Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 62
Found at i:5611627 original size:21 final size:21
Alignment explanation
Indices: 5611601--5611640 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5611591 AGGACAAGGA
*
5611601 GTATCGGTACTTCTTTTATGG
1 GTATCGGTACTTCCTTTATGG
5611622 GTATCGGTACTTCCTTTAT
1 GTATCGGTACTTCCTTTAT
5611641 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.47
Consensus pattern (21 bp):
GTATCGGTACTTCCTTTATGG
Found at i:5613661 original size:38 final size:39
Alignment explanation
Indices: 5613612--5613688 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
5613602 TTACTTTTTG
5613612 AAATTTAGTTTTTATATTAATTATAATT-TGTATATTAT
1 AAATTTAGTTTTTATATTAATTATAATTCTGTATATTAT
* * *
5613650 AAATTTGGTTTTTATATTAATTCTAATTCTTTATATTAT
1 AAATTTAGTTTTTATATTAATTATAATTCTGTATATTAT
5613689 TTATAATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 26 0.74
39 9 0.26
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (39 bp):
AAATTTAGTTTTTATATTAATTATAATTCTGTATATTAT
Found at i:5613684 original size:19 final size:19
Alignment explanation
Indices: 5613622--5613705 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
5613612 AAATTTAGTT
5613622 TTTATATTAATTATAATT-
1 TTTATATTAATTATAATTC
* **
5613640 TGTATATTATAAATT-TGGTT-
1 T-T-TA-TATTAATTATAATTC
*
5613660 TTTATATTAATTCTAATTC
1 TTTATATTAATTATAATTC
*
5613679 TTTATATTATTTATAATTC
1 TTTATATTAATTATAATTC
5613698 -TTATATTA
1 TTTATATTA
5613706 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.13
18 14 0.26
19 19 0.36
20 6 0.11
21 7 0.13
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:5613706 original size:18 final size:19
Alignment explanation
Indices: 5613660--5613706 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5613650 AAATTTGGTT
* *
5613660 TTTATATTAATTCTAATTC
1 TTTATATTATTTATAATTC
5613679 TTTATATTATTTATAATTC
1 TTTATATTATTTATAATTC
5613698 -TTATATTAT
1 TTTATATTAT
5613707 AAATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTATTTATAATTC
Found at i:5613719 original size:13 final size:14
Alignment explanation
Indices: 5613685--5613721 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5613675 ATTCTTTATA
5613685 TTATTTAT-AATTC
1 TTATTTATAAATTC
5613698 TTATATTATAAATT-
1 TTAT-TTATAAATTC
5613712 TTATTTATAA
1 TTATTTATAA
5613722 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:5616210 original size:23 final size:23
Alignment explanation
Indices: 5616184--5616246 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5616174 CATCAGCAAC
*
5616184 CAGCAAGCATCACTGTATCAATT
1 CAGCAAGCATCACTGCATCAATT
*
5616207 CAGCAAGCATCATTGCATCAATT
1 CAGCAAGCATCACTGCATCAATT
*
5616230 CAACAAGCATC-CTGCAT
1 CAGCAAGCATCACTGCAT
5616247 TAAGAAAGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.24
Consensus pattern (23 bp):
CAGCAAGCATCACTGCATCAATT
Found at i:5616357 original size:20 final size:20
Alignment explanation
Indices: 5616332--5616390 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
5616322 AAACCATTAC
5616332 AAATATCAAGCAGAAGCAAG
1 AAATATCAAGCAGAAGCAAG
* *
5616352 AAATATCAAGTAGAAGAAAG
1 AAATATCAAGCAGAAGCAAG
*
5616372 AAATATCAAACAGAAGCAA
1 AAATATCAAGCAGAAGCAA
5616391 ACAATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.12
Consensus pattern (20 bp):
AAATATCAAGCAGAAGCAAG
Found at i:5616396 original size:20 final size:19
Alignment explanation
Indices: 5616332--5616403 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
5616322 AAACCATTAC
*
5616332 AAATATCAAGCAGAAGCAA
1 AAATATCAAACAGAAGCAA
** *
5616351 GAAATATCAAGTAGAAGAAA
1 -AAATATCAAACAGAAGCAA
5616371 GAAATATCAAACAGAAGCAA
1 -AAATATCAAACAGAAGCAA
*
5616391 ACAATATAAAACA
1 A-AATATCAAACA
5616404 TAATCAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.61, C:0.12, G:0.14, T:0.12
Consensus pattern (19 bp):
AAATATCAAACAGAAGCAA
Found at i:5618598 original size:6 final size:6
Alignment explanation
Indices: 5618587--5618710 Score: 68
Period size: 6 Copynumber: 20.5 Consensus size: 6
5618577 TTAGATTTGT
* * * * * * * *
5618587 GTTCGG GTTCGG GTTTTGG TTTTGG GTTTGG GTTCGC GATCAG TTTCGG
1 GTTCGG GTTCGG G-TTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG
* ** * * * *
5618636 GTTCGG GTTCGG GATCAA ATTCGA GTTCGG GTTTGG GTTCAG GTTCGG
1 GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG GTTCGG
** * *
5618684 GTTTAG GTTCGG GTTTGG GTTTGG GTT
1 GTTCGG GTTCGG GTTCGG GTTCGG GTT
5618711 TAGGTTAGGG
Statistics
Matches: 88, Mismatches: 29, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
6 84 0.95
7 4 0.05
ACGTcount: A:0.07, C:0.11, G:0.41, T:0.40
Consensus pattern (6 bp):
GTTCGG
Found at i:5618637 original size:24 final size:24
Alignment explanation
Indices: 5618587--5618696 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
5618577 TTAGATTTGT
* ** *
5618587 GTTCGGGTTCGGGTTTTGGTTTTGG
1 GTTCGGGTTCGGG-ATCAGTTTCGG
* *
5618612 GTTTGGGTTCGCGATCAGTTTCGG
1 GTTCGGGTTCGGGATCAGTTTCGG
** *
5618636 GTTCGGGTTCGGGATCAAATTCGA
1 GTTCGGGTTCGGGATCAGTTTCGG
* * *
5618660 GTTCGGGTTTGGGTTCAGGTTCGG
1 GTTCGGGTTCGGGATCAGTTTCGG
**
5618684 GTTTAGGTTCGGG
1 GTTCGGGTTCGGG
5618697 TTTGGGTTTG
Statistics
Matches: 66, Mismatches: 19, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
24 55 0.83
25 11 0.17
ACGTcount: A:0.08, C:0.13, G:0.41, T:0.38
Consensus pattern (24 bp):
GTTCGGGTTCGGGATCAGTTTCGG
Found at i:5618681 original size:18 final size:18
Alignment explanation
Indices: 5618660--5618728 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
5618650 TCAAATTCGA
5618660 GTTCGGGTTTGGGTTCAG
1 GTTCGGGTTTGGGTTCAG
* *
5618678 GTTCGGGTTTAGGTTCGG
1 GTTCGGGTTTGGGTTCAG
* *
5618696 GTTTGGGTTTGGGTTTAG
1 GTTCGGGTTTGGGTTCAG
* *
5618714 GTTAGGGTTGGGGTT
1 GTTCGGGTTTGGGTT
5618729 AGCGATTAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.06, C:0.06, G:0.46, T:0.42
Consensus pattern (18 bp):
GTTCGGGTTTGGGTTCAG
Found at i:5618697 original size:24 final size:24
Alignment explanation
Indices: 5618591--5618722 Score: 84
Period size: 24 Copynumber: 5.5 Consensus size: 24
5618581 ATTTGTGTTC
** *
5618591 GGGTTCGGGTTTTGGTTTTGGGTTT
1 GGGTTCGGGTTCAGG-TTCGGGTTT
* * * *
5618616 GGGTTCGCGATCAGTTTCGGGTTC
1 GGGTTCGGGTTCAGGTTCGGGTTT
* ** * *
5618640 GGGTTCGGGATCAAATTCGAGTTC
1 GGGTTCGGGTTCAGGTTCGGGTTT
*
5618664 GGGTTTGGGTTCAGGTTCGGGTTT
1 GGGTTCGGGTTCAGGTTCGGGTTT
* ** *
5618688 AGGTTCGGGTTTGGGTTTGGGTTT
1 GGGTTCGGGTTCAGGTTCGGGTTT
* *
5618712 AGGTTAGGGTT
1 GGGTTCGGGTT
5618723 GGGGTTAGCG
Statistics
Matches: 84, Mismatches: 23, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
24 74 0.88
25 10 0.12
ACGTcount: A:0.08, C:0.10, G:0.42, T:0.40
Consensus pattern (24 bp):
GGGTTCGGGTTCAGGTTCGGGTTT
Found at i:5618711 original size:6 final size:6
Alignment explanation
Indices: 5618664--5618728 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
5618654 ATTCGAGTTC
* * * * *
5618664 GGGTTT GGGTTC AGGTTC GGGTTT AGGTTC GGGTTT GGGTTT GGGTTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
* * *
5618712 AGGTTA GGGTTG GGGTT
1 GGGTTT GGGTTT GGGTT
5618729 AGCGATTAGA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.06, C:0.05, G:0.48, T:0.42
Consensus pattern (6 bp):
GGGTTT
Found at i:5618711 original size:12 final size:12
Alignment explanation
Indices: 5618665--5618722 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
5618655 TTCGAGTTCG
* *
5618665 GGTTTGGGTTCA
1 GGTTCGGGTTTA
5618677 GGTTCGGGTTTA
1 GGTTCGGGTTTA
*
5618689 GGTTCGGGTTTG
1 GGTTCGGGTTTA
*
5618701 GGTTTGGGTTTA
1 GGTTCGGGTTTA
*
5618713 GGTTAGGGTT
1 GGTTCGGGTT
5618723 GGGGTTAGCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.07, C:0.05, G:0.45, T:0.43
Consensus pattern (12 bp):
GGTTCGGGTTTA
Found at i:5618727 original size:24 final size:24
Alignment explanation
Indices: 5618677--5618728 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5618667 TTTGGGTTCA
* *
5618677 GGTTCGGGTTTAGGTTCGGGTTTG
1 GGTTCGGGTTTAGGTTAGGGTTGG
*
5618701 GGTTTGGGTTTAGGTTAGGGTTGG
1 GGTTCGGGTTTAGGTTAGGGTTGG
5618725 GGTT
1 GGTT
5618729 AGCGATTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.04, G:0.48, T:0.42
Consensus pattern (24 bp):
GGTTCGGGTTTAGGTTAGGGTTGG
Found at i:5618737 original size:24 final size:24
Alignment explanation
Indices: 5618686--5618737 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5618676 AGGTTCGGGT
* * * * *
5618686 TTAGGTTCGGGTTTGGGTTTGGGT
1 TTAGGTTAGGGTTGGGGTTAGCGA
5618710 TTAGGTTAGGGTTGGGGTTAGCGA
1 TTAGGTTAGGGTTGGGGTTAGCGA
5618734 TTAG
1 TTAG
5618738 AGAAGATGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.04, G:0.44, T:0.40
Consensus pattern (24 bp):
TTAGGTTAGGGTTGGGGTTAGCGA
Found at i:5619058 original size:90 final size:91
Alignment explanation
Indices: 5618929--5619104 Score: 241
Period size: 90 Copynumber: 1.9 Consensus size: 91
5618919 TGAACTTTTG
** * *
5618929 GGTGTTTGATCCAAAAAACATTAATGAGTTTAGGTTTTGGTGTTTGTGAAGATCAAATAATGG-T
1 GGTGTTTGAT-CAAAAAACAGAAATGAGTTTAGGTTTTGGTGTTTCTGAAGATCAAATAAGGGTT
5618993 TTGGGGATGAACACGAGATGAAATATTT
65 TTGGGGATGAACACGA-ATGAAATATTT
* *
5619021 GGTGTTTGAT-AAAAAACACGAAATG-GTTTGGGTTTTGGTGTTTCTGAAGATCAAATGAGGGTT
1 GGTGTTTGATCAAAAAACA-GAAATGAGTTTAGGTTTTGGTGTTTCTGAAGATCAAATAAGGGTT
*
5619084 TTTGGGATGAACACGAATGAA
65 TTGGGGATGAACACGAATGAA
5619105 CAAGTTATGA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
90 45 0.60
91 20 0.27
92 10 0.13
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.34
Consensus pattern (91 bp):
GGTGTTTGATCAAAAAACAGAAATGAGTTTAGGTTTTGGTGTTTCTGAAGATCAAATAAGGGTTT
TGGGGATGAACACGAATGAAATATTT
Found at i:5638054 original size:20 final size:21
Alignment explanation
Indices: 5638015--5638061 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5638005 GAGATTATTT
5638015 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
**
5638036 TCATTTTTGTATTTT-AAAAA
1 TCATTTTTCAATTTTGAAAAA
*
5638056 TAATTT
1 TCATTT
5638062 CTCATAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:5640473 original size:26 final size:27
Alignment explanation
Indices: 5640418--5640508 Score: 80
Period size: 33 Copynumber: 3.2 Consensus size: 27
5640408 TTTCAATTAA
* *
5640418 TATATATGTTTATAT-TAATAAATTAA-
1 TATATATGTTTATATATACT-AATGAAC
5640444 TATATAT-TTTATATATACTAATGAAC
1 TATATATGTTTATATATACTAATGAAC
5640470 TATATAATATATAGTTTATATATACTAATGAAC
1 ----T-ATATAT-GTTTATATATACTAATGAAC
5640503 TATATA
1 TATATA
5640509 ATGTATAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
25 12 0.22
26 10 0.19
28 5 0.09
29 1 0.02
30 1 0.02
31 6 0.11
33 19 0.35
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (27 bp):
TATATATGTTTATATATACTAATGAAC
Found at i:5640478 original size:33 final size:33
Alignment explanation
Indices: 5640441--5640628 Score: 195
Period size: 33 Copynumber: 5.6 Consensus size: 33
5640431 ATTAATAAAT
*
5640441 TAATATATATTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
5640474 TAATATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* **
5640507 TAATGTATAGTTTATATATACCATATAGTTTA-TATA
1 TAATATATAGTTTATATATA-C-TA-A-TGAACTATA
* *
5640543 TACTATATAGTTTATATATACTAATGAAATATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* * *
5640576 TAATATATATAGTTTGTATATAC-CAT-ATACTTTA
1 T-A-ATATATAGTTTATATATACTAATGA-ACTATA
*
5640610 T-ATATATAGTTTTTATATA
1 TAATATATAGTTTATATATA
5640629 TAGTTCATAT
Statistics
Matches: 133, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
31 17 0.13
32 2 0.02
33 58 0.44
34 11 0.08
35 20 0.15
36 23 0.17
37 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:5640493 original size:18 final size:18
Alignment explanation
Indices: 5640470--5640615 Score: 126
