Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 136 of 292
Found at i:40416572 original size:26 final size:27
Alignment explanation
Indices: 40416506--40416572 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
40416496 GACTGTGGAA
*
40416506 TGGGTTTTTGAAATTTTTTCTCAAAAT
1 TGGGTTTTTGAAAGTTTTTCTCAAAAT
* ** *
40416533 TGGGTATTCAAAAGTTTTTCT-AAACCT
1 TGGGTTTTTGAAAGTTTTTCTCAAA-AT
40416560 T-GGTTTTTGAAAG
1 TGGGTTTTTGAAAG
40416573 AGATGATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
26 12 0.39
27 19 0.61
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (27 bp):
TGGGTTTTTGAAAGTTTTTCTCAAAAT
Found at i:40420576 original size:27 final size:28
Alignment explanation
Indices: 40420546--40420611 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
40420536 GACTGTGGAA
40420546 TGGGTTTTTGAAAA-TTTTTCTCAAA-AT
1 TGGGTTTTTGAAAAGTTTTTCT-AAACAT
* *
40420573 TGGG-TTTTCAAAAGTTTTTCTAAACCT
1 TGGGTTTTTGAAAAGTTTTTCTAAACAT
40420600 T-GGTTTTTGAAA
1 TGGGTTTTTGAAA
40420612 GAGATGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (28 bp):
TGGGTTTTTGAAAAGTTTTTCTAAACAT
Found at i:40434508 original size:40 final size:40
Alignment explanation
Indices: 40434448--40434615 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 40
40434438 TATTCGAATG
* * *
40434448 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGCT
* * *
40434488 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGCT
* * * * **
40434528 ATATCCGGGCTATGACCCGAAGGCATTTATGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGCT
* *
40434568 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGCT
40434608 ATATCCGG
1 ATATCCGG
40434616 TTAAATCCCA
Statistics
Matches: 107, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGCT
Found at i:40434581 original size:80 final size:80
Alignment explanation
Indices: 40434448--40434615 Score: 246
Period size: 80 Copynumber: 2.1 Consensus size: 80
40434438 TATTCGAATG
* * * * * *
40434448 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGGCTATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGACCCGAAGGCA
40434513 TTTGTGCGAGTTGCT
66 TTTGTGCGAGTTGCT
* * *
40434528 ATATCCGGGCTATGACCCGAAGGCATTTATGCTAGCGATTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGACCCGAAGGCA
*
40434593 TTTGTGCGAGTTGTT
66 TTTGTGCGAGTTGCT
40434608 ATATCCGG
1 ATATCCGG
40434616 TTAAATCCCA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGACCCGAAGGCA
TTTGTGCGAGTTGCT
Found at i:40442917 original size:40 final size:40
Alignment explanation
Indices: 40442857--40443064 Score: 283
Period size: 40 Copynumber: 5.2 Consensus size: 40
40442847 TATTCGAATG
* * * * *
40442857 ATATCCGGTCTAAGTCCCGAAGGCTTTTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* *
40442897 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * * * *
40442937 ATATCCGGGCTATGACCCGAAGGCATTTATGCTAG-CGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
40442977 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
*
40443017 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
40443057 ATATCCGG
1 ATATCCGG
40443065 TTAAATCCCA
Statistics
Matches: 147, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 145 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
Found at i:40445957 original size:24 final size:24
Alignment explanation
Indices: 40445916--40445967 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
40445906 CCTTCATACC
*
40445916 CATATACACATGAACACAT-CTATA
1 CATATACACATAAACACATAC-ATA
40445940 CATATACACA-AAAGCACATACATA
1 CATATACACATAAA-CACATACATA
40445964 CATA
1 CATA
40445968 CCTTCCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.21
Consensus pattern (24 bp):
CATATACACATAAACACATACATA
Found at i:40447192 original size:126 final size:126
Alignment explanation
Indices: 40447042--40447405 Score: 611
Period size: 126 Copynumber: 2.9 Consensus size: 126
40447032 GGATATTCGA
* * * *
40447042 ATATTCGAATATTCAAAACCAACAAAGAAAGCGAAACCCAGTATGTTAGGGCATGATTCTTCGAA
1 ATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAA
* *
40447107 TTCTTTAAATACCAAACATTGCCTTTATTTTGAAAATTTTTGAGAGTGAACTGGTAAGAGG
66 TTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTGGTAAGAGG
*
40447168 ATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCATTACGTTAGGGCACGATTCTTCGAA
1 ATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAA
*
40447233 TTCTTTAAATATCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTGGTAAGAGG
66 TTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTGGTAAGAGG
* * *
40447294 ATATTCGAATACTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTACGGCACGGTTCTTCGAA
1 ATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAA
*
40447359 TTCTTTAAATACTGAACATTGCCTTTATTTTGAAAGAATTTTGAGAG
66 TTCTTTAAATACCGAACATTGCCTTTATTTTGAAA-AATTTTGAGAG
40447406 AAGATCAATG
Statistics
Matches: 223, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
126 212 0.95
127 11 0.05
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (126 bp):
ATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTCGAA
TTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTGGTAAGAGG
Found at i:40447537 original size:13 final size:12
Alignment explanation
Indices: 40447504--40447554 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
40447494 CTAACCATAT
*
40447504 ATAAATAATAAAA
1 ATAATTAAT-AAA
40447517 ATAA-TAATAATA
1 ATAATTAATAA-A
*
40447529 GTAATTAATAGAA
1 ATAATTAATA-AA
40447542 ATAATTAATAAA
1 ATAATTAATAAA
40447554 A
1 A
40447555 CAACAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 11 0.33
13 19 0.58
14 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
ATAATTAATAAA
Found at i:40447887 original size:14 final size:14
Alignment explanation
Indices: 40447844--40447898 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
40447834 CTTCGCTTAA
40447844 AAATATAT-ATATAT
1 AAATATATAATA-AT
* *
40447858 ATATATTTACATAAT
1 AAATATATA-ATAAT
40447873 AAATATATAATAAT
1 AAATATATAATAAT
*
40447887 AAATAAATAATA
1 AAATATATAATA
40447899 TAATAATATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 22 0.65
15 9 0.26
16 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATAATAAT
Found at i:40447899 original size:19 final size:18
Alignment explanation
Indices: 40447870--40447906 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
40447860 ATATTTACAT
40447870 AATAAATATATAATAATA
1 AATAAATATATAATAATA
40447888 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
40447907 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:40447947 original size:63 final size:64
Alignment explanation
Indices: 40447879--40448028 Score: 177
Period size: 63 Copynumber: 2.4 Consensus size: 64
40447869 TAATAAATAT
* *
40447879 ATAATAATAAATAAATAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-A
1 ATAATAA-AAATAAA-AATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTA
40447940 AA
63 AA
* *
40447942 ATAATAAAAA-AACAAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAAA
1 ATAATAAAAATAA-AAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAA
*
40448006 ATAACAAAAATAAAAA-ATAAAAA
1 ATAATAAAAATAAAAATATAAAAA
40448029 AGGGGTTAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
61 14 0.18
62 11 0.14
63 34 0.45
64 15 0.20
65 2 0.03
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.25
Consensus pattern (64 bp):
ATAATAAAAATAAAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAA
Found at i:40448323 original size:18 final size:18
Alignment explanation
Indices: 40448300--40448372 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
40448290 ATAACAAGTA
*
40448300 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
40448318 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
40448336 ATGGT-TTAGTAGGGT-GTGG
1 -GGGTGAT-GGA-GGTAGTGG
40448355 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
40448373 ATAGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.63
19 10 0.23
20 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.27
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:40448351 original size:29 final size:30
Alignment explanation
Indices: 40448311--40448417 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 30
40448301 GGTGATGGAG
* *
40448311 TTAGTGGGGGTGATGGAGGTAGTGGATGGT
1 TTAGTAGGGGTGATGGAGGTAGTGGATAGT
40448341 TTAGTAGGGTGTGGGGGTGATGGAGGTAGTGGATAGT
1 TTAGTA-------GGGGTGATGGAGGTAGTGGATAGT
*
40448378 TTAGTA-GGGTGATGGAGTTAGTGG-TCAGT
1 TTAGTAGGGGTGATGGAGGTAGTGGAT-AGT
40448407 TTAGT-GGGGTG
1 TTAGTAGGGGTG
40448418 TTTAATTTAG
Statistics
Matches: 65, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
28 1 0.02
29 30 0.46
30 5 0.08
37 29 0.45
ACGTcount: A:0.18, C:0.01, G:0.50, T:0.32
Consensus pattern (30 bp):
TTAGTAGGGGTGATGGAGGTAGTGGATAGT
Found at i:40448364 original size:37 final size:37
Alignment explanation
Indices: 40448314--40448388 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40448304 GATGGAGTTA
*
40448314 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
40448351 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
40448388 G
1 G
40448389 ATGGAGTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
Found at i:40448813 original size:86 final size:85
Alignment explanation
Indices: 40448655--40448947 Score: 455
Period size: 85 Copynumber: 3.4 Consensus size: 85
40448645 AACAAAGATA
* * * *
40448655 AGATTTGT-AATTTTAGCTTGTTACCCTACTGCTTAGGGGGCTAAGGCGAGTCATTGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCTC
*
40448719 CACCACTGCTCGGCGAGCCC
66 CGCCACTGCTCGGCGAGCCC
*
40448739 A-AGTCTGTAAACTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGCCTTTGACCTGC
1 AGA-TCTGTAAA-TTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGC
*
40448803 TCCGCTACTGCTCGGCGAGCCC
64 TCCGCCACTGCTCGGCGAGCCC
* *
40448825 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCTC
* *
40448890 TGCCACTGCTTGGCGAGCCC
66 CGCCACTGCTCGGCGAGCCC
40448910 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGG
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGG
40448948 TACCCTACTG
Statistics
Matches: 191, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
83 1 0.01
