Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 27
Found at i:1264233 original size:21 final size:21
Alignment explanation
Indices: 1264207--1264295 Score: 151
Period size: 21 Copynumber: 4.2 Consensus size: 21
1264197 GATTCGTAAC
1264207 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
* *
1264228 GCGAACTTGGACTATCGCAAC
1 GCGAACTTCGACTATCGCAAT
1264249 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
1264270 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
1264291 GCGAA
1 GCGAA
1264296 TATGTAAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:1264253 original size:42 final size:42
Alignment explanation
Indices: 1264204--1264295 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
1264194 CCAGATTCGT
1264204 AACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGC
1 AACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGC
1264246 AACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGC
1 AACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGC
*
1264288 AATGCGAA
1 AACGCGAA
1264296 TATGTAAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (42 bp):
AACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGC
Found at i:1264308 original size:20 final size:20
Alignment explanation
Indices: 1264283--1264334 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1264273 AACTTGGACT
1264283 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1264303 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1264323 ATCGCAATGCGA
1 ATCGCAATGCGA
1264335 TAGTCCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1265057 original size:6 final size:6
Alignment explanation
Indices: 1265041--1265102 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
1265031 CGTCGTCTCG
1265041 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1265088 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
1265103 AATACGTGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1265212 original size:20 final size:20
Alignment explanation
Indices: 1265187--1265259 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1265177 ATTTTGGACT
1265187 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
1265207 ATCGCAACGCGAACT-TCG-ACT
1 ATCGCAATGCGAA-TAT-GTA-A
1265228 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1265248 ATCGCAATGCGA
1 ATCGCAATGCGA
1265260 TAGTCGAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1265806 original size:25 final size:26
Alignment explanation
Indices: 1265762--1265811 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1265752 AAAATTTCCC
* *
1265762 AATATATTTATAATATATATTTTAAG
1 AATATATTTATAATAAATATATTAAG
*
1265788 AATATA-TTATAGTAAATATATTAA
1 AATATATTTATAATAAATATATTAA
1265812 TCATTTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AATATATTTATAATAAATATATTAAG
Found at i:1269419 original size:1 final size:1
Alignment explanation
Indices: 1269413--1269440 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1269403 GGATCACCCG
1269413 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1269441 GAAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1270254 original size:14 final size:15
Alignment explanation
Indices: 1270230--1270258 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1270220 TCATATCTTT
1270230 AAAGTCCAAAAGCCA
1 AAAGTCCAAAAGCCA
1270245 AAAG-CCAAAAGCCA
1 AAAGTCCAAAAGCCA
1270259 GTGCTTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.28, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAGTCCAAAAGCCA
Found at i:1271473 original size:111 final size:112
Alignment explanation
Indices: 1271277--1271501 Score: 389
Period size: 111 Copynumber: 2.0 Consensus size: 112
1271267 ATTCAGTAGC
1271277 TTTCATTGGTATAGAATATTTGGGTGTTGTTTACTTGCATGGTCTTTAAGAAATTTTGTCATCTC
1 TTTCATTGGTATAGAATATTTGGGTGTTGTTTACTTGCATGGTCTTTAAGAAATTTTGTCATCTC
1271342 TTCGGTATTAGTTTTATGTGGAATTGAGG-TTCAAAGTGCAACTTGT
66 TTCGGTATTAGTTTTATGTGGAATTGAGGTTTCAAAGTGCAACTTGT
* * * *
1271388 TTTCATTGGTCTAGAATATTTGGGTGTTGTTTACTTGTATGTTCTTTAAGAAATTTTGTCATTTC
1 TTTCATTGGTATAGAATATTTGGGTGTTGTTTACTTGCATGGTCTTTAAGAAATTTTGTCATCTC
* *
1271453 TTTGGTATTAGTTTTGTGTGGAATTGAGGTTTCAAAGTGCAACTTGT
66 TTCGGTATTAGTTTTATGTGGAATTGAGGTTTCAAAGTGCAACTTGT
1271500 TT
1 TT
1271502 AGCATTTTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 88 0.82
112 19 0.18
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.48
Consensus pattern (112 bp):
TTTCATTGGTATAGAATATTTGGGTGTTGTTTACTTGCATGGTCTTTAAGAAATTTTGTCATCTC
TTCGGTATTAGTTTTATGTGGAATTGAGGTTTCAAAGTGCAACTTGT
Found at i:1277973 original size:71 final size:71
Alignment explanation
Indices: 1277857--1277999 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
1277847 CTGACAAGAG
*
1277857 ACCAACGAAAGAAATTCAATGCGTCTCAATTCGGAATTTATAGTTTCAAGGCTCACAATCCTTAT
1 ACCAACGAAAGAAATTCAATGCGTCTCAATTCCGAATTTATAGTTTCAAGGCTCACAATCCTTAT
1277922 TGGGTA
66 TGGGTA
* **
1277928 ACCAACGAAAGAAATTCAGTGCGTCTCAATTCCGAATTTATAGTTTCCGGGCTCACAATCCTTAT
1 ACCAACGAAAGAAATTCAATGCGTCTCAATTCCGAATTTATAGTTTCAAGGCTCACAATCCTTAT
1277993 TGGGTA
66 TGGGTA
1277999 A
1 A
1278000 GGACCAAGTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (71 bp):
ACCAACGAAAGAAATTCAATGCGTCTCAATTCCGAATTTATAGTTTCAAGGCTCACAATCCTTAT
TGGGTA
Found at i:1284268 original size:12 final size:12
Alignment explanation
Indices: 1284251--1284279 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1284241 TCCAATATCT
1284251 TCTTCCATCTCA
1 TCTTCCATCTCA
1284263 TCTTCCATCTCA
1 TCTTCCATCTCA
1284275 TCTTC
1 TCTTC
1284280 ATCAACTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (12 bp):
TCTTCCATCTCA
Found at i:1292201 original size:33 final size:33
Alignment explanation
Indices: 1292148--1292254 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
1292138 GAGTTTGGTA
*
1292148 GTAACGGCCTCATCAACCGATGAAGAAGCAGAT
1 GTAACGGCATCATCAACCGATGAAGAAGCAGAT
* *
1292181 GTAGCGGCATTATCAACCGATGAAGAAGCAGAT
1 GTAACGGCATCATCAACCGATGAAGAAGCAGAT
1292214 GTAACGGCATCATCAACCGATGAAGAAGCAGAT
1 GTAACGGCATCATCAACCGATGAAGAAGCAGAT
1292247 GTAACGGC
1 GTAACGGC
1292255 TTTTGGCTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.16
Consensus pattern (33 bp):
GTAACGGCATCATCAACCGATGAAGAAGCAGAT
Found at i:1293216 original size:37 final size:36
Alignment explanation
Indices: 1293141--1293216 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1293131 TTTTTATATT
*
1293141 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1293177 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1293214 TTT
1 TTT
1293217 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1293398 original size:20 final size:20
Alignment explanation
Indices: 1293362--1293399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1293352 ATCTTATTCT
**
1293362 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1293382 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1293400 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1297751 original size:30 final size:30
Alignment explanation
Indices: 1297709--1297780 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1297699 ACTGGTAAAG
* * *
1297709 AACCGGT-AGAACCGACTGAGAACCGATAA
1 AACCGGTGTGAACCGACTGAAAACCGACAA
* *
1297738 AACCAGG-GTGAACCGGCTGAAAACTGACAA
1 AACC-GGTGTGAACCGACTGAAAACCGACAA
1297768 AACCGGTGTGAAC
1 AACCGGTGTGAAC
1297781 TGCCGGTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (30 bp):
AACCGGTGTGAACCGACTGAAAACCGACAA
Found at i:1299139 original size:16 final size:16
Alignment explanation
Indices: 1299118--1299153 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1299108 ATGAACGCTC
1299118 AATCACCTCTTGTTAT
1 AATCACCTCTTGTTAT
1299134 AATCACCTCTTGTTAT
1 AATCACCTCTTGTTAT
1299150 AATC
1 AATC
1299154 GCTGGTACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (16 bp):
AATCACCTCTTGTTAT
Found at i:1299921 original size:24 final size:24
Alignment explanation
Indices: 1299883--1299931 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1299873 AATGAGAAAT
* *
1299883 TTTATAATACAAATATTATTTTAA
1 TTTATAATACAAATATAATGTTAA
1299907 TTTATAATA-AGAATATAATGTTAA
1 TTTATAATACA-AATATAATGTTAA
1299931 T
1 T
1299932 ACATATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTATAATACAAATATAATGTTAA
Found at i:1300018 original size:2 final size:2
Alignment explanation
Indices: 1300011--1300036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1300001 TGTCACTAAA
1300011 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1300037 GCATAATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1300551 original size:22 final size:21
Alignment explanation
Indices: 1300515--1300555 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1300505 AAACTGCCTA
1300515 ATTTAAAATTCATTTCAATAGC
1 ATTTAAAATTCATTT-AATAGC
1300537 ATTTAAAATAT-ATTTAATA
1 ATTTAAAAT-TCATTTAATA
1300556 TACTACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 13 0.72
23 1 0.06
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTAAAATTCATTTAATAGC
Found at i:1300568 original size:19 final size:19
Alignment explanation
Indices: 1300544--1300590 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1300534 AGCATTTAAA
1300544 ATATATTTAATA-TACTACT
1 ATATATTTAATACTACTA-T
1300563 ATATATTT-ATACTACTAT
1 ATATATTTAATACTACTAT
*
