Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008617.1 Hibiscus syriacus cultivar Beakdansim tig00111575_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: 526994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:3474 original size:15 final size:15
Alignment explanation
Indices: 3456--3485 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3446 CCACGGTGCT
3456 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
*
3471 CCCGGAATCTTGCGC
1 CCCGGAATCCTGCGC
3486 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.43, G:0.27, T:0.17
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:5730 original size:23 final size:23
Alignment explanation
Indices: 5683--5730 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5673 AATAACATAT
**
5683 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
5706 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
5729 TA
1 TA
5731 TGCATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:5787 original size:23 final size:23
Alignment explanation
Indices: 5761--5808 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5751 ATCAAGTACA
5761 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
5784 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
5807 AT
1 AT
5809 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:5792 original size:87 final size:86
Alignment explanation
Indices: 5642--5808 Score: 298
Period size: 87 Copynumber: 1.9 Consensus size: 86
5632 CGGTTATGTT
* *
5642 ATATCATTTAACTGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAAT
1 ATATCATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAAT
5707 AGGTAGCGCTTATATAATAAA
66 AGGTAGCGCTTATATAATAAA
*
5728 ATATGCATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAA
1 ATAT-CATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAA
5793 TAGGTAGCGCTTATAT
65 TAGGTAGCGCTTATAT
5809 TGACCTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 4 0.05
87 73 0.95
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (86 bp):
ATATCATTTAACCGGAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAAT
AGGTAGCGCTTATATAATAAA
Found at i:6165 original size:197 final size:197
Alignment explanation
Indices: 5827--6320 Score: 517
Period size: 197 Copynumber: 2.5 Consensus size: 197
5817 TTTCTCATAA
* * * * *
5827 AACCGGTAAATTTAAACCGGTTACATTATAAATTGACCTATTACATTAT-GTATATCGGTTTCGA
1 AACCGGTATATTTTAACCGGTTACATTATAAATTTACCTATTACATTATAAT-TATCGATTTCGA
* * *
5891 TGTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTTATGCATGCAACTCGTTTGTGCTTT
65 TGTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTTATGCATACAACTCGTTTGTCCTTC
* * *
5956 ATTTTGGAAAAAA-GTATCGACACATATTTAAAGAGTGTCGATACACAATGTAGACCTATT-TGC
130 ATTTTGGAAAAAATGTATCAACACA-AATTAAAAAGTGTCGATACACAATGTAGACCTATTCT-C
*
6019 TAATT
193 TAATG
* *
6024 AACCGGTATATTTTAACCGGTTACATTATAAATTTACCTGTTACATAATAATTATCGATTTCGAT
1 AACCGGTATATTTTAACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGATTTCGAT
* ** * *
6089 G-TTTCGATGATCGATA-TTTTTTACAAATGTATCGACACTTTATGCTTACACCTCGTTT-TCCA
66 GTTTTCG-GGATCGATACAATTTT--AAATGTATCGACACTTTATGCATACAACTCGTTTGTCC-
*** *
6151 TTCATTTT-GAAAAAATGTATCAACACAAATTAAAAAGTGTCGATACTTTATGTTGACCTATTCT
127 TTCATTTTGGAAAAAATGTATCAACACAAATTAAAAAGTGTCGATACACAATGTAGACCTATTCT
*
6215 CTCATG
192 CTAATG
* ** * * **
6221 AACCCGGTATATTCT-ACC-G-TACATTGGAAATTTACCTATTACATTATAATTATCGGTCTCTT
1 AA-CCGGTATATTTTAACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGATTTCGA
* *
6283 TGATTT-GGGATCGATAC-TTGTTATAAATGTATCGACAC
65 TGTTTTCGGGATCGATACAAT-TT-TAAATGTATCGACAC
6321 AAAATCTAAT
Statistics
Matches: 251, Mismatches: 34, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
194 24 0.10
195 40 0.16
196 14 0.06
197 112 0.45
198 61 0.24
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (197 bp):
AACCGGTATATTTTAACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGATTTCGAT
GTTTTCGGGATCGATACAATTTTAAATGTATCGACACTTTATGCATACAACTCGTTTGTCCTTCA
TTTTGGAAAAAATGTATCAACACAAATTAAAAAGTGTCGATACACAATGTAGACCTATTCTCTAA
TG
Found at i:7037 original size:18 final size:19
Alignment explanation
Indices: 6998--7048 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 19
6988 TTAGTGACAT
6998 TCTTTCTCTTCATTTCCTCCA
1 TCTTT-TCTTC-TTTCCTCCA
7019 TCTTTTCTTCTTT-CTCCA
1 TCTTTTCTTCTTTCCTCCA
7037 TCTTTTCTTCTT
1 TCTTTTCTTCTT
7049 CAAATTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.57
19 3 0.10
20 5 0.17
21 5 0.17
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (19 bp):
TCTTTTCTTCTTTCCTCCA
Found at i:7424 original size:15 final size:15
Alignment explanation
Indices: 7404--7433 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7394 ACTCTGTTTT
7404 CCCTGACCGTAATCC
1 CCCTGACCGTAATCC
*
7419 CCCTGACCGTCATCC
1 CCCTGACCGTAATCC
7434 ACCCCTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTGACCGTAATCC
Found at i:7749 original size:22 final size:24
Alignment explanation
Indices: 7721--7776 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
7711 AACCTGCATT
7721 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
7743 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
7767 TATAAAAAAA
1 TATAATAAAA
7777 CAAAAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 14 0.52
25 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:9698 original size:20 final size:20
Alignment explanation
Indices: 9652--9698 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
9642 ACCGGTAGCG
9652 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
9672 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
9693 -TTTACC
1 CTTTACC
9699 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:10288 original size:182 final size:182
Alignment explanation
Indices: 9626--10271 Score: 902
Period size: 182 Copynumber: 3.6 Consensus size: 182
9616 ATTAAAGTAC
* * * * *
9626 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * *
9691 TTTTTACCTATTATATTGTTATGGATCGATACGTTT-TCATAAAGTATCGACACTTTTTAGGCGC
66 TTATTACCTATTATATTGCTATGGATCGATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGC
*
9755 TATAATTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* * * * *
9808 CGACACTTTCAATATATCTGATATCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * *
9873 TTATTACTTGTTATATTGCTATAGATCGATACATTTGTATAAAGTATAGACACTTTTTA-GCGCT
66 TTATTACCTATTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
* * *
9937 ATTACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATACTAATGTAT
131 ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
** * * **
9989 CGACACTTTCAATATATATGGTATCTTTTTACCGGTTTTATCATTTCGAGACTTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* *
10054 TTATTACCTATTCTATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGTGCT
66 TTATTACCTATTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
* *
10119 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* * * *
10171 CGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTGTCAT
* * * *
10235 ATTTTTATCTGTTATATTGCTATGGATCCATACATTT
65 ATTATTACCTATTATATTGCTATGGATCGATACATTT
10272 TTAATTTGTA
Statistics
Matches: 411, Mismatches: 50, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
181 169 0.41
182 240 0.58
183 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTATTACCTATTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
ATAACTTATTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
Found at i:12345 original size:15 final size:16
Alignment explanation
Indices: 12308--12338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12298 TTTCATGTTA
*
12308 ATATCATTTTAAATTC
1 ATATCATTTAAAATTC
12324 ATATCATTTAAAATT
1 ATATCATTTAAAATT
12339 TATTCATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATCATTTAAAATTC
Found at i:17088 original size:6 final size:6
Alignment explanation
Indices: 17076--17213 Score: 73
Period size: 6 Copynumber: 23.0 Consensus size: 6
17066 TATTCCTACA
* * * * *
17076 ATTCTT CTTCTT CTTATT CTTCTT ATTCTT ATTCTT ATTCTT ATTATT
1 ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT
* * * * * * * *
17124 ATTATT ATTATT -TTATT ATTATT ATTATT ATTATT A-TATT ATTATT
1 ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT
* * * * * *
17170 ATTATT ATTATTT ATTATT ATTATT ATTATT ATTTATT ATTCTT
1 ATTCTT ATT-CTT ATTCTT ATTCTT ATTCTT A-TTCTT ATTCTT
17214 CACGTTGGTG
Statistics
Matches: 120, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.08
6 99 0.82
7 11 0.09
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTCTT
Found at i:17089 original size:9 final size:9
Alignment explanation
Indices: 17077--17120 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
17067 ATTCCTACAA
*
17077 TTCTTCTTC
1 TTCTTATTC
17086 TTCTTATTC
1 TTCTTATTC
17095 TTCTTATTC
1 TTCTTATTC
* * *
17104 TTATTCTTA
1 TTCTTATTC
17113 TTCTTATT
1 TTCTTATT
17121 ATTATTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.68
Consensus pattern (9 bp):
TTCTTATTC
Found at i:17096 original size:15 final size:15
Alignment explanation
Indices: 17076--17123 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
17066 TATTCCTACA
17076 ATTCTTCTTCTTCTT
1 ATTCTTCTTCTTCTT
*
17091 ATTCTTCTTATTCTT
1 ATTCTTCTTCTTCTT
* *
17106 ATTCTTATTCTTATT
1 ATTCTTCTTCTTCTT
17121 ATT
1 ATT
17124 ATTATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTCTTCTTCTTCTT
Found at i:17124 original size:3 final size:3
Alignment explanation
Indices: 17098--17210 Score: 167
Period size: 3 Copynumber: 37.7 Consensus size: 3
17088 CTTATTCTTC
* * *
17098 TTA TTC TTA TTC TTA TTC TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17145 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
17190 TTA TTA TTA TTA TTTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TT
17211 CTTCACGTTG
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.04
3 90 0.90
4 6 0.06
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17417 original size:79 final size:80
Alignment explanation
Indices: 17279--17530 Score: 316
Period size: 79 Copynumber: 3.2 Consensus size: 80
17269 TCCTTTAAAT
* * * *
17279 TATGGGTGCATTATCGGCATAAAATAATAATGCATATAGG-TGAATTATT-AGCATGAAAGGATT
1 TATGGGTGCATTATCGACATAAAAGAATAATGCATAT-GGATGCATTATTGAGCATGAAAGGATG
*
17342 TCATAGCTGAAATGCA
65 CCATAGCTGAAATGCA
*
17358 TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGATGCATTATTGAG-ATTAAAGGATGC
1 TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGATGCATTATTGAGCATGAAAGGATGC
17422 CATAGCTGAAATGCA
66 CATAGCTGAAATGCA
* * * * ** *
17437 TATAGGTGTATTATCAATATAAAAGAATAATGCATAT-GAGTGCATTATTG-GCATGAAATAAGG
1 TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGA-TGCATTATTGAGCATGAAAGGATG
* *
17500 CCATAACTGAAATGAA
65 CCATAGCTGAAATGCA
17516 TATGGGTGCATTATC
1 TATGGGTGCATTATC
17531 AGTATAAATA
Statistics
Matches: 151, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.03
79 144 0.95
80 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (80 bp):
TATGGGTGCATTATCGACATAAAAGAATAATGCATATGGATGCATTATTGAGCATGAAAGGATGC
CATAGCTGAAATGCA
Found at i:20129 original size:45 final size:43
Alignment explanation
Indices: 20059--20281 Score: 167
Period size: 45 Copynumber: 5.5 Consensus size: 43