84 5 0.03
85 107 0.56
86 77 0.40
87 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTTGACCTGCTC
CGCCACTGCTCGGCGAGCCC
Found at i:40448953 original size:16 final size:16
Alignment explanation
Indices: 40448932--40448963 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40448922 TTTAGCCTGT
40448932 TACCCTACTGCTTAGG
1 TACCCTACTGCTTAGG
40448948 TACCCTACTGCTTAGG
1 TACCCTACTGCTTAGG
40448964 GGGTTAAAGC
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:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (16 bp):
TACCCTACTGCTTAGG
Found at i:40449047 original size:44 final size:43
Alignment explanation
Indices: 40448995--40449277 Score: 159
Period size: 44 Copynumber: 6.5 Consensus size: 43
40448985 ATCTGCTCCA
* *
40448995 TTATTGCTTAGGGAGATAAGATCTATAATCTGCAGCTTGTTACC
1 TTATTGCTTAGGGAGATAA-ATCTGTAATCTTCAGCTTGTTACC
* * * * * *
40449039 TTATTGCTTAGGGCGTTAAAGCGTGT-ATCTT-TGATCTGCT-CC
1 TTATTGCTTAGGGAGATAAATC-TGTAATCTTCAGCT-TGTTACC
* * *
40449081 ACTATTGCTTAGGGAGATAAGATCTGTAATCTTTAGTTTGTTACC
1 -TTATTGCTTAGGGAGATAA-ATCTGTAATCTTCAGCTTGTTACC
* * * * *
40449126 TTATTGCTTAGAGAGTTAAAGCCTGCAATCTTTAGCTTGTTACCC
1 TTATTGCTTAGGGAGATAAA-TCTGTAATCTTCAGCTTGTTA-CC
* * * * * *
40449171 TT-TTGCTTAGGGAGTTAAAGC-CTACAGT-TCTC-GATCT-ATCCC
1 TTATTGCTTAGGGAGATAAATCTGTA-A-TCT-TCAGCT-TGTTACC
* *
40449213 ACTATTGCTTAGGGAGATAAGATCTGTAATTTTCAGCTTGTTACC
1 -TTATTGCTTAGGGAGATAA-ATCTGTAATCTTCAGCTTGTTACC
* *
40449258 CTATTGCTTAGGGAGTTAAA
1 TTATTGCTTAGGGAGATAAA
40449278 GCCTGCTGAA
Statistics
Matches: 182, Mismatches: 37, Indels: 41
0.70 0.14 0.16
Matches are distributed among these distances:
42 7 0.04
43 37 0.20
44 119 0.65
45 17 0.09
46 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (43 bp):
TTATTGCTTAGGGAGATAAATCTGTAATCTTCAGCTTGTTACC
Found at i:40449102 original size:87 final size:87
Alignment explanation
Indices: 40448956--40449147 Score: 312
Period size: 87 Copynumber: 2.2 Consensus size: 87
40448946 GGTACCCTAC
* *
40448956 TGCTTAGGGGGTTAAAGCGTGTATCTTTGATCTGCTCCATTATTGCTTAGGGAGATAAGATCTAT
1 TGCTTAGGGAGTTAAAGCGTGTATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTAT
40449021 AATCTGCAGCTTGTTACCTTAT
66 AATCTGCAGCTTGTTACCTTAT
* *
40449043 TGCTTAGGGCGTTAAAGCGTGTATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT
1 TGCTTAGGGAGTTAAAGCGTGTATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTAT
** *
40449108 AATCTTTAGTTTGTTACCTTAT
66 AATCTGCAGCTTGTTACCTTAT
*
40449130 TGCTTAGAGAGTTAAAGC
1 TGCTTAGGGAGTTAAAGC
40449148 CTGCAATCTT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 97 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (87 bp):
TGCTTAGGGAGTTAAAGCGTGTATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTAT
AATCTGCAGCTTGTTACCTTAT
Found at i:40460792 original size:126 final size:127
Alignment explanation
Indices: 40460567--40460814 Score: 428
Period size: 126 Copynumber: 2.0 Consensus size: 127
40460557 GTTTTAGTCT
*
40460567 TAAGAGGATATTCGAATATTCAAAACCAACAAAGAAAGCAAAACTCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACTCAGTACGTTAGGGCACGATT
* *
40460632 CTTCAAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTTAGA-ATGAACTGG
66 CTTCAAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGATGAACTGG
*
40460693 TAAGAGGATATTCGAATATTCAAGACAAACAAAGAAAGCAAAAC-CTAGTACGTTAGGGCACGAT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACTC-AGTACGTTAGGGCACGAT
*
40460757 TCTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGATGA
65 TCTTCAAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGATGA
40460815 TCAATGGATA
Statistics
Matches: 115, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
125 1 0.01
126 110 0.96
127 4 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (127 bp):
TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACTCAGTACGTTAGGGCACGATT
CTTCAAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGATGAACTGG
Found at i:40460971 original size:21 final size:21
Alignment explanation
Indices: 40460941--40460992 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40460931 AATAGTAATT
* *
40460941 AATAGAAATAATTAATAAAAC
1 AATAGTAATAATAAATAAAAC
* *
40460962 AATAGTAATAATAAATACAAT
1 AATAGTAATAATAAATAAAAC
40460983 AAT-GTAATAA
1 AATAGTAATAA
40460993 ACATTGCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (21 bp):
AATAGTAATAATAAATAAAAC
Found at i:40461236 original size:18 final size:18
Alignment explanation
Indices: 40461213--40461250 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40461203 GTCTATGTAT
40461213 AATAGAAATTTATATTTA
1 AATAGAAATTTATATTTA
40461231 AATAGAAATTTATATTTA
1 AATAGAAATTTATATTTA
40461249 AA
1 AA
40461251 ATAATTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
AATAGAAATTTATATTTA
Found at i:40461313 original size:19 final size:19
Alignment explanation
Indices: 40461266--40461327 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
40461256 TAACTTCGCT
*
40461266 TAAATATATATATATATATATT
1 TAAATA-ATATATATA-ATA-A
*
40461288 TACATAATATATATAATAA
1 TAAATAATATATATAATAA
40461307 TAAATAA-ATAATATAATAA
1 TAAATAATAT-ATATAATAA
40461326 TA
1 TA
40461328 TGAAACATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.06
19 17 0.47
20 3 0.08
21 9 0.25
22 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAATATATATAATAA
Found at i:40461408 original size:58 final size:58
Alignment explanation
Indices: 40461309--40461441 Score: 150
Period size: 58 Copynumber: 2.3 Consensus size: 58
40461299 TATAATAATA
* * * *
40461309 AATAAATAATATAATAAT-ATGAAACATAACTCAAATTAATTAAATTAATAG-AAAGT
1 AATAAAAAATATAAAAATAATGAAACATAACTCAAATTAATTAAATTAACAGTAAAAT
* *
40461365 AATAAAAAATATAAAAATAATGAGA-ATAAAGCTCAAATTAATTAATTTAACAGTAAAAT
1 AATAAAAAATATAAAAATAATGAAACAT-AA-CTCAAATTAATTAAATTAACAGTAAAAT
*
40461424 AA-CAAAAATA-AAAAATAA
1 AATAAAAAATATAAAAATAA
40461442 AAAAGGGGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
56 18 0.27
57 15 0.23
58 27 0.41
59 6 0.09
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (58 bp):
AATAAAAAATATAAAAATAATGAAACATAACTCAAATTAATTAAATTAACAGTAAAAT
Found at i:40461425 original size:56 final size:54
Alignment explanation
Indices: 40461308--40461437 Score: 138
Period size: 56 Copynumber: 2.3 Consensus size: 54
40461298 ATATAATAAT
* * *
40461308 AAATAAATAATATAATAATATGAAACATAACTCAAATTAATTAAATTAATAGAA
1 AAATAAAAAATATAAAAATATGAAACATAACTCAAATTAATTAAATTAACAGAA
* * *
40461362 AGTAATAAAAAATATAAAAATAATGAGA-ATAAAGCTCAAATTAATTAATTTAACAGTA
1 A--AATAAAAAATATAAAAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAACAGAA
40461420 AAATAACAAAA-ATAAAAA
1 AAATAA-AAAATATAAAAA
40461438 ATAAAAAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
54 1 0.02
56 30 0.47
57 11 0.17
58 22 0.34
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (54 bp):
AAATAAAAAATATAAAAATATGAAACATAACTCAAATTAATTAAATTAACAGAA
Found at i:40461739 original size:18 final size:18
Alignment explanation
Indices: 40461716--40461788 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
40461706 ATAAAAAGTA
*
40461716 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
40461734 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
40461752 ATGGT-TTAGTAGGGT-GTGG
1 -GGGTGAT-GGA-GGTAGTGG
40461771 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
40461789 ATGGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.63
19 10 0.23
20 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.27
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:40461767 original size:29 final size:29
Alignment explanation
Indices: 40461734--40461833 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 29
40461724 GAGTTAGTGG
40461734 GGGTGATGGAGGTAGTGGATGGTTTAGTA
1 GGGTGATGGAGGTAGTGGATGGTTTAGTA
40461763 GGGTGTGGGGGTGATGGAGGTAGTGGATGGTTTAGTA
1 --------GGGTGATGGAGGTAGTGGATGGTTTAGTA
* *
40461800 GGGTGATGGAGTTAGTGG-TCGGTTTAGTG
1 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
40461829 GGGTG
1 GGGTG
40461834 TTTAATTTGG
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.02
29 30 0.50
37 29 0.48
ACGTcount: A:0.16, C:0.01, G:0.52, T:0.31
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGATGGTTTAGTA
Found at i:40461780 original size:37 final size:37
Alignment explanation
Indices: 40461730--40461804 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
40461720 GATGGAGTTA
40461730 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
40461767 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
40461804 G
1 G
40461805 ATGGAGTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.55, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
Found at i:40463012 original size:30 final size:31
Alignment explanation
Indices: 40462972--40463034 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
40462962 CCTTTTCATA
*
40462972 TTTCATATTTCATAACACT-GGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40463002 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40463033 TT
1 TT
40463035 ACGGTAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40463283 original size:24 final size:24
Alignment explanation
Indices: 40463228--40463417 Score: 269
Period size: 24 Copynumber: 8.0 Consensus size: 24
40463218 GCTTTATCAT
* *
40463228 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* *
40463253 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTG
* *
40463277 ATCACTGGGGCATAAGCCC-CTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40463300 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
40463324 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
40463348 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40463372 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTG
40463395 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40463418 TCACTTCCTC
Statistics
Matches: 150, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
23 41 0.27
24 97 0.65
25 12 0.08
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:40463307 original size:47 final size:47
Alignment explanation
Indices: 40463253--40463417 Score: 267
Period size: 47 Copynumber: 3.5 Consensus size: 47
40463243 GCCTCTTTTA
