Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 62
Found at i:741062 original size:26 final size:26
Alignment explanation
Indices: 741003--741053 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
740993 TATTTTGGTT
741003 GGGTAAAATTACAAAAATACCCTTAA
1 GGGTAAAATTACAAAAATACCCTTAA
741029 GGGTAAAATTACAAAAATACCCTTA
1 GGGTAAAATTACAAAAATACCCTTA
741054 TATTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.24
Consensus pattern (26 bp):
GGGTAAAATTACAAAAATACCCTTAA
Found at i:742154 original size:35 final size:36
Alignment explanation
Indices: 742112--742220 Score: 134
Period size: 35 Copynumber: 3.1 Consensus size: 36
742102 CTACAGGTTA
*
742112 ACTCGATCAAACTAGTAATTCCTTATATAGGTTCAG
1 ACTCGATCAAACTGGTAATTCCTTATATAGGTTCAG
**
742148 AC-CGATCAAACTGGTAATTCCTTACGGTAGGTTCAG
1 ACTCGATCAAACTGGTAATTCCTTA-TATAGGTTCAG
* *
742184 -CTC-AGTCAAATTGGTTATTCCTTATATAGGTTCAG
1 ACTCGA-TCAAACTGGTAATTCCTTATATAGGTTCAG
742219 AC
1 AC
742221 ATATCAAGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
35 32 0.52
36 30 0.48
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (36 bp):
ACTCGATCAAACTGGTAATTCCTTATATAGGTTCAG
Found at i:742239 original size:35 final size:34
Alignment explanation
Indices: 742117--742243 Score: 121
Period size: 35 Copynumber: 3.6 Consensus size: 34
742107 GGTTAACTCG
* *
742117 ATCAAACTAGTAATTCCTTATATAGGTTCAGACCG
1 ATCAAACTGGTAATTCCTTATATAGGTTCAGA-CT
**
742152 ATCAAACTGGTAATTCCTTACGGTAGGTTCAG-CT
1 ATCAAACTGGTAATTCCTTA-TATAGGTTCAGACT
* *
742186 CAGTCAAATTGGTTATTCCTTATATAGGTTCAGACAT
1 -A-TCAAACTGGTAATTCCTTATATAGGTTCAGAC-T
* **
742223 ATCAAGCTGGCGATTCCTTAT
1 ATCAAACTGGTAATTCCTTAT
742244 GAATCTAAGG
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
34 1 0.01
35 45 0.60
36 28 0.37
37 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (34 bp):
ATCAAACTGGTAATTCCTTATATAGGTTCAGACT
Found at i:749828 original size:17 final size:18
Alignment explanation
Indices: 749791--749831 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
749781 TTATTATGTA
*
749791 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
749809 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
749826 TTTACT
1 TTTACT
749832 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:751911 original size:18 final size:18
Alignment explanation
Indices: 751888--751922 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
751878 TCTACTCAGG
751888 ACGACGACGACAATGACA
1 ACGACGACGACAATGACA
* *
751906 ACGACGATGACGATGAC
1 ACGACGACGACAATGAC
751923 GATGGTGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.26, G:0.26, T:0.09
Consensus pattern (18 bp):
ACGACGACGACAATGACA
Found at i:761744 original size:19 final size:19
Alignment explanation
Indices: 761702--761758 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
761692 TCAATAATCC
761702 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
*
761720 TAATTCCACTGATAATCTTT
1 T-ATTCCACTGGTAATCTTT
761740 TATTCCCACTGGTAATCTT
1 TATT-CCACTGGTAATCTT
761759 ACATTTCGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.03
19 8 0.24
20 25 0.74
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:762391 original size:27 final size:27
Alignment explanation
Indices: 762361--762414 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
762351 TGTTGGCTTT
* *
762361 ACCGAGCGGAGGGAAATCGTTGTTTCC
1 ACCGAGCGGAGGGAAATCATCGTTTCC
762388 ACCGAGCGGAGGGAAATCATCGTTTCC
1 ACCGAGCGGAGGGAAATCATCGTTTCC
762415 GAGGAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.20
Consensus pattern (27 bp):
ACCGAGCGGAGGGAAATCATCGTTTCC
Found at i:764990 original size:25 final size:25
Alignment explanation
Indices: 764956--765008 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
764946 TTACTAAAAG
**
764956 AATTAAAAAAATGATTAAAAATAAA
1 AATTAAAAAAATGACAAAAAATAAA
* * *
764981 AATTATAAAATTGACAAAAAATCAA
1 AATTAAAAAAATGACAAAAAATAAA
765006 AAT
1 AAT
765009 AACTAACGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
AATTAAAAAAATGACAAAAAATAAA
Found at i:766066 original size:18 final size:18
Alignment explanation
Indices: 766043--766095 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
766033 TCTTTTCTAT
766043 AATATTAATAAATAAATA
1 AATATTAATAAATAAATA
766061 AATATTAATAAGAATATAATA
1 AATATTAAT-A-AATA-AATA
*
766082 AATTTTAA-AAATAA
1 AATATTAATAAATAA
766096 TGAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 2 0.06
20 4 0.13
21 11 0.35
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATTAATAAATAAATA
Found at i:766083 original size:21 final size:19
Alignment explanation
Indices: 766043--766107 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
766033 TCTTTTCTAT
766043 AATATTAAT-AAATAAATA
1 AATATTAATAAAATAAATA
766061 AATATTAATAAGAATATAATA
1 AATATTAATAA-AATA-AATA
* *
766082 AATTTTAAAAATAATGAAATA
1 AATATTAATAA-AAT-AAATA
766103 AATAT
1 AATAT
766108 ATACTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 9 0.23
19 1 0.03
20 4 0.10
21 24 0.62
22 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AATATTAATAAAATAAATA
Found at i:766467 original size:34 final size:31
Alignment explanation
Indices: 766400--766460 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
766390 TATCGAAAGT
*
766400 AATAATAAAAATGAAATAAAAATTGTAAATA
1 AATAATAAAAATGAAATAAAAATTATAAATA
*
766431 AATAATGATAAAA-GAAATTAAAATTATAAA
1 AATAAT-A-AAAATGAAATAAAAATTATAAA
766461 ATTAAATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 16 0.62
33 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (31 bp):
AATAATAAAAATGAAATAAAAATTATAAATA
Found at i:772701 original size:762 final size:762
Alignment explanation
Indices: 771238--772761 Score: 3030
Period size: 762 Copynumber: 2.0 Consensus size: 762
771228 TGAGATGAGG
771238 CATCATGGATCAATTTATTGAAGATAATTTCGAGTGATTAAGGCATACTCAAAGAAGAAAAAAGT
1 CATCATGGATCAATTTATTGAAGATAATTTCGAGTGATTAAGGCATACTCAAAGAAGAAAAAAGT
*
771303 GATTAATTTAAATAAATATATCATGCATTAATTACATTGTTTTCATGTAAATGAAAGTTAATCTT
66 GATTAATTAAAATAAATATATCATGCATTAATTACATTGTTTTCATGTAAATGAAAGTTAATCTT
771368 GAATATTCATCCCCTGGAGATACCTCTTTTTACAAAGACTTCTATGTATGAGACGACTGAAATTT
131 GAATATTCATCCCCTGGAGATACCTCTTTTTACAAAGACTTCTATGTATGAGACGACTGAAATTT
771433 GTGCACAGTTTAAGCATGCAATCTCATTGACATATCGCCCAAAGATGAATGGGGCATTTGAAGAA
196 GTGCACAGTTTAAGCATGCAATCTCATTGACATATCGCCCAAAGATGAATGGGGCATTTGAAGAA
771498 GCAAATAAGAACGTTAAGAGGATCATTACAAAGACCACTAAAACTTACAAGGATTGGCACGAGAA
261 GCAAATAAGAACGTTAAGAGGATCATTACAAAGACCACTAAAACTTACAAGGATTGGCACGAGAA
771563 GCTACCTTCTGCCTTATATGCATATCGAAATACTGTTTGAACATCACTGGGGCAACACCTTATTG
326 GCTACCTTCTGCCTTATATGCATATCGAAATACTGTTTGAACATCACTGGGGCAACACCTTATTG
*
771628 TTCAGTCTTACCAATTTGAGATCCCACTACTTTTTATCTTGAAAAAGCTAAAATTAGAGGAGGCT
391 TTCAGTCTTACCAATTTGAAATCCCACTACTTTTTATCTTGAAAAAGCTAAAATTAGAGGAGGCT
771693 GAAGGGATCCAAGCTCGATTTGATCAATTAAACCTTATTGATAAGAAGAGATTGAAAGCTATTTA
456 GAAGGGATCCAAGCTCGATTTGATCAATTAAACCTTATTGATAAGAAGAGATTGAAAGCTATTTA
771758 CCATGGGTAGATGCATCAGAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCGTGAGAGT
521 CCATGGGTAGATGCATCAGAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCGTGAGAGT
771823 TCCAAGAGGGTGATCTAATCTTACCTATACATAAAGATTTCCGTGGGAAATGGATGCCTAATTAG
586 TCCAAGAGGGTGATCTAATCTTACCTATACATAAAGATTTCCGTGGGAAATGGATGCCTAATTAG
771888 GAATGGTCATATGTTGTAAAAAAGGGGACTTTTCCGGAGGAGCATTAGTTTTGGCAGAAATAGAT
651 GAATGGTCATATGTTGTAAAAAAGGGGACTTTTCCGGAGGAGCATTAGTTTTGGCAGAAATAGAT
771953 GAGAAAGTTCTAAGAAAACAAATAAACTCAGATTCTGTCAAGAAAAA
716 GAGAAAGTTCTAAGAAAACAAATAAACTCAGATTCTGTCAAGAAAAA
772000 CATCATGGATCAATTTATTGAAGATAATTTCGAGTGATTAAGGCATACTCAAAGAAGAAAAAAGT
1 CATCATGGATCAATTTATTGAAGATAATTTCGAGTGATTAAGGCATACTCAAAGAAGAAAAAAGT
772065 GATTAATTAAAATAAATATATCATGCATTAATTACATTGTTTTCATGTAAATGAAAGTTAATCTT
66 GATTAATTAAAATAAATATATCATGCATTAATTACATTGTTTTCATGTAAATGAAAGTTAATCTT
772130 GAATATTCATCCCCTGGAGATACCTCTTTTTACAAAGACTTCTATGTATGAGACGACTGAAATTT
131 GAATATTCATCCCCTGGAGATACCTCTTTTTACAAAGACTTCTATGTATGAGACGACTGAAATTT
772195 GTGCACAGTTTAAGCATGCAATCTCATTGACATATCGCCCAAAGATGAATGGGGCATTTGAAGAA
196 GTGCACAGTTTAAGCATGCAATCTCATTGACATATCGCCCAAAGATGAATGGGGCATTTGAAGAA
772260 GCAAATAAGAACGTTAAGAGGATCATTACAAAGACCACTAAAACTTACAAGGATTGGCACGAGAA
261 GCAAATAAGAACGTTAAGAGGATCATTACAAAGACCACTAAAACTTACAAGGATTGGCACGAGAA
772325 GCTACCTTCTGCCTTATATGCATATCGAAATACTGTTTGAACATCACTGGGGCAACACCTTATTG
326 GCTACCTTCTGCCTTATATGCATATCGAAATACTGTTTGAACATCACTGGGGCAACACCTTATTG
772390 TTCAGTCTTACCAATTTGAAATCCCACTACTTTTTATCTTGAAAAAGCTAAAATTAGAGGAGGCT
391 TTCAGTCTTACCAATTTGAAATCCCACTACTTTTTATCTTGAAAAAGCTAAAATTAGAGGAGGCT
772455 GAAGGGATCCAAGCTCGATTTGATCAATTAAACCTTATTGATAAGAAGAGATTGAAAGCTATTTA
456 GAAGGGATCCAAGCTCGATTTGATCAATTAAACCTTATTGATAAGAAGAGATTGAAAGCTATTTA
772520 CCATGGGTAGATGCATCAGAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCGTGAGAGT
521 CCATGGGTAGATGCATCAGAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCGTGAGAGT
772585 TCCAAGAGGGTGATCTAATCTTACCTATACATAAAGATTTCCGTGGGAAATGGATGCCTAATTAG
586 TCCAAGAGGGTGATCTAATCTTACCTATACATAAAGATTTCCGTGGGAAATGGATGCCTAATTAG
