Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008156.1 Hibiscus syriacus cultivar Beakdansim tig00110722_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: 820393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:512353 original size:17 final size:17
Alignment explanation
Indices: 512319--512356 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
512309 TTTTTTTCTC
512319 TTTTTTAATTTTAGCATT
1 TTTTTTAATTTTA-CATT
512337 TTTTTTAATTATT-CATT
1 TTTTTTAATT-TTACATT
512354 TTT
1 TTT
512357 ACCTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 10 0.53
19 2 0.11
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTAATTTTACATT
Found at i:513510 original size:5 final size:5
Alignment explanation
Indices: 513496--513543 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
513486 GTGGGGTATG
*
513496 ATTTT TTTTT ATTTT ATTTT A-TTT ATTTT ATTTT -TTTT ATTTT GATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTT
513544 ACCTCACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
4 8 0.21
5 26 0.68
6 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (5 bp):
ATTTT
Found at i:513520 original size:14 final size:14
Alignment explanation
Indices: 513498--513543 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
513488 GGGGTATGAT
513498 TTTTTTTTATTTTA
1 TTTTTTTTATTTTA
*
513512 TTTTATTTATTTTA
1 TTTTTTTTATTTTA
513526 TTTTTTTTATTTTGA
1 TTTTTTTTATTTT-A
513541 TTT
1 TTT
513544 ACCTCACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTTTTTATTTTA
Found at i:513538 original size:9 final size:9
Alignment explanation
Indices: 513498--513538 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
513488 GGGGTATGAT
513498 TTTTTTTTA
1 TTTTTTTTA
513507 TTTTATTTTA
1 TTTT-TTTTA
*
513517 TTTATTTTA
1 TTTTTTTTA
513526 TTTTTTTTA
1 TTTTTTTTA
513535 TTTT
1 TTTT
513539 GATTTACCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:514224 original size:19 final size:19
Alignment explanation
Indices: 514200--514246 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
514190 ATTTAGACAT
514200 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
514219 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
514238 TTTGC-TTTC
1 TTTGCATTTC
514247 ACATTAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.66
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:517690 original size:84 final size:84
Alignment explanation
Indices: 517547--518296 Score: 776
Period size: 84 Copynumber: 8.9 Consensus size: 84
517537 GCTATCTGCC
* * * * * *
517547 AAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCA
1 AAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
517612 AGAAGGGTTATCTGCTAACA
65 AGAAGGGTTATCTGCTAACA
*
517632 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
* *
517697 GAAGGGTTATCTGCCAACT
66 GAAGGGTTATCTGCTAACA
* * * * * * * * *
517716 AAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCT
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCT
* * *
517781 AGAAGGGATATCTG-TCACC
65 AGAAGGGTTATCTGCTAACA
* * * *
517800 AAAGACCTTTGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
*
517865 GAAGGGCTATCTGC---C-
66 GAAGGGTTATCTGCTAACA
* * * * * *
517880 AAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCA
1 AAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
* *
517945 AGAAGGGTTATCTGCCAACT
65 AGAAGGGTTATCTGCTAACA
* * * * * * * * *
517965 AAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCT
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCT
* *
518030 AGAAGGGTTATCTG-TCACC
65 AGAAGGGTTATCTGCTAACA
* * * * *
518049 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCGGCACAGCTTAAGTCTA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
* * *
518114 GAGGGGTTGTCTGCCAACA
66 GAAGGGTTATCTGCTAACA
* * * * *** * * *
518133 AAAGACCTTCGAGTTTGATTACACTCAGCTTCGGGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCT
* *
518198 AGAAGGGTTATTTG-TGACCA
65 AGAAGGGTTATCTGCT-AACA
* * *
518218 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTCGA
1 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
*
518283 GAAGGGCTATCTGC
66 GAAGGGTTATCTGC
518297 CAAAGACTCC
Statistics
Matches: 544, Mismatches: 109, Indels: 24
0.80 0.16 0.04
Matches are distributed among these distances:
80 25 0.05
81 46 0.08
83 72 0.13
84 211 0.39
85 190 0.35
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (84 bp):
AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
GAAGGGTTATCTGCTAACA
Found at i:517838 original size:168 final size:166
Alignment explanation
Indices: 517522--518379 Score: 865
Period size: 168 Copynumber: 5.2 Consensus size: 166
517512 TGCAGCTTAG
* * * * *
517522 CTCAAAGCCAGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGC
* *
517585 ACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGA
65 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGA
* * *
517650 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAA
130 TTACACTCAGCTCCAAGGCACATCATTTACAGCATAA
* * * * * *
517687 CTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTC-AC-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAA-G
* * * * * * * *
517752 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGATATCTGTC-ACCAAAGACCTTTGAGTTC
63 GCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTC
* * * *
517816 GATTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAG
128 GATTACACTCAGCTCCAAGGCACATCATTTACAGCATAA
* * * * *
517855 CTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTC-AAGGC
* * * *
517918 ACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGA
65 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGA
* *
517983 TTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
130 TTACACTCAGCTCCAA-GGCACATCATTTACAGCATAA
* *
518021 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCA-CAAAGACCCTT-GAGTTCGACTACGCTCAGCTTCAAGG
* * * * * * * * *
518085 CATATCATTTGCGGCACAGCTTAAGTCTAGAGGGGTTGTCTGCCAACAAAAGACCTTCGAGTTTG
64 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCG
***
518150 ATTACACTCAGCTTCGGGGGCACATCATTTACAGCATAA
129 ATTACACTCAGC-TCCAAGGCACATCATTTACAGCATAA
* * * * *
518189 CTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCA-C-AAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGG
* * * * **
518254 CACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGA-CTCCCGAGTTC
64 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCT-TTGAGTTC
* * * * *
518314 GATTACACTCAACTTCGAGGTCATATCATTTACAACATAA
128 GATTACACTCAGCTCCAAGG-CACATCATTTACAGCATAA
* * * *
518354 TTCATGGCGAGAAAGGTTATTTGTCA
1 CTCAAGGCGAGAAGGGTTATCTGTCA
518380 ATAAAATTGT
Statistics
Matches: 581, Mismatches: 95, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
164 71 0.12
165 114 0.20
166 38 0.07
167 2 0.00
168 197 0.34
169 156 0.27
170 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (166 bp):
CTCAAGGCGAGAAGGGTTATCTGTCACAAAGACCCTTGAGTTCGACTACGCTCAGCTTCAAGGCA
CATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGAT
TACACTCAGCTCCAAGGCACATCATTTACAGCATAA
Found at i:518302 original size:249 final size:251
Alignment explanation
Indices: 517522--518303 Score: 986
Period size: 249 Copynumber: 3.1 Consensus size: 251
517512 TGCAGCTTAG
* * * * *
517522 CTCAAAGCCAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCA
1 CTCAAGGCTAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCA
* * * *
517586 CATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGAC
65 CATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGAC
* *
517651 TACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
130 TACGCTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
517715 TAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
195 TAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* * *
517772 CTCAAGGCTAGAAGGGATATCTGTCACCAAAGACCTTTGAGTTCGATTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGCTATCTG--ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * *
517837 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTCGA
64 ACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* *
517898 CTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAA
129 CTACGCTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAA
517963 CTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
194 CTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
*
518021 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGCTATCTG--ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * * * * *
518086 ATATCATTTGCGGCACAGCTTAAGTCTAGAGGGGTTGTCTGCCAACAAAAGACCTTCGAGTTTGA
64 ACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* * ** * * * * * ** *
518151 TTACACTCAGCTTCGGGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGAC
129 CTACGCTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAA
* * * * * * * * * *
518216 CAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATATGCAGCATAG
194 CTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* * *
518273 CTTAAGTCGAGAAGGGCTATCTG-CCAAAGAC
1 CTCAAGGCTAGAAGGGCTATCTGACCAAAGAC
518304 TCCCGAGTTC
Statistics
Matches: 464, Mismatches: 60, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
248 26 0.06
249 212 0.46
250 21 0.05
252 81 0.17
253 124 0.27
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (251 bp):
CTCAAGGCTAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
ATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACT
AAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
Found at i:518315 original size:333 final size:330
Alignment explanation
Indices: 517522--518379 Score: 981
Period size: 333 Copynumber: 2.6 Consensus size: 330
517512 TGCAGCTTAG
* *
517522 CTCAAAGCCAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCAC
1 CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCAC
* *
517587 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACT
66 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGC--ACAAAAGACC-CTGAGTTCGATT
* * * * * * * *
517652 ACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACT
128 ACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-ACC
* * *
517716 AAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCT
192 AAAGACCCTTAAGTTCGACTACACTCAGCTCCAAGGGCATATCATTTACAGCACAACTCAAGGCT
* * * *
517781 AGAAGGGATATCTGTCACCAAAGACCTTTGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTT
257 AGAAGGGATATCTGCCACAAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTT
* *
517846 GCAGAATAG
322 ACAGAATAA
* *
517855 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCAC
1 CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCAC
* *
517920 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATT
66 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTG-C-ACAAAAGACCC-TGAGTTCGATT
*
517985 ACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCA
128 ACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCA
* * * * * * *
518050 AAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCGGCACAGCTTAAGTCT
193 AAGACCCTT-AAGTTCGACTACACTCAGCTCCAAGGGCATATCATTTACAGCACAACTCAAGGCT
* * * * ***
518113 AGAGGGGTTGTCTGCCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTTCGGGGGCACATCAT
257 AGAAGGGATATCTGCC-ACAAAAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCAT
*
518178 TTACAGCATAA
320 TTACAGAATAA
* * * * * * *
518189 CTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAG
1 CTCAAGGCGAGAAGGGCTA--TCTG-CC-AAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAG
* * * * * *
518253 GCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-C-AAAGACTCCCGAGTTCGA
62 GCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCACAAAAGAC-CCTGAGTTCGA
* * * * * * * *
518316 TTACACTCAACTTCGAGGTCATATCATTTACAACATAATTCATGGCGAGAAAGGTTATTTGTCA
126 TTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCA
518380 ATAAAATTGT
Statistics
Matches: 448, Mismatches: 66, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
332 40 0.09
333 254 0.57
334 79 0.18
336 4 0.01
337 45 0.10
338 26 0.06
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (330 bp):
CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCAC
ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCACAAAAGACCCTGAGTTCGATTACA
CTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACCAAAG
ACCCTTAAGTTCGACTACACTCAGCTCCAAGGGCATATCATTTACAGCACAACTCAAGGCTAGAA
GGGATATCTGCCACAAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAG
AATAA
Found at i:519089 original size:36 final size:36
Alignment explanation
Indices: 519000--519317 Score: 186
Period size: 36 Copynumber: 8.9 Consensus size: 36
518990 TTTCAAAAAG
*
519000 AAAACA-TTTTGAAAA-TATGGGTAATATATAGTTTTTT
1 AAAACATTTTTGAAAACTAT--ATAATATATAG-TTTTT
* *
519037 AAAAATATTTTTGAAAACTATATAACATATAGTTTTT
1 -AAAACATTTTTGAAAACTATATAATATATAGTTTTT
* *
519074 AAAACATTTTTGAAAATTATATAACATATA-TTTTT
1 AAAACATTTTTGAAAACTATATAATATATAGTTTTT
* * *
519109 GAAATCA-TTTTGAAAA--A-ATAATGTATAGTTTAAAATA
1 -AAAACATTTTTGAAAACTATATAATATATAGTTT----TT
* *
519146 AAAACATTTTTTGAAAATTTTATATAATATATAGTTTTA
1 AAAACA-TTTTTGAAAA--CTATATAATATATAGTTTTT
* * *
519185 AAAATATTTTGGAAAACT-CAT-ATA-ATA-TTTTT
1 AAAACATTTTTGAAAACTATATAATATATAGTTTTT
* *
519217 AAAATCATTTTTGAAAACTATATGGA-ATATAGTTTTG
1 AAAA-CATTTTTGAAAACTATAT-AATATATAGTTTTT
**
519254 AAAACATTTTT---AA--ATATAATATATAGTTTAA
1 AAAACATTTTTGAAAACTATATAATATATAGTTTTT
* * *
519285 AAAATATTTTTTGAGATA-TATATATTATATAGT
1 AAAACA-TTTTTGA-AAACTATATAATATATAGT
519318 CTATATTATT
Statistics
Matches: 226, Mismatches: 26, Indels: 57
0.73 0.08 0.18
Matches are distributed among these distances:
30 1 0.00
31 18 0.08
32 21 0.09
33 21 0.09
34 5 0.02
35 17 0.08
36 51 0.23
37 27 0.12
38 32 0.14
39 16 0.07
40 3 0.01
42 1 0.00
43 13 0.06
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
AAAACATTTTTGAAAACTATATAATATATAGTTTTT
Found at i:519246 original size:34 final size:33
Alignment explanation
Indices: 519172--519239 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
519162 ATTTTATATA
* *
519172 ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAACTC
1 ATATAATA-TTTTTAAAATCATTTTTGAAAACTC
519204 ATATAATATTTTTAAAATCATTTTTGAAAACT-
1 ATATAATATTTTTAAAATCATTTTTGAAAACTC
519236 ATAT
1 ATAT
519240 GGAATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
ATATAATATTTTTAAAATCATTTTTGAAAACTC
Found at i:519338 original size:144 final size:141
Alignment explanation
Indices: 519021--519298 Score: 341
Period size: 144 Copynumber: 1.9 Consensus size: 141
519011 AAAATATGGG
*
519021 TAATATATAGTTTTTTAAAAATATTTTTGAAAACT-ATATAACATATAGTTTTTAAAACATTTTT
1 TAATATATAG--TTTTAAAAATATTTTGGAAAACTCATAT---A-ATA-TTTTTAAAACATTTTT
* * * *
519085 GAAAATTATATAACATATATTTTTGAAATCATTTTGAAAAAATAATGTATAGTTTAAAATAAAAA
59 GAAAACTATATAACATATAGTTTTGAAAACATTTTGAAAAAATAATATATAGTTT--AATAAAAA
519150 CATTTTTTGAAAATTTTATA
122 CATTTTTTGAAAATTTTATA
519170 TAATATATAGTTTTAAAAATATTTTGGAAAACTCATATAATATTTTTAAAATCATTTTTGAAAAC
1 TAATATATAGTTTTAAAAATATTTTGGAAAACTCATATAATATTTTTAAAA-CATTTTTGAAAAC
* * * *
519235 TATATGGA-ATATAGTTTTGAAAACATTTT-TAAATATAATATATAGTTT-A-AAAAATATTTTT
65 TATAT-AACATATAGTTTTGAAAACATTTTGAAAAAATAATATATAGTTTAATAAAAACATTTTT
519296 TGA
129 TGA
519299 GATATATATA
Statistics
Matches: 117, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
139 14 0.12
140 1 0.01
143 25 0.21
144 39 0.33
145 2 0.02
147 22 0.19
148 4 0.03
149 10 0.09
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (141 bp):
TAATATATAGTTTTAAAAATATTTTGGAAAACTCATATAATATTTTTAAAACATTTTTGAAAACT
ATATAACATATAGTTTTGAAAACATTTTGAAAAAATAATATATAGTTTAATAAAAACATTTTTTG
AAAATTTTATA
Found at i:519371 original size:18 final size:18
Alignment explanation
Indices: 519350--519388 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
519340 ATTATTTCTT
*
519350 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
519368 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
519386 TTC
1 TTC
519389 TGTTTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:521741 original size:14 final size:15
Alignment explanation
Indices: 521717--521758 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
521707 GGATTTAGAA
521717 TATTATTTTAAATAT
1 TATTATTTTAAATAT
*
521732 TATT-TTTTAAGTAT
1 TATTATTTTAAATAT
*
521746 T-TTAGTTTAAATA
1 TATTATTTTAAATA
521759 GTTTTAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 2 0.09
14 17 0.74
15 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTATTTTAAATAT
Found at i:526359 original size:75 final size:76
Alignment explanation
Indices: 526270--526495 Score: 222
Period size: 76 Copynumber: 3.1 Consensus size: 76
526260 TAAACTCAAG
* * *
526270 TTTAGGATAATATTTTAAACATTATATTTTAACTTT-GTATTTT-GTTGTAAATAGGTTTTAGTA
1 TTTAGGATATTATTTTAAATATTATATTTTAACTTTAGTATTTTAGTT-TAAATAAGTTTTAGTA
*
526333 TTTTAATTAAGT
65 TTTTAATTAAGA
* * **
526345 TTTAGGATATTATTTT-TATATTTTATCTTT-GTTTTAGGTATTTTAGTTTAAATAAGTTTTAGT
1 TTTAGGATATTATTTTAAATATTATAT-TTTAACTTTA-GTATTTTAGTTTAAATAAGTTTTAGT
*
526408 ATTTTAATTACGA
64 ATTTTAATTAAGA
*
526421 TTTAGAATATTATTTTAAATA-T-TA-TTT---TTTAGGTATTTTAGTTTAAAT-AGTTTTAAGT
1 TTTAGGATATTATTTTAAATATTATATTTTAACTTTA-GTATTTTAGTTTAAATAAGTTTT-AGT
* *
526479 GTTTTAATTAGGA
64 ATTTTAATTAAGA
526492 TTTA
1 TTTA
526496 AGATGTTTTA
Statistics
Matches: 132, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
70 6 0.05
71 39 0.30
73 3 0.02
74 10 0.08
75 20 0.15
76 48 0.36
77 6 0.05
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (76 bp):
TTTAGGATATTATTTTAAATATTATATTTTAACTTTAGTATTTTAGTTTAAATAAGTTTTAGTAT
TTTAATTAAGA
Found at i:527725 original size:29 final size:29
Alignment explanation
Indices: 527648--527715 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
527638 TTTGATGTAC
527648 TCTTAGTTCATTTATACACAAAATATTAA
1 TCTTAGTTCATTTATACACAAAATATTAA
*
527677 TCTTAGTTCATTTATACACAAAATTTTAA
