Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_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: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 16
Found at i:997716 original size:81 final size:80
Alignment explanation
Indices: 997506--997701 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 80
997496 GTGTACTTGG
* * *
997506 CAGAAAGGTGTCAATTATGAAAGTTAGATGAACA-GTTAAATAACATTGAGTAAAAAATAATTGC
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAA-AGGTTAAATACCATTGAGTAAAAAATAATGGC
* *
997570 CTAACCGTGCATTTGG
65 CTAACCGTACATTTGA
* * * * * *
997586 TAGAAAGGTGTCAATTATGCCAATTAGATGAACGTTTAAATACCGTTGAGTAAAATAATAATGGC
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGTTAAATACCATTGAGTAAAA-AATAATGGC
**
997651 CTAATTGTACATTTGA
65 CTAACCGTACATTTGA
*
997667 CAGAAAGGTGTCATTTATGACAGTTAGATGAAAGG
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAAAGG
997702 ATAAGTTCCT
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
80 46 0.48
81 49 0.52
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (80 bp):
CAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGTTAAATACCATTGAGTAAAAAATAATGGCC
TAACCGTACATTTGA
Found at i:997727 original size:297 final size:298
Alignment explanation
Indices: 997040--997903 Score: 1234
Period size: 297 Copynumber: 2.9 Consensus size: 298
997030 CGGTCTAAAA
* * *
997040 TAAAATATTAATAGGCCTAATTGTGCATTTGACAGAAAGGTGTAATTTATGCTAGTTAGATGAAA
1 TAAAATAATAAT-GGCCTAATTGTACATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAA
* * * *
997105 GGCTAAGAGCCTTTGAGGCCTACCTGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATG
65 GGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATG
* * * *
997170 AAAGGCTAAATGCCTTTGAGGCTTAACTGTGTATTTGGCAGAAATGTGTCAGTTATGCCAGTTAG
130 AAAGGCTAAATGCCTTTGAGGCCTAACTGTGTATTTGGCAGAAAGGTGTCAATTATGCAAGTTAG
* * *
997235 ATGAACAGTTAAATACCGTTGAGTAAAAGAATAATGGTCTAACTGTGCATTTGGCATAAAGGTGT
195 ATGAACAGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACCGTGCATTTGGCAGAAAGGTGT
*
997300 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
260 CAATTATGCCAATTAGATGAACGGTTAAATACCGTTGAG
* * *
997339 TAAAAGAATAATGGCCTAACTGTGTAC--TTGA-ATGGAATGTGTCATTTATGCTAGTTAGATGA
1 TAAAATAATAATGGCCTAA-T-TGTACATTTGACA-GAAAGGTGTCATTTATGCTAGTTAGATGA
*
997401 AAGGCTAAGTGCCTTTGAGGCCAAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGA
63 AAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGA
* * *
997466 TGAAATGCTAAATGCCTTTGAGGCCTAACTGTGTACTTGGCAGAAAGGTGTCAATTATGAAAGTT
128 TGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGTATTTGGCAGAAAGGTGTCAATTATGCAAGTT
* * * *
997531 AGATGAACAGTTAAATAACATTGAGTAAAA-AATAATTGCCTAACCGTGCATTTGGTAGAAAGGT
193 AGATGAACAGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACCGTGCATTTGGCAGAAAGGT
*
997595 GTCAATTATGCCAATTAGATGAACGTTTAAATACCGTTGAG
258 GTCAATTATGCCAATTAGATGAACGGTTAAATACCGTTGAG
997636 TAAAATAATAATGGCCTAATTGTACATTTGACAGAAAGGTGTCATTTATGAC-AGTTAGATGAAA
1 TAAAATAATAATGGCCTAATTGTACATTTGACAGAAAGGTGTCATTTATG-CTAGTTAGATGAAA
* * * *
997700 GGATAAGTTCCTTTGAGGCCTAACTGTGCATTTGATAGAAATGTGCCATTTATGCCAGTTAGATG
65 GGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATG
* * * * *
997765 AAAGGCTAAATGCCTTTGAGGCCTAACTATGCATTTGGCAGAAAGATATCAATTATGCTAGTTAG
130 AAAGGCTAAATGCCTTTGAGGCCTAACTGTGTATTTGGCAGAAAGGTGTCAATTATGCAAGTTAG
* * ** * * * * *
997830 ATGAACGGTTAAATACCGTTGAGTAAAAGACTAATGGATTAGCTGTACATTTGACAGAAAAGTGT
195 ATGAACAGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACCGTGCATTTGGCAGAAAGGTGT
*
997895 CAAATATGC
260 CAATTATGC
997904 AAGTTATATT
Statistics
Matches: 500, Mismatches: 57, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
295 5 0.01
296 1 0.00
297 260 0.52
298 219 0.44
299 11 0.02
300 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (298 bp):
TAAAATAATAATGGCCTAATTGTACATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAG
GCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGA
AAGGCTAAATGCCTTTGAGGCCTAACTGTGTATTTGGCAGAAAGGTGTCAATTATGCAAGTTAGA
TGAACAGTTAAATACCGTTGAGTAAAAGAATAATGGCCTAACCGTGCATTTGGCAGAAAGGTGTC
AATTATGCCAATTAGATGAACGGTTAAATACCGTTGAG
Found at i:997759 original size:68 final size:68
Alignment explanation
Indices: 997648--997809 Score: 225
Period size: 68 Copynumber: 2.4 Consensus size: 68
997638 AAATAATAAT
* * * * *
997648 GGCCTAATTGTACATTTGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGGATAAGTTCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGACAGTTAGATGAAAGGATAAATGCCTT
997713 TGA
66 TGA
* * * *
997716 GGCCTAACTGTGCATTTGATAGAAATGTGCCATTTATGCCAGTTAGATGAAAGGCTAAATGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGACAGTTAGATGAAAGGATAAATGCCTT
997781 TGA
66 TGA
* *
997784 GGCCTAACTATGCATTTGGCAGAAAG
1 GGCCTAACTGTGCATTTGACAGAAAG
997810 ATATCAATTA
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 81 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGACAGTTAGATGAAAGGATAAATGCCTT
TGA
Found at i:997821 original size:68 final size:67
Alignment explanation
Indices: 997660--997852 Score: 224
Period size: 68 Copynumber: 2.8 Consensus size: 67
997650 CCTAATTGTA
* * *
997660 CATTTGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGGATAAGTTCCTTTGAGGCCTAACT
1 CATTTGACAGAAA-GTGTCATTTATGCCAGTTAGATGAAAGGATAAATACCTTTGAGGCCTAACT
*
997725 GTG
65 ATG
* * * *
997728 CATTTGATAGAAATGTGCCATTTATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACT
1 CATTTGACAGAAA-GTGTCATTTATGCCAGTTAGATGAAAGGATAAATACCTTTGAGGCCTAACT
997793 ATG
65 ATG
* * * * * * *
997796 CATTTGGCAGAAAGATATCAATTATGCTAGTTAGATGAACGGTTAAATACCGTTGAG
1 CATTTGACAGAAAG-TGTCATTTATGCCAGTTAGATGAAAGGATAAATACCTTTGAG
997853 TAAAAGACTA
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
67 1 0.01
68 105 0.99
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (67 bp):
CATTTGACAGAAAGTGTCATTTATGCCAGTTAGATGAAAGGATAAATACCTTTGAGGCCTAACTA
TG
Found at i:1001536 original size:37 final size:35
Alignment explanation
Indices: 1001481--1001551 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
1001471 AAAGATAAAA
1001481 GAAATGATTTAAGGAAAGGAAATGAAATGAAAAGAAT
1 GAAATGATTTAAGGAAAGG-AATGAAA-GAAAAGAAT
* *
1001518 GAAATGGTTT-AGGAAAAGGAATGAAAGCAAAGAA
1 GAAATGATTTAAGG-AAAGGAATGAAAGAAAAGAA
1001552 GGAATGGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 7 0.23
36 10 0.32
37 14 0.45
ACGTcount: A:0.55, C:0.01, G:0.27, T:0.17
Consensus pattern (35 bp):
GAAATGATTTAAGGAAAGGAATGAAAGAAAAGAAT
Found at i:1001541 original size:36 final size:36
Alignment explanation
Indices: 1001465--1001551 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 36
1001455 AAGAAGAAAA
*
1001465 AAATGGAAAGATAA-AA-GAAATGATTTAAGGAAAGG
1 AAAT-GAAAGAAAAGAATGAAATGATTTAAGGAAAGG
*
1001500 AAATGAAATGAAAAGAATGAAATGGTTT-AGGAAAAGG
1 AAATGAAA-GAAAAGAATGAAATGATTTAAGG-AAAGG
*
1001537 -AATGAAAGCAAAGAA
1 AAATGAAAGAAAAGAA
1001552 GGAATGGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
34 4 0.09
35 15 0.33
36 12 0.27
37 14 0.31
ACGTcount: A:0.57, C:0.01, G:0.25, T:0.16
Consensus pattern (36 bp):
AAATGAAAGAAAAGAATGAAATGATTTAAGGAAAGG
Found at i:1003668 original size:18 final size:18
Alignment explanation
Indices: 1003645--1003688 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1003635 CTATTTTATT
1003645 TAACCCCACAATTGTCGG
1 TAACCCCACAATTGTCGG
1003663 TAACCCCACAATTGTCGG
1 TAACCCCACAATTGTCGG
1003681 TAACCCCA
1 TAACCCCA
1003689 AATACTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (18 bp):
TAACCCCACAATTGTCGG
Found at i:1012922 original size:16 final size:16
Alignment explanation
Indices: 1012898--1012942 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1012888 CGCATCGAAA
*
1012898 GGGGGCTTTGCGAATT
1 GGGGTCTTTGCGAATT
*
1012914 GGGGTCTTTCCGAATT
1 GGGGTCTTTGCGAATT
1012930 GGGGTCTTATGCG
1 GGGGTCTT-TGCG
1012943 CGATTCCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.11, C:0.16, G:0.40, T:0.33
Consensus pattern (16 bp):
GGGGTCTTTGCGAATT
Found at i:1026271 original size:31 final size:31
Alignment explanation
Indices: 1026229--1026368 Score: 199
Period size: 31 Copynumber: 4.5 Consensus size: 31
1026219 TAGTTATTTC
*
1026229 GGGGACCATATTGCAAACAGACAAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* *
1026260 GGGGACTATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* *
1026291 GGGGACCATATTGCAAATAAACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
1026322 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* **
1026353 GGCGACTGTATTGCAA
1 GGGGACCATATTGCAA
1026369 GTTTTAAAAG
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 96 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:1031448 original size:50 final size:50
Alignment explanation
Indices: 1031373--1031480 Score: 216
Period size: 50 Copynumber: 2.2 Consensus size: 50
1031363 AGTGGATTCA
1031373 CGCCAATAGTAGTCTGTTGCGCCCGCAATCTAATGGGTAATGGTGTATAG
1 CGCCAATAGTAGTCTGTTGCGCCCGCAATCTAATGGGTAATGGTGTATAG
1031423 CGCCAATAGTAGTCTGTTGCGCCCGCAATCTAATGGGTAATGGTGTATAG
1 CGCCAATAGTAGTCTGTTGCGCCCGCAATCTAATGGGTAATGGTGTATAG
1031473 CGCCAATA
1 CGCCAATA
1031481 AGAGGACGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (50 bp):
CGCCAATAGTAGTCTGTTGCGCCCGCAATCTAATGGGTAATGGTGTATAG
Found at i:1036339 original size:51 final size:51
Alignment explanation
Indices: 1036258--1036364 Score: 169
Period size: 51 Copynumber: 2.1 Consensus size: 51
1036248 AGATTGCTAA
* * *
1036258 ACATCTTAACATAGTTAGGTTGCATTAGGTATGTGTTGTTTTAAGTAATGT
1 ACATCTCAACAGAGTTAGGTTGCATGAGGTATGTGTTGTTTTAAGTAATGT
* *
1036309 ACATCTCAACAGAGTTAGGTTGCATGAGGTATGTGTTGTTTTAATTATTGT
1 ACATCTCAACAGAGTTAGGTTGCATGAGGTATGTGTTGTTTTAAGTAATGT
1036360 ACATC
1 ACATC
1036365 GTACTTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.41
Consensus pattern (51 bp):
ACATCTCAACAGAGTTAGGTTGCATGAGGTATGTGTTGTTTTAAGTAATGT
Found at i:1037907 original size:6 final size:6
Alignment explanation
Indices: 1037831--1037906 Score: 134
Period size: 6 Copynumber: 12.7 Consensus size: 6
1037821 CATATATTCT
1037831 ATATCC ATATCC ATATCC ATATCC ATATCC ATATCC ATATCC ATATCC
1 ATATCC ATATCC ATATCC ATATCC ATATCC ATATCC ATATCC ATATCC
* *
1037879 ATATCC ATATCC ATATAC ATATAC ATAT
1 ATATCC ATATCC ATATCC ATATCC ATAT
1037907 ATTACTCATG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATCC
Found at i:1041978 original size:90 final size:90
Alignment explanation
Indices: 1041864--1042041 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
1041854 TAATCCTGAA
* * *
1041864 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1041929 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
1041954 TATTAAATTTCAATTAATTGAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1042019 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
1042042 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1047734 original size:31 final size:31
Alignment explanation