772650 GAATGGTCATATGTTGTAAAAAAGGGGACTTTTCCGGAGGAGCATTAGTTTTGGCAGAAATAGAT
651 GAATGGTCATATGTTGTAAAAAAGGGGACTTTTCCGGAGGAGCATTAGTTTTGGCAGAAATAGAT
772715 GAGAAAGTTCTAAGAAAACAAATAAACTCAGATTCTGTCAAGAAAAA
716 GAGAAAGTTCTAAGAAAACAAATAAACTCAGATTCTGTCAAGAAAAA
772762 TTATACTTGA
Statistics
Matches: 760, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
762 760 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (762 bp):
CATCATGGATCAATTTATTGAAGATAATTTCGAGTGATTAAGGCATACTCAAAGAAGAAAAAAGT
GATTAATTAAAATAAATATATCATGCATTAATTACATTGTTTTCATGTAAATGAAAGTTAATCTT
GAATATTCATCCCCTGGAGATACCTCTTTTTACAAAGACTTCTATGTATGAGACGACTGAAATTT
GTGCACAGTTTAAGCATGCAATCTCATTGACATATCGCCCAAAGATGAATGGGGCATTTGAAGAA
GCAAATAAGAACGTTAAGAGGATCATTACAAAGACCACTAAAACTTACAAGGATTGGCACGAGAA
GCTACCTTCTGCCTTATATGCATATCGAAATACTGTTTGAACATCACTGGGGCAACACCTTATTG
TTCAGTCTTACCAATTTGAAATCCCACTACTTTTTATCTTGAAAAAGCTAAAATTAGAGGAGGCT
GAAGGGATCCAAGCTCGATTTGATCAATTAAACCTTATTGATAAGAAGAGATTGAAAGCTATTTA
CCATGGGTAGATGCATCAGAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCGTGAGAGT
TCCAAGAGGGTGATCTAATCTTACCTATACATAAAGATTTCCGTGGGAAATGGATGCCTAATTAG
GAATGGTCATATGTTGTAAAAAAGGGGACTTTTCCGGAGGAGCATTAGTTTTGGCAGAAATAGAT
GAGAAAGTTCTAAGAAAACAAATAAACTCAGATTCTGTCAAGAAAAA
Found at i:772811 original size:18 final size:18
Alignment explanation
Indices: 772778--772842 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
772768 TTGAAGAAGA
*
772778 AGAAAAAAAG-AGAAAAG
1 AGAAAAAAAGAAAAAAAG
* * *
772795 AGAAAACAGGAAAAAAAA
1 AGAAAAAAAGAAAAAAAG
772813 AGAAAAAAAGAAAAAAAG
1 AGAAAAAAAGAAAAAAAG
772831 TAAGAAAAAAAG
1 --AGAAAAAAAG
772843 TAAGGAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 8 0.21
18 20 0.53
20 10 0.26
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (18 bp):
AGAAAAAAAGAAAAAAAG
Found at i:772821 original size:28 final size:27
Alignment explanation
Indices: 772776--772842 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
772766 ACTTGAAGAA
* *
772776 GAAGAAAAAAAGAGAAAAGAGAAAACAG
1 GAAGAAAAAAAGAAAAAAGA-AAAAAAG
772804 GAA-AAAAAAAGAAAAAAAGAAAAAAAG
1 GAAGAAAAAAAG-AAAAAAGAAAAAAAG
*
772831 TAAGAAAAAAAG
1 GAAGAAAAAAAG
772843 TAAGGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (27 bp):
GAAGAAAAAAAGAAAAAAGAAAAAAAG
Found at i:772827 original size:27 final size:28
Alignment explanation
Indices: 772776--772842 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
772766 ACTTGAAGAA
* *
772776 GAAGAAAAAAAGAGAAAAGAGAAAACAG
1 GAAGAAAAAAAGAAAAAAGAGAAAAAAG
772804 GAA-AAAAAAAGAAAAAA-AGAAAAAAAG
1 GAAGAAAAAAAGAAAAAAGAG-AAAAAAG
*
772831 TAAGAAAAAAAG
1 GAAGAAAAAAAG
772843 TAAGGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.06
27 21 0.62
28 11 0.32
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (28 bp):
GAAGAAAAAAAGAAAAAAGAGAAAAAAG
Found at i:772828 original size:8 final size:8
Alignment explanation
Indices: 772777--772861 Score: 57
Period size: 8 Copynumber: 10.0 Consensus size: 8
772767 CTTGAAGAAG
772777 AAGAAAAA
1 AAGAAAAA
772785 AAGAGAAAA
1 AAGA-AAAA
*
772794 GAGAAAACA
1 AAGAAAA-A
772803 GGAA-AAAAA
1 --AAGAAAAA
772812 AAGAAAAA
1 AAGAAAAA
772820 AAGAAAAA
1 AAGAAAAA
772828 AAGTAAGAAA
1 AAG-AA-AAA
**
772838 AA-AAGTA
1 AAGAAAAA
*
772845 AGGAAAAAA
1 AAG-AAAAA
772854 AAGAAAAA
1 AAGAAAAA
772862 TTGAATCAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
7 4 0.07
8 30 0.50
9 16 0.27
10 9 0.15
11 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:773352 original size:32 final size:32
Alignment explanation
Indices: 773312--773378 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
773302 AGAGTCTGGA
* *
773312 AACAAGAAGTATCTCTACGAGATGAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
773344 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
773376 AAC
1 AAC
773379 CATTTATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (32 bp):
AACAAGAAGTATCTCTACCAGATAAGCATAAC
Found at i:774917 original size:3 final size:3
Alignment explanation
Indices: 774909--774943 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
774899 TTATTTATTA
**
774909 AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
774944 AACGAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:775264 original size:45 final size:45
Alignment explanation
Indices: 775200--775572 Score: 521
Period size: 45 Copynumber: 8.3 Consensus size: 45
775190 TAAAATCTCA
* * * ** *
775200 TTTGAAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
775245 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
775290 TTTGAAAACATCAAGCACTGAAGAACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
*
775335 TTTGAAAACATCACGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
775380 TTTGAAAACATCATGCACTGAAAGACATACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
775425 TTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
775470 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* * * * * *
775515 TTTGTAAACATCATGTACTGTAGGGCTTACAGATGACCCAAAGGC
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
*
775560 TTTGAAAATATCA
1 TTTGAAAACATCA
775573 AAAAGCTCCC
Statistics
Matches: 296, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 296 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
Found at i:775640 original size:76 final size:74
Alignment explanation
Indices: 775506--775648 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 74
775496 TTACAGATGA
* * *
775506 CCCGAAGGTTTTGTAAACATCATGTACTGTAGGGCTTACAGATGACCCAAAGGCTTTGAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGGCTTACAGATGACCCAAAGGCTTTGAAAACAT
775571 CAAAAAGCT
66 CAAAAAGCT
* * *
775580 CCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGGCTTACAGATGACCCAAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGGCTTACAGATGACCCAAAGGCTTTGAAAAC
775645 ATCA
64 ATCA
775649 TGCACTGAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.13
76 53 0.87
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGGCTTACAGATGACCCAAAGGCTTTGAAAACAT
CAAAAAGCT
Found at i:775661 original size:45 final size:45
Alignment explanation
Indices: 775590--775714 Score: 196
Period size: 45 Copynumber: 2.8 Consensus size: 45
775580 CCCGAAGGCT
* * *
775590 TTTTGAAAACATCCTGCATTGTAGGGCTTACAGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
*
775635 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
* *
775680 TTTTGAAAACATCATGCACTAAAGCGCTTACAGAT
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
775715 ATGGGAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
Found at i:775685 original size:121 final size:121
Alignment explanation
Indices: 775469--775693 Score: 351
Period size: 121 Copynumber: 1.9 Consensus size: 121
775459 GACCTGAAGG
* * *
775469 TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGTAAACATCATGTACT
1 TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACT
* *
775534 GTAGGGCTTACAGATGACCCAAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCT
66 GAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* * * *
775590 TTTTGAAAACATCCTGCATTGTAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACT
* *
775655 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
66 GAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCA
775694 TGCACTAAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
121 93 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (121 bp):
TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACT
GAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
Found at i:775711 original size:166 final size:164
Alignment explanation
Indices: 775416--775714 Score: 472
Period size: 166 Copynumber: 1.8 Consensus size: 164
775406 ATACAGATGA
**
775416 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACAT
1 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACAT
* * ** *
775481 CATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGTAAACATCATGTACTGTAGGGCTTACA
66 CATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGCGCTTACA
775546 GATGACCCAAAGGCTTTGAAAATATCAAAAAGCT
131 GATGACCCAAAGGCTTTGAAAATATCAAAAAGCT
* * * *
775580 CCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGGCTTACAGATGACCCAAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAAC
*
775645 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGCGCTTA
64 ATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGCGCTTA
775710 CAGAT
129 CAGAT
775715 ATGGGAAATA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
164 8 0.07
166 113 0.93
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (164 bp):
CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACAT
CATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGCGCTTACA
GATGACCCAAAGGCTTTGAAAATATCAAAAAGCT
Found at i:776348 original size:22 final size:22
Alignment explanation
Indices: 776323--776401 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
776313 AATAAGGCTT
*
776323 TCATATTTGAAAAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
776345 TCATCTTTGAAGAGAGAATCTA
1 TCATATTTGAAGAGAGAATCTA
* *
776367 CCATATTTGAAGAGTGAATCTA
1 TCATATTTGAAGAGAGAATCTA
*