1300581 ATATAATTAA
1 ATATATTTAA
1300591 AGTAGTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATTTAATACTACTAT
Found at i:1300575 original size:16 final size:16
Alignment explanation
Indices: 1300554--1300584 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1300544 ATATATTTAA
1300554 TATACTACTATATATT
1 TATACTACTATATATT
1300570 TATACTACTATATAT
1 TATACTACTATATAT
1300585 AATTAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (16 bp):
TATACTACTATATATT
Found at i:1302771 original size:5 final size:5
Alignment explanation
Indices: 1302757--1302810 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
1302747 CGCCGTCCGT
* * * *
1302757 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1302807 CTCG
1 CTCG
1302811 TGGTCGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:1302819 original size:6 final size:6
Alignment explanation
Indices: 1302808--1302898 Score: 146
Period size: 6 Copynumber: 15.2 Consensus size: 6
1302798 TCGGCTCGGC
* * * *
1302808 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1302856 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1302899 AATACGTGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:1303197 original size:22 final size:22
Alignment explanation
Indices: 1303172--1303226 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1303162 TCAGGAGTTA
* *
1303172 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1303194 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1303216 CGGGAGTTATA
1 CAGGAGTTATA
1303227 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1308766 original size:5 final size:5
Alignment explanation
Indices: 1308752--1308800 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
1308742 GTCCGTCCGT
* * * *
1308752 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1308801 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1308809 original size:6 final size:6
Alignment explanation
Indices: 1308798--1308864 Score: 98
Period size: 6 Copynumber: 11.2 Consensus size: 6
1308788 TCGGCTCGGC
* * * *
1308798 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1308846 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
1308865 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.06, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:1309164 original size:22 final size:22
Alignment explanation
Indices: 1309139--1309193 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1309129 TCATGAGTTA
* *
1309139 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1309161 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1309183 CGGGAGTTATA
1 CAGGAGTTATA
1309194 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1310378 original size:84 final size:84
Alignment explanation
Indices: 1310249--1310402 Score: 290
Period size: 84 Copynumber: 1.8 Consensus size: 84
1310239 CACAAAAATA
* *
1310249 ACAATTTTGAAATAAACTATGCATTTATGGGCCAAATTATACAACTTTTAAAATTATATTTTTGG
1 ACAATTTTGAAATAAACTATGCATTAATGGGCCAAATTATACAACTTTTAAAATTACATTTTTGG
1310314 TCCCTGACCCACGAAAACG
66 TCCCTGACCCACGAAAACG
1310333 ACAATTTTGAAATAAACTATGCATTAATGGGCCAAATTATACAACTTTTAAAATTACATTTTTGG
1 ACAATTTTGAAATAAACTATGCATTAATGGGCCAAATTATACAACTTTTAAAATTACATTTTTGG
1310398 TCCCT
66 TCCCT
1310403 AAACTTTTAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (84 bp):
ACAATTTTGAAATAAACTATGCATTAATGGGCCAAATTATACAACTTTTAAAATTACATTTTTGG
TCCCTGACCCACGAAAACG
Found at i:1313227 original size:28 final size:29
Alignment explanation
Indices: 1313148--1313232 Score: 118
Period size: 28 Copynumber: 2.9 Consensus size: 29
1313138 TACCTAACTC
1313148 TCATCTAACTAAATTGATGTAAGCAATGACA
1 TCAT-TAACTAAA-TGATGTAAGCAATGACA
*
1313179 TCATTAATTAAATGATGTAAGCAATGACA
1 TCATTAACTAAATGATGTAAGCAATGACA
* *
1313208 TC-TTTACTAAATGATATAAGCAATG
1 TCATTAACTAAATGATGTAAGCAATG
1313233 GAATTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 20 0.40
29 19 0.38
30 7 0.14
31 4 0.08
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
TCATTAACTAAATGATGTAAGCAATGACA
Found at i:1316616 original size:15 final size:15
Alignment explanation
Indices: 1316596--1316625 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1316586 CTTTCTCATA
1316596 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
1316611 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
1316626 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:1317938 original size:29 final size:29
Alignment explanation
Indices: 1317895--1317977 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
1317885 TTCACCTAAC
1317895 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1317925 TAAATGATGTAAGCAATGACATCATTACT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
1317954 TAAATGATGTAAGTAATGAAATCA
1 TAAATGATGTAAGCAATGACATCA
1317978 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1318949 original size:79 final size:78
Alignment explanation
Indices: 1318865--1319019 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 78
1318855 TATTATATTA
*
1318865 GAAAATGATAAAAATTCAATTAATTAACTAAAAAGATATAAAGATACAAGTAAACACTTTTTTTC
1 GAAAATGATAAAAATTCAATTAATTAACTAAAAAGATATAAAGAAACAAGTAAACAC-TTTTTTC
1318930 TAA-ATAAACAATTG
65 -AAGATAAACAATTG
*
1318944 GAAAATGATAAAAATTCAATTAATTAACTAAAAAGATATAAAGAAACGAGTAAACACTTTTTTCA
1 GAAAATGATAAAAATTCAATTAATTAACTAAAAAGATATAAAGAAACAAGTAAACACTTTTTTCA
1319009 AGATAAACAAT
66 AGATAAACAAT
1319020 AAAGGATAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
77 2 0.03
78 16 0.22
79 55 0.75
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.28
Consensus pattern (78 bp):
GAAAATGATAAAAATTCAATTAATTAACTAAAAAGATATAAAGAAACAAGTAAACACTTTTTTCA
AGATAAACAATTG
Found at i:1324447 original size:33 final size:29
Alignment explanation
Indices: 1324412--1324498 Score: 115
Period size: 28 Copynumber: 3.0 Consensus size: 29
1324402 TGTGCCACAG
* *
1324412 AGAGGGAAAGGTAGCATCTTGGCTGAAGCT
1 AGAGAGAAAGGTAGCATCTT-GCTCAAGCT
*
1324442 A-AGAGAACGGTAGCATCTTGCTCAAGCT
1 AGAGAGAAAGGTAGCATCTTGCTCAAGCT
*
1324470 A-AGAGAACGGTAGCATCTTGCTCAAGCT
1 AGAGAGAAAGGTAGCATCTTGCTCAAGCT
1324498 A
1 A
1324499 AGAATCTAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 37 0.69
29 16 0.30
30 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (29 bp):
AGAGAGAAAGGTAGCATCTTGCTCAAGCT
Found at i:1324476 original size:28 final size:28
Alignment explanation
Indices: 1324421--1324501 Score: 144
Period size: 28 Copynumber: 2.9 Consensus size: 28
1324411 GAGAGGGAAA
*
1324421 GGTAGCATCTTGGCTGAAGCTAAGAGAAC
1 GGTAGCATCTT-GCTCAAGCTAAGAGAAC
1324450 GGTAGCATCTTGCTCAAGCTAAGAGAAC
1 GGTAGCATCTTGCTCAAGCTAAGAGAAC
1324478 GGTAGCATCTTGCTCAAGCTAAGA
1 GGTAGCATCTTGCTCAAGCTAAGA
1324502 ATCTAGCAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 40 0.78
29 11 0.22
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (28 bp):
GGTAGCATCTTGCTCAAGCTAAGAGAAC
Found at i:1325058 original size:32 final size:35
Alignment explanation
Indices: 1324993--1325058 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 35
1324983 ATTTAGAATT
*
1324993 TAAAATATAAAATATTAAAAGTATTAAATAAATAC
1 TAAAATATAAAATATTAAAAGTATTAAAAAAATAC
*
1325028 TAAAA-ATAAAAT-TT-AAATTATTAAAAAAATA
1 TAAAATATAAAATATTAAAAGTATTAAAAAAATA
1325059 TTATATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.52
33 2 0.07
34 7 0.24
35 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (35 bp):
TAAAATATAAAATATTAAAAGTATTAAAAAAATAC
Found at i:1327438 original size:19 final size:19
Alignment explanation
Indices: 1327414--1327453 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1327404 CACCCTTAAT
1327414 TCTCTTGGAGCGTTTATGG
1 TCTCTTGGAGCGTTTATGG
1327433 TCTCTTGGAGCGTTTATGG
1 TCTCTTGGAGCGTTTATGG
1327452 TC
1 TC
1327454 ATTGGATCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.17, G:0.30, T:0.42
Consensus pattern (19 bp):
TCTCTTGGAGCGTTTATGG
Found at i:1327883 original size:28 final size:30
Alignment explanation
Indices: 1327840--1327898 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1327830 ATATATATTT
*
1327840 ATATATACGTATATTTT-AAAAACTATATA
1 ATATATACGTATATTTTCAAAAACTACATA
*
1327869 ATATATA-TTATATTTTCAAAAACTACATA
1 ATATATACGTATATTTTCAAAAACTACATA
1327898 A
1 A
1327899 CATGTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (30 bp):
ATATATACGTATATTTTCAAAAACTACATA
Found at i:1327953 original size:21 final size:21
Alignment explanation
Indices: 1327914--1327954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1327904 TTTCAAAAAT
* *
1327914 TCTATATATTATATGTTTTCA
1 TCTATATATTACATATTTTCA
*
1327935 TCTATATTTTACATATTTTC
1 TCTATATATTACATATTTTC
1327955 TGAAATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (21 bp):
TCTATATATTACATATTTTCA
Found at i:1330831 original size:20 final size:20
Alignment explanation
Indices: 1330806--1330847 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1330796 ACGAAGAACA
*
1330806 AGTATCGATACTATCCCTAT
1 AGTATCGATACTATACCTAT
*
1330826 AGTATCGATACTCTACCTAT
1 AGTATCGATACTATACCTAT
1330846 AG
1 AG
1330848 AAGTCATAAA
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:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTATACCTAT
Found at i:1332263 original size:13 final size:13
Alignment explanation
