Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold187
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: 2169796
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 45208 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:516497 original size:13 final size:13
Alignment explanation
Indices: 516479--516503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
516469 ACACACAATA
516479 TGTATCGATACAT
1 TGTATCGATACAT
516492 TGTATCGATACA
1 TGTATCGATACA
516504 CCAAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:516500 original size:32 final size:34
Alignment explanation
Indices: 516459--516527 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
516449 GTAGCCAAAT
* * *
516459 TTGTATCGATACA-CACAATA-TGTATCGATACA
1 TTGTATCGATACACCAAAAAATTATATCGATACA
516491 TTGTATCGATACACCAAAAAATTATATCGATACA
1 TTGTATCGATACACCAAAAAATTATATCGATACA
516525 TTG
1 TTG
516528 GCTTGTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 13 0.41
33 5 0.16
34 14 0.44
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (34 bp):
TTGTATCGATACACCAAAAAATTATATCGATACA
Found at i:525183 original size:33 final size:33
Alignment explanation
Indices: 525141--525207 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
525131 ATACAGATTG
*
525141 CATTGTATCGATAGATGACCAAATATATCGATA
1 CATTGTATCGATACATGACCAAATATATCGATA
*
525174 CATTGTATCGATACATGACCAAATGTATCGATA
1 CATTGTATCGATACATGACCAAATATATCGATA
525207 C
1 C
525208 TTGAAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (33 bp):
CATTGTATCGATACATGACCAAATATATCGATA
Found at i:525202 original size:20 final size:21
Alignment explanation
Indices: 525177--525229 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
525167 ATCGATACAT
**
525177 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
525197 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
525218 TGTATCGATACA
1 TGTATCGATACA
525230 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:525299 original size:13 final size:13
Alignment explanation
Indices: 525281--525305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
525271 ACACACAATA
525281 TGTATCGATACAT
1 TGTATCGATACAT
525294 TGTATCGATACA
1 TGTATCGATACA
525306 CCAAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:525302 original size:32 final size:34
Alignment explanation
Indices: 525261--525329 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
525251 GTAGCCAAAT
* *
525261 TTGTATCGATACA-CACAATA-TGTATCGATACA
1 TTGTATCGATACACCAAAAAATTGTATCGATACA
525293 TTGTATCGATACACCAAAAAATTGTATCGATACA
1 TTGTATCGATACACCAAAAAATTGTATCGATACA
525327 TTG
1 TTG
525330 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 13 0.39
33 5 0.15
34 15 0.45
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (34 bp):
TTGTATCGATACACCAAAAAATTGTATCGATACA
Found at i:526480 original size:13 final size:13
Alignment explanation
Indices: 526462--526488 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
526452 ACATTATGCT
526462 TTGTATCGATACA
1 TTGTATCGATACA
526475 TTGTATCGATACA
1 TTGTATCGATACA
526488 T
1 T
526489 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:526498 original size:19 final size:19
Alignment explanation
Indices: 526474--526529 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
526464 GTATCGATAC
**
526474 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
526493 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
526513 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
526530 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:526517 original size:20 final size:20
Alignment explanation
Indices: 526474--526528 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
526464 GTATCGATAC
**
526474 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
526493 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
526513 ATTGTATCGATACATG
1 ATTGTATCGATACATG
526529 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:526583 original size:20 final size:20
Alignment explanation
Indices: 526558--526595 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
526548 TTTCACTGTT
526558 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
*
526578 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
526596 CGATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:526594 original size:13 final size:13
Alignment explanation
Indices: 526578--526603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
526568 CATGGTATAA
526578 TGTATCGATACAT
1 TGTATCGATACAT
526591 TGTATCGATACAT
1 TGTATCGATACAT
526604 GATGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:526599 original size:33 final size:33
Alignment explanation
Indices: 526557--526623 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
526547 CTTTCACTGT
526557 TTGTATCGATACATGGTAT-AA-TGTATCGATACA
1 TTGTATCGATACAT-G-ATGAATTGTATCGATACA
526590 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
526623 T
1 T
526624 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.09
33 27 0.84
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:528347 original size:18 final size:18
Alignment explanation
Indices: 528324--528362 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
528314 GAATTTTTAG
528324 ATAGGTGGAGGATTCGAC
1 ATAGGTGGAGGATTCGAC
528342 ATAGGTGGAGGATTCGAC
1 ATAGGTGGAGGATTCGAC
528360 ATA
1 ATA
528363 CTCAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.23
Consensus pattern (18 bp):
ATAGGTGGAGGATTCGAC
Found at i:528466 original size:13 final size:13
Alignment explanation
Indices: 528448--528472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
528438 AGAGTGTTTG
528448 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
528461 AAAAAAAAAAAA
1 AAAAAAAAAAAA
528473 ATTCCAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:528573 original size:19 final size:19
Alignment explanation
Indices: 528549--528616 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
528539 AATTCAACGA
528549 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
528568 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
528583 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
528600 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
528617 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:528587 original size:32 final size:32
Alignment explanation
Indices: 528551--528613 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
528541 TTCAACGATT
*
528551 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
528583 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
528614 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:528588 original size:13 final size:13
Alignment explanation
Indices: 528570--528594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
528560 ACATAAGTTT
528570 TGTATCGATACAA
1 TGTATCGATACAA
528583 TGTATCGATACA
1 TGTATCGATACA
528595 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:528674 original size:13 final size:13
Alignment explanation
Indices: 528656--528681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
528646 CATTTTTCTG
528656 TGTATCGATACAT
1 TGTATCGATACAT
528669 TGTATCGATACAT
1 TGTATCGATACAT
528682 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:528678 original size:33 final size:33
Alignment explanation
Indices: 528636--528702 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
528626 GCCAAGGAAA
***
528636 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
528669 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
528702 T
1 T
528703 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:531161 original size:52 final size:52
Alignment explanation
Indices: 531042--531174 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 52
531032 TTGAGTTTAT
* ** * *
531042 CAATTCTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCTAATTTTATTTCCAAAACAC
** *
531093 CAATTTTCCTTTAATCGGGGATACTCCAACTCC-AATTTTATTTCCAAAAATAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTCCTAATTTTATTTCC-AAAACAC
* *
531146 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
531175 CTCGTTATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
51 8 0.12
52 43 0.64
53 16 0.24
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCTAATTTTATTTCCAAAACAC
Found at i:531194 original size:28 final size:28
Alignment explanation
Indices: 531158--531232 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
531148 ATTTTTCACA
* * * *
531158 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCATTACTTC
531186 ATCGGGGATACTCCAACCCCATTACTTC
1 ATCGGGGATACTCCAACCCCATTACTTC
*
531214 -TGAGGGGATACTCCAACCC
1 AT-CGGGGATACTCCAACCC
531233 TGGCTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTACTTC
Found at i:531419 original size:80 final size:80
Alignment explanation
Indices: 531188--531422 Score: 183
Period size: 80 Copynumber: 3.0 Consensus size: 80
531178 GTTATTTCAT
* * * * * **
531188 CGGGGATACTCCAACCCCATTA-CTTCTGAGGGGATACTCCAACCCTGGCT-TTAT-TCCCAAAA
1 CGGGGATACTCCAACCCCGTTATTTTC-GAAGGGACACTCCAACCCCGATTATTATCT-CCAAAA
* ** * *
531250 TATTGATTTCTCATAAT
64 CATAAATTTCTCACAAC
* * * * * * * * *
531267 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGACACTCCAACCCCGATTATTATCTCCAAAACA
**
531332 TCGATTTCTCACAAC
66 TAAATTTCTCACAAC
*
531347 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCCCG-TTATTATCTCCAAAAC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ACACTCCAACCCCGATTATTATCTCCAAAAC
531410 ATTAAATTTCTCA
65 A-TAAATTTCTCA
531423 TTGGGAAATA
Statistics
Matches: 123, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
79 54 0.44
80 68 0.55
81 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.31
Consensus pattern (80 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGACACTCCAACCCCGATTATTATCTCCAAAACA
TAAATTTCTCACAAC
Found at i:543807 original size:8 final size:8
Alignment explanation
Indices: 543794--543869 Score: 66
Period size: 8 Copynumber: 9.5 Consensus size: 8
543784 CCTTCTCTTC