1 TCTTAGTTCATTTATACACAAAATATTAA
527706 -CTTTAGTTCA
1 TC-TTAGTTCA
527716 ACTATGCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (29 bp):
TCTTAGTTCATTTATACACAAAATATTAA
Found at i:530082 original size:3 final size:3
Alignment explanation
Indices: 530074--530106 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
530064 TTTCATTCAA
530074 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
530107 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:532045 original size:65 final size:63
Alignment explanation
Indices: 531911--532051 Score: 149
Period size: 65 Copynumber: 2.2 Consensus size: 63
531901 GTGCACTAAG
* * * * *
531911 TGTGCATTGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGAC
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAACAGCCACAATGCATCGATGCATGAC
* * * * *
531974 TGGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAACATCCTCAATGCATCGGTGCATGGT
1 T-GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAAACAGCCACAATGCATCGATGCAT-G-
532039 A-
62 AC
532040 TGTGCATCGATG
1 TGTGCATCGATG
532052 TTCAATTTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.02
64 26 0.41
65 34 0.53
66 2 0.03
67 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAACAGCCACAATGCATCGATGCATGAC
Found at i:538691 original size:22 final size:21
Alignment explanation
Indices: 538649--538688 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
538639 GAGTTTATTT
*
538649 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
538670 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
538689 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:540668 original size:18 final size:17
Alignment explanation
Indices: 540614--540662 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
540604 TTGGACCCTT
* *
540614 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
540632 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
540650 AGTGCATTCGATG
1 AGTGCA-TCGATG
540663 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:540767 original size:65 final size:65
Alignment explanation
Indices: 540634--540793 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
540624 TGCACTAAGA
* * *
540634 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
* * * * *
540698 GTGCATCGATGCATTAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATCGGTGCATGGTA-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCAT-G-AC
540762 T-
64 TG
*
540763 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
540794 CAATTTAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.32
65 54 0.64
66 2 0.02
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
Found at i:540832 original size:65 final size:64
Alignment explanation
Indices: 540634--540843 Score: 193
Period size: 65 Copynumber: 3.2 Consensus size: 64
540624 TGCACTAAGA
* * *
540634 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA--AATAGCCAGAGTGCATCGATGCAT-GAC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAT--TCAG-GTGCATCGATGCATGGAT
540696 TG
63 TG
* * *
540698 GTGCATCGATGCATTAAATGCATTCGATGTTTTC-ATAACATCCTCA-GTGCATCGGTGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATTA-AT--TCAGGTGCATCGATGCATGGA
540760 TAT-
62 T-TG
*
540763 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TTAATTCA-GGTGCATCGATGCATGGATT
540827 G
64 G
* *
540828 GTGCATAGGTGCATCA
1 GTGCATCGATGCATCA
540844 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.39
65 61 0.50
66 3 0.02
67 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAATTCAGGTGCATCGATGCATGGATTG
Found at i:544713 original size:24 final size:24
Alignment explanation
Indices: 544637--544718 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
544627 CAACTTTATA
544637 ATATTT-AAATAAA-TAATTAAT-T
1 ATATTTAAAATAAATTAA-TAATAT
* *
544659 A-ATTGAAAATAACATTTATTAATAT
1 ATATTTAAAATAA-A-TTAATAATAT
*
544684 -TAATTTTAAATAAATTAATAATAT
1 AT-ATTTAAAATAAATTAATAATAT
544708 ATATTTAAAAT
1 ATATTTAAAAT
544719 TTTAATTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
21 3 0.07
22 7 0.15
23 1 0.02
24 21 0.46
25 5 0.11
26 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
ATATTTAAAATAAATTAATAATAT
Found at i:545074 original size:13 final size:13
Alignment explanation
Indices: 545041--545074 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
545031 AAAAATAAAA
*
545041 TAAAATAATTATT
1 TAAAAAAATTATT
*
545054 TATAAAAATTATT
1 TAAAAAAATTATT
545067 TAAAAAAA
1 TAAAAAAA
545075 AATCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAAATTATT
Found at i:545119 original size:20 final size:20
Alignment explanation
Indices: 545096--545133 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
545086 CCTCCCCATT
545096 TCTCTCTCGTTGCCCCCAAC
1 TCTCTCTCGTTGCCCCCAAC
*
545116 TCTCTCTTGTTGCCCCCA
1 TCTCTCTCGTTGCCCCCA
545134 GCTCCTCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.47, G:0.11, T:0.34
Consensus pattern (20 bp):
TCTCTCTCGTTGCCCCCAAC
Found at i:545205 original size:15 final size:15
Alignment explanation
Indices: 545187--545218 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
545177 TCCTAAGCTC
545187 CCTTCCCATCCCCCT
1 CCTTCCCATCCCCCT
*
545202 CCTTCCTATCCCCCT
1 CCTTCCCATCCCCCT
545217 CC
1 CC
545219 CCCTCCCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.66, G:0.00, T:0.28
Consensus pattern (15 bp):
CCTTCCCATCCCCCT
Found at i:545298 original size:7 final size:7
Alignment explanation
Indices: 545286--545316 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
545276 CCTGCTCCCC
545286 TCCCGTT
1 TCCCGTT
545293 TCCCGTT
1 TCCCGTT
545300 TCCCGTT
1 TCCCGTT
*
545307 TCCCTTT
1 TCCCGTT
545314 TCC
1 TCC
545317 TCTTCCTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.10, T:0.45
Consensus pattern (7 bp):
TCCCGTT
Found at i:545566 original size:48 final size:48
Alignment explanation
Indices: 545513--545604 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
545503 GAAAATATAA
*
545513 TTTAAAGATTTTTATTTTAAATAAAATCTTCAAAATTTCCAGAATGTT
1 TTTAAAGATTTTTATTTTAAATAAAATCTTCAAAATTACCAGAATGTT
* *
545561 TTTAAAGTTTTTTATTTTAAATAAAATTTTCAAAATTACCAGAA
1 TTTAAAGATTTTTATTTTAAATAAAATCTTCAAAATTACCAGAA
545605 CATGACATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (48 bp):
TTTAAAGATTTTTATTTTAAATAAAATCTTCAAAATTACCAGAATGTT
Found at i:545709 original size:18 final size:18
Alignment explanation
Indices: 545686--545722 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
545676 AGAGTTAGAC
*
545686 ACCTAAATTGATCGAAAA
1 ACCTAAATTGACCGAAAA
545704 ACCTAAATTGACCGAAAA
1 ACCTAAATTGACCGAAAA
545722 A
1 A
545723 TAGTATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (18 bp):
ACCTAAATTGACCGAAAA
Found at i:553431 original size:20 final size:20
Alignment explanation
Indices: 553416--553461 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
553406 GTTGTGCGTT
553416 TTTCACATTGAATGTGATAC
1 TTTCACATTGAATGTGATAC
553436 TTTCACATTGAATGTGATAC
1 TTTCACATTGAATGTGATAC
553456 TTTCAC
1 TTTCAC
553462 TTGCTGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
TTTCACATTGAATGTGATAC
Found at i:557539 original size:41 final size:41
Alignment explanation
Indices: 557418--557541 Score: 108
Period size: 41 Copynumber: 3.0 Consensus size: 41
557408 TTGTTTATAG
*
557418 TGCACAAACGCCGCTATAGAGTAGTAATGTAGCGGCGTTTAT
1 TGCACAAACGCCGCTATAGA-TAGTAATGTAGCGGCGTTTGT
** * ** * ***
557460 TAAACAAACGCCGCAATA-AT-GTTGTTTATAGTATCGTTTGT
1 TGCACAAACGCCGCTATAGATAG-T-AATGTAGCGGCGTTTGT
*
557501 TGCACAAACGCCGCTCTAGATAGTAATGTAGCGGCGTTTGT
1 TGCACAAACGCCGCTATAGATAGTAATGTAGCGGCGTTTGT
557542 CCTACAAACG
Statistics
Matches: 58, Mismatches: 20, Indels: 9
0.67 0.23 0.10
Matches are distributed among these distances:
39 1 0.02
40 2 0.03
41 36 0.62
42 18 0.31
43 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (41 bp):
TGCACAAACGCCGCTATAGATAGTAATGTAGCGGCGTTTGT
Found at i:557559 original size:82 final size:83
Alignment explanation
Indices: 557418--557573 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 83
557408 TTGTTTATAG
* *
557418 TGCACAAACGCCGCTATAGAGTAGTAATGTAGCGGCGTTTATTAAACAAACGCCGCAATAATGTT
1 TGCACAAACGCCGCTATAGAGTAGTAATGTAGCGGCGTTTATCAAACAAACGCCACAATAATGTT
*
557483 GTTTATAGTATCGTTTGT
66 GTTAATAGTATCGTTTGT
* * ** *
557501 TGCACAAACGCCGCTCTAGA-TAGTAATGTAGCGGCGTTTGTCCTACAAACGCCACAATATTGTT
1 TGCACAAACGCCGCTATAGAGTAGTAATGTAGCGGCGTTTATCAAACAAACGCCACAATAATGTT
557565 GTTAATAGT
66 GTTAATAGT
557574 GGCATTTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 46 0.71
83 19 0.29
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (83 bp):
TGCACAAACGCCGCTATAGAGTAGTAATGTAGCGGCGTTTATCAAACAAACGCCACAATAATGTT
GTTAATAGTATCGTTTGT
Found at i:558014 original size:8 final size:8
Alignment explanation
Indices: 558001--558026 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
557991 CTATACATAG
558001 TGGTTTAC
1 TGGTTTAC
558009 TGGTTTAC
1 TGGTTTAC
558017 TGGTTTAC
1 TGGTTTAC
