Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 42
Found at i:251289 original size:22 final size:22
Alignment explanation
Indices: 251245--251289 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
251235 TTTCTTCGAT
251245 ATTGAAAATAAATAAATATTAA
1 ATTGAAAATAAATAAATATTAA
* *
251267 ATTGATAA-AAATAATTATGTAA
1 ATTGAAAATAAATAAATAT-TAA
251289 A
1 A
251290 AAAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
ATTGAAAATAAATAAATATTAA
Found at i:252698 original size:3 final size:3
Alignment explanation
Indices: 252690--252749 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
252680 GGCCTGTTTG
**
252690 TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
252735 TAA T-A TCAA TAA TAA
1 TAA TAA T-AA TAA TAA
252750 AAAATGGGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:253990 original size:21 final size:21
Alignment explanation
Indices: 253964--254009 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
253954 GATTTATGGG
* *
253964 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
253985 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
254006 CAAG
1 CAAG
254010 CGAATAAAAT
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:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:254080 original size:23 final size:22
Alignment explanation
Indices: 254036--254080 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
254026 AATGTCATGG
*
254036 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
254058 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
254081 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:255318 original size:16 final size:16
Alignment explanation
Indices: 255297--255327 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
255287 AGGAATGATA
255297 TGTGGTCCTTCGGGAT
1 TGTGGTCCTTCGGGAT
255313 TGTGGTCCTTCGGGA
1 TGTGGTCCTTCGGGA
255328 CATATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.39, T:0.35
Consensus pattern (16 bp):
TGTGGTCCTTCGGGAT
Found at i:255433 original size:18 final size:18
Alignment explanation
Indices: 255410--255445 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
255400 AAGGATGATA
255410 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
255428 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
255446 ATGTATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:255609 original size:23 final size:23
Alignment explanation
Indices: 255552--255612 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
255542 CATTATTATA
255552 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
255575 CGGAACTACGGTGTAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
255598 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
255613 TTTATATGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:256496 original size:113 final size:113
Alignment explanation
Indices: 256323--256950 Score: 979
Period size: 113 Copynumber: 5.6 Consensus size: 113
256313 TGAATTCAAA
** *
256323 CAAAAGGTTGAACAATTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
256388 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
256436 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
256501 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
256549 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
256614 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGA--GATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
* *
256660 CAAAATGTTGAACAAGCTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGAAGAGTTC-TCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * ** * * ** *
256721 TTATGAA----CTCTGGCGATGTTGATCCATTAAATGATGAATTCAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
** *
256765 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCG
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
256830 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
* * *
256878 CAAATGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
256943 TTATGAAC
66 TTATGAAC
256951 CCTTCTGGAA
Statistics
Matches: 466, Mismatches: 39, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
103 17 0.04
105 37 0.08
107 12 0.03
108 46 0.10
109 11 0.02
111 43 0.09
113 300 0.64
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAG
Found at i:256778 original size:329 final size:332
Alignment explanation
Indices: 256323--256950 Score: 983
Period size: 329 Copynumber: 1.9 Consensus size: 332
256313 TGAATTCAAA
** *
256323 CAAAAGGTTGAACAATTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATAAA--TCTTCTTCCTTCTTCAGAAGAGTTCTTCTCA
* * * ** * *
256388 TTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
64 TTATGAA---TCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAC
256453 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
126 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
256518 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
191 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
256583 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGA
256 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGA
256648 GATGGATTTGAG
321 GATGGATTTGAG
* *
256660 CAAAATGTTGAACAAGCTCTTCTCATTATGAA-CTTCTTCCTTCTTCAGAAGAGTTC-TCTCATT
1 CAAAAGGTTGAACAAGCTCTTCTCATTATAAATCTTCTTCCTTCTTCAGAAGAGTTCTTCTCATT
** * * * *
256723 ATGAA-CTCTGGCGATGTTGATCCATTAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTC
66 ATGAATCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAACTCTTC
*
256787 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCGTTATGAACTTTCTCTGGAAAAG
131 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
* * *
256852 CTGATCCATCGAGTGATGGATTTGAGCAAATGGTTGAACAAGCTCTTCTCATTATGAATTTCTTC
196 CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
*
256917 TTCCTTCTTCATATGAGTTCTTCTCATTATGAAC
261 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
256951 CCTTCTGGAA
Statistics
Matches: 268, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
329 205 0.76
333 12 0.04
334 23 0.09
337 28 0.10
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (332 bp):
CAAAAGGTTGAACAAGCTCTTCTCATTATAAATCTTCTTCCTTCTTCAGAAGAGTTCTTCTCATT
ATGAATCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAACTCTTC
TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGATGG
ATTTGAG
Found at i:256931 original size:24 final size:23
Alignment explanation
Indices: 256896--256940 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
256886 TGAACAAGCT
*
256896 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
256920 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
256941 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:257774 original size:22 final size:21
Alignment explanation
Indices: 257698--257771 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 21
257688 AATAAAGCTT
*
257698 TCATCTTCGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAA-TTA
257720 TCATC-TT-AAAAGAGAATTA
1 TCATCTTTGAAAAGAGAATTA
*
257739 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAAT-TA
257761 TCATCTTTGAA
1 TCATCTTTGAA
257772 GAGTGTAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.17
20 11 0.23
21 10 0.21
22 18 0.38
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
TCATCTTTGAAAAGAGAATTA
Found at i:259160 original size:76 final size:76
Alignment explanation
Indices: 259007--259181 Score: 217
Period size: 76 Copynumber: 2.3 Consensus size: 76
258997 GGGATGATAT
* * * * *
259007 GGGCCTTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAACAGTCTTGATT
1 GGGCTTTCAGCATGCCCCAACATTTGGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
259071 CTGATTGAAAG
66 CTGATTGAAAG
* * * * * * *
259082 GGGCTTTCAGCATGCCCCAACATTTTGCTGATATAAATATTCAGAATACTTCAATATTCCTGATT
1 GGGCTTTCAGCATGCCCCAACATTTGGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
259147 CTGATTGAAAG
66 CTGATTGAAAG
* *
259158 GGGTTTTCAGCATGCCACAACATT
1 GGGCTTTCAGCATGCCCCAACATT
259182 CGCTTCTTGT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 21 0.25
76 64 0.75
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (76 bp):
GGGCTTTCAGCATGCCCCAACATTTGGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
CTGATTGAAAG
Found at i:260505 original size:114 final size:114
Alignment explanation
Indices: 260305--260528 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 114
260295 GATCATGCAG
* * * *
260305 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTATCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
260370 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAA
* *
260419 TTCATCTATCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTATCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
260484 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAG
260529 AACGAGGCAC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (114 bp):
TTCATCTATCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAA
Found at i:262830 original size:14 final size:14
Alignment explanation
Indices: 262825--262854 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
262815 TTTGTTTTTG
262825 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
262839 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
262853 TT
1 TT
262855 CTTTCTTTGC
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:262842 original size:20 final size:19
Alignment explanation
Indices: 262805--262862 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
