Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003693.1 Hibiscus syriacus cultivar Beakdansim tig00007894_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: 122399
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1539 original size:2 final size:2
Alignment explanation
Indices: 1534--1569 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1524 AGGATATATA
1534 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1570 TCCTCAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2223 original size:70 final size:67
Alignment explanation
Indices: 2132--2323 Score: 210
Period size: 70 Copynumber: 2.8 Consensus size: 67
2122 AAAAAAAACA
*
2132 TAATATATGAAATCATAATATTTGTTTTCCCACTTGTGTCCTTAATTTAAGCTATAGTGGTTTAG
1 TAATATATGAAATCATAATATTTGTTTTCCCAC-TGT-TCCTTAATTTAAGCTATAATGGTTTA-
*
2197 TTTTT
63 CTTTT
* * * * *
2202 TAATATATGGAGTCATTATATTAT-TGTTCCCCACATGTTTCCTTAATTTAAGTTATAATGGTTT
1 TAATATATGAAATCATAATATT-TGT-TTTCCCAC-TG-TTCCTTAATTTAAGCTATAATGGTTT
2266 ACTTTT
62 ACTTTT
* *
2272 TAATATATGAAATTATAATA-TTGGTTTCTCCACT-TTCCTTAATTTAAGCTAT
1 TAATATATGAAATCATAATATTTGTTTTC-CCACTGTTCCTTAATTTAAGCTAT
2324 GTTTGGTGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
66 17 0.17
68 5 0.05
69 5 0.05
70 40 0.39
71 34 0.33
72 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (67 bp):
TAATATATGAAATCATAATATTTGTTTTCCCACTGTTCCTTAATTTAAGCTATAATGGTTTACTT
TT
Found at i:15054 original size:20 final size:22
Alignment explanation
Indices: 15029--15071 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
15019 TGTACCTAAG
15029 ATTAAA-CATAC-AAATAAAAA
1 ATTAAAGCATACTAAATAAAAA
15049 ATTAAAGCATACTTAAATAAAAA
1 ATTAAAGCATAC-TAAATAAAAA
15072 CATGCGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
23 9 0.45
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (22 bp):
ATTAAAGCATACTAAATAAAAA
Found at i:16526 original size:37 final size:37
Alignment explanation
Indices: 16466--16705 Score: 182
Period size: 37 Copynumber: 6.4 Consensus size: 37
16456 ATCATGCTCG
* * *
16466 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTTGGT
1 GAAGGCTTA-AGATTGATTTGCTTCACTACTCTTCGGT
16504 GAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGT
1 GAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGT
* **** **** * * *
16541 GAAGGTTTAA-A-TGGCCCGGAGGACTTAATCATCATGCT
1 GAAGGCTTAAGATTGATTTGCTTCAC-TACTCTTC--GGT
* * *
16579 CGGAAGGCTTACTGA-TGAATTTGTTTCACTACTCTTCCGT
1 --GAAGGCTTA-AGATTG-ATTTGCTTCACTACTCTTCGGT
* *
16619 GAAGGCTTATGA-TGAATTTGCTTCACTACTCTTCAGT
1 GAAGGCTTAAGATTG-ATTTGCTTCACTACTCTTCGGT
16656 GAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGT
1 GAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGT
*
16693 GAAGGTTTAAGAT
1 GAAGGCTTAAGAT
16706 GGCCCGGAGG
Statistics
Matches: 159, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
35 5 0.03
36 7 0.04
37 104 0.65
38 22 0.14
40 9 0.06
42 9 0.06
43 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (37 bp):
GAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGT
Found at i:16592 original size:115 final size:116
Alignment explanation
Indices: 16364--16668 Score: 488
Period size: 115 Copynumber: 2.6 Consensus size: 116
16354 ACTTGAAATT
* *
16364 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTTACTTCACTACTCTTTGGTGAAG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA-TTTGCTTCACTACTCTTCGGTGAAG
16429 GCTTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATG
65 GCTTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATG
*
16481 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
* *
16546 TTTAA-ATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
66 CTTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATG
* * * * *
16596 AATTTGTTTCACTACTCTTCCGTGAAGGCTTATGA-TGAATTTGCTTCACTACTCTTCAGTGAAG
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG-ATTTGCTTCACTACTCTTCGGTGAAG
16660 GCTTAAGAT
65 GCTTAAGAT
16669 TGATTTGCTT
Statistics
Matches: 174, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
114 2 0.01
115 104 0.60
116 30 0.17
117 38 0.22
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (116 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
CTTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATG
Found at i:16762 original size:153 final size:152
Alignment explanation
Indices: 16466--16822 Score: 615
Period size: 153 Copynumber: 2.3 Consensus size: 152
16456 ATCATGCTCG
* *
16466 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACT
1 GAAGGCTTA-TGATGAATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGATTTGCTTCACT
16531 ACTCTTCGGTGAAGGTTTAAATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
65 ACTCTTCGGTGAAGGTTTAAATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
*
16596 AATTTGTTTCACTACTCTTCCGT
130 AATTTGCTTCACTACTCTTCCGT
*
16619 GAAGGCTTATGATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTA
1 GAAGGCTTATGATGAATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGATTTGCTTCACTA
*
16684 CTCTTCGGTGAAGGTTTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTATTGATG
66 CTCTTCGGTGAAGGTTTAA-ATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
16749 AATTTGCTTCACTACTCTTCCGT
130 AATTTGCTTCACTACTCTTCCGT
* * * *
16772 GAAGGCTTATAATAAATTTGCTTCACTACTATTTAGTGAAGGTTTAAGATT
1 GAAGGCTTATGATGAATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATT
16823 ACCCGGAGGA
Statistics
Matches: 193, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
152 72 0.37
153 121 0.63
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (152 bp):
GAAGGCTTATGATGAATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGATTTGCTTCACTA
CTCTTCGGTGAAGGTTTAAATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGA
ATTTGCTTCACTACTCTTCCGT
Found at i:16768 original size:116 final size:115
Alignment explanation
Indices: 16619--16938 Score: 428
Period size: 116 Copynumber: 2.8 Consensus size: 115
16609 ACTCTTCCGT
16619 GAAGGCTTATGATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTA
1 GAAGGCTTATGATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTA
16684 CTCTTCGGTGAAGGTTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
66 CTCTTCGGTGAAGGTTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
* **
16734 GAAGGCTTATTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTATA-ATAAATTTGCTTCAC
1 GAAGGCTTA-TGATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTA-AGATTGATTTGCTTCAC
