Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008821.1 Hibiscus syriacus cultivar Beakdansim tig00111989_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: 1271541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:656898 original size:3 final size:3
Alignment explanation
Indices: 656892--656916 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
656882 GATGATGTTT
656892 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
656917 CTACACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:662541 original size:3 final size:3
Alignment explanation
Indices: 662535--662618 Score: 109
Period size: 3 Copynumber: 27.7 Consensus size: 3
662525 CTCCATTTTC
662535 TAT TAT TAT TATT TAT TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
662581 TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
662619 CAAACAGGCC
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 59 0.82
4 9 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:664361 original size:20 final size:19
Alignment explanation
Indices: 664336--664377 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
664326 TTATTTTATA
664336 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
664356 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
664375 AAT
1 AAT
664378 ATCAAAGAAA
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:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:664365 original size:119 final size:116
Alignment explanation
Indices: 664234--664468 Score: 265
Period size: 120 Copynumber: 2.0 Consensus size: 116
664224 TTTAATCCTA
* * * * * *
664234 TTTTAATATTTATTTATTTTCCAATAT-TAGGAAAGGGCAGTCTTAAAATAACTGGATGTCCATT
1 TTTTAATATTTATTTATTTTCCAATATAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CATT
* * * *
664298 TTTTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTCTGATATTTCTAAATAAATAAACATCTTA-TTTATAAA-TATATATAAATTG
** * ** *
664352 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCAT
1 TTTTAA-TATTTATTTATTTTCCAATAT-AAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
*
664417 TTTCTGATATTTCTAAATAAATAAACATTTTATTTATAAATATATATAAATT
64 TTTCTGATATTTCTAAATAAATAAACATCTTATTTATAAATATATATAAATT
664469 AATATATATT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
118 17 0.18
119 27 0.28
120 31 0.32
121 22 0.23
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.46
Consensus pattern (116 bp):
TTTTAATATTTATTTATTTTCCAATATAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTT
TCTGATATTTCTAAATAAATAAACATCTTATTTATAAATATATATAAATTG
Found at i:668071 original size:16 final size:16
Alignment explanation
Indices: 668050--668083 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
668040 GGTATTCGAG
668050 GCCATGGTACAAATGA
1 GCCATGGTACAAATGA
668066 GCCATGGTACAAATGA
1 GCCATGGTACAAATGA
668082 GC
1 GC
668084 GAAGTTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (16 bp):
GCCATGGTACAAATGA
Found at i:675678 original size:21 final size:19
Alignment explanation
Indices: 675653--675730 Score: 70
Period size: 18 Copynumber: 4.1 Consensus size: 19
675643 TATTATGCTT
675653 GAAGAAAAAATGAAAAAAAAA
1 GAAGAAAAAA--AAAAAAAAA
* * *
675674 GAAG-AAGAAAAAAGAGAA
1 GAAGAAAAAAAAAAAAAAA
*
675692 GAAGAAGAAAAAAAAAAGAA
1 GAAGAA-AAAAAAAAAAAAA
*
675712 G-AGAAAAAAGAAAAAAAA
1 GAAGAAAAAAAAAAAAAAA
675730 G
1 G
675731 GGTCAAGATG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
18 23 0.48
19 5 0.10
20 16 0.33
21 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (19 bp):
GAAGAAAAAAAAAAAAAAA
Found at i:675738 original size:25 final size:24
Alignment explanation
Indices: 675667--675729 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
675657 AAAAAATGAA
* * *
675667 AAAAAAAGAAGAAGAAAA-AAGAG
1 AAAAGAAGAAAAAAAAAAGAAGAG
675690 AAGAAGAAGAAAAAAAAAAGAAGAG
1 AA-AAGAAGAAAAAAAAAAGAAGAG
675715 AAAA-AAGAAAAAAAA
1 AAAAGAAGAAAAAAAA
675730 GGGTCAAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.37
24 15 0.43
25 7 0.20
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (24 bp):
AAAAGAAGAAAAAAAAAAGAAGAG
Found at i:676122 original size:19 final size:17
Alignment explanation
Indices: 676080--676128 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
676070 TATTTTCTCT
676080 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
676096 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
676114 AAAATTCAATTTATT
1 -AAATTCAATTTATT
676129 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 1 0.04
19 13 0.46
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:677596 original size:112 final size:109
Alignment explanation
Indices: 677354--677687 Score: 409
Period size: 112 Copynumber: 3.0 Consensus size: 109
677344 GCAAAGATTT
* * *
677354 AAATCCATCATTTAATGGATCAACAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
677419 AAAGAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
66 --A-AGAAG-A-AA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* *
677469 GAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTTATCTG
1 AAATCCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTC---ATCTG
*
677534 AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * *
677581 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
677645 GAAGAGGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
65 GAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
677688 ATAATTCTAT
Statistics
Matches: 194, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
109 45 0.23
112 79 0.41
113 3 0.02
114 1 0.01
115 57 0.29
116 1 0.01
118 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (109 bp):
AAATCCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:677700 original size:109 final size:112
Alignment explanation
Indices: 677390--677934 Score: 442
Period size: 124 Copynumber: 4.6 Consensus size: 112
677380 TGCCAGTTAG
677390 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGTTCATAATGAGAAGAACTCATCTGAAG--A-AGAAG-AGAAGTTCATAATGAGAAGAACTTGT
* ** * * * * *
677455 TCAACTTTTTGTTTGAATTC-ATCATTTGATGGATCAACATTGCCAG-GTAG
62 TCAACCTTTTGCATCAATTCTATCACTTGATGGATCAACTTTTCCAGAG-AA
*
677505 AGTTCATAATGAGAAGAACTCGTTATCTGAAGAAGAAGA-AA-TTCATAATGAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTC---ATCTGAAGAAGAAGAGAAGTTCATAATGAGAAGAACTTGTT
* * *
677568 CAACCTTTTGC-TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
63 CAACCTTTTGCATCAATTCTATCACTTGATGGATCAACTTTTCCAGAGAA
* *
677617 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-AG-GAAGTTCACAATGAGAAGAGCTTGTTCAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * *
677680 CCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAAAGAA
66 CCTTTTGCATCAATTCTATCAC---------TTGAT--GGATCAACTTTTCCAGAGAA
* * *
677737 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAG-AGAAGTTCATAATGAGAAGAACTTGTTC
* * * ** *
677802 AACCTTTTGAAT-GACTCTATCACAGAAGGAAATAGGTCAACATCAACTTTTCCAGGGAA
64 AACCTTTTGCATCAATTCTATCAC---TTG--AT-GG-----ATCAACTTTTCCAGAGAA
* * * *
677861 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAG-AGAAGTTCATAATGAGAAGAACTTGTTC
677926 AATCCTTTT
64 AA-CCTTTT
677935 CCAAATTACA
Statistics
Matches: 363, Mismatches: 35, Indels: 54
0.80 0.08 0.12
Matches are distributed among these distances:
108 4 0.01
109 50 0.14
110 1 0.00
111 5 0.01
112 74 0.20
113 3 0.01
114 1 0.00
115 26 0.07
116 1 0.00
118 16 0.04
119 2 0.01
120 51 0.14
122 2 0.01
124 120 0.33
125 7 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCATCAATTCTATCACTTGATGGATCAACTTTTCCAGAGAA
Found at i:677831 original size:124 final size:123
Alignment explanation
Indices: 677599--677934 Score: 480
Period size: 124 Copynumber: 2.7 Consensus size: 123
677589 CACTTGATGG
* *
677599 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AG--GAAGTTCACA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* * * * *
677661 ATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
66 ATAAGAAGAGCTTGTTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAAC
*
677719 ATCAACTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCAT
* * *
677784 AATAAGAAGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAAC
65 AATAAGAAGAGCTTGTTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAAC
* * * *
677843 ATCAACTTTTCCAGGGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
*
677908 AATAAGAAGAACTTGTTCAATCCTTTT
65 AATAAGAAGAGCTTGTTCAA-CCTTTT
677935 CCAAATTACA
Statistics
Matches: 192, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
120 48 0.25
122 2 0.01
124 135 0.70
125 7 0.04
