Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 19
Found at i:171656 original size:19 final size:19
Alignment explanation
Indices: 171625--171671 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
171615 AATAAAATTT
*
171625 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTAGAA
*
171643 ATAATATAAAGAATTGGAA
1 ATAATATAAAGAATTAGAA
*
171662 TTAATATAAA
1 ATAATATAAA
171672 AACCAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTAGAA
Found at i:173553 original size:32 final size:32
Alignment explanation
Indices: 173514--173577 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
173504 ATATATTATT
*
173514 AAACAACATACATATATTAATATTATTAATAA
1 AAACAACATACAAATATTAATATTATTAATAA
173546 AAACAACATACAAATATTAATATTATTAATAA
1 AAACAACATACAAATATTAATATTATTAATAA
173578 TTTAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (32 bp):
AAACAACATACAAATATTAATATTATTAATAA
Found at i:178692 original size:23 final size:23
Alignment explanation
Indices: 178652--178717 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
178642 TTGAATGATT
* *
178652 CAGTGCTGAGTGATTCAACAAAA
1 CAGTGTTGAATGATTCAACAAAA
*
178675 CATTGTTGAATGATTCAACAAAA
1 CAGTGTTGAATGATTCAACAAAA
178698 CAGTGTTGAATGATTCAACA
1 CAGTGTTGAATGATTCAACA
178718 TCAGTGTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (23 bp):
CAGTGTTGAATGATTCAACAAAA
Found at i:178830 original size:15 final size:16
Alignment explanation
Indices: 178794--178832 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
178784 AGAGCCTCTA
*
178794 AATCATTCAGCATTTG
1 AATCATTCAGCACTTG
*
178810 AATCATTCAGCGCTT-
1 AATCATTCAGCACTTG
178825 AATCATTC
1 AATCATTC
178833 TGAAGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (16 bp):
AATCATTCAGCACTTG
Found at i:181623 original size:82 final size:81
Alignment explanation
Indices: 181534--181793 Score: 256
Period size: 82 Copynumber: 3.1 Consensus size: 81
181524 CGATATCTTA
* * * *
181534 ATATATAGTGGCATTTTTGGGAAAATGCCACTATAAACTCATAATTTAGTGGCATTTATATAAAA
1 ATATATAGTGGC-TTTTTGGGAAAATGCCGCTATAAACTCATACTTTAGTGGCGTTTATGTAAAA
*
181599 AATGCCGCGATAGCCAG
65 AATGCCGCTATAGCCAG
* * *
181616 ATATATAGTGGCTTTTTGTG-AAATCGCCGCTA-AAAATGCTTACTTTAGTGGCGTTTATGTAAA
1 ATATATAGTGGCTTTTTGGGAAAAT-GCCGCTATAAACT-CATACTTTAGTGGCGTTTATGT-AA
* *
181679 CAAAATGGCCGTTATAGCTAG
63 -AAAAT-GCCGCTATAGCCAG
* * * * *
181700 ATATATAGCGACGTTTTT-GTATAAATGCCGCTATAAACACATACTTTAATGGCGTTTATGTAAA
1 ATATATAGTGGC-TTTTTGGGA-AAATGCCGCTATAAACTCATACTTTAGTGGCGTTTATGTAAA
* * * *
181764 AAACGCTGCTATAACCCG
64 AAATGCCGCTATAGCCAG
181782 ATATATAGTGGC
1 ATATATAGTGGC
181794 GTTTGTGTAG
Statistics
Matches: 143, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
80 8 0.06
81 31 0.22
82 33 0.23
83 9 0.06
84 23 0.16
85 32 0.22
86 7 0.05
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (81 bp):
ATATATAGTGGCTTTTTGGGAAAATGCCGCTATAAACTCATACTTTAGTGGCGTTTATGTAAAAA
ATGCCGCTATAGCCAG
Found at i:181745 original size:85 final size:81
Alignment explanation
Indices: 181547--181766 Score: 226
Period size: 85 Copynumber: 2.7 Consensus size: 81
181537 TATAGTGGCA
* * * * * *
181547 TTTTTGGGAAAATGCCACTATAAACTCATAATTTAGTGGCATTTATAT-AAAAAATGCCGCGATA
1 TTTTTGTG-AAATGCCGCTATAAACACATACTTTAGTGGCGTTTATGTAAAAAAATGCCGCGATA
* *
181611 GCCAGATATATAGTGGC
65 GCCAGATATATAGCGAC
* ** * **
181628 TTTTTGTGAAATCGCCGCTAAAAATGCTTACTTTAGTGGCGTTTATGTAAACAAAATGGCCGTTA
1 TTTTTGTGAAAT-GCCGCTATAAACACATACTTTAGTGGCGTTTATGTAAA-AAAAT-GCCGCGA
*
181693 TAGCTAGATATATAGCGAC
63 TAGCCAGATATATAGCGAC
* *
181712 GTTTTTGTATAAATGCCGCTATAAACACATACTTTAATGGCGTTTATGTAAAAAA
1 -TTTTTGT-GAAATGCCGCTATAAACACATACTTTAGTGGCGTTTATGTAAAAAA
181767 CGCTGCTATA
Statistics
Matches: 113, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
80 4 0.04
81 34 0.30
82 2 0.02
83 5 0.04
84 24 0.21
85 40 0.35
86 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (81 bp):
TTTTTGTGAAATGCCGCTATAAACACATACTTTAGTGGCGTTTATGTAAAAAAATGCCGCGATAG
CCAGATATATAGCGAC
Found at i:182077 original size:24 final size:24
Alignment explanation
Indices: 182050--182095 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
182040 ACTATACGGT
182050 ATGAACAATA-CAGTGAACAGTGTC
1 ATGAACAATACCA-TGAACAGTGTC
*
182074 ATGAACAGTACCATGAACAGTG
1 ATGAACAATACCATGAACAGTG
182096 AAAAAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (24 bp):
ATGAACAATACCATGAACAGTGTC
Found at i:185884 original size:45 final size:48
Alignment explanation
Indices: 185807--185904 Score: 148
Period size: 45 Copynumber: 2.1 Consensus size: 48
185797 TTTATTTTCG
185807 TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGGATTTA
* * *
185854 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGGATTTA
185900 TTTTT
1 TTTTT
185905 GTGAATAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 27 0.57
46 11 0.23
47 9 0.19
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGGATTTA
Found at i:195513 original size:17 final size:17
Alignment explanation
Indices: 195491--195635 Score: 95
Period size: 17 Copynumber: 8.2 Consensus size: 17
195481 GAATAAATGG
195491 AAAAATGAAAAAATGAA
1 AAAAATGAAAAAATGAA
195508 AAAAATGAAAAAA--AA
1 AAAAATGAAAAAATGAA
195523 GAAAAATGAGAAAAATGAA
1 -AAAAATGA-AAAAATGAA
*
195542 AAATGAAGGAAAAAATGAAA
1 AAA--AATGAAAAAATG-AA
*
195562 AGAAAATGAAATAGAAATG-G
1 A-AAAATG-AA-A-AAATGAA
* *
195582 GAAAATGGAAGAAA--AA
1 AAAAAT-GAAAAAATGAA
* *
195598 AGAAATGAAAAAATGATG
1 AAAAATGAAAAAATGA-A
195616 AAAAATG-AAAAATGAA
1 AAAAATGAAAAAATGAA
195632 AAAA
1 AAAA
195636 TAGAGAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
15 8 0.08
16 16 0.16
17 30 0.30
18 9 0.09
19 19 0.19
20 10 0.10
21 3 0.03
22 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAAAATGAA
Found at i:195519 original size:25 final size:25
Alignment explanation
Indices: 195485--195650 Score: 99
Period size: 25 Copynumber: 6.4 Consensus size: 25
195475 CTTAAAGAAT
*
195485 AAATGGAAAAATGAAAAAATGAAAA
1 AAATGAAAAAATGAAAAAATGAAAA
* *
195510 AAATGAAAAAA-AAGAAAAATGAGAA
1 AAATGAAAAAATGA-AAAAATGAAAA
*
195535 AAATGAAAAATGAAGGAAAAAATGAAAAGA
1 AAATG-AAAA--AATGAAAAAATG-AAA-A
** *
195565 AAATGAAATAGAAATGGGAAAATGGAAGA
1 AAATG-AA-A-AAATGAAAAAAT-GAAAA
* *
195594 AAA--AAGAAATGAAAAAATGATGAA
1 AAATGAAAAAATGAAAAAATGA-AAA
*
195618 AAATG-AAAAATGAAAAAATAGAGAA
1 AAATGAAAAAATGAAAAAAT-GAAAA
195643 AAAT-AAAA
1 AAATGAAAA
195651 GGGGGTTCAA
Statistics
Matches: 111, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
23 2 0.02
24 15 0.14
25 48 0.43
26 8 0.07
28 9 0.08
29 7 0.06
30 19 0.17
31 2 0.02
32 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11
Consensus pattern (25 bp):
AAATGAAAAAATGAAAAAATGAAAA
Found at i:196714 original size:16 final size:17
Alignment explanation
Indices: 196677--196711 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
196667 AGGTTTCCCA
196677 AAGATAGTTGAAGATTG
1 AAGATAGTTGAAGATTG
196694 AAGATA-TTGAAGCATTG
1 AAGATAGTTGAAG-ATTG
196711 A
1 A
196712 GATGAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (17 bp):
AAGATAGTTGAAGATTG
Found at i:197091 original size:55 final size:55
Alignment explanation
Indices: 197025--197417 Score: 456
Period size: 55 Copynumber: 7.1 Consensus size: 55
197015 AGATTAAGTC
* * ** *
197025 CTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCATTGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
*
197080 CTATACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTT
*
197135 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTATTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTT
* * ** * *
197190 CTATACTCTCAGAAGAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
*
197245 CTATACTCTTTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGTT
1 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTCGAGTT
* * *
197300 CTATACTCCCTGAACGG-ATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAG-T
1 CTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
* * * * * * ** *
197354 CTTATACTCACTAAATGAATAGGGAGCAGACACGTTTACCGAAGATTGTTTGAG-T
1 C-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
197409 CTTATACTC
1 C-TATACTC
197418 CTTAAAAGAA
Statistics
Matches: 300, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
54 5 0.02
55 291 0.97
56 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (55 bp):
CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTCGAGTT
Found at i:197400 original size:165 final size:165
Alignment explanation
Indices: 197021--197455 Score: 533
Period size: 165 Copynumber: 2.6 Consensus size: 165
197011 TTGAAGATTA
* * * * *
197021 AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCATTGAAGATTGTTCGAGTTCTATAC
1 AGTCTTATACTCTCTAAATGAATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTCTATAC
* * *
197086 TCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
66 TCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
*
197151 AATAGAGAGCGGACCCGTTTTATGAAGATTATTCG
131 AATAGAGAGCAGACCCGTTTTATGAAGATTATTCG
* * * *
197186 AGT-TCTATACTCTC-AGAA-GAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCGAGTTCTA
1 AGTCT-TATACTCTCTA-AATG-AATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTCTA
197248 TACTCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGA
63 TACTCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGA
* *
197313 ACGG-ATAGGGAGCAGACCCG-TTTATTGAAGATTGTTCG
128 A-GGAATAGAGAGCAGACCCGTTTTA-TGAAGATTATTCG
* ** *
197351 AGTCTTATACTCACTAAATGAATAGGGAGCAGACACGTTTACCGAAGATTGTTTGAG-TCTTATA
1 AGTCTTATACTCTCTAAATGAATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTC-TATA
* * * * **
197415 CTCCTTAAAAGAATAGGGAGAAGACCCGTTATT-TGAAGATT
65 CTCTTTGAAGGAATAGAGAGCGGACCCGTT-TTATGAAGATT
197456 TTTCAAGTCT
Statistics
Matches: 231, Mismatches: 29, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
164 7 0.03
165 217 0.94
166 7 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (165 bp):
AGTCTTATACTCTCTAAATGAATAGGGAGCAGACACGTTTATTGAAGATTGTTCGAGTTCTATAC
TCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
AATAGAGAGCAGACCCGTTTTATGAAGATTATTCG
Found at i:197418 original size:110 final size:110
Alignment explanation
Indices: 197021--197466 Score: 469
Period size: 110 Copynumber: 4.1 Consensus size: 110
197011 TTGAAGATTA
* * * *
197021 AGTC-CTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCATTGAAGATTGTTCGAGTTCTAT
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTA-TGAAGATTGTTCGAGTTCTAT
* * *
197084 ACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGTTCG
65 ACTCCCTGAA-GAATAGAGAGCAGACCCGTTTAT-TGAAGATTGTTCG
* *
197131 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTATTCGAGTTCTATA
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATA
* * * * *
