Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 110 of 163
Found at i:35398864 original size:16 final size:16
Alignment explanation
Indices: 35398843--35398884 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35398833 NTATTAAATT
*
35398843 ATATATTTTAATTATA
1 ATATATTTTAATAATA
35398859 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
35398874 AT-TATGTTTAA
1 ATATAT-TTTAA
35398885 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:35398869 original size:15 final size:15
Alignment explanation
Indices: 35398834--35398875 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35398824 NNNNNNNNNN
*
35398834 TATTAAATTAT-ATA
1 TATTTAATTATAATA
35398848 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
35398862 TATTTAATAATAAT
1 TATTTAATTATAAT
35398876 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:35399123 original size:16 final size:16
Alignment explanation
Indices: 35399098--35399135 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
35399088 TTGATTTGCT
35399098 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
35399114 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
35399130 AATACA
1 ATTACA
35399136 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:35399199 original size:14 final size:13
Alignment explanation
Indices: 35399179--35399213 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
35399169 CATAAAAGAG
35399179 ATAAATAATTAAA
1 ATAAATAATTAAA
35399192 ATTAAATAATTAAA
1 A-TAAATAATTAAA
35399206 ATAAATAA
1 ATAAATAA
35399214 GCAAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATAATTAAA
Found at i:35415647 original size:30 final size:31
Alignment explanation
Indices: 35415611--35415672 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
35415601 ATCTTCCACT
*
35415611 CTCTCAAAA-AAATGAAAAGCAAAGTTGGAG
1 CTCTCAAAATAAATGAAAAGCAAAGTTAGAG
*
35415641 CTCTCAAAATAAATGAAAAGCAACGTTAGAG
1 CTCTCAAAATAAATGAAAAGCAAAGTTAGAG
35415672 C
1 C
35415673 GATGATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (31 bp):
CTCTCAAAATAAATGAAAAGCAAAGTTAGAG
Found at i:35435719 original size:85 final size:86
Alignment explanation
Indices: 35435618--35435797 Score: 337
Period size: 85 Copynumber: 2.1 Consensus size: 86
35435608 TTTCTTTTTC
35435618 AATTCTTATTTCTTTTCTTTTATTTGTTTTGTTTTAATAATGATAATAATAATAATAATATATTT
1 AATTCTTATTTCTTTTCTTTTATTTGTTTTGTTTTAATAATGATAATAATAATAATAATATATTT
35435683 ACTTAATTAA-AAGCAATACA
66 ACTTAATTAATAAGCAATACA
35435703 AATTCTTATTTCTTTTCTTTTATTTGTTTTGTTTTAATAATGATAATAATAATAATAATATATTT
1 AATTCTTATTTCTTTTCTTTTATTTGTTTTGTTTTAATAATGATAATAATAATAATAATATATTT
35435768 ACTTAATTAATAAGCAATACA
66 ACTTAATTAATAAGCAATACA
*
35435789 TATT-TTATT
1 AATTCTTATT
35435798 ATTAAATACA
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 80 0.86
86 13 0.14
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (86 bp):
AATTCTTATTTCTTTTCTTTTATTTGTTTTGTTTTAATAATGATAATAATAATAATAATATATTT
ACTTAATTAATAAGCAATACA
Found at i:35435807 original size:19 final size:20
Alignment explanation
Indices: 35435783--35435821 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
35435773 ATTAATAAGC
35435783 AATACATAT-TTTATTATTA
1 AATACATATATTTATTATTA
*
35435802 AATACATATATTTGTTATTA
1 AATACATATATTTATTATTA
35435822 TTACACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATATTTATTATTA
Found at i:35438123 original size:5 final size:5
Alignment explanation
Indices: 35438109--35438199 Score: 64
Period size: 5 Copynumber: 18.6 Consensus size: 5
35438099 GTAGTAGAAT
* * *
35438109 AGAGA A-AGA AGAGA AGGAGA AGGGAA AAAGA GGAGA AGAGA AGAGA AG-GA
1 AGAGA AGAGA AGAGA A-GAGA AGAG-A AGAGA AGAGA AGAGA AGAGA AGAGA
* * * * *
35438159 AAAGG GGAAA AAAGA AGAGA AGAGA AGAGA AG-GA A-AGA AGA
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGA
35438200 AACGGAAAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
4 13 0.20
5 43 0.67
6 8 0.12
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:35438152 original size:32 final size:34
Alignment explanation
Indices: 35438109--35438194 Score: 133
Period size: 34 Copynumber: 2.6 Consensus size: 34
35438099 GTAGTAGAAT
*
35438109 AGAGAA-AGAAGAGAAGGAGAA-GGG-AAAAAGA
1 AGAGAAGAGAAGAGAAGGAAAAGGGGAAAAAAGA
*
35438140 GGAGAAGAGAAGAGAAGGAAAAGGGGAAAAAAGA
1 AGAGAAGAGAAGAGAAGGAAAAGGGGAAAAAAGA
35438174 AGAGAAGAGAAGAGAAGGAAA
1 AGAGAAGAGAAGAGAAGGAAA
35438195 GAAGAAACGG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 5 0.10
32 14 0.29
33 3 0.06
34 27 0.55
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (34 bp):
AGAGAAGAGAAGAGAAGGAAAAGGGGAAAAAAGA
Found at i:35438174 original size:24 final size:25
Alignment explanation
Indices: 35438120--35438180 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
35438110 GAGAAAGAAG
* *
35438120 AGAAGGAGAAGGGAAAAAGAGGAGAAG
1 AGAA-GAGAA-GGAAAAAGAGGAAAAA
*
35438147 AGAAGAGAAGG-AAAAGGGGAAAAA
1 AGAAGAGAAGGAAAAAGAGGAAAAA
35438171 AGAAGAGAAG
1 AGAAGAGAAG
35438181 AGAAGAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.65
25 2 0.06
26 5 0.16
27 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (25 bp):
AGAAGAGAAGGAAAAAGAGGAAAAA
Found at i:35438207 original size:13 final size:13
Alignment explanation
Indices: 35438109--35438199 Score: 52
Period size: 13 Copynumber: 7.2 Consensus size: 13
35438099 GTAGTAGAAT
*
35438109 AGAGAAAGAAGAGA
1 AGAGAAGGAA-AGA
35438123 AGGAGAAGGGAAA-A
1 A-GAGAA-GGAAAGA
*
35438137 AGAGGA-GAAGAGA
1 AGAGAAGGAA-AGA
35438150 AGAGAAGGAAA-A
1 AGAGAAGGAAAGA
* * *
35438162 GGGGAA-AAAAGA
1 AGAGAAGGAAAGA
35438174 AGAGAA-G--AGA
1 AGAGAAGGAAAGA
35438184 AGAGAAGGAAAGA
1 AGAGAAGGAAAGA
35438197 AGA
1 AGA
35438200 AACGGAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
10 9 0.15
11 7 0.12
12 11 0.19
13 17 0.29
14 6 0.10
15 6 0.10
16 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGAGAAGGAAAGA
Found at i:35439455 original size:25 final size:25
Alignment explanation
Indices: 35439424--35439503 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
35439414 TGCTAAACGG
* *
35439424 AGAGCACTGACATGCTAGTAATCAG
1 AGAGCACTGACATGCTAATAATCAA
* * *
35439449 ATAGCACTAACATGTTAATAATCAA
1 AGAGCACTGACATGCTAATAATCAA
* *
35439474 AGAGCACTGA-AGTGCTAAAAATCAG
1 AGAGCACTGACA-TGCTAATAATCAA
35439499 AGAGC
1 AGAGC
35439504 GCGCTAAAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
24 1 0.02
25 43 0.98
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (25 bp):
AGAGCACTGACATGCTAATAATCAA
Found at i:35440369 original size:6 final size:6
Alignment explanation
Indices: 35440354--35440386 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
35440344 AAAACCCCAA
35440354 TTTTCTT TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TT
35440387 CTCCTTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:35443352 original size:25 final size:25
Alignment explanation
Indices: 35443324--35443458 Score: 115
Period size: 25 Copynumber: 5.6 Consensus size: 25
35443314 ACTTTAGTGC
*
35443324 GCTCTCTGATTATTAGCATGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
35443349 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
* * * **
35443374 GCTTTTTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
35443399 GCTCTCCG--T-TTAGCACGTAT-GT
1 GCTCTCTGATTATTAGCACGT-TGGT
* *
35443421 GCTCTCTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTATTAGCACGTTGGT
35443443 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
35443459 TGCATAATAA
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.38
23 2 0.02
24 1 0.01
25 52 0.57
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:35443415 original size:22 final size:21
Alignment explanation
Indices: 35443387--35443448 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
35443377 TTTTGATTAC
*
35443387 TAGCACGTCAGTGCTCTCCGTT
1 TAGCACGT-AGTGCTCTCCGTA
*
35443409 TAGCACGTATGTGCTCTCTGTA
1 TAGCACGTA-GTGCTCTCCGTA
*
35443431 TAGCACTTTAGTGCTCTC
1 TAGCAC-GTAGTGCTCTC
35443449 TGTTCATTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.35
Consensus pattern (21 bp):
TAGCACGTAGTGCTCTCCGTA
Found at i:35444829 original size:19 final size:19
Alignment explanation
Indices: 35444805--35444842 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35444795 ATAACATACT
35444805 TTCATAGGTTCATAAGGAA
1 TTCATAGGTTCATAAGGAA
35444824 TTCATAGGTTCATAAGGAA
1 TTCATAGGTTCATAAGGAA
35444843 GAATTCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
TTCATAGGTTCATAAGGAA
