Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:437754 original size:20 final size:20
Alignment explanation
Indices: 437606--437842 Score: 131
Period size: 20 Copynumber: 11.7 Consensus size: 20
437596 TTTTCCCAAT
* *
437606 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGATTACGTAAA
** *
437626 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
437647 TCGCAATGCGA-TAC-TGACTA
1 TCGCAATGCGATTACGT-A-AA
* * * *
437667 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGA-TTACGTAAA
* *
437688 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGA-TTACGTAAA
** * * *
437708 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-TTACGTAAA
*
437729 TCGCAATGCGAGTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
437749 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGATTACGTAAA
* *
437769 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
437790 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* * * *
437810 TTGCAATGCGAAT-CTTACTA
1 TCGCAATGCGATTACGTA-AA
437830 TCGCAATGCGATT
1 TCGCAATGCGATT
437843 TACATAGCGC
Statistics
Matches: 169, Mismatches: 39, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
19 5 0.03
20 101 0.60
21 59 0.35
22 3 0.02
23 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:437760 original size:41 final size:40
Alignment explanation
Indices: 437593--437800 Score: 129
Period size: 41 Copynumber: 5.1 Consensus size: 40
437583 TTTCGCGTTA
** *
437593 CGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATG
1 CGATTTTCATAATTCGCAATGCG-ATACGTAAATCGCAATG
** * *
437634 CGAATTTGGA-AAATCGCAATGCGATAC-TGACTATCGCAATG
1 CG-ATTTTCATAATTCGCAATGCGATACGT-A-AATCGCAATG
* * * * **
437675 CAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGTTG
1 CGATTTTCATAATTCGCAATGCGA--TACGTAAATCGCAATG
*
437716 CGATTTTCATAATTCGCAATGCGAGTACGTAAATCGCAACG
1 CGATTTTCATAATTCGCAATGCGA-TACGTAAATCGCAATG
* * * *
437757 CGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAATG
1 CGATTTTCA-TAATTCGCAATGCG-A-TACGTAAATCGCAATG
437798 CGA
1 CGA
437801 ATACGTAAAT
Statistics
Matches: 127, Mismatches: 30, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
39 4 0.03
40 26 0.20
41 89 0.70
42 4 0.03
43 3 0.02
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (40 bp):
CGATTTTCATAATTCGCAATGCGATACGTAAATCGCAATG
Found at i:437809 original size:41 final size:41
Alignment explanation
Indices: 437729--437822 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
437719 TTTTCATAAT
* * *
437729 TCGCAATGCG-AGTACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
437769 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
*
437810 TTGCAATGCGAAT
1 TCGCAATGCGAAT
437823 CTTACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.22
41 36 0.78
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:438492 original size:52 final size:51
Alignment explanation
Indices: 438410--438546 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 51
438400 GAAATAAAAA
* * **
438410 TCGCATTGCGATTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATCTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
*
438461 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGAT-CTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
*
438513 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATT
1 T-CGCGTTGCGA-TCTCATT-TCGCGTTGCGATT
438547 TTCATTTCAA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
51 11 0.14
52 37 0.49
53 15 0.20
54 13 0.17
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (51 bp):
TCGCGTTGCGATCTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:438501 original size:33 final size:34
Alignment explanation
Indices: 438464--438529 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
438454 TTTCATTTCG
438464 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
438497 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
438530 ATTATCTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:438884 original size:43 final size:43
Alignment explanation
Indices: 438823--438908 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
438813 CAACATCCGG
438823 GTGGAGATGCTAATTTGACCCATTCGTGGCTTCAGACTATGAC
1 GTGGAGATGCTAATTTGACCCATTCGTGGCTTCAGACTATGAC
438866 GTGGAGATGCTAATTTGACCCATTCGTGGCTTCAGACTATGAC
1 GTGGAGATGCTAATTTGACCCATTCGTGGCTTCAGACTATGAC
438909 TAGCGATCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (43 bp):
GTGGAGATGCTAATTTGACCCATTCGTGGCTTCAGACTATGAC
Found at i:441878 original size:12 final size:12
Alignment explanation
Indices: 441861--441885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
441851 TCTTCGGGGA
441861 CTTTTTCTTCTT
1 CTTTTTCTTCTT
441873 CTTTTTCTTCTT
1 CTTTTTCTTCTT
441885 C
1 C
441886 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:442095 original size:22 final size:23
Alignment explanation
Indices: 442064--442107 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
442054 CACATCAAAA
*
442064 TCCGAGTATTGACCAATATCAAG
1 TCCGAGTATTGACCAAGATCAAG
442087 TCCG-GTATTGACCAAGATCAA
1 TCCGAGTATTGACCAAGATCAA
442108 ATTTCGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (23 bp):
TCCGAGTATTGACCAAGATCAAG
Found at i:442739 original size:20 final size:21
Alignment explanation
Indices: 442714--442765 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
442704 TTTTCCTAAT
*
442714 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
442734 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
442755 TCGCAATGCGA
1 TCGCAATGCGA
442766 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:442839 original size:20 final size:20
Alignment explanation
Indices: 442731--442842 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
442721 GCGAATAAGT
*
442731 AAATCGCAATGCGAATT-TGGA
1 AAATCGCAATGAG-ATTCT-GA
* *
442752 AAATCGCAATGCGATACTGA
1 AAATCGCAATGAGATTCTGA
** * ** *
442772 CTATCGCAACGAGATAATACA
1 AAATCGCAATGAGATTCT-GA
*
442793 AAATCGCAACGAGATTCTGA
1 AAATCGCAATGAGATTCTGA
***
442813 CTTTCGCAATGAGATTCTGA
1 AAATCGCAATGAGATTCTGA
442833 AAATCGCAAT
1 AAATCGCAAT
442843 CATCTTCAAA
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
20 41 0.59
21 29 0.41
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGAGATTCTGA
Found at i:443148 original size:20 final size:20
Alignment explanation
Indices: 443053--443140 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
443043 CAACGGGGAA
*
443053 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
443073 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
443093 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
**
443113 ATCATAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
443133 ATCGCAAC
1 ATCGCAAC
443141 TAGAAAATCG
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 5 0.10
20 41 0.80
21 5 0.10
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:443208 original size:19 final size:19
Alignment explanation
Indices: 443167--443234 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
443157 GAAATGAAAA
443167 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
443183 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
443200 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
443219 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
443235 TCATTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:444859 original size:41 final size:41
Alignment explanation
Indices: 444814--444895 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
444804 CCTCTTCAAC
* *
444814 GATGATAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGATAGGGGCCTC-TGAACGAGTGGAGGGGACTCTTGAGG
*
444855 GATGATAGGGGCCTCTGAACGATTGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTGAACGAGTGGAGGGGACTCTTGAGG
444896 AATGCAGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 6 0.16
41 31 0.84
ACGTcount: A:0.20, C:0.15, G:0.43, T:0.23
Consensus pattern (41 bp):
GATGATAGGGGCCTCTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:445294 original size:20 final size:20
Alignment explanation
Indices: 445269--445352 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
445259 AAACTTACTT
445269 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
445289 TTGCAA-G-G-AAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
445306 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
445326 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
445345 TCGCAACG
1 TCGCAACG
445353 ACAAAATCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
17 14 0.26
18 2 0.04
19 15 0.28
20 22 0.42
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:445321 original size:37 final size:39
