Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 134 of 182
Found at i:41272628 original size:40 final size:40
Alignment explanation
Indices: 41272425--41272628 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
41272415 CGGAATTTAA
** *
41272425 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41272465 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41272505 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
41272544 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41272584 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41272624 CCGGA
1 CCGGA
41272629 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41275533 original size:6 final size:6
Alignment explanation
Indices: 41275522--41275582 Score: 113
Period size: 6 Copynumber: 10.2 Consensus size: 6
41275512 GCATCGATGT
*
41275522 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGAA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA
41275570 AAAGGA AAAGGA A
1 AAAGGA AAAGGA A
41275583 TAGTTTTGAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:41286281 original size:5 final size:5
Alignment explanation
Indices: 41286271--41286298 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41286261 AAGCATTTTG
41286271 ATTTA ATTTA ATTTA ATTTA ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATT
41286299 GACTAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTTA
Found at i:41290917 original size:50 final size:50
Alignment explanation
Indices: 41290792--41290977 Score: 187
Period size: 50 Copynumber: 3.7 Consensus size: 50
41290782 AAATATAACA
* * * * * *
41290792 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTT-TCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAGG
* * *
41290841 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGG
* ** ** * *
41290891 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGG
**
41290941 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
41290978 CCCCTCATAA
Statistics
Matches: 111, Mismatches: 24, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
48 3 0.03
49 36 0.32
50 72 0.65
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGG
Found at i:41294317 original size:18 final size:18
Alignment explanation
Indices: 41294303--41294340 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41294293 GACAAGGGCA
*
41294303 AAGG-AAAGGCTAAGGCT
1 AAGGCAAAGGCAAAGGCT
*
41294320 AAGGCAAAGGCAAAGCCT
1 AAGGCAAAGGCAAAGGCT
41294338 AAG
1 AAG
41294341 TACAATGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.45, C:0.16, G:0.32, T:0.08
Consensus pattern (18 bp):
AAGGCAAAGGCAAAGGCT
Found at i:41313236 original size:8 final size:8
Alignment explanation
Indices: 41313223--41313250 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41313213 TAGTTCAATA
41313223 AAAAAAAG
1 AAAAAAAG
41313231 AAAAAAAG
1 AAAAAAAG
41313239 AAAAAAAG
1 AAAAAAAG
41313247 AAAA
1 AAAA
41313251 GATGATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:41313894 original size:25 final size:25
Alignment explanation
Indices: 41313858--41313918 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
41313848 CTCCTAAATT
* *
41313858 TTAATTTAATTATCTAATTTTTTA-A
1 TTAATTAAATTAT-TAATATTTTATA
*
41313883 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTATA
41313908 TTAATTAAATT
1 TTAATTAAATT
41313919 TTTTAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTATA
Found at i:41315957 original size:22 final size:22
Alignment explanation
Indices: 41315931--41315975 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41315921 ATTATATGTA
41315931 TTAATTCATAAT-ATAATTAATT
1 TTAATTCAT-ATCATAATTAATT
* *
41315953 TTAATTTATATCATATTTAATT
1 TTAATTCATATCATAATTAATT
41315975 T
1 T
41315976 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATCATAATTAATT
Found at i:41316040 original size:14 final size:14
Alignment explanation
Indices: 41316021--41316047 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41316011 GTGGTTCAGT
41316021 TGAACTGAACCGAG
1 TGAACTGAACCGAG
41316035 TGAACTGAACCGA
1 TGAACTGAACCGA
41316048 CCAAGAAATG
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:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:41316799 original size:24 final size:24
Alignment explanation
Indices: 41316767--41316816 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
41316757 ATCATGACTA
41316767 AGTTATTCTTGCATTATAAGTTTT
1 AGTTATTCTTGCATTATAAGTTTT
41316791 AGTTATTCTTGCATTATAAGTTTT
1 AGTTATTCTTGCATTATAAGTTTT
41316815 AG
1 AG
41316817 GTAATTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (24 bp):
AGTTATTCTTGCATTATAAGTTTT
Found at i:41318591 original size:138 final size:137
Alignment explanation
Indices: 41318343--41318763 Score: 630
Period size: 138 Copynumber: 3.1 Consensus size: 137
41318333 AGAGAACATA
* * * * * *
41318343 AATATAATTAATATATGCATTTTATTCATACAAAATATTTATTGTATATGTTTAACCAAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CAGATTTAT
*
41318408 TAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
65 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
* *
41318473 TTAGAAGG
130 TTGGAAAG
* **
41318481 AATATAACTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGATCTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAT-TTAT
**
41318546 TAATATAAACAGTTGCATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
65 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
41318611 TTGGAAAG
130 TTGGAAAG
* *
41318619 AATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAG-ATTTAT
* * *
41318684 TAATATATACAGTTATATTAATTAATTTCAGTCAAAATAT--AAGACATGAAAATTAATATTCTT
65 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
41318747 TTGGAAAG
130 TTGGAAAG
41318755 AATATAATT
1 AATATAATT
41318764 CCTTTTTTCT
Statistics
Matches: 258, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
136 39 0.15
137 2 0.01
138 215 0.83
139 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (137 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGATTTATT
AATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TGGAAAG
Found at i:41318881 original size:75 final size:75
Alignment explanation
Indices: 41318738--41318962 Score: 362
Period size: 75 Copynumber: 3.0 Consensus size: 75
41318728 CATGAAAATT
*
41318738 AATATTCTTTTGGAAAGAATATAATTCCTTTTTTCTAACTTTCCATTTGTCTT-TTCTATTAATT
1 AATATTCTTTTGGAAAGAATATAATTCC-TTTTTCTAACTTTCCATTTGTCTTCTT-TATTAATA
41318802 AGGGAATAATCC
64 AGGGAATAATCC
41318814 AATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGTCTTCTTTATTAATAAG
1 AATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGTCTTCTTTATTAATAAG
*
41318879 GGAATAATAC
66 GGAATAATCC
* * * * *
41318889 AATAATCTTTTGGAAAGAATATAATTTCTTTTTCTAACTTTCCATTTGCCTTCTCTGTTAATAAG
1 AATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGTCTTCTTTATTAATAAG
41318954 GGAATAATC
66 GGAATAATC
41318963 TTGGTTTTTA
Statistics
Matches: 140, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
75 110 0.79
76 30 0.21
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (75 bp):
AATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGTCTTCTTTATTAATAAG
GGAATAATCC
Found at i:41320069 original size:41 final size:41
Alignment explanation
Indices: 41320019--41320146 Score: 247
Period size: 41 Copynumber: 3.1 Consensus size: 41
41320009 ATTCATGTAC
41320019 ATATATACATAGTATACCAATTTCAATCACATTTCATATCAA
1 ATAT-TACATAGTATACCAATTTCAATCACATTTCATATCAA
41320061 ATATTACATAGTATACCAATTTCAATCACATTTCATATCAA
1 ATATTACATAGTATACCAATTTCAATCACATTTCATATCAA
41320102 ATATTACATAGTATACCAATTTCAATCACATTTCATATCAA
1 ATATTACATAGTATACCAATTTCAATCACATTTCATATCAA
41320143 ATAT
1 ATAT
41320147 CATTTAGCTA
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 82 0.95
42 4 0.05
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (41 bp):
ATATTACATAGTATACCAATTTCAATCACATTTCATATCAA
Found at i:41320451 original size:13 final size:13
Alignment explanation
Indices: 41320433--41320498 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
41320423 AGTTTGGCAA
41320433 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
41320446 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
** *
41320459 TGCCGTGGAAAAG
1 TGCTTTTGAAAAG
*
41320472 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
41320485 TGATTTTGAAAAG
1 TGCTTTTGAAAAG
41320498 T
1 T
41320499 TTGGTTTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:41333493 original size:28 final size:28
Alignment explanation
Indices: 41333453--41333552 Score: 139
Period size: 28 Copynumber: 3.5 Consensus size: 28
41333443 NNNNNNNNNN
41333453 TCGCACACTTAGTGCTACATAATCAAAC
1 TCGCACACTTAGTGCTACATAATCAAAC
*
41333481 TCGCACACTTAGTGCTACATAATCAAGC
1 TCGCACACTTAGTGCTACATAATCAAAC
* *
41333509 TCGCACACTTAGTGCTGAACA-ATTTAAAC
1 TCGCACACTTAGTGCT--ACATAATCAAAC
*
41333538 CCGCACACTTAGTGC
1 TCGCACACTTAGTGC
41333553 CAATCTCATG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
28 43 0.66
29 19 0.29
30 3 0.05
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (28 bp):
TCGCACACTTAGTGCTACATAATCAAAC
Found at i:41340144 original size:48 final size:48
Alignment explanation
Indices: 41340073--41340166 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
41340063 ATGCGTACTG
*
41340073 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCA
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCACCA
*
41340121 ATATTCTGTTAAGATACAAGGGTGGCACGGACTATGTGTAGGCCAC
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCAC
41340167 TGAGAGTCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
ATATTCTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCACCA
Found at i:41340177 original size:48 final size:48
Alignment explanation
Indices: 41340077--41340213 Score: 166
Period size: 48 Copynumber: 2.9 Consensus size: 48
41340067 GTACTGATAT
* * * *
41340077 TCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCAATAT
1 TCTGTTAAGATACAAGGGTGGCACGGACTATGTGTAGGCCACCAAGAG
**
41340125 TCTGTTAAGATACAAGGGTGGCACGGACTATGTGTAGGCCACTGAGAG
1 TCTGTTAAGATACAAGGGTGGCACGGACTATGTGTAGGCCACCAAGAG
** * * * *
41340173 TCTGTTATTACACAAAGGTGGTACGGACTATGTATAGGCCA
1 TCTGTTAAGATACAAGGGTGGCACGGACTATGTGTAGGCCA
41340214 TCGAGAAATC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (48 bp):
TCTGTTAAGATACAAGGGTGGCACGGACTATGTGTAGGCCACCAAGAG
Found at i:41351196 original size:89 final size:89
Alignment explanation
Indices: 41351092--41351353 Score: 375
Period size: 89 Copynumber: 2.9 Consensus size: 89
41351082 GAAACCACAA
* * * *
41351092 AGCCTTATCTCCCTGA-ACAACAGTGGAGTAGATTGAAAATAGTAGATCTTGTCTTCTTGTACTG
1 AGCCTTATCTCCCTGAGA-AGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCTTGTACTG
* * *
41351156 GCAGCAAAGTAGATCAAAGATAG-T
65 GTAGCAAAGCAGATCGAAGATAGCT
* * * *
41351180 CAGCCTTATCTCCCTGAGAAGCAGTGGAATAGGTTGAAGATAGCAAATCTTGTCTTCCTGTATTG
