Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:445979 original size:40 final size:40
Alignment explanation
Indices: 445893--446072 Score: 240
Period size: 40 Copynumber: 4.4 Consensus size: 40
445883 CTCATTTCTT
*
445893 AATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGA--TTCTTGG
445935 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG
*
445975 AATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG
*
446015 AAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGG
1 -A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCT-TGG
446058 AATCGCGTTGCGATT
1 AATCGCGTTGCGATT
446073 CTTGGAAGAT
Statistics
Matches: 128, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
38 5 0.04
40 51 0.40
41 18 0.14
42 51 0.40
43 3 0.02
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (40 bp):
AATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG
Found at i:446101 original size:102 final size:102
Alignment explanation
Indices: 445893--446194 Score: 409
Period size: 102 Copynumber: 3.0 Consensus size: 102
445883 CTCATTTCTT
*
445893 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTGAAT
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAAT
* *
445958 CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTT
66 CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTATG
445995 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGGAA
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCT-GAA
446060 TCGCGTTGCGATTCTTGGAAGAT-GCG-TGCGA-TTTATG
65 TCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTATG
* * * ** * * *
446097 AATCGCATTGCGATTCTTGGAAGATCGTGTTGCGATCTTCT-TTTCAACGTTGCGCTTTTCTAAA
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATC-GCGTTGCGATTTTCTGAA
*
446161 TCGCGTTGCGGTT-TT-GATATCGCGTTGCGATTTT
65 TCGCGTTGCGATTCTTGGA-ATCGCGTTGCGATTTT
446195 GTTGGTCATT
Statistics
Matches: 180, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
98 3 0.02
99 4 0.02
100 7 0.04
101 19 0.11
102 115 0.64
103 26 0.14
104 4 0.02
105 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (102 bp):
AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAAT
CGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTATG
Found at i:446132 original size:82 final size:81
Alignment explanation
Indices: 445893--446111 Score: 286
Period size: 82 Copynumber: 2.7 Consensus size: 81
445883 CTCATTTCTT
*
445893 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTTTCTGAAT
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA-TTT-TGAATCGCGTTGCGATTTTCTGAAT
*
445958 CGCGTTGCGATTCT-TGG
64 CGCGTTGCGATTTTCTGG
***
445975 AATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TT-G-A-ATCGCGTTGCGATTTTCTGA
446038 ATCGCGTTGCGATTTTCTGG
62 ATCGCGTTGCGATTTTCTGG
*
446058 AATCGCGTTGCGATTCTTGGAAGAT-GCG-TGCGATTTATGAATCGCATTGCGATT
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTT-TGAATCGCGTTGCGATT
446112 CTTGGAAGAT
Statistics
Matches: 120, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
79 3 0.03
80 26 0.22
81 5 0.04
82 52 0.43
83 26 0.22
84 6 0.05
85 2 0.02
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (81 bp):
AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTGAATCGCGTTGCGATTTTCTGAATCG
CGTTGCGATTTTCTGG
Found at i:446428 original size:77 final size:79
Alignment explanation
Indices: 446300--446446 Score: 271
Period size: 77 Copynumber: 1.9 Consensus size: 79
446290 ATAAAGTTTT
446300 ACCTTTTCCAACTAAGAAAAATCACCATCGGGTTAATTTAAGCGGGAAACAA-TTGATATCGTTT
1 ACCTTTTCCAACTAAGAAAAATCACCATCGGGTTAATTTAAGCGGGAAACAATTTGATATCGTTT
446364 AAACATATATATAC
66 AAACATATATATAC
*
446378 ACCTTTTCCAACT-AGAAAAATCACCATCGGGTTAATTTAAGCGGTAAACAATTTGATATCGTTT
1 ACCTTTTCCAACTAAGAAAAATCACCATCGGGTTAATTTAAGCGGGAAACAATTTGATATCGTTT
446442 AAACA
66 AAACA
446447 AGTCTCGAGT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
77 37 0.55
78 30 0.45
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (79 bp):
ACCTTTTCCAACTAAGAAAAATCACCATCGGGTTAATTTAAGCGGGAAACAATTTGATATCGTTT
AAACATATATATAC
Found at i:449860 original size:15 final size:16
Alignment explanation
Indices: 449834--449863 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
449824 CTTTATCAAA
449834 GTCAACGGTCAAAGTG
1 GTCAACGGTCAAAGTG
449850 GTCAA-GGTCAAAGT
1 GTCAACGGTCAAAGT
449864 CAACTGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (16 bp):
GTCAACGGTCAAAGTG
Found at i:451527 original size:20 final size:21
Alignment explanation
Indices: 451498--451538 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
451488 TTAAAGGATA
451498 AAAAATTTTGATTAATGAAAT
1 AAAAATTTTGATTAATGAAAT
451519 AAAAA-TTTGATTAATGAAAT
1 AAAAATTTTGATTAATGAAAT
451539 TTGGGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
AAAAATTTTGATTAATGAAAT
Found at i:457394 original size:201 final size:202
Alignment explanation
Indices: 457048--457456 Score: 568
Period size: 201 Copynumber: 2.0 Consensus size: 202
457038 CAAGTTAGGC
* *
457048 TAAAAACTCAACTAATTATTTAAGTTTTACTTTTAAAGAATGGTATGGTCTAATGGGATGAGGCA
1 TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGAATGGTATGGTCTAATGGAATGAGGCA
* * * *** *
457113 CTAGGTCACTTAAGCAAGGTCATGTGTTCGAATCCTAGTGTTTGTGAACAGAGCAAACTAGGTTG
66 CTAGGTCACTTAAGCAAGGTAAGGGGTTCGAATCCTAACATTTGCGAACAGAGCAAACTAGGTTG
* * * * * *
457178 GGAGGGTCGTCCTCGTCTTTATAGTACTAGATCT-GATTAGTCGGTTGATAGATCATATATCAGT
131 AGAGAGTCATCCTCGTCTCTATAGTACTAGATCTGGATTAGTCGGTTGATAGACCATATATAAGT
457242 GATTAAT
196 GATTAAT
** * *
457249 TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGTCTGGTTTGGTTTAATGGAATGAGGCA
1 TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGAATGGTATGGTCTAATGGAATGAGGCA
* * ** * * *
457314 CTAGGTCACTTACGTAAGGTAAGGGGTTCGAATCCTAACATTTGCGAATGGATCAAATTGGGTTG
66 CTAGGTCACTTAAGCAAGGTAAGGGGTTCGAATCCTAACATTTGCGAACAGAGCAAACTAGGTTG
*
457379 AGAGAGTCATCCTCGTCTCTATAGTACTAGATCTGGATTATTCGGTTGATAGACCATATATAAGT
131 AGAGAGTCATCCTCGTCTCTATAGTACTAGATCTGGATTAGTCGGTTGATAGACCATATATAAGT
457444 GATTAAT
196 GATTAAT
457451 TAAAAA
1 TAAAAA
457457 AAATCTCGTT
Statistics
Matches: 180, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
201 140 0.78
202 40 0.22
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (202 bp):
TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGAATGGTATGGTCTAATGGAATGAGGCA
CTAGGTCACTTAAGCAAGGTAAGGGGTTCGAATCCTAACATTTGCGAACAGAGCAAACTAGGTTG
AGAGAGTCATCCTCGTCTCTATAGTACTAGATCTGGATTAGTCGGTTGATAGACCATATATAAGT
GATTAAT
Found at i:460773 original size:63 final size:63
Alignment explanation
Indices: 460634--460795 Score: 184
Period size: 63 Copynumber: 2.5 Consensus size: 63
460624 ATTGTTCAAG
* * *
460634 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACA-GTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * * ** *
460698 GTGTATCGATGCACGAGTAGTGCATCTATGCACCCCCTT-AAATACAAGCATCGAATGGGATTTA
1 GTGTATCGATGCAC-AGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TCA
*
460762 -TGTATCGATGCATAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAG-TAGTGCATCGATGCACCC
460796 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.02
63 46 0.55
64 35 0.42
65 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:462505 original size:21 final size:21
Alignment explanation
Indices: 462480--462537 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
462470 AGTATGTACA
462480 GGGGG-AACAGATTCCCCCTGG
1 GGGGGTAAC-GATTCCCCCTGG
*
462501 GGGGGTATCGATTCCCCCT--
1 GGGGGTAACGATTCCCCCTGG
*
462520 GGGGGTATCGATTCCCCC
1 GGGGGTAACGATTCCCCC
462538 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 18 0.51
21 15 0.43
22 2 0.06
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGTAACGATTCCCCCTGG
Found at i:462525 original size:19 final size:20
Alignment explanation
Indices: 462489--462537 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
462479 AGGGGGAACA
462489 GATTCCCCCTGGGGGGGTATC
1 GATTCCCCCT-GGGGGGTATC
462510 GATTCCCCCT-GGGGGTATC
1 GATTCCCCCTGGGGGGTATC
462529 GATTCCCCC
1 GATTCCCCC
462538 CTAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 18 0.64
21 10 0.36
ACGTcount: A:0.10, C:0.35, G:0.31, T:0.24
Consensus pattern (20 bp):
GATTCCCCCTGGGGGGTATC
Found at i:462966 original size:22 final size:22
Alignment explanation
Indices: 462940--463013 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
462930 ATTATATGAA
462940 ATGATATATGAATATGTAATAC
1 ATGATATATGAATATGTAATAC
* * * *
462962 GTGATACATGTGATATG-ATATGAA
1 ATGATATATG-AATATGTA-AT-AC
*
462986 ATGACATATGAATATGTAATAC
1 ATGATATATGAATATGTAATAC
*
463008 TTGATA
1 ATGATA
463014 CATGTGATAT
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
22 14 0.38
23 14 0.38
24 9 0.24
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (22 bp):
ATGATATATGAATATGTAATAC
Found at i:462978 original size:23 final size:23
Alignment explanation
Indices: 462951--463024 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
462941 TGATATATGA
462951 ATATGTAATACGTGATACATGTG
1 ATATGTAATACGTGATACATGTG
* ** *
462974 ATATG--ATATGAAATGACATATG
1 ATATGTAATACGTGAT-ACATGTG
*
462996 AATATGTAATACTTGATACATGTG
1 -ATATGTAATACGTGATACATGTG
463020 ATATG
1 ATATG
463025 ATATGAAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
21 6 0.16
22 6 0.16
23 15 0.39
24 6 0.16
25 5 0.13
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (23 bp):
ATATGTAATACGTGATACATGTG
Found at i:462995 original size:46 final size:46
Alignment explanation
Indices: 462925--463037 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
462915 GAGATAAGCT
*
462925 ATGTGAT-T-ATATGAAATGATATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
*
462969 ATGTGATATGATATGAAATGACATATGAATATGTAATACTTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
463015 ATGTGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
463038 GGTTACACAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 53 0.82
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
Found at i:463280 original size:38 final size:38
Alignment explanation
Indices: 463186--463281 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
463176 TATAAGACAT
** *
463186 ATGACAGGTCCTACGGGACACAAATTACATCATTCGAG
1 ATGACAGGTCCTTTGGGACACAAATGACATCATTCGAG
* * * *
463224 ATGACATGT-CTTTCGGGACACAGATGACATCCTTCGGG
1 ATGACAGGTCCTTT-GGGACACAAATGACATCATTCGAG
*
463262 ATGATAGGTCCTTTGGGACA
1 ATGACAGGTCCTTTGGGACA
463282 TTTATACGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 2 0.04
38 41 0.87
39 4 0.09
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (38 bp):
ATGACAGGTCCTTTGGGACACAAATGACATCATTCGAG
Found at i:465269 original size:2 final size:2
Alignment explanation
