Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 19
Found at i:3265528 original size:20 final size:20
Alignment explanation
Indices: 3265499--3265537 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3265489 ACAGGTCATA
*
3265499 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3265519 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3265538 GTGGCGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3269249 original size:43 final size:42
Alignment explanation
Indices: 3269180--3269278 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
3269170 AATAGGTAAC
* *
3269180 GATATATAGCGGCATTTCTTCAACAAAAGTCGTAATAGGTGCT
1 GATATTTAGCGGCATTTCTT-AACAAAAGCCGTAATAGGTGCT
* **
3269223 GATATTTAGCGGCATTTGTCTT-ACAAATGCCGTAATAGGTTTT
1 GATATTTAGCGGCA-TT-TCTTAACAAAAGCCGTAATAGGTGCT
*
3269266 GAGATTTAGCGGC
1 GATATTTAGCGGC
3269279 GTTTTTTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 42 0.88
44 2 0.04
45 4 0.08
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
GATATTTAGCGGCATTTCTTAACAAAAGCCGTAATAGGTGCT
Found at i:3269343 original size:44 final size:44
Alignment explanation
Indices: 3269288--3269568 Score: 348
Period size: 44 Copynumber: 6.4 Consensus size: 44
3269278 CGTTTTTTGA
*
3269288 ATACAAACGCCGCTAAAGGTCTGGTATATAGCAGCATTTTTAGG
1 ATACAAACGCCGCTAAAGATCTGGTATATAGCAGCATTTTTAGG
* * **
3269332 ATGCAAGCGCCGCTAAAGATCTGGTATATAGCAGTGTTTTTAGG
1 ATACAAACGCCGCTAAAGATCTGGTATATAGCAGCATTTTTAGG
* * * * * * *
3269376 ATACAAACGCCACTGAAGGTCTAGTATATAACGGCATTTTTAGA
1 ATACAAACGCCGCTAAAGATCTGGTATATAGCAGCATTTTTAGG
* *
3269420 ATACAAACGCCGCTAAAGATCTGATATATAGCAGCGTTTTTAGG
1 ATACAAACGCCGCTAAAGATCTGGTATATAGCAGCATTTTTAGG
* * *
3269464 ATACAAACGCCGATAAAGATCTGGTATATAACGGCATTTTTAGG
1 ATACAAACGCCGCTAAAGATCTGGTATATAGCAGCATTTTTAGG
* * * * *
3269508 ATACAAACGTCGCTAAA-AGTTTGGTATATAGCGGTATTTTTAGT
1 ATACAAACGCCGCTAAAGA-TCTGGTATATAGCAGCATTTTTAGG
3269552 ATACAAACGCCGCTAAA
1 ATACAAACGCCGCTAAA
3269569 TGTTTATATA
Statistics
Matches: 199, Mismatches: 37, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
43 1 0.01
44 198 0.99
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (44 bp):
ATACAAACGCCGCTAAAGATCTGGTATATAGCAGCATTTTTAGG
Found at i:3269428 original size:132 final size:132
Alignment explanation
Indices: 3269275--3269568 Score: 399
Period size: 132 Copynumber: 2.2 Consensus size: 132
3269265 TGAGATTTAG
* * * * * *
3269275 CGGCGTTTTTTGAATACAAACGCCGCTAAAGGTCTGGTATATAGCAGCATTTTTAGGATGCAAGC
1 CGGCATTTTTAGAATACAAACGCCGCTAAAGATCTGATATATAGCAGCATTTTTAGGATACAAAC
* * ** * *
3269340 GCCGCTAAAGATCTGGTATATAGCAGTGTTTTTAGGATACAAACGCCACTGAAGGTCTAGTATAT
66 GCCGATAAAGATCTGGTATATAACAGCATTTTTAGGATACAAACGCCACTAAAAGTCTAGTATAT
3269405 AA
131 AA
*
3269407 CGGCATTTTTAGAATACAAACGCCGCTAAAGATCTGATATATAGCAGCGTTTTTAGGATACAAAC
1 CGGCATTTTTAGAATACAAACGCCGCTAAAGATCTGATATATAGCAGCATTTTTAGGATACAAAC
* * * * *
3269472 GCCGATAAAGATCTGGTATATAACGGCATTTTTAGGATACAAACGTCGCTAAAAGTTTGGTATAT
66 GCCGATAAAGATCTGGTATATAACAGCATTTTTAGGATACAAACGCCACTAAAAGTCTAGTATAT
*
3269537 AG
131 AA
* *
3269539 CGGTATTTTTAGTATACAAACGCCGCTAAA
1 CGGCATTTTTAGAATACAAACGCCGCTAAA
3269569 TGTTTATATA
Statistics
Matches: 141, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
132 141 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (132 bp):
CGGCATTTTTAGAATACAAACGCCGCTAAAGATCTGATATATAGCAGCATTTTTAGGATACAAAC
GCCGATAAAGATCTGGTATATAACAGCATTTTTAGGATACAAACGCCACTAAAAGTCTAGTATAT
AA
Found at i:3275890 original size:36 final size:36
Alignment explanation
Indices: 3275850--3275918 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
3275840 AAAATATCGA
3275850 CATTGGTGTAGCTAATTATTCTAGGTAAACTATTTT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATTTT
*
3275886 CATTGGTGTAGTTAATTATTCTAGGTAAACTAT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTAT
3275919 ATATAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (36 bp):
CATTGGTGTAGCTAATTATTCTAGGTAAACTATTTT
Found at i:3283986 original size:12 final size:12
Alignment explanation
Indices: 3283969--3283997 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3283959 ATAGAAACTA
3283969 AAAAAATAAAAT
1 AAAAAATAAAAT
3283981 AAAAAATAAAAT
1 AAAAAATAAAAT
3283993 AAAAA
1 AAAAA
3283998 CACTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:3283990 original size:20 final size:19
Alignment explanation
Indices: 3283952--3283991 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3283942 TAAGAAAGAC
* *
3283952 AAAATAAATAGAAACTAAA
1 AAAATAAATAAAAAATAAA
3283971 AAAATAAAATAAAAAATAAA
1 AAAAT-AAATAAAAAATAAA
3283991 A
1 A
3283992 TAAAAACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAATAAATAAAAAATAAA
Found at i:3285220 original size:103 final size:103
Alignment explanation
Indices: 3284890--3285466 Score: 572
Period size: 103 Copynumber: 5.6 Consensus size: 103
3284880 TGTCTAAGAT
* * * *
3284890 TATTTATTTTGAGTTTACATATTAAAATG--TTCGAATGGTTTGGTAAGTTTAGTTTAAATTTTG
1 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAA--TT-
* *
3284953 TTTTTTGTTTTTTGTTTTTATTTTAATTA-ATAATTATTAGAC
63 TTATTT-TTTTTTGTTTTTATTTTAAATATA-AATTATTAGAC
* * * * * *
3284995 TATTTATTTTTATTTTACAAATTAAA--CTATTTGAGTGGTTTCGT-AGTTTAATGTAAATTTTA
1 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAATTTTA
*
3285057 TGGTTTAATTTTTTAGTTTTTATTTTAAATATAAATTAATTAGAT
66 ---TTT--TTTTTT-GTTTTTATTTTAAATATAAATT-ATTAGAC
* * *
3285102 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGATTTGGTAAATTTAGTTTAAATTTTA
1 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAATTTTA
* *
3285167 TTTTTTTTTGTTTTTATTTTAAATA-ATTATTATTATAC
66 TTTTTTTTTGTTTTTATTTTAAATATA-AATTATTAGAC
* * ** *
3285205 TATTTATTTTGATTTTACATATTAAATCGTATTTGAGTGG-CCCGTAAGTTTAGTGTAAATTTTA
1 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAATTTTA
** **
3285269 TTGTTTCATT-TTTTTATTTTAAATATAAATTAATTAGTT
66 TT-TTTTTTTGTTTTTATTTTAAATATAAATT-ATTAGAC
* ** **
3285308 TATTTATTTTGATTTTACAGACAAAACGGTATTCGAGTGG----GTAAGTTTAGTTTAAATTTTA
1 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAATTTTA
* *
3285369 -TTGTTTAT-TTTTTATTTTAAATATAAATTATTAGAC
66 TTTTTTTTTGTTTTTATTTTAAATATAAATTATTAGAC
* * * *
3285405 TATTTATTTTGATTTTATAGATTAAATTATATTTGAGTGGTTTCGTAAGTTTAGTTTAAATT
1 TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAATT
3285467 AATTAGACTA
Statistics
Matches: 393, Mismatches: 59, Indels: 44
0.79 0.12 0.09
Matches are distributed among these distances:
97 38 0.10
98 24 0.06
99 1 0.00
100 20 0.05
101 20 0.05
102 41 0.10
103 87 0.22
104 33 0.08
105 47 0.12
106 19 0.05
107 34 0.09
109 14 0.04
110 15 0.04
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.55
Consensus pattern (103 bp):
TATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGGTTTCGTAAGTTTAGTTTAAATTTTA
TTTTTTTTTGTTTTTATTTTAAATATAAATTATTAGAC
Found at i:3285325 original size:206 final size:207
Alignment explanation
Indices: 3284886--3285466 Score: 713
Period size: 212 Copynumber: 2.8 Consensus size: 207
3284876 TGCATGTCTA
* *
3284886 AGATTATTTATTTTGAGTTTACATATTAAAATG--TTCGAATGGTTTGGTAAGTTTAGTTTAAAT
1 AGATTATTTATTTTGATTTTACATATTAAAATGTATTCGAGT-GTTTGGTAAGTTTAGTTTAAA-
* * *
3284949 TTTGTTTTTTGTTTTTTGTTTTTATTTTAATTAATAATTATTAGACTATTTATTTTTATTTTACA
64 -TT-TTATTT-TTTTTTGTTTTTATTTTAAATAATAATTATTAGACTATTTATTTTGATTTTACA
*
3285014 AATTAAA-CTATTTGAGTGGTTTCGT-AGTTTAATGTAAATTTTATGGTTTAATTTTTTAGTTTT
126 AATTAAATCTATTTGAGTGGTTTCGTAAGTTTAGTGTAAATTTTATGGTTTAA---TTTA-TTTT
3285077 TATTTTAAATATAAATTAATT
187 TATTTTAAATATAAATTAATT
* *
3285098 AGATTATTTATTTTGATTTTACATATTAAATTGTATTCGAGTGATTTGGTAAATTTAGTTTAAAT
1 AGATTATTTATTTTGATTTTACATATTAAAATGTATTCGAGTG-TTTGGTAAGTTTAGTTTAAAT
* * *
3285163 TTTATTTTTTTTTGTTTTTATTTTAAATAATTATTATTATACTATTTATTTTGATTTTACATATT
65 TTTATTTTTTTTTGTTTTTATTTTAAATAATAATTATTAGACTATTTATTTTGATTTTACAAATT
** * *
3285228 AAATCGTATTTGAGTGG-CCCGTAAGTTTAGTGTAAATTTTATTGTTTCA-TT-TTTTTATTTTA
130 AAATC-TATTTGAGTGGTTTCGTAAGTTTAGTGTAAATTTTATGGTTTAATTTATTTTTATTTTA
3285290 AATATAAATTAATT
194 AATATAAATTAATT
* * * *
3285304 AGTTTATTTATTTTGATTTTACAGA-CAAAACGGTATTCGAGTG---GGTAAGTTTAGTTTAAAT
1 AGATTATTTATTTTGATTTTACATATTAAAA-TGTATTCGAGTGTTTGGTAAGTTTAGTTTAAAT
* * * *
3285365 TTTA-TTGTTTAT-TTTTTATTTTAAAT-ATAAATTATTAGACTATTTATTTTGATTTTATAGAT
65 TTTATTTTTTTTTGTTTTTATTTTAAATAAT-AATTATTAGACTATTTATTTTGATTTTACAAAT
* *
3285427 TAAATTATATTTGAGTGGTTTCGTAAGTTTAGTTTAAATT
129 TAAA-TCTATTTGAGTGGTTTCGTAAGTTTAGTGTAAATT
3285467 AATTAGACTA
Statistics
Matches: 328, Mismatches: 31, Indels: 31
0.84 0.08 0.08
Matches are distributed among these distances:
199 2 0.01
200 58 0.18
201 25 0.08
202 21 0.06
205 3 0.01
206 59 0.18
208 2 0.01
210 56 0.17
211 9 0.03
212 67 0.20
213 1 0.00
214 25 0.08
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.55
Consensus pattern (207 bp):
AGATTATTTATTTTGATTTTACATATTAAAATGTATTCGAGTGTTTGGTAAGTTTAGTTTAAATT
TTATTTTTTTTTGTTTTTATTTTAAATAATAATTATTAGACTATTTATTTTGATTTTACAAATTA
AATCTATTTGAGTGGTTTCGTAAGTTTAGTGTAAATTTTATGGTTTAATTTATTTTTATTTTAAA
TATAAATTAATT
Found at i:3285517 original size:3 final size:3
Alignment explanation
Indices: 3285509--3285540 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3285499 TTTTGTTTAA
3285509 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3285541 AAATTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3285549 original size:15 final size:15
Alignment explanation
Indices: 3285506--3285579 Score: 55
Period size: 18 Copynumber: 4.7 Consensus size: 15
3285496 TTATTTTGTT
3285506 TAAATTATTATTATTA
1 TAAATT-TTATTATTA
*
3285522 TTATTATTATTATTATTA
1 -TA-AATT-TTATTATTA
3285540 TAAATTTTATATATT-
1 TAAATTTTAT-TATTA
*
3285555 T-AATTTT-TTAAATA
1 TAAATTTTATT-ATTA
3285569 TAAATTTTATT
1 TAAATTTTATT
3285580 GTTTCATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
12 1 0.02
13 3 0.06
14 7 0.15
15 11 0.23
16 9 0.19
17 4 0.08
18 13 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATTTTATTATTA
Found at i:3288105 original size:27 final size:27
Alignment explanation
Indices: 3288088--3288204 Score: 139
Period size: 27 Copynumber: 4.3 Consensus size: 27
3288078 TTCATCATGG
*
3288088 TCATTTAAATATGGATATTAATCATAT
1 TCATTCAAATATGGATATTAATCATAT
* ** *
3288115 TCATTCAAATATGGCTATCCATCACAT
1 TCATTCAAATATGGATATTAATCATAT
*
3288142 TCATTCAAATATGGATATTAATCACAT
1 TCATTCAAATATGGATATTAATCATAT
*
3288169 TCATTCAAATATGGTTATCT-ATCACT-T
1 TCATTCAAATATGGATAT-TAATCA-TAT
