Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 62
Found at i:198819 original size:19 final size:19
Alignment explanation
Indices: 198795--198855 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
198785 GCGATTCCCT
198795 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
198814 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
198828 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
198847 CATTGCGAT
1 CGTTGCGAT
198856 AGTCATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:198833 original size:14 final size:14
Alignment explanation
Indices: 198781--198837 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
198771 TTTAGTTTCG
*
198781 CGTTGCGATTCCCT
1 CGTTGCGATTCTCT
*
198795 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
198814 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
198828 CGTTGCGATT
1 CGTTGCGATT
198838 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:198981 original size:14 final size:14
Alignment explanation
Indices: 198962--198998 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
198952 TATCAATTAA
198962 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
198976 ACAAATCATCTTTT
1 ACAAATCAACTTTT
198990 ACAAATCAA
1 ACAAATCAA
198999 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:200907 original size:21 final size:21
Alignment explanation
Indices: 200870--200926 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
200860 TCTGGAACTT
* *
200870 AAAATCACAACGTGAAAAATG
1 AAAATCGCAACGCGAAAAATG
**
200891 ACTATCGCAACGCG--AAATG
1 AAAATCGCAACGCGAAAAATG
200910 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
200927 CCAAAAATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 17 0.61
21 11 0.39
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGCGAAAAATG
Found at i:200932 original size:19 final size:20
Alignment explanation
Indices: 200894--200944 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
200884 AAAAATGACT
**
200894 ATCGCAACGCGAAA-TGAAA
1 ATCGCAACGCGAAACCAAAA
200913 ATCGCAACGCGAAACCAAAA
1 ATCGCAACGCGAAACCAAAA
*
200933 ATCACAACGCGA
1 ATCGCAACGCGA
200945 TTATAGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (20 bp):
ATCGCAACGCGAAACCAAAA
Found at i:200994 original size:19 final size:19
Alignment explanation
Indices: 200970--201025 Score: 112
Period size: 19 Copynumber: 2.9 Consensus size: 19
200960 GCGATTTTGT
200970 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
200989 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
201008 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
201026 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:201226 original size:94 final size:92
Alignment explanation
Indices: 201114--201391 Score: 354
Period size: 94 Copynumber: 3.1 Consensus size: 92
201104 ATGGATTGCA
* *
201114 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
201179 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAAAC-AACAAAT
* *
201207 TTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACATCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
201272 TTAGCAGAATTGGCAGC-AAC--CGAAT
65 TTAGCAGAATTGGCAGCAAACAACAAAT
* * * *
201297 ATACTTCAACCAAAAGCCAAAACAAAAGACAAATATTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * * *
201358 TTAGTAGTATTGGCAGCAACCAAATAAAT
65 TTAGCAGAATTGGCAGCAAAC-AACAAAT
201387 TTACT
1 TTACT
201392 AAGCAATCTA
Statistics
Matches: 162, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
86 24 0.15
87 2 0.01
89 18 0.11
90 38 0.23
93 7 0.04
94 73 0.45
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (92 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACAACAAAT
Found at i:203145 original size:14 final size:14
Alignment explanation
Indices: 203126--203178 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
203116 CGGAAATGAC
203126 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
203140 TCGCAACACGAAATGAAAA
1 TCGC-A-ACG--A-GAGAA
203159 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
203173 TCGCAA
1 TCGCAA
203179 TGCGATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 14 0.44
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.25
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:203214 original size:14 final size:14
Alignment explanation
Indices: 203195--203250 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
203185 TTTGGTTTCG
203195 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
203209 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
203228 CGTTGCGATTATCT
1 CGTTGCGATTATCT
203242 CGTTGCGAT
1 CGTTGCGAT
203251 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:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:203227 original size:33 final size:33
Alignment explanation
Indices: 203179--203271 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
203169 AGAATCGCAA
**
203179 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
203212 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
**
203245 TGCGATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
203272 TTCATTCTCG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 43 0.78
34 12 0.22
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:203276 original size:20 final size:19
Alignment explanation
Indices: 203209--203277 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
203199 GCGATTATCT
203209 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
203228 CGTTGCGA--TT-A--TCT
1 CGTTGCGATTTTCATTTCG
**
203242 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
203262 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
203278 CTCGAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 3 0.08
19 9 0.23
20 15 0.38
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:203845 original size:20 final size:20
Alignment explanation
Indices: 203822--203913 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
203812 CGATAGTCAG
*
203822 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
203842 ATTCGCATTGCGATTTTCAT
1 ATTCGCATTGCGATTTACGT
* *
203862 AATTTGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
203883 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
203903 ATTCGCATTGC
1 ATTCGCATTGC
203914 AAATTATGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 42 0.71
21 17 0.29
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:203879 original size:41 final size:40
Alignment explanation
Indices: 203802--203915 Score: 120
Period size: 41 Copynumber: 2.8 Consensus size: 40
203792 GCGCTATGTA
** *
203802 AATCGCATTGCGATAGTCAGATTCGCATTGCAATTTACGT
1 AATCGCATTGCGATTTTCAAATTCGCATTGCAATTTACGT
* * * *
203842 ATTCGCATTGCGATTTTCATAATTTGCATTGCGATTTACTT
1 AATCGCATTGCGATTTTCA-AATTCGCATTGCAATTTACGT
* * **
203883 AATCGCGTTGCGATTTACGTATTCGCATTGCAA
1 AATCGCATTGCGATTTTCAAATTCGCATTGCAA
203916 ATTATGAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
40 27 0.46
41 32 0.54
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (40 bp):
AATCGCATTGCGATTTTCAAATTCGCATTGCAATTTACGT
Found at i:203948 original size:20 final size:21
Alignment explanation
Indices: 203905--203977 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
203895 ATTTACGTAT
* * *
203905 TCGCATTGCAAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
203926 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
203946 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
203967 TCGCAATGCGA
1 TCGCAATGCGA
203978 TAGTCAGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:203989 original size:41 final size:41
Alignment explanation
Indices: 203905--203999 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
203895 ATTTACGTAT
* *
203905 TCGCATTGCAAATTATGAAAATCGCAACGCGAATACGTAAA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
* *
203946 TCGCAATGCGAATTAGGAAAATCGCAATGCG-ATA-GTCAGAA
1 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGT-A-AA
*
203987 TCGCGTTGCGAAT
1 TCGCATTGCGAAT
204000 CTGGAAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.04
40 4 0.09
41 40 0.87
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (41 bp):
TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
Found at i:204848 original size:182 final size:182
Alignment explanation
Indices: 204555--204993 Score: 650
Period size: 182 Copynumber: 2.4 Consensus size: 182
204545 CGATCCAAAT
* * * * *
204555 TAAAAATGTATCGATCCA-TATCAATATAACATGTAAAAATATGATAAAAACGGTCA-AGAAAAG
1 TAAAAATGTATCGATCCACAAT-GATATAACATGTAAAAATATGATAAAACCGGT-ATCGAAATG
* * *
204618 ACAATACCGGTAAAGTCCTACCAGATATATTGAACGTGTCGATACTTTAATATAAGGATCGACAC
64 ATAAAACCGGTAAAGTCCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
204683 TTTGTGAATTTAAAAGATAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
129 TTTGTGAATTTAAAAGATAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
*
204737 TAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGACAAAACCGGTATCGAAATGAT
1 TAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGATAAAACCGGTATCGAAATGAT
* * * * *
204802 AAAACCGGTAAAG-CACTACCGGATATATTTAAAGTGTCGGTACTTTAATATAAGTATCGACGCT
66 AAAACCGGTAAAGTC-CTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
* * *
204866 TTGTGAATTTAAAAGATAAGCAGTTTTAGCGCTTATAAATTGTCGATACTTTA
130 TTGTGAATTTAAAAGATAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
204919 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGATAAAACCGGTATCGAAATGAT
204984 AAAACCGGTA
66 AAAACCGGTA
204994 TCAAAATGAT
Statistics
Matches: 233, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
181 2 0.01
182 229 0.98
183 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGATAAAACCGGTATCGAAATGAT
AAAACCGGTAAAGTCCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
TGTGAATTTAAAAGATAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
Found at i:204973 original size:20 final size:20
Alignment explanation
Indices: 204950--205013 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
204940 CGATATAACA
204950 GGTA-AAAATATGATAAAACC
1 GGTATAAAA-ATGATAAAACC
*
204970 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
*
204990 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
205010 GGTA
1 GGTA
205014 AAGCGCTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 39 0.93
21 3 0.07
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (20 bp):
GGTATAAAAATGATAAAACC
Found at i:207281 original size:21 final size:21
Alignment explanation
Indices: 207257--207321 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
207247 AAGATAATCA
207257 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
207278 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
207299 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