1 -AGCCTTATCTCCCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCTTGTACTG
*
41351245 GTAGCGAAGCAGATCGAAGATAGCT
65 GTAGCAAAGCAGATCGAAGATAGCT
*
41351270 AGCCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCTTGTACTGG
1 AGCCTTATCTCCCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCTTGTACTGG
41351335 TAGCAAAGCAGATCGAAGA
66 TAGCAAAGCAGATCGAAGA
41351354 CACCAGCCTT
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
89 151 0.99
90 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (89 bp):
AGCCTTATCTCCCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCTTGTACTGG
TAGCAAAGCAGATCGAAGATAGCT
Found at i:41351312 original size:44 final size:44
Alignment explanation
Indices: 41351172--41351312 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 44
41351162 AAGTAGATCA
* *
41351172 AAGATAG-TCAGCCTTATCTCCCTGAGAAGCAGTGGAATAGGTTG
1 AAGATAGCT-AGCCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTG
* ** * *** * * * * * *
41351216 AAGATAGCAAATCTTGTCT-TCCTGTATTGGTAGCGAAGCAGATCG
1 AAGATAGCTAGCCTTATCTCT-CTG-AGAAGCAGTGGAGTAGGTTG
41351261 AAGATAGCTAGCCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTG
1 AAGATAGCTAGCCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTG
41351305 AAGATAGC
1 AAGATAGC
41351313 AGATCTTGTC
Statistics
Matches: 65, Mismatches: 28, Indels: 8
0.64 0.28 0.08
Matches are distributed among these distances:
44 36 0.55
45 28 0.43
46 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (44 bp):
AAGATAGCTAGCCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTG
Found at i:41362179 original size:20 final size:20
Alignment explanation
Indices: 41362154--41362207 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
41362144 CTAAGAACCG
41362154 TTCCATTTACTTAGTTACCA
1 TTCCATTTACTTAGTTACCA
* *
41362174 TTCCATTTACTTACTTTCCA
1 TTCCATTTACTTAGTTACCA
* *
41362194 TTCAATTTAATTAG
1 TTCCATTTACTTAG
41362208 CATAAACTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (20 bp):
TTCCATTTACTTAGTTACCA
Found at i:41363924 original size:23 final size:24
Alignment explanation
Indices: 41363880--41363925 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
41363870 TGAAGAAGAA
* *
41363880 AACCTTTTGTTTTCTTATTTTATT
1 AACCTTTTATTCTCTTATTTTATT
41363904 AACCTTTTATTCT-TTATTTTAT
1 AACCTTTTATTCTCTTATTTTAT
41363926 CTTTATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.20, C:0.13, G:0.02, T:0.65
Consensus pattern (24 bp):
AACCTTTTATTCTCTTATTTTATT
Found at i:41371745 original size:51 final size:50
Alignment explanation
Indices: 41371568--41371905 Score: 329
Period size: 51 Copynumber: 6.7 Consensus size: 50
41371558 TATCATTTGA
* * * * *
41371568 TACACGTAGTAGCCTTCACATAGTACTACACATGTGATCAACCTTTACGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGG
* * *
41371618 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAG-TTTTACGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGG
* *
41371668 TTCACATAGTAGCCTTCACATGGTACTACACACGTGACCAAAGCTTTTCGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGG
* ** * * * *
41371719 TACACATAGTAGTCTTCATTTAGTACTACACATGTGACC-ATCATTTATTGAT
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCG-G
* * * *
41371771 TTCACTTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGG
* * * *** *
41371822 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGA
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTT-TCGG
* *
41371873 TACACGTAGTAGCCTTCACACAGTACTACACAC
1 TACACATAGTAGCCTTCACATAGTACTACACAC
41371906 ATGTTCATCG
Statistics
Matches: 236, Mismatches: 43, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
49 5 0.02
50 84 0.36
51 105 0.44
52 38 0.16
53 2 0.01
54 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (50 bp):
TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGG
Found at i:41371797 original size:103 final size:102
Alignment explanation
Indices: 41371574--41371905 Score: 416
Period size: 103 Copynumber: 3.3 Consensus size: 102
41371564 TTGATACACG
* * * * * * * *
41371574 TAGTAGCCTTCACATAGTACTACACATGTGATC-AACCTTTACGGTTCACGTAGTAGCCTTCACA
1 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACT
* * *** *
41371638 TAGTACTACACACGTGATCAAGTTTTA-CGGTTCACA
66 TAGTACTACACATGTGACCATCATTTATCGATTCACA
** * *
41371674 TAGTAGCCTTCACATGGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGTCTTCATT
1 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACT
* *
41371739 TAGTACTACACATGTGACCATCATTTATTGATTTCACT
66 TAGTACTACACATGTGACCATCATTTATCGA-TTCACA
* *
41371777 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACT
* * *
41371842 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATCATTTATCGATTCACA
41371879 TAGTAGCCTTCACACAGTACTACACAC
1 TAGTAGCCTTCACACAGTACTACACAC
41371906 ATGTTCATCG
Statistics
Matches: 201, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
100 30 0.15
101 46 0.23
102 32 0.16
103 93 0.46
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (102 bp):
TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACT
TAGTACTACACATGTGACCATCATTTATCGATTCACA
Found at i:41372431 original size:30 final size:31
Alignment explanation
Indices: 41372377--41372435 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
41372367 GCTTTGACTC
*
41372377 AACTTTTGTCAAAATTATAATTTTGTCCCTA
1 AACTTTTGTCAAAATTACAATTTTGTCCCTA
* *
41372408 AACTTTTG-CATAATTACATTTTTGTCCC
1 AACTTTTGTCAAAATTACAATTTTGTCCC
41372436 CAAGCTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (31 bp):
AACTTTTGTCAAAATTACAATTTTGTCCCTA
Found at i:41373595 original size:52 final size:52
Alignment explanation
Indices: 41373516--41373620 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
41373506 TGGTTAAGTC
*
41373516 TATCCAAATTTTGTTGGTATTTTTCTTCTTCATGGGCAGCTTTAACCATGGA
1 TATCCAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
41373568 TATCCAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
1 TATCCAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
41373620 T
1 T
41373621 GGTCTTTGGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (52 bp):
TATCCAAATTTTGTTGGTATTTGTCTTCTTCATGGGCAGCTTTAACCATGGA
Found at i:41375796 original size:49 final size:49
Alignment explanation
Indices: 41375671--41376177 Score: 860
Period size: 49 Copynumber: 10.6 Consensus size: 49
41375661 CCCTTCGGGA
* * * * *
41375671 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41375717 CTCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41375765 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41375814 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41375863 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41375912 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41375959 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41376008 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41376057 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41376104 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41376151 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
41376178 TATTCAAATA
Statistics
Matches: 446, Mismatches: 7, Indels: 15
0.95 0.01 0.03
Matches are distributed among these distances:
46 3 0.01
47 200 0.45
48 2 0.00
49 241 0.54
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41375936 original size:145 final size:143
Alignment explanation
Indices: 41375671--41376177 Score: 862
Period size: 145 Copynumber: 3.5 Consensus size: 143
41375661 CCCTTCGGGA
* * * * * *
41375671 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATA
41375733 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATC
41375798 ACATCGGCCATTAGGC
128 ACATCGGCCATTAGGC
41375814 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
41375879 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
41375944 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
41375959 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
41376024 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
41376089 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
41376104 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41376167 ACTTTCACATT
66 ACTTTCACATT
41376178 TATTCAAATA
Statistics
Matches: 353, Mismatches: 6, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
141 19 0.05
143 57 0.16
144 1 0.00
145 227 0.64
146 2 0.01
147 47 0.13
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:41381321 original size:25 final size:25
Alignment explanation
Indices: 41381291--41381373 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
41381281 CTACCGATTC
*
41381291 TCAGCTCGAGAGAGCTTACCGATAT
1 TCAGCTCGAGAGAGCTTACCAATAT
* * * *
41381316 TTAGCTC-ACATGAGCTTTCTAATAT
1 TCAGCTCGAGA-GAGCTTACCAATAT
* *
41381341 TCAGCTCAAGAGAGCTTAACAATAT
1 TCAGCTCGAGAGAGCTTACCAATAT
41381366 TCAGCTCG
1 TCAGCTCG
41381374 TATGAGCTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 2 0.04
25 41 0.91
26 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (25 bp):
TCAGCTCGAGAGAGCTTACCAATAT
Found at i:41381429 original size:25 final size:24
Alignment explanation
Indices: 41381368--41381433 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
41381358 AACAATATTC
* * *
41381368 AGCTCGTATGAGCTTACCGTTTAT
1 AGCTCGTATGAGCATACCGTTCAA
* *
41381392 AGCTCATAAGAGCATACCGATTCAA
1 AGCTCGTATGAGCATACCG-TTCAA
41381417 AGCTCGTATGAGCATAC
1 AGCTCGTATGAGCATAC
41381434 ATGTACAGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (24 bp):
AGCTCGTATGAGCATACCGTTCAA
Found at i:41381635 original size:15 final size:15
Alignment explanation
Indices: 41381594--41381635 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
41381584 GAAATGATGT
41381594 TACATGATATATTGA
1 TACATGATATATTGA
* *
41381609 TATATGAAATATATGA
1 TACATGATATAT-TGA
41381625 TACATG-TATAT
1 TACATGATATAT
41381636 GAAATTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (15 bp):
TACATGATATATTGA
Found at i:41387149 original size:69 final size:68
Alignment explanation
Indices: 41387054--41387182 Score: 186
Period size: 69 Copynumber: 1.9 Consensus size: 68
41387044 ATATATATAT
* * *
41387054 ACATTGCCATGGTCCAACCATGGTCTTACGTCTGAACAAATGTCATAGCCTTGCTATGGTCTTAC
1 ACATTACCATGGTCCAACCATAGTCTTACGTCTGAA-AAATGCCATAGCCTTGCTATGGTCTTAC
41387119 GTAA
65 GTAA
** * *
41387123 ACATTACCATGGTCCAACCATAGTCTTGTGTCTGAAAACTGCCATAGTCTTGCTATGGTC
1 ACATTACCATGGTCCAACCATAGTCTTACGTCTGAAAAATGCCATAGCCTTGCTATGGTC
41387183 CAACCATGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
68 21 0.40
69 32 0.60
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (68 bp):
ACATTACCATGGTCCAACCATAGTCTTACGTCTGAAAAATGCCATAGCCTTGCTATGGTCTTACG
TAA
Found at i:41393111 original size:18 final size:18
Alignment explanation
Indices: 41393088--41393122 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41393078 TGTTTTGATC
41393088 ATCACAAT-TCATCAACAA
1 ATCACAATGTCAT-AACAA