20049 ATAAACGAAT
* *
20059 AATGTATATGGGTGCTTTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCCATAG-TGA
* * *
20104 AATACATATGGGTGAATTATCGGCAT-AAA-A-G--A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTGA
* *
20138 AATGCATATGGATGAATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCCATAG-TGA
* *
20183 AATGCATATAGGTGCATTATTAGCAT-AAA-AT---A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTGA
20217 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAG-ATGCCATAG-TGA
* *
20262 AATACATATAGGTGCATTAT
1 AATGCATATGGGTGCATTAT
20282 CAGCATAAAT
Statistics
Matches: 140, Mismatches: 16, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
34 47 0.34
35 6 0.04
36 2 0.01
37 3 0.02
38 3 0.02
39 2 0.01
40 2 0.01
41 3 0.02
42 3 0.02
43 2 0.01
44 6 0.04
45 61 0.44
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCCATAGTGA
Found at i:20162 original size:79 final size:79
Alignment explanation
Indices: 20035--20290 Score: 377
Period size: 79 Copynumber: 3.2 Consensus size: 79
20025 TTAAATTATG
* * * *
20035 GGTGAATTATCGGCATAAACGAATAATGTATATGGGTGCTTTATTGGCATGAAAGGATGCCATAG
1 GGTGAATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
*
20100 TTGAAATACATATG
66 TTGAAATACATATA
* * *
20114 GGTGAATTATCGGCATAAAAGAATAATGCATATGGATGAATTATTGGCATGAAAGGATGCCATAG
1 GGTGAATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
* *
20179 CTGAAATGCATATA
66 TTGAAATACATATA
* * * *
20193 GGTGCATTATTAGCATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAG
1 GGTGAATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
20258 TTGAAATACATATA
66 TTGAAATACATATA
*
20272 GGTGCATTATCAGCATAAA
1 GGTGAATTATCAGCATAAA
20291 TGTATGTTAT
Statistics
Matches: 159, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 159 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
GGTGAATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG
TTGAAATACATATA
Found at i:24043 original size:20 final size:21
Alignment explanation
Indices: 24020--24069 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
24010 GGCATTACTA
24020 ATAACATTGA-TCATGTTGAG
1 ATAACATTGATTCATGTTGAG
* *
24040 ATAATA-AGATTCATGTTGAG
1 ATAACATTGATTCATGTTGAG
24060 A-AGACATTGA
1 ATA-ACATTGA
24070 GAAAGAACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (21 bp):
ATAACATTGATTCATGTTGAG
Found at i:25707 original size:95 final size:96
Alignment explanation
Indices: 25533--25750 Score: 246
Period size: 95 Copynumber: 2.2 Consensus size: 96
25523 TTTTCCTATC
* * *
25533 TGACCTACAATGAAGAGTAGATGAGAAGATCCTTATTTCTTTGAATCTGACCTACCCCAAAGAGC
1 TGACCTACCATGAAGAGTAGA-GAGAAGATCCCTATTTCTTTGAATCTGACCTACCCCAAAGAAC
*
25598 ACCGAAGAAGATTCCA-ATTTTTCTTTAGATT
65 ACAGAAGAAGATTCCATATTTTTCTTTAGATT
* * **
25629 TGACCTACCATGAAGAGTAGCA-AGAAGATCCCTCTTTCTTTGAATTTGACCTACCCTTAAGAAC
1 TGACCTACCATGAAGAGTAG-AGAGAAGATCCCTATTTCTTTGAATCTGACCTACCCCAAAGAAC
* *
25693 AACAG-AGCAA-ATTCCATTTTTTTTCTTTATATT
65 -ACAGAAG-AAGATTCCA-TATTTTTCTTTAGATT
* *
25726 TGAGCTACCCTGAAGAGTAGTAGAG
1 TGACCTACCATGAAGAGTAG-AGAG
25751 CAAATCTATC
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
95 44 0.43
96 24 0.23
97 33 0.32
98 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (96 bp):
TGACCTACCATGAAGAGTAGAGAGAAGATCCCTATTTCTTTGAATCTGACCTACCCCAAAGAACA
CAGAAGAAGATTCCATATTTTTCTTTAGATT
Found at i:26803 original size:24 final size:24
Alignment explanation
Indices: 26771--26816 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
26761 TCTTCCAGAT
26771 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
26795 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
26817 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:28844 original size:17 final size:17
Alignment explanation
Indices: 28794--28846 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
28784 TGAATAAAGT
*
28794 TAGTTCATTAATTAAAC
1 TAGTTCGTTAATTAAAC
* *
28811 TAGTT-GATTCATCAAAC
1 TAGTTCG-TTAATTAAAC
*
28828 TAGTTCGTTTATTAAAC
1 TAGTTCGTTAATTAAAC
28845 TA
1 TA
28847 ACTCTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 28 0.97
18 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (17 bp):
TAGTTCGTTAATTAAAC
Found at i:36761 original size:17 final size:17
Alignment explanation
Indices: 36728--36780 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
36718 TGAATAAAGT
* *
36728 TAGTTCATTAATTAAAC
1 TAGTTCATTCATCAAAC
*
36745 TAGTTGATTCATCAAAC
1 TAGTTCATTCATCAAAC
* *
36762 TAGTTCATTTATTAAAC
1 TAGTTCATTCATCAAAC
36779 TA
1 TA
36781 ACTCTTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTCATCAAAC
Found at i:41923 original size:28 final size:28
Alignment explanation
Indices: 41889--41957 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
41879 ATATTGAATT
*
41889 TTATTTTCGTTACATATTGGTCCATGTA
1 TTATTTTCATTACATATTGGTCCATGTA
41917 TTATTTTCATTACATATTGGTCCATGTA
1 TTATTTTCATTACATATTGGTCCATGTA
41945 TTATTTTCATTAC
1 TTATTTTCATTAC
41958 TAACTTCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.52
Consensus pattern (28 bp):
TTATTTTCATTACATATTGGTCCATGTA
Found at i:46334 original size:19 final size:18
Alignment explanation
Indices: 46287--46341 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
46277 ATCTAACCCA
**
46287 TTGACTTTGACCCAAAATG
1 TTGACTTTGA-CCAAACCG
*
46306 TTGACTTTGACCTAACCG
1 TTGACTTTGACCAAACCG
46324 TTGACTGTTGACCAAACC
1 TTGACT-TTGACCAAACC
46342 CATTAACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TTGACTTTGACCAAACCG
Found at i:49841 original size:55 final size:54
Alignment explanation
Indices: 49759--49898 Score: 163
Period size: 55 Copynumber: 2.5 Consensus size: 54
49749 CTCGGAGCCA
* * *
49759 GGGGTGTATCGCTACATCAACCAGTGTATCGATACACAAAATGCATTCAATGTAG
1 GGGGTGTATCGATACATCAA-GAGTGTATCGATACACAAAATACATTCAATGTAG
* * * * * *
49814 GGGGTGTATCGATACAACGAAGAGTGTATCGGTACCCAAATTACATTCGATGTTG
1 GGGGTGTATCGATACATC-AAGAGTGTATCGATACACAAAATACATTCAATGTAG
*
49869 GGGGTATATCGATACATCCAAGAGTGTATC
1 GGGGTGTATCGATACAT-CAAGAGTGTATC
49899 AGTACCTCCC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
55 69 0.96
56 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (54 bp):
GGGGTGTATCGATACATCAAGAGTGTATCGATACACAAAATACATTCAATGTAG
Found at i:50516 original size:19 final size:21
Alignment explanation
Indices: 50481--50524 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
50471 AATAAACATT
*
50481 AAATTTAAACTAATC-AAACC
1 AAATTCAAACTAATCAAAACC
50501 AAATTCAAAC-AATCAAAACC
1 AAATTCAAACTAATCAAAACC
50521 AAAT
1 AAAT
50525 ATATATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATTCAAACTAATCAAAACC
Found at i:55259 original size:63 final size:64
Alignment explanation
Indices: 55181--55308 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
55171 ATAACCCAAG
55181 TATCTAGAATAGTCATCTACCAATAC-AAGCAATATTGTTTTCCACCCAAGCTAATCGTTCTAA
1 TATCTAGAATAGTCATCTACCAATACAAAGCAATATTGTTTTCCACCCAAGCTAATCGTTCTAA
55244 TATCTAGAATAGTCATCTACCAATACAAAGCAATATTGTTTTCCACCCAAGCTAATCGTTCTAA
1 TATCTAGAATAGTCATCTACCAATACAAAGCAATATTGTTTTCCACCCAAGCTAATCGTTCTAA
55308 T
1 T
55309 TGGCCCAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 26 0.41
64 38 0.59
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (64 bp):
TATCTAGAATAGTCATCTACCAATACAAAGCAATATTGTTTTCCACCCAAGCTAATCGTTCTAA
Found at i:56427 original size:22 final size:21
Alignment explanation
Indices: 56387--56429 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56377 GAGTTCATTT
*
56387 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTAGAAATA
*
56408 TCATTTTTGAATTTCAGAAATA
1 TCATTTTTCAATTT-AGAAATA
56430 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (21 bp):
TCATTTTTCAATTTAGAAATA
Found at i:59479 original size:34 final size:34
Alignment explanation
Indices: 59419--59487 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 34
59409 TTCAATACCA
*
59419 TTTTATAGCTAAGTGCATAAACTTTA-CTCGAAG
1 TTTTATAGCTAAGTGAATAAACTTTACCTCGAAG
59452 TTTTATAGTCTAAGTGAAT-AACATTTACCTCGAAG
1 TTTTATAG-CTAAGTGAATAAAC-TTTACCTCGAAG
59487 T
1 T
59488 CCCTTCGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 11 0.34
34 13 0.41
35 8 0.25
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (34 bp):
TTTTATAGCTAAGTGAATAAACTTTACCTCGAAG
Found at i:62399 original size:16 final size:17
Alignment explanation
Indices: 62366--62399 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62356 CAATATTTTG
*
62366 TTTATTTTTTTCATTAT
1 TTTATTTATTTCATTAT
62383 TTTATTTATTT-ATTAT
1 TTTATTTATTTCATTAT
62399 T
1 T
62400 AATTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTCATTAT
Found at i:68797 original size:13 final size:13
Alignment explanation
Indices: 68779--68803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68769 ATTCTAATAA
68779 TTTTTTATTTTAC
1 TTTTTTATTTTAC
68792 TTTTTTATTTTA
1 TTTTTTATTTTA
68804 GGGTAAACTA
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:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTATTTTAC
Found at i:70906 original size:2 final size:2
Alignment explanation
Indices: 70899--70971 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
70889 TTGAGGTCTT
70899 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
70941 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 T
70972 GCTTCGTATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:72102 original size:14 final size:14
Alignment explanation
Indices: 72083--72115 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
72073 CGTTCGTGAA
72083 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
72097 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
72111 CGTTC
1 CGTTC
72116 ATTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.18, G:0.27, T:0.48
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:72121 original size:14 final size:14
Alignment explanation
Indices: 72083--72124 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
72073 CGTTCGTGAA
*
72083 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
*
72097 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
*
72111 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
72125 TAACCCAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:73253 original size:26 final size:26
Alignment explanation
Indices: 73224--73276 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
73214 TTTATGTTCG
73224 TGTTCGTTTAT-GTTCATATTCATTTA
1 TGTTCGTTT-TCGTTCATATTCATTTA
* *
73250 TGTTCGTTTTCGTTTATATTCGTTTA
1 TGTTCGTTTTCGTTCATATTCATTTA
73276 T
1 T
73277 TTATTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.60
Consensus pattern (26 bp):
TGTTCGTTTTCGTTCATATTCATTTA
Found at i:73273 original size:16 final size:16
Alignment explanation
Indices: 73210--73274 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
73200 AACGTTTATG
*
73210 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTT
* *
73226 TTCGTTTATGTTCATA
1 TTCGTTTATGTTCGTT
*
73242 TTCATTTATGTTCGTT
1 TTCGTTTATGTTCGTT
*
73258 TTCGTTTATATTCGTT
1 TTCGTTTATGTTCGTT
73274 T
1 T
73275 ATTTATTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (16 bp):
TTCGTTTATGTTCGTT
Found at i:73318 original size:31 final size:31
Alignment explanation
