Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 178 of 208
Found at i:56342093 original size:29 final size:29
Alignment explanation
Indices: 56342061--56342148 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
56342051 TTTTTAATGC
* *
56342061 ATTTTATATTTTTTTATGATTTTTATAAA
1 ATTTTATATTCTTTTACGATTTTTATAAA
*
56342090 ATTTTACATTCTTTTACGATTTTTATAAA
1 ATTTTATATTCTTTTACGATTTTTATAAA
56342119 ATTTTATATTCTTTTACGATTTTTATAAA
1 ATTTTATATTCTTTTACGATTTTTATAAA
56342148 A
1 A
56342149 AAAATTATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (29 bp):
ATTTTATATTCTTTTACGATTTTTATAAA
Found at i:56342162 original size:29 final size:29
Alignment explanation
Indices: 56342064--56342164 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
56342054 TTAATGCATT
* * **
56342064 TTATATTTTTTTATGATTTTTATAAAATT
1 TTATATTCTTTTACGATTTTTATAAAAAA
* **
56342093 TTACATTCTTTTACGATTTTTATAAAATT
1 TTATATTCTTTTACGATTTTTATAAAAAA
56342122 TTATATTCTTTTACGATTTTTATAAAAAAAA
1 TTATATTCTTTTACGATTTTTAT--AAAAAA
56342153 TTATATT-TTTTA
1 TTATATTCTTTTA
56342165 ATAAAATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 48 0.75
30 5 0.08
31 11 0.17
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTATATTCTTTTACGATTTTTATAAAAAA
Found at i:56342170 original size:19 final size:20
Alignment explanation
Indices: 56342137--56342189 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
56342127 TTCTTTTACG
*
56342137 ATTTTTATAAAAAAAATTAT-
1 ATTTTT-TAATAAAAATTATA
*
56342157 ATTTTTTAAT-AAAATTTTA
1 ATTTTTTAATAAAAATTATA
*
56342176 ATTTTTTATTAAAA
1 ATTTTTTAATAAAA
56342190 TCTAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.25
19 12 0.43
20 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTTAATAAAAATTATA
Found at i:56342172 original size:18 final size:18
Alignment explanation
Indices: 56342149--56342201 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
56342139 TTTTATAAAA
56342149 AAAATTATATTTTTTAAT
1 AAAATTATATTTTTTAAT
* *
56342167 AAAATTTTAATTTTTTATT
1 AAAATTAT-ATTTTTTAAT
56342186 AAAATCTAATATTTTT
1 AAAAT-T-ATATTTTT
56342202 AAAATTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 7 0.24
19 14 0.48
20 7 0.24
21 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AAAATTATATTTTTTAAT
Found at i:56342205 original size:16 final size:16
Alignment explanation
Indices: 56342184--56342216 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56342174 TAATTTTTTA
56342184 TTAAAATCTAATATTT
1 TTAAAATCTAATATTT
*
56342200 TTAAAATTTAATATTT
1 TTAAAATCTAATATTT
56342216 T
1 T
56342217 ATAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAAATCTAATATTT
Found at i:56342238 original size:17 final size:16
Alignment explanation
Indices: 56342192--56342239 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
56342182 TATTAAAATC
*
56342192 TAATATTTTTAAAATT
1 TAATATTTTTAATATT
56342208 TAATATTTTATAATATT
1 TAATATTTT-TAATATT
*
56342225 TTATAATTTTTAATA
1 TAAT-ATTTTTAATA
56342240 AGAACTTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 9 0.32
17 14 0.50
18 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATATTTTTAATATT
Found at i:56342240 original size:10 final size:10
Alignment explanation
Indices: 56342208--56342236 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
56342198 TTTTAAAATT
56342208 TAATATTTTA
1 TAATATTTTA
56342218 TAATATTTTA
1 TAATATTTTA
56342228 TAAT-TTTTA
1 TAATATTTTA
56342237 ATAAGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TAATATTTTA
Found at i:56345529 original size:5 final size:5
Alignment explanation
Indices: 56345527--56345576 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
56345517 TTAAAATATA
*
56345527 ATAAT ATAAT ATAAT -TAAT ATAATTT ACAAT ATAAT ATAAT A-AA- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT ATAAT ATAAT ATAAT
56345576 A
1 A
56345577 ACATACTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 1 0.03
4 8 0.21
5 25 0.66
7 4 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:56352352 original size:59 final size:59
Alignment explanation
Indices: 56352260--56352373 Score: 228
Period size: 59 Copynumber: 1.9 Consensus size: 59
56352250 TAAAATATAA
56352260 TATCTTATAAATAAAAAACAAATATTTAATTAGGTACTTCAATATTAAGTAACCTTTAC
1 TATCTTATAAATAAAAAACAAATATTTAATTAGGTACTTCAATATTAAGTAACCTTTAC
56352319 TATCTTATAAATAAAAAACAAATATTTAATTAGGTACTTCAATATTAAGTAACCT
1 TATCTTATAAATAAAAAACAAATATTTAATTAGGTACTTCAATATTAAGTAACCT
56352374 CAAATGGGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.37
Consensus pattern (59 bp):
TATCTTATAAATAAAAAACAAATATTTAATTAGGTACTTCAATATTAAGTAACCTTTAC
Found at i:56353138 original size:153 final size:155
Alignment explanation
Indices: 56352719--56353139 Score: 581
Period size: 153 Copynumber: 2.8 Consensus size: 155
56352709 GATTTTTTAT
* *
56352719 TTTATTT-TAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATATAAAATAA
1 TTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* *
56352783 TAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCG-GGGAAAAAATACGAACAAAAG
66 TAAAATTAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAAG
* * *
56352847 GCCGAAATAAGGTTTTTTTTAAAAA
131 GCCAAAATAAGGGTTTTCTTAAAAA
* * *
56352872 TTTATTTAAAAAA-ATAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* *
56352936 T-AAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAA-TC-AGAAAAAAAATACGAACAA
66 TAAAATTA-GAAAATAGTATA-TTTT-TTGAAAGTAATAAAATTCGAGGAAAAAAATACGAACAA
** * **
56352997 CTGGCCAAAATTAGGGTTTTCTT-CCAA
128 AAGGCCAAAATAAGGGTTTTCTTAAAAA
* *
56353024 TTTATTTAAAAAACACACTAAATGAATACATTTCAAATATAATGTACTAAAATAATGTAAAATGA
1 TTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA
56353089 TAAAATTAGAAAATAGTATA-TTTTTGAAAGTAATAAAATTCGAGGAAAAAA
66 TAAAATTAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAGGAAAAAA
56353140 TATGAATAAA
Statistics
Matches: 234, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
151 17 0.07
152 34 0.15
153 149 0.64
154 32 0.14
155 2 0.01
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (155 bp):
TTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA
TAAAATTAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAGGAAAAAAATACGAACAAAAG
GCCAAAATAAGGGTTTTCTTAAAAA
Found at i:56354747 original size:147 final size:147
Alignment explanation
Indices: 56354480--56354776 Score: 504
Period size: 147 Copynumber: 2.0 Consensus size: 147
56354470 TCAGAGCAAA
*
56354480 TACTTTCTTTTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGATACTT
1 TACTTTCTTCTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGATACTT
*
56354545 CACTGACATTTTCTTTAATATGTTTTACATAATGTTTTCAGTTTCCAAGTAACTGTCCATTTTTC
66 CACTGACATTTTCTTTAATATGCTTTACATAATGTTTTCAGTTTCCAAGTAACTGTCCATTTTTC
*
56354610 TTCTTTCTTATATATGG
131 TTCTTTCTTAGATATGG
* *
56354627 TACTTTCTTCTATTCATCATGTTGATTATTTATGTGCTATGTGATGTGTGATGTACTGGCTACTT
1 TACTTTCTTCTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGATACTT
* * * *
56354692 CACTGACATTTTCTTTAATTTGCTTTACATAATGTTTTCTGTTTCTAAGTAACTGTCCGTTTTTC
66 CACTGACATTTTCTTTAATATGCTTTACATAATGTTTTCAGTTTCCAAGTAACTGTCCATTTTTC
*
56354757 TTCTTTCTTGGATATGG
131 TTCTTTCTTAGATATGG
56354774 TAC
1 TAC
56354777 ATGCAGTTAG
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 140 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (147 bp):
TACTTTCTTCTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGATACTT
CACTGACATTTTCTTTAATATGCTTTACATAATGTTTTCAGTTTCCAAGTAACTGTCCATTTTTC
TTCTTTCTTAGATATGG
Found at i:56355971 original size:42 final size:42
Alignment explanation
Indices: 56355919--56356006 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
56355909 TTTTGGCTGC
*
56355919 TGTATCCATAGTTAATACAACTTGCACTTAGCATTACAATTT
1 TGTACCCATAGTTAATACAACTTGCACTTAGCATTACAATTT
56355961 TGTACCCATAGTTAATACAACTTGCACTTAGCATTACAATTT
1 TGTACCCATAGTTAATACAACTTGCACTTAGCATTACAATTT
56356003 TGTA
1 TGTA
56356007 TCCGTAGTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (42 bp):
TGTACCCATAGTTAATACAACTTGCACTTAGCATTACAATTT
Found at i:56364421 original size:25 final size:25
Alignment explanation
Indices: 56364376--56364423 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
56364366 GTTTAAGTGC
*
56364376 AGAATTCTCTTTGAGTTTTTCTTCA
1 AGAATTCTCTTTGAGGTTTTCTTCA
56364401 AGAATTCTCTCTTG-GGTTTTCTT
1 AGAATTCTCT-TTGAGGTTTTCTT
56364424 TAGAAGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (25 bp):
AGAATTCTCTTTGAGGTTTTCTTCA
Found at i:56369091 original size:28 final size:28
Alignment explanation
Indices: 56369059--56369116 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
56369049 TTCCAGACAC
56369059 TACATTCTTTCTAACTTCTGGTACATAA
1 TACATTCTTTCTAACTTCTGGTACATAA
56369087 TACATTCTTTCTAACTTCTGGTACATAA
1 TACATTCTTTCTAACTTCTGGTACATAA
56369115 TA
1 TA
56369117 TATATCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (28 bp):
TACATTCTTTCTAACTTCTGGTACATAA
Found at i:56369833 original size:9 final size:9
Alignment explanation
Indices: 56369812--56369905 Score: 100
Period size: 9 Copynumber: 10.4 Consensus size: 9
56369802 TTTGGTTAAA
*
56369812 AATTAGCCG
1 AATTAACCG
*
56369821 AATTAACCA
1 AATTAACCG
56369830 AATTAACCG
1 AATTAACCG
*
56369839 AATTACCCG
1 AATTAACCG
*
56369848 AATT-ACTCA
1 AATTAAC-CG
*
56369857 AATTAACCA
1 AATTAACCG
*
56369866 AATTACCCG
1 AATTAACCG
*
56369875 AATTACCCG
1 AATTAACCG
56369884 AATTAACCG
1 AATTAACCG
*
56369893 AATTAACCT
1 AATTAACCG
56369902 AATT
