Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 38
Found at i:5385227 original size:20 final size:20
Alignment explanation
Indices: 5385202--5385252 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
5385192 CCATGGTGTG
5385202 GTATCGATACTAAAAGGTAA
1 GTATCGATACTAAAAGGTAA
5385222 GTATCGATACTAAAAGGTAA
1 GTATCGATACTAAAAGGTAA
5385242 GTATCGATACT
1 GTATCGATACT
5385253 TGTTCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
GTATCGATACTAAAAGGTAA
Found at i:5392742 original size:21 final size:20
Alignment explanation
Indices: 5392703--5392752 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5392693 CTCTAAATCA
**
5392703 TTTTTCAAAAATTTATTTTG
1 TTTTTCAAAAATCAATTTTG
5392723 TTTTTCAAAAATCAACTTTTG
1 TTTTTCAAAAATCAA-TTTTG
*
5392744 -CTTTCAAAA
1 TTTTTCAAAA
5392753 CCAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTTCAAAAATCAATTTTG
Found at i:5394693 original size:45 final size:45
Alignment explanation
Indices: 5394621--5394723 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
5394611 GTTTTCATTA
* *
5394621 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
5394666 CATAAATAAAATGCATAATGGTTCATTAAAGGCATGAAAGGATGC
1 CATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
5394711 CATAAATGAAAAT
1 CATAAAT-AAAAT
5394724 AATTAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 48 0.91
46 5 0.09
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (45 bp):
CATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:5394741 original size:45 final size:45
Alignment explanation
Indices: 5394647--5394741 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
5394637 AACGGTGCAT
* * ** *
5394647 TAAAGGCATGAAATGATGCCATAAATAAAATGCATAATGGTTCAT
1 TAAAGGCATGAAAGGATGCCATAAATAAAATGAATAATAATTCAC
5394692 TAAAGGCATGAAAGGATGCCATAAATGAAAAT-AATTAATAATT-AC
1 TAAAGGCATGAAAGGATGCCATAAAT-AAAATGAA-TAATAATTCAC
5394737 TAAAG
1 TAAAG
5394742 AATAATGGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
45 32 0.74
46 11 0.26
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.25
Consensus pattern (45 bp):
TAAAGGCATGAAAGGATGCCATAAATAAAATGAATAATAATTCAC
Found at i:5396399 original size:17 final size:17
Alignment explanation
Indices: 5396379--5396418 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
5396369 ATTAAAACTC
5396379 ACAAGAACAAAATTTTT
1 ACAAGAACAAAATTTTT
5396396 ACAAGAACAAAATTTTT
1 ACAAGAACAAAATTTTT
5396413 ACAAGA
1 ACAAGA
5396419 GAATAGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (17 bp):
ACAAGAACAAAATTTTT
Found at i:5397064 original size:8 final size:8
Alignment explanation
Indices: 5397053--5397077 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5397043 CGGTGAAGGT
5397053 ACTGGTTC
1 ACTGGTTC
5397061 ACTGGTTC
1 ACTGGTTC
5397069 ACTGGTTC
1 ACTGGTTC
5397077 A
1 A
5397078 ACCGGGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (8 bp):
ACTGGTTC
Found at i:5397630 original size:24 final size:24
Alignment explanation
Indices: 5397598--5397653 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
5397588 CTATTCTTTC
* *
5397598 GCTTAAATTGAGCTCAAATTTTAT
1 GCTTCAATTGAGCTCAAATTTTAG
5397622 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
5397646 GCTTCAAT
1 GCTTCAAT
5397654 CGAACTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:5399625 original size:18 final size:17
Alignment explanation
Indices: 5399578--5399633 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
5399568 AGTATGCTTT
*
5399578 TTCATTCAATAAAGCTAG
1 TTCATTCATTAAA-CTAG
* *
5399596 TTCACTAATTAAACTAG
1 TTCATTCATTAAACTAG
*
5399613 TTCATTCATTTAAACTGG
1 TTCATTCA-TTAAACTAG
5399631 TTC
1 TTC
5399634 GTTAATCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (17 bp):
TTCATTCATTAAACTAG
Found at i:5400640 original size:22 final size:22
Alignment explanation
Indices: 5400613--5400692 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
5400603 ACCGGTGGGA
5400613 GGTATTGGTACCATAGCATAGG
1 GGTATTGGTACCATAGCATAGG
5400635 GGTATTGGTACCATAGCATAGG
1 GGTATTGGTACCATAGCATAGG
*
5400657 GGTATTGGTACCATAGCACAGG
1 GGTATTGGTACCATAGCATAGG
* *
5400679 GGTATCGATACCAT
1 GGTATTGGTACCAT
5400693 GGTGAGGGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (22 bp):
GGTATTGGTACCATAGCATAGG
Found at i:5400754 original size:18 final size:17
Alignment explanation
Indices: 5400733--5400768 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
5400723 AGTTAATTTT
5400733 GGTATCGATACTGTAAGG
1 GGTATCGATACTG-AAGG
5400751 GGTATCGATACTGAAGG
1 GGTATCGATACTGAAGG
5400768 G
1 G
5400769 CCAGAAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.28, C:0.11, G:0.36, T:0.25
Consensus pattern (17 bp):
GGTATCGATACTGAAGG
Found at i:5401155 original size:59 final size:59
Alignment explanation
Indices: 5401092--5401526 Score: 427
Period size: 59 Copynumber: 7.4 Consensus size: 59
5401082 ATGGAACTTT
5401092 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTTCAGATAGAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTTCAGATAGAGCACTAA
* * * *
5401151 GTGTGCT-AAATGGTGAGGAAAATCATACCAAGTGTATGGATTTCCAGATAGAGCACTAA
1 GTGTGCTAAAATGATAAGG-AAATCATACTAAGTGTATGGATTTTCAGATAGAGCACTAA
* * * * *
5401210 GTGTGCT-AAATGGTGAGGAAAAACATACTAAGTGTATGGATTTCCAGATATG-GCACTTCA
1 GTGTGCTAAAATGATAAGG-AAATCATACTAAGTGTATGGATTTTCAGATA-GAGCAC-TAA
* * *
5401270 -TGTGCTAAAATGGTGAGGAAATCATACTAAGTGTATGTA-TTTCTAGATAGAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTTC-AGATAGAGCACTAA
* * * * * * * * * * **
5401328 GAGTGCTACAAGGTTAAGGAAATCATTCTAAGGGTATAGATTTTCAAATAGGGTACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTTCAGATAGAGCACTAA
* * * * **
5401387 GTGTGCTAAAATGAT-AGGGAATCATATTAA-TGGTATGGATTTTTAGATAGGGCACTTC
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGT-GTATGGATTTTCAGATAGAGCACTAA
* * * *
5401445 GTGTGCTAAAATGAGAGGGAAATCATACTAAGTGTAT-GATCTTCCAGATAGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGAT-TTTCAGATAGAGCACTAA
* *
5401504 GAGTGCTAACATGATAAGGAAAT
1 GTGTGCTAAAATGATAAGGAAAT
5401527 TAAATGAATT
Statistics
Matches: 313, Mismatches: 51, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
58 65 0.21
59 229 0.73
60 19 0.06
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.29
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTTCAGATAGAGCACTAA
Found at i:5401393 original size:177 final size:175
Alignment explanation
Indices: 5401093--5401525 Score: 491
Period size: 177 Copynumber: 2.4 Consensus size: 175
5401083 TGGAACTTTG
* * *
5401093 TGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTT-TCAGATAGAGCACTAAGTGTGC
1 TGTGCTAAAATGGTGAGGAAATCATACTAAGTGTAT-GATTTCT-AGATAGAGCACTAAGAGTGC
* * * *
5401157 TAAATGGTGAGGAAAATCATACCAAGTGTATGGATTTCCAGATAGAGCACTAAGTGTGCT-AAAT
64 TAAATGGTAAGGAAAATCATACCAAGGGTATAGATTTCCAAATAGAGCACTAAGTGTGCTAAAAT
* *
5401221 GGTGAGGAAAAACATACTAA-GTGTATGGATTTCCAGATATGGCACTTCA
129 GAT-AGG-AAAACATACTAATG-GTATGGATTTCCAGATAGGGCACTTCA
5401270 TGTGCTAAAATGGTGAGGAAATCATACTAAGTGTATGTATTTCTAGATAGAGCACTAAGAGTGCT
1 TGTGCTAAAATGGTGAGGAAATCATACTAAGTGTATG-ATTTCTAGATAGAGCACTAAGAGTGCT
* * * * * **
5401335 ACAA-GGTTAAGG-AAATCATTCTAAGGGTATAGATTTTCAAATAGGGTACTTTGTGTGCTAAAA
65 A-AATGG-TAAGGAAAATCATACCAAGGGTATAGATTTCCAAATAGAGCACTAAGTGTGCTAAAA
* * * ** *
5401398 TGATAGGGAATCATATTAATGGTATGGATTTTTAGATAGGGCACTTCG
128 TGATAGGAAAACATACTAATGGTATGGATTTCCAGATAGGGCACTTCA
* * *
5401446 TGTGCTAAAAT-GAGAGGGAAATCATACTAAGTGTATGATCTTCCAGATAGAGCACTGAGAGTGC
1 TGTGCTAAAATGGTGA-GGAAATCATACTAAGTGTATGAT-TTCTAGATAGAGCACTAAGAGTGC
*
5401510 TAACATGATAAGGAAA
64 TAA-ATGGTAAGGAAA
5401526 TTAAATGAAT
Statistics
Matches: 219, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
175 6 0.03
176 95 0.43
177 105 0.48
178 13 0.06
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (175 bp):
TGTGCTAAAATGGTGAGGAAATCATACTAAGTGTATGATTTCTAGATAGAGCACTAAGAGTGCTA
AATGGTAAGGAAAATCATACCAAGGGTATAGATTTCCAAATAGAGCACTAAGTGTGCTAAAATGA
TAGGAAAACATACTAATGGTATGGATTTCCAGATAGGGCACTTCA
Found at i:5403635 original size:27 final size:27
Alignment explanation
Indices: 5403592--5403651 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
5403582 TTAGTTCTAG
*
5403592 AAAATATTTTCTATTTT-GTTTTTTAGA
1 AAAATATTTTCTATTTTAG-TTTTTAAA
*
5403619 AAAATGTTTTC-ATTTTTAGTTTTTAAA
1 AAAATATTTTCTA-TTTTAGTTTTTAAA
5403646 AAAATA
1 AAAATA
5403652 GAAAACATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 26 0.93
28 1 0.04
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (27 bp):
AAAATATTTTCTATTTTAGTTTTTAAA
Found at i:5403641 original size:26 final size:27
Alignment explanation
Indices: 5403582--5403651 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
5403572 ATTCATATCA
*
5403582 TTAGTTCTAG-AAAATATTTTCTATTT
1 TTAGTTTTAGAAAAATATTTTCTATTT
* *
5403608 TGT-TTTTTAGAAAAATGTTTTC-ATTT
1 T-TAGTTTTAGAAAAATATTTTCTATTT
*
5403634 TTAGTTTTTAAAAAAATA
1 TTAG-TTTTAGAAAAATA
5403652 GAAAACATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
25 1 0.03
26 11 0.32
27 22 0.65
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (27 bp):
TTAGTTTTAGAAAAATATTTTCTATTT
Found at i:5406546 original size:15 final size:15
Alignment explanation
Indices: 5406526--5406568 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
5406516 TTTACCTGGA
5406526 AAATATAAAATCTTC
1 AAATATAAAATCTTC
5406541 AAATATAAAATCTTC
1 AAATATAAAATCTTC
5406556 AAATATAAAATCT
1 AAATATAAAATCT
5406569 AAATATTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAAAATCTTC
Found at i:5413363 original size:18 final size:18
Alignment explanation
Indices: 5413336--5413383 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
5413326 TTTAATGGCA
*
5413336 AAATGGATATTTCTCATT
1 AAATGAATATTTCTCATT
5413354 AAATGAATATTTCTCATT
1 AAATGAATATTTCTCATT
5413372 AAATGAATATTT
1 AAATGAATATTT
5413384 TATTCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
AAATGAATATTTCTCATT
Found at i:5417285 original size:21 final size:20
Alignment explanation
Indices: 5417247--5417285 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5417237 TCCAATGAAG
5417247 ATTTGAGATTTGAGGTTTGA
1 ATTTGAGATTTGAGGTTTGA
5417267 ATTT-AGAGTTTGAAGGTTT
1 ATTTGAGA-TTTG-AGGTTT
5417286 AAGAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 8 0.47
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
ATTTGAGATTTGAGGTTTGA
Found at i:5428619 original size:76 final size:76
Alignment explanation
Indices: 5428493--5428649 Score: 305
Period size: 76 Copynumber: 2.1 Consensus size: 76
5428483 CAGAGCATTC
5428493 AGAATATCCAGTTGAAGGCCTTGGTACATTTCTTTCCTCTTTATCAACGTTTAGTTAACTATGTT
1 AGAATATCCAGTTGAAGGCCTTGGTACATTTCTTTCCTCTTTATCAACGTTTAGTTAACTATGTT
*
5428558 TAGTTTGAGTT
66 TACTTTGAGTT
5428569 AGAATATCCAGTTGAAGGCCTTGGTACATTTCTTTCCTCTTTATCAACGTTTAGTTAACTATGTT
1 AGAATATCCAGTTGAAGGCCTTGGTACATTTCTTTCCTCTTTATCAACGTTTAGTTAACTATGTT
5428634 TACTTTGAGTT
66 TACTTTGAGTT
5428645 AGAAT
1 AGAAT
5428650 TAATTGGATC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (76 bp):
AGAATATCCAGTTGAAGGCCTTGGTACATTTCTTTCCTCTTTATCAACGTTTAGTTAACTATGTT
TACTTTGAGTT
