Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:4070 original size:23 final size:21
Alignment explanation
Indices: 4017--4079 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
4007 TTTTGGTGCA
*
4017 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
4038 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
4059 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
4080 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:4087 original size:21 final size:21
Alignment explanation
Indices: 4019--4100 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
4009 TTGGTGCAGA
* *
4019 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
4039 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
4063 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
4084 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
4101 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
23 16 0.32
24 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:12616 original size:29 final size:29
Alignment explanation
Indices: 12584--12673 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
12574 AGTCAATTAT
*
12584 TCTTTTACTCAACAGTGTTTAACCATTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
12613 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
12642 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
12671 TCT
1 TCT
12674 AACTCGCAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAACCGTTCA
Found at i:12785 original size:81 final size:81
Alignment explanation
Indices: 12642--12959 Score: 433
Period size: 81 Copynumber: 3.9 Consensus size: 81
12632 TAACCGTTCA
* * * * *
12642 TCTTTTACTCAACAGTGTTTAACCGTTCATCTAACTCGCA-AAGTTGACACATTTCTGTCAAATG
1 TCTTTTACTCAACGGTATTTAACAGTTCATCTAACTGGCATAA-TTGACACATTTCTGCCAAATG
*
12706 CACATTTAGGCCATTAT
65 CACAGTTAGGCCATTAT
* * *
12723 TATTGTACTCAACGGTATTTAACAGTTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACAGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
12788 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
*
12804 TCTTTTACTCAACGATATTTAA-ACGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATG
1 TCTTTTACTCAACGGTATTTAACA-GTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATG
* *
12868 CATAGTTAGCCCATTAT
65 CACAGTTAGGCCATTAT
* * * * * *
12885 TCTTTTACTCAACGGTATTTTACCGTTCATTTAACTAGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACAGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
*
12950 ACAATTAGGC
66 ACAGTTAGGC
12960 ATCAAAGGCA
Statistics
Matches: 209, Mismatches: 25, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.00
81 206 0.99
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACAGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
ACAGTTAGGCCATTAT
Found at i:13019 original size:68 final size:68
Alignment explanation
Indices: 12910--13434 Score: 816
Period size: 68 Copynumber: 7.7 Consensus size: 68
12900 TATTTTACCG
* * * * * *
12910 TTCATTTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAATTAGGCATCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
12975 CCT
66 CCT
* * *
12978 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAATTAGGCCTCCAATGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
13043 CCT
66 CCT
*
13046 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGTCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
13111 CCT
66 CCT
* * * *
13114 TTCATCTAACTGGCATAAATGACAACTTTCAGTCAAATGCACAGTTAGGCCGCAAAGGCATTTAT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
13179 CCT
66 CCT
* *
13182 TTCATCTAACTGGCATAAATGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGACATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
13247 CCT
66 CCT
* * * *
13250 TTCATCTAACTTGCATAAATGACACATTTCTCTCAAATGCACAGTTAGGCCTCAAAGGCGTTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
13315 CCT
66 CCT
* * *
13318 TTTATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGTCGCAAAGGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
13383 CCT
66 CCT
* * *
13386 TTCATCTAACTGGCATAAATGACACTTTTCTGTCAAATGTACAATTAGG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGG
13435 GCTATTAATC
Statistics
Matches: 418, Mismatches: 39, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 418 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
CCT
Found at i:15199 original size:23 final size:24
Alignment explanation
Indices: 15169--15220 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
15159 TAACTTTGAC
*
15169 CTGACCCGGTGA-CTTTGACCAGT
1 CTGACCCGGTGACCTTTGACCAAT
*
15192 CTGACCCGTTGACCTTTGACCAAT
1 CTGACCCGGTGACCTTTGACCAAT
15216 CTGAC
1 CTGAC
15221 TGTTGACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.27
Consensus pattern (24 bp):
CTGACCCGGTGACCTTTGACCAAT
Found at i:16889 original size:19 final size:19
Alignment explanation
Indices: 16846--16893 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16836 TTCTCTAAAA
* *
16846 TTTGATATATGTTTTGATC
1 TTTGATATCTGTTATGATC
* *
16865 TCTGATATCTGTTATGATT
1 TTTGATATCTGTTATGATC
16884 TTTGATATCT
1 TTTGATATCT
16894 CTATTTACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (19 bp):
TTTGATATCTGTTATGATC
Found at i:34551 original size:21 final size:21
Alignment explanation
Indices: 34525--34566 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34515 ACGTAGAATT
*
34525 TGTCCCGAAGGACCACGTATA
1 TGTCCCGAAGGACCACATATA
*
34546 TGTCCCGAATGACCACATATA
1 TGTCCCGAAGGACCACATATA
34567 ACATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:34624 original size:18 final size:18
Alignment explanation
Indices: 34576--34625 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
34566 AACATATATA
*
34576 TCCCGAAGGACCACTATG
1 TCCCGAAGAACCACTATG
*
34594 TCCTGAA-AGACCACTATG
1 TCCCGAAGA-ACCACTATG
34612 TCCCGAAGAACCAC
1 TCCCGAAGAACCAC
34626 GTAAACCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (18 bp):
TCCCGAAGAACCACTATG
Found at i:41904 original size:10 final size:10
Alignment explanation
Indices: 41889--41925 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
41879 GGACCGGCTG
41889 AAAACCGAAA
1 AAAACCGAAA
**
41899 AAAACCGGGA
1 AAAACCGAAA
41909 AAAACCGAAA
1 AAAACCGAAA
41919 AAAACCG
1 AAAACCG
41926 CCAATTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.62, C:0.22, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAACCGAAA
Found at i:59248 original size:17 final size:18
Alignment explanation
Indices: 59205--59250 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
59195 TTTTGACATA
59205 AATAATATTTCAAAAATT
1 AATAATATTTCAAAAATT
59223 ATTATAATATTTCAAAAA-T
1 A--ATAATATTTCAAAAATT
59242 AATAATATT
1 AATAATATT
59251 AAAATTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
18 1 0.04
19 2 0.08
20 15 0.58
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAATATTTCAAAAATT
Found at i:60760 original size:13 final size:15
Alignment explanation
Indices: 60740--60774 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
60730 TACGTATCAC
60740 TATTATTA-TAAAAT
1 TATTATTATTAAAAT
60754 T-TTATTATTAAAAT
1 TATTATTATTAAAAT
60768 TATTATT
1 TATTATT
60775 GTCTTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 8 0.42
15 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATTATTAAAAT
Found at i:60844 original size:3 final size:3
Alignment explanation
Indices: 60791--60825 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
60781 TTGTTAAACA
60791 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
60826 AAATTGTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:85519 original size:24 final size:24
Alignment explanation
Indices: 85490--85553 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
85480 TTAGTCGTTG
* *
85490 ATTTTAATTTAATTCAATAAGTTC
1 ATTTTAATTTAATTCAATAAATTA
85514 ATTTTAATTTAATTCAATAAATTA
1 ATTTTAATTTAATTCAATAAATTA
85538 ATTTGTGAATTTAATT
1 ATTT-T-AATTTAATT
85554 GGTGAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 26 0.72
25 1 0.03
26 9 0.25
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (24 bp):
ATTTTAATTTAATTCAATAAATTA
Found at i:87424 original size:13 final size:13
Alignment explanation
Indices: 87406--87444 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
87396 GTCATAAATC
*
87406 TATGACGCACATT
1 TATGACACACATT
87419 TATGACACACATT
1 TATGACACACATT
*
87432 TATGACACTCATT
1 TATGACACACATT
87445 GCGCGTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (13 bp):
TATGACACACATT
Found at i:87506 original size:85 final size:85
Alignment explanation
Indices: 87416--87581 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
87406 TATGACGCAC
* * *
87416 ATTTATGACACACATTTATGACAC-T-CATTGCGCGTCATTGAAGCCCCCGTC-TTAAATGAAGA
1 ATTTATGACACACATTTAT-A-ACTTACATTGCGCGTCATTGAAGCACACGTCATTAAA-AAAGA
*
87478 CGACACACATTTGTGTGTCATAA
63 CGACACACATTCGTGTGTCATAA
* * **
87501 ATTTATGACACGCATTTATAACTTACATTGCGTGTCATTGAAGCACACGTCATTAAAAAAGTTGA
1 ATTTATGACACACATTTATAACTTACATTGCGCGTCATTGAAGCACACGTCATTAAAAAAGACGA
87566 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
87582 GTGATTGTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
83 2 0.03
84 2 0.03
85 61 0.87
86 5 0.07
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (85 bp):
ATTTATGACACACATTTATAACTTACATTGCGCGTCATTGAAGCACACGTCATTAAAAAAGACGA
CACACATTCGTGTGTCATAA
Found at i:97075 original size:31 final size:31
Alignment explanation
Indices: 97037--97097 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
97027 TCACAATACG
97037 TCTAAAATATTATATTTATACATTTTACAGA
1 TCTAAAATATTATATTTATACATTTTACAGA
97068 TCTAAAATATTATATTTATACATTTTACAG
1 TCTAAAATATTATATTTATACATTTTACAG
97098 TTATCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (31 bp):
TCTAAAATATTATATTTATACATTTTACAGA
Found at i:101341 original size:16 final size:17
Alignment explanation
Indices: 101314--101349 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
101304 GATATAAGAA
101314 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
101331 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
101347 AAA
1 AAA
101350 ATATCGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:103693 original size:16 final size:16
Alignment explanation
Indices: 103672--103703 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
103662 GAGTCTAAAC
103672 AACGTCATTTGGCGAG
1 AACGTCATTTGGCGAG
103688 AACGTCATTTGGCGAG
1 AACGTCATTTGGCGAG
103704 GGCTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (16 bp):
AACGTCATTTGGCGAG
Found at i:103734 original size:11 final size:11
Alignment explanation
Indices: 103718--103750 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
103708 ATATAAACAA
