Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 175 of 211
Found at i:54436585 original size:54 final size:53
Alignment explanation
Indices: 54436522--54436623 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
54436512 ATATTTCTAA
* *
54436522 AATTTTCGTGTTTAAAAAAATT-TCGTATTTTCAAAATTTTTTATTTTTTTCAAC
1 AATTCTCGTGTTT-AAAAAATTCTCGTATTTT-AAAATTTTTTATGTTTTTCAAC
* *
54436576 AATTCTCGTGTTTCACAAATTCTCGTATTTTAAAATTTTTTATGTTTT
1 AATTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTT
54436624 AAAAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
53 22 0.51
54 21 0.49
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (53 bp):
AATTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
Found at i:54436596 original size:71 final size:70
Alignment explanation
Indices: 54436430--54436610 Score: 186
Period size: 71 Copynumber: 2.5 Consensus size: 70
54436420 GAAAAATCAG
* * *
54436430 AAAAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATTCCATTTTTCAAAATTTTTCGTG
1 AAAAATTCTCGTG-TTTC-AAAATTTTCGTGTTTTAAAAAATTCCATTTTTCAAAATTTTTC-TA
54436495 TTTTTTTA
63 TTTTTTTA
* * * * *
54436503 AAAAATTC-CATATTTCTAAAATTTTCGTGTTTAAAAAAATTTCGTATTTTCAAAATTTTT-TAT
1 AAAAATTCTCGTGTTTC-AAAATTTTCGTGTTTTAAAAAATTCCAT-TTTTCAAAATTTTTCTAT
*
54436566 TTTTTTC
64 TTTTTTA
* * *
54436573 AACAATTCTCGTGTTTCACAAATTCTCGTATTTTAAAA
1 AAAAATTCTCGTGTTTCA-AAATTTTCGTGTTTTAAAA
54436611 TTTTTTATGT
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
70 16 0.18
71 50 0.56
72 16 0.18
73 7 0.08
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (70 bp):
AAAAATTCTCGTGTTTCAAAATTTTCGTGTTTTAAAAAATTCCATTTTTCAAAATTTTTCTATTT
TTTTA
Found at i:54436666 original size:16 final size:16
Alignment explanation
Indices: 54436641--54436677 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
54436631 AAATTTCTCG
*
54436641 TGTTTCAAAATTGTCA
1 TGTTTAAAAATTGTCA
*
54436657 TGTTTAAAAATTTTCA
1 TGTTTAAAAATTGTCA
54436673 TGTTT
1 TGTTT
54436678 CTAAAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (16 bp):
TGTTTAAAAATTGTCA
Found at i:54436728 original size:52 final size:50
Alignment explanation
Indices: 54436657--54436828 Score: 170
Period size: 52 Copynumber: 3.3 Consensus size: 50
54436647 AAAATTGTCA
* * *
54436657 TGTTT-AAAAATTTTCATGTTTCTAAAATGTTC-GTATTTCAAAATCCTCG
1 TGTTTCAAAAATTTTCATGTTTCAAAAATCTTCTGT-TTTCAAAATCCTAG
* *
54436706 TGTTTTTCAAAAATTCTCATGTTTCAAAAATCTTCTTGTTTTCAAAATTCTAG
1 TG--TTTCAAAAATTTTCATGTTTCAAAAATCTTC-TGTTTTCAAAATCCTAG
* *
54436759 TGTTTCAAAAATTTTCATGTTTTCAAAAAT-TTCCCCTGTTTTCAAAAATTCTCG
1 TGTTTCAAAAATTTTCATG-TTTCAAAAATCTT---CTGTTTTC-AAAATCCTAG
*
54436813 TATTTCAAAAATTTTC
1 TGTTTCAAAAATTTTC
54436829 TTTTTTTCAA
Statistics
Matches: 105, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
49 2 0.02
51 21 0.20
52 34 0.32
53 21 0.20
54 27 0.26
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.46
Consensus pattern (50 bp):
TGTTTCAAAAATTTTCATGTTTCAAAAATCTTCTGTTTTCAAAATCCTAG
Found at i:54436766 original size:16 final size:16
Alignment explanation
Indices: 54436635--54436768 Score: 53
Period size: 16 Copynumber: 8.0 Consensus size: 16
54436625 AAAAATAAAT
*
54436635 TTCTCGTGTTTCAAAA
1 TTCTAGTGTTTCAAAA
* *
54436651 TTGTCA-TGTTTAAAAA
1 TTCT-AGTGTTTCAAAA
*
54436667 TTTTCA-TGTTTCTAAAA
1 TTCT-AGTGTTTC-AAAA
* *
54436684 TGT-TCGTATTTCAAAA
1 T-TCTAGTGTTTCAAAA
* *
54436700 TCCTCGTGTTTTTCAAAAA
1 TTCTAGTG--TTTC-AAAA
54436719 TTCTCA-TGTTTCAAAAA
1 TTCT-AGTGTTTC-AAAA
*
54436736 TCTTCTTGT-TTTCAAAA
1 --TTCTAGTGTTTCAAAA
54436753 TTCTAGTGTTTCAAAA
1 TTCTAGTGTTTCAAAA
54436769 ATTTTCATGT
Statistics
Matches: 92, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
15 6 0.07
16 39 0.42
17 24 0.26
18 9 0.10
19 14 0.15
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.46
Consensus pattern (16 bp):
TTCTAGTGTTTCAAAA
Found at i:54436897 original size:18 final size:18
Alignment explanation
Indices: 54436874--54436921 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
54436864 ATCTCCGTGT
54436874 TTTCAAAAAATTCTCG-AC
1 TTTCAAAAAATT-TCGTAC
**
54436892 TTTCAAAAAATTTCGTGT
1 TTTCAAAAAATTTCGTAC
54436910 TTTCAAAAAATT
1 TTTCAAAAAATT
54436922 GACATTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAATTTCGTAC
Found at i:54437020 original size:19 final size:20
Alignment explanation
Indices: 54436987--54437061 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 20
54436977 ATCAAAATTT
54436987 TTGTGTTTTCAAAAAATAAAA
1 TTGTGTTTTC-AAAAATAAAA
54437008 TTGTGTTTT-AAAAAT-AAA
1 TTGTGTTTTCAAAAATAAAA
54437026 TTCGTGTTTTCAAAAA-AAAA
1 TT-GTGTTTTCAAAAATAAAA
*
54437046 TTCTCGTGTTTCAAAA
1 TTGT-GT-TTTCAAAA
54437062 TTTTCGTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
18 5 0.10
19 14 0.29
20 12 0.25
21 17 0.35
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (20 bp):
TTGTGTTTTCAAAAATAAAA
Found at i:54437063 original size:16 final size:16
Alignment explanation
Indices: 54437042--54437072 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54437032 TTTTCAAAAA
54437042 AAAATTCTCGTGTTTC
1 AAAATTCTCGTGTTTC
*
54437058 AAAATTTTCGTGTTT
1 AAAATTCTCGTGTTT
54437073 TTTTTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
AAAATTCTCGTGTTTC
Found at i:54449299 original size:195 final size:192
Alignment explanation
Indices: 54448739--54449357 Score: 1094
Period size: 193 Copynumber: 3.2 Consensus size: 192
54448729 CTTTCCAAGG
*
54448739 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
54448804 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
65 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
54448869 GTTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 GTTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
54448932 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTTAAATTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTTTAAATTT
* *
54448997 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATGTTTA
65 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
*
54449062 GTTTATGTTTTAAATTGACTAATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 GTTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
54449125 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCATCAAGACATGTTGAGGTATTTTTAAATTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCC-TCAAGACACGTTGAGGTATTTTTAAATTT
*
54449190 TTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTT
65 TTT--AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTT
*
54449255 TAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
128 TAGTTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* **
54449320 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
54449358 GGCTCACATG
Statistics
Matches: 408, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
193 229 0.56
194 25 0.06
195 122 0.30
196 32 0.08
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (192 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:54449397 original size:16 final size:17
Alignment explanation
Indices: 54449376--54449409 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54449366 TGCTGAGGTA
*
54449376 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
54449392 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
54449409 T
1 T
54449410 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:54449573 original size:85 final size:88
Alignment explanation
Indices: 54449315--54449573 Score: 309
Period size: 91 Copynumber: 2.9 Consensus size: 88
54449305 TAATTTTTGT
*
54449315 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
*
54449379 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
54449406 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
**
54449468 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* *
54449493 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
*
54449557 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
54449574 TCTGTTTTTT
Statistics
Matches: 148, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 29 0.20
88 2 0.01
89 31 0.21
91 41 0.28
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:54449755 original size:54 final size:54
Alignment explanation
Indices: 54449671--54449836 Score: 255
Period size: 54 Copynumber: 3.1 Consensus size: 54
54449661 TCAATTTCTA
54449671 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCT-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
54449726 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCT-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
54449780 CTTTTGCAAATTCTGTTTTC-AAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
54449834 CTT
1 CTT
54449837 GGCTCACATG
Statistics
Matches: 103, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
54 87 0.84
55 10 0.10
56 6 0.06
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTTTCAATTTCTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:54450143 original size:30 final size:30
Alignment explanation
Indices: 54450109--54450210 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
54450099 AAAAAAATAA
*
54450109 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-CT
* *
54450139 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTCT
* * *
54450169 AAATTTCACTTAGACCCCTAAAATTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTC-TCT
54450199 AAATTTCATTTT
1 AAATTTCATTTT
54450211 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 59 0.97
31 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTCT
Found at i:54450224 original size:29 final size:28
Alignment explanation
Indices: 54450109--54450225 Score: 92
Period size: 30 Copynumber: 4.0 Consensus size: 28
54450099 AAAAAAATAA
* * *
54450109 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTT-AACCCTAAA-TTTTCTT
* *
54450139 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTAACCC-TAAATTTTC-TT
* *
54450169 AAATTTCA-CTTAGACCCCTAAAATTTCATT
1 AAATTTCATTTTA-A-CCCTAAATTTTC-TT
*
54450199 AAATTTCATTTTAATCCTAAATTTTCT
1 AAATTTCATTTTAACCCTAAATTTTCT
54450226 AAAAATTACA
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.01
29 19 0.27
30 44 0.63
31 6 0.09
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.44
Consensus pattern (28 bp):
AAATTTCATTTTAACCCTAAATTTTCTT
Found at i:54450792 original size:23 final size:24
Alignment explanation
Indices: 54450755--54450808 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
54450745 AGCAAAAAAA
54450755 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
54450779 AAGCAG-AAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
54450802 AAGCAGC
1 AAGCAGC
54450809 CCAAATGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:54450945 original size:10 final size:9
Alignment explanation
Indices: 54450929--54450990 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 9
54450919 CCCAGCAGAA
54450929 AAAAAAAAG
1 AAAAAAAAG
54450938 AGAAAAAAA-
1 A-AAAAAAAG
54450947 AAAGAAAAAG
1 AAA-AAAAAG
*
54450957 AGAGAAAAAG
1 A-AAAAAAAG
54450967 -AAAAAAAG
1 AAAAAAAAG
54450975 AAAAAACAAG
1 AAAAAA-AAG
54450985 AAAAAA
1 AAAAAA
54450991 GGGGTTCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 9 0.20
9 12 0.27
10 23 0.51
11 1 0.02
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:54450960 original size:21 final size:21
Alignment explanation
Indices: 54450927--54450978 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