Indices: 1047698--1047768 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
1047688 GCAACCCTTG
1047698 GGTAGGCTCCGAGGCCCCGAGAAATGTCTTA
1 GGTAGGCTCCGAGGCCCCGAGAAATGTCTTA
*
1047729 GGTAGGCTCCGAGGCCCCGAGAACTGTCTTA
1 GGTAGGCTCCGAGGCCCCGAGAAATGTCTTA
1047760 GGTAGGCTC
1 GGTAGGCTC
1047769 TCAGTCCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.20
Consensus pattern (31 bp):
GGTAGGCTCCGAGGCCCCGAGAAATGTCTTA
Found at i:1049596 original size:23 final size:25
Alignment explanation
Indices: 1049561--1049627 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 25
1049551 TTATTTTTGT
1049561 TTTAAA-TATTATATTAA-TAATC-A
1 TTTAAATTA-TATATTAAGTAATCAA
*
1049584 TTTAAATTATATATGAAATGTAATCAA
1 TTTAAATTATATAT-TAA-GTAATCAA
1049611 TTATAAATTATATATTA
1 TT-TAAATTATATATTA
1049628 GAAGGATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 11 0.31
24 4 0.11
26 5 0.14
27 4 0.11
28 12 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (25 bp):
TTTAAATTATATATTAAGTAATCAA
Found at i:1049643 original size:14 final size:15
Alignment explanation
Indices: 1049619--1049648 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1049609 AATTATAAAT
1049619 TATATATTAGAAGGA
1 TATATATTAGAAGGA
1049634 TATATA-TAGAAGGA
1 TATATATTAGAAGGA
1049648 T
1 T
1049649 GTAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
TATATATTAGAAGGA
Found at i:1050914 original size:17 final size:18
Alignment explanation
Indices: 1050892--1050927 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1050882 AACAATATAT
1050892 TTAAAAACA-AAAATAAA
1 TTAAAAACATAAAATAAA
*
1050909 TTAAAAATATAAAATAAA
1 TTAAAAACATAAAATAAA
1050927 T
1 T
1050928 GACTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
TTAAAAACATAAAATAAA
Found at i:1052270 original size:20 final size:19
Alignment explanation
Indices: 1052247--1052296 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1052237 TTTTTTTTAT
* *
1052247 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1052267 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1052286 TATTTA-ATATA
1 TATTTATATATA
1052297 ATATAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 7 0.27
20 15 0.58
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1052300 original size:14 final size:15
Alignment explanation
Indices: 1052281--1052392 Score: 108
Period size: 14 Copynumber: 7.4 Consensus size: 15
1052271 TATATGTATT
*
1052281 TAATATAT-TTAATA
1 TAATATATAATAATA
1052295 TAATATAATAATAATA
1 TAATAT-ATAATAATA
1052311 TAATA-ATAATAATA
1 TAATATATAATAATA
1052325 TAATA-ATAATAATAA
1 TAATATATAATAAT-A
*
1052340 TAATGATAATAGTAATAA
1 TAAT-AT-ATAATAAT-A
1052358 TAATA-ATAATAATAA
1 TAATATATAATAAT-A
*
1052373 TAAT-TTTAATAATA
1 TAATATATAATAATA
1052387 TAATAT
1 TAATAT
1052393 GGATAAAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
14 33 0.38
15 28 0.33
16 11 0.13
17 1 0.01
18 13 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TAATATATAATAATA
Found at i:1052307 original size:3 final size:3
Alignment explanation
Indices: 1052290--1052391 Score: 133
Period size: 3 Copynumber: 35.7 Consensus size: 3
1052280 TTAATATATT
1052290 TAA T-A TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * **
1052334 TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1052382 TAA T-A TAA TA
1 TAA TAA TAA TA
1052392 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
2 10 0.12
3 76 0.88
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1052906 original size:113 final size:113
Alignment explanation
Indices: 1052692--1053463 Score: 1348
Period size: 113 Copynumber: 6.9 Consensus size: 113
1052682 ATAGAATGCC
* *
1052692 AAAA-GTTGAACAAGTTCTTCTCATTATGAA--ACTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1052753 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTTAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
*
1052800 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1052865 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
*
1052913 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1052978 TATGAAC-TTCTCTGGAAAAGATGATCCA--AAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1053023 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1053088 TATGAAC-TTCTCTGGAAAAGCTAACCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1053135 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1053200 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1053248 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1053313 TATGAACTTTCTCTGGAAAAGCTAACCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
1053361 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1053426 TATGAACTTTCTCTGGAAAAGCTAA-CTCATCAAATGAT
66 TATGAACTTTCTCTGGAAAAGATAATC-CATCAAATGAT
1053464 AGATTTGAAT
Statistics
Matches: 639, Mismatches: 16, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
108 4 0.01
109 25 0.04
110 106 0.17
111 6 0.01
112 141 0.22
113 357 0.56
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGT
Found at i:1053309 original size:335 final size:337
Alignment explanation
Indices: 1052692--1053463 Score: 1367
Period size: 335 Copynumber: 2.3 Consensus size: 337
1052682 ATAGAATGCC
* *
1052692 AAAA-GTTGAACAAGTTCTTCTCATTATGAA--ACTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
1052753 TATGAACTTCTCTGGAAAAGATAATCCATCAATTGATGAATTTAGGTAAAAGGTTGAACAAATTC
66 TATGAACTTCTCTGGAAAAGCTAACCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTC
*
1052818 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
*
1052883 AAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
196 AAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* *
1052948 TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAAC-TTCTCTGGAAAAGATGATCCA-AAATG
261 TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGGAAAAGATAACCCACAAATG
1053011 ATGAATTCAGGT
326 ATGAATTCAGGT
1053023 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1053088 TATGAACTTCTCTGGAAAAGCTAACCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTC
66 TATGAACTTCTCTGGAAAAGCTAACCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTC
1053153 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1053218 AAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
196 AAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* *
1053283 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAACCCATCAAAT
261 TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGGAAAAGATAACCCA-CAAAT
1053348 GATGAATTCAGGT
325 GATGAATTCAGGT
1053361 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1053426 TATGAACTTTCTCTGGAAAAGCTAACTCATCAAATGAT
66 TATGAAC-TTCTCTGGAAAAGCTAACCCATCAAATGAT
1053464 AGATTTGAAT
Statistics
Matches: 420, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
331 4 0.01
332 25 0.06
334 6 0.01
335 249 0.59
336 18 0.04
338 89 0.21
339 29 0.07
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (337 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTCTGGAAAAGCTAACCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGGAAAAGATAACCCACAAATG
ATGAATTCAGGT
Found at i:1054256 original size:83 final size:83
Alignment explanation
Indices: 1054097--1054300 Score: 304
Period size: 83 Copynumber: 2.5 Consensus size: 83
1054087 CCTACTGAAT
* * * *
1054097 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATGTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCCAAATTAAA
*
1054162 TGATTGGTTCTG-CCAAAC
66 TGATTGATTCTGTCC-AAC
*
1054180 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCAAATTAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACAAATTCATCTTCCAAATTAA
* *
1054244 ATGCTTGATTCTGTCCAAT
65 ATGATTGATTCTGTCCAAC
1054263 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1054301 TGATTCTGTC
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
83 107 0.96
84 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCCAAATTAAA
TGATTGATTCTGTCCAAC
Found at i:1054312 original size:52 final size:52
Alignment explanation
Indices: 1054244--1054508 Score: 530
Period size: 52 Copynumber: 5.1 Consensus size: 52
1054234 TCCAAATTAA
1054244 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1054296 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1054348 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1054400 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1054452 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1054504 ATGCT
1 ATGCT
1054509 ATGAACACAT
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 213 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (52 bp):
ATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:1055658 original size:1 final size:1
Alignment explanation
Indices: 1055652--1055751 Score: 83
Period size: 1 Copynumber: 100.0 Consensus size: 1
1055642 TTGACCTCCC
* * ** ** * * *
1055652 TTTTTTTCTTTCTTTTTTTTTCCTTTTTTTTTCCTTTTTTTTTTCTTTTTTCTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
1055717 TTCTTTTTTTCTTTTTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1055752 CTTCAAGCAT
Statistics
Matches: 77, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:1055669 original size:11 final size:10
Alignment explanation
Indices: 1055653--1055744 Score: 98
Period size: 11 Copynumber: 8.6 Consensus size: 10
1055643 TGACCTCCCT
1055653 TTTTTTCTTTC
1 TTTTTT-TTTC
1055664 TTTTTTTTTCC
1 TTTTTTTTT-C
1055675 TTTTTTTTTCC
1 TTTTTTTTT-C
1055686 TTTTTTTTTTC
1 -TTTTTTTTTC
1055697 TTTTTTCTTT-
1 TTTTTT-TTTC
1055707 TTTTCTTTTT-
1 TTTT-TTTTTC
1055717 TTCTTTTTTTC
1 TT-TTTTTTTC
1055728 TTTTTTTTTTC
1 -TTTTTTTTTC
1055739 TTTTTT
1 TTTTTT
1055745 CTTTTTTCTT
Statistics
Matches: 74, Mismatches: 0, Indels: 15
0.83 0.00 0.17
Matches are distributed among these distances:
10 29 0.39
11 34 0.46
12 11 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1055680 original size:23 final size:23
Alignment explanation
Indices: 1055650--1055737 Score: 110
Period size: 22 Copynumber: 3.9 Consensus size: 23
1055640 CCTTGACCTC
1055650 CCTTTTTTTCTTTCTTTTTTTTT
1 CCTTTTTTTCTTTCTTTTTTTTT
*
1055673 CCTTTTTTT-TTCCTTTTTTTTT
1 CCTTTTTTTCTTTCTTTTTTTTT
* *
1055695 TC-TTTTTTCTTTTTTTCTTTTTT
1 CCTTTTTTTCTTTCTTT-TTTTTT
*
1055718 TCTTTTTTTCTTT-TTTTTTT
1 CCTTTTTTTCTTTCTTTTTTT
1055738 CTTTTTTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.10
22 22 0.38
23 20 0.34
24 10 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (23 bp):
CCTTTTTTTCTTTCTTTTTTTTT
Found at i:1055689 original size:7 final size:7
Alignment explanation
Indices: 1055653--1055754 Score: 104
Period size: 7 Copynumber: 14.3 Consensus size: 7
1055643 TGACCTCCCT
1055653 TTTTTTC
1 TTTTTTC
1055660 TTTCTTT-
1 TTT-TTTC
1055667 TTTTTTCC
1 TTTTTT-C
1055675 TTTTTT-
1 TTTTTTC
*
1055681 TTTCCTTTT
1 TTT--TTTC
1055690 TTTTTTC
1 TTTTTTC
1055697 TTTTTTC
1 TTTTTTC
1055704 TTTTTTTC
1 -TTTTTTC
1055712 TTTTTTTC