197195 CTCTCAGAAGAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCG
66 CTCCCTGAAG-AATAGAGAGCAGACCCGTTTATTGAAGATTGTTCG
* *
197241 AGT-TCTATACTCTTTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATA
* *
197305 CTCCCTGAACGGATAGGGAGCAGACCCGTTTATTGAAGATTGTTCG
66 CTCCCTGAA-GAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCG
* * * * * * *
197351 AGTCT-TATACTCACTAAATGAATAGGGAGCAGACACG-TTTACCGAAGATTGTTTGAG-TCTTA
1 AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTA-TGAAGATTGTTCGAGTTC-TA
* * * * * *
197413 TACTCCTTAAAAGAATAGGGAGAAGACCCG-TTATTTGAAGATTTTTCA
64 TACTCCCT-GAAGAATAGAGAGCAGACCCGTTTA-TTGAAGATTGTTCG
197461 AGTCTC
1 AGTCTC
197467 GTTTATCCAG
Statistics
Matches: 290, Mismatches: 35, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
109 10 0.03
110 272 0.94
111 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (110 bp):
AGTCTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTGTTCGAGTTCTATA
CTCCCTGAAGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCG
Found at i:197465 original size:55 final size:56
Alignment explanation
Indices: 197040--197466 Score: 344
Period size: 55 Copynumber: 7.8 Consensus size: 56
197030 CTCTCTGAAT
* ** * * *
197040 GAATAGGGAGCGGACAAGTTCATTGAAGATTGTTCGAGT-TCTATACT-CTCTGAAG
1 GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCT-TAAAA
* * * * *
197095 GAATAGAGAGCGGACCCATTT-TATGAAGATTGTTCGAGT-TCTATACT-CTCTGAAG
1 GAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTCGAGTCTCTATACTCCT-TAAAA
* * * * *
197150 GAATAGAGAGCGGACCCGTTT-TATGAAGATTATTCGAGT-TCTATACT-CTCAGAA
1 GAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* * * * * * *
197204 GAAATAGAGAGCATACTCGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTTTGAAG
1 G-AATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* * * * *
197260 GAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGT-TCTATACTCCCTGAAC
1 GAATAGGGAGCAGACCCGTTTAT-TGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* *
197315 GGATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCT-TATACTCAC-TAAAT
1 GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTC-CTTAAAA
* ** *
197370 GAATAGGGAGCAGACACGTTTACCGAAGATTGTTTGAGTCT-TATACTCCTTAAAA
1 GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
* * *
197425 GAATAGGGAGAAGACCCG-TTATTTGAAGATTTTTCAAGTCTC
1 GAATAGGGAGCAGACCCGTTTA-TTGAAGATTGTTCGAGTCTC
197467 GTTTATCCAG
Statistics
Matches: 317, Mismatches: 44, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
54 8 0.03
55 302 0.95
56 7 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (56 bp):
GAATAGGGAGCAGACCCGTTTATTGAAGATTGTTCGAGTCTCTATACTCCTTAAAA
Found at i:200577 original size:12 final size:12
Alignment explanation
Indices: 200562--200591 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
200552 AACAATACCG
*
200562 TGAACATTGTCA
1 TGAACATTATCA
200574 TGAACATTATCA
1 TGAACATTATCA
200586 TGAACA
1 TGAACA
200592 GTGAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (12 bp):
TGAACATTATCA
Found at i:201232 original size:24 final size:24
Alignment explanation
Indices: 201205--201275 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
201195 CACCACAACT
*
201205 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
201229 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
201253 CGTAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
201276 TATAAGATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 14 0.33
24 29 0.67
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:202810 original size:8 final size:8
Alignment explanation
Indices: 202784--202823 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
202774 TCTCACGTGG
202784 AGAAG-GA
1 AGAAGAGA
202791 AGAAGA-A
1 AGAAGAGA
202798 AGAAGAGA
1 AGAAGAGA
202806 AGAAGAGA
1 AGAAGAGA
202814 AGAAGAGA
1 AGAAGAGA
202822 AG
1 AG
202824 TGGAGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AGAAGAGA
Found at i:203358 original size:18 final size:19
Alignment explanation
Indices: 203337--203377 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
203327 CTCGCTTTCA
203337 TTTCT-ATTCTCTCGTCAT
1 TTTCTGATTCTCTCGTCAT
*
203355 TTTCTGATTTTCTCGTCAT
1 TTTCTGATTCTCTCGTCAT
203374 TTTC
1 TTTC
203378 ACTAAAGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.10, C:0.24, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTCTGATTCTCTCGTCAT
Found at i:232911 original size:13 final size:13
Alignment explanation
Indices: 232895--232944 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
232885 TTTCGCTTTT
232895 TTTATTTTATTTA
1 TTTATTTTATTTA
*
232908 TTTATTTT-TGTTC
1 TTTATTTTAT-TTA
232921 TTT-TATTTATTTA
1 TTTAT-TTTATTTA
*
232934 TTTAGTTTATT
1 TTTATTTTATT
232945 CTTATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.07
13 27 0.90
14 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:232916 original size:22 final size:22
Alignment explanation
Indices: 232891--233005 Score: 85
Period size: 22 Copynumber: 5.3 Consensus size: 22
232881 TTTATTTCGC
232891 TTTTTTTATTTTATTTATTTAT
1 TTTTTTTATTTTATTTATTTAT
* *
232913 TTTTGTTCTTTTATTTATTTAT
1 TTTTTTTATTTTATTTATTTAT
**
232935 TTAGTTTATTCTTA-TTATTT-T
1 TTTTTTTATT-TTATTTATTTAT
* * **
232956 TCTTTTTACTCAATTCTATTTAT
1 TTTTTTTATTTTATT-TATTTAT
* *
232979 TTTTATT-TTTTATATTA-ATAT
1 TTTTTTTATTTTAT-TTATTTAT
233000 TTTTTT
1 TTTTTT
233006 CCTTTTTTTC
Statistics
Matches: 69, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.23
22 42 0.61
23 10 0.14
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTTATTTTATTTATTTAT
Found at i:235524 original size:31 final size:31
Alignment explanation
Indices: 235486--235579 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
235476 AACTCTAAAT
235486 ATGAGATTCCTTGACTTTCAACAACACCTAG
1 ATGAGATTCCTTGACTTTCAACAACACCTAG
235517 ATGAGATTCCTTGACTTTCAACAACACCTAG
1 ATGAGATTCCTTGACTTTCAACAACACCTAG
235548 ATGAGATTCCTTGACTTTCAACAACACCTAG
1 ATGAGATTCCTTGACTTTCAACAACACCTAG
235579 A
1 A
235580 CTATAACATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.29
Consensus pattern (31 bp):
ATGAGATTCCTTGACTTTCAACAACACCTAG
Found at i:235739 original size:94 final size:95
Alignment explanation
Indices: 235632--235824 Score: 318
Period size: 95 Copynumber: 2.0 Consensus size: 95
235622 GTTATAATAT
*
235632 ATATACAATAAAGCTTGAGCT-TCCCTCTTAAA-CAATTGGTTAAACGCCCCGGCTTTATGGATA
1 ATATACAATAAAGCTTGAACTGTCCCTC-TAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATA
*
235695 AGATTCAACTAGCCTAATAAAGGTGATTTTA
65 AGATTCAACTAGCCTAATAAAGGTGATTATA
*
235726 ATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTTTATGGATAA
1 ATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
* *
235791 GATTCAGCTAGCCTGATAAAGGTGATTATA
66 GATTCAACTAGCCTAATAAAGGTGATTATA
235821 ATAT
1 ATAT
235825 TGAGTTGTCC
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
94 24 0.26
95 68 0.74
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (95 bp):
ATATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
GATTCAACTAGCCTAATAAAGGTGATTATA
Found at i:237172 original size:86 final size:86
Alignment explanation
Indices: 236929--237203 Score: 351
Period size: 86 Copynumber: 3.2 Consensus size: 86
236919 GAAATATTGG
* *
236929 CAGCACAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACCTTCGAGTTTGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAG
* *
236993 CTCAAAGACACATCAAATTCG
66 CTCAAAGGCACATCAAATTCA
* ** * * * *
237014 CAGCATAAG-TTAAGGTAAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGATTACACTCA
1 CAGCAT-AGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCA
*
237078 GCTCAAAGGCACATCAAATTTA
65 GCTCAAAGGCACATCAAATTCA
* *
237100 CAGCATAGCACAAGGCGAGAAGGGCTATCTGTCAACAAAATACCTTCGAGTTCGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAG
* *
237165 CTCAAAGGCATATCCAA-T-A
66 CTCAAAGGCACATCAAATTCA
* *
237184 CAACATAACTCAAGGCGAGA
1 CAGCATAGCTCAAGGCGAGA
237204 TTCGATTACA
Statistics
Matches: 161, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
84 18 0.11
85 30 0.19
86 113 0.70
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (86 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAG
CTCAAAGGCACATCAAATTCA
Found at i:237213 original size:54 final size:55
Alignment explanation
Indices: 237146--237259 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 55
237136 AAAATACCTT
* * * *
237146 CGAG-TTCGATTACATTCAGCTCAAAGGCATATCCAA-TACAACATAACTCAAGG
1 CGAGATTCGATTACACTAAGCTCAAAGGCACATCAAATTACAACATAACTCAAGG
* *
237199 CGAGATTCGATTACACTAAGCTCAAAGGCACATCAAATTTACATCATAGCTCAAGG
1 CGAGATTCGATTACACTAAGCTCAAAGGCACATCAAA-TTACAACATAACTCAAGG
237255 CGAGA
1 CGAGA
237260 AGGGCTATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
53 4 0.08
54 28 0.54
56 20 0.38
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (55 bp):
CGAGATTCGATTACACTAAGCTCAAAGGCACATCAAATTACAACATAACTCAAGG
Found at i:237316 original size:140 final size:140
Alignment explanation
Indices: 237064--237343 Score: 497
Period size: 140 Copynumber: 2.0 Consensus size: 140
237054 GACCTTTGAG
*
237064 TTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCACAAGGCGAGAAGGGCTATC
1 TTCGATTACACTAAGCTCAAAGGCACATCAAATTTACAGCATAGCACAAGGCGAGAAGGGCTATC
*
237129 TGTCAACAAAATACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAATACAACATAACT
66 TGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAATACAACATAACT
237194 CAAGGCGAGA
131 CAAGGCGAGA
* *
237204 TTCGATTACACTAAGCTCAAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATC
1 TTCGATTACACTAAGCTCAAAGGCACATCAAATTTACAGCATAGCACAAGGCGAGAAGGGCTATC
* *
237269 TGTCAACAAAAAACGTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAGTACAACATAACT
66 TGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAATACAACATAACT
*
237334 CAAGGTGAGA
131 CAAGGCGAGA
237344 AGGGTTATCT
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 133 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (140 bp):
TTCGATTACACTAAGCTCAAAGGCACATCAAATTTACAGCATAGCACAAGGCGAGAAGGGCTATC
TGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAATACAACATAACT
CAAGGCGAGA
Found at i:237494 original size:87 final size:87
Alignment explanation
Indices: 237199--237621 Score: 466
Period size: 85 Copynumber: 4.9 Consensus size: 87
237189 TAACTCAAGG
* * * * *
237199 CGAGATTCGATTACACTAAGCTCAAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGG
1 CGAG-TTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAACTCAAGGCGAGAAGGG
*
237264 CTATCTGTCAACAAA-AAACGTT
65 CTATCTGTCAACAAATAAACCTT
* * * *
237286 CGAGTTCGATTACATTCAGCTCAAAGGCATATC-CA-GTACAACATAACTCAAGGTGAGAAGGGT
1 CGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAACTCAAGGCGAGAAGGGC
* *
237349 TATCTGTCAAC-CA-AGACCTT
