Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 5 of 136
Found at i:1246300 original size:52 final size:51
Alignment explanation
Indices: 1246207--1246306 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 51
1246197 ACTTATATAT
1246207 ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
1 ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
* * * *
1246258 ATATAAAATATATTCATGCATTTACT-AAAA-AATGAAATATATAAGTATA
1 ATATAAAATACA-TAATGCATTTA-TGAAAACAAGGAAA-ATATAAATATA
1246307 ATATAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 17 0.40
52 24 0.57
53 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (51 bp):
ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
Found at i:1246589 original size:24 final size:21
Alignment explanation
Indices: 1246573--1246613 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1246563 TATATGTAGG
1246573 TATAATTATAATAATATATAA
1 TATAATTATAATAATATATAA
1246594 TATAATTATAATAATA-ATAA
1 TATAATTATAATAATATATAA
1246614 CAAAATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAATTATAATAATATATAA
Found at i:1246862 original size:20 final size:17
Alignment explanation
Indices: 1246833--1246876 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1246823 CTCTTTTTTT
1246833 TAAAAAAATCGTAAATAAG
1 TAAAAAAATCG-AAA-AAG
1246852 TAAAAATAATCGAAAAAG
1 TAAAAA-AATCGAAAAAG
1246870 -AAAAAAA
1 TAAAAAAA
1246877 AAGAAAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 5 0.21
18 3 0.12
19 9 0.38
20 5 0.21
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (17 bp):
TAAAAAAATCGAAAAAG
Found at i:1246874 original size:18 final size:19
Alignment explanation
Indices: 1246834--1246877 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1246824 TCTTTTTTTT
1246834 AAAAAAATCGTAAATAAGTA
1 AAAAAAATCGTAAATAAG-A
*
1246854 AAAATAATCG-AAA-AAGA
1 AAAAAAATCGTAAATAAGA
1246871 AAAAAAA
1 AAAAAAA
1246878 AGAAAACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 3 0.14
20 9 0.41
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (19 bp):
AAAAAAATCGTAAATAAGA
Found at i:1247100 original size:21 final size:21
Alignment explanation
Indices: 1247074--1247126 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1247064 AATCATATCT
*
1247074 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
1247095 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
1247116 TCTAAGATTGC
1 TCTAAGATTGC
1247127 CTATCCTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:1249578 original size:16 final size:15
Alignment explanation
Indices: 1249557--1249604 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 15
1249547 TAAACAATTA
1249557 TTAAAATGATTTAAAT
1 TTAAAAT-ATTTAAAT
1249573 TTAAAA-A-TT--AT
1 TTAAAATATTTAAAT
*
1249584 TAAAAATATTTAAAT
1 TTAAAATATTTAAAT
1249599 TTAAAA
1 TTAAAA
1249605 AATATGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
13 4 0.15
14 1 0.04
15 7 0.27
16 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TTAAAATATTTAAAT
Found at i:1249589 original size:27 final size:25
Alignment explanation
Indices: 1249546--1249605 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 25
1249536 AAAACTATAA
1249546 TTAAACAATTATTAAAATGATTTAAAT
1 TTAAA-AATTATTAAAAT-ATTTAAAT
1249573 TTAAAAATTATTAAAAATATTTAAAT
1 TTAAAAATTATT-AAAATATTTAAAT
1249599 TTAAAAA
1 TTAAAAA
1249606 ATATGATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAAAATTATTAAAATATTTAAAT
Found at i:1250294 original size:18 final size:17
Alignment explanation
Indices: 1250273--1250336 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
1250263 CTTCATGATT
1250273 TTTTTAAATTTTATGAA
1 TTTTTAAATTTTATGAA
1250290 CTTTTTAAATTCTT-TGAA
1 -TTTTTAAATT-TTATGAA
1250308 TTTTTTAATAATTTTAT-AA
1 -TTTTT-A-AATTTTATGAA
*
1250327 TTTTAAAATT
1 TTTTTAAATT
1250337 ATTTTTTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 4 0.10
17 1 0.03
18 23 0.57
19 7 0.17
20 5 0.12
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTTAAATTTTATGAA
Found at i:1252412 original size:6 final size:7
Alignment explanation
Indices: 1252395--1252420 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1252385 AATATACTTG
1252395 AAAAAAT
1 AAAAAAT
1252402 AAAAAAT
1 AAAAAAT
1252409 AAAAAAT
1 AAAAAAT
1252416 AAAAA
1 AAAAA
1252421 CTATTGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1256514 original size:141 final size:141
Alignment explanation
Indices: 1256245--1256519 Score: 353
Period size: 141 Copynumber: 2.0 Consensus size: 141
1256235 CTTGGAAAAT
* *
1256245 AACAACAACAAGAGCTTCAACAATTCAACAACCAAGATCACTTACTCAACACAACTTCAACTTCT
1 AACAACAACAAGAGCTTCAACAATTCAACAACCAAGATCACTCACTCAACACAACTTCAACTTCC
* * *
1256310 ATACTCTCTTCTACTCCCTCTTTTTGTTCAAAAAACTTGTCAATCAGAGTGCCAAAAACCCCTTA
66 ATAATCTCTTCTACTCCCTCTTTTTGTTCAAAAAACATGTCAATCAGAATGCCAAAAACCCCTTA
1256375 CTCTTTTGACC
131 CTCTTTTGACC
* * * * *
1256386 AACAACAATCAA-AGCTTCAACAATTTAATAACC-AGCATCACTCACTCAACATAGCTTCACCTT
1 AACAACAA-CAAGAGCTTCAACAATTCAACAACCAAG-ATCACTCACTCAACACAACTTCAACTT
* * *
1256449 CCATAATCTCTTCTACT-CCTCGTTTGTTGTTCAAGAAACATG-CTAATTAGAATGCTAAAAA-C
64 CCATAATCTCTTCTACTCCCTC-TTT-TTGTTCAAAAAACATGTC-AATCAGAATGCCAAAAACC
1256511 CCTTACTCT
126 CCTTACTCT
1256520 CTTAACTGGA
Statistics
Matches: 116, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
140 6 0.05
141 79 0.68
142 31 0.27
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.29
Consensus pattern (141 bp):
AACAACAACAAGAGCTTCAACAATTCAACAACCAAGATCACTCACTCAACACAACTTCAACTTCC
ATAATCTCTTCTACTCCCTCTTTTTGTTCAAAAAACATGTCAATCAGAATGCCAAAAACCCCTTA
CTCTTTTGACC
Found at i:1259073 original size:29 final size:29
Alignment explanation
Indices: 1259010--1259067 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1259000 ATACAAATTC
1259010 AAATAAACAAAAGTAATGTTAATGGCAAT
1 AAATAAACAAAAGTAATGTTAATGGCAAT
1259039 AAATAAACAAAAGTAATGTTAATGGCAAT
1 AAATAAACAAAAGTAATGTTAATGGCAAT
1259068 TTATAAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (29 bp):
AAATAAACAAAAGTAATGTTAATGGCAAT
Found at i:1259889 original size:190 final size:190
Alignment explanation
Indices: 1259566--1259947 Score: 764
Period size: 190 Copynumber: 2.0 Consensus size: 190
1259556 TTTATTCGAG
1259566 TTGATTTGAATAACTCCAACTATTTAATTTAATTTTTGATTTTTTTATTAAGTTTTTCTAATCGA
1 TTGATTTGAATAACTCCAACTATTTAATTTAATTTTTGATTTTTTTATTAAGTTTTTCTAATCGA
1259631 ATCAGATTTTTCTCACCCCTAGTTATGAGATAGAAATGATTATTAAAAACATTAAAATAAAATGT
66 ATCAGATTTTTCTCACCCCTAGTTATGAGATAGAAATGATTATTAAAAACATTAAAATAAAATGT
1259696 GTATATATATTAGATTGTCAAATTTTATTTTCAAATTATATTTAAAATAAATAAAATAGA
131 GTATATATATTAGATTGTCAAATTTTATTTTCAAATTATATTTAAAATAAATAAAATAGA
1259756 TTGATTTGAATAACTCCAACTATTTAATTTAATTTTTGATTTTTTTATTAAGTTTTTCTAATCGA
1 TTGATTTGAATAACTCCAACTATTTAATTTAATTTTTGATTTTTTTATTAAGTTTTTCTAATCGA
1259821 ATCAGATTTTTCTCACCCCTAGTTATGAGATAGAAATGATTATTAAAAACATTAAAATAAAATGT
66 ATCAGATTTTTCTCACCCCTAGTTATGAGATAGAAATGATTATTAAAAACATTAAAATAAAATGT
1259886 GTATATATATTAGATTGTCAAATTTTATTTTCAAATTATATTTAAAATAAATAAAATAGA
131 GTATATATATTAGATTGTCAAATTTTATTTTCAAATTATATTTAAAATAAATAAAATAGA
1259946 TT
1 TT
1259948 ATAATTATAT
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 192 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (190 bp):
TTGATTTGAATAACTCCAACTATTTAATTTAATTTTTGATTTTTTTATTAAGTTTTTCTAATCGA
ATCAGATTTTTCTCACCCCTAGTTATGAGATAGAAATGATTATTAAAAACATTAAAATAAAATGT
GTATATATATTAGATTGTCAAATTTTATTTTCAAATTATATTTAAAATAAATAAAATAGA
Found at i:1277920 original size:24 final size:24
Alignment explanation
Indices: 1277886--1277931 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1277876 AGCTTCTGCC
*
1277886 TTTTTTCTTTTTTCTTTGTTTTTT
1 TTTTTTCTTTTTTCGTTGTTTTTT
* *
1277910 TTTTTTTTTTTTTGGTTGTTTT
1 TTTTTTCTTTTTTCGTTGTTTT
1277932 GTTGGGGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (24 bp):
TTTTTTCTTTTTTCGTTGTTTTTT
Found at i:1277931 original size:20 final size:22
Alignment explanation
Indices: 1277886--1277931 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1277876 AGCTTCTGCC
1277886 TTTTTTCTTTTTTCTTT-GTT-
1 TTTTTTCTTTTTTCTTTGGTTG
* *
1277906 TTTTTTTTTTTTTTTTTGGTTG
1 TTTTTTCTTTTTTCTTTGGTTG
1277928 TTTT
1 TTTT
1277932 GTTGGGGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 3 0.14
22 4 0.18
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (22 bp):
TTTTTTCTTTTTTCTTTGGTTG
Found at i:1277951 original size:1 final size:1
Alignment explanation
Indices: 1277945--1277989 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
1277935 GGGGCATGAG
1277945 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1277990 GGTTGTTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1277989 original size:67 final size:68
Alignment explanation
Indices: 1277886--1278016 Score: 201
Period size: 67 Copynumber: 1.9 Consensus size: 68
1277876 AGCTTCTGCC
* * *
1277886 TTTTTTCTTTTTTCTTTGTTTTTTTTTTTTTTTTTTTGGTTGTTT-TGTTGGGGCATGAGTTTTT
1 TTTTTTCTTTTTTCTTTGTTTTTTTTTTTTTTTTTTTGGTTGTTTGAGTTGGGACATGAATTTTT
1277950 TTT
66 TTT
* * *
1277953 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTGTTTGAGTTGGGACATGAATTTT
1 TTTTTTCTTTTTTCTTTGTTTTTTTTTTTTTTTTTTTGGTTGTTTGAGTTGGGACATGAATTTT
