Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 174 of 325
Found at i:54579437 original size:27 final size:27
Alignment explanation
Indices: 54579407--54579762 Score: 430
Period size: 27 Copynumber: 13.2 Consensus size: 27
54579397 AACACCCTAG
* *
54579407 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54579434 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54579461 GGGTAAAACAGTAATTTTTTAAATCTA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* **
54579488 GGGTAAAATAGTAAATTTGTAAATTAA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54579515 GGGTAAAACAGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
54579542 GGGTAAAAT-GATAATTCTGTAAATCGA
1 GGGTAAAATAG-TAATTTTGTAAATCGA
54579569 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
**
54579596 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54579623 GGGTAAAA-CGATAATTCTGTAAATTGA
1 GGGTAAAATAG-TAATTTTGTAAATCGA
*
54579650 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
54579677 GGGTAAAATGGTAATTTTGTAAATTGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
54579704 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
54579731 TGGTAAAATAGTAATTTTG-AAATTTGA
1 GGGTAAAATAGTAATTTTGTAAA-TCGA
54579758 GGGTA
1 GGGTA
54579763 CTTTGATAAT
Statistics
Matches: 286, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
26 5 0.02
27 279 0.98
28 2 0.01
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (27 bp):
GGGTAAAATAGTAATTTTGTAAATCGA
Found at i:54579772 original size:27 final size:25
Alignment explanation
Indices: 54579742--54579847 Score: 79
Period size: 27 Copynumber: 4.0 Consensus size: 25
54579732 GGTAAAATAG
54579742 TAATTTTGAAATTTGAGGGTACTTTGA
1 TAATTTTGAAA-TTGAGGGTA-TTTGA
* *
54579769 TAATTTT-ACAAGTCGAGGGTATTTCA
1 TAATTTTGA-AA-TTGAGGGTATTTGA
*
54579795 GTAATTTTGCAAATTGAGGGTATTTCGG
1 -TAATTTTG-AAATTGAGGGTATTT-GA
* * *
54579823 TAATTTTACAAATCGAGGATATTTG
1 TAATTTT-GAAATTGAGGGTATTTG
54579848 GGTATTTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
26 6 0.09
27 55 0.86
28 2 0.03
29 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (25 bp):
TAATTTTGAAATTGAGGGTATTTGA
Found at i:54579773 original size:54 final size:54
Alignment explanation
Indices: 54579407--54579816 Score: 399
Period size: 54 Copynumber: 7.6 Consensus size: 54
54579397 AACACCCTAG
* * * * *
54579407 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAATGATAATTCTGTAAATCGA
* * **
54579461 GGGTAAAACAGTAATTTTTTAAATCT-AGGGTAAAAT-AGTAAATT-TGTAAATTAA
1 GGGTAAAATAGTAATTTTGTAAAT-TGAGGGTAAAATGA-T-AATTCTGTAAATCGA
* * * *
54579515 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAATGATAATTCTGTAAATCGA
* * * *
54579569 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAATGATAATTCTGTAAATCGA
* * * *
54579623 GGGTAAAA-CGATAATTCTGTAAATTGAGGGTAAAA-CAGTAATTTTGTAAATCGA
1 GGGTAAAATAG-TAATTTTGTAAATTGAGGGTAAAATGA-TAATTCTGTAAATCGA
*
54579677 GGGTAAAATGGTAATTTTGTAAATTGAGGGTAAAAT-AGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAATGA-TAATTCTGTAAATCGA
* ***
54579731 TGGTAAAATAGTAATTTTG-AAATTTGAGGGTACTTTGATAATT-T-TACAAGTCGA
1 GGGTAAAATAGTAATTTTGTAAA-TTGAGGGTAAAATGATAATTCTGTA-AA-TCGA
** *
54579785 GGGT-ATTTCAGTAATTTTGCAAATTGAGGGTA
1 GGGTAAAAT-AGTAATTTTGTAAATTGAGGGTA
54579817 TTTCGGTAAT
Statistics
Matches: 305, Mismatches: 35, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
52 2 0.01
53 13 0.04
54 280 0.92
55 10 0.03
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (54 bp):
GGGTAAAATAGTAATTTTGTAAATTGAGGGTAAAATGATAATTCTGTAAATCGA
Found at i:54579798 original size:81 final size:81
Alignment explanation
Indices: 54579407--54579816 Score: 441
Period size: 81 Copynumber: 5.1 Consensus size: 81
54579397 AACACCCTAG
* * * * *
54579407 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAG
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAATCAG
* * *
54579472 TAATTTTTTAAATCTA
66 TAATTCTGTAAATCGA
* ** ** * * *
54579488 GGGTAAAATAGTAAATTTGTAAATTAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGA
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT-AAATCA
54579553 -TAATTCTGTAAATCGA
65 GTAATTCTGTAAATCGA
* *
54579569 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAAC-G
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAATCAG
*
54579633 ATAATTCTGTAAATTGA
66 -TAATTCTGTAAATCGA
* *
54579650 GGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATTGAGGGTAAAAT-A
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT-AAATCA
54579714 GTAATTCTGTAAATCGA
65 GTAATTCTGTAAATCGA
* * *** * ** * **
54579731 TGGTAAAATAGTAATTTTG-AAATTTGAGGGTACTTTGATAATTTTACAAGTCGAGGGTATTTCA
1 GGGTAAAATAGTAATTTTGTAAA-TCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAATCA
* * *
54579795 GTAATTTTGCAAATTGA
65 GTAATTCTGTAAATCGA
54579812 GGGTA
1 GGGTA
54579817 TTTCGGTAAT
Statistics
Matches: 279, Mismatches: 43, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
80 8 0.03
81 263 0.94
82 8 0.03
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (81 bp):
GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAATCAG
TAATTCTGTAAATCGA
Found at i:54579827 original size:54 final size:54
Alignment explanation
Indices: 54579740--54579907 Score: 168
Period size: 54 Copynumber: 3.1 Consensus size: 54
54579730 ATGGTAAAAT
* *
54579740 AGTAATTTTGAAATTTGAGGGTACTTT-GATAATTTTACAAGTCGAGGGTATTTC
1 AGTAATTTTGAAA-TTGAGGGTACTTTCGGTAATTTTACAAATCGAGGGTATTTC
* *
54579794 AGTAATTTTGCAAATTGAGGGTA-TTTCGGTAATTTTACAAATCGAGGATATTTG
1 AGTAATTTTG-AAATTGAGGGTACTTTCGGTAATTTTACAAATCGAGGGTATTTC
* *** * *
54579848 GGT-ATTTT-ATAAACCAGGGGTACTTTC-GTAATTTTACAACT-GGGGGTATTTC
1 AGTAATTTTGA-AATTGA-GGGTACTTTCGGTAATTTTACAAATCGAGGGTATTTC
54579900 AGTAATTT
1 AGTAATTT
54579908 GGTAAACTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
51 1 0.01
52 13 0.14
53 30 0.32
54 48 0.51
55 3 0.03
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (54 bp):
AGTAATTTTGAAATTGAGGGTACTTTCGGTAATTTTACAAATCGAGGGTATTTC
Found at i:54579851 original size:27 final size:27
Alignment explanation
Indices: 54579756--54579907 Score: 134
Period size: 27 Copynumber: 5.7 Consensus size: 27
54579746 TTTGAAATTT
* *
54579756 GAGGGTACTTT-GATAATTTTACAAGTC
1 GAGGGTA-TTTCGGTAATTTTACAAATC
* * *
54579783 GAGGGTATTTCAGTAATTTTGCAAATT
1 GAGGGTATTTCGGTAATTTTACAAATC
54579810 GAGGGTATTTCGGTAATTTTACAAATC
1 GAGGGTATTTCGGTAATTTTACAAATC
* * *
54579837 GAGGATATTTGGGT-ATTTTATAAA-C
1 GAGGGTATTTCGGTAATTTTACAAATC
* *
54579862 CAGGGGTACTTTC-GTAATTTTACAACT-
1 GA-GGGTA-TTTCGGTAATTTTACAAATC
* *
54579889 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCGGTAATTT
54579908 GGTAAACTAA
Statistics
Matches: 101, Mismatches: 18, Indels: 13
0.77 0.14 0.10
Matches are distributed among these distances:
25 6 0.06
26 30 0.30
27 65 0.64
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (27 bp):
GAGGGTATTTCGGTAATTTTACAAATC
Found at i:54581105 original size:3 final size:3
Alignment explanation
Indices: 54581097--54581129 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
54581087 ATAAATAGAG
54581097 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54581130 GGAATGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54586773 original size:39 final size:39
Alignment explanation
Indices: 54586666--54586921 Score: 236
Period size: 39 Copynumber: 6.6 Consensus size: 39
54586656 TTGAATGCTG
* * * * * *
54586666 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
54586705 TCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCGAAGGCATTCGTGCGAGTTACTAAA
*
54586745 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTA-TTAA
1 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTACTAAA
*
54586783 T-CGGG-TAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAA
1 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTACTAAA
* **
54586820 TCCGGGTTAAGTCCGAAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCG-AAGGCATTCGTGCGAGTTACTAAA
* * *
54586860 TCCGGGTTATGTCCGAAGGCATT-GTGTGAGTTCCTAAA
1 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
54586898 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGT-CCGAAGGCATT
54586922 GAACGAGGAG
Statistics
Matches: 187, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
36 5 0.03
37 29 0.16
38 33 0.18
39 69 0.37
40 44 0.24
41 7 0.04
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (39 bp):
TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:54586841 original size:76 final size:76
Alignment explanation
Indices: 54586704--54586919 Score: 240
Period size: 76 Copynumber: 2.8 Consensus size: 76
54586694 AAGTGAATAT
* * * *
54586704 ATCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCGAAGGCATTC
1 ATCCGGGTTAAG-TCCGAAGG-CATTGTGCGAG-TTCTAAATCCGGGTTAAGTCCGAAGGCAGTC
54586769 GTGCGAGTTATT-A
63 GTGCGAGTTATTAA
*
54586782 AT-CGGG-TAAGTCCCGAAGGCATTCGTGCGAGTTTTAAATCCGGGTTAAGTCCGAAAGGCAGTC
1 ATCCGGGTTAAGT-CCGAAGGCATT-GTGCGAGTTCTAAATCCGGGTTAAGTCCG-AAGGCAGTC
*
54586845 GTGCGAGTTGTTAA
63 GTGCGAGTTATTAA
* * * * *
54586859 ATCCGGGTTATGTCCGAAGGCATTGTGTGAGTTCCTAAAACCGGGCTATGTCCCGAAGGCA
1 ATCCGGGTTAAGTCCGAAGGCATTGTGCGAGTT-CTAAATCCGGGTTAAGT-CCGAAGGCA
54586920 TTGAACGAGG
Statistics
Matches: 118, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
75 24 0.20
76 37 0.31
77 14 0.12
78 36 0.31
79 7 0.06
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (76 bp):
ATCCGGGTTAAGTCCGAAGGCATTGTGCGAGTTCTAAATCCGGGTTAAGTCCGAAGGCAGTCGTG
CGAGTTATTAA
Found at i:54594645 original size:40 final size:40
Alignment explanation
Indices: 54594601--54594824 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
54594591 AAGTGAATAT
* * * * *
54594601 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAA
54594641 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
54594681 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* *
54594721 ATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* * *
54594761 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* * *
54594800 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
54594825 TGAACGAGGA
Statistics
Matches: 169, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 35 0.21
40 134 0.79
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
Found at i:54594844 original size:79 final size:80
Alignment explanation
Indices: 54594601--54594859 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
54594591 AAGTGAATAT
* * * * * * *
