Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_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: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:526901 original size:23 final size:22
Alignment explanation
Indices: 526875--526945 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
526865 ATGATATAAG
526875 ATATATATAATAAAAATAATATA
1 ATATATATAATAAAAA-AATATA
* *
526898 ATATAAATAAAAAAAGAGGAATATA
1 ATATATATAATAAAA-A--AATATA
* *
526923 GTAAATA-AATAAAAAAATATA
1 ATATATATAATAAAAAAATATA
526944 AT
1 AT
526946 TAAAAATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.18
23 14 0.37
24 7 0.18
25 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.27
Consensus pattern (22 bp):
ATATATATAATAAAAAAATATA
Found at i:528282 original size:36 final size:36
Alignment explanation
Indices: 528235--528493 Score: 207
Period size: 36 Copynumber: 7.3 Consensus size: 36
528225 TTTTTTTGTA
* *
528235 TTTCAAGAGAAACTGTCTCAAGAGGGACAAAATTTG
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
528271 TTTCAAAAGAAATTGTTTCAAGAGAGACAAAACTTAG
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* *
528308 -TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 TTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
528344 TTTCAAGGAA-AAGA-TAT-TC-A-A-AG----ATTTTG
1 TTTCAA--AAGAA-ACTGTCTCAAGAGAGACAAAATTTG
**
528373 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
** *
528409 TTTCAAGGGAAACTGTCTCAAGAGAGACAATATTTTG
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAA-AATTTG
** * **
528446 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
*
528482 TTTCAAAGGAAA
1 TTTCAAAAGAAA
528494 TGTTTTCAAT
Statistics
Matches: 183, Mismatches: 23, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 4 0.02
29 13 0.07
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
36 87 0.48
37 68 0.37
38 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:528446 original size:102 final size:102
Alignment explanation
Indices: 528267--528453 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
528257 AGGGACAAAA
* * *
528267 TTTGTTTCAAAAGAAATTGTTTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
528332 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * **
528369 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAGA
528432 GAGAC-AATATTTTGTTTCAAGG
65 GAGACGAA-A-TTTGTTTCAAGG
528454 GAAACTATCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 3 0.04
101 27 0.36
102 44 0.59
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:528515 original size:102 final size:102
Alignment explanation
Indices: 528407--528622 Score: 351
Period size: 102 Copynumber: 2.1 Consensus size: 102
528397 AGACAAAATT
* * *
528407 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGAG
528472 ACAAAATTAATTTCAAAGGAAATGTTTTCAATGTTTA
66 ACAAAATTAATTTCAAAGGAAATGTTTTCAATGTTTA
* * *
528509 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGAG
* * *
528574 ATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTAATTTCAAAGGAAATGTTTTCAATGTTTA
528611 TGTTTCAAGGGA
1 TGTTTCAAGGGA
528623 GACAAAATTT
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGAGAG
ACAAAATTAATTTCAAAGGAAATGTTTTCAATGTTTA
Found at i:528560 original size:37 final size:36
Alignment explanation
Indices: 528509--528595 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
528499 TCAATGTTTA
* ** * *
528509 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAA-TT
*
528546 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
*
528582 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
528596 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
Found at i:528588 original size:138 final size:137
Alignment explanation
Indices: 528235--528595 Score: 422
Period size: 138 Copynumber: 2.6 Consensus size: 137
528225 TTTTTTTGTA
** * *
528235 TTTCAAGAGAAACTGTCTCAAGAGG-GACAAAATTTGTTTCAAAAGAAATTGTTTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAG-GGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * ** * * * **
528299 AAAACTTAGTTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAGATATTCA
65 AAAATTTATTTC-AAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGAAAAGATATTCA
528364 AAGATTTTG
129 AAGATTTTG
* *
528373 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
* * * *
528438 ATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGGAAATG-TTTTCA
66 A-AATTTATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTC-AAGGAAAAGATATTCA
*
528502 ATG-TTTATG
129 AAGATTT-TG
** * * *
528511 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGAT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
528576 AAAATTTATTTCAAGGGAAA
65 AAAATTTATTTCAAGGGAAA
528596 TGTTTTCAAT
Statistics
Matches: 189, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
137 4 0.02
138 142 0.75
139 43 0.23
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (137 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
AAATTTATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAGGAAAAGATATTCAAA
GATTTTG
Found at i:528619 original size:87 final size:87
Alignment explanation
Indices: 528528--528706 Score: 313
Period size: 87 Copynumber: 2.1 Consensus size: 87
528518 AGAAACTGTC
* *
528528 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
528593 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * *
528615 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
528680 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
528702 TCAAG
1 TCAAG
528707 AGAAACTGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:529149 original size:106 final size:106
Alignment explanation
Indices: 528964--529317 Score: 476
Period size: 106 Copynumber: 3.3 Consensus size: 106
528954 TGTATTGTTC
* * * * * **
528964 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * ** * *
529029 GCCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGATGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
529070 CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGCAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
529135 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
529176 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
529241 ACCAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
529282 CGAGTGGCACGATATCCTTCG-TCGTGGAGTTGAAAT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAAT
529318 CGCAGGTGGC
Statistics
Matches: 221, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
106 196 0.89
108 2 0.01
109 23 0.10
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:529934 original size:32 final size:32
Alignment explanation
Indices: 529848--529935 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
529838 TTTGCATCAG
* * *
529848 GATGTTGAAT-TCCCAAAGATGCTCCAATATTC
1 GATGTTGAATCT-ACAAAGATGCCCCAACATTC
* * *
529880 GATGTTGAATCTAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTACAAAGATGCCCCAACATTC
*
529912 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTACAAAGATGCCC
529936 TCATTGTTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTACAAAGATGCCCCAACATTC
Found at i:530980 original size:69 final size:69
Alignment explanation
Indices: 530865--531002 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
530855 TCTCTCTCTC
* * * *
530865 TTGATGCTTCATGATCTTCTAGTGGAGTGATTCAGTAATTTAGAAATGATTGTGATTGATCAATT
1 TTGATGCTTCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGATTGATCAATA
530930 TCAT
66 TCAT
* * * *
530934 TTGATGC-TCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAAT
1 TTGATGCTTC-ATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGATTGATCAAT
530998 ATCAT
65 ATCAT
531003 AGTTTGAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 2 0.03
69 58 0.97
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (69 bp):
TTGATGCTTCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGATTGATCAATA
TCAT
Found at i:531108 original size:25 final size:24
Alignment explanation
Indices: 531074--531131 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
531064 TTTTTCTTCA
*
531074 ATTTTCCTTTGTTTTTTTCTTTTT
1 ATTTTCCTTTGTTTTTTTCTCTTT
531098 ATTTTCTCTTTGTTTTTTTCTCTTT
1 ATTTTC-CTTTGTTTTTTTCTCTTT
531123 -TTTTCCTTT
1 ATTTTCCTTT
531132 TTGCTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 4 0.12
24 11 0.34
25 17 0.53
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (24 bp):
ATTTTCCTTTGTTTTTTTCTCTTT
Found at i:531126 original size:13 final size:13
Alignment explanation
Indices: 531075--531126 Score: 63
Period size: 12 Copynumber: 4.1 Consensus size: 13
531065 TTTTCTTCAA
*
531075 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
531087 TTTT-TCTTTTTA
1 TTTTCTCTTTTTT
531099 TTTTCTCTTTGTTT
1 TTTTCTCTTT-TTT
531113 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
531126 T
1 T
531127 CCTTTTTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 13 0.38
13 9 0.26
14 12 0.35
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:534296 original size:19 final size:19
Alignment explanation
Indices: 534218--534305 Score: 56
Period size: 19 Copynumber: 4.5 Consensus size: 19
534208 CAAACGTGAG
*
534218 AATAATAAATA-AAACAAGA
1 AATAATAAAAATAAACAA-A
*
534237 AAAAATAGAAAAT-AACAAA
1 AATAATA-AAAATAAACAAA
** * *
534256 ACGAGTAAAAAATAATATAAA
1 AATAAT-AAAAATAA-ACAAA
534277 AATAATAAAAATAAAC-AA
1 AATAATAAAAATAAACAAA
534295 AATGAATAAAA
1 AAT-AATAAAA
534306 TGTTAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
18 5 0.09
19 23 0.43
20 18 0.34
21 7 0.13
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.16
Consensus pattern (19 bp):
AATAATAAAAATAAACAAA
Found at i:534668 original size:2 final size:2
Alignment explanation
Indices: 534661--534705 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
534651 TTAATACATC
*
534661 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
534702 TA TA
1 TA TA
534706 ATTAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:534718 original size:25 final size:27
Alignment explanation
Indices: 534670--534720 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
534660 CTATATATAT
* *
534670 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
534697 ATATATATA-AT-TAAAATAATATAA
1 ATATATATATATATAAAATAATATAA
534721 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 2 0.09
27 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:539119 original size:16 final size:16
Alignment explanation
Indices: 539098--539167 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
539088 GTATTACCCG
*
539098 ACCTGTTTTCAACCTA
1 ACCTGTTTTTAACCTA
539114 ACCTGTTTTTAACC-A
1 ACCTGTTTTTAACCTA
*
539129 GACCTGTTTTTAACCTG
1 -ACCTGTTTTTAACCTA
*
539146 ACCTGTTTTTAACCTG
1 ACCTGTTTTTAACCTA
539162 ACCTGT
1 ACCTGT
539168 AAATGATCCG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.02
16 49 0.98
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.40
Consensus pattern (16 bp):
ACCTGTTTTTAACCTA
Found at i:539138 original size:32 final size:32
Alignment explanation
Indices: 539097--539167 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
539087 GGTATTACCC
539097 GACCTGTTTTCAACCTAACCTGTTTTTAACCA
1 GACCTGTTTTCAACCTAACCTGTTTTTAACCA
* * *
539129 GACCTGTTTTTAACCTGACCTGTTTTTAACCT