1 -TTTTTTC
1055720 TTTTTT-
1 TTTTTTC
*
1055726 TCTTTT-
1 TTTTTTC
1055732 TTTTTTC
1 TTTTTTC
1055739 TTTTTTC
1 TTTTTTC
1055746 TTTTTTC
1 TTTTTTC
1055753 TT
1 TT
1055755 CAAGCATAAT
Statistics
Matches: 84, Mismatches: 3, Indels: 16
0.82 0.03 0.16
Matches are distributed among these distances:
6 16 0.19
7 38 0.45
8 27 0.32
9 3 0.04
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:1055725 original size:42 final size:42
Alignment explanation
Indices: 1055653--1055751 Score: 146
Period size: 42 Copynumber: 2.3 Consensus size: 42
1055643 TGACCTCCCT
*
1055653 TTTTTTCTTTCTTTTTTTTTCCTTTTTTTTTCCTTTTTTTTTTC
1 TTTTTTCTTT-TTTTTTTTT-CTTCTTTTTTCCTTTTTTTTTTC
*
1055697 TTTTTTCTTTTTTTCTTTTT-TTCTTTTTTTCTTTTTTTTTTC
1 TTTTTTCTTTTTTT-TTTTTCTTCTTTTTTCCTTTTTTTTTTC
1055739 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
1055752 CTTCAAGCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
42 33 0.63
43 4 0.08
44 15 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (42 bp):
TTTTTTCTTTTTTTTTTTTCTTCTTTTTTCCTTTTTTTTTTC
Found at i:1055743 original size:34 final size:34
Alignment explanation
Indices: 1055650--1055752 Score: 131
Period size: 34 Copynumber: 3.0 Consensus size: 34
1055640 CCTTGACCTC
*
1055650 CCTTTTTTTCTTTCTTTTTTT-TTCCTTT-TTTTTT
1 CCTTTTTTTCTTT-TTTTTTTCTT-TTTTCTTTTTT
*
1055684 CCTTTTTTT-TTTCTTTTTTCTTTTTTTCTTTTTT
1 CCTTTTTTTCTTTTTTTTTTC-TTTTTTCTTTTTT
*
1055718 TCTTTTTTTCTTTTTTTTTTCTTTTTTCTTTTTT
1 CCTTTTTTTCTTTTTTTTTTCTTTTTTCTTTTTT
1055752 C
1 C
1055753 TTCAAGCATA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
32 6 0.10
33 6 0.10
34 38 0.63
35 10 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (34 bp):
CCTTTTTTTCTTTTTTTTTTCTTTTTTCTTTTTT
Found at i:1067184 original size:19 final size:19
Alignment explanation
Indices: 1067163--1067198 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1067153 AATATATTTA
1067163 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
1067181 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
1067199 GACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:1068545 original size:20 final size:20
Alignment explanation
Indices: 1068520--1068576 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1068510 TCTGTAATTA
* *
1068520 TATTTTTATTATTATTTATT
1 TATTTTTAATAATATTTATT
*
1068540 TATTTTTAATAATATTTATA
1 TATTTTTAATAATATTTATT
* *
1068560 TGTATTTAAT-ATATTTA
1 TATTTTTAATAATATTTA
1068577 ATAATAATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTTTAATAATATTTATT
Found at i:1068583 original size:3 final size:3
Alignment explanation
Indices: 1068575--1068672 Score: 153
Period size: 3 Copynumber: 32.7 Consensus size: 3
1068565 TTAATATATT
*
1068575 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1068623 TGA TAA TAGA -AA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1068668 TAA TA
1 TAA TA
1068673 TGGATAAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
2 1 0.01
3 85 0.98
4 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1070574 original size:184 final size:185
Alignment explanation
Indices: 1070260--1070613 Score: 597
Period size: 184 Copynumber: 1.9 Consensus size: 185
1070250 ATTAAATTTT
* *
1070260 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATCATTTAAAACCCAATTAATAA
1070325 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAAA-TT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAAATTT
* *
1070389 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGCTTTTTAATTAAAA
131 TTATTTTATAATTACATATTATTTAAATTAATTATAAACTGCTTTTTAATTAAAA
1070444 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAA-CTATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATC-ATTTAAAACCCAATTAATA
* * **
1070508 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTTATTAATTAGAAAATT-TATCTGAAAT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATAT-AAAAAT
1070572 TTTTATTTTATAATTACATATTATTTAAATTAATTATAAACT
129 TTTTATTTTATAATTACATATTATTTAAATTAATTATAAACT
1070614 TTTTTTTTGA
Statistics
Matches: 159, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
183 4 0.03
184 115 0.72
185 40 0.25
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAAATTT
TTATTTTATAATTACATATTATTTAAATTAATTATAAACTGCTTTTTAATTAAAA
Found at i:1072817 original size:91 final size:91
Alignment explanation
Indices: 1072664--1073181 Score: 849
Period size: 91 Copynumber: 5.7 Consensus size: 91
1072654 GAGCCAGAAG
* * * *
1072664 GAACAAGTTCTTCTCATTATGAACTTTTTCTCCTTCA-CGGATGAGTTCTTCTCGTTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
* *
1072728 TCCAATGGAAATACTGAGCCAAGGTT
66 TCCACTGGAAATGCTGAGCCAAGGTT
* * * *
1072754 GAACAAGTTATTTTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTTATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
*
1072819 TCCACTGGAAATGTTGAGCCAAGGTT
66 TCCACTGGAAATGCTGAGCCAAGGTT
*
1072845 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAATTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
*
1072910 TCCACTGGAAATGCTAAGCCAAGGTT
66 TCCACTGGAAATGCTGAGCCAAGGTT
1072936 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
1073001 TCCACTGGAAATGCTGAGCCAAGGTT
66 TCCACTGGAAATGCTGAGCCAAGGTT
* * *
1073027 GAACAAGTTATTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTATTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
* * *
1073092 TCCACTGGAATTGTTGAGCCAAAGTT
66 TCCACTGGAAATGCTGAGCCAAGGTT
*
1073118 TAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACT
1073182 TTTTCTCCCT
Statistics
Matches: 398, Mismatches: 29, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
90 33 0.08
91 365 0.92
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (91 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
TCCACTGGAAATGCTGAGCCAAGGTT
Found at i:1072883 original size:21 final size:21
Alignment explanation
Indices: 1072857--1072898 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1072847 ACAAGTTCTT
1072857 CTCATT-ATGAACTTCTTCTCC
1 CTCATTGATGAA-TTCTTCTCC
1072878 CTCATTGGATGAATTCTTCTC
1 CTCATT-GATGAATTCTTCTC
1072899 ATTATGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.43
Consensus pattern (21 bp):
CTCATTGATGAATTCTTCTCC
Found at i:1073154 original size:21 final size:21
Alignment explanation
Indices: 1073130--1073195 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1073120 ACAAGTTCTT
1073130 CTCATTATGAACTTCTTCTCC
1 CTCATTATGAACTTCTTCTCC
*
1073151 CTCATTGGATG-AGTTC-T-T--
1 CTCATT--ATGAACTTCTTCTCC
*
1073169 CTCATTATGAACTTTTTCTCC
1 CTCATTATGAACTTCTTCTCC
1073190 CTCATT
1 CTCATT
1073196 GGATGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 7 0.20
19 1 0.03
20 1 0.03
21 13 0.37
22 4 0.11
23 3 0.09
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (21 bp):
CTCATTATGAACTTCTTCTCC
Found at i:1073177 original size:39 final size:39
Alignment explanation
Indices: 1073123--1073220 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
1073113 AAGTTTAACA
1073123 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
*
1073162 AGTTCTTCTCATTATGAACTTTTTCTCCCTCATTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
* *
1073201 ATTTATTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
1073221 CTCTACTAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.46
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
Found at i:1073717 original size:66 final size:66
Alignment explanation
Indices: 1073668--1073935 Score: 195
Period size: 66 Copynumber: 4.1 Consensus size: 66
1073658 TTTTTACAGG
*
1073668 GAGACAAAATTCAG-TTCAAGGGAAACGATCTCAAAGATCGGTGTTTCAAGGAAAACTGTCTCAA
1 GAGACAAAACT-AGTTTCAAGGGAAACGATCTCAAAGATCGGTGTTTCAAGGAAAACTGTCTCAA
1073732 GA
65 GA
***
1073734 GAGACAAAACTAGTTTCAAGGGAAACGATCTCAAAGATTTTATGTTTCAA-GAGAAACTGTC-CT
1 GAGACAAAACTAGTTTCAAGGGAAACGATCTCAAAGA-TCGGTGTTTCAAGGA-AAACTGTCTC-
*
1073797 AAGG
63 AAGA
* * * *
1073801 GAGACAAAATTTGTTTCAA---AATA-TAT-TCAAAGAT---T-TTTCCCAA-AAGAAACTGTCT
1 GAGACAAAACTAGTTTCAAGGGAA-ACGATCTCAAAGATCGGTGTTT--CAAGGA-AAACTGTCT
*
1073856 CAAGC
62 CAAGA
* * * * * * * *
1073861 GAGACAGAACTCGTTTTAAGGGAAACAATCTCAAAGGTTGGTGTTTCAAGTAAAAATGTCTCAA-
1 GAGACAAAACTAGTTTCAAGGGAAACGATCTCAAAGATCGGTGTTTCAAGGAAAACTGTCTCAAG
1073925 A
66 A
1073926 CGAGACAAAA
1 -GAGACAAAA
1073936 ATTGTTTTGA
Statistics
Matches: 163, Mismatches: 20, Indels: 38
0.74 0.09 0.17
Matches are distributed among these distances:
58 3 0.02
59 1 0.01
60 31 0.19
61 1 0.01
62 2 0.01
63 11 0.07
64 11 0.07
65 3 0.02
66 58 0.36
67 39 0.24
68 3 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (66 bp):
GAGACAAAACTAGTTTCAAGGGAAACGATCTCAAAGATCGGTGTTTCAAGGAAAACTGTCTCAAG
A
Found at i:1073808 original size:67 final size:66
Alignment explanation
Indices: 1073665--1073819 Score: 199
Period size: 66 Copynumber: 2.3 Consensus size: 66
1073655 AATTTTTTAC
*
1073665 AGGGAGACAAAATTCAG-TTCAAGGGAAACGATCTCAAAGATCGGTGTTTCAAGGAAAACTGTCT
1 AGGGAGACAAAATT-AGTTTCAAGGGAAACGATCTCAAAGATCGATGTTTCAAGGAAAACTGTCT
1073729 CA
65 CA
* * **
1073731 AGAGAGACAAAACTAGTTTCAAGGGAAACGATCTCAAAGATTTTATGTTTCAA-GAGAAACTGTC
1 AGGGAGACAAAATTAGTTTCAAGGGAAACGATCTCAAAGA-TCGATGTTTCAAGGA-AAACTGTC
1073795 -CTA
64 TC-A
*
1073798 AGGGAGACAAAATTTGTTTCAA
1 AGGGAGACAAAATTAGTTTCAA
1073820 AATATATTCA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
65 2 0.03
66 38 0.49
67 37 0.48
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (66 bp):
AGGGAGACAAAATTAGTTTCAAGGGAAACGATCTCAAAGATCGATGTTTCAAGGAAAACTGTCTC
A
Found at i:1073997 original size:37 final size:37
Alignment explanation
Indices: 1073909--1074017 Score: 150
Period size: 36 Copynumber: 3.0 Consensus size: 37
1073899 TGGTGTTTCA
*
1073909 AGTAAAAA-TGTCTCAAACGAGACAAAAATTGTTTTG
1 AGTAAAAATTGTCTCAAAAGAGACAAAAATTGTTTTG
*
1073945 AG-AAAAATTGTCTCAAAAGAGACAAAACTTGTTTTG
1 AGTAAAAATTGTCTCAAAAGAGACAAAAATTGTTTTG
** *
1073981 AGTAAAAATTGTCTCAAGTGAGACAAAATTTGCTTTT
1 AGTAAAAATTGTCTCAAAAGAGACAAAAATTG-TTTT
1074018 TTTTGTTGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 5 0.08
36 30 0.46
37 26 0.40
38 4 0.06
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (37 bp):
AGTAAAAATTGTCTCAAAAGAGACAAAAATTGTTTTG
Found at i:1074209 original size:90 final size:90
Alignment explanation
Indices: 1074054--1074335 Score: 469
Period size: 90 Copynumber: 3.1 Consensus size: 90
1074044 CTTGAAAATC
* * *
1074054 AGGCTTAGTTTTTAAACA-CTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCTGAA
1 AGGCTTAGTTTCTAAA-ATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAA
*
1074118 GGACTTACAAATCAAGAAACCCCTGA
65 GGACTTACAAATCAAGAAACCCCCGA
*
1074144 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGACCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAG
*
1074209 GACTTACAAATCAAGAAACCCCCAA
66 GACTTACAAATCAAGAAACCCCCGA
1074234 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTA-CACTGAAGGTCTTATGGATGGCCCGAA