Indices: 1332227--1332272 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1332217 ATATTTGTGG
*
1332227 TTATATTAAAAAA
1 TTATATTAAAAAT
*
1332240 TTACA--AAAAAT
1 TTATATTAAAAAT
1332251 TTATATTAAAAAT
1 TTATATTAAAAAT
1332264 TTA-ATTAAA
1 TTATATTAAA
1332273 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.32
12 6 0.21
13 13 0.46
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATATTAAAAAT
Found at i:1333627 original size:13 final size:13
Alignment explanation
Indices: 1333583--1333639 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 13
1333573 ATATTTGTGG
1333583 TTATATTAAAAAA
1 TTATATTAAAAAA
*
1333596 TTACA--AAAAAA
1 TTATATTAAAAAA
*
1333607 TT-T-GTAAAAAA
1 TTATATTAAAAAA
1333618 TTATATTAAAAAA
1 TTATATTAAAAAA
1333631 TTA-ATTAAA
1 TTATATTAAA
1333640 TTTCATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 16 0.43
12 7 0.19
13 14 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
TTATATTAAAAAA
Found at i:1333976 original size:19 final size:20
Alignment explanation
Indices: 1333952--1333995 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1333942 TTATCCGGGA
1333952 AAAAAT-CGGTATGGGGTTT
1 AAAAATCCGGTATGGGGTTT
*
1333971 AAAAATCCGGTTTGGGGTTT
1 AAAAATCCGGTATGGGGTTT
1333991 AAAAA
1 AAAAA
1333996 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (20 bp):
AAAAATCCGGTATGGGGTTT
Found at i:1334045 original size:16 final size:16
Alignment explanation
Indices: 1334024--1334054 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1334014 TTACCGGATT
1334024 AAAAACCGATTTTTTA
1 AAAAACCGATTTTTTA
*
1334040 AAAAACCGGTTTTTT
1 AAAAACCGATTTTTT
1334055 TTCAAACCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (16 bp):
AAAAACCGATTTTTTA
Found at i:1334718 original size:22 final size:22
Alignment explanation
Indices: 1334671--1334719 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1334661 TGTTTAAAAT
* * * *
1334671 TTAATGTTATGAATTGAGCAAT
1 TTAATATTATGAATCGAACAAG
1334693 TTAATATTATGAATCGAACAAG
1 TTAATATTATGAATCGAACAAG
1334715 TTAAT
1 TTAAT
1334720 TTGTGAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (22 bp):
TTAATATTATGAATCGAACAAG
Found at i:1343856 original size:15 final size:16
Alignment explanation
Indices: 1343836--1343875 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1343826 GTTTACTTCA
*
1343836 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
1343851 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
1343867 GAATGATTC
1 GAATGATTC
1343876 GGAGGCTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:1343959 original size:27 final size:27
Alignment explanation
Indices: 1343928--1343994 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
1343918 AATAATGGCT
1343928 CTGAATCATTCAGAATGTACTTTGATG
1 CTGAATCATTCAGAATGTACTTTGATG
1343955 CTGAATCATTCAGAATGTACTTTGATG
1 CTGAATCATTCAGAATGTACTTTGATG
1343982 CTGAATCATTCAG
1 CTGAATCATTCAG
1343995 CACTGTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTTGATG
Found at i:1347076 original size:27 final size:27
Alignment explanation
Indices: 1347037--1347099 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
1347027 GCTAACCCTT
**
1347037 CAGCTGGTTGGTTGCTTTTCTTTTCTC
1 CAGCTGGAAGGTTGCTTTTCTTTTCTC
1347064 CAGCTGGAAGGTTGCTTTTCTTTTCTC
1 CAGCTGGAAGGTTGCTTTTCTTTTCTC
1347091 CAGCTGGAA
1 CAGCTGGAA
1347100 ACTAGATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (27 bp):
CAGCTGGAAGGTTGCTTTTCTTTTCTC
Found at i:1353032 original size:120 final size:120
Alignment explanation
Indices: 1352886--1353104 Score: 384
Period size: 120 Copynumber: 1.8 Consensus size: 120
1352876 CCGAGTCGAG
*
1352886 CTCGAGTATTGCTGACCTCGACTCGAACTCGAAAAGTTTAAAATTAGGCTCAACTCGACTCGAAA
1 CTCGAGTATTGCTGACCTCGACTCGAACTAGAAAAGTTTAAAATTAGGCTCAACTCGACTCGAAA
*
1352951 ACTCTCGAGCTAAAAATTATCAAGCTCAGCTCGAACTCAAAATATAATATTGAAA
66 ACTCGCGAGCTAAAAATTATCAAGCTCAGCTCGAACTCAAAATATAATATTGAAA
* * * *
1353006 CTCGAGTATTGTTGAGCTCGACTCGAACTAGAAAAGTTTAAAATTAGGCTCGACTCGATTCGAAA
1 CTCGAGTATTGCTGACCTCGACTCGAACTAGAAAAGTTTAAAATTAGGCTCAACTCGACTCGAAA
1353071 ACTCGCGAGCTAAAAATTATCAAGCTCAGCTCGA
66 ACTCGCGAGCTAAAAATTATCAAGCTCAGCTCGA
1353105 CTCGAACTCG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 93 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (120 bp):
CTCGAGTATTGCTGACCTCGACTCGAACTAGAAAAGTTTAAAATTAGGCTCAACTCGACTCGAAA
ACTCGCGAGCTAAAAATTATCAAGCTCAGCTCGAACTCAAAATATAATATTGAAA
Found at i:1357693 original size:24 final size:22
Alignment explanation
Indices: 1357666--1357719 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1357656 GAAAACATGC
* *
1357666 CATAAATGAAAAGAAAAAATGTGT
1 CATAAA-G-AAAGAAAAAATATAT
*
1357690 CATAAAGGAAGAAAAAATATAT
1 CATAAAGAAAGAAAAAATATAT
1357712 CATAAAGA
1 CATAAAGA
1357720 CGAAATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 19 0.73
23 1 0.04
24 6 0.23
ACGTcount: A:0.61, C:0.06, G:0.15, T:0.19
Consensus pattern (22 bp):
CATAAAGAAAGAAAAAATATAT
Found at i:1357724 original size:21 final size:22
Alignment explanation
Indices: 1357676--1357718 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1357666 CATAAATGAA
* *
1357676 AAGAAAAAATGTGTCATAAAGG
1 AAGAAAAAATATATCATAAAGG
1357698 AAGAAAAAATATATCATAAAG
1 AAGAAAAAATATATCATAAAG
1357719 ACGAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (22 bp):
AAGAAAAAATATATCATAAAGG
Found at i:1359724 original size:54 final size:54
Alignment explanation
Indices: 1359665--1359770 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
1359655 GAATTCACGC
*
1359665 GTGAATGTTATAATTTTAATAAAATCCTAATGTGTATATTCGTAAGTGTGAGAT
1 GTGAATGTTATAATTTTAATAAAATCCTAATGTGTATATTCGAAAGTGTGAGAT
1359719 GTGAATGTTATAATTTTAATAAAATCCTAATGTGTATATTCGAAAGTGTGAG
1 GTGAATGTTATAATTTTAATAAAATCCTAATGTGTATATTCGAAAGTGTGAG
1359771 GTACAAATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (54 bp):
GTGAATGTTATAATTTTAATAAAATCCTAATGTGTATATTCGAAAGTGTGAGAT
Found at i:1361181 original size:2 final size:2
Alignment explanation
Indices: 1361174--1361198 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1361164 ACTTATATGT
1361174 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
1361199 GTACACATTT
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:1362586 original size:10 final size:10
Alignment explanation
Indices: 1362571--1362604 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1362561 TTCATTTACC
1362571 ATTTATTTTT
1 ATTTATTTTT
1362581 ATTTATTTTT
1 ATTTATTTTT
* *
1362591 ATCTATTTCT
1 ATTTATTTTT
1362601 ATTT
1 ATTT
1362605 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1373038 original size:105 final size:105
Alignment explanation
Indices: 1372854--1373506 Score: 1018
Period size: 105 Copynumber: 6.4 Consensus size: 105
1372844 AGGTTTTACC
*
1372854 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
1372919 ACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
*
1372959 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1373024 ACGAAGGGATCGCTGCTTGTCAACAACAACTTCCCAATCT
66 ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
*
1373064 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1373129 ACGAAGGGACCGCTGCTTGTCAACAACGACTTCCCAATCT
66 ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
*
1373169 CAGAG-C-----CAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1373228 ACGAAGGGACCGCTGCTTGTCAACAACGACTTCCCAATCT
66 ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
1373268 CAGAG-C-----CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1373327 ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
66 ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
1373367 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1373432 ACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-AT-T
66 ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
** * * *
1373467 CAGATTCAATTTCAATTTCACAACGAAGGACATCGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1373507 GAAACAACAC
Statistics
Matches: 522, Mismatches: 19, Indels: 19
0.93 0.03 0.03
Matches are distributed among these distances:
99 195 0.37
100 37 0.07
101 2 0.00
102 1 0.00
103 2 0.00
104 6 0.01
105 279 0.53
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCT
Found at i:1374993 original size:2 final size:2
Alignment explanation
Indices: 1374981--1375024 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1374971 ACTTATATGT
1374981 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1375022 TA T
1 TA T
1375025 GTACACATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1379337 original size:24 final size:24
Alignment explanation
Indices: 1379293--1379363 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
1379283 AAACGGAGAT
* * *
1379293 ATCAGAAATCAAAATAGAATTCAG
1 ATCAAAAATCAGAACAGAATTCAG
*
1379317 ATCAAAAATCAGAACATAATTCAG
1 ATCAAAAATCAGAACAGAATTCAG
* ***
1379341 GTCATGTATCAGAACAGAATTCA
1 ATCAAAAATCAGAACAGAATTCA
1379364 AGTCGTAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAAATCAGAACAGAATTCAG
Found at i:1379375 original size:24 final size:24
Alignment explanation
Indices: 1379298--1379375 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
1379288 GAGATATCAG
* * *
1379298 AAATCAAAATAGAATTC-AGATCAA
1 AAATCAGAACAGAATTCAAG-TCAT
* *
1379322 AAATCAGAACATAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAT
** *
1379346 GTATCAGAACAGAATTCAAGTCGT
1 AAATCAGAACAGAATTCAAGTCAT
1379370 AAATCA
1 AAATCA
1379376 AATAAAATAT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAT
Found at i:1391706 original size:19 final size:20
Alignment explanation
Indices: 1391679--1391727 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1391669 TATTTTTAAA
*
1391679 AATAATATTATTGA-AATAT
1 AATATTATTATTGAGAATAT
1391698 AATATTATT-TTGAGAATAT
1 AATATTATTATTGAGAATAT
**
1391717 TGTATTATTAT
1 AATATTATTAT
1391728 ATTTGATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 20 0.80
20 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
AATATTATTATTGAGAATAT
Found at i:1391878 original size:21 final size:22
Alignment explanation
Indices: 1391840--1391887 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1391830 TTTTAACAAG
*
1391840 TAAAATTTTAATATAAAA-TTA
1 TAAAATTTGAATATAAAATTTA
1391861 TAAATATTTGAATA-AAAATTTA
1 TAAA-ATTTGAATATAAAATTTA
1391883 TAAAA
1 TAAAA
1391888 AAATATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAATTTGAATATAAAATTTA
Found at i:1392273 original size:3 final size:3
Alignment explanation
Indices: 1392265--1392296 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1392255 ACTCTTTGTA
1392265 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1392297 ATTTTGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1393570 original size:22 final size:23
Alignment explanation
Indices: 1393526--1393574 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1393516 AGATAAAAAG
1393526 AAAGAAAACGGCTAGTTTTTTTA
1 AAAGAAAACGGCTAGTTTTTTTA
*
1393549 AAAGAAAACGGCTAGTTTTTTAA
1 AAAGAAAACGGCTAGTTTTTTTA
1393572 AAA
1 AAA
1393575 ATATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (23 bp):
AAAGAAAACGGCTAGTTTTTTTA
Found at i:1395491 original size:21 final size:21
Alignment explanation
Indices: 1395462--1395505 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1395452 TAAACTAAAA
*
1395462 TTAACTACTCAAATTATGTTTT
1 TTAACTACTCAAAATAT-TTTT
*
1395484 TTAA-TACTTAAAATATTTTT
1 TTAACTACTCAAAATATTTTT
1395504 TT
1 TT
1395506 GGTCAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAACTACTCAAAATATTTTT
Found at i:1398335 original size:32 final size:31
Alignment explanation
Indices: 1398299--1398359 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1398289 TTGAATTTTT
*
1398299 GGTCGGGTTAATACCAT-ATCGGTTAGATTTCG
1 GGTCGGGTCAATA-CATGATCGGTT-GATTTCG
*
1398331 GGTCGGGTCAATATATGATCGGTTGATTT
1 GGTCGGGTCAATACATGATCGGTTGATTT
1398360 TCAGTTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (31 bp):
GGTCGGGTCAATACATGATCGGTTGATTTCG
Found at i:1398987 original size:20 final size:18
Alignment explanation
Indices: 1398941--1398989 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1398931 ACTTTCTATT
1398941 ATTTTATTAA-AAATTTA
1 ATTTTATTAATAAATTTA
1398958 ATATTT-TTAATAAATTATCA
1 AT-TTTATTAATAAATT-T-A
1398978 ATTTTATTAATA
1 ATTTTATTAATA
1398990 TTGAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 4 0.15
20 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATTAATAAATTTA
Found at i:1401283 original size:23 final size:24
Alignment explanation
Indices: 1401231--1401286 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
1401221 AAATCAAAAC
*
1401231 ATATAAAAA-TAATAATATTTCGA
1 ATATAAAAATTAATAATATTTCAA
* *
1401254 AGA-AAAAATTAATAAT-TTTTAA
1 ATATAAAAATTAATAATATTTCAA
1401276 ATATAAAAATT
1 ATATAAAAATT
1401287 TAAAGTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATATAAAAATTAATAATATTTCAA
Found at i:1412593 original size:21 final size:21
Alignment explanation
Indices: 1412569--1412616 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1412559 TTCCAACCCT
1412569 GCAAAAGAAGAAAATTTTACA
1 GCAAAAGAAGAAAATTTTACA
1412590 GCAAAAGAAGAAAATTTTACA
1 GCAAAAGAAGAAAATTTTACA
1412611 GCAAAA
1 GCAAAA
1412617 CCTTATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (21 bp):
GCAAAAGAAGAAAATTTTACA
Found at i:1421102 original size:20 final size:20
Alignment explanation
Indices: 1421077--1421114 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1421067 ATCTTAAAGT
*
1421077 TTAAACTCTAAATTCTAAAC
1 TTAAACTCTAAATCCTAAAC
*
1421097 TTAAACTTTAAATCCTAA
1 TTAAACTCTAAATCCTAA
1421115 CTAAATATTT
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:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAACTCTAAATCCTAAAC
Found at i:1421197 original size:11 final size:11
Alignment explanation
Indices: 1421183--1421209 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1421173 ATATTATAAA
1421183 AAGTAATCTGT
1 AAGTAATCTGT
1421194 AAGTAATCTGT
1 AAGTAATCTGT
1421205 AAGTA
1 AAGTA
1421210 TATTTATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (11 bp):
AAGTAATCTGT
Found at i:1421970 original size:19 final size:20
Alignment explanation
Indices: 1421946--1421996 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1421936 AATGACCAAT
1421946 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1421965 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1421985 AAAATCGCAACG
1 AAAATCGCAACG
1421997 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1421990 original size:20 final size:20
Alignment explanation
Indices: 1421946--1422243 Score: 147
Period size: 20 Copynumber: 14.6 Consensus size: 20
1421936 AATGACCAAT
* *
1421946 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1421965 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1421985 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1422005 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1422025 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1422046 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
1422069 AAAATCGCAA--TGATTTTG
1 AAAATCGCAACGCGATTTAG
* * *
1422087 ATTGAATCGCAATGCGATTTAT
1 A--AAATCGCAACGCGATTTAG
* * *
1422109 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1422129 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1422152 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1422172 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1422192 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1422212 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1422232 AAAATCGCAACG
1 AAAATCGCAACG
1422244 TTCAAAAGAA
Statistics
Matches: 221, Mismatches: 42, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 154 0.70
21 19 0.09
22 6 0.03
23 23 0.10
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1422137 original size:40 final size:40
Alignment explanation
Indices: 1422050--1422241 Score: 213
Period size: 40 Copynumber: 4.7 Consensus size: 40
1422040 GCTTCCAAGT
*** **
1422050 TCGCAACGCGATTTAGAAGAAAATCGCAATGATTTTGATTGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
1422093 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
1422133 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
1422176 TCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
1422216 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
1422242 CGTTCAAAAG
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
40 73 0.58
41 2 0.02
42 4 0.03
43 47 0.37
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:1422160 original size:83 final size:83
Alignment explanation
Indices: 1422050--1422233 Score: 278
Period size: 83 Copynumber: 2.2 Consensus size: 83
1422040 GCTTCCAAGT
*** ** * * *
1422050 TCGCAACGCGATTTAGAAGAAAATCGCAATGATTTTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGAGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
1422115 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
*
1422133 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGAGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1422198 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
1422216 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
1422234 AATCGCAACG
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 91 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGAGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:1422397 original size:5 final size:5
Alignment explanation
Indices: 1422333--1422393 Score: 77
Period size: 5 Copynumber: 12.2 Consensus size: 5
1422323 CACGTATTAC
* * *
1422333 CACGA CACGA CACGA CACGA CACGA CACGA CACGA CCCGA CCCGA CCCGA
1 CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
* *
1422383 CCCGA CCCGA C
1 CACGA CACGA C
1422394 CCGAGACGAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.31, C:0.49, G:0.20, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:1422864 original size:21 final size:20
Alignment explanation
Indices: 1422825--1422878 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
1422815 AATAAGCTCG
1422825 CGTTGCGATTTTC-TTTTGA
1 CGTTGCGATTTTCTTTTTGA
1422844 CCGTTGCGATTTTCTTTTTGA
1 -CGTTGCGATTTTCTTTTTGA
1422865 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1422879 AAATCGCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.09, C:0.19, G:0.20, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTTGA
Found at i:1422905 original size:19 final size:20
Alignment explanation
Indices: 1422865--1422915 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1422855 TTCTTTTTGA
*
1422865 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1422885 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1422904 CGTTGCGATTTT
