Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 2 of 279
Found at i:303637 original size:46 final size:46
Alignment explanation
Indices: 303570--303777 Score: 210
Period size: 46 Copynumber: 4.5 Consensus size: 46
303560 TAACCCGCCT
* *
303570 ATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
* *
303616 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCTTCG
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
* * *
303662 ATAAGTGAACTCAGACTTAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCATCC
* * * * * *
303711 -TCA-CGAACTCAGACTCAACTCAATGAGTTCGGACGTTTGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
303755 ATAAGTGAAC-CTGGACTCAACTC
1 ATAAGTGAACTC-GGACTCAACTC
303778 CATGAGTTCG
Statistics
Matches: 134, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
42 3 0.02
43 3 0.02
44 2 0.01
45 3 0.02
46 89 0.66
47 26 0.19
48 2 0.01
49 1 0.01
50 2 0.01
51 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCC
Found at i:303777 original size:93 final size:93
Alignment explanation
Indices: 303622--303792 Score: 227
Period size: 93 Copynumber: 1.8 Consensus size: 93
303612 ATCCATAAGT
* * * *
303622 GAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCTTCGATAAGTGAACTCAGACTTAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
303687 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * * * *
303715 GAACTCAGACTCAACTCAATGAGTTCGGACGTTTGCATCCATAAGTGAAC-CTGGACTCAACTCC
1 GAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTC-AGACTCAACTCA
* *
303779 ATGAGTTCGGATGC
65 ACGAGCTCGGATGC
303793 TCAAATATCC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
92 1 0.02
93 65 0.98
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:314139 original size:40 final size:40
Alignment explanation
Indices: 314060--314236 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
314050 CGGATGATAA
* * * *
314060 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
314100 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
314140 CCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
314180 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
314220 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
314237 ATACTTGGGT
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 100 0.85
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:314198 original size:80 final size:79
Alignment explanation
Indices: 314060--314236 Score: 250
Period size: 80 Copynumber: 2.2 Consensus size: 79
314050 CGGATGATAA
* * *
314060 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGG-CTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
314125 TGCTAG-TGATTATAT
65 TGCGAGTTG-TTATAT
* *
314140 CCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CC-GGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
314205 TGCGAGTTGTTATAT
65 TGCGAGTTGTTATAT
314220 CCGGCTAA-ATCCCGAAG
1 CCGGCTAAGA-CCCGAAG
314237 ATACTTGGGT
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
78 1 0.01
79 13 0.15
80 70 0.80
81 4 0.05
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTAT
GCGAGTTGTTATAT
Found at i:314504 original size:22 final size:22
Alignment explanation
Indices: 314464--314505 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
314454 GAATGTGCAT
*
314464 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
314486 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
314506 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:317201 original size:5 final size:5
Alignment explanation
Indices: 317191--317217 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
317181 GTAGTTTGAT
317191 TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TA
317218 ATGGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:319956 original size:15 final size:16
Alignment explanation
Indices: 319936--319965 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
319926 GCATTTAGTG
319936 TATTTTTAAA-AAAAT
1 TATTTTTAAATAAAAT
319951 TATTTTTAAATAAAA
1 TATTTTTAAATAAAA
319966 ACAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTTTAAATAAAAT
Found at i:324601 original size:14 final size:14
Alignment explanation
Indices: 324582--324611 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
324572 TCACTCATAC
324582 ATAGCTAGTTCTGT
1 ATAGCTAGTTCTGT
324596 ATAGCTAGTTCTGT
1 ATAGCTAGTTCTGT
324610 AT
1 AT
324612 CTGAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (14 bp):
ATAGCTAGTTCTGT
Found at i:327368 original size:28 final size:28
Alignment explanation
Indices: 327337--327393 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
327327 AGTGTGAAAA
* * *
327337 ATATTAAGAATGGCACTTGGTGTGCGGG
1 ATATTAAGAATGACACTTAGTGTACGGG
* *
327365 ATATTGAGTATGACACTTAGTGTACGGG
1 ATATTAAGAATGACACTTAGTGTACGGG
327393 A
1 A
327394 CATCTAGGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.30
Consensus pattern (28 bp):
ATATTAAGAATGACACTTAGTGTACGGG
Found at i:337495 original size:13 final size:13
Alignment explanation
Indices: 337477--337501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337467 AAATAATCAC
337477 ACACGGGCGTGTT
1 ACACGGGCGTGTT
337490 ACACGGGCGTGT
1 ACACGGGCGTGT
337502 CCCTGCCGAG
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:340161 original size:37 final size:37
Alignment explanation
Indices: 340083--340163 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
340073 ATGTGGTACG
* *
340083 TGTAAGACCATAGCTGTGCTATGGCATCGTAATAGCG
1 TGTAAGACCATAGCTGGGCTATGGCATCGTAATAGCA
*
340120 TGTAAGACCATAGCTGGGCTATGGCATCGTGAT-GACA
1 TGTAAGACCATAGCTGGGCTATGGCATCGTAATAG-CA
340157 TGTAAGA
1 TGTAAGA
340164 TCTGTAACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.03
37 39 0.98
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (37 bp):
TGTAAGACCATAGCTGGGCTATGGCATCGTAATAGCA
Found at i:341598 original size:46 final size:46
Alignment explanation
Indices: 341531--341699 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 46
341521 CCGCCCCTAG
* *
341531 GTGAACTCAGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTCAGGCGTTCGCATCCATAA
* * * *
341577 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATTTCA-CA
1 GTGAACTCGGACTCAACTCAACGAGTTC--A-GGC--GTTCGCA-TCCATAA
*
341627 ---AACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTCAGG-CGTTCGCATCCATAA
341670 GTGAACTCGGACTCAACTCAACGAGTTCAG
1 GTGAACTCGGACTCAACTCAACGAGTTCAG
341700 ATGCTCAACC
Statistics
Matches: 99, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 1 0.01
46 51 0.52
47 26 0.26
48 1 0.01
49 2 0.02
50 3 0.03
51 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
GTGAACTCGGACTCAACTCAACGAGTTCAGGCGTTCGCATCCATAA
Found at i:341647 original size:93 final size:93
Alignment explanation
Indices: 341534--341703 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
341524 CCCCTAGGTG
*
341534 AACTCAGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCAGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
341598 CGAGTTCGGATGCCTAGTTACATTTCACA
65 CGAGTTCAGATGCCTAGTTACATTTCACA
* *
341627 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
341692 GAGTTCAGATGC
66 GAGTTCAGATGC
341704 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCAGATGCCTAGTTACATTTCACA
Found at i:344128 original size:15 final size:15
Alignment explanation
Indices: 344102--344157 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
344092 CAAGGAAACC
344102 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
* *
344117 -AGATAGAGAAATACA
1 GA-ATAAAGAAATCCA
344132 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
344147 GAATAAAGAAA
1 GAATAAAGAAA
344158 CCCAAGATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:347191 original size:46 final size:46
Alignment explanation
Indices: 347124--347296 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
347114 AACCCGCCCC
* *
347124 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * * * * *
347170 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCATCCA
* * * *
347216 TTTCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
*
347263 TAAGTGAACCCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
347297 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
45 2 0.02
46 64 0.64
47 32 0.32
48 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:347236 original size:93 final size:93
Alignment explanation
Indices: 347129--347299 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
347119 GCCCCTAAGT
* * * *
347129 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACCCGGACTCAACTCAA
347194 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
*
347222 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACCCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACCCGGACTCAACTCAA
*
347287 CGAGTTCGGATGC
66 CGAGTTCAGATGC
347300 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACCCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:347315 original size:46 final size:45
Alignment explanation
Indices: 347222--347307 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 45
347212 TACATTTCAC
* * *
347222 GAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGT
1 GAACCCGGACTCAACTCAACAAGTTCGGA-ATGCGCAACCATAAGT
* *
347268 GAACCCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACCCGGACTCAACTCAACAAGTTCGGAATGCGCAACCAT
347308 CCTAGTGACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 9 0.26
46 26 0.74
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (45 bp):
GAACCCGGACTCAACTCAACAAGTTCGGAATGCGCAACCATAAGT
Found at i:349686 original size:46 final size:47
Alignment explanation
Indices: 349620--349823 Score: 137
Period size: 46 Copynumber: 4.1 Consensus size: 47
349610 CGCATTGTCA
* * * * *
349620 CACATCACACACCGAAGCCATAGCCCTGCCATGGTCTTACAC-GAAT
1 CACATAACATACCGATGCCATAGCCCAGACATGGTCTTACACGGAAT
* * *
349666 CACATAACATACCGATGCCATATCCCAGATATGGTCTTATACGGAAT
1 CACATAACATACCGATGCCATAGCCCAGACATGGTCTTACACGGAAT
*
349713 CACATTATCACATCACACCGATGCCATAGCCCA-ACTATGGTCTTATACGGGAACT
1 CACA-TA--ACAT---ACCGATGCCATAGCCCAGAC-ATGGTCTTACAC-GGAA-T
* * * *
349768 CGA-ATCACATTGTACCGATGCCATAGCCCAG-CTATGGTCTTATATGGAAG
1 C-ACATAACA---TACCGATGCCATAGCCCAGAC-ATGGTCTTACACGGAAT
349818 CACATA
1 CACATA
349824 TCACATCTAT
Statistics
Matches: 128, Mismatches: 14, Indels: 28
