Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 39
Found at i:430811 original size:34 final size:34
Alignment explanation
Indices: 430759--430838 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
430749 GAAATGAAAA
* * *
430759 TCGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 TCGCGTTGCGATTCTCTCGTTGCGATAGCCAGTT
* *
430793 TTGCGTTGCGATTCTCTCGTTGCGATAGTCAGTT
1 TCGCGTTGCGATTCTCTCGTTGCGATAGCCAGTT
*
430827 TCGTGTTGCGAT
1 TCGCGTTGCGAT
430839 AGTCTGTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.12, C:0.21, G:0.25, T:0.41
Consensus pattern (34 bp):
TCGCGTTGCGATTCTCTCGTTGCGATAGCCAGTT
Found at i:432405 original size:41 final size:42
Alignment explanation
Indices: 432360--432447 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
432350 CCTCTTCAAC
* *
432360 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
432401 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
432443 GATGA
1 GATGA
432448 AAGGTGAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 20 0.48
42 22 0.52
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:432416 original size:21 final size:21
Alignment explanation
Indices: 432387--432447 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
432377 GAACGGTGGG
*
432387 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
432408 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
432429 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
432448 AAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:432803 original size:20 final size:20
Alignment explanation
Indices: 432778--432816 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
432768 GAAGAATAGT
432778 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
432798 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
432817 ATGACTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:432830 original size:20 final size:20
Alignment explanation
Indices: 432804--432876 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
432794 AAACTTACTT
*
432804 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGGCTA
* *
432824 TCACAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
432844 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
432864 TCGCAATGCGAAA
1 TCGCAACGCGAAA
432877 TGAAAATCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:432885 original size:19 final size:19
Alignment explanation
Indices: 432863--432921 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
432853 GGAAATGGCT
432863 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
432882 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
432896 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
432915 ATCGCAA
1 ATCGCAA
432922 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:432898 original size:14 final size:14
Alignment explanation
Indices: 432879--432937 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
432869 ATGCGAAATG
432879 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
432893 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
432912 AAAATCGCAACGAC
1 AAAATCGCAACGAC
432926 AAAATCGCAACG
1 AAAATCGCAACG
432938 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:432953 original size:33 final size:33
Alignment explanation
Indices: 432863--432942 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
432853 GGAAATGGCT
432863 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
432896 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
432929 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
432943 CACAAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:432973 original size:14 final size:14
Alignment explanation
Indices: 432954--433010 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
432944 ACAAATCGCA
432954 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
432968 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
*
432985 CATTGCAATTTTGTCG
1 --TTGCGATTTTGTCG
433001 TTGCGATTTT
1 TTGCGATTTT
433011 CATTTCGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 15 0.44
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 5 0.15
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:432995 original size:19 final size:19
Alignment explanation
Indices: 432968--433026 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
432958 GATTTTGTCG
432968 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
432987 TTGC-AATTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
433001 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
433020 TTGCGAT
1 TTGCGAT
433027 AGTCATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 4 0.13
17 4 0.13
18 4 0.13
19 11 0.35
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:432996 original size:33 final size:33
Alignment explanation
Indices: 432949--433023 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
432939 GAAACACAAA
*
432949 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCAATTTTGTCGTTGCGATTTTCATT
432982 TCGCATTGCAATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCAATTTTGTCGTTGCGATTTTCATT
433015 TCGCATTGC
1 TCGCATTGC
433024 GATAGTCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TCGCATTGCAATTTTGTCGTTGCGATTTTCATT
Found at i:433581 original size:18 final size:18
Alignment explanation
Indices: 433558--433605 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
433548 TCGGTCGATC
433558 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
433576 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
433594 AGGTGATGGCTC
1 AGGTGATGGCTC
433606 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:434943 original size:20 final size:20
Alignment explanation
Indices: 434895--434937 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
434885 AATAGTTTCT
*
434895 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACAC
*
434915 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACAC
434935 GAA
1 GAA
434938 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGACAATCGCAACAC
Found at i:435554 original size:20 final size:20
Alignment explanation
Indices: 435440--435553 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
435430 GATTATGTAT
*
435440 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
435460 TATCGTGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
435480 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
435500 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
435521 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
435541 TATCGCGTTGCGA
1 TATCGCGTTGCGA
435554 TTTTTCCAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:435557 original size:41 final size:41
Alignment explanation
Indices: 435420--435555 Score: 186
Period size: 41 Copynumber: 3.3 Consensus size: 41
435410 CACTTTGAAA
* *
435420 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
435461 ATCGTGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* *
435501 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
435542 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
435556 TTTCCAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 45 0.55
42 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:435615 original size:21 final size:20
Alignment explanation
Indices: 435585--435637 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
435575 ATTTACTTAT
435585 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
435606 TCGCAATGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
435627 TCGCATTGCGA
1 TCGCATTGCGA
435638 TAGTCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:435921 original size:19 final size:19
Alignment explanation
Indices: 435897--435936 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
435887 AAGTAAAACA
435897 CACAAATCTGTTGAAGGCT
1 CACAAATCTGTTGAAGGCT
435916 CACAAATCTGTTGAAGGCT
1 CACAAATCTGTTGAAGGCT
435935 CA
1 CA
435937 ACGGCGGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (19 bp):
CACAAATCTGTTGAAGGCT
Found at i:439112 original size:21 final size:21
Alignment explanation
Indices: 439086--439144 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
439076 TGATTTATTA
439086 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
439107 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
*
439128 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
439145 ATTGGATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.05, G:0.24, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:442635 original size:12 final size:12
Alignment explanation
Indices: 442618--442656 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
442608 TTATTACTCT
442618 TTCAAAACTTGA
1 TTCAAAACTTGA
442630 TTCAAAACTTGA
1 TTCAAAACTTGA
442642 TTC-AAACTTGA
1 TTCAAAACTTGA
442653 TTCA
1 TTCA
442657 GATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (12 bp):
TTCAAAACTTGA
Found at i:442650 original size:11 final size:11
Alignment explanation