558025 TG
1 TG
558027 CTTGAGAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.50
Consensus pattern (8 bp):
TGGTTTAC
Found at i:559244 original size:79 final size:79
Alignment explanation
Indices: 559090--559237 Score: 178
Period size: 79 Copynumber: 1.9 Consensus size: 79
559080 TTGTCTCCAA
* * *
559090 AAACGCCGCAATAAGTTCGTATATAGTGGCTTTTCACAACAAACGCCATTACAGAGTACTGCTTT
1 AAACGCCGCAATAAGTTCATATATAGTGGCTTTTCACAACAAACGCCATTACAGAATACTACTTT
559155 AGCGGAGTTTTCAT
66 AGCGGAGTTTTCAT
* * *
559169 AAACGCCGCAA-AATGGTTCATCTATAGTGG-TGTTT-ACAACAAACGCCGA-TATAGAATAGTA
1 AAACGCCGCAATAA--GTTCATATATAGTGGCT-TTTCACAACAAACGCC-ATTACAGAATACTA
559230 CTTTAGCG
62 CTTTAGCG
559238 ACGTTTTTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
78 2 0.03
79 40 0.68
80 17 0.29
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (79 bp):
AAACGCCGCAATAAGTTCATATATAGTGGCTTTTCACAACAAACGCCATTACAGAATACTACTTT
AGCGGAGTTTTCAT
Found at i:559278 original size:41 final size:41
Alignment explanation
Indices: 559233--559451 Score: 166
Period size: 41 Copynumber: 5.3 Consensus size: 41
559223 AATAGTACTT
* *
559233 TAGCGACGTTTTTATACAAACGCTGCAATATATGTAATCTA
1 TAGCGACATTTTTATACAAACGCCGCAATATATGTAATCTA
* *
559274 TAGCGGCATTTTTCA-ACAAACGCCGCAAGATAGTTGT-A-CGT-
1 TAGCGACATTTTT-ATACAAACGCCGCAATATA--TGTAATC-TA
* *
559315 TAGC-AGCATTTTTATACAAACGCCGCAATAGATGTAATATA
1 TAGCGA-CATTTTTATACAAACGCCGCAATATATGTAATCTA
** * * *
559356 TAGCGGTGTATTTTCA-ACAAACGCCGCAAGATAGTTGT-A-CTT
1 TAGC-G-ACATTTTTATACAAACGCCGCAATATA--TGTAATCTA
* * **
559398 TAGCGGCATTTTTATACAAGCGTTGCAATATATGTAATCTA
1 TAGCGACATTTTTATACAAACGCCGCAATATATGTAATCTA
559439 TAGCGACATTTTT
1 TAGCGACATTTTT
559452 TCAACAAACG
Statistics
Matches: 138, Mismatches: 23, Indels: 34
0.71 0.12 0.17
Matches are distributed among these distances:
39 6 0.04
40 11 0.08
41 85 0.62
42 23 0.17
43 10 0.07
44 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
TAGCGACATTTTTATACAAACGCCGCAATATATGTAATCTA
Found at i:559402 original size:42 final size:42
Alignment explanation
Indices: 559283--559403 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
559273 ATAGCGGCAT
*
559283 TTTTCAACAAACGCCGCAAGATAGTTGTACGTTAGC--AGCA
1 TTTTCAACAAACGCCGCAAGATAGTTGTACTTTAGCGGAGCA
* * * * *
559323 TTTTTATACAAACGCCGC-A-ATAGATGTAATATATAGCGGTGTA
1 TTTTCA-ACAAACGCCGCAAGATAGTTGTACT-T-TAGCGGAGCA
559366 TTTTCAACAAACGCCGCAAGATAGTTGTACTTTAGCGG
1 TTTTCAACAAACGCCGCAAGATAGTTGTACTTTAGCGG
559404 CATTTTTATA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
39 8 0.12
40 7 0.11
41 15 0.23
42 17 0.26
43 9 0.14
44 9 0.14
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (42 bp):
TTTTCAACAAACGCCGCAAGATAGTTGTACTTTAGCGGAGCA
Found at i:559407 original size:83 final size:82
Alignment explanation
Indices: 559227--559493 Score: 372
Period size: 83 Copynumber: 3.2 Consensus size: 82
559217 ATATAGAATA
* * *
559227 GTACTTTAGCGACGTTTTTATACAAACGCTGCAATATATGTAATCTATAGCGGCATTTTTCAACA
1 GTACGTTAGCGGCATTTTTATACAAACGCTGCAATATATGTAATCTATAGCGGCATTTTTCAACA
559292 AACGCCGCAAGATAGTT
66 AACGCCGCAAGATAGTT
* * * * **
559309 GTACGTTAGCAGCATTTTTATACAAACGCCGCAATAGATGTAATATATAGCGGTGTATTTTCAAC
1 GTACGTTAGCGGCATTTTTATACAAACGCTGCAATATATGTAATCTATAGCGGCAT-TTTTCAAC
559374 AAACGCCGCAAGATAGTT
65 AAACGCCGCAAGATAGTT
* * * *
559392 GTACTTTAGCGGCATTTTTATACAAGCGTTGCAATATATGTAATCTATAGCGACATTTTTTCAAC
1 GTACGTTAGCGGCATTTTTATACAAACGCTGCAATATATGTAATCTATAGCGGCA-TTTTTCAAC
* *
559457 AAACGCTGCAAAATAGTT
65 AAACGCCGCAAGATAGTT
*
559475 GTACGTTAGCTGCATTTTT
1 GTACGTTAGCGGCATTTTT
559494 TTTATCAAAA
Statistics
Matches: 160, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
82 47 0.29
83 112 0.70
84 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (82 bp):
GTACGTTAGCGGCATTTTTATACAAACGCTGCAATATATGTAATCTATAGCGGCATTTTTCAACA
AACGCCGCAAGATAGTT
Found at i:559494 original size:42 final size:41
Alignment explanation
Indices: 559274--559493 Score: 166
Period size: 41 Copynumber: 5.3 Consensus size: 41
559264 ATGTAATCTA
*
559274 TAGCGGCATTTTTCAACAAACGCCGCAAGATAGTTGTACGT
1 TAGCGGCATTTTTCAACAAACGCCGCAAAATAGTTGTACGT
* * **
559315 TAGCAGCATTTTT-ATACAAACGCCGC--AATAGATGTAATAT
1 TAGCGGCATTTTTCA-ACAAACGCCGCAAAATAGTTGT-ACGT
** * *
559355 ATAGCGGTGTATTTTCAACAAACGCCGCAAGATAGTTGTACTT
1 -TAGCGGCAT-TTTTCAACAAACGCCGCAAAATAGTTGTACGT
* ** *
559398 TAGCGGCATTTTT-ATACAAGCGTTGCAATATA--TGTAATC-T
1 TAGCGGCATTTTTCA-ACAAACGCCGCAAAATAGTTGT-A-CGT
* *
559438 ATAGCGACATTTTTTCAACAAACGCTGCAAAATAGTTGTACGT
1 -TAGCGGCA-TTTTTCAACAAACGCCGCAAAATAGTTGTACGT
*
559481 TAGCTGCATTTTT
1 TAGCGGCATTTTT
559494 TTTATCAAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 32
0.71 0.12 0.16
Matches are distributed among these distances:
39 10 0.07
40 6 0.04
41 59 0.42
42 48 0.35
43 6 0.04
44 10 0.07
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
TAGCGGCATTTTTCAACAAACGCCGCAAAATAGTTGTACGT
Found at i:562368 original size:25 final size:25
Alignment explanation
Indices: 562334--562392 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
562324 TATGAAGAAA
562334 ATGATAAAAGATTTGGGTCTTGGAT
1 ATGATAAAAGATTTGGGTCTTGGAT
562359 ATGATAAAAGATTTGGGTCTTGGAT
1 ATGATAAAAGATTTGGGTCTTGGAT
*
562384 ATGACAAAA
1 ATGATAAAA
562393 TTCATAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.32
Consensus pattern (25 bp):
ATGATAAAAGATTTGGGTCTTGGAT
Found at i:567581 original size:39 final size:39
Alignment explanation
Indices: 567527--567602 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
567517 TACTTTGATG
*
567527 AGATGTAGTAGGACTAGTTTGAGATTGATGCACAGAGGA
1 AGATGTAGTAGGACTAGTTTGAGACTGATGCACAGAGGA
*
567566 AGATGTAGTAGGACTATTTTGAGACTGATGCACAGAG
1 AGATGTAGTAGGACTAGTTTGAGACTGATGCACAGAG
567603 CAAGGTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (39 bp):
AGATGTAGTAGGACTAGTTTGAGACTGATGCACAGAGGA
Found at i:572744 original size:16 final size:16
Alignment explanation
Indices: 572723--572756 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
572713 TTACTATTCA
*
572723 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
572739 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
572755 CG
1 CG
572757 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:573527 original size:15 final size:16
Alignment explanation
Indices: 573507--573538 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
573497 TGGCAGATCC
573507 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
573522 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
573538 A
1 A
573539 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:577919 original size:41 final size:41
Alignment explanation
Indices: 577874--577970 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
577864 CATTCATTGA
577874 GTATCAATACCAGGGCAGGAGTATTGATACTCCCTATAGGG
1 GTATCAATACCAGGGCAGGAGTATTGATACTCCCTATAGGG
* *
577915 GTATCATTACCAGGGCATGAGTATTGATACTCCCTATAGGG
1 GTATCAATACCAGGGCAGGAGTATTGATACTCCCTATAGGG
* *
577956 GTATCGATACTAGGG
1 GTATCAATACCAGGG
577971 TATTTTTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (41 bp):
GTATCAATACCAGGGCAGGAGTATTGATACTCCCTATAGGG
Found at i:580633 original size:17 final size:16
Alignment explanation
Indices: 580611--580642 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
580601 TTGAAGCGAT
580611 GTATATATATAGTAAAC
1 GTATATAT-TAGTAAAC
580628 GTATATATTAGTAAA
1 GTATATATTAGTAAA
580643 AAAATGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (16 bp):
GTATATATTAGTAAAC
Found at i:580681 original size:2 final size:2
Alignment explanation
Indices: 580676--580722 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
580666 AATGTGTGTG
*
580676 TA TA TA TA TA TA TA TA -A TA -A TT TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
580715 TA TA TA TA
1 TA TA TA TA
580723 AAAGAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:583981 original size:19 final size:20
Alignment explanation
Indices: 583932--583984 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
583922 ACAATCTGGT
583932 AATTTTAAAAAAATTATTTAA
1 AATTTTAAAAAAATTA-TTAA
**
583953 AATTAAAAAAAAATTA-TAA
1 AATTTTAAAAAAATTATTAA
*
583972 ATTTTTAAAAAAA
1 AATTTTAAAAAAA
583985 AGTAAAACAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.48
21 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTTAAAAAAATTATTAA
Found at i:586809 original size:25 final size:25
Alignment explanation
Indices: 586781--586837 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
586771 TCCTTTCCAC
* *
586781 CTTTTTCTTCTTTCCTTCTTCTTTT
1 CTTTTTCTTCTTTCCTTATTCCTTT
*
586806 CTTTTTCTTCTTTTCTTATTCCTTT
1 CTTTTTCTTCTTTCCTTATTCCTTT
586831 CTCTTTT
1 CT-TTTT
586838 GGAGTTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (25 bp):
CTTTTTCTTCTTTCCTTATTCCTTT
Found at i:586813 original size:14 final size:14
Alignment explanation
Indices: 586796--586822 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
586786 TCTTCTTTCC
586796 TTCTTCTTTTCTTT
