Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 51
Found at i:4134182 original size:20 final size:20
Alignment explanation
Indices: 4134159--4134214 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
4134149 TCTGAAACTT
4134159 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
4134179 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
4134199 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
4134215 TTTAACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:4134659 original size:22 final size:22
Alignment explanation
Indices: 4134632--4134673 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4134622 GAGATAGACG
4134632 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
*
4134654 GATTTCGTCGGAGATGGGGA
1 GATTTCGCCGGAGATGGGGA
4134674 TGGATGTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.43, T:0.24
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACT
Found at i:4134926 original size:20 final size:20
Alignment explanation
Indices: 4134849--4134966 Score: 112
Period size: 20 Copynumber: 5.9 Consensus size: 20
4134839 GCGCTTTGAA
* *
4134849 AATCCCATTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
* * *
4134869 CATCGCGTTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
* *
4134889 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
4134909 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
4134929 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
*
4134949 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
4134967 GGAAAATCGC
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 81 0.98
21 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:4142665 original size:3 final size:3
Alignment explanation
Indices: 4142645--4142741 Score: 51
Period size: 3 Copynumber: 32.0 Consensus size: 3
4142635 TACGGATGAC
* *
4142645 ATA AT- ATA ATA TATA ATA ATA CTA AGTA ATA ATA ATA AT- ATA ATG
1 ATA ATA ATA ATA -ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * * *
4142690 ATA ATTA AGAA ATA CTAA ATA ATA AGTA ATA A-A A-A ATA TTA AT- GTA
1 ATA A-TA A-TA ATA AT-A ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
4142736 ATA ATA
1 ATA ATA
4142742 CACTAATACT
Statistics
Matches: 72, Mismatches: 13, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
2 9 0.12
3 47 0.65
4 16 0.22
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4142738 original size:18 final size:17
Alignment explanation
Indices: 4142706--4142739 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4142696 AAGAAATACT
4142706 AAATAATAAGTAATAAA
1 AAATAATAAGTAATAAA
*
4142723 AAATATTAATGTAATAA
1 AAATAATAA-GTAATAA
4142740 TACACTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
AAATAATAAGTAATAAA
Found at i:4142742 original size:38 final size:37
Alignment explanation
Indices: 4142658--4142742 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 37
4142648 ATATAATATA
* *
4142658 TAATAATACTAAGTAATAATAATAATATAATGATAAT
1 TAATAATACTAAATAATAATAATAATAAAATGATAAT
*
4142695 TAAGAAATACTAAATAATAAGTAATAA-AAAAT-ATTAAT
1 TAA-TAATACTAAATAATAA-TAATAATAAAATGA-TAAT
4142733 GTAATAATAC
1 -TAATAATAC
4142743 ACTAATACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
37 4 0.10
38 27 0.68
39 9 0.22
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (37 bp):
TAATAATACTAAATAATAATAATAATAAAATGATAAT
Found at i:4145522 original size:20 final size:21
Alignment explanation
Indices: 4145482--4145523 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4145472 ACAAATGAGA
4145482 ATGTTGTGGCAAAATGAAATGG
1 ATGTTGTGG-AAAATGAAATGG
*
4145504 ATGTTGTGG-AAATGGAATGG
1 ATGTTGTGGAAAATGAAATGG
4145524 TGGTGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAAATGG
Found at i:4155975 original size:37 final size:37
Alignment explanation
Indices: 4155931--4156034 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
4155921 CTTTTCGTCC
*
4155931 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* * *
4155968 TGCTAGGATTCAAACTCCTAAAAATATGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
4156005 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
4156035 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:4156527 original size:2 final size:2
Alignment explanation
Indices: 4156520--4156578 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
4156510 TTATTCCTAT
4156520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4156562 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
4156579 TATTATTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4156584 original size:3 final size:3
Alignment explanation
Indices: 4156576--4156607 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4156566 TATATATATA
4156576 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4156608 CTATGTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:4156638 original size:12 final size:12
Alignment explanation
Indices: 4156621--4156645 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4156611 TGTTTACTTA
4156621 TTTACTATATTT
1 TTTACTATATTT
4156633 TTTACTATATTT
1 TTTACTATATTT
4156645 T
1 T
4156646 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTACTATATTT
Found at i:4156705 original size:29 final size:29
Alignment explanation
Indices: 4156658--4156748 Score: 71
Period size: 29 Copynumber: 3.0 Consensus size: 29
4156648 TAACGTTATA
*
4156658 TATATATATATATTCTTACTTTATTTTATTT
1 TATAT-TATATA-TGTTACTTTATTTTATTT
* *
4156689 TATATT-TCTATGATTACTATT-TTTTAGTT
1 TATATTATATATG-TTACT-TTATTTTATTT
*
4156718 AATATTATATATGTATA-TTTATTTTTATTT
1 TATATTATATATGT-TACTTTA-TTTTATTT
4156748 T
1 T
4156749 TTTATTATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
28 3 0.06
29 22 0.47
30 17 0.36
31 5 0.11
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (29 bp):
TATATTATATATGTTACTTTATTTTATTT
Found at i:4156816 original size:24 final size:24
Alignment explanation
Indices: 4156719--4156841 Score: 74
Period size: 24 Copynumber: 5.0 Consensus size: 24
4156709 TTTTTAGTTA
* *
4156719 ATATTATATATGTATATTTATTTTT
1 ATATT-TATATATATATATATTTTT
* * *
4156744 ATTTTTTTAT-TAT-TATTACTATTT
1 ATATTTATATATATATA-TA-TTTTT
* *
4156768 AGTATTTTATTATATACATACATTTTT
1 A-TA-TTTA-TATATATATATATTTTT
4156795 ATATTTATATATATATATA-TTTT
1 ATATTTATATATATATATATTTTT
* *
4156818 ATTATTTATTTATAT-TATTTTTTT
1 A-TATTTATATATATATATATTTTT
4156842 TTCATTATTT
Statistics
Matches: 76, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
22 1 0.01
23 13 0.17
24 35 0.46
25 9 0.12
26 5 0.07
27 8 0.11
28 3 0.04
29 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
ATATTTATATATATATATATTTTT
Found at i:4156835 original size:16 final size:16
Alignment explanation
Indices: 4156517--4156604 Score: 64
Period size: 14 Copynumber: 5.8 Consensus size: 16
4156507 ATATTATTCC
*
4156517 TATTATATATATATA-
1 TATTATATATTTATAT
*
4156532 TA-TATATATATATA-
1 TATTATATATTTATAT
*
4156546 TA-TATATATATATAT
1 TATTATATATTTATAT
*
4156561 ATATATATATATATATAT
1 -TAT-TATATATTTATAT
4156579 TATTAT-TA-TTATTAT
1 TATTATATATTTA-TAT
4156594 TATTAT-TATTT
1 TATTATATATTT
4156605 TATCTATGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
14 28 0.42
15 15 0.23
16 7 0.11
17 3 0.05
18 13 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATATATTTATAT
Found at i:4157831 original size:20 final size:20
Alignment explanation
Indices: 4157806--4157849 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4157796 AAGGGTCTGG
4157806 CAAGCCCAAGGGGGCACCGA
1 CAAGCCCAAGGGGGCACCGA
*
4157826 CAAGCCCAAGGGGGCACCGG
1 CAAGCCCAAGGGGGCACCGA
4157846 CAAG
1 CAAG
4157850 GAGAACTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.36, T:0.00
Consensus pattern (20 bp):
CAAGCCCAAGGGGGCACCGA
Found at i:4160405 original size:16 final size:14
Alignment explanation
Indices: 4160364--4160405 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 14
4160354 CAAAAAGGGC
4160364 AAAAACAAAAAAGA
1 AAAAACAAAAAAGA
4160378 AAAGAAGCAAAAAAGA
1 AAA-AA-CAAAAAAGA
4160394 AGAAAACAAAAA
1 A-AAAACAAAAA
4160406 TCAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 8 0.32
16 12 0.48
17 2 0.08
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAGA
Found at i:4162143 original size:106 final size:106
Alignment explanation
Indices: 4162021--4163079 Score: 1625
Period size: 106 Copynumber: 10.0 Consensus size: 106
4162011 GTGCCACTTG
* * *
4162021 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCCCAAAT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATT
4162085 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
4162127 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACCACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
4162192 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * *
4162233 AGACAAAGCAAGTTCAACTTCACGACAAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
4162298 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* ** *
4162339 AGACAACGCAAGTTCAACTTCATGACGAAGGGACTACTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