Indices: 442622--442656 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
442612 TACTCTTTCA
442622 AAACTTGATTC
1 AAACTTGATTC
442633 AAAACTTGATTC
1 -AAACTTGATTC
442645 AAACTTGATTC
1 AAACTTGATTC
442656 A
1 A
442657 GATTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (11 bp):
AAACTTGATTC
Found at i:445706 original size:28 final size:29
Alignment explanation
Indices: 445666--445723 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
445656 CCGTGAAGAG
445666 CAGCAATATCCGCTCCG-AAACTGGTTTA
1 CAGCAATATCCGCTCCGAAAACTGGTTTA
445694 CAGCAATATCCGCTCCGAAAACTGGTTTA
1 CAGCAATATCCGCTCCGAAAACTGGTTTA
445723 C
1 C
445724 GGGCAAGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (29 bp):
CAGCAATATCCGCTCCGAAAACTGGTTTA
Found at i:456619 original size:22 final size:21
Alignment explanation
Indices: 456594--456644 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
456584 ACAAATGCTT
456594 AGATTAATC-CTAGGAAATAAGA
1 AGATTAATCACTAGGAAA-AA-A
*
456616 AGA-TATTCACTAGGAAAAAA
1 AGATTAATCACTAGGAAAAAA
*
456636 AAATTAATC
1 AGATTAATC
456645 TTAACCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.12
21 10 0.42
22 11 0.46
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.24
Consensus pattern (21 bp):
AGATTAATCACTAGGAAAAAA
Found at i:456837 original size:2 final size:2
Alignment explanation
Indices: 456830--456859 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
456820 GATTCAAAAG
456830 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
456860 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:461080 original size:25 final size:25
Alignment explanation
Indices: 461033--461082 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
461023 TTAACGAGTT
* *
461033 CCAAAGCCGTGAGTTCCTAGCCATC
1 CCAAAGCCGAGAGTTCCCAGCCATC
*
461058 CCAAAGCCGAGAGTTCCCCGCCATC
1 CCAAAGCCGAGAGTTCCCAGCCATC
461083 TAGATCAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.40, G:0.20, T:0.16
Consensus pattern (25 bp):
CCAAAGCCGAGAGTTCCCAGCCATC
Found at i:461802 original size:24 final size:22
Alignment explanation
Indices: 461782--461838 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
461772 CACTCTCTAA
*
461782 GGCGACATCCGTCCCCATCTCT
1 GGCGAAATCCGTCCCCATCTCT
* *
461804 GACGAAATCAGTCCCCATCTCT
1 GGCGAAATCCGTCCCCATCTCT
461826 GGCGAAATCCGTC
1 GGCGAAATCCGTC
461839 TATCTCCATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.39, G:0.19, T:0.21
Consensus pattern (22 bp):
GGCGAAATCCGTCCCCATCTCT
Found at i:462293 original size:20 final size:20
Alignment explanation
Indices: 462221--462276 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
462211 CGATTTTAGT
462221 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
462241 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
462261 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
462277 AATTTTCGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:462303 original size:20 final size:20
Alignment explanation
Indices: 462218--462303 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
462208 ATGCGATTTT
462218 AGTTTCGCGTTGCGATAGTCA
1 AGTTTCGCGTTGCGATAGT-A
*
462239 A-ATTCGCGTTGCGATAGTCA
1 AGTTTCGCGTTGCGATAGT-A
*
462259 A-ATTCGCGTTGCGATAGTA
1 AGTTTCGCGTTGCGATAGTA
* * **
462278 ATTTTCGTGTTGCGATTTTA
1 AGTTTCGCGTTGCGATAGTA
462298 AGTTTC
1 AGTTTC
462304 AGAAACTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.03
20 55 0.95
21 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (20 bp):
AGTTTCGCGTTGCGATAGTA
Found at i:464298 original size:20 final size:20
Alignment explanation
Indices: 464273--464319 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
464263 GATTCTCTCG
464273 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
464293 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
464313 TTGCGAT
1 TTGCGAT
464320 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:464329 original size:20 final size:20
Alignment explanation
Indices: 464273--464329 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
464263 GATTCTCTCG
*
464273 TTGCGATAGTCAA-ATTCGCA
1 TTGCGATAGT-AAGTTTCGCA
* *
464293 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTAAGTTTCGCA
**
464313 TTGCGATTTTAAGTTTC
1 TTGCGATAGTAAGTTTC
464330 AGATTCTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTAAGTTTCGCA
Found at i:464850 original size:18 final size:19
Alignment explanation
Indices: 464811--464852 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
464801 CTCACCTATC
464811 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
464832 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
464850 ATC
1 ATC
464853 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:464864 original size:42 final size:42
Alignment explanation
Indices: 464805--464897 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
464795 GCCTGACTCA
** * *
464805 CCTATCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCC-CCTCCCACCGTTCAAGAGGCC
*
464847 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* *
464889 ACTGTCATC
1 CCTATCATC
464898 ATTGAAAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:466331 original size:14 final size:14
Alignment explanation
Indices: 466294--466355 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
466284 TTGCTTGTTT
*
466294 AATTGATTTATAAA
1 AATTGATTTGTAAA
466308 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
466322 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
466337 TATTGATGTGTAAA
1 AATTGATTTGTAAA
466351 TAATT
1 -AATT
466356 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:466479 original size:20 final size:20
Alignment explanation
Indices: 466454--466507 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
466444 AGGTACACTT
*
466454 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
466474 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
466494 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
466508 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:466559 original size:34 final size:34
Alignment explanation
Indices: 466516--466652 Score: 139
Period size: 34 Copynumber: 3.9 Consensus size: 34
466506 AGTCAATTCG
* * * *
466516 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTACGATTTTCT
*
466550 CGTTGCGATAGTCAAATACCCGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATACCCGTTACGAT--T----TTCT
* **
466590 CGTTGCGATAGTCAAATTCGTGTTACGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTACGATTTTCT
*
466624 CGTTGCGATAGTCAAATACCCGTTGCGAT
1 CGTTGCGATAGTCAAATACCCGTTACGAT
466653 AATCAAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
34 53 0.63
36 1 0.01
38 1 0.01
40 29 0.35
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACCCGTTACGATTTTCT
Found at i:466671 original size:94 final size:94
Alignment explanation
Indices: 466550--466795 Score: 332
Period size: 94 Copynumber: 2.6 Consensus size: 94
466540 GCGATTTTCT
* * *
466550 CGTTGCGATAGTCAAATACCCGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGTGTTA
1 CGTTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTA
* *
466615 CGATTTTCT-CGTTGCGATAGTCAAATACC
66 CGATTTT-TGAGTTGCGATAATCAAATACC
* * * * * *
466644 CGTTGCGATAATCAAATTCGCATTACGATAGTCAAATTCTCGTTGCGATAGACAAATTTGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTA
* *
466709 CGATTTTTGAGTTGCGATAATCAAATTCG
66 CGATTTTTGAGTTGCGATAATCAAATACC
* *
466738 CGTTGCGATAGTCAAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTC-AAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAAT
466796 GAATGTGTAA
Statistics
Matches: 131, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 91 0.69
95 39 0.30
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATTCGCGTTACGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTA
CGATTTTTGAGTTGCGATAATCAAATACC
Found at i:466681 original size:74 final size:74
Alignment explanation
Indices: 466510--466682 Score: 267
Period size: 74 Copynumber: 2.3 Consensus size: 74
466500 CGCGAAAGTC
* * *
466510 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
1 AATTCGCGTTGCGATAGTCAAATTCGCTTTACGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
*
466575 CGATAGTCA
66 CGATAATCA
466584 AATTCGCGTTGCGATAGTCAAATTCG-TGTTACGATTTTCTCGTTGCGATAGTCAAATACCCGTT
1 AATTCGCGTTGCGATAGTCAAATTCGCT-TTACGATTTTCTCGTTGCGATAGTCAAATACCCGTT
*
466648 GCGATAATCA
65 ACGATAATCA
* *
466658 AATTCGCATTACGATAGTCAAATTC
1 AATTCGCGTTGCGATAGTCAAATTC
466683 TCGTTGCGAT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
73 1 0.01
74 90 0.99
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTCGCTTTACGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
CGATAATCA
Found at i:466723 original size:74 final size:75
Alignment explanation
Indices: 466645--466787 Score: 234
Period size: 75 Copynumber: 1.9 Consensus size: 75
466635 TCAAATACCC
* *
466645 GTTGCGATAATCAAATTCGCATTACGATAGTC-AAATTCTCGTTGCGATAGACAAATTTGCGTTG
1 GTTGCGATAATCAAATTCGCATTACGATAGTCAAAATTCGCGTTGCGATAGACAAATTCGCGTTG