Period size: 18 Copynumber: 8.3 Consensus size: 18
5640460 ACTAATGAAC
*
5640470 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
*
5640488 TATATACTA-AT-G--AA
1 TATATACTATATAGTTTA
* *
5640502 CTATATAATGTATAGTTTA
1 -TATATACTATATAGTTTA
*
5640521 TATATACCATATAGTTTA
1 TATATACTATATAGTTTA
5640539 TATATACTATATAGTTTA
1 TATATACTATATAGTTTA
**
5640557 TATATACTA-AT-GAAATA
1 TATATACTATATAG-TTTA
*
5640574 TATAATA-TATATAGTTTG
1 TAT-ATACTATATAGTTTA
* *
5640592 TATATACCATATACTTTA
1 TATATACTATATAGTTTA
5640610 TATATA
1 TATATA
5640616 TAGTTTTTAT
Statistics
Matches: 101, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
14 1 0.01
15 7 0.07
16 4 0.04
17 15 0.15
18 72 0.71
19 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:5640556 original size:69 final size:71
Alignment explanation
Indices: 5640470--5640615 Score: 233
Period size: 69 Copynumber: 2.1 Consensus size: 71
5640460 ACTAATGAAC
* *
5640470 TATATAATATATAGTTTATATATACTAATGAACTATAT-A-ATGTATAGTTTATATATACCATAT
1 TATATAATATATAGTTTATATATACTAATGAAATATATAATATATATAGTTTATATATACCATAT
*
5640533 AGTTTA
66 ACTTTA
* *
5640539 TATATACTATATAGTTTATATATACTAATGAAATATATAATATATATAGTTTGTATATACCATAT
1 TATATAATATATAGTTTATATATACTAATGAAATATATAATATATATAGTTTATATATACCATAT
5640604 ACTTTA
66 ACTTTA
5640610 TATATA
1 TATATA
5640616 TAGTTTTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 36 0.51
70 1 0.01
71 33 0.47
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (71 bp):
TATATAATATATAGTTTATATATACTAATGAAATATATAATATATATAGTTTATATATACCATAT
ACTTTA
Found at i:5640618 original size:102 final size:101
Alignment explanation
Indices: 5640444--5640628 Score: 257
Period size: 102 Copynumber: 1.8 Consensus size: 101
5640434 AATAAATTAA
* * *
5640444 TATATATTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAACTATATA
1 TATATAGTTTATATATACTAATGAAATATATAATATATAGTTTATATATACCAAT-AACTATATA
*
5640509 ATGTATAGTTTATATATACCATATAGTTTATATATAC
65 ATATATAGTTTATATATACCATATAGTTTATATATAC
* *
5640546 TATATAGTTTATATATACTAATGAAATATATAATATATATAGTTTGTATATACC-ATATACTTTA
1 TATATAGTTTATATATACTAATGAAATATAT-A-ATATATAGTTTATATATACCAATA-ACTATA
*
5640610 T-ATATATAGTTTTTATATA
63 TAATATATAGTTTATATATA
5640629 TAGTTCATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
102 46 0.63
103 9 0.12
104 18 0.25
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (101 bp):
TATATAGTTTATATATACTAATGAAATATATAATATATAGTTTATATATACCAATAACTATATAA
TATATAGTTTATATATACCATATAGTTTATATATAC
Found at i:5640631 original size:13 final size:13
Alignment explanation
Indices: 5640600--5640638 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5640590 TGTATATACC
*
5640600 ATATACTTTATAT
1 ATATAGTTTATAT
*
5640613 ATATAGTTTTTAT
1 ATATAGTTTATAT
*
5640626 ATATAGTTCATAT
1 ATATAGTTTATAT
5640639 GTAAACTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (13 bp):
ATATAGTTTATAT
Found at i:5640765 original size:15 final size:15
Alignment explanation
Indices: 5640750--5640784 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5640740 TACTTTGAAT
5640750 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
5640764 TTATATAAGTATAAA
1 TTATATAAGTATAAA
5640779 TTATAT
1 TTATAT
5640785 TAAATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:5640783 original size:27 final size:28
Alignment explanation
Indices: 5640753--5640815 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
5640743 TTTGAATTTA
* *
5640753 TATAGTATAAAT-TATATAAGTATAAAT
1 TATAGTATAAATATATATAAATATAAAC
*
5640780 TATA-T-TAAATAATATATAAATATCAAC
1 TATAGTATAAAT-ATATATAAATATAAAC
5640807 TATAGTATA
1 TATAGTATA
5640816 TAGTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 5 0.17
26 1 0.03
27 20 0.69
28 1 0.03
29 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (28 bp):
TATAGTATAAATATATATAAATATAAAC
Found at i:5640887 original size:7 final size:7
Alignment explanation
Indices: 5640872--5640938 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
5640862 ATATGTAAAT
*
5640872 TATACTA
1 TATAATA
*
5640879 TATAGTA
1 TATAATA
*
5640886 TATAGTA
1 TATAATA
5640893 TAT-ATA
1 TATAATA
*
5640899 GTTTACATA
1 -TATA-ATA
5640908 TATAATA
1 TATAATA
5640915 TATAATA
1 TATAATA
5640922 TATAATA
1 TATAATA
*
5640929 TATAAAA
1 TATAATA
5640936 TAT
1 TAT
5640939 CAACAATAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
6 2 0.04
7 44 0.85
8 3 0.06
9 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (7 bp):
TATAATA
Found at i:5640908 original size:43 final size:41
Alignment explanation
Indices: 5640850--5640932 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 41
5640840 ATATGGTTTT
* * *
5640850 TATATATAGTTCATATGTAA-ATTATACTATATAGTATATAG
1 TATATATAGTTCATATATAATA-TATAATATATAATATATAG
5640891 TATATATAGTTTACATATATAATATATAATATATAATATATA
1 TATATATAG-TT-CATATATAATATATAATATATAATATATA
5640933 AAATATCAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 9 0.25
42 2 0.06
43 24 0.67
44 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (41 bp):
TATATATAGTTCATATATAATATATAATATATAATATATAG
Found at i:5641052 original size:18 final size:18
Alignment explanation
Indices: 5641031--5641065 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5641021 TAGTATAGTT
*
5641031 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
5641049 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
5641066 TAATTTACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:5641149 original size:22 final size:22
Alignment explanation
Indices: 5641084--5641156 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
5641074 TAATAAATTA
* *
5641084 TATATATATAGTTCATAT-GTA
1 TATATATATAGTTTATATAGTT
* * *
5641105 AAT-TATATAGTTTACATATTT
1 TATATATATAGTTTATATAGTT
5641126 TATATATATAGTTTATATAGTT
1 TATATATATAGTTTATATAGTT
*
5641148 TATACATAT
1 TATATATAT
5641157 TTTAGAATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 12 0.29
21 5 0.12
22 24 0.59
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (22 bp):
TATATATATAGTTTATATAGTT
Found at i:5643266 original size:16 final size:15
Alignment explanation
Indices: 5643242--5643297 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
5643232 TCCGACTTGT
*
5643242 TATTGACCTGATCTGA
1 TATTTACCTGA-CTGA
5643258 TATTTACCTGACTTGA
1 TATTTACCTGAC-TGA
* *
5643274 CATTTACCTGACTTA
1 TATTTACCTGACTGA
5643289 TATATTACC
1 TAT-TTACC
5643298 AATGATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 5 0.15
16 29 0.85
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (15 bp):
TATTTACCTGACTGA
Found at i:5643477 original size:22 final size:21
Alignment explanation
Indices: 5643452--5643617 Score: 79
Period size: 21 Copynumber: 8.0 Consensus size: 21
5643442 ATTATTATTA
5643452 ATATACTTTATATTTAATACTT
1 ATATA-TTTATATTTAATACTT
*
5643474 ATAT-TTATATAGTTTAATTC-T
1 ATATATT-TATA-TTTAATACTT
5643495 -T-TA--T--ATTTAATACTT
1 ATATATTTATATTTAATACTT
*
5643510 ATAT-TATATAGTTTAATACTT
1 ATATATTTATA-TTTAATACTT
*
5643531 ATAT-TATATAGTTTAATACTT
1 ATATATTTATA-TTTAATACTT
* *
5643552 -TATATTATATACTTATGTACTT
1 ATATATT-TATATTTA-ATACTT
*
5643574 ATATACTTATATACTTT-ATATTT
1 ATATA-TT-TATA-TTTAATACTT
*
5643597 A-ATACTTATATTTATATACTT
1 ATATATTTATATTTA-ATACTT
5643618 TAATACTTAT
Statistics
Matches: 115, Mismatches: 10, Indels: 39
0.70 0.06 0.24
Matches are distributed among these distances:
14 7 0.06
15 2 0.02
16 1 0.01
17 2 0.02
18 1 0.01
19 4 0.03
20 11 0.10
21 46 0.40
22 23 0.20
23 9 0.08
24 7 0.06
25 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATATTTATATTTAATACTT
Found at i:5643553 original size:56 final size:56
Alignment explanation
Indices: 5643460--5643597 Score: 181
Period size: 56 Copynumber: 2.4 Consensus size: 56
5643450 TAATATACTT
*
5643460 TATATTTAATACTTATATTTATATAGTTTAATTCTTTATATT-TAATACTTATATTA
1 TATATTTAATACTTATATTTATATAGTTTAATACTTTATATTAT-ATACTTATATTA
5643516 TATAGTTTAATACTTATA-TTATATAGTTTAATACTTTATATTATATACTTATGTACTTA
1 TATA-TTTAATACTTATATTTATATAGTTTAATACTTTATATTATATACTTA--TA-TTA
*
5643575 TATACTTATATACTTTATATTTA
1 TATATTTA-ATAC-TTATATTTA
5643598 ATACTTATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
56 34 0.47
57 14 0.19
58 5 0.07
59 11 0.15
60 5 0.07
61 3 0.04
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (56 bp):
TATATTTAATACTTATATTTATATAGTTTAATACTTTATATTATATACTTATATTA
Found at i:5643576 original size:38 final size:35
Alignment explanation
Indices: 5643516--5643629 Score: 126
Period size: 38 Copynumber: 3.1 Consensus size: 35
5643506 ACTTATATTA
5643516 TATAGTTTAATACTTATA-TTATATAGTTTAATACTT
1 TATA-TTTAATACTTATACTTATATA-TTTAATACTT
*
5643552 TATA-TTATATACTTATGTACTTATATACTTATATACTT
1 TATATTTA-ATACTTA--TACTTATATATTTA-ATACTT
*
5643590 TATATTTAATACTTATATTTATATACTTTAATAC-T
1 TATATTTAATACTTATACTTATATA-TTTAATACTT
5643625 TATAT
1 TATAT
5643630 CCAAACACTT
Statistics
Matches: 68, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
34 3 0.04
35 13 0.19
36 17 0.25
37 8 0.12
38 24 0.35
39 3 0.04
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (35 bp):
TATATTTAATACTTATACTTATATATTTAATACTT
Found at i:5643619 original size:22 final size:22
Alignment explanation
Indices: 5643460--5643679 Score: 121
Period size: 22 Copynumber: 10.2 Consensus size: 22
5643450 TAATATACTT
5643460 TATA-TTTAATACTTATATTTA
1 TATACTTTAATACTTATATTTA
* *
5643481 TATAGTTTAATTCTTTATATTTA
1 TATACTTTAATAC-TTATATTTA
*
5643504 -ATAC-TT-ATATTATATAGTTTA
1 TATACTTTAATACT-TATA-TTTA
*
5643525 -ATAC-TT-ATATTATATAGTTTA
1 TATACTTTAATACT-TATA-TTTA
5643546 -ATACTTT-ATA-TTATATACTTA
1 TATACTTTAATACTTATAT--TTA
*
5643567 TGTAC-TTATATACTTATATACTT-
1 TATACTTTA-ATACTTATAT--TTA
5643590 TATA-TTTAATACTTATATTTA
1 TATACTTTAATACTTATATTTA
**
5643611 TATACTTTAATACTTATATCCA
1 TATACTTTAATACTTATATTTA
* * *
5643633 AACACTTTATTACTT-TATATTA
1 TATACTTTAATACTTATAT-TTA
*
5643655 TATACTTT-ATA-TATATATATA
1 TATACTTTAATACT-TATATTTA
5643676 TATA
1 TATA
5643680 AAGTATAAAG
Statistics
Matches: 165, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.01
20 13 0.08
21 57 0.35
22 65 0.39
23 18 0.11
24 10 0.06
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (22 bp):
TATACTTTAATACTTATATTTA
Found at i:5643624 original size:36 final size:35
Alignment explanation
Indices: 5643454--5643629 Score: 152
Period size: 36 Copynumber: 4.9 Consensus size: 35
5643444 TATTATTAAT
*
5643454 ATACTTTATATTTA-ATACTT-ATATTTATATAGTTTA
1 ATAC-TTATATTTATATACTTAATACTT-TATA-TTTA
*
5643490 ATTCTTTATATTTA-ATACTT-ATA-TTATATAGTTTA
1 ATAC-TTATATTTATATACTTAATACTT-TATA-TTTA
*
5643525 ATACTTATA-TTATATAGTTTAATACTTTATA-TTA
1 ATACTTATATTTATATA-CTTAATACTTTATATTTA
*
5643559 TATACTTATGTACTTATATACTTATATACTTTATATTTA
1 -ATACTTA--TATTTATATACTTA-ATACTTTATATTTA
5643598 ATACTTATATTTATATACTTTAATAC-TTATAT
1 ATACTTATATTTATATAC-TTAATACTTTATAT
5643630 CCAAACACTT
Statistics
Matches: 124, Mismatches: 5, Indels: 23
0.82 0.03 0.15
Matches are distributed among these distances:
33 3 0.02
34 11 0.09
35 30 0.24
36 43 0.35
37 10 0.08
38 24 0.19
39 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (35 bp):
ATACTTATATTTATATACTTAATACTTTATATTTA
Found at i:5643628 original size:14 final size:14
Alignment explanation
Indices: 5643447--5643617 Score: 90
Period size: 14 Copynumber: 11.9 Consensus size: 14
5643437 TAATTATTAT
*
5643447 TATTAATATACTTTA
1 TATTTATATAC-TTA
5643462 TATTTA-ATACTTA
1 TATTTATATACTTA
*
5643475 TATTTATATAGTT-
1 TATTTATATACTTA
* *
5643488 TAATTCTTTATATTTAA
1 T-ATT-TATATACTT-A
*
5643505 TACTTATAT--TATA
1 TATTTATATACT-TA
5643518 TAGTTTA-ATACTTA
1 TA-TTTATATACTTA
*
5643532 TA-TTATATAGTTTAA
1 TATTTATATA-CTT-A
5643547 TACTTTATAT--TATA
1 TA-TTTATATACT-TA
* *
5643561 TACTTATGTACTTA
1 TATTTATATACTTA