* * * *
40463253 ATAACTGGGGCAAAAGCCCTTTTTATCACTGGGGCATAAGCCCCTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTG
*
40463300 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTG
*
40463348 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTA
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTG
40463395 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40463418 TCACTTCCTC
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
47 65 0.59
48 45 0.41
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTG
Found at i:40463328 original size:71 final size:72
Alignment explanation
Indices: 40463228--40463418 Score: 280
Period size: 71 Copynumber: 2.7 Consensus size: 72
40463218 GCTTTATCAT
* * *
40463228 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATCACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAA
40463292 GCCC-CTTG
64 GCCCTCTTG
* * *
40463300 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
*
40463365 CCTTTTG
66 CCTCTTG
40463372 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTT
40463419 CACTTCCTCC
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
71 75 0.69
72 33 0.31
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
CCTCTTG
Found at i:40463490 original size:9 final size:9
Alignment explanation
Indices: 40463476--40463532 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40463466 ATCTCGTGTG
40463476 CATATCATA
1 CATATCATA
*
40463485 CATATCATGTT
1 CATATCA--TA
40463496 CATATCATA
1 CATATCATA
* *
40463505 CATGTCATGTG
1 CATATCA--TA
40463516 CATATCATA
1 CATATCATA
40463525 CATATCAT
1 CATATCAT
40463533 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (9 bp):
CATATCATA
Found at i:40463499 original size:20 final size:20
Alignment explanation
Indices: 40463476--40463535 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
40463466 ATCTCGTGTG
40463476 CATATCATACATATCATGTT
1 CATATCATACATATCATGTT
* *
40463496 CATATCATACATGTCATGTG
1 CATATCATACATATCATGTT
40463516 CATATCATACATATCATGTT
1 CATATCATACATATCATGTT
40463536 TATCAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (20 bp):
CATATCATACATATCATGTT
Found at i:40463617 original size:25 final size:25
Alignment explanation
Indices: 40463571--40463618 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40463561 ATATATAAAC
* * * *
40463571 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40463596 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40463619 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40464772 original size:27 final size:27
Alignment explanation
Indices: 40464742--40464881 Score: 192
Period size: 27 Copynumber: 5.2 Consensus size: 27
40464732 TGTAAATTAG
*
40464742 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTTTATAAATCGA
** *
40464769 GGGTAAAATAGTAATTTTGTAAA-CTGA
1 GGGTAAAACGGTAATTTTATAAATC-GA
* *
40464796 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTTTATAAATCGA
*
40464823 GGGTAAAACGGTAATTTTACAAATCGA
1 GGGTAAAACGGTAATTTTATAAATCGA
*
40464850 GGGTAAAACGGTAATTTTACAAATCGA
1 GGGTAAAACGGTAATTTTATAAATCGA
40464877 GGGTA
1 GGGTA
40464882 TTTCAATAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 1 0.01
27 99 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.28
Consensus pattern (27 bp):
GGGTAAAACGGTAATTTTATAAATCGA
Found at i:40464891 original size:27 final size:27
Alignment explanation
Indices: 40464804--40465055 Score: 197
Period size: 27 Copynumber: 9.4 Consensus size: 27
40464794 GAGGGTAAAA
* * ***
40464804 TGGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTTTACAAATCGAGGGTATTT
* ***
40464831 CGGTAATTTTACAAATCGAGGGTAAAA
1 TGGTAATTTTACAAATCGAGGGTATTT
*
40464858 CGGTAATTTTACAAATCGAGGGTATTT
1 TGGTAATTTTACAAATCGAGGGTATTT
*** ** *
40464885 CAATAATTTTACAGGTTGAGGGTATTT
1 TGGTAATTTTACAAATCGAGGGTATTT
** * *
40464912 CAGTAATTTCACAAAT-TAGGGGTATTT
1 TGGTAATTTTACAAATCGA-GGGTATTT
*
40464939 TGGTAATTTTACAAA-CTAGGGGTATTT
1 TGGTAATTTTACAAATCGA-GGGTATTT
* *
40464966 TGATAATTTTACAAA-CTAGGGGTATTT
1 TGGTAATTTTACAAATCGA-GGGTATTT
* * *
40464993 TGGTAATTTTATAAACCAAGGGTATTT
1 TGGTAATTTTACAAATCGAGGGTATTT
* *
40465020 TAGTAATTTTACAAAGC-AGGGTATTT
1 TGGTAATTTTACAAATCGAGGGTATTT
40465046 TGGTAATTTT
1 TGGTAATTTT
40465056 GTAAACCAAA
Statistics
Matches: 195, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.10
27 174 0.89
28 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
TGGTAATTTTACAAATCGAGGGTATTT
Found at i:40464892 original size:54 final size:54
Alignment explanation
Indices: 40464742--40464897 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 54
40464732 TGTAAATTAG
**
40464742 GGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAT-AGTAATTTTGTAAACTGA
1 GGGTAAAACGGTAATTCTATAAATCGAGGGT-AAATCAGTAATTTTACAAACTGA
* * *
40464796 GGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTACAAA-TCGA
1 GGGTAAAACGGTAATTCTATAAATCGAGGGTAAATCAGTAATTTTACAAACT-GA
* * ** *
40464850 GGGTAAAACGGTAATTTTACAAATCGAGGGTATTTCAATAATTTTACA
1 GGGTAAAACGGTAATTCTATAAATCGAGGGTAAATCAGTAATTTTACA
40464898 GGTTGAGGGT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
53 4 0.05
54 83 0.95
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (54 bp):
GGGTAAAACGGTAATTCTATAAATCGAGGGTAAATCAGTAATTTTACAAACTGA
Found at i:40465069 original size:26 final size:26
Alignment explanation
Indices: 40464932--40465072 Score: 138
Period size: 27 Copynumber: 5.3 Consensus size: 26
40464922 ACAAATTAGG
* * *
40464932 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTATAAACCA-A
* * * *
40464959 GGTATTTTGATAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTATAAACCA-A
40464986 GGTATTTTGGTAATTTTATAAACCAA
1 GGTATTTTGGTAATTTTATAAACCAA
* * * *
40465012 GGGTATTTTAGTAATTTTACAAAGCAG
1 -GGTATTTTGGTAATTTTATAAACCAA
*
40465039 GGTATTTTGGTAATTTTGTAAACCAA
1 GGTATTTTGGTAATTTTATAAACCAA
*
40465065 AGTATTTT
1 GGTATTTT
40465073 AAATAGGGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
26 28 0.29
27 70 0.71
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTATAAACCAA
Found at i:40467894 original size:31 final size:31
Alignment explanation
Indices: 40467853--40467916 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40467843 CCTTTTCATA
*
40467853 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40467884 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40467915 TT
1 TT
40467917 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40468173 original size:23 final size:24
Alignment explanation
Indices: 40468109--40468296 Score: 260
Period size: 23 Copynumber: 8.0 Consensus size: 24
40468099 GCTTTATCAT
* *
40468109 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* *
40468134 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTG
*
40468158 ATAACT-GGGCGTAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40468180 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
40468204 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
40468228 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40468251 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTG
40468274 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40468297 TCACTTCCTC
Statistics
Matches: 150, Mismatches: 8, Indels: 11
0.89 0.05 0.07
Matches are distributed among these distances:
22 9 0.06
23 67 0.45
24 62 0.41
25 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:40468243 original size:47 final size:47
Alignment explanation
Indices: 40468130--40468296 Score: 257
Period size: 47 Copynumber: 3.6 Consensus size: 47
40468120 CCTAGCCTCT
* * *
40468130 TTTAATAACTGGGGCAAAAGCCCTTTTTATAACT-GGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
* *
40468176 TTTGATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
*
40468223 TTTTGATAACT-GGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
40468270 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
40468297 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
46 39 0.35
47 62 0.56
48 10 0.09
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
Found at i:40468368 original size:9 final size:9
Alignment explanation
Indices: 40468354--40468410 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40468344 ATCTCGTGTG
40468354 CATATCATA
1 CATATCATA
*
40468363 CATATCATGTG
1 CATATCA--TA
40468374 CATATCATA
1 CATATCATA
* *
40468383 CATGTCATGTG
1 CATATCA--TA
40468394 CATATCATA
1 CATATCATA
40468403 CATATCAT
1 CATATCAT
40468411 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40468373 original size:20 final size:20
Alignment explanation
Indices: 40468350--40468412 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
40468340 GAACATCTCG
40468350 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
40468370 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
40468390 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
40468410 TGT
1 TGT
40468413 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:40468495 original size:25 final size:25
Alignment explanation
Indices: 40468449--40468496 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40468439 ATATATAAAC
* * * *
40468449 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40468474 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40468497 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40469651 original size:27 final size:27
Alignment explanation
Indices: 40469621--40469841 Score: 291
Period size: 27 Copynumber: 8.2 Consensus size: 27
40469611 TGTAAATTAG
40469621 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
** *
40469648 GGGTAAAATAGTAATTCTGTAAA-CTGA
1 GGGTAAAACGGTAATTCTATAAATC-GA
*
40469675 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
* *
40469702 GGGTAAAACGGTAATTTTACAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
* *
40469729 GGGTAAAATGGCAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
** * *
40469756 GGGTAAAATAGTAATTCTGTAAACCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
*
40469783 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
* *
40469810 GGGTAAAACGGTAATTTTACAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