466709 CGATTTTTGA
66 CGATTTTTGA
* * *
466719 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 GTTGCGATAATCAAATTCGCATTACGATAGTCAAAATTCGCGTTGCGATAGACAAATTCGCGTTG
466784 CGAT
66 CGAT
466788 ATTCAAATGA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 30 0.48
75 33 0.52
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (75 bp):
GTTGCGATAATCAAATTCGCATTACGATAGTCAAAATTCGCGTTGCGATAGACAAATTCGCGTTG
CGATTTTTGA
Found at i:466757 original size:21 final size:20
Alignment explanation
Indices: 466501--466795 Score: 241
Period size: 20 Copynumber: 15.7 Consensus size: 20
466491 AAATCGCAAC
*
466501 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
466520 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
466540 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
466554 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
466574 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
466594 GCGATAGTCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
* *
466614 ACGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
466628 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
* *
466648 GCGATAATCAAATTCGCATT
1 GCGATAGTCAAATTCGCGTT
* *
466668 ACGATAGTCAAATTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
466688 GCGATAGACAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
466708 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
466722 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
466742 GCGATAGTCAAAATTCGCGTT
1 GCGATAGTC-AAATTCGCGTT
466763 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
466783 GCGATATTCAAAT
1 GCGATAGTCAAAT
466796 GAATGTGTAA
Statistics
Matches: 219, Mismatches: 37, Indels: 39
0.74 0.13 0.13
Matches are distributed among these distances:
14 32 0.15
16 3 0.01
18 2 0.01
19 8 0.04
20 154 0.70
21 20 0.09
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:468993 original size:16 final size:16
Alignment explanation
Indices: 468968--469004 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
468958 GTGTAACAAT
* *
468968 CAACTGCTATTTTTAC
1 CAACTACTATATTTAC
468984 CAACTACTATATTTAC
1 CAACTACTATATTTAC
469000 CAACT
1 CAACT
469005 CTTCTTCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (16 bp):
CAACTACTATATTTAC
Found at i:469104 original size:12 final size:12
Alignment explanation
Indices: 469087--469122 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
469077 CTTCGAGGAT
469087 TTTTTCTTCTTC
1 TTTTTCTTCTTC
469099 TTTTTCTTCTTC
1 TTTTTCTTCTTC
469111 TTTTTCTTCTTC
1 TTTTTCTTCTTC
469123 AGTGTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:469331 original size:24 final size:24
Alignment explanation
Indices: 469297--469350 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
469287 CTGAAACATC
469297 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
469321 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
469345 ATCAAA
1 ATCAAA
469351 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:470246 original size:21 final size:21
Alignment explanation
Indices: 470216--470259 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
470206 TTCGCATTGT
*
470216 GAATTCGGAAAATGGCAACGC
1 GAATTCGGAAAATCGCAACGC
* *
470237 GAATTTGGAAAATCGCAATGC
1 GAATTCGGAAAATCGCAACGC
470258 GA
1 GA
470260 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (21 bp):
GAATTCGGAAAATCGCAACGC
Found at i:472126 original size:18 final size:18
Alignment explanation
Indices: 472087--472143 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
472077 TTTTAATATT
*
472087 AAAATATAATTAT-TTATTA
1 AAAATATAAATATCTTA--A
472106 AAAATATAAATATCTTAA
1 AAAATATAAATATCTTAA
* * *
472124 AAAATCTAAAAATCTGAA
1 AAAATATAAATATCTTAA
472142 AA
1 AA
472144 GCGCAAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 18 0.55
19 12 0.36
20 3 0.09
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATATAAATATCTTAA
Found at i:472127 original size:19 final size:19
Alignment explanation
Indices: 472087--472133 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
472077 TTTTAATATT
* *
472087 AAAATATAATTATTTATTA
1 AAAATATAAATATTTATAA
*
472106 AAAATATAAATATCT-TAA
1 AAAATATAAATATTTATAA
*
472124 AAAATCTAAA
1 AAAATATAAA
472134 AATCTGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATAAATATTTATAA
Found at i:476788 original size:22 final size:22
Alignment explanation
Indices: 476740--476807 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
476730 AGAATGGGAG
* *
476740 AAGAAAGAAGAG--GAGAGAGG
1 AAGAAAGAAGAGAAGAGAAAGA
*
476760 AATAAAGAAGAGAAGAGAAAGA
1 AAGAAAGAAGAGAAGAGAAAGA
*
476782 AAGAAAGAAGAAGAATAG-AAGA
1 AAGAAAGAAG-AGAAGAGAAAGA
476804 AAGA
1 AAGA
476808 TAAAGTCGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.28
22 23 0.57
23 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (22 bp):
AAGAAAGAAGAGAAGAGAAAGA
Found at i:476796 original size:18 final size:19
Alignment explanation
Indices: 476740--476801 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
476730 AGAATGGGAG
* *
476740 AAGAAAGAAGAGGAGAGAGG
1 AAGAAAGAAGAGAAGA-AGA
*
476760 AATAAAGAAGAGAAG-AGA
1 AAGAAAGAAGAGAAGAAGA
476778 AAGAAAGAA-AGAAGAAGA
1 AAGAAAGAAGAGAAGAAGA
476796 ATAGAA
1 A-AGAA
476802 GAAAGATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 5 0.14
18 14 0.39
19 4 0.11
20 13 0.36
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (19 bp):
AAGAAAGAAGAGAAGAAGA
Found at i:476889 original size:16 final size:18
Alignment explanation
Indices: 476864--476906 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
476854 TTTTCTTTTT
476864 TAAAATATATATTATTTA
1 TAAAATATATATTATTTA
476882 TAAAATATATATTATTTA
1 TAAAATATATATTATTTA
476900 TAAAATA
1 TAAAATA
476907 GCATGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATATATATTATTTA
Found at i:477164 original size:17 final size:18
Alignment explanation
Indices: 477139--477177 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
477129 ATTATTTATT
*
477139 TTTAGATTAAAT-TAATG
1 TTTAGATTAAATGTAATC
*
477156 TTTATATTAAATGTAATC
1 TTTAGATTAAATGTAATC
477174 TTTA
1 TTTA
477178 AATTGAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTAGATTAAATGTAATC
Found at i:478212 original size:21 final size:21
Alignment explanation
Indices: 478179--478223 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
478169 GAATATCAAT
*
478179 AGTGTATCAATGCACTGCTAC
1 AGTGCATCAATGCACTGCTAC
*
478200 AGTGCATCGATGCACTGCTAC
1 AGTGCATCAATGCACTGCTAC
478221 AGT
1 AGT
478224 ATTGCTACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
AGTGCATCAATGCACTGCTAC
Found at i:479032 original size:32 final size:32
Alignment explanation
Indices: 478918--479069 Score: 120
Period size: 32 Copynumber: 4.9 Consensus size: 32
478908 ACCTCGACAA
* *
478918 CTGTCCATAGGTCCCG-AAAACCTAGGTAA-T
1 CTGTCCATATGTCCCGAAAAACATAGGTAATT
* * ** *
478948 -TGTTCATATGTTCCTTAGAACATAGGT-A-T
1 CTGTCCATATGTCCCGAAAAACATAGGTAATT
* * *
478977 AT-TCCATATGTCTC-AGAAGACATAGGTAATT
1 CTGTCCATATGTCCCGA-AAAACATAGGTAATT
*
479008 CTGTTCATATGTCCCGAAAAACATAGGTAATT
1 CTGTCCATATGTCCCGAAAAACATAGGTAATT
* * *
479040 CTGTCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTCCCGAAAAACATAGGTAA
479070 ACCCTCGACT
Statistics
Matches: 95, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
29 31 0.33
30 11 0.12
31 2 0.02
32 50 0.53
33 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (32 bp):
CTGTCCATATGTCCCGAAAAACATAGGTAATT
Found at i:479236 original size:2 final size:2
Alignment explanation
Indices: 479229--479254 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
479219 TCTCATATTC
479229 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
479255 GGTTCACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:481485 original size:8 final size:8
Alignment explanation
Indices: 481474--481499 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
481464 TATTTATTTA
481474 TTTATAAT
1 TTTATAAT
481482 TTTATAAT
1 TTTATAAT
481490 TTTATAAT
1 TTTATAAT
481498 TT
1 TT
481500 CTTGTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATAAT
Found at i:482629 original size:20 final size:19
Alignment explanation
Indices: 482604--482689 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
482594 CTATGCATAC
482604 ATTATTATAAAATCAAGTTA
1 ATTATTATAAAATCAA-TTA
482624 ATTATTATAAAATC-A--A
1 ATTATTATAAAATCAATTA
* *
482640 A-TA-TATACATAT-ACATAA
1 ATTATTATA-AAATCA-ATTA
482658 ATTATTATAAAATCAAGTTA
1 ATTATTATAAAATCAA-TTA
482678 ATTATTATAAAA
1 ATTATTATAAAA
482690 AATTCAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 3 0.06
18 2 0.04
19 7 0.13
20 33 0.61
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTATTATAAAATCAATTA
Found at i:482664 original size:54 final size:54
Alignment explanation
Indices: 482570--482689 Score: 174
Period size: 54 Copynumber: 2.2 Consensus size: 54
482560 AAAATACATA
* * *
482570 AATTATTAT-AAATAAATTTAATTACTATGCATACATTATTATAAAATCAAGTT