Alignment explanation
Indices: 445269--445352 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 39
445259 AAACTTACTT
* **
445269 TCGCAACGCGAAAATGACTATTGCAA-G-GAAATGACTA
1 TCGCAACGCGAAAATGACTATCGCAATGCGAAATGAAAA
* *
445306 TCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAATGCGAAATGAAAA
445345 TCGCAACG
1 TCGCAACG
445353 ACAAAATCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 23 0.57
38 1 0.03
39 16 0.40
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (39 bp):
TCGCAACGCGAAAATGACTATCGCAATGCGAAATGAAAA
Found at i:445406 original size:19 final size:19
Alignment explanation
Indices: 445379--445530 Score: 103
Period size: 19 Copynumber: 8.6 Consensus size: 19
445369 AAAACACAAA
*
445379 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
445398 TCGCGTTGCGA--TT--TG
1 TCGCGTTGCGATTTTCATT
445413 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
445430 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
445449 TCGCATTGCGA--TT--TG
1 TCGCGTTGCGATTTTCATT
445464 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
445481 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
445500 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
445520 TCGTGTTGCGA
1 TCGCGTTGCGA
445531 AAGTAAACTA
Statistics
Matches: 106, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
13 15 0.14
15 8 0.08
17 8 0.08
19 63 0.59
20 12 0.11
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:445439 original size:51 final size:51
Alignment explanation
Indices: 445379--445511 Score: 230
Period size: 51 Copynumber: 2.6 Consensus size: 51
445369 AAAACACAAA
445379 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTGTCGTTGCGATTTTCATT
*
445430 TCGCATTGCGATTTTCATTTCGCATTGCGATTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTGTCGTTGCGATTTTCATT
***
445481 TCGCATTGCGATAGCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGAT
445512 AGTCATTTTC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44
Consensus pattern (51 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTTGTCGTTGCGATTTTCATT
Found at i:446085 original size:18 final size:18
Alignment explanation
Indices: 446062--446108 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
446052 CGGGTCGATC
446062 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
446080 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
446098 AGGTGA-GGCTC
1 AGGTGATGGCTC
446109 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.15, C:0.13, G:0.47, T:0.26
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:447443 original size:20 final size:20
Alignment explanation
Indices: 447418--447455 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
447408 AATAATTTCT
447418 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
447438 GAAAATGAAAATCGCAAC
1 GAAAATGAAAATCGCAAC
447456 GCAAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:447765 original size:22 final size:22
Alignment explanation
Indices: 447738--447781 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
447728 AGATGGAGAT
447738 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
447760 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
447782 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:448001 original size:20 final size:20
Alignment explanation
Indices: 447976--448042 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
447966 GTATTATCTC
*
447976 GTTGCGAAAGTAAGTATTGA
1 GTTGCGAAAGTAAGTATCGA
* *
447996 GTTGCGAAATTAAGTACCGA
1 GTTGCGAAAGTAAGTATCGA
* *
448016 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTAAGTATCGA
448036 GTTGCGA
1 GTTGCGA
448043 TTTTGTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAGTAAGTATCGA
Found at i:448069 original size:41 final size:41
Alignment explanation
Indices: 447950--448087 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
447940 CGCTTTGAAA
* * * *
447950 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * * *
447991 ATTGAGTTGCGAAATT-AAGTACCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
448031 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
448072 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
448088 CCAAATTCGC
Statistics
Matches: 74, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
40 30 0.41
41 44 0.59
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:448079 original size:20 final size:20
Alignment explanation
Indices: 448008--448084 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
447998 TGCGAAATTA
* *
448008 AGTACCGAGTTGCGAAAGTC
1 AGTACCGCGTTGCGATAGTC
* *
448028 AGTATCGCGTTGCGATTTTGT-
1 AGTACCGCGTTGCGA--TAGTC
* *
448049 ATTATCGCGTTGCGATAGTC
1 AGTACCGCGTTGCGATAGTC
448069 AGTACCGCGTTGCGAT
1 AGTACCGCGTTGCGAT
448085 TTTCCAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.07
20 27 0.59
21 14 0.30
22 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (20 bp):
AGTACCGCGTTGCGATAGTC
Found at i:448103 original size:41 final size:41
Alignment explanation
Indices: 448017--448105 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
448007 AAGTACCGAG
* * ** * *
448017 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTACCGCGTTGCGATTTTCAAATATCGCA
448058 TTGCGATAGTCAGTACCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTACCGCGTTGCGATTTT-CAAATATCGCA
448099 TTGCGAT
1 TTGCGAT
448106 TTACTTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCAGTACCGCGTTGCGATTTTCAAATATCGCA
Found at i:448104 original size:21 final size:20
Alignment explanation
Indices: 448078--448124 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
448068 CAGTACCGCG
*
448078 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACAAATTCGCA
**
448099 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACAAATTCGCA
448119 TTGCGA
1 TTGCGA
448125 ATTGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:448166 original size:21 final size:22
Alignment explanation
Indices: 448117--448166 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
448107 TACTTATTCG
*
448117 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCA
**
448138 CAACGCGAAATT-GGAAAATCA
1 CATTGCGAAATTGGGAAAATCA
448159 CATTGCGA
1 CATTGCGA
448167 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCA
Found at i:449571 original size:35 final size:31
Alignment explanation
Indices: 449502--449567 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
449492 CATATAAGTC
* *
449502 TAATAATTATTTTATAATAATTTAATAAAAT
1 TAATAATTAATTTATAATAATATAATAAAAT
*
449533 TAATAATTAATTTATATATATATATATTTAAAAT
1 TAATAATTAATTTATA-ATA-ATATA-ATAAAAT
449567 T
1 T
449568 TAATGATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 15 0.52
32 3 0.10
33 4 0.14
34 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TAATAATTAATTTATAATAATATAATAAAAT
Found at i:453818 original size:21 final size:20
Alignment explanation
Indices: 453732--453889 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
453722 AAATGACCAA
**
453732 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
453751 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
453771 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
453791 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
453812 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
453833 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
453853 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
453874 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
453890 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:453882 original size:20 final size:20
Alignment explanation
Indices: 453857--454050 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
453847 GATTTTCAAT
* *
453857 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
453877 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
453897 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
453917 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
453937 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
453957 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
453977 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
453997 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
454018 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
454038 AATCGCAACGCGA
1 AATCGCAACGCGA
454051 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:453902 original size:40 final size:39
Alignment explanation
Indices: 453857--454050 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
453847 GATTTTCAAT
* ** *
453857 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
453897 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