1 CGTTGCGATTTT
1422916 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1424106 original size:31 final size:31
Alignment explanation
Indices: 1424065--1424131 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1424055 ATAATAACAC
* ** *
1424065 AAATGATCATTAATGTTATCGATTTGTAATA
1 AAATAATCATTAACATTATCGATTTATAATA
*
1424096 AAATAATCATTAGCATTATCGATTTATAATA
1 AAATAATCATTAACATTATCGATTTATAATA
1424127 AAATA
1 AAATA
1424132 GTCACTCTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (31 bp):
AAATAATCATTAACATTATCGATTTATAATA
Found at i:1425005 original size:31 final size:31
Alignment explanation
Indices: 1424970--1425029 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1424960 AACACAAATG
* *
1424970 ATCATTAATGTTATCGATTTGTAACAAAAAA
1 ATCATTAACGTTATCGATTTATAACAAAAAA
*
1425001 ATCATTAACGTTATCGATTTATAATAAAA
1 ATCATTAACGTTATCGATTTATAACAAAA
1425030 TGGTCACTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (31 bp):
ATCATTAACGTTATCGATTTATAACAAAAAA
Found at i:1425887 original size:31 final size:31
Alignment explanation
Indices: 1425840--1425917 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1425830 ATTGTCAACA
*
1425840 ATAACACAAATGATCATTAATGTTATCGATTT
1 ATAACA-AAATGATCATTAATCTTATCGATTT
* * *
1425872 GTAACAAAATAATCATTAGTCTTATCGATTT
1 ATAACAAAATGATCATTAATCTTATCGATTT
*
1425903 ATAATAAAATGATCA
1 ATAACAAAATGATCA
1425918 CTCCACCGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 34 0.87
32 5 0.13
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (31 bp):
ATAACAAAATGATCATTAATCTTATCGATTT
Found at i:1425913 original size:882 final size:866
Alignment explanation
Indices: 1423733--1426017 Score: 2893
Period size: 900 Copynumber: 2.6 Consensus size: 866
1423723 GTCGGATCGA
* * * * *
1423733 AACCCATCAGGTTCGAATCCCATGTCCATCCATAGATATTGAAGGCAAGTTACGAAGAGCTTAAC
1 AACCCATAAGGTTCGAATCCAATGACCATCC-TAGATATTGAAGGCAAGTTACGAAGCGCTTACC
* *
1423798 ATTGAGTACAAAATCGATAAAAATGAATAAATATAAAAAGTATATAATACGATTTGAAGATAACC
65 ATAGAGTACAAAATCGATAAAAATGAATAAATATAAAAAGTATATAATACGATTTGAAGAGAACC
1423863 TAATCTATCTACTCTCAAAATTTGCAGAACC-AAAAAAAATATTTAAATCATTAAATTTGGGGGA
130 TAATCTATCTACTCTCAAAATTTGCAGAACCTAAAAAAAATATTTAAATCATTAAATTTGGGGGA
* *
1423927 CCAGGGATTAATTTGCGTATTTTTCAAATTATCATGGGCTTTAAAGACCAATTATGGAGATTTAA
195 CCAGGGATTAATTTGCGTATTTTTCACATTATCATGGACTTTAAAGACCAATTATGGAGATTTAA
* *
1423992 GGGCAATTTACACAGATGATCATTAATATTTGATTAAATTTTCATTTTTTCATTGAACTGTCAAT
260 GGGCAATTTACACAAATGATCATTAATATTTGATTAAATTTTCATTTTTTCATTGAACTGTCAAC
*
1424057 AATAACACAAATGATCATTAATGTTATCGATTTGTAATAAAATAATCATTAGCATTATCGATTTA
325 AATAACACAAATGATCATTAATGTTATCGATTTGTAACAAAATAATCATTAGCATTATCGATTTA
* * * * *
1424122 TAATAAAATAGTCACTCTACCATCGTTCCCGTTAAATTGGTGATGTTGTAATGTTAACAAAAAGG
390 TAATAAAATGGTCACTCCACCGTCATTCCCGTTAAATTGGTGATGTTGTAACGTTAACAAAAAGG
1424187 GTAATGTTTAATTTTACTCCTAAACTACTACTAAAACATCAAATAGGTTCTTTATCGAAAAATAT
455 GTAATGTTTAATTTTACTCCTAAACTACTACTAAAACATCAAATAGG-TCTTTATCGAAAAATAT
1424252 ATATACAATAATTTAGATATTGATAAGGATGGGCATGGGTCGAGTTGGGTTTTTGGTCCACCCGA
519 ATATACAATAATTTAGATATTGATAAGGATGGGCATGGGTCGAGTTGGGTTTTTGGTCCACCCGA
* * *
1424317 CCCGAGAACAAGAAATTCGACCTGACCAAAACAAGATTTCACCCGTCCCAAACTCGACCCGATAT
584 CCCGAGAACAAGAAATTCCACCTGACCAAAACAAGATTCCACCCGACCCAAACTCGACCCGATAT
* * *
1424382 ATAACTTAAAAACACGATCCGACCTGAAATAATAAAAAATATTATTGTTATTCAATAAAAAATAG
649 ATAACTTAAAAACACGATCCAACCTAAAATAATAAAAAATATTATTGTTATTAAATAAAAAATAG
*
1424447 TGACTTAATTGGAAAAAAATATATAGAGAGGGGTATTATTATAATTATTCATAAATATATAAGTT
714 TGACTTAATTGG-AAAAAATATATAGAGAGGGGTATTATTATAATTATTCATAAATATATAAGAT
* * * * **
1424512 AAGATTATATGTTTTTTTGGGTCGAGTCGGGTATTTTTCACTTTAAACCCGAACACAACCCGACC
778 AAAATAATATGATTTTTTGGGTCGAGTCGGATATTTTTCACCCTAAACCCGAACACAACCCGACC
*
1424577 CAAATATCACATTAAAAAAAAACG
843 CAAACATCACATTAAAAAAAAACG
* * ** *** * * * *
1424601 ACCCGACCCGACCCTGA-TTTAAAAAAAAAAATCGACACGACTCGATCGGGTCGAGTCGGAACCC
1 A----ACCC-A---TAAGGTT--CGAATCCAAT-GAC-C-A-TC-CT-AGAT--A-T-TGAA---
** * * * * * *** * ** * * *
1424665 ATCAAGTT-TGAATCTCATGCTCACCCCTAGA-TATTGAAGGCCAGTTACGAA-GAGCTTAACAT
43 GGCAAGTTACGAA--GC--GCTTA-CCATAGAGTA--CAAAATC-GATAAAAATGA-ATAAATAT
* * * *** * * *** * * * *
1424727 --AGAGTACAAAAT-CGATAAAAAAAATGAA--TAAATATAAAAAGTATATAATACGATTTGAAG
99 AAAAAGTATATAATACGAT-TTGAAGA-GAACCT-AATCTATCTACTCT-CAA-A--ATTTG--C
*
1424787 AGAACCTAAAAAAATTATTTAAATCATTAAATTTGGGGGACCAGGGATTAATTTGCGTATTTTTC
155 AGAACCTAAAAAAAATATTTAAATCATTAAATTTGGGGGACCAGGGATTAATTTGCGTATTTTTC
*
1424852 ACATTATCATGGACTTTAAAGACCAAATATGGAGATTTAAGGGCAATTTACACAAATGATCATTA
220 ACATTATCATGGACTTTAAAGACCAATTATGGAGATTTAAGGGCAATTTACACAAATGATCATTA
*
1424917 ATATTTGATTAAATTTTCGTTTTTTCATTGAACTGTCAACAATAACACAAATGATCATTAATGTT
285 ATATTTGATTAAATTTTCATTTTTTCATTGAACTGTCAACAATAACACAAATGATCATTAATGTT
* * * *
1424982 ATCGATTTGTAACAAAAAAATCATTAACGTTATCGATTTATAATAAAATGGTCACTCCATCGTCA
350 ATCGATTTGTAACAAAATAATCATTAGCATTATCGATTTATAATAAAATGGTCACTCCACCGTCA
1425047 TTCCCGTTAAATTGGTGATGTTGTAACGTTAACAAAAAGGGTAATGTTTAATTTTACTCCTAAAC
415 TTCCCGTTAAATTGGTGATGTTGTAACGTTAACAAAAAGGGTAATGTTTAATTTTACTCCTAAAC
1425112 TACTACTAAAACATCAAATAGGTCATTTATCGAAAAATATATATACAATAATTTAGATATTGATA
480 TACTACTAAAACATCAAATAGGTC-TTTATCGAAAAATATATATACAATAATTTAGATATTGAT-
*
1425177 AGGATGGGCATGGGCATGGGTCGGGTTGGGTTTTTGGTCCACCCGACCCGAGAACAAGAAATTCT
543 A--A--GG-ATGGGCATGGGTCGAGTTGGGTTTTTGGTCCACCCGACCCGAGAACAAGAAA-T-T
1425242 CCACCTGAGATTCGACCCAACCAAAACAAGATTCCACCCGACCCAAA-TCTGACCCGATATATAA
601 CCACC------T-G-----ACCAAAACAAGATTCCACCCGACCCAAACTC-GACCCGATATATAA
* *
1425306 CTTAAAAACACGATCCAACCTAAAATAAT-GAAAATATTATT-TGTATTAAAT-AGAAATAGTGA
653 CTTAAAAACACGATCCAACCTAAAATAATAAAAAATATTATTGT-TATTAAATAAAAAATAGTGA
* * * * *
1425368 GTTAATTGG-AAATATATATATATAGGGGTATTATTATAATTATTCCTAAATATATAAGATAAAA
717 CTTAATTGGAAAAAATATATAGAGAGGGGTATTATTATAATTATTCATAAATATATAAGATAAAA
* * *
1425432 TAATAT-ATTTTTTGGGTCG-GATCGGATATTTTTCACCCTAAACTCGAATACAACCCGACCTAA
782 TAATATGATTTTTTGGGTCGAG-TCGGATATTTTTCACCCTAAACCCGAACACAACCCGACCCAA
*
1425495 ACATCAC-TTTAAAAAAAA-G
846 ACATCACATTAAAAAAAAACG
* *
1425514 AACCCATAAGGTTCGAATCCTATGACCATTCCTAAATATTGAAGGCAAGTTACGAAGCGCTTACC
1 AACCCATAAGGTTCGAATCCAATGACCA-TCCTAGATATTGAAGGCAAGTTACGAAGCGCTTACC
1425579 ATAGAGTACAAAATCGATAAAAATGAATAAATATAAAAAGTATATAATACGATTTGAAGAGAACC
65 ATAGAGTACAAAATCGATAAAAATGAATAAATATAAAAAGTATATAATACGATTTGAAGAGAACC
*
1425644 TAATCTATCTACTCTCAAAATTTGCAGAACCTAAAGAAAAAAATTTAAATCATTAAATTTGGGGG
130 TAATCTATCTACTCTCAAAATTTGCAGAACCTAAA-AAAAATATTTAAATCATTAAATTTGGGGG
1425709 ACCAGGGATTAATTTGCGTATTTTTCACATTATCATGGACTTTAAAGACCAATTA-GGAGATTTA
194 ACCAGGGATTAATTTGCGTATTTTTCACATTATCATGGACTTTAAAGACCAATTATGGAGATTTA
* * *
1425773 AGGGCAATTTACACAAATCATCATTAATATTTGATTAAATTTTCTTTTTTTCATTGAATTGTCAA
259 AGGGCAATTTACACAAATGATCATTAATATTTGATTAAATTTTCATTTTTTCATTGAACTGTCAA
1425838 CAATAACACAAATGATCATTAATGTTATCGATTTGTAACAAAATAATCATTAGTC-TTATCGATT
324 CAATAACACAAATGATCATTAATGTTATCGATTTGTAACAAAATAATCATTAG-CATTATCGATT
*
1425902 TATAATAAAATGATCACTCCACCGTCATTCCCGTTAAATTGGTGATGTTGTAACGTTAACAAAAA
388 TATAATAAAATGGTCACTCCACCGTCATTCCCGTTAAATTGGTGATGTTGTAACGTTAACAAAAA
1425967 GGGTAATGTTTAATTTTACTCCTAAACTACTACTAAAACATCAAATAGGTC
453 GGGTAATGTTTAATTTTACTCCTAAACTACTACTAAAACATCAAATAGGTC
1426018 CTTAAAGAAT
Statistics
Matches: 1194, Mismatches: 146, Indels: 140
0.81 0.10 0.09
Matches are distributed among these distances:
868 1 0.00
872 4 0.00
873 1 0.00
875 2 0.00
876 2 0.00
877 4 0.00
878 2 0.00
879 1 0.00
880 1 0.00
881 3 0.00
882 257 0.22
883 82 0.07
884 6 0.01
885 1 0.00
886 14 0.01
887 10 0.01
888 29 0.02
889 17 0.01
891 1 0.00
892 17 0.01
893 27 0.02
894 9 0.01
895 14 0.01
896 1 0.00
897 6 0.01
899 9 0.01
900 363 0.30
901 4 0.00
902 1 0.00
903 4 0.00
904 4 0.00
905 4 0.00
906 53 0.04
907 1 0.00
908 6 0.01
909 4 0.00
913 2 0.00
914 12 0.01
915 55 0.05
916 54 0.05
918 19 0.02
919 20 0.02
920 67 0.06
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (866 bp):
AACCCATAAGGTTCGAATCCAATGACCATCCTAGATATTGAAGGCAAGTTACGAAGCGCTTACCA
TAGAGTACAAAATCGATAAAAATGAATAAATATAAAAAGTATATAATACGATTTGAAGAGAACCT
AATCTATCTACTCTCAAAATTTGCAGAACCTAAAAAAAATATTTAAATCATTAAATTTGGGGGAC
CAGGGATTAATTTGCGTATTTTTCACATTATCATGGACTTTAAAGACCAATTATGGAGATTTAAG
GGCAATTTACACAAATGATCATTAATATTTGATTAAATTTTCATTTTTTCATTGAACTGTCAACA
ATAACACAAATGATCATTAATGTTATCGATTTGTAACAAAATAATCATTAGCATTATCGATTTAT
AATAAAATGGTCACTCCACCGTCATTCCCGTTAAATTGGTGATGTTGTAACGTTAACAAAAAGGG
TAATGTTTAATTTTACTCCTAAACTACTACTAAAACATCAAATAGGTCTTTATCGAAAAATATAT
ATACAATAATTTAGATATTGATAAGGATGGGCATGGGTCGAGTTGGGTTTTTGGTCCACCCGACC
CGAGAACAAGAAATTCCACCTGACCAAAACAAGATTCCACCCGACCCAAACTCGACCCGATATAT
AACTTAAAAACACGATCCAACCTAAAATAATAAAAAATATTATTGTTATTAAATAAAAAATAGTG
ACTTAATTGGAAAAAATATATAGAGAGGGGTATTATTATAATTATTCATAAATATATAAGATAAA
ATAATATGATTTTTTGGGTCGAGTCGGATATTTTTCACCCTAAACCCGAACACAACCCGACCCAA
ACATCACATTAAAAAAAAACG
Found at i:1428656 original size:5 final size:5
Alignment explanation
Indices: 1428646--1428679 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1428636 ATAGGCGAAT
1428646 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA CCAA
1 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA CCAA
