Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:442221 original size:23 final size:23
Alignment explanation
Indices: 442195--442242 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
442185 TTTAACTTAT
442195 ATTAAGAAAATACGATATTATAC
1 ATTAAGAAAATACGATATTATAC
442218 ATTAAGAAAATACGATATTATAC
1 ATTAAGAAAATACGATATTATAC
442241 AT
1 AT
442243 AGGTTTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (23 bp):
ATTAAGAAAATACGATATTATAC
Found at i:443469 original size:15 final size:15
Alignment explanation
Indices: 443449--443478 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
443439 TACATGCTTG
*
443449 ATGGTATCGGTACCT
1 ATGGTATCGATACCT
443464 ATGGTATCGATACCT
1 ATGGTATCGATACCT
443479 CTGCTTTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (15 bp):
ATGGTATCGATACCT
Found at i:454353 original size:23 final size:24
Alignment explanation
Indices: 454323--454370 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
454313 CGGGACACAT
454323 TGGTCCTTCAGGAC-ATTTCATAG
1 TGGTCCTTCAGGACAATTTCATAG
454346 TGGTCCTTCAGGACAAATTTCATAG
1 TGGTCCTTCAGGAC-AATTTCATAG
454371 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (24 bp):
TGGTCCTTCAGGACAATTTCATAG
Found at i:456455 original size:23 final size:23
Alignment explanation
Indices: 456429--456478 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
456419 CACCACAGCT
456429 CGTATAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCGAAGTGCCA
** *
456452 CGTATATTTGCACCGAAGTGCCG
1 CGTATAAATGCACCGAAGTGCCA
456475 CGTA
1 CGTA
456479 GAATTACACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTATAAATGCACCGAAGTGCCA
Found at i:456488 original size:23 final size:23
Alignment explanation
Indices: 456439--456494 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
456429 CGTATAAATG
* * *
456439 CACCGAAGTGCCACGTATATTTG
1 CACCGAAGTGCCACGTAGAATTA
*
456462 CACCGAAGTGCCGCGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
*
456485 CACCGTAGTG
1 CACCGAAGTG
456495 TCATATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:465559 original size:417 final size:415
Alignment explanation
Indices: 464769--465584 Score: 1121
Period size: 417 Copynumber: 2.0 Consensus size: 415
464759 ATATTTTAAT
* * * *
464769 TATAGTGATAAAATATATTGTCACAAAGATTTCACTCCATATTTTTTTTGCGTCAAAAAGTCATA
1 TATAGTAACAAAATATATTATCACAAAGATTTCACTCCATATTTTTTTTGCG-CAAAAAATCATA
* * * *
464834 TGGTAACAAAATTTTGTAACTATATGTGTTAATAATTATTACAAAAAAAAGTATTGTCACAAAAA
65 TAGTAACAAAATTTTGTAACTATAAGTGTTAATAATTATTAC-AAAAAAAGCATTGTAACAAAAA
* *
464899 ATAATGATATTCACGTTTTTGTAAAAAATTATATTTTTAGTTATAAATTTTAACTATAATATAGC
129 ATAATGATATTCACGTTTTTGTAAAAAATTATACTTGTAGTTATAAATTTTAACTATAATATAGC
* *
464964 ATATATTGTCATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGACAATTTTTATAA
194 ATATATTGTCATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTGATATTGACAATGTTTATAA
* *
465029 TTATAATTTATAGTTTTTTATAAAAAAATTATCACATCAAATAATAAAATTCAACCTTTTTGTAA
259 TTATAATTTATAGTTTTTTACAAAAAAATTATCACATCAAATAATAAAATTCAAACTTTTTGTAA
465094 TAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACCATTTCTC
324 TAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACCATTTCTC
465159 CATATTTTTCAGTGTAAAAAAATGTTA
389 CATATTTTTCAGTGTAAAAAAATGTTA
*
465186 TATAGTAACAAAATATATTATCATAAAGATTTTC-CTCCATATTTTTTTGTGC-CAAAAAAATCA
1 TATAGTAACAAAATATATTATCACAAAGA-TTTCACTCCATATTTTTTT-TGCGC-AAAAAATCA
* * * *
465249 TATAGTAA-TAATTTTTGTAAGTATAAGTGTTTATAATTATTAC-AAAAAA-CATTGTAAC-AAA
63 TATAGTAACAAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAGCATTGTAACAAAA
* * * * * * *
465310 AATAATGGTATTCACTTTTTTGTGATAAATTATACTTGTAGTTATAAATTTTTATTATAGTGAT-
128 AATAATGATATTCACGTTTTTGTAAAAAATTATACTTGTAGTTATAAATTTTAACTATAAT-ATA
* *
465374 GACATATATTGTGATGAA-TATTTTTCTCCACTTTTTTTCGTTTCAAAAAGTGATATTGATAA-G
192 G-CATATATTGTCAT-AACTATTTTTCTCCAC-TTTTTT-GTTTC-AAAAGTGATATTGACAATG
*
465437 TTTGTAATTATAATTTATAGTTATTGTTACATAAAAAATTATCACATCAAATAATAAAATT-AAA
252 TTTATAATTATAATTTATAGTT-TT-TTACA-AAAAAATTATCACATCAAATAATAAAATTCAAA
* * * * *
465501 GTTTTTTTAATCAATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAGTTATACTATCAGA
314 CTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGA
*
465566 ACCATTTCTCCCTATTTTT
379 ACCATTTCTCCATATTTTT
465585 TGGTGCCAAA
Statistics
Matches: 352, Mismatches: 35, Indels: 24
0.86 0.09 0.06
Matches are distributed among these distances:
412 56 0.16
413 34 0.10
414 14 0.04
415 26 0.07
416 48 0.14
417 138 0.39
418 36 0.10
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (415 bp):
TATAGTAACAAAATATATTATCACAAAGATTTCACTCCATATTTTTTTTGCGCAAAAAATCATAT
AGTAACAAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAAGCATTGTAACAAAAAAT
AATGATATTCACGTTTTTGTAAAAAATTATACTTGTAGTTATAAATTTTAACTATAATATAGCAT
ATATTGTCATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTGATATTGACAATGTTTATAATT
ATAATTTATAGTTTTTTACAAAAAAATTATCACATCAAATAATAAAATTCAAACTTTTTGTAATA
AATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACCATTTCTCCA
TATTTTTCAGTGTAAAAAAATGTTA
Found at i:465909 original size:17 final size:17
Alignment explanation
Indices: 465881--465921 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
465871 ATTTTTTTCT
*
465881 TAATTATAATTATGTAAA
1 TAATT-TAATTAAGTAAA
465899 TAATTTAATTAAGTAAA
1 TAATTTAATTAAGTAAA
465916 TAATTT
1 TAATTT
465922 GTATAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
TAATTTAATTAAGTAAA
Found at i:466106 original size:3 final size:3
Alignment explanation
Indices: 466098--466123 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
466088 CTTCATTTTG
466098 ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC AC
466124 TGTTATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:467834 original size:3 final size:3
Alignment explanation
Indices: 467828--467882 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
467818 TAATATACTA
467828 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
467873 TAT TAT TAT T
1 TAT TAT TAT T
467883 TTTTTTTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:467850 original size:17 final size:17
Alignment explanation
Indices: 467828--467882 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
467818 TAATATACTA
467828 TATTATTATATTATTAT
1 TATTATTATATTATTAT
467845 TATTATTATTATT-TTAT
1 TATTATTA-TATTATTAT
*
467862 TATTATTATTTTATTAT
1 TATTATTATATTATTAT
467879 TATT
1 TATT
467883 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 3 0.09
17 28 0.80
18 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTATATTATTAT
Found at i:467887 original size:14 final size:14
Alignment explanation
Indices: 467830--467886 Score: 91
Period size: 14 Copynumber: 4.1 Consensus size: 14
467820 ATATACTATA
467830 TTATTA-TATTATT
1 TTATTATTATTATT
467843 ATTATTATTATTATT
1 -TTATTATTATTATT
467858 TTATTATTATTATT
1 TTATTATTATTATT
467872 TTATTATTATT-TT
1 TTATTATTATTATT
467885 TT
1 TT
467887 TTTAATTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.10
14 31 0.74
15 7 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:470128 original size:21 final size:22
Alignment explanation
Indices: 470102--470154 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
470092 ATTATTTGTC
470102 TTTTTTATTAAC-TTTTATTTA
1 TTTTTTATTAACATTTTATTTA
* *
470123 TTTTTTGTTATCTATTTTATTTA
1 TTTTTTATTAAC-ATTTTATTTA
470146 TTTTATTAT
1 TTTT-TTAT
470155 CATTATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
23 13 0.50
24 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTATTAACATTTTATTTA
Found at i:470161 original size:23 final size:21
Alignment explanation
Indices: 470114--470192 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 21
470104 TTTTATTAAC
*
470114 TTTTATTTATTTTTTGTTATCTA
1 TTTTATTTATTTTTT-TCAT-TA
470137 TTTTATTTATTTTATTATCATTA
1 TTTTATTTATTTT-TT-TCATTA
* *
470160 TTATATTAATATTTTTTCA-TA
1 TTTTATTTAT-TTTTTTCATTA
470181 TTTT-TTTATTTT
1 TTTTATTTATTTT
470193 ACAATGTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.06
20 4 0.08
21 5 0.10
22 3 0.06
23 25 0.52
24 8 0.17
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTATTTATTTTTTTCATTA
Found at i:474654 original size:253 final size:250
Alignment explanation
Indices: 474201--474857 Score: 967
Period size: 253 Copynumber: 2.6 Consensus size: 250
474191 AATTTTAGAG
**
474201 CCAATTTCAACTTCATAGCGAAGGATATTGGACTCGAAATAATACAACTTACTTGGATTTCAACT
1 CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAATAATACAACTTACTTGGATTTCAACT
* * ** * *
474266 TTATGACCAGTGATATCCAATTCAAGGCTCAACTTCATGACGGAGGGGCCATCCACAGTTTCAAC
66 TCACGAGAAG-GATATCCAATTCAAGGCTCAACTTCACGACGGA-GGG-CATCCACGGTTTCAAC
*
474331 TTCACGACGAAGGGAATCATGCACACAAGCAGCATCCATCTCCAGATTTGGATTTCAACTTCACG
128 TTCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCCAGATTTGGATTTCAACTTCACG
* *
474396 ACGAAGGATATCCATCTCAAAGAATGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAT
193 ACGAAGAATATCCAACTCAAAGAATGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAT
* *
474454 CCAATTTCAACTTCACGGCAAATGATATTGGACTCGAAATAATACAACTTACTTGGATTTCAACT
1 CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAATAATACAACTTACTTGGATTTCAACT
*
474519 TCACGATGAAGGATATCCAATTCAAGGTTCAACTTCACGACGGAGGAGACATCCACGGTTTCAAC
66 TCACGA-GAAGGATATCCAATTCAAGGCTCAACTTCACGACGGAGG-G-CATCCACGGTTTCAAC
* *
474584 TTCACGACGAAGGGAATCGTGCACACAAGCAGTATCCATCTCCAGATTTGGATTTCAACTTCATG
128 TTCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCCAGATTTGGATTTCAACTTCACG
*
474649 ACGAAGAATATTCAACTCAAAGAATGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAT
193 ACGAAGAATATCCAACTCAAAGAATGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAT
* ** * *
474707 CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAGCACAA-ATACTTCGATTTCAACT
1 CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAATAATACAACTTACTTGGATTTCAACT
* * * *
474771 TCACGACGAAGGATATTCAAGTT-AAGGCTCAACTTCACAATGAAAGGGCTATCCACGGTTTCAA
66 TCACGA-GAAGGATATCCAA-TTCAAGGCTCAACTTCACGACG-GAGGGC-ATCCACGGTTTCAA
*
474835 CTTCACGACGAAAGGAATCGTGC
127 CTTCACGACGAAGGGAATCGTGC
474858 TCACCAACAA
Statistics
Matches: 367, Mismatches: 32, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
251 1 0.00
252 88 0.24
253 276 0.75
254 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (250 bp):
CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAATAATACAACTTACTTGGATTTCAACT
TCACGAGAAGGATATCCAATTCAAGGCTCAACTTCACGACGGAGGGCATCCACGGTTTCAACTTC
ACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCCAGATTTGGATTTCAACTTCACGACG
AAGAATATCCAACTCAAAGAATGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAT
Found at i:475103 original size:116 final size:116
Alignment explanation
Indices: 474761--475084 Score: 492
Period size: 116 Copynumber: 2.8 Consensus size: 116
474751 CAAATACTTC
* * *
474761 GATTTCAACTTCACGACGAAGGATAT-TCAAGTT-AAGGCTCAACTTCACAATGAA-AGGGCTAT
1 GATTTCAACTTCACGACGAAGGATATCT-AA-TTCAAGGTTCAACTTCACAACGAAGA-GGCCAT
*
474823 CCACGGTTTCAACTTCACGACGAAAGGAATCGTGCTCACCAACAACATTAATTA
63 CCACGGTTTTAACTTCACGACGAAAGGAATCGTGCTCACCAACAACATTAATTA
* *
474877 GATTTCAACTTCACGACGAAGGATATCTAATTCAAGGTTCAACTTCACAACGAAGGGGACATCCA
1 GATTTCAACTTCACGACGAAGGATATCTAATTCAAGGTTCAACTTCACAACGAAGAGGCCATCCA
474942 CGGTTTTAACTTCACGACGAAAGGAATCGTGCTCACCAACAACATTAATTA
66 CGGTTTTAACTTCACGACGAAAGGAATCGTGCTCACCAACAACATTAATTA
* * * *
474993 GATTTCAACTTCCCGGCGAATGATATCTAATTCAAGGTTCAACTTCATAACGAAGAGGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCTAATTCAAGGTTCAACTTCACAACGAAGAGGCCATCCA
* *
475058 CGATTTTAACTTCACGACGAAGGGAAT
66 CGGTTTTAACTTCACGACGAAAGGAAT
475085 TGTACCCACC
Statistics
Matches: 191, Mismatches: 14, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
115 2 0.01
116 188 0.98
117 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (116 bp):
GATTTCAACTTCACGACGAAGGATATCTAATTCAAGGTTCAACTTCACAACGAAGAGGCCATCCA
CGGTTTTAACTTCACGACGAAAGGAATCGTGCTCACCAACAACATTAATTA
Found at i:475229 original size:21 final size:22
Alignment explanation
Indices: 475192--475235 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
475182 AATTTACTCA
*
475192 AAACAAAGTTTTGTCTCTCTTG
1 AAACAAAGTTTTATCTCTCTTG
475214 AAACAAA-TTTTATCTCTCTTG
1 AAACAAAGTTTTATCTCTCTTG
475235 A
1 A
475236 GACAGTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (22 bp):
AAACAAAGTTTTATCTCTCTTG
Found at i:475251 original size:36 final size:36
Alignment explanation
Indices: 475210--475290 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
475200 TTTTGTCTCT
475210 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCC
* *
475246 CTTGAAACAAATTTTTTCTTTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCC
475282 CTTGAAACA
1 CTTGAAACA
475291 CCAATCTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (36 bp):
CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCC
Found at i:475420 original size:33 final size:34
Alignment explanation
Indices: 475343--475432 Score: 121
Period size: 33 Copynumber: 2.7 Consensus size: 34
475333 CCTTGAGACA
475343 GTTTCTCTTGAAACACAAAAAAATCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAATCTTTGAAATC
* * * *
475377 ATTTCTCTTGAAACAGAAAATAA-CTTT-AAAGTT
1 GTTTCTCTTGAAACACAAAAAAATCTTTGAAA-TC
475410 GTTTCTCTTGAAACACAAAAAAA
1 GTTTCTCTTGAAACACAAAAAAA
475433 AAACCTTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 3 0.06
33 25 0.52
34 20 0.42
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAATCTTTGAAATC
Found at i:475903 original size:3 final size:3
Alignment explanation
Indices: 475895--475934 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
475885 TATATTATAA
475895 TAT TAT TAT T-T TATT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
475935 TAATTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:479009 original size:78 final size:77
Alignment explanation
Indices: 478792--479036 Score: 293
Period size: 77 Copynumber: 3.2 Consensus size: 77
478782 GCATTCCTTC
* * * *
478792 TGTCGTACCGAAA-ATTTACAGTCTCTTTTTGTTTTGCC-CATTTCCTTTCCCTTGATCCTCAGC
1 TGTCGTTCCGAAACACTTGCAGTCTCTTTTTGTTTTGCCTCGTTT-CTTTCCCTTGATCCTCAGC
*
478855 GTTGTCTTCTTTTT
65 ATTGTCTTC-TTTT
* * ** * *
478869 TTTGGTTTGGAAACATTTGCAGTCTC-TTTTGTTTTGCCTCG-TTCTTTTCCCTTGATCTTCAGC
1 TGTCGTTCCGAAACACTTGCAGTCTCTTTTTGTTTTGCCTCGTTTC-TTTCCCTTGATCCTCAGC
478932 ATTGTCTTCTTTT
65 ATTGTCTTCTTTT
* *
478945 TGTCGCTCCGAAACACTTGCAGTCCTCTTTTTGTTTTGCCTCGTTTCTTTCCCTTAATCCTCAGC
1 TGTCGTTCCGAAACACTTGCAGT-CTCTTTTTGTTTTGCCTCGTTTCTTTCCCTTGATCCTCAGC
479010 ATTGTCTTC-TTT
65 ATTGTCTTCTTTT
*
479022 TGTTGTTCCGAAACA
1 TGTCGTTCCGAAACA
479037 TTTGTAGCCC
Statistics
Matches: 143, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
76 22 0.15
77 66 0.46
78 52 0.36
79 3 0.02
ACGTcount: A:0.13, C:0.25, G:0.14, T:0.48
Consensus pattern (77 bp):
TGTCGTTCCGAAACACTTGCAGTCTCTTTTTGTTTTGCCTCGTTTCTTTCCCTTGATCCTCAGCA
TTGTCTTCTTTT
Found at i:481829 original size:15 final size:16
Alignment explanation
Indices: 481811--481843 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
481801 GTGGCAGATC
481811 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
481826 AAAATCCAGAACGGGA
1 AAAATCCAGAACGGGA
481842 AA
1 AA
481844 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:485692 original size:38 final size:38
Alignment explanation
Indices: 485642--485717 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
485632 ATATTGGTCG
485642 TATATGAACCATGGTCTTTCCGCTAGAACCTTAACGTA
1 TATATGAACCATGGTCTTTCCGCTAGAACCTTAACGTA
*
485680 TATATGATCCATGGTCTTTCCGCTAGAACCTTAACGTA
1 TATATGAACCATGGTCTTTCCGCTAGAACCTTAACGTA
485718 GTTTTCATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (38 bp):
TATATGAACCATGGTCTTTCCGCTAGAACCTTAACGTA
Found at i:486974 original size:15 final size:15
Alignment explanation
Indices: 486956--486985 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
486946 ATCTTAACCC
486956 GAGCATGGATTACAT
1 GAGCATGGATTACAT
486971 GAGCATGGATTACAT
1 GAGCATGGATTACAT
486986 CAAGGGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
GAGCATGGATTACAT
Found at i:491187 original size:30 final size:30
Alignment explanation
Indices: 491153--491236 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
491143 AAATGGATAC
* *
491153 AAACATAAACTTAAAGGA-TCAAAATAGAAA
1 AAACAAAAAATTAAAGGACT-AAAATAGAAA
* *
491183 AAACAGAAAATTAAAGGACTAAAATAGTAA
1 AAACAAAAAATTAAAGGACTAAAATAGAAA
* *
491213 AAACAAAAATTTAAATGACTAAAA
1 AAACAAAAAATTAAAGGACTAAAA
491237 CAACAATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (30 bp):
AAACAAAAAATTAAAGGACTAAAATAGAAA
Found at i:491468 original size:2 final size:2
Alignment explanation
Indices: 491461--491487 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
491451 ATATCTACAA
491461 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
491488 AATGCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:493189 original size:43 final size:43
Alignment explanation
Indices: 493128--493335 Score: 192
Period size: 43 Copynumber: 4.9 Consensus size: 43
493118 GTCAGGGATG
*
493128 ACACTGCTCATATGCGATGAGTCTTGGCCATCTAAGGGTGATA
1 ACACTGCTCATATGCGATGAGTCTTGGTCATCTAAGGGTGATA
* * * *
493171 ACACTGCTCATATGCGATGAGTCCTGGTTATCT-AGGG-GTTG
1 ACACTGCTCATATGCGATGAGTCTTGGTCATCTAAGGGTGATA
* *
493212 ACACTGCTCATATACGATGAGTCTTGGTCATATAAGGGTGATA
1 ACACTGCTCATATGCGATGAGTCTTGGTCATCTAAGGGTGATA
* * * * * * * * *
493255 ACACGGTTCCTATGTGATGAGGACGGCTGGTTATCT--GGG-GTTG
1 ACACTGCTCATATGCGATGA-GTC--TTGGTCATCTAAGGGTGATA
* *
493298 ACACAGCTCATATGCGATGAGTCTTGGTCATATAAGGG
1 ACACTGCTCATATGCGATGAGTCTTGGTCATCTAAGGG
493336 ATAGTTTCAA
Statistics
Matches: 128, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
40 7 0.05
41 31 0.24
42 13 0.10
43 65 0.51
44 5 0.04
46 7 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
ACACTGCTCATATGCGATGAGTCTTGGTCATCTAAGGGTGATA
Found at i:493274 original size:84 final size:85
Alignment explanation
Indices: 493126--493335 Score: 307
Period size: 84 Copynumber: 2.5 Consensus size: 85
493116 TGGTCAGGGA
* * *
493126 TGACACTGCTCATATGCGATGAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATATGCGATGA
1 TGACACTGCTCATATGCGATGAGTCTTGGTCATATAAGGGTGATAACACGGCTCATATGCGATGA
*
493191 -GTC-CTGGTTATCTAGGGGT
66 GGACGCTGGTTATCT-GGGGT
* * * *
493210 TGACACTGCTCATATACGATGAGTCTTGGTCATATAAGGGTGATAACACGGTTCCTATGTGATGA
1 TGACACTGCTCATATGCGATGAGTCTTGGTCATATAAGGGTGATAACACGGCTCATATGCGATGA
493275 GGACGGCTGGTTATCTGGGGT
66 GGAC-GCTGGTTATCTGGGGT
*
493296 TGACACAGCTCATATGCGATGAGTCTTGGTCATATAAGGG
1 TGACACTGCTCATATGCGATGAGTCTTGGTCATATAAGGG
493336 ATAGTTTCAA
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 58 0.51
85 2 0.02
86 43 0.38
87 10 0.09
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (85 bp):
TGACACTGCTCATATGCGATGAGTCTTGGTCATATAAGGGTGATAACACGGCTCATATGCGATGA
GGACGCTGGTTATCTGGGGT
Found at i:493579 original size:36 final size:36
Alignment explanation
Indices: 493533--493659 Score: 102
Period size: 36 Copynumber: 3.6 Consensus size: 36
493523 AATAGAGATA
*
493533 TTTCACGAGAAAATATCTCAAGGAAAATAATATTTG
1 TTTCAAGAGAAAATATCTCAAGGAAAATAATATTTG
* * *
493569 TTTCAAGAGAAACAAATCTC-A--AAGATGAT-TGTTG
1 TTTCAAGAGAAA-ATATCTCAAGGAAAATAATAT-TTG
* *** * *
493603 TTTCATGAGAAACGGTCTCAAGGAAAATAAGATATG
1 TTTCAAGAGAAAATATCTCAAGGAAAATAATATTTG
493639 TTTCAAGAG-AAATAATCTCAA
1 TTTCAAGAGAAAAT-ATCTCAA
493660 AGTTTGGTCA
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
33 5 0.07
34 21 0.31
35 2 0.03
36 33 0.49
37 7 0.10
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (36 bp):
TTTCAAGAGAAAATATCTCAAGGAAAATAATATTTG
Found at i:493745 original size:71 final size:71
Alignment explanation
Indices: 493548--493802 Score: 261
Period size: 70 Copynumber: 3.6 Consensus size: 71
493538 CGAGAAAATA
* * *
493548 TCTCAAGGAAAATAATAT-TTGTTTCAAGAGAAACAAATCTCAAAG-ATGATTGTTGTTTCATGA
1 TCTCAAGGAAAATAAGATATTGTTTCAAGAGAAAC-AATCTCAAAGTTTGGTTGTTGTTTCATGA
*
493611 GAAACGG
65 GAAACAG
* ** *
493618 TCTCAAGGAAAATAAGATA-TGTTTCAAGAGAAATAATCTCAAAGTTTGGTCATTGTTTCATTAG
1 TCTCAAGGAAAATAAGATATTGTTTCAAGAGAAACAATCTCAAAGTTTGGTTGTTGTTTCATGAG
*
493682 AGACAG
66 AAACAG
* ** * * *
493688 TCTCAAGGAAACTTTGATATTGTTTCAAGGGAAACAATATCAAAGTTTGGTTGTTGTTTCATAAG
1 TCTCAAGGAAAATAAGATATTGTTTCAAGAGAAACAATCTCAAAGTTTGGTTGTTGTTTCATGAG
493753 AAA-ATG
66 AAACA-G
* * * * *
493759 TCTCGAGGGAGACAAAAT-TTGTTTCAAGAGAAACAGA-CTCAAAG
1 TCTCAAGGAAAATAAGATATTGTTTCAAGAGAAACA-ATCTCAAAG
493803 ATTATAAATT
Statistics
Matches: 151, Mismatches: 29, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
69 10 0.07
70 88 0.58
71 53 0.35
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (71 bp):
TCTCAAGGAAAATAAGATATTGTTTCAAGAGAAACAATCTCAAAGTTTGGTTGTTGTTTCATGAG
AAACAG
Found at i:493894 original size:66 final size:71
Alignment explanation
Indices: 493816--493944 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 71
493806 ATAAATTTTG
* * *
493816 TTTCCAATGAAACAAACTC-AA-A-GA-TTTT-TTTCAAAATAAATTATCTCAAGAGAGAAAAAA
1 TTTCCAAAGAAACAAACTCAAAGATGATTTTTGTTTCAAAAGAAATTATCTCAAGAGACAAAAAA
493876 ACTTTA
66 ACTTTA
* *
493882 TTTCCAAAGAAACATACTCAAAGATGATTTTTGTTTCAAAAGAAATTGTCTCAAGAGACAAAA
1 TTTCCAAAGAAACAAACTCAAAGATGATTTTTGTTTCAAAAGAAATTATCTCAAGAGACAAAA
493945 TTAGTTTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
66 17 0.32
67 2 0.04
68 1 0.02
69 2 0.04
70 4 0.08
71 27 0.51
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (71 bp):
TTTCCAAAGAAACAAACTCAAAGATGATTTTTGTTTCAAAAGAAATTATCTCAAGAGACAAAAAA
ACTTTA
Found at i:494204 original size:34 final size:34
Alignment explanation
Indices: 494156--494222 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
494146 AAAGGAAAAA
*
494156 TGTCTCAAGCGAGACGAAATTTG-TTTTGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGCTTTT-AGAAAT
*
494190 TGTCTCAAGTGAGACAAAATTTGCTTTTAGAAA
1 TGTCTCAAGCGAGACAAAATTTGCTTTTAGAAA
494223 AACACCATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAAATTTGCTTTTAGAAAT
Found at i:495324 original size:3 final size:3
Alignment explanation
Indices: 495316--495368 Score: 61
Period size: 3 Copynumber: 16.7 Consensus size: 3
495306 AATATTTAAT
* *
495316 TAA TAA TAA TAA TAA TATA TAA TATA TAA TAT TAA TAA TAA TATT TAA
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TA-A TAA
495364 TAA TA
1 TAA TA
495369 TTTTTTTCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
3 35 0.81
4 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:495333 original size:23 final size:23
Alignment explanation
Indices: 495306--495368 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 23
495296 CAAAATGTAA
495306 AATATTTAATTAATAATAATAAT
1 AATATTTAATTAATAATAATAAT
* *
495329 AATATATAATATATAATATTAATAAT
1 AATAT-TTA-AT-TAATAATAATAAT
495355 AATATTTAA-TAATA
1 AATATTTAATTAATA
495369 TTTTTTTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.15
23 5 0.15
24 3 0.09
25 4 0.12
26 17 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATTTAATTAATAATAATAAT
Found at i:495369 original size:29 final size:26
Alignment explanation
Indices: 495316--495365 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
495306 AATATTTAAT
495316 TAATAATAATAATAATATATAATATA
1 TAATAATAATAATAATATATAATATA
* *
495342 TAATATTAATAATAATATTTAATA
1 TAATAATAATAATAATATATAATA
495366 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAATAATAATAATAATATATAATATA
Found at i:497247 original size:2 final size:2
Alignment explanation
Indices: 497240--497279 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
497230 AAAATAGGTT
497240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
497280 AAGTTTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:503664 original size:20 final size:20
Alignment explanation
Indices: 503622--503664 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
503612 TTTTCTCTTG
* *
503622 AAAGCAAAATTGGATTTTGA
1 AAAGCAAAATTGAATTTTAA
503642 AAAGCAAAA-TGAAATTTTAA
1 AAAGCAAAATTG-AATTTTAA
503662 AAA
1 AAA
503665 ATGATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (20 bp):
AAAGCAAAATTGAATTTTAA
Found at i:506388 original size:20 final size:20
Alignment explanation
Indices: 506363--506406 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
506353 ACTCCGTTGG
506363 TCAATAACAAAAAACATTGA
1 TCAATAACAAAAAACATTGA
* * *
506383 TCAATAACGAAAAATATTGG
1 TCAATAACAAAAAACATTGA
506403 TCAA
1 TCAA
506407 AGTGTCACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (20 bp):
TCAATAACAAAAAACATTGA
Found at i:509089 original size:2 final size:2
Alignment explanation
Indices: 509082--509118 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
509072 AAAAATAAGA
509082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
509119 GTTATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:509824 original size:2 final size:2
Alignment explanation
Indices: 509817--509873 Score: 75
Period size: 2 Copynumber: 29.5 Consensus size: 2
509807 TATCAATAAT
*
509817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
509858 TA -A GTA T- TA TA TA TA T
1 TA TA -TA TA TA TA TA TA T
509874 TATTTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
1 3 0.06
2 45 0.92
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:510906 original size:3 final size:3
Alignment explanation
Indices: 510900--510927 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
510890 CGGCGGCGGC
510900 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
510928 AGAGTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:518604 original size:45 final size:45
Alignment explanation
Indices: 518313--518577 Score: 387
Period size: 45 Copynumber: 6.0 Consensus size: 45
518303 CCTCCATTCA
* *
518313 TGTTTATAATGCA-CCATTATGCATTTTCAGCTAT---ATA-TTTTC
1 TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTTC
* * *
518355 TGTTGATAATGTACCCATATGCATTTCAACTGTAGCATATTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
518400 TGTTGATAATGCACCCATATGCATTTCAACTGTAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
518445 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
518490 TGTTGATAATGTACCCATATGCATTTCAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * *
518535 TATTGATAATGCACCCATATGCATTTCAACTATGGCATCCTTT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTT
518578 CATTCCAATA
Statistics
Matches: 206, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
41 8 0.04
42 17 0.08
43 3 0.01
44 3 0.01
45 175 0.85
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
Found at i:525385 original size:45 final size:45
Alignment explanation
Indices: 525237--525579 Score: 428
Period size: 45 Copynumber: 7.6 Consensus size: 45
525227 TGTAACCTCC
* *
525237 TTTCATGTTTATAATGCA-CCATTATGCATTTTCAACTATAGCATAC-
1 TTTC-TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAACATACT
* *
525283 TTT-TGTTGATAATACACCCATATGCATTTCAACTAT-AGATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACT
** *
525326 TTTCTGTTGATAATGCACCCATACACATTTCAACTATAATATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACT
**
525371 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATTTCATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACT
*
525416 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACT
* *
525461 TTTTTGTTGATAATGCACCAATATGCATTTCAACTATAGA-ATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATA-ACATACT
* ** *
525506 TTTCTGTTGATAATGCACCCATATGTATTTCAACTATGGCAT-CC
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACT
* * *
525550 TTTCATGCTGATAATACACCCATATACATT
1 TTTC-TGTTGATAATGCACCCATATGCATT
525580 ATTATTTTCA
Statistics
Matches: 262, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
42 4 0.02
43 13 0.05
44 52 0.20
45 190 0.73
46 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAACATACT
Found at i:525496 original size:135 final size:133
Alignment explanation
Indices: 525237--525579 Score: 485
Period size: 135 Copynumber: 2.5 Consensus size: 133
525227 TGTAACCTCC
*
525237 TTTCATGTTTATAATGCA-CCATTATGCATTTTCAACTATAGCATACTTT-TGTTGATAATACAC
1 TTTC-TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTCTGTTGATAATACAC
*
525300 CCATATGCATTTCAACTATAGATACTTTTCTGTTGATAATGCACCCATACACATTTCAACTATA-
63 CCATATGCATTTCAACTATAGATACTTTTCTGTTGATAATGCACCAATACACATTTCAACTATAG
525364 ATATACT
128 A-ATACT
** *
525371 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATTTCATACTTTTCTGTTGATAATGCACCC
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATAC-TTTCTGTTGATAATACACCC
* **
525436 ATATGCATTTCAACTATAGCATACTTTTTTGTTGATAATGCACCAATATGCATTTCAACTATAGA
65 ATATGCATTTCAACTATAG-ATACTTTTCTGTTGATAATGCACCAATACACATTTCAACTATAGA
525501 ATACT
129 ATACT
* * * *
525506 TTTCTGTTGATAATGCACCCATATGTATTTCAACTATGGCATCCTTTCATGCTGATAATACACCC
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTC-TGTTGATAATACACCC
*
525571 ATATACATT
65 ATATGCATT
525580 ATTATTTTCA
Statistics
Matches: 188, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
132 15 0.08
133 21 0.11
134 45 0.24
135 106 0.56
136 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (133 bp):
TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTCTGTTGATAATACACCCA
TATGCATTTCAACTATAGATACTTTTCTGTTGATAATGCACCAATACACATTTCAACTATAGAAT
ACT
Found at i:536397 original size:6 final size:6
Alignment explanation
Indices: 536387--539694 Score: 5490
Period size: 6 Copynumber: 562.2 Consensus size: 6
536377 TCATGACATT
* * * * * * * *
536387 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
** * * * * * *
536435 ACATTT ACAT-- ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
536481 ACATAT ACATAT ATATAC ATATAC ATACATAT ACATAT ACATAT ACATAT
1 ACATAC ACATAC ACATAC ACATAC --ACATAC ACATAC ACATAC ACATAC
* * *
536531 ACATAT ACATAT ACATAT ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536579 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536627 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536675 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536723 ACATACAC ACATAC ACATA- ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACAT--AC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536770 ACATAC ACATAC ACATAC ACATAC ACATAC ACAT-C ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536817 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
536865 ACATAC ACATAC ACATAC ACATAC AC--AC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * *
536911 GCATAC AGATAC ACATAC ACATGC ACATGC ACATGC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* *
536959 ACATGC ACATAC ACATAC ACATAC ACAGAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537007 ACATAC ACATAC ACATACAC ACATAC ACA-AC ACATAC ACATACAC ACATAC
1 ACATAC ACATAC ACAT--AC ACATAC ACATAC ACATAC ACAT--AC ACATAC
537058 ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537104 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537152 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537200 ACATAC ACATAC ACATAC ACATAC ACATAC AC--AC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537246 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537294 ACATAC ACATAC AC--AC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537340 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537388 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537436 ACATAC ACAT-- ACATAC ACATAC ACATACAC ACATAC AC-TAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACAT--AC ACATAC ACATAC ACATAC
537483 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537531 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537579 ACATAC ACATACAC ACATAC ACATAC ACATAC ACAT-- ACA-AC ACATAC
1 ACATAC ACAT--AC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537626 ACATAC ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537672 ACATAC ACATAC ACACCTAC ACATAC ACATAC ACATAC ACAT-- ACATAC
1 ACATAC ACATAC ACA--TAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
537720 ACATAC ACACAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537768 ACATAC AC--AC ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
537812 ACATAC ACATAC ACATAC AC-TAC ACATAC ACATAC ACACAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537859 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATACAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--AC
*
537909 ACATAC ACATAC ACAT-- ACATAC CCATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
537955 ACATAC ACATAC ACATAC AC--AC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
538001 ACATAC ACATAC ACATAC ACATAC ACATAC ACACAAC ACAT-- ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACA-TAC ACATAC ACATAC
538048 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538096 ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538142 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538190 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538236 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538284 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538332 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538380 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538428 ACATAC ACATAC ACATAC ACATAC ACATAC ACACTAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACA-TAC ACATAC ACATAC
538477 ACAT-C ACATAC ACATAC ACATAC AC--AC ACAT-C ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538521 ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538567 AC-TAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538612 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538660 ACATAC ACATAC ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538706 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538752 ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538798 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538846 ACATAC ACATAC ACATAC ACATAC ACATAC ACATA- ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538893 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538939 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
538985 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
539033 ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC AC--AC ACACAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539077 ACATAC ACATAC ACATAC AC-TAC ACAT-- ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539122 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539170 ACATAC ACATAC ATACATAC AC-TAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC --ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539219 ACATAC AC-TAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539266 ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539312 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539360 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539408 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539456 ACATAC ACATAC ACATAC ACAT-- ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539502 ACATAC ACATAC ACATAC ACA-AC ACAT-- ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539547 ACA-AC ACATAC ACATAC ACATAC ACATAC AC--AC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539592 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC AC--AC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539638 ACAT-- ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT--
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
539682 ACATAC ACATAC A
1 ACATAC ACATAC A
539695 TATGCATATA
Statistics
Matches: 3172, Mismatches: 25, Indels: 210
0.93 0.01 0.06
Matches are distributed among these distances:
4 139 0.04
5 73 0.02
6 2897 0.91
7 11 0.00
8 52 0.02
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATAC
Found at i:536448 original size:10 final size:10
Alignment explanation
Indices: 536386--539702 Score: 904
Period size: 10 Copynumber: 352.2 Consensus size: 10
536376 TTCATGACAT
536386 TACATATACATA
1 TACATATAC--A
536398 TACATATACATA
1 TACATATAC--A
536410 TACATATACATA
1 TACATATAC--A
536422 TACATATACATA
1 TACATATAC--A
*
536434 TACATTTACA
1 TACATATACA
536444 TACATATACATA
1 TACATATAC--A
536456 TACATATACATA
1 TACATATAC--A
536468 TACATATACA
1 TACATATACA
* *
536478 T--ATACATA
1 TACATATACA
*
536486 TACATATATA
1 TACATATACA
536496 TACATATACA
1 TACATATACA
536506 TACATATACATA
1 TACATATAC--A
536518 TACATATACATA
1 TACATATAC--A
536530 TACATATACATA
1 TACATATAC--A
536542 TACATATACA
1 TACATATACA
*
536552 TACACATAC-
1 TACATATACA
*
536561 -ACATACACA
1 TACATATACA
*
536570 TACACATAC-
1 TACATATACA
*
536579 -ACATACACA
1 TACATATACA
*
536588 TACACATAC-
1 TACATATACA
*
536597 -ACATACACA
1 TACATATACA
*
536606 TACACATAC-
1 TACATATACA
*
536615 -ACATACACA
1 TACATATACA
*
536624 TACACATAC-
1 TACATATACA
*
536633 -ACATACACA
1 TACATATACA
*
536642 TACACATAC-
1 TACATATACA
*
536651 -ACATACACA
1 TACATATACA
*
536660 TACACATAC-
1 TACATATACA
*
536669 -ACATACACA
1 TACATATACA
*
536678 TACACATAC-
1 TACATATACA
*
536687 -ACATACACA
1 TACATATACA
*
536696 TACACATACACA
1 T--ACATATACA
*
536708 TACACATACACA
1 T--ACATATACA
*
536720 TACACATACA
1 TACATATACA
* *
536730 CACATACACA
1 TACATATACA
*
536740 TAACATACACA
1 T-ACATATACA
*
536751 TACACATAC-
1 TACATATACA
*
536760 -ACATACACA
1 TACATATACA
*
536769 TACATACACA
1 TACATATACA
*
536779 TACACATAC-
1 TACATATACA
*
536788 -ACATACACA
1 TACATATACA
*
536797 TACACATCACA
1 TACATAT-ACA
*
536808 TACACATAC-
1 TACATATACA
*
536817 -ACATACACA
1 TACATATACA
*
536826 TACACATAC-
1 TACATATACA
*
536835 -ACATACACA
1 TACATATACA
*
536844 TACACATAC-
1 TACATATACA
*
536853 -ACATACACA
1 TACATATACA
*
536862 TACACATAC-
1 TACATATACA
*
536871 -ACATACACA
1 TACATATACA
*
536880 TACACATACACA
1 T--ACATATACA
* *
536892 CACATACACA
1 TACATATACA
*
536902 TACACATACGCA
1 TACATATA--CA
*
536914 TACAGATAC-
1 TACATATACA
*
536923 -ACATACACA
1 TACATATACA
**
536932 TGCACATGCACA
1 T--ACATATACA
*
536944 TGCACATACACA
1 T--ACATATACA
*
536956 TACACATGCACA
1 TACATAT--ACA
*
536968 TACACATAC-
1 TACATATACA
*
536977 -ACATACACA
1 TACATATACA
* *
536986 GACACATAC-
1 TACATATACA
*
536995 -ACATACACA
1 TACATATACA
*
537004 TACACATAC-
1 TACATATACA
*
537013 -ACATACACA
1 TACATATACA
*
537022 TAC--ACACA
1 TACATATACA
* *
537030 TACACAACACA
1 TACA-TATACA
*
537041 TACACATACA
1 TACATATACA
* *
537051 CACATACACA
1 TACATATACA
*
537061 TACATACACA
1 TACATATACA
*
537071 TACACATAC-
1 TACATATACA
*
537080 -ACATACACA
1 TACATATACA
*
537089 TACACATAC-
1 TACATATACA
*
537098 -ACATACACA
1 TACATATACA
*
537107 TACACATAC-
1 TACATATACA
*
537116 -ACATACACA
1 TACATATACA
*
537125 TACACATAC-
1 TACATATACA
*
537134 -ACATACACA
1 TACATATACA
*
537143 TACACATAC-
1 TACATATACA
*
537152 -ACATACACA
1 TACATATACA
*
537161 TACACATAC-
1 TACATATACA
*
537170 -ACATACACA
1 TACATATACA
*
537179 TACACATAC-
1 TACATATACA
*
537188 -ACATACACA
1 TACATATACA
*
537197 TACACATAC-
1 TACATATACA
*
537206 -ACATACACA
1 TACATATACA
*
537215 TACACATAC-
1 TACATATACA
*
537224 -ACATACACA
1 TACATATACA
* *
537233 CACATACACA
1 TACATATACA
*
537243 TACACATAC-
1 TACATATACA
*
537252 -ACATACACA
1 TACATATACA
*
537261 TACACATAC-
1 TACATATACA
*
537270 -ACATACACA
1 TACATATACA
*
537279 TACACATAC-
1 TACATATACA
*
537288 -ACATACACA
1 TACATATACA
*
537297 TACACATACA
