Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_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: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:4984 original size:25 final size:22
Alignment explanation
Indices: 4955--5000 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4945 TTTTTAACAC
4955 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
4980 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
5001 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:5584 original size:2 final size:2
Alignment explanation
Indices: 5577--5603 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5567 AAACTAAAGC
5577 TA 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 TA T
5604 GACCATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6595 original size:21 final size:21
Alignment explanation
Indices: 6569--6622 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6559 CATTTCCAAT
* *
6569 AAACTTGACATCTATAACAAC
1 AAACTTGAAATCTATAAAAAC
*
6590 AAACTTGAAATGTATAAAAAC
1 AAACTTGAAATCTATAAAAAC
6611 AAACTTGAAATC
1 AAACTTGAAATC
6623 CAATGAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACTTGAAATCTATAAAAAC
Found at i:17183 original size:164 final size:163
Alignment explanation
Indices: 16891--17189 Score: 370
Period size: 164 Copynumber: 1.8 Consensus size: 163
16881 ATAGCGGCGT
** *
16891 TTTTTTTACATAAACACAACTAAAGTAAGCGTTTGTAGCGGCGTTTGCACTAAAACGCCACTAAA
1 TTTTTTTACATAAACACAACTAAAGTAAGCGTAAGTAGAGGCGTTTGCAC-AAAACGCCACTAAA
** * * ** *
16956 TATCTGGCTATAGCGGTGTTTTTTCATAAACGCCACTAAAGTATAAGTTTTTAGCAGCATTTTCA
65 TATCTGGCTATAGCGGCATTTTTACATAAACGCCACTAAAGTAGAAGTTGGTAACAGCATTTTCA
17021 TAAAAGCACTTCTATATATCTGGCTATCACGGTG
130 TAAAAGCACTTCTATATATCTGGCTATCACGGTG
* * * * * *
17055 TTTTTTTACATAAATACAACTAAAGTACGCGTAAGTAGAGGCTTTTTCA-AAAATTGCCACTATA
1 TTTTTTTACATAAACACAACTAAAGTAAGCGTAAGTAGAGGCGTTTGCACAAAA-CGCCACTAAA
*
17119 TATCTGGCTATAGCGGCATTTGTTACATAAACGCCACTAAAGTACGCA-TTGGTAAC-GACATTT
65 TATCTGGCTATAGCGGCATTT-TTACATAAACGCCACTAAAGTA-GAAGTTGGTAACAG-CATTT
*
17182 TCCTAAAA
127 TCATAAAA
17190 ATGCCATTAT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
162 4 0.04
163 28 0.25
164 80 0.71
165 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (163 bp):
TTTTTTTACATAAACACAACTAAAGTAAGCGTAAGTAGAGGCGTTTGCACAAAACGCCACTAAAT
ATCTGGCTATAGCGGCATTTTTACATAAACGCCACTAAAGTAGAAGTTGGTAACAGCATTTTCAT
AAAAGCACTTCTATATATCTGGCTATCACGGTG
Found at i:21194 original size:2 final size:2
Alignment explanation
Indices: 21187--21214 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21177 AAGCTACATG
21187 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21215 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28855 original size:41 final size:41
Alignment explanation
Indices: 28793--28873 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
28783 TCTCAACAAA
*
28793 AAAGTATACAAGCCTTTAAAGAATATTCATTGAGAGGAGAC
1 AAAGTATACAAGCCTTTAAAGAATATGCATTGAGAGGAGAC
28834 AAAGTATACAAG-CTTTAAAAGAATATGCATTGAGAGGAGA
1 AAAGTATACAAGCCTTT-AAAGAATATGCATTGAGAGGAGA
28874 AATAGGTAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAGTATACAAGCCTTTAAAGAATATGCATTGAGAGGAGAC
Found at i:29405 original size:34 final size:34
Alignment explanation
Indices: 29362--29428 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
29352 AAAAAGTGAC
*
29362 AATAGGGTGTGGTTTCTGGAAGAGATTCGGAGGA
1 AATAGGGTGTAGTTTCTGGAAGAGATTCGGAGGA
29396 AATAGGGTGTAGTTTCTGGAAGAGATTCGGAGG
1 AATAGGGTGTAGTTTCTGGAAGAGATTCGGAGG
29429 TGATACAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.27, C:0.06, G:0.40, T:0.27
Consensus pattern (34 bp):
AATAGGGTGTAGTTTCTGGAAGAGATTCGGAGGA
Found at i:38742 original size:27 final size:26
Alignment explanation
Indices: 38700--38752 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
38690 TTCCAGAAGG
*
38700 TGCTGACTAGATCTTCTAGAAAACTGC
1 TGCTGACTAGACCTTCTAG-AAACTGC
*
38727 TGCTGACTGGACCTTCTAGAAACTGC
1 TGCTGACTAGACCTTCTAGAAACTGC
38753 CACGACAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (26 bp):
TGCTGACTAGACCTTCTAGAAACTGC
Found at i:47059 original size:90 final size:91
Alignment explanation
Indices: 46913--47080 Score: 284
Period size: 90 Copynumber: 1.8 Consensus size: 91
46903 TTTTTTAGCT
*
46913 AAGTTACCCTAATCATATTAGGGTTTTTTTATTATTTCAAATTAATTAAATATATATTTAATTAA
1 AAGTTACCCTAATCATATTAGGG-TATTTTATTATTTCAAATTAATTAAATATATATTTAATTAA
* *
46978 TTGGAATTTAATAATCCTTTTATATCC
65 TTGAAATTAAATAATCCTTTTATATCC
*
47005 AAGTTACCCTAATCATATTAGGG-ATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1 AAGTTACCCTAATCATATTAGGGTATTTTATTATTTCAAATTAATTAAATATATATTTAATTAAT
47069 TGAAATTAAATA
66 TGAAATTAAATA
47081 TTCGAGATTA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
90 49 0.68
92 23 0.32
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (91 bp):
AAGTTACCCTAATCATATTAGGGTATTTTATTATTTCAAATTAATTAAATATATATTTAATTAAT
TGAAATTAAATAATCCTTTTATATCC
Found at i:65148 original size:13 final size:13
Alignment explanation
Indices: 65130--65162 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
65120 CTCTCCTCCT
65130 ATTTTTCTCTATA
1 ATTTTTCTCTATA
65143 ATTTTTCTCTATA
1 ATTTTTCTCTATA
65156 ATTTTTC
1 ATTTTTC
65163 GTTTACTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTCTCTATA
Found at i:66817 original size:6 final size:6
Alignment explanation
Indices: 66806--66835 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
66796 AATTTACTAT
66806 AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
66836 TTAATCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:66979 original size:19 final size:19
Alignment explanation
Indices: 66947--66995 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
66937 AAGTCAATAT
* *
66947 TAAAAGTAAGTAGTTAAAA
1 TAAAATTAAATAGTTAAAA
66966 TAAAATTAAATAGTTAAAA
1 TAAAATTAAATAGTTAAAA
*
66985 TAAATTTAAAT
1 TAAAATTAAAT
66996 TGAATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
TAAAATTAAATAGTTAAAA
Found at i:68881 original size:24 final size:24
Alignment explanation
Indices: 68848--68894 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
68838 TAGCATGTTT
68848 AAAAATAAAACTT-AAAAGAAAAG
1 AAAAATAAAACTTGAAAAGAAAAG
*
68871 AAAAATGAAAACTTGAAAATAAAA
1 AAAAAT-AAAACTTGAAAAGAAAA
68895 TAAAGGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (24 bp):
AAAAATAAAACTTGAAAAGAAAAG
Found at i:72860 original size:294 final size:294
Alignment explanation
Indices: 72331--72916 Score: 1172
Period size: 294 Copynumber: 2.0 Consensus size: 294
72321 CAGCTGAGAC
72331 ATGTTCTCCTAGATTTACCTTCTCATTCCCGATAAGCTTCCTCTTTGTTGTACAAAGGTCCTTCA
1 ATGTTCTCCTAGATTTACCTTCTCATTCCCGATAAGCTTCCTCTTTGTTGTACAAAGGTCCTTCA
72396 AAAATCGGGCTTATCTTGAAACCTTTTGGATAACCTCAAGGAGAGGTATTTTGATTTCCACCTTC
66 AAAATCGGGCTTATCTTGAAACCTTTTGGATAACCTCAAGGAGAGGTATTTTGATTTCCACCTTC
72461 TGAAATACATCTAGTATTTCCTTTTCCTCAGCTTTTTATCCTTTTTTACTAACCTCAATGGAAAA
131 TGAAATACATCTAGTATTTCCTTTTCCTCAGCTTTTTATCCTTTTTTACTAACCTCAATGGAAAA
72526 AGGTGGTGGCACATAACAGGGAGATGGCGTTGGATTTGTTTGTACTTCGTCACCCTTCTTCTGGG
196 AGGTGGTGGCACATAACAGGGAGATGGCGTTGGATTTGTTTGTACTTCGTCACCCTTCTTCTGGG
72591 ATCCTAAGTCAATCGTCTTCTTCCCTTTTTTTGG
261 ATCCTAAGTCAATCGTCTTCTTCCCTTTTTTTGG
72625 ATGTTCTCCTAGATTTACCTTCTCATTCCCGATAAGCTTCCTCTTTGTTGTACAAAGGTCCTTCA
1 ATGTTCTCCTAGATTTACCTTCTCATTCCCGATAAGCTTCCTCTTTGTTGTACAAAGGTCCTTCA
72690 AAAATCGGGCTTATCTTGAAACCTTTTGGATAACCTCAAGGAGAGGTATTTTGATTTCCACCTTC
66 AAAATCGGGCTTATCTTGAAACCTTTTGGATAACCTCAAGGAGAGGTATTTTGATTTCCACCTTC
72755 TGAAATACATCTAGTATTTCCTTTTCCTCAGCTTTTTATCCTTTTTTACTAACCTCAATGGAAAA
131 TGAAATACATCTAGTATTTCCTTTTCCTCAGCTTTTTATCCTTTTTTACTAACCTCAATGGAAAA
72820 AGGTGGTGGCACATAACAGGGAGATGGCGTTGGATTTGTTTGTACTTCGTCACCCTTCTTCTGGG
196 AGGTGGTGGCACATAACAGGGAGATGGCGTTGGATTTGTTTGTACTTCGTCACCCTTCTTCTGGG
72885 ATCCTAAGTCAATCGTCTTCTTCCCTTTTTTT
261 ATCCTAAGTCAATCGTCTTCTTCCCTTTTTTT
72917 TGGAACAGGT
Statistics
Matches: 292, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
294 292 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.39
Consensus pattern (294 bp):
ATGTTCTCCTAGATTTACCTTCTCATTCCCGATAAGCTTCCTCTTTGTTGTACAAAGGTCCTTCA
AAAATCGGGCTTATCTTGAAACCTTTTGGATAACCTCAAGGAGAGGTATTTTGATTTCCACCTTC
TGAAATACATCTAGTATTTCCTTTTCCTCAGCTTTTTATCCTTTTTTACTAACCTCAATGGAAAA
AGGTGGTGGCACATAACAGGGAGATGGCGTTGGATTTGTTTGTACTTCGTCACCCTTCTTCTGGG
ATCCTAAGTCAATCGTCTTCTTCCCTTTTTTTGG
Found at i:75195 original size:25 final size:24
Alignment explanation
Indices: 75134--75185 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
75124 TAGCATGTTT
75134 AAAAAT-AAAACTTAAAAGAAAAG
1 AAAAATGAAAACTTAAAAGAAAAG
*
75157 AAAAATGAAAACTTGAAAAGAAAAT
1 AAAAATGAAAACTT-AAAAGAAAAG
75182 AAAA
1 AAAA
75186 GAGATAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.23
24 7 0.27
25 13 0.50
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.13
Consensus pattern (24 bp):
AAAAATGAAAACTTAAAAGAAAAG
Found at i:75449 original size:27 final size:25
Alignment explanation
Indices: 75393--75455 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
75383 TTTACCCGTC
75393 GACCTTCTAG--AATACGCTGACTA
1 GACCTTCTAGAAAATACGCTGACTA
* *
75416 GATCTTCTAGAAAACTACTGCTGACTG
1 GACCTTCTAGAAAA-TAC-GCTGACTA