54594601 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
54594665 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
54594681 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
54594746 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
54594761 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
54594825 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
54594840 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
54594860 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:54605290 original size:26 final size:26
Alignment explanation
Indices: 54605261--54605338 Score: 156
Period size: 26 Copynumber: 3.0 Consensus size: 26
54605251 ACAAGATAGC
54605261 AAATATTTAGGTATCAAATTAGCCAT
1 AAATATTTAGGTATCAAATTAGCCAT
54605287 AAATATTTAGGTATCAAATTAGCCAT
1 AAATATTTAGGTATCAAATTAGCCAT
54605313 AAATATTTAGGTATCAAATTAGCCAT
1 AAATATTTAGGTATCAAATTAGCCAT
54605339 TTTCGCATGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (26 bp):
AAATATTTAGGTATCAAATTAGCCAT
Found at i:54606224 original size:43 final size:43
Alignment explanation
Indices: 54606176--54606377 Score: 255
Period size: 43 Copynumber: 4.7 Consensus size: 43
54606166 TCCCTGACGT
* * *
54606176 GGTCTTACAT-GTAATCACATATCGATGCCACTATCCCCGAC-A
1 GGTCTTAC-TCGTAATCACATATCGATGCCATTGTCCCAGACAA
* *
54606218 GCGTCTTACTCATAATCCCATATCGATGCCATTGTCCCAGACAA
1 G-GTCTTACTCGTAATCACATATCGATGCCATTGTCCCAGACAA
* * *** * *
54606262 GGTCTTACTCGTAATCACATATTGATGCCAATGTATTAAACAT
1 GGTCTTACTCGTAATCACATATCGATGCCATTGTCCCAGACAA
*
54606305 GGTCTTACTCATAATCACATATCGATGCCATTGTCCCAGACAA
1 GGTCTTACTCGTAATCACATATCGATGCCATTGTCCCAGACAA
54606348 GGTCTTACTCGTAATCACATATCGATGCCA
1 GGTCTTACTCGTAATCACATATCGATGCCA
54606378 ATGTATTAAA
Statistics
Matches: 134, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.01
43 130 0.97
44 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (43 bp):
GGTCTTACTCGTAATCACATATCGATGCCATTGTCCCAGACAA
Found at i:54606310 original size:86 final size:86
Alignment explanation
Indices: 54606220--54606397 Score: 338
Period size: 86 Copynumber: 2.1 Consensus size: 86
54606210 CCCCGACAGC
* *
54606220 GTCTTACTCATAATCCCATATCGATGCCATTGTCCCAGACAAGGTCTTACTCGTAATCACATATT
1 GTCTTACTCATAATCACATATCGATGCCATTGTCCCAGACAAGGTCTTACTCGTAATCACATATC
54606285 GATGCCAATGTATTAAACATG
66 GATGCCAATGTATTAAACATG
54606306 GTCTTACTCATAATCACATATCGATGCCATTGTCCCAGACAAGGTCTTACTCGTAATCACATATC
1 GTCTTACTCATAATCACATATCGATGCCATTGTCCCAGACAAGGTCTTACTCGTAATCACATATC
54606371 GATGCCAATGTATTAAACATG
66 GATGCCAATGTATTAAACATG
54606392 GTCTTA
1 GTCTTA
54606398 TTCGCACACA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (86 bp):
GTCTTACTCATAATCACATATCGATGCCATTGTCCCAGACAAGGTCTTACTCGTAATCACATATC
GATGCCAATGTATTAAACATG
Found at i:54606395 original size:43 final size:43
Alignment explanation
Indices: 54606176--54606415 Score: 225
Period size: 43 Copynumber: 5.6 Consensus size: 43
54606166 TCCCTGACGT
* * * **
54606176 GGTCTTACAT-GTAATCACATATCGATGCCACTATCCCCGAC-A
1 GGTCTTAC-TCGTAATCACATATCGATGCCAATGTACCAAACAA
* * * * *
54606218 GCGTCTTACTCATAATCCCATATCGATGCCATTGTCCCAGACAA
1 G-GTCTTACTCGTAATCACATATCGATGCCAATGTACCAAACAA
* ** *
54606262 GGTCTTACTCGTAATCACATATTGATGCCAATGTATTAAACAT
1 GGTCTTACTCGTAATCACATATCGATGCCAATGTACCAAACAA
* * * *
54606305 GGTCTTACTCATAATCACATATCGATGCCATTGTCCCAGACAA
1 GGTCTTACTCGTAATCACATATCGATGCCAATGTACCAAACAA
** *
54606348 GGTCTTACTCGTAATCACATATCGATGCCAATGTATTAAACAT
1 GGTCTTACTCGTAATCACATATCGATGCCAATGTACCAAACAA
* *
54606391 GGTCTTATTCGCACA-CACATATCGA
1 GGTCTTACTCGTA-ATCACATATCGA
54606416 AATCACATAT
Statistics
Matches: 163, Mismatches: 31, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
42 2 0.01
43 158 0.97
44 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (43 bp):
GGTCTTACTCGTAATCACATATCGATGCCAATGTACCAAACAA
Found at i:54606453 original size:56 final size:56
Alignment explanation
Indices: 54606360--54606472 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
54606350 TCTTACTCGT
* ** * *
54606360 AATCACATATCGATGCCAATGTATTAAACATGGTCTTATTCGCACACACATATCGA
1 AATCACATATCGATGCCAACGTATTAAACATACTCTTACTCACACACACATATCGA
* ** *
54606416 AATCACATATTGATGCCAACGTATTAAATGTACTCTTACTCACACACATATATCGA
1 AATCACATATCGATGCCAACGTATTAAACATACTCTTACTCACACACACATATCGA
54606472 A
1 A
54606473 GTCATGGCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTATTAAACATACTCTTACTCACACACACATATCGA
Found at i:54607641 original size:14 final size:14
Alignment explanation
Indices: 54607622--54607648 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54607612 AATCACGAAG
54607622 ATTTCACACATAAA
1 ATTTCACACATAAA
54607636 ATTTCACACATAA
1 ATTTCACACATAA
54607649 TAAAAATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTTCACACATAAA
Found at i:54610482 original size:39 final size:39
Alignment explanation
Indices: 54610439--54610621 Score: 267
Period size: 39 Copynumber: 4.7 Consensus size: 39
54610429 CATGGTATTT
* *
54610439 GAAATATATCCGGACATGAGGACCGTAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
*
54610478 GAAATATATCCGGACATGAGGTCCCCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
*
54610517 GAAATATATCCGGACATGAAGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* * * *
54610556 GGATTATATCCGGACATGAGGTCTGCAGGCTATATGCTA
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* * *
54610595 GAAATATATCCAGACTTGAAGTCCGCA
1 GAAATATATCCGGACATGAGGTCCGCA
54610622 AGCCACGTGC
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 128 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (39 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
Found at i:54617518 original size:31 final size:31
Alignment explanation
Indices: 54617482--54617551 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
54617472 TACTGGGCTA
*
54617482 AAGCCTTTTCATAAATTATATCACTT-GGCCG
1 AAGCCTTTTCATAAATCATATCA-TTGGGCCG
54617513 AAGCCTTTTCATAAATCATATCATTGGGCCG
1 AAGCCTTTTCATAAATCATATCATTGGGCCG
54617544 AAGCCTTT
1 AAGCCTTT
54617552 ACTGTAAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (31 bp):
AAGCCTTTTCATAAATCATATCATTGGGCCG
Found at i:54617841 original size:26 final size:26
Alignment explanation
Indices: 54617770--54617918 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
54617760 CTCTTTTAAG
*
54617770 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
54617795 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
54617820 AACTGGGGCATAAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* *
54617846 AATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* *
54617872 AACTAGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
54617898 AACTAGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
54617919 GCACTTCCTC
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 33 0.29
26 81 0.71
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGATA
Found at i:54617875 original size:52 final size:52
Alignment explanation
Indices: 54617770--54617918 Score: 248
Period size: 52 Copynumber: 2.9 Consensus size: 52
54617760 CTCTTTTAAG
54617770 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
* *
54617820 AACTGGGGCATAAGCCCTTTTCGATAAATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
* *
54617872 AACTAGGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
54617919 GCACTTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 10 0.11
51 23 0.25
52 58 0.64
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (52 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
Found at i:54618769 original size:27 final size:27
Alignment explanation
Indices: 54618716--54618807 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
54618706 GGGCGTATTC
* *
54618716 GTCATTTTACCATAC-GGGG-TATTACG
1 GTCACTTTACCTTACAGGGGCT-TTACG
54618742 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACCTTACAGGGGCTTTACG
* * *
54618769 GTCTCTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCTTACAGGGGCTTTACG
**
54618796 GTCTTTTTACCT
1 GTCACTTTACCT
54618808 AATAGGGGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
26 13 0.23
27 43 0.75
28 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (27 bp):
GTCACTTTACCTTACAGGGGCTTTACG
Found at i:54618908 original size:27 final size:27
Alignment explanation
Indices: 54618860--54618911 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54618850 GTAAATCTAC
*
54618860 AAACCAAAGGTATTTTAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTTGT
*
54618887 AAACCAATGGTATTTCCA-TAATTTT
1 AAACCAAAGGTATTT-CAGTAATTTT
54618912 TAGAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCAGTAATTTTGT
Found at i:54619019 original size:21 final size:21
Alignment explanation
Indices: 54618995--54619037 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54618985 CGGTAATTTC
* *
54618995 ACAAACCAGTGGTATTTTGGT
1 ACAAAACAGGGGTATTTTGGT
*
54619016 ACAAAATAGGGGTATTTTGGT
1 ACAAAACAGGGGTATTTTGGT
54619037 A
1 A
54619038 ATTTTACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (21 bp):
ACAAAACAGGGGTATTTTGGT
Found at i:54619074 original size:75 final size:75
Alignment explanation
Indices: 54618947--54619087 Score: 257
Period size: 75 Copynumber: 1.9 Consensus size: 75
54618937 CTTTGTAAAT
54618947 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATT
54619011 TTGGTACAAAA
65 TTGGTACAAAA
*
54619022 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTT
54619087 T
66 T
54619088 AGCAATTTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
75 62 0.97
76 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (75 bp):
TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTT
TGGTACAAAA
Found at i:54619145 original size:80 final size:77
Alignment explanation
Indices: 54618922--54619176 Score: 279
Period size: 80 Copynumber: 3.2 Consensus size: 77
54618912 TAGAAAGTCA
54618922 AGGGTATTTCT-GTAACTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC
1 AGGGTATTT-TAGTAA-TTT-TAAA-TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC
*
54618986 GGTAATTTCACAAACC
62 GGTAATTTTACAAACC
*
54619002 AGTGGTATTTTGGTACA----AAATAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGG
1 AG-GGTATTTTAGTA-ATTTTAAATAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGG
54619063 TAATTTTACAAACC
64 TAATTTTACAAACC
* ** * *
54619077 AAGGGTATTTTAGCAATTTTATAGACTA-GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTT
1 -AGGGTATTTTAGTAATTTTA-A-A-TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC
** *
54619141 GGTAATTTTGTAAACTG
62 GGTAATTTTACAAAC-C
54619158 AGGGTATTTTAGTAATTTT
1 AGGGTATTTTAGTAATTTT
54619177 GTAAATCAAG
Statistics
Matches: 152, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
74 1 0.01
75 64 0.42
76 5 0.03
78 1 0.01
79 1 0.01
80 67 0.44
81 12 0.08
82 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (77 bp):
AGGGTATTTTAGTAATTTTAAATAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTA
ATTTTACAAACC
Found at i:54619173 original size:27 final size:27
Alignment explanation
Indices: 54619025--54619181 Score: 165
Period size: 27 Copynumber: 5.9 Consensus size: 27
54619015 TACAAAATAG
* *
54619025 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTTTATAAACTGA
* * **
54619052 GGGTATTTCGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTATAAACTGA
* * *
54619079 GGGTATTTTAGCAATTTTATAGACT-A
1 GGGTATTTTGGTAATTTTATAAACTGA
* *
54619105 GGGTATTTTGGTAATTTTACTGATC-GA
1 GGGTATTTTGGTAATTTTA-TAAACTGA
*
54619132 GGGTATTTTGGTAATTTTGTAAACTGA
1 GGGTATTTTGGTAATTTTATAAACTGA
* *
54619159 GGGTATTTTAGTAATTTTGTAAA
1 GGGTATTTTGGTAATTTTATAAA
54619182 TCAAGGGTAA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.19
27 87 0.81
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACTGA
Found at i:54619188 original size:27 final size:27
Alignment explanation
Indices: 54618868--54619337 Score: 151
Period size: 27 Copynumber: 17.6 Consensus size: 27
54618858 ACAAACCAAA
* * * *
54618868 GGTATTTTAGTAATTTTGTAAACCAAT
1 GGTATTTTAGTAATTTTATAAATCGAG
* * *
54618895 GGTATTTCCA-TAATTTTTAGAAAGTCAAG
1 GGTATTT-TAGTAA-TTTTATAAA-TCGAG
* * *
54618924 GGTATTTCT-GTAACTTTGTAAAT-TAGG
1 GGTATTT-TAGTAATTTTATAAATCGA-G
* * *
54618951 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTAGTAATTTTATAAATCGAG
** * * *
54618978 GGTATTTCGGTAATTTCACAAA-CCAG
1 GGTATTTTAGTAATTTTATAAATCGAG
* * *
54619004 TGGTATTTTGGT-A---CA-AAATAG-G
1 -GGTATTTTAGTAATTTTATAAATCGAG
* * *
54619026 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTAGTAATTTTATAAATCGAG
** * * *
54619053 GGTATTTCGGTAATTTTACAAACCAAG
1 GGTATTTTAGTAATTTTATAAATCGAG
* * *
54619080 GGTATTTTAGCAATTTTATAGA-CTAG
1 GGTATTTTAGTAATTTTATAAATCGAG
* *
54619106 GGTATTTTGGTAATTTTACT-GATCGAG
1 GGTATTTTAGTAATTTTA-TAAATCGAG
* *
54619133 GGTATTTTGGTAATTTTGTAAA-CTGAG
1 GGTATTTTAGTAATTTTATAAATC-GAG
* *
54619160 GGTATTTTAGTAATTTTGTAAATCAAG
1 GGTATTTTAGTAATTTTATAAATCGAG
**** * * *
54619187 GGTAAAACAGTAATTCTGTAAATCAAG
1 GGTATTTTAGTAATTTTATAAATCGAG
*** *
54619214 GGTAAAATAGTAATTCTATAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCGAG
** * *
54619241 GGTA--AAACGATAATTCTGTAAATCGAG
1 GGTATTTTA-G-TAATTTTATAAATCGAG
***** *
54619268 GGTAAAACGGTAATTCTATAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCGAG
* * * * * *
54619295 GGTACTTTGGTAATTTTACAATTTGAA
1 GGTATTTTAGTAATTTTATAAATCGAG
*
54619322 GGTATTTCAGTAATTT
1 GGTATTTTAGTAATTT
54619338 GGTAAACTGA
Statistics
Matches: 354, Mismatches: 65, Indels: 48
0.76 0.14 0.10
Matches are distributed among these distances:
21 11 0.03
22 5 0.01
23 2 0.01
25 3 0.01
26 34 0.10
27 267 0.75
28 17 0.05
29 15 0.04
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
GGTATTTTAGTAATTTTATAAATCGAG
Found at i:54619309 original size:54 final size:54
Alignment explanation
Indices: 54619168--54619298 Score: 190
Period size: 54 Copynumber: 2.4 Consensus size: 54
54619158 AGGGTATTTT
* * * * *
54619168 AGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
* *
54619222 AGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
*
54619276 GGTAATTCTATAAATCGAGGGTA
1 AGTAATTCTATAAATCGAGGGTA
54619299 CTTTGGTAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (54 bp):
AGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:54619336 original size:81 final size:81
Alignment explanation
Indices: 54619127--54619336 Score: 215
Period size: 81 Copynumber: 2.6 Consensus size: 81
54619117 AATTTTACTG
* * * * *
54619127 ATCGAGGGTATTTTGGTAATTTTGTAAACTGAGGGTATTTTAGTAATTTTGTAAATCAAGGGTAA
1 ATCGAGGGTAATTTGGTAATTTTATAAATTGAGGGTATTTCAGTAATTCTGTAAATCAAGGGTAA
*
54619192 AACAGTAATTCTGTAA
66 AACAGTAATTCTATAA
* ** * * * *** *
54619208 ATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAAC-GATAATTCTGTAAATCGAGGGTA
1 ATCGAGGGTAATTTGGTAATTTTATAAATTGAGGGTATTTCAG-TAATTCTGTAAATCAAGGGTA
*
54619272 AAACGGTAATTCTATAA
65 AAACAGTAATTCTATAA
* * * *
54619289 ATCGAGGGTACTTTGGTAATTTTACAATTTGAAGGTATTTCAGTAATT
1 ATCGAGGGTAATTTGGTAATTTTATAAATTGAGGGTATTTCAGTAATT
54619337 TGGTAAACTG
Statistics
Matches: 97, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
80 1 0.01
81 95 0.98
82 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (81 bp):
ATCGAGGGTAATTTGGTAATTTTATAAATTGAGGGTATTTCAGTAATTCTGTAAATCAAGGGTAA
AACAGTAATTCTATAA
Found at i:54621780 original size:39 final size:39
Alignment explanation
Indices: 54621737--54621934 Score: 252
Period size: 39 Copynumber: 5.1 Consensus size: 39
54621727 CATGGTATTT
* * *
54621737 GAAATATATCCGGACATGAGGACTGTAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* * *
54621776 GAAATATATTCGGACATGAGGTCTGTAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
*
54621815 GAAATATATCCGGACATGAAGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* * *
54621854 GGAATGTATCCAGACATGAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* * * * **
54621893 GAAATATATCCAGACTTGAAGTCCGCAAGCTACGTGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
54621932 GAA
1 GAA
54621935 TGGTATACGG
Statistics
Matches: 142, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (39 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
Found at i:54628215 original size:34 final size:34
Alignment explanation
Indices: 54628157--54628237 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
54628147 ATTAGATTTT
*
54628157 TTTCAGTAACAGTAGCAGTCTAGGCCTTAGCAC-A
1 TTTCAGTAATAGTAGCAGTCTAGGCCTTAGC-CTA
*
54628191 TTTCAGTAATAG-AGACAGTTTAGGCCTTAGCCTA
1 TTTCAGTAATAGTAG-CAGTCTAGGCCTTAGCCTA
54628225 TTTCAG-AATAGTA
1 TTTCAGTAATAGTA
54628238 AGCAAGCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 8 0.19
34 34 0.81
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (34 bp):
TTTCAGTAATAGTAGCAGTCTAGGCCTTAGCCTA
Found at i:54633613 original size:42 final size:42
Alignment explanation
Indices: 54633558--54633646 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
54633548 TAGCCCATAG
* * * ** *
54633558 GCCCATTTTAATATAACATGTAATGTCAATGGATGTATGCAA
1 GCCCAATTCAATATAACATGAAATACCAATGAATGTATGCAA
* *
54633600 GCCCAATTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCAATTCAATATAACATGAAATACCAATGAATGTATGCAA
54633642 GCCCA
1 GCCCA
54633647 TTTGGGGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (42 bp):
GCCCAATTCAATATAACATGAAATACCAATGAATGTATGCAA
Found at i:54633864 original size:51 final size:51
Alignment explanation
Indices: 54633788--54633916 Score: 226
Period size: 51 Copynumber: 2.6 Consensus size: 51
54633778 GCCTAGCCTC
54633788 TTTCAAT-AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCT
1 TTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCT
* *
54633837 TTTCAATAAACTGAGGCATAAGCCCTTTTTGGTAAACTGGGGCAAAGCCCT
1 TTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCT
54633888 TTTCAATAAACTGGGGCATAAGCCCTTTT
1 TTTCAATAAACTGGGGCATAAGCCCTTTT
54633917 GCACTTCCTC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
49 7 0.09
50 9 0.12
51 59 0.79
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (51 bp):
TTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCT
Found at i:54633872 original size:26 final size:25
Alignment explanation
Indices: 54633788--54633916 Score: 179
Period size: 25 Copynumber: 5.1 Consensus size: 25
54633778 GCCTAGCCTC
54633788 TTTCAAT-AACTGGGGCAAAGCCCT
1 TTTCAATAAACTGGGGCAAAGCCCT
**
54633812 TTTCGGTAAACTGGGGCAAAGCCCT
1 TTTCAATAAACTGGGGCAAAGCCCT
*
54633837 TTTCAATAAACTGAGGCATAAGCCCT
1 TTTCAATAAACTGGGGCA-AAGCCCT
***
54633863 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTCAATAAACTGGGGCAAAGCCCT
54633888 TTTCAATAAACTGGGGCATAAGCCCT
1 TTTCAATAAACTGGGGCA-AAGCCCT
54633914 TTT
1 TTT
54633917 GCACTTCCTC
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.06
25 54 0.60
26 31 0.34
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
TTTCAATAAACTGGGGCAAAGCCCT
Found at i:54633991 original size:20 final size:20
Alignment explanation
Indices: 54633966--54634052 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
54633956 TTATGAATAC
54633966 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
54633986 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
* *
54634006 ATCGTGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
54634026 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
54634046 ATCATGT
1 ATCATGT
54634053 ATATCATATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:54634821 original size:27 final size:27
Alignment explanation
Indices: 54634760--54634823 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
54634750 GGCGTATTCA
54634760 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
54634787 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
54634814 TCTTTTTACC
1 TCATTTTACC
54634824 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:54634884 original size:27 final size:27
Alignment explanation
Indices: 54634854--54634987 Score: 142
Period size: 27 Copynumber: 5.0 Consensus size: 27
54634844 TTTCATCCTA
* * *
54634854 CAAGGGTGTTTTGGTAAATCTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* **
54634881 CAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
54634908 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * * * *
54634935 TGAGGGTGTTTCGGTAATTTCATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
54634962 CAATGGTATTTTGGTAATTTTACAAA
1 CAAGGGTATTTTGGTAATTTTACAAA
54634988 CTAGGGGTGT
Statistics
Matches: 83, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:54635000 original size:27 final size:27
Alignment explanation
Indices: 54634857--54635007 Score: 126
Period size: 27 Copynumber: 5.6 Consensus size: 27
54634847 CATCCTACAA
* * * *
54634857 GGGTGTTTTGGTAAATCTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAG
* **
54634884 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
*
54634911 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * * * *
54634937 AGGGTGTTTCGGTAATTTCATAAATCAA
1 -GGGTATTTTGGTAATTTTACAAATCAG
*