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
ATAAGAAGAGCTTGTTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAAC
Found at i:677953 original size:124 final size:121
Alignment explanation
Indices: 677599--678017 Score: 459
Period size: 124 Copynumber: 3.5 Consensus size: 121
677589 CACTTGATGG
* *
677599 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAG--GAAGTTCACA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
* *
677661 ATGAGAAGAGCTTGTTCAACCTTTTGCATAATT-CTATCACAGAAGGAGATAGATCAGC
66 ATAAGAAGAGCTTGTTCAACCTTTT-CA-AATTACTATCACAGAAGGAGATAG-TCAAC
* *
677719 ATCAACTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAGAAGAAGTTCAT
* * * *
677784 AATAAGAAGAGCTTATTCAACCTTTT-GAATGACTCTATCACAGAAGGAAATAGGTCAAC
65 AATAAGAAGAGCTTGTTCAACCTTTTCAAATTA--CTATCACAGAAGGAGATA-GTCAAC
* * * *
677843 ATCAACTTTTCCAGGGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
* * * *
677908 AATAAGAAGAACTTGTTCAATCCTTTTCCAAATTAC-ATCATAGAAGGAGATA-TTATC
65 AATAAGAAGAGCTTGTTCAA-CCTTTT-CAAATTACTATCACAGAAGGAGATAGTCAAC
* * *
677965 ATC--C----CCAGCGGAAAGTTCATAATGAGAAGAACTCGTCTGAAGAAAGAGAAGAA
1 ATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAA
678018 TTTATTCAAC
Statistics
Matches: 259, Mismatches: 27, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
116 11 0.04
117 34 0.13
120 48 0.19
121 3 0.01
122 8 0.03
124 143 0.55
125 8 0.03
127 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (121 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
ATAAGAAGAGCTTGTTCAACCTTTTCAAATTACTATCACAGAAGGAGATAGTCAAC
Found at i:678164 original size:3 final size:3
Alignment explanation
Indices: 678158--678237 Score: 99
Period size: 3 Copynumber: 25.7 Consensus size: 3
678148 CTCCATTTTC
678158 TAT TAT TAT TATT TAT TAT TAT TAT TATT TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TAT
* *
678206 T-T TATT TAT TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA
678238 CAAACAAGCA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 2 0.03
3 54 0.79
4 12 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:683191 original size:19 final size:20
Alignment explanation
Indices: 683149--683190 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
683139 AAACAGATTG
*
683149 CCCAAATGGTACCGGTACCC
1 CCCAAATGGTACCGATACCC
*
683169 CCCAGATGGTACCGATACCC
1 CCCAAATGGTACCGATACCC
683189 CC
1 CC
683191 ATGACATTTT
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:0.24, C:0.43, G:0.19, T:0.14
Consensus pattern (20 bp):
CCCAAATGGTACCGATACCC
Found at i:689049 original size:23 final size:22
Alignment explanation
Indices: 689018--689096 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
689008 CTGCGTGCTA
*
689018 GGTATCGATACCCCCTTTGAATG
1 GGTACCGATACCCCC-TTGAATG
*
689041 GGTACCGATACCATCCTTGAATG
1 GGTACCGATACC-CCCTTGAATG
689064 GGTACCGATACCCCCTTG-A-G
1 GGTACCGATACCCCCTTGAATG
*
689084 GGTATCGATACCC
1 GGTACCGATACCC
689097 TCCACGGGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 13 0.25
21 1 0.02
22 5 0.10
23 30 0.59
24 2 0.04
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGAATG
Found at i:689520 original size:20 final size:21
Alignment explanation
Indices: 689497--689537 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
689487 ATTTTTGAAA
689497 TAAAAAAATTG-TTTTGATTT
1 TAAAAAAATTGTTTTTGATTT
**
689517 TAAAATTATTGTTTTTGATTT
1 TAAAAAAATTGTTTTTGATTT
689538 AATTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TAAAAAAATTGTTTTTGATTT
Found at i:699157 original size:17 final size:17
Alignment explanation
Indices: 699135--699167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
699125 TTTGATGTTG
699135 TTGGATTGATATGTTTT
1 TTGGATTGATATGTTTT
*
699152 TTGGATTGTTATGTTT
1 TTGGATTGATATGTTT
699168 AAATTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (17 bp):
TTGGATTGATATGTTTT
Found at i:699888 original size:20 final size:20
Alignment explanation
Indices: 699863--699903 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
699853 AAACAAATTG
*
699863 CCCAGATGGTACCGGTACCC
1 CCCAGATGGTACCGATACCC
699883 CCCAGATGGTACCGATACCC
1 CCCAGATGGTACCGATACCC
699903 C
1 C
699904 AATGCCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.41, G:0.22, T:0.15
Consensus pattern (20 bp):
CCCAGATGGTACCGATACCC
Found at i:706787 original size:22 final size:22
Alignment explanation
Indices: 706762--706804 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
706752 TTATTCATTC
* *
706762 ATTGTTTGTTTGAATTAATATT
1 ATTGTATGTTTGAATAAATATT
*
706784 ATTGTATGTTTGTATAAATAT
1 ATTGTATGTTTGAATAAATAT
706805 ATAAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (22 bp):
ATTGTATGTTTGAATAAATATT
Found at i:706834 original size:19 final size:19
Alignment explanation
Indices: 706811--706855 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
706801 ATATATAAAT
*
706811 ATATTTTTAATATATATTA
1 ATATTTTTAATAAATATTA
* * *
706830 TTATTTATAATAAATCTTA
1 ATATTTTTAATAAATATTA
706849 ATATTTT
1 ATATTTT
706856 ATGATATTGT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTTTAATAAATATTA
Found at i:711296 original size:30 final size:28
Alignment explanation
Indices: 711249--711309 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
711239 TAAACAAATT
* *
711249 CATCATTTAACGTATTACCGATAATATG
1 CATCATTTAACGCATTACCAATAATATG
711277 CATCATTTATAACGCATTACCAATAATATG
1 CATCA-TT-TAACGCATTACCAATAATATG
711307 CAT
1 CAT
711310 TCAAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.17
29 2 0.07
30 22 0.76
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (28 bp):
CATCATTTAACGCATTACCAATAATATG
Found at i:717952 original size:6 final size:6
Alignment explanation
Indices: 717937--718051 Score: 53
Period size: 6 Copynumber: 19.0 Consensus size: 6
717927 ATTATACTTG
* * * * *
717937 AAGAAT AAGAAA AAGAGAA AA-ACA AAGAAA AATGAGA AA-AAG AGGTAAA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA AA-GAAA AAGAAA AAG-AAA
* * *
717986 AGGAAA AA-AAA TTAGAAA ATTAGA-A AAGAAA AATAAA AA-AAA AAGAAA
1 AAGAAA AAGAAA -AAGAAA A--AGAAA AAGAAA AAGAAA AAGAAA AAGAAA
718034 AA-ATAA AAGAAA AAGAAA
1 AAGA-AA AAGAAA AAGAAA
718052 CAAAGGAGAT
Statistics
Matches: 84, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
5 17 0.20
6 44 0.52
7 20 0.24
8 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (6 bp):
AAGAAA
Found at i:718037 original size:18 final size:18
Alignment explanation
Indices: 718009--718051 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
717999 AGAAAATTAG
718009 AAAAG-AAAAATAAAAAA
1 AAAAGAAAAAATAAAAAA
*
718026 AAAAGAAAAAATAAAAGA
1 AAAAGAAAAAATAAAAAA
718044 AAAAGAAA
1 AAAAGAAA
718052 CAAAGGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAATAAAAAA
Found at i:719483 original size:3 final size:3
Alignment explanation
Indices: 719477--719530 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
719467 TTTTATTATC
* * * *
719477 TTA TTA TTA TTA TTA CTA ATA TTAA ATA TTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
719523 TTA TTA TT
1 TTA TTA TT
719531 TACATTTTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:733681 original size:48 final size:49
Alignment explanation
Indices: 733597--733719 Score: 140
Period size: 48 Copynumber: 2.5 Consensus size: 49
733587 TTAGCAGGAA
* * * * *
733597 AGCGCGCCCCTGAACCGCGCTATATGTTGATTTGGCGCCACGTTGGTAT
1 AGCGCGCCCCTGAACCGCGATATACGATGATCTGGCGCCACGTGGGTAT
** *
733646 AGCGC-CCCCTGCCCCGCGATATACGATGATCTGGCGTCACGTGGGTAT
1 AGCGCGCCCCTGAACCGCGATATACGATGATCTGGCGCCACGTGGGTAT
* *
733694 AGCGCGCCTCCTGATCCGCGTTATAC
1 AGCGCGCC-CCTGAACCGCGATATAC
733720 CTGGATATCT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 40 0.66
49 7 0.11
50 14 0.23
ACGTcount: A:0.16, C:0.33, G:0.28, T:0.24
Consensus pattern (49 bp):
AGCGCGCCCCTGAACCGCGATATACGATGATCTGGCGCCACGTGGGTAT
Found at i:733855 original size:10 final size:10
Alignment explanation
Indices: 733840--733874 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
733830 TTTATCACAC
733840 CAAATTCTCT
1 CAAATTCTCT
733850 CAAATTCTCT
1 CAAATTCTCT
733860 -AAATTTCTCT
1 CAAA-TTCTCT
733870 CAAAT
1 CAAAT
733875 ACTATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:762969 original size:20 final size:20
Alignment explanation
Indices: 762944--763003 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
762934 AGTATGCTTG
*
762944 AGGGGGAACCGATTCCCCCC
1 AGGGGGTACCGATTCCCCCC
762964 AGGGGGTACCGATTCCCCCC
1 AGGGGGTACCGATTCCCCCC
762984 AGGGGGTACCGATTCCCCCC
1 AGGGGGTACCGATTCCCCCC
763004 CAGTGTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.17, C:0.40, G:0.30, T:0.13
