Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000914.1 Hibiscus syriacus cultivar Beakdansim tig00001825_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: 1342319
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 6
Found at i:356723 original size:54 final size:54
Alignment explanation
Indices: 356641--356748 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
356631 TATATATATA
*
356641 TATATATCTATCTATCTGTTGGTTATGCGATGAGAGGATAAGGATTAATTTTAT
1 TATATATATATCTATCTGTTGGTTATGCGATGAGAGGATAAGGATTAATTTTAT
356695 TATATATATATCTATCTGTTGGTTATGCGATGAGAGGATAAGGATTAATTTTAT
1 TATATATATATCTATCTGTTGGTTATGCGATGAGAGGATAAGGATTAATTTTAT
356749 GTTAGTAGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (54 bp):
TATATATATATCTATCTGTTGGTTATGCGATGAGAGGATAAGGATTAATTTTAT
Found at i:358642 original size:15 final size:15
Alignment explanation
Indices: 358602--358631 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
358592 CATTGCCAAA
358602 ACTACTCGAACTGTT
1 ACTACTCGAACTGTT
358617 ACTACTCGAACTGTT
1 ACTACTCGAACTGTT
358632 GTTAGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (15 bp):
ACTACTCGAACTGTT
Found at i:368061 original size:3 final size:3
Alignment explanation
Indices: 368039--368086 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
368029 CATTTGCACC
*
368039 CTT CTT C-T CTT -TC CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
368084 CTT
1 CTT
368087 ACTCTCTCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 5 0.12
3 35 0.88
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:374360 original size:7 final size:7
Alignment explanation
Indices: 374348--374377 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
374338 TACATTCTTG
374348 TAAACCC
1 TAAACCC
374355 TAAACCC
1 TAAACCC
*
374362 TAAACTC
1 TAAACCC
374369 TAAACCC
1 TAAACCC
374376 TA
1 TA
374378 TTTGTTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:380449 original size:24 final size:24
Alignment explanation
Indices: 380403--380452 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
380393 CAATTAAGTA
380403 TTATTTTAAAAAACGATTATGATTT
1 TTATTTTAAAAAAC-ATTATGATTT
*
380428 TTATTTTGAAAAA-ATTAGTGATTT
1 TTATTTTAAAAAACATTA-TGATTT
380452 T
1 T
380453 GCAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 7 0.30
25 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (24 bp):
TTATTTTAAAAAACATTATGATTT
Found at i:381176 original size:12 final size:12
Alignment explanation
Indices: 381159--381192 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
381149 ATAAGATGGG
381159 AATAAATATAAA
1 AATAAATATAAA
* *
381171 AGTAAAAATAAA
1 AATAAATATAAA
381183 AATAAATATA
1 AATAAATATA
381193 TTTACAATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAAATATAAA
Found at i:382762 original size:3 final size:3
Alignment explanation
Indices: 382756--382797 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
382746 TATGTATTAT
* *
382756 TAA TAA TAA TTAA TAA TAA TAG TAA TAA TAA TTA TAA -AA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
382798 AACGGGTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:382784 original size:22 final size:20
Alignment explanation
Indices: 382756--382796 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
382746 TATGTATTAT
382756 TAATAATAATTAATAATAATAG
1 TAATAATAATT-ATAA-AATAG
382778 TAATAATAATTATAAAATA
1 TAATAATAATTATAAAATA
382797 AAACGGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TAATAATAATTATAAAATAG
Found at i:384586 original size:21 final size:22
Alignment explanation
Indices: 384551--384591 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
384541 GCGCCACCGT
384551 ATCTCCCTCCGCCTCGTCCCAC
1 ATCTCCCTCCGCCTCGTCCCAC
* *
384573 ATCT-CCTCCTCCTCTTCCC
1 ATCTCCCTCCGCCTCGTCCC
384592 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.59, G:0.05, T:0.29
Consensus pattern (22 bp):
ATCTCCCTCCGCCTCGTCCCAC
Found at i:389072 original size:2 final size:2
Alignment explanation
Indices: 389065--389115 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
389055 TCAATCTACA
389065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
389107 AT AT AT AT A
1 AT AT AT AT A
389116 ATTTACGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:389492 original size:85 final size:85
Alignment explanation
Indices: 389170--389481 Score: 430
Period size: 85 Copynumber: 3.7 Consensus size: 85
389160 AATGATGTGT
** * * * ** * *
389170 GCTTCAATGAAACGCAATGTAAGTCATACATGAGTGCCATATATTTATGATACACAAATATATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
389235 CAAGC--AGATTTATGACGGGG
66 C-ATCTTA-ATTTATGACGGGG
* * *
389255 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGATGCAAAAATATGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
389320 TATCTTAATTTATGACGGGG
66 CATCTTAATTTATGACGGGG
389340 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
389405 CATCTTAATTTATGACGGGA
66 CATCTTAATTTATGACGGGG
* * *
389425 GCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAGATTTATGACACACAA
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAA
389482 TTGCGCGTCA
Statistics
Matches: 207, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
84 2 0.01
85 204 0.99
86 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
CATCTTAATTTATGACGGGG
Found at i:391080 original size:20 final size:20
Alignment explanation
Indices: 391043--391081 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
391033 AAATCCTGAT
*
391043 ATATTTATTATAGGTAATTC
1 ATATTTATTATAAGTAATTC
* *
391063 ATATTTATTTTAATTAATT
1 ATATTTATTATAAGTAATT
391082 TATAAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTTATTATAAGTAATTC
Found at i:398411 original size:21 final size:21
Alignment explanation
Indices: 398385--398433 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
398375 CGCGATCTAT
398385 ATATATATATAGT-CTCATGTC
1 ATATAT-TATAGTACTCATGTC
* *
398406 ATATATTCTTGTACTCATGTC
1 ATATATTATAGTACTCATGTC
398427 ATATATT
1 ATATATT
398434 CTTGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (21 bp):
ATATATTATAGTACTCATGTC
Found at i:398434 original size:21 final size:21
Alignment explanation
Indices: 398398--398439 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
398388 TATATATAGT
398398 CTCATGTCATATATTCTTGTA
1 CTCATGTCATATATTCTTGTA
398419 CTCATGTCATATATTCTTGTA
1 CTCATGTCATATATTCTTGTA
398440 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
CTCATGTCATATATTCTTGTA
Found at i:417911 original size:15 final size:15
Alignment explanation
Indices: 417891--417920 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
417881 CTGCTGACAT
417891 ATATACACATGCAAG
1 ATATACACATGCAAG
417906 ATATACACATGCAAG
1 ATATACACATGCAAG
417921 TATCAGCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
ATATACACATGCAAG
Found at i:419769 original size:6 final size:6
Alignment explanation
Indices: 419758--419786 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
419748 GGTTCTCCTT
419758 CCTCCG CCTCCG CCTCCG CCTCCG CCTCC
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCC
419787 TCCCCATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.14, T:0.17
Consensus pattern (6 bp):
CCTCCG
Found at i:426548 original size:30 final size:32
Alignment explanation
Indices: 426512--426572 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
426502 TATTACTTAA
*
426512 ATGTTTAAATAAA-AATT-ATATTTTCAAATT
1 ATGTTTAAATAAATAATTAATATTTTAAAATT
* *
426542 ATGTTTATATAAATATTTAATATTTTAAAAT
1 ATGTTTAAATAAATAATTAATATTTTAAAAT
426573 AGTTAGAGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 12 0.46
31 3 0.12
32 11 0.42
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (32 bp):
ATGTTTAAATAAATAATTAATATTTTAAAATT
Found at i:435200 original size:17 final size:18
Alignment explanation
Indices: 435175--435209 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
435165 CGGGGACTAT
435175 ATTTAAAAAAAAT-TAAA
1 ATTTAAAAAAAATATAAA
*
435192 ATTTTAAAAAAATATAAA
1 ATTTAAAAAAAATATAAA
435210 CATGCCGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTTAAAAAAAATATAAA
Found at i:436096 original size:24 final size:25
Alignment explanation
Indices: 436068--436123 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
436058 ATTAAAACAA
* *
436068 TTTAATAAATATAAT-ATTTCATAT
1 TTTAATAAAAATAATAATTTAATAT
* *
436092 TTTAA-AAAAATATTAATTTAATTT
1 TTTAATAAAAATAATAATTTAATAT
436116 TTTAATAA
1 TTTAATAA
436124 CCTTGTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.27
24 17 0.65
25 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTAATAAAAATAATAATTTAATAT
Found at i:448918 original size:36 final size:36
Alignment explanation
Indices: 448877--449188 Score: 471
Period size: 36 Copynumber: 8.7 Consensus size: 36
448867 GTGCGCTACA
* * *
448877 TCCTTCCGTTCGACTCGAATCGGAAGTGCCAATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
448913 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* *
448949 TCATTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* *
448985 TACTTCCGTTCGACTTGAATCGGAAGTGCTGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