776389 TCATCTTTGAAGA
1 TCATATTTGAAGA
776402 ATGTAGATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATATTTGAAGAGAGAATCTA
Found at i:777922 original size:75 final size:72
Alignment explanation
Indices: 777733--777966 Score: 212
Period size: 75 Copynumber: 3.2 Consensus size: 72
777723 CATGATGATG
* * *
777733 TGGGCCTTCAGCATGCCCCAAT-ATTTGTTGATATGAACGTTCAAAAT--G-TTATTCCAATTTC
1 TGGGCTTTCAGCATGCCCC-ATCATTTGTTGA-CTGAACGTTCAAAATGCGCATATTCCAATTTC
777794 TGATTGAAA
64 TGATTGAAA
* * * *
777803 TGGGCTTTCAGCATACCCCAGCATTTGCTAAT-ACAG-ACGGTCAAAATGCGCCAATATTCCAAT
1 TGGGCTTTCAGCATGCCCCATCATTTG-T--TGACTGAACGTTCAAAATGCG-C-ATATTCCAAT
777866 TTCTGATTGAAA
61 TTCTGATTGAAA
* *
777878 TGGGCTTTCAGCATGCCCCATCATTTGTTGACGTGAACATTCAAAATGCGTCGATATTCCTGA-T
1 TGGGCTTTCAGCATGCCCCATCATTTGTTGAC-TGAACGTTCAAAATGCG-C-ATATTCC-AATT
* *
777942 TATGATTAAAA
62 TCTGATTGAAA
*
777953 TGGACTTTCAGCAT
1 TGGGCTTTCAGCAT
777967 ACCTTAACAT
Statistics
Matches: 133, Mismatches: 18, Indels: 21
0.77 0.10 0.12
Matches are distributed among these distances:
69 1 0.01
70 32 0.24
71 2 0.02
72 3 0.02
73 3 0.02
74 2 0.02
75 89 0.67
76 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (72 bp):
TGGGCTTTCAGCATGCCCCATCATTTGTTGACTGAACGTTCAAAATGCGCATATTCCAATTTCTG
ATTGAAA
Found at i:779548 original size:2 final size:2
Alignment explanation
Indices: 779537--779565 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
779527 TCTAAAGAAA
779537 AT AT -T 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
779566 TAGGATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:780595 original size:22 final size:22
Alignment explanation
Indices: 780570--780632 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
780560 TCTTCGGCCG
780570 GCCACCGCCAGTCACTATTCCA
1 GCCACCGCCAGTCACTATTCCA
* * *
780592 GCCACCGCTA-TTACTATTCCG
1 GCCACCGCCAGTCACTATTCCA
*
780613 GCCACCACC-GATCACTATTC
1 GCCACCGCCAG-TCACTATTC
780633 ACGGTGGCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.22, C:0.43, G:0.13, T:0.22
Consensus pattern (22 bp):
GCCACCGCCAGTCACTATTCCA
Found at i:781317 original size:3 final size:3
Alignment explanation
Indices: 781309--781349 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
781299 TTATTTATTA
**
781309 AAT AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
781350 AACGAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:782209 original size:3 final size:3
Alignment explanation
Indices: 782201--782267 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
782191 TCATATTAAT
782201 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
782249 GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA G
782268 TGAAAATACC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:782768 original size:50 final size:50
Alignment explanation
Indices: 782674--782774 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
782664 TTAAAATGTT
** *
782674 TGTTAAATCTAACAATATTAAATGATGATGTAATAAAATTCGTAATTTTA
1 TGTTAAATCTAACAATATTAAATGATGATGTAATAAAACACGTAATATTA
*
782724 TGTTAAATCTAACAATGTTAAATGATGATGTAATAAAACACGTAATATTA
1 TGTTAAATCTAACAATATTAAATGATGATGTAATAAAACACGTAATATTA
782774 T
1 T
782775 TTTATATGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (50 bp):
TGTTAAATCTAACAATATTAAATGATGATGTAATAAAACACGTAATATTA
Found at i:783883 original size:24 final size:24
Alignment explanation
Indices: 783851--783903 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
783841 AAGTGGTACT
783851 GATACTACTTTACATAGTAGTATC
1 GATACTACTTTACATAGTAGTATC
783875 GATACTACTTTACATAGTAGTATC
1 GATACTACTTTACATAGTAGTATC
783899 GATAC
1 GATAC
783904 CATAGGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (24 bp):
GATACTACTTTACATAGTAGTATC
Found at i:786561 original size:131 final size:131
Alignment explanation
Indices: 786324--786576 Score: 373
Period size: 131 Copynumber: 1.9 Consensus size: 131
786314 TGAATTTTAG
* * **
786324 GAGAGAAAACGATAACATCTAATTATTTCCAATCGAGAATAAATGACCCCTCATGCCTTAAAACA
1 GAGAGAAAACGATAACATCTAATTATTTACAATCGAAAATAAAAAACCCCTCATGCCTTAAAACA
* *
786389 ATCATTTATTACTCCAATCGAAATGAGGAGATATTATTATTTCGTCCTAAAATTCAATATTGATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCGTCCTAAAATTCAATATTGATT
786454 A
131 A
** * *
786455 GAGAGAAAACGATATTATCTAATTATTTACAATCGAAAATAAAAAACCTCTCATGCCTTAAAGC-
1 GAGAGAAAACGATAACATCTAATTATTTACAATCGAAAATAAAAAACCCCTCATGCCTTAAAACA
* * *
786519 ATCCATTTATTATTCCGATCGAAATGAAGATATATTACTATTTCGTCCTAAAATTCAA
66 AT-CATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCGTCCTAAAATTCAA
786577 AATTAATCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
130 2 0.02
131 106 0.98
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAACATCTAATTATTTACAATCGAAAATAAAAAACCCCTCATGCCTTAAAACA
ATCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCGTCCTAAAATTCAATATTGATT
A
Found at i:787077 original size:24 final size:24
Alignment explanation
Indices: 787031--787080 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
787021 TGACTAAAAT
* *
787031 AAAATAACATAAAAGCAACATGCA
1 AAAATAAAATAAAAGCAAAATGCA
787055 AAAATTAAAATAAAA-CAAAATGCA
1 AAAA-TAAAATAAAAGCAAAATGCA
787079 AA
1 AA
787081 TAGACTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.68, C:0.12, G:0.06, T:0.14
Consensus pattern (24 bp):
AAAATAAAATAAAAGCAAAATGCA
Found at i:788560 original size:3 final size:3
Alignment explanation
Indices: 788539--788620 Score: 58
Period size: 3 Copynumber: 27.3 Consensus size: 3
788529 ATGAAAACAA
* * * * *
788539 AAT AAA AAT -AT ATAT AAT AAT AAT AAT ATT ATT AAT AAT AAC GAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
788584 AAT AAT AAT ATT ATT ATT ACT AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
788621 TCCCGAACAA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:788566 original size:18 final size:17
Alignment explanation
Indices: 788539--788614 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 17
788529 ATGAAAACAA
*
788539 AATAAAAATATATATAAT
1 AATAATAATAT-TATAAT
788557 AATAATAATATTAT--T
1 AATAATAATATTATAAT
* *
788572 AATAATAACGATAATAAT
1 AATAATAA-TATTATAAT
* *
788590 AATATTATTATTACTAAT
1 AATAATAATATTA-TAAT
788608 AATAATA
1 AATAATA
788615 GTAATATCCC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
15 9 0.20
16 4 0.09
17 6 0.13
18 27 0.59
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
AATAATAATATTATAAT
Found at i:788575 original size:27 final size:27
Alignment explanation
Indices: 788545--788621 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
788535 ACAAAATAAA
788545 AATATATATAATAATAATAATATTATT
1 AATATATATAATAATAATAATATTATT
788572 AATA-ATA-ACGATAATAATAATATTATT
1 AATATATATA--ATAATAATAATATTATT
* *
788599 ATTACTA-ATAATAATAGTAATAT
1 AATA-TATATAATAATAATAATAT
788622 CCCGAACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 36 0.84
28 1 0.02
29 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (27 bp):
AATATATATAATAATAATAATATTATT
Found at i:788588 original size:30 final size:30
Alignment explanation
Indices: 788552--788609 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
788542 AAAAATATAT
788552 ATAATAATAATAATATTATTAATAATAACG
1 ATAATAATAATAATATTATTAATAATAACG
* *
788582 ATAATAATAATATTATTATTACTAATAA
1 ATAATAATAATAATATTATTAATAATAA
788610 TAATAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
ATAATAATAATAATATTATTAATAATAACG
Found at i:789859 original size:131 final size:131
Alignment explanation
Indices: 789669--789921 Score: 346
Period size: 131 Copynumber: 1.9 Consensus size: 131
789659 TGAATTTTAG
* * * *
789669 GAGAGAAAGCGATAACATCTAATTATTTTCAATCGATAATAAATGACCTCTCATACCTTAAAGCA
1 GAGAGAAAACGATAACATCTAATTATTTTCAATCGAGAATAAAAGAACTCTCATACCTTAAAGCA
* *** **
789734 ATCATTTATTACTCCAATCAAAATTTGGAGATATTACTATTTTGTCCTAAAATTCAATATTGATT
66 ATCATTTATTACTCAAATCAAAATGAAGAGATATTACTATTCCGTCCTAAAATTCAATATTGATT
789799 C
131 C
* *
789800 GAGAGAAAACGATAATATCTAATTA-TTTCTAATCGAGAATAAAAGAACTCTCATGCCTTAAAGC
1 GAGAGAAAACGATAACATCTAATTATTTTC-AATCGAGAATAAAAGAACTCTCATACCTTAAAGC
** * *
789864 GGTCATTTATTATTCAAATCGAAATGAAGAGATATTACTATTCCGTCCTAAAATTCAA
65 AATCATTTATTACTCAAATCAAAATGAAGAGATATTACTATTCCGTCCTAAAATTCAA
789922 AATTAATCAT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
130 4 0.04
131 101 0.96
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAACATCTAATTATTTTCAATCGAGAATAAAAGAACTCTCATACCTTAAAGCA
ATCATTTATTACTCAAATCAAAATGAAGAGATATTACTATTCCGTCCTAAAATTCAATATTGATT
C
Found at i:790429 original size:24 final size:24
Alignment explanation
Indices: 790380--790429 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
790370 TGACTAAAAT
* *
790380 AAAATAACATAAAAGCAACATACA
1 AAAATAAAATAAAAGCAAAATACA
*
790404 AAAATTAAAATAAAA-CAAAATGCA
1 AAAA-TAAAATAAAAGCAAAATACA
790428 AA
1 AA
790430 TAGGACTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.70, C:0.12, G:0.04, T:0.14
Consensus pattern (24 bp):
AAAATAAAATAAAAGCAAAATACA
Found at i:792651 original size:20 final size:20
Alignment explanation
Indices: 792626--792667 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
792616 CTTTTTATAC