41393106 ATCACAATGTCATAACA
1 ATCACAATGTCATAACA
41393123 TGTACAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (18 bp):
ATCACAATGTCATAACAA
Found at i:41400916 original size:25 final size:25
Alignment explanation
Indices: 41400888--41400940 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
41400878 TAAGCATATT
41400888 TAAGGCATCGCATTATTACACTTAC
1 TAAGGCATCGCATTATTACACTTAC
*
41400913 TAAGGCATCGCATTGTTACACTTAC
1 TAAGGCATCGCATTATTACACTTAC
41400938 TAA
1 TAA
41400941 CTTCCAAATC
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:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (25 bp):
TAAGGCATCGCATTATTACACTTAC
Found at i:41402645 original size:24 final size:24
Alignment explanation
Indices: 41402618--41402686 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
41402608 GACATCATAG
*
41402618 AATATTCCACAAAGGCAATTACAA
1 AATATGCCACAAAGGCAATTACAA
* * * * *
41402642 AATACGCCATAGAGGCATTTACAG
1 AATATGCCACAAAGGCAATTACAA
41402666 AATATGCCACAAAGGCAATTA
1 AATATGCCACAAAGGCAATTA
41402687 TAGTTAACCT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (24 bp):
AATATGCCACAAAGGCAATTACAA
Found at i:41405344 original size:51 final size:51
Alignment explanation
Indices: 41405284--41405418 Score: 182
Period size: 51 Copynumber: 2.6 Consensus size: 51
41405274 AAAGTGATGG
*
41405284 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-GA
* * * * * *
41405335 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGA
*
41405386 TCACATGTGTAGTACTATGTGTAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
41405419 TGAACCGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 72 0.99
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGA
Found at i:41405478 original size:45 final size:45
Alignment explanation
Indices: 41405422--41405516 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
41405412 TACTATGTGA
* *
41405422 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
41405467 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
41405512 ACCGA
1 ACCGA
41405517 GTATCTGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:41408197 original size:4 final size:4
Alignment explanation
Indices: 41408181--41408216 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
41408171 TAATTGGGGA
*
41408181 AATT AACTT AATT AATT AATT AATT AATT TATT AAT
1 AATT AA-TT AATT AATT AATT AATT AATT AATT AAT
41408217 ATTTTGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:41410461 original size:23 final size:23
Alignment explanation
Indices: 41410427--41410470 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41410417 TTCACGCTAA
41410427 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACATC
* *
41410450 AATTTGGGCAGCATATATACA
1 AATTTGGACAGCATAAATACA
41410471 ACAGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACATC
Found at i:41410478 original size:23 final size:23
Alignment explanation
Indices: 41410427--41410478 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
41410417 TTCACGCTAA
*
41410427 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACAAC
* *
41410450 AATTTGGGCAGCATATATACAAC
1 AATTTGGACAGCATAAATACAAC
*
41410473 AGTTTG
1 AATTTG
41410479 AGCAACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACAAC
Found at i:41410531 original size:23 final size:23
Alignment explanation
Indices: 41410497--41410643 Score: 152
Period size: 23 Copynumber: 6.3 Consensus size: 23
41410487 TTTTACACCA
41410497 AAATTGGACAGCATATATGCAAC
1 AAATTGGACAGCATATATGCAAC
* * * * *
41410520 AAACTGGGCAGCATTTAAGCATC
1 AAATTGGACAGCATATATGCAAC
* *
41410543 AAAATTGGATAGCATATATGTAAC
1 -AAATTGGACAGCATATATGCAAC
*
41410567 AAATTGGACAGCATATATGTAAC
1 AAATTGGACAGCATATATGCAAC
* * *
41410590 AAATTGGGCAGCATTTAAT-CATC
1 AAATTGGACAGCATAT-ATGCAAC
*
41410613 AAAATTGGACAGCATATATGTAAC
1 -AAATTGGACAGCATATATGCAAC
41410637 AAATTGG
1 AAATTGG
41410644 TTCAACTCAT
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
23 65 0.66
24 34 0.34
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (23 bp):
AAATTGGACAGCATATATGCAAC
Found at i:41410535 original size:47 final size:48
Alignment explanation
Indices: 41410484--41410580 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 48
41410474 GTTTGAGCAA
* *
41410484 CATTTTTA-CACCAAAATTGGACAGCATATATGCAACAAACTGGGCAG
1 CATTTTAAGCACCAAAATTGGACAGCATATATGCAACAAACTGGACAG
* * * *
41410531 CA-TTTAAGCATCAAAATTGGATAGCATATATGTAACAAATTGGACAG
1 CATTTTAAGCACCAAAATTGGACAGCATATATGCAACAAACTGGACAG
41410578 CAT
1 CAT
41410581 ATATGTAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
46 4 0.10
47 38 0.90
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (48 bp):
CATTTTAAGCACCAAAATTGGACAGCATATATGCAACAAACTGGACAG
Found at i:41410571 original size:70 final size:70
Alignment explanation
Indices: 41410497--41410643 Score: 258
Period size: 70 Copynumber: 2.1 Consensus size: 70
41410487 TTTTACACCA
*
41410497 AAATTGGACAGCATATATGCAACAAACTGGGCAGCATTTAAGCATCAAAATTGGATAGCATATAT
1 AAATTGGACAGCATATATGCAACAAACTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATAT
41410562 GTAAC
66 GTAAC
* * *
41410567 AAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAATCATCAAAATTGGACAGCATATAT
1 AAATTGGACAGCATATATGCAACAAACTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATAT
41410632 GTAAC
66 GTAAC
41410637 AAATTGG
1 AAATTGG
41410644 TTCAACTCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (70 bp):
AAATTGGACAGCATATATGCAACAAACTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATAT
GTAAC
Found at i:41411530 original size:43 final size:43
Alignment explanation
Indices: 41411464--41411587 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 43
41411454 AATTCTTACA
* * ** * *
41411464 ATGCCAACATCCCAGACATGGTCTTACATGTAATCACGTA-TCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACATAAACAC-AAGTCG
41411507 ATGCC-ACTGTCCCAGACAGGGTCTTACACATAAACACAAGTCG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACATAAACACAAGTCG
41411550 ATGCCAACGTCCCAGAC-GTGGTCTTACACGAT-AACACA
1 ATGCCAACGTCCCAGACAG-GGTCTTACAC-ATAAACACA
41411588 TCTCGGAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 62 0.89
44 4 0.06
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACATAAACACAAGTCG
Found at i:41413488 original size:26 final size:27
Alignment explanation
Indices: 41413429--41413488 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
41413419 TAAACAAGAT
* ** *
41413429 TTATAAAATTAAAAGATGTGTAAATTA
1 TTATAAAATTAAAAGATATAAAAATAA
*
41413456 TTTTAAAATTAAAAG-TATAAAAATAA
1 TTATAAAATTAAAAGATATAAAAATAA
41413482 TTATAAA
1 TTATAAA
41413489 CCCCTAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (27 bp):
TTATAAAATTAAAAGATATAAAAATAA
Found at i:41413658 original size:33 final size:34
Alignment explanation
Indices: 41413621--41413697 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
41413611 TACTAAATTC
41413621 AAAATCCAAAC-TCAAAACATTTAAATCAAATAA
1 AAAATCCAAACTTCAAAACATTTAAATCAAATAA
** * *
41413654 AAAATATAGACTTGAAAACATTTAAATCAAATAA
1 AAAATCCAAACTTCAAAACATTTAAATCAAATAA
*
41413688 AAAACCCAAA
1 AAAATCCAAA
41413698 GAAATTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 8 0.23
34 27 0.77
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.21
Consensus pattern (34 bp):
AAAATCCAAACTTCAAAACATTTAAATCAAATAA
Found at i:41424631 original size:30 final size:30
Alignment explanation
Indices: 41424597--41424656 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
41424587 TATTTTATTA
41424597 TTAATTTTGTTATTATTTTAAAGAAATTTG
1 TTAATTTTGTTATTATTTTAAAGAAATTTG
* *
41424627 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGAAATTTG
41424657 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGAAATTTG
Found at i:41426598 original size:24 final size:23
Alignment explanation
Indices: 41426555--41426615 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
41426545 TTTAAAAAAT
41426555 TAAAAAATAATT-AAATT-ATA-A
1 TAAAAAA-AATTAAAATTCATATA
*
41426576 -AAAAAGAATATAAAATTCATATA
1 TAAAAAAAAT-TAAAATTCATATA
*
41426599 TTAAAAAAATTAAAATT
1 TAAAAAAAATTAAAATT
41426616 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 5 0.16
22 3 0.09
23 8 0.25
24 7 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAAAAAAATTAAAATTCATATA
Found at i:41429478 original size:17 final size:17
Alignment explanation
Indices: 41429456--41429489 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41429446 CACTAACATG
* *
41429456 AAAATGTAATGACAATA
1 AAAATGCAATCACAATA
41429473 AAAATGCAATCACAATA
1 AAAATGCAATCACAATA
41429490 TATATTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAATGCAATCACAATA
Found at i:41430003 original size:18 final size:19
Alignment explanation
Indices: 41429943--41430004 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
41429933 TTCTCATTTT
*
41429943 CAGCAACTTCTTCTTCTTCAG
1 CAGCAACTTC-TCTTC-TCAA
*
41429964 CAACAACTTTCTCTTCTGCAA
1 CAGCAAC-TTCTCTTCT-CAA
41429985 CAGCAACTTC-CTTCTCAA
1 CAGCAACTTCTCTTCTCAA
41430003 CA
1 CA
41430005 ACAATGTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.14
19 5 0.14
20 4 0.11
21 19 0.53
22 3 0.08
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (19 bp):
CAGCAACTTCTCTTCTCAA
Found at i:41438114 original size:18 final size:18
Alignment explanation
Indices: 41438091--41438126 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
41438081 TTAGAAAAAA
41438091 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
41438109 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
41438127 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:41442539 original size:78 final size:79
Alignment explanation
Indices: 41442401--41442561 Score: 261
Period size: 78 Copynumber: 2.1 Consensus size: 79
41442391 AATATTGGTC
* *
41442401 CTTTGGTTATCATCATCTTTCATTTGAATGTTAAGGGTTCGGCGAACTACAAGGCATTGAAAATC
1 CTTTGGTTATCATCATCTTTCATCTGAATGATAAGGGTTCGGCGAACTACAAGGCATTGAAAATC
41442466 AGCAAAGTCCCCTT
66 AGCAAAGTCCCCTT
* * *
41442480 CTTT-GTTGTCATCATCTTTCATCTGGATGATAAGGGTTCGGCGAACTACAAGGCATTGAAAGTC
1 CTTTGGTTATCATCATCTTTCATCTGAATGATAAGGGTTCGGCGAACTACAAGGCATTGAAAATC
*
41442544 AGCAAAGTCTCCTT
66 AGCAAAGTCCCCTT
41442558 CTTT
1 CTTT
41442562 TGGTGGTTCG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 72 0.95
79 4 0.05
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (79 bp):
CTTTGGTTATCATCATCTTTCATCTGAATGATAAGGGTTCGGCGAACTACAAGGCATTGAAAATC
AGCAAAGTCCCCTT
Found at i:41443768 original size:36 final size:37
Alignment explanation
Indices: 41443728--41443800 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
41443718 TCAAAAACCT
41443728 GCAAAACAAACACTCAA-CACTCAAAAAGAAAAATTA
1 GCAAAACAAACACTCAATCACTCAAAAAGAAAAATTA
* ** ** *
41443764 GCAAACCTCACTTTTAATCACTCAAAAAGAAAAATTA
1 GCAAAACAAACACTCAATCACTCAAAAAGAAAAATTA
41443801 AATTCTCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