262795 TTCCTTCTTC
* * *
262805 TTTTTTCCTTTTTGTTTTT
1 TTTTTTTCTTCTTCTTTTT
262824 GTTTTTTTCTTCTTCTTTTT
1 -TTTTTTTCTTCTTCTTTTT
*
262844 TTCTTCTTCTTCTTTCTTT
1 TT-TTTTTCTTC-TTCTTT
262863 GCTGGATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.06
20 24 0.75
21 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTTTTCTTCTTCTTTTT
Found at i:263161 original size:2 final size:2
Alignment explanation
Indices: 263154--263178 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
263144 ACAACAAATG
263154 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
263179 AAAGGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:264812 original size:27 final size:27
Alignment explanation
Indices: 264782--264837 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
264772 GTAATTATGT
264782 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
264809 AAAAATGCAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
264836 AA
1 AA
264838 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:264826 original size:12 final size:12
Alignment explanation
Indices: 264811--264838 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
264801 CAAACGTAAA
264811 AAATGCAAATGT
1 AAATGCAAATGT
264823 AAATGCAAATGT
1 AAATGCAAATGT
264835 AAAT
1 AAAT
264839 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:264931 original size:7 final size:7
Alignment explanation
Indices: 264897--264938 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
264887 ATAAAAGTAT
264897 AAATGCA
1 AAATGCA
* *
264904 CAATGAA
1 AAATGCA
264911 AAATGCA
1 AAATGCA
264918 AAGATGCA
1 AA-ATGCA
264926 AAATGC-
1 AAATGCA
264932 AAATGCA
1 AAATGCA
264939 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:268653 original size:3 final size:3
Alignment explanation
Indices: 268645--268704 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
268635 GGCCTGTTTG
**
268645 TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
268690 TAA T-A TCAA TAA TAA
1 TAA TAA T-AA TAA TAA
268705 AAAAATGGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:273666 original size:16 final size:16
Alignment explanation
Indices: 273645--273679 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
273635 AACACCACAT
273645 GTCCCAAAATAACAGA
1 GTCCCAAAATAACAGA
273661 GTCCCAAAATAACAGA
1 GTCCCAAAATAACAGA
273677 GTC
1 GTC
273680 TGAACCTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (16 bp):
GTCCCAAAATAACAGA
Found at i:280196 original size:22 final size:23
Alignment explanation
Indices: 280143--280196 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
280133 TATTAATTAT
* * *
280143 AATAATTAACGATTAAAATAAGA
1 AATAAATAATGATAAAAATAAGA
*
280166 AA-AAGTAATGATAAAAATAA-A
1 AATAAATAATGATAAAAATAAGA
280187 AATAAATAAT
1 AATAAATAAT
280197 ATACTATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (23 bp):
AATAAATAATGATAAAAATAAGA
Found at i:280606 original size:2 final size:2
Alignment explanation
Indices: 280599--280654 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
280589 TCATAAACTT
280599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
280641 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
280655 CATTTGTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:284278 original size:3 final size:3
Alignment explanation
Indices: 284270--284294 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
284260 ACACTATGTT
284270 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
284295 CAACCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:285819 original size:14 final size:14
Alignment explanation
Indices: 285802--285830 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
285792 TTAAAAATAT
285802 ACTAAATATTTTTA
1 ACTAAATATTTTTA
285816 ACTAAATATTTTTA
1 ACTAAATATTTTTA
285830 A
1 A
285831 AAATAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ACTAAATATTTTTA
Found at i:286360 original size:2 final size:2
Alignment explanation
Indices: 286353--286378 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
286343 TAATTAATCA
286353 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
286379 AATCCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:298546 original size:2 final size:2
Alignment explanation
Indices: 298539--298570 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
298529 AAGCTAACAC
298539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298571 GGAAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:300544 original size:21 final size:21
Alignment explanation
Indices: 300502--300544 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
300492 TTAAATTTCG
* * *
300502 TAATTTTGATTAAACTTAAAA
1 TAATTTTAAATAAAATTAAAA
*
300523 TAATTTTAAATAAAATTTAAA
1 TAATTTTAAATAAAATTAAAA
300544 T
1 T
300545 TATAATAAGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATTTTAAATAAAATTAAAA
Found at i:306149 original size:7 final size:8
Alignment explanation
Indices: 306128--306154 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
306118 TTTTATAATT
306128 TTAAAAAA
1 TTAAAAAA
306136 TTAAAAAA
1 TTAAAAAA
306144 TTAAAAAA
1 TTAAAAAA
306152 TTA
1 TTA
306155 CATGTGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
TTAAAAAA
Found at i:306966 original size:31 final size:31
Alignment explanation
Indices: 306931--307001 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
306921 AAAAAAATTA
306931 AGTTTAGGTATCAAAACAGAACAAGAAT-AAT
1 AGTTTAGGTATCAAAACAGAACAA-AATCAAT
* *
306962 AGTTTAGGTATCGAAACGGAACAAAATCAAT
1 AGTTTAGGTATCAAAACAGAACAAAATCAAT
*
306993 AATTTAGGT
1 AGTTTAGGT
307002 GCTAAGCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 3 0.08
31 33 0.92
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (31 bp):
AGTTTAGGTATCAAAACAGAACAAAATCAAT
Found at i:307639 original size:41 final size:41
Alignment explanation
Indices: 307594--307701 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 41
307584 TGATTTTTTA
*
307594 AAAAAAAGAAATAAATAAAAATTTATTATACAGTGAAAA-TT
1 AAAAAAAGAAATAAATAAAAATGT-TTATACAGTGAAAAGTT
* * *
307635 AAAAAAGGGAACAAATACAAAATGTTTATACAGTGAAAATGTT
1 AAAAAAAGAAATAAATA-AAAATGTTTATACAGTGAAAA-GTT
*
307678 AGAAAAAAGTAAATAAATGAAAAT
1 A-AAAAAAG-AAATAAATAAAAAT
307702 AATTATAAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
41 28 0.52
42 6 0.11
43 3 0.06
44 11 0.20
45 6 0.11
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.23
Consensus pattern (41 bp):
AAAAAAAGAAATAAATAAAAATGTTTATACAGTGAAAAGTT
Found at i:307714 original size:25 final size:25
Alignment explanation
Indices: 307683--307733 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
307673 ATGTTAGAAA
307683 AAAGTAAATAAATGAAAATAATTAT
1 AAAGTAAATAAATGAAAATAATTAT
*
307708 AAAGTAATTAAATGAAAATAATTAT
1 AAAGTAAATAAATGAAAATAATTAT
307733 A
1 A
307734 CAGTGAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (25 bp):
AAAGTAAATAAATGAAAATAATTAT
Found at i:307731 original size:14 final size:14
Alignment explanation
Indices: 307691--307731 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
307681 AAAAAGTAAA
307691 TAAATGAAAATAAT
1 TAAATGAAAATAAT
*
307705 T--AT-AAAGTAAT
1 TAAATGAAAATAAT
307716 TAAATGAAAATAAT
1 TAAATGAAAATAAT
307730 TA
1 TA
307732 TACAGTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 2 0.09
14 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (14 bp):
TAAATGAAAATAAT
Found at i:318407 original size:211 final size:212
Alignment explanation
Indices: 317824--318668 Score: 1354
Period size: 212 Copynumber: 4.0 Consensus size: 212
317814 ACTCTCTTAA
* * *
317824 CACATGCTTATCACTCTTCAGAAAATTAAGGCCAATGCCTATTCCATATTGAGAATTATGTAAAA
1 CACATTCTTATCACTCTTCAGTAAATTAAGGCCAATGCCTTTTCCATATTGAGAATTATGTAAAA
* * *
317889 GAAGAGCCAAACTCGAACTTCAT--GAAGCAGAGCACAAGCATTAACTTCTGATTTGATATCTGG
66 GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGATTTAATATCTGG
* * *
317952 AGAAGATACAAAGAGGGAGATGACTATCTGATATTTTGATCACAATCCTCTATCAGACTCCACAT
131 AGAAGATACAAAGAGGGAGATGGCTATCTGATATTTTGATCACAATCATCTATCAGACACCACAT
318017 TTCCCACTTCTCCAATC
196 TTCCCACTTCTCCAATC
* * * * * *
318034 CAGATTCTTATCACTCTTCAGTAAGTTAAGGTCAATGCTTTTTCCACATCGAGAATTATGTAAAA
1 CACATTCTTATCACTCTTCAGTAAATTAAGGCCAATGCCTTTTCCATATTGAGAATTATGTAAAA
*
318099 GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGGTTTAATATCTGG
66 GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGATTTAATATCTGG
* * **
318164 AGAATATACAAAGAGGGTGATGGCTATCTGATATTTTGATCACAATCATCTATCAGATGCCACAT
131 AGAAGATACAAAGAGGGAGATGGCTATCTGATATTTTGATCACAATCATCTATCAGACACCACAT
318229 TTCCCACTTCTCCAATC
196 TTCCCACTTCTCCAATC
* * * *
318246 CACATTCTTATCACTCTTCAGTAAATTAAAGTCAATG-CTTTTTCATATTGAAAATTATGTAAAA
1 CACATTCTTATCACTCTTCAGTAAATTAAGGCCAATGCCTTTTCCATATTGAGAATTATGTAAAA
* * *
318310 GAAGAGCCAAACTTGAACTCCAAGATAAGCAGAGCACAAGCATTAACTTCTGGTTTAATATCTGG
66 GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGATTTAATATCTGG
* * * *
318375 AGAAGATACAAAGAGGGAGATGTCTGTCTGATATTTTGATCACAATCCTCTATCAGACACCACGT
131 AGAAGATACAAAGAGGGAGATGGCTATCTGATATTTTGATCACAATCATCTATCAGACACCACAT
*
318440 TTCCAACTTCTCCAATC
196 TTCCCACTTCTCCAATC
*
318457 CACACTCTTATCACTCTTCAGTAAATTAAGGCCAATGCCTTTTCCATATTGAGAATTATGTAAAA
1 CACATTCTTATCACTCTTCAGTAAATTAAGGCCAATGCCTTTTCCATATTGAGAATTATGTAAAA
*
318522 GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGAATTAATATCTGG
66 GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGATTTAATATCTGG
*
318587 AGAAGATACAAAGAGGGTGATGGCTATCTGATATTTTGATCACAATCATCTATCAGACACCACAT
131 AGAAGATACAAAGAGGGAGATGGCTATCTGATATTTTGATCACAATCATCTATCAGACACCACAT
318652 TTCCCACTTCTCCAATC
196 TTCCCACTTCTCCAATC
318669 GACCCAGGAC
Statistics
Matches: 579, Mismatches: 53, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
210 77 0.13
211 192 0.33
212 310 0.54
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (212 bp):
CACATTCTTATCACTCTTCAGTAAATTAAGGCCAATGCCTTTTCCATATTGAGAATTATGTAAAA
GAAGAGCCAAACTTGAACTCCATGAGAAGCAGAGCACAAGCATTAACTTCTGATTTAATATCTGG
AGAAGATACAAAGAGGGAGATGGCTATCTGATATTTTGATCACAATCATCTATCAGACACCACAT
TTCCCACTTCTCCAATC
Found at i:319490 original size:16 final size:16
Alignment explanation
Indices: 319469--319500 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
319459 TACAGTAAAA
*
319469 CAAATCCAATAAACAT
1 CAAATCCAACAAACAT
319485 CAAATCCAACAAACAT
1 CAAATCCAACAAACAT
319501 AGATTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (16 bp):
CAAATCCAACAAACAT
Found at i:326258 original size:2 final size:2
Alignment explanation
Indices: 326251--326280 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
326241 ATTTTAAAAG
326251 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
326281 GATTAGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:326441 original size:21 final size:21
Alignment explanation
Indices: 326415--326459 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
326405 CAAAATGATG
* *
326415 GTAGAATGGTTGTTTGGTCTT
1 GTAGAATGATTGTTTGGCCTT
*
326436 GTAGAATGATTGTTTTGCCTT
1 GTAGAATGATTGTTTGGCCTT
326457 GTA
1 GTA
326460 TCTTGGCGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.07, G:0.29, T:0.47
Consensus pattern (21 bp):
GTAGAATGATTGTTTGGCCTT
Found at i:332094 original size:22 final size:23
Alignment explanation
Indices: 332063--332109 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
332053 TACAAGTATA
*
332063 AAATTATATATAATTTT-ATTTT
1 AAATTATATAAAATTTTAATTTT
*
332085 AAATTTTATAAAATTTTAATTTT
1 AAATTATATAAAATTTTAATTTT
332108 AA
1 AA
332110 TCTTTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATTATATAAAATTTTAATTTT
Found at i:332946 original size:54 final size:54
Alignment explanation
Indices: 332864--332973 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
332854 CTAGTGTTTC
332864 ATTCTACTAAACCAACTGATTGTTGGTATTATTATTATTTTTCATAATCGACGT
1 ATTCTACTAAACCAACTGATTGTTGGTATTATTATTATTTTTCATAATCGACGT
*
332918 ATTCTACTAAACCAACTGGTTGTTGGTATTATTATTATTTTTCATAATCGACGT
1 ATTCTACTAAACCAACTGATTGTTGGTATTATTATTATTTTTCATAATCGACGT
332972 AT
1 AT
332974 ATTGACATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (54 bp):
ATTCTACTAAACCAACTGATTGTTGGTATTATTATTATTTTTCATAATCGACGT
Found at i:334805 original size:2 final size:2
Alignment explanation
Indices: 334793--334824 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
334783 GCTTTGTTCC
334793 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
334825 AAAGAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:351382 original size:28 final size:28
Alignment explanation
Indices: 351350--351411 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
351340 ATTTATTCCC
* * *
351350 ATCAATTCCTTGATTGTTTTATACTCTT
1 ATCAATTCCTTGACTGCTTTATACTCCT
351378 ATCAATTCCTTGACTGCTTTATACTCCT
1 ATCAATTCCTTGACTGCTTTATACTCCT
351406 ATCAAT
1 ATCAAT
351412 ATTTTATCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (28 bp):
ATCAATTCCTTGACTGCTTTATACTCCT
Found at i:360636 original size:19 final size:19
Alignment explanation
Indices: 360590--360637 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
360580 AGCTATGTAA
360590 CTTTATTTTTTTAAAATGT
1 CTTTATTTTTTTAAAATGT
* * *
360609 CCTTGTTTTTTT-AAATTT
1 CTTTATTTTTTTAAAATGT
360627 CTTTATTTTTT
1 CTTTATTTTTT
360638 ATTTTATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (19 bp):
CTTTATTTTTTTAAAATGT
Found at i:365437 original size:29 final size:30
Alignment explanation
Indices: 365396--365455 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
365386 TAGTAATCAT
365396 TTATAATAATTAATAAATTTAAT-A-AAAAA
1 TTATAATAATTAA-AAATTTAATGATAAAAA
** *
365425 TTATAATTTTTAAAATTTTAATGATAAAAA
1 TTATAATAATTAAAAATTTAATGATAAAAA
365455 T
1 T
365456 AAGTATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.31
29 12 0.46
30 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TTATAATAATTAAAAATTTAATGATAAAAA
Found at i:366090 original size:61 final size:61
Alignment explanation
Indices: 365995--366114 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
365985 TTCATTTTCA
* * *
365995 AATAATTGAGAATCCTTAGAGCAAATATTACTTATAATCATCTTAGATTTATAAAAAAACG
1 AATAATTGAGAATCCTTAGAACAAATATTACTTATAATCATCGTAGATTAATAAAAAAACG
*
366056 AATAATTGAGAATCCTTAGAACATATATTACTTATAATCATCGTAGATTAATAAAAAAA
1 AATAATTGAGAATCCTTAGAACAAATATTACTTATAATCATCGTAGATTAATAAAAAAA
366115 ATTGAATTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (61 bp):
AATAATTGAGAATCCTTAGAACAAATATTACTTATAATCATCGTAGATTAATAAAAAAACG
Found at i:371408 original size:20 final size:20
Alignment explanation
Indices: 371379--371422 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
371369 CAAGACACAT
*
371379 GAAAAAAAT-CAACAAAATA
1 GAAAAAAATCCAACAAAAGA
*
371398 GAAACAAAATCCACCAAAAGA
1 GAAA-AAAATCCAACAAAAGA
371419 GAAA
1 GAAA
371423 GATACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 12 0.57
ACGTcount: A:0.68, C:0.16, G:0.09, T:0.07
Consensus pattern (20 bp):
GAAAAAAATCCAACAAAAGA
Found at i:376169 original size:2 final size:2
Alignment explanation
Indices: 376162--376197 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
376152 GCTAGGGAGT
376162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
376198 CCAAGTGCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:376730 original size:33 final size:34
Alignment explanation
Indices: 376693--376801 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 34
376683 GGTAAGAAAT
* * *
376693 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
376726 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* *
376760 TT-TTTTT-TATTAAAATAATATTTATATAATTATTA
1 TTATTTTTATATT--AAT-ATATTTATGTAAATATTA
376795 TTTATTT
1 -TTATTT
376802 AGATTATTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
32 4 0.06
33 21 0.33
34 11 0.17
35 23 0.36
36 2 0.03
37 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:376755 original size:35 final size:32
Alignment explanation
Indices: 376693--376772 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
376683 GGTAAGAAAT
* * *
376693 TTATTTTTATGTTAGTATTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATTTTTGTAAATA-TTA
376726 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATAT-TTT-TGTAAATATTA
376760 TT-TTTTT-TATTAA
1 TTATTTTTATATTAA
376773 AATAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 6 0.14
33 21 0.50
34 8 0.19
35 7 0.17
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (32 bp):
TTATTTTTATATTAATATTTTTGTAAATATTA
Found at i:378535 original size:21 final size:21
Alignment explanation
Indices: 378505--378552 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
378495 GCAGGGGTAC
* *
378505 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
378526 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
378547 ATGCCA
1 ATGCCA
378553 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:378582 original size:21 final size:21
Alignment explanation
Indices: 378556--378649 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
378546 TATGCCATCT
* *
378556 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
378577 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
378598 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
378619 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
378640 CCGCAGGGTT
1 CCGCAGGGTT
378650 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:379230 original size:33 final size:34
Alignment explanation
Indices: 379171--379234 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
379161 AAATGTTTTT
* *
379171 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATAATATTATTCGAAATTTAAAATA
379205 AAAATAAAAATAATATTATTC-AAATTTAAA
1 AAAATAAAAATAATATTATTCGAAATTTAAA
379235 TTTCAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (34 bp):
AAAATAAAAATAATATTATTCGAAATTTAAAATA
Found at i:379852 original size:124 final size:125
Alignment explanation
Indices: 379613--379956 Score: 614
Period size: 124 Copynumber: 2.8 Consensus size: 125
379603 TTTAAGTTAT
*
379613 TCCCCGAGGGACATGAGTGACATAATAGGGCAATG---ATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
379675 GCGCCCCCGGGAACGCGCCTTCACGTG-A-AGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGA-ATATCTAGTG
379734 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
379799 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTG-ATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGAATATCTAGTG
379858 TCCCCGAGGGACATGAATGACATAATAGGGC-ATGATAATATTCTCTGACGAAATAA-GGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
379921 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
379957 CCGATTATAG
Statistics
Matches: 217, Mismatches: 1, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
121 34 0.16
122 43 0.20
123 25 0.12
124 95 0.44
125 1 0.00
126 19 0.09
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (125 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGAATATCTAGTG
Found at i:397390 original size:18 final size:18
Alignment explanation
Indices: 397367--397410 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
397357 TGAAGAAAGG
*
397367 TAAGATTATCGGTAAGAA
1 TAAGATTATCGATAAGAA
* *
397385 TAAGATTATCTATGAGAA
1 TAAGATTATCGATAAGAA
397403 TAAGATTA
1 TAAGATTA
397411 CTGAGATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (18 bp):
TAAGATTATCGATAAGAA
Found at i:398987 original size:4 final size:4
Alignment explanation
Indices: 398974--399008 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
398964 TGTGTGTGTG
* *
398974 TGTA TTTA TGTA TGTA TGTA TGTA TGTA TGCA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
399009 TTTGGATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:402423 original size:21 final size:21
Alignment explanation
Indices: 402384--402424 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
402374 GGTAAAAAAT
* *
402384 TACCTAAAACATTATTACTTC
1 TACCTAAAACATCAATACTTC
402405 TACCTAAAACATCAATACTT
1 TACCTAAAACATCAATACTT
402425 TTAACAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (21 bp):
TACCTAAAACATCAATACTTC
Found at i:404000 original size:33 final size:33
Alignment explanation
Indices: 403963--404025 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
403953 TGTCTAAAAA
* * * *
403963 ATAATTTTGTCTTGATCGATTAATTGTAAACAG
1 ATAATTTTATCTCGACCGATTAATAGTAAACAG
403996 ATAATTTTATCTCGACCGATTAATAGTAAA
1 ATAATTTTATCTCGACCGATTAATAGTAAA
404026 AAACCAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Consensus pattern (33 bp):
ATAATTTTATCTCGACCGATTAATAGTAAACAG
Found at i:405838 original size:9 final size:9
Alignment explanation
Indices: 405806--405830 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
405796 TACAAGGGAA
405806 AAATAAAAT
1 AAATAAAAT
405815 AAATAAAAT
1 AAATAAAAT
405824 AAATAAA
1 AAATAAA
405831 TAAGATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:406904 original size:37 final size:36
Alignment explanation
Indices: 406861--406962 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
406851 ATAGTATAAC
406861 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
406898 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
406932 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
406963 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:407808 original size:105 final size:105
Alignment explanation
Indices: 407510--408341 Score: 1314
Period size: 105 Copynumber: 8.0 Consensus size: 105
407500 CATTGTTCCA
* * * ** * * *
407510 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* ** * *
407575 CAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
407616 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGAATTTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
407676 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
407716 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
407781 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
407821 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
407886 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
407926 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
407991 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
408031 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
408096 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
408136 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGATGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
408201 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
408241 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
408306 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
408342 CCTCGAGTGC
Statistics
Matches: 678, Mismatches: 42, Indels: 12
0.93 0.06 0.02
Matches are distributed among these distances:
100 81 0.12
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 510 0.75
106 75 0.11
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:409149 original size:65 final size:67
Alignment explanation
Indices: 408984--409151 Score: 214
Period size: 68 Copynumber: 2.5 Consensus size: 67
408974 AAGATATCTG
* * * ** *
408984 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAG
409049 TT
66 TT
* *
409051 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAG-
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
409114 GTT
65 GTT
* * *
409117 TTGTTTCAAGGGAAACTGTCTCTAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
409152 CTTAGTTCCA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
65 30 0.34
66 3 0.03
67 23 0.26
68 32 0.36
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (67 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAG
TT
Found at i:409195 original size:102 final size:101
Alignment explanation
Indices: 409059--409305 Score: 298
Period size: 102 Copynumber: 2.4 Consensus size: 101
409049 TTTGTGTTTC
* * * ** * * * *
409059 AAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTC
1 AAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTATTTC
*
409124 AAGGGAAACTGTCTCTAGAGAGACAAAACTTAGTTCCA
66 AAGGGAAACTGTCTCAAGAGAGACAAAACTTA-TT-CA
* * *
409162 AA-AGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTATTTC
1 AAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTATTTC
* *
409226 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTA
66 AAGGGAAACTGTCTCAAGAGAGACAAAACTTATTCA
* **
409262 AAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAA
1 AAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAA-AGAAA
409306 CTTTCTCAAG
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
100 3 0.02
101 33 0.27
102 85 0.69
103 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (101 bp):
AAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTATTTC
AAGGGAAACTGTCTCAAGAGAGACAAAACTTATTCA
Found at i:409266 original size:36 final size:36
Alignment explanation
Indices: 409218--409361 Score: 225
Period size: 36 Copynumber: 4.0 Consensus size: 36
409208 ATTCAAATAT
409218 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
409254 TTTATTTAAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
409290 TTTGTTTCAAGAGAAACTTTCTCAAGAGAGACAAAA
1 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
409326 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
409362 CTCTTCTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:409402 original size:71 final size:72
Alignment explanation
Indices: 409223--409403 Score: 215
Period size: 72 Copynumber: 2.5 Consensus size: 72
409213 AATATTTTAT
* * *
409223 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACGA
** *
409288 AATTTGT
66 AAACTGC
* *
409295 TTCAAGAGAAACTTTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACGA
409359 AAACT-C
66 AAACTGC
* * * *
409365 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
409404 TAAGAAAAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
70 10 0.11
71 26 0.28
72 58 0.62
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACGA
AAACTGC
Found at i:410317 original size:22 final size:22
Alignment explanation
Indices: 410291--410345 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
410281 TTGTGTTTGG
410291 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
410313 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
410335 TCAAAGGTTTG
1 TCAAAGGTTTG
410346 ATGGGACAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:411008 original size:7 final size:7
Alignment explanation
Indices: 410996--411079 Score: 64
Period size: 8 Copynumber: 11.3 Consensus size: 7
410986 TGATTCTTAT
410996 TTTTTTC
1 TTTTTTC
411003 TTTTTTTCC
1 -TTTTTT-C
411012 TTTTGTTC
1 TTTT-TTC
411020 TTGTTTCTC
1 TT-TTT-TC
411029 TTTTTTC
1 TTTTTTC
411036 TTTGTTT-
1 TTT-TTTC
* *
411043 TTCTTTG
1 TTTTTTC
411050 TTTTTT-
1 TTTTTTC
*
411056 TTTTTGC
1 TTTTTTC
411063 TTCTTTTC
1 TT-TTTTC
411071 TTTTTTC
1 TTTTTTC
411078 TT
1 TT
411080 ATTGATTGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
6 8 0.12
7 21 0.33
8 26 0.41
9 9 0.14
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:411009 original size:9 final size:9
Alignment explanation
Indices: 410995--411076 Score: 57
Period size: 9 Copynumber: 9.6 Consensus size: 9
410985 TTGATTCTTA
410995 TTTTTTTC-
1 TTTTTTTCT
*
411003 TTTTTTTCC
1 TTTTTTTCT
*
411012 TTTTGTTC-
1 TTTTTTTCT
*
411020 -TTGTTTCT
1 TTTTTTTCT
*
411028 CTTTTTTCT
1 TTTTTTTCT
411037 TTGTTTTTCT
1 TT-TTTTTCT
*
411047 TTGTTTT-T
1 TTTTTTTCT
*
411055 TTTTTTGC-
1 TTTTTTTCT
*
411063 TTCTTTTCT
1 TTTTTTTCT
411072 TTTTT
1 TTTTT
411077 CTTATTGATT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
7 5 0.09
8 20 0.35
9 23 0.40
10 9 0.16
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.80
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:411060 original size:17 final size:17
Alignment explanation
Indices: 410996--411073 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 17
410986 TGATTCTTAT
*
410996 TTTTTTCTTT-TTTTCC
1 TTTTTTCTTTGTTTTTC
*
411012 TTTTGTTC-TTGTTTCTC
1 TTTT-TTCTTTGTTTTTC
411029 TTTTTTCTTTGTTTTTC
1 TTTTTTCTTTGTTTTTC
411046 TTTGTTT-TTT-TTTTTGC
1 TTT-TTTCTTTGTTTTT-C
411063 TTCTTTTCTTT
1 TT-TTTTCTTT
411074 TTTCTTATTG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
16 14 0.27
17 31 0.60
18 7 0.13
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTGTTTTTC
Found at i:412203 original size:8 final size:8
Alignment explanation