Indices: 73283--73363 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
73273 TTATTTATTA
73283 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
*
73314 AATGAACGAACATGAACAAGCTATATTCTTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
73345 AATGAACGAACATGAACAA
1 AATGAACGAACATGAACAA
73364 AAAAAATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGCTATATTCCTT
Found at i:77074 original size:3 final size:3
Alignment explanation
Indices: 77055--77095 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
77045 TAGAGTGATT
*
77055 TAA T-A TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
77096 ATATTATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:84929 original size:42 final size:42
Alignment explanation
Indices: 84833--84930 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
84823 TTTCTTGTAC
* * * * * * **
84833 AAACGCTATAATAGAGTAGTAATTTTGCGGCGTTTTTAGTCC
1 AAACGCCACAATAGAGTAGTAATTTAGCGACGTATGTAGTAA
* *
84875 AAACACCGCAATAGAGTAGTAATTTAGCGACGTATGTAGTAA
1 AAACGCCACAATAGAGTAGTAATTTAGCGACGTATGTAGTAA
84917 AAACGCCACAATAG
1 AAACGCCACAATAG
84931 GGTTTTTTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (42 bp):
AAACGCCACAATAGAGTAGTAATTTAGCGACGTATGTAGTAA
Found at i:85458 original size:27 final size:27
Alignment explanation
Indices: 85428--85479 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
85418 TATTGGTTTA
* *
85428 CTGCTTTCGAATAGAAAAATAATAGAT
1 CTGCTTCCGAAAAGAAAAATAATAGAT
*
85455 CTGCTTCCGAAAAGGAAAATAATAG
1 CTGCTTCCGAAAAGAAAAATAATAG
85480 TTTTTGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (27 bp):
CTGCTTCCGAAAAGAAAAATAATAGAT
Found at i:90131 original size:7 final size:7
Alignment explanation
Indices: 90119--90145 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
90109 AACATATTCT
90119 TTATGAA
1 TTATGAA
90126 TTATGAA
1 TTATGAA
90133 TTATGAA
1 TTATGAA
90140 TTATGA
1 TTATGA
90146 TCCAATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
TTATGAA
Found at i:96450 original size:21 final size:21
Alignment explanation
Indices: 96409--96450 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
96399 AAGAAGTAAG
* * *
96409 GGAAGCAGAGAGAGCAGCAAC
1 GGAAGCACAGAGAGAAACAAC
96430 GGAAGCACAGAGAGAAACAAC
1 GGAAGCACAGAGAGAAACAAC
96451 ATATCAGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.19, G:0.33, T:0.00
Consensus pattern (21 bp):
GGAAGCACAGAGAGAAACAAC
Found at i:99572 original size:2 final size:2
Alignment explanation
Indices: 99565--99598 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
99555 ACTAAAGTAA
*
99565 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99599 TTAGGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:101181 original size:3 final size:3
Alignment explanation
Indices: 101175--101209 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
101165 TACTATTATT
101175 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
101210 TTTAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:110236 original size:135 final size:134
Alignment explanation
Indices: 109993--110248 Score: 404
Period size: 135 Copynumber: 1.9 Consensus size: 134
109983 CAGATGCACA
* ** **
109993 TTTTGCATAAAATAGCATTTTATTTCCTCTTCTAAAATTATCTTCTAAAGGTAGGTACACAATTT
1 TTTTGCATAAAATAACATTTTATTTCCTCTTCTAAAATTATCTTAAAAAAATAGGTACACAATTT
* * *
110058 TCTAAAGTTGATATTATTTTAAGGTTCAATTATAAACTAGTATCACTCAACTTTTTTTTTCTCAC
66 TCTAAAGTTAATATTATTTAAAGGCTCAATTATAAACTAGTATCACTCAACTTTTTTTTTCTCAC
110123 TCAT
131 TCAT
*
110127 TTTTGCATAAAATAACATTTTATTTCCTCTTTCTAAAATTATCTTAAAAAAATAGGTACATAATT
1 TTTTGCATAAAATAACATTTTATTTCCTC-TTCTAAAATTATCTTAAAAAAATAGGTACACAATT
* *
110192 TTCTAAAGTTAATATTATTTAAAGGCTCAATTATAAACTTGTATCATTCAACTTTTT
65 TTCTAAAGTTAATATTATTTAAAGGCTCAATTATAAACTAGTATCACTCAACTTTTT
110249 CTCAGTCATA
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
134 28 0.25
135 82 0.75
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (134 bp):
TTTTGCATAAAATAACATTTTATTTCCTCTTCTAAAATTATCTTAAAAAAATAGGTACACAATTT
TCTAAAGTTAATATTATTTAAAGGCTCAATTATAAACTAGTATCACTCAACTTTTTTTTTCTCAC
TCAT
Found at i:111766 original size:42 final size:42
Alignment explanation
Indices: 111707--111790 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
111697 GAAGAGCCAA
*
111707 CCACCACTATACTCTATTTACTACCATACAAAATGCGTACAT
1 CCACCACTATACTCTATTTACTACCATACAAAATGAGTACAT
111749 CCACCACTATACTCTATTTACTACCATACAAAATGAGTACAT
1 CCACCACTATACTCTATTTACTACCATACAAAATGAGTACAT
111791 AAAAAGGCAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.30, G:0.05, T:0.29
Consensus pattern (42 bp):
CCACCACTATACTCTATTTACTACCATACAAAATGAGTACAT
Found at i:112610 original size:25 final size:25
Alignment explanation
Indices: 112565--112628 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
112555 GCGGCAAGTC
*
112565 TAATAATAGAT-TTTTTTTGAAATT
1 TAATAATAGATATTTTATTGAAATT
*
112589 TAATAATAGGTATTTTATTGAAATT
1 TAATAATAGATATTTTATTGAAATT
*
112614 TAATAATAGTTATTT
1 TAATAATAGATATTT
112629 AGGTACCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 10 0.28
25 26 0.72
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (25 bp):
TAATAATAGATATTTTATTGAAATT
Found at i:113364 original size:20 final size:20
Alignment explanation
Indices: 113313--113364 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
113303 GAATCGCAAG
*
113313 GAACCG-TTGAACCTGCTGT
1 GAACCGTTTGAACCGGCTGT
* *
113332 GAACCATTCGAACCGGCTGT
1 GAACCGTTTGAACCGGCTGT
113352 GAACCGTTTGAAC
1 GAACCGTTTGAAC
113365 TGGACCGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (20 bp):
GAACCGTTTGAACCGGCTGT
Found at i:113650 original size:23 final size:22
Alignment explanation
Indices: 113617--113663 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
113607 TGTGGGAATG
113617 TTTTTAGTTTTTTATTAAATATTT
1 TTTTTAG-TTTTTATTAAAT-TTT
*
113641 TTTTTA-TTTTTATTTAATTTT
1 TTTTTAGTTTTTATTAAATTTT
113662 TT
1 TT
113664 AAATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 11 0.50
24 6 0.27
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTAGTTTTTATTAAATTTT
Found at i:114249 original size:3 final size:3
Alignment explanation
Indices: 114237--114268 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
114227 TAGAGTGATT
114237 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
114269 ATAAATAAAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:114283 original size:9 final size:10
Alignment explanation
Indices: 114241--114284 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
114231 GTGATTTAAT
114241 ATAATAAT-A
1 ATAATAATAA
114250 ATAATAAT-A
1 ATAATAATAA
114259 ATAATAATAA
1 ATAATAATAA
114269 AT-A-AATAA
1 ATAATAATAA
114277 ATAA-AATA
1 ATAATAATA
114285 TTATGCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 7 0.21
9 23 0.70
10 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAATAATAA
Found at i:117198 original size:3 final size:3
Alignment explanation
Indices: 117190--117230 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
117180 AACATTTTAA
*
117190 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
117231 ATGATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:118332 original size:2 final size:2
Alignment explanation
Indices: 118325--118438 Score: 72
Period size: 2 Copynumber: 56.5 Consensus size: 2
118315 CATATACAAA
* * *
118325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT -T CAT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * * *
118367 GT GAT TT TT GAT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT
1 AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
118411 -T TT AT AT GT A- AT AT AC AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
118439 GAATTAAGTG
Statistics
Matches: 88, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
1 3 0.03
2 80 0.91
3 5 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (2 bp):
AT
Found at i:118431 original size:50 final size:50
Alignment explanation
Indices: 118327--118438 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
118317 TATACAAAAT
* * * **
118327 ATATATATATATATATATATATATATTTATTTATTCATGTGTGATTTTTG
1 ATATATATATATATATATATATATATTTATTTATTCATATGTGAATATAC
*
118377 ATATATATATATATATATATATATATTTATTTATTTTATATGT-AATATAC
1 ATATATATATATATATATATATATATTTATTTA-TTCATATGTGAATATAC
118427 ATATATCATATA
1 ATATAT-ATATA
118439 GAATTAAGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
50 42 0.78
51 12 0.22
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (50 bp):
ATATATATATATATATATATATATATTTATTTATTCATATGTGAATATAC
Found at i:118597 original size:15 final size:15
Alignment explanation
Indices: 118577--118610 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
118567 TATAACTCGA
*
118577 AGTTCTTTTGAGTCG
1 AGTTCTTTTGAATCG
118592 AGTTCTTTTGAATCG
1 AGTTCTTTTGAATCG
118607 AGTT
1 AGTT
118611 AAGTCGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (15 bp):
AGTTCTTTTGAATCG
Found at i:121507 original size:32 final size:31
Alignment explanation
Indices: 121430--121507 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
121420 CTAAAGTGAC
* * **
121430 CCTTAGGTAGGCTCTTAGGCCCCAAGGTACT
1 CCTTAGGTAGGCTCTAAAGCCCCAAGACACT
*
121461 CCATTGGGTAGGCTCTAAAGCCCCAAGACACT
1 CC-TTAGGTAGGCTCTAAAGCCCCAAGACACT
*
121493 ACCTTAGGTTGGCTC
1 -CCTTAGGTAGGCTC
121508 CTATGTCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 2 0.05
32 34 0.89
33 2 0.05
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (31 bp):
CCTTAGGTAGGCTCTAAAGCCCCAAGACACT
Found at i:121813 original size:16 final size:16
Alignment explanation
Indices: 121789--121826 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
121779 AAATTTCATG
*
121789 CTTGACTATATATCTA
1 CTTGGCTATATATCTA
121805 CTTGGCTATATATCTA
1 CTTGGCTATATATCTA
121821 CTTGGC
1 CTTGGC
121827 CTTTAGCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (16 bp):
CTTGGCTATATATCTA
Found at i:121999 original size:3 final size:3
Alignment explanation
Indices: 121991--122039 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
121981 TTCGTCCCGC
* * * *
121991 TAT TAT TAT TAT TAT TAT TAT TAT TAG TGT TAT TAA TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
122039 T
1 T
122040 TATTTTACAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:123667 original size:61 final size:62
Alignment explanation
Indices: 123536--123654 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 62
123526 TAAAAATGCT
* * **
123536 TATTTTAGTCACTTTTGCATTTTGTTTTGTTTTAATTTTTGACATGATGCTTTGTTTGTTTA
1 TATTTTAGTCACTTTTGCATTTTATTTTGATTTAATTTTTGACATGATGCTTTGCATGTTTA
* *
123598 TATTTTAGTC-CTATTTTCATTTTATTTT-ATTTAATTTTTG-CATGTTGC-TTGCATGTT
1 TATTTTAGTCACT-TTTGCATTTTATTTTGATTTAATTTTTGACATGATGCTTTGCATGTT
123655 ATTTCATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 7 0.14
60 7 0.14
61 13 0.26
62 23 0.46
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (62 bp):
TATTTTAGTCACTTTTGCATTTTATTTTGATTTAATTTTTGACATGATGCTTTGCATGTTTA
Found at i:124381 original size:131 final size:129
Alignment explanation
Indices: 124100--124435 Score: 381
Period size: 131 Copynumber: 2.6 Consensus size: 129
124090 CAATATTGAG
* * *
124100 AATAGTAATATCT-TATCATTTCAGTTGGAGTAATAAAT-AACTGCTTTCAGGCATGAGAGGTCA