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCC-AGCACTGAAGGTCTTATGGATGGCCCGAA
*
1074298 AGACTTACAAATCAAGAAACCCCCGA
65 GGACTTACAAATCAAGAAACCCCCGA
1074324 AGGCTTAGTTTC
1 AGGCTTAGTTTC
1074336 ATTTGAAAAT
Statistics
Matches: 181, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
89 1 0.01
90 179 0.99
91 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (90 bp):
AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAG
GACTTACAAATCAAGAAACCCCCGA
Found at i:1074388 original size:81 final size:81
Alignment explanation
Indices: 1074253--1074747 Score: 677
Period size: 81 Copynumber: 5.9 Consensus size: 81
1074243 TTCTAAAATC
* *
1074253 TCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1074318 CCCCGAAGGCTTAGTT
66 CCCCGAAGGCTTAGTT
*
1074334 TCATTTGAAAATATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
*
1074399 CTCCGAAGGCTTAGTTTCTAAAAT
66 CCCCGAAGGCTTAG----T----T
* * *
1074423 CTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAGGGCTTACAAATCAAGAAA
1 -TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAA
1074488 -CCCCGAAGGCTTAGTT
65 CCCCCGAAGGCTTAGTT
* *
1074504 TCATTTGAAAACATCTTGCACTAAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1074569 CCCCGAAGGCTTAGTTTCTAAAAT
66 CCCCGAAGGCTTAG----T----T
* *
1074593 CTCATTTGAAAACATCCTGTACTGAAGGTCTTATGGATGGCCTGAAGGACTTACAAATCAAGAAA
1 -TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAA
*
1074658 CCCCCAAAGGCTTAGTT
65 CCCCCGAAGGCTTAGTT
* * *
1074675 TCATTTGAAAACATCATGCACTAAAGGTCTTATGGATGGCCCGAAGGACTTAATAAATCAAGAAA
1 TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTT-ACAAATCAAGAAA
1074740 CCCCCGAA
65 CCCCCGAA
1074748 AATCAAGCTT
Statistics
Matches: 369, Mismatches: 25, Indels: 39
0.85 0.06 0.09
Matches are distributed among these distances:
80 59 0.16
81 137 0.37
82 20 0.05
85 3 0.01
86 1 0.00
89 15 0.04
90 134 0.36
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (81 bp):
TCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
CCCCGAAGGCTTAGTT
Found at i:1074424 original size:171 final size:171
Alignment explanation
Indices: 1074054--1074747 Score: 1104
Period size: 171 Copynumber: 4.0 Consensus size: 171
1074044 CTTGAAAATC
* *
1074054 AGGCTTAGTTTTTAAACA-CTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCTGAA
1 AGGCTTAGTTTCTAAA-ATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAA
* *
1074118 GGACTTACAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCA
65 GGACTTACAAATCAAGAAACCCCCGAAGGCTTAG----T----T-TCATTTGAAAACATCCTGCA
* * *
1074183 CTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCAA
121 CTAAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGA
* *
1074234 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAA
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
* *
1074299 GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCATTTGAAAATATCCTGCACTGAAGGTCT
66 GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCATTTGAAAACATCCTGCACTAAAGGTCT
*
1074364 TATGGATGGCCCGAAGGACTTACAAATCAAGAAACCTCCGA
131 TATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGA
1074405 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
* *
1074470 GGCTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCATTTGAAAACATCTTGCACTAAAGGTCT
66 GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCATTTGAAAACATCCTGCACTAAAGGTCT
1074534 TATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGA
131 TATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGA
**
1074575 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGTACTGAAGGTCTTATGGATGGCCTGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
* *
1074640 GACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCATTTGAAAACATCATGCACTAAAGGTCT
66 GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCATTTGAAAACATCCTGCACTAAAGGTCT
*
1074705 TATGGATGGCCCGAAGGACTTAATAAATCAAGAAACCCCCGA
131 TATGGATGGCCCGAAGGACTT-ACAAATCAAGAAACCCCCGA
1074747 A
1 A
1074748 AATCAAGCTT
Statistics
Matches: 488, Mismatches: 23, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
170 163 0.33
171 211 0.43
172 21 0.04
176 1 0.00
179 1 0.00
180 91 0.19
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (171 bp):
AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCATTTGAAAACATCCTGCACTAAAGGTCT
TATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGA
Found at i:1074487 original size:90 final size:89
Alignment explanation
Indices: 1074334--1074505 Score: 299
Period size: 90 Copynumber: 1.9 Consensus size: 89
1074324 AGGCTTAGTT
* *
1074334 TCATTTGAAAATATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1074399 CTCCGAAGGCTTAGTTTCTAAAATC
66 C-CCGAAGGCTTAGTTTCTAAAATC
* *
1074424 TCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAGGGCTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1074489 CCCGAAGGCTTAGTTTC
66 CCCGAAGGCTTAGTTTC
1074506 ATTTGAAAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 16 0.21
90 62 0.79
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (89 bp):
TCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
CCCGAAGGCTTAGTTTCTAAAATC
Found at i:1074657 original size:90 final size:90
Alignment explanation
Indices: 1074504--1074676 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 90
1074494 AGGCTTAGTT
*
1074504 TCATTTGAAAACATCTTGCACTAAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
*
1074569 CCCCGAAGGCTTAGTTTCTAAAATC
66 CCCCAAAGGCTTAGTTTCTAAAATC
* * *
1074594 TCATTTGAAAACATCCTGTACTGAAGGTCTTATGGATGGCCTGAAGGACTTACAAATCAAGAAAC
1 TCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
1074659 CCCCAAAGGCTTAGTTTC
66 CCCCAAAGGCTTAGTTTC
1074677 ATTTGAAAAC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (90 bp):
TCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAAC
CCCCAAAGGCTTAGTTTCTAAAATC
Found at i:1074704 original size:341 final size:346
Alignment explanation
Indices: 1074054--1074747 Score: 1121
Period size: 341 Copynumber: 2.0 Consensus size: 346
1074044 CTTGAAAATC
* *
1074054 AGGCTTAGTTTTTAAACACTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCTGAAG
1 AGGCTTAGTTTCTAAACACTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
1074119 GACTTACAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCAC
66 GACTTACAAATCAAGAAACCCCTGAAGGCTTAG--T-T---ATCTCATTTGAAAACATCCAGCAC
*
1074184 TGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAA
125 TAAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAA
1074249 AATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAG
190 AATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAG
* * * *
1074314 AAACCCCCGAAGGCTTAGTTTCATTTGAAAATATCCTGCACTGAAGGTCTTATGGATGGCCCGAA
255 AAACCCCCAAAGGCTTAGTTTCATTTGAAAACATCATGCACTAAAGGTCTTATGGATGGCCCGAA
*
1074379 GGACTT-ACAAATCAAGAAACCTCCGA
320 GGACTTAACAAATCAAGAAACCCCCGA
1074405 AGGCTTAGTTTCTAAA-ATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAA
1 AGGCTTAGTTTCTAAACA-CTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAA
* **
1074469 GGGCTTACAAATCAAGAAACCCC-GAAGGCTTAG-T-T-TCATTTGAAAACATCTTGCACTAAAG
65 GGACTTACAAATCAAGAAACCCCTGAAGGCTTAGTTATCTCATTTGAAAACATCCAGCACTAAAG
* *
1074530 GTCTTATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCT
130 GTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAAAATCT
** * *
1074595 CATTTGAAAACATCCTGTACTGAAGGTCTTATGGATGGCCTGAAGGACTTACAAATCAAGAAACC
195 CATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACC
1074660 CCCAAAGGCTTAGTTTCATTTGAAAACATCATGCACTAAAGGTCTTATGGATGGCCCGAAGGACT
260 CCCAAAGGCTTAGTTTCATTTGAAAACATCATGCACTAAAGGTCTTATGGATGGCCCGAAGGACT
*
1074725 TAATAAATCAAGAAACCCCCGA
325 TAACAAATCAAGAAACCCCCGA
1074747 A
1 A
1074748 AATCAAGCTT
Statistics
Matches: 323, Mismatches: 18, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
341 209 0.65
342 20 0.06
346 1 0.00
350 11 0.03
351 82 0.25
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (346 bp):
AGGCTTAGTTTCTAAACACTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCTGAAG
GACTTACAAATCAAGAAACCCCTGAAGGCTTAGTTATCTCATTTGAAAACATCCAGCACTAAAGG
TCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAAAATCTC
ATTTGAAAACATCCTACACTGAAGGTCTTATGGATGGCCCGAAAGACTTACAAATCAAGAAACCC
CCAAAGGCTTAGTTTCATTTGAAAACATCATGCACTAAAGGTCTTATGGATGGCCCGAAGGACTT
AACAAATCAAGAAACCCCCGA
Found at i:1076871 original size:19 final size:19
Alignment explanation
Indices: 1076847--1076900 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
1076837 TACTCAAGTG
1076847 TAAAATTAAGTTTTAATCT
1 TAAAATTAAGTTTTAATCT
1076866 TAAAA-TAA---TT--TC-
1 TAAAATTAAGTTTTAATCT
1076878 -AAAATTAAGTTTTAATCT
1 TAAAATTAAGTTTTAATCT
1076896 TAAAA
1 TAAAA
1076901 CAATTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 16
0.63 0.00 0.37
Matches are distributed among these distances:
11 4 0.15
12 3 0.11
13 2 0.07
15 4 0.15
17 2 0.07
18 3 0.11
19 9 0.33
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (19 bp):
TAAAATTAAGTTTTAATCT
Found at i:1076882 original size:30 final size:30
Alignment explanation
Indices: 1076848--1076920 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
1076838 ACTCAAGTGT
*
1076848 AAAATTAAGTTTTAATCTTAAAATAATTTC
1 AAAATTAAGTTTTAATCTTAAAACAATTTC
1076878 AAAATTAAGTTTTAATCTTAAAACAATTTC
1 AAAATTAAGTTTTAATCTTAAAACAATTTC
1076908 AAAA-TAA-TTTTAA
1 AAAATTAAGTTTTAA
1076921 AAAGTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 6 0.14
29 3 0.07
30 33 0.79
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTAAGTTTTAATCTTAAAACAATTTC
Found at i:1082939 original size:20 final size:21
Alignment explanation
Indices: 1082895--1082934 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1082885 CCCCCTTTGA
*
1082895 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1082916 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1082935 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1085474 original size:30 final size:30
Alignment explanation
Indices: 1085440--1085511 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
1085430 ACTCAAGTGT
1085440 AAAATTAAGTTTTAATCTTAAAACAATTTC
1 AAAATTAAGTTTTAATCTTAAAACAATTTC
*
1085470 AAAATTAAGTTTTAATCTTAAAACAGTTTC
1 AAAATTAAGTTTTAATCTTAAAACAATTTC
1085500 AAAA-TAA-TTTTA
1 AAAATTAAGTTTTA
1085512 CAAAGTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 33 0.80
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAATTAAGTTTTAATCTTAAAACAATTTC
Found at i:1086343 original size:7 final size:7
Alignment explanation
Indices: 1086331--1086376 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
1086321 TTTTTAATAT
1086331 TTTTTTC
1 TTTTTTC
1086338 TTTTTTC
1 TTTTTTC
* *
1086345 TTTTATA
1 TTTTTTC
*
1086352 TTTTTCC
1 TTTTTTC
1086359 TTCTTTTC
1 TT-TTTTC
1086367 TTTTTTC
1 TTTTTTC
1086374 TTT
1 TTT
1086377 GCGTTATCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:1086370 original size:22 final size:23
Alignment explanation