36 11 0.37
37 19 0.63
ACGTcount: A:0.55, C:0.22, G:0.05, T:0.18
Consensus pattern (37 bp):
GCAAAACAAACACTCAATCACTCAAAAAGAAAAATTA
Found at i:41444779 original size:18 final size:18
Alignment explanation
Indices: 41444756--41444791 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
41444746 TTAGAAAAAA
41444756 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
41444774 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
41444792 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:41445312 original size:24 final size:23
Alignment explanation
Indices: 41445285--41445336 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
41445275 TTAAAACTAC
41445285 TTCTAAAGAAAACTCAAGAGAGAA
1 TTCTAAAGAAAACTCAAG-GAGAA
**
41445309 TTCTTGGAGAAAACTCAAGGAGAA
1 TTC-TAAAGAAAACTCAAGGAGAA
41445333 TTCT
1 TTCT
41445337 GCACTCAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 11 0.44
25 13 0.52
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (23 bp):
TTCTAAAGAAAACTCAAGGAGAA
Found at i:41450789 original size:26 final size:27
Alignment explanation
Indices: 41450729--41450782 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
41450719 TATTTTCTTG
* * *
41450729 AAATTTTACCAAGGGTAAAATTGTTAA
1 AAATTTTACTAGGGGTAAAATCGTTAA
41450756 AAATTTTACTAGGGGTAAAATCGTTAA
1 AAATTTTACTAGGGGTAAAATCGTTAA
41450783 TTTTTTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (27 bp):
AAATTTTACTAGGGGTAAAATCGTTAA
Found at i:41456278 original size:65 final size:64
Alignment explanation
Indices: 41456193--41456382 Score: 231
Period size: 71 Copynumber: 2.9 Consensus size: 64
41456183 AATAATTCAT
* **
41456193 TTTTTTCA-TTTTTGGTTAAATTGTAAATAAGTATATTATTGATGTAAAAATATAATACAAATGA
1 TTTTTTCATTTTTTCG-TAAATTGTAAATAAGTATATTATTGATGTAAAAATATAATACAAACAA
* *
41456257 TTTTTTCATTTTTTTCGTAAATTATAAATAAGTATATTGTTGATGTAAAAATCCAATACAATATA
1 TTTTTTCA-TTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAAT---AT---A-ATA
*
41456322 CCAACAA
58 CAAACAA
41456329 TTTTTTCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAA-ATAA
1 TTTTTTCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATATAA
41456383 AAATACTTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
63 1 0.01
64 9 0.08
65 33 0.30
66 6 0.06
67 2 0.02
68 2 0.02
71 41 0.38
72 15 0.14
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (64 bp):
TTTTTTCATTTTTTCGTAAATTGTAAATAAGTATATTATTGATGTAAAAATATAATACAAACAA
Found at i:41458732 original size:43 final size:43
Alignment explanation
Indices: 41458677--41458929 Score: 362
Period size: 43 Copynumber: 5.9 Consensus size: 43
41458667 TTTTAGAAAT
* **
41458677 AAACACCGCTATAGGCCACAACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
41458720 AAACGCTGCTATAGGCCACGACCTTTAGAGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
41458763 AAACGCCGCTATAGGTCATGACCTTTAGCGGCACTTTTCCCAA
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
41458806 AAACGCCACTATAGGCCATGACCTTTAGCGACACTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
41458849 AAACGCTGCTATAGGCCATGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
* *
41458892 AAAAGCCGCTATAGGCCATGACCTTTAGTGGCGCTTTT
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTT
41458930 TTTAAAAACG
Statistics
Matches: 188, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 188 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:41459277 original size:21 final size:21
Alignment explanation
Indices: 41459251--41459300 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
41459241 TTCTACTTTG
* *
41459251 CTCTGCTTCTCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCCGC
41459272 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCCGC
41459293 CTCTGCTT
1 CTCTGCTT
41459301 TAAGCTGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCCGC
Found at i:41459417 original size:66 final size:66
Alignment explanation
Indices: 41459271--41459422 Score: 191
Period size: 66 Copynumber: 2.3 Consensus size: 66
41459261 CTCGCTGCTG
* * * *
41459271 CCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGCTGCAGCTGGAGTTCTTCATACTTCTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCCTCTGCTTTAAGCTGCAGCTGAAGTTCTTCATACTTCTTTTGA
41459336 A
66 A
* * * *
41459337 CCTCAGC-TCTTCTCGCTGCTGCTTTTGCTTTAAGTTGTAGCTGAAGTTCTTCATATCTT-TTTT
1 CCTCAGCTTC-TCTCGCTGCTGCCTCTGCTTTAAGCTGCAGCTGAAGTTCTTCATA-CTTCTTTT
41459400 GAA
64 GAA
*
41459403 CCTCAGCTTCTCTCGATGCT
1 CCTCAGCTTCTCTCGCTGCT
41459423 TACCCTTGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
65 2 0.03
66 67 0.91
67 5 0.07
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCCTCTGCTTTAAGCTGCAGCTGAAGTTCTTCATACTTCTTTTGA
A
Found at i:41459540 original size:9 final size:9
Alignment explanation
Indices: 41459526--41459920 Score: 186
Period size: 9 Copynumber: 45.4 Consensus size: 9
41459516 AGTATATATG
41459526 AGTTATGTA
1 AGTTATGTA
41459535 AGTTATGATA
1 AGTTATG-TA
* * *
41459545 TGATATAT-
1 AGTTATGTA
41459553 A-TTATGT-
1 AGTTATGTA
*
41459560 A-TTACGTA
1 AGTTATGTA
*
41459568 AATTATGTA
1 AGTTATGTA
41459577 AGTTATGT-
1 AGTTATGTA
*
41459585 A-TTATATA
1 AGTTATGTA
41459593 AGTTATGTA
1 AGTTATGTA
41459602 AGTTATGT-
1 AGTTATGTA
41459610 A-TTATGTA
1 AGTTATGTA
*
41459618 AGCTATGTA
1 AGTTATGTA
*
41459627 AGTTGTGT-
1 AGTTATGTA
41459635 A-TTATGTA
1 AGTTATGTA
41459643 AGTTATGT-
1 AGTTATGTA
41459651 A-TTATGTA
1 AGTTATGTA
*
41459659 TGTTATGTA
1 AGTTATGTA
*
41459668 AGTTGTGTA
1 AGTTATGTA
*
41459677 TA-ATAT-TA
1 -AGTTATGTA
41459685 A-TTAAT-TA
1 AGTT-ATGTA
41459693 AGTTATGTA
1 AGTTATGTA
41459702 AG-T-TGTA
1 AGTTATGTA
41459709 AGTTATGTA
1 AGTTATGTA
41459718 AGTTATGTA
1 AGTTATGTA
*
41459727 TA-ATAT-TA
1 -AGTTATGTA
41459735 A-TTAAT-TA
1 AGTT-ATGTA
41459743 AGTTATGT-
1 AGTTATGTA
41459751 A-TTATGTA
1 AGTTATGTA
*
41459759 AGTTATTTA
1 AGTTATGTA
41459768 AGTTATGTA
1 AGTTATGTA
*
41459777 AGTTGTGT-
1 AGTTATGTA
* *
41459785 A-TTTTGTG
1 AGTTATGTA
*
41459793 AGTTATGCA
1 AGTTATGTA
*
41459802 ATTTATGTA
1 AGTTATGTA
* * *
41459811 GGCTATAT-
1 AGTTATGTA
41459819 A-TTATGTA
1 AGTTATGTA
41459827 AGTTAT-TA
1 AGTTATGTA
* *
41459835 TGTTATTATATA
1 AG---TTATGTA
*
41459847 AGTTATGCA
1 AGTTATGTA
*
41459856 AGTTTACATATA
1 AG-TT--ATGTA
*
41459868 AGTTTCTATATA
1 AG--T-TATGTA
41459880 AGTTATGTA
1 AGTTATGTA
41459889 AGTTATTATGTA
1 AG---TTATGTA
41459901 AGTTATGT-
1 AGTTATGTA
41459909 A-TTATGTA
1 AGTTATGTA
41459917 AGTT
1 AGTT
41459921 TATATATAAG
Statistics
Matches: 299, Mismatches: 46, Indels: 82
0.70 0.11 0.19
Matches are distributed among these distances:
7 63 0.21
8 38 0.13
9 156 0.52
10 11 0.04
11 4 0.01
12 24 0.08
13 2 0.01
14 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (9 bp):
AGTTATGTA
Found at i:41459585 original size:25 final size:25
Alignment explanation
Indices: 41459554--41459810 Score: 196
Period size: 25 Copynumber: 10.3 Consensus size: 25
41459544 ATGATATATA
* *
41459554 TTATGTATTACGTAAATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
41459579 TTATGTATTATATAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
41459604 TTATGTATTATGTAAGCTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
41459629 TTGTGTATTATGTAAGTTATGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
*
41459652 TTATGTATGTTATGTAAGTTGTGTATA-
1 TTATGTA--TTATGTAAGTTATGTA-AG
*
41459679 ATAT-TAATTAAT-TAAGTTATGTAAG
1 TTATGT-ATT-ATGTAAGTTATGTAAG
41459704 -T-TGTAAGTTATGTAAGTTATGTATA-
1 TTATGT-A-TTATGTAAGTTATGTA-AG
*
41459729 ATAT-TAATTAAT-TAAGTTATGT-A-
1 TTATGT-ATT-ATGTAAGTTATGTAAG
*
41459752 TTATGTAAGTTATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* * * * *
41459779 TTGTGTATTTTGTGAGTTATGCAAT
1 TTATGTATTATGTAAGTTATGTAAG
41459804 TTATGTA
1 TTATGTA
41459811 GGCTATATAT
Statistics
Matches: 194, Mismatches: 19, Indels: 38
0.77 0.08 0.15
Matches are distributed among these distances:
23 11 0.06
24 13 0.07
25 147 0.76
26 12 0.06
27 11 0.06
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:41459588 original size:16 final size:17
Alignment explanation
Indices: 41459568--41459832 Score: 191
Period size: 16 Copynumber: 15.9 Consensus size: 17
41459558 GTATTACGTA
41459568 AATTATGTAAGTTATGT
1 AATTATGTAAGTTATGT
*
41459585 -ATTATATAAGTTATGT
1 AATTATGTAAGTTATGT
41459601 AAGTTATGT-A-TTATGT
1 AA-TTATGTAAGTTATGT
* *
41459617 AAGCTATGTAAGTTGTGT
1 AA-TTATGTAAGTTATGT
41459635 -ATTATGTAAGTTATGT
1 AATTATGTAAGTTATGT
*
41459651 -ATTATGTATGTTATGT
1 AATTATGTAAGTTATGT
* *
41459667 AAGTTGTGTATA-ATAT-T
1 AA-TTATGTA-AGTTATGT
41459684 AATTAAT-TAAGTTATGT
1 AATT-ATGTAAGTTATGT
*
41459701 AAGT-TGTAAGTTATGT
1 AATTATGTAAGTTATGT
*
41459717 AAGTTATGTATA-ATAT-T
1 AA-TTATGTA-AGTTATGT
41459734 AATTAAT-TAAGTTATGT
1 AATT-ATGTAAGTTATGT
*
41459751 -ATTATGTAAGTTATTT
1 AATTATGTAAGTTATGT
*
41459767 AAGTTATGTAAGTTGTGT
1 AA-TTATGTAAGTTATGT
* * *
41459785 -ATTTTGTGAGTTATGC
1 AATTATGTAAGTTATGT
* * *
41459801 AATTTATGTAGGCTATAT
1 AA-TTATGTAAGTTATGT
41459819 -ATTATGTAAGTTAT
1 AATTATGTAAGTTAT
41459833 TATGTTATTA
Statistics
Matches: 195, Mismatches: 31, Indels: 45
0.72 0.11 0.17
Matches are distributed among these distances:
15 5 0.03
16 117 0.60
17 24 0.12
18 48 0.25
19 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (17 bp):
AATTATGTAAGTTATGT
Found at i:41459612 original size:50 final size:49
Alignment explanation
Indices: 41459554--41459776 Score: 218
Period size: 50 Copynumber: 4.6 Consensus size: 49
41459544 ATGATATATA
* *
41459554 TTATGTATTACGTAAATTATGTAAGTTATGTATTATA-TAAGTT-ATGTAAG
1 TTATGTATTA-GTAAGTTATGTAAGTTATGTATAATATTAA-TTAAT-TAAG
* * *
41459604 TTATGTATTATGTAAGCTATGTAAG-T-TG--T-GTATT-A-T--GTAAG
1 TTATGTATTA-GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
* *
41459645 TTATGTATTATGTATGTTATGTAAGTTGTGTATAATATTAATTAATTAAG
1 TTATGTATTA-GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
41459695 TTATGTAAGTT-GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
1 TTATGT-A-TTAGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
*
41459745 TTATGTATTATGTAAGTTATTTAAGTTATGTA
1 TTATGTATTA-GTAAGTTATGTAAGTTATGTA
41459777 AGTTGTGTAT
Statistics
Matches: 147, Mismatches: 12, Indels: 28
0.79 0.06 0.15
Matches are distributed among these distances:
41 27 0.18
42 1 0.01
43 3 0.02
45 4 0.03
46 6 0.04
47 1 0.01
48 5 0.03
49 2 0.01
50 95 0.65
51 1 0.01
52 2 0.01
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (49 bp):
TTATGTATTAGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
Found at i:41459649 original size:75 final size:74
Alignment explanation
Indices: 41459557--41459859 Score: 239
Period size: 75 Copynumber: 4.0 Consensus size: 74
41459547 ATATATATTA
* *
41459557 TGTATTACGTAAATTATGTAAGTTATGTA-TTATATAAGTTATGTAAGTTATGT-ATTATGTAAG
1 TGTATTATGTAAGTTATGTAA-TTATGTAGTTATATAAGTTATGTAA-TTATGTAATTAT-TAAG
*
41459620 CTATGTAAGTTG
63 TTATGTAAGTTG
* * *