* ** **
16798 TACTATTTAGTGAAGGTTTAAGATTACCCGGAGGACTTAATCATCATGCTCG
64 TACTCTTCGGTGAAGGTTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
* * * * * *
16850 GAATGCTTACTGATGGATTTTCTTCACTACTTTTCTGTGAAGGCTTAAGA-TGGTTTGCTTCACT
1 GAAGGCTTA-TGATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACT
* * * * *
16914 ATTCTCCGGTTAAGGCTTAGGATGG
65 ACTCTTCGGTGAAGGTTTAAGATGG
16939 TGCTTCAATT
Statistics
Matches: 175, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
115 36 0.21
116 138 0.79
117 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (115 bp):
GAAGGCTTATGATGAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTA
CTCTTCGGTGAAGGTTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
Found at i:16811 original size:37 final size:38
Alignment explanation
Indices: 16734--16813 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
16724 ATCATGCTCG
* * * *
16734 GAAGGCTTATTGATGAATTTGCTTCACTACTCTTCCGT
1 GAAGGCTTATTAATAAATTTGCTTCACTACTATTCAGT
*
16772 GAAGGCTTA-TAATAAATTTGCTTCACTACTATTTAGT
1 GAAGGCTTATTAATAAATTTGCTTCACTACTATTCAGT
16809 GAAGG
1 GAAGG
16814 TTTAAGATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 28 0.76
38 9 0.24
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (38 bp):
GAAGGCTTATTAATAAATTTGCTTCACTACTATTCAGT
Found at i:16909 original size:268 final size:268
Alignment explanation
Indices: 16365--16970 Score: 873
Period size: 268 Copynumber: 2.3 Consensus size: 268
16355 CTTGAAATTG
*
16365 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTTACTTCACTACTCTTTGGTGAAGG
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGA-TTTGCTTCACTACTCTTTGGTGAAGG
*
16430 CTTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTA
65 CTTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATGAATTTGCTTCACTA
** ** * * *
16495 CTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGGTTTAAATGGCCCGG
130 CTCTTCCGTGAAGGCTTAAGATAAATTTGCTTCACTACTATTCAGTGAAGGTTTAAATGACCCGG
16560 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGAATTTGTTTCACTACTCTTCCGTGAAGGC
195 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGAATTTGTTTCACTACTCTTCCGTGAAGGC
*
16625 TTATGATGA
260 TTAAGATGA
* * *
16634 ATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGGT
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGC
* *
16699 TTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTATTGATGAATTTGCTTCACTAC
66 TTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATGAATTTGCTTCACTAC
* *
16764 TCTTCCGTGAAGGCTTATA-ATAAATTTGCTTCACTACTATTTAGTGAAGGTTTAAGATTACCCG
131 TCTTCCGTGAAGGCTTA-AGATAAATTTGCTTCACTACTATTCAGTGAAGGTTTAA-ATGACCCG
* * * *
16828 GAGGACTTAATCATCATGCTCGGAATGCTTACTGATGGATTT-TCTTCACTACTTTTCTGTGAAG
194 GAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGAATTTGT-TTCACTACTCTTCCGTGAAG
16892 GCTTAAGATG-
258 GCTTAAGATGA
* * * * * * * *
16902 GTTTGCTTCACTATTCTCCGGTTAAGGCTTAGGA-TG--GTGCTTCAATTCTCTTTGGTGAAGGC
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGC
16964 TTAAGAT
66 TTAAGAT
16971 TGATTGCTTC
Statistics
Matches: 302, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
265 28 0.09
267 2 0.01
268 161 0.53
269 111 0.37
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (268 bp):
ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGC
TTAAGATGGCCCGGAGGACTAAATCATCATGCTCGGAAGGCTTACTGATGAATTTGCTTCACTAC
TCTTCCGTGAAGGCTTAAGATAAATTTGCTTCACTACTATTCAGTGAAGGTTTAAATGACCCGGA
GGACTTAATCATCATGCTCGGAAGGCTTACTGATGAATTTGTTTCACTACTCTTCCGTGAAGGCT
TAAGATGA
Found at i:16911 original size:36 final size:36
Alignment explanation
Indices: 16861--17003 Score: 123
Period size: 36 Copynumber: 4.0 Consensus size: 36
16851 AATGCTTACT
* *
16861 GATGGATTTTCTTCACTACTTTTCTGTGAAGGCTTAA
1 GATGG-TTTGCTTCACTACTTTTCGGTGAAGGCTTAA
* * *
16898 GATGGTTTGCTTCACTA-TTCTCCGGTTAAGGCTTAG
1 GATGGTTTGCTTCACTACTT-TTCGGTGAAGGCTTAA
* *
16934 GATGG--TGCTTCAATTCTCTTT-GGTGAAGGCTTAA
1 GATGGTTTGCTTCACTACT-TTTCGGTGAAGGCTTAA
* * * * *
16968 GATTGATTGCTTCTCTACTCTTCAGTGAAGGCTTAA
1 GATGGTTTGCTTCACTACTTTTCGGTGAAGGCTTAA
17004 TATTGACTTG
Statistics
Matches: 84, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
34 23 0.27
35 6 0.07
36 50 0.60
37 5 0.06
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (36 bp):
GATGGTTTGCTTCACTACTTTTCGGTGAAGGCTTAA
Found at i:17859 original size:16 final size:18
Alignment explanation
Indices: 17832--17865 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17822 ACATGCACTG
17832 TCACTGCTTCAT-CATTT
1 TCACTGCTTCATACATTT
17849 TCACT-CTTCATACATTT
1 TCACTGCTTCATACATTT
17866 CTATCCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.29, G:0.03, T:0.47
Consensus pattern (18 bp):
TCACTGCTTCATACATTT
Found at i:18210 original size:125 final size:125
Alignment explanation
Indices: 17988--18219 Score: 295
Period size: 125 Copynumber: 1.9 Consensus size: 125
17978 ACAATATTAT
* * * * * ***
17988 CTCATACTGGTATGGGCCTTCAAAATGCCCCAACATCTTAGATTGTAAGGCTCACTCTTAATGTT
1 CTCATACTGGTACGGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAACTCTTAATACC
** *
18053 TTCTTGGTTTAAATCTTATCATCTCAACATGATTTGGGTTCAGTCATGACCCATCAGTCA
66 ACCTTGGTTTAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGACCCATCAGTCA
* * *
18113 CTCATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTAATTCTTCATACC
1 CTCATACTGGTACGGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAACTCTTAATACC
* * *
18178 ACCTTGGTCTT-AATCTTGTTATTTCAACATGATGTGGGTTCA
66 ACCTTGGT-TTAAATCTTATCATCTCAACATGATGTGGGTTCA
18220 ACCGTAACCC
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
125 87 0.98
126 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (125 bp):
CTCATACTGGTACGGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAACTCTTAATACC
ACCTTGGTTTAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGACCCATCAGTCA
Found at i:19377 original size:2 final size:2
Alignment explanation
Indices: 19361--19396 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
19351 AACTTTATTG
*
19361 TA TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19397 TGTATGCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21514 original size:12 final size:13
Alignment explanation
Indices: 21497--21525 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21487 AAATACATGC
21497 AATGTAAATG-TA
1 AATGTAAATGCTA
21509 AATGTAAATGCTA
1 AATGTAAATGCTA
21522 AATG
1 AATG
21526 CAAGTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.31