Found at i:35445781 original size:3 final size:3
Alignment explanation
Indices: 35445773--35445811 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
35445763 GAATATATAT
35445773 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35445812 ACGGGATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35447760 original size:31 final size:31
Alignment explanation
Indices: 35447722--35447780 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35447712 CACCAGTACT
*
35447722 TTGGTGCCACCTTTCCCATGGGCACCACTCC
1 TTGGTGCCACCTTTCCCATGGACACCACTCC
*
35447753 TTGGTGCCGCCTTTCCCATGGACACCAC
1 TTGGTGCCACCTTTCCCATGGACACCAC
35447781 CACCCAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.14, C:0.41, G:0.20, T:0.25
Consensus pattern (31 bp):
TTGGTGCCACCTTTCCCATGGACACCACTCC
Found at i:35452571 original size:6 final size:6
Alignment explanation
Indices: 35452560--35452602 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
35452550 AATTATTTAC
*
35452560 ATTAAT ATTAAT ATTAAT ATTAAC A-TAAT A-TAAT A-TAAT ATTA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTA
35452603 TTTTTTATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTAAT
Found at i:35452902 original size:21 final size:22
Alignment explanation
Indices: 35452864--35452906 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
35452854 ATTTTCAAAT
35452864 TATTATATAAATTTATATTTTA
1 TATTATATAAATTTATATTTTA
*
35452886 TATTGTATAAA-TTATATTTTA
1 TATTATATAAATTTATATTTTA
35452907 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTATATAAATTTATATTTTA
Found at i:35454065 original size:15 final size:14
Alignment explanation
Indices: 35454045--35454098 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
35454035 TAGTCTTTGT
35454045 ATTTTAATTTGATTA
1 ATTTTAATTTG-TTA
35454060 ATTTTAATTT-TTA
1 ATTTTAATTTGTTA
35454073 TATTTTTTAAATTTGTTA
1 -A--TTTT-AATTTGTTA
35454091 ATTTTAAT
1 ATTTTAAT
35454099 CTTTGTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 14 0.41
16 4 0.12
17 6 0.18
18 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (14 bp):
ATTTTAATTTGTTA
Found at i:35454092 original size:31 final size:31
Alignment explanation
Indices: 35454046--35454110 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
35454036 AGTCTTTGTA
*
35454046 TTTTAATTTGATTAATTTTAATTTTTATATT
1 TTTTAATTTGATTAATTTTAATCTTTATATT
*
35454077 TTTTAAATTTG-TTAATTTTAATCTTTGTATT
1 TTTT-AATTTGATTAATTTTAATCTTTATATT
35454108 TTT
1 TTT
35454111 GGTTAAAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (31 bp):
TTTTAATTTGATTAATTTTAATCTTTATATT
Found at i:35461631 original size:17 final size:18
Alignment explanation
Indices: 35461600--35461633 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35461590 CAAATGTTTT
*
35461600 TTTTTTAAATTTTTATTA
1 TTTTTTAAATGTTTATTA
35461618 TTTTTTAAA-GTTTATT
1 TTTTTTAAATGTTTATT
35461634 CAATTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTTAAATGTTTATTA
Found at i:35461842 original size:23 final size:24
Alignment explanation
Indices: 35461810--35461855 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
35461800 TCATAAATTT
35461810 AATTATAAAAATATATAAAATATC
1 AATTATAAAAATATATAAAATATC
* *
35461834 AATTA-AAAAATATTTTAAATAT
1 AATTATAAAAATATATAAAATAT
35461856 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTATAAAAATATATAAAATATC
Found at i:35463186 original size:66 final size:66
Alignment explanation
Indices: 35463109--35463241 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 66
35463099 ATTCTGAAGC
* * *
35463109 TGTAGTTGGAGTTCGTCATA-TTT-TTTGCTTGCCTCTGCTTCCCCCGCTGCTGCCTCCACTTTA
1 TGTAGCTGGAGTTCGTCATATTTTCTTTG--AGCCTCTGCTTCCCCCGATGCTGCCTCCACTTTA
35463172 AGT
64 AGT
* * *
35463175 TGTAGCTGGAGTTCTTCATATTTTCTTTGAGCCTCTGCTTCCCTCGATGCTGCCTCCGCTTTAAG
1 TGTAGCTGGAGTTCGTCATATTTTCTTTGAGCCTCTGCTTCCCCCGATGCTGCCTCCACTTTAAG
35463240 T
66 T
35463241 T
1 T
35463242 AAGCAATTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
66 52 0.88
67 3 0.05
68 4 0.07
ACGTcount: A:0.11, C:0.28, G:0.20, T:0.41
Consensus pattern (66 bp):
TGTAGCTGGAGTTCGTCATATTTTCTTTGAGCCTCTGCTTCCCCCGATGCTGCCTCCACTTTAAG
T
Found at i:35469465 original size:18 final size:17
Alignment explanation
Indices: 35469444--35469496 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
35469434 ATATAATTTT
35469444 AAAAATAGAATTTAATT-
1 AAAAATAGAA-TTAATTA
*
35469461 AAAAA-AGAAATAATTA
1 AAAAATAGAATTAATTA
*
35469477 AAGAAATAAAATTAATTA
1 AA-AAATAGAATTAATTA
35469495 AA
1 AA
35469497 GTTTAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
17 8 0.27
18 11 0.37
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAATAGAATTAATTA
Found at i:35469476 original size:15 final size:17
Alignment explanation
Indices: 35469426--35469496 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
35469416 GTTAAAGTTT
*
35469426 AAAATATAATATAATTTTA
1 AAAATAGAATATAA--TTA
*
35469445 AAAATAGAATTTAATTA
1 AAAATAGAATATAATTA
35469462 AAAA-AGAA-ATAATTAA
1 AAAATAGAATATAATT-A
*
35469478 AGAAATAAAAT-TAATTA
1 A-AAATAGAATATAATTA
35469495 AA
1 AA
35469497 GTTTAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 5 0.11
16 7 0.16
17 12 0.27
18 8 0.18
19 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAATAGAATATAATTA
Found at i:35469514 original size:11 final size:11
Alignment explanation
Indices: 35469500--35469538 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
35469490 AATTAAAGTT
35469500 TAAAATAGAAA
1 TAAAATAGAAA
* *
35469511 TAAAGATATAAT
1 TAAA-ATAGAAA
35469523 TAAAATAGAAA
1 TAAAATAGAAA
35469534 TAAAA
1 TAAAA
35469539 AATTTTAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (11 bp):
TAAAATAGAAA
Found at i:35470443 original size:35 final size:35
Alignment explanation
Indices: 35470399--35470524 Score: 112
Period size: 35 Copynumber: 3.4 Consensus size: 35
35470389 TATATAATAT
35470399 TTTTTTATATTAACAATGTATTTTTTGAACTATTA
1 TTTTTTATATTAACAATGTATTTTTTGAACTATTA
* * * *
35470434 TTTTTTATATTAATTGAAATAAATAATATATATT-ATA-TAATA
1 TTTTTTATATTAA---CAAT--GT-AT-T-TTTTGA-ACTATTA
35470476 TTTTTTTATATTAACAATGTATTTTTTGAACTATTA
1 -TTTTTTATATTAACAATGTATTTTTTGAACTATTA
35470512 TTTTTTATATTAA
1 TTTTTTATATTAA
35470525 TTGAAATAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
35 30 0.42
36 6 0.08
37 2 0.03
38 4 0.06
40 4 0.06
41 2 0.03
42 6 0.08
43 17 0.24
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTTTTATATTAACAATGTATTTTTTGAACTATTA
Found at i:35470500 original size:78 final size:78
Alignment explanation
Indices: 35470371--35470545 Score: 350
Period size: 78 Copynumber: 2.2 Consensus size: 78
35470361 CGAATTATCC
35470371 GAAATAAATAATATATATTATATAATATTTTTTTATATTAACAATGTATTTTTTGAACTATTATT
1 GAAATAAATAATATATATTATATAATATTTTTTTATATTAACAATGTATTTTTTGAACTATTATT
35470436 TTTTATATTAATT
66 TTTTATATTAATT
35470449 GAAATAAATAATATATATTATATAATATTTTTTTATATTAACAATGTATTTTTTGAACTATTATT
1 GAAATAAATAATATATATTATATAATATTTTTTTATATTAACAATGTATTTTTTGAACTATTATT
35470514 TTTTATATTAATT
66 TTTTATATTAATT
35470527 GAAATAAATAATATATATT
1 GAAATAAATAATATATATT
35470546 TTTAAACTAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (78 bp):
GAAATAAATAATATATATTATATAATATTTTTTTATATTAACAATGTATTTTTTGAACTATTATT
TTTTATATTAATT
Found at i:35472825 original size:2 final size:2
Alignment explanation
Indices: 35472818--35472854 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
35472808 NACTGATTAT
*
35472818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35472855 GTATCATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35475083 original size:18 final size:18
Alignment explanation
Indices: 35475043--35475084 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
35475033 CCAGAAAATC
35475043 CAAGAACAGAAAAACAGA
1 CAAGAACAGAAAAACAGA
* *
35475061 GAAGAAGCAGAGAAA-AGA
1 CAAGAA-CAGAAAAACAGA
35475079 CAAGAA
1 CAAGAA
35475085 AATTTCACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.64, C:0.12, G:0.24, T:0.00
Consensus pattern (18 bp):
CAAGAACAGAAAAACAGA
Found at i:35483296 original size:51 final size:51
Alignment explanation
Indices: 35483219--35483405 Score: 252
Period size: 51 Copynumber: 3.6 Consensus size: 51
35483209 ATGAAAGTGA
*
35483219 GGTCACGTGTTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAAT
1 GGTCACATG-TGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAAT
* * * * *
35483271 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGT-TT
1 GGTCACATGTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGA-TAAT