5643575 TATACTTATATACTTTA
1 TAT--TTATATAC-TTA
5643592 TATTTA-ATACTTA
1 TATTTATATACTTA
5643605 TATTTATATACTT
1 TATTTATATACTT
5643618 TAATACTTAT
Statistics
Matches: 123, Mismatches: 12, Indels: 43
0.69 0.07 0.24
Matches are distributed among these distances:
12 3 0.02
13 33 0.27
14 40 0.33
15 25 0.20
16 9 0.07
17 13 0.11
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTTATATACTTA
Found at i:5643673 original size:15 final size:14
Alignment explanation
Indices: 5643525--5643673 Score: 78
Period size: 14 Copynumber: 10.2 Consensus size: 14
5643515 ATATAGTTTA
5643525 ATAC-TTATATTAT
1 ATACTTTATATTAT
*
5643538 ATAGTTTAATACTT-T
1 ATACTTT-ATA-TTAT
5643553 ATA-TTATATACTTAT
1 ATACTT-TATA-TTAT
*
5643568 GTACTTATATACTTAT
1 ATACTT-TATA-TTAT
5643584 ATACTTTATATT-T
1 ATACTTTATATTAT
5643597 AATAC-TTATATTTAT
1 -ATACTTTATA-TTAT
5643612 ATACTTTAATACTTAT
1 ATACTTT-ATA-TTAT
*** *
5643628 AT-CCAAACACTT-T
1 ATACTTTATA-TTAT
5643641 ATTACTTTATATTAT
1 A-TACTTTATATTAT
5643656 ATACTTTATATATAT
1 ATACTTTATAT-TAT
5643671 ATA
1 ATA
5643674 TATATAAAGT
Statistics
Matches: 109, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
13 11 0.10
14 40 0.37
15 30 0.28
16 28 0.26
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (14 bp):
ATACTTTATATTAT
Found at i:5643804 original size:24 final size:24
Alignment explanation
Indices: 5643777--5643823 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5643767 TTGATTAGGG
*
5643777 GTGAAATTGA-ATTAATTATAAAAT
1 GTGAAACTGATATTAA-TATAAAAT
*
5643801 GTGAAGCTGATATTAATATAAAA
1 GTGAAACTGATATTAATATAAAA
5643824 ATGGACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (24 bp):
GTGAAACTGATATTAATATAAAAT
Found at i:5644668 original size:2 final size:2
Alignment explanation
Indices: 5644657--5644706 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
5644647 TTAAAACAAT
*
5644657 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5644698 -A TA TG TA TA
1 TA TA TA TA TA
5644707 ATGAATGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5644822 original size:534 final size:530
Alignment explanation
Indices: 5643690--5645261 Score: 1492
Period size: 534 Copynumber: 2.9 Consensus size: 530
5643680 AAGTATAAAG
* *
5643690 TATATATGTATATAAAGTACCAAATTGAACAAACATGAATTTGGAAATAAAAAATTGAATAAATT
1 TATATATATATATAAAGTACCAAATTGAACAAACATGAAATTGGAAATAAAAAATT-AATAAATT
* * * *
5643755 AAACAACACGT-ATTGATTAGGGGTGAAATTGAATTAATTATAAAATGTGAAGCTGATATTAATA
65 AAGCAACA--TAATTGATGAGGGATGAAATTGAATTAATTATAAAATTTGAAGCTGATATTAATA
*
5643819 TAAAAATGGACTAAATTGCATACATTTAAAAAGCTGGTGAACATAATTTGAAAAGAAATTTATTA
128 TAAAAATGGACTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTA
* *
5643884 GGTGATTTACATTTTGTAGGG-TTT-TAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATT
193 TGTGATTTACATTTTATAGGGTTTTATAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATT
* * * * *
5643947 TCAGATACAATATAATTTGAAGGACTAAATTGAACAAATATGAAATTATAAATTTAAATTTAAAT
258 TTAGATACAAAATAATTTGAAGGACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAAT
* * * *
5644012 A-AA-AAATAACATAAAAGGATCATATCAAAAAATTGTAAAATGCGAGGGAAAATTGTAAAATGG
323 ACAATAAACAACATAAAATGATCAAAT-AAAAAA-TGTAAAATGTGA-GG-AAATTGTAAAATGG
* * *
5644075 ACTGGATTGCATTAATTTCAAAA-TATGGGGAATATTAAAATAATTATAATATATATAATGA-AT
384 ACTGAATTGCATTAATTTCAAAAGT-T-GGGAAAATTAAAACAATTATAATATATATAAT-ATAT
* * * *
5644138 GT-TATGATAATATGATGCATGTATATATAATGTACATTATACTTTTTATATATATACATATACA
446 ATATATGATAATATGAT-CATGTATATATAATGTA-ATAATACATGTTATATATATACATATACA
* * * *
5644202 TATATACTTATACTTTATAGTT
509 TATATACATATACATTACACTT
* *
5644224 TATATATATGTATAAAGTGCCAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATT
1 TATATATATATATAAAGTACCAAATTGAACAAACATGAAATTGGAAATAAAAAATT-AATAAATT
*
5644289 AAGCAACATACATTGATGAGGGATGAAATTGAATTAATTATAAAATTTAAAGCTGATATTAATAT
65 AAGCAACATA-ATTGATGAGGGATGAAATTGAATTAATTATAAAATTTGAAGCTGATATTAATAT
* * * *
5644354 AAAATTGGACTAAATTGCATATATTTAAAAGGTTGGTGAACATAATTTGAAAAGAAATTTATTTT
129 AAAAATGGACTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTAT
* * *
5644419 ATGATTTACATTTTATAGGGTTTGTTATAAGTAAATTACAAAAACATAAATAAGTATGTGTCAAT
194 GTGATTTACATTTTATAGGG-TT-TTATAAGTAAATTACAAAAATATAAATAAGTATGGGTCAAT
5644484 TTTAGATACGAAAATAATTTGAAGGACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAA
257 TTTAGATAC-AAAATAATTTGAAGGACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAA
* * *
5644549 ATACAATAAACAACATAAAATGATCAAAT-AAAAATGTGAAATGTGAGTAAATTTTGTAAAAGGG
321 ATACAATAAACAACATAAAATGATCAAATAAAAAATGTAAAATGTGAGGAAA--TTGTAAAATGG
5644613 ACTGAATTGCATTAATTTCAAAAGTTGGGAAAAATTAAAACAATTATAATATATAT-ATATATAT
384 ACTGAATTGCATTAATTTCAAAAGTTGGG-AAAATTAAAACAATTATAATATATATAATATATAT
* *
5644677 ATAT-ATATATAT-AT-ATGTATA-AT-ATGT-ATAATGA-ATGTTATGATA-ATAGGATGCATG
448 ATATGATA-ATATGATCATGTATATATAATGTAATAAT-ACATGTTAT-ATATATA-CAT--ATA
* *
5644734 TATATATA-ATGTACATTACACTT
507 CATATATACATATACATTACACTT
* * * * * * *
5644757 TATATATATATATATA-TACACACACATAT-ATACTTACACTTTATAGTT-TATATATGTATATA
1 TATATATATATATAAAGTAC-CA-A-AT-TGA-AC--AAACATGA-AATTGGA-A-A--TA-AAA
* * ***
5644819 AATTACTAAATTGAA-CAAACATGAAGTTGGAAATAAAAAATTGAATAAATTTAGCAACACACAT
53 AATTAATAAATT-AAGC-AACAT-AA-TT-G--ATGAGGGA-TG---AAA-TT-G------A-A-
* *
5644883 TTATGAGGGATGAAATTGAATTAATTATAAAATG-TGA-AGTTGATATTAATACAAAAAATGGAC
97 -T-T-A---AT--TA-T-AA--AATT-T-GAA-GCTGATA-TT-A-A-T-ATA-A--AAATGGAC
* *
5644946 TACATTGCATACATTTAAAAAGTTGGTGAACATAATTAGAAAAGAAATTTATTATGTGATTTACA
139 TAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGTGATTTACA
* * *
5645011 TTTGATAAGGTTTTA-AA-TAAATTACAAAAATATAAATAAGTATGGGTTAATTTTAGATACAAA
204 TTTTATAGGGTTTTATAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTTAGATACAAA
* * *
5645074 TATAATTTGAAGGACTAAATTAAATAAATATAAAATTACAAATTAATATTTAAATACAATAAACA
269 -ATAATTTGAAGGACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATACAATAAACA
* **
5645139 ACATAACATGATCAAATAAAAAAAATGTAAAATGTGAGGAACATTGTAAAATTTACTGAATTGCA
333 ACATAAAATGATCAAAT--AAAAAATGTAAAATGTGAGGAA-ATTGTAAAATGGACTGAATTGCA
* *
5645204 TTAATTTCAAAAGTTGGTG-AAATTTAAACAATTATAATATATATAATATGTATA-ATGA
395 TTAATTTCAAAAGTTGG-GAAAATTAAAACAATTATAATATATATAATATATATATATGA
5645262 ATGTTATGAT
Statistics
Matches: 868, Mismatches: 84, Indels: 126
0.81 0.08 0.12
Matches are distributed among these distances:
531 12 0.01
532 9 0.01
533 30 0.03
534 207 0.24
535 10 0.01
536 8 0.01
537 16 0.02
538 124 0.14
539 64 0.07
540 3 0.00
541 19 0.02
542 10 0.01
543 14 0.02
544 3 0.00
545 1 0.00
547 4 0.00
548 2 0.00
551 3 0.00
552 2 0.00
553 1 0.00
559 1 0.00
560 1 0.00
562 1 0.00
563 1 0.00
564 1 0.00
567 2 0.00
569 1 0.00
570 1 0.00
571 2 0.00
573 4 0.00
574 2 0.00
575 8 0.01
576 2 0.00
577 4 0.00
578 118 0.14
579 31 0.04
580 49 0.06
581 22 0.03
582 75 0.09
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (530 bp):
TATATATATATATAAAGTACCAAATTGAACAAACATGAAATTGGAAATAAAAAATTAATAAATTA
AGCAACATAATTGATGAGGGATGAAATTGAATTAATTATAAAATTTGAAGCTGATATTAATATAA
AAATGGACTAAATTGCATACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGT
GATTTACATTTTATAGGGTTTTATAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTTA
GATACAAAATAATTTGAAGGACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATACA
ATAAACAACATAAAATGATCAAATAAAAAATGTAAAATGTGAGGAAATTGTAAAATGGACTGAAT
TGCATTAATTTCAAAAGTTGGGAAAATTAAAACAATTATAATATATATAATATATATATATGATA
ATATGATCATGTATATATAATGTAATAATACATGTTATATATATACATATACATATATACATATA
CATTACACTT
Found at i:5644938 original size:24 final size:24
Alignment explanation
Indices: 5644893--5644938 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5644883 TTATGAGGGA
*
5644893 TGAAATTGAATTAATTATAAAATG
1 TGAAATTGAATTAATTACAAAATG
*
5644917 TGAAGTTGATATTAA-TACAAAA
1 TGAAATTGA-ATTAATTACAAAA
5644939 AATGGACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (24 bp):
TGAAATTGAATTAATTACAAAATG
Found at i:5645165 original size:581 final size:572
Alignment explanation
Indices: 5644119--5645257 Score: 1707
Period size: 581 Copynumber: 2.0 Consensus size: 572
5644109 TTAAAATAAT
* *
5644119 TATAATATATATAATGAATGTTATGATAATATGATGCATGTATATATAATGTACATTATACTTTT
1 TATAATATATATAATGAATGTTATGATAATAGGATGCATGTATATATAATGTACATTACACTTTT
* * * * *
5644184 TATATATATACATATACATATATACTTATACTTTATAGTTTATATATATGTATAAAGTGCCAAAT
66 TATATATATACACACACATATATACTTACACTTTATAGTTTATATATATATATAAAGTACCAAAT
*
5644249 TGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACATACATTGATGAGGGATG
131 TGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAGGGATG
* * * *
5644314 AAATTGAATTAATTATAAAATTTAAAGCTGATATTAATATAAAATTGGACTAAATTGCATATATT
196 AAATTGAATTAATTATAAAATGTAAAGCTGATATTAATAAAAAAATGGACTAAATTGCATACATT
* * * * *
5644379 TAAAAGGTTGGTGAACATAATTTGAAAAGAAATTTATTTTATGATTTACATTTTATAGGGTTTGT
261 TAAAAAGTTGGTGAACATAATTAGAAAAGAAATTTATTATATGATTTACATTTGATAAGGTTTGT
*
5644444 TATAAGTAAATTACAAAAACATAAATAAGTATGTGTCAATTTTAGATACGAAAATAATTTGAAGG
326 TATAAGTAAATTACAAAAACATAAATAAGTATGGGTCAATTTTAGATACGAAAATAATTTGAAGG
*
5644509 ACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATACAATAAACAACATAAAATGATC
391 ACTAAATTAAACAAATATAAAATTACAAATTAAAATTTAAATACAATAAACAACATAAAATGATC
* *
5644574 AAATAAAAATGTGAAATGTGAGTAA-ATTTTGTAAAAGGGACTGAATTGCATTAATTTCAAAAGT
456 AAATAAAAATGTAAAATGTGAGGAACA--TTGTAAAAGGGACTGAATTGCATTAATTTCAAAAGT
5644638 TGG-GAAAAATTAAAACAATTATAATATATATATATATATATATATATATATATATG
519 TGGTG--AAATTAAAACAATTATAATATATATA-ATATATATATATATATATATATG
*
5644694 TATAATATGTATAATGAATGTTATGATAATAGGATGCATGTATATATAATGTACATTACACTTTA
1 TATAATATATATAATGAATGTTATGATAATAGGATGCATGTATATATAATGTACATTACAC--T-
* *
5644759 TATATATATATATATACACACACATATATACTTACACTTTATAGTTTATATATGTATATAAATTA
63 T-T-T-TATATATATACACACACATATATACTTACACTTTATAGTTTATATATATATATAAAGTA
* * * *
5644824 CTAAATTGAACAAACATGAAGTTGGAAATAAAAAATTGAATAAATTTAGCAACACACATTTATGA
125 CCAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGA
* * *
5644889 GGGATGAAATTGAATTAATTATAAAATGTGAAGTTGATATTAATACAAAAAATGGACTACATTGC
190 GGGATGAAATTGAATTAATTATAAAATGTAAAGCTGATATTAATA-AAAAAATGGACTAAATTGC
*
5644954 ATACATTTAAAAAGTTGGTGAACATAATTAGAAAAGAAATTTATTATGTGATTTACATTTGATAA
254 ATACATTTAAAAAGTTGGTGAACATAATTAGAAAAGAAATTTATTATATGATTTACATTTGATAA
* *
5645019 GG-TT-TTA-AA-TAAATTACAAAAATATAAATAAGTATGGGTTAATTTTAGATAC-AAATATAA
319 GGTTTGTTATAAGTAAATTACAAAAACATAAATAAGTATGGGTCAATTTTAGATACGAAA-ATAA
* *
5645079 TTTGAAGGACTAAATTAAATAAATATAAAATTACAAATTAATATTTAAATACAATAAACAACATA
383 TTTGAAGGACTAAATTAAACAAATATAAAATTACAAATTAAAATTTAAATACAATAAACAACATA
* ***
5645144 ACATGATCAAATAAAAAAAATGTAAAATGTGAGGAACATTGTAAAATTTACTGAATTGCATTAAT
448 AAATGATCAAAT---AAAAATGTAAAATGTGAGGAACATTGTAAAAGGGACTGAATTGCATTAAT
* *
5645209 TTCAAAAGTTGGTGAAATTTAAACAATTATAATATATATAATATGTATA
510 TTCAAAAGTTGGTGAAATTAAAACAATTATAATATATATAATATATATA
5645258 ATGAATGTTA
Statistics
Matches: 509, Mismatches: 42, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
575 58 0.11
577 4 0.01
578 126 0.25
579 28 0.06
580 40 0.08
581 176 0.35
582 77 0.15
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (572 bp):
TATAATATATATAATGAATGTTATGATAATAGGATGCATGTATATATAATGTACATTACACTTTT
TATATATATACACACACATATATACTTACACTTTATAGTTTATATATATATATAAAGTACCAAAT
TGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAGGGATG
AAATTGAATTAATTATAAAATGTAAAGCTGATATTAATAAAAAAATGGACTAAATTGCATACATT
TAAAAAGTTGGTGAACATAATTAGAAAAGAAATTTATTATATGATTTACATTTGATAAGGTTTGT
TATAAGTAAATTACAAAAACATAAATAAGTATGGGTCAATTTTAGATACGAAAATAATTTGAAGG
ACTAAATTAAACAAATATAAAATTACAAATTAAAATTTAAATACAATAAACAACATAAAATGATC
AAATAAAAATGTAAAATGTGAGGAACATTGTAAAAGGGACTGAATTGCATTAATTTCAAAAGTTG
GTGAAATTAAAACAATTATAATATATATAATATATATATATATATATATATG