Indices: 1086306--1086370 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
1086296 TCTCTCTCTC
** *
1086306 TATTTTTTATTTCTTTT-TTTAA
1 TATTTTTTCCTTCTTTTCTTTTA
*
1086328 TATTTTTTTCTT-TTTTCTTTTA
1 TATTTTTTCCTTCTTTTCTTTTA
1086350 TA-TTTTTCCTTCTTTTCTTTT
1 TATTTTTTCCTTCTTTTCTTTT
1086371 TTCTTTGCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.32
22 25 0.68
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (23 bp):
TATTTTTTCCTTCTTTTCTTTTA
Found at i:1086615 original size:2 final size:2
Alignment explanation
Indices: 1086608--1086635 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1086598 ACAACAAGGG
1086608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1086636 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1090385 original size:22 final size:21
Alignment explanation
Indices: 1090328--1090382 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1090318 CAAAATGCAA
1090328 AAATTAAAATAAA-AGTATCT
1 AAATTAAAATAAACAGTATCT
* *
1090348 AAATCAGAAATTAACAGTGAT-T
1 AAATTA-AAATAAACAGT-ATCT
1090370 AAATTAAAATAAA
1 AAATTAAAATAAA
1090383 ACAACACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 5 0.18
21 12 0.43
22 9 0.32
23 2 0.07
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (21 bp):
AAATTAAAATAAACAGTATCT
Found at i:1093354 original size:23 final size:24
Alignment explanation
Indices: 1093323--1093370 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1093313 TTGACTTTAT
*
1093323 AAATTAAATTT-AACTAA-AAAATA
1 AAATAAAATTTCAA-TAATAAAATA
1093346 AAATAAAATTTCAATAATAAAATA
1 AAATAAAATTTCAATAATAAAATA
1093370 A
1 A
1093371 GATTCTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAAATTTCAATAATAAAATA
Found at i:1097463 original size:36 final size:35
Alignment explanation
Indices: 1097422--1097513 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 35
1097412 GAAATCTCTG
1097422 CAGGTTAAGTTCTGATCAATATGGTAATTCCTTATAT
1 CAGGTTAAGTTCTGATCAA-ATGGTAATTCCTTAT-T
** * *
1097459 -AGGTTCAA-CACCGATCAACTGGTAATTCCTTATT
1 CAGGTT-AAGTTCTGATCAAATGGTAATTCCTTATT
*
1097493 GCATGTTAAGTTCTGATCAAA
1 -CAGGTTAAGTTCTGATCAAA
1097514 CTATTAATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
34 1 0.02
35 16 0.38
36 23 0.55
37 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (35 bp):
CAGGTTAAGTTCTGATCAAATGGTAATTCCTTATT
Found at i:1105526 original size:72 final size:72
Alignment explanation
Indices: 1105415--1105579 Score: 210
Period size: 72 Copynumber: 2.3 Consensus size: 72
1105405 TTCAGTTCTG
* *
1105415 ATCAAGCTGGTAATTCC-TA-TGTAGGTTTAGTTCTGATCAAGATGGTAATTCCTTATATAGGTT
1 ATCAA-CTGGTAATTCCTTATTGCAGGTTCAGTTCTGATCAAGATGGTAATTCCTTATATAGGTT
1105478 CAACACCA
65 CAACACCA
* * * *
1105486 ATCAACTGGTAATTCCTTATTGCAGGTTCAGTGT-TGATCAAGCTGGTAATTTCTTATGTATGTT
1 ATCAACTGGTAATTCCTTATTGCAGGTTCAGT-TCTGATCAAGATGGTAATTCCTTATATAGGTT
* * *
1105550 CAGCATCG
65 CAACACCA
1105558 ATCAACTGGTAATTCCTTATTG
1 ATCAACTGGTAATTCCTTATTG
1105580 ACCTAAGACG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
70 11 0.13
71 7 0.09
72 63 0.77
73 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (72 bp):
ATCAACTGGTAATTCCTTATTGCAGGTTCAGTTCTGATCAAGATGGTAATTCCTTATATAGGTTC
AACACCA
Found at i:1105577 original size:35 final size:36
Alignment explanation
Indices: 1105414--1105577 Score: 165
Period size: 35 Copynumber: 4.6 Consensus size: 36
1105404 GTTCAGTTCT
* *
1105414 GATCAAGCTGGTAATTCC-TATGTAGGTTTAG-TTC
1 GATCAAGCTGGTAATTCCTTATGTAGGTTCAGCATC
* * * *
1105448 TGATCAAGATGGTAATTCCTTATATAGGTTCAACACC
1 -GATCAAGCTGGTAATTCCTTATGTAGGTTCAGCATC
* * ** *
1105485 AATCAA-CTGGTAATTCCTTATTGCAGGTTCAGTGTT
1 GATCAAGCTGGTAATTCCTTA-TGTAGGTTCAGCATC
* *
1105521 GATCAAGCTGGTAATTTCTTATGTATGTTCAGCATC
1 GATCAAGCTGGTAATTCCTTATGTAGGTTCAGCATC
1105557 GATCAA-CTGGTAATTCCTTAT
1 GATCAAGCTGGTAATTCCTTAT
1105578 TGACCTAAGA
Statistics
Matches: 102, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
35 44 0.43
36 44 0.43
37 14 0.14
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (36 bp):
GATCAAGCTGGTAATTCCTTATGTAGGTTCAGCATC
Found at i:1109695 original size:65 final size:64
Alignment explanation
Indices: 1109584--1109739 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 64
1109574 ATAAGACTTA
* * * * * * *
1109584 GTGCATCGGTACACTAATTAAATTCGATGTTTCAAAAGAGCCAAGAGTGTATCGATGCATAGTCT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAGAACAAAGAGTGCATCGATGCAT-GACT
* *
1109649 GTGCATCGGTACACAAAATACATTCGATGTTTCAATAA-AATAAAGAGTGCATTGATGCATGACT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAA-AAGAACAAAGAGTGCATCGATGCATGACT
* *
1109713 GTGCATCGATACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATACATTCGA
1109740 ATAGGGTGTG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 28 0.35
65 49 0.62
66 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAGAACAAAGAGTGCATCGATGCATGACT
Found at i:1110650 original size:29 final size:31
Alignment explanation
Indices: 1110613--1110670 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1110603 TGACTAATCA
*
1110613 TTTCAACTAAC-TT-GATTCTTTTTGTCTTG
1 TTTCAACTAACATTGGATTCCTTTTGTCTTG
* *
1110642 TTTCTACTAACATTGGTTTCCTTTTGTCT
1 TTTCAACTAACATTGGATTCCTTTTGTCT
1110671 GCTCTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 2 0.08
31 12 0.50
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTCAACTAACATTGGATTCCTTTTGTCTTG
Found at i:1111365 original size:21 final size:21
Alignment explanation
Indices: 1111341--1111380 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1111331 ATGCATTTTG
1111341 CATTAGCATA-TATACATTGTA
1 CATTA-CATAGTATACATTGTA
*
1111362 CATTACATAGTATTCATTG
1 CATTACATAGTATACATTG
1111381 CATCTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
CATTACATAGTATACATTGTA
Found at i:1112680 original size:23 final size:23
Alignment explanation
Indices: 1112623--1112680 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1112613 TTGACAACAC
* * *
1112623 AAAGAGAAAAAGAAATATATAGA
1 AAAGAAAAAAAAAAATAGATAGA
* * *
1112646 AAATACACAAAAAAATAGATAGA
1 AAAGAAAAAAAAAAATAGATAGA
1112669 AAAGAAAAAAAA
1 AAAGAAAAAAAA
1112681 CAAAAACAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.74, C:0.03, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAGAAAAAAAAAAATAGATAGA
Found at i:1112702 original size:32 final size:30
Alignment explanation
Indices: 1112654--1112763 Score: 100
Period size: 32 Copynumber: 3.6 Consensus size: 30
1112644 GAAAATACAC
* *
1112654 AAAAAAATAGATAGAAAAGAAAAAAAACAAA
1 AAAAAAAAAGAGAGAAAAGAAAAAAAA-AAA
1112685 AACAAAAAAAGAGAGAAAA-AAATTAAAAAAAA
1 AA-AAAAAAAGAGAGAAAAGAAA--AAAAAAAA
**
1112717 TTAAAAAAA-AGAG-AAAGAAAAAGAAAAAA
1 AAAAAAAAAGAGAGAAAAGAAAAA-AAAAAA
* *
1112746 GAAAAATAAGAGAGAAAA
1 AAAAAAAAAGAGAGAAAA
1112764 AAGAATAAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
28 2 0.03
29 15 0.23
30 11 0.17
31 15 0.23
32 17 0.26
33 5 0.08
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (30 bp):
AAAAAAAAAGAGAGAAAAGAAAAAAAAAAA
Found at i:1112713 original size:10 final size:10
Alignment explanation
Indices: 1112700--1112726 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1112690 AAAAAGAGAG
1112700 AAAAAAATTA
1 AAAAAAATTA
1112710 AAAAAAATTA
1 AAAAAAATTA
1112720 AAAAAAA
1 AAAAAAA
1112727 GAGAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:1112723 original size:30 final size:29
Alignment explanation
Indices: 1112719--1112784 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1112709 AAAAAAAATT
1112719 AAAAAAA-AGAGAAAGAAAAAGAAAAAAGA
1 AAAAAAAGAGAGAAA-AAAAAGAAAAAAGA
* * *
1112748 AAAATAAGAGAGAAAAAAGAATAAGAAAGA
1 AAAAAAAGAGAGAAAAAA-AAGAAAAAAGA
*
1112778 AAGAAAA
1 AAAAAAA
1112785 CCGATCAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (29 bp):
AAAAAAAGAGAGAAAAAAAAGAAAAAAGA
Found at i:1112737 original size:12 final size:13
Alignment explanation
Indices: 1112721--1112784 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
1112711 AAAAAATTAA
*
1112721 AAAAAAGAGAAAG
1 AAAAAAGAAAAAG
1112734 -AAAAAGAAAAAAG
1 AAAAAAG-AAAAAG
* *
1112747 AAAAATA-AGAGAG
1 AAAAA-AGAAAAAG
*
1112760 AAAAAAGAATAAG
1 AAAAAAGAAAAAG
1112773 AAAGAAAGAAAA
1 AAA-AAAGAAAA
1112785 CCGATCAAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
12 7 0.18
13 20 0.51
14 11 0.28
15 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:1112773 original size:26 final size:28
Alignment explanation
Indices: 1112682--1112768 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
1112672 GAAAAAAAAC
* *
1112682 AAAAACAAAAAAAGAGAGAAA-AAAATTAAA
1 AAAAAGAAAAAAA-AGAGAAAGAAAA--AGA
*
1112712 AAAAATTAAAAAAAAGAGAAAGAAAAAGA
1 AAAAA-GAAAAAAAAGAGAAAGAAAAAGA
* *
1112741 AAAAAGAAAAATAAGAGAGA-AAAAAGA
1 AAAAAGAAAAAAAAGAGAAAGAAAAAGA
1112768 A
1 A
1112769 TAAGAAAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 8 0.16
28 12 0.24
29 7 0.14
30 12 0.24
31 11 0.22
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.06
Consensus pattern (28 bp):
AAAAAGAAAAAAAAGAGAAAGAAAAAGA
Found at i:1114947 original size:20 final size:20
Alignment explanation
Indices: 1114922--1114967 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1114912 GAGCAAGATG
1114922 ATAAGACCTTCGGGCCATCC
1 ATAAGACCTTCGGGCCATCC
1114942 ATAAGACCTTCGGGCCATCC
1 ATAAGACCTTCGGGCCATCC
1114962 ATAAGA
1 ATAAGA
1114968 TCAGCACCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (20 bp):
ATAAGACCTTCGGGCCATCC
Found at i:1115203 original size:132 final size:132
Alignment explanation
Indices: 1115029--1115316 Score: 360
Period size: 132 Copynumber: 2.2 Consensus size: 132
1115019 TGACATCTGG
* ** * * * * *
1115029 TTCGATTCCATCACAGAAGAATGTGGATTGACATTTTTATTTCTCTCAAATTCATCGCATAAGGA
1 TTCGATTCCATCACAGAAGAAGGTCAATCGACATTTTCATTTCACTCAAATCCATCACATAAGGA
* * * * *
1115094 GTTGGATCAGCATCAACTTTTTGCTCGATTCTATCACAGAAGAAGGTAGATCATCACCAACATAT
66 GCTGGAGCAGCATCAACATTTTGCTCGATTCTATCACAAAAGAAGATAGATCATCACCAACATAT
1115159 CA
131 CA
* *
1115161 TTCGATTCCATCACAGAAGGAGGTCAATCGACATTTTCATTTCACTCAAATCCATCATATAAGGA
1 TTCGATTCCATCACAGAAGAAGGTCAATCGACATTTTCATTTCACTCAAATCCATCACATAAGGA
* * * * *
1115226 GCTGGAGCAGCATCAACATTTTGCTCGATTCTATCACAAAAGGAGATAGATCAGCATCGACATCT
66 GCTGGAGCAGCATCAACATTTTGCTCGATTCTATCACAAAAGAAGATAGATCATCACCAACATAT
**
1115291 TG
131 CA
* *
1115293 TTCGATTCTATCACATAAGAAGGT
1 TTCGATTCCATCACAGAAGAAGGT
1115317 AGATCAAACA
Statistics
Matches: 131, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (132 bp):
TTCGATTCCATCACAGAAGAAGGTCAATCGACATTTTCATTTCACTCAAATCCATCACATAAGGA
GCTGGAGCAGCATCAACATTTTGCTCGATTCTATCACAAAAGAAGATAGATCATCACCAACATAT
CA
Found at i:1115269 original size:44 final size:44
Alignment explanation
Indices: 1115221--1115307 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
1115211 TCCATCATAT
* * *
1115221 AAGGAGCTGGAGCAGCATCAACATTTTGCTCGATTCTATCACAA
1 AAGGAGATAGAGCAGCATCAACATCTTGCTCGATTCTATCACAA
* * *
1115265 AAGGAGATAGATCAGCATCGACATCTTGTTCGATTCTATCACA