Consensus pattern (13 bp):
AATGTAAATGCTA
Found at i:25925 original size:195 final size:194
Alignment explanation
Indices: 25594--25983 Score: 735
Period size: 195 Copynumber: 2.0 Consensus size: 194
25584 AATGTCAAAC
25594 ATTCGAAAAAATATTTTAGTCTAAAATATACATATAACTATACCCTAAAAAAATTATTAAAATTA
1 ATTCGAAAAAATATTTTAGTCTAAAATATACATATAACTATACCCTAAAAAAATTATTAAAATTA
*
25659 TATTAACATGTAATCAATATTGTTTTACGCTAAATCAATTAATAACTACAAATAATACTAGTATT
66 TATTAACATGTAATCAATATTGTTTTACGCTAAATCAATTAATAACTACAAATAATACTAATATT
*
25724 ATTTACCTAAAGTTGAAAATAACATTTAAGGATATAATATATACATTCTAATCACATTAATCAA
131 ATTTACCTAAAGTTGAAAATAACATTTAAGGATATAATATATACATGCTAATCACATTAATCAA
*
25788 ATTCGAAAAAATATTTTAGTCTAAAATATACATATAACTATACCCTGAAAAAACTTATTAAAATT
1 ATTCGAAAAAATATTTTAGTCTAAAATATACATATAACTATACCCT-AAAAAAATTATTAAAATT
*
25853 ATATTAACATGTAATCAATATTTTTTTACGCTAAATCAATTAATAACTACAAATAATACTAATAT
65 ATATTAACATGTAATCAATATTGTTTTACGCTAAATCAATTAATAACTACAAATAATACTAATAT
25918 TATTTACCTAAAGTTGAAAATAACATTTAAGGATATAATATATACATGCTAATCACATTAATCAA
130 TATTTACCTAAAGTTGAAAATAACATTTAAGGATATAATATATACATGCTAATCACATTAATCAA
25983 A
1 A
25984 CTCAACATCA
Statistics
Matches: 191, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
194 46 0.24
195 145 0.76
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (194 bp):
ATTCGAAAAAATATTTTAGTCTAAAATATACATATAACTATACCCTAAAAAAATTATTAAAATTA
TATTAACATGTAATCAATATTGTTTTACGCTAAATCAATTAATAACTACAAATAATACTAATATT
ATTTACCTAAAGTTGAAAATAACATTTAAGGATATAATATATACATGCTAATCACATTAATCAA
Found at i:26462 original size:20 final size:22
Alignment explanation
Indices: 26437--26479 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
26427 TGTACCTAAG
26437 ATTAAA-CATAC-AAATAAAAA
1 ATTAAAGCATACTAAATAAAAA
26457 ATTAAAGCATACTTAAATAAAAA
1 ATTAAAGCATAC-TAAATAAAAA
26480 CATGCGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
23 9 0.45
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (22 bp):
ATTAAAGCATACTAAATAAAAA
Found at i:29333 original size:50 final size:48
Alignment explanation
Indices: 29267--29391 Score: 153
Period size: 48 Copynumber: 2.6 Consensus size: 48
29257 AAACTCTTGT
*
29267 AAGATCTGACATTCCCTTTAGAGTAAGCAGATA-AGGTCTCTCTCTTTCCC
1 AAGATCTGATATTCCCTTTAGAGTAAGCAGA-ACA--TCTCTCTCTTTCCC
* * ** *
29317 AATATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTTCCC
1 AAGATCTGATATTCCCTTTAGAGTAAGCAGAACATCTCTCTCTTTCCC
*
29365 AAGATGTGATATTCCCTTTAGAGTAAG
1 AAGATCTGATATTCCCTTTAGAGTAAG
29392 TGGAACAAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 37 0.57
49 1 0.02
50 27 0.42
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (48 bp):
AAGATCTGATATTCCCTTTAGAGTAAGCAGAACATCTCTCTCTTTCCC
Found at i:29376 original size:48 final size:48
Alignment explanation
Indices: 29305--29403 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 48
29295 AGATAAGGTC
* *
29305 TCTCTCTTTCCCAATATCTGATATTCCCTTCAGAGTAAGTGGAACATG
1 TCTCTCTTTCCCAAGATCTGATATTCCCTTCAGAGTAAGTGGAACAAG
* *
29353 TCTCTCTTTCCCAAGATGTGATATTCCCTTTAGAGTAAGTGGAACAAG
1 TCTCTCTTTCCCAAGATCTGATATTCCCTTCAGAGTAAGTGGAACAAG
29401 TCT
1 TCT
29404 GCCCTGATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (48 bp):
TCTCTCTTTCCCAAGATCTGATATTCCCTTCAGAGTAAGTGGAACAAG
Found at i:29503 original size:48 final size:48
Alignment explanation
Indices: 29432--29566 Score: 216
Period size: 48 Copynumber: 2.8 Consensus size: 48
29422 AAACTCCTGT
*
29432 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCC
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTTCCC
* * *
29480 AAGATCTGATATTCCCTTTAGAGTAAGCGAAACATGTCTCTCTTTCCC
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTTCCC
* *
29528 AAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT
29567 GCCCTGATTC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 79 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (48 bp):
AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTTCCC
Found at i:29528 original size:163 final size:163
Alignment explanation
Indices: 29254--29669 Score: 620
Period size: 163 Copynumber: 2.5 Consensus size: 163
29244 CATTCAGTGG
* * * *
29254 ATCAAACTCTTGTAAGATCTGACATTCCCTTTAGAGTAAGCAGATA-AGGTCTCTCTCTTTCCCA
1 ATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGA-ACAGG--TCTCTCTTTCCCA
* * *
29318 ATATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTCTTTCCCAAGATGTGATATTCCCTT
63 AGATCTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATGTGATATTCCCTT
*
29383 TAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
128 CAGAGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
29419 ATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCCAAGA
1 ATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCCAAGA
* *
29484 TCTGATATTCCCTTTAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAG
66 TCTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATGTGATATTCCCTTCAG
29549 AGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
131 AGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
** * * * *
29582 ATTGAACTCCT-TCAAGATTTGATATTCCCTTCAGTGTAAGCGGAACATGTATCTCTTTCCCAAG
1 ATCAAACTCCTGT-AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCCAAG
* *
29646 ATTTGATATTCCCTTCATAGTAAG
65 ATCTGATATTCCCTTCAGAGTAAG
29670 TGGAACAAGT
Statistics
Matches: 230, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
162 1 0.00
163 185 0.80
164 1 0.00
165 43 0.19
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (163 bp):
ATCAAACTCCTGTAAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCCAAGA
TCTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATGTGATATTCCCTTCAG
AGTAAGTGGAACAAGTCTGCCCTGATTCAAGGA
Found at i:29598 original size:115 final size:115
Alignment explanation
Indices: 29479--29808 Score: 459
Period size: 115 Copynumber: 2.9 Consensus size: 115
29469 CTCTCTTTCC
*
29479 CAAGATCTGATATTCCCTTTAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATTTGATATTCCC
1 CAAGATCTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATTTGATATTCCC
* **
29544 TTCAGAGTAAGTGGAACAAGTCTGCCCTGATTCAA-GGAATTGAACTCCTT
66 TTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGG-ATCAAACTCCTT
* * * *
29594 CAAGATTTGATATTCCCTTCAGTGTAAGCGGAACATGTATCTCTTTCCCAAGATTTGATATTCCC
1 CAAGATCTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATTTGATATTCCC
* *
29659 TTCATAGTAAGTGGAACAAGTCTACCCCGATTCAATGGATCAAACTCCTT
66 TTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCCTT
* * * **
29709 C-ATATCTGATATTTCCTTCAGAGTAAGCGGAAA-AGGTCTCTTCTTTTTCAAGATTTGATATTC
1 CAAGATCTGATATTCCCTTCAGAGTAAGC-GAAACATGTCTC-TCTTTCCCAAGATTTGATATTC
* *
29772 CCTTCAGAGTAAGTGGAACAAGTCTGCCTCAATTCAA
64 CCTTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAA
29809 ATTTCCCTGA
Statistics
Matches: 189, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
114 28 0.15
115 159 0.84
116 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (115 bp):
CAAGATCTGATATTCCCTTCAGAGTAAGCGAAACATGTCTCTCTTTCCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAGTCTGCCCCGATTCAATGGATCAAACTCCTT
Found at i:29808 original size:49 final size:48
Alignment explanation
Indices: 29715--29812 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 48
29705 CCTTCATATC
* * **
29715 TGATATTTCCTTCAGAGTAAGCGGAAAAGGTCTCTTCTTTTTCAAGATT
1 TGATATTCCCTTCAGAGTAAGCGGAAAAGGTCTCCTCTAATTCAA-ATT
*
29764 TGATATTCCCTTCAGAGTAAGTGGAACAA-GTCTGCCTC-AATTCAAATT
1 TGATATTCCCTTCAGAGTAAGCGGAA-AAGGTCT-CCTCTAATTCAAATT
29812 T
1 T
29813 CCCTGAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 4 0.10
49 33 0.79
50 5 0.12
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (48 bp):
TGATATTCCCTTCAGAGTAAGCGGAAAAGGTCTCCTCTAATTCAAATT
Found at i:30079 original size:15 final size:16
Alignment explanation
Indices: 30061--30090 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30051 TTTTTTCGTC
30061 ATTATTTAT-ATTATT
1 ATTATTTATAATTATT
30076 ATTATTTATAATTAT
1 ATTATTTATAATTAT
30091 ATTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATTTATAATTATT
Found at i:30353 original size:26 final size:25
Alignment explanation
Indices: 30290--30389 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 25
30280 GGTTTCCAGA
* *
30290 ACAGCCGCCACCACTTGGACCACTC
1 ACAGCCACCACCGCTTGGACCACTC
* *
30315 A-TGCCACCGCCGCTTGGACCACTC
1 ACAGCCACCACCGCTTGGACCACTC
**
30339 GACAGCCACCACCGCTTGGACCA-GA
1 -ACAGCCACCACCGCTTGGACCACTC
* * *
30364 ACAGCCACCGCCTCTTGGATCACTC
1 ACAGCCACCACCGCTTGGACCACTC
30389 A
1 A
30390 ATAACCACCA
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
24 38 0.64
25 3 0.05
26 18 0.31
ACGTcount: A:0.23, C:0.44, G:0.19, T:0.14
Consensus pattern (25 bp):
ACAGCCACCACCGCTTGGACCACTC
Found at i:30371 original size:50 final size:50
Alignment explanation
Indices: 30290--30388 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
30280 GGTTTCCAGA
* **
30290 ACAGCCGCCACCACTTGGACCACTCATGCCACCGCCGCTTGGACCACTCG
1 ACAGCCACCACCACTTGGACCAAACATGCCACCGCCGCTTGGACCACTCG
* * *
30340 ACAGCCACCACCGCTTGGACCAGAACA-GCCACCGCCTCTTGGATCACTC
1 ACAGCCACCACCACTTGGACCA-AACATGCCACCGCCGCTTGGACCACTC
30389 AATAACCACC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.14
Consensus pattern (50 bp):
ACAGCCACCACCACTTGGACCAAACATGCCACCGCCGCTTGGACCACTCG
Found at i:31052 original size:2 final size:2
Alignment explanation
Indices: 31045--31134 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
31035 GGATCTTTAT
31045 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31087 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31129 TC TC TC
1 TC TC TC
31135 CTCAAAACCA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31843 original size:73 final size:73
Alignment explanation
Indices: 31724--32002 Score: 289
Period size: 73 Copynumber: 3.8 Consensus size: 73
31714 AAAAAATATA
* *
31724 TAATATA-TGAAATCATTATAATATTTGTTTTCCCACGTGTATCCTTAATTTAAGCTATAGTGGT
1 TAATATATTG-AATCATTATAATATTTGTTTTCCCACATGTTTCCTTAATTTAAGCTATAGTGGT
31788 TTAGTTTTT
65 TTAGTTTTT
* * *
31797 TAATATATTGAGTCATTATATTATTTGTTTCCCCACATGTTTCCTTAATTTAAGCTATAGTGGTT
1 TAATATATTGAATCATTATAATATTTGTTTTCCCACATGTTTCCTTAATTTAAGCTATAGTGGTT
*
31862 TACTTTTT
66 TAGTTTTT
* * * * * *
31870 TAATATATGGAATTATTATAATA-TTGGTTTCTC-CATTTTTCC-TAATTTAAGCTACGT-TTGG
1 TAATATATTGAATCATTATAATATTTGTTTTCCCACATGTTTCCTTAATTTAAGCTA--TAGT-G
**
31931 TGTTTAGCTATTAG
63 -GTTTAG-T-TTTT
* * *
31945 TAATATATATAGAATTATTATAGTATTTGTTTTCCCACTTGTTTCCTTAATTTAAGCT
1 TAATATAT-T-GAATCATTATAATATTTGTTTTCCCACATGTTTCCTTAATTTAAGCT
32003 TTGATTTGTT
Statistics
Matches: 170, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
70 12 0.07
71 9 0.05
72 9 0.05
73 88 0.52
74 3 0.02
75 10 0.06
77 13 0.08
78 8 0.05
79 7 0.04
80 11 0.06
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (73 bp):
TAATATATTGAATCATTATAATATTTGTTTTCCCACATGTTTCCTTAATTTAAGCTATAGTGGTT
TAGTTTTT
Found at i:35707 original size:2 final size:2
Alignment explanation
Indices: 35695--35736 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
35685 TTGGTTAAGC
35695 TA TA T- 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
35736 T
1 T
35737 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42072 original size:4 final size:4
Alignment explanation
Indices: 42063--42087 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
42053 TATCAATAAT
42063 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
42088 TCATATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:42297 original size:35 final size:35
Alignment explanation
Indices: 42251--42328 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
42241 GTTGTGACAC
42251 TAAGTCAATCCATTGGGTACGATATTCTTCTTCGT
1 TAAGTCAATCCATTGGGTACGATATTCTTCTTCGT
42286 TAAGTCAATCCATTGGGTACGATATTCTTCTTCGT
1 TAAGTCAATCCATTGGGTACGATATTCTTCTTCGT
*
42321 GAAGTCAA
1 TAAGTCAA
42329 AATCGTAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (35 bp):
TAAGTCAATCCATTGGGTACGATATTCTTCTTCGT
Found at i:42656 original size:83 final size:82
Alignment explanation
Indices: 42468--42705 Score: 284
Period size: 84 Copynumber: 2.9 Consensus size: 82
42458 TACGCCCTCA
* * * *
42468 AGCTGAATGGAATCGAACTCGAAGGTC--TTTGACAGATATCCCTTCTTGCCTTGAGCTATGCTG
1 AGCTGAGTGGAGTCGAACTCGAAGGTCTTTTTGA-AGATAACCCTTCTTGCCTTGAGCTATGATG
*
42531 CAAATGATGGTGCCTTTG
65 CAAATGATGGTGCCTTGG
* *
42549 AGCTGAGTGGAGTCGAACTCGAAGGTCTTTATTGATAGATAACCCTTCTAGCCTTGAGATATGAT
1 AGCTGAGTGGAGTCGAACTCGAAGGTCTTT-TTGA-AGATAACCCTTCTTGCCTTGAGCTATGAT
*
42614 GTAAATGAT-GTGCCTTGG
64 GCAAATGATGGTGCCTTGG
* * * * *
42632 AGTTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGAAAATAGCCCTTCTTGCCTTGAGCTATGT
1 AGCTGAGTGGAGTCGAACTCGAAGGTC-TTT-TT-GAAGATAACCCTTCTTGCCTTGAGCTATGA
42697 TGCAAATGA
63 TGCAAATGA
42706 ACATGATATC
Statistics
Matches: 134, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
81 25 0.19
83 34 0.25
84 73 0.54