4162404 CAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
4162445 AGACAACGCAAGTTCAACTTCACGACGAAGAGACCGCCGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
4162510 CAGAGCCAATTTCAACTTCACAACGATGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
4162551 AGACAACGCAAGTTCAACTTCAGGACGAATGAACAGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
4162616 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
4162657 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* ** *
4162722 CGGAGCCAATTTCAACTTCACAGTGAAAGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
4162763 AGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* **
4162828 CGGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
4162869 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
4162934 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * * * *
4162975 AGACAACACAAGTTCAACTTCACAACGAAAGGACGGCTGGTTGTCAACAAACAATTTCCCGATTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
4163040 CAGAGCCAATTTCAACTTTACGACGGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
4163080 AAAACAATGC
Statistics
Matches: 876, Mismatches: 76, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
106 874 1.00
107 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:4163919 original size:37 final size:37
Alignment explanation
Indices: 4163829--4163925 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
4163819 CCTTTTCGTC
*
4163829 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
4163866 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
4163903 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
4163926 GATAAGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:4164515 original size:2 final size:2
Alignment explanation
Indices: 4164508--4164534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4164498 TTTTCCTAAC
4164508 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4164535 TCTTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4164661 original size:13 final size:14
Alignment explanation
Indices: 4164645--4164703 Score: 59
Period size: 13 Copynumber: 4.1 Consensus size: 14
4164635 TTATACATAC
4164645 ATTTTATATT-TTT
1 ATTTTATATTATTT
4164658 ATTTT-TATTATTT
1 ATTTTATATTATTT
4164671 ATTTATACTATTTATTT
1 ATTT-TA-TA-TTATTT
*
4164688 ATTTTCATATTTTTT
1 ATTTT-ATATTATTT
4164703 A
1 A
4164704 GTTTCTTTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 4 0.10
13 12 0.31
14 1 0.03
15 6 0.15
16 5 0.13
17 11 0.28
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTATATTATTT
Found at i:4164809 original size:20 final size:19
Alignment explanation
Indices: 4164782--4164837 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
4164772 TTTTATCTTC
4164782 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
4164801 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
4164821 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
4164838 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:4168401 original size:19 final size:19
Alignment explanation
Indices: 4168373--4168414 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
4168363 AAAACCAGAA
*
4168373 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGAATCGATT
*
4168391 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGATT
4168410 CCCCT
1 CCCCT
4168415 TCAAAGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.14, C:0.33, G:0.31, T:0.21
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGATT
Found at i:4189928 original size:23 final size:23
Alignment explanation
Indices: 4189902--4189963 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
4189892 TCAGCTGTTA
4189902 TAACTCCTGAAATTAAATCATTG
1 TAACTCCTGAAATTAAATCATTG
*
4189925 TAACTCCTGAAATTAAATCATTT
1 TAACTCCTGAAATTAAATCATTG
* *
4189948 TAACTCTTGATATTAA
1 TAACTCCTGAAATTAA
4189964 CAGCTTGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (23 bp):
TAACTCCTGAAATTAAATCATTG
Found at i:4193473 original size:29 final size:29
Alignment explanation
Indices: 4193431--4193487 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
4193421 TTTTCACCTA
4193431 ACTAAATTGATGTAAGCAATGACATCAAT
1 ACTAAATTGATGTAAGCAATGACATCAAT
4193460 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTGATGTAAGCAATGACATCAA
4193488 ATTAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGACATCAAT
Found at i:4198163 original size:29 final size:29
Alignment explanation
Indices: 4198121--4198177 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
4198111 TTTTCACCTA
4198121 ACTAAATTGATGTAAGCAATGACATCAAT
1 ACTAAATTGATGTAAGCAATGACATCAAT
4198150 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTGATGTAAGCAATGACATCAA
4198178 ATTAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGACATCAAT
Found at i:4199876 original size:40 final size:40
Alignment explanation
Indices: 4199821--4199902 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
4199811 CAACGATTGG
4199821 ATGGCCACCCATCTCCAACAATCTGCGGGATCAAATCAGT
1 ATGGCCACCCATCTCCAACAATCTGCGGGATCAAATCAGT
4199861 ATGGCCACCCATCTCCAACAATCTGCGGGATCAAATCAGT
1 ATGGCCACCCATCTCCAACAATCTGCGGGATCAAATCAGT
4199901 AT
1 AT
4199903 CCTTCAACGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (40 bp):
ATGGCCACCCATCTCCAACAATCTGCGGGATCAAATCAGT
Found at i:4206807 original size:36 final size:36
Alignment explanation
Indices: 4206757--4206832 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
4206747 TTATAGCAAA
*
4206757 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
*
4206793 AAAAATCGTATTTATTCGAATTTTGCCAAAAATATC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
4206829 AAAA
1 AAAA
4206833 TCCCGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:4208904 original size:23 final size:23
Alignment explanation
Indices: 4208878--4208930 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
4208868 GGATAAGAAA
*
4208878 TCATTAAGAATAAATATTCCATC
1 TCATTAAGAATAAATATTCAATC
4208901 TCATTAAGAATAAATATTCAATC
1 TCATTAAGAATAAATATTCAATC
4208924 TCATTAA
1 TCATTAA
4208931 TCGGTGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (23 bp):
TCATTAAGAATAAATATTCAATC
Found at i:4209921 original size:21 final size:21
Alignment explanation
Indices: 4209895--4209965 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
4209885 ATTCAAAAAT
* * *
4209895 TTTTAGTAGTTGCAATCAATC
1 TTTTAGTAGCTACTATCAATC
4209916 TTTTAGTAGCTACTATCAATC
1 TTTTAGTAGCTACTATCAATC
4209937 TTTTAGTAGCTACTATCAATC
1 TTTTAGTAGCTACTATCAATC
4209958 TTTTAGTA
1 TTTTAGTA
4209966 ACACTAATGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.45
Consensus pattern (21 bp):
TTTTAGTAGCTACTATCAATC
Found at i:4212772 original size:2 final size:2
Alignment explanation
Indices: 4212760--4212799 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
4212750 TTGTATAATG
4212760 TA TA TA T- TA TA TA -A TA 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
4212799 T
1 T
4212800 TATTTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4214008 original size:37 final size:37
Alignment explanation
Indices: 4213967--4214054 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
4213957 TTGTTTTTAA
* * *
4213967 TATTTTTATTT-TTGGTTTATTATTATTATTATTTATT
1 TATTTATATTTATTAGTTTATT-TTATTATTATTTACT
* *
4214004 TATTTATATTTATTATTTTATTTTATTCTTATTTACT
1 TATTTATATTTATTAGTTTATTTTATTATTATTTACT
* *
4214041 TATATATTTTTATT
1 TATTTATATTTATT
4214055 TATATATGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 35 0.81
38 8 0.19
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (37 bp):
TATTTATATTTATTAGTTTATTTTATTATTATTTACT
Found at i:4214058 original size:14 final size:14
Alignment explanation
Indices: 4213982--4214075 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
4213972 TTATTTTTGG
4213982 TTTA-TTAT-TATT
1 TTTATTTATATATT
* *
4213994 ATTATTTATTTATT
1 TTTATTTATATATT
*
4214008 TATATTTAT-TA-T
1 TTTATTTATATATT
*
4214020 TTTATTT-TATTCTT
1 TTTATTTATA-TATT
*
4214034 ATTTACTTATATATT
1 -TTTATTTATATATT
*
4214049 TTTATTTATATATG
1 TTTATTTATATATT
* *
4214063 TGTATATATATAT
1 TTTATTTATATAT
4214076 ATATGTATGT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
11 1 0.02
12 10 0.16
13 7 0.11
14 35 0.55
15 9 0.14
16 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTATTTATATATT
Found at i:4214640 original size:22 final size:23
Alignment explanation
Indices: 4214615--4214657 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
4214605 TTTAGCTTTA
4214615 TTTTTATTTATTTA-ATTTTTCT
1 TTTTTATTTATTTATATTTTTCT
*
4214637 TTTTTATTTCTTTATATTTTT
1 TTTTTATTTATTTATATTTTT
4214658 TGTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTATTTATTTATATTTTTCT
Found at i:4214665 original size:21 final size:22
Alignment explanation
Indices: 4214617--4214665 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4214607 TAGCTTTATT
*
4214617 TTTATTTATTTAATTTTTCTTT
1 TTTATTTATTTAATTTTTCTTG
*
4214639 TTTATTTCTTT-ATATTTT-TTG
1 TTTATTTATTTAAT-TTTTCTTG
4214660 TTTATT