Found at i:5432616 original size:31 final size:31
Alignment explanation
Indices: 5432579--5432643 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
5432569 TAGTGTCACG
*
5432579 TCATCATCTATAATGACCTGGACACACCACA
1 TCATCATCTATAATGACCTGAACACACCACA
* *
5432610 TCATCATCTATCATGACCTGAACACGCCACA
1 TCATCATCTATAATGACCTGAACACACCACA
5432641 TCA
1 TCA
5432644 GGATCTAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (31 bp):
TCATCATCTATAATGACCTGAACACACCACA
Found at i:5432650 original size:31 final size:31
Alignment explanation
Indices: 5432583--5432650 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
5432573 GTCACGTCAT
* *
5432583 CATCTATAATGACCTGGACACACCACATCAT
1 CATCTATAATGACCTGAACACACCACATCAG
* *
5432614 CATCTATCATGACCTGAACACGCCACATCAG
1 CATCTATAATGACCTGAACACACCACATCAG
*
5432645 GATCTA
1 CATCTA
5432651 GGTCCTCATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (31 bp):
CATCTATAATGACCTGAACACACCACATCAG
Found at i:5435509 original size:46 final size:47
Alignment explanation
Indices: 5435418--5435517 Score: 114
Period size: 46 Copynumber: 2.1 Consensus size: 47
5435408 ATGTAAGTGA
* * * *
5435418 TTAAAACGTTACTTTTTTTAAAACGGGTGACTAAAGTAAGGTAGATT
1 TTAAAACGTTACTTTTTTCAAAACCGGTAACTAAAGTAAGATAGATT
* *
5435465 TTAAAGCGTTA-TTTTTTCAAAACCGGTAATTCAAA-TAAGATAGATT
1 TTAAAACGTTACTTTTTTCAAAACCGGTAACT-AAAGTAAGATAGATT
5435511 TTGAAAA
1 TT-AAAA
5435518 AATAGGGATC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 28 0.64
47 16 0.36
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (47 bp):
TTAAAACGTTACTTTTTTCAAAACCGGTAACTAAAGTAAGATAGATT
Found at i:5436745 original size:5 final size:5
Alignment explanation
Indices: 5436735--5436759 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5436725 ACCAGTCATA
5436735 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
5436760 TTGACCCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:5436775 original size:15 final size:16
Alignment explanation
Indices: 5436757--5436790 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
5436747 CCGACCCGAC
5436757 CCGTTGACC-CGTTGA
1 CCGTTGACCACGTTGA
5436772 CCGTTGACCGACGTTGA
1 CCGTTGACC-ACGTTGA
5436789 CC
1 CC
5436791 AGTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (16 bp):
CCGTTGACCACGTTGA
Found at i:5439266 original size:24 final size:24
Alignment explanation
Indices: 5439215--5439271 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
5439205 ATTTGATTTC
* * * *
5439215 TGATCTGATACTTGACTTGGATTT
1 TGATATGATACTTGACATGAATTA
5439239 TGATATGATACTTGACATGAATTA
1 TGATATGATACTTGACATGAATTA
*
5439263 TGATTTGAT
1 TGATATGAT
5439272 TTTTGATATA
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:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACATGAATTA
Found at i:5441964 original size:7 final size:7
Alignment explanation
Indices: 5441952--5442040 Score: 85
Period size: 7 Copynumber: 13.1 Consensus size: 7
5441942 AATCAAATTA
5441952 AGGGTTT
1 AGGGTTT
5441959 AGGGTTT
1 AGGGTTT
5441966 AGGGTTT
1 AGGGTTT
5441973 AGGG-TT
1 AGGGTTT
*
5441979 A-TGTTT
1 AGGGTTT
*
5441985 AGAGTTT
1 AGGGTTT
**
5441992 AATGTTT
1 AGGGTTT
*
5441999 ATGGTTT
1 AGGGTTT
5442006 AGGGTTT
1 AGGGTTT
5442013 AGGGTTT
1 AGGGTTT
*
5442020 A-AGTTT
1 AGGGTTT
**
5442026 ATAGTTT
1 AGGGTTT
5442033 AGGGTTT
1 AGGGTTT
5442040 A
1 A
5442041 AGATTTAAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
5 1 0.01
6 11 0.16
7 57 0.83
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
AGGGTTT
Found at i:5442010 original size:40 final size:41
Alignment explanation
Indices: 5441955--5442033 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
5441945 CAAATTAAGG
*
5441955 GTTTAGGGTTTAGGGTTTAGGG-TTATGTTTAGAGTTTAAT
1 GTTTAGGGTTTAGGGTTTAGGGTTTAAGTTTAGAGTTTAAT
* *
5441995 GTTTATGGTTTAGGGTTTAGGGTTTAAGTTTATAGTTTA
1 GTTTAGGGTTTAGGGTTTAGGGTTTAAGTTTAGAGTTTA
5442034 GGGTTTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.49
Consensus pattern (41 bp):
GTTTAGGGTTTAGGGTTTAGGGTTTAAGTTTAGAGTTTAAT
Found at i:5442032 original size:20 final size:20
Alignment explanation
Indices: 5441952--5442047 Score: 86
Period size: 20 Copynumber: 4.7 Consensus size: 20
5441942 AATCAAATTA
* *
5441952 AGGGTTTAGGGTTTAGGGTTT
1 AGGGTTTA-AGTTTAGAGTTT
*
5441973 AGGG-TTATGTTTAGAGTTT
1 AGGGTTTAAGTTTAGAGTTT
** * *
5441992 AATGTTTATGGTTTAGGGTTT
1 AGGGTTTA-AGTTTAGAGTTT
*
5442013 AGGGTTTAAGTTTATAGTTT
1 AGGGTTTAAGTTTAGAGTTT
5442033 AGGGTTTAAGATTTA
1 AGGGTTTAAG-TTTA
5442048 AGGCTCATTG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.20
20 25 0.41
21 24 0.39
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (20 bp):
AGGGTTTAAGTTTAGAGTTT
Found at i:5442033 original size:27 final size:27
Alignment explanation
Indices: 5441981--5442049 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
5441971 TTAGGGTTAT
* *
5441981 GTTTAGAGTTTAATGTTTATGGTTTAGG
1 GTTTAGGGTTTAA-GTTTATAGTTTAGG
5442009 GTTTAGGGTTTAAGTTTATAGTTTAGG
1 GTTTAGGGTTTAAGTTTATAGTTTAGG
* *
5442036 GTTTAAGATTTAAG
1 GTTTAGGGTTTAAG
5442050 GCTCATTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.68
28 12 0.32
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.48
Consensus pattern (27 bp):
GTTTAGGGTTTAAGTTTATAGTTTAGG
Found at i:5442550 original size:30 final size:30
Alignment explanation
Indices: 5442510--5442566 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
5442500 CATATTTTTA
*
5442510 TTTTATTATATTTTTAAAATTTTATAAAAT
1 TTTTAATATATTTTTAAAATTTTATAAAAT
5442540 TTTTAATATATTTTTAAAATTTTATAA
1 TTTTAATATATTTTTAAAATTTTATAA
5442567 TTATCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAATATATTTTTAAAATTTTATAAAAT
Found at i:5442556 original size:11 final size:11
Alignment explanation
Indices: 5442510--5442600 Score: 70
Period size: 11 Copynumber: 8.7 Consensus size: 11
5442500 CATATTTTTA
*
5442510 TTTTATTATAT
1 TTTTAATATAT
5442521 TTTTAA-A-AT
1 TTTTAATATAT
5442530 TTTATAA-A-AT
1 TTT-TAATATAT
5442540 TTTTAATATAT
1 TTTTAATATAT
5442551 TTTTAA-A-AT
1 TTTTAATATAT
5442560 TTTATAAT-TAT
1 TTT-TAATATAT
*** *
5442571 CAATAATGTAT
1 TTTTAATATAT
5442582 TTTTAATATAT
1 TTTTAATATAT
5442593 TTTTAATA
1 TTTTAATA
5442601 ATGTAATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
9 13 0.20
10 19 0.29
11 33 0.51
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:5442567 original size:21 final size:21
Alignment explanation
Indices: 5442508--5442567 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 21
5442498 ATCATATTTT
* *
5442508 TATTTTATTATATTTTTAA-A
1 TATTTTATAAAATTTTTAATA
5442528 -ATTTTATAAAATTTTTAATA
1 TATTTTATAAAATTTTTAATA
5442548 TATTTT-TAAAATTTTATAAT
1 TATTTTATAAAATTTT-TAAT
5442568 TATCAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 16 0.46
20 10 0.29
21 9 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAAAATTTTTAATA
Found at i:5442586 original size:31 final size:30
Alignment explanation
Indices: 5442516--5442587 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
5442506 TTTATTTTAT
***
5442516 TATATTTTTAAAATTTTATAAAATTTTTAA
1 TATATTTTTAAAATTTTATAAAATCAATAA
*
5442546 TATATTTTTAAAATTTTATAATTATCAATAA
1 TATATTTTTAAAATTTTATAA-AATCAATAA
*
5442577 TGTATTTTTAA
1 TATATTTTTAA
5442588 TATATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 21 0.58
31 15 0.42
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (30 bp):
TATATTTTTAAAATTTTATAAAATCAATAA
Found at i:5443848 original size:21 final size:20
Alignment explanation
Indices: 5443822--5443860 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5443812 AAGACACAAA
5443822 AATAAAAAAATAAATAAAAAT
1 AATAAAAAAAT-AATAAAAAT
*
5443843 AATAAAAATATAATAAAA
1 AATAAAAAAATAATAAAA
5443861 CAAACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AATAAAAAAATAATAAAAAT
Found at i:5443855 original size:8 final size:9
Alignment explanation
Indices: 5443819--5443852 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5443809 ACAAAGACAC
5443819 AAAAATAA-
1 AAAAATAAT
5443827 AAAAATAAAT
1 AAAAAT-AAT
5443837 AAAAATAAT
1 AAAAATAAT
5443846 AAAAATA
1 AAAAATA
5443853 TAATAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.25
9 12 0.50
10 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAAATAAT
Found at i:5445452 original size:6 final size:6
Alignment explanation
Indices: 5445441--5445528 Score: 56
Period size: 6 Copynumber: 14.0 Consensus size: 6
5445431 AAAATCAGGA
* **
5445441 AAAAAT AAAAAT --AAAT AAAAAT AAATAAA AATAAAT AAAAAT ATTAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA-AAT AA-AAAT AAAAAT AAAAAT
*
5445489 -AAAAT AATAAAT AATATTAAT ATAATAT AAAAAT AAAAAT
1 AAAAAT AA-AAAT AA-A--AAT A-AAAAT AAAAAT AAAAAT
5445529 CATTTTTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.06
5 3 0.05
6 32 0.49
7 19 0.29
8 1 0.02
9 5 0.08
10 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (6 bp):
AAAAAT
Found at i:5445456 original size:10 final size:10
Alignment explanation
Indices: 5445443--5445502 Score: 84
Period size: 10 Copynumber: 5.6 Consensus size: 10
5445433 AATCAGGAAA
5445443 AAATAAAAAT
1 AAATAAAAAT
5445453 AAATAAAAAT
1 AAATAAAAAT
5445463 AAATAAAAAT
1 AAATAAAAAT
5445473 AAATAAAAAT
1 AAATAAAAAT
5445483 ATTAATAAAATAAT
1 A--AAT-AAA-AAT
5445497 AAATAA
1 AAATAA
5445503 TATTAATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
10 31 0.67
11 2 0.04
12 6 0.13
13 3 0.07
14 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:5445460 original size:16 final size:16
Alignment explanation
Indices: 5445441--5445528 Score: 67
Period size: 16 Copynumber: 5.4 Consensus size: 16
5445431 AAAATCAGGA
5445441 AAAAATAAA-AATAAAT
1 AAAAATAAATAA-AAAT
5445457 AAAAATAAATAAAAAT
1 AAAAATAAATAAAAAT
**
5445473 AAATAA-AAATATTAAT
1 AAA-AATAAATAAAAAT
5445489 -AAAAT-AATAAATAAT
1 AAAAATAAATAAA-AAT
*
5445504 ATTAATATAATATAAAAAT
1 A--AAAATAA-ATAAAAAT
5445523 AAAAAT
1 AAAAAT
5445529 CATTTTTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
14 6 0.11
15 5 0.09
16 24 0.42
17 8 0.14
18 4 0.07
19 5 0.09
20 5 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:5445518 original size:20 final size:19
Alignment explanation
Indices: 5445471--5445523 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
5445461 ATAAATAAAA
5445471 ATAA-ATAAAAATATTAAT
1 ATAATATAAAAATATTAAT
*
5445489 AAAATAATAAATAATATTAAT
1 ATAAT-ATAAA-AATATTAAT
5445510 ATAATATAAAAATA
1 ATAATATAAAAATA
5445524 AAAATCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.10
19 4 0.13
20 10 0.33
21 13 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATATAAAAATATTAAT
Found at i:5445642 original size:12 final size:12
Alignment explanation
Indices: 5445625--5445685 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
5445615 TATATAATAT
5445625 ATATTTTCAAAA
1 ATATTTTCAAAA
5445637 ATATTTTCAAAA
1 ATATTTTCAAAA
* * * * *
5445649 CTATATACTATAT
1 ATATTTTC-AAAA
5445662 ATATTTTCAAAA
1 ATATTTTCAAAA
5445674 ATA-TTTCAAAA
1 ATATTTTCAAAA
5445685 A
1 A
5445686 CTATATAGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
11 9 0.24
12 22 0.58
13 7 0.18
