Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 93 of 100
Found at i:18437014 original size:28 final size:28
Alignment explanation
Indices: 18436983--18437071 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
18436973 CCAAATTGGT
18436983 AGAAAATTTAGAAATCCAACAAAAAAAG
1 AGAAAATTTAGAAATCCAACAAAAAAAG
** * * **
18437011 AG--AATTTCTAAAT-AAACCAAAATGG
1 AGAAAATTTAGAAATCCAACAAAAAAAG
* *
18437036 TGAAAAATTTAGAAATCCAACAAAAAAAA
1 AG-AAAATTTAGAAATCCAACAAAAAAAG
18437065 AGAAAAT
1 AGAAAAT
18437072 ATTTTTAATT
Statistics
Matches: 42, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
25 9 0.21
26 9 0.21
28 16 0.38
29 8 0.19
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (28 bp):
AGAAAATTTAGAAATCCAACAAAAAAAG
Found at i:18437043 original size:54 final size:55
Alignment explanation
Indices: 18436959--18437068 Score: 161
Period size: 54 Copynumber: 2.0 Consensus size: 55
18436949 ATAAGAAAAT
* * * *
18436959 ATTTCTAAATTGACCCAAATTGGTAGAAAATTTAGAAATCCAACAAAAAAAGAGA
1 ATTTCTAAATTAAACCAAAATGGTAGAAAATTTAGAAATCCAACAAAAAAAAAGA
18437014 ATTTCTAAA-TAAACCAAAATGGT-GAAAAATTTAGAAATCCAACAAAAAAAAAGA
1 ATTTCTAAATTAAACCAAAATGGTAG-AAAATTTAGAAATCCAACAAAAAAAAAGA
18437068 A
1 A
18437069 AATATTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 1 0.02
54 40 0.80
55 9 0.18
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (55 bp):
ATTTCTAAATTAAACCAAAATGGTAGAAAATTTAGAAATCCAACAAAAAAAAAGA
Found at i:18438198 original size:23 final size:24
Alignment explanation
Indices: 18438163--18438215 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
18438153 TTAAACAGTA
* * *
18438163 TTATTATTCTTAAAATATT-ATTT
1 TTATTAATATTAAAATATTAATAT
18438186 TTATTAATATTAAAATATTAATAT
1 TTATTAATATTAAAATATTAATAT
18438210 TTATTA
1 TTATTA
18438216 TTAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTAATATTAAAATATTAATAT
Found at i:18438225 original size:15 final size:16
Alignment explanation
Indices: 18438205--18438243 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
18438195 TTAAAATATT
18438205 AATATTTAT-TATTAA
1 AATATTTATATATTAA
18438220 AATATTTATACTATTAA
1 AATATTTATA-TATTAA
18438237 AATATTT
1 AATATTT
18438244 GTTTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATTTATATATTAA
Found at i:18438733 original size:23 final size:25
Alignment explanation
Indices: 18438706--18438754 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
18438696 TCTTGAGTAT
*
18438706 AAATATAAAAATA-TT-TAATATTA
1 AAATATAAAAAGACTTATAATATTA
*
18438729 AAATATTAAAAGACTTATAATATTA
1 AAATATAAAAAGACTTATAATATTA
18438754 A
1 A
18438755 TATTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 2 0.09
25 9 0.41
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATATAAAAAGACTTATAATATTA
Found at i:18438872 original size:168 final size:165
Alignment explanation
Indices: 18438537--18438858 Score: 384
Period size: 168 Copynumber: 1.9 Consensus size: 165
18438527 TTTAATAATA
* * * *
18438537 TATAAA-ATAAAATTATTTAAAATTTAAATATTAAAAAATTTTAAATGTTAATTTTTAAATTTTT
1 TATAAATATAAAAATATTTAAAATTAAAATATTAAAAAATTATAAATATTAATTTTTAAATTTTT
* *
18438601 TTAATTAAAATTAAATAAAATATTTTTATTAATATAATAATATTTCAAGTCGAATCAAATCAAGT
66 TTAAGTAAAATTAAATAAAATATTTTTATTAATATAATAATATTTCAAGTCGAATCAAATCAAAT
* * *
18438666 TCAAATTTAAAATATTATGTTCAAAATCTTTCTTGAG
131 TCAAACTTAAAAAATCATGTT-AAAA-CTTTCTTGAG
* *
18438703 TATAAATATAAAAATATTTAATATTAAAATATTAAAAGACTTAT-AATATTAATATTTT-AA-TT
1 TATAAATATAAAAATATTTAAAATTAAAATATTAAAA-AATTATAAATATTAAT-TTTTAAATTT
***
18438765 TTTTAAGTAAAATTAAATAAAAATATTATTTATTAATATAATAATATTTTGGGTC-ATATCAAAT
64 TTTTAAGTAAAATTAAAT-AAAATATT-TTTATTAATATAATAATATTTCAAGTCGA-ATCAAAT
* * *
18438829 TAAATTTAAGCTTAAAAAATCATGTATAAA
126 CAAATTCAAACTTAAAAAATCATGT-TAAA
18438859 TTTCAAATTG
Statistics
Matches: 132, Mismatches: 17, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
166 25 0.19
167 46 0.35
168 60 0.45
169 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (165 bp):
TATAAATATAAAAATATTTAAAATTAAAATATTAAAAAATTATAAATATTAATTTTTAAATTTTT
TTAAGTAAAATTAAATAAAATATTTTTATTAATATAATAATATTTCAAGTCGAATCAAATCAAAT
TCAAACTTAAAAAATCATGTTAAAACTTTCTTGAG
Found at i:18443097 original size:13 final size:13
Alignment explanation
Indices: 18443079--18443107 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18443069 ATAAACTACA
18443079 ATAAATATAAAAT
1 ATAAATATAAAAT
18443092 ATAAATATAAAAT
1 ATAAATATAAAAT
18443105 ATA
1 ATA
18443108 TTTGTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATATAAAAT
Found at i:18448683 original size:348 final size:348
Alignment explanation
Indices: 18448135--18449176 Score: 1299
Period size: 348 Copynumber: 3.0 Consensus size: 348
18448125 AAATTTTTGG
* * *
18448135 TTATTAAAGGTGTCTTTTATTAT-GACATGCCTTTAATATACCATGATGGTAATGGAAGGTGTTT
1 TTATTAAAGGCGTCTTTTATTATAAAC-CGCCTTTAATATACCATGATGGTAATGGAAGGTGTTT
* * * * * *
18448199 CTTAGAAAAGGCACCTTTAATATACTTTTAAACTTAGTAATCGATTAGTGAAGGCATTTGTTAAT
65 ATTAGAAAAGGAACCTTCAATATAC-TTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAAT
* * * * * *
18448264 AACAAACGCCTTTAAAATTTATTCTTTTAATATTTTAGAAACTATTAAAGGCATCTTCTATTGTA
129 AACAGACGCCTTCAAAATTTATTCTTTTAATATTTTAGGAATTATTAAAGGCTTCTTCTACTGTA
**
18448329 AAATACCTTCTATATACAGCCACATAAATTCTAACACTGTTATTGAAGGCAAACATCCAAGAAAG
194 AAATACCTTCTATATACAGCCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAG
*
18448394 ATGCCTTTAATAATTCTTATCACAGTTTGTAAATAATAACTGAAGGTGGTTACAGAAAATATCAC
259 ATGCCTTTAATAATTCTTATCACAGTTTGTAAATAATAACTGAAGGTGGTTACAGAAAATATCGC
18448459 CTTCAATAATTTTCCTC-TCACAGA
324 CTTCAATAATTTTCCTCATCACAGA
* * * *
18448483 TTTTTAAAGGCGTCTTTTATTATAAACCGCCTTCAATATACCATGATGGTAAGGGAAGATGTTTA
1 TTATTAAAGGCGTCTTTTATTATAAACCGCCTTTAATATACCATGATGGTAATGGAAGGTGTTTA
* * * * *
18448548 TTAGAAAA-AAAGCCTTCAATATATCTTTAAACTTAGAAATCCATGAATGAAAGTGTTTGTTAAT
66 TTAGAAAAGGAA-CCTTCAATATA-CTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAAT
* *
18448612 AACAGACGCATTCAAAATTTATTCTTTTAATATTTTAGGAATTATTAAAGGCTTTTTCTACTGTA
129 AACAGACGCCTTCAAAATTTATTCTTTTAATATTTTAGGAATTATTAAAGGCTTCTTCTACTGTA
* *
18448677 AAATACCTTTTATATACTA-CCACACAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAA
194 AAATACCTTCTATATAC-AGCCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAA
* *
18448741 GATGCCTTTAATAATT-TCTATCATAGTTTGTAAATAATGACTGAAGGTGGTTACAGAAAATAAT
258 GATGCCTTTAATAATTCT-TATCACAGTTTGTAAATAATAACTGAAGGTGGTTACAGAAAAT-AT
* * *
18448805 -GCCTTCAATAATTTCCCTCAAAAATTTTTTACGGA
321 CGCCTTCAATAATTTTCCTC----A----TCACAGA
* * * * * * *
18448840 TTATTAAAGACGTTTTTTATTATAAATCGCCTTTAATATCCCACGATGGTAATGAAAGGCGTTTA
1 TTATTAAAGGCGTCTTTTATTATAAACCGCCTTTAATATACCATGATGGTAATGGAAGGTGTTTA
* * *
18448905 CTAGAAAAGGTACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATA
66 TTAGAAAAGGAACCTTCAATATA-CTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAATA
* * * **
18448970 ACAGATGCCTTCAAAATTT-TCCCATAAAATATTTT-GAGAATTATTAAAGGCTTCTTCTACTGT
130 ACAGACGCCTTCAAAATTTAT-TCTTTTAATATTTTAG-GAATTATTAAAGGCTTCTTCTACTGT
* * * *
18449033 AAAATACCTTCTCTATACCGCCACATAAATTCTAACACTATTATTGAAGGCGTACATCTAAGAAA
193 AAAATACCTTCTATATACAGCCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAA
** * * * * * *
18449098 GACACTTTTAATAATTCTTATCACAGTTTGTAGATAATAACTGAAGGCGGTTGCAGAAAACAACG
258 GATGCCTTTAATAATTCTTATCACAGTTTGTAAATAATAACTGAAGGTGGTTACAGAAAATATCG
18449163 CCTTCAATAATTTT
323 CCTTCAATAATTTT
18449177 TCTTAAAAAA
Statistics
Matches: 593, Mismatches: 80, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
347 2 0.00
348 293 0.49
349 6 0.01
356 3 0.01
357 287 0.48
358 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (348 bp):
TTATTAAAGGCGTCTTTTATTATAAACCGCCTTTAATATACCATGATGGTAATGGAAGGTGTTTA
TTAGAAAAGGAACCTTCAATATACTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAATAA
CAGACGCCTTCAAAATTTATTCTTTTAATATTTTAGGAATTATTAAAGGCTTCTTCTACTGTAAA
ATACCTTCTATATACAGCCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGAT
GCCTTTAATAATTCTTATCACAGTTTGTAAATAATAACTGAAGGTGGTTACAGAAAATATCGCCT
TCAATAATTTTCCTCATCACAGA
Found at i:18449033 original size:357 final size:353
Alignment explanation
Indices: 18448084--18449234 Score: 1385
Period size: 357 Copynumber: 3.2 Consensus size: 353
18448074 TTACAGAAAA
* * *
18448084 TGGTTACAGAAAACAACGCCTTCAATAATTTCTCTGAAAAAAAATTTTT-GG-TTATTAAAGGTG
1 TGGTTACAGAAAACAACGCCTTCAATAATTTCCCT---CAAAAATTTTTCGGATTATTAAAGGCG
* * *
18448147 TCTTTTATTAT-GACATGCCTTTAATATACCATGATGGTAATGGAAGGTGTTT-CTTAGAAAAGG
63 TCTTTTATTATAAAC-CGCCTTCAATATACCATGATGGTAATGGAAGGTGTTTAC-TAGAAAAGG
* * * * * * *
18448210 CACCTTTAATATACTTTTAAACTTAGTAATCGATTAGTGAAGGCATTTGTTAATAACAAACGCCT
126 AACCTTCAATATACCTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAATAACAGACGCCT
* * * *
18448275 TTAAAATTTATTCTTTTAATATTTTAGAAACTATTAAAGGCATCTTCTATTGTAAAATACCTTCT
191 TCAAAATTTATTCTTTTAATATTTTAG-AATTATTAAAGGCTTCTTCTACTGTAAAATACCTTCT
**
18448340 ATATACAGCCACATAAATTCTAACACTGTTATTGAAGGCAAACATCCAAGAAAGATGCCTTTAAT
255 ATATACA-CCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAAT
18448405 AATTCTTATCACAGTTTGTAAATAATAACTGAAGG
319 AATTCTTATCACAGTTTGTAAATAATAACTGAAGG
* * * * ** * *
18448440 TGGTTACAGAAAATATCACCTTCAATAATTTTCCTC-------TCACAGATTTTTAAAGGCGTCT
1 TGGTTACAGAAAACAACGCCTTCAATAATTTCCCTCAAAAATTTTTCGGATTATTAAAGGCGTCT
* * * *
18448498 TTTATTATAAACCGCCTTCAATATACCATGATGGTAAGGGAAGATGTTTATTAGAAAA-AAAGCC
66 TTTATTATAAACCGCCTTCAATATACCATGATGGTAATGGAAGGTGTTTACTAGAAAAGGAA-CC
* * * * * *
18448562 TTCAATATATCTTTAAACTTAGAAATCCATGAATGAAAGTGTTTGTTAATAACAGACGCATTCAA
130 TTCAATATACCTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAATAACAGACGCCTTCAA
* *
18448627 AATTTATTCTTTTAATATTTTAGGAATTATTAAAGGCTTTTTCTACTGTAAAATACCTTTTATAT
195 AATTTATTCTTTTAATATTTTA-GAATTATTAAAGGCTTCTTCTACTGTAAAATACCTTCTATAT
*
18448692 ACTACCACACAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAATT
259 AC-ACCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAATT
* *
18448757 -TCTATCATAGTTTGTAAATAATGACTGAAGG
323 CT-TATCACAGTTTGTAAATAATAACTGAAGG
* * *
18448788 TGGTTACAGAAAATAATGCCTTCAATAATTTCCCTCAAAAATTTTTTACGGATTATTAAAGACGT
1 TGGTTACAGAAAACAACGCCTTCAATAATTTCCCTCAAAAA-TTTTT-CGGATTATTAAAGGCGT
* * * * * * * *
18448853 TTTTTATTATAAATCGCCTTTAATATCCCACGATGGTAATGAAAGGCGTTTACTAGAAAAGGTAC
64 CTTTTATTATAAACCGCCTTCAATATACCATGATGGTAATGGAAGGTGTTTACTAGAAAAGGAAC
* *
18448918 CTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACAGATGCCTTCA
129 CTTCAATATACCTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAATAACAGACGCCTTCA
* * ** *
18448983 AAATTT-TCCCATAAAATATTTTGAGAATTATTAAAGGCTTCTTCTACTGTAAAATACCTTCTCT
194 AAATTTAT-TCTTTTAATATTTT-AGAATTATTAAAGGCTTCTTCTACTGTAAAATACCTTCTAT
* * * ** *
18449047 ATACCGCCACATAAATTCTAACACTATTATTGAAGGCGTACATCTAAGAAAGACACTTTTAATAA
257 ATA-CACCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAA
*
18449112 TTCTTATCACAGTTTGTAGATAATAACTGAAGG
321 TTCTTATCACAGTTTGTAAATAATAACTGAAGG
* * ** * *
18449145 CGGTTGCAGAAAACAACGCCTTCAATAATTTTTCTTAAAAAATTTTCGTTGATTATTAAAGGCGT
1 TGGTTACAGAAAACAACGCCTTCAATAATTTCCCTCAAAAATTTTTCG--GATTATTAAAGGCGT
18449210 CTTTTATTATAAACCGCCTTCAATA
64 CTTTTATTATAAACCGCCTTCAATA
18449235 AATTATTATA
Statistics
Matches: 671, Mismatches: 100, Indels: 47
0.82 0.12 0.06
Matches are distributed among these distances:
346 1 0.00
347 3 0.00
348 292 0.44
349 4 0.01
355 2 0.00
356 36 0.05
357 329 0.49
358 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (353 bp):
TGGTTACAGAAAACAACGCCTTCAATAATTTCCCTCAAAAATTTTTCGGATTATTAAAGGCGTCT
TTTATTATAAACCGCCTTCAATATACCATGATGGTAATGGAAGGTGTTTACTAGAAAAGGAACCT
TCAATATACCTTTAAACTTAGTAATCCATTAATGAAGGCGTTTGTTAATAACAGACGCCTTCAAA
ATTTATTCTTTTAATATTTTAGAATTATTAAAGGCTTCTTCTACTGTAAAATACCTTCTATATAC
ACCACATAAATTCTAACACTGTTATTGAAGGCGTACATCCAAGAAAGATGCCTTTAATAATTCTT
ATCACAGTTTGTAAATAATAACTGAAGG
Found at i:18454962 original size:30 final size:30
Alignment explanation
Indices: 18454926--18454991 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
18454916 TTTCAAATAT
* **
18454926 TTTTTATCCAATTAAA-CCTTTAATCATTTA
1 TTTTTATCAAATTAAATCC-TTAATCATCGA
18454956 TTTTTATCAAATTAAATCCTTAATCATCGA
1 TTTTTATCAAATTAAATCCTTAATCATCGA
18454986 TTTTTA
1 TTTTTA
18454992 AATGGTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTTTATCAAATTAAATCCTTAATCATCGA
Found at i:18456009 original size:10 final size:10
Alignment explanation
Indices: 18455974--18456017 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
18455964 ATTTTTATTT
18455974 TATAAAAAT-
1 TATAAAAATA
18455983 T-TAAAATATA
1 TATAAAA-ATA
18455993 TATAAAAATA
1 TATAAAAATA
*
18456003 AATAAAAATA
1 TATAAAAATA
18456013 TATAA
1 TATAA
18456018 TTCAGTTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 5 0.17
9 3 0.10
10 17 0.57
11 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAAAAATA
Found at i:18461925 original size:48 final size:48
Alignment explanation
Indices: 18461853--18461947 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
18461843 GATTCACAAG
** * *
18461853 AAAGATAGATTAATGAGATTTCAAGTTTCGTAAAGGTTCTAGATTCAC
1 AAAGATAGATTAACAAGATCTCAAGTTTCGCAAAGGTTCTAGATTCAC
* *
18461901 AAAGATAGATTTACAAGATCTCAAGTTTTGCAAAGGTTCTAGATTCA
1 AAAGATAGATTAACAAGATCTCAAGTTTCGCAAAGGTTCTAGATTCA
18461948 TAAAAATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (48 bp):
AAAGATAGATTAACAAGATCTCAAGTTTCGCAAAGGTTCTAGATTCAC
Found at i:18462249 original size:121 final size:121
Alignment explanation
Indices: 18462046--18462581 Score: 514
Period size: 120 Copynumber: 4.5 Consensus size: 121
18462036 AGGAAGAAAC
* * * * * ** *
18462046 CATGAGTCAAAAAATGAAACAACTATGA-TAAGTCAAGGTCAAAAATAAATGATTTGGACAAAAC
1 CATGAGTCAAAAAATGAAACGACCAGGACCAAGTCGAGGTCAAAAATAAATGATCAGGACGAAAC
* * * * *
18462110 CATGAGTCATAAGAAATGATTTGGACTAAGCCAAGATCGAGTGACTGAGACAAAAT
66 CATGAGTCATAAGAAATGATCTAGACTAAGCCAAGATCGAATGACCGAAACAAAAT
* * * * * *
18462166 CATGAGTCAAAAAATGAAACGACCAGGACCAAGTTGAGGTAAAAAATACATGACCGGGACGAAAT
1 CATGAGTCAAAAAATGAAACGACCAGGACCAAGTCGAGGTCAAAAATAAATGATCAGGACGAAAC
* * * * *
18462231 CATGAGTCATAAGAAATGATCTAGACTGAA-CTATGATTGAGTGACCGAAATAAAAT
66 CATGAGTCATAAGAAATGATCTAGACT-AAGCCAAGATCGAATGACCGAAACAAAAT
* * * * * *
18462287 CACGAGTTAAAATAT-AAGATGACCAGGACCAAGTCAAGGTCAAAAATAAATGATCAGGACAAAA
1 CATGAGTCAAAAAATGAA-ACGACCAGGACCAAGTCGAGGTCAAAAATAAATGATCAGGACGAAA
** * * * * *
18462351 CCACAAGTCATAAGAAATG-TCTGGACTAAGCCAAGATCAAATGACCAAAACGAAAC
65 CCATGAGTCATAAGAAATGATCTAGACTAAGCCAAGATCGAATGACCGAAACAAAAT
* * *
18462407 CATGAGTCAAAAAATGAGGAA--ACC-GAGACAAAGTCGAGGTCAAAAGTAAATGA-CAGGATGA
1 CATGAGTCAAAAAATGA--AACGACCAG-GACCAAGTCGAGGTCAAAAATAAATGATCAGGACGA
* * * *
18462468 AACCATGAGTCATAAGAAATGATCTAAACTAAGTCAAGATCGAATGATCGGAACAAAAT
63 AACCATGAGTCATAAGAAATGATCTAGACTAAGCCAAGATCGAATGACCGAAACAAAAT
* * * * *
18462527 CATGAATCAAAAAAT-AAGATGACCAGGATCGAGTCGATGTCAAAAATAAATGATC
1 CATGAGTCAAAAAATGAA-ACGACCAGGACCAAGTCGAGGTCAAAAATAAATGATC
18462582 GAGATGAAAT
Statistics
Matches: 332, Mismatches: 70, Indels: 27
0.77 0.16 0.06
Matches are distributed among these distances:
117 1 0.00
118 1 0.00
119 29 0.09
120 157 0.47
121 140 0.42
122 3 0.01
123 1 0.00
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (121 bp):
CATGAGTCAAAAAATGAAACGACCAGGACCAAGTCGAGGTCAAAAATAAATGATCAGGACGAAAC
CATGAGTCATAAGAAATGATCTAGACTAAGCCAAGATCGAATGACCGAAACAAAAT
Found at i:18467580 original size:15 final size:14
Alignment explanation
Indices: 18467545--18467605 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
18467535 AAAATGAAAG
*
18467545 AAAAAA-AAACTC-
1 AAAAAATAAAATCA
* *
18467557 AAAATATAAAATGA
1 AAAAAATAAAATCA
18467571 ATAAAAATAAAATCA
1 A-AAAAATAAAATCA
18467586 AAAAAATAAAAAT-A
1 AAAAAAT-AAAATCA
18467600 AAAAAA
1 AAAAAA
18467606 GAGATACATG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 14 0.35
15 17 0.43
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAAATAAAATCA
Found at i:18467589 original size:29 final size:29
Alignment explanation
Indices: 18467535--18467596 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
18467525 AATAAATTAA
*
18467535 AAAATGAAAGAAAAAAAAACTCAAAATAT
1 AAAATGAAAGAAAAAAAAACTCAAAAAAT
*
18467564 AAAATGAATA-AAAATAAAA-TCAAAAAAAT
1 AAAATGAA-AGAAAAAAAAACTC-AAAAAAT
18467593 AAAA
1 AAAA
18467597 ATAAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 26 0.90
30 1 0.03
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (29 bp):
AAAATGAAAGAAAAAAAAACTCAAAAAAT
Found at i:18472392 original size:27 final size:27
Alignment explanation
Indices: 18472362--18472419 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
18472352 GTTGTTTAAT
18472362 ATGTAAAATAAATATGTGACACTTTGC
1 ATGTAAAATAAATATGTGACACTTTGC
* *
18472389 ATGTTAAATAAATATGTGACATTTTGC
1 ATGTAAAATAAATATGTGACACTTTGC
18472416 ATGT
1 ATGT
18472420 CAGACACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (27 bp):
ATGTAAAATAAATATGTGACACTTTGC
Found at i:18473745 original size:3 final size:3
Alignment explanation
Indices: 18473737--18473763 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18473727 ACTAGTTACA
18473737 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
18473764 TTCACTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18473861 original size:16 final size:17
Alignment explanation
Indices: 18473832--18473871 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
18473822 TTGATAATTT
*
18473832 TAAATATAATATAAAAA
1 TAAATATAAAATAAAAA
18473849 TAAA-ATAAAAT-AAAA
1 TAAATATAAAATAAAAA
18473864 T-AATATAA
1 TAAATATAA
18473872 TTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.10
15 9 0.43
16 6 0.29
17 4 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAATATAAAATAAAAA
Found at i:18476920 original size:53 final size:53
Alignment explanation
Indices: 18476797--18476921 Score: 157
Period size: 53 Copynumber: 2.4 Consensus size: 53
18476787 TCTCTCTTTA
* * *
18476797 TTTTT-TTTTTTTATTTCTAAATTTTTCATCATTTGGGACAATTTAGAAATT-
1 TTTTTATTTTTTTATTTTTAAATTTTTCACCATTTGGGACTATTTAGAAATTC
* *
18476848 TTTTT-TTTTTTGAAATTTTTAAATTTTTCACCATTTGGGCCTATTTAGAAATTC
1 TTTTTATTTTTT--TATTTTTAAATTTTTCACCATTTGGGACTATTTAGAAATTC
*
18476902 TTTTTATTTTTTTTTTTTTA
1 TTTTTATTTTTTTATTTTTA
18476922 GAAAGAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
51 11 0.17
53 41 0.65
54 5 0.08
55 6 0.10
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.62
Consensus pattern (53 bp):
TTTTTATTTTTTTATTTTTAAATTTTTCACCATTTGGGACTATTTAGAAATTC
Found at i:18477128 original size:196 final size:196
Alignment explanation
Indices: 18476905--18477264 Score: 426
Period size: 196 Copynumber: 1.8 Consensus size: 196
18476895 GAAATTCTTT
* * *
18476905 TTATTTTTTTTTTTTTAGAAAGAAAAT-AATATGATAATTATTTTTATT-AAAATTTCATTTAAA
1 TTATTTTTATTTTTTTAGAAAGAAAATAAATAT--TAATTATTGTTATTGAAAATTT-ATCTAAA
** * * * *
18476968 TT-TTTTACTATTTCAGACAAATTTAAA-GAAATTTCTCACCTAGAGATTTCT-TAAGGAATTTA
63 TTATTCCACAATTTCAGACAAATTTAAACAAAATTTCTCACCTAGAAATTT-TATAA-AAATTTA
* * * *
18477030 TCATTTGAAATTTTTA-AGAATCTCATCCTTGGATAATTATCGAATATTTTCAACCCAAATTTTT
126 CCATTTAAAATTTCTATA-AATCTCATCATTGGATAATTATCGAATATTTTCAACCCAAATTTTT
18477094 ATTTTTA
190 ATTTTTA
* ** *
18477101 TTATTTTTATTTTTTTGGATTGAAAATAAATATTAATTATTGTTATTGAAACTTTATCTAAATTA
1 TTATTTTTATTTTTTTAGAAAGAAAATAAATATTAATTATTGTTATTGAAAATTTATCTAAATTA
** * *
18477166 TTCCACAATTTGGGATAAATTTAAACAAAATTTCTCATCTAGAAATTTTATAAAAATTTACCATT
66 TTCCACAATTTCAGACAAATTTAAACAAAATTTCTCACCTAGAAATTTTATAAAAATTTACCATT
*
18477231 TAAAATTTCTATAAATTTCATCATTGGATAATTA
131 TAAAATTTCTATAAATCTCATCATTGGATAATTA
18477265 ATATTTATTC
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
195 21 0.15
196 87 0.64
197 28 0.21
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (196 bp):