41459632 TGTATTATGTAAGTTATGT-ATTATGTATGTTATGTAAGTTGTGTATAATAT-TAATTAATTAAG
1 TGTATTATGTAAGTTATGTAATTATGTA-GTTATATAAGTTATGTA-ATTATGTAATT-ATTAAG
41459695 TTATGTAAGTTG
63 TTATGTAAGTTG
* * *
41459707 T-AAGTTATGTAAGTTATGTATAATAT-TAATTA-ATTAAGTTATGT-ATTATGTAAGTTATTTA
1 TGTA-TTATGTAAGTTATGTA-ATTATGTAGTTATA-TAAGTTATGTAATTATGTAA-TTA-TTA
41459768 AGTTATGTAAGTTG
61 AGTTATGTAAGTTG
* * * * *
41459782 TGTATTTTGTGAGTTATGCAATTTATGTAGGCTATAT-A-TTATGTAAGTTATTATGTTATTATA
1 TGTATTATGTAAGTTATGTAA-TTATGTA-GTTATATAAGTTATGT-A---ATTATGTAATTAT-
*
41459845 TAAGTTATGCAAGTT
59 TAAGTTATGTAAGTT
41459860 TACATATAAG
Statistics
Matches: 184, Mismatches: 21, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
73 11 0.06
74 8 0.04
75 122 0.66
76 9 0.05
77 7 0.04
78 2 0.01
79 17 0.09
80 8 0.04
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.48
Consensus pattern (74 bp):
TGTATTATGTAAGTTATGTAATTATGTAGTTATATAAGTTATGTAATTATGTAATTATTAAGTTA
TGTAAGTTG
Found at i:41459890 original size:21 final size:21
Alignment explanation
Indices: 41459866--41459909 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41459856 AGTTTACATA
41459866 TAAGTT-TCTATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
41459887 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
41459908 TA
1 TA
41459910 TTATGTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:41459897 original size:12 final size:12
Alignment explanation
Indices: 41459882--41459906 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41459872 TCTATATAAG
41459882 TTATGTAAGTTA
1 TTATGTAAGTTA
41459894 TTATGTAAGTTA
1 TTATGTAAGTTA
41459906 T
1 T
41459907 GTATTATGTA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:41459930 original size:28 final size:28
Alignment explanation
Indices: 41459882--41459935 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
41459872 TCTATATAAG
*
41459882 TTATGTAAGTTATTATGTAAGTTATGTA
1 TTATGTAAGTTATTATATAAGTTATGTA
41459910 TTATGTAAGTT-TATATATAAGTTATG
1 TTATGTAAGTTAT-TATATAAGTTATG
41459936 ATATGATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (28 bp):
TTATGTAAGTTATTATATAAGTTATGTA
Found at i:41460025 original size:15 final size:15
Alignment explanation
Indices: 41459990--41460032 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
41459980 TAAGTTTTGA
*
41459990 AAAAATATATAAATT
1 AAAAATATATATATT
**
41460005 TTAAATATATATATT
1 AAAAATATATATATT
*
41460020 AAAAATGTATATA
1 AAAAATATATATA
41460033 AATATTAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAAATATATATATT
Found at i:41460364 original size:21 final size:21
Alignment explanation
Indices: 41460340--41460379 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41460330 AATTATAAAA
* *
41460340 TTTATTATTGAAAATATAGGT
1 TTTAATATTGAAAAAATAGGT
*
41460361 TTTAATATTTAAAAAATAG
1 TTTAATATTGAAAAAATAG
41460380 CATTTACAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (21 bp):
TTTAATATTGAAAAAATAGGT
Found at i:41460366 original size:69 final size:69
Alignment explanation
Indices: 41460208--41460417 Score: 359
Period size: 69 Copynumber: 3.1 Consensus size: 69
41460198 TGGGGTGATA
* *
41460208 TATTAAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTGTAAAAT
1 TATTGAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
41460273 TT-T
66 TTAT
*
41460276 TATTGAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTAATTTTAAAATTATAAAAT
1 TATTGAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
41460341 TTAT
66 TTAT
* * *
41460345 TATTGAAAATATAGGTTTTAATATTTAAAAAATAGCATTTACAATTATTTTTAAAATTATAAAAT
1 TATTGAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
41460410 TTAT
66 TTAT
41460414 TATT
1 TATT
41460418 AATAAAATTT
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
68 64 0.48
69 70 0.52
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (69 bp):
TATTGAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
TTAT
Found at i:41461188 original size:25 final size:26
Alignment explanation
Indices: 41461144--41461201 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
41461134 ATTAGAATTT
* *
41461144 AATTATTTTATAAGTTATAGAGTAAG
1 AATTATTTGATAAGTCATAGAGTAAG
41461170 AATTATTTGATAAG-CATAGAGTAAG
1 AATTATTTGATAAGTCATAGAGTAAG
41461195 AATTATT
1 AATTATT
41461202 ATGCAACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.40
Consensus pattern (26 bp):
AATTATTTGATAAGTCATAGAGTAAG
Found at i:41462145 original size:24 final size:24
Alignment explanation
Indices: 41462118--41462171 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
41462108 TCTAGATTTG
41462118 GGGGAATTTTGGGGAAAAATTGGA
1 GGGGAATTTTGGGGAAAAATTGGA
*
41462142 GGGGAATTTTGGGGAAAAATTTGA
1 GGGGAATTTTGGGGAAAAATTGGA
41462166 GGGGAA
1 GGGGAA
41462172 AAATGAGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (24 bp):
GGGGAATTTTGGGGAAAAATTGGA
Found at i:41462162 original size:13 final size:14
Alignment explanation
Indices: 41462128--41462175 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
41462118 GGGGAATTTT
*
41462128 GGGGAAAAATTGGA
1 GGGGAAAAATTTGA
*
41462142 GGGG---AATTT-T
1 GGGGAAAAATTTGA
41462152 GGGGAAAAATTTGA
1 GGGGAAAAATTTGA
41462166 GGGGAAAAAT
1 GGGGAAAAAT
41462176 GAGCTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
13 5 0.19
14 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.21
Consensus pattern (14 bp):
GGGGAAAAATTTGA
Found at i:41464054 original size:17 final size:16
Alignment explanation
Indices: 41464028--41464059 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41464018 AAATCTCTAA
41464028 CCCCTAACCCCTAAAT
1 CCCCTAACCCCTAAAT
41464044 CCCCTTAACCCCTAAA
1 CCCC-TAACCCCTAAA
41464060 CCTTAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (16 bp):
CCCCTAACCCCTAAAT
Found at i:41465032 original size:41 final size:40
Alignment explanation
Indices: 41464987--41465220 Score: 261
Period size: 41 Copynumber: 5.7 Consensus size: 40
41464977 AATGTTTTTT
*
41464987 GCGGCGCTTCTACAAAAACGCCGCTAAAACCCCTAACATTA
1 GCGGCGCTTC-ACAAAAACGCCGCTAAAAACCCTAACATTA
* * *
41465028 GCGGCGCTTCTCAAAAAACGCCGCTAAAAACCTTAACTTTA
1 GCGGCGCTTCAC-AAAAACGCCGCTAAAAACCCTAACATTA
*
41465069 GCGGCGCTTCATTAAAAACGCCGCTAAAAACCCTAACATTA
1 GCGGCGCTTCA-CAAAAACGCCGCTAAAAACCCTAACATTA
* * * *
41465110 GCGGCGCTTCCCAAAAAACACCACTAAAAACCGTAACATTA
1 GCGGCGCTTCAC-AAAAACGCCGCTAAAAACCCTAACATTA
* * * *
41465151 GCAGCGCTTCATTAAAAACGCTGCTAAAACACCCTACCATTA
1 GCGGCGCTTCA-CAAAAACGCCGCTAAAA-ACCCTAACATTA
** **
41465193 GCGGCGCAACTTAAAAACGCCGCTAAAA
1 GCGGCGCTTCACAAAAACGCCGCTAAAA
41465221 GTCACAGCAT
Statistics
Matches: 162, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.01
41 144 0.89
42 17 0.10
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.18
Consensus pattern (40 bp):
GCGGCGCTTCACAAAAACGCCGCTAAAAACCCTAACATTA
Found at i:41465125 original size:82 final size:82
Alignment explanation
Indices: 41464987--41465199 Score: 311
Period size: 82 Copynumber: 2.6 Consensus size: 82
41464977 AATGTTTTTT
* * * * *
41464987 GCGGCGCTTC-TACAAAAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAAAAAACGCCG
1 GCGGCGCTTCAT-TAAAAACGCCGCTAAAAACCCTAACATTAGCGGCGCTTCCCAAAAAACACCA
* *
41465051 CTAAAAACCTTAACTTTA
65 CTAAAAACCGTAACATTA
41465069 GCGGCGCTTCATTAAAAACGCCGCTAAAAACCCTAACATTAGCGGCGCTTCCCAAAAAACACCAC
1 GCGGCGCTTCATTAAAAACGCCGCTAAAAACCCTAACATTAGCGGCGCTTCCCAAAAAACACCAC
41465134 TAAAAACCGTAACATTA
66 TAAAAACCGTAACATTA
* * *
41465151 GCAGCGCTTCATTAAAAACGCTGCTAAAACACCCTACCATTAGCGGCGC
1 GCGGCGCTTCATTAAAAACGCCGCTAAAA-ACCCTAACATTAGCGGCGC
41465200 AACTTAAAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
82 100 0.84
83 19 0.16
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.18
Consensus pattern (82 bp):
GCGGCGCTTCATTAAAAACGCCGCTAAAAACCCTAACATTAGCGGCGCTTCCCAAAAAACACCAC
TAAAAACCGTAACATTA
Found at i:41465207 original size:123 final size:123
Alignment explanation
Indices: 41464987--41465220 Score: 303
Period size: 123 Copynumber: 1.9 Consensus size: 123
41464977 AATGTTTTTT
* * * * *
41464987 GCGGCGCTTCTACAAAAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAAAAAACGCCGC
1 GCGGCGCTTCCACAAAAACACCACTAAAAACCCTAACATTAGCAGCGCTTCTCAAAAAACGCCGC
* * **
41465052 TAAAAACCTTAACTTTAGCGGCGCTTCATTAAAAACGCCGCTAAAAACCCTAACATTA
66 TAAAAACCCTAACATTAGCGGCGCAACATTAAAAACGCCGCTAAAAACCCTAACATTA
* * *
41465110 GCGGCGCTTCC-CAAAAAACACCACTAAAAACCGTAACATTAGCAGCGCTTCAT-TAAAAACGCT
1 GCGGCGCTTCCAC-AAAAACACCACTAAAAACCCTAACATTAGCAGCGCTTC-TCAAAAAACGCC
*
41465173 GCTAAAACACCCTACCATTAGCGGCGCAAC-TTAAAAACGCCGCTAAAA
64 GCTAAAA-ACCCTAACATTAGCGGCGCAACATTAAAAACGCCGCTAAAA
41465221 GTCACAGCAT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
122 1 0.01
123 76 0.80
124 18 0.19
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.18
Consensus pattern (123 bp):
GCGGCGCTTCCACAAAAACACCACTAAAAACCCTAACATTAGCAGCGCTTCTCAAAAAACGCCGC
TAAAAACCCTAACATTAGCGGCGCAACATTAAAAACGCCGCTAAAAACCCTAACATTA
Found at i:41465250 original size:123 final size:123
Alignment explanation
Indices: 41465000--41465260 Score: 278
Period size: 123 Copynumber: 2.1 Consensus size: 123
41464990 GCGCTTCTAC
* * * *
41465000 AAAAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAAAAAACGCCGCTAAAAACCTTAAC
1 AAAAACGCCACTAAAAACCCTAACATTAGCAGCGCTTCTCAAAAAACGCCGCTAAAAACCCTAAC
* ** * * **
41465065 TTTAGCGGCGCTTCATTAAAAACGCCGCTAAAAACCCTAACATTAGCGGCGCTTCCCA
66 ATTAGCGGCGCAACATTAAAAACGCCGCTAAAAACACTAACATTAGCGGCACTTAACA
* * * *
41465123 AAAAACACCACTAAAAACCGTAACATTAGCAGCGCTTCAT-TAAAAACGCTGCTAAAACACCCTA
1 AAAAACGCCACTAAAAACCCTAACATTAGCAGCGCTTC-TCAAAAAACGCCGCTAAAA-ACCCTA
* * * *
41465187 CCATTAGCGGCGCAAC-TTAAAAACGCCGCTAAAAGTCAC-AGCATTAGCGGCAC-TAATA
64 ACATTAGCGGCGCAACATTAAAAACGCCGCTAAAA-ACACTAACATTAGCGGCACTTAACA
*
41465245 TAAAAACGCCATTAAA
1 -AAAAACGCCACTAAA
41465261 GCCCTCAGAA
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
122 2 0.02
123 91 0.81
124 20 0.18
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (123 bp):
AAAAACGCCACTAAAAACCCTAACATTAGCAGCGCTTCTCAAAAAACGCCGCTAAAAACCCTAAC
ATTAGCGGCGCAACATTAAAAACGCCGCTAAAAACACTAACATTAGCGGCACTTAACA
Found at i:41466505 original size:76 final size:76
Alignment explanation
Indices: 41466187--41466497 Score: 419
Period size: 76 Copynumber: 4.1 Consensus size: 76
41466177 CGGTTTATTT
* *
41466187 GACTAGCGTTGGGTGCAACTCATTGTTAGTACATCCAACTAGTGTTGGGCACACATTTGATATCG
1 GACTAGCGTTGGGCGCAACTCATTGTTAGTACATCCAACTAGTGCTGGGCACACATTTGATATCG
*
41466252 TCAGTTTACTC
66 TCAGTTTACCC
* * *
41466263 GACTAGCGTTGGGCGCAACTCATTATTGGTACATCCAACTAGTGCTGGGCACACATTTGATATCA
1 GACTAGCGTTGGGCGCAACTCATTGTTAGTACATCCAACTAGTGCTGGGCACACATTTGATATCG
41466328 TC-GATTTACCC
66 TCAG-TTTACCC
* * * *
41466339 GACTAGCGTTGGGCACAACTCATTGTTGGTACATCCAACTAGCGCTGGGCACACATTTGATATTG
1 GACTAGCGTTGGGCGCAACTCATTGTTAGTACATCCAACTAGTGCTGGGCACACATTTGATATCG
*
41466404 TTAGTTTACCC
66 TCAGTTTACCC
* * ** *