1428680 TCCATCACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:1430629 original size:16 final size:17
Alignment explanation
Indices: 1430608--1430640 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1430598 TTTATTCATA
1430608 ATATTTAATTAT-TAAT
1 ATATTTAATTATCTAAT
*
1430624 ATATTTATTTATCTAAT
1 ATATTTAATTATCTAAT
1430641 TTCAATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTAATTATCTAAT
Found at i:1430686 original size:15 final size:17
Alignment explanation
Indices: 1430655--1430686 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1430645 ATGTATTTTT
1430655 ATCTATCTTGTAATTTA
1 ATCTATCTTGTAATTTA
1430672 ATCTA-CTTG-AATTTA
1 ATCTATCTTGTAATTTA
1430687 TTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (17 bp):
ATCTATCTTGTAATTTA
Found at i:1450723 original size:30 final size:30
Alignment explanation
Indices: 1450689--1450757 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
1450679 TAATTACCCA
*
1450689 TTCATACATGAAGTA-TATCAAATTCTCAAT
1 TTCATACATGAA-TATTATAAAATTCTCAAT
* *
1450719 TTCATACGT-AATATTTTAAAATTCTCAAT
1 TTCATACATGAATATTATAAAATTCTCAAT
*
1450748 TTTATACATG
1 TTCATACATG
1450758 GAGTTTTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.06
29 22 0.69
30 8 0.25
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (30 bp):
TTCATACATGAATATTATAAAATTCTCAAT
Found at i:1455603 original size:195 final size:192
Alignment explanation
Indices: 1455240--1455592 Score: 483
Period size: 192 Copynumber: 1.8 Consensus size: 192
1455230 GTTGGTCTAT
** * * *
1455240 TTCCATGTGATTCCCTGCTTCTGACTGATTATCCGAATGTGCATCGTCGACATTCAGAATCACTT
1 TTCCATGTGATTCCCTGCTTCTGACTGAAGATCCAAATGTGCATCGTCAACATTCAGAATCACCT
* * * * *
1455305 CAGACAACTTTCTTTCTCTTGCATACTGCTCATGTGAAAAGAGGGTACCAGTTTCCCCCTCCAAA
66 CAGACAACTTACTTTCACCTGCATACTGCTCATGTGAAAAAAGGGTACCAGTTCCCCCCTCCAAA
* *
1455370 TCTTTTGAGTCAAACTGCACATGAGGTTCACCCAAGCTGACTTCAACTAGCTTCTCAAGGCA
131 TCCTTTGACTCAAACTGCACATGAGGTTCACCCAAGCTGACTTCAACTAGCTTCTCAAGGCA
* * *
1455432 TTCCATGTGATTCCCTGCTTCTGACTGAAGATCCAAATGTGTATTGTCAACATTTAGAATCACCT
1 TTCCATGTGATTCCCTGCTTCTGACTGAAGATCCAAATGTGCATCGTCAACATTCAGAATCACCT
* **
1455497 CAGACAACGTTGGACTTTCACCTGCATTCTGCTCATGTGAACAAAAGGG-GGCAGTTCCCCCCTC
66 CAGACAAC-TT--ACTTTCACCTGCATACTGCTCATGTGAA-AAAAGGGTACCAGTTCCCCCCTC
* *
1455561 TAAATCCTTTGACTCAAACTGCACTTGAGGTT
127 CAAATCCTTTGACTCAAACTGCACATGAGGTT
1455593 TATTCAAGCT
Statistics
Matches: 137, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
192 65 0.47
193 2 0.01
195 64 0.47
196 6 0.04
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (192 bp):
TTCCATGTGATTCCCTGCTTCTGACTGAAGATCCAAATGTGCATCGTCAACATTCAGAATCACCT
CAGACAACTTACTTTCACCTGCATACTGCTCATGTGAAAAAAGGGTACCAGTTCCCCCCTCCAAA
TCCTTTGACTCAAACTGCACATGAGGTTCACCCAAGCTGACTTCAACTAGCTTCTCAAGGCA
Found at i:1457214 original size:351 final size:352
Alignment explanation
Indices: 1456562--1457219 Score: 1282
Period size: 351 Copynumber: 1.9 Consensus size: 352
1456552 GAAATATCTA
*
1456562 ACAATAGATATTTTTTTCTTCAAATTCAGACACCCAATTTGATGTCATAATAGTATGCCTCTTAT
1 ACAACAGATATTTTTTTCTTCAAATTCAGACACCCAATTTGATGTCATAATAGTATGCCTCTTAT
*
1456627 TTGCAGTCAAAGAAGTTATTGGCTATCTTATGTCTCACAAACCTCTTAATACTAGGCCAAGAGAT
66 TTGCAGTCAAAGAAGTTATTGGCTATCTTATGTCTCACAAACCCCTTAATACTAGGCCAAGAGAT
1456692 TATTGGCAATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCA
131 TATTGGCAATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCA
1456757 ACAACAGAAAACATTTAGTTACATTGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTA
196 ACAACAGAAAACATTTAGTTACATTGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTA
1456822 CACTCGAAAGAGAGCTTTCTATTCATTATGATATTACAATTATAGAAATATCTAACAATAGATAT
261 CACTCGAAAGAGAGCTTTCTATTCATTATGATATTACAATTATAGAAATATCTAACAATAGATAT
1456887 TTTATGGCAAGATACACATTGCAAAAG
326 TTTATGGCAAGATACACATTGCAAAAG
*
1456914 ACAACAGA-ATTTTTTTCTTCAAATTCAGACATCCAATTTGATGTCATAATAGTATGCCTCTTAT
1 ACAACAGATATTTTTTTCTTCAAATTCAGACACCCAATTTGATGTCATAATAGTATGCCTCTTAT
1456978 TTGCAGTCAAAGAAGTTATTGGCTATCTTATGTCTCACAAACCCCTTAATACTAGGCCAAGAGAT
66 TTGCAGTCAAAGAAGTTATTGGCTATCTTATGTCTCACAAACCCCTTAATACTAGGCCAAGAGAT
1457043 TATTGGCAATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCA
131 TATTGGCAATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCA
1457108 ACAACAGAAAACATTTAGTTACATTGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTA
196 ACAACAGAAAACATTTAGTTACATTGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTA
1457173 CACTCGAAAGAGAGCTTTCTATTCATTATGATATTACAATTATAGAA
261 CACTCGAAAGAGAGCTTTCTATTCATTATGATATTACAATTATAGAA
1457220 GACTGTGTTG
Statistics
Matches: 303, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
351 296 0.98
352 7 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (352 bp):
ACAACAGATATTTTTTTCTTCAAATTCAGACACCCAATTTGATGTCATAATAGTATGCCTCTTAT
TTGCAGTCAAAGAAGTTATTGGCTATCTTATGTCTCACAAACCCCTTAATACTAGGCCAAGAGAT
TATTGGCAATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCA
ACAACAGAAAACATTTAGTTACATTGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTA
CACTCGAAAGAGAGCTTTCTATTCATTATGATATTACAATTATAGAAATATCTAACAATAGATAT
TTTATGGCAAGATACACATTGCAAAAG
Found at i:1457615 original size:315 final size:306
Alignment explanation
Indices: 1457050--1457669 Score: 1087
Period size: 315 Copynumber: 2.0 Consensus size: 306
1457040 GATTATTGGC
1457050 AATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCAACAACAG
1 AATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCAACAACAG
*
1457115 AAAACATTTAGTTACATTGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTACACTCGA
66 AAAACATTTAGTTACATCGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTACACTCGA
*
1457180 AAGAGAGCTTTCTATTCATTATGATATTACAATTATAGAAGACTGTGTTGGAAAAGTAATCTAGC
131 AAGAGAGATTTCTATTCATTATGATATTACAATTATAGAAGACTGTGTTGGAAAAGTAATCTAGC
1457245 TCAGTTGTGTTAATTCAGATTATAGTAAATTACAAATAGTTTCCAAAGATATAGAGATGCATAAG
196 TCAGTTGTGTTAATTCAGATTATAGTAAATTACAAATAGTTTCCAAAGATATAGAGATGCATAAG
1457310 AAAATAACCACACTGAGAACCTGGAAGAAAGTAGATAATATTAACT
261 AAAATAACCACACTGAGAACCTGGAAGAAAGTAGATAATATTAACT
*
1457356 AATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTTTTATATAGGATTAATTTCAACAACAG
1 AATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCAACAACAG
1457421 AAAACATTTAGTTACATCGCCAAAGAAACATGCTTGAAATTGAAAGTTAATAGAGTTTTAAAAAG
66 AAAACATTTAGTTACATCGCCAAAGAAACATGCTTGAAATT----G---A-A-AGTTTTAAAAAG
*
1457486 TACACTCGAAAGAGAGATTTCTATTCATTATGATATTACAATTATAGAATACTGTGTTGGAAAAG
122 TACACTCGAAAGAGAGATTTCTATTCATTATGATATTACAATTATAGAAGACTGTGTTGGAAAAG
* *
1457551 TAATCTAGCTCAGTTGTGTTAATTCAGATTATAGTAAATTGCAAATAGTTTCCAAAGTTATAGAG
187 TAATCTAGCTCAGTTGTGTTAATTCAGATTATAGTAAATTACAAATAGTTTCCAAAGATATAGAG
* *
1457616 ATGCATAAGAAAATAACCACACTGGGAACCTGGAAGACAGTAGATAATATTAAC
252 ATGCATAAGAAAATAACCACACTGAGAACCTGGAAGAAAGTAGATAATATTAAC
1457670 CAACCTGTCT
Statistics
Matches: 297, Mismatches: 8, Indels: 9
0.95 0.03 0.03
Matches are distributed among these distances:
306 104 0.35
310 1 0.00
313 1 0.00
314 1 0.00
315 190 0.64
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (306 bp):
AATTTGAAAGAAGATCAACACAAGAATAGCATAGTATTGTTATATAGGATTAATTTCAACAACAG
AAAACATTTAGTTACATCGCCAAAGAAACATGCTTGAAATTGAAAGTTTTAAAAAGTACACTCGA
AAGAGAGATTTCTATTCATTATGATATTACAATTATAGAAGACTGTGTTGGAAAAGTAATCTAGC
TCAGTTGTGTTAATTCAGATTATAGTAAATTACAAATAGTTTCCAAAGATATAGAGATGCATAAG
AAAATAACCACACTGAGAACCTGGAAGAAAGTAGATAATATTAACT
Found at i:1464135 original size:18 final size:18
Alignment explanation
Indices: 1464112--1464149 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1464102 CCCTTTTTTT
*
1464112 AAAAAAAATAAATTATAA
1 AAAAAAAAAAAATTATAA
1464130 AAAAAAAAAAAATTATAA
1 AAAAAAAAAAAATTATAA
1464148 AA
1 AA
1464150 TAATCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAAAAAAAATTATAA
Found at i:1481889 original size:3 final size:3
Alignment explanation
Indices: 1481881--1481909 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1481871 ACGACACATA
1481881 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1481910 GAATATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1488775 original size:32 final size:33
Alignment explanation
Indices: 1488721--1488784 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
1488711 AATTTGTTTG
*
1488721 GGTTGCTTTCGGATCAGATT-AAATTCGGTTCT
1 GGTTGCTTTCAGATCAGATTAAAATTCGGTTCT
* * *
1488753 GGTTGCTTTCATATCGGGTTAAAATTCGGTTC
1 GGTTGCTTTCAGATCAGATTAAAATTCGGTTC
1488785 AAGTTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (33 bp):
GGTTGCTTTCAGATCAGATTAAAATTCGGTTCT
Found at i:1488817 original size:22 final size:22
Alignment explanation
Indices: 1488792--1488837 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1488782 TTCAAGTTTC
*
1488792 TTTCG-GTTCGGGTTAATTTTGG
1 TTTCGAGTT-GGGTTAATTTCGG
1488814 TTTCGAGTTGGGTTAATTTCGG
1 TTTCGAGTTGGGTTAATTTCGG
1488836 TT
1 TT
1488838 CTGTTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.11, C:0.09, G:0.30, T:0.50
Consensus pattern (22 bp):
TTTCGAGTTGGGTTAATTTCGG
Found at i:1491314 original size:16 final size:16
Alignment explanation
Indices: 1491295--1491328 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1491285 CAATATACGA
1491295 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1491311 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1491327 AT