207320 AG
1 AG
207322 GCATAAGGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:207392 original size:33 final size:33
Alignment explanation
Indices: 207355--207418 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
207345 AAATAGATGG
*
207355 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
207388 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
207419 CATCTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:209145 original size:19 final size:19
Alignment explanation
Indices: 209118--209166 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
209108 AATGTAGGGT
*
209118 TAATGTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
209137 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
209156 TAATTTTGTAT
1 TAATTTTGTAT
209167 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:209657 original size:200 final size:198
Alignment explanation
Indices: 209408--209964 Score: 843
Period size: 200 Copynumber: 2.8 Consensus size: 198
209398 GTAAGTATAT
* * *
209408 GTGTCGATCCATATATAAAAAGTATCGATCCCAGAAACATCGAAACTCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATTGAAACTCATAAGTATAATGTAAT-
*
209473 AGTAATTTTTCAATGTAACCGGTATAAAATAACCGATTTTACGAGAGAATAGTTCTACAACATAT
65 AGTAATTTTTCAATGTAACCGGTATAAAATAACCGATTTTACGAGAGAATAG-TCTACAACATGT
* *
209538 ATCAACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGACAAAAATGGTACAACC
129 ATTAACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGACAAAAAGGGTACAACC
209603 ATAAA
194 ATAAA
* *
209608 GTGTTGATATATTTATAAAAAGTATCGATCCCAGAAACATTGAAACTCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATTGAAACTCATAAGTATAATGTAATA
* * *
209673 GGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAACATGT
66 -GTAATTTTTCAATGTAACCGGTATAAAATAACCGATTTTACGAGAGAATA-GTCTACAACATGT
* * * *
209738 ATTGACACATTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
129 ATTAACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGACAAAAAGGGTACAACC
209803 ATAAA
194 ATAAA
* * *
209808 GTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATTGAAACCCATAAGTATAATGT-AT-
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATTGAAACTCATAAGTATAATGTAATA
* *
209871 GTAATTTTTCAATGTAACCGGTAT-AAATATACC-AGTTTTATGAGAGAATAAGTATACAACATG
66 GTAATTTTTCAATGTAACCGGTATAAAATA-ACCGA-TTTTACGAGAGAAT-AGTCTACAACATG
209934 TATTAACACTTTTTAATTTTGTGTCGATACT
128 TATTAACACTTTTTAATTTTGTGTCGATACT
209965 AATTTAAATA
Statistics
Matches: 325, Mismatches: 27, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
196 3 0.01
197 80 0.25
198 1 0.00
199 3 0.01
200 237 0.73
201 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATTGAAACTCATAAGTATAATGTAATA
GTAATTTTTCAATGTAACCGGTATAAAATAACCGATTTTACGAGAGAATAGTCTACAACATGTAT
TAACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGACAAAAAGGGTACAACCAT
AAA
Found at i:212971 original size:201 final size:199
Alignment explanation
Indices: 212602--213076 Score: 668
Period size: 201 Copynumber: 2.4 Consensus size: 199
212592 AGTCTCCCAT
* * ** * *
212602 AAAGTGTCGATCCATATAT-AAAAAGTAACGACCCCAAAAACATCGAAACCGATAATTATAATGT
1 AAAGTGTCGATACAT-TTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* * * *
212666 AAT-GAGTAATTTTTCAATGTAACCGATATAAATATACCGGTTTTATGAAAAATAGGTCTACAAC
65 AATAG-GTAATTTTTCAATATAACCGATACAAATATACCGATTTTATGAAAAATAAGTCTACAAC
*
212730 ATGTATCGACACTTATCAATATTGTGTCGATACTTTTTGTCCAAAATGGAAGCCAAAAAGGGTGA
129 ATGTATCGACACTTATCAATATTGTGTCGATAATTTTTGTCCAAAATGGAAGCCAAAAAGGGTGA
212795 ACGCAC
194 ACGCAC
*
212801 AAAGTGTCGATACATTTTCAAAGAGTGTCGATCCCAAAAACATCGAAACCCCATAATTATAATGT
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAA-CCCATAATTATAATGT
* * * *
212866 AATAGGTAATTTTGT-AATATAACCGGTACACATATACCGATTTTATGAGAGAATAAGTCTATAA
65 AATAGGTAATTTT-TCAATATAACCGATACAAATATACCGATTTTATGA-AAAATAAGTCTACAA
* * * *
212930 CATGTATCGACACTTCTTAATATTGTGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGGGTG
128 CATGTATCGACACTTATCAATATTGTGTCGATAATTTTTGTCCAAAATGGAAGCCAAAAAGGGTG
*
212995 AACGCAT
193 AACGCAC
* *
213002 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCTGAAAAATATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCC-CAAAAACATCGAAACCCATAATTATAATGT
213067 AATAGGTAAT
65 AATAGGTAAT
213077 ATACCGGTTT
Statistics
Matches: 246, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
198 2 0.01
199 39 0.16
200 54 0.22
201 139 0.57
202 12 0.05
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (199 bp):
AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
ATAGGTAATTTTTCAATATAACCGATACAAATATACCGATTTTATGAAAAATAAGTCTACAACAT
GTATCGACACTTATCAATATTGTGTCGATAATTTTTGTCCAAAATGGAAGCCAAAAAGGGTGAAC
GCAC
Found at i:213200 original size:178 final size:177
Alignment explanation
Indices: 212897--213253 Score: 554
Period size: 178 Copynumber: 2.0 Consensus size: 177
212887 ACCGGTACAC
* *
212897 ATATACCGATTTTATGAGAGAATAAGTCTATAACATGTATCGACACTTCTTAATATTGTGTCGAT
1 ATATACCGATTTTATGAGAGAATAAGTCTATAACATGTATCGACACTTATAAATATTGTGTCGAT
* * *
212962 AATTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAG
66 AATTTTTGTCCAGAATGGATGCCAAAAAGGATGAACACACAAAGTGTCGATACATTTTCAAAAAG
* *
213027 TGTCGATCCTGAAAAATATCGAAACCCATAATTATAATGTAATAGGTA
131 TGTCGATCC-CAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
* * *
213075 ATATACCGGTTTTATGAGAGAATATGTCTATAATATGTATCGACACTATATAAAT-TTGTGTCGA
1 ATATACCGATTTTATGAGAGAATAAGTCTATAACATGTATCGACACT-TATAAATATTGTGTCGA
* * * * *
213139 TACTTTTTGTCTAGAATGGATGCCAAAAAGGATGAACACACAAAGTGTTGATACTTTTTCAAATA
65 TAATTTTTGTCCAGAATGGATGCCAAAAAGGATGAACACACAAAGTGTCGATACATTTTCAAAAA
213204 GTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
130 GTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
213252 AT
1 AT
213254 TTTTTAATAT
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
177 38 0.23
178 120 0.74
179 5 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (177 bp):
ATATACCGATTTTATGAGAGAATAAGTCTATAACATGTATCGACACTTATAAATATTGTGTCGAT
AATTTTTGTCCAGAATGGATGCCAAAAAGGATGAACACACAAAGTGTCGATACATTTTCAAAAAG
TGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTA
Found at i:216345 original size:205 final size:198
Alignment explanation
Indices: 215788--216351 Score: 592
Period size: 200 Copynumber: 2.8 Consensus size: 198
215778 TAACCGGTAT
** * *
215788 ATTTGTGTCGATACTTATT-GTCCAGGATGAATGCACAAACGAGGTGCACGC-TAAAGTGTCGAT
1 ATTTGTGTCGATACTT-TTGGTCCAAAATGAATGC-CAAA-AAGGTGCAAGCATAAAGTGTCGAT
** *
215851 ACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTATTAGGTAAATT
63 ACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCAATAA-TATAATGTAATAGGTAAATT
* * * *
215916 TACAGTGTAACCGATATAAATATACC-AGTTTTATGATAAACTAAGTCAGCATAAAGTATCGACA
126 TACAATGTAACCGGTATAAATATACCGAGTTTTATGAGAAACTAAGTCAGAATAAAGTATCGACA
215980 CTTGCTAA
191 CTTGCTAA
* *
215988 ATTTGTGTCGATACTTTTGGTCCAAAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTTGATAC
1 ATTTGTGTCGATACTTTTGGTCCAAAATGAATGCCAAAAA-GGTGCAAGCATAAAGTGTCGATAC
* * * *
216053 ATTTATAAAAAGTATCGATCCCGAAAATATCGAAACCCATAAGTATAATGTAATAGGTAAATTTT
65 ATTTAT-AAAAGTATCGATCCCAAAAACATCGAAACCAATAA-TATAATGTAATAGGTAAATTTA
* *
216118 CAATGTAACTGGTATAAATATACCGA-TTTTATGAGAGAA-TATGTCTA-AATAAAGTATCGACA
128 CAATGTAACCGGTATAAATATACCGAGTTTTATGAGA-AACTAAGTC-AGAATAAAGTATCGACA
*
216180 CTTTG-TTA
191 C-TTGCTAA
* * *
216188 GTTTGTGTCGATACTTTT-TTCCAGAATGAAATATGAATGCCCAACCAA-GTGCAAGCATAAAGT
1 ATTTGTGTCGATACTTTTGGTCC------AAA-ATGAATG-CCAA-AAAGGTGCAAGCATAAAGT
* ** *
216251 GTCGATACATTTA-AAATTGTATCGATCTAAAAAACATTGAAACCAATAATAATAATGTAATAGG
57 GTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCAATAAT-ATAATGTAATAGG
* *
216315 TAAATTTGCAATGTTACCGGTATAAATATACCG-GTTT
120 TAAATTTACAATGTAACCGGTATAAATATACCGAGTTT
216352 ACTTCGAAAA
Statistics
Matches: 309, Mismatches: 35, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
198 1 0.00
199 17 0.06
200 167 0.54
201 7 0.02
204 4 0.01
205 74 0.24
206 33 0.11
207 4 0.01
208 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
ATTTGTGTCGATACTTTTGGTCCAAAATGAATGCCAAAAAGGTGCAAGCATAAAGTGTCGATACA
TTTATAAAAGTATCGATCCCAAAAACATCGAAACCAATAATATAATGTAATAGGTAAATTTACAA
TGTAACCGGTATAAATATACCGAGTTTTATGAGAAACTAAGTCAGAATAAAGTATCGACACTTGC
TAA
Found at i:216503 original size:23 final size:23
Alignment explanation
Indices: 216453--216497 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
216443 TGCCTATTTT
*
216453 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
216476 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
216498 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:217516 original size:61 final size:61
Alignment explanation
Indices: 217400--217517 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
217390 GAAAAGTTGT
* * * * * *
217400 CTCATAATGAATTTATATAGTATTTAATCTAAATTGGTATATCTTAATGAGGTGTTAGAAA
1 CTCATAACGAATTTATATAGTACTCAATCTAAATTGATACATCTGAATGAGGTGTTAGAAA
* *
217461 CTCATAACGAGTTTATATAGTACTCAATCTGAATTGATACATCTGAATGCA-GTGTTA
1 CTCATAACGAATTTATATAGTACTCAATCTAAATTGATACATCTGAATG-AGGTGTTA
217518 AGTCATTGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 47 0.98
62 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (61 bp):
CTCATAACGAATTTATATAGTACTCAATCTAAATTGATACATCTGAATGAGGTGTTAGAAA
Found at i:217968 original size:32 final size:32
Alignment explanation
Indices: 217927--218023 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 32
217917 ATAAGTTACG
*
217927 AAATAATCATTAAATTTTATCGAACTATTATA
1 AAATAATCATTAAATTTTATCAAACTATTATA
* ** *
217959 AAATGATCATTTGATTTTATCAAACTGTTATA
1 AAATAATCATTAAATTTTATCAAACTATTATA
* * * * *
217991 AAATAATAATCAACTTTTATCAAAATTTTATA
1 AAATAATCATTAAATTTTATCAAACTATTATA
218023 A
1 A
218024 TTATTACAAC
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (32 bp):
AAATAATCATTAAATTTTATCAAACTATTATA
Found at i:225515 original size:18 final size:18
Alignment explanation
Indices: 225493--225530 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
225483 ACAAAGTAGA
*
225493 CTTTTTTCGAA-GTCGAT
1 CTTTTTACGAATGTCGAT
225510 CTTTTTACGAATGTCGAT
1 CTTTTTACGAATGTCGAT
225528 CTT
1 CTT
225531 ATTGACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (18 bp):
CTTTTTACGAATGTCGAT
Found at i:227175 original size:16 final size:16
Alignment explanation
Indices: 227154--227186 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
227144 TATTCTTTAT
227154 TAATTTTTTTTAACAA
1 TAATTTTTTTTAACAA
227170 TAATTTTTTTTAACAA
1 TAATTTTTTTTAACAA
227186 T
1 T
227187 TTGACTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTTTTTTAACAA
Found at i:227459 original size:18 final size:17
Alignment explanation
Indices: 227418--227461 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
227408 GTTTACTAAT
* *
227418 TTTGAGAGATTATATCTA