66 TATCTGTCAACAAATAAACCTT
* * * * *
237369 CAAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTGCAACATAACTCAAGGCGAGAAGAGC
1 CGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAACTCAAGGCGAGAAGGGC
237434 TATCTGTCAACAAATAAACCTT
66 TATCTGTCAACAAATAAACCTT
* * * *
237456 CGAGTTCGATTACATTCCGTTCAAAGGCATATCCAATTTACAACATAACTCAAGGCGAGAAGGGT
1 CGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAACTCAAGGCGAGAAGGGC
*
237521 TATCTGTCGACAAAT--ACCTT
66 TATCTGTCAACAAATAAACCTT
* * * * * * * * ***
237541 -GAAGTTCGATTCCATTCAGCTCAAGGGCATGTCAAATTCACAGCATAGCTTAAGTCGAGAAAAC
1 CG-AGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAACTCAAGGCGAGAAGGG
237605 CTATCTGTCAACGAAAT
65 CTATCTGTCAAC-AAAT
237622 TATCGAGTTC
Statistics
Matches: 281, Mismatches: 49, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
83 36 0.13
84 36 0.13
85 98 0.35
86 31 0.11
87 80 0.28
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (87 bp):
CGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAACTCAAGGCGAGAAGGGC
TATCTGTCAACAAATAAACCTT
Found at i:237563 original size:172 final size:170
Alignment explanation
Indices: 237204--237621 Score: 577
Period size: 172 Copynumber: 2.4 Consensus size: 170
237194 CAAGGCGAGA
* * *
237204 TTCGATTACACTAAGCTCAAAGGCACATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATC
1 TTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGAGCTATC
*
237269 TGTCAACAAA-AAACGTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAGTACAACATAAC
66 TGTCAACAAATAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAGTACAACATAAC
* *
237333 TCAAGGTGAGAAGGGTTATCTGTCAACCAAGACCTTCAAG
131 TCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAG
* *
237373 TTCGATTACACTCAGCTCAAAGGCACATCAAATTTGCAACATAACTCAAGGCGAGAAGAGCTATC
1 TTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGAGCTATC
* * *
237438 TGTCAACAAATAAACCTTCGAGTTCGATTACATTCCGTTCAAAGGCATATCCAATTTACAACATA
66 TGTCAACAAATAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCC-A-GTACAACATA
* * *
237503 ACTCAAGGCGAGAAGGGTTATCTGTCGACAAATACCTTGAAG
129 ACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAG
* * * ** * * * * * *
237545 TTCGATTCCATTCAGCTCAAGGGCATGTCAAATTCACAGCATAGCTTAAGTCGAGAAAACCTATC
1 TTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGAGCTATC
237610 TGTCAACGAAAT
66 TGTCAAC-AAAT
237622 TATCGAGTTC
Statistics
Matches: 218, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
169 70 0.32
170 38 0.17
171 1 0.00
172 105 0.48
173 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (170 bp):
TTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGAGCTATC
TGTCAACAAATAAACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCCAGTACAACATAAC
TCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAG
Found at i:239365 original size:4 final size:4
Alignment explanation
Indices: 239349--239396 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
239339 TTTATTTCGC
* * *
239349 TTAT TTAT ATAT TTAT TTAT TTTT GTTCTT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT -TT-AT TTAT TTAT TTAT TTAT TT
239397 TTATTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 32 0.84
5 4 0.11
6 2 0.05
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:239405 original size:12 final size:12
Alignment explanation
Indices: 239349--239413 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
239339 TTTATTTCGC
* *
239349 TTATTTATATAT
1 TTATTTATTTTT
239361 TTATTTATTTTT
1 TTATTTATTTTT
* *
239373 GTTCTTTTATTTAT
1 -TT-ATTTATTTTT
239387 TTATTTATTTTT
1 TTATTTATTTTT
239399 ATT-TTTATTATTT
1 -TTATTTATT-TTT
239412 TT
1 TT
239414 CTTTTTACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
12 26 0.60
13 9 0.21
14 8 0.19
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:239407 original size:16 final size:15
Alignment explanation
Indices: 239364--239420 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
239354 TATATATTTA
* *
239364 TTTATTTTTGTT-CT
1 TTTATTTTTATTATT
239378 TTTATTTATTTATTTATT
1 TTTA-TT-TTTA-TTATT
239396 TTTATTTTTATTATT
1 TTTATTTTTATTATT
*
239411 TTTCTTTTTA
1 TTTATTTTTA
239421 CTCAATTGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.11
15 16 0.44
16 7 0.19
17 4 0.11
18 5 0.14
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTATTTTTATTATT
Found at i:239487 original size:21 final size:20
Alignment explanation
Indices: 239444--239487 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
239434 TTCTTTTTTC
* *
239444 TTTTTTATATTAATTTTTCT
1 TTTTTTATATTAATTTCTAT
*
239464 TTTTTTCATATTTATTTCTAT
1 TTTTTT-ATATTAATTTCTAT
239485 TTT
1 TTT
239488 CTAACATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTATATTAATTTCTAT
Found at i:244312 original size:16 final size:16
Alignment explanation
Indices: 244287--244320 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
244277 TAATAAATAA
*
244287 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
244303 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
244319 AC
1 AC
244321 TTTTTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:244459 original size:133 final size:135
Alignment explanation
Indices: 244219--244489 Score: 393
Period size: 133 Copynumber: 2.0 Consensus size: 135
244209 TAGAAAATGG
* * ** * **
244219 TTAGGCCTGTAAACGAACTGACCGTATACGAATTGAGGTATGTTCATGTTCGTTCATTTAATAAA
1 TTAGGCCTGTAAACGAACCGAACACACACGAACGGAGGTATGTTCATGTTCGTTCATTTAATAAA
* * * *
244284 TAAACGAATATAAACGAACACGAACATAAATGAAC-ACTTTTTTT-TCCATGTTCGTTCATTAAG
66 TAAACGAACATAAAAGAACACGAACATAAACGAACAAATTTTTTTGTCCATGTTCGTTCATTAAG
244347 GAATA
131 GAATA
244352 TTAGGCCTGTAAACGAACCGAACACACACGAACGGAGGTATGTTCATGTTCGTTCATTTAATAAA
1 TTAGGCCTGTAAACGAACCGAACACACACGAACGGAGGTATGTTCATGTTCGTTCATTTAATAAA
* *
244417 TAAACGAACATAAAAGAACACGAACATAAACGAATAAATTTTTTTTTGTTCATGTTCGTTCATTA
66 TAAACGAACATAAAAGAACACGAACATAAACGAACAAA--TTTTTTTGTCCATGTTCGTTCATTA
244482 AGGAATA
129 AGGAATA
244489 T
1 T
244490 AGGTTGTTCA
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
133 89 0.74
134 1 0.01
136 7 0.06
137 24 0.20
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (135 bp):
TTAGGCCTGTAAACGAACCGAACACACACGAACGGAGGTATGTTCATGTTCGTTCATTTAATAAA
TAAACGAACATAAAAGAACACGAACATAAACGAACAAATTTTTTTGTCCATGTTCGTTCATTAAG
GAATA
Found at i:244533 original size:10 final size:10
Alignment explanation
Indices: 244518--244557 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
244508 CATTTAAATG
244518 ATAAACGAAC
1 ATAAACGAAC
244528 ATAAACGAAC
1 ATAAACGAAC
*
244538 GTAAACGAAC
1 ATAAACGAAC
*
244548 ACAAACGAAC
1 ATAAACGAAC
244558 GAACACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:244544 original size:20 final size:20
Alignment explanation
Indices: 244519--244558 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
244509 ATTTAAATGA
*
244519 TAAACGAACATAAACGAACG
1 TAAACGAACACAAACGAACG
244539 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
244559 AACACAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:244600 original size:23 final size:23
Alignment explanation
Indices: 244528--244612 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
244518 ATAAACGAAC
*
244528 ATAAACGAACGTAAACGAACACA
1 ATAAACGAACATAAACGAACACA
* * * *
244551 A-ACGAACGAACACAAATGAGCATA
1 ATA--AACGAACATAAACGAACACA
*
244575 ATAAAAGAACATAAACGAACACA
1 ATAAACGAACATAAACGAACACA
*
244598 ATAAACGAATATAAA
1 ATAAACGAACATAAA
244613 AAAAAACACA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
22 1 0.02
23 29 0.62
24 16 0.34
25 1 0.02
ACGTcount: A:0.60, C:0.18, G:0.12, T:0.11
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:247522 original size:15 final size:15
Alignment explanation
Indices: 247504--247596 Score: 114
Period size: 15 Copynumber: 6.2 Consensus size: 15
247494 CGATACTATA
*
247504 AGTACCAATACTGTT
1 AGTACCAATACTGTG
*
247519 AGTACCGATACTGTG
1 AGTACCAATACTGTG
*
247534 AGTGCCAATACTGTG
1 AGTACCAATACTGTG
*
247549 AGTATCAATACTGTG
1 AGTACCAATACTGTG
*
247564 AGTACCAATATTGTG
1 AGTACCAATACTGTG
** *
247579 AGTATTAATACTGCG
1 AGTACCAATACTGTG
247594 AGT
1 AGT
247597 GTAGTACCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 66 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (15 bp):
AGTACCAATACTGTG
Found at i:247530 original size:30 final size:30
Alignment explanation
Indices: 247494--247582 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 30
247484 TTTACATTAT
* * *
247494 CGATACTATAAGTACCAATACTGTTAGTAC
1 CGATACTGTGAGTACCAATACTGTGAGTAC
* *
247524 CGATACTGTGAGTGCCAATACTGTGAGTAT
1 CGATACTGTGAGTACCAATACTGTGAGTAC
* *
247554 CAATACTGTGAGTACCAATATTGTGAGTA
1 CGATACTGTGAGTACCAATACTGTGAGTA
247583 TTAATACTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (30 bp):
CGATACTGTGAGTACCAATACTGTGAGTAC
Found at i:257278 original size:279 final size:280
Alignment explanation
Indices: 256817--257322 Score: 764
Period size: 279 Copynumber: 1.8 Consensus size: 280
256807 TCGTTGGATT
* * *
256817 GTTTGGCTTTATCGCCATCCATTTGCATCGAAGCAGGTCTTATAAAGATCTATGCTATGATTATA
1 GTTTGGCTTTATCGCCATCCATTTGCATCAAAGCAGGTCTTACAAAGATCTATGCTAGGATTATA
* * * *
256882 AGTTTAAAGTTTTCTTAAGAGAACTATTGGCACCAATTTGTGTTTAAGACTGATTCGACAATAGT
66 AGTTTAAAGTTTTCTCAAGAGAACCATTGACACCAAGTTGTGTTTAAGACTGATTCGACAATAGT
* * * *
256947 GGCTAATAAATTGTCTCGTGATGTTGTAGATTTGTCCACTTTAGGATTTCATCTGGCTGAAGCTC
131 GGCTAATAAACTATCTCGTGAAGTGGTAGATTTGTCCACTTTAGGATTTCATCTGGCTGAAGCTC
* *
257012 ATCC-ATTTTGCATACCAATGTATCTTTCAAATTTGGTTTCCATTGGTGTTATAGCTCGAGACTC
196 AGCCTATTTTGCAGACCAATGTATCTTTCAAATTTGGTTTCCATTGGTGTTATAGCTCGAGACTC
257076 TAAAGGTTTACCATTGGACG
261 TAAAGGTTTACCATTGGACG
* * * * * *
257096 GTTTGGCTTTATCGTCATCCATTTGCATCAAAGCGGGTCTTACAGAGATCTATGTTAGGATTGTC
1 GTTTGGCTTTATCGCCATCCATTTGCATCAAAGCAGGTCTTACAAAGATCTATGCTAGGATTATA
* * * *
257161 GGTTTAAAGTTTTCTCAAGAGAACCATTGACACCAAGTTGTGTTTGAGACTGATTCGATAATGGT
66 AGTTTAAAGTTTTCTCAAGAGAACCATTGACACCAAGTTGTGTTTAAGACTGATTCGACAATAGT
257226 GGCTAATAAACTATCTCGTGAAGTGGTAGATTTGTCCA-TATTAGGATTTCATCTGGCTGAAGCT
131 GGCTAATAAACTATCTCGTGAAGTGGTAGATTTGTCCACT-TTAGGATTTCATCTGGCTGAAGCT
* *
257290 CGGCCTATTTTGCAGACTAATGTATCTTTCAAA
195 CAGCCTATTTTGCAGACCAATGTATCTTTCAAA
257323 GTTGTTTTGT
Statistics
Matches: 200, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
278 1 0.00
279 174 0.87
280 25 0.12
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (280 bp):
GTTTGGCTTTATCGCCATCCATTTGCATCAAAGCAGGTCTTACAAAGATCTATGCTAGGATTATA
AGTTTAAAGTTTTCTCAAGAGAACCATTGACACCAAGTTGTGTTTAAGACTGATTCGACAATAGT
GGCTAATAAACTATCTCGTGAAGTGGTAGATTTGTCCACTTTAGGATTTCATCTGGCTGAAGCTC
AGCCTATTTTGCAGACCAATGTATCTTTCAAATTTGGTTTCCATTGGTGTTATAGCTCGAGACTC
TAAAGGTTTACCATTGGACG
Found at i:261175 original size:3 final size:3
Alignment explanation