1278017 ATATATCTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
67 42 0.74
68 15 0.26
ACGTcount: A:0.05, C:0.03, G:0.15, T:0.76
Consensus pattern (68 bp):
TTTTTTCTTTTTTCTTTGTTTTTTTTTTTTTTTTTTTGGTTGTTTGAGTTGGGACATGAATTTTT
TTT
Found at i:1280380 original size:114 final size:112
Alignment explanation
Indices: 1280240--1280645 Score: 413
Period size: 114 Copynumber: 3.6 Consensus size: 112
1280230 AAAAACTTCG
* *
1280240 GCCCAACGACGTCGTTTT-TCGCGCATTCGGGGATTTAGCAGCGTTTTTTATGAAGCGCCGCTAA
1 GCCCAACGACGTCGTTTTCT-GAGCATTCGGGGATTTAGCGGCGTTTTTTA-GAAGCGCCGCTAA
* * *
1280304 AGCTCAGGGATTTAGCGGCGTTTTTGAGAATTCGCTGCAAAGAAACCTAA
64 AGCTCAGGGCTTTAGCGGCGTTTTTGAGAA-GCGCCGCAAAGAAACCTAA
* * * * * * *
1280354 GCCCAACGACGTTGTTTTCTGAGCATTCGGTGACTTAGCGGCGTTTTTTAGGTAGTGCCGCCAAT
1 GCCCAACGACGTCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTTA-GAAGCGCCGCTAAA
* * * *
1280419 GTTCAGTGCTTTAGCGGCGTTTCTGAGGAAGCGCCACAAAGAAACCTAA
65 GCTCAGGGCTTTAGCGGCGTTTTTGA-GAAGCGCCGCAAAGAAACCTAA
* * * * * ** * *
1280468 GCCCAACAACGCCATTCTCTGAGTATTCGGGGATTTAGCGGCGTTTATGGAGAAGCGCTGCTAAT
1 GCCCAACGACGTCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTT-TTTAGAAGCGCCGCTAAA
* * * *
1280533 GCTCAGGGCTTTAGCAGCATTTTTGGGAAAGCGCCGCAGA-AAACCTAA
65 GCTCAGGGCTTTAGCGGCGTTTTTGAG-AAGCGCCGCAAAGAAACCTAA
* * * *
1280581 GCCCAACGATGTCGTTTGACTGAGCATTGGGGGATTTAGCGGCGTTTTTTAACAAGCGCCG-TAA
1 GCCCAACGACGTCGTTT-TCTGAGCATTCGGGGATTTAGCGGCGTTTTTT-AGAAGCGCCGCTAA
1280645 A
64 A
1280646 ATAATTATTT
Statistics
Matches: 234, Mismatches: 52, Indels: 13
0.78 0.17 0.04
Matches are distributed among these distances:
113 25 0.11
114 203 0.87
115 6 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (112 bp):
GCCCAACGACGTCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTTTAGAAGCGCCGCTAAAG
CTCAGGGCTTTAGCGGCGTTTTTGAGAAGCGCCGCAAAGAAACCTAA
Found at i:1280801 original size:8 final size:8
Alignment explanation
Indices: 1280761--1280811 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
1280751 TGGCTTTTTC
1280761 AAAACCCT
1 AAAACCCT
*
1280769 TAAACCCT
1 AAAACCCT
* *
1280777 AAAAACAT
1 AAAACCCT
*
1280785 -AATCCCT
1 AAAACCCT
1280792 AAAACCCT
1 AAAACCCT
*
1280800 AAACCCCT
1 AAAACCCT
1280808 AAAA
1 AAAA
1280812 ATTTCATGTG
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
7 4 0.12
8 28 0.88
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAACCCT
Found at i:1282298 original size:21 final size:21
Alignment explanation
Indices: 1282272--1282349 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
1282262 GTAGAGGCGA
1282272 CAGCGAAGGAAGCAGCGGCTG
1 CAGCGAAGGAAGCAGCGGCTG
*
1282293 CAGCGAAGGAAGCAGCGACTG
1 CAGCGAAGGAAGCAGCGGCTG
* *
1282314 CAGCGAGGGAAGCAGAGGCTG
1 CAGCGAAGGAAGCAGCGGCTG
1282335 CAGCG-AGAGAAGCAG
1 CAGCGAAG-GAAGCAG
1282350 AGCAGAGCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.32, C:0.22, G:0.42, T:0.04
Consensus pattern (21 bp):
CAGCGAAGGAAGCAGCGGCTG
Found at i:1282350 original size:21 final size:21
Alignment explanation
Indices: 1282264--1282351 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
1282254 AACTTAAAGT
1282264 AGAGGC-GACAGCGAAGGAAGC
1 AGAGGCTG-CAGCGAAGGAAGC
*
1282285 AGCGGCTGCAGCGAAGGAAGC
1 AGAGGCTGCAGCGAAGGAAGC
* * *
1282306 AGCGACTGCAGCGAGGGAAGC
1 AGAGGCTGCAGCGAAGGAAGC
1282327 AGAGGCTGCAGCG-AGAGAAGC
1 AGAGGCTGCAGCGAAG-GAAGC
1282348 AGAG
1 AGAG
1282352 CAGAGCAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.43, T:0.03
Consensus pattern (21 bp):
AGAGGCTGCAGCGAAGGAAGC
Found at i:1285719 original size:31 final size:30
Alignment explanation
Indices: 1285659--1285716 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
1285649 TTCATTTTGT
1285659 AATAAATAATAATAATAATGTTTTTTATAAA
1 AATAAAT-ATAATAATAATGTTTTTTATAAA
*
1285690 AATAAAT-TAATAA-AATGTACTTTTATA
1 AATAAATATAATAATAATGT-TTTTTATA
1285717 TAATCTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 13 0.52
31 7 0.28
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (30 bp):
AATAAATATAATAATAATGTTTTTTATAAA
Found at i:1288554 original size:31 final size:31
Alignment explanation
Indices: 1288516--1288578 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1288506 TTGCTAGTTG
1288516 TTGTTTTTTTCAAGTAAGTTCATACGAGACT
1 TTGTTTTTTTCAAGTAAGTTCATACGAGACT
1288547 TTGTTTTTTTCAAGTAAGTTCATACGAGACT
1 TTGTTTTTTTCAAGTAAGTTCATACGAGACT
1288578 T
1 T
1288579 ACTTTATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (31 bp):
TTGTTTTTTTCAAGTAAGTTCATACGAGACT
Found at i:1298796 original size:33 final size:33
Alignment explanation
Indices: 1298754--1298820 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1298744 TGCTCTAAGA
1298754 GGTATATAAAAGCTTGTCGTCACTACCTCTGAG
1 GGTATATAAAAGCTTGTCGTCACTACCTCTGAG
1298787 GGTATATAAAAGCTTGTCGTCACTACCTCTGAG
1 GGTATATAAAAGCTTGTCGTCACTACCTCTGAG
1298820 G
1 G
1298821 CTATCATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (33 bp):
GGTATATAAAAGCTTGTCGTCACTACCTCTGAG
Found at i:1304816 original size:22 final size:21
Alignment explanation
Indices: 1304791--1304834 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1304781 ATCTGTTCCA
*
1304791 CATTCTGCAACTAGATATTTGT
1 CATTCTACAA-TAGATATTTGT
*
1304813 CATTCTACTATAGATATTTGT
1 CATTCTACAATAGATATTTGT
1304834 C
1 C
1304835 CACTTCCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (21 bp):
CATTCTACAATAGATATTTGT
Found at i:1309290 original size:18 final size:18
Alignment explanation
Indices: 1309269--1309311 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1309259 ATAATTTCAA
1309269 TAAAAAATCTTA-AAATTT
1 TAAAAAAT-TTATAAATTT
*
1309287 TAAAAAA-TTATAATTTT
1 TAAAAAATTTATAAATTT
1309304 TAAAAAAT
1 TAAAAAAT
1309312 AGAACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAAATTTATAAATTT
Found at i:1309320 original size:17 final size:17
Alignment explanation
Indices: 1309284--1309322 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1309274 AATCTTAAAA
*
1309284 TTTTAAAAAATTATAAT
1 TTTTAAAAAATTAGAAT
1309301 TTTTAAAAAA-TAGAACT
1 TTTTAAAAAATTAGAA-T
1309318 TTTTA
1 TTTTA
1309323 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTTAAAAAATTAGAAT
Found at i:1309328 original size:21 final size:21
Alignment explanation
Indices: 1309302--1309343 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1309292 AATTATAATT
* *
1309302 TTTAAAAAATAGAACTTTTTA
1 TTTAAAAAATAAAACTCTTTA
1309323 TTTAAAAAATAAAACTCTTTA
1 TTTAAAAAATAAAACTCTTTA
1309344 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTAAAAAATAAAACTCTTTA
Found at i:1309354 original size:24 final size:21
Alignment explanation
Indices: 1309302--1309355 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
1309292 AATTATAATT
* *
1309302 TTTAAAAAATAGAACTTTTTA
1 TTTAAAAAATAAAACTTTTAA
1309323 TTTAAAAAATAAAACTCTTTAAAA
1 TTTAAAAAATAAAACT-TTT--AA
1309347 TTTAAAAAA
1 TTTAAAAAA
1309356 ATCATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 3 0.11
24 10 0.36
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
TTTAAAAAATAAAACTTTTAA
Found at i:1309446 original size:13 final size:13
Alignment explanation
Indices: 1309430--1309470 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1309420 AATTTGAAAA
1309430 TTAAAAATTTATT
1 TTAAAAATTTATT
*
1309443 TTAAAAA-TTATA
1 TTAAAAATTTATT
*
1309455 TTAAAAATTTAAT
1 TTAAAAATTTATT
1309468 TTA
1 TTA
1309471 TTCAACCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAAAAATTTATT
Found at i:1309453 original size:12 final size:12
Alignment explanation
Indices: 1309429--1309463 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1309419 AAATTTGAAA
1309429 ATTAAAAATTTAT
1 ATTAAAAA-TTAT
*
1309442 TTTAAAAATTAT
1 ATTAAAAATTAT
1309454 ATTAAAAATT
1 ATTAAAAATT
1309464 TAATTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTAAAAATTAT
Found at i:1309834 original size:22 final size:22
Alignment explanation
Indices: 1309806--1309902 Score: 116
Period size: 22 Copynumber: 4.7 Consensus size: 22
1309796 ATCCTATCTA
1309806 AATTTCCTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
1309828 AATTTCCTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
**
1309850 AAACT-C-T-C-AAA--CTCTC
1 AATTTCCTTCCAAAATTCTCTC
* *
1309866 AAATTCCTTCCAAAATCCTCTC
1 AATTTCCTTCCAAAATTCTCTC
1309888 AATTTCCTTCCAAAA
1 AATTTCCTTCCAAAA
1309903 ATCTTTAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
16 9 0.14
17 1 0.02
18 4 0.06
19 2 0.03
20 4 0.06
21 1 0.02
22 44 0.68
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (22 bp):
AATTTCCTTCCAAAATTCTCTC
Found at i:1309942 original size:17 final size:18
Alignment explanation
Indices: 1309917--1309950 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1309907 TTAAAATCCA
1309917 TATTAAATTTC-TTTTTC
1 TATTAAATTTCATTTTTC
*
1309934 TATTCAATTTCATTTTT
1 TATTAAATTTCATTTTT
1309951 TAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTAAATTTCATTTTTC
Found at i:1309982 original size:20 final size:18
Alignment explanation
Indices: 1309959--1310013 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 18
1309949 TTTAAGATAA
1309959 TTTTAAATATTTTTATATTT
1 TTTTAAATATTTTTA-A-TT