3288196 TCATTCAAA
1 TCATTCAAA
3288205 AAATAAATAG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 77 0.99
28 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (27 bp):
TCATTCAAATATGGATATTAATCATAT
Found at i:3288152 original size:54 final size:54
Alignment explanation
Indices: 3288088--3288204 Score: 189
Period size: 54 Copynumber: 2.2 Consensus size: 54
3288078 TTCATCATGG
* *
3288088 TCATTTAAATATGGATATTAATCATATTCATTCAAATATGGCTATCCATCACAT
1 TCATTCAAATATGGATATTAATCACATTCATTCAAATATGGCTATCCATCACAT
* * *
3288142 TCATTCAAATATGGATATTAATCACATTCATTCAAATATGGTTATCTATCACTT
1 TCATTCAAATATGGATATTAATCACATTCATTCAAATATGGCTATCCATCACAT
3288196 TCATTCAAA
1 TCATTCAAA
3288205 AAATAAATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (54 bp):
TCATTCAAATATGGATATTAATCACATTCATTCAAATATGGCTATCCATCACAT
Found at i:3291058 original size:19 final size:19
Alignment explanation
Indices: 3291036--3291076 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3291026 AAAATAAAAA
*
3291036 TAATTACTAA-AAATATTAT
1 TAATTA-TAATAAATACTAT
3291055 TAATTATAATAAATACTAT
1 TAATTATAATAAATACTAT
3291074 TAA
1 TAA
3291077 AGTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTATAATAAATACTAT
Found at i:3291771 original size:295 final size:296
Alignment explanation
Indices: 3291216--3291771 Score: 868
Period size: 295 Copynumber: 1.9 Consensus size: 296
3291206 AAAATTATAA
* * *
3291216 TTATGAATAAAATTAAAATAAAATTATTACTAAAAATATTATTAATTATAACTAATATTATTTAA
1 TTATGAATAAAATTAAAATAAAATAATTACTAAAAATATTATAAATTATAACTAATACTATTTAA
* *
3291281 AGTTATTATTAAATTTTGAATTTTTCGTCATTATTTAAATACATTCATCATCACGTGAGTTGACT
66 AGTTATTATTAAATTTCGAATTTTTCGTCATTATTTAAATACATTCATCATCACATGAGTTGACT
* * *
3291346 TATAATTAAATTTATTAACAATATTTTTATAACTACTAGTAATGATCTAATTATTTTAACATTTC
131 TATAATTAAATTTATTAACAATATTTTTATAACTACTAATAATGATCTAACTATTTTAACATTTA
* * * * *
3291411 TACTACAAATACTAAATCAATACTATTAAAATTATAATAATGATTCGTAAGTTAAAATTTAACTA
196 TACTACAAATACTAAATCAAAAATATTAAAATTATAATAATGATTCATAAGGTAAAATGTAACTA
3291476 ACAATGCTATATATTCATCATCACATGATTCCTAAG
261 ACAATGCTATATATTCATCATCACATGATTCCTAAG
* * *
3291512 TTATGATTAAAATTAATATAAAATAATTACTAAACATATTATAAATTATAA-TAAATACTA-TTA
1 TTATGAATAAAATTAAAATAAAATAATTACTAAAAATATTATAAATTATAACT-AATACTATTTA
* * **
3291575 AAGTTATTATTCAATTTCGAATTTTTCGTCATTTTTTAAATATGTTCATCATCACATGAGCTT-A
65 AAGTTATTATTAAATTTCGAATTTTTCGTCATTATTTAAATACATTCATCATCACATGAG-TTGA
*
3291639 CTTATGATTAAATTTATTAACAATATTTTTTATAACTACTAATAATGATCTAACTATTTTAACAT
129 CTTATAATTAAATTTATTAACAATA-TTTTTATAACTACTAATAATGATCTAACTATTTTAACAT
3291704 TTATACTACAAATACTAAATCAAAAAT-TTAAAATTATAATAATGATTCATAAGGTAAAATGTAA
193 TTATACTACAAATACTAAATCAAAAATATTAAAATTATAATAATGATTCATAAGGTAAAATGTAA
3291768 CTAA
258 CTAA
3291772 GAATATTATG
Statistics
Matches: 236, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
295 121 0.51
296 115 0.49
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.41
Consensus pattern (296 bp):
TTATGAATAAAATTAAAATAAAATAATTACTAAAAATATTATAAATTATAACTAATACTATTTAA
AGTTATTATTAAATTTCGAATTTTTCGTCATTATTTAAATACATTCATCATCACATGAGTTGACT
TATAATTAAATTTATTAACAATATTTTTATAACTACTAATAATGATCTAACTATTTTAACATTTA
TACTACAAATACTAAATCAAAAATATTAAAATTATAATAATGATTCATAAGGTAAAATGTAACTA
ACAATGCTATATATTCATCATCACATGATTCCTAAG
Found at i:3293524 original size:18 final size:19
Alignment explanation
Indices: 3293461--3293552 Score: 89
Period size: 18 Copynumber: 4.9 Consensus size: 19
3293451 GGTCAACTCT
* * *
3293461 GGTCAAAGTCAATGGGTTA
1 GGTCAAAGTCAATCGATCA
* * *
3293480 TGTCAAAGTCAATAGGTCA
1 GGTCAAAGTCAATCGATCA
* *
3293499 GGTAAAAGTCAA-CGATTA
1 GGTCAAAGTCAATCGATCA
3293517 GGTCAAAGTCAA-CGATCA
1 GGTCAAAGTCAATCGATCA
*
3293535 GGTCAAAGTCAATGGATC
1 GGTCAAAGTCAATCGATC
3293553 GGGTTGGGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
18 31 0.51
19 30 0.49
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (19 bp):
GGTCAAAGTCAATCGATCA
Found at i:3297931 original size:19 final size:19
Alignment explanation
Indices: 3297903--3297956 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3297893 AACTCTAGTA
* *
3297903 AAAGTCAACGTGTCATGTC
1 AAAGTCAACGGGTCAGGTC
*
3297922 AAAGTTAACGGGTCAGGTC
1 AAAGTCAACGGGTCAGGTC
*
3297941 AAAGTCAATGGGTCAG
1 AAAGTCAACGGGTCAG
3297957 ATCGGGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (19 bp):
AAAGTCAACGGGTCAGGTC
Found at i:3300137 original size:15 final size:16
Alignment explanation
Indices: 3300107--3300137 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3300097 GCCATCAACC
3300107 AGTAAATCAGTAAATT
1 AGTAAATCAGTAAATT
3300123 AGTAAATCA-TAAATT
1 AGTAAATCAGTAAATT
3300138 TCGGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (16 bp):
AGTAAATCAGTAAATT
Found at i:3301720 original size:19 final size:18
Alignment explanation
Indices: 3301697--3301795 Score: 90
Period size: 19 Copynumber: 5.2 Consensus size: 18
3301687 CAAAGTCACT
*
3301697 GGTCAAAGTCAACAGGTC
1 GGTCAAAGTCAACGGGTC
**
3301715 GTGTCAAAGTTGACGGGTC
1 G-GTCAAAGTCAACGGGTC
3301734 AGGTCAAAGTCAACGGGTC
1 -GGTCAAAGTCAACGGGTC
* * *
3301753 GGTTAAAAGTTAATGGGTC
1 GG-TCAAAGTCAACGGGTC
*
3301772 GGGTCAAAGTCAATGGGTC
1 -GGTCAAAGTCAACGGGTC
3301791 AGGTC
1 -GGTC
3301796 GGGTTGACTC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
18 3 0.05
19 60 0.91
20 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.22
Consensus pattern (18 bp):
GGTCAAAGTCAACGGGTC
Found at i:3301753 original size:38 final size:38
Alignment explanation
Indices: 3301697--3301790 Score: 118
Period size: 38 Copynumber: 2.5 Consensus size: 38
3301687 CAAAGTCACT
* * *
3301697 GGTCAAAGTCAACAGGTC-GTGTCAAAGTTGACGGGTCA
1 GGTCAAAGTCAACGGGTCGGT-TAAAAGTTAACGGGTCA
* *
3301735 GGTCAAAGTCAACGGGTCGGTTAAAAGTTAATGGGTCG
1 GGTCAAAGTCAACGGGTCGGTTAAAAGTTAACGGGTCA
*
3301773 GGTCAAAGTCAATGGGTC
1 GGTCAAAGTCAACGGGTC
3301791 AGGTCGGGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 47 0.96
39 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (38 bp):
GGTCAAAGTCAACGGGTCGGTTAAAAGTTAACGGGTCA
Found at i:3304858 original size:23 final size:23
Alignment explanation
Indices: 3304828--3304881 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
3304818 CTTGTAGAAG
3304828 AGCAAACATCTCAACTCAGTCCA
1 AGCAAACATCTCAACTCAGTCCA
3304851 AGCAAACATCTCAACTCAGTCCA
1 AGCAAACATCTCAACTCAGTCCA
*
3304874 AGTAAACA
1 AGCAAACA
3304882 AGACCATGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (23 bp):
AGCAAACATCTCAACTCAGTCCA
Found at i:3306070 original size:17 final size:18
Alignment explanation
Indices: 3306037--3306072 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3306027 AATTCCAATA
3306037 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
3306055 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
3306072 A
1 A
3306073 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:3306419 original size:12 final size:11
Alignment explanation
Indices: 3306389--3306422 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3306379 GACTAATATG
3306389 AAAATAATAAT
1 AAAATAATAAT
3306400 AAAATAATAACT
1 AAAATAATAA-T
*
3306412 AAAGTAATAAT
1 AAAATAATAAT
3306423 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:3308072 original size:3 final size:3
Alignment explanation
Indices: 3308064--3308105 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
3308054 AATATAATTT
3308064 TAA TAA TAA TAA TAA TAA T-A TAA TAA TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
3308106 ATTTAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3308082 original size:21 final size:22
Alignment explanation
Indices: 3308053--3308103 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
3308043 TCTGGGCTTG
*
3308053 TAAT-ATAATTTTAATAATA-A
1 TAATAATAATTATAATAATATA
3308073 TAATAATAA-TATAATAATATA
1 TAATAATAATTATAATAATATA
3308094 TAATAATAAT
1 TAATAATAAT
3308104 AAATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATAATAATTATAATAATATA
Found at i:3308433 original size:22 final size:23
Alignment explanation
Indices: 3308372--3308434 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
3308362 CATTTGAAAA
*
3308372 CATCCTGCACTGTAGGTCTTATG
1 CATCTTGCACTGTAGGTCTTATG
* * *
3308395 GA--TGGCCCTG-AGGTCTTAT-
1 CATCTTGCACTGTAGGTCTTATG
3308414 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
3308435 CATATGACCC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 11 0.37
22 8 0.27
23 1 0.03
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (23 bp):
CATCTTGCACTGTAGGTCTTATG
Found at i:3308480 original size:45 final size:45
Alignment explanation
Indices: 3308431--3308598 Score: 264
Period size: 45 Copynumber: 3.7 Consensus size: 45
3308421 CACTGTAGGT
* * * * *
3308431 CTTACATATGACCCGGAGGCTTTAAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGGG
3308476 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGGG
3308521 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGGG
* * *
3308566 TTTATAGATGACCCGAAGGTTTTGAAAATATCA
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCA
3308599 AAAAGCTCCC
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 115 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTAAAGGG
Found at i:3308654 original size:75 final size:75
Alignment explanation
Indices: 3308532--3308725 Score: 318
Period size: 75 Copynumber: 2.6 Consensus size: 75
3308522 TTACAGATGA
* * * *
3308532 CCCGAAGG-TTTTGAAAACATCATGCACTAAAGGGTTTATAGATGACCCGAAGGTTTTGAAAATA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAATA
3308596 TCAAAAAGCT
66 TCAAAAAGCT
* *
3308606 CCCGAAGGCTTTTGAAAACAGCATGTACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAATA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAATA
*
3308671 TTAAAAAGCT
66 TCAAAAAGCT
3308681 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
3308726 TGGGAAATAT
Statistics
Matches: 110, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
74 8 0.07
75 102 0.93
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (75 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAATA
TCAAAAAGCT
Found at i:3309453 original size:22 final size:22
Alignment explanation
Indices: 3309390--3309455 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
3309380 AAATCCAATA
* *
3309390 AATCTTTCATCTTTGAAA-AGAG
1 AATCTATCATCTTT-AAAGAGTG
**
3309412 AATCTATCATCTTTGGAGAGTG
1 AATCTATCATCTTTAAAGAGTG
3309434 AATCTATCATCTTTAAAGAGTG
1 AATCTATCATCTTTAAAGAGTG