75443 GACCTTCTAGAAA
1 GACCTTCTAGAAA
75456 CTGCCACGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 9 0.27
25 2 0.06
26 3 0.09
27 19 0.58
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (25 bp):
GACCTTCTAGAAAATACGCTGACTA
Found at i:78909 original size:60 final size:60
Alignment explanation
Indices: 78866--78979 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
78856 TTTGGATGAT
* * *
78866 TTGCTTTTGAAGACTACGTTGCTCTTTCGTGTTGAGTACATCTAGTAGTCTTTAGAGAAA
1 TTGCTTTTGAAGACAACATTGCTCATTCGTGTTGAGTACATCTAGTAGTCTTTAGAGAAA
* * * * * *
78926 TTGTTTTTGAATACAACATTGCTCATTCGTGTTGAGGAGACCTAGTTGTCTTTA
1 TTGCTTTTGAAGACAACATTGCTCATTCGTGTTGAGTACATCTAGTAGTCTTTA
78980 AATAACTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (60 bp):
TTGCTTTTGAAGACAACATTGCTCATTCGTGTTGAGTACATCTAGTAGTCTTTAGAGAAA
Found at i:79230 original size:13 final size:13
Alignment explanation
Indices: 79212--79236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79202 TTAATATAGC
79212 TTAAGAGAAATTT
1 TTAAGAGAAATTT
79225 TTAAGAGAAATT
1 TTAAGAGAAATT
79237 CTAAAGGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
TTAAGAGAAATTT
Found at i:80182 original size:5 final size:5
Alignment explanation
Indices: 80172--80209 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
80162 GTATCATTTC
80172 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
80210 TCCTTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:80216 original size:15 final size:15
Alignment explanation
Indices: 80172--80219 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
80162 GTATCATTTC
*
80172 TTTAATTTAATTTAA
1 TTTAATTTAACTTAA
*
80187 TTTAATTTAATTTAA
1 TTTAATTTAACTTAA
**
80202 TTTAATTTTCCTTAA
1 TTTAATTTAACTTAA
80217 TTT
1 TTT
80220 GACATAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATTTAACTTAA
Found at i:80703 original size:512 final size:498
Alignment explanation
Indices: 79721--81074 Score: 1448
Period size: 512 Copynumber: 2.7 Consensus size: 498
79711 AAAACAATAG
* *
79721 TTCATTGAATATCAAAAGAATCAATTGCTCTTTTAAATTTTCAAAGCTATAACTCTTTGACAAGT
1 TTCA-TGAATATCAAAAGAATCAACTGCTCTTTTAAATTTTCAAAGTTATAACTCTTTGACAAGT
* * * *
79786 GTCAGGATTGATGGGTTGATTTCAAGTTGGCTTCTTATTTTGTTCTGAAGTTTCAGTCATCAAGA
65 GTCA-GATTGATGGGTTGGTTT-TAGTT-GCTT-TTATTTT-TTCTAAAGTTT-AATCATCAAGA
* *
79851 TGTCATTCCTTT-CTCAGTCCTTCTGAACATTGTGACATGCCCCTCTTTCTC-GACTTGACATTC
124 TGTCATTCCTTTCCT-AGGCCTTCTAAACATTGTGACATGCCCCTCTTTCTCAG-CTTGACATTC
* * * **
79914 CAAATGGATACA-ACCAAAATGACACAACTAGCATAATTAATTGCTAGACCTTTTAGAACA-AAC
187 CAAATGGATACAGA-CAAAATGACTCAACTAGCATAATCAATTGTTAGACCTTTTAGAACACTTC
* * * * *
79977 TATTTTGATTCTCTGAAATCTTTCATTTGTTCAAGCTTTGTAGATTCCTTCAGTAGAGATAGTGC
251 TATTTCGATTCTCTGAAAT-ATTCATTTGTTCAAGCTTTGTAGATTCCTTTAGTAGAGGTAATGC
* * * *
80042 ATAAATATTGGTCTAAAGATAGAATTCCTAAGTGCTTATGTGAAGTTGACTATAACATGTGTTTC
315 AGAAATATCGGTCTAAAGATAGAATTCCTAAGTGCTTATGTGAAGTTAACTATAACAGGTGTTTC
* * * *
80107 TTAACTTCTTTAGTCCATTTTCACCAAAACGCTTTATTAATTCAAACCTCTAATTGTATCATTTC
380 TTAACTCCCTTAGTCCATCTTCACCAAAACGCCTTATTAATTCAAACCTCTAATTGTATCATTTC
* * *
80172 TTTAATTTAATTTAATTTAATTTAATTTAATTTAATTTTCCTTAATTTGACATAGTTGAAGGA
445 TTGAATTTAA-TT-A---AATTTAATTTAATTT--TTAT--TTAATTTGACATAGCTGAAGGA
* * *
80235 TTCATGAATATAAAAAGAATCAGCTGCTCGTTTAAATTTTCAAAGTTATAACTCTTTGACAAGTG
1 TTCATGAATATCAAAAGAATCAACTGCTCTTTTAAATTTTCAAAGTTATAACTCTTTGACAAGTG
* *
80300 TCATGATTGATAGGTTGGTTTTAGGTTGCTTTTTATTTTTTCTAAAGTTTAACTCATCGAGATGT
66 TCA-GATTGATGGGTTGGTTTTA-GTTGC-TTTTATTTTTTCTAAAGTTTAA-TCATCAAGATGT
* * *** *
80365 CATTCCTTTCCTAGGCCTTCTAAAAATTGTGACACGTTTCTCTTTATCAGCTTGACATTCCAAAT
127 CATTCCTTTCCTAGGCCTTCTAAACATTGTGACATGCCCCTCTTTCTCAGCTTGACATTCCAAAT
* * *
80430 GGATATAGACAAAATGACTCAACTAGCATAATCAATTGTTAGACCTCTTATAACACTTCTATTTC
192 GGATACAGACAAAATGACTCAACTAGCATAATCAATTGTTAGACCTTTTAGAACACTTCTATTTC
* * *
80495 AATACTCTGAAATATTCAATCTGTTCAAGCTTTGTAGATTCCTTTAGTAGAGGTAATGCAGAAAT
257 GATTCTCTGAAATATTC-ATTTGTTCAAGCTTTGTAGATTCCTTTAGTAGAGGTAATGCAGAAAT
* * * * *
80560 ATCGGTTTAAAGATAGAATTCTTGAGTGTTTGTGTGAAGTTAACTATAACAGGTGTTTCTCT-AC
321 ATCGGTCTAAAGATAGAATTCCTAAGTGCTTATGTGAAGTTAACTATAACAGGTGTTTCT-TAAC
** *
80624 TCCCTTAGTCCATCTTCACTGAAACTCCTTATTAATTCAAACCT-TAAACTT-TATCATTTCCTT
385 TCCCTTAGTCCATCTTCACCAAAACGCCTTATTAATTCAAACCTCT-AA-TTGTATCATTT-CTT
* * *
80687 GAATTT-ATTAAATTTAATTTCATTTTTATTTAATTTGGCGTAGCTGAAGGA
447 GAATTTAATTAAATTTAATTTAATTTTTATTTAATTTGACATAGCTGAAGGA
* * * * * *
80738 TTCATTAATATCAAAAGAATCAACTTCTCTTTTAATTTTTCAAACTTATAACTTTTTAACAAGTG
1 TTCATGAATATCAAAAGAATCAACTGCTCTTTTAAATTTTCAAAGTTATAACTCTTTGACAAGTG
* * * *
80803 TCGAGGTTGATGGGTTGGTTTCT-G--G----T-TTTTTCCTAAAGTTTCAATCATCAAGATTTA
66 TC-AGATTGATGGGTTGGTTT-TAGTTGCTTTTATTTTTTCTAAAGTTT-AATCATCAAGATGTC
* * * ** *
80860 ATTCTTTTCTCT--GCCTTTTTAAACATTATGATGTGCCCCTCTTTCTCAACTTGACATTCCAAA
128 ATTCCTTTC-CTAGGCC-TTCTAAACATTGTGACATGCCCCTCTTTCTCAGCTTGACATTCCAAA
** * *
80923 TACACACAGACAAAATGACTCAACTAGCATAATCAATTGTTAAACCTTTTAGAACACTTTCTATT
191 TGGATACAGACAAAATGACTCAACTAGCATAATCAATTGTTAGACCTTTTAGAACAC-TTCTATT
* * * ** * * * * *
80988 TCGGTTCTCTAAAATATTCCTTTTGTTCAATATATGTATATTCCTTTAGTAGAGGTAGTGAAAAA
255 TCGATTCTCTGAAATATT-CATTTGTTCAAGCTTTGTAGATTCCTTTAGTAGAGGTAATGCAGAA
* **
81053 ATAGCAATCTAAAGATAGAATT
319 ATATCGGTCTAAAGATAGAATT
81075 ATTAAGTTTT
Statistics
Matches: 712, Mismatches: 109, Indels: 57
0.81 0.12 0.06
Matches are distributed among these distances:
493 3 0.00
494 118 0.17
495 80 0.11
496 1 0.00
500 1 0.00
502 1 0.00
503 92 0.13
504 2 0.00
505 3 0.00
507 14 0.02
510 2 0.00
511 126 0.18
512 175 0.25
513 90 0.13
514 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (498 bp):
TTCATGAATATCAAAAGAATCAACTGCTCTTTTAAATTTTCAAAGTTATAACTCTTTGACAAGTG
TCAGATTGATGGGTTGGTTTTAGTTGCTTTTATTTTTTCTAAAGTTTAATCATCAAGATGTCATT
CCTTTCCTAGGCCTTCTAAACATTGTGACATGCCCCTCTTTCTCAGCTTGACATTCCAAATGGAT
ACAGACAAAATGACTCAACTAGCATAATCAATTGTTAGACCTTTTAGAACACTTCTATTTCGATT
CTCTGAAATATTCATTTGTTCAAGCTTTGTAGATTCCTTTAGTAGAGGTAATGCAGAAATATCGG
TCTAAAGATAGAATTCCTAAGTGCTTATGTGAAGTTAACTATAACAGGTGTTTCTTAACTCCCTT
AGTCCATCTTCACCAAAACGCCTTATTAATTCAAACCTCTAATTGTATCATTTCTTGAATTTAAT
TAAATTTAATTTAATTTTTATTTAATTTGACATAGCTGAAGGA
Found at i:83067 original size:10 final size:10
Alignment explanation
Indices: 83052--83093 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
83042 CTGGTTCACT
83052 GGTTCAACCG
1 GGTTCAACCG
83062 GGTTCAACCG
1 GGTTCAACCG
83072 GGTTCAACCG
1 GGTTCAACCG
*
83082 TGGTTGAACCG
1 -GGTTCAACCG
83093 G
1 G
83094 ATTTTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:88440 original size:21 final size:21
Alignment explanation
Indices: 88416--88455 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
88406 TATGAGAAAT
*
88416 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
88437 TGTTTCAAAATTGAAAAAT
1 TGTTTCAAAATTGAAAAAT
88456 AAAAATAAGC
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:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:92294 original size:23 final size:22
Alignment explanation
Indices: 92249--92330 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
92239 TAGTGCAGAA
*
92249 GGAATCGATACCCTCTTGAAGG
1 GGAATCGATACCCCCTTGAAGG
*
92271 GGAATCGATTCCCCCTTTGAAGG
1 GGAATCGATACCCCC-TTGAAGG
* * *
92294 GGAACCGATTCCCCC-TGTAGG
1 GGAATCGATACCCCCTTGAAGG
92315 GGAATCGATACCCCCT
1 GGAATCGATACCCCCT
92331 GAGGGTTCTG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.35
22 13 0.25
23 21 0.40
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (22 bp):
GGAATCGATACCCCCTTGAAGG
Found at i:92317 original size:21 final size:20
Alignment explanation
Indices: 92249--92335 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 20
92239 TAGTGCAGAA
* *
92249 GGAATCGATACCCTCTTGAAGG
1 GGAATCGATTCCC-CCTG-AGG
92271 GGAATCGATTCCCCCTTTGAAGG
1 GGAATCGATTCCCCC--TG-AGG
*
92294 GGAACCGATTCCCCCTGTAGG
1 GGAATCGATTCCCCCTG-AGG
*
92315 GGAATCGATACCCCCTGAGG
1 GGAATCGATTCCCCCTGAGG
92335 G
1 G
92336 TTCTGGTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.07
21 21 0.37
22 12 0.21
23 20 0.35
ACGTcount: A:0.23, C:0.28, G:0.29, T:0.21
Consensus pattern (20 bp):
GGAATCGATTCCCCCTGAGG
Found at i:94495 original size:2 final size:2
Alignment explanation
Indices: 94488--94523 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
94478 CAGCTTAAGC
94488 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
94524 ATCAATTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94992 original size:25 final size:26
Alignment explanation
Indices: 94964--95028 Score: 105
Period size: 27 Copynumber: 2.5 Consensus size: 26
94954 TCCAGAGGGA
94964 ACCGATTCCCCCCCCCCCAA-GGGGT
1 ACCGATTCCCCCCCCCCCAATGGGGT
94989 ACCGATTCCCCCCCCCCCCCAATGGGGT
1 ACCGATT--CCCCCCCCCCCAATGGGGT
95017 ACCGATTCCCCC
1 ACCGATTCCCCC
95029 TGAATGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.19
26 5 0.14
27 13 0.35
28 12 0.32
ACGTcount: A:0.15, C:0.54, G:0.17, T:0.14
Consensus pattern (26 bp):
ACCGATTCCCCCCCCCCCAATGGGGT
Found at i:95015 original size:28 final size:27
Alignment explanation
Indices: 94964--95028 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 27
94954 TCCAGAGGGA
94964 ACCGATT--CCCCCCCCCCCAAGGGGT
