Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 141 of 279
Found at i:45683264 original size:24 final size:24
Alignment explanation
Indices: 45683220--45683271 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
45683210 TGAGTGGGCA
* *
45683220 GCTGTTGCTTTGCTTGCTGCTGCT
1 GCTGTTGCTTAGCTTGATGCTGCT
*
45683244 GCTGTTGCATTAG-TTGATGCTTCT
1 GCTGTTGC-TTAGCTTGATGCTGCT
45683268 GCTG
1 GCTG
45683272 CATAATCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.06, C:0.21, G:0.29, T:0.44
Consensus pattern (24 bp):
GCTGTTGCTTAGCTTGATGCTGCT
Found at i:45685785 original size:12 final size:12
Alignment explanation
Indices: 45685768--45685792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45685758 AGAGACCCAA
45685768 GGAATGAGAAGT
1 GGAATGAGAAGT
45685780 GGAATGAGAAGT
1 GGAATGAGAAGT
45685792 G
1 G
45685793 ACAGCTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
GGAATGAGAAGT
Found at i:45687374 original size:3 final size:3
Alignment explanation
Indices: 45687322--45687355 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
45687312 TGATGATATA
*
45687322 GCT GTT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
45687356 TTGAGGAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.35, T:0.35
Consensus pattern (3 bp):
GCT
Found at i:45701330 original size:17 final size:18
Alignment explanation
Indices: 45701308--45701387 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 18
45701298 GTATTTATTT
45701308 AATTTTTAAAAATT-TAA
1 AATTTTTAAAAATTATAA
45701325 AATTTTTAAAAATTAT-A
1 AATTTTTAAAAATTATAA
** *
45701342 AATCATT-AAATTTATTAA
1 AATTTTTAAAAATTA-TAA
* *
45701360 AAATTATAAAAATTAT-A
1 AATTTTTAAAAATTATAA
*
45701377 TATTTTTAAAA
1 AATTTTTAAAA
45701388 TTTTAAAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
16 6 0.12
17 30 0.62
18 6 0.12
19 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTTTAAAAATTATAA
Found at i:45701343 original size:26 final size:25
Alignment explanation
Indices: 45701314--45701396 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 25
45701304 ATTTAATTTT
45701314 TAAAAATTTAAAATTTTTAAAAATTA
1 TAAAAA-TTAAAATTTTTAAAAATTA
*
45701340 TAAATCATT-AAATTTATTAAAAATTA
1 TAAA-AATTAAAATTT-TTAAAAATTA
* *
45701366 TAAAAATTATATATTTTT-AAAATTT
1 TAAAAATTA-AAATTTTTAAAAATTA
45701391 TAAAAA
1 TAAAAA
45701397 ATAATTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
25 21 0.43
26 22 0.45
27 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAAAATTAAAATTTTTAAAAATTA
Found at i:45701398 original size:35 final size:34
Alignment explanation
Indices: 45701308--45701396 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 34
45701298 GTATTTATTT
* * *
45701308 AATTTTTAAAAATTTAAAATTTTTAAAAATTATA
1 AATTTTTAAAATTTTAAAAATTATAAAAATTATA
** *
45701342 AATCATTAAATTTATTAAAAATTATAAAAATTATA
1 AATTTTTAAAATT-TTAAAAATTATAAAAATTATA
*
45701377 TATTTTTAAAATTTTAAAAA
1 AATTTTTAAAATTTTAAAAA
45701397 ATAATTAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
34 16 0.36
35 28 0.64
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
AATTTTTAAAATTTTAAAAATTATAAAAATTATA
Found at i:45704965 original size:99 final size:99
Alignment explanation
Indices: 45704794--45704991 Score: 396
Period size: 99 Copynumber: 2.0 Consensus size: 99
45704784 TTTGGTCAAC
45704794 CTGATTGACTTGCTCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAA
1 CTGATTGACTTGCTCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAA
45704859 GATGATCCCTTTCTCCCTCAGCAGCTTCACGTCG
66 GATGATCCCTTTCTCCCTCAGCAGCTTCACGTCG
45704893 CTGATTGACTTGCTCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAA
1 CTGATTGACTTGCTCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAA
45704958 GATGATCCCTTTCTCCCTCAGCAGCTTCACGTCG
66 GATGATCCCTTTCTCCCTCAGCAGCTTCACGTCG
45704992 TCTCCCGTGT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.31
Consensus pattern (99 bp):
CTGATTGACTTGCTCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAA
GATGATCCCTTTCTCCCTCAGCAGCTTCACGTCG
Found at i:45705011 original size:99 final size:98
Alignment explanation
Indices: 45704807--45705015 Score: 330
Period size: 99 Copynumber: 2.1 Consensus size: 98
45704797 ATTGACTTGC
45704807 TCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAAGATGATCCCTTTC
1 TCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAAGATGATCCCTTTC
* * * *
45704872 TCCCTCAGCAGCTTCACGTCGCTGATTGACTTGC
66 TCCCTCAGCAGCTTCACGTCGCTCAGTGA-TCGA
45704906 TCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAAGATGATCCCTTTC
1 TCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAAGATGATCCCTTTC
*
45704971 TCCCTCAGCAGCTTCACGTCGTCTCCCGTG-TCGA
66 TCCCTCAGCAGCTTCACGTCG-CT-CAGTGATCGA
*
45705005 TGATCCCATTC
1 TCATCCCATTC
45705016 ATCATCTCGG
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
99 98 0.96
100 2 0.02
101 2 0.02
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (98 bp):
TCATCCCATTCCAAACATCTGCAGCTTCTCCATCGCTCTTCAAGTGATTCAAGATGATCCCTTTC
TCCCTCAGCAGCTTCACGTCGCTCAGTGATCGA
Found at i:45708249 original size:31 final size:32
Alignment explanation
Indices: 45708185--45708265 Score: 137
Period size: 31 Copynumber: 2.5 Consensus size: 32
45708175 ACGTACGTGT
45708185 AAATTGAAAGGTAAGTAAAAAAACAAAATAAAA
1 AAATTGAAAGGTAAGT-AAAAAACAAAATAAAA
45708218 AAATTGAAAGGTAAGTAAAAAACAAAA-AAAA
1 AAATTGAAAGGTAAGTAAAAAACAAAATAAAA
*
45708249 AATTTGAAAGGTAAGTA
1 AAATTGAAAGGTAAGTA
45708266 TTGTCTGCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 20 0.43
32 11 0.23
33 16 0.34
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.17
Consensus pattern (32 bp):
AAATTGAAAGGTAAGTAAAAAACAAAATAAAA
Found at i:45710182 original size:19 final size:19
Alignment explanation
Indices: 45710157--45710213 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
45710147 TTTACAAAAA
45710157 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
45710176 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
45710195 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
45710213 A
1 A
45710214 TTATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.32
19 23 0.68
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:45710225 original size:17 final size:18
Alignment explanation
Indices: 45710170--45710242 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
45710160 AATTCAAAAT
*
45710170 AATTTT-TAA-AATTCAA
1 AATTTTATAATAATTTAA
*
45710186 AATATTTATAAAAATTCTAA
1 AAT-TTTATAATAATT-TAA
* *
45710206 AA-TTTATATTATTTTAA
1 AATTTTATAATAATTTAA
45710223 AATTTTATAATAATTTAA
1 AATTTTATAATAATTTAA
45710241 AA
1 AA
45710243 AAATACTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.07
17 8 0.17
18 27 0.59
19 4 0.09
20 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTTATAATAATTTAA
Found at i:45720380 original size:19 final size:19
Alignment explanation
Indices: 45720352--45720388 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45720342 AATATGTAAT
45720352 TATATCAAATTAAAATTTA
1 TATATCAAATTAAAATTTA
*
45720371 TATATTAAATTAAAATTT
1 TATATCAAATTAAAATTT
45720389 TAACATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATCAAATTAAAATTTA
Found at i:45721929 original size:26 final size:28
Alignment explanation
Indices: 45721878--45721946 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
45721868 ATATTCTATA
* * *
45721878 CTTAATTTTTTAAAAATAATTTTTAATAT
1 CTTAA-TTTTTCAAAATAATTATTAAAAT
45721907 -TTAATTTTTCAAAAT-ATTATTAAAAT
1 CTTAATTTTTCAAAATAATTATTAAAAT
*
45721933 CTTAATTTATCAAA
1 CTTAATTTTTCAAA
45721947 TAACAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.26
27 22 0.63
28 4 0.11
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (28 bp):
CTTAATTTTTCAAAATAATTATTAAAAT
Found at i:45728581 original size:18 final size:19
Alignment explanation
Indices: 45728558--45728599 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
45728548 CCGTAACAGT
*
45728558 AAAAAAA-ATTGAAAAAGA
1 AAAAAAACACTGAAAAAGA
*
45728576 AAAAAAACACTGAAAACGA
1 AAAAAAACACTGAAAAAGA
45728595 AAAAA
1 AAAAA
45728600 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (19 bp):
AAAAAAACACTGAAAAAGA
Found at i:45728582 original size:19 final size:19
Alignment explanation
Indices: 45728558--45728604 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
45728548 CCGTAACAGT
*
45728558 AAAAAAAATTGAAAAAGAA
1 AAAAAAAACTGAAAAAGAA
* *
45728577 AAAAAACACTGAAAACGAA
1 AAAAAAAACTGAAAAAGAA
45728596 AAAATAAAA
1 AAAA-AAAA
45728605 ATAAAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAAAACTGAAAAAGAA
Found at i:45728789 original size:22 final size:22
Alignment explanation
Indices: 45728764--45728810 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
45728754 AGGCGGAGAA
*
45728764 AAAGAAAAGAA-AGAGAAGAAGG
1 AAAGAAAAGAAGA-AGAAGAAAG
*
45728786 AAAGAAGAGAAGAAGAAGAAAG
1 AAAGAAAAGAAGAAGAAGAAAG
45728808 AAA
1 AAA
45728811 AAGAAGGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
AAAGAAAAGAAGAAGAAGAAAG
Found at i:45729409 original size:25 final size:26
Alignment explanation
Indices: 45729381--45729442 Score: 65
Period size: 30 Copynumber: 2.3 Consensus size: 26
45729371 GTTTTTTGTT
45729381 AAAATAATA-TAAAAAATAAAATAT-G
1 AAAATAATATTAAAAAATAAAAT-TCG
45729406 AAAATAGTATATTTTAAAAAATAAAATTCG
1 AAAATA--ATA--TTAAAAAATAAAATTCG
45729436 AAAATAA
1 AAAATAA
45729443 AAAAATATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
25 6 0.19
27 3 0.10
28 1 0.03
29 1 0.03
30 20 0.65
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (26 bp):
AAAATAATATTAAAAAATAAAATTCG
Found at i:45729546 original size:136 final size:138
Alignment explanation
Indices: 45729393--45729969 Score: 530
Period size: 154 Copynumber: 4.1 Consensus size: 138