Indices: 465262--465311 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
465252 TATCATTGGA
465262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
465304 AT AT AT AT
1 AT AT AT AT
465312 TGATTGAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:468681 original size:34 final size:35
Alignment explanation
Indices: 468620--468688 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
468610 TATGTACAGG
*
468620 GGGAACAGATTCCCCTTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
468655 GGGAACAGATTCCCCCT-GGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
468689 ATAAATGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.22
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:469117 original size:22 final size:21
Alignment explanation
Indices: 469092--469164 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
469082 TTATATGAAA
469092 TGATATATGAATATGCAATACG
1 TGATATATGAATATG-AATACG
* * **
469114 TGATACATGTGATATGATATGAAA
1 TGATATATG-AATATGA-AT-ACG
*
469138 TGACATATGAATATGTAATACG
1 TGATATATGAATATG-AATACG
469160 TGATA
1 TGATA
469165 CATATGATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 14 0.38
23 14 0.38
24 9 0.24
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (21 bp):
TGATATATGAATATGAATACG
Found at i:469146 original size:46 final size:46
Alignment explanation
Indices: 469076--469188 Score: 178
Period size: 46 Copynumber: 2.5 Consensus size: 46
469066 GAGATAAGCT
*
469076 ATGTGAT-T-ATATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
469120 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
469166 ATATGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
469189 GGTTACACAT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 52 0.81
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
Found at i:469431 original size:38 final size:38
Alignment explanation
Indices: 469337--469432 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
469327 TATAAGACAT
* * * *
469337 ATGATAGGTCCTACGGGACACATATTATATCCTTCGAG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGAG
* * *
469375 ATGACAAGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGAG
* *
469413 ATGATAGGTCATTTGGGACA
1 ATGATAGGTCCTTCGGGACA
469433 TTTATACGAG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGAG
Found at i:470173 original size:15 final size:15
Alignment explanation
Indices: 470149--470196 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
470139 GAGAAATGAA
*
470149 ATAAGGTATGTGATT
1 ATAAGATATGTGATT
*
470164 ATAAGATATGTGATA
1 ATAAGATATGTGATT
* *
470179 ATAAGTTATATGATT
1 ATAAGATATGTGATT
470194 ATA
1 ATA
470197 TGATCATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (15 bp):
ATAAGATATGTGATT
Found at i:470730 original size:23 final size:23
Alignment explanation
Indices: 470634--470737 Score: 136
Period size: 23 Copynumber: 4.5 Consensus size: 23
470624 TCTTAAATGA
* *
470634 CACTACGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATCCTACGCGG
* *
470657 CACTACGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATCCTACGCGG
* *
470680 CACTTCGGTGCAATCCTATGTGG
1 CACTTCGGTGCAATCCTACGCGG
*
470703 CACTTCGGTGCAATCCTACGTGG
1 CACTTCGGTGCAATCCTACGCGG
*
470726 CACTTCGATGCA
1 CACTTCGGTGCA
470738 TTTATATGAG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (23 bp):
CACTTCGGTGCAATCCTACGCGG
Found at i:472453 original size:202 final size:202
Alignment explanation
Indices: 472107--472516 Score: 613
Period size: 202 Copynumber: 2.0 Consensus size: 202
472097 CAAGTTAGGC
* *
472107 TAAAAACTCAACTAATTATTTAAGTTTTACTTTTAAAGAATGGTTTGATCTAATGGGATGAGGCA
1 TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGAATGGTTTGATCTAATGGAATGAGGCA
* * *** **
472172 CTAGGTCACTTAAGCAAGGTCATGTGTTCGAATCCTAGTGTTTGTGAACAGAGCAAACTAGGTTG
66 CTAGGTCACTTAAGCAAGGTCAGGGGTTCGAATCCTAACATTTACGAACAGAGCAAACTAGGTTG
* *
472237 GGAGGGTCGTCCTCGTCTTTATAGTACTAGATTTGAATTAGTCGGTTGATAGACCATATATCAGT
131 GGAGAGTCGTCCTCGTCTTTATAGTACTAGATTTGAATTAGTCGGTTGATAGACCATATATAAGT
472302 GATTAAT
196 GATTAAT
* ** *
472309 TAAAAACTCAACTAATTGCTTAAGTTTTACTTTTAAAGTCTGGTTTGGTCTAATGGAATGAGGCA
1 TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGAATGGTTTGATCTAATGGAATGAGGCA
* * ** * * *
472374 CTAGGTCACTTACGTAAGGTCAGGGGTTCGAATCCTAACATTTACGAATGGATCAAATTGGGTTG
66 CTAGGTCACTTAAGCAAGGTCAGGGGTTCGAATCCTAACATTTACGAACAGAGCAAACTAGGTTG
*
472439 GGAGAGTCGTCCTCGTCTTTATAGTACTAGATTTGGATTAGTCGGTTGATAGACCATATATAAGT
131 GGAGAGTCGTCCTCGTCTTTATAGTACTAGATTTGAATTAGTCGGTTGATAGACCATATATAAGT
472504 GATTAAT
196 GATTAAT
472511 TAAAAA
1 TAAAAA
472517 AATCTCGTTT
Statistics
Matches: 185, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
202 185 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (202 bp):
TAAAAACTCAACTAATTACTTAAGTTTTACTTTTAAAGAATGGTTTGATCTAATGGAATGAGGCA
CTAGGTCACTTAAGCAAGGTCAGGGGTTCGAATCCTAACATTTACGAACAGAGCAAACTAGGTTG
GGAGAGTCGTCCTCGTCTTTATAGTACTAGATTTGAATTAGTCGGTTGATAGACCATATATAAGT
GATTAAT
Found at i:474749 original size:57 final size:57
Alignment explanation
Indices: 474602--474755 Score: 240
Period size: 59 Copynumber: 2.7 Consensus size: 57
474592 GTGACCCTCA
* *
474602 TATTTTT-T-TTAATGTGGCCCTCCCACTCATAAAATAAACTCAACGTGGACCTCGT
1 TATTTTTCTCTTAATGTGACCCTCCCACTCATAAAATAAACCCAACGTGGACCTCGT
*
474657 TATTTTTTTCTCTCAATGTGACCCTCCCACTCATAAAATAAACCCAACGTGGACCTCGT
1 TA--TTTTTCTCTTAATGTGACCCTCCCACTCATAAAATAAACCCAACGTGGACCTCGT
*
474716 TATTTTTCTCTTAATGTGACCCTCTCACTCATAAAATAAA
1 TATTTTTCTCTTAATGTGACCCTCCCACTCATAAAATAAA
474756 TTCAATGTGA
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
55 2 0.02
57 41 0.46
58 1 0.01
59 46 0.51
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.35
Consensus pattern (57 bp):
TATTTTTCTCTTAATGTGACCCTCCCACTCATAAAATAAACCCAACGTGGACCTCGT
Found at i:479212 original size:33 final size:30
Alignment explanation
Indices: 479143--479218 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
479133 ATCTGCAAAA
* *
479143 AAAT-TAATTAAATAAAATATTAAACAATT
1 AAATATAATTAAATAAAATATAAAAAAATT
*
479172 AAA-ATAATTAAATAAATTACTAAAAAAATACT
1 AAATATAATTAAATAAAATA-TAAAAAAAT--T
*
479204 AAATATAATAAAATA
1 AAATATAATTAAATA
479219 TACCTGAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 17 0.45
30 7 0.18
32 4 0.11
33 10 0.26
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (30 bp):
AAATATAATTAAATAAAATATAAAAAAATT
Found at i:485342 original size:5 final size:5
Alignment explanation
Indices: 485332--485472 Score: 282
Period size: 5 Copynumber: 28.2 Consensus size: 5
485322 ATCTAGAGTG
485332 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
485382 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
485432 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
485473 TGTTTGGAAA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 136 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:487761 original size:16 final size:17
Alignment explanation
Indices: 487740--487791 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
487730 TTTTTAATTT
487740 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
487756 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
487771 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
487788 AATT
1 AATT
487792 TATTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:494689 original size:2 final size:2
Alignment explanation
Indices: 494682--494747 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
494672 CGATTATTTG
494682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494724 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
494748 GAACGTACAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:498616 original size:17 final size:17
Alignment explanation
Indices: 498596--498631 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
498586 GACAATAATT
498596 TAAAGAGATTA-TATATA
1 TAAA-AGATTATTATATA
498613 TAAAAGATTATTATATA
1 TAAAAGATTATTATATA
498630 TA
1 TA
498632 TATATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (17 bp):
TAAAAGATTATTATATA
Found at i:499043 original size:20 final size:22
Alignment explanation
Indices: 499013--499053 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
499003 GCATGTATTA
499013 TTTATAATTTAAGA-CTAAATT
1 TTTATAATTTAAGATCTAAATT
499034 TTTA-AATTTAAGATCTAAAT
1 TTTATAATTTAAGATCTAAAT
499054 CCTTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (22 bp):
TTTATAATTTAAGATCTAAATT
Found at i:499059 original size:21 final size:20
Alignment explanation
Indices: 499018--499061 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
499008 TATTATTTAT
**
499018 AATTTAAGACTAAATTTTTA
1 AATTTAAGACTAAATCCTTA
499038 AATTTAAGATCTAAATCCTTA
1 AATTTAAGA-CTAAATCCTTA
499059 AAT
1 AAT
499062 AAAATACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (20 bp):
AATTTAAGACTAAATCCTTA
Found at i:500811 original size:90 final size:90
Alignment explanation
Indices: 500644--500927 Score: 424
Period size: 90 Copynumber: 3.1 Consensus size: 90
500634 GAACAAAAAT
* * * * * *
500644 AGTCCCTGATTATAGGGTATTACTTTATTAAGTCTCTCAATTATTAAAAGTTACAAAATGATTAT
1 AGTCCCCGACTATAGGGTATTACTTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTCAT
500709 TCGACTAGGGAGTGTTGCTTTGTTA
66 TCGACTAGGGAGTGTTGCTTTGTTA
* * * *
500734 AGTCTCCGACTATAGGGTATTACTTTATTAAATCTCTCGACGATTAAAAGTTACAAAATGGTCCT
1 AGTCCCCGACTATAGGGTATTACTTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTCAT
*
500799 TCGACTAAGGAGTGTTGCTTTGTTA
66 TCGACTAGGGAGTGTTGCTTTGTTA
* * *
500824 AGTCCCCAACTATAGGATATTACTTTATTAAGTCTATCGACTATTAAAAGTTACAAAATGGTCAT
1 AGTCCCCGACTATAGGGTATTACTTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTCAT
*
500889 TCGACTAGGGAGTGTTGCTTTGTTG
66 TCGACTAGGGAGTGTTGCTTTGTTA
500914 AGTCCCTCGACTAT
1 AGTCCC-CGACTAT
500928 TGATCACCTG
Statistics
Matches: 172, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
90 166 0.97
91 6 0.03
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (90 bp):
AGTCCCCGACTATAGGGTATTACTTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTCAT
TCGACTAGGGAGTGTTGCTTTGTTA
Found at i:501210 original size:60 final size:58
Alignment explanation
Indices: 501146--501259 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 58
501136 ATAGTCAGAC
* *
501146 GACCATTTTATAACATTTAATAGTTGAGAGACTCAATAAAACAATAATCTATAGTCGAAG
1 GACCATTCTATAACATTTAATAG-TGAGAGACT-AATAAAACAATAACCTATAGTCGAAG
* * * * *
501206 GACCATTCTGTAACTTTTAATAGTGAGTGACTAATAAAGCAATACCCTATAGTC
1 GACCATTCTATAACATTTAATAGTGAGAGACTAATAAAACAATAACCTATAGTC
501260 AGAAATTTGC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 19 0.40
59 8 0.17
60 20 0.43
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (58 bp):