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:5445671 original size:37 final size:37
Alignment explanation
Indices: 5445567--5445739 Score: 179
Period size: 37 Copynumber: 4.9 Consensus size: 37
5445557 AAAAAAATTG
* * * *
5445567 TTTTCAAAACCATATAATATATACATATTCAAAAATTA
1 TTTTCAAAACTATATACTATATATATTTTCAAAAA-TA
*
5445605 TTTTTAAAACTATATA--ATATATATTTTCAAAAATA
1 TTTTCAAAACTATATACTATATATATTTTCAAAAATA
5445640 TTTTCAAAACTATATACTATATATATTTTCAAAAATA
1 TTTTCAAAACTATATACTATATATATTTTCAAAAATA
* *
5445677 -TTTC--AA--A-A-AC--TATATAGTTTCAAAAATG
1 TTTTCAAAACTATATACTATATATATTTTCAAAAATA
* *
5445705 TTTTAAAAACTATATATTATATATATTTTCAAAAA
1 TTTTCAAAACTATATACTATATATATTTTCAAAAA
5445740 CTATACAATA
Statistics
Matches: 114, Mismatches: 10, Indels: 23
0.78 0.07 0.16
Matches are distributed among these distances:
28 16 0.14
29 3 0.03
30 2 0.02
31 3 0.03
32 1 0.01
33 1 0.01
34 3 0.03
35 18 0.16
36 19 0.17
37 34 0.30
38 14 0.12
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (37 bp):
TTTTCAAAACTATATACTATATATATTTTCAAAAATA
Found at i:5445698 original size:28 final size:27
Alignment explanation
Indices: 5445659--5445744 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 27
5445649 CTATATACTA
5445659 TATATATTTTCAAAAATATTTCAAAAAC
1 TATATA-TTTCAAAAATATTTCAAAAAC
* *
5445687 TATATAGTTTCAAAAATGTTTTAAAAAC
1 TATATA-TTTCAAAAATATTTCAAAAAC
* *
5445715 TATATA-TT-ATATATATTTTCAAAAAC
1 TATATATTTCAAAAATA-TTTCAAAAAC
5445741 TATA
1 TATA
5445745 CAATATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.08
26 15 0.30
28 31 0.62
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (27 bp):
TATATATTTCAAAAATATTTCAAAAAC
Found at i:5445698 original size:65 final size:63
Alignment explanation
Indices: 5445620--5445796 Score: 223
Period size: 65 Copynumber: 2.8 Consensus size: 63
5445610 AAAACTATAT
* * *
5445620 AATATATATTTTCAAAAATATTTTCAAAACTATATACTATATATATTTTCAAAAA-TATTTCAAA
1 AATATATATTTTCAAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAAACTA-TAC-AA
* * *
5445684 AACTATATAGTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAAACTATACAA
1 AA-TATATATTTTCAAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAAACTATACAA
* *
5445748 TATATAT-TTTTCAAAAACCGTTTTCAAAACTTATATAATATATATATTT
1 AATATATATTTTCAAAAA-TGTTTTCAAAAC-TATATAATATATATATTT
5445797 CGAAAACCAT
Statistics
Matches: 99, Mismatches: 10, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
62 9 0.09
63 15 0.15
64 22 0.22
65 51 0.52
66 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (63 bp):
AATATATATTTTCAAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAAACTATACAA
Found at i:5445751 original size:26 final size:25
Alignment explanation
Indices: 5445705--5445765 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
5445695 TTCAAAAATG
* *
5445705 TTTT-AAAAACTATATATTATATAT
1 TTTTCAAAAACTATACAATATATAT
5445729 ATTTTCAAAAACTATACAATATATAT
1 -TTTTCAAAAACTATACAATATATAT
5445755 TTTTCAAAAAC
1 TTTTCAAAAAC
5445766 CGTTTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 15 0.45
26 18 0.55
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTCAAAAACTATACAATATATAT
Found at i:5445776 original size:38 final size:38
Alignment explanation
Indices: 5445730--5445879 Score: 207
Period size: 38 Copynumber: 4.0 Consensus size: 38
5445720 ATTATATATA
* * *
5445730 TTTTCAAAAAC-TATACAATATATATTTTTCAAAAACCG
1 TTTTC-AAAACTTATATAATATATATATTTCGAAAACCG
*
5445768 TTTTCAAAACTTATATAATATATATATTTCGAAAACCA
1 TTTTCAAAACTTATATAATATATATATTTCGAAAACCG
*
5445806 TTTTCAAAACTTATATAATATATATATTTCGAAAATCG
1 TTTTCAAAACTTATATAATATATATATTTCGAAAACCG
* *
5445844 TTTCCAAAACTTATATAATA-ATGT-TTTCGAAAACCG
1 TTTTCAAAACTTATATAATATATATATTTCGAAAACCG
5445880 ATATGACAAC
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
36 11 0.11
37 8 0.08
38 83 0.81
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (38 bp):
TTTTCAAAACTTATATAATATATATATTTCGAAAACCG
Found at i:5446516 original size:45 final size:45
Alignment explanation
Indices: 5446450--5446885 Score: 628
Period size: 45 Copynumber: 9.7 Consensus size: 45
5446440 CATCCATTTA
* * * * *
5446450 TGTTTATAATACA-CCATTATGCACTTTAAACTATAACAT-CTTTTC
1 TGTTGATAATGCACCCA-TATGCA-TTTCAACTCTAGCATACTTTTC
* * *
5446495 TGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTT
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
* * * *
5446540 TGTTGATAATGTACCCATATACATTTCAAC-CATAGTATA-TATTTA
1 TGTTGATAATGCACCCATATGCATTTCAACTC-TAGCATACT-TTTC
* * *
5446585 TGTTGATAATGTACCCATATACATTTCAACTCTAGTATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
5446630 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
5446675 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
*
5446720 TGTTGATAATGCACCCATATGCATTTCAACTCTTGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
* * *
5446765 TGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
5446810 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
*
5446855 TGTTGATAATGCACCCATATACATTTCAACT
1 TGTTGATAATGCACCCATATGCATTTCAACT
5446886 AAAGTATGTT
Statistics
Matches: 362, Mismatches: 23, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
44 13 0.04
45 344 0.95
46 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTC
Found at i:5446670 original size:135 final size:135
Alignment explanation
Indices: 5446489--5446969 Score: 655
Period size: 135 Copynumber: 3.6 Consensus size: 135
5446479 ACTATAACAT
* * * *
5446489 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTTTGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCAC
* * * *
5446554 CCATATACATTTCAAC-CATAGTATA-TATTTATGTTGATAATGTACCCATATACATTTCAACTC
66 CCATATGCATTTCAACTC-TAGCATACT-TTTCTGTTGATAATGCACCCATATACATTTCAACTC
5446617 TAGTATA
129 TAGTATA
* *
5446624 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCAC
* *
5446689 CCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTT
66 CCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTA
*
5446754 GCATA
131 GTATA
*
5446759 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCAC
**
5446824 CCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTAAA
66 CCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTA
*
5446889 GTATGT
131 GTAT-A
* * * * * * *** *
5446895 TTTTTTTGTTGATAATG-TCCCATATACATTTCAATTATGGCAT-CCTTTCATGCCAATAATGTA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTC-TGTTGATAATGCA
5446958 CCCATATGCATT
65 CCCATATGCATT
5446970 AGTATTTTCA
Statistics
Matches: 312, Mismatches: 30, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
134 5 0.02
135 290 0.93
136 17 0.05
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (135 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCAC
CCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTA
GTATA
Found at i:5447514 original size:22 final size:20
Alignment explanation
Indices: 5447472--5447529 Score: 89
Period size: 22 Copynumber: 2.8 Consensus size: 20
5447462 TTCAATGTTT
5447472 CATGGTATCGATACCCTTAC
1 CATGGTATCGATACCCTTAC
5447492 CATGGTATCGATACTACCTTAC
1 CATGGTATCGATAC--CCTTAC
*
5447514 CATGGTACCGATACCC
1 CATGGTATCGATACCC
5447530 CCTTATGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 16 0.46
22 19 0.54
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.28
Consensus pattern (20 bp):
CATGGTATCGATACCCTTAC
Found at i:5453239 original size:45 final size:45
Alignment explanation
Indices: 5453201--5453619 Score: 549
Period size: 45 Copynumber: 9.4 Consensus size: 45
5453191 ATGCACTTTA
* * * *
5453201 AACTATAACAT-CTTTTATGTTTATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* *
5453245 AACTATAG--TACTTTTCTATTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * * **
5453288 AACCATAGTATATTTTTCTGTTGATAATTTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * *
5453333 AACTCTAGCATACATTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* *
5453378 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* *
5453423 AACTCTAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * *
5453468 AACTCTAGCATACGTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * *
5453513 AACTCTAGCATACTTTTCTGTTGATAATGTACCCATTTACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
* * * *
5453558 AACTAAAGTATGCTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
*
5453603 AACTATGGCAT-CTTTTC
1 AACTATAGCATACTTTTC
5453620 ATGCCATGCA
Statistics
Matches: 336, Mismatches: 36, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
42 1 0.00
43 35 0.10
44 13 0.04
45 287 0.85
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
AACTATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTC
Found at i:5453421 original size:135 final size:135
Alignment explanation
Indices: 5453218--5453606 Score: 631
Period size: 135 Copynumber: 2.9 Consensus size: 135
5453208 ACATCTTTTA
* * *
5453218 TGTTTATAATGCACCCATATGCATTTCAACTATAG--TACTTTTCTATTGATAATGTACCCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATAT
* *
5453281 ACATTTCAACCATAGTATATTTTTCTGTTGATAATTTACCCATATACATTTCAACTCTAGCATAC
66 ACATTTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATAC
5453346 ATTTC
131 ATTTC
*
5453351 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATAT
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATAT
* *
5453416 GCATTTCAACTC-TAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
66 ACATTTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
*
5453480 CGTTTC
130 CATTTC
*
5453486 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATTT
1 TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATAT
* * *
5453551 ACATTTCAACTAAAGTATGCTTTTCTGTTGATAATGTACCCATATACATTTCAACT
66 ACATTTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACT
5453607 ATGGCATCTT
Statistics
Matches: 236, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
133 33 0.14
135 202 0.86
136 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (135 bp):
TGTTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATAT
ACATTTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATAC
ATTTC
Found at i:5454073 original size:20 final size:20
Alignment explanation
Indices: 5454045--5454104 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
5454035 CTGGTTATGA
*
5454045 AGTATCGATACTACTACCCT
1 AGTACCGATACTACTACCCT
* *
5454065 AGTACCGATACTTCTACACT
1 AGTACCGATACTACTACCCT
*
5454085 AGGGTACCGATACTCCTACC
1 A--GTACCGATACTACTACC
5454105 TGGTATCGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 18 0.55
22 15 0.45
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.27
Consensus pattern (20 bp):
AGTACCGATACTACTACCCT
Found at i:5454094 original size:22 final size:20
Alignment explanation
Indices: 5454045--5454116 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
5454035 CTGGTTATGA
* *
5454045 AGTATCGATACTACTACCCT
1 AGTACCGATACTACTACACT
*
5454065 AGTACCGATACTTCTACACT
1 AGTACCGATACTACTACACT
*
5454085 AGGGTACCGATACTCCTAC-CT
1 A--GTACCGATACTACTACACT
* *
5454106 GGTATCGATAC
1 AGTACCGATAC
5454117 CAAAATTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 9 0.20