1 AATAGTGATATCTCT-TCATTTCA-TTGGAGTAATAAATGAA-TGCTTTAAGGCATGAGCGGTCA
* * * *
124163 TTTATTCTCGATTGGAATAATTTGTTATTAATATTTTCTCTCAAATCATTATTGATTTTTAAGAC
63 TTTATTCTCGATTGGAATAATTAGATATTAATATTTTCACTCAAATCATTATTGAATTTTAAGAC
*
124228 GG
128 GA
* ** * *
124230 AATAGTGACATCTCTTCATTTCGATTGGAGTAATAAATGGTTGCTTTAAGGTATGAGCGGTTATT
1 AATAGTGATATCTCTTCATTTC-ATTGGAGTAATAAATGAATGCTTTAAGGCATGAGCGGTCATT
* * * * * * *
124295 TATTCTCGATTGGAAATCATTAGATATTATTGTTTTCACTTGAATTGA-TATTGAATTTTAAGAT
65 TATTCTCGATTGG-AATAATTAGATATTAATATTTTCAC-TCAAATCATTATTGAATTTTAAGAC
124359 GA
128 GA
** *
124361 AATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGAATGCTTTAAGGCACAAGCAGTCATT
1 AATAGTGATATCTCTTCATTTC-ATTGGAGTAATAAATGAATGCTTTAAGGCATGAGCGGTCATT
124426 TATTCTCGAT
65 TATTCTCGAT
124436 CAGAAATAAT
Statistics
Matches: 172, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
130 65 0.38
131 102 0.59
132 5 0.03
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (129 bp):
AATAGTGATATCTCTTCATTTCATTGGAGTAATAAATGAATGCTTTAAGGCATGAGCGGTCATTT
ATTCTCGATTGGAATAATTAGATATTAATATTTTCACTCAAATCATTATTGAATTTTAAGACGA
Found at i:138446 original size:31 final size:31
Alignment explanation
Indices: 138403--138512 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
138393 CATAGATTTT
* **
138403 GAAGAACCTAGGTATTCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
138434 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* **
138465 GAAGAATATAGGTAAACAGTCCATATGTTTC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
138496 AAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
138513 CCTCGACTCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:141509 original size:3 final size:3
Alignment explanation
Indices: 141495--141526 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
141485 CACTCAAGAG
*
141495 TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
141527 ACCACCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:148408 original size:20 final size:21
Alignment explanation
Indices: 148378--148416 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
148368 ATTACAGATA
148378 CAAATATGACAAAACCGGTCT
1 CAAATATGACAAAACCGGTCT
*
148399 CAAA-ATGACAAAATCGGT
1 CAAATATGACAAAACCGGT
148417 AAAACGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCT
Found at i:148835 original size:182 final size:182
Alignment explanation
Indices: 148345--149214 Score: 933
Period size: 182 Copynumber: 4.8 Consensus size: 182
148335 ATACAAATGA
* * * * * * * *
148345 AAAATGGATCGCTCCATAGCAATATTACAGATACAAATATGACAAAACCGGTCTC-AAAATGACA
1 AAAATGTATCGAT-CATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACA
* * * * * * ** * * * *
148409 AAATCGGTAAAACGCTATCGGATATGCGT-CGAGTGTCAATAATTTAATATAAGTATCAAAATTT
65 AAACCAGTAAAAAGTTACCGGATATG-TTAAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* * * * * **
148473 TCTGAATTTAAAAGATAAGAAGTTATAACGCCTATAAAGTGTCGATACTTTAAA
129 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGACACTTTATG
* * * * * *
148527 AAAATATATTGATCAACAACAATATAACAAGTAAAAATATGATAAAACTGGCCT-AAAAATGACA
1 AAAATGTATCGATC-ATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACA
* * * *
148591 AAACC-GAAAAAAGTTACCGTATATATTAAAAGTGTCGATAATTTAATATTAGTATCGACACTTT
65 AAACCAGTAAAAAGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* *
148655 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAATGTCGACACTTTATG
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGACACTTTATG
* * * *
148708 AAAATGTATTGATCTTTACTAATATAACAGGTGAAAATATGATAAAACAGGTCTCAAAAATGACA
1 AAAATGTATCGATCATAAC-AATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACA
* *
148773 AAACCAG-AAAAAGTTATCGGATATGTTAAAAGTGTTGATAATTTAATATAAGTATCGACACTTT
65 AAACCAGTAAAAAGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * *
148837 CTGAATTTAAAAGAGAAAAAGTTATTGCGCTTAAAAAGTGTCTACACTTTATG
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGACACTTTATG
* * *
148890 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAAACATGTCTCAAAATTGACA
1 AAAATGTATCGAT-CATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACA
* * * * * *
148955 AAACCAGTAAAACGCTACCGAATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
65 AAACCAGTAAAAAGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * * **
149020 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAA
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGACACTTT-ATG
* * * * * * * *
149074 AAAATATATCGATCAACAATAGTATAACAGATACAAATATGATAAAACAGGTCCCAAAATTGACA
1 AAAATGTATCGATC-ATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACA
* * * * * *
149139 AAACTAGTAAAACA-ATACCGGATATATTGAAAGTATCGATAATTTAATATAAATATCGACACTT
65 AAACCAGTAAAA-AGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
149203 TCTGAAATTAAA
129 TCTGAATTTAAA
149215 CTAAAAAGTG
Statistics
Matches: 584, Mismatches: 93, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
180 3 0.01
181 133 0.23
182 227 0.39
183 99 0.17
184 122 0.21
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (182 bp):
AAAATGTATCGATCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAA
AACCAGTAAAAAGTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
TGAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGACACTTTATG
Found at i:149359 original size:530 final size:526
Alignment explanation
Indices: 148685--149713 Score: 1501
Period size: 530 Copynumber: 1.9 Consensus size: 526
148675 GTTATAGCGC
* * * *
148685 CTAAAAAATGTCGACACTTTATGAAAATGTATTGATCTTTACTAATATAACAGGTGAAAATATGA
1 CTAAAAAATGTCGACACTTTATGAAAATGTATCGATCATAACTAATATAACAGGTAAAAATATGA
* * *
148750 TAAAACAGGTCTCAAAAATGACAAAACCAGAAAAAGTTATCGGATATGTTAAAAGTGTTGATAAT
66 TAAAACAGGTCTCAAAAATGACAAAACCAGAAAAAGTTACCGGATATATTAAAAGTGTCGATAAT
148815 TTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTAT-TGCGCTTAAAAAGTGTC
131 TTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATAT-CGCTTAAAAAGTGTC
*
148879 TACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAAACATG-TC
195 GACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAAACA-GATC
* * * * *
148943 TCAAAATTGACAAAACCAGTAAAACGCTACCGAATATATTGAAAGTGTCGATAATTTAATATAAG
259 TCAAAAATGACAAAACC-GAAAAAAGCTACCGAATATATTGAAAATGTCGATAATTTAATATAAC
* *
149008 TATCGAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAA
323 TATCGAAACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGA-ACTTT-AA
* * *
149073 AAAAATATATCGATCAACAATAGTATAACAGATACAAATATGATAAAA-CAGGTCCCAAAATTGA
386 AAAAATATATCGATCAACAACAATATAACAGATAAAAATATGATAAAATC-GGTCCCAAAA-TGA
*
149137 CAAAACTAGTAAA-ACAATACCGGATATATTGAAAGTATCGATAATTTAATATAAATATCGACAC
449 CAAAACCAGTAAATA-AATACCGGATATATTGAAAGTATCGATAATTTAATATAAATATCGACAC
149201 TTTCTGAAATTAAA
513 TTTCTGAAATTAAA
* *
149215 CTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAAC-AATATAACATGTAAAAATATG
1 CTAAAAAATGTCGACACTTTATGAAAATGTATCGAT-CATAACTAATATAACAGGTAAAAATATG
* *
149279 ATAAAACTGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATATTAAAAGTGTCGATAA
65 ATAAAACAGGTCTCAAAAATGACAAAACCAGAAAAAGTTACCGGATATATTAAAAGTGTCGATAA
* *
149344 TTTAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATATCGCTTAAAAAGTGTC
130 TTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATATCGCTTAAAAAGTGTC
* * * * *
149409 GACACTTTATTAAAATGTATCGATCCTTACCAATGTAACAGGTAAAAATATGATAAAACAGATCT
195 GACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAAACAGATCT
* * * * *
149474 CAAAAATGATAAAACCGAAAAAAGTTATCGGATATGTTGAAAATGTCGATAATTTAATATAACTA
260 CAAAAATGACAAAACCGAAAAAAGCTACCGAATATATTGAAAATGTCGATAATTTAATATAACTA
* * **
149539 TCGACACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGAACTTTATGAAA
325 TCGAAACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAACTTTAAAAAA
* * * * *
149604 ATGTATCGATCCAGAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCAAAATGACAAAAC
390 ATATATCGATCAACAACAATATAACAGATAAAAATATGATAAAATCGGTCCCAAAATGACAAAAC
* * * * *
149669 CGGTAAATAGATACCGGATATGTTGAAAGTGTCGATACTTTAATA
455 CAGTAAATAAATACCGGATATATTGAAAGTATCGATAATTTAATA
149714 ATTACGCGTA
Statistics
Matches: 445, Mismatches: 49, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
526 46 0.10
527 51 0.11
528 6 0.01
529 92 0.21
530 245 0.55
531 5 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (526 bp):
CTAAAAAATGTCGACACTTTATGAAAATGTATCGATCATAACTAATATAACAGGTAAAAATATGA
TAAAACAGGTCTCAAAAATGACAAAACCAGAAAAAGTTACCGGATATATTAAAAGTGTCGATAAT
TTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATATCGCTTAAAAAGTGTCG
ACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAAACAGATCTC
AAAAATGACAAAACCGAAAAAAGCTACCGAATATATTGAAAATGTCGATAATTTAATATAACTAT
CGAAACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAACTTTAAAAAAA
TATATCGATCAACAACAATATAACAGATAAAAATATGATAAAATCGGTCCCAAAATGACAAAACC
AGTAAATAAATACCGGATATATTGAAAGTATCGATAATTTAATATAAATATCGACACTTTCTGAA
ATTAAA
Found at i:149704 original size:181 final size:182
Alignment explanation
Indices: 149216--149713 Score: 768
Period size: 182 Copynumber: 2.7 Consensus size: 182
149206 GAAATTAAAC
*
149216 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * *
149281 AAAACTGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATATTAAAAGTGTCGATAATT
66 AAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
* * * *
149346 TAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATATCGCT
131 TAATATAACTATCGACACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCT
* * * *
149398 TAAAAAGTGTCGACACTTTATTAAAATGTATCGATCCTTACCAATGTAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * * * *
149463 AAAACAGATCTCAAAAATGATAAAACCGAAAAAAGTTATCGGATATGTTGAAAATGTCGATAATT
66 AAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
149528 TAATATAACTATCGACACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCT
131 TAATATAACTATCGACACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCT
*
149580 TAAAAAGTGTCGA-ACTTTATGAAAATGTATCGATCCAGAACAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
* * *
149644 AAAATC-GGTCTC-AAAATGACAAAACCGGTAAATAGATACCGGATATGTTGAAAGTGTCGATAC
66 AAAA-CAGGTCTCAAAAATGACAAAACCGG-AAAAAGTTACCGGATATGTTGAAAGTGTCGATAA
149707 TTTAATA
129 TTTAATA
149714 ATTACGCGTA
Statistics
Matches: 284, Mismatches: 30, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
180 14 0.05
181 91 0.32
182 179 0.63
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
AAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAATT
TAATATAACTATCGACACTTTCTAAATTTAAAAGAGAAGAAGTTATAGCGCT
Found at i:150133 original size:19 final size:19
Alignment explanation
Indices: 150102--150165 Score: 112
Period size: 19 Copynumber: 3.4 Consensus size: 19
150092 TAGTTAATAT
150102 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
150120 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
150139 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
150158 TTTTAGGT
1 TTATAGGT
150166 TGTATAAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 9 0.20
19 35 0.80
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:150451 original size:18 final size:18
Alignment explanation
Indices: 150416--150454 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
