996 TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1324044 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1324078 TATTTATTCT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1334431 original size:16 final size:16
Alignment explanation
Indices: 1334406--1334448 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1334396 CAGTTAGTAA
*
1334406 TTAGCGGTTAGAAATG
1 TTAGCGGTTAGAAAAG
*
1334422 TTAGCTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
1334438 TTAGCGGTTAG
1 TTAGCGGTTAG
1334449 CAGAGTCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:1334548 original size:7 final size:7
Alignment explanation
Indices: 1334536--1334566 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1334526 TTAATAAAAT
1334536 AAAATAA
1 AAAATAA
1334543 AAAAT-A
1 AAAATAA
1334549 AAAATAA
1 AAAATAA
1334556 AAAATAA
1 AAAATAA
1334563 AAAA
1 AAAA
1334567 AAGTTAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:1334554 original size:13 final size:13
Alignment explanation
Indices: 1334531--1334565 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1334521 ACAAATTAAT
1334531 AAAAT-AAAATAA
1 AAAATAAAAATAA
1334543 AAAATAAAAATAA
1 AAAATAAAAATAA
1334556 AAAATAAAAA
1 AAAATAAAAA
1334566 AAAGTTAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:1336059 original size:139 final size:138
Alignment explanation
Indices: 1335893--1336448 Score: 698
Period size: 138 Copynumber: 4.0 Consensus size: 138
1335883 ATTTTTGGAT
* * * * * * *
1335893 ATAATTTGGGGACAACACAATTTCTATGTGATGCGAAAGTTTGGTTATCTGAGGATGACGCTGCT
1 ATAATTT-GAGACAACACGATTCCTATGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCT
* *
1335958 CCTACGCGTTGAGGAGATTTAGTCGGTTGACGACATTGTTCTTACGTGATGAGGACGTCTAGCCA
65 CCTACGCGTTGAGGAGATTTAGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCA
1336023 TCTTTAGGG
130 TCTTTAGGG
* * **
1336032 ATAATTTGGAGACAACACGGTTCCTATGTGATGAGGAAGTTTGATTGCCTGAGGATGACGCTGCT
1 ATAATTT-GAGACAACACGATTCCTATGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCT
* * * * * * *
1336097 CCTACGCGTTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTACGTCATGAGGATGTCTAGTCG
65 CCTACGCGTTGAGGAGATTTAGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCA
1336162 TCTTTAGGG
130 TCTTTAGGG
* * * * *
1336171 ATAATTTGAGATAACACGATTCCTATGTGATGATGAAGTCTGGTTATCTGAGGATGACACTGCTT
1 ATAATTTGAGACAACACGATTCCTATGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTC
* * * * * * *
1336236 CTACGTGTTAAGGAGATTTAGTTGGTGGATGACATTATTCCTACGTGATGATGATGTCTAGCCAT
66 CTACGCGTTGAGGAGATTTAGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCAT
1336301 CTTTAGGG
131 CTTTAGGG
* * * * *
1336309 ATAATTTGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTGTCTGAAGATGAAGCTGCTC
1 ATAATTTGAGACAACACGATTCCTATGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTC
** * * * *
1336374 CTATACGTTGAGCAGATTTGGTCGGTGGATGACATTGTTCCTACGTGATAAGGACGTCTAGCCAT
66 CTACGCGTTGAGGAGATTTAGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCAT
*
1336439 ATTTAGGG
131 CTTTAGGG
1336447 AT
1 AT
1336449 TATAACATCC
Statistics
Matches: 357, Mismatches: 60, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
138 228 0.64
139 129 0.36
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (138 bp):
ATAATTTGAGACAACACGATTCCTATGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTC
CTACGCGTTGAGGAGATTTAGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCAT
CTTTAGGG
Found at i:1338086 original size:22 final size:23
Alignment explanation
Indices: 1338038--1338087 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1338028 TTGAGGATTC
*
1338038 TACGCGGTCCTTTGAGACAATTC
1 TACGCGGTCCTTTGAGACAATTA
* * *
1338061 TACGTGGTCC-TTGGGACATTTA
1 TACGCGGTCCTTTGAGACAATTA
1338083 TACGC
1 TACGC
1338088 TGTTATTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (23 bp):
TACGCGGTCCTTTGAGACAATTA
Found at i:1341170 original size:18 final size:17
Alignment explanation
Indices: 1341147--1341180 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1341137 AGAGCCTTGC
1341147 TTCCCATCTTAACTCTAT
1 TTCCCATCTTAA-TCTAT
*
1341165 TTCCCATGTTAATCTA
1 TTCCCATCTTAATCTA
1341181 ACCTAACCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (17 bp):
TTCCCATCTTAATCTAT
Found at i:1344096 original size:20 final size:21
Alignment explanation
Indices: 1344068--1344117 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1344058 CTGGGTTGGC
* * *
1344068 TTCAGATTATGAGAAA-TTAT
1 TTCAAATTATAAGAAAGATAT
1344088 TTCAAATTATAAGAAAGATAT
1 TTCAAATTATAAGAAAGATAT
1344109 TTCGAAATT
1 TTC-AAATT
1344118 GAAAAACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.56
21 6 0.24
22 5 0.20
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (21 bp):
TTCAAATTATAAGAAAGATAT
Found at i:1348006 original size:21 final size:21
Alignment explanation
Indices: 1347935--1348007 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1347925 ATTTTTGTGC
* *
1347935 AAAGTGCATCAATACACTATG
1 AAAGTGCAACGATACACTATG
* * *
1347956 AAGGTGCACCGATGCATTGCT-TG
1 AAAGTGCAACGATACA---CTATG
*
1347979 AATGTGCAACGATACACTATG
1 AAAGTGCAACGATACACTATG
1348000 AAAGTGCA
1 AAAGTGCA
1348008 CCAATTCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.05
21 21 0.52
23 15 0.38
24 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (21 bp):
AAAGTGCAACGATACACTATG
Found at i:1348556 original size:12 final size:13
Alignment explanation
Indices: 1348530--1348562 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1348520 ATAATATAAA
1348530 TTTTCAAACATAG
1 TTTTCAAACATAG
1348543 TTTTCAAA-ATAG
1 TTTTCAAACATAG
1348555 TTTTCAAA
1 TTTTCAAA
1348563 TTTTGCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:1353561 original size:20 final size:20
Alignment explanation
Indices: 1353536--1353586 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1353526 TGGTAGTATC
1353536 GGTACTACCTTGATGATATA
1 GGTACTACCTTGATGATATA
* *
1353556 GGTACTACCTTGATGGTATC
1 GGTACTACCTTGATGATATA
1353576 GGTACTACCTT
1 GGTACTACCTT
1353587 TGTCTAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
GGTACTACCTTGATGATATA
Found at i:1355683 original size:19 final size:19
Alignment explanation
Indices: 1355655--1355712 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