1 AATT
56369906 GAATCATACA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 1 0.01
9 70 0.96
10 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:56369905 original size:27 final size:27
Alignment explanation
Indices: 56369812--56369897 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
56369802 TTTGGTTAAA
*
56369812 AATTAGCCGAATTAACCAAATTAACCG
1 AATTACCCGAATTAACCAAATTAACCG
*
56369839 AATTACCCGAATT-ACTCAAATTAACCA
1 AATTACCCGAATTAAC-CAAATTAACCG
* *
56369866 AATTACCCGAATTACCCGAATTAACCG
1 AATTACCCGAATTAACCAAATTAACCG
56369893 AATTA
1 AATTA
56369898 ACCTAATTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 2 0.04
27 49 0.94
28 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (27 bp):
AATTACCCGAATTAACCAAATTAACCG
Found at i:56374690 original size:13 final size:13
Alignment explanation
Indices: 56374672--56374701 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56374662 TCCAACAACT
56374672 ATGAATTTATTTC
1 ATGAATTTATTTC
*
56374685 ATGAATTTATTTG
1 ATGAATTTATTTC
56374698 ATGA
1 ATGA
56374702 TGATCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:56374873 original size:50 final size:50
Alignment explanation
Indices: 56374794--56375037 Score: 355
Period size: 50 Copynumber: 4.9 Consensus size: 50
56374784 ACATTGGGTA
*
56374794 GAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
56374844 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
56374894 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
** * * * *
56374944 GAGAGGTCCCCCGTAAGACCATGTGTGGGACATTGCATCGGTACCG-GCAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG-AT
** * *
56374994 GAGAACATCCCATGTAAGACTATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
56375038 TGTTATTATT
Statistics
Matches: 173, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 142 0.82
51 30 0.17
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:56381259 original size:50 final size:50
Alignment explanation
Indices: 56381144--56381286 Score: 196
Period size: 50 Copynumber: 2.8 Consensus size: 50
56381134 GATAATAACA
* * ** *
56381144 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
56381195 TGCCTATACCATGTCCCACACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
*
56381245 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
56381287 TTACCCAATG
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 48 0.59
51 33 0.41
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:56386515 original size:3 final size:3
Alignment explanation
Indices: 56386507--56386538 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56386497 ATTAAGAAAA
56386507 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
56386539 TGGTTCACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:56387866 original size:22 final size:23
Alignment explanation
Indices: 56387825--56387868 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
56387815 TATTAATTTT
**
56387825 AAAAATATTAAATTTATTTGTAA
1 AAAAATATTAAAAATATTTGTAA
56387848 AAAAATATTAAAAAT-TTTGTA
1 AAAAATATTAAAAATATTTGTA
56387869 CATTTTCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAAATATTAAAAATATTTGTAA
Found at i:56391157 original size:19 final size:18
Alignment explanation
Indices: 56391133--56391168 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
56391123 ATACACATAT
56391133 TTTTATAATTTATAATTTC
1 TTTTATAATTTA-AATTTC
*
56391152 TTTTATATTTTAAATTT
1 TTTTATAATTTAAATTT
56391169 TTTATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATAATTTAAATTTC
Found at i:56391167 original size:18 final size:18
Alignment explanation
Indices: 56391132--56391180 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
56391122 GATACACATA
*
56391132 TTTTTATAATTTATAATT
1 TTTTTATATTTTATAATT
56391150 TCTTTTATATTTTA-AATT
1 T-TTTTATATTTTATAATT
56391168 TTTTATATATTTT
1 TTTT-TATATTTT
56391181 CTTTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 14 0.50
19 11 0.39
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTATATTTTATAATT
Found at i:56391184 original size:30 final size:32
Alignment explanation
Indices: 56391143--56391206 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
56391133 TTTTATAATT
56391143 TATAATTTCTTTT-ATATTTTAAAT-T-TTTTA
1 TATAATTTCTTTTAAT-TTTTAAATATCTTTTA
*
56391173 TATATTTTCTTTTAATTTTTAAATATCTTTTA
1 TATAATTTCTTTTAATTTTTAAATATCTTTTA
56391205 TA
1 TA
56391207 AAAAATAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 20 0.67
31 3 0.10
32 7 0.23
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (32 bp):
TATAATTTCTTTTAATTTTTAAATATCTTTTA
Found at i:56392638 original size:16 final size:16
Alignment explanation
Indices: 56392589--56392648 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
56392579 GTAATATATA
* *
56392589 TGAACCCTGATATATG
1 TGAACCCTTATATGTG
*
56392605 TGAA-CCTTGT-TGCATG
1 TGAACCCTTATATG--TG
56392621 TGAACCCTTATATGTG
1 TGAACCCTTATATGTG
56392637 TGAACCCTTATA
1 TGAACCCTTATA
56392649 AACTGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 1 0.03
15 4 0.11
16 24 0.67
17 5 0.14
18 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (16 bp):
TGAACCCTTATATGTG
Found at i:56392771 original size:24 final size:23
Alignment explanation
Indices: 56392716--56392781 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
56392706 TTAGTATACT
*
56392716 TATGCGAACCCTATATGTTATTA
1 TATGCGAACCCTAAATGTTATTA
*
56392739 CATGCGAACCCTAAATTGTTATTA
1 TATGCGAACCCTAAA-TGTTATTA
* * *
56392763 TATGAGAACGCTACATGTT
1 TATGCGAACCCTAAATGTT
56392782 TGCCTTGCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (23 bp):
TATGCGAACCCTAAATGTTATTA
Found at i:56395832 original size:125 final size:123
Alignment explanation
Indices: 56395631--56395981 Score: 524
Period size: 125 Copynumber: 2.8 Consensus size: 123
56395621 TAATTTCGAG
* * * * * *
56395631 TTGACATTTCTGATCAAATAGTATAAAATCGCTTCTAGCAAGATGTTATTTTAGAAGAATTTGTG
1 TTGACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
* *
56395696 AAATCGCGCCCTCGTGGACGTGTTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
66 AAATCGCGCCCTTGTGGACGTGCTTTTGCTACAGTAGGTCATGGAAG-AAT-ATTTTTTT
56395756 TTGACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
1 TTGACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
* * *
56395821 AAATCGTGCCCTTGTGGACGTGCTTTTGCTACAGTCGGTCATGGAAGAATTTTTTTTT
66 AAATCGCGCCCTTGTGGACGTGCTTTTGCTACAGTAGGTCATGGAAGAATATTTTTTT
* * *
56395879 TTGA-TGTTTCTAAGCTAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACT-TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
*
56395943 GAAAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAG
65 -AAAATCGCGCCCTTGTGGACGTGCTTTTGCTACAGTAG
56395982 CATGTTTGGG
Statistics
Matches: 207, Mismatches: 17, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
122 1 0.00
123 66 0.32
124 38 0.18
125 102 0.49
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (123 bp):
TTGACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
AAATCGCGCCCTTGTGGACGTGCTTTTGCTACAGTAGGTCATGGAAGAATATTTTTTT
Found at i:56399178 original size:37 final size:36
Alignment explanation
Indices: 56399104--56399180 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
56399094 ATTATGTGAA
* *
56399104 AGTAAAATTATTAATTGATAAATTATATTAATGGTT
1 AGTAAAATTATAAATTGATAAAATATATTAATGGTT
* *
56399140 AGTAAAATTATCAAATTATATAAAAT-TATTAATTGTT
1 AGTAAAATTAT-AAATT-GATAAAATATATTAATGGTT
56399177 AGTA
1 AGTA
56399181 CCAGGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 11 0.31
37 18 0.51
38 6 0.17
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (36 bp):
AGTAAAATTATAAATTGATAAAATATATTAATGGTT
Found at i:56399272 original size:23 final size:23
Alignment explanation
Indices: 56399229--56399272 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56399219 AAGTAAAATT
**
56399229 ATTAACTTAGTTTAATTTTTTTA
1 ATTAACTTAGTTTAAGGTTTTTA
*
56399252 ATTAACTTAGTTTAGGGTTTT
1 ATTAACTTAGTTTAAGGTTTT
56399273 AAAGTTAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (23 bp):
ATTAACTTAGTTTAAGGTTTTTA
Found at i:56399294 original size:22 final size:21
Alignment explanation
Indices: 56399263--56399360 Score: 110
Period size: 21 Copynumber: 4.6 Consensus size: 21
56399253 TTAACTTAGT
*
56399263 TTAGGGTTTTAAAGTTAAGGG
1 TTAGGTTTTTAAAGTTAAGGG
56399284 TTAGGATTTTT-AAGTTAAGGG
1 TTAGG-TTTTTAAAGTTAAGGG
* * *
56399305 TTTAGGGTTTTAAAATTAAGGA
1 -TTAGGTTTTTAAAGTTAAGGG
56399327 TTAGAGTTTTT-AAGTTAAGGG
1 TTAG-GTTTTTAAAGTTAAGGG
56399348 TTAAGGTTTTTAA
1 TT-AGGTTTTTAA
56399361 TTTAATTAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
21 39 0.61
22 25 0.39
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.43
Consensus pattern (21 bp):
TTAGGTTTTTAAAGTTAAGGG
Found at i:56399310 original size:43 final size:43
Alignment explanation
Indices: 56399261--56399360 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
56399251 AATTAACTTA
* *
56399261 GTTTAGGGTTTTAAAGTTAAGGGTTAG-GATTTTTAAGTTAAGG
1 GTTTAGGGTTTTAAAATTAAGGATTAGAG-TTTTTAAGTTAAGG
56399304 GTTTAGGGTTTTAAAATTAAGGATTAGAGTTTTTAAGTTAAGG
1 GTTTAGGGTTTTAAAATTAAGGATTAGAGTTTTTAAGTTAAGG
* *
56399347 GTTAAGGTTTTTAA
1 GTTTAGGGTTTTAA
56399361 TTTAATTAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (43 bp):
GTTTAGGGTTTTAAAATTAAGGATTAGAGTTTTTAAGTTAAGG
Found at i:56399378 original size:23 final size:23
Alignment explanation
Indices: 56399346--56399832 Score: 534