85 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (82 bp):
AGCTGAGTGGAGTCGAACTCGAAGGTCTTTTTGAAGATAACCCTTCTTGCCTTGAGCTATGATGC
AAATGATGGTGCCTTGG
Found at i:42938 original size:124 final size:124
Alignment explanation
Indices: 42760--43231 Score: 775
Period size: 124 Copynumber: 3.8 Consensus size: 124
42750 CTGCTTGTGG
* * * * * *
42760 GCACAATAT-CCTTCATCGTGAAGTTGAAATCGTGGAGGGACCATTTGTTGTGAAGTTGAGCCTT
1 GCACAAT-TCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTT
42824 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGA
65 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGA
*
42884 GCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTATGAAGTTGAGCCTTG
1 GCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTG
*
42949 AATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGA
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGA
* *
43008 GAACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTG
1 GCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTG
* * *
43073 AATTGGATATCCTTCGTCATGAAGTTGAAATCTAATCTAAAGATCAATGTTACTGGTGA
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGA
* *
43132 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTG
1 GCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTG
* *
43197 ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
43232 GCTTGTATTG
Statistics
Matches: 326, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 1 0.00
124 325 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (124 bp):
GCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTG
AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGA
Found at i:43433 original size:249 final size:249
Alignment explanation
Indices: 43076--43536 Score: 692
Period size: 249 Copynumber: 1.9 Consensus size: 249
43066 AGCCTTGAAT
*
43076 TGGATATCCTTCGTCATGAAGTTGAAATCTAATCTAAAGATCAATGTTACTGGTGAGCACGATTC
1 TGGATATCCTTCATCATGAAGTTGAAATCTAATCTAAAGATCAATGTTACTGGTGAGCACGATTC
* * * *
43141 CCTTCGTCGTGAAGTTGAAACCGTGGATGACCCCTTCGTTGTGAAGTTGAGCC-TTGACTTGAAT
66 CCTTCGTCATGAAGTTGAAACCATGGATGACCCCTTCGTTGTGAAGTTGAGCCGTGGAATTGAAT
* ** *
43205 ATCCTTCGTCGTGAAGTTGAAATCCAA-GCTTGTATTGTTTCGAGTCCAATATCCTTCACCGTGA
131 ATCATTCGTCGTGAAGTTGAAATCCAATGAATG--TTGCTTCGAGTCCAATATCCTTCACCGTGA
43269 AGTTGAAATTGGCTCTGAAACTTGAAAGTTTATTGACATACACTCATTCTTTGAGC
194 AGTTGAAATTGGCTCTGAAACTTGAAAGTTTATTGACATACACTCATTCTTTGAGC
* * ** * * * *
43325 TGGATATCCTTCATCGTGAAGTTGAAATCTAATCTAGAGATGGATGTTGCTTGTGTGCATGATTC
1 TGGATATCCTTCATCATGAAGTTGAAATCTAATCTAAAGATCAATGTTACTGGTGAGCACGATTC
* * * *
43390 CCTTCGTCATGAAGTTGAAACTATGGATGGCCCCTTTGTTGTGAAGTTGAGCCGTGGAATTGGAT
66 CCTTCGTCATGAAGTTGAAACCATGGATGACCCCTTCGTTGTGAAGTTGAGCCGTGGAATTGAAT
*
43455 ATCATTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTTCGAGTCCAATATCCTTCGCCGTGAAG
131 ATCATTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTTCGAGTCCAATATCCTTCACCGTGAAG
43520 TTGAAATTGGCTCTGAA
196 TTGAAATTGGCTCTGAA
43537 TGAAACTGGG
Statistics
Matches: 188, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
249 151 0.80
250 34 0.18
251 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (249 bp):
TGGATATCCTTCATCATGAAGTTGAAATCTAATCTAAAGATCAATGTTACTGGTGAGCACGATTC
CCTTCGTCATGAAGTTGAAACCATGGATGACCCCTTCGTTGTGAAGTTGAGCCGTGGAATTGAAT
ATCATTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTTCGAGTCCAATATCCTTCACCGTGAAG
TTGAAATTGGCTCTGAAACTTGAAAGTTTATTGACATACACTCATTCTTTGAGC
Found at i:44453 original size:23 final size:23
Alignment explanation
Indices: 44427--44507 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
44417 AGGGTGTCAA
44427 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
* *
44450 AGTGCATCGATGCACCTACCACT
1 AGTGCATCCATGCACCTGCCACT
*
44473 AGTGCATCGATGCACCATG----T
1 AGTGCATCCATGCACC-TGCCACT
44493 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
44508 TCCATTTCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
20 15 0.28
23 37 0.70
24 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (23 bp):
AGTGCATCCATGCACCTGCCACT
Found at i:47655 original size:21 final size:21
Alignment explanation
Indices: 47629--47668 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47619 AAACAATTGG
47629 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
47650 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
47669 CTATAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:52048 original size:6 final size:6
Alignment explanation
Indices: 52037--52062 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52027 CAAAATTAAG
52037 AATTTA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
52063 AATTCAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:52178 original size:18 final size:16
Alignment explanation
Indices: 52132--52182 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
52122 TAAAGGTAAT
52132 AAAA-TAAAAATAAGAA
1 AAAACTAAAAATAA-AA
*
52148 AAAACAAATAAATAAAA
1 AAAACTAA-AAATAAAA
52165 AATACACTAAAAATAAAA
1 AA-A-ACTAAAAATAAAA
52183 GGAAAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 4 0.14
17 6 0.21
18 15 0.52
19 4 0.14
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAACTAAAAATAAAA
Found at i:52227 original size:43 final size:43
Alignment explanation
Indices: 52157--52245 Score: 135
Period size: 43 Copynumber: 2.0 Consensus size: 43
52147 AAAAACAAAT
52157 AAATAAAAAATACACTAAAAATAAAAGGAAAAAATGAATAACTA
1 AAATAAAAAATA-ACTAAAAATAAAAGGAAAAAATGAATAACTA
* *
52201 AAATAAAAAAT-GCTAAAATTAAAAAGGAAAAAATGAATAACTA
1 AAATAAAAAATAACTAAAAAT-AAAAGGAAAAAATGAATAACTA
52244 AA
1 AA
52246 TTGAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
42 7 0.17
43 24 0.57
44 11 0.26
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.17
Consensus pattern (43 bp):
AAATAAAAAATAACTAAAAATAAAAGGAAAAAATGAATAACTA
Found at i:52261 original size:43 final size:42
Alignment explanation
Indices: 52157--52263 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 42
52147 AAAAACAAAT
*
52157 AAATAAAAAATACACTAAAAAT-AAAAGGAAAAAATGAATAACTA
1 AAATAAAAAAT---CTAAAATTAAAAAGGAAAAAATGAATAACTA
52201 AAATAAAAAATGCTAAAATTAAAAAGGAAAAAATGAATAACTA
1 AAATAAAAAAT-CTAAAATTAAAAAGGAAAAAATGAATAACTA
*
52244 AATTGAAATAAAT-TAAAATT
1 AAAT-AAA-AAATCTAAAATT
52264 GATGGATTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
42 7 0.12
43 32 0.56
44 14 0.25
45 4 0.07
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (42 bp):
AAATAAAAAATCTAAAATTAAAAAGGAAAAAATGAATAACTA