1355645 AGGTATCTAG
1355655 CTTCAATAATAGCCGTCTT
1 CTTCAATAATAGCCGTCTT
*
1355674 CTTCAGTAATAGCCGTCTT
1 CTTCAATAATAGCCGTCTT
*
1355693 CTTCAATAATAACCGTCTT
1 CTTCAATAATAGCCGTCTT
1355712 C
1 C
1355713 CTTACAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (19 bp):
CTTCAATAATAGCCGTCTT
Found at i:1356606 original size:33 final size:33
Alignment explanation
Indices: 1356569--1356632 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1356559 CTTTACAAAC
*
1356569 TCCCTAG-TTGTTCACAGGTTAAGCTAGAACCTT
1 TCCCTAGATT-TTCACAGGCTAAGCTAGAACCTT
* *
1356602 TCCCTAGATTTTCACGGGCTCAGCTAGAACC
1 TCCCTAGATTTTCACAGGCTAAGCTAGAACC
1356633 AAAACCCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (33 bp):
TCCCTAGATTTTCACAGGCTAAGCTAGAACCTT
Found at i:1356947 original size:21 final size:21
Alignment explanation
Indices: 1356922--1356979 Score: 107
Period size: 21 Copynumber: 2.7 Consensus size: 21
1356912 AGAATAGGAA
1356922 GTATCGGTACTCCTTCATAGG
1 GTATCGGTACTCCTTCATAGG
1356943 GTATCGGTACTCCTTCATAGG
1 GTATCGGTACTCCTTCATAGG
1356964 GTATCGGTACTACCTT
1 GTATCGGTACT-CCTT
1356980 TTTTAATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 32 0.89
22 4 0.11
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
GTATCGGTACTCCTTCATAGG
Found at i:1358875 original size:23 final size:23
Alignment explanation
Indices: 1358844--1358897 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 23
1358834 ATGTTTTGAG
*
1358844 CCTTCATGGTAGTATCGGTACAA
1 CCTTGATGGTAGTATCGGTACAA
*
1358867 CCTTGAT-G--GTATCGGTACTA
1 CCTTGATGGTAGTATCGGTACAA
1358887 CCTTGATGGTA
1 CCTTGATGGTA
1358898 TCGGTACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 18 0.69
21 1 0.04
22 1 0.04
23 6 0.23
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (23 bp):
CCTTGATGGTAGTATCGGTACAA
Found at i:1358880 original size:20 final size:20
Alignment explanation
Indices: 1358855--1358910 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1358845 CTTCATGGTA
*
1358855 GTATCGGTACAACCTTGATG
1 GTATCGGTACTACCTTGATG
1358875 GTATCGGTACTACCTTGATG
1 GTATCGGTACTACCTTGATG
1358895 GTATCGGTACTACCTT
1 GTATCGGTACTACCTT
1358911 TGTCTAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (20 bp):
GTATCGGTACTACCTTGATG
Found at i:1361030 original size:19 final size:19
Alignment explanation
Indices: 1360980--1361037 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
1360970 AGGTATCTAG
* *
1360980 CTTCAATAATAGCCATCTT
1 CTTCAATAATAGTCGTCTT
*
1360999 CTTCAGTAATAGTCGTCTT
1 CTTCAATAATAGTCGTCTT
1361018 CTTCAATAATAGTCGTCTT
1 CTTCAATAATAGTCGTCTT
1361037 C
1 C
1361038 CTTACAAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (19 bp):
CTTCAATAATAGTCGTCTT
Found at i:1367686 original size:2 final size:2
Alignment explanation
Indices: 1367679--1367703 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1367669 ATACTTCATT
1367679 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1367704 TAGAGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1368439 original size:30 final size:31
Alignment explanation
Indices: 1368387--1368452 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
1368377 AATCTATTTG
* *
1368387 AAAATCCAATGGTTCATTTTTTTCA-TCGTTT
1 AAAATCAAATGGTTCATTTTTTTAACT-GTTT
1368418 AAAATCAAATGGTTC-TTTTTTTAACTGTTT
1 AAAATCAAATGGTTCATTTTTTTAACTGTTT
1368448 AAAAT
1 AAAAT
1368453 TCAAGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (31 bp):
AAAATCAAATGGTTCATTTTTTTAACTGTTT
Found at i:1375771 original size:42 final size:41
Alignment explanation
Indices: 1375672--1375778 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
1375662 ACCCGAATGT
* * *
1375672 CTTACGGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
* ** * *
1375713 CTTACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGA
* *
1375755 CTTACTGATGGGCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
1375779 CCAATTTCTA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 18 0.35
42 33 0.65
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:1376004 original size:260 final size:251
Alignment explanation
Indices: 1375530--1376156 Score: 793
Period size: 260 Copynumber: 2.5 Consensus size: 251
1375520 GTAGTCAAAT
* *
1375530 CAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGTAATCACTTTCTTAC-TTTT-AAAATTT
1 CAATTTAGAAAATAGTTTACTGGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTTAAAAATTT
* *
1375593 CATTTTCT-AAAAACATTAAATGAGAAACTTTGGAAAAATCGCTTTCTC--GTTTTCATGTGAAA
66 CATTTT-TAAAAAACATTAAATGAGAAAC-TT-G-TAAATCGCTTTCTCATTTTTTCATGTGAAA
* * * *
1375655 ACATCCTACCCGAATGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGACTTACAA
127 ACATCCTACCCAAAGGTCTTACGGATGGCCCAAAGGACATATCATCTTGCTCAAAAGAATTACAA
*
1375720 ATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGGCCGAAGGACTTAC
192 ATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
** * * *
1375780 CAATTTCTAAAATAATTTACATGGGGTAAGAAACTTTGATAATCTCTTTCTTACTTTTTAAAAAT
1 CAATTTAGAAAATAGTTTAC-T-GGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTTAAAAAT
*
1375845 TTCATTTTTAAAAAATATTTAAATGAGAAACTCTGTAAATCGCTTTCTCATTTTCACAATTCATG
64 TTCATTTTTAAAAAACA-TTAAATGAGAAACT-TGTAAATCGCTTTCTCATTTT-----TTCATG
* *
1375910 TGAAAACATCCTACCCAAAGGTCTTACGGATGGCCCGAAGGACATATCGTCTTGCT-AGAAAGAA
122 TGAAAACATCCTACCCAAAGGTCTTACGGATGGCCCAAAGGACATATCATCTTGCTCA-AAAGAA
* * *
1375974 TTACAGATAACTCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGACTTA
186 TTACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
1376039 C
251 C
* * **
1376040 CAATTTAGAAAATAGTTTACTGGGTAAAAAACTTTGGTAACCACTTTCTTACTTTACAACAAATT
1 CAATTTAGAAAATAGTTTACTGGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTTAA-AAATT
* * * *
1376105 T-ATTTTCAGAAAAGATTAAATGAGAAACTT-TAGGAATCTCTTTCTCATTTTT
65 TCATTTTTAAAAAACATTAAATGAGAAACTTGTA--AATCGCTTTCTCATTTTT
1376157 AAAACAACTT
Statistics
Matches: 327, Mismatches: 32, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
250 16 0.05
251 1 0.00
252 30 0.09
253 18 0.06
254 21 0.06
255 18 0.06
256 1 0.00
257 30 0.09
258 43 0.13
259 8 0.02
260 141 0.43
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (251 bp):
CAATTTAGAAAATAGTTTACTGGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTTAAAAATTT
CATTTTTAAAAAACATTAAATGAGAAACTTGTAAATCGCTTTCTCATTTTTTCATGTGAAAACAT
CCTACCCAAAGGTCTTACGGATGGCCCAAAGGACATATCATCTTGCTCAAAAGAATTACAAATAA
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
Found at i:1378293 original size:12 final size:12
Alignment explanation
Indices: 1378263--1378317 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
1378253 TCTTTCTCCT
*
1378263 TTTTTCATCTTC
1 TTTTTCTTCTTC
*
1378275 TCTTTCTTCTTC
1 TTTTTCTTCTTC
*
1378287 TTTTTCTTCTATT
1 TTTTTCTTCT-TC
*
1378300 TTTTCTCTTCTAC
1 TTTT-TCTTCTTC
1378313 TTTTT
1 TTTTT
1378318 TCTCTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 20 0.57
13 9 0.26
14 6 0.17
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:1378293 original size:38 final size:36
Alignment explanation
Indices: 1378250--1378337 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
1378240 ACTTGATTTA
1378250 TTTTCTTTCTCCTTTTTTCATCTTCT-CTTTCTTCTTCT
1 TTTTCTTTCT-CTTTTTTC-TCTTCTACTTTCTTC-TCT
* *
1378288 TTTTC-TTCTATTTTTTCTCTTCTACTTTTTTCTCT
1 TTTTCTTTCTCTTTTTTCTCTTCTACTTTCTTCTCT
1378323 TTTAT-TTTCTCTTTT
1 TTT-TCTTTCTCTTTT
1378338 CTCTTTATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
35 12 0.27
36 23 0.52
37 4 0.09
38 5 0.11
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.72
Consensus pattern (36 bp):
TTTTCTTTCTCTTTTTTCTCTTCTACTTTCTTCTCT
Found at i:1378308 original size:26 final size:27
Alignment explanation
Indices: 1378247--1378339 Score: 74
Period size: 26 Copynumber: 3.6 Consensus size: 27
1378237 AATACTTGAT
*
1378247 TTATTTTCT-TTCTCCTTTTTTCATC--
1 TTATTTTCTCTTCTTCTTTTTTC-TCTA
* *
1378272 TTCTCTT-TCTTCTTC-TTTTTCTTCTA
1 TTATTTTCTCTTCTTCTTTTTTC-TCTA
* *
1378298 TT-TTTTCTCTTCTACTTTTTTCTCTT
1 TTATTTTCTCTTCTTCTTTTTTCTCTA
1378324 TTATTTTCTCTT-TTCT
1 TTATTTTCTCTTCTTCT
1378340 CTTTATTGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
24 9 0.17
25 13 0.24
26 17 0.31
27 15 0.28
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (27 bp):
TTATTTTCTCTTCTTCTTTTTTCTCTA
Found at i:1378310 original size:14 final size:14
Alignment explanation
Indices: 1378287--1378330 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
1378277 TTTCTTCTTC
1378287 TTTT-TCTTCTATT
1 TTTTCTCTTCTATT
1378300 TTTTCTCTTCTACTT
1 TTTTCTCTTCTA-TT
*
1378315 TTTTCTCTTTTATT
1 TTTTCTCTTCTATT
1378329 TT
1 TT
1378331 CTCTTTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 13 0.46
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTCTCTTCTATT
Found at i:1378310 original size:29 final size:29
Alignment explanation
Indices: 1378272--1378343 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
1378262 TTTTTTCATC
*
1378272 TTCTCTTTCTTCTTCTTTT-TCTTCTATTTT
1 TTCTC-TTCTACTT-TTTTCTCTTCTATTTT
*
1378302 TTCTCTTCTACTTTTTTCTCTTTTATTTT
1 TTCTCTTCTACTTTTTTCTCTTCTATTTT
* *
1378331 CTCTTTTCT-CTTT
1 TTCTCTTCTACTTT
1378344 ATTGGATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.22
29 24 0.65
30 5 0.14
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (29 bp):
TTCTCTTCTACTTTTTTCTCTTCTATTTT
Found at i:1378318 original size:15 final size:15
Alignment explanation
Indices: 1378272--1378323 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1378262 TTTTTTCATC
*
1378272 TTCTCTTTCTTCTTCTT
1 TTCTC-TTCTACTT-TT
1378289 TT-TCTTCTA-TTTT
1 TTCTCTTCTACTTTT
1378302 TTCTCTTCTACTTTT
1 TTCTCTTCTACTTTT
1378317 TTCTCTT
1 TTCTCTT
1378324 TTATTTTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 4 0.12
14 9 0.28
15 15 0.47
16 2 0.06
17 2 0.06
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTCTTCTACTTTT
Found at i:1380912 original size:45 final size:45
Alignment explanation
Indices: 1380839--1381159 Score: 398
Period size: 45 Copynumber: 7.2 Consensus size: 45
1380829 TGCATTTAAC
* * **
1380839 TTTT-ATTAATGGCACCTTTTATGACGATAATGCACCATTATGCA
1 TTTTCATTAGTGGCACCTTTTATGTCGATAATGCACTGTTATGCA
* *
1380883 TTTTCATTAGTGGCACCTTTTATGTCGATAATACACTGTTATGTA
1 TTTTCATTAGTGGCACCTTTTATGTCGATAATGCACTGTTATGCA
* * * *
1380928 ATTTCATTAGTGGCACATTTTATGCCGATAATGCACCGTTATGCA
1 TTTTCATTAGTGGCACCTTTTATGTCGATAATGCACTGTTATGCA
* *
1380973 TTTTTATTAGTGGCACCTTTTATG-CTGGTAATGCACTGTTATGCA
1 TTTTCATTAGTGGCACCTTTTATGTC-GATAATGCACTGTTATGCA
* * * *
1381018 TTTTCATTAGTGGCACATTTTATGTTGTTAATGCACTATTATGCA
1 TTTTCATTAGTGGCACCTTTTATGTCGATAATGCACTGTTATGCA
*
1381063 TTTTCATTAGTGGCACATTTTATG-CTGATAATGCACTGTTATGCA
1 TTTTCATTAGTGGCACCTTTTATGTC-GATAATGCACTGTTATGCA
* * * *
1381108 TTTTCATTAGCT-ACACCTTTTATGTTGATAATGCACCGTTATGCT
1 TTTTCATTAG-TGGCACCTTTTATGTCGATAATGCACTGTTATGCA
1381153 TTTTCAT
1 TTTTCAT
1381160 AGATTTAAGC
Statistics
Matches: 241, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
44 5 0.02
45 235 0.98
46 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (45 bp):
TTTTCATTAGTGGCACCTTTTATGTCGATAATGCACTGTTATGCA
Found at i:1380997 original size:26 final size:26
Alignment explanation
Indices: 1380966--1381087 Score: 65
Period size: 26 Copynumber: 5.2 Consensus size: 26
1380956 TAATGCACCG
1380966 TTATGCATTTTTATTAGTGGCACCTT
1 TTATGCATTTTTATTAGTGGCACCTT
** *
1380992 TTATGC--TGGTA--A-T-GCA-CTG
1 TTATGCATTTTTATTAGTGGCACCTT
* *
1381011 TTATGCATTTTCATTAGTGGCACATT
1 TTATGCATTTTTATTAGTGGCACCTT
* *
1381037 TTATG--TTGTTA--A-T-GCA-CTA
1 TTATGCATTTTTATTAGTGGCACCTT
* *
1381056 TTATGCATTTTCATTAGTGGCACATT
1 TTATGCATTTTTATTAGTGGCACCTT
1381082 TTATGC
1 TTATGC
1381088 TGATAATGCA
Statistics
Matches: 66, Mismatches: 16, Indels: 28
0.60 0.15 0.25
Matches are distributed among these distances:
19 14 0.21
20 6 0.09
21 8 0.12
22 2 0.03
23 2 0.03
24 9 0.14
25 6 0.09
26 19 0.29
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (26 bp):
TTATGCATTTTTATTAGTGGCACCTT
Found at i:1381081 original size:135 final size:135
Alignment explanation
Indices: 1380839--1381159 Score: 457
Period size: 135 Copynumber: 2.4 Consensus size: 135
1380829 TGCATTTAAC
* * *
1380839 TTTTATTAATGGCACCTTTTATGAC-GATAATGCACCATTATGCATTTTCATTAGTGGCACCTTT
1 TTTTATTAGTGGCACCTTTTATG-CTGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTT
* *
1380903 TATGTCGATAATACACTGTTATGTAATTTCATTAGTGGCACATTTTATGCCGATAATGCACCGTT
65 TATGTCGATAATACACTATTATGCAATTTCATTAGTGGCACATTTTATGCCGATAATGCACCGTT
1380968 ATGCAT
130 ATGCAT
* *
