Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009164.1 Hibiscus syriacus cultivar Beakdansim tig00112699_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: 622707
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:437962 original size:2 final size:2
Alignment explanation
Indices: 437955--437981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
437945 GCTAGATCAT
437955 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
437982 TTGCTAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:438710 original size:46 final size:48
Alignment explanation
Indices: 438603--438722 Score: 163
Period size: 46 Copynumber: 2.5 Consensus size: 48
438593 CACGTAGGGG
438603 TATAGCGCGGGGCAGGTACCGCGACATACATTTACTCCTGACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGACATACATTTA--CC-GACATAATTTTA
* * * *
438654 TATAACGCGGGACAGGTACCGTGACATACCTTTA-C-ACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGACATACATTTACCGACATAATTTTA
438700 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
438723 TTTTGTATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
46 31 0.50
48 1 0.02
51 30 0.48
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (48 bp):
TATAGCGCGGGGCAGGTACCGCGACATACATTTACCGACATAATTTTA
Found at i:439554 original size:24 final size:24
Alignment explanation
Indices: 439510--439555 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
439500 AAATATTATA
*
439510 TTTTTAATTATTTATATGTTCTTT
1 TTTTTAATTATTTATAGGTTCTTT
*
439534 TTTTATAATT-TTTCTAGGTTCT
1 TTTT-TAATTATTTATAGGTTCT
439556 AATTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (24 bp):
TTTTTAATTATTTATAGGTTCTTT
Found at i:440417 original size:26 final size:27
Alignment explanation
Indices: 440371--440433 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
440361 TTTTAAAAAT
*
440371 ATATTTTGATTTTGTCTTTAACTTATTCA
1 ATATTTT--TTTTGTCTTTAACTTATTAA
440400 ATATTTTTTTTGTC-TTAACTTATTAA
1 ATATTTTTTTTGTCTTTAACTTATTAA
440426 ATATTTTT
1 ATATTTTT
440434 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 19 0.58
27 7 0.21
29 7 0.21
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (27 bp):
ATATTTTTTTTGTCTTTAACTTATTAA
Found at i:442307 original size:17 final size:18
Alignment explanation
Indices: 442285--442319 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
442275 TCTATAAAAA
442285 TATTTTATTA-TATTATT
1 TATTTTATTATTATTATT
442302 TATTTTATTATTATTATT
1 TATTTTATTATTATTATT
442320 ATTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTATTATTATTATT
Found at i:448770 original size:110 final size:105
Alignment explanation
Indices: 448550--448823 Score: 309
Period size: 110 Copynumber: 2.5 Consensus size: 105
448540 GGCTTCCCAG
* *
448550 TTTCATAGCCAAGTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG-ACTCAAGACAACACAAGCTCAACTTC
* *
448615 ACAACGAAGGGGAGATTGATTGTCAACAAAAAACTTTTCAA
65 ACAACGAAGGGGAGATTGACTGTCAACAAAAAACTTTCCAA
* * * *
448656 TTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAATCTCAA
1 --T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT-GACTCAAGACAACACAAGCTCAA
* * * * * *
448721 CTTCACAGCGAAGGGGCGGTTGGCTGTCAACAAACAA-TTTCCCAG
61 CTTCACAACGAAGGGGAGATTGACTGTCAACAAAAAACTTT-CCAA
* *
448766 TTTCAGAGCCAATTTCAATTTCAC-GACGAAGGATATTGGACTCAAAACAACACAAGCT
1 TTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATT-GACTCAAGACAACACAAGCT
448824 TGGATTTCAA
Statistics
Matches: 140, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
105 1 0.01
106 48 0.34
108 2 0.01
109 3 0.02
110 85 0.61
111 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (105 bp):
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGAGATTGACTGTCAACAAAAAACTTTCCAA
Found at i:449341 original size:84 final size:84
Alignment explanation
Indices: 449176--449368 Score: 208
Period size: 84 Copynumber: 2.3 Consensus size: 84
449166 GATATTGTGT
* * * * * *
449176 TCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTTCCAACCAAAGGCCATCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAAAAAGGCTATCTGCCAACCAAAGACCATCGAGTTCGACTA
* * *
449241 CGCTCAGCTCCAAGGCACA
66 CACTCAACTCCAAGGCAAA
* * * *
449260 TCATTTGCAACATAGCTCAAGGCAAAAAAGGCTATCTGCTAACCAAAGATCTTCGAGTTCGATTA
1 TCATTTGCAACATAGCTCAAGGCAAAAAAGGCTATCTGCCAACCAAAGACCATCGAGTTCGACTA
*
449325 CATTCAACT-CAGAGGCAAA
66 CACTCAACTCCA-AGGCAAA
* *
449344 TCAAATTTACAGCATAGCTCAAGGC
1 TC--ATTTGCAACATAGCTCAAGGC
449369 GATAAGGTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
83 2 0.02
84 69 0.77
86 19 0.21
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (84 bp):
TCATTTGCAACATAGCTCAAGGCAAAAAAGGCTATCTGCCAACCAAAGACCATCGAGTTCGACTA
CACTCAACTCCAAGGCAAA
Found at i:461501 original size:42 final size:42
Alignment explanation
Indices: 461454--461591 Score: 116
Period size: 45 Copynumber: 3.1 Consensus size: 42
461444 GTTTAAGGTT
461454 TAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTC
1 TAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTC
* * * * * * * * * *
461496 TAAAAAGAACTTAACAAGGTTGTTTTAATAATTAAAGGTAA-TGCGGTT
1 TAAAAA-ATC-CATCAA-ATTCTATGAACAA-TAGA-GTAACT--GGTC
461544 TAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTC
1 TAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTC
461586 TAAAAA
1 TAAAAA
461592 GAACTTAACA
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
42 15 0.22
43 6 0.09
44 8 0.12
45 16 0.24
46 8 0.12
47 6 0.09
48 9 0.13
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (42 bp):
TAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTC
Found at i:461603 original size:90 final size:90
Alignment explanation
Indices: 461450--461632 Score: 357
Period size: 90 Copynumber: 2.0 Consensus size: 90
461440 CACTGTTTAA
461450 GGTTTAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTCTAAAAAGAACTTAACAAGG
1 GGTTTAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTCTAAAAAGAACTTAACAAGG
*
461515 TTGTTTTAATAATTAAAGGTAATGC
66 TTGTTTTAATAATCAAAGGTAATGC
461540 GGTTTAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTCTAAAAAGAACTTAACAAGG
1 GGTTTAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTCTAAAAAGAACTTAACAAGG
461605 TTGTTTTAATAATCAAAGGTAATGC
66 TTGTTTTAATAATCAAAGGTAATGC
461630 GGT
1 GGT
461633 GAAGTGTGAC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (90 bp):
GGTTTAAAAAATCCATCAAATTCTATGAACAATAGAGTAACTGGTCTAAAAAGAACTTAACAAGG
TTGTTTTAATAATCAAAGGTAATGC
Found at i:465814 original size:94 final size:95
Alignment explanation
Indices: 465648--465841 Score: 381
Period size: 94 Copynumber: 2.1 Consensus size: 95
465638 CACTGAGTAT
465648 ACATCTAAAATGATTCTCCGATTGGTTCACTTCTTTGCAATTTATGAGCTTCGACTTAGGAACCA
1 ACATCTAAAATGATTCTCCGATTGGTTCACTTCTTTGCAATTTATGAGCTTCGACTTAGGAACCA
465713 CAGGGTTTCACCAATTACACTTTTGTATTA
66 CAGGGTTTCACCAATTACACTTTTGTATTA
465743 ACAT-TAAAATGATTCTCCGATTGGTTCACTTCTTTGCAATTTATGAGCTTCGACTTAGGAACCA
1 ACATCTAAAATGATTCTCCGATTGGTTCACTTCTTTGCAATTTATGAGCTTCGACTTAGGAACCA
465807 CAGGGTTTCACCAATTACACTTTTGTATTA
66 CAGGGTTTCACCAATTACACTTTTGTATTA
465837 ACATC
1 ACATC
465842 CTAATAAGGT
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 94 0.96
95 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (95 bp):
ACATCTAAAATGATTCTCCGATTGGTTCACTTCTTTGCAATTTATGAGCTTCGACTTAGGAACCA
CAGGGTTTCACCAATTACACTTTTGTATTA
Found at i:469448 original size:22 final size:22
Alignment explanation
Indices: 469420--469481 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
469410 ATACGATATG
*
469420 AACAGTACCGTGAACATTAATA
1 AACAGTACCGTGAACAGTAATA
*
469442 AACAGTACCGTGAACAGTAATG
1 AACAGTACCGTGAACAGTAATA
* **
469464 AACATTACTATGAACAGT
1 AACAGTACCGTGAACAGT
469482 GAAAAAATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.23
Consensus pattern (22 bp):
AACAGTACCGTGAACAGTAATA
Found at i:470027 original size:31 final size:31
Alignment explanation
Indices: 469988--470112 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
469978 CCCGAAGGAC
* *
469988 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
470019 AAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
470050 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
470081 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
470112 C
1 C
470113 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:470303 original size:59 final size:58
Alignment explanation
Indices: 470215--470327 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 58
470205 TCATTTCTTT
* * * *
470215 TTATAAACACATATCTTTCTTTTCTGTCACGTATCACATGTACGTGTAATCATTGATC
1 TTATAAACACATATCTTTCTCTTCTGTCACATACCACATGTACGTGTAAACATTGATC
* * *
470273 TTATAATCACATATTTCTTT-TCTTCTGTCACATACCATATGTATGTGTAAACATT
1 TTATAAACACATA--TCTTTCTCTTCTGTCACATACCACATGTACGTGTAAACATT
470328 TATTTCATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 12 0.26
59 29 0.63
60 5 0.11
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.43
Consensus pattern (58 bp):
TTATAAACACATATCTTTCTCTTCTGTCACATACCACATGTACGTGTAAACATTGATC
Found at i:477470 original size:20 final size:21
Alignment explanation
Indices: 477447--477526 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
477437 TTAGTTCAGA
477447 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* *
477467 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-ATG-AG
* *
477490 GGGAACCGATACCCCCCA-CAG
1 GGGAATCGATA-CCCCCATGAG
477511 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
477527 CTGGGTTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 20 0.41
21 14 0.29
22 1 0.02
23 9 0.18
24 5 0.10
ACGTcount: A:0.26, C:0.34, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:477514 original size:21 final size:21
Alignment explanation
Indices: 477488--477527 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
477478 CCCCCTTTGA
477488 AGGGGAACCGATACCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
477509 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
477528 TGGGTTCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.40, G:0.25, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:481247 original size:23 final size:23
Alignment explanation
Indices: 481201--481244 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
481191 TGTCAGTGAT
*
481201 TATTATTTTTCTTGTTCTTTTTC
1 TATTATGTTTCTTGTTCTTTTTC
*
481224 TATTATGTTT-TTGTTTTTTTT
1 TATTATGTTTCTTGTTCTTTTT
481245 TCTTTGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (23 bp):
TATTATGTTTCTTGTTCTTTTTC
Found at i:487126 original size:34 final size:34
Alignment explanation
Indices: 487087--487154 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
487077 GCATCTCTAA
487087 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
1 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
487121 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
1 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
487155 TCGGTTTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (34 bp):
CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
Found at i:487735 original size:17 final size:17
Alignment explanation
Indices: 487713--487747 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
487703 TGCGCCCCTT
487713 CGCTTGCTCGACTCTTA
1 CGCTTGCTCGACTCTTA
487730 CGCTTGCTCGACTCTTA
1 CGCTTGCTCGACTCTTA
487747 C
1 C
487748 CCTCGGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.37, G:0.17, T:0.34
Consensus pattern (17 bp):
CGCTTGCTCGACTCTTA
Found at i:490832 original size:34 final size:34
Alignment explanation
Indices: 490793--490860 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
490783 GCATCTCTAA
490793 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
1 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
490827 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
1 CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
490861 TCGGTTTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (34 bp):
CGTAGGAACTCCTTCCTACAAGTCTTGATTTGCC
Found at i:491440 original size:17 final size:17
Alignment explanation
Indices: 491418--491452 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
491408 TGCGCCCCTT
491418 CGCTTGCTCGACTCTTA
1 CGCTTGCTCGACTCTTA
491435 CGCTTGCTCGACTCTTA
1 CGCTTGCTCGACTCTTA
491452 C
1 C
491453 CCTCGGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.37, G:0.17, T:0.34
Consensus pattern (17 bp):
CGCTTGCTCGACTCTTA
Found at i:496438 original size:21 final size:21
Alignment explanation
Indices: 496414--496531 Score: 173
Period size: 21 Copynumber: 5.6 Consensus size: 21
496404 CATAGTTTCT
*
496414 AAATTCGCGACGCGATTATCC
1 AAATTCGCGACGCGATTCTCC
**
496435 AAATTCGCGACGCGATTCTTT
1 AAATTCGCGACGCGATTCTCC
*
496456 AAATTCGTGACGCGATTCTCC
1 AAATTCGCGACGCGATTCTCC
* *
496477 AAATTCGCGTCGCGATTCTCT
1 AAATTCGCGACGCGATTCTCC
496498 AAATTCGCGACGCGATTCTCC
1 AAATTCGCGACGCGATTCTCC
*
496519 AAATTCGTGACGC
1 AAATTCGCGACGC
496532 TAATTACTGA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
AAATTCGCGACGCGATTCTCC
Found at i:496468 original size:42 final size:42
Alignment explanation
Indices: 496411--496531 Score: 197
Period size: 42 Copynumber: 2.9 Consensus size: 42
496401 CAACATAGTT
*
496411 TCTAAATTCGCGACGCGATTATCCAAATTCGCGACGCGATTC
1 TCTAAATTCGCGACGCGATTCTCCAAATTCGCGACGCGATTC
* * *
496453 TTTAAATTCGTGACGCGATTCTCCAAATTCGCGTCGCGATTC
1 TCTAAATTCGCGACGCGATTCTCCAAATTCGCGACGCGATTC
*
496495 TCTAAATTCGCGACGCGATTCTCCAAATTCGTGACGC
1 TCTAAATTCGCGACGCGATTCTCCAAATTCGCGACGC
496532 TAATTACTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (42 bp):
TCTAAATTCGCGACGCGATTCTCCAAATTCGCGACGCGATTC
Found at i:497047 original size:20 final size:21
Alignment explanation
Indices: 497024--497078 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
497014 CAAAAATGAA
*
497024 AATCACGTTGCGAATTT-GAG
1 AATCGCGTTGCGAATTTGGAG
*
497044 AATCGCGTTACGAATTTGGAG
1 AATCGCGTTGCGAATTTGGAG
497065 AATCGCGTTGCGAA
1 AATCGCGTTGCGAA
497079 ATTAGAGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (21 bp):
AATCGCGTTGCGAATTTGGAG
Found at i:499971 original size:28 final size:28
Alignment explanation
Indices: 499942--500030 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
499932 CAAATTTTAG
499942 TTAGTGACTAAAATATAATTTTTGAAAGT
1 TTAGTGAC-AAAATATAATTTTTGAAAGT
* * * **
499971 TTGGTGGCAAAGTATAAACTTTGTAAGAGT
1 TTAGTGACAAAATATAATTTTTG-AA-AGT
* *
500001 TTAGGGACAAAAATATAATTTTTAAAAGT
1 TTAGTGAC-AAAATATAATTTTTGAAAGT
500030 T
1 T
500031 ATATATTTTG
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
28 12 0.27
29 12 0.27
30 10 0.22
31 11 0.24
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (28 bp):
TTAGTGACAAAATATAATTTTTGAAAGT
Found at i:502748 original size:18 final size:17
Alignment explanation
Indices: 502698--502770 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 17
502688 AACGAGAGAG
*
502698 TTATTTAATATTTTTATT
1 TTATTTTAT-TTTTTATT
*
502716 TTGTTTTATTTTTTATT
1 TTATTTTATTTTTTATT
*
502733 TTATTTT-TTTCCTTTAAT
1 TTATTTTATTT--TTTATT
502751 TTATTTAATATTTATTTATT
1 TTATTT--TATTT-TTTATT
502771 ATTTTTTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.07
17 14 0.32
18 18 0.41
20 6 0.14
21 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTTTTATT
Found at i:506844 original size:31 final size:32
Alignment explanation
Indices: 506770--506845 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
506760 AGAGAGCATC
*
506770 TTTGAAGATTCAACATCAAATGTTGAGGCATAT
1 TTTG-AGATTCAACATCAAATATTGAGGCATAT
506803 TTTGAGATTCAACATCAAATATTG-GGCAT-T
1 TTTGAGATTCAACATCAAATATTGAGGCATAT
*
506833 TTTGGGAATTCAA
1 TTTGAG-ATTCAA
506846 TATTCTCTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 6 0.15
31 11 0.28
32 19 0.47
33 4 0.10
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGAGGCATAT
Found at i:507114 original size:61 final size:61
Alignment explanation
Indices: 507019--507171 Score: 227
Period size: 61 Copynumber: 2.5 Consensus size: 61
507009 TAATCTCTTG
* *
507019 CAGCTTTTAGAGTCAATTTCT-ACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTT
1 CAGCTTTAAGAGTCAATTT-TAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTC
* * *
507080 CAGCTTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCAATAAACAACTTTC
1 CAGCTTTAAGAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTC
* *
507141 CAACTTTAAGAGTCAGTTTTAACTTCACAGC
1 CAGCTTTAAGAGTCAATTTTAACTTCACAGC
507172 AAAATATAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 1 0.01
61 82 0.99