103718 TTTTTCTCTAT
1 TTTTTCTCTAT
103729 TTTTTCTC-ATT
1 TTTTTCTCTA-T
103740 TTTTTCTCTAT
1 TTTTTCTCTAT
103751 GCCCTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTCTCTAT
Found at i:105599 original size:19 final size:19
Alignment explanation
Indices: 105567--105623 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
105557 AGTATCAAAT
**
105567 AAACTTGACGTCCATAAAC
1 AAACTTGAAATCCATAAAC
*
105586 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCAT-A-AAC
105607 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
105624 TAATAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 17 0.52
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (19 bp):
AAACTTGAAATCCATAAAC
Found at i:109469 original size:40 final size:41
Alignment explanation
Indices: 109366--109528 Score: 220
Period size: 41 Copynumber: 4.0 Consensus size: 41
109356 TTGTAAACAC
*
109366 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
109407 AAACCCCACTAAAGTATGAGTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
109448 AAACG-CACTAAAGTACAAGTCTATAGTGGCGTTTGTATTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
109488 AAATGCCACTAAAGTAGGAGTCTTTAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
109529 TGTAATGATA
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
40 34 0.33
41 70 0.67
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:109502 original size:81 final size:82
Alignment explanation
Indices: 109366--109528 Score: 229
Period size: 81 Copynumber: 2.0 Consensus size: 82
109356 TTGTAAACAC
* * *
109366 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACCCCACTAAAGTATGAGTCTA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACCCCACTAAAGTAGGAGTCTA
*
109431 TAGCGACGTTTGTATAA
66 TAGCGACGTTTATATAA
* * ** *
109448 AAACG-CACTAAAGTACAAGTCTATAGTGGCGTTTGTATTAAAATGCCACTAAAGTAGGAGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACCCCACTAAAGTAGGAGTCTA
*
109512 TAGCGGCGTTTATATAA
66 TAGCGACGTTTATATAA
109529 TGTAATGATA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 66 0.93
82 5 0.07
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (82 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACCCCACTAAAGTAGGAGTCTA
TAGCGACGTTTATATAA
Found at i:109740 original size:41 final size:41
Alignment explanation
Indices: 109631--109741 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 41
109621 TTACGACGTC
* * * *
109631 TGTATAAAAA-GCAACTAAAGTACAAGTCTTTAGTGGCGTT
1 TGTATAAAAATGCAACTAAAGTACGAGTCTATAGGGGCATT
*
109671 TGTATAAAAATGCCACTAAAGTACGAGTCTATAGGGGCATT
1 TGTATAAAAATGCAACTAAAGTACGAGTCTATAGGGGCATT
* *
109712 TGTATAAAAATGCTACTAAAGTAGGAGTCT
1 TGTATAAAAATGCAACTAAAGTACGAGTCT
109742 TCAACAACAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 10 0.16
41 53 0.84
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (41 bp):
TGTATAAAAATGCAACTAAAGTACGAGTCTATAGGGGCATT
Found at i:109753 original size:41 final size:41
Alignment explanation
Indices: 109669--109778 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
109659 TTTAGTGGCG
****
109669 TTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGGGGCA
1 TTTGTATAAAAATGCCACTAAAGTACGAGTCTATAACAACA
* *
109710 TTTGTATAAAAATGCTACTAAAGTAGGAGTCT-TCAACAACA
1 TTTGTATAAAAATGCCACTAAAGTACGAGTCTAT-AACAACA
* *
109751 TTTGTATACAAACGCCA-TGAAAGTACGA
1 TTTGTATAAAAATGCCACT-AAAGTACGA
109779 TTCTTTAGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 2 0.04
41 55 0.96
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (41 bp):
TTTGTATAAAAATGCCACTAAAGTACGAGTCTATAACAACA
Found at i:110690 original size:43 final size:42
Alignment explanation
Indices: 110580--111032 Score: 275
Period size: 43 Copynumber: 10.4 Consensus size: 42
110570 CAACACCCTA
* * *
110580 TGTGATGGAAGCGAGCGAAATGTTGATGTT-TGACCAA-TTCCTTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTAT--TCAACTT--TTC
* * * *
110624 TATGATGGAATTGAATGAGATGTTGATGTTATTCAACTTATTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTT-TTC
*
110667 TGTCATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTT-TTC
* * ** * *
110710 TGTCATGGAATCGAACGAAATGTTAATGTTTAACCTACTCTTTT
1 TGTGATGGAATCGAACGAAATGTTGATG-TTATTCAACT-TTTC
* * * * **
110754 TGTGATGGAATTGATCAAAATGTTAATGTTTGACCCAACTTCTTC
1 TGTGATGGAATCGAACGAAATGTTGATG-TT-ATTCAACTT-TTC
* * ** *
110799 TGTGATGGAATC-AATAGAAATATTGATGTTTGACCCAACTCCTTC
1 TGTGATGGAATCGAA-CGAAATGTTGATG-TT-ATTCAACT-TTTC
* * * * *
110844 TGTGATAGAATCGAGCGAAATATTGATGTTGTTCAACTCCTTC
1 TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACT-TTTC
* * * ** * *
110887 TATGATGGAATCTAATGAAATGTTGATGAAAAATCAACTCATTC
1 TGTGATGGAATCGAACGAAATGTTGATG-TTATTCAACT-TTTC
* ** * *
110931 TGTGATGGAATTGAACGAAATGTT-AGTGAAATTCATCTCTTTT
1 TGTGATGGAATCGAACGAAATGTTGA-TGTTATTCAACT-TTTC
* *
110974 TGTGATGGAATTGAACGAAATGTTGATGTTGATCCAACTCTTTC
1 TGTGATGGAATCGAACGAAATGTTGATGTT-ATTCAACT-TTTC
*
111018 TGTGATGGAAGCGAA
1 TGTGATGGAATCGAA
111033 ACTTGAATTC
Statistics
Matches: 332, Mismatches: 64, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
43 141 0.42
44 122 0.37
45 68 0.20
46 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
TGTGATGGAATCGAACGAAATGTTGATGTTATTCAACTTTTC
Found at i:110897 original size:177 final size:174
Alignment explanation
Indices: 110597--110955 Score: 389
Period size: 177 Copynumber: 2.0 Consensus size: 174
110587 GAAGCGAGCG
* * * * **
110597 AAATGTTGATGTTTGACCAATTCCTTCTATGATGGAATTGAATGAGATGTTGATGTTATTCAACT
1 AAATGTTAATGTTTGACCAATTCCTTCTATGATGGAATTCAATGAAATATTGATGTTACCCAACT
* * * * *
110662 TATTCTGTCATGGAATCGAACGAAATGTTGATGTTATTCAACTTATTCTGTCATGGAATCGAACG
66 CATTCTGTCATAGAATCGAACGAAATATTGATGTTATTCAACTCATTCTATCATGGAATCGAACG
*** * * * *
110727 AAATGTTAATGTTTAACCTACTCTTTTTGTGATGGAATTGATCA
131 AAATGTTAATGAAAAACCAACTCATTCTGTGATGGAATTGAACA
*
110771 AAATGTTAATGTTTGACCCAACTT-CTTCTGTGATGGAA-TCAATAGAAATATTGATGTTTGACC
1 AAATGTTAATGTTTGA-CCAA-TTCCTTCTATGATGGAATTCAAT-GAAATATTGATG-TT-ACC
* * * * * *
110834 CAACTCCTTCTGTGATAGAATCGAGCGAAATATTGATGTTGTTCAACTCCTTCTATGATGGAATC
61 CAACTCATTCTGTCATAGAATCGAACGAAATATTGATGTTATTCAACTCATTCTATCATGGAATC
* * * * *
110899 TAATGAAATGTTGATGAAAAATCAACTCATTCTGTGATGGAATTGAACG
126 GAACGAAATGTTAATGAAAAACCAACTCATTCTGTGATGGAATTGAACA
110948 AAATGTTA
1 AAATGTTA
110956 GTGAAATTCA
Statistics
Matches: 150, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
174 19 0.13
175 27 0.18
176 4 0.03
177 100 0.67
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (174 bp):
AAATGTTAATGTTTGACCAATTCCTTCTATGATGGAATTCAATGAAATATTGATGTTACCCAACT
CATTCTGTCATAGAATCGAACGAAATATTGATGTTATTCAACTCATTCTATCATGGAATCGAACG
AAATGTTAATGAAAAACCAACTCATTCTGTGATGGAATTGAACA
Found at i:111378 original size:41 final size:41
Alignment explanation
Indices: 111277--111396 Score: 159
Period size: 42 Copynumber: 2.9 Consensus size: 41
111267 CTTATGGATA
* *
111277 GCCCGAAGGACTTAATCACCATGCTCAAAAGACTTACTAGT
1 GCCCGAAGGATTTAATCACCATGCTCAAAAGACTTACTAAT
* * *
111318 GATCCGAAGGATTTAATCACCATGCTCAACAGAGTTACTAAT
1 G-CCCGAAGGATTTAATCACCATGCTCAAAAGACTTACTAAT
* **
111360 GCCCGAAGGATTTAATCACTATGCTCGTAAGACTTAC
1 GCCCGAAGGATTTAATCACCATGCTCAAAAGACTTAC
111397 AGATGGCTCG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 31 0.46
42 36 0.54
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
GCCCGAAGGATTTAATCACCATGCTCAAAAGACTTACTAAT
Found at i:114801 original size:23 final size:23
Alignment explanation
Indices: 114712--114841 Score: 99
Period size: 23 Copynumber: 5.8 Consensus size: 23
114702 GAGTCAAGGG
*
114712 TTCTACGCGGTCCTTCGGGACA-
1 TTCTACGTGGTCCTTCGGGACAT
* *
114734 -TCTATGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
*
114756 TTCTATC-TGGTCCTTTGGGACAT
1 TTCTA-CGTGGTCCTTCGGGACAT
* *
114779 TTCTACGTGATCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * * * *
114802 ATCTAAGTGCTCCATCGTGACA-
1 TTCTACGTGGTCCTTCGGGACAT
*
114824 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
114842 TGCAATTTAT
Statistics
Matches: 84, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
21 20 0.24
22 12 0.14
23 52 0.62
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:118508 original size:23 final size:23
Alignment explanation
Indices: 118419--118548 Score: 106
Period size: 23 Copynumber: 5.8 Consensus size: 23
118409 GAGTCAAGGG
*
118419 TTCTACGCGGTCCTTCGGGACA-
1 TTCTACGTGGTCCTTCGGGACAT
* *
118441 -TCTATGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
* *
118463 TTCTACCTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
118486 TTCTACGTGATCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * * * *
118509 ATCTAAGTGCTCCATCGTGACA-
1 TTCTACGTGGTCCTTCGGGACAT
*
118531 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
118549 TGCAATTTAT
Statistics
Matches: 84, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
21 20 0.24
22 11 0.13
23 53 0.63
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:122183 original size:23 final size:22
Alignment explanation
Indices: 122130--122184 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
122120 GAGTCGAGGG
* *
122130 TTCTACGCGGTCATTTGGGACA
1 TTCTACGTGGTCATTTAGGACA
* *
122152 -TCTATGTGGTCCTTTAGGACAA
1 TTCTACGTGGTCATTTAGGAC-A
122174 TTCTACGTGGT
1 TTCTACGTGGT
122185 TCTTCGGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 16 0.62
22 1 0.04
23 9 0.35
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (22 bp):
TTCTACGTGGTCATTTAGGACA
Found at i:124415 original size:3 final size:3
Alignment explanation
Indices: 124407--124436 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
124397 GAAATCTCTA
124407 TCT TCT TCT TCT TCT TCT TCT TCTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC-T TCT TC
124437 CTTATCTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:125803 original size:15 final size:15
Alignment explanation
Indices: 125767--125805 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
125757 GTGACTATGT
125767 GAAC-ATGTGATACA
1 GAACTATGTGATACA
*
125781 -ATCTATGTGATACA
1 GAACTATGTGATACA
125795 GAACTATGTGA
1 GAACTATGTGA
125806 ATAATTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 2 0.10
14 10 0.48
15 9 0.43
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (15 bp):
GAACTATGTGATACA
Found at i:125967 original size:23 final size:23
Alignment explanation
Indices: 125941--125989 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
125931 TTTGGGATTA
* *
125941 TTCTACGTGGTCCTTAGGAGCAT
1 TTCTACGCGGTCCTTAGGAACAT
*
125964 TTCTATGCGGTCCTTAGGAACAT
1 TTCTACGCGGTCCTTAGGAACAT
125987 TTC
1 TTC
125990 AGGAAATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCTACGCGGTCCTTAGGAACAT
Found at i:126844 original size:30 final size:31