1 TACATATACA
* *
537307 CACACATAC-
1 TACATATACA
*
537316 -ACATACACA
1 TACATATACA
*
537325 TACACATAC-
1 TACATATACA
*
537334 -ACATACACA
1 TACATATACA
*
537343 TACACATAC-
1 TACATATACA
*
537352 -ACATACACA
1 TACATATACA
*
537361 TACACATAC-
1 TACATATACA
*
537370 -ACATACACA
1 TACATATACA
*
537379 TACACATAC-
1 TACATATACA
*
537388 -ACATACACA
1 TACATATACA
*
537397 TACACATAC-
1 TACATATACA
*
537406 -ACATACACA
1 TACATATACA
*
537415 TACACATAC-
1 TACATATACA
*
537424 -ACATACACA
1 TACATATACA
*
537433 TACACATACACA
1 T--ACATATACA
*
537445 TACATACACA
1 TACATATACA
*
537455 TACACATACA
1 TACATATACA
* *
537465 CACATACAC-
1 TACATATACA
*
537474 TACACATAC-
1 TACATATACA
*
537483 -ACATACACA
1 TACATATACA
*
537492 TACACATAC-
1 TACATATACA
*
537501 -ACATACACA
1 TACATATACA
*
537510 TACACATAC-
1 TACATATACA
*
537519 -ACATACACA
1 TACATATACA
*
537528 TACACATAC-
1 TACATATACA
*
537537 -ACATACACA
1 TACATATACA
*
537546 TACACATAC-
1 TACATATACA
*
537555 -ACATACACA
1 TACATATACA
*
537564 TACACATAC-
1 TACATATACA
*
537573 -ACATACACA
1 TACATATACA
*
537582 TACACATACA
1 TACATATACA
* *
537592 CACATACACA
1 TACATATACA
*
537602 TACACATACACA
1 T--ACATATACA
*
537614 TACA-ACACA
1 TACATATACA
*
537623 TACACATAC-
1 TACATATACA
*
537632 -ACATACACA
1 TACATATACA
*
537641 TACACATAC-
1 TACATATACA
*
537650 -ACATACACA
1 TACATATACA
*
537659 TACATACACA
1 TACATATACA
*
537669 TACACATAC-
1 TACATATACA
*
537678 -ACATACACA
1 TACATATACA
*
537687 CCTACACATAC-
1 --TACATATACA
*
537698 -ACATACACA
1 TACATATACA
*
537707 TACACATACA
1 TACATATACA
*
537717 TACACATAC-
1 TACATATACA
* *
537726 -ACACACACA
1 TACATATACA
*
537735 TACACATAC-
1 TACATATACA
*
537744 -ACATACACA
1 TACATATACA
*
537753 TACACATAC-
1 TACATATACA
*
537762 -ACATACACA
1 TACATATACA
* *
537771 TACACACACA
1 TACATATACA
*
537781 TACACATAC-
1 TACATATACA
*
537790 -ACATACACA
1 TACATATACA
*
537799 TACACATACA
1 TACATATACA
*
537809 TACACATAC-
1 TACATATACA
*
537818 -ACATACACA
1 TACATATACA
*
537827 TACACTACACA
1 TACA-TATACA
*
537838 TACACATACA
1 TACATATACA
* * * *
537848 CACACACATA
1 TACATATACA
* *
537858 CACATACACA
1 TACATATACA
*
537868 TACACATAC-
1 TACATATACA
*
537877 -ACATACACA
1 TACATATACA
*
537886 TACACATACACA
1 T--ACATATACA
*
537898 TACACATACA
1 TACATATACA
* *
537908 CACATACACA
1 TACATATACA
*
537918 TACACATACA
1 TACATATACA
*
537928 TACCCATACACA
1 TA--CATATACA
*
537940 TACACATAC-
1 TACATATACA
*
537949 -ACATACACA
1 TACATATACA
*
537958 TACACATAC-
1 TACATATACA
*
537967 -ACATACACA
1 TACATATACA
* *
537976 CACATACACA
1 TACATATACA
*
537986 TACACATAC-
1 TACATATACA
*
537995 -ACATACACA
1 TACATATACA
*
538004 TACACATAC-
1 TACATATACA
*
538013 -ACATACACA
1 TACATATACA
*
538022 TACACATACA
1 TACATATACA
* *
538032 CACA-ACACA
1 TACATATACA
*
538041 TACATACACA
1 TACATATACA
*
538051 TACACATAC-
1 TACATATACA
*
538060 -ACATACACA
1 TACATATACA
*
538069 TACACATAC-
1 TACATATACA
*
538078 -ACATACACA
1 TACATATACA
*
538087 TACACATAC-
1 TACATATACA
*
538096 -ACATACACA
1 TACATATACA
*
538105 TACACATAC-
1 TACATATACA
*
538114 -ACATACACA
1 TACATATACA
*
538123 TACATACACA
1 TACATATACA
*
538133 TACACATAC-
1 TACATATACA
*
538142 -ACATACACA
1 TACATATACA
*
538151 TACACATAC-
1 TACATATACA
*
538160 -ACATACACA
1 TACATATACA
*
538169 TACACATAC-
1 TACATATACA
*
538178 -ACATACACA
1 TACATATACA
*
538187 TACACATAC-
1 TACATATACA
*
538196 -ACATACACA
1 TACATATACA
*
538205 TACACATAC-
1 TACATATACA
*
538214 -ACATACACA
1 TACATATACA
*
538223 TACACATACACA
1 T--ACATATACA
*
538235 TACATACACA
1 TACATATACA
*
538245 TACACATAC-
1 TACATATACA
*
538254 -ACATACACA
1 TACATATACA
*
538263 TACACATAC-
1 TACATATACA
*
538272 -ACATACACA
1 TACATATACA
*
538281 TACACATAC-
1 TACATATACA
*
538290 -ACATACACA
1 TACATATACA
*
538299 TACACATAC-
1 TACATATACA
*
538308 -ACATACACA
1 TACATATACA
*
538317 TACACATAC-
1 TACATATACA
*
538326 -ACATACACA
1 TACATATACA
*
538335 TACACATAC-
1 TACATATACA
*
538344 -ACATACACA
1 TACATATACA
*
538353 TACACATAC-
1 TACATATACA
*
538362 -ACATACACA
1 TACATATACA
*
538371 TACACATAC-
1 TACATATACA
*
538380 -ACATACACA
1 TACATATACA
*
538389 TACACATAC-
1 TACATATACA
*
538398 -ACATACACA
1 TACATATACA
*
538407 TACACATAC-
1 TACATATACA
*
538416 -ACATACACA
1 TACATATACA
*
538425 TACACATAC-
1 TACATATACA
*
538434 -ACATACACA
1 TACATATACA
*
538443 TACACATAC-
1 TACATATACA
*
538452 -ACATACACA
1 TACATATACA
*
538461 CTACACATAC-
1 -TACATATACA
*
538471 -ACATACACA
1 TACATATACA
*
538480 T-CACATAC-
1 TACATATACA
*
538488 -ACATACACA
1 TACATATACA
* *
538497 TACACACACA
1 TACATATACA
*
538507 TCACATACACA
1 T-ACATATACA
*
538518 TACACATAC-
1 TACATATACA
*
538527 -ACATACACA
1 TACATATACA
*
538536 TACACATACA
1 TACATATACA
*
538546 TACACATAC-
1 TACATATACA
*
538555 -ACATACACA
1 TACATATACA
*
538564 TACACTACACA
1 TACA-TATACA
*
538575 TACACATAC-
1 TACATATACA
*
538584 -ACATACACA
1 TACATATACA
*
538593 TACACATACACA
1 T--ACATATACA
*
538605 TACATACACA
1 TACATATACA
*
538615 TACACATAC-
1 TACATATACA
*
538624 -ACATACACA
1 TACATATACA
*
538633 TACACATAC-
1 TACATATACA
*
538642 -ACATACACA
1 TACATATACA
*
538651 TACACATAC-
1 TACATATACA
*
538660 -ACATACACA
1 TACATATACA
*
538669 TACACATAC-
1 TACATATACA
*
538678 -ACATACACA
1 TACATATACA
*
538687 TACACATACA
1 TACATATACA
*
538697 TACACATAC-
1 TACATATACA
*
538706 -ACATACACA
1 TACATATACA
*
538715 TACACATAC-
1 TACATATACA
*
538724 -ACATACACA
1 TACATATACA
*
538733 TACACATAC-
1 TACATATACA
*
538742 -ACATACACA
1 TACATATACA
*
538751 TACATACACA
1 TACATATACA
*
538761 TACACATACACA
1 T--ACATATACA
*
538773 TACATACACA
1 TACATATACA
*
538783 TACACATAC-
1 TACATATACA
*
538792 -ACATACACA
1 TACATATACA
*
538801 TACACATAC-
1 TACATATACA
*
538810 -ACATACACA
1 TACATATACA
*
538819 TACACATAC-
1 TACATATACA
*
538828 -ACATACACA
1 TACATATACA
*
538837 TACACATAC-
1 TACATATACA
*
538846 -ACATACACA
1 TACATATACA
*
538855 TACACATAC-
1 TACATATACA
*
538864 -ACATACACA
1 TACATATACA
*
538873 TACACATAACA
1 TACATAT-ACA
*
538884 TACACATAC-
1 TACATATACA
*
538893 -ACATACACA
1 TACATATACA
*
538902 TACACATAC-
1 TACATATACA
*
538911 -ACATACACA
1 TACATATACA
*
538920 TACACATAC-
1 TACATATACA
*
538929 -ACATACACA
1 TACATATACA
*
538938 TACATACACA
1 TACATATACA
*
538948 TACACATAC-
1 TACATATACA
*
538957 -ACATACACA
1 TACATATACA
*
538966 TACACATAC-
1 TACATATACA
*
538975 -ACATACACA
1 TACATATACA
*
538984 TACATACACA
1 TACATATACA
*
538994 TACACATAC-
1 TACATATACA
*
539003 -ACATACACA
1 TACATATACA
*
539012 TACACATAC-
1 TACATATACA
*
539021 -ACATACACA
1 TACATATACA
*
539030 TACACATACA
1 TACATATACA
*
539040 TACACATAC-
1 TACATATACA
*
539049 -ACATACACA
1 TACATATACA
*
539058 TACACATAC-
1 TACATATACA
* *
539067 -ACACACACA
1 TACATATACA
* *
539076 CACATACACA
1 TACATATACA
*
539086 TACACATACA
1 TACATATACA
*
539096 CTACACATACA
1 -TACATATACA
*
539107 TACACATAC-
1 TACATATACA
*
539116 -ACATACACA
1 TACATATACA
*
539125 TACACATAC-
1 TACATATACA
*
539134 -ACATACACA
1 TACATATACA
*
539143 TACACATAC-
1 TACATATACA
*
539152 -ACATACACA
1 TACATATACA
*
539161 TACACATACACA
1 T--ACATATACA
*
539173 TACACATACA
1 TACATATACA
*
539183 TACATACACTA
1 TACATATAC-A
* *
539194 CACATACACA
1 TACATATACA
*
539204 TACACATAC-
1 TACATATACA
*
539213 -ACATACACA
1 TACATATACA
*
539222 TACACTACACA
1 TACA-TATACA
*
539233 TACACATAC-
1 TACATATACA
*
539242 -ACATACACA
1 TACATATACA
*
539251 TACACATAC-
1 TACATATACA
*
539260 -ACATACACA
1 TACATATACA
*
539269 TACACATAC-
1 TACATATACA
*
539278 -ACATACACA
1 TACATATACA
*
539287 TACATACACA
1 TACATATACA
*
539297 TACACATAC-
1 TACATATACA
*
539306 -ACATACACA
1 TACATATACA
*
539315 TACACATAC-
1 TACATATACA
*
539324 -ACATACACA
1 TACATATACA
*
539333 TACACATAC-
1 TACATATACA
*
539342 -ACATACACA
1 TACATATACA
*
539351 TACACATAC-
1 TACATATACA
*
539360 -ACATACACA
1 TACATATACA
*
539369 TACACATAC-
1 TACATATACA
*
539378 -ACATACACA
1 TACATATACA
*
539387 TACACATAC-
1 TACATATACA
*
539396 -ACATACACA
1 TACATATACA
*
539405 TACACATAC-
1 TACATATACA
*
539414 -ACATACACA
1 TACATATACA
*
539423 TACACATAC-
1 TACATATACA
*
539432 -ACATACACA
1 TACATATACA
*
539441 TACACATAC-
1 TACATATACA
*
539450 -ACATACACA
1 TACATATACA
*
539459 TACACATAC-
1 TACATATACA
*
539468 -ACATACACA
1 TACATATACA
*
539477 TACATACACA
1 TACATATACA
*
539487 TACACATAC-
1 TACATATACA
*
539496 -ACATACACA
1 TACATATACA
*
539505 TACACATAC-
1 TACATATACA
*
539514 -ACATACACA
1 TACATATACA
*
539523 -ACACATACA
1 TACATATACA
*
539532 TACACATAC-
1 TACATATACA
*
539541 -ACATACACAA
1 TACATATAC-A
* *
539551 CACATACACA
1 TACATATACA
*
539561 TACACATAC-
1 TACATATACA
*
539570 -ACATACACA
1 TACATATACA
* *
539579 CACATACACA
1 TACATATACA
*
539589 TACACATAC-
1 TACATATACA
*
539598 -ACATACACA
1 TACATATACA
*
539607 TACACATAC-
1 TACATATACA
*
539616 -ACATACACA
1 TACATATACA
* *
539625 TACACACACA
1 TACATATACA
*
539635 TACACATACA
1 TACATATACA
*
539645 TACACATAC-
1 TACATATACA
*
539654 -ACATACACA
1 TACATATACA
*
539663 TACACATAC-
1 TACATATACA
*
539672 -ACATACACA
1 TACATATACA
*
539681 TACATACACA
1 TACATATACA
*
539691 TACATATGCA
1 TACATATACA
539701 TA
1 TA
539703 TATAATTTTA
Statistics
Matches: 2410, Mismatches: 586, Indels: 620
0.67 0.16 0.17
Matches are distributed among these distances:
8 789 0.33
9 34 0.01
10 1222 0.51
11 111 0.05
12 254 0.11
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (10 bp):
TACATATACA
Found at i:540873 original size:5 final size:5
Alignment explanation
Indices: 540863--540912 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
540853 TGACCGGTCT
* *
540863 GACCC GACCC GACCC GA-CT GACCC GACCC GACCGTT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC
540913 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 31 0.82
7 4 0.11
ACGTcount: A:0.20, C:0.52, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:540883 original size:19 final size:18
Alignment explanation
Indices: 540861--540912 Score: 79
Period size: 19 Copynumber: 2.9 Consensus size: 18
540851 TTTGACCGGT
540861 CTGACCCGACCCGACCCG
1 CTGACCCGACCCGACCCG
540879 ACTGACCCGACCCGA-CCG
1 -CTGACCCGACCCGACCCG
*
540897 TTGACCCGACCCGACC
1 CTGACCCGACCCGACC
540913 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 13 0.42
18 4 0.13
19 14 0.45
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (18 bp):
CTGACCCGACCCGACCCG
Found at i:540903 original size:17 final size:17
Alignment explanation
Indices: 540862--540919 Score: 89
Period size: 17 Copynumber: 3.3 Consensus size: 17
540852 TTGACCGGTC
*
540862 TGACCCGACCCGACCCGAC
1 TGACCCGACCCGA-CCG-T
540881 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
540898 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
540915 TGACC
1 TGACC
540920 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 22 0.58
18 3 0.08
19 13 0.34
ACGTcount: A:0.19, C:0.48, G:0.22, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:540919 original size:7 final size:7
Alignment explanation
Indices: 540909--540939 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
540899 GACCCGACCC
540909 GACCGTT
1 GACCGTT
540916 GACCGTT
1 GACCGTT
540923 GACCGTT
1 GACCGTT
540930 GACCGTT
1 GACCGTT
540937 GAC
1 GAC
540940 TTCCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:547981 original size:14 final size:15
Alignment explanation
Indices: 547957--548008 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 15
547947 CCGGTCTGAA
*
547957 CCGATCTGACCCGAC
1 CCGACCTGACCCGAC
547972 CCGA-CTGACCC-AGC
1 CCGACCTGACCCGA-C
547986 CCGACCATTGACCCGAC
1 CCGACC--TGACCCGAC
548003 CCGACC
1 CCGACC
548009 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.03
14 12 0.38
15 5 0.16
17 13 0.41
18 1 0.03
ACGTcount: A:0.21, C:0.50, G:0.19, T:0.10
Consensus pattern (15 bp):
CCGACCTGACCCGAC
Found at i:547999 original size:17 final size:17
Alignment explanation
Indices: 547963--548015 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
547953 TGAACCGATC
547963 TGACCCGACCCGA-C--
1 TGACCCGACCCGACCAT
547977 TGACCC-AGCCCGACCAT
1 TGACCCGA-CCCGACCAT
*
547994 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCAT
548011 TGACC
1 TGACC
548016 GTTGACTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 1 0.03
14 11 0.33
15 1 0.03
17 19 0.58
18 1 0.03
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCAT
Found at i:551356 original size:141 final size:141
Alignment explanation
Indices: 551102--551357 Score: 377
Period size: 141 Copynumber: 1.8 Consensus size: 141
551092 AACTTGAAAA
* * * *
551102 TGGAGGTTCTAATATTAATCCTAATTTGTTTTAACCAATTATTGAGTAGAATAATCGAAATGGTC
1 TGGAGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATTGAATAGAATAATCGAAATGATC
* * *
551167 CCTCGAGCATGTTAATGCGAAAGCCAATTCAAATTACTCTCTATATTAAAGGACAAAAGTGAAAT
66 CCTCGAGCATGTTAATGCGAAAGCCAAATCAAATTACTCCCTAAATTAAAGGACAAAAGTGAAAT
551232 TAGACCTAAAT
131 TAGACCTAAAT
* * * *
551243 TGGAGGCTCTAATATTAATCTTAATTTATTTTAACCAATTCTTGAATCGAATAATTGAAATGATC
1 TGGAGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATTGAATAGAATAATCGAAATGATC
* * * *
551308 CCTTGAGCATTTTAATGCGAGAGCCAAATCAAATTATTCCCTAAATTAAA
66 CCTCGAGCATGTTAATGCGAAAGCCAAATCAAATTACTCCCTAAATTAAA
551358 AGTTTAGGAA
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