1 AATTATTATAAAATAAATATAATTACTATACATAAATTATTATAAAATCAAGTT
482623 AATTATTATAAAATCAAATAT-A-TACATATACATAAATTATTATAAAATCAAGTT
1 AATTATTATAAAAT-AAATATAATTAC-TATACATAAATTATTATAAAATCAAGTT
482677 AATTATTATAAAA
1 AATTATTATAAAA
482690 AATTCAAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
53 12 0.20
54 44 0.72
55 5 0.08
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.39
Consensus pattern (54 bp):
AATTATTATAAAATAAATATAATTACTATACATAAATTATTATAAAATCAAGTT
Found at i:484747 original size:13 final size:12
Alignment explanation
Indices: 484729--484763 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
484719 GGATTTCTCC
484729 ACATCAATTTTCA
1 ACATCAATTTT-A
484742 ACATCAATTTTA
1 ACATCAATTTTA
484754 ACAGTCAATT
1 ACA-TCAATT
484764 CCGAGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (12 bp):
ACATCAATTTTA
Found at i:485549 original size:35 final size:30
Alignment explanation
Indices: 485510--485591 Score: 74
Period size: 35 Copynumber: 2.5 Consensus size: 30
485500 CTAAAAAAAG
485510 AAAAAAATAATAAAAATATATAACTATTAGGTACA
1 AAAAAAATAATAAAAATA-ATAA--A-TAGG-ACA
* * *
485545 AAAAAAGAAAATAATAATAATAAATAGGAGA
1 AAAAAA-ATAATAAAAATAATAAATAGGACA
*
485576 GAAAAAATAATAAAAA
1 AAAAAAATAATAAAAA
485592 AAGAAAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
30 8 0.20
31 7 0.17
32 4 0.10
33 1 0.03
35 10 0.25
36 10 0.25
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (30 bp):
AAAAAAATAATAAAAATAATAAATAGGACA
Found at i:485848 original size:11 final size:11
Alignment explanation
Indices: 485806--485853 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
485796 AATAAAAAGG
485806 AAATAATAATA
1 AAATAATAATA
485817 ATAATAATAA-A
1 A-AATAATAATA
485828 CAAATAATAAATA
1 -AAATAAT-AATA
485841 AAAT-ATAATA
1 AAATAATAATA
485851 AAA
1 AAA
485854 GTAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.21
11 10 0.30
12 15 0.45
13 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATAATA
Found at i:485852 original size:14 final size:14
Alignment explanation
Indices: 485806--485852 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
485796 AATAAAAAGG
485806 AAATAATAATAATAAT
1 AAATAA-AAT-ATAAT
*
485822 -AATAAACAAATAAT
1 AAATAAA-ATATAAT
485836 AAATAAAATATAAT
1 AAATAAAATATAAT
485850 AAA
1 AAA
485853 AGTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAATATAAT
Found at i:485862 original size:23 final size:25
Alignment explanation
Indices: 485791--485863 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
485781 ATATAACGAT
* *
485791 ATATAAATAAAAAGGAAATAATAATA
1 ATAT-AATAAAAAGTAAAAAATAATA
* *
485817 ATAATAATAAACAAATAATAAATAA-A
1 AT-ATAATAAA-AAGTAAAAAATAATA
485843 ATATAAT-AAAAGTAAAAAATA
1 ATATAATAAAAAGTAAAAAATA
485864 TATAGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
23 10 0.26
24 2 0.05
25 5 0.13
26 11 0.28
27 11 0.28
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.23
Consensus pattern (25 bp):
ATATAATAAAAAGTAAAAAATAATA
Found at i:488356 original size:83 final size:85
Alignment explanation
Indices: 487669--488737 Score: 1248
Period size: 84 Copynumber: 13.0 Consensus size: 85
487659 TAAGTTATAT
** ** * * * *
487669 TGTAAATTTGATATGTCC-TTGAGCT-A-AATAATCGAACTAAAAGGTCTTTGCTGACATATAGC
1 TGTAAATTTGATATG-CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
*
487731 CCTTCTCGCCTTGACCTATGC
65 CCTTCTCGCCTTGAGCTATGC
* * * * * *
487752 TATAAATTT-ATACGCCTTTGAGCTAAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
* * *
487816 CTTTTCGTCTTGAGTTATGC
66 CTTCTCGCCTTGAGCTATGC
* * *** *
487836 TGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTCTTTACTGACAAATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
* *
487901 CTTCTCGCCTTGAGTTATGT
66 CTTCTCGCCTTGAGCTATGC
* * * *
487921 TGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTTGAAGGT-TTGGTTGACAGATAGCC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
487985 CTTCTCG-CTTGAGCTA---
66 CTTCTCGCCTTGAGCTATGC
* *
488001 TGTAAATTTGATATGTCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
* * * *
488066 CTTCTCGCTTTAAGTTATGT
66 CTTCTCGCCTTGAGCTATGC
*
488086 TGT-AA----ATATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTGGTTGACA-ATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
* * *
488145 CTTTTCGCCTTGTGCTATAC
66 CTTCTCGCCTTGAGCTATGC
* * ** *
488165 TATAAATTTGATGTGCCTTTGAGCTTTGTGT-ATCGAACTCGAAGGTCTTGGTTGACATATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
*
488229 CTTCTCGCCTTGAGCTATAC
66 CTTCTCGCCTTGAGCTATGC
* * *
488249 TGTAAATTTGATATGCC-TTAAGCTGAGTGT-ATCGAACTCGAAGGTCTTGGTTGATAGAT-ATC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
*
488311 CTTCTCGCCTTGAGGTATGC
66 CTTCTCGCCTTGAGCTATGC
* *
488331 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTGG--GACAGATAAAC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
*
488394 CTTCTCGCCTTGAGTTATGC
66 CTTCTCGCCTTGAGCTATGC
* *
488414 TGT-AA----ATATGCTTTTGAGCTGAGTGTAATCGAACTCGAA-G--TTGGTTGACAGATAGCC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
*
488471 CTTATCGCCTTGAGCTATGC
66 CTTCTCGCCTTGAGCTATGC
488491 TGTAAA-TTG--ATGCCTTTGAGCTGAGTGTAAT-GAACTCGAAGGTCTTGGTTGACAGATAACC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
*
488552 CTTCTCGCC-TGAGTTATGC
66 CTTCTCGCCTTGAGCTATGC
* * *
488571 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCTAACTCGAAGGTC-T--TTAACAGATAGCC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
* *
488633 CTTTTTG-CTTGAGCTATGC
66 CTTCTCGCCTTGAGCTATGC
* * *
488652 TGCAAACTTGATATGCCTTTGAGCTGAGTATAATCGAACTCGAA-GTCTT--TCTGACAGATAAC
1 TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGT-TGACAGATAAC
488714 CCTTCTCGCCTTGAGCTATGC
65 CCTTCTCGCCTTGAGCTATGC
488735 TGT
1 TGT
488738 CTAGTTCATT
Statistics
Matches: 851, Mismatches: 100, Indels: 70
0.83 0.10 0.07
Matches are distributed among these distances:
75 4 0.00
77 31 0.04
78 43 0.05
79 43 0.05
80 108 0.13
81 119 0.14
82 77 0.09
83 152 0.18
84 162 0.19
85 112 0.13
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
TGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACC
CTTCTCGCCTTGAGCTATGC
Found at i:488412 original size:328 final size:331
Alignment explanation
Indices: 487617--488737 Score: 1329
Period size: 328 Copynumber: 3.4 Consensus size: 331
487607 AGGTGAATGG
* * * ** * * **
487617 AATCGAACTCG-AGTTATTGG-TGATAGATAGCTTTTCTCGACTTAAGTTATATTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCG-CTTGAGCTATGCTGTAAATTTGA
** ** * * *
487680 TATGTCC-TTGAGCT-A-AATAATCGAACTAAAAGGTCTTTGCTGACATATAGCCCTTCTCGCCT
65 TATG-CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTG-GGACAGATAACCCTTCTCGCCT
** * * * * *
487742 TGACCTATGCTATAAATTTATACGCCTTTGAGCTAAATGTAATCAAACTCGAAGGTCTTTGTTGA
127 TGAGTTATGCTGTAAA--TAT--GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGA
* * *
487807 CAGATAACCCTTTTCGTCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCG
188 CAGATAACCCTTTTCGCCTTGAGCTATGCTGTAAATTTGAT-TGCCTTTGAGCTGAGTGTAATCG
* *** * *
487872 AACTCAAAGGTCTTTACTGACAAATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATATGC
252 AACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGC
*
487937 CTTTGAGCTGAATGT
317 CTTTGAGCTGAGTGT
*
487952 AATCGAACTTGAAGGT-TTGGTTGACAGATAGCCCTTCTCGCTTGAGCTA---TGTAAATTTGAT
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCTTGAGCTATGCTGTAAATTTGAT
* * * *
488013 ATGTCTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCTTTA
66 ATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGG--GACAGATAACCCTTCTCGCCTTG
* *
488078 AGTTATGTTGTAAATATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTGGTTGACA-ATA
129 AGTTATGCTGTAAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATA
* * * **
488142 ACCCTTTTCGCCTTGTGCTATACTATAAATTTGATGTGCCTTTGAGCTTTGTGT-ATCGAACTCG
194 ACCCTTTTCGCCTTGAGCTATGCTGTAAATTTGAT-TGCCTTTGAGCTGAGTGTAATCGAACTCG
* * * *
488206 AAGGTCTTGGTTGACATATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCC-TTAA
258 AAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGA
488270 GCTGAGTGT
323 GCTGAGTGT
* * *
488279 -ATCGAACTCGAAGGTCTTGGTTGATAGATA-TCCTTCTCGCCTTGAGGTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCG-CTTGAGCTATGCTGTAAATTTGA
* *
488342 TATGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTGGGACAGATAAACCTTCTCGCCTTGA
65 TATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGGACAGATAACCCTTCTCGCCTTGA
* *
488407 GTTATGCTGTAAATATGCTTTTGAGCTGAGTGTAATCGAACTCGAA-G--TTGGTTGACAGATAG
130 GTTATGCTGTAAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
*
488469 CCCTTATCGCCTTGAGCTATGCTGTAAA-TTGA-TGCCTTTGAGCTGAGTGTAAT-GAACTCGAA
195 CCCTTTTCGCCTTGAGCTATGCTGTAAATTTGATTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
*
488531 GGTCTTGGTTGACAGATAACCCTTCTCGCC-TGAGTTATGCTGTAAATTTGATATGCCTTTGAGC
260 GGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGC
488595 TGAGTGT
325 TGAGTGT
* * * * * *
488602 AATCTAACTCGAAGGTC-T--TTAACAGATAGCCCTTTTTGCTTGAGCTATGCTGCAAACTTGAT