Consensus pattern (20 bp):
AGGGGGTACCGATTCCCCCC
Found at i:786076 original size:17 final size:18
Alignment explanation
Indices: 786054--786087 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
786044 TTGAAAGGTC
*
786054 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
786071 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
786088 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:790554 original size:19 final size:19
Alignment explanation
Indices: 790530--790568 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
790520 TTTGAAAAAG
*
790530 AATAATAGTAGATTATCAA
1 AATAATAGTAGATTACCAA
*
790549 AATAATAGTGGATTACCAA
1 AATAATAGTAGATTACCAA
790568 A
1 A
790569 TAGGTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (19 bp):
AATAATAGTAGATTACCAA
Found at i:796041 original size:73 final size:71
Alignment explanation
Indices: 795900--796045 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 71
795890 TTCATAACAT
*
795900 TATCTATTTATTTTGAATCATATAAAAAAGTAAAAAATAAAATACCTGATCATCTTCATTCCAAA
1 TATCTATTTATTTTGAATCATATAAAAAAGTAAAAAATAAAACACCTGATCATCTTCATTCCAAA
795965 GTTCAC
66 GTTCAC
795971 TATCTATTTATTTTGAATCATATAAAAAAGTAAAAAAAATAAAACACCTGATCATCTTCATTCCA
1 TATCTATTTATTTTGAATCATATAAAAAAGT--AAAAAATAAAACACCTGATCATCTTCATTCCA
796036 AAGTTCAC
64 AAGTTCAC
796044 TA
1 TA
796046 CAGCAAAACA
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 31 0.43
73 41 0.57
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (71 bp):
TATCTATTTATTTTGAATCATATAAAAAAGTAAAAAATAAAACACCTGATCATCTTCATTCCAAA
GTTCAC
Found at i:799922 original size:2 final size:2
Alignment explanation
Indices: 799915--799946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
799905 TATTATGTTA
799915 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
799947 GTTAAATTAG
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:802203 original size:16 final size:16
Alignment explanation
Indices: 802182--802216 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
802172 AATTCGGAAA
*
802182 GTCCACATTGTATTTT
1 GTCCACATTGAATTTT
802198 GTCCACATTGAATTTT
1 GTCCACATTGAATTTT
802214 GTC
1 GTC
802217 TCGTAAGAAT
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:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (16 bp):
GTCCACATTGAATTTT
Found at i:805347 original size:23 final size:23
Alignment explanation
Indices: 805319--805433 Score: 88
Period size: 23 Copynumber: 5.0 Consensus size: 23
805309 GTTCTACACG
805319 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
*** * *
805342 GGTCCTTTAAGACATTTCTACGC
1 GGTCCTTCGGGACAATTCTACGT
* * * * *
805365 GGTCTTTTGGGATAATTATATGT
1 GGTCCTTCGGGACAATTCTACGT
* *
805388 GGTCATTCGGGACATTTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
*
805411 -GTCACTTCGGTACATATTCTACG
1 GGTC-CTTCGGGACA-ATTCTACG
805434 CGGCACTTTG
Statistics
Matches: 68, Mismatches: 22, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
22 3 0.04
23 58 0.85
24 7 0.10
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:805440 original size:24 final size:23
Alignment explanation
Indices: 805393--805441 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
805383 TATGTGGTCA
* *
805393 TTCGGGACATTTCTACGTGTCAC
1 TTCGGGACATTTCTACGCGGCAC
*
805416 TTCGGTACATATTCTACGCGGCAC
1 TTCGGGACAT-TTCTACGCGGCAC
805440 TT
1 TT
805442 TGGTGCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCGGGACATTTCTACGCGGCAC
Found at i:805980 original size:23 final size:23
Alignment explanation
Indices: 805954--806039 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
805944 ATTCGAGGGT
805954 TCTACGTGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* ** **
805977 TCTATGTGGTCCTTCAAGACATT
1 TCTACGTGGTCCTTCGGGACAAA
* *
806000 TCTATGTGGTCATTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
*
806023 TTCTACGTGGTACTTCG
1 -TCTACGTGGTCCTTCG
806040 ATGCAATTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
23 36 0.73
24 13 0.27
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:809915 original size:23 final size:23
Alignment explanation
Indices: 809888--809936 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
809878 TCGAGACAAT
809888 TATGTGGCATTTCGGTGCAAACC
1 TATGTGGCATTTCGGTGCAAACC
*
809911 TATGTGGCATTTTGGTGCAAACC
1 TATGTGGCATTTCGGTGCAAACC
809934 TAT
1 TAT
809937 ATGGTCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (23 bp):
TATGTGGCATTTCGGTGCAAACC
Found at i:815837 original size:3 final size:3
Alignment explanation
Indices: 815829--815887 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
815819 TAAACAGTTC
815829 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT -AT AAT AAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
815876 AAT AAT AAT AAT
1 AAT AAT AAT AAT
815888 GACCAAAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.08
3 46 0.87
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:815877 original size:29 final size:29
Alignment explanation
Indices: 815829--815885 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
815819 TAAACAGTTC
815829 AATAATAATAATAATAATAATAATAATAT
1 AATAATAATAATAATAATAATAATAATAT
815858 AATAAT-ATAATAATACATAATAATAATA
1 AATAATAATAATAATA-ATAATAATAATA
815886 ATGACCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (29 bp):
AATAATAATAATAATAATAATAATAATAT
Found at i:828403 original size:2 final size:2
Alignment explanation
Indices: 828391--828440 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
828381 TTACCTAATC
* *
828391 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
828433 AT AT AT AT
1 AT AT AT AT
828441 GTAAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:830211 original size:16 final size:16
Alignment explanation
Indices: 830190--830241 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
830180 ATTACCCGAT
830190 CTGTTTTCAACCTGAC
1 CTGTTTTCAACCTGAC
830206 CTGTTTTCAACCTGAC
1 CTGTTTTCAACCTGAC
* *
830222 TTGTTTTTAACCTGAC
1 CTGTTTTCAACCTGAC
830238 CTGT
1 CTGT
830242 AAATGATCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.13, T:0.42
Consensus pattern (16 bp):
CTGTTTTCAACCTGAC
Found at i:830539 original size:22 final size:23
Alignment explanation
Indices: 830508--830554 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
830498 TACAAAGGAA
830508 AATTAATATAGTTTAATTTATAT
1 AATTAATATAGTTTAATTTATAT
830531 AATT-ATATAGTTTAATTTATAT
1 AATTAATATAGTTTAATTTATAT
830553 AA
1 AA
830555 AGAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
AATTAATATAGTTTAATTTATAT
Found at i:833095 original size:62 final size:61
Alignment explanation
Indices: 833009--833154 Score: 188
Period size: 62 Copynumber: 2.4 Consensus size: 61
832999 GTCTCTTAGT
* *
833009 TTTAAA-TTTATTCAATTTAGTCCAAATTTAATAATT-TAATATATTAATTTAAGCTTCATA
1 TTTAAATTTTGTTCAATTTAATCCAAATTTAAT-ATTATAATATATTAATTTAAGCTTCATA
* * * * *
833069 TTTCAACTTTTTTTCAATTTAATCCAAATTTAATGTTATCATTTATTAATTTAAGCTTCATA
1 TTT-AAATTTTGTTCAATTTAATCCAAATTTAATATTATAATATATTAATTTAAGCTTCATA
*
833131 TTTAAATTTTGTTCAATTTGATCC
1 TTTAAATTTTGTTCAATTTAATCC
833155 TTATATATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
60 3 0.04
61 22 0.30
62 49 0.66
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (61 bp):
TTTAAATTTTGTTCAATTTAATCCAAATTTAATATTATAATATATTAATTTAAGCTTCATA
Found at i:833230 original size:18 final size:18
Alignment explanation
Indices: 833209--833344 Score: 107
Period size: 18 Copynumber: 8.1 Consensus size: 18
833199 AATAAATTAA
833209 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
833227 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
833245 TA-AT-G--AACTATATA-
1 TATATAGTTTA-TATATAC
*
833259 -ATATAG--TGTATATAC
1 TATATAGTTTATATATAC
* *
833274 TA-AT-GAATTATATATAA
1 TATATAG-TTTATATATAC
*
833291 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
833309 CATATAGTCTATATAT--
1 TATATAGTTTATATATAC
833325 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
833343 TA
1 TA
833345 ATAAACTATA
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.01
14 10 0.11
15 9 0.10
16 16 0.17
17 10 0.11
18 46 0.49
19 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:833304 original size:33 final size:31
Alignment explanation
Indices: 833218--833368 Score: 96
Period size: 33 Copynumber: 4.6 Consensus size: 31
833208 ATATATAGTT
* *
833218 TATATATACTATATAGTTTATATA-TACTAA
1 TATATATAATATATAGTTTATATACTAATAA
*
833248 TGA-ACTAT-ATAATATAGTGTATATACTAATGAA
1 T-ATA-TATAAT-ATATAGTTTATATACTAAT-AA
*
833281 TTATATATAATGTATAGTTTATATA-TACCATATA
