Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008785.1 Hibiscus syriacus cultivar Beakdansim tig00111917_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: 1341157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:665835 original size:32 final size:32
Alignment explanation
Indices: 665799--665872 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
665789 GCATCTTTAA
* *
665799 AGATTCAACAGCAAATGTTGGGGCATATTTGG
1 AGATTCAACAGCAAATATTAGGGCATATTTGG
*** *
665831 AGATTCAACATTGAATATTAGGGCATCTTTGG
1 AGATTCAACAGCAAATATTAGGGCATATTTGG
*
665863 GGATTCAACA
1 AGATTCAACA
665873 TCCTGATGCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (32 bp):
AGATTCAACAGCAAATATTAGGGCATATTTGG
Found at i:666183 original size:83 final size:83
Alignment explanation
Indices: 666019--666215 Score: 227
Period size: 83 Copynumber: 2.3 Consensus size: 83
666009 ACTATTCACA
* * * *
666019 CATACCTCAAGGCGAGAAAGGCTATCTGCCAACCAAGATCTTCGAGTTCGACTACACCCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACC-A-ATCTTCGAGTTCGACTACACCCAGCTCA
*
666084 AAGGCATATCAAATTTACAT
64 AAGGCATATCAAATTTACAG
* * ***
666104 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACC-ATCCTTCGAGTTTGATTACATTTAGCTC-A
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAT-CTTCGAGTTCGACTACACCCAGCTCAA
* *
666167 AGGACATGTCAAATTTACGG
65 AGG-CATATCAAATTTACAG
*
666187 CATAACTCAAGACGAGAAGGGTTATCTGT
1 CATAACTCAAGGCGAGAAGGGTTATCTGT
666216 TAAAAAACAC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
82 6 0.06
83 61 0.63
85 30 0.31
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (83 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAATCTTCGAGTTCGACTACACCCAGCTCAAA
GGCATATCAAATTTACAG
Found at i:667177 original size:159 final size:159
Alignment explanation
Indices: 666968--667277 Score: 539
Period size: 159 Copynumber: 1.9 Consensus size: 159
666958 AGAATCAACA
* * * *
666968 TCATCCTAAGACAATCAGACTTCCTCAACACGAATGAATCGTATTGTCTCCAAATTATCTCCAGA
1 TCATCCTAAGACAATCAAACTTCCTCAACACGAAGGAACCATATTGTCTCCAAATTATCTCCAGA
*
667033 TTGACCCGATTTCCTCAACGCGGAGGAACATCGTCATCTTCAACAAACAATTTACCTGAAAATGA
66 TTGACCCGATTTCCTCAACGCGAAGGAACATCGTCATCTTCAACAAACAATTTACCTGAAAATGA
667098 CCAGATCTCTTCAACACGGATGAGCAGTG
131 CCAGATCTCTTCAACACGGATGAGCAGTG
* *
667127 TCATCCTAAGACAATCAAACTTTCTCAATACGAAGGAACCATATTGTCTCCAAATTATCTCCAGA
1 TCATCCTAAGACAATCAAACTTCCTCAACACGAAGGAACCATATTGTCTCCAAATTATCTCCAGA
667192 TTGACCCGATTTCCTCAACGCGAAGGAACATCGTCATCTTCAACAAACAATTTACCTGAAAATGA
66 TTGACCCGATTTCCTCAACGCGAAGGAACATCGTCATCTTCAACAAACAATTTACCTGAAAATGA
* *
667257 CCAGATCTTTTTAACACGGAT
131 CCAGATCTCTTCAACACGGAT
667278 AAGTAGCGTC
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
159 142 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (159 bp):
TCATCCTAAGACAATCAAACTTCCTCAACACGAAGGAACCATATTGTCTCCAAATTATCTCCAGA
TTGACCCGATTTCCTCAACGCGAAGGAACATCGTCATCTTCAACAAACAATTTACCTGAAAATGA
CCAGATCTCTTCAACACGGATGAGCAGTG
Found at i:667344 original size:61 final size:62
Alignment explanation
Indices: 667177--667351 Score: 149
Period size: 61 Copynumber: 2.9 Consensus size: 62
667167 ATATTGTCTC
* * ** *
667177 CAAATTATCTCCAGATTGACCCGATTTCCTCAACGCGAAGGAACATCGTCATCTTCAACAAA
1 CAAATTATCTCTAGATTGACCCGATCTCCTCAACGCGAAGGAGTAGCGTCATCTTCAACAAA
* * * * ** * * * ** * *
667239 CAATTTA-C-CTGAAAATGACCAGATCTTTTTAACACGGATAAGTAGCGTCGTCTTCAAC-AT
1 CAAATTATCTCT-AGATTGACCCGATCTCCTCAACGCGAAGGAGTAGCGTCATCTTCAACAAA
*
667299 CAAATTATCTCTAGATTGACCCGATCTCCTCAACGCGAAGGAGTAGTGTCATC
1 CAAATTATCTCTAGATTGACCCGATCTCCTCAACGCGAAGGAGTAGCGTCATC
667352 CACAGACAAT
Statistics
Matches: 79, Mismatches: 31, Indels: 7
0.68 0.26 0.06
Matches are distributed among these distances:
60 8 0.10
61 63 0.80
62 8 0.10
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (62 bp):
CAAATTATCTCTAGATTGACCCGATCTCCTCAACGCGAAGGAGTAGCGTCATCTTCAACAAA
Found at i:667552 original size:220 final size:220
Alignment explanation
Indices: 667095--667538 Score: 575
Period size: 220 Copynumber: 2.0 Consensus size: 220
667085 TACCTGAAAA
* * * * * * * *
667095 TGACCAGATCTCTTCAACACGGATGAGCAGTGTCATCCTAAGACAATCAAACTTTCTCAATACGA
1 TGACCCGATCTCCTCAACGCGAAGGAGTAGTGTCATCCTAAGACAATCAAACTTCCTCAACACGA
* * * * * *
667160 AGGAACCATATTGTCTCCAAATTATCTCCAGATTGACCCGATTTCCTCAACGCGAAGGAACATCG
66 AGGAACCATATTATCTCCAAATTATCTCCAGATTAACCCGACTTCCTCAACGAGAAGGAACAACA
* * * *
667225 TCATCTTCAACAAACAATTTACCTGAAAATGACCAGATCTTTTTAACACGGATAAGTAGCGTCGT
131 TCATCTTCAACAAACAATTTACCTGAAAATGACCAGATCTCTTCAACACGGATAAGCAGAGTCGT
* *
667290 CTTCAACATCAAATTATCTCTAGAT
196 CTTCAACACCAAATTATCTCCAGAT
* * *
667315 TGACCCGATCTCCTCAACGCGAAGGAGTAGTGTCATCC-ACAGACAATCAGACTTCCTCAACGCT
1 TGACCCGATCTCCTCAACGCGAAGGAGTAGTGTCATCCTA-AGACAATCAAACTTCCTCAACACG
* * * *
667379 AAGGAACCGTGTTATCTCCAAATTATCTCCAGATTAACCCGACTTCCTTAACGAGAATGAACAAC
65 AAGGAACCATATTATCTCCAAATTATCTCCAGATTAACCCGACTTCCTCAACGAGAAGGAACAAC
* ** * *
667444 ATCATCTTCAATAAACAATTTATTTGAAAGTGACCAGATCTCTTCAACACGGATGAGCAGAGTCG
130 ATCATCTTCAACAAACAATTTACCTGAAAATGACCAGATCTCTTCAACACGGATAAGCAGAGTCG
*
667509 TCTTCAACACCAAATTATCTCCATAT
195 TCTTCAACACCAAATTATCTCCAGAT
667535 TGAC
1 TGAC
667539 TTGATTCCCT
Statistics
Matches: 190, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
219 1 0.01
220 189 0.99
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (220 bp):
TGACCCGATCTCCTCAACGCGAAGGAGTAGTGTCATCCTAAGACAATCAAACTTCCTCAACACGA
AGGAACCATATTATCTCCAAATTATCTCCAGATTAACCCGACTTCCTCAACGAGAAGGAACAACA
TCATCTTCAACAAACAATTTACCTGAAAATGACCAGATCTCTTCAACACGGATAAGCAGAGTCGT
CTTCAACACCAAATTATCTCCAGAT
Found at i:667657 original size:104 final size:104
Alignment explanation
Indices: 667477--667667 Score: 258
Period size: 104 Copynumber: 1.8 Consensus size: 104
667467 TTGAAAGTGA
* * * * *
667477 CCAGATCTCTTCAACACGGATGAGCAGAGTCGTCTTCAACACCAAATTATCTCCATATTGACTTG
1 CCAGACCTCTTCAACACGGATGAACAGAGTCGTCTTCAACACCAAATTATATCCAGATTGACTCG
*
667542 ATTCCCTCAACAAGAAGGAACAACGACATCTTCAAAAGG
66 AGTCCCTCAACAAGAAGGAACAACGACATCTTCAAAAGG
* * * * *
667581 CCAGACCTCTTCAACATGGATGAACAGTGTCGTCTTTAACACTAAATTATATCCAGATTTACTCG
1 CCAGACCTCTTCAACACGGATGAACAGAGTCGTCTTCAACACCAAATTATATCCAGATTGACTCG
*
667646 AAGT-CCTCAACATGAAGGAACA
66 -AGTCCCTCAACAAGAAGGAACA
667668 CTGTAGTCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 72 0.97
105 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (104 bp):
CCAGACCTCTTCAACACGGATGAACAGAGTCGTCTTCAACACCAAATTATATCCAGATTGACTCG
AGTCCCTCAACAAGAAGGAACAACGACATCTTCAAAAGG
Found at i:670278 original size:26 final size:27
Alignment explanation
Indices: 670239--670291 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
670229 CATTTCTAAA
* *
670239 ATTTTTTTTGCTTTT-AATTTCTCTTC
1 ATTTTTGTTACTTTTGAATTTCTCTTC
*
670265 ATTTTTGTTACTTTTGATTTTCTCTTC
1 ATTTTTGTTACTTTTGAATTTCTCTTC
670292 TGTTTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.11, C:0.15, G:0.06, T:0.68
Consensus pattern (27 bp):
ATTTTTGTTACTTTTGAATTTCTCTTC
Found at i:682524 original size:2 final size:2
Alignment explanation
Indices: 682517--682557 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
682507 ACAATACTAA
682517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
682558 CACACTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:682919 original size:24 final size:24
Alignment explanation
Indices: 682891--682937 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
682881 TTTATTGATA
*
682891 ATTTTT-TTATAAT-ATAATATAAT
1 ATTTTTATTTTAATAAT-ATATAAT
682914 ATTTTTATTTTAATAATATATAAT
1 ATTTTTATTTTAATAATATATAAT
682938 TAATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 13 0.62
25 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTATTTTAATAATATATAAT
Found at i:685487 original size:21 final size:21
Alignment explanation
Indices: 685457--685686 Score: 170
Period size: 21 Copynumber: 11.0 Consensus size: 21
685447 GATTTACATA
*
685457 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
685478 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
685499 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
685520 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
685539 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
685562 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
685585 TT--CGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
685604 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
685627 TT--CGTTGCGAGAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
685646 TTCACGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
685669 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
685687 AATCGCAACG
Statistics
Matches: 167, Mismatches: 30, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
19 38 0.23
21 84 0.50
23 45 0.27
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:685537 original size:40 final size:43