1309979 TTTTAAAATAATTTTTAATT
1 TTTT-AAAT-ATTTTTAATT
1309999 TTTT-AATATTTTTAA
1 TTTTAAATATTTTTAA
1310014 CAATGACCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 8 0.24
18 3 0.09
20 10 0.30
21 5 0.15
22 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAAATATTTTTAATT
Found at i:1309983 original size:31 final size:31
Alignment explanation
Indices: 1309946--1310011 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1309936 TTCAATTTCA
*
1309946 TTTTTTAAGATAATTTTAAATATTTTT-ATAT
1 TTTTTTAAAATAATTTTAAAT-TTTTTAATAT
*
1309977 TTTTTTAAAATAATTTTTAATTTTTTAATAT
1 TTTTTTAAAATAATTTTAAATTTTTTAATAT
1310008 TTTT
1 TTTT
1310012 AACAATGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATTTTTTAATAT
Found at i:1310003 original size:8 final size:9
Alignment explanation
Indices: 1309958--1310013 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
1309948 TTTTAAGATA
*
1309958 ATTTTAAAT
1 ATTTTTAAT
1309967 ATTTTTATAT
1 ATTTTTA-AT
*
1309977 TTTTTTAAAAT
1 ATTTTT--AAT
1309988 AATTTTTAAT
1 -ATTTTTAAT
1309998 -TTTTTAAT
1 ATTTTTAAT
1310006 ATTTTTAA
1 ATTTTTAA
1310014 CAATGACCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 8 0.21
9 13 0.33
10 10 0.26
11 2 0.05
12 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:1312356 original size:24 final size:23
Alignment explanation
Indices: 1312298--1312352 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1312288 ATTATTTGAT
*
1312298 ACCCTAACCTAATTTATTTAAAA
1 ACCCTAACCTAATTTAATTAAAA
1312321 ACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCTAATTTAATTAAAA
1312344 ACCCTAACC
1 ACCCTAACC
1312353 CTAACCTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (23 bp):
ACCCTAACCTAATTTAATTAAAA
Found at i:1312358 original size:29 final size:29
Alignment explanation
Indices: 1312320--1312508 Score: 225
Period size: 29 Copynumber: 6.1 Consensus size: 29
1312310 TTTATTTAAA
1312320 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
1312349 AACCCTAACCTAATTTAATTTAATTAAAAACCTT
1 AACCCTAACC-----TAATTTAATTAAAAACCCT
*
1312383 AACCCTAACCTATTTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
1312412 AACCATAACCTAATTTAATTTAATTAAAAGCCCT
1 AACCCTAACCTAATTTAA-TT-A--AAAA-CCCT
*
1312446 AACTCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
1312475 AAACCCTAACCTATTTTAATTAAAACCCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
1312505 AACC
1 AACC
1312509 TAATTTATGT
Statistics
Matches: 139, Mismatches: 10, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
29 51 0.37
30 32 0.23
31 1 0.01
32 1 0.01
33 6 0.04
34 48 0.35
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:1312368 original size:34 final size:34
Alignment explanation
Indices: 1312330--1312495 Score: 208
Period size: 34 Copynumber: 5.1 Consensus size: 34
1312320 AACCCTAACC
1312330 TAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATT
*
1312364 TAATTTAATTAAAAACCTTAACCCTAACCT-A--
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATT
*
1312395 T--TTTAATTAAAAACCCTAACCATAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATT
* *
1312427 TAATTTAATTAAAAGCCCTAACTCTAACC-----
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATT
*
1312456 TAATTTAATTAAAAACCCTAAACCCTAACCTATTT
1 TAATTTAATTAAAAACCCT-AACCCTAACCTAATT
1312491 TAATT
1 TAATT
1312496 AAAACCCCTA
Statistics
Matches: 113, Mismatches: 8, Indels: 21
0.80 0.06 0.15
Matches are distributed among these distances:
29 43 0.38
30 10 0.09
31 1 0.01
32 1 0.01
33 1 0.01
34 52 0.46
35 5 0.04
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (34 bp):
TAATTTAATTAAAAACCCTAACCCTAACCTAATT
Found at i:1312390 original size:63 final size:63
Alignment explanation
Indices: 1312320--1312495 Score: 289
Period size: 63 Copynumber: 2.8 Consensus size: 63
1312310 TTTATTTAAA
*
1312320 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAATTAAAAACCTT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAATTAAAAACCCT
* * *
1312383 AACCCTAACCTATTTTAATTAAAAACCCTAACCATAACCTAATTTAATTTAATTAAAAGCCCT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAATTAAAAACCCT
* *
1312446 AACTCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTATTTTAATT
1 AACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATT
1312496 AAAACCCCTA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 86 0.83
64 18 0.17
ACGTcount: A:0.43, C:0.24, G:0.01, T:0.32
Consensus pattern (63 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAATTAAAAACCCT
Found at i:1312539 original size:24 final size:23
Alignment explanation
Indices: 1312475--1312539 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
1312465 TAAAAACCCT
1312475 AAACCCTAACCT-ATTTTAATTAA
1 AAACCCTAACCTAATTTT-ATTAA
*
1312498 AACCCCTAACCTAA-TTTATGTAA
1 AAACCCTAACCTAATTTTAT-TAA
*
1312521 AAACCCTAACATAATTTTA
1 AAACCCTAACCTAATTTTA
1312540 CCTAATTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 2 0.06
23 29 0.81
24 5 0.14
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (23 bp):
AAACCCTAACCTAATTTTATTAA
Found at i:1312591 original size:56 final size:56
Alignment explanation
Indices: 1312531--1312655 Score: 198
Period size: 56 Copynumber: 2.2 Consensus size: 56
1312521 AAACCCTAAC
* *
1312531 ATAATTTTACCTAATTTGATAATCCTACTAACCATTAAC-ACATTTTTTGGGGCTTA
1 ATAATTTTACATAATTTGATAATCCTACTAACCATTAACAAAATTTTTT-GGGCTTA
**
1312587 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAATCCTACTAACCATTAACAAAATTTTTTGGGCTTA
1312643 ATAATTTTACATA
1 ATAATTTTACATA
1312656 GTTTTAAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 56 0.88
57 8 0.12
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAATCCTACTAACCATTAACAAAATTTTTTGGGCTTA
Found at i:1320322 original size:88 final size:88
Alignment explanation
Indices: 1320051--1320532 Score: 750
Period size: 88 Copynumber: 5.5 Consensus size: 88
1320041 ATCAGTGAAG
* * * * *
1320051 ATAACAGATCTTGCCTTCTTGCACCGACAGCAAAGCAGATCGAAGACACCAACCTTGTCTCTCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
1320116 GGTTGTAGCGGAACAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * *
1320139 ATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGAC-CCAACCTTGCCTCCCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
1320203 GGTTGCAGCGGAGCAAGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * *
1320226 ATAACAGATCTTGCTTTCCTGTACCGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1320291 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * *
1320314 ATAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCTTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
1320379 GGTTACAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
*
1320402 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
1320467 GATTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * *
1320490 ATAACAGATCTTGCCTTCCTACACCGATAGTGAAGCAGATCGA
1 ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
1320533 TGACCCCAAC
Statistics
Matches: 362, Mismatches: 31, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
87 79 0.22
88 283 0.78
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (88 bp):
ATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGTTAAAA
Found at i:1320371 original size:44 final size:44
Alignment explanation
Indices: 1320323--1320461 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 44
1320313 AATAGCAGAT
1320323 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGC
****** * * ** * * * *
1320367 CTTGCC-TCCTTGGGTTACAGCGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAG-C
* *
1320411 CTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGC
1 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGC
1320455 CTTGCCT
1 CTTGCCT
1320462 CCCTGGATTG
Statistics
Matches: 64, Mismatches: 29, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 23 0.36
44 19 0.30
45 22 0.34
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.19
Consensus pattern (44 bp):
CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:1320503 original size:44 final size:44
Alignment explanation
Indices: 1320191--1320505 Score: 177
Period size: 44 Copynumber: 7.2 Consensus size: 44
1320181 AAGACCCAAC
* *
1320191 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGTTAAAAATAACAGAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAACAGAT
* * * ** * * * * * * *
1320235 CTTGCTTTCCTGTACCGACAGCGAAGCAGATCAAAGACACCAG-C
1 CTTGCCTCCCTGGATTG-CAGCGGAGCAGGTTAAAAATAACAGAT
* *
1320279 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAACAGAT
* ** ** * * ** * * * *
1320323 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTGGATTG-CAGCGGAGCAGGTTAAAAATAACAGAT
* * *
1320367 CTTGCCTCCTTGGGTTACAGCGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAACAGAT
* * ** * * * ** * * * *
1320411 CTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAG-C
1 CTTGCCTCCCTGGATTG-CAGCGGAGCAGGTTAAAAATAACAGAT
1320455 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAACAGAT
1320499 CTTGCCT
1 CTTGCCT
1320506 TCCTACACCG
Statistics
Matches: 179, Mismatches: 86, Indels: 12
0.65 0.31 0.04
Matches are distributed among these distances:
43 54 0.30
44 72 0.40
45 53 0.30
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (44 bp):
CTTGCCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAACAGAT
Found at i:1321066 original size:44 final size:44
Alignment explanation
Indices: 1320973--1321080 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
1320963 ATGGCAAATT
* ** *
1320973 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTAAAGCAGATTAAAACCGATAATC
* * * *
1321017 CTATCTCCCTGAAGTTGCAGTAAAGCGGATTAAAACC-TTGGATC
1 TTATCTCCCTGAAGTTGCAGTAAAGCAGATTAAAACCGAT-AATC
*
1321061 TTATCTCTCTGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAG
1321081 AGAGCATAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTAAAGCAGATTAAAACCGATAATC
Found at i:1323290 original size:139 final size:140
Alignment explanation
Indices: 1323131--1323409 Score: 551
Period size: 139 Copynumber: 2.0 Consensus size: 140
1323121 GGGCGTTACG
1323131 AGGGTGCTAATCCTTCCTCATACGTAACTAACTCCCGGATCCATTTTTTTAAAACTTGTAGACCA
1 AGGGTGCTAATCCTTCCTCATACGTAACTAACTCCCGGATCCATTTTTTTAAAACTTGTAGACCA
1323196 AAGCCGTTTTTTTAGGTGATCCAATCACACCTTAATAAAAGATTGGTGGCGACTCCCAAA-TTTC
66 AAGCCGTTTTTTTAGGTGATCCAATCACACCTTAATAAAAGATTGGTGGCGACTCCCAAATTTTC
1323260 ATTTTTTAAA
131 ATTTTTTAAA
1323270 AGGGTGCTAATCCTTCCTCATACGTAACTAACTCCCGGATCCATTTTTTTAAAACTTGTAGACCA
1 AGGGTGCTAATCCTTCCTCATACGTAACTAACTCCCGGATCCATTTTTTTAAAACTTGTAGACCA
1323335 AAGCCGTTTTTTTAGGTGATCCAATCACACCTTAATAAAAGATTGGTGGCGACTCCCAAATTTTC
66 AAGCCGTTTTTTTAGGTGATCCAATCACACCTTAATAAAAGATTGGTGGCGACTCCCAAATTTTC
1323400 ATTTTTTAAA
131 ATTTTTTAAA
1323410 GTCGACAACC
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 125 0.90
140 14 0.10
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (140 bp):
AGGGTGCTAATCCTTCCTCATACGTAACTAACTCCCGGATCCATTTTTTTAAAACTTGTAGACCA
AAGCCGTTTTTTTAGGTGATCCAATCACACCTTAATAAAAGATTGGTGGCGACTCCCAAATTTTC
ATTTTTTAAA
Found at i:1330892 original size:35 final size:35
Alignment explanation
Indices: 1330846--1330918 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
1330836 ACTGGGACAC
1330846 ATGGTTGTCCATGTTCATTTGAATTTAGATAACAA
1 ATGGTTGTCCATGTTCATTTGAATTTAGATAACAA
1330881 ATGGTTGTCCATGTTCATTTGAATTTAGATAACAA
1 ATGGTTGTCCATGTTCATTTGAATTTAGATAACAA
1330916 ATG
1 ATG
1330919 TTTCGATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
ATGGTTGTCCATGTTCATTTGAATTTAGATAACAA
Found at i:1337754 original size:19 final size:18
Alignment explanation
Indices: 1337730--1337772 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1337720 TTACAATTCG
*
1337730 AATAACTTGAATAATTCCA
1 AATAACTTGAATAACT-CA
1337749 AATAACTTGAATAACTCA
1 AATAACTTGAATAACTCA
1337767 AATAAC
1 AATAAC
1337773 AGATTGGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.28
Consensus pattern (18 bp):
AATAACTTGAATAACTCA
Found at i:1337893 original size:17 final size:18
Alignment explanation
Indices: 1337863--1337897 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1337853 AATAAATTCC
*
1337863 AAATAATTTTTAAAATTA
1 AAATAATTTATAAAATTA
1337881 AAAT-ATTTATAAAATTA
1 AAATAATTTATAAAATTA
1337898 CAAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATTTATAAAATTA
Found at i:1337938 original size:19 final size:20
Alignment explanation
Indices: 1337914--1337957 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1337904 TATATTTTTA
1337914 AAAAAAT-TATAAAAATAT-T
1 AAAAAATCTA-AAAAATATAT
*
1337933 AAAAAATCTAAAGAATATAT
1 AAAAAATCTAAAAAATATAT
1337953 AAAAA
1 AAAAA
1337958 TTTTAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAATCTAAAAAATATAT
Found at i:1340645 original size:22 final size:22
Alignment explanation
Indices: 1340619--1340663 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1340609 TATCACTACT
1340619 ATCAG-TCGGCAAAATTATCATG
1 ATCAGATCGGCAAAATTA-CATG
*
1340641 ATCAGATCGGTAAAATTACATG
1 ATCAGATCGGCAAAATTACATG
1340663 A
1 A
1340664 AATTCTGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (22 bp):
ATCAGATCGGCAAAATTACATG
Found at i:1341195 original size:15 final size:15
Alignment explanation
Indices: 1341175--1341203 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1341165 CATCCACCAT
1341175 AATCAAAAGCTTGAA
1 AATCAAAAGCTTGAA
1341190 AATCAAAAGCTTGA
1 AATCAAAAGCTTGA
1341204 CAGCTTTTAA
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:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (15 bp):
AATCAAAAGCTTGAA
Found at i:1341233 original size:2 final size:2
Alignment explanation
Indices: 1341222--1341257 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1341212 AAAGTCAGCA
*
1341222 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1341258 GACACACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1344100 original size:296 final size:299
Alignment explanation
Indices: 1343548--1344124 Score: 738
Period size: 296 Copynumber: 1.9 Consensus size: 299
1343538 TTGACAAACA
** *
1343548 ACAAAAAATATTTAACTCAAAATCATTTAAACACTAGAAAGTATCAGTTTTTTCAACAACAAAAA
1 ACAAAAAATATTTAACTCAAAATCATCCAAACACTAGAAAATATCAGTTTTTT--AC-ACAAAAA
* * *
1343613 AACAATCTATTTTCCAAAAATAAATTTTTGGAAGTTGTTTCCAGTGAAACAAACACAACCTTAAA
63 AACAATCCATTTTCCAAAAATAAATTTTTGAAAGTTGTTTCCAATGAAACAAACACAACCTTAAA
** *
1343678 ATAAGTATAAATATCAGGTTATATGATTTTTTTTTTAGGATAAACTATGTGAACAATCACTAAAT
128 ATAAGTATAAATATCAGGTTATATGA---TTTTTTTAGGATAAAAAATGTGAAAAATCACTAAAT
* * * *
1343743 TTTGATTAAAATTATGTTTTAATCATCCAACTTTTAAAAATTACATCATAGTCGCTAATGTTATC
190 TTTAATTAAAATTATGTTTTAATCATCAAACTTTTAAAAATTACATAATAGTCACTAATGTTATC
1343808 AAGTTGTTACATTTTGGTCACCCAACTTTTAAAATTATGTGAACG
255 AAGTTGTTACATTTTGGTCACCCAACTTTTAAAATTATGTGAACG
* * * *
1343853 ACAAAAAATATTTTACGT-AGAATCATCCAAACACTAGAAAATATCAG-TTTTT-C-CAAACAAT
1 ACAAAAAATATTTAAC-TCAAAATCATCCAAACACTAGAAAATATCAGTTTTTTACACAAAAAAA
* * * * * *
1343914 CAATCCATTTTTCAAAAAT-CATTTTCTGAAAGTTGTTTTCAATGAAACTAACTCAGCCTTAAAA
65 CAATCCATTTTCCAAAAATAAATTTT-TGAAAGTTGTTTCCAATGAAACAAACACAACCTTAAAA
* * *
1343978 TAAGTATAGATATC-GAGTTATCTGA-TTTTTTAGGGTAAAAAATTGTGAAAAATCACTAAATTT
129 TAAGTATAAATATCAG-GTTATATGATTTTTTTAGGATAAAAAA-TGTGAAAAATCACTAAATTT
* *
1344041 TAATTAAAATTATGTTTTGATCA-CTAAACTTTTAAAAATTACATAATAGTCATTAATGTTATCA
192 TAATTAAAATTATGTTTTAATCATC-AAACTTTTAAAAATTACATAATAGTCACTAATGTTATCA
*
1344105 ATTTGTTACATTTTGGTCAC
256 AGTTGTTACATTTTGGTCAC
1344125 TCGTCTGTTA
Statistics
Matches: 238, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
295 15 0.06
296 94 0.39
298 6 0.03
299 76 0.32
301 1 0.00
304 5 0.02
305 40 0.17
306 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (299 bp):
ACAAAAAATATTTAACTCAAAATCATCCAAACACTAGAAAATATCAGTTTTTTACACAAAAAAAC
AATCCATTTTCCAAAAATAAATTTTTGAAAGTTGTTTCCAATGAAACAAACACAACCTTAAAATA
AGTATAAATATCAGGTTATATGATTTTTTTAGGATAAAAAATGTGAAAAATCACTAAATTTTAAT
TAAAATTATGTTTTAATCATCAAACTTTTAAAAATTACATAATAGTCACTAATGTTATCAAGTTG
TTACATTTTGGTCACCCAACTTTTAAAATTATGTGAACG
Found at i:1344347 original size:17 final size:17
Alignment explanation
Indices: 1344325--1344359 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1344315 TCACAATTCA
1344325 TTTTTTAAAATTATAAT
1 TTTTTTAAAATTATAAT
*
1344342 TTTTTTGAAATTATAAT
1 TTTTTTAAAATTATAAT
1344359 T
1 T
1344360 ATACACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTTTAAAATTATAAT
Found at i:1347823 original size:18 final size:19
Alignment explanation
Indices: 1347779--1347837 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1347769 AGAATTTTAG
*
1347779 AAAATTTATTATGAATTTT
1 AAAATTTTTTATGAATTTT
** *
1347798 AATTTTTTTTAT-ATTTTT
1 AAAATTTTTTATGAATTTT
1347816 AAAATTTTGTTA-GAATTGTT
1 AAAATTTT-TTATGAATT-TT
1347836 AA
1 AA
1347838 GAAAAACTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 11 0.37
19 15 0.50
20 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
AAAATTTTTTATGAATTTT
Found at i:1354923 original size:19 final size:19
Alignment explanation
Indices: 1354876--1354923 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1354866 ATATGTTCTA
*
1354876 TATTATTTATCTTTAATAT
1 TATTATTTTTCTTTAATAT
* *
1354895 TATTAATTTTCTTTTATAAT
1 TATTATTTTTCTTTAAT-AT
1354915 TA-TATTTTT
1 TATTATTTTT
1354924 AATTTGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTTTTCTTTAATAT
Found at i:1357320 original size:197 final size:198
Alignment explanation
Indices: 1356985--1357381 Score: 787
Period size: 197 Copynumber: 2.0 Consensus size: 198
1356975 AGATCCATGT
1356985 AATGGGTTAAGCTCGAACTCAACGTATTATGTAATTTTTGTTATATGAGAATTAGACATGTTACA
1 AATGGGTTAAGCTCGAACTCAACGTATTATGTAATTTTTGTTATATGAGAATTAGACATGTTACA
1357050 CTATAATGAAAATATTAAAAATGTTAAATTGTTTATATTTAAAATTTTAAAATATGTATAATGGC
66 CTATAATGAAAATATTAAAAATGTTAAATTGTTTATATTTAAAATTTTAAAATATGTATAATGGC
1357115 ATTAAAATAAATCTATGCATATAAATACTAAATATTAAAACAATATAATATA-TTTTTTATTTTA
131 ATTAAAATAAATCTATGCATATAAATACTAAATATTAAAACAATATAATATATTTTTTTATTTTA
1357179 TTA
196 TTA
1357182 AATGGGTTAAGCTCGAACTCAACGTATTATGTAATTTTTGTTATATGAGAATTAGACATGTTACA
1 AATGGGTTAAGCTCGAACTCAACGTATTATGTAATTTTTGTTATATGAGAATTAGACATGTTACA
1357247 CTATAATGAAAATATTAAAAATGTTAAATTGTTTATATTTAAAATTTTAAAATATGTATAATGGC
66 CTATAATGAAAATATTAAAAATGTTAAATTGTTTATATTTAAAATTTTAAAATATGTATAATGGC