45729383 AATAATATAA
* * * *
45729393 AAAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATTCGAAAATAAAAAAATATGAACAAG
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAATATGAACAAA
* *
45729458 GTGCCAAAGTCAGGGTTATTTATTAAATTAATAT-AAAAA-ACTTAAATAATACATTTGAAAGAT
66 GTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAATAATACATTTGAAACAT
45729521 TTTATGCT
131 TTTATGCT
* *
45729529 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG---A-AAAAAAATATGAATAAA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAATATGAACAAA
* **
45729590 GTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACA
66 GTGCCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAACACTTAAATAATACATTTGAAACA
**
45729655 TTATGTACTAAAATAATAT
130 -T-T-T--T---AT--GCT
* *
45729674 AAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAAAAATTACGA
1 --A-AAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAAT-AAAAAAA-TATGA
* * *
45729739 AGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAGTAATACATTTG
61 ACAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAA-AAACACTTAAATAATACATTTG
*
45729804 AAACATTTTTTGCTAAAATAATAT
125 AAACATTTTATGC----------T
* * *
45729828 AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAATACGAATA
1 --AAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAATATGAACA
* * * * *
45729888 AAGTGCTAAAATCAAGGTTATTTATTGAAA-AAATATAAATAATACTTAAATAATACATTTGAAA
64 AAGTGCCAAAATCAGGGTTATTTATT-AAATTAATATAAAAAACACTTAAATAATACATTTGAAA
* * *
45729952 CATTATGTACT
128 CATTTTATGCT
45729963 AAAATAA
1 AAAATAA
45729970 TATGAAGAAA
Statistics
Matches: 371, Mismatches: 36, Indels: 71
0.78 0.08 0.15
Matches are distributed among these distances:
132 45 0.12
133 8 0.02
134 5 0.01
135 23 0.06
136 40 0.11
137 1 0.00
138 1 0.00
140 1 0.00
143 2 0.01
145 30 0.08
146 39 0.11
147 11 0.03
148 41 0.11
149 1 0.00
151 2 0.01
152 1 0.00
153 52 0.14
154 68 0.18
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (138 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAATATGAACAAA
GTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAATAATACATTTGAAACAT
TTTATGCT
Found at i:45729643 original size:153 final size:146
Alignment explanation
Indices: 45729529--45730026 Score: 472
Period size: 146 Copynumber: 3.3 Consensus size: 146
45729519 ATTTTATGCT
*
45729529 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATATGAATAAAGTGC
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATACGAATAAAGTGC
45729594 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATT--
66 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAAT--A--T-AAAC-TTAA
*
45729657 ATGTAC--T-AAAATAATATAA
125 ATATACTTTGAAAATAATATAA
* *
45729676 AGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAAAAATTACGAAG
1 A-AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAAA-TACGAAT
** * * * *
45729741 AAAGTG-TCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAGT-A-ATACATTT
59 AAAGTGCT-AAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATATAAACTT
* **
45729803 GAAACATTTTTTGCTAAAATAATATAA
123 -AAATATACTTTG--AAAATAATATAA
45729830 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-AAAAAAATACGAATAAAGTGC
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATACGAATAAAGTGC
* * * *
45729894 TAAAATCAAGGTTATTTATTGAAAAAATAT-AAATAATACTTAAATAATACATTTGAAACATT--
66 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAAT--A--T-AAAC-TTAA
*
45729956 ATGTAC--T-AAAATAATATGAA
125 ATATACTTTGAAAATAATAT-AA
*
45729976 GAAATAAAATACGAAAATAATATATTTT-AAAAATAAGT-TACGAAAATAAAA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAA-TATACGAAAA-AAAA
45730027 ATATGNTAAA
Statistics
Matches: 292, Mismatches: 30, Indels: 58
0.77 0.08 0.15
Matches are distributed among these distances:
145 33 0.11
146 73 0.25
147 15 0.05
148 43 0.15
149 3 0.01
150 3 0.01
151 2 0.01
152 2 0.01
153 53 0.18
154 65 0.22
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (146 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATACGAATAAAGTGC
TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATATAAACTTAAATATAC
TTTGAAAATAATATAA
Found at i:45729710 original size:132 final size:132
Alignment explanation
Indices: 45729440--45729698 Score: 308
Period size: 132 Copynumber: 1.9 Consensus size: 132
45729430 AATTCGAAAA
* * **
45729440 TAAAAAAATATGAACAAGGTGCCAAAGTCAGGGTTATTTATTAAATTAATATAAAAAACTTAAAT
1 TAAAAAAATATGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACTTAAAT
* * * * ***
45729505 AATACATTTGAAAGATTTTATGCTAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATA
66 AATACATTTGAAACATTATATACTAAAATAAAATAAGAAAATAATATATACGAAAAAATAATATA
45729570 CG
131 CG
* * *
45729572 AAAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTA
1 TAAAAAAATATGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATAT--AAAAA-ACTTA
* *
45729637 AATAATACATTTGAAACATTATGTACTAAAATAATATAA-AGAAATAA-A-ATACGAAAATAATA
63 AATAATACATTTGAAACATTATATACTAAAATAAAATAAGA-AAATAATATATACGAAAA-AATA
45729699 TATTTTAAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
132 45 0.42
133 6 0.06
134 11 0.10
135 44 0.42
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (132 bp):
TAAAAAAATATGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACTTAAAT
AATACATTTGAAACATTATATACTAAAATAAAATAAGAAAATAATATATACGAAAAAATAATATA
CG
Found at i:45729981 original size:146 final size:145
Alignment explanation
Indices: 45729530--45730026 Score: 714
Period size: 154 Copynumber: 3.3 Consensus size: 145
45729520 TTTTATGCTA
*
45729530 AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATATGAATAAAGTGCT
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATACGAATAAAGTGCT
45729595 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATG
66 AAAATCAGGGTTATTTATT-AAAAAATAT-AAAAAACACTTAAATAATACATTTGAAACATTATG
45729660 TACTAAAATAATATAAAG
129 TACTAAAATAATAT-AAG
* *
45729678 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAAAAAATTACGAAGAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAAA-TACGAATAA
* *
45729743 AGTG-TCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAGTAATACATTTGAAA
60 AGTGCT-AAAATCAGGGTTATTTATTAAA-AAATATAAA-AAACACTTAAATAATACATTTGAAA
* * * *
45729807 CATTTTTTGCTAAAATAATATAAA
122 CATTATGTACTAAAATAATATAAG
45729831 AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-AAAAAAATACGAATAAAGTGCT
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATACGAATAAAGTGCT
* * *
45729895 AAAATCAAGGTTATTTATTGAAAAAATATAAATAATACTTAAATAATACATTTGAAACATTATGT
66 AAAATCAGGGTTATTTATT-AAAAAATATAAAAAACACTTAAATAATACATTTGAAACATTATGT
45729960 ACTAAAATAATATGAAG
130 ACTAAAATAATAT-AAG
45729977 AAATAAAATACGAAAATAATATATTTT-AAAAATAAGT-TACGAAAATAAAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAA-TATACGAAAA-AAAA
45730027 ATATGNTAAA
Statistics
Matches: 314, Mismatches: 20, Indels: 31
0.86 0.05 0.08
Matches are distributed among these distances:
145 52 0.17
146 71 0.23
147 15 0.05
148 41 0.13
153 58 0.18
154 77 0.25
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (145 bp):
AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAATACGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAATATAAAAAACACTTAAATAATACATTTGAAACATTATGTA
CTAAAATAATATAAG
Found at i:45730067 original size:30 final size:30
Alignment explanation
Indices: 45729977--45730085 Score: 130
Period size: 30 Copynumber: 3.6 Consensus size: 30
45729967 TAATATGAAG
45729977 AAATAAAATACGAAAATAATATATTTT-AA
1 AAATAAAATACGAAAATAATATATTTTAAA
** * **
45730006 AAATAAGTTACGAAAATAAAAATATGNTAAA
1 AAATAAAATACGAAAAT-AATATATTTTAAA
* *
45730037 AAATAAAATATGAAAATAGTATATTTTAAA
1 AAATAAAATACGAAAATAATATATTTTAAA
*
45730067 AAATAAAATTCGAAAATAA
1 AAATAAAATACGAAAATAA
45730086 AAAAATATGA
Statistics
Matches: 63, Mismatches: 15, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
29 15 0.24
30 32 0.51
31 16 0.25
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (30 bp):
AAATAAAATACGAAAATAATATATTTTAAA
Found at i:45730321 original size:341 final size:353
Alignment explanation
Indices: 45729664--45730363 Score: 1005
Period size: 342 Copynumber: 2.0 Consensus size: 353
45729654 ATTATGTACT
* *
45729664 AAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAATAAAA
1 AAAAT-ATGTAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAA
* * *
45729729 AAAATTACGAAGAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAGT
65 AAAATTACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAAT
*
45729794 AATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTA
130 AATACATTTGAAACA--TTTT-CT--AAT-ACAT-AAAAATAAAATACGAAAATAATATATTTTA
*
45729859 AAAAATAATATACGAAAAAAATACGAATAAAGTGCTAAAATCAAGGTTATTTATTGAAAAAATAT
188 AAAAATAATATACGAAAAAAATACGAATAAAGTGCTAAAATCAAGCTTATTTATTGAAAAAATAT
* * * *
45729924 AAATAATACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATGAAGAAATAAAATACG
253 AAAAAACACTTAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAGAAATAAAATACG
*
45729989 AAAATAATATATTTT-AAAAATAAGTTACGAAAATA
318 AAAATAATATATTTTAAAAAATAAGATACGAAAATA
* * *
45730024 AAAATATGNTAAA-AAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATTCGAAAAT-AAA
1 AAAATATG-TAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAA
* * *
45730087 AAAA-TATGAACAAGGTGCCAAAGTCAGGGTTATTTATTAAATTAATAT-AA-AAA-ACTTAAAT
65 AAAATTACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAAT
* * * *
45730148 AATACATTTGAAAGA-TTT-T-AT-CCT-AAAATACAATACGCAAATAATATATTTTAAAAAATA
130 AATACATTTGAAACATTTTCTAATACATAAAAATAAAATACGAAAATAATATATTTTAAAAAATA
45730208 ATATACGAAAAAAATACGAATAAAGTGCTAAAATC-AGACTTATTTATT-AAAAAATATAAAAAA