Alignment explanation
Indices: 126810--126884 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
126800 TAATCATCAT
*
126810 TTCTTTCTCTTCTCTTTTT-T-TCTTTTGCTC
1 TTCTTTCTCTTCTATTTTTCTCTCTTTT-CTC
126840 TTCTTTCT-TT-TATTTTTCTCTCTTTTCTC
1 TTCTTTCTCTTCTATTTTTCTCTCTTTTCTC
*
126869 TTTTTTC-CTTC-ATTTT
1 TTCTTTCTCTTCTATTTT
126885 CCTTCAGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 6 0.15
29 19 0.49
30 14 0.36
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.72
Consensus pattern (31 bp):
TTCTTTCTCTTCTATTTTTCTCTCTTTTCTC
Found at i:126846 original size:15 final size:15
Alignment explanation
Indices: 126809--126875 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
126799 TTAATCATCA
*
126809 TTTCTTTCTCTTCTC
1 TTTCTTTCTTTTCTC
*
126824 TTTTTTTCTTTTGCTC
1 TTTCTTTCTTTT-CTC
* *
126840 -TTCTTTCTTTTATT
1 TTTCTTTCTTTTCTC
*
126854 TTTCTCTCTTTTCTC
1 TTTCTTTCTTTTCTC
126869 TTT-TTTC
1 TTTCTTTC
126876 CTTCATTTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
14 4 0.10
15 34 0.83
16 3 0.07
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.73
Consensus pattern (15 bp):
TTTCTTTCTTTTCTC
Found at i:126866 original size:20 final size:21
Alignment explanation
Indices: 126813--126867 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
126803 TCATCATTTC
*
126813 TTTCTCTTCTCTTT-TTTTCTT
1 TTTCTC-TCTCTTTCTTTTATT
*
126834 TTGCTCT-TCTTTCTTTTATT
1 TTTCTCTCTCTTTCTTTTATT
126854 TTTCTCTCT-TTTCT
1 TTTCTCTCTCTTTCT
126868 CTTTTTTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.17
20 18 0.62
21 6 0.21
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTCTCTCTCTTTCTTTTATT
Found at i:127218 original size:167 final size:167
Alignment explanation
Indices: 126896--127218 Score: 348
Period size: 167 Copynumber: 1.9 Consensus size: 167
126886 CTTCAGACTT
* * * *
126896 TTGTTTCTTTCCCTTGCCTTGAGGAATTTATCACGTTAAAATTAATGTCATGATTTAAATATAAC
1 TTGTTTCTTTCCCTTACCTTGAGGAATTCATCACATTAAAATTAATGTCAAGATTTAAATATAAC
* * ** * * *
126961 AACTTTATAAAGCTCTGACTTACATTAATAGCTATTTGAAATTACCTTCAATTTATCAGCTTACT
66 AACTTAATAAAGCCCAAACTTACATCAATAGCTATTTGAAATTACCTCCAATTTATCAGCCTACT
* **
127026 GCTTTTAGTGGAGTGGCCTCATTTTACCTCTTTCTTC
131 GATTTTAGCCGAGTGGCCTCATTTTACCTCTTTCTTC
* * * *
127063 TTGTTTCTTTCTCTTACCTT-AGGAAATTCATCGCATTACAATTAATGTCACAG-TTTGAATATA
1 TTGTTTCTTTCCCTTACCTTGAGG-AATTCATCACATTAAAATTAATGTCA-AGATTTAAATATA
* * * * * *
127126 ACCACTTAATGAAGCCCAAACTTACCTCAATAGCTGTTTGGAATTACCTCCAATTTATCATCCTA
64 ACAACTTAATAAAGCCCAAACTTACATCAATAGCTATTTGAAATTACCTCCAATTTATCAGCCTA
* *
127191 -TTATTTTCAGCCTAGTGGTCC-CATTTTA
129 CTGATTTT-AGCCGAGTGG-CCTCATTTTA
127219 TTACACTCAT
Statistics
Matches: 126, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
166 8 0.06
167 115 0.91
168 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (167 bp):
TTGTTTCTTTCCCTTACCTTGAGGAATTCATCACATTAAAATTAATGTCAAGATTTAAATATAAC
AACTTAATAAAGCCCAAACTTACATCAATAGCTATTTGAAATTACCTCCAATTTATCAGCCTACT
GATTTTAGCCGAGTGGCCTCATTTTACCTCTTTCTTC
Found at i:145549 original size:19 final size:19
Alignment explanation
Indices: 145525--145562 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
145515 GTTTAAGAAC
145525 ATAATCTCTGCTTGTATCA
1 ATAATCTCTGCTTGTATCA
*
145544 ATAATCTCTTCTTGTATCA
1 ATAATCTCTGCTTGTATCA
145563 TCTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (19 bp):
ATAATCTCTGCTTGTATCA
Found at i:148044 original size:38 final size:38
Alignment explanation
Indices: 147989--148081 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
147979 CTACAAAGGA
** * *
147989 GGGGGTTCGGGTAAAAAGGATAGATAAAAGAAAAAAGT
1 GGGGGTTCGGGCGAAAAGGAGAGAAAAAAGAAAAAAGT
*
148027 GGGGGTTCGGGCGAAAAGGAGAGAAAAAATAAAAAAGT
1 GGGGGTTCGGGCGAAAAGGAGAGAAAAAAGAAAAAAGT
*
148065 GGGGGTTCGAGCGAAAA
1 GGGGGTTCGGGCGAAAA
148082 AAGAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.44, C:0.05, G:0.38, T:0.13
Consensus pattern (38 bp):
GGGGGTTCGGGCGAAAAGGAGAGAAAAAAGAAAAAAGT
Found at i:148100 original size:38 final size:38
Alignment explanation
Indices: 148014--148092 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
148004 AAGGATAGAT
* *
148014 AAAAGAAAAAAGTGGGGGTTCGGGCGAAAAGGAGAGAA
1 AAAAGAAAAAAGTGGGGGTTCGAGCGAAAAGAAGAGAA
*
148052 AAAATAAAAAAGTGGGGGTTCGAGCGAAAA-AAGA-AA
1 AAAAGAAAAAAGTGGGGGTTCGAGCGAAAAGAAGAGAA
148088 AAAAG
1 AAAAG
148093 GAGAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 6 0.16
37 3 0.08
38 28 0.76
ACGTcount: A:0.53, C:0.05, G:0.33, T:0.09
Consensus pattern (38 bp):
AAAAGAAAAAAGTGGGGGTTCGAGCGAAAAGAAGAGAA
Found at i:163371 original size:262 final size:258
Alignment explanation
Indices: 162780--163608 Score: 865
Period size: 262 Copynumber: 3.2 Consensus size: 258
162770 GGGTTTCTTG
* * * * * * * *
162780 ATTGGTAAGTCCTT-CGGCCATTAGTAAGCCTATCGAGCATGATTG-TTAAATCCTCCGGGTCAT
1 ATTGGTAAGTCCTTAGGGTCATCAATAAGTCTTTCGAGCATGA-TGATTAAATCCTTCGAGTCAT
* * * * * * ** * * * * * * **
162843 CTATAAGACTTTCGAGCTAGAGGATAAGTCCTTCAGGTCATCCAGAAGGCCTTCGGACAGGATAT
65 CTGTCAGTCTTTCAAGCAAGAAGATAAGTTGTTCAGGCCATCTATAAGACCTTCGGGCAAGATGC
* * * ***
162908 TTTCATATGAAT--TTTGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCTTTTCTC
130 TTTCATAT-AATAATTTGAAAAATGAGAAAACAATTTTCAAAGTTTCTCATTT-AATATTTTAAA
* *
162971 AAAATGAAAATTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAA
193 AAAATG-AATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAA
163036 AA
257 AA
* * * *
163038 ACTGATAAGTCCTTCA-GGTCATCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGAGTCAT
1 ATTGGTAAGTCCTT-AGGGTCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCAT
* * *
163102 TTGTCAGTCTTTCAAGCAAGATGATAAGTCAT-TTGA-GCCATCTATAAGACCTTCGGGCAAGAT
65 CTGTCAGTCTTTCAAGCAAGAAGATAAGT--TGTTCAGGCCATCTATAAGACCTTCGGGCAAGAT
*
163165 GCTTTCATATAATAATTTGAAAAATGAGAAAGCAATTTTCAAAGTTTC-CTATTTAGA-ATTTTA
128 GCTTTCATATAATAATTTGAAAAATGAGAAAACAATTTTCAAAGTTTCTC-ATTTA-ATATTTT-
* * *
163228 AAAAAAAAAATGAATTTTTTGAAAATTAAGAAAACGATTTCCAAAGTTTCTTACCTAGT-AATTA
190 ---AAAAAAATGAA-TTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTA
*
163292 TTTCTAAA
251 TTTCAAAA
* * * * *
163300 TTTGGTAAGTCCTTAGGGTCATCAATAAGTCTTTCGAGCATGTTGTTTAAATCCTTTG-GGCTAT
1 ATTGGTAAGTCCTTAGGGTCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTC-AT
* * *
163364 CTGTCAGTCTTTCGATCAAGAAGATAAGTTGTTCAGGCCATCTATAAGACCTTTGGGCAAGATGC
65 CTGTCAGTCTTTCAAGCAAGAAGATAAGTTGTTCAGGCCATCTATAAGACCTTCGGGCAAGATGC
* * * *
163429 TTTCATATGATAATTTGAAAAATGAGAAAACGATTTTCAAAGTTTCTCATTTAATATTTTCAGAA
130 TTTCATATAATAATTTGAAAAATGAGAAAACAATTTTCAAAGTTTCTCATTTAATATTTTAAAAA
* * * *
163494 AATG-ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGCTTCTTATCTAGTAAACTATTTCCAAA
195 AATGAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAA
* *
163557 ATTGGTAAGTCCTTTGGG-CAATCAATAAGTCTTTCAAGCATGATGATTAAAT
1 ATTGGTAAGTCCTTAGGGTC-ATCAATAAGTCTTTCGAGCATGATGATTAAAT
163609 ATTTCGGGTA
Statistics
Matches: 478, Mismatches: 71, Indels: 45
0.80 0.12 0.08
Matches are distributed among these distances:
256 40 0.08
257 57 0.12
258 24 0.05
259 95 0.20
260 39 0.08
261 7 0.01
262 169 0.35
263 47 0.10
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (258 bp):
ATTGGTAAGTCCTTAGGGTCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATC
TGTCAGTCTTTCAAGCAAGAAGATAAGTTGTTCAGGCCATCTATAAGACCTTCGGGCAAGATGCT
TTCATATAATAATTTGAAAAATGAGAAAACAATTTTCAAAGTTTCTCATTTAATATTTTAAAAAA
ATGAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCAAAA
Found at i:167276 original size:14 final size:15
Alignment explanation
Indices: 167245--167279 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
167235 TATTGAGTCC
*
167245 TTTAATTTTTTTTAT
1 TTTAATTTTGTTTAT
167260 TTTAATTTTGTTT-T
1 TTTAATTTTGTTTAT
167274 TTTAAT
1 TTTAAT
167280 AAATGTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTAATTTTGTTTAT
Found at i:172600 original size:39 final size:39
Alignment explanation
Indices: 172546--172661 Score: 126
Period size: 39 Copynumber: 3.0 Consensus size: 39
172536 TACTTTCTGG
* * *
172546 AGGCTCCTCGGCTTTGTTCTCAGGGTAAGTCCTTACTGC
1 AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGC
* ** * *
172585 AGGCTCCTCTACTTTGTGCACATAAG-AAGACCTTACTGT
1 AGGCTCCTCTGCTTTGTGCACA-GGGTAAGTCCTTACTGC
* *
172624 AGGCTCCTTTGCTTTGTGCACAGGGTAATTCCTTACTG
1 AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTG
172662 GGTGTACAGG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
38 1 0.02
39 59 0.97
40 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (39 bp):
AGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTACTGC
Found at i:176876 original size:39 final size:39
Alignment explanation
Indices: 176833--176952 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 39
176823 TTATCGCTTT
* *
176833 CTGCAGGCTCCT-TGGCTTTGTGCTCAGGGTAAGTCCTTA
1 CTGCAGACTCCTCT-GCTTTGTGCACAGGGTAAGTCCTTA
* * * *
176872 CTGCAGACTCCTCTACTTTGTACACAGGATAAGACCTTA
1 CTGCAGACTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
* * *
176911 CTGCAGACTTCTCTGCTTTGTGCACATGGTAAGTTCTTA
1 CTGCAGACTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
176950 CTG
1 CTG
176953 GATGTACAGG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 66 0.99
40 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (39 bp):
CTGCAGACTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
Found at i:177320 original size:38 final size:38
Alignment explanation
Indices: 177278--177352 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
177268 ATGTATTATC
* * *
177278 GGTATTTTGTTCCGTAAATGTTTTATATAGTTTTCTGT
1 GGTATTTTGATACGTAAATGTTTTATACAGTTTTCTGT
* *
177316 GGTATTTTGATATGTATATGTTTTATACAGTTTTCTG
1 GGTATTTTGATACGTAAATGTTTTATACAGTTTTCTG
177353 ACATATGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.20, C:0.07, G:0.19, T:0.55
Consensus pattern (38 bp):
GGTATTTTGATACGTAAATGTTTTATACAGTTTTCTGT
Found at i:178035 original size:17 final size:17
Alignment explanation
Indices: 178013--178045 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
178003 AATAAACGAA
*
178013 CTAGTTTGATTAATGAT
1 CTAGTTTAATTAATGAT
178030 CTAGTTTAATTAATGA
1 CTAGTTTAATTAATGA
178046 ACTACTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (17 bp):
CTAGTTTAATTAATGAT
Found at i:178716 original size:25 final size:24
Alignment explanation
Indices: 178688--178734 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
178678 ATCTTTATTC
178688 ACAA-TTTGATCAGCGGGTAATGGTA
1 ACAAGTTT-ATCAG-GGGTAATGGTA
*
178713 ACAAGTTTATCAGGGTTAATGG
1 ACAAGTTTATCAGGGGTAATGG
178735 ATTGAACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 9 0.45
26 3 0.15