54450917 AGCCCAGCAG
54450927 AAAAAAAAAAGAG-AAAAA-A
1 AAAAAAAAAAGAGAAAAAAGA
*
54450946 AAAAGAAAAAGAGAGAAAAAGA
1 AAAAAAAAAAGAGA-AAAAAGA
54450968 AAAAAAGAAAA
1 AAAAAA-AAAA
54450979 AACAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.44
21 5 0.19
22 6 0.22
23 4 0.15
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGAGAAAAAAGA
Found at i:54450991 original size:35 final size:34
Alignment explanation
Indices: 54450925--54450989 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
54450915 CCAGCCCAGC
*
54450925 AGAAAAAAAAAAGAGAAAAAAAAAAGAAAAAGAG
1 AGAAAAAAAAAAAAGAAAAAAAAAAGAAAAAGAG
*
54450959 AGAAAAAGAAAAAAAG-AAAAAACAAGAAAAA
1 AGAAAAA-AAAAAAAGAAAAAAAAAAGAAAAA
54450990 AGGGGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (34 bp):
AGAAAAAAAAAAAAGAAAAAAAAAAGAAAAAGAG
Found at i:54451150 original size:5 final size:5
Alignment explanation
Indices: 54451140--54451182 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
54451130 CATTTATATT
* * * *
54451140 TTTAA TTTAA TTTAA TTTAA TTCAA TTTTA TTTTA TTTTA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
54451183 TAAATACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (5 bp):
TTTAA
Found at i:54451381 original size:21 final size:20
Alignment explanation
Indices: 54451349--54451390 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
54451339 TCGCGTTTCG
54451349 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
54451369 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
54451390 A
1 A
54451391 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:54451391 original size:19 final size:19
Alignment explanation
Indices: 54451349--54451390 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
54451339 TCGCGTTTCG
54451349 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
54451369 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
54451389 AA
1 AA
54451391 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:54451534 original size:17 final size:18
Alignment explanation
Indices: 54451495--54451911 Score: 239
Period size: 17 Copynumber: 23.3 Consensus size: 18
54451485 GAAAAATCAG
54451495 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
54451513 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
54451531 AAAAAATTCCAT-TTTTC
1 AAAAATTTTCGTGTTTTC
* *
54451548 AAAATTTTTCGTGTTTTTTTA
1 AAAAATTTTCGTG---TTTTC
* * *
54451569 AAAAATTTCCAT-ATTTC
1 AAAAATTTTCGTGTTTTC
* *
54451586 TAAAATTTTCGTG-TTTA
1 AAAAATTTTCGTGTTTTC
* *
54451603 AAAAAATTTCGTATTTTC
1 AAAAATTTTCGTGTTTTC
* ** *
54451621 AAAATTTTTTATTTTTTTC
1 AAAA-ATTTTCGTGTTTTC
* *
54451640 AACAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
54451657 ACAAATTCTCGTATTTT-
1 AAAAATTTTCGTGTTTTC
* ** *
54451674 AAAATTTTTTATGTTTTA
1 AAAAATTTTCGTGTTTTC
54451692 AAAAATAAATTTC-TCGTGTTTC
1 AAAAAT---TTTCGT-GT-TTTC
* *
54451714 AAAAATTGTCATGTTTT-
1 AAAAATTTTCGTGTTTTC
*
54451731 AAAAATTTTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
54451748 TAAAATGTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
**
54451765 AAAAAATCCTCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
* *
54451784 AAAAATTCTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54451801 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
54451819 -AAAATTCTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54451835 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
54451853 AAAAATTTCCCCTGTTTTC
1 AAAAATTT-TCGTGTTTTC
* *
54451872 AAAAATTCTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
* *
54451889 AAAAATTTTCTTTTTTTC
1 AAAAATTTTCGTGTTTTC
54451907 AAAAA
1 AAAAA
54451912 AAAAAACTTC
Statistics
Matches: 302, Mismatches: 73, Indels: 48
0.71 0.17 0.11
Matches are distributed among these distances:
16 7 0.02
17 134 0.44
18 96 0.32
19 36 0.12
20 2 0.01
21 18 0.06
22 9 0.03
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.47
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:54451595 original size:38 final size:36
Alignment explanation
Indices: 54451509--54451601 Score: 118
Period size: 38 Copynumber: 2.5 Consensus size: 36
54451499 ATTTTCGTGT
*
54451509 TTTCAAAAATTTTCGTG--TTTTCAAAAAATTCCATT
1 TTTC-AAAATTTTCGTGTTTTTTCAAAAAATTCCATA
*
54451544 TTTCAAAATTTTTCGTGTTTTTTTAAAAAATTTCCATA
1 TTTCAAAA-TTTTCGTGTTTTTTCAAAAAA-TTCCATA
54451582 TTTCTAAAATTTTCGTGTTT
1 TTTC-AAAATTTTCGTGTTT
54451602 AAAAAAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.08
35 12 0.24
37 10 0.20
38 21 0.41
39 4 0.08
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (36 bp):
TTTCAAAATTTTCGTGTTTTTTCAAAAAATTCCATA
Found at i:54451654 original size:54 final size:53
Alignment explanation
Indices: 54451589--54451897 Score: 148
Period size: 54 Copynumber: 5.8 Consensus size: 53
54451579 ATATTTCTAA
* *
54451589 AATTTTCGTGTTTAAAAAAATT-TCGTATTTTCAAAATTTTTTATTTTTTTCAAC
1 AATTCTCGTGTTT-AAAAAATTCTCGTATTTT-AAAATTTTTTATGTTTTTCAAC
* * ** *
54451643 AATTCTCGTGTTTCACAAATTCTCGTATTTTAAAATTTTTTATGTTTTAAAAAATA
1 AATTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTT--TCAA-C
* * * * * * *
54451699 AATTTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAATTTTCATGTTTCT-AA-
1 AA-TTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
* * * * * *
54451751 AATGT-TCGTATTTCAAAAAATCCTCGTGTTTTCAAAAATTCTCATG--TTTCAA-
1 AAT-TCTCGTGTTT-AAAAAATTCTCGTATTTT-AAAATTTTTTATGTTTTTCAAC
* ** * * * * * *
54451803 AAATCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATG-TTTTCAAA
1 AATTC-TCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
* * * * *
54451856 AATTTCCCCTGTTTTCAAAAATTCTCGTATTTCAAAAATTTT
1 AA-TTCTCGTG-TTTAAAAAATTCTCGTATTTTAAAATTTTT
54451898 CTTTTTTTCA
Statistics
Matches: 203, Mismatches: 37, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
51 23 0.11
52 40 0.20
53 46 0.23
54 51 0.25
55 2 0.01
56 2 0.01
57 39 0.19
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (53 bp):
AATTCTCGTGTTTAAAAAATTCTCGTATTTTAAAATTTTTTATGTTTTTCAAC
Found at i:54451720 original size:57 final size:55
Alignment explanation
Indices: 54451587--54451752 Score: 160
Period size: 57 Copynumber: 3.0 Consensus size: 55
54451577 CCATATTTCT
* ***
54451587 AAAATTT-TCGTGTTTAAAAAAATTTCGTATTTTCAAAATTTTTTAT-TTTT-TTCA
1 AAAATTTCTCGTGTTT-CAAAAATTTCGTATTTT-AAAATTTTTTATGTTTTAAAAA
* *
54451641 ACAA-TTCTCGTGTTTCACAAATTCTCGTATTTTAAAATTTTTTATGTTTTAAAAA
1 AAAATTTCTCGTGTTTCAAAAATT-TCGTATTTTAAAATTTTTTATGTTTTAAAAA
* * * *
54451696 ATAAATTTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAATTTTCATGTTTCTAAAA
1 A-AAATTTCTCGTGTTTCAAAAATT-TCGTATTTTAAAATTTTTTATGTTT-TAAAA
54451753 TGTTCGTATT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
53 20 0.22
54 24 0.26
55 2 0.02
56 2 0.02
57 39 0.42
58 5 0.05
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (55 bp):
AAAATTTCTCGTGTTTCAAAAATTTCGTATTTTAAAATTTTTTATGTTTTAAAAA
Found at i:54451753 original size:34 final size:34
Alignment explanation
Indices: 54451495--54451895 Score: 186
Period size: 35 Copynumber: 11.2 Consensus size: 34
54451485 GAAAAATCAG
* *
54451495 AAAAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTC
1 AAAAATTCTCATG-TTTCAAAAATTTTCGTG-TTTC
* * *
54451531 AAAAAATTC-CATTTTTCAAAATTTTTCGTGTTTTTTTA
1 -AAAAATTCTCATGTTTCAAAAATTTTCGTG----TTTC
* * *
54451569 AAAAATT-TCCATATTTCTAAAATTTTCGTGTTTAA
1 AAAAATTCT-CATGTTTCAAAAATTTTCGTGTTT-C
* ** *
54451604 AAAAATT-TCGTAT-TTTCAAAATTTTTTATTTTTTTC
1 AAAAATTCTC--ATGTTTCAAAA-ATTTT-CGTGTTTC
* * * * * *
54451640 AACAATTCTCGTGTTTCACAAATTCTCGTATTTT
1 AAAAATTCTCATGTTTCAAAAATTTTCGTGTTTC
* * * *
54451674 AAAATTTTTTATGTTTTAAAAAATAAATTTCTCGTGTTTC
1 AAAAATTCTCATG-TTT---CAA-AAATTT-TCGTGTTTC
* * *
54451714 AAAAATTGTCATGTTTTAAAAATTTTCATGTTTC
1 AAAAATTCTCATGTTTCAAAAATTTTCGTGTTTC
* * * **
54451748 TAAAATGT-TCGTATTTCAAAAAATCCTCGTGTTTTC
1 AAAAAT-TCTCATGTTTC-AAAAATTTTCGTG-TTTC
*
54451784 AAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTC
1 AAAAATTCTCATGTTTCAAAAATTTTCGTG-TTTC
*
54451819 -AAAATTCT-AGTGTTTCAAAAATTTTCATGTTTTC
1 AAAAATTCTCA-TGTTTCAAAAATTTTCGTG-TTTC
* * * *
54451853 AAAAATTTCCCCTGTTTTCAAAAATTCTCGTATTTC
1 AAAAA-TTCTCATG-TTTCAAAAATTTTCGTGTTTC
54451889 AAAAATT
1 AAAAATT
54451896 TTCTTTTTTT
Statistics
Matches: 281, Mismatches: 56, Indels: 56
0.72 0.14 0.14
Matches are distributed among these distances:
33 1 0.00
34 65 0.23
35 80 0.28
36 53 0.19
37 34 0.12
38 23 0.08
39 8 0.03
40 17 0.06
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.47
Consensus pattern (34 bp):
AAAAATTCTCATGTTTCAAAAATTTTCGTGTTTC
Found at i:54451836 original size:16 final size:16
Alignment explanation
Indices: 54451780--54451838 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
54451770 ATCCTCGTGT
54451780 TTTCAAAAATTCTCA-TG
1 TTTC-AAAATTCT-AGTG
* *
54451797 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TAGTG
54451814 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTAGTG
54451831 TTTCAAAA
1 TTTCAAAA
54451839 ATTTTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.40
17 11 0.31
18 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTCAAAATTCTAGTG
Found at i:54451967 original size:18 final size:18
Alignment explanation
Indices: 54451944--54451991 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
54451934 ATCTCCGTGT
54451944 TTTCAAAAAATTCTCG-AC
1 TTTCAAAAAATT-TCGTAC
**
54451962 TTTCAAAAAATTTCGTGT
1 TTTCAAAAAATTTCGTAC
54451980 TTTCAAAAAATT
1 TTTCAAAAAATT
54451992 GACATTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAATTTCGTAC
Found at i:54452085 original size:20 final size:20
Alignment explanation
Indices: 54452060--54452099 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
54452050 CAAAATTTTT
*
54452060 GTGTTTTCAAAATAAAATTC
1 GTGTTTTCAAAAAAAAATTC
54452080 GTGTTTTCAAAAAAAAATTC
1 GTGTTTTCAAAAAAAAATTC
54452100 TCGTGTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
GTGTTTTCAAAAAAAAATTC
Found at i:54452093 original size:22 final size:22
Alignment explanation
Indices: 54452060--54452111 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
54452050 CAAAATTTTT
*
54452060 GTGTTTTC-AAAATAAAAT-TC
1 GTGTTTTCAAAAAAAAAATCTC
*
54452080 GTGTTTTCAAAAAAAAATTCTC
1 GTGTTTTCAAAAAAAAAATCTC
54452102 GTG-TTTCAAA
1 GTGTTTTCAAA
54452112 TTTTTCGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 15 0.54
22 5 0.18
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
GTGTTTTCAAAAAAAAAATCTC
Found at i:54452646 original size:40 final size:40
Alignment explanation
Indices: 54452585--54452796 Score: 230
Period size: 40 Copynumber: 5.3 Consensus size: 40
54452575 CATTTGAATG
* * *
54452585 ATATCCGGGCTAAGTCTCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
54452625 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
54452665 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
54452705 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * *
54452745 AAATCCAGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
54452785 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54452797 ATTCCGAAGA
Statistics
Matches: 138, Mismatches: 32, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
39 8 0.06
40 128 0.93
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:54452725 original size:80 final size:79
Alignment explanation
Indices: 54452592--54452805 Score: 286
Period size: 80 Copynumber: 2.7 Consensus size: 79
