Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 131 of 144
Found at i:40756012 original size:46 final size:44
Alignment explanation
Indices: 40755909--40756012 Score: 102
Period size: 46 Copynumber: 2.3 Consensus size: 44
40755899 TGAAGAAAAT
* * * * **
40755909 AAATA-AAAGATATGTATATGGATTATAAAATATAAAAGCATAA
1 AAATATAAATATAGGTATATAGATTATAAAATAAAAAAAAATAA
*
40755952 ATATATACATATATAGGTATATAGATTATAAAATACAAAAAAAATATA
1 AAATATA-A-ATATAGGTATATAGATTATAAAATA-AAAAAAAATA-A
40756000 AAATATAAATATA
1 AAATATAAATATA
40756013 TACGTTATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
43 4 0.08
44 1 0.02
45 1 0.02
46 27 0.56
47 8 0.17
48 7 0.15
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.30
Consensus pattern (44 bp):
AAATATAAATATAGGTATATAGATTATAAAATAAAAAAAAATAA
Found at i:40756336 original size:3 final size:3
Alignment explanation
Indices: 40756328--40756364 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
40756318 CAAATAAAAC
*
40756328 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
40756365 ATGCTAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40756373 original size:22 final size:22
Alignment explanation
Indices: 40756319--40756366 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40756309 ATAAAATGGC
40756319 AAATAA-AACTAATAATAATAAT
1 AAATAATAA-TAATAATAATAAT
* *
40756341 TAATAATAATAATAATGATAAT
1 AAATAATAATAATAATAATAAT
40756363 AAAT
1 AAAT
40756367 GCTAATACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATAATAATAATAATAATAAT
Found at i:40758445 original size:21 final size:20
Alignment explanation
Indices: 40758421--40758459 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40758411 TGAATTTTAT
40758421 GAATATATATAAGTGTTGGCC
1 GAATATATATAAGT-TTGGCC
* *
40758442 GAATGTTTATAAGTTTGG
1 GAATATATATAAGTTTGG
40758460 GAGCTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (20 bp):
GAATATATATAAGTTTGGCC
Found at i:40761268 original size:16 final size:16
Alignment explanation
Indices: 40761247--40761277 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40761237 AGAGAAGAAC
40761247 AAGCTTCGGCCAAACT
1 AAGCTTCGGCCAAACT
*
40761263 AAGCTTTGGCCAAAC
1 AAGCTTCGGCCAAAC
40761278 CCGGGGATTA
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:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (16 bp):
AAGCTTCGGCCAAACT
Found at i:40762118 original size:37 final size:36
Alignment explanation
Indices: 40762049--40762169 Score: 172
Period size: 36 Copynumber: 3.4 Consensus size: 36
40762039 AAAGGAATAA
40762049 TGATTCTACTG-AAGTGCTCAACAAGCAATATCTAC
1 TGATTCTACTGAAAGTGCTCAACAAGCAATATCTAC
* *
40762084 TGATTCTATTGAAAGTGCTCAAACGAGCAATATCTAC
1 TGATTCTACTGAAAGTGCTC-AACAAGCAATATCTAC
* * *
40762121 TTATTCTACTGAAAGAGCTTAACAAGCAATATCTAC
1 TGATTCTACTGAAAGTGCTCAACAAGCAATATCTAC
*
40762157 TGATCCTACTGAA
1 TGATTCTACTGAA
40762170 TATGTTTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
35 10 0.13
36 34 0.45
37 31 0.41
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (36 bp):
TGATTCTACTGAAAGTGCTCAACAAGCAATATCTAC
Found at i:40762186 original size:73 final size:72
Alignment explanation
Indices: 40762051--40762192 Score: 187
Period size: 73 Copynumber: 2.0 Consensus size: 72
40762041 AGGAATAATG
* * * *
40762051 ATTCTACTGAAGTGCTCAACAAGCAATATCTACTGATTCTATTGAAAGTGCTCAAACGAGCAATA
1 ATTCTACTGAAGAGCTCAACAAGCAATATCTACTGATCCTACTGAAAGTGCTCAAACAAGCAATA
40762116 TCTACTT
66 TCTACTT
* * *
40762123 ATTCTACTGAAAGAGCTTAACAAGCAATATCTACTGATCCTACTGAATA-TGTTTAAACAAGCAA
1 ATTCTACTG-AAGAGCTCAACAAGCAATATCTACTGATCCTACTGAA-AGTGCTCAAACAAGCAA
*
40762187 TGTCTA
64 TATCTA
40762193 GTTGTAATAG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
72 9 0.15
73 50 0.83
74 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (72 bp):
ATTCTACTGAAGAGCTCAACAAGCAATATCTACTGATCCTACTGAAAGTGCTCAAACAAGCAATA
TCTACTT
Found at i:40768318 original size:6 final size:6
Alignment explanation
Indices: 40768307--40768382 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
40768297 AAAAAAAAGG
* * *
40768307 CAAAAT CAAAAT CAAAAA CAAAA- -AAGAA- GAAAAA CAAAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAA-AAT CAAAAT C-AAAAT CAAAAT
* * * *
40768354 CAAAGT CAAAAT GAAAAT GAAAAT GAAAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAA
40768383 AAGAGAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
4 2 0.03
5 4 0.07
6 49 0.82
7 5 0.08
ACGTcount: A:0.71, C:0.11, G:0.08, T:0.11
Consensus pattern (6 bp):
CAAAAT
Found at i:40768398 original size:15 final size:15
Alignment explanation
Indices: 40768372--40768416 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
40768362 AAATGAAAAT
*
40768372 GAAAATGAAAAAAGA
1 GAAAAAGAAAAAAGA
* *
40768387 GAGAAAGAAAAAAGG
1 GAAAAAGAAAAAAGA
*
40768402 GAAAAAGGAAAAAGA
1 GAAAAAGAAAAAAGA
40768417 AAAGGAGAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAAAGA
Found at i:40770823 original size:129 final size:129
Alignment explanation
Indices: 40770567--40770812 Score: 438
Period size: 129 Copynumber: 1.9 Consensus size: 129
40770557 AAAACCTAGC
*
40770567 TCCCTGACCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGC
1 TCCCTGACCAGCAGTGCAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGC
*
40770632 AGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGGAGATTTAAGCCACAAGCCCTATA
66 AGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGCCCTATA
* *
40770696 TCCCTGACCAGCAGTGCAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGC
1 TCCCTGACCAGCAGTGCAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGC
* *
40770761 AGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCATATTTAAGCC
66 AGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
40770813 GATAATCCTA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 111 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (129 bp):
TCCCTGACCAGCAGTGCAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGC
AGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGCCCTATA
Found at i:40770950 original size:44 final size:45
Alignment explanation
Indices: 40770899--40771028 Score: 142
Period size: 45 Copynumber: 2.9 Consensus size: 45
40770889 TGGATCGCAT
40770899 CAGGTCTTACCTCCCTGAGGTTGCAGTGGAGCAGA-CTG-AG-TAA
1 CAGGTCTTACCTCCCTGAGGTTGCAGTGGAGCAGATC-GAAGATAA
*
40770942 GCAGGTCTTATCC-CCCTGAGGTTGCAGTGGGGCAGATCGAAGATAA
1 -CAGGTCTTA-CCTCCCTGAGGTTGCAGTGGAGCAGATCGAAGATAA
* ** * * *
40770988 AAAATCTTATCTCCCTGACGTTGCAGTGGAGCAGATTGAAG
1 CAGGTCTTACCTCCCTGAGGTTGCAGTGGAGCAGATCGAAG
40771029 CCGATAATCC
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
44 33 0.45
45 37 0.51
46 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (45 bp):
CAGGTCTTACCTCCCTGAGGTTGCAGTGGAGCAGATCGAAGATAA
Found at i:40771058 original size:218 final size:218
Alignment explanation
Indices: 40770799--40771195 Score: 645
Period size: 218 Copynumber: 1.8 Consensus size: 218
40770789 AGTGTAAGGA
* *
40770799 AGCATATTTAAGCCGATAATCCTATCTCCCTAAAATTGTAGT-GAAGCGGATTAAAGTAATAGAT
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAA-CGGATTAAAGTAATAGAT
* *
40770863 CTTATCTTTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTACCTCCCTGAGGTTGCAGTGG
65 CTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCACCAGGTCTTACCTCCCTGAGGTTGCAGTGG
* * * * *
40770928 AGCAGACTGAGTAAG-CAGGTCTTATCCCCCTGAGGTTGCAGTGGGGCAGATCGAAGATAAAAAA
130 AACAGACTGAG-AAGACAAGTCTTATCACCCTGAAGTTACAGTGGGGCAGATCGAAGATAAAAAA
40770992 TCTTATCTCCCTGACGTTGCAGTGG
194 TCTTATCTCCCTGACGTTGCAGTGG
* *
40771017 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAACGGATTAAAGTAATAGATC
* *
40771082 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCACCAGGTCTTATCTCCTTGAGGTTGCAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCACCAGGTCTTACCTCCCTGAGGTTGCAGTGGA
40771147 ACAGACTGAGAAGACAAGTCTTATCACCCTGAAGTTACAGTGGGGCAGA
131 ACAGACTGAGAAGACAAGTCTTATCACCCTGAAGTTACAGTGGGGCAGA
40771196 CTGAGAATAG
Statistics
Matches: 164, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
217 3 0.02
218 158 0.96
219 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (218 bp):
AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAACGGATTAAAGTAATAGATC
TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCACCAGGTCTTACCTCCCTGAGGTTGCAGTGGA
ACAGACTGAGAAGACAAGTCTTATCACCCTGAAGTTACAGTGGGGCAGATCGAAGATAAAAAATC
TTATCTCCCTGACGTTGCAGTGG
Found at i:40771087 original size:44 final size:44
Alignment explanation
Indices: 40770990--40771102 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 44
40770980 GAAGATAAAA
* * * *
40770990 AATCTTATCTCCCTGACGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAAT
* * * *
40771034 AATCCTATCTCCCTGAAGTTGTAGTGGAACGGATTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAAT
*
40771077 AGATCTTATCTCTCTGAAGTTGCAGT
1 A-ATCTTATCTCCCTGAAGTTGCAGT
40771103 AGAGTGGATC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 3 0.05
44 54 0.95
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAAT
Found at i:40772081 original size:18 final size:17
Alignment explanation
Indices: 40772036--40772095 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 17
40772026 GGTGATTGGA
*
40772036 TTTTCTTTCTTTTTTTC
1 TTTTCTTTGTTTTTTTC
*
40772053 TTCATCTTTTGTTTTTTTC
1 TT-TTC-TTTGTTTTTTTC
**
40772072 TCTTTCTTTGGGTTTTTC
1 T-TTTCTTTGTTTTTTTC
40772090 TTTTCT
1 TTTTCT
40772096 GTTCGTCCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 7 0.20
18 13 0.37
19 14 0.40
20 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.07, T:0.75
Consensus pattern (17 bp):
TTTTCTTTGTTTTTTTC
Found at i:40773934 original size:197 final size:198
Alignment explanation
Indices: 40773598--40773993 Score: 749
Period size: 197 Copynumber: 2.0 Consensus size: 198
40773588 TTCGCTATTC
*
40773598 TATCATAATTCGTTTGTAAGAAATCTTTTATTTTAAAGCACAACAATCATTCTATTTCACAATAA
1 TATCATAATTCATTTGTAAGAAATCTTTTATTTTAAAGCACAACAATCATTCTATTTCACAATAA
* *
40773663 AAAACCTAGCGTTTATATTTCTTGAGAGAATTGTGCCCTAACTTTCTGGGTTCCAATTCTTCTCG