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (61 bp):
CAGCTTTAAGAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTC
Found at i:507543 original size:21 final size:21
Alignment explanation
Indices: 507517--507653 Score: 67
Period size: 21 Copynumber: 7.4 Consensus size: 21
507507 TGAGACATTT
507517 TCTCTTGAAACAAATTTTTTC
1 TCTCTTGAAACAAATTTTTTC
* *
507538 TCTCTTGAGAC--A--GTTTC
1 TCTCTTGAAACAAATTTTTTC
*
507555 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTTTC
* *
507574 TCTCTTGAGAC--A--GTTTC
1 TCTCTTGAAACAAATTTTTTC
*
507591 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTTTC
* *
507610 TCTCTTGAGAC--A--GTTTC
1 TCTCTTGAAACAAATTTTTTC
*
507627 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTTTC
507646 TCTCTTGA
1 TCTCTTGA
507654 GAAAGTTTCA
Statistics
Matches: 81, Mismatches: 17, Indels: 36
0.60 0.13 0.27
Matches are distributed among these distances:
15 21 0.26
16 3 0.04
17 13 0.16
19 12 0.15
20 3 0.04
21 29 0.36
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTTTC
Found at i:507547 original size:36 final size:36
Alignment explanation
Indices: 507489--507869 Score: 431
Period size: 36 Copynumber: 10.2 Consensus size: 36
507479 AATTTACTCA
* * *
507489 AAACAAA-GTTGTCTCTCTTGAGACATTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
507524 AAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
507560 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
507596 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* **
507632 AAACAAATTTTGTCTCTCTTGAGAAAGTTTCATTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
507668 AAACAAATTTTATATCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
507704 AAAAAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCATCTCCCTTG
1 -AAACAAAT-TTTG----T-CTCT-CTTGAGAC--A-GT--T-TCCCTTG
* * **
507754 AGACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
507790 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
507827 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
507863 AAACAAA
1 AAACAAA
507870 ATCTTTGAAT
Statistics
Matches: 294, Mismatches: 36, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
35 7 0.02
36 203 0.69
37 40 0.14
38 3 0.01
39 1 0.00
40 1 0.00
42 8 0.03
43 3 0.01
44 8 0.03
46 1 0.00
47 1 0.00
48 4 0.01
49 7 0.02
50 7 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:507776 original size:21 final size:21
Alignment explanation
Indices: 507728--507779 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
507718 AATATGTTTT
*
507728 CCTTGAAACAAATTTCATCTC
1 CCTTGAGACAAATTTCATCTC
**
507749 CCTTGAGACAAATTTTGTCTC
1 CCTTGAGACAAATTTCATCTC
507770 CCTTGAGACA
1 CCTTGAGACA
507780 GTTTCTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (21 bp):
CCTTGAGACAAATTTCATCTC
Found at i:507836 original size:159 final size:158
Alignment explanation
Indices: 507589--507918 Score: 527
Period size: 159 Copynumber: 2.1 Consensus size: 158
507579 TGAGACAGTT
* *
507589 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGA
1 TCCCTTGAGACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGA
507654 GAAAGTTTCATTTGAAACAAATTTTATATCTCTTGAGACAGTTTCCCTTGAAAAAAAATCTTTGA
66 GAAAGTTTCATTTGAAACAAATTTTATATCTCTTGAGACAGTTTCCCTTGAAAAAAAATCTTTGA
*
507719 ATATGTTTTCCTTGAAACAAATTTCATC
131 ATATGTTTTCCTTGAAACAAATTCCATC
** * *
507747 TCCCTTGAGACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTG
1 TCCCTTGAGACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTG
* * * *
507812 AGACAGTTTC-TCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
65 AGAAAGTTTCAT-TTGAAACAAATTTTATATCTCTTGAGACAGTTTCCCTTGAAAAAAAATCTTT
*
507876 GAATATGTTTTCCTTGAAACAAATTCCGTC
129 GAATATGTTTTCCTTGAAACAAATTCCATC
507906 TCCCTTGAGACAA
1 TCCCTTGAGACAA
507919 TTTCTCTTGG
Statistics
Matches: 158, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
158 43 0.27
159 115 0.73
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (158 bp):
TCCCTTGAGACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGA
GAAAGTTTCATTTGAAACAAATTTTATATCTCTTGAGACAGTTTCCCTTGAAAAAAAATCTTTGA
ATATGTTTTCCTTGAAACAAATTCCATC
Found at i:507930 original size:138 final size:138
Alignment explanation
Indices: 507749--508007 Score: 455
Period size: 138 Copynumber: 1.9 Consensus size: 138
507739 ATTTCATCTC
* ** * *
507749 CCTTGAGACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAG
507814 ACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAA
66 ACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAA
507879 TATGTTTT
131 TATGTTTT
507887 CCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAG
* *
507952 ATAGTTTCTCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
66 ACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
508008 GTTTTGTCTC
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 114 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.40
Consensus pattern (138 bp):
CCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAG
ACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAA
TATGTTTT
Found at i:507988 original size:36 final size:36
Alignment explanation
Indices: 507884--508036 Score: 170
Period size: 36 Copynumber: 4.3 Consensus size: 36
507874 TTGAATATGT
** * *
507884 TTTC-CTTGAAACAAATTCCGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
507919 TTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
507956 TTTCTCTTGAAACAAATTTTTTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