1 TTTGA-AGATTACATCAA
227436 TTTGAAGATTACATCAA
1 TTTGAAGATTACATCAA
227453 TTATGAAGA
1 TT-TGAAGA
227462 GACCGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (17 bp):
TTTGAAGATTACATCAA
Found at i:228273 original size:55 final size:55
Alignment explanation
Indices: 228207--228315 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 55
228197 GTTGGTCGAA
**
228207 ATTCATATAAATTTTGACATGTTCGAATATTCATGTTTATATTATGGTGATTGAG
1 ATTCATATAAATTTTGACATGTTAAAATATTCATGTTTATATTATGGTGATTGAG
** * * *
228262 ATTCATATAAATTTTGATGTGTTAAAATGTTCATGTTTATATTCTGGTGGTTGA
1 ATTCATATAAATTTTGACATGTTAAAATATTCATGTTTATATTATGGTGATTGA
228316 AAAACATAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.47
Consensus pattern (55 bp):
ATTCATATAAATTTTGACATGTTAAAATATTCATGTTTATATTATGGTGATTGAG
Found at i:236573 original size:2 final size:2
Alignment explanation
Indices: 236566--236590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
236556 AATATTGCTT
236566 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
236591 CACATGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:240383 original size:30 final size:32
Alignment explanation
Indices: 240350--240591 Score: 192
Period size: 32 Copynumber: 7.7 Consensus size: 32
240340 ATATATATAT
* * *
240350 AATTTTATCTAAATATTATAAAATAATCATAATT
1 AATTTTATCTAATTATTACAAAATAATCAT--TA
*
240384 AATTTTA-CTGAATTATTA-AAAA-AGGTCATTA
1 AATTTTATCT-AATTATTACAAAATA-ATCATTA
* * *
240415 AATTTTATCTAAATGTTACAAAATAGTCATT-
1 AATTTTATCTAATTATTACAAAATAATCATTA
* * *
240446 -ATTTTATCTAATTATTGCAAAATTACCATTA
1 AATTTTATCTAATTATTACAAAATAATCATTA
* *
240477 AATTTTATCTAATTATTAAAAAATGATCATTA
1 AATTTTATCTAATTATTACAAAATAATCATTA
* * * ** *
240509 AATTTTATCGAACTGTTACAAAATGGTCTTTA
1 AATTTTATCTAATTATTACAAAATAATCATTA
* * * *
240541 AA-TTTATCGAATT-GTGCAAAATGATCATTA
1 AATTTTATCTAATTATTACAAAATAATCATTA
*
240571 AATTTTATCTAACTATTACAA
1 AATTTTATCTAATTATTACAA
240592 TTTATAAAAT
Statistics
Matches: 169, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
30 39 0.23
31 33 0.20
32 72 0.43
33 11 0.07
34 14 0.08
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (32 bp):
AATTTTATCTAATTATTACAAAATAATCATTA
Found at i:240517 original size:94 final size:93
Alignment explanation
Indices: 240384--240588 Score: 270
Period size: 94 Copynumber: 2.2 Consensus size: 93
240374 AATCATAATT
* *
240384 AATTTTA-CTGAATTATTAAAAAAGGTCATTAAATTTTATCTAAATGTTACAAAATAGTCATT-A
1 AATTTTATCT-AATTATTAAAAAAGATCATTAAATTTTATCGAAATGTTACAAAATAGTCATTAA
* * * *
240447 TTTTATCTAATTATTGCAAAATTACCATTA
65 ATTTATCGAATT-GTGCAAAATGACCATTA
* * *
240477 AATTTTATCTAATTATTAAAAAATGATCATTAAATTTTATCGAACTGTTACAAAATGGTCTTTAA
1 AATTTTATCTAATTATTAAAAAA-GATCATTAAATTTTATCGAAATGTTACAAAATAGTCATTAA
*
240542 ATTTATCGAATTGTGCAAAATGATCATTA
65 ATTTATCGAATTGTGCAAAATGACCATTA
*
240571 AATTTTATCTAACTATTA
1 AATTTTATCTAATTATTA
240589 CAATTTATAA
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
93 20 0.20
94 67 0.68
95 11 0.11
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (93 bp):
AATTTTATCTAATTATTAAAAAAGATCATTAAATTTTATCGAAATGTTACAAAATAGTCATTAAA
TTTATCGAATTGTGCAAAATGACCATTA
Found at i:241561 original size:2 final size:2
Alignment explanation
Indices: 241554--241581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
241544 TCATTGTTAA
241554 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
241582 GATTAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242047 original size:21 final size:21
Alignment explanation
Indices: 242022--242061 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
242012 GTTCATAGAC
*
242022 TTATTTAATTTTTTAAATAAA
1 TTATTTAAATTTTTAAATAAA
242043 TTATTTAAATTTTTAAATA
1 TTATTTAAATTTTTAAATA
242062 TAAAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTAAATTTTTAAATAAA
Found at i:243859 original size:21 final size:22
Alignment explanation
Indices: 243834--243881 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
243824 ACCTTACTTA
*
243834 AAACCCTAAACCAATAACC-CT
1 AAACCATAAACCAATAACCTCT
* *
243855 AAACCATAACCCCATAACCTCT
1 AAACCATAAACCAATAACCTCT
243877 AAACC
1 AAACC
243882 TTAATCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACCATAAACCAATAACCTCT
Found at i:243865 original size:13 final size:14
Alignment explanation
Indices: 243835--243866 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
243825 CCTTACTTAA
243835 AACCCTAAACCAAT
1 AACCCTAAACCAAT
243849 AACCCTAAACC-AT
1 AACCCTAAACCAAT
243862 AACCC
1 AACCC
243867 CATAACCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (14 bp):
AACCCTAAACCAAT
Found at i:248308 original size:31 final size:31
Alignment explanation
Indices: 248238--248359 Score: 129
Period size: 31 Copynumber: 3.9 Consensus size: 31
248228 GTCGAGGGTT
* *
248238 TACCTATGTTCTACGGAACATATGGATAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* *
248269 TTACCTATG-TCTTTCGGGACATATGGACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* * *
248301 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
248332 TACCTATGTTCTTCGGGACCTATGGACA
1 TACCTATGTTCTACGGAACATATGGACA
248360 ATTGCCGAGG
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
31 48 0.65
32 26 0.35
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:248706 original size:20 final size:20
Alignment explanation
Indices: 248681--248719 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
248671 TATATATTTT
248681 GTTATATGAAATGTTTTATG
1 GTTATATGAAATGTTTTATG
* *
248701 GTTATATTATATGTTTTAT
1 GTTATATGAAATGTTTTAT
248720 ATACCTCACT
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:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (20 bp):
GTTATATGAAATGTTTTATG
Found at i:253569 original size:19 final size:19
Alignment explanation
Indices: 253545--253590 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
253535 ATTTAGACAT
253545 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
253564 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
253583 TTTGCATT
1 TTTGCATT
253591 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:256764 original size:84 final size:84
Alignment explanation
Indices: 256615--257536 Score: 1039
Period size: 84 Copynumber: 11.1 Consensus size: 84
256605 TTTTAAACAA
* * * * * *
256615 ATCATTTGCGGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCAACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
256679 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
256698 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
256763 ACGCTCAGCT-CAACGGCAC
66 ACGCTCAGCTCCAA-GGCAC
* * * * ** *
256782 ATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG----GCAAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
** * *
256843 ACATTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
* * *
256863 ATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGGCT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
256928 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
256947 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
257012 ACGCTCAGCT-CAACGACAC
66 ACGCTCAGCTCCAA-GGCAC
* * * ** *
257031 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
257092 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
* *
257112 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGGCT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
257177 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
257196 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
257261 ACGCTCAGCT-CAACGGCAC
66 ACGCTCAGCTCCAA-GGCAC
* * * ** *
257280 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
257341 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
257361 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
257426 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * *
257445 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
257510 ACACTCAACTCAAAGGCACC
66 ACGCTCAGCTCCAAGGCA-C
257530 ATCATTT
1 ATCATTT
257537 ACAACATAGC
Statistics
Matches: 694, Mismatches: 122, Indels: 44
0.81 0.14 0.05
Matches are distributed among these distances:
80 73 0.11
81 124 0.18
82 3 0.00
83 43 0.06
84 369 0.53
85 82 0.12
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:256894 original size:165 final size:163
Alignment explanation
Indices: 256615--257487 Score: 926
Period size: 165 Copynumber: 5.3 Consensus size: 163
256605 TTTTAAACAA
* * * * * ** *
256615 ATCATTTGCGGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGACTA
* * * ** * * *
256680 CGCTCAGCTCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAA
63 CACTCAGCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAA
*
256745 AGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCAC
128 AGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCAC
* * * * *
256782 ATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGGCAAAGACCCCCGAGTTCGATTACAT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACAC
* *
256847 TCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGC-TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
* * *
256912 ACCTTCGAGTTTGGCTACGCTCAGCTCCAAGGCAT
130 ACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCAC
* * * * ***
256947 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT-GC--C-AAAGACCCCCGAGTTCGACT
* * * * * * *
257012 ACGCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-A
62 ACACTCAGCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
** * * *
257073 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
127 AAGACCTTCGAGTTCGACTACGCTCAGC-TC-AAGGCAC
* ** * *
257112 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGGCT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGACT
* * * * * * * *
257177 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
62 ACACTCAGCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
*
257242 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCAC
127 AAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCAC
* * *
257280 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACAC
*
257345 TCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 TCAGC-TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
*
257410 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
130 ACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCAC
* * * *
257445 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
257488 CCAAAGACCT
Statistics
Matches: 585, Mismatches: 102, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
164 74 0.13
165 333 0.57
166 9 0.02
167 34 0.06
168 88 0.15
169 47 0.08
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (163 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACAC
TCAGCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGA
CCTTCGAGTTCGACTACGCTCAGCTCAAGGCAC
Found at i:257052 original size:249 final size:249
Alignment explanation
Indices: 256615--257536 Score: 1603
Period size: 249 Copynumber: 3.7 Consensus size: 249
256605 TTTTAAACAA
* * * * * *
256615 ATCATTTGCGGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCAACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
256679 ACGCTCAGCTCCAAGGCATGTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
66 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
* *
256744 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTACAGCATAGCTTAAGTCGAG
131 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
* *
256809 AAGGGCTATCTGGCAAAGACCCCCGAGTTCGATTACATTCAGCTTCGAGGGCAC
196 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * *
256863 ATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGGCT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
256928 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
66 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
*
256993 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAG
131 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
257058 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
196 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
257112 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGGCT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
257177 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAA
66 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
257242 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
131 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
257307 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
196 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
257361 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
257426 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCA
66 ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
* * * * *
257491 AAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACCATCATTT
131 AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCA-CATCATTT
257537 ACAACATAGC
Statistics
Matches: 645, Mismatches: 27, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
248 35 0.05
249 602 0.93
250 8 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (249 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
AAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:262003 original size:17 final size:18
Alignment explanation
Indices: 261971--262004 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
261961 TACTTACCTA
261971 ATATTAATTTTGTGATTG
1 ATATTAATTTTGTGATTG
*
261989 ATATT-ATTTTTTGATT
1 ATATTAATTTTGTGATT
262005 TCTATGCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (18 bp):
ATATTAATTTTGTGATTG
Found at i:264459 original size:17 final size:17
Alignment explanation
Indices: 264437--264470 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
264427 ATCAAGCGTC
264437 GATAAGTACCATCCGGT
1 GATAAGTACCATCCGGT
*
264454 GATAAGTGCCATCCGGT
1 GATAAGTACCATCCGGT
264471 CAAACCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (17 bp):
GATAAGTACCATCCGGT
Found at i:276560 original size:6 final size:6
Alignment explanation
Indices: 276549--276619 Score: 142
Period size: 6 Copynumber: 11.8 Consensus size: 6
276539 TTATCTGAAT
276549 AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG
1 AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG AGCGAG
276597 AGCGAG AGCGAG AGCGAG AGCGA
1 AGCGAG AGCGAG AGCGAG AGCGA
276620 ACCTCTGAGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.34, C:0.17, G:0.49, T:0.00
Consensus pattern (6 bp):
AGCGAG
Found at i:277491 original size:75 final size:74
Alignment explanation
Indices: 277344--277670 Score: 349
Period size: 74 Copynumber: 4.4 Consensus size: 74
277334 CTTAATCGAT
* * * * * *
277344 TAAAATAAAATAGGTGCT--ATATTATGTTAAACTACCTACCG-GTTATTGAAGGTTACTAATAA
1 TAAAATAAAATAGGCGTTACATATTACGTTAAACTACCTACCGATTTATTTAAAGTTACTAATAA
277406 TGTAAACGG
66 TGTAAACGG
* ** *
277415 TAAAATAAAATAGGCGTTACATATTACGTTAAAATATATACCGGTTTATTTAAAGATTACTAATA
1 TAAAATAAAATAGGCGTTACATATTACGTTAAACTACCTACCGATTTATTTAAAG-TTACTAATA
*
277480 ATATAAACGG
65 ATGTAAACGG
** * * *
277490 TAAAATAAAATAAACATTGTC-TATTACG-TAAACTACCTACCGACTTATTTAAATGTTACTAAT
1 TAAAATAAAATAGGCGTT-ACATATTACGTTAAACTACCTACCGATTTATTTAAA-GTTACTAAT
277553 AATGTAAACGG
64 AATGTAAACGG
* * * * * *
277564 TAAAATAAAATAGGTGTTATATATTACGTTAAACTAGCTATCGATTTTTTTAAAGTTAATAATAA
1 TAAAATAAAATAGGCGTTACATATTACGTTAAACTACCTACCGATTTATTTAAAGTTACTAATAA
*
277629 TGTAAATGG
66 TGTAAACGG
* * * *
277638 TAAAATAAAACAGGCGCTACTTATTATGTTAAA
1 TAAAATAAAATAGGCGTTACATATTACGTTAAA
277671 TAGACTCTAC
Statistics
Matches: 210, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
71 16 0.08
73 19 0.09
74 112 0.53
75 62 0.30
76 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (74 bp):
TAAAATAAAATAGGCGTTACATATTACGTTAAACTACCTACCGATTTATTTAAAGTTACTAATAA
TGTAAACGG
Found at i:277570 original size:149 final size:146
Alignment explanation
Indices: 277371--277647 Score: 401
Period size: 149 Copynumber: 1.9 Consensus size: 146
277361 TATATTATGT
* *
277371 TAAACTACCTACCGGTTATTGAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGGCGTTACA
1 TAAACTACCTACCGCTTATTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGGCGTTACA
* * *
277436 TATTACGTTAAAATATATACCGGTTTATTTAAAGATTACTAATAATATAAACGGTAAAATAAAAT
66 TATTACGTTAAAATAGATACCGATTTATTTAAAG-TTAATAATAATATAAACGGTAAAATAAAAT
277501 AAACATTGTCTATTACG
130 AAACATTGTCTATTACG
* *
277518 TAAACTACCTACCGACTTATTTAAATGTTACTAATAATGTAAACGGTAAAATAAAATAGGTGTTA
1 TAAACTACCTACCG-CTTA-TTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGGCGTTA
* * * * * * *
277583 TATATTACGTTAAACTAGCTATCGATTTTTTTAAAGTTAATAATAATGTAAATGGTAAAATAAAA
64 CATATTACGTTAAAATAGATACCGATTTATTTAAAGTTAATAATAATATAAACGGTAAAATAAAA
277648 CAGGCGCTAC
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
147 14 0.12
148 29 0.25
149 71 0.62
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (146 bp):
TAAACTACCTACCGCTTATTAAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGGCGTTACA
TATTACGTTAAAATAGATACCGATTTATTTAAAGTTAATAATAATATAAACGGTAAAATAAAATA
AACATTGTCTATTACG
Found at i:278232 original size:103 final size:108
Alignment explanation
Indices: 278071--278346 Score: 298
Period size: 107 Copynumber: 2.6 Consensus size: 108
278061 GCAACCTAGT
* * * * *
278071 ATGTTAATATTTATTTATAACAAAATAAGAAATTAACATATTTTGTTGTCGT-GAGATTTCG-AA
1 ATGTTAATAATT-TTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCG-GATTTCGTAA
* * * * *
278134 TGCCCCATCAGCTT-AA-TTTGGTCAT-TTTAGGCGCTACCTAAC
64 GGCCCCATCAGCTTAAACTTTGATAATATTTAGACGATACCTAAC
*
278176 ATGTTAATAATTTTAATAACAAAATAAGTAA-TGACCTATTTTGTTATCGTCGGATTT-GTAAGG
1 ATGTTAATAATTTTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCGTAAGG
* * * *
278239 CCCTATTAGCTTAAACTTTGATAATAATTTAGACGATGCCTAAT
66 CCCCATCAGCTTAAACTTTGATAAT-ATTTAGACGATACCTAAC
* * * *
278283 ATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTC-TAAGG
1 ATGTTAATAATTTTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCGTAAGG
278347 TTTCATCAGC
Statistics
Matches: 143, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
102 1 0.01
103 34 0.24
104 20 0.14
105 18 0.13
107 40 0.28
108 30 0.21
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (108 bp):
ATGTTAATAATTTTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTCGGATTTCGTAAGG
CCCCATCAGCTTAAACTTTGATAATATTTAGACGATACCTAAC
Found at i:282006 original size:20 final size:20
Alignment explanation
Indices: 281969--282007 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
281959 AGATTGAGTG
* *
281969 GATTTTGATGTTGTTTGCAC
1 GATTTTGATGATGATTGCAC
*
281989 GATTTTTATGATGATTGCA
1 GATTTTGATGATGATTGCA
282008 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTGATGATGATTGCAC
Found at i:282188 original size:21 final size:21
Alignment explanation
Indices: 282162--282201 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
282152 CAGAACCCCA
*
282162 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
282183 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
282202 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:282210 original size:23 final size:21
Alignment explanation
Indices: 282184--282241 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
282174 TTCCCCTGTG
282184 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
282207 GGGGGAATCAGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
282227 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
282242 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 2 0.06
22 3 0.10
23 12 0.39
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:290817 original size:19 final size:19
Alignment explanation
Indices: 290793--290861 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
290783 ATAAAACCTG
*
290793 AGTGCATCGATGCATGGTT
1 AGTGCATCGATGCATGGTA
290812 AGTGCATCGATGCAT-G-A
1 AGTGCATCGATGCATGGTA
* *
290829 AATGCATTCGAT--ATGGTG
1 AGTGCA-TCGATGCATGGTA
290847 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
290862 CAATGAGTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 2 0.05
17 11 0.27
18 11 0.27
19 17 0.41
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (19 bp):
AGTGCATCGATGCATGGTA
Found at i:290817 original size:65 final size:65
Alignment explanation
Indices: 290684--290840 Score: 234
Period size: 65 Copynumber: 2.4 Consensus size: 65
290674 GTGCACTAAG
*
290684 AGTGCATCGA-GCATAAAATGCATTCGATGTTTCAAACAAGCTTGAGTGCATCGATGCATGGTCT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGTCT
290748 -GTGCATCGATGCATAAAATGCATTCGATGTTTTTCATAA-AA-CCTGAGTGCATCGATGCATGG
1 AGTGCATCGATGCATAAAATGCATTCGATG--TTTCA-AACAAGCCTGAGTGCATCGATGCATGG
290810 T-T
63 TCT
*
290812 AGTGCATCGATGCATGAAATGCATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
290841 ATGGTGAGTG
Statistics
Matches: 86, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
63 9 0.10
64 20 0.23
65 48 0.56
66 7 0.08
67 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGAGTGCATCGATGCATGGTCT
Found at i:290870 original size:20 final size:20
Alignment explanation
Indices: 290845--290882 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
290835 TTCGATATGG
*
290845 TGAGTGCATCGATGCATCAA
1 TGAGTGCAACGATGCATCAA
*
290865 TGAGTGCAACGGTGCATC
1 TGAGTGCAACGATGCATC
290883 CTTCACAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (20 bp):
TGAGTGCAACGATGCATCAA
Found at i:293397 original size:23 final size:23
Alignment explanation
Indices: 293368--293449 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
293358 CTATGATAGT