GACCATTCTATAACATTTAATAGTGAGAGACTAATAAAACAATAACCTATAGTCGAAG
Found at i:502999 original size:31 final size:29
Alignment explanation
Indices: 502964--503021 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
502954 TTATAACAAA
502964 TAAATACATAAAGTATATTATTTTTATCATT
1 TAAATACATAAAGTAT-TT-TTTTTATCATT
**
502995 TAAATATTTAAAGTATTTTTTTTATCA
1 TAAATACATAAAGTATTTTTTTTATCA
503022 AAATAAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 2 0.08
31 14 0.56
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (29 bp):
TAAATACATAAAGTATTTTTTTTATCATT
Found at i:503046 original size:29 final size:31
Alignment explanation
Indices: 503003--503098 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
502993 TTTAAATATT
* *
503003 TAAAG-TATTTTTTTTATCAAAATAAGTACC
1 TAAAGTTATCTTTTTGATCAAAATAAGTACC
* *
503033 TAAAGTTATCTTTTTGGTC-AAATTAGATACC
1 TAAAGTTATCTTTTTGATCAAAATAAG-TACC
*
503064 TAAA-TTAT-TTTTTGATCAAAATAGGTACC
1 TAAAGTTATCTTTTTGATCAAAATAAGTACC
*
503093 AAAAGT
1 TAAAGT
503099 ATTCAATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 15 0.28
30 21 0.39
31 18 0.33
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (31 bp):
TAAAGTTATCTTTTTGATCAAAATAAGTACC
Found at i:503101 original size:29 final size:29
Alignment explanation
Indices: 503003--503101 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
502993 TTTAAATATT
* *
503003 TAAAGTATTTTTTTTATCAAAATAAGTACC
1 TAAAGTA-TTTTTTGATCAAAATAGGTACC
* * *
503033 TAAAGTTATCTTTTTGGTCAAATTAGATACC
1 TAAAG-TAT-TTTTTGATCAAAATAGGTACC
*
503064 TAAATTATTTTTTGATCAAAATAGGTACC
1 TAAAGTATTTTTTGATCAAAATAGGTACC
*
503093 AAAAGTATT
1 TAAAGTATT
503102 CAATTTTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 25 0.45
30 9 0.16
31 22 0.39
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (29 bp):
TAAAGTATTTTTTGATCAAAATAGGTACC
Found at i:503286 original size:30 final size:30
Alignment explanation
Indices: 503184--503288 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 30
503174 AATTTTTTTG
* * *
503184 AATAGTTTAGATACTTATTTTGA--AATAA
1 AATACTTTAGGTACTTATTTTGACCAAAAA
* *
503212 AATACTTTAGGTAATTATTTTTACC-AAAA
1 AATACTTTAGGTACTTATTTTGACCAAAAA
503241 AATAACTTTAGGTACTTATTTTGACCAAAAA
1 AAT-ACTTTAGGTACTTATTTTGACCAAAAA
*
503272 AATACTTTATGTACTTA
1 AATACTTTAGGTACTTA
503289 AATGAAAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 19 0.29
29 6 0.09
30 33 0.51
31 7 0.11
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (30 bp):
AATACTTTAGGTACTTATTTTGACCAAAAA
Found at i:508739 original size:11 final size:11
Alignment explanation
Indices: 508717--508751 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
508707 ATATAGAGTC
508717 CCCACTTGCTTT
1 CCCAC-TGCTTT
508729 CCCACTGCTTT
1 CCCACTGCTTT
*
508740 ACCACTGCTTT
1 CCCACTGCTTT
508751 C
1 C
508752 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.11, C:0.43, G:0.09, T:0.37
Consensus pattern (11 bp):
CCCACTGCTTT
Found at i:511076 original size:2 final size:2
Alignment explanation
Indices: 511069--511105 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
511059 TGCAATCTGA
511069 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
511106 GATCTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:511195 original size:4 final size:4
Alignment explanation
Indices: 511188--511229 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
511178 TGCATGCATG
511188 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
511230 ACTATTCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:515571 original size:22 final size:23
Alignment explanation
Indices: 515532--515578 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
515522 AACCCTAAAC
*
515532 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCATATCTGCTA
* *
515555 AAGCCC-AGAATCATATCTTCTA
1 AAGCCCAAAAATCATATCTGCTA
515577 AA
1 AA
515579 CTCACGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCATATCTGCTA
Found at i:518413 original size:69 final size:69
Alignment explanation
Indices: 518302--518443 Score: 266
Period size: 69 Copynumber: 2.1 Consensus size: 69
518292 GACGAATCTC
*
518302 ATTAGATCTCGTCTCTCCAATTGTGGTTTGATTTAGTTTATATGGTTGTAGGTGTTGCTTCTCTT
1 ATTAGATCTCGTCTCTCCAATTGTGGTTTGATTTAGTTTATATGATTGTAGGTGTTGCTTCTCTT
518367 TTAT
66 TTAT
*
518371 ATTAGATCTCGTTTCTCCAATTGTGGTTTGATTTAGTTTATATGATTGTAGGTGTTGCTTCTCTT
1 ATTAGATCTCGTCTCTCCAATTGTGGTTTGATTTAGTTTATATGATTGTAGGTGTTGCTTCTCTT
518436 TTAT
66 TTAT
518440 ATTA
1 ATTA
518444 TGTTATCTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.18, C:0.12, G:0.19, T:0.51
Consensus pattern (69 bp):
ATTAGATCTCGTCTCTCCAATTGTGGTTTGATTTAGTTTATATGATTGTAGGTGTTGCTTCTCTT
TTAT
Found at i:518466 original size:31 final size:31
Alignment explanation
Indices: 518424--518492 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
518414 GATTGTAGGT
*
518424 GTTGCTTCTCTTTTATATTATGTTATCTTGC
1 GTTGTTTCTCTTTTATATTATGTTATCTTGC
*
518455 GTTGTTTCTCTTTTATATTATGTTCTCTTGC
1 GTTGTTTCTCTTTTATATTATGTTATCTTGC
518486 GTTGTTT
1 GTTGTTT
518493 TAATCCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.61
Consensus pattern (31 bp):
GTTGTTTCTCTTTTATATTATGTTATCTTGC
Found at i:525424 original size:2 final size:2
Alignment explanation
Indices: 525417--525448 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
525407 TTTTCAAGAA
525417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
525449 GGAGAATCAT
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):
AT
Found at i:535482 original size:4 final size:4
Alignment explanation
Indices: 535475--535629 Score: 55
Period size: 4 Copynumber: 37.0 Consensus size: 4
535465 TTCATTTCTA
* **
535475 ATTT ATTT ATTT -GTT AGTTT ATTT ATTT ATTCT AGTCGA ATTT ATTT
1 ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATT-T A-T-TT ATTT ATTT
* ** * * **
535522 ATTT ATTCC ACTCA AATTT ATTT ATTT AATT GTTT A-AA ATTT ATTT ATTT
1 ATTT ATT-T A-TTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * ** *
535572 AGTT ATTT CGAATTT ATTT ATTT GTTT GTTT -TGA AATT ATTT ATTT ATTT
1 ATTT ATTT ---ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
535622 ATTT ATTT
1 ATTT ATTT
535630 GAAGGGATAT
Statistics
Matches: 110, Mismatches: 29, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
3 4 0.04
4 89 0.81
5 10 0.09
6 3 0.03
7 4 0.04
ACGTcount: A:0.26, C:0.05, G:0.06, T:0.63
Consensus pattern (4 bp):
ATTT
Found at i:535522 original size:23 final size:23
Alignment explanation
Indices: 535492--535624 Score: 103
Period size: 23 Copynumber: 5.8 Consensus size: 23
535482 TATTTGTTAG
* *
535492 TTTATTTATTTATTCTAGTCGAA
1 TTTATTTATTTATTCTATTCAAA
* *
535515 TTTATTTATTTATTCCACTCAAA
1 TTTATTTATTTATTCTATTCAAA
* *
535538 TTTATTTATTTAATTGT-TTAAAA
1 TTTATTTATTT-ATTCTATTCAAA
* *
535561 TTTATTTATTTAGT-TATTTCGAA
1 TTTATTTATTTATTCTA-TTCAAA
* * * *
535584 TTTATTTATTTGTTTGTTTTGAAA
1 TTTATTTATTT-ATTCTATTCAAA
535608 -TTATTTATTTATT-TATT
1 TTTATTTATTTATTCTATT
535625 TATTTGAAGG
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
21 4 0.05
22 4 0.05
23 71 0.81
24 8 0.09
25 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTATTTATTTATTCTATTCAAA
Found at i:535563 original size:46 final size:46
Alignment explanation
Indices: 535513--535620 Score: 123
Period size: 46 Copynumber: 2.3 Consensus size: 46
535503 ATTCTAGTCG
535513 AATTTATTTATTTATTCCA-CTCAAATTTATTTATTTAATTG-TTTAA
1 AATTTATTTATTTATT--ATCTCAAATTTATTTATTTAATTGTTTTAA
* * ** *
535559 AATTTATTTATTTAGTTATTTCGAATTTATTTATTTGTTTGTTTTGA
1 AATTTATTTATTTA-TTATCTCAAATTTATTTATTTAATTGTTTTAA
535606 AA-TTATTTATTTATT
1 AATTTATTTATTTATT
535621 TATTTATTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
45 3 0.06
46 43 0.80
47 8 0.15
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.61
Consensus pattern (46 bp):
AATTTATTTATTTATTATCTCAAATTTATTTATTTAATTGTTTTAA
Found at i:535624 original size:46 final size:46
Alignment explanation
Indices: 535536--535625 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
535526 ATTCCACTCA
535536 AATTTATTTATTTAATTGTTTAAAATTTATTTATTTAGTTATTTCG
1 AATTTATTTATTTAATTGTTTAAAATTTATTTATTTAGTTATTTCG
** * *
535582 AATTTATTTATTTGTTTGTTTTGAAA-TTATTTATTTATTTATTT
1 AATTTATTTATTTAATTG-TTTAAAATTTATTTATTTAGTTATTT
535626 ATTTGAAGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 33 0.85
47 6 0.15
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.64
Consensus pattern (46 bp):
AATTTATTTATTTAATTGTTTAAAATTTATTTATTTAGTTATTTCG
Found at i:537733 original size:2 final size:2
Alignment explanation
Indices: 537726--537753 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
537716 ATTTTATCTA
537726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537754 CTCGAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:539787 original size:66 final size:66
Alignment explanation
Indices: 539676--539807 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
539666 CAGCAGGCTC
* *
539676 TGATGGCCTCTAACAAAGTTGCCTCGGATGAAACCGAAAGTAAAGCGGGTGATTCGACTGAAGCG
1 TGATCGCCTCTAACAAAGTTGCCTCGGATGAAACCGAAAGTAAAGCGAGTGATTCGACTGAAGCG
539741 A
66 A
** * * *
539742 TGATCGCCTCTAACCGAGTTGCCTCGGATGAAGCTGAGAGTAAAGCGAGTGATTCGACTGAAGCG
1 TGATCGCCTCTAACAAAGTTGCCTCGGATGAAACCGAAAGTAAAGCGAGTGATTCGACTGAAGCG
539807 A
66 A
539808 GGAACAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (66 bp):
TGATCGCCTCTAACAAAGTTGCCTCGGATGAAACCGAAAGTAAAGCGAGTGATTCGACTGAAGCG
A
Found at i:541470 original size:16 final size:16
Alignment explanation
Indices: 541449--541481 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
541439 ATTCAAGAGC
541449 TCGATTTTGACCTCGG
1 TCGATTTTGACCTCGG
*
541465 TCGATTTTGAGCTCGG
1 TCGATTTTGACCTCGG
541481 T
1 T
541482 TTAAGCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.39
Consensus pattern (16 bp):
TCGATTTTGACCTCGG
Found at i:542587 original size:42 final size:42
Alignment explanation
Indices: 542526--542636 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
542516 GATAATCTTA
* * * **
542526 AACAACAGTATCAGTCTCAAGAAAGTTATCAGAATTCCGTTC
1 AACAACAGCATCCGCCTCAAGAAAGTTATCAGAATTCCACTC
* * * *
542568 AACAACAGCATCCGCCTCAAAAAAGTGATCAGAGTTCTACTC
1 AACAACAGCATCCGCCTCAAGAAAGTTATCAGAATTCCACTC
*
542610 AACAAAAGCATCCGCCTCAAGAAAGTT
1 AACAACAGCATCCGCCTCAAGAAAGTT
542637 TTCGGAGTTC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (42 bp):
AACAACAGCATCCGCCTCAAGAAAGTTATCAGAATTCCACTC
Found at i:542752 original size:48 final size:48
Alignment explanation
Indices: 542068--542797 Score: 483
Period size: 48 Copynumber: 15.4 Consensus size: 48
542058 CTTCTCGAGG
* * * * * *