54634965 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
* *
54634992 GGGTGTTTTAGTAATT
1 GGGTATTTTGGTAATT
54635008 CTACTTTATA
Statistics
Matches: 95, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
26 2 0.02
27 93 0.98
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:54635006 original size:54 final size:53
Alignment explanation
Indices: 54634854--54635007 Score: 164
Period size: 54 Copynumber: 2.8 Consensus size: 53
54634844 TTTCATCCTA
* * * * * * **
54634854 CAAGGGTGTTTTGGTAAATCTACAAATCAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT-AGGGGTGTTTTAGTAATTTCATAAAT
* * **
54634908 CAGGGGTATTTTGGTAATTTTACAAATTGAGGGTGTTTCGGTAATTTCATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAATAG-GGGTGTTTTAGTAATTTCATAAAT
*
54634962 CAATGGTATTTTGGTAATTTTACAAACTAGGGGTGTTTTAGTAATT
1 CAAGGGTATTTTGGTAATTTTACAAA-TAGGGGTGTTTTAGTAATT
54635008 CTACTTTATA
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 80 0.98
55 2 0.02
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (53 bp):
CAAGGGTATTTTGGTAATTTTACAAATAGGGGTGTTTTAGTAATTTCATAAAT
Found at i:54635033 original size:81 final size:81
Alignment explanation
Indices: 54634877--54635037 Score: 182
Period size: 81 Copynumber: 2.0 Consensus size: 81
54634867 GTAAATCTAC
* ** * * *
54634877 AAATCAAGGGTATTTTTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGT
1 AAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTCTACAAATAGAGGGT
* *
54634942 GTTTCGGTAATTTCAT
66 ATTTCAGTAATTTCAT
* * **
54634958 AAATCAATGGTATTTTGGTAATTTTACAAA-CTAGGGGTGTTTTAGTAATTCTACTTTATAG-GG
1 AAATCAAGGGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTAGTAATTCTAC-AAATAGAGG
54635021 GTATTTCAGTAATTTCA
64 GTATTTCAGTAATTTCA
54635038 CAATCGAGGG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
80 1 0.02
81 62 0.94
82 3 0.05
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.43
Consensus pattern (81 bp):
AAATCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTCTACAAATAGAGGGT
ATTTCAGTAATTTCAT
Found at i:54635069 original size:27 final size:27
Alignment explanation
Indices: 54635039--54635130 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
54635029 GTAATTTCAC
54635039 AATCGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
*
54635066 AATCGAGGGTAAAACAGTAATTCTT-TA
1 AATCGAGGGTAAAACGGTAATT-TTATA
* * *
54635093 AATTGAGGGTAGAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
*
54635120 AATCGGGGGTA
1 AATCGAGGGTA
54635131 CTTTGGTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 53 0.95
28 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTATA
Found at i:54637454 original size:42 final size:42
Alignment explanation
Indices: 54637407--54637498 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
54637397 TGGCCCATAG
* ** *
54637407 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
54637449 GCCCATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
54637491 GCCCATTT
1 GCCCATTT
54637499 GGGAAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:54637715 original size:26 final size:26
Alignment explanation
Indices: 54637631--54637792 Score: 242
Period size: 26 Copynumber: 6.3 Consensus size: 26
54637621 TTGGAGGCCT
54637631 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
54637655 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
*
54637680 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
54637706 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
54637732 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
54637758 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
54637784 AGCCCTTTT
1 AGCCCTTTT
54637793 GCACTTCCTC
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.04
24 5 0.04
25 32 0.26
26 83 0.66
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:54637867 original size:20 final size:20
Alignment explanation
Indices: 54637842--54637908 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
54637832 TTATGAATAC
54637842 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
54637862 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
54637882 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
54637902 ATCATGT
1 ATCATGT
54637909 ATATCATATC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:54638788 original size:54 final size:54
Alignment explanation
Indices: 54638713--54638843 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
54638703 CGTCCTACAA
* * * * *** *
54638713 GGGTGTTTTGGTAAATCTACAAATCAAGAATATTTCTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAAGAATATTTCGGTAATTTCACAAACCAG
* * * *
54638767 GGGTATTTTGGTAATTTTACAAATTAAGGATGTTTCGGTAATTTCACAAGCCAG
1 GGGTATTTTGGTAATTTTACAAATCAAGAATATTTCGGTAATTTCACAAACCAG
*
54638821 TGGTATTTTGGTAATTTTACAAA
1 GGGTATTTTGGTAATTTTACAAA
54638844 CTAGGGGTGT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATCAAGAATATTTCGGTAATTTCACAAACCAG
Found at i:54638790 original size:27 final size:27
Alignment explanation
Indices: 54638713--54638863 Score: 108
Period size: 27 Copynumber: 5.6 Consensus size: 27
54638703 CGTCCTACAA
* * * *
54638713 GGGTGTTTTGGTAAATCTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAG
** **
54638740 GAATATTTCT-GTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAATCAG
* *
54638767 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTGGTAATTTTACAAATCAG
* * * * **
54638794 GGATGTTTCGGTAATTTCACAAGCCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
*
54638821 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
*
54638848 GGGTGTTTTGGTAATT
1 GGGTATTTTGGTAATT
54638864 CTACTTTATT
Statistics
Matches: 91, Mismatches: 30, Indels: 6
0.72 0.24 0.05
Matches are distributed among these distances:
26 2 0.02
27 88 0.97
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:54638986 original size:27 final size:27
Alignment explanation
Indices: 54638895--54638980 Score: 136
Period size: 27 Copynumber: 3.2 Consensus size: 27
54638885 GTAATTTCAC
*
54638895 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTATA
* *
54638922 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
*
54638949 AATCGAGGGTAGAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
54638976 AATCG
1 AATCG
54638981 GAGGTACTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTATA
Found at i:54643417 original size:42 final size:43
Alignment explanation
Indices: 54643370--54643482 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
54643360 TCCCTGATGT
*
54643370 GGTCTTACAT-GTAATCACATATCGATGCCACT-TCCCAGACAG
1 GGTCTTAC-TCGTAATCACATATCGATGCCACTGTCCCAGACAA
* * *
54643412 GGTCTTACTCGTAGTCACATATCGACGCCACTGTCCCAGAGAA
1 GGTCTTACTCGTAATCACATATCGATGCCACTGTCCCAGACAA
*
54643455 GGTCTTACTCGTATTCACATATCGATGC
1 GGTCTTACTCGTAATCACATATCGATGC
54643483 TAATGTATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 28 0.44
43 34 0.54
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (43 bp):
GGTCTTACTCGTAATCACATATCGATGCCACTGTCCCAGACAA
Found at i:54647635 original size:40 final size:40
Alignment explanation
Indices: 54647554--54647775 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
54647544 CAACCAAGTA
** * *
54647554 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
54647593 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
54647633 CCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
54647673 CCTTTGGGACTTAGCCCGGTTATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * * * *
54647713 CCTTCGGGACTTAGCCCAG-AATTAGTCATTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATG
54647753 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
54647776 CATCCGAATA
Statistics
Matches: 160, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 14 0.09
40 145 0.91
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:54649914 original size:127 final size:126
Alignment explanation
Indices: 54649767--54649995 Score: 318
Period size: 127 Copynumber: 1.8 Consensus size: 126
54649757 AATTTTAAAA
* *
54649767 GGATATTCGGTTATTTAGGTTAAACGAGAAAAATCAAA-ACCTAGTAAGTTAGGGCACGATTTCT
1 GGATATTCGGCTATTTAGGTTAAACGAGAAAAATCAAACACC--GTAAGTTAGGGCACGACTTCT
54649831 CGAATTTCC-AAACACGAAATATTGCCTTATTTTAAAAATATCATGCATTTTTTAAAATTGAAG
64 CGAATTTCCAAAACACGAAATATT-CCTTATTTTAAAAATATCATGCATTTTTTAAAATTGAAG
* * * * * *
54649894 GGATATTTGGCTATTTAGGTTTAACGAGAAAATTGAAACACCGTAAGTTATGGTACGACTTCTCG
1 GGATATTCGGCTATTTAGGTTAAACGAGAAAAATCAAACACCGTAAGTTAGGGCACGACTTCTCG
* * *
54649959 TATTTCCAAAACACGAAATATTCCTTGTTTTCAAAAT
66 AATTTCCAAAACACGAAATATTCCTTATTTTAAAAAT
54649996 TTTCTTTTGT
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
126 39 0.44
127 47 0.53
128 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (126 bp):
GGATATTCGGCTATTTAGGTTAAACGAGAAAAATCAAACACCGTAAGTTAGGGCACGACTTCTCG
AATTTCCAAAACACGAAATATTCCTTATTTTAAAAATATCATGCATTTTTTAAAATTGAAG
Found at i:54652248 original size:4 final size:4
Alignment explanation
Indices: 54652241--54652273 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
54652231 GGGGCTAATT
54652241 ATAA AT-A ATAA ATAA ATAA ATAA ATGAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA A
54652274 AGATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:54652359 original size:3 final size:3
Alignment explanation
Indices: 54652351--54652421 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
54652341 ATAAAATGAT
54652351 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* *
54652399 AAC AAC AAC AAT AAC AAT AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AA
54652422 TAATAATAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.68, C:0.30, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:54652431 original size:6 final size:6
Alignment explanation
Indices: 54652349--54652430 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
54652339 GAATAAAATG
* * * * * * *
54652349 ATAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA
* * *
54652397 ACAACA ACAACA ATAACA ATAACA ATAATA ATAA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAA
54652431 TCTAATTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.07
Consensus pattern (6 bp):
ATAACA
Found at i:54655995 original size:41 final size:41
Alignment explanation
Indices: 54655938--54656083 Score: 195
Period size: 41 Copynumber: 3.6 Consensus size: 41
54655928 GGTTTAAATT
54655938 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
*
54655979 CGAGCTTGGTCTCGAAGAGCTTTTGAGCCAGTGTCATAA-C