293368 GTGCATCGATGCACATTCAATGA
1 GTGCATCGATGCACATTCAATGA
*
293391 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAATGA
* * *
293413 -TGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTCAATGA
293435 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
293450 TATTTAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
22 6 0.12
23 15 0.31
24 13 0.27
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAATGA
Found at i:293461 original size:44 final size:44
Alignment explanation
Indices: 293372--293468 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
293362 GATAGTGTGC
* * *
293372 ATCGATGCACATTCAATGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAAGAGTGCATCGATGCATATTCATGATGT
* *
293416 ATCGATGCACATTCAAAGGGATGCATCGATGCACTATTTA-G-TGT
1 ATCGATGCACATTCAAAGAG-TGCATCGATGCA-TATTCATGATGT
293460 ATCGATGCA
1 ATCGATGCA
293469 TTTTGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 30 0.65
45 12 0.26
46 4 0.09
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (44 bp):
ATCGATGCACATTCAAAGAGTGCATCGATGCATATTCATGATGT
Found at i:296206 original size:23 final size:23
Alignment explanation
Indices: 296175--296243 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
296165 CACCACAGCT
* *
296175 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
296198 CGTAGAATTGCACTGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
296221 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
296244 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:296424 original size:100 final size:102
Alignment explanation
Indices: 296262--296468 Score: 346
Period size: 100 Copynumber: 2.0 Consensus size: 102
296252 TGTCCATAAG
***
296262 GACCACATATCATTCCTTAAGAATCATATACATATACTTGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
296327 TT-CACATGTTCCAAA-AATACATATATGTCCCGAAA
66 TTACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
296362 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
296427 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TT-ACACATGTTCCAAAGAATACATATATGTCCCGAAA
296465 GACC
1 GACC
296469 GCGTAGACCC
Statistics
Matches: 99, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
100 63 0.64
102 13 0.13
103 23 0.23
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (102 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:297748 original size:20 final size:20
Alignment explanation
Indices: 297712--297749 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
297702 TTTTCCTTTA
**
297712 GGGGGTATCGATTCCCTACT
1 GGGGGTATCGAAACCCTACT
297732 GGGGGTATCGAAACCCTA
1 GGGGGTATCGAAACCCTA
297750 AGACATTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGAAACCCTACT
Found at i:301132 original size:23 final size:23
Alignment explanation
Indices: 301101--301167 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 23
301091 TCACCACAGC
* *
301101 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
301124 CGTAGAATTGCACCGGAGT--CA
1 CGTAGAATTGCACCGAAGTGCCA
*
301145 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
301168 TATAATAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 20 0.53
23 18 0.47
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:307212 original size:21 final size:21
Alignment explanation
Indices: 307186--307237 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
307176 TTGGGAGCGT
307186 CTGGTGCATCGATGCATAAGG
1 CTGGTGCATCGATGCATAAGG
*
307207 CTGGTGCATTGATGCATAAGG
1 CTGGTGCATCGATGCATAAGG
*
307228 CTAGTGCATC
1 CTGGTGCATC
307238 AGTACACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (21 bp):
CTGGTGCATCGATGCATAAGG
Found at i:307352 original size:64 final size:63
Alignment explanation
Indices: 307302--307458 Score: 230
Period size: 64 Copynumber: 2.5 Consensus size: 63
307292 GTGCACTAAG
307302 AGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CCTGAGTGCATCGATGCATGGT
*
307365 CTGTGCATCGATGCATAAAATGCATTCGATGTTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 -AGTGCATCGATGCATAAAATGCATTCGATG-TTTTCATAAAACCTGAGTGCATCGATGCATGGT
*
307430 AGTGAATCGATGCA-AGAAATGCATTCGAT
1 AGTGCATCGATGCATA-AAATGCATTCGAT
307459 ATGGTAAGTG
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.01
64 54 0.63
65 22 0.26
66 7 0.08
67 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
Found at i:310095 original size:29 final size:29
Alignment explanation
Indices: 310060--310141 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
310050 AAACTAAATT
*
310060 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
310089 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
310118 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
310142 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:314848 original size:29 final size:29
Alignment explanation
Indices: 314813--314894 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
314803 AAACTAAATT
*
314813 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
314842 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
314871 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
314895 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:315802 original size:15 final size:15
Alignment explanation
Indices: 315782--315810 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
315772 TTGATCACTC
315782 ATCAAATTATAAGTG
1 ATCAAATTATAAGTG
315797 ATCAAATTATAAGT
1 ATCAAATTATAAGT
315811 ACAACTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (15 bp):
ATCAAATTATAAGTG
Found at i:317614 original size:33 final size:34
Alignment explanation
Indices: 317518--317867 Score: 199
Period size: 33 Copynumber: 9.9 Consensus size: 34
317508 TGTATAATAA
* *
317518 TTTTAAATATAACTTTTGAAAATATATAATATATAAT
1 TTTTAAA-ATAA-TTTTAAAAACATATAATATAT-AT
** *
317555 TTTTAAAACGATTTTAAAAAATATATAATATATA-
1 TTTTAAAATAATTTT-AAAAACATATAATATATAT
317589 TTTTAAAATAATTTTAAAAACATATAATATATAATTT
1 TTTTAAAATAATTTTAAAAACATATAATATAT-A--T
** * **
317626 TTTTAAAACGATTTT-GAAA-ATATGGTATATAGT
1 TTTTAAAATAATTTTAAAAACATATAATATATA-T
* * *
317659 TTTTAAAGTAATTTTGAAAACATAT-ATATA-AC
1 TTTTAAAATAATTTTAAAAACATATAATATATAT
** * *
317691 TTTTAAAACGATTTTGAAAAACATGTAATATAT-G
1 TTTTAAAATAATTTT-AAAAACATATAATATATAT
* * * *
317725 GTTTAAAATAATCTTGAAAACATATAGTATATAAT
1 TTTTAAAATAATTTTAAAAACATATAATATAT-AT
* * *
317760 TTTCAAAATAAATTTTAAAGAAAACGTATAATATATCGTTT
1 TTTTAAAAT-AATTTT--A-AAAACATATAATATA---TAT
* * * *
317801 TTTTAAAATATTATTTAAAAATATATGATATATGGT
1 TTTTAAAATAAT-TTTAAAAACATATAATATAT-AT
* * *
317837 TTTTAAAACATTTTTAAAAAACTTATAATAT
1 TTTTAAAATAATTTT-AAAAACATATAATAT
317868 GGTTTCTAAA
Statistics
Matches: 242, Mismatches: 49, Indels: 45
0.72 0.15 0.13
Matches are distributed among these distances:
32 12 0.05
33 52 0.21
34 38 0.16
35 29 0.12
36 50 0.21
37 20 0.08
38 12 0.05
39 14 0.06
40 2 0.01
41 12 0.05
42 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (34 bp):
TTTTAAAATAATTTTAAAAACATATAATATATAT
Found at i:317857 original size:36 final size:35
Alignment explanation
Indices: 317800--317913 Score: 135
Period size: 36 Copynumber: 3.2 Consensus size: 35
317790 ATATATCGTT
*
317800 TTTTTAAAATATTATTT-AAAAATATATGATATATGG
1 TTTTTAAAACATT-TTTAAAAAAT-TATGATATATGG
317836 TTTTTAAAACATTTTTAAAAAACTTAT-A-ATATGG
1 TTTTTAAAACATTTTTAAAAAA-TTATGATATATGG
* *
317870 TTTCTAAAACATTTTTTAAAAAATGTATGGTATATGG
1 TTTTTAAAACA-TTTTTAAAAAAT-TATGATATATGG
317907 TTTTTAA
1 TTTTTAA
317914 TTTTTTTGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
34 17 0.25
35 18 0.26
36 20 0.29
37 13 0.19
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (35 bp):
TTTTTAAAACATTTTTAAAAAATTATGATATATGG
Found at i:320732 original size:213 final size:213
Alignment explanation
Indices: 320486--320870 Score: 560
Period size: 213 Copynumber: 1.8 Consensus size: 213
320476 AACAAAATAA
* * *
320486 GTAATTAACATATTTTGTTATCGTCGGATTTCTAAGG-TCCTATCAACTTAAACTTTGATAATAT
1 GTAATTAACATATTTTGTTATCATCAGATTTCTAAGGCTCC-ATCAACTTAAACTTTGATAACAT
** * *
320550 TTT-AGACGCTGCCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTA
65 TTTAAG-CGCAACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTA
* *
320614 TCGTTGGATTTCTAAAGCCTCATCAGCTTTAAAAA-ACGCTACATGAGCGCTATTTGTTATGTTA
129 TCGTCGGATTTCTAAAGAC-CATCAGCTTTAAAAATACGCTACATGAGCGCTATTTGTTATGTTA
320678 TTATGGTTGATAATGTTTCCG
193 TTATGGTTGATAATGTTTCCG
* * * * *
320699 GTAATTAACCTGTTTTGTTATCATCATATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATT
1 GTAATTAACATATTTTGTTATCATCAGATTTCTAAGGCTCCATCAACTTAAACTTTGATAACATT
* *
320764 TTAAGTGCAACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAATATATTTTGTTATC
66 TTAAGCGCAACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATC
* *
320829 GTCGGATTTCTAATGACCATCAGCTTTAAAAATGCGCTACAT
131 GTCGGATTTCTAAAGACCATCAGCTTTAAAAATACGCTACAT
320871 ATTACGTTAC
Statistics
Matches: 151, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
212 15 0.10
213 131 0.87
214 5 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (213 bp):
GTAATTAACATATTTTGTTATCATCAGATTTCTAAGGCTCCATCAACTTAAACTTTGATAACATT
TTAAGCGCAACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATC
GTCGGATTTCTAAAGACCATCAGCTTTAAAAATACGCTACATGAGCGCTATTTGTTATGTTATTA
TGGTTGATAATGTTTCCG
Found at i:320824 original size:108 final size:106
Alignment explanation
Indices: 320343--320859 Score: 427
Period size: 108 Copynumber: 4.8 Consensus size: 106
320333 ATTGGGCACA
* * * * *
320343 ACCTAATATGTTAATATTTATTTATAACAAAATAAGAAATTAACATATTTTGTTGTCGT-GAGAT
1 ACCTAATATGTTGATA-ATATTGATAAC-AAATAAGTAATTAACATATTTTGTTATCGTCG-GAT
* * *
320407 TTCGAAGGTCTCATCAACTTAAAATTTGATAACATTTTAGGCGCT
63 TTCTAAGGTC-CATCAGCTTAAAATTTGATAACATTTTAAGCGCT
* *
320452 ATCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCGGATTT
1 ACCTAATATGTTGATAATATTGATAAC-AAATAAGTAATTAACATATTTTGTTATCGTCGGATTT
* * *
320517 CTAAGGTCCTATCAACTTAAACTTTGATAATATTTT-AGACGCT
65 CTAAGGTCC-ATCAGCTTAAAATTTGATAACATTTTAAG-CGCT
* * *
320560 GCCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTTGGATTT
1 ACCTAATATGTTGATAATATTGATAACAAA-TAAGTAATTAACATATTTTGTTATCGTCGGATTT
* * *** * *
320625 CTAAAGCCTCATCAGCTTTAAAAAACGCT-ACA---TGAGCGCT
65 CTAAGGTC-CATCAGC-TTAAAATTTGATAACATTTTAAGCGCT
** ** * * **** ** * * * **
320665 ATTTGTTATGTT-ATTATGGTTGATAATGTTTCCGGTAATTAACCTGTTTTGTTATCATCATATT
1 ACCTAATATGTTGATAAT-ATTGATAACAAAT-AAGTAATTAACATATTTTGTTATCGTCGGATT
* * * *
320729 TCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAAGTGCA
64 TCTAAGG-TCCATCAGCTTAAAATTTGATAACATTTTAAGCGCT
*
320773 ACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAATATATTTTGTTATCGTCGGATTT
1 ACCTAATATGTTGATAATATTGATAACAAAT-AAGTAATTAACATATTTTGTTATCGTCGGATTT
* *
320838 CTAATGACCATCAGCTTTAAAA
65 CTAAGGTCCATCAGC-TTAAAA
