Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold91
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: 1327174
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 48727 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:481056 original size:13 final size:13
Alignment explanation
Indices: 481038--481083 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
481028 TTTATGATGT
*
481038 AAATATTTAATAA
1 AAATATTAAATAA
*
481051 AAATATAAAATAAA
1 AAATATTAAAT-AA
481065 AAATATTAAAATAA
1 AAATATT-AAATAA
481079 AAATA
1 AAATA
481084 AAATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 9 0.32
14 15 0.54
15 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATTAAATAA
Found at i:481074 original size:15 final size:14
Alignment explanation
Indices: 481049--481109 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 14
481039 AATATTTAAT
481049 AAAAATATAAAATA
1 AAAAATATAAAATA
481063 AAAAATATTAAAATAA
1 AAAAATA-TAAAAT-A
* *
481079 AAATAAAATATAATA
1 AAA-AATATAAAATA
481094 TAAAAATAT-AAATA
1 -AAAAATATAAAATA
481108 AA
1 AA
481110 TTATAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.05
14 11 0.28
15 11 0.28
16 12 0.31
17 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATATAAAATA
Found at i:481084 original size:26 final size:24
Alignment explanation
Indices: 481047--481120 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
481037 TAAATATTTA
481047 ATAAAAATATAAAAT--AA-AAAAT
1 ATAAAAATA-AAAATAAAATAAAAT
* *
481069 ATTAAAATAAAAATAAAATATAAT
1 ATAAAAATAAAAATAAAATAAAAT
* *
481093 ATAAAAATATAAATAAATTATAAAT
1 ATAAAAATAAAAATAAAATA-AAAT
481118 ATA
1 ATA
481121 TATTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
21 5 0.12
22 8 0.19
23 2 0.05
24 21 0.50
25 6 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAAAAATAAAAATAAAATAAAAT
Found at i:481114 original size:19 final size:19
Alignment explanation
Indices: 481052--481122 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
481042 ATTTAATAAA
*
481052 AATAT-AAAATAAAAAATATT
1 AATATAAAAAT-ATAAATA-T
*
481072 AAAATAAAAATA-AAATAT
1 AATATAAAAATATAAATAT
481090 AATATAAAAATATAAATA-
1 AATATAAAAATATAAATAT
*
481108 AATTATAAATATATA
1 AA-TATAAAAATATA
481123 TTTATTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
18 14 0.31
19 21 0.47
20 5 0.11
21 5 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATAAAAATATAAATAT
Found at i:481116 original size:11 final size:11
Alignment explanation
Indices: 481050--481118 Score: 68
Period size: 11 Copynumber: 6.1 Consensus size: 11
481040 ATATTTAATA
481050 AAAATATAAAAT
1 AAAATAT-AAAT
* *
481062 AAAAAAT-ATT
1 AAAATATAAAT
*
481072 AAAATAAAAAT
1 AAAATATAAAT
481083 AAAATATAATAT
1 AAAATATAA-AT
481095 AAAAATATAAAT
1 -AAAATATAAAT
*
481107 AAATTATAAAT
1 AAAATATAAAT
481118 A
1 A
481119 TATATTTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
10 7 0.15
11 21 0.45
12 10 0.21
13 9 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:481120 original size:6 final size:6
Alignment explanation
Indices: 481046--481202 Score: 62
Period size: 6 Copynumber: 26.2 Consensus size: 6
481036 GTAAATATTT
* * * *
481046 AATAAA AATATAA AATAAAA AATATTA AA-ATA AAAATAA AATATA ATATAAA
1 AATATA AATAT-A AAT-ATA AATA-TA AATATA AATAT-A AATATA A-ATATA
* * * * * * *
481098 AATATA AATA-A ATTATA AATATA TAT-TT ATTTTA AA-ATT TATAT-
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
*
481142 ATTATA AAT-T- AATA-A AATATTA AATTATTTA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATA-TA AA-TA--TA AATATA AATATA AATATA
481191 AATATA AA-ATA A
1 AATATA AATATA A
481203 TAAAATACAC
Statistics
Matches: 115, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
4 3 0.03
5 24 0.21
6 54 0.47
7 24 0.21
8 5 0.04
9 5 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AATATA
Found at i:481149 original size:16 final size:17
Alignment explanation
Indices: 481081--481150 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 17
481071 TAAAATAAAA
481081 ATAAA-ATATA-ATA-T
1 ATAAATATATATATATT
* * *
481095 AAAAATATAAATAAATT
1 ATAAATATATATATATT
*
481112 ATAAATATATATTTATT
1 ATAAATATATATATATT
* *
481129 TTAAA-ATTTATATATT
1 ATAAATATATATATATT
481145 ATAAAT
1 ATAAAT
481151 TAATAAAATA
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 15 0.37
17 18 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATATATATATATT
Found at i:492334 original size:79 final size:79
Alignment explanation
Indices: 492202--492448 Score: 363
Period size: 79 Copynumber: 3.1 Consensus size: 79
492192 GATTATAAAA
* * *
492202 AAAAATTGATGCTTTAGAAATAAAGGCCGGGGTTGGAGTATCCCCATGA-AAATAACGGGGTTGG
1 AAAAATTGATGTTTTAGAAATAAA-ACCGGGGTTGGAGTATCCCC-TCAGAAATAACGGGGTTGG
*
492266 AGTATCCCCGATTGTG
64 AGTATCCCCGATTATG
*
492282 AGAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAG
1 AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAG
492347 TATCCCCGATTATG
66 TATCCCCGATTATG
* * * * *
492361 AAAAATTGATATTTTAGAAATAAAATCGGGGTTTGAGTATCCCCTC-GAAAATAACGAGGTTTGA
1 AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGA
492425 GTATCCCCGATTATG
65 GTATCCCCGATTATG
492440 AAAAATTGA
1 AAAAATTGA
492449 GAAAATTAAA
Statistics
Matches: 154, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
78 3 0.02
79 129 0.84
80 22 0.14
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAG
TATCCCCGATTATG
Found at i:493654 original size:21 final size:21
Alignment explanation
Indices: 493628--493679 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
493618 TGTGCCCATC
493628 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTAT
493649 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTAT
*
493670 ATTTCATGCC
1 ATTCCATGCC
493680 CATCATTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (21 bp):
ATTCCATGCCTTCATTTTTAT
Found at i:493685 original size:22 final size:21
Alignment explanation
Indices: 493628--493686 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
493618 TGTGCCCATC
*
493628 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCATCATTTTTAT
*
493649 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCATCATTTTTAT
*
493670 ATTTCATGCCCATCATT
1 ATTCCATG-CCATCATT
493687 CCATGCCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTCCATGCCATCATTTTTAT
Found at i:493730 original size:14 final size:14
Alignment explanation
Indices: 493713--493739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
493703 ATTATTATTT
493713 TTTTTGAATTTTAA
1 TTTTTGAATTTTAA
493727 TTTTTGAATTTTA
1 TTTTTGAATTTTA
493740 CTTATTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTGAATTTTAA
Found at i:494483 original size:61 final size:61
Alignment explanation
Indices: 494395--494537 Score: 171
Period size: 61 Copynumber: 2.3 Consensus size: 61
494385 AAGAAATGTG
* * * * * *
494395 TCCTGCTCTTTGAGGACTGGAAGATGCCACTAACTAGTGTGGGATTTGCAAAAAGAAA-GCA
1 TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTAGTGTGGGATTT-AAAAAAAAAAGGCA
* * *
494456 TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAGGCG
1 TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTAGTGTGGGATTTAAAAAAAAAAGGCA
* *
494517 TCTTGCTCTTTGAAAACTGAA
1 TCCTGCTCTTTGAAGACTGAA
494538 GGTGAAAGGA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
60 8 0.11
61 62 0.89
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (61 bp):
TCCTGCTCTTTGAAGACTGAAAAATGCCACCAACTAGTGTGGGATTTAAAAAAAAAAGGCA
Found at i:494642 original size:55 final size:54
Alignment explanation
Indices: 494558--494689 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 54
494548 GAGAGCGTCT
*
494558 TGCTTTTTAAGGACTAGGAA-GTGCCACCAACTTGTGTAGGCTTTAAAAAAAGTCC
1 TGCTTTTTGAGGACT--GAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAAAGTCC
* * * * ***
494613 TGCTTTTTGAGGACTGAAAGGTGTCACCAACTTTTGTGGGCTTTGAAAGGCGTCC
1 TGCTTTTTGAGGACTG-AAGGTGCCACCAACTTGTGTAGGCTTTAAAAAAAGTCC
*
494668 TGCTTTTTGAAGACTGAAGGTG
1 TGCTTTTTGAGGACTGAAGGTG
494690 AAAGGAGAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
53 1 0.02
54 8 0.12
55 57 0.86
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (54 bp):
TGCTTTTTGAGGACTGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAAAGTCC
Found at i:494706 original size:93 final size:93
Alignment explanation
Indices: 494609--494778 Score: 243
Period size: 93 Copynumber: 1.8 Consensus size: 93
494599 TTTAAAAAAA
* * * * *
494609 GTCCTGCTTTTTGAGGACT-GAAAGGTGTCACCAACTTTTGTGGGCTTTGAAAGGCGTCCTGCTT
1 GTCCTGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCTT
494673 TTTGAAGACTGAAGGTGAAAGGAGAGAGC
65 TTTGAAGACTGAAGGTGAAAGGAGAGAGC
* * *
494702 GTCCTGCTCTTTGAGGATTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGTTTT
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCTTT
*
494767 TTGAGGACTGAA
66 TTGAAGACTGAA
494779 AGGTACCACC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
93 64 0.96
94 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (93 bp):
GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGCTTT
TTGAAGACTGAAGGTGAAAGGAGAGAGC
Found at i:494730 original size:148 final size:148
Alignment explanation
Indices: 494394--494837 Score: 557
Period size: 148 Copynumber: 2.9 Consensus size: 148
494384 AAAGAAATGT
* * *
494394 GTCCTGCTCTTTGAGGACT-GGAAGATGCCACTAACTAGTGTGGGATTTGCAAAAAGAAAGCATC
1 GTCCTGCTCTTTGAGGACTAGGAAG-TGCCACCAACTTGTGTGGGCTTT---AAAA-AAAG--TC
* * ** * *
494458 CTGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAGGCGTCTTGC
59 CTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT------GAAAGGCGTCCTGC
*
494523 TCTTTGAAAACTGAAGGTGAAAGGAGAGAGC
118 TCTTTGAAGACTGAAGGTGAAAGGAGAGAGC
* * * *
494554 GTCTTGCTTTTTAAGGACTAGGAAGTGCCACCAACTTGTGTAGGCTTTAAAAAAAGTCCTGCTTT
1 GTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGTCCTGCTTT
* * *
494619 TTGAGGACTGAAAGGTGTCACCAACTTTTGTGGGCTTTGAAAGGCGTCCTGCTTTTTGAAGACTG
66 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAAGACTG
494684 AAGGTGAAAGGAGAGAGC
131 AAGGTGAAAGGAGAGAGC
* ** *
494702 GTCCTGCTCTTTGAGGATTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGTTTT
1 GTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGTCCTGCTTT
* *
494767 TTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAAGACTA
66 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAAGACTG
494832 AAGGTG
131 AAGGTG
494838 CCACCAACTT
Statistics
Matches: 253, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
148 164 0.65
154 41 0.16
156 4 0.02
157 4 0.02
160 35 0.14
161 5 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (148 bp):
GTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGTCCTGCTTT
TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAAGACTG
AAGGTGAAAGGAGAGAGC
Found at i:494770 original size:55 final size:56
Alignment explanation
Indices: 494702--494947 Score: 302
Period size: 55 Copynumber: 4.4 Consensus size: 56
494692 AGGAGAGAGC
* *
494702 GTCCTGCTCTTTGAGGATTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGA
1 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * * *
494757 GTCCTGTTTTTTGAGGACT-GAAAGGTACCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
494812 GTCCTGCTCTTTGAAGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAGA
1 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA----AGGA
* * *
494871 CGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGC
1 -GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
494928 GTCCTGCTCTTTGAGGACTA
1 GTCCTGCTCTTTGAGGACTA
494948 AAGGGCGAAA
Statistics
Matches: 162, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
54 30 0.19
55 62 0.38
56 19 0.12
57 2 0.01
59 2 0.01
60 17 0.10
61 3 0.02
62 27 0.17
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (56 bp):
GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:494916 original size:116 final size:109
Alignment explanation
Indices: 494700--494951 Score: 353
Period size: 116 Copynumber: 2.2 Consensus size: 109
494690 AAAGGAGAGA
* * *
494700 GCGTCCTGCTCTTTGAGGATTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGTCCTGT
1 GCGTCCTGCTCTTTGAGGACTA--AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGTCCTGC
* *
494764 TTTTTGAGGACTGAAAGGTACCACCAACTTGTGTGGGCTTTGAAAG
64 TTTTTGAGGACTGAAAAGTACCACCAACTTGTGTGGGCTTTAAAAG
*
494810 GCGTCCTGCTCTTTGAAGACTAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGAAGACGTC
1 GCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA----AAGA-GTC
*
494875 CTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
60 CTGCTTTTTGAGGACT-GAAAAGTACCACCAACTTGTGTGGGCTTTAAAAG
494926 GCGTCCTGCTCTTTGAGGACTAAAGG
1 GCGTCCTGCTCTTTGAGGACTAAAGG
494952 GCGAAAGGAG
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
108 2 0.02
109 24 0.19
110 23 0.18
114 3 0.02