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
* * * * * * * * *
54656019 CGAACCTAGTTTCAAAGGGCCTTCGGGCCAATGTCATAATC
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
54656060 CGAGCTTGGTCTCGAAGGGCTTTT
1 CGAGCTTGGTCTCGAAGGGCTTTT
54656084 TGAGTCAGCG
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 30 0.35
41 56 0.65
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.28
Consensus pattern (41 bp):
CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
Found at i:54658278 original size:42 final size:42
Alignment explanation
Indices: 54658229--54658323 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 42
54658219 TCCCAAACAG
* *
54658229 GGTCTTACACG-AAATCAAACACGAAGCCAACGTCCCATACGT
1 GGTCTTACACGAAAACCAAA-ACGAAGCCAACATCCCATACGT
* * *
54658271 GGTCTTACACGTAAAAACCAAATCGATGCCAACATCCTATACGT
1 GGTCTTACACG--AAAACCAAAACGAAGCCAACATCCCATACGT
54658315 GGTCTTACA
1 GGTCTTACA
54658324 TGATTTCACA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 11 0.24
44 27 0.60
45 7 0.16
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (42 bp):
GGTCTTACACGAAAACCAAAACGAAGCCAACATCCCATACGT
Found at i:54659414 original size:13 final size:13
Alignment explanation
Indices: 54659396--54659420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54659386 ACAAACGATA
54659396 AAATTTTCACACG
1 AAATTTTCACACG
54659409 AAATTTTCACAC
1 AAATTTTCACAC
54659421 ATACTAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54662359 original size:31 final size:31
Alignment explanation
Indices: 54662318--54662381 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
54662308 CCTTTTCATA
*
54662318 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
54662349 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
54662380 TT
1 TT
54662382 ACTGTAAACG
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:54662650 original size:23 final size:23
Alignment explanation
Indices: 54662596--54662714 Score: 202
Period size: 23 Copynumber: 5.1 Consensus size: 23
54662586 CCTAGCCTCT
*
54662596 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54662619 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
54662643 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
54662666 TTTAATAACTGGGGCACAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
54662689 TTTAATAACTGGGGCATAAGGCC
1 TTTAATAACTGGGGCATAAGCCC
54662712 TTT
1 TTT
54662715 TTCACTTCCT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
23 69 0.76
24 22 0.24
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:54662793 original size:20 final size:20
Alignment explanation
Indices: 54662765--54662831 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
54662755 TTATGATTAC
*
54662765 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54662785 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54662805 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54662825 ACCATGT
1 ATCATGT
54662832 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54670481 original size:30 final size:31
Alignment explanation
Indices: 54670441--54670503 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
54670431 CCTTTTCATA
54670441 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** *
54670472 TTTCA-ATTTCATATTATTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
54670502 TT
1 TT
54670504 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:54671854 original size:46 final size:46
Alignment explanation
Indices: 54671667--54671844 Score: 284
Period size: 46 Copynumber: 3.9 Consensus size: 46
54671657 CACAATATAT
* * * * *
54671667 ATATACATCTCATACATATCTCACATTAGCCATTCGCCTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
*
54671713 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
* *
54671759 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGACTTTACCTC
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
54671805 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTT
1 ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTT
54671845 CGCCACATAT
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 123 1.00
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.35
Consensus pattern (46 bp):
ATATCCATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
Found at i:54671899 original size:47 final size:45
Alignment explanation
Indices: 54671848--54672202 Score: 467
Period size: 47 Copynumber: 7.5 Consensus size: 45
54671838 TCGGCTTCGC
* * **
54671848 CACATATATACACTTCCACGTTCATCACATTGGCCATTCTACCTTAT
1 CACATATATGCA-TT-CACATTCATCACATTGGCCATTCGGCCTTAT
*
54671895 CACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGCA--TTCACATTCATCACATTGGCCATTCGGCCTTAT
54671942 CACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGCA--TTCACATTCATCACATTGGCCATTCGGCCTTAT
* *
54671989 CACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTAT
1 CACATATATGC-A-TTCACATTCATCACATTGGCCATTCGGCCTTAT
* *
54672036 CACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTAT
1 CACATATATGC-A-TTCACATTCATCACATTGGCCATTCGGCCTTAT
*
54672083 CACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGC-A-TTCACATTCATCACATTGGCCATTCGGCCTTAT
*
54672130 CACGTATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACATATATGCAT-T-CACATTCATCACATTGGCCATTCGGCCTTAT
54672177 CACATATATGCATGTTCACATTCATC
1 CACATATATGCA--TTCACATTCATC
54672203 TCATAAAATC
Statistics
Matches: 291, Mismatches: 11, Indels: 12
0.93 0.04 0.04
Matches are distributed among these distances:
45 1 0.00
46 2 0.01
47 283 0.97
48 4 0.01
49 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (45 bp):
CACATATATGCATTCACATTCATCACATTGGCCATTCGGCCTTAT
Found at i:54671946 original size:94 final size:94
Alignment explanation
Indices: 54671848--54672202 Score: 550
Period size: 94 Copynumber: 3.8 Consensus size: 94
54671838 TCGGCTTCGC
* * ** * * *
54671848 CACATATATACACT-TCCACGTTCATCACATTGGCCATTCTACCTTATCACATATATACATGTTC
1 CACATATATGCA-TGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTC
54671912 ACATTCATCACATTGGCCATTCGGCCTTAT
65 ACATTCATCACATTGGCCATTCGGCCTTAT
*
54671942 CACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
1 CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
*
54672007 CATTGATCACATTGGCCATTCGGCCTTAT
66 CATTCATCACATTGGCCATTCGGCCTTAT
* * * *
54672036 CACACATATGCAAGTTCACATTGATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
1 CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
54672101 CATTCATCACATTGGCCATTCGGCCTTAT
66 CATTCATCACATTGGCCATTCGGCCTTAT
* * *
54672130 CACGTATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCA
1 CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
54672195 CATTCATC
66 CATTCATC
54672203 TCATAAAATC
Statistics
Matches: 240, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
93 1 0.00
94 239 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (94 bp):
CACATATATGCATGTCCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCA
CATTCATCACATTGGCCATTCGGCCTTAT
Found at i:54672019 original size:141 final size:141
Alignment explanation
Indices: 54671862--54672202 Score: 556
Period size: 141 Copynumber: 2.4 Consensus size: 141
54671852 TATATACACT
* ** *
54671862 TCCACGTTCATCACATTGGCCATTCTACCTTATCACATATATACATGTTCACATTCATCACATTG
1 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
54671927 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
54671992 ACATATGCAAG
131 ACATATGCAAG
* * * * *
54672003 TTCACATTGATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCACATTGATCACATTG
1 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
54672068 GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
** *
54672133 GTATATGCATG
131 ACATATGCAAG
54672144 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATC
1 TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATC
54672203 TCATAAAATC
Statistics
Matches: 181, Mismatches: 19, Indels: 0
0.90 0.09 0.00
Matches are distributed among these distances:
141 181 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (141 bp):
TCCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
GCCATTCGGCCTTATCACACATATGCAAGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
ACATATGCAAG
Found at i:54681199 original size:27 final size:27
Alignment explanation
Indices: 54681168--54681345 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54681158 TAAATTGTAC
54681168 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54681195 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54681221 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54681249 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54681277 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54681304 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54681331 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54681346 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54681282 original size:82 final size:81
Alignment explanation
Indices: 54681169--54681324 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54681159 AAATTGTACA
* *
54681169 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54681233 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54681250 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54681315 TGCGAGTTGA
65 TGCGAATTGA
54681325 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54681336 original size:82 final size:81
Alignment explanation
Indices: 54681165--54681345 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
54681155 GATTAAATTG
* *
54681165 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54681230 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54681246 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54681310 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54681328 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54681346 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54685060 original size:30 final size:30
Alignment explanation
Indices: 54685024--54685084 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54685014 TTCCCGAGCC
54685024 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
54685054 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
54685084 T
1 T
54685085 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:54691542 original size:44 final size:43
Alignment explanation
Indices: 54691394--54691552 Score: 191