Found at i:5645345 original size:2 final size:2
Alignment explanation
Indices: 5645328--5645707 Score: 118
Period size: 2 Copynumber: 189.5 Consensus size: 2
5645318 TAATACATTA
5645328 AT AT AT -T AT A- AGT AT AT AT AT AT AT AT AT A- AGT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * *
5645369 -T A- AT AT A- AA AGT AT AT AC AT AT AG GT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
5645409 AT ACT -T AT TT AA AT AT AC AT AT AT AA AA AA AGT AT A- AGT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT
* * *
5645450 AT AT AT AA AGT GT GA- ACT AT AA AGT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT A-T AT -AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * * *
5645492 AT AT GT AT AA ACT AT AA AGT AT AT AT AT -T TT AA AGT GT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
* * * *
5645534 AT AT -T AT AA AGT AT AA AT AA AT -T AT ACT TT AT ACT AT A- ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T
* * * *
5645575 TT AT AT AT AT -T AT AT ACT TT AT AT -T AT AC AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5645616 AT AT AT AT AT AT AT AT AT AA AGT -T TT AGT AT AA AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT
* *
5645658 AC AT AT AT A- AT A- AT AT A- AA AT AT A- AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
5645697 AT AT AT AT AT A
1 AT AT AT AT AT A
5645708 AAGTATAATT
Statistics
Matches: 277, Mismatches: 58, Indels: 86
0.66 0.14 0.20
Matches are distributed among these distances:
1 21 0.08
2 237 0.86
3 19 0.07
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5645482 original size:37 final size:37
Alignment explanation
Indices: 5645441--5645766 Score: 114
Period size: 33 Copynumber: 9.2 Consensus size: 37
5645431 ATAAAAAAAG
* *
5645441 TATAAGTATATATATA-AAGTGTGAACTATAAAGTATA
1 TATAA-TATATATATATAAGTATAAACTATAAAGTATA
*
5645478 TATAATATATATATATATGTATAAACTATAAAGTATA
1 TATAATATATATATATAAGTATAAACTATAAAGTATA
* * * * *
5645515 TAT-AT-TTTAAAGTGT-A-TATATATTATAAAGTATA
1 TATAATATATATA-TATAAGTATAAACTATAAAGTATA
* * * *
5645549 AATAA-AT-TATACTTTATACTAT-AACT-T-TA-TATA
1 TATAATATATATA-TATA-AGTATAAACTATAAAGTATA
* * ** *
5645582 TAT--TATATACTTTAT-ATTATACATTTATATA-TATA
1 TATAATATATA-TATATAAGTATA-AACTATAAAGTATA
** *
5645617 TATATATATATATATATAAAGT-TTTAGTATAAAGTATA
1 TATA-ATATATATATAT-AAGTATAAACTATAAAGTATA
* *
5645655 TAT-ACATATATA-ATAA-TATAAAATAT-AAGTATA
1 TATAATATATATATATAAGTATAAACTATAAAGTATA
*
5645688 TAT-ATATATATATAT-A-TATAAAGTAT-AA-T-TA
1 TATAATATATATATATAAGTATAAACTATAAAGTATA
* * *
5645719 TA-AAGACTAAAGTATATAAATATATAA-TATAAAGTATA
1 TATAATA-TATA-TATATAAGTATA-AACTATAAAGTATA
5645757 TATACATATA
1 TATA-ATATA
5645767 AAGTATAAGT
Statistics
Matches: 218, Mismatches: 38, Indels: 64
0.68 0.12 0.20
Matches are distributed among these distances:
31 10 0.05
32 6 0.03
33 48 0.22
34 36 0.17
35 25 0.11
36 29 0.13
37 39 0.18
38 18 0.08
39 5 0.02
40 2 0.01
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (37 bp):
TATAATATATATATATAAGTATAAACTATAAAGTATA
Found at i:5645592 original size:31 final size:32
Alignment explanation
Indices: 5645556--5645622 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 32
5645546 ATAAATAAAT
5645556 TATACTTTATACTATA-ACTTTATATATAT-TA
1 TATACTTTATACTATACA-TTTATATATATATA
*
5645587 TATACTTTATATTATACATTTATATATATATA
1 TATACTTTATACTATACATTTATATATATATA
5645619 TATA
1 TATA
5645623 TATATATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (32 bp):
TATACTTTATACTATACATTTATATATATATA
Found at i:5645681 original size:27 final size:30
Alignment explanation
Indices: 5645576--5645714 Score: 80
Period size: 27 Copynumber: 4.8 Consensus size: 30
5645566 ACTATAACTT
*** *
5645576 TATATATAT-TATATACTTTATATTATACA
1 TATATATATATATATAAAATATAGTATACA
* *
5645605 T-T-TATATATATAT-ATATATA-TATATA
1 TATATATATATATATAAAATATAGTATACA
* * *
5645631 TATAAAGT-TTTAGTATAAAGTATA-TATACA
1 TATATA-TATATA-TATAAAATATAGTATACA
*
5645661 TATATA-ATA-ATATAAAATATAAGTATATA
1 TATATATATATATATAAAATAT-AGTATACA
5645690 TATATATATATATATATAAAGTATA
1 TATATATATATATATA-AAA-TATA
5645715 ATTATAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
26 6 0.07
27 20 0.24
28 12 0.14
29 17 0.20
30 18 0.21
31 5 0.06
32 4 0.05
33 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (30 bp):
TATATATATATATATAAAATATAGTATACA
Found at i:5645886 original size:13 final size:13
Alignment explanation
Indices: 5645854--5646011 Score: 102
Period size: 13 Copynumber: 12.2 Consensus size: 13
5645844 TATATAGATA
5645854 TATAA-TATAAAG
1 TATAAGTATAAAG
5645866 TATATAAGTATAAAG
1 --TATAAGTATAAAG
5645881 TATAAGTATTAAA-
1 TATAAGTA-TAAAG
5645894 TATAAAGTATATAAG
1 TAT-AAGTATA-AAG
* *
5645909 TATATAATATACA-
1 TATA-AGTATAAAG
5645922 TATACA-TATAAAG
1 TATA-AGTATAAAG
*
5645935 TACAAGTAT-AAG
1 TATAAGTATAAAG
*
5645947 TATAAGTATATA-
1 TATAAGTATAAAG
*
5645959 TAT-A-TATAAAT
1 TATAAGTATAAAG
5645970 TATAAAGTAT-AAG
1 TAT-AAGTATAAAG
5645983 TATATA-TATAAAG
1 TATA-AGTATAAAG
* *
5645996 TTTCAGTATAAAG
1 TATAAGTATAAAG
5646009 TAT
1 TAT
5646012 GTATACATAT
Statistics
Matches: 116, Mismatches: 12, Indels: 33
0.72 0.07 0.20
Matches are distributed among these distances:
10 5 0.04
11 4 0.03
12 25 0.22
13 46 0.40
14 21 0.18
15 15 0.13
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (13 bp):
TATAAGTATAAAG
Found at i:5645887 original size:6 final size:6
Alignment explanation
Indices: 5645868--5645986 Score: 59
Period size: 6 Copynumber: 18.7 Consensus size: 6
5645858 ATATAAAGTA
* *
5645868 TATAAG TATAAAG TATAAG TATTAAA TATAAAG TATATAAG TATATAA
1 TATAAG TAT-AAG TATAAG TA-TAAG TAT-AAG --TATAAG TATA-AG
*
5645916 TATACA- TATACA- TATAAAG TACAAG TATAAG TATAAG TAT-A- TATATA-
1 TATA-AG TATA-AG TAT-AAG TATAAG TATAAG TATAAG TATAAG TATA-AG
*
5645963 TATAAAT TATAAAG TATAAG TATA
1 TAT-AAG TAT-AAG TATAAG TATA
5645987 TATATAAAGT
Statistics
Matches: 94, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
6 52 0.55
7 32 0.34
8 3 0.03
9 3 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (6 bp):
TATAAG
Found at i:5645974 original size:29 final size:29
Alignment explanation
Indices: 5645609--5645774 Score: 102
Period size: 29 Copynumber: 5.8 Consensus size: 29
5645599 TATACATTTA
*
5645609 TATATATATATATATA-TATATATATAAAG
1 TATATATATATATAAAGTATA-ATATAAAG
* *
5645638 T-T-T-TA-GTATAAAGTAT-ATATACA-
1 TATATATATATATAAAGTATAATATAAAG
* *
5645661 TATATA-ATAATATAAAATATAAGTATATATATA
1 TATATATAT-ATATAAAGTATAA-TATA-A-A-G
5645694 TATATATATATATAAAGTATAATTATAAAG
1 TATATATATATATAAAGTATAA-TATAAAG
*
5645724 -ACTA-A-AGTATATAAATATATAATATAAAG
1 TA-TATATA-TATATAAA-GTATAATATAAAG
*
5645753 TATATATACATATAAAGTATAA
1 TATATATATATATAAAGTATAA
5645775 GTGTGTGTAT
Statistics
Matches: 106, Mismatches: 12, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
23 1 0.01
24 7 0.07
25 7 0.07
26 5 0.05
27 10 0.09
28 3 0.03
29 29 0.27
30 16 0.15
31 3 0.03
32 1 0.01
33 22 0.21
34 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (29 bp):
TATATATATATATAAAGTATAATATAAAG
Found at i:5645993 original size:42 final size:43
Alignment explanation
Indices: 5645901--5645993 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
5645891 AAATATAAAG
*
5645901 TATATAAGTATATAATATACATATACATATAAAGTACAAGTATA
1 TATATAAGTATATAATATA-ATATAAATATAAAGTACAAGTATA
*
5645945 -AGTATAAGTATAT-ATAT-ATATAAATTATAAAGTATAAGTATA
1 TA-TATAAGTATATAATATAATATAAA-TATAAAGTACAAGTATA
5645987 TATATAA
1 TATATAA
5645994 AGTTTCAGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
41 6 0.14
42 21 0.48
43 6 0.14
44 11 0.25
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (43 bp):
TATATAAGTATATAATATAATATAAATATAAAGTACAAGTATA
Found at i:5646717 original size:21 final size:21
Alignment explanation
Indices: 5646693--5646734 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5646683 TGGGTCAACA
*
5646693 ACCATGGGGTGTAGCATCTCT
1 ACCATAGGGTGTAGCATCTCT
5646714 ACCATAGGGTGTAGCATCTCT
1 ACCATAGGGTGTAGCATCTCT
5646735 GTCTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (21 bp):
ACCATAGGGTGTAGCATCTCT
Found at i:5647247 original size:22 final size:21
Alignment explanation
Indices: 5647200--5647352 Score: 122
Period size: 21 Copynumber: 7.3 Consensus size: 21
5647190 TGTTGTTGTT
*
5647200 GTATATAAGCATTAAATAT-AA
1 GTATATAAGTA-TAAATATAAA
5647221 GTATATAAGTATTAAATATAAA
1 GTATATAAGTA-TAAATATAAA
**
5647243 GTATATAAGTATATGTATAAA
1 GTATATAAGTATAAATATAAA
* **
5647264 TTATA-AAGTATATGTATAAA
1 GTATATAAGTATAAATATAAA
* *
5647284 TTATA-AAGTATATATATATATAG
1 GTATATAAGTATA-A-ATATA-AA
*
5647307 GTGTAT-A--AT-AATATAAA
1 GTATATAAGTATAAATATAAA
5647324 GTATATAAGTATATAATATAAA
1 GTATATAAGTATA-AATATAAA
5647346 GTATATA
1 GTATATA
5647353 TATATATATA
Statistics
Matches: 111, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.05
18 6 0.05
19 1 0.01
20 29 0.26
21 32 0.29
22 32 0.29
23 5 0.05
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (21 bp):
GTATATAAGTATAAATATAAA
Found at i:5647247 original size:28 final size:26
Alignment explanation
Indices: 5647212--5647281 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 26
5647202 ATATAAGCAT
5647212 TAAA-TATAAGTATATAAGTATTAAA-TA
1 TAAAGTATAAGTATAT--GTA-TAAATTA
5647239 TAAAGTATATAAGTATATGTATAAATTA
1 TAAAG--TATAAGTATATGTATAAATTA
*
5647267 TAAAGTATATGTATA
1 TAAAGTATAAGTATA
5647282 AATTATAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
26 9 0.24
27 8 0.21
28 10 0.26
30 11 0.29
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (26 bp):
TAAAGTATAAGTATATGTATAAATTA
Found at i:5647274 original size:20 final size:20
Alignment explanation
Indices: 5647237--5647301 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
5647227 AAGTATTAAA
*
5647237 TATAAAGTATATAAGTATATG
1 TATAAATTATA-AAGTATATG
5647258 TATAAATTATAAAGTATATG
1 TATAAATTATAAAGTATATG
*
5647278 TATAAATTATAAAGTATATA
1 TATAAATTATAAAGTATATG
5647298 TATA
1 TATA
5647302 TATAGGTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
20 32 0.76
21 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
TATAAATTATAAAGTATATG
Found at i:5647275 original size:14 final size:13
Alignment explanation
Indices: 5647212--5647356 Score: 59
Period size: 14 Copynumber: 10.6 Consensus size: 13
5647202 ATATAAGCAT
5647212 TAAATAT-AAGTA
1 TAAATATAAAGTA
5647224 TATAAGTATTAAA-TA
1 TA-AA-TA-TAAAGTA
5647239 TAAAGTATATAAGTA
1 TAAA-TATA-AAGTA
** *
5647254 TATGTATAAATTA
1 TAAATATAAAGTA
*
5647267 TAAAGTAT-ATGTA
1 TAAA-TATAAAGTA
5647280 TAAATTATAAAGTA
1 TAAA-TATAAAGTA
* *
5647294 TATATATATATAGGTG
1 TA-A-ATATA-AAGTA
*
5647310 TATA-AT-AA-TA
1 TAAATATAAAGTA
5647320 TAAAGTATATAAGTA
1 TAAA-TATA-AAGTA
5647335 TATAATATAAAGTA
1 TA-AATATAAAGTA
*
5647349 TATATATA
1 TAAATATA
5647357 TATATATATA
Statistics
Matches: 100, Mismatches: 16, Indels: 33
0.67 0.11 0.22
Matches are distributed among these distances:
10 4 0.04
11 1 0.01
12 4 0.04
13 27 0.27
14 32 0.32
15 22 0.22
16 10 0.10
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (13 bp):
TAAATATAAAGTA
Found at i:5647299 original size:2 final size:2
Alignment explanation
Indices: 5647292--5647689 Score: 93
Period size: 2 Copynumber: 206.0 Consensus size: 2
5647282 AATTATAAAG
** * *
5647292 TA TA TA TA TA TA TA GG TG TA TA -A TA -A TA TA AA GTA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
5647332 GTA TA TA -A TA TA AA GTA TA TA TA TA TA TA TA TA TA TA T- TA TT
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5647374 TA -A TA CT- TA TA TA T- TT TT TA T- TA TA TA CT- TT TA TA CTT
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * * *
5647412 TA TA T- TA TA TGC T- TA TA TA CTT TA GTC TT TA TA GT- TA TA T-
