Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 51
Found at i:1090841 original size:30 final size:30
Alignment explanation
Indices: 1090805--1090885 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
1090795 TTTCGGAAAA
**
1090805 TGAATTACTGAAATTTGAATTATTGAAATT
1 TGAATTACTGAAAAATGAATTATTGAAATT
*
1090835 TGAATTACTGAAAAATGAATTATTGGAATT
1 TGAATTACTGAAAAATGAATTATTGAAATT
*
1090865 TGAATT-CTGGAAAATGAATTA
1 TGAATTACTGAAAAATGAATTA
1090886 CATTTCTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 14 0.30
30 33 0.70
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (30 bp):
TGAATTACTGAAAAATGAATTATTGAAATT
Found at i:1090892 original size:20 final size:20
Alignment explanation
Indices: 1090869--1090918 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1090859 GGAATTTGAA
1090869 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1090889 TTCTGAAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1090909 TTCTGGAAAA
1 TTCTGGAAAA
1090919 CATCTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1091111 original size:49 final size:50
Alignment explanation
Indices: 1091014--1091112 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
1091004 TACAAATATT
*
1091014 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
1091064 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
1091113 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:1091287 original size:28 final size:29
Alignment explanation
Indices: 1091247--1091426 Score: 116
Period size: 29 Copynumber: 6.3 Consensus size: 29
1091237 CTTTACGAAA
1091247 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTA-TTAAATATATAAATAATTATTAT
1091276 -TCATTATTAAATATATAAA-AATTATTAT
1 AT-ATTATTAAATATATAAATAATTATTAT
* *
1091304 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAATA-ATTAT-TAT
* * *
1091333 ATATTATTATA-ATATAATTGATTATTTTAT
1 ATATTATTAAATATATAAATAATTA--TTAT
* *
1091363 ATAATATTAAAAATAT-AAT-ATTA-TAT
1 ATATTATTAAATATATAAATAATTATTAT
*
1091389 -TATTA-TAAATATTAATAAATATATT-TTAA
1 ATATTATTAAATA-T-ATAAATA-ATTATTAT
1091418 ATATT-TTAA
1 ATATTATTAA
1091427 TAATTAATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 35
0.71 0.08 0.21
Matches are distributed among these distances:
24 5 0.04
25 5 0.04
26 5 0.04
27 11 0.09
28 33 0.28
29 36 0.30
30 21 0.17
31 4 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
ATATTATTAAATATATAAATAATTATTAT
Found at i:1091309 original size:25 final size:28
Alignment explanation
Indices: 1091249--1091323 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
1091239 TTACGAAAAT
1091249 ATTATTTAAATATATAAATAATATTATTC
1 ATTA-TTAAATATATAAATAATATTATTC
1091278 ATTATTAAATATATAAA-AATTATTATAT-
1 ATTATTAAATATATAAATAA-TATTAT-TC
*
1091306 ATTATTAAA-ATAAAAATA
1 ATTATTAAATATATAAATA
1091324 TAATATCTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 8 0.19
28 29 0.69
29 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTATTAAATATATAAATAATATTATTC
Found at i:1091387 original size:22 final size:23
Alignment explanation
Indices: 1091362--1091405 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1091352 GATTATTTTA
1091362 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
1091384 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
1091406 AATATATTTT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:1091410 original size:22 final size:22
Alignment explanation
Indices: 1091366--1091422 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1091356 ATTTTATATA
* *
1091366 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
1091387 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
1091409 ATATTTTAAATATT
1 ATATTATAAATATT
1091423 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:1091421 original size:52 final size:51
Alignment explanation
Indices: 1091302--1091422 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
1091292 AAAAATTATT
**
1091302 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
1091353 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
1091407 ATATATTTTAAATATT
1 ATATATTTTAAATATT
1091423 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:1091665 original size:42 final size:42
Alignment explanation
Indices: 1091611--1091722 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
1091601 ATGAATTACA
*
1091611 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
* *
1091653 TTTCGGAAAACGAATTACGTGAAACAAACACGGAAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
* *
1091695 TTCCAGAAAACGAATTACATGAAACAAA
1 TTCCGGAAAACGAATTACGTGAAACAAA
1091723 TATGAGATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
Found at i:1092109 original size:18 final size:19
Alignment explanation
Indices: 1092088--1092123 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1092078 ATATGTTTTT
1092088 AAATTATTA-AAAATATAA
1 AAATTATTATAAAATATAA
1092106 AAATTATTATAAAATATA
1 AAATTATTATAAAATATA
1092124 CTATTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTATTATAAAATATAA
Found at i:1098367 original size:166 final size:167
Alignment explanation
Indices: 1098166--1098490 Score: 607
Period size: 166 Copynumber: 2.0 Consensus size: 167
1098156 AACACAATAA
1098166 TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1 TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1098231 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
66 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
*
1098296 CCAAAAGTTAAAGTACACCCCAAGAGAATAAATTCTT
131 CCAAAAGCTAAAGTACACCCCAAGAGAATAAATTCTT
* * *
1098333 TTTAACGTGGAAAACTC-CCAAATGGAGAAAAACCACAGGCGTTGTCAAAAGATAACCAAGAGAA
1 TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1098397 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
66 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
1098462 CCAAAAGCTAAAGTACACCCCAAGAGAAT
131 CCAAAAGCTAAAGTACACCCCAAGAGAAT
1098491 TTTAAATTCT
Statistics
Matches: 154, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
166 138 0.90
167 16 0.10
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (167 bp):
TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
CCAAAAGCTAAAGTACACCCCAAGAGAATAAATTCTT
Found at i:1102082 original size:15 final size:15
Alignment explanation
Indices: 1102062--1102127 Score: 87
Period size: 15 Copynumber: 4.4 Consensus size: 15
1102052 TTTCGGAAAA
1102062 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
1102077 TGAATTATTGAAATT
1 TGAATTACTGAAATT
**
1102092 TGAATTACTGAAAAA
1 TGAATTACTGAAATT
* *
1102107 TGAATTATTGGAATT
1 TGAATTACTGAAATT
1102122 TGAATT
1 TGAATT
1102128 CTGGAAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:1102098 original size:30 final size:30
Alignment explanation
Indices: 1102062--1102142 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
1102052 TTTCGGAAAA
**
1102062 TGAATTACTGAAATTTGAATTATTGAAATT
1 TGAATTACTGAAAAATGAATTATTGAAATT
*
1102092 TGAATTACTGAAAAATGAATTATTGGAATT
1 TGAATTACTGAAAAATGAATTATTGAAATT
*
1102122 TGAATT-CTGGAAAATGAATTA
1 TGAATTACTGAAAAATGAATTA
1102143 CATTTCTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 14 0.30
30 33 0.70
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (30 bp):
TGAATTACTGAAAAATGAATTATTGAAATT
Found at i:1102149 original size:20 final size:20
Alignment explanation
Indices: 1102126--1102175 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1102116 GGAATTTGAA
1102126 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1102146 TTCTGAAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1102166 TTCTGGAAAA
1 TTCTGGAAAA
1102176 CATCTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1102368 original size:49 final size:50
Alignment explanation
Indices: 1102271--1102369 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
1102261 TACAAATATT
*
1102271 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
1102321 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
1102370 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:1102539 original size:29 final size:30
Alignment explanation
Indices: 1102504--1102575 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
1102494 CTTTACGAAA
*
1102504 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTATTTAAATATATAAAAAATTATTAT
1102533 -TCATTA-TTAAATATATAAAAAATTATTAT
1 AT-ATTATTTAAATATATAAAAAATTATTAT
*
1102562 ATATTATTAAAATA
1 ATATTATTTAAATA
1102576 AAAATATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 16 0.43
29 14 0.38
30 7 0.19
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATTATTTAAATATATAAAAAATTATTAT
Found at i:1102557 original size:26 final size:27
Alignment explanation
Indices: 1102505--1102671 Score: 94
Period size: 29 Copynumber: 5.9 Consensus size: 27
1102495 TTTACGAAAA
1102505 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
1102533 TCATTATTAAATATATAAAAAATTATTAT
1 T-ATTATTAAATATATAAATAA-TATTAT
*
1102562 ATATTATTAAA-ATAAAAATATAATATCT-T
1 -TATTATTAAATAT-ATAA-ATAATAT-TAT
** * *
1102591 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* * *
1102621 ATAATATTAAAAATAT-AATATTA-TAT
1 -TATTATTAAATATATAAATAATATTAT
1102647 TATTA-TAAATATTAATAAAT-ATATT
1 TATTATTAAATA-T-ATAAATAATATT
1102672 TTAAATATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