**
449021 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* *
449057 TCCTTTCGTTCGACTTGAATCAGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* * *
449093 TCATTCCATTCGACTTGAATCAGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
449129 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
449165 TCCTTCTGTTCGACTTGAATCGGA
1 TCCTTCCGTTCGACTTGAATCGGA
449189 CGTGTAGATG
Statistics
Matches: 253, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 253 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
Found at i:458277 original size:30 final size:27
Alignment explanation
Indices: 458226--458297 Score: 65
Period size: 30 Copynumber: 2.5 Consensus size: 27
458216 CAATACAATA
* *
458226 AATTTTAATAAAATAATAAAATTATTATG
1 AATTCTAATATAATAATAAAA-TATT-TG
458255 TAATTCTAATATAATAGA-AAAATATTTG
1 -AATTCTAATATAATA-ATAAAATATTTG
458283 ACATTCGTAATATAA
1 A-ATTC-TAATATAA
458298 AGATTGATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 1 0.03
28 6 0.16
29 12 0.32
30 17 0.46
31 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (27 bp):
AATTCTAATATAATAATAAAATATTTG
Found at i:469772 original size:31 final size:29
Alignment explanation
Indices: 469721--469790 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
469711 AAATAGTTAT
*
469721 TATTTTTTATATTAATATATTTATGTAAA
1 TATTTTTTATATTAATATATTTATATAAA
*
469750 TATTTTTT-TATTAAAATAATATTTATATAAT
1 TATTTTTTATATT--AAT-ATATTTATATAAA
*
469781 TATTATTTAT
1 TATTTTTTAT
469791 TTAGAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 4 0.12
29 8 0.24
30 3 0.09
31 18 0.53
32 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TATTTTTTATATTAATATATTTATATAAA
Found at i:471548 original size:21 final size:21
Alignment explanation
Indices: 471518--471565 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
471508 GCAGGGGTAC
* *
471518 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
471539 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
471560 ATGCCA
1 ATGCCA
471566 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:471595 original size:21 final size:21
Alignment explanation
Indices: 471569--471641 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
471559 TATGCCATCT
*
471569 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
*
471590 CCGCAGAGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
471611 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
471632 CCGCAGGGTT
1 CCGCAGGGTT
471642 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:472208 original size:33 final size:34
Alignment explanation
Indices: 472149--472245 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
472139 AAATGTTTTT
* *
472149 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
472183 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
472216 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
472246 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:472252 original size:34 final size:32
Alignment explanation
Indices: 472147--472252 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
472137 ATAAATGTTT
*
472147 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
472181 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
472213 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
472248 TTAAA
1 TTAAA
472253 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:472802 original size:128 final size:128
Alignment explanation
Indices: 472642--473296 Score: 1156
Period size: 128 Copynumber: 5.1 Consensus size: 128
472632 TTACCTGATT
472642 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
472707 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
472770 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAAC-TATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* ****
472834 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACACGCCTTCATGT--CCCCTGAGAA-AATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGA-AATAATAGG
472895 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
472960 TGACGAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
473023 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
473088 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGTCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
473151 TACTAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
473216 TGACGAAATAACGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
473279 TACTGATATATCTAGTGT
1 TACTGATATATCTAGTGT
473297 TTCTCTGAAA
Statistics
Matches: 500, Mismatches: 22, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
125 66 0.13
126 52 0.10
127 52 0.10
128 330 0.66
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:477332 original size:3 final size:3
Alignment explanation
Indices: 477326--477404 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
477316 TTACTCATTT
* * * * * * *
477326 TTA TTA TTA TTA TTA CTA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
477374 TTA TAA TTA TTA -TA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
477405 AAAAAAATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:478627 original size:12 final size:12
Alignment explanation
Indices: 478612--478638 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
478602 TGAATTAGGT
478612 TTTTAATTATAA
1 TTTTAATTATAA
478624 TTTTAATTATAA
1 TTTTAATTATAA
478636 TTT
1 TTT
478639 AGTCACTAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTAATTATAA
Found at i:478954 original size:23 final size:22
Alignment explanation
Indices: 478908--478952 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
478898 ATATTATAAA
478908 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
478930 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
478953 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:479006 original size:118 final size:125
Alignment explanation
Indices: 478769--479011 Score: 268
Period size: 118 Copynumber: 2.0 Consensus size: 125
478759 TGTAGTCATA
* *
478769 TAAATATATATATAATAAATAATAATTTATATTTTTTTACATAAATTATTTTAATATTTATTTTT
1 TAAATATATATATAATAAATAATAATTTATATTTTTTTAAATAAATTATATTAATATTTA--TTT
* * * * * *
478834 CAATATCGAAGAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTCTGGTATTT-TAAAAT
64 CAATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTATGATATTTCTAAAAT
* *
478895 TAAATAT-TATA-AA-AAATTATAATTTA-ATTTTATTTAAAT-TATTATATTAATATTTA-TT-
1 TAAATATATATATAATAAATAATAATTTATATTTT-TTTAAATAAATTATATTAATATTTATTTC
* * * * *
478953 AATATCGAAGAAAATAGCAGTCTTAAGGCACCTAGAAGTTCTTTTATGATATTTCTAAA
65 AATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTATGATATTTCTAAA
479012 TAAATAAATA
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
118 43 0.43
119 6 0.06
122 20 0.20
123 18 0.18
124 2 0.02
125 4 0.04
126 7 0.07
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (125 bp):
TAAATATATATATAATAAATAATAATTTATATTTTTTTAAATAAATTATATTAATATTTATTTCA
ATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTATGATATTTCTAAAAT
Found at i:479033 original size:22 final size:25
Alignment explanation
Indices: 479002--479049 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
478992 TCTTTTATGA
*
479002 TATTTCTAAATA-A-ATAAA-TATT
1 TATTTATAAATATATATAAATTATT
479024 TATTTATAAATATATATAAATTATT
1 TATTTATAAATATATATAAATTATT
479049 T
1 T
479050 TTTTCTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 5 0.23
25 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTATAAATATATATAAATTATT
Found at i:484685 original size:3 final size:3
Alignment explanation
Indices: 484677--484733 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
484667 AATATTTATT
* * *
484677 TAA TAA TAA TAA TGTA TAA TAA TGA TAA TAA TAA TTAA TAA CAAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA -TAA TAA -TAA TAA
484725 TAA TAA TAA
1 TAA TAA TAA
484734 AAGAAAACTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 38 0.84
4 7 0.16
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:484698 original size:16 final size:14
Alignment explanation
Indices: 484677--484732 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 14
484667 AATATTTATT
*
484677 TAATAATAATAATG
1 TAATAATAATAATA
*
484691 T-ATAATAATGATAA
1 TAATAATAATAAT-A
*
484705 TAATAATTAATAACA
1 TAATAA-TAATAATA
484720 -AATAATAATAATA
1 TAATAATAATAATA
484733 AAAGAAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 17 0.50
14 7 0.21
15 5 0.15
16 5 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:484715 original size:10 final size:11
Alignment explanation
Indices: 484680--484731 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
484670 ATTTATTTAA
484680 TAATAATAATG
1 TAATAATAATG
484691 T-ATAATAATG
1 TAATAATAATG
484701 ATAATAATAAT-
1 -TAATAATAATG
* *
484712 TAATAACAA-A
1 TAATAATAATG
484722 TAATAATAAT
1 TAATAATAAT
484732 AAAAGAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 25 0.71
11 2 0.06
12 8 0.23
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (11 bp):
TAATAATAATG
Found at i:485018 original size:76 final size:76