453937 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
453977 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
454018 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
454051 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:453940 original size:60 final size:60
Alignment explanation
Indices: 453857--454049 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
453847 GATTTTCAAT
* ** * *
453857 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
453917 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
453977 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
454038 AATCGCAACGCG
1 AATCGCAACGCG
454050 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:454489 original size:31 final size:32
Alignment explanation
Indices: 454428--454496 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
454418 TTCACTTAGA
454428 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTC-GTCGTTGCGAT
* *
454461 TTTCATTTCGCGTTGCTATTC-TCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCGTCGTTGCGAT
454492 TTTCA
1 TTTCA
454497 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 15 0.44
33 19 0.56
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.48
Consensus pattern (32 bp):
TTTCATTTCGCGTTACGATTCGTCGTTGCGAT
Found at i:454636 original size:14 final size:14
Alignment explanation
Indices: 454617--454671 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
454607 AGAATGACTG
454617 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
454631 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
454650 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
454664 TCGCAACG
1 TCGCAACG
454672 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:454654 original size:33 final size:33
Alignment explanation
Indices: 454617--454687 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
454607 AGAATGACTG
**
454617 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
454650 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
454683 TCGCA
1 TCGCA
454688 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:454724 original size:14 final size:14
Alignment explanation
Indices: 454705--454794 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
454695 TTTAATTTCG
454705 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
454719 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
454738 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
454752 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
454769 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
454785 CGTTGCGATT
1 CGTTGCGATT
454795 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:454730 original size:33 final size:33
Alignment explanation
Indices: 454688--454802 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
454678 CAAAATCGCA
*
454688 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
454721 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
454754 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
454787 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
454803 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:454743 original size:19 final size:18
Alignment explanation
Indices: 454683--454800 Score: 71
Period size: 14 Copynumber: 7.1 Consensus size: 18
454673 GAAACCAAAA
* *
454683 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCA-T
454702 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
454716 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
454735 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
454749 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
454767 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
454782 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
454800 T
1 T
454801 TCAACCAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 29
0.67 0.08 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.11
17 7 0.09
18 1 0.01
19 30 0.39
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:456663 original size:92 final size:93
Alignment explanation
Indices: 456496--456871 Score: 708
Period size: 92 Copynumber: 4.1 Consensus size: 93
456486 TAGATTGCTT
*
456496 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
456561 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
456588 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
456652 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
456680 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
456742 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
456770 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
456835 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
456863 AGTAAATTT
1 AGTAAATTT
456872 ATCCATTCAA
Statistics
Matches: 279, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
90 90 0.32
91 8 0.03
92 142 0.51
93 39 0.14
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:456805 original size:182 final size:184
Alignment explanation
Indices: 456496--456873 Score: 708
Period size: 182 Copynumber: 2.1 Consensus size: 184
456486 TAGATTGCTT
456496 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGTA
456561 TTTGTCTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
65 TTTGTCTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
456626 TGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
456680 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-TGTATTCTTTAACACTGTGAAATA-TAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAACACTGTGAAATAGTAT
456743 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTC-TTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
456808 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
456863 AGTAAATTTAT
1 AGTAAATTTAT
456874 CCATTCAAGT
Statistics
Matches: 190, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
181 8 0.04
182 107 0.56
183 40 0.21
184 35 0.18
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (184 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:456955 original size:19 final size:19
Alignment explanation
Indices: 456915--457043 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
456905 TAGTTTACTT
* *
456915 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
456935 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
456954 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
456973 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
456987 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
457006 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
457020 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
457039 TCGCA
1 TCGCA
457044 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:456994 original size:33 final size:32
Alignment explanation
Indices: 456951--457043 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
456941 CGCGAAACCA
**
456951 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
456983 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
457016 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
457044 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:457041 original size:52 final size:52
Alignment explanation
Indices: 456915--457043 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
456905 TAGTTTACTT
**
456915 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
456967 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
457020 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
457044 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:457061 original size:19 final size:19
Alignment explanation
Indices: 457039--457173 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
457029 GAAACCAAAA
*
457039 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
457058 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
457074 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
457091 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
457107 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
457124 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
457143 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
457163 TCGTGTTGCGA
1 TCGCGTTGCGA
457174 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:457080 original size:14 final size:14
Alignment explanation
Indices: 457061--457117 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
457051 TTTCATTTCG
457061 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
457075 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
457092 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