792626 ATTTATAAAATAATTATAAA
1 ATTTATAAAATAATTATAAA
** *
792646 ATTTATTCAATTATTATAAA
1 ATTTATAAAATAATTATAAA
792666 AT
1 AT
792668 AATATTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATAAAATAATTATAAA
Found at i:797982 original size:2 final size:2
Alignment explanation
Indices: 797975--798013 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
797965 TCTTCCTATT
*
797975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
798014 CCTTGTATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:803080 original size:22 final size:21
Alignment explanation
Indices: 803032--803090 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
803022 ATGAATTAAT
803032 AAAATTTTAAAAATAATAAAA
1 AAAATTTTAAAAATAATAAAA
*
803053 ATAAATTATTAATAAA-AATATAA
1 A-AAATT-TTAA-AAATAATAAAA
803076 AAAATTCTTAAAAAT
1 AAAATT-TTAAAAAT
803091 CTCGATCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 4 0.12
22 14 0.44
23 11 0.34
24 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTTTAAAAATAATAAAA
Found at i:803617 original size:68 final size:68
Alignment explanation
Indices: 803482--803643 Score: 251
Period size: 68 Copynumber: 2.4 Consensus size: 68
803472 AATTATTATT
803482 TAATTATAATTCTATTAAAATTATAA----TAAATTTTAACAAATAATAAATTTTAAATAAATCC
1 TAATTATAATTCTATTAAAATTATAATTTTTAAATTTTAACAAATAATAAATTTTAAATAAATCC
*
803543 TTA
66 ATA
* * *
803546 TAATTATAATTCTATTAAAATTATAATTTTTAAATTTTAATAAATGATTAATTTTAAATAAATCC
1 TAATTATAATTCTATTAAAATTATAATTTTTAAATTTTAACAAATAATAAATTTTAAATAAATCC
803611 ATA
66 ATA
*
803614 TAATTATAATTCTATTAAAATTATAGTTTT
1 TAATTATAATTCTATTAAAATTATAATTTT
803644 AATATATACG
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
64 26 0.29
68 63 0.71
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (68 bp):
TAATTATAATTCTATTAAAATTATAATTTTTAAATTTTAACAAATAATAAATTTTAAATAAATCC
ATA
Found at i:805719 original size:2 final size:2
Alignment explanation
Indices: 805712--805745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
805702 GGAAAGGTCC
805712 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
805746 GTGATGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:806062 original size:23 final size:23
Alignment explanation
Indices: 806012--806062 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
806002 AAACCTGTTT
* **
806012 ATTTTGTTGTAGTGTAACAACCT
1 ATTTTGCTGTAGTGTAACAACAA
* *
806035 GTTTTGCTGTAGTGTAACAAGAA
1 ATTTTGCTGTAGTGTAACAACAA
806058 ATTTT
1 ATTTT
806063 CAAAATTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (23 bp):
ATTTTGCTGTAGTGTAACAACAA
Found at i:812532 original size:28 final size:29
Alignment explanation
Indices: 812475--812538 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
812465 ATTTATACTT
* *
812475 ATATATATAATATGTATAATCATGATTAC-
1 ATATA-ATAATATGCATAATCATGAATACA
*
812504 ATATAATAATATGCATAATTA-GTAATACA
1 ATATAATAATATGCATAATCATG-AATACA
812533 ATATAA
1 ATATAA
812539 ACCCAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 18 0.60
29 11 0.37
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (29 bp):
ATATAATAATATGCATAATCATGAATACA
Found at i:812802 original size:55 final size:54
Alignment explanation
Indices: 812743--813157 Score: 351
Period size: 55 Copynumber: 7.6 Consensus size: 54
812733 TGTCCACTCT
* * *
812743 CTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCC
1 CTATTC-TTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTCTGCTCC
* * * * * *
812798 CTATTCGTTCAGGAAGTATA-AGACTCGACCAATCTTCAACAAACGTGTCTTCTCT
1 CTATTC-TTCAGGGAGTATAGA-ACTCGAACAATCTTCATCAAACGGGTCTGCTCC
** * * *
812853 CTATTCACGCAGAGAGTATA-AGACTCGAATAATTTTCAAT-AAACGGGTCTGCTCC
1 CTATTC-TTCAGGGAGTATAGA-ACTCGAACAATCTTC-ATCAAACGGGTCTGCTCC
* *
812908 CTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCTTCGAACGGGT-TCGCTCC
1 CTATTC-TTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTCT-GCTCC
* ** *
812963 CTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTTTTCCAACGGGT-TCGCTCC
1 CTATT-CTTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTCT-GCTCC
* * * *
813018 CTCTTACTACAGGGAGTATAGAACTCGAACAATCTTCTTCGAACGGGT-TCGCTCC
1 CTATT-CTTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTCT-GCTCC
* * ** **
813073 CTCTTGCTTCAGGAAGTATAGAACTCGAAC-ATCTTTTTCTTACGGGT-TCGCTCC
1 CTATT-CTTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTCT-GCTCC
* *
813127 CTCTTTCTTCAGGGAGTATAGAACTTGAACA
1 CT-ATTCTTCAGGGAGTATAGAACTCGAACA
813158 TTTTCTTATG
Statistics
Matches: 309, Mismatches: 43, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
54 47 0.15
55 259 0.84
56 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (54 bp):
CTATTCTTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTCTGCTCC
Found at i:813654 original size:37 final size:37
Alignment explanation
Indices: 813553--813666 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
813543 ATTCTTCCGA
* * *
813553 GAAGGCTTAAAAAGGATATGCTTCACTACTATTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
*
813590 GAAGGCTTAAGATGG-TTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
*
813626 GAAGGCTCAAAATGGATTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
813663 GAAG
1 GAAG
813667 ACTTGGCTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
36 32 0.46
37 38 0.54
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (37 bp):
GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
Found at i:814944 original size:16 final size:16
Alignment explanation
Indices: 814919--814959 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
814909 CTCACATTCT
*
814919 AGTGTCGCTACACAAC
1 AGTGTAGCTACACAAC
814935 AGTGTAGCTACACAAC
1 AGTGTAGCTACACAAC
*
814951 AATGTAGCT
1 AGTGTAGCT
814960 GAATATCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (16 bp):
AGTGTAGCTACACAAC
Found at i:818675 original size:55 final size:55
Alignment explanation
Indices: 818588--818718 Score: 181
Period size: 55 Copynumber: 2.4 Consensus size: 55
818578 AACAACTTCA
* * * * *
818588 GGATGTCTTTTTTTATGGATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATC
1 GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
* *
818643 GGATGTCCTTCTTCATGAATCGTTCTTCAATCAGGTTCAAATTTCTTCATTCGTC
1 GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
* *
818698 GAATGTTCTTCTTCATGAATC
1 GGATGTCCTTCTTCATGAATC
818719 ATCTGAATGC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (55 bp):
GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
Found at i:820649 original size:20 final size:20
Alignment explanation
Indices: 820624--820663 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
820614 CATTATGACT
*
820624 TATACATACA-TATATATATA
1 TATACACACACTA-ATATATA
820644 TATACACACACTAATATATA
1 TATACACACACTAATATATA
820664 ATGTACGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (20 bp):
TATACACACACTAATATATA
Found at i:822518 original size:28 final size:29
Alignment explanation
Indices: 822461--822524 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
822451 ATTTATACTT
*
822461 ATATATATAATATGTATAATCATAATTAC-
1 ATATA-ATAATATGCATAATCATAATTACA
*
822490 ATATAATAATATGCATAATTAGTAA-TACA
1 ATATAATAATATGCATAATCA-TAATTACA
822519 ATATAA
1 ATATAA
822525 ACCCAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (29 bp):
ATATAATAATATGCATAATCATAATTACA
Found at i:826224 original size:18 final size:19
Alignment explanation
Indices: 826185--826224 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
826175 CCCTTTGAAT
*
826185 GGGAACCGATTCCCCCTAG
1 GGGAACCGATACCCCCTAG
*
826204 GGGAATCGATACCCCCT-G
1 GGGAACCGATACCCCCTAG
826222 GGG
1 GGG
826225 TTTTGGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.15
Consensus pattern (19 bp):
GGGAACCGATACCCCCTAG
Found at i:828010 original size:15 final size:15
Alignment explanation
Indices: 827990--828021 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
827980 AAGCGTTTTA
*
827990 AAGAGGAGTATTGTT
1 AAGAGGAGTAGTGTT
828005 AAGAGGAGTAGTGTT
1 AAGAGGAGTAGTGTT
828020 AA
1 AA
828022 AGTAAGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (15 bp):
AAGAGGAGTAGTGTT
Found at i:838533 original size:40 final size:40
Alignment explanation
Indices: 838445--838697 Score: 191
Period size: 40 Copynumber: 6.3 Consensus size: 40
838435 AAATGACCAA
* * * **
838445 CAAATTCGCAACGCGA-ACGCCAATTTCGCAACCCAG-TTT
1 CAAATTCGCAACGCGATA-GTCAAATTCGCAACACAGAAGT
* *
838484 CCAATTTCGCAACGCGAATATGT-AAA-TCGTAACACAGAAGT
1 -CAAATTCGCAACGCG-ATA-GTCAAATTCGCAACACAGAAGT
*
838525 CAAATTCGCAACGCGATAGTCAAATTCGCAACGC-GAA-T
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGT
* *
838563 CTGTAAA-TCGCAACGTGAATTTGT-AAA-TCGCAACACAGAAGT
1 C---AAATTCGCAACGCG-A-TAGTCAAATTCGCAACACAGAAGT
*
838605 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGT
* * * * * * *
838645 CAAATTCGCAACACAAAAGTCAAATTTGCAACGCGGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAA-GT
838686 CAAATTCGCAAC
1 CAAATTCGCAAC
838698 TGAATTTCAA
Statistics
Matches: 172, Mismatches: 25, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
38 7 0.04
39 16 0.09
40 115 0.67