20 18 0.41
21 2 0.05
22 15 0.34
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (20 bp):
AGTACCGATACTACTACACT
Found at i:5463593 original size:16 final size:16
Alignment explanation
Indices: 5463572--5463609 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5463562 AAGACAATGC
5463572 AGATACCTTATAGCCT
1 AGATACCTTATAGCCT
5463588 AGATACCTTATAGCCT
1 AGATACCTTATAGCCT
*
5463604 GGATAC
1 AGATAC
5463610 ATGTCAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (16 bp):
AGATACCTTATAGCCT
Found at i:5469217 original size:15 final size:15
Alignment explanation
Indices: 5469197--5469225 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5469187 AAAAAAAGTT
5469197 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
5469212 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
5469226 CAGTCGGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:5470049 original size:20 final size:21
Alignment explanation
Indices: 5470003--5470063 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
5469993 TCCCCTGTGG
5470003 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
5470026 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
5470046 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
5470064 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:5478188 original size:65 final size:64
Alignment explanation
Indices: 5478048--5478203 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 64
5478038 ACACCCTATT
* * * * * *
5478048 TCGAATGCATTTTATGCACCAATGCACAGGCATGCATCGATGAACTCTAGATTTTATTGAAATA
1 TCGAATACAATTTATGCACCGATGCACAAGCATGCATCGATGAACTCTAGATTGTATTGAAACA
* * * * *
5478112 TCGAATGCAATTTATGCACCGATGCACATATCATGCATCGATGCACTCCTGGCTTGT-TTGAAAC
1 TCGAATACAATTTATGCACCGATGCACA-AGCATGCATCGATGAACT-CTAGATTGTATTGAAAC
5478176 A
64 A
*
5478177 TTGAATACAA-TTAGTGCACCGATGCAC
1 TCGAATACAATTTA-TGCACCGATGCAC
5478204 TCCTAGTGTA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 29 0.37
65 43 0.55
66 6 0.08
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
TCGAATACAATTTATGCACCGATGCACAAGCATGCATCGATGAACTCTAGATTGTATTGAAACA
Found at i:5484041 original size:21 final size:21
Alignment explanation
Indices: 5484017--5484074 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
5484007 CCCTTGAATA
5484017 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCATGAAGG
* * *
5484038 TGCATCGATGCACTCCTTGAATG
1 TGCATCGAT--ACACCATGAAGG
5484061 TGCATCGATACACC
1 TGCATCGATACACC
5484075 CGTCAGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCATGAAGG
Found at i:5484063 original size:23 final size:21
Alignment explanation
Indices: 5484008--5484074 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
5483998 ACAATGCATC
*
5484008 CCTTGAATATGCATCGATACA
1 CCTTGAATGTGCATCGATACA
* * *
5484029 CCATGAAGGTGCATCGATGCACT
1 CCTTGAATGTGCATCGAT--ACA
5484052 CCTTGAATGTGCATCGATACA
1 CCTTGAATGTGCATCGATACA
5484073 CC
1 CC
5484075 CGTCAGTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 19 0.51
23 18 0.49
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTTGAATGTGCATCGATACA
Found at i:5485678 original size:27 final size:27
Alignment explanation
Indices: 5485648--5485705 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
5485638 TGAGAATTTG
5485648 ATCTAAGGTTTGCATCCATTGAATCTC
1 ATCTAAGGTTTGCATCCATTGAATCTC
5485675 ATCTAAGGTTTGCATCCATTGAATCTC
1 ATCTAAGGTTTGCATCCATTGAATCTC
5485702 ATCT
1 ATCT
5485706 CACTGCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (27 bp):
ATCTAAGGTTTGCATCCATTGAATCTC
Found at i:5488294 original size:16 final size:16
Alignment explanation
Indices: 5488223--5488295 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
5488213 TTAGTAGTTT
*
5488223 TTTTTTTCTTTCTCTG
1 TTTTTTTCTTTCTCCG
5488239 TTTTTTTCTTTCTCCGG
1 TTTTTTTCTTTCTCC-G
* * * ***
5488256 TTCTGTCTCTCTCTTTT
1 TT-TTTTTCTTTCTCCG
*
5488273 TTTTTTTCTGTCTCCG
1 TTTTTTTCTTTCTCCG
5488289 TTTTTTT
1 TTTTTTT
5488296 TTCTTCAGGT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
16 29 0.69
17 5 0.12
18 8 0.19
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.70
Consensus pattern (16 bp):
TTTTTTTCTTTCTCCG
Found at i:5488752 original size:17 final size:15
Alignment explanation
Indices: 5488709--5488749 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
5488699 GGTCTGTAAT
5488709 TATTTATTT-ATATA
1 TATTTATTTAATATA
5488723 TATTTATTTAATATA
1 TATTTATTTAATATA
5488738 TATTTA-TTAATA
1 TATTTATTTAATA
5488750 ATAATAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:5488753 original size:3 final size:3
Alignment explanation
Indices: 5488745--5488791 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
5488735 ATATATTTAT
*
5488745 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5488792 TGGATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5489298 original size:117 final size:116
Alignment explanation
Indices: 5489017--5489447 Score: 582
Period size: 117 Copynumber: 3.7 Consensus size: 116
5489007 TAGAATTATG
* * * *
5489017 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCATATGAGGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
* * * * * *
5489082 TCATTATGAACTTTCTTTGG-AA-GAAATAATCCATCCAGTGATGAATTCAGA-
66 TCATTATGAACTTTC-CTGGCAATG--TTGATCCATCAAATGATGAATTCAAAC
* * * *
5489133 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
5489198 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACT-TTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* * *
5489250 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
*
5489315 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACT-TTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* * **
5489367 CAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCTTCAT-ATGAGTTCTT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AGATGATGAGTTCTT
5489431 CTCATTATGAACTTTCC
65 CTCATTATGAACTTTCC
5489448 GCTGGGGATG
Statistics
Matches: 283, Mismatches: 27, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
116 97 0.34
117 183 0.65
118 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (116 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
TCATTATGAACTTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:5489363 original size:233 final size:232
Alignment explanation
Indices: 5489017--5489447 Score: 602
Period size: 233 Copynumber: 1.8 Consensus size: 232
5489007 TAGAATTATG
*
5489017 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCATATGAGGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGGAGTTCTTC
* * * * * * **
5489082 TCATTATGAACTTTCTTTGGAAGAAATAATCCATCCAGTGATGAATTCAGA-TAAAAGGTTGAAC
66 TCATTATGAACTTACTCTGGAAG-AATAATCCATCAAATGATGAATTCAAACCAAAAAATTGAAC
*
5489146 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AGATGACGAGTTCTTCTCATTATGAACT
130 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCTACAT-ACGAGTTCTTCTCATTATGAACT
5489210 CTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
194 -TTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* *
5489250 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTT-TTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTT-CTTCTTCAGATGAGGAGTTCTT
* *
5489314 CTCATTATGAACTCTAC-CTGGCAATG-TTGATCCATCAAATGATGAATTCAAACCAAAAAATTG
65 CTCATTATGAACT-TACTCTGG-AA-GAATAATCCATCAAATGATGAATTCAAACCAAAAAATTG
* * * *
5489377 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCTTCATATGAGTTCTTCTCATTATGAA
127 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCTACATACGAGTTCTTCTCATTATGAA
5489442 CTTTCC
192 CTTTCC
5489448 GCTGGGGATG
Statistics
Matches: 174, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
232 3 0.02
233 98 0.56
234 70 0.40
235 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (232 bp):
CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGGAGTTCTTC
TCATTATGAACTTACTCTGGAAGAATAATCCATCAAATGATGAATTCAAACCAAAAAATTGAACA
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCTACATACGAGTTCTTCTCATTATGAACTTT
CCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:5489520 original size:95 final size:93
Alignment explanation
Indices: 5489406--5489599 Score: 262
Period size: 95 Copynumber: 2.1 Consensus size: 93
5489396 GAACTTCTTC
* * ** * * *
5489406 TTCTTTCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTCCATCAAG
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CGCTGGAAAAGATGATCCATCAAA
*
5489471 TAATGGATTCATGTAAAAGGTTTGAACAAA
65 TAATGGATTCAAGTAAAAGG-TTGAACAAA
* * *
5489501 TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCGCTGGAAAAGATGATCCATCAAAT
*
5489566 GATGGATTCAAGTAAAAGGTTGAACAAA
66 AATGGATTCAAGTAAAAGGTTGAACAAA
5489594 TTCTTC
1 TTCTTC
5489600 TCATTATGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 15 0.17
94 35 0.40
95 37 0.43
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (93 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCGCTGGAAAAGATGATCCATCAAAT
AATGGATTCAAGTAAAAGGTTGAACAAA
Found at i:5489621 original size:113 final size:112
Alignment explanation
Indices: 5489501--5489789 Score: 515
Period size: 113 Copynumber: 2.6 Consensus size: 112
5489491 TTTGAACAAA
* *
5489501 TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-ATGATCCATCAAAT
5489566 GATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
65 GATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
5489614 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAA-TGATCCATCAAAT
* *
5489679 GATGGATTCAGGTAAAAGGTTGAACAAATTCTTTTCATTATGAACTTC
65 GATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
5489727 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAGAAATGATCCATCAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA-AAATGATCCATCAA
5489790 GTGGATTCGA
Statistics
Matches: 170, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
113 167 0.98
114 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATGATCCATCAAATG
ATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
Found at i:5490597 original size:84 final size:84
Alignment explanation
Indices: 5490441--5490664 Score: 409
Period size: 84 Copynumber: 2.7 Consensus size: 84
5490431 GTAGTTCTTA
5490441 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-ATCTTCCA
5490505 AATTCAATGATTGGTTCTG-
65 AATTCAATGATTGGTTCTGT
5490524 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTA-TCTTCCA
5490589 AATTCAATGATTGGTTCTGT
65 AATTCAATGATTGGTTCTGT
5490609 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTA
5490665 CATTTGTTCC
Statistics
Matches: 138, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
83 46 0.33
84 90 0.65
85 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATCTTCCAA
ATTCAATGATTGGTTCTGT
Found at i:5495372 original size:18 final size:19
Alignment explanation
Indices: 5495346--5495382 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5495336 ATTTATGAAA
*
5495346 TAAATAAATGTAAA-AATG
1 TAAAAAAATGTAAAGAATG
5495364 TAAAAAAATGTAAAGAATG
1 TAAAAAAATGTAAAGAATG
5495383 ATTGCCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
TAAAAAAATGTAAAGAATG