* *
35483321 CGATCACGTGTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAAT
*
35483373 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGATACTA
35483406 TGTGAACCGA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
50 2 0.02
51 103 0.90
52 10 0.09
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAAT
Found at i:35483336 original size:102 final size:103
Alignment explanation
Indices: 35483221--35483407 Score: 367
Period size: 102 Copynumber: 1.8 Consensus size: 103
35483211 GAAAGTGAGG
35483221 TCACGTGTTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAATGGTCACATGTGTAGT
1 TCACGTGTTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAATGGTCACATGTGTAGT
35483286 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
66 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
35483324 TCACGTG-TGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAATGGTCACATGTGTAGT
1 TCACGTGTTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAATGGTCACATGTGTAGT
35483388 ACTATGTGCAGGCTACTATG
66 ACTATGTGCAGGCTACTATG
35483408 TGAACCGAAC
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 77 0.92
103 7 0.08
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (103 bp):
TCACGTGTTGTAGTACTATGTGCAGGATACTACGTGTATCGGATGATAATGGTCACATGTGTAGT
ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:35483504 original size:45 final size:45
Alignment explanation
Indices: 35483411--35483505 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
35483401 TACTATGTGA
* * * * *
35483411 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTGC
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCC
*
35483456 ACCGGACATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCC
1 ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCC
35483501 ACCGA
1 ACCGA
35483506 GTATCTGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCC
Found at i:35487833 original size:17 final size:17
Alignment explanation
Indices: 35487813--35487849 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
35487803 AATTTTTGAA
35487813 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
35487830 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
35487847 TTA
1 TTA
35487850 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:35489122 original size:46 final size:46
Alignment explanation
Indices: 35489066--35489250 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
35489056 TGGAAAATTT
*
35489066 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAGCCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* * *
35489112 TGAAATGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* * * *
35489158 TGAAAAGTATGTATGGTGTTTCAGTAAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
*
35489204 TGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
35489250 T
1 T
35489251 AGCATTTTAA
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:35494223 original size:17 final size:17
Alignment explanation
Indices: 35494190--35494237 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
35494180 GAATTTATAA
*
35494190 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
35494206 GAATTTTGTGATTTAGT
1 GAATTTTGTGATTTAGT
35494223 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
35494238 AAAAGAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:35495497 original size:46 final size:45
Alignment explanation
Indices: 35495444--35495583 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 45
35495434 CCATGGAAAA
*
35495444 TTGTGAAATGCAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGAG
1 TTGTGAAATGTAGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAG
*
35495490 TTGTGAAATGTAGGTATGGTGTTTCAGTGACGAAAACCATACTGAG
1 TTGTGAAATGTAGGTATGGTGTTTCAGTGAAG-AAACCATACTGAG
* * *
35495536 TTGTGAAAAGTAGGTATGGTATTCCAGTGAATGAAACCATACTGAG
1 TTGTGAAATGTAGGTATGGTGTTTCAGTGAA-GAAACCATACTGAG
35495582 TT
1 TT
35495584 ATAGCATTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
46 82 0.95
47 4 0.05
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (45 bp):
TTGTGAAATGTAGGTATGGTGTTTCAGTGAAGAAACCATACTGAG
Found at i:35496532 original size:22 final size:25
Alignment explanation
Indices: 35496498--35496542 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
35496488 GTGGAAATTG
35496498 AATTAGAAGCTG-ATGAG-ATATGA
1 AATTAGAAGCTGAATGAGTATATGA
*
35496521 AATTA-AATCTGAATGAGTATAT
1 AATTAGAAGCTGAATGAGTATAT
35496543 TTTCATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (25 bp):
AATTAGAAGCTGAATGAGTATATGA
Found at i:35510432 original size:34 final size:35
Alignment explanation
Indices: 35510388--35510454 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
35510378 CAGTAAAATA
*
35510388 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
35510422 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
35510455 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:35511609 original size:4 final size:4
Alignment explanation
Indices: 35511582--35511636 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
35511572 TAATTGCTAG
* * * * * *
35511582 TGTA TGTG TGTG TGTG TGTG TGTA TGTA TGTA TGTA CGTA TGTA TTTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
35511630 TGTA TGT
1 TGTA TGT
35511637 CTCTTGTCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.16, C:0.02, G:0.31, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:35516858 original size:28 final size:30
Alignment explanation
Indices: 35516807--35516867 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
35516797 TAATACTAAT
35516807 TAAATAATAATAGGAGAAAAAATAATG-ATAA
1 TAAATAATAATA-GAGAAAAAATAA-GAATAA
*
35516838 TAAATAATAATA-AG-AAGAATAAGAATAA
1 TAAATAATAATAGAGAAAAAATAAGAATAA
35516866 TA
1 TA
35516868 CGAACAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 13 0.46
29 2 0.07
31 12 0.43
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (30 bp):
TAAATAATAATAGAGAAAAAATAAGAATAA
Found at i:35516976 original size:13 final size:11
Alignment explanation
Indices: 35516940--35516978 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
35516930 GGAAGAGATA
*
35516940 ATAAATAAATAA
1 ATAAA-AAATAT
35516952 ATAAAAAATAT
1 ATAAAAAATAT
*
35516963 ATAAAAAATCT
1 ATAAAAAATAT
35516974 ATAAA
1 ATAAA
35516979 GGGTCGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:35518966 original size:17 final size:18
Alignment explanation
Indices: 35518934--35518968 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35518924 AAAGGTCATG
35518934 AAGAAAAGCAAAATTACA
1 AAGAAAAGCAAAATTACA
*
35518952 AAGAAAA-CCAAATTACA
1 AAGAAAAGCAAAATTACA
35518969 CAATGTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (18 bp):
AAGAAAAGCAAAATTACA
Found at i:35519811 original size:18 final size:18
Alignment explanation
Indices: 35519790--35519848 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
35519780 TAAAAAATAT
*
35519790 AAATTTTGGAATTTTTAA
1 AAATTTTTGAATTTTTAA
*
35519808 AAATATTTTTAA-TTTTAA
1 AAAT-TTTTGAATTTTTAA
** *
35519826 ATTTTTTTGAATTTTTGA
1 AAATTTTTGAATTTTTAA
35519844 AAATT
1 AAATT
35519849 ATTTTGATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 6 0.19
18 20 0.65
19 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
AAATTTTTGAATTTTTAA
Found at i:35519832 original size:27 final size:25
Alignment explanation
Indices: 35519768--35519832 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
35519758 CTTTAGATTT
*
35519768 TTTTAATTTTTTTAAAAAATATAAA
1 TTTTAAATTTTTTAAAAAATATAAA
* * *
35519793 TTTTGGAA-TTTTTAAAAATATTTTTAA
1 TTTT-AAATTTTTTAAAAA-A-TATAAA
35519820 TTTTAAATTTTTT
1 TTTTAAATTTTTT
35519833 TGAATTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 14 0.45
26 4 0.13
27 13 0.42
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTTAAATTTTTTAAAAAATATAAA
Found at i:35531515 original size:22 final size:22
Alignment explanation
Indices: 35531487--35531609 Score: 74
Period size: 22 Copynumber: 5.4 Consensus size: 22
35531477 TTTCTTTTAA
35531487 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
35531509 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
35531533 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
35531555 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
35531579 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
35531601 TTAGGAGAT
1 TTAGGAGAT
35531610 AATATTTTGG
Statistics
Matches: 73, Mismatches: 16, Indels: 24