1380974 TTTTATTAGTGGCACCTTTTATGCTGGTAATGCACTGTTATGCATTTTCATTAGTGGCACATTTT
1 TTTTATTAGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTT
* * * * * *
1381039 ATGTTGTTAATGCACTATTATGCATTTTCATTAGTGGCACATTTTATGCTGATAATGCACTGTTA
66 ATGTCGATAATACACTATTATGCAATTTCATTAGTGGCACATTTTATGCCGATAATGCACCGTTA
1381104 TGCAT
131 TGCAT
* * * *
1381109 TTTCATTAGCT-ACACCTTTTATGTTGATAATGCACCGTTATGCTTTTTCAT
1 TTTTATTAG-TGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCAT
1381160 AGATTTAAGC
Statistics
Matches: 165, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
134 1 0.01
135 163 0.99
136 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (135 bp):
TTTTATTAGTGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTT
ATGTCGATAATACACTATTATGCAATTTCATTAGTGGCACATTTTATGCCGATAATGCACCGTTA
TGCAT
Found at i:1387908 original size:45 final size:44
Alignment explanation
Indices: 1387843--1388118 Score: 372
Period size: 45 Copynumber: 6.1 Consensus size: 44
1387833 TGCATTTAAC
* * *
1387843 TTTCATTAATGGAACCTTTTATGTCGATAATTCACCGTTATACAT
1 TTTCATTAGTGGAACCTTTTATG-CGATAATGCACCGTTATGCAT
* * *
1387888 TTTCATTAGTGGCACATTTTATGCTGATAATGCACCATTATGCAT
1 TTTCATTAGTGGAACCTTTTATGC-GATAATGCACCGTTATGCAT
* *
1387933 TTTCATTAATGGCACCTTTTATGTCGATAATGCACCGTTATGCAT
1 TTTCATTAGTGGAACCTTTTATG-CGATAATGCACCGTTATGCAT
* *
1387978 TTTCATTAGTGGCACCTTTTATGACGATAATACACCGTTATGCAT
1 TTTCATTAGTGGAACCTTTTATG-CGATAATGCACCGTTATGCAT
* *
1388023 TTTCATTAGTGGAACCTTTTACGCCGATAATGCACCGTTTTGCAT
1 TTTCATTAGTGGAACCTTTTATG-CGATAATGCACCGTTATGCAT
* *
1388068 TTTCATTAGTGGAACTTTTTATGCTGATAATGCACCGTAATGCAT
1 TTTCATTAGTGGAACCTTTTATGC-GATAATGCACCGTTATGCAT
1388113 TTTCAT
1 TTTCAT
1388119 AGATTTAAAC
Statistics
Matches: 207, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
44 2 0.01
45 204 0.99
46 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (44 bp):
TTTCATTAGTGGAACCTTTTATGCGATAATGCACCGTTATGCAT
Found at i:1387980 original size:90 final size:90
Alignment explanation
Indices: 1387843--1388118 Score: 419
Period size: 90 Copynumber: 3.1 Consensus size: 90
1387833 TGCATTTAAC
* *
1387843 TTTCATTAATGGAACCTTTTATGTCGATAATTCACCGTTATACATTTTCATTAGTGGCACATTTT
1 TTTCATTAATGGAACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTT
*
1387908 ATGCTGATAATGCACCATTATGCAT
66 ATGCTGATAATGCACCGTTATGCAT
* *
1387933 TTTCATTAATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTAGTGGCACCTTTT
1 TTTCATTAATGGAACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTT
*
1387998 ATGAC-GATAATACACCGTTATGCAT
66 ATG-CTGATAATGCACCGTTATGCAT
* * * * * *
1388023 TTTCATTAGTGGAACCTTTTACGCCGATAATGCACCGTTTTGCATTTTCATTAGTGGAACTTTTT
1 TTTCATTAATGGAACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTT
*
1388088 ATGCTGATAATGCACCGTAATGCAT
66 ATGCTGATAATGCACCGTTATGCAT
1388113 TTTCAT
1 TTTCAT
1388119 AGATTTAAAC
Statistics
Matches: 169, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
89 1 0.01
90 167 0.99
91 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (90 bp):
TTTCATTAATGGAACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTT
ATGCTGATAATGCACCGTTATGCAT
Found at i:1390189 original size:6 final size:6
Alignment explanation
Indices: 1390175--1390212 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1390165 AAGCAATTCG
* *
1390175 AATGCA AATGTA AATGCC AATGCA AATGCA AATGCA AA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AA
1390213 AATTGTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (6 bp):
AATGCA
Found at i:1393438 original size:21 final size:21
Alignment explanation
Indices: 1393412--1393474 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1393402 GTCGAGGGTT
1393412 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
* * *
1393433 TCATAGGTCTTTCGCGACATAT
1 TCATAGGTCCTTCGGGACA-AC
* *
1393455 TCACAGGTCCTTCAGGACAA
1 TCATAGGTCCTTCGGGACAA
1393475 ATTTCATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:1394047 original size:20 final size:20
Alignment explanation
Indices: 1394022--1394063 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1394012 CGAAGTTTTT
* *
1394022 ATGCATCGGTGCACTGTAGC
1 ATGCATCGATACACTGTAGC
1394042 ATGCATCGATACACTGTAGC
1 ATGCATCGATACACTGTAGC
1394062 AT
1 AT
1394064 TGTAGCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (20 bp):
ATGCATCGATACACTGTAGC
Found at i:1409324 original size:13 final size:12
Alignment explanation
Indices: 1409299--1409332 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1409289 AAATGAATCA
1409299 AAATAAATAAAG
1 AAATAAATAAAG
1409311 AAATAAAGTAAAG
1 AAATAAA-TAAAG
1409324 AAATCAAAT
1 AAAT-AAAT
1409333 TATTTACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 10 0.50
14 3 0.15
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (12 bp):
AAATAAATAAAG
Found at i:1409698 original size:21 final size:20
Alignment explanation
Indices: 1409670--1409715 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1409660 GAATTAATCA
* *
1409670 AAAGGTTATGACCTTTTGAT
1 AAAGGTTAAGACCATTTGAT
1409690 AAAGAGTTAAGACCATTTGAT
1 AAAG-GTTAAGACCATTTGAT
*
1409711 GAAGG
1 AAAGG
1409716 GATTTGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (20 bp):
AAAGGTTAAGACCATTTGAT
Found at i:1411933 original size:131 final size:131
Alignment explanation
Indices: 1411687--1412047 Score: 487
Period size: 131 Copynumber: 2.8 Consensus size: 131
1411677 ATAATTTTAA
* * *
1411687 GAGATAAAACAATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGC-
* *
1411752 AG-CATTTATTACTCCAATCGAAATGAAGAGATACCACTATTTCATCTTAAAATTCAATATCGAT
65 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATATCGAT
1411816 TC
130 TC
* * * * *
1411818 GAGTGAAAACAATAATATCTAATGATTTGCAATAGAGAATAAATGACCTCCCATACCTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGCA
* * *
1411883 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTAT-GTTTTAAAAATCAATATTGAT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATT-TCATCTTAAAAATCAATATCGAT
1411947 TC
130 TC
* * * * *
1411949 TAGAGAAAACGATAATATCAAATTATTTTCAATCGAGAATAAATGACCTCCCATGCTTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGCA
*
1412014 GTCATTTATTA-TCCCAA-CTGAAATGAAAAGATAT
66 GTCATTTATTACT-CCAATC-GAAATGAAGAGATAT
1412048 TATTATTCTC
Statistics