1 TA TA TA TA TA T-A TA TA TA TA -TA TA -TA TA TA TA -TA TA TA TA
* *
5647452 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TG TA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * * *
5647495 T- TA T- TA TA TT TG TA TA TA TA -A TT TA TA CTA -A AA CTT TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * *
5647535 TG TA TA TA TA CA CTT TA TA TA TT TA TA TA CTT TA TA T- TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
5647577 TA TA TG TA TA TA TA TA TA TA CA TA TA TA TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5647618 GTT TA TA T- TA -A TA -A AA TA TA TA -A TT TA TA CA TA -A TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
5647656 TA TA -A TT TA TA -A T- TA TA CA TA -A TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5647690 AGCTTTATAT
Statistics
Matches: 287, Mismatches: 61, Indels: 96
0.65 0.14 0.22
Matches are distributed among these distances:
1 31 0.11
2 240 0.84
3 16 0.06
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5647324 original size:33 final size:32
Alignment explanation
Indices: 5647276--5647338 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
5647266 ATAAAGTATA
*
5647276 TGTATAAATTATAAAGTATATATA-TATATAGG
1 TGTATAAAATATAAAGTATATA-AGTATATAGG
5647308 TGTATAATAATATAAAGTATATAAGTATATA
1 TGTATAA-AATATAAAGTATATAAGTATATA
5647339 ATATAAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (32 bp):
TGTATAAAATATAAAGTATATAAGTATATAGG
Found at i:5647617 original size:11 final size:11
Alignment explanation
Indices: 5647599--5647666 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
5647589 TATATATACA
5647599 TATATATAATT
1 TATATATAATT
*
5647610 TATATATAGTT
1 TATATATAATT
*
5647621 TATAT-TAATAA
1 TATATATAAT-T
*
5647632 AATATATAATT
1 TATATATAATT
*
5647643 TATACATAA--
1 TATATATAATT
5647652 TATATATAATT
1 TATATATAATT
5647663 TATA
1 TATA
5647667 ATTATACATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
9 8 0.18
10 3 0.07
11 30 0.67
12 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
TATATATAATT
Found at i:5647637 original size:33 final size:35
Alignment explanation
Indices: 5647574--5647659 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 35
5647564 CTTTATATTA
*
5647574 TTATATATGTATATATATATATACATATATATAAT
1 TTATATATGTATATATATATATACAAATATATAAT
*
5647609 TTATATATAGTTTATAT-TA-ATA-AAATATATAAT
1 TTATATAT-GTATATATATATATACAAATATATAAT
* *
5647642 TTATACAT-AATATATATA
1 TTATATATGTATATATATA
5647660 ATTTATAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 5 0.11
32 2 0.05
33 17 0.39
34 3 0.07
35 10 0.23
36 7 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (35 bp):
TTATATATGTATATATATATATACAAATATATAAT
Found at i:5650056 original size:24 final size:24
Alignment explanation
Indices: 5650024--5650092 Score: 129
Period size: 24 Copynumber: 2.9 Consensus size: 24
5650014 CTTTCAGATG
5650024 ATGTATAAAACATCTATGTACACA
1 ATGTATAAAACATCTATGTACACA
*
5650048 ATGTATAAAACATCTATGTACACG
1 ATGTATAAAACATCTATGTACACA
5650072 ATGTATAAAACATCTATGTAC
1 ATGTATAAAACATCTATGTAC
5650093 CATGTCATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.30
Consensus pattern (24 bp):
ATGTATAAAACATCTATGTACACA
Found at i:5651507 original size:22 final size:20
Alignment explanation
Indices: 5651469--5651522 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
5651459 GGGGTATTAC
5651469 ACTATAT-ATTTAAATAT-A
1 ACTATATAATTTAAATATCA
*
5651487 ATTCATATATAATTTACATATCA
1 A--C-TATATAATTTAAATATCA
5651510 ACTATATAATTTA
1 ACTATATAATTTA
5651523 TGTTAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 1 0.03
20 12 0.40
21 6 0.20
22 9 0.30
23 2 0.07
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
ACTATATAATTTAAATATCA
Found at i:5651598 original size:2 final size:2
Alignment explanation
Indices: 5651591--5651629 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
5651581 TTATACATGG
*
5651591 TA TA TA TA GTT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5651630 CTTTATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5651653 original size:24 final size:24
Alignment explanation
Indices: 5651626--5651683 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
5651616 TATATATATA
5651626 TATACTTTATAAACTTAAATACTT
1 TATACTTTATAAACTTAAATACTT
* * *
5651650 TATA--TTATATACTTATATATTT
1 TATACTTTATAAACTTAAATACTT
5651672 TAGT-CTTTATAA
1 TA-TACTTTATAA
5651684 TTATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
22 17 0.63
23 1 0.04
24 9 0.33
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (24 bp):
TATACTTTATAAACTTAAATACTT
Found at i:5651699 original size:51 final size:50
Alignment explanation
Indices: 5651644--5651792 Score: 177
Period size: 51 Copynumber: 3.1 Consensus size: 50
5651634 ATAAACTTAA
5651644 ATACTTTATATTATATACTTATATATTTTAGTCTTTATAATTATATTTTAT
1 ATACTTTATATTATATACTTATATATTTTAGTCTTTATAATTATA-TTTAT
* *
5651695 ATACTTTATATT-TAATACTTATATATTTTA-----TATTA-TATACTTAT
1 ATACTTTATATTAT-ATACTTATATATTTTAGTCTTTATAATTATATTTAT
* * *
5651739 ATACTTTATATTATGTGCTTATATACTTTAGTCTTTATAATTATACTTTAT
1 ATACTTTATATTATATACTTATATATTTTAGTCTTTATAATTATA-TTTAT
5651790 ATA
1 ATA
5651793 TATAAGATAC
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
44 29 0.35
45 5 0.06
46 4 0.05
49 4 0.05
50 5 0.06
51 35 0.43
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (50 bp):
ATACTTTATATTATATACTTATATATTTTAGTCTTTATAATTATATTTAT
Found at i:5651701 original size:22 final size:22
Alignment explanation
Indices: 5651691--5651948 Score: 74
Period size: 22 Copynumber: 12.0 Consensus size: 22
5651681 TAATTATATT
5651691 TTATATACTT-TATA-TTTAATA
1 TTATATACTTATATACTTT-ATA
*
5651712 CTTATATA-TTTTATA-TTATATA
1 -TTATATACTTATATACTT-TATA
* *
5651734 CTTATATACTT-TATA-TTATGTGC
1 -TTATATACTTATATACTT-TAT-A
5651757 TTATATACTT-TAGT-CTTTATA
1 TTATATACTTATA-TACTTTATA
*
5651778 AT-TATACTT-TATA---TATA
1 TTATATACTTATATACTTTATA
* *
5651795 TAAGATAC-T-TATACTTTATA
1 TTATATACTTATATACTTTATA
*
5651815 TATATATA-TATATATAATTTATA
1 T-TATATACT-TATATACTTTATA
*
5651838 GTTTATATAAATACTTATGTACTTTATA
1 ---T-TAT--ATACTTATATACTTTATA
* *
5651866 TT-TAAAC-TATATAATTTATA
1 TTATATACTTATATACTTTATA
* *
5651886 TTAATAAAC-TATATAGTTTATA
1 TT-ATATACTTATATACTTTATA
*
5651908 -TATATAATATATATACTTTAT-
1 TTATATACT-TATATACTTTATA
* *
5651929 TTATACAC-TATATAGTTTAT
1 TTATATACTTATATACTTTAT
5651949 GTATAGTTTA
Statistics
Matches: 187, Mismatches: 23, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
17 9 0.05
18 4 0.02
19 1 0.01
20 42 0.22
21 11 0.06
22 81 0.43
23 17 0.09
24 1 0.01
25 1 0.01
26 5 0.03
28 14 0.07
29 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (22 bp):
TTATATACTTATATACTTTATA
Found at i:5651775 original size:73 final size:72
Alignment explanation
Indices: 5651593--5651793 Score: 166
Period size: 73 Copynumber: 2.8 Consensus size: 72
5651583 ATACATGGTA
* * * * *
5651593 TATATAGTTTA-TATATATATATATATATATATATATACTTTAT-A--A-ACTTAAATACTTTAT
1 TATATACTTTAGTATTTATA-AT-TATAT-TTTATATACTTTATAATTATACTTATATATTTTAT
5651653 ATTATATACT
63 ATTATATACT
* * *
5651663 TATATATTTTAGTCTTTATAATTATATTTTATATACTTTATATTTAATACTTATATATTTTATAT
1 TATATACTTTAGTATTTATAATTATATTTTATATACTTTATAATT-ATACTTATATATTTTATAT
5651728 TATATACT
65 TATATACT
* ** *
5651736 TATATACTTTA-TATTATGTGCTTATATACTTTA-GT-CTTTATAATTATACTTTATATAT
1 TATATACTTTAGTATT-TATAATTATAT--TTTATATACTTTATAATTATAC-TTATATAT
5651794 ATAAGATACT
Statistics
Matches: 107, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
68 13 0.12
69 5 0.05
70 12 0.11
71 6 0.06
72 8 0.07
73 58 0.54
74 1 0.01
75 4 0.04
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (72 bp):
TATATACTTTAGTATTTATAATTATATTTTATATACTTTATAATTATACTTATATATTTTATATT
ATATACT
Found at i:5651793 original size:66 final size:66
Alignment explanation
Indices: 5651691--5651815 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 66
5651681 TAATTATATT
* * *
5651691 TTATATACTTTATATTTAATACTTATATATT-T-TATATTATATACTTATATACTTTATATTATG
1 TTATATACTTTATATTTAATAATTATATATTATATATATAAGATAC-T-TATACTTTATATTATG
5651754 TGC
64 TGC
*
5651757 TTATATACTTTAGTCTTT-ATAATTATACT-TTATATATATAAGATACTTATACTTTATAT
1 TTATATACTTTA-TATTTAATAATTATA-TATTATATATATAAGATACTTATACTTTATAT
5651816 ATATATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
66 34 0.67
67 7 0.14
68 10 0.20
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.54
Consensus pattern (66 bp):
TTATATACTTTATATTTAATAATTATATATTATATATATAAGATACTTATACTTTATATTATGTG
C
Found at i:5651815 original size:95 final size:96
Alignment explanation
Indices: 5651616--5651863 Score: 283
Period size: 95 Copynumber: 2.6 Consensus size: 96
5651606 TATATATATA
* * *
5651616 TATATATATATATACTTTATAAACTTAAATACTTTATATTATATACTTATATATTTTAGTCTTTA
1 TATATATATATATA--TTATATACTTATATACTTTATATTATATACTTATATACTTTAGTCTTTA
** *
5651681 TAATTATATTTTATATACTTTATATTTAATACT
64 TAATTATATTTTATATACTAGATACTTAATACT
* * *
5651714 TATATAT-TTTATATTATATACTTATATACTTTATATTATGTGCTTATATACTTTAGTCTTTATA
1 TATATATATATATATTATATACTTATATACTTTATATTATATACTTATATACTTTAGTCTTTATA
5651778 ATTATACTTTATATATA-TAAGATACTT-ATACT
66 ATTATA-TTT-TATATACT-AGATACTTAATACT
* * * *
5651810 T-TATATATATATATATATATAATT-TATAGTTTATA-TAAATACTTATGTACTTTA
1 TATATATATATATAT-TATATACTTATATACTTTATATTATATACTTATATACTTTA
5651864 TATTTAAACT
Statistics
Matches: 129, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
95 72 0.56
96 26 0.20
97 24 0.19
98 7 0.05
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (96 bp):
TATATATATATATATTATATACTTATATACTTTATATTATATACTTATATACTTTAGTCTTTATA
ATTATATTTTATATACTAGATACTTAATACT
Found at i:5651818 original size:2 final size:2
Alignment explanation
Indices: 5651811--5652109 Score: 104
Period size: 2 Copynumber: 148.5 Consensus size: 2
5651801 ACTTATACTT
* * *
5651811 TA TA TA TA TA TA TA TA TA TA -A TT TA TA GTT TA TA TA AA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * * * *
5651853 TA TG TA CTT TA TA TT TA AA CTA TA TA -A TT TA TA T- TA -A TA AA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5651894 CTA TA TA GTT TA TA TA TA TA -A TA TA TA TA CTT TA TT TA TA CA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
5651936 CTA TA TA GTT TA TG TA TA GTT TA TA T- TA -A TA AA CTA TA TA T-
1 -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
5651977 TT TA TA GA TA -A TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* *
5652020 -A TT TA TA TA TA TA -A TA TA TA TA TA TA TA TA CTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
5652061 AA CTT TA GTT TA TA CA TA -A TA -A TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5652103 TA TA TA T
1 TA TA TA T
5652110 TGTTTCAATT
Statistics
Matches: 212, Mismatches: 55, Indels: 60
0.65 0.17 0.18
Matches are distributed among these distances:
1 14 0.07
2 183 0.86
3 15 0.07
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5651961 original size:42 final size:44
Alignment explanation
Indices: 5651814--5651953 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 44
5651804 TATACTTTAT
* *
5651814 ATATATAT-ATATATATAATTTATAGTTTATATAAATACTTATGTACTTT
1 ATATATATAATATATATAATTTATA--TTA-AT-AA-AC-TATATAGTTT
5651863 ATAT-T-TAA-ACTATATAATTTATATTAATAAACTATATAGTTT
1 ATATATATAATA-TATATAATTTATATTAATAAACTATATAGTTT
* *
5651905 ATATATATAATATATATACTTTAT-TT-ATACACTATATAGTTT
1 ATATATATAATATATATAATTTATATTAATAAACTATATAGTTT
*
5651947 ATGTATA
1 ATATATA
5651954 GTTTATATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 17
0.79 0.05 0.17
Matches are distributed among these distances:
42 33 0.41
43 5 0.06
44 16 0.20
45 3 0.04
46 3 0.04
47 2 0.02
48 15 0.19
49 4 0.05
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (44 bp):