0.65 0.14 0.21
Matches are distributed among these distances:
20 8 0.11
21 2 0.03
22 31 0.42
24 22 0.30
25 2 0.03
26 8 0.11
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:35531525 original size:46 final size:46
Alignment explanation
Indices: 35531482--35531622 Score: 282
Period size: 46 Copynumber: 3.1 Consensus size: 46
35531472 TCTATTTTCT
35531482 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
35531528 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
35531574 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
35531620 TTT
1 TTT
35531623 CTATCTTTGT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 95 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.40
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:35531541 original size:24 final size:24
Alignment explanation
Indices: 35531509--35531587 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
35531499 ATGCTAAAGT
35531509 TTAGGAGATAATATTTTGGTTTAA
1 TTAGGAGATAATATTTTGGTTTAA
** * *
35531533 TTAGGAGAT--TA-GAT-GCTAAA
1 TTAGGAGATAATATTTTGGTTTAA
35531553 GTTTAGGAGATAATATTTTGGTTTAA
1 --TTAGGAGATAATATTTTGGTTTAA
35531579 TTAGGAGAT
1 TTAGGAGAT
35531588 TAGATGCTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 11 0.27
24 20 0.49
25 1 0.02
26 4 0.10
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.41
Consensus pattern (24 bp):
TTAGGAGATAATATTTTGGTTTAA
Found at i:35536981 original size:120 final size:120
Alignment explanation
Indices: 35536847--35537085 Score: 451
Period size: 120 Copynumber: 2.0 Consensus size: 120
35536837 AAAATCACGA
35536847 TATGAAAATATATGTAAGAACATGTGTTAGAGACCCATGACATCATATGACAATGAGAATACTCA
1 TATGAAAATATATGTAAGAACATGTGTTAGAGACCCATGACATCATATGACAATGAGAATACTCA
*
35536912 TGGTGTAGCTTCCAGTAAGATGTAAACCAGACTAACATATCACAACATGAAAATT
66 TGGTGTAGCCTCCAGTAAGATGTAAACCAGACTAACATATCACAACATGAAAATT
*
35536967 TATGAAAATATATGTAAGAACATGTGTTAGAGACCCATGGCATCATATGACAATGAGAATACTCA
1 TATGAAAATATATGTAAGAACATGTGTTAGAGACCCATGACATCATATGACAATGAGAATACTCA
*
35537032 TGGTGTAGCCTCCAGTAAGATGTAAACCAGACTAACATATCGCAACATGAAAAT
66 TGGTGTAGCCTCCAGTAAGATGTAAACCAGACTAACATATCACAACATGAAAAT
35537086 ATGTACAAGA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (120 bp):
TATGAAAATATATGTAAGAACATGTGTTAGAGACCCATGACATCATATGACAATGAGAATACTCA
TGGTGTAGCCTCCAGTAAGATGTAAACCAGACTAACATATCACAACATGAAAATT
Found at i:35541110 original size:37 final size:37
Alignment explanation
Indices: 35540924--35541117 Score: 282
Period size: 37 Copynumber: 5.2 Consensus size: 37
35540914 ATCCAACCGA
*
35540924 AACACGCC-AATCGCTCATAAGAGCTAATCCACACAAT
1 AACACGCCAAAT-GCTCATAAGAGCTAATCCACTCAAT
* *
35540961 AACATGCCAAATGCTCATAAGAGCTAATCCACTCAAA
1 AACACGCCAAATGCTCATAAGAGCTAATCCACTCAAT
*
35540998 AACACGCCAAATGCTCATAAGAGCTAATCCACTCAAA
1 AACACGCCAAATGCTCATAAGAGCTAATCCACTCAAT
* *
35541035 AACACGACAAATGCTCATAAGAGCTAATCCACTCGAT
1 AACACGCCAAATGCTCATAAGAGCTAATCCACTCAAT
* * **
35541072 AACACGCCAAATGCTCATAAGATCTAATCCAATTGAT
1 AACACGCCAAATGCTCATAAGAGCTAATCCACTCAAT
35541109 AACACGCCA
1 AACACGCCA
35541118 CAACACTAAG
Statistics
Matches: 145, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
37 142 0.98
38 3 0.02
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (37 bp):
AACACGCCAAATGCTCATAAGAGCTAATCCACTCAAT
Found at i:35542282 original size:22 final size:22
Alignment explanation
Indices: 35542257--35542318 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
35542247 TAAATACGAT
35542257 TGGCACAAAGCCATAATCAAGA
1 TGGCACAAAGCCATAATCAAGA
* * * * *
35542279 TGGCACAGAGCCATATTTAGGT
1 TGGCACAAAGCCATAATCAAGA
35542301 TGGCACAAAGCCATAATC
1 TGGCACAAAGCCATAATC
35542319 GGATTACGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (22 bp):
TGGCACAAAGCCATAATCAAGA
Found at i:35542759 original size:27 final size:27
Alignment explanation
Indices: 35542662--35542759 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 27
35542652 CCCTATAGAG
* * *
35542662 GTATTTTGGTAATTTTTCAAACT-GGA
1 GTATTTCGATAATTTTACAAACTAGGA
* *
35542688 GGTA-TTCAATAATTTTACAAATTGAGG-
1 -GTATTTCGATAATTTTACAAACT-AGGA
*
35542715 GTATTTCGATAACTTTACAAACTAGGA
1 GTATTTCGATAATTTTACAAACTAGGA
* *
35542742 GTATTTCGGTAATATTAC
1 GTATTTCGATAATTTTAC
35542760 CCTATAAGGG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
26 20 0.36
27 34 0.61
28 2 0.04
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (27 bp):
GTATTTCGATAATTTTACAAACTAGGA
Found at i:35544236 original size:15 final size:17
Alignment explanation
Indices: 35544218--35544249 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35544208 CAGAATAGAA
35544218 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
35544233 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
35544250 GGGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:35545329 original size:45 final size:46
Alignment explanation
Indices: 35545265--35545365 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
35545255 CCGACTACTG
*
35545265 TTACTGTTACCGATTCGGCAC-TTTGTGTGTCAAATACTGTTACCA
1 TTACTGTTACCAATTCGGCACTTTTGTGTGTCAAATACTGTTACCA
** *
35545310 TTACTGTTACCAATTCGGCACTTTTGTGTGTTGAATACTGTTACTA
1 TTACTGTTACCAATTCGGCACTTTTGTGTGTCAAATACTGTTACCA
*
35545356 TTATTGTTAC
1 TTACTGTTAC
35545366 TGCTACCGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 20 0.40
46 30 0.60
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (46 bp):
TTACTGTTACCAATTCGGCACTTTTGTGTGTCAAATACTGTTACCA
Found at i:35556725 original size:40 final size:40
Alignment explanation
Indices: 35556670--35556787 Score: 236
Period size: 40 Copynumber: 3.0 Consensus size: 40
35556660 GGATCGACAG
35556670 ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTATAA
1 ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTATAA
35556710 ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTATAA
1 ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTATAA
35556750 ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTAT
1 ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTAT
35556788 CCGATAAGTA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (40 bp):
ATATGCTTAGCCATATTTATGAAAGTATGAATGCTTATAA
Found at i:35570102 original size:42 final size:42
Alignment explanation
Indices: 35570038--35570166 Score: 141
Period size: 42 Copynumber: 3.1 Consensus size: 42
35570028 AGGATAAAAA
* * * *
35570038 GAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAACG
* * * *
35570080 GAAGCTCGTAAGAGCTGAACAGAAACCCAAAATGGTTAAACT
1 GAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAACG
* * * * *
35570122 GAAGGTTAAAAGAGCTGAACAAAAACCCATTAGGGTTAAACG
1 GAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAACG
35570164 GAA
1 GAA
35570167 ACTTATATGA
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAACG
Found at i:35580128 original size:20 final size:20
Alignment explanation
Indices: 35580077--35580116 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
35580067 TGAAGTAAGG
35580077 CAAAATATGTATATGCAAGT
1 CAAAATATGTATATGCAAGT
35580097 CAAAATATGTATATGCAAGT
1 CAAAATATGTATATGCAAGT
35580117 ATTATATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (20 bp):
CAAAATATGTATATGCAAGT
Found at i:35582098 original size:19 final size:20
Alignment explanation
Indices: 35582056--35582101 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
35582046 GTACGACATT
* *
35582056 TTTTTATATTTTTTTATGAA
1 TTTTTATATTTCTTTATCAA
35582076 -TTTTATATTTCTTTA-CAA
1 TTTTTATATTTCTTTATCAA
35582094 TTTTTATA
1 TTTTTATA
35582102 ATTTTCTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTATATTTCTTTATCAA
Found at i:35582193 original size:10 final size:11
Alignment explanation
Indices: 35582170--35582194 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35582160 AAAATTACAA
35582170 TTTTTCTAATT
1 TTTTTCTAATT
35582181 TTTTTCTAATT
1 TTTTTCTAATT
35582192 TTT
1 TTT
35582195 AATAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTCTAATT
Found at i:35582210 original size:29 final size:27
Alignment explanation
Indices: 35582176--35582250 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
35582166 ACAATTTTTC
* *
35582176 TAATTTTTTTCTAATTTTTAATAAATTT
1 TAATTTTTTT-TATTTTTTAATAAAATT
* *
35582204 TATATTTTTTATATTTTTTATTAAAATT
1 TA-ATTTTTTTTATTTTTTAATAAAATT
35582232 TAATTTTTTTTATTTTTTA
1 TAATTTTTTTTATTTTTTA
35582251 TTTTTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.39
28 18 0.44
29 7 0.17
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (27 bp):
