Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008511.1 Hibiscus syriacus cultivar Beakdansim tig00111366_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: 2221980
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 9
Found at i:684 original size:24 final size:24
Alignment explanation
Indices: 657--717 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
647 ATCATTAAAT
*
657 TTAGGTATGTACAATATCTACATA
1 TTAGGTATGTACAATAACTACATA
****
681 TTAGGTATGTTTGTTAACTACATA
1 TTAGGTATGTACAATAACTACATA
*
705 TTAGGTATATACA
1 TTAGGTATGTACA
718 TCTTTTGAGT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (24 bp):
TTAGGTATGTACAATAACTACATA
Found at i:1856 original size:38 final size:39
Alignment explanation
Indices: 1809--1894 Score: 138
Period size: 38 Copynumber: 2.2 Consensus size: 39
1799 TCCGATGCTC
* *
1809 ATCATAATCCAAAGCTCATATGGTGCCAA-CAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
1847 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1886 ATCAAAATC
1 ATCAAAATC
1895 TACAACTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 26 0.59
39 18 0.41
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.19
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2346 original size:23 final size:23
Alignment explanation
Indices: 2315--2387 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2305 ATAGGTAAAA
* *
2315 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGATT
* *
2338 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGATT
*
2361 ATATAATGTAATAGGTAGTGATT
1 ATATAATGTAATAGGTAGCGATT
2384 ATAT
1 ATAT
2388 TGTAAGTATC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:2769 original size:23 final size:22
Alignment explanation
Indices: 2743--2819 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
2733 ATAGGTAAAA
2743 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
* *
2766 ATATATGTAATAGGTATCGTTT
1 ATATATGTAATAGGTAGCGCTT
* *
2788 ATATAATGTAATAGGTAGTGGTT
1 ATAT-ATGTAATAGGTAGCGCTT
2811 ATAT-TGTAA
1 ATATATGTAA
2820 GTATCTATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 5 0.10
22 20 0.42
23 23 0.48
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (22 bp):
ATATATGTAATAGGTAGCGCTT
Found at i:2838 original size:45 final size:45
Alignment explanation
Indices: 2743--2838 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
2733 ATAGGTAAAA
* * *
2743 ATATGATGTAATAGGTAGCGCTTATATATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCATTT
* * *
2788 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAGTATCTATCATTT
1 ATATAATGTAATAGGTAGCGCTTATATATGTAA-TAGCTATCATTT
*
2833 TTATAA
1 ATATAA
2839 AAGTGTCCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 5 0.12
45 38 0.88
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCATTT
Found at i:2909 original size:427 final size:428
Alignment explanation
Indices: 2113--3584 Score: 2619
Period size: 427 Copynumber: 3.5 Consensus size: 428
2103 GTTAATGTTG
* * *
2113 TTAAATT-TAAATTCTAAATATTATTTTATAAAATATCAAAACAATAAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
2177 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
2242 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
2307 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATAT-ATGTAATAGGTATCGTTTATATAATGTAA
2372 TAGGTAGTGATTATATTGTAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
260 TAGGTAGTGATTATATTGTAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
* * * *
2437 GAAAATATTAATTTAAGGTTATCATTTGAGTGGGTTTTAAGATATTAATTTAGTAATTATAGGTG
325 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
2502 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
390 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
2541 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
* * * *
2606 CTGAAATTATTAAATTAATATTATAGGTGGAAAACACGAAACGCTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
*
2671 AAATTACATAACTTTAAAAGAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC-A-ATAA
130 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
2734 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATATGTAATAGGTATCGTTTATATAATGTAA
195 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATATGTAATAGGTATCGTTTATATAATGTAA
* *
2799 TAGGTAGTGGTTATATTGTAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
260 TAGGTAGTGATTATATTGTAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
*
2864 GAAAACATTAATTTAAGGTTATCTTTTGAGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCG
325 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
2929 TCTAATGATTTATTTTTTACGTTACG--ATATA-TATTA
390 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
2965 TTAAATTAAAAATTCTAAATAATATTTTAT--AATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
3028 ATGAAATTATTAAATTAAT-TTGTAGGTGGAAAACATGAAACACTTTTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
3092 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
130 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
3157 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATATTGTAATAGGTAGCGTTTATATAATGTA
195 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATA-TGTAATAGGTATCGTTTATATAATGTA
*
3222 ATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
259 ATAGGTAGTGATTATATTGT-AAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
3287 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATA-TAATTTAGT-ATTATAGG
323 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
3350 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
388 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
3391 TTAAATTAAAAATTCTAAAT--TATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
3454 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
* *
3519 AATTACATAACTTTAAATGAAGTATCGATCCTTTTTATAAAAAGTATGGACAGTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
3584 A
196 A
3585 TAATGTAATA
Statistics
Matches: 1003, Mismatches: 29, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
421 98 0.10
422 52 0.05
423 77 0.08
424 97 0.10
425 98 0.10
426 158 0.16
427 205 0.20
428 47 0.05
429 98 0.10
430 73 0.07
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (428 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
AGGTAAAAATATGATGTAATAGGTAGCGCTTATATATGTAATAGGTATCGTTTATATAATGTAAT
AGGTAGTGATTATATTGTAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
CTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:3198 original size:23 final size:23
Alignment explanation
Indices: 3166--3238 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
3156 ATAGGTAAAA
*
3166 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3189 ATATATTGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
3212 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
3235 ATAT
1 ATAT
3239 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:5442 original size:2 final size:2
Alignment explanation
Indices: 5435--5481 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5425 CGAGTAACTC
5435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5477 AT AT A
1 AT AT A
5482 AAACTCATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6307 original size:26 final size:26
Alignment explanation
Indices: 6278--6363 Score: 109
Period size: 26 Copynumber: 3.1 Consensus size: 26
6268 AGGGGCCTAC
*
6278 GGCCTGACCTGTATAAAGCCTGGTCT
1 GGCCTGACATGTATAAAGCCTGGTCT
6304 GGCCTGACATGTATAAAGCCTGGCCTGGTCT
1 GGCCTGACATGTATAAA-----GCCTGGTCT
*
6335 GGCCTGACATGTATAAAGCCTGGCCT
1 GGCCTGACATGTATAAAGCCTGGTCT
6361 GGC
1 GGC
6364 ATGGCCTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 27 0.51
31 26 0.49
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (26 bp):
GGCCTGACATGTATAAAGCCTGGTCT
Found at i:6330 original size:31 final size:31
Alignment explanation
Indices: 6295--6370 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
6285 CCTGTATAAA
6295 GCCTGGTCTGGCCTGACATGTATAAAGCCTG
1 GCCTGGTCTGGCCTGACATGTATAAAGCCTG
6326 GCCTGGTCTGGCCTGACATGTATAAAGCCTG
1 GCCTGGTCTGGCCTGACATGTATAAAGCCTG
6357 GCCTGG-CATGGCCT
1 GCCTGGTC-TGGCCT
6371 ATTTAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 1 0.02
31 43 0.98
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (31 bp):
GCCTGGTCTGGCCTGACATGTATAAAGCCTG
Found at i:7344 original size:60 final size:60
Alignment explanation
Indices: 7232--7350 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
7222 CTTTCATCCC
* * * *
7232 TAAACTTTTAAATATTTTAATTGCATCCCTAAACTATGACTATCATTTTAAATTAGTCCT
1 TAAACTTTTAAACATTTCAATTGCATCCCCAAACTATGACTATCATTCTAAATTAGTCCT
* * * * *
7292 TAAACTTTTGAACATTTCAATTTCATCCCCAAACTGTGACCT-TCGTTCTAAATTGGTCC
1 TAAACTTTTAAACATTTCAATTGCATCCCCAAACTATGA-CTATCATTCTAAATTAGTCC
7351 CCCAGACTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (60 bp):
TAAACTTTTAAACATTTCAATTGCATCCCCAAACTATGACTATCATTCTAAATTAGTCCT
Found at i:7608 original size:60 final size:60
Alignment explanation
Indices: 7544--7664 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 60
7534 TCATGGTTTA
* *
7544 GGGATGAAATT-AGAATATTCAAAAGTTTTAGGA-CTAATTTAGAATGA-AATACATAATTTG
1 GGGATGAAATTGA-AATATTCAAAAGTTTAAGGATC-AATTTAAAATGAGAAT-CATAATTTG
* *
7604 GGGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATGAGAATTATAATTTG
1 GGGATGAAATTGAAATATTCAAAAGTTTAAGGATCAATTTAAAATGAGAATCATAATTTG
7664 G
1 G
7665 AAACATATGA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
60 49 0.91
61 5 0.09
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTGAAATATTCAAAAGTTTAAGGATCAATTTAAAATGAGAATCATAATTTG
Found at i:8700 original size:53 final size:53
Alignment explanation
Indices: 8643--8754 Score: 206
Period size: 53 Copynumber: 2.1 Consensus size: 53
8633 AACACTTTCT
8643 ATTATTAAAAAAGAATCGTCTTTATTGTCCATTTAATTCTTCATTTTCACTCA
1 ATTATTAAAAAAGAATCGTCTTTATTGTCCATTTAATTCTTCATTTTCACTCA
* *
8696 ATTATTAAAAAGGAATTGTCTTTATTGTCCATTTAATTCTTCATTTTCACTCA
1 ATTATTAAAAAAGAATCGTCTTTATTGTCCATTTAATTCTTCATTTTCACTCA
8749 ATTATT
1 ATTATT
8755 TGAAGCGTGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.47
Consensus pattern (53 bp):
ATTATTAAAAAAGAATCGTCTTTATTGTCCATTTAATTCTTCATTTTCACTCA
Found at i:11675 original size:6 final size:6
Alignment explanation
Indices: 11664--11709 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
11654 TCACTAACTT
11664 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT- TTTTTCA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTTT
11710 GTTCTCATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.13
6 29 0.76
7 4 0.11
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:12367 original size:19 final size:19
Alignment explanation
Indices: 12333--12377 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