1357312 ATTAAAATAAATCTATGCATATAAATACTAAATATTAAAACAATATAATATATTTTTTTATTTTA
131 ATTAAAATAAATCTATGCATATAAATACTAAATATTAAAACAATATAATATATTTTTTTATTTTA
1357377 TTA
196 TTA
1357380 AA
1 AA
1357382 AAAATAATAT
Statistics
Matches: 199, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
197 182 0.91
198 17 0.09
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (198 bp):
AATGGGTTAAGCTCGAACTCAACGTATTATGTAATTTTTGTTATATGAGAATTAGACATGTTACA
CTATAATGAAAATATTAAAAATGTTAAATTGTTTATATTTAAAATTTTAAAATATGTATAATGGC
ATTAAAATAAATCTATGCATATAAATACTAAATATTAAAACAATATAATATATTTTTTTATTTTA
TTA
Found at i:1358048 original size:16 final size:16
Alignment explanation
Indices: 1358008--1358069 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
1357998 AAAATTCAGA
1358008 AAAATTA-TAAAAATT
1 AAAATTATTAAAAATT
*
1358023 ---ATTTTTAAAAATT
1 AAAATTATTAAAAATT
1358036 AAAATTATTAAAAATT
1 AAAATTATTAAAAATT
** *
1358052 AAAAAAAATAAAAATT
1 AAAATTATTAAAAATT
1358068 AA
1 AA
1358070 TTAAATGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 3 0.08
13 8 0.21
16 27 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTATTAAAAATT
Found at i:1362590 original size:83 final size:84
Alignment explanation
Indices: 1362494--1362667 Score: 325
Period size: 83 Copynumber: 2.1 Consensus size: 84
1362484 ATTTAAAAAT
1362494 AATT-ATTAAATTATCATAATTTAAAAGGGATCAATAATGCTATTAATAAAAATTTAATACAGGA
1 AATTAATTAAATTATCATAATTTAAAAGGGATCAATAATGCTATTAATAAAAATTTAATACAGGA
1362558 CTTTTTTAAAATGAT-ATA
66 CTTTTTTAAAATGATAATA
1362576 AATTAATTAAATTATCATAATTTAAAAGGGATCAATAATGCTATTAATAAAAATTTAATACAGGA
1 AATTAATTAAATTATCATAATTTAAAAGGGATCAATAATGCTATTAATAAAAATTTAATACAGGA
1362641 CTTTTTTAAAATGATAAATA
66 CTTTTTTAAAATGAT-AATA
1362661 AATTAAT
1 AATTAAT
1362668 AGTTTTAATT
Statistics
Matches: 89, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
82 4 0.04
83 75 0.84
85 10 0.11
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (84 bp):
AATTAATTAAATTATCATAATTTAAAAGGGATCAATAATGCTATTAATAAAAATTTAATACAGGA
CTTTTTTAAAATGATAATA
Found at i:1371433 original size:135 final size:136
Alignment explanation
Indices: 1371260--1371506 Score: 379
Period size: 136 Copynumber: 1.8 Consensus size: 136
1371250 AAACTCTGAT
* * * *
1371260 ACCACTTGATGAAGATCAACCTGATTAAGCAACGAACAAGTAAAAATAGCAGAA-AAATTGAGAG
1 ACCACTTGATGAAGATCAACCCGATTAAGCAACAAACAAGTAAAAATAGCAGAAGAAATTAAGAA
*
1371324 ATTGAACACACAAATTTTTTTTAACTTGACTTGCAAGCAATCTCTTATTTTATTTAACATGAATT
66 ATTGAACACACAAATTTTGTTTAACTTGACTTGCAAGCAATCTCTTATTTTATTTAACATGAATT
1371389 TAGGTC
131 TAGGTC
** * **
1371395 ACCACTTGATGGGGATCGACCCGATTAAGCAACAAACAAGTAAAAATAGTGGAAGAAATTAAGAA
1 ACCACTTGATGAAGATCAACCCGATTAAGCAACAAACAAGTAAAAATAGCAGAAGAAATTAAGAA
* *
1371460 ATTGAACACACGAATTTTGTTTAACTTGACTTGCAAGTAATCTCTTA
66 ATTGAACACACAAATTTTGTTTAACTTGACTTGCAAGCAATCTCTTA
1371507 ACAAGAATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
135 47 0.47
136 52 0.53
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (136 bp):
ACCACTTGATGAAGATCAACCCGATTAAGCAACAAACAAGTAAAAATAGCAGAAGAAATTAAGAA
ATTGAACACACAAATTTTGTTTAACTTGACTTGCAAGCAATCTCTTATTTTATTTAACATGAATT
TAGGTC
Found at i:1372694 original size:33 final size:32
Alignment explanation
Indices: 1372589--1372701 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
1372579 TGTGTGGTTC
* * * *
1372589 TGTGAAATGAGAATAAATATCAGCTTTCATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* * *
1372621 TGTGAAATGGTAACAAAT-TACAAGTTCAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
1372653 TGTGAAATGATAACAAATATCAACTTTAATTTT
1 TGTGAAATGATAACAAATATCAACTTTAA-TTT
*
1372686 TGTTAAATGATAACAA
1 TGTGAAATGATAACAA
1372702 TATTCCTCTA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
31 1 0.01
32 47 0.70
33 19 0.28
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:1376225 original size:43 final size:43
Alignment explanation
Indices: 1376108--1376226 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
1376098 TTTTTGTCCT
* *
1376108 GATGTGGTTGCTGCCACGTTGCTTCTTTTTTTGTCTGGACATA
1 GATGTGGTTCCTTCCACGTTGCTTCTTTTTTTGTCTGGACATA
* *
1376151 GATGCGGTTCCTTCCACATTGCTTAC-TTTTTTGTCTGGATGCA-A
1 GATGTGGTTCCTTCCACGTTGCTT-CTTTTTTTGTCTGGA--CATA
* * *
1376195 -TTGTGGTTTCTTCCACGTAGCTTCTTTTTTTG
1 GATGTGGTTCCTTCCACGTTGCTTCTTTTTTTG
1376227 GTCTTTTTCT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
42 1 0.02
43 58 0.92
44 2 0.03
45 2 0.03
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (43 bp):
GATGTGGTTCCTTCCACGTTGCTTCTTTTTTTGTCTGGACATA
Found at i:1378150 original size:15 final size:16
Alignment explanation
Indices: 1378130--1378162 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1378120 GACTATTAGT
*
1378130 TTTTTCTATTAA-TCC
1 TTTTTCTAATAATTCC
1378145 TTTTTCTAATAATTCC
1 TTTTTCTAATAATTCC
1378161 TT
1 TT
1378163 AATTTCTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTCTAATAATTCC
Found at i:1387885 original size:30 final size:30
Alignment explanation
Indices: 1387851--1387910 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1387841 TATTTTATTA
1387851 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
1387881 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
1387911 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:1393420 original size:11 final size:11
Alignment explanation
Indices: 1393404--1393442 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1393394 TATATAAATA
1393404 TATAAATTAAT
1 TATAAATTAAT
*
1393415 TATAAAGTATAT
1 TATAAATTA-AT
1393427 TATTAAATTAAT
1 TA-TAAATTAAT
1393439 TATA
1 TATA
1393443 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:1393454 original size:14 final size:17
Alignment explanation
Indices: 1393422--1393459 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
1393412 AATTATAAAG
1393422 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
1393439 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
1393453 TATATTA
1 TATATTA
1393460 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:1394601 original size:16 final size:16
Alignment explanation
Indices: 1394580--1394618 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1394570 TTATGTGTAT
1394580 GGTAAG-CAAATAATAA
1 GGTAAGTCAAAT-ATAA
*
1394596 GGTAAGTGAAATATAA
1 GGTAAGTCAAATATAA
1394612 GGTAAGT
1 GGTAAGT
1394619 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (16 bp):
GGTAAGTCAAATATAA
Found at i:1394988 original size:23 final size:21
Alignment explanation
Indices: 1394961--1395091 Score: 138
Period size: 21 Copynumber: 6.1 Consensus size: 21
1394951 GGCTTGACCG
1394961 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
1394982 GCATCAGGCACTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
* *
1395005 ATCTCAGGCATTTTATGTGTTGT
1 A--TCAGGCACTTTATGTGTCGT
* **
1395028 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* **
1395049 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
1395070 TTCAGGCAC-TTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
1395090 AT
1 AT
1395092 ATTGATTAGG
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.11
21 45 0.47
23 40 0.42
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:1395047 original size:44 final size:45
Alignment explanation
Indices: 1394962--1395051 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 45
1394952 GCTTGACCGA
* *
1394962 TCAGGCACTTTATGTGTCGTGCATCAGGCACTTTATGTGTCGTATC
1 TCAGGCACTTTATGTGTC-TGCATCAGGCACCTCATGTGTCGTATC
* * *
1395008 TCAGGCATTTTATGTGT-TGTATCAGGCACCTCGTGTGTCGTATC
1 TCAGGCACTTTATGTGTCTGCATCAGGCACCTCATGTGTCGTATC
1395052 AGGCACCTCG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 23 0.59
46 16 0.41
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (45 bp):
TCAGGCACTTTATGTGTCTGCATCAGGCACCTCATGTGTCGTATC
Found at i:1395128 original size:19 final size:19
Alignment explanation
Indices: 1395106--1395152 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1395096 ATTAGGTACT
1395106 ATGTGCCGTTTTAGGCACA
1 ATGTGCCGTTTTAGGCACA
*
1395125 ATGTGCCGTTTTAGGCATA
1 ATGTGCCGTTTTAGGCACA
1395144 ATGTGCCGT
1 ATGTGCCGT
1395153 ATTGGTGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (19 bp):
ATGTGCCGTTTTAGGCACA
Found at i:1400591 original size:9 final size:9
Alignment explanation
Indices: 1400577--1400613 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1400567 TATAGTTTGA
1400577 TATTCGAAT
1 TATTCGAAT
1400586 TATTCGAAT
1 TATTCGAAT
*
1400595 TATTCGAGT
1 TATTCGAAT
1400604 TATTCGAAT
1 TATTCGAAT
1400613 T
1 T
1400614 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1403636 original size:39 final size:39
Alignment explanation
Indices: 1403582--1403659 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
1403572 AAATGAACAA
*
1403582 ATTAAACCCTGTACGTTAAACTAAAGAGCAAATTAGTTC
1 ATTAAACCCTGTACGTTAAACTAAAGAGCAAATCAGTTC
1403621 ATTAAACCCTGTACGTTAAACTAAAGAGCAAATCAGTTC
1 ATTAAACCCTGTACGTTAAACTAAAGAGCAAATCAGTTC
1403660 TTTCTATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (39 bp):
ATTAAACCCTGTACGTTAAACTAAAGAGCAAATCAGTTC
Found at i:1407278 original size:10 final size:11
Alignment explanation