66 AAAACCTAGCGTTTATATTTCTTGAGAGAATTGTGCCCTAACTTACTAGGTTCCAATTCTTCTCG
40773728 ATGAATTTAGATCACAATGTGTTTATTTAATTAAAACCATACAATTTTAAAACTAAGCATTTAGG
131 ATGAATTTAGATCACAATGTGTTTATTTAATTAAAACCATACAATTTTAAAACTAAGCATTTAGG
40773793 ATT
196 ATT
*
40773796 TATCATAATTCATTTGTAAGAATTCTTTTATTTTAAAGCACAACAATCATTCTATTTCACAAT-A
1 TATCATAATTCATTTGTAAGAAATCTTTTATTTTAAAGCACAACAATCATTCTATTTCACAATAA
40773860 AAAACCTAGCGTTTATATTTCTTGAGAGAATTGTGCCCTAACTTACTAGGTTCCAATTCTTCTCG
66 AAAACCTAGCGTTTATATTTCTTGAGAGAATTGTGCCCTAACTTACTAGGTTCCAATTCTTCTCG
40773925 ATGAATTTAGATCACAATGTGTTTATTTAATTAAAACCATACAATTTTAAAACTAAGCATTTAGG
131 ATGAATTTAGATCACAATGTGTTTATTTAATTAAAACCATACAATTTTAAAACTAAGCATTTAGG
40773990 ATT
196 ATT
40773993 T
1 T
40773994 CAAAATGTCG
Statistics
Matches: 194, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
197 133 0.69
198 61 0.31
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (198 bp):
TATCATAATTCATTTGTAAGAAATCTTTTATTTTAAAGCACAACAATCATTCTATTTCACAATAA
AAAACCTAGCGTTTATATTTCTTGAGAGAATTGTGCCCTAACTTACTAGGTTCCAATTCTTCTCG
ATGAATTTAGATCACAATGTGTTTATTTAATTAAAACCATACAATTTTAAAACTAAGCATTTAGG
ATT
Found at i:40774636 original size:36 final size:37
Alignment explanation
Indices: 40774565--40774909 Score: 374
Period size: 36 Copynumber: 9.3 Consensus size: 37
40774555 TCGACACTAG
*
40774565 TGATTCTACTAAAAGTTCTCAAACGAGCAATATCTAC
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
*
40774602 TGATTCTACTAAAAGTGCTC-AATGAGCAATATCTAC
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
* * * *
40774638 TGATCCTACTAAATGTGCTCAAACGAGCAATGTCTAG
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
* *
40774675 TGGTTCTACT-GAAGTGCTCAAACGAGCAATATCTAC
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
* * * *
40774711 TGATTCTACAAAAAGTGTTC-AATGAGCAATATCTAT
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
* * * * *
40774747 TGATCCTACTAAATGTGCTCAAACGACCAATGTGTAC
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
* * *
40774784 TGATTCTACT-GATGTGCTCAAATGAGCAATATCTAC
1 TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
* *
40774820 TGATTCTACTAAATAGTTGCTCAAACGAGCAATATCCAT
1 TGATTCTACTAAA-AG-TGCTCAAACGAGCAATATCTAC
* * * * *
40774859 TGATTATACTGAATGCTTGCTCAAACGAGCATTATCCAC
1 TGATTCTACTAAAAG--TGCTCAAACGAGCAATATCTAC
*
40774898 TGATTATACTAA
1 TGATTCTACTAA
40774910 TAAGATTTTC
Statistics
Matches: 256, Mismatches: 45, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
36 124 0.48
37 68 0.27
38 2 0.01
39 62 0.24
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (37 bp):
TGATTCTACTAAAAGTGCTCAAACGAGCAATATCTAC
Found at i:40774659 original size:73 final size:74
Alignment explanation
Indices: 40774565--40774909 Score: 383
Period size: 73 Copynumber: 4.7 Consensus size: 74
40774555 TCGACACTAG
* * *
40774565 TGATTCTACTAAAAGTTCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTC-AATGAGC
1 TGATTCTACTAAATGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAACGAGC
40774629 AATATCTAC
66 AATATCTAC
* * * * *
40774638 TGATCCTACTAAATGTGCTCAAACGAGCAATGTCTAGTGGTTCTACT-GAAGTGCTCAAACGAGC
1 TGATTCTACTAAATGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAACGAGC
40774702 AATATCTAC
66 AATATCTAC
* * * * * * * *
40774711 TGATTCTACAAAAAGTGTTC-AATGAGCAATATCTATTGATCCTACTAAATGTGCTCAAACGACC
1 TGATTCTACTAAATGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAACGAGC
* *
40774775 AATGTGTAC
66 AATATCTAC
* *
40774784 TGATTCTACT-GATGTGCTCAAATGAGCAATATCTACTGATTCTACTAAATAGTTGCTCAAACGA
1 TGATTCTACTAAATGTGCTCAAACGAGCAATATCTACTGATTCTACTAAA-AG-TGCTCAAACGA
* *
40774848 GCAATATCCAT
64 GCAATATCTAC
* * * * *
40774859 TGATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTGATTATACTAA
1 TGATTCTACTAAATG--TGCTCAAACGAGCAATATCTACTGATTCTACTAA
40774910 TAAGATTTTC
Statistics
Matches: 224, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
72 35 0.16
73 129 0.58
74 1 0.00
75 26 0.12
76 3 0.01
78 30 0.13
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (74 bp):
TGATTCTACTAAATGTGCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAAACGAGC
AATATCTAC
Found at i:40774733 original size:109 final size:109
Alignment explanation
Indices: 40774561--40774889 Score: 451
Period size: 109 Copynumber: 3.0 Consensus size: 109
40774551 GGTTTCGACA
* * *
40774561 CTAGTGATTCTACTAAAAGTTCTCAAACGAGCAATATCTACTGATTCTACTAAAAGTGCTCAATG
1 CTAGTGATTCTACT-GAAGTGCTCAAACGAGCAATATCTACTGATTCTACAAAAAGTGCTCAATG
*
40774626 AGCAATATCTACTGATCCTACTAAATGTGCTCAAACGAGCAATGT
65 AGCAATATCTATTGATCCTACTAAATGTGCTCAAACGAGCAATGT
* *
40774671 CTAGTGGTTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACAAAAAGTGTTCAATGA
1 CTAGTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACAAAAAGTGCTCAATGA
*
40774736 GCAATATCTATTGATCCTACTAAATGTGCTCAAACGACCAATGT
66 GCAATATCTATTGATCCTACTAAATGTGCTCAAACGAGCAATGT
* * * * *
40774780 GTACTGATTCTACTGATGTGCTCAAATGAGCAATATCTACTGATTCTACTAAATAGTTGCTCAAA
1 CTAGTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTAC-AAAAAG-TGCTC-AA
* * ** *
40774845 CGAGCAATATCCATTGATTATACTGAATGCTTGCTCAAACGAGCA
63 TGAGCAATATCTATTGATCCTACTAAATG--TGCTCAAACGAGCA
40774890 TTATCCACTG
Statistics
Matches: 194, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
109 133 0.69
110 18 0.09
111 4 0.02
112 26 0.13
114 13 0.07
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (109 bp):
CTAGTGATTCTACTGAAGTGCTCAAACGAGCAATATCTACTGATTCTACAAAAAGTGCTCAATGA
GCAATATCTATTGATCCTACTAAATGTGCTCAAACGAGCAATGT
Found at i:40776622 original size:17 final size:17
Alignment explanation
Indices: 40776600--40776667 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 17
40776590 TAATTTGAAA
40776600 AAAAATTAAAAATATTT
1 AAAAATTAAAAATATTT
*
40776617 AAAAA-TGAAAATATTT
1 AAAAATTAAAAATATTT
* *
40776633 --ACA--AAAATTATTT
1 AAAAATTAAAAATATTT
*
40776646 AAAAATT-AAAATAATT
1 AAAAATTAAAAATATTT
40776662 AAAAAT
1 AAAAAT
40776668 AATTAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 2 0.05
16 23 0.57
17 5 0.12
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (17 bp):
AAAAATTAAAAATATTT
Found at i:40776627 original size:16 final size:15
Alignment explanation
Indices: 40776608--40776669 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 15
40776598 AAAAAAATTA
40776608 AAAATATTTAAAAAT
1 AAAATATTTAAAAAT
*
40776623 GAAAATATTT-ACAA-
1 -AAAATATTTAAAAAT
*
40776637 AAATTATTTAAAAATT
1 AAAATATTTAAAAA-T
*
40776653 AAAATAATTAAAAAT
1 AAAATATTTAAAAAT
40776668 AA
1 AA
40776670 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 8 0.21
14 3 0.08
15 6 0.16
16 21 0.55
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAATATTTAAAAAT
Found at i:40776646 original size:29 final size:29
Alignment explanation
Indices: 40776607--40776672 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
40776597 AAAAAAAATT
* *
40776607 AAAAA-TATTTAAAAATGAAAATATTTAC
1 AAAAATTATTTAAAAATGAAAATAATTAA
*
40776635 AAAAATTATTTAAAAATTAAAATAATTAA
1 AAAAATTATTTAAAAATGAAAATAATTAA
40776664 AAATAATTA
1 AAA-AATTA
40776673 AAATTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 5 0.15
29 23 0.70
30 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTATTTAAAAATGAAAATAATTAA
Found at i:40776913 original size:39 final size:41
Alignment explanation
Indices: 40776856--40776957 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 41
40776846 TAGGTGATAA
* *
40776856 ATTTTAATTTTTTCAAATTATTTAATAAATAAAAATAAAAAT
1 ATTTTCATTATTT-AAATTATTTAATAAATAAAAATAAAAAT
* * ** *
40776898 A-TTT-ATTATTTAAATTA-TTATTTAATTGAAATTAAAAT
1 ATTTTCATTATTTAAATTATTTAATAAATAAAAATAAAAAT
*
40776936 ATTTTCATTATTTAAATAATTT
1 ATTTTCATTATTTAAATTATTT
40776958 GAAAAAAAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
38 17 0.34
39 9 0.18
40 18 0.36
41 5 0.10
42 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (41 bp):
ATTTTCATTATTTAAATTATTTAATAAATAAAAATAAAAAT
Found at i:40777165 original size:20 final size:19
Alignment explanation
Indices: 40777117--40777175 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
40777107 TTTAAAAATA
*
40777117 TTAAAATTTCTAATATATT
1 TTAAAATTTTTAATATATT
40777136 TTAAAATTTTTAATA-AGTT
1 TTAAAATTTTTAATATA-TT
40777155 TTAATAATTTTT--TATATT
1 TTAA-AATTTTTAATATATT
40777173 TTA
1 TTA
40777176 TATTTTTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 8 0.22
19 21 0.58
20 7 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAAAATTTTTAATATATT
Found at i:40777166 original size:10 final size:10
Alignment explanation
Indices: 40777117--40777203 Score: 60
Period size: 10 Copynumber: 9.1 Consensus size: 10
40777107 TTTAAAAATA
40777117 TTAA-AATTT
1 TTAATAATTT
*
40777126 CTAAT-ATATT
1 TTAATAAT-TT
40777136 TTAA-AATTT
1 TTAATAATTT
*
40777145 TTAATAAGTT
1 TTAATAATTT
40777155 TTAATAATTT
1 TTAATAATTT
*
40777165 TTTAT-A-TT
1 TTAATAATTT
*
40777173 TT-ATATTTT
1 TTAATAATTT
**
40777182 TTTGTAATTT
1 TTAATAATTT
40777192 TATAATAATTT
1 T-TAATAATTT
40777203 T
1 T
40777204 AATTTTAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 16 0.27
10 30 0.50
11 8 0.13
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (10 bp):
TTAATAATTT
Found at i:40777206 original size:9 final size:9
Alignment explanation
Indices: 40777105--40777165 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
40777095 GATTTATAAG
*
40777105 ATTTTAAAA
1 ATTTTAATA
*
40777114 ATATTAA-A
1 ATTTTAATA
40777122 ATTTCTAATA
1 ATTT-TAATA
40777132 TATTTTAA-A
1 -ATTTTAATA
40777141 ATTTTTAATA
1 A-TTTTAATA
40777151 AGTTTTAATA
1 A-TTTTAATA
40777161 ATTTT
1 ATTTT
40777166 TTATATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 5 0.11
9 20 0.45
10 15 0.34
11 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (9 bp):
ATTTTAATA
Found at i:40777208 original size:17 final size:18
Alignment explanation
Indices: 40777186--40777220 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40777176 TATTTTTTTG
*
40777186 TAATTTTATAATA-ATTT
1 TAATTTTAAAATATATTT
40777203 TAATTTTAAAATATATTT