Alignment explanation
Indices: 685472--685574 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 43
685462 ATTGCGATAG
*
685472 TCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-T
1 TCCAAATTC-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
685514 TCCAAATT-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
685556 TCCAAATTCGCGTTGCGAT
1 TCCAAATTC-CGTTGCGAT
685575 TTATTCCAAG
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
40 29 0.52
41 2 0.04
42 16 0.29
44 9 0.16
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (43 bp):
TCCAAATTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:685597 original size:65 final size:63
Alignment explanation
Indices: 685463--685630 Score: 250
Period size: 65 Copynumber: 2.7 Consensus size: 63
685453 CATATTCGCA
* * * *
685463 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATTTTCCAAATTCG
*
685524 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGA-TT-TTCCAAATTCG
*
685589 TTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
685631 TTGCGAGAGT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
61 26 0.27
63 18 0.19
64 2 0.02
65 51 0.53
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (63 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATTTTCCAAATTCG
Found at i:685617 original size:42 final size:42
Alignment explanation
Indices: 685562--685683 Score: 208
Period size: 42 Copynumber: 2.9 Consensus size: 42
685552 TTATTCCAAA
* *
685562 TTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
*
685604 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGAGAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
*
685646 TTCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
685684 CAAAATCGCA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:685655 original size:107 final size:105
Alignment explanation
Indices: 685456--685686 Score: 346
Period size: 107 Copynumber: 2.2 Consensus size: 105
685446 CGATTTACAT
*
685456 ATTCGCATTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
1 ATTCGCGTTGCGATTAGTCCAAGTTC-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA
* *
685520 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA
65 TTCGTTGCGAGAGTCGAAGTTCACGTTGCGATTTATTCCAA
* *
685561 ATTCGCGTTGCGATTTATTCCAAGTT-CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCA
1 ATTCGCGTTGCGA-TTAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCA
685625 AATTCGTTGCGAGAGTCGAAGTTCACGTTGCGATTTATTCCAA
63 AATTCGTTGCGAGAGTCGAAGTTCACGTTGCGATTTATTCCAA
685668 ATT--CGTTGCGA-TAGTCCAA
1 ATTCGCGTTGCGATTAGTCCAA
685687 AATCGCAACG
Statistics
Matches: 116, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
103 7 0.06
105 48 0.41
106 2 0.02
107 59 0.51
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (105 bp):
ATTCGCGTTGCGATTAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAAT
TCGTTGCGAGAGTCGAAGTTCACGTTGCGATTTATTCCAA
Found at i:685856 original size:6 final size:6
Alignment explanation
Indices: 685775--685852 Score: 120
Period size: 6 Copynumber: 13.0 Consensus size: 6
685765 AGACACGTAT
685775 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
* * * *
685823 TACCAC GACCAC GACCAC GACCAC GACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC
685853 GACCCGAGAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.33, C:0.50, G:0.05, T:0.12
Consensus pattern (6 bp):
TACCAC
Found at i:686385 original size:6 final size:6
Alignment explanation
Indices: 686355--686402 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
686345 TCTCGTCTCG
*
686355 GGTCG- GGTCG- GGTCG- GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
686400 GGT
1 GGT
686403 AATACGTGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 15 0.37
6 26 0.63
ACGTcount: A:0.02, C:0.17, G:0.54, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:686498 original size:19 final size:19
Alignment explanation
Indices: 686474--686530 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
686464 AAATGCAATA
686474 CGCAACGAATTTGGAAAAT
1 CGCAACGAATTTGGAAAAT
* * **
686493 CGCAACGCGAACTTCGACTAT
1 CGCAA--CGAATTTGGAAAAT
686514 CGCAACGAATTTGGAAA
1 CGCAACGAATTTGGAAA
686531 GTTTGATATC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (19 bp):
CGCAACGAATTTGGAAAAT
Found at i:692772 original size:24 final size:24
Alignment explanation
Indices: 692745--692799 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
692735 ATGAAAATGA
*
692745 TGGCAAAAGGTTGCATAGCTTTCT
1 TGGCAAAAGGTTGCACAGCTTTCT
692769 TGGCAAAAGGTTGCACAGCTTTCT
1 TGGCAAAAGGTTGCACAGCTTTCT
692793 TGGCAAA
1 TGGCAAA
692800 TGTGATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (24 bp):
TGGCAAAAGGTTGCACAGCTTTCT
Found at i:697208 original size:62 final size:63
Alignment explanation
Indices: 697139--697258 Score: 199
Period size: 62 Copynumber: 1.9 Consensus size: 63
697129 TAGTAGTGGC
* *
697139 ATGTGTATTTATGTTATCAGTTTGCT-TGTCAGTTTTATTTAAATGGTCTAT-ATAGTATTTGT
1 ATGTGTATTTATGTTATCAGTCTGCTAT-TCAGTTTTATTTAAACGGTCTATAATAGTATTTGT
697201 ATGTGTATTTATGTTATCAGTCTGCTATTCAGTTTTATTTAAACGGTCTATAATAGTA
1 ATGTGTATTTATGTTATCAGTCTGCTATTCAGTTTTATTTAAACGGTCTATAATAGTA
697259 AATTAGGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 47 0.87
63 7 0.13
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (63 bp):
ATGTGTATTTATGTTATCAGTCTGCTATTCAGTTTTATTTAAACGGTCTATAATAGTATTTGT
Found at i:700106 original size:14 final size:14
Alignment explanation
Indices: 700069--700099 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
700059 TAAGAAATGT
700069 AATTCATTTTACGG
1 AATTCATTTTACGG
*
700083 AATTCATTTTTCGG
1 AATTCATTTTACGG
700097 AAT
1 AAT
700100 CAGTTTTATG
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:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (14 bp):
AATTCATTTTACGG
Found at i:705209 original size:31 final size:30
Alignment explanation
Indices: 705110--705225 Score: 87
Period size: 29 Copynumber: 3.9 Consensus size: 30
705100 TTAAATTATT
* * * *
705110 AAATATATTTTATTCTTGTCTTAACCT-AA
1 AAATATATTTTAATATTTTCTTAACTTAAA
* * * *
705139 AAGTATATTTTATTCTTATT-TTAGCTT--A
1 AAATATATTTTAATATT-TTCTTAACTTAAA
705167 AAATATATTTTAATATTTATCTTAACTTAAA
1 AAATATATTTTAATATTT-TCTTAACTTAAA
* * *
705198 AAATATGTTTTATTCTTTTCTTAACTTA
1 AAATATATTTTAATATTTTCTTAACTTA
705226 TTACATAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.01
28 16 0.23
29 27 0.38
30 11 0.15
31 16 0.23
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (30 bp):
AAATATATTTTAATATTTTCTTAACTTAAA
Found at i:705359 original size:30 final size:29
Alignment explanation
Indices: 705067--705424 Score: 212
Period size: 30 Copynumber: 12.2 Consensus size: 29
705057 CTAATTTTAC
* * *
705067 ATCTTAACATTAAAATTTTATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTCTT
* * *
705097 ATATTAAATTATTAAATATATTTTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * *
705127 GTCTTAACCTAAAAGTATATTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
705156 ATTTTAGCTT-AAAATATATTTTAATAT-TT
1 ATCTTAACTTAAAAATATATTTT-AT-TCTT
*
705185 ATCTTAACTTAAAAAATATGTTTTATTCTT
1 ATCTTAACTT-AAAAATATATTTTATTCTT
* * * * * *
705215 TTCTTAACTTATTACATAAATTATGTTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * ** **
705245 AACTTAAATTCTTAAATATATTCAATTCTT
1 ATCTTAACTT-AAAAATATATTTTATTCTT
* * * * *
705275 ACCTTAAATTATTAAATATAATTAATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * *
705305 GTTTTAACTTAAAACATAT-CTTTATTCTT
1 ATCTTAACTTAAAA-ATATATTTTATTCTT
705334 ATCTTAACTTAAAAATATATTTTTATT-TT
1 ATCTTAACTTAAAAATATA-TTTTATTCTT
* * *
705363 AAC-T-AC--AAAAATGTATTTTATTTTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
705388 ATCTTAAC-TACAAAATTATATTATATTTTT
1 ATCTTAACTTA-AAAA-TATATTTTATTCTT
705418 ATCTTAA
1 ATCTTAA
705425 ATTTAAATAT
Statistics
Matches: 255, Mismatches: 55, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
24 7 0.03
25 12 0.05
26 1 0.00
27 4 0.02
28 17 0.07
29 69 0.27
30 134 0.53
31 11 0.04
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:705379 original size:25 final size:24
Alignment explanation
Indices: 705327--705386 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
705317 AACATATCTT
* * *
705327 TATTCTTATCTTAACTTAAAAATA
1 TATTTTTATTTTAACTCAAAAATA
*
705351 TATTTTTATTTTAACTACAAAAATG
1 TATTTTTATTTTAACT-CAAAAATA
705376 TA-TTTTATTTT
1 TATTTTTATTTT
705387 TATCTTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 23 0.74
25 8 0.26
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTTTTATTTTAACTCAAAAATA
Found at i:705506 original size:30 final size:30
Alignment explanation
Indices: 705450--705537 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 30
705440 AAATAAAATA
* * *
705450 TAAA-TAAGATAAGAATAAATTGTATTTTT
1 TAAACTAAAATAAGAATAAAATATATTTTT
** * *
705479 TAATTTAATATAAGATTAAAATATA-TTTT