54452582 ATGATATCCG
* * *
54452592 GGCTAAGTCTCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 GGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGATCCGAAGGCATTTGTGC
* * *
54452657 GAGTTGCTATACCCG
65 GAGTTACTAAACCCA
*
54452672 GGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTGTGC
1 GGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGATCCGAAGGCATTTGTGC
*
54452737 GAGTTACTAAATCCA
65 GAGTTACTAAACCCA
* * * *
54452752 GGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA-ATTCCGAAG
1 GGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGA-TCCGAAG
54452806 AAACTTGGGT
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 13 0.11
80 105 0.88
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (79 bp):
GGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAGGCATTTGTGCG
AGTTACTAAACCCA
Found at i:54458871 original size:38 final size:39
Alignment explanation
Indices: 54458820--54458939 Score: 125
Period size: 38 Copynumber: 3.0 Consensus size: 39
54458810 CTCAATCTGC
*
54458820 TCCACTACAACTTCAGGGAGATAATATTTGTAGCTTGT-
1 TCCACTACAACTTCAGGGAGATAAAATTTGTAGCTTGTA
* ** * *
54458858 TCCACTACAACTTCAAGGAGATAAGGTTTGTGGCTTTAATCTA
1 TCCACTACAACTTCAGGGAGATAAAATTTGTAGC--T--TGTA
*
54458901 CTCCACTACAAATTCAGGGAGATAAAATTTGTAGCTTGT
1 -TCCACTACAACTTCAGGGAGATAAAATTTGTAGCTTGT
54458940 CTTCAATCTG
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
38 30 0.46
40 3 0.05
42 3 0.05
44 29 0.45
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (39 bp):
TCCACTACAACTTCAGGGAGATAAAATTTGTAGCTTGTA
Found at i:54458922 original size:44 final size:47
Alignment explanation
Indices: 54458858--54458978 Score: 149
Period size: 49 Copynumber: 2.6 Consensus size: 47
54458848 TGTAGCTTGT
* * *
54458858 TCCACTACAACTTCAAGGAGATAAGGTTTGT-G-G-CTTTAATCTAC
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAGTGTCTTCAATCTAC
* * *
54458902 TCCACTACAAATTCAGGGAGATAAAATTTGTAGCTTGTCTTCAATCTGC
1 TCCACTACAACTTCAGGGAGATAAGATTTGTAG--TGTCTTCAATCTAC
54458951 TCCACTACAACTTCAGGGAGATAAGATT
1 TCCACTACAACTTCAGGGAGATAAGATT
54458979 GGTTGATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
44 27 0.42
45 1 0.02
48 1 0.02
49 35 0.55
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (47 bp):
TCCACTACAACTTCAGGGAGATAAGATTTGTAGTGTCTTCAATCTAC
Found at i:54459202 original size:44 final size:44
Alignment explanation
Indices: 54459133--54459383 Score: 133
Period size: 44 Copynumber: 5.6 Consensus size: 44
54459123 CTTCAGTTTG
* *
54459133 CTCCACTGCAACTTTAGTG-ATATAAGACTTGTAACTTCAACCTA
1 CTCCACTGCAACTTCAG-GAAGATAAGACTTGTAACTTCAACCTA
* * * * * *
54459177 CTCTACTGCAACTTCAAGAAGATAAG-GTT-T-GCTAT-GATCTA
1 CTCCACTGCAACTTCAGGAAGATAAGACTTGTAACT-TCAACCTA
* *
54459218 CTCTACTGCAACTTCA-GAGAGATAAGATCTGCAATTTATAGCTTCAATCC-A
1 CTCCACTGCAACTTCAGGA-AGATAAGA-CT----TGTA-A-CTTCAA-CCTA
* * **
54459269 TTCCACTGCAACTTCAGGGAA-ATAAGA-TTCGCTATCTTCAGTCTA
1 CTCCACTGCAACTTCA-GGAAGATAAGACTT-G-TAACTTCAACCTA
* * * *
54459314 CTCCATTGCAACTTTAGGGAGATAAGACTTGTAACTTTAACCTA
1 CTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAACCTA
* *
54459358 CTCCACTACAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGAAGATAAG
54459384 GTTTGATATG
Statistics
Matches: 156, Mismatches: 29, Indels: 44
0.68 0.13 0.19
Matches are distributed among these distances:
40 2 0.01
41 29 0.19
42 2 0.01
43 4 0.03
44 56 0.36
45 27 0.17
46 2 0.01
47 3 0.02
48 1 0.01
49 1 0.01
50 1 0.01
51 24 0.15
52 2 0.01
53 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAACCTA
Found at i:54459216 original size:181 final size:181
Alignment explanation
Indices: 54458939--54459397 Score: 616
Period size: 181 Copynumber: 2.5 Consensus size: 181
54458929 TTGTAGCTTG
* * * * ** * **
54458939 TCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGA-TTGGTTGATTTTTAACCTGTTCCACT
1 TCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTT-G-T-AACTTCAACCTACTCCACT
* * * *
54459003 GTAACTTTAAGGAGATAAGGTTCGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAAAAT-T
63 GCAACTTCAAGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGAT-AAAATCT
*
54459067 GCAATTTATAGCTTAAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCACTA
127 GCAATTTATAGCTTAAATCCATTCCACTGCAACTTCAGGGAAATAAGATTCACTA
* * * * *
54459122 TCTTCAGTTTGCTCCACTGCAACTTTAGTGATATAAGACTTGTAACTTCAACCTACTCTACTGCA
1 TCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTGCA
* * *
54459187 ACTTCAAGAAGATAAGGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGCAA
66 ACTTCAAGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGCAA
* *
54459252 TTTATAGCTTCAATCCATTCCACTGCAACTTCAGGGAAATAAGATTCGCTA
131 TTTATAGCTTAAATCCATTCCACTGCAACTTCAGGGAAATAAGATTCACTA
* * *
54459303 TCTTCAGTCTACTCCATTGCAACTTTAGGGAGATAAGACTTGTAACTTTAACCTACTCCACTACA
1 TCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTGCA
*
54459368 ACTTCAGGGAGATAAGGTTTGATATGATCT
66 ACTTCAAGGAGATAAGGTTTGATATGATCT
54459398 TCAATCCATC
Statistics
Matches: 241, Mismatches: 33, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
180 4 0.02
181 201 0.83
182 1 0.00
183 33 0.14
184 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (181 bp):
TCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTGCA
ACTTCAAGGAGATAAGGTTTGATATGATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGCAA
TTTATAGCTTAAATCCATTCCACTGCAACTTCAGGGAAATAAGATTCACTA
Found at i:54459376 original size:89 final size:89
Alignment explanation
Indices: 54459089--54459383 Score: 296
Period size: 89 Copynumber: 3.3 Consensus size: 89
54459079 TTAAATCTAT
* * * * *
54459089 TCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTCAGTTTGCTCCACTGCAACTTTAGTGAT
1 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTTAGAGAG
54459154 ATAAGACTTGTAACTTCAACCTAC
66 ATAAGACTTGTAACTTCAACCTAC
* * * * * * *
54459178 TCTACTGCAACTTCA-AGAAGATAAGGTTTGCTA---TGA-TCTACTCTACTGCAACTTCAGAGA
1 TCCACTGCAACTTCAGGGAA-ATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTTAGAGA
* *
54459238 GATAAGATCTGCAATTTATAGCTTCAATCC-AT
65 GATAAGA-CT----TGTA-A-CTTCAA-CCTAC
* *
54459270 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCATTGCAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTTAGAGAG
*
54459335 ATAAGACTTGTAACTTTAACCTAC
66 ATAAGACTTGTAACTTCAACCTAC
* *
54459359 TCCACTACAACTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAAATAAG
54459384 GTTTGATATG
Statistics
Matches: 163, Mismatches: 28, Indels: 30
0.74 0.13 0.14
Matches are distributed among these distances:
85 25 0.15
86 4 0.02
88 5 0.03
89 53 0.33
90 4 0.02
91 4 0.02
92 32 0.20
93 5 0.03
95 4 0.02
96 27 0.17
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (89 bp):
TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTTAGAGAG
ATAAGACTTGTAACTTCAACCTAC
Found at i:54471214 original size:44 final size:44
Alignment explanation
Indices: 54471151--54471571 Score: 569
Period size: 44 Copynumber: 9.6 Consensus size: 44
54471141 AAACTATAAA
*
54471151 TCCTAGCTCCTTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
* * ** *
54471195 TCCTAGCTCTCTGAACAGCAGTGGAATAGGCAGAAGATTGTAAA-
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTG-AAAG
54471239 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
* * * *
54471283 TCCTACCTCCCTGAACAGTAGTGGAATAGGTGGAAGGCTGAAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
* * *
54471327 TCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAA-
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTG-AAAG
* *
54471371 TCCTAGCTCTCTGACCAGCAGTGGAATAGGTGGAAGGCTGAAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
* * *
54471415 TCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAA-
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTG-AAAG
* *
54471459 TCCTAGCTCCTTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
* * *
54471503 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTAGAAGATTGGAAG
1 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
* *
54471547 TCCTAGCTCCCTGAGCAGCTGTGGA
1 TCCTAGCTCCCTGACCAGCAGTGGA
54471572 GGAGGTTAAA
Statistics
Matches: 330, Mismatches: 41, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
43 8 0.02
44 313 0.95
45 9 0.03
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (44 bp):
TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAAAG
Found at i:54471388 original size:132 final size:132
Alignment explanation
Indices: 54471151--54471571 Score: 637
Period size: 132 Copynumber: 3.2 Consensus size: 132
54471141 AAACTATAAA
* * *
54471151 TCCTAGCTCCTTGACCAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCTCTGAACAGCAG
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
*
54471216 TGGAATAGGCAGAAGATTGTAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAA
66 TGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAA
54471281 AG
131 AG
* * *
54471283 TCCTACCTCCCTGAACAGTAGTGGAATAGGTGGAAGGCTGAAAGTCCTAGCTCCCTGAACAGCAG
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
* *
54471348 TGGAATAGGCGGAAGATTGTAAATCCTAGCTCTCTGACCAGCAGTGGAATAGGTGGAAGGCTGAA
66 TGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAA
54471413 AG
131 AG
* * * *
54471415 TCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAA-TCCTAGCTCCTTGACCAGCA
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTG-AAAGTCCTAGCTCCCTGAACAGCA
* * * * * *
54471479 GTGGAATAGGTGGAAGACTGTAAGTCCTAGCTCCCTGACCAGCAGTGGAATAGGTAGAAGATTGG
65 GTGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGA
54471544 AAG
130 AAG
* *
54471547 TCCTAGCTCCCTGAGCAGCTGTGGA
1 TCCTAGCTCCCTGAACAGCAGTGGA
54471572 GGAGGTTAAA
Statistics
Matches: 262, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
132 259 0.99
133 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (132 bp):
TCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTGAAAGTCCTAGCTCCCTGAACAGCAG
TGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGAA
AG
Found at i:54471696 original size:88 final size:88
Alignment explanation
Indices: 54471592--54471935 Score: 517
Period size: 88 Copynumber: 3.9 Consensus size: 88
54471582 AATTACAGAT
* * *
54471592 CTTATCTCCTTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAG
1 CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAG
54471657 CGAAGCAGATCGAAGACACAAGC
66 CGAAGCAGATCGAAGACACAAGC
* * *
54471680 CTTATCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCATATCTTGCCTTCCTACATCGACAT
1 CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAG
*
54471745 CGAAGAAGATCGAAGACACAAGC
66 CGAAGCAGATCGAAGACACAAGC
* * * *
54471768 CTTGCCACCCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAG
1 CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAG
* *
54471833 TGAAGTAGATCGAAGACACAAGC
66 CGAAGCAGATCGAAGACACAAGC
* * * *
54471856 CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCATTCCTGCATCGATAG
1 CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAG
* *
54471921 TGAAGCAAATCGAAG
66 CGAAGCAGATCGAAG
54471936 CCAATGGTCT
Statistics
Matches: 234, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 234 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (88 bp):
CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACATCGACAG
CGAAGCAGATCGAAGACACAAGC
Found at i:54471816 original size:44 final size:44
Alignment explanation
Indices: 54471768--54471904 Score: 109
Period size: 44 Copynumber: 3.1 Consensus size: 44
54471758 AGACACAAGC