Period size: 23 Copynumber: 21.9 Consensus size: 23
56399336 TTAAGTTAAG
*
56399346 GGTTAAGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
56399369 GGTTAGGGTTTTTTAAGTTAATTA
1 GGTTAGGG-TTTTTAATTTAATTA
*
56399393 GGTTAAGGTTTTTAA-TTAA--A
1 GGTTAGGGTTTTTAATTTAATTA
*
56399413 --ATAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
56399434 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
56399457 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
56399480 GGTTAGGGTTTTTTTAAGTTAATTA
1 GGTTAGGG--TTTTTAATTTAATTA
56399505 GGTTAGGGTTTTTAA-TTAA--A
1 GGTTAGGGTTTTTAATTTAATTA
*
56399525 --ATAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
56399546 GGTT-GGGATTTTTAATTTAATTA
1 GGTTAGGG-TTTTTAATTTAATTA
* *
56399569 GGTTAGGGTTTTTAAGTTAA--G
1 GGTTAGGGTTTTTAATTTAATTA
*
56399590 GGTTAGGGTTTTAAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
56399613 GGTTAGGGGTTTTTAATTTAATTG
1 GGTTA-GGGTTTTTAATTTAATTA
*
56399637 GGTTAGGGTTTTTTAAGTTAATTA
1 GGTTAGGG-TTTTTAATTTAATTA
*
56399661 GGTTAGGTTTTTTAA-TTAA--A
1 GGTTAGGGTTTTTAATTTAATTA
* * *
56399681 --ATAAGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
56399702 GGTTAGGGTTTTTTAAGTTAATTA
1 GGTTAGGG-TTTTTAATTTAATTA
*
56399726 GGTTAGTGTTTTTAA-TTAA--A
1 GGTTAGGGTTTTTAATTTAATTA
*
56399746 --ATAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
56399767 GGTTAGAGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
56399790 GGTTAGAGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
56399813 GGTTAGGATTTTTAAGTTAA
1 GGTTAGGGTTTTTAATTTAA
56399833 GGGTATTAAT
Statistics
Matches: 395, Mismatches: 39, Indels: 60
0.80 0.08 0.12
Matches are distributed among these distances:
18 44 0.11
19 15 0.04
20 4 0.01
21 22 0.06
22 19 0.05
23 185 0.47
24 85 0.22
25 21 0.05
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.49
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTTAATTA
Found at i:56399435 original size:18 final size:18
Alignment explanation
Indices: 56399399--56399458 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
56399389 ATTAGGTTAA
* *
56399399 GGTTTTTAATTAAAATAG
1 GGTTTTTAATTTAATTAG
56399417 GGTTTTTAATTTAATTAGGTTAG
1 GGTTTTTAATTT-A--A--TTAG
56399440 GGTTTTTAATTTAATTAG
1 GGTTTTTAATTTAATTAG
56399458 G
1 G
56399459 TTAGGGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
18 16 0.46
19 1 0.03
20 1 0.03
21 1 0.03
22 1 0.03
23 15 0.43
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (18 bp):
GGTTTTTAATTTAATTAG
Found at i:56399545 original size:89 final size:88
Alignment explanation
Indices: 56399306--56399832 Score: 460
Period size: 89 Copynumber: 5.9 Consensus size: 88
56399296 AGTTAAGGGT
* * * * ** * *
56399306 TTAGGGTTTTAAAATT-AAGGATTAGAGTTTTTAAGTTAAGGGTTAAGGTTTTTAATTTAATTAG
1 TTAGGGTTTTTAAGTTAAAGG-TTAGGGTTTTTAATTTAATAGATAGGGTTTTTAATTTAATTAG
56399370 GTTAGGGTTTTTTAAGTT-AATTAGG
65 GTTAGGG-TTTTTAA-TTAAATTAGG
* * *
56399395 TTAAGGTTTTTAA-TTAAA--ATAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAA-TA-GATAGGGTTTTTAATTTAATTA
56399457 GGTTAGGGTTTTTAATTAAATTAGG
64 GGTTAGGGTTTTTAATTAAATTAGG
56399482 TTAGGGTTTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTAA-A-ATAGGGTTTTTAATTTAAT
1 TTAGGG--TTTTTAAGTTAA--AGGTTAGGGTTTTTAATTTAATAGATAGGGTTTTTAATTTAAT
*
56399544 TAGGTT-GGGATTTTTAATTTAATTAGG
62 TAGGTTAGGG-TTTTTAATTAAATTAGG
* * *
56399571 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTAAATTTAATTAGGTTAGGGGTTTTTAATTTAATT
1 TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAA-TA-GATA-GGGTTTTTAATTTAATT
*
56399636 GGGTTAGGGTTTTTTAAGTT-AATTAGG
63 AGGTTAGGG-TTTTTAA-TTAAATTAGG
* * * * * *
56399663 TTAGGTTTTTTAA-TTAAA--ATAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTTAAGTTAATT
1 TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAA-TA-GATAGGG-TTTTTAATTTAATT
*
56399725 AGGTTAGTGTTTTTAATTAAA--A--
63 AGGTTAGGGTTTTTAATTAAATTAGG
* * * * *
56399747 -TAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAATTAAAT
1 TTAGGGTTTTTAAGTTAA--AGGTTAGGGTTTTTAATTTAA-TA-GATAGGGTTTTTAATTTAAT
*
56399811 TAGGTTAGGATTTTTAAGTTAA
62 TAGGTTAGGGTTTTTAA-TTAA
56399833 GGGTATTAAT
Statistics
Matches: 374, Mismatches: 36, Indels: 57
0.80 0.08 0.12
Matches are distributed among these distances:
83 11 0.03
84 4 0.01
85 14 0.04
86 23 0.06
87 59 0.16
88 75 0.20
89 108 0.29
90 6 0.02
91 26 0.07
92 30 0.08
93 6 0.02
94 12 0.03
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (88 bp):
TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAATAGATAGGGTTTTTAATTTAATTAGG
TTAGGGTTTTTAATTAAATTAGG
Found at i:56399669 original size:29 final size:27
Alignment explanation
Indices: 56399610--56399669 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 27
56399600 TTAAATTTAA
*
56399610 TTAGGTTAGGGGTTTTTAATTTAATTG
1 TTAGGTTAGGGGTTTTTAAGTTAATTG
*
56399637 ---GGTTAGGGTTTTTTAAGTTAATTAGG
1 TTAGGTTAGGGGTTTTTAAGTTAATT--G
56399663 TTAGGTT
1 TTAGGTT
56399670 TTTTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
24 21 0.81
26 1 0.04
29 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (27 bp):
TTAGGTTAGGGGTTTTTAAGTTAATTG
Found at i:56399704 original size:17 final size:18
Alignment explanation
Indices: 56399663--56399705 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
56399653 GTTAATTAGG
56399663 TTAGGTTTTTTAATTAAAA
1 TTAGG-TTTTTAATTAAAA
*
56399682 TAAGGTTTTTAATT-AAA
1 TTAGGTTTTTAATTAAAA
56399699 TTAGGTT
1 TTAGGTT
56399706 AGGGTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 9 0.41
19 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
TTAGGTTTTTAATTAAAA
Found at i:56399740 original size:244 final size:240
Alignment explanation
Indices: 56399317--56399836 Score: 626
Period size: 244 Copynumber: 2.1 Consensus size: 240
56399307 TAGGGTTTTA
* * *
56399317 AAATTAAGGATTAGAGTTTTTAAGTTAAGGGTTAAGGTTTTTAATTTAATTAGGTTAGGGTTTTT
1 AAATT-AGG-TTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTAAATTTAATTAGGTTAGGGGTTTT
*** *
56399382 TAAGTTAATTAGGTTAAGGTTTTTAATTAAAATAGGGTTTTTAATTTAATTAGGTTAGGGTTTTT
64 TAAGTTAATTAGGTTAAGGTTTTTAATTAAAATAGGGTTTTT-ATTTAATTAAAATAAGGTTTTT
* * *
56399447 AATTTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTTTAAGTTAATTAGGTTAGG
128 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTGTTTTTAA-TTAA--A--ATAGG
* *
56399512 GTTTTTAA-TTAA-A-ATAGGGTTTTTAATTTAATTAGGTT-GGGATTTTTAATT
187 GTTTTTAATTTAATAGATAGAGTTTTTAATTTAATTAGGTTAGAG-TTTTTAATT
* *
56399563 TAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTAAATTTAATTAGGTTAGGGGTTTTTA
1 AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTAAATTTAATTAGGTTAGGGGTTTTTA
* * * *
56399628 ATTTAATTGGGTTAGGGTTTTTTAAGTT-AATTA-GGTTAGGTTT-TTTAATTAAAATAAGGTTT
66 AGTTAATTAGGTTAAGG-TTTTTAA-TTAAAATAGGGTT---TTTATTTAATTAAAATAAGGTTT
56399690 TTAATTAAATTAGGTTAGGGTTTTTTAAGTT-AATTAGGTTA-GTGTTTTTAATTAAAATAGGGT
126 TTAATTAAATTAGGTTAGGG-TTTTTAA-TTAAATTAGGTTAGGTGTTTTTAATTAAAATAGGGT
*
56399753 TTTTAATTTAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAATT
189 TTTTAATTTAA-TA-GATAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAATT
*
56399807 AAATTAGGTTAGGATTTTTAAGTTAAGGGT
1 AAATTAGGTTAGGGTTTTTAAGTTAAGGGT
56399837 ATTAATGGTT
Statistics
Matches: 240, Mismatches: 21, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
239 12 0.05
240 4 0.02
241 1 0.00
242 1 0.00
243 4 0.02
244 140 0.58
245 50 0.21
246 23 0.10
247 5 0.02
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (240 bp):
AAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTAAATTTAATTAGGTTAGGGGTTTTTA
AGTTAATTAGGTTAAGGTTTTTAATTAAAATAGGGTTTTTATTTAATTAAAATAAGGTTTTTAAT
TAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTGTTTTTAATTAAAATAGGGTTTTTAAT
TTAATAGATAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAATT
Found at i:56399770 original size:17 final size:17
Alignment explanation
Indices: 56399728--56399770 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
56399718 GTTAATTAGG
56399728 TTAGTGTTTTTAATTAAA
1 TTAG-GTTTTTAATTAAA
* *
56399746 ATAGGGTTTTTAATTTAA
1 TTA-GGTTTTTAATTAAA
56399764 TTAGGTT
1 TTAGGTT
56399771 AGAGTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 4 0.19
18 16 0.76
19 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (17 bp):
TTAGGTTTTTAATTAAA
Found at i:56399804 original size:41 final size:41
Alignment explanation
Indices: 56399361--56399807 Score: 314
Period size: 41 Copynumber: 10.2 Consensus size: 41
56399351 AGGTTTTTAA
* *
56399361 TTTAATTAGGTTAGGGTTTTTTAAGTTAATTAGGTTAAGGTT
1 TTTAATTAGGTTAGGG-TTTTTAATTTAATTAGGTTAGGGTT
***
56399403 TTTAATTAAAATAGGGTTTTTAATTTAATTAGGTTAGGGTTTTT
1 TTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG---TT
*
56399447 AATTTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTT
1 --TTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG----TT
* * *
56399494 TAAGTTAATTAGGTTAGGGTTTTTAATTAAAATAGGGTT---TTT
1 T---TTAATTAGGTTAGGGTTTTTAATTTAATTA-GGTTAGGGTT
56399536 AATTTAATTAGGTT-GGGATTTTTAATTTAATTAGGTTAGGGTT
1 --TTTAATTAGGTTAGGG-TTTTTAATTTAATTAGGTTAGGGTT
*
56399579 TTTAAGTTAAGGGTTAGGGTTTTAAATTTAATTAGGTTAGGGGTT
1 TTTAA-TT-A-GGTTAGGGTTTTTAATTTAATTAGGTTA-GGGTT
* *
56399624 TTTAATTTAATTGGGTTAGGGTTTTTTAAGTTAATTAGGTTAGGTTT
1 TTTAA-TT-A---GGTTAGGG-TTTTTAATTTAATTAGGTTAGGGTT
*** * *
56399671 TTTAATTAAAATAAGGTTTTTAATTAAATTAGGTTAGGGTTTTT
1 TTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG---TT
* * * *