1 ACCGATTCCCCCCCCCCCCCAAGGGGT
94989 ACCGATTCCCCCCCCCCCCCAATGGGGT
1 ACCGATTCCCCCCCCCCCCCAA-GGGGT
95017 ACCGATTCCCCC
1 ACCGATTCCCCC
95029 TGAATGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
25 7 0.19
27 13 0.35
28 17 0.46
ACGTcount: A:0.15, C:0.54, G:0.17, T:0.14
Consensus pattern (27 bp):
ACCGATTCCCCCCCCCCCCCAAGGGGT
Found at i:98161 original size:15 final size:15
Alignment explanation
Indices: 98141--98175 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
98131 GATGTATGAT
*
98141 CTGAATAACATATAA
1 CTGAATAACACATAA
*
98156 CTGAATAACACATAT
1 CTGAATAACACATAA
98171 CTGAA
1 CTGAA
98176 CACGTGTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (15 bp):
CTGAATAACACATAA
Found at i:99507 original size:2 final size:2
Alignment explanation
Indices: 99502--99535 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
99492 TATCCAAATA
99502 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
99536 TCTTAATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100781 original size:2 final size:2
Alignment explanation
Indices: 100776--100812 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
100766 TTTTTTTATT
*
100776 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
100813 ATTTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:100852 original size:38 final size:38
Alignment explanation
Indices: 100809--101221 Score: 251
Period size: 38 Copynumber: 10.7 Consensus size: 38
100799 ATTTATATAG
100809 TATAATTTTTGAAAATATTTTTTGAAAA-AAATATAATA
1 TATAATTTTTGAAAATA-TTTTTGAAAATAAATATAATA
** * * *
100847 TATAATTTTTAGAAAACGGTATTCGAAAATATATAT-ATA
1 TATAATTTTT-GAAAA-TATTTTTGAAAATAAATATAATA
** ** * * *
100886 TCATATAGCTTTGAAAACGGTTTTCGAAAATATATATATTA
1 T-ATA-ATTTTTGAAAA-TATTTTTGAAAATAAATATAATA
* *
100927 TAT-AGTTTTGAAAATA-TTTTAAAAATATATATATAATA
1 TATAATTTTTGAAAATATTTTTGAAAATA-A-ATATAATA
* * * *
100965 TATAGTTTTGGAAAATATTTTTGAAAATATATATAACA
1 TATAATTTTTGAAAATATTTTTGAAAATAAATATAATA
* * *
101003 TATAA-TTTTGAAAACATTTTTAAAAAATATATATAATA
1 TATAATTTTTGAAAATATTTTT-GAAAATAAATATAATA
* * *
101041 TAT-AGTTTTGAAAACATTTTTGAAAACATATATATAATA
1 TATAATTTTTGAAAATATTTTTG-AAA-ATAAATATAATA
*
101080 TAATATATAGTTTTGAAAATA-TTTTGAAAACATATATATAATA
1 T-ATA-AT--TTTTGAAAATATTTTTG-AAA-ATAAATATAATA
* * *
101123 TAT-AGTTTT---AACA-TTTTGAAAATATATAT-ATA
1 TATAATTTTTGAAAATATTTTTGAAAATAAATATAATA
* *
101155 TAATATATGGTTTTTAAAATA-TTTTGAAAATATATATAATA
1 T-ATA-AT--TTTTGAAAATATTTTTGAAAATAAATATAATA
* *
101196 TATAGTTTTGGAAAATATTTTTGAAA
1 TATAATTTTTGAAAATATTTTTGAAA
101222 GTTTTTGAAA
Statistics
Matches: 309, Mismatches: 37, Indels: 58
0.76 0.09 0.14
Matches are distributed among these distances:
32 4 0.01
33 10 0.03
34 3 0.01
35 9 0.03
36 9 0.03
37 28 0.09
38 89 0.29
39 41 0.13
40 69 0.22
41 11 0.04
42 3 0.01
43 23 0.07
44 10 0.03
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (38 bp):
TATAATTTTTGAAAATATTTTTGAAAATAAATATAATA
Found at i:100952 original size:36 final size:37
Alignment explanation
Indices: 100872--101300 Score: 319
Period size: 38 Copynumber: 11.0 Consensus size: 37
100862 ACGGTATTCG
* * * **
100872 AAAATATATATATATCATATAGCTTTGAAAACGGTTTT
1 AAAAAATATATATATTATATAGTTTTGAAAA-TATTTT
**
100910 CGAAAATATATATATTATATAGTTTTGAAAATATTTT
1 AAAAAATATATATATTATATAGTTTTGAAAATATTTT
*
100947 AAAAATATATATATAATATATAGTTTTGGAAAATATTTT
1 AAAAA-ATATATATATTATATAGTTTT-GAAAATATTTT
** ** * *
100986 TGAAAATATATATAACATATAATTTTGAAAACATTTTT
1 AAAAAATATATATATTATATAGTTTTGAAAATA-TTTT
* *
101024 AAAAAATATATATAATATATAGTTTTGAAAACATTTTT
1 AAAAAATATATATATTATATAGTTTTGAAAATA-TTTT
101062 GAAAACATATATATAATATAATATATAGTTTTGAAAATATTTT
1 -AAAA-A-ATATAT-ATAT--TATATAGTTTTGAAAATATTTT
* * * *
101105 GAAAACATATATATAATATATAGTTTT-AACAT-TTTG
1 -AAAAAATATATATATTATATAGTTTTGAAAATATTTT
* * *
101141 AAAATATATATATATAATATATGGTTTTTAAAATATTTT
1 AAAA-A-ATATATATATTATATAGTTTTGAAAATATTTT
* *
101180 -GAAAATATATATAATATATAGTTTTGGAAAATATTTTT
1 AAAAAATATATATATTATATAGTTTT-GAAAATA-TTTT
*
101218 GAAAGTTTTTGAAAATATATATATTATATGGTTTTGAAAATAATTTT
1 --AA-------AAAATATATATATTATATAGTTTTGAAAAT-ATTTT
* * *
101265 TAAAAACATATA-A-TATATAGTTTTAAAAATGATTTT
1 AAAAAATATATATATTATATAGTTTTGAAAAT-ATTTT
101301 TTATATATTA
Statistics
Matches: 325, Mismatches: 40, Indels: 54
0.78 0.10 0.13
Matches are distributed among these distances:
35 4 0.01
36 43 0.13
37 45 0.14
38 133 0.41
39 21 0.06
40 4 0.01
41 12 0.04
42 3 0.01
43 9 0.03
44 17 0.05
45 1 0.00
47 10 0.03
48 23 0.07
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
AAAAAATATATATATTATATAGTTTTGAAAATATTTT
Found at i:101212 original size:26 final size:24
Alignment explanation
Indices: 101176--101259 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
101166 TTTTAAAATA
101176 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAATATATAT-ATATATAG
*
101201 TTTTGGAAAATAT-T-T-T-TGAAAG
1 TTTT-GAAAATATATATATAT-ATAG
*
101223 TTTTTGAAAATATATATATTATATGG
1 -TTTTGAAAATATATATA-TATATAG
101249 TTTTGAAAATA
1 TTTTGAAAATA
101260 ATTTTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
21 1 0.02
22 12 0.25
23 5 0.10
24 2 0.04
25 16 0.33
26 11 0.23
27 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (24 bp):
TTTTGAAAATATATATATATATAG
Found at i:101237 original size:75 final size:77
Alignment explanation
Indices: 100875--101221 Score: 383
Period size: 76 Copynumber: 4.5 Consensus size: 77
100865 GTATTCGAAA
* * * *
100875 ATATATATATATCATATAGCTTTGAAAACGGTTTTCGAAAATATATAT--ATTATATAGTTTTGA
1 ATATATATA-AT-ATATAGTTTTGAAAAC-ATTTTTGAAAATATATATAAAATATATAGTTTTGA
*
100938 AAATATTTTAAAAAT
63 AAATATTTTAAAAAC
* *
100953 ATATATATAATATATAGTTTTGGAAAATATTTTTGAAAATATATATAACATATA-A-TTTTGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTGAAAATATATATAAAATATATAGTTTTGAAA
*
101016 ACATTTTTAAAAA-
65 ATA-TTTTAAAAAC
101029 ATATATATAATATATAGTTTTGAAAACATTTTTGAAAACATATATATAATATAATATATAGTTTT
1 ATATATATAATATATAGTTTTGAAAACATTTTTG-AAA-ATATATAT-A-A-AATATATAGTTTT
*
101094 GAAAATATTTTGAAAAC
61 GAAAATATTTTAAAAAC
* *
101111 ATATATATAATATATAGTTTT---AACA-TTTTGAAAATATATATATATAATATATGGTTTTTAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATA-A-AATATATAGTTTTGAA
*
101172 AATATTTT-GAAA-
64 AATATTTTAAAAAC
*
101184 ATATATATAATATATAGTTTTGGAAAATATTTTTGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTGAAA
101222 GTTTTTGAAA
Statistics
Matches: 237, Mismatches: 15, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
73 21 0.09
74 3 0.01
75 38 0.16
76 67 0.28
77 31 0.13
78 27 0.11
79 5 0.02
80 5 0.02
81 9 0.04
82 31 0.13
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (77 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAAAATATATAGTTTTGAAAA
TATTTTAAAAAC
Found at i:101249 original size:84 final size:84
Alignment explanation
Indices: 101148--101301 Score: 231
Period size: 84 Copynumber: 1.8 Consensus size: 84
101138 TTGAAAATAT
* * *
101148 ATATATATAATATATGGTTTTTAAAAT-ATTTTGAAAATATATATAATATATAGTTTTGGAAAAT
1 ATATATATAATATATGGTTTTGAAAATAATTTTGAAAA-ACATATAATATATAGTTTT-AAAAAT
101212 -ATTTTTGAAAGTTTTTGAAA
64 GATTTTTGAAAGTTTTTGAAA
* *
101232 ATATATATATTATATGGTTTTGAAAATAATTTTTAAAAACATATAATATATAGTTTTAAAAATGA
1 ATATATATAATATATGGTTTTGAAAATAATTTTGAAAAACATATAATATATAGTTTTAAAAATGA
101297 TTTTT
66 TTTTT
101302 TATATATTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
83 5 0.08
84 49 0.78
85 9 0.14
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.47
Consensus pattern (84 bp):
ATATATATAATATATGGTTTTGAAAATAATTTTGAAAAACATATAATATATAGTTTTAAAAATGA
TTTTTGAAAGTTTTTGAAA
Found at i:101363 original size:22 final size:22
Alignment explanation
Indices: 101319--101363 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
101309 TATATTAATA
**
101319 TTATTATTTATTTTTTTTGTTT
1 TTATTATTTATTTTCCTTGTTT
101341 TTATTATTTATTATTCCTT-TTT
1 TTATTATTTATT-TTCCTTGTTT
101363 T
1 T
101364 ATTTACGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTATTTATTTTCCTTGTTT
Found at i:102689 original size:33 final size:32
Alignment explanation
Indices: 102622--102690 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
102612 TCTTTTTTTT
* *
102622 ATTTAAAATCTTTTTTATTTTTTTATTTTCCA
1 ATTTAAAATCTTTTTTATTTTTTTAATATCCA
* *
102654 ATTTAACATTTTTTTTATTTTTTTTCAATAT-CA
1 ATTTAAAATCTTTTTTA-TTTTTTT-AATATCCA
102687 ATTT
1 ATTT
102691 CAATCGATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 15 0.48
33 13 0.42
34 3 0.10
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (32 bp):
ATTTAAAATCTTTTTTATTTTTTTAATATCCA
Found at i:104400 original size:20 final size:20
Alignment explanation
Indices: 104375--104412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
104365 CTCCAACACT
* *
104375 AAATTAGGACCAAATAGTTG
1 AAATTAGAAACAAATAGTTG
104395 AAATTAGAAACAAATAGT
1 AAATTAGAAACAAATAGT
104413 CAAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.24
Consensus pattern (20 bp):
AAATTAGAAACAAATAGTTG
Found at i:104418 original size:20 final size:20
Alignment explanation
Indices: 104375--104420 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
104365 CTCCAACACT
* * **
104375 AAATTAGGACCAAATAGTTG
1 AAATTAGAAACAAATAGTCA
104395 AAATTAGAAACAAATAGTCA
1 AAATTAGAAACAAATAGTCA
104415 AAATTA
1 AAATTA