24 5 0.05
25 5 0.05
26 7 0.06
27 7 0.06
28 20 0.18
29 40 0.37
30 21 0.19
31 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:1102645 original size:22 final size:23
Alignment explanation
Indices: 1102620--1102663 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1102610 GATTATTTTA
1102620 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
1102642 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
1102664 AATATATTTT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:1102668 original size:22 final size:22
Alignment explanation
Indices: 1102624--1102680 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1102614 ATTTTATATA
* *
1102624 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
1102645 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
1102667 ATATTTTAAATATT
1 ATATTATAAATATT
1102681 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:1102679 original size:52 final size:51
Alignment explanation
Indices: 1102560--1102680 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
1102550 AAAAATTATT
**
1102560 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
1102611 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
1102665 ATATATTTTAAATATT
1 ATATATTTTAAATATT
1102681 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:1102923 original size:42 final size:42
Alignment explanation
Indices: 1102869--1102980 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
1102859 ATGAATTACA
*
1102869 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
* *
1102911 TTTCGGAAAACGAATTACGTGAAACAAACACGGAAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
* *
1102953 TTCCAGAAAACGAATTACATGAAACAAA
1 TTCCGGAAAACGAATTACGTGAAACAAA
1102981 TATGAGATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
Found at i:1103458 original size:51 final size:52
Alignment explanation
Indices: 1103342--1103458 Score: 129
Period size: 51 Copynumber: 2.3 Consensus size: 52
1103332 TAAAATATGT
*
1103342 TTTTAAATTATTAA-AAATATAAAAATATTATAAAATATACTATTTTAACCA
1 TTTTAAAATATTAATAAATATAAAAATATTATAAAATATACTATTTTAACCA
* **
1103393 -TTTAAAAT-TATAATAAATAATTATAAATA-TATAAAATATA-TA-TTTAATTA
1 TTTTAAAATAT-TAATAAAT-A-TAAAAATATTATAAAATATACTATTTTAACCA
1103443 TTTTAAAATATTAATA
1 TTTTAAAATATTAATA
1103459 TATTCAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
49 1 0.02
50 16 0.29
51 19 0.34
52 13 0.23
53 7 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (52 bp):
TTTTAAAATATTAATAAATATAAAAATATTATAAAATATACTATTTTAACCA
Found at i:1109458 original size:17 final size:16
Alignment explanation
Indices: 1109427--1109460 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1109417 CACGTGAGGA
1109427 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1109443 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1109460 T
1 T
1109461 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1115838 original size:19 final size:21
Alignment explanation
Indices: 1115801--1115843 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1115791 TAACTTTTTC
1115801 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1115821 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1115841 TTT
1 TTT
1115844 ACCTTTTCTC
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:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1115849 original size:19 final size:20
Alignment explanation
Indices: 1115800--1115849 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1115790 TTAACTTTTT
*
1115800 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
1115820 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
1115839 CTTTTACCTTT
1 CTTTTACCTTT
1115850 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:1119694 original size:17 final size:16
Alignment explanation
Indices: 1119663--1119696 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1119653 CACGTGAGGA
1119663 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1119679 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1119696 T
1 T
1119697 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1121555 original size:166 final size:167
Alignment explanation
Indices: 1121354--1121678 Score: 616
Period size: 166 Copynumber: 2.0 Consensus size: 167
1121344 AACACAATAA
1121354 TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1 TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1121419 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
66 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
*
1121484 CCAAAAGTTAAAGTACACCCCAAGAGAATAAATTCTT
131 CCAAAAGCTAAAGTACACCCCAAGAGAATAAATTCTT
* *
1121521 TTTAACGTGGAAAACTC-CCAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1 TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
1121585 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
66 AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
1121650 CCAAAAGCTAAAGTACACCCCAAGAGAAT
131 CCAAAAGCTAAAGTACACCCCAAGAGAAT
1121679 TTTAAATTCT
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
166 139 0.90
167 16 0.10
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (167 bp):
TTTAACGTGAAAAACTCTCAAAATGGAGAAAAACCACAGGCGTTGTCAAAAGACAACCAAGAGAA
AAAAATATTTACTATGTGGAAAATTATTACAACCACACTACAAAATATTTAACTCTCACACATGC
CCAAAAGCTAAAGTACACCCCAAGAGAATAAATTCTT
Found at i:1123777 original size:32 final size:30
Alignment explanation
Indices: 1123741--1123799 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1123731 GATTAGCACA
1123741 GAACCGG-TAAAGAACCGGCTGAAAACCGGGGT
1 GAACCGGCTAAA-AACCGGC--AAAACCGGGGT
*
1123773 GAACCGGCTGAAAACCGGCAAAACCGG
1 GAACCGGCTAAAAACCGGCAAAACCGG
1123800 TTTGAACTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
32 14 0.56
33 3 0.12
ACGTcount: A:0.36, C:0.25, G:0.32, T:0.07
Consensus pattern (30 bp):
GAACCGGCTAAAAACCGGCAAAACCGGGGT
Found at i:1124585 original size:12 final size:12
Alignment explanation
Indices: 1124562--1124594 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1124552 ATATAAAATC
1124562 CGGTTC-AACCG
1 CGGTTCGAACCG
1124573 CGGTTCGAACCG
1 CGGTTCGAACCG
1124585 CGGTT-GAACC
1 CGGTTCGAACC
1124595 AGTGAACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18
Consensus pattern (12 bp):
CGGTTCGAACCG
Found at i:1128982 original size:137 final size:138
Alignment explanation
Indices: 1128650--1129035 Score: 542
Period size: 137 Copynumber: 2.8 Consensus size: 138
1128640 GTAAATTTGG
* * * * *
1128650 AGATAACACGGTTCCTACGTGATGAGCAAATATGGTTATCTAAGGGTGACACTGCTCCTATGTGA
1 AGATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACTGCTCCTACGTGA
* ** * * *
1128715 TGAGGAGATCTGGTCGATGGATGACACTATTCCTATGTGATGAGGACGTCTTGGCCATCTTTAGG
66 TGAGGAGATCTGGTCGGTGGATGACACGGTTCCTATGTGATGAGGACGACTTGACCATATTTAGG
*
1128780 GATAATGT
131 GATAATGA
*
1128788 AGATAACATGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACA-TGGCTCCTACGTG
1 AGATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACT-GCTCCTACGTG
* * * * *
1128852 ATGAAGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGTATGAC-TGATCATATTTAG
65 ATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTATGTGATGAGGACGACTTGACCATATTTAG
*
1128916 GGATGATGA
130 GGATAATGA
* *
1128925 AGATAACACGGTTCCTATGTGATAAGGAAGTCTGGCTATCTAAGGGTGACACTGCTCCTACGTGA
1 AGATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACTGCTCCTACGTGA
* *
1128990 TGAGGAGATCTGGTTGGTAGATGACACGGTTCCTATGTGATGAGGA
66 TGAGGAGATCTGGTCGGTGGATGACACGGTTCCTATGTGATGAGGA
1129036 TGGCTAGCCA
Statistics
Matches: 219, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
137 119 0.54
138 100 0.46
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (138 bp):
AGATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACTGCTCCTACGTGA
TGAGGAGATCTGGTCGGTGGATGACACGGTTCCTATGTGATGAGGACGACTTGACCATATTTAGG
GATAATGA
Found at i:1129169 original size:66 final size:66
Alignment explanation
Indices: 1129063--1129256 Score: 280
Period size: 66 Copynumber: 2.9 Consensus size: 66
1129053 GGATAATTTG
**
1129063 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAACAAACTCAAAGATTTTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTTTT
1129128 A
66 A
* * *
1129129 TTTCAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACATACTCAAAGATTTTT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTTTT
*
1129194 G
66 A
* * ** * *
1129195 TTTCAAGAGAAATTGTCTTAAGCGAGACAAAATTTGTTTTGAGGGAAATAATCTCAAAGATT
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATT
1129257 AATTTTGTTT
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 113 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (66 bp):
TTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATTTTT
A
Found at i:1129195 original size:30 final size:30
Alignment explanation
Indices: 1129097--1129206 Score: 87
Period size: 30 Copynumber: 3.5 Consensus size: 30
1129087 AGACAAAACA
* *
1129097 TGTTTCAAGGGAAACAAACTCAAAGATTTT
1 TGTTTCAAGAGAAACATACTCAAAGATTTT
* * **
1129127 TATTTCAAGAGAAAC-TGTCTCAAGAGAAACAAAATT
1 TGTTTCAAGAGAAACAT-ACTCAA-AG-----ATTTT
*
1129163 TGTTTCAAGGGAAACATACTCAAAGATTTT
1 TGTTTCAAGAGAAACATACTCAAAGATTTT
1129193 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