TTATTTTTATTTTTTTAGAAAGAAAATAAATATTAATTATTGTTATTGAAAATTTATCTAAATTA
TTCCACAATTTCAGACAAATTTAAACAAAATTTCTCACCTAGAAATTTTATAAAAATTTACCATT
TAAAATTTCTATAAATCTCATCATTGGATAATTATCGAATATTTTCAACCCAAATTTTTATTTTT
A
Found at i:18477221 original size:26 final size:26
Alignment explanation
Indices: 18477192--18477245 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
18477182 AAATTTAAAC
18477192 AAAATTT-CTCATCTAGAAATTT-TATA
1 AAAATTTAC-CATCTA-AAATTTCTATA
*
18477218 AAAATTTACCATTTAAAATTTCTATA
1 AAAATTTACCATCTAAAATTTCTATA
18477244 AA
1 AA
18477246 TTTCATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 18 0.72
27 1 0.04
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAATTTACCATCTAAAATTTCTATA
Found at i:18477255 original size:25 final size:26
Alignment explanation
Indices: 18477192--18477255 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
18477182 AAATTTAAAC
*
18477192 AAAATTTC-TCATCTAGAAATTTTAT
1 AAAATTTCATCATTTAGAAATTTTAT
*
18477217 AAAAATTT-ACCATTTA-AAATTTCTAT
1 -AAAATTTCATCATTTAGAAATTT-TAT
18477243 -AAATTTCATCATT
1 AAAATTTCATCATT
18477256 GGATAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 6 0.19
25 11 0.34
26 15 0.47
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (26 bp):
AAAATTTCATCATTTAGAAATTTTAT
Found at i:18478305 original size:18 final size:18
Alignment explanation
Indices: 18478274--18478308 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18478264 AACACACTTA
*
18478274 TTTTTGTTTGTTTTTTTG
1 TTTTTGTTTATTTTTTTG
*
18478292 TTTTTTTTTATTTTTTT
1 TTTTTGTTTATTTTTTT
18478309 TAAACTTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.89
Consensus pattern (18 bp):
TTTTTGTTTATTTTTTTG
Found at i:18478453 original size:36 final size:37
Alignment explanation
Indices: 18478402--18478480 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 37
18478392 TTTGAAAAAT
* * *
18478402 AAAATGCTCACCTAAATAAAGGCACCACTAC-TTTGA
1 AAAATGCTCACCTAAACAAAAGCACCACAACTTTTGA
*
18478438 AAAATGCTCATCTAAACAAAAGCACCACAACTTTTTGA
1 AAAATGCTCACCTAAACAAAAGCACCACAAC-TTTTGA
18478476 AAAAT
1 AAAAT
18478481 AAATTGTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 27 0.73
38 10 0.27
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (37 bp):
AAAATGCTCACCTAAACAAAAGCACCACAACTTTTGA
Found at i:18478496 original size:79 final size:78
Alignment explanation
Indices: 18478365--18478521 Score: 201
Period size: 79 Copynumber: 2.0 Consensus size: 78
18478355 AATAAATTAA
* * * *
18478365 GCTCATCTAAACAGAGGCACCATAATTTTTGAAAAATAAAATGCTCACCTAAATA-AAGGCACCA
1 GCTCATCTAAACAAAAGCACCACAATTTTTGAAAAATAAAATGCTCACCTAAACAGAA-GCACCA
*
18478429 CTACTTTGAAAAAT
65 CAACTTTGAAAAAT
* *
18478443 GCTCATCTAAACAAAAGCACCACAACTTTTTGAAAAATAAATTGTTC-CTCTAAACAGAAGCACC
1 GCTCATCTAAACAAAAGCACCACAA-TTTTTGAAAAATAAAATGCTCAC-CTAAACAGAAGCACC
*
18478507 ACAACTTTGTAAAAT
64 ACAACTTTGAAAAAT
18478522 AAATTTCTCC
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 23 0.34
79 43 0.63
80 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (78 bp):
GCTCATCTAAACAAAAGCACCACAATTTTTGAAAAATAAAATGCTCACCTAAACAGAAGCACCAC
AACTTTGAAAAAT
Found at i:18478547 original size:41 final size:41
Alignment explanation
Indices: 18478365--18478697 Score: 279
Period size: 41 Copynumber: 8.1 Consensus size: 41
18478355 AATAAATTAA
* * * *
18478365 GCTCATCTAAACAGAGGCACCATAATTTTTGAAAAATAAAAT
1 GCTCCTCTAAACAAAGGCACCACAA-CTTTGAAAAATAAAAT
* *
18478407 GCTCAC-CTAAATAAAGGCACCACTACTTTG----A-AAAAT
1 GCTC-CTCTAAACAAAGGCACCACAACTTTGAAAAATAAAAT
* * *
18478443 GCTCATCTAAACAAAAGCACCACAACTTTTTGAAAAATAAATT
1 GCTCCTCTAAACAAAGGCACCACAAC--TTTGAAAAATAAAAT
* * *
18478486 GTTCCTCTAAACAGAA-GCACCACAACTTTGTAAAATAAATT
1 GCTCCTCTAAACA-AAGGCACCACAACTTTGAAAAATAAAAT
* * * * * *
18478527 TCTCCTTTAAATAGAGGCACCACAACTTTGAAAAAAAAAAA
1 GCTCCTCTAAACAAAGGCACCACAACTTTGAAAAATAAAAT
* *
18478568 GCTCCTCTAAACAAAGGCACCATAACTTTAAAAAAATAAAAT
1 GCTCCTCTAAACAAAGGCACCACAACTTT-GAAAAATAAAAT
*
18478610 GCTCCTCTAAAAAAAGGCACCACAACTTTG-AAAATCAAAAT
1 GCTCCTCTAAACAAAGGCACCACAACTTTGAAAAAT-AAAAT
* * * * ***
18478651 GCT-TTTTAAACAGAGACACTGTAACTTTGAAAAAATAAAAT
1 GCTCCTCTAAACAAAGGCACCACAACTTTG-AAAAATAAAAT
18478692 GCTCCT
1 GCTCCT
18478698 TGACGATTAT
Statistics
Matches: 232, Mismatches: 43, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
36 26 0.11
37 1 0.00
38 4 0.02
40 24 0.10
41 88 0.38
42 62 0.27
43 25 0.11
44 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAAAGGCACCACAACTTTGAAAAATAAAAT
Found at i:18478636 original size:124 final size:124
Alignment explanation
Indices: 18478437--18478697 Score: 312
Period size: 124 Copynumber: 2.1 Consensus size: 124
18478427 CACTACTTTG
* ** * * *
18478437 AAAAATGCTCATCTAAACAAAAGCACCACAACTTTTTGAAAAATAAATTGTTCCTCTAAACAGAA
1 AAAAATGCTCCTCTAAACAAAAGCACCACAACTTTTAAAAAAATAAAATGCTCCTCTAAACAAAA
* * * *
18478502 GCACCACAACTTTGTAAAAT-AAATTTCTCCTTTAAATAGAGGCACCACAACTTTGAAAAA
66 GCACCACAACTTTG-AAAATCAAAATGCT-CTTTAAACAGAGACACCACAACTTTGAAAAA
* * *
18478562 AAAAAAGCTCCTCTAAACAAAGGCACCATAAC-TTTAAAAAAATAAAATGCTCCTCTAAA-AAAA
1 AAAAATGCTCCTCTAAACAAAAGCACCACAACTTTTAAAAAAATAAAATGCTCCTCTAAACAAAA
* ***
18478625 GGCACCACAACTTTGAAAATCAAAATGCTTTTTAAACAGAGACACTGTAACTTTGAAAAA
66 -GCACCACAACTTTGAAAATCAAAATGCTCTTTAAACAGAGACACCACAACTTTGAAAAA
18478685 ATAAAATGCTCCT
1 A-AAAATGCTCCT
18478698 TGACGATTAT
Statistics
Matches: 115, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
123 34 0.30
124 53 0.46
125 28 0.24
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.24
Consensus pattern (124 bp):
AAAAATGCTCCTCTAAACAAAAGCACCACAACTTTTAAAAAAATAAAATGCTCCTCTAAACAAAA
GCACCACAACTTTGAAAATCAAAATGCTCTTTAAACAGAGACACCACAACTTTGAAAAA
Found at i:18479113 original size:58 final size:58
Alignment explanation
Indices: 18479048--18479199 Score: 227
Period size: 58 Copynumber: 2.6 Consensus size: 58
18479038 CATTTGAAAT
* *
18479048 TCAAAGATTCTCATTTGAGTTTAAAGATTCACATT-AGACAAATTTTGGGTTTCACACC
1 TCAAAGATTCTCATTTGAGTTCAAAGATTCACATTCA-ACAAATTTTGAGTTTCACACC
18479106 TCAAAGATTCTCATTTGAGTTCGAAA-ATTCACATTCAACAAATTTTGAGTTTCACACC
1 TCAAAGATTCTCATTTGAGTTC-AAAGATTCACATTCAACAAATTTTGAGTTTCACACC
* *
18479164 TCAAAGATTCTCATTTGAAATTCAAAGATTCTCATT
1 TCAAAGATTCTCATTTG-AGTTCAAAGATTCACATT
18479200 TGAAATTCAA
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
58 70 0.81
59 16 0.19
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (58 bp):
TCAAAGATTCTCATTTGAGTTCAAAGATTCACATTCAACAAATTTTGAGTTTCACACC
Found at i:18479188 original size:21 final size:21
Alignment explanation
Indices: 18479164--18479225 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
18479154 GTTTCACACC
18479164 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAT
18479185 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAT
* *
18479206 TCAAAGATTCACACTTGAAA
1 TCAAAGATTCTCATTTGAAA
18479226 ACTCAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAT
Found at i:18479287 original size:75 final size:71
Alignment explanation
Indices: 18479163--18479307 Score: 184
Period size: 75 Copynumber: 2.0 Consensus size: 71
18479153 AGTTTCACAC
* * *
18479163 CTCAAAGATTCTCATTTGAAATTCAAAGATTCTCATTTGAAATTCAAAGATTCACACTTGAAAAC
1 CTCAAAAATTCTCATTTGAAATTCAAAGATTATCATTTGAAACTCAAAGATTCACACTTGAAAAC
18479228 TCAAAA
66 TCAAAA
* * *
18479234 CTCAAAAATTCTCATTTGAAAATGCCTTAAAGATTATCATTT-AAGACTCAAAGATTCTCATTTG
1 CTCAAAAATTCTCATTTG-AAAT---TCAAAGATTATCATTTGAA-ACTCAAAGATTCACACTTG
18479298 AAAACTCAAA
61 AAAACTCAAA
18479308 GATTCTCATT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
71 17 0.27
72 4 0.06
74 2 0.03
75 40 0.63
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (71 bp):
CTCAAAAATTCTCATTTGAAATTCAAAGATTATCATTTGAAACTCAAAGATTCACACTTGAAAAC
TCAAAA
Found at i:18479307 original size:22 final size:22
Alignment explanation
Indices: 18479230--18479322 Score: 116
Period size: 22 Copynumber: 4.1 Consensus size: 22
18479220 TTGAAAACTC
*
18479230 AAAACTCAAAAATTCTCATTTG
1 AAAACTCAAAGATTCTCATTTG
* *
18479252 AAAATGCCTTAAAGATTATCATTT-
1 AAAA---CTCAAAGATTCTCATTTG
*
18479276 AAGACTCAAAGATTCTCATTTG
1 AAAACTCAAAGATTCTCATTTG
18479298 AAAACTCAAAGATTCTCATTTG
1 AAAACTCAAAGATTCTCATTTG
18479320 AAA
1 AAA
18479323 TTCAAAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.25
22 28 0.47
24 3 0.05
25 14 0.23
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (22 bp):
AAAACTCAAAGATTCTCATTTG
Found at i:18480725 original size:21 final size:20
Alignment explanation
Indices: 18480699--18480743 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
18480689 CATTTTCATC
18480699 TTTTTTCCATTCTTTCATTTT
1 TTTTTTCCATTCTTTC-TTTT
** *
18480720 TTTTTTCTTTTTTTTCTTTT
1 TTTTTTCCATTCTTTCTTTT
18480740 TTTT
1 TTTT
18480744 CTTTTTCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCCATTCTTTCTTTT
Found at i:18480730 original size:9 final size:9
Alignment explanation
Indices: 18480718--18480749 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
18480708 TTCTTTCATT
18480718 TTTTTTTTC
1 TTTTTTTTC
18480727 TTTTTTTTC
1 TTTTTTTTC
18480736 TTTTTTTTC
1 TTTTTTTTC
18480745 TTTTT
1 TTTTT
18480750 CATCTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:18480755 original size:18 final size:18
Alignment explanation
Indices: 18480691--18480757 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
18480681 TTTTCTCTCA
*
18480691 TTTTCATC-TTTTTTCCAT
1 TTTTCATCTTTTTTTTC-T
*
18480709 TCTTTCATTTTTTTTTTCT
1 T-TTTCATCTTTTTTTTCT
**
18480728 TTTTTTTCTTTTTTTTCT
1 TTTTCATCTTTTTTTTCT
18480746 TTTTCATCTTTT
1 TTTTCATCTTTT
18480758 GCCATCCATG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 25 0.62
19 8 0.20
20 7 0.17
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCATCTTTTTTTTCT
Found at i:18487375 original size:20 final size:20
Alignment explanation