1 GACCTGTTTTCAACCTAACCTGTTTTTAACCA
539161 GACCTGT
1 GACCTGT
539168 AAATGATCCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (32 bp):
GACCTGTTTTCAACCTAACCTGTTTTTAACCA
Found at i:539387 original size:9 final size:9
Alignment explanation
Indices: 539373--539402 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
539363 ATAAAATTAT
539373 TTAATAAAA
1 TTAATAAAA
539382 TTAATAAAA
1 TTAATAAAA
539391 TTAATAAAA
1 TTAATAAAA
539400 TTA
1 TTA
539403 TTTAAATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TTAATAAAA
Found at i:539645 original size:21 final size:21
Alignment explanation
Indices: 539607--539659 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
539597 TTATATTATG
**
539607 GTTTATGATTTAGTGTTTAGT
1 GTTTATGATTTAAAGTTTAGT
*
539628 GTTTATGGTTTAAAGTTTAAG-
1 GTTTATGATTTAAAGTTT-AGT
*
539649 GTTTAGGATTT
1 GTTTATGATTT
539660 CTTTAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (21 bp):
GTTTATGATTTAAAGTTTAGT
Found at i:539754 original size:15 final size:15
Alignment explanation
Indices: 539734--539787 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
539724 TAATTTATTT
539734 TATATAGTTTATATA
1 TATATAGTTTATATA
*
539749 TATATA-TACTATACATA
1 TATATAGT--T-TATATA
539766 TATATAGTTTATATA
1 TATATAGTTTATATA
539781 TACTATA
1 TA-TATA
539788 CATGGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.03
15 13 0.41
16 6 0.19
17 11 0.34
18 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:539761 original size:13 final size:13
Alignment explanation
Indices: 539745--539787 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
539735 ATATAGTTTA
539745 TATATATATATAC
1 TATATATATATAC
*
539758 TATACATATATA-
1 TATATATATATAC
*
539770 TAGTTTATATATAC
1 TA-TATATATATAC
539784 TATA
1 TATA
539788 CATGGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (13 bp):
TATATATATATAC
Found at i:539795 original size:20 final size:21
Alignment explanation
Indices: 539753--539807 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
539743 TATATATATA
*
539753 TATACTATACATATATATAGTT
1 TATA-TATACATATACATAGTT
*
539775 TATATATAC-TATACATGGTT
1 TATATATACATATACATAGTT
*
539795 TATACATACATAT
1 TATATATACATAT
539808 TATATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.59
21 8 0.28
22 4 0.14
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (21 bp):
TATATATACATATACATAGTT
Found at i:539821 original size:13 final size:13
Alignment explanation
Indices: 539811--539837 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
539801 TACATATTAT
539811 ATAAAATTATTTA
1 ATAAAATTATTTA
539824 ATAAAATTATTTA
1 ATAAAATTATTTA
539837 A
1 A
539838 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:539847 original size:15 final size:14
Alignment explanation
Indices: 539811--539853 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
539801 TACATATTAT
539811 ATAAAATTATTT-A
1 ATAAAATTATTTAA
539824 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
539838 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
539853 A
1 A
539854 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:539960 original size:20 final size:19
Alignment explanation
Indices: 539935--539972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
539925 TGTCATATTA
*
539935 ATTTTATTTGCATGATTAGC
1 ATTTTAGTTGCATG-TTAGC
539955 ATTTTAGTTGCATGTTAG
1 ATTTTAGTTGCATGTTAG
539973 GTTAATTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (19 bp):
ATTTTAGTTGCATGTTAGC
Found at i:540145 original size:7 final size:7
Alignment explanation
Indices: 540133--540214 Score: 60
Period size: 7 Copynumber: 11.7 Consensus size: 7
540123 TTTACATTAG
540133 GGTTTAT
1 GGTTTAT
540140 GGTTTA-
1 GGTTTAT
540146 GTGTTTA-
1 G-GTTTAT
540153 GTGTTTAT
1 G-GTTTAT
*
540161 GGTTTAA
1 GGTTTAT
*
540168 AGTTTAT
1 GGTTTAT
* *
540175 GATTTAG
1 GGTTTAT
540182 GGTTTAT
1 GGTTTAT
* *
540189 GATTTAG
1 GGTTTAT
540196 GGTTTAT
1 GGTTTAT
* *
540203 GATTTAG
1 GGTTTAT
540210 GGTTT
1 GGTTT
540215 CTATAAACTA
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
6 1 0.02
7 56 0.97
8 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (7 bp):
GGTTTAT
Found at i:540151 original size:14 final size:14
Alignment explanation
Indices: 540135--540214 Score: 99
Period size: 14 Copynumber: 5.7 Consensus size: 14
540125 TACATTAGGG
*
540135 TTTATGGTTTAGTG-
1 TTTAGGGTTTA-TGA
* *
540149 TTTAGTGTTTATGG
1 TTTAGGGTTTATGA
**
540163 TTTAAAGTTTATGA
1 TTTAGGGTTTATGA
540177 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
540191 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
540205 TTTAGGGTTT
1 TTTAGGGTTT
540215 CTATAAACTA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
13 2 0.03
14 56 0.97
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:541028 original size:30 final size:31
Alignment explanation
Indices: 540963--541028 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
540953 GAAAAAAATT
* *
540963 AATAGGATTACTTTTTAAATGTAATTAAAAA
1 AATATGATTACTTTTTAAATATAATTAAAAA
* *
540994 AATATGATTACTTTTTAAATATTA-TAATAA
1 AATATGATTACTTTTTAAATATAATTAAAAA
541024 AATAT
1 AATAT
541029 TTATTATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (31 bp):
AATATGATTACTTTTTAAATATAATTAAAAA
Found at i:541152 original size:22 final size:23
Alignment explanation
Indices: 541116--541160 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
541106 TAATGCAAAG
541116 GAAAATTAATATAGTTTAATTTA
1 GAAAATTAATATAGTTTAATTTA
541139 GAAAATT-ATATAGTTTAATTTA
1 GAAAATTAATATAGTTTAATTTA
541161 TATAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (23 bp):
GAAAATTAATATAGTTTAATTTA
Found at i:541353 original size:21 final size:21
Alignment explanation
Indices: 541329--541396 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
541319 TCCATTTATA
541329 TTAGGGTTTATGGTTTAGGAT
1 TTAGGGTTTATGGTTTAGGAT
** * *
541350 TTAGTATTTTTGGTTTA-AAGT
1 TTAGGGTTTATGGTTTAGGA-T
* *
541371 TTAGGGTTTAGGGTTTAGGGT
1 TTAGGGTTTATGGTTTAGGAT
541392 TTAGG
1 TTAGG
541397 TTTCTATAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAGGAT
Found at i:541379 original size:7 final size:7
Alignment explanation
Indices: 541369--541396 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
541359 TTGGTTTAAA
541369 GTTTAGG
1 GTTTAGG
541376 GTTTAGG
1 GTTTAGG
541383 GTTTAGG
1 GTTTAGG
541390 GTTTAGG
1 GTTTAGG
541397 TTTCTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:541395 original size:14 final size:14
Alignment explanation
Indices: 541329--541396 Score: 64
Period size: 14 Copynumber: 4.9 Consensus size: 14
541319 TCCATTTATA
*
541329 TTAGGGTTTATGGT
1 TTAGGGTTTAGGGT
* **
541343 TTAGGATTTAGTAT
1 TTAGGGTTTAGGGT
** **
541357 TTTTGGTTTAAAGT
1 TTAGGGTTTAGGGT
541371 TTAGGGTTTAGGGT
1 TTAGGGTTTAGGGT
541385 TTAGGGTTTAGG
1 TTAGGGTTTAGG
541397 TTTCTATAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTAGGGT
Found at i:541626 original size:2 final size:2
Alignment explanation
Indices: 541615--541741 Score: 58
Period size: 2 Copynumber: 66.0 Consensus size: 2
541605 ATAATATTTC
* *
541615 TA TA -A TA TA TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
541654 TA T- TA GT- TA TA CA TA CA TA TA TA TA CTA TA T- TA -A TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
541693 TT TA TA AA CTA TA TA T- TT TA TA TA GTT TA TA TA CA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
541736 TA TA TA
1 TA TA TA
541742 GAAAATTAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 30
0.66 0.12 0.21
Matches are distributed among these distances:
1 10 0.11
2 77 0.83
3 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:541739 original size:25 final size:24
Alignment explanation
Indices: 541673--541742 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
541663 TACATACATA
*
541673 TATATACTATAT-TA-ATATAATT
1 TATATACTATATATATATATAGTT
* *
541695 TATAAACTATATATTTTATATAGTT
1 TATATACTATATA-TATATATAGTT
541720 TATATACATATATATATATATAG
1 TATATAC-TATATATATATATAG
541743 AAAATTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.28
24 1 0.03
25 21 0.54
26 6 0.15
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (24 bp):
TATATACTATATATATATATAGTT
Found at i:541995 original size:19 final size:19
Alignment explanation
Indices: 541927--542005 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
541917 AATAAAATCT
*
541927 AATTATCAATTTCCCTCCAA
1 AATTATCAATTTCCCT-CTA
* **
541947 AATTTTTTA-TTCCCTCTA
1 AATTATCAATTTCCCTCTA
*
541965 AATTTCTCAATTTCCCTCTA
1 AA-TTATCAATTTCCCTCTA
*
541985 AATTATCAATTTCCCTATA
1 AATTATCAATTTCCCTCTA
542004 AA
1 AA
542006 AAAATTCACA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 4 0.08
19 27 0.56
20 17 0.35
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTATCAATTTCCCTCTA
Found at i:542073 original size:2 final size:2
Alignment explanation
Indices: 542066--542240 Score: 63
Period size: 2 Copynumber: 90.0 Consensus size: 2
542056 ACTTTGAATA
* *
542066 AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AA AT -T AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
542106 AT AC AT AT AT AGT TT AT AT AT AT AGT TT AT AT AT AT AGT -T CAT
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT -AT
* * *
542149 AT AA AC AT A- AT TT AT AT AT AT A- ACT -T AT A- AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
542186 AT AGT TT AT A- AT AT AA AT AT AGT TT AT AT AT AA ACT -T AT AT
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
542227 -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
542241 TTTTTTCAAT
Statistics
Matches: 127, Mismatches: 23, Indels: 46
0.65 0.12 0.23
Matches are distributed among these distances:
1 14 0.11
2 106 0.83
3 7 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:542113 original size:28 final size:30
Alignment explanation
Indices: 542063--542200 Score: 105
Period size: 28 Copynumber: 4.8 Consensus size: 30
542053 CTCACTTTGA
*
542063 ATAATATATATA-TATATATATATA-TTAAT
1 ATAA-ATATATAGTTTATATATATACTTAAT
* *
542092 ATAAAT-TATAGTTTATACATATA--TAGT
1 ATAAATATATAGTTTATATATATACTTAAT
* * * *
542119 TTATATATATAGTTTATATATATAGTTCAT
1 ATAAATATATAGTTTATATATATACTTAAT
*
542149 ATAAACATA-A-TTTATATATATAACTT-AT
1 ATAAATATATAGTTTATATATAT-ACTTAAT
*
542177 AATAATTATATAGTTTATA-ATATA
1 -ATAAATATATAGTTTATATATATA
542201 AATATAGTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
27 11 0.13
28 41 0.47
29 16 0.18
30 13 0.15
31 6 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (30 bp):
ATAAATATATAGTTTATATATATACTTAAT
Found at i:542126 original size:13 final size:13
Alignment explanation
Indices: 542066--542170 Score: 88
Period size: 13 Copynumber: 7.7 Consensus size: 13
542056 ACTTTGAATA
*
542066 ATATATATA-TAT
1 ATATATATAGTTT
542078 ATATATATA-TTAAT
1 ATATATATAGTT--T
*
542092 ATAAATTATAGTTT
1 ATATA-TATAGTTT
542106 ATACATATATAGTTT
1 AT--ATATATAGTTT
542121 ATATATATAGTTT
1 ATATATATAGTTT
542134 ATATATATAGTTCAT
1 ATATATATAGTT--T
* * *
542149 ATAAACATAATTT
1 ATATATATAGTTT
542162 ATATATATA
1 ATATATATA
542171 ACTTATAATA
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
12 10 0.13
13 31 0.40
14 8 0.10
15 24 0.31
16 4 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATATATAGTTT
Found at i:542171 original size:13 final size:13
Alignment explanation
Indices: 542063--542232 Score: 79
Period size: 13 Copynumber: 13.2 Consensus size: 13
542053 CTCACTTTGA
*
542063 ATAATATATATAT
1 ATAATTTATATAT
*
542076 AT-ATATATATAT
1 ATAATTTATATAT
* *
542088 -TAATATAAAT-T
1 ATAATTTATATAT
*
542099 ATAGTTTATACATAT
1 ATAATTTAT--ATAT
*
542114 ATAGTTTATATAT
1 ATAATTTATATAT
*
542127 ATAGTTTATATAT
1 ATAATTTATATAT
* * *
542140 ATAGTTCATATAAAC
1 ATAATT--TATATAT
542155 ATAATTTATATAT
1 ATAATTTATATAT
*
542168 ATAA-CT-TATA-
1 ATAATTTATATAT
*
542178 ATAATTATATAGTTT
1 ATAATT-TATA-TAT
*
542193 ATAA--TATAAAT
1 ATAATTTATATAT
*
542204 ATAGTTTATATAT
1 ATAATTTATATAT
*
542217 A-AACTTATATTAT
1 ATAATTTATA-TAT
542230 ATA
1 ATA
542233 TATTATATTT
Statistics
Matches: 123, Mismatches: 18, Indels: 31
0.72 0.10 0.18
Matches are distributed among these distances:
10 4 0.03
11 10 0.08
12 34 0.28
13 47 0.38
14 4 0.03
15 24 0.20
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (13 bp):
ATAATTTATATAT
Found at i:545066 original size:24 final size:24
Alignment explanation
Indices: 545039--545153 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
545029 CATAATTCAT
* * *
545039 GTCAAGCATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
545063 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* *
545087 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAA
*
545111 GTCATA-TATCAAATCAGAAT-CAA
1 GTCA-AGTATCATATCAGAATCCAA
*
545134 TGTCAAGTATCAGATCAGAA
1 -GTCAAGTATCATATCAGAA
545154 ATCAAATAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.04
24 76 0.95
25 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:545121 original size:48 final size:48
Alignment explanation
Indices: 545037--545153 Score: 157
Period size: 48 Copynumber: 2.4 Consensus size: 48
545027 ACCATAATTC
* * * *
545037 ATGTCAAGCATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCA
1 ATGTCAAGTATCAGATCAGAATCCAGGTCAAGTATCAAATCAGAAT-CA
*
545086 A-GTCAAGTATCAGATCAGAATCCATGTCATA-TATCAAATCAGAATCA
1 ATGTCAAGTATCAGATCAGAATCCAGGTCA-AGTATCAAATCAGAATCA
545133 ATGTCAAGTATCAGATCAGAA
1 ATGTCAAGTATCAGATCAGAA
545154 ATCAAATAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
47 3 0.05
48 56 0.92
49 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (48 bp):
ATGTCAAGTATCAGATCAGAATCCAGGTCAAGTATCAAATCAGAATCA
Found at i:552698 original size:7 final size:7
Alignment explanation
Indices: 552677--552766 Score: 62
Period size: 7 Copynumber: 12.4 Consensus size: 7
552667 ACACAAAAGG
552677 AAAGTAAA
1 AAAG-AAA
552685 AATAGAAA
1 AA-AGAAA
552693 AAAG--A
1 AAAGAAA
552698 AAA-AAA
1 AAAGAAA
*
552704 ATAGAAA
1 AAAGAAA
552711 AAAGAAA
1 AAAGAAA
552718 AAA-AGAA
1 AAAGA-AA
*
552725 AGAGAAA
1 AAAGAAA
*
552732 ACAGAAGAA
1 AAAG-A-AA
552741 AAAGAAAA
1 AAAG-AAA
552749 AAAGAAA
1 AAAGAAA
552756 AAAGAAGA
1 AAAGAA-A
552764 AAA
1 AAA
552767 TAGACAGATC
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
5 4 0.06
6 4 0.06
7 32 0.47
8 19 0.28
9 9 0.13
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:552705 original size:18 final size:18
Alignment explanation
Indices: 552682--552758 Score: 93
Period size: 18 Copynumber: 4.2 Consensus size: 18
552672 AAAGGAAAGT
552682 AAAAATAGAAAAAAGAAA
1 AAAAATAGAAAAAAGAAA
552700 AAAAATAGAAAAAAGAAA
1 AAAAATAGAAAAAAGAAA
* *
552718 AAAAGAAAGAGAAAACAGAAG
1 AAAA-ATAGA-AAAA-AGAAA
*
552739 AAAAAGA-AAAAAAGAAA
1 AAAAATAGAAAAAAGAAA
552756 AAA
1 AAA
552759 GAAGAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.13
18 26 0.50
19 5 0.10
20 6 0.12
21 8 0.15
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAATAGAAAAAAGAAA
Found at i:552739 original size:24 final size:24
Alignment explanation
Indices: 552691--552766 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
552681 TAAAAATAGA
* *
552691 AAAAAGAAAAAAA-ATAGAAAAAAG
1 AAAAAGAAAAAAAGA-AAAAAGAAG
* *
552715 AAAAA-AAGAAAGAGAAAACAGAAG
1 AAAAAGAA-AAAAAGAAAAAAGAAG
552739 AAAAAGAAAAAAAGAAAAAAGAAG
1 AAAAAGAAAAAAAGAAAAAAGAAG
552763 AAAA
1 AAAA
552767 TAGACAGATC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
23 2 0.05
24 38 0.88
25 3 0.07
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (24 bp):
AAAAAGAAAAAAAGAAAAAAGAAG
Found at i:553440 original size:28 final size:29
Alignment explanation
Indices: 553408--553468 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
553398 ACATATTGCC
*
553408 TCCCCAAATTGACCTGAAACACATTA-CT
1 TCCCCAAATTAACCTGAAACACATTACCT
553436 TCCCCAAATTAACCTGAAACACATTACCT
1 TCCCCAAATTAACCTGAAACACATTACCT
553465 TCCC
1 TCCC
553469 AAGGAATCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 25 0.81
29 6 0.19
ACGTcount: A:0.34, C:0.36, G:0.05, T:0.25
Consensus pattern (29 bp):
TCCCCAAATTAACCTGAAACACATTACCT
Found at i:553759 original size:54 final size:53
Alignment explanation
Indices: 553695--554045 Score: 349
Period size: 54 Copynumber: 6.6 Consensus size: 53
553685 TGTTTTTTTG
** * *
553695 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGA-TATTTTCAAATGA-ATTTTAAA
* ** * *
553750 GAAAC-AAGTCTGATTGTCAGAAGTTTC---AT-TTTT-AAATGACCTTTCAAA
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGA-ATTTTAAA
* * * *
553798 GAAACTAAGTCTGATTTTTAAGGGTTTCTTGATGTTTTCAAATGAATTTGAAA
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAA
* * * * * *
553851 GAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATAAATTTTTAAA
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAA-TTTTAAA
* * *
553905 GAAATTAAGCCTGAATTTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAA
1 GAAACTAAGTCTG-ATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTT-AAA
553959 GAAACTAAG-CTTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTTAAA
1 GAAACTAAGTC-TGATTTTCAGGGGTTTCTTGATATTTTCAAATGAA-TTTTAAA
* * *
554013 GAAACTAAGTCTAATTTTTAGGAGTTTCTTGAT
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGAT
554046 GATAACTGAA
Statistics
Matches: 257, Mismatches: 26, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
48 18 0.07
49 21 0.08
51 1 0.00
52 2 0.01
53 61 0.24
54 139 0.54
55 15 0.06
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (53 bp):
GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAA
Found at i:553868 original size:53 final size:54
Alignment explanation
Indices: 553795--554046 Score: 355
Period size: 54 Copynumber: 4.7 Consensus size: 54
553785 ATGACCTTTC
* * * *
553795 AAAGAAACTAAGTCTGATTTTTAAGGGTTTCTTGATGTTTTCAAATGAA-TTTG
1 AAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTT
* *
553848 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATAAATTTTT
1 AAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTT
* *
553902 AAAGAAATTAAGCCTGAA-TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTC
1 AAAGAAACTAAGCCT-AATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTT
* * * *
553956 AAAGAAACTAAGCTTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTT
1 AAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTT
* *
554010 AAAGAAACTAAGTCTAATTTTTAGGAGTTTCTTGATG
1 AAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG
554047 ATAACTGAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
53 45 0.26
54 127 0.73
55 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (54 bp):
AAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTT
Found at i:553997 original size:108 final size:107
Alignment explanation
Indices: 553695--554104 Score: 381
Period size: 108 Copynumber: 3.8 Consensus size: 107
553685 TGTTTTTTTG
** ** *
553695 GAAACTAAGTCTG-ATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAAC-AAG
1 GAAACTAAGTCTGAATTTT-AGGGGTTTCTTGA-TGTTTTCAAATGA-ATTTTAAAGAAACTAAG
* ** * ** *
553758 -TCTGATTGTCAGAAGTTTC---AT-TTTT-AAATGACCTTTCAAA
63 CT-TGATTTTCAGGGGTTTCTTGATATTTTCAAATAAATTTTTAAA
* * * * *
553798 GAAACTAAGTCTGATTTTTAAGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCT
1 GAAACTAAGTCTGAATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAACTAAGCTT
* * *
553863 AATTTTTAGGGGTTTCTTGATGTTTTCAAATAAATTTTTAAA
66 GATTTTCAGGGGTTTCTTGATATTTTCAAATAAATTTTTAAA
* *
553905 GAAATTAAGCCTGAATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAACTAAGCT
1 GAAACTAAGTCTGAATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTT-AAAGAAACTAAGCT
*
553970 TGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTTAAA
65 TGATTTTCAGGGGTTTCTTGATATTTTCAAATAAATTTTTAAA
* ***
554013 GAAACTAAGTCT-AATTTTTAGGAGTTTCTTGATGATAACTGAAAAATGAAAGATTTT-AAGAAA
1 GAAACTAAGTCTGAA-TTTTAGGGGTTTCTTGATG-T---TTTCAAATG--A-ATTTTAAAGAAA
*
554076 CTAAGCTTGATTTTCAAGGGTTTCTTGAT
58 CTAAGCTTGATTTTCAGGGGTTTCTTGAT
554105 GAATAAGTCT
Statistics
Matches: 253, Mismatches: 37, Indels: 24
0.81 0.12 0.08
Matches are distributed among these distances:
101 10 0.04
102 26 0.10
103 23 0.09
104 4 0.02
105 2 0.01
106 4 0.02
107 58 0.23
108 79 0.31
109 1 0.00
112 6 0.02
113 34 0.13
114 1 0.00
115 5 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (107 bp):
GAAACTAAGTCTGAATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAACTAAGCTT
GATTTTCAGGGGTTTCTTGATATTTTCAAATAAATTTTTAAA
Found at i:554089 original size:59 final size:54
Alignment explanation
Indices: 553795--554106 Score: 203
Period size: 54 Copynumber: 5.7 Consensus size: 54
553785 ATGACCTTTC
*** *
553795 AAAGAAACTAAG-TCTGATTTTTAAGGGTTTCTTGATG-TTTTCAAATG-AATTTG
1 AAAGAAACTAAGCT-TGA-TTTTAAGGGTTTCTTGATGATTGAAAAATGAAATTTT
* * * * ***
553848 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAAT-AAATTTTT
1 AAAGAAACTAAGCTTGA-TTTTAAGGGTTTCTTGATGATTGAAAAATGAAA-TTTT
* * * ***
553902 AAAGAAATTAAGCCTGAATTTTAGGGGTTTCTTGATG-TTTTCAAATG-AATTTT
1 AAAGAAACTAAGCTTG-ATTTTAAGGGTTTCTTGATGATTGAAAAATGAAATTTT
* *** *
553955 CAAAGAAACTAAGCTTGATTTTCAGGGGTTTCTTGAT-ATTTTCAAATGAATTTTT
1 -AAAGAAACTAAGCTTGATTTT-AAGGGTTTCTTGATGATTGAAAAATGAAATTTT
* *
554010 AAAGAAACTAAG-TCTAATTTTTAGGAGTTTCTTGATGATAACTGAAAAATGAAAGATTTT
1 AAAGAAACTAAGCT-TGATTTTAAGG-GTTTCTTGATGAT---TGAAAAATG-AA-ATTTT
554070 -AAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 AAAGAAACTAAGCTTGATTTT-AAGGGTTTCTTGATGA
554107 ATAAGTCTTT
Statistics
Matches: 220, Mismatches: 20, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
53 55 0.25
54 112 0.51
55 8 0.04
58 6 0.03
59 31 0.14
60 8 0.04
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (54 bp):
AAAGAAACTAAGCTTGATTTTAAGGGTTTCTTGATGATTGAAAAATGAAATTTT
Found at i:555377 original size:139 final size:139
Alignment explanation
Indices: 555127--555655 Score: 789
Period size: 139 Copynumber: 3.8 Consensus size: 139
555117 AGATGAACCA
* *
555127 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCGT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* * * * * *
555192 AATGAGAAAAACTTGTTCGATCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGTAACACATC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
555257 ACTCGAGGG
131 ACTCGAGGG
*
555266 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* * *
555331 AATGAGAATAGCTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
555396 ACTCGAGGG
131 ACTCGAGGG
* *
555405 ATCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCAATGAAGGAGAAG-A---CAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* * * * *