141 100 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (141 bp):
TGGAGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATTGAATAGAATAATCGAAATGATC
CCTCGAGCATGTTAATGCGAAAGCCAAATCAAATTACTCCCTAAATTAAAGGACAAAAGTGAAAT
TAGACCTAAAT
Found at i:551901 original size:23 final size:24
Alignment explanation
Indices: 551874--551925 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
551864 AAAACATCTT
* *
551874 AAAATAAAT-AACTTAGAAGGAAA
1 AAAATAAATAAAATAAGAAGGAAA
*
551897 AAAATAATTAAAATAAGAAGGAAA
1 AAAATAAATAAAATAAGAAGGAAA
551921 AAAAT
1 AAAAT
551926 TAAAGAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (24 bp):
AAAATAAATAAAATAAGAAGGAAA
Found at i:554086 original size:44 final size:44
Alignment explanation
Indices: 554000--554087 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
553990 AAAATAATAT
* *
554000 TGATGCTATTCCAACTCCTTATGTGAAGGAAACGAGCGAAATGG
1 TGATGCTATTCCAACTCCTTATGTGAAGGAAACGAACAAAATGG
* * * *
554044 TGATGCTGA-TCCAACTTCTTATGTGATGGAATCTAACAAAATGG
1 TGATGCT-ATTCCAACTCCTTATGTGAAGGAAACGAACAAAATGG
554088 AAATGTTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.97
45 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
TGATGCTATTCCAACTCCTTATGTGAAGGAAACGAACAAAATGG
Found at i:557017 original size:35 final size:35
Alignment explanation
Indices: 556970--557044 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
556960 AAAATACTTT
556970 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGA
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGA
* * *
557005 AATTT-GGAGTTTAGAATGTAATTTAAGTGTTTTGG
1 AATTTAGG-GTTTAGAATGTAATTAAAGTATTTTGA
557040 AATTT
1 AATTT
557045 TGAACATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 2 0.06
35 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGA
Found at i:558151 original size:35 final size:35
Alignment explanation
Indices: 558096--558172 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
558086 TCTAAACCCT
* *
558096 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATA
1 AAATTGAATTATTTTAGAATTTAGGGTTTAAAATA
* * * *
558131 TAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
1 AAATTGAATTATTTTAGAATTTAGGGTTTAAAATA
558166 AAATTGA
1 AAATTGA
558173 GGACTGTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGGTTTAAAATA
Found at i:560888 original size:21 final size:22
Alignment explanation
Indices: 560862--560909 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
560852 TTTTATTGAA
560862 TTTTATT-CACTTTTAATT-ATT
1 TTTTATTGCA-TTTTAATTGATT
*
560883 TTTTATTGCATTTTTATTGATT
1 TTTTATTGCATTTTAATTGATT
560905 TTTTA
1 TTTTA
560910 AAAAGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATTGCATTTTAATTGATT
Found at i:560909 original size:11 final size:10
Alignment explanation
Indices: 560852--560907 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
560842 TTACATTATG
*
560852 TTTTATTGAA
1 TTTTATTGAT
*
560862 TTTTATTCACT
1 TTTTATTGA-T
*
560873 TTTAATT-ATT
1 TTTTATTGA-T
560883 TTTTATTGCAT
1 TTTTATTG-AT
560894 TTTTATTGAT
1 TTTTATTGAT
560904 TTTT
1 TTTT
560908 TAAAAAGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 22 0.58
11 15 0.39
12 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTATTGAT
Found at i:561534 original size:16 final size:16
Alignment explanation
Indices: 561513--561543 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
561503 TCAAACTAGA
561513 TTGAGTTTAATGGGAT
1 TTGAGTTTAATGGGAT
561529 TTGAGTTTAATGGGA
1 TTGAGTTTAATGGGA
561544 CTTATCACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (16 bp):
TTGAGTTTAATGGGAT
Found at i:564059 original size:22 final size:23
Alignment explanation
Indices: 564033--564090 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
564023 AATTTATATG
564033 ATATGTGTTATATGG-AAATGATT
1 ATATGTGTTATATGGAAAATG-TT
*
564056 -TATGTATTATA-GGAAAATGTT
1 ATATGTGTTATATGGAAAATGTT
*
564077 ATATGAGTTATATG
1 ATATGTGTTATATG
564091 AACATGAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 4 0.14
22 24 0.83
23 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (23 bp):
ATATGTGTTATATGGAAAATGTT
Found at i:564409 original size:2 final size:2
Alignment explanation
Indices: 564402--564429 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
564392 AACATGGAGT
564402 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
564430 GACTAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:566986 original size:39 final size:39
Alignment explanation
Indices: 566943--567065 Score: 138
Period size: 39 Copynumber: 3.2 Consensus size: 39
566933 AAATAATCAC
* * *
566943 CCTCACCTTAGGTGTTATCTCCTTTATTACATTCAACAT
1 CCTCACCTTAGGTATTATCACCTTTATTACACTCAACAT
* * * *
566982 CCTCACCTCAGGAATTATCACCTTTATTACGCTCACCAT
1 CCTCACCTTAGGTATTATCACCTTTATTACACTCAACAT
* * * * *
567021 CATTACCTTAGGTATTACCGCCTTTATTACACTCATCAT
1 CCTCACCTTAGGTATTATCACCTTTATTACACTCAACAT
567060 CCTCAC
1 CCTCAC
567066 ATTAAGCATT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (39 bp):
CCTCACCTTAGGTATTATCACCTTTATTACACTCAACAT
Found at i:571288 original size:20 final size:18
Alignment explanation
Indices: 571238--571285 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
571228 AGTAAAGTGT
571238 AAAGGTAAATACAAATGC
1 AAAGGTAAATACAAATGC
* *
571256 AAAGATGCAAATACATGATGC
1 AAAG--GTAAATACA-AATGC
571277 AAAGGTAAA
1 AAAGGTAAA
571286 ATATATTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 8 0.33
21 8 0.33
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (18 bp):
AAAGGTAAATACAAATGC
Found at i:573316 original size:140 final size:140
Alignment explanation
Indices: 573167--573426 Score: 362
Period size: 140 Copynumber: 1.9 Consensus size: 140
573157 TAAAATATGT
*
573167 AGGCTCTAATATTAACCCTAATTTGTTTTAACCAATTAT-T-GTGTCGAATAATCAAAATAGTCC
1 AGGCTCTAATATTAACCCTAATTTATTTTAACCAATTATCTAGT-T-GAATAATCAAAATAGTCC
* * * * ** *
573230 CTCGGGCATGTTAATGCGATAGCTTATTCAAATTACCCCTTAAATTAAAGGACTAAAATGATAAT
64 ATAGAGCATGTTAATGCGAGAGCCAATTCAAATTACCCCTTAAATTAAAGAACTAAAATGATAAT
573295 AAACCTAAAGTG
129 AAACCTAAAGTG
* * * *
573307 AGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATCTAGTTGAATAATCTAAATGGTCTAT
1 AGGCTCTAATATTAACCCTAATTTATTTTAACCAATTATCTAGTTGAATAATCAAAATAGTCCAT
* *
573372 AGAGCATGTTAATGTGAGAGCCAATTCAAATTACTCCTTAAATTAAAGAACTAAA
66 AGAGCATGTTAATGCGAGAGCCAATTCAAATTACCCCTTAAATTAAAGAACTAAA
573427 GTATGGGAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
140 100 0.96
141 2 0.02
142 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (140 bp):
AGGCTCTAATATTAACCCTAATTTATTTTAACCAATTATCTAGTTGAATAATCAAAATAGTCCAT
AGAGCATGTTAATGCGAGAGCCAATTCAAATTACCCCTTAAATTAAAGAACTAAAATGATAATAA
ACCTAAAGTG
Found at i:578114 original size:2 final size:2
Alignment explanation
Indices: 578107--578141 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
578097 TCAATCTACA
578107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
578142 ATTTCCGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:578494 original size:85 final size:85
Alignment explanation
Indices: 578189--578496 Score: 438
Period size: 85 Copynumber: 3.6 Consensus size: 85
578179 GTCTTTTTAA
* * * * * *
578189 ATGACGTGTGCTTCAATGACACACAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACACACA
* **
578254 AATGTATGTCA-AACAGATTT
66 AATGTGTGTCATATTA-ATTT
*
578274 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACGCACA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACACACA
*
578339 AATGTGTGTCATCTTAATTT
66 AATGTGTGTCATATTAATTT
* * *
578359 ATGACGGGGGCTTTAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACAAACA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACACACA
*
578424 AATATGTGTCATATTAATTT
66 AATGTGTGTCATATTAATTT
* * *
578444 ATGACGGAGGCTTCAATGACGCGCAATGTAAGTCATACATACGCGCCATAAAT
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAAT
578497 GTGCATCATA
Statistics
Matches: 200, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
85 199 1.00
86 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (85 bp):
ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACACACA
AATGTGTGTCATATTAATTT
Found at i:580919 original size:34 final size:36
Alignment explanation
Indices: 580881--581126 Score: 120
Period size: 34 Copynumber: 6.7 Consensus size: 36
580871 ATTTGTTAAA
580881 AAAAATTGTTTTAAAACTATATA-TA-AT-ATGTTTC
1 AAAAATT-TTTTAAAACTATATATTATATAATGTTTC
* *
580915 AAAAATATTTTCAAAACTATATATTATATAATTTTTC
1 AAAAAT-TTTTTAAAACTATATATTATATAATGTTTC
* * * *
580952 AAAAATATTTTCAAACTATATGTTATATAGT-TTTC
1 AAAAATTTTTTAAAACTATATATTATATAATGTTTC
***
580987 --AAATTTAAAAAAAAAC-ATATATTATATATAT-TTTC
1 AAAAATTT--TTTAAAACTATATATTATATA-ATGTTTC
*
581022 AAAATGTTTTTTTTAAAAAAAC-ATATATTATATATAT-TTTC
1 AAAA---ATTTTTT---AAAACTATATATTATATA-ATGTTTC
** * *
581063 -AAAATGACTTAAAAACTATATATTATATATAATTTTTC
1 AAAAAT-TTTTTAAAACTATATA-T-TATATAATGTTTC
**
581101 -AAAATGTTTTGGAAACTATATATTAT
1 AAAAAT-TTTTTAAAACTATATATTAT
581127 GTATAAATTT
Statistics
Matches: 166, Mismatches: 26, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
33 5 0.03
34 31 0.19
35 21 0.13
36 30 0.18
37 19 0.11
38 30 0.18
40 6 0.04
41 24 0.14
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAAATTTTTTAAAACTATATATTATATAATGTTTC
Found at i:580972 original size:13 final size:12
Alignment explanation
Indices: 580905--580966 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
580895 AACTATATAT
580905 AATATGTTTCAAA
1 AATAT-TTTCAAA
580918 AATATTTTCAAA
1 AATATTTTCAAA
* *
580930 ACTATATATT-ATAT
1 A--ATATTTTCA-AA
580944 AAT-TTTTCAAA
1 AATATTTTCAAA
580955 AATATTTTCAAA
1 AATATTTTCAAA
580967 CTATATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.17
12 19 0.47
13 6 0.15
14 8 0.20
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (12 bp):
AATATTTTCAAA
Found at i:580978 original size:36 final size:37
Alignment explanation
Indices: 580840--581142 Score: 164
Period size: 38 Copynumber: 8.1 Consensus size: 37
580830 TAATAAATAT
* * *
580840 AAAAATATTTTCAAAACTATATAATACATATATTTGTTA
1 AAAAATATTTTCAAAACTATATATTATATA-ATTT-TTC
* * *
580879 AAAAAAATTGTTTTAAAACTATATA-TA-AT-ATGTTTC
1 AAAAATA-T-TTTCAAAACTATATATTATATAATTTTTC
580915 AAAAATATTTTCAAAACTATATATTATATAATTTTTC
1 AAAAATATTTTCAAAACTATATATTATATAATTTTTC
* *
580952 AAAAATATTTTC-AAACTATATGTTATAT-AGTTTTC
1 AAAAATATTTTCAAAACTATATATTATATAATTTTTC
** ****
580987 AAATTTA-AAAAAAAAC-ATATATTATAT-ATATTTTC
1 AAAAATATTTTCAAAACTATATATTATATAAT-TTTTC
* * *
581022 AAAATGTTTTTTTTAAAAAAAC-ATATATTATAT-ATATTTTC
1 AAAA---ATATTTT--CAAAACTATATATTATATAAT-TTTTC
* *
581063 -AAAATGA-CTTAAAAACTATATATTATATATAATTTTTC
1 AAAAAT-ATTTTCAAAACTATATA-T-TATATAATTTTTC
* ** *
581101 -AAAATGTTTTGGAAACTATATATTATGTATAAATTTTC
1 AAAAATATTTTCAAAACTATATATTA--TATAATTTTTC
581139 AAAA
1 AAAA
581143 TGCTTTATAG
Statistics
Matches: 212, Mismatches: 30, Indels: 44
0.74 0.10 0.15
Matches are distributed among these distances:
34 25 0.12
35 32 0.15
36 32 0.15
37 26 0.12
38 39 0.18
39 13 0.06
40 6 0.03
41 39 0.18
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAAATATTTTCAAAACTATATATTATATAATTTTTC
Found at i:581049 original size:77 final size:78
Alignment explanation
Indices: 580964--581110 Score: 194
Period size: 77 Copynumber: 1.9 Consensus size: 78
580954 AAATATTTTC
* *
580964 AAACTATATGT-TATATAGTTTTCAAATTTAAAAAAAAAC-ATATATTATATAT-A-TTTTCAAA
1 AAACTATAT-TATATATA-TTTTCAAAATGAAAAAAAAACTATATATTATATATAATTTTTCAAA
581025 ATGTTTTTTTTAAAA
64 ATGTTTTTTTTAAAA
***
581040 AAACATATATTATATATATTTTCAAAATGACTTAAAAACTATATATTATATATAATTTTTCAAAA
1 AAAC-TATATTATATATATTTTCAAAATGAAAAAAAAACTATATATTATATATAATTTTTCAAAA
581105 TGTTTT
65 TGTTTT
581111 GGAAACTATA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
76 21 0.34
77 24 0.39
78 1 0.02
79 15 0.25
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (78 bp):
AAACTATATTATATATATTTTCAAAATGAAAAAAAAACTATATATTATATATAATTTTTCAAAAT
GTTTTTTTTAAAA
Found at i:581824 original size:80 final size:81
Alignment explanation
Indices: 581725--581982 Score: 270
Period size: 80 Copynumber: 3.2 Consensus size: 81
581715 AATTTATTGA
* ** * *
581725 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCATAGTCGA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCCTTGGAGCTGAGCGTAATCGA
581789 ACTCGAAGGTCTTTGG
66 ACTCGAAGGTCTTTGG
* ** * * * * *
581805 CAGATAGCCCTTCTAGCCTTGAGCTATACCCCAAATGATGTGTCATT-GAGTTAAGCGTAATCAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCCTTGGAGCTGAGCGTAATCGA
*
581869 ACTCAAAGGTCTTTGTTGG
66 ACTCGAAGGTC--T-TTGG
* * * * * *
581888 CAGATAACCCTTCTAGCATTGAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCCTTGGAGCTGAGCGTAATCGA
*
581953 ACTCG-AGAGTCTTTAG
66 ACTCGAAG-GTCTTTGG
581969 CAGATAGCCCTTCT
1 CAGATAGCCCTTCT
581983 CGACTTAAGT
Statistics
Matches: 143, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
80 59 0.41
81 19 0.13
82 2 0.01
83 44 0.31
84 19 0.13
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (81 bp):
CAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCCCTTGGAGCTGAGCGTAATCGA
ACTCGAAGGTCTTTGG
Found at i:588269 original size:36 final size:36