3309456 TAGATATGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTAAAGAGTG
Found at i:3310916 original size:74 final size:75
Alignment explanation
Indices: 3310782--3310960 Score: 222
Period size: 74 Copynumber: 2.4 Consensus size: 75
3310772 ATAAGATGAT
* * * ** *
3310782 ATGGGCCTTCACCATGCCCCAGCATTTACTGATATGAACATTCAAAATATATCAACATTCC-TTA
1 ATGGGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACATTCAAAATATATCAACATTCCAAT-
3310846 TTCTGATTGAA
65 TTCTGATTGAA
* *
3310857 AT-GGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACGTTCAAAATGAGT-T-AATATTCCAA
1 ATGGGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACATTCAAAAT-A-TATCAACATTCCAA
3310919 TTTCTGATTGAA
64 TTTCTGATTGAA
*
3310931 ATGGGCTTTCAGCATGCCCCAGTATTTGCT
1 ATGGGCTTTCAGCATGCCCCAGCATTTGCT
3310961 TCTTATTAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
74 59 0.65
75 31 0.34
76 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAGCATTTGCTGATACAAACATTCAAAATATATCAACATTCCAATT
TCTGATTGAA
Found at i:3313094 original size:72 final size:72
Alignment explanation
Indices: 3312974--3313115 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 72
3312964 GTATAATAGT
* *
3312974 ATAACAAATTAGTTGAATATTATCCATAAAGCCGGGGCGATTAGCCAATTGCTTTAGGGGGATAA
1 ATAACAAATTAGTTGAATATTATCCATAAAGCCGGAGCGATTAACCAATTGCTTTAGGGGGATAA
3313039 CTCAAAC
66 CTCAAAC
* *
3313046 ATAACAGATTAGCTT-AATATTATCCATAAAGCCGGAGCTATTAACCAATTGCTTTAGGGGGATA
1 ATAACAAATTAG-TTGAATATTATCCATAAAGCCGGAGCGATTAACCAATTGCTTTAGGGGGATA
3313110 ACTCAA
65 ACTCAA
3313116 GCTTTATTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
72 63 0.97
73 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (72 bp):
ATAACAAATTAGTTGAATATTATCCATAAAGCCGGAGCGATTAACCAATTGCTTTAGGGGGATAA
CTCAAAC
Found at i:3315491 original size:14 final size:14
Alignment explanation
Indices: 3315471--3315550 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 14
3315461 AGTTTGAAAC
3315471 AAAATGCAAATATG
1 AAAATGCAAATATG
* *
3315485 CAAATGCAAAAATG
1 AAAATGCAAATATG
*
3315499 AAAATGTAAATAT-
1 AAAATGCAAATATG
* * *
3315512 -AAACGTAAAAATG
1 AAAATGCAAATATG
3315525 CAAATATGCAAA-ATG
1 -AAA-ATGCAAATATG
*
3315540 AAAATACAAAT
1 AAAATGCAAAT
3315551 GTAAATATGT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
12 10 0.20
13 6 0.12
14 25 0.49
15 5 0.10
16 5 0.10
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (14 bp):
AAAATGCAAATATG
Found at i:3315545 original size:35 final size:34
Alignment explanation
Indices: 3315486--3315555 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
3315476 GCAAATATGC
* *
3315486 AAATGCAAAAATGAAAATGTAAATATAAACGTAA
1 AAATGCAAAAATGAAAATGAAAATACAAACGTAA
* *
3315520 AAATGCAAATATGCAAAATGAAAATACAAATGTAA
1 AAATGCAAAAATG-AAAATGAAAATACAAACGTAA
3315555 A
1 A
3315556 TATGTGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.20
Consensus pattern (34 bp):
AAATGCAAAAATGAAAATGAAAATACAAACGTAA
Found at i:3315643 original size:8 final size:7
Alignment explanation
Indices: 3315615--3315655 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
3315605 ATAAAAATAC
3315615 AAATGCA
1 AAATGCA
*
3315622 AAAT-AA
1 AAATGCA
3315628 AAATGCA
1 AAATGCA
3315635 AAGATGCA
1 AA-ATGCA
3315643 AAATGC-
1 AAATGCA
3315649 AAATGCA
1 AAATGCA
3315656 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 11 0.38
7 11 0.38
8 7 0.24
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:3315655 original size:13 final size:13
Alignment explanation
Indices: 3315608--3315651 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
3315598 AGAAAACATA
3315608 AAAATACAAATGC
1 AAAATACAAATGC
*
3315621 AAAATAAAAATGC
1 AAAATACAAATGC
*
3315634 AAAGATGCAAAATGC
1 AAA-ATAC-AAATGC
3315649 AAA
1 AAA
3315652 TGCATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 2 0.08
15 9 0.35
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (13 bp):
AAAATACAAATGC
Found at i:3315794 original size:43 final size:43
Alignment explanation
Indices: 3315733--3315814 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
3315723 TGCATCAAAT
*
3315733 AAAACTTTACATATAGGGGACAACTTTCAGTCCTAACTTTAAC
1 AAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTTAAC
* *
3315776 AAAACTTTACATATAGGGGATAACTTTCCCTCCTAACTT
1 AAAACTTTACATATAGGGGACAACTTTCACTCCTAACTT
3315815 CTCTAAAGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (43 bp):
AAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTTAAC
Found at i:3316341 original size:36 final size:36
Alignment explanation
Indices: 3316281--3316352 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3316271 TCTTATCGTA
* *
3316281 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
*
3316317 GAATACTTTTGGTATTAATATAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
3316353 TGCATAGCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:3317758 original size:27 final size:26
Alignment explanation
Indices: 3317714--3317765 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3317704 AAATATATTA
* *
3317714 ATTTTTATAAATATATATTTTTTTAT
1 ATTTTTATAAATAAATATTTATTTAT
3317740 ATTTTTATAAATAAAATATTTATTTA
1 ATTTTTATAAAT-AAATATTTATTTA
3317766 CATAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTATAAATAAATATTTATTTAT
Found at i:3318075 original size:11 final size:11
Alignment explanation
Indices: 3318061--3318094 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3318051 GACTAATATG
3318061 AAAATAATAAT
1 AAAATAATAAT
3318072 AAAATAATAATT
1 AAAATAATAA-T
*
3318084 AAAGTAATAAT
1 AAAATAATAAT
3318095 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:3318091 original size:12 final size:12
Alignment explanation
Indices: 3318061--3318095 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3318051 GACTAATATG
3318061 AAAATAATAA-T
1 AAAATAATAATT
3318072 AAAATAATAATT
1 AAAATAATAATT
*
3318084 AAAGTAATAATT
1 AAAATAATAATT
3318096 TAAACATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:3318376 original size:6 final size:6
Alignment explanation
Indices: 3318367--3318406 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
3318357 ACCTTAACCC
* *
3318367 TAAATA TAAATA TAAATA TAAATA TATATA TATATA TAAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAA
3318407 CATGTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATA
Found at i:3319684 original size:3 final size:3
Alignment explanation
Indices: 3319676--3319709 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
3319666 AATATAATTT
3319676 TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
3319710 ATTTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3319691 original size:19 final size:19
Alignment explanation
Indices: 3319667--3319715 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
3319657 TGGGCTTGTA
3319667 ATATAATTTTAATAATAAT
1 ATATAATTTTAATAATAAT
**
3319686 ATATAATAATAATAATAAT
1 ATATAATTTTAATAATAAT
*
3319705 A-ATAAATTTAA
1 ATATAATTTTAA
3319716 AAATGGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAATTTTAATAATAAT
Found at i:3321224 original size:21 final size:20
Alignment explanation
Indices: 3321199--3321238 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3321189 GTCAAGTTTA
*
3321199 TAAAAATTTAAAACTTTTATT
1 TAAAAAATTAAAA-TTTTATT
3321220 TAAAAAATTAAAATTTTAT
1 TAAAAAATTAAAATTTTAT
3321239 ATGTCTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAAATTAAAATTTTATT
Found at i:3328862 original size:14 final size:14
Alignment explanation
Indices: 3328843--3328880 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3328833 GAGTTTTAAG
3328843 TTAGAGATTAAGGT
1 TTAGAGATTAAGGT
*
3328857 TTAGAGTTTAAGGT
1 TTAGAGATTAAGGT
3328871 TTAGAGATTA
1 TTAGAGATTA
3328881 TGGAGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.39
Consensus pattern (14 bp):
TTAGAGATTAAGGT
Found at i:3330111 original size:8 final size:8
Alignment explanation
Indices: 3330098--3330129 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
3330088 TATCCTTTCA
3330098 ATTTTTTT
1 ATTTTTTT
3330106 A-TTTTTT
1 ATTTTTTT
3330113 A-TTTTTT
1 ATTTTTTT
3330120 ATTTTTTT
1 ATTTTTTT
3330128 AT
1 AT
3330130 ACATCTGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.61
8 9 0.39
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:3330117 original size:6 final size:7
Alignment explanation
Indices: 3330100--3330126 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3330090 TCCTTTCAAT
3330100 TTTTTTA
1 TTTTTTA
3330107 TTTTTTA
1 TTTTTTA
3330114 TTTTTTA
1 TTTTTTA
3330121 TTTTTT
1 TTTTTT
3330127 TATACATCTG
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:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:3334652 original size:23 final size:23
Alignment explanation
Indices: 3334617--3334689 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
3334607 ATACTTTACA
*
3334617 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3334640 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3334663 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
3334686 ATAT
1 ATAT
3334690 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3335141 original size:23 final size:23
Alignment explanation
Indices: 3335106--3335178 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3335096 ATACTTTACA
* *
3335106 ATATAAGCACTACTTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
3335129 ATATAAACGCTACCTATTATATT
1 ATATAAGCGCTACCTATTACATT
*
3335152 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
3335175 ATAT
1 ATAT
3335179 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3335452 original size:490 final size:489
Alignment explanation
Indices: 3334215--3337324 Score: 5639
Period size: 490 Copynumber: 6.4 Consensus size: 489
3334205 TTATAATATG
* *
3334215 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATATTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
3334280 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
3334344 CAAAAACTTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
* *
3334409 TAAACAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* ** *
3334474 ACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
*
3334539 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATAGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
3334604 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
3334669 GCGCTACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
3334704 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