12323 ATTTAGACAT
12333 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
12351 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
12370 TTTGCATT
1 TTTGCATT
12378 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:15972 original size:84 final size:84
Alignment explanation
Indices: 15817--16852 Score: 1007
Period size: 84 Copynumber: 12.6 Consensus size: 84
15807 GGACTATCTG
** * * * *
15817 CCAAAGACCCCCGAGTTCGATTACACTCAGCCTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAG-CTCCAAGGCACATCATTTGCAGCATAACTTAAGT
15882 CGAGAAGGGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * *
15902 CCAAAGACCTTCGAGTTCGAATACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
15967 TAGAAGGGTTGTCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* * * * * *
15986 CAAAAGACCTTTGAGTTCGACTATGCTCAGCT-CAACGGTACATCATTTGCAGTATAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGT
*
16050 CGAGAAGGGCTATCTG----
65 CGAGAAGGGTTATCTGCCAA
** * * * *
16066 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
16131 CGAGAAGGGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * *
16151 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
16216 TAGAAGGGTTGTCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* * * * *
16235 CAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTACAGTATAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGT
*
16299 CGAGAAGGGCTATCTG----
65 CGAGAAGGGTTATCTGCCAA
** * * * *
16315 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
16380 CGAGAAGGGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * *
16400 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
16465 TAGAAGGGTTGTCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* * * * * *
16484 CAAAAGACCTTTGAGTTCGACTACACTCGGCT-CAACGGCATATCATTTGCAGCACAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGT
* * * *
16548 CTATAAGGGTTGTATGCCAA
65 CGAGAAGGGTTATCTGCCAA
** * * * * * * * *
16568 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACTTCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
16633 CTAGAA--G------G-C-A
65 CGAGAAGGGTTATCTGCCAA
* * * *
16643 --AAAGACCTTTGAGTTCGACTACGCTTAGCT-CAACGGCACATCATTTGTAGCATAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGT
* *
16705 CGAGAAGAGCTATCTG----
65 CGAGAAGGGTTATCTGCCAA
* * * * * * * * *
16721 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
16786 CTATG-AGGGTTATCTGTC-A
65 CGA-GAAGGGTTATCTGCCAA
*
16805 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
16853 ACAACATAGC
Statistics
Matches: 780, Mismatches: 137, Indels: 70
0.79 0.14 0.07
Matches are distributed among these distances:
71 1 0.00
72 28 0.04
73 23 0.03
74 1 0.00
75 1 0.00
76 1 0.00
77 1 0.00
80 74 0.09
81 116 0.15
82 4 0.01
83 24 0.03
84 397 0.51
85 108 0.14
86 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
GAGAAGGGTTATCTGCCAA
Found at i:16219 original size:249 final size:249
Alignment explanation
Indices: 15781--16627 Score: 1442
Period size: 249 Copynumber: 3.4 Consensus size: 249
15771 CAAACAAACT
* * *
15781 ATTTGCAACATAGCTTAAGTCAAGAAGGACTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
15846 GCCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
15911 TTCGAGTTCGAATACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
* *
15976 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTATGCTCAGCTCAACGGTACATC
196 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
*
16030 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
16095 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
16160 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
16225 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
196 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
* *
16279 ATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
16344 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
16409 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACACAACTTAAGTCTAGAAGGGT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
* * *
16474 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCGGCTCAACGGCATATC
196 TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
* * * * * **
16528 ATTTGCAGCACAACTTAAGTCTATAAGGGTTGTATGCCAACCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGG--CTAT--CTGCCAAAGACCCCCGAGTTCGATTACA
* *
16593 CTCAGCTTCGAGGGCACTTCATTTACAGCATAACT
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACT
16628 CAAGGCTAGA
Statistics
Matches: 568, Mismatches: 26, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
249 506 0.89
251 3 0.01
253 59 0.10
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (249 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGT
TGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
Found at i:16447 original size:333 final size:328
Alignment explanation
Indices: 15817--16852 Score: 1232
Period size: 333 Copynumber: 3.1 Consensus size: 328
15807 GGACTATCTG
** * * * *
15817 CCAAAGACCCCCGAGTTCGATTACACTCAGCCTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAG-CTCCAAGGCACATCATTTGCAGCACAACTTAAGT
* * *
15882 CGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGAATACGCTCAGCTCCAAGGCATATCA
65 CTAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGAATACGCTCAGCT-CAAGGCACATCA
* * * * *
15947 TTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTATGC
129 TTTACAGCATAACTTAAGTCTAGAAGGGCTATCTG-C--C-AAAGACCTTTGAGTTCGACTACGC
* * *
16012 TCAGCTCAACGGTACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC
190 TCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCT
* *
16077 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
255 CGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTT
16142 ATCTGCCAA
320 ATCTGCCAA
* * *
16151 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTC
* * *
16216 TAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCAT
66 TAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGAATACGCTCAGCTCAA-GGCACATCAT
* * * *** * *
16281 TTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGC
130 TTACAGCATAACTTAAGTCTAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCAGC
* * * * *
16346 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTT
195 -TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCT
* * * * * *
16411 CGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAACACAACTTAAGTCTAGAAGGGTT
255 CGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTT
*
16475 GTCTGCCAA
320 ATCTGCCAA
* * * *
16484 CAAAAGACCTTTGAGTTCGACTACACTCGGCT-CAACGGCATATCATTTGCAGCACAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCACAACTTAAGT
* * ** * * * *
16548 CTATAAGGGTTGTATGCCAACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACTTC
65 CTAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGAATACGCTCAGC-TC-AAGGCACATC
* * *
16613 ATTTACAGCATAACTCAAGGCTAGAA-GGC-A------AAAGACCTTTGAGTTCGACTACGCTTA
128 ATTTACAGCATAACTTAAGTCTAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCA
* *
16670 GCTCAACGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCGA
193 GCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGA
* * *
16735 GTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTATG-AGGGTTAT
258 GTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTCTA-GAAGGGTTAT
*
16799 CTGTC-A
322 CTGCCAA
* *
16805 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
16853 ACAACATAGC
Statistics
Matches: 595, Mismatches: 95, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
321 68 0.11
322 42 0.07
323 1 0.00
325 43 0.07
326 23 0.04
329 23 0.04
330 44 0.07
332 8 0.01
333 259 0.44
334 83 0.14
335 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (328 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTC
TAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGAATACGCTCAGCTCAAGGCACATCATT
TACAGCATAACTTAAGTCTAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCAGCT
CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTT
CGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGC
CAA
Found at i:19840 original size:16 final size:17
Alignment explanation
Indices: 19790--19841 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
19780 AAAAAAATTA
19790 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
19807 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
19822 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
19838 AATT
1 AATT
19842 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:26976 original size:16 final size:17
Alignment explanation
Indices: 26951--26983 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
26941 GACGTGTTTC
*
26951 TATATCACAT-TTCATG
1 TATATAACATGTTCATG
26967 TATATAACATGTTCATG
1 TATATAACATGTTCATG
26984 AAGATTGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATAACATGTTCATG
Found at i:36058 original size:29 final size:31
Alignment explanation
Indices: 35983--36130 Score: 202
Period size: 30 Copynumber: 5.0 Consensus size: 31
35973 CCCGAAGGAC
* *
35983 CAGTCCATA-GATTCCGAAGAACCTAGGT-AT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
36013 CAGTCCATATGTCCCGAAGGACATA-GTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
36043 CAGT-CATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
36073 CAGTCCATATGTTCCGAAGAAC-TAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
36103 CAGTCCATATG-T-CGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
36131 CCCTCGACCT
Statistics
Matches: 107, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
28 8 0.07
29 28 0.26
30 53 0.50
31 18 0.17
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:36119 original size:59 final size:60
Alignment explanation
Indices: 35994--36130 Score: 192
Period size: 59 Copynumber: 2.3 Consensus size: 60
35984 AGTCCATAGA
* * *
35994 TTCCGAAGAACCTAGGT-ATCAGTCCATATGTCCCGAAGGACATAGTAAACAGTCATATG
1 TTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGTAAACAGTCATATG
*
36053 TTCCGAAGAACATAGGTAAACAGTCCATATGTTCCGAAGAAC-TAGGTAAACAGTCCATATG
1 TTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATA-GTAAACAGT-CATATG
36114 -T-CGAAGAACATAGGTAA
1 TTCCGAAGAACATAGGTAA
36131 CCCTCGACCT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
59 34 0.48
60 31 0.44
61 6 0.08
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (60 bp):
TTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGTAAACAGTCATATG
Found at i:40647 original size:22 final size:21
Alignment explanation
Indices: 40622--40667 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
40612 GTCTTTGCTA
* *
40622 AATGTTAGACTCCTTAGCAATG
1 AATGATAGACTCCTCAGCAA-G
40644 AATGATAGACTCCTCAGCAAG