1 -TATATATAATATATAGTTTATATACTA--ATA-A
* *
833315 GTCTATATATTATATAGTTTATATATACTAATAA
1 -TATATATAATATATAG-TT-TATATACTAATAA
*
833349 -ACTATATAATGTATAGTTTA
1 TA-TATATAATATATAGTTTA
833369 GGGTTTAGGA
Statistics
Matches: 94, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
30 3 0.03
31 19 0.20
32 7 0.07
33 31 0.33
34 21 0.22
35 5 0.05
36 6 0.06
37 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (31 bp):
TATATATAATATATAGTTTATATACTAATAA
Found at i:833384 original size:14 final size:14
Alignment explanation
Indices: 833365--833395 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
833355 TAATGTATAG
*
833365 TTTAGGGTTTAGGA
1 TTTAGGGTTTAGAA
833379 TTTAGGGTTTAGAA
1 TTTAGGGTTTAGAA
833393 TTT
1 TTT
833396 TTATATATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTTAGAA
Found at i:833436 original size:2 final size:2
Alignment explanation
Indices: 833419--833489 Score: 56
Period size: 2 Copynumber: 34.0 Consensus size: 2
833409 ATATGTAAAT
*
833419 TA TA CTA TA TA T- TA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* *
833462 TA TA AA TA TA AA CTA TA GTA TA TA TA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA
833490 GGTCATATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 2 0.04
2 46 0.82
3 8 0.14
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:833439 original size:34 final size:36
Alignment explanation
Indices: 833396--833465 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
833386 TTTAGAATTT
*
833396 TTATATATAGTTCATATGTA-AAT-TATACTATATA
1 TTATATATAGTTCATATATATAATATATACTATATA
* *
833430 TTATATATAGTTTATATATATAATATATAGTATATA
1 TTATATATAGTTCATATATATAATATATACTATATA
833466 AATATAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 18 0.58
35 3 0.10
36 10 0.32
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (36 bp):
TTATATATAGTTCATATATATAATATATACTATATA
Found at i:833449 original size:20 final size:20
Alignment explanation
Indices: 833419--833489 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
833409 ATATGTAAAT
833419 TATACTATATATTATATATAG
1 TATA-TATATATTATATATAG
* *
833440 TTTATATATATAATATATAG
1 TATATATATATTATATATAG
* *
833460 TATATAAATA-TAAACTATAG
1 TATATATATATTATA-TATAG
833480 TATATATATA
1 TATATATATA
833490 GGTCATATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.05
20 37 0.88
21 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATATATATTATATATAG
Found at i:833489 original size:33 final size:33
Alignment explanation
Indices: 833442--833671 Score: 124
Period size: 33 Copynumber: 7.0 Consensus size: 33
833432 ATATATAGTT
833442 TATA-TATATAATATATAGTATATAAATATAAAC
1 TATAGTATAT-ATATATAGTATATAAATATAAAC
* * *
833475 TATAGTATATATATA-GGT-CAT--ATGTAAAC
1 TATAGTATATATATATAGTATATAAATATAAAC
* *** ** *
833504 TATATAGTATATAAATATCAACCT-TAGTGTATATA-
1 --TATAGTATATATATAT-AGTATATA-AATATAAAC
* *
833539 TATA-TTTATATATATAGT-TCAT--ATGTAAAC
1 TATAGTATATATATATAGTAT-ATAAATATAAAC
833569 TATAGTTCATATATATATAGTATATAAATATAAAC
1 TATAG-T-ATATATATATAGTATATAAATATAAAC
* * *
833604 TATAGTTTATATAAATAGTATATAAATATAAAT
1 TATAGTATATATATATAGTATATAAATATAAAC
* *
833637 TATAGTATGTAGTTTATATA-AATATAAATATAAAC
1 TATAGTA--TA-TATATATAGTATATAAATATAAAC
833672 CCTAAACTCT
Statistics
Matches: 148, Mismatches: 28, Indels: 40
0.69 0.13 0.19
Matches are distributed among these distances:
29 11 0.07
30 5 0.03
31 17 0.11
32 13 0.09
33 58 0.39
34 7 0.05
35 27 0.18
36 10 0.07
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (33 bp):
TATAGTATATATATATAGTATATAAATATAAAC
Found at i:833508 original size:51 final size:51
Alignment explanation
Indices: 833414--833540 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 51
833404 AGTTCATATG
* * *
833414 TAAAT-TATACTATA-TATTATATATAGTTTATATATATAATATATAGTATA
1 TAAATATAAACTATAGTA-TATATATAGGTCATATATATAATATATAGTATA
*
833464 TAAATATAAACTATAGTATATATATAGGTCATATGTA-AACTATATAGTATA
1 TAAATATAAACTATAGTATATATATAGGTCATATATATAA-TATATAGTATA
* *
833515 TAAATATCAACCT-TAGTGTATATATA
1 TAAATAT-AAACTATAGTATATATATA
833541 TATTTATATA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
50 7 0.10
51 54 0.81
52 6 0.09
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (51 bp):
TAAATATAAACTATAGTATATATATAGGTCATATATATAATATATAGTATA
Found at i:833607 original size:20 final size:19
Alignment explanation
Indices: 833577--833644 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
833567 ACTATAGTTC
*
833577 ATATATATATAGTATATAA
1 ATATAAATATAGTATATAA
833596 ATATAAACTATAGT-T-T--
1 ATATAAA-TATAGTATATAA
833612 ATAT-AA-ATAGTATATAA
1 ATATAAATATAGTATATAA
833629 ATATAAATTATAGTAT
1 ATATAAA-TATAGTAT
833645 GTAGTTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
13 5 0.12
14 1 0.03
15 3 0.08
16 4 0.10
17 4 0.10
18 3 0.08
19 7 0.17
20 13 0.32
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (19 bp):
ATATAAATATAGTATATAA
Found at i:833724 original size:22 final size:22
Alignment explanation
Indices: 833706--833751 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
833696 ATATATATAT
833706 ATAAACTATATAATTTATATCA
1 ATAAACTATATAATTTATATCA
833728 ATAAACTATATAATTTATA-CA
1 ATAAACTATATAATTTATATCA
833749 ATA
1 ATA
833752 TATATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAACTATATAATTTATATCA
Found at i:833894 original size:2 final size:2
Alignment explanation
Indices: 833887--833979 Score: 50
Period size: 2 Copynumber: 46.5 Consensus size: 2
833877 TTATACATTG
* * * *
833887 TA TA TA TA -A TT TA TA CTT TA TA CA TA -A TA TA TA TA TA AA GTA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
833929 TA TA GTT TA TA TA TA TA -A TA CA TA TA CTT TA TA T- 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
*
833971 TA TC TA TA T
1 TA TA TA TA T
833980 TAGTTGTTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
1 4 0.06
2 59 0.88
3 4 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:833899 original size:20 final size:19
Alignment explanation
Indices: 833867--833919 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
833857 AAACTATATA
*
833867 GTAT-TATAGTTTATACATT
1 GTATATATAATTTATAC-TT
833886 GTATATATAATTTATACTT
1 GTATATATAATTTATACTT
* *
833905 -TATACATAATATATA
1 GTATATATAATTTATA
833920 TATAAAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 13 0.43
19 6 0.20
20 11 0.37
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (19 bp):
GTATATATAATTTATACTT
Found at i:833907 original size:27 final size:28
Alignment explanation
Indices: 833861--833921 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
833851 ATATATAAAC
* * **
833861 TATATAGTATTATAGTTTATACATTGTA
1 TATATAATATTATACTTTATACATAATA
833889 TATATAAT-TTATACTTTATACATAATA
1 TATATAATATTATACTTTATACATAATA
833916 TATATA
1 TATATA
833922 TAAAGTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (28 bp):
TATATAATATTATACTTTATACATAATA
Found at i:833939 original size:22 final size:22
Alignment explanation
Indices: 833914--833968 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
833904 TTATACATAA
* *
833914 TATATATATAA-AGTATATAGTT
1 TATATATATAATA-CATATACTT
833936 TATATATATAATACATATACTT
1 TATATATATAATACATATACTT
833958 TATATTATATA
1 TATA-TATATA
833969 TATATCTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATATATAATACATATACTT
Found at i:834385 original size:211 final size:213
Alignment explanation
Indices: 834004--834816 Score: 1139
Period size: 211 Copynumber: 3.8 Consensus size: 213
833994 TTTTTTCTCA
* * * * * *
834004 ACTTAATACTTATTTATATTTATT-AATTAGCTCATAACTTTTTAAATGAGTATAATTTAGTACA
1 ACTTATTACTTATTTCTATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
*
834068 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCC-C-T-TTTGTGTTGT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCCTCATATGTGTGTTGT
* *
834130 TTATTATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCATCCAAATTTTATTT
130 TTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
* *
834195 GCACCTAAAATTGACCCAT
195 GCATCTGAAATTGACCCAT
*
834214 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATGATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* *
834279 TTTTGGTATTAATTTTAACCTCAAAATTTAAAATTATTTTGATTTGAT-CTC-T-TTTGTGTTGT
66 TTTT-GTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCCTCATATGTGTGTTGT
* * * *
834341 TTAACATATTTAAATTTTTATTTTTAATTTTATATTTATTCAATTTAGTCCTCCAAATTTTATTT
130 TTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
834406 GCATCTGAAATTGACCCAT
195 GCATCTGAAATTGACCCAT
834425 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACCTTTTTAAATGGGTATAATTTAGTACT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAA-CTTTTTAAATGGGTATAATTTAGTACT