507992 TTTCCCTTGAAACAAAGTTTTG--TCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
508027 TCTT-TCTTGA
1 T-TTCTCTTGA
508037 GACAGTTTCT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
35 23 0.23
36 44 0.44
37 33 0.33
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:508010 original size:73 final size:72
Alignment explanation
Indices: 507884--508018 Score: 189
Period size: 73 Copynumber: 1.9 Consensus size: 72
507874 TTGAATATGT
* * *
507884 TTTCCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCTCTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTT
507949 GAGATAG
66 GAGATAG
*** * *
507956 TTTCTCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCT
1 TTTC-CTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCT
508019 TGAGACAGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
72 4 0.07
73 50 0.93
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (72 bp):
TTTCCTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTT
GAGATAG
Found at i:508033 original size:73 final size:72
Alignment explanation
Indices: 507884--508036 Score: 186
Period size: 73 Copynumber: 2.1 Consensus size: 72
507874 TTGAATATGT
** * * * *
507884 TTTC-CTTGAAACAAATTCCGTCTCCCTTGAGACAATTTCTCTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTG-CTCTCT
*
507948 TGAGATAG
65 TGAGACAG
* *
507956 TTTCTCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTG-TCTCTT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGCTCTCTT
508020 GAGACAG
66 GAGACAG
508027 TCTT-TCTTGA
1 T-TTCTCTTGA
508037 GACAGTTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
71 19 0.27
72 6 0.09
73 45 0.64
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (72 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGCTCTCTT
GAGACAG
Found at i:508036 original size:15 final size:15
Alignment explanation
Indices: 508014--508051 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
508004 CAAAGTTTTG
508014 TCTCTTGAGACAGTCT
1 TCTCTTGAGACAGT-T
508030 T-TCTTGAGACAGTT
1 TCTCTTGAGACAGTT
508044 TCTCTTGA
1 TCTCTTGA
508052 AACACCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (15 bp):
TCTCTTGAGACAGTT
Found at i:508158 original size:33 final size:33
Alignment explanation
Indices: 508113--508261 Score: 189
Period size: 33 Copynumber: 4.6 Consensus size: 33
508103 GACTGTTTCT
508113 CTTGAAACACAAAAAACCTTTGAAATCGTTTAA
1 CTTGAAACACAAAAAACCTTTGAAATCGTTTAA
*
508146 CTTGAAATACAAAAAACCTTTGAAATCGTTTAA
1 CTTGAAACACAAAAAACCTTTGAAATCGTTTAA
* **
508179 CTTGAAATACAAAAAACCTTTGAAATCGTTTCC
1 CTTGAAACACAAAAAACCTTTGAAATCGTTTAA
* * **
508212 CTCGGAA-A-AAAAAACCTTTGAAAAT-GTTTCT
1 CTTGAAACACAAAAAACCTTTG-AAATCGTTTAA
508243 CTTGAAACAC-AAAAACCTT
1 CTTGAAACACAAAAAACCTT
508262 CGAGTTCGAC
Statistics
Matches: 105, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
31 22 0.21
32 15 0.14
33 68 0.65
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (33 bp):
CTTGAAACACAAAAAACCTTTGAAATCGTTTAA
Found at i:508170 original size:18 final size:18
Alignment explanation
Indices: 508147--508204 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
508137 ATCGTTTAAC
508147 TTGAAATACAAAAAACCT
1 TTGAAATACAAAAAACCT
****
508165 TTGAAAT-CGTTTAA-C-
1 TTGAAATACAAAAAACCT
508180 TTGAAATACAAAAAACCT
1 TTGAAATACAAAAAACCT
508198 TTGAAAT
1 TTGAAAT
508205 CGTTTCCCTC
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
17 4 0.14
18 14 0.48
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (18 bp):
TTGAAATACAAAAAACCT
Found at i:510252 original size:22 final size:22
Alignment explanation
Indices: 510224--510275 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
510214 GAGCACTAAG
510224 AATGTCAAGAGTGTGAACGTTC
1 AATGTCAAGAGTGTGAACGTTC
*
510246 AATGTCAAGAGTGTGAGCGTTC
1 AATGTCAAGAGTGTGAACGTTC
510268 AATGTCAA
1 AATGTCAA
510276 ATGGTTGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (22 bp):
AATGTCAAGAGTGTGAACGTTC
Found at i:511577 original size:23 final size:24
Alignment explanation
Indices: 511538--511582 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
511528 ATCACAAAAC
*
511538 AATGAATTATGATAATAATAAAGA
1 AATGAAGTATGATAATAATAAAGA
511562 AATGAAGTAT-ATAATAATAAA
1 AATGAAGTATGATAATAATAAA
511583 AAAGTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (24 bp):
AATGAAGTATGATAATAATAAAGA
Found at i:513085 original size:2 final size:2
Alignment explanation
Indices: 513078--513156 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
513068 GATGATGGAG
513078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
513120 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
513157 GAGTTAGGAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:520419 original size:16 final size:14
Alignment explanation
Indices: 520375--520422 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
520365 TTCTATTCCC
520375 CATCTCTTCTTCTT
1 CATCTCTTCTTCTT
*
520389 TATCTCTT-TTCTT
1 CATCTCTTCTTCTT
520402 CATCTCTTTCTTCATT
1 CATCTC-TTCTTC-TT
520418 CATCT
1 CATCT
520423 TCAACAATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 10 0.34
14 9 0.31
15 3 0.10
16 7 0.24
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.58
Consensus pattern (14 bp):
CATCTCTTCTTCTT
Found at i:521221 original size:66 final size:66
Alignment explanation
Indices: 521147--521280 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
521137 GGGTTTAAGA
* * *
521147 AATTAGATGGTTCCAATCCATTTTTTATATATTTATAATCTTGTGAAGTATTTTAAAACCCTCCT