115 18 0.14
116 56 0.44
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (109 bp):
GCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGTCCTGCTT
TTTGAGGACTGAAAAGTACCACCAACTTGTGTGGGCTTTAAAAG
Found at i:495061 original size:61 final size:61
Alignment explanation
Indices: 494965--495110 Score: 186
Period size: 61 Copynumber: 2.4 Consensus size: 61
494955 AAAGGAGGGA
* * * *
494965 GCGTCTTGCTCTTTGAGGACTAGGAAGCGCCACCAACTTATGTGGGTTTTAAAAGGAGAAG
1 GCGTCTTGCTCTTTGAGGACTAGAAAACGCCACCAACTTATGTGGGCTTTAAAAGGAAAAG
* * * * *
495026 GCGTCTTACTCTTTGAGGACT-GAAAAATGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAT
1 GCGTCTTGCTCTTTGAGGACTAG-AAAACGCCACCAACTTATGTGGGCTTTAAAAGGAAAAG
*
495087 GCGTCCTGCTCTTTGAGGACTAGA
1 GCGTCTTGCTCTTTGAGGACTAGA
495111 GAAGTAGAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
60 1 0.01
61 70 0.97
62 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (61 bp):
GCGTCTTGCTCTTTGAGGACTAGAAAACGCCACCAACTTATGTGGGCTTTAAAAGGAAAAG
Found at i:497541 original size:13 final size:13
Alignment explanation
Indices: 497523--497548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
497513 CAATTTTTTG
497523 TGTATCGATACAT
1 TGTATCGATACAT
497536 TGTATCGATACAT
1 TGTATCGATACAT
497549 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:497632 original size:20 final size:20
Alignment explanation
Indices: 497607--497645 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
497597 ACATCTTTTT
497607 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
497627 CATGTATCGATACATTGCA
1 CATGTATCGATACATTGCA
497646 CTTTGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:501797 original size:27 final size:27
Alignment explanation
Indices: 501767--501820 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
501757 GACTTGGGGT
*
501767 GAAATTCATTGTTGGAACAACCCCGGC
1 GAAATTAATTGTTGGAACAACCCCGGC
501794 GAAATTAATTGTTGGAACAACCCCGGC
1 GAAATTAATTGTTGGAACAACCCCGGC
501821 AGAATGCACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (27 bp):
GAAATTAATTGTTGGAACAACCCCGGC
Found at i:507611 original size:79 final size:79
Alignment explanation
Indices: 507507--507785 Score: 477
Period size: 79 Copynumber: 3.5 Consensus size: 79
507497 GCTAGAGTTG
* * *
507507 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATTGATATTTTAGAGA
1 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGA
*
507572 TAAAACTGGGGTTA
66 TAAAACCGGGGTTA
* * *
507586 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCTCGATTATTAAAAATTGATGTTTTAGAAA
1 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGA
507651 TAAAACCGGGGTTA
66 TAAAACCGGGGTTA
507665 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGA
1 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGA
*
507730 TAAAACCGGGGTTG
66 TAAAACCGGGGTTA
*
507744 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATT
1 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATT
507786 GTAAGAAATT
Statistics
Matches: 188, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 188 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (79 bp):
GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGA
TAAAACCGGGGTTA
Found at i:509227 original size:35 final size:35
Alignment explanation
Indices: 509202--509344 Score: 252
Period size: 35 Copynumber: 4.1 Consensus size: 35
509192 TATTTTTTTG
*
509202 TGCCCATCATTCTATGCCTTCATTTTTATATTCCA
1 TGCCCATCATTCCATGCCTTCATTTTTATATTCCA
*
509237 TGCCCATCATTCCATGCCTCCATTTTTATATTCCA
1 TGCCCATCATTCCATGCCTTCATTTTTATATTCCA
*
509272 TGCCCATCATTCTATGCCTTCATTTTTATATTCCA
1 TGCCCATCATTCCATGCCTTCATTTTTATATTCCA
509307 TGCCCATCATTCCATG-CTTCATTTTTATATTCCA
1 TGCCCATCATTCCATGCCTTCATTTTTATATTCCA
509341 TGCC
1 TGCC
509345 TTCATTTTTA
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
34 22 0.21
35 81 0.79
ACGTcount: A:0.20, C:0.31, G:0.06, T:0.43
Consensus pattern (35 bp):
TGCCCATCATTCCATGCCTTCATTTTTATATTCCA
Found at i:509340 original size:20 final size:21
Alignment explanation
Indices: 509315--509355 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
509305 CATGCCCATC
509315 ATTCCATG-CTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTAT
509335 ATTCCATGCCTTCATTTTTAT
1 ATTCCATGCCTTCATTTTTAT
509356 TATTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.54
Consensus pattern (21 bp):
ATTCCATGCCTTCATTTTTAT
Found at i:509401 original size:6 final size:6
Alignment explanation
Indices: 509367--509394 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
509357 ATTATTATTT
509367 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
509395 TGATTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:509536 original size:25 final size:26
Alignment explanation
Indices: 509507--509563 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
509497 TTACTGTTAT
509507 TATTTTTAGA-TATAATTTATTAAAA
1 TATTTTTAGATTATAATTTATTAAAA
* * *
509532 TATTTGTAGATTTTATTTTATTAAAA
1 TATTTTTAGATTATAATTTATTAAAA
509558 TATTTT
1 TATTTT
509564 AAAATAACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (26 bp):
TATTTTTAGATTATAATTTATTAAAA
Found at i:513260 original size:13 final size:14
Alignment explanation
Indices: 513227--513304 Score: 59
Period size: 15 Copynumber: 5.4 Consensus size: 14
513217 GTTTTTGAAA
* *
513227 TATTTCTAAAACTAC
1 TATTTTTAAAA-TAT
513242 TATTTTTAAAATA-
1 TATTTTTAAAATAT
* *
513255 TATTTTTGATATAT
1 TATTTTTAAAATAT
*
513269 TATTTTCTAATATAT
1 TATTTT-TAAAATAT
*
513284 TAATATTTTAAAATAA
1 T-AT-TTTTAAAATAT
513300 TATTT
1 TATTT
513305 ATAATTTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 11 0.21
14 10 0.19
15 20 0.38
16 9 0.17
17 3 0.06
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (14 bp):
TATTTTTAAAATAT
Found at i:513321 original size:24 final size:24
Alignment explanation
Indices: 513290--513335 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
513280 ATATTAATAT
*
513290 TTTAAAATAATATTTATAATTTCA
1 TTTAAAATAATATTTAAAATTTCA
*
513314 TTTAAAATTATATTTAAAATTT
1 TTTAAAATAATATTTAAAATTT
513336 AACCAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAAAATAATATTTAAAATTTCA
Found at i:515192 original size:21 final size:21
Alignment explanation
Indices: 515166--515235 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
515156 AGAGGCTCGA
*
515166 GCTGCTGCCGTGTTCATGGAT
1 GCTGCTGCCATGTTCATGGAT
*
515187 GCTGCTATTGCCATGTTCGTGGAT
1 GCTGC---TGCCATGTTCATGGAT
** *
515211 GCTGCTGCTTTGTTCATGGAA
1 GCTGCTGCCATGTTCATGGAT
515232 GCTG
1 GCTG
515236 AAAGAGGCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 21 0.52
24 19 0.47
ACGTcount: A:0.11, C:0.21, G:0.31, T:0.36
Consensus pattern (21 bp):
GCTGCTGCCATGTTCATGGAT
Found at i:515203 original size:24 final size:24
Alignment explanation
Indices: 515171--515216 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
515161 CTCGAGCTGC
*
515171 TGCCGTGTTCATGGATGCTGCTAT
1 TGCCATGTTCATGGATGCTGCTAT
*
515195 TGCCATGTTCGTGGATGCTGCT
1 TGCCATGTTCATGGATGCTGCT
515217 GCTTTGTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.30, T:0.37
Consensus pattern (24 bp):
TGCCATGTTCATGGATGCTGCTAT
Found at i:515265 original size:31 final size:31
Alignment explanation
Indices: 515225--515315 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
515215 CTGCTTTGTT
*
515225 CATGGAAGCT-GAAAGAGGCTCGAGTTGCTA-
1 CATGGAAGCTGGAAA-AGGCTCGAGCTGCTAG
*
515255 CAGTGGAAGCTGGAAAAGGCTTGAGCTGCTAG
1 CA-TGGAAGCTGGAAAAGGCTCGAGCTGCTAG
* * *
515287 CATGGAAGTTAGAAAAAGCTCGAGCTGCT
1 CATGGAAGCTGGAAAAGGCTCGAGCTGCT
515316 GGTTTCGGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
30 2 0.04
31 44 0.85
32 6 0.12
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (31 bp):
CATGGAAGCTGGAAAAGGCTCGAGCTGCTAG
Found at i:515873 original size:31 final size:31
Alignment explanation
Indices: 515838--515897 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
515828 TCCATTTGCT
*
515838 TGTGTC-CCTCATGATTGCATGCTACATTGTA
1 TGTGTCTCC-CATGATTGCAAGCTACATTGTA
515869 TGTGTCTCCCATGATTGCAAGCTACATTG
1 TGTGTCTCCCATGATTGCAAGCTACATTG
515898 CCTTGCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (31 bp):
TGTGTCTCCCATGATTGCAAGCTACATTGTA
Found at i:515977 original size:19 final size:20
Alignment explanation
Indices: 515955--515999 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
515945 ATTTTTTTAT
*
515955 ATTTTTTTTATT-TCTATTA
1 ATTTTTATTATTATCTATTA
* *
515974 ATTTTTATTATTATTTTTTA
1 ATTTTTATTATTATCTATTA
515994 ATTTTT
1 ATTTTT
516000 GATTTCTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTATTATTATCTATTA
Found at i:517056 original size:42 final size:42
Alignment explanation
Indices: 516502--517050 Score: 609
Period size: 42 Copynumber: 13.1 Consensus size: 42
516492 TAGATAAGGC
* * *
516502 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAAA-AA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-AAAGAA
* * * * * *
516544 AGTCTCTAAGGTCAACGCCGACAAGCAGACTGAGGGAATGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
** *
516586 AGTCTCCAGGGTCAAAGTTGACAGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
*
516628 AGTCTCCAGCGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAG-AA
* *** *
516670 AATCTCCAAATTCAAAGCCGACAGGCAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
*
516712 AGTCTCCAGGGTCAAAGCCGACAGGCAGAATAAGGGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
* * *
516754 AGTCTCCAGTGTCAAAACCGACAGGCAGATTAAGGGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
* * * * *
516796 AGTCTACAGTGTCAAAGTCAATAGGCAGACTAAGGGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
* * * * *
516838 AGCCTCCAGGGTCAAAGCCGACAGGTAGACTGAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
* * * * * *
516880 AGTCTCCACGATAAAAGCCGACAGGCAGACTGACGGTAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
* * *
516922 AGTCTCCAAGGTCAAAGCCGACAGACAGACTAAGGG-TAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAG-AA
* * * * * *
516964 AGTCTCTAGGGTCAAAGTCAACGGGAAGACTAAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
* *
517006 AGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAGGGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
517048 AGT
1 AGT
517051 TTCTAGAAGT
Statistics
Matches: 428, Mismatches: 74, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
41 6 0.01
42 419 0.98
43 3 0.01
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.13
Consensus pattern (42 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAA
Found at i:527329 original size:13 final size:13
Alignment explanation
Indices: 527311--527335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
527301 ATTACTCAAA
527311 TGTATCGATACAT
1 TGTATCGATACAT
527324 TGTATCGATACA
1 TGTATCGATACA
527336 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:527383 original size:52 final size:50
Alignment explanation
Indices: 527324--527468 Score: 200
Period size: 52 Copynumber: 2.8 Consensus size: 50
527314 ATCGATACAT
*
527324 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
527376 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
527428 TGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAA
527469 CTTTTCATAT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:535669 original size:31 final size:31
Alignment explanation
Indices: 535631--536079 Score: 366
Period size: 30 Copynumber: 14.7 Consensus size: 31
535621 ATACCTTTTT
535631 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
535662 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
* * *
535692 AAAGTCCACGACTTAGTGGC-GTCCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAAT-CTCTTC-TC
* * * * * *
535724 AAAGCCCACGAATCAGTGGCATTTTGTCCT-
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
535754 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* * * * * *
535785 AAAGTCCACGATTCAATGGCATTTTGTCCT-
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
535815 AAAGTCCACGACTCAGTGGCAATCTCTTCCC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* * * * *
535846 AAAGTCCATGACTCAGTGGCATTTTGTCCT-
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
535876 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
535907 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
* *
535937 AAAGTCCACGACTTAGTGGC-ATCCTTTTCCTC
1 AAAGTCCACGACTCAGTGGCAAT-CTCTT-CTC
* * * * * * *
535969 AAAGCCCATGACTCAGTGGCATTTTGTCCTA
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* * *
536000 AAAGTCCACAATTCAGTGGC-ATCCCTT-T-
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
* * * *
536028 TAAGTCCACGACTCCGTGGC-ACCTTCTTTTC
1 AAAGTCCACGACTCAGTGGCAATC-TCTTCTC
* * *
536059 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
536080 CTCTTTGTTC
Statistics
Matches: 333, Mismatches: 68, Indels: 33