543794 AAAAAGAA
1 AAAAAGAA
*
543802 AAAAAGGCA
1 AAAAA-GAA
543811 AAAAA-AA
1 AAAAAGAA
*
543818 AAAAGGAA
1 AAAAAGAA
*
543826 AAAAACAA
1 AAAAAGAA
*
543834 AAAAACAA
1 AAAAAGAA
543842 AACAAAGAA
1 AA-AAAGAA
*
543851 AAAGAG-A
1 AAAAAGAA
*
543858 GAAAAGAA
1 AAAAAGAA
543866 AAAA
1 AAAA
543870 CCTACTTAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
7 10 0.19
8 30 0.56
9 14 0.26
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:543818 original size:15 final size:15
Alignment explanation
Indices: 543793--543836 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
543783 ACCTTCTCTT
543793 CAAAAAGAAAAAAAGG
1 CAAAAA-AAAAAAAGG
543809 CAAAAAAAAAAAAGG
1 CAAAAAAAAAAAAGG
543824 -AAAAAAACAAAAA
1 CAAAAAAA-AAAAA
543837 AACAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.26
15 14 0.52
16 6 0.22
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAGG
Found at i:544861 original size:29 final size:29
Alignment explanation
Indices: 544828--544974 Score: 80
Period size: 29 Copynumber: 5.3 Consensus size: 29
544818 GAGCAGGACG
544828 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * **
544857 CCTTTC--AGTCCC-C-GAAG-AGCAGGACA
1 CCTTTCAAAG-CCCACACAAGTTGGTGG-CA
*
544883 CCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * **
544912 -TTTTC-CAGTCCTCA-AAG-AGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGG-CA
544938 CCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA
544967 CCTTTCAA
1 CCTTTCAA
544975 TCCTCAAAGA
Statistics
Matches: 80, Mismatches: 24, Indels: 28
0.61 0.18 0.21
Matches are distributed among these distances:
25 6 0.08
26 15 0.19
27 13 0.16
28 19 0.24
29 21 0.26
30 6 0.08
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:544893 original size:55 final size:55
Alignment explanation
Indices: 544808--545838 Score: 1244
Period size: 55 Copynumber: 18.3 Consensus size: 55
544798 TCCGCTTTTT
* * *
544808 AGTCCCCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
544863 AGTCCCCGAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
544918 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** *
544973 AATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
**
545028 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
545089 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
545144 AGTCCCCGAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTTGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
545199 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** *
545254 AATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
**
545309 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
545370 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGTA--TTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * * * **
545424 AGTCCTCAAAGAGCAGGGCACCTTTTGAAGCCCATACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** *
545479 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
545540 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGATGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * * **
545595 AGTCCTCAAAAAGCAGGACACTTTTTAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
**
545650 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
545711 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
545766 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
545821 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
545839 TACAGTTTAT
Statistics
Matches: 845, Mismatches: 98, Indels: 66
0.84 0.10 0.07
Matches are distributed among these distances:
53 3 0.00
54 53 0.06
55 562 0.67
56 29 0.03
57 4 0.00
59 4 0.00
60 19 0.02
61 171 0.20
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:545087 original size:226 final size:221
Alignment explanation
Indices: 544808--545838 Score: 1302
Period size: 226 Copynumber: 4.6 Consensus size: 221
544798 TCCGCTTTTT
* * * *
544808 AGTCCCCAAAGAGCAGGACGCC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCGA
1 AGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
*
544872 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
66 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGA
* * *
544936 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAATCCTCAAAGAGCAGGACACCTTTTA
130 CACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTA
* ** *
545000 AAGCCCACACAGGTTGGTGGCATTTTTT
194 AAGCCCACACAAGTTGGTGGCACCTTTC
**
545028 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * *
545093 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCGAAGAGC
61 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
* *
545158 AGGACACCTTTTAAAGCCCACACAAGTTTGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
126 AGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
545223 TTAAAGCCCACACAAGTTGGTGGCACCTTTC
191 TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** *
545254 AATCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* * *
545318 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
66 AGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAG
* * *
545383 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGTA-TTTCCAGTCCTCAAAGAGCAGGGCACCT
125 CAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT
* * * **
545447 TTTGAAGCCCATACAGGTTGGTGGCATTTTTC
190 TTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** *
545479 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * *
545544 CCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGATGGTGGCA-TTTTCCAGTCCTCAAAAAG
61 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAG
* * *
545608 CAGGACACTTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTT
125 CAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C--
**
545673 TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
186 -ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
545711 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* * * * * *
545775 AGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGAAGGA
66 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
545839 TACAGTTTAT
Statistics
Matches: 704, Mismatches: 78, Indels: 52
0.84 0.09 0.06
Matches are distributed among these distances:
220 60 0.09
221 5 0.01
222 2 0.00
224 4 0.01
225 146 0.21
226 378 0.54
227 12 0.02
228 1 0.00
229 1 0.00
230 6 0.01
231 48 0.07
232 41 0.06
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (221 bp):
AGTCCTCAAAGAGCAGGACACCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
ACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAA
GCCCACACAAGTTGGTGGCACCTTTC
Found at i:545109 original size:171 final size:168
Alignment explanation
Indices: 544802--545838 Score: 1301
Period size: 171 Copynumber: 6.1 Consensus size: 168
544792 TCTCCGTCCG
* * *
544802 CTTTTTAGTCCCCAAAGAGCAGGA-C-GCC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
1 CTTTTCAGTCCTCAAAGAGCAGGAGCTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* *
544864 GTCCCCGAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAG
66 GTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAG
*
544929 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA
131 AGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * ** *
544967 CCTTTCAATCCTCAAAGAGCAGGA-C-ACCTTTT-AAAGCCCACACAGGTTGGTGGCATTTTTTA
1 CTTTTCAGTCCTCAAAGAGCAGGAGCTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* **
545029 GTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTC
66 GTCCCCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTC
*
545093 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
124 CTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
545138 CCTTTCAGTCCCCGAAGAGCAGGA-C-ACCTTTT-AAAGCCCACACAAGTTTGTGGCA-TTTTCC
1 CTTTTCAGTCCTCAAAGAGCAGGAGCTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
545199 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAATCCTCAA
65 AGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAA
*
545263 AGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
129 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
545303 TTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTTCAGTCCTCAAAGAGCAGGA-GC--TTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * *
545368 TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGTA-TTTCCAGTCCTCA
63 TCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * * *
545432 AAGAGCAGGGCACCTTTTGAAGCCCATACAGGTTGGTGGCA
128 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
545473 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTT
1 CTTTTCAGTCCTCAAAGAGCAGGA-GC--TTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * *
545538 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGATGGTGGCATTTTCCAGTCCTCA
63 TCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * *
545603 AAAAGCAGGACACTTTTTAAAGCCCACACAGGTTGGTGGCA
128 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
545644 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTTCAGTCCTCAAAGAGCAGGA-GC--TTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
545709 TCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTC
63 TCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTC
* * *
545773 AAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
127 AAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
545815 CTTTTTACTCCTCAATGAGAAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
545839 TACAGTTTAT
Statistics
Matches: 783, Mismatches: 70, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
165 158 0.20
166 7 0.01
167 2 0.00
169 4 0.01
170 171 0.22
171 432 0.55
172 9 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (168 bp):
CTTTTCAGTCCTCAAAGAGCAGGAGCTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
GTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAG
AGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:545111 original size:26 final size:26
Alignment explanation
Indices: 545081--545168 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