Period size: 43 Copynumber: 3.7 Consensus size: 43
54691384 AGCTCATACA
*
54691394 ATGCCAACGTCCCAGACGTGGTCTTACAAGT-AATCAAATATAG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAATAT-G
* * *
54691437 ATG-CAATTGTCCCAGACATGGTCTTACACG-AAATCAAATACG
1 ATGCCAA-CGTCCCAGACGTGGTCTTACACGTAAATCAAATATG
* *
54691479 AAGCCAACGTCCCAGACGTGGTCTTACACGTAAAAACCAAAT-TG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGT--AAATCAAATATG
*
54691523 ATGCCAACGTCCCATACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
54691553 ATTTCACATA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
42 27 0.27
43 35 0.35
44 29 0.29
45 8 0.08
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAATATG
Found at i:54694889 original size:25 final size:25
Alignment explanation
Indices: 54694861--54694911 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
54694851 CCCTTATAAT
* *
54694861 GTGAAAATGACCATTTTGCCCCTAG
1 GTGAAAATGACCATTATACCCCTAG
54694886 GTGAAAATGACCATTATACCCCTAG
1 GTGAAAATGACCATTATACCCCTAG
54694911 G
1 G
54694912 GATGTGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (25 bp):
GTGAAAATGACCATTATACCCCTAG
Found at i:54694977 original size:11 final size:10
Alignment explanation
Indices: 54694955--54694989 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
54694945 TTTATACAAT
54694955 ATATGCCATG
1 ATATGCCATG
54694965 ATATGCACATG
1 ATATGC-CATG
54694976 ATATGCCATG
1 ATATGCCATG
54694986 ATAT
1 ATAT
54694990 ATTCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:54695091 original size:24 final size:24
Alignment explanation
Indices: 54695035--54695091 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
54695025 AAGGAAGTGC
*
54695035 AAAAAGGCTTTGCCCCAGTTTATC
1 AAAAAGGCTTTGCCCCAGTTTATA
* * *
54695059 GAAAGGGCTTTGCCCTAG-TTATTA
1 AAAAAGGCTTTGCCCCAGTTTA-TA
54695083 AAAAAGGCT
1 AAAAAGGCT
54695092 AGGCCTCCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAAGGCTTTGCCCCAGTTTATA
Found at i:54702636 original size:25 final size:25
Alignment explanation
Indices: 54702607--54702657 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54702597 CCCTTATAAT
* *
54702607 GTGAAAATAACCATTTTGCCCCTAG
1 GTGAAAATAACCATTATACCCCTAG
*
54702632 GTGAAAATGACCATTATACCCCTAG
1 GTGAAAATAACCATTATACCCCTAG
54702657 G
1 G
54702658 GATGTGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (25 bp):
GTGAAAATAACCATTATACCCCTAG
Found at i:54702710 original size:10 final size:10
Alignment explanation
Indices: 54702697--54702735 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
54702687 CTGTTTTATA
54702697 CATGATATGC
1 CATGATATGC
54702707 CATGATATGC
1 CATGATATGC
54702717 ACATGATATGC
1 -CATGATATGC
54702728 CATGATAT
1 CATGATAT
54702736 ATTCATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:54702722 original size:21 final size:21
Alignment explanation
Indices: 54702696--54702735 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54702686 ACTGTTTTAT
54702696 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
54702717 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
54702736 ATTCATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:54702815 original size:25 final size:24
Alignment explanation
Indices: 54702780--54702849 Score: 122
Period size: 25 Copynumber: 2.9 Consensus size: 24
54702770 GGAGGAAGTA
54702780 CAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAGGGCTTTGCCCCAGTTTAC
*
54702804 CGAAAAGGGCTTTGCCCCAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAC
54702829 CAAAAGGGCTTTGCCCCAGTT
1 CAAAAGGGCTTTGCCCCAGTT
54702850 ATGAAAAGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 21 0.48
25 23 0.52
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAC
Found at i:54702838 original size:24 final size:24
Alignment explanation
Indices: 54702780--54702862 Score: 123
Period size: 24 Copynumber: 3.4 Consensus size: 24
54702770 GGAGGAAGTA
*
54702780 CAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAGGGCTTTGCCCCAGTTTAT
54702804 CGAAAAGGGCTTTGCCCCAGTTTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
54702829 CAAAAGGGCTTTGCCCCAG-TTAT
1 CAAAAGGGCTTTGCCCCAGTTTAT
*
54702852 GAAAAGAGGCT
1 CAAAAG-GGCT
54702863 AGGCCTCCAG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
23 9 0.16
24 23 0.42
25 23 0.42
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:54702873 original size:49 final size:49
Alignment explanation
Indices: 54702780--54702874 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 49
54702770 GGAGGAAGTA
**
54702780 CAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTAT
1 CAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTAT
*
54702829 CAAAAGGGCTTTGCCCCAG-TTA-TGAAAAGAGGCTAGGCCTCCAGTT
1 CAAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
54702875 ATATGATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 6 0.15
48 10 0.24
49 25 0.61
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.24
Consensus pattern (49 bp):
CAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTAT
Found at i:54704388 original size:9 final size:9
Alignment explanation
Indices: 54704374--54704401 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54704364 AAAAGGGACT
54704374 AAATTGTAA
1 AAATTGTAA
54704383 AAATTGTAA
1 AAATTGTAA
54704392 AAATTGTAA
1 AAATTGTAA
54704401 A
1 A
54704402 TGTTAGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (9 bp):
AAATTGTAA
Found at i:54706428 original size:40 final size:39
Alignment explanation
Indices: 54706344--54706528 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
54706334 TCGAATGATG
* * * *
54706344 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
54706384 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54706424 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
54706463 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
54706504 -CCGGGCTATGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCC-GAAGGCATTTG
54706529 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 37 0.30
40 78 0.62
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54706480 original size:79 final size:81
Alignment explanation
Indices: 54706344--54706526 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
54706334 TCGAATGATG
* *
54706344 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
54706408 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
54706423 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
54706485 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* * *
54706503 ACCGGGCTATGTCCTGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
54706527 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 29 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:54706550 original size:79 final size:79
Alignment explanation
Indices: 54706397--54706551 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
54706387 GGACTAAGAT
* **
54706397 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
54706462 ATCCGGGTTAAGTC
66 ATCCAGGTTAAGTC
* * *
54706476 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCTGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
54706539 TATAT-CAGGTTAA
63 TAAATCCAGGTTAA
54706552 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 42 0.65
80 21 0.32
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCAGGTTAAGTC
Found at i:54719450 original size:27 final size:27
Alignment explanation
Indices: 54719411--54719808 Score: 328
Period size: 27 Copynumber: 14.7 Consensus size: 27
54719401 TAATAAAGAG
** *
54719411 AAATTACTAAAATACCCCTAATTTGTA
1 AAATTACCGAAATACCCCTGATTTGTA
** *
54719438 AAATTATTGAAATACCCCCGATTTGTA
1 AAATTACCGAAATACCCCTGATTTGTA
*
54719465 AAATTACCGAAATA-CTCTCGATTTGTA
1 AAATTACCGAAATACCCCT-GATTTGTA
* ** *
54719492 AAATTACCAAAATACCCCCAATTTGTG
1 AAATTACCGAAATACCCCTGATTTGTA
* *
54719519 AAATTACTGAAACA-CCCTCGATTTGTA
1 AAATTACCGAAATACCCCT-GATTTGTA
* *
54719546 AAATTACCGAAACA-CCCTCAATTTGTA
1 AAATTACCGAAATACCCCT-GATTTGTA
* * * *
54719573 AAATTATCGAAACA-CCTTCAATTTGTA
1 AAATTACCGAAATACCCCT-GATTTGTA
*
54719600 AAATTACC-AAA-ACACCTTCGATTTGTA
1 AAATTACCGAAATAC-CCCT-GATTTGTA
* *
54719627 AAATTACCAAAATA-CCCTCAATTTGTA
1 AAATTACCGAAATACCCCT-GATTTGTA
* *
54719654 AAATTACCAAAATACCCTTGATTTGTA
1 AAATTACCGAAATACCCCTGATTTGTA
**
54719681 AAATTACCGAAATACCATTGATTTGTA
1 AAATTACCGAAATACCCCTGATTTGTA
* *
54719708 AAATTACCGAAACACCCCTGATTTATA
1 AAATTACCGAAATACCCCTGATTTGTA
* * *
54719735 AAATTATCGAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCCTGAT-TTGTA
* * *
54719762 AAATTATCGAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCCTGAT-TTGTA
* *
54719789 AAATGACCGACATACCCCTG
1 AAATTACCGAAATACCCCTG
54719809 TAGGGTAAAA
Statistics
Matches: 318, Mismatches: 44, Indels: 18
0.84 0.12 0.05
Matches are distributed among these distances:
25 1 0.00
26 9 0.03
27 299 0.94
28 8 0.03
29 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCGAAATACCCCTGATTTGTA
Found at i:54719493 original size:54 final size:54
Alignment explanation
Indices: 54719431--54719778 Score: 383
Period size: 54 Copynumber: 6.4 Consensus size: 54
54719421 AATACCCCTA
** *
54719431 ATTTGTAAAATTATTGAAATACCCCCGATTTGTAAAATTACCGAAATACTCTCG
1 ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
* * * * *
54719485 ATTTGTAAAATTACCAAAATACCCCCAATTTGTGAAATTACTGAAACACCCTCG
1 ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
* * * * * * *
54719539 ATTTGTAAAATTACCGAAACACCCTCAATTTGTAAAATTATCGAAACACCTTCA
1 ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
* * ** * *
54719593 ATTTGTAAAATTACCAAAACACCTTCGATTTGTAAAATTACCAAAATACCCTCA
1 ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
* ** * *
54719647 ATTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCGAAATACCATTG
1 ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
* * * * *
54719701 ATTTGTAAAATTACCGAAACACCCCTGATTTATAAAATTATCGAAATACCCTTG
1 ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
* *
54719755 -TAGTGTAAAATTATCGAAATACCC
1 AT-TTGTAAAATTACCGAAATACCC
54719779 TTGTAGTGTA
Statistics
Matches: 254, Mismatches: 39, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 1 0.00
54 253 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
ATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAATTACCGAAATACCCTCG
Found at i:54719752 original size:81 final size:81
Alignment explanation
Indices: 54719411--54719805 Score: 406
Period size: 81 Copynumber: 4.9 Consensus size: 81