Indices: 261169--261259 Score: 84
Period size: 3 Copynumber: 31.0 Consensus size: 3
261159 CCATTTGCTT
* *
261169 TTA TTA TTA TTA ATA TAA TTA TTA -TA TTA -TA TTA -TA TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
261214 TTA TTA TTA TTA TTA TTA TT- TTA TTTC TTAA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA
261260 CAGGCCCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
2 9 0.12
3 58 0.81
4 5 0.07
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:261196 original size:5 final size:5
Alignment explanation
Indices: 261188--261229 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
261178 TTAATATAAT
261188 TATTA TATTA TATTA TATTA T-TTA TATTA TTATTA TTATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA -TATTA -TATTA T
261230 TATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 20 0.57
6 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:262690 original size:15 final size:15
Alignment explanation
Indices: 262670--262699 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
262660 AAAAATCCTT
262670 TATAAATTAATTTTA
1 TATAAATTAATTTTA
*
262685 TATAAATTACTTTTA
1 TATAAATTAATTTTA
262700 GGAAATATAC
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:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAAATTAATTTTA
Found at i:262826 original size:147 final size:147
Alignment explanation
Indices: 262669--262963 Score: 359
Period size: 147 Copynumber: 2.0 Consensus size: 147
262659 TAAAAATCCT
262669 TTATAAATTAATTTTATATAAATTACTTTTAG-GAAATATACTATT-TTAATATTTATTT-GTTT
1 TTATAAATTAA-TTTATATAAATTACTTTTAGAGAAATAT--T-TTATTAATATTTATTTAGTTT
* * * *
262731 TTTAATATTAAGAAATGG-CTGTCTTAAAGCA-ACTAGAAGTCCTTTTTTGATATTTTTAACTAA
62 TTTAATATTAAGAAATGGACTGTCTTAAAGCACA-TAGAAGTCATATTCTGATATTTCTAACTAA
262794 ATAAATATCATATTT-TAATAAA
126 ATAAATATCATATTTAT-ATAAA
* * * * * * * *
262816 TTATATATTAATTTATTTTAGTTATTTTTAGAGAAATGTTTTATTGATATTTATTTATTTTTTTA
1 TTATAAATTAATTTATATAAATTACTTTTAGAGAAATATTTTATTAATATTTATTTAGTTTTTTA
* *
262881 ATATTAAGAAATGGACTGTCTTAAAGCACATAGATGTCATATTCTGATATTTCTAAGTAAATAAA
66 ATATTAAGAAATGGACTGTCTTAAAGCACATAGAAGTCATATTCTGATATTTCTAACTAAATAAA
*
262946 TATCTTATTTATATAAA
131 TATCATATTTATATAAA
262963 T
1 T
262964 ATTTTCTTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
144 2 0.02
145 13 0.10
146 37 0.29
147 73 0.57
148 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (147 bp):
TTATAAATTAATTTATATAAATTACTTTTAGAGAAATATTTTATTAATATTTATTTAGTTTTTTA
ATATTAAGAAATGGACTGTCTTAAAGCACATAGAAGTCATATTCTGATATTTCTAACTAAATAAA
TATCATATTTATATAAA
Found at i:263488 original size:28 final size:26
Alignment explanation
Indices: 263457--263514 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
263447 TAATTCTCTC
*
263457 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAAAATATTTATATATA-TTATT
*
263484 ATTTTCATAATATTTATATATATTATT
1 -TTTTCAAAATATTTATATATATTATT
263511 TTTT
1 TTTT
263515 ATTATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 5 0.18
28 19 0.68
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATATTTATATATATTATT
Found at i:278764 original size:18 final size:18
Alignment explanation
Indices: 278737--278774 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
278727 CAAGTTTATC
278737 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
*
278755 TTTTCTAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
278773 TT
1 TT
278775 CTTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:279427 original size:22 final size:22
Alignment explanation
Indices: 279400--279484 Score: 143
Period size: 22 Copynumber: 3.9 Consensus size: 22
279390 ACATCTACAT
279400 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
279422 TTTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
279444 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
279466 TCTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
279485 TATTGGATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:280037 original size:113 final size:113
Alignment explanation
Indices: 279839--280406 Score: 680
Period size: 113 Copynumber: 4.9 Consensus size: 113
279829 CAAAGATTTA
* *
279839 AATTCATCATTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTCGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
279904 AGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* *
279952 AATTCATCATTCGATGGATCAGCATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAATA
1 AATTCATCATTCGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
280017 AGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * *
280065 AATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGA
1 AATTCATCATTCGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * **
280130 AGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAATCTTTTGCTCA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * ** * * *
280178 AATTCATCATTAGATGAATCAATGTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG
1 AATTCATCATTCGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
280242 AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGCATG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * * * * *
280289 -ACTCTATCACAGAAAGAGATAGATCAGCATCAACTTTTTCCAGAG-AAAGTTCATAATGAGAAG
1 AATTC-AT--C------A-TTCGAT--GGATCAAC-ATTGCCA-AGTAGAGTTCATAATGAGAAG
* *
280352 AACTAATCTGAAG-AGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
52 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
280407 GCATGACTGT
Statistics
Matches: 402, Mismatches: 37, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
110 3 0.01
111 7 0.02
112 34 0.08
113 267 0.66
114 1 0.00
119 1 0.00
120 5 0.01
122 7 0.02
123 75 0.19
124 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AATTCATCATTCGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:280276 original size:20 final size:20
Alignment explanation
Indices: 280214--280277 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
280204 TCCAGAGAAA
280214 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
280234 -ATC-TGAA-GAAGAAGAAGAA
1 GTTCAT-AATG-AGAAGAACTT
280253 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
280273 GTTCA
1 GTTCA
280278 ACCTTTGCAT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:280338 original size:123 final size:122
Alignment explanation
Indices: 280202--280496 Score: 475
Period size: 123 Copynumber: 2.4 Consensus size: 122
280192 TGAATCAATG
*
280202 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* *
280267 GAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATCAACTT
66 GAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATAAAC-A
* *
280325 TTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTGAAGAGGAAGAAAAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
* *
280390 GAACTTGTTCAACCTTTGCATGACTGTATCACAGAAGGAGATAGATCAGCATAAACA
66 GAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATAAACA
** * *
280447 TTTCCAGA-ATTGTTCATAATGAGAAGAACTCATATGAAGAAGAAGAAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAGAAGAA
280497 CTTGTTCAAC
Statistics
Matches: 159, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
121 36 0.23
122 8 0.05
123 115 0.72
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (122 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATAAACA
Found at i:280392 original size:20 final size:21
Alignment explanation
Indices: 280334--280393 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 21
280324 TTTTCCAGAG
280334 AAAGTTCATAATGAGAAGAAC
1 AAAGTTCATAATGAGAAGAAC
*
280355 TAA--TC-TGAA-GAGGAAGAA-
1 AAAGTTCAT-AATGA-GAAGAAC
280373 AAAGTTCATAATGAGAAGAAC
1 AAAGTTCATAATGAGAAGAAC
280394 TTGTTCAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 10 0.33
21 5 0.17
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (21 bp):
AAAGTTCATAATGAGAAGAAC
Found at i:280785 original size:3 final size:3
Alignment explanation
Indices: 280779--280913 Score: 131
Period size: 3 Copynumber: 46.0 Consensus size: 3
280769 CCATTTGCTT
* * *
280779 TTA TTA TTA TTA ATA TTA TTA TTA -TG TTA TT- TTA TT- TATA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
280822 TTA TTA TTA TT- TTA TT- TTA TT- TATA CTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
280864 TTTC TTA GTTT 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
280911 TTA
1 TTA
280914 CAGGCCTAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
2 11 0.10
3 94 0.86
4 4 0.04
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:280823 original size:28 final size:29
Alignment explanation
Indices: 280777--280903 Score: 156
Period size: 28 Copynumber: 4.4 Consensus size: 29
280767 ATCCATTTGC
280777 TTTTATTATTA-TTA-A-TATTATTATTA
1 TTTTATTATTATTTATACTATTATTATTA
*
280803 TGTTATT-TTATTTATACTATTATTATTA
1 TTTTATTATTATTTATACTATTATTATTA
280831 TTTTATT-TTATTTATACTATTATTATTA
1 TTTTATTATTATTTATACTATTATTATTA
* * *
280859 TTTTATTTCTTAGTTTTTATTATTATTATTA
1 TTTTA-TTATTA-TTTATACTATTATTATTA
280890 TTATTATTATTATT
1 TT-TTATTATTATT
280904 ATTATTATTA
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
25 3 0.03
26 9 0.10
27 1 0.01
28 43 0.48
29 2 0.02
30 5 0.06
31 23 0.26
32 3 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTATTATTATTTATACTATTATTATTA
Found at i:282398 original size:146 final size:146
Alignment explanation
Indices: 282104--282400 Score: 361
Period size: 146 Copynumber: 2.0 Consensus size: 146
282094 TATTTATTTG
282104 TTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAAT
1 TTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAAT
* ** * * * * *
282169 AAATAAATATCTTATTTTAATAAATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTT
66 AAATAAATATCTTATTTTAATAAATTATATATTAAATTATACTAATAAATTTGAAAGAAATGTAT
* ** *
282234 TATTAATATTTATTTA
131 TATGAATATAAATATA
* *
282250 TTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATT-TCTAAG
1 TTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCT-TAAA
* * *
282314 TAAATAAATATCTTA-TTTATATAAA-TATTTTCTTAAAATTATACTAATAAATTTGAAATAATA
65 TAAATAAATATCTTATTTTA-ATAAATTA-TATATT-AAATTATACTAATAAATTTGAAAGAA-A
282377 TG-ATTATGAAT-TAAATATA
126 TGTATTATGAATATAAATATA
282396 TTTTT
1 TTTTT
282401 GAATTCTTAA
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
145 7 0.05
146 94 0.73
147 25 0.19
148 3 0.02
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (146 bp):
TTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAAT
AAATAAATATCTTATTTTAATAAATTATATATTAAATTATACTAATAAATTTGAAAGAAATGTAT
TATGAATATAAATATA
Found at i:290894 original size:2 final size:2
Alignment explanation
Indices: 290887--290921 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
290877 CTTAAAACAT
290887 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