56399715 TAAGTTAATTAGGTTAGTGTTTTTAATTAAAATAGGGTT---TTT
1 T---TTAATTAGGTTAGGGTTTTTAATTTAATTA-GGTTAGGGTT
* *
56399757 AATTTAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGAGTT
1 --TTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTT
56399800 TTTAATTA
1 TTTAATTA
56399808 AATTAGGTTA
Statistics
Matches: 332, Mismatches: 37, Indels: 73
0.75 0.08 0.17
Matches are distributed among these distances:
40 11 0.03
41 105 0.32
42 23 0.07
43 5 0.02
44 30 0.09
45 19 0.06
46 37 0.11
47 47 0.14
48 51 0.15
49 4 0.01
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (41 bp):
TTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTT
Found at i:56399827 original size:41 final size:41
Alignment explanation
Indices: 56399282--56399827 Score: 223
Period size: 41 Copynumber: 12.4 Consensus size: 41
56399272 TAAAGTTAAG
56399282 GGTTAGGATTTTTAAGTTAAGGGTTTAGGG-TTTT-A--AAATTAA
1 GGTTAGGATTTTTAA-TT-A-GG-TTAGGGTTTTTAATTAAATT-A
* *
56399324 GGATTA-GAGTTTTTAAGTTAAGGGTTAAGGTTTTTAATTTAATTA
1 GG-TTAGGA-TTTTTAA-TT-A-GGTTAGGGTTTTTAATTAAATTA
* * *
56399369 GGTTAGGGTTTTTTAAGTTAATTAGGTTAAGGTTTTTAATTAAAATA
1 GGTTA-GG--ATTT---TTAATTAGGTTAGGGTTTTTAATTAAATTA
*** * *
56399416 GGGTTTTTA-ATTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 -GGTTAGGATTTTTAATTAGGTTAGGGTTTTTAATTAAATTA
*
56399457 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTTTAAGTT-AATTA
1 GGTTA-GG-ATTT--TT-AATTAGGTTAGGG--TTTTTAA-TTAAATTA
* *** *
56399505 GGTTAGGGTTTTTAATTAAAATAGGGTTTTTAATTTAATTA
1 GGTTAGGATTTTTAATTAGGTTAGGGTTTTTAATTAAATTA
* *
56399546 GGTTGGGATTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTA
1 GGTTAGGA---TT--TTTAATTAGGTTAGGGTTTTTAA-TTAA--ATTA
** ** * *
56399595 GGGTT-TTAAATTTAATTAGGTTAGGGGTTTTTAATTTAATTG
1 -GGTTAGGATTTTTAATTAGGTTA-GGGTTTTTAATTAAATTA
* * *
56399637 GGTTAGGGTTTTTTAAGTTAATTAGGTTAGGTTTTTTAATTAAAATAA
1 GGTTA-GG--ATTT---TTAATTAGGTTAGGGTTTTTAATT-AAATTA
*** * *
56399685 GGTTTTTA-ATTAAATTAGGTTAGGGTTTTTTAAGTT-AATTA
1 GGTTAGGATTTTTAATTAGGTTAGGG-TTTTTAA-TTAAATTA
*** *
56399726 GGTTAGTG-TTTTTAATTAAAATAGGGTTTTTAATTTAATTA
1 GGTTAG-GATTTTTAATTAGGTTAGGGTTTTTAATTAAATTA
* *
56399767 GGTTAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAATTAAATTA
1 GGTTAG-G--ATT--TTTAATTAGGTTAGGGTTTTTAATTAAATTA
56399813 GGTTAGGATTTTTAA
1 GGTTAGGATTTTTAA
56399828 GTTAAGGGTA
Statistics
Matches: 384, Mismatches: 68, Indels: 105
0.69 0.12 0.19
Matches are distributed among these distances:
40 8 0.02
41 94 0.24
42 30 0.08
43 37 0.10
44 28 0.07
45 17 0.04
46 73 0.19
47 40 0.10
48 41 0.11
49 8 0.02
50 8 0.02
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (41 bp):
GGTTAGGATTTTTAATTAGGTTAGGGTTTTTAATTAAATTA
Found at i:56399881 original size:9 final size:9
Alignment explanation
Indices: 56399863--56399903 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
56399853 ATTCTCAAAT
56399863 AATA-TCAA
1 AATATTCAA
56399871 AATATTCAA
1 AATATTCAA
*
56399880 AATATGCAA
1 AATATTCAA
56399889 AATATTCAA
1 AATATTCAA
56399898 AA-ATTC
1 AATATTC
56399904 TATTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (9 bp):
AATATTCAA
Found at i:56399891 original size:18 final size:17
Alignment explanation
Indices: 56399863--56399899 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
56399853 ATTCTCAAAT
56399863 AATATCAAAATATTCAA
1 AATATCAAAATATTCAA
56399880 AATATGCAAAATATTCAA
1 AATAT-CAAAATATTCAA
56399898 AA
1 AA
56399900 ATTCTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (17 bp):
AATATCAAAATATTCAA
Found at i:56399920 original size:22 final size:23
Alignment explanation
Indices: 56399894--56399945 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
56399884 TGCAAAATAT
*
56399894 TCAAAAA-TTCTATTTTATTACA
1 TCAAAAACTTCAATTTTATTACA
56399916 TCAAATAAACTTCAATTTTATTACA
1 TC-AA-AAACTTCAATTTTATTACA
56399941 TCAAA
1 TCAAA
56399946 TAATATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 3 0.12
24 5 0.19
25 16 0.62
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (23 bp):
TCAAAAACTTCAATTTTATTACA
Found at i:56401588 original size:50 final size:50
Alignment explanation
Indices: 56401466--56401711 Score: 253
Period size: 50 Copynumber: 4.8 Consensus size: 50
56401456 TAATAACATA
* * ** * *
56401466 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGGTG
* *
56401517 CCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTG
* ** *
56401567 CCAACGCCATGTCCCAGACATGGTCTTACTTGGGACCTCTCGTCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTG
* * *
56401617 CCCATGCCATGT-CCAGACATGGTCTTACAGAGGACCTCTCATGATCTTAAGGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG-TG
* *
56401672 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
56401712 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
49 26 0.16
50 63 0.39
51 31 0.19
52 2 0.01
53 1 0.01
54 2 0.01
55 13 0.08
56 24 0.15
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTG
Found at i:56401689 original size:105 final size:100
Alignment explanation
Indices: 56401466--56401711 Score: 316
Period size: 105 Copynumber: 2.4 Consensus size: 100
56401456 TAATAACATA
**
56401466 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATGTCC
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATGTCC
* * *
56401531 CAGACATGGTCTTATAGGGGACCTCTCATCTCGGTG
65 CAGACATGGTCTTACAGAGGACCTCTCATCTAGGTG
* * *
56401567 CCAACGCCATGTCCCAGACATGGTCTTACTTGGGACCTCTCGT-CTCGGTGCCCATGCCATGT-C
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATGTCC
56401630 CAGACATGGTCTTACAGAGGACCTCTCATGATCTTAAGGATG
65 CAGACATGGTCTTACAGAGGACCTCTC---ATC-T-AGG-TG
* *
56401672 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56401712 TTACCCAAAT
Statistics
Matches: 127, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 27 0.21
100 22 0.17
101 33 0.26
102 3 0.02
103 1 0.01
104 2 0.02
105 39 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (100 bp):
CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGTCCC
AGACATGGTCTTACAGAGGACCTCTCATCTAGGTG
Found at i:56401827 original size:13 final size:13
Alignment explanation
Indices: 56401806--56401837 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56401796 GCTTGGATCA
*
56401806 TCATCAAATAAAT
1 TCATAAAATAAAT
56401819 TCATAAAATAAAT
1 TCATAAAATAAAT
56401832 TCATAA
1 TCATAA
56401838 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56402085 original size:30 final size:30
Alignment explanation
Indices: 56402049--56402106 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56402039 CCTCGACTCT
*
56402049 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
56402079 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
56402107 AAGGTTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:56402875 original size:40 final size:40
Alignment explanation
Indices: 56402813--56402907 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 40
56402803 CTTTTCTTTC
* *
56402813 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
*
56402854 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
56402894 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
56402908 TTCTTTGTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.00, C:0.28, G:0.08, T:0.63
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:56402933 original size:3 final size:3
Alignment explanation
Indices: 56402925--56402978 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
56402915 TCATATATAT
*
56402925 ATA ATA ATA AT- ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56402968 ATA AT- ATA ATA
1 ATA ATA ATA ATA
56402979 TAAAAACATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 12 0.28
3 31 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:56402941 original size:5 final size:5
Alignment explanation
Indices: 56402917--56402981 Score: 75
Period size: 5 Copynumber: 13.2 Consensus size: 5
56402907 TTTCTTTGTC
56402917 ATATA TATATA ATAATA ATAT- A-ATA ATATA ATATA ATATA ATAT- AT-TA
1 ATATA -ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
56402965 ATAATA ATATA ATATA A
1 AT-ATA ATATA ATATA A
56402982 AAACATAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.06
4 6 0.11
5 30 0.57
6 14 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:56402941 original size:8 final size:8
Alignment explanation
Indices: 56402928--56402981 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
56402918 TATATATATA
56402928 ATAATAAT
1 ATAATAAT
56402936 ATAATAAT
1 ATAATAAT
56402944 ATAATATAAT
1 AT-A-ATAAT
56402954 ATAAT-AT
1 ATAATAAT
56402961 ATTAATAAT
1 A-TAATAAT
56402970 A-ATATAAT
1 ATA-ATAAT
56402978 ATAA
1 ATAA
56402982 AAACATAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 4 0.10
8 23 0.57
9 6 0.15
10 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATAAT
Found at i:56402968 original size:29 final size:28
Alignment explanation
Indices: 56402917--56402981 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
56402907 TTTCTTTGTC
56402917 ATATATATATAATAATAATATAATAATATA
1 ATATA-ATATAAT-ATAATATAATAATATA
*
56402947 ATATAATATAATATATTAATAATAATATA
1 ATATAATATAATATAAT-ATAATAATATA
56402976 ATATAA
1 ATATAA
56402982 AAACATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAATATAATATAATATAATAATATA
Found at i:56402989 original size:13 final size:13
Alignment explanation
Indices: 56402931--56402990 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
56402921 ATATATAATA
*
56402931 ATAATATAATAAT