Indices: 412187--412225 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
412177 AATGTAGATG
412187 AAAATGCA
1 AAAATGCA
*
412195 AAAAGGCA
1 AAAATGCA
412203 AAAATGC-
1 AAAATGCA
412210 AAAATGCA
1 AAAATGCA
*
412218 AGAATGCA
1 AAAATGCA
412226 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:412213 original size:15 final size:15
Alignment explanation
Indices: 412187--412225 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
412177 AATGTAGATG
412187 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
412203 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
412218 AGAATGCA
1 AAAATGCA
412226 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:413714 original size:16 final size:16
Alignment explanation
Indices: 413693--413759 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 16
413683 AATGAAAGTC
413693 CTACCCCACATGATAT
1 CTACCCCACATGATAT
413709 CTACCCCACATGCTTATTATT
1 CTACCCCACATG---A-TA-T
*
413730 CCTACCCGGACATGATAT
1 -CTACCC-CACATGATAT
413748 CTACCCCACATG
1 CTACCCCACATG
413760 CTTATTATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
16 17 0.40
17 6 0.14
18 1 0.02
19 3 0.07
20 3 0.07
21 1 0.02
22 6 0.14
23 5 0.12
ACGTcount: A:0.27, C:0.37, G:0.09, T:0.27
Consensus pattern (16 bp):
CTACCCCACATGATAT
Found at i:413746 original size:39 final size:39
Alignment explanation
Indices: 413691--413800 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
413681 AAAATGAAAG
*
413691 TCCTACCC-CACATGATATCTACCCCACATGCTTATTAT
1 TCCTACCCGGACATGATATCTACCCCACATGCTTATTAT
413729 TCCTACCCGGACATGATATCTACCCCACATGCTTATTAT
1 TCCTACCCGGACATGATATCTACCCCACATGCTTATTAT
* * *
413768 TCCTACCCGGACATGATCTCTATCCCGCATGCT
1 TCCTACCCGGACATGATATCTACCCCACATGCT
413801 AGTCTCAAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 8 0.12
39 59 0.88
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.30
Consensus pattern (39 bp):
TCCTACCCGGACATGATATCTACCCCACATGCTTATTAT
Found at i:415129 original size:24 final size:25
Alignment explanation
Indices: 415075--415130 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
415065 AGGTTTTTTT
* *
415075 AAAAA-AAATAAATGTATAATAATA
1 AAAAATAAAAAAATGTAAAATAATA
**
415099 ATGAATAAAAAAATG-AAAATAATA
1 AAAAATAAAAAAATGTAAAATAATA
415123 AAAAATAA
1 AAAAATAA
415131 TATAAATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.21
Consensus pattern (25 bp):
AAAAATAAAAAAATGTAAAATAATA
Found at i:415369 original size:53 final size:56
Alignment explanation
Indices: 415277--415404 Score: 145
Period size: 55 Copynumber: 2.3 Consensus size: 56
415267 AGATAATTAC
* * ** * * *
415277 AATATATATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGAAATAT
1 AATATATATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAAGAAAAAT
*
415333 -ATATATATATATATATAATAATAATA-AAATAT-AGTAAAAAAATAAATAAAAAT
1 AATATATATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAAGAAAAAT
*
415386 AATTTAATATATATATATA
1 AATAT-ATATATATATATA
415405 TATATACATA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
53 17 0.28
54 7 0.11
55 37 0.61
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (56 bp):
AATATATATATATATATAATAATAATAGAAATATAAGTAAAAAAATAAAGAAAAAT
Found at i:415435 original size:18 final size:17
Alignment explanation
Indices: 415414--415456 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
415404 ATATATACAT
415414 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
415432 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
415449 ATAA-AATA
1 ATAATAATA
415457 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:415894 original size:37 final size:35
Alignment explanation
Indices: 415846--415947 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
415836 ATAGTATAAC
*
415846 TCTATCATATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAAT
*
415883 TTTATCCTATTTTTAGGAGTTTGAATCCT-AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
415917 TCTATCCTATTTTTAGGAGTTTGAATCCTAA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAA
415948 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 33 0.54
35 1 0.02
37 27 0.44
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:420431 original size:2 final size:2
Alignment explanation
Indices: 420424--420471 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
420414 ATTTAAATTA
* * * *
420424 AT AT AT AT AT AT AT AT AT TT AT AT AT TT A- AT TT AA 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
420465 AT AT AT A
1 AT AT AT A
420472 CCGACCCGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:424212 original size:29 final size:29
Alignment explanation
Indices: 424178--424268 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
424168 CTATGACTCT
424178 TATTTTAAATTAGTCCATAAACTTTTGAA
1 TATTTTAAATTAGTCCATAAACTTTTGAA
* * * *
424207 TATTTTAATTTCA-TCCTTAAAC-TATGAC
1 TATTTTAAATT-AGTCCATAAACTTTTGAA
* ** *
424235 TCATTTTAAATTGGTCCCCAAACTTTTAAA
1 T-ATTTTAAATTAGTCCATAAACTTTTGAA
424265 TATT
1 TATT
424269 CCAAATTCAT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
28 5 0.11
29 37 0.79
30 5 0.11
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.45
Consensus pattern (29 bp):
TATTTTAAATTAGTCCATAAACTTTTGAA
Found at i:424260 original size:58 final size:58
Alignment explanation
Indices: 424160--424352 Score: 260
Period size: 60 Copynumber: 3.3 Consensus size: 58
424150 TCAACATATG
* ** * **
424160 TCCTTAAACTATGACTCTTATTTTAAATTAGTCCATAAACTTTTGAATATTTTAATTTCA
1 TCCTTAAACTATGACTC--ATTTTAAATTGGTCCCCAAACTTTTAAATATTCCAATTTCA
*
424220 TCCTTAAACTATGACTCATTTTAAATTGGTCCCCAAACTTTTAAATATTCCAAATTCA
1 TCCTTAAACTATGACTCATTTTAAATTGGTCCCCAAACTTTTAAATATTCCAATTTCA
* *
424278 TCCTTAAACTACGACTCTCATTTTAAATTGATCCCCAAACTTTTAAATATTCCAATTTCA
1 TCCTTAAACTATGA--CTCATTTTAAATTGGTCCCCAAACTTTTAAATATTCCAATTTCA
*
424338 TCATTAAACTATGAC
1 TCCTTAAACTATGAC
424353 CCTTATTCTA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
58 48 0.40
60 71 0.60
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (58 bp):
TCCTTAAACTATGACTCATTTTAAATTGGTCCCCAAACTTTTAAATATTCCAATTTCA
Found at i:424320 original size:60 final size:59
Alignment explanation
Indices: 424160--424400 Score: 254
Period size: 60 Copynumber: 4.1 Consensus size: 59
424150 TCAACATATG
* ** * ** *
424160 TCCTTAAACTATGACTCTTATTTTAAATTAGTCCATAAACTTTTGAATATTTTAATTTCA
1 TCCTTAAACTATGACTCTCATTTTAAATTA-TCCCCAAACTTTTAAATATTCCAAATTCA
*
424220 TCCTTAAACTATGA--CTCATTTTAAATTGGTCCCCAAACTTTTAAATATTCCAAATTCA
1 TCCTTAAACTATGACTCTCATTTTAAATT-ATCCCCAAACTTTTAAATATTCCAAATTCA
* *
424278 TCCTTAAACTACGACTCTCATTTTAAATTGATCCCCAAACTTTTAAATATTCCAATTTCA
1 TCCTTAAACTATGACTCTCATTTTAAATT-ATCCCCAAACTTTTAAATATTCCAAATTCA
* * * * * * * *
424338 TCATTAAACTATGACCCTTATTCTAAATTAGCCCTGAAACTTTTGAACATTCCAATATT-A
1 TCCTTAAACTATGACTCTCATTTTAAATTATCCC-CAAACTTTTAAATATTCCAA-ATTCA
424398 TCC
1 TCC
424401 CCCCTAAATC
Statistics
Matches: 154, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
58 48 0.31
59 4 0.03
60 100 0.65
61 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (59 bp):
TCCTTAAACTATGACTCTCATTTTAAATTATCCCCAAACTTTTAAATATTCCAAATTCA
Found at i:430414 original size:36 final size:36
Alignment explanation
Indices: 430346--430420 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
430336 AACTCGATTT
* * *
430346 GAAAATTCACGAGTTTAAAATTGTCAAGCTCGACCC
1 GAAAACTCACGAGCTTAAAATTGTCAAACTCGACCC
* *
430382 GAAAACTCGCGAGCTTAAAATT-TCAAAACTCGACTC
1 GAAAACTCACGAGCTTAAAATTGTC-AAACTCGACCC
430418 GAA
1 GAA
430421 CTCGAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (36 bp):
GAAAACTCACGAGCTTAAAATTGTCAAACTCGACCC
Found at i:434122 original size:18 final size:18
Alignment explanation
Indices: 434099--434133 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
434089 TCGGTTCTTC
434099 CGACCGATCGAACCAGTT
1 CGACCGATCGAACCAGTT
* *
434117 CGACCGGTTGAACCAGT
1 CGACCGATCGAACCAGT
434134 AAACTGGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (18 bp):
CGACCGATCGAACCAGTT
Found at i:434255 original size:31 final size:31
Alignment explanation
Indices: 434215--434318 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
434205 TAAAATGTTT
* *
434215 AAATTTTAATTTGACTCTTAAATTTTAAACA
1 AAATATTAATTTGACTCTTAAATTTTAAATA
* * * *
434246 AAATATTAATTTGA-TCATAAACTCTAGATA
1 AAATATTAATTTGACTCTTAAATTTTAAATA
* * *
434276 AAATATTAATCTAACCCTTAAATTTTAAATA
1 AAATATTAATTTGACTCTTAAATTTTAAATA
*
434307 AAATATCAATTT
1 AAATATTAATTT
434319 AACACTTGAA
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
30 23 0.40
31 34 0.60
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (31 bp):
AAATATTAATTTGACTCTTAAATTTTAAATA
Found at i:436991 original size:2 final size:2
Alignment explanation
Indices: 436984--437014 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
436974 GTAAATTGTA
436984 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
437015 AAACCAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:442658 original size:88 final size:88
Alignment explanation
Indices: 442509--442684 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
442499 AAAGAAAAAA
442509 ACGAGTCATGTCCCCATTTTTTGTTTAATTAATTTTTAAATCCTTATAAATTTTAAAGTTACACA
1 ACGAGTCATGTCCCCATTTTTTGTTTAATTAATTTTTAAATCCTTATAAATTTTAAAGTTACACA
442574 ATGTAATCCCAATGTTCCTTGCC
66 ATGTAATCCCAATGTTCCTTGCC
442597 ACGAGTCATGTCCCCATTTTTTGTTTAATTAATTTTTAAATCCTTATAAATTTTAAAGTTACACA
1 ACGAGTCATGTCCCCATTTTTTGTTTAATTAATTTTTAAATCCTTATAAATTTTAAAGTTACACA