542068 AAGTTATCAGAGCTCCGATGATCATCAACAGCAGCATCAGTCTCAAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * * * * * * *
542116 AAGTT-TGATTAGTTTTAATAATGTTGAACAAAAGCATC-GACCT-AAGGA
1 AAGTTATCA-GAGTTCTGATCATCTTCAACAACAGCATCAG-CCTCAA-GA
** * * *
542164 AAGTTATCAGAGTTCCAACCATCTTCAACAACAGCATCAGTCTCGAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * * * * *
542212 AAGTGATCAGAGTTCCGACCATCTTCAACAACAACATCAGTCTCGAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * * * *
542260 AAGTTACCTGAGTTCTGATCATCTTGAACAAAAGCATCGGCCT-AAGGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAA-GA
* ** * * **
542308 AAGTTACCAGAGTTCCCACCATCTTCAACAACAGCATCAGTCTCGGGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * *
542356 AAGTTATCAGAGTTCTGATAATCTTCAACAAAAGCATCAACCT-AAGGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAA-GA
* * * * * *
542404 AAGTTATCAGAGTTCCGACCGTCTTCAACAACAACAGT-AGTCTAAAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCA-TCAGCCTCAAGA
* * * * *
542452 AAGTTACCAGAATTCTGATCATCTTCAACAAAAGCATCAACCT-AAGGG
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAA-GA
* * * * *
542500 AAGTTATCAAAGTTCTGATAATCTTAAACAACAGTATCAGTCTCAAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * * *
542548 AAGTTATCAGAATTC----C--GTTCAACAACAGCATCCGCCTCAAAA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * *
542590 AAGTGATCAGAGTTC---T-A-C-TCAACAAAAGCATCCGCCTCAAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * * ** * * *
542632 AAGTTTTCGGAGTTCCGATCATCTTCAACAATGGAACCAGGCTCCTCAGGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCA-G--CCTCAAGA
*** * *
542683 AAACGATCAGAGTTCTAATCATCTTCAACAACAGCATCAGCCTCGAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
* * * *
542731 AAGGTATCAGGGTTCTGATCATCTTCAGCATCAGCAT-ATGCCTCAAGA
1 AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCA-GCCTCAAGA
* *
542779 AAGTTATCAGGGTTTTGAT
1 AAGTTATCAGAGTTCTGAT
542798 GGTTCAATTG
Statistics
Matches: 524, Mismatches: 132, Indels: 52
0.74 0.19 0.07
Matches are distributed among these distances:
42 67 0.13
45 1 0.00
46 1 0.00
47 11 0.02
48 398 0.76
49 10 0.02
50 1 0.00
51 35 0.07
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (48 bp):
AAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCAAGA
Found at i:544549 original size:48 final size:48
Alignment explanation
Indices: 544478--545456 Score: 691
Period size: 48 Copynumber: 20.8 Consensus size: 48
544468 TCAAGAGCCG
**
544478 ACAGCATCAGCCTCGGGAAAGTTATCAGAGTTCTGATCATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * *
544526 ACAGCATCAGACTCAAGAAAGTTATCAGAGTTCGGATAATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * *
544574 AAAGCATCTA-CCT-AAGGAGAGTTATCAGCGTTCCGATCATCTTCAACA
1 ACAGCATC-AGCCTCAA-GAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * * * * * * *
544622 AGATCAT-AGGGCTCGAGTAGGTCATCACAGTTC----C--GTTCAACA
1 ACAGCATCA-GCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * * * *
544664 ACAGCATCGGGGTTCTCAGGGAAGTTATCAGAGTTCTGATCAACGTCAAC-
1 ACAGCATC--AG-CCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * *
544714 A-A-CATCAGACTC-AGAAAAGTTATCAGAGCTT-TGATCATCTTAAACT
1 ACAGCATCAGCCTCAAG-AAAGTTATCAGAG-TTCTGATCATCTTCAACA
* * * * *
544760 ACAGCCTCAGCCTCAGGAAAATTATCAAAGTTC-CATTCATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGA-TCATCTTCAACA
* * *
544808 ACAGCATCAGCCTCAGGAAAGTTATCAGAGTTCCGATAATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
**
544856 ACAGCATCAGCCTCGGGAAAGTTATCAGAGTTCTGATCATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* ***
544904 ACAGCATCAACCTTGGGAAAGTTATCAGAGTTCTGATCATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* *
544952 ACAGCAT-AGGCCTGAGGAAAGTTATCAGAGTTCTGATCATCTTCAACA
1 ACAGCATCA-GCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * *
545000 ACAGCATCAACCT-AAGGAAAGTTATCAGAGTTCCGACCATCTTCAACA
1 ACAGCATCAGCCTCAA-GAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * *
545048 ACAACATCAGTCTCAAGAAAGTTACCAGAATTCTGATCATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * * *
545096 AAAGCATCAACC-CAAGGACAGTTATCAAAGTTCTGATAATCTTCAACA
1 ACAGCATCAGCCTCAA-GAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * * * * *
545144 AAAACATC-GACCT-AAGGAAAGTTGTCAAAATTCTG---ATCTACAAGA
1 ACAGCATCAG-CCTCAA-GAAAGTTATCAGAGTTCTGATCATCTTCAACA
** * * *
545189 ACAATATCAGTCTCAAGAAAGTTATCAGAATTC----C--GTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* *
545231 ACAGCATCCA-CCTCAAAAAAGTGATCAGAGTTCT-A--A---TCAACA
1 ACAGCAT-CAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * * *
545273 AAAGCATCCGCCTCAAGAAAGTTTTCGGAGTTCCGATCATCTTCAACA
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
** * * * *** *
545321 ATGGAACCAGGATCCTCAGGAAAACGATCAGAGTTCTAATCATCTTCAACA
1 ACAGCATCA-G--CCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * * * *
545372 ACAGCATCAGCCCCGAGAAAGGTATCAGGGTTCTGATCATCTTCAGCG
1 ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
* * * *
545420 TCAGCAT-ATTCCTCAAGAAAGTTATCAGGGTTTTGAT
1 ACAGCATCA-GCCTCAAGAAAGTTATCAGAGTTCTGAT
545457 GGTTCAACTG
Statistics
Matches: 739, Mismatches: 143, Indels: 98
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.00
42 72 0.10
43 3 0.00
44 3 0.00
45 74 0.10
46 8 0.01
47 12 0.02
48 514 0.70
49 10 0.01
50 2 0.00
51 40 0.05
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (48 bp):
ACAGCATCAGCCTCAAGAAAGTTATCAGAGTTCTGATCATCTTCAACA
Found at i:545258 original size:42 final size:42
Alignment explanation
Indices: 545200--545294 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
545190 CAATATCAGT
* ** *
545200 CTCAAGAAAGTTATCAGAATTCCGTTCAACAACAGCATCCAC
1 CTCAAGAAAGTGATCAGAATTCCAATCAACAAAAGCATCCAC
* * * *
545242 CTCAAAAAAGTGATCAGAGTTCTAATCAACAAAAGCATCCGC
1 CTCAAGAAAGTGATCAGAATTCCAATCAACAAAAGCATCCAC
545284 CTCAAGAAAGT
1 CTCAAGAAAGT
545295 TTTCGGAGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (42 bp):
CTCAAGAAAGTGATCAGAATTCCAATCAACAAAAGCATCCAC
Found at i:547909 original size:30 final size:30
Alignment explanation
Indices: 547848--547910 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
547838 AAATAATAAT
** * *
547848 AATAAATAGTAAGTTAAAGTAATGAAATTA
1 AATAAATAAAAAGTAAAAGGAATGAAATTA
547878 AATAAATAAAAAGTAAAAGGAA-GAAATTTA
1 AATAAATAAAAAGTAAAAGGAATGAAA-TTA
547908 AAT
1 AAT
547911 GTGCATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (30 bp):
AATAAATAAAAAGTAAAAGGAATGAAATTA
Found at i:548061 original size:4 final size:4
Alignment explanation
Indices: 548052--548082 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
548042 TTCAAACATA
*
548052 AAAT AAAT AAAT AAGT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
548083 AAGTTAGCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:548305 original size:130 final size:129
Alignment explanation
Indices: 548140--548480 Score: 420
Period size: 130 Copynumber: 2.6 Consensus size: 129
548130 GTTTGGATCG
* * *
548140 TAATAATGTGGATTATACCCCGGATCGGGTCACCACAAGGTCGTATAATAATTCAAAAATAAAAT
1 TAATAAAGTGGATCATACCCCGAATCGGGTCACCACAAGGTCGTATAATAATTCAAAAATAAAAT
* * * *
548205 AAAATAAATAAATAAAAAGTTAGTGGTTAAAAGTTAGCGGTTAGATATTAACATAG-TCTGAACC
66 AAAATAAATAAATAAAAAGTTAGTGCTTAAAAGTTA-CGGTTAGATATTAAAAGAGTTCAG-ACC
548269 A
129 A
* * * *
548270 TAATAAAGTGGACCATACCCCGAATCGGGTCACCACAAGGTCGTATAATTATTCGAACATAAAAT
1 TAATAAAGTGGATCATACCCCGAATCGGGTCACCACAAGGTCGTATAATAATTCAAAAATAAAAT
* *
548335 AAAATACATAAATAAAAAAAGTTAGTGCTTAAAAGTTACGGTTAGATGTTAAAAGAGTTCAGACC
66 AAAATAAATAAAT--AAAAAGTTAGTGCTTAAAAGTTACGGTTAGATATTAAAAGAGTTCAGACC
548400 A
129 A
* * * * * *
548401 TTATAATA-TGAATCGTACCCTGAATCAGGTCACCACAAGGTCGTATAATAATTCGAAAACT--A
1 TAATAA-AGTGGATCATACCCCGAATCGGGTCACCACAAGGTCGTATAATAATTC-AAAAATAAA
548463 ATAACAATAAATAAATAA
64 ATAA-AATAAATAAATAA
548481 TGGAATTAAT
Statistics
Matches: 181, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
129 2 0.01
130 75 0.41
131 75 0.41
132 29 0.16
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (129 bp):
TAATAAAGTGGATCATACCCCGAATCGGGTCACCACAAGGTCGTATAATAATTCAAAAATAAAAT
AAAATAAATAAATAAAAAGTTAGTGCTTAAAAGTTACGGTTAGATATTAAAAGAGTTCAGACCA
Found at i:548448 original size:131 final size:130
Alignment explanation
Indices: 548154--548480 Score: 412
Period size: 131 Copynumber: 2.5 Consensus size: 130
548144 AATGTGGATT
* * *
548154 ATACCCCGGATCGGGTCACCACAAGGTCGTATAATAATTCAAAAATAAAATAAAATAAATAAATA
1 ATACCCCGAATCAGGTCACCACAAGGTCGTATAATAATTCGAAAATAAAATAAAATAAATAAATA
* * * * *
548219 AAAAGTTAGTGGTTAAAAGTTAGCGGTTAGATATTAACATAGTCTGAACCATAATAAAGTGGACC
66 AAAAGTTAGTGCTTAAAAGTTAGCGGTTAGATATTAAAAGAGTCAGAACCATAATAAAGTGAACC
* * * *
548284 ATACCCCGAATCGGGTCACCACAAGGTCGTATAATTATTCGAACATAAAATAAAATACATAAATA
1 ATACCCCGAATCAGGTCACCACAAGGTCGTATAATAATTCGAAAATAAAATAAAATAAATAAAT-
* *
548349 AAAAAAGTTAGTGCTTAAAAGTTA-CGGTTAGATGTTAAAAGAGTTCAG-ACCATTATAATA-TG
65 -AAAAAGTTAGTGCTTAAAAGTTAGCGGTTAGATATTAAAAGAG-TCAGAACCATAATAA-AGTG
*
548411 AATC
127 AACC
* *
548415 GTACCCTGAATCAGGTCACCACAAGGTCGTATAATAATTCGAAAACT--AATAACAATAAATAAA
1 ATACCCCGAATCAGGTCACCACAAGGTCGTATAATAATTCGAAAA-TAAAATAA-AATAAATAAA
548478 TAA
64 TAA
548481 TGGAATTAAT
Statistics
Matches: 172, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
129 2 0.01
130 64 0.37
131 79 0.46
132 27 0.16
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (130 bp):
ATACCCCGAATCAGGTCACCACAAGGTCGTATAATAATTCGAAAATAAAATAAAATAAATAAATA
AAAAGTTAGTGCTTAAAAGTTAGCGGTTAGATATTAAAAGAGTCAGAACCATAATAAAGTGAACC
Found at i:563509 original size:15 final size:15
Alignment explanation
Indices: 563489--563525 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
563479 ATATTTAATT
*
563489 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
563504 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
563519 GGGCGGG
1 GGGCGGG
563526 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:564354 original size:27 final size:28
Alignment explanation
Indices: 564304--564357 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
564294 CCACTGTGGC
*
564304 TTTCAAGCATCGACTCGACGACATAATA
1 TTTCAAGCATCGACTCGAAGACATAATA
*
564332 TTTCAAGCATTG-CTCGAAGACATAAT
1 TTTCAAGCATCGACTCGAAGACATAAT
564358 GTAAATAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (28 bp):
TTTCAAGCATCGACTCGAAGACATAATA
Found at i:570441 original size:14 final size:14
Alignment explanation
Indices: 570408--570450 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
570398 TTATATTTTT
570408 TAAAAA-TAAT-TA
1 TAAAAATTAATATA
*
570420 TAATAATTAATATA
1 TAAAAATTAATATA
*
570434 TAAAAATTAATAAA
1 TAAAAATTAATATA
570448 TAA
1 TAA
570451 TTTAAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAAATTAATATA
Found at i:570469 original size:30 final size:27
Alignment explanation
Indices: 570434--570502 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 27
570424 AATTAATATA
*
570434 TAAAAATTAATAAATAATTTAAACTCATT
1 TAAAAATTAATAAA-AA-TTAAACTAATT
*
570463 TAAAAAATGGTAA-AAAAATTAAATTAATT
1 T-AAAAAT--TAATAAAAATTAAACTAATT
570492 TAAAAATTAAT
1 TAAAAATTAAT
570503 GCATAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
26 3 0.09
28 6 0.18
29 11 0.32
30 8 0.24
31 3 0.09
32 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (27 bp):
TAAAAATTAATAAAAATTAAACTAATT
Found at i:570524 original size:172 final size:173
Alignment explanation
Indices: 570259--570602 Score: 609
Period size: 172 Copynumber: 2.0 Consensus size: 173
570249 AAAAACTTCG
*
570259 TATAAAAATTAATAAATAATTTAAACTCATTTAAAAAATGGTAAAAAAAATTAATTTAATTTAAA
1 TATAAAAATTAATAAATAATTTAAACTCATTTAAAAAATGGTAAAAAAAATTAAATTAATTTAAA
*
570324 AATTAATGTATAGTTTAAATTTTTTATATTTTAAAATTAAAATAATTTTTTTCTATTTTCCATTA
66 AATTAATGCATAGTTTAAATTTTTTATATTTTAAAATTAAAATAATTTTTTTCTATTTTCCATTA
** *
570389 ATAATTTGCTTATATTTTTTAAAAATAATTATAATAATTAATA
131 ATAATTTAATTATATATTTTAAAAATAATTATAATAATTAATA
570432 TATAAAAATTAATAAATAATTTAAACTCATTTAAAAAATGGT-AAAAAAATTAAATTAATTTAAA
1 TATAAAAATTAATAAATAATTTAAACTCATTTAAAAAATGGTAAAAAAAATTAAATTAATTTAAA
* **
570496 AATTAATGCATAGTTTAAATTTTTTATATTTTAAAATTAAATTAATTTTTTTCTATTTTTTATTA
66 AATTAATGCATAGTTTAAATTTTTTATATTTTAAAATTAAAATAATTTTTTTCTATTTTCCATTA
570561 ATAATTTAATTATATATTTTAAAAATAATTATAATAATTAAT
131 ATAATTTAATTATATATTTTAAAAATAATTATAATAATTAAT
570603 TTAATTTTAA
Statistics
Matches: 163, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
172 121 0.74
173 42 0.26
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (173 bp):
TATAAAAATTAATAAATAATTTAAACTCATTTAAAAAATGGTAAAAAAAATTAAATTAATTTAAA
AATTAATGCATAGTTTAAATTTTTTATATTTTAAAATTAAAATAATTTTTTTCTATTTTCCATTA
ATAATTTAATTATATATTTTAAAAATAATTATAATAATTAATA
Found at i:570605 original size:24 final size:24
Alignment explanation
Indices: 570560--570606 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
570550 ATTTTTTATT
* *
570560 AATAATTTAATTATATATTTTAAA
1 AATAATTTAATAATATAATTTAAA
570584 AATAATTATAATAAT-TAATTTAA
1 AATAATT-TAATAATATAATTTAA
570607 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAATTTAATAATATAATTTAAA
Found at i:570610 original size:30 final size:31
Alignment explanation
Indices: 570559--570633 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
570549 TATTTTTTAT
570559 TAATAATTTAATTATATATTTTAAAAATAATTA
1 TAATAATTTAATT-TATATTTTAAAAATAA-TA
570592 TAATAA-TTAATTTA-ATTTTAAAAATAATA
1 TAATAATTTAATTTATATTTTAAAAATAATA
570621 T-ATAATTTAATTT
1 TAATAATTTAATTT
570634 TTTATATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.10
29 10 0.24
30 13 0.32
31 2 0.05
32 6 0.15
33 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATAATTTAATTTATATTTTAAAAATAATA
Found at i:570643 original size:33 final size:32
Alignment explanation
Indices: 570561--570645 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 32
570551 TTTTTTATTA
*
570561 ATAATTTAA--TTATATATTTTAAAAATAATT
1 ATAATTTAATTTTTTATATTTTAAAAATAATT
*
570591 ATAA--TAATTAATTTA-ATTTTAAAAATAATAT
1 ATAATTTAATT-TTTTATATTTTAAAAATAAT-T
570622 ATAATTTAATTTTTTATATTTTAA
1 ATAATTTAATTTTTTATATTTTAA
570646 TACTAATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
28 3 0.07
30 18 0.40
31 8 0.18
32 4 0.09
33 12 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATAATTTAATTTTTTATATTTTAAAAATAATT
Found at i:572142 original size:16 final size:16
Alignment explanation
Indices: 572121--572168 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
572111 ATATTAAATT
572121 TTTCGAATCAAACTCA
1 TTTCGAATCAAACTCA
*
572137 TTTCGAATCAAATTCA
1 TTTCGAATCAAACTCA
572153 TTTC-AAGTCAAACTCA
1 TTTCGAA-TCAAACTCA
572169 ACAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 2 0.07
16 27 0.93
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (16 bp):
TTTCGAATCAAACTCA
Found at i:572386 original size:15 final size:17
Alignment explanation
Indices: 572352--572408 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
572342 TATTTTAGAG
* *
572352 TTTAG-GGTTTCATGGA
1 TTTAGAGGTTTAAAGGA
572368 TTTAGAGGTTT-AA-GA
1 TTTAGAGGTTTAAAGGA
572383 TTTAG-GGTTTAAAGGA
1 TTTAGAGGTTTAAAGGA
*
572399 TTTAAAGGTT
1 TTTAGAGGTT
572409 AAGTGATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 5 0.14
15 9 0.26
16 12 0.34
17 9 0.26
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (17 bp):
TTTAGAGGTTTAAAGGA
Found at i:577085 original size:29 final size:29
Alignment explanation
Indices: 577040--577098 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
577030 ATAAAATGGG
*
577040 TAGCGCCTAACAATGTTTTCGATCATTTT
1 TAGCGCCTAACAATGTTTCCGATCATTTT
* * *
577069 TAGCGCCTAATATTGTTTCCGGTCATTTT
1 TAGCGCCTAACAATGTTTCCGATCATTTT
577098 T
1 T
577099 TTGAAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.44
Consensus pattern (29 bp):
TAGCGCCTAACAATGTTTCCGATCATTTT
Found at i:577484 original size:60 final size:59
Alignment explanation
Indices: 577416--577644 Score: 268
Period size: 60 Copynumber: 3.8 Consensus size: 59
577406 CATCATATGT
*
577416 CCCAAAATATGACCATCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCTATTCCATC
1 CCCAAAATATGACC-TCATTTTAAATTAGTCCTTAAACTTTTGAATATTTCTATTCCATC
*
577476 CCCAAAATATGACCTTCATTTTAAATTAATCCTTAAACTTTTGAATA-TTCATATTCCAT-
1 CCCAAAATATGACC-TCATTTTAAATTAGTCCTTAAACTTTTGAATATTTC-TATTCCATC
* * *
577535 CCCAAACTATGACTCTCATTTTAAATTAGTCCTTACACTTTTGAATATTT-TAATTTCATC
1 CCCAAAATATGAC-CTCATTTTAAATTAGTCCTTAAACTTTTGAATATTTCT-ATTCCATC
* * * **
577595 CCTAAACTATGACCCTC-TTTCTAAATTGGTCCCAAAACTTTTTGAATATT
1 CCCAAAATATGA-CCTCATTT-TAAATTAGTCCTTAAAC-TTTTGAATATT
577645 CCAATTTCAT
Statistics
Matches: 149, Mismatches: 12, Indels: 15
0.85 0.07 0.09
Matches are distributed among these distances:
58 1 0.01
59 54 0.36
60 82 0.55
61 12 0.08
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.41
Consensus pattern (59 bp):
CCCAAAATATGACCTCATTTTAAATTAGTCCTTAAACTTTTGAATATTTCTATTCCATC
Found at i:577633 original size:119 final size:120
Alignment explanation
Indices: 577415--577658 Score: 309
Period size: 119 Copynumber: 2.0 Consensus size: 120
577405 GCATCATATG
*
577415 TCCCAAAATATGACCATCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCTATTCCATCCCCA
1 TCCCAAAATATGACCATCATTTTAAATTAGTCCTTAAACTTTTGAATATTTCTATTCCATCCCCA
* **
577480 AAATATGACCTTCATTTTAAATTAATCCTTAAAC-TTTTGAATATT-CATATTCCA
66 AAATATGACCCTCATTTTAAATTAATCCCAAAACTTTTTGAATATTCCA-ATTCCA
* * *
577534 TCCCAAACTATGACTC-TCATTTTAAATTAGTCCTTACACTTTTGAATATTT-TAATTTCATCCC
1 TCCCAAAATATGAC-CATCATTTTAAATTAGTCCTTAAACTTTTGAATATTTCT-ATTCCATCCC
* * ** *
577597 TAAACTATGACCCTC-TTTCTAAATTGGTCCCAAAACTTTTTGAATATTCCAATTTCA
64 CAAAATATGACCCTCATTT-TAAATTAATCCCAAAACTTTTTGAATATTCCAATTCCA
577654 TCCCA
1 TCCCA
577659 GATTCATCCA
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 80 0.74
120 22 0.20
121 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (120 bp):
TCCCAAAATATGACCATCATTTTAAATTAGTCCTTAAACTTTTGAATATTTCTATTCCATCCCCA
AAATATGACCCTCATTTTAAATTAATCCCAAAACTTTTTGAATATTCCAATTCCA
Found at i:579283 original size:21 final size:21
Alignment explanation
Indices: 579241--579291 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
579231 GGACTGCTAT
* **
579241 GTCAACACCGTGAAGTGTCAC
1 GTCAACACCGTGAACTACCAC
*
579262 GTCAACATCGTGAACTACCAC
1 GTCAACACCGTGAACTACCAC
*
579283 GCCAACACC
1 GTCAACACC
579292 ATAAATGTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (21 bp):
GTCAACACCGTGAACTACCAC
Found at i:579533 original size:22 final size:22
Alignment explanation
Indices: 579506--579565 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
579496 GACGAAATTT
579506 ATATTTAAATAATAAA-TAATA
1 ATATTTAAATAATAAATTAATA
** *
579527 ATAATTTATTTAAGAAATTAATA
1 AT-ATTTAAATAATAAATTAATA
579550 ATATATTAAA-AATAAA
1 ATAT-TTAAATAATAAA
579566 GAACATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.07
22 18 0.60
23 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATTTAAATAATAAATTAATA
Found at i:580990 original size:4 final size:4
Alignment explanation
Indices: 580991--582955 Score: 2680
Period size: 4 Copynumber: 492.5 Consensus size: 4
580981 CGCACGCACG
580991 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581039 CACA CA-A CACA CA-A CACA CACA CACA CACA CACA CACA CACA CA-A
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
*
581084 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * *
581132 CGCA CACG CACG CACA CGCA CGCA CACG CACA CGCA CACG CACA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* *
581180 CACG CACA CGCA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581228 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581276 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581324 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581372 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581420 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
*
581468 CACA CACA CACA CACA CACA CACA CACA CACA CACA CGCA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581516 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * *
581564 CACA CACA CGCA CACG CACG CACG CACG CACG CACT CACA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
581612 CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
581660 CGCA CTCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * *
581708 CACA CGCA CGCA CACG CACG CACA CGCA CGCA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
581756 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
581804 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
581852 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
581900 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * *
581948 CACG CACG CACG CACG CACG CACA CGCA CGCA CGCA CGCA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
581996 CTCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * * * *
582044 CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* * * * * * * * * *
582092 CGCA CGCA CGCA CACG CACA CGCA CACG CACG CGCA CACG CGCA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
* *