* * * *
834490 TTTTTGTATTAATTTCAACATCACAATTTAAATTTATTTAGATTTGATCCCTCATCAATGTGTGT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGAT-CCTCAT--ATGTGTGT
* *
834555 TGTTTAATTTATTT-AATTTTT-TTT-TAAATTTCATATTTTTTCAATTTAGTCCTCCAAATTTT
127 TGTTTAATATATTTAAATTTTTATTTGT-AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
* *
834617 ATTTGCATATGAAATTGATCCAT
191 ATTTGCATCTGAAATTGACCCAT
* * * *
834640 ACTTTTTACTTAATTCAATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAG---T
1 ACTTATTACTTATTTCTA-TTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
* *
834702 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCATCATCAATGTGTGT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCC-TCAT--ATGTGTGT
*
834767 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
127 TGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
834817 ATTCTTAAAT
Statistics
Matches: 550, Mismatches: 37, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
209 2 0.00
210 60 0.11
211 207 0.38
212 105 0.19
213 10 0.02
214 26 0.05
215 97 0.18
216 25 0.05
217 18 0.03
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (213 bp):
ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCCTCATATGTGTGTTGTT
TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
CATCTGAAATTGACCCAT
Found at i:837135 original size:17 final size:17
Alignment explanation
Indices: 837110--837146 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
837100 GATGAGCTGA
837110 TATAAAAAAAATAGGTT
1 TATAAAAAAAATAGGTT
*
837127 TATATAAAAAATAGGTT
1 TATAAAAAAAATAGGTT
837144 TAT
1 TAT
837147 GTCCGTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TATAAAAAAAATAGGTT
Found at i:837211 original size:32 final size:32
Alignment explanation
Indices: 837174--837265 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 32
837164 ATAAAAGTAA
837174 AATAAAGTGATATATCACTGAAAAGTTTATAC
1 AATAAAGTGATATATCACTGAAAAGTTTATAC
* * * *
837206 AATAAATTGATTTATCACTGAAAGGTTTCTAC
1 AATAAAGTGATATATCACTGAAAAGTTTATAC
* ** *
837238 AGTGGAGTGATATATCAATGAAAAGTTT
1 AATAAAGTGATATATCACTGAAAAGTTT
837266 TTGAAGTGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (32 bp):
AATAAAGTGATATATCACTGAAAAGTTTATAC
Found at i:837318 original size:65 final size:65
Alignment explanation
Indices: 837238--837360 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 65
837228 AGGTTTCTAC
* *
837238 AGTGGAGTGATATATCAATGAAAAGTTTTTGAAGTGAATTAATTTTTGTATGAAAAAGTTTCTGT
1 AGTGAAGTGATATATCAATGAAAAGTGTTTGAAGTGAATTAATTTTTGTATGAAAAAGTTTCTGT
* * * * *
837303 AGTGAAGTGATATATCAATTACAAGTGTTTGAAGTGAATTATTTTTTGTTTGGAAAAG
1 AGTGAAGTGATATATCAATGAAAAGTGTTTGAAGTGAATTAATTTTTGTATGAAAAAG
837361 GACGTTTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (65 bp):
AGTGAAGTGATATATCAATGAAAAGTGTTTGAAGTGAATTAATTTTTGTATGAAAAAGTTTCTGT
Found at i:837464 original size:23 final size:23
Alignment explanation
Indices: 837437--837486 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
837427 AAAGTGTCTG
837437 AAGTGAATTAATTAGCCACTGAA
1 AAGTGAATTAATTAGCCACTGAA
*
837460 AAGTGTATTAATTAGCCACTGAA
1 AAGTGAATTAATTAGCCACTGAA
837483 AAGT
1 AAGT
837487 TTCTGAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (23 bp):
AAGTGAATTAATTAGCCACTGAA
Found at i:840076 original size:25 final size:27
Alignment explanation
Indices: 840017--840076 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
840007 GATCCATACT
*
840017 CATATGTTGATGATTGTTATAGCATGCATA
1 CATA-GTTGATCATTGTTATAGCA--CATA
840047 C-TAGTTGATCATTGTTATAGC-C-TA
1 CATAGTTGATCATTGTTATAGCACATA
840071 CATAGT
1 CATAGT
840077 ATTATGCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 3 0.11
25 5 0.18
28 17 0.61
29 2 0.07
30 1 0.04
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (27 bp):
CATAGTTGATCATTGTTATAGCACATA
Found at i:849944 original size:23 final size:23
Alignment explanation
Indices: 849910--849996 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
849900 CACATATTTA
*
849910 TCCCGAATGACCACATAGTTTTG
1 TCCCGAAGGACCACATAGTTTTG
* *
849933 TCCCTAAGGACCGCATAGTTTTG
1 TCCCGAAGGACCACATAGTTTTG
** *
849956 TCCCGAAATACCACATAAG-ATTG
1 TCCCGAAGGACCACAT-AGTTTTG
*
849979 TCCCGAAGAACCACATAG
1 TCCCGAAGGACCACATAG
849997 GATAGAAACC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 2 0.04
23 49 0.92
24 2 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGTTTTG
Found at i:850678 original size:22 final size:22
Alignment explanation
Indices: 850650--850706 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
850640 TACCCCCATT
850650 TCAGTATCGATACCTTCTTCAA
1 TCAGTATCGATACCTTCTTCAA
850672 TCAGTATCGATACCTTCTTCAA
1 TCAGTATCGATACCTTCTTCAA
850694 TCAGTATCGATAC
1 TCAGTATCGATAC
850707 TGATCCTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (22 bp):
TCAGTATCGATACCTTCTTCAA
Found at i:851236 original size:34 final size:32
Alignment explanation
Indices: 851183--851252 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
851173 CCTTACAAAC
*
851183 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
851215 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
851249 TCCC
1 TCCC
851253 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:851572 original size:20 final size:21
Alignment explanation
Indices: 851535--851575 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
851525 CCAGAATGGG
*
851535 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
851556 GGGAATCGATA-CCCTTCATA
1 GGGAATCGATACCCCTTCATA
851576 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:851813 original size:29 final size:31
Alignment explanation
Indices: 851779--851838 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
851769 AAATTTTGAA
*
851779 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
851808 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
851839 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:853613 original size:3 final size:3
Alignment explanation
Indices: 853605--853645 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
853595 TACGTCCTCA
* *
853605 TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
853646 CCTTTCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:853651 original size:14 final size:15
Alignment explanation
Indices: 853634--853663 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
853624 TCTTCTTGTT
853634 TTTCTTC-TCTTCCC
1 TTTCTTCATCTTCCC
853648 TTTCTTCATCTTCCC
1 TTTCTTCATCTTCCC
853663 T
1 T
853664 CACCATCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTCTTCATCTTCCC
Found at i:854598 original size:161 final size:165
Alignment explanation
Indices: 854333--854659 Score: 617
Period size: 161 Copynumber: 2.0 Consensus size: 165
854323 GAATTGGTAG
854333 AGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACCTTCTTAATGAGTTAGGCTCTGATGCCAATT
1 AGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACCTTCTTAATGAGTTAGGCTCTGATGCCAATT
854398 GTTGGGATTTTCGGAAGCTCGAAACGACAACCGGAACGATTTGCAAAGAGGGGTCAGAACGG-TT
66 GTTGGGATTTTCGGAAGCTCGAAACGACAACCGGAACGATTTGCAAAGAGGGGTCAGAACGGTTT
854462 T-TGTTTA-G-GTAAGGAGATTGAAAGATAGAGAA
131 TGTGTTTAGGAGTAAGGAGATTGAAAGATAGAGAA
854494 AGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACCTTCTTAATGAGTTAGGCTCTGATGCCAATT
1 AGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACCTTCTTAATGAGTTAGGCTCTGATGCCAATT
854559 GTTGGGATTTTCGGAAGCTCGAAACGACAACCGGAACGATTTGCAAAGAGGGGTCAGAACGGTTT
66 GTTGGGATTTTCGGAAGCTCGAAACGACAACCGGAACGATTTGCAAAGAGGGGTCAGAACGGTTT
854624 TGTGTTTAGGGAGTAAGGAGATTGAAAGATAGAGAA
131 TGTGTTTA-GGAGTAAGGAGATTGAAAGATAGAGAA
854660 TTGGACAGCG
Statistics
Matches: 161, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
161 127 0.79
162 3 0.02
163 6 0.04
165 1 0.01
166 24 0.15
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (165 bp):
AGCTTCTTCTAGGATCGTCTCAAGGTGGTTAAACCTTCTTAATGAGTTAGGCTCTGATGCCAATT
GTTGGGATTTTCGGAAGCTCGAAACGACAACCGGAACGATTTGCAAAGAGGGGTCAGAACGGTTT
TGTGTTTAGGAGTAAGGAGATTGAAAGATAGAGAA
Found at i:855105 original size:21 final size:21
Alignment explanation
Indices: 855079--855120 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
855069 CAGAATTGGG
* *
855079 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACACCTTCATA
855100 GGGAATCGATACACCTTCATA
1 GGGAATCGATACACCTTCATA
855121 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACACCTTCATA
Found at i:855216 original size:25 final size:25
Alignment explanation