41466415 GACTAACGTTGGGCGCAACTCATTGTCAGTTTATCCGAA-TAGTGCTGGGCACACGTTTGATATC
1 GACTAGCGTTGGGCGCAACTCATTGTTAGTACATCC-AACTAGTGCTGGGCACACATTTGATATC
* *
41466479 GTCGGTTTATCC
65 GTCAGTTTACCC
*
41466491 AACTAGC
1 GACTAGC
41466498 ACTGGGCGTA
Statistics
Matches: 206, Mismatches: 26, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
75 1 0.00
76 202 0.98
77 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (76 bp):
GACTAGCGTTGGGCGCAACTCATTGTTAGTACATCCAACTAGTGCTGGGCACACATTTGATATCG
TCAGTTTACCC
Found at i:41466541 original size:152 final size:151
Alignment explanation
Indices: 41466214--41466544 Score: 376
Period size: 152 Copynumber: 2.2 Consensus size: 151
41466204 ACTCATTGTT
* *
41466214 AGTACATCCAACTAGTGTTGGGCACACATTTGATATCGTCAGTTTACTCGACTAGCGTTGGGCGC
1 AGTACATCCAACTAGTG-TGGGCACACATTTGATATCGTCAGTTTACCCGACTAACGTTGGGCGC
** *
41466279 AACTCATTATTGGTACATCCAACTAGTGCTGGGCACACATTTGATATCATCGATTTACCCGACTA
65 AACTCATTATCAGTACATCCAACTAGTGCTGGGCACACATTTGATATCATCGATTTACCCAACTA
** ** * *
41466344 GCGTTGGGCACAACTCATTGTT
130 GCACTGGGCACAAAACATTATC
* * * *
41466366 GGTACATCCAACTAGCGCTGGGCACACATTTGATATTGTTAGTTTACCCGACTAACGTTGGGCGC
1 AGTACATCCAACTAGTG-TGGGCACACATTTGATATCGTCAGTTTACCCGACTAACGTTGGGCGC
* ** * * * *
41466431 AACTCATTGTCAGTTTATCCGAA-TAGTGCTGGGCACACGTTTGATATCGTCGGTTTATCCAACT
65 AACTCATTATCAGTACATCC-AACTAGTGCTGGGCACACATTTGATATCATCGATTTACCCAACT
**
41466495 AGCACTGGGCGTAAAACATTATC
129 AGCACTGGGCACAAAACATTATC
** *
41466518 AGTTTATCCGACTAGTGTAGGGCACAC
1 AGTACATCCAACTAGTGT-GGGCACAC
41466545 CTATCGTTGG
Statistics
Matches: 147, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
151 1 0.01
152 144 0.98
153 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (151 bp):
AGTACATCCAACTAGTGTGGGCACACATTTGATATCGTCAGTTTACCCGACTAACGTTGGGCGCA
ACTCATTATCAGTACATCCAACTAGTGCTGGGCACACATTTGATATCATCGATTTACCCAACTAG
CACTGGGCACAAAACATTATC
Found at i:41469784 original size:20 final size:20
Alignment explanation
Indices: 41469761--41469806 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
41469751 CTTTCACTTC
*
41469761 TCTTTTCATTTACTTTCTCT
1 TCTTTTCATTTACTTTATCT
*
41469781 TCTTTTCCTTTACTTTATCT
1 TCTTTTCATTTACTTTATCT
41469801 TCTTTT
1 TCTTTT
41469807 AACTTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTTTCATTTACTTTATCT
Found at i:41478956 original size:41 final size:41
Alignment explanation
Indices: 41478899--41479086 Score: 306
Period size: 41 Copynumber: 4.6 Consensus size: 41
41478889 AGTAAGATGA
*
41478899 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
41478940 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
* *
41478981 TTC-GAGCTTTACGTCTAGCAGGCTTGATGCCAGTGAAATGT
1 TTCAGA-CTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
* *
41479022 TTCAGACTTTATGTCTAGCAGGCTCGATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
*
41479063 TTCAGACTTTACGTCTAACAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
41479087 AATTGTTGGT
Statistics
Matches: 136, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 2 0.01
41 132 0.97
42 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
Found at i:41479611 original size:71 final size:70
Alignment explanation
Indices: 41479535--41479691 Score: 199
Period size: 71 Copynumber: 2.2 Consensus size: 70
41479525 GATAAATACA
*
41479535 TATATACATTTGGTTATAATATTTGTTAAG-TATATGTATATATATGCATTCGGCTATTCATGTT
1 TATATACATTTGGTTATAATATATGTTAAGATATATGTATATA-A-GCATTCGGCTATTCATGTT
41479599 CAAAGTG
64 CAAAGTG
* *** *
41479606 TATATACATTTTGAGCTAATATATGTTAAGCATATATGTATATAAGCATTCGGCTATTCATGTTT
1 TATATACATTTGGTTATAATATATGTTAAG-ATATATGTATATAAGCATTCGGCTATTCATGTTC
*
41479671 ATAGTG
65 AAAGTG
* *
41479677 AATATACATTCGGTT
1 TATATACATTTGGTT
41479692 CTAAGAGTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
71 59 0.82
72 1 0.01
73 12 0.17
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (70 bp):
TATATACATTTGGTTATAATATATGTTAAGATATATGTATATAAGCATTCGGCTATTCATGTTCA
AAGTG
Found at i:41481441 original size:66 final size:66
Alignment explanation
Indices: 41481352--41481492 Score: 165
Period size: 66 Copynumber: 2.1 Consensus size: 66
41481342 ATCGAGCTTC
* * * * * * *
41481352 GGTCTTACATAATATACCTATGTTTTTTGTCCCAACGAATTCACTATGCTACCATAGATGAGCCA
1 GGTCTTACAGAACAGACCCATGTTTTCTGTCCCAACGAACTCACTATGCTACCATAAATGAGCCA
41481417 T
66 T
* * * * * *
41481418 GGTCTTACAGAACAGACCCATGTTTTCTGTCTCAATGGACTCTCTATGCTTCCATAAATGAGCTA
1 GGTCTTACAGAACAGACCCATGTTTTCTGTCCCAACGAACTCACTATGCTACCATAAATGAGCCA
41481483 T
66 T
41481484 GGTCTTACA
1 GGTCTTACA
41481493 CATCATACCC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (66 bp):
GGTCTTACAGAACAGACCCATGTTTTCTGTCCCAACGAACTCACTATGCTACCATAAATGAGCCA
T
Found at i:41481548 original size:67 final size:67
Alignment explanation
Indices: 41481477--41481660 Score: 217
Period size: 67 Copynumber: 2.7 Consensus size: 67
41481467 TTCCATAAAT
* * ** * *
41481477 GAGCTATGGTCTTACACATCATACCCCGTGTTTACTGTTCCGACGGACTCTCTATGTTGCTATAG
1 GAGCTATGGTCTTACACAACATACCCTGTGTTTACTGTTCCGACGGACTCTCTATGTCACCACAG
41481542 TC
66 TC
* * * *
41481544 GAGCTATGGTCTTAGACAACATACCCTGTGTTTACTG-TCCTGATGGACTGTTTATGTCACCACA
1 GAGCTATGGTCTTACACAACATACCCTGTGTTTACTGTTCC-GACGGACTCTCTATGTCACCACA
41481608 GTC
65 GTC
* * * * *
41481611 GAGCCATGATCTTACACAACATACCCTGTGTTTACTATCCCAACGGACTC
1 GAGCTATGGTCTTACACAACATACCCTGTGTTTACTGTTCCGACGGACTC
41481661 CATTGTTTGT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
66 3 0.03
67 92 0.95
68 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (67 bp):
GAGCTATGGTCTTACACAACATACCCTGTGTTTACTGTTCCGACGGACTCTCTATGTCACCACAG
TC
Found at i:41483546 original size:68 final size:68
Alignment explanation
Indices: 41483462--41483622 Score: 198
Period size: 68 Copynumber: 2.4 Consensus size: 68
41483452 CTCATTATAA
* * * * *
41483462 CCCATTTTTAATGTCCTAACGGACTCTATTGGTTGCCATAGTGGAGCTACAGTTTTACACTTGTA
1 CCCATTTTTAATGTCCTAACGGACTCTAGTGGATGCCATAGTGGAGCTACAGTCTTACACCTGCA
41483527 ATC
66 ATC
* * * * * *
41483530 CCCATGTTTAATGTCCTAGCAGACTCTAGTGGATGTCATAGTTGAGCTATAGTCTTACACCTGCA
1 CCCATTTTTAATGTCCTAACGGACTCTAGTGGATGCCATAGTGGAGCTACAGTCTTACACCTGCA
41483595 ATC
66 ATC
*
41483598 CCAATTTTTAATG-CTCTAACGGACT
1 CCCATTTTTAATGTC-CTAACGGACT
41483623 TCCCCGTTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 1 0.01
68 76 0.99
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (68 bp):
CCCATTTTTAATGTCCTAACGGACTCTAGTGGATGCCATAGTGGAGCTACAGTCTTACACCTGCA
ATC
Found at i:41502844 original size:44 final size:44
Alignment explanation
Indices: 41502795--41503193 Score: 178
Period size: 44 Copynumber: 9.2 Consensus size: 44
41502785 TTGAATTTGC
* *
41502795 AGTGGAGCGGATTAAAAATCATAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCGGATTCAAAATCACAGATCTTATCTCCCTAAGCAGT
* * * * * *
41502839 AGTGGAGC--ATATCGAAGTCCCCAG-CCTTATCTCCCTGAGCAGC
1 AGTGGAGCGGAT-TCAAAAT-CACAGATCTTATCTCCCTAAGCAGT
** * *
41502882 AGTGGAATAGG-TTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGG-AGCGGATTCAAAATCACAGATCTTATCTCCCTAAGCAGT
* * * * * * * * *
41502926 AATGGAGCAGA-TCGAAGTCCCCAG-CCTTATCTCCCTGAGTAGC
1 AGTGGAGCGGATTCAAAAT-CACAGATCTTATCTCCCTAAGCAGT
* * *
41502969 AGTGGAGTAGG-TTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAG-CGGATTCAAAATCACAGATCTTATCTCCCTAAGCAGT
* * * * * *
41503013 AGTGGAGC--ATATCGAAGTCCCCAG-CCTTATCTCCCTGAGCAGC
1 AGTGGAGCGGAT-TCAAAAT-CACAGATCTTATCTCCCTAAGCAGT
* * * * * *
41503056 AATGGAGTAGG-TTGAAAATTACAGATCTTAACTCCCTAAGCAAT
1 AGTGGAG-CGGATTCAAAATCACAGATCTTATCTCCCTAAGCAGT
* * * * * * * **
41503100 AGTGGAGCAGA-TCGAAGTCCCCAG-CCTTATCTCCTTGAGCAAC
1 AGTGGAGCGGATTCAAAAT-CACAGATCTTATCTCCCTAAGCAGT
* * *
41503143 AGTGGAGTAGG-TTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAG-CGGATTCAAAATCACAGATCTTATCTCCCTAAGCAGT
41503187 AGTGGAG
1 AGTGGAG
41503194 TAGATCGAAG
Statistics
Matches: 243, Mismatches: 89, Indels: 46
0.64 0.24 0.12
Matches are distributed among these distances:
42 3 0.01
43 116 0.48
44 122 0.50
45 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (44 bp):
AGTGGAGCGGATTCAAAATCACAGATCTTATCTCCCTAAGCAGT
Found at i:41502871 original size:43 final size:43
Alignment explanation
Indices: 41502821--41503203 Score: 243
Period size: 43 Copynumber: 8.8 Consensus size: 43
41502811 AATCATAGAT
*
41502821 CTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
* * ** * * * ** *
41502864 CTTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-C
*
41502908 CTTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
* * * * * * * ** *
41502951 CTTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-C
*
41502995 CTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
* * * * * * * ** *
41503038 CTTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-C
* *
41503082 CTTAACTCCCTAAGCAATAGTGGAGCAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
* * ** * * * * ** *
41503125 CTTATCTCCTTGAGCAACAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-C
*
41503169 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
41503204 ACACTAGCCT
Statistics
Matches: 244, Mismatches: 85, Indels: 22
0.70 0.24 0.06
Matches are distributed among these distances:
43 123 0.50
44 121 0.50
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.25
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGC
Found at i:41503194 original size:44 final size:44
Alignment explanation
Indices: 41502864--41503196 Score: 255
Period size: 44 Copynumber: 7.6 Consensus size: 44
41502854 AGTCCCCAGC
* *
41502864 CTTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * * * * * ** *
41502908 CTTATCTCCCTAAGCAGTAATGGAGCAGATCG-AAGTCCCCAG-C
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
* *
41502951 CTTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * ** * * ** *
41502995 CTTATCTCCCTAAGCAGTAGTGGAGCATATCG-AAGTCCCCAG-C
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
* *
41503038 CTTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* ** * * * * ** *
41503082 CTTAACTCCCTAAGCAATAGTGGAGCAGATCG-AAGTCCCCAG-C
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
* * *
41503125 CTTATCTCCTTGAGCAACAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
*
41503169 CTTATCTCCCTAAGCAGTAGTGGAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGTAG
41503197 ATCGAAGACA
Statistics
Matches: 209, Mismatches: 71, Indels: 18
0.70 0.24 0.06
Matches are distributed among these distances:
43 93 0.44
44 116 0.56
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
Found at i:41503259 original size:87 final size:87
Alignment explanation
Indices: 41502817--41503203 Score: 675
Period size: 87 Copynumber: 4.4 Consensus size: 87
41502807 TAAAAATCAT
*
41502817 AGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
*
41502882 AGTGGAATAGGTTGAAAATTAC
66 AGTGGAGTAGGTTGAAAATTAC
* *