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (24 bp):
ACAAGTTTATCAGGGGTAATGGTA
Found at i:182764 original size:17 final size:17
Alignment explanation
Indices: 182742--182774 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
182732 TTAGTAATGA
182742 AAAAAATAACCTCACAG
1 AAAAAATAACCTCACAG
182759 AAAAAATAACCTCACA
1 AAAAAATAACCTCACA
182775 AAACACTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAAATAACCTCACAG
Found at i:183773 original size:21 final size:22
Alignment explanation
Indices: 183731--183776 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
183721 TTGGCTGAAT
* **
183731 AATCTAGATCATTTTGGGGATG
1 AATCTAGATCAATTTGAAGATG
183753 AATCTAGA-CAATTTGAAGATG
1 AATCTAGATCAATTTGAAGATG
183774 AAT
1 AAT
183777 TTGACCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (22 bp):
AATCTAGATCAATTTGAAGATG
Found at i:184355 original size:17 final size:17
Alignment explanation
Indices: 184323--184372 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
184313 TAAGAGTTAA
* *
184323 TTTAATAAACGAACTAG
1 TTTAATTAATGAACTAG
*
184340 TTTGATTAATGAACTAG
1 TTTAATTAATGAACTAG
184357 TTTAATTAATGAACTA
1 TTTAATTAATGAACTA
184373 CTTCCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTAATTAATGAACTAG
Found at i:186603 original size:13 final size:13
Alignment explanation
Indices: 186585--186609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186575 ATTAAAGAAG
186585 TGCATATGAAGAC
1 TGCATATGAAGAC
186598 TGCATATGAAGA
1 TGCATATGAAGA
186610 TTGTTCAACT
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
TGCATATGAAGAC
Found at i:187887 original size:14 final size:14
Alignment explanation
Indices: 187868--187895 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
187858 AGCAAAAGCC
187868 TACACTCTCACATG
1 TACACTCTCACATG
187882 TACACTCTCACATG
1 TACACTCTCACATG
187896 AAGAGTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
TACACTCTCACATG
Found at i:192322 original size:19 final size:20
Alignment explanation
Indices: 192280--192323 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
192270 TACTATTTAC
192280 TTTATTTTTATATATTCATT
1 TTTATTTTTATATATTCATT
*
192300 TTTATTGTTTAT-TTTTC-TT
1 TTTATT-TTTATATATTCATT
192319 TTTAT
1 TTTAT
192324 ATATTTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 10 0.45
21 5 0.23
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTATTTTTATATATTCATT
Found at i:195384 original size:51 final size:51
Alignment explanation
Indices: 195324--195438 Score: 176
Period size: 51 Copynumber: 2.3 Consensus size: 51
195314 AGGATTAGAT
* *
195324 TTATTATTTTATTAGGAATTAAGATAGAGTCAAAACATTACCTTTAGTTTA
1 TTATTATTTTATTAAGAATTAAGATAGAATCAAAACATTACCTTTAGTTTA
* * * *
195375 TTGTTATTTTATTAAGAATTAGGATAGAATCAAAATATTATCTTTAGTTTA
1 TTATTATTTTATTAAGAATTAAGATAGAATCAAAACATTACCTTTAGTTTA
195426 TTATTATTTTATT
1 TTATTATTTTATT
195439 CAGTAGTTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (51 bp):
TTATTATTTTATTAAGAATTAAGATAGAATCAAAACATTACCTTTAGTTTA
Found at i:196224 original size:7 final size:7
Alignment explanation
Indices: 196214--196238 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
196204 TGAAAATGAA
196214 AAAAGAC
1 AAAAGAC
196221 AAAAGAC
1 AAAAGAC
196228 AAAAGAC
1 AAAAGAC
196235 AAAA
1 AAAA
196239 AAACAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAC
Found at i:202063 original size:193 final size:191
Alignment explanation
Indices: 201705--202083 Score: 715
Period size: 193 Copynumber: 2.0 Consensus size: 191
201695 TAACCCTTAA
*
201705 TGATTACATCTTAATTAAATAAAAATAAAATGATCAAATATTATGTTTTTGAATTCTATGAATAA
1 TGATCACATCTTAATTAAATAAAAATAAAATGATCAAATATTATGTTTTTGAATTCTATGAATAA
201770 AATTATATAAAACTTAAAAAATGATCAACCATTTAATTTATCATTTTAATAAATATTAGGGGCTA
66 AATTATATAAAACTTAAAAAATGATCAACCATTTAATTTATCATTTTAATAAATATTAGGGGCTA
201835 GTTTTGATATTATACCTTTATTATAATGGATAGTTACATCTCAGGTATGATTCTTTATTAG
131 GTTTTGATATTATACCTTTATTATAATGGATAGTTACATCTCAGGTATGATTCTTTATTAG
201896 TGATCACATCTTAATTAAATAAAAATAAAATGATCAAATATTATGTTTTTGAATTCTATGAATAA
1 TGATCACATCTTAATTAAATAAAAATAAAATGATCAAATATTATGTTTTTGAATTCTATGAATAA
201961 AATTATATAAAACTTAAACAAAAAT-ATCAACCATTTAATTTATCATTTTAATAAATATTAGGGG
66 AATTATATAAAACTT--A-AAAAATGATCAACCATTTAATTTATCATTTTAATAAATATTAGGGG
202025 CTAGTTTTGATATTATACCTTTATTATAATGGATAGTTACATCTCAGGTATGATTCTTT
128 CTAGTTTTGATATTATACCTTTATTATAATGGATAGTTACATCTCAGGTATGATTCTTT
202084 TTAAAAAAAA
Statistics
Matches: 184, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
191 79 0.43
193 99 0.54
194 6 0.03
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (191 bp):
TGATCACATCTTAATTAAATAAAAATAAAATGATCAAATATTATGTTTTTGAATTCTATGAATAA
AATTATATAAAACTTAAAAAATGATCAACCATTTAATTTATCATTTTAATAAATATTAGGGGCTA
GTTTTGATATTATACCTTTATTATAATGGATAGTTACATCTCAGGTATGATTCTTTATTAG
Found at i:202325 original size:23 final size:23
Alignment explanation
Indices: 202299--202346 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
202289 ATAAAGTACA
*
202299 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
202322 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
202345 AT
1 AT
202347 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:202749 original size:21 final size:20
Alignment explanation
Indices: 202719--202772 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
202709 GATAGACACT
*
202719 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
202740 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
202763 TTACATTATA
1 TTACATTATA
202773 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:202760 original size:23 final size:23
Alignment explanation
Indices: 202734--202796 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
202724 ATATAACCAT
202734 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
202757 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
202780 TACCTATTACATCATAT
1 TACCTATTACATTATAT
202797 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:203117 original size:431 final size:427
Alignment explanation
Indices: 202458--203326 Score: 1702
Period size: 431 Copynumber: 2.0 Consensus size: 427
202448 GGATCGATAC
202458 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
202523 ATTTGATTGTTTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAATAATATATACCGTAA
66 ATTTGATTGTTTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAATAATATATACCGTAA
202588 CGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
131 CGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
202653 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
196 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
202718 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
261 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
202783 CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
326 CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
202848 CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
202885 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
202950 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAA-TT--TAATAATATATACC
203015 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
127 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
203080 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
192 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
203145 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
257 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
203210 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
322 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
203275 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
387 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
203316 TTTAACAGTGT
1 TTTAACAGTGT
203327 ACTGCGAATT
Statistics
Matches: 438, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
427 88 0.20
428 22 0.05
429 2 0.00
431 326 0.74
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (427 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAATATTATTTAGAATTTTTAATTTAATAATATATACCGTAA
CGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
Found at i:203180 original size:21 final size:20
Alignment explanation
Indices: 203150--203203 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
203140 GATAGACACT
*
203150 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
203171 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
203194 TTACATTATA
1 TTACATTATA
203204 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:203191 original size:23 final size:23
Alignment explanation
Indices: 203165--203227 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
203155 ATATAACCAT
203165 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
203188 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
203211 TACCTATTACATCATAT
1 TACCTATTACATTATAT
203228 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:206320 original size:184 final size:184
Alignment explanation
Indices: 205775--206626 Score: 1528
Period size: 184 Copynumber: 4.7 Consensus size: 184
205765 TTTTAAATGG
*
205775 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
205840 TAAAACCGGTATATTTATA-CGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
205904 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
205958 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAG----A--CGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
206017 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
206082 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
206136 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
206201 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
206266 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
206320 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
206385 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
206450 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACA--TTT-TTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
206501 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGGTTGTAGACCTAT
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCG--ATA-----TAGGTTGTAGACCTAT
**
206566 TCGCGCATAAGACCGGTATATTTATA-CGGTTATATTACAAAATTATCTATTTTATTATAAT
59 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
206627 ATGTTGAAAG
Statistics
Matches: 651, Mismatches: 4, Indels: 24
0.96 0.01 0.04
Matches are distributed among these distances:
177 23 0.04
178 151 0.23
179 1 0.00
181 45 0.07
182 4 0.01
183 55 0.08
184 297 0.46
187 33 0.05
188 42 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:207991 original size:3 final size:3
Alignment explanation