*
54471768 CTTGCCACCCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGAT
* * * * * * * * *
54471812 CTTGCCTTCCT-GCATCGACAGTGAAGTAGATCGAAGACA-CA-AGC
1 CTTGCCTCCCTCG-GTTG-TAGTGGAGTAGGTTGAAGATAGCAGA-T
* * *
54471856 CTTACCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGT
1 CTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGAT
54471900 CTTGC
1 CTTGC
54471905 ATTCCTGCAT
Statistics
Matches: 64, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
43 17 0.27
44 30 0.47
45 17 0.27
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGAT
Found at i:54477584 original size:23 final size:23
Alignment explanation
Indices: 54477553--54477597 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
54477543 TAAAAGATTT
54477553 ATTACTGAAATGAATTCAAATGA
1 ATTACTGAAATGAATTCAAATGA
*
54477576 ATTATTGAAATGAATTCAAATG
1 ATTACTGAAATGAATTCAAATG
54477598 GCATAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (23 bp):
ATTACTGAAATGAATTCAAATGA
Found at i:54478787 original size:26 final size:26
Alignment explanation
Indices: 54478758--54478821 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
54478748 ATATTTTCTT
* **
54478758 AAAATTTTACCACGGGTATAATTGTC
1 AAAATTTTACCACGGGTACAATCATC
* **
54478784 AAAATTTTATCGGGGGTACAATCATC
1 AAAATTTTACCACGGGTACAATCATC
54478810 AAAATTTTACCA
1 AAAATTTTACCA
54478822 ATGGTAAAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (26 bp):
AAAATTTTACCACGGGTACAATCATC
Found at i:54486214 original size:28 final size:28
Alignment explanation
Indices: 54486143--54486246 Score: 131
Period size: 28 Copynumber: 3.8 Consensus size: 28
54486133 CAAAATAGGT
** *
54486143 AAAATGACCAAAATACCCCTAA-AG-GG
1 AAAATGACCATTATACCCCTAATAGATG
** *
54486169 TAAAATGATTATTTTACCCCTAATAGATG
1 -AAAATGACCATTATACCCCTAATAGATG
54486198 AAAATGACCATTATACCCCTAATAGATG
1 AAAATGACCATTATACCCCTAATAGATG
54486226 AAAATGACCATTATACCCCTA
1 AAAATGACCATTATACCCCTA
54486247 GAGGTAGGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.26
28 48 0.73
29 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (28 bp):
AAAATGACCATTATACCCCTAATAGATG
Found at i:54486468 original size:29 final size:26
Alignment explanation
Indices: 54486371--54486479 Score: 139
Period size: 26 Copynumber: 4.1 Consensus size: 26
54486361 TGGAGGAAGT
*
54486371 ATACTGTTACTGGCAGC-TTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
54486396 ATGCTATTACTGGCAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTTGCTGCG
*
54486422 ATACTATTACTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTTGCTGCG
*
54486448 ATACTTTTATTACTGGTAGCTTTGCTGCG
1 ATAC---TATTACTGGCAGCTTTGCTGCG
54486477 ATA
1 ATA
54486480 TTGGTGTGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
25 15 0.21
26 34 0.47
29 23 0.32
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:54486473 original size:55 final size:51
Alignment explanation
Indices: 54486371--54486479 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 51
54486361 TGGAGGAAGT
* * * *
54486371 ATACTGTTACTGGCAGCTTGCTGCGATGCTATTACTGGCAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTGCTACGATACTATTACTGGCAGCTTTGCTGCG
*
54486422 ATACTATTACTGGCAGCTTTGCTACGATACTTTTATTACTGGTAGCTTTGCTGCG
1 ATACTATTACTGGCAGC-TTGCTACGATAC---TATTACTGGCAGCTTTGCTGCG
54486477 ATA
1 ATA
54486480 TTGGTGTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 16 0.33
52 10 0.20
55 23 0.47
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (51 bp):
ATACTATTACTGGCAGCTTGCTACGATACTATTACTGGCAGCTTTGCTGCG
Found at i:54489844 original size:101 final size:102
Alignment explanation
Indices: 54489728--54489912 Score: 329
Period size: 101 Copynumber: 1.8 Consensus size: 102
54489718 AAAGTGATGG
*
54489728 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGATAATGGTCACATGTGTAGT
54489791 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
*
54489829 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGATAATGGTCACATGTGTAGTA
54489894 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
54489913 TGAACCGAAC
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
100 4 0.05
101 42 0.52
102 34 0.43
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:54489858 original size:51 final size:51
Alignment explanation
Indices: 54489724--54489910 Score: 236
Period size: 51 Copynumber: 3.7 Consensus size: 51
54489714 AGTGAAAGTG
* *
54489724 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTA
* * * * *
54489773 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTA
* * * *
54489824 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTA
54489876 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
54489911 TGTGAACCGA
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.33
51 73 0.63
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATAGTA
Found at i:54489914 original size:26 final size:26
Alignment explanation
Indices: 54489834--54489914 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
54489824 TTCGATCACG
54489834 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
54489860 CGTGTA-T-CAGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
54489885 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
54489911 TGTG
1 TGTG
54489915 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:54490131 original size:38 final size:37
Alignment explanation
Indices: 54490085--54490157 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
54490075 AGGTGTGGAA
*
54490085 TTGAATTGAATAT-TGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAAT-TGTGA-TT-GAAAGTGAAAAAGTGAATT
54490123 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
54490158 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAATT
Found at i:54496001 original size:46 final size:48
Alignment explanation
Indices: 54495910--54496029 Score: 120
Period size: 47 Copynumber: 2.5 Consensus size: 48
54495900 CAACCAGTGG
* * * *
54495910 TTACTTTTCATAAGTCTCACCCATGTGTCTGGGAGTAGAGCCAC-TTA
1 TTACCTTTCATAAGCCTCACCCATGTGTCTAGGAGCAGAGCCACTTTA
* *
54495957 TTACCTTTCTTAAGCCTC-CCCATGTGTCTAGGAGCA-ATGTCACTTTA
1 TTACCTTTCATAAGCCTCACCCATGTGTCTAGGAGCAGA-GCCACTTTA
* * *
54496004 TTACCTTCCGTAAGCCTTCTCCCATG
1 TTACCTTTCATAAGCC-TCACCCATG
54496030 CGTTTGGAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.02
46 20 0.33
47 32 0.52
48 2 0.03
49 6 0.10
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (48 bp):
TTACCTTTCATAAGCCTCACCCATGTGTCTAGGAGCAGAGCCACTTTA
Found at i:54496306 original size:39 final size:37
Alignment explanation
Indices: 54496219--54496338 Score: 117
Period size: 39 Copynumber: 3.3 Consensus size: 37
54496209 CGAATATAAT
* *
54496219 AAATA-TTTTAATTTTTTTTAATTTTAAAATACTTTTA
1 AAATATTTTTAA-TTTTTTAAATTTTAAAATATTTTTA
* * *
54496256 AAATA-----ATTTTTTTAAATTTTTAAATTTTTTTA
1 AAATATTTTTAATTTTTTAAATTTTAAAATATTTTTA
*
54496288 AAATACGTTTTTAATTTTTTTAATTTTAAAATATTTTTA
1 AAATA--TTTTTAATTTTTTAAATTTTAAAATATTTTTA
54496327 AAATATTTTTAA
1 AAATATTTTTAA
54496339 AATTTTTGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
32 26 0.39
33 1 0.01
37 12 0.18
39 28 0.42
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (37 bp):
AAATATTTTTAATTTTTTAAATTTTAAAATATTTTTA
Found at i:54496307 original size:31 final size:31
Alignment explanation
Indices: 54496233--54496306 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
54496223 ATTTTAATTT
* ** **
54496233 TTTTTAATTTTAAAATACTTTTAAAATAATT
1 TTTTTAATTTTTAAATTTTTTTAAAATAACG
54496264 TTTTTAAATTTTTAAATTTTTTTAAAAT-ACG
1 TTTTT-AATTTTTAAATTTTTTTAAAATAACG
54496295 TTTTTAATTTTT
1 TTTTTAATTTTT
54496307 TTAATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 7 0.19
31 11 0.30
32 19 0.51
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTTAATTTTTAAATTTTTTTAAAATAACG
Found at i:54496327 original size:11 final size:11
Alignment explanation
Indices: 54496311--54496345 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
54496301 ATTTTTTTAA
54496311 TTTTAAAATAT
1 TTTTAAAATAT
54496322 TTTTAAAATAT
1 TTTTAAAATAT
54496333 TTTTAAAAT-T
1 TTTTAAAATAT
54496343 TTT
1 TTT
54496346 GTTTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54496335 original size:28 final size:27
Alignment explanation
Indices: 54496283--54496338 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
54496273 TTTTAAATTT
*
54496283 TTTTAAAATACGTTTTTAATTTTTTTAA
1 TTTTAAAATAC-TTTTTAATATTTTTAA
54496311 TTTTAAAATA-TTTTTAAAATATTTTTAA
1 TTTTAAAATACTTTTT--AATATTTTTAA
54496339 AATTTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 5 0.20
28 20 0.80
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTAAAATACTTTTTAATATTTTTAA
Found at i:54496370 original size:71 final size:72
Alignment explanation
Indices: 54496216--54496370 Score: 199
Period size: 71 Copynumber: 2.2 Consensus size: 72
54496206 GCCCGAATAT
*
54496216 AATAAATATTTTAATTTTTTTTAATTTTAAAATACTTTTAAAATAATTTTTTTAAATTTTTAAAT
1 AATAAAT-TTTTAATTTTTTTTAATTTTAAAATACTTTTAAAATAATTTTTTAAAATTTTTAAAT
54496281 TTTTTTAA
65 TTTTTTAA
** * ***
54496289 AATACGTTTTTAA-TTTTTTTAATTTTAAAATATTTTTAAAAT-A-TTTTTAAAATTTTTGTTTT
1 AATAAATTTTTAATTTTTTTTAATTTTAAAATACTTTTAAAATAATTTTTTAAAATTTTTAAATT
54496351 AATTTTTAA
66 --TTTTTAA
54496360 AATAAATTTTT
1 AATAAATTTTT
54496371 GGTATTTATT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
69 15 0.21
70 1 0.01
71 44 0.62
72 6 0.08
73 5 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (72 bp):
AATAAATTTTTAATTTTTTTTAATTTTAAAATACTTTTAAAATAATTTTTTAAAATTTTTAAATT
TTTTTAA
Found at i:54501294 original size:19 final size:19
Alignment explanation
Indices: 54501252--54501309 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
54501242 AATTAAAAAC
54501252 TAAATAAATTTATAATAAAT
1 TAAATAAATTT-TAATAAAT
54501272 TAAATAAATTTTAA-AATAT
1 TAAATAAATTTTAATAA-AT
*
54501291 TAAATTAATTATTAATAAA
1 TAAATAAATT-TTAATAAA
54501310 AGTAAAAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 2 0.06
19 14 0.41
20 16 0.47
21 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATAAATTTTAATAAAT
Found at i:54501987 original size:30 final size:29
Alignment explanation
Indices: 54501944--54502042 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 29
54501934 TGTGTTAATA
*
54501944 ATATACAAGAATTGGATC-AAATCAAAATTTC
1 ATATATAA-AATTGGA-CAAAATCAAAA-TTC
*
54501975 ATATATAAAATTGTACAAAATCAAAATTC
1 ATATATAAAATTGGACAAAATCAAAATTC
* * * *
54502004 ATGTATACAATTGCACATTAAA-CTATAATTC
1 ATATATAAAATTGGACA--AAATC-AAAATTC
54502035 ATATATAA
1 ATATATAA
54502043 TTATGAGATT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 18 0.32
30 16 0.29
31 22 0.39
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.32
Consensus pattern (29 bp):
ATATATAAAATTGGACAAAATCAAAATTC
Found at i:54502005 original size:29 final size:30
Alignment explanation
Indices: 54501962--54502042 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
54501952 GAATTGGATC
*
54501962 AAATCAAAATTTCATATATAAAATTGTACA-
1 AAATCAAAA-TTCATATATAAAATTGCACAT
* *
54501992 AAATCAAAATTCATGTATACAATTGCACATT
1 AAATCAAAATTCATATATAAAATTGCACA-T
*
54502023 AAA-CTATAATTCATATATAA
1 AAATC-AAAATTCATATATAA
54502043 TTATGAGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 17 0.40
30 10 0.24
31 15 0.36
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTCATATATAAAATTGCACAT
Found at i:54502891 original size:11 final size:11
Alignment explanation