Found at i:52447 original size:16 final size:16
Alignment explanation
Indices: 52426--52469 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
52416 TTTCCCTCTC
52426 GAAAATGCAACAAAGG
1 GAAAATGCAACAAAGG
52442 GAAAATGCAACAAAGG
1 GAAAATGCAACAAAGG
52458 GAAAATGCAACA
1 GAAAATGCAACA
52470 GTGCACGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.23, T:0.07
Consensus pattern (16 bp):
GAAAATGCAACAAAGG
Found at i:54207 original size:42 final size:41
Alignment explanation
Indices: 54126--54215 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
54116 TCGAAATCCT
* * *
54126 GTGTTTGTTTCACGTAATTCATTTTTCGGAAAATATTTTCTC
1 GTGTTTGTTTCACGTAATTCAGTTTTCCGAAAATATTTTC-A
* *
54168 GTGTTTGTTTTACGTAATTC-GTTTTCCGAAATATGTTTTCA
1 GTGTTTGTTTCACGTAATTCAGTTTTCCGAAA-ATATTTTCA
54209 GTGTTTG
1 GTGTTTG
54216 GTTGGAGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (41 bp):
GTGTTTGTTTCACGTAATTCAGTTTTCCGAAAATATTTTCA
Found at i:54530 original size:19 final size:18
Alignment explanation
Indices: 54506--54574 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
54496 ATATTATTAA
54506 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
54525 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
54543 ATTAATATAATAATTTAATAAT
1 ATT-AT-TAATAA--TAATAAT
54565 ATT-TTAATAA
1 ATTATTAATAA
54575 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:54595 original size:23 final size:23
Alignment explanation
Indices: 54555--54613 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
54545 TAATATAATA
**
54555 ATTTAATAATATTTTAATAAAGAT
1 ATTTAA-AATATACTAATAAAGAT
* *
54579 ATTTAAAATATACTAATTAATAT
1 ATTTAAAATATACTAATAAAGAT
*
54602 TTTTAAAATATA
1 ATTTAAAATATA
54614 ATATAATTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAAAATATACTAATAAAGAT
Found at i:54670 original size:22 final size:23
Alignment explanation
Indices: 54642--54689 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
54632 AATTTCATCC
54642 TTATATTATATAA-TATA-TATAT
1 TTATATTATA-AATTATATTATAT
54664 TTATATTATAAATTATATTATAT
1 TTATATTATAAATTATATTATAT
54687 TTA
1 TTA
54690 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATTATAAATTATATTATAT
Found at i:56956 original size:15 final size:14
Alignment explanation
Indices: 56902--56958 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
56892 TTCCAAAAAT
56902 ATAATTCATTTTCC
1 ATAATTCATTTTCC
* **
56916 ACAATTCAAATTCC
1 ATAATTCATTTTCC
56930 AATAATTCATTTTCC
1 -ATAATTCATTTTCC
56945 ATAATTCAATTTTC
1 ATAATTC-ATTTTC
56959 AGAAAACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 18 0.51
15 17 0.49
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATTCATTTTCC
Found at i:80702 original size:18 final size:19
Alignment explanation
Indices: 80679--80721 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
80669 CAGTAATCCT
*
80679 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
80697 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
80717 ATTCC
1 ATTCC
80722 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:89199 original size:23 final size:22
Alignment explanation
Indices: 89169--89247 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
89159 GCATGGCCTT
89169 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
89191 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
89213 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
89236 GATGCATCGATG
1 G-TGCATCGATG
89248 TACTGTTAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 19 0.42
24 9 0.20
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:89225 original size:21 final size:22
Alignment explanation
Indices: 89169--89231 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
89159 GCATGGCCTT
89169 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * *
89192 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGA
*
89213 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
89232 AAGGGATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:94949 original size:21 final size:21
Alignment explanation
Indices: 94923--94974 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
94913 TTGAAAGCGT
94923 CTGGTGCATCGATGCATAAGG
1 CTGGTGCATCGATGCATAAGG
94944 CTGGTGCATCGATGCATAAGG
1 CTGGTGCATCGATGCATAAGG
*
94965 CTAGTGCATC
1 CTGGTGCATC
94975 AGTACACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (21 bp):
CTGGTGCATCGATGCATAAGG
Found at i:95112 original size:64 final size:64
Alignment explanation
Indices: 95042--95197 Score: 199
Period size: 64 Copynumber: 2.4 Consensus size: 64
95032 GCACTAAGAG
* * * * *
95042 TGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AACATGCCCGAGTGCATCGATGCATGGTCT
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-A-ACCCGAGTGCATCGATGCATGATAT
95105 A
64 A
* * *
95106 TGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGATATG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCGAGTGCATCGATGCATGATATA
*
95170 TGCATCGATACATAAAATGCATTCGATG
1 TGCATCGATGCATAAAATGCATTCGATG
95198 ATCAATTTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 72 0.90
65 6 0.08
66 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCGAGTGCATCGATGCATGATATA
Found at i:96567 original size:11 final size:11
Alignment explanation
Indices: 96551--96584 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
96541 CAACACCATG
96551 CATTGCATTTA
1 CATTGCATTTA
*
96562 CATTGCATCTA
1 CATTGCATTTA
96573 CATTGCATTTA
1 CATTGCATTTA
96584 C
1 C
96585 TTTCGCATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (11 bp):
CATTGCATTTA
Found at i:96598 original size:22 final size:22
Alignment explanation
Indices: 96549--96598 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
96539 ATCAACACCA
96549 TGCATTGCATTTACATTGCATC
1 TGCATTGCATTTACATTGCATC
* *
96571 TACATTGCATTTACTTTCGCAT-
1 TGCATTGCATTTACATT-GCATC
96593 TGCATT
1 TGCATT
96599 TTATTCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (22 bp):
TGCATTGCATTTACATTGCATC
Found at i:99531 original size:1 final size:1
Alignment explanation
Indices: 99521--99595 Score: 60
Period size: 1 Copynumber: 75.0 Consensus size: 1
99511 ACAACACTCG
* * * * * * * * * *
99521 AAAAAGAAAAAAAGAAAAAAAAAAATAAAAGAAGAAAATAAAAGAAAAAGAAACAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
99586 AAAAAAAAAA
1 AAAAAAAAAA
99596 GAAAGAAAAG
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.87, C:0.01, G:0.09, T:0.03
Consensus pattern (1 bp):