1 TTTATT
4214666 ATCTCCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTATTTATTTAATTTTTCTTG
Found at i:4218895 original size:95 final size:95
Alignment explanation
Indices: 4218724--4218983 Score: 305
Period size: 95 Copynumber: 2.7 Consensus size: 95
4218714 GAATACCTAT
* * * * **
4218724 ATTATAA-A-ACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACGCCATGGGTTTAT
1 ATTATAATATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCACGACTTTAT
*
4218787 GGATAAGATTCAACTAGCCTGATAAAGGTG
66 GGATAAAATTCAACTAGCCTGATAAAGGTG
4218817 ATTATAATATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGTCC-CGACTTTA
1 ATTATAATATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CCACGACTTTA
*
4218881 TGTATAAAATTCAACTAGCCTGATAAAGGTG
65 TGGATAAAATTCAACTAGCCTGATAAAGGTG
* * * * * *
4218912 ATTATAATAT-CTATATAATGATA-TCGAGATGTCCCTCTAGATCAATTGGTTAAATGCCTCGGC
1 ATTATAATATAC-A-ATAA--A-ACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCACGAC
4218975 TTTATGGAT
61 TTTATGGAT
4218984 TCAGCTAGCC
Statistics
Matches: 144, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
93 7 0.05
94 2 0.01
95 85 0.59
96 6 0.04
97 2 0.01
98 41 0.28
99 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCACGACTTTAT
GGATAAAATTCAACTAGCCTGATAAAGGTG
Found at i:4220119 original size:147 final size:147
Alignment explanation
Indices: 4219933--4220534 Score: 972
Period size: 147 Copynumber: 4.1 Consensus size: 147
4219923 GTGGTTGTTG
* * * *
4219933 AACTTCACAGCGAAGGAGCGTCTGTCAACAAACAACTTTCCAGTTTTATTCGGAGAT-AATTTCA
1 AACTTCACAGCGAAGGAGCATCTGTCAACAAACACCTTTCCAGTTTCATTCAGAG-TCAATTTCA
*
4219997 ACTTCACAGCGAAGGATATTGGACTTGAAACAACACAAGATTGGATTTCAACTTCACAACGAAGG
65 ACTTCACAGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGAAGG
4220062 ATATCCAATTCAAAGCTC
130 ATATCCAATTCAAAGCTC
* *
4220080 AACTTCACAGCGAAGGAGCATCTGTCAACAAACACCTTTCCAGTTGCATTCAGAGTCAATTTTAA
1 AACTTCACAGCGAAGGAGCATCTGTCAACAAACACCTTTCCAGTTTCATTCAGAGTCAATTTCAA
* * *
4220145 CTTCACAGCGAAGAATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCATAACGAACGA
66 CTTCACAGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGAAGGA
4220210 TATCCAATTCAAAGCTC
131 TATCCAATTCAAAGCTC
* * * *
4220227 AACTTCACAGCGAATGAGCATCTGCCAACAAACACCTTTCCAGTTTCATTCATAATCAATTTCAA
1 AACTTCACAGCGAAGGAGCATCTGTCAACAAACACCTTTCCAGTTTCATTCAGAGTCAATTTCAA
* *
4220292 CTTCACAGCGAAGGATATTGGACTTGAAACAACACAAGATTGGATTTCAACTTCACAACGAATGA
66 CTTCACAGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGAAGGA
4220357 TATCCAATTCAAAGCTC
131 TATCCAATTCAAAGCTC
* *
4220374 AACTTCACAGCGAAGGAGCATCTGTCAACAAACACTTTTCCAGTTTCATTTAGAGTCAATTTCAA
1 AACTTCACAGCGAAGGAGCATCTGTCAACAAACACCTTTCCAGTTTCATTCAGAGTCAATTTCAA
* * *
4220439 CTTCACGGCGAATGATATTGGACTCGAAACAACACAATATTGGATTTCAACTTCACAACGAAGGA
66 CTTCACAGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGAAGGA
* *
4220504 TATCCAATTTAAAGCCC
131 TATCCAATTCAAAGCTC
*
4220521 AACTTCACAACGAA
1 AACTTCACAGCGAA
4220535 TGAACCATCC
Statistics
Matches: 420, Mismatches: 34, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
146 1 0.00
147 419 1.00
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (147 bp):
AACTTCACAGCGAAGGAGCATCTGTCAACAAACACCTTTCCAGTTTCATTCAGAGTCAATTTCAA
CTTCACAGCGAAGGATATTGGACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGAAGGA
TATCCAATTCAAAGCTC
Found at i:4221051 original size:85 final size:85
Alignment explanation
Indices: 4220936--4221125 Score: 299
Period size: 85 Copynumber: 2.2 Consensus size: 85
4220926 TATGTTAACA
* * * *
4220936 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCACATTTACATCATAACTCAAGGC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACTCAAGCC
4221001 GAGAAGGATTATCTGTCAAC
66 GAGAAGGATTATCTGTCAAC
* * *
4221021 CAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTATAGCATAGCTCAAGCC
1 AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACTCAAGCC
*
4221086 GAGAAGGGTTATCTGTCAAC
66 GAGAAGGATTATCTGTCAAC
*
4221106 AAACACCTTCGAGTTTGATT
1 AAAGACCTTCGAGTTTGATT
4221126 CTATTCAACT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 95 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (85 bp):
AAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACTCAAGCC
GAGAAGGATTATCTGTCAAC
Found at i:4221762 original size:2 final size:2
Alignment explanation
Indices: 4221751--4221804 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
4221741 ATCCTTATTG
4221751 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4221792 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
4221805 TTACACCCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4222198 original size:21 final size:22
Alignment explanation
Indices: 4222174--4222226 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
4222164 ATTTCGTCCT
* *
4222174 TATTGTATAATGTATATAT-TA
1 TATTATATAATATATATATATA
4222195 TATTATATAATATATATATATA
1 TATTATATAATATATATATATA
4222217 TATATATATA
1 TAT-TATATA
4222227 TTATTTACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 17 0.61
22 5 0.18
23 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
TATTATATAATATATATATATA
Found at i:4222203 original size:2 final size:2
Alignment explanation
Indices: 4222186--4222227 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
4222176 TTGTATAATG
4222186 TA TA TA T- TA TA T- TA TA 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
4222225 TA T
1 TA T
4222228 TATTTACACC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4223380 original size:2 final size:2
Alignment explanation
Indices: 4223375--4223441 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
4223365 TTTATGTGTG
4223375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
4223417 TA TA TA TG TA TA TG TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4223442 TTTACCTTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4223680 original size:18 final size:18
Alignment explanation
Indices: 4223659--4223696 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4223649 GAAGTGATTG
*
4223659 TTTTCT-TTTTTTATTATT
1 TTTTCTCTTTTCT-TTATT
4223677 TTTTCTCTTTTCTTTATT
1 TTTTCTCTTTTCTTTATT
4223695 TT
1 TT
4223697 GTTTGTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTCTTTTCTTTATT
Found at i:4223741 original size:2 final size:2
Alignment explanation
Indices: 4223734--4223768 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4223724 CCTATTAATT
4223734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4223769 TTACATGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4224007 original size:34 final size:34
Alignment explanation
Indices: 4223938--4224006 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
4223928 TCTTCCATTG
* **
4223938 TTCCTTATTTTTAGTTTTGGTTATTAATTTATTT
1 TTCCTTATTTTTAGCTTTATTTATTAATTTATTT
*
4223972 TTCCTTATTTTTAGCTTTATTTA-TATTTTATTT
1 TTCCTTATTTTTAGCTTTATTTATTAATTTATTT
4224005 TT
1 TT
4224007 TTCTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.17, C:0.07, G:0.06, T:0.70
Consensus pattern (34 bp):
TTCCTTATTTTTAGCTTTATTTATTAATTTATTT
Found at i:4224523 original size:30 final size:30
Alignment explanation
Indices: 4224437--4224529 Score: 118
Period size: 31 Copynumber: 3.0 Consensus size: 30
4224427 CAGTATGTAT
4224437 TAATATTGTTTTAGGGTTTAGTTGCAATAAAA
1 TAATA-TGTTTTAGGGTTT-GTTGCAATAAAA
*
4224469 CAATATGTTTTAGGGTTTGGTTGCAATAAAA
1 TAATATGTTTTAGGGTTT-GTTGCAATAAAA
*
4224500 TAGTATGTTTTA-GGTTTGCTTGC-ATAAAA
1 TAATATGTTTTAGGGTTTG-TTGCAATAAAA
4224529 T
1 T
4224530 TTGTTGAAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
29 8 0.14
30 9 0.16
31 35 0.62
32 4 0.07
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.43
Consensus pattern (30 bp):
TAATATGTTTTAGGGTTTGTTGCAATAAAA
Found at i:4230717 original size:19 final size:19
Alignment explanation
Indices: 4230693--4230773 Score: 126
Period size: 19 Copynumber: 4.3 Consensus size: 19
4230683 CGCTGTTGCA
* *
4230693 GCTCCATAGGTCGTCAAGT
1 GCTCCATAGGTCGCCATGT
*
4230712 GCTCCATAGGTTGCCATGT
1 GCTCCATAGGTCGCCATGT
4230731 GCTCCATAGGTCGCCATGT
1 GCTCCATAGGTCGCCATGT
*
4230750 GCTCCATAGGTCGTCATGT
1 GCTCCATAGGTCGCCATGT
4230769 GCTCC
1 GCTCC
4230774 TGGAGACCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 57 1.00
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (19 bp):
GCTCCATAGGTCGCCATGT
Found at i:4235572 original size:43 final size:43
Alignment explanation
Indices: 4235511--4235630 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
4235501 ATAGGTCTAG
*
4235511 ACGCCACAAAAGGTCAAGCTCTATAGCGGCGTTTCTATTTAAA
1 ACGCCGCAAAAGGTCAAGCTCTATAGCGGCGTTTCTATTTAAA
* * * *
4235554 ACGCCGCAAAAGGTCAAGCTCAATAGCGGCATTTTTCTTTAAA
1 ACGCCGCAAAAGGTCAAGCTCTATAGCGGCGTTTCTATTTAAA
* ** *
4235597 ACACCGCAAAATATCAAGATCTATAGCGGCGTTT
1 ACGCCGCAAAAGGTCAAGCTCTATAGCGGCGTTT
4235631 TTAAGAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (43 bp):
ACGCCGCAAAAGGTCAAGCTCTATAGCGGCGTTTCTATTTAAA
Found at i:4239211 original size:41 final size:41
Alignment explanation