3334769 TCAATTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
3334834 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
3334899 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
*
3334964 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACTC
*
3335029 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATAGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGAT
* *
3335094 AGATACTTTACAATATAAGCACTACTTATTACATTATATAAACGCTACCTATTATATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
3335159 CGCTACCTATTACATCATATTTTTACCTATTATA
456 CGCTACCTATTACATCATATTTTTACCTATTATA
*
3335193 TTGAAAGTGTCCATACTTTTTTTTAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
3335258 TTCAATTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
3335323 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
3335388 TAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
3335453 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
*
3335518 CAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
* *
3335583 TAGATACTTTACAATATAAGTACTACTTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
3335648 GCGCTACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
3335683 TTGAAAGTGTACATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
3335748 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
3335813 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
3335878 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* ** *
3335943 ACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
*
3336008 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGAACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
*
3336073 TAGATACTTTACAATATAAGCATTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
3336138 GCGCTACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
3336173 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
** **
3336238 TCAATTTTTTTTAATAGTGTTTCATAATTTCCACCTACAATATTAATTTAATAATTTCATTTATA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
3336303 CAAAAAATTATTTGATTCTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
* *
3336368 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* *
3336433 ATCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACT
3336498 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
*
3336563 TAGGTACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
*
3336628 GAGCTACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
3336663 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
3336728 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
* * *
3336793 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAATAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
3336858 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
*
3336923 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACTC
*
3336988 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAA-AATGTATGGGCACTTTTATAAAAAGGA
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAA-GTATGGACACTTTTATAAAAAGGA
3337052 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
* *
3337117 GCGCTACCTATTATATCATATTTTTAACTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
* *
3337152 TTGAAAGTGTTCATATTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
**
3337217 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTATA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
3337282 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
3337325 AATTTGGGTC
Statistics
Matches: 2537, Mismatches: 79, Indels: 9
0.97 0.03 0.00
Matches are distributed among these distances:
488 54 0.02
489 957 0.38
490 1526 0.60
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (489 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
CGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:3335631 original size:23 final size:23
Alignment explanation
Indices: 3335605--3335668 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
3335595 AATATAAGTA
*
3335605 CTACTTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
*
3335628 CTACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
*
3335651 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
3335669 TTTTACCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:3336122 original size:23 final size:23
Alignment explanation
Indices: 3336096--3336158 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
3336086 ATATAAGCAT
3336096 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGC
*
3336119 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGC
*
3336142 TACCTATTACATCATAT
1 TACCTATTACATTATAT
3336159 TTTTACCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:3336208 original size:979 final size:980
Alignment explanation
Indices: 3334215--3337324 Score: 5676
Period size: 979 Copynumber: 3.2 Consensus size: 980
3334205 TTATAATATG
* *
3334215 TTGAAAGTGTCTATACTTTTTTATAAAAAGGATCGATATTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* *
3334280 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
*
3334343 ACAAAAACTTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
3334408 TTAAACAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
* * ** *
3334473 TACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCAC
261 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
*
3334538 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATAGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
3334603 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
3334668 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAG
456 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAG
3334733 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT
521 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT
*
3334798 TCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
586 CCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
*
3334863 ATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATAT
651 ATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATAT
*
3334928 ATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACG
716 ATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACG
3334993 CCTATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCA
781 CCTATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCA
*
3335058 CAGTGAAATAAGTAT-AGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACTTA
846 CAGTGAAATAAGTATGA-ACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTA
*
3335122 TTACATTATATAAACGCTACCTATTATATTATATAAGCGCTACCTATTACATCATATTTTTACCT
910 TTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
3335187 ATTATA
975 ATTATA
*
3335193 TTGAAAGTGTCCATACTTTTTTTTAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* *
3335258 TTCAA-TTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
3335322 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
* *
3335387 TTAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
3335452 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
261 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
*
3335517 TCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
* *
3335582 ATAGATACTTTACAATATAAGTACTACTTATTACATTATATAAACGCTACCTATTACATTATATA
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
3335647 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTACATACTTTTTATAAAAAG
456 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAG
3335712 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTT
521 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTT
*
3335777 TCCACCTACAATATTAATTTAATAATTTTATTTGCACAAAAAATTATTTGATTGTTTTGATATTT
585 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTT
3335842 TATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATA
650 TATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATA
* * *
3335907 TATATGTTTATTGTTTTTAATTTAATGATAATATATACCGTAACATAAAAAATAAATCATTAGAT
715 TATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGAC
* *
3335972 ACATATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
780 GCCTATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCC
*
3336037 ACAGTGAAATAAGTATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCATTACCTA
845 ACAGTGAAATAAGTATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTA
3336102 TTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
910 TTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
3336167 ATTATA
975 ATTATA
*
3336173 TTGAAAGTGTCCATAC-TTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
** *
3336237 TTCAATTTTTTTTAATAGTGTTTCATAATTTCCACCTACAATATTAATTTAATAATTTCATTTAT
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
*
3336302 ACAAAAAATTATTTGATTCTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
3336367 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATGATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
*
3336432 TATCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
261 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
3336497 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
*
3336562 ATAGGTACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
3336627 AGAGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAG
456 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAG
3336692 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT
521 GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT
*
3336757 CCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTT
586 CCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
* *
3336822 ATAAAATATTATTTAGATTTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATAT
651 ATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATAT
3336887 ATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACG
716 ATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACG
*
3336952 CCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCA
781 CCTATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCA
**
3337017 CAGTGAAA-AATGTATGGGCACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTA
846 CAGTGAAATAA-GTATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTA
* *
3337081 TTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTATATCATATTTTTAACT
910 TTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCT
3337146 ATTATA
975 ATTATA
*