290922 CCACTTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:291140 original size:2 final size:2
Alignment explanation
Indices: 291135--291166 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
291125 TAAGAGGATA
291135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
291167 GAATAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291654 original size:31 final size:32
Alignment explanation
Indices: 291606--291674 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 32
291596 ATATTCTTCA
* *
291606 ATATTTAATTTTTTAAATATTTGAATATTTTT
1 ATATTTAATGTTTTAAATATTGGAATATTTTT
291638 ATATTTAA-GTTTTAAATATTGGAATATTTTT
1 ATATTTAATGTTTTAAATATTGGAATATTTTT
291669 ATATTT
1 ATATTT
291675 TAAATTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 27 0.77
32 8 0.23
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (32 bp):
ATATTTAATGTTTTAAATATTGGAATATTTTT
Found at i:297418 original size:15 final size:15
Alignment explanation
Indices: 297398--297428 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
297388 ATTTATATAA
297398 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
297413 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
297428 T
1 T
297429 ATCAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTAATTACCTAGAC
Found at i:304667 original size:40 final size:40
Alignment explanation
Indices: 304622--304701 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
304612 TTGTGAAAGC
304622 TTTTAAGGTAAATATGATTTACTAGCTCTATTGTGGTAGT
1 TTTTAAGGTAAATATGATTTACTAGCTCTATTGTGGTAGT
304662 TTTTAAGGTAAATATGATTTACTAGCTCTATTGTGGTAGT
1 TTTTAAGGTAAATATGATTTACTAGCTCTATTGTGGTAGT
304702 CTGAGATGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (40 bp):
TTTTAAGGTAAATATGATTTACTAGCTCTATTGTGGTAGT
Found at i:307053 original size:20 final size:20
Alignment explanation
Indices: 307028--307069 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
307018 CTAAGAGCCT
*
307028 ATTTAGGATCATATAGATGC
1 ATTTAGGAGCATATAGATGC
*
307048 ATTTAGGAGCATATAGTTGC
1 ATTTAGGAGCATATAGATGC
307068 AT
1 AT
307070 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTAGGAGCATATAGATGC
Found at i:309370 original size:178 final size:179
Alignment explanation
Indices: 309071--309428 Score: 700
Period size: 178 Copynumber: 2.0 Consensus size: 179
309061 TTTTTAGTGC
309071 TGATATTTGGTGTCAATATTGTTCTATCAGTATATATATTGATATATTCCAGTATCGATACGACT
1 TGATATTTGGTGTCAATATTGTTCTATCAGTATATATATTGATATATTCCAGTATCGATACGACT
309136 ACTTTCCATTACTTGTACCATTTTTCAACGTTGGAATTTCCAATTTCCAATGTTGGTATTTAGTA
66 ACTTTCCATTACTTGTACCATTTTTCAACGTTGGAATTTCCAATTTCCAATGTTGGTATTTAGTA
309201 TCGATACTGTTATTCTAG-TCGGTACTCGAACCTAGAAATGCATTGTTT
131 TCGATACTGTTATTCTAGATCGGTACTCGAACCTAGAAATGCATTGTTT
309249 TGATATTTGGTGTCAATATTGTTCTATCAGTATATATATTGATATATTCCAGTATCGATACGACT
1 TGATATTTGGTGTCAATATTGTTCTATCAGTATATATATTGATATATTCCAGTATCGATACGACT
309314 ACTTTCCATTACTTGTACCATTTTTCAACGTTGGAATTTCCAATTTCCAATGTTGGTATTTAGTA
66 ACTTTCCATTACTTGTACCATTTTTCAACGTTGGAATTTCCAATTTCCAATGTTGGTATTTAGTA
309379 TCGATACTGTTATTCTAGTATCGGTACTCGAACCTAGAAATGCATTGTTT
131 TCGATACTGTTATTCTAG-ATCGGTACTCGAACCTAGAAATGCATTGTTT
309429 AAGCTCGAAA
Statistics
Matches: 178, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
178 148 0.83
180 30 0.17
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (179 bp):
TGATATTTGGTGTCAATATTGTTCTATCAGTATATATATTGATATATTCCAGTATCGATACGACT
ACTTTCCATTACTTGTACCATTTTTCAACGTTGGAATTTCCAATTTCCAATGTTGGTATTTAGTA
TCGATACTGTTATTCTAGATCGGTACTCGAACCTAGAAATGCATTGTTT
Found at i:311096 original size:24 final size:25
Alignment explanation
Indices: 311063--311109 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
311053 ACATGGTCAT
311063 AATTCATATAA-CACTTATATTACA
1 AATTCATATAATCACTTATATTACA
* *
311087 AATTCCTATAATTACTTATATTA
1 AATTCATATAATCACTTATATTA
311110 ATATCACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTCATATAATCACTTATATTACA
Found at i:316524 original size:85 final size:85
Alignment explanation
Indices: 316424--316588 Score: 269
Period size: 85 Copynumber: 1.9 Consensus size: 85
316414 TACAATCACC
* * *
316424 ACACACGAATGTGTGTTATTTTCATTTATGACGGGGGCTTCAAT-GACACGCAATGTAAGTCATA
1 ACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAG-CACGCAATGTAAGTCATA
**
316488 AATGCGTGTCATAAATTTATG
65 AATGCACGTCATAAATTTATG
316509 ACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAGCACGCAATGTAAGTCATAA
1 ACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAGCACGCAATGTAAGTCATAA
316574 ATGCACGTCATAAAT
66 ATGCACGTCATAAAT
316589 GTGCGTCATA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 73 0.99
86 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (85 bp):
ACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATAGCACGCAATGTAAGTCATAA
ATGCACGTCATAAATTTATG
Found at i:316583 original size:13 final size:13
Alignment explanation
Indices: 316567--316653 Score: 129
Period size: 13 Copynumber: 6.7 Consensus size: 13
316557 CGCAATGTAA
*
316567 GTCATAAATGCAC
1 GTCATAAATGCGC
*
316580 GTCATAAATGTGC
1 GTCATAAATGCGC
316593 GTCATAAATGCGC
1 GTCATAAATGCGC
*
316606 GTCATAAATGTGC
1 GTCATAAATGCGC
*
316619 GTCATAAATGCGT
1 GTCATAAATGCGC
316632 GTCATAAATGCGC
1 GTCATAAATGCGC
*
316645 GTAATAAAT
1 GTCATAAAT
316654 TTATGACGCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 66 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:319162 original size:31 final size:31
Alignment explanation
Indices: 319124--319251 Score: 127
Period size: 31 Copynumber: 4.1 Consensus size: 31
319114 GAACCTCGAC
* *
319124 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
319155 AACTGTCCATATGT-TCATTAGAACATAGGTA
1 AACTGTCCATATGTCCCA-AAGAACATAGGTA
*
319186 TACTGTCCATATGTCCCAAA-AGACATAGGTA
1 AACTGTCCATATGTCCCAAAGA-ACATAGGTA
* * *
319217 ATTA-TGTCCATATGTTCTATAGAACATAGGTA
1 A--ACTGTCCATATGTCCCAAAGAACATAGGTA
319249 AAC
1 AAC
319252 CCTCAACTCT
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
30 4 0.05
31 47 0.59
32 26 0.33
33 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:319240 original size:63 final size:62
Alignment explanation
Indices: 319125--319248 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 62
319115 AACCTCGACA
*
319125 ACTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCATTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCATTAGAACATAGGTAT
*
319187 ACTGTCCATATGTCCCAAA-AGACATAGGTAATTA-TGTCCATATGTTC-TATAGAACATAGGTA
1 ACTGTCCATAGGTCCCAAAGA-ACATAGGTAA--ACTGTCCATATGTTCAT-TAGAACATAGGTA
319249 AACCCTCAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
61 1 0.02
62 28 0.50
63 26 0.46
64 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCATTAGAACATAGGTAT
Found at i:319589 original size:24 final size:25
Alignment explanation
Indices: 319556--319602 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
319546 ACATGGTCAT
319556 AATTCATATAA-CACTTATATTACA
1 AATTCATATAATCACTTATATTACA
* *
319580 AATTCCTATAATTACTTATATTA
1 AATTCATATAATCACTTATATTA
319603 ATATCACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTCATATAATCACTTATATTACA
Found at i:321069 original size:32 final size:32
Alignment explanation
Indices: 321032--321118 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 32
321022 ATTAACACTA
* *
321032 TTGTGCATTATTTGAATGTGACACTGAAATTG
1 TTGTGCATTATATGAATGTGACACCGAAATTG
* * *
321064 TTGTGCATTATCTAAATGTG-CACCGACATTG
1 TTGTGCATTATATGAATGTGACACCGAAATTG
* * *
321095 CTATGTATTATATGAATGTGACAC
1 TTGTGCATTATATGAATGTGACAC
321119 ATTACAAGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 24 0.53
32 21 0.47
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
TTGTGCATTATATGAATGTGACACCGAAATTG
Found at i:324903 original size:5 final size:5
Alignment explanation
Indices: 324893--324919 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
324883 TCCTGCTTTG
324893 CCTTC CCTTC CCTTC CCTTC CCTTC CC
1 CCTTC CCTTC CCTTC CCTTC CCTTC CC
324920 AGGAACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (5 bp):
CCTTC
Found at i:339498 original size:17 final size:16
Alignment explanation
Indices: 339467--339500 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
339457 CACGTGAGGA
339467 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
339483 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
339500 T
1 T
339501 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:343489 original size:2 final size:2
Alignment explanation
Indices: 343482--343506 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
343472 TGAATGTTTC
343482 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
343507 TTGGTTTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:344340 original size:22 final size:22
Alignment explanation
Indices: 344312--344362 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
344302 TTTTACACAT
344312 AGTGTACCGATACACTCTTGAG
1 AGTGTACCGATACACTCTTGAG
344334 AGTGTACCGATACACTCTTGAG
1 AGTGTACCGATACACTCTTGAG
344356 AGTGTAC
1 AGTGTAC
344363 GATGCACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (22 bp):
AGTGTACCGATACACTCTTGAG
Found at i:345426 original size:26 final size:26
Alignment explanation
Indices: 345397--345449 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
345387 CTAAATTTAG
345397 AGTAGAAAGGAGACTACAATTGTCTA
1 AGTAGAAAGGAGACTACAATTGTCTA
345423 AGTAGAAAGGAGACTACAATTGTCTA
1 AGTAGAAAGGAGACTACAATTGTCTA
345449 A
1 A
345450 ATACTACGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (26 bp):
AGTAGAAAGGAGACTACAATTGTCTA
Found at i:346386 original size:167 final size:166
Alignment explanation
Indices: 346101--346602 Score: 828
Period size: 167 Copynumber: 3.0 Consensus size: 166
346091 GTCACTAAAA
* * * *
346101 AGAAAGTTGACATTCAATGTATAACCATATTAATCGATAAAATATTTAGATTAAAATAAAATTTT
1 AGAAAGTTGACATTCAATGTATAACCAAATTAATTGATAAAATATTTTGATTAAAATAATATTTT
* * * * * * *
346166 T-ATTTTATATTTTAATTGAAATATTTTAAAATTAATTTAAATCCTGCACATAATTTAATGGGAA
66 TGATTTGATGTTTTAATTAAAATATTTTAAAGTTAATTTAAATCCTGTACATAATTTGATGTGAA
346230 CTTTTATGTAACAGTAGCTTACAATCATATGTGCGG
131 CTTTTATGTAACAGTAGCTTACAATCATATGTGCGG
*
346266 AGAAATGTTGACA-TCTAATGTTTAACCAAATTAATTGATAAAATATTTTGATTAAAATAATATT
1 AGAAA-GTTGACATTC-AATGTATAACCAAATTAATTGATAAAATATTTTGATTAAAATAATATT
346330 TTTGATTTGATGTTTTAATTAAAATATTTTAAAGTTAATTTAAATCCTGTACATAATTTGATGTG
64 TTTGATTTGATGTTTTAATTAAAATATTTTAAAGTTAATTTAAATCCTGTACATAATTTGATGTG
346395 AACTTTTATGTAACAGTAGCTTACAATCATATGTGCGG
129 AACTTTTATGTAACAGTAGCTTACAATCATATGTGCGG
346433 AGAAAAGTTGACATTCAATGTATAACCAAATTAATTGATAAAATATTTTGATTAAAATAATATTT
1 AG-AAAGTTGACATTCAATGTATAACCAAATTAATTGATAAAATATTTTGATTAAAATAATATTT
*
346498 TTGATTTGATGTTTTAATTAAAATATTTTAAAGTTAATTTAAATCCTGTACATAATTTGATATGA