1 AATTAGATGGTTCCAATCCATTTTTTAGATATTTATAACCTTATGAAGTATTTTAAAACCCTCCT
521212 T
66 T
* * * * *
521213 AATTAGATGGTTCTAATCCATTTTTTAGATATTTCTAGCCTTATGAAGTGTTTTAAAACCCTTCT
1 AATTAGATGGTTCCAATCCATTTTTTAGATATTTATAACCTTATGAAGTATTTTAAAACCCTCCT
521278 T
66 T
521279 AA
1 AA
521281 CCCCTAACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (66 bp):
AATTAGATGGTTCCAATCCATTTTTTAGATATTTATAACCTTATGAAGTATTTTAAAACCCTCCT
T
Found at i:523906 original size:45 final size:46
Alignment explanation
Indices: 523819--523910 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 46
523809 TTGAAAAACC
* *
523819 TGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAT
523865 TGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCAT
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAT
523910 T
1 T
523911 CGATGTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 24 0.55
46 20 0.45
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (46 bp):
TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAT
Found at i:527374 original size:46 final size:45
Alignment explanation
Indices: 527322--527413 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
527312 TTGAAAAACC
* * *
527322 TGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATACAT
527368 TGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATACAT
1 TGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATACAT
527413 T
1 T
527414 CGATGTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 23 0.53
46 20 0.47
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
TGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATACAT
Found at i:536099 original size:45 final size:46
Alignment explanation
Indices: 536011--536100 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 46
536001 TTAAAAAACA
* * **
536011 TGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCGAATGCAC
1 TGAGTGCATCAATGCATGGTCATGTGCATCAATGCATAAAATGCAC
*
536057 TGAGTGCATCAATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 TGAGTGCATCAATGCATGGTCATGTGCATCAATGCATAAAATGCA
536101 TTCGATGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (46 bp):
TGAGTGCATCAATGCATGGTCATGTGCATCAATGCATAAAATGCAC
Found at i:539505 original size:33 final size:33
Alignment explanation
Indices: 539463--539530 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
539453 CTGTTAATAA
539463 CTAAGTAGTTTAGATA-TCCTACAACTCTTATCT
1 CTAAGTAGTTTAGATATTCC-ACAACTCTTATCT
**
539496 CTAAGTAGTTTAGATATTCCATGACTCTTATCT
1 CTAAGTAGTTTAGATATTCCACAACTCTTATCT
539529 CT
1 CT
539531 TAATAAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (33 bp):
CTAAGTAGTTTAGATATTCCACAACTCTTATCT
Found at i:541165 original size:31 final size:31
Alignment explanation
Indices: 541100--541185 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
541090 AAACTATACA
** * *
541100 TTTAGTACCTAAACTACTAGTTTTGGTCCAT
1 TTTAGTACCTAAACTTTTAATTTTAGTCCAT
**
541131 TTTAGTACCTAAACTTTTAATTTTAGTCTGT
1 TTTAGTACCTAAACTTTTAATTTTAGTCCAT
* *
541162 TTTAGTACCAAAACTTTCAATTTT
1 TTTAGTACCTAAACTTTTAATTTT
541186 TTTAAAAACC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (31 bp):
TTTAGTACCTAAACTTTTAATTTTAGTCCAT
Found at i:544918 original size:38 final size:38
Alignment explanation
Indices: 544867--544955 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
544857 TTTCGCACCT
*
544867 CTGAATGATTCAGTGATGACTGATTCAGTAAAACAGTA
1 CTGAATGATTCAGTGATGACTGATTCAGCAAAACAGTA
* *
544905 CTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTG
1 CTGAATGATTCAGTGATGACTGATTCAGCAAAACAGTA
*
544943 TTGAATGATTCAG
1 CTGAATGATTCAG
544956 CAAAACAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (38 bp):
CTGAATGATTCAGTGATGACTGATTCAGCAAAACAGTA
Found at i:544951 original size:23 final size:23
Alignment explanation
Indices: 544915--545003 Score: 160
Period size: 23 Copynumber: 3.9 Consensus size: 23
544905 CTGAATGATT
* *
544915 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGTTGAATGATTCAGCAAAA
544938 CAGTGTTGAATGATTCAGCAAAA
1 CAGTGTTGAATGATTCAGCAAAA
544961 CAGTGTTGAATGATTCAGCAAAA
1 CAGTGTTGAATGATTCAGCAAAA
544984 CAGTGTTGAATGATTCAGCA
1 CAGTGTTGAATGATTCAGCA
545004 TCAAAGTACA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (23 bp):
CAGTGTTGAATGATTCAGCAAAA
Found at i:545848 original size:2 final size:2
Alignment explanation
Indices: 545841--545869 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
545831 TTAAAATTAT
545841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
545870 TAAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:558246 original size:51 final size:53
Alignment explanation
Indices: 558149--558256 Score: 193
Period size: 52 Copynumber: 2.1 Consensus size: 53
558139 CTTTTGTAAG
558149 CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTAC-AAA
1 CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTACAAAA
*
558201 CTAACTAAATATTTTTTTCTTCC-TGTAGTTGAGTGTACCTGGATGTACAAAA
1 CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTACAAAA
558253 CTAA
1 CTAA
558257 GTGTCGATGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
51 25 0.46
52 29 0.54
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (53 bp):
CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTACAAAA
Found at i:565829 original size:43 final size:43
Alignment explanation
Indices: 565782--565863 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
565772 TTTAACCCTT
*
565782 TAATTTTATTTAAT-TTAATTTTTATATTTATAATTGAGGTCTC