545071 AAGTTGGTGG
*
545081 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
545107 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
545136 CACCTTTCAGTCCCCGAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
545162 CACCTTT
1 CACCTTT
545169 TAAAGCCCAC
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
25 3 0.07
26 18 0.39
27 5 0.11
28 6 0.13
29 11 0.24
30 3 0.07
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:545317 original size:281 final size:282
Alignment explanation
Indices: 544808--545838 Score: 1501
Period size: 281 Copynumber: 3.7 Consensus size: 282
544798 TCCGCTTTTT
* * *
544808 AGTCCCCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCGAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
544873 GAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
66 GAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
544938 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCTTTTAAA
131 CCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCTTTTAAA
545002 GCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
196 GCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
545067 ACACAAGTTGGTGGCACCTTTC
261 ACACAAGTTGGTGGCACCTTTC
*
545089 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCGAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
*
545154 GAGCAGGACACCTTTTAAAGCCCACACAAGTTTGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
66 GAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
545219 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCTTTTAAA
131 CCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCTTTTAAA
545283 GCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
196 GCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
545348 ACACAAGTTGGTGGCACCTTTC
261 ACACAAGTTGGTGGCACCTTTC
* *
545370 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGTA--TTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAA
* * * * *
545433 AGAGCAGGGCACCTTTTGAAGCCCATACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGAT
65 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA-
** * * * *
545498 GCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCT
129 -C---ACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCT
* * * ** * * *
545563 TTCAAAGCCCACACAAGATGGTGGCATTTTCCAGTCCTCAAAAAGCAGGA--C----ACTTTTTA
190 TTTAAAGCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCA
* **
545622 AAGCCCACACAGGTTGGTGGCATTTTTC
255 AAGCCCACACAAGTTGGTGGCACCTTTC
* *
545650 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
545715 CCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAG
60 CCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAG
* * * * * * *
545779 CAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGAAGGA
124 CAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGA
545839 TACAGTTTAT
Statistics
Matches: 685, Mismatches: 49, Indels: 32
0.89 0.06 0.04
Matches are distributed among these distances:
279 3 0.00
280 115 0.17
281 368 0.54
282 4 0.01
284 1 0.00
285 5 0.01
286 120 0.18
287 63 0.09
288 6 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (282 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
GAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
CCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCTTTTAAA
GCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
ACACAAGTTGGTGGCACCTTTC
Found at i:545762 original size:29 final size:28
Alignment explanation
Indices: 545682--545764 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 28
545672 TTTTCTTTTC
545682 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
* * **
545710 -CAGTCCC-CA-AAG-AGCAGGACACCTCTT
1 AAAG-CCCACACAAGTTGGTGG-CACCT-TT
545737 AAAGCCCACACAAGTTGGTGGCACCTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT
545765 CAGTCCTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
25 3 0.08
26 8 0.20
27 9 0.22
28 9 0.22
29 8 0.20
30 3 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.19
Consensus pattern (28 bp):
AAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:546357 original size:18 final size:18
Alignment explanation
Indices: 546334--546372 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
546324 GAATTTTTAG
546334 ATAGGTGGAGGATTCGAC
1 ATAGGTGGAGGATTCGAC
546352 ATAGGTGGAGGATTCGAC
1 ATAGGTGGAGGATTCGAC
546370 ATA
1 ATA
546373 CTCAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.23
Consensus pattern (18 bp):
ATAGGTGGAGGATTCGAC
Found at i:546587 original size:19 final size:19
Alignment explanation
Indices: 546563--546629 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
546553 ATTCAACGAT
546563 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
546582 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
546596 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
546614 TTGTATCGATACATAA
1 TTGTATCGATACATAA
546630 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 1 0.02
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:546600 original size:32 final size:32
Alignment explanation
Indices: 546564--546626 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
546554 TTCAACGATT
546564 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
546596 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
546627 TAATTAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:546601 original size:13 final size:13
Alignment explanation
Indices: 546583--546607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546573 ACATAAGTAT
546583 TGTATCGATACAA
1 TGTATCGATACAA
546596 TGTATCGATACA
1 TGTATCGATACA
546608 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:546687 original size:13 final size:13
Alignment explanation
Indices: 546669--546694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
546659 CATTTTTCTG
546669 TGTATCGATACAT
1 TGTATCGATACAT
546682 TGTATCGATACAT
1 TGTATCGATACAT
546695 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:546691 original size:33 final size:33
Alignment explanation
Indices: 546649--546715 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
546639 GCCAAGGAAA
***
546649 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
546682 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
546715 T
1 T
546716 ATAAGTTCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:547127 original size:20 final size:20
Alignment explanation
Indices: 547102--547151 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
547092 CCCTGAAAAC
*
547102 TATCGATACACATTTAAATG
1 TATCGATACACATTGAAATG
* * *
547122 TATCGATACAGATTGCATTG
1 TATCGATACACATTGAAATG
547142 TATCGATACA
1 TATCGATACA
547152 TGACCAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (20 bp):
TATCGATACACATTGAAATG
Found at i:547179 original size:33 final size:33
Alignment explanation
Indices: 547137--547203 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
547127 ATACAGATTG
547137 CATTGTATCGATACATGACCAAATATATCGATA
1 CATTGTATCGATACATGACCAAATATATCGATA
*
547170 CATTGTATCGATACATGACCAAATGTATCGATA
1 CATTGTATCGATACATGACCAAATATATCGATA
547203 C
1 C
547204 TTGAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (33 bp):
CATTGTATCGATACATGACCAAATATATCGATA
Found at i:547198 original size:20 final size:20
Alignment explanation
Indices: 547140--547225 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
547130 CAGATTGCAT
547140 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
*
547160 TATATCGATACAT-------
1 TGTATCGATACATGACCAAA
547173 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
* **
547193 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGACCAA-A
547214 TGTATCGATACA
1 TGTATCGATACA
547226 GGTCATTGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
13 12 0.23
20 28 0.54
21 12 0.23
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:547295 original size:13 final size:13
Alignment explanation
Indices: 547277--547301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
547267 ACCCACAATA
547277 TGTATCGATACAT
1 TGTATCGATACAT
547290 TGTATCGATACA
1 TGTATCGATACA
547302 CCAAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:547320 original size:34 final size:32
Alignment explanation
Indices: 547257--547325 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 32
547247 GTAGCCAAAT
* *
547257 TTGTATCGATACCCACAATATGTATCGATACA
1 TTGTATCGATACCCAAAAAATGTATCGATACA
547289 TTGTATCGATACACCAAAAAATTGTATCGATACA
1 TTGTATCGATAC-CCAAAAAA-TGTATCGATACA
547323 TTG
1 TTG
547326 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 12 0.36
33 6 0.18
34 15 0.45
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACCCAAAAAATGTATCGATACA
Found at i:548476 original size:13 final size:13
Alignment explanation
Indices: 548458--548484 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
548448 ACATTATGCT
548458 TTGTATCGATACA
1 TTGTATCGATACA
548471 TTGTATCGATACA
1 TTGTATCGATACA
548484 T
1 T
548485 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:548494 original size:19 final size:19
Alignment explanation
Indices: 548470--548525 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
548460 GTATCGATAC
**
548470 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
548489 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
548509 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
548526 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:548513 original size:20 final size:20
Alignment explanation
Indices: 548470--548524 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
548460 GTATCGATAC
**
548470 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
548489 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
548509 ATTGTATCGATACATG
1 ATTGTATCGATACATG
548525 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:548579 original size:20 final size:20
Alignment explanation
Indices: 548554--548591 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