1 AATGATAGACTCCTCAGCAAG
40665 AAT
1 AAT
40668 CTGCTCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (21 bp):
AATGATAGACTCCTCAGCAAG
Found at i:53491 original size:15 final size:15
Alignment explanation
Indices: 53433--53503 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
53423 TTTAATTAAA
53433 TTAT-ATTTAA-ATT
1 TTATAATTTAATATT
*
53446 TTAACTAATTT-ATA-A
1 TT-A-TAATTTAATATT
*
53461 TTATACATTTAGTATT
1 TTATA-ATTTAATATT
53477 TTATAATTTAATATT
1 TTATAATTTAATATT
*
53492 TTATAAATTAAT
1 TTATAATTTAAT
53504 TTAATAGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 26 0.57
16 10 0.22
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:53699 original size:42 final size:42
Alignment explanation
Indices: 53640--53753 Score: 210
Period size: 42 Copynumber: 2.7 Consensus size: 42
53630 CGAATTCTCT
*
53640 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAGTGTTTTCCCG
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCG
53682 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCG
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCG
*
53724 TGTTTGTTTCACGTAATTAGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAA
53754 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.46
Consensus pattern (42 bp):
TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCG
Found at i:54001 original size:18 final size:17
Alignment explanation
Indices: 53946--54005 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 17
53936 TATTATATAT
53946 TTATAATAATAT-AATA
1 TTATAATAATATAAATA
53962 TTAT-ATAAATAATCAATTATA
1 TTATAAT-AAT-AT-AA--ATA
53983 TTATAATAATATAAGATA
1 TTATAATAATATAA-ATA
54001 TTATA
1 TTATA
54006 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
15 2 0.06
16 7 0.19
17 2 0.06
18 8 0.22
19 3 0.08
20 2 0.06
21 10 0.28
22 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTATAATAATATAAATA
Found at i:54049 original size:28 final size:28
Alignment explanation
Indices: 54018--54081 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
54008 TTTATTTTAA
54018 TAATATAT-AATAAAAAAATTTATATATT
1 TAATA-ATGAATAAAAAAATTTATATATT
* **
54046 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAAAAAAATTTATATATT
54074 TAAATAAT
1 T-AATAAT
54082 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 23 0.74
29 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATAATGAATAAAAAAATTTATATATT
Found at i:54061 original size:19 final size:19
Alignment explanation
Indices: 54039--54091 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
54029 AAAAAAATTT
*
54039 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
54058 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
54080 ATAT-TTTAATAA
1 ATATATTTAATAA
54092 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:54112 original size:23 final size:23
Alignment explanation
Indices: 54086--54130 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54076 AATAATATTT
54086 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
54109 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
54131 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:57595 original size:38 final size:38
Alignment explanation
Indices: 57553--57634 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 38
57543 TTTATTAAAC
* *
57553 ATTTTTAT-ATTTTCAAT-TTTGTAAAAAAAATTATATAA
1 ATTTTTATGAATTTAAATCTTT-TAAAAAAAA-TATATAA
*
57591 A-TTTTATGAATTTAAATCTTTTAAAGAAAATATATAA
1 ATTTTTATGAATTTAAATCTTTTAAAAAAAATATATAA
57628 ATATTTT
1 AT-TTTT
57635 TTAACTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
37 14 0.38
38 16 0.43
39 7 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (38 bp):
ATTTTTATGAATTTAAATCTTTTAAAAAAAATATATAA
Found at i:59209 original size:18 final size:19
Alignment explanation
Indices: 59171--59213 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
59161 AATCAAATCC
*
59171 TTTTTTTAATAGAAATAAT
1 TTTTTTTAATAAAAATAAT
59190 TTTTTTTAATAAAAAT-AT
1 TTTTTTTAATAAAAATAAT
59208 TTTTTT
1 TTTTTT
59214 GGGTCTGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTTTAATAAAAATAAT
Found at i:60790 original size:21 final size:21
Alignment explanation
Indices: 60766--60812 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
60756 ACTGGAAATA
*
60766 TTATTATTTT-TATCGGTTTTG
1 TTATT-TTTTCTACCGGTTTTG
*
60787 TTATTTTTTCTACCGTTTTTG
1 TTATTTTTTCTACCGGTTTTG
60808 TTATT
1 TTATT
60813 GTTGGGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.68
Consensus pattern (21 bp):
TTATTTTTTCTACCGGTTTTG
Found at i:60911 original size:22 final size:22
Alignment explanation
Indices: 60883--60925 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
60873 TTTTAAGTAA
* *
60883 TTTTTTATCGATTTTGTTATTC
1 TTTTTTACCGATTTTATTATTC
60905 TTTTTTACCGATTTTATTATT
1 TTTTTTACCGATTTTATTATT
60926 TAAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTTTTACCGATTTTATTATTC
Found at i:64902 original size:30 final size:30
Alignment explanation
Indices: 64839--64901 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
64829 AGAGACAAAA
*
64839 TTTTGTTTCCAAAGAAACCGACTCAAAGAT
1 TTTTGTTTCCAAAGAAACCAACTCAAAGAT
64869 TTTTGTTTCCAAAGAAA-CAACTCAAAGAT
1 TTTTGTTTCCAAAGAAACCAACTCAAAGAT
64898 TTTT
1 TTTT
64902 TCACGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (30 bp):
TTTTGTTTCCAAAGAAACCAACTCAAAGAT
Found at i:64928 original size:91 final size:88
Alignment explanation
Indices: 64826--64989 Score: 238
Period size: 91 Copynumber: 1.8 Consensus size: 88
64816 GATTTGTTTT
* * * * *
64826 AAGAGAGACAAAATTTTGTTTCCAAAGAAACCGACTCAAAGATTTTTGTTTCCAAAGAAACAACT
1 AAGAGAGACAAAACTTTCTTTCAAAAGAAACAGACTCAAAGA--TTT-TTTCAAAAGAAACAACT
64891 CAAAGATTTTTTCACGAAATTGTCTC
63 CAAAGATTTTTTCACGAAATTGTCTC
* *
64917 AAGAGAGACAAAACTTTCTTTCAAAAGAAATAGACTCAAAGATTTTTTCAAAATAAACAACTCAA
1 AAGAGAGACAAAACTTTCTTTCAAAAGAAACAGACTCAAAGATTTTTTCAAAAGAAACAACTCAA
64982 AGATTTTT
66 AGATTTTT
64990 ATTCAAAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
88 26 0.39
89 3 0.05
91 37 0.56
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (88 bp):
AAGAGAGACAAAACTTTCTTTCAAAAGAAACAGACTCAAAGATTTTTTCAAAAGAAACAACTCAA
AGATTTTTTCACGAAATTGTCTC
Found at i:65015 original size:29 final size:28
Alignment explanation
Indices: 64740--65031 Score: 137
Period size: 29 Copynumber: 10.3 Consensus size: 28
64730 ATTTGTTTTT
*
64740 AAAGAAATAGACTCAAAGATGATTTTGTT-A
1 AAAGAAACAGACTCAAAGAT--TTTT-TTCA
** *
64770 GTAGAAACAAACTCAAAGATTTTTTTTCA
1 AAAGAAACAGACTCAAAGA-TTTTTTTCA
* *
64799 AAATG-AGCATACTCAAAGATTTGTTTT--
1 AAA-GAAACAGACTCAAAGATTT-TTTTCA
* *
64826 -AAG--AGAGA--CAAA-ATTTTGTTTCC
1 AAAGAAACAGACTCAAAGATTTT-TTTCA
* *
64849 AAAGAAACCGACTCAAAGATTTTTGTTTCC
1 AAAGAAACAGACTCAAAGA-TTTT-TTTCA
64879 AAAGAAACA-ACTCAAAGA-TTTTTTCA
1 AAAGAAACAGACTCAAAGATTTTTTTCA
* * ** *
64905 CGAAATTGTCTCAAGAGAGACAAA-ACTTTCTTTCA
1 --AAA--G---AAACAGACTCAAAGA-TTTTTTTCA
*
64940 AAAGAAATAGACTCAAAGA-TTTTTTCA
1 AAAGAAACAGACTCAAAGATTTTTTTCA
*
64967 AAATAAACA-ACTCAAAGATTTTTATTCA
1 AAAGAAACAGACTCAAAGATTTTT-TTCA
*
64995 AAAGGAACAGACTCAAAGATTTTGTTTCA
1 AAAGAAACAGACTCAAAGATTTT-TTTCA
*
65024 AGAGAAAC
1 AAAGAAAC
65032 TGTCTCTAGA
Statistics
Matches: 202, Mismatches: 31, Indels: 59
0.69 0.11 0.20
Matches are distributed among these distances:
20 1 0.00
21 7 0.03
22 4 0.02
24 5 0.02
25 1 0.00
26 18 0.09
27 21 0.10
28 32 0.16
29 56 0.28
30 36 0.18
31 2 0.01
33 7 0.03
34 5 0.02
35 7 0.03
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (28 bp):
AAAGAAACAGACTCAAAGATTTTTTTCA
Found at i:65521 original size:2 final size:2
Alignment explanation
Indices: 65514--65543 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
65504 TGCACCTTTC
*
65514 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65544 CCACGCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:65873 original size:30 final size:30
Alignment explanation
Indices: 65813--65944 Score: 187
Period size: 30 Copynumber: 4.4 Consensus size: 30
65803 CCCGAAGGAC
*
65813 CTATCCAGAGGTCACAAAGA-CC-CAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTC-GGTAA
65842 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
65872 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
65902 CTGTCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
65932 CTGTCCATAGGTC
1 CTATCCAGAGGTC
65945 CCGAAGAACC
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.20
30 76 0.79
31 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:65961 original size:60 final size:60
Alignment explanation
Indices: 65813--65961 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 60
65803 CCCGAAGGAC
**
65813 CTATCCAGAGGTCACAAAG-ACCCAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACATAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
65872 CTATCCAGAGGTCATAAAGATCATCGGTAACTGTCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCACAAAGAACATAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
65932 CTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACATAGGTAA
65962 ACTTTCCATA
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 18 0.24
60 56 0.76
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGAACATAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:70064 original size:30 final size:30
Alignment explanation
Indices: 70008--70136 Score: 206
Period size: 30 Copynumber: 4.3 Consensus size: 30
69998 GAAGGACCTA
* * *
70008 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
70037 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
70067 TCCAGAGGTCATAAAGATCATCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
70097 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
70127 TCCATAGGTC
1 TCCAGAGGTC
70137 CCGAAGAACC
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 16 0.17
30 77 0.83
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:70153 original size:30 final size:30
Alignment explanation
Indices: 70029--70172 Score: 90
Period size: 30 Copynumber: 4.8 Consensus size: 30
70019 CAAAGACCCC
* * ** * *
70029 GGTAACTATCCAGAGGTCATAAAGATCCTC
1 GGTAACTGTCCATAGGTCACGAAGAACCTA
* ** * * *
70059 GGTAACTGTCCAGAGGTCATAAAGATCATC
1 GGTAACTGTCCATAGGTCACGAAGAACCTA
* ** * *
70089 GGTAACTGTCCAGAGGTCATAAAGATCCTC
1 GGTAACTGTCCATAGGTCACGAAGAACCTA
*
70119 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATAGGTCACGAAGAACCTA
* * *
70149 GGTAAACTTTCCATATGTCTCGAA
1 GGT-AACTGTCCATAGGTCACGAA
70173 AGACATAGGT
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
30 84 0.83
31 17 0.17
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (30 bp):
GGTAACTGTCCATAGGTCACGAAGAACCTA
Found at i:70153 original size:60 final size:60
Alignment explanation
Indices: 70008--70153 Score: 186