457108 CGTTGCGATT
1 CGTTGCGATT
457118 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:457086 original size:33 final size:33
Alignment explanation
Indices: 457044--457136 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
457034 CAAAATCGCA
*
457044 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
457077 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
457110 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
457137 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:457676 original size:21 final size:21
Alignment explanation
Indices: 457620--457682 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
457610 TTCCTCGAGA
*
457620 GTCCCTCCCACCGTTCAAGAG
1 GTCCCTCCCACCATTCAAGAG
** * *
457641 G-CCACTGTCATCATTGAAGAG
1 GTCC-CTCCCACCATTCAAGAG
457662 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCATTCAAGAG
457683 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
GTCCCTCCCACCATTCAAGAG
Found at i:459072 original size:14 final size:14
Alignment explanation
Indices: 459053--459091 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
459043 GATTGTTAAT
459053 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
459067 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
459081 TGATTGTGTAA
1 TGATT-TGTAA
459092 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:459261 original size:20 final size:19
Alignment explanation
Indices: 459193--459275 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
459183 AAAAATGACT
459193 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
459212 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
459226 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
459245 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
459265 ATCGCAATGCG
1 ATCGCAATGCG
459276 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:459328 original size:19 final size:19
Alignment explanation
Indices: 459304--459577 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
459294 GATTATCTCG
459304 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
459323 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
459342 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
459356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
459375 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
459394 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
459413 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
459432 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
459451 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
459465 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
459484 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
459503 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
459517 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
459537 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
459551 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
459570 TTGCGATT
1 TTGCGATT
459578 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 137 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:459344 original size:52 final size:52
Alignment explanation
Indices: 459282--459549 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
459272 TGCGTTTATA
*
459282 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
459334 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
459386 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
459443 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
459495 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
459548 AT
1 AT
459550 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:459433 original size:109 final size:105
Alignment explanation
Indices: 459282--459549 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
459272 TGCGTTTATA
459282 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
459346 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
459386 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
459451 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
459495 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
459550 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:461866 original size:12 final size:12
Alignment explanation
Indices: 461849--461873 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
461839 TCTTCGGGGA
461849 CTTTTTCTTCTT
1 CTTTTTCTTCTT
461861 CTTTTTCTTCTT
1 CTTTTTCTTCTT
461873 C
1 C
461874 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:462081 original size:24 final size:24
Alignment explanation
Indices: 462047--462093 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
462037 CTGAAACATC
462047 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
462071 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
462094 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:462794 original size:20 final size:20
Alignment explanation
Indices: 462766--463155 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
462756 AAATTTCAGT
* * * *
462766 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
462786 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
462806 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
462826 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
462846 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
462866 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
462886 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
462906 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
462926 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
462946 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
462966 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
462986 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
463007 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
463027 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
463047 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
463067 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
463087 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
463107 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
463127 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
463147 GTTGCGATT
1 GTTGCGATT
463156 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:477386 original size:24 final size:25
Alignment explanation
Indices: 477344--477391 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
477334 TTTTGATCTA
* *
477344 AAAAAATTAAAGAACAAAATACTAC
1 AAAAAATAAAAGAACAAAAAACTAC
*
477369 AAAAAATAAAATAA-AAAAAACTA
1 AAAAAATAAAAGAACAAAAAACTA
477392 TTTAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (25 bp):
AAAAAATAAAAGAACAAAAAACTAC
Found at i:479806 original size:59 final size:59
Alignment explanation
Indices: 479743--479856 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
479733 AATAGTTGGG
* * * *
479743 TGATCATTTTATAATTTTTAATAGTCAGGAAACTTAATAAAATAATGTCCTATAGCCAA
1 TGATCATTTTATAACTTTTAATAATCAGGAAACTCAACAAAATAATGTCCTATAGCCAA
* * * * *
479802 TGATCATTTTATAGCTTTTAATAATCATGAGACTCAACAAAATAATTTCTTATAG
1 TGATCATTTTATAACTTTTAATAATCAGGAAACTCAACAAAATAATGTCCTATAG
479857 TCGGAGGACC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (59 bp):
TGATCATTTTATAACTTTTAATAATCAGGAAACTCAACAAAATAATGTCCTATAGCCAA
Found at i:483279 original size:27 final size:27
Alignment explanation
Indices: 483262--483316 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
483252 TTAGGGACCT
*
483262 AATTATAAATATAGAAATTGAGAGCCC
1 AATTATAAATATAAAAATTGAGAGCCC
483289 AATTATAAATATAAAAATTG-GAGGCCC
1 AATTATAAATATAAAAATTGAGA-GCCC
483316 A
1 A
483317 TAGCTACTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (27 bp):
AATTATAAATATAAAAATTGAGAGCCC
Found at i:483963 original size:18 final size:19
Alignment explanation
Indices: 483940--483981 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
483930 CAGTAATCCT
483940 ATTCT-CTGATAATCTTAC
1 ATTCTACTGATAATCTTAC
*
483958 ATTCTCACTGGTAATCTTAC
1 ATTCT-ACTGATAATCTTAC
483978 ATTC
1 ATTC
483982 GGTGAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
20 16 0.76
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTCTACTGATAATCTTAC
Found at i:484906 original size:14 final size:13
Alignment explanation
Indices: 484883--484925 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 13
484873 ATTAGTTATG
484883 AAAATATATTTTA
1 AAAATATATTTTA
484896 AAAACTATATTTT-
1 AAAA-TATATTTTA
484909 -AAATATATTTTA
1 AAAATATATTTTA
*
484921 TAAAT
1 AAAAT
484926 TTAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.30
12 3 0.11