150406 TTGAAATGGT
150416 AATTGGATTAAAACTTTA
1 AATTGGATTAAAACTTTA
*
150434 AATT-GATTACAAATTTTA
1 AATTGGATTA-AAACTTTA
150452 AAT
1 AAT
150455 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTGGATTAAAACTTTA
Found at i:150887 original size:128 final size:128
Alignment explanation
Indices: 150659--150914 Score: 485
Period size: 128 Copynumber: 2.0 Consensus size: 128
150649 ATCACACAAT
*
150659 CAAGGAATGATAGTAAAGAATACAAAGAATGGATGAAAGCACATGAAAAGAAGGTATTCATTAAA
1 CAAGGAATGATAGTAAAGAATACAAAGAACGGATGAAAGCACATGAAAAGAAGGTATTCATTAAA
*
150724 CTTGTAAATACGTTGATACAAGATATATAAGAACAATAACATTATATATTGTTAAAAAATGTA
66 CTTGTAAATACATTGATACAAGATATATAAGAACAATAACATTATATATTGTTAAAAAATGTA
150787 CAAGGAATGATAGTAAAGAATACAAAGAACGGATGAAAGCACATGAAAAGAAGGTATTCATTAAA
1 CAAGGAATGATAGTAAAGAATACAAAGAACGGATGAAAGCACATGAAAAGAAGGTATTCATTAAA
*
150852 CTTGTAAATACATTGATACAAGATATATAAGAACAATAACATTATATATTGTTAAAATATGTA
66 CTTGTAAATACATTGATACAAGATATATAAGAACAATAACATTATATATTGTTAAAAAATGTA
150915 GGAAGTGTCG
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 125 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (128 bp):
CAAGGAATGATAGTAAAGAATACAAAGAACGGATGAAAGCACATGAAAAGAAGGTATTCATTAAA
CTTGTAAATACATTGATACAAGATATATAAGAACAATAACATTATATATTGTTAAAAAATGTA
Found at i:152324 original size:22 final size:18
Alignment explanation
Indices: 152275--152313 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
152265 GAAAAAATTT
*
152275 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATGGAG
152293 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
152311 GAA
1 GAA
152314 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:153806 original size:19 final size:19
Alignment explanation
Indices: 153782--153825 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
153772 GCATGGTTAA
*
153782 TTGTATAAGATTTTTAATT
1 TTGTATAAGATTTATAATT
*
153801 TTGTATACGATTTATAATT
1 TTGTATAAGATTTATAATT
153820 TTGTAT
1 TTGTAT
153826 GTGAATGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (19 bp):
TTGTATAAGATTTATAATT
Found at i:154510 original size:199 final size:199
Alignment explanation
Indices: 154170--155609 Score: 2239
Period size: 199 Copynumber: 7.3 Consensus size: 199
154160 GTAAACTTAT
*
154170 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAATCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
*
154235 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
154300 TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
154365 AAAA
196 AAAA
154369 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* *
154434 GGTAAATTAGCAATATAACCGGTCTAAATATACCAGTTTTTGAGAAAACAAGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
154499 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
154564 AAAA
196 AAAA
* *
154568 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAA-ATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
*
154632 GGTAAATTAGCAATATAACCGGTCTAAATATACCGG-TTTTGAGAAAACCGGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
154696 TCGACACAAATCGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGAACTA
131 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
154761 AAAA
196 AAAA
*
154765 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAATATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
154830 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
154895 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAAAATGTATTTCAAAACCAAGTGCACTA
131 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
154960 AAAA
196 AAAA
* *
154964 GTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACAT-------CA-AA--A-ACTGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* *
155018 GGTAAATTAGCAATATAACCGGTCTAAATATACTGGTTTTTGAGAAAACAGGTGTACAAACAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * * *
155083 TCGACACAAATTGAACAAGTATCGATACTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACAT
131 TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCAC-T
155148 AAAAA
195 AAAAA
* ** *
155153 -TGTCGATACATTTAAAACAAGTGTCGATCCCAAAAACATAAAAAAACATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * *
155217 GGTAAATTATTC-ATATAAACGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGT
66 GGTAAATTA-GCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGT
** * *
155281 ATCGACACAAATATAACAAGTGTCGATACTTTTTCTCCAAAATGTATTTCAAAACCAAGTGCACT
130 ATCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACT
155346 AAAAA
195 AAAAA
*
155351 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
* * * * * * * **
155416 GGTAAATTAACAATGTAACCGGTCTAAATGTACCAGTTTATGAGAAAACAAGTATACATGAAGTA
66 GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * * * *
155481 TCGACACAAATAC-ATCAAGTTTCGATACATTTTTGTCCAGACTATATTTTAAAAACCAAGTGCA
131 TCGACACAAAT-CGAACAAGTGTCGATAC-TTTTTGTCCAGAATGTA-TTTCAAAACCAAGTGCA
155545 C-AACAAA
193 CTAA-AAA
* * * *
155552 GTTTCGATACATTTATAACAATTGTCGATCCCAAAAATATCGAAAAACATAATTATAA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAA
155610 CCAAATGTCT
Statistics
Matches: 1147, Mismatches: 73, Indels: 40
0.91 0.06 0.03
Matches are distributed among these distances:
188 166 0.14
189 7 0.01
191 2 0.00
192 2 0.00
195 2 0.00
196 2 0.00
197 129 0.11
198 131 0.11
199 617 0.54
200 16 0.01
201 73 0.06
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (199 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATA
GGTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
TCGACACAAATCGAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCACTA
AAAA
Found at i:158035 original size:198 final size:195
Alignment explanation
Indices: 157529--158201 Score: 703
Period size: 198 Copynumber: 3.4 Consensus size: 195
157519 TTTTCAAAAA
* * ** * * *
157529 GTATCGACCCCAAAAACATCGAAAC-AAATATTATAATGTAATATTTAAATTAATAATGTAACCA
1 GTATCGATCCCAAAAACATCAAAACGAAA-ATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * * * *
157593 TTATACATATATCGG-TTAATTATAAAATATGTCAACATAAAGTATCGACACTTTTTAAGTTTGT
65 GTATAAATATATCGGTTTTATGAGAAAATAGGTCAA-ATAAAGTATCGACACTTTATAA-TTTGT
* * * * *
157657 GTCGATACTTTTTTCCA-AAAGAAAGCACAAAC-AAGTTCACA-CATAAAGTGTCGATACATTTA
128 GTCGATACTTTTTTCCATAATGAATGC-CCAACGAGGTGCA-AGCATAAAGTGTCGATACATTTA
157719 AAATT
191 AAATT
* * * * * *
157724 GCATCGATCACAAAAACATCGAAACCGATAATTATAATGTAATATGTCAATTTACAATGTAACCG
1 GTATCGATCCCAAAAACATC-AAAACGAAAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * *
157789 GTTTAAATTTACCGCTTTTATGAGAAAATAGGTCAGAATAAAGTATCGACACTTGTGTAATTTGT
65 GTATAAATATATCGGTTTTATGAGAAAATAGGTCA-AATAAAGTATCGACACTT-TATAATTTGT
* * *
157854 GTCGATACATTTTGTCCATAATGAATGCCCAACGAGGTGCAAGAATAACGTGTCGATACATTTAA
128 GTCGATAC-TTTTTTCCATAATGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAA
157919 AATT
192 AATT
* * *
157923 GTATCGATCCCAAAAACATCAAAACGAAAATTACAATGTTATAGGTAAATTTACAATGTACCCGG
1 GTATCGATCCCAAAAACATCAAAACGAAAATTATAATGTAATAGGTAAATTTACAATGTAACCGG
* *
157988 TATAAATATATCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACACCTTTATAGTTTGTG
66 TATAAATATATCGGTTTTATGAGAAAATAGGTC-AAATAAAGTATCGACA-CTTTATAATTTGTG
*
158053 TCGATACTTTTTTCCAGAATGAATTAGGAATG-CCAACGAGATGCAAGCATAAAGTGTCGATACA
129 TCGATACTTTTTTCC---AT-AA-T--GAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACA
158117 TTTAAAATT
187 TTTAAAATT
* * * * * * *
158126 GTATCGATCCAAAAAACAACGAAACTAATAATTATAATGCAATCGGTAAATTTATAATGCT-ACC
1 GTATCGATCCCAAAAACATCAAAACGAA-AATTATAATGTAATAGGTAAATTTACAATG-TAACC
158190 GGTATAAATATA
64 GGTATAAATATA
158202 CTGGTTAAAT
Statistics
Matches: 398, Mismatches: 60, Indels: 31
0.81 0.12 0.06
Matches are distributed among these distances:
195 17 0.04
196 42 0.11
197 54 0.14
198 115 0.29
199 58 0.15
200 2 0.01
201 2 0.01
202 1 0.00
203 62 0.16
204 44 0.11
205 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (195 bp):
GTATCGATCCCAAAAACATCAAAACGAAAATTATAATGTAATAGGTAAATTTACAATGTAACCGG
TATAAATATATCGGTTTTATGAGAAAATAGGTCAAATAAAGTATCGACACTTTATAATTTGTGTC
GATACTTTTTTCCATAATGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATT
Found at i:158239 original size:23 final size:23
Alignment explanation
Indices: 158213--158294 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
158203 TGGTTAAATG
*
158213 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
* *
158236 CCTATTAGATTATATAAGTGCTA
1 CCTATTATATTATATAAGCGCTA
*
158259 CCTATTACATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
*
158282 CCTAATATATTAT
1 CCTATTATATTAT
158295 TGTGCTTGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Found at i:159062 original size:22 final size:22
Alignment explanation
Indices: 159036--159080 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
159026 TTATTAACAG
*
159036 AAAATGCTATGAATAAA-GTAAC
1 AAAATGCTA-GAAAAAATGTAAC
*
159058 AAAATGTTAGAAAAAATGTAAC
1 AAAATGCTAGAAAAAATGTAAC
159080 A
1 A
159081 TGTTAGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.58, C:0.07, G:0.13, T:0.22
Consensus pattern (22 bp):
AAAATGCTAGAAAAAATGTAAC
Found at i:161251 original size:19 final size:19
Alignment explanation
Indices: 161229--161318 Score: 55
Period size: 18 Copynumber: 4.8 Consensus size: 19
161219 AAAGTGTAAA
161229 AAATATAAAAAATATATAT
1 AAATATAAAAAATATATAT
161248 AAATACT--AAAATAT-TAT
1 AAATA-TAAAAAATATATAT
* * * *
161265 AAACATATAAATTA-ATAA
1 AAATATAAAAAATATATAT
***
161283 AAATATTTTAAAT-TATAT
1 AAATATAAAAAATATATAT
161301 AAAATATAAAAAACTATA
1 -AAATATAAAAAA-TATA
161319 AAAATTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
16 1 0.02
17 7 0.13
18 26 0.50
19 14 0.27
20 2 0.04
21 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATAAAAAATATATAT
Found at i:163585 original size:24 final size:22
Alignment explanation
Indices: 163536--163588 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
163526 TAGGTTTTAT
*
163536 ATATT-TATTTTGTTTGTATTA
1 ATATTATATATTGTTTGTATTA
*
163557 TTATTATATATTGCTTTGTATATA
1 ATATTATATATTG-TTTGTAT-TA
163581 ATATTATA
1 ATATTATA
163589 GCATGATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 6 0.23
23 7 0.27
24 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (22 bp):
ATATTATATATTGTTTGTATTA
Found at i:170173 original size:38 final size:37
Alignment explanation
Indices: 170131--170219 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
170121 TTGGGTGTTG
170131 TTTCTCTCGAAACAAAATGTCATCTCACTTGAGACATT
1 TTTCT-TCGAAACAAAATGTCATCTCACTTGAGACATT
** * ** *
170169 TTTCTGTTAAAAC-AAATTTTGTTTCACTTGAGACATT
1 TTTCT-TCGAAACAAAATGTCATCTCACTTGAGACATT
*
170206 TTTCTTCGGAACAA
1 TTTCTTCGAAACAA
170220 TAATTTCAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
36 4 0.10
37 26 0.65
38 10 0.25
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTCTTCGAAACAAAATGTCATCTCACTTGAGACATT
Found at i:170384 original size:38 final size:37
Alignment explanation
Indices: 170335--170527 Score: 188
Period size: 37 Copynumber: 5.5 Consensus size: 37
170325 TTCAAAGTTG
*
170335 TTTTTCT-TAAAAACAAATTTTGTTTCACTTGAGACA
1 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACA
*
170371 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATA
1 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACA
** ** * **
170408 TTTTTCT-TTGGAAC-AA--TAATTTCA---AAGTTA
1 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACA
* * * *
170438 TTTTTCT-TAAAAATAAATTTTGTCTCGCTTGAGACA
1 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACA
*
170474 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATA
1 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACA
*
170511 TTTTTCTCTCAAAACAA
1 TTTTTCTCTTAAAACAA
170528 GCATCGTCTC
Statistics
Matches: 124, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
30 14 0.11
31 2 0.02
33 10 0.08
35 2 0.02
36 22 0.18
37 74 0.60
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (37 bp):
TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACA
Found at i:170410 original size:103 final size:103
Alignment explanation
Indices: 170153--170517 Score: 612
Period size: 103 Copynumber: 3.6 Consensus size: 103
170143 CAAAATGTCA
* *
170153 TCTCACTTGAGACATTTTTCTGTTAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAAC
1 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCTTCGGAAC
170218 AATAATTTCAAAGTTGTTTTTCTTAAAAATAAA--TTG
66 AATAATTTCAAAGTTGTTTTTCTTAAAAATAAATTTTG
*
170254 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCT-TTTCACTTGAGTTATTTTTCTTCGGAA
1 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTT-TGTTTCACTTGAGATATTTTTCTTCGGAA
*
170318 CACA-AATTTCAAAGTTGTTTTTCTTAAAAACAAATTTTG
65 CA-ATAATTTCAAAGTTGTTTTTCTTAAAAATAAATTTTG
* *
170357 TTTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCTTTGGAAC
1 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCTTCGGAAC
*
170422 AATAATTTCAAAGTTATTTTTCTTAAAAATAAATTTTG
66 AATAATTTCAAAGTTGTTTTTCTTAAAAATAAATTTTG
*
170460 TCTCGCTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCT
1 TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCT
170518 CTCAAAACAA
Statistics
Matches: 247, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
101 90 0.36
102 4 0.02
103 153 0.62
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.46
Consensus pattern (103 bp):
TCTCACTTGAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGATATTTTTCTTCGGAAC
AATAATTTCAAAGTTGTTTTTCTTAAAAATAAATTTTG
Found at i:170543 original size:37 final size:37
Alignment explanation
Indices: 170459--170549 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 37
170449 AATAAATTTT
* ** *
170459 GTCTCGCTTGAGACATTTTTCTCTTAAAACAAATTTT
1 GTCTCGCTTGAGACATTTTTCTCTCAAAACAAACATC
* * * *
170496 GTTTCACTTGAGATATTTTTCTCTCAAAACAAGCATC
1 GTCTCGCTTGAGACATTTTTCTCTCAAAACAAACATC
170533 GTCTCGCTTGAGACATT
1 GTCTCGCTTGAGACATT
170550 CTCCCAAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (37 bp):
GTCTCGCTTGAGACATTTTTCTCTCAAAACAAACATC
Found at i:170836 original size:76 final size:74
Alignment explanation
Indices: 170745--170923 Score: 200
Period size: 74 Copynumber: 2.4 Consensus size: 74
170735 GATAGTTTCC
* * * * *
170745 CTTAAAACAGACTTTGTCTCGCTTGAGACATTCTTTTCTCACAACAAGACAT-TTCGTTTCA-TT
1 CTTAAAACAAACTTTGTCTCGCTTGAGACA-T-TTTACTCAAAACAAGA-ATATTCATTTCACTC
170808 ACAAATTATTTTT
63 A-AAATTATTTTT
* * *
170821 CTTAAAACATACTTTGTCTCGCTTAAGACATTTTACTCAAAACAAGAATATTTATTTCACTCAAA
1 CTTAAAACAAACTTTGTCTCGCTTGAGACATTTTACTCAAAACAAGAATATTCATTTCACTCAAA
*
170886 ATTGTTTTT
66 ATTATTTTT
* *
170895 CTTAAAACCAAAATTTATCTCGCTTGAGA
1 CTTAAAA-CAAACTTTGTCTCGCTTGAGA
170924 TAGTTTCCCT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
73 2 0.02
74 38 0.43
75 20 0.23
76 28 0.32
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (74 bp):
CTTAAAACAAACTTTGTCTCGCTTGAGACATTTTACTCAAAACAAGAATATTCATTTCACTCAAA
ATTATTTTT
Found at i:171120 original size:52 final size:52
Alignment explanation
Indices: 170996--171243 Score: 210
Period size: 52 Copynumber: 4.6 Consensus size: 52
170986 GAAGACTTTT
* * * * *
170996 AGAAACTAGGCCTAATTTTCAGGGGTTCCTCGATGTTTTTAAATGAACTTGAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTTAAATGAA-TTTAA
* * *
171049 AGAAGCTAAACCTAA-TTTTAGGGGTTTCTTAATGTTTTTAAATGAATTTAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTTAAATGAATTTAA
* * ** * * * **
171100 AGAAATTATGCCTAATTTTTAGGTATTTCTTGATATTTTCAAATGAGTTTTT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTTAAATGAATTTAA
* * * *
171152 AGAAACTAAGCCTGATTTTTATGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG-T--TTTTAAATGA--ATTT-AA
* *
171210 AGGAAACTAAGCCTAATTCTTAGGGGTTCCTTGA
1 A-GAAACTAAGCCTAATTTTTAGGGGTTTCTTGA
171244 CAACTAAGAA
Statistics
Matches: 151, Mismatches: 36, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
51 15 0.10
52 83 0.55
53 13 0.09
55 8 0.05
57 3 0.02
58 1 0.01
59 28 0.19
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTTAAATGAATTTAA
Found at i:172509 original size:105 final size:105
Alignment explanation
Indices: 172254--172645 Score: 558
Period size: 102 Copynumber: 3.7 Consensus size: 105
172244 GGATAAACCG
* * *
172254 ATCAACATTTCCATAAGAGTTCATAATAAGAAGAACTCGTCCTAAAGGAGAAAGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
**
172319 AAGAACTTGTTCCTTTCAAATTTACCCCAGAAGG-A--GA
66 AAGAACTTGTTCCTTTCAAATCCACCCCAGAAGGAAGTGA
* * *
172356 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
* * *
172421 AAGAGCATGTTCCTTTCAAATCCACCACAGAAGGAAGTGA
66 AAGAACTTGTTCCTTTCAAATCCACCCCAGAAGGAAGTGA
* * *
172461 ACCAACATTTACAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
**
172526 AAGAACTTGTTTTTTTCAAATCCACTCCCAGAA-GAAGGTGA
66 AAGAACTTGTTCCTTTCAAATCCAC-CCCAGAAGGAA-GTGA
* *
172567 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCGTTCTAAAGGAGAAGAAGTTCATAATG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAG-A-AAGTTCATAATG
172632 AGAAGAACTTGTTC
64 AGAAGAACTTGTTC
172646 AACCTTAGCT
Statistics
Matches: 257, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
102 90 0.35
103 1 0.00
105 85 0.33
106 55 0.21
107 1 0.00
108 25 0.10
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (105 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAG
AAGAACTTGTTCCTTTCAAATCCACCCCAGAAGGAAGTGA
Found at i:172638 original size:20 final size:19
Alignment explanation
Indices: 172579--172638 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 19
172569 CAACATTTCC
172579 AGAAGAGTTCATAATGAGA
1 AGAAGAGTTCATAATGAGA
** *
172598 AGAATTCGTTC-TAA--AGG
1 AGAA-GAGTTCATAATGAGA
172615 AGAAGAAGTTCATAATGAGA
1 AGAAG-AGTTCATAATGAGA
172635 AGAA
1 AGAA
172639 CTTGTTCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
17 10 0.33
18 3 0.10
19 7 0.23
20 10 0.33
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.22
Consensus pattern (19 bp):
AGAAGAGTTCATAATGAGA
Found at i:172645 original size:20 final size:19
Alignment explanation
Indices: 172585--172646 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
172575 TTCCAGAAGA
172585 GTTCATAATGAGAAGAATT
1 GTTCATAATGAGAAGAATT
*
172604 CGTTC-TAAAGGAGAAGAA--
1 -GTTCAT-AATGAGAAGAATT
172622 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAA-TT
172642 GTTCA
1 GTTCA
172647 ACCTTAGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 14 0.40
18 1 0.03
19 1 0.03
20 19 0.54
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (19 bp):
GTTCATAATGAGAAGAATT
Found at i:172748 original size:136 final size:136
Alignment explanation
Indices: 172582--172930 Score: 574
Period size: 136 Copynumber: 2.5 Consensus size: 136
172572 CATTTCCAGA
* *
172582 AGAGTTCATAATGAGAAGAATTCGTTCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGAGTTCATAATGAGAAGAACTC-ATCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
172647 ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGG-CCAATATTT
65 ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGACCAATATTT
172711 TCAATGG
130 TCAATGG
172718 AGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGAGTTCATAATGAGAAGAACTCAT-CTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
172783 ACCTTAGCTCGATTCATCGCATATGGTGTTGAATCAGCAATACCTCACTCGAGGGATCAATATTT
65 ACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGACCAATATTT
*
172848 TCAGTGG
130 TCAATGG
*
172855 AGAGTTCATAATGAGAAGAACTCATCTGATAAGGGAGAAGAAGTTAATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCT-A-AA-GGAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
172920 CGACCTTAGCT
63 CAACCTTAGCT
172931 TGTTTCCATC
Statistics
Matches: 200, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
135 1 0.00
136 116 0.58
137 40 0.20
138 2 0.01
139 41 0.20
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (136 bp):
AGAGTTCATAATGAGAAGAACTCATCTAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGACCAATATTTT
CAATGG
Found at i:172781 original size:20 final size:19
Alignment explanation
Indices: 172721--172782 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
172711 TCAATGGAGA
172721 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
** * *
172740 CATCCTAAAGGAGAAGAA--
1 GTTCAT-AATGAGAAGAACT
172758 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
172778 GTTCA
1 GTTCA
172783 ACCTTAGCTC
Statistics
Matches: 31, Mismatches: 8, Indels: 7
0.67 0.17 0.15
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 3 0.10
20 15 0.48
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:174456 original size:27 final size:28
Alignment explanation
Indices: 174403--174458 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
174393 GCTTTAGGTT
* * * *
174403 TTATATATTTATTTTGTTTTTATTATTA
1 TTATATATTTACTTTGTATATAATATTA
174431 TTATATA-TTACTTTGTATATAATATTA
1 TTATATATTTACTTTGTATATAATATTA
174458 T
1 T
174459 AGCATGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (28 bp):
TTATATATTTACTTTGTATATAATATTA
Found at i:176598 original size:20 final size:21
Alignment explanation
Indices: 176573--176627 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
176563 ACCCAGGGTG
176573 AGTATCGATACTCAAGAG-TT
1 AGTATCGATACTCAAGAGCTT
* *
176593 AGTATCGATACTAAAGGGCTT
1 AGTATCGATACTCAAGAGCTT
176614 AGTATCGATA-TCAA
1 AGTATCGATACTCAA
176628 CATACTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (21 bp):
AGTATCGATACTCAAGAGCTT
Found at i:189377 original size:20 final size:20
Alignment explanation
Indices: 189349--189418 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
189339 GGCTTGATTT
*
189349 TACTATAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
189369 TACTGTAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
189389 TACTGTAGCAGTATCGATAC
1 TACTGTAGCAGTATCGATAC
189409 TACTGTAGCA
1 TACTGTAGCA
189419 ATATGGATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (20 bp):
TACTGTAGCAGTATCGATAC
Found at i:189820 original size:198 final size:197
Alignment explanation
Indices: 189483--189878 Score: 724
Period size: 198 Copynumber: 2.0 Consensus size: 197
189473 TACTATTCAT
*
189483 ACGAAACTATTCATACATATTTTTTTAAATTGCAATAAAATGTAATTTGAATTATTTTTGAAAAC
1 ACGAAACTATTCATACATATTTTTTTAAATTGCAATAAAATGTAATTTGAATTAGTTTTGAAAAC
189548 TTTGAATAAATTCAATTCAAGTCCAAAAATGTTTTGCCATAATTGTTATATGAATCATAGTTCTA
66 TTTGAATAAATTCAATTCAAGTCCAAAAATGTTTTGCCATAATTGTTATATGAATCATAGTTCTA
*
189613 CAATCTCCCCCTTTTTTATATAAC-AAACATTTGAAAATTTGTTTTTGACAAAAGTCCCCCTTAG
131 CAATCTCCCCATTTTTTATATAACAAAACATTTGAAAATTTGTTTTTGAC-AAAGTCCCCCTTAG
189677 TAA
195 TAA