1 AAGGAGATAGAGCAGCATCAACATCTTGCTCGATTCTATCACA
1115308 TAAGAAGGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (44 bp):
AAGGAGATAGAGCAGCATCAACATCTTGCTCGATTCTATCACAA
Found at i:1115300 original size:176 final size:175
Alignment explanation
Indices: 1115089--1115499 Score: 441
Period size: 176 Copynumber: 2.3 Consensus size: 175
1115079 TTCATCGCAT
* * * * * *
1115089 AAGGAGTTGGATCAGCATCAACTTTTTGCTCGATTCTATCACAGAAGAAGGTAGATCATCACCAA
1 AAGGAGATAGATCAGCATCGAC-ATTTGTTCGATTCTATCACAGAAGAAGGTAGATCA--AACAA
*
1115154 C-A-TATCATTCGATTCCATCACAGAAGGAGGTCAATCGACATTTTCATTTCACTCAAATCCATC
63 CGAGTATCATTCGATTCCATCACAGAAGGAGGTCAATCAACATTTTCATTTCACTCAAATCCATC
* * * * *
1115217 ATATAAGGAGCTGGAGCAGCATCAACATTTTGCTCGATTCTATCACAA
128 ACATAAGGAGCTGGAGCAACATCAACATTTTGCTAGATTCCATAACAA
* *
1115265 AAGGAGATAGATCAGCATCGACATCTTGTTCGATTCTATCACATAAGAAGGTAGATCAAACATCG
1 AAGGAGATAGATCAGCATCGACAT-TTGTTCGATTCTATCACAGAAGAAGGTAGATCAAACAACG
* ** * ** * *
1115330 AGTTTTGTTCGATTCCATCATAGAAGGAGGTGGATCAACATTTTCATTTCGCTCAAATCCATCGC
65 AGTATCATTCGATTCCATCACAGAAGGAGGTCAATCAACATTTTCATTTCACTCAAATCCATCAC
* * * * *
1115395 ATAAGGAGTTGGATCAACATCAACGTTTTGCTAGATTCCATAATAG
130 ATAAGGAGCTGGAGCAACATCAACATTTTGCTAGATTCCATAACAA
* * * * * * *
1115441 AATGAGGTAGATCATCA-CTGACATTATGTTTGATTCCATCACAGAAGGAGGTGGATCAA
1 AAGGAGATAGATCAGCATC-GACATT-TGTTCGATTCTATCACAGAAGAAGGTAGATCAA
1115500 TATTGATATT
Statistics
Matches: 195, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
174 4 0.02
175 4 0.02
176 187 0.96
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (175 bp):
AAGGAGATAGATCAGCATCGACATTTGTTCGATTCTATCACAGAAGAAGGTAGATCAAACAACGA
GTATCATTCGATTCCATCACAGAAGGAGGTCAATCAACATTTTCATTTCACTCAAATCCATCACA
TAAGGAGCTGGAGCAACATCAACATTTTGCTAGATTCCATAACAA
Found at i:1115320 original size:44 final size:44
Alignment explanation
Indices: 1115233--1115349 Score: 137
Period size: 44 Copynumber: 2.7 Consensus size: 44
1115223 GGAGCTGGAG
* * *
1115233 CAGCATCAACATTTTGCTCGATTCTATCACAAAAGGAGATAGAT
1 CAGCATCGACATTTTGTTCGATTCTATCACAAAAGAAGATAGAT
* * *
1115277 CAGCATCGACATCTTGTTCGATTCTATCACATAAGAAGGTAGAT
1 CAGCATCGACATTTTGTTCGATTCTATCACAAAAGAAGATAGAT
* * *
1115321 CAAACATCGA-GTTTTGTTCGATTCCATCA
1 C-AGCATCGACATTTTGTTCGATTCTATCA
1115350 TAGAAGGAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
44 55 0.89
45 7 0.11
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (44 bp):
CAGCATCGACATTTTGTTCGATTCTATCACAAAAGAAGATAGAT
Found at i:1116742 original size:29 final size:28
Alignment explanation
Indices: 1116653--1116743 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 28
1116643 AACTTTGAAA
* * * *
1116653 TTTAGTCAATGTTTTATATTTATT-CAT
1 TTTAGTCACTATTTTTTAATTATTGCAT
*
1116680 TTTAGTCAC---TTTTTAATTTTTG-A-
1 TTTAGTCACTATTTTTTAATTATTGCAT
*
1116703 TTTAGTTACTATTATTTTAATTATTGCAT
1 TTTAGTCACTATT-TTTTAATTATTGCAT
1116732 TTTAGTCACTAT
1 TTTAGTCACTAT
1116744 AATTAGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
23 8 0.16
24 10 0.20
26 1 0.02
27 19 0.38
28 1 0.02
29 11 0.22
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.58
Consensus pattern (28 bp):
TTTAGTCACTATTTTTTAATTATTGCAT
Found at i:1122614 original size:11 final size:11
Alignment explanation
Indices: 1122598--1122633 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1122588 AGTCAAAACA
1122598 TTTATTTTTAG
1 TTTATTTTTAG
*
1122609 TTTATTTTTAT
1 TTTATTTTTAG
1122620 TTTATTTTTCAG
1 TTTATTTTT-AG
1122632 TT
1 TT
1122634 GCTTAAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (11 bp):
TTTATTTTTAG
Found at i:1123754 original size:22 final size:22
Alignment explanation
Indices: 1123685--1123783 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
1123675 ATCAATTCAC
*
1123685 ATGAATAATTACATCCT-TACAT
1 ATGAATAATTACA-CCTATCCAT
* * * *
1123707 TTTAATAATCACTCCTAAT-CAT
1 ATGAATAATTACACCT-ATCCAT
* *
1123729 ATGAACAATTACATCTATCCAT
1 ATGAATAATTACACCTATCCAT
** *
1123751 ATGAATGGTTACACCTATTCAT
1 ATGAATAATTACACCTATCCAT
1123773 ATGAATAATTA
1 ATGAATAATTA
1123784 TACTCCTTAA
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
21 5 0.09
22 51 0.89
23 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (22 bp):
ATGAATAATTACACCTATCCAT
Found at i:1125115 original size:14 final size:14
Alignment explanation
Indices: 1125098--1125127 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1125088 CATTTGATCC
1125098 TTAATATTTATACA
1 TTAATATTTATACA
1125112 TTAATATTTATACA
1 TTAATATTTATACA
1125126 TT
1 TT
1125128 CTATCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAATATTTATACA
Found at i:1126544 original size:93 final size:92
Alignment explanation
Indices: 1126425--1126689 Score: 324
Period size: 93 Copynumber: 2.8 Consensus size: 92
1126415 TGTGATATCT
* * * * **
1126425 TATCATTTTAATTAATAAATATTATGGTAATTACTTTTATTAGGTATATCTTTTATTTATTACAA
1 TATCATATTAATT-ATTACTATTATGGTAATTACTTTTATTATGTATAT-TTTTATTTATTATTA
*
1126490 TATTATGATATATATTTCCATATTTTAGTG
64 TATTATGATATATA-TTCCATATTTTAATG
* *
1126520 TATCATATTAATT-TTACT-TCTATGGTAATTACTTTTACCATCTGTATA-TTTTATTTATTATT
1 TATCATATTAATTATTACTAT-TATGGTAATTACTTTTA--TTATGTATATTTTTATTTATTATT
1126582 ATATTATGATATATA-TCCATATTTTAATG
63 ATATTATGATATATATTCCATATTTTAATG
* *
1126611 TATGATATTAATTATTACTATTATGGTAATTCCTTTTTATTATGTATATTTTT-TGTTATTATTA
1 TATCATATTAATTATTACTATTATGGTAATTAC-TTTTATTATGTATATTTTTAT-TTATTATTA
1126675 TATTATGATATATAT
64 TATTATGATATATAT
1126690 ATTTATATAT
Statistics
Matches: 148, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
91 33 0.22
92 44 0.30
93 53 0.36
95 18 0.12
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (92 bp):
TATCATATTAATTATTACTATTATGGTAATTACTTTTATTATGTATATTTTTATTTATTATTATA
TTATGATATATATTCCATATTTTAATG
Found at i:1126692 original size:14 final size:13
Alignment explanation
Indices: 1126673--1126705 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1126663 TTGTTATTAT
1126673 TATATTATGATATA
1 TATATTAT-ATATA
1126687 TATATT-TATATA
1 TATATTATATATA
1126699 TATATTA
1 TATATTA
1126706 ATGTACACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.61
13 1 0.06
14 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TATATTATATATA
Found at i:1126695 original size:26 final size:24
Alignment explanation
Indices: 1126666--1126732 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 24
1126656 ATATTTTTTG
*
1126666 TTATTATTATATTATGATATATATAT
1 TTATTATTATATTATG-TACA-ATAT
*
1126692 TTA-TATATATATTAATGTACACTAT
1 TTATTAT-TATATT-ATGTACAATAT
1126717 TTATTATTATTATTAT
1 TTATTATTA-TATTAT
1126733 TATTTTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
25 13 0.37
26 19 0.54
27 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (24 bp):
TTATTATTATATTATGTACAATAT
Found at i:1126734 original size:12 final size:13
Alignment explanation
Indices: 1126717--1126765 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
1126707 TGTACACTAT
1126717 TTATTATTATT-A
1 TTATTATTATTGA
1126729 TTATTATT-TTGA
1 TTATTATTATTGA
*
1126741 TT-TTATTTTTGGA
1 TTATTATTATT-GA
1126754 TTATATATTATT
1 TTAT-TATTATT
1126766 AATTGATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 7 0.23
12 13 0.42
13 4 0.13
14 1 0.03
15 6 0.19
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (13 bp):
TTATTATTATTGA
Found at i:1135878 original size:53 final size:50
Alignment explanation
Indices: 1135798--1135903 Score: 176
Period size: 53 Copynumber: 2.1 Consensus size: 50
1135788 AAATAAATCT
1135798 GATAAAACAACCCTGTAGATATCACGTACATGCCACTAATAAGTCAAAGTAAG
1 GATAAAACAACCCTGTAGATATCACGTACATGCCAC---TAAGTCAAAGTAAG
*
1135851 GATAAAACAACCCTGTAGATATCACGTACATTCCACTAAGTCAAAGTAAG
1 GATAAAACAACCCTGTAGATATCACGTACATGCCACTAAGTCAAAGTAAG
1135901 GAT
1 GAT
1135904 GTCTTACTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
50 17 0.33
53 35 0.67
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (50 bp):
GATAAAACAACCCTGTAGATATCACGTACATGCCACTAAGTCAAAGTAAG
Found at i:1139923 original size:53 final size:52
Alignment explanation
Indices: 1139816--1139932 Score: 121
Period size: 53 Copynumber: 2.2 Consensus size: 52
1139806 AACAACACAA
** * *
1139816 CAAACCAACACAAGACGTGCAAAATAAAAATATTACATAAGAGTATAAAGTCT
1 CAAA-CAACACAAGACGTGCAAAATAAAAATACCACACAAGAATATAAAGTCT
* * * *
1139869 CAAATCAACACAAGATGTTCATATTAAAAATACCACACAAGAATATCAAA-TCT
1 CAAA-CAACACAAGACGTGCAAAATAAAAATACCACACAAGAATAT-AAAGTCT
1139922 C-AACAACACAA
1 CAAACAACACAA
1139933 TAAAATCAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 8 0.15
52 2 0.04
53 41 0.76
54 3 0.06
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.19
Consensus pattern (52 bp):
CAAACAACACAAGACGTGCAAAATAAAAATACCACACAAGAATATAAAGTCT
Found at i:1139991 original size:64 final size:65
Alignment explanation
Indices: 1139870--1140001 Score: 194
Period size: 64 Copynumber: 2.0 Consensus size: 65
1139860 ATAAAGTCTC
* *
1139870 AAATCAACACAAGATGTTCATATTAAAAATACCACACAAGAATATCAAATCTCAACAACACAATA
1 AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAATATCAAATCTCAACAACACAATA
* * * * *
1139935 AAATCAACACAAGATGTTCAAAAT-AAAATACCACACAATAGTATCAAGTCTTAACAACATAATA
1 AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAATATCAAATCTCAACAACACAATA
1139999 AAA
1 AAA
1140002 GAGATAGTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
64 38 0.63
65 22 0.37
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (65 bp):
AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAATATCAAATCTCAACAACACAATA
Found at i:1150949 original size:19 final size:19
Alignment explanation
Indices: 1150925--1150968 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1150915 AATTCAATGG
*
1150925 CGATCAACAGTCAACTGCT
1 CGATCAACAGTCAACGGCT
* *
1150944 CGATCAACGGTCAGCGGCT
1 CGATCAACAGTCAACGGCT
1150963 CGATCA
1 CGATCA
1150969 GCGGCTCGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (19 bp):
CGATCAACAGTCAACGGCT
Found at i:1151029 original size:19 final size:19
Alignment explanation
Indices: 1151005--1151041 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1150995 GCTCGGTCCA
*
1151005 GACCGGTCTAGACAGTTCT
1 GACCGGTCCAGACAGTTCT
*
1151024 GACCGGTCCAGCCAGTTC
1 GACCGGTCCAGACAGTTC
1151042 CCCAAGCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (19 bp):
GACCGGTCCAGACAGTTCT
Found at i:1157426 original size:17 final size:18
Alignment explanation
Indices: 1157404--1157443 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
1157394 TGATCGGTCT
1157404 GACCCGGCCCGTTGA-CC
1 GACCCGGCCCGTTGACCC
1157421 GACCCGGCCCGTTGACCC
1 GACCCGGCCCGTTGACCC
1157439 GACCC
1 GACCC
1157444 AACCCGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.12, C:0.50, G:0.28, T:0.10
Consensus pattern (18 bp):
GACCCGGCCCGTTGACCC
Found at i:1157449 original size:18 final size:18
Alignment explanation
Indices: 1157411--1157454 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1157401 TCTGACCCGG