40469837 GGGTA
1 GGGTA
40469842 TTTCAATAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 168 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.27
Consensus pattern (27 bp):
GGGTAAAACGGTAATTCTATAAATCGA
Found at i:40469851 original size:27 final size:27
Alignment explanation
Indices: 40469820--40470015 Score: 168
Period size: 27 Copynumber: 7.3 Consensus size: 27
40469810 GGGTAAAACG
* *
40469820 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCTAGGGTATTTTA
* ** * * *
40469847 ATAATTTTACAGGTCGAGGGCATTTCA
1 GTAATTTTACAAATCTAGGGTATTTTA
* *
40469874 GTAATTTCACAAAT-TAGGGGTATTTTG
1 GTAATTTTACAAATCTA-GGGTATTTTA
40469901 GTAATTTTACAAA-CTAGGGGTATTTT-
1 GTAATTTTACAAATCTA-GGGTATTTTA
*
40469927 GATAATTTTACAAA-CTAGGGGTATTTTG
1 G-TAATTTTACAAATCTA-GGGTATTTTA
* * *
40469955 GTAATTTTATAAACCAAGGGTATTTTA
1 GTAATTTTACAAATCTAGGGTATTTTA
* * *
40469982 GTAACTTTACAAAGC-AGGGTATTTTG
1 GTAATTTTACAAATCTAGGGTATTTTA
40470008 GTAATTTT
1 GTAATTTT
40470016 GTAAACCAAA
Statistics
Matches: 143, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.13
27 121 0.85
28 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAATCTAGGGTATTTTA
Found at i:40470011 original size:26 final size:27
Alignment explanation
Indices: 40469874--40470015 Score: 189
Period size: 27 Copynumber: 5.3 Consensus size: 27
40469864 GGGCATTTCA
* *
40469874 GTAATTTCACAAATTAGGGGTATTTTG
1 GTAATTTTACAAACTAGGGGTATTTTG
40469901 GTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACTAGGGGTATTTTG
*
40469928 ATAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAACTAGGGGTATTTTG
* * * *
40469955 GTAATTTTATAAACCAAGGGTATTTTA
1 GTAATTTTACAAACTAGGGGTATTTTG
*
40469982 GTAACTTTACAAAGC-A-GGGTATTTTG
1 GTAATTTTACAAA-CTAGGGGTATTTTG
40470008 GTAATTTT
1 GTAATTTT
40470016 GTAAACCAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
26 16 0.16
27 85 0.83
28 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
GTAATTTTACAAACTAGGGGTATTTTG
Found at i:40470029 original size:26 final size:26
Alignment explanation
Indices: 40469892--40470032 Score: 129
Period size: 27 Copynumber: 5.3 Consensus size: 26
40469882 ACAAATTAGG
* * *
40469892 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTATAAACCA-A
* * * *
40469919 GGTATTTTGATAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTATAAACCA-A
40469946 GGTATTTTGGTAATTTTATAAACCAA
1 GGTATTTTGGTAATTTTATAAACCAA
* * * * *
40469972 GGGTATTTTAGTAACTTTACAAAGCAG
1 -GGTATTTTGGTAATTTTATAAACCAA
*
40469999 GGTATTTTGGTAATTTTGTAAACCAA
1 GGTATTTTGGTAATTTTATAAACCAA
*
40470025 AGTATTTT
1 GGTATTTT
40470033 AAATAGGGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
26 27 0.28
27 69 0.72
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTATAAACCAA
Found at i:40476970 original size:35 final size:35
Alignment explanation
Indices: 40476922--40476992 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
40476912 TACCAGAACA
*
40476922 TACACATGCAATCGTATAAAACTGAGACATAATTT
1 TACACATGAAATCGTATAAAACTGAGACATAATTT
40476957 TACACATGAAATCGTATAAAACTGAGACATAATTT
1 TACACATGAAATCGTATAAAACTGAGACATAATTT
40476992 T
1 T
40476993 TACATCCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (35 bp):
TACACATGAAATCGTATAAAACTGAGACATAATTT
Found at i:40481290 original size:51 final size:52
Alignment explanation
Indices: 40481213--40481346 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 52
40481203 CGGATACCGG
* *
40481213 GTGGCCTGCACATAGTACCACCCTTGTAGTCAAAGCTA-CCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTAGTCAAAGCTATCCTTCTTCACAAA
* * * *
40481264 GTGGCCTTCACATAGTATCACACTTGT-GACCAAAGCTATCTTTCTTCATAAA
1 GTGGCCTTCACATAGTACCACACTTGTAG-TCAAAGCTATCCTTCTTCACAAA
40481316 GTGGCCTTCACATAGTACCACACTTG-AGTCA
1 GTGGCCTTCACATAGTACCACACTTGTAGTCA
40481347 TTAGTGACAT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.01
51 34 0.47
52 37 0.51
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTAGTCAAAGCTATCCTTCTTCACAAA
Found at i:40482611 original size:22 final size:21
Alignment explanation
Indices: 40482549--40482613 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
40482539 GTCACTAGGA
40482549 ATTATGTGATTTGAACTCATTG
1 ATTATGTGATTTGAACTCA-TG
* * **
40482571 AGT-TGTGGTTTGAGTTCATG
1 ATTATGTGATTTGAACTCATG
*
40482591 ATTTATGTGATTTGACCTCATG
1 A-TTATGTGATTTGAACTCATG
40482613 A
1 A
40482614 GTTGGCATCG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 17 0.52
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (21 bp):
ATTATGTGATTTGAACTCATG
Found at i:40482611 original size:43 final size:41
Alignment explanation
Indices: 40482550--40482634 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 41
40482540 TCACTAGGAA
** *
40482550 TTATGTGATTTGAACTCATTGAGTTGTGGTTTGAGTTCATGAT
1 TTATGTGATTTGAACTCA-TGAGTTG-GCATCGAGTTCATGAT
*
40482593 TTATGTGATTTGACCTCATGAGTTGGCATCGAGTTCATGAT
1 TTATGTGATTTGAACTCATGAGTTGGCATCGAGTTCATGAT
40482634 T
1 T
40482635 ATGACACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 14 0.37
42 7 0.18
43 17 0.45
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.44
Consensus pattern (41 bp):
TTATGTGATTTGAACTCATGAGTTGGCATCGAGTTCATGAT
Found at i:40485070 original size:41 final size:40
Alignment explanation
Indices: 40484992--40485110 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 40
40484982 CCTGGCCAGG
* * *
40484992 CCATGTGGCCCACAAGGCTGGCACACAACCT-CACACAC-A
1 CCATGTGACCCACATGGCTGACACACAACCTAC-CACACGA
40485031 TCCATGTGACCCACATGAGCTGACACACAACCTACCACACGA
1 -CCATGTGACCCACATG-GCTGACACACAACCTACCACACGA
* * *
40485073 CTATGTGACCTACATGGGCT-ATCACACAGCCTACCACA
1 CCATGTGACCCACAT-GGCTGA-CACACAACCTACCACA
40485111 TGGCCGTATG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
40 15 0.22
41 50 0.74
42 3 0.04
ACGTcount: A:0.31, C:0.38, G:0.16, T:0.15
Consensus pattern (40 bp):
CCATGTGACCCACATGGCTGACACACAACCTACCACACGA
Found at i:40492562 original size:48 final size:48
Alignment explanation
Indices: 40492426--40492605 Score: 192
Period size: 48 Copynumber: 3.9 Consensus size: 48
40492416 GGTTATGTAC
* *
40492426 GATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATCGATATGT
* **** * *
40492474 AATTTTTTGTAAGACCATAG-CT-GG-GCT---ATCGGCATCGATATGT
1 GATCCCATGTAAGACCAT-GTCTGGGAGATGGCATTGGCATCGATATGT
*
40492517 GATCCCATGTAAGACCATGTCTAGGAGATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATCGATATGT
* * *
40492565 GATCCCATGTAAGACCATATCTGGGATATGGCAGTGGCATC
1 GATCCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATC
40492606 CTACCATGTG
Statistics
Matches: 105, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 29 0.28
44 2 0.02
45 2 0.02
46 1 0.01
47 2 0.02
48 67 0.64
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATCGATATGT
Found at i:40492581 original size:91 final size:90
Alignment explanation
Indices: 40492426--40492597 Score: 245
Period size: 91 Copynumber: 1.9 Consensus size: 90
40492416 GGTTATGTAC
* * ****
40492426 GATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGATATGTAATTTTTTGTAAGACCA
1 GATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTAATCCCATGTAAGACCA
*
40492491 TAGCTGGGCTATCGGCATCGATATGT
66 TAGCTGGGATAT-GGCATCGATATGT
* *
40492517 GATCCCATGTAAGACCATGTCTAGGAGATGGCATTGGCATCGATATGTGATCCCATGTAAGACCA
1 GATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTAATCCCATGTAAGACCA
*
40492582 TATCTGGGATATGGCA
66 TAGCTGGGATATGGCA
40492598 GTGGCATCCT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 4 0.06
91 67 0.94
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (90 bp):
GATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTAATCCCATGTAAGACCA
TAGCTGGGATATGGCATCGATATGT
Found at i:40495394 original size:40 final size:40
Alignment explanation
Indices: 40495345--40495550 Score: 254
Period size: 40 Copynumber: 5.2 Consensus size: 40
40495335 TCTTCGGAAT
* * *
40495345 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * ** * *
40495384 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
40495424 TTAGCCCGGATATAA-CAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* *
40495464 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
40495504 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
40495544 TTAGCCC
1 TTAGCCC
40495551 AGGTATCATT
Statistics
Matches: 144, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 3 0.02
40 140 0.97
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:40502482 original size:17 final size:17
Alignment explanation
Indices: 40502460--40502498 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
40502450 TTGAGAAACA
40502460 AAAGTATTGCCCTTGTG
1 AAAGTATTGCCCTTGTG
*
40502477 AAAGTATTGTCCTTGTG
1 AAAGTATTGCCCTTGTG
40502494 AAAGT
1 AAAGT
40502499 GTTATGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (17 bp):
AAAGTATTGCCCTTGTG
Found at i:40512026 original size:47 final size:47
Alignment explanation
Indices: 40511972--40512208 Score: 375
Period size: 47 Copynumber: 5.0 Consensus size: 47
40511962 GATTTTATGA
** * * *
40511972 GATGAATGTGAATGTGTATATATGAGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
40512019 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
40512066 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
40512113 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* ** *
40512160 GATGAATGTGAACATGCATATGTGTGATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
40512207 GA
1 GA
40512209 GATATGTATG
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 179 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:40512068 original size:22 final size:22
Alignment explanation
Indices: 40512041--40512162 Score: 65
Period size: 22 Copynumber: 5.3 Consensus size: 22
40512031 CATGCATATG
40512041 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40512063 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
40512088 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
40512110 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
40512133 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGCCGAATGGCCAA
40512157 TGTGAT
1 TGTGAT
40512163 GAATGTGAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 32
0.64 0.09 0.28