A
Found at i:99538 original size:5 final size:5
Alignment explanation
Indices: 99522--99606 Score: 54
Period size: 5 Copynumber: 17.2 Consensus size: 5
99512 CAACACTCGA
* *
99522 AAAAG -AAA- AAAAG AAAA- AAAA- AAATAA AAGAAG AAAAT AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AA-AAG AAAAG AAAAG -AAAAG
* * *
99571 AAACAA AAAAG AAAAA AAAAA AAAAG -AAAG AAAAG A
1 AAA-AG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
99607 TAGATAAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
4 17 0.26
5 33 0.51
6 14 0.22
7 1 0.02
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:99566 original size:30 final size:27
Alignment explanation
Indices: 99527--99604 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 27
99517 CTCGAAAAAG
99527 AAAAAAAGAAAAAAAAAAATAAAAGAAGA
1 AAAAAAAGAAAAAAAAAAA-AAAAGAA-A
*
99556 AAATAAAAGAAAAAGAAACAAAAAAGAAA
1 AAA-AAAAGAAAAA-AAAAAAAAAAGAAA
* *
99585 AAAAAAA-AAAAGAAAGAAAA
1 AAAAAAAGAAAAAAAAAAAAA
99605 GATAGATAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.16
27 4 0.09
28 4 0.09
29 7 0.16
30 17 0.39
31 5 0.11
ACGTcount: A:0.86, C:0.01, G:0.10, T:0.03
Consensus pattern (27 bp):
AAAAAAAGAAAAAAAAAAAAAAAGAAA
Found at i:106725 original size:18 final size:18
Alignment explanation
Indices: 106704--106741 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
106694 CCATCATCAA
106704 AGGAAGAAACGAAAGATG
1 AGGAAGAAACGAAAGATG
106722 A-G--GAAACGAAAGATG
1 AGGAAGAAACGAAAGATG
106737 AGGAA
1 AGGAA
106742 ACTCATGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 6
0.74 0.00 0.26
Matches are distributed among these distances:
15 14 0.82
16 1 0.06
17 1 0.06
18 1 0.06
ACGTcount: A:0.55, C:0.05, G:0.34, T:0.05
Consensus pattern (18 bp):
AGGAAGAAACGAAAGATG
Found at i:106729 original size:15 final size:15
Alignment explanation
Indices: 106709--106743 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
106699 ATCAAAGGAA
106709 GAAACGAAAGATGAG
1 GAAACGAAAGATGAG
106724 GAAACGAAAGATGAG
1 GAAACGAAAGATGAG
106739 GAAAC
1 GAAAC
106744 TCATGATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.09, G:0.31, T:0.06
Consensus pattern (15 bp):
GAAACGAAAGATGAG
Found at i:108744 original size:23 final size:22
Alignment explanation
Indices: 108702--108762 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
108692 ATAGGGCAGA
* *
108702 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
108724 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
108747 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
108763 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:108788 original size:20 final size:22
Alignment explanation
Indices: 108702--108783 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
108692 ATAGGGCAGA
*
108702 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
108724 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
*
108747 GGGAACCGATTCCCCC---ACAG
1 GGGAACCGATACCCCCTTGA-AG
*
108767 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
108784 GAGGGTTCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.02
20 16 0.30
22 14 0.26
23 22 0.42
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:117155 original size:233 final size:232
Alignment explanation
Indices: 116741--117241 Score: 716
Period size: 233 Copynumber: 2.2 Consensus size: 232
116731 TTTATAAGGT
* * *
116741 AAAAAATTGAGAAATGTTTCTCATTTAAAGCTAAAAATTGAAATTGTTGAAAACTAAGAAAAGTT
1 AAAAAA-TGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTGTTGAAAACTAAGAAAAGTT
** * * * *
116806 TCTTACCTAGTAAACTATTTTTAAAATTTGTAAGTCCTTCGGGCCATCTATAAGTTTTTCGAGCA
65 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCA
* * *
116871 TGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTCGAGCCAT
130 TGATGCTTAAATCCTTCGGGACATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCAT
* * * * *
116936 CCATAAGACCTTCAAGTAGGATGTTTTTACATGTCTCTT
195 CCACAAAACCTT-AAGCAGGATGTTTTCACATGTCTCTC
* * *
116975 GAAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAGTTGAAAATT-TTGAAAAGTAAGAAAAGTT
1 AAAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTG-AAATTGTTGAAAACTAAGAAAAGTT
*
117039 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCTATCAATAAGTCTTTCAAGCA
65 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCA
* *
117104 TGATGCTTAAATCCTTCGGGACATCTATAAGTCTTTCGAGTAAGATGATAAGTCCTTCGGGCCAT
130 TGATGCTTAAATCCTTCGGGACATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCAT
* ** *
117169 TCACAAAACCTTGGGCGGGATGTTTTCACATGTCTCTC
195 CCACAAAACCTTAAGCAGGATGTTTTCACATGTCTCTC
*
117207 AAAAAATTAGAAAGGTTTCTCATTTAAATCTGAAA
1 AAAAAATGAGAAAGGTTTCTCATTTAAATCTGAAA
117242 TTTTTAAAAA
Statistics
Matches: 237, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
232 53 0.22
233 174 0.73
234 10 0.04
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (232 bp):
AAAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTGTTGAAAACTAAGAAAAGTTT
CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCAT
GATGCTTAAATCCTTCGGGACATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGCCATC
CACAAAACCTTAAGCAGGATGTTTTCACATGTCTCTC
Found at i:117683 original size:233 final size:233
Alignment explanation
Indices: 117276--119011 Score: 2248
Period size: 233 Copynumber: 7.5 Consensus size: 233
117266 CTCCCGTTAT
* * *
117276 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTATAAGTCTATCGAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* * * * *
117341 AGTCTTTCGAGCCATCCATAAGACCTTCGGGCAG-GATGTTTTCACATGTCTCTCAAAAAATGAG
66 AGTCATTCGGGCCATCCATAAGACCTTC-GGCCGTGATGTTTTCACATATCTCTCGAAAAATGAG
** *
117405 AAAATTTTCTCATTTAAATCTGAAAGTTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT
130 AAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT
* * *
117470 AAAATATTTCCAAAATTGGTAAGTCCTTCGGGCTATCAG
195 AAACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* **
117509 TAAGTCTTTCGAGTATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTTAAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* ** * * * * *
117574 AATTTTTCGAGCTATCCATAAGACCTTCAGCCGTGATGTTTTCATATATCTCTTGAAAAATGAGA
66 AGTCATTCGGGCCATCCATAAGACCTTCGGCCGTGATGTTTTCACATATCTCTCGAAAAATGAGA
* *
117639 AAGGTTTCTCATTTAAATATGAAAACTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTA
131 AAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTA
* * *
117704 AACCATTTCCAAAATTTGTAAGTCCTTCGAGCCATTAG