Alignment explanation
Indices: 588229--588300 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
588219 TTTAGATGTG
588229 CCATATTAATTACATAAGAAGAAATCAAATCAATAA
1 CCATATTAATTACATAAGAAGAAATCAAATCAATAA
588265 CCATATTAATTACATAAGAAGAAATCAAATCAATAA
1 CCATATTAATTACATAAGAAGAAATCAAATCAATAA
588301 TTATTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (36 bp):
CCATATTAATTACATAAGAAGAAATCAAATCAATAA
Found at i:590335 original size:3 final size:3
Alignment explanation
Indices: 590327--590356 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
590317 TGGGTCTTAA
590327 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
590357 TATAACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:596993 original size:34 final size:34
Alignment explanation
Indices: 596950--597032 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
596940 GCAACAATCA
596950 TGTGCATTGAACTTTTTTTCTTTATTAATCTGGG
1 TGTGCATTGAACTTTTTTTCTTTATTAATCTGGG
596984 TGTGCATTGAACTTTTTTTCTTTATTAATCTGGG
1 TGTGCATTGAACTTTTTTTCTTTATTAATCTGGG
597018 TGTGCATTGAACTTT
1 TGTGCATTGAACTTT
597033 AAATAAATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (34 bp):
TGTGCATTGAACTTTTTTTCTTTATTAATCTGGG
Found at i:597740 original size:21 final size:22
Alignment explanation
Indices: 597714--597754 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
597704 TCAAAGGGAA
597714 AAGAAAAAA-ATAAAATAAAAC
1 AAGAAAAAATATAAAATAAAAC
*
597735 AAGAAAAAATATTAAATAAA
1 AAGAAAAAATATAAAATAAA
597755 TCAAAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (22 bp):
AAGAAAAAATATAAAATAAAAC
Found at i:597766 original size:26 final size:25
Alignment explanation
Indices: 597690--597771 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
597680 AATAATCAAT
597690 AAATACTAAATAAATC-AAAGGGAAA
1 AAATA-TAAATAAATCAAAAGGGAAA
* **
597715 AGAA-AAAAATAAAAT-AAAACAAGAAA
1 A-AATATAAAT-AAATCAAAA-GGGAAA
597741 AAATATTAAATAAATCAAAAGGGAAA
1 AAATA-TAAATAAATCAAAAGGGAAA
597767 AAATA
1 AAATA
597772 AAAAAGAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
24 4 0.09
25 11 0.25
26 21 0.48
27 8 0.18
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (25 bp):
AAATATAAATAAATCAAAAGGGAAA
Found at i:597849 original size:15 final size:15
Alignment explanation
Indices: 597837--597903 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 15
597827 GAAAAAAAAC
597837 AAAATAAATAAAATA
1 AAAATAAATAAAATA
*
597852 AAGATAAATAAAATTGA
1 AAAATAAATAAAA-T-A
*
597869 GAAAAT-ATTAAAAT-
1 -AAAATAAATAAAATA
597883 AAAA-AAATAAAA-A
1 AAAATAAATAAAATA
597896 AAAATAAA
1 AAAATAAA
597904 AAAGGTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
13 14 0.33
14 3 0.07
15 12 0.29
16 2 0.05
17 7 0.17
18 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:597906 original size:7 final size:8
Alignment explanation
Indices: 597817--597897 Score: 51
Period size: 8 Copynumber: 9.9 Consensus size: 8
597807 TAAGTATAAC
597817 AAAAAAAT
1 AAAAAAAT
597825 AAGAAAAA-
1 AA-AAAAAT
597833 AAACAAAAT
1 AAA-AAAAT
597842 AAATAAAAT
1 AAA-AAAAT
597851 AAAGATAAAT
1 AAA-A-AAAT
*
597861 --AAAATT
1 AAAAAAAT
* *
597867 GAGAAAAT
1 AAAAAAAT
**
597875 ATTAAAAT
1 AAAAAAAT
597883 AAAAAAAT
1 AAAAAAAT
597891 AAAAAAA
1 AAAAAAA
597898 AATAAAAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
6 3 0.05
7 2 0.04
8 31 0.54
9 17 0.30
10 4 0.07
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:597914 original size:18 final size:18
Alignment explanation
Indices: 597812--597906 Score: 66
Period size: 18 Copynumber: 5.0 Consensus size: 18
597802 ATATATAAGT
*
597812 ATAACAAAAAAATAAGAAA
1 ATAA-AAAAAAATAAAAAA
*
597831 A-AAAACAAAATAAATAAA
1 ATAAAAAAAAATAAA-AAA
* * **
597849 ATAAAGATAAATAAAATTG
1 ATAAAAAAAAATAAAA-AA
*
597868 AGAAAATATTAAAATAAAAAA
1 ATAAAA-A--AAAATAAAAAA
597889 ATAAAAAAAAATAAAAAA
1 ATAAAAAAAAATAAAAAA
597907 GGTAAAAATT
Statistics
Matches: 57, Mismatches: 13, Indels: 13
0.69 0.16 0.16
Matches are distributed among these distances:
17 9 0.16
18 18 0.32
19 15 0.26
20 2 0.04
21 5 0.09
22 8 0.14
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (18 bp):
ATAAAAAAAAATAAAAAA
Found at i:599406 original size:37 final size:37
Alignment explanation
Indices: 599305--599768 Score: 478
Period size: 37 Copynumber: 12.5 Consensus size: 37
599295 AATATGTATT
* *
599305 TTTTCAAAAT-TATTT-TAAAACTATATATGATATATATA
1 TTTTCAAAATGT-TTTCAAAAACTATATAT--TATATATG
**
599343 TTTTTTAAATGTTTTC-AAAACTATATATTATATATG
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATG
* * * *
599379 TCTTCAAAAATATTTTC-AAAACAATATATTATATAAG
1 TTTTC-AAAATGTTTTCAAAAACTATATATTATATATG
* *
599416 TTTTCAAAAAATGTTTTC-AAAACTCTATATTATATAAG
1 TTTTC--AAAATGTTTTCAAAAACTATATATTATATATG
* *
599454 TTTTCAAAAAATATTTTCAAAAACTATATATTATATATA
1 TTTTC--AAAATGTTTTCAAAAACTATATATTATATATG
599493 TTTTCAAAATGTTTTCAAAAAACTATATATTATATAT-
1 TTTTCAAAATGTTTTC-AAAAACTATATATTATATATG
* *
599530 ATTTCAAAATGTTTTCAAAAAACTATATATTATATAAG
1 TTTTCAAAATGTTTTC-AAAAACTATATATTATATATG
599568 TTTTCAAAAAAATGTTTTC-AAAACTATATA-T-TATA--
1 TTTTC---AAAATGTTTTCAAAAACTATATATTATATATG
* *
599603 ---T---AA-GTTTTCAAAAACTATATATTACACATATA
1 TTTTCAAAATGTTTTCAAAAACTATATATT--ATATATG
*
599635 TTTTCAAAATGTTTTCAAAAAACTATATATTATATATA
1 TTTTCAAAATGTTTTC-AAAAACTATATATTATATATG
599673 TTTTCAAAATGTTTTCAAAAACTATATATTATATATG
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATG
*
599710 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATT
1 TTTTCAAAATGTTTTCAAAAACTATATA-T-TATATATG
599749 TTTTCAAAATGTTTTCAAAA
1 TTTTCAAAATGTTTTCAAAA
599769 TCCGCTTTCT
Statistics
Matches: 374, Mismatches: 25, Indels: 53
0.83 0.06 0.12
Matches are distributed among these distances:
25 6 0.02
26 13 0.03
27 1 0.00
30 3 0.01
32 1 0.00
35 1 0.00
36 10 0.03
37 128 0.34
38 119 0.32
39 67 0.18
40 14 0.04
41 11 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTCAAAATGTTTTCAAAAACTATATATTATATATG
Found at i:599413 original size:75 final size:73
Alignment explanation
Indices: 599305--599768 Score: 411
Period size: 75 Copynumber: 6.3 Consensus size: 73
599295 AATATGTATT
* **
599305 TTTTCAAAATTATTTT-AAAACTATATATGATATATATATTTTTTAAATGTTTTC-AAAACTATA
1 TTTTCAAAA-TATTTTCAAAA-AATATAT-ATATATATATTTTAAAAATGTTTTCAAAAACTATA
599368 TATTATATATG
63 TATTATATATG
* *
599379 TCTTCAAAAATATTTTCAAAACAATATAT-TATATA-AGTTTTCAAAAAATGTTTTC-AAAACTC
1 TTTTC-AAAATATTTTCAAAA-AATATATATATATATA-TTTT--AAAAATGTTTTCAAAAACTA
*
599441 TATATTATATAAG
61 TATATTATATATG
* *
599454 TTTTCAAAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAAACTAT
1 TTTTC--AAAATATTTTCAAAAAATATATA-TATATATATTTTAAAAATGTTTTC-AAAAACTAT
599519 ATATTATATAT-
62 ATATTATATATG
* *
599530 ATTTCAAAATGTTTTCAAAAAACTATATAT-TATATAAGTTTTCAAAAAAATGTTTTC-AAAACT
1 TTTTCAAAATATTTTCAAAAAA-TATATATATATAT-A-TTTT---AAAAATGTTTTCAAAAACT
*
599593 ATATATTATATAAG
60 ATATATTATATATG
* * * * *
599607 TTTTCAAAA-A----C--TATATAT-TACACATATATTTTCAAAATGTTTTCAAAAAACTATATA
1 TTTTCAAAATATTTTCAAAAAATATATATATATATATTTTAAAAATGTTTTC-AAAAACTATATA
*
599664 TTATATATA
65 TTATATATG
* * * *
599673 TTTTCAAAATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATATA
1 TTTTCAAAATATTTTCAAAAAATATATA-TATATATATTTTAAAAATGTTTTCAAAAACTATATA
*
599738 TTATATATATT
65 -T-TATATATG
*
599749 TTTTCAAAATGTTTTCAAAA
1 TTTTCAAAATATTTTCAAAA
599769 TCCGCTTTCT
Statistics
Matches: 325, Mismatches: 33, Indels: 62
0.77 0.08 0.15
Matches are distributed among these distances:
64 11 0.03
66 27 0.08
67 4 0.01
68 3 0.01
69 7 0.02
70 2 0.01
71 1 0.00
72 2 0.01
73 19 0.06
74 41 0.13
75 96 0.30
76 65 0.20
77 35 0.11
78 12 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (73 bp):
TTTTCAAAATATTTTCAAAAAATATATATATATATATTTTAAAAATGTTTTCAAAAACTATATAT
TATATATG
Found at i:599552 original size:114 final size:113
Alignment explanation
Indices: 599349--599768 Score: 518
Period size: 114 Copynumber: 3.8 Consensus size: 113
599339 TATATTTTTT
* * * *
599349 AAATGTTTTCAAAACTATATATTATATATGTCTTCAAAAATATTTTC-AAAACAATATATTATAT
1 AAATGTTTTCAAAACTATATATTATATATATTTTC-AAAATGTTTTCAAAAACTATATATTATAT
*
599413 A-AGTTTTCAAAAAATGTTTTC--AAAACTCTATATTATATAAGTTTTCAAA
65 ATA-TTTTC--AAAATGTTTTCAAAAAACTATATATTATATAAGTTTTCAAA
*
599462 AAATATTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAAACTATATATTATA
1 AAATGTTTTC-AAAACTATATATTATATATATTTTCAAAATGTTTTC-AAAAACTATATATTATA
599527 TATA-TTTCAAAATGTTTTCAAAAAACTATATATTATATAAGTTTTCAAAA
64 TATATTTTCAAAATGTTTTCAAAAAACTATATATTATATAAGTTTTC-AAA
*
599577 AAATGTTTTCAAAAC--TATA-TAT-TATA---T---AA-GTTTTCAAAAACTATATATTACACA
1 AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATT--ATA
599631 TATATTTTCAAAATGTTTTCAAAAAACTATATATTATATATA-TTTTC--A
64 TATATTTTCAAAATGTTTTCAAAAAACTATATATTATATA-AGTTTTCAAA
*
599679 AAATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATAT
1 AAATGTTTTC-AAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
599744 ATATTTTTTCAAAATGTTTTCAAAA
65 ATA--TTTTCAAAATGTTTTCAAAA
599769 TCCGCTTTCT
Statistics
Matches: 272, Mismatches: 10, Indels: 49
0.82 0.03 0.15
Matches are distributed among these distances:
102 25 0.09
103 11 0.04
104 8 0.03
105 44 0.16
106 4 0.01
107 4 0.01
110 5 0.02
111 3 0.01
112 21 0.08
113 21 0.08
114 96 0.35
115 29 0.11
116 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (113 bp):
AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
TATTTTCAAAATGTTTTCAAAAAACTATATATTATATAAGTTTTCAAA
Found at i:599610 original size:66 final size:66
Alignment explanation
Indices: 599540--599757 Score: 198
Period size: 66 Copynumber: 3.2 Consensus size: 66
599530 ATTTCAAAAT
*
599540 GTTTTCAAAAAACTATATATT-ATATA-AGTTTTCAAAAAAATGTTTTC-AAAACTATATATTAT
1 GTTTTCAAAAAACTATATATTAACATATA-TTTTC---AAAATGTTTTCAAAAACTATATATTAT
599602 ATA-A
62 ATATA
599606 GTTTTC-AAAAACTATATATTACACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATAT
1 GTTTTCAAAAAACTATATATTA-ACATATATTTTCAAAATGTTTTC-AAAAACTATATATTATAT
599670 ATA
64 ATA
* *
599673 -TTTTCAAAATGTTTTCAAAAACTATATATT-ATATATGTTTTCAAAATGTTTTCAAAAACTATA
1 GTTTTC---A-------AAAAACTATATATTAACATATATTTTCAAAATGTTTTCAAAAACTATA
599736 TATTATATATA
56 TATTATATATA
*
599747 TTTTTTCAAAA
1 -GTTTTCAAAA
599758 TGTTTTCAAA
Statistics
Matches: 130, Mismatches: 3, Indels: 38
0.76 0.02 0.22
Matches are distributed among these distances:
64 11 0.08
65 14 0.11
66 32 0.25
67 10 0.08
68 1 0.01
73 1 0.01
74 21 0.16
75 21 0.16
76 5 0.04
77 14 0.11
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (66 bp):
GTTTTCAAAAAACTATATATTAACATATATTTTCAAAATGTTTTCAAAAACTATATATTATATAT
A
Found at i:599662 original size:142 final size:138
Alignment explanation
Indices: 599467--599744 Score: 470
Period size: 142 Copynumber: 2.0 Consensus size: 138
599457 TCAAAAAATA
*
599467 TTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATATA-
1 TTTTCAAAAACTATATATTACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATATAT
599531 TTTCAAAATGTTTTCAAAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTC-AAAACTAT
66 TTTCAAAATGTTTTC-AAAAACTATATATTATATAAGTTTTC---AAAATGTTTTCAAAAACTAT
599595 ATATTATATAAG
127 ATATTATATAAG
599607 TTTTCAAAAACTATATATTACACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATAT
1 TTTTCAAAAACTATATATT--ACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATAT
*
599672 ATTTTCAAAATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATAT
64 ATTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAAACTATAT
599737 ATTATATA
129 ATTATATA
599745 TATTTTTTCA
Statistics
Matches: 132, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
139 11 0.08
140 37 0.28
142 69 0.52
143 15 0.11
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (138 bp):
TTTTCAAAAACTATATATTACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATATAT
TTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAAACTATATAT
TATATAAG
Found at i:600440 original size:54 final size:53
Alignment explanation
Indices: 600358--600459 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 53
600348 TACCATACGG
600358 TTGATATGTCATCGAGCTGAATAAAATCGAACTCGACAGTTTTTTGTTGTAAAT
1 TTGATATGTCATCGAGCTGAATAAAATCGAACTCGA-AGTTTTTTGTTGTAAAT
* **
600412 TTGATATGTTC-TTGAGCTGAATGGAATCGAACTCGAAGTTTTTTGTTG
1 TTGATATG-TCATCGAGCTGAATAAAATCGAACTCGAAGTTTTTTGTTG
600460 GCAGATAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
53 12 0.27
54 30 0.68
55 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (53 bp):
TTGATATGTCATCGAGCTGAATAAAATCGAACTCGAAGTTTTTTGTTGTAAAT
Found at i:606062 original size:5 final size:5
Alignment explanation
Indices: 606052--606216 Score: 62
Period size: 5 Copynumber: 31.8 Consensus size: 5
606042 TCAAAAGGGA
*
606052 AAAAT AAAAT AAAAT AAAAT AAATATT AAATATT AAATATT AAATT ACGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAA-A-T AAA-A-T AAA-A-T AAAAT A--AAAT
* * *
606105 -ATAT AAATAT AACA- AAAA- AAGAT AAGAAAT AAAAT AAAAT AAAAT
1 AAAAT AAA-AT AAAAT AAAAT AAAAT -A-AAAT AAAAT AAAAT AAAAT
*
606150 -AAAT AAAGAT -AAAT AAAATT GAAAA- AATATT AAAAT -AAA- AAAAT
1 AAAAT AAA-AT AAAAT AAAA-T -AAAAT AA-AAT AAAAT AAAAT AAAAT