Period size: 60 Copynumber: 2.5 Consensus size: 60
69998 GAAGGACCTA
***
70008 TCCAGAGGTCACAAAG-ACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACATAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
* * * *
70067 TCCAGAGGTCATAAAGATCATCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACATAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
* * * *
70127 TCCATAGGTCCCGAAGAACCTAGGTAA
1 TCCAGAGGTCACAAAGAACATAGGTAA
70154 ACTTTCCATA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 15 0.20
60 59 0.80
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGAACATAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:71891 original size:31 final size:30
Alignment explanation
Indices: 71835--71894 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
71825 TACAGAAACG
71835 ACTCAAAGATGGTTTGTTTTAAGAGAAACAA
1 ACTCAAAGAT-GTTTGTTTTAAGAGAAACAA
*
71866 ACTCAAAGAT-TTTGTATTTCTAGAGAAAC
1 ACTCAAAGATGTTTGT-TTT-AAGAGAAAC
71895 TGCTTCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 5 0.19
30 3 0.12
31 18 0.69
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (30 bp):
ACTCAAAGATGTTTGTTTTAAGAGAAACAA
Found at i:71969 original size:30 final size:29
Alignment explanation
Indices: 71935--71998 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
71925 AGAAATGATT
* * *
71935 TCAAAGGTGGGTGTTTCAAGAGAAATTAAC
1 TCAAAGATAGGTGTTTCAAAAGAAA-TAAC
* *
71965 TCAAATATAGGTGTTTCAAAAGAAATGAC
1 TCAAAGATAGGTGTTTCAAAAGAAATAAC
71994 TCAAA
1 TCAAA
71999 AATATTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (29 bp):
TCAAAGATAGGTGTTTCAAAAGAAATAAC
Found at i:72261 original size:30 final size:31
Alignment explanation
Indices: 72206--72264 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
72196 ATTTTTTTAT
** *
72206 TTTGTTTCAAGTGAAACATACTCAAAGATCC
1 TTTGTTTCAAAAGAAACAGACTCAAAGATCC
72237 TTTGTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
72265 GATGTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATCC
Found at i:72379 original size:37 final size:37
Alignment explanation
Indices: 72302--72396 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
72292 ATAATTTGGA
* * *
72302 AAATTGTCTCAAATGAGAC-AACATTTATTTTTAGAG
1 AAATTGTCTCAAACGAGACAAAAAATTATTTTTAGAG
* *
72338 AAATTGTCTCAAACGAGACAAAAAATTGTTTTTAGAT
1 AAATTGTCTCAAACGAGACAAAAAATTATTTTTAGAG
*
72375 AAATTATCTCAAACGAGACAAA
1 AAATTGTCTCAAACGAGACAAA
72397 GTTTGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 18 0.35
37 34 0.65
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
AAATTGTCTCAAACGAGACAAAAAATTATTTTTAGAG
Found at i:72624 original size:36 final size:36
Alignment explanation
Indices: 72530--72638 Score: 94
Period size: 38 Copynumber: 2.9 Consensus size: 36
72520 AAACTTTGTG
* * *
72530 GAAAAATATCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATATCTCTAGCGAGACAAAATTTGTTTTTAA
* *
72566 GAGAAAGT-TGTCTCATGCGAGACAAAATTTGTTTTTAA
1 GA-AAAATATCTCT-A-GCGAGACAAAATTTGTTTTTAA
* * * *
72604 GAAAACTATCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAAATATCTCTAGCGAGAC-AAAATTTGTTTTT
72639 TTAAAGAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
36 11 0.19
37 21 0.36
38 26 0.45
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (36 bp):
GAAAAATATCTCTAGCGAGACAAAATTTGTTTTTAA
Found at i:72990 original size:4 final size:4
Alignment explanation
Indices: 72981--73041 Score: 54
Period size: 4 Copynumber: 15.0 Consensus size: 4
72971 CTCATGTAAC
* * *
72981 ATGT ATGT ATGT GT-T GATGT ATGT ATGT ATTT GATGT ATAT ATGT AT-T
1 ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT
73029 GATGT ATGT ATGT
1 -ATGT ATGT ATGT
73042 TGATCTGTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
3 2 0.04
4 39 0.85
5 5 0.11
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:73002 original size:16 final size:16
Alignment explanation
Indices: 72981--73041 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
72971 CTCATGTAAC
*
72981 ATGTATGTATGTGTTG
1 ATGTATGTATGTATTG
72997 ATGTATGTATGTATTTG
1 ATGTATGTATGTA-TTG
*
73014 ATGTATATATGTATTG
1 ATGTATGTATGTATTG
73030 ATGTATGTATGT
1 ATGTATGTATGT
73042 TGATCTGTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 26 0.63
17 15 0.37
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:74224 original size:5 final size:5
Alignment explanation
Indices: 74216--74303 Score: 50
Period size: 5 Copynumber: 15.6 Consensus size: 5
74206 GCTCTTTGCT
*
74216 TTTTC TTTTC TTTTC TTTTTC TTTGATT TTTTC TTTTC TCTTTGC TTTTTC
1 TTTTC TTTTC TTTTC -TTTTC TTT--TC TTTTC TTTTC T-TTT-C -TTTTC
* * *
74267 TTTGCTC TTTTTC TTTATT TTTTC TTTGC TCTTC TTT
1 TTT--TC -TTTTC TTT-TC TTTTC TTTTC TTTTC TTT
74304 ATTCTTTTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
5 36 0.55
6 15 0.23
7 10 0.15
8 4 0.06
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:74274 original size:18 final size:18
Alignment explanation
Indices: 74203--74299 Score: 87
Period size: 18 Copynumber: 5.5 Consensus size: 18
74193 TTGTTTTCTT
*
74203 TTTGCTCTTTGCTTTTTC
1 TTTGCTCTTTTCTTTTTC
74221 TTT--TCTTTTCTTTTTC
1 TTTGCTCTTTTCTTTTTC
* *
74237 TTTGATTTTTTCTTTTCTC
1 TTTGCTCTTTTCTTTT-TC
*
74256 TTTGCT-TTTTCTTTGCTC
1 TTTGCTCTTTTCTTT-TTC
*
74274 TTT-TTCTTTAT-TTTTTC
1 TTTGCTCTTT-TCTTTTTC
74291 TTTGCTCTT
1 TTTGCTCTT
74300 CTTTATTCTT
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
16 15 0.23
17 6 0.09
18 36 0.55
19 8 0.12
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (18 bp):
TTTGCTCTTTTCTTTTTC
Found at i:74308 original size:7 final size:6
Alignment explanation
Indices: 74196--74330 Score: 79
Period size: 6 Copynumber: 22.5 Consensus size: 6
74186 ATGCTCATTG
* *
74196 TTTTCT TTTTGCT CTTTGCT TTTTC- TTTTC- TTTTCT TTTTCT TTGAT-T
1 TTTTCT TTTT-CT -TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT
* * *
74244 TTTTC- TTTTCT CTTTGCT TTTTCT TTGCTCT TTTTCT TTAT-T TTTTC-
1 TTTTCT TTTTCT -TTTTCT TTTTCT TT-TTCT TTTTCT TTTTCT TTTTCT
* *
74291 TTTGC- TCTTCT TTATTCT TTTTCT ATTTAT-T TTTTCT TTT
1 TTTTCT TTTTCT TT-TTCT TTTTCT -TTT-TCT TTTTCT TTT
74331 GCTTCTATTA
Statistics
Matches: 101, Mismatches: 14, Indels: 28
0.71 0.10 0.20
Matches are distributed among these distances:
5 28 0.28
6 44 0.44
7 25 0.25
8 4 0.04
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTTCT
Found at i:74324 original size:35 final size:34
Alignment explanation
Indices: 74196--74334 Score: 120
Period size: 35 Copynumber: 3.9 Consensus size: 34
74186 ATGCTCATTG
** *
74196 TTTTCTTTTTGCTCTTTGCTTTTTCTTTTCTTTTCT
1 TTTTCTTTTT-CT-TTTATTTTTTCTTTGCTTTTCT
* *
74232 TTTTCTTTGATT-TTTTCTTTTCTCTTTGCTTTTTCT
1 TTTTCTTT--TTCTTTTATTTTTTCTTTGC-TTTTCT
* *
74268 TTGCTCTTTTTC-TTTATTTTTTCTTTGCTCTTCT
1 TT-TTCTTTTTCTTTTATTTTTTCTTTGCTTTTCT
74302 TTATTCTTTTTCTATTTATTTTTTCTTTTGCTT
1 TT-TTCTTTTTCT-TTTATTTTTTC-TTTGCTT
74335 CTATTATGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
34 15 0.18
35 28 0.33
36 28 0.33
37 11 0.13
38 2 0.02
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (34 bp):
TTTTCTTTTTCTTTTATTTTTTCTTTGCTTTTCT
Found at i:75163 original size:21 final size:21
Alignment explanation
Indices: 75138--75178 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
75128 TCTGGGCAAA
* *
75138 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
75159 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
75179 ACGACAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:75890 original size:31 final size:31
Alignment explanation
Indices: 75852--76036 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
75842 GGGTCGAGGG
75852 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
75883 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
75914 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
75945 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
75976 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
76007 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
76037 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:78482 original size:30 final size:30
Alignment explanation
Indices: 78446--78698 Score: 497
Period size: 30 Copynumber: 8.4 Consensus size: 30
78436 TCCGAAGGAC
78446 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78476 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78506 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78536 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78566 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78596 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78626 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
78656 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
78686 CTATCCATAGGTC
1 CTATCCAGAGGTC
78699 CCGAACAACC
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 222 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:78958 original size:4 final size:4
Alignment explanation
Indices: 78949--78977 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
78939 ATATAACCAT
78949 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
78978 GTCATCCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:79146 original size:2 final size:2
Alignment explanation
Indices: 79134--79184 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
79124 TACACAACTC
79134 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79175 AT AT AT AT AT
1 AT AT AT AT AT
79185 GTAACATGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83618 original size:12 final size:12
Alignment explanation
Indices: 83601--83626 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
83591 ATGGCCACCT
83601 GCTGAACTCACG
1 GCTGAACTCACG
83613 GCTGAACTCACG
1 GCTGAACTCACG
83625 GC
1 GC
83627 GGAGTTCACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.27, T:0.15
Consensus pattern (12 bp):
GCTGAACTCACG
Found at i:84488 original size:3 final size:3
Alignment explanation
Indices: 84480--84558 Score: 113
Period size: 3 Copynumber: 25.3 Consensus size: 3
84470 AAAAAATTTG
*
84480 TAA TAA TAA TAA TTAT TAA TAA TAA TAA TAA TTAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA
*
84528 TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
84559 TAAATGGTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
3 61 0.88
4 8 0.12
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:102773 original size:17 final size:17
Alignment explanation
Indices: 102747--102794 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
102737 ATCCATAAAA
102747 TTAT-TTTTATTATATT
1 TTATATTTTATTATATT
*
102763 TTATATTTTATAATATT
1 TTATATTTTATTATATT
* *
102780 ATGTATTTTATTATA
1 TTATATTTTATTATA
102795 ATATAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTATATTTTATTATATT
Found at i:109020 original size:36 final size:36
Alignment explanation
Indices: 108987--109054 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
108977 TACAAATTGT
108987 AAAATATTTATATAT-TTCTTTAAAAAATTAAATTC
1 AAAATATTTATATATATTCTTTAAAAAATTAAATTC
* * *
109022 ATAATATTTATATATATTTTTTACAAAATTAAA
1 AAAATATTTATATATATTCTTTAAAAAATTAAA
109055 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 14 0.48
36 15 0.52
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATATATTCTTTAAAAAATTAAATTC
Found at i:116203 original size:16 final size:16
Alignment explanation
Indices: 116182--116212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
116172 CTTCTCCTGT
*
116182 GGTCCTAGCTCACTGC
1 GGTCCTACCTCACTGC
116198 GGTCCTACCTCACTG
1 GGTCCTACCTCACTG
116213 TTCTGTTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.39, G:0.23, T:0.26
Consensus pattern (16 bp):
GGTCCTACCTCACTGC
Found at i:116318 original size:6 final size:6
Alignment explanation
Indices: 116307--116338 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
116297 TAAATTTATT
*
116307 AAATTA AAATTA AAATTA AAATTA AAACTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
116339 TAGATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:116664 original size:120 final size:119
Alignment explanation
Indices: 116447--116682 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 119
116437 CTGTTTGAAA
*
116447 AAAATAGAAGAGCATTGGTCAACTTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
1 AAAATAGAAGAGCATTGGTCAAATTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
** *
116512 CCTAATTGTTTTTTACCCGAACTTCCTCAGCTAAAGACTTAAGAGTTAATTGGTG
66 CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTT-AGAATTAATTGGTG
* * *
116567 AAAATAGAAGATCATTGGTCAAATTAGAATTTTTCTATAATTATGTGGTCATAGGTGTAATTTAC
1 AAAATAGAAGAGCATTGGTCAAATTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
116632 CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTTAGAATTAATTG
66 CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTTAGAATTAATTG
116683 CATCATAAGT
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 10 0.09
120 99 0.91
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (119 bp):
AAAATAGAAGAGCATTGGTCAAATTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTTAGAATTAATTGGTG
Found at i:116811 original size:59 final size:60
Alignment explanation
Indices: 116718--116878 Score: 186
Period size: 60 Copynumber: 2.7 Consensus size: 60
116708 CTTATTCTTG
* * *
116718 ATTAGTCCT-AAACTTTTAAATATTTTAATTTCATCCCT-AACAATGA-CTATCATTCTAT
1 ATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCTAAACAATGACCT-TCATTCTAA
* * * * * *
116776 ATTAGTCCTCCAACTTTTGAACATTTTATTTTCATCCTTAAACTATGACCTTCGTTTTAA
1 ATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCTAAACAATGACCTTCATTCTAA
*
116836 ATTAGTCCTCAAACTTTTTGAACATTTCAATTTCATCCC-AAAC
1 ATTAGTCCTCAAAC-TTTTGAACATTTTAATTTCATCCCTAAAC
116879 TATGTGTATA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 9 0.10
59 24 0.28
60 30 0.35
61 23 0.27
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (60 bp):
ATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCTAAACAATGACCTTCATTCTAA
Found at i:124772 original size:2 final size:2
Alignment explanation
Indices: 124765--124795 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
124755 GATTCCTCAG
124765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
124796 CAATTGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129711 original size:25 final size:25
Alignment explanation
Indices: 129677--129726 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
129667 CTTCACTTGA
129677 TTGACACTGAAATAAAACATCATCG
1 TTGACACTGAAATAAAACATCATCG
* *
129702 TTGACACTGAAATGAAACGTCATCG
1 TTGACACTGAAATAAAACATCATCG
129727 ACACCATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
TTGACACTGAAATAAAACATCATCG
Found at i:135988 original size:2 final size:2
Alignment explanation
Indices: 135981--136011 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
135971 ATGTCATGCA
135981 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
136012 TTATTTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:136842 original size:36 final size:36
Alignment explanation
Indices: 136764--136977 Score: 299
Period size: 36 Copynumber: 6.0 Consensus size: 36
136754 TGAACAATTA
* *
136764 AATCGAAAGTGCGGATGCTTCCTTCCGTTC-ACTTG
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCTTCTTG
* *
136799 AATCGAAAGTACCGATGCTTCCTTTCGTTCTTCTTG
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCTTCTTG
136835 AATCGAAAGTGCCGATGCTTCCTTCCGTTCATT-TTG
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTC-TTCTTG
** *
136871 AATCGAAAGTGATGATGCTTCCTTTCGTTCTTCTTG
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCTTCTTG
* *
136907 AATCGAAAGTGTCGATGCTTCCTTCCGTTC-ACTTTG
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC-TTG
*
136943 AATCGAAAGTGCCGATGCTTCCTTTCGTTCTTCTT
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCTTCTT
136978 CCTCACCTTC
Statistics
Matches: 158, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
35 30 0.19
36 125 0.79
37 3 0.02
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (36 bp):
AATCGAAAGTGCCGATGCTTCCTTCCGTTCTTCTTG
Found at i:136900 original size:72 final size:71
Alignment explanation
Indices: 136764--136977 Score: 349
Period size: 72 Copynumber: 3.0 Consensus size: 71
136754 TGAACAATTA
* *
136764 AATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTGAATCGAAAGT-ACCGATGCTTCCTTTCGTT
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGA-CGATGCTTCCTTTCGTT
136828 CTTCTTG
65 CTTCTTG
*
136835 AATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTTGAATCGAAAGTGATGATGCTTCCTTTCGTT
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCA-TTTGAATCGAAAGTGACGATGCTTCCTTTCGTT
136900 CTTCTTG
65 CTTCTTG
* *
136907 AATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTCGTT
1 AATCGAAAGTGCCGATGCTTCCTTCCGTTCA-TTTGAATCGAAAGTGACGATGCTTCCTTTCGTT
136972 CTTCTT
65 CTTCTT
136978 CCTCACCTTC
Statistics
Matches: 134, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
71 30 0.22
72 103 0.77
73 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (71 bp):
AATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGACGATGCTTCCTTTCGTTC
TTCTTG
Found at i:140795 original size:19 final size:19
Alignment explanation
Indices: 140771--140849 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 19
140761 GCGATTTTGA
140771 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
140790 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
140810 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
*
140834 AAAAAGTGTTGCGATA
1 AAAATGTGTTGCGATA
140850 ATGAAAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 26 0.52
20 3 0.06
22 8 0.16
24 3 0.06
25 10 0.20
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:140843 original size:44 final size:41
Alignment explanation
Indices: 140766--140847 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
140756 GCAACGCGAT
* *
140766 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
140807 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
140848 TAATGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 25 0.69
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:140854 original size:19 final size:19
Alignment explanation
Indices: 140821--140857 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
140811 AAAAACGTGT
*
140821 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAATGAAAAAG
140840 TGTTGCGATAATGAAAAA
1 TGTTGCGATAATGAAAAA
140858 TCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAATGAAAAAG
Found at i:151527 original size:18 final size:17
Alignment explanation
Indices: 151498--151544 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
151488 TTTTCAAAAG
151498 TAATAATTAAACCGATT
1 TAATAATTAAACCGATT
*
151515 TAATAACTTAAACTGATT
1 TAATAA-TTAAACCGATT
*
151533 AAATTAATTAAA
1 TAA-TAATTAAA
151545 TAAACCACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 17 0.65
19 3 0.12
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (17 bp):
TAATAATTAAACCGATT
Found at i:151771 original size:21 final size:21
Alignment explanation
Indices: 151745--151785 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
151735 CTCGACTGAG
151745 GTCACTTGATAATTGAGTTAT
1 GTCACTTGATAATTGAGTTAT
151766 GTCACTTGATAATTGAGTTA
1 GTCACTTGATAATTGAGTTA
151786 CGGGTCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (21 bp):
GTCACTTGATAATTGAGTTAT
Found at i:152496 original size:21 final size:21
Alignment explanation
Indices: 152451--152496 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
152441 AAAGTTTTGT
*
152451 AGATTTTCAGGGAAGGACATG
1 AGATTTTCAGGGAAGGACATA
* *
152472 AGATTTTCAGTGAAGGACTTA
1 AGATTTTCAGGGAAGGACATA
152493 AGAT
1 AGAT
152497 GTTGGAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (21 bp):
AGATTTTCAGGGAAGGACATA
Found at i:156070 original size:51 final size:51
Alignment explanation
Indices: 155943--156668 Score: 813
Period size: 51 Copynumber: 14.0 Consensus size: 51
155933 TCTTTTGCCT
* * * * *
155943 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-T-T-CAA
*
155997 ACGGGTTTGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
156048 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * * * **
156098 ACTGGGTTCGCTCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAATCTTCTTCTT
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTC-GAA-CATCTTCAA
* *
156152 ACGGGTTCGCTCCTTCTCTCTTTAA--AGCATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
156201 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * * * **
156251 ACTGGGTTCGCTCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTT
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTC--GAA-CATCTTCAA
* * *
156306 ACGGGTTCGCTCCTTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
156357 ACGGGTTCGCTCCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G
1 ACGGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * * * **
156408 ACTGGGTTCGCTCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTT
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTC--GAA-CATCTTCAA
* * *
156463 ACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
** *
156514 ACGGGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * *
156565 ACGGGTTCGCTACTTCTTTCATTAAGGAGTATGGAACTCGGATATC-TCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC-GA-A-CATCTTCAA
* *
156618 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
156669 CAATCGTGTA
Statistics
Matches: 577, Mismatches: 69, Indels: 55
0.82 0.10 0.08