442662 ATGTAATCCCAATGTTCCTTGCC
66 ATGTAATCCCAATGTTCCTTGCC
442685 CCATTTTTCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (88 bp):
ACGAGTCATGTCCCCATTTTTTGTTTAATTAATTTTTAAATCCTTATAAATTTTAAAGTTACACA
ATGTAATCCCAATGTTCCTTGCC
Found at i:447091 original size:20 final size:20
Alignment explanation
Indices: 447066--447111 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
447056 TTATCTAGAA
*
447066 AAAAATCCGGTCTAGGGTTT
1 AAAAATCCAGTCTAGGGTTT
*
447086 AAAAATCCAGTCTGGGGTTT
1 AAAAATCCAGTCTAGGGTTT
447106 AAAAAT
1 AAAAAT
447112 TAGATGACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (20 bp):
AAAAATCCAGTCTAGGGTTT
Found at i:454263 original size:25 final size:25
Alignment explanation
Indices: 454235--454285 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
454225 TTATATTCTG
454235 AAAATAAAATAT-TAAAAATAATTAT
1 AAAA-AAAATATATAAAAATAATTAT
* * *
454260 AAAAATAATATATAATATTAATTAT
1 AAAAAAAATATATAAAAATAATTAT
454285 A
1 A
454286 GTAATAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAAAAATATATAAAAATAATTAT
Found at i:454264 original size:12 final size:12
Alignment explanation
Indices: 454247--454285 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
454237 AATAAAATAT
454247 TAAAAATAATTA
1 TAAAAATAATTA
454259 TAAAAATAATATA
1 TAAAAATAAT-TA
* *
454272 TAATATTAATTA
1 TAAAAATAATTA
454284 TA
1 TA
454286 GTAATAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAAATAATTA
Found at i:454264 original size:13 final size:13
Alignment explanation
Indices: 454235--454274 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
454225 TTATATTCTG
*
454235 AAAATAAAATATTA
1 AAAATAATATA-TA
454249 AAAATAAT-TATA
1 AAAATAATATATA
454261 AAAATAATATATA
1 AAAATAATATATA
454274 A
1 A
454275 TATTAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 10 0.42
13 7 0.29
14 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAATATATA
Found at i:456568 original size:356 final size:351
Alignment explanation
Indices: 455867--456586 Score: 1336
Period size: 356 Copynumber: 2.0 Consensus size: 351
455857 GGAATAACAA
455867 CATTTTCTTTTTTTTAATAAAATCACTCAAAAAATTCTAAGTTATAATTAGAATCGTGAATTTTT
1 CATTTT-TTTTTTTTAATAAAATCACTCAAAAAATTCTAAGTTATAATTAGAATCGTGAATTTTT
455932 TAAAAAAAAAATATTATTGCAGATTTTATTACCGAGCTTATAAGATATAATTTGTGTCCTCTCAT
65 TAAAAAAAAAATATTATTGCAGATTTTATTACCGAGCTTATAAGATATAATTTGTGTCCTCTCAT
455997 GGACATATGTCAATAGTGCCTTGGGCTTTGTTTAGTCCATTAAAATGAGAGGCAAAGATTGTTGG
130 GGACATATGTCAATAGTGCCTTGGGCTTTGTTTAGTCCATTAAAATGAGAGGCAAAGATTGTTGG
*
456062 GTTGGGACTTAGCGTATATTTAAAGTTTTAAACCCCATTGAGTATATGAAAATTGGAAAACAGCC
195 GTTGGGACTTAGAGTATATTTAAAGTTTTAAACCCCATTGAGTATATGAAAATTGGAAAACAGCC
456127 CAATCCATCTACGGCCCACAATGTTATAGGAATTTTGAGATGCTGACGTGGCTGCCCGAACAAAA
260 CAATCCATCTACGGCCCACAATGTTATAGGAATTTTGAGATGCTGACGTGGCTGCCCGAACAAAA
456192 TATCCGACACTCGTGGCTCTCCAATTT
325 TATCCGACACTCGTGGCTCTCCAATTT
456219 CATTTTTTTTTTTTAATAAAATCACTCAAAAAATTCTAAGTTATAATTAGAATCGTGAATTTTTT
1 CATTTTTTTTTTTTAATAAAATCACTCAAAAAATTCTAAGTTATAATTAGAATCGTGAATTTTTT
456284 -AAAAAAAAATATTATTGCAGATTTTATTACCGAGCTTATAAGATATATAATTTGTGTCCTCTCA
66 AAAAAAAAAATATTATTGCAGATTTTATTACCGAGCTTATAAG--ATATAATTTGTGTCCTCTCA
456348 TGGACATATGTCAATAGTGCCTTGGGCTTTGTTTAGTCCATTAAAAATGAGAGGCAAAGATTGTT
129 TGGACATATGTCAATAGTGCCTTGGGCTTTGTTTAGTCCATT-AAAATGAGAGGCAAAGATTGTT
456413 GGGTTGGGACTTAAGAGTATAGATTTAAAGTTTTAAA-CCCATTGAGTATATGAAAATTGGAAAA
193 GGGTTGGGACTT-AGAGTAT--ATTTAAAGTTTTAAACCCCATTGAGTATATGAAAATTGGAAAA
456477 CAGCCCAATCCATCTACGGCCCACAATGTTTATAGGAATTTTGAGATGCTGACGTGGCTGCCCGA
255 CAGCCCAATCCATCTACGGCCCACAATG-TTATAGGAATTTTGAGATGCTGACGTGGCTGCCCGA
456542 ACAAAATATCCGACACTCGTGGCTCTCCAATTT
319 ACAAAATATCCGACACTCGTGGCTCTCCAATTT
*
456575 CATTTTTCTTTT
1 CATTTTTTTTTT
456587 GTCGGCGGCT
Statistics
Matches: 359, Mismatches: 2, Indels: 10
0.97 0.01 0.03
Matches are distributed among these distances:
350 42 0.12
351 59 0.16
352 68 0.19
353 34 0.09
354 6 0.02
355 55 0.15
356 95 0.26
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (351 bp):
CATTTTTTTTTTTTAATAAAATCACTCAAAAAATTCTAAGTTATAATTAGAATCGTGAATTTTTT
AAAAAAAAAATATTATTGCAGATTTTATTACCGAGCTTATAAGATATAATTTGTGTCCTCTCATG
GACATATGTCAATAGTGCCTTGGGCTTTGTTTAGTCCATTAAAATGAGAGGCAAAGATTGTTGGG
TTGGGACTTAGAGTATATTTAAAGTTTTAAACCCCATTGAGTATATGAAAATTGGAAAACAGCCC
AATCCATCTACGGCCCACAATGTTATAGGAATTTTGAGATGCTGACGTGGCTGCCCGAACAAAAT
ATCCGACACTCGTGGCTCTCCAATTT
Found at i:465874 original size:5 final size:5
Alignment explanation
Indices: 465864--465893 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
465854 GTATTTATTC
465864 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
465894 AAGAATACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:482553 original size:15 final size:15
Alignment explanation
Indices: 482533--482578 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
482523 GGTTCTTGTA
482533 GTTGTTGTTGTAGCT
1 GTTGTTGTTGTAGCT
*
482548 GTTGTTGTTGCAG-T
1 GTTGTTGTTGTAGCT
*
482562 AGTTGTTGTTGTTGCT
1 -GTTGTTGTTGTAGCT
482578 G
1 G
482579 CTGCTGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.07, C:0.07, G:0.35, T:0.52
Consensus pattern (15 bp):
GTTGTTGTTGTAGCT
Found at i:482556 original size:18 final size:18
Alignment explanation
Indices: 482542--482576 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
482532 AGTTGTTGTT
482542 GTAGCTGTTGTTGTTGCA
1 GTAGCTGTTGTTGTTGCA
*
482560 GTAGTTGTTGTTGTTGC
1 GTAGCTGTTGTTGTTGC
482577 TGCTGCTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (18 bp):
GTAGCTGTTGTTGTTGCA
Found at i:485123 original size:27 final size:27
Alignment explanation
Indices: 485082--485150 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
485072 TTGAGACTGT
485082 TGCTGCTGCTGCTGGCTTTGTTGTTGC
1 TGCTGCTGCTGCTGGCTTTGTTGTTGC
* *
485109 TGTTGCTGCTGCTGGCTTTGTTGTTGT
1 TGCTGCTGCTGCTGGCTTTGTTGTTGC
485136 TGCTGCTGCTGCTGG
1 TGCTGCTGCTGCTGG
485151 AGTTGGTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.00, C:0.20, G:0.35, T:0.45
Consensus pattern (27 bp):
TGCTGCTGCTGCTGGCTTTGTTGTTGC
Found at i:485155 original size:24 final size:24
Alignment explanation
Indices: 485079--485155 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 24
485069 GTATTGAGAC
**
485079 TGTTGCTGCTGCTGCTGGCTTTGT
1 TGTTGCTGCTGCTGCTGGAGTTGT
*
485103 TGTTGCTGTTGCTGCTGCTGGCTTTGTTGT
1 TGTTGC---TGCTGCTGCTGG---AGTTGT
485133 TGTTGCTGCTGCTGCTGGAGTTG
1 TGTTGCTGCTGCTGCTGGAGTTG
485156 GTTCATACGT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
24 10 0.23
27 24 0.55
30 10 0.23
ACGTcount: A:0.01, C:0.18, G:0.35, T:0.45
Consensus pattern (24 bp):
TGTTGCTGCTGCTGCTGGAGTTGT
Found at i:485642 original size:2 final size:2
Alignment explanation
Indices: 485635--485674 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
485625 AAGAAAACGG
485635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
485675 ATTTTAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:485953 original size:2 final size:2
Alignment explanation
Indices: 485946--486001 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
485936 CTATTGCGTT
485946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
485987 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
486002 TGAAAATCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:486263 original size:8 final size:8
Alignment explanation
Indices: 486250--486274 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
486240 ACGAAACCGA
486250 AAAAATCG
1 AAAAATCG
486258 AAAAATCG
1 AAAAATCG
486266 AAAAATCG
1 AAAAATCG
486274 A
1 A
486275 CATGAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAATCG
Found at i:489043 original size:20 final size:20
Alignment explanation
Indices: 489018--489081 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
489008 TTTTCCCAAT
489018 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
489038 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
*
489058 T-TCAATGCGAATAAGT-AA
1 TCGCAATGCGAATAAGTAAA
489076 TCGCAA
1 TCGCAA
489082 CACGAATTGG
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
20 17 0.52
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:489088 original size:38 final size:39
Alignment explanation
Indices: 489021--489095 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
489011 TCCCAATTCG
*
489021 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAATT
1 CAATGCGAATAAGTAAATCGCAACACGAATTGGGAAATT
489060 CAATGCGAATAAGT-AATCGCAACACGAATTGGGAAA
1 CAATGCGAATAAGTAAATCGCAACACGAATTGGGAAA
489096 ATCGCAATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 21 0.60
39 14 0.40
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (39 bp):
CAATGCGAATAAGTAAATCGCAACACGAATTGGGAAATT
Found at i:489121 original size:20 final size:20
Alignment explanation
Indices: 489096--489189 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
489086 AATTGGGAAA
*
489096 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
489116 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
489137 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
489157 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
489177 TTCGCAACGCGAT
1 ATCGCAACGCGAT
489190 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:489138 original size:41 final size:41
Alignment explanation
Indices: 489093--489170 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
489083 ACGAATTGGG