Indices: 4239144--4239610 Score: 266
Period size: 41 Copynumber: 11.4 Consensus size: 41
4239134 CGTTTATTCA
** ** * *
4239144 AAAAACGCCACTAAAGTTTGGGTCTTTGGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGTAT
* * * * *
4239185 AAAAACGCCACTAAAGTACGAATCTTTGGTGGCATTTGTGCT
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGT-AT
* * * * ** * *
4239227 TAAAATGCTACTAAAGTACTAGCATTTAGCGGTGTTTGTGCT
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGT-AT
* * * * ** *
4239269 TAAAACACCACTAAAGTA-TAGTATTTAGCGGCGTTTAAAC
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGTAT
* * * ** *
4239309 AAAAGCACCACTAAAGTATGAGCATTTAGCGGTGTTTGTGAT
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGT-AT
* * * * ** *
4239351 TAAAACGCCACTAAAGTAC-AGTATTTATCGGCATTTAAAC
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGTAT
* * *
4239391 AAAAATGCCACTAAAGTATGAGA-ATTTAGCGGCGTTTGTGCT
1 AAAAACGCCACTAAAGTACGA-ATATTTAGCGGCGTTTGT-AT
* * * * * *
4239433 TAAAACGCCACTAAAGTA-TAGTATTTACCGGCGTTTATAC
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGTAT
* *
4239473 AAAAACACCACTAAAGTACGACA-ATTTAGCGGCGTTTGTGCT
1 AAAAACGCCACTAAAGTACGA-ATATTTAGCGGCGTTTGT-AT
** * * * *
4239515 TCAAACGCTACTAAAGTAC-ATTATTTAGCGTCGTTTATAT
1 AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGTAT
* *
4239555 AAAAACGCCACTAAAGCAC-AAGTATTTACCGGCGTTTGT-T
1 AAAAACGCCACTAAAGTACGAA-TATTTAGCGGCGTTTGTAT
*
4239595 CAAAAACGCCGCTAAA
1 -AAAAACGCCACTAAA
4239611 AACCCATTTT
Statistics
Matches: 324, Mismatches: 89, Indels: 26
0.74 0.20 0.06
Matches are distributed among these distances:
40 67 0.21
41 163 0.50
42 94 0.29
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACGAATATTTAGCGGCGTTTGTAT
Found at i:4239335 original size:82 final size:82
Alignment explanation
Indices: 4239236--4239610 Score: 441
Period size: 82 Copynumber: 4.6 Consensus size: 82
4239226 TTAAAATGCT
* * *
4239236 ACTAAAGTACT-AGCATTTAGCGGTGTTTGTGCTTAAAACACCACTAAAGTATAGTATTTAGCGG
1 ACTAAAGTA-TGAGCATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGG
*
4239300 CGTTTAAACAAAAGCACC
65 CGTTTAAACAAAAACACC
* * *
4239318 ACTAAAGTATGAGCATTTAGCGGTGTTTGTGATTAAAACGCCACTAAAGTACAGTATTTATCGGC
1 ACTAAAGTATGAGCATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGC
* **
4239383 ATTTAAACAAAAATGCC
66 GTTTAAACAAAAACACC
* * *
4239400 ACTAAAGTATGAGAATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTACCGGC
1 ACTAAAGTATGAGCATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGC
*
4239465 GTTTATACAAAAACACC
66 GTTTAAACAAAAACACC
* * * * *
4239482 ACTAAAGTACGA-CAATTTAGCGGCGTTTGTGCTTCAAACGCTACTAAAGTACATTATTTAGCGT
1 ACTAAAGTATGAGC-ATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGG
* * *
4239546 CGTTTATATAAAAACGCC
65 CGTTTAAACAAAAACACC
* ** * * * * *
4239564 ACTAAAGCACAAGTATTTACCGGCGTTTGTTC-AAAAACGCCGCTAAA
1 ACTAAAGTATGAGCATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAA
4239611 AACCCATTTT
Statistics
Matches: 254, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
81 12 0.05
82 242 0.95
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (82 bp):
ACTAAAGTATGAGCATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTAGCGGC
GTTTAAACAAAAACACC
Found at i:4239422 original size:164 final size:164
Alignment explanation
Indices: 4239172--4239593 Score: 499
Period size: 164 Copynumber: 2.6 Consensus size: 164
4239162 TGGGTCTTTG
* * * * * *** * *
4239172 GCGGCGTTTGT-ATAAAAACGCCACTAAAGTACGAATCTTTGGTGGCATTTGTGCTTAAAATGCT
1 GCGGCGTTTGTGATTAAAACGCCACTAAAGTAC-AGTATTTAGCGGCATTTAAAC-AAAAATGCC
* * *
4239236 ACTAAAGTACTAGCATTTAGCGGTGTTTGTGCTTAAAACACCACTAAAGTATAGTATTTAGCGGC
64 ACTAAAGTACTAGAATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTATAGTATTTACCGGC
* *
4239301 GTTTAAACAAAAGCACCACTAAAGTATGAGC-ATTTA
129 GTTTAAACAAAAACACCACTAAAGTACGA-CAATTTA
* *
4239337 GCGGTGTTTGTGATTAAAACGCCACTAAAGTACAGTATTTATCGGCATTTAAACAAAAATGCCAC
1 GCGGCGTTTGTGATTAAAACGCCACTAAAGTACAGTATTTAGCGGCATTTAAACAAAAATGCCAC
*
4239402 TAAAGTA-TGAGAATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTACCGGCG
66 TAAAGTACT-AGAATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTATAGTATTTACCGGCG
*
4239466 TTTATACAAAAACACCACTAAAGTACGACAATTTA
130 TTTAAACAAAAACACCACTAAAGTACGACAATTTA
* * * * * * * * *
4239501 GCGGCGTTTGTGCTTCAAACGCTACTAAAGTACATTATTTAGCGTCGTTTATATAAAAACGCCAC
1 GCGGCGTTTGTGATTAAAACGCCACTAAAGTACAGTATTTAGCGGCATTTAAACAAAAATGCCAC
* * * *
4239566 TAAAGCACAAGTATTTACCGGCGTTTGT
66 TAAAGTACTAGAATTTAGCGGCGTTTGT
4239594 TCAAAAACGC
Statistics
Matches: 219, Mismatches: 34, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
163 2 0.01
164 174 0.79
165 23 0.11
166 20 0.09
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (164 bp):
GCGGCGTTTGTGATTAAAACGCCACTAAAGTACAGTATTTAGCGGCATTTAAACAAAAATGCCAC
TAAAGTACTAGAATTTAGCGGCGTTTGTGCTTAAAACACCACTAAAGTATAGTATTTACCGGCGT
TTAAACAAAAACACCACTAAAGTACGACAATTTA
Found at i:4240791 original size:27 final size:27
Alignment explanation
Indices: 4240761--4240812 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
4240751 AGTATAATGA
* *
4240761 AACTAAACATAGATAAATGAATAAAAT
1 AACTAAACAGAGATAAAAGAATAAAAT
* *
4240788 AACTAATCAGAGGTAAAAGAATAAA
1 AACTAAACAGAGATAAAAGAATAAA
4240813 TACATGAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.19
Consensus pattern (27 bp):
AACTAAACAGAGATAAAAGAATAAAAT
Found at i:4241238 original size:2 final size:2
Alignment explanation
Indices: 4241231--4241277 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
4241221 TGTCAAAGGA
* *
4241231 AT AT AT AT AT AT AT AT AT AT AT -T AT AT A- AT AT GT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4241271 AA AT AT A
1 AT AT AT A
4241278 ATACATGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4242429 original size:9 final size:9
Alignment explanation
Indices: 4242417--4242489 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
4242407 TAAACAAAAT
4242417 AATAATAAA
1 AATAATAAA
* *
4242426 AATATTAAT
1 AATAATAAA
*
4242435 AATAA-AAT
1 AATAATAAA
4242443 AA-AATAAA
1 AATAATAAA
* *
4242451 TATAATAAT
1 AATAATAAA
4242460 AATAATAATA
1 AATAATAA-A
4242470 AATAA-ACAA
1 AATAATA-AA
*
4242479 GATAATAAA
1 AATAATAAA
4242488 AA
1 AA
4242490 ATAAACCCAG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
7 2 0.04
8 8 0.16
9 32 0.65
10 7 0.14
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:4242447 original size:31 final size:30
Alignment explanation
Indices: 4242406--4242489 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
4242396 TTTTTAACCT
* *
4242406 ATAAACAAAATAATAATAAAAATATTAATA
1 ATAAATAAAATAATAATAAAAATAATAATA
*
4242436 ATAAAATAAAATAA-ATATAATAATAATAATA
1 AT-AAATAAAATAATA-ATAAAAATAATAATA
4242467 ATAAATAAACA-AGATAATAAAAA
1 ATAAATAAA-ATA-ATAATAAAAA
4242490 ATAAACCCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
30 11 0.24
31 33 0.73
32 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.25
Consensus pattern (30 bp):
ATAAATAAAATAATAATAAAAATAATAATA
Found at i:4242459 original size:25 final size:25
Alignment explanation
Indices: 4242412--4242494 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 25
4242402 ACCTATAAAC
*
4242412 AAAATAATAATAAAAATATTAATAAT
1 AAAATAA-AATAAAAATAATAATAAT
*
4242438 AAAATAAAATAAATATAATAATAAT
1 AAAATAAAATAAAAATAATAATAAT
*
4242463 AATAAT-AAATAAACAA-GATAATAA-
1 AA-AATAAAATAAA-AATAATAATAAT
4242487 AAAATAAA
1 AAAATAAA
4242495 CCCAGATGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 3 0.06
24 4 0.08
25 32 0.64
26 11 0.22
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (25 bp):
AAAATAAAATAAAAATAATAATAAT
Found at i:4242486 original size:3 final size:3
Alignment explanation
Indices: 4242414--4242470 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
4242404 CTATAAACAA
* *
4242414 AAT AAT AAT AAA AAT ATT AAT AAT AA- AAT AA- AAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
4242457 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
4242471 ATAAACAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.11
3 40 0.87
4 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4243349 original size:188 final size:188
Alignment explanation
Indices: 4243032--4243479 Score: 662
Period size: 188 Copynumber: 2.4 Consensus size: 188
4243022 AGGTTGTATT
* * * *
4243032 TGAAGACAACATTGTTCATTCTTGTTGAGGAAATCTTATTGCCTAGAGACAATTTGATGTTGGAA
1 TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTGCTTAGAGATAATTTGATGTTGGAA
* * * * **
4243097 ACGACACGGCTCCTATGTGATGAGGAGAAACTAGTCATTTATGATGACATTGTTTTTTCATGTTA
66 ACGACATGGCTCCTACGTGATGAGGAGAAACTAGTCAATTATGATGACATTGCTCCTTCATGTTA
* * *
4243162 AGAAGGTCTAGTCAGTGGACGATATTGTTCTTACTTGATGAGGACGTCTAGCCACATC
131 AGAAGGTATAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACGTCTAGCCACATC
* ** * *
4243220 TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATATGATTTTTTAAAGATATTTTGATGTTGGAA
1 TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTGCTTAGAGATAATTTGATGTTGGAA
* * *