Indices: 54502870--54502930 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
54502860 ACTAATCCTA
54502870 TCTCAAATTTCC
1 TCTC-AATTTCC
*
54502882 TCTCAATTTCT
1 TCTCAATTTCC
*
54502893 TCTAAATTTCC
1 TCTCAATTTCC
*
54502904 TCTCAATTTGC
1 TCTCAATTTCC
*
54502915 TCTCAAATTCC
1 TCTCAATTTCC
54502926 T-TCAA
1 TCTCAA
54502931 AATTTCTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 4 0.10
11 34 0.81
12 4 0.10
ACGTcount: A:0.25, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:54502925 original size:22 final size:22
Alignment explanation
Indices: 54502870--54502944 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 22
54502860 ACTAATCCTA
54502870 TCTCAAATTTCCTCTCAATTTC
1 TCTCAAATTTCCTCTCAATTTC
54502892 T-TCTAAATTTCCTCTCAATTTGC
1 TCTC-AAATTTCCTCTCAATTT-C
54502915 TCTCAAA-TTCCT-TCAAAATTTC
1 TCTCAAATTTCCTCTC--AATTTC
*
54502937 TCTTAAAT
1 TCTCAAAT
54502945 CTCTATTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
21 4 0.09
22 30 0.65
23 10 0.22
24 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (22 bp):
TCTCAAATTTCCTCTCAATTTC
Found at i:54502934 original size:34 final size:34
Alignment explanation
Indices: 54502870--54502944 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
54502860 ACTAATCCTA
* *
54502870 TCTCAAATTTCCTCTCAATTTCTTCTAAATTTCC
1 TCTCAAATTTCCTCTCAATTCCTTCAAAATTTCC
*
54502904 TCTC-AATTTGCTCTCAAATTCCTTCAAAATTT-C
1 TCTCAAATTTCCTCTC-AATTCCTTCAAAATTTCC
*
54502937 TCTTAAAT
1 TCTCAAAT
54502945 CTCTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 14 0.40
34 21 0.60
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (34 bp):
TCTCAAATTTCCTCTCAATTCCTTCAAAATTTCC
Found at i:54504648 original size:18 final size:18
Alignment explanation
Indices: 54504621--54504655 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54504611 CAGGTGCGTT
* *
54504621 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
54504639 TCCTAACCCTTATATGT
1 TCCTAACCCTTATATGT
54504656 TTCTTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.43
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:54505231 original size:22 final size:21
Alignment explanation
Indices: 54505206--54505286 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
54505196 TTTAATTGAC
54505206 AAACCTTTAACCCTTAACCTAA
1 AAACC-TTAACCCTTAACCTAA
* **
54505228 AAACCCTAACCCTTAAATTTAA
1 AAACCTTAACCCTT-AACCTAA
* *
54505250 AACCCTAAACCCTTAACCTAA
1 AAACCTTAACCCTTAACCTAA
* *
54505271 AAACCCTAAACCTTAA
1 AAACCTTAACCCTTAA
54505287 ACCTTAAACC
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
21 25 0.54
22 21 0.46
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCTTAACCCTTAACCTAA
Found at i:54505266 original size:29 final size:29
Alignment explanation
Indices: 54505206--54505344 Score: 72
Period size: 29 Copynumber: 4.8 Consensus size: 29
54505196 TTTAATTGAC
* *
54505206 AAACCTTTAACCCTT-AACCTAAAAACCCT
1 AAACC-TTAAACCTTAAACCTTAAAACCCT
* * *
54505235 AACCCTTAAA-TTTAAAACCCT-AAACCCT
1 AAACCTTAAACCTT-AAACCTTAAAACCCT
* * * *
54505263 TAACCTAAAAACCCTAAACCTT-AAACCTT
1 AAACCT-TAAACCTTAAACCTTAAAACCCT
* * *
54505292 AAACCTAAAAACCCTAAACCTT-AAACCTT
1 AAACCT-TAAACCTTAAACCTTAAAACCCT
* *
54505321 AAACCCTAAAACCCTAAACCTTAA
1 AAA-CCTTAAACCTTAAACCTTAA
54505345 CTTTAAAACC
Statistics
Matches: 91, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
27 2 0.02
28 15 0.16
29 69 0.76
30 5 0.05
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.22
Consensus pattern (29 bp):
AAACCTTAAACCTTAAACCTTAAAACCCT
Found at i:54505267 original size:43 final size:43
Alignment explanation
Indices: 54505214--54505860 Score: 487
Period size: 43 Copynumber: 14.8 Consensus size: 43
54505204 ACAAACCTTT
* *
54505214 AACCCTTAACCTAAAAACCCTAACCCTTAAATTTAAAACCCTA
1 AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTA
* *
54505257 AACCCTTAACCTAAAAACCCTAAACCTTAAACCTTAAACCTAAAAACCCTA
1 AACCCTTAACTTAAAAACCCT-AA-C-----CCTTAAA-TTAAAAACCCTA
* * *
54505308 AA-CCTTAAACCTTAAACCCTAAAACCCTAAACCTTAACTTTAAAACCCTA
1 AACCCTT-AA-CTT--A----AAAACCCTAACCCTTAAATTAAAAACCCTA
* *
54505358 AACCCTTAACTTAAAAACCATAAACCCTTAACTTAAAAACCCT-
1 AACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTA
* * ** * *
54505401 AACCCTTAAATTAAAAACCCTAAACCATTAACCTGAAAA-CCTT
1 AACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTA
* ** * * *
54505444 AACCCTTAACCTAAAAACCCTAAATCTTAACTTTAAAACCTTA
1 AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTA
* * * *
54505487 AACCATTAACTTTAAAACCCTAAACCCTTCACTTAAAAACCCT-
1 AACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTA
* * ** *
54505530 AACCCTTAAATTAAAAACCCTAAACCATTAACCTAAAAACCAT-
1 AACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTA
*
54505573 AACCCTTAACTT-AAAA--C---CCC-TAAATCT-CAAACCCTA
1 AACCCTTAACTTAAAAACCCTAACCCTTAAAT-TAAAAACCCTA
* * * * * *
54505609 AA-CCTTAACCTAAAAGCCCTAAACTTTAACTTTAAAACCCTA
1 AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTA
* * * *
54505651 GACCCTTAACTTAAAAACCCTAAACCATTAACTTAAAACCCCT-
1 AACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTA
* * *
54505694 AACCCTTAAATTAAAAATCCTAAACCCTTAAATTAAAAATCCTA
1 AACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTA
* * **
54505738 AACCATTAACCTAAAAACCCTAACCCTTAACCTAAAAACCCTA
1 AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTA
* * * *
54505781 AACCCTTAACTTTAAAACCATAGACCCTTAACTTTAAAACCCTA
1 AACCCTTAACTTAAAAACCCTA-ACCCTTAAATTAAAAACCCTA
* *
54505825 AACTCTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAA
54505861 TATAATTTGA
Statistics
Matches: 487, Mismatches: 82, Indels: 70
0.76 0.13 0.11
Matches are distributed among these distances:
35 17 0.03
36 8 0.02
38 1 0.00
40 1 0.00
41 2 0.00
42 32 0.07
43 250 0.51
44 109 0.22
45 1 0.00
47 1 0.00
49 3 0.01
50 25 0.05
51 24 0.05
52 2 0.00
54 1 0.00
57 2 0.00
58 8 0.02
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (43 bp):
AACCCTTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTA
Found at i:54505275 original size:65 final size:65
Alignment explanation
Indices: 54505214--54505860 Score: 656
Period size: 65 Copynumber: 9.9 Consensus size: 65
54505204 ACAAACCTTT
* * * *
54505214 AACCCTTAACCTAAAAACCCTAACCCTTAAATTTAAAACCCTAAACCCTTAACCTAAAAACCCTA
1 AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
*
54505279 AACCTTAAACCTTAAACCTAAAAACCCTAAACCTTAAACCTTAAACCCTAAAACCCTAAA-CCTT
1 AACC----A--TT-AACCTAAAAACCCTAACCCTT-AA-CTT--A----AAAACCCTAAACCCTT
*
54505343 AACTTTAAAACCCTA
51 AACTTAAAAACCCTA
* * * *
54505358 AACCCTTAACTTAAAAACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCT
1 AACCATTAACCTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT
54505422 A
65 A
* * * * * *
54505423 AACCATTAACCTGAAAACCTTAACCCTTAACCTAAAAACCCTAAA-TCTTAACTTTAAAACCTTA
1 AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * * *
54505487 AACCATTAACTTTAAAACCCTAAACCCTTCACTTAAAAACCCT-AACCCTTAAATTAAAAACCCT
1 AACCATTAACCTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT
54505551 A
65 A
* * *
54505552 AACCATTAACCTAAAAACCATAACCCTTAACTTAAAACCCCTAAA----T--C-T-CAAACCCTA
1 AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * * * *
54505609 AACC-TTAACCTAAAAGCCCTAAACTTTAACTTTAAAACCCTAGACCCTTAACTTAAAAACCCTA
1 AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * * * * *
54505673 AACCATTAACTTAAAACCCCTAACCCTTAAATTAAAAATCCTAAACCCTTAAATTAAAAATCCTA
1 AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * *
54505738 AACCATTAACCTAAAAACCCTAACCCTTAACCTAAAAACCCTAAACCCTTAACTTTAAAACCATA
1 AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
* * * * *
54505803 GACCCTTAACTTTAAAACCCTAAACTCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
1 AACCATTAACCTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
54505861 TATAATTTGA
Statistics
Matches: 480, Mismatches: 71, Indels: 62
0.78 0.12 0.10
Matches are distributed among these distances:
56 33 0.07
57 12 0.03
58 1 0.00
60 1 0.00
61 1 0.00
62 1 0.00
63 1 0.00
64 88 0.18
65 239 0.50
66 19 0.04
69 1 0.00
71 5 0.01
72 34 0.07
73 10 0.02
74 2 0.00
79 21 0.04
80 11 0.02
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (65 bp):
AACCATTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTA
Found at i:54505290 original size:22 final size:21
Alignment explanation
Indices: 54505217--54505286 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
54505207 AACCTTTAAC
*
54505217 CCTTAACCTAAAAACCCTAAC
1 CCTTAACCTAAAAACCCTAAA
** *
54505238 CCTTAAATTTAAAACCCTAAA
1 CCTTAACCTAAAAACCCTAAA
54505259 CCCTTAACCTAAAAACCCTAAA
1 -CCTTAACCTAAAAACCCTAAA
54505281 CCTTAA
1 CCTTAA
54505287 ACCTTAAACC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 23 0.56
22 18 0.44
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (21 bp):
CCTTAACCTAAAAACCCTAAA
Found at i:54505344 original size:22 final size:20
Alignment explanation
Indices: 54505253--54505341 Score: 88
Period size: 22 Copynumber: 4.2 Consensus size: 20
54505243 AATTTAAAAC
* *
54505253 CCTAAACCCTTAACCTAAAAA
1 CCTAAACCCTAAACCT-TAAA
*
54505274 CCCTAAACCTTAAACCTTAAA
1 -CCTAAACCCTAAACCTTAAA
54505295 CCTAAAAACCCTAAACCTTAAA
1 CCT--AAACCCTAAACCTTAAA
*
54505317 CCTTAAACCCTAAAACCCTAAA
1 CC-TAAACCCT-AAACCTTAAA
54505339 CCT
1 CCT
54505342 TAACTTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.05
21 11 0.19
22 43 0.74
23 1 0.02
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (20 bp):
CCTAAACCCTAAACCTTAAA
Found at i:54505353 original size:29 final size:29
Alignment explanation
Indices: 54505249--54505372 Score: 143
Period size: 29 Copynumber: 4.3 Consensus size: 29
54505239 CTTAAATTTA
*
54505249 AAACCCTAAACCCTT-AA-CCTAAAAACCCT
1 AAACCTTAAA-CCTTAAACCCT-AAAACCCT
54505278 AAACCTTAAACCTTAAA-CCTAAAAACCCT
1 AAACCTTAAACCTTAAACCCT-AAAACCCT
54505307 AAACCTTAAACCTTAAACCCTAAAACCCT
1 AAACCTTAAACCTTAAACCCTAAAACCCT
*
54505336 AAACCTT-AACTTTAAAACCCT-AAACCCT
1 AAACCTTAAACCTT-AAACCCTAAAACCCT
*
54505364 TAA-CTTAAA
1 AAACCTTAAA
54505373 AACCATAAAC
Statistics
Matches: 88, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
27 3 0.03
28 20 0.23
29 62 0.70
30 3 0.03
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (29 bp):
AAACCTTAAACCTTAAACCCTAAAACCCT
Found at i:54505364 original size:22 final size:22
Alignment explanation
Indices: 54505328--54505860 Score: 503
Period size: 22 Copynumber: 24.1 Consensus size: 22
54505318 CTTAAACCCT
*
54505328 AAAACCCTAAA-CCTTAACTTT
1 AAAACCCTAAACCCTTAACTTA
54505349 AAAACCCTAAACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
*
54505371 AAAACCATAAACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
*
54505393 AAAACCCT-AACCCTTAAATTA
1 AAAACCCTAAACCCTTAACTTA
* * *
54505414 AAAACCCTAAACCATTAACCTG
1 AAAACCCTAAACCCTTAACTTA
* *
54505436 AAAA-CCTTAACCCTTAACCTA
1 AAAACCCTAAACCCTTAACTTA
* *
54505457 AAAACCCTAAA-TCTTAACTTT
1 AAAACCCTAAACCCTTAACTTA
* * *
54505478 AAAACCTTAAACCATTAACTTT
1 AAAACCCTAAACCCTTAACTTA
*
54505500 AAAACCCTAAACCCTTCACTTA
1 AAAACCCTAAACCCTTAACTTA
*
54505522 AAAACCCT-AACCCTTAAATTA
1 AAAACCCTAAACCCTTAACTTA
* *
54505543 AAAACCCTAAACCATTAACCTA
1 AAAACCCTAAACCCTTAACTTA
*
54505565 AAAACCAT-AACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
* * * *
54505586 AAACCCCTAAA-TCTCAAACCCTA
1 AAAACCCTAAACCCT-TAA-CTTA
*
54505609 AACCTTAA-CCTAAAAGCCCTAAACTTTA
1 AA----AACCCT-AAA-CCCTTAAC-TTA
* * *
54505637 ACTTTAAAACCCTAGACCCTTAACTTA
1 A----AAACCCT-AAACCCTTAACTTA
*
54505664 AAAACCCTAAACCATTAACTTA