41502904 AGATCTTATCTCCCTAAGCAGTAATGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGTAGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
41502969 AGTGGAGTAGGTTGAAAATTAC
66 AGTGGAGTAGGTTGAAAATTAC
*
41502991 AGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
*
41503056 AATGGAGTAGGTTGAAAATTAC
66 AGTGGAGTAGGTTGAAAATTAC
* * * *
41503078 AGATCTTAACTCCCTAAGCAATAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCTTGAGCAAC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
41503143 AGTGGAGTAGGTTGAAAATTAC
66 AGTGGAGTAGGTTGAAAATTAC
*
41503165 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
41503204 ACACTAGCCT
Statistics
Matches: 283, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 283 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.25
Consensus pattern (87 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTATCTCCCTGAGCAGC
AGTGGAGTAGGTTGAAAATTAC
Found at i:41503439 original size:44 final size:44
Alignment explanation
Indices: 41503322--41503445 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 44
41503312 GAGCAGTAGT
* ** *
41503322 GGAGCAGATTGAAGACGGCAAATCTTATCTCCCTAAGGTTACAGT
1 GGAGCAGATTAAAGACAAC-AATCTTATCTCCCTAAGGTTACAGC
* * *
41503367 GGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAGGTTACAGC
1 GGAGCAGATTAAAGACAACAATCTTATCTCCCTAAGGTTACAGC
* * * *
41503411 GGATCGGATTAAA-ATAACAGATCTTATCTCTCTAA
1 GGAGCAGATTAAAGACAACA-ATCTTATCTCCCTAA
41503446 AGTTGTAGAG
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
43 3 0.05
44 47 0.73
45 14 0.22
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (44 bp):
GGAGCAGATTAAAGACAACAATCTTATCTCCCTAAGGTTACAGC
Found at i:41503520 original size:84 final size:88
Alignment explanation
Indices: 41503432--41503591 Score: 204
Period size: 89 Copynumber: 1.9 Consensus size: 88
41503422 AAATAACAGA
* * *
41503432 TCTTAT-CTCTCTAAAGTTGTAGAGAG-CAGA-T-CACAT-CTAGTCTTATCTCCCTGAAGTTGC
1 TCTTATCCT-TCTAAAGTTGTAGAGAGACAGACTGAACATGCGAATCTTATCTCCCTGAAGTTGC
*
41503492 AGTGGAGCAGACTAAGTAAGCAGG
65 AGTGAAGCAGACTAAGTAAGCAGG
* * *
41503516 TCTTATCCTTCTAAAGTTGTAGTGAGACAGACTGAAGATGGCGAATCTTATCTCCTTGAAGTTGC
1 TCTTATCCTTCTAAAGTTGTAGAGAGACAGACTGAACAT-GCGAATCTTATCTCCCTGAAGTTGC
41503581 AGTGAAGCAGA
65 AGTGAAGCAGA
41503592 TTAAAGCCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
84 22 0.35
85 6 0.10
86 1 0.02
87 3 0.05
89 31 0.49
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (88 bp):
TCTTATCCTTCTAAAGTTGTAGAGAGACAGACTGAACATGCGAATCTTATCTCCCTGAAGTTGCA
GTGAAGCAGACTAAGTAAGCAGG
Found at i:41503521 original size:44 final size:43
Alignment explanation
Indices: 41503471--41503765 Score: 140
Period size: 44 Copynumber: 6.8 Consensus size: 43
41503461 ATCACATCTA
41503471 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAG
* * * *
41503515 GTCTTATC-CTTCTAAAGTTGTAGT-GAGACAGACTGAAGATGGC-G
1 GTCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGACT-AAGA-AGCAG
* * * * *
41503559 AATCTTATCTCCTTGAAGTTGCAGTGAAGCAGA-TTA-AAGCCAATA
1 -GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-G
* * * * * * *
41503604 ATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAA-AACCACTG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA--G
* * * * * *
41503648 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCA-TATCAG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAG
* * * * *
41503688 GTCTTATCTTCCTAAAGTTGCAGTGGAGCAGACCAAGAAAGTAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAG
* * * *
41503732 GTCTTATCCCCCTGAAATTGTAGTGGGGCAGACT
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
41503766 GAATAAACAA
Statistics
Matches: 187, Mismatches: 47, Indels: 34
0.70 0.18 0.13
Matches are distributed among these distances:
40 20 0.11
41 8 0.04
42 8 0.04
43 12 0.06
44 106 0.57
45 30 0.16
46 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAG
Found at i:41503717 original size:217 final size:216
Alignment explanation
Indices: 41503317--41503768 Score: 579
Period size: 217 Copynumber: 2.1 Consensus size: 216
41503307 TCCATGAGCA
* *
41503317 GTAGTGGAGCAGATTGAAGACGGCAAATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTAAAGC
1 GTAGTGGA-CAGACTGAAGACGGCAAATCTTATCTCCCTAAGGTTACAGTGAAGCAGATTAAAGC
* *
41503382 CAATAATCCTATCTCCCTAAGGTTACAGCGGATCGGATTAAAATAACAGATCTTATCTCTCTAAA
65 CAATAATCCTATCTCCCTAAGGTTACAGCGGAGCGGATTAAAACAACAGATCTTATCTCTCTAAA
* * * *
41503447 GTTGTAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
130 GTTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACCAAGAAAG
* **
41503512 CAGGTCTTATCCTTCT-AAAGTT
195 CAAGTCTTATCCCCCTGAAA-TT
* * * *
41503534 GTAGTGAGACAGACTGAAGATGGCGAATCTTATCTCCTTGAA-GTTGCAGTGAAGCAGATTAAAG
1 GTAGTG-GACAGACTGAAGACGGCAAATCTTATCTCCCT-AAGGTTACAGTGAAGCAGATTAAAG
* ** * * * *
41503598 CCAATAATCCTATCTCCTTGAA-GTTGTAGTGGAGCGGATTAAAACCACTGATCTTATCTCTCTG
64 CCAATAATCCTATCTCCCT-AAGGTTACAGCGGAGCGGATTAAAACAACAGATCTTATCTCTCTA
* *
41503662 AAGTTGCAGAGAGCAGATCATATC-AGGTCTTATCTTCCTAAAGTTGCAGTGGAGCAGACCAAGA
128 AAGTTGCAGAGAGCAGATCACATCTA-GTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACCAAGA
*
41503726 AAGTAAGTCTTATCCCCCTGAAATT
192 AAGCAAGTCTTATCCCCCTGAAATT
*
41503751 GTAGTGGGGCAGACTGAA
1 GTAGT-GGACAGACTGAA
41503769 TAAACAAATC
Statistics
Matches: 203, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
216 1 0.00
217 192 0.95
218 10 0.05
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (216 bp):
GTAGTGGACAGACTGAAGACGGCAAATCTTATCTCCCTAAGGTTACAGTGAAGCAGATTAAAGCC
AATAATCCTATCTCCCTAAGGTTACAGCGGAGCGGATTAAAACAACAGATCTTATCTCTCTAAAG
TTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACCAAGAAAGC
AAGTCTTATCCCCCTGAAATT
Found at i:41505589 original size:26 final size:25
Alignment explanation
Indices: 41505540--41505612 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
41505530 TTTTAACACA
* *
41505540 TATTTTTTTATTTTATATATATACAT
1 TATTTATTT-TTTTATATAAATACAT
41505566 ATATTTATGTTTTTTA-ATAAATACAT
1 -TATTTAT-TTTTTTATATAAATACAT
*
41505592 TATTTATTTTGTTATATAAAT
1 TATTTATTTTTTTATATAAAT
41505613 TTTATAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.15
25 13 0.32
26 9 0.22
27 11 0.27
28 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (25 bp):
TATTTATTTTTTTATATAAATACAT
Found at i:41509532 original size:41 final size:41
Alignment explanation
Indices: 41509475--41509558 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
41509465 TCTGGTTTTT
41509475 ACCCCTAGTATTGATGTTCATTTTTTAGATACGAGAATTAC
1 ACCCCTAGTATTGATGTTCATTTTTTAGATACGAGAATTAC
41509516 ACCCCTAGTATTGATGTTCATTTTTTAGATACGAGAATTAC
1 ACCCCTAGTATTGATGTTCATTTTTTAGATACGAGAATTAC
41509557 AC
1 AC
41509559 GTTTGTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (41 bp):
ACCCCTAGTATTGATGTTCATTTTTTAGATACGAGAATTAC
Found at i:41513828 original size:68 final size:68
Alignment explanation
Indices: 41513734--41513887 Score: 229
Period size: 68 Copynumber: 2.3 Consensus size: 68
41513724 ACTTATCATG
* *
41513734 CCTCATGTTTAATGTCCTGGCAGACTCTATTGGTTTCCATAGTCGAGCTATGATCTTACACCTGT
1 CCTCATGTTTAATGTCCTGGAAGACTCTATTGGTTGCCATAGTCGAGCTATGATCTTACACCTGT
41513799 AAT
66 AAT
* * * *
41513802 CCTCATGTCTAATGTCCT-GAAGGACTCTATTGGTTGCCATAGTTGAGTTATGGTCTTACACCTG
1 CCTCATGTTTAATGTCCTGGAA-GACTCTATTGGTTGCCATAGTCGAGCTATGATCTTACACCTG
41513866 TAAT
65 TAAT
*
41513870 CCCCATGTTTAATGTCCT
1 CCTCATGTTTAATGTCCT
41513888 AGCAGACTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
67 2 0.03
68 75 0.97
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.37
Consensus pattern (68 bp):
CCTCATGTTTAATGTCCTGGAAGACTCTATTGGTTGCCATAGTCGAGCTATGATCTTACACCTGT
AAT
Found at i:41516177 original size:42 final size:43
Alignment explanation
Indices: 41516130--41516233 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
41516120 ATCATGTGAT
* * *
41516130 CCTATTTTGAATTGCACACGGTCT-ACAACACGGCCGTATGAC
1 CCTATTTCGAATTGCACACGGTATGACAACACGACCGTATGAC
* * * * *
41516172 CCTATTTGGAATTGCACACGGTATGGCAACACGACTGTGTGGC
1 CCTATTTCGAATTGCACACGGTATGACAACACGACCGTATGAC
41516215 CCTATTTCGAATTGCACAC
1 CCTATTTCGAATTGCACAC
41516234 AATCTAGAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 22 0.42
43 31 0.58
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (43 bp):
CCTATTTCGAATTGCACACGGTATGACAACACGACCGTATGAC
Found at i:41516247 original size:43 final size:42
Alignment explanation
Indices: 41516130--41516248 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 42
41516120 ATCATGTGAT
* * *
41516130 CCTATTTTGAATTGCACACGGTCTACAACACGGCCGTATGAC
1 CCTATTTCGAATTGCACACGGTCTAGAACACGACCGTATGAC
* * * * * *
41516172 CCTATTTGGAATTGCACACGGTATGGCAACACGACTGTGTGGC
1 CCTATTTCGAATTGCACACGGTCTAG-AACACGACCGTATGAC
**
41516215 CCTATTTCGAATTGCACACAATCTAGAGACACGA
1 CCTATTTCGAATTGCACACGGTCTAGA-ACACGA
41516249 ATTGTACATG
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
42 23 0.37
43 39 0.63
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (42 bp):
CCTATTTCGAATTGCACACGGTCTAGAACACGACCGTATGAC
Found at i:41521597 original size:33 final size:33
Alignment explanation
Indices: 41521533--41521750 Score: 182
Period size: 33 Copynumber: 6.4 Consensus size: 33
41521523 ATATAAAGGG
*
41521533 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
41521560 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
41521593 GGTTGCTAAGTGCTGATCCCACCGTATCGTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AT--T-CAT-TG---GT
41521635 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
41521668 GGTTGCTAAGTGCTGATTCCACC-A-TAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGATTCAT-TG---GT
* *
41521704 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
41521737 GGTTGCTAAGTGCT
1 GGTTGCTAAGTGCT
41521751 AAATCCACCG
Statistics
Matches: 157, Mismatches: 12, Indels: 38
0.76 0.06 0.18
Matches are distributed among these distances:
27 22 0.14
31 2 0.01
32 5 0.03
33 58 0.37
34 5 0.03
35 4 0.03
36 26 0.17
37 5 0.03
38 3 0.02
39 2 0.01
40 2 0.01
41 3 0.02
42 20 0.13
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:41521679 original size:75 final size:69
Alignment explanation
Indices: 41521556--41521750 Score: 309
Period size: 75 Copynumber: 2.7 Consensus size: 69
41521546 TGATTCCCCC
41521556 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACC--A--
41521621 GTAAATGTGA
62 -T-AATGTGA
*
41521631 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATAAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATAAT
41521696 GTGA
66 GTGA
* *
41521700 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCT
41521751 AAATCCACCG
Statistics
Matches: 117, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
69 56 0.48
70 1 0.01
73 1 0.01
75 59 0.50
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (69 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATAAT
GTGA
Found at i:41521737 original size:69 final size:70