4243285 ACGACATGGCTCCTACGTGATGAGGAGAAACTGGTCAATTCTGATGGCATTGCTCCTTCATGTTA
66 ACGACATGGCTCCTACGTGATGAGGAGAAACTAGTCAATTATGATGACATTGCTCCTTCATGTTA
* * *
4243350 AGAAGGTATAGTTAGTGGACGACATTGTTCCTACTTGATGAGGACGTCTAGTCATATC
131 AGAAGGTATAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACGTCTAGCCACATC
*
4243408 TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTGCTTAGAGATAATTTGATGTTGAAA
1 TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTGCTTAGAGATAATTTGATGTTGGAA
*
4243473 ATGACAT
66 ACGACAT
4243480 TGTTCATCCA
Statistics
Matches: 229, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
188 229 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (188 bp):
TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTGCTTAGAGATAATTTGATGTTGGAA
ACGACATGGCTCCTACGTGATGAGGAGAAACTAGTCAATTATGATGACATTGCTCCTTCATGTTA
AGAAGGTATAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACGTCTAGCCACATC
Found at i:4244253 original size:16 final size:17
Alignment explanation
Indices: 4244235--4244268 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
4244225 ATGCTTTATG
4244235 AAAATTTTAAATAATGAA
1 AAAATTTTAAATAATG-A
4244253 AAAATTTTAAATAATG
1 AAAATTTTAAATAATG
4244269 TTTGATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
AAAATTTTAAATAATGA
Found at i:4245592 original size:21 final size:21
Alignment explanation
Indices: 4245568--4245620 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
4245558 AGAACTAGAA
4245568 GTATCGGTACTCCACTATGGG
1 GTATCGGTACTCCACTATGGG
4245589 GTATCGGTACTCCACTATGGG
1 GTATCGGTACTCCACTATGGG
4245610 GTATCGGTACT
1 GTATCGGTACT
4245621 ACCTTTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTACTCCACTATGGG
Found at i:4247346 original size:20 final size:20
Alignment explanation
Indices: 4247314--4247351 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
4247304 CATTTTGATT
*
4247314 TTCAAAATCAACT-TTTTCA
1 TTCAAAACCAACTATTTTCA
4247333 TTCAAAACCAAACTATTTT
1 TTCAAAACC-AACTATTTT
4247352 TATTTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (20 bp):
TTCAAAACCAACTATTTTCA
Found at i:4249435 original size:16 final size:16
Alignment explanation
Indices: 4249377--4249435 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 16
4249367 TATCATTTTT
*
4249377 TCATGTAATCACATAGG
1 TCATGTAA-CACATAGA
*
4249394 TCATGTAACACGTAGGA
1 TCATGTAACACATA-GA
*
4249411 TGACATGTAACACATACA
1 T--CATGTAACACATAGA
4249429 TCATGTA
1 TCATGTA
4249436 GAACAATGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 11 0.31
17 10 0.29
18 2 0.06
19 12 0.34
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (16 bp):
TCATGTAACACATAGA
Found at i:4256213 original size:23 final size:23
Alignment explanation
Indices: 4256187--4256249 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
4256177 CCACATAGTA
4256187 TTGTCCCGAAGGACCGCGTAGAG
1 TTGTCCCGAAGGACCGCGTAGAG
* * *
4256210 TTGTCCCGAATGACCACGTATAG
1 TTGTCCCGAAGGACCGCGTAGAG
4256233 TTGTCCCGAAGGACCGC
1 TTGTCCCGAAGGACCGC
4256250 ACAGAACCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.21
Consensus pattern (23 bp):
TTGTCCCGAAGGACCGCGTAGAG
Found at i:4262354 original size:27 final size:27
Alignment explanation
Indices: 4262323--4262374 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4262313 AATATCATGA
*
4262323 AACTAAAGAG-GGATAAATGAATAAAAT
1 AACTAAAGAGAGG-TAAAAGAATAAAAT
*
4262350 AACTAAATAGAGGTAAAAGAATAAA
1 AACTAAAGAGAGGTAAAAGAATAAA
4262375 TACATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (27 bp):
AACTAAAGAGAGGTAAAAGAATAAAAT
Found at i:4263810 original size:3 final size:3
Alignment explanation
Indices: 4263802--4263880 Score: 83
Period size: 3 Copynumber: 27.0 Consensus size: 3
4263792 GGCTATTTGG
* * * *
4263802 TAA TAA TAA TAA TAA TAA AAA TAA -AA AAA T-A GAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4263848 TAAA TAA -GA TAA TAA TAA TAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4263881 ATTGAGAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:4264025 original size:21 final size:20
Alignment explanation
Indices: 4263983--4264044 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
4263973 CAACGCGAAC
*
4263983 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
* *
4264003 TCCAAATTCGTAACACGATTT
1 TCCAAATTCGCAACAC-AGTT
*
4264024 TCCCAAATTCGCAACTCAGTT
1 T-CCAAATTCGCAACACAGTT
4264045 GCTACAATCG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 14 0.41
21 7 0.21
22 13 0.38
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:4264056 original size:42 final size:42
Alignment explanation
Indices: 4263984--4264067 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
4263974 AACGCGAACT
* * *
4263984 CCAATTTCGCAACACAGTTTCCAAATTCGTAACACGATTTTC
1 CCAAATTCGCAACACAGTTGCCAAATTCGTAACACGAATTTC
* * *
4264026 CCAAATTCGCAACTCAGTTGCTACAA-TCGTAACGCGAATTTC
1 CCAAATTCGCAACACAGTTGCCA-AATTCGTAACACGAATTTC
4264068 TTTCTCGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (42 bp):
CCAAATTCGCAACACAGTTGCCAAATTCGTAACACGAATTTC
Found at i:4264158 original size:20 final size:20
Alignment explanation
Indices: 4264133--4264181 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4264123 GATTTCTGAA
* *
4264133 TTCGCAACGCGAA-TTTCTTT
1 TTCGCAACAC-AAGTTTCCTT
4264153 TTCGCAACACAAGTTTCCTT
1 TTCGCAACACAAGTTTCCTT
4264173 TTCGCAACA
1 TTCGCAACA
4264182 AGATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCGCAACACAAGTTTCCTT
Found at i:4264170 original size:82 final size:81
Alignment explanation
Indices: 4263988--4264170 Score: 192
Period size: 82 Copynumber: 2.2 Consensus size: 81
4263978 CGAACTCCAA
* *
4263988 TTTCGCAACACAGTTTCCAAATTCGTAACACGATTTTCCCAAATTCGCAACTCAGTTGCTACAAT
1 TTTCGCAACACAGTTTCCAAATTCGAAACACGAATTT-CCAAATTCGCAACTCAGTTGCTACAAT
*
4264053 CGTAACGCGAATTTCTT
65 CGCAACGCGAATTTCTT
* ** * * * *
4264070 TCTCGCAACGTGATTTTCCAAATTCGAAACACGGAATTT-CAAATTTGTAACTC-GATTTCTGA-
1 TTTCGCAAC-ACAGTTTCCAAATTCGAAACAC-GAATTTCCAAATTCGCAACTCAG-TTGCT-AC
*
4264132 ATTCGCAACGCGAATTTCTT
62 AATCGCAACGCGAATTTCTT
4264152 TTTCGCAACACAAGTTTCC
1 TTTCGCAACAC-AGTTTCC
4264171 TTTTCGCAAC
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
81 1 0.01
82 56 0.69
83 19 0.23
84 5 0.06
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (81 bp):
TTTCGCAACACAGTTTCCAAATTCGAAACACGAATTTCCAAATTCGCAACTCAGTTGCTACAATC
GCAACGCGAATTTCTT
Found at i:4265204 original size:24 final size:24
Alignment explanation
Indices: 4265177--4265230 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4265167 GTATTCGAAA
*
4265177 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTCGGTCAATACCCGGAC
* *
4265201 TTTGATCTCGGTCAATACTCGGAT
1 TTTGATCTCGGTCAATACCCGGAC
4265225 TTTGAT
1 TTTGAT
4265231 GATGTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTCGGTCAATACCCGGAC
Found at i:4267768 original size:29 final size:29
Alignment explanation
Indices: 4267726--4267798 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
4267716 AATTCGCAAC
*
4267726 GCGAAATTCAAATTCAT-GTTGCGATTGTT
1 GCGAAAGTCAAATTC-TCGTTGCGATTGTT
4267755 GCGAAAGTCAAATTCTCGTTGCGATTGTT
1 GCGAAAGTCAAATTCTCGTTGCGATTGTT
4267784 GCGAAAGTCAAATTC
1 GCGAAAGTCAAATTC
4267799 GCAACGACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (29 bp):
GCGAAAGTCAAATTCTCGTTGCGATTGTT
Found at i:4269211 original size:21 final size:21
Alignment explanation
Indices: 4269187--4269282 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
4269177 GTGAATCGGG
* *
4269187 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
4269208 CTCTTGAACGATGAGAGGGGT
1 CTCTTGAACGATGAGAGGGGC
* * *
4269229 CTTTTAAACGACGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
4269250 CTCTTGAATGAT-ATGAGGAGC
1 CTCTTGAACGATGA-GAGGGGC
4269271 CTCTTGAACGAT
1 CTCTTGAACGAT
4269283 AACAAGTGAA
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 1 0.02
21 60 0.98
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:4269613 original size:42 final size:41
Alignment explanation
Indices: 4269567--4269675 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
4269557 GAAACAATCT
* *
4269567 CACGTAGAGCGGCTACCTCATCACGTAAAGTATATACCTCAC
1 CACGTAAAGC-GCTACCTCATCACGTAAAATATATACCTCAC
* * ** * *
4269609 CACGTAAAGCACCATTTTCATCGCGTAAAATATCTACCTCAC
1 CACGTAAAGCGCTA-CCTCATCACGTAAAATATATACCTCAC
4269651 CACGTAAAGAC-CGTACCTCATCACG
1 CACGTAAAG-CGC-TACCTCATCACG
4269676 CCATGCACCA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
41 2 0.04
42 48 0.92
43 2 0.04
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (41 bp):
CACGTAAAGCGCTACCTCATCACGTAAAATATATACCTCAC
Found at i:4271479 original size:20 final size:20
Alignment explanation
Indices: 4271456--4271555 Score: 166
Period size: 20 Copynumber: 5.0 Consensus size: 20
4271446 CTTAAATTCA
*
4271456 CAACACGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
*
4271476 CAACGCGAAAATAAAAATCG
1 CAACGCGAAAATGAAAATCG
4271496 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
4271516 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
*
4271536 CAACGCGAAACT-AAAATCG