1129207 TTGTCTTAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
30 34 0.57
31 2 0.03
35 2 0.03
36 21 0.35
37 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACATACTCAAAGATTTT
Found at i:1129554 original size:35 final size:37
Alignment explanation
Indices: 1129508--1129593 Score: 122
Period size: 35 Copynumber: 2.4 Consensus size: 37
1129498 TGCGATACAT
* *
1129508 TGTCTCAAGCGAGACAAAATTTGATTTTA-G-AAAAC
1 TGTCTCAAGCGAGAAAAAAATTGATTTTATGAAAAAC
*
1129543 TGTCTCAAGCGAGAAAAAAATTGTTTTTATGAAAAAC
1 TGTCTCAAGCGAGAAAAAAATTGATTTTATGAAAAAC
*
1129580 TGTCTCTAGCGAGA
1 TGTCTCAAGCGAGA
1129594 TGACACTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 26 0.58
36 1 0.02
37 18 0.40
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (37 bp):
TGTCTCAAGCGAGAAAAAAATTGATTTTATGAAAAAC
Found at i:1154440 original size:24 final size:24
Alignment explanation
Indices: 1154413--1154466 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1154403 GACTAAGAAG
* *
1154413 TGGCGTGAGAAAATACTTTTGCCA
1 TGGCATGAGAAAATACATTTGCCA
* *
1154437 TGGCATGAGAAAATGCATTTGCTA
1 TGGCATGAGAAAATACATTTGCCA
1154461 TGGCAT
1 TGGCAT
1154467 TTTCATGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCATGAGAAAATACATTTGCCA
Found at i:1172249 original size:2 final size:2
Alignment explanation
Indices: 1172242--1172267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1172232 TTTTCCATTT
1172242 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1172268 AATCCTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1172793 original size:3 final size:3
Alignment explanation
Indices: 1172785--1172846 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
1172775 TTTGAAGCCT
1172785 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1172832 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1172847 GGGTAGATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1186803 original size:301 final size:296
Alignment explanation
Indices: 1186216--1186811 Score: 1147
Period size: 301 Copynumber: 2.0 Consensus size: 296
1186206 CTCTCTTCCT
1186216 TTCCACCACTTACTTGATTACCAATATCATGGAGTGCAAAGTAATACATATGTTCTGGATAAACT
1 TTCCACCACTTACTTGATTACCAATATCATGGAGTGCAAAGTAATACATATGTTCTGGATAAACT
1186281 CCAAGATCACTAAACTGATGAAGCCCCAGAATGTGATTTTCCTCGTAACCACTCTTTATGGAACT
66 CCAAGATCACTAAACTGATGAAGCCCCAGAATGTGATTTTCCTCGTAACCACTCTTTATGGAACT
1186346 GCACAAGCCGGCTGCACCTCGTAAGATAAAAGCAAGCGGTATGTAGTTGTTTGGGGACTCCCATT
131 GCACAAGCCGGCTGCACCTCGTAAGATAAAAGCAAGCGGTATGTAGTTGTTTGGGGACTCCCATT
1186411 GATAGTTCCTGCCGTCTGTCATCTAAATTCTGAACAATGCCTTCACATTTGACCCAGAATTCACA
196 GATAGTTCCTGCCGTCTGTCATCTAAATTCTGAACAATGCCTTCACATTTGACCCAGAATTCACA
1186476 AGCCGGCATCTTTGCACAACGCCGTGCTACAACCAC
261 AGCCGGCATCTTTGCACAACGCCGTGCTACAACCAC
1186512 TTCCACCACTTACTTGATTACCAATATCATGGAGTGCAAAGTAATACATATGTTCTGGATAAACT
1 TTCCACCACTTACTTGATTACCAATATCATGGAGTGCAAAGTAATACATATGTTCTGGATAAACT
1186577 CCAAGATCACTAAACTGATGAAGCCCCAGAATGTGATTTTCCTCGTAACCACTCTCTTTATGGAA
66 CCAAGATCACTAAACTGATGAAGCCCCAGAATGTGATTTTCCTCGTAACCA--CTCTTTATGGAA
1186642 CTGCACAAGCCGGCTGCACCTCGTAAGAATAAAAAGCAAGCGGGTATGTAGTTGTTTGGGGACTC
129 CTGCACAAGCCGGCTGCACCTCGTAAG-AT-AAAAGCAAGC-GGTATGTAGTTGTTTGGGGACTC
1186707 CCATTGATAGTTCCTGCCGTCTGTCATCTAAATTCTGAACAATGCCTTCACATTTGACCCAGAAT
191 CCATTGATAGTTCCTGCCGTCTGTCATCTAAATTCTGAACAATGCCTTCACATTTGACCCAGAAT
1186772 TCACAAGCCGGCATCTTTGCACAACGCCGTGCTACAACCA
256 TCACAAGCCGGCATCTTTGCACAACGCCGTGCTACAACCA
1186812 GCAAATCCTC
Statistics
Matches: 295, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
296 116 0.39
298 39 0.13
299 2 0.01
300 10 0.03
301 128 0.43
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (296 bp):
TTCCACCACTTACTTGATTACCAATATCATGGAGTGCAAAGTAATACATATGTTCTGGATAAACT
CCAAGATCACTAAACTGATGAAGCCCCAGAATGTGATTTTCCTCGTAACCACTCTTTATGGAACT
GCACAAGCCGGCTGCACCTCGTAAGATAAAAGCAAGCGGTATGTAGTTGTTTGGGGACTCCCATT
GATAGTTCCTGCCGTCTGTCATCTAAATTCTGAACAATGCCTTCACATTTGACCCAGAATTCACA
AGCCGGCATCTTTGCACAACGCCGTGCTACAACCAC
Found at i:1191433 original size:223 final size:227
Alignment explanation
Indices: 1191039--1191519 Score: 837
Period size: 223 Copynumber: 2.1 Consensus size: 227
1191029 GTAAATTATC
* * *
1191039 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* *
1191104 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATATTT
1191169 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
1191233 AAACATAAATTACATAACTTTCAAA-AA-ATA
196 AAACATAAATTACATAACTTTCAAAGAAGATA
*
1191263 TATCA-TTTTATAAAAGTGTCCATACTTATTTCACTGTTG-AAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1191326 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATATT
*
1191391 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
1191456 GAAACATAAATTACATAACTTTCAAAGAAGTATA
195 GAAACATAAATTACATAACTTTCAAAGAAG-ATA
1191490 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
1191520 AAAGTAGGTC
Statistics
Matches: 243, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
223 172 0.71
224 37 0.15
225 2 0.01
227 8 0.03
228 24 0.10
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATAAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTCAAAGAAGATA
Found at i:1191820 original size:20 final size:19
Alignment explanation
Indices: 1191797--1191843 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1191787 CGATATACCA
1191797 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1191817 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1191837 GGTAAAA
1 GGTAAAA
1191844 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1191931 original size:181 final size:182
Alignment explanation
Indices: 1191585--1192056 Score: 689
Period size: 181 Copynumber: 2.6 Consensus size: 182
1191575 GATCCAAATT
* * * *
1191585 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
1191649 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
1191714 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
1191767 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * *
1191832 AAACCGGTAAAACGTTACCGGATATATTAAAAGTTTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
1191896 GTGAATTTAAAAGAGAAGCAGTTATACCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * *
1191948 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
1192013 AAACCGGTAAAATGATA-CGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
1192057 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
180 25 0.10
181 141 0.54
182 96 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:1192001 original size:20 final size:19
Alignment explanation
Indices: 1191978--1192024 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1191968 CGATATAACA
1191978 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1191998 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1192018 GGTAAAA
1 GGTAAAA
1192025 TGATACGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1192026 original size:17 final size:19
Alignment explanation
Indices: 1191987--1192029 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1191977 AGGTAAAAAT
1191987 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1192007 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1192024 ATGATA
1 ATGATA
1192030 CGGATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1194278 original size:21 final size:21
Alignment explanation
Indices: 1194251--1194315 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1194241 AAGACAATCA
*
1194251 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
1194272 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1194293 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1194314 AG
1 AG
1194316 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1194391 original size:33 final size:33
Alignment explanation
Indices: 1194349--1194414 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1194339 AAATAGATGG
*
1194349 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1194382 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1194415 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1196230 original size:19 final size:19
Alignment explanation
Indices: 1196206--1196252 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1196196 AATGTAGGGT
1196206 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1196225 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1196244 T--TTTTGTAT
1 TAATTTTGTAT
1196253 GTGAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
19 19 0.70
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1197124 original size:198 final size:199
Alignment explanation
Indices: 1196361--1197315 Score: 1733
Period size: 198 Copynumber: 4.8 Consensus size: 199
1196351 GGCAAATTTA
* * *
1196361 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
*
1196426 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
1196491 ATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
1196555 TGCAC
195 TGCAC
* *
1196560 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCAAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
1196625 GTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTATGAGA-TA-ATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
1196688 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1196753 GCAC