104421 AAAGTAAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (20 bp):
AAATTAGAAACAAATAGTCA
Found at i:104453 original size:20 final size:20
Alignment explanation
Indices: 104406--104461 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
104396 AATTAGAAAC
*
104406 AAATAG-TCAAAATTAAAAGT
1 AAATAGTTC-AAATAAAAAGT
**
104426 AAGCAGTTCAAATAAAAAGT
1 AAATAGTTCAAATAAAAAGT
*
104446 AAATAGTTGAAATAAA
1 AAATAGTTCAAATAAA
104462 TTTAAATTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.23
Consensus pattern (20 bp):
AAATAGTTCAAATAAAAAGT
Found at i:106647 original size:22 final size:22
Alignment explanation
Indices: 106621--106681 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
106611 GGCATGTGAA
106621 ATTTGTCCCGAAAGACCTATGT
1 ATTTGTCCCGAAAGACCTATGT
*
106643 ATTTGTCCCGAATA-ACCTCTGT
1 ATTTGTCCCGAA-AGACCTATGT
* *
106665 ATATGTCCCGAATGACC
1 ATTTGTCCCGAAAGACC
106682 GCGTAGACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAAAGACCTATGT
Found at i:114780 original size:32 final size:32
Alignment explanation
Indices: 114744--114812 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
114734 TCATTTAAAT
**
114744 CCTTATACACTTTTATTGATAACCAAAT-AAGC
1 CCTTATACACTTCAATTGATAACCAAATGAA-C
114776 CCTTATACACTTCAATTGATAACCAAATGAAC
1 CCTTATACACTTCAATTGATAACCAAATGAAC
114808 CCTTA
1 CCTTA
114813 ATCTATTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (32 bp):
CCTTATACACTTCAATTGATAACCAAATGAAC
Found at i:117329 original size:57 final size:59
Alignment explanation
Indices: 117257--117372 Score: 157
Period size: 57 Copynumber: 2.0 Consensus size: 59
117247 ACTAATATTT
**
117257 TAATGAATTTGGGGATGAA-ATAAGGTGATTCAAAAGTTTGAGGATTAATTTAGAATGAG
1 TAATGAATTTGGGGATGAATATAAAATG-TTCAAAAGTTTGAGGATTAATTTAGAATGAG
* * *
117316 TAAT-AATTT-GGGATGAATCTAAAATGTTCAAAAGTTTTAGGATTAATTTGGAATGAG
1 TAATGAATTTGGGGATGAATATAAAATGTTCAAAAGTTTGAGGATTAATTTAGAATGAG
117373 AGTCGGTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 37 0.73
58 10 0.20
59 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (59 bp):
TAATGAATTTGGGGATGAATATAAAATGTTCAAAAGTTTGAGGATTAATTTAGAATGAG
Found at i:122626 original size:30 final size:30
Alignment explanation
Indices: 122592--122670 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
122582 ATTTTTCATT
* *
122592 TAAGTACCTAAAGTATTTTTTTGGTTAAAA
1 TAAGTATCTAAAGTATTTTTTTGGTCAAAA
*
122622 TAAGTATCTAAAGTTATATTTTTGGTCAAAA
1 TAAGTATCTAAAG-TATTTTTTTGGTCAAAA
*
122653 TAGGTATC-AAAGTATTTT
1 TAAGTATCTAAAGTATTTT
122671 ATGTTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.12
30 16 0.37
31 22 0.51
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (30 bp):
TAAGTATCTAAAGTATTTTTTTGGTCAAAA
Found at i:122679 original size:27 final size:29
Alignment explanation
Indices: 122599--122684 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 29
122589 ATTTAAGTAC
*
122599 CTAAAGTATTTTTTTGGTTAAAATAAGTAT
1 CTAAAGTA-TTTTTTGGTTAAAATAGGTAT
*
122629 CTAAAGTTATATTTTTGGTCAAAATAGGTAT
1 CTAAAG-TAT-TTTTTGGTTAAAATAGGTAT
*
122660 C-AAAGTATTTTAT-GTTAAAATAGGT
1 CTAAAGTATTTTTTGGTTAAAATAGGT
122685 GCTTAAACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.22
28 4 0.08
29 3 0.06
30 11 0.22
31 21 0.42
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (29 bp):
CTAAAGTATTTTTTGGTTAAAATAGGTAT
Found at i:123457 original size:27 final size:29
Alignment explanation
Indices: 123404--123474 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 29
123394 TTTGTTATTT
* *
123404 TTTTACTTTCTTTTGTTATTTTCTTTT-TC
1 TTTT-CTTTCTTTTGTTATATTATTTTCTC
123433 TTTTCTTT-TTTTGTTATATTATTTTCTC
1 TTTTCTTTCTTTTGTTATATTATTTTCTC
*
123461 TTATTCTATCTTTT
1 TT-TTCTTTCTTTT
123475 ATGATTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.42
28 8 0.22
29 9 0.25
30 4 0.11
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.75
Consensus pattern (29 bp):
TTTTCTTTCTTTTGTTATATTATTTTCTC
Found at i:123548 original size:15 final size:17
Alignment explanation
Indices: 123528--123559 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
123518 TATAATATAA
123528 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
123543 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
123560 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:124359 original size:182 final size:182
Alignment explanation
Indices: 124052--124395 Score: 616
Period size: 182 Copynumber: 1.9 Consensus size: 182
124042 TTGTAGAGTA
124052 GAGATGAAGACTGGAGATGACCTTAGCCAACAATGGAGCGTTAATTTAATCATCCATATAAGGCG
1 GAGATGAAGACTGGAGATGACCTTAGCCAACAATGGAGCGTTAATTTAATCATCCATATAAGGCG
124117 GGATGTCAATGCCACGATTGATAACCTTGCTCATATGGGAACTAATGGCCCCCTGTATCTCGTGA
66 GGATGTCAATGCCACGATTGATAACCTTGCTCATATGGGAACTAATGGCCCCCTGTATCTCGTGA
124182 TATATCAACATCCACCGAGAGAAATCCATCTCCAGCTACTTCCTTAAAGCTG
131 TATATCAACATCCACCGAGAGAAATCCATCTCCAGCTACTTCCTTAAAGCTG
* * * * *
124234 GAGATGAGGGCTGGAGATGGCCTTAGCCAGCAATGGAGCGTTAATTTCATCATCCATATAAGGCG
1 GAGATGAAGACTGGAGATGACCTTAGCCAACAATGGAGCGTTAATTTAATCATCCATATAAGGCG
* * *
124299 GGATGTCAATGCCTCGATTGATAGCCTTGCTCATCTGGGAACTAATGGCCCCCTGTATCTCGTGA
66 GGATGTCAATGCCACGATTGATAACCTTGCTCATATGGGAACTAATGGCCCCCTGTATCTCGTGA
124364 TATATCAACATCCACCGAGAGAAATCCATCTC
131 TATATCAACATCCACCGAGAGAAATCCATCTC
124396 TCTCTACAAG
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 154 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (182 bp):
GAGATGAAGACTGGAGATGACCTTAGCCAACAATGGAGCGTTAATTTAATCATCCATATAAGGCG
GGATGTCAATGCCACGATTGATAACCTTGCTCATATGGGAACTAATGGCCCCCTGTATCTCGTGA
TATATCAACATCCACCGAGAGAAATCCATCTCCAGCTACTTCCTTAAAGCTG
Found at i:137732 original size:25 final size:26
Alignment explanation
Indices: 137685--137733 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
137675 AGCTTTCTCT
* *
137685 TTTTACTTTTTAAGTTTTCATTTTTC
1 TTTTACTTTTCAAGCTTTCATTTTTC
*
137711 TTTTA-TTTTCAAGCTTTGATTTT
1 TTTTACTTTTCAAGCTTTCATTTT
137734 AATATGCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTACTTTTCAAGCTTTCATTTTTC
Found at i:157171 original size:30 final size:30
Alignment explanation
Indices: 157135--157197 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
157125 TCATATCGCG
* *
157135 TAGACATATTATTTCCATACCTTTACCACA
1 TAGACATATCATTTACATACCTTTACCACA
*
157165 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTACCACA
157195 TAG
1 TAG
157198 CTCATATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTACCACA
Found at i:163668 original size:13 final size:13
Alignment explanation
Indices: 163650--163710 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
163640 AACCCGACCC
163650 GACCCGACCCGTT
1 GACCCGACCCGTT
*
163663 GACCCGACCAGTT
1 GACCCGACCCGTT
163676 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
163694 GACCCGACCCGTT
1 GACCCGACCCGTT
163707 GACC
1 GACC
163711 GTTGACCCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:163668 original size:18 final size:18
Alignment explanation
Indices: 163645--163704 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
163635 GTCATAACCC
163645 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
163663 GACCCGA-CC-A---GTT
1 GACCCGACCCGACCCGTT
163676 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
163694 GACCCGACCCG
1 GACCCGACCCG
163705 TTGACCGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 21 0.57
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:163681 original size:31 final size:31
Alignment explanation
Indices: 163645--163710 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
163635 GTCATAACCC
163645 GACCCGACCCGACCCGTTGACCCGACCAGTT
1 GACCCGACCCGACCCGTTGACCCGACCAGTT
*
163676 GACCCGACCCGACCCGTTGACCCGACCCGTT
1 GACCCGACCCGACCCGTTGACCCGACCAGTT
163707 GACC
1 GACC
163711 GTTGACCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCCGACCAGTT
Found at i:165035 original size:18 final size:18
Alignment explanation
Indices: 165009--165044 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
164999 TCGAAAGGAC
*
165009 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
165027 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
165045 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:167555 original size:23 final size:23
Alignment explanation
Indices: 167492--167574 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
167482 TATAAAGTTA
167492 CACCGAAGTGCCACGTAGAATTTG
1 CACCGAAGTGCCACGTAGAA-TTG
* *
167516 TC-CCGAAG-GACCGCGTAGAAATG
1 -CACCGAAGTG-CCACGTAGAATTG
167539 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
167562 CACCGTAGTGCCA
1 CACCGAAGTGCCA
167575 TATAATATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 32 0.64
24 16 0.32
25 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:168814 original size:9 final size:9
Alignment explanation
Indices: 168790--168818 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
168780 GGTTTCACGT
168790 TGAAGAAGA
1 TGAAGAAGA
168799 T-AAGAAGA
1 TGAAGAAGA
168807 TGAAGAAGA
1 TGAAGAAGA
168816 TGA
1 TGA
168819 GTATCTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (9 bp):
TGAAGAAGA
Found at i:188668 original size:2 final size:2
Alignment explanation
Indices: 188661--188826 Score: 114
Period size: 2 Copynumber: 83.5 Consensus size: 2