1 TAATTTTAAAATATATTT
40777221 GGAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTTAAAATATATTT
Found at i:40779403 original size:9 final size:9
Alignment explanation
Indices: 40779389--40779447 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
40779379 TTTGGTTAAA
40779389 AATTACCCG
1 AATTACCCG
40779398 AATTACCCG
1 AATTACCCG
*
40779407 -ATTAACCG
1 AATTACCCG
*
40779415 AATTAACCG
1 AATTACCCG
40779424 AATTACCCG
1 AATTACCCG
40779433 AAAATTACCCG
1 --AATTACCCG
40779444 AATT
1 AATT
40779448 GCCCAAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 7 0.16
9 29 0.64
11 9 0.20
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:40779415 original size:17 final size:17
Alignment explanation
Indices: 40779390--40779444 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
40779380 TTGGTTAAAA
40779390 ATTACCCGAATTACCCG
1 ATTACCCGAATTACCCG
* *
40779407 ATTAACCGAATTAACCG
1 ATTACCCGAATTACCCG
40779424 AATTACCCGAAAATTACCCG
1 -ATTACCCG--AATTACCCG
40779444 A
1 A
40779445 ATTGCCCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 15 0.48
18 7 0.23
19 1 0.03
20 8 0.26
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (17 bp):
ATTACCCGAATTACCCG
Found at i:40779456 original size:20 final size:20
Alignment explanation
Indices: 40779415--40779456 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40779405 CGATTAACCG
*
40779415 AATTAACCGAATTACCCGAA
1 AATTAACCGAATTACCCAAA
* *
40779435 AATTACCCGAATTGCCCAAA
1 AATTAACCGAATTACCCAAA
40779455 AA
1 AA
40779457 GTTCGGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (20 bp):
AATTAACCGAATTACCCAAA
Found at i:40781677 original size:18 final size:18
Alignment explanation
Indices: 40781642--40781678 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40781632 TACAAATGGA
*
40781642 TCATTTCCATTTTAATTT
1 TCATTTCCATTTCAATTT
*
40781660 TCATTTCCATTTCCATTT
1 TCATTTCCATTTCAATTT
40781678 T
1 T
40781679 TGGAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCAATTT
Found at i:40782957 original size:18 final size:18
Alignment explanation
Indices: 40782922--40782958 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40782912 TACAAATGGA
*
40782922 TCATTTCCATTTTAATTT
1 TCATTTCCATTTCAATTT
*
40782940 TCATTTCCATTTCCATTT
1 TCATTTCCATTTCAATTT
40782958 T
1 T
40782959 TGGAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCAATTT
Found at i:40792288 original size:15 final size:16
Alignment explanation
Indices: 40792268--40792297 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40792258 ATAGAAGTTA
40792268 GCGAAG-TTGTACATT
1 GCGAAGATTGTACATT
40792283 GCGAAGATTGTACAT
1 GCGAAGATTGTACAT
40792298 CTTCATGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (16 bp):
GCGAAGATTGTACATT
Found at i:40794319 original size:36 final size:35
Alignment explanation
Indices: 40794279--40794346 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
40794269 TGTGAAAGAG
* * *
40794279 AATATATTGGTATGTTATTCATGCTATGTGATAGTA
1 AATATATGGGTATGTT-TTCATACCATGTGATAGTA
*
40794315 AATATGTGGGTATGTTTTCATACCATGTGATA
1 AATATATGGGTATGTTTTCATACCATGTGATA
40794347 TTGATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 14 0.50
36 14 0.50
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (35 bp):
AATATATGGGTATGTTTTCATACCATGTGATAGTA
Found at i:40797740 original size:15 final size:15
Alignment explanation
Indices: 40797723--40797756 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
40797713 TGTGTATAAT
40797723 AAAATAAAATAAAATA
1 AAAATAAAA-AAAATA
*
40797739 AAAATAATAAAAATA
1 AAAATAAAAAAAATA
40797754 AAA
1 AAA
40797757 GTACGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAAAAAATA
Found at i:40801319 original size:8 final size:8
Alignment explanation
Indices: 40801298--40801326 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40801288 TGTAAGAATA
40801298 AAAATATT
1 AAAATATT
40801306 -AAATATT
1 AAAATATT
40801313 AAAATATT
1 AAAATATT
40801321 AAAATA
1 AAAATA
40801327 AAAAAGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:40801331 original size:15 final size:15
Alignment explanation
Indices: 40801295--40801330 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
40801285 ATCTGTAAGA
40801295 ATAAAAATATTAAAT
1 ATAAAAATATTAAAT
*
40801310 ATTAAAATATTAAA-
1 ATAAAAATATTAAAT
40801324 ATAAAAA
1 ATAAAAA
40801331 AGACTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAAATATTAAAT
Found at i:40814521 original size:25 final size:25
Alignment explanation
Indices: 40814493--40814540 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
40814483 ATAGTACGAA
40814493 AAATGATAA-ATAAATAGATTAAACT
1 AAATGATAATATAAA-AGATTAAACT
* *
40814518 AAATTATAATATAAAGGATTAAA
1 AAATGATAATATAAAAGATTAAA
40814541 GTGCAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATGATAATATAAAAGATTAAACT
Found at i:40818572 original size:32 final size:32
Alignment explanation
Indices: 40818531--40818595 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40818521 ATCATATCAC
40818531 TTAGGGGAACATATTTGGAGAATCGGAGTGGA
1 TTAGGGGAACATATTTGGAGAATCGGAGTGGA
40818563 TTAGGGGAACATATTTGGAGAATCGGAGTGGA
1 TTAGGGGAACATATTTGGAGAATCGGAGTGGA
40818595 T
1 T
40818596 CAGATCACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.37, T:0.26
Consensus pattern (32 bp):
TTAGGGGAACATATTTGGAGAATCGGAGTGGA
Found at i:40825657 original size:17 final size:18
Alignment explanation
Indices: 40825637--40825671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40825627 TTATTTCATT
40825637 TAAAATT-TTATTAAATA
1 TAAAATTATTATTAAATA
*
40825654 TAAAATTATTTTTAAATA
1 TAAAATTATTATTAAATA
40825672 AATTATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAATTATTATTAAATA
Found at i:40825949 original size:16 final size:16
Alignment explanation
Indices: 40825897--40825955 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
40825887 AAAAAAAATC
*
40825897 AAATATTAATAAT-TTT
1 AAAT-TTAATAATATAT
*
40825913 AAATTTAA-AATAAAAT
1 AAATTTAATAAT-ATAT
*
40825929 TAATTTAATAATATAT
1 AAATTTAATAATATAT
*
40825945 AAATTAAATAA
1 AAATTTAATAA
40825956 ACTATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 24 0.71
17 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAATAATATAT
Found at i:40826397 original size:17 final size:17
Alignment explanation
Indices: 40826375--40826412 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40826365 TTTTTTCATT
*
40826375 AATAAT-AATAATTTTTA
1 AATAATAAATAA-CTTTA
40826392 AATAATAAATAACTTTA
1 AATAATAAATAACTTTA
40826409 AATA
1 AATA
40826413 TCAACCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATAAATAACTTTA
Found at i:40826909 original size:5 final size:5
Alignment explanation
Indices: 40826901--40826932 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
40826891 TATGTAACAT
40826901 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
40826933 ACCATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:40827600 original size:30 final size:31
Alignment explanation
Indices: 40827573--40827667 Score: 126
Period size: 30 Copynumber: 3.2 Consensus size: 31
40827563 TAAAAATTAT
*
40827573 ATTTTGACCCCTAAACTTTTC-CTAAATTTC
1 ATTTTGACCCTTAAACTTTTCTCTAAATTTC
*
40827603 ATTTTGACCCTTAAAC-TTTCTTTAAATTTC
1 ATTTTGACCCTTAAACTTTTCTCTAAATTTC
*
40827633 ATTTAGACCCTTAAAC-TTTCAT-TAAATTTC
1 ATTTTGACCCTTAAACTTTTC-TCTAAATTTC
40827663 ATTTT
1 ATTTT
40827668 AATCCTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.07
30 54 0.92
31 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTTGACCCTTAAACTTTTCTCTAAATTTC
Found at i:40827642 original size:60 final size:60
Alignment explanation
Indices: 40827563--40827710 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 60
40827553 AATTAAAAAA
* * *
40827563 TAAAAATTATATTTTGACCCCTAAACTTTTC-CTAAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTACATTTAGACCCCTAAACTTTTCACTAAATTTCATTTTAACCC-TAAACTTTC
** * * * * *
40827623 TTTAAATTTCATTTAGACCCTTAAAC-TTTCATTAAATTTCATTTTAATCCTAAATTTTC
1 TAAAAATTACATTTAGACCCCTAAACTTTTCACTAAATTTCATTTTAACCCTAAACTTTC
* *
40827682 TAAAAATTACATTTAG-CCCCAAAAGTTTT
1 TAAAAATTACATTTAGACCCCTAAACTTTT
40827711 GCTGCATTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
58 6 0.09
59 28 0.40
60 36 0.51
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (60 bp):
TAAAAATTACATTTAGACCCCTAAACTTTTCACTAAATTTCATTTTAACCCTAAACTTTC
Found at i:40828051 original size:3 final size:3
Alignment explanation
Indices: 40828043--40828101 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
40828033 GCTCGGTTTT
40828043 GAA GAA GAA GAA GAA GGAA GAA GAA GAA GAA GAAA GAAA GAGA GAA GAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA G-AA G-AA GA-A GAA GAA
40828092 GAAA GAA GAA
1 G-AA GAA GAA
40828102 AAAAAAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 36 0.69
4 16 0.31
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40828064 original size:13 final size:13
Alignment explanation
Indices: 40828043--40828101 Score: 77
Period size: 13 Copynumber: 4.5 Consensus size: 13
40828033 GCTCGGTTTT
40828043 GAAGAAGAAG-AA
1 GAAGAAGAAGAAA
40828055 GAAGGAAGAAG-AA
1 GAA-GAAGAAGAAA
40828068 GAAGAAGAAAGAAA
1 GAAGAAG-AAGAAA
40828082 GAGAGAAGAAGAAA
1 GA-AGAAGAAGAAA
40828096 GAAGAA
1 GAAGAA
40828102 AAAAAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.16
13 19 0.44
14 12 0.28
15 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAA
Found at i:40828100 original size:10 final size:10
Alignment explanation
Indices: 40828043--40828101 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
40828033 GCTCGGTTTT
40828043 GAAG-AAGAA
1 GAAGAAAGAA
*
40828052 GAAGAAGGAA
1 GAAGAAAGAA
40828062 GAAG-AAGAA
1 GAAGAAAGAA
40828071 GAAGAAAG-A
1 GAAGAAAGAA
*
40828080 -AAGAGAGAA
1 GAAGAAAGAA
40828089 GAAGAAAGAA
1 GAAGAAAGAA
40828099 GAA
1 GAA
40828102 AAAAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 6 0.14
9 14 0.33
10 22 0.52
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:40828191 original size:18 final size:18