41 27 0.16
42 7 0.04
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGT
Found at i:838547 original size:20 final size:20
Alignment explanation
Indices: 838522--838697 Score: 139
Period size: 20 Copynumber: 8.8 Consensus size: 20
838512 GTAACACAGA
838522 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
838542 AGTCAAATTCGCAACGCGAAT
1 AGTCAAATTCGCAACGCG-AT
* *
838563 CTGT-AAA-TCGCAACGTGAATT
1 -AGTCAAATTCGCAACGCG-A-T
* *
838584 TGT-AAA-TCGCAACACAGA-
1 AGTCAAATTCGCAACGC-GAT
838602 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * *
838622 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
* * *
838642 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
*
838662 AGTCAAATTTGCAACGCGGA-
1 AGTCAAATTCGCAACGC-GAT
*
838682 ATTTCAAATTCGCAAC
1 A-GTCAAATTCGCAAC
838698 TGAATTTCAA
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
18 2 0.02
19 5 0.04
20 104 0.78
21 20 0.15
22 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:838654 original size:80 final size:81
Alignment explanation
Indices: 838489--838656 Score: 252
Period size: 80 Copynumber: 2.1 Consensus size: 81
838479 AGTTTCCAAT
*
838489 TTCGCAACGCGAATATGTAAATCGTAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
* **
838554 AACGCGAATCTGTAAA
66 AACACGAATAAGTAAA
* *
838570 -TCGCAACGTGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
1 TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
838634 AACAC-AA-AAGTCAAA
66 AACACGAATAAGT-AAA
838649 TTCGCAAC
1 TTCGCAAC
838657 ACAAAAGTCA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
78 2 0.03
79 5 0.06
80 72 0.91
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (81 bp):
TTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
AACACGAATAAGTAAA
Found at i:838708 original size:60 final size:61
Alignment explanation
Indices: 838489--838776 Score: 224
Period size: 60 Copynumber: 4.8 Consensus size: 61
838479 AGTTTCCAAT
* * * * * *
838489 TTCGCAACGCGAATATGT-AAA-TCGTAACACAGAA-GTCAAATTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAATAT-TCAAATTCGCAACA-TGAATTTCAAATTCGCAACACAAAAGTCAAA
* * * *
838549 TTCGCAACGCGAATCTGT-AAA-TCGCAACGTGAATTTGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAATAT-TCAAATTCGCAACATGAATTT-CAAATTCGCAACACAAAAGTCAAA
* ** **
838609 TTCGCAACGCG-ATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATATTCAAATTCGCAACATGAATTTCAAATTCGCAACACAAAAGTCAAA
* ** **
838669 TTTGCAACGCGGAAT-TTCAAATTCGCAAC-TGAATTTCAAATTCGCAAC-TGAATTTCAAA
1 TTCGCAACGC-GAATATTCAAATTCGCAACATGAATTTCAAATTCGCAACACAAAAGTCAAA
* * *
838728 TTCGTAAC-TGAAT-TTCAAATTCGCAAC-TAGATTTTCAAATTCGCAACAC
1 TTCGCAACGCGAATATTCAAATTCGCAACAT-GAATTTCAAATTCGCAACAC
838777 GAATTTAATT
Statistics
Matches: 185, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
57 19 0.10
58 18 0.10
59 24 0.13
60 105 0.57
61 17 0.09
62 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (61 bp):
TTCGCAACGCGAATATTCAAATTCGCAACATGAATTTCAAATTCGCAACACAAAAGTCAAA
Found at i:838809 original size:58 final size:57
Alignment explanation
Indices: 838524--838812 Score: 180
Period size: 60 Copynumber: 4.9 Consensus size: 57
838514 AACACAGAAG
* *
838524 TCAAATTCGCAACGCG-ATAGTCAAATTCGCAACGCGAATCTGT-AAA-TCGCAACGTGAATT
1 TCAAATTCGCAAC-CGAAT-TTCAAATTCGCAAC-TGAAT-T-TCAAATTCGCAAC-TGAATT
* * * * ** **
838584 TGTAAA-TCGCAACACAGAA-GTCAAATTCGCAAC-GCGATAGTCAAATTCGCAACACAAAAG
1 T-CAAATTCGCAAC-C-GAATTTCAAATTCGCAACTG-AAT-TTCAAATTCGCAAC-TGAATT
* ** * *
838644 TCAAATTCGCAACACAAAAGTCAAATTTGCAACGCGGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAAC-CGAATTTCAAATTCGCAA--CTGAATTTCAAATTCGCAACTGAATT
* * *
838704 TCAAATTCGCAACTGAATTTCAAATTCGTAACTGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACCGAATTTCAAATTCGCAACTGAATTTCAAATTCGCAACT-GAATT
* *
838762 TCAAATTCGCAACACGAATTT-AATTTCGCAACATGAATTT-AATTTCGCAAC
1 TCAAATTCGCAAC-CGAATTTCAAATTCGCAAC-TGAATTTCAAATTCGCAAC
838813 AGGTTTTAGT
Statistics
Matches: 184, Mismatches: 31, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
57 20 0.11
58 38 0.21
59 35 0.19
60 69 0.38
61 17 0.09
62 4 0.02
63 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (57 bp):
TCAAATTCGCAACCGAATTTCAAATTCGCAACTGAATTTCAAATTCGCAACTGAATT
Found at i:838813 original size:19 final size:19
Alignment explanation
Indices: 838680--838812 Score: 180
Period size: 19 Copynumber: 6.9 Consensus size: 19
838670 TTGCAACGCG
838680 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
838699 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
*
838718 GAATTTCAAATTCGTAACT
1 GAATTTCAAATTCGCAACT
838737 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* *
838756 AGATTTTCAAATTCGCAACAC
1 -GAATTTCAAATTCGCAAC-T
*
838777 GAATTT-AATTTCGCAACAT
1 GAATTTCAAATTCGCAAC-T
*
838796 GAATTT-AATTTCGCAAC
1 GAATTTCAAATTCGCAAC
838813 AGGTTTTAGT
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
19 83 0.79
20 22 0.21
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:838825 original size:18 final size:19
Alignment explanation
Indices: 838680--838831 Score: 116
Period size: 19 Copynumber: 7.9 Consensus size: 19
838670 TTGCAACGCG
*
838680 GAATTTCAAATTCGCAAC-T
1 GAATTT-AATTTCGCAACAT
*
838699 GAATTTCAAATTCGCAAC-T
1 GAATTT-AATTTCGCAACAT
* *
838718 GAATTTCAAATTCGTAAC-T
1 GAATTT-AATTTCGCAACAT
*
838737 GAATTTCAAATTCGCAAC-T
1 GAATTT-AATTTCGCAACAT
* * *
838756 AGATTTTCAAATTCGCAACAC
1 -GAATTT-AATTTCGCAACAT
838777 GAATTTAATTTCGCAACAT
1 GAATTTAATTTCGCAACAT
838796 GAATTTAATTTCGCAACA-
1 GAATTTAATTTCGCAACAT
** *
838814 GGTTTTAGTTTCGCAACA
1 GAATTTAATTTCGCAACA
838832 CAAATGTTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.12
19 84 0.69
20 22 0.18
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (19 bp):
GAATTTAATTTCGCAACAT
Found at i:838991 original size:14 final size:15
Alignment explanation
Indices: 838972--839009 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
838962 TCCCCATCTC
838972 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
838986 TAATTTTGTTTCTATA
1 TAATTTT-TTTCTACA
839002 TAATTTTT
1 TAATTTTT
839010 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:839625 original size:12 final size:12
Alignment explanation
Indices: 839604--839637 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
839594 ACCACATTTC
*
839604 CAATACCAAACA
1 CAATATCAAACA
839616 CAATATCAAACA
1 CAATATCAAACA
*
839628 CAATCTCAAA
1 CAATATCAAA
839638 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:842080 original size:18 final size:18
Alignment explanation
Indices: 842057--842092 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
842047 AAGCAAAAGG
842057 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
842075 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
842093 CAACCGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:842499 original size:34 final size:35
Alignment explanation
Indices: 842456--842522 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
842446 CGAATTTGAC
842456 TTTCGCGTTGCAAATTTGAC-TATCGCAACGCTTA
1 TTTCGCGTTGCAAATTTGACATATCGCAACGCTTA
*
842490 TTTCGCGTTGCGAATTTGACAATATCGCAACGC
1 TTTCGCGTTGCAAATTTGAC-ATATCGCAACGC
842523 GAATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 19 0.63
36 11 0.37
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (35 bp):
TTTCGCGTTGCAAATTTGACATATCGCAACGCTTA
Found at i:842544 original size:20 final size:21
Alignment explanation
Indices: 842521--842575 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
842511 ATATCGCAAC
*
842521 GCGAATTTTA-CTTTCGCGTT
1 GCGAATTTTACCTTTCGCATT
842541 GCGAA-TTTACCTTTCGCATT
1 GCGAATTTTACCTTTCGCATT
842561 GCGAATTTGTACCTT
1 GCGAATTT-TACCTT
842576 CAACAGGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 4 0.13
20 19 0.61
21 2 0.06
22 6 0.19
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
GCGAATTTTACCTTTCGCATT
Found at i:842765 original size:65 final size:66
Alignment explanation
Indices: 842623--842767 Score: 213
Period size: 66 Copynumber: 2.2 Consensus size: 66
842613 AATTTAAAAC
* * *
842623 AACAAATCAACTTTTACATATCAATTAAACAAGCAAAAAAATAATTTTTATTTACACATAAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATAAAATT
842688 A
66 A
* * *
842689 AACAAATCAACTTTTACAAATCAATTAAACAA-AATAAAAAATAATTCTTATTTCCTCAT-CAAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAA-AAAAAATAATTCTTATTTACACATAAAAT
842752 TA
65 TA
842754 AACAAATCAACTTT
1 AACAAATCAACTTT
842768 CAATGTAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
65 20 0.28
66 52 0.72
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (66 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACACATAAAATT
A
Found at i:844225 original size:21 final size:21
Alignment explanation
Indices: 844160--844240 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
844150 GAATGATGAC
* *
844160 AGGGGCCTTTTGAACGGT-GG
1 AGGGGCCTCTTGAACGATAGG
844180 AAGGGGCCTCTT---CGATAATGAG
1 -AGGGGCCTCTTGAACGAT-A-G-G
844202 AGGGGCCTCTTGAACGATAGG
1 AGGGGCCTCTTGAACGATAGG
*
844223 AGGTGCCTCTTGAACGAT
1 AGGGGCCTCTTGAACGAT