1 CAACGCGAAAATGAAAATCG
4271555 C
1 C
4271556 GTTGCGAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
19 8 0.11
20 68 0.89
ACGTcount: A:0.51, C:0.22, G:0.17, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:4272127 original size:20 final size:20
Alignment explanation
Indices: 4272082--4272127 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4272072 ACGCGCTTTG
*
4272082 CGAATTTGACTTATGTGTTG
1 CGAATTTGACTTATGTGTTA
*
4272102 CAAATTT-AGCTTATGTGTTA
1 CGAATTTGA-CTTATGTGTTA
4272122 CGAATT
1 CGAATT
4272128 ACAAATTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTATGTGTTA
Found at i:4272149 original size:27 final size:27
Alignment explanation
Indices: 4272119--4272174 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
4272109 AGCTTATGTG
4272119 TTACGAATTACAAATTCGCGTTGCGAA
1 TTACGAATTACAAATTCGCGTTGCGAA
* * *
4272146 TTACGATTTATATATTCGCGTTGCGAA
1 TTACGAATTACAAATTCGCGTTGCGAA
4272173 TT
1 TT
4272175 TCAAAACTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (27 bp):
TTACGAATTACAAATTCGCGTTGCGAA
Found at i:4278260 original size:22 final size:21
Alignment explanation
Indices: 4278235--4278285 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
4278225 AATCAATACG
*
4278235 ATTAATAATATAAAATAATGAA
1 ATTAATAATATAAAA-AATAAA
* *
4278257 ATTAAATAATTTCAAAAATAAA
1 ATT-AATAATATAAAAAATAAA
4278279 ATTAATA
1 ATTAATA
4278286 CTAAAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 11 0.44
23 10 0.40
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTAATAATATAAAAAATAAA
Found at i:4282995 original size:13 final size:13
Alignment explanation
Indices: 4282977--4283009 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4282967 AATATACTTA
4282977 GAAAATCATTTTG
1 GAAAATCATTTTG
4282990 GAAAATCATTTTG
1 GAAAATCATTTTG
4283003 GAAAATC
1 GAAAATC
4283010 TTAAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (13 bp):
GAAAATCATTTTG
Found at i:4284864 original size:21 final size:21
Alignment explanation
Indices: 4284838--4284877 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4284828 CAGAACCCCA
*
4284838 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
4284859 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
4284878 TCAAATGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:4289016 original size:117 final size:117
Alignment explanation
Indices: 4288794--4289017 Score: 274
Period size: 117 Copynumber: 1.9 Consensus size: 117
4288784 AACTTTCAAA
* * *
4288794 TTGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGTTATAAATCCTTCTTCAAGAT
1 TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACAT
* *
4288859 TTCATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAAT
66 TTCATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAAT
* * * * *
4288911 TTGAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAAC
1 TTGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCT-TCAAC
* * **
4288974 ATTTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 ATTTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
4289018 ATCATTTTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
116 2 0.02
117 84 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACAT
TTCATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAAT
Found at i:4291194 original size:23 final size:23
Alignment explanation
Indices: 4291168--4291215 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4291158 CATTGTGTCT
4291168 TTATTTTATCTGTCGTTA-TTTAC
1 TTATTTTATCT-TCGTTATTTTAC
* *
4291191 TTATTTTCTCTTCTTTATTTTAC
1 TTATTTTATCTTCGTTATTTTAC
4291214 TT
1 TT
4291216 TCTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATTTTATCTTCGTTATTTTAC
Found at i:4291208 original size:14 final size:13
Alignment explanation
Indices: 4291191--4291226 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
4291181 CGTTATTTAC
4291191 TTATTTTCTCTTCT
1 TTATTTTCT-TTCT
4291205 TTATTTTACTTTCT
1 TTATTTT-CTTTCT
4291219 TTATTTTC
1 TTATTTTC
4291227 AATTTATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.86
15 2 0.10
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTCTTTCT
Found at i:4300978 original size:8 final size:8
Alignment explanation
Indices: 4300931--4300959 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4300921 GTCCTAAATT
4300931 GAAAAA-A
1 GAAAAAGA
4300938 GAAAAAGA
1 GAAAAAGA
4300946 GAAAAAGA
1 GAAAAAGA
4300954 GAAAAA
1 GAAAAA
4300960 ATAACAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
GAAAAAGA
Found at i:4302302 original size:110 final size:107
Alignment explanation
Indices: 4302099--4302578 Score: 499
Period size: 110 Copynumber: 4.5 Consensus size: 107
4302089 AGCTTCCCAA
* *
4302099 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC-AAGACAACACAAGCTCAACTT
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAA-ACAGCACAAGCTCAACTT
* * * *
4302163 CACAACGAAGGGGTGAG-TGATTGTTAACAAACAACTTT-TCAGTT
65 CACAACGAAGGGGCG-GCTGACTGTCAACAAACAA-TTTCCCAG-T
* * *
4302207 TCATTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTAGACTCGAAACAGCACAAGCTCAACT
1 T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAGCACAAGCTCAACT
** * * * * * *
4302272 TCACAGTGAAAGGGCGGTTGGCTATCAACAAATAATTTCCCA-A
64 TCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGT
* *
4302315 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC-AAGACA-AACAAGCTCAACTT
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAA-ACAGCACAAGCTCAACTT
* * * *
4302378 CACAACGAAGGGGTGACTGATTGTCAACAAACAACTTT-TCAGTT
65 CACAACGAAGGGGCGGCTGACTGTCAACAAACAA-TTTCCCAG-T
* * *
4302422 TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACT
1 T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAGCACAAGCTCAACT
** * **
4302487 TCACAGTGAAGGGGCGGCTGGCTGTCAACAAGTAATTTCCCAGT
64 TCACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGT
* * *
4302531 TTT-AGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTTGAAACA
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACA
4302579 ATACAACTTA
Statistics
Matches: 305, Mismatches: 53, Indels: 30
0.79 0.14 0.08
Matches are distributed among these distances:
105 41 0.13
106 83 0.27
107 3 0.01
108 2 0.01
109 51 0.17
110 123 0.40
111 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (107 bp):
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAGCACAAGCTCAACTTC
ACAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGT
Found at i:4302464 original size:215 final size:216
Alignment explanation
Indices: 4302092--4302571 Score: 836
Period size: 215 Copynumber: 2.2 Consensus size: 216
4302082 AAAAAGGAGC
4302092 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCT
* *
4302157 CAACTTCACAACGAAGGGGTGAGTGATTGTTAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
66 CAACTTCACAACGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
*
4302222 TTCAACTTCACGGCGAAGGATATTAGACTCGAAACAGCACAAGCTCAACTTCACAGTGAAAGGGC
131 TTCAACTTCACAGCGAAGGATATTAGACTCGAAACAGCACAAGCTCAACTTCACAGTGAAAGGGC
*
4302287 GGTTGGCTATCAACAAATAAT
196 GGCTGGCTATCAACAAATAAT
4302308 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAA-ACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCT
4302372 CAACTTCACAACGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
66 CAACTTCACAACGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
* *
4302437 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGTGAAGGGGC
131 TTCAACTTCACAGCGAAGGATATTAGACTCGAAACAGCACAAGCTCAACTTCACAGTGAAAGGGC
* *
4302502 GGCTGGCTGTCAACAAGTAAT
196 GGCTGGCTATCAACAAATAAT
* * ** *
4302523 TTCCCAGTTTTAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
4302572 TGAAACAATA
Statistics
Matches: 251, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
215 194 0.77
216 57 0.23
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (216 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCT
CAACTTCACAACGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
TTCAACTTCACAGCGAAGGATATTAGACTCGAAACAGCACAAGCTCAACTTCACAGTGAAAGGGC
GGCTGGCTATCAACAAATAAT
Found at i:4304145 original size:100 final size:100
Alignment explanation
Indices: 4303972--4304171 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 100
4303962 CATGAACTGG
4303972 GCAGAGAAGAAGGGAGGGGTTCGGTGAGAGAAAAGAGGAAATGAAGTTTTTTTAAAAAAATTTGA
1 GCAGAGAAGAAGGGAGGGGTTCGGTGAGAGAAAAGAGGAAATGAAGTTTTTTTAAAAAAATTTGA
4304037 CTTTTATATTGAGCCCACTCGACCCGCGTATCGAC
66 CTTTTATATTGAGCCCACTCGACCCGCGTATCGAC
*
4304072 GCAGAGAAGAAGGGAGGGGTTCGGTGAGAGAGAAGAGGAAATGAAG-TTTTTTAAAAAAATTTTG
1 GCAGAGAAGAAGGGAGGGGTTCGGTGAGAGAAAAGAGGAAATGAAGTTTTTTTAAAAAAA-TTTG
4304136 ACTTTTATATTGAGCCCACTCGACCCGCGTATCGAC
65 ACTTTTATATTGAGCCCACTCGACCCGCGTATCGAC
4304172 CCGATGGGTC
Statistics
Matches: 98, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
99 13 0.13
100 85 0.87
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (100 bp):
GCAGAGAAGAAGGGAGGGGTTCGGTGAGAGAAAAGAGGAAATGAAGTTTTTTTAAAAAAATTTGA
CTTTTATATTGAGCCCACTCGACCCGCGTATCGAC