Matches are distributed among these distances:
22 23 0.31
23 17 0.23
24 17 0.23
25 17 0.23
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40513779 original size:40 final size:40
Alignment explanation
Indices: 40513726--40514044 Score: 494
Period size: 40 Copynumber: 8.0 Consensus size: 40
40513716 TTGAGAGTTA
*
40513726 TATAGCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
40513766 TATGTCAGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
*
40513806 TATGTCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
40513846 TATGTCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
40513886 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * * * *
40513926 TATATTCGGGCTAAGTCTCGGAGAGCATTCGTGCTAGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* *
40513966 TATATCAGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
* * *
40514006 TATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
40514045 ATGTGTATTC
Statistics
Matches: 255, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 255 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGT
Found at i:40516532 original size:40 final size:40
Alignment explanation
Indices: 40516487--40516653 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40516477 CGGAATATAA
40516487 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40516527 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40516567 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40516607 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40516646 CCGGATAT
1 CCGGATAT
40516654 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40516637 original size:80 final size:79
Alignment explanation
Indices: 40516487--40516653 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
40516477 CGGAATATAA
* *
40516487 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
40516552 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
40516567 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
40516629 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
40516646 CCGGATAT
1 CCGGATAT
40516654 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:40517501 original size:17 final size:19
Alignment explanation
Indices: 40517478--40517523 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40517468 AAGAAGCATG
40517478 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40517496 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40517514 AATCATGCTC
1 AATCATGCTC
40517524 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40524528 original size:40 final size:39
Alignment explanation
Indices: 40524483--40524648 Score: 172
Period size: 40 Copynumber: 4.2 Consensus size: 39
40524473 CGGAATATAA
40524483 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC
* * * *
40524523 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
** * *
40524562 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC
** * * * *
40524602 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
40524641 CCGGATAT
1 CCGGATAT
40524649 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 46 0.44
40 59 0.56
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
Found at i:40524605 original size:79 final size:79
Alignment explanation
Indices: 40524499--40524648 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 79
40524489 ATAATCACGT
*
40524499 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAAC-CAGCA-GAATTGCCTTCGGGCTTAGC
40524562 CCGGATATAGCCACTA
64 CCGGATATAGCCACTA
* * ** * *
40524578 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGCCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC
40524643 GGATAT
66 GGATAT
40524649 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 3 0.05
79 59 0.95
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40525495 original size:17 final size:19
Alignment explanation
Indices: 40525472--40525517 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40525462 AAGAAGCATG
40525472 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40525490 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40525508 AATCATGCTC
1 AATCATGCTC
40525518 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40529653 original size:40 final size:40
Alignment explanation
Indices: 40529608--40529774 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
40529598 CGGAATATAA
40529608 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40529648 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40529688 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40529728 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40529767 CCGGATAT
1 CCGGATAT
40529775 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40529758 original size:80 final size:79
Alignment explanation
Indices: 40529624--40529774 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
40529614 ATAATCACGT
*
40529624 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
40529689 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
40529704 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
40529767 CCGGATAT
64 CCGGATAT
40529775 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40530621 original size:17 final size:19
Alignment explanation
Indices: 40530598--40530643 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40530588 AAGAAGCATG
40530598 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40530616 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40530634 AATCATGCTC
1 AATCATGCTC
40530644 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40537639 original size:40 final size:40
Alignment explanation
Indices: 40537594--40537760 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40537584 CGGAATATAA
40537594 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40537634 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40537674 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40537714 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40537753 CCGGATAT
1 CCGGATAT
40537761 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40537744 original size:80 final size:79
Alignment explanation
Indices: 40537594--40537760 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
40537584 CGGAATATAA
* *
40537594 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
40537659 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
40537674 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
40537736 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
40537753 CCGGATAT
1 CCGGATAT
40537761 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:40538608 original size:17 final size:19
Alignment explanation
Indices: 40538585--40538630 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40538575 AAGAAGCATG
40538585 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40538603 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40538621 AATCATGCTC
1 AATCATGCTC
40538631 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40545461 original size:41 final size:41
Alignment explanation
Indices: 40545416--40545533 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
40545406 TGAAAGATAA
40545416 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
40545457 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
40545487 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
40545528 ATGTAG
1 ATGTAG
40545534 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:40545472 original size:71 final size:71
Alignment explanation
Indices: 40545384--40545547 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
40545374 GAGATGTATC
40545384 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40545449 AGGACA
66 AGGACA
40545455 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
40545520 AGGACA
66 AGGACA
40545526 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
40545548 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:40548279 original size:16 final size:16
Alignment explanation
Indices: 40548260--40548360 Score: 84
Period size: 16 Copynumber: 6.2 Consensus size: 16
40548250 GAAATAAAAA
40548260 AAATATAATAATATAT
1 AAATATAATAATATAT
40548276 AAATATAATATAATATAT
1 AAATAT-A-ATAATATAT
*
40548294 AAATATAAAAATATAT
1 AAATATAATAATATAT
*
40548310 AAA-ATATTTAGA-ATAT
1 AAATATA-ATA-ATATAT
*
40548326 ATATATAATAA-A-AT
1 AAATATAATAATATAT
* *
40548340 AGATATAATATATAAAT
1 AAATATAATA-ATATAT
40548357 AAAT
1 AAAT
40548361 TGAACATAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.16
15 6 0.09
16 27 0.39
17 11 0.16
18 15 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATATAATAATATAT
Found at i:40548290 original size:18 final size:18
Alignment explanation
Indices: 40548267--40548357 Score: 89
Period size: 18 Copynumber: 4.8 Consensus size: 18
40548257 AAAAAATATA
40548267 ATAATATATAAATATAAT
1 ATAATATATAAATATAAT
40548285 ATAATATATAAATATAA-
1 ATAATATATAAATATAAT
40548302 A-AATATATAAAATATTTAGAAT
1 ATAATATAT-AAATA--T--AAT
40548324 ATATATATAATAAA-ATAGAT
1 ATA-ATAT-ATAAATATA-AT
40548344 ATAATATATAAATA
1 ATAATATATAAATA
40548358 AATTGAACAT
Statistics
Matches: 62, Mismatches: 0, Indels: 21
0.75 0.00 0.25
Matches are distributed among these distances:
16 7 0.11
17 6 0.10
18 22 0.35
19 7 0.11
20 5 0.08
21 3 0.05
22 1 0.02
23 2 0.03
24 7 0.11
25 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAATATATAAATATAAT
Found at i:40548307 original size:34 final size:34
Alignment explanation
Indices: 40548260--40548358 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 34
40548250 GAAATAAAAA
*
40548260 AAATATAATAATATATAAATATAATATAATATAT
1 AAATATAAAAATATATAAATATAATATAATATAT
* *
40548294 AAATATAAAAATATATAAA-ATATTTAGAATATAT
1 AAATATAAAAATATATAAATATA-ATATAATATAT
* *
40548328 ATATAATAAAATAGATATAATATATAA-ATAA
1 AAAT-ATAAAA-ATATATAA-ATATAATATAA
40548359 ATTGAACATA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
33 3 0.06
34 30 0.57
35 6 0.11
36 10 0.19
37 1 0.02
38 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (34 bp):
AAATATAAAAATATATAAATATAATATAATATAT
Found at i:40550490 original size:43 final size:42