0.75 0.08 0.16
Matches are distributed among these distances:
46 34 0.27
47 8 0.06
48 2 0.02
49 1 0.01
50 7 0.05
51 4 0.03
52 34 0.27
53 28 0.22
54 5 0.04
55 4 0.03
56 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (47 bp):
CACATAACATACCGATGCCATAGCCCAGACATGGTCTTACACGGAAT
Found at i:349793 original size:52 final size:52
Alignment explanation
Indices: 349664--349830 Score: 187
Period size: 52 Copynumber: 3.2 Consensus size: 52
349654 TCTTACACGA
*
349664 ATCACATAACATACCGATGCCATATCCCAGA-TATGGTCTTATACGGAATCACATT
1 ATCACAT--CATACCGATGCCATAGCCCA-ACTATGGTCTTATACGGAATCACA-T
* *
349719 ATCACATCACACCGATGCCATAGCCCAACTATGGTCTTATACGGGAACTC-GA-
1 ATCACATCATACCGATGCCATAGCCCAACTATGGTCTTATAC-GGAA-TCACAT
** * * *
349771 ATCACATTGTACCGATGCCATAGCCCAGCTATGGTCTTATATGGAAGCACAT
1 ATCACATCATACCGATGCCATAGCCCAACTATGGTCTTATACGGAATCACAT
349823 ATCACATC
1 ATCACATC
349831 TATTCCGTCA
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
50 1 0.01
51 5 0.05
52 45 0.47
53 31 0.32
54 5 0.05
55 9 0.09
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (52 bp):
ATCACATCATACCGATGCCATAGCCCAACTATGGTCTTATACGGAATCACAT
Found at i:364584 original size:53 final size:52
Alignment explanation
Indices: 364502--364668 Score: 169
Period size: 52 Copynumber: 3.2 Consensus size: 52
364492 TCTTACACGA
* * * *
364502 ATCACATAACATACTGATGCCATATCCCAGATATGGTCTTATACAGAATCACATT
1 ATCACATCACAT-C-GATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACATT
* *
364557 ATCACATCACATCGATGCCATAGCCCAGCTATGGTCTTATATGGGA-AC-TT
1 ATCACATCACATCGATGCCATAGCCCAGCTATGGTCTTATACGGAACACATT
*** *
364607 GGATCACATTGTACCGATGCCATAGCCCAGCTATGGTCTTATACGGAAGCACA-T
1 --ATCACATCACATCGATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACATT
364661 ATCACATC
1 ATCACATC
364669 TTTTTCGTCA
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
50 2 0.02
51 2 0.02
52 47 0.50
53 28 0.30
54 4 0.04
55 11 0.12
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (52 bp):
ATCACATCACATCGATGCCATAGCCCAGCTATGGTCTTATACGGAACACATT
Found at i:366090 original size:42 final size:41
Alignment explanation
Indices: 366038--366377 Score: 234
Period size: 42 Copynumber: 7.7 Consensus size: 41
366028 CTGTGATACA
* * *
366038 TGTAAGACCATGTATGGGACATGGCATCGATATGAGATACTG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGAT-CTG
366080 TGTAAGACCATATCTGGGATATGGCATCAGCATCAATATGAGATCTTG
1 TGTAAGACCATATCTGGGATATGGCATC-G-----ATATGAGATC-TG
366128 TGTAAGACCATATCTGGGATATGGCATCAGCTTCGATATGAGATCTTG
1 TGTAAGACCATATCTGGGATATGG---CA---TCGATATGAGATC-TG
* *
366176 TGTAAGACCATATCTAGGATATGATATCGGCATCGCTATGAGATTATG
1 TGTAAGACCATATCT-GG----GATAT-GGCATCGATATGAGA-TCTG
* * * *
366224 TGTAAGACCATATCTGGGATATGGCTTCGGTATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCT-G
* * *** * *
366266 TGTAAGACCATGTCTAGGATGCAGCATCGATATGTGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCT-G
* * * * *
366308 TATAAGACCATGTCTGGTACATGGCATCGATATGAGACTTTG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TCTG
366350 TGTAAGACCATAGT-T-GGACTATGGCATC
1 TGTAAGACCATA-TCTGGGA-TATGGCATC
366378 AAGTAAAAGA
Statistics
Matches: 244, Mismatches: 30, Indels: 48
0.76 0.09 0.15
Matches are distributed among these distances:
41 4 0.02
42 120 0.49
43 10 0.04
47 3 0.01
48 90 0.37
49 3 0.01
51 4 0.02
53 6 0.02
54 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (41 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCTG
Found at i:366120 original size:48 final size:48
Alignment explanation
Indices: 366061--366248 Score: 281
Period size: 48 Copynumber: 3.9 Consensus size: 48
366051 ATGGGACATG
366061 GCATCGATATGAGATAC-TGTGTAAGACCATATCTGGGATATGGCATCA
1 GCATCGATATGAGAT-CTTGTGTAAGACCATATCTGGGATATGGCATCA
*
366109 GCATCAATATGAGATCTTGTGTAAGACCATATCTGGGATATGGCATCA
1 GCATCGATATGAGATCTTGTGTAAGACCATATCTGGGATATGGCATCA
* * ** *
366157 GCTTCGATATGAGATCTTGTGTAAGACCATATCTAGGATATGATATCG
1 GCATCGATATGAGATCTTGTGTAAGACCATATCTGGGATATGGCATCA
*
366205 GCATCGCTATGAGAT-TATGTGTAAGACCATATCTGGGATATGGC
1 GCATCGATATGAGATCT-TGTGTAAGACCATATCTGGGATATGGC
366249 TTCGGTATGA
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
47 2 0.02
48 124 0.98
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (48 bp):
GCATCGATATGAGATCTTGTGTAAGACCATATCTGGGATATGGCATCA
Found at i:366298 original size:96 final size:92
Alignment explanation
Indices: 366038--366285 Score: 258
Period size: 96 Copynumber: 2.7 Consensus size: 92
366028 CTGTGATACA
* * * * * *
366038 TGTAAGACCATGTATGGGACAT-G-GCATCGATATGAGATAC-TGTGTAAGACCATATCTGGGAT
1 TGTAAGACCATATCTGGGATATGGAGCTTCGATATGAGAT-CTTATGTAAGACCATATCTAGGAT
** * **
366100 ATGGCATCAGCATCAATATGAGATCTTG
65 ATGATATCGGCATCGCTATGAGATCTTG
*
366128 TGTAAGACCATATCTGGGATATGGCATCAGCTTCGATATGAGATCTTGTGTAAGACCATATCTAG
1 TGTAAGACCATATCTGGGATATGG----AGCTTCGATATGAGATCTTATGTAAGACCATATCTAG
366193 GATATGATATCGGCATCGCTATGAGAT-TATG
62 GATATGATATCGGCATCGCTATGAGATCT-TG
* *
366224 TGTAAGACCATATCTGGGATAT-G-GCTTCGGTATGAGAT-TTCATGTAAGACCATGTCTAGGAT
1 TGTAAGACCATATCTGGGATATGGAGCTTCGATATGAGATCTT-ATGTAAGACCATATCTAGGAT
366286 GCAGCATCGA
Statistics
Matches: 136, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
89 2 0.01
90 52 0.38
91 1 0.01
95 3 0.02
96 78 0.57
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (92 bp):
TGTAAGACCATATCTGGGATATGGAGCTTCGATATGAGATCTTATGTAAGACCATATCTAGGATA
TGATATCGGCATCGCTATGAGATCTTG
Found at i:370955 original size:46 final size:47
Alignment explanation
Indices: 370887--371028 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 47
370877 AGGACATGAC
* *
370887 AAGACAGAAATGAGTCATGTAAGTCCATATCAG-ATATATGGCTTTG
1 AAGACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTG
* * *
370933 GAGACAGGAATGAGTCATGTAAGCCCATATTAGATATATATATGGCATTG
1 AAGACAGGAATGAGTCATGTAAGTCCATATCAG--A-ATATATGGCATTG
* * * * *
370983 AAGACAGGAATAATTCATGTAAGTCCATGTC-GAAGACATGGCATTG
1 AAGACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTG
371029 GCAGGATGTT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
46 40 0.51
47 1 0.01
49 1 0.01
50 37 0.47
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (47 bp):
AAGACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTG
Found at i:375297 original size:46 final size:47
Alignment explanation
Indices: 375229--375370 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 47
375219 AGGACATGAC
* *
375229 AAGACAGAAATGAGTCATGTAAGTCCATATCAG-ATATATGGCTTTG
1 AAGACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTG
* * *
375275 GAGACAGGAATGAGTCATGTAAGCCCATATTAGATATATATATGGCATTG
1 AAGACAGGAATGAGTCATGTAAGTCCATATCAG--A-ATATATGGCATTG
* * * * *
375325 AAGACAGGAATAATTCATGTAAGTCCATGTC-GAAGACATGGCATTG
1 AAGACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTG
375371 GTAGGATGTT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
46 40 0.51
47 1 0.01
49 1 0.01
50 37 0.47
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (47 bp):
AAGACAGGAATGAGTCATGTAAGTCCATATCAGAATATATGGCATTG
Found at i:375956 original size:129 final size:129
Alignment explanation
Indices: 375726--375982 Score: 487
Period size: 129 Copynumber: 2.0 Consensus size: 129
375716 GTCGGAGACT
*
375726 CGATCACACTATCGAAGAAATAACATTGGTATAGTTAGTCGTTTCGTTTTGTGTATGGCATGTAT
1 CGATCACACTATCGAAGAAATAACATTGGTATAGTTAGACGTTTCGTTTTGTGTATGGCATGTAT
375791 AGGAACTTGGTTTCTTTTGATACGATATGATCAATGAATGATGTGTAAATACTTGCTAGTGATC
66 AGGAACTTGGTTTCTTTTGATACGATATGATCAATGAATGATGTGTAAATACTTGCTAGTGATC
*
375855 CGATCACACTATCGAAGAAATCACATTGGTATAGTTAGACGTTTCGTTTTGTGTATGGCATGTAT
1 CGATCACACTATCGAAGAAATAACATTGGTATAGTTAGACGTTTCGTTTTGTGTATGGCATGTAT
*
375920 AGGAACTTGGTTTCTTTTGATATGATATGATCAATGAATGATGTGTAAATACTTGCTAGTGAT
66 AGGAACTTGGTTTCTTTTGATACGATATGATCAATGAATGATGTGTAAATACTTGCTAGTGAT
375983 TAGCTAATAG
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (129 bp):
CGATCACACTATCGAAGAAATAACATTGGTATAGTTAGACGTTTCGTTTTGTGTATGGCATGTAT
AGGAACTTGGTTTCTTTTGATACGATATGATCAATGAATGATGTGTAAATACTTGCTAGTGATC
Found at i:376284 original size:87 final size:87
Alignment explanation
Indices: 376176--376340 Score: 294
Period size: 87 Copynumber: 1.9 Consensus size: 87
376166 CATATGGACT
376176 AAGCAAAACAGGTAAAGGTTTTGAATTTTATAGGGTATCTGAGTTTTGGTGAAATAGGGCCAGAG
1 AAGCAAAACAGGTAAAGGTTTTGAATTTTATAGGGTATCTGAGTTTTGGTGAAATAGGGCCAGAG
376241 CAATTTCTAGATCATTTGGAAG
66 CAATTTCTAGATCATTTGGAAG
* *
376263 AAGCAAAACAGGTAAAGGTTTTGTATTTTATAGGGTATTTGAGTTTTGGTGAAATAGGGCCAGAG
1 AAGCAAAACAGGTAAAGGTTTTGAATTTTATAGGGTATCTGAGTTTTGGTGAAATAGGGCCAGAG
* *
376328 CGATTTCTGGATC
66 CAATTTCTAGATC
376341 CCCTGTTCTA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (87 bp):
AAGCAAAACAGGTAAAGGTTTTGAATTTTATAGGGTATCTGAGTTTTGGTGAAATAGGGCCAGAG
CAATTTCTAGATCATTTGGAAG
Found at i:377733 original size:28 final size:28
Alignment explanation
Indices: 377663--377733 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
377653 TTTATATGTA
*
377663 TATGGCACTTACTGTGCCAAATATTAAG
1 TATGGCACTTAGTGTGCCAAATATTAAG
* * *
377691 AATGGCACTTGGTGTG-CAAGATATTGAG
1 TATGGCACTTAGTGTGCCAA-ATATTAAG
377719 TATGGCACTTAGTGT
1 TATGGCACTTAGTGT
377734 ACGAGACATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 3 0.08
28 33 0.92
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (28 bp):
TATGGCACTTAGTGTGCCAAATATTAAG
Found at i:383228 original size:45 final size:45
Alignment explanation
Indices: 383176--383349 Score: 215
Period size: 45 Copynumber: 3.8 Consensus size: 45
383166 TCATTTCATC
*
383176 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGGATAGTATCTCACA
1 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCTCACA
* ** *
383221 GGCATTATAGCCTGCTAGGCTTGAAGGCCCGAATAGTATCTCACT
1 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCTCACA
* * * * * *
383266 GGCATTATAGCCTGTTAGGCTCAAAGGCTCGAATAGTATCACCCC
1 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCTCACA
*
383311 GGCATTATAGCCTA-CTAGGCTCAAAAGGCTCGAATAGTA
1 GGCATTATAGCC-AGCTAGGCTC-AAAGGCCCGAATAGTA
383350 CTATACGATA
Statistics
Matches: 113, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
45 97 0.86
46 16 0.14
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (45 bp):
GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCTCACA
Found at i:383274 original size:90 final size:91