195 ATATACGAAAAAAATACGAATAAAGTGCTAAAATCAAG-CTTATTTATTGAAAAAATATAAAAAA
*
45730271 CACTTAAATAATACATTTAAAATATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATA
259 CACTTAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATA
45730336 ATATATTTTAAAAAATAAGATACGAAAA
324 ATATATTTTAAAAAATAAGATACGAAAA
45730364 AAATACGAAT
Statistics
Matches: 314, Mismatches: 23, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
341 86 0.27
342 95 0.30
344 1 0.00
346 2 0.01
349 1 0.00
351 3 0.01
354 21 0.07
355 3 0.01
356 2 0.01
357 39 0.12
358 7 0.02
359 45 0.14
360 9 0.03
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (353 bp):
AAAATATGTAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAA
AAATTACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAGAAACACTTAAATA
ATACATTTGAAACATTTTCTAATACATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAA
TATACGAAAAAAATACGAATAAAGTGCTAAAATCAAGCTTATTTATTGAAAAAATATAAAAAACA
CTTAAATAATACATTTAAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAAT
ATATTTTAAAAAATAAGATACGAAAATA
Found at i:45730322 original size:145 final size:145
Alignment explanation
Indices: 45730173--45730626 Score: 680
Period size: 147 Copynumber: 3.1 Consensus size: 145
45730163 TTTTATCCTA
* * *
45730173 AAATACAATACGCAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTA
** *
45730238 AAATCAGACTTATTTATTAAAAAATATAAAAAACACTTAAATAATACATTTAAAATATTATGTAC
66 AAATCAGGGTTATTTATTAAAAAATATAAAAAACACTTAAATAATACATTTAAAACATTATGTAC
45730303 TAAAATAATATAAAG
131 TAAAATAATATAAAG
*
45730318 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATGAAGTGCTA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTA
* *
45730383 AAATCAGGGTTATTTATTAAAAAAATATAAAAAAAAACTTAAATAATACATTCAAAACATTATGT
66 AAATCAGGGTTATTTATT-AAAAAATAT-AAAAAACACTTAAATAATACATTTAAAACATTATGT
*
45730448 ACTAAAATGATATAAAG
129 ACTAAAATAATATAAAG
* *
45730465 AAATAAAATATGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAAGAAAGTG-TC
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCT-
* * * * *
45730529 AAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTACATAATACATTTGAAACATTTTTT
65 AAAATCAGGGTTATTTATTAAA-AAATATAAAAAACACTTAAATAATACATTTAAAACATTATGT
*
45730594 GCTAAAATAATAT-AA-
129 ACTAAAATAATATAAAG
*
45730609 AAATAATATACGAAAATA
1 AAATAAAATACGAAAATA
45730627 TTTTACTTAT
Statistics
Matches: 281, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
144 16 0.06
145 79 0.28
146 54 0.19
147 132 0.47
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.28
Consensus pattern (145 bp):
AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAATACGAATAAAGTGCTA
AAATCAGGGTTATTTATTAAAAAATATAAAAAACACTTAAATAATACATTTAAAACATTATGTAC
TAAAATAATATAAAG
Found at i:45732380 original size:50 final size:50
Alignment explanation
Indices: 45732321--45732425 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 50
45732311 TTACATGACT
45732321 AATACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATATTAC
1 AATACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATATTAC
45732371 AATACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATATTAC
1 AATACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATATTAC
45732421 -ATACT
1 AATACT
45732426 CACATTAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 5 0.09
50 50 0.91
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (50 bp):
AATACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATATTAC
Found at i:45737128 original size:46 final size:44
Alignment explanation
Indices: 45737054--45737303 Score: 186
Period size: 46 Copynumber: 5.5 Consensus size: 44
45737044 ATTAATGCCG
* * *
45737054 TGTCCCAGACAGGTCTTACACTGACACATGTAACCGT-GCTGACGCA
1 TGTCCCAGACATGTCTTACACTGACACATCT---CGTAGCCGACGCA
*
45737100 TGTTCCAGACATGTCTTACACT-AGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTGA-CACATCTCGTAGCCGACGCA
* * * *
45737144 TGTCCCAGACATGTCTGACACTGGCTAAAATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAC--ACATCTCGTA-GCCGACGCA
* * * * *
45737190 TGTCCTAGACATGTCTTACACTGGCTC-TCATACTGTGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGACACATC-T-C-GTAGCCGACGCA
* * * * *
45737236 TGTCCCAGACATGTCTTACACTGGCTC-TCATACTGTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTGACACATC-T-C-GTAGCCGACGCA
45737282 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
45737304 AGCCCTCGTC
Statistics
Matches: 178, Mismatches: 16, Indels: 20
0.83 0.07 0.09
Matches are distributed among these distances:
43 5 0.03
44 30 0.17
45 3 0.02
46 140 0.79
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (44 bp):
TGTCCCAGACATGTCTTACACTGACACATCTCGTAGCCGACGCA
Found at i:45737257 original size:92 final size:89
Alignment explanation
Indices: 45737097--45737354 Score: 279
Period size: 92 Copynumber: 2.8 Consensus size: 89
45737087 CCGTGCTGAC
* * *
45737097 GCATGTTCCAGACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
1 GCATG-TCCAGACATGTCTTACACTAGCCTCATCTCGT-GCCGATGCATGTCCCAGACATGTCTT
45737161 ACACTGGCTAAAAT-CTCGAGGCCGAT
64 ACACTGGCTAAAATACT-GAGGCCGAT
*
45737187 GCATGTCCTAGACATGTCTTACACTGGCTCTCATACT-GTGGCCGATGCATGTCCCAGACATGTC
1 GCATGTCC-AGACATGTCTTACACTAGC-CTCAT-CTCGT-GCCGATGCATGTCCCAGACATGTC
*** * *
45737251 TTACACTGGCTCTCATACTGTGGCTGAT
62 TTACACTGGCTAAAATACTGAGGCCGAT
* * *
45737279 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGATGCCATGTCCCATACATGGT
1 GCATGT-CCAGACATGTCTTACACTAG-CCTCATCTC-GTGCCGATG-CATGTCCCAGACAT-GT
45737344 CTTACACTGGC
61 CTTACACTGGC
45737355 ACACAAATCT
Statistics
Matches: 143, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
89 3 0.02
90 22 0.15
91 2 0.01
92 82 0.57
93 21 0.15
94 13 0.09
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (89 bp):
GCATGTCCAGACATGTCTTACACTAGCCTCATCTCGTGCCGATGCATGTCCCAGACATGTCTTAC
ACTGGCTAAAATACTGAGGCCGAT
Found at i:45737326 original size:46 final size:44
Alignment explanation
Indices: 45737097--45737354 Score: 241
Period size: 46 Copynumber: 5.6 Consensus size: 44
45737087 CCGTGCTGAC
* * * *
45737097 GCATGTTCCAGACATGTCTTACACTAGCACATC-TCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTGGCTC-TCATC-TATGCCGAT
* *** *
45737141 GCATGTCCCAGACATGTCTGACACTGGCTAAAATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCATCT--ATGCCGAT
* *
45737187 GCATGTCCTAGACATGTCTTACACTGGCTCTCATACTGTGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCAT-CTAT-GCCGAT
* *
45737233 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCAT-CTAT-GCCGAT
* * *
45737279 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTCTCATCT--ATGCCGAT
*
45737325 GCCATGTCCCATACATGGTCTTACACTGGC
1 G-CATGTCCCAGACAT-GTCTTACACTGGC
45737355 ACACAAATCT
Statistics
Matches: 180, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.01
44 27 0.15
45 3 0.02
46 121 0.67
47 16 0.09
48 12 0.07
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (44 bp):
GCATGTCCCAGACATGTCTTACACTGGCTCTCATCTATGCCGAT
Found at i:45742717 original size:29 final size:29
Alignment explanation
Indices: 45742675--45742732 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
45742665 TCTTCCAAAG
45742675 TTGGTCTAAAACGATTTGATGTTCTCGTT
1 TTGGTCTAAAACGATTTGATGTTCTCGTT
45742704 TTGGTCTAAAACGATTTGATGTTCTCGTT
1 TTGGTCTAAAACGATTTGATGTTCTCGTT
45742733 CTATTAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (29 bp):
TTGGTCTAAAACGATTTGATGTTCTCGTT
Found at i:45743440 original size:16 final size:15
Alignment explanation
Indices: 45743414--45743499 Score: 50
Period size: 16 Copynumber: 5.3 Consensus size: 15
45743404 AAAATTTATA
*
45743414 CCTTCTTTTTTCTTTT
1 CCTTC-TTTTTCTTCT
*
45743430 CTTTCTGTTTTCCTTCT
1 CCTTCT-TTTT-CTTCT
45743447 CCTTCTTTTTCTTCATT
1 CCTTCTTTTTCTTC--T
*
45743464 CTCTTCTCCTTTCTT-T
1 C-CTTCT-TTTTCTTCT
45743480 CCCTT-TATTTTCTTCT
1 -CCTTCT-TTTTCTTCT
45743496 CCTT
1 CCTT
45743500 GCTGCTGATT
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 16 0.29
16 17 0.30
17 12 0.21
18 5 0.09
19 6 0.11
ACGTcount: A:0.02, C:0.31, G:0.01, T:0.65
Consensus pattern (15 bp):
CCTTCTTTTTCTTCT
Found at i:45743493 original size:25 final size:25
Alignment explanation
Indices: 45743437--45743499 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
45743427 TTTCTTTCTG
**
45743437 TTTTCCTTCTCC-TTCTTTTTCTTCA
1 TTTT-CTTCTCCTTTCTTTCCCTTCA
* *
45743462 TTCTCTTCTCCTTTCTTTCCCTTTA
1 TTTTCTTCTCCTTTCTTTCCCTTCA
45743487 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
45743500 GCTGCTGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTCTTCTCCTTTCTTTCCCTTCA
Found at i:45743647 original size:19 final size:19
Alignment explanation
Indices: 45743623--45743667 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
45743613 TTTATTTTTA
45743623 TTTTTTTCGTTTTCAGTGT-
1 TTTTTTTCGTTTTCAGT-TC
*
45743642 TTTTTTTCTTTTTCAGTTC
1 TTTTTTTCGTTTTCAGTTC
45743661 TTTTTTT
1 TTTTTTT
45743668 TATTGTTGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (19 bp):
TTTTTTTCGTTTTCAGTTC
Found at i:45744531 original size:28 final size:28
Alignment explanation
Indices: 45744478--45744532 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
45744468 ATAATCACAA
* **
45744478 AATTTAAATCTTAATCATCATTCAAACC
1 AATTTAAATCTCAATCATCACCCAAACC
45744506 AATTTAAATCATCAATCAT-ACCCAAAC
1 AATTTAAATC-TCAATCATCACCCAAAC
45744533 ACATATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (28 bp):
AATTTAAATCTCAATCATCACCCAAACC
Found at i:45747140 original size:21 final size:21
Alignment explanation
Indices: 45747114--45747156 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
45747104 TTAAGACTTA
45747114 TCTCCCACCCTGACTAAAACC
1 TCTCCCACCCTGACTAAAACC
45747135 TCTCCCACCCTGACTAAAACC
1 TCTCCCACCCTGACTAAAACC
45747156 T
1 T