Indices: 207983--208033 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
207973 ACTTGTTTGG
* * * *
207983 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
208031 ATC
1 ATC
208034 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:208000 original size:12 final size:12
Alignment explanation
Indices: 207983--208045 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
207973 ACTTGTTTGG
207983 ATCATCATCTTC
1 ATCATCATCTTC
*
207995 ATCATCATCGTC
1 ATCATCATCTTC
*
208007 ATCATCATCATC
1 ATCATCATCTTC
*
208019 ATCGTCATCTTC
1 ATCATCATCTTC
* *
208031 ATCGTCAGCTTC
1 ATCATCATCTTC
208043 ATC
1 ATC
208046 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:208044 original size:18 final size:18
Alignment explanation
Indices: 207987--208048 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
207977 GTTTGGATCA
207987 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
208005 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
208023 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
208041 TCATCTTC
1 TCATCTTC
208049 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:208048 original size:6 final size:6
Alignment explanation
Indices: 207987--208048 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
207977 GTTTGGATCA
* * * * * *
207987 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
208035 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
208049 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:209994 original size:200 final size:200
Alignment explanation
Indices: 209508--210915 Score: 2580
Period size: 200 Copynumber: 7.1 Consensus size: 200
209498 TTTAAATTAG
* *
209508 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
209573 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * * ***
209638 CGACAC-TTTTTATATATGGATCGACACTTTATTGATTCACCTTG-TAAAAATTCATTCT-GGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
209700 AAAAA
196 AAAAA
*
209705 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTTTTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
209770 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
209835 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
209900 AAAAA
196 AAAAA
209905 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
209970 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
210035 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
210099 AAAAA
196 AAAAA
210104 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210169 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
210234 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
210299 AAAAA
196 AAAAA
210304 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210369 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
210434 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
210499 AAAAA
196 AAAAA
210504 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
210569 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
210634 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
210699 AAAAA
196 AAAAA
210704 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210768 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *** *
210833 CGACAC-TTTTT-TATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
210895 AAAAA
196 AAAAA
210900 TATCGACACAAACTAT
1 TATCGACACAAACTAT
210916 TAGTATCGAC
Statistics
Matches: 1181, Mismatches: 26, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
196 36 0.03
197 163 0.14
198 40 0.03
199 281 0.24
200 661 0.56
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
AAAAA
Found at i:210268 original size:399 final size:398
Alignment explanation
Indices: 209508--210915 Score: 2633
Period size: 399 Copynumber: 3.5 Consensus size: 398
209498 TTTAAATTAG
* *
209508 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
209573 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
209638 CGACACTTTTTATATATGGATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGG-AAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
*
209702 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTTTTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
209767 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
209832 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
209897 GAAAAAAA
391 GAAAAAAA
209905 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
209970 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
***
210035 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
210100 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
210165 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
210230 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
325 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
210295 GGAAAAAAA
390 GGAAAAAAA
210304 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210369 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *** *
210434 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
210499 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
194 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
210564 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
259 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
210629 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
324 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
210694 GGGAAAAAAA
389 GGGAAAAAAA
210704 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210768 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
210833 CGACACTTTTT-TATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
210897 AAATATCGACACAAACTAT
196 AAATATCGACACAAACTAT
210916 TAGTATCGAC
Statistics
Matches: 989, Mismatches: 19, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
396 36 0.04
397 200 0.20
398 18 0.02
399 417 0.42
400 318 0.32
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
GAAAAAAA
Found at i:210642 original size:599 final size:598
Alignment explanation
Indices: 209508--210915 Score: 2653
Period size: 599 Copynumber: 2.4 Consensus size: 598
209498 TTTAAATTAG
* *
209508 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
209573 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
209638 CGACACTTTTTATATATGGATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCT-GGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGGAAAA
*
209702 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTTTTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
209767 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
209832 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
209897 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
391 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
209962 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
456 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
*
210027 TTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCAT
521 TTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCAT
210091 TCTGGAAAAAAAA
586 TCTGGAAAAAAAA
210104 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210169 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * ***
210234 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGGAA
210299 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
194 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
210364 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
259 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
210429 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
324 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
210494 GGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAA
389 GGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAA
210559 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
454 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
*
210624 ATTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTC
519 ATTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTC
*
210689 ATTCTGGGAAAAAAA
584 ATTCTGGAAAAAAAA
210704 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
210768 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
210833 CGACACTTTTT-TATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGGAAAA
210897 AAATATCGACACAAACTAT
196 AAATATCGACACAAACTAT
210916 TAGTATCGAC
Statistics
Matches: 790, Mismatches: 18, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
596 170 0.22
597 65 0.08
598 16 0.02
599 420 0.53
600 119 0.15
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (598 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
TTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTTAATTCAT
TCTGGAAAAAAAA
Found at i:211034 original size:19 final size:19
Alignment explanation
Indices: 211012--211069 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
211002 ACATAAAAAA
211012 ATAAATCGTATACAAAATT
1 ATAAATCGTATACAAAATT
211031 ATAAATCGTATACAAAATT
1 ATAAATCGTATACAAAATT
*
211050 ATAAATCTTATACAAAATT
1 ATAAATCGTATACAAAATT
211069 A
1 A
211070 ACTCGACATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAATCGTATACAAAATT
Found at i:212656 original size:18 final size:17
Alignment explanation
Indices: 212621--212674 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
212611 TGGGCCTCTC
*
212621 CTTCCTCCTCATTTCTT
1 CTTCCTCCTCTTTTCTT
*
212638 C--CAT-CTCTTCTTCTT
1 CTTCCTCCTCTT-TTCTT
212653 CTTCCTCCCTCTTTTCTT
1 CTTCCT-CCTCTTTTCTT
212671 CTTC
1 CTTC
212675 ATATTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
17 3 0.10
18 9 0.31
19 5 0.17
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.54
Consensus pattern (17 bp):
CTTCCTCCTCTTTTCTT
Found at i:212669 original size:15 final size:15
Alignment explanation
Indices: 212621--212671 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
212611 TGGGCCTCTC
*
212621 CTTCCT-CCTCATTT
1 CTTCCTCCCTCTTTT
*
212635 CTTCCATCTCTTCTTCTT
1 CTTCC-TC-CCTCTT-TT
212653 CTTCCTCCCTCTTTT
1 CTTCCTCCCTCTTTT
212668 CTTC
1 CTTC
212672 TTCATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 5 0.17
17 6 0.20
18 7 0.23
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTCCTCCCTCTTTT
Found at i:212894 original size:33 final size:33
Alignment explanation
Indices: 212857--212922 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
212847 CATCTTAATA
*
212857 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
212890 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
212923 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:215283 original size:20 final size:19
Alignment explanation