13 8 0.30
14 8 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AAAATATATTTTA
Found at i:485489 original size:31 final size:31
Alignment explanation
Indices: 485444--485504 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
485434 AAATCAAAAT
* *
485444 ATTTTGTCATTTTCGTCTTTATTTAATTAAA
1 ATTTGGTCAATTTCGTCTTTATTTAATTAAA
* *
485475 ATTTGGTCAATTTCGTTTTTGTTTAATTAA
1 ATTTGGTCAATTTCGTCTTTATTTAATTAA
485505 GATGTGATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (31 bp):
ATTTGGTCAATTTCGTCTTTATTTAATTAAA
Found at i:489574 original size:2 final size:2
Alignment explanation
Indices: 489567--489601 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
489557 ATTATATCAT
489567 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 T
489602 TAATGATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:489904 original size:15 final size:14
Alignment explanation
Indices: 489879--489908 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
489869 ATGCGGGCTT
489879 TTTAACCCGCACCG
1 TTTAACCCGCACCG
489893 TTTAAGCCCGCACCG
1 TTTAA-CCCGCACCG
489908 T
1 T
489909 CAAAACCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (14 bp):
TTTAACCCGCACCG
Found at i:489991 original size:24 final size:20
Alignment explanation
Indices: 489964--490021 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
489954 TAATAAGGAG
*
489964 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TG-T-A-GAA
*
489988 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
490008 TGCATCGATGCACT
1 TGCATCGATGCACT
490022 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:491653 original size:23 final size:23
Alignment explanation
Indices: 491585--491653 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
491575 CAATCTTATA
* *
491585 TGGCACTTCAGTGCATTTCTAAG
1 TGGCACTTCGGTGCATTTCTACG
* * *
491608 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
491631 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
491654 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:494687 original size:142 final size:143
Alignment explanation
Indices: 494498--494780 Score: 424
Period size: 143 Copynumber: 2.0 Consensus size: 143
494488 TTTTTTGAAT
* * * * *
494498 AATTCCTACTTAGGGGAAGAGAAGGGGAATTTTGATTTTAATGGATATTAAACCCACAACCTA-G
1 AATTCCTACTTAGAGGAAGAGAAGGAGAATTTTGATTCTAATAGATATTAAACCAACAACCTAGG
* * * *
494562 GAGAGAAAATATGTCAACTGAGAACTTTTAACTATTTACTCTAAAGATTATTGACTAATATATAT
66 GAAAGAAAATATGTCAACCGAGAACTTTTAACTATCTACTCTAAAGATTATCGACTAATATATAT
494627 ACATTTTTTAAGC
131 ACATTTTTTAAGC
* * *
494640 AATTCCTACTTAGAGTAGGAGAAGGAGAATTTTGCTTCTAATAGATATTAAACCAACAACCTAGG
1 AATTCCTACTTAGAGGAAGAGAAGGAGAATTTTGATTCTAATAGATATTAAACCAACAACCTAGG
* * *
494705 GAAAGAAAATATGTCAACCGAGAACTTTTAATTATCTACTCTGAAGATTATCGATTAATATATAT
66 GAAAGAAAATATGTCAACCGAGAACTTTTAACTATCTACTCTAAAGATTATCGACTAATATATAT
494770 ACATTTTTTAA
131 ACATTTTTTAA
494781 ACGATTAAAG
Statistics
Matches: 125, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
142 55 0.44
143 70 0.56
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (143 bp):
AATTCCTACTTAGAGGAAGAGAAGGAGAATTTTGATTCTAATAGATATTAAACCAACAACCTAGG
GAAAGAAAATATGTCAACCGAGAACTTTTAACTATCTACTCTAAAGATTATCGACTAATATATAT
ACATTTTTTAAGC
Found at i:496371 original size:89 final size:89
Alignment explanation
Indices: 496220--496397 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
496210 TGAAATTGAA
496220 AACGGCTCCATGACGTGCTAGCATTTGAGCAATCGAGAGGTAACCGTCTCGGTACCTTGTGTTAT
1 AACGGCTCCATGACGTGCTAGCATTTGAGCAATCGAGAGGTAACCGTCTCGGTACCTTGTGTTAT
496285 AGTACCCTGCTGTGAGTTCAGGAG
66 AGTACCCTGCTGTGAGTTCAGGAG
496309 AACGGCTCCATGACGTGCTAGCATTTGAGCAATCGAGAGGTAACCGTCTCGGTACCTTGTGTTAT
1 AACGGCTCCATGACGTGCTAGCATTTGAGCAATCGAGAGGTAACCGTCTCGGTACCTTGTGTTAT
496374 AGTACCCTGCTGTGAGTTCAGGAG
66 AGTACCCTGCTGTGAGTTCAGGAG
496398 CATGGGATCG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (89 bp):
AACGGCTCCATGACGTGCTAGCATTTGAGCAATCGAGAGGTAACCGTCTCGGTACCTTGTGTTAT
AGTACCCTGCTGTGAGTTCAGGAG
Found at i:501898 original size:18 final size:19
Alignment explanation
Indices: 501870--501906 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
501860 GGTCATCACA
501870 AAAATCCAAACAAATACTG
1 AAAATCCAAACAAATACTG
*
501889 AAAA-CCAAACAAGTACTG
1 AAAATCCAAACAAATACTG
501907 CTAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.57, C:0.22, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAATCCAAACAAATACTG
Found at i:503233 original size:22 final size:22
Alignment explanation
Indices: 503216--503282 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
503206 CTCGTATAAA
503216 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
503238 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
503260 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
503282 T
1 T
503283 ATGTCCATAA
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:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:503532 original size:29 final size:31
Alignment explanation
Indices: 503500--503558 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
503490 TAGACATAGT
*
503500 ATTTCCATACCTTTA-CACATAG-GCATATC
1 ATTTACATACCTTTATCACATAGTGCATATC
503529 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTATCACATAGTGCATAT
503559 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.52
30 7 0.26
31 6 0.22
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTATCACATAGTGCATATC
Found at i:503610 original size:26 final size:27
Alignment explanation
Indices: 503574--503653 Score: 103
Period size: 26 Copynumber: 3.0 Consensus size: 27
503564 TTCTGCATAA
503574 TCATGTCATGTAATACAT-ATATGAAT
1 TCATGTCATGTAATACATAATATGAAT
**
503600 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACA--TAATATGAAT
503629 TCATGTCATGT-AT-CATAATATGAAT
1 TCATGTCATGTAATACATAATATGAAT
503654 GTAATCATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 8 0.17
26 17 0.36
27 2 0.04
28 3 0.06
29 17 0.36
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (27 bp):
TCATGTCATGTAATACATAATATGAAT
Found at i:503639 original size:29 final size:26
Alignment explanation
Indices: 503574--503640 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 26
503564 TTCTGCATAA
**
503574 TCATGTCATGTAATACATATATGAAT
1 TCATGTCATGTAATACATATACAAAT
503600 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACA--T-ATACAAAT
503629 TCATGTCATGTA
1 TCATGTCATGTA
503641 TCATAATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 17 0.47
28 1 0.03
29 18 0.50
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (26 bp):
TCATGTCATGTAATACATATACAAAT
Found at i:504078 original size:66 final size:67
Alignment explanation
Indices: 503941--504089 Score: 212
Period size: 66 Copynumber: 2.2 Consensus size: 67
503931 TTTTCTCATG
* *
503941 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAGCAATCTGGAATTTCATATACGATG
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAGCAATCTGGAAATTCATATACGATG
*
504006 AG
66 AA
* * * *
504008 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTT
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTC-AGCAATCTGGAAATTCATATACGAT
504071 GAA
65 GAA
504074 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
504090 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 40 0.54
67 34 0.46
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.29
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAGCAATCTGGAAATTCATATACGATG
AA
Found at i:504099 original size:21 final size:21
Alignment explanation
Indices: 504069--504111 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
504059 ATTCATTTCG
* *
504069 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
504090 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
504111 T
1 T
504112 AACCCAGAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:510136 original size:22 final size:22
Alignment explanation
Indices: 510119--510185 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
510109 CTCGTATAAA
510119 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
510141 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
510163 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
510185 T
1 T
510186 ATGTCCATAA
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:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:510446 original size:30 final size:31
Alignment explanation
Indices: 510405--510464 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
510395 TAGACATAGT
*
510405 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
510435 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