Alignment explanation
Indices: 40828154--40828196 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40828144 AACCGGGTAT
* * *
40828154 AACCCGACCCGATCCGGC
1 AACCCAACCCGACCCAGC
40828172 AACCCAACCCGACCCAGC
1 AACCCAACCCGACCCAGC
40828190 AAGCCCA
1 AA-CCCA
40828197 TTAGCCAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.30, C:0.51, G:0.16, T:0.02
Consensus pattern (18 bp):
AACCCAACCCGACCCAGC
Found at i:40829210 original size:17 final size:17
Alignment explanation
Indices: 40829183--40829493 Score: 181
Period size: 17 Copynumber: 18.2 Consensus size: 17
40829173 GTTTTCGTAT
40829183 TTTCAAAAAATTTTCGTG
1 TTTC-AAAAATTTTCGTG
*
40829201 TTTCAAAAATCTTCGTG
1 TTTCAAAAATTTTCGTG
40829218 TTTTCAAAAA-TTTCGGTG
1 -TTTCAAAAATTTTC-GTG
*
40829236 TTTCAAAGATTTTCGTG
1 TTTCAAAAATTTTCGTG
* *
40829253 TTTTCAAAAA-CTCCGGTG
1 -TTTCAAAAATTTTC-GTG
* ***
40829271 ATTTTAAAAAAAAATCGTTG
1 --TTTCAAAAATTTTCG-TG
*
40829291 TTTCAAAAATTTTCATG
1 TTTCAAAAATTTTCGTG
*
40829308 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
*
40829325 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* * *
40829342 TTTTAAAAATTCTCGTA
1 TTTCAAAAATTTTCGTG
*
40829359 TTT--TAAATTTT--T-
1 TTTCAAAAATTTTCGTG
* **
40829371 TTTAAGAAAAAAAATT-GTG
1 TTT---CAAAAATTTTCGTG
* * **
40829390 TTTCAAAAAATGTATTG
1 TTTCAAAAATTTTCGTG
* *
40829407 TTTTAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTG
* *
40829424 TTTCAAAAAATGTCGTG
1 TTTCAAAAATTTTCGTG
*
40829441 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
** *
40829458 TTTCTGAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
*
40829475 TTT-AAAAATTCTCGTG
1 TTTCAAAAATTTTCGTG
40829491 TTT
1 TTT
40829494 TTAAAAAAAA
Statistics
Matches: 230, Mismatches: 47, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
12 3 0.01
13 1 0.00
15 6 0.03
16 19 0.08
17 143 0.62
18 42 0.18
19 13 0.06
20 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:40829327 original size:34 final size:34
Alignment explanation
Indices: 40829174--40829493 Score: 208
Period size: 34 Copynumber: 9.3 Consensus size: 34
40829164 AAATTTCGTG
* *
40829174 TTTTCGTATTTTCAAAAAATTTTCGTGTTTCAAAAA
1 TTTTCGT-GTTTC-AAAAATTTTCGTGTTTTAAAAA
* * *
40829210 TCTTCGTGTTTTCAAAAA-TTTCGGTGTTTCAAAGA
1 TTTTCGTG-TTTCAAAAATTTTC-GTGTTTTAAAAA
* *
40829245 TTTTCGTGTTTTCAAAAA-CTCCGGTGATTTTAAAAAA
1 TTTTCGTG-TTTCAAAAATTTTC-GTG-TTTT-AAAAA
*** *
40829282 AAATCGTTGTTTCAAAAATTTTCATGTTTTAAAAA
1 TTTTCG-TGTTTCAAAAATTTTCGTGTTTTAAAAA
*
40829317 TTTTCGTGTTTTAAAAATTTTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
* * * *
40829351 TTCTCGTATTT--TAAATTTT--T-TTTAAGAAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTT---TAAAAA
** * * **
40829383 AATT-GTGTTTCAAAAAATGTATTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
* * *
40829416 TTCTCGTGTTTCAAAAAATGTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
** *
40829450 TTTTCGTGTTTCTGAAATTTCCGTG-TTTAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
*
40829483 TTCTCGTGTTT
1 TTTTCGTGTTT
40829494 TTAAAAAAAA
Statistics
Matches: 226, Mismatches: 43, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
29 3 0.01
30 1 0.00
31 5 0.02
32 13 0.06
33 29 0.13
34 85 0.38
35 48 0.21
36 20 0.09
37 18 0.08
38 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (34 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTAAAAA
Found at i:40829392 original size:99 final size:100
Alignment explanation
Indices: 40829277--40829456 Score: 265
Period size: 99 Copynumber: 1.8 Consensus size: 100
40829267 GGTGATTTTA
* * * * * *
40829277 AAAAAAAATCGTTGTTTCAAAAATTTTCA-TGTTTTAAAAATTTTCGTGTTTTAAAAATTTTCGT
1 AAAAAAAATCGTTGTTTCAAAAAATGT-ATTGTTTTAAAAATTCTCGTGTTTCAAAAAATGTCGT
40829341 GTTTTAAAAATTCTCGTATTTTAAATTTTTTTTAAG
65 GTTTTAAAAATTCTCGTATTTTAAATTTTTTTTAAG
*
40829377 AAAAAAAATTG-TGTTTCAAAAAATGTATTGTTTTAAAAATTCTCGTGTTTCAAAAAATGTCGTG
1 AAAAAAAATCGTTGTTTCAAAAAATGTATTGTTTTAAAAATTCTCGTGTTTCAAAAAATGTCGTG
*
40829441 TTTTAAAAATTTTCGT
66 TTTTAAAAATTCTCGT
40829457 GTTTCTGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
98 1 0.01
99 60 0.85
100 10 0.14
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (100 bp):
AAAAAAAATCGTTGTTTCAAAAAATGTATTGTTTTAAAAATTCTCGTGTTTCAAAAAATGTCGTG
TTTTAAAAATTCTCGTATTTTAAATTTTTTTTAAG
Found at i:40829514 original size:20 final size:20
Alignment explanation
Indices: 40829491--40829528 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40829481 AATTCTCGTG
*
40829491 TTTTTAAAAAAAACTTTCAT
1 TTTTTAAAAAAAAATTTCAT
40829511 TTTTTAAAAAAAAATTTC
1 TTTTTAAAAAAAAATTTC
40829529 GTGCTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTTAAAAAAAAATTTCAT
Found at i:40841710 original size:73 final size:73
Alignment explanation
Indices: 40841605--40842294 Score: 1334
Period size: 73 Copynumber: 9.5 Consensus size: 73
40841595 TTTGTTTTTC
40841605 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40841670 TAAAAAAA
66 TAAAAAAA
40841678 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40841743 TAAAAAAA
66 TAAAAAAA
40841751 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40841816 TAAAAAAA
66 TAAAAAAA
40841824 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40841889 TAAAAAAA
66 TAAAAAAA
40841897 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40841962 TAAAAAAA
66 TAAAAAAA
40841970 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40842035 TAAAAAAA
66 TAAAAAAA
40842043 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40842108 TAAAAAAA
66 TAAAAAAA
40842116 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40842181 TAAAAAAA
66 TAAAAAAA
40842189 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA--TT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
40842252 T--AAAAA
66 TAAAAAAA
* *
40842258 AAAATCAACTCATACTGCGAGAAGTGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
40842295 GGGGCACGCC
Statistics
Matches: 615, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
69 40 0.07
71 3 0.00
73 572 0.93
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TAAAAAAA
Found at i:40842634 original size:85 final size:88
Alignment explanation
Indices: 40842381--40842634 Score: 290
Period size: 85 Copynumber: 2.9 Consensus size: 88
40842371 TTGTTTTTCA
*
40842381 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTTTCAATT
*
40842445 TATGTTTTTTTTCAA-TCTATGCTTCTC
65 TCTG--TTTTTT-AATTCTA-GCTTCTC
* *
40842472 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTTTCAAT
1 -AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTTTCAAT
** *
40842534 TTCTGCTTTACTAATTCTA-CTTTTC
64 TTCTG-TTTTTTAATTCTAGCTTCTC
* * *
40842559 -AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTCAAATT
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTCAATTT
40842623 CTG-TTTTTAATT
66 CTGTTTTTTAATT
40842635 TCTGTTTTTT
Statistics
Matches: 141, Mismatches: 15, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
84 3 0.02
85 40 0.28
87 28 0.20
88 2 0.01
89 8 0.06
90 23 0.16
92 35 0.25
94 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (88 bp):
AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTCAATTT
CTGTTTTTTAATTCTAGCTTCTC
Found at i:40842637 original size:13 final size:13
Alignment explanation
Indices: 40842621--40842654 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
40842611 TCTTTTCAAA
40842621 TTCTGTTTTTAAT
1 TTCTGTTTTTAAT
40842634 TTCTGTTTTTTTAAT
1 TTCTG--TTTTTAAT
40842649 TTCTGT
1 TTCTGT
40842655 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (13 bp):
TTCTGTTTTTAAT
Found at i:40842646 original size:15 final size:15
Alignment explanation
Indices: 40842626--40842654 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40842616 TCAAATTCTG
40842626 TTTTTAATTTCTGTT
1 TTTTTAATTTCTGTT
40842641 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
40842655 GTTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTGTT
Found at i:40842827 original size:54 final size:54
Alignment explanation
Indices: 40842743--40843065 Score: 448
Period size: 54 Copynumber: 6.1 Consensus size: 54
40842733 TCAATTTCTA
*
40842743 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTT-AATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
40842798 CTTTTAATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGC
1 CTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40842852 C--TT--TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
40842903 CTTTTAATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGC
1 CTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40842957 C--TT--TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
40843008 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT--AATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40843063 CTT
1 CTT
40843066 GGCTCACGTG
Statistics
Matches: 240, Mismatches: 16, Indels: 24
0.86 0.06 0.09
Matches are distributed among these distances:
50 24 0.10
51 66 0.28
52 4 0.02
53 4 0.02
54 79 0.33
55 54 0.22
56 5 0.02
57 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (54 bp):
CTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:40842932 original size:105 final size:105
Alignment explanation
Indices: 40842751--40843065 Score: 537
Period size: 105 Copynumber: 3.0 Consensus size: 105
40842741 TACTTTTCAA
*
40842751 TTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTT
1 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTT
40842815 TCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGCCTT
66 TCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGCCTT
40842855 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTT
1 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTT
40842920 TCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGCCTT
66 TCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGCCTT
* *
40842960 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCT-GT
1 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--AATTTCTATT