555466 AACGAGAAGAACTTGTTCAACCTTAGATCGATTCGTCACATATGGAGTTGAATCAGCAATACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
555531 ACTCGAGGG
131 ACTCGAGGG
*
555540 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAT-AAGGGAGACGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAA-GGAGAAGAAGTTCA
* * * *
555604 TAATGAGAAGAACTTGTTCAATCTTAGCTTGTTTCCATCGCATAAGGAGTTG
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCGCATATGGAGTTG
555656 GAACATCATT
Statistics
Matches: 351, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
134 2 0.01
135 120 0.34
136 1 0.00
138 1 0.00
139 213 0.61
140 14 0.04
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (139 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
ACTCGAGGG
Found at i:555622 original size:274 final size:277
Alignment explanation
Indices: 555127--555655 Score: 796
Period size: 274 Copynumber: 1.9 Consensus size: 277
555117 AGATGAACCA
* *
555127 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCGT
1 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAA--TCAT
* * * * * * *
555192 AATGAGAAAAACTTGTTCGATCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGTAACACATC
64 AACGAGAAAAACTTGTTCAACCTTAGATCGATTCATCACATATGGAGTTGAATCAGCAACACATC
555257 ACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAA
129 ACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAA
* * *
555322 GAAGTTCATAATGAGAATAGCTTGTTCAACCTTAGCTCGATT-CATCGCATATGGAGTTGAATCA
194 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCGCATAAGGAGTTGAATCA
555386 ACAACACCTCACTCGAGGG
259 ACAACACCTCACTCGAGGG
* *
555405 ATCAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCAATGAAGGAGAAG-A-CATAA
1 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAATCATAA
* * * *
555468 CGAGAAGAACTTGTTCAACCTTAGATCGATTCGTCACATATGGAGTTGAATCAGCAATACCTCAC
66 CGAGAAAAACTTGTTCAACCTTAGATCGATTCATCACATATGGAGTTGAATCAGCAACACATCAC
* *
555533 TCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAT-AAGGGAGACG
131 TCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAA-GAAGAAG
* * *
555597 AAGTTCATAATGAGAAGAACTTGTTCAATCTTAGCTTGTTTCCATCGCATAAGGAGTTG
195 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCGCATAAGGAGTTG
555656 GAACATCATT
Statistics
Matches: 226, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
273 2 0.01
274 153 0.68
275 16 0.07
277 1 0.00
278 54 0.24
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (277 bp):
ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAATCATAA
CGAGAAAAACTTGTTCAACCTTAGATCGATTCATCACATATGGAGTTGAATCAGCAACACATCAC
TCGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCGCATAAGGAGTTGAATCAAC
AACACCTCACTCGAGGG
Found at i:558978 original size:10 final size:10
Alignment explanation
Indices: 558965--559083 Score: 69
Period size: 10 Copynumber: 10.9 Consensus size: 10
558955 TGAACGGATG
558965 TAAACGAACA
1 TAAACGAACA
*
558975 TAAAGGAACACAA
1 TAAACG-A-AC-A
*
558988 TAAACGAACG
1 TAAACGAACA
*
558998 TAAATGAACACA
1 TAAACG-A-ACA
* *
559010 AACAAACGAACG
1 TA-A-ACGAACA
559022 TAAACGAACACAA
1 TAAACG-A-AC-A
*
559035 TAAATGAACA
1 TAAACGAACA
*
559045 TAAACGAACG
1 TAAACGAACA
559055 TAAACGAACA
1 TAAACGAACA
559065 TAAACGAA-A
1 TAAACGAACA
559074 GTAAACGAAC
1 -TAAACGAAC
559084 GTGAATGAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
9 1 0.01
10 47 0.57
11 8 0.10
12 12 0.14
13 13 0.16
14 2 0.02
ACGTcount: A:0.58, C:0.18, G:0.13, T:0.10
Consensus pattern (10 bp):
TAAACGAACA
Found at i:559021 original size:24 final size:24
Alignment explanation
Indices: 558966--559053 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 24
558956 GAACGGATGT
* * *
558966 AAACGAACATAAAGGAACAC-AAT
1 AAACGAACGTAAACGAACACAAAC
*
558989 AAACGAACGTAAATGAACACAAAC
1 AAACGAACGTAAACGAACACAAAC
*
559013 AAACGAACGTAAACGAACAC-AAT
1 AAACGAACGTAAACGAACACAAAC
* *
559036 AAATGAACATAAACGAAC
1 AAACGAACGTAAACGAAC
559054 GTAAACGAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 36 0.63
24 21 0.37
ACGTcount: A:0.59, C:0.19, G:0.12, T:0.09
Consensus pattern (24 bp):
AAACGAACGTAAACGAACACAAAC
Found at i:559029 original size:57 final size:57
Alignment explanation
Indices: 558941--559069 Score: 147
Period size: 57 Copynumber: 2.3 Consensus size: 57
558931 ATTTAAATGA
** * *
558941 TAAATGAACACAAATGAACGGATGTAAACG-A-AC-ATAAAGGAACACAATAAACGAACG
1 TAAATGAACACAAACAAACGAACGTAAACGAACACAATAAAGG-A-AC-ATAAACGAACG
*
558998 TAAATGAACACAAACAAACGAACGTAAACGAACACAATAAATGAACATAAACGAACG
1 TAAATGAACACAAACAAACGAACGTAAACGAACACAATAAAGGAACATAAACGAACG
* *
559055 TAAACGAACATAAAC
1 TAAATGAACACAAAC
559070 GAAAGTAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 50 0.81
58 3 0.05
59 3 0.05
60 6 0.10
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.12
Consensus pattern (57 bp):
TAAATGAACACAAACAAACGAACGTAAACGAACACAATAAAGGAACATAAACGAACG
Found at i:559093 original size:20 final size:20
Alignment explanation
Indices: 559035--559083 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
559025 ACGAACACAA
* *
559035 TAAATGAACATAAACGAACG
1 TAAACGAACATAAACGAAAG
559055 TAAACGAACATAAACGAAAG
1 TAAACGAACATAAACGAAAG
559075 TAAACGAAC
1 TAAACGAAC
559084 GTGAATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.12
Consensus pattern (20 bp):
TAAACGAACATAAACGAAAG
Found at i:559273 original size:10 final size:10
Alignment explanation
Indices: 559258--559310 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
559248 GATTATGCTA
*
559258 AACATAAATG
1 AACATAAACG
*
559268 AACATAAACA
1 AACATAAACG
* *
559278 AATATAAATG
1 AACATAAACG
559288 AACATAAACG
1 AACATAAACG
559298 AACATAAACG
1 AACATAAACG
559308 AAC
1 AAC
559311 GAACATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (10 bp):
AACATAAACG
Found at i:559286 original size:20 final size:20
Alignment explanation
Indices: 559257--559310 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
559247 AGATTATGCT
559257 AAACATAAATGAACATAAAC
1 AAACATAAATGAACATAAAC
*
559277 AAATATAAATGAACATAAAC
1 AAACATAAATGAACATAAAC
* *
559297 GAACATAAACGAAC
1 AAACATAAATGAAC
559311 GAACATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (20 bp):
AAACATAAATGAACATAAAC
Found at i:559313 original size:14 final size:14
Alignment explanation
Indices: 559294--559338 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
559284 AATGAACATA
559294 AACGAACATAAACG
1 AACGAACATAAACG
*
559308 AACGAACATAAATG
1 AACGAACATAAACG
* *
559322 AGCGAACATAACCG
1 AACGAACATAAACG
559336 AAC
1 AAC
559339 ATATTACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.53, C:0.22, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:566199 original size:16 final size:16
Alignment explanation
Indices: 566178--566217 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
566168 GGATTTTAGA
*
566178 CTCTGGTTGTGGATTT
1 CTCTGGTTGTGGATGT
566194 CTCTGGTTGTGGATGT
1 CTCTGGTTGTGGATGT
566210 CTCTGGTT
1 CTCTGGTT
566218 TCGTCGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.15, G:0.33, T:0.47
Consensus pattern (16 bp):
CTCTGGTTGTGGATGT
Found at i:567322 original size:55 final size:55
Alignment explanation
Indices: 567272--567778 Score: 688
Period size: 55 Copynumber: 9.4 Consensus size: 55
567262 GGAGTATGGA
* *
567272 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
567327 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * *
567380 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
567435 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * *
567488 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
567543 AC-C-CACAATCTTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
567596 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTAAAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
567651 ACCCGAACAATCTTCAACTATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
567706 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCCATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
567759 ACTCGAACAATCTTCAACAA
1 ACTCGAACAATCTTCAACAA
567779 ATGGGTTCGC
Statistics
Matches: 392, Mismatches: 52, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
53 184 0.47
54 8 0.02
55 200 0.51
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:567403 original size:108 final size:108
Alignment explanation
Indices: 567272--567774 Score: 742
Period size: 108 Copynumber: 4.6 Consensus size: 108
567262 GGAGTATGGA
* * ** *
567272 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
567337 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
567380 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
567445 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
567488 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
*
567553 TTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
567596 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTAAAAGACCCGAACAA
1 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCC--ACAA
* * * *
567661 TCTTCAACTATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
567706 AC-C-CACAATCTTC-ATCAATCGCGTCTGCCCCCCATTTCTTCAGAGAGTATAAGACTCGAACA
1 ACTCGAACAATCTTCAAT-GATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-C-CACA
567768 ATCTTCA
63 ATCTTCA
567775 ACAAATGGGT
Statistics
Matches: 365, Mismatches: 25, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
107 1 0.00
108 314 0.86
109 2 0.01
110 48 0.13
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (108 bp):
ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:567611 original size:163 final size:161
Alignment explanation
Indices: 567272--567778 Score: 709
Period size: 163 Copynumber: 3.1 Consensus size: 161
567262 GGAGTATGGA
* * *
567272 ACTCGAATAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACC-CACAAT
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCGAACAAT
* * *
567336 CTTC-ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT-G
66 CTTCAAT--ATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTC-ATCA
* *
567399 ATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAG
126 ATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
567435 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-CGAACAA
* *
567498 TCTTCAATGATCGTGTCTGCCCCCTATATCTTTAGAGAGTATAAGACCCACAATCTTCATCAATC
65 TCTTCAAT-ATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
567563 GTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
129 GTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
567596 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTAAAAGACCCGAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-CCGAACAA
*
567661 TCTTCAACTATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
65 TCTTCAA-TATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
* *
567726 GCGTCTGCCCCCCATTTCTTCAGAGAGTATAAG
129 GTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
567759 ACTCGAACAATCTTCAACAA
1 ACTCGAACAATCTTCAACAA
567779 ATGGGTTCGC
Statistics
Matches: 307, Mismatches: 29, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
160 2 0.01
161 92 0.30
162 4 0.01
163 205 0.67
164 4 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (161 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCGAACAAT
CTTCAATATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGT
GTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:567809 original size:55 final size:55
Alignment explanation
Indices: 567270--568231 Score: 421
Period size: 51 Copynumber: 18.1 Consensus size: 55
567260 AAGGAGTATG
* * * * * *
567270 GAACTCGAATAATCTTTAACAAT-CGTGTCTGCCCCCTATTTCTTCAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAA
* * * * * *
567326 G-AC-C-CACAATCTTCATCAATCGCG-TCTGCCCCCTATTTCTTCAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAAT-GGGTTC-GCTCCCTCTTTCTTTAGAGAGTATAA
** * * * *
567379 G-ACTCGAACAATCTTCAATGAT-CGTGTCTGCCCCCTATATCTTTAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAA
* * * * * *
567434 G-AC-C-CACAATCTTCATCAATCGCG-TCTGCCCCCTATTTCTTCAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAAT-GGGTTC-GCTCCCTCTTTCTTTAGAGAGTATAA
** * * * *
567487 G-ACTCGAACAATCTTCAATGAT-CGTGTCTGCCCCCTATATCTTTAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAA
* * * * * *
567542 G-AC-C-CACAATCTTCATCAAT-CGTGTCTGCCCCCTATTTCTTCAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAA
* * * * * * * *
567595 G-ACTCGAACGATCTTCAACGAT-TGTGTCTGCCCCCTATATCTTCAGAGAGTAAAA
1 GAACTCGAACAATCTTCAACAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAA
* * * * * *
567650 G-ACCCGAACAATCTTCAACTAT-TGTGTCTGCCCCCTATTTCTTCAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAA
* * * * *
567705 G-AC-C-CACAATCTTCATCAATCGCG-TCTGC-CCCCCATTTCTTCAGAGAGTATAA
1 GAACTCGAACAATCTTCAACAAT-GGGTTC-GCTCCCTC-TTTCTTTAGAGAGTATAA
*
567758 G-ACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTAT-A
1 GAACTCGAACAATCTTCAAC-AATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAA
* * * *
567812 GAACTCGAACATCTCTTC-AC---GGGTTCGCTCCCTCTTTCTCTAGGGAGTAT-G
1 GAACTCGAACA-ATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAA
* *
567863 GAACTCGAAC-ATCTTCAAC--TGGGTTCGCTCCCTCTTTCTTCAGGGAGTAT-A
1 GAACTCGAACAATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAA
* ** * * * * * *
567914 GAACTC-AAAAATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTCTAAAGAGTAT-A
1 GAACTCGAACAATCTTCAAC-AATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAA
* ** * *
567968 GAACTCGAAC-ATCTTC-A-AACGGGTTCGCTCATTCTTTCATTA-AGGAGTAT-G
1 GAACTCGAACAATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGA-GAGTATAA
* * * * * *
568019 GAACTCGGA-TATCTTC-AC-ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT-G
1 GAACTCGAACAATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAA
* * * *
568070 GAACTC-AGACATCTCTTC-A-AACGGGTTCGCTCCTTCTTTCTTTA-AGGAGTAT-G
1 GAACTCGA-ACA-ATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGA-GAGTATAA
* *
568123 GAACTCGAAC-ATCTTC-A-AACGGGTTCGCTCCTTCTTTCTTTA-AGGAGTAT-A
1 GAACTCGAACAATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGA-GAGTATAA
* *
568174 GAACTCGAAC-ATCTTC-A-AACGGGTTCGCTCCTTCTTTCTTTA-AGGAGTAT-A
1 GAACTCGAACAATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGA-GAGTATAA
568225 GAACTCG
1 GAACTCG
568232 CATATCTTCA
Statistics
Matches: 774, Mismatches: 91, Indels: 87
0.81 0.10 0.09
Matches are distributed among these distances:
49 5 0.01
50 5 0.01
51 252 0.33
52 3 0.00
53 218 0.28
54 48 0.06
55 228 0.29
56 15 0.02
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (55 bp):
GAACTCGAACAATCTTCAACAATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAA
Found at i:567856 original size:51 final size:50
Alignment explanation
Indices: 567750--568241 Score: 531
Period size: 51 Copynumber: 9.5 Consensus size: 50
567740 TTTCTTCAGA
* *
567750 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAGG
1 GAGTATAGA-ACTCGAAC-ATCTTCAAC----GGGTTCGCTCCTTCTTTCTTTAAG
* * *
567805 GAGTATAGAACTCGAACATCTCTTC-ACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACA--TCTTCAACGGGTTCGCTCCTTCTTTCTTTAAG
* * * *
567856 GAGTATGGAACTCGAACATCTTCAACTGGGTTCGCTCCCTCTTTCTTCAGG
1 GAGTATAGAACTCGAACATCTTCAAC-GGGTTCGCTCCTTCTTTCTTTAAG
* * * * * *
567907 GAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTCTAAA
1 GAGTATAGAACTC--GAA-CATCTTC-AACGGGTTCGCTCCTTCTTTCTTTAAG
* *
567961 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCATTCTTTCATTAAG
1 GAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTCTTTAAG
* * * * * *
568012 GAGTATGGAACTCGGATATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCA-ACGGGTTCGCTCCTTCTTTCTTTAAG
*
568063 GAGTATGGAACTC-AGACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGA-ACA--TCTTC-AACGGGTTCGCTCCTTCTTTCTTTAAG
*
568116 GAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTCTTTAAG
568167 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTCTTTAAG
* *
568218 GAGTATAGAACTCGCATATCTTCA
1 GAGTATAGAACTCGAACATCTTCA
568242 TTTGCTTCAC
Statistics
Matches: 383, Mismatches: 39, Indels: 35
0.84 0.09 0.08
Matches are distributed among these distances:
49 5 0.01
50 4 0.01
51 261 0.68
52 2 0.01
53 46 0.12
54 40 0.10
55 19 0.05
56 6 0.02
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (50 bp):
GAGTATAGAACTCGAACATCTTCAACGGGTTCGCTCCTTCTTTCTTTAAG
Found at i:568158 original size:155 final size:153
Alignment explanation
Indices: 567740--568230 Score: 612
Period size: 156 Copynumber: 3.1 Consensus size: 153
567730 CTGCCCCCCA
* * ** * * *
567740 TTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAG
1 TTTCTT-AGGGAGTATAGA-ACTC-AAAAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
* *
567804 GGAGTATAGAACTCGAACATCTCTTC--ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
63 GGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTCTTTCT-TAAGGAGTATGGAAC
567867 TCGAACATCTTCAACTGGGTTCGCTCCCTC
125 TCGAACATCTTCAAC-GGGTTCGCTCCCTC
** * * *
567897 TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTCTAAAG
1 TTTCTT-AGGGAGTATAGAACTCAAAAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
* *
567962 AGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCATTCTTTCATTAAGGAGTATGGAACTCGG
65 AGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTC-TTAAGGAGTATGGAACTCGA
*
568027 ATATCTTCACACGGGTTCGCTCCCTC
129 ACATCTTCA-ACGGGTTCGCTCCCTC
* * *
568053 TTTCTCTAGGGAGTATGGAACTCAGACATC-TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
1 TTTCT-TAGGGAGTATAGAACTCAAAAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
* *
568117 AGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGA
65 AGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTC-TTAAGGAGTATGGAACTCGA
*
568182 ACATCTTCAAACGGGTTCGCTCCTTC
129 ACATCTTC-AACGGGTTCGCTCCCTC
*
568208 TTTCTTTAAGGAGTATAGAACTC
1 TTTC-TTAGGGAGTATAGAACTC
568231 GCATATCTTC
Statistics
Matches: 292, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
154 5 0.02
155 130 0.45
156 132 0.45
157 24 0.08
158 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (153 bp):
TTTCTTAGGGAGTATAGAACTCAAAAATCTTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGA
GTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTAAGGAGTATGGAACTCGAAC
ATCTTCAACGGGTTCGCTCCCTC
Found at i:568671 original size:36 final size:36
Alignment explanation
Indices: 568611--568873 Score: 293
Period size: 36 Copynumber: 7.4 Consensus size: 36
568601 ACTCTTCTGA
* * **
568611 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
568648 GAAGACTTAAGATGGTTTACTTCAC---TCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
568681 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
568717 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
568753 GAAGGCTTCAGATGGTTAGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* **
568789 GAAGGCTTAGGATGGTTTGCTTCACTATTCTCTAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
568825 GAAGGCTTCAGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
568861 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
568874 TAACTTTGCT
Statistics
Matches: 194, Mismatches: 27, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
32 1 0.01
33 28 0.14
35 1 0.01
36 151 0.78
37 13 0.07
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:576647 original size:16 final size:16
Alignment explanation
Indices: 576626--576665 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
576616 GGGATTTAGA
*
576626 CTCTGGTTGTGGATTT
1 CTCTGGTTGTGGATGT
576642 CTCTGGTTGTGGATGT
1 CTCTGGTTGTGGATGT
576658 CTCTGGTT
1 CTCTGGTT
576666 TCGTCGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.15, G:0.33, T:0.47
Consensus pattern (16 bp):
CTCTGGTTGTGGATGT
Found at i:579291 original size:43 final size:43
Alignment explanation
Indices: 579243--579327 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
579233 AAAATAAAAT
579243 TAAAATATAACATTA-A-ATATAATTTAAA-AAATAAATAGATAAC
1 TAAAATA-AA-ATTACACATATAA-TTAAATAAATAAATAGATAAC
* *
579286 TAAAATAAAATTACACATATAATTAAATAATTAAATATATAA
1 TAAAATAAAATTACACATATAATTAAATAAATAAATAGATAA
579328 TTTATCCGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
41 4 0.11
42 8 0.22
43 25 0.68
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (43 bp):
TAAAATAAAATTACACATATAATTAAATAAATAAATAGATAAC
Found at i:579654 original size:17 final size:18
Alignment explanation
Indices: 579620--579671 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
579610 GATTTTTATT
579620 TATATAATATTAAAATTAA
1 TATATAATATT-AAATTAA
*
579639 TATATAATATT-TATTAA
1 TATATAATATTAAATTAA
* *
579656 AATGATCATATTAAAT
1 TAT-ATAATATTAAAT
579672 CTTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATAATATTAAATTAA
Found at i:581527 original size:4 final size:4
Alignment explanation
Indices: 581520--581545 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
581510 TCTTTCGTCA
581520 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
581546 TTATTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:590335 original size:11 final size:11
Alignment explanation
Indices: 590319--590383 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
590309 AGAAATTAGG
590319 AGCTCGATTGA
1 AGCTCGATTGA
590330 AGCTCGAGACTTG-
1 AGCTC--GA-TTGA
*
590343 AGCTCGAATGA
1 AGCTCGATTGA
590354 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
590366 AGCTCGATTCA
1 AGCTCGATTGA
590377 AGCTCGA
1 AGCTCGA
590384 ACTCAAACTC
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 4 0.09
11 21 0.48
12 7 0.16
13 9 0.20
14 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:590345 original size:24 final size:23
Alignment explanation
Indices: 590318--590386 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
590308 AAGAAATTAG
590318 GAGCTCGATTGAAGCTCGAGACTT
1 GAGCTCGATTGAAGCTCGA-ACTT
* **
590342 GAGCTCGAATGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTT
*
590365 GAGCTCGATTCAAGCTCGAACT
1 GAGCTCGATTGAAGCTCGAACT
590387 CAAACTCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGAACTT
Found at i:593316 original size:11 final size:11
Alignment explanation
Indices: 593300--593362 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
593290 TTATTATAGA
593300 ATTTTTAATAT
1 ATTTTTAATAT
593311 ATTTTTAA-A-
1 ATTTTTAATAT
593320 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
593331 ATCAATAATGT
1 ATTTTTAATAT
593342 ATTTTTAATAT
1 ATTTTTAATAT
593353 ATTTTTAATA
1 ATTTTTAATA
593363 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:594355 original size:12 final size:12