188651 ATCAATTTTA
* ** *
188661 AT AT AT AT AT AT AT AT AT AT AT GT -T AT GC AT ACT TT AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T
* *
188703 AT ACT -T AT AA AT AT AT A- AT AT AT ACT AT AC AT -T AT ACT -T
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
*
188742 GT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
188784 AT AT AT AT AT GT AT GT AT ACT -T AT AT CT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
188826 A
1 A
188827 CACACGCATA
Statistics
Matches: 129, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
1 8 0.06
2 113 0.88
3 8 0.06
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:188895 original size:20 final size:18
Alignment explanation
Indices: 188870--188916 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
188860 ATGTATATAA
188870 ATATATATAAGTATAAAGT
1 ATATATATAAGTATAAA-T
*
188889 ATAATATATAAGTATATAT
1 AT-ATATATAAGTATAAAT
188908 ATATATATA
1 ATATATATA
188917 CCAATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 5 0.19
20 14 0.54
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
ATATATATAAGTATAAAT
Found at i:189275 original size:45 final size:45
Alignment explanation
Indices: 189203--189288 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
189193 ATTTGTCAAT
*
189203 AAATAAAATTTCCCTCTTCCCTTTTCTAAATTC-CAAAAAAAAAA
1 AAATAAAATTTCCCTCTTCCCTCTTCTAAATTCTCAAAAAAAAAA
* *
189247 AAATCAAATTTTCCCTCTTCTCTCTTCTAAATTCTCAAAAAA
1 AAAT-AAAATTTCCCTCTTCCCTCTTCTAAATTCTCAAAAAA
189289 TCAATTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 4 0.11
45 26 0.70
46 7 0.19
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (45 bp):
AAATAAAATTTCCCTCTTCCCTCTTCTAAATTCTCAAAAAAAAAA
Found at i:189869 original size:19 final size:19
Alignment explanation
Indices: 189845--189882 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
189835 TTTCTTTGTT
189845 TTTTAAATATAA-TTTTAAA
1 TTTTAAATA-AACTTTTAAA
*
189864 TTTTAATTAAACTTTTAAA
1 TTTTAAATAAACTTTTAAA
189883 ATTACGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAATAAACTTTTAAA
Found at i:192679 original size:20 final size:20
Alignment explanation
Indices: 192654--192696 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
192644 CAAAATCATT
*
192654 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
192674 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
192694 TTT
1 TTT
192697 CGAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:193745 original size:14 final size:14
Alignment explanation
Indices: 193723--193775 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
193713 TCAATTATAT
*
193723 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
193737 GTTCATTTA---T-
1 GTTCATTTATGTTC
*
193747 GTTCATTTATGTCC
1 GTTCATTTATGTTC
*
193761 ATTCATTTATGTTC
1 GTTCATTTATGTTC
193775 G
1 G
193776 AACAAAGGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
10 9 0.30
11 1 0.03
14 20 0.67
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:193755 original size:24 final size:24
Alignment explanation
Indices: 193710--193774 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
193700 ATTTCGTGAA
* *
193710 CATTCAATTATATGTTCGTTTATGTT
1 CATTC-ATT-TATGTTCATTTATGTC
*
193736 CGTTCATTTATGTTCATTTATGTC
1 CATTCATTTATGTTCATTTATGTC
193760 CATTCATTTATGTTC
1 CATTCATTTATGTTC
193775 GAACAAAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 28 0.80
25 3 0.09
26 4 0.11
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (24 bp):
CATTCATTTATGTTCATTTATGTC
Found at i:194112 original size:19 final size:20
Alignment explanation
Indices: 194088--194126 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
194078 TTATTATGTC
*
194088 CGTTCG-TTGTGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
194107 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
194127 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.54
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:194127 original size:10 final size:10
Alignment explanation
Indices: 194097--194127 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
194087 CCGTTCGTTG
194097 TGTTCGTTTA
1 TGTTCGTTTA
*
194107 CGTTCGTTTA
1 TGTTCGTTTA
194117 TGTTCGTTTA
1 TGTTCGTTTA
194127 T
1 T
194128 CATTTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:200474 original size:3 final size:3
Alignment explanation
Indices: 200466--200496 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
200456 AATTAATTTG
200466 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
200497 GCAAATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:200486 original size:14 final size:14
Alignment explanation
Indices: 200467--200495 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
200457 ATTAATTTGA
200467 ATAATAATAATAAT
1 ATAATAATAATAAT
200481 ATAATAATAATAAT
1 ATAATAATAATAAT
200495 A
1 A
200496 AGCAAATGAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:202568 original size:21 final size:21
Alignment explanation
Indices: 202544--202591 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
202534 AATATAATTT
202544 AATAATTAATATTTTTATTAA
1 AATAATTAATATTTTTATTAA
202565 AATAATTAATATTTTTATTAA
1 AATAATTAATATTTTTATTAA
202586 AATAAT
1 AATAAT
202592 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTAATATTTTTATTAA
Found at i:202570 original size:17 final size:20
Alignment explanation
Indices: 202544--202607 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
202534 AATATAATTT
202544 AATAATTAATATTTTTATTAA
1 AATAATTAATATTTTTATT-A
202565 AATAATTAATATTTTTATT-
1 AATAATTAATATTTTTATTA
202584 AA-AA-TAATATTTTAATATTA
1 AATAATTAATATTTT--TATTA
202604 AATA
1 AATA
202608 TATAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.23
18 2 0.05
19 6 0.15
20 2 0.05
21 20 0.51
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTAATATTTTTATTA
Found at i:204049 original size:3 final size:3
Alignment explanation
Indices: 203985--204036 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
203975 TTCATTTAAA
203985 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
204032 TAT TA
1 TAT TA
204037 ATAAATATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:207914 original size:20 final size:21
Alignment explanation
Indices: 207881--207920 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
207871 TTTTAACGTA
207881 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
207901 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
207921 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:207928 original size:22 final size:20
Alignment explanation
Indices: 207880--207924 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
207870 ATTTTAACGT
207880 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
207900 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
207921 AATT
1 AATT
207925 TGATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:211308 original size:21 final size:21
Alignment explanation
Indices: 211282--211321 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
211272 CCCCCTTTGA
*
211282 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
211303 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
211322 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:214219 original size:23 final size:23
Alignment explanation
Indices: 214193--214242 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
214183 TTTAAAATTA
214193 AATTTTATAAAAAATTATTAT-TT
1 AATTTTAT-AAAAATTATTATATT
**
214216 AATTTTATTTAAATTATTATATT
1 AATTTTATAAAAATTATTATATT
214239 AATT
1 AATT
214243 AATATCGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATTTTATAAAAATTATTATATT
Found at i:214324 original size:23 final size:26
Alignment explanation
Indices: 214292--214341 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
214282 CCTTTTCTGA
*
214292 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
214315 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
214341 T
1 T
214342 TTCTCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:225546 original size:13 final size:12
Alignment explanation
Indices: 225532--225604 Score: 80
Period size: 12 Copynumber: 6.2 Consensus size: 12
225522 ATGCTTGAAG
225532 AAAAAAAAAG--
1 AAAAAAAAAGAA
*
225542 AAGAAAAAAGAA
1 AAAAAAAAAGAA
225554 AAAAAAGAAAG-A
1 AAAAAA-AAAGAA
*
225566 AAAAAAAGAGAA
1 AAAAAAAAAGAA
*
225578 AAGAAAAAAGAA
1 AAAAAAAAAGAA
*
225590 AAAGAAAAAGAA
1 AAAAAAAAAGAA
225602 AAA
1 AAA
225605 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
10 9 0.17
11 3 0.06
12 36 0.69
13 4 0.08
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:225554 original size:20 final size:19
Alignment explanation
Indices: 225529--225604 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
225519 ATTATGCTTG
225529 AAGAAAAAAAAAGAAGAAAA
1 AAGAAAAAAAAA-AAGAAAA
225549 AAGAAAAAAAAGAAAG--AA
1 AAGAAAAAAAA-AAAGAAAA
* *
225567 AA-AAAAGAGAAAAGAAAA
1 AAGAAAAAAAAAAAGAAAA
*
225585 AAGAAAAAGAAAAAGAAAA
1 AAGAAAAAAAAAAAGAAAA
225604 A
1 A
225605 GGGGGTCAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.09
17 6 0.13
18 8 0.17
19 14 0.30
20 14 0.30
21 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAAAAGAAAA
Found at i:225563 original size:29 final size:26