189680 ACGAAACTATTCATACATATTTTTTTTAAATTGCAATAAAATGTAATTTGAATTAGTTTTGAAAA
1 ACGAAACTATTCATACATA-TTTTTTTAAATTGCAATAAAATGTAATTTGAATTAGTTTTGAAAA
189745 CTTTGAATAAATTCAATTCAAGT-CAAAAATGTTTTGCCATAATTGTTATATTGAATCATAGTTC
65 CTTTGAATAAATTCAATTCAAGTCCAAAAATGTTTTGCCATAATTGTTATA-TGAATCATAGTTC
*
189809 TACAATCTCCCCATTTTTTATATAACAAAACATTTGAAAATTTGTTTTTGGCAAAGTCCCCCTTA
129 TACAATCTCCCCATTTTTTATATAACAAAACATTTGAAAATTTGTTTTTGACAAAGTCCCCCTTA
189874 GTAA
194 GTAA
189878 A
1 A
189879 ATGTTTAATG
Statistics
Matches: 193, Mismatches: 3, Indels: 5
0.96 0.01 0.02
Matches are distributed among these distances:
197 46 0.24
198 123 0.64
199 24 0.12
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (197 bp):
ACGAAACTATTCATACATATTTTTTTAAATTGCAATAAAATGTAATTTGAATTAGTTTTGAAAAC
TTTGAATAAATTCAATTCAAGTCCAAAAATGTTTTGCCATAATTGTTATATGAATCATAGTTCTA
CAATCTCCCCATTTTTTATATAACAAAACATTTGAAAATTTGTTTTTGACAAAGTCCCCCTTAGT
AA
Found at i:195021 original size:21 final size:23
Alignment explanation
Indices: 194995--195047 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 23
194985 TGTTCTCAAT
194995 GTATCGATACCCTCCA-CATA-G
1 GTATCGATACCCTCCACCATAGG
*
195016 GTATCGATA-CCTCTACCATAGG
1 GTATCGATACCCTCCACCATAGG
195038 GTATCGATAC
1 GTATCGATAC
195048 TGTTCATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 10 0.36
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (23 bp):
GTATCGATACCCTCCACCATAGG
Found at i:198108 original size:18 final size:18
Alignment explanation
Indices: 198077--198111 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
198067 ACTATAAATT
*
198077 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
198095 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
198112 CATTAAGAAC
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:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:200396 original size:14 final size:14
Alignment explanation
Indices: 200324--200411 Score: 56
Period size: 14 Copynumber: 6.3 Consensus size: 14
200314 AACCTACATC
* *
200324 CTAATTCTTACACT
1 CTAAATCTTAAACT
* *
200338 TTAAACCTTAAACAT
1 CTAAATCTTAAAC-T
*
200353 -TAAA-CTTTAAACC
1 CTAAATC-TTAAACT
*
200366 CTAAATCCTT-AATT
1 CTAAAT-CTTAAACT
200380 CTAAATCTTAAACT
1 CTAAATCTTAAACT
* *
200394 CTAATTCCTAAACT
1 CTAAATCTTAAACT
200408 CTAA
1 CTAA
200412 TTCTAATAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
13 4 0.07
14 50 0.86
15 3 0.05
16 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (14 bp):
CTAAATCTTAAACT
Found at i:200414 original size:14 final size:14
Alignment explanation
Indices: 200360--200411 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
200350 CATTAAACTT
*
200360 TAAACCCTAAATCC
1 TAAACTCTAAATCC
* * *
200374 TTAATTCTAAATCT
1 TAAACTCTAAATCC
*
200388 TAAACTCTAATTCC
1 TAAACTCTAAATCC
200402 TAAACTCTAA
1 TAAACTCTAA
200412 TTCTAATAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAACTCTAAATCC
Found at i:200579 original size:2 final size:2
Alignment explanation
Indices: 200572--200609 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
200562 ATCTTAACCC
200572 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
200610 ATATATATAT
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:200614 original size:2 final size:2
Alignment explanation
Indices: 200609--200639 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
200599 TCTCTCTCTC
200609 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 T
200640 CTTTACTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:203311 original size:3 final size:3
Alignment explanation
Indices: 203291--203357 Score: 91
Period size: 3 Copynumber: 22.7 Consensus size: 3
203281 AGATAAGAAA
* * * *
203291 AAT AAT AA- AGT AAA AAT AAT AAA AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
203338 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
203358 GGTAAAATAG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 1 0.02
3 54 0.98
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:204767 original size:25 final size:26
Alignment explanation
Indices: 204713--204769 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
204703 AAAATAGTAA
* **
204713 ATAAATATACATGTATATATATACGT
1 ATAAATAAACATAAATATATATACGT
*
204739 -TAAATAAACATAAATATATATA-TT
1 ATAAATAAACATAAATATATATACGT
204763 ATAAATA
1 ATAAATA
204770 TGTGCTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (26 bp):
ATAAATAAACATAAATATATATACGT
Found at i:208818 original size:4 final size:4
Alignment explanation
Indices: 208809--208833 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
208799 ACTTTAACCA
208809 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
208834 GTTTCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:209004 original size:126 final size:116
Alignment explanation
Indices: 208851--209140 Score: 364
Period size: 118 Copynumber: 2.4 Consensus size: 116
208841 TTATTACTCA
* *
208851 ATCTTGTGGTGACTAGATATGGGGTATGATCCACATTATTATGGTTTGGATTATGCTAACCACTA
1 ATCTTGTGGTGACCAGAT-T-GGGTATGATCCACATTATTATGGTTTGGACTATGCTAACCACTA
*
208916 ACCTTTTTTATTTGATTTATTTTATTTTCTTTTTATATATTTGTTTGAATTATTCAATTCG
64 A-C-----T-TTT-ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
* * *
208977 ATCTTGCGGTGACCAGATCTGAGGTATGATTCACATTATTATGGTTTGGACTCTGCTAACCACTA
1 ATCTTGTGGTGACCAGAT-TG-GGTATGATCCACATTATTATGGTTTGGACTATGCTAACCACTA
* *
209042 ACTTTTATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCGATTTG
64 ACTTTTATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
* *
209095 ACCTTGTGGTGACCCGATTCGGGATATGATCCACATTATTATGGTT
1 ATCTTGTGGTGACCAGATT-GGG-TATGATCCACATTATTATGGTT
209141 CGAACCTTAC
Statistics
Matches: 148, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
117 3 0.02
118 81 0.55
119 3 0.02
120 1 0.01
125 2 0.01
126 58 0.39
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (116 bp):
ATCTTGTGGTGACCAGATTGGGTATGATCCACATTATTATGGTTTGGACTATGCTAACCACTAAC
TTTTATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCG
Found at i:209154 original size:118 final size:118
Alignment explanation
Indices: 208930--209165 Score: 325
Period size: 118 Copynumber: 2.0 Consensus size: 118
208920 TTTTTATTTG
* *
208930 ATTTATTTTATTTTCTTTTTATATATTTGTTTGAATTATTCAATTCGATCTTGCGGTGACCAGAT
1 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGACCTTGCGGTGACCAGAT
* * * *
208995 CTGAGGTATGATTCACATTATTATGGTTTGGACTCTGCTAACCACTAACTTTT
66 CTGAGGTATGATCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTT
* * * *
209048 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCGATTTGACCTTGTGGTGACCCGAT
1 ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGACCTTGCGGTGACCAGAT
*
209113 -TCG-GGATATGATCCACATTATTATGGTTCGAAC-CTTACTAACCGCTAACTTTT
66 CT-GAGG-TATGATCCACATTATTATGGTTCGAACTC-TACTAACCACTAACTTTT
209166 CTAACTTAAC
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
117 4 0.04
118 100 0.96
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (118 bp):
ATTTATTTTATTTTATTTTTATATATTTGTTTGAATTATTCAATTCGACCTTGCGGTGACCAGAT
CTGAGGTATGATCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTT
Found at i:209212 original size:32 final size:33
Alignment explanation
Indices: 209176--209369 Score: 173
Period size: 32 Copynumber: 5.8 Consensus size: 33
209166 CTAACTTAAC
209176 AACATTCTAAC-TTTTATTTTATTGTTCATACT
1 AACATTCTAACTTTTTATTTTATTGTTCATACT
209208 AACATTCTAAC-TTTTATTTTATTGTTCATACT
1 AACATTCTAACTTTTTATTTTATTGTTCATACT
* * * *
209240 AACATTCTAGCTTTTTTTATTGTTCTTATTAACTTACT
1 AACATTCTAAC--TTTTTATT-TTATTGTT--CATACT
* * *
209278 AACATTCTAA-TTTATATTTTATTGCTCATATT
1 AACATTCTAACTTTTTATTTTATTGTTCATACT
* *
209310 AACATACTTACCTTTTTATTTCTATTGTT-ATTACT
1 AACATTC-TAACTTTTTATTT-TATTGTTCA-TACT
**
209345 AAC-TTACTAACACTTTATTTTATTG
1 AACATT-CTAACTTTTTATTTTATTG
209370 CACAAACTAA
Statistics
Matches: 131, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
32 52 0.40
33 7 0.05
34 25 0.19
35 27 0.21
36 6 0.05
38 14 0.11
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (33 bp):
AACATTCTAACTTTTTATTTTATTGTTCATACT
Found at i:209287 original size:70 final size:74
Alignment explanation
Indices: 209204--209356 Score: 199
Period size: 70 Copynumber: 2.1 Consensus size: 74
209194 TTATTGTTCA
* * *
209204 TACTAACATTCTAACTTT-TATTTTATTGTTCATACTAACATTC-TAGC-TTT-TTT-TATTGTT
1 TACTAACATTCTAA-TTTATATTTTATTGCTCATACTAACATACTTACCTTTTATTTCTATTGTT
* *
209264 CTTATTAACT
65 ATTACTAACT
*
209274 TACTAACATTCTAATTTATATTTTATTGCTCATATTAACATACTTACCTTTTTATTTCTATTGTT
1 TACTAACATTCTAATTTATATTTTATTGCTCATACTAACATACTTACC-TTTTATTTCTATTGTT
209339 ATTACTAACT
65 ATTACTAACT
209349 TACTAACA
1 TACTAACA
209357 CTTTATTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
69 3 0.04
70 36 0.51
71 3 0.04
73 3 0.04
74 3 0.04
75 23 0.32
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.52
Consensus pattern (74 bp):
TACTAACATTCTAATTTATATTTTATTGCTCATACTAACATACTTACCTTTTATTTCTATTGTTA
TTACTAACT
Found at i:209310 original size:40 final size:38
Alignment explanation
Indices: 209234--209317 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 38
209224 TTTTATTGTT
* * *
209234 CATACTAACATTCTAGCTTTTTTTATTGTTCTTATTAA
1 CATACTAACATTCTAACTTTTTTTATTGCTCATATTAA
* *
209272 CTTACTAACATTCTAATTTATATTTTATTGCTCATATTAA
1 CATACTAACATTCTAACTT-T-TTTTATTGCTCATATTAA
209312 CATACT
1 CATACT
209318 TACCTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 16 0.42
39 1 0.03
40 21 0.55
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.50
Consensus pattern (38 bp):
CATACTAACATTCTAACTTTTTTTATTGCTCATATTAA
Found at i:210059 original size:6 final size:5
Alignment explanation
Indices: 210022--210056 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
210012 TTTCCCCTCG
*
210022 TTTTA TTTTTA TTTTG TTTTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
210057 TATCTTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:213628 original size:39 final size:39
Alignment explanation
Indices: 213574--213655 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
213564 AGAATAAAGA
*
213574 CCTGCGGTAAGGACTTACCCTGAGCACAAAGCAGAGGAG
1 CCTGCGATAAGGACTTACCCTGAGCACAAAGCAGAGGAG
* *
213613 CCTGCGATATGGACTTACCCTGAGCACAAAGTAGAGGAG
1 CCTGCGATAAGGACTTACCCTGAGCACAAAGCAGAGGAG
213652 CCTG
1 CCTG
213656 TGGTAAGATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (39 bp):
CCTGCGATAAGGACTTACCCTGAGCACAAAGCAGAGGAG
Found at i:213669 original size:39 final size:38
Alignment explanation
Indices: 213574--213669 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 38
213564 AGAATAAAGA
213574 CCTGCGGTAAGGACTTACCCTGAGCACAAAGCAGAGGAG
1 CCTGCGGTAA-GACTTACCCTGAGCACAAAGCAGAGGAG
* * *
213613 CCTGCGATATGGACTTACCCTGAGCACAAAGTAGAGGAG
1 CCTGCGGTA-AGACTTACCCTGAGCACAAAGCAGAGGAG
*
213652 CCTGTGGTAAGATCTTAC
1 CCTGCGGTAAGA-CTTAC
213670 AAGTCATAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.04
39 47 0.96
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (38 bp):
CCTGCGGTAAGACTTACCCTGAGCACAAAGCAGAGGAG
Found at i:216091 original size:64 final size:64
Alignment explanation
Indices: 215979--216100 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 64
215969 CATCGAAGCT
* ** *