320860 ATGCGCTACA
Statistics
Matches: 319, Mismatches: 73, Indels: 33
0.75 0.17 0.08
Matches are distributed among these distances:
104 12 0.04
105 60 0.19
106 3 0.01
107 13 0.04
108 204 0.64
109 27 0.08
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (106 bp):
ACCTAATATGTTGATAATATTGATAACAAATAAGTAATTAACATATTTTGTTATCGTCGGATTTC
TAAGGTCCATCAGCTTAAAATTTGATAACATTTTAAGCGCT
Found at i:325788 original size:23 final size:23
Alignment explanation
Indices: 325753--325802 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
325743 ATTAAGCACA
*
325753 ATAACATATTAGGTAGCGCGTAT
1 ATAACATAATAGGTAGCGCGTAT
* *
325776 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCGTAT
325799 ATAA
1 ATAA
325803 TAAAATAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCGTAT
Found at i:325809 original size:23 final size:23
Alignment explanation
Indices: 325753--325809 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
325743 ATTAAGCACA
* *
325753 ATAACATATTAGGTAGCGCGTAT
1 ATAACAAAATAGGTAGCGCGTAT
** *
325776 ATAACGTAATAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCGTAT
*
325799 ATAATAAAATA
1 ATAACAAAATA
325810 AGTTAATTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCGCGTAT
Found at i:326253 original size:2 final size:2
Alignment explanation
Indices: 326246--326282 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
326236 TAAGTATGAA
326246 AT AT AT AT 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 AT AT AT AT A
326283 ATGTGTGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:328488 original size:197 final size:201
Alignment explanation
Indices: 328250--328658 Score: 646
Period size: 202 Copynumber: 2.0 Consensus size: 201
328240 CGTTTTTTCA
328250 AAACCGGTATCTATTGACCGATTACATTGTATATTGAAACCAA-TTTTATCAATTTTTAACC-TT
1 AAACCGGTATCTATTGACCGATTACATTGTATATTGAAACCAATTTTTATCAATTTTTAACCTTT
*
328313 TATATCATTATGTATCGATA-TTTTATAGGTATAGATACTTCTTACGTGCATGTAGTTTTGA-AA
66 TATATCATTATGTATAGATACTTTTATAGGTATAGATACTTCTTACGTGCATGTAGTTTTGAGAA
** * *
328376 GTACACTGGACAAAAAGTATCGATACATATACAAAATGTATCGATACTTTATATAAAATTATGTT
131 ACACACTGGACAAAAAGTATCGATACATATAAAAAAAGTATCGATACTTTATATAAAATTATGTT
328441 ACCATT
196 ACCATT
* * *
328447 AAACTGGTATCTATTGATCGGTTACATTGTATATTGAAACCAATTTTTATCAATTTTTAACCTTT
1 AAACCGGTATCTATTGACCGATTACATTGTATATTGAAACCAATTTTTATCAATTTTTAACCTTT
**
328512 TATATCATTATGTATAGATACGTTTTATAGGTATCTATACTTCTTACGTGCATGTAGTTTTGAGA
66 TATATCATTATGTATAGATAC-TTTTATAGGTATAGATACTTCTTACGTGCATGTAGTTTTGAGA
* * * *
328577 AACATACTGGACAAAAAGTATCGATACATATAAAAAAAGTATCGGTACTTTATATTAACTTATGT
130 AACACACTGGACAAAAAGTATCGATACATATAAAAAAAGTATCGATACTTTATATAAAATTATGT
328642 TACCATT
195 TACCATT
*
328649 AAATCGGTAT
1 AAACCGGTAT
328659 ATTTTTACAC
Statistics
Matches: 191, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
197 40 0.21
198 18 0.09
199 21 0.11
201 39 0.20
202 73 0.38
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (201 bp):
AAACCGGTATCTATTGACCGATTACATTGTATATTGAAACCAATTTTTATCAATTTTTAACCTTT
TATATCATTATGTATAGATACTTTTATAGGTATAGATACTTCTTACGTGCATGTAGTTTTGAGAA
ACACACTGGACAAAAAGTATCGATACATATAAAAAAAGTATCGATACTTTATATAAAATTATGTT
ACCATT
Found at i:330300 original size:6 final size:6
Alignment explanation
Indices: 330279--330326 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
330269 TTTTATATTG
* * * *
330279 AAATTC AAACTC AAATTG AAATTG AAATTG AAATTC AAATTC AAATTC
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
330327 CAATAACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (6 bp):
AAATTC
Found at i:330324 original size:18 final size:18
Alignment explanation
Indices: 330275--330326 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
330265 CAAATTTTAT
*
330275 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAATTCAA
* *
330293 ATTGAAATTGAAATTGAA
1 ATTGAAATTCAAATTCAA
*
330311 ATTCAAATTCAAATTC
1 ATTGAAATTCAAATTC
330327 CAATAACATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.33
Consensus pattern (18 bp):
ATTGAAATTCAAATTCAA
Found at i:333286 original size:156 final size:160
Alignment explanation
Indices: 332984--333315 Score: 460
Period size: 158 Copynumber: 2.1 Consensus size: 160
332974 TCATAATGAA
* * * * * *
332984 ACCGGTTTTATCATATTTTACCTGTTATATGTTATGGATCGATACATTTTTATAAAGTATCGATA
1 ACCGGTTTTGTCATATTTTACATGTTATATGTTATCGATCGATACAATGTTATAAAGTATCAATA
*
333049 CTTTATAGGCGCTATTACTGCTTTTATTTTAAATTCCAAAAGTGTTGATACTTATTTCAATGGAA
66 CTTTATAGGCGCTATTACTGCTTTTATTTTAAATTCCAAAAGTGTCGA-ACTTATTTCAATGGAA
**
333114 TCGATACTTTCAACATAT-CGGTAGCGCTTT
130 TAAATACTTTCAACATATCCGGTAGCGCTTT
* *
333144 ACCGGTTTTGTCATATTTTACATGTTATATTGTTTTCTATCG-TA-AATGTTATAAAGTATCAAT
1 ACCGGTTTTGTCATATTTTACATGTTATA-TGTTATCGATCGATACAATGTTATAAAGTATCAAT
* * *
333207 ACTTT-TAGG-GTGTATTATTGCTTTTCTTTTAAATTCCAAAAGTGTCG-ACTTATTTCAATGGA
65 ACTTTATAGGCG-CTATTACTGCTTTTATTTTAAATTCCAAAAGTGTCGAACTTATTTCAATGGA
*
333269 ATAAATACTTTCAACATATCCGGTAGCGTTTT
129 ATAAATACTTTCAACATATCCGGTAGCGCTTT
333301 ACCGGTTTTGTCATA
1 ACCGGTTTTGTCATA
333316 ATGAAACCAG
Statistics
Matches: 154, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
156 32 0.21
157 27 0.18
158 36 0.23
159 21 0.14
160 29 0.19
161 9 0.06
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43
Consensus pattern (160 bp):
ACCGGTTTTGTCATATTTTACATGTTATATGTTATCGATCGATACAATGTTATAAAGTATCAATA
CTTTATAGGCGCTATTACTGCTTTTATTTTAAATTCCAAAAGTGTCGAACTTATTTCAATGGAAT
AAATACTTTCAACATATCCGGTAGCGCTTT
Found at i:333472 original size:183 final size:181
Alignment explanation
Indices: 333227--333571 Score: 480
Period size: 183 Copynumber: 1.9 Consensus size: 181
333217 TGTATTATTG
*
333227 CTTTTCTTTTAAATTCCAAAAGTGTCGACTTATTTCAATGGAATAAATACTTTCAACATATCCGG
1 CTTTTCTTTTAAATTCCAAAAGTGTCGACTTATTTCAATAGAATAAATACTTTCAACATATCCGG
* * *
333292 TAGCGTTTTACCGGTTTTGTCATAATGAAAC-CAGTTTTGTTATATTTTTACCT-ATTATATTGT
66 TAGCGCTTTACCGGTTTTGTCATAATG-AACTCAGTTTTCTCATATTTTTACCTGA-TATATTGT
*
333355 TGTGTATCGATACATATTTATAAAT-TATCGATACTTTTTAGACGCTCTTAATA
129 TATGTATCGATACATATTT-TAAATGTATCGATACTTTTTAGACGCTCTTAATA
** * ** *
333408 CTTTTCTTTTAAATTTTAAAAGTGTCGATACTTATTTCAGTAGAATCGATACTTTCTACATATCC
1 CTTTTCTTTTAAATTCCAAAAGTGTCG--ACTTATTTCAATAGAATAAATACTTTCAACATATCC
* * *
333473 GGTAGCGCTTTACCGGTTTTGTTATATTGAACTCGGTTTTCTCATATTTTTACCTGATATATTGT
64 GGTAGCGCTTTACCGGTTTTGTCATAATGAACTCAGTTTTCTCATATTTTTACCTGATATATTGT
* *
333538 TATGTGTCGATACATATTTTAATTGTATCGATAC
129 TATGTATCGATACATATTTTAAATGTATCGATAC
333572 GTACCGACAA
Statistics
Matches: 143, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
181 25 0.17
182 7 0.05
183 110 0.77
184 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (181 bp):
CTTTTCTTTTAAATTCCAAAAGTGTCGACTTATTTCAATAGAATAAATACTTTCAACATATCCGG
TAGCGCTTTACCGGTTTTGTCATAATGAACTCAGTTTTCTCATATTTTTACCTGATATATTGTTA
TGTATCGATACATATTTTAAATGTATCGATACTTTTTAGACGCTCTTAATA
Found at i:333977 original size:38 final size:36
Alignment explanation
Indices: 333926--334124 Score: 282
Period size: 38 Copynumber: 5.5 Consensus size: 36
333916 TATCTATATA
333926 ATATAGTTTTTAAAACATTTTGAAAACATATATATAAT
1 ATATAGTTTTTAAAACATTTTGAAAAC-T-TATATAAT
333964 ATATAGTTTTTAAAACATTTTG--AA--TATAT-AT
1 ATATAGTTTTTAAAACATTTTGAAAACTTATATAAT
*
333995 ATATAGTTTTTGAAAACATTTTAAAAACTTATATAAT
1 ATATAGTTTTT-AAAACATTTTGAAAACTTATATAAT
334032 ATATAGTTTTTAAAAAACATTTTGAAAACTTATATAAT
1 ATATAGTTTTT--AAAACATTTTGAAAACTTATATAAT
*
334070 ATATAGTTTTGAAAACATTTTTGAAAACTTATATAAT
1 ATATAGTTTTTAAAACA-TTTTGAAAACTTATATAAT
*
334107 ATATAGTTTTGAAAACAT
1 ATATAGTTTTTAAAACAT
334125 ATATAATATA
Statistics
Matches: 149, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
31 13 0.09
32 15 0.10
34 2 0.01
36 14 0.09
37 49 0.33
38 56 0.38
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (36 bp):
ATATAGTTTTTAAAACATTTTGAAAACTTATATAAT
Found at i:334037 original size:37 final size:37
Alignment explanation
Indices: 333926--334124 Score: 281
Period size: 37 Copynumber: 5.5 Consensus size: 37
333916 TATCTATATA
333926 ATATAGTTTTT-AAAACATTTTGAAAACATATATATAAT
1 ATATAGTTTTTGAAAACATTTTGAAAAC-T-TATATAAT
333964 ATATAGTTTTT-AAAACATTTTG--AA--TATAT-AT
1 ATATAGTTTTTGAAAACATTTTGAAAACTTATATAAT
*
333995 ATATAGTTTTTGAAAACATTTTAAAAACTTATATAAT
1 ATATAGTTTTTGAAAACATTTTGAAAACTTATATAAT
*
334032 ATATAGTTTTTAAAAAACATTTTGAAAACTTATATAAT
1 ATATAGTTTTT-GAAAACATTTTGAAAACTTATATAAT
334070 ATATAG-TTTTGAAAACATTTTTGAAAACTTATATAAT
1 ATATAGTTTTTGAAAACA-TTTTGAAAACTTATATAAT
334107 ATATAG-TTTTGAAAACAT
1 ATATAGTTTTTGAAAACAT
334125 ATATAATATA
Statistics
Matches: 149, Mismatches: 4, Indels: 18
0.87 0.02 0.11
Matches are distributed among these distances:
31 13 0.09
32 15 0.10
34 2 0.01
36 14 0.09
37 53 0.36
38 52 0.35
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATAGTTTTTGAAAACATTTTGAAAACTTATATAAT
Found at i:334149 original size:26 final size:26
Alignment explanation
Indices: 334087--334150 Score: 112
Period size: 25 Copynumber: 2.5 Consensus size: 26
334077 TTTGAAAACA
*
334087 TTTTTGAAAACTTATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
334113 -TTTTGAAAACATATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
334138 TTTTTGAAAACAT
1 TTTTTGAAAACAT
334151 TTTAAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 24 0.67
26 12 0.33
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATAG
Found at i:334197 original size:69 final size:67
Alignment explanation
Indices: 334113--334317 Score: 186
Period size: 69 Copynumber: 3.0 Consensus size: 67
334103 TAATATATAG
*
334113 TTTTGAAAACATATATAATATATAGTTTTTGAAAACATTTT-AAAA-ATAATATGTAGTTTTTGA
1 TTTTG-AAA-ATATATAATATATAG-TTTTGAAAACATTTTGAAAATATAATATATAG-TTTT-A
334176 AAAT-AT
61 AAATAAT
* * *
334182 TTTTGAAAATGTAT-ATAATATAG-TTTGAAAATATTTTTTGAAAATATATTATATAGTTTTAAA
1 TTTTGAAAATATATAAT-ATATAGTTTTGAAAACA--TTTTGAAAATATAATATATAGTTTTAAA
334245 ATAAT
63 ATAAT
* * * * *
334250 TTTTGAAAATATATATTATATGGTTTTGAAAACAATTTTTGAAAGCATATAATAAATAATTTAAA
1 TTTTGAAAATATATAATATATAGTTTTGAAAAC-A-TTTTGAAA--ATATAATATATAGTTTTAA
334315 AAT
62 AAT
334318 GTTTTTTATT
Statistics
Matches: 113, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
65 9 0.08
66 2 0.02
67 20 0.18
68 31 0.27
69 32 0.28
70 1 0.01
71 18 0.16
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (67 bp):
TTTTGAAAATATATAATATATAGTTTTGAAAACATTTTGAAAATATAATATATAGTTTTAAAATA
AT
Found at i:334222 original size:35 final size:34
Alignment explanation
Indices: 334171--334293 Score: 160
Period size: 33 Copynumber: 3.6 Consensus size: 34
334161 ATATGTAGTT
*
334171 TTTGAAAAT-ATTTTTGAAAATGTATATAATATAG
1 TTTGAAAATAATTTTTGAAAAT-TATATTATATAG
*
334205 TTTGAAAATATTTTTTGAAAA-TATATTATATAG
1 TTTGAAAATAATTTTTGAAAATTATATTATATAG
* *
334238 TTTTAAAATAATTTTTGAAAATATATATTATATGG