Alignment explanation
Indices: 484863--485428 Score: 997
Period size: 76 Copynumber: 7.4 Consensus size: 76
484853 GAAGTGTTGA
*
484863 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCAG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
484928 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
484940 AAACATCATGCACTGAAGGGCTTACAGATGAGCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
485005 AGGCTTTTTGG
66 AGGCTTTTTGG
485016 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
485081 AGGCTTTTTGG
66 AGGCTTTTTGG
*
485092 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
485157 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
485168 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
485233 AGGCTTTTTAG
66 AGGCTTTTTGG
*
485244 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCGAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
485309 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
485320 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGATTTTGAAAACATCAAAACGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
485385 AGGCTTTTTTTTGG
66 AGGC---TTTTTGG
485399 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
485429 TGGGAAATAG
Statistics
Matches: 467, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
76 393 0.84
77 38 0.08
79 36 0.08
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:486130 original size:22 final size:22
Alignment explanation
Indices: 486105--486159 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
486095 CATAAAGCTT
486105 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
486127 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
486149 TCATCTTTGAA
1 TCATCTTTGAA
486160 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:488983 original size:115 final size:115
Alignment explanation
Indices: 488776--489330 Score: 1013
Period size: 115 Copynumber: 4.8 Consensus size: 115
488766 AATCATGTAG
* * * *
488776 TTCACCTTTCAATTCCAATGATTGGTTCTG-GGATTCATACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
* *
488840 AATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
488890 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
*
488955 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
489005 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
489070 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
489120 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
*
489185 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
489235 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
* *
489300 AACACTTTCAGGAGATGCTATTGAGTCTCCT
66 AACACTTCCAGAAGATGCTATTGAGTCTCCT
489331 CTTCAAAATT
Statistics
Matches: 429, Mismatches: 11, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
114 28 0.07
115 401 0.93
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAACAAA
Found at i:491349 original size:12 final size:11
Alignment explanation
Indices: 491320--491362 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
491310 CTTGATTCAA
*
491320 TTTTTTCTTT-
1 TTTTTTTTTTG
*
491330 TTCTTTTTTTG
1 TTTTTTTTTTG
491341 TTTTGTTTTTTG
1 TTTT-TTTTTTG
491353 TTTTTTTTTT
1 TTTTTTTTTT
491363 CTTCTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.29
11 9 0.32
12 11 0.39
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:496837 original size:19 final size:18
Alignment explanation
Indices: 496792--496839 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
496782 CTAAATATTA
496792 AAATAATTTATTTTTAAAT
1 AAAT-ATTTATTTTTAAAT
*
496811 AAATATTTATTTATTATAT
1 AAATATTTATTT-TTAAAT
*
496830 ATATATTTAT
1 AAATATTTAT
496840 GACTACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATTTATTTTTAAAT
Found at i:498301 original size:3 final size:3
Alignment explanation
Indices: 498293--498349 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
498283 AATATTTATT
* * *
498293 TAA TAA TAA TAA TGTA TAA TAA TGA TAA TAA TAA TTAA TAA CAAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA -TAA TAA -TAA TAA
498341 TAA TAA TAA
1 TAA TAA TAA
498350 AAGCAAACTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 38 0.84
4 7 0.16
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:498314 original size:16 final size:14
Alignment explanation
Indices: 498293--498348 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 14
498283 AATATTTATT
*
498293 TAATAATAATAATG
1 TAATAATAATAATA
*
498307 T-ATAATAATGATAA
1 TAATAATAATAAT-A
*
498321 TAATAATTAATAACA
1 TAATAA-TAATAATA
498336 -AATAATAATAATA
1 TAATAATAATAATA
498349 AAAGCAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 17 0.50
14 7 0.21
15 5 0.15
16 5 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:498331 original size:10 final size:11
Alignment explanation
Indices: 498296--498347 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
498286 ATTTATTTAA
498296 TAATAATAATG
1 TAATAATAATG
498307 T-ATAATAATG
1 TAATAATAATG
498317 ATAATAATAAT-
1 -TAATAATAATG
* *
498328 TAATAACAA-A
1 TAATAATAATG
498338 TAATAATAAT
1 TAATAATAAT
498348 AAAAGCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 25 0.71
11 2 0.06
12 8 0.23
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (11 bp):
TAATAATAATG
Found at i:498653 original size:15 final size:15
Alignment explanation
Indices: 498633--498664 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
498623 ATCAATACCT
498633 TTTTGCATACATACA
1 TTTTGCATACATACA
*
498648 TTTTGCATACATTCA
1 TTTTGCATACATACA
498663 TT
1 TT
498665 ATTCATTTCA
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:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:502801 original size:18 final size:18
Alignment explanation
Indices: 502778--502823 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
502768 ATTATGCTTG
*
502778 AAGAAAAAAAAAGGAAG-A
1 AAGAAAAAAAAA-AAAGAA
502796 AAGAAAAGAAAAAAAAGAA
1 AAGAAAA-AAAAAAAAGAA
502815 AAGAAAAAA
1 AAGAAAAAA
502824 GGGGGGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAAAAGAA
Found at i:502812 original size:14 final size:14
Alignment explanation
Indices: 502795--502823 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
502785 AAAAAGGAAG
502795 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
502809 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
502823 A
1 A
502824 GGGGGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAA
Found at i:504416 original size:94 final size:93
Alignment explanation
Indices: 504199--504487 Score: 433
Period size: 94 Copynumber: 3.1 Consensus size: 93
504189 AACAAGTGCC
*
504199 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC--ATCTGGTTTGGTATAAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCACA
* * *
504262 AAACCCCATCATTGGACTTGAAAGATGA
66 AAAACCAATCATTGGAATTGAAAGATGA
* *
504290 GTGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCACA
* *
504355 AAAACCAATCATTGGATTTAGAAATATGA
66 AAAACCAATCATTGGAATT-GAAAGATGA
* *
504384 ATGCGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCAC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AAACCAC
504449 -AAAACCAATCATT-GAATTGAAAGATGA
65 AAAAACCAATCATTGGAATTGAAAGATGA
*
504476 ATGTGATCATAG
1 ATGTGCTCATAG
504488 TAGAAATAAG
Statistics
Matches: 179, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
91 39 0.22
92 18 0.10
93 41 0.23
94 74 0.41
95 7 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCACA
AAAACCAATCATTGGAATTGAAAGATGA
Found at i:505606 original size:113 final size:112
Alignment explanation
Indices: 505274--506173 Score: 1086
Period size: 113 Copynumber: 8.0 Consensus size: 112
505264 TAGCAAAGAT
* * *
505274 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCA-ATAGAGTTCATAATGAGAAGAACTCATCTGA
*
505339 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
505387 TTAAATTCATCATTTGATGGATTAAC-ATT-GAAGGTAGAGTTCATAATGAGAAGAACTCATCAT
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAA--TAGAGTTCATAATGAGAAGAA--C-TCAT
* * * *
505450 CTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTCGC
61 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
505502 TCAAATCCATCATTTGATGGATCAGCTTTTCCAATTTGAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAA-TAGAGTTCATAATGAGAAGAACTCATCTGA
*
505567 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
505615 TTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAACTTTTCCA-ATAGAGTTCATAATGAGAAGAA--C-TCATC
*
505680 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
505731 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCA-ATAGAGTTCATAATGAGAAGAACTCATCTGA
505796 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
505844 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCA-ATAGAGTTCATAATGAGAAGAACTCATCTGA
*
505909 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** *
505957 TCAAATCCATCACTTGATGGATCAGTTTTTCC-AGAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAATAG-AGTTCATAATGAGAAGAACTCATCTGA
* ** *
506021 AGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* ** * * * * *