1 TTCTTCTTTTCTTT
586810 TTCTTCTTTTCTT
1 TTCTTCTTTTCTT
586823 ATTCCTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTCTTTTCTTT
Found at i:593353 original size:2 final size:2
Alignment explanation
Indices: 593346--593412 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
593336 TCTAGAATAA
593346 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
593388 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
593413 ACACTCCTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:594686 original size:2 final size:2
Alignment explanation
Indices: 594681--594747 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
594671 AAAAAGAACT
594681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
594723 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
594748 TGCAATTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:601137 original size:31 final size:31
Alignment explanation
Indices: 601102--601168 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
601092 TCAAAAAATA
*
601102 TAAGATATGATCACTTTCTTTTTTATTTAAT
1 TAAGATATGATCACTTTCGTTTTTATTTAAT
601133 TAAGATATGATCACTTTCGTTTTTATTTAAT
1 TAAGATATGATCACTTTCGTTTTTATTTAAT
601164 TAAGA
1 TAAGA
601169 CGTGGTCATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (31 bp):
TAAGATATGATCACTTTCGTTTTTATTTAAT
Found at i:601967 original size:22 final size:23
Alignment explanation
Indices: 601942--601992 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
601932 TTTTATATAT
601942 ATATATATATATTAAATTA-AAA
1 ATATATATATATTAAATTATAAA
* * * *
601964 ATATTTTTATATTAACTTATTAA
1 ATATATATATATTAAATTATAAA
601987 ATATAT
1 ATATAT
601993 TTTATTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATATATATTAAATTATAAA
Found at i:601992 original size:25 final size:27
Alignment explanation
Indices: 601956--602022 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 27
601946 ATATATATTA
601956 AATTAAAAATATTTTTA-TATTAACTT
1 AATTAAAAATATTTTTATTATTAACTT
* *
601982 -ATTAAATATA-TTTTATTATTAGCTT
1 AATTAAAAATATTTTTATTATTAACTT
602007 AATTTAAAAATATTTT
1 AA-TTAAAAATATTTT
602023 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 5 0.15
25 17 0.50
26 1 0.03
27 8 0.24
28 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (27 bp):
AATTAAAAATATTTTTATTATTAACTT
Found at i:602038 original size:27 final size:27
Alignment explanation
Indices: 601953--602046 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 27
601943 TATATATATA
* *
601953 TTAAATTAAAAATATTTT-TATATTAAC
1 TTAATTTAAAAATATTTTAT-TATTAGC
*
601980 TT-A-TTAAATATATTTTATTATTAGC
1 TTAATTTAAAAATATTTTATTATTAGC
* **
602005 TTAATTTAAAAATATTTTATTTTTATT
1 TTAATTTAAAAATATTTTATTATTAGC
*
602032 TTCATTTAAAAATAT
1 TTAATTTAAAAATAT
602047 ATATATTTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 20 0.35
26 3 0.05
27 34 0.60
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
TTAATTTAAAAATATTTTATTATTAGC
Found at i:604818 original size:15 final size:15
Alignment explanation
Indices: 604798--604828 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
604788 TATAACAAAC
604798 ATTATTAAATAGTAT
1 ATTATTAAATAGTAT
604813 ATTATTAAATAGTAT
1 ATTATTAAATAGTAT
604828 A
1 A
604829 AATTAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTATTAAATAGTAT
Found at i:610541 original size:22 final size:21
Alignment explanation
Indices: 610487--610567 Score: 84
Period size: 18 Copynumber: 4.0 Consensus size: 21
610477 TAATCGAGAG
610487 ATATACAGTGGTCCTTCGGGAC
1 ATATA-AGTGGTCCTTCGGGAC
*
610509 --ATAA-TGGTCCTTCGTGAC
1 ATATAAGTGGTCCTTCGGGAC
610527 ATATATAGTGGTCCTTCGGGAC
1 ATATA-AGTGGTCCTTCGGGAC
*
610549 --AT-AGTGGTCATTCGGGAC
1 ATATAAGTGGTCCTTCGGGAC
610567 A
1 A
610568 AATATTTAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
18 28 0.55
19 1 0.02
20 8 0.16
21 1 0.02
22 13 0.25
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (21 bp):
ATATAAGTGGTCCTTCGGGAC
Found at i:610542 original size:40 final size:40
Alignment explanation
Indices: 610487--610572 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
610477 TAATCGAGAG
* * *
610487 ATATACAGTGGTCCTTCGGGACATAATGGTCCTTCGTGAC
1 ATATATAGTGGTCCTTCGGGACATAATGGTCATTCGGGAC
*
610527 ATATATAGTGGTCCTTCGGGACATAGTGGTCATTCGGGAC
1 ATATATAGTGGTCCTTCGGGACATAATGGTCATTCGGGAC
*
610567 AAATAT
1 ATATAT
610573 TTAGTGCCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (40 bp):
ATATATAGTGGTCCTTCGGGACATAATGGTCATTCGGGAC
Found at i:614398 original size:25 final size:25
Alignment explanation
Indices: 614367--614419 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
614357 TTACAACTAG
*
614367 AAATGAGATAAATTAGGGCTATATA
1 AAATGAGATAAATTAGGGCGATATA
614392 AAATGAGATAAATTAGGGCGATATA
1 AAATGAGATAAATTAGGGCGATATA
614417 AAA
1 AAA
614420 CTTGCCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.25
Consensus pattern (25 bp):
AAATGAGATAAATTAGGGCGATATA
Found at i:624550 original size:20 final size:20
Alignment explanation
Indices: 624521--624570 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
624511 CATTAATAGA
624521 GTATCGATACT-ACAAGGTTG
1 GTATCGATACTCACAAGG-TG
* *
624541 GTATCAATACTCACGAGGTG
1 GTATCGATACTCACAAGGTG
624561 GTATCGATAC
1 GTATCGATAC
624571 CGGGATCGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (20 bp):
GTATCGATACTCACAAGGTG
Found at i:625755 original size:21 final size:20
Alignment explanation
Indices: 625744--625786 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
625734 GTCCATCTTT
*
625744 TATTTCAACTTGTTTATGCTC
1 TATTTCAACTTGTTCAT-CTC
625765 TATTTCAACTTGTTCATC-C
1 TATTTCAACTTGTTCATCTC
625784 TAT
1 TAT
625787 ACTTCTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 1 0.05
21 16 0.76
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (20 bp):
TATTTCAACTTGTTCATCTC
Found at i:628581 original size:15 final size:16
Alignment explanation
Indices: 628554--628583 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
628544 ATTATTTTAT
628554 TAATATATAATTAAAA
1 TAATATATAATTAAAA
628570 TAATAT-TAATTAAA
1 TAATATATAATTAAA
628584 TTACACCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATATAATTAAAA
Found at i:629136 original size:32 final size:34
Alignment explanation
Indices: 629100--629168 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 34
629090 TAATTATTAA
*
629100 ATTATA-TTTATTG-ATAATTTTAATAATATAAT
1 ATTATATTTTATTGTATAATTATAATAATATAAT
* *
629132 ATTATATTTTATTGTTATAATTATATTATTATAAT
1 ATTATATTTTATTG-TATAATTATAATAATATAAT
629167 AT
1 AT
629169 ATAATATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 6 0.19
33 7 0.23
35 18 0.58
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (34 bp):
ATTATATTTTATTGTATAATTATAATAATATAAT
Found at i:629142 original size:21 final size:21
Alignment explanation
Indices: 629075--629185 Score: 54
Period size: 21 Copynumber: 5.2 Consensus size: 21
629065 TTTAGTCTCG
629075 TTTTAATAA-A-AATATTA-A
1 TTTTAATAATATAATATTATA
* *
629093 TTATTAA-ATTATATTTATTGATAA
1 TT-TTAATAATATA-ATATT-AT-A
629117 TTTTAATAATATAATATTATA
1 TTTTAATAATATAATATTATA
* **
629138 TTTTATTGTTATAAT-TATATTA
1 TTTTAATAATATAATAT-TA-TA
* *
629160 TTATAAT-ATATAATATCATA
1 TTTTAATAATATAATATTATA
629180 CTTTTA
1 -TTTTA
629186 TTTCAATAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 21
0.68 0.12 0.21
Matches are distributed among these distances:
18 3 0.04
19 5 0.07
20 4 0.06
21 30 0.43
22 11 0.16
23 8 0.12
24 8 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTAATAATATAATATTATA
Found at i:629446 original size:32 final size:31
Alignment explanation
Indices: 629344--629476 Score: 105
Period size: 32 Copynumber: 4.1 Consensus size: 31
629334 AACAATGTTA
* *
629344 TTATTTTAATAATAATTAATAATATATTATT
1 TTATTTTAATAATAATTAATAATTTAATATT
629375 CTTATTTTAATAAGTAATTAATATAATTTATAATAATT
1 -TTATTTTAATAA-TAATT-A-ATAA-TT-TAAT-ATT
629413 TTATTTTAATAA-AATATAATAATCTTAATATT
1 TTATTTTAATAATAAT-TAATAAT-TTAATATT
*
629445 TT-TATTT-ATAA-AATT-ATAGATATAATATT
1 TTAT-TTTAATAATAATTAATA-ATTTAATATT
629474 TTA
1 TTA
629477 ATAATAATAT
Statistics
Matches: 87, Mismatches: 3, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
29 12 0.14
30 3 0.03
31 8 0.09
32 20 0.23
33 10 0.11
34 6 0.07
35 8 0.09
36 2 0.02
37 15 0.17
38 3 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (31 bp):
TTATTTTAATAATAATTAATAATTTAATATT
Found at i:629468 original size:69 final size:70
Alignment explanation
Indices: 629344--629481 Score: 160
Period size: 69 Copynumber: 2.0 Consensus size: 70
629334 AACAATGTTA
*
629344 TTATTTTAATAATAATTAATAATATATTATTCTTATTTTAATAAGTAATTAATATAAT-TTATAA
1 TTATTTTAATAATAATTAATAATATAATATTCTTATTTTAATAAGTAATTAATATAATATTATAA
629408 TAATT
66 TAATT
* * *
629413 TTATTTTAATAA-AATATAATAATCTTAATATTTTTATTTATAA-AA-TTA-TAGATATAATATT
1 TTATTTTAATAATAAT-TAATAAT-ATAATATTCTTATTT-TAATAAGTAATTA-ATATAATATT
*
629474 TTAATAAT
62 ATAATAAT
629482 AATATTGACA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
68 5 0.08
69 28 0.47