1 TTTGAAAATAATTTTTGAAAAT-TATATTATATAG
*
334273 TTTTGAAAACAATTTTTGAAA
1 -TTTGAAAATAATTTTTGAAA
334294 GCATATAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
33 30 0.38
34 9 0.12
35 21 0.27
36 18 0.23
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (34 bp):
TTTGAAAATAATTTTTGAAAATTATATTATATAG
Found at i:335749 original size:13 final size:13
Alignment explanation
Indices: 335721--335757 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
335711 TTAACCTTTT
*
335721 TTTTATCTACTCAA
1 TTTTATTTA-TCAA
335735 TTTTATTTATCAA
1 TTTTATTTATCAA
335748 TTTTATTTAT
1 TTTTATTTAT
335758 TTTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTATTTATCAA
Found at i:335799 original size:26 final size:26
Alignment explanation
Indices: 335757--335809 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
335747 ATTTTATTTA
335757 TTTTATTATTATTATATTAATATATT
1 TTTTATTATTATTATATTAATATATT
* *
335783 TTTTATT-TTGTTCATATTTATATATT
1 TTTTATTATTATT-ATATTAATATATT
335809 T
1 T
335810 CGCAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTATTATTATTATATTAATATATT
Found at i:335900 original size:12 final size:13
Alignment explanation
Indices: 335878--335906 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
335868 GAATCGGGTT
335878 TTTTAAATTTTAA
1 TTTTAAATTTTAA
335891 TTTT-AATTTTAA
1 TTTTAAATTTTAA
335903 TTTT
1 TTTT
335907 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:338848 original size:23 final size:23
Alignment explanation
Indices: 338822--338899 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
338812 CACCATAGCT
*
338822 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* *
338845 CATAGAATTGCACCGAAGTGTCA
1 CATAGAAATGCACCGAAGTGCCA
* *
338868 CGTAGAATTGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
*
338891 TATA-AAATG
1 CATAGAAATG
338900 TCCCTAAGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 4 0.09
23 43 0.91
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:341920 original size:103 final size:103
Alignment explanation
Indices: 341741--342048 Score: 571
Period size: 103 Copynumber: 3.0 Consensus size: 103
341731 GGGTCTACGC
*
341741 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAATTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
341806 CCCTAGTATATGTATATAATTCTTAAGGAATGATATGT
66 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
*
341844 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
341909 CCCTAATATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
*
341947 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
342012 CCCTAGTATATGTATATGATTCTTAAGGAATGATATG
66 CCCTAGTATATGTATATGATTCTTAAGGAATGATATG
342049 CAGTCCTTAT
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 198 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
Found at i:342106 original size:23 final size:23
Alignment explanation
Indices: 342073--342140 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
342063 ATTATTATAT
342073 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
342096 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
342119 GGCACTTCGTTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
342141 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:347292 original size:103 final size:102
Alignment explanation
Indices: 347114--347431 Score: 542
Period size: 103 Copynumber: 3.2 Consensus size: 102
347104 GGGTCTACGC
347114 GGTCCTTCGGGACATATA-GTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGT-TGAAGTCTGGTGAGACACATACTTGAT
347178 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
65 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
347216 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGT-TGAAGTCTGGTGAGACACATACTTGAT
347281 CCCTAGTATATG--TATGATTCTTAAGGAATGATATGT
65 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
347317 GGTCCTTCGGG--ATATATGTATTCTTTGGAACATG-TGAAGTCTGGTGAGACACATACTTGAT-
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTTGAAGTCTGGTGAGACACATACTTGATC
347378 CCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCTAGTATATGTATATGATTCTTAAGGAATGATATGT
* **
347415 AGTCCTTATGGACATAT
1 GGTCCTTCGGGACATAT
347432 TATATGGCAC
Statistics
Matches: 207, Mismatches: 4, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
96 11 0.05
97 27 0.13
98 32 0.15
99 23 0.11
100 4 0.02
101 35 0.17
102 18 0.09
103 57 0.28
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTTGAAGTCTGGTGAGACACATACTTGATC
CCTAGTATATGTATATGATTCTTAAGGAATGATATGT
Found at i:347470 original size:23 final size:23
Alignment explanation
Indices: 347437--347504 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
347427 CATATTATAT
*
347437 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * *
347460 GGCACTCCGGTTCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
* *
347483 GGCTCTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
347505 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:347724 original size:16 final size:16
Alignment explanation
Indices: 347669--347725 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
347659 GAGAACAATA
*
347669 TGTGATATGTATATGATT
1 TGTGATATG-ATAT-ATG
* *
347687 TGTGATATGATGTGTG
1 TGTGATATGATATATG
**
347703 CATGATATGATATATG
1 TGTGATATGATATATG
347719 TGTGATA
1 TGTGATA
347726 GGGGTTTGGT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 18 0.60
17 3 0.10
18 9 0.30
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.44
Consensus pattern (16 bp):
TGTGATATGATATATG
Found at i:349375 original size:24 final size:20
Alignment explanation
Indices: 349318--349375 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
349308 TTCTTATTAA
*
349318 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
349338 AGTGTATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATT-C-T-AC
349361 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
349376 CTACCCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:352822 original size:23 final size:23
Alignment explanation
Indices: 352796--352850 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
352786 TCGTAAAATG
352796 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* *
352819 CACCAAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTA
352842 CACCGAAGT
1 CACCGAAGT
352851 TCCATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:357006 original size:25 final size:25
Alignment explanation
Indices: 356977--357029 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
356967 TAAATAAGGT
356977 GTTTCAGCAAAGATGGACTAAGGGA
1 GTTTCAGCAAAGATGGACTAAGGGA
357002 GTTTCAGCAAAGATGGACTAAGGGA
1 GTTTCAGCAAAGATGGACTAAGGGA
357027 GTT
1 GTT
357030 AAGGAACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (25 bp):
GTTTCAGCAAAGATGGACTAAGGGA
Found at i:358265 original size:79 final size:77
Alignment explanation
Indices: 358151--358387 Score: 253
Period size: 79 Copynumber: 3.0 Consensus size: 77
358141 TTCCATTCAA
* * * * *
358151 CTCAAGGGCATATTAAATTTATAACATAGCTCAAGGCGAGAAGGGTTATCTGTCAAGAAAAACCT
1 CTCAAGGGAATATTAAATTTACAGCATAACACAAGGCGAGAAGGGTTATCTGTC-A-AAAAACCT
358216 TCGAGTTCGATCAG
64 TCGAGTTCGATCAG
* *
358230 CTCAA-GGATATATTAAATTTACAGTATAACACAAGGCGAGAAGGGTTATTTGTCGATAAAAACC
1 CTCAAGGGA-ATATTAAATTTACAGCATAACACAAGGCGAGAAGGGTTATCTGTC-A-AAAAACC
358294 TTCGAGTTCGATTACATTCAG
63 TTCGAGTTCG-----A-TCAG
* * * * *
358315 CTCAAGGGAATGTTAAATTTACAGCATAACTCAAGGCAAGAAGGGCTATCTGT-AACAAACCTTC
1 CTCAAGGGAATATTAAATTTACAGCATAACACAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTC
358379 GAGTTCGAT
66 GAGTTCGAT
358388 TACATTCAGC
Statistics
Matches: 134, Mismatches: 16, Indels: 19
0.79 0.09 0.11
Matches are distributed among these distances:
76 1 0.01
77 1 0.01
78 2 0.01
79 62 0.46
82 16 0.12
83 1 0.01
84 1 0.01
85 47 0.35
86 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (77 bp):
CTCAAGGGAATATTAAATTTACAGCATAACACAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTC
GAGTTCGATCAG
Found at i:359185 original size:37 final size:37
Alignment explanation
Indices: 359140--359338 Score: 296
Period size: 37 Copynumber: 5.3 Consensus size: 37
359130 GATTTTTGAA
*
359140 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTAAAAACATTTTG
*
359177 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTAAAAACATTTTG
359214 AAAACT-TATATAATATATAGTTTTTAAAAAACATTTTG
1 AAAA-TATATATAATATATAGTTTTT-AAAAACATTTTG
359252 AAAACT-TATATAATATATAG-TTTTAAAAACATTTTTG
1 AAAA-TATATATAATATATAGTTTTTAAAAACA-TTTTG
* *
359289 AAAACATATATAATATATAGTTTTTAAAAACATTTTA
1 AAAATATATATAATATATAGTTTTTAAAAACATTTTG
359326 AAAATAATATATA
1 AAAAT-ATATATA
359339 GTTTTTGAAA
Statistics
Matches: 152, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
36 7 0.05
37 95 0.62
38 50 0.33
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTTAAAAACATTTTG
Found at i:359262 original size:75 final size:74
Alignment explanation
Indices: 359131--359349 Score: 308
Period size: 75 Copynumber: 3.0 Consensus size: 74
359121 TTAAAAATCG
* *
359131 ATTTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATA
1 ATTTTTG--AAAACATATATAATATATAGTTTTTAAAAACATTTTGAAAAT-TATATAATATATA
359196 GTTTTTGAAAAC
63 GTTTTTGAAAAC
*
359208 A-TTTTGAAAACTTATATAATATATAGTTTTTAAAAAACATTTTGAAAACTTATATAATATATAG
1 ATTTTTGAAAACATATATAATATATAGTTTTT-AAAAACATTTTGAAAA-TTATATAATATATAG
*
359272 -TTTTAAAAAC
64 TTTTTGAAAAC
359282 ATTTTTGAAAACATATATAATATATAGTTTTTAAAAACATTTT--AAA--A-ATAATATATAGTT
1 ATTTTTGAAAACATATATAATATATAGTTTTTAAAAACATTTTGAAAATTATATAATATATAGTT
359342 TTTGAAAA
66 TTTGAAAA
359350 TGTATATAAT
Statistics
Matches: 132, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
68 11 0.08
69 9 0.07
72 3 0.02
74 44 0.33
75 58 0.44
76 6 0.05
77 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (74 bp):
ATTTTTGAAAACATATATAATATATAGTTTTTAAAAACATTTTGAAAATTATATAATATATAGTT
TTTGAAAAC
Found at i:359380 original size:92 final size:96
Alignment explanation
Indices: 359247--359442 Score: 264
Period size: 92 Copynumber: 2.1 Consensus size: 96
359237 TTAAAAAACA
359247 TTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTTGAAAACATATATAATATATAGTTT
1 TTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTTG-AAA-ATATATAATATATAG-TT
*
359312 TTAAAAAC-A-TTTTAAAAATA-ATA-TATA-GT
63 TTAAAAACAATTTTTAAAAATATATATTATATGG
* *
359341 TTTTGAAAA-TGTATAT-A-ATATAGTTTTAAAAATATTTTTGAAAATATATATTATATAGTTTT
1 TTTTGAAAACT-TATATAATATATAGTTTTAAAAACATTTTTGAAAATATATAATATATAGTTTT
*
359403 AAAAACAATTTTTGAAAATATATATTATATGG
65 AAAAACAATTTTTAAAAATATATATTATATGG
359435 TTTTGAAA
1 TTTTGAAA
359443 CAATTTTTGA
Statistics
Matches: 92, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
89 10 0.11
90 15 0.16
91 13 0.14
92 25 0.27
93 6 0.07
