Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 129 of 150
Found at i:38935912 original size:44 final size:41
Alignment explanation
Indices: 38935841--38936211 Score: 350
Period size: 44 Copynumber: 8.5 Consensus size: 41
38935831 TTGTAAATCC
*
38935841 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAATTCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAA--AAGCAAGTCT
*
38935885 TATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAAATGGCAAGTCT
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACT-AAAA--GCAAGTCT
* * * *
38935930 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAAAGC-A-AGTCT
* * * *
38935974 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCT
1 TATCTCC-TGAAGTTGCAGTGGAGCAGACTAAAAGC-AAG-TCT
* *** * *
38936018 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAAAGCAAGTCT
*
38936058 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAA--AAGCAAGTCT
38936102 TATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAATTGGCAAGTCT
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACTAAAA---GCAAGTCT
38936147 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACT-AA-AAGCAAGTCT
38936191 TATCCTCCTGAAGTTGCAGTG
1 TAT-CTCCTGAAGTTGCAGTG
38936212 AGGCAGATTG
Statistics
Matches: 277, Mismatches: 27, Indels: 46
0.79 0.08 0.13
Matches are distributed among these distances:
40 20 0.07
41 10 0.04
42 7 0.03
43 12 0.04
44 149 0.54
45 75 0.27
46 2 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (41 bp):
TATCTCCTGAAGTTGCAGTGGAGCAGACTAAAAGCAAGTCT
Found at i:38935946 original size:89 final size:86
Alignment explanation
Indices: 38935841--38936211 Score: 359
Period size: 89 Copynumber: 4.2 Consensus size: 86
38935831 TTGTAAATCC
*
38935841 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAATTCTTATC-CTCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTC-CCTGAAGTTGCAGT
*
38935905 GGGGCAGACTGAAAATGGCAAGTCT
64 GGAGCAGACT-AAAAT-GCAAGTCT
* * * * *
38935930 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCGATAATCCTATCTCCTTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A-AGTCTTATCTCCCTGAAGTTGCAGT
* *
38935994 GGAGCGGATTAAAACCT-C-AGATCT
64 GGAGCAGACTAAAA--TGCAAG-TCT
* * * * * *
38936018 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTCCCTGAAGTTGCAGTGG
*
38936080 AGCAGACTAAGTAA-GCAAGTCC
66 AGCAGACTAA--AATGCAAGTCT
38936102 TATC-CTCCTGAAGTTGCAGTGGAGCAGACTAA-AATTGGCAAGTCTTATCTCCCTGAAGTTGCA
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACTAAGAA---GCAAGTCTTATCTCCCTGAAGTTGCA
*
38936165 GTGGAGCAGACTAAATAAGCAAGTCT
62 GTGGAGCAGACTAAA-ATGCAAGTCT
38936191 TATC-CTCCTGAAGTTGCAGTG
1 TATCTC-CCTGAAGTTGCAGTG
38936212 AGGCAGATTG
Statistics
Matches: 235, Mismatches: 27, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
83 1 0.00
84 51 0.22
85 9 0.04
86 7 0.03
87 13 0.06
88 28 0.12
89 124 0.53
90 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (86 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTCCCTGAAGTTGCAGTGG
AGCAGACTAAAATGCAAGTCT
Found at i:38936114 original size:128 final size:129
Alignment explanation
Indices: 38935836--38936174 Score: 356
Period size: 128 Copynumber: 2.6 Consensus size: 129
38935826 GAAGATTGTA
* *
38935836 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA--GCAATTCTTATC-CTCCTGAAG
1 AATCCTATCTCCTTGAAGTTGCAGTGGAGCAGACTAA--AACTGCAAGTCTTATCTC-CCTGAAG
* * * * *
38935898 TTGCAGTGGGGCAGA-CTGAAAATGGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA
63 TTGCAGTAGAGCAGATC-G--CAT--CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
38935962 AACCGAT
123 AACCGAT
* * *
38935969 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACCT-C-AGATCTTATCTCTCTGAAGT
1 AATCCTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAAA-CTGCAAG-TCTTATCTCCCTGAAGT
*
38936032 TGCAG-AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
64 TGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AACC
38936096 -A-
127 GAT
* *
38936097 AGTCCTATCCTCC-TGAAGTTGCAGTGGAGCAGACTAAAATTGGCAAGTCTTATCTCCCTGAAGT
1 AATCCTAT-CTCCTTGAAGTTGCAGTGGAGCAGACTAAAACT-GCAAGTCTTATCTCCCTGAAGT
*
38936161 TGCAGTGGAGCAGA
64 TGCAGTAGAGCAGA
38936175 CTAAATAAGC
Statistics
Matches: 176, Mismatches: 17, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
127 1 0.01
128 68 0.39
129 27 0.15
130 14 0.08
131 2 0.01
132 8 0.05
133 55 0.31
134 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (129 bp):
AATCCTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAAACTGCAAGTCTTATCTCCCTGAAGTTG
CAGTAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACCGAT
Found at i:38936420 original size:19 final size:19
Alignment explanation
Indices: 38936396--38936499 Score: 145
Period size: 19 Copynumber: 5.4 Consensus size: 19
38936386 AATTTTTGAG
*
38936396 GATATGCAATCTAAGATAT
1 GATATGCAATCTTAGATAT
**
38936415 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
38936434 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
38936455 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
38936474 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38936493 GATATGC
1 GATATGC
38936500 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 59 0.78
21 17 0.22
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38936441 original size:40 final size:40
Alignment explanation
Indices: 38936397--38936499 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
38936387 ATTTTTGAGG
*
38936397 ATATGCAATCTAAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
**
38936437 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
38936477 ATAT--AATCTTAGATATGATATGC
1 ATATGCAATCTTAGATATGATATGC
38936500 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 19 0.32
40 41 0.68
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:38937272 original size:23 final size:25
Alignment explanation
Indices: 38937218--38937266 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
38937208 TATGTACATG
*
38937218 TATATTTTTTTAACGAATATTTTCC
1 TATATTTTTTTAAAGAATATTTTCC
38937243 TATATTTTTTTAAAGAATATTTTC
1 TATATTTTTTTAAAGAATATTTTC
38937267 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATTTTTTTAAAGAATATTTTCC
Found at i:38938064 original size:98 final size:98
Alignment explanation
Indices: 38937940--38938136 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
38937930 TAAAAAATAA
* *
38937940 TAAAGGAAATATTCCGAGTTTAGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTAGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
38938005 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGAATAAGTGGATGTTCTTTTAAAG
* *
38938038 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTAGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
38938103 TTAAATCTTGAATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGAATAAGTGGATGTTCTTTTAAAG
38938136 T
1 T
38938137 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTAGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGAATAAGTGGATGTTCTTTTAAAG
Found at i:38938998 original size:10 final size:10
Alignment explanation
Indices: 38938983--38939017 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
38938973 TGCTGTTTAA
38938983 TTCTTTTTTT
1 TTCTTTTTTT
38938993 TTC-TTTTTT
1 TTCTTTTTTT
38939002 TTCTTTTTTT
1 TTCTTTTTTT
38939012 TT-TTTT
1 TTCTTTT
38939018 GCATGCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.54
10 11 0.46
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:38939345 original size:22 final size:22
Alignment explanation
Indices: 38939310--38939355 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
38939300 CAAATTCCAA
38939310 TCAAGTTTCAAAAGTCCAAA-AT
1 TCAAGTTTCAAAAGT-CAAATAT
38939332 TCAA-TTTCACAAAGTCAAATAT
1 TCAAGTTTCA-AAAGTCAAATAT
38939354 TC
1 TC
38939356 TAGTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (22 bp):
TCAAGTTTCAAAAGTCAAATAT
Found at i:38944953 original size:35 final size:36
Alignment explanation
Indices: 38944900--38944967 Score: 129
Period size: 35 Copynumber: 1.9 Consensus size: 36
38944890 ATTGAGAAAA
38944900 AAAATCAATGTTTAAATCGGTTTACAATTTTTTTTT
1 AAAATCAATGTTTAAATCGGTTTACAATTTTTTTTT
38944936 AAAATCAAT-TTTAAATCGGTTTACAATTTTTT
1 AAAATCAATGTTTAAATCGGTTTACAATTTTTT
38944968 AGGCTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.72
36 9 0.28
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (36 bp):
AAAATCAATGTTTAAATCGGTTTACAATTTTTTTTT
Found at i:38945198 original size:16 final size:16
Alignment explanation
Indices: 38945177--38945219 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
38945167 GTCTTTAATT
38945177 ATTTTAAGAAATTA-AA
1 ATTTTAA-AAATTATAA
*
38945193 ATTTTAAATATATATAA
1 ATTTTAAAAAT-TATAA
38945210 ATTTTAAAAA
1 ATTTTAAAAA
38945220 ATTTTGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 9 0.39
17 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTTAAAAATTATAA
Found at i:38946201 original size:18 final size:19
Alignment explanation