196 AACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* * * *
117742 TAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGAT-ATTTGTAAGTCATTCGAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* * * * * * *
117806 AGACAATCGGGCCAT-CACAAGACCTTCGGGCAG-GATATTTTCCCATGTCTCTCGAAAAATGAG
66 AGTCATTCGGGCCATCCATAAGACCTTC-GGCCGTGATGTTTTCACATATCTCTCGAAAAATGAG
* * *
117869 AAAGGTTTCTCATTCAAATCTAAAAATTGAAATTTTTGAAAACTAAGAAAAGTTTCTTACCTAGT
130 AAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT
* * * ** *
117934 AAACTATTTTCAAAATTGGTAAGTCCTTAGGGCCGCCAA
195 AAACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* * * *
117973 TAAGTCTTTCAAGCATGATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTTGAACAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* * * * * * *
118038 AGTCATTCGGGCCATCCAAAAGACCTTCAGACATGAT-TTTTCACATGTCTCTTGAAAAATAAGA
66 AGTCATTCGGGCCATCCATAAGACCTTCGGCCGTGATGTTTTCACATATCTCTCGAAAAATGAGA
** *
118102 AATATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTAACCTAGTA
131 AAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTA
*
118167 AACTATTTCCAAAATTTGTTAGTCCTTCGGGCCATCAG
196 AACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* * * **
118205 TAATTCTTTTGAGCATGATGTTTAAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* * * * * *
118270 AGTCTTTCAGGCCATCTATAAGACCTTCAGGCAG-GATGTTTTCATATATCTCTCAAAAAATGAG
66 AGTCATTCGGGCCATCCATAAGACCTTC-GGCCGTGATGTTTTCACATATCTCTCGAAAAATGAG
* *
118334 AAAGGTTTCTCATTTAAATCAGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTTGT
130 AAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT
*
118399 AAACTATTTCCAAAATTTGTAAATCCTTCGGGCCATCAG
195 AAACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* * * *
118438 TAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGTTATCTATAAGTATTTCGAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* ** * * * *
118503 AATCATTCGGGTTATCCATAAGACCTTCGGACATGATGTTTTCACATATCTCTCGAACAATGAGG
66 AGTCATTCGGGCCATCCATAAGACCTTCGGCCGTGATGTTTTCACATATCTCTCGAAAAATGAGA
* *
118568 AAGTTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTA
131 AAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTA
*
118633 AACTATTTCCAAAATTTGTAAGTCCTTCGGGCAATCAG
196 AACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* * *
118671 TAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCTGTAATTCTTTCAAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
* * * * *
118736 AGCCCTTCGGGCCATCCATAAGACCTTCGGGCATGATGTTTTCACATATCTATCGAAAAATGAGA
66 AGTCATTCGGGCCATCCATAAGACCTTCGGCCGTGATGTTTTCACATATCTCTCGAAAAATGAG-
* * * * *
118801 AAAGTTTTCTCATTTAAATATGGAAATTGAAATTTTTAAAAAGTAAGAAAAGTTTCTTACCTACT
130 AAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT
* ****
118866 AAACTATTTCCAAAATTGGTAAGTCCTTCGAATAATCAG
195 AAACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
* * * * * * *
118905 TTAGTCTTTCGAGCATTATGCTTAAATTCTTCAGGG-CAAT-AGTAAGACTTTTGAGTAAGATGA
1 TAAGTCTTTCGAGCATGATGCTTAAATCCTTC-GGGTC-ATCTGTAAGTCTTTCGAGCAAGATGA
* * * *
118968 TAAGTCCTTCGTGACATCCATAAGTCCTTCGGCCAG-GATGTTTT
64 TAAGTCATTCGGGCCATCCATAAGACCTTCGGCC-GTGATGTTTT
119012 TCATGATTTT
Statistics
Matches: 1304, Mismatches: 187, Indels: 23
0.86 0.12 0.02
Matches are distributed among these distances:
231 160 0.12
232 275 0.21
233 685 0.53
234 179 0.14
235 5 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (233 bp):
TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATA
AGTCATTCGGGCCATCCATAAGACCTTCGGCCGTGATGTTTTCACATATCTCTCGAAAAATGAGA
AAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTA
AACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAG
Found at i:118517 original size:41 final size:42
Alignment explanation
Indices: 118438--118524 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
118428 GGGCCATCAG
* * * * * *
118438 TAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGTTATCTA
1 TAAGTATTTCGAGCAAGATGCATAAATCATTCGGGTTATCCA
118480 TAAGTATTTCGAGCAAGATG-ATAAATCATTCGGGTTATCCA
1 TAAGTATTTCGAGCAAGATGCATAAATCATTCGGGTTATCCA
118521 TAAG
1 TAAG
118525 ACCTTCGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 21 0.54
42 18 0.46
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (42 bp):
TAAGTATTTCGAGCAAGATGCATAAATCATTCGGGTTATCCA
Found at i:119736 original size:3 final size:3
Alignment explanation
Indices: 119722--119774 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
119712 CGACATTTTA
* * *
119722 TAT TAT TCT TAT TAT TAT TAT TAA TAT TAT TAT TAAT TAAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT T-AT TAT TAT
119769 T-T TAT T
1 TAT TAT T
119775 TTACATATCC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.79
4 7 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:121563 original size:21 final size:20
Alignment explanation
Indices: 121514--121584 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
121504 CATAAAATTT
121514 ATTATTTTTACA-TTTTTAT-
1 ATTATTTTTA-ATTTTTTATA
**
121533 ATTAAATTTAATGTTTTTATA
1 ATTATTTTTAAT-TTTTTATA
*
121554 ATTATTTTTATTATTTTTATA
1 ATTATTTTTAAT-TTTTTATA
*
121575 TTTATTTTTA
1 ATTATTTTTA
121585 GAAATATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.02
19 8 0.19
20 7 0.17
21 26 0.62
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (20 bp):
ATTATTTTTAATTTTTTATA
Found at i:121582 original size:20 final size:20
Alignment explanation
Indices: 121515--121582 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
121505 ATAAAATTTA
* *
121515 TTATTTTTACATTTTTATAT
1 TTATTTTAATATTTTTATAT
* * * *
121535 TAAATTTAATGTTTTTATAA
1 TTATTTTAATATTTTTATAT
*
121555 TTATTTTTATTATTTTTATAT
1 TTA-TTTTAATATTTTTATAT
121576 TTATTTT
1 TTATTTT
121583 TAGAAATATA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (20 bp):
TTATTTTAATATTTTTATAT
Found at i:121669 original size:49 final size:50
Alignment explanation
Indices: 121593--121692 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 50
121583 TAGAAATATA
121593 AATATGAAAAATACTGAATTTAATTTAAAA-TAT-AAAAATAATAAATTT
1 AATATGAAAAATACTGAATTTAATTTAAAATTATAAAAAATAATAAATTT
* *
121641 AATATGAAAAAGTA-TTACATTTAATTTAAAATTTTAAAAAATAATAAATTT
1 AATATGAAAAA-TACTGA-ATTTAATTTAAAATTATAAAAAATAATAAATTT
121692 A
1 A
121693 TTTTAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
48 13 0.28
49 15 0.33
50 2 0.04
51 16 0.35
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (50 bp):
AATATGAAAAATACTGAATTTAATTTAAAATTATAAAAAATAATAAATTT
Done.