196 GCAC
*
1196757 CCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * * *
1196821 GTAATATGTAA-TTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
1196885 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1196950 GCAC
196 GCAC
1196954 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1197019 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
1197084 TAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
1197148 GCAC
196 GCAC
1197152 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1197217 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
1197282 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
1197316 CTAATTTAAA
Statistics
Matches: 733, Mismatches: 18, Indels: 11
0.96 0.02 0.01
Matches are distributed among these distances:
195 38 0.05
196 95 0.13
197 158 0.22
198 313 0.43
199 129 0.18
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (199 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
GCAC
Found at i:1198799 original size:6 final size:6
Alignment explanation
Indices: 1198775--1198854 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
1198765 AGCGGTCGCA
* * * * **
1198775 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GAAGCT GGCGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * *
1198823 GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1198855 TGATCCAAAC
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:1198806 original size:24 final size:24
Alignment explanation
Indices: 1198778--1198824 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1198768 GGTCGCAGAA
1198778 GATGAAGCTGACGATGAAGATGAC
1 GATGAAGCTGACGATGAAGATGAC
*
1198802 GATGAAGCTGGCGATGAAGATGA
1 GATGAAGCTGACGATGAAGATGA
1198825 TGACGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (24 bp):
GATGAAGCTGACGATGAAGATGAC
Found at i:1198835 original size:3 final size:3
Alignment explanation
Indices: 1198814--1198858 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1198804 TGAAGCTGGC
* * *
1198814 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1198859 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:1198858 original size:12 final size:12
Alignment explanation
Indices: 1198778--1198854 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
1198768 GGTCGCAGAA
*
1198778 GATGAAGCTGAC
1 GATGAAGATGAC
1198790 GATGAAGATGAC
1 GATGAAGATGAC
* *
1198802 GATGAAGCTGGC
1 GATGAAGATGAC
*
1198814 GATGAAGATGAT
1 GATGAAGATGAC
* * *
1198826 GACGATGATGAT
1 GATGAAGATGAC
* *
1198838 GATGATGATGAA
1 GATGAAGATGAC
1198850 GATGA
1 GATGA
1198855 TGATCCAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1200001 original size:20 final size:21
Alignment explanation
Indices: 1199976--1200018 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1199966 TTTTAATATA
*
1199976 TTAT-AAAGTATCTATCCTTT
1 TTATAAAAGTATCTATACTTT
*
1199996 TTATAAAAGTGTCTATACTTT
1 TTATAAAAGTATCTATACTTT
1200017 TT
1 TT
1200019 CCACTGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (21 bp):
TTATAAAAGTATCTATACTTT
Found at i:1200633 original size:183 final size:182
Alignment explanation
Indices: 1200323--1200808 Score: 855
Period size: 183 Copynumber: 2.7 Consensus size: 182
1200313 TTCAACATAT
* *
1200323 TATAAATATACCGGTTTTTTGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* *
1200388 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATTT
*
1200453 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
1200506 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
1200571 TCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATTT
*
1200636 ACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
* *
1200689 TATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
1200754 TCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCATTTAAAAAAGT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
1200809 GTCGGTAATT
Statistics
Matches: 290, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
183 286 0.99
184 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTTA
CACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:1203314 original size:25 final size:25
Alignment explanation
Indices: 1203280--1203344 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1203270 TTATCATTAA
1203280 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1203305 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1203330 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1203345 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1203722 original size:23 final size:23
Alignment explanation
Indices: 1203691--1203763 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1203681 ATAGGTAAAC
*
1203691 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1203714 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1203737 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1203760 ATAT
1 ATAT
1203764 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1204031 original size:9 final size:9
Alignment explanation
Indices: 1204017--1204042 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1204007 ATTCCAACCA
1204017 TGTGACAAG
1 TGTGACAAG
1204026 TGTGACAAG
1 TGTGACAAG
1204035 TGTGACAA
1 TGTGACAA
1204043 CTCAATCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.23
Consensus pattern (9 bp):
TGTGACAAG
Found at i:1204219 original size:18 final size:18
Alignment explanation
Indices: 1204198--1204234 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1204188 GTAATTGGAG
1204198 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1204216 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1204234 T
1 T
1204235 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1204242 original size:24 final size:24
Alignment explanation
Indices: 1204190--1204236 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1204180 TTTCATATGT
* *
1204190 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1204214 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1204237 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1204537 original size:39 final size:39
Alignment explanation
Indices: 1204494--1204580 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1204484 TCCGATGCTC
*
1204494 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
1204533 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1204572 ATCAAAATC
1 ATCAAAATC
1204581 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1205033 original size:23 final size:23
Alignment explanation
Indices: 1205002--1205074 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1204992 ATAGGTAAAC
*
1205002 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1205025 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1205048 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
1205071 ATAT
1 ATAT
1205075 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1205279 original size:30 final size:29
Alignment explanation
Indices: 1205220--1205286 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1205210 GTTACGATAT
* *
1205220 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
1205250 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
1205280 ATTTTTT
1 ATATTTT
1205287 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:1210618 original size:25 final size:25
Alignment explanation
Indices: 1210583--1210683 Score: 80
Period size: 25 Copynumber: 4.0 Consensus size: 25
1210573 ACAAAAAAGG
*
1210583 AAATAGAAAATAATAAATAAATACAT
1 AAATA-AAAATAATAAATAAATAAAT
* * *
1210609 AAATAAAAATAATATATATATATAT
1 AAATAAAAATAATAAATAAATAAAT
* * *
1210634 ATAATAAAATGTAGT-ATTAAATAAAT
1 A-AATAAAA-ATAATAAATAAATAAAT
*
1210660 AAAATAAAAAGAA-AAATAAATAAA
1 -AAATAAAAATAATAAATAAATAAA
1210684 AAAACATGAA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
25 28 0.48
26 26 0.45
27 4 0.07
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (25 bp):
AAATAAAAATAATAAATAAATAAAT
Found at i:1212289 original size:32 final size:31
Alignment explanation
Indices: 1212229--1212289 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1212219 CTTTTAAAAT
* **
1212229 TAATAATTTAATTATTAATATTTTCAATTTA
1 TAATAAATTAATTATTAATATTAACAATTTA
1212260 TAATAAATTAATTATTTAATATTAACAATT
1 TAATAAATTAATTA-TTAATATTAACAATT
1212290 ATTATTGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
TAATAAATTAATTATTAATATTAACAATTTA
Found at i:1213177 original size:16 final size:16
Alignment explanation
Indices: 1213158--1213283 Score: 93
Period size: 16 Copynumber: 7.8 Consensus size: 16
1213148 TTTCATCATT
1213158 TTTTCCTTTTTTTTCA
1 TTTTCCTTTTTTTTCA
*
1213174 TTTTCATTTTTTTCTTGCA
1 TTTTC-CTTTTTT-TT-CA
*
1213193 TTTTCCCTTTTTTTC-
1 TTTTCCTTTTTTTTCA
*
1213208 TTTT-CTTTTTTCATCA
1 TTTTCCTTTTTT-TTCA
* *
1213224 TTTTTCATTTTTTTCA
1 TTTTCCTTTTTTTTCA
1213240 TTTT--TTCTTTTCTTC-
1 TTTTCCTT-TTTT-TTCA
*
1213255 TTTT-CTTCTTTTTTCC
1 TTTTCCTT-TTTTTTCA
1213271 TTTTCCTTTTTTT
1 TTTTCCTTTTTTT
1213284 ATTTTTTTTA
Statistics
Matches: 91, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
14 7 0.08
15 17 0.19
16 36 0.40
17 17 0.19
18 7 0.08
19 7 0.08
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTTCCTTTTTTTTCA
Found at i:1213211 original size:7 final size:7
Alignment explanation
Indices: 1213199--1213353 Score: 72
Period size: 7 Copynumber: 21.4 Consensus size: 7
1213189 TGCATTTTCC
1213199 CTTTTTT
1 CTTTTTT
*
1213206 -TCTTTT
1 CTTTTTT
1213212 CTTTTTT
1 CTTTTTT
1213219 CATCATTTTT
1 C-T--TTTTT
1213229 CATTTTTTT
1 C--TTTTTT
1213238 CATTTTTT
1 C-TTTTTT
1213246 CTTTTCTT
1 CTTTT-TT
1213254 CTTTTCTT
1 CTTTT-TT
1213262 CTTTTTT
1 CTTTTTT
* *
1213269 CCTTTTC
1 CTTTTTT
1213276 CTTTTTT
1 CTTTTTT
1213283 -TATTTTT
1 CT-TTTTT
1213290 -TTTATTT
1 CTTT-TTT
1213297 -TTATTTT
1 CTT-TTTT
1213304 -TATTTTT
1 CT-TTTTT
*
1213311 -ATTTTT
1 CTTTTTT
*
1213317 ATTTTTT
1 CTTTTTT
*
1213324 ATTTTTT
1 CTTTTTT
*
1213331 -ATTTTT
1 CTTTTTT
*
1213337 ATTTTTT
1 CTTTTTT
*
1213344 ATTTTTT
1 CTTTTTT
1213351 CTT
1 CTT
1213354 CAAGCGAAAT
Statistics
Matches: 123, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
6 18 0.15
7 67 0.54
8 25 0.20
9 6 0.05
10 6 0.05
11 1 0.01
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:1213281 original size:1 final size:1
Alignment explanation
Indices: 1213277--1213350 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
1213267 TTCCTTTTCC
* * * * * * * * *
1213277 TTTTTTTATTTTTTTTATTTTTATTTTTATTTTTATTTTTATTTTTTATTTTTTATTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1213342 TTATTTTTT
1 TTTTTTTTT
1213351 CTTCAAGCGA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:1213283 original size:9 final size:8
Alignment explanation
Indices: 1213224--1213353 Score: 63
Period size: 8 Copynumber: 16.0 Consensus size: 8
1213214 TTTTTCATCA
1213224 TTTTTCATT
1 TTTTTC-TT
*
1213233 TTTTTCAT
1 TTTTTCTT
1213241 TTTTTCTT
1 TTTTTCTT
*
1213249 TTCTTCTT
1 TTTTTCTT
*
1213257 TTCTTC-T
1 TTTTTCTT
*
1213264 TTTTTC-C
1 TTTTTCTT
*
1213271 TTTTCCTT
1 TTTTTCTT
*
1213279 TTTTTATT
1 TTTTTCTT
*
1213287 TTTTT-TA
1 TTTTTCTT
*
1213294 TTTTTATT
1 TTTTTCTT
1213302 TTTATT-TT
1 TTT-TTCTT
1213310 TATTTT-TAT
1 T-TTTTCT-T
*
1213319 TTTTTATT
1 TTTTTCTT
*
1213327 TTTTATTTT
1 TTTT-TCTT
*
1213336 TATTTTTTAT
1 T-TTTTCT-T
1213346 TTTTTCTT
1 TTTTTCTT
1213354 CAAGCGAAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 19
0.76 0.10 0.15
Matches are distributed among these distances:
7 17 0.17
8 52 0.53
9 25 0.25
10 5 0.05
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1213288 original size:6 final size:6
Alignment explanation
Indices: 1213288--1213349 Score: 97
Period size: 6 Copynumber: 9.8 Consensus size: 6
1213278 TTTTTTATTT
1213288 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTTA TTTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA -TTTTTA TTTTTA
1213338 TTTTTTA TTTTT
1 -TTTTTA TTTTT
1213350 TCTTCAAGCG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
6 35 0.65
7 19 0.35
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:1213303 original size:20 final size:20
Alignment explanation
Indices: 1213287--1213350 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
1213277 TTTTTTTATT
1213287 TTTTTTATTTTTA-TTTTTA
1 TTTTTTATTTTTATTTTTTA
1213306 -TTTTTATTTTTATTTTTTA
1 TTTTTTATTTTTATTTTTTA
1213325 TTTTTTATTTTTATTTTTTA
1 TTTTTTATTTTTATTTTTTA
1213345 TTTTTT
1 TTTTTT
1213351 CTTCAAGCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 12 0.28
19 6 0.14
20 25 0.58
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTATTTTTATTTTTTA
Found at i:1224826 original size:17 final size:17
Alignment explanation
Indices: 1224790--1224829 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1224780 AAAACATAAA
* **
1224790 AAATAAAATAAGGGTTT
1 AAATAAAATAAGCGCAT
1224807 AAATAAAATAAGCGCAT
1 AAATAAAATAAGCGCAT
1224824 AAATAA
1 AAATAA
1224830 GGTACCTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (17 bp):
AAATAAAATAAGCGCAT
Found at i:1228337 original size:20 final size:20
Alignment explanation
Indices: 1228314--1228366 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1228304 GTTTCCAGAT
1228314 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1228334 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1228354 TCGCAACGCGATT
1 TCGCAACGCGATT
1228367 TACATAGCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1228567 original size:22 final size:22
Alignment explanation
Indices: 1228542--1228607 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1228532 GGCGACATCC
1228542 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1228564 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
1228586 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1228608 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1228701 original size:20 final size:20
Alignment explanation
Indices: 1228676--1228722 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1228666 TATTTTTATT
*
1228676 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1228696 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1228716 TTGCGAT
1 TTGCGAT
1228723 TTACGTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1228734 original size:20 final size:21
Alignment explanation
Indices: 1228709--1228770 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
1228699 CGATAGTCAG
1228709 ATTCGCGTTGCGATTTACGTA
1 ATTCGCGTTGCGATTTACGTA
* * * **
1228730 A-TCGCATTACGATTTTCCAA
1 ATTCGCGTTGCGATTTACGTA
1228750 ATTCGCGTTGCGATTTACGTA
1 ATTCGCGTTGCGATTTACGTA
1228771 TTCACATTGC
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (21 bp):
ATTCGCGTTGCGATTTACGTA
Found at i:1228780 original size:20 final size:20
Alignment explanation
Indices: 1228709--1228782 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1228699 CGATAGTCAG
*
1228709 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * **
1228729 AATCGCATTACGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1228750 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1228770 ATTCACATTGCGA
1 ATTCGCATTGCGA
1228783 ATTAGGAAAA
Statistics
Matches: 39, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1228824 original size:21 final size:21
Alignment explanation
Indices: 1228778--1228824 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1228768 GTATTCACAT
1228778 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
* * *
1228799 CGCGAATTTGGAAAATCGCTA
1 TGCGAATTAGGAAAATCGCAA
1228820 TGCGA
1 TGCGA
1228825 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:1230093 original size:17 final size:16
Alignment explanation
Indices: 1230070--1230113 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
1230060 TACTATTTTT
1230070 TATTTTAAAACTCATAAA
1 TATTTTAAAACT--TAAA
1230088 -ATTTTAATAACTTAAA
1 TATTTTAA-AACTTAAA
1230104 TATTTTAAAA
1 TATTTTAAAA
1230114 TAATTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.25
17 14 0.58
18 4 0.17
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTTAAAACTTAAA
Found at i:1237275 original size:3 final size:3
Alignment explanation
Indices: 1237267--1237299 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1237257 GGTTCTCGTT
*
1237267 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1237300 ATTTACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1239711 original size:126 final size:126
Alignment explanation
Indices: 1239486--1239738 Score: 407
Period size: 126 Copynumber: 2.0 Consensus size: 126
1239476 GACCAACATT
* * *
1239486 TGGGCGTTGTGGATGTGCTAACCATTCCCTACACGTAACCGACTCCCGAACTCTTAAAAATGAAT
1 TGGGCGTTGTGGAGGTGCTAACCATTCCCCACACGTAACCGACTCCCGAACTCTTAAAAACGAAT
* ** * *
1239551 CTTTGGTAAAACACATACTGTTTTTTGACGTTTAAGGTTTTCAACCTACCTAATTTAATGG
66 CTTTGGTAAAACACAGACCATTTTTTAACGTTTAAGGTTTCCAACCTACCTAATTTAATGG
* * *
1239612 TGGGCGTTGTGGGGGTGCTAACCCTTCCCCACACGTAACCGACTCTCGAACTCTTAAAAACGAAT
1 TGGGCGTTGTGGAGGTGCTAACCATTCCCCACACGTAACCGACTCCCGAACTCTTAAAAACGAAT
1239677 CTTTGGTAAAACACAGACCATTTTTTAACGTTTAAGGTTTCCAACCTACCTAATTTAATGG
66 CTTTGGTAAAACACAGACCATTTTTTAACGTTTAAGGTTTCCAACCTACCTAATTTAATGG
1239738 T
1 T
1239739 TGGTAGTGAC
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 116 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (126 bp):
TGGGCGTTGTGGAGGTGCTAACCATTCCCCACACGTAACCGACTCCCGAACTCTTAAAAACGAAT
CTTTGGTAAAACACAGACCATTTTTTAACGTTTAAGGTTTCCAACCTACCTAATTTAATGG
Found at i:1241447 original size:13 final size:13
Alignment explanation
Indices: 1241429--1241455 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1241419 TTTTGCTTGA
1241429 AATTGAATTCCTT
1 AATTGAATTCCTT
1241442 AATTGAATTCCTT
1 AATTGAATTCCTT
1241455 A
1 A
1241456 TCAGATAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
AATTGAATTCCTT
Found at i:1244217 original size:60 final size:60
Alignment explanation
Indices: 1244082--1244234 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
1244072 CATCAATTTT
* * * * *
1244082 AATTGGTCCCTAAAATTTTAAATATTTCAATTTTATCCCTAACCTATGAGTGTCATTCTA
1 AATTGGTCCCTAAACTTTTAAACATTTCAATTCTATCCCCAAACTATGAGTGTCATTCTA
* *
1244142 AATTAGTCCTTAAACTTTTAAACATTTCAATTCTATCCCCAAACTATG-GCCT-TCATTCTA
1 AATTGGTCCCTAAACTTTTAAACATTTCAATTCTATCCCCAAACTATGAG--TGTCATTCTA
* * * *
1244202 AATTGGCCCCCAAACTTTTTGAACATTCCAATT
1 AATTGGTCCCTAAAC-TTTTAAACATTTCAATT
1244235 TCATCCCAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 60 0.78
61 16 0.21
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (60 bp):