65 TTGATTTGATGTTTTAATTAAAATATTTTAAAGTTAATTTAAATCCTGTACATAATTTGATGTGA
* *
346563 ACTTTTATGCAACAGTATCTTACAATCATATGTGCGG
130 ACTTTTATGTAACAGTAGCTTACAATCATATGTGCGG
346600 AGA
1 AGA
346603 GATCGGGATG
Statistics
Matches: 316, Mismatches: 16, Indels: 9
0.93 0.05 0.03
Matches are distributed among these distances:
165 7 0.02
166 54 0.17
167 250 0.79
168 5 0.02
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.40
Consensus pattern (166 bp):
AGAAAGTTGACATTCAATGTATAACCAAATTAATTGATAAAATATTTTGATTAAAATAATATTTT
TGATTTGATGTTTTAATTAAAATATTTTAAAGTTAATTTAAATCCTGTACATAATTTGATGTGAA
CTTTTATGTAACAGTAGCTTACAATCATATGTGCGG
Found at i:350637 original size:16 final size:16
Alignment explanation
Indices: 350616--350650 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
350606 TTTTTATGTA
*
350616 TTCCTCTTAAGTATAT
1 TTCCTCCTAAGTATAT
350632 TTCCTCCTAAGTATAT
1 TTCCTCCTAAGTATAT
350648 TTC
1 TTC
350651 AATTTATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (16 bp):
TTCCTCCTAAGTATAT
Found at i:351990 original size:60 final size:63
Alignment explanation
Indices: 351895--352067 Score: 203
Period size: 64 Copynumber: 2.8 Consensus size: 63
351885 ATTCGCTGTG
* * *
351895 AAATTGAGCTTTGAATTGGATATTCTTT-GTTGTGAAGTTGAAATCCAA-GGA-T-TGTTTCACC
1 AAATTGA-TTTTGAGTTGGATA-TCTTTCGTTGTGAAGTTGAAATCCAATGGAGTAAGTTTCACC
* *
351956 AAATTGATTTTGAGTTGGATATCTTTCGTCGTGAAGTTG-AATCCAATCTTGAGTAAGTTTCACC
1 AAATTGATTTTGAGTTGGATATCTTTCGTTGTGAAGTTGAAATCCAA--TGGAGTAAGTTTCACC
* * *
352020 AAATTGGTTTTGAGTTAGATATCCTTCGTTGTGAAGTTGAAATCCAAT
1 AAATTGATTTTGAGTTGGATATCTTTCGTTGTGAAGTTGAAATCCAAT
352068 CTTGAGTAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
59 12 0.12
60 23 0.24
61 7 0.07
62 2 0.02
63 2 0.02
64 43 0.45
65 7 0.07
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (63 bp):
AAATTGATTTTGAGTTGGATATCTTTCGTTGTGAAGTTGAAATCCAATGGAGTAAGTTTCACC
Found at i:352031 original size:64 final size:65
Alignment explanation
Indices: 351948--352076 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 65
351938 TCCAAGGATT
* *
351948 GTTTCACCAAATTGATTTTGAGTTGGATATCTTTCGTCGTGAAGTTG-AATCCAATCTTGAGTAA
1 GTTTCACCAAATTGATTTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAA
* *
352012 GTTTCACCAAATTGGTTTTGAGTTAGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAA
1 GTTTCACCAAATTGATTTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAA
352077 ATTGTGTCAC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 43 0.72
65 17 0.28
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (65 bp):
GTTTCACCAAATTGATTTTGAGTTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAA
Found at i:353767 original size:201 final size:201
Alignment explanation
Indices: 353422--353823 Score: 804
Period size: 201 Copynumber: 2.0 Consensus size: 201
353412 TACTGAAACT
353422 CCTTATTTAGATAAATTTAATTTAATTTTCCATTGTCTGGCTAGCTGAATCCATAAAGTCGGGGT
1 CCTTATTTAGATAAATTTAATTTAATTTTCCATTGTCTGGCTAGCTGAATCCATAAAGTCGGGGT
353487 GTTTAACCAATTACTCTAGAGGGACAACTCAATATATAAACATATTTATCAAGTTAGCTGAATCT
66 GTTTAACCAATTACTCTAGAGGGACAACTCAATATATAAACATATTTATCAAGTTAGCTGAATCT
353552 TATCCATAAAGTCGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATATAT
131 TATCCATAAAGTCGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATATAT
353617 ATTATA
196 ATTATA
353623 CCTTATTTAGATAAATTTAATTTAATTTTCCATTGTCTGGCTAGCTGAATCCATAAAGTCGGGGT
1 CCTTATTTAGATAAATTTAATTTAATTTTCCATTGTCTGGCTAGCTGAATCCATAAAGTCGGGGT
353688 GTTTAACCAATTACTCTAGAGGGACAACTCAATATATAAACATATTTATCAAGTTAGCTGAATCT
66 GTTTAACCAATTACTCTAGAGGGACAACTCAATATATAAACATATTTATCAAGTTAGCTGAATCT
353753 TATCCATAAAGTCGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATATAT
131 TATCCATAAAGTCGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATATAT
353818 ATTATA
196 ATTATA
353824 ATCACCTTTA
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (201 bp):
CCTTATTTAGATAAATTTAATTTAATTTTCCATTGTCTGGCTAGCTGAATCCATAAAGTCGGGGT
GTTTAACCAATTACTCTAGAGGGACAACTCAATATATAAACATATTTATCAAGTTAGCTGAATCT
TATCCATAAAGTCGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTATATAT
ATTATA
Found at i:353918 original size:98 final size:98
Alignment explanation
Indices: 353748--353924 Score: 302
Period size: 99 Copynumber: 1.8 Consensus size: 98
353738 AAGTTAGCTG
* *
353748 AATCTTATCCATAAAGTCGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTGTA
1 AATCTTATCCATAAAGTCGGGAGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTATA
353813 TATATATTATAATCACCTTTATCATGCTAGTTA
66 TATATATTATAATCACCTTTATCATGCTAGTTA
* *
353846 AATCTTATCCATAAAGTCGGGGAGTTTAACCAATTGCTTTAGAGGGATAACTCAAGCTTTATTAT
1 AATCTTATCCATAAAGTC-GGGAGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTAT
353911 ATA-ATATTATAATC
65 ATATATATTATAATC
353925 TGGGTATACG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
98 29 0.39
99 45 0.61
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (98 bp):
AATCTTATCCATAAAGTCGGGAGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTTTATTATA
TATATATTATAATCACCTTTATCATGCTAGTTA
Found at i:357601 original size:30 final size:29
Alignment explanation
Indices: 357562--357620 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
357552 GAGAATTTAC
* *
357562 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
357591 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
357621 TATATTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:357894 original size:23 final size:23
Alignment explanation
Indices: 357841--357894 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
357831 TCCTTAGGGA
* * *
357841 CATTT-TATATGGCACTTCGGTG
1 CATTTCTACATGGCACTACAGTG
* *
357863 CAATCCTACATGGCACTACAGTG
1 CATTTCTACATGGCACTACAGTG
357886 CATTTCTAC
1 CATTTCTAC
357895 GCGGAACTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (23 bp):
CATTTCTACATGGCACTACAGTG
Found at i:362431 original size:23 final size:23
Alignment explanation
Indices: 362405--362467 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
362395 ACATTTTATA
*
362405 TGGCACTTCGGTGCAATCCTATG
1 TGGCACTTCGGTGCAATCCTACG
* * *
362428 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATCCTACG
* *
362451 CGGCACTTTGGTGCAAT
1 TGGCACTTCGGTGCAAT
362468 TATATAAGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATCCTACG
Found at i:362645 original size:28 final size:26
Alignment explanation
Indices: 362583--362647 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
362573 TACATGTGAT
*
362583 TTGTATGATTTTATGCTATGAATTGTA
1 TTGTATGATTTTATGC-ATGAATTGGA
*
362610 TTATATGATTTATATG-ATGATATGTGGA
1 TTGTATGATTT-TATGCATGA-AT-TGGA
362638 TTGTATGATT
1 TTGTATGATT
362648 AAATGAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 4 0.12
27 12 0.38
28 16 0.50
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.51
Consensus pattern (26 bp):
TTGTATGATTTTATGCATGAATTGGA
Found at i:368775 original size:14 final size:14
Alignment explanation
Indices: 368753--368791 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
368743 ACTTTTTATA
368753 TTAATTATAATCT-
1 TTAATTATAATCTC
368766 TTATATTATAA-CTC
1 TTA-ATTATAATCTC
368780 TTAATTATAATC
1 TTAATTATAATC
368792 ATTAAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATTATAATCTC
Found at i:368788 original size:13 final size:13
Alignment explanation
Indices: 368753--368796 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
368743 ACTTTTTATA
368753 TTAATTATAATCT
1 TTAATTATAATCT
368766 TTATATTATAA-CT
1 TTA-ATTATAATCT
*
368779 CTTAATTATAATCA
1 -TTAATTATAATCT
368793 TTAA
1 TTAA
368797 ACTAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTATAATCT
Found at i:369269 original size:29 final size:30
Alignment explanation
Indices: 369203--369274 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
369193 GGCGATTTGA
*
369203 CCTAACTAACACCTTATAAACCTATAATGC
1 CCTAACTAACACCTTATAAACCAATAATGC
* * *
369233 CCGAACTAACACCGTT-T-AACCAATATTTC
1 CCTAACTAACACC-TTATAAACCAATAATGC
369262 CCTAACTAACACC
1 CCTAACTAACACC
369275 CTTTCGGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.58
30 13 0.36
31 2 0.06
ACGTcount: A:0.38, C:0.33, G:0.04, T:0.25
Consensus pattern (30 bp):
CCTAACTAACACCTTATAAACCAATAATGC
Found at i:372891 original size:137 final size:137
Alignment explanation
Indices: 372657--372990 Score: 483
Period size: 137 Copynumber: 2.4 Consensus size: 137
372647 TGAAAACAAG
* * * *
372657 TTTCAGGGGGCGCGCCTTCCATTATTTTGTCGGA-AATAGGTTATAATTGCCTTATTATGACTCA
1 TTTCAAGGGGCGTGCCTTCCATTATTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGACTCA
** * *
372721 TGTCCCCCAGGGGCACTATTCATGTTAGTACCTATCATGTTTGAGAGGACGCAGCAAAGTGGTGA
66 TGTCCCCCAGACGAACTATTCATGTTAGTACCTATCATGTTTGAGAGAACGCAGCAAAGTGGTGA
372786 AAGCGCA
131 AAGCGCA
* *
372793 TTTCAAGGGGCGTGCCTTCCAATATTTTGTCATAGAATAGGTTATAATTGCCCTATTATGACTCA
1 TTTCAAGGGGCGTGCCTTCCATTATTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGACTCA
* *
372858 TGTCCCCCAGACGAACTATTCATGTTAGTACCTATCATGTTTGAGAGAACGCAGTAAAGTTGTGA
66 TGTCCCCCAGACGAACTATTCATGTTAGTACCTATCATGTTTGAGAGAACGCAGCAAAGTGGTGA
*
372923 AAGCGCG
131 AAGCGCA
* * * * *
372930 TTTC-AGGGAGCGTGCCTTTCATTGTTTTGTCAGAGAATAGGTCATAATTTCCCTATCATGA
1 TTTCAAGGG-GCGTGCCTTCCATTATTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGA
372991 ATGCATCAAA
Statistics
Matches: 176, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
136 33 0.19
137 143 0.81
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (137 bp):
TTTCAAGGGGCGTGCCTTCCATTATTTTGTCAGAGAATAGGTTATAATTGCCCTATTATGACTCA
TGTCCCCCAGACGAACTATTCATGTTAGTACCTATCATGTTTGAGAGAACGCAGCAAAGTGGTGA
AAGCGCA
Found at i:373056 original size:85 final size:85
Alignment explanation
Indices: 372913--373070 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
372903 AGAACGCAGT
* ** * *
372913 AAAGTTGTGAAAGCGCGTTTCAGGGAGCGTGCCTTTCATTGTTTTGTCAGAGAATAGGTCATAAT
1 AAAGTGGTGAAAGCGCGTTTCAGGGAGCACGACTTTCATTATTTTGTCAGAGAATAGGTCATAAT
372978 TTCCCTATCATGAATGCATC
66 TTCCCTATCATGAATGCATC
* * * *
372998 AAAGTGGTGAAAGTGCGTTTCAGGGGGCACGAC-TTCTATTATTTTGTCATAGAATAGGTTATAA
1 AAAGTGGTGAAAGCGCGTTTCAGGGAGCACGACTTTC-ATTATTTTGTCAGAGAATAGGTCATAA
373062 TTTCCCTAT
65 TTTCCCTAT
373071 TATGTGACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 3 0.05
85 60 0.95
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (85 bp):
AAAGTGGTGAAAGCGCGTTTCAGGGAGCACGACTTTCATTATTTTGTCAGAGAATAGGTCATAAT
TTCCCTATCATGAATGCATC
Found at i:373200 original size:361 final size:359
Alignment explanation
Indices: 372656--373348 Score: 917
Period size: 361 Copynumber: 1.9 Consensus size: 359
372646 GTGAAAACAA
* * * *
372656 GTTTCAGGGGGCGCGCCTTCCATTATTTTGTCGGAAATAGGTTATAATTGCCTTATTATGACTCA
1 GTTTCAGGGGGCACGACTTCCATTATTTTGTCAGAAATAGGTTATAATTGCCCTATTATGACTCA