Matches are distributed among these distances:
49 30 0.05
50 6 0.01
51 278 0.48
52 72 0.12
53 77 0.13
54 110 0.19
55 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (51 bp):
ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
Found at i:156429 original size:157 final size:156
Alignment explanation
Indices: 155945--156668 Score: 1111
Period size: 157 Copynumber: 4.7 Consensus size: 156
155935 TTTTGCCTAC
* ** * ** *
155945 GGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACGGGTTTGCTCC
1 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
* * *
156010 TTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
66 TTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
156075 AGTATAGAACTCGAACATCTTCGACT
131 AGTATAGAACTCGAACATCTTCGACT
156101 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTC-AAAATCTTCTTCTTACGGGTTCGCTCC
1 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
156165 TTCTCTCTTT-AA-AGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
66 TTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
156228 AGTATAGAACTCGAACATCTTCGACT
131 AGTATAGAACTCGAACATCTTCGACT
156254 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
1 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
156319 TTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTTCTTTCTTTAAG
66 TTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCT-CCTTCTTTCTTTAAG
156384 GAGTATAGAACTCGAACATCTTCGACT
130 GAGTATAGAACTCGAACATCTTCGACT
156411 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
1 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
* * ** *
156476 TTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTCACTTTAAAG
66 TTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
*
156541 AGTATAGAACTCGAACATCTTCAAAC-
131 AGTATAGAACTCGAACATCTTC-GACT
* * * ** * **
156567 GGGTTCGCT-ACTTCTTTCATT-AAGGAGTATGGAACTCGGATATC-TCTTCAAACGGGTTCGCT
1 GGGTTCGCTCCCTT-TTTC-TTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
* * * *
156629 CCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAA
64 CCTTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAA
156669 CAATCGTGTA
Statistics
Matches: 534, Mismatches: 27, Indels: 15
0.93 0.05 0.03
Matches are distributed among these distances:
153 113 0.21
154 38 0.07
155 89 0.17
156 136 0.25
157 158 0.30
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (156 bp):
GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
TTCTCTCTTTAAAGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
AGTATAGAACTCGAACATCTTCGACT
Found at i:160926 original size:8 final size:8
Alignment explanation
Indices: 160913--160940 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
160903 AAAAGAAGAT
160913 ATATATAC
1 ATATATAC
160921 ATATATAC
1 ATATATAC
160929 ATATATAC
1 ATATATAC
160937 ATAT
1 ATAT
160941 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:169181 original size:38 final size:37
Alignment explanation
Indices: 169075--169252 Score: 173
Period size: 38 Copynumber: 4.9 Consensus size: 37
169065 CAAGAACAAT
*
169075 ATGTTCAAAGTTTGGCCACCAACCAA-A-GAATTTTCC
1 ATGTTCAAAGTTTGGCCACCAACCAAGATGAA-ATTCC
* *
169111 AATGTGT-ACAAG-TTAGCCACC-A--AATATGAAATTCAC
1 -ATGT-TCA-AAGTTTGGCCACCAACCAAGATGAAATTC-C
169147 ATGTTCAAAGTTTGGCCACCAACCAAGATGAAATTCAC
1 ATGTTCAAAGTTTGGCCACCAACCAAGATGAAATTC-C
169185 ATGTTCAAAGTTTGGCCACCAACCAAGATGAAATTTCC
1 ATGTTCAAAGTTTGGCCACCAACCAAGATGAAA-TTCC
*
169223 A--AT--AAG-TTGGCCACCAACCAAGATGAAATT
1 ATGTTCAAAGTTTGGCCACCAACCAAGATGAAATT
169253 TCTAACTTGT
Statistics
Matches: 125, Mismatches: 5, Indels: 27
0.80 0.03 0.17
Matches are distributed among these distances:
32 2 0.02
33 22 0.18
34 9 0.07
35 17 0.14
36 7 0.06
37 13 0.10
38 52 0.42
39 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (37 bp):
ATGTTCAAAGTTTGGCCACCAACCAAGATGAAATTCC
Found at i:185270 original size:14 final size:14
Alignment explanation
Indices: 185251--185280 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
185241 ACTCTTCTGG
*
185251 TTATGAATTTTACT
1 TTATGAATATTACT
185265 TTATGAATATTACT
1 TTATGAATATTACT
185279 TT
1 TT
185281 TCTACTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTATGAATATTACT
Found at i:194157 original size:19 final size:19
Alignment explanation
Indices: 194119--194159 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
194109 ACAGTCAACA
* * *
194119 GTCGGGTCGGGTCGGGTCG
1 GTCGAGTCGGGTCAGATCG
194138 GTCGAGTCGGGTCAGATCG
1 GTCGAGTCGGGTCAGATCG
194157 GTC
1 GTC
194160 AAACCGGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.07, C:0.22, G:0.49, T:0.22
Consensus pattern (19 bp):
GTCGAGTCGGGTCAGATCG
Found at i:195405 original size:108 final size:108
Alignment explanation
Indices: 195216--195425 Score: 323
Period size: 108 Copynumber: 1.9 Consensus size: 108
195206 GATTCTGGCG
* **
195216 GATCGCCTCACCGGAGTTATCACCTCGTTATTGCTTCCTAACTCTTTCCCTTTCCTCTTGGCAGC
1 GATCGCCTCACCGGAGTTATCACCTCGTTATTCCCACCTAACTCTTTCCCTTTCCTCTTGGCAGC
*
195281 AGTCGTCGAAACTGATCTATCAGATGAATTGGAGTTCACGGCC
66 AGACGTCGAAACTGATCTATCAGATGAATTGGAGTTCACGGCC
*
195324 GATCGCCTCACCGGAGTTATCACCTCGTTGCTTCCCACC-AACTCTTTCCCTTTCCTCTTGGCAG
1 GATCGCCTCACCGGAGTTATCACCTCGTT-ATTCCCACCTAACTCTTTCCCTTTCCTCTTGGCAG
* ** *
195388 CTGACGTCGAATTTGATCTCTCAGATGAATTGGAGTTC
65 CAGACGTCGAAACTGATCTATCAGATGAATTGGAGTTC
195426 TCGACAGGAA
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 87 0.95
109 5 0.05
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (108 bp):
GATCGCCTCACCGGAGTTATCACCTCGTTATTCCCACCTAACTCTTTCCCTTTCCTCTTGGCAGC
AGACGTCGAAACTGATCTATCAGATGAATTGGAGTTCACGGCC
Found at i:198341 original size:22 final size:21
Alignment explanation
Indices: 198310--198356 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
198300 TCCTAAATTA
* *
198310 ATAACCCTAAACTATAACCTC
1 ATAACCCTAAACAATAAACTC
198331 ATAACCTCTAAACAATAAACTC
1 ATAACC-CTAAACAATAAACTC
198353 -TAAC
1 ATAAC
198357 TTAAAATCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAACCCTAAACAATAAACTC
Found at i:207982 original size:32 final size:35
Alignment explanation
Indices: 207935--208009 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 35
207925 TATTATATAT
207935 ATATATAATATTAATAAATT-TA-ATTTAAATTAAA-
1 ATATAT-ATATTAAT-AATTATATATTTAAATTAAAC
* *
207969 ATATATATA-TAATATTTATATATTTAATTTAAAC
1 ATATATATATTAATAATTATATATTTAAATTAAAC
208003 ATATATA
1 ATATATA
208010 CTCGGCCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 3 0.08
32 6 0.17
33 14 0.39
34 13 0.36
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (35 bp):
ATATATATATTAATAATTATATATTTAAATTAAAC
Found at i:208509 original size:20 final size:20
Alignment explanation
Indices: 208484--208771 Score: 406
Period size: 20 Copynumber: 14.2 Consensus size: 20
208474 AATAGTTTAG
208484 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
208504 AATCGCAACGCGATTCAG-A
1 AATCGCAACGCGATTCAGAA
208523 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
208543 AATCGCAACGCGATTCAG-A
1 AATCGCAACGCGATTCAGAA
208562 AATCGCCAACGCGATTCAGAA
1 AATCG-CAACGCGATTCAGAA
208583 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
208603 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
208623 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
*
208643 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGA--TT-CAGAA
*
208665 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGA--TT-CAGAA
*
208687 AATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAA
208707 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
*
208727 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGA--TT-CAGAA
*
208749 AATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAA
208769 AAT
1 AAT
208772 GAGTAAATTC
Statistics
Matches: 250, Mismatches: 7, Indels: 22
0.90 0.03 0.08
Matches are distributed among these distances:
19 27 0.11
20 159 0.64
21 6 0.02
22 54 0.22
23 4 0.02
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGATTCAGAA
Found at i:208723 original size:84 final size:79
Alignment explanation
Indices: 208484--208768 Score: 391
Period size: 84 Copynumber: 3.5 Consensus size: 79
208474 AATAGTTTAG
208484 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTC-AGAAATCGCAACGCGATTCAGAAAATCG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAG-AATCGCAACGCGATTCAGAAAATCG
208548 CAACGCGATTCAG-A
65 CAACGCGATTCAGAA
*
208562 AATCGCCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATC
1 AATCG-CAACGCGATTCAGAAAATCGCAACGCGATTCA-AGAATCGCAACGCGATTCAGAAAATC
208627 GCAACGCGATTCAGAA
64 GCAACGCGATTCAGAA
* *
208643 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGA--TT-CAAGAATCGCAACGCGATTCAGAA
208707 AATCGCAACGCGATTCAGAA
60 AATCGCAACGCGATTCAGAA
*
208727 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-AAGAA
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAAGAA
208769 AATGAGTAAA
Statistics
Matches: 193, Mismatches: 4, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
78 5 0.03
79 31 0.16
80 51 0.26
81 7 0.04
82 18 0.09
83 2 0.01
84 77 0.40
85 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (79 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAGAATCGCAACGCGATTCAGAAAATCGC
AACGCGATTCAGAA
Found at i:208881 original size:6 final size:6
Alignment explanation
Indices: 208870--208918 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
208860 ACGTATTACA
208870 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
208916 ACC
1 ACC
208919 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.24
6 32 0.76
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:209395 original size:20 final size:19
Alignment explanation
Indices: 209372--209593 Score: 146
Period size: 20 Copynumber: 10.9 Consensus size: 19
209362 CGTTGAAAAG
*
209372 AAGATCGCAACACGATCTTC
1 AAGATCGCAACGCGAT-TTC
*
209392 AAGAATCGCAATGCGA-TTC
1 AAG-ATCGCAACGCGATTTC
*
209411 ATAAAATCGCAACGCGATCTTCC
1 --AAGATCGCAACGCGAT-TT-C
209434 AAGAATCGCAACGCGA-TTC
1 AAG-ATCGCAACGCGATTTC
*
209453 AGAAAATCGCAACGCGA-TTC
1 --AAGATCGCAACGCGATTTC
*
209473 AGAAATCGCAACGCGATCTTC
1 A-AGATCGCAACGCGAT-TTC
* **
209494 CAGAATCGCAACGCGATTAAG
1 AAG-ATCGCAACGCGATT-TC
* *
209515 AAAATCGCAACGCGATTCC
1 AAGATCGCAACGCGATTTC
209534 AAGAATCGCAACGCGA-TTC
1 AAG-ATCGCAACGCGATTTC
*
209553 AGAAAATCGCAACGCGATCTTCC
1 --AAGATCGCAACGCGAT-TT-C
209576 AAGAATCGCAACGCGATT
1 AAG-ATCGCAACGCGATT
209594 AAGAAATGAG
Statistics
Matches: 163, Mismatches: 18, Indels: 41
0.73 0.08 0.18
Matches are distributed among these distances:
18 1 0.01
19 22 0.13
20 71 0.44
21 38 0.23
22 29 0.18
23 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (19 bp):
AAGATCGCAACGCGATTTC
Found at i:209517 original size:40 final size:39