Matches: 203, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
130 4 0.02
131 198 0.98
132 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (131 bp):
GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATATCGATT
C
Found at i:1414050 original size:3 final size:3
Alignment explanation
Indices: 1414042--1414080 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1414032 TAATTTGGGG
1414042 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1414081 ATAATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:1414085 original size:3 final size:3
Alignment explanation
Indices: 1414079--1414104 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1414069 CTACTACTAC
1414079 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1414105 GTGGGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1414592 original size:135 final size:134
Alignment explanation
Indices: 1414269--1414853 Score: 627
Period size: 134 Copynumber: 4.3 Consensus size: 134
1414259 ATCAGATCGA
* * * * *
1414269 GAGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATCGAATCGAGGTAGACTTATTCCACTACT
1 GAGACATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCT
** * * * * *
1414334 ACTCAGGGAAGATCAAATCTT-GAAATGGATGGGATATGTTATGCTATTTATTCAGGAGAAAACC
66 ACTCAGGGAAGATCAAAT-TTGGAAAACGA-GGGATTTGTTACGCTGTTTCTTCAGG-GAAAATC
*
1414398 AGATTTG
128 AGATATG
* * * * * *
1414405 GGGACATTGATTCATTCTAATTTTCTTCAAGGAATATTGAATCGAGGAAGACTTGTTCCACTGCT
1 GAGACATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCT
* * * *
1414470 ACTCAGGGAAGATCAAATTTGGAAAGA-GATGGGATTTGTTCCCCTGTTTCTTCAAGGAAAATTA
66 ACTCAGGGAAGATCAAATTTGGAAA-ACGA-GGGATTTGTTACGCTGTTTCTTCAGGGAAAATCA
1414534 GATAT-
129 GATATG
*** * * *
1414539 GAGGGTGTTGATTCATTCCACTATTCTTCATGGAAGATTGAATCGAGGAAGACTTGTTCCACTGT
1 GA-GACATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGC
* * * * * * * *
1414604 TCCTTAGGAAAGATCAAATTTGGAAAATGAGGGATTTGTTCCGCTGCTTCTTGAGGGAAAATTAG
65 TACTCAGGGAAGATCAAATTTGGAAAACGAGGGATTTGTTACGCTGTTTCTTCAGGGAAAATCAG
1414669 ATATG
130 ATATG
* * *
1414674 GAGACATTGATTCATTTCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTT
1 GAGACATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCT
* * * * * *
1414739 CCTCAGGGAATATCAAATCTGGAAAACGAGGGATTTGTTATGATGTTTCTTGAGGGAAAATCAGA
66 ACTCAGGGAAGATCAAATTTGGAAAACGAGGGATTTGTTACGCTGTTTCTTCAGGGAAAATCAGA
*
1414804 TATA
131 TATG
* * * * *
1414808 GAAATATTGATTCATTTCACTTTTCTTCAGGGAAGATTTAATCGAG
1 GAGACATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
1414854 TTCGATTTAC
Statistics
Matches: 383, Mismatches: 61, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
134 193 0.50
135 92 0.24
136 98 0.26
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (134 bp):
GAGACATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCT
ACTCAGGGAAGATCAAATTTGGAAAACGAGGGATTTGTTACGCTGTTTCTTCAGGGAAAATCAGA
TATG
Found at i:1414756 original size:269 final size:270
Alignment explanation
Indices: 1414274--1414853 Score: 670
Period size: 269 Copynumber: 2.2 Consensus size: 270
1414264 ATCGAGAGAC
* * *
1414274 GTTGATTCATTCCACTGTTCTTCAGGGAAGATCGAATCGAGGTAGACTTATTCCACTACTACTCA
1 GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGAAGACTTATTCCACTACTACTCA
* * * *
1414339 GGGAAGATCAAATCTTGAAATGGATGGGATATGTTATGCTATTTATTCAGGAGAAAACCAGATTT
66 GGAAAGATCAAATCTTGAAATGGATGGGATATGTTACGCTACTTATTCAGGAGAAAACCAGATAT
* * *
1414404 GGGGACATTGATTCATTCTAATTTTCTTCAAGGAATATTGAATCGAGGAAGACTTGTTCCACTGC
131 GGAGACATTGATTCATTCTAATGTTCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGC
* * * *
1414469 TACTCAGGGAAGATCAAATTTGGAAAGA-GATGGGATTTGTTCCCCTGTTTCTTCAAGGAAAATT
196 TACTCAGGGAAGATCAAATCTGGAAA-ACGA-GGGATTTGTTACCATGTTTCTTCAAGGAAAATC
**
1414533 AGATAT-GAGGGT
259 AGATATAGA-AAT
* * ** * *
1414545 GTTGATTCATTCCACTATTCTTCATGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTCCTTA
1 GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGAAGACTTATTCCACTACTACTCA
* * * * * **
1414610 GGAAAGATCAAAT-TTGGAAAAT-GA-GGGATTTGTTCCGCTGCTTCTTGAGG-GAAAATTAGAT
66 GGAAAGATCAAATCTT-G-AAATGGATGGGATATGTTACGCTACTTATTCAGGAGAAAACCAGAT
* * *
1414671 ATGGAGACATTGATTCATT-TCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCAC
129 ATGGAGACATTGATTCATTCT-AATGTTCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCAC
* * * ** * *
1414735 TGTTCCTCAGGGAATATCAAATCTGGAAAACGAGGGATTTGTTATGATGTTTCTTGAGGGAAAAT
193 TGCTACTCAGGGAAGATCAAATCTGGAAAACGAGGGATTTGTTACCATGTTTCTTCAAGGAAAAT
1414800 CAGATATAGAAAT
258 CAGATATAGAAAT
* * * *
1414813 ATTGATTCATTTCACTTTTCTTCAGGGAAGATTTAATCGAG
1 GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAG
1414854 TTCGATTTAC
Statistics
Matches: 260, Mismatches: 44, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
268 71 0.27
269 93 0.36
270 21 0.08
271 71 0.27
272 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (270 bp):
GTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGAAGACTTATTCCACTACTACTCA
GGAAAGATCAAATCTTGAAATGGATGGGATATGTTACGCTACTTATTCAGGAGAAAACCAGATAT
GGAGACATTGATTCATTCTAATGTTCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGC
TACTCAGGGAAGATCAAATCTGGAAAACGAGGGATTTGTTACCATGTTTCTTCAAGGAAAATCAG
ATATAGAAAT
Found at i:1416140 original size:16 final size:15
Alignment explanation
Indices: 1416115--1416170 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
1416105 GAAGCCCCCT
* *
1416115 TTTTTTTCTTTCTTTC
1 TTTTTCTCTTT-TTTA
1416131 TTTTTCTCTTTTTTA
1 TTTTTCTCTTTTTTA
**
1416146 TTTTT-TAATTTTTA
1 TTTTTCTCTTTTTTA
*
1416160 TTTTTTTCTTT
1 TTTTTCTCTTT
1416171 CTTTTTCCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.36
15 11 0.33
16 10 0.30
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTCTTTTTTA
Found at i:1416190 original size:41 final size:40
Alignment explanation
Indices: 1416114--1416190 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
1416104 TGAAGCCCCC
**
1416114 TTTTTTTTCTTTCTTTCTTTTTCTCTTTTTTATTTTTTAA
1 TTTTTTTTCTTTCTTTCTTTTTCTCTTTTCCATTTTTTAA
*
1416154 TTTTTATTTTTTTCTTTCTTTTTC-CATTTTCCATTTT
1 TTTTT-TTTCTTTCTTTCTTTTTCTC-TTTTCCATTTT
1416191 CTTCTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 6 0.19
41 26 0.81
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (40 bp):