ATATATATAATATATATAATTTATATTAATAAACTATATAGTTT
Found at i:5652017 original size:13 final size:13
Alignment explanation
Indices: 5652001--5652106 Score: 79
Period size: 13 Copynumber: 7.5 Consensus size: 13
5651991 AAATATAAAC
*
5652001 TATATAGTTTATA
1 TATATAATTTATA
5652014 TATATAATTTATA
1 TATATAATTTATA
5652027 TATATAATATATATA
1 TATATAAT-T-TATA
5652042 TATATATACTTTATA
1 TATATA-A-TTTATA
5652057 TATA-AACTTTAGTTTA
1 TATATAA-TTTA---TA
* *
5652073 TACATAATAATATA
1 TATATAAT-TTATA
*
5652087 TATATATATATATA
1 TATATA-ATTTATA
5652101 TATATA
1 TATATA
5652107 TATTGTTTCA
Statistics
Matches: 79, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
13 26 0.33
14 20 0.25
15 20 0.25
16 8 0.10
17 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (13 bp):
TATATAATTTATA
Found at i:5652027 original size:53 final size:53
Alignment explanation
Indices: 5651889--5652029 Score: 139
Period size: 53 Copynumber: 2.7 Consensus size: 53
5651879 ATTTATATTA
* **
5651889 ATAAACTATATAGTTTATATATATAATATATATACTTTATTTATACACTATAT
1 ATAAACTATATAGTTTATATATATAATATATATATTTTATAGATACACTATAT
** *
5651942 AGTTTA-TGTATAGTTTATAT-TAATAA-ACTATATATTTTATAGATA-A-TATAAAT
1 A-TAAACTATATAGTTTATATAT-ATAATA-TATATATTTTATAGATACACTAT--AT
*
5651995 ATAAACTATATAGTTTATATATATAATTTATATAT
1 ATAAACTATATAGTTTATATATATAATATATATAT
5652030 ATAATATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
51 3 0.04
52 5 0.07
53 59 0.84
54 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (53 bp):
ATAAACTATATAGTTTATATATATAATATATATATTTTATAGATACACTATAT
Found at i:5654820 original size:23 final size:23
Alignment explanation
Indices: 5654772--5654835 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
5654762 CAAATGAACA
*
5654772 AACATAAACGAATGA-ATGTAAACG
1 AACATAAACGAAT-ATA-ATAAACG
5654796 AACATAAACGAATATAATAAACG
1 AACATAAACGAATATAATAAACG
* * *
5654819 AACGTAAATGAAAATAA
1 AACATAAACGAATATAA
5654836 GCGAACACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.59, C:0.11, G:0.12, T:0.17
Consensus pattern (23 bp):
AACATAAACGAATATAATAAACG
Found at i:5655160 original size:14 final size:14
Alignment explanation
Indices: 5655141--5655181 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5655131 TAACATACAC
5655141 GAACATAAATGAAA
1 GAACATAAATGAAA
*
5655155 GAACATAAAT-AGAC
1 GAACATAAATGA-AA
5655169 GAACATAAATGAA
1 GAACATAAATGAA
5655182 TGGATTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (14 bp):
GAACATAAATGAAA
Found at i:5656380 original size:284 final size:282
Alignment explanation
Indices: 5655870--5656435 Score: 1078
Period size: 284 Copynumber: 2.0 Consensus size: 282
5655860 CCATGATAAG
5655870 CCATTTTGATTATGTAACAATTTGCCTAATTTGATTACGAGTTCCAAAGACTAAACTTTATGCCT
1 CCATTTTGATTATGTAACAATTTGCCTAATTTGATTACGAGTTCCAAAGACTAAACTTTATGCCT
*
5655935 AATTTGCAGTTCATGTAGCAATTCAGATGTTGCTTTTGTTTCTTGTAATCAGATCGAACCAGAGT
66 AATTTGCAGTTCATGTAGCAATTCAGATGTTGCTTTTGTTTCTTGTAATCAAATCGAACCAGAGT
5656000 AAGATTGGTATGCTGATTAGTAGAATTTGAGTCCTCTTATCCTAGAAATGGATCTCATTGTAGCT
131 AAGATTGGTATGCTGATTAGTAGAATTTGAGTCCTCTTATCCTAGAAATGGATCTCATTGTAGCT
*
5656065 GGGAAACCACATGAAGCAGCATGGATGACATTCTTTTTTTTTACTTTTACTTTAGTATAGATGAC
196 GGGAAACCACATGAAGCAGCATGGATGACATTC-TTTTTCTT-CTTTTACTTTAGTATAGATGAC
*
5656130 ATTCAGTTGCTTGAAATGGGACAT
259 ATTCAGTTGCTTGAAATGAGACAT
*
5656154 CCATTTTGATTATGTAACAATTTGCCTAATTTGCTTACGAGTTCCAAAGACTAAACTTTATGCCT
1 CCATTTTGATTATGTAACAATTTGCCTAATTTGATTACGAGTTCCAAAGACTAAACTTTATGCCT
5656219 AATTTGCAGTTCATGTAGCAATTCAGATGTTGCTTTTGTTTCTTGTAATCAAATCGAACCAGAGT
66 AATTTGCAGTTCATGTAGCAATTCAGATGTTGCTTTTGTTTCTTGTAATCAAATCGAACCAGAGT
5656284 AAGATTGGTATGCTGATTAGTAGAATTTGAGTCCTCTTATCCTAGAAATGGATCTCATTGTAGCT
131 AAGATTGGTATGCTGATTAGTAGAATTTGAGTCCTCTTATCCTAGAAATGGATCTCATTGTAGCT
5656349 GGGAAACCACATGAAGCAGCATGGATGACATTCTTTTTCTTCTTTTACTTTAGTATAGATGACAT
196 GGGAAACCACATGAAGCAGCATGGATGACATTCTTTTTCTTCTTTTACTTTAGTATAGATGACAT
5656414 TCAGTTGCTTGAAATGAGACAT
261 TCAGTTGCTTGAAATGAGACAT
5656436 TTTTTGCTTA
Statistics
Matches: 278, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
282 45 0.16
283 7 0.03
284 226 0.81
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (282 bp):
CCATTTTGATTATGTAACAATTTGCCTAATTTGATTACGAGTTCCAAAGACTAAACTTTATGCCT
AATTTGCAGTTCATGTAGCAATTCAGATGTTGCTTTTGTTTCTTGTAATCAAATCGAACCAGAGT
AAGATTGGTATGCTGATTAGTAGAATTTGAGTCCTCTTATCCTAGAAATGGATCTCATTGTAGCT
GGGAAACCACATGAAGCAGCATGGATGACATTCTTTTTCTTCTTTTACTTTAGTATAGATGACAT
TCAGTTGCTTGAAATGAGACAT
Found at i:5661280 original size:22 final size:22
Alignment explanation
Indices: 5661255--5661300 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5661245 CCATGAACAT
5661255 ACTTCATGAATCATGCAAGCTA
1 ACTTCATGAATCATGCAAGCTA
5661277 ACTTCATGAATCATGCAAGCTA
1 ACTTCATGAATCATGCAAGCTA
5661299 AC
1 AC
5661301 AAACTCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (22 bp):
ACTTCATGAATCATGCAAGCTA
Found at i:5679373 original size:20 final size:20
Alignment explanation
Indices: 5679350--5679387 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5679340 CAGTGTTGGT
5679350 CTTTGGGTATCAATACTAAC
1 CTTTGGGTATCAATACTAAC
*
5679370 CTTTGGGTATCGATACTA
1 CTTTGGGTATCAATACTA
5679388 CTGGCTTGTT
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:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
CTTTGGGTATCAATACTAAC
Found at i:5681718 original size:22 final size:24
Alignment explanation
Indices: 5681673--5681726 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
5681663 AAGAACGTGC
* *
5681673 CACAAGAGCAGAGAGAAAATGTGT
1 CACAAGAGCAGAGAAAAAAAGTGT
5681697 CACAAGAGCA-A-AAAAAAAGTGT
1 CACAAGAGCAGAGAAAAAAAGTGT
5681719 CACAAGAG
1 CACAAGAG
5681727 TAGATGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 17 0.61
23 1 0.04
24 10 0.36
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (24 bp):
CACAAGAGCAGAGAAAAAAAGTGT
Found at i:5684828 original size:2 final size:2
Alignment explanation
Indices: 5684823--5684848 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5684813 GATTTGCTTA
5684823 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
5684849 TACAATTTTT
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:5685189 original size:15 final size:15
Alignment explanation
Indices: 5685169--5685212 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5685159 TACCCACCCT
5685169 GCATCCGCCCGCCCC
1 GCATCCGCCCGCCCC
*
5685184 GCATCCACCCGCCCC
1 GCATCCGCCCGCCCC
* *
5685199 ACATTCGCCCGCCC
1 GCATCCGCCCGCCC
5685213 AGCTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.11, C:0.64, G:0.16, T:0.09
Consensus pattern (15 bp):
GCATCCGCCCGCCCC
Found at i:5695481 original size:22 final size:22
Alignment explanation
Indices: 5695456--5695497 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5695446 TCAGATGTTA
5695456 TAACTCCC-GAAATTATATCATG
1 TAAC-CCCTGAAATTATATCATG
*
5695478 TAACCCCTGGAATTATATCA
1 TAACCCCTGAAATTATATCA
5695498 CGTATTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (22 bp):
TAACCCCTGAAATTATATCATG
Found at i:5697067 original size:29 final size:28
Alignment explanation
Indices: 5696971--5697184 Score: 146
Period size: 29 Copynumber: 7.4 Consensus size: 28
5696961 ACCCGATCCG
* *
5696971 GTGATATTTTGGGAATTATTTTGAAAAAT
1 GTGATATTTTGGAAATTATTTT-AAAAAA
* * * *
5697000 GTGACATTTAAGG-AATTATTTGGAAAAAG
1 GTGATATTT-TGGAAATTATTT-TAAAAAA
*
5697029 GTGACATTTTGGAAATTATTTTAAAAAA
1 GTGATATTTTGGAAATTATTTTAAAAAA
* *
5697057 GGTGATATTTTGGGAATTTTTTTTTAAAATAA
1 -GTGATATTTT-GGAA-ATTATTTTAAAA-AA
* * * * *
5697089 -TGACATTCTAGTAATTATTTTTAAAACA
1 GTGATATTTTGGAAATTA-TTTTAAAAAA
* *
5697117 -TGATATTTTGGGAATTATTTGTAAAATA
1 GTGATATTTTGGAAATTATTT-TAAAAAA
* *
5697145 GTGATATTTTCGTAATTATTTTTAATAAAA
1 GTGATATTTTGGAAATTA-TTTTAA-AAAA
5697175 GTGATATTTT
1 GTGATATTTT
5697185 TGTAATTTTT
Statistics
Matches: 148, Mismatches: 25, Indels: 23
0.76 0.13 0.12
Matches are distributed among these distances:
27 3 0.02
28 29 0.20
29 75 0.51
30 29 0.20
31 10 0.07
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.44
Consensus pattern (28 bp):
GTGATATTTTGGAAATTATTTTAAAAAA
Found at i:5697073 original size:58 final size:58
Alignment explanation
Indices: 5696971--5697184 Score: 218
Period size: 58 Copynumber: 3.7 Consensus size: 58
5696961 ACCCGATCCG
* * * * * ** *
5696971 GTGATATTTTGGGAATTATTTTGAAAAATGTGACATTTAAGGAATTATTTGGAAAA-A
1 GTGACATTTTGGTAATTATTTTTAAAAAAGTGATATTTTGGGAATTATTTGTAAAATA
* * *
5697028 GGTGACATTTTGGAAATTA-TTTTAAAAAAGGTGATATTTTGGGAATTTTTTTTTAAAATA
1 -GTGACATTTTGGTAATTATTTTTAAAAAA-GTGATATTTTGGGAA-TTATTTGTAAAATA
* * * *
5697088 ATGACATTCTAGTAATTATTTTTAAAACA-TGATATTTTGGGAATTATTTGTAAAATA
1 GTGACATTTTGGTAATTATTTTTAAAAAAGTGATATTTTGGGAATTATTTGTAAAATA
* *
5697145 GTGATATTTTCGTAATTATTTTTAATAAAAGTGATATTTT
1 GTGACATTTTGGTAATTATTTTTAA-AAAAGTGATATTTT
5697185 TGTAATTTTT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
57 41 0.32
58 45 0.35
59 32 0.25
60 10 0.08
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.44
Consensus pattern (58 bp):
GTGACATTTTGGTAATTATTTTTAAAAAAGTGATATTTTGGGAATTATTTGTAAAATA
Found at i:5697125 original size:87 final size:87
Alignment explanation
Indices: 5696970--5697166 Score: 222
Period size: 87 Copynumber: 2.3 Consensus size: 87
5696960 GACCCGATCC
*
5696970 GGTGATATTTTGGGAATTATTTTGAAAAATGTGACATTTAAGGAATTATTTGGAAAAAGGTGACA
1 GGTGATATTTTGGGAATTATTTTGAAAAATATGACATTTAAGGAATTATTTGGAAAAA-GTGACA
5697035 TTTTGGAAATTATTT-TAAAAAA
65 TTTTGGAAATTATTTGTAAAAAA
* ** * **
5697057 GGTGATATTTTGGGAATTTTTTTTTAAAATAATGACATTCT-AGTAATTATTTTTAAAACA-TGA
1 GGTGATATTTTGGGAATTATTTTGAAAAAT-ATGACATT-TAAGGAATTATTTGGAAAA-AGTGA
* * *
5697120 TATTTTGGGAATTATTTGTAAAATA
63 CATTTTGGAAATTATTTGTAAAAAA
* *
5697145 -GTGATATTTTCGTAATTATTTT
1 GGTGATATTTTGGGAATTATTTT
5697167 TAATAAAAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
87 64 0.69
88 27 0.29
89 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (87 bp):
GGTGATATTTTGGGAATTATTTTGAAAAATATGACATTTAAGGAATTATTTGGAAAAAGTGACAT
TTTGGAAATTATTTGTAAAAAA
Found at i:5711207 original size:20 final size:20
Alignment explanation
Indices: 5711182--5711219 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5711172 TTTTTCTTTA
5711182 TCTTTCATTATTAA-TTTTTC
1 TCTTTCATT-TTAACTTTTTC
5711202 TCTTTCATTTTAACTTTT
1 TCTTTCATTTTAACTTTT
5711220 ACATTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TCTTTCATTTTAACTTTTTC
Found at i:5712936 original size:15 final size:15
Alignment explanation
Indices: 5712916--5712946 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5712906 TGATACCCGA
5712916 TGATAATAATTTTGT
1 TGATAATAATTTTGT
5712931 TGATAATAATTTTGT
1 TGATAATAATTTTGT
5712946 T
1 T
5712947 AGCTAGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (15 bp):
TGATAATAATTTTGT
Found at i:5713959 original size:19 final size:19
Alignment explanation
Indices: 5713935--5713973 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5713925 TGCTGGCACT
*
5713935 GGACAGCTGTCACTGGACA
1 GGACAGCTGGCACTGGACA
5713954 GGACAGCTGGCACTGGACA
1 GGACAGCTGGCACTGGACA
5713973 G
1 G
5713974 CTGTCTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (19 bp):
GGACAGCTGGCACTGGACA
Found at i:5715811 original size:12 final size:12
Alignment explanation
Indices: 5715794--5715832 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5715784 CCGATTCGAC
5715794 CCGACCCGTTGA
1 CCGACCCGTTGA
*
5715806 CCGACCTGTTGA
1 CCGACCCGTTGA
*
5715818 CCCGACCCGGTGA
1 -CCGACCCGTTGA
5715831 CC
1 CC
5715833 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.15, C:0.44, G:0.26, T:0.15
Consensus pattern (12 bp):
CCGACCCGTTGA
Found at i:5715822 original size:13 final size:13