Indices: 1407262--1407302 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1407252 TTATTAAAAT
1407262 TTAATAATTTC
1 TTAATAATTTC
1407273 TT-ATAA-TTC
1 TTAATAATTTC
1407282 TTAATAATTTC
1 TTAATAATTTC
**
1407293 AAAATAATTT
1 TTAATAATTT
1407303 TATTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 5 0.19
10 8 0.31
11 13 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAATAATTTC
Found at i:1411135 original size:3 final size:3
Alignment explanation
Indices: 1411121--1411155 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1411111 AAAAGTGAGC
*
1411121 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1411156 CCAGTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1412636 original size:15 final size:13
Alignment explanation
Indices: 1412601--1412644 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
1412591 TAGATTTAGA
1412601 TTATTTATAATTTT
1 TTATTTA-AATTTT
1412615 TTATTTAAATTTT
1 TTATTTAAATTTT
*
1412628 TTAAGTTTAGATTTT
1 TT-A-TTTAAATTTT
1412643 TT
1 TT
1412645 TCGACCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.30
14 8 0.30
15 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (13 bp):
TTATTTAAATTTT
Found at i:1413741 original size:15 final size:15
Alignment explanation
Indices: 1413709--1413757 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
1413699 ATTGCTATAG
*
1413709 TATATATATATAATTAT
1 TATAT-TATGTAA-TAT
1413726 TATATTATGTAATAT
1 TATATTATGTAATAT
1413741 TATATTATGT-ATAT
1 TATATTATGTAATAT
1413755 TAT
1 TAT
1413758 GATTTATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 7 0.23
15 13 0.42
16 6 0.19
17 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (15 bp):
TATATTATGTAATAT
Found at i:1413753 original size:24 final size:25
Alignment explanation
Indices: 1413712--1413758 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
1413702 GCTATAGTAT
1413712 ATATATATAATTATTATATTATGTA
1 ATATATATAATTATTATATTATGTA
1413737 ATAT-TAT-ATTATGTATATTATG
1 ATATATATAATTAT-TATATTATG
1413759 ATTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
ATATATATAATTATTATATTATGTA
Found at i:1415034 original size:45 final size:45
Alignment explanation
Indices: 1414965--1415057 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
1414955 CACCATAAAA
* *
1414965 TATGATGCAGAAGTTGGTTCTAGAGACTCACTAGAAACCTACCTT
1 TATGATGCAGAAGTCGGTTCTAGAGACTCACCAGAAACCTACCTT
* * *
1415010 TATGATGCAGAAGTCGGTTTTAGAGACTCACCAGAGACCTACTTT
1 TATGATGCAGAAGTCGGTTCTAGAGACTCACCAGAAACCTACCTT
1415055 TAT
1 TAT
1415058 CTCGACCTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (45 bp):
TATGATGCAGAAGTCGGTTCTAGAGACTCACCAGAAACCTACCTT
Found at i:1418175 original size:19 final size:18
Alignment explanation
Indices: 1418151--1418186 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1418141 TAATTAAAAA
*
1418151 TTAATTAATCATAGTTTAT
1 TTAATTAAACAT-GTTTAT
1418170 TTAATTAAACATGTTTA
1 TTAATTAAACATGTTTA
1418187 ACTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TTAATTAAACATGTTTAT
Found at i:1418994 original size:50 final size:49
Alignment explanation
Indices: 1418823--1418992 Score: 187
Period size: 50 Copynumber: 3.4 Consensus size: 49
1418813 AGTTGTTACA
* * * * * * *
1418823 GGGTTTCTCGTCACGACGTGACATATTGTCCTGACCTCGTCGTGATGATG
1 GGGTTCCTCGTCACGACGTGACAAATTGTCC-CACCTCATCATGACGACG
* * * * *
1418873 GGGTTCCTTGTCACAACGTGACAAACTGTCCCGACCTCATCTTGGCGACG
1 GGGTTCCTCGTCACGACGTGACAAATTGTCCC-ACCTCATCATGACGACG
*
1418923 GGGTTCCTCGTCACGACGTGGCAAATTGTCCCACCCTCATCATGACGACG
1 GGGTTCCTCGTCACGACGTGACAAATTGTCCCA-CCTCATCATGACGACG
*
1418973 GGGTTCCTAGTCACGACGTG
1 GGGTTCCTCGTCACGACGTG
1418993 GCCTGGAACT
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.01
50 99 0.99
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (49 bp):
GGGTTCCTCGTCACGACGTGACAAATTGTCCCACCTCATCATGACGACG
Found at i:1423392 original size:43 final size:43
Alignment explanation
Indices: 1423344--1423430 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1423334 AAGCAAAACA
*
1423344 AATTTTAAATAAATTCAGAATGAAAGATTGCAAGCCTATAGCC
1 AATTTTAAATAAATTCAGAATGAAAGATTACAAGCCTATAGCC
* *
1423387 AATTTTAAATAAATTCAGAATGAAAGATTACAAGCTTGTAGCC
1 AATTTTAAATAAATTCAGAATGAAAGATTACAAGCCTATAGCC
1423430 A
1 A
1423431 CATCAGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.29
Consensus pattern (43 bp):
AATTTTAAATAAATTCAGAATGAAAGATTACAAGCCTATAGCC
Found at i:1430861 original size:14 final size:15
Alignment explanation
Indices: 1430832--1430864 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1430822 AAATTAATAA
*
1430832 TTTAATTCAAATATT
1 TTTAATACAAATATT
1430847 TTTAATACAAA-ATT
1 TTTAATACAAATATT
1430861 TTTA
1 TTTA
1430865 GTTTTGTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATACAAATATT
Found at i:1431499 original size:29 final size:30
Alignment explanation
Indices: 1431435--1431500 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
1431425 ATTTGAACTT
* *
1431435 ATTTGATTCTTTTTAATAGTATAAGGACTA
1 ATTTGATTCTATTTAATAATATAAGGACTA
* *
1431465 AATTGATTC-ATTTAATAATATAAGGACTC
1 ATTTGATTCTATTTAATAATATAAGGACTA
1431494 ATTTGAT
1 ATTTGAT
1431501 CCAAACCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (30 bp):
ATTTGATTCTATTTAATAATATAAGGACTA
Found at i:1432215 original size:22 final size:23
Alignment explanation
Indices: 1432190--1432233 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1432180 TTAAAAATAA
*
1432190 AAAAATAAAATAAAAT-TATTTT
1 AAAAATAAAAAAAAATATATTTT
*
1432212 AAAATTAAAAAAAAATATATTT
1 AAAAATAAAAAAAAATATATTT
1432234 ATTATATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAAATAAAAAAAAATATATTTT
Found at i:1432505 original size:18 final size:17
Alignment explanation
Indices: 1432452--1432511 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
1432442 CGTAGTGTTT
*
1432452 GTGAGCTCGC-GATCTTG
1 GTGAGCTCGCACAT-TTG
1432469 GTGAGCTCGCACATTTG
1 GTGAGCTCGCACATTTG
*
1432486 GTGAGCTCGTACATTTTG
1 GTGAGCTCGCACA-TTTG
1432504 GTGAGCTC
1 GTGAGCTC
1432512 ATAGTTCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
17 25 0.64
18 14 0.36
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.32
Consensus pattern (17 bp):
GTGAGCTCGCACATTTG
Found at i:1432522 original size:18 final size:18
Alignment explanation
Indices: 1432466--1432528 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
1432456 GCTCGCGATC
**
1432466 TTGGTGAGCTCGCACA-T
1 TTGGTGAGCTCATACATT
*
1432483 TTGGTGAGCTCGTACATT
1 TTGGTGAGCTCATACATT
*
1432501 TTGGTGAGCTCATA-GTT
1 TTGGTGAGCTCATACATT
1432518 CTTGGTGAGCT
1 -TTGGTGAGCT
1432529 GTTCTGGTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.16, C:0.17, G:0.30, T:0.37
Consensus pattern (18 bp):
TTGGTGAGCTCATACATT
Found at i:1435062 original size:27 final size:26
Alignment explanation
Indices: 1435012--1435191 Score: 193
Period size: 27 Copynumber: 6.7 Consensus size: 26
1435002 ACACCGAGAC
*
1435012 CCCCATAGGGT-AAATGACCGAAATT
1 CCCCATAGGGTAAAATGACCGAAATA
**
1435037 CTCCCATAGGGTAAAATGACATAAATA
1 C-CCCATAGGGTAAAATGACCGAAATA
* *
1435064 CCCCCATAAGGTAAAATGACCAAAATA
1 -CCCCATAGGGTAAAATGACCGAAATA
*
1435091 TCCCCATAGGATAAAATGACCGAAATA
1 -CCCCATAGGGTAAAATGACCGAAATA
*
1435118 CCCTAATAGGGTAAAATGACCGAAATA
1 CCC-CATAGGGTAAAATGACCGAAATA
* **
1435145 CCCCCATAGGGTAAAATGACTGTTATA
1 -CCCCATAGGGTAAAATGACCGAAATA
1435172 CCCC-TAGGAGATAAAATGAC
1 CCCCATAGG-G-TAAAATGAC
1435192 TGTTATACCC
Statistics
Matches: 132, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
25 5 0.04
26 18 0.14
27 105 0.80
28 4 0.03
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (26 bp):
CCCCATAGGGTAAAATGACCGAAATA
Found at i:1435099 original size:54 final size:54
Alignment explanation
Indices: 1435010--1435164 Score: 215
Period size: 54 Copynumber: 2.9 Consensus size: 54
1435000 CTACACCGAG
*
1435010 ACCCCCATAGGGT-AAATGACCGAAAT-TCTCCCATAGGGTAAAATGACATAAAT
1 ACCCCCATAGGGTAAAATGACCGAAATATC-CCCATAGGGTAAAATGACAGAAAT
* * * *
1435063 ACCCCCATAAGGTAAAATGACCAAAATATCCCCATAGGATAAAATGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAATATCCCCATAGGGTAAAATGACAGAAAT
** *
1435117 ACCCTAATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGAC
1 ACCCCCATAGGGTAAAATGACCGAAATATCCCCATAGGGTAAAATGAC
1435165 TGTTATACCC
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 12 0.13
54 75 0.84
55 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (54 bp):
ACCCCCATAGGGTAAAATGACCGAAATATCCCCATAGGGTAAAATGACAGAAAT
Found at i:1435202 original size:81 final size:81
Alignment explanation
Indices: 1435012--1435164 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 81
1435002 ACACCGAGAC
* * * *
1435012 CCCCATAGGGT-AAATGACCGAAATTCTCC-CATAGGGTAAAATGACATAAATACCCCCATAAGG
1 CCCCATAGGATAAAATGACCGAAATAC-CCTAATAGGGTAAAATGACAGAAATACCCCCATAAGG
1435075 TAAAATGACCAAAATAT
65 TAAAATGACCAAAATAT
* *
1435092 CCCCATAGGATAAAATGACCGAAATACCCTAATAGGGTAAAATGACCGAAATACCCCCATAGGGT
1 CCCCATAGGATAAAATGACCGAAATACCCTAATAGGGTAAAATGACAGAAATACCCCCATAAGGT
1435157 AAAATGAC
66 AAAATGAC
1435165 TGTTATACCC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 12 0.18
81 53 0.82
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.18
Consensus pattern (81 bp):