1 AT
1491329 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1491402 original size:16 final size:18
Alignment explanation
Indices: 1491370--1491403 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1491360 TATTAATGTA
1491370 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1491388 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1491404 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1492078 original size:130 final size:130
Alignment explanation
Indices: 1491874--1492121 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
1491864 AATTTTCTTC
* *
1491874 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGATAACACATGTCAGAT
** *
1491939 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
1492004 TAATTAGGTGGTGACATGTGTCACCAATGACACATGTCATGATCATGTGATAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGATAACACATGTCAGAT
1492069 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1492122 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGATAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1492568 original size:35 final size:35
Alignment explanation
Indices: 1492518--1492591 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
1492508 AATTGAATTT
* *
1492518 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1492553 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1492588 AATT
1 AATT
1492592 AAGGAATGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1494034 original size:30 final size:30
Alignment explanation
Indices: 1493998--1494063 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1493988 CCAAGCAAAG
1493998 ATTTATCATGAATATCATTCTTTTAGTTTT
1 ATTTATCATGAATATCATTCTTTTAGTTTT
*
1494028 ATTTATCATGAATATTATTCTTTTAGTTTT
1 ATTTATCATGAATATCATTCTTTTAGTTTT
1494058 ATTTAT
1 ATTTAT
1494064 TAAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.59
Consensus pattern (30 bp):
ATTTATCATGAATATCATTCTTTTAGTTTT
Found at i:1496673 original size:449 final size:448
Alignment explanation
Indices: 1495801--1496690 Score: 1717
Period size: 449 Copynumber: 2.0 Consensus size: 448
1495791 TTAAATATTG
*
1495801 ATAGAGGTCAAAATATTAGATTATTTAAAATCTTGTCAGATATTTAAACTCAAAATTCAGCTTAA
1 ATAGAGGTCAAAATATTAGATTATTTAAAATCTTGTCAGATATTTAAACTCAAAATTAAGCTTAA
*
1495866 ATCAAGCGACTTTAGTGATTAAGGGATTGTTGTTATCTTTGAGGTCCCGAATTCAAGCACTGTGT
66 ATCAAGCGACTTTAGTGATTAAGAGATTGTTGTTATCTTTGAGGTCCCGAATTCAAGCACTGTGT
*
1495931 ATGTAGGGATATGAGCGTTCATTATCAAATAGTTAAAAATCTTTGTACATGTACTACCTTGTATT
131 ACGTAGGGATATGAGCGTTCATTATCAAATAGTTAAAAATCTTTGTACATGTACTACCTTGTATT
1495996 CAACTTAAATTTATAAAAAAAAAACCTCAAAATTCACAAGACAACTTCTAATTTGTCTAATATTT
196 CAACTTAAATTTATAAAAAAAAAACCTCAAAATTCACAAGACAACTTCTAATTTGTCTAATATTT
1496061 AAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTTAAGAACACAGGCTTATCATTCTTTA
261 AAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTTAAGAACACAGGCTTATCATTCTTTA
1496126 GTTCGACCTATACTTGATTAAATATTTAATAAATGTGTATATTTTTAAAATTTTAAAATTTATTT
326 GTTCGACCTATACTTGATTAAATATTTAATAAATGTGTATATTTTTAAAATTTTAAAATTTATTT
1496191 TTACATAAACTAAAATATTATTAAACCAAAATTATATCAAATAAACAAATTATATTTA
391 TTACATAAACTAAAATATTATTAAACCAAAATTATATCAAATAAACAAATTATATTTA
*
1496249 ATAGAGGTCAAAATATTAGATTATTTAAAATCTTGTTAGATATTTAAACTCAAAATTAAGCTTAA
1 ATAGAGGTCAAAATATTAGATTATTTAAAATCTTGTCAGATATTTAAACTCAAAATTAAGCTTAA
*
1496314 ATCAAGCGACTTTAGTGATTAAGAGATTGTTGTTATCTTTGAGGTCTCGAATTCAAGCACTGTGT
66 ATCAAGCGACTTTAGTGATTAAGAGATTGTTGTTATCTTTGAGGTCCCGAATTCAAGCACTGTGT
1496379 ACGTAGGGATATGAGCGTTCATTATCAAATAGTTAAAAATCTTTGTACATGTACTACCTTGTATT
131 ACGTAGGGATATGAGCGTTCATTATCAAATAGTTAAAAATCTTTGTACATGTACTACCTTGTATT
1496444 CAACTTAAATTTATAAAAAAAAAAACCTCAAAATTCACAAGACAACTTCTAATTTGTCTAATATT
196 CAACTTAAATTTAT-AAAAAAAAAACCTCAAAATTCACAAGACAACTTCTAATTTGTCTAATATT
*
1496509 TAAACTTATAATGACTTAAATTGTAATTAGACCAAAAATTTAAGAACACAGGCTTATCATTCTTT
260 TAAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTTAAGAACACAGGCTTATCATTCTTT
1496574 AGTTCGACCTATACTTGATTAAATATTTAATAAATGTGTATATTTTTAAAATTTTAAAATTTATT
325 AGTTCGACCTATACTTGATTAAATATTTAATAAATGTGTATATTTTTAAAATTTTAAAATTTATT
1496639 TTTACATAAACTAAAATATTATTAAACCAAAATTATATCAAATAAACAAATT
390 TTTACATAAACTAAAATATTATTAAACCAAAATTATATCAAATAAACAAATT
1496691 TTAACAGAAG
Statistics
Matches: 435, Mismatches: 6, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
448 204 0.47
449 231 0.53
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (448 bp):
ATAGAGGTCAAAATATTAGATTATTTAAAATCTTGTCAGATATTTAAACTCAAAATTAAGCTTAA
ATCAAGCGACTTTAGTGATTAAGAGATTGTTGTTATCTTTGAGGTCCCGAATTCAAGCACTGTGT
ACGTAGGGATATGAGCGTTCATTATCAAATAGTTAAAAATCTTTGTACATGTACTACCTTGTATT
CAACTTAAATTTATAAAAAAAAAACCTCAAAATTCACAAGACAACTTCTAATTTGTCTAATATTT
AAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTTAAGAACACAGGCTTATCATTCTTTA
GTTCGACCTATACTTGATTAAATATTTAATAAATGTGTATATTTTTAAAATTTTAAAATTTATTT
TTACATAAACTAAAATATTATTAAACCAAAATTATATCAAATAAACAAATTATATTTA
Found at i:1497483 original size:19 final size:19
Alignment explanation
Indices: 1497459--1497496 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1497449 TGTCTCGTGG
1497459 CAATCATTCTTTAGGATAA
1 CAATCATTCTTTAGGATAA
1497478 CAATCATTCTTTAGGATAA
1 CAATCATTCTTTAGGATAA
1497497 AGAAGATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
CAATCATTCTTTAGGATAA
Found at i:1506396 original size:158 final size:159
Alignment explanation
Indices: 1506147--1506494 Score: 448
Period size: 158 Copynumber: 2.2 Consensus size: 159
1506137 CCTTGTTTCA
* * * **
1506147 TTATTTCTTCAATTCCTCCTTCATTTTAAGTCCATTTTTTTACCAAATTTGAACCATGTGCTCCT
1 TTATTTCTACAATTCCTCATTCATTTTAAATCCATTTTTTTACCAAATTTGAACCACATGCTCCT
* *
1506212 AAAACATAGTATAATACATGTATACTTTCAATTCCACTTTTTGATAATAATTTTTTTTATTTTTC
66 AAAACATAGTAGAATACATGTATACTTTCAATTCCACTTTTTGATAACAA-TTTTTTTATTTTTC
1506277 AATTTAGTCCTTCAATTTTTCACAATCTTG
130 AATTTAGTCCTTCAATTTTTCACAATCTTG
* * **
1506307 TTATTTCTACAATTCGTCATTTATTTTAAAT-CA-TTTTTTACCAAATTTGAGTCACATGCTCCT
1 TTATTTCTACAATTCCTCATTCATTTTAAATCCATTTTTTTACCAAATTTGAACCACATGCTCCT
* * * * *
1506370 AAATCATAGTAGAATACATGTGTACTTTTAATTCCTCTTTTTTATAACAATTTTTTTATTTTTCA
66 AAAACATAGTAGAATACATGTATACTTTCAATTCCACTTTTTGATAACAATTTTTTTATTTTTCA
* * **
1506435 ATTTAGTTCTTCAATTTTTCATAATCTCC
131 ATTTAGTCCTTCAATTTTTCACAATCTTG
* * ** *
1506464 TTATTCCTTCAATTTTTGATTCATTTTAAAT
1 TTATTTCTACAATTCCTCATTCATTTTAAAT
1506495 TCCACACTCT
Statistics
Matches: 162, Mismatches: 26, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
157 65 0.40
158 69 0.43
159 2 0.01
160 26 0.16
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (159 bp):
TTATTTCTACAATTCCTCATTCATTTTAAATCCATTTTTTTACCAAATTTGAACCACATGCTCCT
AAAACATAGTAGAATACATGTATACTTTCAATTCCACTTTTTGATAACAATTTTTTTATTTTTCA
ATTTAGTCCTTCAATTTTTCACAATCTTG
Found at i:1514641 original size:32 final size:33
Alignment explanation
Indices: 1514601--1514662 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1514591 CAACAGTTAA
1514601 TAATATTTATTT-AT-TTTTAATAAAATTAAATT
1 TAATATTTATTTAATATTTT-ATAAAATTAAATT
*
1514633 TAATATTTATTTAATATTTTTTAAAATTAA
1 TAATATTTATTTAATATTTTATAAAATTAA
1514663 TATTAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 11 0.41
34 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TAATATTTATTTAATATTTTATAAAATTAAATT
Found at i:1514751 original size:21 final size:21
Alignment explanation
Indices: 1514714--1514772 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1514704 CTTTACATTA
* *
1514714 TATTTTTATTGAATTTTATT-
1 TATTTTTATTCATTTTTATTG
1514734 TATTTTTAATTCATTTTTATTG
1 TATTTTT-ATTCATTTTTATTG
* *
1514756 CATTTTTATTTATTTTT
1 TATTTTTATTCATTTTT
1514773 TTAAAAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (21 bp):
TATTTTTATTCATTTTTATTG
Found at i:1514770 original size:10 final size:10
Alignment explanation
Indices: 1514714--1514772 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
1514704 CTTTACATTA
1514714 TATTTTTATT
1 TATTTTTATT
* *
1514724 GAATTTTATT
1 TATTTTTATT
1514734 TATTTTTAATT
1 TATTTTT-ATT
*
1514745 CATTTTTATT
1 TATTTTTATT
*
1514755 GCATTTTTATT
1 -TATTTTTATT
1514766 TATTTTT
1 TATTTTT
1514773 TTAAAAAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 22 0.54
11 19 0.46
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1528107 original size:2 final size:2
Alignment explanation
Indices: 1528100--1528130 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1528090 CGATAGTATT
1528100 TA TA TA 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 TA TA TA T
1528131 TCAGCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1530283 original size:25 final size:25
Alignment explanation
Indices: 1530246--1530295 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1530236 AAGTTACCAG
*
1530246 AATCATTTTATGCTTTGATCTTAGT
1 AATCATTTAATGCTTTGATCTTAGT
1530271 AATCATTTAATGCTTTGATCTTAGT
1 AATCATTTAATGCTTTGATCTTAGT
1530296 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (25 bp):
AATCATTTAATGCTTTGATCTTAGT
Found at i:1536092 original size:20 final size:20
Alignment explanation
Indices: 1536067--1536105 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536057 AGGTTCGAGC
1536067 ACCGTGTACTTAAGGGTGTG
1 ACCGTGTACTTAAGGGTGTG
1536087 ACCGTGTACTTAAGGGTGT
1 ACCGTGTACTTAAGGGTGT