*
606194 GAAAT -AAA- AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT -AAAAT AAAA
606217 AATTGAAATT
Statistics
Matches: 128, Mismatches: 11, Indels: 42
0.71 0.06 0.23
Matches are distributed among these distances:
4 29 0.23
5 54 0.42
6 17 0.13
7 28 0.22
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:606075 original size:14 final size:14
Alignment explanation
Indices: 606052--606216 Score: 74
Period size: 15 Copynumber: 11.3 Consensus size: 14
606042 TCAAAAGGGA
606052 AAAATAAAATAAAAT
1 AAAAT-AAATAAAAT
606067 AAAATAAATATTAAAT
1 AAAATAAATA--AAAT
* *
606083 ATTAAAT-ATTAAATT
1 A--AAATAAATAAAAT
*
606098 ACGAAATATAT-AAAT
1 A--AAATAAATAAAAT
* * *
606113 ATAACAAA-AAAAG
1 AAAATAAATAAAAT
* *
606126 ATAAGAAATAAAAT
1 AAAATAAATAAAAT
606140 AAAATAAA-ATAAAT
1 AAAATAAATA-AAAT
606154 AAAGATAAATAAAATT
1 AAA-ATAAATAAAA-T
606170 GAAAA-AATATTAAAAT
1 -AAAATAA-A-TAAAAT
*
606186 AAAA-AAATGAAAT
1 AAAATAAATAAAAT
606199 AAAA-AAATAAAAAT
1 AAAATAAAT-AAAAT
606213 AAAA
1 AAAA
606217 AATTGAAATT
Statistics
Matches: 118, Mismatches: 17, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
13 28 0.24
14 31 0.26
15 33 0.28
16 11 0.09
17 11 0.09
18 4 0.03
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:606083 original size:7 final size:7
Alignment explanation
Indices: 606071--606096 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
606061 TAAAATAAAA
606071 TAAATAT
1 TAAATAT
606078 TAAATAT
1 TAAATAT
606085 TAAATAT
1 TAAATAT
606092 TAAAT
1 TAAAT
606097 TACGAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAAATAT
Found at i:606143 original size:22 final size:22
Alignment explanation
Indices: 606109--606151 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
606099 CGAAATATAT
*
606109 AAATATAACAAAA-AAAGATAAG
1 AAATAAAACAAAATAAA-ATAAG
*
606131 AAATAAAATAAAATAAAATAA
1 AAATAAAACAAAATAAAATAA
606152 ATAAAGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (22 bp):
AAATAAAACAAAATAAAATAAG
Found at i:606148 original size:27 final size:25
Alignment explanation
Indices: 606109--606216 Score: 76
Period size: 27 Copynumber: 4.1 Consensus size: 25
606099 CGAAATATAT
* *
606109 AAATATAACAAAAAAAGATAAGAAATA
1 AAATAAAATAAAAAAA-ATAA-AAATA
* *
606136 AAATAAAATAAAATAAATAAAGAT-
1 AAATAAAATAAAAAAAATAAAAATA
* *
606160 AAATAAAATTGAAAAAATATTAAAATA
1 AAATAAAA-T-AAAAAAAATAAAAATA
*
606187 AAA-AAATGAAATAAAAAAATAAAAATA
1 AAATAAA--ATA-AAAAAAATAAAAATA
606214 AAA
1 AAA
606217 AATTGAAATT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
24 8 0.12
25 4 0.06
26 19 0.30
27 32 0.50
28 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.19
Consensus pattern (25 bp):
AAATAAAATAAAAAAAATAAAAATA
Found at i:606198 original size:13 final size:13
Alignment explanation
Indices: 606182--606225 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
606172 AAAAATATTA
606182 AAATAAAAAAATG
1 AAATAAAAAAATG
*
606195 AAATAAAAAAATAA
1 AAATAAAAAAAT-G
*
606209 AAATAAAAAATTG
1 AAATAAAAAAATG
606222 AAAT
1 AAAT
606226 TTTGAAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AAATAAAAAAATG
Found at i:606217 original size:14 final size:14
Alignment explanation
Indices: 606131--606218 Score: 74
Period size: 14 Copynumber: 6.1 Consensus size: 14
606121 AAAAGATAAG
606131 AAAT-AAAATAAAA
1 AAATAAAAATAAAA
*
606144 TAAA-ATAAATAAAGA
1 -AAATAAAAATAAA-A
*
606159 TAAATAAAATTGAAAA
1 -AAATAAAAAT-AAAA
*
606175 AATATTAAAATAAAA
1 AA-ATAAAAATAAAA
*
606190 AAAT-GAAATAAAA
1 AAATAAAAATAAAA
606203 AAATAAAAATAAAA
1 AAATAAAAATAAAA
606217 AA
1 AA
606219 TTGAAATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
13 12 0.20
14 22 0.36
15 13 0.21
16 11 0.18
17 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:606217 original size:27 final size:27
Alignment explanation
Indices: 606135--606225 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
606125 GATAAGAAAT
* *
606135 AAAATAAAATAAAATAAATAAAGATAAA
1 AAAATGAAATAAAA-AAATAAAAATAAA
* *
606163 TAAAATTG--A-AAAAATATTAAAATAAA
1 -AAAA-TGAAATAAAAAAATAAAAATAAA
606189 AAAATGAAATAAAAAAATAAAAATAAA
1 AAAATGAAATAAAAAAATAAAAATAAA
*
606216 AAATTGAAAT
1 AAAATGAAAT
606226 TTTGAAAGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
24 2 0.04
25 4 0.08
26 11 0.22
27 28 0.55
28 1 0.02
29 4 0.08
30 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (27 bp):
AAAATGAAATAAAAAAATAAAAATAAA
Found at i:606259 original size:15 final size:15
Alignment explanation
Indices: 606235--606269 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
606225 TTTTGAAAGT
606235 AAAA-AAATGTTAAG
1 AAAATAAATGTTAAG
*
606249 AAAATAAATGTTAAT
1 AAAATAAATGTTAAG
606264 AAAATA
1 AAAATA
606270 CAAAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
AAAATAAATGTTAAG
Found at i:606970 original size:11 final size:11
Alignment explanation
Indices: 606929--606971 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
606919 GTGTAGTTGC
* *
606929 TTTGTTTGTGT
1 TTTGGTTGTTT
* *
606940 TTTGGTTGGTG
1 TTTGGTTGTTT
606951 TTTGGTTGTTT
1 TTTGGTTGTTT
606962 TTTGGTTGTT
1 TTTGGTTGTT
606972 GGTTTTTTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (11 bp):
TTTGGTTGTTT
Found at i:607481 original size:25 final size:28
Alignment explanation
Indices: 607449--607511 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
607439 TGGACCTTAA
* *
607449 AATAAAATAA-AAA-AAGAA-AAATATT
1 AATAAAATAATAAATAAAAACAAATAAT
607474 AATAAAATAATAAATAAAAACAAATAAT
1 AATAAAATAATAAATAAAAACAAATAAT
607502 AATAATAATA
1 AATAA-AATA
607512 TATTATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 10 0.31
26 3 0.09
27 4 0.12
28 11 0.34
29 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (28 bp):
AATAAAATAATAAATAAAAACAAATAAT
Found at i:607508 original size:31 final size:32
Alignment explanation
Indices: 607446--607524 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
607436 TGTTGGACCT
*
607446 TAAAAT-A-AAATAAAAAAAGAAAAATATTAA
1 TAAAATAATAAATAAAAAAAGAAAAATAATAA
* *
607476 TAAAATAATAAATAAAAACA-AATAATAATAA
1 TAAAATAATAAATAAAAAAAGAAAAATAATAA
* *
607507 TAATATATTATAATAAAA
1 TAAAATAATA-AATAAAA
607525 TTTTTCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
31 18 0.44
32 17 0.41
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (32 bp):
TAAAATAATAAATAAAAAAAGAAAAATAATAA
Found at i:607598 original size:38 final size:38
Alignment explanation
Indices: 607535--608015 Score: 347
Period size: 38 Copynumber: 12.9 Consensus size: 38
607525 TTTTTCAAAA
*
607535 ATATTATATAT-TTTT-AAAAATTGTTTTC-AAAGCTAT
1 ATATTATATATGTTTTCAAAAA-TGTTTTCAAAAACTAT
*
607571 ATATTATATATGTCTTCAAAATATGTTTTC-AAAACTAT
1 ATATTATATATGTTTTCAAAA-ATGTTTTCAAAAACTAT
*
607609 ATATTATATAAGTTTTCAAAAAAATGTTTTC-AAAACTAT
1 ATATTATATATGTTTTC--AAAAATGTTTTCAAAAACTAT
* *
607648 ATATTATATAAGTTTTCAAAAAAAATGTTTTCAAAAATTAT
1 ATATTATATATGTTTTC---AAAAATGTTTTCAAAAACTAT
*
607689 ATATTATATATATTTTC-AAAATGTTTTCAAAAACTAT
1 ATATTATATATGTTTTCAAAAATGTTTTCAAAAACTAT
*
607726 ATATTATATATATATTTTC-AAAATGTTTTCAAAAAACTAT
1 ATA-T-TATATATGTTTTCAAAAATGTTTTC-AAAAACTAT
*
607766 ATATTATATAT-ATTTC-AAAATGTTTTCAAAAACTAT
1 ATATTATATATGTTTTCAAAAATGTTTTCAAAAACTAT
* * *
607802 ATATTATATAAGTTTTC-AAAA------C-TATA-TAT
1 ATATTATATATGTTTTCAAAAATGTTTTCAAAAACTAT
**
607831 -TA-TATA-AGT-TTTCAAAAAATGTTTTCAAAACTA-TAT
1 ATATTATATA-TGTTTTCAAAAATGTTTTCAAAA--ACTAT
** ** * **
607867 AT-TATATA-AGT-TTTCAAAATGTTTTCA--AAAACTAT
1 ATAT-TATATA-TGTTTTCAAAAATGTTTTCAAAAACTAT
*
607902 ATATTATACATATATTTTC-AAAATGTTTTCAAAAAACTAT
1 ATATTAT--ATATGTTTTCAAAAATGTTTTC-AAAAACTAT
*
607942 ATATTATATATATTTTC-AAAATGTTTTCAAAAACTAT
1 ATATTATATATGTTTTCAAAAATGTTTTCAAAAACTAT
* **
607979 ATATTATATATATATATTTTAAAATGTTTTCAAAAAC
1 ATATTATATATGT-T-TTCAAAAATGTTTTCAAAAAC
608016 AATTTTATAA
Statistics
Matches: 377, Mismatches: 31, Indels: 70
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.01
27 8 0.02
28 2 0.01
29 3 0.01
30 2 0.01
31 1 0.00
33 1 0.00
34 2 0.01
35 8 0.02
36 38 0.10
37 78 0.21
38 85 0.23
39 61 0.16
40 62 0.16
41 22 0.06
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (38 bp):
ATATTATATATGTTTTCAAAAATGTTTTCAAAAACTAT
Found at i:607647 original size:39 final size:39
Alignment explanation
Indices: 607535--607822 Score: 334
Period size: 39 Copynumber: 7.5 Consensus size: 39
607525 TTTTTCAAAA
* * *
607535 ATATTATAT-A-TTTTTAAAAATTGTTTTC-AAAGCTAT
1 ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
* * *
607571 ATATTATATATGTCTTCAAAATATGTTTTC-AAAACTAT
1 ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
607609 ATATTATATAAGTTTTCAAAAAAATGTTTTC-AAAACTAT
1 ATATTATATAAGTTTTC-AAAAAATGTTTTCAAAAACTAT
*
607648 ATATTATATAAGTTTTCAAAAAAAATGTTTTCAAAAATTAT
1 ATATTATATAAGTTTTC--AAAAAATGTTTTCAAAAACTAT
607689 ATATTATATATA-TTTTC--AAAATGTTTTCAAAAACTAT
1 ATATTATATA-AGTTTTCAAAAAATGTTTTCAAAAACTAT
*
607726 ATATTATATATATATTTTC--AAAATGTTTTCAAAAAACTAT
1 ATATTATATA-A-GTTTTCAAAAAATGTTTTC-AAAAACTAT
607766 ATATTATAT-A-TATTTC--AAAATGTTTTCAAAAACTAT
1 ATATTATATAAGT-TTTCAAAAAATGTTTTCAAAAACTAT
607802 ATATTATATAAGTTTTCAAAA
1 ATATTATATAAGTTTTCAAAA
607823 CTATATATTA
Statistics
Matches: 227, Mismatches: 11, Indels: 25
0.86 0.04 0.10
Matches are distributed among these distances:
36 28 0.12
37 51 0.22
38 38 0.17
39 55 0.24
40 32 0.14
41 22 0.10
42 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (39 bp):
ATATTATATAAGTTTTCAAAAAATGTTTTCAAAAACTAT
Found at i:607849 original size:27 final size:26
Alignment explanation
Indices: 607787--607848 Score: 117
Period size: 25 Copynumber: 2.4 Consensus size: 26
607777 ATTTCAAAAT
607787 GTTTTCAAAAACTATATATTATATAA
1 GTTTTCAAAAACTATATATTATATAA
607813 GTTTTC-AAAACTATATATTATATAA
1 GTTTTCAAAAACTATATATTATATAA
607838 GTTTTCAAAAA
1 GTTTTCAAAAA
607849 ATGTTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 25 0.71
26 10 0.29
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (26 bp):
GTTTTCAAAAACTATATATTATATAA
Found at i:607905 original size:176 final size:179
Alignment explanation
Indices: 607634--607988 Score: 646
Period size: 176 Copynumber: 2.0 Consensus size: 179
607624 TCAAAAAAAT
*
607634 GTTTTCAAAACTATATATTATATAAGTTTTCAAAAAAAATGTTTTCAAAAATTATATATTATATA
1 GTTTTCAAAACTATATATTATATAAGTTTTC-AAAAAAATGTTTTCAAAAACTATATATTATATA
*
607699 TATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAATGTTTTCAAAAAACT
65 TATTTTCAAAATGTTTTCAAAAACTATATATTATACATATATTTTCAAAATGTTTTCAAAAAACT
607764 ATATATTATATATA-TTTCAAAATGTTTTCAAAAACTATATATTATATAA
130 ATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATAA
607813 GTTTTCAAAACTATATATTATATAAGTTTTC-AAAAAATGTTTTC-AAAACTATATATTATATA-
1 GTTTTCAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTCAAAAACTATATATTATATAT
607875 AGTTTTCAAAATGTTTTCAAAAACTATATATTATACATATATTTTCAAAATGTTTTCAAAAAACT
66 A-TTTTCAAAATGTTTTCAAAAACTATATATTATACATATATTTTCAAAATGTTTTCAAAAAACT
607940 ATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
130 ATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
607989 TATATATTTT
Statistics
Matches: 172, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
175 1 0.01
176 93 0.54
177 47 0.27
179 31 0.18
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (179 bp):
GTTTTCAAAACTATATATTATATAAGTTTTCAAAAAAATGTTTTCAAAAACTATATATTATATAT
ATTTTCAAAATGTTTTCAAAAACTATATATTATACATATATTTTCAAAATGTTTTCAAAAAACTA
TATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATAA
Found at i:608015 original size:77 final size:76
Alignment explanation
Indices: 607813--608015 Score: 290
Period size: 77 Copynumber: 2.7 Consensus size: 76
607803 TATTATATAA
*
607813 GTTTTC-AAAACTATATATTATATA-AGT-TTTCAAAAAATGTTTTC-AAAACTATATATTATAT
1 GTTTTCAAAAACTATATATTATATATA-TATTT-TAAAAATGTTTTCAAAAACTATATATTATAT
607874 AAGTTTTCAAAAT
64 AAGTTTTCAAAAT
* *
607887 GTTTTCAAAAACTATATATTATACATATATTTTCAAAATGTTTTCAAAAAACTATATATTATATA
1 GTTTTCAAAAACTATATATTATATATATATTTTAAAAATGTTTTC-AAAAACTATATATTATATA
607952 TA-TTTTCAAAAT
65 -AGTTTTCAAAAT
*
607964 GTTTTCAAAAACTATATATTATATATATATATTTTAAAATGTTTTCAAAAAC
1 GTTTTCAAAAACTATATATTATATATATAT-TTTAAAAATGTTTTCAAAAAC
608016 AATTTTATAA
Statistics
Matches: 117, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
74 6 0.05
75 29 0.25
76 4 0.03
77 63 0.54
78 15 0.13
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (76 bp):
GTTTTCAAAAACTATATATTATATATATATTTTAAAAATGTTTTCAAAAACTATATATTATATAA
GTTTTCAAAAT
Found at i:609107 original size:16 final size:16
Alignment explanation
Indices: 609086--609118 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
609076 CGATTGATTT
*
609086 TTGGGTTGGGTCAATA
1 TTGGGTTAGGTCAATA
609102 TTGGGTTAGGTCAATA
1 TTGGGTTAGGTCAATA
609118 T
1 T
609119 CGCATCGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.33, T:0.39
Consensus pattern (16 bp):
TTGGGTTAGGTCAATA
Found at i:609729 original size:21 final size:21
Alignment explanation
Indices: 609689--609729 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
609679 TTTTCTATTA
* *
609689 TTTTTATTATAAATATGATAT
1 TTTTTATTACAAATAAGATAT
*
609710 TTTTTATTACAAGTAAGATA
1 TTTTTATTACAAATAAGATA