1 TAATTTT-TGTAATCTTAATTTTTATATTTATAATTGAGGTCTC
* *
565825 TAATTTTTGTAATCTTACTTTTTATCTTTATAATTGAGG
1 TAATTTTTGTAATCTTAATTTTTATATTTATAATTGAGG
565864 CCCCTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (43 bp):
TAATTTTTGTAATCTTAATTTTTATATTTATAATTGAGGTCTC
Found at i:566157 original size:43 final size:43
Alignment explanation
Indices: 565808--566140 Score: 313
Period size: 43 Copynumber: 7.7 Consensus size: 43
565798 AATTTTTATA
* * *
565808 TTTATAATTGAGGTCTCTAATTTTTGT-AATCTTACTTTTTATC
1 TTTATAATTGAGGTCCCTAATTTTT-TCAATCTCACTTTTTACC
* * *
565851 TTTATAATTGAGGCCCCTTAATTTTTTCAATCCCATTTTTTTACC
1 TTTATAATTGAGGTCCC-TAATTTTTTCAATCTCA-CTTTTTACC
* * * * *
565896 TTTATAATTGA-TTATCCTAAGTTTTTCAATCCCA-TTTTGTGCC
1 TTTATAATTGAGGT-CCCTAATTTTTTCAATCTCACTTTT-TACC
* * * *
565939 TTTATAATT-AAGTTCCTGATTTTTTCAATATCACTTTTTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
* *
565981 TTTATAATTGAAGTCACTAATTTTTTTCAATCTCA-TTTTTA-C
1 TTTATAATTGAGGTCCCTAA-TTTTTTCAATCTCACTTTTTACC
* *
566023 TTATATAATTTAGG-CCACTAATTTTTTCAATCTCACTTTTTAAC
1 TT-TATAATTGAGGTCC-CTAATTTTTTCAATCTCACTTTTTACC
* * * **
566067 ATTAAAATCGAGACCCCTAATTTTTT-AATCTCACTTTTTACC
1 TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
566109 TTTATAATTGAGGTCCCTAATTTTTTTCAATC
1 TTTATAATTGAGGTCCCTAA-TTTTTTCAATC
566141 ATAATTTTAC
Statistics
Matches: 239, Mismatches: 35, Indels: 31
0.78 0.11 0.10
Matches are distributed among these distances:
42 81 0.34
43 88 0.37
44 50 0.21
45 20 0.08
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (43 bp):
TTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:566683 original size:41 final size:40
Alignment explanation
Indices: 566637--566717 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 40
566627 CAGACCGTTA
* * *
566637 TTTAAGTAATTGTTCC-TAATAACAAGTGTTGAAAAATAAAT
1 TTTAAG-AATAGTTCCATAATAACAAATATTGAAAAA-AAAT
**
566678 TTTAAGGGTAGTTCCATAATAACAAATATTGAAAAAAAAT
1 TTTAAGAATAGTTCCATAATAACAAATATTGAAAAAAAAT
566718 GACCCCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 10 0.29
41 24 0.71
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (40 bp):
TTTAAGAATAGTTCCATAATAACAAATATTGAAAAAAAAT
Found at i:568514 original size:16 final size:16
Alignment explanation
Indices: 568495--568551 Score: 78
Period size: 16 Copynumber: 3.4 Consensus size: 16
568485 AATGATGTCA
*
568495 ATAAAAACTATTAAAT
1 ATAAAAAATATTAAAT
568511 ATAAAAAATATTAATTAT
1 ATAAAAAATATTAA--AT
*
568529 AAAAAAAATATTAAAT
1 ATAAAAAATATTAAAT
568545 ATAAAAA
1 ATAAAAA
568552 TACGAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 21 0.58
18 15 0.42
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAAATATTAAAT
Found at i:568534 original size:18 final size:18
Alignment explanation
Indices: 568497--568551 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
568487 TGATGTCAAT
*
568497 AAAAACTATTAAATAT--
1 AAAAAATATTAAATATAA
*
568513 AAAAAATATTAATTATAA
1 AAAAAATATTAAATATAA
568531 AAAAAATATTAAATATAA
1 AAAAAATATTAAATATAA
568549 AAA
1 AAA
568552 TACGAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 14 0.41
18 20 0.59
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATATTAAATATAA
Found at i:568675 original size:40 final size:40
Alignment explanation
Indices: 568627--568704 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
568617 ATAAAAACCT
*
568627 TTATCTCTGTCGAGTGAGACGCTTTACAAAATGATAAAAA
1 TTATCTCTGTCGAATGAGACGCTTTACAAAATGATAAAAA
* *
568667 TTATCTCTGTCGAATGAGATGCTTTACGAAATGATAAA
1 TTATCTCTGTCGAATGAGACGCTTTACAAAATGATAAA
568705 GAAGTGGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (40 bp):
TTATCTCTGTCGAATGAGACGCTTTACAAAATGATAAAAA
Found at i:572985 original size:44 final size:44
Alignment explanation
Indices: 572922--573018 Score: 176
Period size: 44 Copynumber: 2.2 Consensus size: 44
572912 GAAAAAAATA
572922 TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
1 TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
* *
572966 TAAATTATATTGTAATGAATCGTTATCTTAAAAGCAATCTTAAC
1 TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
573010 TAAATTATA
1 TAAATTATA
573019 ATGCCTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.38
Consensus pattern (44 bp):
TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
Found at i:575096 original size:21 final size:21
Alignment explanation
Indices: 575070--575122 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
575060 TTAGCTGAGT
575070 AGTATCGATATTGATTCAATC
1 AGTATCGATATTGATTCAATC
*
575091 AGTATCGATATTGATTCAATT
1 AGTATCGATATTGATTCAATC
*
575112 AATATCGATAT
1 AGTATCGATAT
575123 CGACGAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (21 bp):
AGTATCGATATTGATTCAATC
Found at i:576291 original size:68 final size:68
Alignment explanation
Indices: 575949--576272 Score: 459
Period size: 68 Copynumber: 4.8 Consensus size: 68
575939 CTAAAATAAA
* * *
575949 AGGCCTAACTGTGCATTTTACAGAAAAGTGTTAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
576014 TTG
66 TTG
* * * *
576017 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAAATATGCCAATTAGATGAAAGACTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
576082 TTG
66 TTG
* * *
576085 AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATTCCAGTTAGATGAAAGGCTAAATGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
576150 TTG
66 TTG
* * * *
576153 AGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAATTAGATGAAATGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