* * *
489093 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
489134 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
489171 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:489766 original size:19 final size:19
Alignment explanation
Indices: 489744--489961 Score: 178
Period size: 19 Copynumber: 12.1 Consensus size: 19
489734 GAAACCAAAA
*
489744 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
489763 TCGCATTGCGA-TTTCA-T
1 TCGCGTTGCGATTTTCATT
* *
489780 TCGCATTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
489799 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
489818 TCGCGTTGTGA-TTTAATT
1 TCGCGTTGCGATTTTCATT
489836 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
489856 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
489872 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
489889 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
489903 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
489922 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
489942 AT--CGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
489960 TC
1 TC
489962 AACCAAAAGA
Statistics
Matches: 164, Mismatches: 18, Indels: 35
0.76 0.08 0.16
Matches are distributed among these distances:
14 20 0.12
15 1 0.01
16 3 0.02
17 15 0.09
18 36 0.22
19 63 0.38
20 25 0.15
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:489810 original size:55 final size:57
Alignment explanation
Indices: 489744--489868 Score: 182
Period size: 55 Copynumber: 2.2 Consensus size: 57
489734 GAAACCAAAA
* * *
489744 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCA-TTCGC-ATTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTAATTTCGCGATTGCGATTTTCATT
* * *
489799 TCGCGTTGCGATTTTCATTTCGCGTTGTGATTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTAATTTCGCGATTGCGATTTTCATT
489856 TCGCGTTGCGATT
1 TCGCGTTGCGATT
489869 GTCTGGTCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
55 31 0.50
56 5 0.08
57 26 0.42
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (57 bp):
TCGCGTTGCGATTTTCATTTCGCATTGCGATTTAATTTCGCGATTGCGATTTTCATT
Found at i:489940 original size:20 final size:18
Alignment explanation
Indices: 489884--489961 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 18
489874 GTCGCGATAG
489884 TCATTTCGCGTTGCGATTC
1 TCATTTC-CGTTGCGATTC
**
489903 TC---T-CGTTGCGATAG
1 TCATTTCCGTTGCGATTC
489917 TCATTTCCGCGTTGCGATTC
1 TCATTT-C-CGTTGCGATTC
*
489937 TCATTAT-CGTTGCGATTT
1 TCATT-TCCGTTGCGATTC
489955 TCATTTC
1 TCATTTC
489962 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
14 11 0.24
16 1 0.02
17 2 0.04
18 15 0.33
19 2 0.04
20 14 0.30
21 1 0.02
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (18 bp):
TCATTTCCGTTGCGATTC
Found at i:489959 original size:38 final size:33
Alignment explanation
Indices: 489802--489961 Score: 140
Period size: 33 Copynumber: 4.5 Consensus size: 33
489792 TTTCATTTCG
* * *
489802 CGTTGCGATTTTCATTTCGCGTTGTGATTTAATTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGA--T--TCTCT
*
489839 CGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT
1 C-GTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* * **
489873 GGTCGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
**
489906 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATTAT
1 CGTTGCGATTTTCATTT-CGCGTTGCGATTCTC----T
489944 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
489962 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
33 43 0.41
34 18 0.17
36 1 0.01
37 2 0.02
38 41 0.39
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:492009 original size:21 final size:21
Alignment explanation
Indices: 491985--492051 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
491975 TCATTCCTCG
491985 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
492006 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
492027 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
492048 AGAG
1 AGAG
492052 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:492009 original size:42 final size:42
Alignment explanation
Indices: 491929--492051 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
491919 GCCCGACTCG
* * * * * *
491929 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
491971 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
492013 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
492052 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:494297 original size:14 final size:14
Alignment explanation
Indices: 494278--494314 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
494268 CATCAATTAA
494278 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
494292 ACAAATCATCTTTT
1 ACAAATCAACATTT
494306 ACAAATCAA
1 ACAAATCAA
494315 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:494879 original size:14 final size:14
Alignment explanation
Indices: 494860--494896 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
494850 CATCAATTAA
494860 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
494874 ACAAATCATCTTTT
1 ACAAATCAACATTT
494888 ACAAATCAA
1 ACAAATCAA
494897 TTAACAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:495451 original size:14 final size:14
Alignment explanation
Indices: 495432--495468 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
495422 CATCAATTAA
495432 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
495446 ACAAATCATCTTTT
1 ACAAATCAACATTT
495460 ACAAATCAA
1 ACAAATCAA
495469 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:496100 original size:579 final size:588
Alignment explanation
Indices: 493908--498621 Score: 8448
Period size: 579 Copynumber: 8.1 Consensus size: 588
493898 TTTAACAATT
*
493908 ATTATTGAATTCTAGGTACTTAACCAAATA-TTTCAAACCAAAAGGAG--TATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
493970 CTTGCATTATGTGTATTTTATGTGTGCAC-TTTAACATTTTCAGTTAGGCATGTATGAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
494034 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
494099 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
494164 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCATTCAACATAAAGCAGATTG-AAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
494228 TCAAC-AATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
494292 ACAAATCATCTTTTACAAATCAATTAAACAATC-AAAA-AATAATAATTCTTATTTCTTCATCAA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
494355 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
*
494420 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAATAG
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
494485 CAA
586 CAA
494488 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
494553 CTTGCATTATGTGTA-TTT-TGTGTGCACTTTTAACA-TTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
494615 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
494680 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
494745 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
494810 TCAACAAATC-ACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
494874 ACAAATCATCTTTTACAAATCAATT-AACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
494938 TT-TTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCTCCA-TTCACGCAGCTCACTTAAG
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACA--TCCATTTCACGCAGCTCACTTAAG
495001 GATTAACCTGCAGAAACCAAACATTTGCTC-AACAAGACTTCCTACACATCT-AAACCTACAAAC
519 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
495064 AGCAA
584 AGCAA
495069 ATTATTGAATTCTAGGTACTTAACC-AACATTTTCAAACCAAAAGGAG--TATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
495131 CTTGCATTA--TGTA-TTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
495193 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTAT--C
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
495256 AATG-AAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATG-AAATCGCATTGCGA-TTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
495318 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAGA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
495383 TCAAC-AATCAACTATTACATTTCAACAC-AATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
495446 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC-
391 ACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCA
495510 ATTA-TGAATCAAGAATC-ACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
455 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
*
495573 ATTAACCTGCAGAAACCAAACATTTGCTC-AACAAGACTTCATAC-CATCTAAAACCTACAAACA
520 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
*
495636 ACAA
585 GCAA
495640 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAA-CAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
* *
495704 CTTGCATTATGTGTA-TTTATGTGTGCACTTTTAACATTTTCAGTTAGACATGTA-TAGTAATTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
495767 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
495832 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
495897 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACAT-AAGCA-TTTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
495960 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
496025 ACAAATCATCTTTTAC-AATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
496089 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