609730 AGTAAACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTTTATTACAAATAAGATAT
Found at i:610660 original size:2 final size:2
Alignment explanation
Indices: 610653--610708 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
610643 ATGACCCTCG
610653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
610695 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
610709 GTGTGTGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:610713 original size:2 final size:2
Alignment explanation
Indices: 610708--610737 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
610698 TATATATATA
610708 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
610738 CGCGCGCGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:611777 original size:19 final size:20
Alignment explanation
Indices: 611720--611785 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 20
611710 ATAAATAAAC
* *
611720 ATAATAATATA-ATATATATA
1 ATAA-AATATATACATATACA
* *
611740 ATATAATA-ATACATGTACA
1 ATAAAATATATACATATACA
611759 ATAAAATATATA-ATATACA
1 ATAAAATATATACATATACA
611778 TATAAAAT
1 -ATAAAAT
611786 GTTTTCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 23 0.62
20 13 0.35
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAATATATACATATACA
Found at i:611831 original size:39 final size:38
Alignment explanation
Indices: 611781--612060 Score: 253
Period size: 37 Copynumber: 6.9 Consensus size: 38
611771 ATATACATAT
611781 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATAT-TTTTC
* * *
611820 AAAATATTTTCAAAAACTATATTATACATACATATATATATAT-
1 AAAATGTTTTCAAAAACTATA-TAT---T--ATATATATTTTTC
* * * ** *
611863 ATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATATTTTC
1 A-AAATGTTTTCAAAA---ACT--ATA-TAT-TA-TATATAT-T-TT-TC
*
611913 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTT
1 AAAATGTTTTCAAAAACTATATATTATATATAT-TTTTC
611952 AAAATGTTTTCAAAAAC--TATATTATATATATTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATATTTTTC
611988 AAAATGTTTTCAAAAACTATATATTATATAT-TTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATATTTTTC
*
612025 AAAATGTTTTCAAAAACTATATATTATACATATTTT
1 AAAATGTTTTCAAAAACTATATATTATATATATTTT
612061 AAAAAAAAAT
Statistics
Matches: 200, Mismatches: 21, Indels: 41
0.76 0.08 0.16
Matches are distributed among these distances:
36 21 0.10
37 50 0.25
38 16 0.08
39 38 0.19
40 5 0.03
41 8 0.04
42 2 0.01
43 5 0.03
44 16 0.08
45 9 0.05
46 8 0.04
47 3 0.01
48 1 0.00
49 17 0.09
50 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (38 bp):
AAAATGTTTTCAAAAACTATATATTATATATATTTTTC
Found at i:611892 original size:93 final size:91
Alignment explanation
Indices: 611764--611934 Score: 281
Period size: 93 Copynumber: 1.9 Consensus size: 91
611754 GTACAATAAA
*
611764 ATATATAATATACATATAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATATTT
1 ATATATAATATACATATAAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAATATTT
611829 TCAAAAACTATATTATACATACATAT
66 TCAAAAACTATATTATACATACATAT
* *
611855 ATATATATATATATATATTCAAAATGTTTT-AAAAACTATATATTATATATATATTTTCAAAATG
1 ATATATA-ATATACATA-T-AAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAATA
611919 TTTTCAAAAACTATAT
63 TTTTCAAAAACTATAT
611935 ATTATATATA
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
91 7 0.09
92 8 0.11
93 49 0.66
94 10 0.14
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (91 bp):
ATATATAATATACATATAAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAATATTT
TCAAAAACTATATTATACATACATAT
Found at i:611943 original size:37 final size:37
Alignment explanation
Indices: 611854--612065 Score: 304
Period size: 37 Copynumber: 5.6 Consensus size: 37
611844 TACATACATA
*
611854 TATATATATATATATATATTCAAAATGTTTT-AAAAAC
1 TATATAT-TATATATATTTTCAAAATGTTTTCAAAAAC
611891 TATATATTATATATATATTTTCAAAATGTTTTCAAAAAC
1 TATATA-T-TATATATATTTTCAAAATGTTTTCAAAAAC
*
611930 TATATATTATATATATGTTTTTAAAATGTTTTCAAAAAC
1 TATATATTATATATA--TTTTCAAAATGTTTTCAAAAAC
611969 --TATATTATATATATTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATA-TTTTCAAAATGTTTTCAAAAAC
*
612005 TATATATTATATATTTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
* *
612042 TATATATTATACATATTTTAAAAA
1 TATATATTATATATATTTTCAAAA
612066 AAAATTATAT
Statistics
Matches: 161, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
36 21 0.13
37 70 0.43
38 37 0.23
39 33 0.20
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:612637 original size:32 final size:32
Alignment explanation
Indices: 612596--612673 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
612586 GTTACTTTCT
* *
612596 GTTCTGGTTGCTTTCA-GGTCGAGCTAAATTCG
1 GTTCGGGTTGCTTT-AGGGTCGAGCTAAATTCA
* *
612628 GTTCGGGTTGCTTTAGGGTCGGGTTAAATTCA
1 GTTCGGGTTGCTTTAGGGTCGAGCTAAATTCA
* *
612660 ATTCGAGTTGCTTT
1 GTTCGGGTTGCTTT
612674 TAGACCGGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (32 bp):
GTTCGGGTTGCTTTAGGGTCGAGCTAAATTCA
Found at i:613407 original size:153 final size:152
Alignment explanation
Indices: 613133--613412 Score: 352
Period size: 153 Copynumber: 1.8 Consensus size: 152
613123 ATTTTAGAAT
* * * *
613133 GAAACACAATAATATTTAATTATTTTCTATTGATAAAAATCGACCTCTCATGCCTTAAAGCAATC
1 GAAAAACAATAATATTTAATTATTTCCTATCGAAAAAAATC-ACCTCTCATGCCTTAAAGCAATC
* * *
613198 AAGTCCTCTTCCAATAAAAATAAAGAAATATTACAATTCCATTCCAAAGTTCATTATTAATTTCA
65 AAGTCCTCCTCCAATAAAAATAAAGAAATAATACAATTCCATTCCAAAATTCATTATTAATTTCA
613263 ACACATTCCTTAAATTTTTGTAC
130 ACACATTCCTTAAATTTTTGTAC
613286 GAAAAACAATAATATTTAATTATTTCCTATCGAGAAGAAAAT-ACCTCTCATGCCTTAAAGCAAT
1 GAAAAACAATAATATTTAATTATTTCCTATCGA-AA-AAAATCACCTCTCATGCCTTAAAGCAAT
* * * * * * *
613350 C-ATTTCTCACTCCAAATGAAAA-AGAGAAATAATACTATTTCC-TTCTAAAATTTATTATTAAT
64 CAAGTCCTC-CTCC-AATAAAAATAAAGAAATAATAC-AATTCCATTCCAAAATTCATTATTAAT
613412 T
126 T
613413 CTAATGCATA
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
152 5 0.05
153 85 0.79
154 13 0.12
155 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (152 bp):
GAAAAACAATAATATTTAATTATTTCCTATCGAAAAAAATCACCTCTCATGCCTTAAAGCAATCA
AGTCCTCCTCCAATAAAAATAAAGAAATAATACAATTCCATTCCAAAATTCATTATTAATTTCAA
CACATTCCTTAAATTTTTGTAC
Found at i:614000 original size:2 final size:2
Alignment explanation
Indices: 613993--614027 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
613983 TAACTAAAAC
613993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
614028 ACATTAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:615482 original size:13 final size:11
Alignment explanation
Indices: 615431--615490 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
615421 TTTGGCCTGC
*
615431 AATAATAATAAT
1 AATAA-AATAAA
*
615443 AATAAAATAAC
1 AATAAAATAAA
*
615454 ATTAAAATAAA
1 AATAAAATAAA
615465 AATAAAATAGATA
1 AATAAAATA-A-A
615478 AATAAAAATAAA
1 AAT-AAAATAAA
615490 A
1 A
615491 GAACCGGGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 22 0.54
12 8 0.20
13 5 0.12
14 6 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:615566 original size:26 final size:26
Alignment explanation
Indices: 615528--615580 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
615518 CGGGTATGGG
** *
615528 TCGGGTATCGGATTGAATTTGATTAT
1 TCGGGTATCGGATCAAATTTGAATAT
*
615554 TCGGGTATTGGATCAAATTTGAATAT
1 TCGGGTATCGGATCAAATTTGAATAT
615580 T
1 T
615581 TTATTCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (26 bp):
TCGGGTATCGGATCAAATTTGAATAT
Found at i:616801 original size:26 final size:26
Alignment explanation
Indices: 616786--616867 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
616776 GTCAAGTCGA
616786 GCTCAACAATACTCGAGCTCGAATCG
1 GCTCAACAATACTCGAGCTCGAATCG
616812 GCTCAACAATACTCGAGCTCGAATCG
1 GCTCAACAATACTCGAGCTCGAATCG
*
616838 GCTCAACAATACTAGAGCTCGAATCG
1 GCTCAACAATACTCGAGCTCGAATCG
616864 GCTC
1 GCTC
616868 GATTACACCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (26 bp):
GCTCAACAATACTCGAGCTCGAATCG
Found at i:617176 original size:43 final size:43
Alignment explanation
Indices: 617128--617222 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
617118 AATTTCTATA
617128 TTTATAATTGAGACCCCTAAGTTTTTTCAATCTC-AGTTATACC
1 TTTATAATTGAGACCCCT-AGTTTTTTCAATCTCGAGTTATACC
* * * * * * *
617171 TTTATAATTGAGGCCTCTATTTTTTTTAATGTCGATTTCTACC
1 TTTATAATTGAGACCCCTAGTTTTTTCAATCTCGAGTTATACC
617214 TTTATAATT
1 TTTATAATT
617223 AAGGTCACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 12 0.27
43 32 0.73
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.48
Consensus pattern (43 bp):
TTTATAATTGAGACCCCTAGTTTTTTCAATCTCGAGTTATACC
Found at i:621773 original size:440 final size:440
Alignment explanation
Indices: 620952--621834 Score: 1640
Period size: 440 Copynumber: 2.0 Consensus size: 440
620942 ATGTGCTTCG
620952 TCCTGGAATGAAAAGACGGATTCTGTTGTCGAACCTCTTGATGTAGCAACAATGATCTGCTTGAC
1 TCCTGGAATGAAAAGACGGATTCTGTTGTCGAACCTCTTGATGTAGCAACAATGATCTGCTTGAC
*
621017 ATATGGTAAAACCACTGCTACTCATGAAACTATCAAACTTCTTGTACCATTATCTAGGAGTTTGT
66 ATATGGTAAAACCACTGCTACTCATGAAACTATCAAACTTCTTGTACAATTATCTAGGAGTTTGT
*
621082 TTTAAACCATACAAGCTCTTCTTCAAACTGCATACCAAGTTTTTCTTGCCTGCCTCTATGAAGCC
131 TTTAAACCATACAAGCTCTTCTTCAAACTGCATACCAAGTTTTTCTTGCCTGCCCCTATGAAGCC
*
621147 TTCTGGTTGCCTCATATATATTTCTTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
196 TTCTGGCTGCCTCATATATATTTCTTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
* *
621212 ACTGCTCAAGATGTAGATTTTCTGCAGCTACAATTTTCAACACCAGTCTGATTGTAGACAGTTTC
261 ACTGCTCAAGATGTAGATTTTCTGCAACTACAATTTTCAACACCAGTCTGATTATAGACAGTTTC
*
621277 ATGATTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
326 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
*
621342 TCTGGCTTTGTAGCGTTTGCTCCCATCGTGCTCTTCCTTGATCCTGTAAA
391 TCTGGCTTTATAGCGTTTGCTCCCATCGTGCTCTTCCTTGATCCTGTAAA
621392 TCCTGGAATGAAAAGACGGATTCTGTTGTCGAACCTCTTGATGTAGCAACAATGATCTGCTTGAC
1 TCCTGGAATGAAAAGACGGATTCTGTTGTCGAACCTCTTGATGTAGCAACAATGATCTGCTTGAC
* * *
621457 ATCTGGTAAAACCATTGCTACTCATGAAACTATCAAACTTCTTGTACAATTGTCTAGGAGTTTGT
66 ATATGGTAAAACCACTGCTACTCATGAAACTATCAAACTTCTTGTACAATTATCTAGGAGTTTGT
*
621522 TTTAAACCATACAAGCTCTTCTTCAAACTGCATACCAGGTTTTTCTTGCCTGCCCCTATGAAGCC
131 TTTAAACCATACAAGCTCTTCTTCAAACTGCATACCAAGTTTTTCTTGCCTGCCCCTATGAAGCC
621587 TTCTGGCTGCCTCATATATATTTCTTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
196 TTCTGGCTGCCTCATATATATTTCTTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
* *
621652 ACTGCTCAAGATGTAGATTTTCTGTAACTACAATTTTTAACACCAGTCTGATTATAGACAGTTTC
261 ACTGCTCAAGATGTAGATTTTCTGCAACTACAATTTTCAACACCAGTCTGATTATAGACAGTTTC
621717 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
326 ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
*
621782 TCTGGCTTTATAGCGTTTTCTCCCATCGTGCTCTTCCTTGATCCTGTAAA
391 TCTGGCTTTATAGCGTTTGCTCCCATCGTGCTCTTCCTTGATCCTGTAAA
621832 TCC
1 TCC
621835 ACTTGTTGTG
Statistics
Matches: 429, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
440 429 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (440 bp):
TCCTGGAATGAAAAGACGGATTCTGTTGTCGAACCTCTTGATGTAGCAACAATGATCTGCTTGAC
ATATGGTAAAACCACTGCTACTCATGAAACTATCAAACTTCTTGTACAATTATCTAGGAGTTTGT
TTTAAACCATACAAGCTCTTCTTCAAACTGCATACCAAGTTTTTCTTGCCTGCCCCTATGAAGCC
TTCTGGCTGCCTCATATATATTTCTTCCTCCAAATCACCATGAAGGAAAGCTGTCTTTACATCTA
ACTGCTCAAGATGTAGATTTTCTGCAACTACAATTTTCAACACCAGTCTGATTATAGACAGTTTC
ATGACTGGAGAGAAAATTTCATTGTAGTCAATACCTTCTTTTTGCTGAAAACCTTTGACAACCAA
TCTGGCTTTATAGCGTTTGCTCCCATCGTGCTCTTCCTTGATCCTGTAAA
Found at i:624714 original size:28 final size:28
Alignment explanation
Indices: 624682--624743 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
624672 TGGGAGAAAG
*
624682 AAATGATTTTTGGGATGGTTTTGAAGCT
1 AAATGATTTTTGGGACGGTTTTGAAGCT
624710 AAATGATTTTTGGGACGGTTTTGAAGCT
1 AAATGATTTTTGGGACGGTTTTGAAGCT
624738 AAATGA
1 AAATGA
624744 GCTAGGGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (28 bp):
AAATGATTTTTGGGACGGTTTTGAAGCT
Found at i:627396 original size:79 final size:79
Alignment explanation
Indices: 627258--627594 Score: 559
Period size: 79 Copynumber: 4.3 Consensus size: 79
627248 TATGCTCTTT
*
627258 ATGCA-CCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGATATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
*
627322 TTTTCATGCCAATA
66 CTTTCATGCCAATA
** * * *
627336 ACACACCTATATGCATTATTCTTTTATGCTGATAATGTACCCATATTCATTTCAGCTATGACATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
627401 CTTTCATGCCAATA
66 CTTTCATGCCAATA
627415 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
* *
627480 CTCTCATGTCAATA
66 CTTTCATGCCAATA
* * *
627494 ATGCACCCATATGCATTATTCTTTTATACTGACAATGTACCCATATACATTTCAGCCATGGCATC
1 ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
627559 CTTTCATGCCAATA
66 CTTTCATGCCAATA
627573 ATGCACCCATATGCATTATTCT
1 ATGCACCCATATGCATTATTCT
627595 CTTACTCAAC
Statistics
Matches: 239, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
78 3 0.01
79 236 0.99
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (79 bp):
ATGCACCCATATGCATTATTCTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATC
CTTTCATGCCAATA
Done.