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCTTGAGCTATGCTGTAAATTTGAT
* **
488664 ATGCCTTTGAGCTGAGTATAATCGAACTCGAA-GTCTTTCTGACAGATAACCCTTCTCGCCTTGA
66 ATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGGACAGATAACCCTTCTCGCCTTGA
*
488728 GCTATGCTGT
130 GTTATGCTGT
488738 CTAGTTCATT
Statistics
Matches: 682, Mismatches: 86, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
320 3 0.00
321 93 0.14
322 31 0.05
323 67 0.10
324 17 0.02
325 14 0.02
326 49 0.07
327 33 0.05
328 125 0.18
329 48 0.07
330 88 0.13
331 1 0.00
332 24 0.04
333 4 0.01
334 45 0.07
335 21 0.03
336 19 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (331 bp):
AATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCTTGAGCTATGCTGTAAATTTGAT
ATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGGACAGATAACCCTTCTCGCCTTGAG
TTATGCTGTAAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
CCTTTTCGCCTTGAGCTATGCTGTAAATTTGATTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
GTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCT
GAGTGT
Found at i:489663 original size:236 final size:233
Alignment explanation
Indices: 489322--489793 Score: 917
Period size: 236 Copynumber: 2.0 Consensus size: 233
489312 AGAATTGACC
489322 ATGCCCCATTTCTTCTTGGGTTGAAGCCTTTCACTTTGAGATTGTCCTGTTTGAAAATGTTTTTT
1 ATGCCCCATTTCTTCTTGGGTTGAAGCCTTTCACTTTGAGATTGTCCTGTTTGAAAATGTTTTTT
489387 CTCTTTCTTTATTTTAGGAGGAAAAAAAGATATGAGGATATAAGAATTTTGTAAAGTAAGGCCCC
66 CTCTTTCTTTATTTTAGGAGGAAAAAAAGATATGAGGATATAAGAATTTTGTAAAGTAAGGCCCC
489452 TTAATTCAGGCTCGCAATCAAATCAAATCATAAACATGAGTTCATAGAAAATCAAATTAATCAAT
131 TTAATTCAGGCTCGCAATCAAATCAAATCATAAACATGAGTTCATAGAAAATCAAATTAATCAAT
489517 AGTTCTTTAATGTTTTTAGAGTTATAGCTCTTTGACAA
196 AGTTCTTTAATGTTTTTAGAGTTATAGCTCTTTGACAA
489555 ATGCCCCATTTTCTTCTTGGGTTGAAGCCTTTCACATTTGAGATTGTCCTGTTTGAAAATGTTTT
1 ATGCCCCA-TTTCTTCTTGGGTTGAAGCCTTTCAC-TTTGAGATTGTCCTGTTTGAAAATGTTTT
489620 TTCTCTTTCTTTTATTTTAGGAGGAAAAAAAGATATGAGGATATAAGAATTTTGTAAAGTAAGGC
64 TTCTCTTTC-TTTATTTTAGGAGGAAAAAAAGATATGAGGATATAAGAATTTTGTAAAGTAAGGC
489685 CCCTTAATTCAGGCTCGCAATCAAATCAAATCATAAACATGAGTTCATAGAAAATCAAATTAATC
128 CCCTTAATTCAGGCTCGCAATCAAATCAAATCATAAACATGAGTTCATAGAAAATCAAATTAATC
489750 AATAGTTCTTTAATGTTTTTAGAGTTATAGCTCTTTGACAA
193 AATAGTTCTTTAATGTTTTTAGAGTTATAGCTCTTTGACAA
489791 ATG
1 ATG
489794 TCGAAGTTGA
Statistics
Matches: 236, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
233 8 0.03
234 26 0.11
235 38 0.16
236 164 0.69
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (233 bp):
ATGCCCCATTTCTTCTTGGGTTGAAGCCTTTCACTTTGAGATTGTCCTGTTTGAAAATGTTTTTT
CTCTTTCTTTATTTTAGGAGGAAAAAAAGATATGAGGATATAAGAATTTTGTAAAGTAAGGCCCC
TTAATTCAGGCTCGCAATCAAATCAAATCATAAACATGAGTTCATAGAAAATCAAATTAATCAAT
AGTTCTTTAATGTTTTTAGAGTTATAGCTCTTTGACAA
Found at i:494101 original size:19 final size:19
Alignment explanation
Indices: 494077--494119 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
494067 AAATAAAATT
494077 AAAAACAAAAAA-AAATACA
1 AAAAACAAAAAACAAA-ACA
494096 AAAAACAAAAAACAAAACA
1 AAAAACAAAAAACAAAACA
494115 AAAAA
1 AAAAA
494120 ATAAATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAACAAAAAACAAAACA
Found at i:494453 original size:63 final size:65
Alignment explanation
Indices: 494325--494468 Score: 147
Period size: 63 Copynumber: 2.2 Consensus size: 65
494315 ACTAAGTAGG
* * *
494325 TAAATATATATAATATAGTATTAAATAAGTAAAATAAAATAAAAATAGTAAAAATAGAATAAAAA
1 TAAA-ATATATAATATAGTATTAAATAAG-AAAATAAAATAAAAATAATAAAAAAAAAATAAAAA
*
494390 AC
64 AA
*
494392 TAAAATATATAATGATA-T-TTAAATAA-AAAA-AGAAATAATAATAATAAAAAAACAAAT-AAA
1 TAAAATATATAAT-ATAGTATTAAATAAGAAAATA-AAATAAAAATAATAAAAAAA-AAATAAAA
494452 AAA
63 AAA
494455 TAATAA-ATATAATA
1 TAA-AATATATAATA
494469 AAAGTAAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
62 2 0.03
63 36 0.53
64 5 0.07
65 8 0.12
66 10 0.15
67 7 0.10
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (65 bp):
TAAAATATATAATATAGTATTAAATAAGAAAATAAAATAAAAATAATAAAAAAAAAATAAAAAAA
Found at i:494523 original size:82 final size:85
Alignment explanation
Indices: 494374--494612 Score: 221
Period size: 87 Copynumber: 2.9 Consensus size: 85
494364 TAAAAATAGT
* * * * *
494374 AAAAATAGA-ATAA-AAAACTAAAAT-ATATAAT-GATATTTAAATAAA-AAAAGAAAT-AATAA
1 AAAAATAAATATAATAAAAGTAAAATAATATAATAG-TATTT-AATAAATGAAATAAGTAAATAA
* *
494433 TAATAAAAAAACAAATA-AA-A-
64 -AAAAAAAAAACAAACACAAGAC
*
494453 AATAATAAATATAATAAAAGTAAAATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAA
1 AAAAATAAATATAATAAAAGTAAAATAATATAATAGTATTTAATAAATGAAATAAGTAAAT-AAA
*
494518 AAAAAAAGAAGAAACACAATGAC
65 AAAAAAA-AACAAACACAA-GAC
* * *
494541 AAAAATGAATGT-ATATAAG-AATAATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAA
1 AAAAATAAATATAATAAAAGTAA-AATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAA
*
494604 AAAGAAAAA
65 AAAAAAAAA
494613 GAAGAAACAA
Statistics
Matches: 133, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
79 7 0.05
80 4 0.03
81 16 0.12
82 18 0.14
83 11 0.08
84 8 0.06
85 4 0.03
86 11 0.08
87 45 0.34
88 9 0.07
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (85 bp):
AAAAATAAATATAATAAAAGTAAAATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAA
AAAAAAAACAAACACAAGAC
Found at i:494579 original size:87 final size:89
Alignment explanation
Indices: 494476--494651 Score: 329
Period size: 87 Copynumber: 2.0 Consensus size: 89
494466 ATAAAAGTAA
494476 AATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAAAA-AAAAAGAAGAAAC-ACAATG
1 AATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAAAAGAAAAAGAAGAAACAACAATG
494539 ACAAAAATGAATGTATATAAGAAT
66 ACAAAAATGAATGTATATAAGAAT
*
494563 AATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAAAAGAAAAAGAAGAAACAATAATG
1 AATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAAAAGAAAAAGAAGAAACAACAATG
494628 ACAAAAATGAATGTATATAAGAAT
66 ACAAAAATGAATGTATATAAGAAT
494652 TTAAAACGAA
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
87 44 0.51
88 13 0.15
89 29 0.34
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (89 bp):
AATAATATAATAGTATTTAATAAATGAAATAAGTAAATAAAAAAGAAAAAGAAGAAACAACAATG
ACAAAAATGAATGTATATAAGAAT
Found at i:494674 original size:89 final size:87
Alignment explanation
Indices: 494484--494674 Score: 260
Period size: 89 Copynumber: 2.2 Consensus size: 87
494474 AAAATAATAT
* *
494484 AATAGTATTTAATAAATGAAATAAGTAAATAAAAAAAAAAAGAAGAAACACAATGACAAAAATGA
1 AATAGTAATAAATAAATGAAATAAGTAAATAAAAAAAAAAAGAAGAAACACAATGACAAAAATGA
* *
494549 ATGTATATAAGAATAATAATAT
66 ATGTATATAAGAATAATAAAAG
* * *
494571 AATAGTATTTAATAAATGAAATAAGTAAATAAAAAAGAAAAAGAAGAAACAATAATGACAAAAAT
1 AATAGTAATAAATAAATGAAATAAGTAAATAAAAAA-AAAAAGAAGAAAC-ACAATGACAAAAAT
*
494636 GAATGTATATAAGAAT-TTAAAACG
64 GAATGTATATAAGAATAATAAAA-G
494660 AATA-TAAATAAATAA
1 AATAGT-AATAAATAA
494675 TAAAATATAT
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
87 36 0.38
88 18 0.19
89 40 0.43
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.23
Consensus pattern (87 bp):
AATAGTAATAAATAAATGAAATAAGTAAATAAAAAAAAAAAGAAGAAACACAATGACAAAAATGA
ATGTATATAAGAATAATAAAAG
Found at i:494756 original size:2 final size:2
Alignment explanation
Indices: 494751--494784 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
494741 AAAATAAAAA
494751 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
494785 ATAATGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:495448 original size:23 final size:24
Alignment explanation
Indices: 495417--495461 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
495407 AAAAAATTAC
*
495417 AAATATTTCTTGCT-ATTTTTTCTG
1 AAATATTTCGTG-TGATTTTTTCTG
495441 AAAT-TTTCGTGTGATTTTTTC
1 AAATATTTCGTGTGATTTTTTC
495462 ATCCCTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.74
24 4 0.21
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (24 bp):
AAATATTTCGTGTGATTTTTTCTG
Found at i:495845 original size:19 final size:19
Alignment explanation
Indices: 495821--495857 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
495811 ATGTAAAAAA
495821 ATAAATACATGATATAAAC
1 ATAAATACATGATATAAAC
* *
495840 ATAAATATATTATATAAA
1 ATAAATACATGATATAAA
495858 TATACAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
ATAAATACATGATATAAAC
Found at i:497988 original size:22 final size:21
Alignment explanation
Indices: 497963--498015 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
497953 GTTTTATTTA
*
497963 TATTATGGATTATTAGATTTTG
1 TATT-TGGATTATTAAATTTTG
** *
497985 TATTTTTAATTTTTAAATTTTG
1 TA-TTTGGATTATTAAATTTTG
498007 TATTTGGAT
1 TATTTGGAT
498016 GTTGAATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 5 0.21
22 17 0.71
23 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.60
Consensus pattern (21 bp):
TATTTGGATTATTAAATTTTG
Found at i:503374 original size:164 final size:162
Alignment explanation
Indices: 503106--503431 Score: 609
Period size: 164 Copynumber: 2.0 Consensus size: 162
503096 TAGCTGCGGC