1 ATAATATAAAAAT
56402944 ATAATATAATATAAT
1 ATAATATAA-A-AAT
* *
56402959 ATATTAATAATAAT
1 ATAAT-ATAAAAAT
*
56402973 ATAATATAAAAAC
1 ATAATATAAAAAT
56402986 ATAAT
1 ATAAT
56402991 TATTACTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 20 0.53
14 7 0.18
15 7 0.18
16 4 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATATAAAAAT
Found at i:56402990 original size:24 final size:23
Alignment explanation
Indices: 56402923--56402981 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
56402913 TGTCATATAT
*
56402923 ATATAATAATAATATAATAATATA
1 ATATAAT-ATAATATAATAAAATA
*
56402947 ATATAATATAATATATTAATAATA
1 ATATAATATAATATAATAA-AATA
56402971 ATATAATATAA
1 ATATAATATAA
56402982 AAACATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAATATAATATAATAAAATA
Found at i:56403733 original size:18 final size:18
Alignment explanation
Indices: 56403695--56403734 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
56403685 GACTCGGAAA
* *
56403695 AGGATACATATAAGGGTT
1 AGGATACATATAAGAGCT
56403713 AGGATACATATAAGAGCT
1 AGGATACATATAAGAGCT
56403731 AGGA
1 AGGA
56403735 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGAGCT
Found at i:56404395 original size:7 final size:7
Alignment explanation
Indices: 56404385--56404417 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
56404375 TTATATACAT
56404385 AATACTA
1 AATACTA
56404392 AATACTA
1 AATACTA
56404399 AATACTA
1 AATACTA
56404406 AATACTA
1 AATACTA
56404413 AATAC
1 AATAC
56404418 CAATCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:56405644 original size:17 final size:16
Alignment explanation
Indices: 56405605--56405636 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
56405595 ATTTTGGAAG
56405605 GAAATTGAGAGAATAA
1 GAAATTGAGAGAATAA
56405621 GAAAATTGAGAGAATA
1 G-AAATTGAGAGAATA
56405637 TTGAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (16 bp):
GAAATTGAGAGAATAA
Found at i:56408593 original size:20 final size:19
Alignment explanation
Indices: 56408564--56408603 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
56408554 CTCCAAATTT
*
56408564 TGTTCTCTGCTGGTGCTGG
1 TGTTCTCTGCTGGCGCTGG
56408583 TGTTCCTCTGCTGGCGCTGG
1 TGTT-CTCTGCTGGCGCTGG
56408603 T
1 T
56408604 TCTTTGTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.00, C:0.25, G:0.35, T:0.40
Consensus pattern (19 bp):
TGTTCTCTGCTGGCGCTGG
Found at i:56408613 original size:25 final size:25
Alignment explanation
Indices: 56408583--56408641 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
56408573 CTGGTGCTGG
56408583 TGTTCCTCTGCTGGCGCTGGTTCTT
1 TGTTCCTCTGCTGGCGCTGGTTCTT
* *
56408608 TGTTCCTCAGCTGGTGCTGGTTCTT
1 TGTTCCTCTGCTGGCGCTGGTTCTT
56408633 TGTTCCTCT
1 TGTTCCTCT
56408642 TCTCCACATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.46
Consensus pattern (25 bp):
TGTTCCTCTGCTGGCGCTGGTTCTT
Found at i:56410088 original size:41 final size:42
Alignment explanation
Indices: 56410043--56410126 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
56410033 TGTTCAACAG
*
56410043 TTCCGAAGACAATCAGTCTAATA-TTTTTCTCTTAATCAGTA
1 TTCCGAAGACAATCAATCTAATATTTTTTCTCTTAATCAGTA
56410084 TTCCGAAGACAATCAATCTAATATTTTTTCTCTTAATCAGTA
1 TTCCGAAGACAATCAATCTAATATTTTTTCTCTTAATCAGTA
56410126 T
1 T
56410127 CCCAACCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 22 0.54
42 19 0.46
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.40
Consensus pattern (42 bp):
TTCCGAAGACAATCAATCTAATATTTTTTCTCTTAATCAGTA
Found at i:56417892 original size:10 final size:9
Alignment explanation
Indices: 56417874--56417907 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
56417864 AAGCCATTTT
56417874 AAATTTTAA
1 AAATTTTAA
56417883 AAATTATTAA
1 AAATT-TTAA
56417893 AAATTTATAA
1 AAATTT-TAA
56417903 AAATT
1 AAATT
56417908 ATATACTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATTTTAA
Found at i:56417912 original size:11 final size:11
Alignment explanation
Indices: 56417880--56417912 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
56417870 TTTTAAATTT
56417880 TAAAAATTAT-
1 TAAAAATTATA
56417890 TAAAAATT-TA
1 TAAAAATTATA
56417900 TAAAAATTATA
1 TAAAAATTATA
56417911 TA
1 TA
56417913 CTCATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 16 0.76
11 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:56421963 original size:32 final size:33
Alignment explanation
Indices: 56421927--56421998 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
56421917 AATTTATATG
56421927 AAATATTTT-CA-AGAAATC-TACCAAACAACAGA
1 AAATATTTTACACAG-AATCAT-CCAAACAACAGA
* *
56421959 AAATATTTTACACAGATTCATCCAAACACCAGA
1 AAATATTTTACACAGAATCATCCAAACAACAGA
56421992 AAATATT
1 AAATATT
56421999 AGCTTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 9 0.26
33 23 0.66
34 3 0.09
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (33 bp):
AAATATTTTACACAGAATCATCCAAACAACAGA
Found at i:56425095 original size:13 final size:13
Alignment explanation
Indices: 56425074--56425132 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
56425064 ACTCTCAAAT
56425074 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
56425087 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
56425100 TTTTTC--AAGCAC
1 -TTTTCAAAAGCAC
*
56425112 -TTTCAAAAGTAC
1 TTTTCAAAAGCAC
56425124 TTTTCAAAA
1 TTTTCAAAA
56425133 ACAATGAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 4 0.11
12 10 0.27
13 19 0.51
14 4 0.11
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:56425121 original size:24 final size:25
Alignment explanation
Indices: 56425081--56425127 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
56425071 AATTTTTCAA
56425081 AAGCACTTCTCAAAAGTACTTTTTC
1 AAGCACTTCTCAAAAGTACTTTTTC
56425106 AAGCACTT-TCAAAAGTACTTTT
1 AAGCACTTCTCAAAAGTACTTTT
56425128 CAAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (25 bp):
AAGCACTTCTCAAAAGTACTTTTTC
Found at i:56427824 original size:13 final size:13
Alignment explanation
Indices: 56427789--56427847 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
56427779 GATATATTTG
*
56427789 TAATTTGAAAGCT
1 TAATTTGAAAACT
56427802 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
56427816 TAATTTG--AA--
1 TAATTTGAAAACT
56427825 -AATTTGAAAACT
1 TAATTTGAAAACT
56427837 TAATTTGAAAA
1 TAATTTGAAAA
56427848 TTTGAAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
8 6 0.15
10 2 0.05
11 2 0.05
13 17 0.44
14 12 0.31
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:56427830 original size:8 final size:8
Alignment explanation
Indices: 56427817--56427865 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
56427807 TTGAAAACTT
56427817 AATTTGAA
1 AATTTGAA
56427825 AATTTGAA
1 AATTTGAA
*
56427833 AACTT---
1 AATTTGAA
56427838 AATTTGAA
1 AATTTGAA
56427846 AATTTGAA
1 AATTTGAA
* *
56427854 AACTTAAA
1 AATTTGAA
56427862 AATT
1 AATT
56427866 AAATTTGGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
5 4 0.12
8 29 0.88
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (8 bp):
AATTTGAA
Found at i:56427832 original size:21 final size:21
Alignment explanation
Indices: 56427806--56427860 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
56427796 AAAGCTTAAG
56427806 TTTGAAAACTTAATTTGAAAA
1 TTTGAAAACTTAATTTGAAAA
56427827 TTTGAAAACTTAATTTGAAAA
1 TTTGAAAACTTAATTTGAAAA
56427848 TTTGAAAACTTAA
1 TTTGAAAACTTAA
56427861 AAATTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.38
Consensus pattern (21 bp):
TTTGAAAACTTAATTTGAAAA
Found at i:56427863 original size:29 final size:29
Alignment explanation
Indices: 56427817--56427872 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
56427807 TTGAAAACTT
* *
56427817 AATTTGAAAATTTGAAAACTT-AATTTGAA
1 AATTTGAAAACTT-AAAAATTAAATTTGAA
56427846 AATTTGAAAACTTAAAAATTAAATTTG
1 AATTTGAAAACTTAAAAATTAAATTTG
56427873 GTAAACTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (29 bp):
AATTTGAAAACTTAAAAATTAAATTTGAA
Found at i:56427869 original size:21 final size:22
Alignment explanation
Indices: 56427806--56427884 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 22
56427796 AAAGCTTAAG
*
56427806 TTTGAAAACTT--AATTTGAAAA
1 TTTGAAAACTTAAAAATT-AAAA
*
56427827 TTTGAAAACTT--AATTTGAAAA
1 TTTGAAAACTTAAAAATT-AAAA
56427848 TTTGAAAACTTAAAAATT-AAA
1 TTTGAAAACTTAAAAATTAAAA
*
56427869 TTTGGTAAACTTAAAA
1 TTT-GAAAACTTAAAA
56427885 GTTTTGAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
21 38 0.72
22 11 0.21
23 4 0.08
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTGAAAACTTAAAAATTAAAA
Found at i:56428148 original size:35 final size:35
Alignment explanation
Indices: 56428104--56428280 Score: 230
Period size: 35 Copynumber: 5.1 Consensus size: 35
56428094 TTCACTTGTC
* * * *
56428104 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
*
56428139 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
** *
56428174 TTTTGTTATAGGGAATCTCTCCTGTTCACACATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
* *
56428209 -TTTATTGCAGGGAATCTCTCATGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
* * *
56428243 TTTTGTTGCAAGGAATCTCTCATGTTCACACATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
56428278 TTT
1 TTT
56428281 CTTTTTGGAC
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
34 29 0.23
35 97 0.77
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
Found at i:56428224 original size:69 final size:69
Alignment explanation