Alignment explanation
Indices: 5715791--5715832 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
5715781 GAACCGATTC
5715791 GACCCGACCCGTT
1 GACCCGACCCGTT
*
5715804 GA-CCGACCTGTT
1 GACCCGACCCGTT
*
5715816 GACCCGACCCGGT
1 GACCCGACCCGTT
5715829 GACC
1 GACC
5715833 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.17, C:0.43, G:0.26, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:5715986 original size:58 final size:56
Alignment explanation
Indices: 5715840--5716076 Score: 233
Period size: 57 Copynumber: 4.1 Consensus size: 56
5715830 ACCTTTTAAA
* *
5715840 AATTATTTTGAAAAATGTGATATTTTAGGAATTATTTTGAAAAATGTGACATTTTGAG-
1 AATTATTTT-AAAAATGTGACATTTTGGGAATTATTTT-AAAAATGTGACATTTTG-GT
* * *
5715898 AATTATTTTAAAAAAGTGACATTTTGGGAATTGTTTTAAAAATAGTGACATTCTGGT
1 AATTATTTTAAAAATGTGACATTTTGGGAATTATTTTAAAAAT-GTGACATTTTGGT
* ** *
5715955 AATTATTTTTAAAATGATGACATTTTGGGAATTATTTGTAAAACGGTGATATTTTGGT
1 AATTATTTTAAAAATG-TGACATTTTGGGAATTATTT-TAAAAATGTGACATTTTGGT
* * * * * * *
5716013 AATTATTTTTAATAAAGGTGATATTTTGGTATTTATTTTTAATAAAGGTGATATTTTTGT
1 AATTA-TTTTAA-AAATGTGACATTTTGGGAATTA-TTTTAA-AAATGTGACATTTTGGT
5716073 AATT
1 AATT
5716077 TTTGAATGTG
Statistics
Matches: 152, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
56 7 0.05
57 48 0.32
58 44 0.29
59 27 0.18
60 26 0.17
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.46
Consensus pattern (56 bp):
AATTATTTTAAAAATGTGACATTTTGGGAATTATTTTAAAAATGTGACATTTTGGT
Found at i:5716055 original size:30 final size:29
Alignment explanation
Indices: 5715840--5716076 Score: 221
Period size: 29 Copynumber: 8.1 Consensus size: 29
5715830 ACCTTTTAAA
* * *
5715840 AATTATTTTGAAAAATGTGATATTTTAGG-
1 AATTATTTTTAAAAAGGTGACATTTT-GGT
* *
5715869 AATTATTTTGAAAAATGTGACATTTTGAG-
1 AATTATTTTTAAAAAGGTGACATTTTG-GT
* *
5715898 AATTA-TTTTAAAAAAGTGACATTTTGGG
1 AATTATTTTTAAAAAGGTGACATTTTGGT
* * *
5715926 AATT-GTTTTAAAAATAGTGACATTCTGGT
1 AATTATTTTTAAAAA-GGTGACATTTTGGT
* * *
5715955 AATTATTTTTAAAATGATGACATTTTGGG
1 AATTATTTTTAAAAAGGTGACATTTTGGT
* * *
5715984 AATTATTTGTAAAACGGTGATATTTTGGT
1 AATTATTTTTAAAAAGGTGACATTTTGGT
*
5716013 AATTATTTTTAATAAAGGTGATATTTTGGT
1 AATTATTTTTAA-AAAGGTGACATTTTGGT
* * *
5716043 ATTTATTTTTAATAAAGGTGATATTTTTGT
1 AATTATTTTTAA-AAAGGTGACATTTTGGT
5716073 AATT
1 AATT
5716077 TTTGAATGTG
Statistics
Matches: 181, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.01
28 33 0.18
29 92 0.51
30 55 0.30
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.46
Consensus pattern (29 bp):
AATTATTTTTAAAAAGGTGACATTTTGGT
Found at i:5727278 original size:14 final size:14
Alignment explanation
Indices: 5727259--5727301 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
5727249 TTCAACTCAA
5727259 TCTGAGTCAACCTG
1 TCTGAGTCAACCTG
5727273 TCTGAGTCAA-CTCG
1 TCTGAGTCAACCT-G
*
5727287 TCCGAGTCAACCTG
1 TCTGAGTCAACCTG
5727301 T
1 T
5727302 TGACTTTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (14 bp):
TCTGAGTCAACCTG
Found at i:5740493 original size:20 final size:21
Alignment explanation
Indices: 5740429--5740494 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
5740419 GGTTAAGACA
5740429 TTTCGATGAAAAGACTTAACC
1 TTTCGATGAAAAGACTTAACC
** * **
5740450 TTTTAATTAAAAGACTTATTC
1 TTTCGATGAAAAGACTTAACC
5740471 TTTCGATGAAAAG-CTTAACC
1 TTTCGATGAAAAGACTTAACC
5740491 TTTC
1 TTTC
5740495 CTGAAAGGAT
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (21 bp):
TTTCGATGAAAAGACTTAACC
Found at i:5742693 original size:2 final size:2
Alignment explanation
Indices: 5742688--5742721 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5742678 TAAGAGAGTA
5742688 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
5742722 GTATGTATGT
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:5742726 original size:4 final size:4
Alignment explanation
Indices: 5742719--5745978 Score: 5630
Period size: 4 Copynumber: 836.8 Consensus size: 4
5742709 TATATATATA
5742719 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5742767 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5742815 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5742863 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5742911 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5742958 TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743005 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5743052 TATG TATG TATG TATG TATG TATG TATG TATG TAT- TATG GATG TA-G
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743098 TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743144 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743190 TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TA-G
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
5743235 TATG TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATA TGTA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743282 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743330 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743378 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743424 TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743470 TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5743516 T-TG TATG TAGG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743563 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743610 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743658 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743705 TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATGG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT-G
5743752 ATATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG
1 -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5743799 TATG TATG TATG TA-G TATG TATG TATG TATG TCTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743846 TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5743893 TATG TATG TATG TATG TATG TATG TATG TATG GATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5743941 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA--
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5743987 TATG TATG TATG TAGG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744035 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5744083 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAGG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744131 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744179 TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744226 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744274 TATG TATG TATG -ATG TATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744320 TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744366 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T-TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744411 TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744457 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744505 TATG -ATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744552 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG -ATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744599 TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744645 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744692 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5744739 TATG TGTAG TATG TATG T-TG TATG TATG TATG TATG TATG --TG TATG
1 TATG TAT-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744785 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744833 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5744880 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TCTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744928 TATG TATG TATG TATG TA-G TA-G TATG TATG TATG TATG TATG -ATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5744973 TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5745017 TAT- TATG TATG TCTG TATG TA-- TATG T-TG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745060 TATG TATG TATG TATTG TATG TATG TATG TA-- TATG TATG TATG TATG
1 TATG TATG TATG TA-TG TATG TATG TATG TATG TATG TATG TATG TATG
5745107 TATG TATG TATG TATG TATG TTATG TATG TATG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG -TATG TATG TATG TATG TATG TATG TATG
5745155 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745203 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5745251 T-CG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745294 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745342 TA-G TATG TATG TATG --TG TATG TATG TATG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745386 TATG TA-G TATG TATG TATG TATG T-TG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745430 TATG TATG TATG TATG TATG TATG TATG T-TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745477 TATG --TG TATG TATG --TG TATG TATG TATG TCTATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG --TATG TATG TATG TATG
5745523 TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5745569 TATG TATG TATG TATG TATG --TG TATG TCTG TATG TATG T-TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
5745614 TATG TATG TA-G TATG TAGG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745661 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745708 TATG TATG TATG TA-G TATG TATG TTATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG -TATG TATG TATG TATG TATG TATG
* *
5745756 TCTG TATG TATG TATG TATG --TG TATG TATG TCTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745802 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745850 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745898 TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
5745944 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
5745979 AAATGGCGTG
Statistics
Matches: 3122, Mismatches: 32, Indels: 204
0.93 0.01 0.06
Matches are distributed among these distances:
2 54 0.02
3 122 0.04
4 2922 0.94
5 17 0.01
6 7 0.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:5748951 original size:7 final size:7
Alignment explanation
Indices: 5748939--5748963 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5748929 GGTCAAAGGA
5748939 GGTCAAC
1 GGTCAAC
5748946 GGTCAAC
1 GGTCAAC
5748953 GGTCAAC
1 GGTCAAC
5748960 GGTC
1 GGTC
5748964 GGGTCGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:5756017 original size:13 final size:14
Alignment explanation
Indices: 5755999--5756029 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5755989 GGTCAAAGGA
5755999 GGTCAACGGTC-AC
1 GGTCAACGGTCAAC
5756012 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
5756026 GGTC
1 GGTC
5756030 GGGTCGGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:5756020 original size:7 final size:7
Alignment explanation
Indices: 5755999--5756029 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5755989 GGTCAAAGGA
5755999 GGTCAAC
1 GGTCAAC
5756006 GGTC-AC
1 GGTCAAC
5756012 GGTCAAC
1 GGTCAAC
5756019 GGTCAAC
1 GGTCAAC
5756026 GGTC
1 GGTC
5756030 GGGTCGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:5756079 original size:19 final size:19
Alignment explanation
Indices: 5756057--5756135 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 19
5756047 TCGGGTCGGG
*
5756057 TCAGCCCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
** *
5756076 TCAGACCGGTCAGTCTGGT
1 TCAGACCGGTCAAACCGGT
* *
5756095 TCGGACCGGTCAAAACCGAT
1 TCAGACCGGTC-AAACCGGT
*
5756115 TCAAAACCGGTCAAACCGGT
1 TC-AGACCGGTCAAACCGGT
5756135 T
1 T
5756136 TTCAGCCACT
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 25 0.54