TAATTTTTTTTATTTTTTAATAAAATT
Found at i:35582213 original size:9 final size:9
Alignment explanation
Indices: 35582201--35582256 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
35582191 TTTTAATAAA
35582201 TTTTATATT
1 TTTTATATT
35582210 TTTTATATT
1 TTTTATATT
**
35582219 TTTTATTAAA
1 TTTTA-TATT
*
35582229 ATTTA-ATT
1 TTTTATATT
*
35582237 TTTTTTATT
1 TTTTATATT
35582246 TTTTAT-TT
1 TTTTATATT
35582254 TTT
1 TTT
35582257 ATTTTTGCCA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
8 9 0.24
9 22 0.59
10 6 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATATT
Found at i:35582249 original size:27 final size:27
Alignment explanation
Indices: 35582176--35582252 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
35582166 ACAATTTTTC
* * *
35582176 TAATTTTTTTCTAATTTTTAATAAATTT
1 TAATTTTTTT-TATTTTTTATTAAAATT
*
35582204 TATATTTTTTATATTTTTTATTAAAATT
1 TA-ATTTTTTTTATTTTTTATTAAAATT
35582232 TAATTTTTTTTATTTTTTATT
1 TAATTTTTTTTATTTTTTATT
35582253 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 18 0.42
28 18 0.42
29 7 0.16
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (27 bp):
TAATTTTTTTTATTTTTTATTAAAATT
Found at i:35582262 original size:7 final size:7
Alignment explanation
Indices: 35582237--35582262 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35582227 AAATTTAATT
35582237 TTTTTTA
1 TTTTTTA
35582244 TTTTTTA
1 TTTTTTA
35582251 TTTTTTA
1 TTTTTTA
35582258 TTTTT
1 TTTTT
35582263 GCCACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:35583381 original size:20 final size:20
Alignment explanation
Indices: 35583358--35583432 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
35583348 ACTTAGGGGG
* *
35583358 ACTTCTAACCATATAGGTCC
1 ACTTCTAACCATACAAGTCC
*
35583378 ACTTAT-ACCGATACAAGTCC
1 ACTTCTAACC-ATACAAGTCC
* *
35583398 ATTTCTACCCATACAAGTCC
1 ACTTCTAACCATACAAGTCC
* *
35583418 ACTTTTACCCATACA
1 ACTTCTAACCATACA
35583433 TCTTGTAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.07
20 40 0.89
21 2 0.04
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.29
Consensus pattern (20 bp):
ACTTCTAACCATACAAGTCC
Found at i:35588584 original size:69 final size:67
Alignment explanation
Indices: 35588509--35588644 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 67
35588499 CACAATAATG
* *
35588509 TCAACTTAAACAAATATTTAATGACATATAAAAACAGAAAT-AAATTAGGAAAAGAGCATGAAAT
1 TCAACTTAAACAAATATTTAATGAC--ATAAAAACAGAAATAAAATCA-GAAAAGAACATGAAAT
35588573 CAACT
63 CAACT
* * *
35588578 TCAACTTAAACCAGTATTTAATGACATAAAAACTGAAATAAAAATCAGAAAAGAACATGAAATCA
1 TCAACTTAAACAAATATTTAATGACATAAAAACAGAAAT-AAAATCAGAAAAGAACATGAAATCA
35588643 AC
65 AC
35588645 AGCAAGGGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
67 13 0.22
68 19 0.32
69 28 0.47
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.22
Consensus pattern (67 bp):
TCAACTTAAACAAATATTTAATGACATAAAAACAGAAATAAAATCAGAAAAGAACATGAAATCAA
CT
Found at i:35590221 original size:3 final size:3
Alignment explanation
Indices: 35590213--35590244 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35590203 GAAAAGCAAA
35590213 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
35590245 ATAAGGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35591389 original size:16 final size:16
Alignment explanation
Indices: 35591368--35591420 Score: 106
Period size: 16 Copynumber: 3.3 Consensus size: 16
35591358 TTGGTTCGCT
35591368 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
35591384 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
35591400 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
35591416 GTAAT
1 GTAAT
35591421 AGATAATCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:35591454 original size:46 final size:44
Alignment explanation
Indices: 35591402--35591495 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
35591392 ATAGAGGCGT
*
35591402 AATGGAATAGAGGCGTAATAGATAATCCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAG-T-ATCCTTGTGTTTGGTTGAATGG
*
35591448 AATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTATCCTTGTGTTTGGTTGAATGG
35591492 AATG
1 AATG
35591496 ATGGTGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.52
45 1 0.02
46 21 0.46
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGTATCCTTGTGTTTGGTTGAATGG
Found at i:35591505 original size:39 final size:42
Alignment explanation
Indices: 35591402--35591506 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 42
35591392 ATAGAGGCGT
*
35591402 AATGGAATAGA-GGCGTAATAGATAATCCTTTTGTTTGGTTG
1 AATGGAATAGATGGCGTAATAGATAATCCTTGTGTTTGGTTG
* *
35591443 AATGGAATGGAATAGAGGCGTAATAG-T-ATTCTTGTGTTTGGTTG
1 AATGGAATAG-AT---GGCGTAATAGATAATCCTTGTGTTTGGTTG
*
35591487 AATGGAAT-GATGGTGTAATA
1 AATGGAATAGATGGCGTAATA
35591507 ACATAAGGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
39 8 0.15
41 9 0.16
42 3 0.05
43 1 0.02
44 23 0.42
45 1 0.02
46 10 0.18
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (42 bp):
AATGGAATAGATGGCGTAATAGATAATCCTTGTGTTTGGTTG
Found at i:35593216 original size:49 final size:49
Alignment explanation
Indices: 35593146--35593249 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
35593136 GAAAAAAAAT
* * ** * *
35593146 AAATTAAAATTAAGTTTAATATCATGACTCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTATATA
*
35593195 AAATTAAAATTGAGTTCAATATCATGAATCAAAAACTCAACACTATATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTATATA
35593244 AAATTA
1 AAATTA
35593250 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTATATA
Found at i:35596877 original size:20 final size:21
Alignment explanation
Indices: 35596827--35596883 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
35596817 GAAAGAATGC
*
35596827 TCAAGATTTGCTCCTAAAATA
1 TCAAGATTTGCACCTAAAATA
* *
35596848 TCTAATATTTGCACCTAATAT-
1 TC-AAGATTTGCACCTAAAATA
35596869 TCAAGATTT-CACCTA
1 TCAAGATTTGCACCTA
35596884 GTGGACTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.19
20 6 0.19
21 4 0.13
22 15 0.48
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (21 bp):
TCAAGATTTGCACCTAAAATA
Found at i:35600624 original size:18 final size:19
Alignment explanation
Indices: 35600593--35600656 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
35600583 TTTGCTATTA
*
35600593 TTATTATTTTTACTACTAT
1 TTATTATTTATACTACTAT
*
35600612 TTATTA-TTATACTGCTAT
1 TTATTATTTATACTACTAT
* * *
35600630 GTACCTATTTATA-TATTATT
1 TTA-TTATTTATACTACTA-T
35600650 TTATTAT
1 TTATTAT
35600657 ACTATTATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 12 0.35
19 14 0.41
20 8 0.24
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTATTTATACTACTAT
Found at i:35600662 original size:16 final size:15
Alignment explanation
Indices: 35600638--35600667 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35600628 ATGTACCTAT
35600638 TTATATATTATTTTA
1 TTATATATTATTTTA
35600653 TTATACTATTATTTT
1 TTATA-TATTATTTT
35600668 TTAAACCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATTATTTTA
Found at i:35605583 original size:26 final size:26
Alignment explanation
Indices: 35605554--35605613 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
35605544 AAAAATGGTC
35605554 AAAATCAAAATAAAAAACAAAAAAGA
1 AAAATCAAAATAAAAAACAAAAAAGA
* * **
35605580 AAAATCAAAGTCAAAAGTAAAAAAGA
1 AAAATCAAAATAAAAAACAAAAAAGA
*
35605606 GAAATCAA
1 AAAATCAA
35605614 TTAAAGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.73, C:0.08, G:0.08, T:0.10
Consensus pattern (26 bp):
AAAATCAAAATAAAAAACAAAAAAGA
Found at i:35607383 original size:87 final size:87
Alignment explanation
Indices: 35607237--35607496 Score: 412
Period size: 87 Copynumber: 3.0 Consensus size: 87
35607227 GTGAATATAA
*
35607237 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
35607302 GCGTTGACAGTGAAGCAGATCG
66 GCGTTGACAGTGAAGCAGATCG
35607324 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * * * *
35607389 GTGTTAACAGCGGAGCAAATCG
66 GCGTTGACAGTGAAGCAGATCG
* * * * *
35607411 AAAACAAAGCATTGCCTCCATTGGTTTTAGTGAAGCTGGTTAAAGATAGCAGATCTTGCCCTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
35607476 GCGTCGACAGTGAAGCAGATC
66 GCGTTGACAGTGAAGCAGATC
35607497 AAAGATTACA
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 156 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (87 bp):
AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
GCGTTGACAGTGAAGCAGATCG
Found at i:35607647 original size:44 final size:44