94 23 0.25
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (96 bp):
TTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTTGAAAATATATAATATATAGTTTTA
AAAACAATTTTTAAAAATATATATTATATGG
Found at i:359391 original size:35 final size:34
Alignment explanation
Indices: 359340--359486 Score: 170
Period size: 35 Copynumber: 4.1 Consensus size: 34
359330 TAATATATAG
*
359340 TTTTTGAAAATGTATATAATATAGTTTTAAAAATA
1 TTTTTGAAAATATATATAATATAGTTTTAAAAA-A
*
359375 TTTTTGAAAATATATATTATATAGTTTTAAAAACAA
1 TTTTTGAAAATATATATAATATAGTTTT-AAAA-AA
* * *
359411 TTTTTGAAAATATATATTATATGGTTTTGAAACAA
1 TTTTTGAAAATATATATAATATAGTTTT-AAAAAA
*
359446 TTTTTGAAAACATATATAATATA-TAATTTAAAAAA
1 TTTTTGAAAATATATATAATATAGT--TTTAAAAAA
359481 TGTTTT
1 T-TTTT
359487 TTATTTTTAT
Statistics
Matches: 98, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
34 1 0.01
35 54 0.55
36 42 0.43
37 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (34 bp):
TTTTTGAAAATATATATAATATAGTTTTAAAAAA
Found at i:359421 original size:36 final size:36
Alignment explanation
Indices: 359340--359468 Score: 181
Period size: 35 Copynumber: 3.6 Consensus size: 36
359330 TAATATATAG
* *
359340 TTTTTGAAAATGTATATAATATAGTTTTAAAAA-TA
1 TTTTTGAAAATATATATAATATAGTTTTAAAAACAA
*
359375 TTTTTGAAAATATATATTATATAGTTTTAAAAACAA
1 TTTTTGAAAATATATATAATATAGTTTTAAAAACAA
* * *
359411 TTTTTGAAAATATATATTATATGGTTTT-GAAACAA
1 TTTTTGAAAATATATATAATATAGTTTTAAAAACAA
*
359446 TTTTTGAAAACATATATAATATA
1 TTTTTGAAAATATATATAATATA
359469 TAATTTAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
35 57 0.67
36 28 0.33
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (36 bp):
TTTTTGAAAATATATATAATATAGTTTTAAAAACAA
Found at i:359499 original size:5 final size:6
Alignment explanation
Indices: 359484--359564 Score: 56
Period size: 6 Copynumber: 12.8 Consensus size: 6
359474 TAAAAAATGT
* **
359484 TTTTTA TTTTTA TTTTTA TTTTTAA TATTATA TTAATA TTATTTA TTTTGTA
1 TTTTTA TTTTTA TTTTTA TTTTT-A T-TTTTA TTTTTA TT-TTTA TTTT-TA
** *
359536 TTTATTA -TTTTA TTAATA TTTTTC TTTTT
1 TTT-TTA TTTTTA TTTTTA TTTTTA TTTTT
359565 TTGATTTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
5 3 0.05
6 38 0.63
7 15 0.25
8 4 0.07
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:359505 original size:18 final size:18
Alignment explanation
Indices: 359484--359564 Score: 56
Period size: 20 Copynumber: 4.3 Consensus size: 18
359474 TAAAAAATGT
*
359484 TTTTTATTTTTATTTTTA
1 TTTTTATTTATATTTTTA
**
359502 TTTTTAATATTATATTAATA
1 TTTTT-AT-TTATATTTTTA
*
359522 TTATTTATTTTGTATTTATTA
1 TT-TTTA-TTTATATTT-TTA
* *
359543 -TTTTATTAATATTTTTC
1 TTTTTATTTATATTTTTA
359560 TTTTT
1 TTTTT
359565 TTGATTTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.04
18 16 0.33
19 6 0.12
20 18 0.38
21 6 0.12
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTTTATTTATATTTTTA
Found at i:361230 original size:2 final size:2
Alignment explanation
Indices: 361218--361291 Score: 139
Period size: 2 Copynumber: 36.5 Consensus size: 2
361208 TGTGAACAAG
361218 AT AT GAT 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
361261 AT 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 AT A
361292 GGTTTATGTG
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 69 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:361748 original size:31 final size:31
Alignment explanation
Indices: 361623--361748 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
361613 AGAGTCGAGG
*
361623 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAG-T
* * *
361655 TTACCTATG-TCTTTCGGGACATATGGATAGT
1 TTACCTATGTTC-TACGGAACATATGGACAGT
* *
361686 ATACCTATGTTCTAAGGAACATATGGACAGT
1 TTACCTATGTTCTACGGAACATATGGACAGT
* * * *
361717 TTACCTAGGTTCTTCGGGACCTATGGACAGT
1 TTACCTATGTTCTACGGAACATATGGACAGT
361748 T
1 T
361749 GTCGAGGTTC
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
31 51 0.66
32 26 0.34
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAGT
Found at i:362484 original size:22 final size:22
Alignment explanation
Indices: 362453--362496 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
362443 TGTAGCAGGG
* *
362453 TACTGTTCACGGTGCTGTTCAT
1 TACTGGTCACGGTACTGTTCAT
362475 TACTGGTCACGGTACTGTTCAT
1 TACTGGTCACGGTACTGTTCAT
362497 ACCATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (22 bp):
TACTGGTCACGGTACTGTTCAT
Found at i:363763 original size:22 final size:22
Alignment explanation
Indices: 363715--363755 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
363705 TATCTACTCA
*
363715 ATTTTATTTATCTATTTTATTT
1 ATTTTATTTATCTATTATATTT
363737 ATTTTA-TTAT-TATTATATT
1 ATTTTATTTATCTATTATATT
363756 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTATTTATCTATTATATTT
Found at i:366487 original size:20 final size:19
Alignment explanation
Indices: 366458--366498 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
366448 CGTCTTTTAA
366458 TTCCCCCTTATTTTCATCCT
1 TTCCCCCTTATTTTCA-CCT
*
366478 TTCCCGCTTATTTTCACCT
1 TTCCCCCTTATTTTCACCT
366497 TT
1 TT
366499 TGCCTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.10, C:0.37, G:0.02, T:0.51
Consensus pattern (19 bp):
TTCCCCCTTATTTTCACCT
Found at i:370031 original size:13 final size:13
Alignment explanation
Indices: 370013--370037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
370003 GACGCACAAT
370013 ACGTCATAAATGC
1 ACGTCATAAATGC
370026 ACGTCATAAATG
1 ACGTCATAAATG
370038 TGTGTCATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
ACGTCATAAATGC
Found at i:370713 original size:19 final size:20
Alignment explanation
Indices: 370677--370714 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
370667 TTGATTACGT
* *
370677 ATTTGAATTTCATTTTTTTG
1 ATTTGAATTTAATATTTTTG
370697 ATTT-AATTTAATATTTTT
1 ATTTGAATTTAATATTTTT
370715 TCCATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTGAATTTAATATTTTTG
Found at i:370713 original size:20 final size:20
Alignment explanation
Indices: 370677--370715 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
370667 TTGATTACGT
*
370677 ATTTGAATTTCATTTTTTTG
1 ATTTGAATTTAATTTTTTTG
370697 ATTT-AATTTAATATTTTTT
1 ATTTGAATTTAAT-TTTTTT
370716 CCATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (20 bp):
ATTTGAATTTAATTTTTTTG
Found at i:382571 original size:16 final size:17
Alignment explanation
Indices: 382550--382582 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
382540 ACCAAGTCAA
*
382550 ATGAAATGTAA-ATTAT
1 ATGAAATATAATATTAT
382566 ATGAAATATAATATTAT
1 ATGAAATATAATATTAT
382583 CCATATAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
ATGAAATATAATATTAT
Found at i:385685 original size:50 final size:51
Alignment explanation
Indices: 385618--385724 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 51
385608 ATTTTTAATT
*
385618 CTATTAATCAAATCACTT-A-ATTATTTAAACAAGACCAATCAAACTAATAA
1 CTATTAATCAAACCACTTAATATTATTTAAA-AAGACCAATCAAACTAATAA
* * *
385668 CTATTAATCAGACCACTTAATTATTATTTAAAGAGACCAATCAAGCTAATAA
1 CTATTAATCAAACCACTTAA-TATTATTTAAAAAGACCAATCAAACTAATAA
385720 CTATT
1 CTATT
385725 GACAATTACC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
50 16 0.32
51 1 0.02
52 23 0.46
53 10 0.20
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (51 bp):
CTATTAATCAAACCACTTAATATTATTTAAAAAGACCAATCAAACTAATAA
Found at i:391282 original size:14 final size:14
Alignment explanation
Indices: 391263--391296 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
391253 ATAGAATATT
*
391263 AATAATGAGAGATA
1 AATAATGAGAGACA
391277 AATAATGAGAGACA
1 AATAATGAGAGACA
391291 AATAAT
1 AATAAT
391297 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (14 bp):
AATAATGAGAGACA
Found at i:392911 original size:18 final size:17
Alignment explanation
Indices: 392883--392919 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
392873 TTTATAGATT
392883 AATTTAAAATAAAAGTA
1 AATTTAAAATAAAAGTA
*
392900 AATTTAAAAATAAAATTA
1 AATTT-AAAATAAAAGTA
392918 AA
1 AA
392920 AATTTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AATTTAAAATAAAAGTA
Found at i:395853 original size:190 final size:188
Alignment explanation
Indices: 395535--395912 Score: 690
Period size: 190 Copynumber: 2.0 Consensus size: 188
395525 TCAGAAGTTA
395535 CCAGTTCACTCACCAATATAATATATATATACACTCGATCAAAAGTTATTTCACTTACAGATCAC
1 CCAGTTCACTCACCAATATAATATATATATACACTCGATCAAAAGTTATTTCACTTACAGATCAC
395600 CATATGACCCAGATGCAACTTTGTTCTCGAACTTCAAGTGTCTAGGGTCAATTTCCCAAACATCA
66 CATATGACCCAGATGCAACTTTGTTCTCGAACTTCAAGTGTCTAGGGTCAATTTCCCAAACATCA
395665 ATCCCGTCA-TAGGAA-TGCCACAT-ATTCTGGTCATCATTGGTGCCCATTTCCTCAT
131 ATCCCGTCATTAGGAATTGCCACATAATTCTGGTCATCATTGGTGCCCATTTCCTCAT
395720 CCAGTTCACTCACCAATATATATATATATATACACTCGATCAGAAAGTTGTTATTTCACTTACAG
1 CCAGTTCACTCACCAATATA-ATATATATATACACTCGATCA-AAA---GTTATTTCACTTACAG
395785 ATCACCATATGACCCAGATGCAACTTTGTTCTCGAACTTCAAGTGTCTAGGGTCAATTTCCCAAA
61 ATCACCATATGACCCAGATGCAACTTTGTTCTCGAACTTCAAGTGTCTAGGGTCAATTTCCCAAA
395850 CATCAATCCCGTCATTAGGAATTGCCACATAATTCTGGTCATCATTGGTGCCCATTTCCTCAT
126 CATCAATCCCGTCATTAGGAATTGCCACATAATTCTGGTCATCATTGGTGCCCATTTCCTCAT
395913 GGTCTCTCGA
Statistics
Matches: 185, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
185 20 0.11
186 21 0.11
187 3 0.02
190 95 0.51
191 6 0.03
192 8 0.04
193 32 0.17
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (188 bp):
CCAGTTCACTCACCAATATAATATATATATACACTCGATCAAAAGTTATTTCACTTACAGATCAC
CATATGACCCAGATGCAACTTTGTTCTCGAACTTCAAGTGTCTAGGGTCAATTTCCCAAACATCA
ATCCCGTCATTAGGAATTGCCACATAATTCTGGTCATCATTGGTGCCCATTTCCTCAT
Found at i:397874 original size:18 final size:18
Alignment explanation
Indices: 397848--397890 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
397838 CTTTAAATGA
* * *
397848 TTTAATTAATTATTTTCT
1 TTTATTTAATTATTATAT
397866 TTTATTTAATTATTATAT
1 TTTATTTAATTATTATAT
397884 TTTATTT
1 TTTATTT
397891 TAAAAACACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:397875 original size:22 final size:23
Alignment explanation
Indices: 397847--397892 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
397837 ACTTTAAATG
*
397847 ATTTAATTAAT-TATTTTCTTTT
1 ATTTAATTAATATATTTTATTTT
*
397869 ATTTAATTATTATATTTTATTTT
1 ATTTAATTAATATATTTTATTTT
397892 A
1 A
397893 AAAACACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTAATTAATATATTTTATTTT
Found at i:399865 original size:31 final size:32
Alignment explanation
Indices: 399810--399871 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
399800 CAAGGTATCC
399810 TAGATTTCTTAAAGACTTTTGTACTAAAAAAA
1 TAGATTTCTTAAAGACTTTTGTACTAAAAAAA
*
399842 TAGATTTCTTAAAGAC-TTTGTACTACAAAA
1 TAGATTTCTTAAAGACTTTTGTACTAAAAAA
399872 GAAAAGCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (32 bp):
TAGATTTCTTAAAGACTTTTGTACTAAAAAAA
Done.