506066 AT-AATTTTATCA---CA-GCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 -TCAAATCCATCATTTGATGGATCAACTTTTCCA-ATAGAGTTCATAATGAGAAGAACTCATCTG
* * ** *
506126 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
64 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
506174 AATGACTCTA
Statistics
Matches: 695, Mismatches: 72, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
105 10 0.01
106 31 0.04
107 3 0.00
108 26 0.04
109 22 0.03
110 32 0.05
111 3 0.00
112 52 0.07
113 315 0.45
114 3 0.00
115 74 0.11
116 122 0.18
117 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (112 bp):
TCAAATCCATCATTTGATGGATCAACTTTTCCAATAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:505762 original size:229 final size:226
Alignment explanation
Indices: 505274--506173 Score: 1232
Period size: 229 Copynumber: 4.0 Consensus size: 226
505264 TAGCAAAGAT
* ***
505274 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGATTGAGTTCATAATGAGAAGAACTCATCTGA
*
505339 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
* *
505404 TGGATTAACATTG-AAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAAGAAGAA
131 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAAGAAGAA
*
505468 ATTCATAATGAGAAGAATTTATTCAACCTTTCGC
193 ATTCATAATGAGAAGAATTTATTCAACCTTTTGC
* *
505502 TCAAATCCATCATTTGATGGATCAGCTTTTCCA-ATTTGAGTTCATAATGAGAAGAACTCATCTA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGA-TTGAGTTCATAATGAGAAGAACTCATCTG
*
505566 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTG
* *
505631 ATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGA
130 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAAGAAGA
*
505696 AATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
192 AATTCATAATGAGAAGAATTTATTCAACCTTTTGC
*
505731 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGATTGAGTTCATAATGAGAAGAACTCATCTGA
* * *
505796 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
* * * * * *
505861 TGGATCAACTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
131 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATT
* *
505926 CATAATGAGAAGAATTTGTTCAACTTTTTGC
196 CATAATGAGAAGAATTTATTCAACCTTTTGC
*
505957 TCAAATCCATCACTTGATGGATCAGTTTTTCCAGA--GAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGATTG-AGTTCATAATGAGAAGAACTCATCTG
* ** * * * *
506020 AAGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGCATAATTTTATCA---
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTTAAATTCATCATTT
* * * * * *
506078 CA-GCATCAACCTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAA
129 GATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
* **
506141 GTTCATAATGAGAAGAGCTTATTCAACCTTTTG
193 ATTCATAATGAGAAGAATTTATTCAACCTTTTG
506174 AATGACTCTA
Statistics
Matches: 621, Mismatches: 45, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
218 82 0.13
219 1 0.00
221 26 0.04
222 15 0.02
223 1 0.00
224 2 0.00
225 31 0.05
226 87 0.14
227 2 0.00
228 137 0.22
229 237 0.38
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (226 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGATTGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGA
TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATT
CATAATGAGAAGAATTTATTCAACCTTTTGC
Found at i:505905 original size:342 final size:336
Alignment explanation
Indices: 505274--506173 Score: 1206
Period size: 342 Copynumber: 2.7 Consensus size: 336
505264 TAGCAAAGAT
* *
505274 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGA
* *
505339 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTAAATTCATCACTTGA
* * ** * *
505404 TGGATTAACATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAAGAAGAAA
129 TGGATCAACTTTCCAGATAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAAGAAGAAG
* * *
505469 TTCATAATGAGAAGAATTTATTCAACCTTTCGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
191 TTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCC
505534 AATTTGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
256 AATTTGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
*
505599 TTGTTCAACCTTTTGT
321 TTGTTCAACCTTTTGC
* * * * * *
505615 TTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGG-AGAGTTCATAATGAGAAGAA--C-TCATC
* *
505680 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACT
62 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT-AAATTCATCACT
* * * *
505745 TGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
126 TGATGGATCAAC-TTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
*
505810 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
190 GTTCATAATGAGAAGAATTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTC
* *
505875 CAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
255 CAATTTGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
*
505940 TTTGTTCAACTTTTTGC
320 TTTGTTCAACCTTTTGC
* *
505957 TCAAATCCATCACTTGATGGATCAGTTTTTCCA-GAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGAG-AGTTCATAATGAGAAGAACTCATCTGA
* ** * * *
506021 AGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGCATAATTTTATCAC---
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC-TAAATTCATCACTTG
* * * *
506079 A-GCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGT
128 ATGGATCAA-CTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGT
**
506143 TCATAATGAGAAGAGCTTATTCAACCTTTTG
192 TCATAATGAGAAGAATTTATTCAACCTTTTG
506174 AATGACTCTA
Statistics
Matches: 493, Mismatches: 56, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
331 81 0.16
332 2 0.00
334 25 0.05
335 16 0.03
336 2 0.00
337 1 0.00
338 12 0.02
339 1 0.00
340 2 0.00
341 66 0.13
342 184 0.37
343 3 0.01
344 74 0.15
345 24 0.05
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (336 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTAAATTCATCACTTGATG
GATCAACTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAT
AATGAGAAGAATTTATTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAATTT
GAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGC
Found at i:506396 original size:3 final size:3
Alignment explanation
Indices: 506390--506465 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
506380 TTACCCATTT
* * * * *
506390 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
506438 TAA TTA TTA -TA TATA TTA TTA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
506466 AAAAAAAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:506415 original size:15 final size:15
Alignment explanation
Indices: 506390--506467 Score: 99
Period size: 15 Copynumber: 5.4 Consensus size: 15
506380 TTACCCATTT
*
506390 TTATTATTATTATTA
1 TTATAATTATTATTA
*
506405 CTATAATTATTATTA
1 TTATAATTATTATTA
* *
506420 TTATAATTATAATAA
1 TTATAATTATTATTA
506435 TTATAATTATTA-TA
1 TTATAATTATTATTA
506449 -TAT-ATTATTATTA
1 TTATAATTATTATTA
506462 TTATAA
1 TTATAA
506468 AAAAAATAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
12 7 0.13
13 5 0.09
14 4 0.08
15 37 0.70
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATAATTATTATTA
Found at i:506490 original size:36 final size:36
Alignment explanation
Indices: 506415--506492 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
506405 CTATAATTAT
* ** **
506415 TATTATTATAATTATAATAATTATAATTATTATATA
1 TATTATTATAATTATAAAAAAAATAATTAAAATATA
*
506451 TATTATTATTATTATAAAAAAAATAATTACAAATA-A
1 TATTATTATAATTATAAAAAAAATAATTA-AAATATA
506487 TATTAT
1 TATTAT
506493 AGGCCCAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 32 0.91
37 3 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (36 bp):
TATTATTATAATTATAAAAAAAATAATTAAAATATA
Found at i:507687 original size:12 final size:12
Alignment explanation
Indices: 507672--507698 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
507662 TGAATTAGGT
507672 TTTTAATTATAA
1 TTTTAATTATAA
507684 TTTTAATTATAA
1 TTTTAATTATAA
507696 TTT
1 TTT
507699 AGTCACTAAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTAATTATAA
Found at i:507978 original size:22 final size:22
Alignment explanation
Indices: 507953--507996 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
507943 GGTATTTTAA
507953 AATTAAATATTATAAAAATTAT
1 AATTAAATATTATAAAAATTAT
* * **
507975 AATTTAATTTTATTTAAATTAT
1 AATTAAATATTATAAAAATTAT
507997 TATATTAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAATATTATAAAAATTAT
Found at i:508014 original size:23 final size:22
Alignment explanation
Indices: 507968--508012 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
507958 AATATTATAA
507968 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
507990 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
508013 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:508058 original size:115 final size:124
Alignment explanation
Indices: 507834--508069 Score: 274
Period size: 115 Copynumber: 2.0 Consensus size: 124
507824 TCATATAAAT
* * *
507834 ATATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATTTTAATATTTATTTTTCAAT
1 ATATATATAATAAATAATAATTTATATTTTATTTAAATAAATTATATTAATATTTA--TTTCAAT
* * * *
507899 ATCGAAGAAAAGGACAGTCTTAATACAACTGGATGTCCTATTCTGGTATTT-TAAAATTAA
64 ATCGAAGAAAAGGACAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAAATTAA
* *
507959 ATAT-TATAA-AAATTATAATTTA-ATTTTATTTAAAT-TATTATATTAATATTTA-TT-AATAT
1 ATATATATAATAAATAATAATTTATATTTTATTTAAATAAATTATATTAATATTTATTTCAATAT
* * * *
508018 CGAAGAAAA-G-CTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTCTAAA
66 CGAAGAAAAGGACAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAA
508070 TAAATAAATA
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
115 29 0.30
116 5 0.05
117 14 0.14
118 2 0.02
121 15 0.15
122 11 0.11
123 12 0.12
124 5 0.05
125 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (124 bp):
ATATATATAATAAATAATAATTTATATTTTATTTAAATAAATTATATTAATATTTATTTCAATAT
CGAAGAAAAGGACAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAAATTAA
Found at i:508092 original size:23 final size:26
Alignment explanation
Indices: 508060--508109 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
508050 CCTTTTCTGA
*
508060 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
508083 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
508109 T
1 T
508110 TTTCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:527904 original size:23 final size:23
Alignment explanation
Indices: 527842--527904 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
527832 GAGTCGATGG
*
527842 TTCTACGCGGTCCTTCGGGACAC
1 TTCTACGCGGTCCTTCGGGACAA
*** *
527865 TTCTATATGGTCATTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
*
527888 TTCTACGCGATCCTTCG
1 TTCTACGCGGTCCTTCG
527905 AGATAAATCT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:528948 original size:9 final size:9
Alignment explanation
Indices: 528936--529162 Score: 83
Period size: 9 Copynumber: 23.9 Consensus size: 9
528926 GAAATGAAAG
528936 TAAATAAAA
1 TAAATAAAA
*
528945 TAAAGAAAA
1 TAAATAAAA
*
528954 TAAA-AGGAA
1 TAAATA-AAA
528963 TAAAT-AAA
1 TAAATAAAA
528971 TAAAT-AAA
1 TAAATAAAA
528979 TAAATAAAA
1 TAAATAAAA
*
528988 TGGGATAAAAATAA
1 T---A-AATAA-AA
*
529002 TACAAAAAAA
1 TA-AATAAAA
**
529012 TGATGTAAAGA
1 T-AAATAAA-A
*
529023 TAAAAAAAA
1 TAAATAAAA
529032 GT-AATAAAA
1 -TAAATAAAA
529041 TAAATAAAA
1 TAAATAAAA
*
529050 TAAGTAAAA
1 TAAATAAAA
529059 GTAAAAGTAAGAAA
1 -T-AAA-T-A-AAA
* *
529073 TGAAGAAAA
1 TAAATAAAA
529082 TAAATAAAA
1 TAAATAAAA
* **
529091 TAAAGATCA
1 TAAATAAAA
*
529100 T-GATAATAA
1 TAAATAA-AA
*
529109 TATAATATAA
1 TA-AATAAAA
529119 TAAAT-AAA
1 TAAATAAAA
529127 TAAA-AACAA
1 TAAATAA-AA
529136 -AAATAAAA
1 TAAATAAAA
529144 TAAAATAAAAA
1 T-AAAT-AAAA
529155 TAAATAAA
1 TAAATAAA
529163 GAAACAAAAC
Statistics
Matches: 164, Mismatches: 28, Indels: 52
0.67 0.11 0.21
Matches are distributed among these distances:
8 31 0.19
9 73 0.45
10 25 0.15
11 19 0.12
12 4 0.02
13 6 0.04
14 6 0.04
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.20
Consensus pattern (9 bp):
TAAATAAAA
Found at i:528959 original size:34 final size:29
Alignment explanation
Indices: 528921--529012 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 29
528911 TTAGAGGAAA
528921 AAAAGGAAATGAAAGTAAATAAAATAAAGAAAAT
1 AAAAGG-AAT-AAA-TAAAT-AAATAAA-AAAAT
*
528955 AAAAGGAATAAATAAATAAATAAATAAAT
1 AAAAGGAATAAATAAATAAATAAAAAAAT
* *
528984 AAAATGGGAT-AA-AAATAATACAAAAAAAT
1 AAAA-GGAATAAATAAATAA-ATAAAAAAAT
529013 GATGTAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
28 6 0.12
29 18 0.35
30 11 0.21
31 5 0.10
32 3 0.06
33 3 0.06
34 6 0.12
ACGTcount: A:0.71, C:0.01, G:0.11, T:0.17
Consensus pattern (29 bp):
AAAAGGAATAAATAAATAAATAAAAAAAT
Found at i:528970 original size:4 final size:4
Alignment explanation
Indices: 528961--528986 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
528951 AAATAAAAGG
528961 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
528987 ATGGGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:529120 original size:13 final size:11
Alignment explanation
Indices: 529102--529161 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 11
529092 AAAGATCATG
529102 ATAATAATATAA
1 ATAATAA-ATAA
529114 TATAATAAATAA
1 -ATAATAAATAA
*
529126 ATAA-AAACAA
1 ATAATAAATAA
529136 A-AATAAAATAAA
1 ATAAT-AAAT-AA
529148 ATAA-AAATAA
1 ATAATAAATAA
529158 ATAA
1 ATAA
529162 AGAAACAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 2 0.05
10 12 0.29
11 11 0.27
12 7 0.17
13 9 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
ATAATAAATAA
Found at i:529141 original size:33 final size:34
Alignment explanation
Indices: 529104--529181 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 34
529094 AGATCATGAT
*
529104 AATAATATAATATAATAAATAAAT-AA-AAACAAA
1 AATAATATAAAATAA-AAATAAATAAAGAAACAAA
*
529137 AATAAAATAAAATAAAAATAAATAAAGAAACAAA
1 AATAATATAAAATAAAAATAAATAAAGAAACAAA
529171 ACA-AATATAAA
1 A-ATAATATAAA
529182 GGAAATAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 8 0.21
33 15 0.38
34 15 0.38
35 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (34 bp):
AATAATATAAAATAAAAATAAATAAAGAAACAAA
Found at i:529181 original size:39 final size:39
Alignment explanation
Indices: 529129--529203 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
529119 TAAATAAATA
*
529129 AAAACAAAAATAAAATAAAATA-AAAATAAATAAAGAAAC
1 AAAACAAAAAT-AAAGAAAATAGAAAATAAATAAAGAAAC
* * *
529168 AAAACAAATATAAAGGAAATAGAAAATAAGTAAAGA
1 AAAACAAAAATAAAGAAAATAGAAAATAAATAAAGA
529204 TAGAGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 8 0.26
39 23 0.74
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (39 bp):
AAAACAAAAATAAAGAAAATAGAAAATAAATAAAGAAAC
Found at i:529339 original size:2 final size:2
Alignment explanation
Indices: 529332--529358 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
529322 AATGAAAATA
529332 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 A
529359 ACGAATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:529947 original size:15 final size:15
Alignment explanation
Indices: 529924--529956 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
529914 AAAACCAAGC
*
529924 ATCGGGGGAGCGTAG
1 ATCGAGGGAGCGTAG
529939 ATCGAGGGAGCGTAG
1 ATCGAGGGAGCGTAG
529954 ATC
1 ATC
529957 TAAGAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.45, T:0.15
Consensus pattern (15 bp):
ATCGAGGGAGCGTAG
Found at i:531412 original size:9 final size:9
Alignment explanation
Indices: 531398--531431 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
531388 TAACATATGC
531398 AATGAAAAA
1 AATGAAAAA
*
531407 AATGAAAAG
1 AATGAAAAA
*
531416 AATGAACAA
1 AATGAAAAA
531425 AATGAAA
1 AATGAAA
531432 TATCAACATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (9 bp):
AATGAAAAA
Found at i:536650 original size:33 final size:34
Alignment explanation
Indices: 536595--536669 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
536585 GATCTTTTTC
536595 ATAACTTATCTTAAAAAAATGAATGACCCTAACA
1 ATAACTTATCTTAAAAAAATGAATGACCCTAACA
*
536629 ATAACTTGTCTT-AAAAAATGAATGACCCTAACA
1 ATAACTTATCTTAAAAAAATGAATGACCCTAACA
536662 ATAA-TTAT
1 ATAACTTAT
536670 ATAAGATAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
32 3 0.08
33 25 0.64
34 11 0.28
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (34 bp):
ATAACTTATCTTAAAAAAATGAATGACCCTAACA
Found at i:537284 original size:17 final size:18
Alignment explanation
Indices: 537245--537292 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
537235 TGTTTATGAG
537245 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
* *
537263 GGAATTGGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
537280 GGAATTAGAATCT
1 GGAATTAGAATCT
537293 AATCTCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:537915 original size:33 final size:33
Alignment explanation
Indices: 537873--537979 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 33
537863 AACCCGAACC
*
537873 CGACCCGACCCGAATATCATACTTAAAAAAATT
1 CGACCCGACCCGAATATCACACTTAAAAAAATT
*
537906 CGACCCGACCTGAATATCACACTT-AAAAAA--
1 CGACCCGACCCGAATATCACACTTAAAAAAATT
* ***
537936 --ACCCGACCTGAATATCACACTT-AAAAACCC
1 CGACCCGACCCGAATATCACACTTAAAAAAATT
537966 CGACCCGACCCGAA
1 CGACCCGACCCGAA
537980 CAAAATAAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
28 27 0.41
32 17 0.26
33 22 0.33
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (33 bp):
CGACCCGACCCGAATATCACACTTAAAAAAATT
Found at i:542169 original size:20 final size:21
Alignment explanation
Indices: 542124--542170 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
542114 ATTTGAAATG
* *
542124 TTTAACTAACATAATATTATA
1 TTTAACTAACATAATATCACA
542145 TTTAACTAACATAA-ATCACA
1 TTTAACTAACATAATATCACA
542165 TTTAAC
1 TTTAAC
542171 CATTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAACTAACATAATATCACA
Found at i:542839 original size:33 final size:33
Alignment explanation
Indices: 542793--542866 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
542783 GTGATGACGA
*
542793 CGATGACGGTGAAAGATGAGCAGGTTCGAGCGG
1 CGATGACGATGAAAGATGAGCAGGTTCGAGCGG
** *
542826 CGATGACGATGAAAGATGAGTGGGTTCGGGCGG
1 CGATGACGATGAAAGATGAGCAGGTTCGAGCGG
*
542859 CCATGACG
1 CGATGACG