Indices: 56428112--56428280 Score: 230
Period size: 69 Copynumber: 2.4 Consensus size: 69
56428102 TCTTTTCTTG
* * * * * * *
56428112 CAGGGAATATTTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
1 CAGGGAATCTCTCCTGTTCACACATCA-TTTATTGCAGGGAATCTCTCATGTTCACACATTATTT
56428177 TGTTA
65 TGTTA
*
56428182 TAGGGAATCTCTCCTGTTCACACATCATTTATTGCAGGGAATCTCTCATGTTCACACATTATTTT
1 CAGGGAATCTCTCCTGTTCACACATCATTTATTGCAGGGAATCTCTCATGTTCACACATTATTTT
*
56428247 GTTG
66 GTTA
* *
56428251 CAAGGAATCTCTCATGTTCACACATCATTT
1 CAGGGAATCTCTCCTGTTCACACATCATTT
56428281 CTTTTTGGAC
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 65 0.75
70 22 0.25
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (69 bp):
CAGGGAATCTCTCCTGTTCACACATCATTTATTGCAGGGAATCTCTCATGTTCACACATTATTTT
GTTA
Found at i:56431115 original size:20 final size:23
Alignment explanation
Indices: 56431080--56431124 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
56431070 GAACAAATTG
56431080 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
56431102 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
56431123 TT
1 TT
56431125 CTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:56436115 original size:105 final size:105
Alignment explanation
Indices: 56436003--56436204 Score: 262
Period size: 105 Copynumber: 1.9 Consensus size: 105
56435993 AACATCAGGC
* **
56436003 TCAATGCCTCGTTTTATCATTGTGTCAACAATATCCT-CAGCTTTAGAAACCATCCCTTCTTTGC
1 TCAATGCCTCGCTTTATCATTGTGTCAACAATAT-CTACAGCTTTAGAAACCATCCCTTCCGTGC
* *
56436067 AATGTGCATCAACCAATGTAGAATACGTGACAACATTGGGT
65 AAAGTGCATCAACCAATATAGAATACGTGACAACATTGGGT
* * * * * * *
56436108 TCAATGCCTTGCTTTCTCATTGTGTTAACGATCTCTACAGCTTTAGAAATCATTCCTTCCGTGCA
1 TCAATGCCTCGCTTTATCATTGTGTCAACAATATCTACAGCTTTAGAAACCATCCCTTCCGTGCA
* *
56436173 AAGTGCATCAACCAATATGGTATACGTGACAA
66 AAGTGCATCAACCAATATAGAATACGTGACAA
56436205 TATCAAGTGA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 2 0.02
105 80 0.98
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (105 bp):
TCAATGCCTCGCTTTATCATTGTGTCAACAATATCTACAGCTTTAGAAACCATCCCTTCCGTGCA
AAGTGCATCAACCAATATAGAATACGTGACAACATTGGGT
Found at i:56439793 original size:16 final size:17
Alignment explanation
Indices: 56439749--56439799 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
56439739 TTAAAAATTT
56439749 AAAAAAAGTATTTTAAA
1 AAAAAAAGTATTTTAAA
*
56439766 ATTAAAAA--A-TTTAAA
1 A-AAAAAAGTATTTTAAA
56439781 AAAAAAAGTATTTTAAA
1 AAAAAAAGTATTTTAAA
56439798 AA
1 AA
56439800 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
16 2 0.07
17 9 0.32
18 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
AAAAAAAGTATTTTAAA
Found at i:56439817 original size:32 final size:31
Alignment explanation
Indices: 56439726--56439819 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 31
56439716 GGCCCATTTT
56439726 TATTTTAAAAT-TTTTAAAAATTTAAAAAAAG
1 TATTTTAAAATATTTT-AAAATTTAAAAAAAG
**
56439757 TATTTT-AAA-ATTAAAAAATTTAAAAAAAAAAG
1 TATTTTAAAATATTTTAAAATTT---AAAAAAAG
56439789 TATTTTAAAAATATTTTAAAATTTAAAAAAA
1 TATTTT-AAAATATTTTAAAATTTAAAAAAA
56439820 ATTAAAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
29 7 0.13
30 5 0.10
31 6 0.12
32 21 0.40
34 3 0.06
35 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAATATTTTAAAATTTAAAAAAAG
Found at i:56441336 original size:31 final size:29
Alignment explanation
Indices: 56441293--56441372 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
56441283 ATCTCAAAAG
56441293 TATATATGAACTTT-AGTTTAATGTGTAATTT
1 TATATATGAACTTTGA-TTT--TGTGTAATTT
*
56441324 TATATATTAACTTTGATTTTGTGTAATTT
1 TATATATGAACTTTGATTTTGTGTAATTT
* *
56441353 TATACATGAAATTTTGATTT
1 TATATATG-AACTTTGATTT
56441373 GATCCAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 16 0.37
30 10 0.23
31 16 0.37
32 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (29 bp):
TATATATGAACTTTGATTTTGTGTAATTT
Found at i:56443269 original size:23 final size:23
Alignment explanation
Indices: 56443239--56443302 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
56443229 TTTTATGCAC
56443239 GCAAGTGATAGTGGCACTACGAT
1 GCAAGTGATAGTGGCACTACGAT
* *** * *
56443262 GCAAGTGAAAGCAACACTATGGT
1 GCAAGTGATAGTGGCACTACGAT
*
56443285 GCAAGTGTTAGTGGCACT
1 GCAAGTGATAGTGGCACT
56443303 TCTGTACAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (23 bp):
GCAAGTGATAGTGGCACTACGAT
Found at i:56445629 original size:50 final size:50
Alignment explanation
Indices: 56445514--56445756 Score: 396
Period size: 50 Copynumber: 4.8 Consensus size: 50
56445504 GATAATAACA
* ** * *
56445514 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
56445565 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
56445615 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
56445665 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
56445715 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56445757 TTACCCAAAT
Statistics
Matches: 179, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 146 0.82
51 33 0.18
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:56445872 original size:13 final size:13
Alignment explanation
Indices: 56445851--56445881 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56445841 GCTTAGATCA
*
56445851 TCATCAAATAAAT
1 TCATAAAATAAAT
56445864 TCATAAAATAAAT
1 TCATAAAATAAAT
56445877 TCATA
1 TCATA
56445882 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56446130 original size:29 final size:30
Alignment explanation
Indices: 56446092--56446151 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
56446082 ACCCTCGACT
*
56446092 CTAAA-TTTTTCAAAATTACAATTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
* * *
56446121 CTAAACTTTTACATAATTACATTTTTTCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
56446151 C
1 C
56446152 AAGGCTCGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (30 bp):
CTAAACTTTTACAAAATTACAATTTTGCCC
Found at i:56453206 original size:50 final size:50
Alignment explanation
Indices: 56453091--56453332 Score: 387
Period size: 50 Copynumber: 4.8 Consensus size: 50
56453081 GATAATAACA
* ** * *
56453091 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
56453142 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
56453192 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
56453242 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
56453292 TGCCAATGCCATGTCCCA-ACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56453333 TTACCCAAAT
Statistics
Matches: 178, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 23 0.13
50 122 0.69
51 33 0.19
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:56453448 original size:13 final size:13
Alignment explanation
Indices: 56453427--56453457 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56453417 GCTTAGATCA
*
56453427 TCATCAAATAAAT
1 TCATAAAATAAAT
56453440 TCATAAAATAAAT
1 TCATAAAATAAAT
56453453 TCATA
1 TCATA
56453458 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56453704 original size:30 final size:30
Alignment explanation
Indices: 56453669--56453726 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56453659 CCTCGACTCT
* *
56453669 AACTTTTTCAAAATTATAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
56453699 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
56453727 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:56456987 original size:6 final size:6
Alignment explanation
Indices: 56456976--56457002 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56456966 AAAACATGAA
56456976 AAACAT AAACAT AAACAT AAACAT AAA
1 AAACAT AAACAT AAACAT AAACAT AAA
56457003 AGACATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAACAT
Found at i:56466737 original size:45 final size:44
Alignment explanation
Indices: 56466681--56466767 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
56466671 AACTTAATTT
*
56466681 AATTGTTTTATTATT-TATTTTGAAGCAAATAAAATTATATTTTTA
1 AATTATTTTATT-TTATATTTTGAAGCAAATAAAATTAT-TTTTTA
*
56466726 AATTATTTTATTTTATATTTTGAAGCAAATAAGATTATTTTT
1 AATTATTTTATTTTATATTTTGAAGCAAATAAAATTATTTTT
56466768 AGGTGAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
44 6 0.15
45 33 0.85
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (44 bp):
AATTATTTTATTTTATATTTTGAAGCAAATAAAATTATTTTTTA
Found at i:56468788 original size:16 final size:16
Alignment explanation
Indices: 56468767--56468798 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56468757 TTCTCATTAG
56468767 TAGATGGTACAGTTTA
1 TAGATGGTACAGTTTA
56468783 TAGATGGTACAGTTTA
1 TAGATGGTACAGTTTA
56468799 GGGCCACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
TAGATGGTACAGTTTA
Found at i:56471800 original size:16 final size:16
Alignment explanation
Indices: 56471767--56471800 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56471757 GAATATTGTT
* *
56471767 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
56471783 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
56471799 AA
1 AA
56471801 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:56476518 original size:16 final size:16
Alignment explanation
Indices: 56476485--56476518 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56476475 GGAGATTGTT
* *
56476485 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
56476501 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
56476517 AA
1 AA
56476519 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:56479324 original size:14 final size:15