Found at i:5504189 original size:20 final size:18
Alignment explanation
Indices: 5504164--5504205 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
5504154 CTTTCTCCGG
5504164 TTCTGTCTCTCTCTTTTTTT
1 TTCTGTCTC-C-CTTTTTTT
*
5504184 TTCTGTCTCCGTTTTTTT
1 TTCTGTCTCCCTTTTTTT
5504202 TTCT
1 TTCT
5504206 TCAGGTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 1 0.05
20 9 0.43
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.69
Consensus pattern (18 bp):
TTCTGTCTCCCTTTTTTT
Found at i:5504658 original size:17 final size:15
Alignment explanation
Indices: 5504615--5504655 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
5504605 GGTCTGTAAT
5504615 TATTTATTT-ATATA
1 TATTTATTTAATATA
5504629 TATTTATTTAATATA
1 TATTTATTTAATATA
5504644 TATTTA-TTAATA
1 TATTTATTTAATA
5504656 ATAATAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:5504659 original size:3 final size:3
Alignment explanation
Indices: 5504651--5504727 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
5504641 ATATATTTAT
* * *
5504651 TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5504699 TAA TAA AAA TAA TAA TAA AAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5504728 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5507902 original size:134 final size:138
Alignment explanation
Indices: 5507559--5507913 Score: 315
Period size: 143 Copynumber: 2.6 Consensus size: 138
5507549 CATGGTCTTT
* * * * * ** * * * *
5507559 TTCTTTCAGATTTGGTCTTCCTGAAGAGGAGCGAAGCAAATCAAGTTTGATTCAATCTTCTCTAA
1 TTCTTTCAAATTTGGTATTCCTAAAGAGCAGCGAAGCAAATCAACTTCAATTAAACCTTCACTGA
* * * * *
5507624 AGAGCAGCAAAGTGGATCAAAAATATTTTATTTTCGAGTCTGATCTCCCTTAAAGTGTAGTGGAG
66 AGAGCAACGAAGTGGATC----ACATTTTATTTTCGAGTCTAATCTCCCTTAAAGCGTAGTGGAG
*
5507689 CAGAATCTTCTTC
127 CAGAATC-TCTCC
* * * * * * * *
5507702 TTCTTTCAAATTTGGTATTCTTGAAGAGCAGCGAGGCAAATCAAGTTCGATTCAATCTTCCCTGA
1 TTCTTTCAAATTTGGTATTCCTAAAGAGCAGCGAAGCAAATCAACTTCAATTAAACCTTCACTGA
5507767 AGAGCAACGAAGTGGATCACATTTT-TTTT-GAGTCTAATCTCGCC-TAAAGCGTAGTGGAGCAG
66 AGAGCAACGAAGTGGATCACATTTTATTTTCGAGTCTAATCTC-CCTTAAAGCGTAGTGGAGCAG
5507829 -ATC-CTCC
130 AATCTCTCC
* * * * ** * *
5507836 TTCTTTCATATTTGGTCTTCCTAAAGAGTAGTGAAGCAAATTGACTTCAATTAAACCTTTATTGA
1 TTCTTTCAAATTTGGTATTCCTAAAGAGCAGCGAAGCAAATCAACTTCAATTAAACCTTCACTGA
*
5507901 AGAGCAGCGAAGT
66 AGAGCAACGAAGT
5507914 AAATCAAAAT
Statistics
Matches: 180, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
134 64 0.36
136 3 0.02
137 28 0.16
138 6 0.03
139 6 0.03
143 73 0.41
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (138 bp):
TTCTTTCAAATTTGGTATTCCTAAAGAGCAGCGAAGCAAATCAACTTCAATTAAACCTTCACTGA
AGAGCAACGAAGTGGATCACATTTTATTTTCGAGTCTAATCTCCCTTAAAGCGTAGTGGAGCAGA
ATCTCTCC
Found at i:5509659 original size:22 final size:20
Alignment explanation
Indices: 5509618--5509660 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
5509608 CCTATTTCTT
*
5509618 TGTTTTATTTTACATTTTAA
1 TGTTTTATTTTAAATTTTAA
5509638 TGTTTTATATTTAAATTGTTAA
1 TGTTTTAT-TTTAAATT-TTAA
5509660 T
1 T
5509661 TTCAAGCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
TGTTTTATTTTAAATTTTAA
Found at i:5509780 original size:31 final size:31
Alignment explanation
Indices: 5509740--5509842 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
5509730 AATTCTAATT
5509740 TAACCGCTAACTTTGCTAATTTATTAACCAC
1 TAACCGCTAACTTTGCTAATTTATTAACCAC
* * **
5509771 TAACTGCTAACTTTGTTAATTTATTAACTGC
1 TAACCGCTAACTTTGCTAATTTATTAACCAC
** * *
5509802 TGTCTGCTAACTTTGCTAATTTATTAATCAC
1 TAACCGCTAACTTTGCTAATTTATTAACCAC
*
5509833 TGACCGCTAA
1 TAACCGCTAA
5509843 TTGTTATATT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (31 bp):
TAACCGCTAACTTTGCTAATTTATTAACCAC
Found at i:5510003 original size:30 final size:30
Alignment explanation
Indices: 5509969--5510073 Score: 176
Period size: 30 Copynumber: 3.5 Consensus size: 30
5509959 TTCGATTTCT
* *
5509969 TTTAATTTCTATCATTTACATTTTTTTCCC
1 TTTAATTTCTATTATTTACATTTTTTGCCC
5509999 TTTAATTTCTATTATTTACATTTTTTGCCC
1 TTTAATTTCTATTATTTACATTTTTTGCCC
5510029 TTTAATTTCTATTATTTACA-TTTTTGCCC
1 TTTAATTTCTATTATTTACATTTTTTGCCC
*
5510058 TTTAATTTATATTATT
1 TTTAATTTCTATTATT
5510074 CTAATTTCAA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 24 0.33
30 48 0.67
ACGTcount: A:0.22, C:0.15, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTAATTTCTATTATTTACATTTTTTGCCC
Found at i:5510622 original size:15 final size:15
Alignment explanation
Indices: 5510585--5510614 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5510575 TTTAAATTTT
5510585 ATTTAAATTAATCTA
1 ATTTAAATTAATCTA
5510600 ATTTAAATTAATCTA
1 ATTTAAATTAATCTA
5510615 GATTAAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATTAATCTA
Found at i:5510747 original size:15 final size:15
Alignment explanation
Indices: 5510727--5510756 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5510717 GTGCAACACC
5510727 CTCATAAATAATTTT
1 CTCATAAATAATTTT
5510742 CTCATAAATAATTTT
1 CTCATAAATAATTTT
5510757 GAAATGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
CTCATAAATAATTTT
Found at i:5511446 original size:23 final size:23
Alignment explanation
Indices: 5511396--5511448 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5511386 AGACCTAAGA
* *
5511396 CGTTGTTTTAATAAAATTAAAAT
1 CGTTTTTTTAATAAAATGAAAAT
* * *
5511419 TGTTTTTTTATTAAAATGACAAT
1 CGTTTTTTTAATAAAATGAAAAT
5511442 CGTTTTT
1 CGTTTTT
5511449 GGTGCCCAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (23 bp):
CGTTTTTTTAATAAAATGAAAAT
Found at i:5511632 original size:28 final size:28
Alignment explanation
Indices: 5511601--5511661 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
5511591 AATAGTTTCG
* *
5511601 ACACACTTATCTAATAAAATAATTTTAA
1 ACACACTTATCAAAAAAAATAATTTTAA
** * *
5511629 ACACTTTTTTGAAAAAAAATAATTTTAA
1 ACACACTTATCAAAAAAAATAATTTTAA
5511657 ACACA
1 ACACA
5511662 TAAAATGAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (28 bp):
ACACACTTATCAAAAAAAATAATTTTAA
Found at i:5514075 original size:30 final size:30
Alignment explanation
Indices: 5514040--5514112 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
5514030 TATTTGAGCC
5514040 TAACTTTATATAAAATACTAACTTGAT-CT
1 TAACTTTATATAAAATACTAACTTGATGCT
* *
5514069 TAAACTTTATATTAAATACTAATTTGATGCT
1 T-AACTTTATATAAAATACTAACTTGATGCT
*
5514100 TAACTTTAAATAA
1 TAACTTTATATAA
5514113 TATATTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.03
30 34 0.89
31 3 0.08
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (30 bp):
TAACTTTATATAAAATACTAACTTGATGCT
Found at i:5514122 original size:30 final size:29
Alignment explanation
Indices: 5514031--5514125 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
5514021 CAAACACCCT
* *
5514031 ATTTGA-GCCTAACTTTATATAAAATACTA
1 ATTTGATGCTTAACTTTAAAT-AAATACTA
* *
5514060 ACTTGAT-CTTAAACTTTATATTAAATACTA
1 ATTTGATGCTT-AACTTTA-AATAAATACTA
*
5514090 ATTTGATGCTTAACTTTAAATAATATATTA
1 ATTTGATGCTTAACTTTAAATAA-ATACTA
5514120 ATTTGA
1 ATTTGA
5514126 CTCCTAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 11 0.20
30 39 0.72
31 4 0.07
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (29 bp):
ATTTGATGCTTAACTTTAAATAAATACTA
Found at i:5514568 original size:106 final size:106
Alignment explanation
Indices: 5514455--5514790 Score: 238
Period size: 106 Copynumber: 3.1 Consensus size: 106
5514445 GTTATGTTTA
5514455 TAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACTGA
1 TAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACTGA
*
5514520 AGTCATATCTTTAATATTTATAAATATTAAAAATTTATAAT
66 AGTCATATATTTAATATTTATAAATATTAAAAATTTATAAT
* ***** * * * *** * * *
5514561 TAATATT-ATAAATATACCAAAAAATATAACATAATAAAAA--AATTT-GCAAGCA-GATTATAC
1 TAATATTAAT-AATAAAATTTTAATTATAAC-T-TTAAAAATTTATTTGGGGTGAACTATTAGAC
* ** * *
5514621 ATGAGATGTCACTA-ATTAAGATATGCAAAAATCTCAAGTTAATATTATTTA-ACAT
63 -TGA-A-GTCA-TATATTTA-ATATTTATAAA--T--A-TTAA-A-AATTTATA-AT
* *
5514676 ATAATATTAATAAT-AAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTTTTAGACTA
1 -TAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACTG
*
5514740 AAGTCATATATTTAATATTTACTAAATATAAAAAATTTATAAT
65 AAGTCATATATTTAATATTTA-TAAATATTAAAAATTTATAAT
5514783 TAATATTA
1 TAATATTA
5514791 TAAATATACC
Statistics
Matches: 161, Mismatches: 44, Indels: 50
0.63 0.17 0.20
Matches are distributed among these distances:
104 6 0.04
105 8 0.05
106 33 0.20
107 15 0.09
108 18 0.11
109 3 0.02
110 2 0.01
112 2 0.01
113 17 0.11
114 14 0.09
115 21 0.13
116 15 0.09
117 7 0.04
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (106 bp):
TAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACTGA
AGTCATATATTTAATATTTATAAATATTAAAAATTTATAAT
Found at i:5514589 original size:30 final size:30
Alignment explanation
Indices: 5514530--5514589 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
5514520 AGTCATATCT
**
5514530 TTAATATTTATAAATATTAAAAATTTATAA
1 TTAATATTTATAAATATTAAAAAAATATAA
5514560 TTAATA-TTATAAATA-TACCAAAAAATATAA
1 TTAATATTTATAAATATTA--AAAAAATATAA
5514590 CATAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 2 0.08
29 9 0.35
30 15 0.58
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAATATTTATAAATATTAAAAAAATATAA
Found at i:5514868 original size:221 final size:222
Alignment explanation
Indices: 5514453--5514877 Score: 705
Period size: 221 Copynumber: 1.9 Consensus size: 222
5514443 TTGTTATGTT
5514453 TATAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACT
1 TATAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACT
* * *
5514518 GAAGTCATATCTTTAATATTTATAAATATTAAAAATTTATAATTAATATTATAAATATACCAAAA
66 AAAGTCATATATTTAATATTTATAAATATAAAAAATTTATAATTAATATTATAAATATACCAAAA
* *
5514583 AATATAACATAATAAAAAAATTTGCAAGCAGATTATACATGAGATGTCACTAATTAAGATATGCA
131 AATATAACATAATAAAAAAATTTGCAAGCAGATTATACATGACAAGTCACTAATTAAGATATGCA
5514648 AAAATCTCAAGTTAATATTATTTAACA
196 AAAATCTCAAGTTAATATTATTTAACA
*
5514675 TATAATATTAATAAT-AAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTTTTAGACT
1 TATAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACT
*
5514739 AAAGTCATATATTTAATATTTACTAAATATAAAAAATTTATAATTAATATTATAAATATACCAAC
66 AAAGTCATATATTTAATATTTA-TAAATATAAAAAATTTATAATTAATATTATAAATATACCAAA
* * *
5514804 AAATATAATATAAT-AAAAAA-TTGCAAGCAGCA-TATACATGACAAGTTACTAATTATGCATAT
130 AAATATAACATAATAAAAAAATTTGCAAGCAG-ATTATACATGACAAGTCACTAATTAAG-ATAT
5514866 GCAAAAATCTCA
193 GCAAAAATCTCA
5514878 CGTCAACAAC
Statistics
Matches: 190, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
220 31 0.16
221 91 0.48
222 68 0.36
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (222 bp):
TATAATATTAATAATAAAATTTTAATTATAACTTTAAAAATTTATTTGGGGTGAACTATTAGACT
AAAGTCATATATTTAATATTTATAAATATAAAAAATTTATAATTAATATTATAAATATACCAAAA
AATATAACATAATAAAAAAATTTGCAAGCAGATTATACATGACAAGTCACTAATTAAGATATGCA
AAAATCTCAAGTTAATATTATTTAACA
Found at i:5516161 original size:14 final size:14
Alignment explanation
Indices: 5516142--5516168 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5516132 AATTTTTAGT