3337152 TTGAAAGTGTTCATA-TTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
3337216 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAT
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
3337281 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATT
3337325 AATTTGGGTC
Statistics
Matches: 2057, Mismatches: 69, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
978 69 0.03
979 1092 0.53
980 895 0.44
981 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (980 bp):
TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTGATATCTTAAAACTCAC
TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAG
GATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT
CCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
ATAAAATAATATTTAGAATTTAAATTTAATAATATTAACCAAAGATAATAATAAATATGTAATAT
ATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACG
CCTATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCA
CAGTGAAATAAGTATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTAT
TACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTA
TTATA
Found at i:3336611 original size:23 final size:23
Alignment explanation
Indices: 3336576--3336648 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
3336566 GTACTTTACA
* *
3336576 ATATAAGCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
3336599 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
3336622 ATATAAGA-GCTACCTATTACATC
1 ATATAA-ACGCTACCTATTACATT
3336645 ATAT
1 ATAT
3336649 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 45 0.98
24 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:3337137 original size:23 final size:23
Alignment explanation
Indices: 3337065--3337129 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
3337055 ATACTTTACA
*
3337065 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3337088 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
3337111 ATATAAGCGCTACCTATTA
1 ATATAAGCGCTACCTATTA
3337130 TATCATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3340240 original size:120 final size:120
Alignment explanation
Indices: 3340027--3340271 Score: 418
Period size: 120 Copynumber: 2.0 Consensus size: 120
3340017 TTTTTCTTCC
* * * *
3340027 ATTCTGGACATAAAGTACCGACACAAGATTAACAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGAACTATTCGCT
3340092 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
3340147 ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGAACTATTCGCT
1 ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGAACTATTCGCT
* * *
3340212 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
3340267 ATTCT
1 ATTCT
3340272 GGGTTCCGAT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (120 bp):
ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGAACTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:3340409 original size:303 final size:303
Alignment explanation
Indices: 3339862--3340642 Score: 1481
Period size: 303 Copynumber: 2.6 Consensus size: 303
3339852 TTAAAATTAG
*
3339862 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
3339927 AAACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
3339992 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAGATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAGATT
* * *
3340057 AACAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AACAAGTGTCGACATAGGTTATAAACATATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
3340122 TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
*
3340165 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGAACTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
3340230 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
3340295 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAGATT
3340360 AACAAGTGTCGACATAGGTTATAAACATATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AACAAGTGTCGACATAGGTTATAAACATATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
*
3340425 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
3340468 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
3340533 ATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
3340598 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACA
3340643 CAATATTAAA
Statistics
Matches: 468, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
303 468 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAGATT
AACAAGTGTCGACATAGGTTATAAACATATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
Found at i:3340543 original size:120 final size:120
Alignment explanation
Indices: 3340330--3340576 Score: 404
Period size: 120 Copynumber: 2.1 Consensus size: 120
3340320 TTTTTCTTCC
* *
3340330 ATTCTGGACATAAAGTACCGACACAATATTAACAAGTGTCGACATAGGTTATAAACATATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTATAAACATATTCGCT
3340395 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
* * * *
3340450 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTATAAACATATTCGCT
* * * *
3340515 CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
3340570 ATTCTGG
1 ATTCTGG
3340577 GTTCCGATGT
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTATAAACATATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:3341875 original size:3 final size:3
Alignment explanation
Indices: 3341867--3341917 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3341857 ACTTGTTTGG
* * * * *
3341867 ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3341915 ATC
1 ATC
3341918 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:3341918 original size:12 final size:12
Alignment explanation
Indices: 3341871--3341934 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
3341861 GTTTGGATCA
* *
3341871 TCATCATCATCA
1 TCATCTTCATCG
* *
3341883 TCATCATCGTCG
1 TCATCTTCATCG
3341895 TCATCTTCATCG
1 TCATCTTCATCG
3341907 TCATCTTCATCG
1 TCATCTTCATCG
* *
3341919 TCAGCTTCATCT
1 TCATCTTCATCG
3341931 TCAT
1 TCAT
3341935 TGACCGCTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:3341932 original size:6 final size:6
Alignment explanation
Indices: 3341871--3341934 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
3341861 GTTTGGATCA
* * * * * * *
3341871 TCATCA TCATCA TCATCA TCGTCG TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
3341919 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
3341935 TGACCGCTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.20, C:0.33, G:0.08, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:3344059 original size:201 final size:200
Alignment explanation
Indices: 3343419--3344174 Score: 1329
Period size: 200 Copynumber: 3.8 Consensus size: 200
3343409 TTTAAATTAG
* * *
3343419 TATCGACA-AAACATTAAACAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTAT
1 TATCGACACAAAC-TAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTAT
* * * *
3343483 ACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTAAACTTATGGGTTTAGATATTTAT-GG
65 ACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGG
* *
3343547 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGAC
130 ATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGAC
3343612 CAAAAA
195 CAAAAA
* *
3343618 TATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
*
3343683 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGA
3343748 TCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACC
3343813 AAAAA
196 AAAAA
3343818 TATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACC-AGTTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTA-TTCTCTCATAAAACCGGTAT
3343882 ACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGG
65 ACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGG
* *
3343947 ATCGACACTTTTTTATAAATGGATCGACATTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGA
130 ATCGACAC-TTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGA
3344012 CCAAAAA
194 CCAAAAA
*
3344019 TATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
3344084 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGA
66 CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGA
3344149 TCGACACTTTTTATATATGGATCGAC
131 TCGACACTTTTTATATATGGATCGAC
3344175 CCTTAATGTG
Statistics
Matches: 535, Mismatches: 17, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
199 114 0.21
200 225 0.42
201 195 0.36
202 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGA
TCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACC
AAAAA
Found at i:3344160 original size:401 final size:399
Alignment explanation
Indices: 3343419--3344174 Score: 1327
Period size: 401 Copynumber: 1.9 Consensus size: 399
3343409 TTTAAATTAG
* * *
3343419 TATCGACAAAACATTAAACAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACAAAACATAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
3343484 CTTGTACCGGTTAGATTGAAAAATTACCTAATACATTAAACTTATGGGTTTAGATATTTATGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACCTAATACATTAAACTTATGGGTTTAGATATTTATGGAT
*
3343549 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCA
131 CGACACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCA
* *
3343614 AAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGG
3343679 TATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTAT
261 TATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTAT
*
3343744 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTG
326 CGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTG
3343809 GACCAAAAA
391 GACCAAAAA
3343818 TATCGACACAAAC-TAAAAAAGTGTCGAAACATTATTTAGACC-AGTTCTCTCATAAAACCGGTA
1 TATCGACA-AAACATAAAAAAGTGTCGAAACATTATTTAGACCTA-TTCTCTCATAAAACCGGTA
* * * *
3343881 TACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCG
64 TACTTGTACCGGTTAGATTGAAAAATTACCTAATACATTAAACTTATGGGTTTAGATATTTAT-G
* * *
3343946 GATCGACACTTTTTTATAAATGGATCGACATTTTATTGTTGCACCCTGTTTGCCATTCATTCTGG
128 GATCGACAC-TTTTTATAAATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGG
3344011 ACCAAAAATATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAA
192 ACCAAAAATATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAA
*
3344076 TCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
257 CCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
3344141 TTATCGGATCGACACTTTTTATATATGGATCGAC
322 TTATCGGATCGACACTTTTTATATATGGATCGAC
3344175 CCTTAATGTG
Statistics
Matches: 338, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
398 1 0.00
399 112 0.33
400 14 0.04
401 211 0.62