45747157 TATTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.47, G:0.05, T:0.21
Consensus pattern (21 bp):
TCTCCCACCCTGACTAAAACC
Found at i:45748390 original size:27 final size:27
Alignment explanation
Indices: 45748360--45748422 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
45748350 GTGGGGATTG
*
45748360 AGGTGGAGGGGAGGGGGGTTGTGATGA
1 AGGTGGAGGGGAGGGGGGTGGTGATGA
45748387 AGGTGGAGGGGAGGGGGGTGGTGATGA
1 AGGTGGAGGGGAGGGGGGTGGTGATGA
45748414 AGGTGGAGG
1 AGGTGGAGG
45748423 AGAAGAGACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.00, G:0.65, T:0.16
Consensus pattern (27 bp):
AGGTGGAGGGGAGGGGGGTGGTGATGA
Found at i:45752909 original size:21 final size:21
Alignment explanation
Indices: 45752883--45752922 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
45752873 CTAATGGAGG
45752883 GTTAAAAAGGCTAATGTAATT
1 GTTAAAAAGGCTAATGTAATT
45752904 GTTAAAAAGGCTAATGTAA
1 GTTAAAAAGGCTAATGTAA
45752923 CCTTAAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (21 bp):
GTTAAAAAGGCTAATGTAATT
Found at i:45752928 original size:20 final size:21
Alignment explanation
Indices: 45752884--45752929 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
45752874 TAATGGAGGG
**
45752884 TTAAAAAGGCTAATGTAATTG
1 TTAAAAAGGCTAATGTAATCC
45752905 TTAAAAAGGCTAATGTAA-CC
1 TTAAAAAGGCTAATGTAATCC
45752925 TTAAA
1 TTAAA
45752930 TGCAGTGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (21 bp):
TTAAAAAGGCTAATGTAATCC
Found at i:45753246 original size:15 final size:14
Alignment explanation
Indices: 45753210--45753262 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
45753200 TCCTTCAATT
*
45753210 TTTTAAAAAAAAAA
1 TTTTAAAAATAAAA
**
45753224 TTAAAAAAATATAAA
1 TTTTAAAAATA-AAA
45753239 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
45753253 GTTGTTAAAA
1 -TT-TTAAAA
45753263 TCTTGATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 11 0.35
15 14 0.45
16 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:45754214 original size:19 final size:20
Alignment explanation
Indices: 45754175--45754214 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
45754165 TATTAAAAAA
*
45754175 TATATTTTTAGTAATTAAGT
1 TATATTATTAGTAATTAAGT
*
45754195 TATATTATTA-TAATTGAGT
1 TATATTATTAGTAATTAAGT
45754214 T
1 T
45754215 TTTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
TATATTATTAGTAATTAAGT
Found at i:45755897 original size:35 final size:35
Alignment explanation
Indices: 45755851--45755923 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
45755841 CTTTGTTTTT
45755851 GACTTTATTAAAAATTTTGGAAGTTTTCATTGATG
1 GACTTTATTAAAAATTTTGGAAGTTTTCATTGATG
45755886 GACTTTATTAAAAATTTTGGAAGTTTTCATTGATG
1 GACTTTATTAAAAATTTTGGAAGTTTTCATTGATG
45755921 GAC
1 GAC
45755924 ATTAGATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (35 bp):
GACTTTATTAAAAATTTTGGAAGTTTTCATTGATG
Found at i:45757695 original size:20 final size:22
Alignment explanation
Indices: 45757670--45757725 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
45757660 CAGAATACCC
45757670 GACACATAAAGTGCCT-AAAT-
1 GACACATAAAGTGCCTAAAATA
** *
45757690 GACACACGAGGTGCCTAAAATA
1 GACACATAAAGTGCCTAAAATA
45757712 CGACACATAAAGTG
1 -GACACATAAAGTG
45757726 TCTGATCGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 13 0.48
21 4 0.15
23 10 0.37
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (22 bp):
GACACATAAAGTGCCTAAAATA
Found at i:45758903 original size:23 final size:23
Alignment explanation
Indices: 45758876--45758932 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
45758866 AAATTAGTTA
*
45758876 TTTTATTACAAGTGTA-C-ATAT
1 TTTTATTACAAATGTACCAATAT
45758897 CTATTTATTACAAATGTACCAATAT
1 -T-TTTATTACAAATGTACCAATAT
45758922 TTTTATTACAA
1 TTTTATTACAA
45758933 TTGTCATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 24 0.77
24 2 0.06
25 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (23 bp):
TTTTATTACAAATGTACCAATAT
Found at i:45759180 original size:3 final size:3
Alignment explanation
Indices: 45759172--45759248 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
45759162 ATATGAAACC
*
45759172 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- TTA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** *
45759218 ATA A-A ACC ATA CTA ATA ATTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
45759249 AATTTTAGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 5 0.08
3 55 0.87
4 3 0.05
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:45763870 original size:24 final size:24
Alignment explanation
Indices: 45763834--45763975 Score: 117
Period size: 24 Copynumber: 5.9 Consensus size: 24
45763824 GGGTCAACAT
*
45763834 TGGCACTAAGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
45763858 TGGCACTATGTGTGCGGAATTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* *
45763882 TGGCACTATGTGTGCTGATTTGGA
1 TGGCACTATGTGTGCGGATTTGAA
* * ** * * * *
45763906 TGTCAATACATGAGTGAATCTTCAA
1 TGGCACTATGTGTGCGGAT-TTGAA
* *
45763931 -GGCACTATGTGTGCGG-TGTAGCA
1 TGGCACTATGTGTGCGGAT-TTGAA
*
45763954 TGGCACTATGTGTGCGAATTTG
1 TGGCACTATGTGTGCGGATTTG
45763976 TTTAGCACTA
Statistics
Matches: 87, Mismatches: 28, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
23 3 0.03
24 80 0.92
25 4 0.05
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:45767210 original size:40 final size:40
Alignment explanation
Indices: 45767157--45767358 Score: 172
Period size: 40 Copynumber: 5.0 Consensus size: 40
45767147 TTTTAAAATT
*
45767157 CAGAGCAATAGCGGCGTTTTAAAAAAAACGCCGGTAAAAA
1 CAGAGCAATAGCGGCGTTTTAAAAAAAACGCCGCTAAAAA
* * * *
45767197 CAGAGCAACAGCGGCGTTTTAGTAAAAAATGCCGCTAAAAC
1 CAGAGCAATAGCGGCGTTTTA-AAAAAAACGCCGCTAAAAA
* * * * *
45767238 CATAGCATTAGCGGCGCTTTCAATAAAACGCCGCTAAAAA
1 CAGAGCAATAGCGGCGTTTTAAAAAAAACGCCGCTAAAAA
* * ** ****
45767278 CTGAGCATTAGCGGCACTTTCGGTAAAACGCCGCTAAAAA
1 CAGAGCAATAGCGGCGTTTTAAAAAAAACGCCGCTAAAAA
* ***
45767318 CCAGAGCATTAGCGGCGCTTTT-GCTAAAACGCCGCTAAAAA
1 -CAGAGCAATAGCGGCG-TTTTAAAAAAAACGCCGCTAAAAA
45767359 TCCCATAACC
Statistics
Matches: 136, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 70 0.51
41 63 0.46
42 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.18
Consensus pattern (40 bp):
CAGAGCAATAGCGGCGTTTTAAAAAAAACGCCGCTAAAAA
Found at i:45767318 original size:81 final size:80
Alignment explanation
Indices: 45767157--45767358 Score: 226
Period size: 81 Copynumber: 2.5 Consensus size: 80
45767147 TTTTAAAATT
* * * * * *
45767157 CAGAGCAATAGCGGCGTTTTAAAAAAAACGCCGGTAAAAACAGAGCAACAGCGGCGTTTTAGTAA
1 CAGAGCATTAGCGGCGCTTTAAATAAAACGCCGCTAAAAACAGAGCAACAGCGGCCTTTCAGT-A
*
45767222 AAAATGCCGCTAAAAC
65 AAAACGCCGCTAAAAC
* * * ** *
45767238 CATAGCATTAGCGGCGCTTTCAATAAAACGCCGCTAAAAACTGAGCATTAGCGGCACTTTCGGT-
1 CAGAGCATTAGCGGCGCTTTAAATAAAACGCCGCTAAAAACAGAGCAACAGCGGC-CTTTCAGTA
45767302 AAAACGCCGCTAAAAAC
65 AAAACGCCGCT-AAAAC
***
45767319 CAGAGCATTAGCGGCGCTTTTGCTAAAACGCCGCTAAAAA
1 CAGAGCATTAGCGGCGCTTTAAATAAAACGCCGCTAAAAA
45767359 TCCCATAACC
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 10 0.10
81 87 0.85
82 5 0.05
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.18
Consensus pattern (80 bp):
CAGAGCATTAGCGGCGCTTTAAATAAAACGCCGCTAAAAACAGAGCAACAGCGGCCTTTCAGTAA
AAACGCCGCTAAAAC
Found at i:45767524 original size:14 final size:14
Alignment explanation
Indices: 45767502--45767541 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
45767492 TTAATTATCA
* *
45767502 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
45767516 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
45767530 ATATGGTTTAAG
1 TTATGGTTTAAG
45767542 CAGGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:45768372 original size:28 final size:25
Alignment explanation
Indices: 45768341--45768399 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
45768331 AGGTTTAGTG
*
45768341 TTTAGAGTATTAGATTTAGGGTTTTAAA
1 TTTAGAGTA-TA-ATTTAGGATTTT-AA
*
45768369 TTTAGAGTATAATTTTGGATTTTAA
1 TTTAGAGTATAATTTAGGATTTTAA
45768394 TTTAGA
1 TTTAGA
45768400 AGATAAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 10 0.34
27 2 0.07
28 9 0.31
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (25 bp):
TTTAGAGTATAATTTAGGATTTTAA
Found at i:45768419 original size:15 final size:15
Alignment explanation
Indices: 45768399--45768430 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
45768389 TTTAATTTAG
*
45768399 AAGATAAATGTATAT
1 AAGATAAATATATAT
45768414 AAGATAAATATATAT
1 AAGATAAATATATAT
45768429 AA
1 AA
45768431 AATATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:45768469 original size:24 final size:24
Alignment explanation
Indices: 45768402--45768469 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
45768392 AATTTAGAAG
* *
45768402 ATAAATGTATATAAGATAAATATAT
1 ATAAATATATATATGA-AAATATAT
* *
45768427 ATAAA-ATATTATTTTAAAATATAT
1 ATAAATATA-TATATGAAAATATAT
45768451 ATAAATATATATATGAAAA
1 ATAAATATATATATGAAAA
45768470 GTGGTTTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATAAATATATATATGAAAATATAT
Found at i:45770011 original size:18 final size:17
Alignment explanation
Indices: 45769990--45770032 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
45769980 ATCTTAATGA
45769990 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
45770008 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
45770025 TCGATGAT
1 T-GATGAT
45770033 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:45773060 original size:44 final size:44
Alignment explanation
Indices: 45773000--45773129 Score: 192
Period size: 43 Copynumber: 3.0 Consensus size: 44
45772990 AACTGCGCAA
* * * *
45773000 ATTAGCGGCGTTTTTTAAAAAAGCGCTGCTAAAGGTCCTGGTC-