1536106 ATGAATCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ACCGTGTACTTAAGGGTGTG
Found at i:1539265 original size:27 final size:25
Alignment explanation
Indices: 1539211--1539272 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
1539201 CCCTATTATA
*
1539211 TATATATATTTTTAATAAATTGAAT
1 TATATATAATTTTAATAAATTGAAT
*
1539236 TATACTATAATTTTACTATAATT-AAT
1 TATA-TATAATTTTAATA-AATTGAAT
1539262 T-TATAT-ATTTT
1 TATATATAATTTT
1539273 CTTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 5 0.15
24 3 0.09
25 6 0.18
26 15 0.45
27 4 0.12
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (25 bp):
TATATATAATTTTAATAAATTGAAT
Found at i:1543116 original size:21 final size:23
Alignment explanation
Indices: 1543090--1543139 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
1543080 TAATTATTAA
1543090 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
*
1543111 AATATTTATAATAATATTATATT
1 AATATTTAAAATAATATTATATT
1543134 -ATATTT
1 AATATTT
1543140 TTAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:1543117 original size:10 final size:10
Alignment explanation
Indices: 1543102--1543147 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
1543092 TATTTAAAAT
1543102 ATATTTATTA
1 ATATTTATTA
1543112 ATATTTATAATA
1 ATATTTAT--TA
1543124 ATATTATATT-
1 ATATT-TATTA
1543134 ATATTT-TTA
1 ATATTTATTA
1543143 ATATT
1 ATATT
1543148 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 13 0.41
11 1 0.03
12 7 0.22
13 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATTA
Found at i:1543135 original size:26 final size:25
Alignment explanation
Indices: 1543073--1543135 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
1543063 CATTTTCATC
1543073 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
*
1543097 AAAATA-TAT-TTATTAATAT-TTAT
1 AAAATATTATATTATTAAAATATT-T
1543120 AATAATATTATATTAT
1 AA-AATATTATATTAT
1543136 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:1543137 original size:22 final size:22
Alignment explanation
Indices: 1543090--1543145 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1543080 TAATTATTAA
*
1543090 AATATTTAAAAT-ATATTTATT
1 AATATTTATAATAATATTTATT
1543111 AATATTTATAATAATATTATATT
1 AATATTTATAATAATATT-TATT
*
1543134 -ATATTTTTAATA
1 AATATTTATAATA
1543146 TTATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 11 0.35
22 16 0.52
23 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTATAATAATATTTATT
Found at i:1543167 original size:32 final size:31
Alignment explanation
Indices: 1543087--1543180 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 31
1543077 TATTAATTAT
* *
1543087 TAAAATATTTAAAATATATTTATTAATATTTA
1 TAAAATAATT-AATTATATTTATTAATATTTA
1543119 TAATAAT-ATTATATTATATTT-TTAATATTATAA
1 TAA-AATAATTA-ATTATATTTATTAATATT-T-A
*
1543152 TAAAATAATTAATTATATTATAATAATAT
1 TAAAATAATTAATTATATT-TATTAATAT
1543181 AAGATATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
31 9 0.17
32 25 0.48
33 12 0.23
34 6 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TAAAATAATTAATTATATTTATTAATATTTA
Found at i:1543189 original size:23 final size:23
Alignment explanation
Indices: 1543143--1543193 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1543133 TATATTTTTA
*
1543143 ATATTATAATAAAATAATTAATT
1 ATATTATAATAAAATAAATAATT
*
1543166 ATATTATAATAATATAAGAT-ATT
1 ATATTATAATAAAATAA-ATAATT
1543189 ATATT
1 ATATT
1543194 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATTATAATAAAATAAATAATT
Found at i:1543215 original size:55 final size:54
Alignment explanation
Indices: 1543098--1543225 Score: 135
Period size: 53 Copynumber: 2.4 Consensus size: 54
1543088 AAAATATTTA
* *
1543098 AAATATATTTATTAATATTTATAATAATATTATATTATATTTTTAATATTATAAT
1 AAATATA-TAATTAATATTTATAATAATATGATATTATATTTTTAATATTATAAT
1543153 -AA-A-ATAATTAATTATATTATAATAATATAAGATATTATATTTTT-AT-TT-TAAT
1 AAATATATAATTAA-TAT-TTATAATAATAT--GATATTATATTTTTAATATTATAAT
*
1543205 AAATATATAA-TAAAATTTATA
1 AAATATATAATTAATATTTATA
1543226 TATATTTAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
51 6 0.10
52 13 0.21
53 19 0.30
54 8 0.13
55 17 0.27
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (54 bp):
AAATATATAATTAATATTTATAATAATATGATATTATATTTTTAATATTATAAT
Found at i:1543310 original size:23 final size:23
Alignment explanation
Indices: 1543290--1543334 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1543280 AATAATATTT
1543290 TAATGAAGATATTTAAAATATAC
1 TAATGAAGATATTTAAAATATAC
* * *
1543313 TAATTAATATTTTTAAAATATA
1 TAATGAAGATATTTAAAATATA
1543335 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATGAAGATATTTAAAATATAC
Found at i:1547087 original size:15 final size:16
Alignment explanation
Indices: 1547057--1547090 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1547047 TAATTTCTTC
*
1547057 AAAATTTAATCTATTT
1 AAAATTAAATCTATTT
1547073 AAAATTAAATC-ATTT
1 AAAATTAAATCTATTT
1547088 AAA
1 AAA
1547091 GAGATTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTAAATCTATTT
Found at i:1548183 original size:15 final size:15
Alignment explanation
Indices: 1548152--1548229 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 15
1548142 ACATAGTTAT
*
1548152 TATATTT-TATATTAA
1 TATATTTATATA-AAA
*
1548167 TATAATTATATAAAA
1 TATATTTATATAAAA
*
1548182 TATTATTTTTATTAAAA
1 TA-TATTTATA-TAAAA
*
1548199 TAATATTTATATAAAT
1 T-ATATTTATATAAAA
*
1548215 TATTATTTATTTAAA
1 TA-TATTTATATAAA
1548230 TTTATTAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
15 11 0.22
16 26 0.51
17 13 0.25
18 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTTATATAAAA
Found at i:1548196 original size:30 final size:33
Alignment explanation
Indices: 1548154--1548230 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
1548144 ATAGTTATTA
1548154 TATTTTATATT-AAT-ATAATTATATAAAATAT
1 TATTTTATATTAAATAATAATTATATAAAATAT
* *
1548185 TATTTT-TATTAAAATAATATTTATATAAATTAT
1 TATTTTATATT-AAATAATAATTATATAAAATAT
1548218 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
1548231 TTATTAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.10
31 10 0.25
32 8 0.20
33 18 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTTTATATTAAATAATAATTATATAAAATAT
Found at i:1548199 original size:17 final size:17
Alignment explanation
Indices: 1548172--1548222 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
1548162 ATTAATATAA
1548172 TTATATAAAATATTATTT
1 TTAT-TAAAATATTATTT
*
1548190 TTATTAAAATAATATTT
1 TTATTAAAATATTATTT
* *
1548207 ATA-TAAATTATTATTT
1 TTATTAAAATATTATTT
1548223 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 11 0.38
17 14 0.48
18 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTAAAATATTATTT
Found at i:1548231 original size:16 final size:16
Alignment explanation
Indices: 1548172--1548229 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
1548162 ATTAATATAA
1548172 TTATATAAAATATTAT
1 TTATATAAAATATTAT
* *
1548188 TTTTATTAAAATAATAT
1 TTATA-TAAAATATTAT
*
1548205 TTATATAAATTATTAT
1 TTATATAAAATATTAT
*
1548221 TTATTTAAA
1 TTATATAAA
1548230 TTTATTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 21 0.60
17 14 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATAAAATATTAT
Found at i:1555739 original size:78 final size:78
Alignment explanation
Indices: 1555610--1555766 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
1555600 TTTTGGTCAC
*
1555610 TAAAATCTAAAAGTTTTCAATTTCAAAAACCCTAGAGACTTCAGGGACTAAGGCTGTAGTTAACT
1 TAAAATCTAAAAGTTTTCAATTTCAAAAACCCTAGAGACTTCAGCGACTAAGGCTGTAGTTAACT
1555675 CATTTTACCCCCA
66 CATTTTACCCCCA
1555688 TAAAATCTAAAAGTTTTCAATTTCAAAAACCCTAGAGACTTCAGCGACTAAGGCTGTAGTTAACT
1 TAAAATCTAAAAGTTTTCAATTTCAAAAACCCTAGAGACTTCAGCGACTAAGGCTGTAGTTAACT
1555753 CATTTTACCCCCA
66 CATTTTACCCCCA
1555766 T
1 T
1555767 TTCTCTAACT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (78 bp):
TAAAATCTAAAAGTTTTCAATTTCAAAAACCCTAGAGACTTCAGCGACTAAGGCTGTAGTTAACT
CATTTTACCCCCA
Found at i:1560201 original size:170 final size:173
Alignment explanation
Indices: 1559919--1560261 Score: 665
Period size: 170 Copynumber: 2.0 Consensus size: 173
1559909 CCGTCATTAA
1559919 TAGTTTTTGGTATTTATTCTTCATAGATTGTGCCTGCAATGCTTGGGATGCTTGCATACAAAGCA
1 TAGTTTTTGGTATTTATTCTTCATAGATTGTGCCTGCAATGCTTGGGATGCTTGCATACAAAGCA
1559984 GCTGCTCTTGTTCAAGTATACAGGGACAATGAAGACCTGCAGTTTCTCTTTCCGGAAAACGAGTA
66 GCTGCTCTTGTTCAAGTATACAGGGACAATGAAGACCTGCAGTTTCTCTTTCCGGAAAACGAGTA
1560049 ACAGTCTAGTAA-CGAGTCTCCAA-TTATAGAACAC-TCAAAC
131 ACAGTCTAGTAACCGAGTCTCCAATTTATAGAACACTTCAAAC
1560089 TAGTTTTTGGTATTTATTCTTCATAGATTGTGCCTGCAATGCTTGGGATGCTTGCATACAAAGCA
1 TAGTTTTTGGTATTTATTCTTCATAGATTGTGCCTGCAATGCTTGGGATGCTTGCATACAAAGCA
1560154 GCTGCTCTTGTTCAAGTATACAGGGACAATGAAGACCTGCAGTTTCTCTTTCCGGAAAACGAGTA
66 GCTGCTCTTGTTCAAGTATACAGGGACAATGAAGACCTGCAGTTTCTCTTTCCGGAAAACGAGTA
1560219 ACAGTCTAGTAACCGAGTCTCCAATTTATAGAACACTTCAAAC
131 ACAGTCTAGTAACCGAGTCTCCAATTTATAGAACACTTCAAAC
1560262 ACTGAACTGA
Statistics
Matches: 170, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
170 142 0.84
171 11 0.06
172 11 0.06
173 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (173 bp):
TAGTTTTTGGTATTTATTCTTCATAGATTGTGCCTGCAATGCTTGGGATGCTTGCATACAAAGCA
GCTGCTCTTGTTCAAGTATACAGGGACAATGAAGACCTGCAGTTTCTCTTTCCGGAAAACGAGTA
ACAGTCTAGTAACCGAGTCTCCAATTTATAGAACACTTCAAAC
Done.