Alignment explanation
Indices: 40550395--40550504 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
40550385 GACTTATGAT
40550395 TTACGTGTAAGACCATGTCTGGGACATCAGCATCATATTTAA
1 TTACGTGTAAGACCATGTCTGGGACATCAGCATCATATTTAA
* * * * *
40550437 TTTCGTGTAAGACCTTGTCTGGGACAGT-GGTATCGATATTTGA
1 TTACGTGTAAGACCATGTCTGGGACA-TCAGCATC-ATATTTAA
* * *
40550480 TTACATGTAAGACCACGTTTGGGAC
1 TTACGTGTAAGACCATGTCTGGGAC
40550505 TTGGCATTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
42 28 0.50
43 28 0.50
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACATCAGCATCATATTTAA
Found at i:40555343 original size:20 final size:20
Alignment explanation
Indices: 40555315--40555407 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
40555305 ATTCATTTCT
*
40555315 ATTCGTATAAACTGTAATTC
1 ATTCGTATAAACAGTAATTC
* * * * *
40555335 ATTCATATAACCTGCAGTTC
1 ATTCGTATAAACAGTAATTC
*
40555355 A-TCTGTATAAACAGTAGTTC
1 ATTC-GTATAAACAGTAATTC
40555375 A-TCAGTA-ATAACAGTAATTC
1 ATTC-GTATA-AACAGTAATTC
40555395 ATTCGTATAAACA
1 ATTCGTATAAACA
40555408 CATATTTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.05
20 53 0.90
21 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (20 bp):
ATTCGTATAAACAGTAATTC
Found at i:40555633 original size:26 final size:26
Alignment explanation
Indices: 40555569--40555639 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 26
40555559 CTCCGCCTAT
* *
40555569 TGAGCTGA-AAA-GGTAAGCTCTTTC
1 TGAGCTGATAAACGGTAAGCTCCTCC
* *
40555593 -GAGC-CATAATCGGTAAGCTCCTCC
1 TGAGCTGATAAACGGTAAGCTCCTCC
*
40555617 TGAGCTGATAAACGGTATGCTCC
1 TGAGCTGATAAACGGTAAGCTCC
40555640 AAATAGCTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
22 1 0.03
23 6 0.17
24 11 0.31
25 4 0.11
26 14 0.39
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (26 bp):
TGAGCTGATAAACGGTAAGCTCCTCC
Found at i:40555681 original size:23 final size:23
Alignment explanation
Indices: 40555626--40555681 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
40555616 CTGAGCTGAT
* * *
40555626 AAACGGTATGCTCCAAATAGCTG
1 AAACGGTAAGCCCCAAAGAGCTG
* *
40555649 -AATGGTAAGCCCCGAAGAGCTG
1 AAACGGTAAGCCCCAAAGAGCTG
40555671 AAACGGTAAGC
1 AAACGGTAAGC
40555682 TCATATGAGC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (23 bp):
AAACGGTAAGCCCCAAAGAGCTG
Found at i:40555875 original size:23 final size:24
Alignment explanation
Indices: 40555844--40555889 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
40555834 TCAATTTACG
*
40555844 AAATCATATATGTACAATTCAATC
1 AAATCATATATATACAATTCAATC
*
40555868 AAAT-ATATATATACATTTCAAT
1 AAATCATATATATACAATTCAAT
40555890 ACTCAATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATCATATATATACAATTCAATC
Found at i:40559210 original size:94 final size:93
Alignment explanation
Indices: 40559063--40559368 Score: 253
Period size: 94 Copynumber: 3.3 Consensus size: 93
40559053 TATGTGTGCT
* ***** *
40559063 AGTGTAAGACATGTCTGAGACATGCATCAACCACAGTATGAGAGCTAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGTTTGAG-ATGAGAGTTAGTGTAAGACATGTCTGGG
*
40559128 ACATGCATC-AGCTTCGAGATATTTAAGCC
65 ACATGCATCGA-CTTCGAGATATTCAAGCC
* * * *
40559157 AGTGTAAGACATGTTTGGGACATGCATCAGTATTGAGATGAGAGTTAGTGTAAGAAATATTTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGT-TTGAGATGAGAGTTAGTGTAAGACATGTCTGGG
* * * * *
40559222 ACAAGCATCGGCCTT-GTGATATACAAGCT
65 ACATGCATC-GACTTCGAGATATTCAAGCC
* * * * * * *
40559251 AGTGTAAGACCTATCTGGGACATGGCATCAGTTTGTGAT--GTGTCAGTGTAAGACCTGTCTAGG
1 AGTGTAAGACATGTCTGGGACAT-GCATCAGTTTGAGATGAGAGTTAGTGTAAGACATGTCTGGG
* * * *
40559314 ACATGGCATCGACATCGATAGA-TGAGAGCC
65 ACAT-GCATCGACTTCGAGATATTCA-AGCC
40559344 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
40559369 GCGTCAATAT
Statistics
Matches: 165, Mismatches: 39, Indels: 17
0.75 0.18 0.08
Matches are distributed among these distances:
92 24 0.15
93 21 0.13
94 107 0.65
95 13 0.08
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (93 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGTTTGAGATGAGAGTTAGTGTAAGACATGTCTGGGA
CATGCATCGACTTCGAGATATTCAAGCC
Found at i:40559289 original size:48 final size:47
Alignment explanation
Indices: 40559060--40559285 Score: 165
Period size: 46 Copynumber: 4.8 Consensus size: 47
40559050 AGATATGTGT
* * * *** *
40559060 GCTAGTGTAAGACATGTCTGAGACATGCATCAAC-CACAG-TATGAGA
1 GCTAGTGTAAGACATATCTGGGACATGCATCAGCTTTGAGATAT-AAA
* * *
40559106 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTTCGAGATATTTAA
1 GCTAGTGTAAGACATATCTGGGACATGCATCAGCTTTGAGATA-TAAA
* * * * *
40559154 GCCAGTGTAAGACATGTTTGGGACATGCATCAG-TATTGAGAT-GAGA
1 GCTAGTGTAAGACATATCTGGGACATGCATCAGCT-TTGAGATATAAA
* * * * * * *
40559200 GTTAGTGTAAGAAATATTTGGGACAAGCATCGGCCTTGTGATATACAA
1 GCTAGTGTAAGACATATCTGGGACATGCATCAGCTTTGAGATATA-AA
*
40559248 GCTAGTGTAAGACCTATCTGGGACATGGCATCAG-TTTG
1 GCTAGTGTAAGACATATCTGGGACAT-GCATCAGCTTTG
40559286 TGATGTGTCA
Statistics
Matches: 142, Mismatches: 30, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
46 66 0.46
47 4 0.03
48 65 0.46
49 7 0.05
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (47 bp):
GCTAGTGTAAGACATATCTGGGACATGCATCAGCTTTGAGATATAAA
Found at i:40563010 original size:28 final size:28
Alignment explanation
Indices: 40562962--40563030 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
40562952 TTTAAAACCC
* *
40562962 TAGGGGT-ATATCAGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
40562989 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
40563017 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
40563031 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:40563696 original size:27 final size:27
Alignment explanation
Indices: 40563665--40563825 Score: 205
Period size: 27 Copynumber: 6.0 Consensus size: 27
40563655 TTCTACCCTA
*
40563665 CAAGGGTATTTCGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
40563692 AAAGGGTATTTTAGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
40563719 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
40563746 CAAGGGTATTTTAGTAATTATACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
40563773 TAGGGGTATTTTGGTGATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
*
40563800 CAAGGGTATTTTGGTAATTCTATAAA
1 CAAGGGTATTTTGGTAATTTTATAAA
40563826 TTGAAGGTAA
Statistics
Matches: 110, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAC
Found at i:40563735 original size:54 final size:54
Alignment explanation
Indices: 40563668--40563818 Score: 239
Period size: 54 Copynumber: 2.8 Consensus size: 54
40563658 TACCCTACAA
* * *
40563668 GGGTATTTCGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTATACAAACCAG
* *
40563722 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTATACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTATACAAACCAG
* *
40563776 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTGGTAATT
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATT
40563819 CTATAAATTG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 89 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGTAATTATACAAACCAG
Found at i:40564183 original size:27 final size:27
Alignment explanation
Indices: 40563813--40564161 Score: 431
Period size: 27 Copynumber: 12.9 Consensus size: 27
40563803 GGGTATTTTG
* * * *
40563813 GTAATTCTATAAATTGAAGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACA
* *
40563840 GTAATTCTGTAAA-CTAAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACA
* *
40563867 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACA
*
40563894 GTAATTCTGTAAA-CTGAGGGGAAAACA
1 GTAATTCTGTAAATC-GAGGGTAAAACA
* *
40563921 GTAATTCTGTAAATCGAGGATAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACA
*
40563948 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACA
*
40563975 GTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACA
*
40564002 GTAATTCTGTAAA-CTGAGGGGAAAACA
1 GTAATTCTGTAAATC-GAGGGTAAAACA
* *
40564029 GTAATTCTGTAAATCGAGGATAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACA
*
40564056 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACA
40564083 GTAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACA
**
40564110 GTAATTCTGTAAA-CTGAGGGTAAAATG
1 GTAATTCTGTAAATC-GAGGGTAAAACA
40564137 GTAATTCTGTAAATCGAGGGTAAAA
1 GTAATTCTGTAAATCGAGGGTAAAA
40564162 TGGTAATTTT
Statistics
Matches: 280, Mismatches: 30, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.02
27 269 0.96
28 6 0.02
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACA
Found at i:40564183 original size:54 final size:54
Alignment explanation
Indices: 40563812--40564169 Score: 572
Period size: 54 Copynumber: 6.6 Consensus size: 54
40563802 AGGGTATTTT
* * * ** *
40563812 GGTAATTCTATAAATTGAAGGTAAAACGGTAATTCTGTAAACTAAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
* *
40563866 GGTAATTCTATAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGGAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
* *
40563920 AGTAATTCTGTAAATCGAGGATAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
*
40563974 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGGAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
* *
40564028 AGTAATTCTGTAAATCGAGGATAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
* *
40564082 GGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAAT
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
*
40564136 GGTAATTCTGTAAATCGAGGGTAAAATGGTAATT
1 GGTAATTCTGTAAATCGAGGGTAAAATAGTAATT
40564170 TTACAAGTCG
Statistics
Matches: 282, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 282 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.28
Consensus pattern (54 bp):
GGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAAC
Found at i:40581242 original size:15 final size:15
Alignment explanation
Indices: 40581222--40581290 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
40581212 GTATCTTGGG
40581222 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
40581237 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
40581252 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