Indices: 855182--855232 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
855172 CCCCTTGGGG
855182 GGAATCGGTTCCCCTTTTACATACT
1 GGAATCGGTTCCCCTTTTACATACT
855207 GGAATCGGTTCCCCTTTTACATACT
1 GGAATCGGTTCCCCTTTTACATACT
855232 G
1 G
855233 TTCAAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (25 bp):
GGAATCGGTTCCCCTTTTACATACT
Found at i:855352 original size:29 final size:31
Alignment explanation
Indices: 855320--855379 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
855310 AAATTTTGAA
*
855320 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
855349 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
855380 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:861371 original size:23 final size:22
Alignment explanation
Indices: 861345--861412 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
861335 GTGCCATATA
*
861345 TTTGTCTCGAATGACCACATAGT
1 TTTGTC-CGAATGACCACATAGG
861368 TTTGTCCCGAATGACCACATAGG
1 TTTGT-CCGAATGACCACATAGG
* *
861391 ATTGTCCAGAAGGACCACATAG
1 TTTGTCC-GAATGACCACATAG
861413 AACCCTCGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.05
23 37 0.93
24 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (22 bp):
TTTGTCCGAATGACCACATAGG
Found at i:863087 original size:14 final size:14
Alignment explanation
Indices: 863049--863087 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
863039 TTTTATCTAT
* *
863049 TTTTAAATATATAA
1 TTTTAAATTTTTAA
*
863063 TTTTAATTTTTTAA
1 TTTTAAATTTTTAA
863077 TTTTAAATTTT
1 TTTTAAATTTT
863088 CAAAATTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATTTTTAA
Found at i:863525 original size:15 final size:16
Alignment explanation
Indices: 863497--863532 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
863487 TAAACTTCAT
863497 TTAATTTATTAATTTA
1 TTAATTTATTAATTTA
863513 TTAATTT-TTAATTTA
1 TTAATTTATTAATTTA
*
863528 ATAAT
1 TTAAT
863533 AATTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTATTAATTTA
Found at i:863545 original size:8 final size:8
Alignment explanation
Indices: 863497--863532 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
863487 TAAACTTCAT
863497 TTAATTTA
1 TTAATTTA
863505 TTAATTTA
1 TTAATTTA
863513 TTAATTT-
1 TTAATTTA
863520 TTAATTTA
1 TTAATTTA
*
863528 ATAAT
1 TTAAT
863533 AATTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTAATTTA
Found at i:863761 original size:23 final size:23
Alignment explanation
Indices: 863730--863774 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
863720 CATATTTTAC
*
863730 TTTAGAACTACTAAAATAATTTT
1 TTTAAAACTACTAAAATAATTTT
* *
863753 TTTAAAACTATTAAATTAATTT
1 TTTAAAACTACTAAAATAATTT
863775 ATAAATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTAAAACTACTAAAATAATTTT
Found at i:863947 original size:12 final size:12
Alignment explanation
Indices: 863930--863964 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
863920 ATAATAATAT
863930 AATATATTTATA
1 AATATATTTATA
863942 AATATATTTA-A
1 AATATATTTATA
863953 AATAATATTTAT
1 AAT-ATATTTAT
863965 TCAAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATATTTATA
Found at i:868527 original size:2 final size:2
Alignment explanation
Indices: 868520--868601 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
868510 CCTGTATTCA
868520 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
868562 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
868602 TCCTTTATAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:871147 original size:13 final size:13
Alignment explanation
Indices: 871129--871153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
871119 TCACAACCCG
871129 ACCCGACCCGTTT
1 ACCCGACCCGTTT
871142 ACCCGACCCGTT
1 ACCCGACCCGTT
871154 GACTCGACCT
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:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:871161 original size:13 final size:13
Alignment explanation
Indices: 871132--871170 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
871122 CAACCCGACC
* *
871132 CGACCCGTTTACC
1 CGACCCGTTGACT
871145 CGACCCGTTGACT
1 CGACCCGTTGACT
*
871158 CGACCTGTTGACT
1 CGACCCGTTGACT
871171 GGCGTTGACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.15, C:0.38, G:0.21, T:0.26
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:873816 original size:24 final size:24
Alignment explanation
Indices: 873720--873828 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
873710 GAATATTTTA
* *
873720 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
873744 TTTGACATCCGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
873768 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
873792 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
873816 TTTGATTTCTGAT
1 TCTGATATCTGAT
873829 ATCTCTGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:875914 original size:13 final size:13
Alignment explanation
Indices: 875896--875920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
875886 TTACAACCCG
875896 ACCCGACCCGTTT
1 ACCCGACCCGTTT
875909 ACCCGACCCGTT
1 ACCCGACCCGTT
875921 GACCGGCGTT
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:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:878448 original size:24 final size:24
Alignment explanation
Indices: 878362--878460 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
878352 CTTATATGAA
* *
878362 TGATTTGAATTATGTT-TGACATC
1 TGATCTGAATTATGTTCTGATATC
878385 TGATCTGAAATT-TGTTCTGAT-TCC
1 TGATCTG-AATTATGTTCTGATAT-C
* * * *
878409 TAACCTGGATTCTGTTCTGATATC
1 TGATCTGAATTATGTTCTGATATC
* *
878433 TGATCTGAATTATGTTTTGATTTC
1 TGATCTGAATTATGTTCTGATATC
878457 TGAT
1 TGAT
878461 ATCTCTGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 14 0.23
24 45 0.75
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATCTGAATTATGTTCTGATATC
Found at i:880522 original size:13 final size:13
Alignment explanation
Indices: 880504--880528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
880494 ACACCCGACC
880504 CGACCCGTTGACT
1 CGACCCGTTGACT
880517 CGACCCGTTGAC
1 CGACCCGTTGAC
880529 CGGCGTTGAC
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:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:880749 original size:17 final size:18
Alignment explanation
Indices: 880717--880750 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
880707 TTGATTTTGA
*
880717 CCGAAAATTCCAAATTTT
1 CCGAAAAGTCCAAATTTT
880735 CCGAAAAGT-CAAATTT
1 CCGAAAAGTCCAAATTT
880751 ATGCTTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (18 bp):
CCGAAAAGTCCAAATTTT
Found at i:881864 original size:218 final size:218
Alignment explanation
Indices: 881485--881921 Score: 849
Period size: 218 Copynumber: 2.0 Consensus size: 218
881475 CAAGATCAGA
881485 GAGTGTTCAAGAAAGCAATTAATCATAGGATCTCTCTAAATTATATTATTTTCGTTAAGAGCTAA
1 GAGTGTTCAAGAAAGCAATTAATCATAGGA-CTCTCTAAATTATATTATTTTCGTTAAGAGCTAA
881550 TATCGAACTTATTGGTTAAGAAATTACAGAAATGCCCTTAAGAGGTAGAATAGTCTGAGATGACT
65 TATCGAACTTATTGGTTAAGAAATTACAGAAATGCCCTTAAGAGGTAGAATAGTCTGAGATGACT
881615 CTGAATGAGAAAATACTTAGAGGATTCGTACTTAACTCGATTAAGTACGGATTTAATTGTTAAGA
130 CTGAATGAGAAAATACTTAGAGGATTCGTACTTAACTCGATTAAGTACGGATTTAATTGTTAAGA
881680 TCCCGACTTAGTGCAGGAAAATTC
195 TCCCGACTTAGTGCAGGAAAATTC
881704 GAGTGTTCAAGAAAGCAATTAATCATAGGA-TCTCTAAATTATATTATTTTCGTTAAGAGCTAAT
1 GAGTGTTCAAGAAAGCAATTAATCATAGGACTCTCTAAATTATATTATTTTCGTTAAGAGCTAAT
881768 ATCGAACTTATCTGGTTAAGAAATTACAGAAATGCCCTTAAGAGGTAGAATAGTCTGAGATGACT
66 ATCGAACTTAT-TGGTTAAGAAATTACAGAAATGCCCTTAAGAGGTAGAATAGTCTGAGATGACT
881833 CTGAATGAGAAAATACTTAGAGGATTCGTACTTAACTCGATTAAGTACGGATTTAATTGTTAAGA
130 CTGAATGAGAAAATACTTAGAGGATTCGTACTTAACTCGATTAAGTACGGATTTAATTGTTAAGA
881898 TCCCGACTTAGTGCAGGAAAATTC
195 TCCCGACTTAGTGCAGGAAAATTC
881922 TGATATTCCG
Statistics
Matches: 217, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
217 45 0.21
218 142 0.65
219 30 0.14
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31
Consensus pattern (218 bp):
GAGTGTTCAAGAAAGCAATTAATCATAGGACTCTCTAAATTATATTATTTTCGTTAAGAGCTAAT
ATCGAACTTATTGGTTAAGAAATTACAGAAATGCCCTTAAGAGGTAGAATAGTCTGAGATGACTC
TGAATGAGAAAATACTTAGAGGATTCGTACTTAACTCGATTAAGTACGGATTTAATTGTTAAGAT
CCCGACTTAGTGCAGGAAAATTC
Found at i:882065 original size:18 final size:18
Alignment explanation
Indices: 882039--882074 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
882029 TCGAAATGAC
*
882039 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
882057 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
882075 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:884429 original size:122 final size:119