Alignment explanation
Indices: 383176--383349 Score: 242
Period size: 90 Copynumber: 1.9 Consensus size: 91
383166 TCATTTCATC
* * *
383176 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGGATAGTATCTCACAGGCATTATAGCCTGCTAGGC
1 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCACACAGGCATTATAGCCTACTAGGC
**
383241 T-TGAAGGCCCGAATAGTATCTCACT
66 TCAAAAGGCCCGAATAGTATCTCACT
* * * * *
383266 GGCATTATAGCCTGTTAGGCTCAAAGGCTCGAATAGTATCACCCCGGCATTATAGCCTACTAGGC
1 GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCACACAGGCATTATAGCCTACTAGGC
*
383331 TCAAAAGGCTCGAATAGTA
66 TCAAAAGGCCCGAATAGTA
383350 CTATACGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 58 0.81
91 14 0.19
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (91 bp):
GGCATTATAGCCAGCTAGGCTCAAAGGCCCGAATAGTATCACACAGGCATTATAGCCTACTAGGC
TCAAAAGGCCCGAATAGTATCTCACT
Found at i:384203 original size:47 final size:47
Alignment explanation
Indices: 384152--384247 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
384142 AAAATTTTCT
* * * *
384152 TTAACTAAGTACCTTATCTGGAAATATTAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGAAAATATTAAGAGCAAATTTAACAAGC
384199 TTAACTAAGTAACTTATCCGAAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGAAAATATTAAGAGCAAATTTAACAAGC
384246 TT
1 TT
384248 TAAATTCAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGAAAATATTAAGAGCAAATTTAACAAGC
Found at i:390895 original size:45 final size:45
Alignment explanation
Indices: 390792--390967 Score: 250
Period size: 45 Copynumber: 4.0 Consensus size: 45
390782 CTGAATTCAT
* * *
390792 TCACCGGCATTATAGCCTACTAGGCTCGAAGG-CCG-ATA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
390835 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * * *
390880 TCACCGGTATTATAGCCTGCTAGGCTCGAAGGCCTGAATAGCATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
390925 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
390968 CTGTACGATA
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
43 30 0.25
44 3 0.03
45 84 0.71
46 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:390896 original size:88 final size:90
Alignment explanation
Indices: 390792--390967 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
390782 CTGAATTCAT
* *
390792 TCACCGGCATTATAGCCTACTAGGCTCGAAGGCC-G-ATATCATTTCACCGGCATTATAGCCTGC
1 TCACCGGCATTATAGCCTACTAGGCTCGAAGGCCTGAATAGCATCTCACCGGCATTATAGCCTGC
390855 TAGGCTCAAAGGCCCGAATAGTATC
66 TAGGCTCAAAGGCCCGAATAGTATC
* * *
390880 TCACCGGTATTATAGCCTGCTAGGCTCGAAGGCCTGAATAGCATCTCACTGGCATTATAGCCTGC
1 TCACCGGCATTATAGCCTACTAGGCTCGAAGGCCTGAATAGCATCTCACCGGCATTATAGCCTGC
390945 TAGGCTCAAAGGCCCGAATAGTA
66 TAGGCTCAAAGGCCCGAATAGTA
390968 CTGTACGATA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 32 0.40
89 1 0.01
90 48 0.59
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (90 bp):
TCACCGGCATTATAGCCTACTAGGCTCGAAGGCCTGAATAGCATCTCACCGGCATTATAGCCTGC
TAGGCTCAAAGGCCCGAATAGTATC
Found at i:391831 original size:47 final size:47
Alignment explanation
Indices: 391778--391873 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 47
391768 AAAATTTTCT
391778 TTAACTAAGTAACTTATCC-AGAAATATTAA-AGGAAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGA-AAATATTAAGA-GAAAATTTAACAAGC
*
391825 TTAACTAAGTAACTTATCCGAAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGAAAATATTAAGAGAAAATTTAACAAGC
391872 TT
1 TT
391874 TAAATTCAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
47 44 0.96
48 2 0.04
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGAAAATATTAAGAGAAAATTTAACAAGC
Found at i:402690 original size:27 final size:27
Alignment explanation
Indices: 402660--402766 Score: 112
Period size: 27 Copynumber: 3.9 Consensus size: 27
402650 GGCTGCCAGG
*
402660 ACAGATAATGTGACAGAGTCACCAGAT
1 ACAGATAATGTGACAGAGCCACCAGAT
402687 ACAGATAATCGT-AGCAGAGCCACCAGA-
1 ACAGATAAT-GTGA-CAGAGCCACCAGAT
* *
402714 ACAGAAATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGACAGAGCCACCAGAT
* *
402742 -CAGATAATTGTGGCATAGCCACCAG
1 ACAGATAA-TGTGACAGAGCCACCAG
402767 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.01
27 52 0.75
28 16 0.23
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (27 bp):
ACAGATAATGTGACAGAGCCACCAGAT
Found at i:407392 original size:40 final size:40
Alignment explanation
Indices: 407322--407472 Score: 225
Period size: 40 Copynumber: 3.8 Consensus size: 40
407312 CGGATGATAA
* *
407322 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
407362 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
407402 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
**
407442 CGAAGGCATTTAAGCGAG-TAGCTATATCCGG
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGG
407473 TTAAATCCCT
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
39 2 0.02
40 101 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:413971 original size:27 final size:26
Alignment explanation
Indices: 413936--414047 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
413926 AGCATGGCTG
* *
413936 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
413962 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
413990 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
414017 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
414044 CCAG
1 CCAG
414048 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:414028 original size:54 final size:54
Alignment explanation
Indices: 413936--414047 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
413926 AGCATGGCTG
* *
413936 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
413990 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
414044 CCAG
1 CCAG
414048 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:419814 original size:43 final size:43
Alignment explanation
Indices: 419767--419898 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
419757 AAATAGGGTT
* *
419767 TTACACGAAATCA-TATAACAATGCCAATGTCCCAGACATGGTG
1 TTACACGAAAT-AGCATAACAATGCCAATGTCCCAGACATGGTC
* * * *
419810 TTACACGTAATAGCATAACGATGCTAATGTCCCTGACATGGTC
1 TTACACGAAATAGCATAACAATGCCAATGTCCCAGACATGGTC
* * * *
419853 TTACAC-ACAATTGCA-ATACAATGCCAATGCCCCAAACGTGGTC
1 TTACACGA-AATAGCATA-ACAATGCCAATGTCCCAGACATGGTC
419896 TTA
1 TTA
419899 AATGTAATCT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 2 0.03
43 70 0.97
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
TTACACGAAATAGCATAACAATGCCAATGTCCCAGACATGGTC
Found at i:422171 original size:13 final size:13
Alignment explanation
Indices: 422153--422182 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
422143 TGGCTTGAGA
422153 ATTCTATTAGAGT
1 ATTCTATTAGAGT
422166 ATTCTATTAGAGT
1 ATTCTATTAGAGT
422179 ATTC
1 ATTC
422183 GTTGAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (13 bp):
ATTCTATTAGAGT
Found at i:425457 original size:48 final size:48
Alignment explanation
Indices: 425386--426163 Score: 1224
Period size: 48 Copynumber: 16.2 Consensus size: 48
425376 CAAGATAAAT
* * *
425386 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
425434 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
425482 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
* * *
425530 ATATATATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
*
425578 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
* **
425626 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
* *
425674 ATATATATATATATGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 --ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
* *
425724 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
**
425772 ATATGTATATGTGGTAAAGT-CGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAA-TCCGAATGGCTAATGTGAAATATGTATGAG
* * **
425820 ATATATATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
425868 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
* *
425916 ATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
**
425964 ATATGTATATGTGGTAAAGT-CGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAA-TCCGAATGGCTAATGTGAAATATGTATGAG
* * *
426012 ATATATATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
426060 ATA--TATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
426106 ATATGTATATGTGGTAAAGT-CGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAA-TCCGAATGGCTAATGTGAAATATGTATGAG
*
426154 ATGTGTATAT
1 ATATGTATAT
426164 ATTGTGGCCG
Statistics
Matches: 680, Mismatches: 41, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
46 44 0.06
48 592 0.87
49 1 0.00
50 43 0.06
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:426346 original size:37 final size:37
Alignment explanation
Indices: 426296--426366 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
426286 GGAAATATAT
* *
426296 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACATGTGGAGATTTTG
*
426333 TCCGGGTAAGACCCGATAACTACATGTGGGGATT
1 TCCGGGTAAGACCCGATAACTACATGTGGAGATT
426367 ATTCGAGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACATGTGGAGATTTTG
Found at i:431896 original size:27 final size:27
Alignment explanation
Indices: 431866--431957 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
431856 ATTACCAAAG
* * *
431866 TACCCTCGACTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTATCGTTT
* *
431893 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTATCGTTT
*
431920 TACCCTCAATTTACAAAATT-TCTGTTT
1 TACCCTCGATTTACAAAATTATC-GTTT
431947 TACCCTCGATT
1 TACCCTCGATT
431958 GTGAAATTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.02
27 54 0.98
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTATCGTTT
Found at i:431911 original size:54 final size:54
Alignment explanation
Indices: 431853--431957 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
431843 CTCGACTTGT
* * *
431853 AAAATTACCAAAGTACCCTCGACTTATAGAATTATC-GTTTTACCCTCGATTTAC
1 AAAATTACCAAAGTACCCTCAACTTACAAAATT-TCTGTTTTACCCTCGATTTAC
*** *
431907 AAAATTACCATTTTACCCTCAATTTACAAAATTTCTGTTTTACCCTCGATT
1 AAAATTACCAAAGTACCCTCAACTTACAAAATTTCTGTTTTACCCTCGATT
431958 GTGAAATTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.05
54 41 0.95
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (54 bp):
AAAATTACCAAAGTACCCTCAACTTACAAAATTTCTGTTTTACCCTCGATTTAC
Found at i:431979 original size:27 final size:26