40581267 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
40581282 TTTCTTTAT
1 TTTCTTTAT
40581291 TCAGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:40581291 original size:30 final size:30
Alignment explanation
Indices: 40581213--40581292 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
40581203 TATAGTATCG
* * *
40581213 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* *
40581243 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
40581273 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
40581293 AGTTTTCTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:40585380 original size:18 final size:18
Alignment explanation
Indices: 40585357--40585392 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40585347 GAGATGCCTG
40585357 GAGTTGATAAAAGACTAT
1 GAGTTGATAAAAGACTAT
*
40585375 GAGTTGATAATAGACTAT
1 GAGTTGATAAAAGACTAT
40585393 CACCTGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
GAGTTGATAAAAGACTAT
Found at i:40588316 original size:48 final size:48
Alignment explanation
Indices: 40588200--40588365 Score: 178
Period size: 48 Copynumber: 3.5 Consensus size: 48
40588190 TATTTGTGCT
* * * *
40588200 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-CG-TATGA-GAGAC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAT-ACAAGCC
* * **
40588246 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGGTATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAGCC
* * *
40588294 AGTGTAAGACATGTCAT-GGACATGTATCAGCCTCGCGATATACAAGCT
1 AGTGTAAGACATGTC-TGGGACATGCATCAGCCTCGAGATATACAAGCC
*
40588342 AGTGTAAGACCTGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
40588366 GCGTCAGCTT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
46 32 0.32
47 2 0.02
48 66 0.65
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAGCC
Found at i:40591548 original size:16 final size:16
Alignment explanation
Indices: 40591519--40591552 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40591509 AATATATTTA
40591519 GATAACATTCTCATAT
1 GATAACATTCTCATAT
* *
40591535 GATAAGATTTTCATAT
1 GATAACATTCTCATAT
40591551 GA
1 GA
40591553 AAATATACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
GATAACATTCTCATAT
Found at i:40593837 original size:21 final size:21
Alignment explanation
Indices: 40593794--40593833 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40593784 TTAATTCATA
* *
40593794 AAACATGTGGTTCATCTGTAT
1 AAACATGTAGTTCATCAGTAT
40593815 AAACA-GTAGTTCATCAGTA
1 AAACATGTAGTTCATCAGTA
40593834 ATAATAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
AAACATGTAGTTCATCAGTAT
Found at i:40594129 original size:22 final size:23
Alignment explanation
Indices: 40594101--40594144 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
40594091 ACGGTTAGCT
40594101 CTGAAGAGCTG-AATGGTAAGCC
1 CTGAAGAGCTGAAATGGTAAGCC
40594123 CTGAAGAGCTGAAATGGTAAGC
1 CTGAAGAGCTGAAATGGTAAGC
40594145 TTATATGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (23 bp):
CTGAAGAGCTGAAATGGTAAGCC
Found at i:40600184 original size:40 final size:39
Alignment explanation
Indices: 40600126--40600215 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 39
40600116 CATTTCTATT
* **
40600126 CGTATAAACTATAATTCATTCA-T-ATAACCTGTGGTTCATC
1 CGTATAAAC-ATAATTCA-TCAGTAATAA-CAGTAATTCATC
*
40600166 CGTATAAACAGTAGTTCATCAGTAATAACAGTAATTCATC
1 CGTATAAACA-TAATTCATCAGTAATAACAGTAATTCATC
40600206 CGTATAAACA
1 CGTATAAACA
40600216 CATATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
39 4 0.09
40 35 0.81
41 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (39 bp):
CGTATAAACATAATTCATCAGTAATAACAGTAATTCATC
Found at i:40600215 original size:20 final size:20
Alignment explanation
Indices: 40600160--40600215 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
40600150 TAACCTGTGG
*
40600160 TTCATCCGTATAAACAGTAG
1 TTCATCCGTATAAACAGTAA
*
40600180 TTCATCAGTA-ATAACAGTAA
1 TTCATCCGTATA-AACAGTAA
40600200 TTCATCCGTATAAACA
1 TTCATCCGTATAAACA
40600216 CATATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
TTCATCCGTATAAACAGTAA
Found at i:40600485 original size:72 final size:72
Alignment explanation
Indices: 40600342--40600486 Score: 177
Period size: 72 Copynumber: 2.0 Consensus size: 72
40600332 ATCATTTATA
* * *
40600342 CTCTTTCGAGCCATGATCGGTAAGCTCCTCCTGAGCTGGAAACAGTAAGCTCTATTGAGCTGAAA
1 CTCTTTCGAGCCATGATCAGTAAGCTCCTCCTGAGCTGGAAACAGTAAGCTCGATAGAGCTGAAA
40600407 TGGTAAG
66 TGGTAAG
* * * * *
40600414 CTCTTTCGAGCCATGATTAGTAAGCTCCTCTTGAGCTGATAAACGGTATGCTCCGA-AGAGCTGA
1 CTCTTTCGAGCCATGATCAGTAAGCTCCTCCTGAGCTG-GAAACAGTAAGCT-CGATAGAGCTGA
*
40600478 ACT-GTAAG
64 AATGGTAAG
40600486 C
1 C
40600487 CCCGAAGAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
72 41 0.66
73 19 0.31
74 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (72 bp):
CTCTTTCGAGCCATGATCAGTAAGCTCCTCCTGAGCTGGAAACAGTAAGCTCGATAGAGCTGAAA
TGGTAAG
Found at i:40603263 original size:93 final size:93
Alignment explanation
Indices: 40603151--40603322 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
40603141 CGCCCATAAG
* *
40603151 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40603216 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* *
40603244 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40603309 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40603323 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:40603319 original size:46 final size:46
Alignment explanation
Indices: 40603144--40603319 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
40603134 TGTAACCCGC
* * * *
40603144 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * *
40603190 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
40603240 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
40603283 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40603320 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 2 0.02
46 63 0.58
47 29 0.27
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40605079 original size:27 final size:27
Alignment explanation
Indices: 40605048--40605100 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
40605038 GGGGTAACAC
*
40605048 AGTCACCTTAACATAAAAGGGCAAAAT
1 AGTCACCTTAACACAAAAGGGCAAAAT
* *
40605075 AGTCATCTTACCACAAAAGGGCAAAA
1 AGTCACCTTAACACAAAAGGGCAAAA
40605101 CAAGCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (27 bp):
AGTCACCTTAACACAAAAGGGCAAAAT
Found at i:40605112 original size:27 final size:27
Alignment explanation
Indices: 40605064--40605303 Score: 238
Period size: 27 Copynumber: 8.9 Consensus size: 27
40605054 CTTAACATAA
* * *
40605064 AAGGGCAAAA-TAGTCATCTTACCACAA
1 AAGGGCAAAACAAG-CATTTTACCACAT
*
40605091 AAGGGCAAAACAAGCATTTTACCTCAT
1 AAGGGCAAAACAAGCATTTTACCACAT
* *
40605118 AAAGGG-AAAACAATCATTTTACCTCAT
1 -AAGGGCAAAACAAGCATTTTACCACAT
* * ** *
40605145 ATGGGCAAAA-TAGTCATTTTACCTTAA
1 AAGGGCAAAACAAG-CATTTTACCACAT
* *
40605172 AAGGGCAAAACAATCATTTTACCACGT
1 AAGGGCAAAACAAGCATTTTACCACAT
* *
40605199 AAGGGCAAAACAATCATTTTACCATAT
1 AAGGGCAAAACAAGCATTTTACCACAT
*
40605226 AAGGGTAAAAC-AGTCATTTTACCACAT
1 AAGGGCAAAACAAG-CATTTTACCACAT
* *
40605253 AAGGGCAAAACAATCATTTTCCCACAT
1 AAGGGCAAAACAAGCATTTTACCACAT
40605280 AAGGGCAAAAC-AGTCATTTTACCA
1 AAGGGCAAAACAAG-CATTTTACCA
40605304 ATTAGGGGTC
Statistics
Matches: 178, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
26 7 0.04
27 162 0.91
28 9 0.05
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (27 bp):
AAGGGCAAAACAAGCATTTTACCACAT
Found at i:40605151 original size:54 final size:55
Alignment explanation
Indices: 40605063--40605303 Score: 278
Period size: 54 Copynumber: 4.5 Consensus size: 55
40605053 CCTTAACATA
* * * *
40605063 AAAGGGCAAAATAGTCATCTTACCACAAAAGGGCAAAACAAGCATTTTACCTCAT
1 AAAGGGCAAAACAATCATTTTACCACATAAGGGCAAAACAAGCATTTTACCTCAT
* * * *
40605118 AAAGGG-AAAACAATCATTTTACCTCATATGGGCAAAA-TAGTCATTTTACCTTA-
1 AAAGGGCAAAACAATCATTTTACCACATAAGGGCAAAACAAG-CATTTTACCTCAT
* *
40605171 AAAGGGCAAAACAATCATTTTACCACGTAAGGGCAAAACAATCATTTTA-C-CAT
1 AAAGGGCAAAACAATCATTTTACCACATAAGGGCAAAACAAGCATTTTACCTCAT
* * * * *
40605224 ATAAGGGTAAAACAGTCATTTTACCACATAAGGGCAAAACAATCATTTTCCCACAT
1 A-AAGGGCAAAACAATCATTTTACCACATAAGGGCAAAACAAGCATTTTACCTCAT
*
40605280 -AAGGGCAAAACAGTCATTTTACCA
1 AAAGGGCAAAACAATCATTTTACCA
40605304 ATTAGGGGTC
Statistics
Matches: 160, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
52 1 0.01
53 10 0.06
54 138 0.86
55 8 0.05
56 3 0.02
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (55 bp):
AAAGGGCAAAACAATCATTTTACCACATAAGGGCAAAACAAGCATTTTACCTCAT
Found at i:40605209 original size:81 final size:81
Alignment explanation
Indices: 40605059--40605303 Score: 341
Period size: 81 Copynumber: 3.0 Consensus size: 81
40605049 GTCACCTTAA
* * * *
40605059 CATAAAAGGGCAAAATAGTCATCTTACCACAAAAGGGCAAAACAAGCATTTTACCTCATAAAGGG
1 CATATAAGGGCAAAATAGTCATTTTACCACAAAAGGGCAAAACAATCATTTTACCACAT-AAGGG
40605124 -AAAACAATCATTTTAC
65 CAAAACAATCATTTTAC
* ** *
40605140 C-TCATATGGGCAAAATAGTCATTTTACCTTAAAAGGGCAAAACAATCATTTTACCACGTAAGGG
1 CAT-ATAAGGGCAAAATAGTCATTTTACCACAAAAGGGCAAAACAATCATTTTACCACATAAGGG
40605204 CAAAACAATCATTTTAC
65 CAAAACAATCATTTTAC
* * * *
40605221 CATATAAGGGTAAAACAGTCATTTTACCACATAAGGGCAAAACAATCATTTTCCCACATAAGGGC
1 CATATAAGGGCAAAATAGTCATTTTACCACAAAAGGGCAAAACAATCATTTTACCACATAAGGGC
*
40605286 AAAACAGTCATTTTAC
66 AAAACAATCATTTTAC
40605302 CA
1 CA
40605304 ATTAGGGGTC
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
80 6 0.04
81 137 0.95
82 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (81 bp):
CATATAAGGGCAAAATAGTCATTTTACCACAAAAGGGCAAAACAATCATTTTACCACATAAGGGC
AAAACAATCATTTTAC
Found at i:40607086 original size:3 final size:3
Alignment explanation
Indices: 40607069--40607109 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
40607059 GCCTTTTTTA
40607069 TAT TA- TAT ATAT TAT TAT TAT TAT TAT TAT T-T T-T TAT TAT T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40607110 TACCTGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40630610 original size:24 final size:24
Alignment explanation
Indices: 40630578--40630640 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