AATTGGTCCCTAAACTTTTAAACATTTCAATTCTATCCCCAAACTATGAGTGTCATTCTA
Found at i:1244526 original size:60 final size:59
Alignment explanation
Indices: 1244376--1244560 Score: 180
Period size: 60 Copynumber: 3.1 Consensus size: 59
1244366 GGATGAATTT
** * *
1244376 GGGATGAAATTGGAATATTCAAAAAGTTTGGGGACTAATTAAGAA-AGAGGGTCATATATTA
1 GGGATGAAATT-GAATATTC-AAAAGTTTAAGGACTAATTTAGAATA-AGAGTCATATATTA
* * * * *
1244437 GGGATTAAAATTGAAATGTTCAAAAGTTTAAGGACTAGTTTAGAATAATAGTCATAGT-TTG
1 GGGA-TGAAATTG-AATATTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTCATA-TATTA
*
1244498 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATAA-AGATTATATATT-
1 GGGATGAAATT-GAATATTCAAAAGTTTAAGGACTAATTTAGAATAAGAG-TCATATATTA
1244557 GGGA
1 GGGA
1244561 GCATGTGATG
Statistics
Matches: 104, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
59 7 0.07
60 44 0.42
61 39 0.38
62 14 0.13
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (59 bp):
GGGATGAAATTGAATATTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTCATATATTA
Found at i:1244539 original size:29 final size:29
Alignment explanation
Indices: 1244455--1244543 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
1244445 AATTGAAATG
*
1244455 TTCAAAAGTTTAAGGACTAGTTTAGAATAA
1 TTCAAAAGTTTAAGGACTAATTTAGAAT-A
* ** *
1244485 TAGTC-ATAGTTTGGGGA-TGAAATTAGAATA
1 T--TCAAAAGTTTAAGGACT-AATTTAGAATA
1244515 TTCAAAAGTTTAAGGACTAATTTAGAATA
1 TTCAAAAGTTTAAGGACTAATTTAGAATA
1244544 AAGATTATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
28 2 0.04
29 19 0.42
30 5 0.11
31 17 0.38
32 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.34
Consensus pattern (29 bp):
TTCAAAAGTTTAAGGACTAATTTAGAATA
Found at i:1244874 original size:49 final size:50
Alignment explanation
Indices: 1244801--1244911 Score: 188
Period size: 49 Copynumber: 2.2 Consensus size: 50
1244791 AAAATAAAAA
* * *
1244801 CTATATAAAAAAAAACCTTCTCATACACTCTTTTCTCTAACTGCACGAAG
1 CTATATAAAAAAAAACCTTCTCATACACTCTTCTCTCCAACTGCACAAAG
1244851 CTATATAAAAAAAAA-CTTCTCATACACTCTTCTCTCCAACTGCACAAAG
1 CTATATAAAAAAAAACCTTCTCATACACTCTTCTCTCCAACTGCACAAAG
1244900 CTATATAAAAAA
1 CTATATAAAAAA
1244912 GAAGCCTTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
49 43 0.74
50 15 0.26
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (50 bp):
CTATATAAAAAAAAACCTTCTCATACACTCTTCTCTCCAACTGCACAAAG
Found at i:1248608 original size:254 final size:254
Alignment explanation
Indices: 1248159--1248669 Score: 1022
Period size: 254 Copynumber: 2.0 Consensus size: 254
1248149 GTGTTAAGGT
1248159 AATCCTGAACCTGCTTCAGGCGATCACTCTGCACAAGAGAGAGATCAGTTACTGAGAAAATTCTT
1 AATCCTGAACCTGCTTCAGGCGATCACTCTGCACAAGAGAGAGATCAGTTACTGAGAAAATTCTT
1248224 TGGAAACAATAAAGACATAAGGAAGGGAAGTTGACCTTCTCTTTCTGAAGTTCATGGAGCTGTCT
66 TGGAAACAATAAAGACATAAGGAAGGGAAGTTGACCTTCTCTTTCTGAAGTTCATGGAGCTGTCT
1248289 ATGCAATTCTTCAAGCTTCCTTAAGGATAAGTCAGTTTCATCCACTACTGCTTTGGAAGAAATTG
131 ATGCAATTCTTCAAGCTTCCTTAAGGATAAGTCAGTTTCATCCACTACTGCTTTGGAAGAAATTG
1248354 ATACGGAGGATCCATAAATCTCATTTGTGATCTTTTGTATCTGCTCTAAAACATCTACA
196 ATACGGAGGATCCATAAATCTCATTTGTGATCTTTTGTATCTGCTCTAAAACATCTACA
1248413 AATCCTGAACCTGCTTCAGGCGATCACTCTGCACAAGAGAGAGATCAGTTACTGAGAAAATTCTT
1 AATCCTGAACCTGCTTCAGGCGATCACTCTGCACAAGAGAGAGATCAGTTACTGAGAAAATTCTT
1248478 TGGAAACAATAAAGACATAAGGAAGGGAAGTTGACCTTCTCTTTCTGAAGTTCATGGAGCTGTCT
66 TGGAAACAATAAAGACATAAGGAAGGGAAGTTGACCTTCTCTTTCTGAAGTTCATGGAGCTGTCT
1248543 ATGCAATTCTTCAAGCTTCCTTAAGGATAAGTCAGTTTCATCCACTACTGCTTTGGAAGAAATTG
131 ATGCAATTCTTCAAGCTTCCTTAAGGATAAGTCAGTTTCATCCACTACTGCTTTGGAAGAAATTG
1248608 ATACGGAGGATCCATAAATCTCATTTGTGATCTTTTGTATCTGCTCTAAAACATCTACA
196 ATACGGAGGATCCATAAATCTCATTTGTGATCTTTTGTATCTGCTCTAAAACATCTACA
1248667 AAT
1 AAT
1248670 TGATTTCTTC
Statistics
Matches: 257, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
254 257 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (254 bp):
AATCCTGAACCTGCTTCAGGCGATCACTCTGCACAAGAGAGAGATCAGTTACTGAGAAAATTCTT
TGGAAACAATAAAGACATAAGGAAGGGAAGTTGACCTTCTCTTTCTGAAGTTCATGGAGCTGTCT
ATGCAATTCTTCAAGCTTCCTTAAGGATAAGTCAGTTTCATCCACTACTGCTTTGGAAGAAATTG
ATACGGAGGATCCATAAATCTCATTTGTGATCTTTTGTATCTGCTCTAAAACATCTACA
Found at i:1251649 original size:21 final size:21
Alignment explanation
Indices: 1251620--1251666 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1251610 ATTCTGACTA
1251620 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1251641 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1251662 TCGCA
1 TCGCA
1251667 ATGTGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1251726 original size:41 final size:41
Alignment explanation
Indices: 1251681--1251773 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
1251671 GAATACGTAA
* *
1251681 ATCGCAACATGAATTTGGAAAATCGCAACGAGA-TTCTGACT
1 ATCGCAACATGAATTT-CAAAATCGCAACGAGATTTCTGAAT
* * **
1251722 ATCGCAATACTGAATTTCAAATTCGCAACTCGATTTCTGAAT
1 ATCGCAACA-TGAATTTCAAAATCGCAACGAGATTTCTGAAT
1251764 -TCGCAACATG
1 ATCGCAACATG
1251774 TTTTAGTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.05
41 27 0.63
42 14 0.33
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (41 bp):
ATCGCAACATGAATTTCAAAATCGCAACGAGATTTCTGAAT
Found at i:1252605 original size:24 final size:24
Alignment explanation
Indices: 1252578--1252631 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1252568 GTATTCGAAA
1252578 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1252602 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1252626 TTTGAT
1 TTTGAT
1252632 GATATTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1255085 original size:20 final size:20
Alignment explanation
Indices: 1255060--1255132 Score: 105
Period size: 20 Copynumber: 3.6 Consensus size: 20
1255050 CAACGCGGAA
1255060 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
*
1255080 ATCGCAACACAGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
1255100 ATCGCAACGCGTAAT-TGACT
1 ATCGCAACGCG-AATATGACT
1255120 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1255133 CGCGTTGCGA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.06
20 42 0.88
21 3 0.06
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:1255173 original size:34 final size:34
Alignment explanation
Indices: 1255135--1255230 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
1255125 AACGCGAACG
1255135 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
1255169 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
1255202 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1255231 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:1255351 original size:14 final size:14
Alignment explanation
Indices: 1255332--1255368 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1255322 TATCAATTAA
1255332 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1255346 ACAAATCATCTTTT
1 ACAAATCAACATTT
1255360 ACAAATCAA
1 ACAAATCAA
1255369 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1257351 original size:34 final size:34
Alignment explanation
Indices: 1257304--1257457 Score: 139
Period size: 34 Copynumber: 4.4 Consensus size: 34
1257294 TGAAACTTAA
*
1257304 AATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
** * * *
1257338 AATCGCAATGCG-AAATGAAAATCGCAACAACAA
1 AATCGCAATGCGAAAATGACTATCGCAACGAGAG
** * *
1257371 AATCGCAACACGAAAATGATTATCGCAATGCGAAAATG
1 AATCGCAATGCGAAAATGACTATCGCAA--CG-AGA-G
**
1257409 ACTATCGCAATGCGAATTTGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAAAATGACTATCGCAACGAGAG
1257445 AATCGCAATGCGA
1 AATCGCAATGCGA
1257458 TTTTCATTTC
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
33 26 0.28
34 36 0.38
36 3 0.03
37 4 0.04
38 3 0.03
40 22 0.23
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.16
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGACTATCGCAACGAGAG
Found at i:1257386 original size:14 final size:15
Alignment explanation
Indices: 1257354--1257387 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1257344 AATGCGAAAT
1257354 GAAAATCGCAACAAC
1 GAAAATCGCAACAAC
1257369 -AAAATCGCAAC-AC
1 GAAAATCGCAACAAC
1257382 GAAAAT
1 GAAAAT
1257388 GATTATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.09
Consensus pattern (15 bp):
GAAAATCGCAACAAC
Found at i:1257397 original size:20 final size:20
Alignment explanation
Indices: 1257372--1257439 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1257362 CAACAACAAA
*
1257372 ATCGCAACACGAAAATGATT
1 ATCGCAACACGAAAATGACT
**
1257392 ATCGCAATGCGAAAATGACT
1 ATCGCAACACGAAAATGACT
** **
1257412 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
1257432 ATCGCAAC
1 ATCGCAAC
1257440 GAGAGAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1257540 original size:54 final size:53
Alignment explanation
Indices: 1257447--1257568 Score: 172
Period size: 54 Copynumber: 2.3 Consensus size: 53
1257437 AACGAGAGAA
* ** * *
1257447 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTGCAATTCTCTCGTTGCGATAGTCAAAT
**
1257500 TCGCATTGCGATAGTCATTTTCGCATTGCAATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCAATTCTCTCGTTGCGATAGTCAAAT
1257554 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
1257569 AAACTATTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 14 0.23