1 TAAACTAAAATAAGAATAAAATATATTTTT
705508 TAAACTAAAATAAGAATAAAATATATTTTT
1 TAAACTAAAATAAGAATAAAATATATTTTT
705538 AGGTTATGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 28 0.58
30 20 0.42
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
TAAACTAAAATAAGAATAAAATATATTTTT
Found at i:705845 original size:16 final size:16
Alignment explanation
Indices: 705824--705857 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
705814 TTGGTTGGTG
* *
705824 AAAATATATTAAATTA
1 AAAATAAATTAAAATA
705840 AAAATAAATTAAAATA
1 AAAATAAATTAAAATA
705856 AA
1 AA
705858 TTTAATTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAATTAAAATA
Found at i:707189 original size:40 final size:41
Alignment explanation
Indices: 707135--707224 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
707125 TACCTAAAGT
*
707135 TTAG-TTTTTATTTCATTGTAGTATCC-GCGGTT-ACAAAAA
1 TTAGTTTTTTATTTCATTGTAGTACCCAGCGGTTCA-AAAAA
* *
707174 TTAGTTTTTTCTTTCATTTTAGTACCCAGCGGTTCAAAAAA
1 TTAGTTTTTTATTTCATTGTAGTACCCAGCGGTTCAAAAAA
707215 TTAGTTTTTT
1 TTAGTTTTTT
707225 TCATTTTAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 4 0.09
40 19 0.42
41 21 0.47
42 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (41 bp):
TTAGTTTTTTATTTCATTGTAGTACCCAGCGGTTCAAAAAA
Found at i:707218 original size:41 final size:38
Alignment explanation
Indices: 707135--707235 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 38
707125 TACCTAAAGT
* *
707135 TTAGTTTTTATTTCATTGTAGTATCCGCGGTTACAAAAA
1 TTAGTTTTT-TTTCATTTTAGTACCCGCGGTTACAAAAA
707174 TTAGTTTTTTCTTTCATTTTAGTACCCAGCGGTT-CAAAAAA
1 TTAG-TTTTT-TTTCATTTTAGTACCC-GCGGTTAC-AAAAA
707215 TTAG-TTTTTTTCATTTTAGTA
1 TTAGTTTTTTTTCATTTTAGTA
707236 TCTCATTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
38 13 0.23
39 8 0.14
40 20 0.36
41 15 0.27
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (38 bp):
TTAGTTTTTTTTCATTTTAGTACCCGCGGTTACAAAAA
Found at i:710256 original size:14 final size:14
Alignment explanation
Indices: 710239--710266 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
710229 ATCATAACAA
710239 AATTATATAACTAT
1 AATTATATAACTAT
710253 AATTATATAACTAT
1 AATTATATAACTAT
710267 TCTTTTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:710763 original size:26 final size:26
Alignment explanation
Indices: 710732--710789 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
710722 TCTAACGTGC
710732 TTCGATTCTTTAGGTCTTTCGTATTT
1 TTCGATTCTTTAGGTCTTTCGTATTT
710758 TTCGATTCTTTAGGTCTTTCGTATTT
1 TTCGATTCTTTAGGTCTTTCGTATTT
710784 TTCGAT
1 TTCGAT
710790 CTTCGTGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.57
Consensus pattern (26 bp):
TTCGATTCTTTAGGTCTTTCGTATTT
Found at i:717175 original size:16 final size:15
Alignment explanation
Indices: 717155--717201 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
717145 TTTTTATAAA
717155 ATATATATTTTAATT
1 ATATATATTTTAATT
*
717170 ACTATAT-TTATATATT
1 A-TATATATTTTA-ATT
717186 AT-TATATTTTAATT
1 ATATATATTTTAATT
717200 AT
1 AT
717202 TTATTATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 9 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATATATTTTAATT
Found at i:717202 original size:14 final size:14
Alignment explanation
Indices: 717158--717206 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
717148 TTATAAAATA
*
717158 TATATTTTAATTAC
1 TATATTTTAATTAT
717172 TATATTTATATATTAT
1 TATATTT-TA-ATTAT
717188 TATATTTTAATTAT
1 TATATTTTAATTAT
717202 T-TATT
1 TATATT
717207 ATGATTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.12
14 13 0.41
15 4 0.12
16 11 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTTAATTAT
Found at i:717206 original size:29 final size:30
Alignment explanation
Indices: 717128--717206 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
717118 AAATTTTAAA
* *
717128 ATATATTATAATTATTT-TTTTTATAAAAT
1 ATATATTTTAATTATTTATTTATATAAAAT
* **
717157 ATATATTTTAATTACTATATTTATATATTAT
1 ATATATTTTAATTA-TTTATTTATATAAAAT
717188 -TATATTTTAATTATTTATT
1 ATATATTTTAATTATTTATT
717207 ATGATTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 18 0.43
30 15 0.36
31 9 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (30 bp):
ATATATTTTAATTATTTATTTATATAAAAT
Found at i:717231 original size:16 final size:16
Alignment explanation
Indices: 717210--717243 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
717200 ATTTATTATG
717210 ATTAATAATTAATATT
1 ATTAATAATTAATATT
717226 ATTAATAATTAATATT
1 ATTAATAATTAATATT
717242 AT
1 AT
717244 ATTTATTTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATAATTAATATT
Found at i:717883 original size:12 final size:12
Alignment explanation
Indices: 717866--717892 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
717856 TCATTTTTCT
717866 TAATTTTAAATA
1 TAATTTTAAATA
717878 TAATTTTAAATA
1 TAATTTTAAATA
717890 TAA
1 TAA
717893 CCTTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATTTTAAATA
Found at i:718500 original size:29 final size:29
Alignment explanation
Indices: 718442--718500 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
718432 TAATCAAATA
* *
718442 AATACCTCCTAAAATGTTCATATAAGACT
1 AATACCTCCTAAAATGTCCATATAAAACT
* *
718471 AATACCTCCTAAATTGTCCATGTAAAACT
1 AATACCTCCTAAAATGTCCATATAAAACT
718500 A
1 A
718501 CCTAGCCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.31
Consensus pattern (29 bp):
AATACCTCCTAAAATGTCCATATAAAACT
Found at i:719101 original size:17 final size:16
Alignment explanation
Indices: 719079--719112 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
719069 ATCCTTAATG
719079 TTAATAAAAATTAAATT
1 TTAATAAAAA-TAAATT
719096 TTAATAAAAATAAATT
1 TTAATAAAAATAAATT
719112 T
1 T
719113 ATCAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAATAAAAATAAATT
Found at i:719104 original size:16 final size:17
Alignment explanation
Indices: 719079--719112 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
719069 ATCCTTAATG
*
719079 TTAATAAAAATTAAATT
1 TTAATAAAAAATAAATT
719096 TTAAT-AAAAATAAATT
1 TTAATAAAAAATAAATT
719112 T
1 T
719113 ATCAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAATAAAAAATAAATT
Found at i:720883 original size:6 final size:6
Alignment explanation
Indices: 720876--720919 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
720866 TGTACCTTTC
*
720876 AATTTC AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AA
720920 AAACCTCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:725373 original size:19 final size:19
Alignment explanation
Indices: 725326--725376 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
725316 AAAACTATAT
725326 AATATAT-TATATTTTCAA
1 AATATATATATATTTTCAA
*
725344 AATCATA-ATATGTTTTCAA
1 AAT-ATATATATATTTTCAA
*
725363 TATATATATATATT
1 AATATATATATATT
725377 ACATATGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (19 bp):
AATATATATATATTTTCAA
Found at i:725464 original size:22 final size:22
Alignment explanation
Indices: 725400--725642 Score: 198
Period size: 22 Copynumber: 11.0 Consensus size: 22
725390 AAAAACTATG
*
725400 TATATTATATGTTTTC-AAAAC
1 TATACTATATGTTTTCAAAAAC
*
725421 TATATAACAATATGTTTT--AAAAC
1 --TAT-ACTATATGTTTTCAAAAAC
*
725444 TATACTATATATTTTCAAAAAC
1 TATACTATATGTTTTCAAAAAC
** *
725466 TATA-TATTATGTGTTTTTATAAC
1 TATACTA-TATGT-TTTCAAAAAC
725489 TATA-TAATATGTTTTCAAAAAC
1 TATACT-ATATGTTTTCAAAAAC
725511 TATACTATATGTTTT--AAAAC
1 TATACTATATGTTTTCAAAAAC
* *
725531 TATACTATATATTTTCAAAATC
1 TATACTATATGTTTTCAAAAAC
* *
725553 TATATATTATATGTTTTTTC-TAAAC
1 --TATACTATATG--TTTTCAAAAAC
*
725578 TATA-TAACATGTTTTCAAAAAC
1 TATACT-ATATGTTTTCAAAAAC
*
725600 TATACTATATGTTTTTAAAAAC
1 TATACTATATGTTTTCAAAAAC
* *
725622 TACACTATATATTTTCAAAAA
1 TATACTATATGTTTTCAAAAA
725643 TCATATATTT
Statistics
Matches: 180, Mismatches: 24, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
20 29 0.16
21 10 0.06
22 78 0.43
23 35 0.19
24 20 0.11
25 3 0.02
26 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (22 bp):
TATACTATATGTTTTCAAAAAC
Found at i:725505 original size:89 final size:89
Alignment explanation
Indices: 725400--725651 Score: 359
Period size: 89 Copynumber: 2.8 Consensus size: 89
725390 AAAAACTATG
* *
725400 TATATTATATGTTTTC-AAAACTATATAACAATATGTTTTAAAACTATACTATATATTTTCAAAA
1 TATATAATATGTTTTCAAAAAC--TAT-ACTATATGTTTTAAAACTATACTATATATTTTCAAAA
*
725464 ACTATATATTATGTG-TTTTTAT-AAC
63 ACTATATATTATATGTTTTTTATAAAC
*
725489 TATATAATATGTTTTCAAAAACTATACTATATGTTTTAAAACTATACTATATATTTTCAAAATCT
1 TATATAATATGTTTTCAAAAACTATACTATATGTTTTAAAACTATACTATATATTTTCAAAAACT
*
725554 ATATATTATATGTTTTTTCTAAAC
66 ATATATTATATGTTTTTTATAAAC
* *
725578 TATATAACATGTTTTCAAAAACTATACTATATGTTTTTAAAAACTACACTATATATTTTCAAAAA
1 TATATAATATGTTTTCAAAAACTATACTATATG-TTTT-AAAACTATACTATATATTTTCAAAAA
725643 -TCATATATT
64 CT-ATATATT
725652 TTTTTTGACT
Statistics
Matches: 149, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