Alignment explanation
Indices: 209395--209600 Score: 231
Period size: 42 Copynumber: 5.1 Consensus size: 39
209385 GATCTTCAAG
* *
209395 AATCGCAATGCGATT-CATAAAATCGCAACGCGATCTTCCAAG-
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT--AAGA
* *
209437 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCAGA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTAAGA
209476 AATCGCAACGCGATCTTCC-AGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG-A
*
209517 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG-A
209557 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAGA
209598 AAT
1 AAT
209601 GAGTAAATTC
Statistics
Matches: 149, Mismatches: 7, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
38 2 0.01
39 17 0.11
40 54 0.36
41 20 0.13
42 56 0.38
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17
Consensus pattern (39 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGA
Found at i:209706 original size:6 final size:6
Alignment explanation
Indices: 209695--209768 Score: 99
Period size: 6 Copynumber: 13.5 Consensus size: 6
209685 GACACGTATT
209695 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-C-C-
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
209740 ACCACG ACC-CG ACCA-G ACCAC- A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
209769 CGAGACGAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
3 1 0.02
4 5 0.08
5 14 0.23
6 41 0.67
ACGTcount: A:0.34, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:210262 original size:6 final size:6
Alignment explanation
Indices: 210251--210289 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
210241 CTCGTCTCGG
210251 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
210290 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:210424 original size:20 final size:20
Alignment explanation
Indices: 210382--210617 Score: 241
Period size: 20 Copynumber: 11.4 Consensus size: 20
210372 CATTTCTGAA
210382 GTTGCGATTCTTGGAAGATCGC
1 GTTGCGATTCTTGG-A-ATCGC
210404 GTTGCGATTCTTGGAATCGC
1 GTTGCGATTCTTGGAATCGC
*
210424 GTTGCGATT-TTCTGAATCGC
1 GTTGCGATTCTT-GGAATCGC
*
210444 ATTGCGATTCTTGGAATCGC
1 GTTGCGATTCTTGGAATCGC
210464 GTTGCGATTTTCTT--AATCGC
1 GTTGCGA--TTCTTGGAATCGC
210484 GTTGCGATTCTTGGAAGATCGC
1 GTTGCGATTCTTGG-A-ATCGC
*
210506 GTTGCGATT-TTCTGAATCGC
1 GTTGCGATTCTT-GGAATCGC
*
210526 GTTGCGATT-TTCTGAATCGC
1 GTTGCGATTCTT-GGAATCGC
*
210546 GTTGCGATTCTTGGAAGATCAC
1 GTTGCGATTCTTGG-A-ATCGC
*
210568 GTTGCGATT-TTATGAATCGC
1 GTTGCGATTCTT-GGAATCGC
*
210588 ATTGCGATTCTTGGAAGATCGC
1 GTTGCGATTCTTGG-A-ATCGC
210610 GTTGCGAT
1 GTTGCGAT
210618 CTTCTTTTCA
Statistics
Matches: 186, Mismatches: 12, Indels: 32
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.03
19 2 0.01
20 103 0.55
21 16 0.09
22 60 0.32
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
GTTGCGATTCTTGGAATCGC
Found at i:210449 original size:40 final size:40
Alignment explanation
Indices: 210399--210679 Score: 261
Period size: 42 Copynumber: 6.9 Consensus size: 40
210389 TTCTTGGAAG
210399 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGA
* *
210439 ATCGCATTGCGATTCTTGGAATCGCGTTGCGATTTTCTTA
1 ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGA
210479 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGA
* *
210521 ATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTCTT-GGAA
1 ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTCTG-A
* * * *
210562 GATCACGTTGCGATT-TTATGAATCGCATTGCGATTCTT-GGAA
1 -ATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATT-TTCTG-A
**** * * *
210604 GATCGCGTTGCGA-TCTTCTTTTCAACGTTGCGCTTTTCTAA
1 -ATCGCGTTGCGATTCTTGGAATC-GCGTTGCGATTTTCTGA
*
210645 ATCGCGTTGCGGTT-TT-GATATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTCTTGGA-ATCGCGTTGCGATTTT
210680 GTTGGTCATT
Statistics
Matches: 205, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
39 11 0.05
40 86 0.42
41 14 0.07
42 94 0.46
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (40 bp):
ATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTGA
Found at i:210477 original size:62 final size:61
Alignment explanation
Indices: 210382--210617 Score: 250
Period size: 62 Copynumber: 3.8 Consensus size: 61
210372 CATTTCTGAA
*
210382 GTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCGATT-TTCTG-A-ATCG
1 GTTGCGATT-TTAGG-A-ATCGCGTTGCGATTCTT-GAATCGCGTTGCGATTCTT-GGAAGATCG
210443 C
61 C
*
210444 ATTGCGATTCTT-GGAATCGCGTTGCGATTTTCTT-AATCGCGTTGCGATTCTTGGAAGATCGC
1 GTTGCGATT-TTAGGAATCGCGTTGCGA--TTCTTGAATCGCGTTGCGATTCTTGGAAGATCGC
** * *
210506 GTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCAC
1 GTTGCGATTTTAGGAATCGCGTTGCGATTCT-TGAATCGCGTTGCGATTCTTGGAAGATCGC
* *
210568 GTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGAT
1 GTTGCGATTTTAGGAATCGCGTTGCGATTCTT-G-A-ATCGCGTTGCGAT
210618 CTTCTTTTCA
Statistics
Matches: 154, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
60 31 0.20
61 8 0.05
62 101 0.66
63 1 0.01
64 13 0.08
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (61 bp):
GTTGCGATTTTAGGAATCGCGTTGCGATTCTTGAATCGCGTTGCGATTCTTGGAAGATCGC
Found at i:210652 original size:20 final size:20
Alignment explanation
Indices: 210399--210679 Score: 210
Period size: 20 Copynumber: 13.8 Consensus size: 20
210389 TTCTTGGAAG
**
210399 ATCGCGTTGCGATTCTT-GGA
1 ATCGCGTTGCGATT-TTCTAA
*
210419 ATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTTTCTAA
* **
210439 ATCGCATTGCGATTCTT-GGA
1 ATCGCGTTGCGATT-TTCTAA
*
210459 ATCGCGTTGCGATTTTCTTA
1 ATCGCGTTGCGATTTTCTAA
**
210479 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
*
210500 GATCGCGTTGCGATTTTCTGA
1 -ATCGCGTTGCGATTTTCTAA
*
210521 ATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTTTCTAA
**
210541 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
* * *
210562 GATCACGTTGCGATTTTATGA
1 -ATCGCGTTGCGATTTTCTAA
* **
210583 ATCGCATTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
* *
210604 GATCGCGTTGCGATCTTCT-T
1 -ATCGCGTTGCGATTTTCTAA
* * *
210624 TTCAACGTTGCGCTTTTCTAA
1 ATC-GCGTTGCGATTTTCTAA
* * *
210645 ATCGCGTTGCGGTTTT-GAT
1 ATCGCGTTGCGATTTTCTAA
210664 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
210680 GTTGGTCATT
Statistics
Matches: 210, Mismatches: 40, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
19 22 0.10
20 128 0.61
21 21 0.10
22 39 0.19
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:212091 original size:26 final size:28
Alignment explanation
Indices: 212039--212091 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
212029 TAAGGTTTTT
*
212039 TTTTATAAATATAATAATATTTTAAATA
1 TTTTATAAATATAATAATATTTAAAATA
212067 TTTT-TAAA-ATAATAA-ATTTCAAAAT
1 TTTTATAAATATAATAATATTT-AAAAT
212092 TACGAGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 11 0.48
27 4 0.17
28 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTATAAATATAATAATATTTAAAATA
Found at i:212210 original size:29 final size:30
Alignment explanation
Indices: 212160--212219 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
212150 CCCATTTTGA
*
212160 GTAACGAAATGGAACGTTAGGCACCAAACT
1 GTAACGAAATGAAACGTTAGGCACCAAACT
*
212190 GTAACGAAAT-AAACGTTAGGCACTAAACT
1 GTAACGAAATGAAACGTTAGGCACCAAACT
212219 G
1 G
212220 AAAAAATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (30 bp):
GTAACGAAATGAAACGTTAGGCACCAAACT
Found at i:212406 original size:10 final size:10
Alignment explanation
Indices: 212387--212454 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
212377 CATTTAAATG
212387 ATAAACGAAC
1 ATAAACGAAC
*
212397 ATAAATGAAC
1 ATAAACGAAC
*
212407 GTAAACGAAC
1 ATAAACGAAC
212417 ATAAACGAAC
1 ATAAACGAAC
*
212427 --GAAC-ATA-
1 ATAAACGA-AC
*
212434 ATAAATGAAC
1 ATAAACGAAC
212444 ATAAACGAAC
1 ATAAACGAAC
212454 A
1 A
212455 ACACAAACAC
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 3 0.07
10 37 0.82
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:212727 original size:14 final size:14
Alignment explanation
Indices: 212708--212736 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
212698 GCTCTATGTT
212708 CGAACATAAATGAA
1 CGAACATAAATGAA
212722 CGAACATAAATGAA
1 CGAACATAAATGAA
212736 C
1 C
212737 ATAAATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:212736 original size:10 final size:10
Alignment explanation
Indices: 212723--212747 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
212713 ATAAATGAAC
212723 GAACATAAAT
1 GAACATAAAT
212733 GAACATAAAT
1 GAACATAAAT
212743 GAACA
1 GAACA
212748 AACATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (10 bp):
GAACATAAAT
Found at i:212738 original size:24 final size:26
Alignment explanation
Indices: 212709--212762 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 26
212699 CTCTATGTTC
*
212709 GAACATAAATGAACGAACATA-AA-T
1 GAACATAAATGAACAAACATATAATT
212733 GAACATAAATGAACAAACATATAATT
1 GAACATAAATGAACAAACATATAATT
212759 GAAC
1 GAAC
212763 GTTTACGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 20 0.74
25 2 0.07
26 5 0.19
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.19
Consensus pattern (26 bp):
GAACATAAATGAACAAACATATAATT
Found at i:212762 original size:16 final size:14
Alignment explanation
Indices: 212710--212753 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
212700 TCTATGTTCG
*
212710 AACATAAATGAACG
1 AACATAAATGAACA
212724 AACATAAATG----
1 AACATAAATGAACA
212734 AACATAAATGAACA
1 AACATAAATGAACA
212748 AACATA
1 AACATA
212754 TAATTGAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 10 0.38
14 16 0.62
ACGTcount: A:0.61, C:0.14, G:0.09, T:0.16
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:213131 original size:51 final size:47
Alignment explanation
Indices: 213076--213172 Score: 140
Period size: 50 Copynumber: 2.0 Consensus size: 47
213066 TTTCTTATAT
*
213076 CTTAAACTAATATAAAAATGAACTGGATTTAGAAAGATAATTAATATTTAC
1 CTTAAACTAATAT-AAAATGAACTGGATTTA-AAA-ATAATAAAT-TTTAC
*
213127 CTTAAACTAATATAAAATGAATTGGATTTAAAAATAATAAATTTTA
1 CTTAAACTAATATAAAATGAACTGGATTTAAAAATAATAAATTTTA
213173 ATTTTAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.09
48 8 0.18
49 3 0.07
50 16 0.36
51 13 0.30
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (47 bp):
CTTAAACTAATATAAAATGAACTGGATTTAAAAATAATAAATTTTAC
Found at i:214196 original size:72 final size:72
Alignment explanation
Indices: 214079--214223 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
214069 TGGTTTCAAC
214079 TTTGAAGGCTAATCCTTTCAAGTCGATTTTCTAAAATATGTTACTTGAATTTGAATGCATTTGTT
1 TTTGAAGGCTAATCCTTTCAAGTCGATTTTCTAAAATATGTTACTTGAATTTGAATGCATTTGTT
214144 GCAGATT
66 GCAGATT
214151 TTTGAAGGCTAATCCTTTCAAGTCGATTTTCTAAAATATGTTACTTGAATTTGAATGCATTTGTT