548544 TTCCACTGTT
548554 TGTATCGATACATGGTATAA
1 TGTATCGATACATGGTATAA
*
548574 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
548592 CGATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:548590 original size:13 final size:13
Alignment explanation
Indices: 548574--548599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
548564 CATGGTATAA
548574 TGTATCGATACAT
1 TGTATCGATACAT
548587 TGTATCGATACAT
1 TGTATCGATACAT
548600 GATGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:548595 original size:33 final size:33
Alignment explanation
Indices: 548553--548619 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
548543 CTTCCACTGT
548553 TTGTATCGATACATGGTAT-AA-TGTATCGATACA
1 TTGTATCGATACAT-G-ATGAATTGTATCGATACA
548586 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
548619 T
1 T
548620 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.09
33 27 0.84
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:550342 original size:18 final size:18
Alignment explanation
Indices: 550319--550357 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
550309 GAATTTTTAG
550319 ATAGGTGGAGGATTCGAC
1 ATAGGTGGAGGATTCGAC
550337 ATAGGTGGAGGATTCGAC
1 ATAGGTGGAGGATTCGAC
550355 ATA
1 ATA
550358 CTCAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.36, T:0.23
Consensus pattern (18 bp):
ATAGGTGGAGGATTCGAC
Found at i:550572 original size:19 final size:19
Alignment explanation
Indices: 550548--550615 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
550538 AATTCAACGA
550548 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
550567 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
550582 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
550599 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
550616 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:550586 original size:32 final size:32
Alignment explanation
Indices: 550550--550612 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
550540 TTCAACGATT
*
550550 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
550582 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
550613 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:550587 original size:13 final size:13
Alignment explanation
Indices: 550569--550593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
550559 ACATAAGTTT
550569 TGTATCGATACAA
1 TGTATCGATACAA
550582 TGTATCGATACA
1 TGTATCGATACA
550594 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:550673 original size:13 final size:13
Alignment explanation
Indices: 550655--550680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
550645 CATTTTTCTA
550655 TGTATCGATACAT
1 TGTATCGATACAT
550668 TGTATCGATACAT
1 TGTATCGATACAT
550681 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:550677 original size:33 final size:33
Alignment explanation
Indices: 550635--550701 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
550625 GCCAAGGAAA
***
550635 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
550668 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
550701 T
1 T
550702 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:553163 original size:52 final size:52
Alignment explanation
Indices: 553044--553176 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 52
553034 TTGAGTTTAT
* * * *
553044 CAATTCTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCTGATTTTATTTCCAAAACAC
** *
553095 CAATTTTCCTTTAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAATAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTCCTGATTTTATTTCC-AAAACAC
* *
553148 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
553177 CTCGTTATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
51 8 0.12
52 44 0.65
53 16 0.24
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCTGATTTTATTTCCAAAACAC
Found at i:553196 original size:28 final size:28
Alignment explanation
Indices: 553160--553236 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
553150 ATTTTTCACA
* * *
553160 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
553188 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
553216 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
553237 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:553303 original size:107 final size:107
Alignment explanation
Indices: 553111--553315 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 107
553101 TCCTTTAATC
* * *
553111 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
553176 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCTGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCTGA
* * *** * * *
553219 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
553283 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
553316 AATTTTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
105 3 0.04
107 58 0.71
108 21 0.26
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCTGA
Found at i:553421 original size:80 final size:77
Alignment explanation
Indices: 553190--553424 Score: 222
Period size: 80 Copynumber: 2.9 Consensus size: 77
553180 GTTATTTCAT
* * * *
553190 CGGGGATACTCCAACCCCGTTA-CTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTTC-GAAGGGATACTCCAACCCC-GTTTTATT-CCAAAACA
* *
553254 TTGATTTCTCATAAT
63 TTGATTTCTCACAAC
* * * * * *
553269 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGAATTTTTTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG---TTTTATTCCAAAACA
*
553334 TCGATTTCTCACAAC
63 TTGATTTCTCACAAC
* *
553349 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCCCGTTATTATCTCCAAAACA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCGTT-TTAT-TCCAAAACA
*
553413 TTAAATTTCTCA
63 TT-GATTTCTCA
553425 TTGGGAAATA
Statistics
Matches: 125, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 50 0.40
80 64 0.51
81 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (77 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGTTTTATTCCAAAACATTG
ATTTCTCACAAC
Found at i:559089 original size:20 final size:22
Alignment explanation
Indices: 559045--559091 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
559035 AATTTTCCAC
559045 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
559067 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
559087 AAATC
1 AAATC
559092 ATCAACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATCTTTCACTTTTTCACTCA
Found at i:561430 original size:20 final size:20
Alignment explanation
Indices: 561391--561441 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
561381 CGATACATTA
**
561391 TATCGATACAT-GTTAATTG
1 TATCGATACATGGACAATTG
561410 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTG
561430 TATCGATACATG
1 TATCGATACATG
561442 AGATTGGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTG
Found at i:561528 original size:33 final size:33
Alignment explanation
Indices: 561470--561536 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
561460 CTTCCACTGT
*
561470 TTGTATCGATACATGGTACAATGTATCAATACA
1 TTGTATCGATACATGATACAATGTATCAATACA
* *
561503 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACAATGTATCAATACA
561536 T
1 T
561537 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCAATACA
Found at i:562910 original size:20 final size:20
Alignment explanation
Indices: 562885--562934 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
562875 AACGCCAGAT
*
562885 GTATCGATACTGCGTTCTTA
1 GTATCGATACTACGTTCTTA
562905 GTATCGATACTACGTTCTTA
1 GTATCGATACTACGTTCTTA
*
562925 GTATTGATAC
1 GTATCGATAC
562935 ATAGTATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (20 bp):
GTATCGATACTACGTTCTTA
Found at i:562945 original size:33 final size:33
Alignment explanation
Indices: 562903--562999 Score: 151
Period size: 33 Copynumber: 2.9 Consensus size: 33
562893 ACTGCGTTCT
562903 TAGTATCGATACTACGTTCTTAGTATTGATACA
1 TAGTATCGATACTACGTTCTTAGTATTGATACA
*
562936 TAGTATCGATACTGCGTTCTTAGTATTGATACA
1 TAGTATCGATACTACGTTCTTAGTATTGATACA
* *
562969 TAGTATCGATACTGA-GTTCTTTGTATCGATA
1 TAGTATCGATACT-ACGTTCTTAGTATTGATA
563000 TATGGGTACT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (33 bp):
TAGTATCGATACTACGTTCTTAGTATTGATACA
Found at i:567160 original size:22 final size:19
Alignment explanation
Indices: 567135--567176 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
567125 CTGACTTAAC
567135 ATGAATTTAATAAAAATATTTA
1 ATGAATTT--TAAAAAT-TTTA
567157 ATGAATTTTAAAAATTTTA
1 ATGAATTTTAAAAATTTTA
567176 A
1 A
567177 ATTTAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATGAATTTTAAAAATTTTA
Found at i:569658 original size:35 final size:34
Alignment explanation
Indices: 569606--569671 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
569596 CTTACAACAC
*
569606 TATCTGTTCAAAGGCTAAGATAGAACTTCTTCCA
1 TATCTGTTCAAAGGCTAAGATAGAACCTCTTCCA
* *
569640 TATCTTTTGCAAATGCTAAGATAGAACCTCTT
1 TATCTGTT-CAAAGGCTAAGATAGAACCTCTT
569672 AATCACTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 7 0.25
35 21 0.75
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.35
Consensus pattern (34 bp):
TATCTGTTCAAAGGCTAAGATAGAACCTCTTCCA
Found at i:570271 original size:13 final size:13
Alignment explanation
Indices: 570253--570279 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
570243 TACAAAGAAC
570253 ATGTATCAATACT
1 ATGTATCAATACT
570266 ATGTATCAATACT
1 ATGTATCAATACT
570279 A
1 A
570280 AGCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
ATGTATCAATACT
Found at i:570417 original size:25 final size:23
Alignment explanation
Indices: 570389--570439 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
570379 GTATTGATAC
570389 TTTGAATTATTTGACTTGAAAAACA
1 TTTGAATTA-TTG-CTTGAAAAACA
* *
570414 TTTGATTTATTGTTTGAAAAACA
1 TTTGAATTATTGCTTGAAAAACA
570437 TTT
1 TTT
570440 AAACTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.54
24 3 0.12
25 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (23 bp):