* *
40843024 TTTCAAAAATCAACTCATATTGCGAGA-AGTGAGTTGAGCCTT
64 TTTCAAAAACCAACTCATATTGCGAGAGA-TAAGTTGAGCCTT
40843066 GGCTCACGTG
Statistics
Matches: 202, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
104 11 0.05
105 146 0.72
106 39 0.19
107 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (105 bp):
TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTT
TCAAAAACCAACTCATATTGCGAGAGATAAGTTGAGCCTT
Found at i:40843369 original size:30 final size:31
Alignment explanation
Indices: 40843335--40843436 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
40843325 TAAAAAATAA
*
40843335 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
40843365 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
**
40843395 AAATTTCATTTAAACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
40843425 AAATTTCATTTT
1 AAATTTCATTTT
40843437 AATCCTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
29 4 0.06
30 58 0.92
31 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:40843457 original size:29 final size:29
Alignment explanation
Indices: 40843335--40843464 Score: 111
Period size: 30 Copynumber: 4.4 Consensus size: 29
40843325 TAAAAAATAA
* * *
40843335 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTT-AACCCTAAACTTTCT-AT
* *
40843365 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTAACCC-TAAACTTTCTAT
*
40843395 AAATTTCATTTAAACCCCTAAACTTTC-ATT
1 AAATTTCATTTTAA-CCCTAAACTTTCTA-T
* * *
40843425 AAATTTCATTTTAATCCTAAATTTTCTAA
1 AAATTTCATTTTAACCCTAAACTTTCTAT
*
40843454 AAATTACATTT
1 AAATTTCATTT
40843465 AGCCCCAGAA
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
29 23 0.28
30 56 0.67
31 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (29 bp):
AAATTTCATTTTAACCCTAAACTTTCTAT
Found at i:40843801 original size:3 final size:3
Alignment explanation
Indices: 40843795--40843866 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
40843785 GCTAGACTTT
* *
40843795 GAA GAA GAA GAA TGAA GAA GAA GGAA AAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
40843842 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
40843867 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 36 0.63
4 13 0.23
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:40843835 original size:18 final size:17
Alignment explanation
Indices: 40843795--40843866 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 17
40843785 GCTAGACTTT
*
40843795 GAAGAAGAAGAATGAAGAA
1 GAAGAAAAAGAA--AAGAA
*
40843814 GAAGGAAAAAGAAAAGAG
1 GAA-GAAAAAGAAAAGAA
40843832 GAAGAAGAAAG-AAAGAAA
1 GAAGAA-AAAGAAAAG-AA
*
40843850 AAAGAAAAAGAAAAGAA
1 GAAGAAAAAGAAAAGAA
40843867 ATAATAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 13 0.29
18 21 0.47
19 3 0.07
20 8 0.18
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (17 bp):
GAAGAAAAAGAAAAGAA
Found at i:40843836 original size:24 final size:24
Alignment explanation
Indices: 40843808--40843854 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40843798 GAAGAAGAAT
*
40843808 GAAGAAGAAGGAAA-AAGAAAAGAG
1 GAAGAAGAAAGAAAGAA-AAAAGAG
40843832 GAAGAAGAAAGAAAGAAAAAAGA
1 GAAGAAGAAAGAAAGAAAAAAGA
40843855 AAAAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAGAAAGAAAAAAGAG
Found at i:40843843 original size:28 final size:29
Alignment explanation
Indices: 40843799--40843857 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
40843789 GACTTTGAAG
*
40843799 AAGAAGAATGAAGAAG-AAGGAAAAAGAA
1 AAGAAGAATGAAGAAGAAAGAAAAAAGAA
*
40843827 AAGAGGAA-GAAGAAAGAAAGAAAAAAGAA
1 AAGAAGAATGAAG-AAGAAAGAAAAAAGAA
40843856 AA
1 AA
40843858 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 10 0.37
29 13 0.48
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (29 bp):
AAGAAGAATGAAGAAGAAAGAAAAAAGAA
Found at i:40843857 original size:35 final size:34
Alignment explanation
Indices: 40843798--40843865 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
40843788 AGACTTTGAA
* * *
40843798 GAAGAAGAATGAAGAAGAAGGAAAAAGAAAAGAG
1 GAAGAAGAAAGAAGAAAAAAGAAAAAGAAAAGAG
40843832 GAAGAAGAAAGAAAGAAAAAAGAAAAAGAAAAGA
1 GAAGAAGAAAG-AAGAAAAAAGAAAAAGAAAAGA
40843866 AATAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (34 bp):
GAAGAAGAAAGAAGAAAAAAGAAAAAGAAAAGAG
Found at i:40843860 original size:24 final size:24
Alignment explanation
Indices: 40843809--40843861 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
40843799 AAGAAGAATG
* **
40843809 AAGAAGAAGGAAAAAGAAAAGAGG
1 AAGAAGAAAGAAAAAGAAAAGAAA
40843833 AAGAAGAAAGAAAGAA-AAAAGAAA
1 AAGAAGAAAGAAA-AAGAAAAGAAA
40843857 AAGAA
1 AAGAA
40843862 AAGAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
AAGAAGAAAGAAAAAGAAAAGAAA
Found at i:40844040 original size:13 final size:13
Alignment explanation
Indices: 40844015--40844049 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40844005 AACAGCAATA
*
40844015 AAGAAGAAGAAAG
1 AAGAAGAAAAAAG
*
40844028 AAGCAGAAAAAAG
1 AAGAAGAAAAAAG
40844041 AAGAAGAAA
1 AAGAAGAAA
40844050 GAAGCAGCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAAG
Found at i:40844190 original size:8 final size:8
Alignment explanation
Indices: 40844177--40844225 Score: 55
Period size: 8 Copynumber: 5.8 Consensus size: 8
40844167 GCCCAGCAAA
40844177 AAAAAAAG
1 AAAAAAAG
40844185 AAAAAAAG
1 AAAAAAAG
40844193 AGAGAAAAAG
1 A-A-AAAAAG
40844203 -AAAAAAG
1 AAAAAAAG
40844210 ATAAAACAAG
1 A-AAAA-AAG
40844220 AAAAAA
1 AAAAAA
40844226 GAGGTTCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 6 0.17
8 11 0.31
9 9 0.25
10 10 0.28
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:40844206 original size:17 final size:16
Alignment explanation
Indices: 40844178--40844228 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 16
40844168 CCCAGCAAAA
40844178 AAAAAAGAAAAAAAGAG
1 AAAAAAG-AAAAAAGAG
*
40844195 AGAAAAAGAAAAAAGAT
1 A-AAAAAGAAAAAAGAG
40844212 AAAACAAGAAAAAAGAG
1 AAAA-AAGAAAAAAGAG
40844229 GTTCAATTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 3 0.10
17 21 0.70
18 6 0.20
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAG
Found at i:40844215 original size:25 final size:24
Alignment explanation
Indices: 40844174--40844227 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
40844164 CCAGCCCAGC
40844174 AAAA-AAAAAAGAAAAAA-AGAGAGA
1 AAAAGAAAAAAGAAAAAACA-AGA-A
*
40844198 AAAAGAAAAAAGATAAAACAAGAA
1 AAAAGAAAAAAGAAAAAACAAGAA
40844222 AAAAGA
1 AAAAGA
40844228 GGTTCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 11 0.41
25 15 0.56
26 1 0.04
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAAAGAAAAAACAAGAA
Found at i:40844393 original size:16 final size:17
Alignment explanation
Indices: 40844367--40844404 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
40844357 TTATATTTAT
40844367 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
40844384 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
40844400 ATTTT
1 ATTTT
40844405 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:40844601 original size:18 final size:18
Alignment explanation
Indices: 40844545--40844714 Score: 95
Period size: 18 Copynumber: 9.5 Consensus size: 18
40844535 AAAATTGTAA
* *
40844545 TTTCAATAATCCTCGTGCT
1 TTTCAAAAATCTTCGTG-T
*
40844564 TTT-AAAAAT-TCTCATG-
1 TTTCAAAAATCT-TCGTGT
40844580 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATCTTCGTGT
* *
40844598 TTTCAAAATTC-TAGTG-
1 TTTCAAAAATCTTCGTGT
* *
40844614 TTTCAAAAATTTTCTTGT
1 TTTCAAAAATCTTCGTGT
*
40844632 TTTCAGAAAAAATTTTCGTGT
1 TTTC---AAAAATCTTCGTGT
* *
40844653 TTT-ATAAAT-TTCCGTAT
1 TTTCAAAAATCTT-CGTGT
** *
40844670 TTTCAAAAA-AATCATGT
1 TTTCAAAAATCTTCGTGT
*
40844687 CTTTCAAAAATTTTCGTGT
1 -TTTCAAAAATCTTCGTGT
40844706 TTTCAAAAA
1 TTTCAAAAA
40844715 AANGTCGGGC
Statistics
Matches: 117, Mismatches: 20, Indels: 29
0.70 0.12 0.17
Matches are distributed among these distances:
16 14 0.12
17 32 0.27
18 47 0.40
19 8 0.07
21 16 0.14
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (18 bp):
TTTCAAAAATCTTCGTGT
Found at i:40844616 original size:34 final size:34
Alignment explanation
Indices: 40844545--40844713 Score: 117
Period size: 34 Copynumber: 4.8 Consensus size: 34
40844535 AAAATTGTAA
* * *
40844545 TTTCAATAATCCTCGTGCTTTTAAAAATTCTCATG
1 TTTCAAAAATCTTCGTG-TTTTCAAAATTCTCATG
40844580 TTTCAAAAATCTTCGTGTTTTCAAAATTCT-AGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAATTCTCA-TG
* * * *
40844614 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTG
1 TTTCAAAAATCTTCGTGTTTTC----AAAATTCTCATG
* * * ***
40844652 TTTTATAAAT-TTCCGTATTTTCAAAAAAATCATG
1 TTTCAAAAATCTT-CGTGTTTTCAAAATTCTCATG
*
40844686 TCTTTCAAAAATTTTCGTGTTTTCAAAA
1 --TTTCAAAAATCTTCGTGTTTTCAAAA
40844714 AAANGTCGGG
Statistics
Matches: 106, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
33 1 0.01
34 42 0.40
35 15 0.14
36 20 0.19
37 4 0.04
38 24 0.23
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAATTCTCATG
Found at i:40844619 original size:16 final size:16
Alignment explanation
Indices: 40844568--40844621 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
40844558 CGTGCTTTTA
40844568 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
40844584 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
40844602 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
40844618 AAAA
1 AAAA
40844622 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:40844632 original size:17 final size:17
Alignment explanation
Indices: 40844545--40844714 Score: 78
Period size: 17 Copynumber: 9.5 Consensus size: 17
40844535 AAAATTGTAA
* *
40844545 TTTCAATAATCCTCGTG
1 TTTCAAAAATTCTCGTG
* *
40844562 CTTTTAAAAATTCTCATG
1 -TTTCAAAAATTCTCGTG
40844580 TTTCAAAAA-TCTTCGTG
1 TTTCAAAAATTC-TCGTG
*
40844597 TTTTC-AAAATTCTAGTG
1 -TTTCAAAAATTCTCGTG
* *
40844614 TTTCAAAAATTTTCTTG
1 TTTCAAAAATTCTCGTG
*
40844631 TTTTCAGAAAAAATTTTCGTG
1 -TTTC---AAAAATTCTCGTG
* * *
40844652 TTTTATAAATT-TCCGTAT
1 TTTCAAAAATTCT-CGT-G
* *
40844670 TTTCAAAAAAATCAT-GTC
1 TTTC-AAAAATTC-TCGTG