Alignment explanation
Indices: 884278--884506 Score: 329
Period size: 121 Copynumber: 1.9 Consensus size: 119
884268 TGTTATTATC
884278 TTAAGAAAAATGTTTTTATATTTATTTA-TTTTTAATATCAAAGAAAAGAGCTGTCTTAAGTCAC
1 TTAAGAAAAATGTTTTTATATTTATTTATTTTTTAATATCAAAGAAAAGAG-TGTCTTAAGT-AC
*
884342 CTAGAAGCCATTTTCTGATATTTTTAAATAAATAAGTATCTTATTTAATTTTTATTTT
64 CTAGAAGCCATTTTCTGATATTTCT-AATAAATAA-TATCTTATTTAATTTTTATTTT
* * *
884400 TTAAG-AAAATGTTTTTAGTTATTT-TTTATTTTTTAATATCGAAGAAAATAGTGTCTTAGGTAC
1 TTAAGAAAAATGTTTTTA--TATTTATTTATTTTTTAATATCAAAGAAAAGAGTGTCTTAAGTAC
* *
884463 CTAGAAGCCCTTTTCTGATATTTCTAATAAGTAATATCTTATTT
64 CTAGAAGCCATTTTCTGATATTTCTAATAAATAATATCTTATTT
884507 TGTGTATTAA
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
119 10 0.10
120 8 0.08
121 37 0.38
122 18 0.18
123 25 0.26
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (119 bp):
TTAAGAAAAATGTTTTTATATTTATTTATTTTTTAATATCAAAGAAAAGAGTGTCTTAAGTACCT
AGAAGCCATTTTCTGATATTTCTAATAAATAATATCTTATTTAATTTTTATTTT
Found at i:885375 original size:18 final size:19
Alignment explanation
Indices: 885327--885389 Score: 76
Period size: 18 Copynumber: 3.3 Consensus size: 19
885317 ATGTTTAATG
885327 AAAAATG-TACCAATTGTTT
1 AAAAATGATACCAATTG-TT
*
885346 ACAAAATTATACCAATTGTT
1 A-AAAATGATACCAATTGTT
885366 AAAAA-GATACCAATTGTT
1 AAAAATGATACCAATTGTT
885384 GAAAAA
1 -AAAAA
885390 ATATGAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 12 0.31
19 10 0.26
20 8 0.21
21 9 0.23
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (19 bp):
AAAAATGATACCAATTGTT
Found at i:891727 original size:28 final size:28
Alignment explanation
Indices: 891678--891747 Score: 113
Period size: 28 Copynumber: 2.4 Consensus size: 28
891668 ATTAAAATTT
891678 CAAACAAACAATTCGGATAAATGATTGATA
1 CAAACAAAC-A-TCGGATAAATGATTGATA
891708 CAAACAAACATCGGATAAATGATTGATA
1 CAAACAAACATCGGATAAATGATTGATA
*
891736 CAAACGAACATC
1 CAAACAAACATC
891748 ATTGTCGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 29 0.74
29 1 0.03
30 9 0.23
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
CAAACAAACATCGGATAAATGATTGATA
Found at i:897052 original size:18 final size:19
Alignment explanation
Indices: 897017--897053 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
897007 CACGGAATGT
897017 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
897037 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
897054 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:897200 original size:17 final size:18
Alignment explanation
Indices: 897170--897208 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
897160 AAATTGTCCT
* *
897170 TATTATAAATTTGTATAA
1 TATTACAAATTTGTAAAA
897188 TATTACAAA-TTGTAAAA
1 TATTACAAATTTGTAAAA
897205 TATT
1 TATT
897209 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
TATTACAAATTTGTAAAA
Found at i:897235 original size:37 final size:36
Alignment explanation
Indices: 897201--897269 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
897191 TACAAATTGT
897201 AAAATATTTATAT-ATTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAATTAAATTC
* *
897237 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
897270 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:905914 original size:138 final size:137
Alignment explanation
Indices: 905647--905927 Score: 384
Period size: 138 Copynumber: 2.0 Consensus size: 137
905637 GTCATATGTG
* * ** * *
905647 CATTTCGGCATAAATTGTATATAATGGTTATCGATTGATTTTGTGTAATGCGTAACGGTGCATTT
1 CATTTCGACATAAATTATATATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATTT
* * * * *
905712 TCGTATCAGTACTATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTTATAATGAGTTTGT
66 TCGTATCAATACTATATGTACTTTCGACACTAGATGTGCAACCATGGAATTCATAATGAGTTTGT
905777 GAATTAC
131 GAATTAC
* * *
905784 CATTTCGACATACAATTATTTATAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATT
1 CATTTCGACATA-AATTATATATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATT
* *
905849 TTCGTATCAATATTATATGTACTTTCGACACTATG-TGTGCATCCATGGAATTCATAATGAGTTT
65 TTCGTATCAATACTATATGTACTTTCGACACTA-GATGTGCAACCATGGAATTCATAATGAGTTT
*
905913 GTGAATTTC
129 GTGAATTAC
905922 CATTTC
1 CATTTC
905928 AACACTTAGG
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
137 11 0.09
138 113 0.90
139 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.41
Consensus pattern (137 bp):
CATTTCGACATAAATTATATATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATTT
TCGTATCAATACTATATGTACTTTCGACACTAGATGTGCAACCATGGAATTCATAATGAGTTTGT
GAATTAC
Found at i:929904 original size:23 final size:23
Alignment explanation
Indices: 929849--929913 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
929839 CCCTTACTAG
*
929849 GTATCGATACCCTCTTTGAATAT
1 GTATCGATACCCTCTTTGAACAT
*
929872 GCA-CTGATACCCTCTTTGAACAT
1 GTATC-GATACCCTCTTTGAACAT
*
929895 GTATCAATACCCCTCTTTG
1 GTATCGATA-CCCTCTTTG
929914 CCCAAACCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.03
23 24 0.69
24 10 0.29
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (23 bp):
GTATCGATACCCTCTTTGAACAT
Found at i:930309 original size:20 final size:20
Alignment explanation
Indices: 930272--930314 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
930262 AAAAAAATGC
*
930272 TTTTGATTTTAAATTGTTGT
1 TTTTGATTTTAAATTGTTAT
*
930292 TTTTGA-TTTAATTATGTTAT
1 TTTTGATTTTAAAT-TGTTAT
930312 TTT
1 TTT
930315 CATGAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTTGATTTTAAATTGTTAT
Found at i:930368 original size:12 final size:13
Alignment explanation
Indices: 930339--930371 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
930329 ATATTATGAT
*
930339 TTTTCAAACATCG
1 TTTTCAAACATAG
930352 TTTTCAAA-ATAG
1 TTTTCAAACATAG
930364 TTTTCAAA
1 TTTTCAAA
930372 TTTTGCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:931275 original size:64 final size:64
Alignment explanation
Indices: 931204--931362 Score: 241
Period size: 64 Copynumber: 2.5 Consensus size: 64
931194 GAATAAATTG
* *
931204 AACATCGAATGCATTTTATGCATTGATGCACATACCATGCATCGATGCACTC-AGGTT-TTATGA
1 AACATCGAATGCATTTTATGCATTGATGCACAGACCATGCATCGATGCACTCGAGCTTGTT-TG-
931267 A
64 A
931268 AACATCGAATGCATTTTATGCATTGATGCACAGACCATGCATCGATGCACTCGAGCTTGTTTGA
1 AACATCGAATGCATTTTATGCATTGATGCACAGACCATGCATCGATGCACTCGAGCTTGTTTGA
* * *
931332 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATTGATGCAC
931363 TCTTAGTGAA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
64 80 0.91
65 6 0.07
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATTGATGCACAGACCATGCATCGATGCACTCGAGCTTGTTTGA
Found at i:936830 original size:20 final size:21
Alignment explanation
Indices: 936778--936899 Score: 88
Period size: 21 Copynumber: 5.6 Consensus size: 21
936768 TTGTGCATAA
* *
936778 TGCATCAATACACTATGAAAG
1 TGCATCGATGCACTATGAAAG
936799 TGCATCGATGCACTATGAAAG
1 TGCATCGATGCACTATGAAAG
* *
936820 TGCAT-GATGCATCCCTTTGAATG
1 TGCATCGATGCA---CTATGAAAG
*
936843 TGCATCGATACA-TCATG-AAG
1 TGCATCGATGCACT-ATGAAAG
* * *
936863 ATGCACCGATGCACTCCTTGAATG
1 -TGCATCGATGCACT--ATGAAAG
936887 TGCATCGATGCAC
1 TGCATCGATGCAC
936900 AAATCCATGC
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
20 9 0.11
21 36 0.45
22 1 0.01
23 27 0.34
24 7 0.09
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (21 bp):
TGCATCGATGCACTATGAAAG
Found at i:936848 original size:44 final size:45
Alignment explanation
Indices: 936793--936899 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 45
936783 CAATACACTA
* *
936793 TGAAAGTGCATCGATGCACT-ATGAA-AGTGCA-TGATGCA-TCCCTT
1 TGAATGTGCATCGATGCACTCATGAAGA-TGCACCGATGCACT-CC-T
*
936837 TGAATGTGCATCGATACA-TCATGAAGATGCACCGATGCACTCCT
1 TGAATGTGCATCGATGCACTCATGAAGATGCACCGATGCACTCCT
936881 TGAATGTGCATCGATGCAC
1 TGAATGTGCATCGATGCAC
936900 AAATCCATGC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 1 0.02
44 43 0.80
45 9 0.17
46 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (45 bp):
TGAATGTGCATCGATGCACTCATGAAGATGCACCGATGCACTCCT
Found at i:939694 original size:64 final size:64
Alignment explanation
Indices: 939626--939784 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 64
939616 GAATAAATTG
*
939626 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGG-TT-TTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTATT-TG-
939689 A
64 A
** *
939690 AACATCGAATGCATTTTATGCATCGATGCACAGACTGTGCATCGATGCACTCGGGCTTATTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTATTTGA
* * * *
939754 AACATCTAATGCACTTCATGAATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