0.77 0.16 0.08
Matches are distributed among these distances:
28 18 0.05
29 8 0.02
30 128 0.38
31 127 0.38
32 50 0.15
33 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:535710 original size:61 final size:61
Alignment explanation
Indices: 535630--536048 Score: 564
Period size: 61 Copynumber: 6.9 Consensus size: 61
535620 AATACCTTTT
535630 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGT-C
1 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGTCC
* * * * *
535690 TCAAAGTCCACGACTTAGTGGC-GTCCTTTTCTTCAAAGCCCACGAATCAGTGGCATTTTGTCC
1 T-AAAGTCCACGACTCAGTGGCAAT-CTCTTC-TCAAAGTCCACGACTCAGTGGCATTTTGTCC
* *
535753 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGATTCAATGGCATTTTGTCC
1 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGTCC
* *
535814 TAAAGTCCACGACTCAGTGGCAATCTCTTCCCAAAGTCCATGACTCAGTGGCATTTTGTCC
1 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGTCC
535875 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGT-C
1 TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGTCC
* * * *
535935 TCAAAGTCCACGACTTAGTGGC-ATCCTTTTCCTCAAAGCCCATGACTCAGTGGCATTTTGTCC
1 T-AAAGTCCACGACTCAGTGGCAAT-CTCTT-CTCAAAGTCCACGACTCAGTGGCATTTTGTCC
* * * * *
535998 TAAAAGTCCACAATTCAGTGGC-ATCCCTT-T-TAAGTCCACGACTCCGTGGCA
1 T-AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCA
536049 CCTTCTTTTC
Statistics
Matches: 319, Mismatches: 31, Indels: 19
0.86 0.08 0.05
Matches are distributed among these distances:
59 17 0.05
60 7 0.02
61 189 0.59
62 82 0.26
63 24 0.08
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (61 bp):
TAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATTTTGTCC
Found at i:535733 original size:32 final size:30
Alignment explanation
Indices: 535631--536021 Score: 395
Period size: 30 Copynumber: 12.7 Consensus size: 30
535621 ATACCTTTTT
*
535631 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1 AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
535662 AAAGTCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTC
* *
535692 AAAGTCCACGACTTAGTGGCGTCCTTT-TCTTC
1 AAAGTCCACGACTCAGTGGCAT--TTTGTC-TC
* *
535724 AAAGCCCACGAATCAGTGGCATTTTGTC-C
1 AAAGTCCACGACTCAGTGGCATTTTGTCTC
*
535753 TAAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1 -AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
* *
535785 AAAGTCCACGATTCAATGGCATTTTGTC-C
1 AAAGTCCACGACTCAGTGGCATTTTGTCTC
* *
535814 TAAAGTCCACGACTCAGTGGCAATCTCT-TCCC
1 -AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
*
535846 AAAGTCCATGACTCAGTGGCATTTTGTC-C
1 AAAGTCCACGACTCAGTGGCATTTTGTCTC
*
535875 TAAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1 -AAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
535907 AAAGTCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTC
*
535937 AAAGTCCACGACTTAGTGGCATCCTTT-TCCTC
1 AAAGTCCACGACTCAGTGGCAT--TTTGT-CTC
* * *
535969 AAAGCCCATGACTCAGTGGCATTTTGTCCTA
1 AAAGTCCACGACTCAGTGGCATTTTGT-CTC
* *
536000 AAAGTCCACAATTCAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
536022 CCCTTTTAAG
Statistics
Matches: 306, Mismatches: 30, Indels: 48
0.80 0.08 0.12
Matches are distributed among these distances:
29 11 0.04
30 122 0.40
31 116 0.38
32 57 0.19
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCTC
Found at i:536119 original size:27 final size:28
Alignment explanation
Indices: 536089--536141 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
536079 ACTCTTTGTT
* * *
536089 CCTTTT-AAGTCCATAACTCCGTGGCCC
1 CCTTTTAAAGCCCACAACTCCATGGCCC
536116 CCTTTTAAAGCCCACAACTCCATGGC
1 CCTTTTAAAGCCCACAACTCCATGGC
536142 ACCTTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (28 bp):
CCTTTTAAAGCCCACAACTCCATGGCCC
Found at i:536146 original size:27 final size:27
Alignment explanation
Indices: 536089--536148 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
536079 ACTCTTTGTT
* * * *
536089 CCTTTTAAGTCCATAACTCCGTGGCCC
1 CCTTTTAAGCCCACAACTCCATGGCCA
536116 CCTTTTAAAGCCCACAACTCCATGG-CA
1 CCTTTT-AAGCCCACAACTCCATGGCCA
536143 CCTTTT
1 CCTTTT
536149 TCTTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.22, C:0.37, G:0.12, T:0.30
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCATGGCCA
Found at i:536154 original size:33 final size:33
Alignment explanation
Indices: 536024--536429 Score: 438
Period size: 37 Copynumber: 12.0 Consensus size: 33
536014 AGTGGCATCC
* *
536024 CTTTT-AAGTCCACGACTCCGTGGCACC---TT
1 CTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
536053 CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTGTT
1 CTTTT-AAAGCCCACAACTCCGTGGCAC-CTTT-TT
* * *
536089 CCTTTT-AAGTCCATAACTCCGTGGC-CC----C
1 -CTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
536117 CTTTTAAAGCCCACAACTCCATGGCACCTTTTT
1 CTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* *
536150 CTTTTTAAAGCCCGCAACTCCGTGGCACTTTTTTT
1 C-TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
*
536185 CCCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTT
1 --CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTT
536221 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
536255 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 --CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTT
*
536291 CTTTTAAAGCCCACAACTCCATGGCACTCTTTTT
1 CTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
*
536325 CCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1 --CTTTT-AAAGCCCACAACTCCGTGGCACCTTTTT
536361 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
* *
536395 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTTT
1 --CTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
536429 C
1 C
536430 CCTTCCTAAA
Statistics
Matches: 325, Mismatches: 22, Indels: 57
0.80 0.05 0.14
Matches are distributed among these distances:
27 5 0.02
28 16 0.05
29 7 0.02
31 19 0.06
32 2 0.01
33 66 0.20
34 63 0.19
35 41 0.13
36 37 0.11
37 69 0.21
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (33 bp):
CTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:536239 original size:70 final size:70
Alignment explanation
Indices: 536115--536429 Score: 528
Period size: 70 Copynumber: 4.5 Consensus size: 70
536105 CTCCGTGGCC
* *
536115 CCCTTTT-AAAGCCCACAACTCCATGGCACCTTTTTCTTTTTAAAGCCCGCAACTCCGTGGCACT
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCGTGGCACT
*
536179 TTTTTT
65 CTTTTT
*
536185 CCCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
536250 TTTTT
66 TTTTT
*
536255 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCATGGCACTC
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
536320 TTTTT
66 TTTTT
*
536325 CCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
536390 TTTTT
66 TTTTT
* *
536395 CCCTTTT--AAGTCCACAACTCCGTGGCATCTTTTTC
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
536430 CCTTCCTAAA
Statistics
Matches: 233, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
68 25 0.11
70 181 0.78
71 27 0.12
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.35
Consensus pattern (70 bp):
CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
TTTTT
Found at i:536318 original size:140 final size:140
Alignment explanation
Indices: 536053--536429 Score: 551
Period size: 140 Copynumber: 2.7 Consensus size: 140
536043 GTGGCACCTT
* *
536053 CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTGTTCCTTTT-AAGTCCATAACTCCGTGG--C-
1 CTTTTCAAAGCCCACAACTCCGTGGCAC-CTTT-TT-CTTTTAAAGCCCACAACTCCGTGGCACT
* * *
536114 C-----CCCTTTTAAAGCCCACAACTCCATGGCACCTTTTTCTTTTTAAAGCCCGCAACTCCGTG
63 CTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCATG
*
536174 GCACTTTTTTTCC
128 GCACTCTTTTTCC
*
536187 CTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
536252 TTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTAAAGCCCACAACTCCATGGC
66 TTTCCCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCATGGC
536316 ACTCTTTTTCC
130 ACTCTTTTTCC
*
536327 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
* *
536392 TTTCCCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTC
66 TTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
536430 CCTTCCTAAA
Statistics
Matches: 222, Mismatches: 11, Indels: 16
0.89 0.04 0.06
Matches are distributed among these distances:
131 5 0.02
132 18 0.08
133 4 0.02
134 28 0.13
135 1 0.00
138 26 0.12
140 112 0.50
141 28 0.13
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (140 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
TTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCATGGCA
CTCTTTTTCC
Found at i:536474 original size:34 final size:35
Alignment explanation
Indices: 536431--536501 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
536421 ATCTTTTTCC
536431 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
536465 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
536500 CT
1 CT
536502 AAGCCCAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.21
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:536508 original size:30 final size:32
Alignment explanation
Indices: 536429--536508 Score: 128
Period size: 34 Copynumber: 2.5 Consensus size: 32
536419 GCATCTTTTT
536429 CCCTTCCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCCTAAAGCCCACACAAGTCGGTGGCAA
536461 CCTTCTTCCTAAAGCCCACACAAGTCGGTGGCAA
1 CC--CTTCCTAAAGCCCACACAAGTCGGTGGCAA
536495 CCCTT-CT-AAGCCCA
1 CCCTTCCTAAAGCCCA
536509 ATATAGCTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 7 0.15
31 2 0.04
32 5 0.11
34 32 0.70
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (32 bp):
CCCTTCCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:536565 original size:49 final size:49
Alignment explanation
Indices: 536501--537125 Score: 640
Period size: 49 Copynumber: 13.0 Consensus size: 49
536491 GCAACCCTTC
* *
536501 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
536550 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---A---T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
*
536593 TAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCACC---A---T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * *
536636 TAAGTCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * * *
536685 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * *
536733 TAAGTCCAATGTAGCTGGCCGTGACTCAGCACATTGGCACC---A---T
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
*
536776 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * * * * *
536825 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
536874 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * * * * * *
536923 TAAGGCCAATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
536972 TAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTT
* * * *
537024 TAAGTTCAATGTAGCTGGCCTTGCATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CC---TT-T-ATCTT
* * * * * * *
537079 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
537126 ACTTTTCTCA
Statistics
Matches: 491, Mismatches: 66, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
43 119 0.24
46 4 0.01
48 46 0.09
49 239 0.49
50 3 0.01
51 2 0.00
52 36 0.07
53 2 0.00
54 1 0.00
55 38 0.08
56 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
Found at i:536910 original size:98 final size:98
Alignment explanation
Indices: 536501--537059 Score: 753
Period size: 98 Copynumber: 5.9 Consensus size: 98
536491 GCAACCCTTC
*
536501 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
536566 GGCCTTGACTCAGCACATTGG------CACCAT
66 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
* * *
536593 TAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCACC---A---TTAAGTCCAATATAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
* * * * *
536652 GGCCCTGAATCAGCATATTGGCACCTTCATCTT
66 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
* * * * *
536685 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
*
536749 GGCCGTGACTCAGCACATTGG------CACCAT
66 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
*
536776 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
536841 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
66 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
* * *
536874 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGGCCAATGTAGTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
536939 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
66 GGCCTTGACTCAGCACATTGGCACCTTCACCAT
* *
536972 TAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAATGTA
537037 GCTGGCCTTG-CATCAGCACATTG
63 GCTGGCCTTGAC-TCAGCACATTG
537060 ACATCCTTTT
Statistics
Matches: 414, Mismatches: 31, Indels: 35
0.86 0.06 0.07
Matches are distributed among these distances:
86 34 0.08
89 1 0.00
91 42 0.10
92 122 0.29
94 1 0.00
97 34 0.08
98 140 0.34
99 3 0.01
100 1 0.00
101 36 0.09
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (98 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
GGCCTTGACTCAGCACATTGGCACCTTCACCAT
Found at i:538044 original size:13 final size:13
Alignment explanation
Indices: 538026--538050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
538016 ATTACTCAAA
538026 TGTATCGATACAT
1 TGTATCGATACAT
538039 TGTATCGATACA
1 TGTATCGATACA
538051 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:538115 original size:52 final size:52
Alignment explanation
Indices: 538059--538183 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
538049 CACTGATCTT
* *
538059 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
538111 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
538163 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
538184 CTTTTCATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:545028 original size:16 final size:16
Alignment explanation
Indices: 545007--545064 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
544997 GTAAACACAC
545007 AAACAAAAAAAAAACA
1 AAACAAAAAAAAAACA
545023 AAACAAAACAAAAAA-A
1 AAACAAAA-AAAAAACA
545039 AAACAAAAAATAACAACA
1 AAACAAAAAA-AA-AACA
545057 AAA-AAAAA
1 AAACAAAAA
545065 GAGAGAATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.05
16 19 0.50
17 13 0.34
18 4 0.11
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (16 bp):
AAACAAAAAAAAAACA
Found at i:545031 original size:21 final size:20
Alignment explanation
Indices: 545007--545063 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 20
544997 GTAAACACAC
545007 AAACAAAAAAAAAACAAAACA
1 AAACAAAAAAAAAACAAAA-A
545028 AAACAAAAAAAAAACAAAAA
1 AAACAAAAAAAAAACAAAAA
545048 ATAACAACAAAAAAAA
1 A-AACAA-AAAAAAAA
545064 AGAGAGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.06
21 24 0.71
22 8 0.24
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (20 bp):
AAACAAAAAAAAAACAAAAA
Found at i:545031 original size:29 final size:29
Alignment explanation
Indices: 545011--545064 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
545001 ACACACAAAC
545011 AAAA-AAAAAACAA-AACAAAACAAAAAA
1 AAAACAAAAAACAACAACAAAACAAAAAA
*
545038 AAAACAAAAAATAACAACAAAA-AAAAA
1 AAAACAAAAAACAACAACAAAACAAAAA
545065 GAGAGAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 13 0.54
29 7 0.29
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (29 bp):
AAAACAAAAAACAACAACAAAACAAAAAA
Found at i:546382 original size:34 final size:34
Alignment explanation
Indices: 546314--546429 Score: 159
Period size: 34 Copynumber: 3.5 Consensus size: 34
546304 ATCTCTCTTC
*
546314 TCAAAGTCCATGACTCAGTGGCATC---TTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTTTCT
546345 TCAAAGTCCACGACTCAGTGGCATCTTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTTTTCT
546379 TCAAAGTCCACGACTCAGTGGCATCTTTTCTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTT-T-TTCT
* *
546414 CCAAAGTCCACAACTC
1 TCAAAGTCCACGACTC
546430 CGGGCACCCT
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.31
34 35 0.45
35 16 0.21
36 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (34 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTTTTCT
Found at i:546442 original size:35 final size:33
Alignment explanation
Indices: 546314--546442 Score: 138
Period size: 34 Copynumber: 3.9 Consensus size: 33
546304 ATCTCTCTTC
* *
546314 TCAAAGTCCATGACTCAGTGGCATC-TTT-TCT
1 TCAAAGTCCACGACTCAGTGGCACCTTTTCTCT
* *
546345 TCAAAGTCCACGACTCAGTGGCATCTTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCA-CCTTTTCTCT
*
546379 TCAAAGTCCACGACTCAGTGGCATCTTTTCTCTT
1 TCAAAGTCCACGACTCAGTGGCACCTTTTCTC-T
* *
546413 TCCAAAGTCCACAACTCCG-GGCACCCTTTT
1 T-CAAAGTCCACGACTCAGTGGCA-CCTTTT
546443 AAGCCCACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
31 22 0.27
33 9 0.11
34 32 0.39
35 20 0.24
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (33 bp):
TCAAAGTCCACGACTCAGTGGCACCTTTTCTCT
Found at i:546475 original size:34 final size:33
Alignment explanation
Indices: 546437--547024 Score: 402
Period size: 34 Copynumber: 18.9 Consensus size: 33
546427 CTCCGGGCAC
**
546437 CCTTTTAAGCCCACAACTTTGTGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTT
* *
546471 CCTTTTAAGCCCATAACTTCGTGGCACTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTT
*
546505 CCTTTTAAGTCCACAACTCCGTGGCA------T
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
546532 CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTT
*
546566 CCTTTTAAGCCCACAACTCCATGGCACTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTT
* * *
546600 CCTTTTAAGTCCACAATTCCATGGCA------T
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
*
546627 CCTTTTAAGCCCACAACTTCGTGGCA------T
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* * *
546654 CCTTTTAAGCTCGCAACTCCGTGGCACTCTTTTC
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTT
* * *** * *
546688 CCTTTTAAGTCCATAACTTTATGGCAACATTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* *
546721 CTTTTTAAAGCCCACAACTCTGTGGCA-C-----
1 CCTTTT-AAGCCCACAACTCCGTGGCATCTTTTT
*
546749 CCTTTTAAGTCCACAACTCCGTGGCATC-TTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* *
546781 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* * **
546813 CTTTTTAAGTCCATGACTCCGTGGCA-C-----
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* **
546840 CCTTTCAAGCCCACAACTTTGTGGCAATCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGC-ATCTTTTT
* * *
546874 CCCTTTAAGTCCACGACTCCGTGGCACTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTT
* * *
546908 CCCTTTAGGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* *
546935 CCTTTGAAGCCCACAACTCCATGGCA-C-----
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
*
546962 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* *
546995 CC-TTTAAGTCCACAACTCCGTGGCACCTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTT
547025 AAAACCAATG
Statistics
Matches: 455, Mismatches: 64, Indels: 72
0.77 0.11 0.12
Matches are distributed among these distances:
27 154 0.34
28 8 0.02
29 1 0.00
31 1 0.00
32 82 0.18
33 13 0.03
34 196 0.43
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
CCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
Found at i:546495 original size:95 final size:94
Alignment explanation
Indices: 546417--546812 Score: 405
Period size: 95 Copynumber: 4.3 Consensus size: 94
546407 TCTCTTTCCA
* *
546417 AAGTCCACAACTCCGGGCACCCTTTTAAGCCCACAACTTTGTGGCATTCTTTTTCCTTTTAAGCC
1 AAGTCCACAACTCCGGGCATCCTTTTAAGCCCACAACTTCGTGGCATTCTTTTTCCTTTTAAGCC
* *
546482 CATAACTTCGTGGCACTCTTTTTCCTTTT
66 CACAACTCCGTGGCACTCTTTTTCCTTTT
*
546511 AAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACTCCGTGGCATTCTTTTTCCTTTTAAGC
1 AAGTCCACAACTCCG-GGCATCCTTTTAAGCCCACAACTTCGTGGCATTCTTTTTCCTTTTAAGC
*
546576 CCACAACTCCATGGCACTCTTTTTCCTTTT
65 CCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
546606 AAGTCCACAATTCCATGGCATCCTTTTAAGCCCACAACTTCGTGGCA-------TCCTTTTAAGC
1 AAGTCCACAACTCC-GGGCATCCTTTTAAGCCCACAACTTCGTGGCATTCTTTTTCCTTTTAAGC
* * *
546664 TCGCAACTCCGTGGCACTCTTTTCCCTTTT
65 CCACAACTCCGTGGCACTCTTTTTCCTTTT
* ** * *
546694 AAGTCCATAACTTTATGGCAACATTTTCTTTTTAAAGCCCACAAC-TCTGTGGCA--C-----CC
1 AAGTCCACAAC--TCCGG--GCA---TCCTTTT-AAGCCCACAACTTC-GTGGCATTCTTTTTCC
*
546751 TTTTAAGTCCACAACTCCGTGGCA-TC-TTTTCCTTTT
57 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
546787 AAGTCCACAACTCCGTGGCA-CCTTTT
1 AAGTCCACAACTCCG-GGCATCCTTTT
546813 CTTTTTAAGT
Statistics
Matches: 260, Mismatches: 29, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
86 5 0.02
88 46 0.18
89 1 0.00
90 3 0.01
91 4 0.02
92 1 0.00
93 19 0.07
94 25 0.10
95 156 0.60
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (94 bp):
AAGTCCACAACTCCGGGCATCCTTTTAAGCCCACAACTTCGTGGCATTCTTTTTCCTTTTAAGCC
CACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:546534 original size:27 final size:27
Alignment explanation
Indices: 546504--547024 Score: 200
Period size: 27 Copynumber: 17.2 Consensus size: 27
546494 GCACTCTTTT
546504 TCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
*
546531 TCCTTTTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
* *
546558 TTCTTTTTCCTTTTAAGCCCACAACTCCATGGCA
1 -------TCCTTTTAAGTCCACAACTCCGTGGCA
* *
546592 CTCTTTTTCCTTTTAAGTCCACAATTCCATGGCA
1 -------TCCTTTTAAGTCCACAACTCCGTGGCA
* *
546626 TCCTTTTAAGCCCACAACTTCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
*
546653 TCCTTTTAAG-CTCGCAACTCCGTGGCA
1 TCCTTTTAAGTC-CACAACTCCGTGGCA
* ***
546680 CTCTTTTCCCTTTTAAGTCCATAACTTTATGGCAACA
1 ------T-CCTTTTAAGTCCACAACTCCGTGG---CA
* * *
546717 TTTTCTTTTTAAAGCCCACAACTCTGTGGCA
1 ---TCCTTTT-AAGTCCACAACTCCGTGGCA
*
546748 CCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
546775 TCTTTTCCTTTTAAGTCCACAACTCCGTGGCA
1 -----TCCTTTTAAGTCCACAACTCCGTGGCA
* **
546807 CCTTTTCTTTTTAAGTCCATGACTCCGTGGCA
1 -----TCCTTTTAAGTCCACAACTCCGTGGCA
* * * **
546839 CCCTTTCAAGCCCACAACTTTGTGGCAA
1 TCCTTTTAAGTCCACAACTCCGTGGC-A
* *
546867 TCTTTTTCCCTTTAAGTCCACGACTCCGTGGCA
1 ------TCCTTTTAAGTCCACAACTCCGTGGCA
* *
546900 CTCTTTTTCCCTTTAGGTCCACAACTCCGTGGCA
1 -------TCCTTTTAAGTCCACAACTCCGTGGCA
* * * *
546934 CCCTTTGAAGCCCACAACTCCATGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
*
546961 CCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
*
546988 TCTTTTTCCTTTAAGTCCACAACTCCGTGGCA
1 TC-----CTTTTAAGTCCACAACTCCGTGGCA
547020 -CCTTT
1 TCCTTT
547025 AAAACCAATG
Statistics
Matches: 397, Mismatches: 59, Indels: 77
0.74 0.11 0.14
Matches are distributed among these distances:
26 4 0.01
27 154 0.39
28 6 0.02
31 3 0.01
32 78 0.20
33 7 0.02
34 142 0.36
35 1 0.00
37 2 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (27 bp):
TCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:546540 original size:61 final size:60
Alignment explanation
Indices: 546470--547024 Score: 360
Period size: 61 Copynumber: 9.1 Consensus size: 60
546460 GCATTCTTTT
* *
546470 TCCTTTTAAGCCCATAACTTCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* *
546531 TCCTTTTAAGCCCACAACTCCGTGGCATTCTTTTTCCTTTTAAGCCCACAACTCCATGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * * * *
546592 CTCTTTTTCCTTTTAAGTCCACAATTCCATGGCA------TCCTTTTAAGCCCACAACTTCGTGG
1 -------TCCTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGG
546651 CA
59 CA
* * * * ***
546653 TCCTTTTAAGCTCGCAACTCCGTGGCACTCTTTTCCCTTTTAAGTCCATAACTTTATGGCAACA
1 TCCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGG---CA
* *
546717 TTTTCTTTTTAAAGCCCACAACTCTGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCA
1 ---TCCTTTT-AAGCCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * * **
546775 TCTTTTCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTCTTTTTAAGTCCATGACTCCGTGGCA
1 -----TCCTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * ** * *
546839 CCCTTTCAAGCCCACAACTTTGTGGCAATCTTTTTCCCTTTAAGTCCACGACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGC-ATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
* * * * * *
546900 CTCTTTTTCCCTTTAGGTCCACAACTCCGTGGCA-C-----CCTTTGAAGCCCACAACTCCATGG
1 -------TCCTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGG
546959 CA
59 CA
* *
546961 CCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCC-TTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
547020 -CCTTT
1 TCCTTT
547025 AAAACCAATG
Statistics
Matches: 390, Mismatches: 61, Indels: 89
0.72 0.11 0.16
Matches are distributed among these distances:
54 46 0.12
55 1 0.00
58 7 0.02
59 60 0.15
60 12 0.03
61 170 0.44
64 25 0.06
66 2 0.01
67 7 0.02
68 60 0.15
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (60 bp):
TCCTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:547167 original size:87 final size:87
Alignment explanation
Indices: 547021--547489 Score: 695
Period size: 87 Copynumber: 5.4 Consensus size: 87
547011 TCCGTGGCAC
* *
547021 CTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
*
547086 AATTAGCATATTGGCACCTTAT
66 AATCAGCATATTGGCACCTTAT
* *
547108 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCATAAGCCCAATATCGCTGGCCTTA
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
547173 AATCAGCATATTGGCACCTTAT
66 AATCAGCATATTGGCACCTTAT
* * * * * * *
547195 CTTTAAGACCAATGTCGCTGGCCTTGAATCAACACGTTGGCACAAACCCAATATCACTGGCCGTG
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
*
547260 AATCAGCATGTTGGCACCTTCAT
66 AATCAGCATATTGGCACCTT-AT
* * *
547283 CTTTAAGACCAATGTCGCTGGCCTTAAATTAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
* *
547348 AATCAGCATATAGGCACATTAT