*
40844688 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
40844705 TTTTCAAAAA
1 -TTTCAAAAA
40844715 AANGTCGGGC
Statistics
Matches: 116, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
16 8 0.07
17 46 0.40
18 39 0.34
19 7 0.06
20 3 0.03
21 13 0.11
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:40865645 original size:313 final size:311
Alignment explanation
Indices: 40864969--40865634 Score: 719
Period size: 314 Copynumber: 2.1 Consensus size: 311
40864959 CTTTAGAGAC
* * * * * *
40864969 TTCTGAACTTGTGAATGTGTGTTGAATAGCTT-GAAAGC-ACCAC--TTTTATAGTGTCAATCAC
1 TTCTGAACTTATGAATGCGTGTTGAATGGCTTAG-AGGCTACCCCTGTTTTATAGTATCAATCAC
* * * * *
40865030 TTGAATATAAGAGAGTTCTCGTAGAATTTTGACCGCCTTTGAATAAAAGAGGGCTCTTGAAACTA
65 TTGAATAAAAGAGAATTCTCGTAGAATTTTGACCACCTTTGAATAAAAGAGAGCTCTTGAAACGA
* *
40865095 GTTTGGACCTCCTTTCTACAACTGAATAAGATCGAAAGGTGGCTTTTTCATAAAGAAATTTTGAC
130 GTTTGGACCTCCTTTCTACAACTGAAT-AGATCGAAAGGTGACTTTTTCAGAAAGAAATTTTGAC
* * * * *
40865160 CTCCTTTCCTCGGTTGAACTAGATTAGAAGGTGACTTTATTCATAACCGATACGGTGTTCATCAA
194 CTCCTTTCCTCGGTTGAACTAGATAAGAAGGAGACTTTATTCAGAACAGATACGGTGCTCATCAA
* * * * * *
40865225 AATTTCTTCAAGTTCTCTAGTTTCCTTAAATACTTCTTTAGAGAACATTTGAAG
259 AATTTCTTAAAGTTCTCAAGCTTCCATAAATA-TTATTCAGAGAACATTTGAAG
* * * * *
40865279 TTCTGAACTTGTGAATGTGTTTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTATTAGTCACT
1 TTCTGAACTTATGAATGCGTGTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTATCAATCACT
* * *
40865344 TGAATAAAAGAGAATTGTTGTAGAATTTTGACCACCTTTGAATAAAATAGAGCTCTTGAAACGAG
66 TGAATAAAAGAGAATTCTCGTAGAATTTTGACCACCTTTGAATAAAAGAGAGCTCTTGAAACGAG
*
40865409 TTTGGACCTCCTTTCTACAATTGAACT-GACTCGAAAGGTGACTTTCTTCAGAAACG-AATTTTG
131 TTTGGACCTCCTTTCTACAACTGAA-TAGA-TCGAAAGGTGACTTT-TTCAGAAA-GAAATTTTG
* * *
40865472 ACCTCCTTTCCTCGGTTGAACTGGATAAGAAGGCAG-CTTTATTCAGAACTAG-TATGGTGCTCG
192 ACCTCCTTTCCTCGGTTGAACTAGATAAGAAGG-AGACTTTATTCAGAAC-AGATACGGTGCTCA
* * * **
40865535 TTAGAATTTCTTAAAGTTCTTCAAAGACTT-CATAGAT-TTATTCAGA-AATTTTTTGTACA-
255 TCAAAATTTCTTAAAGTTC-TC-AAG-CTTCCATAAATATTATTCAGAGAA-CATTTG-A-AG
* *
40865594 TT-TGAATTTATGAATGCGTGTTGAATGGCTTAGAGGTTACC
1 TTCTGAACTTATGAATGCGTGTTGAATGGCTTAGAGGCTACC
40865635 GTTTTTTATA
Statistics
Matches: 298, Mismatches: 42, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
310 33 0.11
311 5 0.02
312 2 0.01
313 113 0.38
314 127 0.43
315 8 0.03
316 8 0.03
317 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (311 bp):
TTCTGAACTTATGAATGCGTGTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTATCAATCACT
TGAATAAAAGAGAATTCTCGTAGAATTTTGACCACCTTTGAATAAAAGAGAGCTCTTGAAACGAG
TTTGGACCTCCTTTCTACAACTGAATAGATCGAAAGGTGACTTTTTCAGAAAGAAATTTTGACCT
CCTTTCCTCGGTTGAACTAGATAAGAAGGAGACTTTATTCAGAACAGATACGGTGCTCATCAAAA
TTTCTTAAAGTTCTCAAGCTTCCATAAATATTATTCAGAGAACATTTGAAG
Found at i:40865665 original size:313 final size:311
Alignment explanation
Indices: 40864969--40865665 Score: 729
Period size: 313 Copynumber: 2.2 Consensus size: 311
40864959 CTTTAGAGAC
* * * * * *
40864969 TTCTGAACTTGTGAATGTGTGTTGAATAGCTT-GAAAGC-ACCAC--TTTTATAGTGTCAATCAC
1 TTCTGAACTTATGAATGCGTGTTGAATGGCTTAG-AGGCTACCCCTGTTTTATAGTGTCAGTCAC
* * * * *
40865030 TTGAATATAAGAGAGTTCTCGTAGAATTTTGACCGCCTTTGAATAAAAGAGGGCTCTTGAAACTA
65 TTGAATAAAAGAGAATTCTCGTAGAATTTTGACCACCTTTGAATAAAAGAGAGCTCTTGAAACGA
* *
40865095 GTTTGGACCTCCTTTCTACAACTGAATAAGATCGAAAGGTGGCTTTTTCATAAAGAAATTTTGAC
130 GTTTGGACCTCCTTTCTACAACTGAAT-AGATCGAAAGGTGACTTTTTCAGAAAGAAATTTTGAC
* * * * *
40865160 CTCCTTTCCTCGGTTGAACTAGATTAGAAGGTGACTTTATTCATAACCGATACGGTGTTCATCAA
194 CTCCTTTCCTCGGTTGAACTAGATAAGAAGGAGACTTTATTCAGAACAGATACGGTGCTCATCAA
* * * * * *
40865225 AATTTCTTCAAGTTCTCTAGTTTCCTTAAATACTTCTTTAGAGAACATTTGAAG
259 AATTTCTTAAAGTTCTCAAGCTTCCATAAATA-TTATTCAGAGAACATTTGAAG
* * * * *
40865279 TTCTGAACTTGTGAATGTGTTTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTATTAGTCACT
1 TTCTGAACTTATGAATGCGTGTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTGTCAGTCACT
* * *
40865344 TGAATAAAAGAGAATTGTTGTAGAATTTTGACCACCTTTGAATAAAATAGAGCTCTTGAAACGAG
66 TGAATAAAAGAGAATTCTCGTAGAATTTTGACCACCTTTGAATAAAAGAGAGCTCTTGAAACGAG
*
40865409 TTTGGACCTCCTTTCTACAATTGAACT-GACTCGAAAGGTGACTTTCTTCAGAAACG-AATTTTG
131 TTTGGACCTCCTTTCTACAACTGAA-TAGA-TCGAAAGGTGACTTT-TTCAGAAA-GAAATTTTG
* * *
40865472 ACCTCCTTTCCTCGGTTGAACTGGATAAGAAGGCAG-CTTTATTCAGAACTAG-TATGGTGCTCG
192 ACCTCCTTTCCTCGGTTGAACTAGATAAGAAGG-AGACTTTATTCAGAAC-AGATACGGTGCTCA
* * * **
40865535 TTAGAATTTCTTAAAGTTCTTCAAAGACTT-CATAGAT-TTATTCAGA-AATTTTTTGTACA-
255 TCAAAATTTCTTAAAGTTC-TC-AAG-CTTCCATAAATATTATTCAGAGAA-CATTTG-A-AG
* * * * * *
40865594 TT-TGAATTTATGAATGCGTGTTGAATGGCTTAGAGGTTA-CCGTTTTTTATAGCGTCAGTCATT
1 TTCTGAACTTATGAATGCGTGTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTGTCAGTCACT
*
40865657 TAAATAAAA
66 TGAATAAAA
40865666 AAAGTTCTTA
Statistics
Matches: 322, Mismatches: 49, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
310 33 0.10
311 5 0.02
312 2 0.01
313 139 0.43
314 125 0.39
315 8 0.02
316 8 0.02
317 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (311 bp):
TTCTGAACTTATGAATGCGTGTTGAATGGCTTAGAGGCTACCCCTGTTTTATAGTGTCAGTCACT
TGAATAAAAGAGAATTCTCGTAGAATTTTGACCACCTTTGAATAAAAGAGAGCTCTTGAAACGAG
TTTGGACCTCCTTTCTACAACTGAATAGATCGAAAGGTGACTTTTTCAGAAAGAAATTTTGACCT
CCTTTCCTCGGTTGAACTAGATAAGAAGGAGACTTTATTCAGAACAGATACGGTGCTCATCAAAA
TTTCTTAAAGTTCTCAAGCTTCCATAAATATTATTCAGAGAACATTTGAAG
Found at i:40873184 original size:26 final size:27
Alignment explanation
Indices: 40873129--40873186 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
40873119 AATAGTGCCC
* *
40873129 CATTATTTTTCTTTCAAAAAATAGTCA
1 CATTATTATTATTTCAAAAAATAGTCA
* *
40873156 CATTATTATTATTTTAAATAAT-GTCA
1 CATTATTATTATTTCAAAAAATAGTCA
40873182 CATTA
1 CATTA
40873187 GCAATGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (27 bp):
CATTATTATTATTTCAAAAAATAGTCA
Found at i:40873856 original size:21 final size:21
Alignment explanation
Indices: 40873819--40873875 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
40873809 CGAAATGATA
40873819 GCAAAACAATG-AAAAAAGTG
1 GCAAAACAATGAAAAAAAGTG
40873839 GCAAAACAATGAAAAAAAGTG
1 GCAAAACAATGAAAAAAAGTG
* *
40873860 ACAAAACAGT-AAAAAA
1 GCAAAACAATGAAAAAA
40873876 CAACAACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.65, C:0.11, G:0.16, T:0.09
Consensus pattern (21 bp):
GCAAAACAATGAAAAAAAGTG
Found at i:40875677 original size:18 final size:18
Alignment explanation
Indices: 40875632--40875679 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
40875622 GGTCAACTAC
*
40875632 TTTTCTTATTTCTTTGTT
1 TTTTCTTTTTTCTTTGTT
* ** *
40875650 GTTTGATTTTTGTTTGTT
1 TTTTCTTTTTTCTTTGTT
40875668 TTTTCTTTTTTC
1 TTTTCTTTTTTC
40875680 AAAAATGTTT
Statistics
Matches: 21, Mismatches: 9, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.04, C:0.08, G:0.10, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTGTT
Found at i:40877067 original size:24 final size:26
Alignment explanation
Indices: 40877021--40877081 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
40877011 CCTAAATATT
*
40877021 TTTTTATTTTTATAATTATAA-TT-A
1 TTTTTATTTTTAAAATTATAATTTGA
40877045 TTTTTATTTTTAAAATT-TGAATTTGA
1 TTTTTATTTTTAAAATTAT-AATTTGA
*
40877071 ATTTTATTTTT
1 TTTTTATTTTT
40877082 TAGTAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.03
24 18 0.56
25 2 0.06
26 11 0.34
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTTATTTTTAAAATTATAATTTGA
Found at i:40883945 original size:29 final size:30
Alignment explanation
Indices: 40883899--40883969 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
40883889 AGCATGTTTC
* *
40883899 TATTTTGGTCACTCAAGTT-TAAAATTTTT
1 TATTTTAGTCACTAAAGTTATAAAATTTTT
* * **
40883928 TATTTTAGTTACTAAAGTTATCAAATTTAA
1 TATTTTAGTCACTAAAGTTATAAAATTTTT
*
40883958 TATTTTGGTCAC
1 TATTTTAGTCAC
40883970 ATCCATTAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (30 bp):
TATTTTAGTCACTAAAGTTATAAAATTTTT
Found at i:40884234 original size:20 final size:20
Alignment explanation
Indices: 40884191--40884234 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40884181 AATTTTTCGA
* *
40884191 TAAAAATACATAAGATTTTC
1 TAAAAATACATAAAAATTTC
40884211 TAAAAATACATACAAAATTT-
1 TAAAAATACATA-AAAATTTC
40884231 TAAA
1 TAAA
40884235 TGAATGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATACATAAAAATTTC
Found at i:40887308 original size:12 final size:12
Alignment explanation
Indices: 40887291--40887315 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40887281 CTCATAGTTG
40887291 AAGTTGAATGGT
1 AAGTTGAATGGT
40887303 AAGTTGAATGGT
1 AAGTTGAATGGT
40887315 A
1 A
40887316 CAGTGTCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AAGTTGAATGGT
Found at i:40894894 original size:43 final size:43
Alignment explanation
Indices: 40894813--40894902 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
40894803 ATTATATAAA
* * *
40894813 ATAAGTATAAATATAATTTTAATAAATCAAATACAATTTCTATT
1 ATAAGTATAAAAATAATTTTAATAAATCAAATAAAATTTATA-T
* *
40894857 ATAATTATAAAAAT-ATTTTAATAAAT-ACATTAAAATTTATAT
1 ATAAGTATAAAAATAATTTTAATAAATCA-AATAAAATTTATAT
40894899 ATAA
1 ATAA
40894903 ATTGTCATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 6 0.15
43 22 0.55
44 12 0.30
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (43 bp):
ATAAGTATAAAAATAATTTTAATAAATCAAATAAAATTTATAT
Found at i:40896729 original size:22 final size:22
Alignment explanation
Indices: 40896701--40896742 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
40896691 ACACAATAAG
40896701 TTTCACACAACTTTGAGAAAAT
1 TTTCACACAACTTTGAGAAAAT
*
40896723 TTTCACATAACTTTGAGAAA
1 TTTCACACAACTTTGAGAAA
40896743 TTATTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
TTTCACACAACTTTGAGAAAAT
Found at i:40900165 original size:16 final size:16
Alignment explanation
Indices: 40900125--40900166 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
40900115 TTTTTCATTT
*
40900125 TAAT-AAATTATTTAA
1 TAATAAAATTTTTTAA