Alignment explanation
Indices: 56479292--56479329 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
56479282 GATAAAATAA
56479292 TAATTTAA-TATTAT
1 TAATTTAATTATTAT
56479306 T-ATTTAATTATT-T
1 TAATTTAATTATTAT
56479319 TAATTTAATTA
1 TAATTTAATTA
56479330 ATGATAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATTTAATTATTAT
Found at i:56482673 original size:12 final size:12
Alignment explanation
Indices: 56482656--56482682 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56482646 AAATTTTAAG
56482656 TTTTTTATAATT
1 TTTTTTATAATT
56482668 TTTTTTATAATT
1 TTTTTTATAATT
56482680 TTT
1 TTT
56482683 ATAATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:56492056 original size:193 final size:194
Alignment explanation
Indices: 56491681--56492067 Score: 505
Period size: 195 Copynumber: 2.0 Consensus size: 194
56491671 TAAAAGGTTA
56491681 AATAATATTCTCAAGATCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACTA
1 AATAATATTCTCAAGATCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACTA
* *
56491746 TCACGTCCTCTTTGAGATGGTTCCTATATAGATGAATTTCTCACTTTCTTTCAGTGCCCTGCTTG
66 TCACGTCCGCTTTGAGATGGTTCCTATATAGATGAA-TCCTCACTTTCTTTCAGTGCCCTGCTTG
*
56491811 CAAGGAATCCTTACGTTAAATTAGTAATATGAGTAGTGACACCAAAATCAATCCACCAAGTATTT
130 CAAGGAATCCTTACATTAAATTAGTAATATGAGTAGTGACACCAAAATCAATCCACCAAGTATTT
* * * * *
56491876 AATAATCTTCTCAAGAGTC-ATTTGATTATTAGTCTCTAAGATTAAGCGTTAGGTTCCAATAGCT
1 AATAATATTCTCAAGA-TCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACT
* * * ** * *
56491940 ATTACTTCCGCTTTGAGATGGTTCCTCATGTAGATG-A-CCTCACTTTCTTTC-GATTTCTTGGT
65 ATCACGTCCGCTTTGAGATGGTTCCT-ATATAGATGAATCCTCACTTTCTTTCAG-TGCCCTGCT
* ** * * *
56492002 TGTAAGGAATCCTTACATTGGATTAGTAATGTGAGTAGT-AGCTCCAGAATCAATCCACCAAGTA
128 TGCAAGGAATCCTTACATTAAATTAGTAATATGAGTAGTGA-CACCAAAATCAATCCACCAAGTA
56492066 TT
192 TT
56492068 AGAAAGATCT
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
192 2 0.01
193 75 0.45
195 80 0.48
196 10 0.06
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (194 bp):
AATAATATTCTCAAGATCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACTA
TCACGTCCGCTTTGAGATGGTTCCTATATAGATGAATCCTCACTTTCTTTCAGTGCCCTGCTTGC
AAGGAATCCTTACATTAAATTAGTAATATGAGTAGTGACACCAAAATCAATCCACCAAGTATTT
Found at i:56494895 original size:2 final size:2
Alignment explanation
Indices: 56494884--56494918 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
56494874 TGCGCGCGCG
*
56494884 CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
56494919 TCACCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.51, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:56498602 original size:17 final size:17
Alignment explanation
Indices: 56498580--56498616 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
56498570 CATCTTCATC
56498580 CACAGTAGTTGAAGATG
1 CACAGTAGTTGAAGATG
56498597 CACAGTAGTTGAAGATG
1 CACAGTAGTTGAAGATG
56498614 CAC
1 CAC
56498617 CAAAGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (17 bp):
CACAGTAGTTGAAGATG
Found at i:56505950 original size:29 final size:29
Alignment explanation
Indices: 56505917--56505975 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
56505907 AATACCAAAG
*
56505917 ATATATAAAATTCTGCATTTGAAGATGTA
1 ATATATAAAATTCAGCATTTGAAGATGTA
56505946 ATATATAAAATTCAGCATTTGAAGATGTA
1 ATATATAAAATTCAGCATTTGAAGATGTA
56505975 A
1 A
56505976 AAATTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.36
Consensus pattern (29 bp):
ATATATAAAATTCAGCATTTGAAGATGTA
Found at i:56514946 original size:13 final size:13
Alignment explanation
Indices: 56514928--56514956 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56514918 AAACAATGGA
56514928 TTTATTTTTATTT
1 TTTATTTTTATTT
56514941 TTTATTTTTATTT
1 TTTATTTTTATTT
56514954 TTT
1 TTT
56514957 CAGAGCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:56516972 original size:2 final size:2
Alignment explanation
Indices: 56516967--56517022 Score: 50
Period size: 2 Copynumber: 29.0 Consensus size: 2
56516957 ATATATTAAA
56516967 AT AT AT A- AT AT A- AT AT AT -T A- AT AT AT AT GAT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT
56517007 AT CAT AT AT AT -T AT AT
1 AT -AT AT AT AT AT AT AT
56517023 TAAAAGGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
1 5 0.11
2 35 0.76
3 6 0.13
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:56516982 original size:22 final size:22
Alignment explanation
Indices: 56516956--56517000 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56516946 TGAAATTATA
56516956 AATATATTAAAATATATAATAT
1 AATATATTAAAATATATAATAT
* *
56516978 AATATATTAATATATATGATAT
1 AATATATTAAAATATATAATAT
56517000 A
1 A
56517001 TCATATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATATATTAAAATATATAATAT
Found at i:56517588 original size:32 final size:30
Alignment explanation
Indices: 56517514--56517588 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
56517504 CGAAACTATA
*
56517514 AATATATTAAAATATATAATATAATTTATT
1 AATATATTAAAATATATAATATAATATATT
*
56517544 AATATATATAAAATCATATCATAT-ATCATATAT
1 AATATAT-TAAAAT-ATATAATATAAT-ATAT-T
*
56517577 ATTATATTAAAA
1 AATATATTAAAA
56517589 GGCATACTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 7 0.18
31 8 0.21
32 16 0.42
33 7 0.18
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATATTAAAATATATAATATAATATATT
Found at i:56521641 original size:25 final size:25
Alignment explanation
Indices: 56521613--56521691 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
56521603 CTAATGGCCG
56521613 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
56521638 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
56521660 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
56521685 ATGTGAT
1 ATGTGAT
56521692 AAGGGCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:56521663 original size:47 final size:47
Alignment explanation
Indices: 56521597--56521820 Score: 394
Period size: 47 Copynumber: 4.7 Consensus size: 47
56521587 GAAATGATAG
*
56521597 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
*
56521644 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
*
56521691 TAAGGGCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
*
56521738 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
*
56521785 TAGGGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGA-AAGT
56521821 CCCGAAGGGC
Statistics
Matches: 170, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 167 0.98
48 3 0.02
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
Found at i:56523877 original size:43 final size:43
Alignment explanation
Indices: 56523829--56523931 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
56523819 TTGGTTTTCA
56523829 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
56523872 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
56523915 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
56523932 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:56523948 original size:29 final size:29
Alignment explanation
Indices: 56523913--56523986 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
56523903 GTTGTGAGAT
* *
56523913 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
56523942 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
*
56523971 TGGCACTAAGTATGCG
1 TGGCACTAAGTGTGCG
56523987 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:56524420 original size:40 final size:40
Alignment explanation
Indices: 56524297--56524479 Score: 158
Period size: 40 Copynumber: 4.6 Consensus size: 40
56524287 TCGAATGATG
** *
56524297 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
56524337 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
56524377 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
56524417 TCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
56524457 TCTGTGCTAAATCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
56524480 ATATGCTGGT
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 97 0.83
41 19 0.16
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:56527959 original size:47 final size:47
Alignment explanation
Indices: 56527893--56528069 Score: 318
Period size: 47 Copynumber: 3.7 Consensus size: 47
56527883 GAAATGATAG
*
56527893 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
56527940 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
*
56527987 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
*
56528034 TAGGGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGA-AAGT
56528070 CCCGAAGGGC
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 122 0.98
48 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGA
Found at i:56531434 original size:23 final size:25
Alignment explanation
Indices: 56531408--56531456 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
56531398 AAATAATTTT
56531408 TGAAAAAT-GAAAAT-AAAAATATG
1 TGAAAAATAGAAAATAAAAAATATG
* *
56531431 TGAAAATTAGAGAATAAAAAATATG
1 TGAAAAATAGAAAATAAAAAATATG
56531456 T
1 T
56531457 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.24
Consensus pattern (25 bp):
TGAAAAATAGAAAATAAAAAATATG
Found at i:56534691 original size:21 final size:19
Alignment explanation
Indices: 56534653--56534699 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
56534643 GAAGCGCAGT
56534653 ATTTCTTTTTTAAAACGA-A