1 AAAACCCTAAACCCTTAACTTA
* *
54505686 AAACCCCT-AACCCTTAAATTA
1 AAAACCCTAAACCCTTAACTTA
* *
54505707 AAAATCCTAAACCCTTAAATTA
1 AAAACCCTAAACCCTTAACTTA
* * *
54505729 AAAATCCTAAACCATTAACCTA
1 AAAACCCTAAACCCTTAACTTA
*
54505751 AAAACCCT-AACCCTTAACCTA
1 AAAACCCTAAACCCTTAACTTA
*
54505772 AAAACCCTAAACCCTTAACTTT
1 AAAACCCTAAACCCTTAACTTA
* * *
54505794 AAAACCATAGACCCTTAACTTT
1 AAAACCCTAAACCCTTAACTTA
*
54505816 AAAACCCTAAACTCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
54505838 AAAACCCT-AACCCTTAACTTA
1 AAAACCCTAAACCCTTAACTTA
54505859 AA
1 AA
54505861 TATAATTTGA
Statistics
Matches: 424, Mismatches: 65, Indels: 46
0.79 0.12 0.09
Matches are distributed among these distances:
21 155 0.37
22 225 0.53
23 10 0.02
26 3 0.01
27 9 0.02
28 15 0.04
29 6 0.01
32 1 0.00
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (22 bp):
AAAACCCTAAACCCTTAACTTA
Found at i:54505495 original size:8 final size:7
Alignment explanation
Indices: 54505249--54505366 Score: 87
Period size: 7 Copynumber: 16.3 Consensus size: 7
54505239 CTTAAATTTA
*
54505249 AAACCCT
1 AAACCTT
54505256 AAACCCTT
1 AAA-CCTT
*
54505264 -AACCTAA
1 AAACCT-T
*
54505271 AAACCCT
1 AAACCTT
54505278 AAACCTT
1 AAACCTT
54505285 AAACCTT
1 AAACCTT
*
54505292 AAACCTAA
1 AAACCT-T
*
54505300 AAACCCT
1 AAACCTT
54505307 AAACCTT
1 AAACCTT
54505314 AAACCTT
1 AAACCTT
*
54505321 AAACCCTA
1 AAA-CCTT
*
54505329 AAACCCT
1 AAACCTT
54505336 AAACCTT
1 AAACCTT
*
54505343 -AACTTT
1 AAACCTT
*
54505349 AAAACCCT
1 -AAACCTT
54505357 AAACCCTT
1 AAA-CCTT
54505365 AA
1 AA
54505367 CTTAAAAACC
Statistics
Matches: 86, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
6 8 0.09
7 51 0.59
8 27 0.31
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCTT
Found at i:54509286 original size:126 final size:124
Alignment explanation
Indices: 54509031--54509592 Score: 687
Period size: 126 Copynumber: 4.5 Consensus size: 124
54509021 CCAAACATGT
* * **
54509031 TACTGTAGAAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
1 TACTGTAGCAAAAGCGCATCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* * * * * *
54509096 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCTAGGACC
66 TGAAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACC
* *
54509155 AACTGTAGCAAAAGCGCATCCACGAT-GGCACGATTTCACAAATTCTTCTCA-AATAGCATGCTG
1 TACTGTAGCAAAAGCGCATCCACG-TGGGCACGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * * *
54509218 CTTGCAGCGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACC
64 CTTGAAGCG-T-TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACC
* * * * *
54509281 TACTGTAGCAAAAGCGCATCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGTATCATGCT
1 TACTGTAGCAAAAGCGCATCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* *
54509346 TGAAGCATTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAAGACC
66 TGAAGC-GTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAAGACC
* * ** * * * *
54509407 AACTGTAGTAAAAGCGCGCCCACGAGGGCATGATTTCACAAATTCTTCTCACAAAACATCCTGCT
1 TACTGTAGCAAAAGCGCATCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
*
54509472 TGAAGCGTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACC
66 TGAAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACC
* * * * * * * *
54509531 TACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCCT
1 TACTGTAGCAAAAGCGCATCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCT
54509593 ACTTTGATTT
Statistics
Matches: 374, Mismatches: 56, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
123 2 0.01
124 118 0.32
125 80 0.21
126 172 0.46
127 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (124 bp):
TACTGTAGCAAAAGCGCATCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
TGAAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACC
Found at i:54509492 original size:250 final size:250
Alignment explanation
Indices: 54509031--54509590 Score: 777
Period size: 250 Copynumber: 2.2 Consensus size: 250
54509021 CCAAACATGT
* * * *
54509031 TACTGTAGAAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCATGCT
* * * * *
54509096 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCTAGGACCAACTGT
66 AGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAAGACCAACTGT
* * * * *
54509161 AGCAAAAGCGCATCCACGATGGCACGATTTCACAAATTCTTCTCAAATAGCATGCTGCTTGCAGC
131 AGCAAAAGCGCACCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAACATCCTGCTTGAAGC
* * *
54509226 GTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACC
196 GTTATTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACC
* * *
54509281 TACTGTAGCAAAAGCGCATCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGTATCATGCT
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCATGCT
*
54509346 TGAAGC-ATTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAAGACCAAC
66 AGAAGCGA--TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTT-TTCCAAGACCAAC
* * *
54509410 TGTAGTAAAAGCGCGCCCACGAGGGCATGATTTCACAAATTCTTCTCACAA-AACATCCTGCTTG
128 TGTAGCAAAAGCGCACCCACGAGGGCACGATTTCACAAATTCTTCTCA-AATAACATCCTGCTTG
* *
54509474 AAGCG-T-TTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACC
192 AAGCGTTATTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACC
* * * * *
54509531 TACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATC
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATC
54509591 CTACTTTGAT
Statistics
Matches: 273, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
249 1 0.00
250 162 0.59
251 39 0.14
252 69 0.25
253 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (250 bp):
TACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCATGCT
AGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAAGACCAACTGT
AGCAAAAGCGCACCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAACATCCTGCTTGAAGC
GTTATTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACC
Found at i:54532161 original size:62 final size:57
Alignment explanation
Indices: 54532048--54532222 Score: 147
Period size: 62 Copynumber: 2.9 Consensus size: 57
54532038 TTTGTGAGAT
* * * * * *
54532048 TAATAAAAATTTTCAAAAATTTTAAGAGAGCTTAATTAAATTCTTTAAAAAATTAAAAGGTA
1 TAATAAGAATTTTTAAAAATTTT-AG-GGGCCTAATTAAATTTTTTTAAAAATT--AA-GTA
54532110 TAATAAGAATTTTTAAAAATTTTGAGGGGCCTAATTAAATTTTTTTTAAAAAGTTAAGTA
1 TAATAAGAATTTTTAAAAATTTT-AGGGGCCTAATTAAA-TTTTTTTAAAAA-TTAAGTA
* * * *
54532170 -AAAAATGAAATTTTTTAAAAAATTTAGGGACCTAATTAAA-GTTTTTAAAAATT
1 TAATAA-G-AA-TTTTTAAAAATTTTAGGGGCCTAATTAAATTTTTTTAAAAATT
54532223 TTAAGGGAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 14 0.14
60 4 0.04
61 29 0.30
62 46 0.47
63 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.38
Consensus pattern (57 bp):
TAATAAGAATTTTTAAAAATTTTAGGGGCCTAATTAAATTTTTTTAAAAATTAAGTA
Found at i:54532215 original size:31 final size:31
Alignment explanation
Indices: 54532048--54532230 Score: 97
Period size: 30 Copynumber: 5.9 Consensus size: 31
54532038 TTTGTGAGAT
* * * * * *
54532048 TAATAAAAATTTTCAAAAATTTTAAGAGAGCT
1 TAATTAAATTTTTTAAAAAATTTAAGGGA-CC
* * *
54532080 TAATTAAATTCTTTAAAAAATTAAAAGGTA--
1 TAATTAAATTTTTTAAAAAATT-TAAGGGACC
* * * *
54532110 TAA-TAAGAATTTTTAAAAATTTTGAGGGGCC
1 TAATTAA-ATTTTTTAAAAAATTTAAGGGACC
* * * **
54532141 TAATTAAATTTTTTTTAAAAAGTTAA-GTAAA
1 TAATTAAA-TTTTTTAAAAAATTTAAGGGACC
* *
54532172 AAATGAAATTTTTTAAAAAATTT-AGGGACC
1 TAATTAAATTTTTTAAAAAATTTAAGGGACC
* *
54532202 TAATTAAAGTTTTTAAAAATTTTAAGGGA
1 TAATTAAATTTTTTAAAAAATTTAAGGGA
54532231 AAAATAAAAA
Statistics
Matches: 108, Mismatches: 35, Indels: 17
0.68 0.22 0.11
Matches are distributed among these distances:
29 7 0.06
30 49 0.45
31 16 0.15
32 32 0.30
33 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (31 bp):
TAATTAAATTTTTTAAAAAATTTAAGGGACC
Found at i:54532234 original size:61 final size:61
Alignment explanation
Indices: 54532119--54532235 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
54532109 ATAATAAGAA
* * * *
54532119 TTTTTAAAAATTTTGAGGGGCCTAATTAAATTTTTTTTAAAAAGTTAAGTAAAAAATGAAAT
1 TTTTTAAAAAATTTGAGGGACCTAATTAAA-TGTTTTTAAAAAGTTAAGGAAAAAATGAAAT
* *
54532181 TTTTTAAAAAATTT-AGGGACCTAATTAAA-GTTTTTAAAAATTTTAAGGGAAAAAT
1 TTTTTAAAAAATTTGAGGGACCTAATTAAATGTTTTTAAAAA-GTTAAGGAAAAAAT
54532236 AAAAAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 10 0.21
60 11 0.23
61 14 0.29
62 13 0.27
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.39
Consensus pattern (61 bp):
TTTTTAAAAAATTTGAGGGACCTAATTAAATGTTTTTAAAAAGTTAAGGAAAAAATGAAAT
Found at i:54532238 original size:29 final size:28
Alignment explanation
Indices: 54532152--54532238 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 28
54532142 AATTAAATTT
* ** *
54532152 TTTTTAAAAAGTTAAGTAAAAAATGAAAT
1 TTTTTAAAAATTTAAGGGAAAAAT-AAAG
* *
54532181 TTTTTAAAAAATTT-AGGGACCTAATTAAAG
1 TTTTT-AAAAATTTAAGGGA--AAAATAAAG
54532211 TTTTTAAAAATTTTAAGGGAAAAATAAA
1 TTTTTAAAAA-TTTAAGGGAAAAATAAA
54532239 AAAATTTCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
29 19 0.42
30 18 0.40
31 8 0.18
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (28 bp):
TTTTTAAAAATTTAAGGGAAAAATAAAG
Found at i:54533417 original size:15 final size:17
Alignment explanation
Indices: 54533391--54533422 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54533381 TAACTAAGGT
54533391 TTGGGACATA-TTGGAG
1 TTGGGACATATTTGGAG
54533407 TTGGG-CATATTTGGAG
1 TTGGGACATATTTGGAG
54533423 AGAGTTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.22, C:0.06, G:0.38, T:0.34
Consensus pattern (17 bp):
TTGGGACATATTTGGAG
Found at i:54533621 original size:12 final size:12
Alignment explanation
Indices: 54533583--54533622 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54533573 GAATTCAAAA
54533583 GATGAAAG-CTT
1 GATGAAAGACTT
54533594 GATTGAAA-ACTT
1 GA-TGAAAGACTT
54533606 GATGAAAGACTT
1 GATGAAAGACTT
54533618 GATGA
1 GATGA
54533623 TTAAATGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (12 bp):
GATGAAAGACTT
Found at i:54534961 original size:14 final size:14
Alignment explanation
Indices: 54534942--54534981 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
54534932 TTGATTGGCA
54534942 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
54534956 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
54534970 GGAAAATGTTTT
1 GTAAAATGTTTT
54534982 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:54534994 original size:34 final size:35
Alignment explanation
Indices: 54534950--54535016 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
54534940 CAGTAAAATG
* *
54534950 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
54534984 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
54535017 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:54535003 original size:20 final size:20
Alignment explanation
Indices: 54534965--54535004 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54534955 CGTAAAATGA
**
54534965 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
54534985 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
54535005 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:54536393 original size:27 final size:27
Alignment explanation
Indices: 54536363--54536432 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
54536353 AATAATCAAT
*
54536363 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
54536390 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