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (399 bp):
TATCGACAAAACATAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACCTAATACATTAAACTTATGGGTTTAGATATTTATGGAT
CGACACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCA
AAAATATCGACACAAACTAAAAAAGTGTCGAAACATTATTTAGACCTATTCTCTCATAAAACCGG
TATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTAT
CGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTG
GACCAAAAA
Found at i:3344259 original size:18 final size:18
Alignment explanation
Indices: 3344236--3344296 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
3344226 TCTCATTCAT
*
3344236 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
3344254 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
3344273 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
3344292 AATTA
1 AATTA
3344297 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:3344272 original size:19 final size:19
Alignment explanation
Indices: 3344248--3344296 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3344238 TTATATTCAC
3344248 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
3344267 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
3344286 ATACAAAATTA
1 ATACAAAATTA
3344297 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:3346126 original size:33 final size:33
Alignment explanation
Indices: 3346089--3346153 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3346079 ATCTTAATAT
* *
3346089 CACCCCTTAACACCCCAACTTCTTTCACCACTA
1 CACCCCTCAACACACCAACTTCTTTCACCACTA
* *
3346122 CACCCCTCAACACATCTACTTCTTTCACCACT
1 CACCCCTCAACACACCAACTTCTTTCACCACT
3346154 CCATCTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (33 bp):
CACCCCTCAACACACCAACTTCTTTCACCACTA
Found at i:3346212 original size:21 final size:21
Alignment explanation
Indices: 3346187--3346251 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
3346177 CCCCTTGTGC
* *
3346187 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3346208 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
3346229 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3346250 CT
1 CT
3346252 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:3348538 original size:20 final size:19
Alignment explanation
Indices: 3348483--3348529 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3348473 TCCGGTATCG
3348483 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
3348502 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
3348523 TTTTACC
1 TTTTACC
3348530 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:3348710 original size:20 final size:19
Alignment explanation
Indices: 3348664--3348710 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3348654 TCCGGTAACG
3348664 TTTTACCAGTTTTATCATT
1 TTTTACCAGTTTTATCATT
* *
3348683 TTGATACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
3348704 TTTTACC
1 TTTTACC
3348711 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:3348754 original size:181 final size:182
Alignment explanation
Indices: 3348450--3348922 Score: 723
Period size: 181 Copynumber: 2.6 Consensus size: 182
3348440 CATACTTACG
* *
3348450 AAAGTATCGACACTTTCAATAAATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
3348515 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
3348580 AGGCGCTAAAACTGCTTCTCTTTTAAATTCTCAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
3348631 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCAGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
3348696 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
3348761 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * **
3348813 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
3348878 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
3348923 AATTTGGATC
Statistics
Matches: 265, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
181 167 0.63
182 98 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:3351208 original size:14 final size:14
Alignment explanation
Indices: 3351189--3351224 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3351179 AACCCAGATT
*
3351189 GAGTCAACTCGTTC
1 GAGTCAACTCATTC
3351203 GAGTCAACTCATTC
1 GAGTCAACTCATTC
*
3351217 AAGTCAAC
1 GAGTCAAC
3351225 ATGTTGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (14 bp):
GAGTCAACTCATTC
Found at i:3354914 original size:15 final size:15
Alignment explanation
Indices: 3354894--3354927 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3354884 CATACTTAGA
3354894 CAAAGTGCTTTACCT
1 CAAAGTGCTTTACCT
3354909 CAAAGTGCTTTACCT
1 CAAAGTGCTTTACCT
3354924 CAAA
1 CAAA
3354928 ATATTCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (15 bp):
CAAAGTGCTTTACCT
Found at i:3356974 original size:27 final size:28
Alignment explanation
Indices: 3356918--3356976 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
3356908 TATTTGGATA
**
3356918 AAAATTACCAAAAATAGCCCTATGGGGT
1 AAAATTACCAAAAATAGCCCTATACGGT
*
3356946 AAAATTA-CAAAAAT-GCCCTTATACTGT
1 AAAATTACCAAAAATAGCCC-TATACGGT
3356973 AAAA
1 AAAA
3356977 GACCAAGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 16 0.59
28 7 0.26
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (28 bp):
AAAATTACCAAAAATAGCCCTATACGGT
Found at i:3357877 original size:2 final size:2
Alignment explanation
Indices: 3357870--3357899 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3357860 TGATAATTCA
3357870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3357900 TCTTAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3359956 original size:24 final size:25
Alignment explanation
Indices: 3359924--3359970 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3359914 TAAAATTTTA
3359924 AATAATTTAATAAAAAAT-TATATT
1 AATAATTTAATAAAAAATATATATT
* *
3359948 AATATTTTAATAATAAATATATA
1 AATAATTTAATAAAAAATATATA
3359971 AATTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAATTTAATAAAAAATATATATT
Found at i:3359974 original size:32 final size:34
Alignment explanation
Indices: 3359898--3359977 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 34
3359888 ATATTATTTT
* *
3359898 AATATATGAAATTGT-TTAAAATTTTAAATAATTT
1 AATATAT-AAATTATATTAAAATTTTAAATAATTA
* *
3359932 AATA-AAAAATTATATTAATATTTT-AATAA-TA
1 AATATATAAATTATATTAAAATTTTAAATAATTA
3359963 AATATATAAATTATA
1 AATATATAAATTATA
3359978 ATTTGTAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
31 5 0.13
32 20 0.51
33 10 0.26
34 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (34 bp):
AATATATAAATTATATTAAAATTTTAAATAATTA
Found at i:3359979 original size:21 final size:22
Alignment explanation
Indices: 3359927--3359979 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
3359917 AATTTTAAAT
3359927 AATTTAATAAAAAATTATATTA
1 AATTTAATAAAAAATTATATTA
*
3359949 ATATTTTAATAATAAA-TATA-TA
1 A-A-TTTAATAAAAAATTATATTA
3359971 AATTATAAT
1 AATT-TAAT
3359980 TTGTAAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.07
21 5 0.19
22 4 0.15
23 5 0.19
24 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTAATAAAAAATTATATTA
Found at i:3362985 original size:17 final size:19
Alignment explanation
Indices: 3362953--3362987 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3362943 ATTTAAAGTA
3362953 TAAAAAATATTCAAATATC
1 TAAAAAATATTCAAATATC
3362972 TAAAAAA-ATT-AAATAT
1 TAAAAAATATTCAAATAT
3362988 AAAATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAATATTCAAATATC
Found at i:3363000 original size:24 final size:23
Alignment explanation
Indices: 3362965--3363029 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 23
3362955 AAAAATATTC
3362965 AAATATCT-AAAAAAATTAAATATA
1 AAATA-CTAAAAAAAATTAAAT-TA
*
3362989 AAATACTAAAAATAA--AAATTA
1 AAATACTAAAAAAAATTAAATTA
* *
3363010 AATTAATAAAAAAAATTAAA
1 AAATACTAAAAAAAATTAAA
3363030 ACAATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 14 0.41
22 4 0.12
23 5 0.15
24 11 0.32
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (23 bp):
AAATACTAAAAAAAATTAAATTA
Found at i:3363011 original size:21 final size:20
Alignment explanation
Indices: 3362954--3363024 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
3362944 TTTAAAGTAT
* *
3362954 AAAAAATATTCAAATATCTAA
1 AAAAAAAATTAAAATA-CTAA
3362975 AAAAATTAAATATAAAATACTAA
1 AAAAA--AAAT-TAAAATACTAA
* *
3362998 AAATAAAAATTAAATTAATAA
1 AAA-AAAAATTAAAATACTAA
3363019 AAAAAA
1 AAAAAA
3363025 TTAAAACAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 3 0.07
21 17 0.40
22 4 0.10
23 10 0.24
24 8 0.19
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAAAATTAAAATACTAA
Found at i:3363043 original size:19 final size:19
Alignment explanation
Indices: 3363021--3363070 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
3363011 ATTAATAAAA
*
3363021 AAAATTAAAACAATA-TATT
1 AAAA-TAAAAAAATACTATT
3363040 AAAATAATAAAAATACTATT
1 AAAATAA-AAAAATACTATT
3363060 AAAAATAAAAA
1 -AAAATAAAAA
3363071 TAAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 10 0.37
20 7 0.26
21 7 0.26
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATAAAAAAATACTATT
Found at i:3363043 original size:22 final size:20
Alignment explanation
Indices: 3363018--3363072 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 20
3363008 TAAATTAATA
3363018 AAAAAAATTAAAACAATA-TATT
1 AAAAAAA-T-AAA-AATACTATT
*
3363040 AAAATAATAAAAATACTATT
1 AAAAAAATAAAAATACTATT
3363060 --AAAAATAAAAATA
1 AAAAAAATAAAAATA
3363073 AAAATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 12 0.40
19 4 0.13
20 7 0.23
21 1 0.03
22 6 0.20
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAAATAAAAATACTATT
Found at i:3363068 original size:18 final size:19
Alignment explanation
Indices: 3363032--3363072 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3363022 AAATTAAAAC
3363032 AATATATTAAAATAATAAA
1 AATATATTAAAATAATAAA
3363051 AATACTATT-AAA-AATAAA
1 AATA-TATTAAAATAATAAA
3363069 AATA
1 AATA
3363073 AAAATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 7 0.33
20 4 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AATATATTAAAATAATAAA
Found at i:3363908 original size:16 final size:15
Alignment explanation
Indices: 3363878--3363928 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3363868 ATTAATAGTA
3363878 TTTTTAATA-TTAAT
1 TTTTTAATATTTAAT
3363892 TTTTTGAATATTTAATT
1 TTTTT-AATATTTAA-T
3363909 ATTTTTAGAT-TTTAAT
1 -TTTTTA-ATATTTAAT
3363925 TTTT
1 TTTT