66 AATCAGCATATTGGCACCTTAT
* * *
547370 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCTACAAACCCAATGTCGCTGGCCTT
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGC-ATAAGCCCAATATCGCTGGCCTT
*
547435 GAATCAGCACATTGGCACCTTCAT
65 GAATCAGCATATTGGCACCTT-AT
* *
547459 CTTTAAGTCCAATATCACTGGCCTTGAATCA
1 CTTTAAGACCAATGTCACTGGCCTTGAATCA
547490 ACATAATGGC
Statistics
Matches: 342, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 197 0.58
88 114 0.33
89 31 0.09
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (87 bp):
CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
AATCAGCATATTGGCACCTTAT
Found at i:547323 original size:49 final size:49
Alignment explanation
Indices: 547242--547938 Score: 499
Period size: 49 Copynumber: 14.6 Consensus size: 49
547232 TGGCACAAAC
* * * **
547242 CCAATATCACTGGCCGTGAATCAGCATGTTGGCACCTTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * *
547291 CCAATGTCGCTGGCCTTAAATTAGCACATTGG------CA----TAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * *
547330 CCAATATCGCTGGCCTTGAATCAGCATATAGGCACATT-ATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
*
547378 CCAATGTCACTGGCCTTGAATCAGCACATTGG---C-T-A-C---AA-A
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
*
547417 CCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 -CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * * *
547467 CCAATATCACTGGCCTTGAATCAACATAATGGCACCTTCGTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGA
547519 CCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAG-
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * *
547557 CCAGATATCGCTAGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGA
1 CCA-ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * * *
547607 TCGATGTCGTTGGCCTTGAATTAGCACATTGGCACCTTAACCATCTTTAAAA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGA
* * * *
547659 CCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAGT
1 -CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * * ** *
547709 CTAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTTTAAAA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGA
* * *
547761 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCCTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * ** * * * *
547810 CCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATTCCTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-TT--TAAGA
* ** * * *
547862 CCAATGTCGTTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
* * *
547909 CTAATGTCGCTGACCATGAATCAGCACATT
1 CCAATGTCGCTGGCCTTGAATCAGCACATT
547939 ATCATTTTTC
Statistics
Matches: 510, Mismatches: 92, Indels: 94
0.73 0.13 0.14
Matches are distributed among these distances:
38 3 0.01
39 61 0.12
40 33 0.06
42 1 0.00
43 6 0.01
44 4 0.01
45 3 0.01
46 2 0.00
47 27 0.05
48 32 0.06
49 166 0.33
50 15 0.03
51 1 0.00
52 122 0.24
53 34 0.07
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGA
Found at i:547330 original size:175 final size:175
Alignment explanation
Indices: 547021--547489 Score: 724
Period size: 175 Copynumber: 2.7 Consensus size: 175
547011 TCCGTGGCAC
* * *
547021 CTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTG
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTG
* *
547086 AATTAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTAGCA
66 AATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTAAATCAGCACATTAGCA
* *
547150 TAAGCCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTAT
131 TAAGCCCAATATCGCTGGCCTTAAATCAGCATATAGGCACATTAT
* * * *
547195 CTTTAAGACCAATGTCGCTGGCCTTGAATCAACACGTTGGCACAAACCCAATATCACTGGCCGTG
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTG
* * * *
547260 AATCAGCATGTTGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTAAATTAGCACATTGGCA
66 AATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTAAATCAGCACATTAGCA
*
547325 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATAGGCACATTAT
131 TAAGCCCAATATCGCTGGCCTTAAATCAGCATATAGGCACATTAT
* *
547370 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCTACAAACCCAATGTCGCTGGCCTT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGC-ACAAACCCAATATCGCTGGCCTT
* * * *
547435 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCCTTGAATCA
65 GAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTAAATCA
547490 ACATAATGGC
Statistics
Matches: 264, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
174 76 0.29
175 120 0.45
176 68 0.26
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (175 bp):
CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTG
AATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTAAATCAGCACATTAGCA
TAAGCCCAATATCGCTGGCCTTAAATCAGCATATAGGCACATTAT
Found at i:547623 original size:88 final size:90
Alignment explanation
Indices: 547470--547641 Score: 249
Period size: 88 Copynumber: 1.9 Consensus size: 90
547460 TTTAAGTCCA
*
547470 ATATCACTGGCCTTGAATCAACATAATGGCACCTTCGTCATCTTTAAGACCAATGTCGCTGGCCT
1 ATATCACTAGCCTTGAATCAACATAATGGCACCTTCG-CATCTTTAAGACCAATGTCGCTGGCCT
547535 TGAATCAGCACATTGGCACAAGCCAG
65 TGAATCAGCACATTGGCACAAGCCAG
* * * * * *
547561 ATATCGCTAGCCTTGAATCAGCATATTGGCACC-TC-CATCTTTAAGATCGATGTCGTTGGCCTT
1 ATATCACTAGCCTTGAATCAACATAATGGCACCTTCGCATCTTTAAGACCAATGTCGCTGGCCTT
*
547624 GAATTAGCACATTGGCAC
66 GAATCAGCACATTGGCAC
547642 CTTAACCATC
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
88 42 0.58
90 2 0.03
91 29 0.40
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (90 bp):
ATATCACTAGCCTTGAATCAACATAATGGCACCTTCGCATCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACAAGCCAG
Found at i:547809 original size:101 final size:101
Alignment explanation
Indices: 547564--547934 Score: 367
Period size: 101 Copynumber: 3.7 Consensus size: 101
547554 AAGCCAGATA
* * * * *
547564 TCGCTAGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGATCGATGTCGTTGGCCTTGAATT
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAG-TCAATATCGTTGGCCTTGAATC
*
547629 AGCACATTGGCACCTTAACCATCTTTAAAACCCAATG
65 AGCATATTGGCACCTTAACCATCTTTAAAACCCAATG
* * * * *
547666 TCGTTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAGTCTAATATCGCTGGCCTTGAATC
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC-AATATCGTTGGCCTTGAATC
** ***
547731 AGCATATTGGTGCCTTCGTCATCTTTAAAA-CCAATG
65 AGCATATTGGCACCTTAACCATCTTTAAAACCCAATG
*
547767 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCCTTAAGTCCAATATCGTTGGCCTTGAATC
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT-CAATATCGTTGGCCTTGAATC
* * * *
547832 AGCGTATTGGCATCTTTAA-CAT-TCCT-AAGCCCAATG
65 AGCATATTGGCA-CCTTAACCATCT-TTAAAACCCAATG
* ** * * * * * * *
547868 TCGTTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGTCGCTGACCATGAATC
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC-AATATCGTTGGCCTTGAATC
547931 AGCA
65 AGCA
547935 CATTATCATT
Statistics
Matches: 221, Mismatches: 42, Indels: 15
0.79 0.15 0.05
Matches are distributed among these distances:
98 1 0.00
99 29 0.13
100 3 0.01
101 108 0.49
102 80 0.36
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (101 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCAATATCGTTGGCCTTGAATCA
GCATATTGGCACCTTAACCATCTTTAAAACCCAATG
Found at i:548737 original size:19 final size:18
Alignment explanation
Indices: 548713--548775 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
548703 AAACAAAAAA
*
548713 TGTATCGATACATAAGTG
1 TGTATCAATACATAAGTG
548731 TTGTATCAATAC--AA---
1 -TGTATCAATACATAAGTG
*
548745 TGTATCGATACATAAGTG
1 TGTATCAATACATAAGTG
548763 CTGTATCAATACA
1 -TGTATCAATACA
548776 ATGTATCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (18 bp):
TGTATCAATACATAAGTG
Found at i:548752 original size:32 final size:32
Alignment explanation
Indices: 548711--548782 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
548701 ATAAACAAAA
*
548711 AATGTATCGATACATAAGTGTTGTATCAATAC
1 AATGTATCGATACATAAGTGCTGTATCAATAC
548743 AATGTATCGATACATAAGTGCTGTATCAATAC
1 AATGTATCGATACATAAGTGCTGTATCAATAC
548775 AATGTATC
1 AATGTATC
548783 ACTACAAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGCTGTATCAATAC
Found at i:555240 original size:10 final size:10
Alignment explanation
Indices: 555205--555248 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
555195 ACACATAAAC
555205 CAAAAAAAAA
1 CAAAAAAAAA
*
555215 CAAAACAAAA
1 CAAAAAAAAA
555225 CAAAAAAAAA
1 CAAAAAAAAA
555235 CAAAAAAACAA
1 CAAAAAAA-AA
555246 CAA
1 CAA
555249 CGCAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 26 0.84
11 5 0.16
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:555241 original size:31 final size:30
Alignment explanation
Indices: 555201--555262 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
555191 GCAAACACAT
*
555201 AAACCAAAAAAAAACAAAACAAAACAAAAAA
1 AAACAAAAAAAAAACAAAACAAAA-AAAAAA
* **
555232 AAACAAAAAAACAACAACGCAAAAAAAAAA
1 AAACAAAAAAAAAACAAAACAAAAAAAAAA
555262 A
1 A
555263 GAGAATACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (30 bp):
AAACAAAAAAAAAACAAAACAAAAAAAAAA
Found at i:555247 original size:26 final size:27
Alignment explanation
Indices: 555208--555260 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
555198 CATAAACCAA
555208 AAAAAAACAAAACAAAACAAAAAAAAAC
1 AAAAAAAC-AAACAAAACAAAAAAAAAC
**
555236 AAAAAAAC-AACAACGCAAAAAAAAA
1 AAAAAAACAAACAAAACAAAAAAAAA
555261 AAGAGAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
28 8 0.35
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (27 bp):
AAAAAAACAAACAAAACAAAAAAAAAC
Found at i:555262 original size:5 final size:5
Alignment explanation
Indices: 555186--555239 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
555176 ATGAAAAAGT
* *
555186 CAAAA GCAAACA CATAAA CCAAAA AAAAA CAAAA CAAAA CAAAA AAAAA
1 CAAAA -CAAA-A CA-AAA -CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
555235 CAAAA
1 CAAAA
555240 AAACAACAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
5 26 0.63
6 10 0.24
7 5 0.12
ACGTcount: A:0.78, C:0.19, G:0.02, T:0.02
Consensus pattern (5 bp):
CAAAA
Found at i:555278 original size:25 final size:26
Alignment explanation
Indices: 555250--555299 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
555240 AAACAACAAC
555250 GCAAAAAAAAAAAGAGAAT-ACAAAG
1 GCAAAAAAAAAAAGAGAATAACAAAG
** *
555275 GCAAAATCAAAAAGGGAATAACAAA
1 GCAAAAAAAAAAAGAGAATAACAAA
555300 AGTCGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.68, C:0.10, G:0.16, T:0.06
Consensus pattern (26 bp):
GCAAAAAAAAAAAGAGAATAACAAAG
Found at i:556588 original size:34 final size:33
Alignment explanation
Indices: 556510--556664 Score: 215
Period size: 34 Copynumber: 4.6 Consensus size: 33
556500 TTCAAATATC
* *
556510 TCTTCTCAAAGTCCATGACTCTGTGGCATC-TTT
1 TCTT-TCAAAGTCCACGACTCAGTGGCATCTTTT
556543 TC-TTCAAAGTCCACGACTCAGTGGCATCTTTT
1 TCTTTCAAAGTCCACGACTCAGTGGCATCTTTT
556575 TCTGTTCAAAGTCCACGACTCAGTGGCATCTTTT
1 TCT-TTCAAAGTCCACGACTCAGTGGCATCTTTT
*
556609 TTTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
1 TCT-TTCAAAGTCCACGACTCAGTGGCATCTTTT
*
556643 CTCTTTCCAAAGTCCACAACTC
1 -TCTTT-CAAAGTCCACGACTC
556665 CGTGACACCC
Statistics
Matches: 111, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.21
32 6 0.05
33 2 0.02
34 64 0.58
35 16 0.14
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.35
Consensus pattern (33 bp):
TCTTTCAAAGTCCACGACTCAGTGGCATCTTTT
Found at i:556719 original size:34 final size:33
Alignment explanation
Indices: 556676--557381 Score: 459
Period size: 34 Copynumber: 22.8 Consensus size: 33
556666 GTGACACCCA
*
556676 TTTAAGCCCACAACTCTGTGGCATTCTTTTTCCT
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
*
556710 TTTAAGCCCACAACTCCGTGGCACTCTTTTTCTT
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
* * *
556744 TTTAAGTCCATAACTCTGTGGCA------TCCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* * *
556771 TTTAAGCCCACAACTTCGTGACATTCATTTTCCT
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
556805 TTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
* **
556839 TTTAAGTCCACAACTTTGTGGCA------TCCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
556866 TTTAAGCCCACAACTCCGTGGCA------TCCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* * *
556893 TTTAAGCCCGCAACTCCATGGCACTCTTTTCCCT
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
* * *
556927 TTTAAGTCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
*
556960 TTTAAAGCCCACAACTTCGTGGCA-C-----CCT
1 TTT-AAGCCCACAACTCCGTGGCATCTTTTTCCT
556988 TTTAA-CTCCACAACTCCGTGGCATC-TTTTCTCT
1 TTTAAGC-CCACAACTCCGTGGCATCTTTTTC-CT
* * *
557021 TTTAAGTCCACAACTCCATGGCATCTTGTTCCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* * * * *