844241 GATAGGTGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.06
21 40 0.80
22 2 0.04
23 1 0.02
24 4 0.08
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATAGG
Found at i:844247 original size:21 final size:21
Alignment explanation
Indices: 844197--844249 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
844187 CTCTTCGATA
*
844197 ATGAGAGGGGCCTCTTGAACG
1 ATGAGAGGTGCCTCTTGAACG
844218 AT-AGGAGGTGCCTCTTGAACG
1 ATGA-GAGGTGCCTCTTGAACG
*
844239 ATGATAGGTGC
1 ATGAGAGGTGC
844250 ATCGAGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.23
Consensus pattern (21 bp):
ATGAGAGGTGCCTCTTGAACG
Found at i:844678 original size:21 final size:21
Alignment explanation
Indices: 844602--844699 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
844592 TAAAAAATCC
*
844602 ACCTCACCACGTAAAG-ACCG
1 ACCTCATCACGTAAAGCACCG
*
844622 AACCTCATCACG-ACATGCACC-
1 -ACCTCATCACGTA-AAGCACCG
** * *
844643 ATTATCTTCACGTAAAGTACCG
1 A-CCTCATCACGTAAAGCACCG
*
844665 ACCTCATGACGTAAAGCACCG
1 ACCTCATCACGTAAAGCACCG
844686 ACCTCATCACGTAA
1 ACCTCATCACGTAA
844700 CTCCCCTAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.03
21 52 0.88
22 5 0.08
ACGTcount: A:0.34, C:0.35, G:0.13, T:0.18
Consensus pattern (21 bp):
ACCTCATCACGTAAAGCACCG
Found at i:846974 original size:20 final size:20
Alignment explanation
Indices: 846949--847126 Score: 221
Period size: 20 Copynumber: 8.8 Consensus size: 20
846939 TAATATTGTG
846949 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
846969 TTTCGCGTTGCAAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
846989 TTTCGCGTTGCAAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
* *
847009 TATCGCGTTGCGAATTTGAA
1 TTTCGCGTTGCGAATTTGAC
* *
847029 ATTCAGTGTTGCGAATTTGAC
1 TTTC-GCGTTGCGAATTTGAC
*
847050 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* **
847070 TTTTGTATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
847090 TATCGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
847110 TATCGCGTTGCGAATTT
1 TTTCGCGTTGCGAATTT
847127 AGAAACTGGG
Statistics
Matches: 136, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
20 120 0.88
21 16 0.12
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:847092 original size:81 final size:81
Alignment explanation
Indices: 846955--847108 Score: 236
Period size: 81 Copynumber: 1.9 Consensus size: 81
846945 TGTGTTTCGC
* *
846955 GTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTTCGCGTTGCAAATTTAACTATCGCGTTGC
1 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTTCGCATTGCAAATTTAACTATCGCGTTGC
847020 GAATTTGAAATTCAGT
66 GAATTTGAAATTCAGT
* * * * * *
847036 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTATTGCGAATTTGACTATCGTGTTGC
1 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTTCGCATTGCAAATTTAACTATCGCGTTGC
847101 GAATTTGA
66 GAATTTGA
847109 CTATCGCGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.40
Consensus pattern (81 bp):
GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTTCGCATTGCAAATTTAACTATCGCGTTGC
GAATTTGAAATTCAGT
Found at i:847160 original size:60 final size:59
Alignment explanation
Indices: 846956--847167 Score: 153
Period size: 60 Copynumber: 3.5 Consensus size: 59
846946 GTGTTTCGCG
* * * * * * *
846956 TTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTTCGCGTTGCAAATTTAACTA-TCGCG-
1 TTGCGAATTGGAC-ATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACAACT-G-GA
* * * *** *
847016 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTA
1 TTGCGAATTGGACA-TC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACAACTGGA
* * *
847077 TTGCGAATTTGACTATCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAGA-AACTGGG
1 TTGCGAATTGGAC-ATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTT-GACAACTGGA
*
847137 TTGTGAAATTGGA-AGTCGCGTTGCGAATTTG
1 TTGCG-AATTGGACA-TCGCGTTGCGAATTTG
847168 TTGGTCATTT
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
59 1 0.01
60 68 0.54
61 55 0.44
62 2 0.02
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (59 bp):
TTGCGAATTGGACATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACAACTGGA
Found at i:848560 original size:3 final size:3
Alignment explanation
Indices: 848552--848576 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
848542 CTTTGATGTT
848552 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
848577 AACCATATTC
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:848808 original size:14 final size:14
Alignment explanation
Indices: 848789--848828 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
848779 AATGTGACGT
848789 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
848803 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
848817 AATCTCTGCATA
1 AATCCCTGCATA
848829 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:858725 original size:11 final size:12
Alignment explanation
Indices: 858709--858737 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
858699 TAATCATCTA
858709 AATTATAATT-T
1 AATTATAATTAT
858720 AATTATAATTAT
1 AATTATAATTAT
858732 AATTAT
1 AATTAT
858738 TCTGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATTATAATTAT
Found at i:858728 original size:6 final size:6
Alignment explanation
Indices: 858709--858737 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
858699 TAATCATCTA
858709 AATTAT AATT-T AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT
858738 TCTGATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AATTAT
Found at i:867436 original size:10 final size:10
Alignment explanation
Indices: 867423--867462 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
867413 GTTCGTGAAC
*
867423 GTTCGGTTAT
1 GTTCGTTTAT
867433 GTTCGTTTAT
1 GTTCGTTTAT
867443 GTTCGTTTAT
1 GTTCGTTTAT
*
867453 GTTCATTTAT
1 GTTCGTTTAT
867463 TTATGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.12, C:0.10, G:0.20, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:868229 original size:16 final size:16
Alignment explanation
Indices: 868204--868260 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
868194 CCAACGTTTA
*
868204 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
868220 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
* *
868236 TGTTCGTTTATATTCG
1 TGTTCATTTATGTTCG
868252 T-TT-ATTTAT
1 TGTTCATTTAT
868261 TAAATTTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.14
15 2 0.05
16 30 0.81
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:871663 original size:2 final size:2
Alignment explanation
Indices: 871656--871696 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
871646 ATATGAATTA
871656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
871697 GTATGAGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:873166 original size:20 final size:21
Alignment explanation
Indices: 873143--873182 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
873133 GTAAATATAT
*
873143 TTTTATTTTTTTAT-ATTTTA
1 TTTTATGTTTTTATCATTTTA
*
873163 TTTTCTGTTTTTATCATTTT
1 TTTTATGTTTTTATCATTTT
873183 TCTTTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTATGTTTTTATCATTTTA
Found at i:875260 original size:12 final size:13
Alignment explanation
Indices: 875238--875269 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
875228 CGTTTGTTGT
875238 GCTTGCTCCTCGG
1 GCTTGCTCCTCGG
875251 GCTT-CTCCTCGG
1 GCTTGCTCCTCGG
875263 GC-TGCTC
1 GCTTGCTC
875270 AGGCTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 13 0.72
13 4 0.22
ACGTcount: A:0.00, C:0.41, G:0.28, T:0.31
Consensus pattern (13 bp):
GCTTGCTCCTCGG
Found at i:879849 original size:29 final size:29
Alignment explanation
Indices: 879814--879881 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
879804 AAAACCGAAT
* *
879814 TAAACGGGTATGGGAAAAACCGTTTATGC
1 TAAACGGGGAGGGGAAAAACCGTTTATGC
* *
879843 TAAACGGGGCGGGGAAAAACCGTTTATGT
1 TAAACGGGGAGGGGAAAAACCGTTTATGC
*
879872 TAAATGGGGA
1 TAAACGGGGA
879882 CGGGTTTAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (29 bp):
TAAACGGGGAGGGGAAAAACCGTTTATGC
Found at i:882407 original size:6 final size:6
Alignment explanation
Indices: 882364--882405 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
882354 AGTGGTCGAT
* *
882364 GGAGAT GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG AGAGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
882406 AGCCTCAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.62, T:0.02
Consensus pattern (6 bp):
GGAGAG
Found at i:884849 original size:138 final size:139
Alignment explanation
Indices: 884520--884851 Score: 407
Period size: 138 Copynumber: 2.4 Consensus size: 139
884510 AATTCTAACT
* *
884520 AAACAATTTGAACACGAATACAATCGAGATAACCCTAAAATCTGAGAATGAAGCTAAAAACAAGT
1 AAACAATTCGAACGCGAATACAATCGAGATAACCCTAAAATCTGAGAATGAAGCTAAAAACAAGT
** * * * * * * * *
884585 TTTGATTTGATTTGATCATAAAAAGGTCAACAACCTGGATTCTGATAGATCTGAATCCAAGCCAA
66 ACTAATTCGATTTGATCATAAAAAGGCCAACAACCCGAATTCTAATAGATCTGAACCCAAACCAA
*
884650 CTGTACTCC
131 CTGTACTCA
* * * * *
884659 AAACAATTCGAACTCGAATACGACCCAGATAA-CCTAAAATCAGAGAATGAAGCTAAAAACAAGT