54536418 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
54536433 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:54546870 original size:15 final size:17
Alignment explanation
Indices: 54546844--54546875 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54546834 TAACTAAGGT
54546844 TTGGGACATA-TTGGAG
1 TTGGGACATATTTGGAG
54546860 TTGGG-CATATTTGGAG
1 TTGGGACATATTTGGAG
54546876 AGAGTTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.22, C:0.06, G:0.38, T:0.34
Consensus pattern (17 bp):
TTGGGACATATTTGGAG
Found at i:54547073 original size:12 final size:12
Alignment explanation
Indices: 54547035--54547074 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54547025 GAATTCAAAA
54547035 GATGAAAG-CTT
1 GATGAAAGACTT
54547046 GATTGAAA-ACTT
1 GA-TGAAAGACTT
54547058 GATGAAAGACTT
1 GATGAAAGACTT
54547070 GATGA
1 GATGA
54547075 TTAAATGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (12 bp):
GATGAAAGACTT
Found at i:54548046 original size:30 final size:30
Alignment explanation
Indices: 54548010--54548072 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
54548000 TTTTGTTATC
54548010 TTGTACTTGTTGATTGCATGATTGGTTGAA
1 TTGTACTTGTTGATTGCATGATTGGTTGAA
54548040 TTGTACTTGTTGATTGCATGATTGGTTGAA
1 TTGTACTTGTTGATTGCATGATTGGTTGAA
54548070 TTG
1 TTG
54548073 GATATGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.06, G:0.27, T:0.48
Consensus pattern (30 bp):
TTGTACTTGTTGATTGCATGATTGGTTGAA
Found at i:54550764 original size:20 final size:21
Alignment explanation
Indices: 54550728--54550766 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54550718 CAAAATCATA
*
54550728 TGATTTATCAAACTAAAAATT
1 TGATTTATCAAAATAAAAATT
54550749 TGATTT-TCAAAATAAAAA
1 TGATTTATCAAAATAAAAA
54550767 CTCTAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (21 bp):
TGATTTATCAAAATAAAAATT
Found at i:54552038 original size:27 final size:28
Alignment explanation
Indices: 54551993--54552052 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
54551983 TTTAAAAATT
54551993 ATAAAAATATTCCAAAAATTTTCAAAAA
1 ATAAAAATATTCCAAAAATTTTCAAAAA
*
54552021 ATAAAAATATT-CATAAATTTTCAAAAA
1 ATAAAAATATTCCAAAAATTTTCAAAAA
54552048 A-AAAA
1 ATAAAA
54552053 TCCCATGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 4 0.13
27 16 0.52
28 11 0.35
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAAAAATATTCCAAAAATTTTCAAAAA
Found at i:54558498 original size:63 final size:63
Alignment explanation
Indices: 54558399--54558525 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
54558389 TATTTTACCC
54558399 ATGGTTTTCAAAACTAAACTAGATTAGCTGATTGAATTGATTGACTGAGAACATGGTCAAACT
1 ATGGTTTTCAAAACTAAACTAGATTAGCTGATTGAATTGATTGACTGAGAACATGGTCAAACT
54558462 ATGGTTTTCAAAACTAAACTAGATTAGCTGATTGAATTGATTGACTGAGAACATGGTCAAACT
1 ATGGTTTTCAAAACTAAACTAGATTAGCTGATTGAATTGATTGACTGAGAACATGGTCAAACT
54558525 A
1 A
54558526 GTTTAATAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (63 bp):
ATGGTTTTCAAAACTAAACTAGATTAGCTGATTGAATTGATTGACTGAGAACATGGTCAAACT
Found at i:54561325 original size:17 final size:17
Alignment explanation
Indices: 54561303--54561337 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54561293 ACTTTCTTTC
54561303 TTTCTCTCTTCTTCTCA
1 TTTCTCTCTTCTTCTCA
54561320 TTTCTCTCTTCTTCTCA
1 TTTCTCTCTTCTTCTCA
54561337 T
1 T
54561338 GTTGGATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTCTCTCTTCTTCTCA
Found at i:54569162 original size:30 final size:30
Alignment explanation
Indices: 54569128--54569185 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54569118 TTTTCAACCC
* *
54569128 AACATATATATAAG-CAAAATTATAATTATT
1 AACATATACAGAAGACAAAATT-TAATTATT
*
54569158 AACATTTACAGAAGACAAAATTTAATTA
1 AACATATACAGAAGACAAAATTTAATTA
54569186 AATCCATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (30 bp):
AACATATACAGAAGACAAAATTTAATTATT
Found at i:54569616 original size:21 final size:21
Alignment explanation
Indices: 54569590--54569767 Score: 112
Period size: 21 Copynumber: 8.5 Consensus size: 21
54569580 ACGGACGCTG
*
54569590 AACAGAAGCTCATGAGAGTTA
1 AACAGAAGCTCATAAGAGTTA
* * * *
54569611 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
54569632 AAC-GAAAGCTCATAAGAGTTA
1 AACAG-AAGCTCATAAGAGTTA
* * * *
54569653 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
* * **
54569674 AACAAAATCTTGTAAGAGCTT-
1 AACAGAAGCTCATAAGAG-TTA
* *
54569695 AACAGAAACCCATAA-AGGTTA
1 AACAGAAGCTCATAAGA-GTTA
* * *
54569716 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGTTA
* *
54569737 AA-AGAAAACTCATATGAGTTA
1 AACAG-AAGCTCATAAGAGTTA
54569758 AACAGAAGCT
1 AACAGAAGCT
54569768 TGTGAGAGCT
Statistics
Matches: 114, Mismatches: 35, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
20 6 0.05
21 102 0.89
22 6 0.05
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGTTA
Found at i:54569734 original size:42 final size:42
Alignment explanation
Indices: 54569590--54569767 Score: 182
Period size: 42 Copynumber: 4.2 Consensus size: 42
54569580 ACGGACGCTG
* *
54569590 AACAGAAGCTCATGAGAGTTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTAAACAGAAACCCATAAGGGTTA
*
54569632 AAC-GAAAGCTCATAAGAGTTAAACAGAAACCCATAAGGGTTG
1 AACAG-AAGCTCATAAGAGTTAAACAGAAACCCATAAGGGTTA
* * ** *
54569674 AACAAAATCTTGTAAGAGCTT-AACAGAAACCCATAAAGGTTA
1 AACAGAAGCTCATAAGAG-TTAAACAGAAACCCATAAGGGTTA
* * * * * *
54569716 AACAGAAGCTCAAAAGAGCTGAA-AGAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGTTAAACAG-AAACCCATAAGGGTTA
54569758 AACAGAAGCT
1 AACAGAAGCT
54569768 TGTGAGAGCT
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.04
42 108 0.95
43 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGTTAAACAGAAACCCATAAGGGTTA
Found at i:54569770 original size:84 final size:84
Alignment explanation
Indices: 54569604--54569786 Score: 199
Period size: 84 Copynumber: 2.2 Consensus size: 84
54569594 GAAGCTCATG
* * * * *
54569604 AGAGTTAAACAGAAACCCATAAGGGTTGAACGAAAGCTCATAAGAGTTAAACAGAAACCCATAAG
1 AGAGCTAAACAGAAACCCATAAAGGTTAAACGAAAGCTCAAAAGAGTGAAACAGAAACCCATAAG
* * *
54569669 GGTTGAACAAAATCTTGTA
66 AGTTAAACAAAAGCTTGTA
* * *
54569688 AGAGCTTAACAGAAACCCATAAAGGTTAAAC-AGAAGCTCAAAAGAGCTGAAAGA-AAACTCATA
1 AGAGCTAAACAGAAACCCATAAAGGTTAAACGA-AAGCTCAAAAGAG-TGAAACAGAAACCCATA
* * *
54569751 TGAGTTAAACAGAAGCTTGTG
64 AGAGTTAAACAAAAGCTTGTA
*
54569772 AGAGCTAAACGGAAA
1 AGAGCTAAACAGAAA
54569787 ATAAACACTA
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
83 1 0.01
84 75 0.93
85 5 0.06
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (84 bp):
AGAGCTAAACAGAAACCCATAAAGGTTAAACGAAAGCTCAAAAGAGTGAAACAGAAACCCATAAG
AGTTAAACAAAAGCTTGTA
Found at i:54572490 original size:17 final size:17
Alignment explanation
Indices: 54572468--54572501 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54572458 TGCTAATATC
54572468 TCTTTCAAGCATAAGAG
1 TCTTTCAAGCATAAGAG
*
54572485 TCTTTCGAGCATAAGAG
1 TCTTTCAAGCATAAGAG
54572502 CAATTGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (17 bp):
TCTTTCAAGCATAAGAG
Found at i:54573216 original size:25 final size:27
Alignment explanation
Indices: 54573182--54573232 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
54573172 ATATTATTAA
54573182 TATAATATA-TAA-ATGTTATAATAAG
1 TATAATATATTAATATGTTATAATAAG
54573207 TATAATATATTAATATGTTATAATAA
1 TATAATATATTAATATGTTATAATAA
54573233 ACATTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
26 3 0.12
27 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
TATAATATATTAATATGTTATAATAAG
Found at i:54574176 original size:43 final size:43
Alignment explanation
Indices: 54574114--54574243 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 43
54574104 CATAGGATTT
**
54574114 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGTTTAAGTGTAAGACCACGTCTGGGACGTTGGCA
* * *
54574157 TCGATTTGTGTTTAAGTGTAAGACC-CTGTCTGGGACAG-CGACA
1 TCGATATGTGTTTAAGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* * * *
54574200 TCGATCTGAGATTACA-TGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGTTTA-AGTGTAAGACCACGTCTGGGACGTTGGCA
54574243 T
1 T
54574244 TGTATGAGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.01
43 67 0.94
44 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
TCGATATGTGTTTAAGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:54579090 original size:98 final size:98
Alignment explanation
Indices: 54578975--54579169 Score: 372
Period size: 98 Copynumber: 2.0 Consensus size: 98
54578965 TAAAAAATAA
* *
54578975 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
54579040 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
54579073 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
54579138 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
54579170 AGTTTTATTG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:54584188 original size:6 final size:6
Alignment explanation
Indices: 54584177--54584228 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
54584167 TGAAAGTGAT
54584177 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
54584225 AAAA
1 AAAA
54584229 TAAAATGGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:54585844 original size:217 final size:217
Alignment explanation
Indices: 54585469--54585928 Score: 762
Period size: 217 Copynumber: 2.1 Consensus size: 217
54585459 GGAGCAAATC
* **
54585469 GAAGATGGCAAGTCTTATC-CTCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCT
1 GAAGATGGCAAGTCTTATCTC-CCTAAAGTTACAAAGGAGCAGATTAAAGCCGATAATCCTATCT
* * * *
54585533 CCCTGAAGTTGCATTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGTAG
65 CCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAGAGCAC
54585598 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTC
130 ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTC
*
54585663 CTGAAGTTGCAGTGGGGCAGACT
195 CTGAAGTTGCAGTGAGGCAGACT
*
54585686 GAAGATGGCAAGTCTTATCTCCCTGAAGTTACAAAGGAGCAGATTAAAGCCGATAATCCTATCTC
1 GAAGATGGCAAGTCTTATCTCCCTAAAGTTACAAAGGAGCAGATTAAAGCCGATAATCCTATCTC
54585751 CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAGAGCACA
66 CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAGAGCACA
* *
54585816 TTGCATTTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
131 TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
54585881 TGAAGTTGCAGTGAGGCAGACT
196 TGAAGTTGCAGTGAGGCAGACT
* **
54585903 AAAGATTTC-AGATCTTATCTCCCTAA
1 GAAGATGGCAAG-TCTTATCTCCCTAA
54585929 GCAGTAGTGG
Statistics
Matches: 226, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
216 2 0.01
217 223 0.99
218 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
GAAGATGGCAAGTCTTATCTCCCTAAAGTTACAAAGGAGCAGATTAAAGCCGATAATCCTATCTC
CCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTAAAGTTGCAGAGAGCACA
TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCC
TGAAGTTGCAGTGAGGCAGACT
Found at i:54585874 original size:84 final size:85
Alignment explanation
Indices: 54585607--54585891 Score: 231
Period size: 89 Copynumber: 3.3 Consensus size: 85
54585597 GATCGCATCT
* * * * *
54585607 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AGTCTTATC-CTCCTGAAGT
1 AGTCTTATCTCTCTGAAGTTGCAGAGGAGCACA-TTAG-CAG-ATAGTCTTATCTC-CCTGAAGT
* *
54585670 TGCAGTGGGGCAGACTGAAGATGGCA
62 TGCAGTGGAGCAGACT-AAGA-AGCA
* * * * * * *
54585696 AGTCTTATCTCCCTGAAGTTACAAAGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AGTCTTATCTCTCTGAAGTTGCAGAGGAGCACATT--AGCAGATAGTCTTATCTCCCTGAAGTTG