TTTTTTTTCTTTCTTTCTTTTTCTCTTTTCCATTTTTTAA
Found at i:1419684 original size:6 final size:6
Alignment explanation
Indices: 1419673--1420964 Score: 2189
Period size: 6 Copynumber: 217.2 Consensus size: 6
1419663 CGAACAATAG
1419673 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1419721 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1419769 TATACA TATACA TATACA TATACA TATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1419815 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1419863 TATACA TATACA TATACA TATACA TATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1419909 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1419957 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420005 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420053 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420100 -ATACA TATACA TATACA TATACA TATAC- TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420146 TATACA TATACA TACATACA TATACA TATACA TATACA TATACA TATACATA
1 TATACA TATACA T--ATACA TATACA TATACA TATACA TATACA TATAC--A
1420198 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420246 TATACA TATAC- -ATACA TATACA TATACA TACATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA T--ATACA TATACA TATACA
* *
1420294 TGTACA TATACA TACATACA TATAC- -ATACA TATACA TATACA TGTACA
1 TATACA TATACA T--ATACA TATACA TATACA TATACA TATACA TATACA
* * * *
1420342 TGTACA TATACA TATACA TGTACA TGTACA TATAC- -ATACA TGTACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * * *
1420388 TGTACA TATACA TGTACA TGTACA T-TAC- -ATACA TGTACA TGTACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
1420433 TACTGTACA TATACA TATACA TGTACA TATACA TATACA TATACA TATACA
1 TA---TACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420484 TATACA TATACA TAT-CA TATACA TATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420529 TATACA TATACA TATACA TA-ACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420576 TATACA TATACA TATAC- TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420623 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420671 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420719 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
1420767 TATACA TATACA TATATA CATACA TATACA TATACA TATAACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TAT-ACA TATACA
1420816 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420862 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420910 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1420958 TATACA T
1 TATACA T
1420965 GAGAATCTAT
Statistics
Matches: 1234, Mismatches: 17, Indels: 70
0.93 0.01 0.05
Matches are distributed among these distances:
4 35 0.03
5 23 0.02
6 1140 0.92
7 6 0.00
8 24 0.02
9 6 0.00
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:1425509 original size:24 final size:24
Alignment explanation
Indices: 1425470--1425526 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1425460 ATCGAAACTA
*
1425470 CCACATAGAATTTGCACCGAAGTG
1 CCACATAGAATATGCACCGAAGTG
* *
1425494 TCACGTAGAATATGCACCGAAGTG
1 CCACATAGAATATGCACCGAAGTG
1425518 CCACATAGA
1 CCACATAGA
1425527 TTTATCCTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (24 bp):
CCACATAGAATATGCACCGAAGTG
Found at i:1425588 original size:23 final size:23
Alignment explanation
Indices: 1425518--1425588 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
1425508 CACCGAAGTG
* *
1425518 CCACATAGATTTATCCTGAAGGA
1 CCACATAGAATTGTCCTGAAGGA
** *
1425541 CTGCGTAGAATTGT-CTCGAAGGA
1 CCACATAGAATTGTCCT-GAAGGA
* *
1425564 CCACATAGAGTTGTCCTGAATGA
1 CCACATAGAATTGTCCTGAAGGA
1425587 CC
1 CC
1425589 GCGTAGAACC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
CCACATAGAATTGTCCTGAAGGA
Found at i:1425595 original size:23 final size:23
Alignment explanation
Indices: 1425531--1425596 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1425521 CATAGATTTA
*
1425531 TCCTGAAGGACTGCGTAGAATTG
1 TCCTGAAGGACCGCGTAGAATTG
* * *
1425554 T-CTCGAAGGACCACATAGAGTTG
1 TCCT-GAAGGACCGCGTAGAATTG
*
1425577 TCCTGAATGACCGCGTAGAA
1 TCCTGAAGGACCGCGTAGAA
1425597 CCTTTGACTC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (23 bp):
TCCTGAAGGACCGCGTAGAATTG
Found at i:1426851 original size:2 final size:2
Alignment explanation
Indices: 1426844--1426868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1426834 CCCCACATGT
1426844 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1426869 CATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1432387 original size:17 final size:18
Alignment explanation
Indices: 1432345--1432387 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
1432335 CTAGAACTCA
*
1432345 AGGTATGTGATTACTTTG
1 AGGTATGTGAGTACTTTG
1432363 A-GTATGTGAGTACTTTG
1 AGGTATGTGAGTACTTTG
1432380 AGGT-TGTG
1 AGGTATGTG
1432388 CATTGTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.42
Consensus pattern (18 bp):
AGGTATGTGAGTACTTTG
Found at i:1432513 original size:23 final size:23
Alignment explanation
Indices: 1432487--1432537 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1432477 AATGTCCGCG
1432487 TAGAATTGTCCCAAAGGACCACA
1 TAGAATTGTCCCAAAGGACCACA
* * * *
1432510 TAGAGTTGTTCCGAAGGACCACG
1 TAGAATTGTCCCAAAGGACCACA
1432533 TAGAA
1 TAGAA
1432538 CTCTCGAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (23 bp):
TAGAATTGTCCCAAAGGACCACA
Found at i:1432719 original size:19 final size:20
Alignment explanation
Indices: 1432692--1432733 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1432682 ATGCTTATGA
*
1432692 AATACAATTT-AGATAAAAT
1 AATAAAATTTAAGATAAAAT
*
1432711 AATAAAATTTAATATAAAAT
1 AATAAAATTTAAGATAAAAT
1432731 AAT
1 AAT
1432734 TCAAATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAATTTAAGATAAAAT
Found at i:1437224 original size:26 final size:26
Alignment explanation
Indices: 1437189--1437241 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1437179 AAGCATTCAT
1437189 TTATTACTCCAATCGAAATGAAGAGA
1 TTATTACTCCAATCGAAATGAAGAGA
1437215 TTATTACTCCAATCGAAATGAAGAGA
1 TTATTACTCCAATCGAAATGAAGAGA
1437241 T
1 T
1437242 ATCACTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (26 bp):
TTATTACTCCAATCGAAATGAAGAGA