510465 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:510522 original size:29 final size:29
Alignment explanation
Indices: 510480--510549 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
510470 TTCTGCATAA
**
510480 TCATGTCATGTAATACATACAATATGAAT
1 TCATGTCATGTAATACATACAATACAAAT
**
510509 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATACAATACAAAT
510538 TCATGTCATGTA
1 TCATGTCATGTA
510550 TCATAATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (29 bp):
TCATGTCATGTAATACATACAATACAAAT
Found at i:510971 original size:68 final size:66
Alignment explanation
Indices: 510853--511004 Score: 205
Period size: 68 Copynumber: 2.3 Consensus size: 66
510843 TTTTTCTCAT
* *
510853 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGA
510918 TGA
64 TGA
** * * *
510921 GGGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTT
1 -GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGAT
510986 GA
65 GA
*
510988 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
511005 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
66 16 0.21
67 6 0.08
68 41 0.55
69 12 0.16
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:511014 original size:21 final size:21
Alignment explanation
Indices: 510984--511026 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
510974 ATTCATTTCG
* *
510984 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
511005 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
511026 T
1 T
511027 AACCCAGAAA
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:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:513109 original size:13 final size:13
Alignment explanation
Indices: 513091--513117 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
513081 TAATATATGT
513091 TATTTGACATGAA
1 TATTTGACATGAA
513104 TATTTGACATGAA
1 TATTTGACATGAA
513117 T
1 T
513118 TCTGATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TATTTGACATGAA
Found at i:513164 original size:24 final size:24
Alignment explanation
Indices: 513137--513207 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
513127 ATATCTAACA
* * *
513137 TGGATTCTAATCTGATACTTGACT
1 TGGATTCTGATATGATACTTGACC
513161 TGGATTCTGATATGATACTTGACC
1 TGGATTCTGATATGATACTTGACC
* *
513185 TAGATTTTGATATGATACTTGAC
1 TGGATTCTGATATGATACTTGAC
513208 ATGAATTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
TGGATTCTGATATGATACTTGACC
Found at i:524117 original size:56 final size:57
Alignment explanation
Indices: 524004--524117 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
523994 ATGGAACCTT
524004 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
1 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
*
524061 CAGCACCTCTGCAGCAAAACCAAGAATC-GATCCTGGTCCAAGATCTTGTGAAGATC
1 CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
524117 C
1 C
524118 TTTAGGTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 28 0.50
57 28 0.50
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.20
Consensus pattern (57 bp):
CAGCACCTCTGCAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATC
Found at i:541320 original size:146 final size:146
Alignment explanation
Indices: 541075--541370 Score: 592
Period size: 146 Copynumber: 2.0 Consensus size: 146
541065 AATTGAATTC
541075 AAGATGAGAACAATCTTATATTTGAGAAGTGAACAAAATTCTTCATGCATAATTTGACAAGCACA
1 AAGATGAGAACAATCTTATATTTGAGAAGTGAACAAAATTCTTCATGCATAATTTGACAAGCACA
541140 AACTTATAAATCCATCTAAACGATGTAATTAGATTCACAAACCAAATTCAATTCTCACTCCCTTA
66 AACTTATAAATCCATCTAAACGATGTAATTAGATTCACAAACCAAATTCAATTCTCACTCCCTTA
541205 AAAATTGGTCCCTACA
131 AAAATTGGTCCCTACA
541221 AAGATGAGAACAATCTTATATTTGAGAAGTGAACAAAATTCTTCATGCATAATTTGACAAGCACA
1 AAGATGAGAACAATCTTATATTTGAGAAGTGAACAAAATTCTTCATGCATAATTTGACAAGCACA
541286 AACTTATAAATCCATCTAAACGATGTAATTAGATTCACAAACCAAATTCAATTCTCACTCCCTTA
66 AACTTATAAATCCATCTAAACGATGTAATTAGATTCACAAACCAAATTCAATTCTCACTCCCTTA
541351 AAAATTGGTCCCTACA
131 AAAATTGGTCCCTACA
541367 AAGA
1 AAGA
541371 CAATAATGAA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 150 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (146 bp):
AAGATGAGAACAATCTTATATTTGAGAAGTGAACAAAATTCTTCATGCATAATTTGACAAGCACA
AACTTATAAATCCATCTAAACGATGTAATTAGATTCACAAACCAAATTCAATTCTCACTCCCTTA
AAAATTGGTCCCTACA
Found at i:541711 original size:195 final size:195
Alignment explanation
Indices: 541379--541766 Score: 670
Period size: 195 Copynumber: 2.0 Consensus size: 195
541369 GACAATAATG
541379 AACATACCAAGTAACTTTTTAAAAAAGGATGAGACATGAAAAAACATATGAAATTAATTCTCGAC
1 AACATACCAAGTAACTTTTTAAAAAAGGATGAGACATGAAAAAACATATGAAATTAATTCTCGAC
*
541444 TTACATTTTAAATCCATCTAAGGTGAAAACCTCCAACACGTTCTGTATTCTTCGATCAAATGCAA
66 TTACATTTTAAATCCATCTAAGGTGAAAACCTCCAACACATTCTGTATTCTTCGATCAAATGCAA
*
541509 CAGCCCTTCCCCTGTTGTAATATTCGAGAAGAACTTGCCTCTCAGCTCTGACCTGAGAATACATA
131 CAGCCCTTCCCCTGTTGTAATATTCGACAAGAACTTGCCTCTCAGCTCTGACCTGAGAATACATA
* * *
541574 AACATACCAAGTAACTTTTTTAAAAAGGATGAGACACT-AAACAACATATGAAATTAGTTCTCGA
1 AACATACCAAGTAACTTTTTAAAAAAGGATGAGACA-TGAAAAAACATATGAAATTAATTCTCGA
* * *
541638 CTTGCATTTTAAATCCATCTAAGGTGAAAACCTCGAACACATTTTGTATTCTTCGATCAAATGCA
65 CTTACATTTTAAATCCATCTAAGGTGAAAACCTCCAACACATTCTGTATTCTTCGATCAAATGCA
* *
541703 ACAGCCCTTCCCCTGTTGTAATCTTCGACAATAACTTGCCTCTCAGCTCTGACCTGAGAATACA
130 ACAGCCCTTCCCCTGTTGTAATATTCGACAAGAACTTGCCTCTCAGCTCTGACCTGAGAATACA
541767 AAAAATGTTA
Statistics
Matches: 182, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
195 181 0.99
196 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (195 bp):
AACATACCAAGTAACTTTTTAAAAAAGGATGAGACATGAAAAAACATATGAAATTAATTCTCGAC
TTACATTTTAAATCCATCTAAGGTGAAAACCTCCAACACATTCTGTATTCTTCGATCAAATGCAA
CAGCCCTTCCCCTGTTGTAATATTCGACAAGAACTTGCCTCTCAGCTCTGACCTGAGAATACATA
Found at i:550371 original size:35 final size:35
Alignment explanation
Indices: 550305--550409 Score: 176
Period size: 35 Copynumber: 3.0 Consensus size: 35
550295 AACATCTACC
*
550305 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
*
550340 AAACATTTACCAAACTTTGAAAACCACTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
550375 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
550410 TCGGTTGCCA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 46 0.70
36 20 0.30
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:554854 original size:21 final size:21
Alignment explanation
Indices: 554830--554890 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
554820 TTCAAAGAAA
554830 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
554851 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
554865 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
554886 CATTT
1 CATTT
554891 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:554857 original size:35 final size:35
Alignment explanation
Indices: 554792--554896 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
554782 AACATCTACC
*
554792 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
554827 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
554862 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
554897 TTGGTTGCCA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 48 0.71
36 20 0.29
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:555337 original size:173 final size:170
Alignment explanation
Indices: 555044--555388 Score: 636
Period size: 173 Copynumber: 2.0 Consensus size: 170
555034 ATTACATCTC
555044 TTCCCTTAGGTATTGTAACATTACAGGCGTTTTGGACTAAAATGCCCTTAAATTTTTTTTTCTTC
1 TTCCCTTAGGTATTGTAACATTACAGGCGTTTTGGACTAAAATGCCCTTAAATTTTTTTTTCTTC
* *
555109 AAAAATATCATTATTCTGTTATTGAATAATAAAATTTCTACAAAGGTTAAATTACAAATTTATCC
66 AAAAATATCATTATTCTGTTATTGAAAAATAAAATTTCTACAAAGATTAAATTACAAATTTATCC
555174 TTAAATTATTTTATATTTACAAAAAATCTATAATTAAAAT
131 TTAAATTATTTTATATTTACAAAAAATCTATAATTAAAAT
*
555214 TTCCCTTAGGTATTGTAACATTACAGGCGTTTTGGACTAAAATGCCCTTAAATTTTTATTTTTTT
1 TTCCCTTAGGTATTGTAACATTACAGGCGTTTTGGACTAAAATGCCCTTAAA--TTT-TTTTTTC
555279 TTCAAAAATATCATTATTCTGTTATTGAAAAATAAAATTTCTACAAAGATTAAATTACAAATTTA
63 TTCAAAAATATCATTATTCTGTTATTGAAAAATAAAATTTCTACAAAGATTAAATTACAAATTTA
555344 TCCTTAAATTATTTTATATTTACAAAAAATCTATAATTAAAAT
128 TCCTTAAATTATTTTATATTTACAAAAAATCTATAATTAAAAT
555387 TT
1 TT
555389 ATATGAAGTT
Statistics
Matches: 169, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
170 52 0.31
172 3 0.02
173 114 0.67
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (170 bp):
TTCCCTTAGGTATTGTAACATTACAGGCGTTTTGGACTAAAATGCCCTTAAATTTTTTTTTCTTC
AAAAATATCATTATTCTGTTATTGAAAAATAAAATTTCTACAAAGATTAAATTACAAATTTATCC
TTAAATTATTTTATATTTACAAAAAATCTATAATTAAAAT
Found at i:564423 original size:19 final size:19