**
1157411 CCCGTTGA-CCGACCCGG
1 CCCGTTGACCCGACCCAA
1157428 CCCGTTGACCCGACCCAA
1 CCCGTTGACCCGACCCAA
*
1157446 CCCGGTGAC
1 CCCGTTGAC
1157455 ATTTTGGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.16, C:0.48, G:0.25, T:0.11
Consensus pattern (18 bp):
CCCGTTGACCCGACCCAA
Found at i:1157505 original size:27 final size:28
Alignment explanation
Indices: 1157453--1157533 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
1157443 CAACCCGGTG
*
1157453 ACATTTTGGGAATTATTTTTGAAAAAGGTA
1 ACATTTTCGGAATTA-TTTTG-AAAAGGTA
*
1157483 ACA-TTTCGGAATT-TTTGTGAAAAGGTG
1 ACATTTTCGGAATTATTT-TGAAAAGGTA
*
1157510 ACATTTTGGGAATTATTTTGAAAA
1 ACATTTTCGGAATTATTTTGAAAA
1157534 AAGTGACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
27 13 0.29
28 17 0.38
29 12 0.27
30 3 0.07
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (28 bp):
ACATTTTCGGAATTATTTTGAAAAGGTA
Found at i:1157543 original size:29 final size:29
Alignment explanation
Indices: 1157449--1157552 Score: 133
Period size: 29 Copynumber: 3.6 Consensus size: 29
1157439 GACCCAACCC
1157449 GGTGACATTTTGGGAATTATTTTTGAAAAA
1 GGTGACATTTTGGGAATTA-TTTTGAAAAA
* *
1157479 GGTAACA-TTTCGGAATT-TTTGTG-AAAA
1 GGTGACATTTTGGGAATTATTT-TGAAAAA
1157506 GGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
1157535 AGTGACATTTTGGTAATT
1 GGTGACATTTTGGGAATT
1157553 TTGAATGTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.20
28 13 0.20
29 32 0.50
30 6 0.09
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (29 bp):
GGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:1164816 original size:19 final size:19
Alignment explanation
Indices: 1164792--1164837 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1164782 GGTTGACCGA
1164792 TCCAAACCGGTCTGATCGG
1 TCCAAACCGGTCTGATCGG
1164811 TCCAAACCGGTCTGATCGG
1 TCCAAACCGGTCTGATCGG
*
1164830 TCCGAACC
1 TCCAAACC
1164838 AGGTTGACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.20
Consensus pattern (19 bp):
TCCAAACCGGTCTGATCGG
Found at i:1164879 original size:17 final size:18
Alignment explanation
Indices: 1164859--1164902 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1164849 TCTGACCCGG
1164859 CCCGTTGACC-GACCCAA
1 CCCGTTGACCGGACCCAA
*
1164876 CCCGTTGACCGGACCCGA
1 CCCGTTGACCGGACCCAA
*
1164894 CCCGATGAC
1 CCCGTTGAC
1164903 ATTTTGGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.20, C:0.45, G:0.23, T:0.11
Consensus pattern (18 bp):
CCCGTTGACCGGACCCAA
Found at i:1164963 original size:29 final size:29
Alignment explanation
Indices: 1164898--1165002 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
1164888 ACCCGACCCG
*
1164898 ATGACATTTTGGGAATTATTTTCGAAAAGG
1 ATGACATTTTGGGAATTATTTT-GAAAAGA
* * * *
1164928 GTGACATTTTGGGAATTCTTGTGAAAAGT
1 ATGACATTTTGGGAATTATTTTGAAAAGA
*
1164957 ATGACATTCTGGGAATTATTTTGAAAA-A
1 ATGACATTTTGGGAATTATTTTGAAAAGA
*
1164985 AGTGACATTTTGGTAATT
1 A-TGACATTTTGGGAATT
1165003 TTCGAATGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 1 0.02
29 43 0.68
30 19 0.30
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (29 bp):
ATGACATTTTGGGAATTATTTTGAAAAGA
Found at i:1168011 original size:2 final size:2
Alignment explanation
Indices: 1168004--1168057 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1167994 TAGTCCCTGA
1168004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1168046 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1168058 GTTTAATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1173876 original size:55 final size:55
Alignment explanation
Indices: 1173795--1173932 Score: 177
Period size: 55 Copynumber: 2.5 Consensus size: 55
1173785 TTTCATGGTT
* * ** ** *
1173795 TTGCACACATAGTGTCGATACAGAAATTCATAAACTTGTTATGAATTTTGTGGGG
1 TTGCACACATAGTGACAATACAGAAATTCATAAACTCATTATGAATTTCATGAGG
* *
1173850 TTGCACACATAATGACAATACGGAAATTCATAAACTCATTATGAATTTCATGAGG
1 TTGCACACATAGTGACAATACAGAAATTCATAAACTCATTATGAATTTCATGAGG
* *
1173905 TTGCACACATAGTGCCAATATAGAAATT
1 TTGCACACATAGTGACAATACAGAAATT
1173933 TGCAACATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (55 bp):
TTGCACACATAGTGACAATACAGAAATTCATAAACTCATTATGAATTTCATGAGG
Found at i:1176071 original size:30 final size:27
Alignment explanation
Indices: 1176016--1176072 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
1176006 TTTCCTTGTT
*
1176016 CTTAAATCATTTCTTTCTTTTCATTTC
1 CTTAAATCATTTCTTTCTTTCCATTTC
1176043 CTTAAATCATTTCTTTTATCTTTCCATTTC
1 CTTAAATCATTTC--TT-TCTTTCCATTTC
1176073 TTTTTTCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.50
29 2 0.08
30 11 0.42
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (27 bp):
CTTAAATCATTTCTTTCTTTCCATTTC
Found at i:1180492 original size:50 final size:50
Alignment explanation
Indices: 1180410--1180505 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
1180400 TTGCACATGA
** * * *
1180410 TGACTTTGGCGCCACGATGAATAAGCACATCACCATTTGACCAAGGGAGG
1 TGACTTTGGCGCCAAAATGAACAAACACATCACCATTCGACCAAGGGAGG
* * *
1180460 TGACTTTGGTGCCAAAATGAACAAACATATCACCATTCGGCCAAGG
1 TGACTTTGGCGCCAAAATGAACAAACACATCACCATTCGACCAAGG
1180506 ACAGGTTGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (50 bp):
TGACTTTGGCGCCAAAATGAACAAACACATCACCATTCGACCAAGGGAGG
Found at i:1187662 original size:55 final size:55
Alignment explanation
Indices: 1187603--1187737 Score: 155
Period size: 55 Copynumber: 2.5 Consensus size: 55
1187593 CATGGTTTTG
*** * * *
1187603 CACACATAGTGCCGTTACGGAAATTCATAAACTCCTTATGAATTTTGTG-GGATTA
1 CACACATAGTGCCAAGACGGAAATTCATAAACTCATTATAAATTTTGCGAGG-TTA
* *
1187658 CACACATAGTGCTAAGACGGAAATTCATAAACTCATTATAAATTTTGCGAGGTTG
1 CACACATAGTGCCAAGACGGAAATTCATAAACTCATTATAAATTTTGCGAGGTTA
* * *
1187713 CACACATAGTACCAATACAGAAATT
1 CACACATAGTGCCAAGACGGAAATT
1187738 TGCAACATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
55 65 0.97
56 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (55 bp):
CACACATAGTGCCAAGACGGAAATTCATAAACTCATTATAAATTTTGCGAGGTTA
Found at i:1192055 original size:22 final size:21
Alignment explanation
Indices: 1192030--1192074 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1192020 AAATTAAGAA
1192030 GATGTT-TATGGTCTTGATGGAT
1 GATGTTGTA-GGTCTTGAT-GAT
*
1192052 GATGTTGTAGGTGTTGATGAT
1 GATGTTGTAGGTCTTGATGAT
1192073 GA
1 GA
1192075 AATGGAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.42
Consensus pattern (21 bp):
GATGTTGTAGGTCTTGATGAT
Found at i:1197320 original size:15 final size:15
Alignment explanation
Indices: 1197300--1197340 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1197290 GGTGAAGGAG
1197300 CATCTTCATGGGCAA
1 CATCTTCATGGGCAA
1197315 CATCTTCATGGGCAA
1 CATCTTCATGGGCAA
1197330 CATCATTCATG
1 CATC-TTCATG
1197341 AAAGGACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (15 bp):
CATCTTCATGGGCAA
Found at i:1205025 original size:22 final size:21
Alignment explanation
Indices: 1205000--1205044 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1204990 GAATTAAGAA
1205000 GATGTT-TATGGTCTTGATGGAT
1 GATGTTGT-TGGTCTTGAT-GAT
*
1205022 GATGTTGTTGGTGTTGATGAT
1 GATGTTGTTGGTCTTGATGAT
1205043 GA
1 GA
1205045 AATGGAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 15 0.71
23 1 0.05
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.44
Consensus pattern (21 bp):
GATGTTGTTGGTCTTGATGAT
Found at i:1206693 original size:15 final size:16
Alignment explanation
Indices: 1206669--1206701 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1206659 TCATAATTTC
1206669 ATCAAAATC-ACAATA
1 ATCAAAATCAACAATA
*
1206684 ATCAACATCAACAATA
1 ATCAAAATCAACAATA
1206700 AT
1 AT
1206702 ATACTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (16 bp):
ATCAAAATCAACAATA
Found at i:1214938 original size:53 final size:53
Alignment explanation
Indices: 1214860--1214977 Score: 148
Period size: 53 Copynumber: 2.2 Consensus size: 53
1214850 CGTCATTTCC
* * * * * *
1214860 AGATGTAGGTGTTGTCTAAAGTTATTATCTTTTAATTTGATACATTAAAAGTT
1 AGATGTAGGTATAGTCAAAAATTATTATATTTTAATTTGACACATTAAAAGTT
* *
1214913 AGATGTAGGTATAGTCAAAAATTATTTTATTTTAATTTGACACATTAAATGTT
1 AGATGTAGGTATAGTCAAAAATTATTATATTTTAATTTGACACATTAAAAGTT
1214966 -GTATGTAGGTAT
1 AG-ATGTAGGTAT
1214978 TAGCCCACCC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.02
53 55 0.98
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (53 bp):
AGATGTAGGTATAGTCAAAAATTATTATATTTTAATTTGACACATTAAAAGTT
Found at i:1220291 original size:7 final size:7
Alignment explanation
Indices: 1220266--1220365 Score: 75
Period size: 7 Copynumber: 14.9 Consensus size: 7
1220256 TTTTCCTTTG
1220266 TTTTTTC
1 TTTTTTC
* *
1220273 TGTTGT-
1 TTTTTTC
1220279 TTTTTTC
1 TTTTTTC
1220286 -TTTTT-
1 TTTTTTC
*
1220291 TTTTTTG
1 TTTTTTC
**
1220298 TTGATT-
1 TTTTTTC
1220304 TTTTTTC
1 TTTTTTC
* *
1220311 TCTTTAC
1 TTTTTTC
1220318 -TTTTTC
1 TTTTTTC
1220324 TTTTTTTC
1 -TTTTTTC
1220332 TTTTTTC
1 TTTTTTC
1220339 TTTTTTC
1 TTTTTTC
*
1220346 TCTTTTC
1 TTTTTTC
*
1220353 TCTTTTC
1 TTTTTTC
1220360 TTTTTT
1 TTTTTT
1220366 TTCTTTGCTT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
6 22 0.30
7 45 0.62
8 6 0.08
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:1220292 original size:21 final size:21
Alignment explanation
Indices: 1220266--1220371 Score: 76
Period size: 23 Copynumber: 5.1 Consensus size: 21
1220256 TTTTCCTTTG
*
1220266 TTTTTTCTGTTGTTTTTTTCT
1 TTTTTTCTTTTGTTTTTTTCT
**
1220287 TTTTTT-TTTTGTTGATTT-T
1 TTTTTTCTTTTGTTTTTTTCT
* **
1220306 TTTTCTC-TTT-ACTTTTTCT
1 TTTTTTCTTTTGTTTTTTTCT
*
1220325 TTTTTTCTTTTTTCTTTTTTCT
1 TTTTTTCTTTTGT-TTTTTTCT
* *
1220347 CTTTTCTCTTTTCTTTTTTTTCT
1 -TTTTTTCTTTT-GTTTTTTTCT
1220370 TT
1 TT
1220372 GCTTTGATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
18 3 0.05
19 16 0.24
20 12 0.18
21 6 0.09
22 9 0.14
23 18 0.27
24 2 0.03
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTGTTTTTTTCT
Found at i:1220307 original size:23 final size:24
Alignment explanation
Indices: 1220255--1220307 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1220245 GCTTCTTATC
* *
1220255 TTTTTCCTTTGTTTTTTCTGTTGT
1 TTTTTTCTTTGTTTTTTCTGTTGA
*
1220279 TTTTTTCTTT-TTTTTTTTGTTGA
1 TTTTTTCTTTGTTTTTTCTGTTGA
1220302 TTTTTT
1 TTTTTT
1220308 TTCTCTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.02, C:0.08, G:0.09, T:0.81
Consensus pattern (24 bp):
TTTTTTCTTTGTTTTTTCTGTTGA
Found at i:1220370 original size:14 final size:13
Alignment explanation
Indices: 1220266--1220371 Score: 79
Period size: 13 Copynumber: 7.8 Consensus size: 13
1220256 TTTTCCTTTG
* *
1220266 TTTTTTCTGTTGT
1 TTTTTTCTTTTTT
1220279 TTTTTTC-TTTTT
1 TTTTTTCTTTTTT
* **
1220291 TTTTTTGTTGATT
1 TTTTTTCTTTTTT
* *
1220304 TTTTTTCTCTTTA
1 TTTTTTCTTTTTT
*
1220317 CTTTTTCTTTTTTT
1 TTTTTTC-TTTTTT
1220331 CTTTTTTCTTTTTT
1 -TTTTTTCTTTTTT
1220345 CTCTTTTCTCTTTTCTT
1 -T-TTTT-TCTTTT-TT
1220362 TTTTTTCTTT
1 TTTTTTCTTT
1220372 GCTTTGATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