CCCCATAGGATAAAATGACCGAAATACCCTAATAGGGTAAAATGACAGAAATACCCCCATAAGGT
AAAATGACCAAAATAT
Found at i:1435231 original size:27 final size:27
Alignment explanation
Indices: 1435156--1435224 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
1435146 CCCCATAGGG
*
1435156 TAAAATGACTGTTATACCCCTAGGAGA
1 TAAAATGACTGTTATACCCTTAGGAGA
1435183 TAAAATGACTGTTATACCCTTAGGAGA
1 TAAAATGACTGTTATACCCTTAGGAGA
*
1435210 TGAAATGACTGTTAT
1 TAAAATGACTGTTAT
1435225 GGCCTTATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (27 bp):
TAAAATGACTGTTATACCCTTAGGAGA
Found at i:1440580 original size:17 final size:16
Alignment explanation
Indices: 1440560--1440606 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
1440550 GTTAGCGATC
1440560 TTGGTGAGCTCACATAT
1 TTGGTGAGCTCACAT-T
*
1440577 TTGGTGAGCTTGTACATT
1 TTGGTGAGC-T-CACATT
1440595 TTGGTGAGCTCA
1 TTGGTGAGCTCA
1440607 TAGTTCTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 11 0.42
19 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (16 bp):
TTGGTGAGCTCACATT
Found at i:1448332 original size:4 final size:4
Alignment explanation
Indices: 1448323--1448445 Score: 237
Period size: 4 Copynumber: 30.8 Consensus size: 4
1448313 ATCACAAATA
1448323 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1448371 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1448419 ATAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1448446 AACACAATAA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 117 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1451797 original size:91 final size:91
Alignment explanation
Indices: 1451642--1451851 Score: 269
Period size: 91 Copynumber: 2.3 Consensus size: 91
1451632 TAAAATTCAT
* * * * * * * *
1451642 ATATGAGCAGACACCGTTTCGAGGGTACTACTTGCTAAGTTAATAGCAGAGCCGTTGTTAGCCTT
1 ATATGAGCACACACCCTTTTGAGGGTACTACTCGATAAGTTAATAGCAAAGCCGATGCTAGCCTT
* *
1451707 TTAAGGCAGTTAGCCAAATTTTAATA
66 CTAAGGCACTTAGCCAAATTTTAATA
* *
1451733 ATATGAGCACACACCCTTTTGAGGGTACTTCTCGATAAGTTAATAGCAAAGCGGATGCTAGCCTT
1 ATATGAGCACACACCCTTTTGAGGGTACTACTCGATAAGTTAATAGCAAAGCCGATGCTAGCCTT
* *
1451798 CTAAGTCACTTAGCCAAATTTTAATT
66 CTAAGGCACTTAGCCAAATTTTAATA
* *
1451824 ATTTGAGCACACATCC-TTTGAGGGTACT
1 ATATGAGCACACACCCTTTTGAGGGTACT
1451852 GCATGCTAGG
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 12 0.12
91 91 0.88
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (91 bp):
ATATGAGCACACACCCTTTTGAGGGTACTACTCGATAAGTTAATAGCAAAGCCGATGCTAGCCTT
CTAAGGCACTTAGCCAAATTTTAATA
Found at i:1451899 original size:90 final size:90
Alignment explanation
Indices: 1451716--1451959 Score: 244
Period size: 90 Copynumber: 2.7 Consensus size: 90
1451706 TTTAAGGCAG
* * * * * **
1451716 TTAGCC-AAATTTTAATAATATGAGCACACACCCTTTTGAGGGTACTTCTCGATAAGTTAATAGC
1 TTAGCCAAAATTTTAATTATCTGAGCACACACCC-TTT-AGGGTACTGCACGATAGGTTAATAAT
* * * * **
1451780 A-AAGCG-GATGCTAGCCTTCTAAGTCAC
64 AGAATCGCCA--ATAACCTTCTAAGGAAC
* * * *
1451807 TTAGCC-AAATTTTAATTATTTGAGCACACATCCTTTGAGGGTACTGCATGCTAGGTTAATAATA
1 TTAGCCAAAATTTTAATTATCTGAGCACACACCCTTT-AGGGTACTGCACGATAGGTTAATAATA
1451871 GAATCGCCAATAACCTTCTAAGGAAC
65 GAATCGCCAATAACCTTCTAAGGAAC
1451897 TTAGCCAATAAATTTTAATTATCTGAGCACACACCCTTTAGGGTACTGCACGATAGGTTAATA
1 TTAGCC-A-AAATTTTAATTATCTGAGCACACACCCTTTAGGGTACTGCACGATAGGTTAATA
1451960 CGGATATGAT
Statistics
Matches: 128, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
90 43 0.34
91 34 0.27
92 23 0.18
93 28 0.22
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (90 bp):
TTAGCCAAAATTTTAATTATCTGAGCACACACCCTTTAGGGTACTGCACGATAGGTTAATAATAG
AATCGCCAATAACCTTCTAAGGAAC
Found at i:1452712 original size:20 final size:20
Alignment explanation
Indices: 1452687--1452729 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1452677 AATTTAGTTT
1452687 AAATATAAAATT-AAATATAA
1 AAATAT-AAATTCAAATATAA
*
1452707 AAATATCAATTCAAATATAA
1 AAATATAAATTCAAATATAA
1452727 AAA
1 AAA
1452730 ATTATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATATAAATTCAAATATAA
Found at i:1455428 original size:26 final size:25
Alignment explanation
Indices: 1455399--1455472 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 25
1455389 TCTCATTATT
1455399 ATTTTACCACTAGTAAAATTTTGATG
1 ATTTTACC-CTAGTAAAATTTTGATG
*
1455425 ATTTTACCCTTGATAAAAATTTTGATG
1 ATTTTACCCTAG-T-AAAATTTTGATG
*
1455452 ATTTTACCTCTAGAAAAATTT
1 ATTTTACC-CTAGTAAAATTT
1455473 CGAGAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 3 0.07
26 16 0.38
27 20 0.48
28 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTGATG
Found at i:1461164 original size:21 final size:21
Alignment explanation
Indices: 1461140--1461195 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1461130 ATGTGGCTTC
*
1461140 TGGTCAAAATTATTATGGATA-
1 TGGTCAAAATTATT-TGGAAAT
*
1461161 TGGTCAAAA-TAGTTTTGAAAT
1 TGGTCAAAATTA-TTTGGAAAT
1461182 TGGTCAAAATTATT
1 TGGTCAAAATTATT
1461196 GTGATGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (21 bp):
TGGTCAAAATTATTTGGAAAT
Found at i:1462242 original size:15 final size:15
Alignment explanation
Indices: 1462222--1462250 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1462212 TATCGTGTTA
1462222 AATAAAGTTGCTATG
1 AATAAAGTTGCTATG
1462237 AATAAAGTTGCTAT
1 AATAAAGTTGCTAT
1462251 AAGTGATGTT
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:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
AATAAAGTTGCTATG
Found at i:1466868 original size:15 final size:15
Alignment explanation
Indices: 1466848--1466876 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1466838 TATCGTGTTA
1466848 AATAAAGTTGCTATG
1 AATAAAGTTGCTATG
1466863 AATAAAGTTGCTAT
1 AATAAAGTTGCTAT
1466877 AAGTGATGTT
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:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
AATAAAGTTGCTATG
Found at i:1475971 original size:18 final size:18
Alignment explanation
Indices: 1475933--1475968 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1475923 TTATTATTTT
*
1475933 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
1475951 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
1475969 TAATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:1475988 original size:22 final size:22
Alignment explanation
Indices: 1475961--1476006 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1475951 TAAAATTTAA
1475961 ATATTAAATAAT-TTAATAAATT
1 ATATT-AATAATATTAATAAATT
* *
1475983 ATATTAATTATATTAATAATTT
1 ATATTAATAATATTAATAAATT
1476005 AT
1 AT
1476007 TATATGACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATAATATTAATAAATT
Found at i:1480458 original size:42 final size:42
Alignment explanation
Indices: 1480399--1480480 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
1480389 AATTTAAACG
*
1480399 AGCAGATAAGAAAGAATCTGCTTTTACAAAGTAACAGACACA
1 AGCAGATAAGAAAGAATCTGCTTTTACAAAGTAAAAGACACA
* *
1480441 AGCAGATAAGAAGGAATCTGTTTTTACAAAGTAAAAGACA
1 AGCAGATAAGAAAGAATCTGCTTTTACAAAGTAAAAGACA
1480481 ATAATATACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (42 bp):
AGCAGATAAGAAAGAATCTGCTTTTACAAAGTAAAAGACACA
Found at i:1485959 original size:15 final size:15
Alignment explanation
Indices: 1485939--1485978 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1485929 TATAAAAGTA
1485939 TGTTATGTATATTAC
1 TGTTATGTATATTAC
*
1485954 TGTTATGTTTATTAC
1 TGTTATGTATATTAC
*
1485969 TATTATGTAT
1 TGTTATGTAT
1485979 GTTGTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.57
Consensus pattern (15 bp):
TGTTATGTATATTAC
Found at i:1486078 original size:9 final size:9
Alignment explanation
Indices: 1485972--1486088 Score: 55
Period size: 9 Copynumber: 14.1 Consensus size: 9
1485962 TTATTACTAT
1485972 TATG-TATG
1 TATGTTATG
1485980 T-TGTTAT-
1 TATGTTATG
1485987 TATGTT-TG
1 TATGTTATG
*
1485995 TTAT-ATATG
1 -TATGTTATG
*
1486004 TATGTTTTG
1 TATGTTATG
1486013 TATGTTATG
1 TATGTTATG
**
1486022 -A-AATATG
1 TATGTTATG
1486029 CT-TGTTATG
1 -TATGTTATG
1486038 TATGTCTA--
1 TATGT-TATG
1486046 T-TGTTAT-
1 TATGTTATG
1486053 TATGTT-TG
1 TATGTTATG
1486061 TTATG-TATG
1 -TATGTTATG
1486070 TATGTTATG
1 TATGTTATG
*
1486079 TATGTCATG
1 TATGTTATG
1486088 T
1 T
1486089 TTATTACTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 33
0.66 0.07 0.26
Matches are distributed among these distances:
6 2 0.02
7 13 0.16
8 24 0.29
9 42 0.51
10 2 0.02
ACGTcount: A:0.21, C:0.03, G:0.20, T:0.56
Consensus pattern (9 bp):
TATGTTATG
Found at i:1486168 original size:33 final size:33
Alignment explanation
Indices: 1486090--1486159 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1486080 ATGTCATGTT
*
1486090 TATTACTATTATGTATGTAACTGTTATATGGTA
1 TATTACTTTTATGTATGTAACTGTTATATGGTA
* * *
1486123 TATTACTTTTATGTATGTGATTGTTATGTGGTA
1 TATTACTTTTATGTATGTAACTGTTATATGGTA
1486156 TATT
1 TATT
1486160 GTTGTTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (33 bp):
TATTACTTTTATGTATGTAACTGTTATATGGTA
Found at i:1486181 original size:33 final size:34
Alignment explanation
Indices: 1486110--1486184 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
1486100 ATGTATGTAA
* * *
1486110 CTGTTATATGGTATATTACTTTTATGTATGTGAT