557054 TTTCAGTCCACAACTTCGTGGCA-CCTTTTCTT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* * *
557086 TTTAAG-TCACGACTCTGTGGCA-C-----CCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* * *
557112 TTTAAGCCCATAACTTCGTGGCACTCTTTTTCCC
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
* *
557146 TTTAAGTCCACGACTCCGTGGCA-C-----CCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* *
557173 TTTAAGCCCACAACTTCGTGGCACTCTTTTTCCC
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
* **
557207 TTTAAGTCCATGACTCCGTGGCA-C-----CCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* *
557234 TTTAAGCCCACAACTTCGTGGCACTCTTTTTCCC
1 TTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCT
* *
557268 TTTAAGTCTACAACTCCGTGGCA-C-----CCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* * *
557295 TTGAAGCTCACAACTTCGTGGCA-C-----CCT
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
*
557322 TTTAAGTCCACAACTCCGTGGCATCTTTTTCC-
1 TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
* *
557354 TTTAAGTCCACAACTCCGTGGCACCTTT
1 TTTAAGCCCACAACTCCGTGGCATCTTT
557382 AAAACCAATG
Statistics
Matches: 531, Mismatches: 89, Indels: 106
0.73 0.12 0.15
Matches are distributed among these distances:
26 9 0.02
27 184 0.35
28 7 0.01
29 3 0.01
31 13 0.02
32 42 0.08
33 59 0.11
34 214 0.40
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.35
Consensus pattern (33 bp):
TTTAAGCCCACAACTCCGTGGCATCTTTTTCCT
Found at i:556727 original size:61 final size:60
Alignment explanation
Indices: 556621--557344 Score: 478
Period size: 61 Copynumber: 11.8 Consensus size: 60
556611 TCTTCAAAGT
* * * * *
556621 CCACGACTCAGTGGCATC-TTTTCTCTTTCCAAAGTCCACAACTCCGTGACACCCATTTAAGC
1 CCACAACTCTGTGGCATCTTTTTC-CTTT--TAAGTCCACAACTCCGTGGCACCCTTTTAAGC
*
556683 CCACAACTCTGTGGCATTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTTA
1 CCACAACTCTGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-C-----C-TTTTA
*
556748 AGT
58 AGC
* * * *
556751 CCATAACTCTGTGGCA------TCCTTTTAAGCCCACAACTTCGTGACATTCATTTTCCTTTTAA
1 CCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA--C-----CCTTTTAA
556810 GC
59 GC
* ** *
556812 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCATCCTTTTAAGC
1 CCACAACTCTGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * * *
556873 CCACAACTCCGTGGCA------TCCTTTTAAGCCCGCAACTCCATGGCACTCTTTTCCCTTTTAA
1 CCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA-------CCCTTTTAA
*
556932 GT
59 GC
* * * * *
556934 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCACCCTTTTAA-C
1 CCACAACTCTGTGGCATCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
556994 TCCACAACTCCGTGGCATC-TTTTCTCTTTTAAGTCCACAACTCCATGGCATCTTGTTCCTTTTC
1 -CCACAACTCTGTGGCATCTTTTTC-CTTTTAAGTCCACAACTCCGTGGCA-C-----CCTTTTA
*
557058 AGT
58 AGC
* * * *
557061 CCACAACT-TCGTGGCA-CCTTTTCTTTTTAAGT-CACGACTCTGTGGCACCCTTTTAAGC
1 CCACAACTCT-GTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
557119 CCATAACT-TCGTGGCACTCTTTTTCCCTTTAAGTCCACGACTCCGTGGCACCCTTTTAAGC
1 CCACAACTCT-GTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* **
557180 CCACAACT-TCGTGGCACTCTTTTTCCCTTTAAGTCCATGACTCCGTGGCACCCTTTTAAGC
1 CCACAACTCT-GTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
557241 CCACAACT-TCGTGGCACTCTTTTTCCCTTTAAGTCTACAACTCCGTGGCACCCTTTGAAGC
1 CCACAACTCT-GTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
*
557302 TCACAACT-TCGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCA
1 CCACAACTCT-GTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
557345 TCTTTTTCCT
Statistics
Matches: 555, Mismatches: 57, Indels: 108
0.77 0.08 0.15
Matches are distributed among these distances:
54 46 0.08
58 23 0.04
59 1 0.00
60 35 0.06
61 303 0.55
62 16 0.03
63 8 0.01
64 17 0.03
65 9 0.02
66 26 0.05
67 9 0.02
68 62 0.11
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (60 bp):
CCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
Found at i:556775 original size:95 final size:92
Alignment explanation
Indices: 556652--557381 Score: 520
Period size: 95 Copynumber: 7.9 Consensus size: 92
556642 TCTCTTTCCA
* * *
556652 AAGTCCACAACTCCGTGACACCCATTTAAGCCCACAAC-TCTGTGGCATTCTTTTTCCTTTTAAG
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACTTC-GTGGCA--C-TTTTCCTTTTAAG
*
556716 CCCACAACTCCGTGGCACTCTTTTTCTTTTT
62 CCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * *
556747 AAGTCCATAACTCTGTGGCATCCTTTTAAGCCCACAACTTCGTGACATTCATTTTCCTTTTAAGC
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACTTCGTGGCA--C-TTTTCCTTTTAAGC
556812 CCACAACTCCGTGGCACTCTTTTTCCTTTT
63 CCACAACTCCGTGGCACTCTTTTTCCTTTT
** * *
556842 AAGTCCACAACTTTGTGGCATCCTTTTAAGCCCACAACTCCGTGGCA----TCCTTTTAAGCCCG
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACTTCGTGGCACTTTTCCTTTTAAGCCCA
* *
556903 CAACTCCATGGCACTCTTTTCCCTTTT
66 CAACTCCGTGGCACTCTTTTTCCTTTT
*
556930 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCAC----CCTTTT
1 AAGTCCACAACTCCGTGGCA------TCCTTTT-AAGCCCACAACTTCGTGGCACTTTTCCTTTT
556991 AA-CTCCACAACTCCGTGGCA-TC-TTTTCTCTTTT
59 AAGC-CCACAACTCCGTGGCACTCTTTTTC-CTTTT
* * * *
557024 AAGTCCACAACTCCATGGCATCTTGTTCCTTTTCAGTCCACAACTTCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCA------TCCTTTTAAGCCCACAACTTCGTGGCA-CTTTTCCTTTT
* * *
557089 AAG-TCACGACTCTGTGGCA--C-----CCTTTT
59 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * * * *
557115 AAGCCCATAACTTCGTGGCACTCTTTTTCCCTTTAAGTCCACGACTCCGTGGCAC----CCTTTT
1 AAGTCCACAACTCCGTGGCA-------TCCTTTTAAGCCCACAACTTCGTGGCACTTTTCCTTTT
* *
557176 AAGCCCACAACTTCGTGGCACTCTTTTTCCCTTT
59 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
** * * *
557210 AAGTCCATGACTCCGTGGCACCCTTTTAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTAAGT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACTTCGTGGCA--C-TTTTCCTTTTAAGC
* *
557275 CTACAACTCCGTGGCA--C-----CCTTTG
63 CCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * *
557298 AAG-CTCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCC-TTTAAGT
1 AAGTC-CACAACTCCGTGGCATCCTTTTAAGCCCACAACTTCGTGGCA-C-TTTTCCTTTTAAGC
557361 CCACAACTCCGTGGCAC-CTTT
63 CCACAACTCCGTGGCACTCTTT
557382 AAAACCAATG
Statistics
Matches: 530, Mismatches: 67, Indels: 81
0.78 0.10 0.12
Matches are distributed among these distances:
86 22 0.04
87 19 0.04
88 134 0.25
90 2 0.00
91 22 0.04
92 29 0.05
93 23 0.04
94 44 0.08
95 212 0.40
96 3 0.01
97 13 0.02
98 7 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (92 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGCCCACAACTTCGTGGCACTTTTCCTTTTAAGCCCA
CAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:556876 original size:27 final size:27
Alignment explanation
Indices: 556835--557351 Score: 165
Period size: 27 Copynumber: 17.3 Consensus size: 27
556825 GCACTCTTTT
* **
556835 TCCTTTTAAGTCCACAACTTTGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
556862 TCCTTTTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
* *
556889 TCCTTTTAAGCCCGCAACTCCATGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
556916 CTCTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 ------T-CCTTTTAAGCCCACAACTCCGTGGCA
* *
556950 CCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCA
1 ------TCCTTTT-AAGCCCACAACTCCGTGGCA
*
556984 CCCTTTTAA-CTCCACAACTCCGTGGCA
1 TCCTTTTAAGC-CCACAACTCCGTGGCA
* *
557011 TCTTTTCTCTTTTAAGTCCACAACTCCATGGCA
1 -----TC-CTTTTAAGCCCACAACTCCGTGGCA
* * *
557044 TCTTGTTCCTTTTCAGTCCACAACTTCGTGGCA
1 ------TCCTTTTAAGCCCACAACTCCGTGGCA
* * * *
557077 CCTTTTCTTTTTAAG-TCACGACTCTGTGGCA
1 -----TCCTTTTAAGCCCACAACTCCGTGGCA
* * *
557108 CCCTTTTAAGCCCATAACTTCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
* * *
557135 CTCTTTTTCCCTTTAAGTCCACGACTCCGTGGCA
1 -------TCCTTTTAAGCCCACAACTCCGTGGCA
* *
557169 CCCTTTTAAGCCCACAACTTCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
* * **
557196 CTCTTTTTCCCTTTAAGTCCATGACTCCGTGGCA
1 -------TCCTTTTAAGCCCACAACTCCGTGGCA
* *
557230 CCCTTTTAAGCCCACAACTTCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
* * *
557257 CTCTTTTTCCCTTTAAGTCTACAACTCCGTGGCA
1 -------TCCTTTTAAGCCCACAACTCCGTGGCA
* * * *
557291 CCCTTTGAAGCTCACAACTTCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
* *
557318 CCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
557345 TCTTTTT
1 TCCTTTT
557352 CCTTTAAGTC
Statistics
Matches: 370, Mismatches: 81, Indels: 78
0.70 0.15 0.15
Matches are distributed among these distances:
26 9 0.02
27 168 0.45
28 5 0.01
31 12 0.03
32 12 0.03
33 50 0.14
34 114 0.31
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.34
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:557257 original size:122 final size:120
Alignment explanation
Indices: 556621--557344 Score: 533
Period size: 122 Copynumber: 5.9 Consensus size: 120
556611 TCTTCAAAGT
* * * * *
556621 CCACGACTCAGTGGCATC-TTTTCTCTTTCCAAAGTCCACAACTCCGTGACACCCATTTAAGCCC
1 CCACAACTCCGTGGCATCTTTTTCCCTTT---AAGTCCACAACTCCGTGGCACCCTTTTAAGCCC
* *
556685 ACAAC-TCTGTGGCATTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTTAA
63 ACAACTTC-GTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-C-----C-TTTTAA
*
556749 GT
119 GC
* * * * * *
556751 CCATAACTCTGTGGCA------TCCTTTTAAGCCCACAACTTCGTGACATTCATTTTCCTTTTAA
1 CCACAACTCCGTGGCATCTTTTTCCCTTTAAGTCCACAACTCCGTGGCA--C-----CCTTTTAA
* ** *
556810 GCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTTGTGGCATCCTTTTAAGC
59 GCCCACAACTTCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * * *
556873 CCACAACTCCGTGGCA------TCCTTTTAAGCCCGCAACTCCATGGCACTCTTTTCCCTTTTAA
1 CCACAACTCCGTGGCATCTTTTTCCCTTTAAGTCCACAACTCCGTGGCA-------CCCTTTTAA
* * * * *
556932 GTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTTCGTGGCACCCTTTTAA-C
59 GCCCACAACTTCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
556994 TCCACAACTCCGTGGCATC-TTTTCTCTTTTAAGTCCACAACTCCATGGCATCTTGTTCCTTTTC
1 -CCACAACTCCGTGGCATCTTTTTC-CCTTTAAGTCCACAACTCCGTGGCA-C-----CCTTTTA
* * * *
557058 AGTCCACAACTTCGTGGCACC-TTTTCTTTTTAAGT-CACGACTCTGTGGCACCCTTTTAAGC
58 AGCCCACAACTTCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * *
557119 CCATAACTTCGTGGCACTCTTTTTCCCTTTAAGTCCACGACTCCGTGGCACCCTTTTAAGCCCAC
1 CCACAACTCCGTGGCA-TCTTTTTCCCTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCAC
* **
557184 AACTTCGTGGCACTCTTTTTCCCTTTAAGTCCATGACTCCGTGGCACCCTTTTAAGC
65 AACTTCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
* * * *
557241 CCACAACTTCGTGGCACTCTTTTTCCCTTTAAGTCTACAACTCCGTGGCACCCTTTGAAGCTCAC
1 CCACAACTCCGTGGCA-TCTTTTTCCCTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCAC
557306 AACTTCGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCA
65 AACTTCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
557345 TCTTTTTCCT
Statistics
Matches: 508, Mismatches: 53, Indels: 81
0.79 0.08 0.13
Matches are distributed among these distances:
115 23 0.05
119 25 0.05
120 2 0.00
121 24 0.05
122 228 0.45
123 1 0.00
124 37 0.07
125 33 0.06
126 15 0.03
127 31 0.06
128 24 0.05
129 51 0.10
130 14 0.03
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (120 bp):
CCACAACTCCGTGGCATCTTTTTCCCTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACA
ACTTCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGC
Found at i:557451 original size:49 final size:49
Alignment explanation
Indices: 557378--557959 Score: 441
Period size: 52 Copynumber: 11.8 Consensus size: 49
557368 TCCGTGGCAC
* * * *
557378 CTTTAAAACCAATGTCGCTAGCCTTGAATCAACACATTGGCATCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
557427 CTTTAAGACCAATATCGCTGGCCTTGAATTAGCATAATGGCACCTTCGACAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CAT
*
557479 CTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGG------CA-
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
557521 C---AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
557567 CTTTAAGACCGATGTCGTTGGCCTTGAATTAGCACAATGGCACCTTAACCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT---CAT
* * * *
557619 CTTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGA-CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * *
557669 CTTTAAGTCCAATATCGCTGGCCGTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGC-AC-CT-TCAT
* * * * **
557721 CTTTAAAACCAATGTCGCTGGCCTTGAATTAACATATTGGTGCCTTCGTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCAT
* *
557773 CTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGAACCTTCAT
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * ** ** * *
557822 CCTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATTTTTAA
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * ** *
557871 CATTCCTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCA--TTCTT