70 23 0.39
71 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (70 bp):
TTATTTTAATAATAATTAATAATATAATATTCTTATTTTAATAAGTAATTAATATAATATTATAA
TAATT
Found at i:629473 original size:29 final size:32
Alignment explanation
Indices: 629394--629475 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 32
629384 ATAAGTAATT
* *
629394 AATATAAT-TTATAATAATTTTATTTTAATAA
1 AATATAATAATATAATATTTTTATTTTAATAA
*
629425 AATATAATAATCTTAATATTTTTA-TTT-ATAA
1 AATATAATAAT-ATAATATTTTTATTTTAATAA
629456 AAT-T-ATAGATATAATATTTT
1 AATATAATA-ATATAATATTTT
629476 AATAATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 12 0.27
30 3 0.07
31 15 0.34
32 4 0.09
33 10 0.23
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
AATATAATAATATAATATTTTTATTTTAATAA
Found at i:631262 original size:3 final size:3
Alignment explanation
Indices: 631254--631284 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
631244 CCTTTAAGAC
631254 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
631285 ATTCCTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:642939 original size:9 final size:9
Alignment explanation
Indices: 642909--642960 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
642899 ATCTGCAAAA
*
642909 AAATTAATT
1 AAATTAAAT
642918 AAA-TAAA-
1 AAATTAAAT
*
642925 ATATTAAAT
1 AAATTAAAT
642934 AAATTAAAT
1 AAATTAAAT
*
642943 -ACTTAAAT
1 AAATTAAAT
642951 AAATTAAAT
1 AAATTAAAT
642960 A
1 A
642961 TAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:642941 original size:17 final size:16
Alignment explanation
Indices: 642911--642967 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
642901 CTGCAAAAAA
* *
642911 ATTAATTAAATAAAAT
1 ATTAAATAAATTAAAT
642927 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
642943 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
642960 ATAAAATA
1 ATTAAATA
642968 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:647941 original size:18 final size:19
Alignment explanation
Indices: 647904--647941 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
647894 CACTAAACAC
*
647904 TATCCATTTTGCCACGACA
1 TATCCATTTTGCCACCACA
*
647923 TATCCA-TTTGCTACCACA
1 TATCCATTTTGCCACCACA
647941 T
1 T
647942 TGCCATCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.34
Consensus pattern (19 bp):
TATCCATTTTGCCACCACA
Found at i:660486 original size:15 final size:15
Alignment explanation
Indices: 660466--660496 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
660456 TTTGGCCCTT
*
660466 TAATTTCTGAATAAA
1 TAATTTATGAATAAA
660481 TAATTTATGAATAAA
1 TAATTTATGAATAAA
660496 T
1 T
660497 TTTAGGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (15 bp):
TAATTTATGAATAAA
Found at i:661590 original size:13 final size:13
Alignment explanation
Indices: 661511--661590 Score: 54
Period size: 13 Copynumber: 6.1 Consensus size: 13
661501 AGATTAAAGC
661511 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
* *
661524 ATTAGGGTTAAGG
1 TTTAGGGTTTAGG
* *
661537 -TTAGAGTTTGGGG
1 TTTAGGGTTT-AGG
**
661550 TTTAGGGTTTAAA
1 TTTAGGGTTTAGG
* * *
661563 ATAAGAGTTTAAGG
1 TTTAGGGTTT-AGG
661577 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
661590 T
1 T
661591 AAAAAGAGAT
Statistics
Matches: 47, Mismatches: 17, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
12 7 0.15
13 24 0.51
14 16 0.34
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (13 bp):
TTTAGGGTTTAGG
Found at i:661634 original size:23 final size:25
Alignment explanation
Indices: 661590--661639 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
661580 AGGGTTTAGG
*
661590 TAAAAAGAGATGTTTTACTATGAGT
1 TAAAAAGAGATGTTATACTATGAGT
* *
661615 TAAAAAGATAT-TTATA-TATGGGT
1 TAAAAAGAGATGTTATACTATGAGT
661638 TA
1 TA
661640 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (25 bp):
TAAAAAGAGATGTTATACTATGAGT
Found at i:661796 original size:18 final size:18
Alignment explanation
Indices: 661773--661818 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
661763 TCACGATATA
661773 ATAAAAATAATATTTTAT
1 ATAAAAATAATATTTTAT
661791 ATAAAAATAATATTTTAT
1 ATAAAAATAATATTTTAT
661809 ATAAAAATAA
1 ATAAAAATAA
661819 GAAAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAATAATATTTTAT
Found at i:662620 original size:19 final size:19
Alignment explanation
Indices: 662596--662669 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
662586 TATTATTCAT
*
662596 AGTTTGGAAACTTTGTAAG
1 AGTTTGGAAACTTTGTAAA
662615 AGTTTGGAAACTTT-TATTAA
1 AGTTTGGAAACTTTGTA--AA
* **
662635 TAGTTTCGAAACTTTACAAA
1 -AGTTTGGAAACTTTGTAAA
*
662655 AGTTTTGAAACTTTG
1 AGTTTGGAAACTTTG
662670 CACCCATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.04
19 27 0.59
20 3 0.07
21 13 0.28
22 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (19 bp):
AGTTTGGAAACTTTGTAAA
Found at i:662645 original size:21 final size:21
Alignment explanation
Indices: 662588--662649 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
662578 TACACGAGTA
*
662588 TTATTCATAGTTTGGAAAC-T
1 TTATTAATAGTTTGGAAACTT
* *
662608 TT-GTAAGAGTTTGGAAACTT
1 TTATTAATAGTTTGGAAACTT
*
662628 TTATTAATAGTTTCGAAACTT
1 TTATTAATAGTTTGGAAACTT
662649 T
1 T
662650 ACAAAAGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 13 0.38
20 5 0.15
21 16 0.47
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (21 bp):
TTATTAATAGTTTGGAAACTT
Found at i:662646 original size:40 final size:40
Alignment explanation
Indices: 662588--662668 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
662578 TACACGAGTA
* * ** *
662588 TTATTCATAGTTTGGAAACTTTGTAAGAGTTTGGAAACTT
1 TTATTAATAGTTTCGAAACTTTACAAAAGTTTGGAAACTT
*
662628 TTATTAATAGTTTCGAAACTTTACAAAAGTTTTGAAACTT
1 TTATTAATAGTTTCGAAACTTTACAAAAGTTTGGAAACTT
662668 T
1 T
662669 GCACCCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (40 bp):
TTATTAATAGTTTCGAAACTTTACAAAAGTTTGGAAACTT
Found at i:664126 original size:12 final size:12
Alignment explanation
Indices: 664111--664150 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
664101 GATGACCAAG
664111 AAGAAGAAAAGA
1 AAGAAGAAAAGA
*
664123 AAGAAGAGAAGA
1 AAGAAGAAAAGA
664135 AA-AAGAAAAAGA
1 AAGAAG-AAAAGA
664147 AAGA
1 AAGA
664151 GGTGAGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.12
12 20 0.83
13 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAGA
Found at i:664134 original size:17 final size:16
Alignment explanation
Indices: 664112--664150 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
664102 ATGACCAAGA
664112 AGAAGAAAAGAAAGAAG
1 AGAAGAAAAGAAA-AAG
664129 AGAAGAAAAAGAAAAAG
1 AGAAG-AAAAGAAAAAG
664146 A-AAGA
1 AGAAGA
664151 GGTGAGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 9 0.43
18 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAGAAAAAG
Found at i:664134 original size:20 final size:18
Alignment explanation
Indices: 664109--664150 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
664099 AGGATGACCA
664109 AGAAGAAGAAAAGAAAGAAG
1 AGAAGAA-AAAAGAAA-AAG
664129 AGAAG-AAAAAGAAAAAG
1 AGAAGAAAAAAGAAAAAG
664146 A-AAGA
1 AGAAGA
664151 GGTGAGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 4 0.19
18 8 0.38
19 1 0.05
20 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AGAAGAAAAAAGAAAAAG
Found at i:666100 original size:19 final size:19
Alignment explanation
Indices: 666076--666114 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
666066 AACTTTTATT
666076 AATAGTTTCAAAACTTTAC
1 AATAGTTTCAAAACTTTAC
*
666095 AATAGTTTCCAAACTTTAC
1 AATAGTTTCAAAACTTTAC
666114 A
1 A
666115 CCCAGAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (19 bp):
AATAGTTTCAAAACTTTAC
Found at i:666291 original size:20 final size:20
Alignment explanation
Indices: 666220--666293 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
666210 CAATGTGTTT
*
666220 AAAAGTTTCGATA-TTT-TC
1 AAAAGTTTCGAAACTTTCTC
* *
666238 ACGAAGTTTTGAAACTTTCTC
1 A-AAAGTTTCGAAACTTTCTC
* *
666259 AAAAGTTTTGAAACTTTCTTT
1 AAAAGTTTCGAAACTTTC-TC
666280 AAAA-TTTCGAAACT
1 AAAAGTTTCGAAACT
666294 ACATGTCCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.02
19 9 0.20
20 28 0.61
21 8 0.17
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (20 bp):
AAAAGTTTCGAAACTTTCTC
Found at i:670900 original size:14 final size:14
Alignment explanation
Indices: 670883--670915 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
670873 ATCAAAGAAA
670883 GAAACAAAAATGAG
1 GAAACAAAAATGAG
*
670897 GAAACGAAAATGAG
1 GAAACAAAAATGAG
670911 GAAAC
1 GAAAC
670916 TGATCCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.09, G:0.24, T:0.06
Consensus pattern (14 bp):
GAAACAAAAATGAG
Found at i:679946 original size:14 final size:14
Alignment explanation
Indices: 679929--679965 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
679919 TGGATAAATT
679929 GGTTCGGGTAATCG
1 GGTTCGGGTAATCG
679943 GGTTCGGGTAATCG
1 GGTTCGGGTAATCG
679957 GGTTCGGGT
1 GGTTCGGGT
679966 CAAGTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.14, G:0.46, T:0.30