Alignment explanation
Indices: 431949--432085 Score: 75
Period size: 27 Copynumber: 5.1 Consensus size: 26
431939 TTCTGTTTTA
* **
431949 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
*
431976 CCCTG-TAGGATAAAATTACCAAAATAC
1 CCCTGAT-TG-TAAAATTACCAAAATAC
* * **
432003 CACTGGTT-TGAGAAATTACTGAAATA-
1 CCCTGATTGT-A-AAATTACCAAAATAC
*
432029 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GA-TTGTAAAATTACCAAAATAC
*
432057 CCCTGATT-TACAAAATTACAAAAATAC
1 CCCTGATTGT--AAAATTACCAAAATAC
432084 CC
1 CC
432086 TTGACTTTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
25 3 0.04
26 8 0.10
27 64 0.76
28 8 0.10
29 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (26 bp):
CCCTGATTGTAAAATTACCAAAATAC
Found at i:433103 original size:25 final size:24
Alignment explanation
Indices: 433069--433138 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
433059 AGGAAGTGCT
433069 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTCTGCCCCAGTTTACC
*
433093 GAAAAGGGCTCTGCCCCAGTTTATC
1 -AAAAGGGCTCTGCCCCAGTTTACC
* *
433118 AGAAAGGGCTTTGCCCAAGTT
1 A-AAAGGGCTCTGCCCCAGTT
433139 ATTAAAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTCTGCCCCAGTTTACC
Found at i:433148 original size:25 final size:25
Alignment explanation
Indices: 433069--433149 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
433059 AGGAAGTGCT
* ***
433069 AAAAGGGCTCTGCCCCAGTTTACCG
1 AAAAGGGCTCTGCCCAAGTTTATAA
* *
433094 AAAAGGGCTCTGCCCCAGTTTATCA
1 AAAAGGGCTCTGCCCAAGTTTATAA
* *
433119 GAAAGGGCTTTGCCCAAG-TTATTAA
1 AAAAGGGCTCTGCCCAAGTTTA-TAA
433144 AAAAGG
1 AAAAGG
433150 CTAGGCCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 3 0.06
25 45 0.94
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (25 bp):
AAAAGGGCTCTGCCCAAGTTTATAA
Found at i:433345 original size:42 final size:42
Alignment explanation
Indices: 433286--433377 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
433276 TAGTCTCCCC
* ** *
433286 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
433328 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
433370 AAATGGGC
1 AAATGGGC
433378 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:433436 original size:31 final size:31
Alignment explanation
Indices: 433401--433479 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
433391 CGTTTACAGT
* *
433401 AAAGGCTTCGGCCGAGTGATATGATTTATTA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
433432 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
433463 AAAGGCTTTGGTCCAGT
1 AAAGGCTTCGGCCCAGT
433480 AACCGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:435880 original size:33 final size:33
Alignment explanation
Indices: 435838--435907 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
435828 GTAAGAATGC
435838 TAATGAGTAAGCTAAGCCTAAAATACTTGATGA
1 TAATGAGTAAGCTAAGCCTAAAATACTTGATGA
*
435871 TAATGAGTAAGCTAAGCCTAAAATACTTGATTA
1 TAATGAGTAAGCTAAGCCTAAAATACTTGATGA
435904 TAAT
1 TAAT
435908 TATGCTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (33 bp):
TAATGAGTAAGCTAAGCCTAAAATACTTGATGA
Found at i:444720 original size:50 final size:50
Alignment explanation
Indices: 444611--444736 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 50
444601 TGGGTTAAGT
* *
444611 TGCTGATGCCATGTCCCAGACATGGTATTACACTAGCTCTCGTACTTATG
1 TGCTAATGCCATGTCCCAGACATGGTATTACACTAGCTCTCGTACTCATG
* *
444661 TGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTGCGTA-TCCATG
1 TGCTAATGCCATGTCCCAGACATGGTATTACACTAGCTC-T-CGTACT-CATG
*
444713 T-C-AATGCCATGTCCTAGACATGGT
1 TGCTAATGCCATGTCCCAGACATGGT
444737 TTATACTGAC
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
50 58 0.84
51 3 0.04
52 8 0.12
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (50 bp):
TGCTAATGCCATGTCCCAGACATGGTATTACACTAGCTCTCGTACTCATG
Found at i:445620 original size:12 final size:12
Alignment explanation
Indices: 445603--445627 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
445593 AAAAAATGTA
445603 AAAATCATCAAG
1 AAAATCATCAAG
445615 AAAATCATCAAG
1 AAAATCATCAAG
445627 A
1 A
445628 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:453785 original size:11 final size:11
Alignment explanation
Indices: 453769--453793 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
453759 TGCTGTAGAA
453769 AATAAAATAAT
1 AATAAAATAAT
453780 AATAAAATAAT
1 AATAAAATAAT
453791 AAT
1 AAT
453794 TTCTACCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:457567 original size:40 final size:40
Alignment explanation
Indices: 457490--457667 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
457480 AAACCAAGTA
* *
457490 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
457529 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
457569 CCTTCGGGACCTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
457609 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
457649 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
457668 TTATCATCCG
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 15 0.12
40 111 0.88
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:462314 original size:12 final size:12
Alignment explanation
Indices: 462297--462339 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
462287 GTTGCTTGTA
462297 TTATATATATAT
1 TTATATATATAT
462309 TTATATATATAT
1 TTATATATATAT
*
462321 TT-TTTATAGTA-
1 TTATATATA-TAT
462332 TTATATAT
1 TTATATAT
462340 TTTGATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATATATATAT
Found at i:462665 original size:16 final size:16
Alignment explanation
Indices: 462644--462684 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
462634 TGAATTACTT
*
462644 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
*
462660 ATTACAGCCCTATTTC
1 ATTACAGCCCTATTCC
*
462676 ATTATAGCC
1 ATTACAGCC
462685 AACCAAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.37
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:463086 original size:28 final size:28
Alignment explanation
Indices: 463047--463116 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
463037 TCCCCCTAAA
*
463047 CCCTCAAAACTTTTTTCCTTTTATTTTCTT
1 CCCT-AAAACTTTTTTCCTTTTACTTTC-T
*
463077 CCC-AAGACTTTTTTCCTTTTACTTTCT
1 CCCTAAAACTTTTTTCCTTTTACTTTCT
463104 CCCTAAAACTTTT
1 CCCTAAAACTTTT
463117 ACTTCCCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.11
28 29 0.81
30 3 0.08
ACGTcount: A:0.19, C:0.29, G:0.01, T:0.51
Consensus pattern (28 bp):
CCCTAAAACTTTTTTCCTTTTACTTTCT
Found at i:463267 original size:28 final size:27
Alignment explanation
Indices: 463236--463294 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 27
463226 CCCACAAATT
463236 TTTTTTCCTTTTACTTTCTCCCCAAAAC
1 TTTTTTCCTTTTACTTTC-CCCCAAAAC
*
463264 TTTTTTCCTTTTGCTTTCCCCCAAAAC
1 TTTTTTCCTTTTACTTTCCCCCAAAAC
463291 TTTT
1 TTTT
463295 ACTTCCCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.15, C:0.31, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTTTTCCTTTTACTTTCCCCCAAAAC
Found at i:463300 original size:82 final size:80
Alignment explanation
Indices: 463163--463323 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 80
463153 TTCTTAAAAA
* *
463163 TTTTACTTTCCACAAAACTTTTTTCCTTTTATTTTCTCCCCAAAACTGTTACTTCCCTCCAAACC
1 TTTTACTTTCCACAAAACTTTTTTCCTTTTACTTTCTCCCCAAAACTGTTACTTCCCCCCAAACC
463228 CACAAATTTTTTTTCC
66 C-CAAATTTTTTTTCC
* * *
463244 TTTTACTTTCTCCCCAAAACTTTTTTCCTTTTGCTTTC-CCCCAAAACTTTTACTTCCCCCCAAA
1 TTTTAC-TT-TCCACAAAACTTTTTTCCTTTTACTTTCTCCCCAAAACTGTTACTTCCCCCCAAA
* *
463308 CTCCAATTTTTTTTTC
64 CCCCAAATTTTTTTTC
463324 AAATTTATGT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
81 18 0.25
82 28 0.39
83 25 0.35
ACGTcount: A:0.21, C:0.32, G:0.01, T:0.45
Consensus pattern (80 bp):
TTTTACTTTCCACAAAACTTTTTTCCTTTTACTTTCTCCCCAAAACTGTTACTTCCCCCCAAACC
CCAAATTTTTTTTCC
Found at i:463303 original size:19 final size:19
Alignment explanation
Indices: 463271--463307 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
463261 AACTTTTTTC
* *
463271 CTTTTGCTTTCCCCCAAAA
1 CTTTTACTTCCCCCCAAAA
463290 CTTTTACTTCCCCCCAAA
1 CTTTTACTTCCCCCCAAA
463308 CTCCAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.41, G:0.03, T:0.35
Consensus pattern (19 bp):
CTTTTACTTCCCCCCAAAA
Found at i:464421 original size:26 final size:26
Alignment explanation
Indices: 464392--464454 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
464382 TATATTCGAT
* *
464392 TCGATTCGATTTGAATTTCATCTCAC
1 TCGACTCGATTTGAATTCCATCTCAC
*
464418 TCGACTCGTTTTGAATTCCATCTCAC
1 TCGACTCGATTTGAATTCCATCTCAC
464444 TCGACTCGATT
1 TCGACTCGATT
464455 CGAGAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.40
Consensus pattern (26 bp):
TCGACTCGATTTGAATTCCATCTCAC
Found at i:465087 original size:11 final size:11
Alignment explanation
Indices: 465071--465095 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
465061 ATTAGTCATG
465071 TACATATTATA
1 TACATATTATA
465082 TACATATTATA
1 TACATATTATA
465093 TAC
1 TAC
465096 CTAAACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (11 bp):
TACATATTATA
Found at i:467710 original size:24 final size:23
Alignment explanation
Indices: 467681--467725 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
467671 ATAATTTACA
*
467681 ATTAAAATAACAAAAAAAAGAAAT
1 ATTAAAAGAA-AAAAAAAAGAAAT
*
467705 ATTAAAAGAAATAAAAAAGAA
1 ATTAAAAGAAAAAAAAAAGAA
467726 TTTAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
ATTAAAAGAAAAAAAAAAGAAAT
Found at i:478884 original size:16 final size:16
Alignment explanation
Indices: 478863--478897 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
478853 TTCAAGATAA
478863 TTAATTTTAATAAATT
1 TTAATTTTAATAAATT
478879 TTAATTTTAATAAATT
1 TTAATTTTAATAAATT
478895 TTA
1 TTA
478898 CTCTTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATTTTAATAAATT
Found at i:483603 original size:45 final size:45
Alignment explanation
Indices: 483552--483637 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
483542 ATGTAATCTG
*
483552 AACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGACATCCA
1 AACTCATTGAGTTGTGGTCTGAGTTCATGAAATATGTGACATCCA
* * *
483597 AACTCATTGAGTTGTGGTTTGAGTTCGTGAAATTTGTGACA
1 AACTCATTGAGTTGTGGTCTGAGTTCATGAAATATGTGACA
483638 CATGTTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (45 bp):