Indices: 215237--215283 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
215227 TCCGGTATCA
*
215237 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
215256 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
215277 TTTTACC
1 TTTTACC
215284 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:215449 original size:20 final size:20
Alignment explanation
Indices: 215401--215450 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
215391 TCGACACTTT
215401 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTTATCA
*
215421 T-TTTGTTACCGGTTTTATCA
1 TAATT-TTACCGGTTTTATCA
215441 TAATTTTACC
1 TAATTTTACC
215451 TGGTATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (20 bp):
TAATTTTACCGGTTTTATCA
Found at i:215933 original size:229 final size:227
Alignment explanation
Indices: 215516--215964 Score: 774
Period size: 229 Copynumber: 2.0 Consensus size: 227
215506 TTAAAACTGC
*
215516 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
215581 TTAATTTATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TTAATTTATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
215646 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
215711 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
*
215743 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
215808 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTT-ATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
215873 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAAATATATTTTC-ACAGTGAAAT
129 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAAT-AAATATATTTTCAACAGTGAAAT
215937 AAGTATGGACACTTTTATAAAAAGGATA
193 AAGTATGGACACTTTTATAAAAAGGATA
215965 GATAATTTAC
Statistics
Matches: 209, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
227 4 0.02
228 66 0.32
229 128 0.61
230 11 0.05
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:217030 original size:14 final size:14
Alignment explanation
Indices: 217013--217040 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
217003 ATCATAACAA
217013 AATTATATAACTAT
1 AATTATATAACTAT
217027 AATTATATAACTAT
1 AATTATATAACTAT
217041 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:219685 original size:30 final size:30
Alignment explanation
Indices: 219650--219727 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
219640 ATCAGATTTA
* *
219650 AAGGTTAAATTAAAATTTTATTTGAAGTTG
1 AAGGTTAAATTAAAATTTTATCTAAAGTTG
* * *
219680 AAGGTTAAATTGATATTTTATCTAAATTTG
1 AAGGTTAAATTAAAATTTTATCTAAAGTTG
* * *
219710 ATGATCAAATTAAAATTT
1 AAGGTTAAATTAAAATTT
219728 AATCCCTTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (30 bp):
AAGGTTAAATTAAAATTTTATCTAAAGTTG
Found at i:222034 original size:39 final size:39
Alignment explanation
Indices: 221974--222058 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
221964 ACCCATAGTT
* ** * *
221974 GCAACTTGAAAGATGTTTAAAAGGGAATCAGCAAGAGCA
1 GCAACTGGAAAGATGAATAAAAGAGAAACAGCAAGAGCA
**
222013 GCAACTGGAAAGATGAATAAAAGAGAAACAGTGAGAGCA
1 GCAACTGGAAAGATGAATAAAAGAGAAACAGCAAGAGCA
222052 GCAACTG
1 GCAACTG
222059 AGTCGACAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.13, G:0.27, T:0.14
Consensus pattern (39 bp):
GCAACTGGAAAGATGAATAAAAGAGAAACAGCAAGAGCA
Found at i:228662 original size:23 final size:23
Alignment explanation
Indices: 228614--228663 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
228604 ATAATTCTAT
* * * *
228614 CGAAGGACCATATAGGTTTGTGC
1 CGAAGAACCACATAGGTTTATCC
228637 CGAAGAACCACATAGGTTTATCC
1 CGAAGAACCACATAGGTTTATCC
228660 CGAA
1 CGAA
228664 AGTCCACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
CGAAGAACCACATAGGTTTATCC
Found at i:242819 original size:261 final size:261
Alignment explanation
Indices: 242212--243327 Score: 1160
Period size: 261 Copynumber: 4.3 Consensus size: 261
242202 AGTTGTAGCG
* * * * * *
242212 ATAATAAAAGTGATTGCGCCTAAAATATTAT-AAA-TTTTTAGCCGATGGAGCCCTAGAGTTCAC
1 ATAATAAAAGTGATTGCGACTAAAATATTATGAAAGGTTTTAGCTGATGGAGCCTTGGAGTTCCC
* * * ** ** * * * *
242275 CACGGTAATAAAATAAGGTAAGAGCACAATGTTTTATGATTTGGTATACTAGATACGACTGTACC
66 CACGATAATAAAATAAGTTAAAAGCACAAAATTTTATGAAATGGAATAATAGATACGACTGCACA
* * * * *
242340 CAATAATATCATGGTTCTAAATGAAATAAATTGCTACTTGTAATGTTAAATTTGGTACTAATAGA
131 CAATAATATAATGGTTCTAAATGAAATAAGTTGCGACTTGTAATGTTAAATTTAGTATTAATAGA
* *
242405 ATAGATTGCACCCAGAATGTCATGACCCCTAAGAAAGCATGTTGTAATATGGAATCTTATTATTT
196 ATAGATTACACCCAGAATGTCATGACCCCTAAGAAAGCATGTTGCAATATGGAATC---TTATTT
242470 TTTT
258 TTTT
* * * * * *
242474 ATAATAAAATTGACTGTGCCTAAAATATTATG-AAGGTTTTAGCTGATAGAGCTTTGGAGTTCCC
1 ATAATAAAAGTGATTGCGACTAAAATATTATGAAAGGTTTTAGCTGATGGAGCCTTGGAGTTCCC
* * * * ***
242538 CACAATAATAAAATAAGTTAAAAGAATAAAATTTTATGAAAAT-GAATAATAGATACGATTGTGT
66 CACGATAATAAAATAAGTTAAAAGCACAAAATTTTATG-AAATGGAATAATAGATACGACTGCAC
* *
242602 ACAATAACATAATGGTTCTAAATGAAATAAGTTGCGATTTGTAATGTTAACA-TTAGTATTAATA
130 ACAATAATATAATGGTTCTAAATGAAATAAGTTGCGACTTGTAATGTTAA-ATTTAGTATTAATA
* * ** *
242666 TAATAGATTACGCTTAGAATGTCATGACCCCATAAGAAAGCATTTTGCAATATGGAATCTTATTT
194 GAATAGATTACACCCAGAATGTCATGACCCC-TAAGAAAGCATGTTGCAATATGGAATCTTATTT
242731 TTTT
258 TTTT
* *
242735 ATAATAAAAGTGATTGCGACTAAAATATTATGAAATG-TTTAGCTAATGGAGCCTTGGAGTTCCC
1 ATAATAAAAGTGATTGCGACTAAAATATTATGAAAGGTTTTAGCTGATGGAGCCTTGGAGTTCCC
* ** **
242799 CACGATAATAAAATAAGTTAAAATCTTAAAATTTTATGAAAAT-GAATAACTA-ATACGGTTGCA
66 CACGATAATAAAATAAGTTAAAAGCACAAAATTTTATG-AAATGGAATAA-TAGATACGACTGCA
* ** * * *
242862 CACAATAATATAATGGTTCTAAATAAAATAAGTTGTAATTTGTAATGTTAAAATTAATATTAATA
129 CACAATAATATAATGGTTCTAAATGAAATAAGTTGCGACTTGTAATGTTAAATTTAGTATTAATA
* * * * ** *
242927 GAATAGATCACGCCCAAAATTTCATTTCCCCCTAAGATAGCATGTTGCAATATGGAATCTTATTA
194 GAATAGATTACACCCAGAATGTCA-TGACCCCTAAGAAAGCATGTTGCAATATGGAATCTTATT-
*
242992 GTTTT
257 TTTTT
* * *
242997 ATTATAAAAATGATTGC-ACCTAAAATATTAT--AAGGTTTTAGCCGATGGAGCCTTGGAGTTCC
1 ATAATAAAAGTGATTGCGA-CTAAAATATTATGAAAGGTTTTAGCTGATGGAGCCTTGGAGTTCC
* * * * ** * * *
243059 CCATGATAATAAAATAAGATAAGAGCACAAAGTTTTATGATTTGGTATAATAGATATGACTACGA
65 CCACGATAATAAAATAAGTTAAAAGCACAAAATTTTATGAAATGGAATAATAGATACGACTGC-A
* * *
243124 C-CAAT-A-AT-AT-GAT-T--ATGAAATAAGTTACGACTTGTAATGTTAAATTTTGTATTAATA
129 CACAATAATATAATGGTTCTAAATGAAATAAGTTGCGACTTGTAATGTTAAATTTAGTATTAATA
* * * *
243181 GAATAGATTGCACCCAGAATGTCATGGCCTCCTAATAAATCATGTTGCAATATGGAATCTTATTA
194 GAATAGATTACACCCAGAATGTCATGACC-CCTAAGAAAGCATGTTGCAATATGGAATCTTA-T-
243246 TTTTTT
256 TTTTTT
* *
243252 ATAATAAAATTGATTGC-ACCTAAAATATTATGAAA-GTTTTAG-TGATGGATCCTTGGAGTTCC
1 ATAATAAAAGTGATTGCGA-CTAAAATATTATGAAAGGTTTTAGCTGATGGAGCCTTGGAGTTCC
243314 CCACGATAATAAAA
65 CCACGATAATAAAA
243328 GTTGAGGATA
Statistics
Matches: 718, Mismatches: 116, Indels: 47
0.81 0.13 0.05
Matches are distributed among these distances:
253 3 0.00
254 83 0.12
255 65 0.09
256 9 0.01
257 4 0.01
258 2 0.00
259 2 0.00
260 9 0.01
261 292 0.41
262 73 0.10
263 148 0.21
264 28 0.04
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (261 bp):
ATAATAAAAGTGATTGCGACTAAAATATTATGAAAGGTTTTAGCTGATGGAGCCTTGGAGTTCCC
CACGATAATAAAATAAGTTAAAAGCACAAAATTTTATGAAATGGAATAATAGATACGACTGCACA
CAATAATATAATGGTTCTAAATGAAATAAGTTGCGACTTGTAATGTTAAATTTAGTATTAATAGA
ATAGATTACACCCAGAATGTCATGACCCCTAAGAAAGCATGTTGCAATATGGAATCTTATTTTTT
T
Found at i:244784 original size:39 final size:38
Alignment explanation
Indices: 244724--244878 Score: 159
Period size: 39 Copynumber: 4.0 Consensus size: 38
244714 AGTATACCTA
* *
244724 GTGCAATTGGTGGATACAACCTTATGCCTAAGCACTTCG
1 GTGCAAATGGTGGAT-CAACCTTATGCGTAAGCACTTCG
*
244763 GTGCAAATGGTGGATGTAACCTTATGCGTAAGCACTTCG
1 GTGCAAATGGTGGAT-CAACCTTATGCGTAAGCACTTCG
* * ** * * *
244802 ATACTTATGGTGGACTCAACCTTATGTGTAAGCAATTCA
1 GTGCAAATGGTGGA-TCAACCTTATGCGTAAGCACTTCG
*
244841 GTGCAAATGGTGGA-CACATTCTTATGCGTAAGCACTTC
1 GTGCAAATGGTGGATCA-A-CCTTATGCGTAAGCACTTC
244879 AATGTAACTC
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 90 0.96
40 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (38 bp):
GTGCAAATGGTGGATCAACCTTATGCGTAAGCACTTCG
Found at i:244865 original size:78 final size:78
Alignment explanation
Indices: 244731--244878 Score: 199
Period size: 78 Copynumber: 1.9 Consensus size: 78
244721 CTAGTGCAAT
* * ***
244731 TGGTGGATACAACCTTATGCCTAAGCACTTCGGTGCAAATGGTGGATGTAACCTTATGCGTAAGC
1 TGGTGGATACAACCTTATGCCTAAGCAATTCAGTGCAAATGGTGGACACAACCTTATGCGTAAGC
244796 ACTTCGATACTTA
66 ACTTCGATACTTA
** **
244809 TGGTGGACT-CAACCTTATGTGTAAGCAATTCAGTGCAAATGGTGGACACATTCTTATGCGTAAG
1 TGGTGGA-TACAACCTTATGCCTAAGCAATTCAGTGCAAATGGTGGACACAACCTTATGCGTAAG
244873 CACTTC
65 CACTTC
244879 AATGTAACTC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
78 59 0.98
79 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (78 bp):
TGGTGGATACAACCTTATGCCTAAGCAATTCAGTGCAAATGGTGGACACAACCTTATGCGTAAGC
ACTTCGATACTTA
Found at i:247403 original size:3 final size:3
Alignment explanation
Indices: 247395--247455 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
247385 TAGATTTTCA
247395 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
247443 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
247456 TTAGGTTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:248031 original size:12 final size:12
Alignment explanation
Indices: 247995--248030 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
247985 AAGAGGGGAT
*
247995 TAGAAAAAAAAA
1 TAGAAAGAAAAA
248007 TAGAAAGAAAAA
1 TAGAAAGAAAAA
248019 TCAGAAAGAAAA
1 T-AGAAAGAAAA
248031 TGAGAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (12 bp):
TAGAAAGAAAAA
Found at i:248865 original size:18 final size:17
Alignment explanation
Indices: 248844--248885 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
248834 CATATTTATA
248844 TATATTTATGAAATACAT
1 TATATTTAT-AAATACAT
*
248862 TATATTATATAAATATAT
1 TATATT-TATAAATACAT
248880 T-TATTT
1 TATATTT
248886 TATTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 4 0.18
18 14 0.64
19 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TATATTTATAAATACAT
Found at i:249129 original size:2 final size:2
Alignment explanation
Indices: 249102--249163 Score: 78
Period size: 2 Copynumber: 32.5 Consensus size: 2
249092 GCTTACTAAG
*
249102 TA TA -A TA TA -A TA AA TA CTA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
249142 TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
249164 TTATGCTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 4 0.08
2 47 0.89
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:253844 original size:47 final size:46
Alignment explanation
Indices: 253777--253996 Score: 268
Period size: 47 Copynumber: 4.8 Consensus size: 46
253767 TATAAAATCT
* *