Consensus pattern (14 bp):
GGTTCGGGTAATCG
Found at i:682948 original size:19 final size:21
Alignment explanation
Indices: 682924--682965 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
682914 AATTTAATAT
682924 TAATTTTAAT-T-CAATTAAA
1 TAATTTTAATATCCAATTAAA
682943 TAATTTTAATATCCAATTAAA
1 TAATTTTAATATCCAATTAAA
682964 TA
1 TA
682966 GTGACATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTTTAATATCCAATTAAA
Found at i:684544 original size:24 final size:24
Alignment explanation
Indices: 684506--684582 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
684496 AAGTTCCACA
684506 TAGAA-TTGTCCCGAAGGACCGCG
1 TAGAATTTGTCCCGAAGGACCGCG
* *
684529 TAGAATTTATCCCGAAGGACCACG
1 TAGAATTTGTCCCGAAGGACCGCG
* *
684553 TAGAAATTTGTCCCGATGGACTGCG
1 TAG-AATTTGTCCCGAAGGACCGCG
684578 TAGAA
1 TAGAA
684583 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.11
24 21 0.46
25 20 0.43
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
TAGAATTTGTCCCGAAGGACCGCG
Found at i:684566 original size:25 final size:25
Alignment explanation
Indices: 684511--684582 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
684501 CCACATAGAA
684511 TTGTCCCGAAGGACCGCGTAG-AAT
1 TTGTCCCGAAGGACCGCGTAGAAAT
* *
684535 TTATCCCGAAGGACCACGTAGAAAT
1 TTGTCCCGAAGGACCGCGTAGAAAT
* *
684560 TTGTCCCGATGGACTGCGTAGAA
1 TTGTCCCGAAGGACCGCGTAGAA
684583 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (25 bp):
TTGTCCCGAAGGACCGCGTAGAAAT
Found at i:684734 original size:15 final size:15
Alignment explanation
Indices: 684716--684795 Score: 97
Period size: 15 Copynumber: 5.3 Consensus size: 15
684706 ATAGGGTATC
*
684716 TTCACGTAGAACATT
1 TTCACATAGAACATT
* *
684731 TTCACTTAGCACATT
1 TTCACATAGAACATT
684746 TTCACATAGAACATT
1 TTCACATAGAACATT
* * *
684761 TTCATATAAAACATA
1 TTCACATAGAACATT
*
684776 TTCACATATAACATT
1 TTCACATAGAACATT
684791 TTCAC
1 TTCAC
684796 TTACCAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (15 bp):
TTCACATAGAACATT
Found at i:690858 original size:16 final size:17
Alignment explanation
Indices: 690837--690869 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
690827 AGGTGTCACA
690837 TTGACTT-TTCAAAACT
1 TTGACTTGTTCAAAACT
*
690853 TTGACTTGTTGAAAACT
1 TTGACTTGTTCAAAACT
690870 CATTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TTGACTTGTTCAAAACT
Found at i:691466 original size:24 final size:24
Alignment explanation
Indices: 691434--691507 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
691424 TGCCACATAG
*
691434 ATTTTTCCCGAATGACCGCGTAGA
1 ATTTGTCCCGAATGACCGCGTAGA
* *
691458 ATTTGTCCCGAATGACCACATAGAA
1 ATTTGTCCCGAATGACCGCGTAG-A
*
691483 ATTTGTCCCGAAGGACCGCGTAGA
1 ATTTGTCCCGAATGACCGCGTAGA
691507 A
1 A
691508 CCATTGACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 22 0.51
25 21 0.49
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (24 bp):
ATTTGTCCCGAATGACCGCGTAGA
Found at i:691491 original size:25 final size:24
Alignment explanation
Indices: 691426--691499 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
691416 GTACGAAGTG
*
691426 CCACATAG-ATTTTTCCCGAATGA
1 CCACATAGAATTTGTCCCGAATGA
* *
691449 CCGCGTAGAATTTGTCCCGAATGA
1 CCACATAGAATTTGTCCCGAATGA
*
691473 CCACATAGAAATTTGTCCCGAAGGA
1 CCACATAG-AATTTGTCCCGAATGA
691498 CC
1 CC
691500 GCGTAGAACC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.14
24 20 0.47
25 17 0.40
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAATGA
Found at i:691506 original size:25 final size:25
Alignment explanation
Indices: 691434--691507 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
691424 TGCCACATAG
*
691434 ATTTTTCCCGAATGACCGCGTAG-A
1 ATTTGTCCCGAATGACCGCGTAGAA
* *
691458 ATTTGTCCCGAATGACCACATAGAA
1 ATTTGTCCCGAATGACCGCGTAGAA
*
691483 ATTTGTCCCGAAGGACCGCGTAGAA
1 ATTTGTCCCGAATGACCGCGTAGAA
691508 CCATTGACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAATGACCGCGTAGAA
Found at i:691655 original size:15 final size:15
Alignment explanation
Indices: 691637--691704 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
691627 CACATAGGGT
*
691637 ATTTTCACGTAAAAC
1 ATTTTCACATAAAAC
* **
691652 ATTTTCACTTAGCAC
1 ATTTTCACATAAAAC
*
691667 ATTTTCACATAGAAC
1 ATTTTCACATAAAAC
*
691682 ATTTTCATATAAAAC
1 ATTTTCACATAAAAC
*
691697 ATATTCAC
1 ATTTTCAC
691705 TTACCAAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (15 bp):
ATTTTCACATAAAAC
Found at i:693353 original size:12 final size:12
Alignment explanation
Indices: 693336--693360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
693326 AAGATTTGAA
693336 AATTTAAGATGC
1 AATTTAAGATGC
693348 AATTTAAGATGC
1 AATTTAAGATGC
693360 A
1 A
693361 CTTTGGTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AATTTAAGATGC
Found at i:694031 original size:20 final size:19
Alignment explanation
Indices: 694006--694057 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
693996 TGATTCAATC
694006 AGTATCGATACCGAAGGAGA
1 AGTATCGATACCGAAGG-GA
*
694026 AGTATCAATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
694045 AGGTATCGATACC
1 A-GTATCGATACC
694058 ATTTTAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:694655 original size:34 final size:34
Alignment explanation
Indices: 694612--694676 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
694602 TCATAACTGA
*
694612 AATGTATATGGGTGCATTATTGACATAAAAGAAT
1 AATGCATATGGGTGCATTATTGACATAAAAGAAT
* *
694646 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATTGACATAAAAG
694677 GATTCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGACATAAAAGAAT
Found at i:694691 original size:79 final size:79
Alignment explanation
Indices: 694560--694721 Score: 245
Period size: 79 Copynumber: 2.1 Consensus size: 79
694550 CAAATGAATG
**
694560 AAAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGTCATAACTGAAATGTATATGGGT
1 AAAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGTCATAACTGAAATACATATGGGT
*
694625 GCATTATTGACATA
66 GCATTATCGACATA
* *
694639 AAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGAT-TCCATAGCTGAAATACATATGGG
1 AAAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGT-CATAACTGAAATACATATGGG
* *
694703 TGTATTATCGGCATA
65 TGCATTATCGACATA
694718 AAAG
1 AAAG
694722 TATACTCTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
78 1 0.01
79 74 0.99
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (79 bp):
AAAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGTCATAACTGAAATACATATGGGT
GCATTATCGACATA
Found at i:697294 original size:23 final size:21
Alignment explanation
Indices: 697247--697295 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
697237 GATATAATAG
* *
697247 TTATCTTAATAAAAATTATAT
1 TTATATTAATAAAAATTATAA
*
697268 TTATATTATATAAAAATATTTAA
1 TTATATTA-ATAAAAAT-TATAA
697291 TTATA
1 TTATA
697296 AAAAGTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
23 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATATTAATAAAAATTATAA
Found at i:697305 original size:18 final size:18
Alignment explanation
Indices: 697255--697306 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 18
697245 AGTTATCTTA
697255 ATAAAAATTATATTTATATT
1 ATAAAAA-T-TATTTATATT
*
697275 ATATAAAAATATTTA-ATT
1 ATA-AAAATTATTTATATT
697293 ATAAAAAGTTATTT
1 ATAAAAA-TTATTT
697307 TAAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 6 0.21
20 3 0.11
21 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAAAAATTATTTATATT
Found at i:697308 original size:19 final size:18
Alignment explanation
Indices: 697255--697315 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
697245 AGTTATCTTA
697255 ATAAAAATTATATTTATATT
1 ATAAAAATTAT-TTTA-ATT
*
697275 ATATAAAAATA-TTTAATT
1 ATA-AAAATTATTTTAATT
*
697293 ATAAAAAGTTATTTTAAAT
1 ATAAAAA-TTATTTTAATT
697312 ATAA
1 ATAA
697316 TTAATTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 4 0.11
18 8 0.23
19 14 0.40
20 3 0.09
21 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAAAAATTATTTTAATT
Found at i:702835 original size:60 final size:61
Alignment explanation
Indices: 702769--702885 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 61
702759 ATAAAGACCT
*
702769 TGACTATAG-GATATTGATTT-ATTAAGT-TCCTTAACTATTAAAAGTTACAAAATGGTTCTC
1 TGACTATAGAGA-ATTGATTTCATTAAGTCT-CTTAACTATTAAAAATTACAAAATGGTTCTC
* * * * *
702829 TGACTATAGAGAGTTGCTTTCATTGAGTCTCTTGATTATTAAAAATTACAAAATGGT
1 TGACTATAGAGAATTGATTTCATTAAGTCTCTTAACTATTAAAAATTACAAAATGGT
702886 CATCCAACTC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
60 15 0.31
61 32 0.67
62 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (61 bp):
TGACTATAGAGAATTGATTTCATTAAGTCTCTTAACTATTAAAAATTACAAAATGGTTCTC
Found at i:703224 original size:60 final size:59
Alignment explanation
Indices: 703099--703225 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 59
703089 TAATGAATAA
* * *
703099 TCGAGTGGTCATTTTGTAACTTTTAATAGTCAAGTGACTCAATAAATAAGCTTCCTATGG