Found at i:4304844 original size:14 final size:14
Alignment explanation
Indices: 4304825--4304859 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
4304815 TGTTATTTAC
4304825 TTATTTT-CTCTTCT
1 TTATTTTACT-TTCT
4304839 TTATTTTACTTTCT
1 TTATTTTACTTTCT
4304853 TTATTTT
1 TTATTTT
4304860 TAATTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.90
15 2 0.10
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTACTTTCT
Found at i:4305108 original size:16 final size:16
Alignment explanation
Indices: 4305087--4305125 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4305077 ACACATTTCT
4305087 GGTAAGACGCAGATCA
1 GGTAAGACGCAGATCA
*
4305103 GGTAAGACGCATATCA
1 GGTAAGACGCAGATCA
4305119 GGTAAGA
1 GGTAAGA
4305126 AATAAGGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (16 bp):
GGTAAGACGCAGATCA
Found at i:4306566 original size:13 final size:13
Alignment explanation
Indices: 4306548--4306572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4306538 TCATAACCCG
4306548 ACCCGACCCGTTT
1 ACCCGACCCGTTT
4306561 ACCCGACCCGTT
1 ACCCGACCCGTT
4306573 GACCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:4309092 original size:12 final size:12
Alignment explanation
Indices: 4309077--4309146 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
4309067 GATACATTAC
4309077 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
4309089 CTGATTTCTGAT
1 CTGAATTCTGTT
*
4309101 CTGGATTCTGTT
1 CTGAATTCTGTT
*
4309113 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
4309125 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
4309137 TTGATTTCTG
1 CTGAATTCTG
4309147 ATATCTCCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:4309108 original size:24 final size:24
Alignment explanation
Indices: 4309077--4309148 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
4309067 GATACATTAC
4309077 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
4309101 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
4309125 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
4309149 ATCTCCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:4309115 original size:48 final size:49
Alignment explanation
Indices: 4309044--4309148 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 49
4309034 ATTTTATCTA
*
4309044 ATTTCTGA-CTTGAATTATGTTCTGATA-CATTACCTGAATTCTGTTCTG
1 ATTTCTGATCTTGAATTATGTTCTGATATC-TGACCTGAATTCTGTTCTG
* * * *
4309092 ATTTCTGATC-TGGATTCTGTTCTGATATCTGATCTGAATTCTGTTTTG
1 ATTTCTGATCTTGAATTATGTTCTGATATCTGACCTGAATTCTGTTCTG
4309140 ATTTCTGAT
1 ATTTCTGAT
4309149 ATCTCCATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 48 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (49 bp):
ATTTCTGATCTTGAATTATGTTCTGATATCTGACCTGAATTCTGTTCTG
Found at i:4310330 original size:15 final size:15
Alignment explanation
Indices: 4310312--4310367 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
4310302 TAACCGGTTT
4310312 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
4310327 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
4310344 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
4310359 CGATTTTAA
1 CGGTTTTAA
4310368 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:4310340 original size:17 final size:17
Alignment explanation
Indices: 4310315--4310365 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
4310305 CCGGTTTCGG
4310315 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
4310332 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
4310347 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
4310364 TT
1 TT
4310366 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:4310562 original size:21 final size:21
Alignment explanation
Indices: 4310538--4310590 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
4310528 ACACTTAGGG
4310538 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
4310559 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
4310580 TACCGATTCCC
1 AACCGATTCCC
4310591 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:4310807 original size:13 final size:13
Alignment explanation
Indices: 4310786--4310840 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
4310776 AAGTTCGATA
*
4310786 AATTCAAATACTT
1 AATTGAAATACTT
4310799 AATTGAAATACTT
1 AATTGAAATACTT
* *
4310812 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
4310826 AATTGAAATACTT
1 AATTGAAATACTT
4310839 AA
1 AA
4310841 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:4310922 original size:32 final size:33
Alignment explanation
Indices: 4310826--4310924 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
4310816 AACTCAACAT
* * *
4310826 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4310859 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4310892 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
4310924 A
1 A
4310925 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:4310943 original size:21 final size:21
Alignment explanation
Indices: 4310919--4310958 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4310909 ACTTCAAGTT
4310919 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
4310940 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
4310959 ATAAAATAAA
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:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:4313283 original size:12 final size:12
Alignment explanation
Indices: 4313266--4313311 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
4313256 TCCAGATAAA
4313266 AACCGGTTTTTT
1 AACCGGTTTTTT
4313278 AACCGGTTTTTTT
1 AACCGG-TTTTTT
4313291 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
4313305 ATCCGGT
1 AACCGGT
4313312 AAAAAACCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:4313296 original size:15 final size:14
Alignment explanation
Indices: 4313265--4313304 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
4313255 TTCCAGATAA
4313265 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
4313278 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
4313291 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
4313305 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:4316378 original size:34 final size:34
Alignment explanation
Indices: 4316339--4316447 Score: 119
Period size: 39 Copynumber: 3.0 Consensus size: 34
4316329 TTGGGTCGAG
* *
4316339 TTTTTTAAGTTTGATATTCGGGTCAGGTTGGATT
1 TTTTTTAAGTGTGATATTCGGGTCGGGTTGGATT
* * *
4316373 TTTTTTAAGTGTGATATTCAGGTTGGGTTCGGGTCGAGT
1 TTTTTTAAGTGTGATATTCGGGTCGGGTT---G--GATT
4316412 TTTTTTAAGTGTGATATTCGGGTCGGGTTTGGATT
1 TTTTTTAAGTGTGATATTCGGGTCGGG-TTGGATT
4316447 T
1 T
4316448 AGGGTGAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
34 25 0.41
35 4 0.07
37 2 0.03
39 28 0.46
40 2 0.03
ACGTcount: A:0.16, C:0.06, G:0.30, T:0.48
Consensus pattern (34 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGTTGGATT
Found at i:4318428 original size:20 final size:21
Alignment explanation
Indices: 4318389--4318429 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4318379 TTCTTTAAAA
4318389 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
4318410 TATAATTTTA-GATTATATTT
1 TATAATATTATGAATATATTT
4318430 GATATTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:4321832 original size:23 final size:23
Alignment explanation
Indices: 4321780--4321832 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
4321770 CGATTCCCCT
4321780 AAGGGGGGAATCAGTTCCCATTC
1 AAGGGGGGAATCAGTTCCCATTC
* ** *
4321803 AAAGGGGGAATGGGTTCCCCTTC
1 AAGGGGGGAATCAGTTCCCATTC
*
4321826 ATGGGGG
1 AAGGGGG
4321833 TATCGATTCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (23 bp):
AAGGGGGGAATCAGTTCCCATTC
Found at i:4327397 original size:11 final size:11
Alignment explanation
Indices: 4327375--4327410 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
4327365 GTTTGATGCT
4327375 TTCTCT-TTGA
1 TTCTCTCTTGA
4327385 TTCTCTCTTGA
1 TTCTCTCTTGA
4327396 TTCTCTCTTGA
1 TTCTCTCTTGA
4327407 TTCT
1 TTCT
4327411 AGTTGCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:4331335 original size:30 final size:30
Alignment explanation
Indices: 4331301--4331357 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
4331291 GTAATATTAG
4331301 AAATCAGGAGTAAGATGTATTTAGTATCAT
1 AAATCAGGAGTAAGATGTATTTAGTATCAT
* *
4331331 AAATCAGTAGTCAGATGTATTTAGTAT
1 AAATCAGGAGTAAGATGTATTTAGTAT
4331358 TAGAAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (30 bp):
AAATCAGGAGTAAGATGTATTTAGTATCAT
Found at i:4336945 original size:19 final size:21
Alignment explanation
Indices: 4336921--4336975 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
4336911 TCTAGGAAGG
4336921 GTATCGATACTGTAGT-A-AA
1 GTATCGATACTGTAGTAAGAA
* *
4336940 GTATCGATACCGCAGTAAGGAA
1 GTATCGATACTGTAGTAA-GAA
4336962 GTATCGATACTGTA
1 GTATCGATACTGTA
4336976 CCTTGGGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 1 0.03
22 14 0.48
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (21 bp):
GTATCGATACTGTAGTAAGAA