253777 CTTACCATT-TATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
253822 CTTACCATCTAAATTCCATAAGCTCATAAGCTTATTTATA-CAAAATA
1 CTTACCAT-TAAATTCCATAAGCTCGTAAGCTTATTT-TACCAAAATA
* *
253869 CTTACCATATAAATTCCATAAGCTCATAAGCTTATTTTATACAAAATA
1 CTTACCAT-TAAATTCCATAAGCTCGTAAGCTTATTTTA-CCAAAATA
* * * * *
253917 CTTACCATTTAGTCCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
253963 CTTGCCATT--ATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTAAATTCCATAAGCTCGTAAGCTTATTT
253997 GTATGCTTAC
Statistics
Matches: 155, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.14
45 8 0.05
46 16 0.10
47 92 0.59
48 17 0.11
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.36
Consensus pattern (46 bp):
CTTACCATTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:254145 original size:40 final size:40
Alignment explanation
Indices: 254101--254258 Score: 289
Period size: 40 Copynumber: 4.0 Consensus size: 40
254091 ACCGTAGTGC
*
254101 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
*
254141 TACACATAAGTTCGTACCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
*
254181 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
254221 TACACATAAGGTCGTACCCACCATATACACCGAAGTGT
1 TACACATAAGGTCGTACCCACCATATACACCGAAGTGT
254259 CTTATAAACC
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
Found at i:256221 original size:34 final size:34
Alignment explanation
Indices: 256183--256250 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
256173 TCTCAAGAGT
256183 AAACCATCAATTTATGGAATAAAATTCTTTTTAG
1 AAACCATCAATTTATGGAATAAAATTCTTTTTAG
256217 AAACCATCAATTTATGGAATAAAATTCTTTTTAG
1 AAACCATCAATTTATGGAATAAAATTCTTTTTAG
256251 GAAATTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (34 bp):
AAACCATCAATTTATGGAATAAAATTCTTTTTAG
Found at i:260762 original size:16 final size:15
Alignment explanation
Indices: 260730--260770 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
260720 TTCATATTTG
*
260730 AGAAAAAG--AAAAG
1 AGAAAAAGAAAAAAA
260743 AGAAAAGAGAAAAAAA
1 AGAAAA-AGAAAAAAA
260759 AGAAAAAGAAAA
1 AGAAAAAGAAAA
260771 TAGAATAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 2 0.08
15 6 0.25
16 10 0.42
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAAAA
Found at i:260768 original size:22 final size:23
Alignment explanation
Indices: 260732--260775 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
260722 CATATTTGAG
260732 AAAAAGAAAAGAGAAAAGAGAAA
1 AAAAAGAAAAGAGAAAAGAGAAA
*
260755 AAAAAGAAAA-AGAAAATAGAA
1 AAAAAGAAAAGAGAAAAGAGAA
260776 TAAGTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAAGAGAAAAGAGAAA
Found at i:262813 original size:7 final size:7
Alignment explanation
Indices: 262803--262854 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
262793 ATATTTGAGA
262803 AAAAAAG
1 AAAAAAG
* *
262810 AAAAGAT
1 AAAAAAG
*
262817 AAAAAAT
1 AAAAAAG
262824 AAAAAA-
1 AAAAAAG
262830 ATAAAAAG
1 A-AAAAAG
262838 AAAAAAG
1 AAAAAAG
262845 AAAAAAG
1 AAAAAAG
262852 AAA
1 AAA
262855 TAAAAGAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 1 0.03
7 38 0.95
8 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:262813 original size:8 final size:8
Alignment explanation
Indices: 262800--262868 Score: 52
Period size: 9 Copynumber: 8.1 Consensus size: 8
262790 TTCATATTTG
262800 AGAAAAAA
1 AGAAAAAA
262808 AGAAAAGATA
1 AGAAAA-A-A
*
262818 AAAAATAAA
1 AGAAA-AAA
*
262827 AAAATAAAA
1 AGAA-AAAA
262836 AG-AAAAA
1 AGAAAAAA
262843 AG-AAAAA
1 AGAAAAAA
262850 AGAAATAAA
1 AGAAA-AAA
262859 AGAAATAAA
1 AGAAA-AAA
262868 A
1 A
262869 TATAATAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
7 13 0.25
8 9 0.17
9 23 0.43
10 7 0.13
11 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (8 bp):
AGAAAAAA
Found at i:262822 original size:14 final size:13
Alignment explanation
Indices: 262802--262859 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
262792 CATATTTGAG
262802 AAAAAAAGAAAAGA
1 AAAAAAAGAAAA-A
* *
262816 TAAAAAATAAAAA
1 AAAAAAAGAAAAA
262829 AATAAAAAGAAAAA
1 AA-AAAAAGAAAAA
262843 AGAAAAAAGAAATAA
1 A-AAAAAAGAAA-AA
262858 AA
1 AA
262860 GAAATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 2 0.05
14 31 0.84
15 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:262836 original size:23 final size:23
Alignment explanation
Indices: 262802--262873 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 23
262792 CATATTTGAG
*
262802 AAAAAAA-GAAAAGATAAAAAAT
1 AAAAAAATAAAAAGATAAAAAAT
*
262824 AAAAAAATAAAAAGA-AAAAAGAA
1 AAAAAAATAAAAAGATAAAAA-AT
* *
262847 AAAAGAAATAAAAGAAATAAAATAT
1 AAAA-AAATAAAA-AGATAAAAAAT
262872 AA
1 AA
262874 TAAGTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 12 0.30
23 11 0.28
24 8 0.20
25 5 0.12
26 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (23 bp):
AAAAAAATAAAAAGATAAAAAAT
Found at i:262839 original size:28 final size:32
Alignment explanation
Indices: 262804--262868 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
262794 TATTTGAGAA
*
262804 AAAAAG-AAAAG-ATAAA-AAATAAAA-AAAT
1 AAAAAGAAAAAGAAAAAAGAAATAAAAGAAAT
262832 AAAAAGAAAAAAGAAAAAAGAAATAAAAGAAAT
1 AAAAAG-AAAAAGAAAAAAGAAATAAAAGAAAT
262865 AAAA
1 AAAA
262869 TATAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
30 5 0.16
31 4 0.13
32 8 0.26
33 8 0.26
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.08
Consensus pattern (32 bp):
AAAAAGAAAAAGAAAAAAGAAATAAAAGAAAT
Found at i:264993 original size:16 final size:17
Alignment explanation
Indices: 264969--265001 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
264959 CATTTAAATC
*
264969 TTTTCTGAAAATTAAAA
1 TTTTCTGAAAAGTAAAA
264986 TTTT-TGAAAAGTAAAA
1 TTTTCTGAAAAGTAAAA
265002 AAAATGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTTCTGAAAAGTAAAA
Found at i:266974 original size:4 final size:4
Alignment explanation
Indices: 266965--267292 Score: 638
Period size: 4 Copynumber: 82.0 Consensus size: 4
266955 TTTTTATACT
266965 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
267013 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
267061 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
267109 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
267157 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
267205 CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
267253 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
267293 GTGTGTTTAT
Statistics
Matches: 320, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 320 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:267354 original size:2 final size:2
Alignment explanation
Indices: 267347--267371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267337 AAGTTAAAAG
267347 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
267372 GTAAATGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:282543 original size:22 final size:22
Alignment explanation
Indices: 282501--282542 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
282491 TCCAGAATGC
282501 TAGGAGGGAACCGATTCCCCCA
1 TAGGAGGGAACCGATTCCCCCA
*
282523 TAGG-GGGTACCGATTCCCCC
1 TAGGAGGGAACCGATTCCCCC
282543 CTGTTCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (22 bp):
TAGGAGGGAACCGATTCCCCCA
Found at i:292902 original size:34 final size:36
Alignment explanation
Indices: 292858--292959 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
292848 TTTCGTCCTA
292858 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
292893 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
292928 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
292960 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:296818 original size:21 final size:20
Alignment explanation
Indices: 296773--296841 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
296763 CAAAAAGGGC
*
296773 AAAAAGAAAAAAGAAAATAAGCA
1 AAAAAGAAAAAA-CAAA-AA-CA
*
296796 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAAAACA
* *
296817 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAAAACA
296837 AAAAA
1 AAAAA
296842 AAGGGACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.43
21 7 0.17
22 2 0.05
23 7 0.17
24 7 0.17
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:297504 original size:22 final size:22
Alignment explanation
Indices: 297479--297527 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
297469 CCATCAATCT
* *
297479 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
297501 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
297523 TTTGA
1 TTTGA
297528 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:297966 original size:18 final size:18
Alignment explanation
Indices: 297943--297978 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
297933 TCAACATCAA
* *
297943 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
297961 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
297979 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:298446 original size:36 final size:35
Alignment explanation
Indices: 298406--298739 Score: 200
Period size: 36 Copynumber: 9.5 Consensus size: 35
298396 ACTCATGATT
* * *
298406 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * ** *
298442 GTTT-TCACTATAAGAGTTTTGTCTCTCTTGAAACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* *
298477 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * *
298513 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGATA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * *
298549 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * * * *
298585 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* * *
298613 TGTTT-TCTTTGAAACAAATTCCGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATT-TGTCTCTCTTGAGACA
* ** *
298650 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * *
298687 GTTTCTCTTGAAACAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
298723 GTTTCCCTTGAAACAAA
1 GTTTCTCTTAAAACAAA
298740 ACCTTTGAAT
Statistics
Matches: 237, Mismatches: 42, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.01
29 18 0.08
30 2 0.01
35 33 0.14
36 145 0.61
37 34 0.14
38 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:298567 original size:72 final size:71
Alignment explanation
Indices: 298459--298739 Score: 290
Period size: 72 Copynumber: 4.0 Consensus size: 71
298449 CTATAAGAGT
* * *
298459 TTTGTCTCTCTTGAAACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
298524 AACAAA
66 AACAAA
* *
298530 TTTCGTCTATCTTGAGATAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
298595 AAACAAA
65 AAACAAA
* * * * ** * **
298602 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