Indices: 38946178--38946223 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
38946168 AACTCTTTTT
38946178 ATTCTCTCTAAA-CTC-CAA
1 ATTCTCTC-AAATCTCTCAA
38946196 ATTCTCTCAAATCTCTCAA
1 ATTCTCTCAAATCTCTCAA
38946215 ATT-TCTCAA
1 ATTCTCTCAA
38946224 TTTTTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.12
18 17 0.65
19 6 0.23
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTCTCAAATCTCTCAA
Found at i:38950011 original size:50 final size:50
Alignment explanation
Indices: 38949908--38950100 Score: 242
Period size: 50 Copynumber: 3.7 Consensus size: 50
38949898 GGGAATGAGA
38949908 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC---GAG---ATGAGAGG
*
38949964 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
** * * * **
38950014 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
* *
38950064 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
38950101 ATACAGAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
50 82 0.67
53 3 0.02
56 38 0.31
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
Found at i:38957310 original size:50 final size:50
Alignment explanation
Indices: 38957192--38957384 Score: 242
Period size: 50 Copynumber: 3.8 Consensus size: 50
38957182 GATAATAACA
* * *** *
38957192 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGGTGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTCGG
* * * * *
38957243 TGCCCATGCCATATCCCAGATATGGTCTTACGGGGGACCTCTAATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
38957293 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
38957343 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
38957385 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 96 0.79
51 26 0.21
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:38957371 original size:100 final size:101
Alignment explanation
Indices: 38957192--38957384 Score: 271
Period size: 100 Copynumber: 1.9 Consensus size: 101
38957182 GATAATAACA
* *** *
38957192 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGGTGTTCTCATATCGGTGCCCATGCCATAT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGACCTCTCATATCGGTGCCAATGCCATAT
* *
38957257 CCCAGATATGGTCTTACGGGGGACCTCTAATCTCGG
66 CCCAGACATGGTCTTACAGGGGACCTCTAATCTCGG
* * * *
38957293 TGCCAACGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTTGGTGCCAATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGACCTCTCATATCGGTGCCAATGCCATAT
*
38957357 CCCAGACATGGTCTTACATGGGACCTCT
66 CCCAGACATGGTCTTACAGGGGACCTCT
38957385 TTACCCAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 49 0.61
101 31 0.39
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGACCTCTCATATCGGTGCCAATGCCATAT
CCCAGACATGGTCTTACAGGGGACCTCTAATCTCGG
Found at i:38968423 original size:28 final size:28
Alignment explanation
Indices: 38968360--38968423 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
38968350 TATTAATTTT
* *
38968360 AATTTTTATAATATAAAAATAAATATTT
1 AATTTTTAAAATATAAAAATAAATATTA
*
38968388 AATATTTAAAATAATAAAAAT-AAT-TTAA
1 AATTTTTAAAAT-ATAAAAATAAATATT-A
38968416 AATTTTTA
1 AATTTTTA
38968424 TATTATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 2 0.07
28 20 0.67
29 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTTTTAAAATATAAAAATAAATATTA
Found at i:38972941 original size:31 final size:31
Alignment explanation
Indices: 38972868--38972941 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
38972858 CAAATTGAAA
* * *
38972868 AAACTCAAGTACCAAAATAAATATCGAAGCT
1 AAACTCAAGTATCAAAATAAATATCAAAGCC
* *
38972899 AAACTCAAGTATCAAAGTAAATATTAAAGCC
1 AAACTCAAGTATCAAAATAAATATCAAAGCC
*
38972930 AAACTTAAGTAT
1 AAACTCAAGTAT
38972942 TAAATTAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (31 bp):
AAACTCAAGTATCAAAATAAATATCAAAGCC
Found at i:38975382 original size:17 final size:17
Alignment explanation
Indices: 38975362--38975394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38975352 CTCTTTTTTT
*
38975362 TTTCTTTTAAATTATTG
1 TTTCATTTAAATTATTG
38975379 TTTCATTTAAATTATT
1 TTTCATTTAAATTATT
38975395 TGTCTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTCATTTAAATTATTG
Found at i:38975402 original size:18 final size:17
Alignment explanation
Indices: 38975367--38975402 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38975357 TTTTTTTTCT
*
38975367 TTTAAATTATTGTTTCA
1 TTTAAATTATTGTCTCA
38975384 TTTAAATTATTTGTCTCA
1 TTTAAATTA-TTGTCTCA
38975402 T
1 T
38975403 CTCCACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTAAATTATTGTCTCA
Found at i:38975562 original size:12 final size:14
Alignment explanation
Indices: 38975533--38975561 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38975523 CATGCATGAG
38975533 AAATATAAAGATAA
1 AAATATAAAGATAA
38975547 AAATA-AAAGATAA
1 AAATATAAAGATAA
38975560 AA
1 AA
38975562 TGGAGAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAATATAAAGATAA
Found at i:38984932 original size:46 final size:46
Alignment explanation
Indices: 38984881--38985144 Score: 469
Period size: 46 Copynumber: 5.8 Consensus size: 46
38984871 GTGATAAGTA
* *
38984881 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
* *
38984927 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
38984973 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
38985019 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
38985065 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
*
38985111 CTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
38985145 ATCATACGTA
Statistics
Matches: 213, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
44 12 0.06
45 5 0.02
46 196 0.92
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (46 bp):
CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAG
Found at i:38987809 original size:13 final size:12
Alignment explanation
Indices: 38987783--38987841 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
38987773 AGGCAACCCA
38987783 ATTTTTATTTTT
1 ATTTTTATTTTT
*
38987795 ATTTTTGTTTATT
1 ATTTTTATTT-TT
*
38987808 ATTTATT-TATTT
1 ATTT-TTATTTTT
38987820 ATTTATTA-TTTT
1 ATTT-TTATTTTT
38987832 ATTATTTATT
1 ATT-TTTATT
38987842 ACTTATTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 27 0.69
13 10 0.26
14 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:38987811 original size:19 final size:18
Alignment explanation
Indices: 38987783--38987841 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
38987773 AGGCAACCCA
*
38987783 ATTT-TTATTTTTATTTTT
1 ATTTATTATTTTT-TATTT
*
38987801 GTTTATTATTTATTTATTT
1 ATTTATTATTT-TTTATTT
38987820 ATTTATTATTTTATTATTT
1 ATTTATTATTTT-TTATTT
38987839 ATT
1 ATT
38987842 ACTTATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.11
19 29 0.83
20 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTATTATTTTTTATTT
Found at i:38987815 original size:4 final size:4
Alignment explanation
Indices: 38987802--38987841 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
38987792 TTTATTTTTG
38987802 TTTA -TTA TTTA TTTA TTTA TTTA -TTA TTT- TATTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TT
38987842 ACTTATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 7 0.22
4 24 0.75
5 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:38987819 original size:27 final size:27
Alignment explanation
Indices: 38987792--38987849 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
38987782 AATTTTTATT
38987792 TTTATTT-TT-GTTTATTATTTATTTA
1 TTTATTTATTAGTTTATTATTTATTTA
*
38987817 TTTATTTATTATTTTATTATTTA-TTA
1 TTTATTTATTAGTTTATTATTTATTTA
*
38987843 CTTATTT
1 TTTATTT
38987850 GGATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.24
26 11 0.38
27 11 0.38
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTATTTATTAGTTTATTATTTATTTA
Found at i:38987822 original size:15 final size:15
Alignment explanation
Indices: 38987792--38987849 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
38987782 AATTTTTATT
*
38987792 TTTATT-TTTGTTTA
1 TTTATTATTTATTTA
38987806 -TTATTTATTTATTTA
1 TTTA-TTATTTATTTA
38987821 TTTATTATTT-TATTA
1 TTTATTATTTAT-TTA
*
38987836 TTTATTACTTATTT
1 TTTATTATTTATTT
38987850 GGATATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 3 0.08
14 3 0.08
15 27 0.73
16 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:38987842 original size:7 final size:7
Alignment explanation
Indices: 38987783--38987848 Score: 61
Period size: 7 Copynumber: 10.0 Consensus size: 7
38987773 AGGCAACCCA
38987783 ATTT-TT
1 ATTTATT
38987789 ATTT-TT
1 ATTTATT
38987795 ATTT-TT
1 ATTTATT
*
38987801 GTTTATT
1 ATTTATT
38987808 ATTTATT
1 ATTTATT
*
38987815 -TAT-TT
1 ATTTATT
38987820 ATTTATT
1 ATTTATT
38987827 ATTTTATT
1 A-TTTATT
38987835 ATTTATT
1 ATTTATT
*
38987842 ACTTATT
1 ATTTATT
38987849 TGGATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
5 2 0.04
6 19 0.37
7 23 0.45
8 7 0.14
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (7 bp):
ATTTATT
Found at i:38988028 original size:22 final size:23