1 ATTT-TTTTTTAAAACGAGA
56534672 AGTTTTTTTTTAAAATACGAGA
1 A-TTTTTTTTT-AAA-ACGAGA
56534694 ATTTTT
1 ATTTTT
56534700 GAAAACACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 9 0.38
22 2 0.08
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (19 bp):
ATTTTTTTTTAAAACGAGA
Found at i:56534698 original size:17 final size:17
Alignment explanation
Indices: 56534678--56535085 Score: 167
Period size: 17 Copynumber: 23.3 Consensus size: 17
56534668 CGAAAGTTTT
*
56534678 TTTTTAAAATACGAGAA
1 TTTTTAAAACACGAGAA
56534695 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAGAA
*
56534713 TTTGT-AAACACGA-AA
1 TTTTTAAAACACGAGAA
* *
56534728 ATTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
*
56534746 TTTTTGGAAAAAACGA-AA
1 TTTTT--AAAACACGAGAA
* *
56534764 TTTTCTTAAAACACGACATTT
1 -TTT-TTAAAACACGAGA--A
* *
56534785 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAGAA
* * *
56534802 TTTTTAAAACAAGACATT
1 TTTTTAAAACACGAGA-A
* *
56534820 TTTTTGAAACAC-A-ATT
1 TTTTTAAAACACGAGA-A
*
56534836 TTTTCTTAAA-A--A-AA
1 TTTT-TAAAACACGAGAA
*
56534850 -TTTT-AAATACGAGAA
1 TTTTTAAAACACGAGAA
*
56534865 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAGAA
56534882 TTTTTAAAACACG-GAAA
1 TTTTTAAAACACGAG-AA
*
56534899 TTTTTTTTTAAAAACACGAAAA
1 ----TTTTT-AAAACACGAGAA
* *
56534921 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-T-AAAACACGAGAA
* *
56534942 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAGAA
*
56534959 TTTTGAAAACACGA-AGA
1 TTTTTAAAACACGAGA-A
* *
56534976 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAGAA
*
56534993 TTTTTAAAAGCACGAGGA
1 TTTTTAAAA-CACGAGAA
* * *
56535011 TTATTGAAAGCACGAAAA
1 TT-TTTAAAACACGAGAA
* * *
56535029 TTTGTAAAAAACGACAA
1 TTTTTAAAACACGAGAA
* *
56535046 TTTTTGAAATACGAGAAA
1 TTTTTAAAACACGAG-AA
* * *
56535064 TTTTTTAAACGCGAAAA
1 TTTTTAAAACACGAGAA
56535081 TTTTT
1 TTTTT
56535086 TTCAAACACG
Statistics
Matches: 302, Mismatches: 57, Indels: 64
0.71 0.13 0.15
Matches are distributed among these distances:
11 3 0.01
12 2 0.01
13 3 0.01
14 1 0.00
15 9 0.03
16 21 0.07
17 122 0.40
18 72 0.24
19 30 0.10
20 12 0.04
21 17 0.06
22 10 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:56534845 original size:36 final size:37
Alignment explanation
Indices: 56534763--56534846 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
56534753 AAAAAACGAA
* **
56534763 ATTTTCTTAAAACACGACATTTTTTTTGAAACACGGG
1 ATTTTCTTAAAACAAGACATTTTTTTTGAAACACAAG
* *
56534800 AATTT-TTAAAACAAGACA-TTTTTTTGAAACACAAT
1 ATTTTCTTAAAACAAGACATTTTTTTTGAAACACAAG
*
56534835 TTTTTCTTAAAA
1 ATTTTCTTAAAA
56534847 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 17 0.44
36 18 0.46
37 4 0.10
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (37 bp):
ATTTTCTTAAAACAAGACATTTTTTTTGAAACACAAG
Found at i:56534869 original size:16 final size:16
Alignment explanation
Indices: 56534845--56535119 Score: 100
Period size: 17 Copynumber: 15.4 Consensus size: 16
56534835 TTTTTCTTAA
* *
56534845 AAAAATTTTAAATACG
1 AAAATTTTTAAACACG
*
56534861 AGAATTTTTAAAACACG
1 AAAATTTTT-AAACACG
56534878 AAAATTTTTAAAACACGG
1 AAAATTTTT-AAACAC-G
*
56534896 AAATTTTTTTTTAAAAACACG
1 AAA---ATTTTT--AAACACG
*
56534917 AAAATTTTTTCTGAAAACAAG
1 AAAA--TTTT-T--AAACACG
*
56534938 AAAATTTTTGAAACACT
1 AAAATTTTT-AAACACG
* *
56534955 AGAATTTTGAAAACACG
1 AAAATTTT-TAAACACG
* *
56534972 AAGATTTTTGAAACATG
1 AAAATTTTT-AAACACG
*
56534989 AGAATTTTTAAAAGCACG
1 AAAATTTTT-AAA-CACG
** *
56535007 AGGATTATTGAAAGCACG
1 AAAATT-TTTAAA-CACG
* *
56535025 AAAATTTGTAAAAAACG
1 AAAATTT-TTAAACACG
* *
56535042 ACAATTTTTGAAATACG
1 AAAATTTTT-AAACACG
*
56535059 AGAAATTTTTTAAACGCG
1 A-AAA-TTTTTAAACACG
56535077 AAAATTTTTTTCAAACACG
1 AAAA--TTTTT-AAACACG
* *
56535096 AAAACTTTTGAAAACGCG
1 AAAA-TTTT-TAAACACG
56535114 AAAATT
1 AAAATT
56535120 CGAAAATTTC
Statistics
Matches: 201, Mismatches: 38, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
16 8 0.04
17 83 0.41
18 57 0.28
19 21 0.10
20 4 0.02
21 21 0.10
22 7 0.03
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (16 bp):
AAAATTTTTAAACACG
Found at i:56534912 original size:22 final size:21
Alignment explanation
Indices: 56534865--56534946 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
56534855 AATACGAGAA
56534865 TTTTTAAAACACGAAAA----
1 TTTTTAAAACACGAAAATTTT
*
56534882 TTTTTAAAACACGGAAATTTT
1 TTTTTAAAACACGAAAATTTT
56534903 TTTTTAAAAACACGAAAATTTT
1 TTTTT-AAAACACGAAAATTTT
* * *
56534925 TTCTGAAAACAAGAAAATTTT
1 TTTTTAAAACACGAAAATTTT
56534946 T
1 T
56534947 GAAACACTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
17 16 0.29
21 21 0.38
22 18 0.33
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTTAAAACACGAAAATTTT
Found at i:56535053 original size:35 final size:32
Alignment explanation
Indices: 56534930--56535085 Score: 114
Period size: 35 Copynumber: 4.5 Consensus size: 32
56534920 ATTTTTTCTG
* *
56534930 AAAACAAGAAAATTTTTGAAACACTAGAATTTT
1 AAAACACG-AAATTTTTGAAACACGAGAATTTT
*
56534963 GAAAACACGAAGATTTTTGAAACATGAGAATTTTT
1 -AAAACACGAA-ATTTTTGAAACACGAGAA-TTTT
* * *
56534998 AAAAGCACGAGGATTATTGAAAGCACGAAAATTTGT
1 AAAA-CACGA-AATTTTTGAAA-CACGAGAATTT-T
* *
56535034 AAAAAACGACAATTTTTGAAATACGAGAAATTTTT
1 AAAACACGA-AATTTTTGAAACACGAG-AA-TTTT
* *
56535069 TAAACGCGAAAATTTTT
1 AAAACACG-AAATTTTT
56535086 TTCAAACACG
Statistics
Matches: 97, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
33 2 0.02
34 31 0.32
35 49 0.51
36 15 0.15
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (32 bp):
AAAACACGAAATTTTTGAAACACGAGAATTTT
Found at i:56535115 original size:18 final size:19
Alignment explanation
Indices: 56535070--56535118 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
56535060 GAAATTTTTT
* **
56535070 AAACGCGAAAATTTTTTTC
1 AAACGCGAAAATCTTTTGA
*
56535089 AAACACGAAAA-CTTTTGA
1 AAACGCGAAAATCTTTTGA
56535107 AAACGCGAAAAT
1 AAACGCGAAAAT
56535119 TCGAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (19 bp):
AAACGCGAAAATCTTTTGA
Found at i:56535163 original size:18 final size:17
Alignment explanation
Indices: 56535114--56535164 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
56535104 TGAAAACGCG
56535114 AAAATTCGAAAATTTCT
1 AAAATTCGAAAATTTCT
* * *
56535131 AAAATACGAGTAATTTTT
1 AAAATTCGA-AAATTTCT
56535149 AAAGATTCGAAAATTT
1 AAA-ATTCGAAAATTT
56535165 GAAACAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAATTCGAAAATTTCT
Found at i:56535689 original size:26 final size:26
Alignment explanation
Indices: 56535650--56535706 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
56535640 CTTTTTTTTT
* *
56535650 CTGCTGCAGGATTCAGGCCTGGGGGC
1 CTGCTGCAGAATTCAGGCCAGGGGGC
* *
56535676 CTGCTGCCGAATTCGGGCCAGGGGGC
1 CTGCTGCAGAATTCAGGCCAGGGGGC
56535702 CTGCT
1 CTGCT
56535707 TGGTCTGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.30, G:0.40, T:0.19
Consensus pattern (26 bp):
CTGCTGCAGAATTCAGGCCAGGGGGC
Found at i:56535838 original size:20 final size:19
Alignment explanation
Indices: 56535813--56535856 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
56535803 TGGCTGTGGC
56535813 CTGCTTCTATTTTATTTTTT
1 CTGCTT-TATTTTATTTTTT
* *
56535833 CTGCTTTGTTTTGTTTTTT
1 CTGCTTTATTTTATTTTTT
*
56535852 TTGCT
1 CTGCT
56535857 GCTTTGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.05, C:0.14, G:0.11, T:0.70
Consensus pattern (19 bp):
CTGCTTTATTTTATTTTTT
Found at i:56535849 original size:19 final size:21
Alignment explanation
Indices: 56535813--56535866 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
56535803 TGGCTGTGGC
*
56535813 CTGCTTCTATTTTA-TTTTTT-
1 CTGCTT-TGTTTTATTTTTTTG
*
56535833 CTGCTTTGTTTTGTTTTTTTTG
1 CTGCTTTGTTTT-ATTTTTTTG
56535855 CTGCTTTGTTTT
1 CTGCTTTGTTTT
56535867 TTTCAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.17
20 6 0.21
21 6 0.21
22 12 0.41
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (21 bp):
CTGCTTTGTTTTATTTTTTTG
Found at i:56535868 original size:19 final size:19
Alignment explanation
Indices: 56535822--56535869 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
56535812 CCTGCTTCTA
*
56535822 TTTTATTTTTTCTGCTTTG
1 TTTTTTTTTTTCTGCTTTG
56535841 TTTTGTTTTTTTTGCTGCTTTG
1 -TTT-TTTTTTTT-CTGCTTTG
56535863 TTTTTTT
1 TTTTTTT
56535870 CAAAAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
21 10 0.40
22 8 0.32
ACGTcount: A:0.02, C:0.08, G:0.12, T:0.77
Consensus pattern (19 bp):
TTTTTTTTTTTCTGCTTTG
Found at i:56536451 original size:29 final size:29
Alignment explanation
Indices: 56536418--56536534 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
56536408 TGTAATTTTT
*
56536418 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
56536447 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
56536477 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
56536506 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
56536535 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:56536473 original size:30 final size:30
Alignment explanation
Indices: 56536433--56536534 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
56536423 ATTTAGGATT
*
56536433 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
56536463 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
56536493 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
56536523 AAAATGCAATTT
1 AAAATGAAATTT
56536535 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Done.