298660 GAACTAAGT
65 AAAC-AA-A
* * *
298669 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
298733 AAACAAA
65 AAACAAA
298740 ACCTTTGAAT
Statistics
Matches: 168, Mismatches: 30, Indels: 24
0.76 0.14 0.11
Matches are distributed among these distances:
64 3 0.02
65 45 0.27
66 5 0.03
71 3 0.02
72 71 0.42
73 39 0.23
74 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:298697 original size:102 final size:102
Alignment explanation
Indices: 298514--298702 Score: 281
Period size: 102 Copynumber: 1.9 Consensus size: 102
298504 CTTGAGACAG
* * *
298514 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGATAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
298579 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
298616 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
298680 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
298703 TTTTCGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 32 0.42
102 45 0.58
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:298734 original size:138 final size:137
Alignment explanation
Indices: 298478--298802 Score: 431
Period size: 138 Copynumber: 2.4 Consensus size: 137
298468 CTTGAAACAG
* *
298478 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* * *
298543 GAGATAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
298608 GAATATGT-
131 GAAT-T-TA
** * * * * *
298616 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
298680 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
298744 TTGAATTTA
129 TTGAATTTA
* * *
298753 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
298803 CAAAATCTTC
Statistics
Matches: 161, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
136 1 0.01
137 51 0.32
138 109 0.68
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATTTA
Found at i:298798 original size:65 final size:65
Alignment explanation
Indices: 298688--298871 Score: 201
Period size: 65 Copynumber: 2.8 Consensus size: 65
298678 CTTGAGACAG
* * ** * **
298688 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCTTTGAATTT
1 TTTCTCCTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTT
298752 A
65 A
* *
298753 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAACCTTCAAATT
298818 TA
64 TA
* * *
298820 TTTC-CCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTCTCC-TAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
298872 CAGATATCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
65 32 0.32
66 14 0.14
67 28 0.28
68 27 0.27
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (65 bp):
TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTA
Found at i:298832 original size:67 final size:67
Alignment explanation
Indices: 298688--298870 Score: 203
Period size: 68 Copynumber: 2.7 Consensus size: 67
298678 CTTGAGACAG
* * ** * **
298688 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAAT
298750 TTA
65 TTA
* *
298753 TTTCTCC-TAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAAT
1 TTTC-CCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAAT
298817 TTA
65 TTA
* * *
298820 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
298871 ACAGATATCT
Statistics
Matches: 99, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
65 30 0.30
66 11 0.11
67 26 0.26
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATT
TA
Found at i:299591 original size:105 final size:105
Alignment explanation
Indices: 299395--300542 Score: 1797
Period size: 105 Copynumber: 11.0 Consensus size: 105
299385 GCACTCGAGG
* * * *
299395 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* * *
299460 AGTCAATCTCAACTTCACAATGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
299501 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAATAAATTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
299566 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
299606 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTGCTTTTCAACAACAACTTCTCAATTTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGA-C-C-GCTGCTTGTCAACAACAACTTCTCAATTTC
299671 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
299714 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
299779 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
299819 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
299884 GCCAATTTCAACTTCACAACGAA-GA-ATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
299922 CAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
299987 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
300027 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
300092 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
300132 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
300197 GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
300237 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
300302 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
300342 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
300402 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
300442 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* * *
300507 AACCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
300543 TGGAACAATG
Statistics
Matches: 970, Mismatches: 61, Indels: 22
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.08
101 3 0.00
102 3 0.00
103 100 0.10
104 7 0.01
105 600 0.62
106 78 0.08
107 2 0.00
108 95 0.10
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:300081 original size:313 final size:315
Alignment explanation
Indices: 299395--300542 Score: 1819
Period size: 313 Copynumber: 3.7 Consensus size: 315
299385 GCACTCGAGG
* * *
299395 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* * * *
299460 AGTCAATCTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACG
* * * * * *
299525 AAGGGACCGCTGCCTGTCAACAATAAATTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
130 AAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAG
* * *
299590 GATATTGGACTTCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTGCTTTTCAACA
195 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGC--C-TGTCAACA
299655 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
257 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
299714 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
299779 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
299844 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAA-G
131 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
*
299908 A-ATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGCCTGTCAACAACAA
196 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAA
299972 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
261 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
300027 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
300092 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
*
300157 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCTAATTTCAACTTCACAACGAAGG
131 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
300222 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA
196 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAA
* * *
300287 CTTCCCAATCTAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
261 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
300342 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
300402 TTCAATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACG
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACG
* * * ** * * *
300466 AAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGT-TCCAGAACCAATTTCAACTTCACGACGG
130 AAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCAATTTCAACTTCACAACGA
300530 AGGATATTGGACT
193 AGGATATTGGACT
300543 TGGAACAATG
Statistics
Matches: 784, Mismatches: 40, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
309 2 0.00
310 82 0.10
311 47 0.06
312 2 0.00
313 259 0.33
314 5 0.01
315 159 0.20
316 47 0.06
317 2 0.00
318 137 0.17
319 42 0.05
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (315 bp):
CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAA
CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:301134 original size:34 final size:36
Alignment explanation
Indices: 301090--301191 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
301080 TTTCGTCCTA
301090 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
301125 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
301160 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
301192 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:301659 original size:11 final size:13
Alignment explanation
Indices: 301634--301663 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
301624 TTATTAGTGT
301634 TATTATATATATA
1 TATTATATATATA
*
301647 TATTATATTTATA
1 TATTATATATATA
301660 TATT
1 TATT
301664 TCTTATTTTG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATATATATA
Found at i:303809 original size:66 final size:66
Alignment explanation
Indices: 303687--303823 Score: 177
Period size: 66 Copynumber: 2.1 Consensus size: 66
303677 TCGATTTCAT
* * *
303687 TAACAGCGACTCCGATAACAGTAACTCTGTTAATAAAATACAATCCCTTAACCCCCGATATTCCA
1 TAACAACGACTCCGATAACAGTAACTCTGATAATAAAATACAATCCCTTAACCCCCGATACTCCA
303752 A
66 A
* * * * *
303753 TAACAACGACTCCGTTAACAGTGACTTTGATAATAAAAATATAATCTCTTAA-CCCCGATACTCC
1 TAACAACGACTCCGATAACAGTAACTCTGATAAT-AAAATACAATCCCTTAACCCCCGATACTCC
*
303817 AT
65 AA
303819 TAACA
1 TAACA
303824 GATGCTCCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 46 0.75
67 15 0.25
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (66 bp):
TAACAACGACTCCGATAACAGTAACTCTGATAATAAAATACAATCCCTTAACCCCCGATACTCCA
A
Found at i:305458 original size:12 final size:12
Alignment explanation
Indices: 305441--305465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
305431 GTAGTTTGGA
305441 GGTGGCTGCCAC
1 GGTGGCTGCCAC
305453 GGTGGCTGCCAC
1 GGTGGCTGCCAC
305465 G
1 G
305466 ATCAGAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.44, T:0.16
Consensus pattern (12 bp):
GGTGGCTGCCAC
Found at i:317592 original size:15 final size:15
Alignment explanation
Indices: 317559--317603 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
317549 ATAAAAGAAG
*
317559 AAAAAAAGAAAATTGAA
1 AAAAAAAGAAAA--AAA
317576 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
*
317591 AAGAAAAGAAAAA
1 AAAAAAAGAAAAA
317604 TAAATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 14 0.54
17 12 0.46
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.04
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Done.