AACTCATTGAGTTGTGGTCTGAGTTCATGAAATATGTGACATCCA
Found at i:485622 original size:28 final size:28
Alignment explanation
Indices: 485589--485656 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
485579 CGATTTTTTT
*
485589 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCGCAATATCTC
*
485617 GCACACTAAGTGTCATTCGCAATATTTC
1 GCACACTAAGTGTCATTCGCAATATCTC
485645 GCACACTAAGTG
1 GCACACTAAGTG
485657 CCATATTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCGCAATATCTC
Found at i:485756 original size:40 final size:40
Alignment explanation
Indices: 485692--485775 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
485682 GTGTTGTACA
*
485692 TAGCTGAAGCTATCTCAAATCGCACACTAAATGCCAAATT
1 TAGCTGAAGCTATCTCAAACCGCACACTAAATGCCAAATT
* * * * *
485732 TAGCTGAAGCTATAC-CGAACCGCACATTGAGTGCCATATT
1 TAGCTGAAGCTAT-CTCAAACCGCACACTAAATGCCAAATT
485772 TAGC
1 TAGC
485776 CGATATGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
TAGCTGAAGCTATCTCAAACCGCACACTAAATGCCAAATT
Found at i:486952 original size:24 final size:24
Alignment explanation
Indices: 486920--486974 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
486910 AATTTTACCC
486920 AAGT-ATGAATTTTGGGTCATTTT
1 AAGTAATGAATTTTGGGTCATTTT
* *
486943 GAGTAATGAATTTTGGGTCGTTTT
1 AAGTAATGAATTTTGGGTCATTTT
486967 AAGTAATG
1 AAGTAATG
486975 CATGTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44
Consensus pattern (24 bp):
AAGTAATGAATTTTGGGTCATTTT
Found at i:491850 original size:47 final size:47
Alignment explanation
Indices: 491772--492083 Score: 246
Period size: 47 Copynumber: 6.6 Consensus size: 47
491762 ATGGGTGATT
491772 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATC-CAGA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCATCACAGA
* * * * **
491820 CGAGGGCTAGTGTAAGACATGTCTGGGACATGCGTCAGCAAT-A-TTA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGC-ATCACAGA
** * *
491866 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGTGTCGGCA-CAGAGA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCATCACAGA
* * * * * *
491914 TAAGTGCCAGAGTAAGACATGTCTGAGACATGCATCGGCCTCGACAGA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATC-ACAGA
* * * *
491962 -GACAGCCAGTGTAAGACATGTCTAGGACACGCATCGGC-T-A-AGA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATCACAGA
* * * * * *
492005 -GTTGTGCTAGTGTAAGACATGTCTAGGACATGCATCAGCACGCACATA
1 TG-AGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCA-TCACAGA
492053 TGAGAGCCAGTGTAAGACCATGTCTGGGACA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACA
492084 CGGCATCGGC
Statistics
Matches: 209, Mismatches: 40, Indels: 29
0.75 0.14 0.10
Matches are distributed among these distances:
43 4 0.02
44 32 0.15
46 29 0.14
47 78 0.37
48 53 0.25
49 13 0.06
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.20
Consensus pattern (47 bp):
TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATCACAGA
Found at i:491933 original size:94 final size:92
Alignment explanation
Indices: 491772--492094 Score: 320
Period size: 94 Copynumber: 3.5 Consensus size: 92
491762 ATGGGTGATT
* *
491772 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCAGACG--AGGGCTAGTGTAA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--CAGA-GATAGTGCTAGTGTAA
*
491835 GACATGTCTGGGACATGCGTCAGCAATATTA
63 GACATGTCTGGGACATGCATCAGCAATA-TA
** * *
491866 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGTGTCGGCACAGAGATAAGTGCCAGAGTAAGA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGAT-AGTGCTAGTGTAAGA
* * * *
491931 CATGTCTGAGACATGCATCGGC-CTCGACA
65 CATGTCTGGGACATGCATCAGCAAT--ATA
* * *
491960 -GAGACAGCCAGTGTAAGA-CATGTCTAGGACA-CGCATCGGCTA-AGAG-TTGTGCTAGTGTAA
1 TGAG--AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACAGAGATAGTGCTAGTGTAA
* *
492020 GACATGTCTAGGACATGCATCAGCACGCACATA
63 GACATGTCTGGGACATGCATCAGCA---ATATA
*
492053 TGAGAGCCAGTGTAAGACCATGTCTGGGACACGGCATCGGCA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
492095 ATATATCCCA
Statistics
Matches: 188, Mismatches: 26, Indels: 31
0.77 0.11 0.13
Matches are distributed among these distances:
91 32 0.17
92 18 0.10
93 29 0.15
94 95 0.51
95 14 0.07
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (92 bp):
TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATAGTGCTAGTGTAAGAC
ATGTCTGGGACATGCATCAGCAATATA
Found at i:492792 original size:30 final size:30
Alignment explanation
Indices: 492757--492814 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
492747 CTAATTTGTC
* *
492757 CACACGGGTAAGACACATGGGCGTGTGTGA
1 CACACGGCTAACACACATGGGCGTGTGTGA
* *
492787 CACACGGCTCACACCCATGGGCGTGTGT
1 CACACGGCTAACACACATGGGCGTGTGT
492815 CATGGCCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (30 bp):
CACACGGCTAACACACATGGGCGTGTGTGA
Found at i:499318 original size:46 final size:48
Alignment explanation
Indices: 499208--499533 Score: 202
Period size: 47 Copynumber: 7.0 Consensus size: 48
499198 TTGGGTGATT
* * * *
499208 TGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATCTAGA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATATATA
* * *
499256 TGAGGGCTAGTGTAAGA-CATGTCTGGGACAT-GCTTCAGCCATAT-TA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCCATATATA
*
499302 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACA-ATGT-
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GC-CATATATA
* * ** *
499350 TGAGTG-CAGAGTAAGA-CATGTCTGGGACAT-GCATCGGCC-TCGACA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCCATATATA
** * * * * *
499395 -GTTAGCCAGTGTGAGA-CGTGTCTGGGACA-CGCATCGGC-TA-AGA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATATATA
* * ** ** *
499438 -GTTGTGCTGGTGTAAGA-CATGTCTGGGACAT-GCATCAGCACGCACATA
1 TG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GC-CATATATA
* *
499486 TGAGAGCCAGTGTAAGACCATGTCTGGGACACGGCATCGGCA-ATATA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATATATA
499533 T
1 T
499534 CCCATGTTGA
Statistics
Matches: 217, Mismatches: 43, Indels: 37
0.73 0.14 0.12
Matches are distributed among these distances:
43 3 0.01
44 33 0.15
45 34 0.16
46 35 0.16
47 47 0.22
48 42 0.19
49 18 0.08
50 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (48 bp):
TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCCATATATA
Found at i:499473 original size:44 final size:42
Alignment explanation
Indices: 499264--499473 Score: 145
Period size: 45 Copynumber: 4.7 Consensus size: 42
499254 GATGAGGGCT
* * * * * *
499264 AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAAAGT-T--GTG-C
499310 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACAATGTTGAGTGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-AA-GTT--GTGC
* * *
499357 AGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGTTAG-CC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CT--AAAGTT-GTGC
* * *
499402 AGTGTGAGACGTGTCTGGGACACGCATCGGCTAAGAGTTGTGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAA-AGTTGTGC
*
499445 TGGTGTAAGACATGTCTGGGACATGCATC
1 -AGTGTAAGACATGTCTGGGACATGCATC
499474 AGCACGCACA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.01
43 5 0.04
44 26 0.19
45 34 0.25
46 26 0.19
47 27 0.20
48 13 0.10
49 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (42 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTAAAGTTGTGC
Found at i:500808 original size:28 final size:28
Alignment explanation
Indices: 500775--500852 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
500765 TTTGAATCAT
500775 TCAATATTTCGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGTCATTC
* *
500803 TCAATATCTCGCACACTAAGCGTCATTC
1 TCAATATTTCGCACACTAAGTGTCATTC
* *
500831 TCAATATTTCGTACACTGAGTG
1 TCAATATTTCGCACACTAAGTG
500853 CCATATTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGTCATTC
Found at i:501414 original size:44 final size:44
Alignment explanation
Indices: 501366--501454 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
501356 AATGCAAATT
*
501366 TATGAAATTGAGTAAAATTCTACTATAGCCGATTATCACTAGTG
1 TATGAAATTGAGTAAAACTCTACTATAGCCGATTATCACTAGTG
501410 TATGAAATTGAGTAAAACTCTACTATAGCCGATTATCACTAGTG
1 TATGAAATTGAGTAAAACTCTACTATAGCCGATTATCACTAGTG
501454 T
1 T
501455 CTCTAGCAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (44 bp):
TATGAAATTGAGTAAAACTCTACTATAGCCGATTATCACTAGTG
Found at i:502976 original size:18 final size:18
Alignment explanation
Indices: 502953--502988 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
502943 CCGAAAAAGG
502953 TGTGTAACCACACCCTTC
1 TGTGTAACCACACCCTTC
502971 TGTGTAACCACACCCTTC
1 TGTGTAACCACACCCTTC
502989 CTTACTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.39, G:0.11, T:0.28
Consensus pattern (18 bp):
TGTGTAACCACACCCTTC
Found at i:506600 original size:48 final size:48
Alignment explanation
Indices: 506535--506667 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
506525 TGGTTGATAT
*
506535 GAGAGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAC
1 GAGAGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGACAC
* * * * * * * *
506583 GAGAGCTAGTGTAAGACCATGTTTTGAATATGGTATCGGCCTTGACAT
1 GAGAGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGACAC
* * *
506631 GTGAGCCAGTGTAA-ACCATGTCTGGGACATGACATCG
1 GAGAGCAAGTGTAAGACCATGTCTGGGACATGGCATCG
506668 ACACTTTACA
Statistics
Matches: 68, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
47 17 0.25
48 51 0.75
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
GAGAGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGACAC
Found at i:511606 original size:44 final size:44
Alignment explanation
Indices: 511538--511654 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
511528 ACATGTACCG
* *
511538 CATCTATAATGAACTCAGACCAACTCAACGAGCTCGGATGCTCA
1 CATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTCA
** * *
511582 CATCCATAATGAACTTGGACCAACTCAATGAGCTCAGATGC-CT
1 CATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTCA
* * *
511625 CATACATATCACGAACCCAGACCAACTCAA
1 CATCCATA--ATGAACTCAGACCAACTCAA
511655 AGAGTCCGGG
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 8 0.13
44 36 0.60
45 16 0.27
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.20
Consensus pattern (44 bp):
CATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTCA
Found at i:514561 original size:55 final size:54