* *
40900140 TATTATAATTTTTTAA
1 TAATAAAATTTTTTAA
40900156 TAATAAAATTT
1 TAATAAAATTT
40900167 AACAATAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAAAATTTTTTAA
Found at i:40903966 original size:31 final size:31
Alignment explanation
Indices: 40903931--40903996 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
40903921 GTCATTAAAT
*
40903931 TATTCAAAAATTT-TCATTTAAGTCACTGAAC
1 TATTCAAAAATTTGTC-TTTAAGTAACTGAAC
* *
40903962 TATTCAAAAGTTTGTCTTTAAGTAACTGGAC
1 TATTCAAAAATTTGTCTTTAAGTAACTGAAC
40903993 TATT
1 TATT
40903997 AAGGTTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (31 bp):
TATTCAAAAATTTGTCTTTAAGTAACTGAAC
Found at i:40908954 original size:47 final size:47
Alignment explanation
Indices: 40908896--40909008 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
40908886 CTGCCAAGAG
* * * *
40908896 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAACGTAATGAATGTGAA
* * * *
40908943 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAACGTAATGAATGTGAA
* *
40908990 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
40909009 TCCCGAAAGG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCGAATGGCCAACGTAATGAATGTGAA
Found at i:40909183 original size:37 final size:37
Alignment explanation
Indices: 40909127--40909205 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40909117 CCGAGCTCTA
* * *
40909127 AAGACCCGATGACTACGTGTGGGGATTTTGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
* *
40909164 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
40909201 AAGAC
1 AAGAC
40909206 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:40917467 original size:76 final size:75
Alignment explanation
Indices: 40917372--40917584 Score: 248
Period size: 75 Copynumber: 2.8 Consensus size: 75
40917362 CCAAACAAGG
* * *
40917372 CCTTTGTGGCGAGTTACCTGAAAAGCCTATGTGGCATATTATTTGGGAGGCCTTAATGGCTAATT
1 CCTTTGTGG-GAGTTACCTGAAAAGCCTATGTGGCATATTATTTGGGAAGCCTTAGTGGCGAATT
40917437 TATCTAGAAAA
65 TATCTAGAAAA
* * * * * *
40917448 CCTTTGTGGTGAGTTACCTGAAAAGCTTATGTGACATATTGTTT-AGAAGCTTTAGTGGAGAATT
1 CCTTTGTGG-GAGTTACCTGAAAAGCCTATGTGGCATATTATTTGGGAAGCCTTAGTGGCGAATT
* * **
40917512 TATTTGGAATG
65 TATCTAGAAAA
* * *
40917523 CCTTTGCGAGGAGTTACTTGAAAAGCCTATGTAGCATATTATTTGGGAAGCCTTAGTGGCGA
1 CCTTTGTG-GGAGTTACCTGAAAAGCCTATGTGGCATATTATTTGGGAAGCCTTAGTGGCGA
40917585 GATATGAGTA
Statistics
Matches: 112, Mismatches: 23, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
75 57 0.51
76 55 0.49
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (75 bp):
CCTTTGTGGGAGTTACCTGAAAAGCCTATGTGGCATATTATTTGGGAAGCCTTAGTGGCGAATTT
ATCTAGAAAA
Found at i:40919542 original size:23 final size:23
Alignment explanation
Indices: 40919516--40919587 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
40919506 TATCTGGAAA
*
40919516 GCCTTTGTGGCGTATTCTGTGAT
1 GCCTTTGTGGCGTATTCTGTAAT
* * *
40919539 GCCTTTATGACATATTCTGTAAT
1 GCCTTTGTGGCGTATTCTGTAAT
*
40919562 GCCTTTGTAGCGTATT-TCGTAAT
1 GCCTTTGTGGCGTATTCT-GTAAT
40919585 GCC
1 GCC
40919588 CTTATGGTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (23 bp):
GCCTTTGTGGCGTATTCTGTAAT
Found at i:40924684 original size:45 final size:45
Alignment explanation
Indices: 40924617--40924706 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
40924607 TGAACACTTC
* *
40924617 GGAATTAGCACATAGCAACCACCTTATTAATCAATGATGTCCGGT
1 GGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
* *
40924662 GGAATCAGCACATAGCAGCCACCTTACTAATCAATGATGTTCGGT
1 GGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
40924707 TCACATAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (45 bp):
GGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
Found at i:40926678 original size:10 final size:10
Alignment explanation
Indices: 40926663--40926696 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
40926653 AAGTTGAAAA
*
40926663 AGGCGTGGAT
1 AGGCGTGGAC
40926673 AGGCGTGGAC
1 AGGCGTGGAC
*
40926683 AGGCGTTGAC
1 AGGCGTGGAC
40926693 AGGC
1 AGGC
40926697 AAGAATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.18, G:0.47, T:0.15
Consensus pattern (10 bp):
AGGCGTGGAC
Found at i:40929209 original size:76 final size:77
Alignment explanation
Indices: 40929005--40929210 Score: 263
Period size: 76 Copynumber: 2.7 Consensus size: 77
40928995 CCAAATAAAG
* ** * **
40929005 CCTTTGTGGCGAGTTACCTGAAAAGCCTATGTGATGTATTATTTGGGAAGTCAAAATGGCAAATT
1 CCTTTGTGGCGAGTTACTTGAAAAGCCTATGTGGCGTATTATTTGGGAAGCCTTAATGGCAAATT
* *
40929070 TATCTTGAACGT
66 TATCTGGAACAT
* ** * *
40929082 -CTTTGTAGCGAGTTACTTGAAACCCCTATATGGCGTATTATTTGGGAAGCCTTAGTGGCAAATT
1 CCTTTGTGGCGAGTTACTTGAAAAGCCTATGTGGCGTATTATTTGGGAAGCCTTAATGGCAAATT
40929146 TATCTGGAA-AT
66 TATCTGGAACAT
* *
40929157 CCTTTATGGCGAGTTACTTGAAAAGCTTATGTGGCGTATTATTTGGGAAGCCTT
1 CCTTTGTGGCGAGTTACTTGAAAAGCCTATGTGGCGTATTATTTGGGAAGCCTT
40929211 TGCAGCGAGT
Statistics
Matches: 109, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
75 1 0.01
76 108 0.99
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (77 bp):
CCTTTGTGGCGAGTTACTTGAAAAGCCTATGTGGCGTATTATTTGGGAAGCCTTAATGGCAAATT
TATCTGGAACAT
Found at i:40929219 original size:50 final size:50
Alignment explanation
Indices: 40929165--40929260 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
40929155 ATCCTTTATG
* * * *
40929165 GCGAGTTACTTGAAAAGCTTATGTGGCGTATTATTTGGGAAGCCTTTGCA
1 GCGAGTTACCTGAAAAGCCTATATGGCATATTATTTGGGAAGCCTTTGCA
*
40929215 GCGAGTTACCTGGAAAGCCTATATGGCATATTATTTGGGAAGCCTT
1 GCGAGTTACCTGAAAAGCCTATATGGCATATTATTTGGGAAGCCTT
40929261 AGTGGTGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (50 bp):
GCGAGTTACCTGAAAAGCCTATATGGCATATTATTTGGGAAGCCTTTGCA
Found at i:40929257 original size:25 final size:25
Alignment explanation
Indices: 40929106--40929259 Score: 66
Period size: 25 Copynumber: 6.1 Consensus size: 25
40929096 ACTTGAAACC
* *
40929106 CCTATATGGCGTATTATTTGGGAAG
1 CCTATATGGCATATTATTTGGAAAG
* * *
40929131 CCT-TAGTGGCAAATTTATCTGGAAAT
1 CCTATA-TGGCATA-TTATTTGGAAAG
* * * *
40929157 CCTTTATGGCGA-GTTACTTGAAAAG
1 CCTATATGGC-ATATTATTTGGAAAG
* * * *
40929182 CTTATGTGGCGTATTATTTGGGAAG
1 CCTATATGGCATATTATTTGGAAAG
* **
40929207 CCT-T-TGCAGCGA-GTTACCTGGAAAG
1 CCTATATG--GC-ATATTATTTGGAAAG
*
40929232 CCTATATGGCATATTATTTGGGAAG
1 CCTATATGGCATATTATTTGGAAAG
40929257 CCT
1 CCT
40929260 TAGTGGTGAG
Statistics
Matches: 90, Mismatches: 28, Indels: 22
0.64 0.20 0.16
Matches are distributed among these distances:
23 2 0.02
24 4 0.04
25 62 0.69
26 17 0.19
27 5 0.06
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (25 bp):
CCTATATGGCATATTATTTGGAAAG
Found at i:40931045 original size:11 final size:11
Alignment explanation
Indices: 40931031--40931085 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
40931021 TATTATTTTC
*
40931031 ATATTTTTATA
1 ATATTTTAATA
40931042 ATA-TTTAATA
1 ATATTTTAATA
40931052 ATA-TTTAATA
1 ATATTTTAATA
*
40931062 AAATTTATAATA
1 ATATTT-TAATA
*
40931074 TTATGTTTAATA
1 ATAT-TTTAATA
40931086 TCGCAATGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 18 0.49
11 5 0.14
12 12 0.32
13 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:40931054 original size:10 final size:10
Alignment explanation
Indices: 40931039--40931075 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
40931029 TCATATTTTT
40931039 ATAATATTTA
1 ATAATATTTA
40931049 ATAATATTTA
1 ATAATATTTA
*
40931059 ATAAAATTT-
1 ATAATATTTA
40931068 ATAATATT
1 ATAATATT
40931076 ATGTTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATAATATTTA
Found at i:40931819 original size:21 final size:24
Alignment explanation
Indices: 40931794--40931836 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40931784 TAAATACATC
40931794 AATTT-ATT-TTTA-TATTGGATA
1 AATTTAATTATTTATTATTGGATA
40931815 AATTTAATTATTTATTATTGGA
1 AATTTAATTATTTATTATTGGA
40931837 ATATATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 4 0.21
24 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (24 bp):
AATTTAATTATTTATTATTGGATA
Found at i:40934333 original size:3 final size:3
Alignment explanation
Indices: 40934325--40934442 Score: 236
Period size: 3 Copynumber: 39.3 Consensus size: 3
40934315 TCCTTAACCC
40934325 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40934373 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40934421 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
40934443 GAGAATTTAG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40936262 original size:15 final size:16
Alignment explanation
Indices: 40936242--40936271 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40936232 AGTTGTCCCG
40936242 ATCGTCTA-ATTTAGT
1 ATCGTCTAGATTTAGT
40936257 ATCGTCTAGATTTAG
1 ATCGTCTAGATTTAG
40936272 CATTGAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (16 bp):
ATCGTCTAGATTTAGT
Found at i:40937420 original size:52 final size:50
Alignment explanation
Indices: 40937356--40937484 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 50
40937346 ATGAACATAT
* *
40937356 GAGTTACTTAATGCATGACTTAATCTAATGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACTTAAT-TAATGATGCAAAC-TTAACTAACATGA
* * * *
40937408 GAGTTACATAATGCATGTCATAATTTATGATGCAAACTTACCTAACATGA
1 GAGTTACATAATGCATGACTTAATTAATGATGCAAACTTAACTAACATGA
* * *
40937458 GAGTTATATAATGTATGACTTTATTAA
1 GAGTTACATAATGCATGACTTAATTAA
40937485 ATCCAGAATA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 32 0.49
51 12 0.18
52 21 0.32
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (50 bp):
GAGTTACATAATGCATGACTTAATTAATGATGCAAACTTAACTAACATGA
Found at i:40939333 original size:15 final size:15
Alignment explanation
Indices: 40939309--40939340 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40939299 TCCATTCTCC
40939309 TTTTTCTCTTTTTCA
1 TTTTTCTCTTTTTCA
*
40939324 TTTTTTTCTTTTTCA
1 TTTTTCTCTTTTTCA
40939339 TT
1 TT
40939341 CTCAAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTCTTTTTCA
Found at i:40939413 original size:14 final size:14