87 49 0.33
88 9 0.06
89 50 0.34
90 10 0.07
91 31 0.21
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (89 bp):
TATATAATATGTTTTCAAAAACTATACTATATGTTTTAAAACTATACTATATATTTTCAAAAACT
ATATATTATATGTTTTTTATAAAC
Found at i:726158 original size:21 final size:21
Alignment explanation
Indices: 726088--726151 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
726078 CATGGGTTAG
*
726088 GCGAAGATTCCTTGCCATTAA
1 GCGAAGATTCCTCGCCATTAA
726109 GCGAAGATTCCTCGCCATTAA
1 GCGAAGATTCCTCGCCATTAA
726130 GCGAAGATTCCTCGCCATTAA
1 GCGAAGATTCCTCGCCATTAA
726151 G
1 G
726152 TTAAGATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (21 bp):
GCGAAGATTCCTCGCCATTAA
Found at i:732156 original size:24 final size:24
Alignment explanation
Indices: 732091--732158 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
732081 TACAGAGGCG
* *
732091 TGTGATTTTGCAGCAGACGAAGCT
1 TGTGCTTTTGCAGCAGATGAAGCT
** *
732115 TGCACTTTTGTAGCAGATGAAGCT
1 TGTGCTTTTGCAGCAGATGAAGCT
*
732139 TGTGCTTTTGCAGTAGATGA
1 TGTGCTTTTGCAGCAGATGA
732159 GTCCCTTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.34
Consensus pattern (24 bp):
TGTGCTTTTGCAGCAGATGAAGCT
Found at i:733547 original size:31 final size:31
Alignment explanation
Indices: 733509--733604 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
733499 GAACCTCGGC
*
733509 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
733540 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* * * *
733571 ATCTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCCCGAAGA-ACCTAGGTA
733602 AAC
1 AAC
733605 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 1 0.02
31 57 0.98
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:734528 original size:24 final size:24
Alignment explanation
Indices: 734476--734556 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
734466 TCCCCTTGAA
*
734476 GTGCATCGATGCATGC--T-ACA-
1 GTGCATCGATGCATTCTTTAACAT
734496 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
734520 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
734544 GTGCATCGATGCA
1 GTGCATCGATGCA
734557 CTACCCATGC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
20 15 0.27
22 1 0.02
23 3 0.05
24 37 0.66
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:734621 original size:64 final size:63
Alignment explanation
Indices: 734544--734684 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
734534 TCTTTAACAT
* *
734544 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
734607 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
734671 GTGCATCGATGCAC
1 GTGCATCGATGCAC
734685 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:735191 original size:19 final size:20
Alignment explanation
Indices: 735157--735194 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
735147 GCCTAGCTTG
*
735157 AGCAAGTTGGAGAAGAAGAA
1 AGCAAGTTGAAGAAGAAGAA
735177 AGCAAG-TGAAGAAGAAGA
1 AGCAAGTTGAAGAAGAAGA
735195 GAGTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.53, C:0.05, G:0.34, T:0.08
Consensus pattern (20 bp):
AGCAAGTTGAAGAAGAAGAA
Found at i:754804 original size:37 final size:37
Alignment explanation
Indices: 754754--754827 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
754744 AGCAGTATCA
*
754754 TCAACACCTCCCCTATCACAATCTAACTCATCCTGTT
1 TCAACACCTCCCCTATCACAATCTAACCCATCCTGTT
*
754791 TCAACACCTCCCCTATCACAATCTAACCCGTCCTGTT
1 TCAACACCTCCCCTATCACAATCTAACCCATCCTGTT
754828 CTGCAACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.42, G:0.04, T:0.28
Consensus pattern (37 bp):
TCAACACCTCCCCTATCACAATCTAACCCATCCTGTT
Found at i:754847 original size:39 final size:37
Alignment explanation
Indices: 754754--754847 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
754744 AGCAGTATCA
** *
754754 TCAACACCTCCCCTATCACAATCTAACTCATCCTGTT
1 TCAACACCTCCAATATCACAATCTAACCCATCCTGTT
** *
754791 TCAACACCTCCCCTATCACAATCTAACCCGTCCTGTT
1 TCAACACCTCCAATATCACAATCTAACCCATCCTGTT
*
754828 CTGCAACATCTCCAATATCA
1 -T-CAACACCTCCAATATCA
754848 TCAAGACAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
37 35 0.70
38 1 0.02
39 14 0.28
ACGTcount: A:0.28, C:0.40, G:0.04, T:0.28
Consensus pattern (37 bp):
TCAACACCTCCAATATCACAATCTAACCCATCCTGTT
Found at i:754892 original size:12 final size:12
Alignment explanation
Indices: 754875--754937 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
754865 AACTACATTT
*
754875 TCAGCAACACTC
1 TCAGCAACACCC
* **
754887 TCAGCAGCACAA
1 TCAGCAACACCC
*
754899 TCAACAACACCC
1 TCAGCAACACCC
754911 TCAGCAACACCC
1 TCAGCAACACCC
**
754923 TCAGTTACACCC
1 TCAGCAACACCC
754935 TCA
1 TCA
754938 CTAGCACCCT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.35, C:0.43, G:0.08, T:0.14
Consensus pattern (12 bp):
TCAGCAACACCC
Found at i:758956 original size:20 final size:21
Alignment explanation
Indices: 758923--758977 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
758913 AAACTGTATA
*
758923 ATATATTATATTTCAAAAT-T
1 ATATAATATATTTCAAAATAT
* *
758943 ATATAATATGTTTCAATATAT
1 ATATAATATATTTCAAAATAT
*
758964 ATATATACATATTT
1 ATATA-ATATATTT
758978 TTTTTTCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 6 0.21
22 6 0.21
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATAATATATTTCAAAATAT
Found at i:759058 original size:20 final size:20
Alignment explanation
Indices: 759025--759144 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 20
759015 CTATATACAA
759025 TATGT-TTTTAAAAATTATAC
1 TATGTATTTT-AAAATTATAC
*
759045 TATGTATTTTAAAAACTATATAGTA
1 TATGTATTTT-AAAA-T-TATA--C
* * *
759070 TATGTTTTTTAAATTTATAA
1 TATGTATTTTAAAATTATAC
*
759090 TATGT-TTTCAAAAATTATAC
1 TATGTATTT-TAAAATTATAC
* *
759110 TATATATTTTTAAAACTATAC
1 TATGTA-TTTTAAAATTATAC
*
759131 TATATATTTTAAAA
1 TATGTATTTTAAAA
759145 AATTATATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.04
20 31 0.37
21 24 0.29
22 8 0.10
23 5 0.06
24 3 0.04
25 9 0.11
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (20 bp):
TATGTATTTTAAAATTATAC
Found at i:759062 original size:45 final size:45
Alignment explanation
Indices: 758995--759198 Score: 197
Period size: 45 Copynumber: 4.6 Consensus size: 45
758985 AAAAACTATA
* * * * *
758995 TATATTATATGTTTTCAAAACTATATACAATATGTTTTTAAAAAT
1 TATACTATATATTTTAAAAACTATATACTATATGTTTTTAAAAAC
* * * **
759040 TATACTATGTATTTTAAAAACTATATAGTATATGTTTTTTAAATT
1 TATACTATATATTTTAAAAACTATATACTATATGTTTTTAAAAAC
* *
759085 TATA--ATATGTTTTCAAAAA-T-TATACTATATATTTTT-AAAAC
1 TATACTATATATTTT-AAAAACTATATACTATATGTTTTTAAAAAC
* *
759126 TATACTATATATTTTAAAAAATTATATATTATATGTTTTTTAAAAAC
1 TATACTATATATTTT-AAAAACTATATACTATATG-TTTTTAAAAAC
759173 TATA-T-TATATTTTCAAAAACTATATA
1 TATACTATATATTTT-AAAAACTATATA
759199 TTATTTAAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
41 7 0.05
42 14 0.11
43 21 0.16
44 6 0.05
45 69 0.52
46 6 0.05
47 9 0.07
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (45 bp):
TATACTATATATTTTAAAAACTATATACTATATGTTTTTAAAAAC
Found at i:759104 original size:65 final size:64
Alignment explanation
Indices: 758995--759215 Score: 213
Period size: 65 Copynumber: 3.4 Consensus size: 64
758985 AAAAACTATA
* * * * *
758995 TATATTATATGTTTTCAAAACTATATACAATATGTTTTTAAAAATTATACTATGTATTTTAAAAA
1 TATA-TATATATTTTAAAAAAT-TATATAATATGTTTTTAAAAATTATACTATATATTTTAAAAA
759060 C
64 C
*** * *
759061 TATATAGTATATGTTTTTTAAATT-TATAATATGTTTTCAAAAATTATACTATATATTTTTAAAA
1 TATATA-TATAT-TTTAAAAAATTATATAATATGTTTTTAAAAATTATACTATATATTTTAAAAA
759125 C
64 C
*
759126 TATACTATATATTTTAAAAAATTATATATTATATGTTTTTTAAAAACTATA-T-TATATTTTCAA
1 TATA-TATATATTTTAAAAAATTATATA--ATATG-TTTTTAAAAATTATACTATATATTTT-AA
759189 AAAC
61 AAAC
759193 TATATAT-TA-TTT--AAAATTATATA
1 TATATATATATTTTAAAAAATTATATA
759216 TTATATATCT
Statistics
Matches: 132, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
62 11 0.08
64 11 0.08
65 54 0.41
66 22 0.17
67 21 0.16
68 13 0.10
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (64 bp):
TATATATATATTTTAAAAAATTATATAATATGTTTTTAAAAATTATACTATATATTTTAAAAAC
Found at i:759152 original size:87 final size:88
Alignment explanation
Indices: 759001--759204 Score: 254
Period size: 87 Copynumber: 2.3 Consensus size: 88
758991 TATATATATT
* * * * *
759001 ATATGTTTTCAAAACTATATACAATATGTTTTTAAAAATTATACTATGTATTTTAAAAACTATAT
1 ATATGTTTTCAAAAAT-TATACTATATATTTTTAAAAACTATACTATATATTTTAAAAACTATAT
**
759066 AGTATATGTTTTTT-AAATTTATA
65 AGTATATGTTTTTTAAAAACTATA
*
759089 ATATGTTTTCAAAAATTATACTATATATTTTT-AAAACTATACTATATATTTTAAAAAATTATAT
1 ATATGTTTTCAAAAATTATACTATATATTTTTAAAAACTATACTATATATTTT-AAAAACTATAT
*
759153 ATTATATGTTTTTTAAAAACTATA
65 AGTATATGTTTTTTAAAAACTATA
* * *
759177 TTATATTTTCAAAAACTATA-TAT-TATTT
1 ATATGTTTTCAAAAATTATACTATATATTT
759205 AAAATTATAT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
86 23 0.23
87 40 0.39
88 39 0.38
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (88 bp):