1 ATTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCG
*
45773043 ATTAGCGGCGTTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCG
1 ATTAGCGGCG-TTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCG
45773088 A-TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTC
1 ATTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTC
45773130 TATAACGGCG
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
43 42 0.53
44 36 0.46
45 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
ATTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCG
Found at i:45775212 original size:50 final size:50
Alignment explanation
Indices: 45775136--45775312 Score: 230
Period size: 50 Copynumber: 3.5 Consensus size: 50
45775126 CCATGGAAAC
*
45775136 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTTATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * * *
45775186 AAGTGATAAGTAATAACTTCGACTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
45775236 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * *
45775286 CAACTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
45775313 CTGATCAGTG
Statistics
Matches: 108, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
50 85 0.79
51 23 0.21
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:45775498 original size:31 final size:31
Alignment explanation
Indices: 45775290--45775491 Score: 314
Period size: 31 Copynumber: 6.5 Consensus size: 31
45775280 AAATGACAAC
45775290 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
45775321 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
45775352 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
45775383 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
45775414 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* **
45775445 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
45775476 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
45775492 TGGCTACAAG
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 157 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:45775509 original size:7 final size:7
Alignment explanation
Indices: 45775497--45775525 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
45775487 AGCTTTGGCT
45775497 ACAAGTG
1 ACAAGTG
45775504 ACAAGTG
1 ACAAGTG
45775511 ACAAGTG
1 ACAAGTG
45775518 ACAAGTG
1 ACAAGTG
45775525 A
1 A
45775526 TTTCTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ACAAGTG
Found at i:45775598 original size:47 final size:48
Alignment explanation
Indices: 45775529--45775654 Score: 166
Period size: 47 Copynumber: 2.7 Consensus size: 48
45775519 CAAGTGATTT
* *
45775529 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * *
45775576 CTGTATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * *
45775624 C-GTGTAAGACCATAGCTGGGCTATGGCATCA
1 CTGTATAAGACCATATCTGGGATATGGCATCA
45775655 TTATGTAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 66 0.96
48 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (48 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
Found at i:45781890 original size:6 final size:6
Alignment explanation
Indices: 45781842--45781874 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
45781832 AAGGGGAATT
45781842 GCCTAA GCCTAA GCCTAA GCCTAA GCCTAA GCC
1 GCCTAA GCCTAA GCCTAA GCCTAA GCCTAA GCC
45781875 AAACCAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.15
Consensus pattern (6 bp):
GCCTAA
Found at i:45782319 original size:42 final size:42
Alignment explanation
Indices: 45782266--45782368 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 42
45782256 TTAAGATTTA
* * *
45782266 AAAAATATAAAAAATATTCTTTTATA-ATTTTA-T-ACATTTTT
1 AAAAATTTAAAAAATAAT-TTTTATATATTTAATTGA-ATTTTT
45782307 AATAAATTT-AAAAATAATTTTTATATATTTAATTGAATTTTT
1 AA-AAATTTAAAAAATAATTTTTATATATTTAATTGAATTTTT
*
45782349 AAAATTTTAAAAAATTAATT
1 AAAAATTTAAAAAA-TAATT
45782369 AAATATTGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
40 7 0.13
41 20 0.38
42 19 0.37
43 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (42 bp):
AAAAATTTAAAAAATAATTTTTATATATTTAATTGAATTTTT
Found at i:45791528 original size:20 final size:20
Alignment explanation
Indices: 45791490--45791545 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
45791480 GCCGAAACTT
* *
45791490 CATTTTAA-CATAATATTTA
1 CATTTTAATTATATTATTTA
45791509 CATTTTAATTATATTATTTA
1 CATTTTAATTATATTATTTA
45791529 CATTTTAATTATATTAT
1 CATTTTAATTATATTAT
45791546 GCATACTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
CATTTTAATTATATTATTTA
Found at i:45791555 original size:20 final size:20
Alignment explanation
Indices: 45791512--45791555 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
45791502 ATATTTACAT
** *
45791512 TTTAATTATATTATTTACAT
1 TTTAATTATATTATGCACAC
*
45791532 TTTAATTATATTATGCATAC
1 TTTAATTATATTATGCACAC
45791552 TTTA
1 TTTA
45791556 TTACCACTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAATTATATTATGCACAC
Found at i:45806758 original size:31 final size:29
Alignment explanation
Indices: 45806718--45806803 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 29
45806708 TATGATATTT
* *
45806718 TAAA-ATAAAAAATAATTTACTTATTAATTA
1 TAAATATAAAAAATAATTTA--TAATAAATA
45806748 TATAAT-TAAAAAATAATATTATAATAAATA
1 TA-AATATAAAAAATAAT-TTATAATAAATA
45806778 TAAATATAACAAAATAATTT-TAATAA
1 TAAATATAA-AAAATAATTTATAATAA
45806804 TATTGATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
29 9 0.18
30 16 0.33
31 21 0.43
32 3 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAATATAAAAAATAATTTATAATAAATA
Found at i:45806806 original size:28 final size:26
Alignment explanation
Indices: 45806741--45806806 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
45806731 AATTTACTTA
*
45806741 TTAATTATATAATTAAAAAATAATAT
1 TTAATAATATAATTAAAAAATAATAT
45806767 TATAATAAATATAAATATAACAAAATAAT-T
1 T-TAAT-AATAT-AAT-TAA-AAAATAATAT
45806797 TTAATAATAT
1 TTAATAATAT
45806807 TGATAATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 1 0.03
27 4 0.12
28 9 0.26
29 7 0.21
30 5 0.15
31 8 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TTAATAATATAATTAAAAAATAATAT
Found at i:45821831 original size:120 final size:120
Alignment explanation
Indices: 45821665--45822252 Score: 1122
Period size: 120 Copynumber: 4.9 Consensus size: 120
45821655 ACTAGCATCA
* * *
45821665 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
*
45821730 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
45821785 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
* *
45821850 AATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
45821905 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
45821970 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
45822025 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
45822090 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
45822145 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
45822210 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
45822253 TAAATATGAT
Statistics
Matches: 460, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 460 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
Found at i:45821989 original size:18 final size:17
Alignment explanation
Indices: 45821961--45821995 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45821951 ATTATTAAGA
*
45821961 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
45821978 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
45821996 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:45822109 original size:18 final size:17
Alignment explanation
Indices: 45822081--45822115 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45822071 ATTATTAAGA
*
45822081 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
45822098 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
45822116 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:45822229 original size:18 final size:17
Alignment explanation
Indices: 45822201--45822235 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45822191 ATTATTAAGA
*
45822201 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
45822218 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
45822236 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:45822449 original size:44 final size:45
Alignment explanation
Indices: 45822400--45822490 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
45822390 ACCTCTATTC
* * *
45822400 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
45822444 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
45822489 CA
1 CA
45822491 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:45822492 original size:16 final size:16
Alignment explanation
Indices: 45822471--45822539 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
45822461 GATTAGCTAT
45822471 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
45822487 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
45822504 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
45822520 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
45822536 TACA
1 TACA
45822540 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:45822513 original size:33 final size:32
Alignment explanation
Indices: 45822471--45822539 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
45822461 GATTAGCTAT
45822471 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
45822504 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
45822536 TACA
1 TACA
45822540 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:45842115 original size:51 final size:51
Alignment explanation