Alignment explanation
Indices: 40939396--40939441 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
40939386 TTCACTTTTC
*
40939396 TTTCAATCTTTCTT
1 TTTCATTCTTTCTT
**
40939410 TTTCATTCAATCTT
1 TTTCATTCTTTCTT
40939424 TTTCATTCATTTCTT
1 TTTCATTC-TTTCTT
40939439 TTT
1 TTT
40939442 TTCTTCTCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTCATTCTTTCTT
Found at i:40939432 original size:18 final size:18
Alignment explanation
Indices: 40939397--40939434 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40939387 TCACTTTTCT
*
40939397 TTCAATCTTTCTTTTTCA
1 TTCAATCTTTCTTATTCA
40939415 TTCAATCTTT-TTCATTCA
1 TTCAATCTTTCTT-ATTCA
40939433 TT
1 TT
40939435 TCTTTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (18 bp):
TTCAATCTTTCTTATTCA
Found at i:40940349 original size:15 final size:15
Alignment explanation
Indices: 40940331--40940360 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40940321 TTTTTTTTCA
40940331 AATTTTTTTCACTTT
1 AATTTTTTTCACTTT
*
40940346 AATTTTTTTTACTTT
1 AATTTTTTTCACTTT
40940361 TTTTGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTTTTTCACTTT
Found at i:40945369 original size:50 final size:50
Alignment explanation
Indices: 40945237--40945462 Score: 240
Period size: 50 Copynumber: 4.5 Consensus size: 50
40945227 TGATCATAAC
** * *
40945237 ATGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTTATATCG
1 ATGCCAACA-CCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * ** ** *
40945288 GTGCCCATTCCATGTCCCAGACATGGTCTTACGGGGGACCTCTAATCTCG
1 ATGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
**
40945338 ATGCCAACACCATGTCCCAGACATGGTCTTACATAAGACCTCTCATCTC-
1 ATGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
40945387 AGTGCCAACGCGATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 A-TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* ** *
40945438 GTGCCAATGCCATGTCCCATACATG
1 ATGCCAACACCATGTCCCAGACATG
40945463 CCAAAGCCAT
Statistics
Matches: 146, Mismatches: 26, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
49 1 0.01
50 113 0.77
51 32 0.22
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (50 bp):
ATGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:40945427 original size:100 final size:100
Alignment explanation
Indices: 40945237--40945462 Score: 265
Period size: 100 Copynumber: 2.2 Consensus size: 100
40945227 TGATCATAAC
** ** * * * **
40945237 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTTATATCGGTGCCCATTCCATG
1 ATGCCAAA-CCATGTCCCAGACATGGTCTTACATAAGATCCTCTCATATCAGTGCCAACGCCATG
*
40945302 TCCCAGACATGGTCTTACGGGGGACCTCTAATCTCG
65 TCCCAGACATGGTCTTACAGGGGACCTCTAATCTCG
* *
40945338 ATGCCAACACCATGTCCCAGACATGGTCTTACATAAGA-CCTCTCATCTCAGTGCCAACGCGATG
1 ATGCCAA-ACCATGTCCCAGACATGGTCTTACATAAGATCCTCTCATATCAGTGCCAACGCCATG
* *
40945402 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
65 TCCCAGACATGGTCTTACAGGGGACCTCTAATCTCG
* * *
40945438 GTGCCAATGCCATGTCCCATACATG
1 ATGCCAA-ACCATGTCCCAGACATG
40945463 CCAAAGCCAT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
100 71 0.67
101 34 0.32
102 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (100 bp):
ATGCCAAACCATGTCCCAGACATGGTCTTACATAAGATCCTCTCATATCAGTGCCAACGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTAATCTCG
Found at i:40952268 original size:28 final size:28
Alignment explanation
Indices: 40952237--40952293 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
40952227 TCTATGCATG
40952237 ATTTATCACCTAGACATTTGCAACAACA
1 ATTTATCACCTAGACATTTGCAACAACA
40952265 ATTTATCACCTAGACATTTGCAACAACA
1 ATTTATCACCTAGACATTTGCAACAACA
40952293 A
1 A
40952294 ACACCTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (28 bp):
ATTTATCACCTAGACATTTGCAACAACA
Found at i:40957008 original size:40 final size:40
Alignment explanation
Indices: 40956949--40957063 Score: 178
Period size: 40 Copynumber: 2.9 Consensus size: 40
40956939 GAGTGTTACC
40956949 TACTGAAACGTATGCGCTATTGAGCCATACCTACTGAATCT
1 TACTGAAACGTATGCGCTATTGAGCCATACCTACTGAAT-T
* *
40956990 T-CTGAAATGTATGTGCTATTGAGCCATACCTACTGAATT
1 TACTGAAACGTATGCGCTATTGAGCCATACCTACTGAATT
* *
40957029 TACTGAAACGTATGCGTTATCGAGCCATACCTACT
1 TACTGAAACGTATGCGCTATTGAGCCATACCTACT
40957064 AAATAAGTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.03
40 64 0.96
41 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (40 bp):
TACTGAAACGTATGCGCTATTGAGCCATACCTACTGAATT
Found at i:40957198 original size:49 final size:49
Alignment explanation
Indices: 40957124--40957219 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
40957114 GAGTGTTACC
* *
40957124 TACTGAAATGTATGTGCTATTGAGCCATACCCACTGAATCTACTGAATT
1 TACTGAAATGTATGCGCTATCGAGCCATACCCACTGAATCTACTGAATT
* * *
40957173 TACTGAAATGTATGCGTTATCGAGCCATACCTACTGATTCTACTGAA
1 TACTGAAATGTATGCGCTATCGAGCCATACCCACTGAATCTACTGAA
40957220 ATGTAGGAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (49 bp):
TACTGAAATGTATGCGCTATCGAGCCATACCCACTGAATCTACTGAATT
Found at i:40957207 original size:40 final size:40
Alignment explanation
Indices: 40957163--40957295 Score: 144
Period size: 40 Copynumber: 3.4 Consensus size: 40
40957153 CCCACTGAAT
*
40957163 CTACTGAATT-TACTGAAATGTATGCGTTATCGAGCCATAC
1 CTACTG-ATTCTACTGAAATGTATGCATTATCGAGCCATAC
* * * *
40957203 CTACTGATTCTACTGAAATGTAGGAACTATCGAGCCACAC
1 CTACTGATTCTACTGAAATGTATGCATTATCGAGCCATAC
* * * * *
40957243 CTATTGGTTGTACT-AAAAGTATGCTTTATCGAGCCATAC
1 CTACTGATTCTACTGAAATGTATGCATTATCGAGCCATAC
*
40957282 CTACTGGTTCTACT
1 CTACTGATTCTACT
40957296 AAAAGCTGTT
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 34 0.45
40 42 0.55
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (40 bp):
CTACTGATTCTACTGAAATGTATGCATTATCGAGCCATAC
Found at i:40957284 original size:39 final size:40
Alignment explanation
Indices: 40957173--40957300 Score: 143
Period size: 39 Copynumber: 3.2 Consensus size: 40
40957163 CTACTGAATT
* * *
40957173 TACTGAAATGTATGCGTTATCGAGCCATACCTACTGATTC
1 TACTGAAAAGTATGCATTATCGAGCCATACCTACTGGTTC
* * * * * * *
40957213 TACTGAAATGTAGGAACTATCGAGCCACACCTATTGGTTG
1 TACTGAAAAGTATGCATTATCGAGCCATACCTACTGGTTC
*
40957253 TACT-AAAAGTATGCTTTATCGAGCCATACCTACTGGTTC
1 TACTGAAAAGTATGCATTATCGAGCCATACCTACTGGTTC
40957292 TACT-AAAAG
1 TACTGAAAAG
40957301 CTGTTCAAAC
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
39 36 0.50
40 36 0.50
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (40 bp):
TACTGAAAAGTATGCATTATCGAGCCATACCTACTGGTTC
Found at i:40960321 original size:24 final size:24
Alignment explanation
Indices: 40960289--40960335 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
40960279 ATAATATGAA
40960289 TAAATATATTAATTACAATTACAT
1 TAAATATATTAATTACAATTACAT
40960313 TAAATATATTAATTACAATTACA
1 TAAATATATTAATTACAATTACA
40960336 AAAGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAATATATTAATTACAATTACAT
Found at i:40960349 original size:24 final size:24
Alignment explanation
Indices: 40960288--40960349 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
40960278 TATAATATGA
40960288 ATAAATATAT-TAATTACAATTAC
1 ATAAATATATATAATTACAATTAC
40960311 ATTAAATATAT-TAATTACAATTAC
1 A-TAAATATATATAATTACAATTAC
*
40960335 A-AAAGTTTATATAAT
1 ATAAA-TATATATAAT
40960350 ATGAATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 3 0.09
23 5 0.14
24 27 0.77
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAAATATATATAATTACAATTAC
Found at i:40966435 original size:43 final size:43
Alignment explanation
Indices: 40966379--40966564 Score: 264
Period size: 43 Copynumber: 4.3 Consensus size: 43
40966369 TTTTAAAAAT
* *
40966379 AAACGCCGCTAAAGACCAAGACCTTTAGAGGCACTTTTACAAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCAAC
* * * *
40966422 AAACGCCGTTAAAGACCAATACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCAAC
* *
40966465 AAACGCCGCTAAAGACCAAGACCTCTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCAAC
* **
40966508 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCCTGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCAC-TTTTCCAAC
40966552 AAACGCCGCTAAA
1 AAACGCCGCTAAA
40966565 AAAGCATTAC
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 107 0.84
44 20 0.16
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCAAC
Found at i:40966599 original size:44 final size:42
Alignment explanation
Indices: 40966379--40966590 Score: 237
Period size: 43 Copynumber: 4.9 Consensus size: 42
40966369 TTTTAAAAAT
* * * *
40966379 AAACGCCGCTAAAGACCAAGACCTTTAGAGGCACTTTTACAAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-CCAC
*
40966422 AAACGCCGTTAAAGACCAAT-ACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACC-ATGACCTTTAGCGGCGCTTTT-CCAC
* *
40966465 AAACGCCGCTAAAGACCAAGACCTCTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCC-AC
* *
40966508 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCCTGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC-TTTTCC-AC
* * * *
40966552 AAACGCCGCTAAAAAAGCATTACCTTTAGCGACGCTTTT
1 AAACGCCGCT-AAAGACCATGACCTTTAGCGGCGCTTTT
40966591 AGCTCAAACC
Statistics
Matches: 145, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
42 3 0.02
43 101 0.70
44 22 0.15
45 19 0.13
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCAC
Found at i:40976688 original size:16 final size:17
Alignment explanation
Indices: 40976664--40976696 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40976654 TAGCAAAAGT
*
40976664 TTAATAATGGAAAAGAA
1 TTAATAATGAAAAAGAA
40976681 TTAA-AATGAAAAAGAA
1 TTAATAATGAAAAAGAA
40976697 CTGTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
TTAATAATGAAAAAGAA
Found at i:40992298 original size:16 final size:17
Alignment explanation
Indices: 40992274--40992306 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40992264 TAGCAAAAGT
*
40992274 TTAATAATGGAAAAGAA
1 TTAATAATGAAAAAGAA
40992291 TTAA-AATGAAAAAGAA
1 TTAATAATGAAAAAGAA
40992307 CTGTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
TTAATAATGAAAAAGAA
Done.