Alignment explanation
Indices: 225532--225604 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 26
225522 ATGCTTGAAG
*
225532 AAAAAA-AAAGAAGAAAAAAGAAAAA
1 AAAAAAGAAAAAAGAAAAAAGAAAAA
*
225557 AAAGAAAGAAAAAAAAGAGAAAAGAAAAA
1 AAA-AAAG--AAAAAAGAAAAAAGAAAAA
225586 AGAAAAAG-AAAAAGAAAAA
1 A-AAAAAGAAAAAAGAAAAA
225605 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
25 3 0.08
26 13 0.32
29 22 0.55
30 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAAGAAAAAAGAAAAA
Found at i:226761 original size:93 final size:93
Alignment explanation
Indices: 226602--226801 Score: 373
Period size: 93 Copynumber: 2.2 Consensus size: 93
226592 AACAAGTGCC
*
226602 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCAC
1 ATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCAC
226667 AGAACCAATCATTGAATTTGAAAGATGA
66 AGAACCAATCATTGAATTTGAAAGATGA
*
226695 ATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCAC
1 ATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCAC
226760 AGAACCAATCATTGAATTTGAAAGATGA
66 AGAACCAATCATTGAATTTGAAAGATGA
*
226788 ATGTGATCATAGTA
1 ATGTGCTCATAGTA
226802 GAAATAAGAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 104 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (93 bp):
ATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCAC
AGAACCAATCATTGAATTTGAAAGATGA
Found at i:227059 original size:115 final size:115
Alignment explanation
Indices: 226703--227017 Score: 580
Period size: 115 Copynumber: 2.7 Consensus size: 115
226693 GAATGTGCTC
*
226703 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
226768 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
66 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
226818 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
226883 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
66 TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
*
226933 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GGAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
*
226997 TCATTGGAA-TTAAAAGATGAA
66 TCATT-GAATTTGAAAGATGAA
227018 CTGCATGATC
Statistics
Matches: 196, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
114 31 0.16
115 165 0.84
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (115 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
TCATTGAATTTGAAAGATGAATGTGATCATAGTAGAAATAAGAAGACCCA
Found at i:227406 original size:21 final size:21
Alignment explanation
Indices: 227381--227431 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
227371 AAAGATCACT
227381 TCATAATCAGATGAGTTGTTA
1 TCATAATCAGATGAGTTGTTA
227402 TCATAATCAGATGAGTTGTTA
1 TCATAATCAGATGAGTTGTTA
*
227423 TCAAAATCA
1 TCATAATCA
227432 ACATGTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (21 bp):
TCATAATCAGATGAGTTGTTA
Found at i:227947 original size:73 final size:73
Alignment explanation
Indices: 227819--227984 Score: 206
Period size: 73 Copynumber: 2.3 Consensus size: 73
227809 AGGAAGAAGA
* * * ** ** *
227819 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTAACATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGACCAACATTA
227884 CCAGGTAG
66 CCAGGTAG
* * *
227892 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGACCAGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGACCAACATTA
* *
227957 CCAGTTCG
66 CCAGGTAG
*
227965 AGTTCATAATAAGAAGAACT
1 AGTTCATAATGAGAAGAACT
227985 CATCTGAAGA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (73 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGACCAACATTA
CCAGGTAG
Found at i:228062 original size:186 final size:186
Alignment explanation
Indices: 227748--228097 Score: 619
Period size: 186 Copynumber: 1.9 Consensus size: 186
227738 GATTCAAATC
** * * * *
227748 CATCATTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGACCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
*
227813 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATTA
227878 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
131 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
*
227934 CATCATTCAATGGACCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAGGGA
1 CATCATTCAATGGACCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
*
227999 ATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATTA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATTA
228064 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
131 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
228098 CATCATCTGA
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
186 155 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (186 bp):
CATCATTCAATGGACCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATTA
ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:228151 original size:116 final size:113
Alignment explanation
Indices: 227892--228483 Score: 581
Period size: 113 Copynumber: 5.2 Consensus size: 113
227882 TGCCAGGTAG
* * ** * * *
227892 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCAATGGACCAGCATT
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAGCATT
* * * *
227956 ACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAGGGAATAAGA
65 ACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * * * * *
228005 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATTATTTGATGGATTAACATTG
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTA
*
228070 CCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGA
66 CCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGA
* * *
228121 AATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTT
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTA
*
228186 CCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* ** *
228234 AGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCAGTTTTT
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTA
**
228299 TTAG--AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-AA-A
66 CCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* ** * * * ** * *
228342 AGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCAT-AATTCTATCACAGAAGCAGATAGATTA
1 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCCATCAC-----TTGATGGATCA
* * *
228406 GCATCAACC-TTTCCAGAGATAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
60 GCAT-TACCAGTT----AG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
228466 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
228484 CTCATCTGAA
Statistics
Matches: 403, Mismatches: 53, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
108 40 0.10
109 3 0.01
110 1 0.00
111 2 0.00
112 31 0.08
113 170 0.42
114 3 0.01
115 1 0.00
116 99 0.25
119 2 0.00
120 31 0.08
122 1 0.00
123 2 0.00
124 17 0.04
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTA
CCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
Found at i:228481 original size:40 final size:40
Alignment explanation
Indices: 228426--228522 Score: 185
Period size: 40 Copynumber: 2.4 Consensus size: 40
228416 TTCCAGAGAT
228426 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
228466 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
*
228506 AGTTCATAATAAGAAGA
1 AGTTCATAATGAGAAGA
228523 GCTTATTCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.19
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
Found at i:228821 original size:3 final size:3
Alignment explanation
Indices: 228763--228808 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
228753 TTCATTTAAA
228763 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
228807 TA
1 TA
228809 ATAAATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:228895 original size:19 final size:20
Alignment explanation
Indices: 228873--228913 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
228863 CAACTGGCCC
* *
228873 ATCAGGAAGCCC-AAACCCA
1 ATCAGGAAACCCTAAAACCA
228892 ATCAGGAAACCCTAAAACCA
1 ATCAGGAAACCCTAAAACCA
228912 AT
1 AT
228914 TTAGGATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.46, C:0.32, G:0.12, T:0.10
Consensus pattern (20 bp):
ATCAGGAAACCCTAAAACCA
Found at i:230531 original size:23 final size:26
Alignment explanation
Indices: 230499--230548 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
230489 CCTTTTCTGA
*
230499 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
230522 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
230548 T
1 T
230549 TTTCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:233229 original size:19 final size:19
Alignment explanation
Indices: 233185--233230 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
233175 TTTTTTTTTA
233185 TTATA-TATATATAATTAT
1 TTATATTATATATAATTAT
* *
233203 ATAAATTATA-ATGAATTAT
1 TTATATTATATAT-AATTAT
233222 TTATATTAT
1 TTATATTAT
233231 GGATTATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATATTATATATAATTAT
Found at i:233382 original size:15 final size:15
Alignment explanation
Indices: 233372--233428 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
233362 AACCGAGTAT
233372 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
** *
233387 CGGGTACCCGCAAAATT
1 CGGGTACCCG-ATTA-C
233404 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