Indices: 18487346--18487397 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
18487336 ACATTGATAT
18487346 CAAT-TTCAGGCATATCAGA
1 CAATGTTCAGGCATATCAGA
18487365 CAATGTTCAGGCATATCAGA
1 CAATGTTCAGGCATATCAGA
18487385 CAATGTTCAGGCA
1 CAATGTTCAGGCA
18487398 AATAAATCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
CAATGTTCAGGCATATCAGA
Found at i:18490494 original size:20 final size:21
Alignment explanation
Indices: 18490458--18490509 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
18490448 CCCGAAATTA
18490458 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
18490480 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
18490501 AT-AAATATT
1 ATAAAATATT
18490510 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:18490500 original size:21 final size:22
Alignment explanation
Indices: 18490458--18490509 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
18490448 CCCGAAATTA
18490458 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
18490480 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
18490501 AT-AAATATT
1 ATAAAATATT
18490510 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:18492853 original size:8 final size:9
Alignment explanation
Indices: 18492840--18492872 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
18492830 ATATAAAATA
18492840 ATTTTTA-T
1 ATTTTTATT
18492848 ATTTTTATT
1 ATTTTTATT
18492857 ATATTTTATT
1 AT-TTTTATT
18492867 ATTTTT
1 ATTTTT
18492873 CAAAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.30
9 7 0.30
10 9 0.39
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTATT
Found at i:18493252 original size:17 final size:17
Alignment explanation
Indices: 18493223--18493269 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
18493213 ACGTGCATTT
*
18493223 TTATT-TTTATTTTTTTC
1 TTATTCTTT-TTTTTTCC
18493240 TTATTCTTTTTTTTTCC
1 TTATTCTTTTTTTTTCC
*
18493257 TT-TCCTTTTTTTT
1 TTATTCTTTTTTTT
18493270 AGTAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 10 0.37
17 14 0.52
18 3 0.11
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (17 bp):
TTATTCTTTTTTTTTCC
Found at i:18493265 original size:15 final size:16
Alignment explanation
Indices: 18493232--18493269 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
18493222 TTTATTTTTA
* *
18493232 TTTTTTTCTTATTCTT
1 TTTTTTTCCTATTCCT
18493248 TTTTTTTCCT-TTCCT
1 TTTTTTTCCTATTCCT
18493263 TTTTTTT
1 TTTTTTT
18493270 AGTAACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTCCTATTCCT
Found at i:18495271 original size:3 final size:3
Alignment explanation
Indices: 18495263--18495314 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
18495253 ATAATTACCT
18495263 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18495311 TTA T
1 TTA T
18495315 CAAGATTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18501781 original size:20 final size:20
Alignment explanation
Indices: 18501756--18501800 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18501746 TTTAAAAATG
*
18501756 GAAAAAATGGAAGAAATTAA
1 GAAAAAATCGAAGAAATTAA
*
18501776 GAAAAAATCTAAGAAATTAA
1 GAAAAAATCGAAGAAATTAA
18501796 -AAAAA
1 GAAAAA
18501801 TTCAATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (20 bp):
GAAAAAATCGAAGAAATTAA
Found at i:18501886 original size:27 final size:27
Alignment explanation
Indices: 18501841--18501897 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
18501831 AAAATTGTGG
*
18501841 AAAATCCAAAAAACCAAAAACTTTAAA
1 AAAATCCAAAAAACCAAAAAATTTAAA
* ** *
18501868 AAAATCCCAAAAATTAAAAAATTTTAA
1 AAAATCCAAAAAACCAAAAAATTTAAA
18501895 AAA
1 AAA
18501898 TTGAAATAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (27 bp):
AAAATCCAAAAAACCAAAAAATTTAAA
Found at i:18502030 original size:20 final size:18
Alignment explanation
Indices: 18502007--18502043 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
18501997 AACATATATT
18502007 TAAAAAATCTAAGAAAAATA
1 TAAAAAAT-TAA-AAAAATA
18502027 TAAAAAATTAAAAAAAT
1 TAAAAAATTAAAAAAAT
18502044 CCAAAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
TAAAAAATTAAAAAAATA
Found at i:18502141 original size:9 final size:9
Alignment explanation
Indices: 18502098--18502161 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
18502088 ATCAAATTTT
18502098 TTAAAAAAA
1 TTAAAAAAA
18502107 TTCAAACAAAA
1 TT-AAA-AAAA
*
18502118 TTGAAAAAA
1 TTAAAAAAA
**
18502127 GAAAAAAAA
1 TTAAAAAAA
18502136 TT--AAAAA
1 TTAAAAAAA
*
18502143 TTTAAAAAA
1 TTAAAAAAA
18502152 TCTAAAAAAA
1 T-TAAAAAAA
18502162 GAAAAATCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
7 7 0.16
9 18 0.42
10 12 0.28
11 6 0.14
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:18502413 original size:17 final size:17
Alignment explanation
Indices: 18502388--18502420 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18502378 ATTTGTTATT
18502388 TTTTAATTTTGATTTTC
1 TTTTAATTTTGATTTTC
*
18502405 TTTTGATTTTGATTTT
1 TTTTAATTTTGATTTT
18502421 TTATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (17 bp):
TTTTAATTTTGATTTTC
Found at i:18502709 original size:16 final size:17
Alignment explanation
Indices: 18502688--18502721 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18502678 ACATTTTATG
18502688 TTATTGCAAGAT-TTTT
1 TTATTGCAAGATATTTT
*
18502704 TTATTGCATGATATTTT
1 TTATTGCAAGATATTTT
18502721 T
1 T
18502722 GTATGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
TTATTGCAAGATATTTT
Found at i:18503898 original size:13 final size:13
Alignment explanation
Indices: 18503880--18503904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18503870 ATTTTAATTC
18503880 AATTAATTTATAT
1 AATTAATTTATAT
18503893 AATTAATTTATA
1 AATTAATTTATA
18503905 AAATAACATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTTATAT
Found at i:18504962 original size:18 final size:18
Alignment explanation
Indices: 18504941--18504980 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18504931 TAAATAATAT
18504941 ATTTATATTCAATATTTA
1 ATTTATATTCAATATTTA
* * *
18504959 ATTTGTTTTCAGTATTTA
1 ATTTATATTCAATATTTA
18504977 ATTT
1 ATTT
18504981 TTAATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTATATTCAATATTTA
Found at i:18508012 original size:18 final size:17
Alignment explanation
Indices: 18507991--18508039 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
18507981 AAATATTATT
18507991 TTAAATATAAATATAAAA
1 TTAAATATAAATA-AAAA
*
18508009 TTAAATATATATAAAAA
1 TTAAATATAAATAAAAA
* *
18508026 -TATATATAATTAAA
1 TTAAATATAAATAAA
18508040 TGTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 11 0.41
17 4 0.15
18 12 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAATATAAATAAAAA
Found at i:18508032 original size:16 final size:16
Alignment explanation
Indices: 18507995--18508033 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18507985 ATTATTTTAA
* *
18507995 ATATAAATATAAAATT
1 ATATATATATAAAAAT
*
18508011 AAATATATATAAAAAT
1 ATATATATATAAAAAT
18508027 ATATATA
1 ATATATA
18508034 ATTAAATGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATATATAAAAAT
Found at i:18512244 original size:2 final size:2
Alignment explanation
Indices: 18512233--18512268 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18512223 AATTGAAACC
18512233 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18512269 TATTTTGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18512881 original size:27 final size:29
Alignment explanation
Indices: 18512830--18512884 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
18512820 AAATAAACAA
*
18512830 ATATAAGTGTAATTATTAATATAAATTAT
1 ATATAAATGTAATTATTAATATAAATTAT
*
18512859 ATATAAATGTAATT-TTAA-CTAAATTA
1 ATATAAATGTAATTATTAATATAAATTA
18512885 AGGTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 4 0.17
29 13 0.54
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (29 bp):
ATATAAATGTAATTATTAATATAAATTAT
Found at i:18513524 original size:17 final size:17
Alignment explanation
Indices: 18513504--18513544 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18513494 AGTAAAAATT
*
18513504 AAAAAAAAGACCCAAAA
1 AAAAAAAAAACCCAAAA
**
18513521 AAAAAAAAAACTTAAAA
1 AAAAAAAAAACCCAAAA
18513538 AAAAAAA
1 AAAAAAA
18513545 GAGTTAGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.83, C:0.10, G:0.02, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAACCCAAAA
Found at i:18513776 original size:30 final size:28
Alignment explanation
Indices: 18513743--18513810 Score: 66
Period size: 31 Copynumber: 2.3 Consensus size: 28
18513733 AATTTATTTA
*
18513743 ATAAAAAAATAACT-AATTAATAAATAATAA
1 ATAAAAAAATAA-TAAAATAAT-AATAAT-A
**
18513773 ATAATAAATTTAATAAAATAATAATAATA
1 ATAA-AAAAATAATAAAATAATAATAATA
18513802 ATAAAAAAA
1 ATAAAAAAA
18513811 GAAAAGAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.10
29 5 0.16
30 11 0.35
31 12 0.39
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAAAAAAATAATAAAATAATAATAATA
Found at i:18513779 original size:14 final size:14
Alignment explanation
Indices: 18513749--18513802 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
18513739 TTTAATAAAA
*
18513749 AAATAACTAATTAAT
1 AAATAA-TAAATAAT
18513764 AAATAATAAATAAT
1 AAATAATAAATAAT
18513778 AAATTTAATAAAATAAT
1 AAA--TAAT-AAATAAT
18513795 -AATAATAA
1 AAATAATAA
18513803 TAAAAAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 2 0.06
14 14 0.40
15 6 0.17
16 6 0.17
17 7 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATAATAAATAAT
Found at i:18513785 original size:23 final size:23
Alignment explanation
Indices: 18513759--18513802 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
18513749 AAATAACTAA
18513759 TTAAT-AAATAATAAATAATAAAT
1 TTAATAAAATAAT-AATAATAAAT
18513782 TTAATAAAATAATAATAATAA
1 TTAATAAAATAATAATAATAA
18513803 TAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAATAAAATAATAATAATAAAT
Found at i:18514232 original size:16 final size:16
Alignment explanation
Indices: 18514211--18514241 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18514201 TTCATACGTG
18514211 ATTAAGTAAAAGTAAA
1 ATTAAGTAAAAGTAAA
18514227 ATTAAGTAAAAGTAA
1 ATTAAGTAAAAGTAA
18514242 CTAAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (16 bp):
ATTAAGTAAAAGTAAA
Found at i:18534765 original size:33 final size:33
Alignment explanation
Indices: 18534728--18534814 Score: 77
Period size: 33 Copynumber: 2.6 Consensus size: 33
18534718 ATATAGGATA
* *
18534728 TTTAAGAGCTTATATTATAAT-TTTTGAGATTTT
1 TTTAAGAGCTTAAATTATAATCTTTAGAGA-TTT
* * ** *
18534761 TTTAAAAACTTAGGTTATGATCTTTAGAGATTT
1 TTTAAGAGCTTAAATTATAATCTTTAGAGATTT
* *
18534794 TGTAAGAGGTTAAATTATAAT
1 TTTAAGAGCTTAAATTATAAT
18534815 AATTAGATTA
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
33 33 0.82
34 7 0.17
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.47
Consensus pattern (33 bp):
TTTAAGAGCTTAAATTATAATCTTTAGAGATTT
Found at i:18535030 original size:27 final size:27
Alignment explanation
Indices: 18535000--18535078 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
18534990 TGGTGAGTAT
**
18535000 AAGTAAATGATTCAATGAATTTTGGAG
1 AAGTAAATGATTCAATGAATTTTAAAG
* *
18535027 AAGTTAAA-GTTTCAATAAATTTTAAAG
1 AAG-TAAATGATTCAATGAATTTTAAAG
* *
18535054 AA-TCAATGATTTAATGAATTCTTAA
1 AAGTAAATGATTCAATGAATT-TTAA
18535079 TATAATTACT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
25 3 0.07
26 10 0.24
27 24 0.59
28 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (27 bp):
AAGTAAATGATTCAATGAATTTTAAAG
Found at i:18540434 original size:15 final size:15
Alignment explanation
Indices: 18540411--18540440 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18540401 TTAATTTTGT
*
18540411 TAATGAATAATAAAA
1 TAATAAATAATAAAA
18540426 TAATAAATAATAAAA
1 TAATAAATAATAAAA
18540441 ATAACAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:18541654 original size:56 final size:57
Alignment explanation
Indices: 18541532--18541651 Score: 136
Period size: 56 Copynumber: 2.1 Consensus size: 57
18541522 CAATTGGTGA
* * **
18541532 AAAATTTAGAAATCCAACAAAGAAAAGAGAGAATTTCTAACTAGGCCCAAATTGTGG
1 AAAATTTAGAAATCCAACAAAGAAAAGAGAAAATTTCTAACTAGGCCAAAATAATGG
* * * *
18541589 AAAATTTAGAAATCTAAGAAA-AAAAGA-AAATATTTCTAATTTGGCCAAAATAATGG
1 AAAATTTAGAAATCCAACAAAGAAAAGAGAAA-ATTTCTAACTAGGCCAAAATAATGG
18541645 AATAATT
1 AA-AATT
18541652 AGATATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
55 2 0.04
56 28 0.53
57 23 0.43
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (57 bp):
AAAATTTAGAAATCCAACAAAGAAAAGAGAAAATTTCTAACTAGGCCAAAATAATGG
Found at i:18545139 original size:23 final size:24
Alignment explanation
Indices: 18545112--18545157 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
18545102 TCTCAAATAG
*
18545112 AAAGGAAAAAG-GAAAAGCAAAAC
1 AAAGGAAAAAGAGAAAAGAAAAAC
18545135 AAAGGAAAAAGAGAAAAGAAAAA
1 AAAGGAAAAAGAGAAAAGAAAAA
18545158 TAAATACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (24 bp):
AAAGGAAAAAGAGAAAAGAAAAAC
Found at i:18545539 original size:16 final size:16
Alignment explanation
Indices: 18545501--18545556 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
18545491 CTAATAGATG
*
18545501 GAAAAAAGAGAAAAAAA
1 GAAAAAAG-GAAAAAAT
*
18545518 GGAAAAAGGAAAAAAT
1 GAAAAAAGGAAAAAAT
** *
18545534 GAAAAAAATAATAAAT
1 GAAAAAAGGAAAAAAT
18545550 GAAAAAA
1 GAAAAAA
18545557 AAGGTAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 26 0.79
17 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (16 bp):
GAAAAAAGGAAAAAAT
Found at i:18546288 original size:70 final size:70
Alignment explanation
Indices: 18546209--18546340 Score: 160
Period size: 70 Copynumber: 1.9 Consensus size: 70
18546199 ATGGCTAGTA
*
18546209 CTGAAAAGCCTGTCAA-TGGTGATCAAATGAT-GAGGGCCAATGGACGAAATTCATTCTGAAATG
1 CTGAAAAGCCTGT-AAGTGATGATCAAATGATAGAGGG-CAATGGACGAAATTCATTCTGAAATG
18546272 GTTAATG
64 GTTAATG
* * * * * * *
18546279 CTGACAAGCCTGTAAGTTATGATTAAATGATATAGGGTAATGGATGAAATTTATTCTGAAAT
1 CTGAAAAGCCTGTAAGTGATGATCAAATGATAGAGGGCAATGGACGAAATTCATTCTGAAAT
18546341 TTCTAGTGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
69 2 0.04
70 46 0.88
71 4 0.08
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (70 bp):
CTGAAAAGCCTGTAAGTGATGATCAAATGATAGAGGGCAATGGACGAAATTCATTCTGAAATGGT
TAATG
Found at i:18546835 original size:46 final size:46
Alignment explanation
Indices: 18546768--18547538 Score: 677
Period size: 46 Copynumber: 16.8 Consensus size: 46
18546758 ATGAATCTTC
* * * * *
18546768 AAATGAAAACCTCTAAGTCTTAAATGAGAATCTTTAATACATTTTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * **
18546814 AAATGTGAACCTTTGAGTCTTAAATGAGAATCTCTAAGATATTTTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * * *
18546860 AAATGAGAAGCTTTGAGTCTTTAATGAAAATCTTTAAGATGTTTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * *
18546906 AAATGAGAACCTTTGAGTGTTAAATGAGAATCTTTAAAATGTTTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * * *
18546952 AATTAAGAACCTTTGAGTCTTAAATGTGAATCTTTAAGATGTTTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * * * *
18546998 AAATAAGAATCTTTAAGATGTTTTCAATTGAGAACCTTT--GA-G-TCTT
1 AAATGAGAACCTTT--GA-GTCTT-AAATGAGAATCTTTAAGACGTTTTT
* * * *
18547044 AAATGAGAATCTTTAATATGTTTTCAAATGAGAATCTTT--GA-G-TCTT
1 AAATGAGAACCTTT--GA-GTCTT-AAATGAGAATCTTTAAGACGTTTTT
* ** * * *
18547090 AAATGAAAATATTTAAAATGTTTTCAAATGAGAATCTTTAAGATGTTTTT
1 AAATGAGAACCTTT--GA-GTCTT-AAATGAGAATCTTTAAGACGTTTTT
* ** *
18547140 AAATGAGAACCTTTGATTCTTAAATGAGAATCTTTAAGACAATTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * *
18547186 AAATGAAAACCTTTGAGTATTAAATGAGAATCCTTAAGACGTTTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * ** *
18547232 AAATGAGAACCTTTAAGTCTTAAATGTGAATCTTTAAGATATTTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * *
18547278 AAATGAGAAACTTTGAGTATTAAATGAGAATCTTTAAGATGTTTTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * *
18547324 AAACGAGAACCTTTAAGTATTAAATGAGAATCTTTAAGATGTTTTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * *
18547370 AAACGAGAACCTTTAAGTATTAAATGAGAATCTTTAAGACGCTTTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * * * *
18547416 AAATGAGAACCTTTTAGTCTTAAATGATAATTTTTAAGACATTTTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* *
18547462 AAATGAGAACCTTTGAGTTTTAAATGAGAATCTTT--GA-G-TCTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
* * *
18547504 AAATAAGAATCTTTGAGT-TTCAAATAAGAATCTTT
1 AAATGAGAACCTTTGAGTCTT-AAATGAGAATCTTT
18547539 GAAAATCTTT
Statistics
Matches: 624, Mismatches: 92, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.00
42 31 0.05
44 2 0.00
46 548 0.88
47 4 0.01
48 7 0.01
49 5 0.01
50 25 0.04
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (46 bp):
AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTT
Found at i:18546886 original size:21 final size:20
Alignment explanation
Indices: 18546856--18547540 Score: 130
Period size: 21 Copynumber: 29.9 Consensus size: 20
18546846 TCTAAGATAT
*
18546856 TTTTAAATGAGAAGCTTTGAG
1 TTTT-AATGAGAATCTTTGAG
*
18546877 TCTTTAATGAAAATCTTTAAGATG
1 T-TTTAATGAGAATCTTT--GA-G
*
18546901 TTTTCAAATGAGAACCTTTGAG
1 TTTT--AATGAGAATCTTTGAG
* *
18546923 TGTTAAATGAGAATCTTTAAAATG
1 T-TTTAATGAGAATCTTT--GA-G
* *
18546947 TTTTCAATTAAGAACCTTTGAG
1 TTTT-AA-TGAGAATCTTTGAG
* *
18546969 TCTTAAATGTGAATCTTTAAGATG
1 T-TTTAATGAGAATCTTT--GA-G
*
18546993 TTTTCAAATAAGAATCTTTAAGATG
1 TTTT--AATGAGAATCTTT--GA-G
*
18547018 TTTTCAATTGAGAACCTTTGAG
1 TTTT-AA-TGAGAATCTTTGAG
* *
18547040 TCTTAAATGAGAATCTTTAATATG
1 T-TTTAATGAGAATCTTT--GA-G
18547064 TTTTCAAATGAGAATCTTTGAG
1 TTTT--AATGAGAATCTTTGAG
* * * *
18547086 TCTTAAATGAAAATATTTAAAATG
1 T-TTTAATGAGAATCTTT--GA-G
18547110 TTTTCAAATGAGAATCTTTAAGATG
1 TTTT--AATGAGAATCTTT--GA-G
*
18547135 TTTTTAAATGAGAACCTTTGA-
1 -TTTT-AATGAGAATCTTTGAG
*
18547156 TTCTTAAATGAGAATCTTTAAGACAA
1 TT-TT-AATGAGAATCTTT--G--AG
* * *
18547182 TTTCAAATGAAAACCTTTGAG
1 TTT-TAATGAGAATCTTTGAG
* *
18547203 TATTAAATGAGAATCCTTAAGACG
1 T-TTTAATGAGAAT-CTT-TGA-G
* *
18547227 TTTTCAAATGAGAACCTTTAAG
1 TTTT--AATGAGAATCTTTGAG
* * *
18547249 TCTTAAATGTGAATCTTTAAGATA
1 T-TTTAATGAGAATCTTT--GA-G
*
18547273 TTTTCAAATGAGAAACTTTGAG
1 TTTT--AATGAGAATCTTTGAG
*
18547295 TATTAAATGAGAATCTTTAAGATG
1 T-TTTAATGAGAATCTTT--GA-G
* * *
18547319 TTTTTAAACGAGAACCTTTAAG
1 -TTTT-AATGAGAATCTTTGAG
*
18547341 TATTAAATGAGAATCTTTAAGATG
1 T-TTTAATGAGAATCTTT--GA-G
* * *
18547365 TTTTTAAACGAGAACCTTTAAG
1 -TTTT-AATGAGAATCTTTGAG
*
18547387 TATTAAATGAGAATCTTTAAGACG
1 T-TTTAATGAGAATCTTT--GA-G
* *
18547411 CTTTTAAATGAGAACCTTTTAG
1 -TTTT-AATGAGAATCTTTGAG
* * * *
18547433 TCTTAAATGATAATTTTTAAGACA
1 T-TTTAATGAGAATCTTT--GA-G
*
18547457 TTTTCAAATGAGAACCTTTGAG
1 TTTT--AATGAGAATCTTTGAG
18547479 TTTTAAATGAGAATCTTTGAG
1 TTTT-AATGAGAATCTTTGAG
* *
18547500 TCTTAAATAAGAATCTTTGAG
1 T-TTTAATGAGAATCTTTGAG
* *
18547521 TTTCAAATAAGAATCTTTGA
1 TTT-TAATGAGAATCTTTGA
18547541 AAATCTTTAA
Statistics
Matches: 496, Mismatches: 91, Indels: 154
0.67 0.12 0.21
Matches are distributed among these distances:
20 4 0.01
21 185 0.37
22 38 0.08
23 62 0.12
24 30 0.06
25 171 0.34
26 6 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTTAATGAGAATCTTTGAG
Found at i:18546929 original size:92 final size:92
Alignment explanation
Indices: 18546768--18547538 Score: 749
Period size: 92 Copynumber: 8.4 Consensus size: 92
18546758 ATGAATCTTC
* * * * * * * *
18546768 AAATGAAAACCTCTAAGTCTTAAATGAGAATCTTTAATACATTTTTAAATGTGAACCTTTGAGTC
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
* *
18546833 TTAAATGAGAATCTCTAAGATATTTTT
66 TTAAATGAGAATCTTTAAGATGTTTTT
* * * * *
18546860 AAATGAGAAGCTTTGAGTCTTTAATGAAAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTG
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
* *
18546925 TTAAATGAGAATCTTTAAAATGTTTTC
66 TTAAATGAGAATCTTTAAGATGTTTTT
* * * * * *
18546952 AATTAAGAACCTTTGAGTCTTAAATGTGAATCTTTAAGATGTTTTCAAATAAGAATCTTTAAGAT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTT--GA-
* * * *
18547017 GTTTTCAATTGAGAACCTTT--GA-G-TCTT
63 GTATT-AAATGAGAATCTTTAAGATGTTTTT
* * * * * * **
18547044 AAATGAGAATCTTTAATATGTTTTCAAATGAGAATCTTT--GA-GTCTT-AAATGAAAATATTTA
1 AAATGAGAACCTTT--GA-GTCTT-AAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTT-
* *
18547105 AAATGTTTTCAAATGAGAATCTTTAAGATGTTTTT
61 -GA-GTATT-AAATGAGAATCTTTAAGATGTTTTT
* * * *
18547140 AAATGAGAACCTTTGATTCTTAAATGAGAATCTTTAAGACAATTTCAAATGAAAACCTTTGAGTA
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
* * *
18547205 TTAAATGAGAATCCTTAAGACGTTTTC
66 TTAAATGAGAATCTTTAAGATGTTTTT
* * *
18547232 AAATGAGAACCTTTAAGTCTTAAATGTGAATCTTTAAGATATTTTCAAATGAGAAACTTTGAGTA
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
18547297 TTAAATGAGAATCTTTAAGATGTTTTT
66 TTAAATGAGAATCTTTAAGATGTTTTT
* * * * * * *
18547324 AAACGAGAACCTTTAAGTATTAAATGAGAATCTTTAAGATGTTTTTAAACGAGAACCTTTAAGTA
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
* *
18547389 TTAAATGAGAATCTTTAAGACGCTTTT
66 TTAAATGAGAATCTTTAAGATGTTTTT
* * * * *
18547416 AAATGAGAACCTTTTAGTCTTAAATGATAATTTTTAAGACATTTTCAAATGAGAACCTTTGAGTT
1 AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
*
18547481 TTAAATGAGAATCTTT--GA-G-TCTT
66 TTAAATGAGAATCTTTAAGATGTTTTT
* * *
18547504 AAATAAGAATCTTTGAGT-TTCAAATAAGAATCTTT
1 AAATGAGAACCTTTGAGTCTT-AAATGAGAATCTTT
18547539 GAAAATCTTT
Statistics
Matches: 566, Mismatches: 96, Indels: 38
0.81 0.14 0.05
Matches are distributed among these distances:
87 2 0.00
88 29 0.05
89 1 0.00
90 2 0.00
92 444 0.78
93 12 0.02
94 12 0.02
95 11 0.02
96 53 0.09
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (92 bp):
AAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATATTTTCAAATGAGAACCTTTGAGTA
TTAAATGAGAATCTTTAAGATGTTTTT
Found at i:18547030 original size:117 final size:117
Alignment explanation
Indices: 18546882--18547517 Score: 570
Period size: 117 Copynumber: 5.5 Consensus size: 117
18546872 TTGAGTCTTT
* *
18546882 AATGAAAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTGTTAAATGAGAATCTTTAAAATG
1 AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAAATG
*
18546947 TTTTCAATTAAGAACCTTTGAGTCTTAAATGTGAATCTTTAAGATGTTTTCA
66 TTTTCAATTAAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCA
* * *
18546999 AATAAGAATCTTTAAGATGTTTTCAATTGAGAACCTTTGAGTCTTAAATGAGAATCTTTAATATG
1 AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAAATG
* * * * * *
18547064 TTTTCAAATGAGAATCTTTGAGTCTTAAATGAAAATATTTAAAATGTTTTCA
66 TTTTCAATTAAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCA
* * * **
18547116 AATGAGAATCTTTAAGATGTTTTTAAATGAGAACCTTTGATTCTTAAATGAGAATCTTTAAGACA
1 AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAAATG
* * * * *
18547181 ATTTCAAATGAA-AACCTTTGAGTATTAAATGAGAATCCTTAAGACGTTTTCA
66 TTTTC-AATTAAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCA
* * * * * * *
18547233 AATGAGAACCTTT-A-A-GTCTT-AAATGTGAATCTTTAAGATATTTTCAAATGAGAAACTTT--
1 AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTT--GA-GTCTT-AAATGAGAATCTTTAA
* * * * * * * * *
18547292 GA-GTATT-AAATGAGAATCTTTAAGATGTTTTTAAACGAGAACCTTT-A-A-GTATT-A
62 AATGTTTTCAATTAAGAACCTTT--GA-G-TCTTAAATGAGAATCTTTAAGATGTTTTCA
* * * * * *
18547346 AATGAGAATCTTTAAGATGTTTTTAAACGAGAACCTTTAAGTATTAAATGAGAATCTTTAAGACG
1 AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAAATG
* * * * * **
18547411 CTTTT-AAATGAGAACCTTTTAGTCTTAAATGATAATTTTTAAGACATTTTCA
66 -TTTTCAATTAAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCA
* * *
18547463 AATGAGAACCTTT--GA-GTTTT-AAATGAGAATCTTTGAGTCTTAAATAAGAATCTTT
1 AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTCTTAAATGAGAATCTTT
18547518 GAGTTTCAAA
Statistics
Matches: 423, Mismatches: 74, Indels: 48
0.78 0.14 0.09
Matches are distributed among these distances:
112 3 0.01
113 87 0.21
114 21 0.05
115 16 0.04
116 14 0.03
117 279 0.66
118 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (117 bp):
AATGAGAATCTTTAAGATGTTTTCAAATGAGAACCTTTGAGTCTTAAATGAGAATCTTTAAAATG
TTTTCAATTAAGAACCTTTGAGTCTTAAATGAGAATCTTTAAGATGTTTTCA
Found at i:18547554 original size:31 final size:32
Alignment explanation
Indices: 18547511--18547576 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
18547501 CTTAAATAAG
* *
18547511 AATCTTTGAG-TTTCAAATAAGAATCTTTGAA
1 AATCTTTAAGTTTTCAAATAAGAATCTTTAAA
*
18547542 AATCTTTAAGTTTTTCAAATGAGAATCTTTAAA
1 AATCTTTAAG-TTTTCAAATAAGAATCTTTAAA
18547575 AA
1 AA
18547577 GAACTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 9 0.30
33 21 0.70
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (32 bp):
AATCTTTAAGTTTTCAAATAAGAATCTTTAAA
Found at i:18553352 original size:21 final size:21
Alignment explanation
Indices: 18553306--18553353 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
18553296 ATAATAAAAT
18553306 ATTATTTTTTTTAAAATATAA
1 ATTATTTTTTTTAAAATATAA
18553327 A-TATTATTTTTT-AAATATAA
1 ATTATT-TTTTTTAAAATATAA
18553347 ATTATTT
1 ATTATTT
18553354 AAAATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTTTTTTTAAAATATAA
Found at i:18553353 original size:18 final size:21
Alignment explanation
Indices: 18553298--18553348 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
18553288 GACCCGAAAT
18553298 AATA-AAATATTATTTTTTTTAA
1 AATATAAATATTA--TTTTTTAA
18553320 AATATAAATATTATTTTTT-A
1 AATATAAATATTATTTTTTAA
18553340 AATATAAAT
1 AATATAAAT
18553349 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.36
21 6 0.21
22 4 0.14
23 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATATTATTTTTTAA
Found at i:18553405 original size:19 final size:21
Alignment explanation
Indices: 18553367--18553405 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
18553357 ATATCATATA
18553367 TAAATATATATAAATAAAAAT
1 TAAATATATATAAATAAAAAT
*
18553388 TAAATA-AT-TAATTAAAAA
1 TAAATATATATAAATAAAAA
18553406 AAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATATATATAAATAAAAAT
Found at i:18555787 original size:8 final size:9
Alignment explanation
Indices: 18555774--18555806 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
18555764 ATATAAAATA
18555774 ATTTTTA-T
1 ATTTTTATT
18555782 ATTTTTATT
1 ATTTTTATT
18555791 ATATTTTATT
1 AT-TTTTATT
18555801 ATTTTT
1 ATTTTT
18555807 CAAAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.30
9 7 0.30
10 9 0.39
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTATT
Found at i:18556188 original size:20 final size:19
Alignment explanation
Indices: 18556163--18556204 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
18556153 TGCATTTTTA
*
18556163 TTTTTTTT-CTTTCTTATTC
1 TTTTTTTTCCTTTCCT-TTC
18556182 TTTTTTTTCCTTTCCTTTC
1 TTTTTTTTCCTTTCCTTTC
18556201 TTTT
1 TTTT
18556205 AGTAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTTCCTTTCCTTTC
Found at i:18558210 original size:3 final size:3
Alignment explanation
Indices: 18558202--18558249 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
18558192 ATAATTACCT
18558202 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18558250 AATACAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18564735 original size:20 final size:20
Alignment explanation
Indices: 18564710--18564754 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18564700 TTTAAAAATG
*
18564710 GAAAAAATGGAAGAAATTAA
1 GAAAAAATCGAAGAAATTAA
*
18564730 GAAAAAATCTAAGAAATTAA
1 GAAAAAATCGAAGAAATTAA
18564750 -AAAAA
1 GAAAAA
18564755 TTCAATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (20 bp):
GAAAAAATCGAAGAAATTAA
Found at i:18565000 original size:20 final size:20
Alignment explanation
Indices: 18564962--18564998 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
18564952 AACATATATT
*
18564962 TAAAAAATCTAAGAAAAATA
1 TAAAAAATCTAAAAAAAATA
18564982 TAAAAAAT-TAAAAAAAA
1 TAAAAAATCTAAAAAAAA
18564999 ATCCAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (20 bp):
TAAAAAATCTAAAAAAAATA
Found at i:18565098 original size:17 final size:16
Alignment explanation
Indices: 18565066--18565126 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 16
18565056 TTTTAAAATT
*
18565066 CAAACAAAATTGAAAAA
1 CAAAAAAAATT-AAAAA
*
18565083 GGAAAAAAAATTAAAAA
1 -CAAAAAAAATTAAAAA
**
18565100 TTAAAAAAATCTAAAAAA
1 CAAAAAAAAT-T-AAAAA
18565118 CAAAAAAAA
1 CAAAAAAAA
18565127 ATCCTACAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 8 0.23
17 6 0.17
18 21 0.60
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.13
Consensus pattern (16 bp):
CAAAAAAAATTAAAAA
Found at i:18565374 original size:17 final size:17
Alignment explanation
Indices: 18565349--18565381 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18565339 ATTTGTTATT
18565349 TTTTAATTTTGATTTTC
1 TTTTAATTTTGATTTTC
*
18565366 TTTTGATTTTGATTTT
1 TTTTAATTTTGATTTT
18565382 TTATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (17 bp):
TTTTAATTTTGATTTTC
Found at i:18565669 original size:16 final size:17
Alignment explanation
Indices: 18565648--18565682 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18565638 ACATTTTATG
18565648 TTATTGCAAGAT-TTTT
1 TTATTGCAAGATATTTT
*
18565664 TTATTGCATGATATTTT
1 TTATTGCAAGATATTTT
18565681 TT
1 TT
18565683 GTATGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TTATTGCAAGATATTTT
Found at i:18566891 original size:13 final size:13
Alignment explanation
Indices: 18566873--18566898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18566863 TAACATCTAA
18566873 TAAATTTTAAAAT
1 TAAATTTTAAAAT
18566886 TAAATTTTAAAAT
1 TAAATTTTAAAAT
18566899 ATTTAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATTTTAAAAT
Found at i:18566916 original size:23 final size:21
Alignment explanation
Indices: 18566874--18566919 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
18566864 AACATCTAAT
18566874 AAATTTTAAAATTAAATTTTA
1 AAATTTTAAAATTAAATTTTA
* *
18566895 AAATATTTAAATATTTATTTTTA
1 AAAT-TTTAAA-ATTAAATTTTA
18566918 AA
1 AA
18566920 TTGCTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTTTAAAATTAAATTTTA
Found at i:18566920 original size:22 final size:21
Alignment explanation
Indices: 18566873--18566921 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
18566863 TAACATCTAA
18566873 TAAATTTTAAAATTAAATTTT
1 TAAATTTTAAAATTAAATTTT
* *
18566894 AAAATATTTAAATATT-TATTTT
1 TAAAT-TTTAAA-ATTAAATTTT
18566916 TAAATT
1 TAAATT
18566922 GCTGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 5 0.22
22 15 0.65
23 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATTTTAAAATTAAATTTT
Found at i:18567929 original size:18 final size:18
Alignment explanation
Indices: 18567908--18567947 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18567898 TAAATAATAT
18567908 ATTTATATTCAATATTTA
1 ATTTATATTCAATATTTA
* * *
18567926 ATTTGTTTTCAGTATTTA
1 ATTTATATTCAATATTTA
18567944 ATTT
1 ATTT
18567948 TTAATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTATATTCAATATTTA
Found at i:18572659 original size:19 final size:19
Alignment explanation
Indices: 18572637--18572674 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18572627 TATTTTAATT
*
18572637 AATATAATATATAAATATA
1 AATATAATAAATAAATATA
*
18572656 AATATAATAAATAATTATA
1 AATATAATAAATAAATATA
18572675 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATAATAAATAAATATA
Found at i:18572916 original size:28 final size:27
Alignment explanation
Indices: 18572871--18572926 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
18572861 CAAAATAGTA
18572871 ATATTTAATAACTAAAAAAT-AAAAAT
1 ATATTTAATAACTAAAAAATGAAAAAT
*
18572897 ATATTGTAAGTAACTGAAAAATGAAAAAT
1 ATATT-TAA-TAACTAAAAAATGAAAAAT
18572926 A
1 A
18572927 AAAGATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 3 0.12
28 11 0.42
29 7 0.27
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.29
Consensus pattern (27 bp):
ATATTTAATAACTAAAAAATGAAAAAT
Found at i:18575258 original size:9 final size:9
Alignment explanation
Indices: 18575246--18575343 Score: 51
Period size: 8 Copynumber: 11.0 Consensus size: 9
18575236 AAATTTATCT
18575246 AATAAAAAA
1 AATAAAAAA
18575255 AAT-AAAAA
1 AATAAAAAA
*
18575263 AATTAAAAA
1 AATAAAAAA
** *
18575272 GGTAACCCAAA
1 AATAA--AAAA
**
18575283 AATGTAAAA
1 AATAAAAAA
* *
18575292 ACTTAAAAA
1 AATAAAAAA
* *
18575301 AACAAAGAA
1 AATAAAAAA
18575310 AATGAAAAAA
1 AAT-AAAAAA
18575320 AA-AAAAAA
1 AATAAAAAA
18575328 AA-AAAAAA
1 AATAAAAAA
18575336 AA-AAAAAA
1 AATAAAAAA
18575344 CAAAAGGAGG
Statistics
Matches: 67, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
8 30 0.45
9 26 0.39
10 7 0.10
11 4 0.06
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (9 bp):
AATAAAAAA
Found at i:18575318 original size:1 final size:1
Alignment explanation
Indices: 18575314--18575348 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
18575304 AAAGAAAATG
*
18575314 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18575349 GGAGGGGGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18576728 original size:17 final size:17
Alignment explanation
Indices: 18576698--18576746 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
18576688 TAAAATTTAT
*
18576698 TTAATAAAAAAATAACAA
1 TTAATAAAATAATAA-AA
*
18576716 TTAAT-AAATAATAAAT
1 TTAATAAAATAATAAAA
18576732 TTAATAAAATAATAA
1 TTAATAAAATAATAA
18576747 TAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 17 0.61
18 5 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAATAAAATAATAAAA
Found at i:18578359 original size:1 final size:1
Alignment explanation
Indices: 18578327--18578352 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
18578317 CTTGAGTACC
18578327 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
18578353 CATTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18586790 original size:26 final size:26
Alignment explanation
Indices: 18586747--18586798 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
18586737 TCTCAATTAT
*
18586747 TTTAAATTAAAAATTAAATAA-TTGAA
1 TTTAAATTAAAAAGTAAA-AACTTGAA
*
18586773 TTTAAATTAATAAGTAAAAACTTGAA
1 TTTAAATTAAAAAGTAAAAACTTGAA
18586799 GTAACCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TTTAAATTAAAAAGTAAAAACTTGAA
Found at i:18588582 original size:32 final size:31
Alignment explanation
Indices: 18588546--18588666 Score: 109
Period size: 32 Copynumber: 3.8 Consensus size: 31
18588536 ATTTTCTTTG
18588546 AAAAATTTCATATCACTTTAAAAAATTAAGTA
1 AAAAATTTCATATCA-TTTAAAAAATTAAGTA
* * *
18588578 AAAAATTTTATAGCAGTTTAAAAAATTAAAT-
1 AAAAATTTCATATCA-TTTAAAAAATTAAGTA
* * * **
18588609 AAAAACTTCATATCTTTTTCAAGTATTAAGTA
1 AAAAATTTCATATC-ATTTAAAAAATTAAGTA
* * *
18588641 AAAAATTTTAAATTATTTAAAAAATT
1 AAAAATTTCATATCATTTAAAAAATT
18588667 TATTTATTAA
Statistics
Matches: 67, Mismatches: 20, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
31 30 0.45
32 37 0.55
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (31 bp):
AAAAATTTCATATCATTTAAAAAATTAAGTA
Found at i:18588682 original size:25 final size:26
Alignment explanation
Indices: 18588648--18588703 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
18588638 GTAAAAAATT
*
18588648 TTAAATTATTTA-AAAAATTTATT-TA
1 TTAAACTATTTATAAAAATTT-TTATA
*
18588673 TTAAACTATTTATAATAATTTTTATA
1 TTAAACTATTTATAAAAATTTTTATA
18588699 TTAAA
1 TTAAA
18588704 AATTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAACTATTTATAAAAATTTTTATA
Found at i:18594016 original size:2 final size:2
Alignment explanation
Indices: 18594009--18594033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18593999 CAATTTCAAA
18594009 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
18594034 AGAGATCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18595544 original size:26 final size:24
Alignment explanation
Indices: 18595515--18595562 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
18595505 GATATGTATA
18595515 ATAATATAAATTATTAAATTATAATT
1 ATAATATAAATTA-T-AATTATAATT
18595541 ATAATATAAATTATAATTATAA
1 ATAATATAAATTATAATTATAA
18595563 GTACGATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATATAAATTATAATTATAATT
Found at i:18595571 original size:24 final size:26
Alignment explanation
Indices: 18595517--18595572 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
18595507 TATGTATAAT
* *
18595517 AATATAAATTATTAAATTATAATTAT
1 AATATAAATTATTAAATTATAAGTAC
18595543 AATATAAATTA-T-AATTATAAGTAC
1 AATATAAATTATTAAATTATAAGTAC
*
18595567 GATATA
1 AATATA
18595573 TTTATTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 1 0.04
26 11 0.41
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (26 bp):
AATATAAATTATTAAATTATAAGTAC
Found at i:18596142 original size:18 final size:18
Alignment explanation
Indices: 18596119--18596158 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18596109 TAAATTAAAA
*
18596119 TAAATATAAAAAATGTAT
1 TAAATATAAAAAACGTAT
**
18596137 TAAATATATTAAACGTAT
1 TAAATATAAAAAACGTAT
18596155 TAAA
1 TAAA
18596159 CATGTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (18 bp):
TAAATATAAAAAACGTAT
Found at i:18596166 original size:18 final size:18
Alignment explanation
Indices: 18596133--18596167 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18596123 TATAAAAAAT
*
18596133 GTATTAAATATATTAAAC
1 GTATTAAACATATTAAAC
*
18596151 GTATTAAACATGTTAAA
1 GTATTAAACATATTAAA
18596168 TGTGTATTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (18 bp):
GTATTAAACATATTAAAC
Found at i:18596691 original size:24 final size:25
Alignment explanation
Indices: 18596659--18596706 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
18596649 AATTGATCAT
18596659 TAAAGATATTAATATAAATATATAA
1 TAAAGATATTAATATAAATATATAA
*
18596684 TAAA-ATATTAATATATATATATA
1 TAAAGATATTAATATAAATATATA
18596707 CTAATACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TAAAGATATTAATATAAATATATAA
Found at i:18596914 original size:58 final size:58
Alignment explanation
Indices: 18596852--18596974 Score: 210
Period size: 58 Copynumber: 2.1 Consensus size: 58
18596842 AGTAATACTG
* * *
18596852 ATAACAACTGTAAATATTATTTAACAAAATAGTATTAAACATATGAAATATCAAATTT
1 ATAACAACTGCAAATATTATTTAACAAAATAGTATTAAACATATGAAATATAAAATAT
*
18596910 ATAACAACTGCAAATGTTATTTAACAAAATAGTATTAAACATATGAAATATAAAATAT
1 ATAACAACTGCAAATATTATTTAACAAAATAGTATTAAACATATGAAATATAAAATAT
18596968 ATAACAA
1 ATAACAA
18596975 AATTAAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.32
Consensus pattern (58 bp):
ATAACAACTGCAAATATTATTTAACAAAATAGTATTAAACATATGAAATATAAAATAT
Found at i:18598618 original size:19 final size:18
Alignment explanation
Indices: 18598572--18598620 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
18598562 TGGCTAGGGT
**
18598572 TAGGTTTAAGGTTTAAGTT
1 TAGGTTT-AGGTTTAAGCC
18598591 TAGGTTTTAGGTTTAAAGCC
1 TAGG-TTTAGGTTT-AAGCC
18598611 TAGGTTTAGG
1 TAGGTTTAGG
18598621 GTTTGGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.29, T:0.43
Consensus pattern (18 bp):
TAGGTTTAGGTTTAAGCC
Found at i:18598623 original size:7 final size:7
Alignment explanation
Indices: 18598613--18598673 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
18598603 TTAAAGCCTA
18598613 GGTTTAG
1 GGTTTAG
18598620 GGTTT--
1 GGTTTAG
18598625 GGTTTAG
1 GGTTTAG
* *
18598632 AGTCTA-
1 GGTTTAG
18598638 GGTTTAG
1 GGTTTAG
18598645 GGTTT-G
1 GGTTTAG
*
18598651 AGTTTAG
1 GGTTTAG
18598658 GGTTTA-
1 GGTTTAG
*
18598664 GATTTAG
1 GGTTTAG
18598671 GGT
1 GGT
18598674 CTAGTTTGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
5 5 0.12
6 14 0.34
7 22 0.54