Alignment explanation
Indices: 35607553--35607665 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 44
35607543 AAATTACAAG
*
35607553 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGACATAAGAAATCAA
1 TCTTATCTCCCTAAAGCAGTAGTGGAGCAGACATAAAAAATCAA
* ** *
35607596 TCCTATCTCCCTAAAGTTGTAGTGGAGCAGA-TTAAAACAAT-ATA
1 TCTTATCTCCCTAAAGCAGTAGTGGAGCAGACATAAAA-AATCA-A
35607640 TCTTATCTCCCT-AAGCAGTAGTGGAG
1 TCTTATCTCCCTAAAGCAGTAGTGGAG
35607666 AAAATCACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 28 0.47
44 31 0.53
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTAAAGCAGTAGTGGAGCAGACATAAAAAATCAA
Found at i:35607970 original size:129 final size:129
Alignment explanation
Indices: 35607740--35608001 Score: 335
Period size: 129 Copynumber: 2.0 Consensus size: 129
35607730 AAGAAGCAAA
* * ** * *
35607740 TCTTATCTCCTTGAGGTTGTAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATTGAAGCCGATAATCCTACCTCCCTAAAGTTGTA
* * * * ** * *
35607805 GTGGGGCGGATTAAGGTAATAGATCTTACCTCTCTGAAGTTGCAGTAGAGTGGATTGCATCAGG
66 GTAGAGCGGATTAAAGTAATAGATCTTACCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAG
* ** * *
35607869 TCTTATCTCCCTGAGATTACAGTGGAACAGATTGAGGTTGGTAATCCTACCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATTGAAGCCGATAATCCTACCTCCCTAAAGTTGTA
* *
35607934 GTAGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAG
66 GTAGAGCGGATTAAAGTAATAGATCTTACCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAG
35607998 TCTT
1 TCTT
35608002 GCCGACTAGA
Statistics
Matches: 112, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
129 112 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (129 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATTGAAGCCGATAATCCTACCTCCCTAAAGTTGTA
GTAGAGCGGATTAAAGTAATAGATCTTACCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAAG
Found at i:35609566 original size:16 final size:15
Alignment explanation
Indices: 35609542--35609571 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35609532 ATGTACCTAT
35609542 TTATATATTATTTTA
1 TTATATATTATTTTA
35609557 TTATACTATTATTTT
1 TTATA-TATTATTTT
35609572 TTAAACTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATTATTTTA
Found at i:35609811 original size:8 final size:8
Alignment explanation
Indices: 35609798--35609836 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
35609788 TTGAAACTCT
35609798 TACATATA
1 TACATATA
35609806 TACATATA
1 TACATATA
*
35609814 TACATACA
1 TACATATA
*
35609822 TATATATA
1 TACATATA
*
35609830 TATATAT
1 TACATAT
35609837 TATTTGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (8 bp):
TACATATA
Found at i:35609823 original size:20 final size:20
Alignment explanation
Indices: 35609798--35609835 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35609788 TTGAAACTCT
35609798 TACATATATACATATATACA
1 TACATATATACATATATACA
*
35609818 TACATATATATATATATA
1 TACATATATACATATATA
35609836 TTATTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
TACATATATACATATATACA
Found at i:35632709 original size:17 final size:17
Alignment explanation
Indices: 35632687--35632722 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35632677 CTGAAGAACA
35632687 TTGAGAAACCATAGAGT
1 TTGAGAAACCATAGAGT
35632704 TTGAGAAACCATAGAGT
1 TTGAGAAACCATAGAGT
35632721 TT
1 TT
35632723 TTGTTACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (17 bp):
TTGAGAAACCATAGAGT
Found at i:35637105 original size:17 final size:18
Alignment explanation
Indices: 35637069--35637106 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35637059 ATTGCTTCTC
* *
35637069 AAAAGTACTTTTGGGCCA
1 AAAAGCACTTTTGAGCCA
35637087 AAAAGCACTTTTGAG-CA
1 AAAAGCACTTTTGAGCCA
35637104 AAA
1 AAA
35637107 GCTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (18 bp):
AAAAGCACTTTTGAGCCA
Found at i:35639707 original size:12 final size:12
Alignment explanation
Indices: 35639690--35639714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35639680 GGTGTTCATT
35639690 CGGTTAACCGAC
1 CGGTTAACCGAC
35639702 CGGTTAACCGAC
1 CGGTTAACCGAC
35639714 C
1 C
35639715 CGAAATTACT
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:35639968 original size:9 final size:9
Alignment explanation
Indices: 35639875--35639969 Score: 102
Period size: 9 Copynumber: 10.4 Consensus size: 9
35639865 TTTGGTTAAA
35639875 AATTACCCG
1 AATTACCCG
* *
35639884 AATTATCCA
1 AATTACCCG
35639893 AATTACCCG
1 AATTACCCG
*
35639902 AATTAACCG
1 AATTACCCG
35639911 AATTACCCG
1 AATTACCCG
*
35639920 AATTAACCG
1 AATTACCCG
*
35639929 AATTAACCG
1 AATTACCCG
35639938 AATTA-CCG
1 AATTACCCG
* *
35639946 AAAAATATCCG
1 --AATTACCCG
35639957 AATTACCCG
1 AATTACCCG
35639966 AATT
1 AATT
35639970 TTTTTTATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
8 3 0.04
9 63 0.86
10 4 0.05
11 3 0.04
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:35642854 original size:87 final size:88
Alignment explanation
Indices: 35642700--35642925 Score: 237
Period size: 87 Copynumber: 2.6 Consensus size: 88
35642690 TGCCTTCTTC
* * *
35642700 TTTTTCCACTCAATTTA-GTACTTGAACTTTTAAAATGCATAAAAAGGCCCCCGAACATTTTCAA
1 TTTTTACACTCAA-TTAGGTACTTGAACTTTCAAAATGCATAAAAA-GACCCCGAACATTTTCAA
*
35642764 AAAAAAGCTATAAAGCCC-CA-TTT
64 AAAAAAGCAATAAAGCCCTCACTTT
* * *** *
35642787 TTTTTGCATTCAATTAGGTACTTGAACTTTCAAAATGCATCAAAAAGACCTTTAACCTTTTTC-A
1 TTTTTACACTCAATTAGGTACTTGAACTTTCAAAATGCAT-AAAAAGACCCCGAA-CATTTTCAA
* *
35642851 AAAAAAGCAATTAAGCCCTTACTTT
64 AAAAAAGCAATAAAGCCCTCACTTT
* *
35642876 TTTTTACACTCAATTGGGTACTT-AAATTGTCAAAATGCATTAAAAAGACC
1 TTTTTACACTCAATTAGGTACTTGAACTT-TCAAAATGCA-TAAAAAGACC
35642926 ATTTGATTGT
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
86 3 0.03
87 55 0.47
88 16 0.14
89 42 0.36
90 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (88 bp):
TTTTTACACTCAATTAGGTACTTGAACTTTCAAAATGCATAAAAAGACCCCGAACATTTTCAAAA
AAAAGCAATAAAGCCCTCACTTT
Found at i:35643049 original size:17 final size:18
Alignment explanation
Indices: 35643027--35643141 Score: 69
Period size: 19 Copynumber: 6.3 Consensus size: 18
35643017 CATGTGGCAA
*
35643027 AAAAATTTATAAAAA-AT
1 AAAAATTAATAAAAATAT
*
35643044 AAAAATCAATAAAAATTAT
1 AAAAATTAATAAAAA-TAT
* * *
35643063 AAAAATT-ATTAAACTTT
1 AAAAATTAATAAAAATAT
* *
35643080 AATAAAATATTAAAAAT-T
1 AA-AAATTAATAAAAATAT
35643098 AAAAAATTAGA-AAAAATAT
1 -AAAAATTA-ATAAAAATAT
*
35643117 AAAAATCATAA-AAAAATTT
1 AAAAAT--TAATAAAAATAT
35643136 AAAAAT
1 AAAAAT
35643142 GTATTTTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
17 17 0.22
18 27 0.36
19 30 0.39
20 2 0.03
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.29
Consensus pattern (18 bp):
AAAAATTAATAAAAATAT
Found at i:35643064 original size:9 final size:9
Alignment explanation
Indices: 35643027--35643130 Score: 81
Period size: 9 Copynumber: 11.6 Consensus size: 9
35643017 CATGTGGCAA
35643027 AAAAATTTAT
1 AAAAA-TTAT
35643037 AAAAA--AT
1 AAAAATTAT
*
35643044 AAAAATCAAT
1 AAAAAT-TAT
35643054 AAAAATTAT
1 AAAAATTAT
35643063 AAAAATTAT
1 AAAAATTAT
* *
35643072 TAAACTT-T
1 AAAAATTAT
*
35643080 AATAAAATATT
1 AA-AAATTA-T
35643091 AAAAATTA-
1 AAAAATTAT
*
35643099 AAAAATTAG
1 AAAAATTAT
*
35643108 AAAAAATAT
1 AAAAATTAT
*
35643117 AAAAATCAT
1 AAAAATTAT
35643126 AAAAA
1 AAAAA
35643131 AATTTAAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
7 7 0.09
8 10 0.13
9 38 0.50
10 18 0.24
11 3 0.04
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35643373 original size:21 final size:20
Alignment explanation
Indices: 35643347--35643407 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
35643337 TTGGTACGAT
35643347 AATTTTTATAATTTTTTTAC
1 AATTTTTATAATTTTTTTAC
*
35643367 GAA-TTTTATAACTTTTTTAC
1 -AATTTTTATAATTTTTTTAC
*
35643387 ATTTTTTTATAATTTATTTTA
1 A-ATTTTTATAATTT-TTTTA
35643408 AAAAATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 16 0.47
21 12 0.35
22 5 0.15
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
AATTTTTATAATTTTTTTAC
Found at i:35643709 original size:91 final size:89
Alignment explanation
Indices: 35643554--35643740 Score: 234
Period size: 91 Copynumber: 2.1 Consensus size: 89
35643544 TCAAAGGGTT
* * * * * *
35643554 TTTTTTATGCATTTTGGCAATTCAAGTATCCAATTAAGTGCAAAAAAAAAAGTAGGGGCTTAATT
1 TTTTTTATACATTTTGGAAATTCAAGTACCCAATTAAGTGAAAAAAAAAAAGCAGAGGCTTAATT
* * *
35643619 GCTTTTTTTGAAAGAGTTTGAGGG
66 ACTCTTTTTGAAAAAGTTTGAGGG
*
35643643 CCTTTTTTATACATTTT-GAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGAAGCA-AGGCTT