542867 GACGACAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.16, G:0.42, T:0.16
Consensus pattern (33 bp):
CGATGACGATGAAAGATGAGCAGGTTCGAGCGG
Found at i:548933 original size:21 final size:21
Alignment explanation
Indices: 548909--548950 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
548899 AGTTTATTTT
548909 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
548930 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
548951 AACTTAGAAG
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:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:548987 original size:33 final size:32
Alignment explanation
Indices: 548939--549015 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
548929 GTAAACTTTG
* *
548939 TTTCAATTATCGAACTTAGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTAGAAGTATTTAAATA
* *
548971 TTTGAATTTATCGAACTTGGAAGTATTTAAATA
1 TTTCAA-TTATCGAACTTAGAAGTATTTAAATA
549004 TTTCAATTATCG
1 TTTCAATTATCG
549016 TAAACTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTCAATTATCGAACTTAGAAGTATTTAAATA
Found at i:549077 original size:15 final size:15
Alignment explanation
Indices: 549057--549089 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
549047 TTTAATAATA
549057 TTATAATCGATTTTT
1 TTATAATCGATTTTT
549072 TTATAATCGATTTTT
1 TTATAATCGATTTTT
549087 TTA
1 TTA
549090 AAAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (15 bp):
TTATAATCGATTTTT
Found at i:553307 original size:30 final size:34
Alignment explanation
Indices: 553243--553321 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
553233 TTAATAATTC
* *
553243 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
553277 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
553309 TAAAAAATAATAA
1 TAAAAAATAATAA
553322 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:558164 original size:5 final size:5
Alignment explanation
Indices: 558154--558178 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
558144 ATGGAAATGG
558154 TCCCC TCCCC TCCCC TCCCC TCCCC
1 TCCCC TCCCC TCCCC TCCCC TCCCC
558179 AGCCGACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
TCCCC
Found at i:563352 original size:3 final size:3
Alignment explanation
Indices: 563344--563392 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
563334 ATTTATTTAT
*
563344 TTA TTA TTA TTA TTA TTAA TTA TTA TTAA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TTA TTA TTA
563391 TT
1 TT
563393 TTTAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.88
4 5 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:563365 original size:16 final size:15
Alignment explanation
Indices: 563344--563392 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 15
563334 ATTTATTTAT
563344 TTATTATTATTATTA
1 TTATTATTATTATTA
*
563359 TTAATTATTATTAACTA
1 TT-ATTATTATT-ATTA
563376 TTATTATTATTATTA
1 TTATTATTATTATTA
563391 TT
1 TT
563393 TTTAATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 7 0.23
16 18 0.60
17 5 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:576425 original size:17 final size:18
Alignment explanation
Indices: 576394--576427 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
576384 AAAATGATGG
576394 AAAAATGAAAAAAAGGAA
1 AAAAATGAAAAAAAGGAA
*
576412 AAAAAT-AAATAAAGGA
1 AAAAATGAAAAAAAGGA
576428 GGGTTCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAAAATGAAAAAAAGGAA
Found at i:577702 original size:141 final size:134
Alignment explanation
Indices: 577353--577801 Score: 437
Period size: 141 Copynumber: 3.3 Consensus size: 134
577343 TTAACATCAG
* * ** *
577353 CTGACCAGATCTCCTCATCATGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACG
1 CTGATCAGATCTCCTCATCACGTAGGAGCAGTGTCAACCTTAGATAACCAGCCGTCCTCATTACG
*
577418 TAGGAA-CTATGTTATCA--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGTATG-AGCAGTG
66 TAGGAACCTA-GTTATCACCCTTCATAAAGATGGCC-AGAACTCTTCATCACGTATGAACCA-TG
577476 TCATCCC
128 TCATCCC
* ** * * ** **
577483 CTGATTAGATCTCCTCATCACGTAGGAGTTGTGTCACCCCTAGATAACCAGTTGTCCTCATCGCG
1 CTGATCAGATCTCCTCATCACGTAGGAGCAGTGTCAACCTTAGATAACCAGCCGTCCTCATTACG
* * * *
577548 TAGGAACCAAGTTATCACCCTTCCTAAAGATGGCCAGAATTCTTCATCATGTATGAACCATGTCA
66 TAGGAACCTAGTTATCACCCTTCATAAAGATGGCCAGAACTCTTCATCACGTATGAACCATGTCA
577613 TCTACC
131 TC--CC
* * * *
577619 CTTAGACGATCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAATCAGCCATCCTCA
1 C-T----GATCAGATCTCCTCATCACGTAGGAGCAGTGTCAACCTTAGATAACCAGCCGTCCTCA
* * * * * *
577684 TTACGTAGGAACCTAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTTATCGCGTATGAGCCG
61 TTACGTAGGAACCTAGTTATCACCCTTCATAAAGATGGCCAGAACTCTTCATCACGTATGAACCA
577749 TGTCATCCC
126 TGTCATCCC
* * * * *
577758 TTGACCAGATTTCCTCATCACGTAGGAATCA-TGTCACCCTTAGA
1 CTGATCAGATCTCCTCATCACGTAGG-AGCAGTGTCAACCTTAGA
577802 CGACCCGAAC
Statistics
Matches: 257, Mismatches: 47, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
130 64 0.25
131 2 0.01
132 1 0.00
133 1 0.00
134 62 0.24
135 11 0.04
136 3 0.01
137 1 0.00
138 1 0.00
139 2 0.01
141 109 0.42
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (134 bp):
CTGATCAGATCTCCTCATCACGTAGGAGCAGTGTCAACCTTAGATAACCAGCCGTCCTCATTACG
TAGGAACCTAGTTATCACCCTTCATAAAGATGGCCAGAACTCTTCATCACGTATGAACCATGTCA
TCCC
Found at i:578002 original size:3 final size:3
Alignment explanation
Indices: 577994--578058 Score: 94
Period size: 3 Copynumber: 20.7 Consensus size: 3
577984 TTATATTTAT
*
577994 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTAA TTA TTA TTAA CTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TT-A TTA
578042 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
578059 TTTAATTTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 49 0.86
4 8 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:578003 original size:10 final size:9
Alignment explanation
Indices: 577994--578058 Score: 94
Period size: 10 Copynumber: 6.9 Consensus size: 9
577984 TTATATTTAT
577994 TTATTATTA
1 TTATTATTA
578003 TTATTATTA
1 TTATTATTA
578012 TTATTAATTA
1 TTATT-ATTA
578022 TTATTAATTA
1 TTATT-ATTA
*
578032 TTATTAACTA
1 TTATT-ATTA
578042 TTATTATTA
1 TTATTATTA
578051 TTATTATT
1 TTATTATT
578059 TTTAATTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
9 25 0.47
10 28 0.53
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TTATTATTA
Found at i:586276 original size:182 final size:182
Alignment explanation
Indices: 585969--586424 Score: 752
Period size: 182 Copynumber: 2.5 Consensus size: 182
585959 ACTTTTTTAC
* * *
585969 TACCGGTTTTGTTATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* *
586034 TACATTTTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTGACGCTATAACTTATTCTCTTTTAAATTCCAAAAG
* * *
586099 TGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCGGGTAGCGCTT
*
586151 TACCGGTTTTGTCATTTCGAGACCGGTTTTGCCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
586216 TACATTTTTATAAAGTATCGACACTTTATT-AGCGCTATAACTTATTCTCTTTTTAATTCCAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTGA-CGCTATAACTTATTCTCTTTTAAATTCCAAAA
586280 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCGGGTAGCGCTT
130 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCGGGTAGCGCTT
* ** * * *
586333 TACCTGTTTTGTCATTTATAGACCGGTTTTGTTATTTTTTTACATGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
586398 TACATTTTTATAAAGTATCGACACTTT
66 TACATTTTTATAAAGTATCGACACTTT
586425 CAATATATCC
Statistics
Matches: 256, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
181 1 0.00
182 255 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTGACGCTATAACTTATTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCGGGTAGCGCTT
Found at i:595959 original size:21 final size:21
Alignment explanation
Indices: 595933--595992 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
595923 GGATTCTGGG
595933 CAGAGTGCATCGATGCATATT
1 CAGAGTGCATCGATGCATATT
595954 CAGAGTGCATCGATGCATATT
1 CAGAGTGCATCGATGCATATT
*
595975 CATAGTGCATCGATGCAT
1 CAGAGTGCATCGATGCAT
595993 CAAGGTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
CAGAGTGCATCGATGCATATT
Found at i:596097 original size:64 final size:64
Alignment explanation
Indices: 596028--596182 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 64
596018 GAAGGTGTAT
* ** *
596028 CGATGCACAGGTAGTGCATCAATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGTGC
1 CGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-TGC
*
596090 AT
63 AC
* * * *
596092 TGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGCAC
1 CGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGCAC
*
596156 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAGGTAGTGCATCGATGCAT
596183 ACCTTCATTA
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 3 0.04
64 59 0.81
65 11 0.15
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
CGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGCAC
Found at i:596719 original size:15 final size:15
Alignment explanation
Indices: 596701--596734 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
596691 GAGGGTATAA