Alignment explanation
Indices: 514433--514639 Score: 256
Period size: 53 Copynumber: 3.8 Consensus size: 54
514423 ATTAAGGTCT
* * *
514433 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGC
* * ** *
514487 AAGGAAATCATGTAAGACCATTTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-CTATAAGGC
* * *
514542 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGC
* * *
514595 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
514640 TAAAAAAAGA
Statistics
Matches: 128, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
52 4 0.03
53 41 0.32
54 39 0.30
55 40 0.31
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGC
Found at i:514638 original size:108 final size:109
Alignment explanation
Indices: 514444--514639 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 109
514434 AGGATACCAA
* * *
514444 GTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAGGAAATCATGTAAGACCATT
1 GTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAGGAAACCACGTAAGACCATG
*
514509 TCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCAT
66 TCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCAT
* * *
514553 GTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACGTAAGACCATG
1 GTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAGGAAACCACGTAAGACCATG
*
514617 TCAAGACATGGCAATGGTAAGTT
66 TCAAGACATGGCAATGATAAGTT
514640 TAAAAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 45 0.57
109 34 0.43
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (109 bp):
GTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAGGAAACCACGTAAGACCATG
TCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCAT
Found at i:524613 original size:20 final size:19
Alignment explanation
Indices: 524581--524619 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
524571 GTCGATCTCT
524581 ATTTAGCTCAATTCAGCTC
1 ATTTAGCTCAATTCAGCTC
* *
524600 ATTTGAGCTTAATTTAGCTC
1 ATTT-AGCTCAATTCAGCTC
524620 GTTGAGCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (19 bp):
ATTTAGCTCAATTCAGCTC
Found at i:524922 original size:17 final size:18
Alignment explanation
Indices: 524900--524937 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
524890 GCTACAGTCA
524900 AATTTA-TG-TTGTGTCTT
1 AATTTATTGTTTGTGT-TT
524917 AATTTATTGTTTGTGTTT
1 AATTTATTGTTTGTGTTT
524935 AAT
1 AAT
524938 ATGTCTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.61
Consensus pattern (18 bp):
AATTTATTGTTTGTGTTT
Found at i:532068 original size:27 final size:27
Alignment explanation
Indices: 531741--532057 Score: 526
Period size: 27 Copynumber: 11.7 Consensus size: 27
531731 TACTAAAATG
* * *
531741 CCCTCAATTTGTAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
531768 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
531795 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
531822 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
531849 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
531876 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
531903 CCCTCGATTTATAGAATTATCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
531930 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
531957 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
531984 CCCTCGATTTATAGAATTATCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
532011 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
532038 CCCTCGATTTATAAAATTAC
1 CCCTCGATTTATAGAATTAC
532058 TAAAATACCC
Statistics
Matches: 273, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 273 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:532094 original size:54 final size:54
Alignment explanation
Indices: 531766--532233 Score: 204
Period size: 54 Copynumber: 8.6 Consensus size: 54
531756 ATTACCGTTT
* *** * * ***
531766 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* *** * * * ***
531820 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* **** * * * * ***
531874 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTATCATTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* **** * * * ****
531928 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* * *** * * * * ****
531982 TACCCTCGATTTATAGAATTATCATTTTACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* *
532036 TACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* * * *
532090 TACCCTCGA-TCAGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTAAAATTACTAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAATA-CCCTTGGTT-T---A-TAAAATTACCAAAA
* * * *
532150 TACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGCTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
* * * *
532204 TACCACT-GATTTGTGAAATTATCGAAATAC
1 TACC-CTCGATTTATAAAATTACCAAAATAC
532234 TCAATTTGTA
Statistics
Matches: 364, Mismatches: 39, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 308 0.85
55 9 0.02
56 1 0.00
58 1 0.00
59 9 0.02
60 33 0.09
61 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAA
Found at i:532141 original size:33 final size:33
Alignment explanation
Indices: 532103--532170 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
532093 CCTCGATCAG
532103 TAAAATTACCAAAATACCCCTAGTTTGTAAAAT
1 TAAAATTACCAAAATACCCCTAGTTTGTAAAAT
*
532136 TAAAATTACTAAAATACCCCTAGTTTGTAAAAT
1 TAAAATTACCAAAATACCCCTAGTTTGTAAAAT
532169 TA
1 TA
532171 CCAAAATACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (33 bp):
TAAAATTACCAAAATACCCCTAGTTTGTAAAAT
Found at i:532151 original size:60 final size:60
Alignment explanation
Indices: 532077--532197 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
532067 CTTGGTTTAC
*
532077 AAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCAAAATACCCCTAGTTTGTAAAATT
1 AAAATTACCAAAATACCC-CGAGTCAGTAAAATTACCAAAATACCCCTAGCTTGTAAAATT
* * ** * *
532137 AAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGCTTGTAAAATT
1 AAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAAAATACCCCTAGCTTGTAAAATT
532197 A
1 A
532198 CCAAAATACC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
59 2 0.04
60 51 0.96
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (60 bp):
AAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAAAATACCCCTAGCTTGTAAAATT
Found at i:532174 original size:87 final size:87
Alignment explanation
Indices: 532049--532224 Score: 239
Period size: 87 Copynumber: 2.0 Consensus size: 87
532039 CCTCGATTTA
* * *
532049 TAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTC-GATCAGTAAAATTACC
1 TAAAATTACTAAAATACCCCTAGTTTACAAAATTACCAAAATACCCTCGGCT-AGTAAAATTACC
*
532113 AAAATACCCCT-AGTTTGTAAAAT
65 AAAATACCACTGA-TTTGTAAAAT
** * *
532136 TAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGCTTGTAAAATTACCA
1 TAAAATTACTAAAATACCCCTAGTTTACAAAATTACCAAAATACCCTCGGCTAGTAAAATTACCA
*
532201 AAATACCACTGATTTGTGAAAT
66 AAATACCACTGATTTGTAAAAT
532223 TA
1 TA
532225 TCGAAATACT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 75 0.96
88 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (87 bp):
TAAAATTACTAAAATACCCCTAGTTTACAAAATTACCAAAATACCCTCGGCTAGTAAAATTACCA
AAATACCACTGATTTGTAAAAT
Found at i:532217 original size:27 final size:26
Alignment explanation
Indices: 532036--532259 Score: 141
Period size: 27 Copynumber: 8.2 Consensus size: 26
532026 ATTACCGTTT
* *
532036 TACCCTCGATTTATAAAATTACTAAAA
1 TACCCT-GATTTGTAAAATTACCAAAA
* **
532063 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCC-TGATTTGTAAAATTACCAAAA
**
532090 TACCCTCGATCAGTAAAATTACCAAAA
1 TACCCT-GATTTGTAAAATTACCAAAA
*
532117 TACCCCT-AGTTTGTAAAATTAAAATTACTAAAA
1 TA-CCCTGA-TTTG------TAAAATTACCAAAA
532150 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TA-CCCTGA-TTTGTAAAATTACCAAAA
**
532177 TACCCTTGGCTTGTAAAATTACCAAAA
1 TACCC-TGATTTGTAAAATTACCAAAA
* * *
532204 TACCACTGATTTGTGAAATTATCGAAA
1 TACC-CTGATTTGTAAAATTACCAAAA
* * *
532231 TACTC-AATTTGTAAAA-TATCAAAA
1 TACCCTGATTTGTAAAATTACCAAAA
532255 TACCC
1 TACCC
532260 CTGTACGGTA
Statistics
Matches: 160, Mismatches: 24, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
24 11 0.07
25 9 0.06
26 6 0.04
27 102 0.64
28 6 0.04
33 26 0.16
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (26 bp):
TACCCTGATTTGTAAAATTACCAAAA
Found at i:532291 original size:27 final size:27
Alignment explanation
Indices: 532252--532467 Score: 297
Period size: 27 Copynumber: 8.0 Consensus size: 27
532242 TAAAATATCA
*
532252 AAATACCCCTGTACGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
532279 AAATACCCTTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
532306 AAATAACCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
532333 AAATACCCCTGTAGGGTAGAATGACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
532360 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
532387 AAATACCCTTGTAGGGTAAAAATACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
532414 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
532441 AGATACCCTTGTGGGGTAAAAATTACC
1 AAATACCCCTGTAGGGT-AGAATTACC
532468 ATTTTGCCCC
Statistics
Matches: 165, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 157 0.95
28 8 0.05
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:532324 original size:54 final size:54
Alignment explanation
Indices: 532252--532458 Score: 342
Period size: 54 Copynumber: 3.8 Consensus size: 54
532242 TAAAATATCA
*
532252 AAATACCCCTGTACGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTG
* * *
532306 AAATAACCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATGACTG
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTG
* *
532360 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAAAAATACTG
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTG
* *
532414 AAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTA
1 AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTA
532459 AAAATTACCA
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 142 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (54 bp):
AAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTG
Found at i:532685 original size:358 final size:358
Alignment explanation
Indices: 532276--532985 Score: 1402
Period size: 358 Copynumber: 2.0 Consensus size: 358
532266 GGTAGAATTA
532276 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTACCGAAATACCC
1 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTACCGAAATACCC
532341 CTGTAGGGTAGAATGACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAA
66 CTGTAGGGTAGAATGACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAA
532406 AAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAAATTACCATT
131 AAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAAATTACCATT
*
532471 TTGCCCCTAGGGTGTTAAATGACTGTTTTGCCCTTGTGGGCAAGTGACTGACTTGGACTGTGTGG
196 TTGCCCCTAGGGTGTTAAATGACTGTTTTGCCCTTGTGGGCAAGTGACTGACTTGGACCGTGTGG
532536 TTGACGGATTTGATTGTGAATATATGTTGGTGATATGAATGACTTGACTATGATTGTTTGATTCA
261 TTGACGGATTTGATTGTGAATATATGTTGGTGATATGAATGACTTGACTATGATTGTTTGATTCA
532601 AATATGGGCATGACATTCTGCATACATGACATG
326 AATATGGGCATGACATTCTGCATACATGACATG
532634 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTACCGAAATACCC
1 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTACCGAAATACCC
*
532699 CTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAA
66 CTGTAGGGTAGAATGACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAA
532764 AAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAAATTACCATT
131 AAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAAATTACCATT
532829 TTGCCCCTAGGGTGTTAAATGACTGTTTTGCCCTTGTGGGCAAGTGACTGACTTGGACCGTGTGG
196 TTGCCCCTAGGGTGTTAAATGACTGTTTTGCCCTTGTGGGCAAGTGACTGACTTGGACCGTGTGG
532894 TTGACGGATTTGATTGTGAATATATGTTGGTGATATGAATGACTTGACTATGATTGTTTGATTCA
261 TTGACGGATTTGATTGTGAATATATGTTGGTGATATGAATGACTTGACTATGATTGTTTGATTCA
532959 AATATGGGCATGACATTCTGCATACAT
326 AATATGGGCATGACATTCTGCATACAT
532986 NNNNNNNNNN
Statistics
Matches: 350, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
358 350 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (358 bp):
CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTACCGAAATACCC
CTGTAGGGTAGAATGACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAA
AAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTAAAAATTACCATT
TTGCCCCTAGGGTGTTAAATGACTGTTTTGCCCTTGTGGGCAAGTGACTGACTTGGACCGTGTGG
TTGACGGATTTGATTGTGAATATATGTTGGTGATATGAATGACTTGACTATGATTGTTTGATTCA
AATATGGGCATGACATTCTGCATACATGACATG
Found at i:532716 original size:54 final size:54
Alignment explanation
Indices: 532634--532816 Score: 312
Period size: 54 Copynumber: 3.4 Consensus size: 54
532624 ACATGACATG
*
532634 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTA
*
532688 CCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTA
* *
532742 CCGAAATACCCTTGTAGGGTAAAAATACTGAAATACCCCTGTAGGGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTA
* *
532796 CCGAGATACCCTTGTGGGGTA
1 CCGAAATACCCTTGTAGGGTA
532817 AAAATTACCA
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 122 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (54 bp):
CCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTA
Found at i:532804 original size:27 final size:27
Alignment explanation
Indices: 532634--532825 Score: 267
Period size: 27 Copynumber: 7.1 Consensus size: 27
532624 ACATGACATG
*
532634 CCGAAATACCCTTGTAGGGTAGAATTA
1 CCGAAATACCCCTGTAGGGTAGAATTA
* *
532661 CTGAAATAACCCTGTAGGGTAGAATTA
1 CCGAAATACCCCTGTAGGGTAGAATTA
532688 CCGAAATACCCCTGTAGGGTAGAATTA
1 CCGAAATACCCCTGTAGGGTAGAATTA
*
532715 CTGAAATACCCCTGTAGGGTAGAATTA
1 CCGAAATACCCCTGTAGGGTAGAATTA
* * *
532742 CCGAAATACCCTTGTAGGGTAAAAATA
1 CCGAAATACCCCTGTAGGGTAGAATTA
*
532769 CTGAAATACCCCTGTAGGGTAGAATTA
1 CCGAAATACCCCTGTAGGGTAGAATTA
* * * *
532796 CCGAGATACCCTTGTGGGGTAAAAATTA
1 CCGAAATACCCCTGTAGGGT-AGAATTA
532824 CC
1 CC
532826 ATTTTGCCCC
Statistics
Matches: 145, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
27 137 0.94
28 8 0.06
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
CCGAAATACCCCTGTAGGGTAGAATTA
Found at i:534560 original size:27 final size:27
Alignment explanation
Indices: 534522--534699 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
534512 NNNNNNNNNN
534522 AATTACTATTTTACCCTCAATTTACAA
1 AATTACTATTTTACCCTCAATTTACAA
* *
534549 AATTACTATTTTACCCTCGATTTACAG
1 AATTACTATTTTACCCTCAATTTACAA
*
534576 AATTA-TCGTTTTACCCTCAATTTACAA
1 AATTACT-ATTTTACCCTCAATTTACAA
* * * *
534603 AATTACTATTTTATCTTCGATTTACAG
1 AATTACTATTTTACCCTCAATTTACAA
** * * *
534630 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACTATTTTACCCTCAATTTACAA
* ** *
534657 AATAACCGTTTTACCCTCAATTTATAA
1 AATTACTATTTTACCCTCAATTTACAA
*
534684 AATTACCATTTTACCC
1 AATTACTATTTTACCC
534700 CTAGGTGTTA
Statistics
Matches: 129, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 1 0.01
27 127 0.98
28 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (27 bp):
AATTACTATTTTACCCTCAATTTACAA
Found at i:534604 original size:54 final size:54
Alignment explanation
Indices: 534530--534699 Score: 223
Period size: 54 Copynumber: 3.1 Consensus size: 54
534520 NNAATTACTA
*
534530 TTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTATCG
1 TTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCG
* *
534584 TTTTACCCTCAATTTACAAAATTACTATTTTATCTTCGATTTACAGAATTACCG
1 TTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCG
* * * * ** * * * *
534638 TTTTACCCTCGATTTATAGAATAACCGTTTTACCCTCAATTTATAAAATTACCA
1 TTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCG
534692 TTTTACCC
1 TTTTACCC
534700 CTAGGTGTTA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (54 bp):
TTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCG
Found at i:534659 original size:81 final size:81
Alignment explanation
Indices: 534522--534699 Score: 257
Period size: 81 Copynumber: 2.2 Consensus size: 81
534512 NNNNNNNNNN
* * *
534522 AATTACTATTTTACCCTCAATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTATCGTTT
1 AATTACTATTTTACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATAACCGTTT
534587 TACCCTCAATTTACAA
66 TACCCTCAATTTACAA
* * * * * *
534603 AATTACTATTTTATCTTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATAACCGTTT
1 AATTACTATTTTACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATAACCGTTT
*
534668 TACCCTCAATTTATAA
66 TACCCTCAATTTACAA
*
534684 AATTACCATTTTACCC
1 AATTACTATTTTACCC
534700 CTAGGTGTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (81 bp):
AATTACTATTTTACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTACAGAATAACCGTTT
TACCCTCAATTTACAA
Found at i:534896 original size:27 final size:27
Alignment explanation
Indices: 534856--535047 Score: 242
Period size: 27 Copynumber: 7.1 Consensus size: 27
534846 ACATGACATG
*
534856 CCGAAATACCCTTGTAGGGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTA
* * *
534883 CTGAAATAACCTTGTAGGGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTA
*
534910 CCGAAATACCCCTGTAGGGTAAAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTA
* * *
534937 CTGAAATACGCC-TGTAGAGTAGAATTA
1 CCGAAATAC-CCTTGTAGGGTAAAATTA
*
534964 CCGAAATACCCTTGTAGGGTAAAAATA
1 CCGAAATACCCTTGTAGGGTAAAATTA
* *
534991 CTGAAATACCCCTGTAGGGTAAAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTA
* *
535018 CCGAGATACCCTTGTGGGGTAAAAATTA
1 CCGAAATACCCTTGTAGGGT-AAAATTA
535046 CC
1 CC
535048 ATTTTGCCCC
Statistics
Matches: 142, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 129 0.91
28 11 0.08
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (27 bp):
CCGAAATACCCTTGTAGGGTAAAATTA
Found at i:534938 original size:54 final size:54
Alignment explanation
Indices: 534856--535046 Score: 276
Period size: 54 Copynumber: 3.5 Consensus size: 54
534846 ACATGACATG
* *
534856 CCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCTTGTAGGGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTACTGAAATAACCCTGTAGGGTAGAATTA
* *
534910 CCGAAATACCCCTGTAGGGTAAAATTACTGAAAT-ACGCCTGTAGAGTAGAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTACTGAAATAAC-CCTGTAGGGTAGAATTA
* * *
534964 CCGAAATACCCTTGTAGGGTAAAAATACTGAAATACCCCTGTAGGGTAAAATTA
1 CCGAAATACCCTTGTAGGGTAAAATTACTGAAATAACCCTGTAGGGTAGAATTA
* *
535018 CCGAGATACCCTTGTGGGGTAAAAATTAC
1 CCGAAATACCCTTGTAGGGT-AAAATTAC
535047 CATTTTGCCC
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
53 2 0.02
54 112 0.92
55 8 0.07
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (54 bp):
CCGAAATACCCTTGTAGGGTAAAATTACTGAAATAACCCTGTAGGGTAGAATTA
Found at i:535302 original size:25 final size:25
Alignment explanation
Indices: 535250--535344 Score: 115
Period size: 25 Copynumber: 3.8 Consensus size: 25
535240 AGGAAGTGCT
*
535250 AAAAGGGCTATG-CCCAGTTTAGC-A
1 AAAAGGGCTTTGCCCCAGTTTA-CTA
535274 AAAAGGGCTTTGCCCCAGTTTACTGA
1 AAAAGGGCTTTGCCCCAGTTTACT-A
* *
535300 AAAAGGGCCTTGCCCCAATTTA-TCA
1 AAAAGGGCTTTGCCCCAGTTTACT-A
535325 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
535345 ATTAAAGGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
24 12 0.19
25 29 0.47
26 21 0.34
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACTA
Found at i:543075 original size:50 final size:50
Alignment explanation
Indices: 543016--543112 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
543006 GCGATGCGTC
543016 CTTAAATGGACTGGGTTGTGTGCTTATGCAAAATGACAAAGTAATAGTCG
1 CTTAAATGGACTGGGTTGTGTGCTTATGCAAAATGACAAAGTAATAGTCG
543066 CTTAAATGGACTGGGTTGTGTGCTTATGCAAAATGACAAAGTAATAG
1 CTTAAATGGACTGGGTTGTGTGCTTATGCAAAATGACAAAGTAATAG
543113 CTTATGCTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (50 bp):
CTTAAATGGACTGGGTTGTGTGCTTATGCAAAATGACAAAGTAATAGTCG
Found at i:549460 original size:14 final size:15
Alignment explanation
Indices: 549441--549473 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
549431 TAGAATTGAT
549441 GTGTGGATG-TTTGG
1 GTGTGGATGTTTTGG
*
549455 GTGTGGCTGTTTTGG
1 GTGTGGATGTTTTGG
549470 GTGT
1 GTGT
549474 TTGTTTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.03, C:0.03, G:0.48, T:0.45
Consensus pattern (15 bp):
GTGTGGATGTTTTGG
Found at i:565178 original size:37 final size:37
Alignment explanation
Indices: 565128--565206 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
565118 TTATTACGAA
* * *
565128 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
565165 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
565202 GTCTT
1 GTCTT
565207 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:565403 original size:47 final size:47
Alignment explanation
Indices: 565325--565623 Score: 490