496154 TTAACCTGCAGAAACCAAACATTTGCTCAAAC-AGACTTCCTACACATCTAAAACCTACAAACAG
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
496218 CAA
586 CAA
496221 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
496286 C-TGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
496350 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTT-TTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
496414 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATG-AAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
496478 TCGTTGCGATAGCC--TTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGA-TGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
496540 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAAC-AATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
496604 AC-AATCATCTTTTACAAATC-ATTAAACAATC--AAA-AATAATAATTCTTATTTCTTCATCAA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
496664 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
*
496729 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAT
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
496794 CAA
586 CAA
496797 ATTATTGAATTCTAGGTACTTAACC-AACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
496861 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
* *
496926 GAGTGTGAACATTGCTA-GATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTCACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
496990 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATG-AAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGA-----
497054 TCGTTGCGATAGCCATTCGCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAA
256 T--TT----T---C--T--CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAA
497119 CATAAAGCAGATTGAAAATCAACAAATCAACTATTACA-TTCAACACAAATTATGTACACATCAA
308 CATAAAGCAGATTGAAAATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAA
497183 TTAAACAAATCAACATTTAC-AA--ATCTTTTACAAATCAATTAAACAATC-AAAATAATAATAA
373 TTAAACAAATCAACATTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAA
497244 TTCTTA-TTC-TCATCAATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTC
438 TTCTTATTTCTTCATCAATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTC
497307 ACGCAGCTCACTTAAGGA-TAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACA
503 ACGCAGCTCACTTAAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACA
497371 TCTAAAACCTACAAACAGCAA
568 TCTAAAACCTACAAACAGCAA
497392 ATTATTGAATTCTAGGTACTTAACCAAAC--TTTCAAACC-AAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
497454 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTA-TAGTAATTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
497518 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
497583 AATGCGAAAATGGTTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTT
196 AATGCGAAAATGG-TTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTT
497648 CTCGTTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAA
260 CTCG-TTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAA
497713 AATCAAC-AATCAACTATTACATTTCAACAC-AATTATGTACACATCAATTAAACAAATCAACA-
324 AATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACAT
497775 TTACAAATCATCTTTTACAAATC-ATTAAAC-ATCAAAAATAATAATAATTCTTATTTCTTCATC
389 TTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATC
497838 AATTATTGAATCAAGAATC-ACAACTTTGTGACCCCGTACATCCA-TTCACGCAGCTCACTTAAG
454 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
497901 GATTAACCTGCAGAAACC-AACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
519 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
497965 AGCAA
584 AGCAA
497970 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
498035 CTTGCATTA--TGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
498098 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
498163 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
498228 TCGTTGTGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
498293 TCAACAAATCAACTATTACATTTCAACACAAATTATGT--ACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
498356 ACAAATCATCTTTTACAAATCAATTAAAC-ATCAAAAATAATAATAATTCTTA-TTCTTCATC-A
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
*
498418 TTATTGAATTAAGAATCAACAACTTTGTGA-CCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
*
498482 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTA-ACATCTAAAACCTACAAACAA
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
498546 CAA
586 CAA
498549 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
498614 CTGGCATT
66 CTTGCATT
498622 TGACTTACCA
Statistics
Matches: 4011, Mismatches: 30, Indels: 187
0.95 0.01 0.04
Matches are distributed among these distances:
570 9 0.00
571 113 0.03
572 97 0.02
573 138 0.03
574 114 0.03
575 267 0.07
576 243 0.06
577 150 0.04
578 518 0.13
579 525 0.13
580 383 0.10
581 434 0.11
582 291 0.07
583 162 0.04
584 5 0.00
587 1 0.00
588 2 0.00
590 2 0.00
592 25 0.01
593 138 0.03
594 54 0.01
595 119 0.03
596 160 0.04
597 47 0.01
598 14 0.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (588 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAA
TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
CAA
Found at i:497093 original size:19 final size:19
Alignment explanation
Indices: 497050--497102 Score: 90
Period size: 18 Copynumber: 2.8 Consensus size: 19
497040 GCATTGCGAT
*
497050 TTTCTCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
497069 -TTCGCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
497087 TTTCGCGTTGCGATAG
1 TTTCGCGTTGCGATAG
497103 TCTGTTTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:498361 original size:14 final size:14
Alignment explanation
Indices: 498342--498378 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
498332 CATCAATTAA
498342 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
498356 ACAAATCATCTTTT
1 ACAAATCAACATTT
498370 ACAAATCAA
1 ACAAATCAA
498379 TTAAACATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:500261 original size:18 final size:19
Alignment explanation
Indices: 500208--500277 Score: 90
Period size: 18 Copynumber: 3.7 Consensus size: 19
500198 GAAACTTAAA
500208 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
500227 ATCGCAACGCAGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
500247 ATCGC-ATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
500264 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
500278 AATCGCATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 5 0.11
18 13 0.30
19 13 0.30
20 13 0.30
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:500346 original size:31 final size:31
Alignment explanation
Indices: 500280--500354 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
500270 ACGCGAAAAA
500280 TCGCATTGCGATTTTGTCGTTGCGATTTCATT
1 TCGCATTGCGA-TTTGTCGTTGCGATTTCATT
*
500312 TCGCGTTGGCGATTTGTCG-TGCGATTTTCA-T
1 TCGCATT-GCGATTTGTCGTTGCGA-TTTCATT
500343 TCGCATTGCGAT
1 TCGCATTGCGAT
500355 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 5 0.13
31 12 0.31
32 18 0.46
33 4 0.10
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (31 bp):
TCGCATTGCGATTTGTCGTTGCGATTTCATT
Found at i:500881 original size:18 final size:18
Alignment explanation
Indices: 500855--500899 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
500845 GTCGATCAGA
*
500855 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
500873 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
500891 TGATGGCTC
1 TGATGGCTC
500900 CCGAAGTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:502110 original size:19 final size:19
Alignment explanation
Indices: 502086--502136 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
502076 GAATAGTTTT
502086 GAAAATGAAATCGCAACAC
1 GAAAATGAAATCGCAACAC
** *
502105 GAAAATGACTTCGCAACGC
1 GAAAATGAAATCGCAACAC
*
502124 GAAACT-AAATCGC
1 GAAAATGAAATCGC
502137 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATGAAATCGCAACAC
Found at i:502383 original size:22 final size:22
Alignment explanation
Indices: 502358--502401 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
502348 GATTTAGATA
502358 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
502380 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
502402 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:502611 original size:20 final size:20
Alignment explanation
Indices: 502586--502679 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
502576 GATTATGTAT
502586 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
502606 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
502626 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
502647 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
502667 TATCGCATTGCGA
1 TATCGCGTTGCGA
502680 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:502680 original size:20 final size:20
Alignment explanation
Indices: 502566--502680 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
502556 CGCTTTGAAA
*
502566 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
502587 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
502607 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
502627 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
502648 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
502668 ATCGCATTGCGAT
1 ATCGCATTGCGAT
502681 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Done.