1 AAACAATTCGAACGCGAATACAATCGAGATAACCCTAAAATCTGAGAATGAAGCTAAAAACAAGT
* *
884723 ACTAATTCGATTTGATCATAAAAA-GCCAACAACCCGAATTCTAATCGATCTGAACCCAAACTAA
66 ACTAATTCGATTTGATCATAAAAAGGCCAACAACCCGAATTCTAATAGATCTGAACCCAAACCAA
884787 CTGTACTCA
131 CTGTACTCA
** * * * * *
884796 AAAGGATTCGAAGGCGAATACAATTGAAATAACCCTGAAATCTGAGGATGAAGCTA
1 AAACAATTCGAACGCGAATACAATCGAGATAACCCTAAAATCTGAGAATGAAGCTA
884852 TGAAGAAATA
Statistics
Matches: 161, Mismatches: 31, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
137 63 0.39
138 71 0.44
139 27 0.17
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (139 bp):
AAACAATTCGAACGCGAATACAATCGAGATAACCCTAAAATCTGAGAATGAAGCTAAAAACAAGT
ACTAATTCGATTTGATCATAAAAAGGCCAACAACCCGAATTCTAATAGATCTGAACCCAAACCAA
CTGTACTCA
Found at i:886295 original size:12 final size:12
Alignment explanation
Indices: 886278--886313 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
886268 AGTAAGATAA
886278 TTATATAAAAAT
1 TTATATAAAAAT
886290 TTATATAAAAAT
1 TTATATAAAAAT
*
886302 TCTAAATAAAAA
1 T-TATATAAAAA
886314 AGATCACAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TTATATAAAAAT
Found at i:892635 original size:34 final size:34
Alignment explanation
Indices: 892569--892654 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
892559 GCCCCGATTA
* *
892569 TATATATATAATATATTTTTATTTTTTATATTAAT
1 TATATATATAATAT-TTTATATATTTTATATTAAT
892604 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
892638 TATATATATAATATTTT
1 TATATATATAATATTTT
892655 CGAGTTCGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 35 0.71
35 14 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:892651 original size:9 final size:9
Alignment explanation
Indices: 892569--892651 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 9
892559 GCCCCGATTA
892569 TATATATAT
1 TATATATAT
*
892578 AATATAT-T
1 TATATATAT
* * *
892586 TTTATTTTT
1 TATATATAT
892595 TATAT-TAAT
1 TATATAT-AT
892604 TATATATA-
1 TATATATAT
*
892612 TA-ATATTT
1 TATATATAT
*
892620 TATATATTT
1 TATATATAT
892629 TATAT-TAAT
1 TATATAT-AT
892638 TATATATAT
1 TATATATAT
*
892647 AATAT
1 TATAT
892652 TTTCGAGTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
7 4 0.07
8 11 0.19
9 41 0.71
10 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATAT
Found at i:893808 original size:12 final size:12
Alignment explanation
Indices: 893791--893815 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
893781 ATTTTATGCG
893791 AGGTTACTATTC
1 AGGTTACTATTC
893803 AGGTTACTATTC
1 AGGTTACTATTC
893815 A
1 A
893816 TGTGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:894623 original size:15 final size:15
Alignment explanation
Indices: 894599--894630 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
894589 TGGCAGATCC
*
894599 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
894614 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
894629 AA
1 AA
894631 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:898945 original size:23 final size:21
Alignment explanation
Indices: 898915--898961 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
898905 TGTGTGCTGG
*
898915 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAA-AAAAAAGA-TA
898938 AAACAAGATAAAAAAAAGATA
1 AAACAAGATAAAAAAAAGATA
898959 AAA
1 AAA
898962 GAATTGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 11 0.48
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (21 bp):
AAACAAGATAAAAAAAAGATA
Found at i:898951 original size:11 final size:11
Alignment explanation
Indices: 898915--898961 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
898905 TGTGTGCTGG
898915 AAACAAGATAA
1 AAACAAGATAA
* *
898926 GAAATAAGATTA
1 -AAACAAGATAA
898938 AAACAAGATAA
1 AAACAAGATAA
*
898949 AAAAAAGATAA
1 AAACAAGATAA
898960 AA
1 AA
898962 GAATTGCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:901471 original size:15 final size:15
Alignment explanation
Indices: 901451--901506 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
901441 AGGGGGTATC
901451 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
901466 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
901484 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
901499 GATTCCCC
1 GATTCCCC
901507 CTGCATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:901485 original size:33 final size:34
Alignment explanation
Indices: 901424--901507 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 34
901414 ATTGTCCAGG
901424 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCAGGGGGTATCGATTCCCC
901459 GGGAACAGATTCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
*
901492 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
901508 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 31 0.65
34 6 0.12
35 11 0.23
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:901489 original size:18 final size:18
Alignment explanation
Indices: 901431--901491 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
901421 AGGGGGAACA
901431 GATTCCCCCCAGGGGGTATC
1 GATT-CCCCCA-GGGGTATC
*
901451 GATT-CCCC--GGG-AAC
1 GATTCCCCCAGGGGTATC
901465 AGATTCCCCCAGGGGTATC
1 -GATTCCCCCAGGGGTATC
901484 GATTCCCC
1 GATTCCCC
901492 GGGTACAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 4 0.12
18 15 0.44
19 2 0.06
20 4 0.12
ACGTcount: A:0.18, C:0.36, G:0.26, T:0.20
Consensus pattern (18 bp):
GATTCCCCCAGGGGTATC
Found at i:901646 original size:21 final size:21
Alignment explanation
Indices: 901620--901661 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
901610 ATTTGAATAT
*
901620 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
901641 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
901662 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:901723 original size:21 final size:21
Alignment explanation
Indices: 901690--901729 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
901680 TTTTTGCAGA
*
901690 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
901712 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
901730 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:901983 original size:34 final size:32
Alignment explanation
Indices: 901944--902013 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
901934 TTTTGTAAAG
*
901944 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
901978 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
902010 GGGA
1 GGGA
902014 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:905004 original size:20 final size:20
Alignment explanation
Indices: 904979--905060 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
904969 ATCAGATTGT
*
904979 CCAGGGGTAA-AGATTCCCCC
1 CCAGGGGGAACAGATT-CCCC
*
904999 CCAGGGGGAACAGATTCCTC
1 CCAGGGGGAACAGATTCCCC
*
905019 CCAGGGGGTATC-GATT--CC
1 CCAGGGGG-AACAGATTCCCC
905037 CC---GGGAACAGATTCCCC
1 CCAGGGGGAACAGATTCCCC
905054 CCAGGGG
1 CCAGGGG
905061 TATCGATTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
14 2 0.04
15 7 0.14
17 4 0.08
18 3 0.06
20 26 0.53
21 7 0.14
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (20 bp):
CCAGGGGGAACAGATTCCCC
Found at i:905066 original size:34 final size:35
Alignment explanation
Indices: 905004--905087 Score: 134
Period size: 34 Copynumber: 2.4 Consensus size: 35
904994 CCCCCCCAGG
*
905004 GGGAACAGATTCCTCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
905039 GGGAACAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
* *
905073 GGGTATAGATTCCCC
1 GGGAACAGATTCCCC
905088 TTGCATGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 29 0.63
35 17 0.37
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:905078 original size:15 final size:15
Alignment explanation
Indices: 905024--905087 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 15
905014 TCCTCCCAGG
905024 GGGTATCGATTCCCC
1 GGGTATCGATTCCCC
*
905039 GGG-AACAGATTCCCCCC
1 GGGTATC-GATT--CCCC
905056 AGGGGTATCGATTCCCC
1 --GGGTATCGATTCCCC
*
905073 GGGTATAGATTCCCC
1 GGGTATCGATTCCCC
905088 TTGCATGGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.05
15 21 0.52
17 8 0.20
19 7 0.17
20 2 0.05
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.22
Consensus pattern (15 bp):
GGGTATCGATTCCCC
Found at i:905226 original size:21 final size:21
Alignment explanation
Indices: 905200--905241 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
905190 ATTTGAATAT
*
905200 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
905221 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
905242 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:905303 original size:21 final size:21
Alignment explanation
Indices: 905270--905309 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
905260 TTTTTGCAGA
*
905270 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
905292 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
905310 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:905563 original size:34 final size:32
Alignment explanation
Indices: 905524--905593 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
905514 TTTTGTAAAG