Period size: 47 Copynumber: 6.3 Consensus size: 47
565315 CCCTTCGGGA
* * * * * *
565325 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
565372 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
565419 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
565466 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
565513 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
565560 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
565609 CTTATCACATATATA
1 CTTATCACATATATA
565624 TACNNNNNNN
Statistics
Matches: 239, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 192 0.80
49 47 0.20
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:574198 original size:37 final size:37
Alignment explanation
Indices: 574139--574217 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
574129 AGCTCAGACG
* *
574139 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
574176 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
574213 TAATC
1 AAATC
574218 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:576616 original size:85 final size:85
Alignment explanation
Indices: 576487--576665 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
576477 TTTTTTATTG
*
576487 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCATTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
576552 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
576572 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
576637 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
576657 CCCATGCTC
1 CCCATGCTC
576666 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.27, G:0.08, T:0.39
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:583736 original size:31 final size:31
Alignment explanation
Indices: 583698--583768 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
583688 GGAAAAAGAA
*
583698 AGCAAAATTTGTCCATCTTCTTCTTTCTTGT
1 AGCAAAATTTGTCCATCTTCTTCTTGCTTGT
583729 AGCAAAATTTGTCCATCTTCTTCTTGCTTGT
1 AGCAAAATTTGTCCATCTTCTTCTTGCTTGT
583760 -GCCAAAATT
1 AG-CAAAATT
583769 CCAAGGGTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (31 bp):
AGCAAAATTTGTCCATCTTCTTCTTGCTTGT
Found at i:584724 original size:21 final size:21
Alignment explanation
Indices: 584655--584724 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
584645 TAATATGAAC
584655 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
* * * **
584676 TCA-TGATATATGTGCCATCCGAAC
1 TCATTGA-GT-TGTG--GTCTGAGT
584700 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
584721 TCAT
1 TCAT
584725 AATATTTGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 4 0.12
23 4 0.12
24 8 0.24
25 3 0.09
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.39
Consensus pattern (21 bp):
TCATTGAGTTGTGGTCTGAGT
Found at i:586195 original size:20 final size:20
Alignment explanation
Indices: 586170--586213 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
586160 TAGTTACATA
586170 GGCGAGACCCATGTCACACG
1 GGCGAGACCCATGTCACACG
* *
586190 GGCGAGTCCCATGTTACACG
1 GGCGAGACCCATGTCACACG
586210 GGCG
1 GGCG
586214 TGTGTGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.32, G:0.34, T:0.14
Consensus pattern (20 bp):
GGCGAGACCCATGTCACACG
Found at i:588483 original size:12 final size:11
Alignment explanation
Indices: 588463--588498 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
588453 ACATGTTGAA
588463 TTTTAATTAAT
1 TTTTAATTAAT
588474 TTTATAATTAAT
1 TTT-TAATTAAT
588486 TTTT-ATTAAT
1 TTTTAATTAAT
588496 TTT
1 TTT
588499 GGTTATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.38
11 4 0.17
12 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:588689 original size:12 final size:11
Alignment explanation
Indices: 588669--588704 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
588659 ACATGTTGAA
588669 TTTTAATTAAT
1 TTTTAATTAAT
588680 TTTATAATTAAT
1 TTT-TAATTAAT
588692 TTTT-ATTAAT
1 TTTTAATTAAT
588702 TTT
1 TTT
588705 GGTTATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.38
11 4 0.17
12 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:588765 original size:206 final size:206
Alignment explanation
Indices: 588411--588822 Score: 824
Period size: 206 Copynumber: 2.0 Consensus size: 206
588401 TCAAAAAAAT
588411 AATTAATTATTATAAAATAATTAATTTGTACTTAAATTATGAACATGTTGAATTTTAATTAATTT
1 AATTAATTATTATAAAATAATTAATTTGTACTTAAATTATGAACATGTTGAATTTTAATTAATTT
588476 TATAATTAATTTTTATTAATTTTGGTTATTTTCGATAGAATTGCACAAAGGGCGAAAAATGGCTC
66 TATAATTAATTTTTATTAATTTTGGTTATTTTCGATAGAATTGCACAAAGGGCGAAAAATGGCTC
588541 GGCAAACACTACTAGAAGCAGAAAATCGAGAAGCAATTTGAAGTACCAAGGCAAATTAATTTCCA
131 GGCAAACACTACTAGAAGCAGAAAATCGAGAAGCAATTTGAAGTACCAAGGCAAATTAATTTCCA
588606 GCCTAAGACGG
196 GCCTAAGACGG
588617 AATTAATTATTATAAAATAATTAATTTGTACTTAAATTATGAACATGTTGAATTTTAATTAATTT
1 AATTAATTATTATAAAATAATTAATTTGTACTTAAATTATGAACATGTTGAATTTTAATTAATTT
588682 TATAATTAATTTTTATTAATTTTGGTTATTTTCGATAGAATTGCACAAAGGGCGAAAAATGGCTC
66 TATAATTAATTTTTATTAATTTTGGTTATTTTCGATAGAATTGCACAAAGGGCGAAAAATGGCTC
588747 GGCAAACACTACTAGAAGCAGAAAATCGAGAAGCAATTTGAAGTACCAAGGCAAATTAATTTCCA
131 GGCAAACACTACTAGAAGCAGAAAATCGAGAAGCAATTTGAAGTACCAAGGCAAATTAATTTCCA
588812 GCCTAAGACGG
196 GCCTAAGACGG
588823 TCCAAAATTA
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 206 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (206 bp):
AATTAATTATTATAAAATAATTAATTTGTACTTAAATTATGAACATGTTGAATTTTAATTAATTT
TATAATTAATTTTTATTAATTTTGGTTATTTTCGATAGAATTGCACAAAGGGCGAAAAATGGCTC
GGCAAACACTACTAGAAGCAGAAAATCGAGAAGCAATTTGAAGTACCAAGGCAAATTAATTTCCA
GCCTAAGACGG
Found at i:598064 original size:29 final size:28
Alignment explanation
Indices: 598007--598068 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
597997 AATAAGGAAA
* *
598007 TCAAAAGCCTAATTAAAAATTTAATCCC
1 TCAAAAGCCTAATTAAAAATTAAAACCC
* *
598035 TCAAAGGCCTTATTACAAAATTAAAACCC
1 TCAAAAGCCTAATTA-AAAATTAAAACCC
598064 T-AAAA
1 TCAAAA
598069 TATAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (28 bp):
TCAAAAGCCTAATTAAAAATTAAAACCC
Found at i:598434 original size:27 final size:27
Alignment explanation
Indices: 598384--598436 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
598374 CAGTAACAGT
* *
598384 TGGGCCTAGCCCATTAACAGAATCAGG
1 TGGGCCTAGCCCAATAACAAAATCAGG
598411 TGGGCCTAAGCCCAAT-ACAAAATCAG
1 TGGGCCT-AGCCCAATAACAAAATCAG
598437 TATCAGATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (27 bp):
TGGGCCTAGCCCAATAACAAAATCAGG
Found at i:598983 original size:27 final size:27
Alignment explanation
Indices: 598853--598983 Score: 131
Period size: 27 Copynumber: 4.9 Consensus size: 27
598843 GGGCATAATC
* *
598853 GTCATTCTACCATAC-AGGAGTATTACG
1 GTCATTTTACCCTACAAGG-GTATTACG
598880 GTCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAAGGGTATTACG
* * * * *
598907 GTCA-ATTACCTTACAGGGGCATTACA
1 GTCATTTTACCCTACAAGGGTATTACG
*
598933 GTCATTTTACCCTACAAGGATATTACG
1 GTCATTTTACCCTACAAGGGTATTACG
* * **
598960 CTCATTTTACACTACCGGGGTATT
1 GTCATTTTACCCTACAAGGGTATT
598984 TTGATAATTT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.25
27 60 0.71
28 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGTATTACG
Found at i:599006 original size:27 final size:27
Alignment explanation
Indices: 598963--599039 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
598953 TATTACGCTC
* *
598963 ATTTTACACTACCGGGGTATTTTGA-TA
1 ATTTTACA-AACCGGGGTATTTTCAGTA
*
598990 ATTTTACAAACCGGGGGATATTTCAGTA
1 ATTTTACAAACCGGGGTAT-TTTCAGTA
* *
599018 ATTTTCCAAACCAAGGGTATTT
1 ATTTTACAAACC-GGGGTATTT
599040 ATGACCCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
26 9 0.22
27 12 0.29
28 15 0.37
29 5 0.12
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (27 bp):
ATTTTACAAACCGGGGTATTTTCAGTA
Found at i:602719 original size:27 final size:27
Alignment explanation
Indices: 602695--602764 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
602685 ATTCTACCAC
602695 ACAGGGGTATTACGGTCATTTTACCCT
1 ACAGGGGTATTACGGTCATTTTACCCT
* * *
602722 ATAGGGGCATTACGATCATTTTACCCT
1 ACAGGGGTATTACGGTCATTTTACCCT
*
602749 ACAAGGGTATTACGGT
1 ACAGGGGTATTACGGT
602765 TAATTACCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (27 bp):
ACAGGGGTATTACGGTCATTTTACCCT
Found at i:602794 original size:53 final size:53
Alignment explanation
Indices: 602699--602824 Score: 146
Period size: 53 Copynumber: 2.4 Consensus size: 53
602689 TACCACACAG
* *
602699 GGGTATTACGGTCATTTTACCCTATAGGGGCATTACGATCATTTTACCCTACAA
1 GGGTATTACGGTTA-TTTACCCTATAGGGGCATTACGATCATTTTACACTACAA
* * * * *
602753 GGGTATTACGGTTAATTACCTTATAGTGGCCTTAC-AGTCATTTTACACTTCAA
1 GGGTATTACGGTTATTTACCCTATAGGGGCATTACGA-TCATTTTACACTACAA
* *
602806 GTGTATTATGGTTATTTAC
1 GGGTATTACGGTTATTTAC
602825 AGTACCAAGG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.77
54 13 0.21
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (53 bp):
GGGTATTACGGTTATTTACCCTATAGGGGCATTACGATCATTTTACACTACAA
Found at i:602884 original size:27 final size:26
Alignment explanation
Indices: 602833--602902 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 26
602823 ACAGTACCAA
* *
602833 GGTATTTCAGTAATTTTTGAACCAGG
1 GGTATTTCGGTAATTTTTAAACCAGG
*
602859 GGTATTTCGGTTATTTTTCAAACCAGG
1 GGTATTTCGGTAATTTTT-AAACCAGG
*
602886 GGTATTTCGATAATTTT
1 GGTATTTCGGTAATTTT
602903 CCAAATTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
26 16 0.42
27 22 0.58
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.43
Consensus pattern (26 bp):
GGTATTTCGGTAATTTTTAAACCAGG
Found at i:606689 original size:17 final size:18
Alignment explanation
Indices: 606669--606704 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
606659 AAATCTTGTT
606669 TTAATAAATTAATA-GCA
1 TTAATAAATTAATATGCA
*
606686 TTAATAATTTAATATGCA
1 TTAATAAATTAATATGCA
606704 T
1 T
606705 ATGTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
TTAATAAATTAATATGCA
Found at i:608901 original size:27 final size:27
Alignment explanation
Indices: 608878--608930 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
608868 TAGAATGATC
* *
608878 GTAATACCCCTGTCGAGTAAAATGACT
1 GTAATACCCCTATAGAGTAAAATGACT
*
608905 GTAATACCCCTATAGGGTAAAATGAC
1 GTAATACCCCTATAGAGTAAAATGAC
608931 AATTTTTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAATACCCCTATAGAGTAAAATGACT
Done.