1 --TTTTTTATACATTTTGGAAA-TTCAAGTACCCAATTAAGTGAAAAAAAAA-AAGCAGAGGCTT
35643706 AATTACTCTTTTTGAAAAAGTTTGAGGG
62 AATTACTCTTTTTGAAAAAGTTTGAGGG
35643734 TTTTTTA
1 TTTTTTA
35643741 CGCCCTTAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
89 7 0.08
90 3 0.04
91 70 0.83
92 4 0.05
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (89 bp):
TTTTTTATACATTTTGGAAATTCAAGTACCCAATTAAGTGAAAAAAAAAAAGCAGAGGCTTAATT
ACTCTTTTTGAAAAAGTTTGAGGG
Found at i:35647666 original size:33 final size:34
Alignment explanation
Indices: 35647528--35647667 Score: 97
Period size: 33 Copynumber: 4.1 Consensus size: 34
35647518 TTATCATCAG
*
35647528 AATGCCATAGCCCAGCTATGGTCTTACACATGTATCTAT
1 AATGCCATAGCCCAGCTATGGTCTT-CACA--T-T-TAA
* * * * * *
35647567 ACTGCCATAGTCCAACCATGGTCTT-ACGTTCAA
1 AATGCCATAGCCCAGCTATGGTCTTCACATTTAA
* * * * **
35647600 GATGCCATAACCCAGTTATAGTCTTTTCA-TTAA
1 AATGCCATAGCCCAGCTATGGTCTTCACATTTAA
35647633 AATGCCATAGCCCAGCTATGGTC-TCACATTTAA
1 AATGCCATAGCCCAGCTATGGTCTTCACATTTAA
35647666 AA
1 AA
35647668 ATTTCCATGG
Statistics
Matches: 75, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
32 3 0.04
33 46 0.61
34 2 0.03
35 1 0.01
37 2 0.03
39 21 0.28
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (34 bp):
AATGCCATAGCCCAGCTATGGTCTTCACATTTAA
Found at i:35655940 original size:22 final size:22
Alignment explanation
Indices: 35655915--35655959 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35655905 AACTAACTGC
35655915 ACAACTAACTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
*
35655937 ACAACTAATTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
35655959 A
1 A
35655960 ACAGTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (22 bp):
ACAACTAACTAACTGATAAGCT
Found at i:35662151 original size:78 final size:77
Alignment explanation
Indices: 35662022--35662238 Score: 346
Period size: 78 Copynumber: 2.8 Consensus size: 77
35662012 AACAGCAGGT
* * *
35662022 TCTAGACGT-GGTGCTTCTGGTAACGAGTCCGATAAAGCTTGAGAAGAAGATGCTGCTGCTGTTG
1 TCTAGAC-TAGGTGCGTCTGGTAATGAATCCGA-AAAGCTTGAGAAGAAGATGCTGCTGCTGTTG
35662086 GAGAACTAGTCGGA
64 GAGAACTAGTCGGA
35662100 TCTAGACTAGGTGCGTCTGGTAATGAATCCGAAAACGCTTGAGAAGAAGATGCTGCTGCTGTTGG
1 TCTAGACTAGGTGCGTCTGGTAATGAATCCGAAAA-GCTTGAGAAGAAGATGCTGCTGCTGTTGG
35662165 AGAACTAGTCGGA
65 AGAACTAGTCGGA
* *
35662178 TCTAGACTAGGTGCGTCTGGTAATGAATCTGAAAATGCTTGAGAAGAAGATGCTACTGCTG
1 TCTAGACTAGGTGCGTCTGGTAATGAATCCGAAAA-GCTTGAGAAGAAGATGCTGCTGCTG
35662239 GAGAAAATTC
Statistics
Matches: 131, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
77 4 0.03
78 127 0.97
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (77 bp):
TCTAGACTAGGTGCGTCTGGTAATGAATCCGAAAAGCTTGAGAAGAAGATGCTGCTGCTGTTGGA
GAACTAGTCGGA
Found at i:35664932 original size:22 final size:22
Alignment explanation
Indices: 35664907--35664951 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35664897 AACTAACTGC
35664907 ACAACTAACTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
*
35664929 ACAACTAATTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
35664951 A
1 A
35664952 ACAGTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (22 bp):
ACAACTAACTAACTGATAAGCT
Found at i:35665986 original size:22 final size:22
Alignment explanation
Indices: 35665961--35666005 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
35665951 AACTAACTGC
35665961 ACAACTAACTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
*
35665983 ACAACTAATTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
35666005 A
1 A
35666006 ATAGTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (22 bp):
ACAACTAACTAACTGATAAGCT
Found at i:35666584 original size:25 final size:24
Alignment explanation
Indices: 35666535--35666585 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
35666525 GTGTATTTCA
35666535 TTTTTTTTTGAATTTTATAATTTT
1 TTTTTTTTTGAATTTTATAATTTT
35666559 TTTTATTTTTGAATATATTAT-ATTTT
1 TTTT-TTTTTGAAT-T-TTATAATTTT
35666585 T
1 T
35666586 AAATTATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 4 0.17
25 9 0.38
26 7 0.29
27 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTTTTTTGAATTTTATAATTTT
Found at i:35682677 original size:16 final size:16
Alignment explanation
Indices: 35682656--35682687 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35682646 ACTTAATTGG
*
35682656 ATTTTTTATTTTTAAT
1 ATTTTTTATTCTTAAT
35682672 ATTTTTTATTCTTAAT
1 ATTTTTTATTCTTAAT
35682688 TAGTTCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTCTTAAT
Found at i:35686395 original size:39 final size:43
Alignment explanation
Indices: 35686291--35686399 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
35686281 GAAAAGAGGC
35686291 GTAATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTT--AT
* * *
35686336 GTAATGGAATAGAGGCGTAATAG-TAATC-TTGTGTTTGG-T-T
1 GTAATGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTAT
35686376 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGTGTAATAGCA
35686400 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 2 0.04
44 11 0.19
45 22 0.39
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
GTAATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTAT
Found at i:35687389 original size:13 final size:13
Alignment explanation
Indices: 35687373--35687401 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35687363 ACCTTACCAA
35687373 AACGATAGAAGAG
1 AACGATAGAAGAG
35687386 AACGATAGAAGAG
1 AACGATAGAAGAG
35687399 AAC
1 AAC
35687402 AGGGGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.10, G:0.28, T:0.07
Consensus pattern (13 bp):
AACGATAGAAGAG
Found at i:35711777 original size:38 final size:38
Alignment explanation
Indices: 35711735--35711875 Score: 158
Period size: 38 Copynumber: 4.0 Consensus size: 38
35711725 GCAGAAACTG
* *
35711735 GCAAATCGGTAGAAAAGAAAAGAAAAGAAACAAAGGGA
1 GCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGGGA
*
35711773 GCAAATCGGCAGAAAAGAAAAGAAAATAAAC--A--GA
1 GCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGGGA
*
35711807 G------GGCAGAAAAGAAAAGAAAAGAAACGGAGGGA
1 GCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGGGA
* *
35711839 GCAAATCGGCAGGAAAGAAAAGAAAATAAACAGAGGG
1 GCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGGG
35711876 CAGAAAAGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
28 23 0.26
30 1 0.01
32 3 0.03
34 3 0.03
36 1 0.01
38 56 0.64
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.04
Consensus pattern (38 bp):
GCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGGGA
Found at i:35711811 original size:28 final size:28
Alignment explanation
Indices: 35711780--35711891 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 28
35711770 GGAGCAAATC
35711780 GGCAGAAAAGAAAAGAAAATAAACAGAG
1 GGCAGAAAAGAAAAGAAAATAAACAGAG
* *
35711808 GGCAGAAAAGAAAAGAAAAGAAACGGAG
1 GGCAGAAAAGAAAAGAAAATAAACAGAG
35711836 GG-AGCAAATCGGCAGGAAAGAAAAGAAAATAAACAGAG
1 GGCAG-AAA-----A-G----AAAAGAAAATAAACAGAG
35711874 GGCAGAAAAGAAAAGAAA
1 GGCAGAAAAGAAAAGAAA
35711892 CGGAGGGAGC
Statistics
Matches: 68, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
27 2 0.03
28 39 0.57
32 1 0.01
33 2 0.03
34 1 0.01
38 21 0.31
39 2 0.03
ACGTcount: A:0.61, C:0.08, G:0.29, T:0.03
Consensus pattern (28 bp):
GGCAGAAAAGAAAAGAAAATAAACAGAG
Found at i:35711815 original size:66 final size:66
Alignment explanation
Indices: 35711745--35711891 Score: 267
Period size: 66 Copynumber: 2.2 Consensus size: 66
35711735 GCAAATCGGT
35711745 AGAAAAGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGG
1 AGAAAAGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGG
35711810 C
66 C
** *
35711811 AGAAAAGAAAAGAAAAGAAACGGAGGGAGCAAATCGGCAGGAAAGAAAAGAAAATAAACAGAGGG
1 AGAAAAGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGG
35711876 C
66 C
35711877 AGAAAAGAAAAGAAA
1 AGAAAAGAAAAGAAA
35711892 CGGAGGGAGC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.62, C:0.08, G:0.27, T:0.03
Consensus pattern (66 bp):
AGAAAAGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGG
C
Found at i:35711825 original size:61 final size:61
Alignment explanation
Indices: 35711750--35711912 Score: 245
Period size: 66 Copynumber: 2.6 Consensus size: 61
35711740 TCGGTAGAAA
35711750 AGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGGC
1 AGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGGC
* *