Alignment explanation
Indices: 41521556--41521764 Score: 321
Period size: 69 Copynumber: 2.9 Consensus size: 70
41521546 TGATTCCCCC
*
41521556 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG-A--
41521621 GTAAATGTGA
63 -T-AATGTGA
41521631 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACC-ATAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGATAA
41521695 TGTGA
66 TGTGA
* * * *
41521700 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAAATCCACCGATAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGATAA
41521765 CGGATAACAT
Statistics
Matches: 128, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
69 63 0.49
70 5 0.04
73 1 0.01
75 59 0.46
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (70 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGATAA
TGTGA
Found at i:41529105 original size:33 final size:33
Alignment explanation
Indices: 41529063--41529197 Score: 117
Period size: 33 Copynumber: 3.8 Consensus size: 33
41529053 ATGTGAAAGG
41529063 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
41529096 GGTTGCTAAGTGCTGATTGCACCATATGATTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATT-C-CC---CGATT-CAT-TG---GT
* *
41529139 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
41529172 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
41529198 AACGGATAAC
Statistics
Matches: 81, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
33 38 0.47
34 5 0.06
35 2 0.02
36 2 0.02
37 1 0.01
38 7 0.09
39 2 0.02
40 2 0.02
41 2 0.02
42 1 0.01
43 19 0.23
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:41529107 original size:75 final size:76
Alignment explanation
Indices: 41528984--41529187 Score: 293
Period size: 76 Copynumber: 2.7 Consensus size: 76
41528974 TGATTCCCCC
* * ** * *
41528984 AAGGGGTTGCTAAGTGCTAATTCCCCGATTCATTAGCAGTTGCTAAGTGCTGATCCCGCCGTAT-
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATG
*
41529048 CTTAAATGTGA
66 ATTAAATGTGA
**
41529059 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTGCACCATATG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATG
*
41529124 ATTGAATGTGA
66 ATTAAATGTGA
* *
41529135 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGA
41529188 ATCCACCGAT
Statistics
Matches: 116, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 56 0.48
76 60 0.52
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATG
ATTAAATGTGA
Found at i:41529229 original size:24 final size:24
Alignment explanation
Indices: 41529201--41529246 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
41529191 CACCGATAAC
41529201 GGATAACATTCCGAGTGTTCAACG
1 GGATAACATTCCGAGTGTTCAACG
41529225 GGATAACATTCCGAGTGTTCAA
1 GGATAACATTCCGAGTGTTCAA
41529247 AGGTGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (24 bp):
GGATAACATTCCGAGTGTTCAACG
Found at i:41541591 original size:39 final size:39
Alignment explanation
Indices: 41541521--41541642 Score: 172
Period size: 39 Copynumber: 3.0 Consensus size: 39
41541511 ACCAAAAATT
41541521 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAGTATTTTAAAAA
41541564 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
41541603 AATTTTAAAATATAAAAAATTTAAAAAAAGTATTTTAAAA
1 TATTTTAAAAT-TAAAAAAATT-AAAAAAGTATTTTAAAA
41541643 TTAAAAATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
39 35 0.47
40 11 0.15
41 17 0.23
42 6 0.08
43 6 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:41541621 original size:41 final size:40
Alignment explanation
Indices: 41541539--41541642 Score: 174
Period size: 39 Copynumber: 2.6 Consensus size: 40
41541529 AAATTAAAAC
*
41541539 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAAT-TAA
1 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATATAA
41541578 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATATAA
1 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATATAA
*
41541618 AAAATTTAAAAAAAGTATTTTAAAA
1 AAAAATT-AAAAAAGTATTTTAAAA
41541643 TTAAAAATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 35 0.57
40 9 0.15
41 17 0.28
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATATAA
Found at i:41543261 original size:20 final size:21
Alignment explanation
Indices: 41543236--41543274 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41543226 TTTTTTAAAT
41543236 ATTTTTTAA-AAAAATAATTA
1 ATTTTTTAAGAAAAATAATTA
*
41543256 ATTTTTTAAGTAAAATAAT
1 ATTTTTTAAGAAAAATAAT
41543275 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTTTTTAAGAAAAATAATTA
Found at i:41545219 original size:33 final size:32
Alignment explanation
Indices: 41545185--41545255 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 32
41545175 AAAAATAAAT
*
41545185 TTTTTAAATAATACAAATGTGTTAATATCTAA
1 TTTTTAAATAATACAAATGTATTAATATCTAA
41545217 --TTTAAATAATACAAATGTATTAATATCTAA
1 TTTTTAAATAATACAAATGTATTAATATCTAA
41545247 TTATTTAAA
1 TT-TTTAAA
41545256 ATATAGATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 29 0.83
33 6 0.17
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (32 bp):
TTTTTAAATAATACAAATGTATTAATATCTAA
Found at i:41545221 original size:30 final size:30
Alignment explanation
Indices: 41545187--41545248 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
41545177 AAATAAATTT
*
41545187 TTTAAATAATACAAATGTGTTAATATCTAA
1 TTTAAATAATACAAATGTATTAATATCTAA
41545217 TTTAAATAATACAAATGTATTAATATCTAA
1 TTTAAATAATACAAATGTATTAATATCTAA
41545247 TT
1 TT
41545249 ATTTAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTAAATAATACAAATGTATTAATATCTAA
Found at i:41545562 original size:13 final size:12
Alignment explanation
Indices: 41545530--41545582 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
41545520 AAACTTTATA
*
41545530 AAAGTACTTTTC
1 AAAGCACTTTTC
41545542 AAAGCACTTTTCC
1 AAAGCACTTTT-C
* *
41545555 ACAGCACTTTTTA
1 AAAGCAC-TTTTC
*
41545568 AAAGCATTTTTC
1 AAAGCACTTTTC
41545580 AAA
1 AAA
41545583 AGCAACACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 17 0.52
13 12 0.36
14 4 0.12
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (12 bp):
AAAGCACTTTTC
Found at i:41545583 original size:13 final size:13
Alignment explanation
Indices: 41545537--41545586 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
41545527 ATAAAAGTAC
*
41545537 TTTTC-AAAGCAC
1 TTTTCAAAAGCAT
* *
41545549 TTTTCCACAGCACT
1 TTTTCAAAAGCA-T
41545563 TTTT-AAAAGCAT
1 TTTTCAAAAGCAT
41545575 TTTTCAAAAGCA
1 TTTTCAAAAGCA
41545587 ACACTAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 10 0.32
13 17 0.55
14 4 0.13
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:41545586 original size:26 final size:25
Alignment explanation
Indices: 41545529--41545586 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
41545519 CAAACTTTAT
* *
41545529 AAAAGTACTTTTCAAAGCACTTTTC
1 AAAAGCACTTTTAAAAGCACTTTTC
* * *
41545554 CACAGCACTTTTTAAAAGCATTTTTC
1 AAAAGCAC-TTTTAAAAGCACTTTTC
41545580 AAAAGCA
1 AAAAGCA
41545587 ACACTAAACT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (25 bp):
AAAAGCACTTTTAAAAGCACTTTTC
Found at i:41551105 original size:57 final size:57
Alignment explanation
Indices: 41551017--41551130 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
41551007 AAGGAAAGAA
41551017 ACAAAATGGAAAGAAAATCAAAGGTTGAGAATCAAATCCAACAGATTTACTTTCTAT
1 ACAAAATGGAAAGAAAATCAAAGGTTGAGAATCAAATCCAACAGATTTACTTTCTAT
41551074 ACAAAATGGAAAGAAAATCAAAGGTTGAGAATCAAATCCAACAGATTTACTTTCTAT
1 ACAAAATGGAAAGAAAATCAAAGGTTGAGAATCAAATCCAACAGATTTACTTTCTAT
41551131 GTTGTTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (57 bp):
ACAAAATGGAAAGAAAATCAAAGGTTGAGAATCAAATCCAACAGATTTACTTTCTAT
Found at i:41552900 original size:9 final size:9
Alignment explanation
Indices: 41552886--41552911 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41552876 TCTCCTCCCT
41552886 AATTTCACA
1 AATTTCACA
41552895 AATTTCACA
1 AATTTCACA
41552904 AATTTCAC
1 AATTTCAC
41552912 TTTCACACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTTCACA
Found at i:41555329 original size:24 final size:24
Alignment explanation
Indices: 41555272--41555330 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
41555262 GGTTTAATGC
* *
41555272 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
41555296 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
41555320 AAATGGATATA
1 AAATGGATATA
41555331 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:41555422 original size:20 final size:19
Alignment explanation
Indices: 41555396--41555460 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
41555386 AATATTTTTA
41555396 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
41555415 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
41555433 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
41555452 ATTTATGTA
1 A-TTATGTA
41555461 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:41555425 original size:37 final size:37
Alignment explanation
Indices: 41555371--41555483 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
41555361 TTATGTTTTA
*
41555371 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
41555407 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
41555444 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
41555481 ATT
1 ATT
41555484 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:41555439 original size:17 final size:17
Alignment explanation
Indices: 41555383--41555477 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
41555373 TCAAGACTTG
41555383 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
41555400 TGTAGTGATTCAAAGACTTA
1 TGTAAT-ATTTTTA-A-TTA
41555420 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
41555437 TGTAGTGATTCAAAGATTTA
1 TGTAAT-ATTTTTA-A-TTA
*
41555457 TGTAATGTTTTTAATTA
1 TGTAATATTTTTAATTA
41555474 TGTA
1 TGTA
41555478 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
17 20 0.36
18 10 0.18
19 9 0.16
20 16 0.29
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TGTAATATTTTTAATTA
Found at i:41555498 original size:9 final size:9
Alignment explanation
Indices: 41555484--41555620 Score: 193
Period size: 9 Copynumber: 14.6 Consensus size: 9
41555474 TGTAGTGATT
41555484 TAATTCGGG
1 TAATTCGGG
41555493 TAATTCGGG
1 TAATTCGGG
41555502 TAATTTTCGGG
1 TAA--TTCGGG
41555513 TAATTTTCGGG
1 TAA--TTCGGG
41555524 TAATTCGGG
1 TAATTCGGG
*
41555533 TAATTTGGG
1 TAATTCGGG
41555542 TAATTTTCGGG
1 TAA--TTCGGG
41555553 TAATTCGGG
1 TAATTCGGG
41555562 TAATTCGGG
1 TAATTCGGG
*
41555571 TAAGTCGGG
1 TAATTCGGG
41555580 TAATTCGGG
1 TAATTCGGG
*
41555589 TAAGTCGGG
1 TAATTCGGG
41555598 TAATTCGGG
1 TAATTCGGG
41555607 TAATTCGGG
1 TAATTCGGG
41555616 TAATT
1 TAATT
41555621 TTTAACCAAA
Statistics
Matches: 118, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
9 90 0.76
11 28 0.24
ACGTcount: A:0.22, C:0.09, G:0.32, T:0.36
Consensus pattern (9 bp):
TAATTCGGG
Done.