20 14 0.30
21 7 0.15
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:5757087 original size:28 final size:29
Alignment explanation
Indices: 5756934--5757069 Score: 186
Period size: 29 Copynumber: 4.7 Consensus size: 29
5756924 TTCTATGAAC
* * **
5756934 TTTTGTATTTTATTGTAATTTATAAAATA-
1 TTTTGTACTTTATTGTAAATTCCAAAA-AG
*
5756963 TTTTGTAATTTATTGTAAATTCCAAAAAG
1 TTTTGTACTTTATTGTAAATTCCAAAAAG
5756992 TTTTGTACTTTATTGTAAATTCCAAAAAG
1 TTTTGTACTTTATTGTAAATTCCAAAAAG
*
5757021 TTTTGTATTTTATTGTAAATTCCAAAAAG
1 TTTTGTACTTTATTGTAAATTCCAAAAAG
*
5757050 TTTTG-CCTTTATTGTAAATT
1 TTTTGTACTTTATTGTAAATT
5757070 TTAAAATGTT
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.14
29 84 0.86
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (29 bp):
TTTTGTACTTTATTGTAAATTCCAAAAAG
Found at i:5757089 original size:57 final size:58
Alignment explanation
Indices: 5756934--5757091 Score: 212
Period size: 58 Copynumber: 2.7 Consensus size: 58
5756924 TTCTATGAAC
* * *
5756934 TTTTGTATTTTATTGT-AATTTATAAAATATTTTGTAATTTATTGTAAATTCCAAAAAG
1 TTTTGTACTTTATTGTAAATTT-TAAAATGTTTTGTATTTTATTGTAAATTCCAAAAAG
** *
5756992 TTTTGTACTTTATTGTAAATTCCAAAAAGTTTTGTATTTTATTGTAAATTCCAAAAAG
1 TTTTGTACTTTATTGTAAATTTTAAAATGTTTTGTATTTTATTGTAAATTCCAAAAAG
* **
5757050 TTTTG-CCTTTATTGTAAATTTTAAAATGTTTTGCCTTTTATT
1 TTTTGTACTTTATTGTAAATTTTAAAATGTTTTGTATTTTATT
5757092 ATAATTTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 31 0.36
58 52 0.60
59 4 0.05
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (58 bp):
TTTTGTACTTTATTGTAAATTTTAAAATGTTTTGTATTTTATTGTAAATTCCAAAAAG
Found at i:5757097 original size:28 final size:28
Alignment explanation
Indices: 5756971--5757100 Score: 100
Period size: 29 Copynumber: 4.6 Consensus size: 28
5756961 TATTTTGTAA
* ** *
5756971 TTTATTGTAAATTCCAAAAAGTTTTGTAC
1 TTTATTATAAATTTTAAAAAGTTTTG-CC
* ** **
5757000 TTTATTGTAAATTCCAAAAAGTTTTGTAT
1 TTTATTATAAATTTTAAAAAGTTTTG-CC
* **
5757029 TTTATTGTAAATTCCAAAAAGTTTTGCC
1 TTTATTATAAATTTTAAAAAGTTTTGCC
* *
5757057 TTTATTGTAAATTTTAAAATGTTTTGCC
1 TTTATTATAAATTTTAAAAAGTTTTGCC
5757085 TTTTATTAT-AATTTTA
1 -TTTATTATAAATTTTA
5757101 TATTTTTTAT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
28 32 0.34
29 61 0.66
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.50
Consensus pattern (28 bp):
TTTATTATAAATTTTAAAAAGTTTTGCC
Found at i:5760907 original size:27 final size:28
Alignment explanation
Indices: 5760842--5760907 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 28
5760832 TGAGTCATTG
5760842 AAGTTAAAATTTTCAATTATGAGAATTCT
1 AAGTTAAAA-TTTCAATTATGAGAATTCT
* * * *
5760871 ACGTTGAAATTT-AATATTTG-GAATTTT
1 AAGTTAAAATTTCAAT-TATGAGAATTCT
5760898 AAGTTAAAAT
1 AAGTTAAAAT
5760908 GTTGATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
27 17 0.57
28 6 0.20
29 7 0.23
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (28 bp):
AAGTTAAAATTTCAATTATGAGAATTCT
Found at i:5764401 original size:19 final size:20
Alignment explanation
Indices: 5764379--5764424 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5764369 TGGTTTCGAC
5764379 CGGTTC-GAACCGGTTTGAA
1 CGGTTCTGAACCGGTTTGAA
*
5764398 CGG-TCTGAACCGGTTTGAT
1 CGGTTCTGAACCGGTTTGAA
5764417 CGG-TCTGA
1 CGGTTCTGA
5764425 CCCGAACGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (20 bp):
CGGTTCTGAACCGGTTTGAA
Found at i:5764449 original size:5 final size:5
Alignment explanation
Indices: 5764434--5764510 Score: 64
Period size: 5 Copynumber: 14.2 Consensus size: 5
5764424 ACCCGAACGA
* * *
5764434 CCGAC CTGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC
1 CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C--CGAC CCGAC
*
5764483 CCGAC CCGAC CGTTGAC CCGAC CCGAC C
1 CCGAC CCGAC C--CGAC CCGAC CCGAC C
5764511 GTTGACCGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
5 46 0.79
7 12 0.21
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (5 bp):
CCGAC
Found at i:5764459 original size:22 final size:22
Alignment explanation
Indices: 5764434--5764510 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
5764424 ACCCGAACGA
*
5764434 CCGACCTGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
5764456 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
5764478 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
5764500 CCGACCCGACC
1 CCGACCCGACC
5764511 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:5764461 original size:17 final size:17
Alignment explanation
Indices: 5764458--5764517 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 17
5764448 CCGTTGACCC
5764458 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
5764475 GACCCGACCCGACCCGACCGTT
1 G-----ACCCGACCCGACCGTT
5764497 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
5764514 GACC
1 GACC
5764518 GTTGACTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 21 0.55
22 17 0.45
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.10
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:5771590 original size:9 final size:9
Alignment explanation
Indices: 5771577--5771645 Score: 84
Period size: 9 Copynumber: 7.3 Consensus size: 9
5771567 GCTGCTGGAA
*
5771577 ACCGGTTTA
1 ACCGGTTTG
5771586 ACCGGTTCTG
1 ACCGGTT-TG
5771596 ACCGGTTTG
1 ACCGGTTTG
5771605 ACCGGTTTCG
1 ACCGGTTT-G
*
5771615 ACCGGTTCG
1 ACCGGTTTG
5771624 AACCGGTTTG
1 -ACCGGTTTG
*
5771634 ACCGGTCTG
1 ACCGGTTTG
5771643 ACC
1 ACC
5771646 CGACCGACCG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
9 29 0.55
10 24 0.45
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5771601 original size:19 final size:18
Alignment explanation
Indices: 5771577--5771639 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
5771567 GCTGCTGGAA
5771577 ACCGGTTTAACCGGTTCTG
1 ACCGGTTTAACCGGTT-TG
*
5771596 ACCGGTTTGACCGGTTTCG
1 ACCGGTTTAACCGGTTT-G
*
5771615 ACCGGTTCGAACCGGTTTG
1 ACCGGTT-TAACCGGTTTG
5771634 ACCGGT
1 ACCGGT
5771640 CTGACCCGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 1 0.03
19 30 0.77
20 8 0.21
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (18 bp):
ACCGGTTTAACCGGTTTG
Found at i:5771622 original size:29 final size:29
Alignment explanation
Indices: 5771578--5771645 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
5771568 CTGCTGGAAA
*
5771578 CCGGTTTAACCGGTTCTG-ACCGGTTTGA
1 CCGGTTTGACCGGTTCTGAACCGGTTTGA
5771606 CCGGTTTCGACCGGTTC-GAACCGGTTTGA
1 CCGGTTT-GACCGGTTCTGAACCGGTTTGA
*
5771635 CCGGTCTGACC
1 CCGGTTTGACC
5771646 CGACCGACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.28
Consensus pattern (29 bp):
CCGGTTTGACCGGTTCTGAACCGGTTTGA
Found at i:5771661 original size:5 final size:5
Alignment explanation
Indices: 5771642--5771690 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
5771632 TGACCGGTCT
*
5771642 GACCC GA-CC GA-CC GACCC GACCC GACCC GACCGTT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC
5771691 GTTGACTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
7 4 0.10
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:5771682 original size:17 final size:17
Alignment explanation
Indices: 5771660--5771696 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5771650 CGACCGACCC
5771660 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
5771677 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
5771694 GAC
1 GAC
5771697 TGTTGACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:5774505 original size:64 final size:65
Alignment explanation
Indices: 5774437--5774589 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 65
5774427 GCACTTGGGA
* * *
5774437 TGCATCGGTGCACTAATTTGC-TTCGATGTTTCAAAATAG-TC-GGGGTGCATCAATGCATGACT
1 TGCATCGGTGCACTAA-ATGCATTCGATGTTTCAAAAT-GTTCAGGAGTGCATCAATACATGACT
5774499 TG
64 TG
* * *
5774501 TGCATCGATGCACTAAATGCATTCGATGTTTCAAAATGTTCAGGAGTGCATCGATACATGGCTTG
1 TGCATCGGTGCACTAAATGCATTCGATGTTTCAAAATGTTCAGGAGTGCATCAATACATGACTTG
* * *
5774566 TGCATCAGTGCATTAAATGTATTC
1 TGCATCGGTGCACTAAATGCATTC
5774590 AAAATTCAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 4 0.05
64 33 0.43
65 39 0.51
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (65 bp):
TGCATCGGTGCACTAAATGCATTCGATGTTTCAAAATGTTCAGGAGTGCATCAATACATGACTTG
Found at i:5784255 original size:12 final size:12
Alignment explanation
Indices: 5784238--5784280 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5784228 TATCTTTTAA
5784238 AGCAACAACCAC
1 AGCAACAACCAC
* **
5784250 AGCAACAAACGT
1 AGCAACAACCAC
5784262 A-CAACAACCAC
1 AGCAACAACCAC
5784273 AGCAACAA
1 AGCAACAA
5784281 ACATGCAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.53, C:0.35, G:0.09, T:0.02
Consensus pattern (12 bp):
AGCAACAACCAC
Found at i:5784267 original size:23 final size:23
Alignment explanation
Indices: 5784240--5784291 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
5784230 TCTTTTAAAG
*
5784240 CAACAACCACAGCAACAAACGTA
1 CAACAACCACAGCAACAAACATA
*
5784263 CAACAACCACAGCAACAAACATG
1 CAACAACCACAGCAACAAACATA
5784286 CAACAA
1 CAACAA
5784292 TCGAGCAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.35, G:0.08, T:0.04
Consensus pattern (23 bp):
CAACAACCACAGCAACAAACATA
Found at i:5784738 original size:2 final size:2
Alignment explanation
Indices: 5784731--5784774 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
5784721 TTTATTAATT
* *
5784731 TA TA TA TA TA TA TT TA CTA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
5784774 T
1 T
5784775 TATTTTTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5784804 original size:5 final size:5
Alignment explanation
Indices: 5784786--5784943 Score: 57
Period size: 5 Copynumber: 31.6 Consensus size: 5
5784776 ATTTTTACTT
* * *
5784786 TTTTA TTATTA TTTTA -TTT- TTTTG TTTTA -TTTA -TATA TTTTA TTCT-
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * *
5784832 TTTT- CTTTA TTTTT TTTTA TATTTA TTTTA CTTACTA TTTTA TCTTTG
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA -TT-TTA TTTTA T-TTTA
* * * *
5784880 TTTT- CTTTA TCTTATC TTTTA TTTAA TTTTT TTCTTCA TTTTAA TTTTA
1 TTTTA TTTTA T-TT-TA TTTTA TTTTA TTTTA TT-TT-A TTTT-A TTTTA
5784929 -TTTA -TTTA -TTTA TTT
1 TTTTA TTTTA TTTTA TTT
5784944 CTTACCTTTT
Statistics
Matches: 117, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
4 34 0.29
5 46 0.39
6 31 0.26
7 6 0.05
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:5784813 original size:13 final size:12
Alignment explanation
Indices: 5784774--5784860 Score: 59
Period size: 13 Copynumber: 6.8 Consensus size: 12
5784764 TATATATATA
5784774 TTATTTTTACTTTT
1 TTATTTTT--TTTT
* *
5784788 TTA-TTATTATT
1 TTATTTTTTTTT
5784799 TTATTTTTTTGTT
1 TTATTTTTTT-TT
* *
5784812 TTATTTATATATT
1 TTATTT-TTTTTT
*
5784825 TTATTCTTTTTCT
1 TTATT-TTTTTTT
5784838 TTATTTTTTTTT
1 TTATTTTTTTTT
*
5784850 ATATTTATTTT
1 TTATTT-TTTT
5784861 ACTTACTATT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
11 6 0.11
12 15 0.26
13 30 0.53
14 6 0.11
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (12 bp):
TTATTTTTTTTT
Found at i:5784813 original size:26 final size:25
Alignment explanation
Indices: 5784772--5784860 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 25
5784762 TATATATATA
5784772 TATTATTTTTACTTTTTTATTATTATTT
1 TATT-TTTTT-CTTTTTT-TTATTATTT
* *
5784800 TATTTTTTTGTTTTATTTATATATTT
1 TATTTTTTTCTTTTTTTTAT-TATTT
*
5784826 TATTCTTTTTCTTTATTTTTTTTTATATT
1 TATT-TTTTTC-TT-TTTTTTATTAT-TT
5784855 TATTTT
1 TATTTT
5784861 ACTTACTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
25 4 0.08
26 14 0.27
27 10 0.20
28 11 0.22
29 12 0.24
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (25 bp):
TATTTTTTTCTTTTTTTTATTATTT
Done.