582140 CACA CGCA CACG CACA CACA C-CA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582187 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582235 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582283 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CAC- CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582330 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582378 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582426 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582474 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582522 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582570 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582618 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582666 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582714 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582762 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582810 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582858 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582906 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
582954 CA
1 CA
582956 TATATGTATG
Statistics
Matches: 1897, Mismatches: 59, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
3 15 0.01
4 1882 0.99
ACGTcount: A:0.43, C:0.50, G:0.07, T:0.00
Consensus pattern (4 bp):
CACA
Found at i:586560 original size:21 final size:22
Alignment explanation
Indices: 586536--586577 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
586526 TACGAAAGTC
*
586536 TCGATTTTTATATCGG-GTTTT
1 TCGATCTTTATATCGGAGTTTT
586557 TCGATCTTTATATCGGAGTTT
1 TCGATCTTTATATCGGAGTTT
586578 GAACGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (22 bp):
TCGATCTTTATATCGGAGTTTT
Found at i:589925 original size:22 final size:22
Alignment explanation
Indices: 589900--589944 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
589890 TATATCAATC
589900 AGCATGTTAACATTCAACTCAT
1 AGCATGTTAACATTCAACTCAT
589922 AGCATGTTAACATTCAACTCAT
1 AGCATGTTAACATTCAACTCAT
589944 A
1 A
589945 TGACTGCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (22 bp):
AGCATGTTAACATTCAACTCAT
Found at i:590115 original size:59 final size:59
Alignment explanation
Indices: 590006--590121 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
589996 GATAATTTTG
* *
590006 TAACTTTTAATAGTCAAGAAACTCAACAAAACAACACCTTATAGTCGAAAACTATTTCA
1 TAACTTTTAATAGTCAAGAAACTCAACAAAACAACACCTTATAATCGAAAACAATTTCA
* * *
590065 TAACTTTTAATTA-TCGAGAAACTCAACAAAACAATATCC-TATAATTGAAAACAATTT
1 TAACTTTTAA-TAGTCAAGAAACTCAACAAAACAACA-CCTTATAATCGAAAACAATTT
590122 GTATACTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 46 0.92
60 4 0.08
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (59 bp):
TAACTTTTAATAGTCAAGAAACTCAACAAAACAACACCTTATAATCGAAAACAATTTCA
Found at i:590130 original size:59 final size:59
Alignment explanation
Indices: 590002--590130 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
589992 AGATGATAAT
* *
590002 TTTGTA-ACTTTTAATAGTCAAGAAACTCAACAAAACAACACCTTATAGTCGAAAACTA
1 TTTGTATACTTTTAATAGTCAAGAAACTCAACAAAACAACACCTTATAATCGAAAACAA
* * * *
590060 TTT-CATAACTTTTAATTA-TCGAGAAACTCAACAAAACAATATCC-TATAATTGAAAACAA
1 TTTGTAT-ACTTTTAA-TAGTCAAGAAACTCAACAAAACAACA-CCTTATAATCGAAAACAA
590119 TTTGTATACTTT
1 TTTGTATACTTT
590131 ATCTTATTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
57 1 0.02
58 3 0.05
59 49 0.83
60 6 0.10
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (59 bp):
TTTGTATACTTTTAATAGTCAAGAAACTCAACAAAACAACACCTTATAATCGAAAACAA
Found at i:595250 original size:21 final size:20
Alignment explanation
Indices: 595220--595258 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
595210 GGTAAAAGAC
595220 TATTAAAATATTATTATTAT
1 TATTAAAATATTATTATTAT
595240 TATTAAAAATATTATTATT
1 TATT-AAAATATTATTATT
595259 GAGTGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAAAATATTATTATTAT
Found at i:598268 original size:2 final size:2
Alignment explanation
Indices: 598261--598309 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
598251 CTTTCTCATT
* * * *
598261 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
598303 TA TA TA T
1 TA TA TA T
598310 TGGCAAGTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:600290 original size:26 final size:24
Alignment explanation
Indices: 600238--600309 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 24
600228 AGGACGTAGG
* **
600238 AATTTAAAGTTTTTTTTTCTTTGAGA
1 AATTTAAAATTTTAGTTT-TTT-AGA
600264 AATTATAAAATTTTGAGTTTTTTAGA
1 AATT-TAAAATTTT-AGTTTTTTAGA
*
600290 AATTTTAAATTTTAGTTTTT
1 AATTTAAAATTTTAGTTTTT
600310 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 7 0.17
25 8 0.20
26 11 0.28
27 11 0.28
28 3 0.08
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (24 bp):
AATTTAAAATTTTAGTTTTTTAGA
Found at i:600576 original size:2 final size:2
Alignment explanation
Indices: 600535--600560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
600525 CTTTAATGTA
600535 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
600561 CAAATGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:601344 original size:2 final size:2
Alignment explanation
Indices: 601337--601375 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
601327 CTGAATGGAT
601337 TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
601376 GGAGTTGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:601358 original size:18 final size:18
Alignment explanation
Indices: 601335--601370 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
601325 TTCTGAATGG
601335 ATTATATATATATATATA
1 ATTATATATATATATATA
601353 ATTATATATATATATATA
1 ATTATATATATATATATA
601371 TATATGGAGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATATATATATATATA
Found at i:603392 original size:21 final size:21
Alignment explanation
Indices: 603368--603410 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
603358 TTCTTCTAGC
* *
603368 AAGTGGTTCTTTTCTGATTCT
1 AAGTGATTCTTTTCCGATTCT
603389 AAGTGATTCTTTTCCGATTCT
1 AAGTGATTCTTTTCCGATTCT
603410 A
1 A
603411 GGTCTGGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (21 bp):
AAGTGATTCTTTTCCGATTCT
Found at i:605975 original size:21 final size:21
Alignment explanation
Indices: 605944--605993 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
605934 CGTTATATTT
*
605944 TTTATTTTTTAATAATAAA-AA
1 TTTA-TTTTTAATAAAAAATAA
605965 TATTATTTTTAATAAAAAATAA
1 T-TTATTTTTAATAAAAAATAA
605987 TTTATTT
1 TTTATTT
605994 ACAAATAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATTTTTAATAAAAAATAA
Found at i:606959 original size:2 final size:2
Alignment explanation
Indices: 606952--606983 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
606942 CAATATTCTC
606952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
606984 TTGTCTTACG
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):
AT
Found at i:608644 original size:116 final size:116
Alignment explanation
Indices: 608440--608780 Score: 560
Period size: 116 Copynumber: 3.0 Consensus size: 116
608430 TGAAAAGTCA
608440 CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATGACTCGACGCCGTTAACAAATCGTTAA
1 CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATGACTCGACGCCGTTAACAAATCGTTAA
*
608505 CAAATCAACGGAATGCTGATGTGGCACATTAAATCAACTAATCCTCCTCCT
66 CAAATCAACGGAATGCTGATGTGGCACATTAAATCAGCTAATCCTCCTCCT
608556 CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATGACTCGACGCCGTTAACAAATCGTTAA
1 CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATGACTCGACGCCGTTAACAAATCGTTAA
608621 CAAATCAACGGAATGCTGATGTGGCACATTAAATCAGCTAATCCTCCTCCTCCT
66 CAAATCAACGGAATGCTGATGTGGCACATTAAATCAGCTAA---TCCTCCTCCT
*
608675 CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATCACTCGACGCCGTTAACAAAT-G----
1 CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATGACTCGACGCCGTTAACAAATCGTTAA
608735 ------AACGGAATGCTGATGTGGCACATTAAATCAGCTAATCCTCCTCCT
66 CAAATCAACGGAATGCTGATGTGGCACATTAAATCAGCTAATCCTCCTCCT
608780 C
1 C
608781 CTCCTCCTCC
Statistics
Matches: 220, Mismatches: 2, Indels: 17
0.92 0.01 0.07
Matches are distributed among these distances:
105 11 0.05
108 35 0.16
116 105 0.48
118 1 0.00
119 68 0.31
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (116 bp):
CAAATCGGTCACTAACATATCATTTGTTAAAAAATAATGACTCGACGCCGTTAACAAATCGTTAA
CAAATCAACGGAATGCTGATGTGGCACATTAAATCAGCTAATCCTCCTCCT
Found at i:608778 original size:3 final size:3
Alignment explanation
Indices: 608770--608874 Score: 203
Period size: 3 Copynumber: 35.3 Consensus size: 3
608760 AATCAGCTAA
608770 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
608818 TCC TCC TCC TCC TCC TCC T-C TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
608865 TCC TCC TCC T
1 TCC TCC TCC T
608875 GCTGCTGCTG
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 99 0.98
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:609158 original size:145 final size:145
Alignment explanation
Indices: 608895--609170 Score: 543
Period size: 145 Copynumber: 1.9 Consensus size: 145
608885 CTGCTGCTGC
608895 TGAACATTTAGCTTGTTGAGTTCCTCGTGGATATGAAAGCAAACGACAACAAGAGCCACGAACCA
1 TGAACATTTAGCTTGTTGAGTTCCTCGTGGATATGAAAGCAAACGACAACAAGAGCCACGAACCA
*
608960 TTTGAGCCATTTCTGCATTCAAAATACCAAAAGCTAAATGAACTAAGAAAATACTATGAACCAAT
66 TTTGAGCCATTTCTGCATTCAAAATACCAAAAACTAAATGAACTAAGAAAATACTATGAACCAAT
609025 GACTGTTTCACAACA
131 GACTGTTTCACAACA
609040 TGAACATTTAGCTTGTTGAGTTCCTCGTGGATATGAAAGCAAACGACAACAAGAGCCACGAACCA
1 TGAACATTTAGCTTGTTGAGTTCCTCGTGGATATGAAAGCAAACGACAACAAGAGCCACGAACCA
609105 TTTGAGCCATTTCTGCATTCAAAATACCAAAAACTAAATGAACTAAGAAAATACTATGAACCAAT
66 TTTGAGCCATTTCTGCATTCAAAATACCAAAAACTAAATGAACTAAGAAAATACTATGAACCAAT
609170 G
131 G
609171 CGGGTGAGTT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 130 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (145 bp):
TGAACATTTAGCTTGTTGAGTTCCTCGTGGATATGAAAGCAAACGACAACAAGAGCCACGAACCA
TTTGAGCCATTTCTGCATTCAAAATACCAAAAACTAAATGAACTAAGAAAATACTATGAACCAAT
GACTGTTTCACAACA
Found at i:609478 original size:30 final size:30
Alignment explanation
Indices: 609442--609498 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
609432 CCTGGCGGTA
609442 CCCCTTCTTCCTTCTGTTGTTCTCCATGTT
1 CCCCTTCTTCCTTCTGTTGTTCTCCATGTT
609472 CCCCTTCTTCCTTCTGTTGTTCTCCAT
1 CCCCTTCTTCCTTCTGTTGTTCTCCAT
609499 CTGCTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.04, C:0.39, G:0.09, T:0.49
Consensus pattern (30 bp):
CCCCTTCTTCCTTCTGTTGTTCTCCATGTT
Found at i:615732 original size:31 final size:32
Alignment explanation
Indices: 615694--615755 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
615684 ATTATTTATG
615694 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
615725 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
615756 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:617838 original size:20 final size:20
Alignment explanation
Indices: 617813--617850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
617803 AAGATCAAAC