503106 TGAGGCAGTTTCGGAAGCAGATCCATAACCTGTAAAACCAATCACGAACATGTGGATTCTATGGA
1 TGAGGCAGTTTCGGAAGCAGATCCATAACCTGTAAAACCAATCACGAACATGTGGATTCTATGGA
*
503171 TTATTAACATAAGATTTCAAATAAAAACTGACAATAAAATCCAAACAGTTACATGATTAGCATTT
66 TTATTAACATAAGATTTCAAATAAAAACTGACAATAAAATCCAAACAGTTACATGATTAGCATTC
503236 ACTCAGACGCCCAA-GAACTTTAGAGGACATA
131 ACTCAGACGCCCAATGAACTTTAGAGGACATA
503267 TGAGGCAGTTTCGGAAGCAGATCCATAACCTGTAAAACCAATCACGAACAATATGTGGATTCTAT
1 TGAGGCAGTTTCGGAAGCAGATCCATAACCTGTAAAACCAATCACGAAC---ATGTGGATTCTAT
503332 GGATTATTAACATAAGATTTCAAATAAAAACTGACAATAAAATCCAAACAGTTACATGATTAGCA
63 GGATTATTAACATAAGATTTCAAATAAAAACTGACAATAAAATCCAAACAGTTACATGATTAGCA
503397 TTCACTCAGACGCCCAATGAACTTTAGAGGACATA
128 TTCACTCAGACGCCCAATGAACTTTAGAGGACATA
503432 ATAACAAATT
Statistics
Matches: 160, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
161 49 0.31
164 94 0.59
165 17 0.11
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (162 bp):
TGAGGCAGTTTCGGAAGCAGATCCATAACCTGTAAAACCAATCACGAACATGTGGATTCTATGGA
TTATTAACATAAGATTTCAAATAAAAACTGACAATAAAATCCAAACAGTTACATGATTAGCATTC
ACTCAGACGCCCAATGAACTTTAGAGGACATA
Found at i:511787 original size:16 final size:16
Alignment explanation
Indices: 511747--511787 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
511737 GCCCATTGTT
*
511747 CAAATTCCCAAACTGC
1 CAAATTCCTAAACTGC
*
511763 CAAATTCCTAATCTGC
1 CAAATTCCTAAACTGC
511779 CAAATTCCT
1 CAAATTCCT
511788 TCTCATCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (16 bp):
CAAATTCCTAAACTGC
Found at i:536223 original size:15 final size:15
Alignment explanation
Indices: 536205--536239 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
536195 ATAAAAGTCA
* *
536205 TAAATTTAAAATAAT
1 TAAAATTAAAAAAAT
536220 TAAAATTAAAAAAAT
1 TAAAATTAAAAAAAT
536235 TAAAA
1 TAAAA
536240 AATTAAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATTAAAAAAAT
Found at i:536247 original size:15 final size:16
Alignment explanation
Indices: 536210--536247 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
536200 AGTCATAAAT
536210 TTAAAATAATT-AAAA
1 TTAAAATAATTAAAAA
*
536225 TTAAAAAAATTAAAAAA
1 TTAAAATAATT-AAAAA
536242 TTAAAA
1 TTAAAA
536248 CGAGTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
17 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAATAATTAAAAA
Found at i:538518 original size:20 final size:20
Alignment explanation
Indices: 538495--538537 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
538485 ATTCCACCAC
* *
538495 ATGCAACTAAATGTTTCTAA
1 ATGCAACTAAATGGTCCTAA
*
538515 ATGCAACTACATGGTCCTAA
1 ATGCAACTAAATGGTCCTAA
538535 ATG
1 ATG
538538 AGCTATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGGTCCTAA
Found at i:547440 original size:23 final size:23
Alignment explanation
Indices: 547397--547440 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
547387 GCAGATGTAT
*
547397 ATGTCGTAGCAAAGTGGATTGAA
1 ATGTCGTAGCAAAGTGAATTGAA
* *
547420 ATGTCGTGGCAAATTGAATTG
1 ATGTCGTAGCAAAGTGAATTG
547441 TGTTGAGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (23 bp):
ATGTCGTAGCAAAGTGAATTGAA
Found at i:550383 original size:15 final size:15
Alignment explanation
Indices: 550357--550404 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
550347 TTCAAATATA
*
550357 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
550373 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
550390 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
550405 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:552432 original size:23 final size:23
Alignment explanation
Indices: 552399--552458 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
552389 CCCCTGTGGA
*
552399 GGGAATCGGTTCCCCTTTAAAGG
1 GGGAATCGGTTCCCCTTCAAAGG
*
552422 GGGAATTGGTTCCCCTTCAAAGG
1 GGGAATCGGTTCCCCTTCAAAGG
552445 GGGAATCGGTTCCC
1 GGGAATCGGTTCCC
552459 TCATAGGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (23 bp):
GGGAATCGGTTCCCCTTCAAAGG
Found at i:557627 original size:24 final size:24
Alignment explanation
Indices: 557587--557635 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
557577 TGTCCGGACA
557587 TCTATTAAAAATAAACATA-TCAT
1 TCTATTAAAAATAAACATACTCAT
* *
557610 TCTATTAGCAAATTAACATACTCAT
1 TCTATTA-AAAATAAACATACTCAT
557635 T
1 T
557636 ACCATACCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (24 bp):
TCTATTAAAAATAAACATACTCAT
Found at i:558043 original size:22 final size:22
Alignment explanation
Indices: 558011--558055 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
558001 GTTTACAAAT
*
558011 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
558033 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
558055 A
1 A
558056 TACTGCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:558593 original size:22 final size:21
Alignment explanation
Indices: 558567--558625 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 21
558557 ATATGAAATT
* *
558567 TTGTCCCAAAGGACCTGTGAA
1 TTGTCCCAAAGAACCTATGAA
* *
558588 TATGTCCCGAAGAACCTATGAG
1 T-TGTCCCAAAGAACCTATGAA
558610 TTGTCCC-AAG-ACCTAT
1 TTGTCCCAAAGAACCTAT
558626 AAACCCTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.18
20 3 0.09
21 7 0.21
22 17 0.52
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TTGTCCCAAAGAACCTATGAA
Found at i:561443 original size:22 final size:21
Alignment explanation
Indices: 561401--561440 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
561391 GAGTTTATTT
*
561401 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
561422 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
561441 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:567439 original size:65 final size:66
Alignment explanation
Indices: 567307--567452 Score: 176
Period size: 66 Copynumber: 2.3 Consensus size: 66
567297 ACCCATTCAA
* * *
567307 GGGGAACCGATA-CCCTTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
567371 G
66 G
* * *
567372 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTA-A-GGG-ATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGC-TAGAGGGGAATCGATACCCCCA
567433 GGG
65 -GG
*
567436 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
567453 ATGAGAAAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
63 5 0.07
64 24 0.34
65 15 0.21
66 25 0.35
67 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
G
Found at i:567787 original size:29 final size:29
Alignment explanation
Indices: 567753--567824 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
567743 CATATTATGA
**
567753 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
567782 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
567811 TACATGACATGAAT
1 TACATGACATGAAT
567825 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:567879 original size:30 final size:31
Alignment explanation
Indices: 567839--567897 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
567829 AGAAAAGTTC
*
567839 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
567870 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
567898 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:568187 original size:22 final size:22
Alignment explanation
Indices: 568113--568179 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
568103 TTATGGACAA
568113 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
568135 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
568157 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
568179 A
1 A
568180 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:574215 original size:21 final size:21
Alignment explanation
Indices: 574189--574231 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
574179 TTTCTGGGTT
* *
574189 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
574210 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
574231 A
1 A
574232 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:574291 original size:65 final size:65
Alignment explanation
Indices: 574189--574358 Score: 200
Period size: 65 Copynumber: 2.6 Consensus size: 65
574179 TTTCTGGGTT
* * * *
574189 AGGGGAATCGGTACCCATTCAAGGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGC-
1 AGGGGAATCGGTACCC--CCAGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCT
574253 TA
64 TA
* * *
574255 GAGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTT
1 -AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTT
574320 A
65 A
* *
574321 AGGGGAATCGATA-CCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA--GGGGGAACCGATACCCCC
574359 ATGAGAAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 5 0.05
65 51 0.56
66 19 0.21
67 16 0.18
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (65 bp):
AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTTA
Found at i:574695 original size:29 final size:29
Alignment explanation
Indices: 574661--574732 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
574651 CATATTATGA
**
574661 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