5516142 ATCCTTTTTAATGC
1 ATCCTTTTTAATGC
5516156 ATCCTTTTTAATG
1 ATCCTTTTTAATG
5516169 TAAACAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
ATCCTTTTTAATGC
Found at i:5522732 original size:12 final size:12
Alignment explanation
Indices: 5522715--5522871 Score: 68
Period size: 12 Copynumber: 12.2 Consensus size: 12
5522705 GACCTAATGA
*
5522715 AAATAAATTAAT
1 AAATAAAATAAT
5522727 AAATAAAATAAT
1 AAATAAAATAAT
*
5522739 AAAATATATATAATAT
1 -AAATA-AAAT-A-AT
*
5522755 AAATATAATAAT
1 AAATAAAATAAT
*
5522767 -AATAATATAAT
1 AAATAAAATAAT
5522778 AAA-AGAAATAAT
1 AAATA-AAATAAT
5522790 AAATTAAATATATAT
1 AAA-TAAA-ATA-AT
* * *
5522805 ACATCATATAAT
1 AAATAAAATAAT
**
5522817 ATGTAACTAATATAT
1 AAATAA--AATA-AT
*
5522832 ATATAAAATATAT
1 AAATAAAATA-AT
*
5522845 AAATATAAT-AT
1 AAATAAAATAAT
5522856 ATAATAATAATAAT
1 A-AATAA-AATAAT
5522870 AA
1 AA
5522872 TAATAATATA
Statistics
Matches: 111, Mismatches: 18, Indels: 31
0.69 0.11 0.19
Matches are distributed among these distances:
11 13 0.12
12 33 0.30
13 29 0.26
14 17 0.15
15 17 0.15
16 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:5522753 original size:9 final size:9
Alignment explanation
Indices: 5522723--5523206 Score: 221
Period size: 9 Copynumber: 54.6 Consensus size: 9
5522713 GAAAATAAAT
*
5522723 TAATAAATA
1 TAATATATA
*
5522732 AAATA-ATA
1 TAATATATA
*
5522740 AAATATATA
1 TAATATATA
5522749 TAATATAAATA
1 TAATAT--ATA
5522760 TAATA-ATAA
1 TAATATAT-A
5522769 TAATATA-A
1 TAATATATA
* * *
5522777 TAAAAGAAA
1 TAATATATA
*
5522786 TAATAAAT-
1 TAATATATA
5522794 TAAATATATA
1 T-AATATATA
*
5522804 TACAT-CATA
1 TA-ATATATA
*
5522813 TAATATGTA
1 TAATATATA
*
5522822 -ACTA-ATA
1 TAATATATA
5522829 T-ATATATA
1 TAATATATA
*
5522837 AAATATATA
1 TAATATATA
5522846 -AATATA-A
1 TAATATATA
5522853 T-ATATA-A
1 TAATATATA
5522860 TAATAATAATAA
1 TAAT-AT-AT-A
5522872 TAATAATATA
1 TAAT-ATATA
*
5522882 TACTATATA
1 TAATATATA
5522891 T-ATATATA
1 TAATATATA
*
5522899 TAATATACA
1 TAATATATA
*
5522908 CT-ATGT-TA
1 -TAATATATA
5522916 TAATATA-A
1 TAATATATA
5522924 T-ATATATA
1 TAATATATA
5522932 T-ATATATA
1 TAATATATA
5522940 TATATATAATA
1 TA-ATAT-ATA
5522951 TAA-ATATA
1 TAATATATA
5522959 TAATA-ATA
1 TAATATATA
5522967 -AATATATA
1 TAATATATA
*
5522975 -AACATATA
1 TAATATATA
5522983 TAATATATA
1 TAATATATA
5522992 TATATATATA
1 TA-ATATATA
5523002 TAACTA-ATA
1 TAA-TATATA
*
5523011 TAATATATG
1 TAATATATA
5523020 TATATAATATA
1 TA-AT-ATATA
*
5523031 TAATAAATA
1 TAATATATA
* *
5523040 T-ATACCATT
1 TAATA-TATA
5523049 TAATA-ATAA
1 TAATATAT-A
5523058 TAATA-ATAA
1 TAATATAT-A
5523067 TAATA-ATAA
1 TAATATAT-A
5523076 TAATA-ATAA
1 TAATATAT-A
5523085 TAATAATATA
1 TAAT-ATATA
*
5523095 TAACATATAA
1 TAATATAT-A
5523105 TAATAATATA
1 TAAT-ATATA
*
5523115 TAACATA-A
1 TAATATATA
* *
5523123 TATTATATG
1 TAATATATA
* *
5523132 CAATA-ATG
1 TAATATATA
5523140 TAATATATA
1 TAATATATA
5523149 TACCATATACTA
1 TA--ATATA-TA
5523161 T-A-AT-TA
1 TAATATATA
5523167 TAATATATA
1 TAATATATA
*
5523176 TACTATATA
1 TAATATATA
5523185 CT-ATAT-TA
1 -TAATATATA
5523193 T-ATATTATA
1 TAATA-TATA
5523202 TAATA
1 TAATA
5523207 AAAAATAATT
Statistics
Matches: 380, Mismatches: 41, Indels: 107
0.72 0.08 0.20
Matches are distributed among these distances:
6 3 0.01
7 27 0.07
8 102 0.27
9 155 0.41
10 50 0.13
11 32 0.08
12 11 0.03
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (9 bp):
TAATATATA
Found at i:5522804 original size:2 final size:2
Alignment explanation
Indices: 5522797--5523043 Score: 166
Period size: 2 Copynumber: 133.5 Consensus size: 2
5522787 AATAAATTAA
* *
5522797 AT AT AT AT AC AT CAT AT A- AT AT GT A- ACT A- AT AT AT AT AT A-
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
5522837 AA AT AT AT AA AT AT A- AT AT AT A- AT A- AT A- AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5522873 A- AT A- AT AT AT ACT AT AT AT AT AT AT AT A- AT AT AC ACT AT GT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
5522914 -T AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5522952 AA AT AT AT A- AT A- AT AA AT AT AT AA AC AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5522991 AT AT AT AT AT AT A- ACT A- AT AT A- AT AT AT GT AT AT A- AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5523030 AT A- AT AA AT AT AT A
1 AT AT AT AT AT AT AT A
5523044 CCATTTAATA
Statistics
Matches: 194, Mismatches: 21, Indels: 60
0.71 0.08 0.22
Matches are distributed among these distances:
1 25 0.13
2 162 0.84
3 7 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:5522829 original size:55 final size:51
Alignment explanation
Indices: 5522723--5523125 Score: 164
Period size: 55 Copynumber: 7.6 Consensus size: 51
5522713 GAAAATAAAT
*
5522723 TAATAAATAAAATAATAAAATATATATAATATAAATATAATAATAATAATA
1 TAATAAATAAAATAATAAAATAAATATAATATAAATATAATAATAATAATA
* *
5522774 TAATAAA-AGAAATAATAAATTAAATAT-ATATACATCATATAATATGTAACTAATA
1 TAATAAATA-AAATAATAAAATAAATATAATATA-A--ATATAATA-ATAA-TAATA
*
5522829 T-ATATATAAAATATATAAATATAATATATAATA-ATAATAATAATAATAATATATA
1 TAATAAATAAAATA-ATAAA-ATAA-ATATAATATA-AAT-ATAATAATAATA-ATA
* * * **
5522884 CTATATATATATATATAATATACACTATGTTATAATAT-AATAT-AT-ATATATATATA
1 -TA-ATAAATA-AAATAATA-A-AATA-AATATAATATAAATATAATAATA-ATA-ATA
5522940 TATATATAATATAAATATATAATAATAAATAT-ATA-AACATAT-ATAAT-AT-ATA
1 TA-ATA-AATA-AAATA-ATAA-AATAAATATAATATAA-ATATAATAATAATAATA
* * * * *
5522992 TATATATATATAACTAATATAATATATGT-ATAT-AATAT-ATAAT-A-AATA
1 TA-ATAAATA-AAATAATAAAATAAATATAATATAAATATAATAATAATAATA
* **
5523040 T-ATACCATTTAATAATAATAAT-AATAATAATA-ATAATAATAATAATAATAATA
1 TAATA-AATAAAATAATAA-AATAAAT-ATAATATA-AAT-ATAATAATAATAATA
* * *
5523093 T-ATAACATATAATAATAATATATAACATAATAT
1 TAATAA-ATAAAATAATAAAATA-AATATAATAT
5523126 TATATGCAAT
Statistics
Matches: 276, Mismatches: 33, Indels: 83
0.70 0.08 0.21
Matches are distributed among these distances:
46 11 0.04
47 6 0.02
48 17 0.06
49 14 0.05
50 11 0.04
51 37 0.13
52 12 0.04
53 33 0.12
54 22 0.08
55 38 0.14
56 33 0.12
57 11 0.04
58 16 0.06
59 14 0.05
60 1 0.00
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (51 bp):
TAATAAATAAAATAATAAAATAAATATAATATAAATATAATAATAATAATA
Found at i:5522892 original size:62 final size:61
Alignment explanation
Indices: 5522812--5523117 Score: 222
Period size: 62 Copynumber: 4.9 Consensus size: 61
5522802 TATACATCAT
*
5522812 ATAATATGTAACTAATATATATATAAAATATATAAATATAATATATAATAATAATAATAATA
1 ATAATATAT-ACTAATATATATATAAAATATATAAATATAATATATAATAATAATAATAATA
* * * *
5522874 ATAATATATACTATATATATATATATAATATA-CACTAT-GT-TATAAT-ATAATATATATATA
1 ATAATATATACTA-ATATATATATAAAATATATAAATATAATATATAATAATAATA-ATA-ATA
* * *
5522934 TATATATATATA-TAATATAAATATATAATAATAAATATATAAACATATATAATATATATATATA
1 -ATA-ATATATACTAATAT--ATATATAA-AATATATAAATATA-ATATATAATA-ATA-ATA-A
5522998 TATATA
57 TA-ATA
* * * *
5523004 ACTAATATA-A-T-ATATGTATATAATATATAATAAATATATACCATTTAATAATAATAATAATA
1 A-TAATATATACTAATATATATATAAAATAT-ATAAATATA-A-TATATAATAATAATAATAATA
*
5523066 ATAATA-ATAATAATA-ATA-ATAATAATATATAACATATAATA-ATAATATATAA
1 ATAATATATACTAATATATATATAA-AATATATAA-ATATAATATATAATA-ATAA
5523118 CATAATATTA
Statistics
Matches: 196, Mismatches: 24, Indels: 50
0.73 0.09 0.19
Matches are distributed among these distances:
58 6 0.03
59 14 0.07
60 14 0.07
61 28 0.14
62 55 0.28
63 11 0.06
64 8 0.04
65 18 0.09
66 8 0.04
67 10 0.05
68 2 0.01
69 9 0.05
70 13 0.07
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (61 bp):
ATAATATATACTAATATATATATAAAATATATAAATATAATATATAATAATAATAATAATA
Found at i:5522941 original size:60 final size:60
Alignment explanation
Indices: 5522734--5523206 Score: 190
Period size: 56 Copynumber: 8.2 Consensus size: 60
5522724 AATAAATAAA
* * * * *
5522734 ATAATAAAATATATATA-ATATAAATATAATA-ATA-ATA-ATATAATA-AAAGAAATA-
1 ATAATATAATATATATATATATATATATACTATATATATATATATAATATAAATATATAT
* *
5522788 ATAA-ATTAA-ATATATATACATCATATA-A-TATGTA-ACTA-ATATATATATAAA-ATATAT
1 ATAATA-TAATATATATATATAT-ATATATACTATATATA-TATATATA-ATATAAATATATAT
* *
5522845 A-AATATAATATATA-ATA-ATA-ATA-A-TA-ATA-ATAATATATACTATATATATATAT
1 ATAATATAATATATATATATATATATATACTATATATAT-ATATATAATATAAATATATAT
*
5522898 ATAATATACACTATGTTATAATATAATATATATA-TATATATATATATATAATATAAATATATA-
1 ATAATATA-A-TAT-ATAT-ATAT-ATATATATACTATATATATATATATAATATAAATATATAT
* * *
5522961 ATAATA-AATATATAAACATATATA-ATA-TATATATATATATATAA-CT-AATATAATAT
1 ATAATATAATATATATATATATATATATACTATATATATATATATAATATAAATAT-ATAT
* * *
5523017 ATGTATATAATATATA-ATA-A-ATATATACCATTTA-ATA-ATAATAATA-ATAATA-ATA-
1 AT-AATATAATATATATATATATATATATACTATATATATATAT-ATAATATA-AATATATAT
*
5523072 ATAATAATAATA-ATA-ATA-ATATATA-AC-ATATAATAATAATATATAACAT-AATAT-TAT
1 ATAAT-ATAATATATATATATATATATATACTATAT-AT-AT-ATATATAATATAAATATATAT
* * * *
5523129 ATGCA-ATAATGTA-ATATATATACCATATACTATAATTATAATATATATACTATATACTATATT
1 AT-AATATAATATATATATATATA-TATATACTAT-A-TAT-ATATATATA--ATATA-AATA-T
5523192 ATAT
57 ATAT
*
5523196 ATTATATAATA
1 ATAATATAATA
5523207 AAAAATAATT
Statistics
Matches: 328, Mismatches: 30, Indels: 109
0.70 0.06 0.23
Matches are distributed among these distances:
51 1 0.00
52 9 0.03
53 31 0.09
54 37 0.11
55 36 0.11
56 68 0.21
57 38 0.12
58 21 0.06
59 8 0.02
60 5 0.02
61 13 0.04
62 10 0.03
63 13 0.04
64 21 0.06
65 5 0.02
66 2 0.01
67 10 0.03
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (60 bp):
ATAATATAATATATATATATATATATATACTATATATATATATATAATATAAATATATAT
Found at i:5523060 original size:6 final size:6
Alignment explanation
Indices: 5523049--5523117 Score: 102
Period size: 6 Copynumber: 11.0 Consensus size: 6
5523039 ATATACCATT
5523049 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TATATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TA-ATAA
*
5523098 CATATAA TAATAA TATATAA
1 TA-ATAA TAATAA TA-ATAA
5523118 CATAATATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
6 44 0.75
7 15 0.25
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (6 bp):
TAATAA
Found at i:5523069 original size:15 final size:15
Alignment explanation
Indices: 5522723--5523117 Score: 130
Period size: 17 Copynumber: 24.6 Consensus size: 15
5522713 GAAAATAAAT
5522723 TAATAAATAA-AATAA
1 TAAT-AATAATAATAA
5522738 TAA-AAT-ATATATAA
1 TAATAATAATA-ATAA
5522752 T-ATAA-ATATAATAA
1 TAATAATA-ATAATAA
5522766 TAATAAT-ATAATAA
1 TAATAATAATAATAA
* *
5522780 -AAGAAATAATAA-AT
1 TAA-TAATAATAATAA
*
5522794 TAA-ATATATATACATCA
1 TAATA-ATA-ATA-ATAA
*
5522811 T-ATAATATGTAACTAA
1 TAATAATA-ATAA-TAA
5522827 TATATATATAA-AATATA
1 TA-ATA-ATAATAATA-A
5522844 TAA-ATATAATATATAA
1 TAATA-ATAATA-ATAA
5522860 TAATAATAATAATAA
1 TAATAATAATAATAA
*
5522875 TAATATATACT-ATATA
1 TAATA-ATAATAATA-A
5522891 TATATATATAAT-ATACA
1 TA-ATA-ATAATAATA-A
* *
5522908 CTATGTTATAAT-ATAA
1 -TA-ATAATAATAATAA
5522924 T-ATATATATATATATATA
1 TAATA-ATA-ATA-ATA-A
5522942 TATATAAT-ATAAATATA
1 TA-ATAATAAT-AATA-A
5522959 TAATAATAAATATATAA
1 TAATAAT-AATA-ATAA
5522976 -ACATATATAATATATATA
1 TA-ATA-ATAATA-ATA-A
5522994 TATATATATAACTAAT-A
1 TA-ATA-ATAA-TAATAA
*
5523011 TAAT-ATATGTATATAA
1 TAATAATA-ATA-ATAA