35711811 AGAAAAGAAAAGAAAAGAAACGGAGGGAGCAAATCGGCAGGAAAGAAAAGAAAATAAACAGAGGG
1 AGAAAAGAAAAG-AAA-CAA---AGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGG
35711876 C
61 C
**
35711877 AGAAAAGAAAAGAAACGGAGGGAGCAAATCGGCAGA
1 AGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGA
35711913 GGCTAGAAGG
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
61 29 0.32
62 3 0.03
63 2 0.02
65 3 0.03
66 54 0.59
ACGTcount: A:0.58, C:0.10, G:0.29, T:0.03
Consensus pattern (61 bp):
AGAAAAGAAAAGAAACAAAGGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGGC
Found at i:35711880 original size:23 final size:23
Alignment explanation
Indices: 35711854--35711898 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35711844 TCGGCAGGAA
*
35711854 AGAAAAGAAAATAAACAGAGGGC
1 AGAAAAGAAAAGAAACAGAGGGC
*
35711877 AGAAAAGAAAAGAAACGGAGGG
1 AGAAAAGAAAAGAAACAGAGGG
35711899 AGCAAATCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.31, T:0.02
Consensus pattern (23 bp):
AGAAAAGAAAAGAAACAGAGGGC
Found at i:35713474 original size:22 final size:23
Alignment explanation
Indices: 35713441--35713506 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 23
35713431 TTCAGTTATG
*
35713441 AAAT-TATCTTTTATAGATAAAT
1 AAATATATATTTTATAGATAAAT
35713463 AAATAT-TATTTTA-AGAGT--AT
1 AAATATATATTTTATAGA-TAAAT
*
35713483 TAATATATATTTT-TA-ATAAAT
1 AAATATATATTTTATAGATAAAT
35713504 AAA
1 AAA
35713507 GAAAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
19 1 0.03
20 8 0.23
21 14 0.40
22 11 0.31
23 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
AAATATATATTTTATAGATAAAT
Found at i:35714167 original size:20 final size:20
Alignment explanation
Indices: 35714142--35714180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35714132 ATTATTAAAA
**
35714142 ATACTTTTTTTATAATTTTT
1 ATACTTTTTCAATAATTTTT
35714162 ATACTTTTTCAATAATTTT
1 ATACTTTTTCAATAATTTT
35714181 AATGATTTTT
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:0.08, G:0.00, T:0.64
Consensus pattern (20 bp):
ATACTTTTTCAATAATTTTT
Found at i:35714180 original size:29 final size:28
Alignment explanation
Indices: 35714148--35714217 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
35714138 AAAAATACTT
*
35714148 TTTTTATAATTTTTATACTTTTT-CAATAA
1 TTTTTATAATTTTTA-A-TTTTTAAAATAA
* *
35714177 TTTTAATGATTTTTAATTTTTAAAAATAA
1 TTTTTATAATTTTTAATTTTT-AAAATAA
*
35714206 ATTTTATAATTT
1 TTTTTATAATTT
35714218 ATTCGAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.15
28 1 0.03
29 27 0.82
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTTTATAATTTTTAATTTTTAAAATAA
Found at i:35718440 original size:11 final size:11
Alignment explanation
Indices: 35718411--35718461 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
35718401 ATATCCAAAC
*
35718411 AATAATAACAA
1 AATAATAGCAA
35718422 AATAATAGCAA
1 AATAATAGCAA
*
35718433 CATAATAG-AGA
1 AATAATAGCA-A
**
35718444 AATGGTAGCAA
1 AATAATAGCAA
35718455 AATAATA
1 AATAATA
35718462 AAAAAGAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
10 1 0.03
11 29 0.94
12 1 0.03
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.20
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:35718507 original size:22 final size:22
Alignment explanation
Indices: 35718477--35718519 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35718467 GAAGAAGAAG
*
35718477 AAAATAGCAACAAAACAATAAA
1 AAAACAGCAACAAAACAATAAA
* *
35718499 AAAACAGCAAGAAAATAATAA
1 AAAACAGCAACAAAACAATAA
35718520 TGGAACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAACAGCAACAAAACAATAAA
Found at i:35718528 original size:92 final size:93
Alignment explanation
Indices: 35718422--35718607 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 93
35718412 ATAATAACAA
35718422 AATAATAGCAACATAATAGAGAAATGGTAGCAAAATAATAAAAAAGAAGAAGAAGAAAATAGCAA
1 AATAATAGCAACATAATAGAGAAATGGTAGCAAAATAATAAAAAAGAAGAAGAAGAAAATAGCAA
35718487 CAAAACAATAAAAAAACAGCAAGAAAAT
66 CAAAACAATAAAAAAACAGCAAGAAAAT
*
35718515 AATAAT-GGAACATAATAGAGAAATGGTAGCAAAATAATAAAAAAGAAGAAGAAGAAAATAGCAA
1 AATAATAGCAACATAATAGAGAAATGGTAGCAAAATAATAAAAAAGAAGAAGAAGAAAATAGCAA
35718579 CAAAACAATAAAAAAACAGCAAGAAAAT
66 CAAAACAATAAAAAAACAGCAAGAAAAT
35718607 A
1 A
35718608 GTAAAAAAAA
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 86 0.93
93 6 0.07
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.12
Consensus pattern (93 bp):
AATAATAGCAACATAATAGAGAAATGGTAGCAAAATAATAAAAAAGAAGAAGAAGAAAATAGCAA
CAAAACAATAAAAAAACAGCAAGAAAAT
Found at i:35718599 original size:22 final size:22
Alignment explanation
Indices: 35718569--35718616 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
35718559 GAAGAAGAAG
*
35718569 AAAATAGCAACAAAACAATAAA
1 AAAACAGCAACAAAACAATAAA
* * *
35718591 AAAACAGCAAGAAAATAGTAAA
1 AAAACAGCAACAAAACAATAAA
35718613 AAAA
1 AAAA
35718617 ATAGCTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.10, G:0.08, T:0.08
Consensus pattern (22 bp):
AAAACAGCAACAAAACAATAAA
Found at i:35719827 original size:20 final size:21
Alignment explanation
Indices: 35719802--35719858 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 21
35719792 TAATTAAATC
35719802 TAAATAAT-TATTTATATTTT
1 TAAATAATCTATTTATATTTT
*
35719822 TAAAT-ATCTATTT-TAATTT
1 TAAATAATCTATTTATATTTT
*
35719841 T-AATAATGTATTTA-ATTT
1 TAAATAATCTATTTATATTT
35719859 GTGAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.10
19 18 0.58
20 10 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TAAATAATCTATTTATATTTT
Found at i:35720953 original size:22 final size:23
Alignment explanation
Indices: 35720909--35720954 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35720899 CATTCACTCA
* *
35720909 TTTTTTATATTAATTCGTAAGTT
1 TTTTTTATATAAAATCGTAAGTT
*
35720932 TTTTTTATATAAAAT-GTGAGTT
1 TTTTTTATATAAAATCGTAAGTT
35720954 T
1 T
35720955 AGTATTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (23 bp):
TTTTTTATATAAAATCGTAAGTT
Found at i:35729055 original size:5 final size:5
Alignment explanation
Indices: 35729045--35729076 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
35729035 TCCTAGTATG
35729045 TGAAT TGAAT TGAAT TGAAT TGAAT ATGAAT T
1 TGAAT TGAAT TGAAT TGAAT TGAAT -TGAAT T
35729077 TTATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:35729800 original size:25 final size:25
Alignment explanation
Indices: 35729729--35729800 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 25
35729719 CTTCCTGAGT
* *
35729729 ATGACTCTTATGAGCTTCCTGTTAT
1 ATGACTCATATGAGCTTCCTGTTAC
* * *
35729754 A-G-CCCAGATAAGCTTCCTGTTAC
1 ATGACTCATATGAGCTTCCTGTTAC
*
35729777 ATGACTCATATGAGCTTCCCGTTA
1 ATGACTCATATGAGCTTCCTGTTA
35729801 TATAGCTCGA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
23 17 0.47
24 2 0.06
25 17 0.47
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (25 bp):
ATGACTCATATGAGCTTCCTGTTAC
Found at i:35730654 original size:16 final size:17
Alignment explanation
Indices: 35730626--35730660 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
35730616 GAATCACACC
*
35730626 ATGAATGTCACAAGTGA
1 ATGAATGTCACAAATGA
35730643 ATGAAT-TCACAAATGA
1 ATGAATGTCACAAATGA
35730659 AT
1 AT
35730661 TCAGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (17 bp):
ATGAATGTCACAAATGA
Found at i:35732918 original size:38 final size:38
Alignment explanation
Indices: 35732861--35732936 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
35732851 CTTGCTTCAT
** * *
35732861 TTTCTTTTCCGGTTTAAACACCCTAGCTGAAGTCCCAA
1 TTTCTTTTCCAATTCAAACACCCAAGCTGAAGTCCCAA
35732899 TTTCTTTTCCAATTCAAACACCCAAGCTGAAGTCCCAA
1 TTTCTTTTCCAATTCAAACACCCAAGCTGAAGTCCCAA
35732937 CTACTTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.32
Consensus pattern (38 bp):
TTTCTTTTCCAATTCAAACACCCAAGCTGAAGTCCCAA
Found at i:35741432 original size:15 final size:17
Alignment explanation
Indices: 35741402--35741434 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35741392 TGTTAACACC
35741402 TAAAATATATTATATAG
1 TAAAATATATTATATAG
35741419 TAAAATA-ATATATATA
1 TAAAATATAT-TATATA
35741435 CAAAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAATATATTATATAG
Found at i:35741480 original size:18 final size:18
Alignment explanation
Indices: 35741449--35741483 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35741439 AAATGTAAAT
35741449 AAATATATAAACTAATAC
1 AAATATATAAACTAATAC
35741467 AAATA-ATAATACTAATA
1 AAATATATAA-ACTAATA
35741484 ATTATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATATAAACTAATAC
Done.