574690 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
574719 TACATGACATGAAT
1 TACATGACATGAAT
574733 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:574787 original size:30 final size:31
Alignment explanation
Indices: 574747--574805 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
574737 AGAAAAGTTC
*
574747 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
574778 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
574806 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:575099 original size:22 final size:22
Alignment explanation
Indices: 575025--575091 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
575015 TTATGGACAA
575025 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
575047 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
575069 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
575091 A
1 A
575092 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:576628 original size:14 final size:14
Alignment explanation
Indices: 576609--576644 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
576599 AGTAAACAAC
576609 GAAGCAATTGAAGT
1 GAAGCAATTGAAGT
576623 GAAGCAATTGAAGT
1 GAAGCAATTGAAGT
576637 GAAGCAAT
1 GAAGCAAT
576645 GGTCATCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.28, T:0.19
Consensus pattern (14 bp):
GAAGCAATTGAAGT
Found at i:584023 original size:22 final size:22
Alignment explanation
Indices: 583995--584037 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
583985 GTAGCGGCCA
*
583995 GGCCAGCCACGCGATCAGTAGT
1 GGCCAGCCACACGATCAGTAGT
584017 GGCCAGCCACACGATCAGTAG
1 GGCCAGCCACACGATCAGTAG
584038 CGGTCCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.30, T:0.12
Consensus pattern (22 bp):
GGCCAGCCACACGATCAGTAGT
Found at i:584822 original size:34 final size:34
Alignment explanation
Indices: 584709--584928 Score: 247
Period size: 34 Copynumber: 6.6 Consensus size: 34
584699 TGCAACCGTT
** *
584709 TAAGTACACAGTGCAAAAGAG--ATGCAGGCGTA
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
* * ** *
584741 TAAGCACACAGTGC--AAGAGAGATGCAATCGTA
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
*
584773 TACA-T--ACAGTACAAAAGAGAAACACAAGCGTA
1 TA-AGTACACAGTGCAAAAGAGAAACACAAGCGTA
* *
584805 TAAGTACACAGTGCAAAAGAGAAACACAATCATA
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
584839 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
** * *
584873 TAAGTACACAGTGTTAAAGAGAAACACAATCATA
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
584907 TAAGTACACAGTGCAAAAGAGA
1 TAAGTACACAGTGCAAAAGAGA
584929 TGCAAAATCC
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
30 11 0.07
31 1 0.01
32 41 0.26
33 1 0.01
34 106 0.66
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (34 bp):
TAAGTACACAGTGCAAAAGAGAAACACAAGCGTA
Found at i:584871 original size:68 final size:67
Alignment explanation
Indices: 584709--584928 Score: 281
Period size: 68 Copynumber: 3.3 Consensus size: 67
584699 TGCAACCGTT
** * * * ** *
584709 TAAGTACACAGTGCAAAAGAG--ATGCAGGCGTATAAGCACACAGTGC-AAGAGAGATGCAATCG
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTATAAGTACACAGTGCAAAGAGAAACACAATCA
584771 TA
66 TA
*
584773 TACA-T--ACAGTACAAAAGAGAAACACAAGCGTATAAGTACACAGTGCAAAAGAGAAACACAAT
1 TA-AGTACACAGTGCAAAAGAGAAACACAAGCGTATAAGTACACAGTGC-AAAGAGAAACACAAT
584835 CATA
64 CATA
*
584839 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTATAAGTACACAGTGTTAAAGAGAAACACAATC
1 TAAGTACACAGTGCAAAAGAGAAACACAAGCGTATAAGTACACAGTG-CAAAGAGAAACACAATC
584904 ATA
65 ATA
584907 TAAGTACACAGTGCAAAAGAGA
1 TAAGTACACAGTGCAAAAGAGA
584929 TGCAAAATCC
Statistics
Matches: 136, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
62 13 0.10
64 24 0.18
65 2 0.01
66 17 0.12
68 80 0.59
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (67 bp):
TAAGTACACAGTGCAAAAGAGAAACACAAGCGTATAAGTACACAGTGCAAAGAGAAACACAATCA
TA
Found at i:588155 original size:39 final size:39
Alignment explanation
Indices: 588106--588244 Score: 149
Period size: 39 Copynumber: 3.6 Consensus size: 39
588096 ACATAGCATA
*
588106 AGGA-CATGCGATAAGGACATACCCTGAGCACAAAG-CTG
1 AGGAGCATGCGATAAGGACTTACCCTGAGCACAAAGTC-G
** * * *
588144 AGGCTCCTGCGATAAGAACTTATCCTGAGCACAAAGTCG
1 AGGAGCATGCGATAAGGACTTACCCTGAGCACAAAGTCG
*
588183 AGGAGCATGC-AGTAAGGATTTACCCTGAGCACAAAGTCG
1 AGGAGCATGCGA-TAAGGACTTACCCTGAGCACAAAGTCG
* * *
588222 AGGAGCCTACGGTAAGGACTTAC
1 AGGAGCATGCGATAAGGACTTAC
588245 AAGTCATAGA
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
38 4 0.05
39 77 0.94
40 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (39 bp):
AGGAGCATGCGATAAGGACTTACCCTGAGCACAAAGTCG
Found at i:589031 original size:18 final size:18
Alignment explanation
Indices: 589005--589056 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
588995 AACGTCGGTC
*
589005 AACGATCAACGGTTGGTT
1 AACGATCAACGGTTGATT
* * *
589023 AACGGTCAACAGTCGATT
1 AACGATCAACGGTTGATT
589041 AACGATCAACGGTTGA
1 AACGATCAACGGTTGA
589057 CCGGTTCAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (18 bp):
AACGATCAACGGTTGATT
Found at i:592019 original size:21 final size:21
Alignment explanation
Indices: 591994--592139 Score: 121
Period size: 21 Copynumber: 6.8 Consensus size: 21
591984 GCCATAAAAA
*
591994 ATGTCCCGAATGACCACATAT
1 ATGTCCCGAAGGACCACATAT
* *
592015 ATGTCCCGTAGGACCACATAGA
1 ATGTCCCGAAGGACCACATA-T
* * *
592037 ATTGTCCCGTATGACCATATAT
1 A-TGTCCCGAAGGACCACATAT
* * *
592059 ATGTTCCAAAGGACCAAATAT
1 ATGTCCCGAAGGACCACATAT
** ***
592080 ATGTCCAAAAAGGATTGCATAT
1 ATGTCC-CGAAGGACCACATAT
* *
592102 ATGTTCCGAAGGATCACATAT
1 ATGTCCCGAAGGACCACATAT
592123 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
592140 GTAGAACCCT
Statistics
Matches: 98, Mismatches: 24, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
21 64 0.65
22 17 0.17
23 17 0.17
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAT
Found at i:592772 original size:19 final size:19
Alignment explanation
Indices: 592745--592791 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
592735 CTTTACGATG
*
592745 GTATTGATATTGTACTTGA
1 GTATCGATATTGTACTTGA
592764 GTATCGATATTGTACTTGA
1 GTATCGATATTGTACTTGA
592783 GTATCGATA
1 GTATCGATA
592792 CCCTTTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (19 bp):
GTATCGATATTGTACTTGA
Found at i:598858 original size:21 final size:21
Alignment explanation
Indices: 598833--598970 Score: 98
Period size: 21 Copynumber: 6.5 Consensus size: 21
598823 GCCATACAAA
598833 ATGTCCCGAATGACCACATAT
1 ATGTCCCGAATGACCACATAT
* *
598854 ATGTCCCGTATGACCACATAGA
1 ATGTCCCGAATGACCACATA-T
* * *
598876 ATTATCCAGTATGACCACATAT
1 A-TGTCCCGAATGACCACATAT
* * *
598898 ATGTGCCAAATGACCAAATAT
1 ATGTCCCGAATGACCACATAT
**** *
598919 ATGTTAAAAATGA-TAGCATAT
1 ATGTCCCGAATGACCA-CATAT
* * *
598940 ATGTTCCGAAAGATCACATAT
1 ATGTCCCGAATGACCACATAT
598961 ATGTCCCGAA
1 ATGTCCCGAA
598971 GAACCACGTA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.01
21 70 0.77
22 3 0.03
23 17 0.19
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (21 bp):
ATGTCCCGAATGACCACATAT
Found at i:599192 original size:21 final size:22
Alignment explanation
Indices: 599151--599192 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
599141 GTCTTCTAAT
*
599151 ACATATCATATAAGTTCATGCC
1 ACATATCATATAAGTTAATGCC
599173 ACATATC-TATAA-TGTAATGC
1 ACATATCATATAAGT-TAATGC
599193 AACCAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 1 0.06
21 10 0.56
22 7 0.39
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ACATATCATATAAGTTAATGCC
Found at i:604323 original size:39 final size:38
Alignment explanation
Indices: 604193--604327 Score: 157
Period size: 39 Copynumber: 3.5 Consensus size: 38
604183 ACATAGGATA
* *
604193 AGGA-CATGCGGTAAGGACTTACCCTGAGAACAAAGCTA
1 AGGAGCATGCGGTAAGGACTTACCCTGAGCACAAAGC-G
* * *
604231 AGGAGCTTACGGTAAGGACTTACCCTGATCACAAAGCCG
1 AGGAGCATGCGGTAAGGACTTACCCTGAGCACAAAG-CG
*
604270 AGGAGTC-TGAGGTAAGGACTTACCCTGAGCACAAAGTCG
1 AGGAG-CATGCGGTAAGGACTTACCCTGAGCACAAAG-CG
*
604309 ATGAGCATGCGGTAAGGAC
1 AGGAGCATGCGGTAAGGAC
604328 ATACAAGTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
38 5 0.06
39 75 0.91
40 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (38 bp):
AGGAGCATGCGGTAAGGACTTACCCTGAGCACAAAGCG
Found at i:606931 original size:30 final size:27
Alignment explanation
Indices: 606877--606932 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
606867 ATTTTGGGCT
*
606877 TTGTTTTAATAAAAAAATATTTTAAAG
1 TTGTTTTAATAAAAAAAAATTTTAAAG
606904 TTGTTTTATATTAAATAAAAAATTTTAAA
1 TTGTTTTA-A-TAAA-AAAAAATTTTAAA
606933 TTATCAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 8 0.32
28 1 0.04
29 4 0.16
30 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (27 bp):
TTGTTTTAATAAAAAAAAATTTTAAAG
Found at i:621921 original size:30 final size:30
Alignment explanation
Indices: 621865--621932 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
621855 TTAATATATA
*
621865 TTTA-ATTTTTTAGTAATTTACTTTTTATT