3363929 AAAATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 5 0.16
17 7 0.22
18 7 0.22
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTTTAATATTTAAT
Found at i:3365103 original size:17 final size:19
Alignment explanation
Indices: 3365080--3365121 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3365070 TGAAAAAACT
3365080 TATAAATT-TTAAGAAAAA
1 TATAAATTATTAAGAAAAA
*
3365098 -ATAAATTATTAATAAAAA
1 TATAAATTATTAAGAAAAA
3365116 TATAAA
1 TATAAA
3365122 AAATATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 9 0.43
19 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TATAAATTATTAAGAAAAA
Found at i:3370345 original size:12 final size:12
Alignment explanation
Indices: 3370328--3370356 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3370318 TGTCAAAGTA
3370328 TTTTTATTTTAC
1 TTTTTATTTTAC
3370340 TTTTTATTTTAC
1 TTTTTATTTTAC
3370352 TTTTT
1 TTTTT
3370357 TTTAGATAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTAC
Found at i:3376557 original size:10 final size:9
Alignment explanation
Indices: 3376542--3376566 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3376532 CCCACTTTGT
3376542 AAAAAAAGA
1 AAAAAAAGA
3376551 AAAAAAAGA
1 AAAAAAAGA
3376560 AAAAAAA
1 AAAAAAA
3376567 TGAAGTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:3377212 original size:20 final size:20
Alignment explanation
Indices: 3377183--3377221 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3377173 AAAGATCATA
*
3377183 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3377203 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3377222 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3383584 original size:19 final size:19
Alignment explanation
Indices: 3383537--3383590 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3383527 GAACTGCTCT
3383537 AACCTGTTGACCTTGACCCG
1 AACC-GTTGACCTTGACCCG
* * *
3383557 ACCCATTGACCTTGACCTG
1 AACCGTTGACCTTGACCCG
* *
3383576 AATCGTTGACTTTGA
1 AACCGTTGACCTTGA
3383591 TTTGACCATT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 24 0.89
20 3 0.11
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (19 bp):
AACCGTTGACCTTGACCCG
Found at i:3383590 original size:25 final size:26
Alignment explanation
Indices: 3383562--3383617 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
3383552 ACCCGACCCA
* *
3383562 TTGACCTTGACC-TGAATCGTTGACT
1 TTGACCTTGACCATGAACCGTTAACT
* *
3383587 TTGA-TTTGACCATTAACCGTTAACT
1 TTGACCTTGACCATGAACCGTTAACT
3383612 TTGACC
1 TTGACC
3383618 AAAAAGTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (26 bp):
TTGACCTTGACCATGAACCGTTAACT
Found at i:3385579 original size:2 final size:2
Alignment explanation
Indices: 3385498--3385563 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3385488 ATAACAAGTC
3385498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3385540 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
3385564 GTCACATACA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3385732 original size:23 final size:23
Alignment explanation
Indices: 3385703--3385757 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
3385693 CATATAAAAT
3385703 TGTCCCGAAGGACCACATAGAAA
1 TGTCCCGAAGGACCACATAGAAA
3385726 TGTCCCGAAGGACCACATAGAAA
1 TGTCCCGAAGGACCACATAGAAA
*
3385749 TGTCACGAA
1 TGTCCCGAA
3385758 TAATCACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
TGTCCCGAAGGACCACATAGAAA
Found at i:3385787 original size:21 final size:21
Alignment explanation
Indices: 3385703--3385811 Score: 76
Period size: 23 Copynumber: 5.0 Consensus size: 21
3385693 CATATAAAAT
* *
3385703 TGTCCCGAAGGACCACATAGAAA
1 TGTCCCGAAAGACCACAT--ATA
* *
3385726 TGTCCCGAAGGACCACATAGAAA
1 TGTCCCGAAAGACCACAT--ATA
* * *
3385749 TGTCACGAATA-ATCACATTTA
1 TGTCCCGAA-AGACCACATATA
*
3385770 TGTCCCGAAAGACGACATATA
1 TGTCCCGAAAGACCACATATA
* *
3385791 TGTCTCGAAGGACCACATATA
1 TGTCCCGAAAGACCACATATA
3385812 ACCCTCGACT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.01
21 34 0.47
23 37 0.51
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (21 bp):
TGTCCCGAAAGACCACATATA
Found at i:3388347 original size:24 final size:24
Alignment explanation
Indices: 3388293--3388347 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
3388283 TTTTAAAACC
*
3388293 TGTTTTATTGAAATAAACAACTAT
1 TGTTTTTTTGAAATAAACAACTAT
*
3388317 TGTTTTTTTGAAATAAACTACTAT
1 TGTTTTTTTGAAATAAACAACTAT
3388341 TGTTTTT
1 TGTTTTT
3388348 AAACTATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (24 bp):
TGTTTTTTTGAAATAAACAACTAT
Found at i:3391149 original size:3 final size:3
Alignment explanation
Indices: 3391137--3391171 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3391127 ATAATATTTT
*
3391137 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA CATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
3391172 AAGTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3391667 original size:117 final size:117
Alignment explanation
Indices: 3391484--3391700 Score: 337
Period size: 117 Copynumber: 1.9 Consensus size: 117
3391474 TTTGAACTAG
* * *
3391484 TTCTTATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTACAAACTCTTCACTAGAA
1 TTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTATTCTCATTACAAACTCTCCACTAGAA
*
3391549 ATGTCGATCCACCTCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTC
66 ATGTCAATCCACCTCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTC
* * * *
3391601 TTCTCATTATGAACTT-TATCTCCCTCATTGGATGAGTTATTCTCATTATAAATTCTCCACTGGA
1 TTCTCATTATGAACTTCT-TCTCCCTCATCGGATGAGTTATTCTCATTACAAACTCTCCACTAGA
*
3391665 AATGTTAATCCACCTCCTTCTGTGATGGAATCGAAC
65 AATGTCAATCCACCTCCTTCTGTGATGGAATCGAAC
3391701 AAAGTGATGA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
116 1 0.01
117 89 0.99
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (117 bp):
TTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTATTCTCATTACAAACTCTCCACTAGAA
ATGTCAATCCACCTCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTC
Found at i:3391936 original size:203 final size:202
Alignment explanation
Indices: 3391568--3392149 Score: 851
Period size: 203 Copynumber: 2.9 Consensus size: 202
3391558 CACCTCCTTC
* * **
3391568 TGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TATCTCCCTCATTGG
1 TGTGATGGAAACGAGCTGAGGTTGAACAAGTTCTTCTCATTATGAACTTCT-TCTCCCTCATTGG
* * * *
3391632 ATGAGTTATTCTCATTATAAATTCTCCACTGGAAATGTTAATCCACCTCCTTCTGTGATGGAATC
65 ATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCT-CTTCTGTGATGGAATC
** * * * *
3391697 GAACAAAGTGATGATACTGATCCAACTCCGTATGCGATGGATGAGCCAAGTATTGGTGTTGTTCT
129 GAACAAAGTGATGATGTTGATCCAACTCCATATGCGATGGATGAGCCAAGTATTGATGATGTTCC
*
3391762 AACTCCTTA
194 AACTCATTA
*
3391771 TGTGATGGAAACGAGTTGAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGA
1 TGTGATGGAAACGAGCTGAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGA
* * * * *
3391836 TGAGTTCTTCTCGTTATGAAGTCTCCACTGGAACTGTTGATCCATCTCATTATGTGATGGAATCG
66 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTC-TTCTGTGATGGAATCG
* *
3391901 AACAAAGTGACGATGTTGATCTAACTCCATATGCGATGGATGAGCCAAGTATTGATGATGTTCCA
130 AACAAAGTGATGATGTTGATCCAACTCCATATGCGATGGATGAGCCAAGTATTGATGATGTTCCA
3391966 ACTCATTA
195 ACTCATTA
* * *
3391974 TGTGATGGAAACGAGCTGAAGTTGAACAAGTTTCTTCTCATTATGAACTTCTTCTCCCTCATCGA
1 TGTGATGGAAACGAGCTGAGGTTGAACAAG-TTCTTCTCATTATGAACTTCTTCTCCCTCATTGG
* * *
3392039 ATGAGTTCTTATCATTATGAACTTTCCACTGGAAATGTTGATCCACCTTCTTCTATGATGGAATC
65 ATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACC-TCTTCTGTGATGGAATC
3392104 GAACAAAGTGATGATGTTGATCCAACTCCATATGCGATGGATGAGC
129 GAACAAAGTGATGATGTTGATCCAACTCCATATGCGATGGATGAGC
3392150 TAAGGTTGAA
Statistics
Matches: 339, Mismatches: 36, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
202 1 0.00
203 205 0.60
204 131 0.39
205 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (202 bp):
TGTGATGGAAACGAGCTGAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGA
TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCTTCTGTGATGGAATCGA
ACAAAGTGATGATGTTGATCCAACTCCATATGCGATGGATGAGCCAAGTATTGATGATGTTCCAA
CTCATTA
Found at i:3393371 original size:28 final size:28
Alignment explanation
Indices: 3393337--3393392 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3393327 ATACTCTCTA
*
3393337 GAGAGATTTTCATGTTTGAAAATATTTT
1 GAGAGATTGTCATGTTTGAAAATATTTT
3393365 GAGAGATTGTCATGTTTGAAAATATTTT
1 GAGAGATTGTCATGTTTGAAAATATTTT
3393393 TCTTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (28 bp):
GAGAGATTGTCATGTTTGAAAATATTTT
Found at i:3401447 original size:2 final size:2
Alignment explanation
Indices: 3401440--3401471 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3401430 ATACATCTAC
3401440 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
3401472 AAATTACCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3403209 original size:2 final size:2
Alignment explanation
Indices: 3403202--3403235 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3403192 ATATTTTAAA
3403202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3403236 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3404171 original size:29 final size:28
Alignment explanation
Indices: 3404029--3404178 Score: 95
Period size: 29 Copynumber: 5.2 Consensus size: 28
3404019 TGGTCTTAAC
* * * **
3404029 TATAATTTATAAAAAGTTTGTCCTCTGC
1 TATAATTTATAAAAAGTTTGACATTTAT
* * * **
3404057 TGTAATTTAAAAAATAATTTGTTATTTAT
1 TATAATTTATAAAA-AGTTTGACATTTAT
* *
3404086 TATCATTTATAAAAATGTTT-ACATCTTTT
1 TATAATTTATAAAAA-GTTTGACAT-TTAT
* * *
3404115 TATATTTTATAAAAACTTTAGACTTTTAT
1 TATAATTTATAAAAAGTTT-GACATTTAT
*
3404144 TATAATTTATAAAAGGTTTGGACATTTAT
1 TATAATTTATAAAAAGTTT-GACATTTAT
*
3404173 TTTAAT
1 TATAAT
3404179 GTAACTGTTT
Statistics
Matches: 91, Mismatches: 26, Indels: 9
0.72 0.21 0.07
Matches are distributed among these distances:
28 18 0.20
29 70 0.77
30 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (28 bp):
TATAATTTATAAAAAGTTTGACATTTAT
Found at i:3408895 original size:2 final size:2
Alignment explanation
Indices: 3408890--3408918 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3408880 ACACACATAC
3408890 AT 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 A
3408919 GTAACTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3412668 original size:2 final size:2
Alignment explanation
Indices: 3412661--3412726 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3412651 ACATCCAAAC