Alignment explanation
Indices: 594338--594382 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
594328 GCCCTAAATT
*
594338 GAAAAAAAAAGA
1 GAAAAAAAAAAA
594350 GAAAAAGAACAAAA
1 GAAAAA-AA-AAAA
594364 GAAAAAACAAAAA
1 GAAAAAA-AAAAA
594377 GAAAAA
1 GAAAAA
594383 TAAGGTGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 6 0.21
13 13 0.45
14 10 0.34
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:595712 original size:110 final size:110
Alignment explanation
Indices: 595519--595716 Score: 306
Period size: 110 Copynumber: 1.8 Consensus size: 110
595509 ATTTCATAGC
*
595519 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* *
595584 GGGCGGTTGATTGTCAACAAACAACTTTTTAGTTTCATTCAGAGT
66 GGGCGGCTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGT
* * * * * *
595629 CAATTTTAACTTCACATCGAAGGATATTAGACTCAAGATAGCACAAGCTCAACTTCACAGCTAAG
1 CAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
*
595694 GGGTGGCTGACTGTCAACAAACA
66 GGGCGGCTGACTGTCAACAAACA
595717 GTTTCCCAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 78 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (110 bp):
CAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
GGGCGGCTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGT
Found at i:597525 original size:33 final size:33
Alignment explanation
Indices: 597483--597555 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
597473 GATCAGAGAA
* *
597483 GAAGAGAGATAGGGGAGGGCTCGGTTTTGACCT
1 GAAGAGAGATAGGGGAGGGCTCAGTTTTAACCT
*
597516 GAAGAGAGATAGGGGAGGGCTCAGTTTTAAGCT
1 GAAGAGAGATAGGGGAGGGCTCAGTTTTAACCT
597549 GAAGAGA
1 GAAGAGA
597556 AAATGAAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.30, C:0.10, G:0.41, T:0.19
Consensus pattern (33 bp):
GAAGAGAGATAGGGGAGGGCTCAGTTTTAACCT
Found at i:598090 original size:19 final size:20
Alignment explanation
Indices: 598061--598107 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
598051 TGTATATATG
598061 CTTTT-TTTTTTACTTT-TT
1 CTTTTATTTTTTACTTTATT
598079 CTTTTATTTTTTACTTTATT
1 CTTTTATTTTTTACTTTATT
*
598099 TTTTTATTT
1 CTTTTATTT
598108 CATTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 10 0.38
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.81
Consensus pattern (20 bp):
CTTTTATTTTTTACTTTATT
Found at i:598117 original size:13 final size:12
Alignment explanation
Indices: 598062--598118 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
598052 GTATATATGC
598062 TTTTTTT-TTTA
1 TTTTTTTATTTA
*
598073 CTTTTTCT-TTTA
1 -TTTTTTTATTTA
598085 -TTTTTTACTTTA
1 TTTTTTTA-TTTA
598097 TTTTTTTATTTCA
1 TTTTTTTATTT-A
598110 TTTTTTTAT
1 TTTTTTTAT
598119 ATTCTTGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 5 0.13
12 17 0.44
13 17 0.44
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:601055 original size:7 final size:7
Alignment explanation
Indices: 601036--601090 Score: 94
Period size: 7 Copynumber: 7.9 Consensus size: 7
601026 CAATACACTG
601036 TTCTTTCT
1 TTCTTT-T
601044 TTCTTTT
1 TTCTTTT
601051 TTCTTTT
1 TTCTTTT
601058 TTCTTTT
1 TTCTTTT
601065 TTCTTTT
1 TTCTTTT
601072 TTCTTTT
1 TTCTTTT
601079 TTC-TTT
1 TTCTTTT
601085 TTCTTT
1 TTCTTT
601091 AGTTTTTAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.13
7 34 0.74
8 6 0.13
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTCTTTT
Found at i:602767 original size:11 final size:11
Alignment explanation
Indices: 602751--602826 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
602741 ATATTTTAAT
602751 AATAATAATAA
1 AATAATAATAA
*
602762 AATAATCATGAA
1 AATAATAAT-AA
*
602774 GATAATAATTTAA
1 AATAATAA--TAA
602787 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
602798 AAGTAATAATAA
1 AA-TAATAATAA
602810 AATAA-AATAA
1 AATAATAATAA
602820 TAATAAT
1 -AATAAT
602827 TAAAATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.14
11 20 0.39
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:602822 original size:16 final size:17
Alignment explanation
Indices: 602796--602855 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 17
602786 AACATATATC
602796 AAAAGTAATAATAAAAT
1 AAAAGTAATAATAAAAT
*
602813 AAAA-TAATAAT-AATT
1 AAAAGTAATAATAAAAT
* *
602828 AAAA-TGA-AAGAAAAT
1 AAAAGTAATAATAAAAT
602843 AAAAGTAATAATA
1 AAAAGTAATAATA
602856 TTAAAACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.47
16 9 0.26
17 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAAGTAATAATAAAAT
Found at i:602843 original size:19 final size:19
Alignment explanation
Indices: 602801--602844 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
602791 ATATCAAAAG
*
602801 TAATAATAAAATAAAATAA
1 TAATAATAAAATAAAAGAA
*
602820 TAATAATTAAAATGAAAGAA
1 TAATAA-TAAAATAAAAGAA
602840 -AATAA
1 TAATAA
602845 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATAATAAAATAAAAGAA
Found at i:604235 original size:3 final size:3
Alignment explanation
Indices: 604216--604280 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
604206 TTGTAATATT
* *
604216 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAG TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
604263 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
604281 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:604237 original size:24 final size:23
Alignment explanation
Indices: 604209--604280 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
604199 ATGGGCTTTG
604209 TAAT-ATTTAATAAATAATATATAA
1 TAATAATTTAAT-AATAATA-ATAA
604233 TAATAATTATAATAATAATAATAA
1 TAATAATT-TAATAATAATAATAA
*
604257 TAGTAATTTTAATAATAATAATAA
1 TAATAA-TTTAATAATAATAATAA
604281 ATTTAAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 28 0.64
25 12 0.27
26 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
TAATAATTTAATAATAATAATAA
Found at i:604590 original size:75 final size:76
Alignment explanation
Indices: 604408--604593 Score: 304
Period size: 75 Copynumber: 2.5 Consensus size: 76
604398 GATGTAAATG
* **
604408 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTTAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
604473 CCCGAAGGCTT
66 CCCGAAGGCTT
*
604484 TTTGGAAACATCATGCACTGAAGGACCTACAGATGACCCTG-AGGCTTTGAAAACATC-AAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
604547 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
604559 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
604594 TGGGAAATAG
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 51 0.50
76 51 0.50
77 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:605170 original size:24 final size:23
Alignment explanation
Indices: 605135--605179 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
605125 TGAACAAATT
*
605135 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
605159 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
605180 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:605260 original size:113 final size:111
Alignment explanation
Indices: 605007--605489 Score: 632
Period size: 113 Copynumber: 4.3 Consensus size: 111
604997 GAATTATGCA
*
605007 AAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
605072 ATGAACT-TCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGC
66 ATGAACTCT-TCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGC
* *
605118 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
605183 TATGAACTCGATCTGGTAATGCTGAAT-CATCGAA-TGATGAATTTAAAC
65 TATGAACTC-TTCTGGAAAAGCTG-ATCCATC-AAGTGATGAATTTAAGC
605231 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
605296 TATGAACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGC
65 TATGAACTCTT-CTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGC
* *
605344 GAAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
605409 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAGC
65 TATGAACTCT-TCTGGAAAAGCTGATCCATC-AAGTGATGAATTTAAGC
*
605457 GAAAAGTTGAACAAGTTCTTCTCATTATGAACT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACT
605490 CGATCTGGTA
Statistics
Matches: 332, Mismatches: 29, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
111 4 0.01
112 70 0.21
113 248 0.75
114 10 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (111 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAGC
Found at i:605400 original size:226 final size:224
Alignment explanation
Indices: 605007--605489 Score: 727
Period size: 226 Copynumber: 2.1 Consensus size: 224
604997 GAATTATGCA
*
605007 AAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
605072 ATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
66 ATGAACTTCTCTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCT
* * *
605137 TCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCGATCTGGTAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGATCTGGAAA
* *
605202 TGCTGAAT-CATCGAATGATGAATTTAAAC
196 AGCTG-ATCCATCGAATGATGAATTCAAAC
605231 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
605296 TATGAACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCGAAAA-TTTGAACAAGT
65 TATGAACTTCT-CTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGC-AAAAGGTTGAACAAAT
***
605360 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
128 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGATCTGG
* *
605425 AAAAGTTGATCCATCGAATGATGAATTCAAGC
193 AAAAGCTGATCCATCGAATGATGAATTCAAAC
*
605457 GAAAAGTTGAACAAGTTCTTCTCATTATGAACT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACT
605490 CGATCTGGTA
Statistics
Matches: 234, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
224 4 0.02
225 71 0.30
226 151 0.65
227 8 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (224 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTCTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGATCTGGAAA
AGCTGATCCATCGAATGATGAATTCAAAC
Found at i:605484 original size:73 final size:73
Alignment explanation
Indices: 605397--605563 Score: 221
Period size: 73 Copynumber: 2.3 Consensus size: 73
605387 TCTTCAGATG
** * *
605397 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTG-ATCCATCGAATGATGAATTCAAGCGAAA
1 AGTTCTTCTCATTATGAACTTGATCTGGAAAAGCTGAAT-CATCGAATGATGAATTCAAAC-AAA
605461 A-GTTGAACA
64 AGGTTGAACA
* * * *
605470 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTTGATCTGGAAAAGCTGAATCATCGAATGATGAATTCAAACAAAAG
605535 GTTGAACA
66 GTTGAACA
*
605543 AATTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
605564 CTTCTTCCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
72 4 0.05
73 76 0.93
74 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTTGATCTGGAAAAGCTGAATCATCGAATGATGAATTCAAACAAAAG
GTTGAACA
Found at i:605516 original size:299 final size:299
Alignment explanation
Indices: 605171--605788 Score: 1116
Period size: 299 Copynumber: 2.1 Consensus size: 299
605161 TCTTCATATG
605171 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
605236 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
605301 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCGAAAA-TTTGAACAAGTTCTTC
131 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGC-AAAAGGTTGAACAAATTCTTC
****
605365 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-A
195 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATA
*
605429 GTTG-ATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
260 -CTGAAT-CATCGAATGATGAATTCAAGCGAAAAGTTGAACA
605470 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
605535 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
605600 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
*
605665 CATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATAC
196 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATAC
605730 TGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
261 TGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
605769 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
605789 TCTTCTTTTT
Statistics
Matches: 308, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
298 4 0.01
299 301 0.98
300 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (299 bp):
AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATAC
TGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
Found at i:605587 original size:113 final size:113
Alignment explanation
Indices: 605470--606089 Score: 942
Period size: 113 Copynumber: 5.5 Consensus size: 113
605460 AAGTTGAACA
* *
605470 AGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGCAAAAG
605535 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*** * * * * *
605583 AGTTCTTCTCATTATGAACTTTTACTGGCAATGTTG-ATCCATC-AAGAGATGGATTTGAGCAAA
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAAT-CATCGAA-TGATGAATTTAAGCAAA
*
605646 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
64 AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
605696 AGTTCTTCTCATTATGAACTCGAACTGGAAATACTGAATCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGC-AAAA
* **
605761 -GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATG
65 GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* *
605809 AGTTCTTCTCATTATGAACTCGAACTGGTAATGATGAATCATCGAATGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGCAAAAG
605874 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* ** *
605922 AGTTCTTCTCATTATGAACTCGAACTGGAAATATTGAATCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGC-AAAA
* **
605987 -GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATG
65 GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
606035 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATT
1 AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATT
606090 CATATCTTTG
Statistics
Matches: 456, Mismatches: 44, Indels: 14
0.89 0.09 0.03
Matches are distributed among these distances:
112 8 0.02
113 436 0.96
114 12 0.03
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCGAACTGGTAATGCTGAATCATCGAATGATGAATTTAAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:606000 original size:525 final size:524
Alignment explanation
Indices: 605005--606014 Score: 1627
Period size: 525 Copynumber: 1.9 Consensus size: 524
604995 TAGAATTATG
*
605005 CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
605070 TTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATT
* * *
605135 CTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCGATCTGGT
131 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
* *
605200 AATGCTGAATCATCGAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 AATACTGAATCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
*** *
605265 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTACTGGCAATGTTGATCCATCAAG
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGCAATGATGATCCATCAAG
* * * * *
605330 AGATGGATTTGAGCGAAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
326 AGATGAATTTAAACGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
****
605395 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAA
391 TGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAA
605460 AAGTTGAACAAGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATT
456 AAGTTGAACAAGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATT
605525 TAAA
521 TAAA
*
605529 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
605594 TTATGAACTTTTACTGGCAATGTTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTCT-CTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAAT
605659 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
130 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* *
605724 AAATACTGAATCATCGAATGATGAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAAC
195 AAATACTGAATCATCGAATGATGAATTCAAAC-AAAAGGTTGAACAAATTCTTCTCATTATGAAC
** *
605788 TTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGTAATGATGAAT-CATC
259 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGCAATGATG-ATCCATC
*
605852 GAA-TGATGAATTTAAAC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
323 -AAGAGATGAATTTAAACGAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
605915 TCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAATA-TTGAAT-CATCGAATGATGAATTC
386 TCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAA-AGTTG-ATCCATCGAATGATGAATTC
605978 AAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
449 AAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
606015 TCTTCTTTTT
Statistics
Matches: 447, Mismatches: 32, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
524 78 0.17
525 358 0.80
526 11 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (524 bp):
CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAAGCTGATCCATCAAGAGATGGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
AATACTGAATCATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGCAATGATGATCCATCAAG
AGATGAATTTAAACGAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAA
AAGTTGAACAAGTTCTTCTCATTATGAACTCGATCTGGTAATGCTGAATCATCGAATGATGAATT
TAAA
Found at i:606518 original size:22 final size:22
Alignment explanation
Indices: 606493--606547 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
606483 CATAAAGTTT
*
606493 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
606515 TCATCTTT-ATAAAGAGAATCTA
1 TCATCTTTGA-AAAGAGAATCTA
606537 TCATCTTTGAA
1 TCATCTTTGAA
606548 GAGCGTAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:606963 original size:54 final size:54
Alignment explanation
Indices: 606881--607049 Score: 218
Period size: 54 Copynumber: 3.2 Consensus size: 54
606871 TAGCAGGTTT
* *** * *
606881 GTAAAACATTTAACAGTGCATTCATCCTTGCCTGTGGCTTCTGCTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGATGTTC
* *
606935 GTAAAACATTTGACAACACATTCATCCTTTCATGTGGTTTCTGTTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGATGTTC
**
606989 GTAAAACATTTGACAACACATTCAT--TTTTTTGTGGCTTCTGCTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGATGTTC
*
607041 -TCAAACATT
1 GTAAAACATT
607050 GAACCTCTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
51 8 0.08
52 23 0.23
54 71 0.70
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCTCAGATGTTC
Found at i:609470 original size:115 final size:114
Alignment explanation
Indices: 609157--609490 Score: 542
Period size: 114 Copynumber: 2.9 Consensus size: 114
609147 GATCATGCAG
* * * * * * *
609157 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
609222 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
*
609271 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
609336 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGGAAT
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
609385 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
609450 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACT
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACT
609491 GAGTACATGG
Statistics
Matches: 206, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
114 126 0.61
115 80 0.39
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:613753 original size:27 final size:27
Alignment explanation
Indices: 613723--613778 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
613713 GTAATTATGT
*
613723 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGCAAATACAAACGTA
* * *
613750 AAAAATGCAAATGCAAATGCAAATGTA
1 AAAAATGAAAATGCAAATACAAACGTA
613777 AA
1 AA
613779 TATGTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (27 bp):
AAAAATGAAAATGCAAATACAAACGTA
Found at i:613872 original size:7 final size:7
Alignment explanation
Indices: 613838--613879 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
613828 ATAAAAGTAT
613838 AAATGCA
1 AAATGCA
* *
613845 CAATGAA
1 AAATGCA
613852 AAATGCA
1 AAATGCA
613859 AAGATGCA
1 AA-ATGCA
613867 AAATGC-
1 AAATGCA
613873 AAATGCA
1 AAATGCA
613880 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:616349 original size:16 final size:17
Alignment explanation
Indices: 616323--616382 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 17
616313 AACATATATC
616323 AAAAGTAATAATAAAAT
1 AAAAGTAATAATAAAAT
*
616340 AAAA-TAATAAT-AATT
1 AAAAGTAATAATAAAAT
* *
616355 AAAA-TGA-AAGAAAAT
1 AAAAGTAATAATAAAAT
616370 AAAAGTAATAATA
1 AAAAGTAATAATA
616383 TTAAAACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.47
16 9 0.26
17 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAAGTAATAATAAAAT
Found at i:616370 original size:19 final size:19
Alignment explanation
Indices: 616328--616371 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
616318 ATATCAAAAG
*
616328 TAATAATAAAATAAAATAA
1 TAATAATAAAATAAAAGAA
*
616347 TAATAATTAAAATGAAAGAA
1 TAATAA-TAAAATAAAAGAA
616367 -AATAA
1 TAATAA
616372 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATAATAAAATAAAAGAA
Found at i:617765 original size:3 final size:3
Alignment explanation
Indices: 617746--617813 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
617736 TTGTAATATT
* *
617746 TAA TAAA TAA TATA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAG
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
617793 TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
617814 ACTTAAATGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:620766 original size:141 final size:141
Alignment explanation
Indices: 620512--620793 Score: 510
Period size: 141 Copynumber: 2.0 Consensus size: 141
620502 GGGTGAGGTG
*
620512 GCAGCTAGTGCTGATGAGGTGGCACCTATTCATGAAACTCATGATAATGTTGGTGTAATTGAGCC
1 GCAGCTAGTGCTGATGAGGTGGCACCTATTCATGAAACTCACGATAATGTTGGTGTAATTGAGCC
* **
620577 AAATGAACAAGTTATATTGAACACATCTGGGCATGTATTTAGTGATGATGTCACGAACCAAATAC
66 AAATGAACAAGGTATATTGAACACATCTGGGCACCTATTTAGTGATGATGTCACGAACCAAATAC
620642 AAATTGATGAT
131 AAATTGATGAT
*
620653 GCAGCTAGTGGTGATGAGGTGGCACCTATTCATGAAACTCACGATAATGTTGGTGTAATTGAGCC
1 GCAGCTAGTGCTGATGAGGTGGCACCTATTCATGAAACTCACGATAATGTTGGTGTAATTGAGCC
*
620718 AAATGAACAAGGTATATTGAACACATCTGGGCACCTATTTGGTGATGATGTCACGAACCAAATAC
66 AAATGAACAAGGTATATTGAACACATCTGGGCACCTATTTAGTGATGATGTCACGAACCAAATAC
620783 AAATTGATGAT
131 AAATTGATGAT
620794 ATGGTGCAAG
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 135 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (141 bp):
GCAGCTAGTGCTGATGAGGTGGCACCTATTCATGAAACTCACGATAATGTTGGTGTAATTGAGCC
AAATGAACAAGGTATATTGAACACATCTGGGCACCTATTTAGTGATGATGTCACGAACCAAATAC
AAATTGATGAT
Found at i:629483 original size:22 final size:21
Alignment explanation
Indices: 629451--629493 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