576218 TTG
66 TTG
* ** * * * *
576221 AGTCCTAGTTGTGGATTTGGCAGAAAGGTGTCAAGTATTCCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
576273 TGGTTAAAGA
Statistics
Matches: 227, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 227 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:576416 original size:80 final size:81
Alignment explanation
Indices: 576224--576482 Score: 371
Period size: 81 Copynumber: 3.2 Consensus size: 81
576214 GCCTTTGAGT
* * *
576224 CCTAGTTGTGGATTTGGCAGAAAGGTGTCAAGTATT-CCAGTTAGATGAATGGTTAAAGACCGTT
1 CCTAGCTGTGCATTTGGCAGAAAGGTGTCAA-TTTTGCCAGTTAGATGAATGGTTAAAGACCGTT
576288 GAGTAAAAGATAAATGG
65 GAGTAAAAGATAAATGG
* * * *
576305 CCTAGCTGTGCATTTGGCAGAAATGTGTCAATTTTGCCAGTTAGACGAATAGTTAAAAACCGTTG
1 CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTTTGCCAGTTAGATGAATGGTTAAAGACCGTTG
576370 AGTAAAAGA-AAATGG
66 AGTAAAAGATAAATGG
* * * *
576385 CCTAGCTGTGCATTTGGCAGAACA-ATGTCAATTATGCTAGTTAGGTGAATGGTTAAAGACCGTT
1 CCTAGCTGTGCATTTGGCAGAA-AGGTGTCAATTTTGCCAGTTAGATGAATGGTTAAAGACCGTT
576449 GAGTAAAAGATAAATGG
65 GAGTAAAAGATAAATGG
*
576466 CCTAGATGTGCATTTGG
1 CCTAGCTGTGCATTTGG
576483 AAGTCCTAAA
Statistics
Matches: 160, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
80 74 0.46
81 86 0.54
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (81 bp):
CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTTTGCCAGTTAGATGAATGGTTAAAGACCGTTG
AGTAAAAGATAAATGG
Found at i:592541 original size:35 final size:35
Alignment explanation
Indices: 592502--592572 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
592492 CTATTTGAAT
**
592502 AACTTTAACCAAATATTATCCAAAAAGGTCTATGA
1 AACTTTAACCAAATATTATCCAAAAAGAACTATGA
*
592537 AACTTTAACCTAATATTATCCAAAAAGAACTATGA
1 AACTTTAACCAAATATTATCCAAAAAGAACTATGA
592572 A
1 A
592573 TGACGACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (35 bp):
AACTTTAACCAAATATTATCCAAAAAGAACTATGA
Found at i:594426 original size:18 final size:18
Alignment explanation
Indices: 594403--594437 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
594393 GTCATCGGTC
594403 AATTAGAGCCTACACATA
1 AATTAGAGCCTACACATA
594421 AATTAGAGCCTACACAT
1 AATTAGAGCCTACACAT
594438 CAGATATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (18 bp):
AATTAGAGCCTACACATA
Found at i:594777 original size:16 final size:17
Alignment explanation
Indices: 594755--594791 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
594745 ATTTAATTTT
*
594755 TTTTTTAAATAGAAGTG
1 TTTTTAAAATAGAAGTG
*
594772 TTTTTAAAATTGAAGTG
1 TTTTTAAAATAGAAGTG
594789 TTT
1 TTT
594792 GTGATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (17 bp):
TTTTTAAAATAGAAGTG
Found at i:602867 original size:13 final size:14
Alignment explanation
Indices: 602846--602891 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
602836 AGTGGCGAGG
602846 AGAAG-AAAAGTGA
1 AGAAGAAAAAGTGA
*
602859 A-AAGAAAAAATGA
1 AGAAGAAAAAGTGA
602872 AGAAG-AAAAGTGA
1 AGAAGAAAAAGTGA
602885 AGAAGAA
1 AGAAGAA
602892 GATGGGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.11
13 21 0.75
14 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.07
Consensus pattern (14 bp):
AGAAGAAAAAGTGA
Found at i:608508 original size:84 final size:82
Alignment explanation
Indices: 608409--608619 Score: 262
Period size: 84 Copynumber: 2.5 Consensus size: 82
608399 TTCTTAAACT
* *
608409 AACGCCGTGATAGAGTAGTACTTTAGCTGCGTTTTTATACAAA-TGCCAGAATAGGGATCGTTTA
1 AACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACT-CCACAATAGGGATCGTTTA
* *
608473 TAGTGGCATTTTTTCTAATA
64 TAGTGGCA-TTTTTCCAACA
* * *
608493 AACGCCGCGATAGAGTAGTACTTTATCAGTGTTTTTATACAAACTCCTCAATAGGGATCGTTTAT
1 AACGCCGCGATAGAGTAGTACTTTA-CTGCGTTTTTATACAAACTCCACAATAGGGATCGTTTAT
*
608558 ATTGGCATTTTTCCAACA
65 AGTGGCATTTTTCCAACA
* * * *
608576 AATGTCGCGATAGAGTAGTACTTTAATGGCGTTTTTATATAAAC
1 AACGCCGCGATAGAGTAGTACTTTACT-GCGTTTTTATACAAAC
608620 ACTGTAATAG
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
83 46 0.42
84 63 0.57
85 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (82 bp):
AACGCCGCGATAGAGTAGTACTTTACTGCGTTTTTATACAAACTCCACAATAGGGATCGTTTATA
GTGGCATTTTTCCAACA
Found at i:608962 original size:38 final size:40
Alignment explanation
Indices: 608872--608963 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
608862 TTATCTTTTA
608872 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGTAG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAG-AG
* *
608913 TGGCGTTTTTAAACAAACGCCGCAATAAGTTAGTG-A-AG
1 TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
*
608951 TGGTGTTTTTAAA
1 TGGCGTTTTTAAA
608964 TACAAACACC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
38 14 0.29
40 1 0.02
41 33 0.69
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (40 bp):
TGGCGTTTTTAAACAAACGCCGCAATAAATCAGTGCAGAG
Found at i:613217 original size:62 final size:62
Alignment explanation
Indices: 613115--613240 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
613105 ACCCGTTTTT
* *
613115 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATTATGTATTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTACTTATGTTAATGCATTTCCTA
613177 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTACTTATGTTAATGCATTTCCTA
1 ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTACTTATGTTAATGCATTTCCTA
613239 AT
1 AT
613241 GATACGTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (62 bp):
ATAGTTTACACACTTTTGTATTACCTCTTCTTAATAATGTACTTATGTTAATGCATTTCCTA
Done.