1 C-TT--TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
557921 CTTCAAGTCTAATGTCGCTAGCCATGAATCAGCACATTG
1 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTG
557960 TCATTCTTCG
Statistics
Matches: 423, Mismatches: 85, Indels: 52
0.76 0.15 0.09
Matches are distributed among these distances:
39 32 0.08
42 1 0.00
43 2 0.00
45 2 0.00
46 1 0.00
47 28 0.07
49 144 0.34
50 13 0.03
51 4 0.01
52 163 0.39
53 33 0.08
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:557608 original size:88 final size:90
Alignment explanation
Indices: 557435--557609 Score: 264
Period size: 88 Copynumber: 2.0 Consensus size: 90
557425 ATCTTTAAGA
*
557435 CCAATATCGCTGGCCTTGAATTAGCATAATGGCACCTTCGACATCTTTAAGACCAATGTCGCTAG
1 CCAATATCGCTGGCCTTGAATCAGCATAATGGCACCTTC-ACATCTTTAAGACCAATGTCGCTAG
*
557500 CCTTGAATCAGCACATTGGCACAAGC
65 CCTTGAATCAGCACAATGGCACAAGC
* * * *
557526 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TC-CATCTTTAAGACCGATGTCGTTGGC
1 CCAATATCGCTGGCCTTGAATCAGCATAATGGCACCTTCACATCTTTAAGACCAATGTCGCTAGC
*
557589 CTTGAATTAGCACAATGGCAC
66 CTTGAATCAGCACAATGGCAC
557610 CTTAACCATC
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 41 0.53
90 2 0.03
91 34 0.44
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (90 bp):
CCAATATCGCTGGCCTTGAATCAGCATAATGGCACCTTCACATCTTTAAGACCAATGTCGCTAGC
CTTGAATCAGCACAATGGCACAAGC
Found at i:557722 original size:102 final size:101
Alignment explanation
Indices: 557526--557915 Score: 354
Period size: 101 Copynumber: 3.8 Consensus size: 101
557516 TGGCACAAGC
* * * * *
557526 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGCTGGCCT
* *
557591 TGAATTAGCACAATGGCACCTTAACCATCTTTAAAA
66 TGAATCAGCACATTGGCACCTTAACCATCTTTAAAA
* * * * *
557627 CCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCC
1 -CCAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGCTGGCC
* * ** ***
557692 GTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAAA
65 TTGAATCAGCACATTGGCACCTTAACCATCTTTAAAA
* * * * *
557729 CCAATGTCGCTGGCCTTGAATTAACATATTGGTGCCTTCGTCATCTTTAAAACCAATGTCGCTGG
1 CCAATGTCGCTGGCCTTGAATCAGCATATT-G-G-CATCTTCATCTTTAAGACCAATGTCGCTGG
* * **
557794 CCTTGAATCAGCACATTGGAACCTT---CATCCTTAAGT
63 CCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAAA
* * * * * * * *
557830 CCAATATCGTTGGCCTTGAATCAGCGTATTGGCATTTTTAACATTCCTAAGCCCAATGTCGTTGG
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC-TT--TAAGACCAATGTCGCTGG
**
557895 CCTTGTCTCAGCACATTGGCA
63 CCTTGAATCAGCACATTGGCA
557916 TTCTTCTTCA
Statistics
Matches: 229, Mismatches: 53, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
98 5 0.02
99 3 0.01
100 1 0.00
101 91 0.40
102 83 0.36
103 1 0.00
104 45 0.20
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (101 bp):
CCAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTCGCTGGCCT
TGAATCAGCACATTGGCACCTTAACCATCTTTAAAA
Found at i:557828 original size:153 final size:151
Alignment explanation
Indices: 557526--557863 Score: 444
Period size: 153 Copynumber: 2.2 Consensus size: 151
557516 TGGCACAAGC
* * *
557526 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAAACCAATGTCGCTGGCCT
* * *
557591 TGAATTAGCACAATGGCACCTTAACCATCTTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACA
66 TGAATTAACACAATGGCACCTTAACCATCTTTAAAACCCAATGTCGCTGGCCTTGAATCAGCACA
* * *
557656 TTGGCATCTTCATCTTTAAGT
131 TTGGAACCTTCATCCTTAAGT
* * * *
557677 CCAATATCGCTGGCCGTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAAACCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-CCATCTTTAAAACCAATGTCGCTGG
* * ** ***
557742 CCTTGAATTAACATATTGGTGCCTTCGTCATCTTTAAAA-CCAATGTCGCTGGCCTTGAATCAGC
63 CCTTGAATTAACACAATGGCACCTTAACCATCTTTAAAACCCAATGTCGCTGGCCTTGAATCAGC
557806 ACATTGGAACCTTCATCCTTAAGT
128 ACATTGGAACCTTCATCCTTAAGT
* *
557830 CCAATATCGTTGGCCTTGAATCAGCGTATTGGCA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA
557864 TTTTTAACAT
Statistics
Matches: 160, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
151 32 0.20
152 1 0.01
153 75 0.47
154 52 0.32
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (151 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCCATCTTTAAAACCAATGTCGCTGGCCT
TGAATTAACACAATGGCACCTTAACCATCTTTAAAACCCAATGTCGCTGGCCTTGAATCAGCACA
TTGGAACCTTCATCCTTAAGT
Found at i:557913 original size:153 final size:154
Alignment explanation
Indices: 557526--557913 Score: 408
Period size: 153 Copynumber: 2.5 Consensus size: 154
557516 TGGCACAAGC
* * * * * * *
557526 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C-CT-CCATCTTTAAGACCGATGTCGTTGG
1 CCAATATCGCTGGCCGTGAATCAGCATATTGGCATCTTTAACATCTCTAAAACCAATGTCGCTGG
* * * ** *** * *
557588 CCTTGAATTAGCACAATGGCACCTTAACCATCTTTAAAACCCAATGTTGTTGGCCTTGAATCAGC
66 CCTTGAATCAACACATTGGTGCCTTCGTCATCTTTAAAACCCAATGTCGCTGGCCTTGAATCAGC
* * *
557653 ACATTGGCATCTTCATCTTTAAGT
131 ACATTGGAACCTTCATCCTTAAGT
* ** *
557677 CCAATATCGCTGGCCGTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAAACCAATGTCGCTGG
1 CCAATATCGCTGGCCGTGAATCAGCATATTGGCATCTTTAACATCTCTAAAACCAATGTCGCTGG
* *
557742 CCTTGAATTAACATATTGGTGCCTTCGTCATCTTTAAAA-CCAATGTCGCTGGCCTTGAATCAGC
66 CCTTGAATCAACACATTGGTGCCTTCGTCATCTTTAAAACCCAATGTCGCTGGCCTTGAATCAGC
557806 ACATTGGAACCTTCATCCTTAAGT
131 ACATTGGAACCTTCATCCTTAAGT
* * * * ** *
557830 CCAATATCGTTGGCCTTGAATCAGCGTATTGGCATTTTTAACAT-TCCTAAGCCCAATGTCGTTG
1 CCAATATCGCTGGCCGTGAATCAGCATATTGGCATCTTTAACATCT-CTAAAACCAATGTCGCTG
** *
557894 GCCTTGTCTCAGCACATTGG
65 GCCTTGAATCAACACATTGG
557914 CATTCTTCTT
Statistics
Matches: 197, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
151 32 0.16
152 2 0.01
153 111 0.56
154 52 0.26
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (154 bp):
CCAATATCGCTGGCCGTGAATCAGCATATTGGCATCTTTAACATCTCTAAAACCAATGTCGCTGG
CCTTGAATCAACACATTGGTGCCTTCGTCATCTTTAAAACCCAATGTCGCTGGCCTTGAATCAGC
ACATTGGAACCTTCATCCTTAAGT
Found at i:558832 original size:13 final size:13
Alignment explanation
Indices: 558814--558841 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
558804 CATTCTTCAA
558814 TGTATTGATACAT
1 TGTATTGATACAT
558827 TGTATTGATACAT
1 TGTATTGATACAT
558840 TG
1 TG
558842 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (13 bp):
TGTATTGATACAT
Found at i:565293 original size:20 final size:19
Alignment explanation
Indices: 565247--565303 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
565237 CTTTATCGAT
*
565247 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
565266 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
565285 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
565304 AAACTAGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:565367 original size:13 final size:13
Alignment explanation
Indices: 565349--565378 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
565339 GATACATAAG
*
565349 ACATTGTATTGAT
1 ACATTGTATCGAT
565362 ACATTGTATCGAT
1 ACATTGTATCGAT
565375 ACAT
1 ACAT
565379 GATGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:565388 original size:33 final size:33
Alignment explanation
Indices: 565332--565399 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
565322 CTACCACTGT
**
565332 TTGTATCGATACATAAGACATTGTATTGATACA
1 TTGTATCGATACATAAGACATTGTATCAATACA
*
565365 TTGTATCGATACATGATGA-ATTGTATCAATACA
1 TTGTATCGATACAT-AAGACATTGTATCAATACA
565398 TT
1 TT
565400 TCTTATAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATAAGACATTGTATCAATACA
Found at i:567645 original size:20 final size:21
Alignment explanation
Indices: 567597--567646 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
567587 AAGATGATAT
*
567597 TAAAAAATTAGCTAATGAAAA
1 TAAAGAATTAGCTAATGAAAA
*
567618 TAATGAATTAGCTAA-GAAAA
1 TAAAGAATTAGCTAATGAAAA
567638 -ACAAGAATT
1 TA-AAGAATT
567647 TGCATGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 11 0.44
21 13 0.52
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (21 bp):
TAAAGAATTAGCTAATGAAAA
Found at i:573460 original size:21 final size:22
Alignment explanation
Indices: 573420--573460 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
573410 TTTTTTAAGA
573420 TTTGAGAAAAGGGGAGAAATGC
1 TTTGAGAAAAGGGGAGAAATGC
* *
573442 TTTGATAAAGGGGGA-AAAT
1 TTTGAGAAAAGGGGAGAAAT
573461 ATGTTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.02, G:0.34, T:0.22
Consensus pattern (22 bp):
TTTGAGAAAAGGGGAGAAATGC
Found at i:574070 original size:19 final size:19
Alignment explanation
Indices: 574048--574102 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
574038 ACATTATGCT
***
574048 TTGTATCGATACATGTTTA
1 TTGTATCGATACATGACAA
574067 TTGTATCGATACATGGACAA
1 TTGTATCGATACAT-GACAA
574087 TTGTATCGATACATGA
1 TTGTATCGATACATGA
574103 AACTGGCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATGACAA
Found at i:574091 original size:20 final size:20
Alignment explanation
Indices: 574048--574101 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
574038 ACATTATGCT
***
574048 TTGTATCGATACAT-GTTTA
1 TTGTATCGATACATGGACAA
574067 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
574087 TTGTATCGATACATG
1 TTGTATCGATACATG
574102 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:574165 original size:13 final size:13
Alignment explanation
Indices: 574147--574176 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
574137 GATACATAAG
574147 ACATTGTATCGAT
1 ACATTGTATCGAT
574160 ACATTGTATCGAT
1 ACATTGTATCGAT
574173 ACAT
1 ACAT
574177 GATGAATTGT
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:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:574172 original size:33 final size:33
Alignment explanation
Indices: 574130--574197 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
574120 CTACCACTGT
574130 TTGTATCGATACAT-AAGACATTGTATCGATACA
1 TTGTATCGATACATGAAGA-ATTGTATCGATACA
*
574163 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGAAGAATTGTATCGATACA
574196 TT
1 TT
574198 TCTTATAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGAAGAATTGTATCGATACA
Found at i:576451 original size:50 final size:49
Alignment explanation
Indices: 576376--576503 Score: 202
Period size: 50 Copynumber: 2.6 Consensus size: 49
576366 ATTTGTATCA
576376 ATACATTCTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGCATTG
1 ATACATT-TTCATTGTATCGATACATTCTAGGTTTTACCCAGATGCATTG
* *
576426 ATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATTG
1 ATACATT-TTCATTGTATCGATACATTCTAGGTTTTACCCAGATGCATTG
*
576476 ATACATTTCTCAATGTATCGATACATTC
1 ATACATTT-TCATTGTATCGATACATTC
576504 AGGCATTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 1 0.01
50 72 0.99
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (49 bp):
ATACATTTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGCATTG
Found at i:579048 original size:79 final size:77
Alignment explanation
Indices: 578780--579051 Score: 266
Period size: 78 Copynumber: 3.5 Consensus size: 77
578770 CAAAACACTG
* * * * * **
578780 ATTTTTCATAATCGAAGACACTCCAACCC-GTTATTTCTAAGGGATACTCCAATCCTGGCTTTAT
1 ATTTTTCATCATCGAGGATACTCCAACCCTGTTATTTCGAGGGGATACTCCAA-CCCCGCTTTAT
**
578844 TTCTAAAATATTG
65 TTCTAAAATATCA
** * * *
578857 ATTTTTCA-CAGTCGAGGATACTCCAACCCCATTATTTCTGAGGGGATACTCTAACCCCGATTTT
1 ATTTTTCATCA-TCGAGGATACTCCAACCCTGTTATTTC-GAGGGGATACTCCAACCCCGCTTTA
* *
578921 TTTCCAAAATACCA
64 TTTCTAAAATATCA
* *
578935 A-TTTTCGACCATC-AGGGTTACTCCAA-CCTCGTTATTTTCGAGGGGATACTCCAACCCCAGCT
1 ATTTTTC-ATCATCGA-GGATACTCCAACCCT-GTTA-TTTCGAGGGGATACTCCAACCCC-GCT
578997 TTATTTCTAAAATATCA
61 TTATTTCTAAAATATCA
*
579014 ATTTTTCATCATCGGGGATACTCCAACCCTGTTATTTC
1 ATTTTTCATCATCGAGGATACTCCAACCCTGTTATTTC
579052 CGAAAGCAAA
Statistics
Matches: 157, Mismatches: 26, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
76 1 0.01
77 32 0.20
78 62 0.39
79 54 0.34
80 8 0.05
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (77 bp):
ATTTTTCATCATCGAGGATACTCCAACCCTGTTATTTCGAGGGGATACTCCAACCCCGCTTTATT
TCTAAAATATCA
Found at i:579065 original size:79 final size:78
Alignment explanation
Indices: 578780--579069 Score: 259
Period size: 79 Copynumber: 3.7 Consensus size: 78
578770 CAAAACACTG
* * * * **
578780 ATTTTTCATAATCGAAGACACTCCAACCC-GTTATTT-CTAAGGGATACTCCAATCCTGGCTTTA
1 ATTTTTCATCATCGAGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCCAA-CCCCGCTTTA
**
578843 TTTCTAAAATATTG
65 TTTCTAAAATATCA
** * * * * *
578857 ATTTTTCA-CAGTCGAGGATACTCCAACCCCATTATTTCTGAGGGGATACTCTAACCCCGATTTT
1 ATTTTTCATCA-TCGAGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCCAACCCCGCTTTA
* *
578921 TTTCCAAAATACCA
65 TTTCTAAAATATCA
* * * *
578935 A-TTTTCGACCATC-AGGGTTACTCCAA-CCTCGTTATTTTCGAGGGGATACTCCAACCCCAGCT
1 ATTTTTC-ATCATCGA-GGATACTCCAACCCT-GTTATTTCCGAAGGGATACTCCAACCCC-GCT
578997 TTATTTCTAAAATATCA