215979 ATTTTATGTACCGATGCACAGCCATGCATCAATACACTCCTATTTTTATTGAAACATCAAATGC
1 ATTTTATGTACCGATACACAGCCATGCATCAATACACTCCTACCTTTATTAAAACATCAAATGC
* * * * *
216043 ATTTTGTGTACCGATACACATCCTATGCATCGATGCACT-CTGCCTTTATTAAAACATC
1 ATTTTATGTACCGATACACAGCC-ATGCATCAATACACTCCTACCTTTATTAAAACATC
216101 GAAGGTAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
64 35 0.73
65 13 0.27
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (64 bp):
ATTTTATGTACCGATACACAGCCATGCATCAATACACTCCTACCTTTATTAAAACATCAAATGC
Found at i:218732 original size:65 final size:64
Alignment explanation
Indices: 218652--218775 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
218642 TTGCATAGCC
** * *
218652 ATGCATCAATACACTCCTATTTTTATTGAAAA-ATCAAATGCATTTTGTGTACCGATACACATCC
1 ATGCATCAATACACT-CTAGCTTTATT-AAAATATCAAATGCAATTAGTGTACCGATACACATCC
218716 T
64 T
* * * *
218717 ATGCATCGATGCACTCTGGCTTTATTAAAATATCGAATGCAATTAGTGTACCGATACAC
1 ATGCATCAATACACTCTAGCTTTATTAAAATATCAAATGCAATTAGTGTACCGATACAC
218776 CCCAAGTGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 4 0.08
64 33 0.66
65 13 0.26
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (64 bp):
ATGCATCAATACACTCTAGCTTTATTAAAATATCAAATGCAATTAGTGTACCGATACACATCCT
Found at i:240214 original size:21 final size:21
Alignment explanation
Indices: 240190--240268 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
240180 ACCCTCGCTA
*
240190 TGTATCAATACACTATGATAG
1 TGTATCGATACACTATGATAG
*
240211 TGTATCGATGCATTCCT-TGA-ATG
1 TGTATCGATACA---CTATGATA-G
*
240234 TGTATCGATACACTATCATAG
1 TGTATCGATACACTATGATAG
240255 TGTATCGATACACT
1 TGTATCGATACACT
240269 CGTCAGGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.04
21 27 0.56
22 2 0.04
23 15 0.31
24 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (21 bp):
TGTATCGATACACTATGATAG
Found at i:240766 original size:18 final size:19
Alignment explanation
Indices: 240730--240766 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
240720 TACATATTGA
240730 TTTTTCAAACATTGTTTTT
1 TTTTTCAAACATTGTTTTT
240749 TTTTTCAAA-ATTAGTTTT
1 TTTTTCAAACATT-GTTTT
240767 CAAATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTCAAACATTGTTTTT
Found at i:241353 original size:15 final size:15
Alignment explanation
Indices: 241333--241374 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
241323 CTAATATCTT
241333 TGGTTTAGATAATGA
1 TGGTTTAGATAATGA
241348 TGGTTTAGATAATGA
1 TGGTTTAGATAATGA
241363 TGGTTTAGATAA
1 TGGTTTAGATAA
241375 CGAAAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (15 bp):
TGGTTTAGATAATGA
Found at i:244467 original size:13 final size:13
Alignment explanation
Indices: 244449--244476 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
244439 CAAAGTTAAC
244449 GAGTTGACTTAGT
1 GAGTTGACTTAGT
244462 GAGTTGACTTAGT
1 GAGTTGACTTAGT
244475 GA
1 GA
244477 CTGGACCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (13 bp):
GAGTTGACTTAGT
Found at i:245715 original size:2 final size:2
Alignment explanation
Indices: 245704--245735 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
245694 AAATTTATTA
245704 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
245736 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252461 original size:21 final size:20
Alignment explanation
Indices: 252443--253447 Score: 566
Period size: 21 Copynumber: 48.4 Consensus size: 20
252433 CGTGGAATAA
*
252443 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
252462 AAATCGCAACGCGAACTT-CACT
1 --ATCGCAA-GCGAACTTGGAAT
252484 ATCGCAA-CGAACTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
252503 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
252526 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* * *
252545 AAATCACAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
* *
252568 ATCGCAA-CCAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
252587 AAATCGCAA-CCAATTTGGAAT
1 --ATCGCAAGCGAACTTGGAAT
*
252608 AAATCGCAA-CGAATTTGGAAT
1 --ATCGCAAGCGAACTTGGAAT
* *
252629 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
* * *
252652 ATCGCAA-CGAATTTGAAAA
1 ATCGCAAGCGAACTTGGAAT
*
252671 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
*
252692 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
*
252711 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
252734 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
252753 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
252776 ATCGCAA-CGAAGTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* * *
252795 AAATCACAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
252818 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
252837 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
252860 ATCGCAA-CGAACTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
252879 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
252902 ATCGCAATGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
*
252923 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* * *
252942 AAATCACAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
252965 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* * *
252984 AAATCGCAACGCGAAGTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
* *
253007 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTGGAAT
*
253026 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
* * *
253047 ACCGCAA--GAATTTGGAAA
1 ATCGCAAGCGAACTTGGAAT
*
253065 ATCGCAATGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
*
253086 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
253105 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
* *
253128 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTGGAAT
*
253149 ATCGCAATGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
*
253170 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
253189 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
* *
253212 ATCGCAA-CGAATTTTGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
253231 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
253254 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
253273 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
253296 ATCGCAATGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
*
253317 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* * *
253336 AAATCACAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
*
253359 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTGGAAT
* *
253378 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTGGAAT
* * *
253401 ATCACAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTGGAAT
*
253420 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAT
253441 ATCGCAA
1 ATCGCAA
253448 TACGAATATG
Statistics
Matches: 771, Mismatches: 137, Indels: 152
0.73 0.13 0.14
Matches are distributed among these distances:
18 21 0.03
19 186 0.24
20 7 0.01
21 402 0.52
22 2 0.00
23 153 0.20
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTGGAAT
Found at i:252542 original size:42 final size:42
Alignment explanation
Indices: 252443--252908 Score: 780
Period size: 42 Copynumber: 11.2 Consensus size: 42
252433 CGTGGAATAA
252443 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC-ACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
252484 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
252526 ATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
252568 ATCGCAACCAATTTGGAATAAATCGCAAC-C-AATTTGGAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
252608 AAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
252652 ATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
252692 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
252734 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* *
252776 ATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
252818 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
252860 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
252902 ATCGCAA
1 ATCGCAA
252909 TGCGAACTTG
Statistics
Matches: 399, Mismatches: 19, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
40 43 0.11
41 44 0.11
42 304 0.76
43 1 0.00
44 7 0.02
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:253201 original size:394 final size:394
Alignment explanation
Indices: 252505--253447 Score: 1597
Period size: 394 Copynumber: 2.4 Consensus size: 394
252495 CTTGGAATAA
* *
252505 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
1 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
* * * *
252570 CGCAACCAATTTGGAATAAATCGCAAC-C-AATTTGGAATAAATCGCAACGAATTTGGAATAAAT
66 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAATTTGG-A-AAAT
*
252633 CGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTGGACTATCGCA
127 CGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTGGACTATCGCA
* * *
252698 ACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAAC
192 ACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAAT-AATCGCAAC
252763 GCGAACTTCGACTATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGA
256 GCGAACTTCGACTATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGA
252828 ATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGA
321 ATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGA
252893 ACTTCGACT
386 ACTTCGACT
252902 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
1 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
*
252967 CGCAACGAATTTGGAATAAATCGCAACGCGAAGTTCGACTATCGCAACGAATTTGGAAAATCGCA
66 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
* * *
253032 ACGCGAACTTGGACTACCGCAA-GAATTTGGAAAATCGCAATGCGAACTTGGACTATCGCAACGA
131 ACGCGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACGA
* *
253096 ATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACT-ATCGCAATGCG
196 ATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTCGAATAATCGCAACGCG
* * *
253160 AACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATT
259 AACTTCGACTATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATT
* *
253225 TTGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACT
324 TGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACT
253290 TCGACT
389 TCGACT
253296 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
1 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
*
253361 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAAATCGCA
66 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
253426 ACGCGAACTTGGACTATCGCAA
131 ACGCGAACTTGGACTATCGCAA
253448 TACGAATATG
Statistics
Matches: 519, Mismatches: 23, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
394 368 0.71
395 28 0.05
396 10 0.02
397 105 0.20
398 1 0.00
399 7 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (394 bp):
ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTAT
CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
ACGCGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACGA
ATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAATAATCGCAACGCGAA
CTTCGACTATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTG
GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
GACT
Done.