* * * *
54585761 CAGTGGAGCGGATTAA-AACCTC
64 CAGTGGAGCAGACTAAGAAGC-A
* **
54585783 AGATCTTATCTCTCTAAAGTTGCAGA-GAGCACATT-GCATTTAGTCTTATCTCCCTGAAGTTGC
1 AG-TCTTATCTCTCTGAAGTTGCAGAGGAGCACATTAGCAGATAGTCTTATCTCCCTGAAGTTGC
54585846 AGTGGAGCAGACTAAGTAAGCA
65 AGTGGAGCAGACTAAG-AAGCA
54585868 AGTCTTATC-CTCCTGAAGTTGCAG
1 AGTCTTATCTCT-CTGAAGTTGCAG
54585892 TGAGGCAGAC
Statistics
Matches: 158, Mismatches: 29, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
83 2 0.01
84 54 0.34
85 2 0.01
86 4 0.03
87 11 0.07
88 23 0.15
89 59 0.37
90 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (85 bp):
AGTCTTATCTCTCTGAAGTTGCAGAGGAGCACATTAGCAGATAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTAAGAAGCA
Found at i:54585876 original size:44 final size:43
Alignment explanation
Indices: 54585476--54585904 Score: 251
Period size: 44 Copynumber: 9.9 Consensus size: 43
54585466 ATCGAAGATG
* *
54585476 GCAAGTCTTATC-CTCCTAAAGTTGCAGTGGAGCAGA-TTA-AA
1 GCAAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAGAA
* * * * *
54585517 GCCGATAATCCTATCTCCCTGAAGTTGCATTGGAGCGGATTAA-AA
1 G-C-A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA
* * * * * * *
54585562 CCTCAGATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T-CGCA
1 GC-AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA
* *
54585604 TCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 GCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AA
* *
54585648 GCAAGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATG
1 GCAAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGA-A
* ** *
54585693 GCAAGTCTTATCTCCCTGAAGTTACAAAGGAGCAGA-TTA-AA
1 GCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA
* * * *
54585734 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AA
1 G-C-A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA
* * * * * * * *
54585779 CCTCAGATCTTATCTCTCTAAAGTTGCAG-AGAGCACA-T-TGCA
1 GC-AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA
***
54585821 TTTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA
1 GCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AA
54585865 GCAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAA
1 GCAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAA
54585905 AGATTTCAGA
Statistics
Matches: 295, Mismatches: 66, Indels: 51
0.72 0.16 0.12
Matches are distributed among these distances:
40 41 0.14
41 18 0.06
42 10 0.03
43 21 0.07
44 162 0.55
45 42 0.14
46 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
GCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA
Found at i:54587441 original size:98 final size:98
Alignment explanation
Indices: 54587326--54587520 Score: 372
Period size: 98 Copynumber: 2.0 Consensus size: 98
54587316 TAAAAAATAA
* *
54587326 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
54587391 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
54587424 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
54587489 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
54587521 AGTTTTATTG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:54589305 original size:45 final size:45
Alignment explanation
Indices: 54589229--54589350 Score: 131
Period size: 45 Copynumber: 2.7 Consensus size: 45
54589219 TAATCAGTAA
* * * * *
54589229 CGGTAGCAATAACAGTAACAATATTCAACACACAATGTG-CTGAAT
1 CGGTAACAATAACAGTAACAGTAGTCGACACACAAAGTGTC-GAAT
* * *
54589274 CTGTAACAATAACGGTTACAGTA-TCCGACACACAAAGTGTCGAAT
1 CGGTAACAATAACAGTAACAGTAGT-CGACACACAAAGTGTCGAAT
*
54589319 CGGTAACAGTAACAGTAACAGTAGTCGACACA
1 CGGTAACAATAACAGTAACAGTAGTCGACACA
54589351 TAAGTGCCTG
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
44 1 0.02
45 60 0.95
46 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (45 bp):
CGGTAACAATAACAGTAACAGTAGTCGACACACAAAGTGTCGAAT
Found at i:54590046 original size:19 final size:19
Alignment explanation
Indices: 54590011--54590065 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
54590001 CTTTACTTTA
* *
54590011 TATT-ATAATAATATAATT
1 TATTAATAATCATTTAATT
54590029 TATTAATAATCATTTAATT
1 TATTAATAATCATTTAATT
* * *
54590048 AATAAAT-ATCTTTTAATT
1 TATTAATAATCATTTAATT
54590066 ATAACACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATAATCATTTAATT
Found at i:54590297 original size:3 final size:3
Alignment explanation
Indices: 54590289--54590328 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
54590279 AATTTATTCC
*
54590289 ATA ATA ATA ATG ATA ATA ATA AT- ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54590329 TGCAACAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:54590523 original size:24 final size:23
Alignment explanation
Indices: 54590470--54590534 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
54590460 ACATATTTTG
*
54590470 ATTT-ATTTAATAATATAATATC
1 ATTTAATTTAATTATATAATATC
54590492 ATTATAATTTAATTATCATAA-ATTC
1 ATT-TAATTTAATTAT-ATAATA-TC
*
54590517 ATTTAATATAAATTATAT
1 ATTTAAT-TTAATTATAT
54590535 TTAAATATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 3 0.08
23 1 0.03
24 16 0.44
25 16 0.44
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAATTTAATTATATAATATC
Found at i:54591890 original size:17 final size:18
Alignment explanation
Indices: 54591853--54591893 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54591843 CTATTTCCAA
*
54591853 AAATAAATATTATTTATT
1 AAATAAATATTATTAATT
*
54591871 AAATTAATATT-TTAATT
1 AAATAAATATTATTAATT
54591888 AAATAA
1 AAATAA
54591894 TTTTCTCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAATATTATTAATT
Found at i:54592886 original size:23 final size:23
Alignment explanation
Indices: 54592855--54592906 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
54592845 GTCCAATGTA
*
54592855 TTGTTAGTCCAGTCAGTCACATC
1 TTGTCAGTCCAGTCAGTCACATC
54592878 TTGTCAGTCCAGTCAGTCACATC
1 TTGTCAGTCCAGTCAGTCACATC
54592901 TATGTC
1 T-TGTC
54592907 TCTATCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (23 bp):
TTGTCAGTCCAGTCAGTCACATC
Found at i:54597090 original size:18 final size:17
Alignment explanation
Indices: 54597059--54597092 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54597049 TTATCTTGTA
*
54597059 TTTTTTGTTGTTTTTAT
1 TTTTTTGTTATTTTTAT
54597076 TTTTTTGTATATTTTTA
1 TTTTTTGT-TATTTTTA
54597093 ATTAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTTTGTTATTTTTAT
Found at i:54599361 original size:25 final size:27
Alignment explanation
Indices: 54599302--54599362 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
54599292 AATTAACAAC
54599302 ATATTATAACTTTTTTTATTTACCAAA
1 ATATTATAACTTTTTTTATTTACCAAA
54599329 ATATTATAA-TTTTTTTATTTACCAAA
1 ATATTATAACTTTTTTTATTTACCAAA
54599355 ATA-TATAA
1 ATATTATAA
54599363 AAAAAGACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 5 0.15
26 20 0.59
27 9 0.26
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (27 bp):
ATATTATAACTTTTTTTATTTACCAAA
Found at i:54599483 original size:27 final size:27
Alignment explanation
Indices: 54599410--54599467 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
54599400 CCTTGGTCAG
54599410 GCCAAAGCCATTGGCGGCACCAAAGGT
1 GCCAAAGCCATTGGCGGCACCAAAGGT
*
54599437 GCCAAAGCCATTGGCGGCACCAATGGT
1 GCCAAAGCCATTGGCGGCACCAAAGGT
54599464 GCCA
1 GCCA
54599468 TACTGATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.12
Consensus pattern (27 bp):
GCCAAAGCCATTGGCGGCACCAAAGGT
Found at i:54599635 original size:9 final size:9
Alignment explanation
Indices: 54599623--54599702 Score: 56
Period size: 9 Copynumber: 8.8 Consensus size: 9
54599613 TAATTGATTA
54599623 TATTGTTGT
1 TATTGTTGT
*
54599632 TATTGTTTT
1 TATTGTTGT
*
54599641 GTATAGTT-T
1 -TATTGTTGT
*
54599650 TAGTTAG-TAT
1 TA-TT-GTTGT
54599660 TATTGTTGT
1 TATTGTTGT
*
54599669 TGTTGTTGT
1 TATTGTTGT
*
54599678 TGTTGTTGT
1 TATTGTTGT
*
54599687 TGTTGTTGT
1 TATTGTTGT
*
54599696 TGTTGTT
1 TATTGTT
54599703 AGTATTAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
8 3 0.05
9 48 0.79
10 10 0.16
ACGTcount: A:0.10, C:0.00, G:0.25, T:0.65
Consensus pattern (9 bp):
TATTGTTGT
Found at i:54599668 original size:3 final size:3
Alignment explanation
Indices: 54599662--54599702 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54599652 GTTAGTATTA
54599662 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
54599703 AGTATTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:54605561 original size:27 final size:27
Alignment explanation
Indices: 54605519--54605574 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
54605509 TTAGCCACAT
*
54605519 ATTGGTGCCGCCTTTTCATTCCGCTCC
1 ATTGGTGCCGCCTTTTCATTCCCCTCC
* *
54605546 ATTGGTGCCGCTTTTTTATTCCCCTCC
1 ATTGGTGCCGCCTTTTCATTCCCCTCC
54605573 AT
1 AT
54605575 CACCCTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (27 bp):
ATTGGTGCCGCCTTTTCATTCCCCTCC
Found at i:54606323 original size:29 final size:30
Alignment explanation
Indices: 54606274--54606341 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
54606264 ATTACCTTTT
*
54606274 TTTTTCTTTTTTTTCCTTCC-TTCCATCTTC
1 TTTTTCTTTTTATTCCTTCCTTTCC-TCTTC
54606304 TTTTTCTTTTCTATT-C-TCCTTTCCTCTTC
1 TTTTTCTTTT-TATTCCTTCCTTTCCTCTTC
*
54606333 TTCTTCTTT
1 TTTTTCTTT
54606342 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 16 0.47
30 15 0.44
31 3 0.09
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTTCTTTTTATTCCTTCCTTTCCTCTTC
Found at i:54606352 original size:38 final size:41
Alignment explanation
Indices: 54606304--54606391 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 41
54606294 TTCCATCTTC
54606304 TTTTTCTTTTCTATTCTCCTTTCCTCTTC-TT-CTTCTTTG
1 TTTTTCTTTTCTATTCTCCTTTCCTCTTCTTTCCTTCTTTG
* *
54606343 TTTTT-TTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTT-
1 TTTTTCTTTTCTATTCTCCTTTCCTCTTCTTTCCTTCTTTG
54606382 TTCTTTCTTT
1 TT-TTTCTTT
54606392 CCTCTCCTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
38 21 0.49
39 9 0.21
40 10 0.23
41 3 0.07
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.70
Consensus pattern (41 bp):
TTTTTCTTTTCTATTCTCCTTTCCTCTTCTTTCCTTCTTTG
Found at i:54606381 original size:18 final size:19
Alignment explanation
Indices: 54606348--54606404 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 19
54606338 CTTTGTTTTT
54606348 TTTTCTCTT-CTC-CTTTCC
1 TTTTCT-TTCCTCTCTTTCC
*
54606366 TTTTCTTTCCT-TCTTT-T
1 TTTTCTTTCCTCTCTTTCC
*
54606383 TCTTTCTTTCCTCTCCTTCC
1 T-TTTCTTTCCTCTCTTTCC
54606403 TT
1 TT
54606405 CCTTCCTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
17 3 0.10
18 22 0.71
19 5 0.16
20 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTCTTTCCTCTCTTTCC
Found at i:54606398 original size:38 final size:36
Alignment explanation
Indices: 54606299--54606404 Score: 103
Period size: 38 Copynumber: 2.9 Consensus size: 36
54606289 CTTCCTTCCA
* *
54606299 TCTTCTTTTTCTTTTCTAT--TCTCCTTTCCTCTTCT
1 TCTTCTTTTTC-TTTCTTTCCTCTCCTTTCCTTTTCT
*
54606334 TCTTCTTTGTT-TTTTTTTCTCTTCTCCTTTCCTTTTCTT
1 TCTTCTTT-TTCTTTCTTTC-C-TCTCCTTTCCTTTTC-T
54606373 TCCTTCTTTTTCTTTCTTTCCTCTCC-TTCCTT
1 T-CTTCTTTTTCTTTCTTTCCTCTCCTTTCCTT
54606405 CCTTCCTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
34 5 0.08
35 8 0.14
36 2 0.03
37 6 0.10
38 19 0.32
39 5 0.08
40 14 0.24
ACGTcount: A:0.01, C:0.31, G:0.01, T:0.67
Consensus pattern (36 bp):
TCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCT
Done.