233419 CGGGTACCCG
1 CGGGTACCCG
233429 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:233440 original size:17 final size:16
Alignment explanation
Indices: 233372--233440 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
233362 AACCGAGTAT
**
233372 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
233387 CGGGTACCCGCAAAATT
1 CGGGTACCCG-AAAATC
**
233404 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
233419 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
233436 CGGGT
1 CGGGT
233441 CGGGACACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:233440 original size:32 final size:32
Alignment explanation
Indices: 233372--233440 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
233362 AACCGAGTAT
*
233372 CGGGTACCCGATTACCGGGTACCCGCAAAATT
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
233404 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
233436 CGGGT
1 CGGGT
233441 CGGGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:243389 original size:2 final size:2
Alignment explanation
Indices: 243349--243381 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
243339 TTTAATCAAG
243349 TA TA TA TA 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 TA TA TA TA T
243382 TGATATATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:244094 original size:16 final size:16
Alignment explanation
Indices: 244075--244105 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
244065 TTTAAATTTC
*
244075 TTTTGGTTTAGGTTAA
1 TTTTGGTTCAGGTTAA
244091 TTTTGGTTCAGGTTA
1 TTTTGGTTCAGGTTA
244106 GTTTCGATTC
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:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (16 bp):
TTTTGGTTCAGGTTAA
Found at i:250377 original size:3 final size:3
Alignment explanation
Indices: 250369--250393 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
250359 TATTTTGTGA
250369 GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG G
250394 GTGATAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:251955 original size:41 final size:41
Alignment explanation
Indices: 251907--252144 Score: 123
Period size: 41 Copynumber: 5.7 Consensus size: 41
251897 TAACTTTAGC
* *
251907 GGCGTTTTTATACAAATGCCGCAATAGGATTCAT-CTATAGT
1 GGCGTTTTTATACAAACGCCGCAATA-GAGTCATACTATAGT
* * *
251948 GGCGTTTTTCA-ACAAACGCCGCAACAGAGTAATACTTTAGCT
1 GGCGTTTTT-ATACAAACGCCGCAATAGAGTCATACTATAG-T
* * *
251990 -GCGTTTTTATACAAACAAACGCCACAATAGAGT-AGTACTTTAGC
1 GGCGTTTTTAT----ACAAACGCCGCAATAGAGTCA-TACTATAGT
* *
252034 GGCGTTTTTATACAAATC-CAGCAATAGGATTCAT-CTATAGT
1 GGCGTTTTTATACAAA-CGCCGCAATA-GAGTCATACTATAGT
* * * * * * *
252075 GGAGTTTTTCCAAAACATATGTCGCAATAGAGT-AGTACTTTAGA
1 GGCGTTTTT---ATACAAACGCCGCAATAGAGTCA-TACTATAGT
* *
252119 GGCGCTTTTA-ACAAACGCCGTAATAG
1 GGCGTTTTTATACAAACGCCGCAATAG
252145 GGTTCATCTA
Statistics
Matches: 150, Mismatches: 28, Indels: 39
0.69 0.13 0.18
Matches are distributed among these distances:
40 18 0.12
41 60 0.40
42 8 0.05
43 5 0.03
44 24 0.16
45 35 0.23
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCAATAGAGTCATACTATAGT
Found at i:252022 original size:45 final size:45
Alignment explanation
Indices: 251958--252049 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
251948 GGCGTTTTTC
* *
251958 AACAAACGCCGCAACAGAGTAATACTTTAGCTGCGTTTTTATACA
1 AACAAACGCCACAACAGAGTAATACTTTAGCGGCGTTTTTATACA
* *
252003 AACAAACGCCACAATAGAGTAGTACTTTAGCGGCGTTTTTATACA
1 AACAAACGCCACAACAGAGTAATACTTTAGCGGCGTTTTTATACA
252048 AA
1 AA
252050 TCCAGCAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (45 bp):
AACAAACGCCACAACAGAGTAATACTTTAGCGGCGTTTTTATACA
Found at i:252113 original size:85 final size:80
Alignment explanation
Indices: 252014--252223 Score: 217
Period size: 85 Copynumber: 2.6 Consensus size: 80
252004 ACAAACGCCA
* *
252014 CAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAATC-CAGCAATAGGATTCATCTATAGTGGA
1 CAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAA-CGCAGCAATAGGATTCATCTACAGTGCA
*
252078 GTTTTTCCAAAACATATGTCG
65 -TTTTT-CAAAA-A-A-GCCG
* * * * *
252099 CAATAGAGTAGTACTTTAGAGGCGCTTTTA-ACAAACGCCGTAATAGGGTTCATCTACAGTGCAT
1 CAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCAGCAATAGGATTCATCTACAGTGCAT
252163 TTTTCAAAAAAGCCG
66 TTTTCAAAAAAGCCG
** * * * * *
252178 CAACGGAGTATTACTTTAGCGTCGTTTTTTTACAAACACCGCAATA
1 CAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCAGCAATA
252224 ATTTGGTATG
Statistics
Matches: 106, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
79 26 0.25
80 14 0.13
81 1 0.01
82 5 0.05
83 6 0.06
84 26 0.25
85 28 0.26
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (80 bp):
CAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCAGCAATAGGATTCATCTACAGTGCAT
TTTTCAAAAAAGCCG
Found at i:254932 original size:21 final size:21
Alignment explanation
Indices: 254908--254970 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
254898 CATATAAAAT
* * *
254908 TGTCCCTAAGGACCTCATATA
1 TGTCCCAAAAGACCACATATA
* *
254929 TGTCCCGAATGACCACATATA
1 TGTCCCAAAAGACCACATATA
254950 TGTCCCAAAAGACCACATATA
1 TGTCCCAAAAGACCACATATA
254971 ATTCTCTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.24
Consensus pattern (21 bp):
TGTCCCAAAAGACCACATATA
Found at i:255006 original size:21 final size:21
Alignment explanation
Indices: 254939--255013 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
254929 TGTCCCGAAT
* * * *
254939 GACCACATATATGTCCCAAAA
1 GACCACATATATATTCTAAAG
*
254960 GACCACATATA-ATTCTCTTGAAG
1 GACCACATATATA-T-TC-TAAAG
254983 GACCACATATATATTCTAAAG
1 GACCACATATATATTCTAAAG
*
255004 GACCAAATAT
1 GACCACATAT
255014 GTGTCAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 25 0.58
22 3 0.07
23 14 0.33
24 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (21 bp):
GACCACATATATATTCTAAAG
Found at i:263891 original size:20 final size:20
Alignment explanation
Indices: 263866--263935 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 20
263856 TATTATTTCA
263866 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTATATTT
263886 AATTAATTGAAAT-TAAATATTT
1 AATTAATT-AAATCT--ATATTT
*
263908 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAATC-TATATTT
263930 AATTAA
1 AATTAA
263936 CTCTATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
20 12 0.29
21 5 0.12
22 17 0.41
23 3 0.07
24 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTAATTAAATCTATATTT
Found at i:265637 original size:18 final size:21
Alignment explanation
Indices: 265601--265648 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
265591 TTTTCATAAT
265601 TATAATTATAATTATTATTAA
1 TATAATTATAATTATTATTAA
265622 TATAA-TATAA-TA-TATTAA
1 TATAATTATAATTATTATTAA
*
265640 TATTATTAT
1 TATAATTAT
265649 TATTTATTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 10 0.40
19 5 0.20
20 5 0.20
21 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATAATTATAATTATTATTAA
Found at i:267089 original size:3 final size:3
Alignment explanation
Indices: 267081--267141 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
267071 TTTCATTTTG
*
267081 ATT ATT ATT ATT -TT ATT ATT ATAT ATGT -TT A-A ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT ATT
267124 CATT ATT ATT ATT ATT AT
1 -ATT ATT ATT ATT ATT AT
267142 CTTAAGTCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:267093 original size:15 final size:14
Alignment explanation
Indices: 267075--267141 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 14
267065 AATTTCTTTC
267075 ATTTTGATTATTATT
1 ATTTT-ATTATTATT
267090 ATTTTATTATTATAT
1 ATTTTATTATTAT-T
*
267105 ATGTTTA-AATTATT
1 AT-TTTATTATTATT
267119 ATTTTCATTATTATT
1 ATTTT-ATTATTATT
267134 ATTATTAT
1 ATT-TTAT
267142 CTTAAGTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 3 0.07
14 12 0.27
15 24 0.53
16 6 0.13
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:267244 original size:13 final size:14
Alignment explanation
Indices: 267215--267256 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
267205 TAAAATTCTA
267215 TTTATAAATTTAAT
1 TTTATAAATTTAAT
*
267229 TTTATAAA-TTACT
1 TTTATAAATTTAAT
*
267242 TTTATCATATTTAAT
1 TTTAT-AAATTTAAT
267257 ATATCTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:267485 original size:21 final size:20
Alignment explanation
Indices: 267461--267508 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
267451 TTCTAAATAA
267461 ATAAATATCTTAT-TTAAAAAT
1 ATAAATAT-TT-TCTTAAAAAT
*
267482 ATAATATATTTTCTTAAAATT
1 ATAA-ATATTTTCTTAAAAAT
267503 ATAAAT
1 ATAAAT
267509 TTAAGATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATATTTTCTTAAAAAT
Found at i:272026 original size:32 final size:32
Alignment explanation
Indices: 271990--272051 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
271980 GTCAGACACA
*
271990 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
272022 AGAAGTATCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
272052 TCATTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:275512 original size:54 final size:55
Alignment explanation
Indices: 275415--275520 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 55
275405 TGATTGAGAA
* * * *