617813 CAAAGAAAAAAAACAAAGAG
1 CAAAGAAAAAAAACAAAGAG
* *
617833 CAAAGAGAAAAATCAAAG
1 CAAAGAAAAAAAACAAAG
617851 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.11, G:0.16, T:0.03
Consensus pattern (20 bp):
CAAAGAAAAAAAACAAAGAG
Found at i:617849 original size:13 final size:12
Alignment explanation
Indices: 617833--617880 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
617823 AAACAAAGAG
617833 CAAAGAGAAAAAT
1 CAAAGA-AAAAAT
*
617846 CAAAGCAAAAAT
1 CAAAGAAAAAAT
*
617858 CAAAG-AAAAAG
1 CAAAGAAAAAAT
617869 CAAAGAACAAAA
1 CAAAGAA-AAAA
617881 AGAGGACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.32
12 12 0.39
13 9 0.29
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:617866 original size:11 final size:11
Alignment explanation
Indices: 617838--617875 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
617828 AAGAGCAAAG
617838 AGAAAAATCAA
1 AGAAAAATCAA
617849 AGCAAAAATCAA
1 AG-AAAAATCAA
*
617861 AGAAAAAGCAA
1 AGAAAAATCAA
617872 AGAA
1 AGAA
617876 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:619060 original size:4 final size:4
Alignment explanation
Indices: 619051--619120 Score: 126
Period size: 4 Copynumber: 18.0 Consensus size: 4
619041 AAAAGTATAC
619051 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
619099 ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT
619121 GATACATAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
4 62 0.97
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:619778 original size:99 final size:97
Alignment explanation
Indices: 619577--619808 Score: 254
Period size: 99 Copynumber: 2.3 Consensus size: 97
619567 TGAGAATTTT
* *
619577 AAAACAAATTGCGTCTCGCTTGAGACATTTTCCTTTGAGATACAAATTTGAATTGATTCACTAAA
1 AAAACAAATT-TGTCTCGCTTGAGACATTTCCCTTTGAGATACAAATTTGAATTGATTCACTAAA
*
619642 AACAAAATTAATCACCTTAGATTGTTGTTTCTTTC-
65 AACAAAATTAATCACCTTAGA-T-TCGTTTC-TTCA
* * * *
619677 AAAACAAATTTGTCTCGCTTGAGACCTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACATT
1 AAAACAAATTTGTCTCGCTTGAGACATTTCCCTTTGAGATACAAATTT-GAA-TTGATTCAC-TA
* * *
619742 AAAACAAAGTTGATCTCACTTGAGA-TCGTTTC-TCA
63 AAAACAAAATTAATCAC-CTT-AGATTCGTTTCTTCA
619777 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTGTCTCGCTTGAGAC-ATTTC
619809 TAAAACAAAT
Statistics
Matches: 113, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
99 36 0.32
100 21 0.19
101 31 0.27
102 19 0.17
103 3 0.03
104 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (97 bp):
AAAACAAATTTGTCTCGCTTGAGACATTTCCCTTTGAGATACAAATTTGAATTGATTCACTAAAA
ACAAAATTAATCACCTTAGATTCGTTTCTTCA
Found at i:619823 original size:33 final size:34
Alignment explanation
Indices: 619777--619870 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
619767 TCGTTTCTCA
* *
619777 AAAACAAACTTTGTCTCGCTTGAGACAATTTC-T
1 AAAACAAATTTTGTCTCGCTTGAGACAATATCTT
** *
619810 AAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAACAAATTTTGTCTCGCTTGAGACAATATCTT
* *
619844 AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
619871 TCATTTCTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (34 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATATCTT
Found at i:620173 original size:27 final size:27
Alignment explanation
Indices: 620115--620213 Score: 155
Period size: 26 Copynumber: 3.6 Consensus size: 27
620105 TTTCTTTTGA
620115 GAAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAATCTTTGAGTTTGTTCCTCTT
620142 GAAAAAATC-TTGAGTTTGTTCCTCTT
1 GAAAAAATCTTTGAGTTTGTTCCTCTT
*
620168 GAAAAAATCTTTGAGTTTGTTCCTTTT
1 GAAAAAATCTTTGAGTTTGTTCCTCTT
*
620195 GAATAAAAATTTTTGAGTT
1 G-A-AAAAATCTTTGAGTT
620214 GTTTCGTTTG
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
26 26 0.39
27 26 0.39
28 1 0.01
29 14 0.21
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (27 bp):
GAAAAAATCTTTGAGTTTGTTCCTCTT
Found at i:620314 original size:52 final size:53
Alignment explanation
Indices: 620252--620354 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 53
620242 CTATTTATTT
*
620252 TGAAACAAAGTTTTGCCTCTCTTGAGACAATTTCGT-GAAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGCCTCTCTTGAGACAATTTCGTAAAAAAATCTTTGAGTC
* *
620304 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGCCTCTCTTGAGACAATTTCGTAAAAAAATCTTTGAG
620355 ATTGTTTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 34 0.72
53 13 0.28
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGCCTCTCTTGAGACAATTTCGTAAAAAAATCTTTGAGTC
Found at i:620390 original size:28 final size:29
Alignment explanation
Indices: 620334--620542 Score: 97
Period size: 30 Copynumber: 6.7 Consensus size: 29
620324 CTTGAGACAA
620334 TTTTGTAAA-AAAATCTTTGAGATTGTTTC
1 TTTTG-AAACAAAATCTTTGAGATTGTTTC
620363 TTTTGAAACAAAATC-TTGAG-TTGGTTTC
1 TTTTGAAACAAAATCTTTGAGATT-GTTTC
* * **
620391 TTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
1 TTTTGAAACAAAA-------TCT-TTGAGATTGTTTC
620428 TTTTGAAACAAAAATCTTTGAG-TCTGTTTC
1 TTTTGAAAC-AAAATCTTTGAGAT-TGTTTC
* * **
620458 TTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
1 TTTTGAAACAAAA-------TCT-TTGAGATTGTTTC
620495 TTTTGAAACAAAAATCTTTGAG-TCTGTTTC
1 TTTTGAAAC-AAAATCTTTGAGAT-TGTTTC
*
620525 TTTGGAAACAAAAT-TTTG
1 TTTTGAAACAAAATCTTTG
620543 TCTCTCTTAA
Statistics
Matches: 138, Mismatches: 17, Indels: 51
0.67 0.08 0.25
Matches are distributed among these distances:
27 2 0.01
28 29 0.21
29 22 0.16
30 32 0.23
31 6 0.04
35 2 0.01
36 3 0.02
37 32 0.23
38 10 0.07
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (29 bp):
TTTTGAAACAAAATCTTTGAGATTGTTTC
Found at i:620428 original size:37 final size:37
Alignment explanation
Indices: 620387--620570 Score: 143
Period size: 37 Copynumber: 5.3 Consensus size: 37
620377 CTTGAGTTGG
620387 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* **
620424 TTTCTTTTGAAACAAAAATCTTTG--AGTC-T--G----
1 TTTCTTTGGAAAC-AAAAT-TTTGTCTCTCTTAAGATAA
620454 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* **
620491 TTTCTTTTGAAACAAAAATCTTTG--AGTC-T--G----
1 TTTCTTTGGAAAC-AAAAT-TTTGTCTCTCTTAAGATAA
620521 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
620558 TTTCTTTTGGAAA
1 TTTC-TTTGGAAA
620571 AAATCTTTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 45
0.66 0.07 0.27
Matches are distributed among these distances:
28 8 0.07
29 10 0.09
30 28 0.25
31 2 0.02
33 2 0.02
34 2 0.02
36 2 0.02
37 32 0.29
38 18 0.16
39 8 0.07
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:620463 original size:67 final size:67
Alignment explanation
Indices: 620359--620590 Score: 402
Period size: 67 Copynumber: 3.5 Consensus size: 67
620349 TTTGAGATTG
620359 TTTCTTTTGAAAC-AAAATC-TTGAGT-TGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTGAAACAAAAATCTTTGAGTCT-GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
620421 TAA
65 TAA
620424 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
620489 AA
66 AA
620491 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
620556 AA
66 AA
* *
620558 TTTCTTTTG-GA-AAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
620591 CTTAAAATGA
Statistics
Matches: 162, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
65 34 0.21
66 7 0.04
67 120 0.74
68 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:620639 original size:64 final size:64
Alignment explanation
Indices: 620386--620660 Score: 261
Period size: 67 Copynumber: 4.2 Consensus size: 64
620376 TCTTGAGTTG
* * * * *
620386 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGT
1 GTTTCTTT-GAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTG-GA-AAAAATCTTTGAAT
620451 CT
63 CT
* * * * *
620453 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGT
1 GTTTCTTT-GAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTG-GA-AAAAATCTTTGAAT
620518 CT
63 CT
* * *
620520 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGGAAAAAATCTTTGAATCT
1 GTTTCTTT-GAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGGAAAAAATCTTTGAATCT
* * * *
620585 GTTTCTCTT-AAA-ATGAATTTTGTATCTCTTGAGACAGTTTCTCTT-GAAGTAAATCTTTGAAT
1 GTTTCT-TTGAAACA-AAATTTTGTATCTCTTAAGACAATTTCTCTTGGAA-AAAATCTTTGAAT
*
620647 AT
63 CT
620649 G-TTCATTTGAAA
1 GTTTC-TTTGAAA
620661 ATCTTTGAGT
Statistics
Matches: 193, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
63 9 0.05
64 46 0.24
65 21 0.11
66 3 0.02
67 114 0.59
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (64 bp):
GTTTCTTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGGAAAAAATCTTTGAATCT
Found at i:620706 original size:29 final size:26
Alignment explanation
Indices: 620658--620711 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
620648 TGTTCATTTG
* *
620658 AAAATCTTTGAGTTTGTTTCTCTTAAC
1 AAAATCTTTGAGTCTATTTCT-TTAAC
620685 AAAATCATCTTGAGTCTATTTCTTTAA
1 AAAATC-T-TTGAGTCTATTTCTTTAA
620712 AACAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 5 0.22
29 12 0.52
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (26 bp):
AAAATCTTTGAGTCTATTTCTTTAAC
Found at i:620949 original size:66 final size:66
Alignment explanation
Indices: 620812--620977 Score: 155
Period size: 66 Copynumber: 2.5 Consensus size: 66
620802 GTAATCCATT
* * * *
620812 TTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGGCAATTTCTTTTGAGAAAAAAAT
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAGAAAAAAAC
620877 C
66 C
* * * ** **
620878 ATTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTCTTTTGA-AAATACCC
1 TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAGAAA-A-AA
620941 ACC
64 ACC
620944 TTTGAGATC-GTTT-CTATT-AAAC-AAATTTTATCTC
1 TTTGAG-TCTGTTTCCT-TTGAAACAAAATTTTATCTC
620978 GCATGAGACA
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
64 14 0.17
65 22 0.27
66 45 0.55
67 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (66 bp):
TTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAGAAAAAAAC
C
Found at i:621640 original size:28 final size:27
Alignment explanation
Indices: 621605--621685 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 27
621595 GAAACACATT
621605 ATCTTTGAGCTTGTTTCTCTTGAAACAA
1 ATCTTTGAG-TTGTTTCTCTTGAAACAA
*
621633 ATCTTTGAGTCTGTTTCTTTTGAAACAA
1 ATCTTTGAGT-TGTTTCTCTTGAAACAA
*
621661 ATCTTTGAATTGGTTTCTCTTGAAA
1 ATCTTTGAGTT-GTTTCTCTTGAAA
621686 TCATAACTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
27 2 0.04
28 46 0.96
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (27 bp):
ATCTTTGAGTTGTTTCTCTTGAAACAA
Found at i:621907 original size:40 final size:40
Alignment explanation
Indices: 621850--622039 Score: 127
Period size: 40 Copynumber: 4.5 Consensus size: 40
621840 CAGTCGTCCC
* *