ATATGTTTTCAAAAATTATACTATATATTTTTAAAAACTATACTATATATTTTAAAAACTATATA
GTATATGTTTTTTAAAAACTATA
Found at i:760492 original size:2 final size:2
Alignment explanation
Indices: 760487--760522 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
760477 TTATTGTTTA
760487 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
760523 TGTTGGAAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:761212 original size:100 final size:102
Alignment explanation
Indices: 761037--761242 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 102
761027 TTATATTTAA
761037 ATGTATTTTGGTATAAATTCTCAAAAGCTCAACTTTTCTTATGCAGCCCATATGAACATCACCCT
1 ATGTATTTTGGTATAAATTCTCAAAAGCTCAACTTTTCTTAT--AGCCCATATGAACATCACCCT
761102 AAAGTTCAGTTCAAAGTTAGAAAGCGCGCGCATATGTGT
64 AAAGTTCAGTTCAAAGTTAGAAAGCGCGCGCATATGTGT
761141 ATGTATTTTGGTATAAATTCTCAAAAGCTCAAC-TTTCTTAT-GCCCATATGAACATCACCCTAA
1 ATGTATTTTGGTATAAATTCTCAAAAGCTCAACTTTTCTTATAGCCCATATGAACATCACCCTAA
761204 AGTTCAGTTCAAAGTTAGAAAGCGCGCGCATATGTGT
66 AGTTCAGTTCAAAGTTAGAAAGCGCGCGCATATGTGT
761241 AT
1 AT
761243 ATATATATAT
Statistics
Matches: 102, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
100 61 0.60
103 8 0.08
104 33 0.32
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (102 bp):
ATGTATTTTGGTATAAATTCTCAAAAGCTCAACTTTTCTTATAGCCCATATGAACATCACCCTAA
AGTTCAGTTCAAAGTTAGAAAGCGCGCGCATATGTGT
Found at i:762518 original size:2 final size:2
Alignment explanation
Indices: 762511--762543 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
762501 CTTCAATTTG
762511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
762544 GTCTTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:775090 original size:43 final size:43
Alignment explanation
Indices: 775025--775132 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 43
775015 CTCTCCATAA
* * * *
775025 AGGATCCCATGTAGAATTAGGACGTAGATTATGCCCTTTGTAG
1 AGGATCCCATGCAGAATCAGGACGTAGATTATACCCTCTGTAG
*
775068 AGGATCCCATGCAGAATCAGGACGTGGATTATACCCTCTGTAG
1 AGGATCCCATGCAGAATCAGGACGTAGATTATACCCTCTGTAG
775111 AGGATCCCATGCAGAATCAGGA
1 AGGATCCCATGCAGAATCAGGA
775133 TAGGTATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (43 bp):
AGGATCCCATGCAGAATCAGGACGTAGATTATACCCTCTGTAG
Found at i:789171 original size:36 final size:37
Alignment explanation
Indices: 789095--789204 Score: 106
Period size: 37 Copynumber: 3.1 Consensus size: 37
789085 TATATAATAT
* * *
789095 TATATTACATGTTTTCAAAAATCATTTTT--TAAA--A
1 TATATTATACGTTTTCAAAAAT-ATTTTTAAAAAACTA
*
789129 TATATTATACG-TTTCAAAACCT-TTTTTAAAAAACTA
1 TATATTATACGTTTTCAAAA-ATATTTTTAAAAAACTA
* *
789165 TATATTATACGTTTTTAAAAATATTTTTTAAAAACTA
1 TATATTATACGTTTTCAAAAATATTTTTAAAAAACTA
789202 TAT
1 TAT
789205 TCAAAAATGT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
32 5 0.08
33 8 0.13
34 13 0.21
36 13 0.21
37 23 0.37
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATTATACGTTTTCAAAAATATTTTTAAAAAACTA
Found at i:789394 original size:3 final size:3
Alignment explanation
Indices: 789381--789423 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
789371 AAAAACTATA
789381 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
789424 CACTAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:789598 original size:71 final size:72
Alignment explanation
Indices: 789480--789632 Score: 191
Period size: 71 Copynumber: 2.1 Consensus size: 72
789470 GATCACACGT
* * *
789480 AGAATCAAGACGACGATTAAGCCCTCCGTAGAGGATCCTAGGCAGAATC-AGATGGGGATACAAT
1 AGAATCAAGACAACGATTAAGCCCTCCGTAGAGGATCCTAGACAGAATCAAGATGAGGATACAAT
*
789544 CCCGTGC
66 CCCATGC
* * * * * * *
789551 AGAATCAGGACAAGGATTATGCCCTCCGTAGTGGATCCTATATAGAATCAAGATGAGTATACAAT
1 AGAATCAAGACAACGATTAAGCCCTCCGTAGAGGATCCTAGACAGAATCAAGATGAGGATACAAT
*
789616 CCCATGT
66 CCCATGC
789623 AGAATCAAGA
1 AGAATCAAGA
789633 TGGTGATACA
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
71 41 0.60
72 27 0.40
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (72 bp):
AGAATCAAGACAACGATTAAGCCCTCCGTAGAGGATCCTAGACAGAATCAAGATGAGGATACAAT
CCCATGC
Found at i:789627 original size:29 final size:29
Alignment explanation
Indices: 789593--789668 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
789583 GGATCCTATA
789593 TAGAATCAAGATGAGT-ATACAATCCCATG
1 TAGAATCAAGATG-GTGATACAATCCCATG
*
789622 TAGAATCAAGATGGTGATACAATCTCATG
1 TAGAATCAAGATGGTGATACAATCCCATG
* * *
789651 CAGAATCATGACGGTGAT
1 TAGAATCAAGATGGTGAT
789669 TATGCCCTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 2 0.05
29 40 0.95
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (29 bp):
TAGAATCAAGATGGTGATACAATCCCATG
Found at i:792586 original size:15 final size:15
Alignment explanation
Indices: 792546--792586 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
792536 CATAACATTT
792546 TAATGAAAATTTGAA
1 TAATGAAAATTTGAA
*
792561 TAATAAAAATTTGAA
1 TAATGAAAATTTGAA
* *
792576 TGATGATAATT
1 TAATGAAAATT
792587 CCCTCCACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (15 bp):
TAATGAAAATTTGAA
Found at i:796036 original size:24 final size:24
Alignment explanation
Indices: 796008--796061 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
795998 TCATAGGGGT
796008 ATTTCATAATTTTATAATTAGGTA
1 ATTTCATAATTTTATAATTAGGTA
*
796032 ATTTCTTAATTTTATAATTAGGTA
1 ATTTCATAATTTTATAATTAGGTA
796056 ATTTCA
1 ATTTCA
796062 GTATTAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (24 bp):
ATTTCATAATTTTATAATTAGGTA
Found at i:811498 original size:19 final size:21
Alignment explanation
Indices: 811461--811503 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
811451 TAACTTTTTC
811461 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
811481 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
811501 TTT
1 TTT
811504 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:811509 original size:19 final size:20
Alignment explanation
Indices: 811460--811509 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
811450 TTAACTTTTT
*
811460 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
811480 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
811499 CTTTTACCTTT
1 CTTTTACCTTT
811510 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:822614 original size:27 final size:27
Alignment explanation
Indices: 822584--822636 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
822574 CCTGTCTGAG
822584 AGTTTTTACGGCAAGAGCAAACCTATT
1 AGTTTTTACGGCAAGAGCAAACCTATT
*
822611 AGTTTTTACGGCAAGTGCAAACCTAT
1 AGTTTTTACGGCAAGAGCAAACCTAT
822637 CTTCTTGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (27 bp):
AGTTTTTACGGCAAGAGCAAACCTATT
Found at i:824006 original size:20 final size:21
Alignment explanation
Indices: 823983--824031 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
823973 AATATTTCTT
823983 TTATTTAAAAAAT-AAATTTA
1 TTATTTAAAAAATAAAATTTA
**
824003 TTATTTTTAAAATTTAAAATTTA
1 TTA--TTTAAAAAATAAAATTTA
824026 TTATTT
1 TTATTT
824032 TTTGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 8 0.33
23 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATTTAAAAAATAAAATTTA
Found at i:825065 original size:6 final size:6
Alignment explanation
Indices: 825042--825124 Score: 60
Period size: 6 Copynumber: 13.3 Consensus size: 6
825032 ACACTAGTTT
* * * *
825042 TTTTTCA TTTTGTC TTTTTA TTTTTA TTTATT- TGTTTA TTATTA TTATTA
1 TTTTT-A TTTT-TA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA
* * *
825092 TTATTA TTATTTA TTATTA TTATTA TTTTTA TT
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TT
825125 ATTAATAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
5 2 0.03
6 46 0.72
7 15 0.23
8 1 0.02
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:825085 original size:3 final size:3
Alignment explanation
Indices: 825077--825145 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
825067 ATTTATTTGT
*
825077 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
825123 TTA TTA ATA ATA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
825146 CAAACAGACC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:828387 original size:36 final size:36
Alignment explanation
Indices: 828347--828416 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
828337 CGAGAAATAC
* ** *
828347 ACACAGAGATCCTGTTATATTAATACCAAAAGTATT
1 ACACAAAGATCCTGCCAGATTAATACCAAAAGTATT
*
828383 ACACAAAGATCCTGCCAGATTGATACCAAAAGTA
1 ACACAAAGATCCTGCCAGATTAATACCAAAAGTA
828417 GTCTACGGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (36 bp):
ACACAAAGATCCTGCCAGATTAATACCAAAAGTATT
Found at i:828875 original size:43 final size:44
Alignment explanation
Indices: 828810--828897 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 44
828800 TGGCTTTAGA
* * *
828810 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
*
828853 GAAGTTAGGACTGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