629441 CATTATTTTA
* *
629451 TTGTTGTATGTTGATGACATGC
1 TTGTTGCATGTTCA-GACATGC
629473 TTGTTGCATGTTCAGACATGC
1 TTGTTGCATGTTCAGACATGC
629494 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (21 bp):
TTGTTGCATGTTCAGACATGC
Found at i:637774 original size:32 final size:33
Alignment explanation
Indices: 637738--637812 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
637728 GATACCAAAG
*
637738 GGTGTCGCCAAG-CTTTCC-AGCTGACTCCCAAC
1 GGTGTCGCCAAGCCGTTCCAAGC-GACTCCCAAC
637770 GGTGTCGCC-AGCCGTTCCAAGCGACTCCCAAC
1 GGTGTCGCCAAGCCGTTCCAAGCGACTCCCAAC
*
637802 GATGTCGCCAA
1 GGTGTCGCCAA
637813 CACTTCCAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 2 0.05
32 32 0.84
33 4 0.11
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.19
Consensus pattern (33 bp):
GGTGTCGCCAAGCCGTTCCAAGCGACTCCCAAC
Found at i:637820 original size:32 final size:32
Alignment explanation
Indices: 637740--637830 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
637730 TACCAAAGGG
* * *
637740 TGTCGCCAAGCTTTCC-AGCTGACTCCCAACGG
1 TGTCGCCAACCGTTCCAAGC-GACTCCCAACGA
*
637772 TGTCGCCAGCCGTTCCAAGCGACTCCCAACGA
1 TGTCGCCAACCGTTCCAAGCGACTCCCAACGA
* *
637804 TGTCGCCAACAC-TTCCAGGCGAATCCC
1 TGTCGCCAAC-CGTTCCAAGCGACTCCC
637831 TCTCGTGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 46 0.92
33 4 0.08
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.19
Consensus pattern (32 bp):
TGTCGCCAACCGTTCCAAGCGACTCCCAACGA
Found at i:639879 original size:21 final size:20
Alignment explanation
Indices: 639849--639892 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
639839 CCGAAAATAT
639849 TAAAAAAATAATATTTTAAA
1 TAAAAAAATAATATTTTAAA
639869 TAAAAATAATAATATTTTAAA
1 TAAAAA-AATAATATTTTAAA
639890 TAA
1 TAA
639893 TTTTCCATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAAAATAATATTTTAAA
Found at i:641233 original size:49 final size:49
Alignment explanation
Indices: 641160--641254 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
641150 ATCTAATAAA
* *
641160 CAGGGGCGGACCTCCATGAAGCCCGGGGTATCCCAGGCAACCCCTCATC
1 CAGGGGCGGACCTCCATGAAGCCCGGGATATCCCAAGCAACCCCTCATC
* ** *
641209 CAGGGGTGGACCTCCATGGTGCCCGGGATATCCCAAGCAATCCCTC
1 CAGGGGCGGACCTCCATGAAGCCCGGGATATCCCAAGCAACCCCTC
641255 CACAAGTGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGAAGCCCGGGATATCCCAAGCAACCCCTCATC
Found at i:644563 original size:60 final size:60
Alignment explanation
Indices: 644430--644575 Score: 172
Period size: 60 Copynumber: 2.4 Consensus size: 60
644420 ATATAATGAG
* *
644430 TAGTCAGGTGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAGCAACATATTA
1 TAGTCAGGAGATCATTTTGTAACTTTTAATAGTCGAGAGACTAAATAAAGCAACATATTA
* ** *
644490 TAGCCAATAGATCATTTTGTAATTTTTAATAGTCGATGA-ACTAAATAAAGCAACATCA-TA
1 TAGTCAGGAGATCATTTTGTAACTTTTAATAGTCGA-GAGACTAAATAAAGCAACAT-ATTA
* *
644550 TAGTTAGGGGATCATTTGTGT-ACTTT
1 TAGTCAGGAGATCATTT-TGTAACTTT
644576 ACCCAATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
60 65 0.92
61 6 0.08
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (60 bp):
TAGTCAGGAGATCATTTTGTAACTTTTAATAGTCGAGAGACTAAATAAAGCAACATATTA
Found at i:644840 original size:78 final size:74
Alignment explanation
Indices: 644698--644935 Score: 246
Period size: 78 Copynumber: 3.0 Consensus size: 74
644688 AAACATTTTG
* * * *
644698 AAAATATATAATATATAGCTTTT-AAAACATTTTGAAAACATTTATATATTATATAATTTGTTTA
1 AAAAAATATAATATATAG-TTTTCAAAACATTTTGAAAATATATATATATTATAT-ATTTTTTTA
644762 AAATGTTTTTACA
64 AAAT-TTTTTA-A
644775 AAAAAATATAATATATAGTTTTCAAAACATTTTTGAAAATATATATATATTATATAGTTTTTTTA
1 AAAAAATATAATATATAGTTTTCAAAACA-TTTTGAAAATATATATATATTATATA-TTTTTTTA
*
644840 AACA-TTTTGAA
64 AA-ATTTTTTAA
* * *
644851 AATAAATATATAATATATAATTTTTCAAAAAACATTTTGAAAATATATAATATATAATATATAAT
1 AA-AAA-ATATAATATAT-AGTTTTC--AAAACATTTTGAAAATATAT-ATATATTATATAT-TT
*
644916 TTTTAAAATATTTTTGA
59 TTTTAAAAT-TTTTTAA
644933 AAA
1 AAA
644936 TTATATGGTT
Statistics
Matches: 138, Mismatches: 10, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
76 7 0.05
77 32 0.23
78 43 0.31
79 7 0.05
80 16 0.12
81 26 0.19
82 7 0.05
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (74 bp):
AAAAAATATAATATATAGTTTTCAAAACATTTTGAAAATATATATATATTATATATTTTTTTAAA
ATTTTTTAA
Found at i:644860 original size:41 final size:41
Alignment explanation
Indices: 644699--644936 Score: 189
Period size: 39 Copynumber: 6.0 Consensus size: 41
644689 AACATTTTGA
* *
644699 AAATATATA-ATATATAG-CTTTTAAAACA-TTTTGAAAAC
1 AAATATATATATATATAGTTTTTTAAAACATTTTTGAAAAT
** * **
644737 ATTTATATAT-TATATAATTTGTTTAAAATGTTTTT-ACAAA-
1 AAATATATATATATATAGTTT-TTTAAAACATTTTTGA-AAAT
*
644777 AAA-ATATA-ATATATAG-TTTTCAAAACATTTTTGAAAAT
1 AAATATATATATATATAGTTTTTTAAAACATTTTTGAAAAT
* *
644815 ATATATATAT-TATATAGTTTTTTTAAACA-TTTTGAAAAT
1 AAATATATATATATATAGTTTTTTAAAACATTTTTGAAAAT
* *
644854 AAATATATA-ATATATAATTTTTCAAAAAACA-TTTTGAAAAT
1 AAATATATATATATATAGTTTTT--TAAAACATTTTTGAAAAT
* * *
644895 ATATAATATATAATATATA-ATTTTTAAAATATTTTTGAAAAT
1 AAAT-ATATAT-ATATATAGTTTTTTAAAACATTTTTGAAAAT
644937 TATATGGTTT
Statistics
Matches: 159, Mismatches: 23, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
37 14 0.09
38 18 0.11
39 53 0.33
40 18 0.11
41 30 0.19
42 15 0.09
43 4 0.03
44 7 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (41 bp):
AAATATATATATATATAGTTTTTTAAAACATTTTTGAAAAT
Found at i:644953 original size:18 final size:16
Alignment explanation
Indices: 644926--644986 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 16
644916 TTTTAAAATA
*
644926 TTTTTGAAAATTATAT
1 TTTTTAAAAATTATAT
644942 GGTTTTTAAAAA--ATAT
1 --TTTTTAAAAATTATAT
*
644958 TTTTTGAAAATTATACAT
1 TTTTTAAAAATTAT--AT
644976 TTTTTAAAAAT
1 TTTTTAAAAAT
644987 ATTTTTGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.25
16 6 0.17
18 21 0.58
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (16 bp):
TTTTTAAAAATTATAT
Found at i:644967 original size:32 final size:32
Alignment explanation
Indices: 644908--645017 Score: 120
Period size: 31 Copynumber: 3.5 Consensus size: 32
644898 TAATATATAA
*
644908 TATATAATTTTT--AAAATA-TTTTTGAAAAT
1 TATATCATTTTTAAAAAATATTTTTTGAAAAT
**
644937 TATATGGTTTTTAAAAAATATTTTTTGAAAAT
1 TATATCATTTTTAAAAAATATTTTTTGAAAAT
* * *
644969 TATA-CATTTTTTAAAAATATTTTTGGAAATT
1 TATATCATTTTTAAAAAATATTTTTTGAAAAT
645000 TATATCTAATTTTTAAAA
1 TATATC--ATTTTTAAAA
645018 GAAACGGTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
29 10 0.15
31 32 0.48
32 16 0.24
34 9 0.13
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (32 bp):
TATATCATTTTTAAAAAATATTTTTTGAAAAT
Found at i:645064 original size:3 final size:3
Alignment explanation
Indices: 645056--645120 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
645046 GTTTTTATAT
* * *
645056 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TCA CTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
645102 TT- TTA TTA CTTA TT- TTA TT
1 TTA TTA TTA -TTA TTA TTA TT
645121 TTAATTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:645607 original size:15 final size:15
Alignment explanation
Indices: 645587--645624 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
645577 AAACACGAGA
645587 AAGAACCAC-AAACGC
1 AAGAACCACAAAAC-C
*
645602 AAGAACAACAAAACC
1 AAGAACCACAAAACC
645617 AAGAACCA
1 AAGAACCA
645625 TTTTTTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.61, C:0.29, G:0.11, T:0.00
Consensus pattern (15 bp):
AAGAACCACAAAACC
Found at i:646613 original size:10 final size:10
Alignment explanation
Indices: 646600--646652 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
646590 TTTTCCTTTG
646600 TTTTTTTTTA
1 TTTTTTTTTA
*
646610 TTTTTGTTTA
1 TTTTTTTTTA
*
646620 TTATTTTTT-
1 TTTTTTTTTA
* *
646629 TTATATTTTA
1 TTTTTTTTTA
*
646639 TTTTTGTTTA
1 TTTTTTTTTA
646649 TTTT
1 TTTT
646653 ATCATTCTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 8 0.23
10 27 0.77
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:646626 original size:22 final size:22
Alignment explanation
Indices: 646601--646664 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
646591 TTTCCTTTGT
*
646601 TTTTTTTTAT-TTTTGTTTATTA
1 TTTTTTTTATATTTTATTT-TTA
*
646623 TTTTTTTTATATTTTATTTTTG
1 TTTTTTTTATATTTTATTTTTA
* *
646645 TTTATTTTATCATTCTATTT
1 TTTTTTTTAT-ATTTTATTT
646665 ATTTTGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (22 bp):
TTTTTTTTATATTTTATTTTTA
Found at i:646649 original size:26 final size:28
Alignment explanation
Indices: 646605--646677 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
646595 CTTTGTTTTT
* **
646605 TTTTATTTTTGTTTATTATTTTTTTTATA
1 TTTTATTTTTGTTTATT-TTATCATTATA
*
646634 TTTTATTTTTGTTTATTTTATCATTCTA
1 TTTTATTTTTGTTTATTTTATCATTATA
646662 -TTTA-TTTTGTTTATTT
1 TTTTATTTTTGTTTATTT
646678 CCCTTTACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 12 0.30
27 4 0.10
28 7 0.17
29 17 0.43
ACGTcount: A:0.16, C:0.03, G:0.04, T:0.77
Consensus pattern (28 bp):
TTTTATTTTTGTTTATTTTATCATTATA
Found at i:649811 original size:15 final size:15
Alignment explanation
Indices: 649791--649826 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
649781 GAATGAGAAA
* *
649791 GTACTTTGAGAATTC
1 GTACTTTAAAAATTC
649806 GTACTTTAAAAATTC
1 GTACTTTAAAAATTC
649821 GTACTT
1 GTACTT
649827 AACTCGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (15 bp):
GTACTTTAAAAATTC
Found at i:651102 original size:24 final size:24
Alignment explanation
Indices: 651075--651183 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
651065 AAATATTTTA
*
651075 TCTGATTTCCGA-CTTGAATTATGT
1 TCTGATTTCTGATC-TGAATTATGT
* * *
651099 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTATGT
*
651123 TCTGATTTCTGATCTGGATTATGT
1 TCTGATTTCTGATCTGAATTATGT
* *
651147 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTATGT
*
651171 TTTGATTTCTGAT
1 TCTGATTTCTGAT
651184 ATCTCCGTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 65 0.93
25 3 0.04
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTATGT
Found at i:651127 original size:12 final size:12
Alignment explanation
Indices: 651112--651181 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
651102 GATACATGAC
651112 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
651124 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
651136 CTGGATTATGTT
1 CTGAATTCTGTT
*
651148 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
651160 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
651172 TTGATTTCTG
1 CTGAATTCTG
651182 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:651180 original size:48 final size:48
Alignment explanation
Indices: 651075--651183 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
651065 AAATATTTTA
* *
651075 TCTGATTTCCGA-CTTGAATTATGTTCTGATACATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTATGTTCTGATACATGACCTGAATTCTGT
*
651123 TCTGATTTCTGATCTGGATTATGTTCTGATATC-TGATCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTATGTTCTGATA-CATGACCTGAATTCTGT
*
651171 TTTGATTTCTGAT
1 TCTGATTTCTGAT
651184 ATCTCCGTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 53 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTATGTTCTGATACATGACCTGAATTCTGT
Done.