54719401 TAATAAAGAG
* * ** **
54719411 AAATTACTAAAATACCCCTAATTTGTAAAATTATTGAAATACCCCCGATTTGTAAAATTACCGAA
1 AAATTACCAAAATACCCTTAATTTGTAAAATTACCGAAATACCCTTGATTTGTAAAATTACCGAA
*
54719476 ATACTCTCGATTTGTA
66 ATACCCTCGATTTGTA
** * * * *
54719492 AAATTACCAAAATACCCCCAATTTGTGAAATTACTGAAACACCCTCGATTTGTAAAATTACCGAA
1 AAATTACCAAAATACCCTTAATTTGTAAAATTACCGAAATACCCTTGATTTGTAAAATTACCGAA
* *
54719557 ACACCCTCAATTTGTA
66 ATACCCTCGATTTGTA
* * *
54719573 AAATTATCGAAACA-CCTTCAATTTGTAAAATTACC-AAA-ACACCTTCGATTTGTAAAATTACC
1 AAATTACCAAAATACCCTT-AATTTGTAAAATTACCGAAATAC-CCTT-GATTTGTAAAATTACC
* *
54719635 AAAATACCCTCAATTTGTA
63 GAAATACCCTCGATTTGTA
* *
54719654 AAATTACCAAAATACCCTTGATTTGTAAAATTACCGAAATACCATTGATTTGTAAAATTACCGAA
1 AAATTACCAAAATACCCTTAATTTGTAAAATTACCGAAATACCCTTGATTTGTAAAATTACCGAA
* *
54719719 ACACCC-CTGATTTATA
66 ATACCCTC-GATTTGTA
* * * * * * *
54719735 AAATTATCGAAATACCCTT-GTAGTGTAAAATTATCGAAATACCCTTG-TAGTGTAAAATGACCG
1 AAATTACCAAAATACCCTTAAT-TTGTAAAATTACCGAAATACCCTTGAT-TTGTAAAATTACCG
*
54719798 ACATACCC
64 AAATACCC
54719806 CTGTAGGGTA
Statistics
Matches: 267, Mismatches: 38, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
79 2 0.01
80 11 0.04
81 242 0.91
82 10 0.04
83 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (81 bp):
AAATTACCAAAATACCCTTAATTTGTAAAATTACCGAAATACCCTTGATTTGTAAAATTACCGAA
ATACCCTCGATTTGTA
Found at i:54720274 original size:11 final size:11
Alignment explanation
Indices: 54720258--54720285 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54720248 TCATTGCATC
54720258 TATGATATTAT
1 TATGATATTAT
54720269 TATGATATTAT
1 TATGATATTAT
54720280 TATGAT
1 TATGAT
54720286 GTGGGCTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (11 bp):
TATGATATTAT
Found at i:54721847 original size:28 final size:27
Alignment explanation
Indices: 54721797--54721908 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 27
54721787 AGCATGGCTG
* * *
54721797 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAAATAATGTGGCAGAGCCA
54721823 CCAGATACAAATAATCGTGGCAGAGCCA
1 CCAGATACAAATAAT-GTGGCAGAGCCA
* *
54721851 CCAGAATAGAAAT-ATGTGGCAGGGCCA
1 CCAG-ATACAAATAATGTGGCAGAGCCA
* * *
54721878 CCAGAT-CAGATAATTGTGGTATAGCCA
1 CCAGATACAAATAA-TGTGGCAGAGCCA
54721905 CCAG
1 CCAG
54721909 GATGCTTCCT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
25 3 0.04
26 8 0.11
27 37 0.52
28 16 0.23
29 7 0.10
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (27 bp):
CCAGATACAAATAATGTGGCAGAGCCA
Found at i:54728900 original size:17 final size:18
Alignment explanation
Indices: 54728878--54728911 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54728868 TTTTGGGCTA
54728878 TGTGGG-CCACACGGGCG
1 TGTGGGACCACACGGGCG
*
54728895 TGTGGGACCACATGGGC
1 TGTGGGACCACACGGGC
54728912 CCACAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.44, T:0.15
Consensus pattern (18 bp):
TGTGGGACCACACGGGCG
Found at i:54729150 original size:80 final size:81
Alignment explanation
Indices: 54729017--54729209 Score: 257
Period size: 80 Copynumber: 2.4 Consensus size: 81
54729007 TGTACCTGGA
54729017 CCCTTA-ATCGGTAAAATGACTATTTTGCCCTTATAAAGTAAAATAACTGTTTTGCCCTTATGAG
1 CCCTTATAT-GGTAAAATGACTATTTTGCCCTTATAAAGTAAAATAACTGTTTTGCCCTTATGAG
* *
54729081 GTAAAATGATTGTTTTG
65 GTAAAATGACTATTTTG
* * * * * *
54729098 CCCTTATGA-GGTAAAATGA-TTTTTTTCCCTTATGAGGTTAAATGACTGTTTTGCCCTTATGAG
1 CCCTTAT-ATGGTAAAATGACTATTTTGCCCTTATAAAGTAAAATAACTGTTTTGCCCTTATGAG
*
54729161 GTAAAATGACTATTTTT
65 GTAAAATGACTATTTTG
*
54729178 CCCTTATATGGTAAAATGACTGTTTTGCCCTT
1 CCCTTATATGGTAAAATGACTATTTTGCCCTT
54729210 TTATGGTAAG
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
79 1 0.01
80 69 0.71
81 26 0.27
83 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (81 bp):
CCCTTATATGGTAAAATGACTATTTTGCCCTTATAAAGTAAAATAACTGTTTTGCCCTTATGAGG
TAAAATGACTATTTTG
Found at i:54729218 original size:27 final size:27
Alignment explanation
Indices: 54729026--54729209 Score: 255
Period size: 27 Copynumber: 6.9 Consensus size: 27
54729016 ACCCTTAATC
* *
54729026 GGTAAAATGACTATTTTGCCCTTATAA
1 GGTAAAATGACTGTTTTGCCCTTATGA
* *
54729053 AGTAAAATAACTGTTTTGCCCTTATGA
1 GGTAAAATGACTGTTTTGCCCTTATGA
*
54729080 GGTAAAATGATTGTTTTGCCCTTATGA
1 GGTAAAATGACTGTTTTGCCCTTATGA
* *
54729107 GGTAAAATGA-TTTTTTTCCCTTATGA
1 GGTAAAATGACTGTTTTGCCCTTATGA
*
54729133 GGTTAAATGACTGTTTTGCCCTTATGA
1 GGTAAAATGACTGTTTTGCCCTTATGA
* *
54729160 GGTAAAATGACTATTTTTCCCTTAT-A
1 GGTAAAATGACTGTTTTGCCCTTATGA
54729186 TGGTAAAATGACTGTTTTGCCCTT
1 -GGTAAAATGACTGTTTTGCCCTT
54729210 TTATGGTAAG
Statistics
Matches: 138, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
26 24 0.17
27 114 0.83
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (27 bp):
GGTAAAATGACTGTTTTGCCCTTATGA
Found at i:54729550 original size:18 final size:17
Alignment explanation
Indices: 54729518--54729558 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
54729508 ATTTACTATT
*
54729518 ACTGCACTGTTACTGTA
1 ACTGTACTGTTACTGTA
*
54729535 ACTGTACTGTTTACTGTT
1 ACTGTACTG-TTACTGTA
54729553 ACTGTA
1 ACTGTA
54729559 ATGGGCCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (17 bp):
ACTGTACTGTTACTGTA
Found at i:54735756 original size:17 final size:19
Alignment explanation
Indices: 54735720--54735761 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
54735710 TATAAACATT
54735720 TTAAATTAAACAAAATAAA
1 TTAAATTAAACAAAATAAA
*
54735739 TTAAATTAGA-AAAA-AAA
1 TTAAATTAAACAAAATAAA
54735756 TTAAAT
1 TTAAAT
54735762 CTTAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
TTAAATTAAACAAAATAAA
Found at i:54740058 original size:34 final size:33
Alignment explanation
Indices: 54739973--54740059 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
54739963 CTGTATTGAG
*
54739973 ATGGGCTAAGGCCCAGACTACCTATGTTACTGAA
1 ATGGGCT-AGGCCCAGACTGCCTATGTTACTGAA
* *
54740007 ATGGGCTAGGCCAAGACTGCCTCTGTTACTGAA
1 ATGGGCTAGGCCCAGACTGCCTATGTTACTGAA
54740040 ATGGGCTCAGGCCCAGACTG
1 ATGGGCT-AGGCCCAGACTG
54740060 ATACTATTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 30 0.62
34 18 0.38
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (33 bp):
ATGGGCTAGGCCCAGACTGCCTATGTTACTGAA
Found at i:54740070 original size:34 final size:33
Alignment explanation
Indices: 54739960--54740074 Score: 112
Period size: 34 Copynumber: 3.5 Consensus size: 33
54739950 CTTTGTTTGC
* *
54739960 ATACTG-TATTGAGATGGGCTAAGGCCCAGACT-
1 ATACTGTTACTGAAATGGGCT-AGGCCCAGACTG
*
54739992 ACCTA-TGTTACTGAAATGGGCTAGGCCAAGACTG
1 A--TACTGTTACTGAAATGGGCTAGGCCCAGACTG
*
54740026 CCT-CTGTTACTGAAATGGGCTCAGGCCCAGACTG
1 -ATACTGTTACTGAAATGGGCT-AGGCCCAGACTG
*
54740060 ATACTATTACTGAAA
1 ATACTGTTACTGAAA
54740075 AAGGGGATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
32 1 0.01
33 31 0.46
34 36 0.53
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (33 bp):
ATACTGTTACTGAAATGGGCTAGGCCCAGACTG
Found at i:54747199 original size:28 final size:27
Alignment explanation
Indices: 54747167--54747260 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 27
54747157 GAATATATGA
54747167 ACTATGTGTGCGAGATCGGGTGTAAGGC
1 ACTATGTGTGCGAGATC-GGTGTAAGGC
* * ** *
54747195 ACTATGTGTGTGAAAT-TAT-TAACCGAGA
1 ACTATGTGTGCGAGATCGGTGTAA--G-GC
54747223 ACTATGTGTGCGAGATCAGGTGTAAGGC
1 ACTATGTGTGCGAGATC-GGTGTAAGGC
*
54747251 ACTGTGTGTG
1 ACTATGTGTG
54747261 TGCAAAATTA
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 1 0.02
28 39 0.80
29 1 0.02
30 1 0.02
31 3 0.06
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.29
Consensus pattern (27 bp):
ACTATGTGTGCGAGATCGGTGTAAGGC
Found at i:54747251 original size:56 final size:57
Alignment explanation
Indices: 54747165--54747272 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 57
54747155 ATGAATATAT
*
54747165 GAACTATGTGTGCGAGATCGGGTGTAAGGCACTATGTGTGTG-AAATTATTAACCGA
1 GAACTATGTGTGCGAGATCAGGTGTAAGGCACTATGTGTGTGAAAATTATTAACCGA
*
54747221 GAACTATGTGTGCGAGATCAGGTGTAAGGCACTGTGTGTGTGCAAAATTATT
1 GAACTATGTGTGCGAGATCAGGTGTAAGGCACTATGTGTGTG-AAAATTATT
54747273 TAGGGAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 40 0.83
58 8 0.17
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.30
Consensus pattern (57 bp):
GAACTATGTGTGCGAGATCAGGTGTAAGGCACTATGTGTGTGAAAATTATTAACCGA
Found at i:54754889 original size:28 final size:28
Alignment explanation
Indices: 54754858--54754959 Score: 113
Period size: 28 Copynumber: 3.6 Consensus size: 28
54754848 ATGAATATAT
54754858 GCACTATGTGTGCGAGATTAGTAACCGA
1 GCACTATGTGTGCGAGATTAGTAACCGA
54754886 GCACTATGTGTGCGAGATCGGGT-GTAA--G-
1 GCACTATGTGTGCGAGAT----TAGTAACCGA
* *
54754914 GCACTATGTGTGCGAAATTATTAACCGA
1 GCACTATGTGTGCGAGATTAGTAACCGA
*
54754942 GCACTATGTGTACGAGAT
1 GCACTATGTGTGCGAGAT
54754960 CGGGTGTAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 3 0.05
27 1 0.02
28 51 0.82
29 1 0.02
31 4 0.06
32 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATTAGTAACCGA
Found at i:54754944 original size:56 final size:56
Alignment explanation
Indices: 54754858--54754974 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
54754848 ATGAATATAT
* *
54754858 GCACTATGTGTGCGAGATTAGTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAAATTAGTAACCGAGCACTATGTGTACGAGATCGGGTGTAAG
*
54754914 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTACGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAAATTAGTAACCGAGCACTATGTGTACGAGATCGGGTGTAAG
54754970 GCACT
1 GCACT
54754975 GTGATACGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (56 bp):
GCACTATGTGTGCGAAATTAGTAACCGAGCACTATGTGTACGAGATCGGGTGTAAG
Found at i:54754973 original size:28 final size:28
Alignment explanation
Indices: 54754886--54754974 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
54754876 TAGTAACCGA
54754886 GCACTATGTGTGCGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAGATCGGGTGTAAG
* **
54754914 GCACTATGTGTGCGAAAT--TAT-TAACCG
1 GCACTATGTGTGCGAGATCGGGTGTAA--G
*
54754941 AGCACTATGTGTACGAGATCGGGTGTAAG
1 -GCACTATGTGTGCGAGATCGGGTGTAAG
54754970 GCACT
1 GCACT
54754975 GTGATACGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 1 0.02
28 38 0.79
29 1 0.02
30 1 0.02
31 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGGTGTAAG
Found at i:54758283 original size:13 final size:14
Alignment explanation
Indices: 54758262--54758294 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54758252 TTTATTAATG
54758262 AAATATATTAAA-AT
1 AAAT-TATTAAATAT