828897 G
1 G
828898 GATGCACGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.70
44 12 0.30
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
Found at i:828994 original size:6 final size:7
Alignment explanation
Indices: 828974--829002 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
828964 CATACATACA
828974 TTTGCAT
1 TTTGCAT
828981 TTTGCAT
1 TTTGCAT
828988 TTT-CAT
1 TTTGCAT
828994 TTTGCAT
1 TTTGCAT
829001 TT
1 TT
829003 ATAGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (7 bp):
TTTGCAT
Found at i:828994 original size:13 final size:13
Alignment explanation
Indices: 828972--829002 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
828962 TTCATACATA
828972 CATTTGCATTTTG
1 CATTTGCATTTTG
*
828985 CATTTTCATTTTG
1 CATTTGCATTTTG
828998 CATTT
1 CATTT
829003 ATAGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (13 bp):
CATTTGCATTTTG
Found at i:837174 original size:22 final size:23
Alignment explanation
Indices: 837146--837202 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 23
837136 ACATCTACAT
837146 TCTTCAAAGATGA-TAGATTCTC
1 TCTTCAAAGATGAGTAGATTCTC
837168 TCTTCAAAGAT-AGTAGATTCTC
1 TCTTCAAAGATGAGTAGATTCTC
*
837190 TTTTCAAAGATGA
1 TCTTCAAAGATGA
837203 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (23 bp):
TCTTCAAAGATGAGTAGATTCTC
Found at i:838100 original size:113 final size:113
Alignment explanation
Indices: 837902--838429 Score: 830
Period size: 113 Copynumber: 4.7 Consensus size: 113
837892 TATTTCCAGA
837902 AGAGTTCATAAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
837966 TTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGCATTGCCAGTT
65 TTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGCATTGCCAGTT
*
838015 AGAGTTCATAATGAGAAGAACGT-ATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTG
1 AGAGTTCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
*
838079 TTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAACATTGCCAGTT
65 TTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGCATTGCCAGTT
*
838128 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTCCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
838193 TCAACCTTTTGCTTTAATTCATCA-TCCGATGGATCAGCATTGCCAGGT
66 TCAACCTTTTGCTTTAATTCATCACT-CGATGGATTAGCATTGCCAGTT
* *
838241 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
** * * **
838306 TCAACCTTTTGCTCGAATTCATCACTCGATGGATTAGCTTTTCCAGAG
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGCATTGCCAGTT
* * * * * *
838354 AAATTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAAAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
838418 TCAACCTTTTGC
66 TCAACCTTTTGC
838430 ACGACTCTAT
Statistics
Matches: 385, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
112 46 0.12
113 337 0.88
114 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTTTAATTCATCACTCGATGGATTAGCATTGCCAGTT
Found at i:838851 original size:3 final size:3
Alignment explanation
Indices: 838843--838896 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
838833 GTTTATTTGT
*
838843 TTA TTA TTA TTA TTA -TA TTA TTA TT- TT- TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
838888 TTA TTA TTA
1 TTA TTA TTA
838897 CAAACAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:838863 original size:25 final size:26
Alignment explanation
Indices: 838813--838892 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 26
838803 GTTTTTTTCA
* *
838813 ATTTGTTT-TTTTTATTTTTAGT-TT
1 ATTTGTTTATTATTATTATTAGTATT
838837 ATTTGTTTATTATTATTATTA-TATT
1 ATTTGTTTATTATTATTATTAGTATT
* * *
838862 ATTATTTTTTATTATTAATATTATTATT
1 A-T-TTGTTTATTATTATTATTAGTATT
838890 ATT
1 ATT
838893 ATTACAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
24 9 0.19
25 13 0.28
26 2 0.04
27 18 0.38
28 5 0.11
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (26 bp):
ATTTGTTTATTATTATTATTAGTATT
Found at i:850242 original size:34 final size:31
Alignment explanation
Indices: 850161--850385 Score: 98
Period size: 29 Copynumber: 7.0 Consensus size: 31
850151 CGAGTCATAT
850161 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGG
1 TTTTTTAAGT-TGATATTCGGGTCGGGTCGGG
* *
850193 TTTTTTAA---AAAATTCGGGCTCGGGTCGGG
1 TTTTTTAAGTTGATATTCGGG-TCGGGTCGGG
*
850222 TTTTTTAGAGTTTGATATTCGAGT----T----
1 TTTTTTA-AG-TTGATATTCGGGTCGGGTCGGG
** * *
850247 TTTTTTAA--AAAAATTTGGGCTCGGGTCGGG
1 TTTTTTAAGTTGATATTCGGG-TCGGGTCGGG
850277 TTTTTTAGAGTTTGATATTCGAGTCGGTCGGGTCGGG
1 TTTTTTA-AG-TTGATATTC--G--GGTCGGGTCGGG
850314 TTTTTTAAGTGTGATATTTGGGTCGGGGTCGGGTCGGG
1 TTTTTTAAGT-TGATA--T---TC-GGGTCGGGTCGGG
* *
850352 TTTTTTTAAGTGTGATATTCGAGTCAGGTCGGG
1 -TTTTTTAAGT-TGATATTCGGGTCGGGTCGGG
850385 T
1 T
850386 GAAACTTTAT
Statistics
Matches: 146, Mismatches: 17, Indels: 60
0.65 0.08 0.27
Matches are distributed among these distances:
21 6 0.04
22 1 0.01
24 1 0.01
25 7 0.05
26 1 0.01
28 8 0.05
29 18 0.12
30 8 0.05
31 1 0.01
32 9 0.06
33 12 0.08
34 13 0.09
35 1 0.01
36 8 0.05
37 18 0.12
38 15 0.10
39 16 0.11
40 1 0.01
41 2 0.01
ACGTcount: A:0.16, C:0.09, G:0.33, T:0.41
Consensus pattern (31 bp):
TTTTTTAAGTTGATATTCGGGTCGGGTCGGG
Found at i:850281 original size:54 final size:54
Alignment explanation
Indices: 850193--850300 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 54
850183 TCGGGTCGGG
850193 TTTTTTAAAAAATTCGGGCTCGGGTCGGGTTTTTTAGAGTTTGATATTCGAGTT
1 TTTTTTAAAAAATTCGGGCTCGGGTCGGGTTTTTTAGAGTTTGATATTCGAGTT
*
850247 TTTTTTAAAAAAATTTGGGCTCGGGTCGGGTTTTTTAGAGTTTGATATTCGAGT
1 TTTTTT-AAAAAATTCGGGCTCGGGTCGGGTTTTTTAGAGTTTGATATTCGAGT
850301 CGGTCGGGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 6 0.12
55 46 0.88
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.44
Consensus pattern (54 bp):
TTTTTTAAAAAATTCGGGCTCGGGTCGGGTTTTTTAGAGTTTGATATTCGAGTT
Found at i:850308 original size:37 final size:37
Alignment explanation
Indices: 850267--850385 Score: 168
Period size: 39 Copynumber: 3.2 Consensus size: 37
850257 AAATTTGGGC
*
850267 TCGGGTCGGGTTTTTTAGAGTTTGATATTCGAGTC-GG
1 TCGGGTCGGGTTTTTTA-AGTGTGATATTCGAGTCGGG
* *
850304 TCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGGGG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGAGTC-GGG
*
850342 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGAGTCAGG
1 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGAGTCGGG
850380 TCGGGT
1 TCGGGT
850386 GAAACTTTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
36 14 0.19
37 17 0.23
38 20 0.27
39 22 0.30
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.39
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGAGTCGGG
Found at i:850452 original size:39 final size:39
Alignment explanation
Indices: 850398--850528 Score: 228
Period size: 39 Copynumber: 3.4 Consensus size: 39
850388 AACTTTATTT
*
850398 TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCTTTGTTCTC
1 TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCCTTGTTCTC
850437 TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCCTTGTTCTC
1 TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCCTTGTTCTC
850476 TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCCTTGTTCT-
1 TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCCTTGTTCTC
*
850514 TAGGTTGGGTCGGGT
1 T-GGTCGGGTCGGGT
850529 GGTATTGGGT
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
38 1 0.01
39 88 0.99
ACGTcount: A:0.03, C:0.20, G:0.43, T:0.34
Consensus pattern (39 bp):
TGGTCGGGTCGGGTCTCGGGTGGAGGTTCCCTTGTTCTC
Found at i:850666 original size:20 final size:20
Alignment explanation
Indices: 850637--850677 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
850627 TATAATTTAT
*
850637 TGAAATGAATAATCAATCAA
1 TGAAACGAATAATCAATCAA
850657 TGAAACGAATAATCAATCAA
1 TGAAACGAATAATCAATCAA
850677 T
1 T
850678 AAAATGAAAA
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:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (20 bp):
TGAAACGAATAATCAATCAA
Found at i:862623 original size:16 final size:15
Alignment explanation
Indices: 862580--862615 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
862570 TAATGAATGA
*
862580 TTAAATATGTTTTTG
1 TTAAGTATGTTTTTG
*
862595 TTAAGTATATTTTTG
1 TTAAGTATGTTTTTG
862610 TTAAGT
1 TTAAGT
862616 GTTGTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (15 bp):
TTAAGTATGTTTTTG
Found at i:873864 original size:2 final size:2
Alignment explanation
Indices: 873857--873881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
873847 TAGTGTGAGA
873857 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
873882 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:873886 original size:2 final size:2
Alignment explanation
Indices: 873881--873906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
873871 TCTCTCTCTC
873881 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