1 TTTATATTTTTTAGTAATTTAATTTTTATT
621894 TTTAGTATTTTTTA-T-ATTTAATGTTTTATT
1 TTTA-TATTTTTTAGTAATTTAAT-TTTTATT
621924 TTTATATTT
1 TTTATATTT
621933 AAAATTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 15 0.43
30 12 0.34
31 8 0.23
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (30 bp):
TTTATATTTTTTAGTAATTTAATTTTTATT
Found at i:622519 original size:28 final size:29
Alignment explanation
Indices: 622460--622514 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
622450 TTAAAATTTT
622460 TAAAAGAAAATCCCAAAATTTTATAAAAC
1 TAAAAGAAAATCCCAAAATTTTATAAAAC
*
622489 TAAAA-AAAA-CCCAAAACTTT-TAAAAC
1 TAAAAGAAAATCCCAAAATTTTATAAAAC
622515 CCTAATTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 10 0.40
28 4 0.16
29 5 0.20
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (29 bp):
TAAAAGAAAATCCCAAAATTTTATAAAAC
Found at i:623601 original size:29 final size:31
Alignment explanation
Indices: 623552--623621 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
623542 GTAAAATATT
623552 TTATTTTATTAAAATAAATTA-A-TAATTTA
1 TTATTTTATTAAAATAAATTATATTAATTTA
* ** *
623581 TTATTTTATTAAATTGTATTATATTAATTTT
1 TTATTTTATTAAAATAAATTATATTAATTTA
*
623612 TTATTATATT
1 TTATTTTATT
623622 TTACAGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 15 0.44
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
TTATTTTATTAAAATAAATTATATTAATTTA
Found at i:628271 original size:60 final size:60
Alignment explanation
Indices: 628178--628292 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
628168 TACACTGTTC
* * * * * *
628178 ACATTTAGGTCGAACAAGCTGGTAGTTGCATGCCTCCCCTTTAAGCTTGAAGGCATCTCG
1 ACATTGAGGTCAAACAAGCTCGTAGTTGAATGCCTCCCCATGAAGCTTGAAGGCATCTCG
* * *
628238 ACATTGAGGTCAAAGAAGCTCGTAGTTGAATGCCTCTCCATGGAGCTTGAAGGCA
1 ACATTGAGGTCAAACAAGCTCGTAGTTGAATGCCTCCCCATGAAGCTTGAAGGCA
628293 CCGTGTCAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (60 bp):
ACATTGAGGTCAAACAAGCTCGTAGTTGAATGCCTCCCCATGAAGCTTGAAGGCATCTCG
Found at i:630419 original size:20 final size:20
Alignment explanation
Indices: 630382--630420 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
630372 TAATCATATT
* **
630382 ACTGGTAATCTTTTATTCCC
1 ACTGATAATCTTACATTCCC
630402 ACTGATAATCTTACATTCC
1 ACTGATAATCTTACATTCC
630421 GTGAACCAAA
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:0.26, C:0.26, G:0.08, T:0.41
Consensus pattern (20 bp):
ACTGATAATCTTACATTCCC
Found at i:635718 original size:156 final size:156
Alignment explanation
Indices: 635531--635841 Score: 622
Period size: 156 Copynumber: 2.0 Consensus size: 156
635521 ATCTCTTTTA
635531 CAGACTTTCTGTAAGAATGAAACTTTATTACTATTTTTTCAGCTTGCTCTTAAGGATGCTGAGAG
1 CAGACTTTCTGTAAGAATGAAACTTTATTACTATTTTTTCAGCTTGCTCTTAAGGATGCTGAGAG
635596 GTTAATGAGCTTGCAAAATAATGAAGTAAGATCCTATATCTTAAAGGCCAATGCTCTAATTCTGG
66 GTTAATGAGCTTGCAAAATAATGAAGTAAGATCCTATATCTTAAAGGCCAATGCTCTAATTCTGG
635661 TAAGTGATGGATTGATTGATATAAAG
131 TAAGTGATGGATTGATTGATATAAAG
635687 CAGACTTTCTGTAAGAATGAAACTTTATTACTATTTTTTCAGCTTGCTCTTAAGGATGCTGAGAG
1 CAGACTTTCTGTAAGAATGAAACTTTATTACTATTTTTTCAGCTTGCTCTTAAGGATGCTGAGAG
635752 GTTAATGAGCTTGCAAAATAATGAAGTAAGATCCTATATCTTAAAGGCCAATGCTCTAATTCTGG
66 GTTAATGAGCTTGCAAAATAATGAAGTAAGATCCTATATCTTAAAGGCCAATGCTCTAATTCTGG
635817 TAAGTGATGGATTGATTGATATAAA
131 TAAGTGATGGATTGATTGATATAAA
635842 TGGATCCAAG
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (156 bp):
CAGACTTTCTGTAAGAATGAAACTTTATTACTATTTTTTCAGCTTGCTCTTAAGGATGCTGAGAG
GTTAATGAGCTTGCAAAATAATGAAGTAAGATCCTATATCTTAAAGGCCAATGCTCTAATTCTGG
TAAGTGATGGATTGATTGATATAAAG
Found at i:649285 original size:12 final size:12
Alignment explanation
Indices: 649268--649294 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
649258 TTAAAATACA
649268 TTGCTATCAAGT
1 TTGCTATCAAGT
649280 TTGCTATCAAGT
1 TTGCTATCAAGT
649292 TTG
1 TTG
649295 AGTACTATTT
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:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (12 bp):
TTGCTATCAAGT
Found at i:652107 original size:29 final size:29
Alignment explanation
Indices: 652051--652107 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
652041 GAAGTATACT
* * *
652051 AAATTCTCAGTTTCATATATAATGTTTTA
1 AAATTCTCAATTTCATACATAATATTTTA
* *
652080 AAATTTTCAATTTCATACATGATATTTT
1 AAATTCTCAATTTCATACATAATATTTT
652108 CTGCCGTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (29 bp):
AAATTCTCAATTTCATACATAATATTTTA
Found at i:652340 original size:51 final size:51
Alignment explanation
Indices: 652278--652386 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 51
652268 CTTACGACGA
652278 TGTAAGTGAATAAAATAAAA-ATGTATAGCACTAAACACATACATACAC-TGG
1 TGTAAGTGAATAAAATAAAATA-GTATAGCACTAAACACATACATACACAT-G
* * *
652329 TGTAAGTGAATAAAATAAAATAGTGTAGCACTTAACACATACTTACACATG
1 TGTAAGTGAATAAAATAAAATAGTATAGCACTAAACACATACATACACATG
652380 TGTAAGT
1 TGTAAGT
652387 ATGTATCTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
51 51 0.96
52 2 0.04
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.27
Consensus pattern (51 bp):
TGTAAGTGAATAAAATAAAATAGTATAGCACTAAACACATACATACACATG
Found at i:653736 original size:11 final size:11
Alignment explanation
Indices: 653720--653744 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
653710 TTTTAATAAA
653720 AAATATTTTTT
1 AAATATTTTTT
653731 AAATATTTTTT
1 AAATATTTTTT
653742 AAA
1 AAA
653745 GTGTCACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:653850 original size:29 final size:29
Alignment explanation
Indices: 653808--653864 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
653798 TTAATGACAG
*
653808 AAAACATCATGTATGAAACCGAGAATTTT
1 AAAACATCATGTATGAAACCGAAAATTTT
* *
653837 AAAACATTATGTATGAAACTGAAAATTT
1 AAAACATCATGTATGAAACCGAAAATTT
653865 GGTATACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (29 bp):
AAAACATCATGTATGAAACCGAAAATTTT
Found at i:654516 original size:34 final size:31
Alignment explanation
Indices: 654478--654572 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
654468 TTCATTAAAT
654478 TTTCAAATATTTTAATACAATCATTTTGTAATAG
1 TTTCAAATA-TTTAATA-AAT-ATTTTGTAATAG
* *
654512 TTTCATATATTTAATAACTATTTTGTAATAG
1 TTTCAAATATTTAATAAATATTTTGTAATAG
* ***
654543 TTT-AATAAATTTAATGGTTATTTTGTAATA
1 TTTCAA-ATATTTAATAAATATTTTGTAATA
654573 TTTAAAAGTC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
30 1 0.02
31 35 0.66
32 2 0.04
33 7 0.13
34 8 0.15
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (31 bp):
TTTCAAATATTTAATAAATATTTTGTAATAG
Found at i:654538 original size:31 final size:31
Alignment explanation
Indices: 654500--654577 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
654490 TAATACAATC
* *
654500 ATTTTGTAATAGTTTCATATATTTAATAACT
1 ATTTTGTAATAGTTTAATAAATTTAATAACT
***
654531 ATTTTGTAATAGTTTAATAAATTTAATGGTT
1 ATTTTGTAATAGTTTAATAAATTTAATAACT
654562 ATTTTGTAATA-TTTAA
1 ATTTTGTAATAGTTTAA
654578 AAGTCTACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.53
Consensus pattern (31 bp):
ATTTTGTAATAGTTTAATAAATTTAATAACT
Found at i:655170 original size:36 final size:37
Alignment explanation
Indices: 655087--655171 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 37
655077 CTCTAATATT
*
655087 AATATAAGATATTTATATATTTTCTTTTAAAAAAATTAA
1 AATATAA-A-ATTTATATAATTTCTTTTAAAAAAATTAA
* *
655126 ATTCATAAAATTTATATAATTT-TTTT-ATAAAATTGAA
1 AAT-ATAAAATTTATATAATTTCTTTTAAAAAAATT-AA
655163 AATATAAAA
1 AATATAAAA
655172 AGGTTTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
36 13 0.32
37 8 0.20
38 12 0.30
39 3 0.08
40 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (37 bp):
AATATAAAATTTATATAATTTCTTTTAAAAAAATTAA
Found at i:656842 original size:2 final size:2
Alignment explanation
Indices: 656835--656866 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
656825 TTTTTGTAAT
656835 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
656867 ACCAGGAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:658710 original size:55 final size:55
Alignment explanation
Indices: 658658--658951 Score: 441
Period size: 55 Copynumber: 5.4 Consensus size: 55
658648 TTCCATGGTT
* * * * *
658658 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACATG-GG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* * *
658712 GTGTACACATAGTGTCAATAC-GATAATTCATAAACTCATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTATGAATTTCGTGAGG
* *
658767 ATGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGGGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
* *
658822 TTGCACACATAGTTCCAATACGGAAATTCATAAACTCGTTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
*
658877 TTGCACATATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
658932 TTGCACACATAGTG-CAATAC
1 TTGCACACATAGTGCCAATAC
658952 AAAAATCTCC
Statistics
Matches: 217, Mismatches: 20, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
53 1 0.00
54 48 0.22
55 166 0.76
56 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
Done.