275415 ATTTGAGCAGAAGCCACAGGAAATGACGAATGTATTGTTAAATG-TTTACAAAAT
1 ATTTGAGCAGAAACCACAAGAAATGACGAACGTATTGTCAAATGTTTTACAAAAT
* * * *
275469 ATTTGTGCAGAAATCACAAGAAATGATGAACGTGTTGTCAAATGTTTTACAA
1 ATTTGAGCAGAAACCACAAGAAATGACGAACGTATTGTCAAATGTTTTACAA
275521 TAAGAAACTA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
54 36 0.84
55 7 0.16
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (55 bp):
ATTTGAGCAGAAACCACAAGAAATGACGAACGTATTGTCAAATGTTTTACAAAAT
Found at i:276428 original size:45 final size:47
Alignment explanation
Indices: 276350--276440 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 47
276340 CTATTTCCCA
* * * *
276350 CATCTGTAAGCACTTCAGTGCATGATGCTTTC-AAAA-CCTTCGGGT
1 CATCCGTAAGCACTGCAATGCAGGATGCTTTCAAAAAGCCTTCGGGT
* *
276395 CATCCGTAAGCCCTGCAATGCAGGATGTTTTCAAAAAGCCTTCGGG
1 CATCCGTAAGCACTGCAATGCAGGATGCTTTCAAAAAGCCTTCGGG
276441 AGATTTTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 26 0.68
46 4 0.11
47 8 0.21
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (47 bp):
CATCCGTAAGCACTGCAATGCAGGATGCTTTCAAAAAGCCTTCGGGT
Found at i:276504 original size:76 final size:76
Alignment explanation
Indices: 276378--276590 Score: 306
Period size: 76 Copynumber: 2.8 Consensus size: 76
276368 TGCATGATGC
*
276378 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAATGCAGGATGTTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAATGCAGAATGTTTTCAAAAAGCCTTCGGGAG
276443 ATTTTTGATAT
66 ATTTTTGATAT
* * *
276454 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGTAGAATGTTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAATGCAGAATGTTTTCAAAAAGCCTTCGGGAG
*
276519 CTTTTTGATAT
66 ATTTTTGATAT
* * * * *
276530 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG-ATGCTTTC-AAAA-CCTTCGGG
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAATGCA-GAATGTTTTCAAAAAGCCTTCGGG
276591 TCATCCGTAA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
74 8 0.06
75 4 0.03
76 112 0.90
77 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (76 bp):
TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAATGCAGAATGTTTTCAAAAAGCCTTCGGGAG
ATTTTTGATAT
Found at i:276591 original size:121 final size:121
Alignment explanation
Indices: 276454--276753 Score: 397
Period size: 121 Copynumber: 2.4 Consensus size: 121
276444 TTTTTGATAT
*
276454 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGTAGAATGTTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAG-ATGTTTTCAAAAAGCCTTCGGGAG
* *
276519 CTTTTTGATATTTTC-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
65 CTTTTTGATATTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
* * * *
276575 TTTCAAAACCTTCGGGTCATCCGTAAGCCTTGCAATGCAGGATGTTTTTAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCA-GATGTTTTCAAAAAGCCTTCGGGAG
* * * *
276640 CTTTTTGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTTCATGATGT
65 CTTTTTGATATTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
* * *
276697 TTTCAAAAAAGCCTTTGGGTCATCTGTAAGTCCT-TCAGTGCATGATGTTTTCAAAAA
1 TTTC--AAAA-CCTTCGGGTCATCCGTAAGCCCTGT-AGTGCA-GATGTTTTCAAAAA
276754 AAAGCCTTCG
Statistics
Matches: 154, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
121 71 0.46
122 42 0.27
124 4 0.03
125 37 0.24
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (121 bp):
TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAGATGTTTTCAAAAAGCCTTCGGGAGC
TTTTTGATATTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
Found at i:276766 original size:98 final size:96
Alignment explanation
Indices: 276655--276945 Score: 476
Period size: 98 Copynumber: 3.0 Consensus size: 96
276645 TGATGTTATC
* * *
276655 AAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTTCATGATGTTTTCAAAAAAGCCTTTGGGTCAT
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAA-CCTTCGGGTCAT
*
276720 CTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
65 CTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
*
276752 AAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAAAAACCTTCGGGTCA
1 AAAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAAACCTTCGGGTCA
*
276817 TCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAA
64 TCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAA
*
276851 AAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGTCATC
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATC
276915 TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
66 TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
276946 CATTTCCATC
Statistics
Matches: 182, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
95 3 0.02
96 45 0.25
97 5 0.03
98 115 0.63
99 14 0.08
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (96 bp):
AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATC
TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
Found at i:276776 original size:50 final size:48
Alignment explanation
Indices: 276655--276945 Score: 460
Period size: 50 Copynumber: 6.0 Consensus size: 48
276645 TGATGTTATC
* *
276655 AAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTTCATGATGTTTTCAA
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
* * *
276703 AAAAGCCTTTGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AA
*
276752 AAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAA
1 AAAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
276801 AAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAA
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AA
*
276851 AAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCATGATGTTTTC--
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
276897 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
276945 A
1 A
276946 CATTTCCATC
Statistics
Matches: 225, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
46 45 0.20
48 83 0.37
49 13 0.06
50 84 0.37
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (48 bp):
AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
Found at i:278603 original size:3 final size:3
Alignment explanation
Indices: 278595--278655 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
278585 TTTCATTTTG
*
278595 ATT ATT ATT ATT -TT ATT ATT ATAT ATGT -TT A-A ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT ATT
278638 CATT ATT ATT ATT ATT AT
1 -ATT ATT ATT ATT ATT AT
278656 CTTAAGTCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:278607 original size:15 final size:14
Alignment explanation
Indices: 278589--278655 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 14
278579 AATTTCTTTC
278589 ATTTTGATTATTATT
1 ATTTT-ATTATTATT
278604 ATTTTATTATTATAT
1 ATTTTATTATTAT-T
*
278619 ATGTTTA-AATTATT
1 AT-TTTATTATTATT
278633 ATTTTCATTATTATT
1 ATTTT-ATTATTATT
278648 ATTATTAT
1 ATT-TTAT
278656 CTTAAGTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 3 0.07
14 12 0.27
15 24 0.53
16 6 0.13
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:278758 original size:13 final size:14
Alignment explanation
Indices: 278729--278770 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
278719 TAAAATTCTA
278729 TTTATAAATTTAAT
1 TTTATAAATTTAAT
*
278743 TTTATAAA-TTACT
1 TTTATAAATTTAAT
*
278756 TTTATCATATTTAAT
1 TTTAT-AAATTTAAT
278771 ATATCTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:279010 original size:22 final size:20
Alignment explanation
Indices: 278978--279025 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
278968 TTCTAAATAA
*
278978 ATAAATATTTTATTTAAAAAT
1 ATAAATATTTT-CTTAAAAAT
*
278999 ATAATATATTTTCTTAAAATT
1 ATAA-ATATTTTCTTAAAAAT
279020 ATAAAT
1 ATAAAT
279026 TTAAAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAATATTTTCTTAAAAAT
Found at i:280752 original size:42 final size:42
Alignment explanation
Indices: 280704--280820 Score: 144
Period size: 43 Copynumber: 2.8 Consensus size: 42
280694 TTTATGATGA
* *
280704 AAAACGCCGCTATAGATCTAACCTTTTGCGGTGTTTATTTCG
1 AAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTATTCCG
* * * *
280746 CAAACGCTGCTATAGATCTCAACATTTTGTGGCGTTTATTCCG
1 AAAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTTATTCCG
* * *
280789 AAAATGTCGCTATAGATCTGACCTTTTGCGGC
1 AAAACGCCGCTATAGATCTAACCTTTTGCGGC
280821 ATTTGTATAA
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 27 0.44
43 34 0.56
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
AAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTATTCCG
Found at i:280879 original size:44 final size:43
Alignment explanation
Indices: 280770--280921 Score: 130
Period size: 45 Copynumber: 3.5 Consensus size: 43
280760 GATCTCAACA
* * * * *
280770 TTTTGTGGCGTTTATTCC-GAAAATGTCGCTATAGATCTGACC
1 TTTTGCGGCGTTTGTTCCAAAAAATGACGCTATATATCTGACC
* **
280812 TTTTGCGGCATTTGTATAAAAAAAATGACGCTATATATCTAGACC
1 TTTTGCGGCGTTTGT-TCCAAAAAATGACGCTATATATCT-GACC
* * *
280857 TTTTGCGACGTTTGTTCCAAAAACACCGATG-TATATAT-TGACC
1 TTTTGCGGCGTTTGTTCCAAAAA-A-TGACGCTATATATCTGACC
* *
280900 TTTTACGGTGTTTGTTCCAAAA
1 TTTTGCGGCGTTTGTTCCAAAA
280922 CGCCGCTGTA
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 12 0.14
43 24 0.27
44 24 0.27
45 25 0.28
46 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (43 bp):
TTTTGCGGCGTTTGTTCCAAAAAATGACGCTATATATCTGACC
Done.