873907 CAAGGGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:880157 original size:27 final size:29
Alignment explanation
Indices: 880103--880157 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
880093 GGTTTTAGGT
*
880103 AGAAATCGTTGTATATTTCTAACGACTTTC
1 AGAAATCGTTG-ATATTTCTAACAACTTTC
880133 AGAAATCGTTG-TA-TTCTAACAACTT
1 AGAAATCGTTGATATTTCTAACAACTT
880158 CCATCGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 11 0.46
28 2 0.08
30 11 0.46
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (29 bp):
AGAAATCGTTGATATTTCTAACAACTTTC
Found at i:880389 original size:2 final size:2
Alignment explanation
Indices: 880382--880451 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
880372 CTGTGACCAT
880382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
880424 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
880452 CATCCTATTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:880940 original size:2 final size:2
Alignment explanation
Indices: 880928--880960 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
880918 GGTTAAGTGG
*
880928 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
880961 AAGATATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:882652 original size:22 final size:22
Alignment explanation
Indices: 882634--882675 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
882624 AGGTTTAAAT
*
882634 TTTAGATATTT-AGATTTTAACA
1 TTTAGAT-TTTAAAATTTTAACA
882656 TTTAGATTTTAAAATTTTAA
1 TTTAGATTTTAAAATTTTAA
882676 GGTCCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTAGATTTTAAAATTTTAACA
Found at i:882660 original size:14 final size:14
Alignment explanation
Indices: 882627--882672 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
882617 TTTTTTAAGG
* *
882627 TTTAAATTTTAGATA
1 TTTAGATTTTA-AAA
*
882642 TTTAGATTTTAACA
1 TTTAGATTTTAAAA
882656 TTTAGATTTTAAAA
1 TTTAGATTTTAAAA
882670 TTT
1 TTT
882673 TAAGGTCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (14 bp):
TTTAGATTTTAAAA
Found at i:887390 original size:15 final size:16
Alignment explanation
Indices: 887361--887395 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
887351 AAATATATTT
*
887361 ATATAATTATTTTAAC
1 ATATAATTATTTTAAA
887377 ATATAATT-TTTTAAA
1 ATATAATTATTTTAAA
887392 ATAT
1 ATAT
887396 TTTAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATTATTTTAAA
Found at i:887412 original size:20 final size:21
Alignment explanation
Indices: 887387--887431 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
887377 ATATAATTTT
*
887387 TTAAAATATTTTAATT-TTAA
1 TTAAAATATATTAATTATTAA
*
887407 TTAAAATATATTATTTATTAA
1 TTAAAATATATTAATTATTAA
887428 TTAA
1 TTAA
887432 CGATGATGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAATATATTAATTATTAA
Found at i:889344 original size:23 final size:22
Alignment explanation
Indices: 889318--889409 Score: 60
Period size: 23 Copynumber: 4.0 Consensus size: 22
889308 AAAAAGCAAG
889318 AAAAAAAAAAAAAATGAGATAAA
1 AAAAAAAAAAAAAATGA-ATAAA
** * *
889341 AAAAAGTAATAAAATGAAT-GA
1 AAAAAAAAAAAAAATGAATAAA
* *
889362 AAAAATAAAAGAAATAGAAGTAAA
1 AAAAAAAAAAAAAAT-GAA-TAAA
* * *
889386 AATAAACAAAGAAAATAAATAAA
1 AA-AAAAAAAAAAAATGAATAAA
889409 A
1 A
889410 TACAAAACAT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
21 12 0.23
22 5 0.10
23 20 0.38
24 5 0.10
25 10 0.19
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.13
Consensus pattern (22 bp):
AAAAAAAAAAAAAATGAATAAA
Found at i:889411 original size:9 final size:9
Alignment explanation
Indices: 889348--889453 Score: 51
Period size: 9 Copynumber: 11.8 Consensus size: 9
889338 AAAAAAAAGT
*
889348 AATAAAATG
1 AATAAAATA
*
889357 AATGAAA-A
1 AATAAAATA
*
889365 AATAAAAGA
1 AATAAAATA
*
889374 AATAGAAGTA
1 AATA-AAATA
* *
889384 AAAATAAACA
1 AATA-AAATA
*
889394 AAGAAAATA
1 AATAAAATA
889403 AATAAAATA
1 AATAAAATA
*
889412 CAA-AACAT-
1 -AATAAAATA
*
889420 AATGATAATA
1 AAT-AAAATA
889430 TAAT-AAATA
1 -AATAAAATA
889439 AAT-AAATA
1 AATAAAATA
889447 AATAAAA
1 AATAAAA
889454 AGAAAATAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
7 2 0.03
8 17 0.23
9 37 0.51
10 14 0.19
11 3 0.04
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:889460 original size:15 final size:15
Alignment explanation
Indices: 889442--889474 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
889432 ATAAATAAAT
889442 AAATAAATAA-AAAGA
1 AAATAAA-AAGAAAGA
889457 AAATAAAAAGAAAGA
1 AAATAAAAAGAAAGA
889472 AAA
1 AAA
889475 AGTATAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (15 bp):
AAATAAAAAGAAAGA
Found at i:889798 original size:3 final size:3
Alignment explanation
Indices: 889785--889820 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
889775 AATAAAGTAA
*
889785 AAT ACT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
889821 TAAATGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:889814 original size:11 final size:11
Alignment explanation
Indices: 889790--889823 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
889780 AGTAAAATAC
889790 TAATAATAATAA
1 TAATAAT-ATAA
889802 TAATAATATAA
1 TAATAATATAA
889813 TAATAATATAA
1 TAATAATATAA
889824 ATGTAAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAATATAA
Found at i:889917 original size:13 final size:12
Alignment explanation
Indices: 889899--889937 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
889889 TTAATAGTAT
889899 TAAAAGTAAAAA
1 TAAAAGTAAAAA
889911 GTAAAAGTAAAAA
1 -TAAAAGTAAAAA
889924 TAAAA-T-AAAA
1 TAAAAGTAAAAA
889934 TAAA
1 TAAA
889938 TAAAACAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 8 0.31
11 1 0.04
12 5 0.19
13 12 0.46
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (12 bp):
TAAAAGTAAAAA
Found at i:890109 original size:25 final size:24
Alignment explanation
Indices: 890073--890120 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
890063 AAACAAGGTG
* * *
890073 TAAAAAACATAATAAGTATTAAAA
1 TAAAAAAAATAAAAAGGATTAAAA
890097 TAAAAAATAATAAAAAGGATTAAA
1 TAAAAAA-AATAAAAAGGATTAAA
890121 TCGAAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (24 bp):
TAAAAAAAATAAAAAGGATTAAAA
Found at i:892326 original size:52 final size:53
Alignment explanation
Indices: 892255--892398 Score: 175
Period size: 54 Copynumber: 2.7 Consensus size: 53
892245 AAGTTGAGCC
* * * * *
892255 TTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT-TGTATGTTGCT
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTCAGAAAGTTGCT
* *
892307 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTCGAGAAAGTTGTT
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTC-AGAAAGTTGCT
* *
892361 TTGAGTTGGATATCCTCCATCGT-AGAGTTGAAATCCAA
1 TTGAGTTGGATATCCTTCGTCGTGA-AGTTGAAATCCAA
892399 TTTCAAACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 38 0.47
53 1 0.01
54 41 0.51
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (53 bp):
TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTCAGAAAGTTGCT
Found at i:893515 original size:83 final size:87
Alignment explanation
Indices: 893418--893643 Score: 257
Period size: 94 Copynumber: 2.6 Consensus size: 87
893408 GGCTAGCTGA
893418 ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGGACAGA-TCAA-TA-TG-TAG-A-CA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTACT-TAGAGGGACA-ACTCAATTATTGATAGAATCA
* * *
893477 CCTTTATCAGGTTAGCTGAATCTT
64 CCTCTATCAGGCTAGCTGAACCTT
*
893501 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTAGAGGGACAACTCAAGCTTTATTGTATAGTAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTACTTAGAGGGACAACTCAA---TTATTG-ATAG---
* *
893566 AATCACCTCTATCAGGCTAGTTGGACCTT
59 AATCACCTCTATCAGGCTAGCTGAACCTT
*
893595 ATCCATAAAGCCGGGGCGTTTAACCAATTCCTTTAGAGGGACAACTCAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTAC-TTAGAGGGACAACTCAA
893644 GCTTTATTGT
Statistics
Matches: 122, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
81 1 0.01
82 14 0.11
83 31 0.25
86 2 0.02
87 2 0.02
89 3 0.02
93 1 0.01
94 51 0.42
95 17 0.14
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTACTTAGAGGGACAACTCAATTATTGATAGAATCACC
TCTATCAGGCTAGCTGAACCTT
Found at i:894489 original size:23 final size:23
Alignment explanation
Indices: 894452--894515 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
894442 CATCTCGTAT
894452 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
894475 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
894498 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
894516 TATAAGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:896013 original size:20 final size:21
Alignment explanation
Indices: 895985--896024 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
895975 CTCGATATCT
895985 ATATAAGTATAC-ATTGATAC
1 ATATAAGTATACAATTGATAC
* *
896005 ATATTAGTATCCAATTGATA
1 ATATAAGTATACAATTGATA
896025 TACTCCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATAAGTATACAATTGATAC
Found at i:896138 original size:24 final size:22
Alignment explanation
Indices: 896081--896144 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 22
896071 TTTCCCTTGA
*
896081 AGTGCATCGATGCAT--TCTAC
1 AGTGCATCGATGCATCCTTTAC
*
896101 AGTGTATCGATGCATCCTTTAAC
1 AGTGCATCGATGCATCCTTT-AC
896124 ATGTGCATCGATGCACTCCTT
1 A-GTGCATCGATGCA-TCCTT
896145 ATGCATCGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.39
22 2 0.06
23 3 0.08
24 12 0.33
25 5 0.14
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTTAC
Found at i:896651 original size:21 final size:21
Alignment explanation
Indices: 896626--896673 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
896616 ATCCTTTGCT
896626 TTTAAGATGATTTAAGCTTTC
1 TTTAAGATGATTTAAGCTTTC
896647 TTTAAGATGATTTAAGCTTTC
1 TTTAAGATGATTTAAGCTTTC
896668 TTTAAG
1 TTTAAG
896674 CTTAATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (21 bp):
TTTAAGATGATTTAAGCTTTC
Found at i:901117 original size:24 final size:22
Alignment explanation
Indices: 901060--901123 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 22
901050 TTTCCCTTGA
*
901060 AGTGCATCGATGCAT--TCTAC
1 AGTGCATCGATGCATCCTTTAC
*
901080 AGTGTATCGATGCATCCTTTAAC
1 AGTGCATCGATGCATCCTTT-AC
901103 ATGTGCATCGATGCACTCCTT
1 A-GTGCATCGATGCA-TCCTT
901124 ATGTATCGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.39
22 2 0.06
23 3 0.08
24 12 0.33
25 5 0.14
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTTAC
Found at i:904435 original size:78 final size:77
Alignment explanation
Indices: 904242--904448 Score: 285
Period size: 77 Copynumber: 2.7 Consensus size: 77
904232 CCGTTGTACA
* * * *
904242 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
**
904305 ACAAAACTGTTT
66 ACAAAACCATTT
904317 AGGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGG
1 A-GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTC-G
**
904381 GGCCAAAACCATTT
64 GAACAAAACCATTT
* *
904395 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTG
904449 TAATTTTTGG
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
75 1 0.01
76 24 0.21
77 52 0.44
78 40 0.34
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
ACAAAACCATTT
Found at i:905080 original size:17 final size:17
Alignment explanation
Indices: 905058--905101 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
905048 TTCATAAATC
905058 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
905075 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
905092 -AAATATCCAA
1 CAAA-ATCCAA
905102 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:905093 original size:9 final size:8
Alignment explanation
Indices: 905053--905103 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
905043 CACCATTCAT
905053 AAATCC-A
1 AAATCCAA
905060 AAATCCAA
1 AAATCCAA
*
905068 CAATCCACA
1 AAATCCA-A
905077 AAAT-CAA
1 AAATCCAA
905084 ACAATCCAA
1 A-AATCCAA
905093 AATATCCAA
1 AA-ATCCAA
905102 AA
1 AA
905104 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:907056 original size:21 final size:21
Alignment explanation
Indices: 907030--907069 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
907020 CAGAACCCCA
*
907030 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
907051 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
907070 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:907104 original size:20 final size:21
Alignment explanation
Indices: 907050--907112 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
907040 GATTCCCCTG
907050 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
907074 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
907094 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
907113 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:913006 original size:75 final size:77
Alignment explanation
Indices: 912878--913086 Score: 289
Period size: 77 Copynumber: 2.8 Consensus size: 77
912868 CCGTTGTACA
* * * *
912878 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTC-GGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGGA
**
912941 ACAAAACTGTTT
66 ACAAAACCATTT
* *
912953 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGGA
*
913017 CCAAAACCATTT
66 ACAAAACCATTT
* * *
913029 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
913087 TTTGGCTTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
74 17 0.14
75 37 0.31
76 12 0.10
77 52 0.44
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGGA
ACAAAACCATTT
Found at i:915340 original size:10 final size:9
Alignment explanation
Indices: 915317--915450 Score: 51
Period size: 9 Copynumber: 14.4 Consensus size: 9
915307 GTTAGAGGAA
915317 AAAAGAAAT
1 AAAAGAAAT
*
915326 GAAAGTAAAT
1 AAAAG-AAAT
915336 AAAAGAAAAT
1 AAAAG-AAAT
* *
915346 AGAAGCAA-
1 AAAAGAAAT
* *
915354 AAAATAAAA
1 AAAAGAAAT
*
915363 AAAATGAGAT
1 AAAA-GAAAT
*
915373 AAAA-AATAA
1 AAAAGAA-AT
*
915382 AAAAGTAAT
1 AAAAGAAAT
915391 AAAATG-AAT
1 AAAA-GAAAT
915400 GAAAA-AAAT
1 -AAAAGAAAT
915409 AAAAGAAAT
1 AAAAGAAAT
* *
915418 ATAAGTAAAA
1 AAAAG-AAAT
* *
915428 ATAAACAAAG
1 A-AAAGAAAT
*
915438 AAAATAAAT
1 AAAAGAAAT
915447 AAAA
1 AAAA
915451 TACAGAACAT
Statistics
Matches: 92, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
8 10 0.11
9 44 0.48
10 36 0.39
11 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.14
Consensus pattern (9 bp):
AAAAGAAAT
Found at i:915362 original size:23 final size:21
Alignment explanation
Indices: 915332--915385 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
915322 AAATGAAAGT
915332 AAATAAAAGAAAAT-AGAAGCAAA
1 AAATAAAA-AAAATGAG-A-CAAA
*
915355 AAATAAAAAAAATGAGATAAA
1 AAATAAAAAAAATGAGACAAA
915376 AAATAAAAAA
1 AAATAAAAAA
915386 GTAATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 13 0.45
22 6 0.21
23 10 0.34
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (21 bp):
AAATAAAAAAAATGAGACAAA
Found at i:915366 original size:9 final size:9
Alignment explanation
Indices: 915352--915450 Score: 56
Period size: 9 Copynumber: 10.2 Consensus size: 9
915342 AAATAGAAGC
915352 AAAAAATAA
1 AAAAAATAA
915361 AAAAAATGAGA
1 AAAAAAT-A-A
915372 TAAAAAATAA
1 -AAAAAATAA
915382 AAAAGTAATAA
1 AAAA--AATAA
** *
915393 AATGAATGA
1 AAAAAATAA
915402 AAAAAATAA
1 AAAAAATAA
915411 AAGAAATATAA
1 AA-AAA-ATAA
*
915422 GTAAAAAT-A
1 -AAAAAATAA
* *
915431 AACAAAGAA
1 AAAAAATAA
*
915440 AATAAATAA
1 AAAAAATAA
915449 AA
1 AA
915451 TACAGAACAT
Statistics
Matches: 69, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
8 4 0.06
9 34 0.49
10 7 0.10
11 16 0.23
12 8 0.12
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:915394 original size:29 final size:27
Alignment explanation
Indices: 915352--915412 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
915342 AAATAGAAGC
915352 AAAAAATAAAAAAAATGAGAT-AAAAAAT
1 AAAAAAT-AAAAAAATGA-ATAAAAAAAT
*
915380 AAAAAAGTAATAAAATGAATGAAAAAAAT
1 AAAAAA-TAAAAAAATGAAT-AAAAAAAT
915409 AAAA
1 AAAA
915413 GAAATATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.07
28 15 0.52
29 12 0.41
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAATAAAAAAATGAATAAAAAAAT
Found at i:915452 original size:9 final size:9
Alignment explanation
Indices: 915375--915526 Score: 53
Period size: 9 Copynumber: 16.4 Consensus size: 9
915365 AATGAGATAA
915375 AAAATAAA-
1 AAAATAAAT
*
915383 AAAGT-AAT
1 AAAATAAAT
*
915391 AAAATGAAT
1 AAAATAAAT
915400 GAAAA-AAAT
1 -AAAATAAAT
*
915409 AAAAGAAAT
1 AAAATAAAT
* *
915418 ATAAGTAAAA
1 A-AAATAAAT
* *
915428 ATAAACAAAG
1 A-AAATAAAT
915438 AAAATAAAT
1 AAAATAAAT
* *
915447 AAAATACAG
1 AAAATAAAT
*
915456 AACAT-AAT
1 AAAATAAAT
*
915464 GATAATATAAT
1 -AAAATA-AAT
*
915475 -AAATAAAC
1 AAAATAAAT
*
915483 AAACAAAAAT
1 AAA-ATAAAT
915493 AAAATACAAAT
1 AAAAT--AAAT
*
915504 AAAAATAAAG
1 -AAAATAAAT
*
915514 AAAATAAAG
1 AAAATAAAT
915523 AAAA
1 AAAA
915527 AGTATAAAGG
Statistics
Matches: 107, Mismatches: 24, Indels: 25
0.69 0.15 0.16
Matches are distributed among these distances:
7 2 0.02
8 15 0.14
9 51 0.48
10 27 0.25
11 7 0.07
12 5 0.05
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (9 bp):
AAAATAAAT
Found at i:916101 original size:43 final size:40
Alignment explanation
Indices: 915993--916107 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 40
915983 AAATATAATT
*
915993 AAATATATATATATATGTTAATAGTAAAAAAAGAAAAAAA
1 AAATATATATATATATATTAATAGTAAAAAAAGAAAAAAA
* *
916033 AGAATATACATATAATGATAATAATAGTAACAAAAGAGAAAAATAA
1 A-AATATATATAT-AT-ATATTAATAGTAA-AAAA-AGAAAAA-AA
* *
916079 AAATATATTTATATACATTAATAGTAAAA
1 AAATATATATATATATATTAATAGTAAAA
916108 TAATAATAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
40 1 0.02
41 10 0.16
42 4 0.06
43 22 0.35
44 6 0.10
45 16 0.26
46 3 0.05
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (40 bp):
AAATATATATATATATATTAATAGTAAAAAAAGAAAAAAA
Done.