1 TTTGAAGGCTAATCCTTTCAAGTCGATTTTCTAAAATATGTTACTTGAATTTGAATGCATTTGTT
214216 GCAGATT
66 GCAGATT
214223 T
1 T
214224 AACATAGATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (72 bp):
TTTGAAGGCTAATCCTTTCAAGTCGATTTTCTAAAATATGTTACTTGAATTTGAATGCATTTGTT
GCAGATT
Found at i:218253 original size:2 final size:2
Alignment explanation
Indices: 218246--218287 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
218236 CCACCCCCAA
218246 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218287 A
1 A
218288 AACACTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:221729 original size:18 final size:18
Alignment explanation
Indices: 221706--221741 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
221696 ATCAGAAATA
*
221706 TTATTATTTTTATCAATT
1 TTATTATTATTATCAATT
*
221724 TTATTATTATTATTAATT
1 TTATTATTATTATCAATT
221742 ATTGATATTG
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:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATTATTATCAATT
Found at i:224683 original size:23 final size:22
Alignment explanation
Indices: 224647--224695 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
224637 AATTTATTAC
224647 TTTATTATCAATTA-ATTATTATA
1 TTTATTATCAATTACA-TA-TATA
**
224670 TTTATTATTTATTACATATATA
1 TTTATTATCAATTACATATATA
224692 TTTA
1 TTTA
224696 GATATTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 14 0.61
24 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATTATCAATTACATATATA
Found at i:233736 original size:153 final size:146
Alignment explanation
Indices: 233465--233764 Score: 537
Period size: 153 Copynumber: 2.0 Consensus size: 146
233455 TACGTAGTGT
233465 AAAATATATTCAATTCTAAACAGAATAAATTTAGATCAGATCCACACGATGAACTATTGTCATAA
1 AAAATATATTCAATTCTAAACAGAATAAATTTAGATCAGATCCACACGATGAACTATTGTCATAA
233530 CCATTTTAGGTGAAATATTAAATATTATTTTAAAAACGATTATGACTTTAATAAAAAATTGGTGA
66 CCATTTTAGGTGAAATATTAAATATTATTTTAAAAACGATTATGACTTTAATAAAAAATTGGTGA
233595 TTTTGGATTGATTTGA
131 TTTTGGATTGATTTGA
233611 AAAATATATTCAATTCTAAATCAGAATAAATTTAGATCAGATCCACACACGATGAACTATATGTC
1 AAAATATATTCAATTCTAAA-CAGAATAAATTTAGATCAGAT-C-CACACGATGAACTAT-TGTC
233676 ATAACCATTTTTAGGTGAAATAATTAAATATTATTTTTAAAAACGATTATGACTTTAATAAAAAA
62 ATAACCA-TTTTAGGTGAAAT-ATTAAATATTA-TTTTAAAAACGATTATGACTTTAATAAAAAA
233741 TTGGTGATTTTGGATTGATTTGA
124 TTGGTGATTTTGGATTGATTTGA
233764 A
1 A
233765 TTAAATTGAA
Statistics
Matches: 147, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
146 20 0.14
147 21 0.14
148 1 0.01
149 15 0.10
150 11 0.07
151 13 0.09
152 11 0.07
153 55 0.37
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (146 bp):
AAAATATATTCAATTCTAAACAGAATAAATTTAGATCAGATCCACACGATGAACTATTGTCATAA
CCATTTTAGGTGAAATATTAAATATTATTTTAAAAACGATTATGACTTTAATAAAAAATTGGTGA
TTTTGGATTGATTTGA
Found at i:236440 original size:13 final size:13
Alignment explanation
Indices: 236436--236488 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
236426 ATTAATAAAC
236436 ATAATAATAATAA
1 ATAATAATAATAA
236449 ATAATAATAAT-A
1 ATAATAATAATAA
*
236461 ATAATAA-ATATAT
1 ATAATAATA-ATAA
236474 ATAAATAATAATAA
1 AT-AATAATAATAA
236488 A
1 A
236489 AAAGACCCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 1 0.03
12 10 0.29
13 13 0.38
14 9 0.26
15 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:236444 original size:3 final size:3
Alignment explanation
Indices: 236436--236487 Score: 61
Period size: 3 Copynumber: 16.3 Consensus size: 3
236426 ATTAATAAAC
236436 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA A-A TATA TATAA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A ATA ATA
236484 ATA A
1 ATA A
236488 AAAAGACCCG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 34 0.76
4 9 0.20
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:236451 original size:19 final size:18
Alignment explanation
Indices: 236424--236488 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
236414 TTGTAATATG
*
236424 TAATTAATAAACATAATAA
1 TAATAAATAAA-ATAATAA
236443 TAATAAATAATAATAATAA
1 TAATAAATAA-AATAATAA
*
236462 TAATAAATATATATAAATAA
1 TAATAAATA-AAAT-AATAA
236482 TAATAAA
1 TAATAAA
236489 AAAGACCCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
19 27 0.66
20 14 0.34
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAAATAAAATAATAA
Found at i:236453 original size:10 final size:10
Alignment explanation
Indices: 236438--236488 Score: 79
Period size: 10 Copynumber: 5.2 Consensus size: 10
236428 TAATAAACAT
236438 AATAATAATA
1 AATAATAATA
236448 AATAATAAT-
1 AATAATAATA
236457 AATAATAATA
1 AATAATAATA
236467 AAT-ATATATA
1 AATAATA-ATA
236477 AATAATAATA
1 AATAATAATA
236487 AA
1 AA
236489 AAAGACCCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.32
10 23 0.61
11 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAATA
Found at i:236455 original size:16 final size:16
Alignment explanation
Indices: 236436--236487 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
236426 ATTAATAAAC
236436 ATAATAATAATAAATA
1 ATAATAATAATAAATA
236452 ATAATAATAAT-AAT-
1 ATAATAATAATAAATA
236466 A-AAT-ATATATAAATA
1 ATAATAATA-ATAAATA
236481 ATAATAA
1 ATAATAA
236488 AAAAGACCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 3 0.10
13 5 0.16
14 4 0.13
15 4 0.13
16 14 0.45
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:236872 original size:40 final size:41
Alignment explanation
Indices: 236710--237076 Score: 174
Period size: 40 Copynumber: 8.6 Consensus size: 41
236700 TGGTCGGGGA
* ** *
236710 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGCTCATACGTGATGAGGAGAGCTGG--TTCT--AGG-G
* * * *
236756 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGG
1 ATGACACGGCTCATACGTGATGAGGA-GAGCTGG-T-TCTAGGG
* * * *
236799 TTGACACGGCTCCTACGTGATAAGGAGATCTGG-TCT-GGG
1 ATGACACGGCTCATACGTGATGAGGAGAGCTGGTTCTAGGG
* *
236838 AATGACCCGGCTCATACGTGATGAGGACG-GCTGGTTATCTATGG
1 -ATGACACGGCTCATACGTGATGAGGA-GAGCTGG-T-TCTAGGG
* * * *
236882 TTGACACGGCTCCTACGTGATAAGGAGATCTGG-TCT-GGG
1 ATGACACGGCTCATACGTGATGAGGAGAGCTGGTTCTAGGG
* ** *
236921 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 -ATGACACGGCTCATACGTGATGAGGAGAGCTGG--TTCT--AGG-G
* * * *
236968 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGG
1 ATGACACGGCTCATACGTGATGAGGA-GAGCTGG-T-TCTAGGG
* * * * * *
237011 TTGACACGGCTCCTACGTGATAAGGAAATCTGG-TCTGGGG
1 ATGACACGGCTCATACGTGATGAGGAGAGCTGGTTCTAGGG
* * *
237051 ATGACACGGTTCCTACATGATGAGGA
1 ATGACACGGCTCATACGTGATGAGGA
237077 CGGCTGGCCA
Statistics
Matches: 249, Mismatches: 51, Indels: 48
0.72 0.15 0.14
Matches are distributed among these distances:
39 4 0.02
40 87 0.35
41 1 0.00
42 2 0.01
43 86 0.35
44 6 0.02
46 60 0.24
47 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (41 bp):
ATGACACGGCTCATACGTGATGAGGAGAGCTGGTTCTAGGG
Found at i:236875 original size:83 final size:83
Alignment explanation
Indices: 236759--236944 Score: 345
Period size: 83 Copynumber: 2.2 Consensus size: 83
236749 AAAGGTGATA
* *
236759 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
236824 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
*
236842 ACCCGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
236907 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
236925 ACACGGCTCATACGTGATGA
1 ACACGGCTCATACGTGATGA
236945 AGAGTTCTGG
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 99 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (83 bp):
ACACGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
AGATCTGGTCTGGGAATG
Found at i:236961 original size:83 final size:83
Alignment explanation
Indices: 236759--236993 Score: 301
Period size: 83 Copynumber: 2.8 Consensus size: 83
236749 AAAGGTGATA
* * * **
236759 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAAGACGGCTGGCCATCTATGGTTGACACGGCTCCTACGTGATAAGG
236824 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
* * **
236842 ACCCGGCTCATACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGG
1 ACACGGCTCATACGTGATGAAGACGGCTGGCCATCTATGGTTGACACGGCTCCTACGTGATAAGG
236907 AGATCTGGTCTGGGAATG
66 AGATCTGGTCTGGGAATG
* * * *
236925 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 ACACGGCTCATACGTGATGAAGACG-GCTGGCCATCT-ATGGT--TGACACGGCTCCTACGTGAT
*
236989 GAGGA
62 AAGGA
236994 CGGCTGGTTA
Statistics
Matches: 136, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
82 1 0.01
83 109 0.80
84 4 0.03
86 22 0.16
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (83 bp):
ACACGGCTCATACGTGATGAAGACGGCTGGCCATCTATGGTTGACACGGCTCCTACGTGATAAGG
AGATCTGGTCTGGGAATG
Found at i:237002 original size:212 final size:212
Alignment explanation
Indices: 236680--237083 Score: 736
Period size: 212 Copynumber: 1.9 Consensus size: 212
236670 TTAACGCGGT
236680 TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
236745 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
* * *
236810 CCTACGTGATAAGGAGATCTGGTCTGGGAATGACCCGGCTCATACGTGATGAGGACGGCTGGTTA
131 CCTACGTGATAAGGAAATCTGGTCTGGGAATGACACGGCTCATACATGATGAGGACGGCTGGTTA
236875 TCTATGGTTGACACGGC
196 TCTATGGTTGACACGGC
* *
236892 TCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
236957 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
* * *
237022 CCTACGTGATAAGGAAATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGCTGG
131 CCTACGTGATAAGGAAATCTGGTCTGGGAATGACACGGCTCATACATGATGAGGACGGCTGG
237084 CCATCTTTAG
Statistics
Matches: 184, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
212 184 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (212 bp):
TCCTACGTGATAAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCT
CCTACGTGATAAGGAAATCTGGTCTGGGAATGACACGGCTCATACATGATGAGGACGGCTGGTTA
TCTATGGTTGACACGGC
Found at i:237084 original size:129 final size:129
Alignment explanation
Indices: 236852--237089 Score: 397
Period size: 129 Copynumber: 1.8 Consensus size: 129
236842 ACCCGGCTCA
*
236852 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTC
1 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAAATCTGGTC
* *
236917 TGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
66 TGGGAATGACACGGCTCATACATGATGAAGAGTGCTGGCCATCTAAAGGTGATAACACGGTTCC
236981 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAAATCTGGTC
1 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAAATCTGGTC
* * * *
237046 TGGGGATGACACGGTTCCTACATGATGAGGACG-GCTGGCCATCT
66 TGGGAATGACACGGCTCATACATGATGAAGA-GTGCTGGCCATCT
237090 TTAGGAGCTA
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
129 100 0.99
130 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (129 bp):
TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAAATCTGGTC
TGGGAATGACACGGCTCATACATGATGAAGAGTGCTGGCCATCTAAAGGTGATAACACGGTTCC
Done.