Indices: 45842039--45842152 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
45842029 AGGGACAAGC
* *
45842039 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
*
45842090 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
45842141 GACAAGTGATAA
1 GACAAGTGATAA
45842153 ATGTGATCAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:45877233 original size:30 final size:30
Alignment explanation
Indices: 45877171--45877233 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
45877161 TTTCAATTAC
*
45877171 AATCAAATTTTCATATATATAATTGCATCA
1 AATCAAATTTTCATATATATAATTGCACCA
*
45877201 AATCAAA-TTTCAATATATATAATTGTACCA
1 AATCAAATTTTC-ATATATATAATTGCACCA
45877231 AAT
1 AAT
45877234 TAAAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (30 bp):
AATCAAATTTTCATATATATAATTGCACCA
Found at i:45877365 original size:21 final size:20
Alignment explanation
Indices: 45877326--45877365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
45877316 TTAATGTTTA
* *
45877326 ATATTATTTATGTTGTATTG
1 ATATTATTTAGGTTATATTG
45877346 ATATTACTTTAGGTTATATT
1 ATATTA-TTTAGGTTATATT
45877366 TTTCGTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (20 bp):
ATATTATTTAGGTTATATTG
Found at i:45882613 original size:10 final size:10
Alignment explanation
Indices: 45882598--45882622 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45882588 GACATTTTAC
45882598 TATTTATTAT
1 TATTTATTAT
45882608 TATTTATTAT
1 TATTTATTAT
45882618 TATTT
1 TATTT
45882623 TATTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTATTAT
Found at i:45884336 original size:40 final size:40
Alignment explanation
Indices: 45884280--45884416 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
45884270 CTCGAGAATA
* * * * * *
45884280 TAAAGTGAATAAGATTTGTTCCTGATTCACTATGGTAATT
1 TAAAGCGAATAGGATTTATTCATGATTCACTACGGTAACT
*
45884320 TAAAGTGAATAGGATTTATTCATGATTCACTACGGTAACT
1 TAAAGCGAATAGGATTTATTCATGATTCACTACGGTAACT
* * * **
45884360 TAAGGCGGATAGAATTTATTTTTGATTCACTACGGTAACT
1 TAAAGCGAATAGGATTTATTCATGATTCACTACGGTAACT
* *
45884400 TAAGGCGGATAGGATTT
1 TAAAGCGAATAGGATTT
45884417 GACCTGAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (40 bp):
TAAAGCGAATAGGATTTATTCATGATTCACTACGGTAACT
Found at i:45891419 original size:29 final size:29
Alignment explanation
Indices: 45891386--45891443 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
45891376 CAAATCATAG
45891386 TATGTCATGCAAATTTCGGAATCCATTGA
1 TATGTCATGCAAATTTCGGAATCCATTGA
45891415 TATGTCATGCAAATTTCGGAATCCATTGA
1 TATGTCATGCAAATTTCGGAATCCATTGA
45891444 CAACTCATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (29 bp):
TATGTCATGCAAATTTCGGAATCCATTGA
Found at i:45891451 original size:29 final size:29
Alignment explanation
Indices: 45891390--45891451 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
45891380 TCATAGTATG
* **
45891390 TCATGCAAATTTCGGAATCCATTGATATG
1 TCATGCAAATTTCGGAATCCATTGACAAC
45891419 TCATGCAAATTTCGGAATCCATTGACAAC
1 TCATGCAAATTTCGGAATCCATTGACAAC
45891448 TCAT
1 TCAT
45891452 CTCATCAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (29 bp):
TCATGCAAATTTCGGAATCCATTGACAAC
Found at i:45894656 original size:14 final size:14
Alignment explanation
Indices: 45894637--45894667 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
45894627 TGCTACTATT
45894637 TTACTATTATGTTG
1 TTACTATTATGTTG
*
45894651 TTACTATTTTGTTG
1 TTACTATTATGTTG
45894665 TTA
1 TTA
45894668 TGGTTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:45894733 original size:30 final size:30
Alignment explanation
Indices: 45894698--45894760 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
45894688 ACTTATTTTA
45894698 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
45894728 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
45894758 TTG
1 TTG
45894761 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:45894905 original size:12 final size:12
Alignment explanation
Indices: 45894884--45894917 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
45894874 TATATTTTTT
*
45894884 AAAATTATATAA
1 AAAATAATATAA
45894896 AAAATAATATAA
1 AAAATAATATAA
*
45894908 AAATTAATAT
1 AAAATAATAT
45894918 GGGCGGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:45895803 original size:12 final size:12
Alignment explanation
Indices: 45895786--45895810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45895776 CATCAATTAA
45895786 CCTAATGTATTT
1 CCTAATGTATTT
45895798 CCTAATGTATTT
1 CCTAATGTATTT
45895810 C
1 C
45895811 ATATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (12 bp):
CCTAATGTATTT
Found at i:45900885 original size:13 final size:14
Alignment explanation
Indices: 45900869--45900904 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
45900859 CAATCTCATA
45900869 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
45900882 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
45900895 TCTC-ATTTCA
1 TCTCAATTTCA
45900905 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:45900894 original size:18 final size:19
Alignment explanation
Indices: 45900856--45900896 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
45900846 TGGTTCATGT
45900856 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
45900875 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
45900893 TTTC
1 TTTC
45900897 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:45901028 original size:23 final size:23
Alignment explanation
Indices: 45901001--45901058 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
45900991 GCAGATTCCT
*
45901001 CCCAAACACGCCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
*
45901024 TCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
45901047 CCCAAACACACC
1 CCCAAACACACC
45901059 CGGAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.41, G:0.05, T:0.09
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:45902445 original size:31 final size:32
Alignment explanation
Indices: 45902387--45902450 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
45902377 CATACATTTG
*
45902387 TCATAATTTAATATATTTATTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
45902419 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
45902450 T
1 T
45902451 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:45902982 original size:13 final size:14
Alignment explanation
Indices: 45902964--45902992 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
45902954 GATTAACTTC
45902964 ATAAATATTTT-TA
1 ATAAATATTTTCTA
45902977 ATAAATATTTTCTA
1 ATAAATATTTTCTA
45902991 AT
1 AT
45902993 CTATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:45906574 original size:42 final size:42
Alignment explanation
Indices: 45906528--45906614 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
45906518 TGTCAAATAT
*
45906528 AAATATTACATTAGACCAAAATATATATAATCACGGCTTTAA
1 AAATATTACATTAGACCAAAATATATATAATCACGGCATTAA
45906570 AAATATTACATTAGACCAAAATATATATAATCACGGCATTAA
1 AAATATTACATTAGACCAAAATATATATAATCACGGCATTAA
45906612 AAA
1 AAA
45906615 ATATCAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.29
Consensus pattern (42 bp):
AAATATTACATTAGACCAAAATATATATAATCACGGCATTAA
Found at i:45917680 original size:24 final size:25
Alignment explanation
Indices: 45917634--45917682 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
45917624 TCAAATATAC
*
45917634 TTAAATATATATTTATATCAAATTT
1 TTAAATATATATTAATATCAAATTT
*
45917659 TTAAATATA-ATTAATATTAAATTT
1 TTAAATATATATTAATATCAAATTT
45917683 AAACAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAATATATATTAATATCAAATTT
Found at i:45917937 original size:3 final size:3
Alignment explanation
Indices: 45917929--45917953 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45917919 GTAAAATGAT
45917929 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
45917954 AAGTGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45934660 original size:67 final size:67
Alignment explanation
Indices: 45934546--45934680 Score: 207
Period size: 67 Copynumber: 2.0 Consensus size: 67
45934536 AACACTACAA
* *
45934546 AACAAGGGAAAAGGAAATAGGGTAAGCACTTTATGCTTAGTAAGCTCATATAGCAAGAATTATAC
1 AACAAGGGAAAAGGAAATAAGGTAAGCACTTTATGCTTAGTAAGCTCATATAACAAGAATTATAC
45934611 TT
66 TT
* * * * *
45934613 AACAGGGGAAAAGGAAATAAGGTAAGCACTTTGTGCTTAGTACGCTCATGTAACAAGAATTATGC
1 AACAAGGGAAAAGGAAATAAGGTAAGCACTTTATGCTTAGTAAGCTCATATAACAAGAATTATAC
45934678 TT
66 TT
45934680 A
1 A
45934681 CCTAATATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (67 bp):
AACAAGGGAAAAGGAAATAAGGTAAGCACTTTATGCTTAGTAAGCTCATATAACAAGAATTATAC
TT
Found at i:45936435 original size:16 final size:16
Alignment explanation
Indices: 45936414--45936445 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45936404 TATTAACACT
45936414 CCATAAATATTTATAA
1 CCATAAATATTTATAA
45936430 CCATAAATATTTATAA
1 CCATAAATATTTATAA
45936446 AAATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
CCATAAATATTTATAA
Found at i:45947432 original size:54 final size:54
Alignment explanation
Indices: 45947370--45947478 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
45947360 AAAGGACTGA
* **
45947370 ATTGTAATAGGTGTAAAAGTTGCTAGAGTGATTAAATAGCTTATTAGTCTAATG
1 ATTGTAATAGGTGTAAAAGTTGCTAGAGTGATTAAATAACTTAAGAGTCTAATG
45947424 ATTGTAATAGGTGTAAAAGTTGCTAGAGTGATTAAATAACTTAAGAGTCTAATG
1 ATTGTAATAGGTGTAAAAGTTGCTAGAGTGATTAAATAACTTAAGAGTCTAATG
45947478 A
1 A
45947479 GAAAGGATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.35
Consensus pattern (54 bp):
ATTGTAATAGGTGTAAAAGTTGCTAGAGTGATTAAATAACTTAAGAGTCTAATG
Found at i:45955065 original size:25 final size:25
Alignment explanation
Indices: 45955035--45955152 Score: 98