54 47 0.77
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (53 bp):
TCGCATTGCGATAGTCATTTCGCATTGCAATTCTCTCGTTGCGATAGTCAAAT
Found at i:1257564 original size:20 final size:20
Alignment explanation
Indices: 1257485--1257568 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
1257475 GATTCTTTCG
**
1257485 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1257505 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1257525 TTGC-A-ATTC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
1257539 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1257559 TTGCGATAGT
1 TTGCGATAGT
1257569 AAACTATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.08
15 1 0.02
16 7 0.13
18 7 0.13
19 1 0.02
20 32 0.62
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1259457 original size:20 final size:20
Alignment explanation
Indices: 1259434--1259521 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
1259424 CTGAAACTTT
*
1259434 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
1259454 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
1259474 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
1259494 CTATCGCAACGCG-AAATG-
1 AAATCGCAACACGAAAATGA
1259512 AAATCGCAAC
1 AAATCGCAAC
1259522 GACAGAATCG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 8 0.14
19 3 0.05
20 47 0.81
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1264233 original size:14 final size:15
Alignment explanation
Indices: 1264214--1264242 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1264204 ACCTTTATGA
1264214 TTTAAAT-TAATATT
1 TTTAAATATAATATT
1264228 TTTAAATATAATATT
1 TTTAAATATAATATT
1264243 ACATATTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAATATAATATT
Found at i:1264380 original size:99 final size:99
Alignment explanation
Indices: 1264270--1264775 Score: 985
Period size: 99 Copynumber: 5.1 Consensus size: 99
1264260 GCCAGCTAAA
*
1264270 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAATTAAATTTTACTGTAATTAT
1 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
* *
1264335 CGTAAAATATCCTAAAACAACTTCTATAAATATG
66 CGTAAAATATCCTAATACAACTTCCATAAATATG
1264369 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1264434 CGTAAAATATCCTAATACAACTTCCATAAATATG
66 CGTAAAATATCCTAATACAACTTCCATAAATATG
1264468 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1264533 CGTAAAATATCCTAATACAACTTCCATAAATATG
66 CGTAAAATATCCTAATACAACTTCCATAAATATG
1264567 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1264632 CGTAAAATATCCTAATACAACTTCCATAAATATG
66 CGTAAAATATCCTAATACAACTTCCATAAATATG
1264666 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1 TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
1264731 CGTAAAATATCCTAATACAACTTCCATAAATATG
66 CGTAAAATATCCTAATACAACTTCCATAAATATG
1264765 TTGAGAAACAA
1 TTGAGAAACAA
1264776 CTTGTATATG
Statistics
Matches: 404, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 404 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (99 bp):
TTGAGAAACAATATACTATTTTATCATTTAGAATTCATATATCAACTAAATTTTACTGTAATTAT
CGTAAAATATCCTAATACAACTTCCATAAATATG
Found at i:1266173 original size:18 final size:20
Alignment explanation
Indices: 1266152--1266189 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1266142 TTATTTTTAT
1266152 GTTAGTAT-TTTT-TTAATA
1 GTTAGTATATTTTATTAATA
*
1266170 GTTATTATATTTTATTAATA
1 GTTAGTATATTTTATTAATA
1266190 TTTATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
GTTAGTATATTTTATTAATA
Found at i:1266182 original size:20 final size:22
Alignment explanation
Indices: 1266148--1266208 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
1266138 AAATTTATTT
*
1266148 TTATGTTAGTATTTTTTTAATAG
1 TTATG-TAATATTTTTTTAATAG
* *
1266171 TTAT-T-ATATTTTATTAATAT
1 TTATGTAATATTTTTTTAATAG
1266191 TTATGTAATATTATTTTT
1 TTATGTAATATT-TTTTT
1266209 TATTAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 16 0.52
21 2 0.06
22 5 0.16
23 8 0.26
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
TTATGTAATATTTTTTTAATAG
Found at i:1267969 original size:21 final size:21
Alignment explanation
Indices: 1267939--1267986 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1267929 GTAAGGGTAC
* * *
1267939 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCAATTCAT
*
1267960 ATGCCAAGCCCACCAATTTAT
1 ATGCCAAGCCCACCAATTCAT
1267981 ATGCCA
1 ATGCCA
1267987 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.40, G:0.10, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCAATTCAT
Found at i:1268016 original size:21 final size:21
Alignment explanation
Indices: 1267990--1268061 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
1267980 TATGCCATCT
*
1267990 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
1268011 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1268032 CCGCCA-GGTTACATGCCTA-C
1 CCG-CAGGGTTACATTCCTAGC
1268052 CCGCAGGGTT
1 CCGCAGGGTT
1268062 TTATACCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.04
20 8 0.17
21 35 0.74
22 2 0.04
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1268243 original size:21 final size:21
Alignment explanation
Indices: 1268213--1268260 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1268203 GTAAGGGTAC
* * *
1268213 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCAATTCAT
*
1268234 ATGCCAAGCCCACCAATTTAT
1 ATGCCAAGCCCACCAATTCAT
1268255 ATGCCA
1 ATGCCA
1268261 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.40, G:0.10, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCAATTCAT
Found at i:1268290 original size:21 final size:21
Alignment explanation
Indices: 1268264--1268336 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
1268254 TATGCCATCT
*
1268264 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
1268285 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1268306 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
1268327 CCGCAGGGTT
1 CCGCAGGGTT
1268337 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1268447 original size:275 final size:275
Alignment explanation
Indices: 1267929--1268480 Score: 1088
Period size: 275 Copynumber: 2.0 Consensus size: 275
1267919 CGTCAATGCC
1267929 GTAAGGGTACATGCCCAGCCCTCCACTTCATATGCCAAGCCCACCAATTTATATGCCATCTCCGC
1 GTAAGGGTACATGCCCAGCCCTCCACTTCATATGCCAAGCCCACCAATTTATATGCCATCTCCGC
1267994 AGGGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTACCCGCAGG
66 AGGGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTACCCGCAGG
1268059 GTTTTATACCATATGGAGGTGCATATACGACTATGTTTAATGATCCAGCATATGGTTCATATGCA
131 GTTTTATACCATATGGAGGTGCATATACGACTATGTTTAATGATCCAGCATATGGTTCATATGCA
1268124 TCTTATTTGGCTGGTGGTGCTTCTCCGCAGACACCTCAATCTCCATCTGGATCACAGACATCGAT
196 TCTTATTTGGCTGGTGGTGCTTCTCCGCAGACACCTCAATCTCCATCTGGATCACAGACATCGAT
1268189 GCCAATG-TTCCACA
261 GCCAATGTTTCCACA
1268203 GTAAGGGTACATGCCCAGCCCTCCACTTCATATGCCAAGCCCACCAATTTATATGCCATCTCCGC
1 GTAAGGGTACATGCCCAGCCCTCCACTTCATATGCCAAGCCCACCAATTTATATGCCATCTCCGC
1268268 AGGGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTAGCCCGCAG
66 AGGGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTA-CCCGCAG
1268333 GGTTTTATACCATATGGAGGTGCATATACGACTATGTTTAATGATCCAGCATATGGTTCATATGC
130 GGTTTTATACCATATGGAGGTGCATATACGACTATGTTTAATGATCCAGCATATGGTTCATATGC
1268398 ATCTTATTTGGCTGGTGGTGCTTCTCCGCAGACACCTCAATCTCCATCTGGATCACAGACATCGA
195 ATCTTATTTGGCTGGTGGTGCTTCTCCGCAGACACCTCAATCTCCATCTGGATCACAGACATCGA
1268463 TGCCAATGTTTCCACA
260 TGCCAATGTTTCCACA
1268479 GT
1 GT
1268481 TTTCACAGTT
Statistics
Matches: 276, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
274 122 0.44
275 145 0.53
276 9 0.03
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (275 bp):
GTAAGGGTACATGCCCAGCCCTCCACTTCATATGCCAAGCCCACCAATTTATATGCCATCTCCGC
AGGGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTACCCGCAGG
GTTTTATACCATATGGAGGTGCATATACGACTATGTTTAATGATCCAGCATATGGTTCATATGCA
TCTTATTTGGCTGGTGGTGCTTCTCCGCAGACACCTCAATCTCCATCTGGATCACAGACATCGAT
GCCAATGTTTCCACA
Found at i:1272161 original size:276 final size:276
Alignment explanation
Indices: 1271779--1272283 Score: 735
Period size: 276 Copynumber: 1.8 Consensus size: 276
1271769 AGTGGTGGGC
* ** * *
1271779 TTAATGGCTCTTGAAGAGCTCATTGTATCTTCTAACTCTAATGAATTTAATTCATATTCTTTTAA
1 TTAATGACTCTTGAAGAGCTCAAGGTATATTCTAACTCTAATGAATTTAATTCATATTATTTTAA
** ** * * *
1271844 TGAGTTTTAAGATGCTTATGATGAATTATTTTTTAAATTTGAGACCATGAATTTCAAATACAA-C
66 TGAGTTACAAGACACTTATGATGAATTATTTTTGAAATTTGAGACCATGAATTCCAAATACAAGA
* * * * *
1271908 AAATTACTTTTTAAATTTAAAGTTGAAAACAATTTTCTTTTGAAAGTAAAATTGGA-TTTTAAAA
131 AAATGA-TTTTTAAATTTAAAGTTAAAAACAATTTTCTTTTGAAAGAAAAACTGGACTTTGAAAA
* *
1271972 TTCAAAATGAAATTTTGAGAAAATATTTAGAATTTTTTTAAATGAAAACACTAAACCTACTATCT
195 -TAAAAATGAAATTTTGAGAAAAGATTTAGAATTTTTTTAAATGAAAACACTAAACCTACTATCT
1272037 AATCCATATGTAGTGTGT
259 AATCCATATGTAGTGTGT
* * *
1272055 TTAATGACTCTTGAAGAGTTTAAGGTATATTCTAATTCTAATGAATTTAATTCATATTATTTTAA
1 TTAATGACTCTTGAAGAGCTCAAGGTATATTCTAACTCTAATGAATTTAATTCATATTATTTTAA
* * *
1272120 TGAGTTACAAGACATTTATGATGAATTATTTTTGGAATTTGAGACCATTAATTCCAAATACAAGA
66 TGAGTTACAAGACACTTATGATGAATTATTTTTGAAATTTGAGACCATGAATTCCAAATACAAGA
**
1272185 AAATGATTTTTAAATTTAAAGTTAAAAATGATTTTCTTTTGAAAGAAAAACTGGACTTTGAAAAT