*
905524 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
905558 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
905590 GGGA
1 GGGA
905594 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:907899 original size:11 final size:11
Alignment explanation
Indices: 907885--907921 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
907875 AAATTTTGGC
907885 TTTTTTGTTTT
1 TTTTTTGTTTT
907896 TTTTTTGTTTT
1 TTTTTTGTTTT
907907 TTTTTTGTTTT
1 TTTTTTGTTTT
907918 TTTT
1 TTTT
907922 AAATAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:937212 original size:20 final size:20
Alignment explanation
Indices: 937189--937252 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 20
937179 AACTTAAATC
937189 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-AAATAATATAT
*
937209 AAAAT--TTTAATAATATAT
1 AAAATAATTAAATAATATAT
*
937227 AAAATAATT-TAT-ATGATAT
1 AAAATAATTAAATAAT-ATAT
937246 AAAATAA
1 AAAATAA
937253 ATTTAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.13
18 13 0.34
19 13 0.34
20 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATAATTAAATAATATAT
Found at i:937273 original size:20 final size:20
Alignment explanation
Indices: 937250--937333 Score: 57
Period size: 20 Copynumber: 4.0 Consensus size: 20
937240 TGATATAAAA
937250 TAAATTTAAAAAATTAATAT
1 TAAATTTAAAAAATTAATAT
* * **
937270 TAAAATTAATATCTATAATA-
1 TAAATTTAAAAAAT-TAATAT
937290 T-AATATT-AAAAATTAATATT
1 TAAAT-TTAAAAAATTAATA-T
937310 TAATTTATTTAAAAAATTAATAT
1 TAA---ATTTAAAAAATTAATAT
937333 T
1 T
937334 TGTTGAGTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 15
0.67 0.11 0.21
Matches are distributed among these distances:
18 5 0.11
19 5 0.11
20 14 0.30
21 6 0.13
23 4 0.09
24 13 0.28
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATTTAAAAAATTAATAT
Found at i:937308 original size:27 final size:24
Alignment explanation
Indices: 937261--937334 Score: 89
Period size: 24 Copynumber: 3.0 Consensus size: 24
937251 AAATTTAAAA
937261 AATTAATATT-AAAATTAATATCTAT
1 AATTAATATTAAAAATTAATAT-T-T
937286 AATATAATATTAAAAATTAATATTT
1 AAT-TAATATTAAAAATTAATATTT
*
937311 AATTTAT-TTAAAAAATTAATATTT
1 AATTAATATT-AAAAATTAATATTT
937335 GTTGAGTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
23 2 0.04
24 17 0.38
25 7 0.16
26 8 0.18
27 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTAATATTAAAAATTAATATTT
Found at i:937344 original size:23 final size:24
Alignment explanation
Indices: 937297--937344 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
937287 ATATAATATT
* *
937297 AAAAATTAATATTTAATTTATTTA
1 AAAAATTAATATTTAATTGAGTTA
*
937321 AAAAATTAATATTT-GTTGAGTTA
1 AAAAATTAATATTTAATTGAGTTA
937344 A
1 A
937345 TCGAATGACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
AAAAATTAATATTTAATTGAGTTA
Found at i:938132 original size:74 final size:75
Alignment explanation
Indices: 938033--938237 Score: 263
Period size: 74 Copynumber: 2.7 Consensus size: 75
938023 CGTTGAACAT
* *
938033 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
** *
938097 AAACTGTTTA
66 AAACCATTCA
* * * * *
938107 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
938171 AAACCATTCA
66 AAACCATTCA
**
938181 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCA-ATCTGGAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
938238 TTTGGCTTTG
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
74 83 0.74
75 6 0.05
76 23 0.21
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
AAACCATTCA
Found at i:938855 original size:17 final size:17
Alignment explanation
Indices: 938833--938876 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
938823 TTCATAAATC
938833 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
938850 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
938867 -AAATATCCAA
1 CAAA-ATCCAA
938877 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:938868 original size:9 final size:8
Alignment explanation
Indices: 938828--938878 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
938818 CACCATTCAT
938828 AAATCC-A
1 AAATCCAA
938835 AAATCCAA
1 AAATCCAA
*
938843 CAATCCACA
1 AAATCCA-A
938852 AAAT-CAA
1 AAATCCAA
938859 ACAATCCAA
1 A-AATCCAA
938868 AATATCCAA
1 AA-ATCCAA
938877 AA
1 AA
938879 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:940844 original size:21 final size:21
Alignment explanation
Indices: 940818--940857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
940808 CAGAACCCCA
*
940818 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
940839 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
940858 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:946768 original size:75 final size:76
Alignment explanation
Indices: 946668--946874 Score: 249
Period size: 75 Copynumber: 2.7 Consensus size: 76
946658 CGTTGAACAT
* *
946668 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
** *
946732 AAACTGTTTAG
66 AAACCATTCAG
** * * * * *
946743 GGGGGAATCGGTTTTTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
946807 AAACCATTCAG
66 AAACCATTCAG
**
946818 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCA-ATCTGGAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
946875 TTTGGCTTTG
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
75 80 0.73
76 6 0.06
77 23 0.21
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.25
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
AAACCATTCAG
Found at i:952948 original size:24 final size:24
Alignment explanation
Indices: 952922--953036 Score: 167
Period size: 24 Copynumber: 4.8 Consensus size: 24
952912 TTTTCTGCAC
* * *
952922 CTCAATTTTATTCACCTCAAATTC
1 CTCAATTTTCTGCACCTCAAATTA
*
952946 CTCAATTTTTTGCACCTCAAATTA
1 CTCAATTTTCTGCACCTCAAATTA
952970 CTCAATTTTCTGCACCTCAAATTA
1 CTCAATTTTCTGCACCTCAAATTA
*
952994 CTCAATTTTCTGCACCTCAAATTT
1 CTCAATTTTCTGCACCTCAAATTA
*
953018 CTTAATTTTCTGCAGCCTC
1 CTCAATTTTCTGCA-CCTC
953037 TCAAGTTCCT
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
24 80 0.95
25 4 0.05
ACGTcount: A:0.26, C:0.29, G:0.04, T:0.41
Consensus pattern (24 bp):
CTCAATTTTCTGCACCTCAAATTA
Found at i:954964 original size:21 final size:22
Alignment explanation
Indices: 954913--954966 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
954903 CTACTTCATC
* *
954913 TCCATCACCATCTCCACCTCCA
1 TCCATCACCACCTCCAACTCCA
* *
954935 TCC-TTACCACCTCCAACTTCA
1 TCCATCACCACCTCCAACTCCA
954956 -CCATCACCACC
1 TCCATCACCACC
954967 ATCATCTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.24, C:0.54, G:0.00, T:0.22
Consensus pattern (22 bp):
TCCATCACCACCTCCAACTCCA
Found at i:967470 original size:30 final size:30
Alignment explanation
Indices: 967434--967536 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
967424 TCCGAAGGAC
967434 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
967464 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
967494 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
967524 CTGTCCATAGGTC
1 CTATCCAGAGGTC
967537 TCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:967553 original size:30 final size:30
Alignment explanation
Indices: 967510--967603 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
967500 AGAGGTCATA
* * *
967510 AAGATCCTCGGTAACTGTCCATAGGTCTCG
1 AAGAACCTAGGTAACTGTCCATATGTCTCG
* *
967540 AAGAACCTAGGTAAACTATCCATATGT-TCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCT-CG
* * *
967571 TAGAACATAGGTATACTGTTCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCTCG
967602 AA
1 AA
967604 AGACATAGGT
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
30 12 0.24
31 36 0.73
32 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCTCG
Found at i:967553 original size:60 final size:61
Alignment explanation
Indices: 967434--967561 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 61
967424 TCCGAAGGAC
* *
967434 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGAACCTAGGTAAA
* * *
967494 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC-TCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCAT-AAAGAACCTAGGTAAA
967555 CTATCCA
1 CTATCCA
967562 TATGTTCCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 51 0.84
61 9 0.15
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGAACCTAGGTAAA
Found at i:968754 original size:64 final size:63
Alignment explanation
Indices: 968685--968825 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 63
968675 GCAGTACCCG
* * *
968685 TGCATCGATGCACAAATTACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATACAC-TCCTTA
1 TGCATCGATGCACAAATTACATTCGATGTTTCCATTTTAAGAGG-TGCATCGATACACTTCC-TA
* * * * *
968749 TGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAGGTGCATCGATGCACTTCCTG
1 TGCATCGATGCACAAATTACATTCGATGTTTCCATTTTAAGAGGTGCATCGATACACTTCCTA
*
968812 TGCATCGATACACA
1 TGCATCGATGCACA
968826 CTGAAAAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
63 25 0.38
64 41 0.62
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
TGCATCGATGCACAAATTACATTCGATGTTTCCATTTTAAGAGGTGCATCGATACACTTCCTA
Done.