Alignment explanation
Indices: 564399--564435 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
564389 ACCATCATCT
564399 CATGCAGATACAGCAATAA
1 CATGCAGATACAGCAATAA
564418 CATGCAGATACAGCAATA
1 CATGCAGATACAGCAATA
564436 TAAGTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (19 bp):
CATGCAGATACAGCAATAA
Found at i:569804 original size:2 final size:2
Alignment explanation
Indices: 569797--569830 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
569787 TGAAGCTCTG
569797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
569831 TATTAGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:570060 original size:2 final size:2
Alignment explanation
Indices: 570053--570090 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
570043 ATTTAAAACA
570053 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
570091 ACACTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:575715 original size:12 final size:13
Alignment explanation
Indices: 575698--575726 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
575688 TTTACTTGCG
575698 AAAATTAAAA-TT
1 AAAATTAAAATTT
575710 AAAATTAAAATTT
1 AAAATTAAAATTT
575723 AAAA
1 AAAA
575727 CGTTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:577168 original size:3 final size:3
Alignment explanation
Indices: 577145--577208 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
577135 AGCCTGCAAA
* * *
577145 AAT AAT ATT AAT AGT ATT AAT AAT -AT AAT AAT AAT AAT AAGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
*
577190 TAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
577209 TATATTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:577196 original size:19 final size:19
Alignment explanation
Indices: 577145--577212 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
577135 AGCCTGCAAA
* *
577145 AATAATAT-TAATAGTATT
1 AATAATATATAATAATAAT
577163 AATAATATAATAATAATAAT
1 AATAATAT-ATAATAATAAT
577183 AAGTAAT-TATAATAATAAT
1 AA-TAATATATAATAATAAT
577202 AATAATATATA
1 AATAATATATA
577213 TTATTTAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 12 0.27
19 17 0.39
20 11 0.25
21 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATAATATATAATAATAAT
Found at i:577572 original size:84 final size:83
Alignment explanation
Indices: 577438--577710 Score: 332
Period size: 84 Copynumber: 3.2 Consensus size: 83
577428 CTGAATGAAA
* * *
577438 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
577503 TGCCTCGAAGCTGAGCGTAG
65 TGCCT-GAAGCTGAGCGTAG
* * * * *
577523 TCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
577588 ACCTTGGAGCTGAGCGTAG
66 GCC-TGAAGCTGAGCGTAG
* * * *
577607 TCGAACTCAAAGGTATTTGGTTGG-AAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
1 TCGAACTCGAAGGTCTTTGGTTGGCAA-ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* *
577671 TGCCTTAGAGCTGAGCGTAA
65 TGCCTGA-AGCTGAGCGTAG
**
577691 TCGAACTCGGGGGTCTTTGG
1 TCGAACTCGAAGGTCTTTGG
577711 CAGATAGCCT
Statistics
Matches: 158, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
83 3 0.02
84 146 0.92
85 9 0.06
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTGAAGCTGAGCGTAG
Found at i:577944 original size:106 final size:106
Alignment explanation
Indices: 577752--579226 Score: 2459
Period size: 106 Copynumber: 13.9 Consensus size: 106
577742 TCGTGAAGTT
* *
577752 GAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTC
1 GAAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* * * * * *
577817 CAATATCATTTGCTATAAAGTTGAAATTGACTCTGAAATTGG
65 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
577859 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
577924 AATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
577965 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
578030 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * *
578071 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
578136 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
578177 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
578242 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGG
*
578284 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
578349 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * *
578390 G-AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
578454 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
578495 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
578560 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-ATTGG
* *
578602 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
578667 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * *
578708 GAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
578773 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
578814 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
578879 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
*
578920 GAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
578985 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-G
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * *
579025 AAAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTCTGGAGTC
1 GAAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
579090 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
65 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
*
579132 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
579197 AATATCCTTCGTTGTGAAGTTGAAATTGGC
66 AATATCCTTCGTTGTGAAGTTGAAATTGGC
579227 ACTCGAGCAA
Statistics
Matches: 1288, Mismatches: 75, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
105 103 0.08
106 973 0.76
107 212 0.16
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
Found at i:583696 original size:37 final size:36
Alignment explanation
Indices: 583646--583783 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
583636 GTGCTTGTGG
* * * * *
583646 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
583683 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
583720 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
583754 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
583784 GGACGAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:583757 original size:34 final size:35
Alignment explanation
Indices: 583680--583780 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
583670 TTAGTAGAAC
583680 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
583718 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
583751 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
583781 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:586806 original size:29 final size:30
Alignment explanation
Indices: 586780--586836 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
586770 TGTATTTTGT
* *
586780 AAGTATAGGTA-CAACATTAGGCATTTTAA
1 AAGTATAGGAATCAACATTAGACATTTTAA
*
586809 AAGTATATGAATCAACATTAGACATTTT
1 AAGTATAGGAATCAACATTAGACATTTT
586837 TATCAATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (30 bp):
AAGTATAGGAATCAACATTAGACATTTTAA
Found at i:588290 original size:21 final size:21
Alignment explanation
Indices: 588264--588314 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
588254 AATAGGTTCT
588264 TGTAGGGCTGTAAACGTGTCA
1 TGTAGGGCTGTAAACGTGTCA
588285 TGTAGGGCTGTAAACGTGTCA
1 TGTAGGGCTGTAAACGTGTCA
* *
588306 AGTTGGGCT
1 TGTAGGGCT
588315 CGAGTATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.35, T:0.29
Consensus pattern (21 bp):
TGTAGGGCTGTAAACGTGTCA
Found at i:594600 original size:29 final size:29
Alignment explanation
Indices: 594558--594616 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
594548 ATTTTCACCT
594558 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
594587 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
594616 A
1 A
594617 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:599286 original size:29 final size:29
Alignment explanation
Indices: 599244--599302 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
599234 ATTTTCACCT
599244 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
599273 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
599302 A
1 A
599303 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:599384 original size:15 final size:15
Alignment explanation
Indices: 599364--599396 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
599354 TCTTCCGTGA
599364 AAACAGCAAGCATTG
1 AAACAGCAAGCATTG
599379 AAACAGCAAGCATTG
1 AAACAGCAAGCATTG
599394 AAA
1 AAA
599397 GAAGAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.12
Consensus pattern (15 bp):
AAACAGCAAGCATTG
Found at i:600402 original size:23 final size:23