131 AAATGATTTTTAAATTTAAAGTTAAAAACAATTTTCTTTTGAAAGAAAAACTGGACTTTGAAAAT
1272250 AAAAATGAAATTTTGAGAAAAGATTTAGAATTTT
196 AAAAATGAAATTTTGAGAAAAGATTTAGAATTTT
1272284 CAAAAAAGAA
Statistics
Matches: 200, Mismatches: 27, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
276 188 0.94
277 12 0.06
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (276 bp):
TTAATGACTCTTGAAGAGCTCAAGGTATATTCTAACTCTAATGAATTTAATTCATATTATTTTAA
TGAGTTACAAGACACTTATGATGAATTATTTTTGAAATTTGAGACCATGAATTCCAAATACAAGA
AAATGATTTTTAAATTTAAAGTTAAAAACAATTTTCTTTTGAAAGAAAAACTGGACTTTGAAAAT
AAAAATGAAATTTTGAGAAAAGATTTAGAATTTTTTTAAATGAAAACACTAAACCTACTATCTAA
TCCATATGTAGTGTGT
Found at i:1273432 original size:18 final size:18
Alignment explanation
Indices: 1273411--1273450 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1273401 AGTTTTGTTT
1273411 TTAAAATGCTTT-TTTTAC
1 TTAAAAT-CTTTATTTTAC
*
1273429 TTAAACTCTTTATTTTAC
1 TTAAAATCTTTATTTTAC
1273447 TTAA
1 TTAA
1273451 CCTACACTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (18 bp):
TTAAAATCTTTATTTTAC
Found at i:1277307 original size:22 final size:22
Alignment explanation
Indices: 1277259--1277325 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1277249 TATCTTATAT
* * * *
1277259 TATTATAATATAATTGATTATTT
1 TATTATAATATTA-TAAATATTA
1277282 TATTATAATATTATAAATATTA
1 TATTATAATATTATAAATATTA
* *
1277304 TATTATATTATTAGAAATATTA
1 TATTATAATATTATAAATATTA
1277326 ATAAATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 26 0.68
23 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
TATTATAATATTATAAATATTA
Found at i:1277333 original size:22 final size:22
Alignment explanation
Indices: 1277255--1277329 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
1277245 ATAATATCTT
*
1277255 ATATTATTATAATATAATT-G-A
1 ATATTA-TATAATATTATTAGAA
* * * * *
1277276 TTATTTTATTATAATATTATAA
1 ATATTATATAATATTATTAGAA
*
1277298 ATATTATATTATATTATTAGAA
1 ATATTATATAATATTATTAGAA
1277320 ATATTA-ATAA
1 ATATTATATAA
1277330 ATATATTTTA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 9 0.22
21 7 0.17
22 25 0.61
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTATATAATATTATTAGAA
Found at i:1278806 original size:15 final size:15
Alignment explanation
Indices: 1278786--1278827 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1278776 GTAAGCAACA
1278786 ACAACAACAGTAGCG
1 ACAACAACAGTAGCG
*
1278801 ACAACAACAATAGCG
1 ACAACAACAGTAGCG
*
1278816 ACAACAGCAGTA
1 ACAACAACAGTA
1278828 ACGGCAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.26, G:0.17, T:0.07
Consensus pattern (15 bp):
ACAACAACAGTAGCG
Found at i:1279721 original size:35 final size:36
Alignment explanation
Indices: 1279675--1279749 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
1279665 ACTAAACCCG
*
1279675 TCCCCGTCCCCGTTTAACATAAAC-GATTTTCCCCA
1 TCCCCATCCCCGTTTAACATAAACGGATTTTCCCCA
* * *
1279710 TCCCCATCCCCGTTTAGCATAAACGGTTTTTCCCCG
1 TCCCCATCCCCGTTTAACATAAACGGATTTTCCCCA
1279746 TCCC
1 TCCC
1279750 TGTTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.19, C:0.41, G:0.11, T:0.29
Consensus pattern (36 bp):
TCCCCATCCCCGTTTAACATAAACGGATTTTCCCCA
Found at i:1280116 original size:15 final size:15
Alignment explanation
Indices: 1280092--1280263 Score: 67
Period size: 15 Copynumber: 11.3 Consensus size: 15
1280082 ATGACGGTAG
*
1280092 CGACAGCGACGACAA
1 CGACAACGACGACAA
* *
1280107 CGTCAACGACGACAT
1 CGACAACGACGACAA
* *
1280122 CGACAACGATGGCAA
1 CGACAACGACGACAA
* *
1280137 CGACAACAACTACAA
1 CGACAACGACGACAA
* *
1280152 TGACAACGATGGA-AA
1 CGACAACGA-CGACAA
**
1280167 CGACAGTGACGGTAACAA
1 CGACAACGAC-G--ACAA
* * * *
1280185 CAACAACAACAATAA
1 CGACAACGACGACAA
*
1280200 TGACAACGACGACAA
1 CGACAACGACGACAA
* ** *
1280215 TGACAGGGACAACAA
1 CGACAACGACGACAA
* *
1280230 CAACAACGATGACAA
1 CGACAACGACGACAA
* ** *
1280245 TGGTAACGACAACAA
1 CGACAACGACGACAA
1280260 CGAC
1 CGAC
1280264 TGTGACAACA
Statistics
Matches: 104, Mismatches: 48, Indels: 10
0.64 0.30 0.06
Matches are distributed among these distances:
15 94 0.90
16 1 0.01
17 1 0.01
18 8 0.08
ACGTcount: A:0.46, C:0.26, G:0.20, T:0.08
Consensus pattern (15 bp):
CGACAACGACGACAA
Found at i:1280138 original size:30 final size:30
Alignment explanation
Indices: 1280104--1280171 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1280094 ACAGCGACGA
* *
1280104 CAACGTCAACGACGAC-ATCGACAACGATGG
1 CAACGACAACAACGACAAT-GACAACGATGG
*
1280134 CAACGACAACAACTACAATGACAACGATGG
1 CAACGACAACAACGACAATGACAACGATGG
*
1280164 AAACGACA
1 CAACGACA
1280172 GTGACGGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (30 bp):
CAACGACAACAACGACAATGACAACGATGG
Found at i:1280220 original size:48 final size:45
Alignment explanation
Indices: 1280134--1280236 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 45
1280124 ACAACGATGG
* * * *
1280134 CAACGACAACAACTACAATGACAACGATGGAAACGACAGTGACGGTAA
1 CAACAACAACAACAACAATGACAACGATCGAAACGACAGGGAC---AA
* *
1280182 CAACAACAACAACAATAATGACAACGA-CGACAATGACAGGGACAA
1 CAACAACAACAACAACAATGACAACGATCGA-AACGACAGGGACAA
1280227 CAACAACAAC
1 CAACAACAAC
1280237 GATGACAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
45 12 0.25
47 2 0.04
48 34 0.71
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.08
Consensus pattern (45 bp):
CAACAACAACAACAACAATGACAACGATCGAAACGACAGGGACAA
Found at i:1280613 original size:33 final size:33
Alignment explanation
Indices: 1280565--1280630 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1280555 AGTCCGACTC
1280565 GATAAAATAACCATGGACAATGAATAATCGTAA
1 GATAAAATAACCATGGACAATGAATAATCGTAA
* *
1280598 GATAAGATAATCATGGACAATGAATAATCGTAA
1 GATAAAATAACCATGGACAATGAATAATCGTAA
1280631 TAATATTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.23
Consensus pattern (33 bp):
GATAAAATAACCATGGACAATGAATAATCGTAA
Found at i:1280626 original size:17 final size:17
Alignment explanation
Indices: 1280570--1280626 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1280560 GACTCGATAA
*
1280570 AATAACCATGGACAATG
1 AATAATCATGGACAATG
* * *
1280587 AATAATCGTAAGATAA-G
1 AATAATCAT-GGACAATG
1280604 -ATAATCATGGACAATG
1 AATAATCATGGACAATG
1280620 AATAATC
1 AATAATC
1280627 GTAATAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.13
16 8 0.27
17 14 0.47
18 4 0.13
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (17 bp):
AATAATCATGGACAATG
Found at i:1289166 original size:30 final size:29
Alignment explanation
Indices: 1289130--1289246 Score: 132
Period size: 30 Copynumber: 3.9 Consensus size: 29
1289120 GAGATAGAAC
1289130 AAAATAAAAAAGAAGAAGGAAAAAAGAAGA
1 AAAATAAAAAAGAAGAAGG-AAAAAGAAGA
1289160 AAAATAAAAAAGAAGAAGGAAAAAGAAGA
1 AAAATAAAAAAGAAGAAGGAAAAAGAAGA
* *
1289189 AAAAGAAAAAAGATAGAA--AAATATGAAGAA
1 AAAATAAAAAAGA-AGAAGGAAA-AAGAAG-A
*
1289219 AAAAGAAAAAAGCAA-AAGAGAAAAAGAA
1 AAAATAAAAAAG-AAGAAG-GAAAAAGAA
1289247 AAAGGAGAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.04
29 29 0.38
30 37 0.48
31 5 0.06
32 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (29 bp):
AAAATAAAAAAGAAGAAGGAAAAAGAAGA
Found at i:1289168 original size:16 final size:16
Alignment explanation
Indices: 1289130--1289249 Score: 85
Period size: 16 Copynumber: 7.6 Consensus size: 16
1289120 GAGATAGAAC
*
1289130 AAAATAAAAAAGAAG-
1 AAAAGAAAAAAGAAGA
*
1289145 -AAGGAAAAAAGAAGA
1 AAAAGAAAAAAGAAGA
*
1289160 AAAATAAAAAAGAAG-
1 AAAAGAAAAAAGAAGA
*
1289175 --AAGGAAAAAGAAGA
1 AAAAGAAAAAAGAAGA
1289189 AAAAGAAAAAAGATAGAA
1 AAAAGAAAAAAGA-AG-A
1289207 AAATATGAAGAAAA-AAGA
1 AAA-A-GAA-AAAAGAAGA
*
1289225 AAAA-AGCAAAAG-AGA
1 AAAAGA-AAAAAGAAGA
1289240 AAAAGAAAAA
1 AAAAGAAAAA
1289250 GGAGAAAATA
Statistics
Matches: 83, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
13 11 0.13
14 12 0.14
15 15 0.18
16 23 0.28
17 3 0.04
18 8 0.10
19 3 0.04
20 4 0.05
21 4 0.05
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAAAGAAGA
Found at i:1289195 original size:38 final size:38
Alignment explanation
Indices: 1289149--1289229 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
1289139 AAGAAGAAGG
*
1289149 AAAAAAGAAGAAAA-ATA-AAAAAGAAGAAGGAAAAAGA
1 AAAAAAGAA-AAAAGATAGAAAAAGAAGAAGAAAAAAGA
* *
1289186 AGAAAAAGAAAAAAGATAGAAAAATATGAAGAAAAAAGA
1 A-AAAAAGAAAAAAGATAGAAAAAGAAGAAGAAAAAAGA
1289225 AAAAA
1 AAAAA
1289230 GCAAAAGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 5 0.13
38 15 0.39
39 18 0.47
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (38 bp):
AAAAAAGAAAAAAGATAGAAAAAGAAGAAGAAAAAAGA
Found at i:1289218 original size:12 final size:10
Alignment explanation
Indices: 1289135--1289229 Score: 65
Period size: 9 Copynumber: 9.4 Consensus size: 10
1289125 AGAACAAAAT
1289135 AAAAAAGAAG
1 AAAAAAGAAG
1289145 AAGGAAAA-AAG
1 AA--AAAAGAAG
* *
1289156 AAGAAA-AAT
1 AAAAAAGAAG
1289165 AAAAAAGAAG
1 AAAAAAGAAG
*
1289175 AAGGAAA-AAG
1 AA-AAAAGAAG
*
1289185 AAGAAA-AAG
1 AAAAAAGAAG
1289194 AAAAAAGATAG
1 AAAAAAGA-AG
1289205 AAAAATATGAAG
1 AAAAA-A-GAAG
1289217 AAAAAAGAA-
1 AAAAAAGAAG
1289226 AAAA
1 AAAA
1289230 GCAAAAGAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
9 26 0.37
10 15 0.21
11 16 0.23
12 12 0.17
13 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (10 bp):
AAAAAAGAAG
Done.