12 9 0.12
13 24 0.33
14 17 0.23
15 14 0.19
16 7 0.10
17 2 0.03
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:1224238 original size:51 final size:51
Alignment explanation
Indices: 1224176--1224290 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
1224166 AAATAAAATA
1224176 AAATAAA-AGTGACAAAAATGCAAGAAAATAAAAGTAA-A-TAACTAAATCAG
1 AAATAAACAGTGACAAAAATGCAA-AAAATAAAA-TAACAGTAACTAAATCAG
* * * *
1224226 AAATAAACAGTGACCAAAATGTAAAAATTAAAATAACAGTAGCTAAATCAG
1 AAATAAACAGTGACAAAAATGCAAAAAATAAAATAACAGTAACTAAATCAG
1224277 AAACT-AACAGTGAC
1 AAA-TAAACAGTGAC
1224291 TAGATTAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
49 3 0.05
50 16 0.28
51 37 0.65
52 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.12, T:0.17
Consensus pattern (51 bp):
AAATAAACAGTGACAAAAATGCAAAAAATAAAATAACAGTAACTAAATCAG
Found at i:1229734 original size:20 final size:20
Alignment explanation
Indices: 1229709--1230165 Score: 88
Period size: 20 Copynumber: 19.6 Consensus size: 20
1229699 AACTAAAAAT
* * *
1229709 GCATGAACTGATGCATTTAG
1 GCATGAACGGATGCATTAAA
1229729 GCATGAACGGATGCATTAAA
1 GCATGAACGGATGCATTAAA
*
1229749 GCATGAAAGGATGCCATAACTAAAAA
1 GCATGAACGGATG-CAT---T--AAA
*
1229775 TGCATGAACGGATGCATTAAG
1 -GCATGAACGGATGCATTAAA
*
1229796 GCATGAAAGGATGCCATAACTAAAACA
1 GCATGAACGGATG-CAT---T--AA-A
*
1229823 TGCATGAACGGATGTCAAAACTAAACA
1 -GCATGAACGGATG-C---A-TTAA-A
* *
1229850 TGCATGAATGGATGCATTAAG
1 -GCATGAACGGATGCATTAAA
*
1229871 GCATGAACGGATACCATAACTAAAAA
1 GCATGAACGGAT-GCAT---T--AAA
* *
1229897 TGCATGAACGGCTGCATTAAG
1 -GCATGAACGGATGCATTAAA
*
1229918 GCATGAAAGGATGCCATAACTAAAAA
1 GCATGAACGGATG-CAT---T--AAA
* *
1229944 TGCATGAA-AGACTGCATTAAG
1 -GCATGAACGGA-TGCATTAAA
*
1229965 GCATGAAAGGATGCCATAACTAAAAA
1 GCATGAACGGATG-CAT---T--AAA
*
1229991 TGCATGAACGGATGCATTAAG
1 -GCATGAACGGATGCATTAAA
* *
1230012 GCATAAAAGGATGCCATAACTAAACA
1 GCATGAACGGATG-CAT---T-AA-A
*
1230038 TGCATGAACGGATGCATTAAG
1 -GCATGAACGGATGCATTAAA
*
1230059 GCATGAAAGGATGCCATAACTAAAAA
1 GCATGAACGGATG-CAT---T--AAA
*
1230085 TGCATGAACGGATGCATTAAG
1 -GCATGAACGGATGCATTAAA
**
1230106 GCATGAAATGATGTCATAACTAAAAA
1 GCATGAACGGATG-CAT---T--AAA
*
1230132 TGCATGAACGGATGCATTAAG
1 -GCATGAACGGATGCATTAAA
*
1230153 GCATGAAAGGATG
1 GCATGAACGGATG
1230166 TCATAACTAA
Statistics
Matches: 328, Mismatches: 46, Indels: 126
0.66 0.09 0.25
Matches are distributed among these distances:
20 118 0.36
21 38 0.12
22 5 0.02
23 8 0.02
24 8 0.02
25 2 0.01
26 39 0.12
27 95 0.29
28 13 0.04
31 1 0.00
32 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
GCATGAACGGATGCATTAAA
Found at i:1229800 original size:47 final size:48
Alignment explanation
Indices: 1229729--1229836 Score: 200
Period size: 47 Copynumber: 2.3 Consensus size: 48
1229719 ATGCATTTAG
1229729 GCATGAACGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAA-AT
1 GCATGAACGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAACAT
*
1229776 GCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAACAT
1 GCATGAACGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAACAT
1229824 GCATGAACGGATG
1 GCATGAACGGATG
1229837 TCAAAACTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
47 44 0.75
48 15 0.25
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.19
Consensus pattern (48 bp):
GCATGAACGGATGCATTAAAGCATGAAAGGATGCCATAACTAAAACAT
Found at i:1229872 original size:75 final size:74
Alignment explanation
Indices: 1229749--1230052 Score: 251
Period size: 75 Copynumber: 4.2 Consensus size: 74
1229739 ATGCATTAAA
* * *
1229749 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATA
1 GCATGAACGGATGCCAAAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATACCATA
1229814 ACTAAAACAT
66 ACTAAAA-AT
* * * *
1229824 GCATGAACGGATGTCAAAACTAAACATGCATGAATGGATGCATTAAGGCATGAACGGATACCATA
1 GCATGAACGGATGCCAAAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATACCATA
1229889 ACTAAAAAT
66 ACTAAAAAT
* * * * *
1229898 GCATGAACGGCTG-C---A-T--TAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAA-GA
1 GCATGAACGGATGCCAAAACTAAAAATGCATGAACGGATG-CAT---T---AAGGCATGAAAGGA
* *
1229955 CT-GCAT---T---AAG
59 -TACCATAACTAAAAAT
* * * *
1229965 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAGGCATAAAAGGATGCCATA
1 GCATGAACGGATGCCAAAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATACCATA
*
1230030 ACTAAACAT
66 ACTAAAAAT
1230039 GCATGAACGGATGC
1 GCATGAACGGATGC
1230053 ATTAAGGCAT
Statistics
Matches: 179, Mismatches: 27, Indels: 47
0.71 0.11 0.19
Matches are distributed among these distances:
67 36 0.20
68 9 0.05
69 1 0.01
70 3 0.02
71 3 0.02
72 1 0.01
73 9 0.05
74 52 0.29
75 65 0.36
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.19
Consensus pattern (74 bp):
GCATGAACGGATGCCAAAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATACCATA
ACTAAAAAT
Found at i:1229893 original size:47 final size:47
Alignment explanation
Indices: 1229824--1230175 Score: 562
Period size: 47 Copynumber: 7.5 Consensus size: 47
1229814 ACTAAAACAT
* * * * *
1229824 GCATGAACGGATGTCAAAACTAAACATGCATGAATGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
* * *
1229871 GCATGAACGGATACCATAACTAAAAATGCATGAACGGCTGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
*
1229918 GCATGAAAGGATGCCATAACTAAAAATGCATGAA-AGACTGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA-TGCATTAAG
1229965 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
* *
1230012 GCATAAAAGGATGCCATAACTAAACATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
1230059 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
* *
1230106 GCATGAAATGATGTCATAACTAAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
*
1230153 GCATGAAAGGATGTCATAACTAA
1 GCATGAAAGGATGCCATAACTAA
1230176 GATTAAAGAA
Statistics
Matches: 285, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 282 0.99
48 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (47 bp):
GCATGAAAGGATGCCATAACTAAAAATGCATGAACGGATGCATTAAG
Found at i:1230052 original size:27 final size:26
Alignment explanation
Indices: 1229749--1230005 Score: 141
Period size: 27 Copynumber: 10.5 Consensus size: 26
1229739 ATGCATTAAA
*
1229749 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAACGGATGCCATAACT-AAAAT
*
1229776 GCATGAACGGATG-CAT---T--AAG
1 GCATGAACGGATGCCATAACTAAAAT
*
1229796 GCATGAAAGGATGCCATAACTAAAACAT
1 GCATGAACGGATGCCATAACT-AAA-AT
* *
1229824 GCATGAACGGATGTCAAAACTAAACAT
1 GCATGAACGGATGCCATAACTAAA-AT
* *
1229851 GCATGAATGGATG-CAT---T--AAG
1 GCATGAACGGATGCCATAACTAAAAT
*
1229871 GCATGAACGGATACCATAACTAAAAAT
1 GCATGAACGGATGCCATAACT-AAAAT
* *
1229898 GCATGAACGGCTG-CAT---T--AAG
1 GCATGAACGGATGCCATAACTAAAAT
*
1229918 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAACGGATGCCATAACT-AAAAT
* *
1229945 GCATGAA-AGACTG-CAT---T--AAG
1 GCATGAACGGA-TGCCATAACTAAAAT
*
1229965 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAACGGATGCCATAACT-AAAAT
1229992 GCATGAACGGATGC
1 GCATGAACGGATGC
1230006 ATTAAGGCAT
Statistics
Matches: 175, Mismatches: 24, Indels: 62
0.67 0.09 0.24
Matches are distributed among these distances:
20 50 0.29
21 15 0.09
23 4 0.02
24 4 0.02
26 13 0.07
27 70 0.40
28 19 0.11
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.19
Consensus pattern (26 bp):
GCATGAACGGATGCCATAACTAAAAT
Found at i:1230097 original size:27 final size:27
Alignment explanation
Indices: 1230059--1230146 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
1230049 ATGCATTAAG
1230059 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCCATAACTAAAAAT
* *
1230086 GCATGAACGGATG-CAT---T---AAG
1 GCATGAAAGGATGCCATAACTAAAAAT
* *
1230106 GCATGAAATGATGTCATAACTAAAAAT
1 GCATGAAAGGATGCCATAACTAAAAAT
*
1230133 GCATGAACGGATGC
1 GCATGAAAGGATGC
1230147 ATTAAGGCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
20 13 0.28
21 3 0.07
23 1 0.02
24 1 0.02
26 3 0.07
27 25 0.54
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (27 bp):
GCATGAAAGGATGCCATAACTAAAAAT
Found at i:1231137 original size:7 final size:8
Alignment explanation
Indices: 1231095--1231152 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
1231085 TTTAAATTTT
*
1231095 AAATATAA
1 AAATATTA
*
1231103 AAATATTC
1 AAATATTA
1231111 AAATATTCA
1 AAATATT-A
*
1231120 AAAAAGTTA
1 AAATA-TTA
1231129 AAATA-TA
1 AAATATTA
1231136 AAATATTA
1 AAATATTA
1231144 AAA-ATTA
1 AAATATTA
1231151 AA
1 AA
1231153 TTACTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
7 13 0.31
8 18 0.43
9 9 0.21
10 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (8 bp):
AAATATTA
Found at i:1231147 original size:16 final size:15
Alignment explanation
Indices: 1231128--1231192 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
1231118 CAAAAAAGTT
*
1231128 AAAATATAAAATATTA
1 AAAAT-TAAAATACTA
*
1231144 AAAATTAAATTACTA
1 AAAATTAAAATACTA
* *
1231159 AAAATTTAAAT-GTA
1 AAAATTAAAATACTA
* * *
1231173 TATATTAAAAAACTA
1 AAAATTAAAATACTA
1231188 AAAAT
1 AAAAT
1231193 ACTATTAAAA
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
14 9 0.25
15 22 0.61
16 5 0.14
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAATTAAAATACTA
Found at i:1231283 original size:2 final size:2
Alignment explanation
Indices: 1231276--1231326 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1231266 AACATTTCAA
*
1231276 AT AT AT AT AT -T AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1231316 AT AT AT AT AT A
1 AT AT AT AT AT A
1231327 GTCATATCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1231807 original size:21 final size:22
Alignment explanation
Indices: 1231757--1231807 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
1231747 TATTTTAATA
1231757 TATATTTATTTTTTAGTAATTT
1 TATATTTATTTTTTAGTAATTT
*
1231779 AACT-TTTA-TTTTTAG-AACTTT
1 TA-TATTTATTTTTTAGTAA-TTT
1231800 TATATTTA
1 TATATTTA
1231808 ACTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 5 0.21
23 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TATATTTATTTTTTAGTAATTT
Found at i:1231988 original size:21 final size:21
Alignment explanation
Indices: 1231964--1232009 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1231954 TCGTAGACCG
* *
1231964 CCACACCAGTATCGTGAACTA
1 CCACACCAGCATCGTAAACTA
*
1231985 CCACATCAGCATCGTAAACTA
1 CCACACCAGCATCGTAAACTA
1232006 CCAC
1 CCAC
1232010 GTCAACATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.37, G:0.11, T:0.17
Consensus pattern (21 bp):
CCACACCAGCATCGTAAACTA
Found at i:1232018 original size:21 final size:21
Alignment explanation
Indices: 1231974--1232022 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1231964 CCACACCAGT
* *
1231974 ATCGTGAACTACCACATCAGC
1 ATCGTAAACTACCACATCAAC
*
1231995 ATCGTAAACTACCACGTCAAC
1 ATCGTAAACTACCACATCAAC
1232016 ATCGTAA
1 ATCGTAA
1232023 TGATCAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (21 bp):
ATCGTAAACTACCACATCAAC
Done.