596701 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
596716 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
596731 TAGT
1 TAGT
596735 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:603508 original size:29 final size:29
Alignment explanation
Indices: 603471--603550 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
603461 TATGTGATAT
*
603471 GAGACATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
603500 GAGAAATGACATGAGCTACATAATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
603529 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
603551 ACATATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 6 0.12
29 42 0.88
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:605873 original size:32 final size:30
Alignment explanation
Indices: 605835--605914 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 30
605825 AATATAATTT
605835 ATAATATTTTAT-TTCAATAAAA-TATACAAA
1 ATAATATTTTATATT-AATAAAATTATA-AAA
605865 TATTAATATTTT-TATTAATAAAATTATAAAA
1 -A-TAATATTTTATATTAATAAAATTATAAAA
605896 ATAATATTTTA-A-TAATAAA
1 ATAATATTTTATATTAATAAA
605915 TAAATTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
28 7 0.16
29 10 0.22
30 1 0.02
31 12 0.27
32 15 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAATATTTTATATTAATAAAATTATAAAA
Found at i:605888 original size:31 final size:28
Alignment explanation
Indices: 605835--605914 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 28
605825 AATATAATTT
605835 ATAATATTTTATTTCAATAAAA-TATACAAA
1 ATAATATTTTA-TT-AATAAAATTATA-AAA
605865 TATTAATATTTTTATTAATAAAATTATAAAA
1 -A-TAATA-TTTTATTAATAAAATTATAAAA
*
605896 ATAATATTTTAATAATAAA
1 ATAATATTTTATTAATAAA
605915 TAAATTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
28 12 0.27
29 5 0.11
30 1 0.02
31 11 0.24
32 11 0.24
33 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAATATTTTATTAATAAAATTATAAAA
Found at i:606156 original size:14 final size:14
Alignment explanation
Indices: 606103--606155 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
606093 CATACGCGCA
606103 TATGAAGACTGCAT
1 TATGAAGACTGCAT
606117 TATGAAGACTGCAT
1 TATGAAGACTGCAT
* *
606131 TATGAAAACTGTAT
1 TATGAAGACTGCAT
606145 TATGAAGACTG
1 TATGAAGACTG
606156 TTCAACTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (14 bp):
TATGAAGACTGCAT
Found at i:606833 original size:22 final size:21
Alignment explanation
Indices: 606787--606840 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
606777 ATAATTATTT
*
606787 AAAAAATTAAATAAAAATACTA
1 AAAAAATTTAATAAAAATAC-A
*
606809 AAAATATTTAATAAAAA-ATCAA
1 AAAAAATTTAATAAAAATA-C-A
606831 AAAAAATTTA
1 AAAAAATTTA
606841 GGTTAAACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTTAATAAAAATACA
Found at i:607041 original size:18 final size:18
Alignment explanation
Indices: 607005--607043 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
606995 AACACTGCTC
*
607005 AAAATACATATAAAGAAG
1 AAAATACAAATAAAGAAG
607023 AAAATGACAAATAAA-AAG
1 AAAAT-ACAAATAAAGAAG
607041 AAA
1 AAA
607044 CGGCTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAATACAAATAAAGAAG
Found at i:609364 original size:23 final size:23
Alignment explanation
Indices: 609338--609425 Score: 131
Period size: 23 Copynumber: 3.8 Consensus size: 23
609328 CACCACAGCT
*
609338 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
609361 CGTAGAATTGCATCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
609384 CTTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
609407 TGTAGAATTTCACCGAAGT
1 CGTAGAATTGCACCGAAGT
609426 TCCATATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:615711 original size:46 final size:46
Alignment explanation
Indices: 615579--615737 Score: 237
Period size: 46 Copynumber: 3.4 Consensus size: 46
615569 TCTATGGTAT
* * * *
615579 AATGGCAAGTGTATTGGTAAAATAAGTTTACGAGCTTATGATATTA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTA
* *
615625 AATGATAAGTATATTTGTAAAAATAAGCTTACGAGCTTATGAAATTA
1 AATGGTAAGTATATTGGT-AAAATAAGCTTACGAGCTTATGAAATTA
* *
615672 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAGTTA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTA
615718 AATGGTAAGTATATTGGTAA
1 AATGGTAAGTATATTGGTAA
615738 GAAACTTTAT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 60 0.59
47 42 0.41
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.34
Consensus pattern (46 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTA
Found at i:620322 original size:23 final size:23
Alignment explanation
Indices: 620296--620351 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
620286 CGTATAAATA
620296 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
620319 CACCGAAGTGCCATGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
620342 CACCAAAGTG
1 CACCGAAGTG
620352 TCATATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:645761 original size:20 final size:20
Alignment explanation
Indices: 645733--645804 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
645723 TTCCTAATTT
645733 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* ** *
645753 GCAACGCGAATTTGGAAAATC
1 GCAATGCGAA-TACGTAAATC
645774 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
645794 GCAATGTGAAT
1 GCAATGCGAAT
645805 CTGACTATCG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:646023 original size:22 final size:22
Alignment explanation
Indices: 645998--646063 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
645988 GGCGACATAT
645998 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
646020 GTCCCCAT-TGCCGACGATATCA
1 GTCCCCATCT-CCGACGAAATCA
* *
646042 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
646064 TTCACGATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:646435 original size:20 final size:19
Alignment explanation
Indices: 646353--646436 Score: 79
Period size: 20 Copynumber: 4.6 Consensus size: 19
646343 GCGATTTTGT
646353 TGTTGCGATTTTCATTTCG
1 TGTTGCGATTTTCATTTCG
*
646372 CGTTGCGA--TTC--TT-G
1 TGTTGCGATTTTCATTTCG
* **
646386 CGTTGCGATAGTCATTTTCG
1 TGTTGCGATTTTCA-TTTCG
646406 TGTTGCGATTTTCATTTTCG
1 TGTTGCGATTTTCA-TTTCG
646426 TGTTGCGATTT
1 TGTTGCGATTT
646437 AAAGATTCAG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 2 0.04
17 3 0.06
19 9 0.17
20 29 0.54
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.49
Consensus pattern (19 bp):
TGTTGCGATTTTCATTTCG
Found at i:648340 original size:20 final size:20
Alignment explanation
Indices: 648315--648471 Score: 144
Period size: 20 Copynumber: 8.5 Consensus size: 20
648305 AGAATAGTTT
648315 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
648335 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
648355 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
648371 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
648388 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
648404 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
648422 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
648442 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
648462 ACTATCGCAA
1 ACTATCGCAA
648472 CGAGAGAATA
Statistics
Matches: 117, Mismatches: 6, Indels: 28
0.77 0.04 0.19
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 8 0.07
18 5 0.04
19 7 0.06
20 73 0.62
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:648384 original size:34 final size:34
Alignment explanation
Indices: 648338--648490 Score: 146
Period size: 34 Copynumber: 4.4 Consensus size: 34
648328 GAAAATGACT
*
648338 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
** * * *
648372 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
* *
648405 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AGA-GA
**
648443 CTATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
*
648479 ATAGCAATGCGA
1 ATCGCAATGCGA
648491 TTTTCATTTC
Statistics
Matches: 95, Mismatches: 17, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
33 27 0.28
34 34 0.36
36 3 0.03
37 4 0.04
38 3 0.03
40 24 0.25
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
Found at i:648570 original size:20 final size:20
Alignment explanation
Indices: 648521--648581 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
648511 TCTTTCGTTA
** *
648521 CGATAGTCAAATTCACATTG
1 CGATAGTCATTTTCGCATTG
648541 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
648561 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
648581 C
1 C
648582 TATTTTATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:648613 original size:33 final size:34
Alignment explanation
Indices: 648497--648655 Score: 133
Period size: 34 Copynumber: 4.5 Consensus size: 34
648487 GCGATTTTCA
* *
648497 TTTCGCATTGCGATTCTT-TCGTTACGATAGTCAA
1 TTTCGCATTGCGATT-TTATCGTTGCGATAGTCAT
* * *
648531 ATTCACATTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--T--TTATCG--TTGCGATAGTCAT
* * **
648571 TTTCGCATTGCTATTTTATTGTTGCGATTTTCA-
1 TTTCGCATTGCGATTTTATCGTTGCGATAGTCAT
* *
648604 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTTTATCGTTGCGATAGTCAT
*
648638 TTTCGCGTTGCGATTTTA