ACGTcount: A:0.16, C:0.02, G:0.38, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:18598639 original size:19 final size:20
Alignment explanation
Indices: 18598617--18598677 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
18598607 AGCCTAGGTT
18598617 TAGGGTTT-GGTTTAGAGTC
1 TAGGGTTTAGGTTTAGAGTC
*
18598636 TA-GGTTTAGGGTTT-GAGTT
1 TAGGGTTTA-GGTTTAGAGTC
* *
18598655 TAGGGTTTAGATTTAGGGTC
1 TAGGGTTTAGGTTTAGAGTC
18598675 TAG
1 TAG
18598678 TTTGAGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 5 0.15
19 12 0.35
20 17 0.50
ACGTcount: A:0.18, C:0.03, G:0.36, T:0.43
Consensus pattern (20 bp):
TAGGGTTTAGGTTTAGAGTC
Found at i:18598655 original size:13 final size:12
Alignment explanation
Indices: 18598540--18598680 Score: 79
Period size: 13 Copynumber: 11.3 Consensus size: 12
18598530 AGAATTTAGG
*
18598540 GTTT-GGGTTGA
1 GTTTAGGGTTTA
*
18598551 GTTTAGGGTTTT
1 GTTTAGGGTTTA
**
18598563 GGCTAGGG-TTA
1 GTTTAGGGTTTA
*
18598574 GGTTTAAGGTTTAA
1 -GTTTAGGGTTT-A
*
18598588 GTTTAGGTTTTA
1 GTTTAGGGTTTA
** **
18598600 GGTTTAAAGCCTA
1 -GTTTAGGGTTTA
*
18598613 GGTTTAGGGTTTG
1 -GTTTAGGGTTTA
* *
18598626 GTTTAGAGTCTA
1 GTTTAGGGTTTA
18598638 GGTTTAGGGTTTGA
1 -GTTTAGGGTTT-A
18598652 GTTTAGGGTTTA
1 GTTTAGGGTTTA
*
18598664 GATTTAGGGTCTA
1 G-TTTAGGGTTTA
18598677 GTTT
1 GTTT
18598681 GAGGTTTGGT
Statistics
Matches: 96, Mismatches: 26, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
11 6 0.06
12 31 0.32
13 57 0.59
14 2 0.02
ACGTcount: A:0.18, C:0.04, G:0.34, T:0.45
Consensus pattern (12 bp):
GTTTAGGGTTTA
Found at i:18598669 original size:26 final size:25
Alignment explanation
Indices: 18598589--18598673 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 25
18598579 AAGGTTTAAG
* * * *
18598589 TTTAGGTTTTAGGTTTAAAGCCTAGG
1 TTTAGGGTTT-GGTTTAGAGTCTAGA
*
18598615 TTTAGGGTTTGGTTTAGAGTCTAGG
1 TTTAGGGTTTGGTTTAGAGTCTAGA
* *
18598640 TTTAGGGTTTGAGTTTAGGGTTTAGA
1 TTTAGGGTTTG-GTTTAGAGTCTAGA
18598666 TTTAGGGT
1 TTTAGGGT
18598674 CTAGTTTGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
25 24 0.46
26 28 0.54
ACGTcount: A:0.19, C:0.04, G:0.33, T:0.45
Consensus pattern (25 bp):
TTTAGGGTTTGGTTTAGAGTCTAGA
Found at i:18598738 original size:13 final size:13
Alignment explanation
Indices: 18598722--18598746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18598712 TAGGTTTAAA
18598722 GTCTAGGTTTGGG
1 GTCTAGGTTTGGG
18598735 GTCTAGGTTTGG
1 GTCTAGGTTTGG
18598747 TGTTTGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.44, T:0.40
Consensus pattern (13 bp):
GTCTAGGTTTGGG
Found at i:18598863 original size:23 final size:23
Alignment explanation
Indices: 18598819--18598865 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
18598809 TTAAACTAAG
* *
18598819 TGCATGAGATTAATCAACTATAA
1 TGCATGAAATTAAACAACTATAA
18598842 TGCATGAAATTAAACTAA-TATAA
1 TGCATGAAATTAAAC-AACTATAA
18598865 T
1 T
18598866 TAAGTTGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (23 bp):
TGCATGAAATTAAACAACTATAA
Found at i:18600587 original size:13 final size:13
Alignment explanation
Indices: 18600503--18600604 Score: 65
Period size: 13 Copynumber: 8.1 Consensus size: 13
18600493 TAAAATTTGA
18600503 TTTAGGGTTTAAGG
1 TTTA-GGTTTAAGG
*
18600517 TTT-GG-TTAAGAA
1 TTTAGGTTTAAG-G
*
18600529 TTTAGG-TTCA-G
1 TTTAGGTTTAAGG
18600540 TTTAGGGTTTAAGG
1 TTTA-GGTTTAAGG
* **
18600554 GTTAGGTTGGAGG
1 TTTAGGTTTAAGG
18600567 ATTT-GGTTTAAGG
1 -TTTAGGTTTAAGG
18600580 TTTAGGTTT--GG
1 TTTAGGTTTAAGG
*
18600591 TTTGGGTTTAAGG
1 TTTAGGTTTAAGG
18600604 T
1 T
18600605 CTAAGTTCAA
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
11 19 0.28
12 10 0.15
13 30 0.44
14 9 0.13
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.44
Consensus pattern (13 bp):
TTTAGGTTTAAGG
Found at i:18600760 original size:18 final size:18
Alignment explanation
Indices: 18600703--18600760 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
18600693 GTTGACTTAA
*
18600703 GTTTAGAGTTTAGGCTCG
1 GTTTAGAGTTTAGGCTTG
** * *
18600721 AATTAGGGTTTGAGG-TTT
1 GTTTAGAGTTT-AGGCTTG
18600739 GTTTAGAGTTTAGGCTTG
1 GTTTAGAGTTTAGGCTTG
18600757 GTTT
1 GTTT
18600761 TGGGTAGATT
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
17 3 0.10
18 23 0.79
19 3 0.10
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.45
Consensus pattern (18 bp):
GTTTAGAGTTTAGGCTTG
Found at i:18600828 original size:27 final size:28
Alignment explanation
Indices: 18600788--18600851 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
18600778 AATTTTGGGA
*
18600788 TTGGTTTTGGTTTAGGATAGGTTTAGGG
1 TTGGTTTTGATTTAGGATAGGTTTAGGG
*
18600816 TTGG-TTTGATTTAGGATAGGTTTAGGT
1 TTGGTTTTGATTTAGGATAGGTTTAGGG
*
18600843 TTGATTTTG
1 TTGGTTTTG
18600852 GGTTTAGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (28 bp):
TTGGTTTTGATTTAGGATAGGTTTAGGG
Found at i:18600914 original size:19 final size:20
Alignment explanation
Indices: 18600890--18600927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18600880 TTAAAGATTG
*
18600890 AGGGTTT-AGTTTTGGGTTC
1 AGGGTTTAAGTTTAGGGTTC
18600909 AGGGTTTAAGTTTAGGGTT
1 AGGGTTTAAGTTTAGGGTT
18600928 TGGTTTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.16, C:0.03, G:0.37, T:0.45
Consensus pattern (20 bp):
AGGGTTTAAGTTTAGGGTTC
Found at i:18600939 original size:12 final size:13
Alignment explanation
Indices: 18600904--18600947 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
18600894 TTTAGTTTTG
*
18600904 GGTTCAGGGTTTA
1 GGTTTAGGGTTTA
*
18600917 AGTTTAGGGTTT-
1 GGTTTAGGGTTTA
*
18600929 GGTTTATGGTTTA
1 GGTTTAGGGTTTA
18600942 GGTTTA
1 GGTTTA
18600948 AGTTTAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:18602898 original size:10 final size:10
Alignment explanation
Indices: 18602878--18602922 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
18602868 ATTTCAAGGA
18602878 TTGACTCAAGT
1 TTGA-TCAAGT
18602889 TTGATCAAGT
1 TTGATCAAGT
* *
18602899 TTGATCGATT
1 TTGATCAAGT
*
18602909 TTGACCAAGT
1 TTGATCAAGT
18602919 TTGA
1 TTGA
18602923 CTTTATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 25 0.86
11 4 0.14
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (10 bp):
TTGATCAAGT
Found at i:18613173 original size:15 final size:15
Alignment explanation
Indices: 18613124--18613173 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
18613114 TATCATCTTG
* *
18613124 AATAACAAATTAAAGT
1 AATAAAAAATTTAA-T
* *
18613140 AATAAAAAATGTAAC
1 AATAAAAAATTTAAT
18613155 AATAAAAAATTTAAT
1 AATAAAAAATTTAAT
18613170 AATA
1 AATA
18613174 TCTTTTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (15 bp):
AATAAAAAATTTAAT
Found at i:18613903 original size:15 final size:17
Alignment explanation
Indices: 18613871--18613904 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18613861 CGTTTGGTTA
18613871 TATTAAAAATATTTTCT
1 TATTAAAAATATTTTCT
18613888 TATTAAAAA-A-TTTCT
1 TATTAAAAATATTTTCT
18613903 TA
1 TA
18613905 AAAAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAAAATATTTTCT
Found at i:18614328 original size:192 final size:191
Alignment explanation
Indices: 18613980--18614335 Score: 443
Period size: 192 Copynumber: 1.9 Consensus size: 191
18613970 AAAGTTACAT
** *
18613980 TTTTATTTTTTATTTTTTGAGAATAAATATAAATTAGTTTTATTAAAATTTTCCCAAAATTTTCA
1 TTTTATTTACTATTTTTTGAAAATAAATATAAATTAGTTTTATTAAAATTTTCCCAAAATTTTCA
* *
18614045 TCGTTTGGGATACTTTTAGGAAAAATTCTCATCTAAAAAATTTTAAGAAATTAACCATTTCTAAA
66 TCATTTGGGATACTTTTAGGAAAAATTCTCATCTAAAAAATTTTAAGAAATCAACCATTTCTAAA
* *
18614110 TTTTTAGAATTTTATCCTTAGAATAATTTTCATTGATTTCTAAACTTTTACAAGGATTAAA
131 CTTTTAGAATTTTATCATTAGAATAATTTTCATTGATTTCTAAACTTTTACAAGGATTAAA
* * *
18614171 TTTTATTTACTATTTGTTTGAAAATAAATATAAATTATTTTTTATTGAAATTTTCCTAAAATTTT
1 TTTTATTTACTATTT-TTTGAAAATAAATATAAATTA-GTTTTATTAAAATTTTCCCAAAATTTT
* * ** * ***
18614236 CA-CTATTTGGTATA-TGTTTA-GAAATATT-TTTTGCCTAAAAATTTTTAAGAAATCGGTCA-T
64 CATC-ATTTGGGATACT-TTTAGGAAAAATTCTCAT--CTAAAAAATTTTAAGAAATCAACCATT
**
18614296 TCTTGACTTTTAGAATTTTATCATTAGAATAATTTTCATT
125 TCTAAACTTTTAGAATTTTATCATTAGAATAATTTTCATT
18614336 TACTTTCAAA
Statistics
Matches: 139, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
191 15 0.11
192 66 0.47
193 58 0.42
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (191 bp):
TTTTATTTACTATTTTTTGAAAATAAATATAAATTAGTTTTATTAAAATTTTCCCAAAATTTTCA
TCATTTGGGATACTTTTAGGAAAAATTCTCATCTAAAAAATTTTAAGAAATCAACCATTTCTAAA
CTTTTAGAATTTTATCATTAGAATAATTTTCATTGATTTCTAAACTTTTACAAGGATTAAA
Found at i:18621402 original size:2 final size:2
Alignment explanation
Indices: 18621395--18621421 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18621385 AGGAGTTATG
18621395 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18621422 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18623453 original size:16 final size:17
Alignment explanation
Indices: 18623431--18623472 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
18623421 ATTTCAAATA
*
18623431 AAAAAATAATTTATATT
1 AAAAATTAATTTATATT
*
18623448 AAAAATTTATTTATA-T
1 AAAAATTAATTTATATT
*
18623464 ACAAATTAA
1 AAAAATTAA
18623473 AAGTTTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAATTAATTTATATT
Found at i:18623527 original size:29 final size:29
Alignment explanation
Indices: 18623445--18623549 Score: 129
Period size: 30 Copynumber: 3.6 Consensus size: 29
18623435 AATAATTTAT
18623445 ATTAAAAATTTATTTATATACAAATTAAA
1 ATTAAAAATTTATTTATATACAAATTAAA
* *
18623474 AGTTTAAGATTTATTTATATACAAATTAAA
1 A-TTAAAAATTTATTTATATACAAATTAAA
* * * *
18623504 AATAAAAATTTATTTAGATGCAAATCAAA
1 ATTAAAAATTTATTTATATACAAATTAAA
*
18623533 TATTAAAGATTTATTTA
1 -ATTAAAAATTTATTTA
18623550 AATGTAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.36
30 41 0.64
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (29 bp):
ATTAAAAATTTATTTATATACAAATTAAA
Done.