5523027 TATATAATAAATATATACCA
1 TA-ATAAT-AATA-ATA--A
*
5523047 T-TTAATAATAATAA
1 TAATAATAATAATAA
5523061 TAATAATAATAATAA
1 TAATAATAATAATAA
5523076 TAATAATAATAATAA
1 TAATAATAATAATAA
*
5523091 TATATAACATATAATAA
1 TA-ATAATA-ATAATAA
5523108 TAATATATAA
1 TAATA-ATAA
5523118 CATAATATTA
Statistics
Matches: 304, Mismatches: 21, Indels: 109
0.70 0.05 0.25
Matches are distributed among these distances:
12 1 0.00
13 9 0.03
14 36 0.12
15 72 0.24
16 56 0.18
17 76 0.25
18 30 0.10
19 17 0.06
20 7 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (15 bp):
TAATAATAATAATAA
Found at i:5523124 original size:15 final size:14
Alignment explanation
Indices: 5522717--5523130 Score: 159
Period size: 13 Copynumber: 29.1 Consensus size: 14
5522707 CCTAATGAAA
5522717 ATAAATTAATAA-AT
1 ATAAA-TAATAATAT
*
5522731 A-AAATAATAAAAT
1 ATAAATAATAATAT
* *
5522744 ATATATAATATAAAT
1 ATAAATAATA-ATAT
5522759 ATAATAATAATAATAT
1 AT-A-AATAATAATAT
5522775 AATAAA-AGA-AATA-
1 -ATAAATA-ATAATAT
5522788 ATAAATTAA-ATATAT
1 ATAAA-TAATA-ATAT
*
5522803 ATACATCATATAATAT
1 ATAAAT-A-ATAATAT
* *
5522819 GTAACTAAT-ATAT
1 ATAAATAATAATAT
5522832 AT--ATAA-AATAT
1 ATAAATAATAATAT
5522843 ATAAAT-ATAATAT
1 ATAAATAATAATAT
5522856 AT-AATAATAATA-
1 ATAAATAATAATAT
5522868 AT-AATAATAATAT
1 ATAAATAATAATAT
*
5522881 AT-ACTATATATATAT
1 ATAAATA-ATA-ATAT
5522896 ATATAAT-ATACACTAT
1 ATA-AATAATA-A-TAT
*
5522912 GTTATAAT-ATAATAT
1 -ATA-AATAATAATAT
*
5522927 ATATATATATATATAT
1 ATAAATA-ATA-ATAT
5522943 ATATAAT-ATAA-AT
1 ATA-AATAATAATAT
5522956 ATATAATAATAAATAT
1 ATA-AATAAT-AATAT
5522972 ATAAACATATATAATAT
1 AT-AA-ATA-ATAATAT
*
5522989 ATATAT-ATATATAT
1 ATAAATAATA-ATAT
5523003 AACTAATATAAT-ATAT
1 -A-TAA-ATAATAATAT
* *
5523019 GTATATAAT-ATAT
1 ATAAATAATAATAT
*
5523032 AATAAATATATACCATTT
1 -ATAAATA-ATA--ATAT
5523050 A-ATAATAATAATA-
1 ATA-AATAATAATAT
5523063 AT-AATAATAATA-
1 ATAAATAATAATAT
5523075 AT-AATAATAATA-
1 ATAAATAATAATAT
*
5523087 AT-AATATATAACAT
1 ATAAATA-ATAATAT
5523101 AT-AATAATAATAT
1 ATAAATAATAATAT
*
5523114 ATAACATAATATTAT
1 ATAA-ATAATAATAT
5523129 AT
1 AT
5523131 GCAATAATGT
Statistics
Matches: 321, Mismatches: 27, Indels: 103
0.71 0.06 0.23
Matches are distributed among these distances:
11 9 0.03
12 55 0.17
13 70 0.22
14 48 0.15
15 52 0.16
16 40 0.12
17 40 0.12
18 7 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (14 bp):
ATAAATAATAATAT
Found at i:5531299 original size:21 final size:22
Alignment explanation
Indices: 5531275--5531350 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 22
5531265 TATGCATGGC
5531275 GTATCGATACCTACAT-GAA-CA
1 GTATCGATACC-ACATGGAAGCA
* * *
5531296 GTATTGATACCATATGGAAGGA
1 GTATCGATACCACATGGAAGCA
* *
5531318 GTATCGATACCATTAT-GAAG-G
1 GTATCGATACCA-CATGGAAGCA
5531339 GTATCGATACCA
1 GTATCGATACCA
5531351 GGGAACATTG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
20 3 0.06
21 25 0.53
22 16 0.34
23 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (22 bp):
GTATCGATACCACATGGAAGCA
Found at i:5531326 original size:22 final size:22
Alignment explanation
Indices: 5531295--5531350 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
5531285 CTACATGAAC
*
5531295 AGTATTGATACCA-TATGGAAGG
1 AGTATCGATACCATTAT-GAAGG
5531317 AGTATCGATACCATTATGAAGG
1 AGTATCGATACCATTATGAAGG
5531339 -GTATCGATACCA
1 AGTATCGATACCA
5531351 GGGAACATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 12 0.38
22 17 0.53
23 3 0.09
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATTATGAAGG
Found at i:5539104 original size:23 final size:24
Alignment explanation
Indices: 5539076--5539128 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
5539066 TCCCAAAGGA
5539076 CCACATAAG-TTTGCAACCAAGTG
1 CCACATAAGATTTGCAACCAAGTG
* * *
5539099 CCACAT-AGATTTGTAGCGAAGTG
1 CCACATAAGATTTGCAACCAAGTG
5539122 CCACATA
1 CCACATA
5539129 TTTGTCCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (24 bp):
CCACATAAGATTTGCAACCAAGTG
Found at i:5539139 original size:21 final size:21
Alignment explanation
Indices: 5539094--5539149 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
5539084 GTTTGCAACC
*
5539094 AAGTGCCACATAGATTTGTAGCG
1 AAGTGCCACAT--ATTTGTACCG
*
5539117 AAGTGCCACATATTTGTCCCG
1 AAGTGCCACATATTTGTACCG
**
5539138 AAGAACCACATA
1 AAGTGCCACATA
5539150 AAACCCTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
23 11 0.38
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
AAGTGCCACATATTTGTACCG
Found at i:5539829 original size:21 final size:21
Alignment explanation
Indices: 5539799--5539871 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
5539789 TACCCTTACA
* *
5539799 GTATCGATACCTCTTAAACAT
1 GTATCAATACCTCTTCAACAT
5539820 GTATCAATACCTCTTCAACAT
1 GTATCAATACCTCTTCAACAT
5539841 GTATCAATACCTCTTCAACAT
1 GTATCAATACCTCTTCAACAT
*
5539862 GTATTAATAC
1 GTATCAATAC
5539872 TACCCTTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (21 bp):
GTATCAATACCTCTTCAACAT
Found at i:5546004 original size:23 final size:23
Alignment explanation
Indices: 5545978--5546022 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5545968 GACCATATAA
5545978 GTTTGCACCAAAGTGCCACATAG
1 GTTTGCACCAAAGTGCCACATAG
*
5546001 GTTTGCACCGAAGTGCCACATA
1 GTTTGCACCAAAGTGCCACATA
5546023 TTTGTCTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (23 bp):
GTTTGCACCAAAGTGCCACATAG
Found at i:5546202 original size:21 final size:21
Alignment explanation
Indices: 5546176--5546226 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5546166 CATAGAGTTT
5546176 GTTCACATTCACTGATTCAAA
1 GTTCACATTCACTGATTCAAA
*
5546197 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTGATTCAAA
5546218 GTTCACATT
1 GTTCACATT
5546227 TCCATAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:5550951 original size:12 final size:12
Alignment explanation
Indices: 5550926--5550995 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
5550916 ACAGAGATAT
* *
5550926 CAGAAATCAAAA
1 CAGAATTCAGAA
5550938 CAGAATTCAGAA
1 CAGAATTCAGAA
5550950 CA-AATATCAGAA
1 CAGAAT-TCAGAA
* * *
5550962 CAGAATCCGGAT
1 CAGAATTCAGAA
* *
5550974 CAGAAATCATAA
1 CAGAATTCAGAA
*
5550986 TAGAATTCAG
1 CAGAATTCAG
5550996 GTTATGTATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 3 0.07
12 37 0.86
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:5550982 original size:24 final size:24
Alignment explanation
Indices: 5550924--5550991 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
5550914 AAACAGAGAT
*
5550924 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * *
5550948 AACA-AATATCAGAACAGAATCCGG
1 ATCAGAA-ATCAAAACAGAATCCAG
* *
5550972 ATCAGAAATCATAATAGAAT
1 ATCAGAAATCAAAACAGAAT
5550992 TCAGGTTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:5555564 original size:12 final size:12
Alignment explanation
Indices: 5555547--5555600 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
5555537 AACCCAATGA
*
5555547 AAATAAATTAAT
1 AAATAAAATAAT
5555559 AAATAAAATAAT
1 AAATAAAATAAT
5555571 AATATAATAA-AAT
1 AA-ATAA-AATAAT
* *
5555584 AAATAACATATT
1 AAATAAAATAAT
5555596 AAATA
1 AAATA
5555601 TATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 1 0.03
12 24 0.67
13 9 0.25
14 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:5555605 original size:2 final size:2
Alignment explanation
Indices: 5555598--5555921 Score: 208
Period size: 2 Copynumber: 173.5 Consensus size: 2
5555588 AACATATTAA
* *
5555598 AT AT AT AT AT AT AT AT CAT A- AA AT AT GT A- ACT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
5555639 AT AT AT AT A- AT AT AA AT AT A- AT A- AT AT AT ACT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
5555679 -T AT AT AT AT A- AT AT AC ACT AT GT -T AT A- AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
5555717 AT A- AT AT AA AT AT AT A- AT A- AT AG AT AT AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5555754 AT AA AT AT AT A- AA AC AT AT AT A- AT GAT AT AT A- ACT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT AT AT
* * *
5555794 A- AT AT AT GT AT AT A- AT AT AT A- AT AA AT AT AT ACC AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
5555833 AT A- AT A- AT A- AT A- AT AGT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
5555872 AT AT AT AT AT AT AT A- AT AT AT A- AT A- AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5555910 AT AT ACT AT AT A
1 AT AT A-T AT AT A
5555922 CCCCAAACGA
Statistics
Matches: 255, Mismatches: 26, Indels: 82
0.70 0.07 0.23
Matches are distributed among these distances:
1 32 0.13
2 209 0.82
3 14 0.05
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:5555619 original size:33 final size:31
Alignment explanation
Indices: 5555582--5555914 Score: 138
Period size: 33 Copynumber: 10.1 Consensus size: 31
5555572 ATATAATAAA
5555582 ATAAATAACATATTAAATATATATATATATAT
1 ATAAATAA-ATATTAAATATATATATATATAT
*
5555614 CAT--A-AAATATGTAACTAATATATATATATAT
1 -ATAAATAAATAT-TAAAT-ATATATATATATAT
* *
5555645 ATAATATAAATATAATAATATATACTAAATATATT
1 ATAA-ATAAATATTA-AATATATA-TATATATA-T
* *
5555680 ATATATATAATA-TACACTATGTTATAATAATATATAT
1 ATAAATA-AATATTA-A--AT-ATAT-AT-ATATATAT
*
5555717 ATAATATAAATA-TATAATA-ATAGATATATAT
1 ATAA-ATAAATATTA-AATATATATATATATAT
*
5555748 ATAATAATAAATATATAAA-ACATATATAATGATAT
1 AT-A-AATAAATAT-TAAATATATATAT-AT-ATAT
* *
5555783 ATAACT-AATA-T-AATATATGTATATA-AT
1 ATAAATAAATATTAAATATATATATATATAT
*
5555810 ATATAATAAATATATACCATATA-ATA-ATA-AT
1 ATA-AATAAATAT-TA-AATATATATATATATAT
*
5555841 AATAATAGTATATATGTATATATATATATATATATAT
1 -ATAA-A-TAAATAT-TA-A-ATATATATATATATAT
*
5555878 ATATATATAATA-TATAATAATATATATAATATAT
1 ATAAATA-AATATTA-AAT-ATATATAT-ATATAT
5555912 ATA
1 ATA
5555915 CTATATACCC
Statistics
Matches: 234, Mismatches: 26, Indels: 79
0.69 0.08 0.23
Matches are distributed among these distances:
27 5 0.02
28 3 0.01
29 12 0.05
30 15 0.06
31 32 0.14
32 22 0.09
33 46 0.20
34 41 0.18
35 23 0.10
36 8 0.03
37 17 0.07
38 10 0.04
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
ATAAATAAATATTAAATATATATATATATAT
Found at i:5557128 original size:23 final size:24
Alignment explanation
Indices: 5557091--5557145 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
5557081 TTTTATTATT
* *
5557091 AAATATTTTTAAAATATG-TCGTCA
1 AAATCTTTTTAAAATAGGAT-GTCA
*
5557115 AAATCTTTTT-AAATGGGATGTCA
1 AAATCTTTTTAAAATAGGATGTCA
5557138 AAATCTTT
1 AAATCTTT
5557146 CTAGAATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (24 bp):
AAATCTTTTTAAAATAGGATGTCA
Found at i:5559700 original size:20 final size:20
Alignment explanation
Indices: 5559675--5559717 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5559665 TCTAAGAGCC
*
5559675 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
5559695 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
5559715 CAT
1 CAT
5559718 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:5564646 original size:20 final size:20
Alignment explanation
Indices: 5564621--5564663 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5564611 TCTAAGAGCC
*