Period size: 24 Copynumber: 4.8 Consensus size: 25
45955025 GCCCTCTCTC
*
45955035 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGT
* *
45955060 GAGCCAT-TAACGGGAAGCTTATCT
1 GAGCCATATAACGGGAAGCTCATGT
* * * * **
45955084 GGGCTATATAATGGAAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATGT
* *
45955109 GAGCCATA-ATCGGGAAGCTCATGG
1 GAGCCATATAACGGGAAGCTCATGT
* *
45955133 GAGGCA-ATAACGGGTAGCTC
1 GAGCCATATAACGGGAAGCTC
45955153 CGAAGAGCTA
Statistics
Matches: 71, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.01
24 45 0.63
25 25 0.35
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:45955075 original size:24 final size:24
Alignment explanation
Indices: 45955035--45955201 Score: 88
Period size: 24 Copynumber: 6.9 Consensus size: 24
45955025 GCCCTCTCTC
*
45955035 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCAT-TAACGGGAAGCTCATGT
* *
45955060 GAGCCATTAACGGGAAGCTTATCT
1 GAGCCATTAACGGGAAGCTCATGT
* * * * **
45955084 GGGCTATATAATGGAAAGCTCATAA
1 GAGCCAT-TAACGGGAAGCTCATGT
*
45955109 GAGCCA-TAATCGGGAAGCTCATGG
1 GAGCCATTAA-CGGGAAGCTCATGT
* * * * *
45955133 GAGGCAATAACGGGTAGCTC-CGAA
1 GAGCCATTAACGGGAAGCTCATG-T
* * **
45955157 GAGCTATTAACGGGAAGTTCCGGAT
1 GAGCCATTAACGGGAAGCTCATG-T
*
45955182 -AGCCATTAAAGGGAAGCTCA
1 GAGCCATTAACGGGAAGCTCA
45955202 CAAAGAGCCT
Statistics
Matches: 106, Mismatches: 31, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
23 4 0.04
24 74 0.70
25 28 0.26
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.20
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCATGT
Found at i:45955215 original size:25 final size:26
Alignment explanation
Indices: 45955182--45955238 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
45955172 AGTTCCGGAT
45955182 AGCCATTAA-AGGGAAGCTCACAAAG
1 AGCCATTAATAGGGAAGCTCACAAAG
* * * *
45955207 AGCCTTTAATCGGGACGCTCACGAAG
1 AGCCATTAATAGGGAAGCTCACAAAG
45955233 AGCCAT
1 AGCCAT
45955239 ATAACGGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.16
Consensus pattern (26 bp):
AGCCATTAATAGGGAAGCTCACAAAG
Found at i:45955226 original size:26 final size:26
Alignment explanation
Indices: 45955089--45955253 Score: 78
Period size: 24 Copynumber: 6.7 Consensus size: 26
45955079 TATCTGGGCT
* * *
45955089 ATATAATGGAAAGCTCA-TAAGAGCC
1 ATATAACGGGAAGCTCACAAAGAGCC
* *** *
45955114 ATA-ATCGGGAAGCTCA-TGGGAGGC
1 ATATAACGGGAAGCTCACAAAGAGCC
* * *
45955138 A-ATAACGGGTAGCTC-CGAAGAGCT
1 ATATAACGGGAAGCTCACAAAGAGCC
* ** *
45955162 AT-TAACGGGAAGTTC-CGGATAGCC
1 ATATAACGGGAAGCTCACAAAGAGCC
*
45955186 AT-TAAAGGGAAGCTCACAAAGAGCC
1 ATATAACGGGAAGCTCACAAAGAGCC
* * *
45955211 -TTTAATCGGGACGCTCACGAAGAGCC
1 ATATAA-CGGGAAGCTCACAAAGAGCC
*
45955237 ATATAACGGGATGCTCA
1 ATATAACGGGAAGCTCA
45955254 TAAGAACTGT
Statistics
Matches: 105, Mismatches: 28, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
23 1 0.01
24 61 0.58
25 12 0.11
26 27 0.26
27 4 0.04
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
ATATAACGGGAAGCTCACAAAGAGCC
Found at i:45956997 original size:17 final size:16
Alignment explanation
Indices: 45956962--45957006 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
45956952 CCTTATATAC
*
45956962 TAAATAAAATAATAAT
1 TAAATAAAATAAAAAT
*
45956978 TAAATATAATTAAAAAT
1 TAAATA-AAATAAAAAT
45956995 TAAATCAAAATA
1 TAAAT-AAAATA
45957007 TTAATAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 17 0.71
18 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAAAATAAAAAT
Found at i:45957421 original size:273 final size:273
Alignment explanation
Indices: 45956934--45957483 Score: 1046
Period size: 273 Copynumber: 2.0 Consensus size: 273
45956924 AGATGAAGAG
*
45956934 AATTCTTCATATTTCTTTCCTTATATACTAAATAAAATAATAATTAAATATAATTAAAAATTAAA
1 AATTCTTCATATTTCTTTCCTTATATACTAAATAAAATAATAATAAAATATAATTAAAAATTAAA
*
45956999 TCAAAATATTAATAAACTAATATTTATTTGATTAATCTAAAATATCATCAACATCATCAATACCC
66 TCAAAATATTAATAAACTAAGATTTATTTGATTAATCTAAAATATCATCAACATCATCAATACCC
45957064 TTCAAAATTATCTTTCTTGCTAAATGACCATTTTGCCCCTTATGATTCTTCAAATTCCTTCATTG
131 TTCAAAATTATCTTTCTTGCTAAATGACCATTTTGCCCCTTATGATTCTTCAAATTCCTTCATTG
45957129 ACTCATCACTTATTTTGATAAAATTATGATTTAACCCTTCATACTTTTTTCATTTATTCAATTTG
196 ACTCATCACTTATTTTGATAAAATTATGATTTAACCCTTCATACTTTTTTCATTTATTCAATTTG
45957194 GTCCTAATTCATC
261 GTCCTAATTCATC
45957207 AATTCTTCATATTTCTTTCCTTATATACTAAATAAAATAATAATAAAATATAATTAAAAATTAAA
1 AATTCTTCATATTTCTTTCCTTATATACTAAATAAAATAATAATAAAATATAATTAAAAATTAAA
* * *
45957272 TCAAGATATTAGTAAACTAAGATTTATTTGATTAATCTAAAATATCATCAACATCATCATTACCC
66 TCAAAATATTAATAAACTAAGATTTATTTGATTAATCTAAAATATCATCAACATCATCAATACCC
*
45957337 TTCAAAATTATCTTTCTTGCTAAATGACCATTTTGCCCCTTATGATTCTTCAAATTCTTTCATTG
131 TTCAAAATTATCTTTCTTGCTAAATGACCATTTTGCCCCTTATGATTCTTCAAATTCCTTCATTG
45957402 ACTCATCACTTATTTTGATAAAATTATGATTTAACCCTTCATACTTTTTTCATTTATTCAATTTG
196 ACTCATCACTTATTTTGATAAAATTATGATTTAACCCTTCATACTTTTTTCATTTATTCAATTTG
45957467 GTCCTAATTCATC
261 GTCCTAATTCATC
45957480 AATT
1 AATT
45957484 TTCCTTAGTT
Statistics
Matches: 271, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
273 271 1.00
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (273 bp):
AATTCTTCATATTTCTTTCCTTATATACTAAATAAAATAATAATAAAATATAATTAAAAATTAAA
TCAAAATATTAATAAACTAAGATTTATTTGATTAATCTAAAATATCATCAACATCATCAATACCC
TTCAAAATTATCTTTCTTGCTAAATGACCATTTTGCCCCTTATGATTCTTCAAATTCCTTCATTG
ACTCATCACTTATTTTGATAAAATTATGATTTAACCCTTCATACTTTTTTCATTTATTCAATTTG
GTCCTAATTCATC
Found at i:45958681 original size:30 final size:30
Alignment explanation
Indices: 45958647--45958709 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
45958637 ACTTAACAAG
45958647 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
45958677 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
45958707 CAA
1 CAA
45958710 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:45960455 original size:16 final size:16
Alignment explanation
Indices: 45960434--45960468 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
45960424 TAAAAAATTG
* *
45960434 ATATTTGTTTTTTTTA
1 ATATTTATTTATTTTA
45960450 ATATTTATTTATTTTA
1 ATATTTATTTATTTTA
45960466 ATA
1 ATA
45960469 CCTTATAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATATTTATTTATTTTA
Found at i:45975276 original size:3 final size:3
Alignment explanation
Indices: 45975268--45975293 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45975258 CACCCTTTTC
45975268 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
45975294 GTTGAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:45976387 original size:21 final size:20
Alignment explanation
Indices: 45976359--45976401 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
45976349 ATCTGTAAGG
45976359 GGGGGGGGGGGTCTTGATTT
1 GGGGGGGGGGGTCTTGATTT
*
45976379 GGNGGGGGGGGTTCTTGATTT
1 GG-GGGGGGGGGTCTTGATTT
45976400 GG
1 GG
45976402 CTATCTCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.05, C:0.05, G:0.58, T:0.30
Consensus pattern (20 bp):
GGGGGGGGGGGTCTTGATTT
Found at i:46001093 original size:13 final size:14
Alignment explanation
Indices: 46001069--46001100 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
46001059 TTTTTTTCGT
46001069 TTAAATAAATGAAA
1 TTAAATAAATGAAA
46001083 TTAAA-AAATGAAA
1 TTAAATAAATGAAA
46001096 -TAAAT
1 TTAAAT
46001101 TATAAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
TTAAATAAATGAAA
Found at i:46002461 original size:38 final size:38
Alignment explanation
Indices: 46002410--46002482 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
46002400 TCACATGTCT
46002410 AAGTTAGATAAAGTATAATAATCAATAAAAAATTATAA
1 AAGTTAGATAAAGTATAATAATCAATAAAAAATTATAA
46002448 AAGTTAGATAAAGTATAATAATCAATAAAAAATTA
1 AAGTTAGATAAAGTATAATAATCAATAAAAAATTA
46002483 CAAACATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (38 bp):
AAGTTAGATAAAGTATAATAATCAATAAAAAATTATAA
Found at i:46003384 original size:6 final size:6
Alignment explanation
Indices: 46003373--46003410 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
46003363 TTTTATTCTG
46003373 TCTGCT TCTGCT TCTGCT TCTGCT TCTGCT TCTGCT TC
1 TCTGCT TCTGCT TCTGCT TCTGCT TCTGCT TCTGCT TC
46003411 CTAATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.16, T:0.50
Consensus pattern (6 bp):
TCTGCT
Found at i:46006817 original size:35 final size:36
Alignment explanation
Indices: 46006771--46006847 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
46006761 TTCAGCTTGG
46006771 TATTCTCAGAAATTA-GAGGGCATTCTGCATTGGAT
1 TATTCTCAGAAATTAGGAGGGCATTCTGCATTGGAT
46006806 TATTCTCAGAAATTAGGAGGGCATTCTGCATTGGAT
1 TATTCTCAGAAATTAGGAGGGCATTCTGCATTGGAT
46006842 TATTCT
1 TATTCT
46006848 AAAATATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 15 0.37
36 26 0.63
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (36 bp):
TATTCTCAGAAATTAGGAGGGCATTCTGCATTGGAT
Found at i:46007636 original size:38 final size:38
Alignment explanation
Indices: 46007593--46007665 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
46007583 TATTATAAAA
46007593 AATAAAATAAGAATAAAAACATTCCCACTAACCTTTAT
1 AATAAAATAAGAATAAAAACATTCCCACTAACCTTTAT
46007631 AATAAAATAAGAATAAAAACATTCCCACTAACCTT
1 AATAAAATAAGAATAAAAACATTCCCACTAACCTT
46007666 GATAGTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (38 bp):
AATAAAATAAGAATAAAAACATTCCCACTAACCTTTAT
Found at i:46008999 original size:3 final size:3
Alignment explanation
Indices: 46008991--46009015 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46008981 CTGTTGATCG
46008991 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
46009016 AATAGTCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:46018205 original size:17 final size:17