Found at i:1437454 original size:130 final size:131
Alignment explanation
Indices: 1437215--1437456 Score: 369
Period size: 130 Copynumber: 1.9 Consensus size: 131
1437205 AATGAAGAGA
* * *
1437215 TTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATCAATTCGAGT
1 TTATTACTCCAATAGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATCAATTCGAGA
* * * * *
1437280 GAAAATGATAATATCTAATGATTTCCAATCGAGAATTAATGACCTCTTATACCTTAAAGCAATTA
66 GAAAACGATAATATCAAATGATTTCAAATAGAGAATAAATGACCTCTTATACCTTAAAGCAATTA
1437345 T
131 T
* **
1437346 TTATTACTCCAATAGAAATGAAGAGATATCACTATTTTGTCTTAAAAAT-AATATTGATTCGAGA
1 TTATTACTCCAATAGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATCAATTCGAGA
*
1437410 GAAAACGATAATATCAAATTATTTCAAATAGAGAATAAATGACCTCT
66 GAAAACGATAATATCAAATGATTTCAAATAGAGAATAAATGACCTCT
1437457 CATGTCTTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
130 53 0.54
131 46 0.46
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (131 bp):
TTATTACTCCAATAGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATCAATTCGAGA
GAAAACGATAATATCAAATGATTTCAAATAGAGAATAAATGACCTCTTATACCTTAAAGCAATTA
T
Found at i:1439461 original size:34 final size:34
Alignment explanation
Indices: 1439363--1439479 Score: 164
Period size: 35 Copynumber: 3.4 Consensus size: 34
1439353 GGGGCCTTTA
* * *
1439363 GGGTTTGGGTTACTGGGTCGATTCTGTTGGGCTCT
1 GGGTTTGGGTAACTGGATCG-TTTTGTTGGGCTCT
* *
1439398 GGGTTTGGGTAACTGGTTCGGTTTTGTTGGGCTCC
1 GGGTTTGGGTAACTGGATC-GTTTTGTTGGGCTCT
1439433 GGGTTTGGGTAACTGGATCGTTTTGTTGGGCTCT
1 GGGTTTGGGTAACTGGATCGTTTTGTTGGGCTCT
1439467 GGGTTTGGG-AACT
1 GGGTTTGGGTAACT
1439480 TTGGCCAGTT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
33 4 0.05
34 23 0.31
35 47 0.63
36 1 0.01
ACGTcount: A:0.08, C:0.13, G:0.40, T:0.39
Consensus pattern (34 bp):
GGGTTTGGGTAACTGGATCGTTTTGTTGGGCTCT
Found at i:1439893 original size:42 final size:40
Alignment explanation
Indices: 1439804--1439893 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
1439794 ATTACATTGA
* *** *
1439804 GAAAAACCAATTACAGTTATCAAATACTGAAAATGTTTTT
1 GAAAAATCAATTACACCCATCAAACACTGAAAATGTTTTT
* *
1439844 CATAAAATCAATTACACCCATCAAACACTAGAAAATATTTTTT
1 GA-AAAATCAATTACACCCATCAAACACT-GAAAAT-GTTTTT
1439887 GAAAAAT
1 GAAAAAT
1439894 ATCTTTCAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
40 1 0.03
41 21 0.54
42 11 0.28
43 6 0.15
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (40 bp):
GAAAAATCAATTACACCCATCAAACACTGAAAATGTTTTT
Found at i:1440563 original size:17 final size:17
Alignment explanation
Indices: 1440522--1440590 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
1440512 ATTCACGCAT
1440522 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
1440539 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1440557 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
1440574 CTAGTTTATTTATTAAA
1 CTAGTTCATTAATTAAA
1440591 ATAACTCTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 30 0.70
18 13 0.30
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1442199 original size:20 final size:21
Alignment explanation
Indices: 1442161--1442200 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1442151 GGAGTGTTTG
1442161 GTGAGGTTATTCCTTTTATTT
1 GTGAGGTTATTCCTTTTATTT
*
1442182 GTGAGGTTATT-TTTTTATT
1 GTGAGGTTATTCCTTTTATT
1442201 ACTAATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.15, C:0.05, G:0.20, T:0.60
Consensus pattern (21 bp):
GTGAGGTTATTCCTTTTATTT
Found at i:1448567 original size:17 final size:17
Alignment explanation
Indices: 1448526--1448595 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
1448516 ATTCATGCAT
1448526 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
1448543 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1448561 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
1448578 CTAGTTTATTTATTAAA
1 CTAGTTCATTAATTAAA
1448595 C
1 C
1448596 AAACTCTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 31 0.70
18 13 0.30
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1450061 original size:32 final size:31
Alignment explanation
Indices: 1449992--1450062 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
1449982 GAGGGGTGGG
* *
1449992 TATTTAGA-AAAAATATTAAAAATTTTATAA
1 TATTTATATAAAAATATTAAAAATTTAATAA
*
1450022 TATTTATATAAAAATATTTAATAA-TTAATAA
1 TATTTATATAAAAATA-TTAAAAATTTAATAA
*
1450053 TTTATTATAT
1 TAT-TTATAT
1450063 TATTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 7 0.21
31 15 0.44
32 12 0.35
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TATTTATATAAAAATATTAAAAATTTAATAA
Found at i:1452913 original size:20 final size:20
Alignment explanation
Indices: 1452884--1452921 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1452874 TTTCATGGGC
1452884 ATGCACCGATGCACCAATCT
1 ATGCACCGATGCACCAATCT
* *
1452904 ATGCATCGATGCATCAAT
1 ATGCACCGATGCACCAAT
1452922 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCT
Found at i:1458642 original size:24 final size:24
Alignment explanation
Indices: 1458610--1458690 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1458600 CACTTAACAC
1458610 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
1458634 TGCATCGATTCAT-CATGTTGAA--
1 TGCATCGATGCATCCCT-TTGAATG
*
1458656 -GCATCGATGCA-CGCC-TAGAATG
1 TGCATCGATGCATC-CCTTTGAATG
1458678 TGCATCGATGCAT
1 TGCATCGATGCAT
1458691 AGGGTCATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
20 4 0.09
21 10 0.22
22 1 0.02
23 13 0.29
24 17 0.38
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:1460332 original size:19 final size:20
Alignment explanation
Indices: 1460308--1460347 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1460298 GAGAACTGTA
*
1460308 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
1460327 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
1460348 TAATTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:1460720 original size:20 final size:20
Alignment explanation
Indices: 1460682--1460720 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1460672 TTTTCAAGGG
*
1460682 CATGCACCGATGTACCAATC
1 CATGCACCGATGCACCAATC
* *
1460702 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