3412661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3412703 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
3412727 CATTCTGTAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3413132 original size:23 final size:23
Alignment explanation
Indices: 3413105--3413166 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
3413095 GCTCGTATAA
*
3413105 ATGCACCGAAGTGCCACGTAGA-
1 ATGCACCAAAGTGCCACGTAGAT
* *
3413127 ATTGCACCTAAGTGCCGCGTAGAT
1 A-TGCACCAAAGTGCCACGTAGAT
3413151 ATGCACCAAAGTGCCA
1 ATGCACCAAAGTGCCA
3413167 TATAAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
ATGCACCAAAGTGCCACGTAGAT
Found at i:3414586 original size:63 final size:64
Alignment explanation
Indices: 3414511--3414633 Score: 158
Period size: 64 Copynumber: 1.9 Consensus size: 64
3414501 CACCACACCC
* ** *
3414511 TGCATCGATGCATAAATCGTATTCGATG-TTTAAATTTAAGGGGGTGCATCGATGCACTTTTTA
1 TGCATCGATGCATAAATCGCATTCGATGTTTTAAATTTAAAAGAGTGCATCGATGCACTTTTTA
** * * *
3414574 TGCATCGATGCATTGATGGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTT
1 TGCATCGATGCATAAATCGCATTCGATGTTTTAAATTTAAAAGAGTGCATCGATGCACTT
3414634 ACATATACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
63 24 0.48
64 26 0.52
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (64 bp):
TGCATCGATGCATAAATCGCATTCGATGTTTTAAATTTAAAAGAGTGCATCGATGCACTTTTTA
Found at i:3416473 original size:20 final size:20
Alignment explanation
Indices: 3416445--3416497 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3416435 GATTTTCCAG
* *
3416445 AATCACAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
3416465 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
3416485 AATCGCAACGCGA
1 AATCGCAACGCGA
3416498 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:3416550 original size:20 final size:20
Alignment explanation
Indices: 3416506--3416719 Score: 198
Period size: 20 Copynumber: 10.6 Consensus size: 20
3416496 GATTCTGACT
*
3416506 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
3416527 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3416547 ATCGCAATGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
3416568 ATCACAACGCCTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3416588 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3416608 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3416628 ATCGCAATGCATATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3416648 ATCGCAATGCATATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3416668 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
3416689 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
3416709 ATCGCAACGCG
1 ATCGCAACGCG
3416720 ATTTTTAAAG
Statistics
Matches: 162, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
20 114 0.70
21 48 0.30
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:3416551 original size:41 final size:41
Alignment explanation
Indices: 3416506--3416717 Score: 259
Period size: 41 Copynumber: 5.2 Consensus size: 41
3416496 GATTCTGACT
** * *
3416506 ATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
3416547 ATCGCAATGACAATACGTAAAATCACAACGCCTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
3416588 ATCGCAACGAGAATACGT-AAATCGCAACGAGAATACGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
3416628 ATCGCAATG-CATATCCGT-AAATCGCAATGCATATCCGTAA
1 ATCGCAACGACA-ATACGTAAAATCGCAACGCGTATCCGTAA
3416668 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
3416709 ATCGCAACG
1 ATCGCAACG
3416718 CGATTTTTAA
Statistics
Matches: 142, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 60 0.42
41 81 0.57
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:3417338 original size:21 final size:21
Alignment explanation
Indices: 3417277--3417355 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
3417267 TTCTAAACTT
3417277 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
3417297 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
3417317 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
3417338 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
3417356 TCGCAACGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:3417378 original size:19 final size:19
Alignment explanation
Indices: 3417277--3417398 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
3417267 TTCTAAACTT
**
3417277 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
3417297 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
3417317 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
3417338 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
3417352 AGAATCGCAACGTGAAATG
1 AAAATCGCAACGCGAAATG
**
3417371 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
3417390 AAAATCGCA
1 AAAATCGCA
3417399 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 25 0.31
20 28 0.35
21 13 0.16
22 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:3417416 original size:19 final size:19
Alignment explanation
Indices: 3417394--3417520 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
3417384 GAAACCAAAA
*
3417394 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3417413 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3417427 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3417446 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
3417460 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
3417479 TCCGCGTTGTGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
3417499 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3417519 TC
1 TC
3417521 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.24
16 5 0.06
17 6 0.07
19 23 0.27
20 30 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3417435 original size:14 final size:14
Alignment explanation
Indices: 3417416--3417471 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
3417406 TTTCATTTCG
3417416 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3417430 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3417449 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3417463 CGTTGCGAT
1 CGTTGCGAT
3417472 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3417441 original size:33 final size:33
Alignment explanation
Indices: 3417399--3417520 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
3417389 CAAAATCGCA
3417399 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3417432 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
3417465 TTGCGATAGTCATTTCCGCGTTGTGATAGTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCG-T-TG--CG--ATTCTCTCG
3417505 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3417521 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
33 46 0.60
34 4 0.05
35 1 0.01
36 2 0.03
38 1 0.01
39 1 0.01
40 22 0.29
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3417617 original size:25 final size:25
Alignment explanation
Indices: 3417589--3417652 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
3417579 ATGTTTATTA
3417589 TTTTTGGTATATCTTCACAGTGTAG
1 TTTTTGGTATATCTTCACAGTGTAG
3417614 TTTTTGGTATATCTTCACAGTGTAG
1 TTTTTGGTATATCTTCACAGTGTAG
3417639 TTTTTGGTATATCT
1 TTTTTGGTATATCT
3417653 AACTTGGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.52
Consensus pattern (25 bp):
TTTTTGGTATATCTTCACAGTGTAG
Found at i:3419384 original size:94 final size:94
Alignment explanation
Indices: 3419223--3419602 Score: 665
Period size: 94 Copynumber: 4.1 Consensus size: 94
3419213 TAGATTGCTT
* * *
3419223 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3419288 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
3419317 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACAGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3419382 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3419411 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3419476 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
3419505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3419570 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3419598 AGTAA
1 AGTAA
3419603 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 251 0.91
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3419716 original size:20 final size:20
Alignment explanation
Indices: 3419691--3419740 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3419681 AAAATGAATT
3419691 GCATTGCGATAGTCATTTTC
1 GCATTGCGATAGTCATTTTC
3419711 GCATTGCGATAGTCATTTTC
1 GCATTGCGATAGTCATTTTC
*
3419731 GCGTTGCGAT
1 GCATTGCGAT
3419741 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
GCATTGCGATAGTCATTTTC
Found at i:3420315 original size:21 final size:21
Alignment explanation
Indices: 3420224--3420328 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
3420214 GACTCACCTG
*
3420224 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
3420246 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
3420266 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
3420287 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
3420308 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
3420329 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3420321 original size:42 final size:42
Alignment explanation
Indices: 3420221--3420331 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
3420211 CCCGACTCAC
* * * *
3420221 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
3420263 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
3420305 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
3420332 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:3421708 original size:14 final size:14
Alignment explanation
Indices: 3421689--3421724 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3421679 ATTGTTTAAT
3421689 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3421703 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3421717 TGATTTGT
1 TGATTTGT
3421725 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3421861 original size:19 final size:20
Alignment explanation
Indices: 3421822--3421862 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3421812 ATGCAAAACA
*
3421822 GACTATCGCAACGCGGAAAT
1 GACTAGCGCAACGCGGAAAT
*
3421842 GACTAGCGCAATGC-GAAAT
1 GACTAGCGCAACGCGGAAAT
3421861 GA
1 GA
3421863 AAATCGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.15
Consensus pattern (20 bp):
GACTAGCGCAACGCGGAAAT
Done.