54758276 AAATTATTAAATAT
1 AAATTATTAAATAT
54758290 AAATT
1 AAATT
54758295 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTATTAAATAT
Found at i:54759218 original size:21 final size:20
Alignment explanation
Indices: 54759189--54759228 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54759179 AATGGCTCCG
54759189 ATCTAATTGAAAGAATTGAA
1 ATCTAATTGAAAGAATTGAA
* *
54759209 ATCTCAATTGCAAGAGTTGA
1 ATCT-AATTGAAAGAATTGA
54759229 CAGATAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
ATCTAATTGAAAGAATTGAA
Found at i:54760875 original size:30 final size:30
Alignment explanation
Indices: 54760841--54760899 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
54760831 ATTTTCGGGC
* *
54760841 CTAGGGGTAAAATGGTCATTTTGTCAAAGT
1 CTAGGGGCAAAATGGTCATTTTGCCAAAGT
*
54760871 CTAGGGGCACAATGGTCATTTTGCCAAAG
1 CTAGGGGCAAAATGGTCATTTTGCCAAAG
54760900 ATATGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
CTAGGGGCAAAATGGTCATTTTGCCAAAGT
Found at i:54763780 original size:93 final size:93
Alignment explanation
Indices: 54763673--54763843 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54763663 GCCCCTAAGT
* *
54763673 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54763738 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * *
54763766 GAACTCGGACTCAACTCAATAAGTTCGGACATTCGCATCCATAAGTGAACTCGGGCTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54763831 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54763844 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54763840 original size:46 final size:46
Alignment explanation
Indices: 54763668--54763840 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
54763658 AACCCGCCCC
* * *
54763668 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCA
* * *
54763714 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGA---C-A-TTCGCATCCA
* * *
54763762 TCA-CGAACTCGGACTCAACTCAATAAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCA
* *
54763807 TAAGTGAACTCGGGCTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
54763841 TGCTCAACCA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 57 0.56
47 27 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCA
Found at i:54769096 original size:40 final size:40
Alignment explanation
Indices: 54769036--54769209 Score: 208
Period size: 40 Copynumber: 4.4 Consensus size: 40
54769026 TGATAACCAA
* **
54769036 GCTAAGTCCCGAAGGAATTTGTGCGAGTTACTATGTCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
* * *
54769076 GCTAAGTCCCGAAGGCATTTGTGTGAGTTACCATAACTGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
* *
54769116 GCTAAGTCCCGAAGGCAATTGTGTGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
** *
54769156 GCTAAGTCCCGAAGGCATTTAAGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAACCGG
**
54769195 GCTAAACCCCGAAGG
1 GCTAAGTCCCGAAGG
54769210 TACTTGGTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 16 0.14
40 101 0.86
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
Found at i:54775374 original size:93 final size:93
Alignment explanation
Indices: 54775262--54775433 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54775252 CGCCCATAAG
* *
54775262 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54775327 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
54775355 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54775420 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54775434 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54775430 original size:46 final size:46
Alignment explanation
Indices: 54775255--54775430 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54775245 TGTAACCCGC
* * *
54775255 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54775301 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54775351 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54775394 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54775431 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54777364 original size:30 final size:30
Alignment explanation
Indices: 54777320--54777408 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
54777310 CAAAGATAAC
54777320 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
54777349 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
54777379 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
54777409 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:54777368 original size:15 final size:15
Alignment explanation
Indices: 54777320--54777399 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
54777310 CAAAGATAAC
*
54777320 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54777334 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54777349 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
54777364 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54777379 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54777394 AAGAAA
1 AAGAAA
54777400 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54777408 original size:15 final size:15
Alignment explanation
Indices: 54777331--54777408 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
54777321 AGAAAACCGA
54777331 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
54777346 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
54777360 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
54777375 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
54777391 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
54777406 ATA
1 ATA
54777409 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:54780392 original size:46 final size:46
Alignment explanation
Indices: 54780291--54780378 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
54780281 TGTAACCCGC
* * * *
54780291 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
54780337 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
54780379 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:54781864 original size:93 final size:92
Alignment explanation
Indices: 54781706--54781875 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 92
54781696 GCCCCTAAGT
* * *
54781706 GAACTCGGACTCAACTCAACAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACAGCTCGGACATTCGCATCCATAAGTGAACTCCGACTCAACTCAAC
*
54781771 GAGTTCGGATGCCTAGTTACATTTCAC
66 GAGTTCGAATGCCTAGTTACATTTCAC
* * *
54781798 GAACTCGGACTCAACTCAATGAGTTCGGACATTTGCATCCATAAGTGAACTCCGACTCAACTCAA
1 GAACTCGGACTCAACTCAA-CAGCTCGGACATTCGCATCCATAAGTGAACTCCGACTCAACTCAA
54781863 CGAGTTCGAATGC
65 CGAGTTCGAATGC
54781876 TCAACCATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 19 0.27
93 51 0.73
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACAGCTCGGACATTCGCATCCATAAGTGAACTCCGACTCAACTCAAC
GAGTTCGAATGCCTAGTTACATTTCAC
Found at i:54781868 original size:46 final size:46
Alignment explanation
Indices: 54781701--54781870 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
54781691 AACCTGCCCC
* * * *
54781701 TAAGTGAACTCGGACTCAACTCAAC-AGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
54781746 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* * *
54781794 TCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
54781839 TAAGTGAACTCCGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
54781871 AATGCTCAAC
Statistics
Matches: 100, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 27 0.27
46 31 0.31
47 28 0.28
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:54782328 original size:30 final size:30
Alignment explanation
Indices: 54782294--54782353 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
54782284 ATTTAATACG
*
54782294 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTGTTGCCCCTA
* * *
54782324 AACTTTTGCATAATTACACTGTTGCCCCTA
1 AACTTTGGAAAAATTACACTGTTGCCCCTA
54782354 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTGTTGCCCCTA
Found at i:54788024 original size:30 final size:30
Alignment explanation
Indices: 54787990--54788049 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54787980 CAAGAAAACT
* *
54787990 GAATAAAGAAATCCATGATAGAGAAACCCA
1 GAATAAAGAAATCCAGGATAAAGAAACCCA
*
54788020 GAATAAAGAGATCCAGGATAAAGAAACCCA
1 GAATAAAGAAATCCAGGATAAAGAAACCCA
54788050 AGATACGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.53, C:0.17, G:0.18, T:0.12
Consensus pattern (30 bp):
GAATAAAGAAATCCAGGATAAAGAAACCCA
Found at i:54788040 original size:15 final size:15
Alignment explanation
Indices: 54787992--54788045 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
54787982 AGAAAACTGA
*
54787992 ATAAAGAAATCCATG
1 ATAAAGAAATCCAGG
* * *
54788007 ATAGAGAAACCCAGA
1 ATAAAGAAATCCAGG
*
54788022 ATAAAGAGATCCAGG
1 ATAAAGAAATCCAGG
54788037 ATAAAGAAA
1 ATAAAGAAA
54788046 CCCAAGATAC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.56, C:0.13, G:0.19, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAGG
Found at i:54788054 original size:15 final size:15
Alignment explanation
Indices: 54787992--54788054 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
54787982 AGAAAACTGA
* *
54787992 ATAAAGAAATCCATG
1 ATAAAGAAACCCAAG
*
54788007 ATAGAGAAACCC-AG
1 ATAAAGAAACCCAAG
* * *
54788021 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
54788037 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
54788052 ATA
1 ATA
54788055 CGATACTATG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
14 1 0.03
15 34 0.94
16 1 0.03
ACGTcount: A:0.54, C:0.16, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:54803649 original size:27 final size:27
Alignment explanation
Indices: 54803590--54803650 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
54803580 AAACATATCA
* * *
54803590 TAGGGGTATATCAGTCATTTTACTTAT
1 TAGGGGTATAACAGTCATTTCACTTAG
54803617 TAGGGGTATAACAGTCATTTCA-TTAG
1 TAGGGGTATAACAGTCATTTCACTTAG
54803643 TATGGGGT
1 TA-GGGGT
54803651 CTAAGTGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (27 bp):
TAGGGGTATAACAGTCATTTCACTTAG
Found at i:54813870 original size:27 final size:27
Alignment explanation
Indices: 54813840--54813895 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
54813830 CCCCAAAATA
*
54813840 GGTAAAATAACCATAATGCCCCTGTAG
1 GGTAAAATAACCATAATACCCCTGTAG
* * * *
54813867 GGTATAATGATCGTAATACCCCTGTAG
1 GGTAAAATAACCATAATACCCCTGTAG
54813894 GG
1 GG
54813896 CGAAATGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (27 bp):
GGTAAAATAACCATAATACCCCTGTAG
Done.