939785 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
64 79 0.93
65 4 0.05
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTATTTGA
Found at i:942155 original size:18 final size:18
Alignment explanation
Indices: 942140--942181 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
942130 AAAGGGTATG
942140 GATACCCCATAGGGTACC
1 GATACCCCATAGGGTACC
942158 GATACCCCATAGGGTACC
1 GATACCCCATAGGGTACC
942176 GATACC
1 GATACC
942182 TCTATACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (18 bp):
GATACCCCATAGGGTACC
Found at i:943474 original size:19 final size:20
Alignment explanation
Indices: 943430--943475 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
943420 AATTTTAAGG
943430 GAAAAAACATTTTATCCAGA
1 GAAAAAACATTTTATCCAGA
* *
943450 GAAAAATCATTTTATCCAGT
1 GAAAAAACATTTTATCCAGA
943470 GAAAAA
1 GAAAAA
943476 CACAATGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (20 bp):
GAAAAAACATTTTATCCAGA
Found at i:945696 original size:20 final size:20
Alignment explanation
Indices: 945671--945764 Score: 98
Period size: 20 Copynumber: 4.5 Consensus size: 20
945661 ATATATATAA
945671 GTATCGATACTCCTTGGACG
1 GTATCGATACTCCTTGGACG
* ** *
945691 GTATCGATACTACTATTTATAG
1 GTATCGATACTCCT-TGGA-CG
*
945713 AAGTATTGATACTCCTTGGACG
1 --GTATCGATACTCCTTGGACG
*
945735 GTATCGATACTCCTTGGATG
1 GTATCGATACTCCTTGGACG
945755 GTATCGATAC
1 GTATCGATAC
945765 CGTTGCTTTC
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 41 0.69
21 2 0.03
22 2 0.03
23 2 0.03
24 12 0.20
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
GTATCGATACTCCTTGGACG
Found at i:945697 original size:44 final size:44
Alignment explanation
Indices: 945647--945745 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
945637 CCATTGTCTA
*
945647 GTATCGATACTACTATATATATAAGTATCGATACTCCTTGGACG
1 GTATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACG
* *
945691 GTATCGATACTACTATTTATAGAAGTATTGATACTCCTTGGACG
1 GTATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACG
945735 GTATCGATACT
1 GTATCGATACT
945746 CCTTGGATGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (44 bp):
GTATCGATACTACTATATATAGAAGTATCGATACTCCTTGGACG
Found at i:945718 original size:24 final size:24
Alignment explanation
Indices: 945646--945725 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
945636 ACCATTGTCT
*
945646 AGTATCGATACTACTATATATATA
1 AGTATCGATACTACTATATATAGA
* ** *
945670 AGTATCGATACTCCT-TGGA-CG-
1 AGTATCGATACTACTATATATAGA
*
945691 -GTATCGATACTACTATTTATAGA
1 AGTATCGATACTACTATATATAGA
*
945714 AGTATTGATACT
1 AGTATCGATACT
945726 CCTTGGACGG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 13 0.31
21 2 0.05
22 1 0.02
23 2 0.05
24 24 0.57
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (24 bp):
AGTATCGATACTACTATATATAGA
Found at i:946087 original size:15 final size:15
Alignment explanation
Indices: 946067--946097 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
946057 ATTATCAATG
946067 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
946082 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
946097 A
1 A
946098 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:948021 original size:21 final size:21
Alignment explanation
Indices: 947996--948063 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
947986 AGTCGCTTGT
*
947996 CGTCCGCCGTCCTCCGACCAT
1 CGTCCGCCGTCCTCCGACCAC
*
948017 CGTCCGCCGTCCTCCAACCAC
1 CGTCCGCCGTCCTCCGACCAC
* *
948038 CGTTCGCCGTCTTCCGACCAC
1 CGTCCGCCGTCCTCCGACCAC
948059 CGTCC
1 CGTCC
948064 ACCGCCGCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.10, C:0.53, G:0.18, T:0.19
Consensus pattern (21 bp):
CGTCCGCCGTCCTCCGACCAC
Found at i:954538 original size:15 final size:15
Alignment explanation
Indices: 954515--954548 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
954505 AATATTACGA
*
954515 ACTCTATAAATTAAT
1 ACTCGATAAATTAAT
954530 ACTCGATAAATTAAT
1 ACTCGATAAATTAAT
954545 ACTC
1 ACTC
954549 TCTCTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (15 bp):
ACTCGATAAATTAAT
Found at i:962073 original size:18 final size:18
Alignment explanation
Indices: 962025--962074 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
962015 GAAGCTAAAT
*
962025 TTTTATTATATTATAATCA
1 TTTTATTATATT-TTATCA
*
962044 -TTTA--ATAGTTTATCA
1 TTTTATTATATTTTATCA
962059 TTTTATTATATTTTAT
1 TTTTATTATATTTTAT
962075 AATAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
15 5 0.20
16 8 0.32
18 12 0.48
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATTATATTTTATCA
Found at i:963762 original size:23 final size:23
Alignment explanation
Indices: 963704--963807 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 23
963694 AGTTGAGGGT
* *
963704 TTCTACGTGGTCCTTTGGGACAAA
1 TTCTACGTGGTCATTCGGGAC-AA
* *
963728 TTTTACGCGGTCATTCGGGACAA
1 TTCTACGTGGTCATTCGGGACAA
* *
963751 TTCTATGTGGTCATTCGGGATAA
1 TTCTACGTGGTCATTCGGGACAA
* *
963774 ATCTATGTGG-CACTTCGGTG-CATA
1 TTCTACGTGGTCA-TTCGG-GACA-A
963798 TTCTACGTGG
1 TTCTACGTGG
963808 CACTTCAGTG
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
22 2 0.03
23 36 0.55
24 27 0.42
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCATTCGGGACAA
Found at i:963807 original size:24 final size:24
Alignment explanation
Indices: 963775--963852 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
963765 TCGGGATAAA
*
963775 TCTATGTGGCACTTCGGTGCATAT
1 TCTACGTGGCACTTCGGTGCATAT
*
963799 TCTACGTGGCACTTCAGTGCATAT
1 TCTACGTGGCACTTCGGTGCATAT
* * *
963823 TCTACGTGGCACTTCGATACAAAT
1 TCTACGTGGCACTTCGGTGCATAT
963847 TCTACG
1 TCTACG
963853 CGGAAGTTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (24 bp):
TCTACGTGGCACTTCGGTGCATAT
Found at i:971654 original size:18 final size:18
Alignment explanation
Indices: 971624--971678 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
971614 TTTTCGTTTG
971624 ATGTTTTTCTTTTTCTCTT
1 ATGTTTTT-TTTTTCTCTT
*
971643 ATGTTTTTTTTTGCTC-T
1 ATGTTTTTTTTTTCTCTT
* *
971660 CTGTTTTGTTCTTTCTCTT
1 ATGTTTT-TTTTTTCTCTT
971679 TTTTTCTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.04, C:0.16, G:0.09, T:0.71
Consensus pattern (18 bp):
ATGTTTTTTTTTTCTCTT
Found at i:973348 original size:10 final size:10
Alignment explanation
Indices: 973333--973357 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
973323 AAAAAAAATC
973333 CCGGTTTTTT
1 CCGGTTTTTT
973343 CCGGTTTTTT
1 CCGGTTTTTT
973353 CCGGT
1 CCGGT
973358 CCGGTTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.24, T:0.52
Consensus pattern (10 bp):
CCGGTTTTTT
Found at i:973381 original size:17 final size:18
Alignment explanation
Indices: 973359--973392 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
973349 TTTTCCGGTC
973359 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
973376 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
973393 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:973406 original size:24 final size:24
Alignment explanation
Indices: 973376--973437 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
973366 AACGGTTCAA
973376 CGGTTCTGACCGGTTCACTAATAG
1 CGGTTCTGACCGGTTCACTAATAG
* * *
973400 CGGTTCTGGCCGATTTACTAATAG
1 CGGTTCTGACCGGTTCACTAATAG
* *
973424 CAGTTC-AACCGGTT
1 CGGTTCTGACCGGTT
973438 TAGATTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (24 bp):
CGGTTCTGACCGGTTCACTAATAG
Found at i:973657 original size:30 final size:29
Alignment explanation
Indices: 973623--973692 Score: 122
Period size: 30 Copynumber: 2.4 Consensus size: 29
973613 AGTATTTAAA
973623 ATTAAAATTAAACAAAAATCTTATTTTATT
1 ATTAAAATTAAACAAAAATCTTA-TTTATT
*
973653 ATTAAAATTAAATAAAAATCTTATTTATT
1 ATTAAAATTAAACAAAAATCTTATTTATT
973682 ATTAAAATTAA
1 ATTAAAATTAA
973693 TTAGTTCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTAAAATTAAACAAAAATCTTATTTATT
Found at i:985009 original size:67 final size:68
Alignment explanation
Indices: 984880--985015 Score: 265
Period size: 67 Copynumber: 2.0 Consensus size: 68
984870 CATCGGTTGA
984880 CTTGAGCTCCTCCACGTTGCAGCTTCGATCTTTCTGAGTTGCTAAAACGATAGGACCTTTCTGAA
1 CTTGAGCTCCTCCACGTTGCAGCTTCGATCTTTCTGAGTTGCTAAAACGATAGGACCTTTCTGAA
984945 TGG
66 TGG
984948 CTTGAGCTCCTCCACGTTGCAGCTTCGATC-TTCTGAGTTGCTAAAACGATAGGACCTTTCTGAA
1 CTTGAGCTCCTCCACGTTGCAGCTTCGATCTTTCTGAGTTGCTAAAACGATAGGACCTTTCTGAA
985012 TGG
66 TGG
985015 C
1 C
985016 CATCTGCCTT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 38 0.56
68 30 0.44
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (68 bp):
CTTGAGCTCCTCCACGTTGCAGCTTCGATCTTTCTGAGTTGCTAAAACGATAGGACCTTTCTGAA
TGG
Done.