1 TTTCGCATTGCGATTTTA
648656 AGTTTCAGAT
Statistics
Matches: 97, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
33 27 0.28
34 37 0.38
36 5 0.05
37 2 0.02
38 4 0.04
40 22 0.23
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.44
Consensus pattern (34 bp):
TTTCGCATTGCGATTTTATCGTTGCGATAGTCAT
Found at i:648640 original size:53 final size:53
Alignment explanation
Indices: 648486--648654 Score: 139
Period size: 53 Copynumber: 3.2 Consensus size: 53
648476 AGAATAGCAA
* * * *
648486 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTACGATAGTCAAATTCACAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCAATTTTACGT
** ** * * * *
648539 TGCGATAGTCATTTTCGCATTGCGATAGTCAT--TTTCGCATTG-CTATTTTATTGT
1 TGCGATTTTCA-TTTCGCATTGCGATTCTC-TCGTTACG-ATAGTCAATTTTA-CGT
* *
648593 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTC-ATTTTCGCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCAATTTT-ACGT
648646 TGCGATTTT
1 TGCGATTTT
648655 AAGTTTCAGA
Statistics
Matches: 88, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
52 1 0.01
53 53 0.60
54 33 0.38
55 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATAGTCAATTTTACGT
Found at i:649220 original size:42 final size:42
Alignment explanation
Indices: 649150--649230 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
649140 TCCCCTATCA
* *
649150 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCG
1 TTCAAGAGGCCACTATCATCACTCAAGAGGT-CCCTCCCACCG
* * *
649192 TTCAAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCA
649231 ACATTCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCACCG
Found at i:650608 original size:14 final size:14
Alignment explanation
Indices: 650589--650624 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
650579 ATTGTTTAAT
650589 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
650603 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
650617 TGATTTGT
1 TGATTTGT
650625 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:650809 original size:33 final size:33
Alignment explanation
Indices: 650718--650796 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
650708 AAAACAGACT
* **
650718 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
650752 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
650785 ATCGCAATGCGA
1 ATCGCAATGCGA
650797 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 32 0.78
34 9 0.22
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:650847 original size:20 final size:20
Alignment explanation
Indices: 650822--650955 Score: 182
Period size: 20 Copynumber: 6.7 Consensus size: 20
650812 GCGATTCTCT
*
650822 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
* *
650842 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
650862 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
650882 TGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
650902 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
650922 CGTTGCGATAGTCATATT-CA
1 CGTTGCGATAGTCAT-TTCCG
650942 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
650956 AATGAATGTC
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 103 0.98
21 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:650925 original size:60 final size:60
Alignment explanation
Indices: 650822--650955 Score: 202
Period size: 60 Copynumber: 2.2 Consensus size: 60
650812 GCGATTCTCT
650822 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCAATTCTGCGTTGCGATAGTCAT-TTC-
1 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCAATTCTGCGTTGCGATAGTCATATTCA
**
650880 CGTGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC-GCGTTGCGATAGTCATATTCA
1 C--GTTGCGATAGTCATTTCCACGTTGCGATAGTCA-ATTCTGCGTTGCGATAGTCATATTCA
650942 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
650956 AATGAATGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
58 1 0.01
60 60 0.87
61 7 0.10
62 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (60 bp):
CGTTGCGATAGTCATTTCCACGTTGCGATAGTCAATTCTGCGTTGCGATAGTCATATTCA
Found at i:654274 original size:20 final size:20
Alignment explanation
Indices: 654249--654315 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
654239 AAATTCAATA
*
654249 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
654269 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
* *
654289 TTGCGAT-TTACAGATTCGCG
1 TTGCGATAGT-CAGAATCGCG
654309 TTGCGAT
1 TTGCGAT
654316 TTACGTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:654316 original size:20 final size:20
Alignment explanation
Indices: 654282--654455 Score: 251
Period size: 20 Copynumber: 8.7 Consensus size: 20
654272 CGATAGTCAG
*
654282 ATTCGCGTTGCGATTTACAG-
1 ATTCGCATTGCGATTTAC-GT
*
654302 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
654322 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
654342 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
654362 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
**
654382 AACCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
654402 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
654423 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
654443 ATTCGCATTGCGA
1 ATTCGCATTGCGA
654456 ATTAGGAAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.01
20 122 0.88
21 16 0.12
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:656465 original size:26 final size:26
Alignment explanation
Indices: 656436--656487 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
656426 GTCTGTCAAG
656436 CTTTTAACCCAGGATTTGAGAGTAAA
1 CTTTTAACCCAGGATTTGAGAGTAAA
656462 CTTTTAACCCAGGATTTGAGAGTAAA
1 CTTTTAACCCAGGATTTGAGAGTAAA
656488 AAAACAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (26 bp):
CTTTTAACCCAGGATTTGAGAGTAAA
Found at i:658112 original size:33 final size:33
Alignment explanation
Indices: 658014--658114 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
658004 ACTCCTTCAA
*
658014 GCATGAATCACCCAGTAGTTTCTGGAGGAGTTA
1 GCATGAATCACCCAGTAGTTTCTGGAGGAGTTG
* * *
658047 CCATGAATAACCCAATAGTTTCTGGAGGAGTTG
1 GCATGAATCACCCAGTAGTTTCTGGAGGAGTTG
*
658080 GCATGAATCACCCGGTAGTTTCTGGAGGAGTTG
1 GCATGAATCACCCAGTAGTTTCTGGAGGAGTTG
658113 GC
1 GC
658115 CTTGGTGGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (33 bp):
GCATGAATCACCCAGTAGTTTCTGGAGGAGTTG
Found at i:673825 original size:19 final size:19
Alignment explanation
Indices: 673801--673839 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
673791 GCTAGGATGG
*
673801 AAGCAATTAGAATGTTATT
1 AAGCAATTAGAATATTATT
673820 AAGCAATTAGAATATTATT
1 AAGCAATTAGAATATTATT
673839 A
1 A
673840 GCATTTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (19 bp):
AAGCAATTAGAATATTATT
Found at i:675369 original size:20 final size:22
Alignment explanation
Indices: 675346--675425 Score: 85
Period size: 21 Copynumber: 3.7 Consensus size: 22
675336 TTGGTGCAGA
*
675346 GGGAATCGA-TCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
*
675366 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
*
675389 GGGAACCGATTCCCCCC-AGAG
1 GGGAACCGATTCCCCCCTTGAG
* *
675410 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
675426 TAGGGTTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.16
21 25 0.49
22 2 0.04
23 16 0.31
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:675396 original size:23 final size:21
Alignment explanation
Indices: 675344--675405 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
675334 TTTTGGTGCA
*
675344 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
675364 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
675385 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
675406 AGAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:677657 original size:13 final size:13
Alignment explanation
Indices: 677639--677666 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
677629 AAAGGGGGAG
677639 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
677652 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
677665 AA
1 AA
677667 AATAAGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:680073 original size:16 final size:17
Alignment explanation
Indices: 680037--680090 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
680027 CACGCATGGC
* *
680037 TAATAATAATATTATATG
1 TAATAATAAT-TAATAAG
*
680055 TAATCATAATTAAT-AG
1 TAATAATAATTAATAAG
*
680071 TAATAATTATTAATAAG
1 TAATAATAATTAATAAG
680088 TAA
1 TAA
680091 CCCATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 13 0.43
17 8 0.27
18 9 0.30
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (17 bp):
TAATAATAATTAATAAG
Found at i:683511 original size:18 final size:19
Alignment explanation
Indices: 683461--683512 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
683451 AATATTAACA
683461 AAAATAATATA-AAAATATG
1 AAAAT-ATATAGAAAATATG
* * *
683480 CAAATAAATTGAAAATAT-
1 AAAATATATAGAAAATATG
683498 AAAATATATAGAAAA
1 AAAATATATAGAAAA
683513 ATTATTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (19 bp):
AAAATATATAGAAAATATG
Done.