* * * *
372721 TGTCCCCCAGGGGCACTATTCATGTTAGTACCTATCATGTTTGAGAGGACGCAGCAAAGTGGTGA
66 TGCCCCCCAGGGGCACTATTCATGTCAGTACATATCATGTTTGAGAGGACGCAACAAAGTGGTGA
* ** * *
372786 AAGCGCATTTCAAGGGGCGTGCCTTCCAATATTTTGTCATAGAATAGGTTATAATTGCCCTATTA
131 AAACGCATTTCAAGGGGCACGCCTTCCAATATTTCGTCAGAGAATAGGTTATAATTGCCCTATTA
* *
372851 -TGACTCATGTCCCCCAGACGAACTATTCATGTTAGTACCTATCATGTTTGAGAGAACGCAGTAA
196 GTGACTCATGTCCCCC-GACGAACTATTCATGTAAGTACCTATCATGTTTGAGAGAACGCAGCAA
* * * *
372915 AGTTGTGAAAGCGCGTTTCAGG-GAGCGTGCCTTTCATT-GTTTTGTCAGAGAATAGGTCATAAT
260 AGTGGTGAAAGCACGTTTCAGGTG-GCGCGCCTTCCATTAGTTTTGTCAGAGAATAGGTCATAAT
372978 TTCCCTATCATGAATGCATCAAAGTGGTGAAAGTGC
324 TTCCCTATCATGAATGCATCAAAGTGGTGAAAGTGC
* * *
373014 GTTTCAGGGGGCACGACTTCTATTATTTTGTCATAGAATAGGTTATAATTTCCCTATTATGTGAC
1 GTTTCAGGGGGCACGACTTCCATTATTTTGTCAGA-AATAGGTTATAATTGCCCTATTA--TGAC
* * *
373079 TCATGCCCCCCGGGGGCACTATTCATGTCGGTACATATCATGTTTGATG-GGACGCAATAAAGTG
63 TCATGCCCCCCAGGGGCACTATTCATGTCAGTACATATCATGTTTGA-GAGGACGCAACAAAGTG
* * * * * * *
373143 GTGAAAATGCATTTTAGGGGGCACGCCTTCTATTATTTCGTTAGAGAATATGTTATAATTGCCCT
127 GTGAAAACGCATTTCAAGGGGCACGCCTTCCAATATTTCGTCAGAGAATAGGTTATAATTGCCCT
** * * * *
373208 ATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTAAGTATCTATCATGTTTGAGGGGACGCA
192 ATTA-GTGACTCATGTCCCCCGACGAACTATTCATGTAAGTACCTATCATGTTTGAGAGAACGCA
* * * *
373273 GCAAAGTGGTGAAAGCACGTTTCAGGTGGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTAT
256 GCAAAGTGGTGAAAGCACGTTTCAGGTGGCGCGCCTTCCATTAGTTTTGTCAGAGAATAGGTCAT
373338 AATTTCCCTAT
321 AATTTCCCTAT
373349 TATGTGACTC
Statistics
Matches: 285, Mismatches: 42, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
358 30 0.11
359 21 0.07
361 116 0.41
362 73 0.26
363 45 0.16
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (359 bp):
GTTTCAGGGGGCACGACTTCCATTATTTTGTCAGAAATAGGTTATAATTGCCCTATTATGACTCA
TGCCCCCCAGGGGCACTATTCATGTCAGTACATATCATGTTTGAGAGGACGCAACAAAGTGGTGA
AAACGCATTTCAAGGGGCACGCCTTCCAATATTTCGTCAGAGAATAGGTTATAATTGCCCTATTA
GTGACTCATGTCCCCCGACGAACTATTCATGTAAGTACCTATCATGTTTGAGAGAACGCAGCAAA
GTGGTGAAAGCACGTTTCAGGTGGCGCGCCTTCCATTAGTTTTGTCAGAGAATAGGTCATAATTT
CCCTATCATGAATGCATCAAAGTGGTGAAAGTGC
Found at i:373358 original size:139 final size:137
Alignment explanation
Indices: 372997--373624 Score: 762
Period size: 139 Copynumber: 4.6 Consensus size: 137
372987 ATGAATGCAT
* * * * * *
372997 CAAAGTGGTGAAAGTGCGTTTCAGGGGGCACGACTTCTATTATTTTGTCATAGAATAGGTTATAA
1 CAAAGTGGTGAAAGCGCGTTTCA-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAA
* * *
373062 TTTCCCTATTATGTGACTCATGCCCCCCGGGGGCACTATTCATGTCGGTA-CATATCATGTTTGA
65 TTGCCCTATTATGTGACTCATGTCCCCC-GGGGCACTATTCATGTCAGTATC-TATCATGTTTGA
*
373126 TGGGACGCAA
128 GGGGACGCAA
* ** * * * * * *
373136 TAAAGTGGTGAAAATGCATTTTAGGGGGCACGCCTTCTATTATTTCGTTAGAGAATATGTTATAA
1 CAAAGTGGTGAAAGCGCGTTTCA-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAA
*
373201 TTGCCCTATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTAAGTATCTATCATGTTTGAGG
65 TTGCCCTATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTCAGTATCTATCATGTTTGAGG
*
373266 GGACGCAG
130 GGACGCAA
* *
373274 CAAAGTGGTGAAAGCACGTTTCAGGTGGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTATA
1 CAAAGTGGTGAAAGCGCGTTTCAGG-GGCGCGCCTTCCATTA-TTTTGTCAGAGAATATGTTATA
* * * *
373339 ATTTCCCTATTATGTGACTCATGTCCCCCGGGGCTCTATTTATGTCAGTACCTATCATGTTTGAG
64 ATTGCCCTATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTCAGTATCTATCATGTTTGAG
*
373404 GGGACGTAA
129 GGGACGCAA
* * *
373413 TAAAGTGTTGAAAGCGCGTTTCAGGGGACGCGCCTTCCATTATTTTGTCAGAAAATATGTTATAA
1 CAAAGTGGTGAAAGCGCGTTTCAGGGG-CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAA
* * * * * * *
373478 TTGCCCTATTATATGAATCATGTCGCCCGGGGCACTATTTATGTCAGTGTCTATCATGTTTAAAG
65 TTGCCCTATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTCAGTATCTATCATGTTTGAGG
*
373543 GGACGCAG
130 GGACGCAA
* * * *
373551 CAAAGTGGTGAAAGCGCGTTTCAAGGGGTGCGCCTTCCCTT-TTTT-T-TG-TAATATGTTATAA
1 CAAAGTGGTGAAAGCGCGTTTC-AGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAA
373612 TTGCCCTATTATG
65 TTGCCCTATTATG
373625 CTTGAAATTT
Statistics
Matches: 429, Mismatches: 55, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
134 24 0.06
135 1 0.00
136 1 0.00
137 6 0.01
138 187 0.44
139 210 0.49
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (137 bp):
CAAAGTGGTGAAAGCGCGTTTCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATAAT
TGCCCTATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTCAGTATCTATCATGTTTGAGGG
GACGCAA
Found at i:373501 original size:277 final size:277
Alignment explanation
Indices: 372997--373624 Score: 847
Period size: 277 Copynumber: 2.3 Consensus size: 277
372987 ATGAATGCAT
* * * * * * *
372997 CAAAGTGGTGAAAGTGCGTTTCAGGGGGCACGACTTCTATTA-TTTTGTCATAGAATAGGTTATA
1 CAAAGTGGTGAAAGCGCGTTTCA-GGGGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTATA
*
373061 ATTTCCCTATTATGTGACTCATGCCCCCCGGGGGCACTATTCATGTCGGTACATATCATGTTTGA
65 ATTTCCCTATTATGTGACTCATGCCCCCCGGGGGCACTATTCATGTCAGTACATATCATGTTTGA
* * * * * * *
373126 TGGGACGCAATAAAGTGGTGAAAATGCATTTTAGGGGGCACGCCTTCTATTATTTCGTTAGAGAA
130 GGGGACGCAATAAAGTGGTGAAAACGCATTTCAGGGGACACGCCTTCCATTATTTCGTCAGAAAA
* *
373191 TATGTTATAATTGCCCTATTATGTGACTCATGTCCCCCGGGGCACTATTCATGTAAGTATCTATC
195 TATGTTATAATTGCCCTATTATATGAATCATGTCCCCCGGGGCACTATTCATGTAAGTATCTATC
* *
373256 ATGTTTGAGGGGACGCAG
260 ATGTTTAAAGGGACGCAG
*
373274 CAAAGTGGTGAAAGCACGTTTCAGGTGGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTATA
1 CAAAGTGGTGAAAGCGCGTTTCAGG-GGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTATA
* * * *
373339 ATTTCCCTATTATGTGACTCATGTCCCCC-GGGGCTCTATTTATGTCAGTACCTATCATGTTTGA
65 ATTTCCCTATTATGTGACTCATGCCCCCCGGGGGCACTATTCATGTCAGTACATATCATGTTTGA
* * * * * *
373403 GGGGACGTAATAAAGTGTTGAAAGCGCGTTTCAGGGGACGCGCCTTCCATTATTTTGTCAGAAAA
130 GGGGACGCAATAAAGTGGTGAAAACGCATTTCAGGGGACACGCCTTCCATTATTTCGTCAGAAAA
* * * *
373468 TATGTTATAATTGCCCTATTATATGAATCATGTCGCCCGGGGCACTATTTATGTCAGTGTCTATC
195 TATGTTATAATTGCCCTATTATATGAATCATGTCCCCCGGGGCACTATTCATGTAAGTATCTATC
373533 ATGTTTAAAGGGACGCAG
260 ATGTTTAAAGGGACGCAG
* *
373551 CAAAGTGGTGAAAGCGCGTTTCAAGGGGTGCGCCTTCCCTT-TTTTT-T--G-TAATATGTTATA
1 CAAAGTGGTGAAAGCGCGTTTC-AGGGGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTATA
*
373611 ATTGCCCTATTATG
65 ATTTCCCTATTATG
373625 CTTGAAATTT
Statistics
Matches: 310, Mismatches: 38, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
272 25 0.08
273 1 0.00
275 1 0.00
276 7 0.02
277 226 0.73
278 50 0.16
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (277 bp):
CAAAGTGGTGAAAGCGCGTTTCAGGGGCGCGCCTTCCATTATTTTTGTCAGATAATATGTTATAA
TTTCCCTATTATGTGACTCATGCCCCCCGGGGGCACTATTCATGTCAGTACATATCATGTTTGAG
GGGACGCAATAAAGTGGTGAAAACGCATTTCAGGGGACACGCCTTCCATTATTTCGTCAGAAAAT
ATGTTATAATTGCCCTATTATATGAATCATGTCCCCCGGGGCACTATTCATGTAAGTATCTATCA
TGTTTAAAGGGACGCAG
Found at i:374513 original size:21 final size:21
Alignment explanation
Indices: 374484--374550 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
374474 TGTGTCATAA
*
374484 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
* * *
374505 AACCTTGCGGGCTGGGTATGT
1 AACCCTGCGGGCTAGGAATGT
* *
374526 ACCCCTGTGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
374547 AACC
1 AACC
374551 ATGCAGAGAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.22
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:374943 original size:11 final size:11
Alignment explanation
Indices: 374915--374944 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
374905 CCGGTTCTCC
*
374915 CTAATCGCAAT
1 CTAATCTCAAT
374926 CTAATCTCAAT
1 CTAATCTCAAT
374937 CTAATCTC
1 CTAATCTC
374945 TGTGTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (11 bp):
CTAATCTCAAT
Found at i:375217 original size:17 final size:17
Alignment explanation
Indices: 375195--375230 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
375185 CCACTGAAAC
375195 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
375212 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
375229 AT
1 AT
375231 TATATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:376457 original size:30 final size:29
Alignment explanation
Indices: 376395--376488 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
376385 TAGCATATAT
* * * *
376395 AATAATTA-ATTAATAAATTTAAATAAAT
1 AATAATTATATAAATATATTTTAATAAAA
376423 AATAATTATATAAATACTATTTTAATAAAA
1 AATAATTATATAAATA-TATTTTAATAAAA
* *
376453 AATAATATTTATATAAT-TATATTAATAAAA
1 AATAAT-TATATA-AATATATTTTAATAAAA
376483 AATAAT
1 AATAAT
376489 AACTATTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.14
29 6 0.11
30 34 0.61
31 5 0.09
32 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
AATAATTATATAAATATATTTTAATAAAA
Found at i:376489 original size:30 final size:32
Alignment explanation
Indices: 376414--376499 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 32
376404 TTAATAAATT
*
376414 TAAATAAATAATAATTATATAAATACTATTTTAA
1 TAAA-AAATAATAATTATATAAATA-TATATTAA
*
376448 TAAAAAATAATATTTATAT-AAT-TATATTAA
1 TAAAAAATAATAATTATATAAATATATATTAA
* *
376478 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
376500 AAATATACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 23 0.50
31 2 0.04
32 3 0.07
33 14 0.30
34 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATATTAA
Found at i:376837 original size:61 final size:61
Alignment explanation
Indices: 376740--376887 Score: 201
Period size: 61 Copynumber: 2.4 Consensus size: 61
376730 AATACCTGCA
* * *
376740 AAAGCGCGACCTCAGGGATGCTCCTTACCCGCGTGGCATCCCAGTCAGCTAAAATCCC--GT
1 AAAGCGCGTCCCCAGGGATGCACCTTACCCGCGTGGCATCCCAGTCAGCTAAAA-CCCTGGT
* * * *
376800 GAAAGCGCGTCCCCAGGGATGCGCCTTACCCGTGTGGCATCCTAGTTAGCTAAAACCCTGGT
1 -AAAGCGCGTCCCCAGGGATGCACCTTACCCGCGTGGCATCCCAGTCAGCTAAAACCCTGGT
376862 AAAGCGCGTCCCCAGGGATGCACCTT
1 AAAGCGCGTCCCCAGGGATGCACCTT
376888 TGTGCCAGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
60 3 0.04
61 73 0.94
62 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (61 bp):
AAAGCGCGTCCCCAGGGATGCACCTTACCCGCGTGGCATCCCAGTCAGCTAAAACCCTGGT
Found at i:377723 original size:2 final size:2
Alignment explanation
Indices: 377712--377741 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
377702 TACATATTAC
377712 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
377742 CTTATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:377873 original size:20 final size:19
Alignment explanation
Indices: 377838--377879 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
377828 TTAACTTTTT
*
377838 TTAATTTTTTTTATTTGAA
1 TTAATTTTTATTATTTGAA
*
377857 TTAATTTCTTATTATTTTAA