TTTGAATTATTGCTTGAAAAACA
Found at i:576385 original size:13 final size:13
Alignment explanation
Indices: 576367--576392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
576357 ACATTTGGTC
576367 ATGTATCGATACA
1 ATGTATCGATACA
576380 ATGTATCGATACA
1 ATGTATCGATACA
576393 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:576387 original size:33 final size:32
Alignment explanation
Indices: 576345--576412 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
576335 CGTTACAAGC
576345 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
576378 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
576410 CAA
1 CAA
576413 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:576489 original size:20 final size:20
Alignment explanation
Indices: 576442--576515 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
576432 GCCAATCACC
*
576442 TGTATCGATACATTCT-TTGCA
1 TGTATCGATACATT-TGAT-CA
* *
576463 AGTATCGATACATTTGGTCA
1 TGTATCGATACATTTGATCA
* *
576483 TGTATCGATAC-TGTGCATTA
1 TGTATCGATACATTTG-ATCA
576503 TGTATCGATACAT
1 TGTATCGATACAT
576516 CTGAAGGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 26 0.59
21 15 0.34
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTGATCA
Found at i:579471 original size:3 final size:3
Alignment explanation
Indices: 579463--579493 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
579453 TCTGAGTCAC
*
579463 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
579494 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:581110 original size:19 final size:20
Alignment explanation
Indices: 581066--581117 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
581056 TTACAAGCCA
581066 ATGTATCGATACATCTGGTC
1 ATGTATCGATACATCTGGTC
*
581086 ATGTATCGATACATCTTGT-
1 ATGTATCGATACATCTGGTC
581105 ATGTATCGATACA
1 ATGTATCGATACA
581118 AACAGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATCTGGTC
Found at i:581206 original size:20 final size:21
Alignment explanation
Indices: 581159--581211 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
581149 GCCAATCACC
*
581159 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
581180 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
581200 TGTATCGATACA
1 TGTATCGATACA
581212 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:581217 original size:13 final size:13
Alignment explanation
Indices: 581199--581223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
581189 ACATTTGGTC
581199 ATGTATCGATACA
1 ATGTATCGATACA
581212 ATGTATCGATAC
1 ATGTATCGATAC
581224 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:583574 original size:33 final size:32
Alignment explanation
Indices: 583519--583581 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
583509 GTTACAAGCT
* *
583519 ATGTATCGATACATTTCTTCATGTATCGATATA
1 ATGTATCAATACATTTCATCATGTAT-GATATA
583552 ATGTATCAATACATTGT-ATCATGTATGATA
1 ATGTATCAATACATT-TCATCATGTATGATA
583582 CAAATAGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 22 0.81
34 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (32 bp):
ATGTATCAATACATTTCATCATGTATGATATA
Found at i:591450 original size:33 final size:32
Alignment explanation
Indices: 591392--591458 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
591382 GTTACAAGCT
* *
591392 ATGTATCGATACATTTCTTCTTGTATTGATACA
1 ATGTATCGATACATTTC-TCATGTATCGATACA
591425 ATGTATCGATACATTGTAC-CATGTATCGATACA
1 ATGTATCGATACATT-T-CTCATGTATCGATACA
591458 A
1 A
591459 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCGATACA
Found at i:591531 original size:19 final size:19
Alignment explanation
Indices: 591487--591542 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
591477 CTGCTAGTTT
**
591487 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
591507 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
591526 CATGTATCGATACAATG
1 CATGTATCGATACAATG
591543 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:591545 original size:13 final size:13
Alignment explanation
Indices: 591527--591553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
591517 TACAATGAAC
591527 ATGTATCGATACA
1 ATGTATCGATACA
591540 ATGTATCGATACA
1 ATGTATCGATACA
591553 A
1 A
591554 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:591568 original size:33 final size:32
Alignment explanation
Indices: 591508--591572 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
591498 ACAATTGTCC
*
591508 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
591540 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
591573 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:594481 original size:15 final size:15
Alignment explanation
Indices: 594461--594497 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
594451 GAAAAAGTAA
594461 AAAAAAAACAAAAAC
1 AAAAAAAACAAAAAC
* *
594476 AAAAAAAACACACAC
1 AAAAAAAACAAAAAC
594491 AAAAAAA
1 AAAAAAA
594498 GTACAAAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAAAAAC
Found at i:595837 original size:27 final size:27
Alignment explanation
Indices: 595799--596647 Score: 460
Period size: 27 Copynumber: 28.5 Consensus size: 27
595789 CTTTTCTTCA
595799 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
595826 AAGTCCACAACTCCATGGCACCCTTTTTTTT
1 AAGTCCACAACTCCGTGGCACCC----TTTT
* *
595857 CAAAGCCCAAAACTCCGTGGCACCTTTTTCTTTT
1 --AAGTCCACAACTCCGTGGCACC-----CTTTT
**
595891 CAAAGTCCACAACTCTATGGCACCCTTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
* * *
595920 AAGTCAACGACTCCATGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* **
595947 AAGTTCAGGACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
595974 AAAGCCCACAACTCTGTGGCACCTTTTTCTTTT
1 -AAGTCCACAACTCCGTGGCACC-----CTTTT
* * *
596007 CAAAGTCCAAAACTCTGTGGCACCATTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
* *
596036 AAAGCCCACAACTCTGTGGCACCTTTTTCTTTT
1 -AAGTCCACAACTCCGTGGCACC-----CTTTT
* *
596069 CAAAGTCCCCAACTCTGTGGCACCCTTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
** * * *
596098 AAGTTTACAGCTCTGTAGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
596125 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
1 -AAGTCCACAACTCCGTGGCACC-----CTTTT
* * * *
596158 CATAGCCCATAACTCCATGGCACCGTTTT
1 -A-AGTCCACAACTCCGTGGCACCCTTTT
* *
596187 AAGTCTACAAATCCGTGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACC-----CTTTT
* * *
596219 CAAAGCCCACAACTCTGTGGCACCTTTTTTTTTT
1 --AAGTCCACAACTCCGTGGCACC-----CTTTT
* ** *
596253 CAAAGTCCAAAACTCTATGGCACCATTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
596282 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
596309 AAGTCCACGACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
596336 AAAG-CTTACAACTTCGTGGCACCTTTTTCTTTT
1 -AAGTC-CACAACTCCGTGGCACC-----CTTTT
* *
596369 CAAAGTCTACAACTCTGTGGCACCCTTTT
1 --AAGTCCACAACTCCGTGGCACCCTTTT
* * *
596398 AAGCCCACAACTCCATGGTATTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA--C-----CCTTTT
596432 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
596459 AAGCCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
596486 AAGCCCACAACTTCGTGGCAAACTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGC--AC-----CCTTTT
* *
596520 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA--C-----CCTTTT
* *
596554 AAGTCCACAACTTCGTGGCAACCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
596581 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
596608 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
596635 AA-TCCACAACTCC
1 AAGTCCACAACTCC
596648 ACGGCATCTT
Statistics
Matches: 671, Mismatches: 88, Indels: 127
0.76 0.10 0.14
Matches are distributed among these distances:
26 10 0.01
27 281 0.42
28 73 0.11
29 30 0.04
31 4 0.01
32 6 0.01
33 39 0.06
34 226 0.34
35 1 0.00
38 1 0.00
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:595871 original size:33 final size:34
Alignment explanation
Indices: 595834--595919 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 34
595824 TTAAGTCCAC
595834 AACTCCATGGCACCCTTTT-TTTTCAAAGCCCAA
1 AACTCCATGGCACCCTTTTCTTTTCAAAGCCCAA
* * * *
595867 AACTCCGTGGCACCTTTTTCTTTTCAAAGTCCAC
1 AACTCCATGGCACCCTTTTCTTTTCAAAGCCCAA
*
595901 AACTCTATGGCACCCTTTT
1 AACTCCATGGCACCCTTTT
595920 AAGTCAACGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 17 0.38
34 28 0.62
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.34
Consensus pattern (34 bp):
AACTCCATGGCACCCTTTTCTTTTCAAAGCCCAA
Found at i:596293 original size:61 final size:59
Alignment explanation
Indices: 595803--596718 Score: 565
Period size: 61 Copynumber: 15.3 Consensus size: 59
595793 TCTTCAAAGT
*
595803 CCACAACTCCGTGGCACC-----CTTTTAAGTCCACAACTCCATGGCACCCTTTTTTTTCAAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCC----TTTT--AAGC
* ** *
595863 CCAAAACTCCGTGGCACCTTTTTCTTTTCAAAGTCCACAACTCTATGGCACCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * * * **
595924 CAACGACTCCATGGCACC-----CTTTTAAGTTCAGGACTCCGTGGCACCCTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGC
* * * *
595979 CCACAACTCTGTGGCACCTTTTTCTTTTCAAAGTCCAAAACTCTGTGGCACCATTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCCTTTT-AAGC
* * * *
596041 CCACAACTCTGTGGCACCTTTTTCTTTTCAAAGTCCCCAACTCTGTGGCACCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCCTTTTAAGC
** * * *
596102 TTACAGCTCTGTAGCACC-----CTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCATA
1 CCACAACTCCGTGGCACCTTTTTCTTTT-AAGTCCACAACTCCGTGGCACC-----CTTTT-A-A
596162 GC
58 GC
* * * * *
596164 CCATAACTCCATGGCACC-----GTTTTAAGTCTACAAATCCGTGGCACCTTTTTCTTTTCAAAG
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACC-----CTTTT--AAG
596224 C
59 C
* * * ** * *
596225 CCACAACTCTGTGGCACCTTTTTTTTTTCAAAGTCCAAAACTCTATGGCACCATTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCCTTTTAAGC
*
596286 CCACAACTCCGTGGCACC-----CTTTTAAGTCCACGACTCCGTGGCACCCTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGC
** * * *
596341 TTACAACTTCGTGGCACCTTTTTCTTTTCAAAGTCTACAACTCTGTGGCACCCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
596402 CCACAACTCCATGGTATTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
1 CCACAACTCCGTGGCA-CCTTTTT-CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* *
596463 CCACAACTCCGTGGCACC-----CTTTTAAGCCCACAACTTCGTGGCAAACTTTTTCCTTTTAAG
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGC--AC-----CCTTTTAAG
596523 C
59 C
* * * *
596524 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAACCTTTTAAGT
1 CCACAACTCCGTGGCAC-CTTTTT-CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
596585 CCACAACTCTGTGGCACC-----CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAA-T
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
** * * * *
596638 CCACAACTCCACGGCATCTTTCTTCTTTTAAG-CTCACAAGTCAGTGGAACCCTTTTCAAAAGC
1 CCACAACTCCGTGGCACCTTT-TTCTTTTAAGTC-CACAACTCCGTGGCACCCTTTT---AAGC
* *
596701 CCACAAGTCGGTGGCACC
1 CCACAACTCCGTGGCACC
596719 CCTTTCAAAG
Statistics
Matches: 689, Mismatches: 102, Indels: 127
0.75 0.11 0.14
Matches are distributed among these distances:
53 15 0.02
54 97 0.14
55 56 0.08
56 16 0.02
58 1 0.00
59 27 0.04
60 34 0.05
61 213 0.31
62 132 0.19
63 26 0.04
65 5 0.01
66 5 0.01
67 22 0.03
68 40 0.06
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (59 bp):
CCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
Found at i:596346 original size:150 final size:147
Alignment explanation
Indices: 596009--596666 Score: 605
Period size: 150 Copynumber: 4.4 Consensus size: 147
595999 TTTCTTTTCA
* * * *
596009 AAGTCCAAAACTCTGTGGCACCATTTTAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTCAAAG
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAG
** * *
596074 TCCC-CAACTCTGTGGCACC-----CTTTTAAGTTTACAGCTCTGTAGCACCCTTTTAAAGTCCA
66 -CCCACAACTCTGTGGCACCTTTTTCTTTTAAGTCCACAACTCTGTGGCA-CCTTTT-AAGTCCA
596133 CAACTCCGTGGCACCTTTTTCTTTT
128 CAACTCCGTGGCACC-----CTTTT
* * * * * * *
596158 CATAGCCCATAACTCCATGGCACCGTTTT-AAGTCTACAAATCCGTGGCACCTTTTTCTTTTCAA
1 -A-AGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAA
* * *
596222 AGCCCACAACTCTGTGGCACCTTTTTTTTTTCAAAGTCCAAAACTCTATGGCACCATTTTAAGTC
64 AGCCCACAACTCTGTGGCACCTTTTTCTTTT--AAGTCCACAACTCTGTGGCACC-TTTTAAGTC
596287 CACAACTCCGTGGCACCCTTTT
126 CACAACTCCGTGGCACCCTTTT
* ** *
596309 AAGTCCACGACTCCGTGGCACCCTTTTAAAGCTTACAACTTCGTGGCACCTTTTTCTTTTCAAAG
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAG
* * * ** *
596374 TCTACAACTCTGTGGCACC-----CTTTTAAGCCCACAACTCCATGGTATTCTTTTTCCTTTTAA
66 CCCACAACTCTGTGGCACCTTTTTCTTTTAAGTCCACAACT-C-T-GT-GGC----ACCTTTTAA
596434 GTCCACAACTCCGTGGCACCCTTTT
123 GTCCACAACTCCGTGGCACCCTTTT
* * *
596459 AAGCCCACAACTCCGTGGCACCCTTTT-AAGCCCACAACTTCGTGGCAAACTTTTTCCTTTT--A
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGC-ACCTTTTT-CTTTTCAA
596521 AGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACT-TCGTGGCAACCTTTTAAGT
64 AGCCCACAACTCTGTGGCAC-CTTTTT-CTTTTAAGTCCACAACTCT-GTGGC-ACCTTTTAAGT
*
596585 CCACAACTCTGTGGCACCCTTTT
125 CCACAACTCCGTGGCACCCTTTT
* * ** *
596608 AAGTCCACAACTCTGTGGCACCCTTTT-AA-TCCACAACTCCACGGCATCTTTCTTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCTTT-TTCTTTT
596667 AAGCTCACAA
Statistics
Matches: 424, Mismatches: 55, Indels: 61
0.79 0.10 0.11
Matches are distributed among these distances:
143 10 0.02
144 1 0.00
145 5 0.01
146 1 0.00
147 11 0.03
148 14 0.03
149 119 0.28
150 164 0.39
151 33 0.08
152 1 0.00
153 3 0.01
155 4 0.01
156 40 0.09
157 18 0.04
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (147 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAG
CCCACAACTCTGTGGCACCTTTTTCTTTTAAGTCCACAACTCTGTGGCACCTTTTAAGTCCACAA
CTCCGTGGCACCCTTTT
Found at i:596356 original size:211 final size:211
Alignment explanation
Indices: 596071--596458 Score: 496
Period size: 211 Copynumber: 1.8 Consensus size: 211
596061 TTTCTTTTCA
* * ** *
596071 AAGTCCCCAACTCTGTGGCACCCTTTTAAGTTTACAGCTCTGTAGCACCCTTTTAAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAGCTCCGTAGCACCCTTTTAAAGTCCACAA
* * * * *
596136 CTCCGTGGCACCTTTTTCTTTTCATAGCCCATAACTCCATGGCACCGTTTTAAGTCTACAAATCC
66 CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTAAGCCCACAAATCC
* * *
596201 GTGGCA-CCTTTTT-CTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTTTTTTCAAAGTCCAAA
131 ATGGCATCCTTTTTCCTTTT--AAGCCCACAACTCCGTGGCACCCTTTTTTTTTCAAAGTCCAAA
596264 ACTCTATGGCACCATTTT
194 ACTCTATGGCACCATTTT
* *
596282 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAC-GACTCCGTGGCACCCTTTTAAAG-CTTAC
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAG-CTCCGTAGCACCCTTTTAAAGTC-CAC
* * * ** *
596345 AACTTCGTGGCACCTTTTTCTTTTCAAAGTCTACAACTCTGTGGCACCCTTTTAAGCCCACAACT
64 AACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTAAGCCCACAAAT
* * *
596410 CCATGGTATTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
129 CCATGGCATCCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCCTTTT
596459 AAGCCCACAA
Statistics
Matches: 149, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
210 2 0.01
211 136 0.91
212 6 0.04
213 5 0.03
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (211 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAGCTCCGTAGCACCCTTTTAAAGTCCACAA
CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCATGGCACCCTTTTAAGCCCACAAATCC
ATGGCATCCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCCTTTTTTTTTCAAAGTCCAAAAC
TCTATGGCACCATTTT
Found at i:596489 original size:88 final size:86
Alignment explanation
Indices: 595799--596647 Score: 590
Period size: 89 Copynumber: 9.5 Consensus size: 86
595789 CTTTTCTTCA
* *
595799 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCCTTTTTTTTCAAAGCC
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC----TTTT--AAGCC
*
595864 CAAAACTCCGTGGCACCTTTTT-CTTTT
60 CACAACTCCGTGGCA-CTTTTTCCTTTT
* * * * ** **
595891 CAAAGTCCACAACTCTATGGCACCCTTTTAAGTCAACGACTCCATGGCACCCTTTTAAGTTCAGG
1 --AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACA
595956 ACTCCGTGGCAC-----CCTTTT
64 ACTCCGTGGCACTTTTTCCTTTT
* * * *
595974 AAAGCCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGTCCAAAACTCTGTGGCACCATTTTAAA
1 -AAGTCCACAACTCTGTGGCACC-----CTTTT--AAGTCCACAACTCCGTGGCACCCTTTT-AA
*
596039 GCCCACAACTCTGTGGCACCTTTTT-CTTTT
57 GCCCACAACTCCGTGGCA-CTTTTTCCTTTT
* ** * * * *
596069 CAAAGTCCCCAACTCTGTGGCACCCTTTTAAGTTTACAGCTCTGTAGCACCCTTTTAAAGTCCAC
1 --AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGCCCAC
596134 AACTCCGTGGCACCTTTTT-CTTTT
63 AACTCCGTGGCA-CTTTTTCCTTTT
* * ** * * *
596158 CATAGCCCATAACTCCATGGCACCGTTTTAAGTCTACAAATCCGTGGCACCTTTTTCTTTTCAAA
1 -A-AGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC-----CTTTT--AA
* *
596223 GCCCACAACTCTGTGGCACCTTTTT-TTTTT
57 GCCCACAACTCCGTGGCA-CTTTTTCCTTTT
* * * * *
596253 CAAAGTCCAAAACTCTATGGCACCATTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACG
1 --AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACA
596318 ACTCCGTGGCAC-----CCTTTT
64 ACTCCGTGGCACTTTTTCCTTTT
* * *
596336 AAAG-CTTACAACT-TCGTGGCACCTTTTTCTTTTCAAAGTCTACAACTCTGTGGCACCCTTTTA
1 -AAGTC-CACAACTCT-GTGGCACC-----CTTTT--AAGTCCACAACTCCGTGGCACCCTTTTA
* *
596399 AGCCCACAACTCCATGGTATTCTTTTTCCTTTT
56 AGCCCACAACTCCGTGGCA--CTTTTTCCTTTT
* *
596432 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAAC
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAAC
*
596497 TTCGTGGCAAACTTTTTCCTTTT
66 TCCGTGGC--ACTTTTTCCTTTT
* * * *
596520 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAACCTTTTAAGT
1 AAGTCCACAACTCTGTGGCA--C-----CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
*
596585 CCACAACTCTGTGGCAC-----CCTTTT
59 CCACAACTCCGTGGCACTTTTTCCTTTT
596608 AAGTCCACAACTCTGTGGCACCCTTTTAA-TCCACAACTCC
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCC
596648 ACGGCATCTT
Statistics
Matches: 618, Mismatches: 85, Indels: 118
0.75 0.10 0.14
Matches are distributed among these distances:
80 10 0.02
81 10 0.02
82 37 0.06
83 9 0.01
86 1 0.00
87 11 0.02
88 129 0.21
89 151 0.24
90 31 0.05
91 7 0.01
93 2 0.00
94 51 0.08
95 140 0.23
96 29 0.05
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (86 bp):
AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAAC
TCCGTGGCACTTTTTCCTTTT
Found at i:596738 original size:29 final size:30
Alignment explanation
Indices: 596667--596762 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
596657 TTCTTCTTTT
* * *
596667 AAGCTCACAAGTCAGTGGAACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
*
596697 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
*
596726 AAGCCCACAAGTCAGTGGCA-ACC-TTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
596754 AAGCCCACA
1 AAGCCCACA
596763 CAAGTTGGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
27 3 0.05
28 12 0.20
29 20 0.34
30 24 0.41
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCCTTTCAA
Found at i:596767 original size:30 final size:29
Alignment explanation
Indices: 596667--596762 Score: 117
Period size: 29 Copynumber: 3.3 Consensus size: 29
596657 TTCTTCTTTT
*
596667 AAGCTCACAAGTCAGTGG-AACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAA-CC-TTTCAA
* *
596697 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCA-ACCTTTCAA
596726 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
596754 AAGCCCACA
1 AAGCCCACA
596763 CAAGTTGGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.05
28 12 0.21
29 20 0.34
30 20 0.34
31 3 0.05
ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:596860 original size:49 final size:49
Alignment explanation
Indices: 596784--597626 Score: 607
Period size: 49 Copynumber: 17.9 Consensus size: 49
596774 CGTCTTTTTC
* * * *
596784 TAAGTCCAACATCGATGGCCTTAAATCAGCATATTGGCACCTTTATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
596833 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
596881 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG---C---A-C--