62 TTATTTCTAAAATATCA
* * * *
579014 ATTTTTCATCATCGGGGATACTCCAACCCTGTTATTTCCGAAAGCAAACTCCAACC
1 ATTTTTCATCATCGAGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCCAACC
579070 TTGTTATTTT
Statistics
Matches: 168, Mismatches: 34, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
76 1 0.01
77 32 0.19
78 60 0.36
79 67 0.40
80 8 0.05
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (78 bp):
ATTTTTCATCATCGAGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCCAACCCCGCTTTAT
TTCTAAAATATCA
Found at i:581166 original size:4 final size:4
Alignment explanation
Indices: 581157--581190 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
581147 TTTTAAGGTG
*
581157 TTTA TTTA TTTA TTTA TTCA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
581191 TGTTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:584177 original size:27 final size:27
Alignment explanation
Indices: 584143--584217 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
584133 TTCAAGGTGC
584143 CAGAATTTGAGAAATATAATGGGACCA
1 CAGAATTTGAGAAATATAATGGGACCA
*
584170 CAGGATTTGAGAAATATAATGGGACCA
1 CAGAATTTGAGAAATATAATGGGACCA
584197 CAGAATTTGAGAAATATAATG
1 CAGAATTTGAGAAATATAATG
584218 TAGCACACCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (27 bp):
CAGAATTTGAGAAATATAATGGGACCA
Found at i:591274 original size:13 final size:13
Alignment explanation
Indices: 591256--591281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
591246 CTATTTATGA
591256 TGTATCGATACAC
1 TGTATCGATACAC
591269 TGTATCGATACAC
1 TGTATCGATACAC
591282 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:591392 original size:22 final size:22
Alignment explanation
Indices: 591337--591392 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
591327 ACAGTGATCT
591337 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
591359 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
591380 ATGAACAGTGATG
1 ATGAACAGTGATG
591393 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:591399 original size:10 final size:10
Alignment explanation
Indices: 591380--591410 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
591370 GTATCGATAC
591380 ATGAACAGTG
1 ATGAACAGTG
*
591390 ATGAATAGTG
1 ATGAACAGTG
591400 ATGAACAGTG
1 ATGAACAGTG
591410 A
1 A
591411 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:591508 original size:53 final size:53
Alignment explanation
Indices: 591434--591570 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
591424 CTACTTCCAA
*
591434 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGGTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
591487 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
591540 TGTATCGATACATATTTTTGTGTATCGATAC
1 TGTATCGATACATA-TTTTGTGTATCGATAC
591571 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 63 0.81
54 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:591565 original size:20 final size:20
Alignment explanation
Indices: 591540--591610 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
591530 GCCAATGTCT
591540 TGTATCGATACATATTTTTG
1 TGTATCGATACATATTTTTG
**
591560 TGTATCGATAC-TATGCAATT-
1 TGTATCGATACATAT--TTTTG
*
591580 TGTATCGATACAT-TTATATG
1 TGTATCGATACATATT-TTTG
591600 TGTATCGATAC
1 TGTATCGATAC
591611 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.10
20 34 0.83
21 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:591676 original size:21 final size:21
Alignment explanation
Indices: 591650--591690 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
591640 GTCAACCTTG
591650 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
591671 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
591691 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:593334 original size:13 final size:13
Alignment explanation
Indices: 593316--593340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593306 ACTGAAGCAA
593316 TGTATCGATACAT
1 TGTATCGATACAT
593329 TGTATCGATACA
1 TGTATCGATACA
593341 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:597104 original size:13 final size:13
Alignment explanation
Indices: 597086--597111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
597076 CTATTTATGA
597086 TGTATCGATACAC
1 TGTATCGATACAC
597099 TGTATCGATACAC
1 TGTATCGATACAC
597112 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:597222 original size:22 final size:22
Alignment explanation
Indices: 597167--597222 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
597157 ACAGTGATCT
597167 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
597189 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
597210 ATGAACAGTGATG
1 ATGAACAGTGATG
597223 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:597229 original size:10 final size:10
Alignment explanation
Indices: 597210--597240 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
597200 GTATCGATAC
597210 ATGAACAGTG
1 ATGAACAGTG
*
597220 ATGAATAGTG
1 ATGAACAGTG
597230 ATGAACAGTG
1 ATGAACAGTG
597240 A
1 A
597241 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:597338 original size:53 final size:53
Alignment explanation
Indices: 597264--597400 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
597254 CTACTTCCAA
*
597264 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGGTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
597317 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
597370 TGTATCGATACATATTTTTGTGTATCGATAC
1 TGTATCGATACATA-TTTTGTGTATCGATAC
597401 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 63 0.81
54 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:597395 original size:20 final size:20
Alignment explanation
Indices: 597370--597440 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
597360 GCCAATGTCT
597370 TGTATCGATACATATTTTTG
1 TGTATCGATACATATTTTTG
**
597390 TGTATCGATAC-TATGCAATT-
1 TGTATCGATACATAT--TTTTG
*
597410 TGTATCGATACAT-TTATATG
1 TGTATCGATACATATT-TTTG
597430 TGTATCGATAC
1 TGTATCGATAC
597441 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.10
20 34 0.83
21 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:597506 original size:21 final size:21
Alignment explanation
Indices: 597480--597520 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
597470 GTCAACCTTG
597480 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
597501 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
597521 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:599208 original size:166 final size:163
Alignment explanation
Indices: 598848--599310 Score: 419
Period size: 167 Copynumber: 2.8 Consensus size: 163
598838 CAAAATCCCT
598848 TTTA-TTTCATGAGTTTTTCATTTTTCTCC-TAAATTCCTCCTATTTTCGAAATATG-AGATTTT
1 TTTATTTTCATGAGTTTTTCATTTTT-TCCTTAAATT-CTCCTATTTTCGAAATATGAAG-TTTT
* * * * * *
598910 -T-TTCTCCGTAAATTTTTTTTTCA-AGAGGA-TTTTCATCGGTTCAAAATTTTTAATATTCATC
63 CTATT-T-CATAAA---TATTTTCAGGGA-GATTTTTC-TTGGTTTAAAATTTTTAAAATTCATC
* * * * *
598971 AAGTATTATTATTTAACTCGAGTAAATCAATTTTAAAAAATTTA
121 AA-TATTGTCATTTAACTCCAGTAAATCAATTTTAAAAAAATCA
*
599015 TTTATTTTCATGAGTTTTCCATTTTTTCCTTAAATTCTCCTATTTTCGAAATATGAAGTTTTCTA
1 TTTATTTTCATGAGTTTTTCATTTTTTCCTTAAATTCTCCTATTTTCGAAATATGAAGTTTTCTA
*
599080 TTTCATAAATATTTTCAGGGAGATTTTTCTTGGTTTAAATTTTTTAAAATTCATCTAATATTGTC
66 TTTCATAAATATTTTCAGGGAGATTTTTCTTGGTTTAAAATTTTTAAAATTCATC-AATATTGTC
* *
599145 ATTTAA-TCCATGGTAAATTAGTTTTGAAAAAAATCA
130 ATTTAACTCCA--GTAAATCAATTTT-AAAAAAATCA
* * ** * *
599181 TTTATTTTCATGAGTTTTTTATTTTTTCCTTAAAATT-TCCCTGTTCCCAAAAAATTGAA-TTTT
1 TTTATTTTCATGAGTTTTTCATTTTTTCCTT-AAATTCT-CCTATTTTCGAAATA-TGAAGTTTT
* * * * *
599244 CTATTTCATAAAAATTTTC-GAGAAAATTTTTC-TGAGTTTAAAACTTTTAAAATTTATCAAATA
63 CTATTTCATAAATATTTTCAG-GGAGATTTTTCTTG-GTTTAAAATTTTTAAAATTCATC-AATA
599307 TTGT
125 TTGT
599311 TATAAAAATC
Statistics
Matches: 251, Mismatches: 29, Indels: 32
0.80 0.09 0.10
Matches are distributed among these distances:
163 3 0.01
164 42 0.17
165 20 0.08
166 41 0.16
167 109 0.43
168 34 0.14
169 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (163 bp):
TTTATTTTCATGAGTTTTTCATTTTTTCCTTAAATTCTCCTATTTTCGAAATATGAAGTTTTCTA
TTTCATAAATATTTTCAGGGAGATTTTTCTTGGTTTAAAATTTTTAAAATTCATCAATATTGTCA
TTTAACTCCAGTAAATCAATTTTAAAAAAATCA
Found at i:600540 original size:21 final size:20
Alignment explanation
Indices: 600514--600553 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
600504 AAAGGTCAAA
600514 ACCTAGAAAGTATCGATACAC
1 ACCTAG-AAGTATCGATACAC
*
600535 ACCTAGATGTATCGATACA
1 ACCTAGAAGTATCGATACA
600554 TATTATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
ACCTAGAAGTATCGATACAC
Found at i:600566 original size:20 final size:19
Alignment explanation
Indices: 600542--600614 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
600532 CACACCTAGA
600542 TGTATCGATACATATTATT
1 TGTATCGATACATATTATT
*
600561 TAGTATCGATACATGTT-TT
1 T-GTATCGATACATATTATT
* * * *
600580 TGGAATCGATACACACTGAAT
1 T-GTATCGATACATA-TTATT
600601 TGTATCGATACATA
1 TGTATCGATACATA
600615 AAACTGGCAG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 14 0.33
20 26 0.62
21 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATATTATT
Found at i:600589 original size:19 final size:20
Alignment explanation
Indices: 600545--600592 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
600535 ACCTAGATGT
*
600545 ATCGATACATATTATTTAGT
1 ATCGATACATATTATTTAGA
* *
600565 ATCGATACATGTT-TTTGGA
1 ATCGATACATATTATTTAGA
600584 ATCGATACA
1 ATCGATACA
600593 CACTGAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (20 bp):
ATCGATACATATTATTTAGA
Found at i:600678 original size:21 final size:20
Alignment explanation
Indices: 600652--600707 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
600642 GTATCGATAC
* *
600652 ATTGTATTGATACATACTTGA
1 ATTGTATCGATACATA-GTGA
* *
600673 ATTGTATCGGTACATAGTGC
1 ATTGTATCGATACATAGTGA
600693 ATTGTATCGATACAT
1 ATTGTATCGATACAT
600708 TAAGCCCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTGTATCGATACATAGTGA
Found at i:600916 original size:20 final size:20
Alignment explanation
Indices: 600891--600929 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
600881 CCAACAACTG
600891 AAGAAA-AGAAGAGAATCAAT
1 AAGAAAGAGAA-AGAATCAAT
*
600911 AAGAAAGAGCAAGAATCAA
1 AAGAAAGAGAAAGAATCAA
600930 CAACAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.64, C:0.08, G:0.21, T:0.08
Consensus pattern (20 bp):
AAGAAAGAGAAAGAATCAAT
Found at i:605879 original size:20 final size:20
Alignment explanation
Indices: 605837--605909 Score: 105
Period size: 20 Copynumber: 3.6 Consensus size: 20
605827 GTTACAAGCT
605837 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
*
605857 ATGTGTCGATACATTGTACC
1 ATGTATCGATACATTGTACC
605877 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
605897 ATGTATCGATACA
1 ATGTATCGATACA
605910 AATAGTGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 47 0.96
21 1 0.02
22 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:605977 original size:13 final size:13
Alignment explanation
Indices: 605959--605985 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
605949 TACAATAAAC
605959 ATGTATCGATACA
1 ATGTATCGATACA
605972 ATGTATCGATACA
1 ATGTATCGATACA
605985 A
1 A
605986 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:609569 original size:48 final size:49
Alignment explanation
Indices: 609504--609630 Score: 195
Period size: 48 Copynumber: 2.6 Consensus size: 49
609494 CATTTTTTTT
*
609504 ATAACAAAAACGAGGAGAGATATTTGAAATAAATTTTTTTTATAAAGAGGG
1 ATAACAAAAA-G-GGAGAGATATTTGAAATAAATTTATTTTATAAAGAGGG
609555 ATAA-AAAAAGGGAGAGATATTTGAAATAAATTTATTTTATAAAGAGGG
1 ATAACAAAAAGGGAGAGATATTTGAAATAAATTTATTTTATAAAGAGGG
* *
609603 ATAACAAAAAGGGGGAGA-ATTTGCAATA
1 ATAACAAAAAGGGAGAGATATTTGAAATA
609631 TTTGTTTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
48 50 0.69
49 13 0.18
50 5 0.07
51 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.27
Consensus pattern (49 bp):
ATAACAAAAAGGGAGAGATATTTGAAATAAATTTATTTTATAAAGAGGG
Found at i:614043 original size:50 final size:52
Alignment explanation
Indices: 613966--614080 Score: 180
Period size: 50 Copynumber: 2.2 Consensus size: 52
613956 TGGCTGCATT
* *
613966 TATTGATACATTTGAGTTAAAAACCTAGAATGTATCGATACAATGAAAAA-G
1 TATTGATACATTTGAGGTAAAAACCTAGAATGCATCGATACAATGAAAAATG
* *
614017 TATTGATACATTTG-GGTCAAAACCTAGAATGCATCGATATAATGAAAAATG
1 TATTGATACATTTGAGGTAAAAACCTAGAATGCATCGATACAATGAAAAATG
614068 TATTGATACATTT
1 TATTGATACATTT
614081 TCTTTTCGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 31 0.53
51 28 0.47
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (52 bp):
TATTGATACATTTGAGGTAAAAACCTAGAATGCATCGATACAATGAAAAATG
Done.