40630568 AATCTCAAAT
40630578 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
40630602 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
40630626 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
40630641 ACATAATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:40638460 original size:24 final size:24
Alignment explanation
Indices: 40638428--40638490 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
40638418 AATCTCAAAT
40638428 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
40638452 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
40638476 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
40638491 ACATAATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:40643329 original size:40 final size:40
Alignment explanation
Indices: 40643274--40643437 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
40643264 TGAATGATAC
* * * *
40643274 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAAAT
* *
40643314 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTAAAT
* * **
40643354 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAAAT
* * *
40643394 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAAAT
40643434 CCGG
1 CCGG
40643438 TTAAATCCCG
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.03
40 96 0.92
41 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTAAAT
Found at i:40649138 original size:53 final size:54
Alignment explanation
Indices: 40649071--40649277 Score: 211
Period size: 53 Copynumber: 3.8 Consensus size: 54
40649061 TTCCTTTTTA
* * *
40649071 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * *
40649124 AACTTACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * * *
40649178 TAGTTTATCAATGCTATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* *
40649233 AACTTACCAATGCCATGCCTT-AGCATAGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGA-CATGGTCTTACATGGTATCCTT
40649278 AAACCCTAAT
Statistics
Matches: 123, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
53 48 0.39
54 35 0.28
55 40 0.33
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:40653270 original size:42 final size:42
Alignment explanation
Indices: 40653159--40653313 Score: 161
Period size: 42 Copynumber: 3.7 Consensus size: 42
40653149 TACCATACCA
* **** *
40653159 ATGCCATATCCCAGATATGGTCTTACATGTCATCTCGTATCG
1 ATGCCATATCCCAGATACGGTCTTACACAAAATCTCATATCG
* *
40653201 ATGCCAATAGCCCAGCTACGGTCTTACACAAAATCTC-TCATCG
1 ATGCC-ATATCCCAGATACGGTCTTACACAAAATCTCAT-ATCG
* * *
40653244 ATGCCATATCCCAGATACGGCCTTACACGAAGTCTCATATCG
1 ATGCCATATCCCAGATACGGTCTTACACAAAATCTCATATCG
* *
40653286 ATG-CATATCCTAGATATGGTCTTACACA
1 ATGCCATATCCCAGATACGGTCTTACACA
40653314 TAGTCTCAGT
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
41 21 0.22
42 39 0.41
43 34 0.36
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATACGGTCTTACACAAAATCTCATATCG
Found at i:40655615 original size:21 final size:20
Alignment explanation
Indices: 40655591--40655630 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40655581 ACTTGTATAT
*
40655591 CTATCAACAAGCATTCAAAAC
1 CTATCAACAAACA-TCAAAAC
*
40655612 CTATCATCAAACATCAAAA
1 CTATCAACAAACATCAAAA
40655631 TACATGCTTA
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:0.50, C:0.28, G:0.03, T:0.20
Consensus pattern (20 bp):
CTATCAACAAACATCAAAAC
Found at i:40659972 original size:27 final size:27
Alignment explanation
Indices: 40659657--40659973 Score: 362
Period size: 27 Copynumber: 11.7 Consensus size: 27
40659647 TTAGTTTACC
*
40659657 AAATTACCAAAATA-CCCTCGATTAGCT-
1 AAATTACCAAAATACCCCT-GATTTG-TA
* * * * *
40659684 AAATTACC-AAATGCCCTTCATTAGCA
1 AAATTACCAAAATACCCCTGATTTGTA
*
40659710 AAATTACCAAAACTACCCCTGGTTTGTA
1 AAATTACCAAAA-TACCCCTGATTTGTA
*
40659738 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
40659765 AAATTACTAAAATACCCATTG-TTTGTA
1 AAATTACCAAAATACCC-CTGATTTGTA
40659792 AAATTACCAAAATACCCCTTG-TTTGCT-
1 AAATTACCAAAATACCCC-TGATTTG-TA
40659819 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* *
40659846 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
*
40659873 AAATTACCAAAATA-CCCTCGATTAGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*
40659900 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
*
40659927 AAATTACCAAAATACCCCTGATTTTTA
1 AAATTACCAAAATACCCCTGATTTGTA
*
40659954 AAATTACTAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
40659974 TAAGGTAGAA
Statistics
Matches: 254, Mismatches: 23, Indels: 26
0.84 0.08 0.09
Matches are distributed among these distances:
26 23 0.09
27 202 0.80
28 29 0.11
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:40659985 original size:27 final size:27
Alignment explanation
Indices: 40659955--40660068 Score: 167
Period size: 27 Copynumber: 4.2 Consensus size: 27
40659945 TGATTTTTAA
40659955 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACTAAAATACCCCTGTAAGGTAG
* * *
40659982 AATTAAC-AAAATACCCTTATAGGGTAG
1 AATT-ACTAAAATACCCCTGTAAGGTAG
*
40660009 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTAAAATACCCCTGTAAGGTAG
*
40660036 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTAAAATACCCCTGTAAGGTAG
40660063 AATTAC
1 AATTAC
40660069 CGAGATACCC
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.03
27 74 0.95
28 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (27 bp):
AATTACTAAAATACCCCTGTAAGGTAG
Found at i:40659986 original size:54 final size:54
Alignment explanation
Indices: 40659711--40660054 Score: 294
Period size: 54 Copynumber: 6.4 Consensus size: 54
40659701 TCATTAGCAA
* ** *
40659711 AATTACCAAAACTACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGT-TTGTAA
1 AATTACCAAAA-TACCCCTGATTTGTAAAATTACCAAAATACCCCT-GTAAGGTAG
* * ** *
40659766 AATTACTAAAATACCCATTG-TTTGTAAAATTACCAAAATACCCCTTGTTTGCTA-
1 AATTACCAAAATACCC-CTGATTTGTAAAATTACCAAAATACCCC-TGTAAGGTAG
*
40659820 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCC--TAATTTGT-G
1 AATTACCAAAATACCCCTGA-TTTGTAAAATTACCAAAATACCCCTGTAA--GGTAG
* ** *
40659873 AAATTACCAAAATA-CCCTCGATTAGTAAAATTACCAAAATACCCCTGGT-TTGTAA
1 -AATTACCAAAATACCCCT-GATTTGTAAAATTACCAAAATACCCCT-GTAAGGTAG
* *
40659928 AATTACCAAAATACCCCTGATTTTTAAAATTACTAAAATACCCCTGTAAGGTAG
1 AATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTGTAAGGTAG
* * ** * **
40659982 AATTAACAAAATA-CCCTTATAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCAAAATACCCCTGAT-TTGTAAAATTACCAAAATACCCCTGTAAGGTAG
**
40660036 AATTACTGAAATACCCCTG
1 AATTACCAAAATACCCCTG
40660055 TAAGGTAGAA
Statistics
Matches: 240, Mismatches: 30, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
51 1 0.00
53 14 0.06
54 199 0.83
55 25 0.10
57 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (54 bp):
AATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTGTAAGGTAG
Found at i:40659986 original size:81 final size:80
Alignment explanation
Indices: 40659709--40660078 Score: 345
Period size: 81 Copynumber: 4.6 Consensus size: 80
40659699 CTTCATTAGC
** * *
40659709 AAAATTACCAAAACTACCCCTGGT-TTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACT
1 AAAATTACCAAAA-TACCCCT-GTAAGGTAGAATTACCAAAATACCCCTGGTTTGTAAAATTACC
*
40659773 AAAATACCCATTGTTTGT
64 AAAATACCC-CTGTTTGT
** * *
40659791 AAAATTACCAAAATACCCCTTGTTTGCTA-AATTACCAAAATACCCCTAGTTTGTAAAATTACCA
1 AAAATTACCAAAATACCCC-TGTAAGGTAGAATTACCAAAATACCCCTGGTTTGTAAAATTACCA
*
40659855 AAATACCCCTAATTTGT
65 AAATACCCCT-GTTTGT
* * *
40659872 GAAATTACCAAAATA-CCCTCGATTA-GTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACC
1 AAAATTACCAAAATACCCCT-G-TAAGGTAGAATTACCAAAATACCCCTGGTTTGTAAAATTACC
*
40659935 AAAATACCCCTGATTTTT
64 AAAATACCCCTG-TTTGT
* * ** ** * **
40659953 AAAATTACTAAAATACCCCTGTAAGGTAGAATTAACAAAATA-CCCTTATAGGGTAGAATTACTG
1 AAAATTACCAAAATACCCCTGTAAGGTAGAATTACCAAAATACCCCTGGT-TTGTAAAATTACCA
**
40660017 AAATACCCCTGTAAGGT
65 AAATACCCCTGT-TTGT
* ** * *
40660034 AGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAGATACCC
1 AAAATTACCAAAATACCCCTGTAAGGTAGAATTACCAAAATACCC
40660079 TCGTGGGGTA
Statistics
Matches: 244, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.00
80 15 0.06
81 205 0.84
82 23 0.09
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTGTAAGGTAGAATTACCAAAATACCCCTGGTTTGTAAAATTACCAA
AATACCCCTGTTTGT
Found at i:40660094 original size:54 final size:54
Alignment explanation
Indices: 40659963--40660095 Score: 144
Period size: 54 Copynumber: 2.5 Consensus size: 54
40659953 AAAATTACTA
* * * * *
40659963 AAATACCCCTGTAAGGTAGAATTAAC-AAAATACCCTTATAGGGTAGAATTACTG
1 AAATACCCCTGTAAGGTAAAATT-ACTGAAATACCCCTATAAGGTAGAATTACCG
* *
40660017 AAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCG
1 AAATACCCCTGTAAGGTAAAATTACTGAAATACCCCTATAAGGTAGAATTACCG
* **
40660071 AGATA-CCCTCGTGGGGTAAAATTAC
1 AAATACCCCT-GTAAGGTAAAATTAC
40660096 CATTTTGCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 6 0.09
54 62 0.91
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (54 bp):
AAATACCCCTGTAAGGTAAAATTACTGAAATACCCCTATAAGGTAGAATTACCG
Found at i:40660456 original size:8 final size:8
Alignment explanation
Indices: 40660443--40660468 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40660433 ATGGGCCGAA
40660443 AATGGGCC
1 AATGGGCC
40660451 AATGGGCC
1 AATGGGCC
40660459 AATGGGCC
1 AATGGGCC
40660467 AA
1 AA
40660469 CGGACCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.35, T:0.12
Consensus pattern (8 bp):
AATGGGCC
Found at i:40660773 original size:27 final size:26
Alignment explanation
Indices: 40660729--40660780 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40660719 CTCGCTGCAA
*
40660729 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
40660756 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
40660781 GCAGCCTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:40663576 original size:15 final size:16
Alignment explanation
Indices: 40663556--40663585 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40663546 AAGATATTGT
40663556 AATCATAA-CTTACTC
1 AATCATAACCTTACTC
40663571 AATCATAACCTTACT
1 AATCATAACCTTACT
40663586 GATGGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
AATCATAACCTTACTC
Done.