Alignment explanation
Indices: 46018185--46018218 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46018175 AGGTTTAGGT
46018185 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
46018202 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
46018219 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:46021236 original size:16 final size:15
Alignment explanation
Indices: 46021210--46021244 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
46021200 TGATGTGAAT
46021210 AATATAAAATATTAA
1 AATATAAAATATTAA
*
46021225 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
46021241 AATA
1 AATA
46021245 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:46021416 original size:20 final size:20
Alignment explanation
Indices: 46021359--46021418 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
46021349 AATACTACAT
46021359 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
46021378 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
46021401 AAATATGTACATAATATA
1 AAATATGTACATAATATA
46021419 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:46021477 original size:27 final size:25
Alignment explanation
Indices: 46021371--46021538 Score: 91
Period size: 25 Copynumber: 6.7 Consensus size: 25
46021361 ATATGTACAT
* * *
46021371 ATATAAAAAATAAATACGT-GAT-A
1 ATATAAAAAATATATACATAAATAA
* *
46021394 ATATTAAAAATATGTACAT-AATATA
1 ATATAAAAAATATATACATAAATA-A
* * *
46021419 GTGTAAAAAATACATACAT-AATATA
1 ATATAAAAAATATATACATAAATA-A
46021444 AT-T--AAAATATATACATAAGATAA
1 ATATAAAAAATATATACATAA-ATAA
*
46021467 CATATAAAAAATATATATATAAATAA
1 -ATATAAAAAATATATACATAAATAA
*
46021493 TATAGTATTAAAGATATATACATAAA-ATA
1 -ATA-TA--AAAAATATATACATAAATA-A
* *
46021522 ATATAATATATATATAC
1 ATATAAAAAATATATAC
46021539 TTAATATAGA
Statistics
Matches: 115, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
22 12 0.10
23 19 0.17
24 6 0.05
25 33 0.29
26 7 0.06
27 18 0.16
28 4 0.03
29 16 0.14
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (25 bp):
ATATAAAAAATATATACATAAATAA
Found at i:46021488 original size:15 final size:15
Alignment explanation
Indices: 46021468--46021533 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
46021458 ATAAGATAAC
46021468 ATATAAAAAATATAT
1 ATATAAAAAATATAT
*
46021483 ATATAAATAATATAGT
1 ATATAAAAAATATA-T
*
46021499 AT-T-AAAGATATAT
1 ATATAAAAAATATAT
*
46021512 ACATAAAATAATATAAT
1 ATATAAAA-AATAT-AT
46021529 ATATA
1 ATATA
46021534 TATACTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 2 0.05
14 8 0.20
15 17 0.43
16 7 0.17
17 6 0.15
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (15 bp):
ATATAAAAAATATAT
Found at i:46021509 original size:29 final size:27
Alignment explanation
Indices: 46021428--46021526 Score: 112
Period size: 27 Copynumber: 3.6 Consensus size: 27
46021418 AGTGTAAAAA
*
46021428 ATACATACATAATATA-ATTAAAATAT
1 ATACATAAATAATATATATTAAAATAT
* *
46021454 ATACATAAGATAACATATA-AAAAATAT
1 ATACATAA-ATAATATATATTAAAATAT
*
46021481 ATATATAAATAATATAGTATTAAAGATAT
1 ATACATAAATAATATA-TATTAAA-ATAT
46021510 ATACATAAAATAATATA
1 ATACAT-AAATAATATA
46021527 ATATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 14 0.23
27 23 0.38
28 4 0.07
29 9 0.15
30 10 0.17
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (27 bp):
ATACATAAATAATATATATTAAAATAT
Found at i:46021517 original size:25 final size:25
Alignment explanation
Indices: 46021481--46021614 Score: 86
Period size: 25 Copynumber: 5.6 Consensus size: 25
46021471 TAAAAAATAT
* *
46021481 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAATATTAAAG
* *
46021506 ATATATACATAAAATAATA-TAATAT
1 ATATATACATAATATAATATTAA-AG
* *
46021531 ATATATACTTAATATAGA-ATT-TAG
1 ATATATACATAATATA-ATATTAAAG
* *
46021555 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
* *
46021577 AATATATATATAATACAATATT-AAG
1 -ATATATACATAATATAATATTAAAG
*
46021602 AAATATA-ATAATA
1 ATATATACATAATA
46021615 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
21 2 0.02
22 2 0.02
23 19 0.23
24 21 0.25
25 37 0.44
26 3 0.04
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:46022150 original size:18 final size:18
Alignment explanation
Indices: 46022127--46022182 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
46022117 GTGGAATAGG
46022127 TAGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
46022145 TAGT-G-G--AGT-TGG-
1 TAGTGGAGCAAGTGTGGC
*
46022157 TGGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
46022175 TAGTGGAG
1 TAGTGGAG
46022183 TTGGTGGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.10
13 4 0.13
14 4 0.13
16 4 0.13
17 4 0.13
18 11 0.37
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.25
Consensus pattern (18 bp):
TAGTGGAGCAAGTGTGGC
Found at i:46022182 original size:30 final size:30
Alignment explanation
Indices: 46022094--46022192 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
46022084 TAGGTACAAG
* *
46022094 TGGTGGTGAAGCAAGTGTGGCTAGTGGAAT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
46022124 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
46022154 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
46022184 TGGTGGTGG
1 TGGTGGTGG
46022193 CAAATGATAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.19, C:0.06, G:0.48, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:46033699 original size:48 final size:48
Alignment explanation
Indices: 46033614--46033712 Score: 146
Period size: 48 Copynumber: 2.1 Consensus size: 48
46033604 ATCAACTCAT
* *
46033614 ATTGCGAGAGGTGAGTTGAGCCTCAGGACACATGCTGAGGTATTTTCA
1 ATTGCAAGAGGTGAGTTGAGCCTCAGGACACACGCTGAGGTATTTTCA
* *
46033662 ATTGCAAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTTCA
1 ATTGCAAGAGGTGAGTTGAGCCTCAGG-ACACACGCTGAGGTATTTTCA
46033710 ATT
1 ATT
46033713 TCTGGTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 2 0.04
48 44 0.96
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (48 bp):
ATTGCAAGAGGTGAGTTGAGCCTCAGGACACACGCTGAGGTATTTTCA
Found at i:46033723 original size:14 final size:14
Alignment explanation
Indices: 46033704--46033738 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
46033694 CGCTGAGGTA
46033704 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
46033718 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
46033732 TTTTCAA
1 TTTTCAA
46033739 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:46034007 original size:149 final size:149
Alignment explanation
Indices: 46033718--46034333 Score: 1042
Period size: 149 Copynumber: 4.1 Consensus size: 149
46033708 CAATTTCTGG
* * * * * * * *
46033718 TTTTCAATTTCTGTTTTTC--AAAAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCGAGACA
1 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
* *
46033781 CGCTAAGGTAATTTCAATTTATGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
46033846 TCAGGACACGCTGAGGTAT
131 TCAGGACACGCTGAGGTAT
46033865 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
1 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
46033930 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
46033995 TCAGGACACGCTGAGGTAT
131 TCAGGACACGCTGAGGTAT
46034014 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
1 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
46034079 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
46034144 TCAGGACACGCTGAGGTAT
131 TCAGGACACGCTGAGGTAT
46034163 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
1 TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
*
46034228 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTC
66 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
46034293 TC-GGCTCACATGCTGAGGTCT
131 TCAGG---ACACGCTGAGGTAT
* *
46034314 TTTT-AATTTCTGCTTTTCAA
1 TTTTAAATTTTTGTTTTTCAA
46034334 TTTCTGTTTT
Statistics
Matches: 449, Mismatches: 15, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
147 17 0.04
148 2 0.00
149 400 0.89
150 14 0.03
151 16 0.04
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (149 bp):
TTTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACA
CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAGGACACGCTGAGGTAT
Found at i:46034296 original size:73 final size:73
Alignment explanation
Indices: 46033719--46034296 Score: 760
Period size: 73 Copynumber: 7.8 Consensus size: 73
46033709 AATTTCTGGT
* * * *
46033719 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCGAGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
*
46033784 TAAGGTAA
66 TGAGGTAA
* * *
46033792 TTTCAATTTATGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
*
46033857 TGAGGTATT
66 TGAGGTA-A
* * * * * *
46033866 TTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACAC
1 TTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
46033931 GCTGAGGTAA
64 GCTGAGGTAA
* *
46033941 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
*
46034006 TGAGGTATT
66 TGAGGTA-A
* * * * * *
46034015 TTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACAC
1 TTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
46034080 GCTGAGGTAA
64 GCTGAGGTAA
* *
46034090 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
*
46034155 TGAGGTATT
66 TGAGGTA-A
* * * * * *
46034164 TTTAAATTTTTGTTTTTCAAAAAAATCAATTCATATTGCGAAAGGTGAGTTAAGCCTCGGGACAC
1 TTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
46034229 GCTGAGGTAA
64 GCTGAGGTAA
* *
46034239 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
46034297 CTCACATGCT
Statistics
Matches: 434, Mismatches: 62, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
73 197 0.45
74 45 0.10
75 45 0.10
76 147 0.34
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
TGAGGTAA
Done.