5564621 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
5564641 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
5564661 CAT
1 CAT
5564664 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:5567353 original size:240 final size:242
Alignment explanation
Indices: 5566888--5567450 Score: 869
Period size: 240 Copynumber: 2.3 Consensus size: 242
5566878 GAATTTAGAC
* * * * **
5566888 TTTTACCCAAAGGAATATAGCCTTTCATCTAACTTGCATGATTGACATATTTCTGTCAAATGCAC
1 TTTTACTCAAAGGTATTTA-CCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCAC
* ***
5566953 AGCTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTGGTACC
65 AACTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTAACACC
* *
5567018 TTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTTATCTAAC
130 TTTCTGCCAAATGCACAGCTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC
* *
5567083 TGGTATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATC
195 TGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATA
*
5567131 TTTTACTCAAAGTTATTT-CCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCACA
1 TTTTACTCAAAGGTATTTACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCACA
* * *
5567195 ACTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAA-TAACATCT
66 ACTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTAACACCT
5567259 TTCTGCCAAATGCACAGCTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT
131 TTCTGCCAAATGCACAGCTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT
*
5567324 GGCATAATTGACATATTTCTGTCAAATGCACAGCTAGGCCATTAATA
196 GGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATA
* * * * *
5567371 TTTTACTCTAAGGTATTTAACTTTTAATCTAACTTGCATAATTGACACCTTTCAGTCATATGCAC
1 TTTTACTCAAAGGTATTT-ACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCAC
*
5567436 ATCTAGGCCATTAAT
65 AACTAGGCCATTAAT
5567451 CGTTTACTTT
Statistics
Matches: 292, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
240 127 0.43
241 96 0.33
242 55 0.19
243 14 0.05
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (242 bp):
TTTTACTCAAAGGTATTTACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCACA
ACTAGGCCATTAATATTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTAACACCT
TTCTGCCAAATGCACAGCTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT
GGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTAATA
Found at i:5567457 original size:81 final size:81
Alignment explanation
Indices: 5566887--5567458 Score: 799
Period size: 81 Copynumber: 7.1 Consensus size: 81
5566877 AGAATTTAGA
* * * * * * **
5566887 CTTTTACCCAAAGGAATATAGCCTTTCATCTAACTTGCATGATTGACATATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
5566952 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* * ** *
5566968 ATTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTGGTACCTTTCTGCCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
5567033 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* * *
5567049 CTTTTACTCAAAGGTATTTAACCTTTTATCTAACTGGTATAATTGACACATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
5567114 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* *
5567130 CTTTTACTCAAAGTTATTT--CCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
5567193 CAACTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* * * * *
5567209 ATTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATAA-TAACATCTTTCTGCCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
5567273 CAGCTAGACCATTAAT
66 CAGCTAGGCCATTAAT
**
5567289 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
5567354 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* * * * * * *
5567370 ATTTTACTCTAAGGTATTTAACTTTTAATCTAACTTGCATAATTGACACCTTTCAGTCATATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
5567435 CATCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
*
5567451 CGTTTACT
1 CTTTTACT
5567459 TTGGAATAGT
Statistics
Matches: 434, Mismatches: 54, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
79 72 0.17
80 73 0.17
81 289 0.67
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
CAGCTAGGCCATTAAT
Found at i:5568693 original size:18 final size:18
Alignment explanation
Indices: 5568672--5568712 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5568662 CATTCCTTAA
5568672 GTTTCTATCATACTCAAT
1 GTTTCTATCATACTCAAT
5568690 GTTTCTATCATACTCAAT
1 GTTTCTATCATACTCAAT
5568708 GTTTC
1 GTTTC
5568713 AAAACCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (18 bp):
GTTTCTATCATACTCAAT
Found at i:5570713 original size:16 final size:15
Alignment explanation
Indices: 5570692--5570732 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
5570682 TATTTTTGTT
5570692 ATTTAATTTTATGCAC
1 ATTTAATTTTATGC-C
*
5570708 ATTTAAATTTATGCC
1 ATTTAATTTTATGCC
*
5570723 ATTTACTTTT
1 ATTTAATTTT
5570733 TATTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (15 bp):
ATTTAATTTTATGCC
Found at i:5570727 original size:15 final size:16
Alignment explanation
Indices: 5570692--5570727 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5570682 TATTTTTGTT
*
5570692 ATTTAATTTTATGCAC
1 ATTTAAATTTATGCAC
5570708 ATTTAAATTTATGC-C
1 ATTTAAATTTATGCAC
5570723 ATTTA
1 ATTTA
5570728 CTTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTAAATTTATGCAC
Found at i:5572487 original size:23 final size:23
Alignment explanation
Indices: 5572461--5572510 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5572451 AATAACAAAG
*
5572461 ATAAA-AATAAATCCACCATTAAA
1 ATAAAGAATAAA-CAACCATTAAA
**
5572484 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGAATAAACAACCATTAAA
5572507 ATAA
1 ATAA
5572511 CCACCACCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (23 bp):
ATAAAGAATAAACAACCATTAAA
Found at i:5575827 original size:20 final size:20
Alignment explanation
Indices: 5575804--5575869 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
5575794 AGAGAAAAGT
* *
5575804 AAAAGTTAAGAGTGAAAGAG
1 AAAAATTAAGAATGAAAGAG
*
5575824 AAAAATTAAGATTGAAAGAG
1 AAAAATTAAGAATGAAAGAG
5575844 AAAAAATTAAGAATGAAAGAG
1 -AAAAATTAAGAATGAAAGAG
5575865 AAAAA
1 AAAAA
5575870 GAAAAAGTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
20 23 0.55
21 19 0.45
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (20 bp):
AAAAATTAAGAATGAAAGAG
Found at i:5575848 original size:21 final size:21
Alignment explanation
Indices: 5575804--5575869 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
5575794 AGAGAAAAGT
* *
5575804 AAAAGTTAAGAGTGAAAGAG-
1 AAAAATTAAGAATGAAAGAGA
*
5575824 AAAAATTAAGATTGAAAGAGA
1 AAAAATTAAGAATGAAAGAGA
5575845 AAAAATTAAGAATGAAAGAGA
1 AAAAATTAAGAATGAAAGAGA
5575866 AAAA
1 AAAA
5575870 GAAAAAGTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 18 0.43
21 24 0.57
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAAATTAAGAATGAAAGAGA
Found at i:5582754 original size:17 final size:17
Alignment explanation
Indices: 5582724--5582756 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5582714 TGAAGCATGC
5582724 ATAAGCAAAGTAAACAA
1 ATAAGCAAAGTAAACAA
5582741 ATAA-CAAAGATAAACA
1 ATAAGCAAAG-TAAACA
5582757 TAAATCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (17 bp):
ATAAGCAAAGTAAACAA
Found at i:5587568 original size:14 final size:14
Alignment explanation
Indices: 5587551--5587795 Score: 90
Period size: 15 Copynumber: 16.9 Consensus size: 14
5587541 TACACCTAAA
*
5587551 GAAAAGAAAAAAAT
1 GAAAAGAAAAAAAG
*
5587565 GAAATGAAAAAAATG
1 GAAAAGAAAAAAA-G
*
5587580 AAAAAGAAAAAAGAG
1 GAAAAGAAAAAA-AG
5587595 AGAGAAA-AAGAAAAAG
1 -GA-AAAGAA-AAAAAG
5587611 GAAAAGAGAAAAAAG
1 GAAAAGA-AAAAAAG
*
5587626 GAAAAGAATATATAAAA
1 GAAAAGAA-A-A-AAAG
*
5587643 TAAAAGAAAAAGAA-
1 GAAAAGAAAAA-AAG
* *
5587657 -AAATG-AAAAATG
1 GAAAAGAAAAAAAG
* *
5587669 AAAAATGAAAAAATG
1 GAAAA-GAAAAAAAG
* * *
5587684 AAAAATAAAAAAGG
1 GAAAAGAAAAAAAG
** *
5587698 GAAAAGGGAAAAGG
1 GAAAAGAAAAAAAG
* *
5587712 GAAAAAAAGAAAAAA
1 GAAAAGAA-AAAAAG
*
5587727 GAAAAAAGAAAAAAG
1 GAAAAGA-AAAAAAG
*
5587742 AGAAAAG-AGAAAAG
1 -GAAAAGAAAAAAAG
*
5587756 AGAAAAGAGAAAAGAG
1 -GAAAAGA-AAAAAAG
* * *
5587772 AAAAATAAAGAAA-
1 GAAAAGAAAAAAAG
5587785 -AAAAGAAAAAA
1 GAAAAGAAAAAA
5587796 GAAAATTGAA
Statistics
Matches: 179, Mismatches: 32, Indels: 42
0.71 0.13 0.17
Matches are distributed among these distances:
11 1 0.01
12 13 0.07
13 7 0.04
14 57 0.32
15 64 0.36
16 20 0.11
17 17 0.09
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (14 bp):
GAAAAGAAAAAAAG
Found at i:5587590 original size:7 final size:7
Alignment explanation
Indices: 5587580--5587800 Score: 134
Period size: 7 Copynumber: 31.4 Consensus size: 7
5587570 GAAAAAAATG
5587580 AAAAAGA
1 AAAAAGA
5587587 AAAAAG-
1 AAAAAGA
* *
5587593 AGAGAG-
1 AAAAAGA
5587599 AAAAAGA
1 AAAAAGA
*
5587606 AAAAGGA
1 AAAAAGA
*
5587613 AAAGAGA
1 AAAAAGA
5587620 AAAAAG-
1 AAAAAGA
*
5587626 GAAAAGA
1 AAAAAGA
5587633 ATATATAA-A
1 A-A-A-AAGA
5587642 ATAAAAG-
1 A-AAAAGA
5587649 AAAAAGA
1 AAAAAGA
*
5587656 AAAATGA
1 AAAAAGA
*
5587663 AAAATGA
1 AAAAAGA
*
5587670 AAAATGA
1 AAAAAGA
5587677 AAAAATGA
1 AAAAA-GA
5587685 AAAATA-A
1 AAAA-AGA
*
5587692 AAAAGGGA
1 AAAA-AGA
**
5587700 AAAGGGA
1 AAAAAGA
**
5587707 AAAGGGAA
1 AAAAAG-A
5587715 AAAAAGA
1 AAAAAGA
5587722 AAAAAGA
1 AAAAAGA
5587729 AAAAAGA
1 AAAAAGA
5587736 AAAAAGA
1 AAAAAGA
*
5587743 GAAAAGA
1 AAAAAGA
*
5587750 GAAAAGA
1 AAAAAGA
*
5587757 GAAAAGA
1 AAAAAGA
*
5587764 GAAAAG-
1 AAAAAGA
*
5587770 AGAAA-A
1 AAAAAGA
*
5587776 ATAAAGAA
1 AAAAAG-A
5587784 AAAAAGA
1 AAAAAGA
5587791 AAAAAGA
1 AAAAAGA
5587798 AAA
1 AAA
5587801 TTGAAAGGAG
Statistics
Matches: 178, Mismatches: 22, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
6 25 0.14
7 122 0.69
8 23 0.13
9 6 0.03
10 2 0.01
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (7 bp):
AAAAAGA
Found at i:5587603 original size:20 final size:20
Alignment explanation
Indices: 5587548--5587800 Score: 137
Period size: 22 Copynumber: 12.1 Consensus size: 20
5587538 AATTACACCT
*
5587548 AAAGAAAAGAAAAAAATGAAA
1 AAAGAAAAGAGAAAAA-GAAA
*
5587569 TGAAA-AAAA-TGAAAAAGAAA
1 --AAAGAAAAGAGAAAAAGAAA
*
5587589 AAAG-AGAGAGAAAAAGAAA
1 AAAGAAAAGAGAAAAAGAAA
*
5587608 AAGGAAAAGAGAAAAAAGGAAA
1 AAAGAAAAGAG-AAAAA-GAAA
*
5587630 AGAATATATAA-A-ATAAAAG-AA
1 A-AAGA-A-AAGAGA-AAAAGAAA
5587651 AAAGAAAA-ATGAAAAATGAAA
1 AAAGAAAAGA-GAAAAA-GAAA
* * *
5587672 AATGAAAAAATGAAAAATAAA
1 AAAGAAAAGA-GAAAAAGAAA
* *
5587693 AAAGGGAAAAGGGAAAAGGGAAAA
1 AAA--GAAAAGAGAAAA-AG-AAA
*
5587717 AAAGAAAAAAGAAAAAAGAAAA
1 AAAGAAAAGAG-AAAAAG-AAA
5587739 AAGAGAAAAGAGAAAAGAGAAA
1 AA-AGAAAAGAGAAAA-AGAAA
* *
5587761 AGAGAAAAGAGAAAAATAAA
1 AAAGAAAAGAGAAAAAGAAA
5587781 GAAA-AAAAGA-AAAAAGAAA
1 -AAAGAAAAGAGAAAAAGAAA
5587800 A
1 A
5587801 TTGAAAGGAG
Statistics
Matches: 184, Mismatches: 24, Indels: 49
0.72 0.09 0.19
Matches are distributed among these distances:
18 9 0.05
19 26 0.14
20 24 0.13
21 42 0.23
22 45 0.24
23 28 0.15
24 8 0.04
25 2 0.01
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.05
Consensus pattern (20 bp):
AAAGAAAAGAGAAAAAGAAA
Done.