1 TTAATTT-TTATTATTTGAA
377877 TTA
1 TTA
377880 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTAATTTTTATTATTTGAA
Found at i:378076 original size:2 final size:2
Alignment explanation
Indices: 378069--378179 Score: 215
Period size: 2 Copynumber: 56.0 Consensus size: 2
378059 ATTTAAGCCC
378069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378153 AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378180 TTTTTCCTCA
Statistics
Matches: 108, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 107 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:379398 original size:13 final size:13
Alignment explanation
Indices: 379380--379404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379370 AAAATGATCG
379380 TAATTCAAATTTC
1 TAATTCAAATTTC
379393 TAATTCAAATTT
1 TAATTCAAATTT
379405 GTAAAATTAT
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:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTCAAATTTC
Found at i:380476 original size:16 final size:17
Alignment explanation
Indices: 380455--380487 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
380445 CTTGAAAAAT
380455 AAAGCATGT-TGGGTAG
1 AAAGCATGTCTGGGTAG
380471 AAAGCATGTCTGGGTAG
1 AAAGCATGTCTGGGTAG
380488 GATTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.24
Consensus pattern (17 bp):
AAAGCATGTCTGGGTAG
Found at i:382303 original size:13 final size:13
Alignment explanation
Indices: 382285--382311 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
382275 GGTTGAGAAC
382285 AAGCGCTAGCTGA
1 AAGCGCTAGCTGA
382298 AAGCGCTAGCTGA
1 AAGCGCTAGCTGA
382311 A
1 A
382312 TAAGCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.30, T:0.15
Consensus pattern (13 bp):
AAGCGCTAGCTGA
Found at i:383170 original size:22 final size:22
Alignment explanation
Indices: 383139--383188 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
383129 AGATGAGTCT
*
383139 AAGAGTTAGACCATATATGTAA
1 AAGAGATAGACCATATATGTAA
383161 AAGAGATAGACCATATATGTAA
1 AAGAGATAGACCATATATGTAA
383183 AAGAGA
1 AAGAGA
383189 ATAGTACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (22 bp):
AAGAGATAGACCATATATGTAA
Found at i:388863 original size:21 final size:21
Alignment explanation
Indices: 388828--388928 Score: 166
Period size: 21 Copynumber: 4.8 Consensus size: 21
388818 TAAATATTAC
*
388828 AAAGGTAGTATCGATACTCATT
1 AAAGG-AGTACCGATACTCATT
388850 AAAGGAGTACCGATACTCATT
1 AAAGGAGTACCGATACTCATT
388871 AAAGGAGTACCGATACTCATT
1 AAAGGAGTACCGATACTCATT
*
388892 AAAAGAGTACCGATACTCATT
1 AAAGGAGTACCGATACTCATT
*
388913 AAAGGAGTACTGATAC
1 AAAGGAGTACCGATAC
388929 CCCTTGTCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
21 70 0.93
22 5 0.07
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (21 bp):
AAAGGAGTACCGATACTCATT
Found at i:390133 original size:24 final size:24
Alignment explanation
Indices: 390101--390153 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
390091 AAACAAAAGA
* *
390101 GTGAAGAGAAAATTCGA-GAAGAGT
1 GTGAGGAGAAAATTC-ATGAAGAAT
*
390125 GTGAGGAGATAATTCATGAAGAAT
1 GTGAGGAGAAAATTCATGAAGAAT
390149 GTGAG
1 GTGAG
390154 ATTGAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.42, C:0.04, G:0.34, T:0.21
Consensus pattern (24 bp):
GTGAGGAGAAAATTCATGAAGAAT
Found at i:394451 original size:2 final size:2
Alignment explanation
Indices: 394434--394521 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
394424 TGAAATAACT
* *
394434 TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394518 TA TA
1 TA TA
394522 ATAGCTTTAT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:397877 original size:39 final size:39
Alignment explanation
Indices: 397814--398048 Score: 314
Period size: 39 Copynumber: 6.0 Consensus size: 39
397804 GGTGCAGCAC
*
397814 GCAAACTA-ATGTATCTCCTTTCACCAGAATCAACATTAT
1 GCAAACTAGA-GTACCTCCTTTCACCAGAATCAACATTAT
* * *
397853 GCAAACTAGAGCAACT-CTTCTCACCAGAATCAACATTAC
1 GCAAACTAGAGTACCTCCTT-TCACCAGAATCAACATTAT
* * * *
397892 GCAAACTATAATACCTCCTTTCATCAAAATCAACATT-T
1 GCAAACTAGAGTACCTCCTTTCACCAGAATCAACATTAT
*
397930 CGCAAACTAGAGTACCTCCTTTCACCAAAATCAACATTAT
1 -GCAAACTAGAGTACCTCCTTTCACCAGAATCAACATTAT
*
397970 GCAAACTAGAGTACCTCCTTTCACCAGAATCAACATTAC
1 GCAAACTAGAGTACCTCCTTTCACCAGAATCAACATTAT
* *
398009 ACAAACTAGAGTACCTCCTTTCACCATAATCAACATTAT
1 GCAAACTAGAGTACCTCCTTTCACCAGAATCAACATTAT
398048 G
1 G
398049 GCTACAATTT
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
38 3 0.02
39 164 0.95
40 5 0.03
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (39 bp):
GCAAACTAGAGTACCTCCTTTCACCAGAATCAACATTAT
Found at i:397994 original size:117 final size:117
Alignment explanation
Indices: 397813--398045 Score: 353
Period size: 117 Copynumber: 2.0 Consensus size: 117
397803 TGGTGCAGCA
* *
397813 CGCAAACTAATGTATCTCCTTTCACCAGAATCAACATTATGCAAACTAGAGCAACTCTTCTCACC
1 CGCAAACTAATGTACCTCCTTTCACCAAAATCAACATTATGCAAACTAGAGCAACTCTTCTCACC
* * *
397878 AGAATCAACATTACGCAAACTATAATACCTCCTTTCATCAAAATCAACATTT
66 AGAATCAACATTACACAAACTAGAATACCTCCTTTCACCAAAATCAACATTT
* *
397930 CGCAAACTAGA-GTACCTCCTTTCACCAAAATCAACATTATGCAAACTAGAGTACCTCCTT-TCA
1 CGCAAACTA-ATGTACCTCCTTTCACCAAAATCAACATTATGCAAACTAGAGCAACT-CTTCTCA
* *
397993 CCAGAATCAACATTACACAAACTAGAGTACCTCCTTTCACCATAATCAACATT
64 CCAGAATCAACATTACACAAACTAGAATACCTCCTTTCACCAAAATCAACATT
398046 ATGGCTACAA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
117 101 0.96
118 4 0.04
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.26
Consensus pattern (117 bp):
CGCAAACTAATGTACCTCCTTTCACCAAAATCAACATTATGCAAACTAGAGCAACTCTTCTCACC
AGAATCAACATTACACAAACTAGAATACCTCCTTTCACCAAAATCAACATTT
Found at i:403862 original size:21 final size:22
Alignment explanation
Indices: 403836--403885 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
403826 AATTATGTAA
*
403836 AAAAATAAATATAAAT-A-TACT
1 AAAAATAAA-AAAAATAATTACT
403857 AAAAATAAAAAAAATAATTACT
1 AAAAATAAAAAAAATAATTACT
403879 AAAAATA
1 AAAAATA
403886 TTAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 11 0.42
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAATAAAAAAAATAATTACT
Found at i:403878 original size:22 final size:21
Alignment explanation
Indices: 403836--403906 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
403826 AATTATGTAA
*
403836 AAAAATAAATATAAATATACT
1 AAAAATAAATAAAAATATACT
403857 AAAAATAAA-AAAAATAATTACT
1 AAAAATAAATAAAAAT-A-TACT
* *
403879 AAAAAT-ATTAAAATATATATT
1 AAAAATAAATAAAA-ATATACT
403900 AAAAATA
1 AAAAATA
403907 TTGAAAACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
20 5 0.12
21 20 0.48
22 15 0.36
23 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATAAATAAAAATATACT
Found at i:403891 original size:21 final size:21
Alignment explanation
Indices: 403850--403913 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
403840 ATAAATATAA
* *
403850 ATATACTAAAAATA-AAAAAA
1 ATATACTAAAAATATTAAAAT
403870 ATAATTACTAAAAATATTAAAAT
1 AT-A-TACTAAAAATATTAAAAT
*
403893 ATATATTAAAAATATTGAAAA
1 ATATACTAAAAATATT-AAAA
403914 CTCTATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 16 0.43
23 6 0.16
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (21 bp):
ATATACTAAAAATATTAAAAT
Found at i:403893 original size:30 final size:30
Alignment explanation
Indices: 403834--403891 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
403824 TCAATTATGT
*
403834 AAAAAAATAAATATAAATATACTAAAAATA
1 AAAAAAATAAATATAAAAATACTAAAAATA
* *
403864 AAAAAAATAATTACTAAAAATATTAAAA
1 AAAAAAATAAATA-TAAAAATACTAAAA
403892 TATATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (30 bp):
AAAAAAATAAATATAAAAATACTAAAAATA
Found at i:403900 original size:24 final size:22
Alignment explanation
Indices: 403833--403900 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
403823 TTCAATTATG
*
403833 TAAAAA-AATAAATATAAATATAC
1 TAAAAATAAAAAATAT-AAT-TAC
*
403856 TAAAAATAAAAAAAATAATTAC
1 TAAAAATAAAAAATATAATTAC
*
403878 TAAAAATATTAAAATATATATTA
1 TAAAAATA-AAAAATATA-ATTA
403901 AAAATATTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 11 0.29
23 16 0.42
24 11 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAATAAAAAATATAATTAC
Found at i:404394 original size:16 final size:17
Alignment explanation
Indices: 404375--404419 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
404365 ATTAACATAT
*
404375 TTAAAAATATAAAG-AA
1 TTAAAAATAAAAAGTAA
*
404391 TTAAATATAAAAAGTAA
1 TTAAAAATAAAAAGTAA
404408 -TAAAAATAAAAA
1 TTAAAAATAAAAA
404420 TTTATTTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 23 0.92
17 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
TTAAAAATAAAAAGTAA
Found at i:404493 original size:29 final size:29
Alignment explanation
Indices: 404452--404510 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 29
404442 TATTTATATT
404452 AAATAATAAAAATACT-ATTAAAA-ATTAAA
1 AAATAATAAAAATA-TGA-TAAAATATTAAA
404481 AAAT-ATATAAAATATGATAAAATATTAAA
1 AAATAATA-AAAATATGATAAAATATTAAA
404510 A
1 A
404511 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (29 bp):
AAATAATAAAAATATGATAAAATATTAAA
Found at i:404500 original size:10 final size:9
Alignment explanation
Indices: 404480--404513 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
404470 TAAAAATTAA
404480 AAAATATAT
1 AAAATATAT
404489 AAAATATGAT
1 AAAATAT-AT
404499 AAAATAT-T
1 AAAATATAT
404507 AAAATAT
1 AAAATAT
404514 TTTAAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATATAT
Found at i:404519 original size:18 final size:18
Alignment explanation
Indices: 404467--404519 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
404457 ATAAAAATAC
*
404467 TATTAAAA-ATTAAAAAA
1 TATTAAAATATTATAAAA
*
404484 TATATAAAATATGATAAAA
1 TAT-TAAAATATTATAAAA
*
404503 TATTAAAATATTTTAAA
1 TATTAAAATATTATAAA
404520 TACATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 17 0.57
19 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TATTAAAATATTATAAAA
Found at i:405201 original size:22 final size:24
Alignment explanation
Indices: 405161--405204 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
405151 ATATATATTA
*
405161 ATATTTTTAGTAATTTATTTTTTT
1 ATATTGTTAGTAATTTATTTTTTT
405185 ATATTGTTA-TAA-TTATTTTT
1 ATATTGTTAGTAATTTATTTTT
405205 AAAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (24 bp):
ATATTGTTAGTAATTTATTTTTTT
Found at i:405520 original size:13 final size:13
Alignment explanation
Indices: 405492--405542 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
405482 CAGTAGCTGG
* *
405492 TTTGATCAACTAA
1 TTTGATTAACTGA
*
405505 TTTGATTAGCTGA
1 TTTGATTAACTGA
**
405518 TTTGAGAAACTGA
1 TTTGATTAACTGA
405531 TTTGATTAACTG
1 TTTGATTAACTG
405543 TTTATATAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (13 bp):
TTTGATTAACTGA
Done.