1 CTGTTATGTGGTATATTACTTTTATGAATATGAT
*
1486144 -TGTTATGTGGTATATT-GTTGTTATGAATATG-T
1 CTGTTATGTGGTATATTACTT-TTATGAATATGAT
1486176 CTGTTATGT
1 CTGTTATGT
1486185 ATGTTATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.09
33 32 0.91
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.53
Consensus pattern (34 bp):
CTGTTATGTGGTATATTACTTTTATGAATATGAT
Found at i:1486273 original size:13 final size:13
Alignment explanation
Indices: 1486255--1486279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1486245 TGTTTAAAAT
1486255 ATGTATGTATATC
1 ATGTATGTATATC
1486268 ATGTATGTATAT
1 ATGTATGTATAT
1486280 TACAGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTATGTATATC
Found at i:1492830 original size:27 final size:27
Alignment explanation
Indices: 1492800--1492876 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 27
1492790 CATATGACAA
*
1492800 ATGGTTTTATTTTGTTGGATCATTTTG
1 ATGGTTTTATTTTGTTGGATCATTCTG
*
1492827 ATGGATGATTTAATTTTGTTGAATCATTCTG
1 ATGG-T--TTT-ATTTTGTTGGATCATTCTG
* *
1492858 ATGGTTGTATTTTGATGGA
1 ATGGTTTTATTTTGTTGGA
1492877 AAATTTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 13 0.32
28 3 0.07
30 4 0.10
31 21 0.51
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.52
Consensus pattern (27 bp):
ATGGTTTTATTTTGTTGGATCATTCTG
Found at i:1494067 original size:29 final size:29
Alignment explanation
Indices: 1494021--1494077 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1494011 TAGTGGATAG
*
1494021 AAAAAAATATTTAGGTACCAATCTGAGAT
1 AAAAAAATATTTAAGTACCAATCTGAGAT
* *
1494050 AAAAAAA-ATTATAAGTACTAATTTGAGA
1 AAAAAAATATT-TAAGTACCAATCTGAGA
1494078 GATATAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (29 bp):
AAAAAAATATTTAAGTACCAATCTGAGAT
Found at i:1495251 original size:12 final size:12
Alignment explanation
Indices: 1495228--1495261 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1495218 AATTTTTAGA
*
1495228 AAATGAATATGG
1 AAATGAAAATGG
*
1495240 AAATGGAAATGG
1 AAATGAAAATGG
1495252 AAATGAAAAT
1 AAATGAAAAT
1495262 ATGTGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:1502516 original size:27 final size:26
Alignment explanation
Indices: 1502466--1502537 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
1502456 TTGCGTGATT
* *
1502466 TCCATGATTGCTATCTAGGAGGACTA
1 TCCATGTTTACTATCTAGGAGGACTA
* * * *
1502492 CTCTATTTTTACTATCTTGGTGGACTA
1 -TCCATGTTTACTATCTAGGAGGACTA
1502519 TCCATGTTTACTATACTAG
1 TCCATGTTTACTAT-CTAG
1502538 CGGACTACCT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (26 bp):
TCCATGTTTACTATCTAGGAGGACTA
Found at i:1502792 original size:67 final size:67
Alignment explanation
Indices: 1502686--1503373 Score: 730
Period size: 67 Copynumber: 10.3 Consensus size: 67
1502676 CTACATGTTC
* * * * * *
1502686 CCATAGCCAAACTATGGCCTTACACATCATAACCC-ATGTTTAATGACCTGTCAAACTCTCTATG
1 CCATAGCCGAGCTATGGTCTTACACATCAT-ACCCTATGTTTAATGTCCTGGCGAACTCTCTATG
*
1502750 TTG
65 CTG
* ** * *
1502753 CCATAACCGAGCTATGGTCTTACACATCATACCCTATGTTTAATGTCCTGGCGGGCTTTCTATGT
1 CCATAGCCGAGCTATGGTCTTACACATCATACCCTATGTTTAATGTCCTGGCGAACTCTCTATGC
1502818 TG
66 TG
* *
1502820 CCATAGCCGAGCTATGGTCTTA-AGCATCATACCCTATGTTTAATGTCTTGGC-AGACTCTCAAT
1 CCATAGCCGAGCTATGGTCTTACA-CATCATACCCTATGTTTAATGTCCTGGCGA-ACTCTCTAT
*
1502883 GTTG
64 GCTG
* * * * *
1502887 GCGTAGCCGAGCTATGGTCTTACACATCATACCCCATGTTTAATGTCCTGGCGAACTCTCCATGT
1 CCATAGCCGAGCTATGGTCTTACACATCATACCCTATGTTTAATGTCCTGGCGAACTCTCTATGC
1502952 TG
66 TG
* * *
1502954 CCATAGCTGAGTTATGGTCTTACACATCATACCAC-ATGTTTAATGTCCTGGCGAACTCTCTATA
1 CCATAGCCGAGCTATGGTCTTACACATCATACC-CTATGTTTAATGTCCTGGCGAACTCTCTATG
1503018 CTG
65 CTG
* * * * * *
1503021 CCATAGTCGAACTATAGTATTACACATCATACACC-ATGTCTAATGTCCTAGCGAACTCTCTATG
1 CCATAGCCGAGCTATGGTCTTACACATCATAC-CCTATGTTTAATGTCCTGGCGAACTCTCTATG
*
1503085 TTG
65 CTG
* * * * * * * * * *
1503088 TCATAGACAAGATCTGGTCTTACACGTCATACCCCATGTTTAATGTCCTGACGAACTCCCTATAC
1 CCATAGCCGAGCTATGGTCTTACACATCATACCCTATGTTTAATGTCCTGGCGAACTCTCTATGC
1503153 T-
66 TG
* * * **
1503154 CCATAGTCGAGCTATGGTCTTACACATCATA-CCTCATGTTTAATGTCCTAGTGGGCTCTCTATG
1 CCATAGCCGAGCTATGGTCTTACACATCATACCCT-ATGTTTAATGTCCTGGCGAACTCTCTATG
1503218 CTG
65 CTG
* * * * **
1503221 TCATAGCCAAGCTATGGTCTTACACATCATA-CCTCATGTTTAATGTCCTAGTGGGCTCTCTATG
1 CCATAGCCGAGCTATGGTCTTACACATCATACCCT-ATGTTTAATGTCCTGGCGAACTCTCTATG
1503285 CTG
65 CTG
* * *
1503288 TCATAGCCAAGCTATGGTCTTACACATCATA-CCTCATGTTTAATGTCCTAGC-AGACTCTCTAT
1 CCATAGCCGAGCTATGGTCTTACACATCATACCCT-ATGTTTAATGTCCTGGCGA-ACTCTCTAT
1503351 GCTG
64 GCTG
*
1503355 CCATAGCCAAGCTATGGTC
1 CCATAGCCGAGCTATGGTC
1503374 ACCTATGTTT
Statistics
Matches: 536, Mismatches: 74, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
65 2 0.00
66 56 0.10
67 474 0.88
68 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (67 bp):
CCATAGCCGAGCTATGGTCTTACACATCATACCCTATGTTTAATGTCCTGGCGAACTCTCTATGC
TG
Found at i:1516204 original size:27 final size:27
Alignment explanation
Indices: 1516163--1516215 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1516153 TTAGAAATAG
*
1516163 GGGTTTTCAGAGTTGACTACGAGCTAA
1 GGGTTTACAGAGTTGACTACGAGCTAA
* *
1516190 GGGTTTACAGGGTTGACTGCGAGCTA
1 GGGTTTACAGAGTTGACTACGAGCTA
1516216 GCAAGGTGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (27 bp):
GGGTTTACAGAGTTGACTACGAGCTAA
Found at i:1526759 original size:106 final size:107
Alignment explanation
Indices: 1526646--1526860 Score: 423
Period size: 106 Copynumber: 2.0 Consensus size: 107
1526636 AAAATCAACT
1526646 TAATATTTTCTACAATAAATGATAAGTAGTTACCTACTTATTTATCTTATTCAACTCTTTTTTGT
1 TAATATTTTCTACAATAAATGATAAGTAGTTACCTACTTATTTATCTTATTCAACTCTTTTTTGT
1526711 TGAAAAATTATATTAAATAAAAATTAAAATGA-TATCAAACA
66 TGAAAAATTATATTAAATAAAAATTAAAATGATTATCAAACA
1526752 TAATATTTTCTACAATAAATGATAAGTAGTTACCTACTTATTTATCTTATTCAACTCTTTTTTGT
1 TAATATTTTCTACAATAAATGATAAGTAGTTACCTACTTATTTATCTTATTCAACTCTTTTTTGT
1526817 TGAAAAATTATATTAAATAAAAATTAAAATGATTATCAAACA
66 TGAAAAATTATATTAAATAAAAATTAAAATGATTATCAAACA
1526859 TA
1 TA
1526861 TTTAAAATAT
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 97 0.90
107 11 0.10
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (107 bp):
TAATATTTTCTACAATAAATGATAAGTAGTTACCTACTTATTTATCTTATTCAACTCTTTTTTGT
TGAAAAATTATATTAAATAAAAATTAAAATGATTATCAAACA
Found at i:1529972 original size:43 final size:43
Alignment explanation
Indices: 1529924--1530106 Score: 298
Period size: 43 Copynumber: 4.3 Consensus size: 43
1529914 GGAAAACTAT
* * *
1529924 TAGGATATTATC-CTTTAGCAATTTTATTTC-AATTGCGATATTG
1 TAGGATATTATCTC-TTAGCAATTTGATTCCTAA-TGGGATATTG
1529967 TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTG
1 TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTG
1530010 TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTG
1 TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTG
*
1530053 TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTA
1 TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTG
1530096 TAGGATATTAT
1 TAGGATATTAT
1530107 TACAGGATAT
Statistics
Matches: 134, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
43 131 0.98
44 3 0.02
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (43 bp):
TAGGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTG
Found at i:1530103 original size:10 final size:10
Alignment explanation
Indices: 1530088--1530129 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
1530078 ATTCCTAATG
1530088 GGATATTATA
1 GGATATTATA
1530098 GGATATTATTACA
1 GGATATTA-T--A
1530111 GGATATTATA
1 GGATATTATA
1530121 GGATATTAT
1 GGATATTAT
1530130 TACAGAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 18 0.62
11 1 0.03
12 1 0.03
13 9 0.31
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (10 bp):
GGATATTATA
Found at i:1530113 original size:13 final size:13
Alignment explanation
Indices: 1530091--1530142 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
1530081 CCTAATGGGA
*
1530091 TATTATAGGATAT
1 TATTACAGGATAT
1530104 TATTACAGGATAT
1 TATTACAGGATAT
1530117 TA-T--AGGATAT
1 TATTACAGGATAT
*
1530127 TATTACAGAATAT
1 TATTACAGGATAT
1530140 TAT
1 TAT
1530143 CTTTTAGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
12 1 0.03
13 23 0.68
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (13 bp):
TATTACAGGATAT
Found at i:1530118 original size:23 final size:23
Alignment explanation
Indices: 1530088--1530142 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1530078 ATTCCTAATG
1530088 GGATATTATAGGATATTATTACA
1 GGATATTATAGGATATTATTACA
1530111 GGATATTATAGGATATTATTACA
1 GGATATTATAGGATATTATTACA
*
1530134 GAATATTAT
1 GGATATTAT
1530143 CTTTTAGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (23 bp):
GGATATTATAGGATATTATTACA
Found at i:1531312 original size:21 final size:21
Alignment explanation
Indices: 1531286--1531328 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1531276 CACCACTGAG
*
1531286 TATATATTACTCAGTGTATGA
1 TATATATTACTCAATGTATGA
1531307 TATATATTACTCAATGTATGA
1 TATATATTACTCAATGTATGA
1531328 T
1 T
1531329 TTTGTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (21 bp):
TATATATTACTCAATGTATGA
Done.