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
596921 -AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * *
596969 TAAGACCGATGTCGTTGGCCTTGAATCATCACATTGGCA-CTTTAACCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT----ATCTT
* * *
597021 TAAGACCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* ** * *
597070 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCATCTTTAACATT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-TT
* ** ** *
597120 CCTAAGCCCAACGT-GACTGGCCTTGTCTCAGCACATTGGCA--TTCT-TCTTT
1 --TAAGACCAATATCG-CTGGCCTTGAATCAGCATATTGGCACCTT-TATC-TT
*
597170 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * *
597219 TAAGACCAATGTCACTGGCCTTGAATTAGTACATTAGG-------A-C--
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATT-GGCACCTTTATCTT
* * *
597259 -AAGCCCAATATCGTTGGCCTTAAATCAGCATATTGGCACC-TTATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
597306 TAAGACCAATATCGCCGGCCTTGAATCAGCACATTGG---C---A----
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * ** * *
597345 TAAGCCCAATATCGCTGGTCC-TAAATCAAAATATTAGCACC-TCATCTT
1 TAAGACCAATATCGCTGG-CCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
597393 TAAGACCAATATCACTGGCCTTGAATTAGCACATTGG---C---A-C--
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
597433 -AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * * * *
597481 TAAGACCGATGTTGTTGGCCTTAAATCAGCACATTGGCACCTTAACCATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT---TATCTT
* * * * *
597533 TAAGACCAATGTCGCTGGCGTTGAATCAGCACATTGGAACCTTAATCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * *
597582 TGAGTCCAATAGCGTTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
597627 ACATTCCTAA
Statistics
Matches: 628, Mismatches: 107, Indels: 118
0.74 0.13 0.14
Matches are distributed among these distances:
38 2 0.00
39 119 0.19
40 2 0.00
42 6 0.01
43 4 0.01
44 2 0.00
45 6 0.01
46 2 0.00
47 2 0.00
48 133 0.21
49 221 0.35
50 13 0.02
51 1 0.00
52 112 0.18
53 3 0.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (49 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:597007 original size:88 final size:87
Alignment explanation
Indices: 596838--597008 Score: 297
Period size: 88 Copynumber: 2.0 Consensus size: 87
596828 ATCTTTAAGA
596838 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATATCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATATCGCTGGCCTT
596903 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* * *
596925 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATCTTTAAGACCAATATCGCTGGCCT
*
596990 TGAATCATCACATTGGCAC
65 TGAATCAGCACATTGGCAC
597009 TTTAACCATC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 36 0.46
88 43 0.54
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATATCGCTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:597106 original size:101 final size:101
Alignment explanation
Indices: 596933--597620 Score: 424
Period size: 101 Copynumber: 7.3 Consensus size: 101
596923 GCCCAATATC
* * * *
596933 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAATCAT
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAG
*
596998 CACATTGGCA-CTTTAACCATCTTTAAGACCAATGTT
66 CATATTGGCACCTTTAA-CATCTTTAAGACCAATGTT
*
597034 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCATTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAG
* * * *
597099 CATATTGGCATCTTTAACAT-TCCTAAGCCCAACG-T
66 CATATTGGCACCTTTAACATCT-TTAAGACCAATGTT
** * * *
597134 GACTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTTTAAGTCCAATATCGCTGGCCTTGAATC
1 G-CTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATATCGTTGGCCTTGAATC
*
597197 AGCATATTGGCACCTTT---ATCTTTAAGACCAATGTC
64 AGCATATTGGCACCTTTAACATCTTTAAGACCAATGTT
* * * * * *
597232 ACTGGCCTTGAATTAGTACATTAGG-------A-C---AAGCCCAATATCGTTGGCCTTAAATCA
1 GCTGGCCTTGAATCAGCATATT-GGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCA
* *
597286 GCATATTGGCACC-TT---ATCTTTAAGACCAATATC
65 GCATATTGGCACCTTTAACATCTTTAAGACCAATGTT
* * * * *
597319 GCCGGCCTTGAATCAGCACATTGG------CA----TAAGCCCAATATCGCTGGTCC-TAAATCA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTTGG-CCTTGAATCA
** * * *
597373 AAATATTAGCACC--T--CATCTTTAAGACCAATATC
65 GCATATTGGCACCTTTAACATCTTTAAGACCAATGTT
* * * * *
597406 ACTGGCCTTGAATTAGCACATTGG------CA-C---AAGCCCAATATCGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAG
*
597461 CATATTGGCACC-TT--CATCTTTAAGACCGATGTT
66 CATATTGGCACCTTTAACATCTTTAAGACCAATGTT
* * * * * * *
597494 GTTGGCCTTAAATCAGCACATTGGCACCTTAACCATCTTTAAGACCAATGTCGCTGGCGTTGAAT
1 GCTGGCCTTGAATCAGCATATTGGCACCTT---CATCTTTAAGTCCAATATCGTTGGCCTTGAAT
* * * * *
597559 CAGCACATTGGAACC-TT-A-ATCTTTGAGTCCAATAG-C
63 CAGCATATTGGCACCTTTAACATCTTTAAGACCAAT-GTT
*
597595 GTTGGCCTTGAATCAGCATATTGGCA
1 GCTGGCCTTGAATCAGCATATTGGCA
597621 TCTTTAACAT
Statistics
Matches: 495, Mismatches: 63, Indels: 58
0.80 0.10 0.09
Matches are distributed among these distances:
86 5 0.01
87 145 0.29
88 76 0.15
92 1 0.00
97 30 0.06
98 4 0.01
99 5 0.01
100 46 0.09
101 176 0.36
102 7 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (101 bp):
GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAG
CATATTGGCACCTTTAACATCTTTAAGACCAATGTT
Found at i:597350 original size:87 final size:87
Alignment explanation
Indices: 597175--597520 Score: 462
Period size: 87 Copynumber: 4.0 Consensus size: 87
597165 TCTTTTAAGT
* *
597175 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCACTGGCCT
1 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACC-TTATCTTTAAGACCAATATCACTGGCCT
* *
597240 TGAATTAGTACATTAGG-ACAAGC
65 TGAATCAGCACATT-GGCACAAGC
* * *
597263 CCAATATCGTTGGCCTTAAATCAGCATATTGGCACCTTATCTTTAAGACCAATATCGCCGGCCTT
1 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTATCTTTAAGACCAATATCACTGGCCTT
*
597328 GAATCAGCACATTGGCATAAGC
66 GAATCAGCACATTGGCACAAGC
** * *
597350 CCAATATCGCTGGTCC-TAAATCAAAATATTAGCACCTCATCTTTAAGACCAATATCACTGGCCT
1 CCAATATCGCTGG-CCTTAAATCAGCATATTGGCACCTTATCTTTAAGACCAATATCACTGGCCT
*
597414 TGAATTAGCACATTGGCACAAGC
65 TGAATCAGCACATTGGCACAAGC
* * * ***
597437 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTTGTTGGCCT
1 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATATCACTGGCCT
*
597502 TAAATCAGCACATTGGCAC
65 TGAATCAGCACATTGGCAC
597521 CTTAACCATC
Statistics
Matches: 225, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
86 4 0.02
87 147 0.65
88 74 0.33
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTATCTTTAAGACCAATATCACTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:597643 original size:101 final size:101
Alignment explanation
Indices: 597433--597668 Score: 271
Period size: 101 Copynumber: 2.3 Consensus size: 101
597423 ACATTGGCAC
* * * * * *
597433 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTTGTTG
1 AAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGAACCTTAATCTTTAAGACCAATGTCGTTG
*
597498 GCCTTAAATCAGCACATTGGCACCTTAACCATCTTT
66 GCCTTAAATCAGCACATTGGCACCTTAACCATCTCT
* * * *
597534 AAGACCAATGTCGCTGGCGTTGAATCAGCACATTGGAACCTTAATCTTTGAGTCCAATAG-CGTT
1 AAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGAACCTTAATCTTTAAGACCAAT-GTCGTT
* * *
597598 GGCCTTGAATCAGCATATTGGCATCTTTAA-CAT-TCCT
65 GGCCTTAAATCAGCACATTGGCA-CCTTAACCATCT-CT
* **
597635 AAGCCCAATGTCGCTAGCCTTGTCTCAGCACATT
1 AAGCCCAATGTCGCTGGCCTTGAATCAGCACATT
597669 CGCATTCTTC
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
100 1 0.01
101 106 0.94
102 6 0.05
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (101 bp):
AAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGAACCTTAATCTTTAAGACCAATGTCGTTG
GCCTTAAATCAGCACATTGGCACCTTAACCATCTCT
Found at i:598515 original size:19 final size:19
Alignment explanation
Indices: 598491--598553 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
598481 AAATAGTAAA
598491 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
598510 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
598523 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
598542 TGTATCGATACA
1 TGTATCGATACA
598554 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:598528 original size:13 final size:13
Alignment explanation
Indices: 598510--598567 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
598500 ACATAAGTGT
598510 TGTATCGATACAA
1 TGTATCGATACAA
598523 TGTATCGATACATAA
1 TGTATCGATAC--AA
598538 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
598555 TGTATCGCTACAA
1 TGTATCGATACAA
598568 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:598530 original size:32 final size:32
Alignment explanation
Indices: 598489--598566 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
598479 ACAAATAGTA
598489 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
598521 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
598553 AATGTATCGCTACA
1 AATGTATCGATACA
598567 AAGCTACTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:598623 original size:13 final size:13
Alignment explanation
Indices: 598605--598630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
598595 CATTATTCAA
598605 TGTATCGATACAT
1 TGTATCGATACAT
598618 TGTATCGATACAT
1 TGTATCGATACAT
598631 CTAGGAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:600240 original size:13 final size:13
Alignment explanation
Indices: 600222--600247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
600212 CAATTTTTTG
600222 TGTATCGATACAT
1 TGTATCGATACAT
600235 TGTATCGATACAT
1 TGTATCGATACAT
600248 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:600333 original size:20 final size:20
Alignment explanation
Indices: 600308--600380 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
600298 ATCTTTTTTT
600308 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
600328 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
600349 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
600369 ATGTATCGATAC
1 ATGTATCGATAC
600381 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:600359 original size:41 final size:42