621850 CATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCTT
1 CATCACGTAGGAGCCGTGTCATCACCTGACCAGAACTCCT
* * *
621890 CATCACGTAAGAGCCGTGTCA--ACCGGATAACCAG-TCGTCCT
1 CATCACGTAGGAGCCGTGTCATCACC---TGACCAGAAC-TCCT
* * *
621931 CATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCCAAGAACTCTT
1 CATCACGTAGGAGCCGTGTCATCA--CCT---GA---CC-AGAACTCCT
* * * *
621980 CATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCT
1 CATCACGTAGGAGCCGTGTCATCACCTGACCAGAACTCCT
622020 CATCACGTAGGAGCCG-GTCA
1 CATCACGTAGGAGCCGTGTCA
622040 CCTTAGACAA
Statistics
Matches: 114, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
38 3 0.03
39 4 0.04
40 41 0.36
41 29 0.25
42 1 0.01
43 1 0.01
44 2 0.02
45 3 0.03
47 3 0.03
48 2 0.02
49 24 0.21
50 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (40 bp):
CATCACGTAGGAGCCGTGTCATCACCTGACCAGAACTCCT
Found at i:622034 original size:130 final size:131
Alignment explanation
Indices: 621691--622053 Score: 396
Period size: 134 Copynumber: 2.8 Consensus size: 131
621681 TGAAATCATA
* * * * * * * *
621691 ACTCCTAAAGATGGCCAGCCGTCCTCGTCACATAGGAACCGTGTCAT-TCCTCAACCAGACCTCC
1 ACTCCTAAAGATGGCCAGACGTCCCCATCACGTAGGAACAGTGTCATCACCT-GACCAGAACTCC
*
621755 TCATCACGTAGGAGCCGGGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTA
65 TCATCACGTAGGAGCC-GGTCAACC-TAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTA
621820 TCACC
128 TCA-C
* * *
621825 ACTCCTAAAGATGGCCAGTCGTCCCCATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCTT
1 ACTCCTAAAGATGGCCAGACGTCCCCATCACGTAGGAACAGTGTCATCACCTGACCAGAACTCCT
* * * *
621890 CATCACGTAAGAGCCGTGTCAACC-GGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATC
66 CATCACGTAGGAGCCG-GTCAACCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
621954 A-
130 AC
* ** * * * *
621955 TC-CCTAAAGATGGCCAAGAAC-TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTC
1 ACTCCTAAAGATGGCC-AG-ACGTCCCCATCACGTAGGAACAGTGTCATCACCTGACCAGAACTC
*
622018 CTCATCACGTAGGAGCCGGTC-ACCTTAGACAACCAG
64 CTCATCACGTAGGAGCCGGTCAACC-TAGATAACCAG
622054 ACCTCTTCAT
Statistics
Matches: 197, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
128 3 0.02
129 16 0.08
130 62 0.31
131 1 0.01
132 38 0.19
133 1 0.01
134 73 0.37
135 3 0.02
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (131 bp):
ACTCCTAAAGATGGCCAGACGTCCCCATCACGTAGGAACAGTGTCATCACCTGACCAGAACTCCT
CATCACGTAGGAGCCGGTCAACCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCA
C
Found at i:622246 original size:3 final size:3
Alignment explanation
Indices: 622240--622288 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
622230 TTTTTTTTAA
** *
622240 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
622287 TA
1 TA
622289 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:624785 original size:84 final size:86
Alignment explanation
Indices: 624688--624857 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 86
624678 GTTATCCTTC
624688 CTACACGTAACCGATTCCCGAATCCATTT-ATCGAATC-TTGGTGACGCATACCAAATTTTGTCT
1 CTACACGTAACCGATTCCCGAATCCATTTAATCGAATCTTTGGTGACGCATACCAAATTTTGTCT
624751 TATAAAATGATTTTTTTAAAA
66 TATAAAATGATTTTTTTAAAA
624772 CTACACGTAACCGATTCCCGAATCCATTTAATCGAATCTTTGGTGACGCATACCAAATTTTGTCT
1 CTACACGTAACCGATTCCCGAATCCATTTAATCGAATCTTTGGTGACGCATACCAAATTTTGTCT
624837 TATAAAATGATTTTTTTAAAA
66 TATAAAATGATTTTTTTAAAA
624858 TTGTTTTAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 29 0.35
85 8 0.10
86 47 0.56
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (86 bp):
CTACACGTAACCGATTCCCGAATCCATTTAATCGAATCTTTGGTGACGCATACCAAATTTTGTCT
TATAAAATGATTTTTTTAAAA
Found at i:629186 original size:44 final size:44
Alignment explanation
Indices: 629123--629211 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
629113 ACACATGAGC
629123 AGTGGCTATGAGTGCTAATCATGTGTACCATGCACAGTCGAAGT
1 AGTGGCTATGAGTGCTAATCATGTGTACCATGCACAGTCGAAGT
629167 AGTGGCTATGAGTGCTAATCATGTGTACCATGCACAGTCGAAGT
1 AGTGGCTATGAGTGCTAATCATGTGTACCATGCACAGTCGAAGT
629211 A
1 A
629212 TATAGATCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (44 bp):
AGTGGCTATGAGTGCTAATCATGTGTACCATGCACAGTCGAAGT
Found at i:635285 original size:140 final size:144
Alignment explanation
Indices: 635083--635366 Score: 508
Period size: 144 Copynumber: 2.0 Consensus size: 144
635073 AATTAATTAT
635083 TAAGAAATTTAAAATTTTGGCTATGATTAATTCGGTTCGAATCGATTGATTAATTGAATTAATCA
1 TAAGAAATTTAAAATTTTGGCTATGATTAATTCGGTTCGAATCGATTGATTAATTGAATTAATCA
635148 AAACATA-TTAATATTTACTTTAG-TTTT-TAT-TTTTAAGTTTGATTTCATTAAGAATCAAGAT
66 AAACATATTTAATATTTACTTTAGTTTTTATATATTTTAAGTTTGATTTCATTAAGAATCAAGAT
635209 CCACCAACGGGTTG
131 CCACCAACGGGTTG
635223 TAAGAAAATTT-AAATTTTGGCTATGATTAATGTCGGTTCGAATCGATTGATT-ATTGAATTAAT
1 TAAG-AAATTTAAAATTTTGGCTATGATTAAT-TCGGTTCGAATCGATTGATTAATTGAATTAAT
635286 CAAAACATATTTAATATTTACTTTAGTTTTTATATATTTTAAGTTTGATTTCATTAAGAATCAAG
64 CAAAACATATTTAATATTTACTTTAGTTTTTATATATTTTAAGTTTGATTTCATTAAGAATCAAG
635351 ATCCACCAACGGGTTG
129 ATCCACCAACGGGTTG
635367 GTTCAAGTGG
Statistics
Matches: 138, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
140 44 0.32
141 42 0.30
142 4 0.03
143 3 0.02
144 45 0.33
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.42
Consensus pattern (144 bp):
TAAGAAATTTAAAATTTTGGCTATGATTAATTCGGTTCGAATCGATTGATTAATTGAATTAATCA
AAACATATTTAATATTTACTTTAGTTTTTATATATTTTAAGTTTGATTTCATTAAGAATCAAGAT
CCACCAACGGGTTG
Found at i:641541 original size:28 final size:28
Alignment explanation
Indices: 641485--641541 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
641475 ATATTAATTT
* *
641485 ATATTCTATTATTTCAAAATTATATAAA
1 ATATTCTATTATTTCAAAAATATAGAAA
641513 ATATT-TATTTATTT-AAAAATATCAGAAA
1 ATATTCTA-TTATTTCAAAAATAT-AGAAA
641541 A
1 A
641542 GAACTTCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
ATATTCTATTATTTCAAAAATATAGAAA
Found at i:641688 original size:22 final size:25
Alignment explanation
Indices: 641663--641713 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
641653 ATTTTCTTTG
641663 ATATTGA-AAAATAA-ATAT-TAAA
1 ATATTGATAAAATAATATATGTAAA
*
641685 ATA-TGATAAAATAATTTATGTAAA
1 ATATTGATAAAATAATATATGTAAA
641709 ATATT
1 ATATT
641714 TAAATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.12
22 10 0.42
23 3 0.12
24 7 0.29
25 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
ATATTGATAAAATAATATATGTAAA
Found at i:643149 original size:3 final size:3
Alignment explanation
Indices: 643114--643183 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
643104 GGCCCGTTTG
* * * * * *
643114 TAA TAA TAT TATA TAA TAT TAG TAA TAAA TAA TAA TAT TAG TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
643161 TAA TTA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
643184 ATATATTTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:643189 original size:11 final size:11
Alignment explanation
Indices: 643114--643183 Score: 63
Period size: 12 Copynumber: 6.3 Consensus size: 11
643104 GGCCCGTTTG
*
643114 TAATAATATTA
1 TAATAATATAA
*
643125 T-ATAATATTAG
1 TAATAATA-TAA
643136 TAATAA-ATAA
1 TAATAATATAA
*
643146 TAATATTAGTAA
1 TAATAATA-TAA
*
643158 TTATAATTATAA
1 TAATAA-TATAA
643170 TAATAATATAA
1 TAATAATATAA
643181 TAA
1 TAA
643184 ATATATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
10 13 0.28
11 13 0.28
12 19 0.40
13 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TAATAATATAA
Found at i:643786 original size:113 final size:113
Alignment explanation
Indices: 643405--644083 Score: 808
Period size: 113 Copynumber: 6.0 Consensus size: 113
643395 TAGAGTCATT
* * *
643405 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCTTTTTTTTCTTCAGATGACGAGT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-----CTTCTTCAGAT---GAGT
*** * * * *
643470 TCTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
58 TCTTCTCATTATGAACTCGAACTGGAAATGCTGATCCATCGAATGATGAATTTAAG
643526 CAAAAGGTTGAACAA-TTCTTCTCATTATGAACTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * *
643589 TTATGAACTTTTTCTGGAAA-GCTGATCCATC-AAGAGATGGATTTGAG
66 TTATGAACTCGAACTGGAAATGCTGATCCATCGAA-TGATGAATTTAAG
* *
643636 CAAAAGGTTG-ACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
643700 TTATGAACTCGAACTGGAAATACTGAAT-CATCGAATGATGAATTCAAG
66 TTATGAACTCGAACTGGAAATGCTG-ATCCATCGAATGATGAATTTAAG
**
643748 CGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
643812 ATTATGAACTTGAACTGGTAATGCTGAATCC-TCGAATGATGAATTTAAG
65 ATTATGAACTCGAACTGGAAATGCTG-ATCCATCGAATGATGAATTTAAG
* **
643861 CGAAAA-TTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTC
1 C-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
643925 ATTATGAACTCGAACT-GTAATGCTGATCCATCGAATGATGGATTTGAG
65 ATTATGAACTCGAACTGGAAATGCTGATCCATCGAATGATGAATTTAAG
* *
643973 CAAAAGGTTGAACAAATTCTTCTCA-TATGAATTTCTTCTTTCCTTCTTCAGATGAGGTTCTTCT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGA-GTTCTTCT
* * *
644037 CATTATGAACTCGACCTGG-AATG-TGATCCATTGAATGATGGATTTAA
64 CATTATGAACTCGAACTGGAAATGCTGATCCATCGAATGATGAATTTAA
644084 ACTTTGCTAA
Statistics
Matches: 503, Mismatches: 41, Indels: 37
0.87 0.07 0.06
Matches are distributed among these distances:
109 6 0.01
110 58 0.12
111 83 0.17
112 100 0.20
113 206 0.41
114 8 0.02
115 3 0.01
120 25 0.05
121 14 0.03
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAATGCTGATCCATCGAATGATGAATTTAAG
Found at i:644508 original size:21 final size:22
Alignment explanation
Indices: 644482--644522 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
644472 CATAAAGTTT
*
644482 TCATCTTT-GAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTG
644503 TCATCTTTAAAAAGAGAATC
1 TCATCTTTAAAAAGAGAATC
644523 CATCTCTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTG
Found at i:646999 original size:83 final size:84
Alignment explanation
Indices: 646857--647112 Score: 430
Period size: 83 Copynumber: 3.1 Consensus size: 84
646847 ATTTCTACTA
646857 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCCA-ATCAGATAACTCAAAGA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA-CCAGATCAGATAACTCAAAGA
646921 ACACTTCCAGAAGATGCTAT
65 ACACTTCCAGAAGATGCTAT
*
646941 TG-GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
*
647005 CATTTCCAGAAGATGCTA-
66 CACTTCCAGAAGATGCTAT
*
647023 TGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGA
647087 ACACTTCCAGAAGATGCTAT
65 ACACTTCCAGAAGATGCTAT
*
647107 GGAGCA
1 TGAGCA
647113 CATTACATTT
Statistics
Matches: 162, Mismatches: 6, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
82 5 0.03
83 148 0.91
84 9 0.06
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.27
Consensus pattern (84 bp):
TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTAT
Done.