1 TCGAGGGGTCATTTTGTAACTTTTAATAGTCAAGTGACTCAATAAACAA-CTTCCTATAG
* * *
703159 CCGAGGGGTCATTTTGTAACTTTTAATAGTC-AGTGGACTCGATAAAGCAA-TATCTTATAG
1 TCGAGGGGTCATTTTGTAACTTTTAATAGTCAAGT-GACTCAATAAA-CAACT-TCCTATAG
703219 TCGAGGG
1 TCGAGGG
703226 ACCATGTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 4 0.07
60 51 0.89
61 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (59 bp):
TCGAGGGGTCATTTTGTAACTTTTAATAGTCAAGTGACTCAATAAACAACTTCCTATAG
Found at i:705014 original size:11 final size:11
Alignment explanation
Indices: 704998--705023 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
704988 AATCATTATT
704998 TATTTTTAGAA
1 TATTTTTAGAA
705009 TATTTTTAGAA
1 TATTTTTAGAA
705020 TATT
1 TATT
705024 CTGAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TATTTTTAGAA
Found at i:709077 original size:27 final size:27
Alignment explanation
Indices: 709023--709078 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
709013 TTATTATTTC
***
709023 TATCAGTTTTGTTATTATTGGGTGCTT
1 TATCAGTTTTGTTATTATTGGACACTT
*
709050 TATCGGTTTTGTTATTATTGGACACTT
1 TATCAGTTTTGTTATTATTGGACACTT
709077 TA
1 TA
709079 CCGGAAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.54
Consensus pattern (27 bp):
TATCAGTTTTGTTATTATTGGACACTT
Found at i:709850 original size:21 final size:22
Alignment explanation
Indices: 709825--709865 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
709815 TTCAACCACT
709825 CTTAA-AA-TTTGATTTTTTTTA
1 CTTAAGAATTTTG-TTTTTTTTA
709846 CTTAAGAATTTTGTTTTTTT
1 CTTAAGAATTTTGTTTTTTT
709866 GTTGTTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (22 bp):
CTTAAGAATTTTGTTTTTTTTA
Found at i:733345 original size:7 final size:7
Alignment explanation
Indices: 733333--733359 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
733323 TAGAGATTTC
733333 AAAATTG
1 AAAATTG
733340 AAAATTG
1 AAAATTG
733347 AAAATTG
1 AAAATTG
733354 AAAATT
1 AAAATT
733360 TTGAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (7 bp):
AAAATTG
Found at i:735241 original size:19 final size:20
Alignment explanation
Indices: 735219--735272 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
735209 GTATTGTTAT
735219 AGTTTAGAAACTTT-GTAAG
1 AGTTTAGAAACTTTAGTAAG
* *
735238 AGTTTTGAAACTTTTATTAAG
1 AGTTTAGAAAC-TTTAGTAAG
*
735259 AGTTTCGAAACTTT
1 AGTTTAGAAACTTT
735273 CAAAACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.33
20 6 0.20
21 14 0.47
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (20 bp):
AGTTTAGAAACTTTAGTAAG
Found at i:741095 original size:10 final size:8
Alignment explanation
Indices: 741073--741106 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
741063 TAATACTATA
741073 TATTTTTT
1 TATTTTTT
741081 TATTTTTT
1 TATTTTTT
*
741089 CTAATTTTT
1 -TATTTTTT
741098 TATTTTTT
1 TATTTTTT
741106 T
1 T
741107 GAAAATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
TATTTTTT
Found at i:750200 original size:23 final size:24
Alignment explanation
Indices: 750156--750200 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
750146 AGGTTCATGT
* * *
750156 TTGAGTTTGAGTTTGAGGTTTTAA
1 TTGAGTTTAAGTTTAAGATTTTAA
750180 TTGAG-TTAAGTTTAAGATTTT
1 TTGAGTTTAAGTTTAAGATTTT
750201 TTTTTTCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (24 bp):
TTGAGTTTAAGTTTAAGATTTTAA
Found at i:753010 original size:2 final size:2
Alignment explanation
Indices: 753003--753043 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
752993 AACAATTTTA
753003 AT AT AT AT AT 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 AT AT AT AT AT A
753044 AAGCATATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:753737 original size:37 final size:36
Alignment explanation
Indices: 753662--753737 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
753652 TTTTTATATT
*
753662 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
753698 TTTAATTTTTTAAAGAAAATT-TATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
753735 TTT
1 TTT
753738 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 24 0.69
37 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:754463 original size:46 final size:45
Alignment explanation
Indices: 754404--754492 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 45
754394 GTATCTATAA
* *
754404 TATTATAAAAATATTTATTTAATT-TTTAAAATCATATTATTTACT
1 TATTATAAAAATA-TTAATTAATTATTTAAAATAATATTATTTACT
* * *
754449 TATTTTAAATAATATTAATTATTTATTTGAAATAATATTATTTA
1 TATTATAAA-AATATTAATTAATTATTTAAAATAATATTATTTA
754493 TAAATTATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 16 0.43
46 21 0.57
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (45 bp):
TATTATAAAAATATTAATTAATTATTTAAAATAATATTATTTACT
Found at i:754493 original size:23 final size:23
Alignment explanation
Indices: 754413--754493 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
754403 ATATTATAAA
*
754413 AATATTTATTTAATT-TTTAAAAT
1 AATA-TTATTTATTTATTTAAAAT
* * *
754436 CATATTATTTACTTATTTTAAAT
1 AATATTATTTATTTATTTAAAAT
* *
754459 AATATTAATTATTTATTTGAAAT
1 AATATTATTTATTTATTTAAAAT
754482 AATATTATTTAT
1 AATATTATTTAT
754494 AAATTATCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 9 0.18
23 40 0.82
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (23 bp):
AATATTATTTATTTATTTAAAAT
Found at i:754497 original size:16 final size:18
Alignment explanation
Indices: 754466--754523 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
754456 AATAATATTA
*
754466 ATTATTTATTTGAAATAAT
1 ATTATTTAATT-AAATAAT
754485 ATTATTT-A-TAAAT--T
1 ATTATTTAATTAAATAAT
754499 ATCTATTTAATTTAAATAAT
1 AT-TATTTAA-TTAAATAAT
754519 ATTAT
1 ATTAT
754524 AAGGAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.09
15 5 0.16
16 5 0.16
17 1 0.03
18 5 0.16
19 10 0.31
20 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTATTTAATTAAATAAT
Found at i:754689 original size:22 final size:23
Alignment explanation
Indices: 754656--754716 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
754646 TAAAAATTAA
754656 ATAAATAT--TTTTATAAT-ATT
1 ATAAATATAATTTTATAATGATT
754676 ATAAATATAATTTTTATAATGATT
1 ATAAATATAA-TTTTATAATGATT
*
754700 -T-CATATACATTTTATAA
1 ATAAATATA-ATTTTATAA
754717 AAATATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 8 0.23
22 13 0.37
23 11 0.31
24 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (23 bp):
ATAAATATAATTTTATAATGATT
Found at i:757699 original size:96 final size:95
Alignment explanation
Indices: 757526--757715 Score: 272
Period size: 96 Copynumber: 2.0 Consensus size: 95
757516 AATAGTAACC
* ** * * *
757526 AGTAAATTTTATGATCCATAAATCAGAAATGATCATATTTTCAATGAAAACATGTAACCATATAA
1 AGTAAATTTCATGATCCATAAATCAGAAACAATCATATTTTCAATGAAAACAGGTAACCAGAGAA
757591 CACATTTCAGGTAACCATAGTTCATAAATT
66 CACATTTCAGGTAACCATAGTTCATAAATT
* * * *
757621 AGTAGATTTCATGATTCATAAATCAGGAACAATCATATTTTACACTGAAAACAGGTAACCAGAGA
1 AGTAAATTTCATGATCCATAAATCAGAAACAATCATATTTT-CAATGAAAACAGGTAACCAGAGA
*
757686 ACATATTTCAGGTAACCATAGTTCATAAAT
65 ACACATTTCAGGTAACCATAGTTCATAAAT
757716 AGGCCTGTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 35 0.42
96 48 0.58
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (95 bp):
AGTAAATTTCATGATCCATAAATCAGAAACAATCATATTTTCAATGAAAACAGGTAACCAGAGAA
CACATTTCAGGTAACCATAGTTCATAAATT
Found at i:757914 original size:24 final size:24
Alignment explanation
Indices: 757887--757935 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
757877 CATTCGTGAA
757887 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
757911 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
757935 C
1 C
757936 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:757915 original size:14 final size:14
Alignment explanation
Indices: 757887--757928 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
757877 CATTCGTGAA
757887 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
757901 CG-T---TTATGTT
1 CGTTCGGTTATGTT
757911 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
757925 CGTT
1 CGTT
757929 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:757945 original size:24 final size:24
Alignment explanation
Indices: 757893--757948 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
757883 TGAACGTTCG
* *
757893 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
757917 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
757941 TTTATGTT
1 GTTATGTT
757949 TAACCCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:759051 original size:16 final size:16
Alignment explanation
Indices: 759008--759063 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
758998 GTCTCCAACA
* *
759008 TTTATGTTCGTCTTCA
1 TTTATGTTCGTGTTCG
759024 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCG
**
759040 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCG
759056 TTTATGTT
1 TTTATGTT
759064 TGTTTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.09, C:0.14, G:0.21, T:0.55
Consensus pattern (16 bp):
TTTATGTTCGTGTTCG
Done.