Found at i:4337795 original size:23 final size:23
Alignment explanation
Indices: 4337766--4337841 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
4337756 GGGATAATTA
4337766 TATGTGGTCTTTCGGGACATTTC
1 TATGTGGTCTTTCGGGACATTTC
* * ** * *
4337789 TACGTGGTTTTTCAAGACAATAC
1 TATGTGGTCTTTCGGGACATTTC
4337812 TATGTGGTCCTTT-GGGACATTTC
1 TATGTGGT-CTTTCGGGACATTTC
4337835 TATGTGG
1 TATGTGG
4337842 CACTTCGGTG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
23 37 0.93
24 3 0.08
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (23 bp):
TATGTGGTCTTTCGGGACATTTC
Found at i:4338043 original size:18 final size:18
Alignment explanation
Indices: 4337965--4338036 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 18
4337955 AATGAACTGC
4337965 GATAATGATAATAAT-AGT
1 GATAATGATAATAATGA-T
* *
4337983 GACAATGATAATAATGTT
1 GATAATGATAATAATGAT
* *
4338001 GATAATGATATTGATGAT
1 GATAATGATAATAATGAT
* * *
4338019 GCTGATGATGATAATGAT
1 GATAATGATAATAATGAT
4338037 AATGATGTTG
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.35
Consensus pattern (18 bp):
GATAATGATAATAATGAT
Found at i:4338071 original size:2 final size:2
Alignment explanation
Indices: 4338066--4338103 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4338056 TATATATATA
4338066 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4338104 CACTTATGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4344545 original size:12 final size:12
Alignment explanation
Indices: 4344528--4344579 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
4344518 ATTATATTTC
4344528 TTTAATTTAAAT
1 TTTAATTTAAAT
*
4344540 TTTAATATAAAT
1 TTTAATTTAAAT
*
4344552 TTT-ATTTCAATT
1 TTTAATTT-AAAT
*
4344564 ATTTAATTTGAAT
1 -TTTAATTTAAAT
4344577 TTT
1 TTT
4344580 TGAACTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.09
12 20 0.62
13 5 0.16
14 4 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTAATTTAAAT
Found at i:4344748 original size:23 final size:24
Alignment explanation
Indices: 4344712--4344784 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
4344702 CCGAATTATA
4344712 TATAATATAATTTTTATATATTAACT
1 TATAA-AT-ATTTTTATATATTAACT
4344738 TA-AAATA-TTTT-TATATTAACT
1 TATAAATATTTTTATATATTAACT
*
4344759 TATTAAATATATTTTA-CTATTAACT
1 TA-TAAATAT-TTTTATATATTAACT
4344784 T
1 T
4344785 TAATTTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
21 12 0.29
22 4 0.10
23 6 0.15
24 2 0.05
25 15 0.37
26 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TATAAATATTTTTATATATTAACT
Found at i:4344779 original size:25 final size:24
Alignment explanation
Indices: 4344728--4344803 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 24
4344718 ATAATTTTTA
4344728 TATATTAACTTA--AAATAT-TTT
1 TATATTAACTTATTAAATATATTT
4344749 TATATTAACTTATTAAATATATTT
1 TATATTAACTTATTAAATATATTT
*
4344773 TACTATTAACTTTAATTTAAAAATATTT
1 TA-TATTAAC-TT-A-TTAAATATATTT
4344801 TAT
1 TAT
4344804 TTTTATTTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 12 0.26
23 6 0.13
24 5 0.11
25 7 0.15
26 2 0.04
27 2 0.04
28 13 0.28
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTAACTTATTAAATATATTT
Found at i:4349657 original size:3 final size:3
Alignment explanation
Indices: 4349649--4349710 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
4349639 TATGTAAAAT
*
4349649 TAA TAA TAA TAGT TAA TAA TAA TTAA TAA TAA -AA -AA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* *
4349694 -AA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
4349711 ATATAAAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 6 0.12
3 38 0.78
4 5 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:4349667 original size:10 final size:10
Alignment explanation
Indices: 4349652--4349691 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
4349642 GTAAAATTAA
*
4349652 TAATAATAGT
1 TAATAATAAT
4349662 TAATAATAAT
1 TAATAATAAT
*
4349672 TAATAATAAA
1 TAATAATAAT
*
4349682 AAATAATAAT
1 TAATAATAAT
4349692 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (10 bp):
TAATAATAAT
Found at i:4349678 original size:13 final size:12
Alignment explanation
Indices: 4349649--4349710 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
4349639 TATGTAAAAT
*
4349649 TAATAATAATAGT
1 TAATAATAATA-A
4349662 TAATAATAATTAA
1 TAATAATAA-TAA
4349675 TAATAA-AA-AA
1 TAATAATAATAA
4349685 TAATAATAA-AA
1 TAATAATAATAA
* *
4349696 TAAAAATAAAAA
1 TAATAATAATAA
4349708 TAA
1 TAA
4349711 ATATAAAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
10 8 0.18
11 12 0.27
12 7 0.16
13 15 0.34
14 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:4349686 original size:17 final size:17
Alignment explanation
Indices: 4349663--4349718 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
4349653 AATAATAGTT
4349663 AATAATAATTAATAATAAAA
1 AATAATAA-TAA-AAT-AAA
4349683 AATAATAATAAAATAAA
1 AATAATAATAAAATAAA
*
4349700 AATAAAAATAAATATAAA
1 AATAATAATAAA-ATAAA
4349718 A
1 A
4349719 GACCCGGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.41
18 9 0.26
19 3 0.09
20 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAATAATAAAATAAA
Found at i:4349710 original size:23 final size:24
Alignment explanation
Indices: 4349662--4349707 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4349652 TAATAATAGT
* *
4349662 TAATAAT-AATTAATAATAAAAAA
1 TAATAATAAAATAAAAATAAAAAA
4349685 TAATAATAAAATAAAAATAAAAA
1 TAATAATAAAATAAAAATAAAAA
4349708 TAAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
TAATAATAAAATAAAAATAAAAAA
Found at i:4349711 original size:6 final size:6
Alignment explanation
Indices: 4349680--4349718 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
4349670 ATTAATAATA
* *
4349680 AAAAAT AATAAT -AAAAT AAAAAT AAAAAT AAATAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
4349719 GACCCGGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:4349968 original size:40 final size:40
Alignment explanation
Indices: 4349919--4350072 Score: 110
Period size: 40 Copynumber: 3.6 Consensus size: 40
4349909 ACACGATTCC
*
4349919 TACGTGATGAAGAAATCTGGTCAAGGGATGACACGGCTCA
1 TACGCGATGAAGAAATCTGGTCAAGGGATGACACGGCTCA
** * * * *
4349959 TACGCGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCC
1 TACGCGATGAAGAAATCTGG---TC------AA-GG-GATGACACGGCTCA
* *
4350010 TACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCA
1 TACGCGATGAAGAAATCTGGTCAAGGGATGACACGGCTCA
**
4350050 TACGCGATGAAGAGTTCTGGTCA
1 TACGCGATGAAGAAATCTGGTCA
4350073 TCTTTAAGAA
Statistics
Matches: 84, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
40 46 0.55
41 2 0.02
42 2 0.02
43 2 0.02
48 2 0.02
49 2 0.02
50 2 0.02
51 26 0.31
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (40 bp):
TACGCGATGAAGAAATCTGGTCAAGGGATGACACGGCTCA
Found at i:4350070 original size:91 final size:91
Alignment explanation
Indices: 4349915--4350113 Score: 389
Period size: 91 Copynumber: 2.2 Consensus size: 91
4349905 GGAAACACGA
*
4349915 TTCCTACGTGATGAAGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGT
1 TTCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGT
4349980 CATCTTTAAGAAGGGTGATAACTCGG
66 CATCTTTAAGAAGGGTGATAACTCGG
4350006 TTCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGT
1 TTCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGT
4350071 CATCTTTAAGAAGGGTGATAACTCGG
66 CATCTTTAAGAAGGGTGATAACTCGG
4350097 TTCCTACGTGATGAGGA
1 TTCCTACGTGATGAGGA
4350114 CGGCTGATTA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 107 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (91 bp):
TTCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGT
CATCTTTAAGAAGGGTGATAACTCGG
Found at i:4350254 original size:141 final size:137
Alignment explanation
Indices: 4350007--4350306 Score: 394
Period size: 141 Copynumber: 2.2 Consensus size: 137
4349997 ATAACTCGGT
* * **
4350007 TCCTACGTGATGAGGAAATCT-G--GTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTG
1 TCCTACGTGATGAGGAAGTCTGGTCGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
*
4350069 GTCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTAT-CTAAGGTT
66 GCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCCTAAGGTT
4350133 GACACGGC
131 GACAC-GC
* * *
4350141 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAGTCTGGTCGTC-AA-GG--GATGACACGGCTCATACACGATGAAGAAC
* *
4350206 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
62 TCTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCCTAA
* *
4350271 TGTTGACACTC
127 GGTTGACACGC
*
4350282 TCCTATGTGATGAGG-AGATCTGGTC
1 TCCTACGTGATGAGGAAG-TCTGGTC
4350307 AGTTGATGTT
Statistics
Matches: 144, Mismatches: 13, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
134 20 0.14
135 1 0.01
137 3 0.02
138 2 0.01
139 2 0.01
140 2 0.01
141 102 0.71
142 12 0.08
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (137 bp):
TCCTACGTGATGAGGAAGTCTGGTCGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
GCCATCTTTAAGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGATTATCCTAAGGTT
GACACGC
Done.