Alignment explanation
Indices: 600367--600421 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
600357 AAACAATTAT
* *
600367 TTTTTTATTTATATGCAATT-AAA
1 TTTTATATATATAT-CAATTAAAA
600390 TTTTATATATATATCAATTAAAA
1 TTTTATATATATATCAATTAAAA
600413 TATTTATAT
1 T-TTTATAT
600422 TTTGATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 5 0.18
23 16 0.57
24 7 0.25
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTATATATATATCAATTAAAA
Found at i:602198 original size:42 final size:42
Alignment explanation
Indices: 602132--602214 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
602122 TTCTTGATTT
* * *
602132 TTAAATCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGC
1 TTAAACCCTTCGAGCCATCAGTAAGCCTTTCGAGCAAGATGC
* * *
602174 TTAAACCCTTCGAGTCATCTGTAAGCCTTTTGAGCAAGATG
1 TTAAACCCTTCGAGCCATCAGTAAGCCTTTCGAGCAAGATG
602215 ATAAGTCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (42 bp):
TTAAACCCTTCGAGCCATCAGTAAGCCTTTCGAGCAAGATGC
Found at i:607842 original size:32 final size:30
Alignment explanation
Indices: 607806--607882 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
607796 CGGGGCCGTG
*
607806 AGGCCTACCTAAGAACACATCTTAGGGCCGC
1 AGGCCTACCTAAGAA-ACATCTCAGGGCCGC
** **
607837 AAGGCCTACCCGAGAATGATCTCAGGGCCGC
1 -AGGCCTACCTAAGAAACATCTCAGGGCCGC
607868 AGAGCCTACCTAAGA
1 AG-GCCTACCTAAGA
607883 GTCACATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 2 0.05
31 22 0.59
32 13 0.35
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.14
Consensus pattern (30 bp):
AGGCCTACCTAAGAAACATCTCAGGGCCGC
Found at i:608787 original size:17 final size:17
Alignment explanation
Indices: 608765--608821 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
608755 AACGGTCACA
608765 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
608782 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
*
608799 GTCAACAGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
608816 GTCAAC
1 GTCAAC
608822 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.16, C:0.25, G:0.42, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:608839 original size:19 final size:19
Alignment explanation
Indices: 608815--608904 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
608805 AGTCGGGTCG
*
608815 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
608834 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
608853 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
608872 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
608892 GGTCAAACCGGTT
1 GGTCAAACCGGTT
608905 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.02
19 49 0.75
20 15 0.23
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:608887 original size:10 final size:10
Alignment explanation
Indices: 608817--608904 Score: 94
Period size: 9 Copynumber: 9.1 Consensus size: 10
608807 TCGGGTCGGG
*
608817 TCAACCCGGT
1 TCAAACCGGT
*
608827 TCAGACCGG-
1 TCAAACCGGT
608836 TCAAACCGGT
1 TCAAACCGGT
*
608846 TCAGACCGG-
1 TCAAACCGGT
608855 TCAAACCGGT
1 TCAAACCGGT
*
608865 TCGAACCGG-
1 TCAAACCGGT
608874 TCAAACCGGT
1 TCAAACCGGT
*
608884 TCAAAACTGG-
1 TC-AAACCGGT
608894 TCAAACCGGT
1 TCAAACCGGT
608904 T
1 T
608905 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 30 0.47
10 28 0.44
11 6 0.09
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:615196 original size:32 final size:30
Alignment explanation
Indices: 615160--615236 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
615150 CGGGGCCGTG
*
615160 AGGCCTACCTAAGAACACATCTTAGGGCCGC
1 AGGCCTACCTAAGAA-ACATCTCAGGGCCGC
** **
615191 AAGGCCTACCCGAGAATGATCTCAGGGCCGC
1 -AGGCCTACCTAAGAAACATCTCAGGGCCGC
615222 AGAGCCTACCTAAGA
1 AG-GCCTACCTAAGA
615237 GTCACATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 2 0.05
31 22 0.59
32 13 0.35
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.14
Consensus pattern (30 bp):
AGGCCTACCTAAGAAACATCTCAGGGCCGC
Found at i:615219 original size:63 final size:63
Alignment explanation
Indices: 615113--615236 Score: 148
Period size: 63 Copynumber: 2.0 Consensus size: 63
615103 CCCTAAGGGA
* * *
615113 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
*
615176 ACATCTTAGGGCC-GCA-AGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGA-GCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
615237 GTCACATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
62 3 0.06
63 48 0.91
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:616123 original size:13 final size:13
Alignment explanation
Indices: 616105--616141 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
616095 AGTCAAAGAA
616105 AGTCAACGGTCAC
1 AGTCAACGGTCAC
616118 AGTCAACGGTCAC
1 AGTCAACGGTCAC
*
616131 GGTCAACGGTC
1 AGTCAACGGTC
616142 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (13 bp):
AGTCAACGGTCAC
Found at i:616153 original size:17 final size:17
Alignment explanation
Indices: 616131--616171 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
616121 CAACGGTCAC
616131 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
616148 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
616165 GGTCAAC
1 GGTCAAC
616172 CCGGTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:616185 original size:10 final size:10
Alignment explanation
Indices: 616167--616235 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
616157 TCGGGTCGGG
*
616167 TCAACCCGGT
1 TCAAACCGGT
*
616177 TCAGACCGG-
1 TCAAACCGGT
616186 TCAAACCGGT
1 TCAAACCGGT
*
616196 TCAGACCGG-
1 TCAAACCGGT
616205 TCAAACCGGT
1 TCAAACCGGT
*
616215 TCAAAACTGG-
1 TC-AAACCGGT
616225 TCAAACCGGT
1 TCAAACCGGT
616235 T
1 T
616236 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:616187 original size:19 final size:19
Alignment explanation
Indices: 616165--616235 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
616155 GGTCGGGTCG
*
616165 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
616184 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
616203 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
616223 GGTCAAACCGGTT
1 GGTCAAACCGGTT
616236 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:625159 original size:10 final size:10
Alignment explanation
Indices: 625131--625160 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
625121 ATAAATGAAT
*
625131 GAACATAAAC
1 GAACATAACC
625141 GAACATAACC
1 GAACATAACC
625151 GAACATAACC
1 GAACATAACC
625161 AAACGTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.27, G:0.10, T:0.10
Consensus pattern (10 bp):
GAACATAACC
Found at i:626132 original size:37 final size:37
Alignment explanation
Indices: 626056--626132 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
626046 TTTTTATATT
**
626056 TTTAATTTTGTAAAAAATATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAATATTATATAAATATTAACAA
*
626093 TTTAATTTTTTAAATAAA-A-TATATAAATATTTAACAA
1 TTTAATTTTGTAAA-AAATATTATATAAATA-TTAACAA
626130 TTT
1 TTT
626133 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 10 0.29
37 22 0.63
38 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATTATATAAATATTAACAA
Found at i:626295 original size:18 final size:19
Alignment explanation
Indices: 626272--626315 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
626262 TCAGTATTCC
*
626272 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
626290 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
626310 TATTCC
1 TATTCC
626316 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:626303 original size:20 final size:20
Alignment explanation
Indices: 626278--626315 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
626268 TTCCTATTCC
*
626278 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
626298 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
626316 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:633618 original size:2 final size:2
Alignment explanation
Indices: 633611--633660 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
633601 ATTACATCAT
633611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
633654 TA T- TA TA
1 TA TA TA TA
633661 ATTAACGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:637232 original size:19 final size:17
Alignment explanation
Indices: 637190--637232 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
637180 AAAACAGTAA
637190 AATTTATATAAAATATT
1 AATTTATATAAAATATT
637207 ATTATTTATACCTAAAATATT
1 A--ATTTATA--TAAAATATT
637228 AATTT
1 AATTT
637233 TTTAACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
19 11 0.50
21 10 0.45
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTATATAAAATATT
Done.