Alignment explanation
Indices: 600286--600380 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
600276 CTGCCAAGAA
*
600286 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
600328 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
600369 ATGTATCGATAC
1 ATGTATCGATAC
600381 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:601041 original size:23 final size:23
Alignment explanation
Indices: 601012--601058 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
601002 AAAAAATCTC
601012 CCCCTTAATCAAGTAATTCATAT
1 CCCCTTAATCAAGTAATTCATAT
601035 CCCCTTAATCAAGTAATTCATAT
1 CCCCTTAATCAAGTAATTCATAT
601058 C
1 C
601059 AAAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (23 bp):
CCCCTTAATCAAGTAATTCATAT
Found at i:602865 original size:13 final size:13
Alignment explanation
Indices: 602847--602885 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
602837 ATAATCACCC
*
602847 TGTATCGATACAG
1 TGTATCGATACAA
602860 TGTATCGATACAA
1 TGTATCGATACAA
602873 TGTATCGATACAA
1 TGTATCGATACAA
602886 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:602896 original size:20 final size:20
Alignment explanation
Indices: 602871--602949 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
602861 GTATCGATAC
602871 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
602891 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
602916 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
602936 CATGTATCGATACA
1 AATGTATCGATACA
602950 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:604979 original size:15 final size:15
Alignment explanation
Indices: 604959--604989 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
604949 ATTTCGTTTG
*
604959 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
604974 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
604989 G
1 G
604990 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:609071 original size:13 final size:13
Alignment explanation
Indices: 609053--609078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
609043 CAATTTTTTG
609053 TGTATCGATACAT
1 TGTATCGATACAT
609066 TGTATCGATACAT
1 TGTATCGATACAT
609079 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:609164 original size:20 final size:20
Alignment explanation
Indices: 609139--609211 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
609129 ATCTTTTTTT
609139 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
609159 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
609180 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
609200 ATGTATCGATAC
1 ATGTATCGATAC
609212 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:609190 original size:41 final size:42
Alignment explanation
Indices: 609117--609211 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
609107 CTGCCAAGAA
*
609117 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
609159 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
609200 ATGTATCGATAC
1 ATGTATCGATAC
609212 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:617403 original size:20 final size:22
Alignment explanation
Indices: 617365--617404 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
617355 AGCCTTTGAC
*
617365 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTCATTATGTTT
617387 CATGCA-TTTTTCA-TATGT
1 CATGCATTTTTTCATTATGT
617405 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (22 bp):
CATGCATTTTTTCATTATGTTT
Found at i:620836 original size:20 final size:20
Alignment explanation
Indices: 620811--620849 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
620801 ACACGATCCT
*
620811 ATGTATCGATATAATACATA
1 ATGTATCGATAAAATACATA
*
620831 ATGTATTGATAAAATACAT
1 ATGTATCGATAAAATACAT
620850 TTGAAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGTATCGATAAAATACATA
Found at i:620950 original size:52 final size:52
Alignment explanation
Indices: 620854--620961 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 52
620844 ATACATTTGA
* * * *
620854 AATTCTAGCCGTTGGACTCAATGTATTTATACAATTCATAATGTATTGATAC
1 AATTATAGCCGTTGGACTCAATGTATTGATACAATTCACAATGTATCGATAC
* * * *
620906 AATTATAGCCGTTAGG-CTTAATGTATTGATACAATTTACCATGTATCGATAT
1 AATTATAGCCGTT-GGACTCAATGTATTGATACAATTCACAATGTATCGATAC
620958 AATT
1 AATT
620962 CACTTGGGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 45 0.96
53 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (52 bp):
AATTATAGCCGTTGGACTCAATGTATTGATACAATTCACAATGTATCGATAC
Found at i:622218 original size:20 final size:20
Alignment explanation
Indices: 622193--622246 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
622183 GTTTAAGACA
* *
622193 ATGTATCAATACAAT-TCCTC
1 ATGTATCGATACAATGTAC-C
622213 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
622233 ATGTATCGATACAA
1 ATGTATCGATACAA
622247 ACAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:622321 original size:19 final size:20
Alignment explanation
Indices: 622275--622328 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
622265 CTTCCAGTTT
* *
622275 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGATA
*
622295 CTTGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
622314 CATGTATCGATACAA
1 CATGTATCGATACAA
622329 AACAGCGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:622328 original size:39 final size:39
Alignment explanation
Indices: 622275--622450 Score: 169
Period size: 39 Copynumber: 4.4 Consensus size: 39
622265 CTTCCAGTTT
622275 CATGTATCGATACAATTATGCTTGTATCGATACAATGAA
1 CATGTATCGATACAATTATGCTTGTATCGATACAATGAA
* * * * * * *
622314 CATGTATCGATACAA-AACAGC-GGTA-GGGTAGCTACTGCCAGTTT
1 CATGTATCGATACAATTA-TGCTTGTATCGATA-C-AATG--A---A
* *
622358 CATGTATCGATACAATTGTGCTTGTATCAATACAATGAA
1 CATGTATCGATACAATTATGCTTGTATCGATACAATGAA
*
622397 CATGTATCGATACAATTATGCTTGTATTGATACAATGAA
1 CATGTATCGATACAATTATGCTTGTATCGATACAATGAA
622436 CATGTATCGATACAA
1 CATGTATCGATACAA
622451 AACATTATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
37 3 0.03
38 5 0.05
39 71 0.66
41 1 0.01
42 1 0.01
44 20 0.19
45 4 0.04
46 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (39 bp):
CATGTATCGATACAATTATGCTTGTATCGATACAATGAA
Found at i:622332 original size:83 final size:83
Alignment explanation
Indices: 622214--622411 Score: 326
Period size: 83 Copynumber: 2.4 Consensus size: 83
622204 CAATTCCTCA
* * *
622214 TGTATCGATACAATGTACCATGTATCGATAC-AAACAGTGATAGGGTAGCTACTTCCAGTTTCAT
1 TGTATCGATACAATG-AACATGTATCGATACAAAACAGCGATAGGGTAGCTACTGCCAGTTTCAT
622278 GTATCGATACAATTATGCT
65 GTATCGATACAATTATGCT
*
622297 TGTATCGATACAATGAACATGTATCGATACAAAACAGCGGTAGGGTAGCTACTGCCAGTTTCATG
1 TGTATCGATACAATGAACATGTATCGATACAAAACAGCGATAGGGTAGCTACTGCCAGTTTCATG
*
622362 TATCGATACAATTGTGCT
66 TATCGATACAATTATGCT
*
622380 TGTATCAATACAATGAACATGTATCGATACAA
1 TGTATCGATACAATGAACATGTATCGATACAA
622412 TTATGCTTGT
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 14 0.13
83 94 0.87
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (83 bp):
TGTATCGATACAATGAACATGTATCGATACAAAACAGCGATAGGGTAGCTACTGCCAGTTTCATG
TATCGATACAATTATGCT
Found at i:622404 original size:19 final size:19
Alignment explanation
Indices: 622358--622450 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
622348 CTGCCAGTTT
**
622358 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
* *
622378 CTTGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
* *
622397 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGA-A
* *
622417 CTTGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
622436 CATGTATCGATACAA
1 CATGTATCGATACAA
622451 AACATTATTT
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
19 30 0.52
20 28 0.48
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:622469 original size:39 final size:39
Alignment explanation
Indices: 622358--622488 Score: 120
Period size: 39 Copynumber: 3.3 Consensus size: 39
622348 CTGCCAGTTT
*** *
622358 CATGTATCGATACAATTGTGCTTGTATCAATACAATGAA
1 CATGTATCGATACAAACATGATTGTATCAATACAATGAA
** * **
622397 CATGTATCGATACAATTATGCTTGTATTGATACAATGAA
1 CATGTATCGATACAAACATGATTGTATCAATACAATGAA
* * *
622436 CATGTATCGATACAAAACATTATT-TATCAATACATCTGGA
1 CATGTATCGATAC-AAACATGATTGTATCAATACA-ATGAA
*
622476 TATGTATCGATAC
1 CATGTATCGATAC
622489 TTTCAAAGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 57 0.73
40 21 0.27
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (39 bp):
CATGTATCGATACAAACATGATTGTATCAATACAATGAA
Found at i:625002 original size:13 final size:13
Alignment explanation
Indices: 624984--625021 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
624974 AGTAACCCAA
*
624984 GTATCGATACATT
1 GTATCGATACAAT
624997 GTATCGATACAAT
1 GTATCGATACAAT
*
625010 GTATAGATACAA
1 GTATCGATACAA
625022 AGAACATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:629151 original size:13 final size:13
Alignment explanation
Indices: 629133--629157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
629123 TTCAACAATT
629133 TGTATCGATACAA
1 TGTATCGATACAA
629146 TGTATCGATACA
1 TGTATCGATACA
629158 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:641168 original size:28 final size:28
Alignment explanation
Indices: 641124--641177 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
641114 TCGATGATCA
641124 GAAAAAATCGGGATTGGAGTATCCCTTC
1 GAAAAAATCGGGATTGGAGTATCCCTTC
*
641152 GAAAATAA-CGGGGTTGGAGTATCCCT
1 GAAAA-AATCGGGATTGGAGTATCCCT
641178 AATTATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (28 bp):
GAAAAAATCGGGATTGGAGTATCCCTTC
Found at i:641251 original size:28 final size:28
Alignment explanation
Indices: 641211--641282 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
641201 GGAATAAAGC
** *
641211 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
641239 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
641267 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
641283 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Done.