1460721 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:1460800 original size:26 final size:26
Alignment explanation
Indices: 1460767--1460832 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
1460757 TGCACATACC
1460767 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
1460793 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
*
1460819 ATGCATTGATGCAC
1 ATGCATCGATGCAC
1460833 AAGACCACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGTGCATTTG
Found at i:1467569 original size:19 final size:20
Alignment explanation
Indices: 1467545--1467582 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1467535 TTTGAATCCT
1467545 AATATAAATTTT-AATTTAA
1 AATATAAATTTTAAATTTAA
*
1467564 AATATATATTTTAAATTTA
1 AATATAAATTTTAAATTTA
1467583 GCAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATAAATTTTAAATTTAA
Found at i:1468121 original size:13 final size:14
Alignment explanation
Indices: 1468091--1468132 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
1468081 ATTCAAATTT
1468091 TCGGATCTAATCA-A
1 TCGGATC-AATCAGA
1468105 -CGGATCAAT-AGA
1 TCGGATCAATCAGA
1468117 TCGGATCAATCAGA
1 TCGGATCAATCAGA
1468131 TC
1 TC
1468133 AAATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 4 0.16
13 15 0.60
14 5 0.20
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (14 bp):
TCGGATCAATCAGA
Found at i:1474822 original size:20 final size:20
Alignment explanation
Indices: 1474777--1474825 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1474767 CGCCGTCCGT
*
1474777 CTCGTCTCGACTCGGCACGG
1 CTCGGCTCGACTCGGCACGG
* **
1474797 CACGGCTCGACTCGGCTTGG
1 CTCGGCTCGACTCGGCACGG
1474817 CTCGGCTCG
1 CTCGGCTCG
1474826 TGGTCGTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.08, C:0.39, G:0.33, T:0.20
Consensus pattern (20 bp):
CTCGGCTCGACTCGGCACGG
Found at i:1475142 original size:22 final size:22
Alignment explanation
Indices: 1475117--1475171 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1475107 TCAGGAGTTA
* *
1475117 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1475139 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1475161 CAGGAGTTATA
1 CAGGAGTTATA
1475172 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1479282 original size:77 final size:76
Alignment explanation
Indices: 1479065--1479282 Score: 233
Period size: 77 Copynumber: 2.8 Consensus size: 76
1479055 AAAGTGGAAT
**
1479065 AGAAGGAAGCATTGCACTTTCGATTCAAGTAGAACGGGAGAAA-A-CATCGCACTTTCGATTCTC
1 AGAAGGAAGCATTGCACTTTCGATTCAAGTAGAAC--GA-AAAGAGCATAACACTTTCGATTCTC
* *
1479128 ATCTAAAGTAGAAC
63 GTCTAAAGTAAAAC
* * ** * * * *
1479142 AGAAGAAAGCATTGTACTTTTAATTAAAATAGAATGAAAGGAGGCATAACACTTTCGATTCTCGT
1 AGAAGGAAGCATTGCACTTTCGATTCAAGTAGAACGAAAAGA-GCATAACACTTTCGATTCTCGT
1479207 CTAAAGTAAAAC
65 CTAAAGTAAAAC
* * * *
1479219 GGAAGGAAGAATCGCACTTTCGATTCAAGTAGAACGAAAAGATGCATATCACTTTCGATTCTCG
1 AGAAGGAAGCATTGCACTTTCGATTCAAGTAGAACGAAAAGA-GCATAACACTTTCGATTCTCG
1479283 ATGACAAACG
Statistics
Matches: 113, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
74 2 0.02
75 3 0.03
77 108 0.96
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (76 bp):
AGAAGGAAGCATTGCACTTTCGATTCAAGTAGAACGAAAAGAGCATAACACTTTCGATTCTCGTC
TAAAGTAAAAC
Found at i:1480580 original size:21 final size:21
Alignment explanation
Indices: 1480551--1480674 Score: 212
Period size: 21 Copynumber: 5.9 Consensus size: 21
1480541 TCCAAAATCA
1480551 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
1480572 TTACGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
1480593 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
1480614 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
1480635 TTGCGATAACACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
1480656 TTGCTATAACACTGTTCAC
1 TTGCGATAGCACTGTTCAC
1480675 ATTTTATAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 99 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:1480799 original size:16 final size:17
Alignment explanation
Indices: 1480770--1480821 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1480760 ATCATAAATA
*
1480770 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
1480787 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
1480802 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
1480820 AT
1 AT
1480822 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:1481201 original size:16 final size:17
Alignment explanation
Indices: 1481172--1481223 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1481162 ATCATAAATA
*
1481172 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
1481189 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
1481204 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
1481222 AT
1 AT
1481224 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:1481406 original size:21 final size:21
Alignment explanation
Indices: 1481380--1481463 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
1481370 AATTCGCAAT
*
1481380 GTGAACAATGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
1481401 GTGAACAGTTCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
1481422 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
1481443 GTAAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
1481464 CGAATTCTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:1481478 original size:42 final size:42
Alignment explanation
Indices: 1481390--1481484 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
1481380 GTGAACAATG
* * * * *
1481390 CTATCGCAACGGTGAACAGTTCTATCGCAACGGTGAACAGTG
1 CTATCGCAACGGTAAACAGTGCTATCGCAACGGCGAACACTA
**
1481432 CTATCGCAACGGTAAACAGTGCTATCGCAAC-GCGAATTCTAA
1 CTATCGCAACGGTAAACAGTGCTATCGCAACGGCGAACACT-A
1481474 CTATCGCAACG
1 CTATCGCAACG
1481485 TGAATTTGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (42 bp):
CTATCGCAACGGTAAACAGTGCTATCGCAACGGCGAACACTA
Found at i:1481587 original size:20 final size:19
Alignment explanation
Indices: 1481564--1481609 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1481554 GAAAATTTAT
*
1481564 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCG
*
1481584 TTGCGATTTAGAGATCGCG
1 TTGCGATCTAGAGATCGCG
1481603 TTGCGAT
1 TTGCGAT
1481610 TTTGTAGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCG
Done.