Alignment explanation
Indices: 38988000--38988050 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
38987990 AGAACGCCTC
* *
38988000 CAGCCAAACTACCC-TATTCCTG
1 CAGCCAAACCACCCTTATCCCTG
38988022 CAGCC-AACCACCCTTATCCCTG
1 CAGCCAAACCACCCTTATCCCTG
38988044 CAGCCAA
1 CAGCCAA
38988051 GCATCACCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.28
22 17 0.68
23 1 0.04
ACGTcount: A:0.27, C:0.45, G:0.10, T:0.18
Consensus pattern (23 bp):
CAGCCAAACCACCCTTATCCCTG
Found at i:38989155 original size:99 final size:100
Alignment explanation
Indices: 38988984--38989174 Score: 289
Period size: 99 Copynumber: 1.9 Consensus size: 100
38988974 TTTAAGAACA
38988984 TGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
* *
38989049 GTGTTCCT-AAG-AAAAAAATAATAAATTAGGAGTC
66 ATATTCCTAAAGCAAAAAAAT-ATAAATTAGGAGTC
* **
38989083 TGTTGGGCTGAGTAATCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTC-AG
1 TGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGA-
*
38989147 TATATTCCTAAAGCATAAAAATATAAAT
65 TATATTCCTAAAGCAAAAAAATATAAAT
38989175 AATAAATAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
98 1 0.01
99 66 0.80
100 9 0.11
101 7 0.08
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (100 bp):
TGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGAT
ATATTCCTAAAGCAAAAAAATATAAATTAGGAGTC
Found at i:38989183 original size:19 final size:18
Alignment explanation
Indices: 38989161--38989202 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
38989151 TTCCTAAAGC
38989161 ATAAAAATATAAATAATAA
1 ATAAAAATATAAA-AATAA
*
38989180 AT--AAATATCAAAATAA
1 ATAAAAATATAAAAATAA
38989196 ATAAAAA
1 ATAAAAA
38989203 AGAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 3 0.15
19 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATATAAAAATAA
Found at i:38989196 original size:16 final size:17
Alignment explanation
Indices: 38989165--38989200 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
38989155 TAAAGCATAA
38989165 AAATATAAATAATAAAT
1 AAATATAAATAATAAAT
*
38989182 AAATATCAA-AATAAAT
1 AAATATAAATAATAAAT
38989198 AAA
1 AAA
38989201 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATATAAATAATAAAT
Found at i:38989806 original size:15 final size:15
Alignment explanation
Indices: 38989786--38989815 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38989776 TATTTTAAAT
*
38989786 ATATTAGGATAATTA
1 ATATTAAGATAATTA
38989801 ATATTAAGATAATTA
1 ATATTAAGATAATTA
38989816 TTCAGGATTA
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:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:38995312 original size:32 final size:32
Alignment explanation
Indices: 38995271--38995334 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
38995261 GATCAAAGTA
38995271 GAATAGATCCTGAATCTGTTTATGGATTTATT
1 GAATAGATCCTGAATCTGTTTATGGATTTATT
38995303 GAATAGATCCTGAATCTGTTTATGGATTTATT
1 GAATAGATCCTGAATCTGTTTATGGATTTATT
38995335 CACTTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (32 bp):
GAATAGATCCTGAATCTGTTTATGGATTTATT
Found at i:38996110 original size:18 final size:18
Alignment explanation
Indices: 38996087--38996121 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38996077 GTTGGTTTTC
*
38996087 AAAAATAGAAACGGAAAT
1 AAAAATAAAAACGGAAAT
*
38996105 AAAAATAAAAATGGAAA
1 AAAAATAAAAACGGAAA
38996122 CTTGCAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAATAAAAACGGAAAT
Found at i:38996288 original size:26 final size:25
Alignment explanation
Indices: 38996259--38996331 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
38996249 AATTTTGTAG
38996259 AAATTTTATCAAGGGT-AAATTCGTCA
1 AAATTTTAT-AAGGGTAAAATT-GTCA
**
38996285 AAATTTTATGGGGGTAAAATTGTCA
1 AAATTTTATAAGGGTAAAATTGTCA
* *
38996310 AATTTTTAT-TGAGGTAAAATTG
1 AAATTTTATAAG-GGTAAAATTG
38996332 GGGTGAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 26 0.63
26 14 0.34
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (25 bp):
AAATTTTATAAGGGTAAAATTGTCA
Found at i:38996309 original size:25 final size:25
Alignment explanation
Indices: 38996271--38996331 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
38996261 ATTTTATCAA
38996271 GGGT-AAATTCGTCAAAATTTTATGG
1 GGGTAAAATT-GTCAAAATTTTATGG
* *
38996296 GGGTAAAATTGTCAAATTTTTATTG
1 GGGTAAAATTGTCAAAATTTTATGG
*
38996321 AGGTAAAATTG
1 GGGTAAAATTG
38996332 GGGTGAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (25 bp):
GGGTAAAATTGTCAAAATTTTATGG
Found at i:39003230 original size:64 final size:64
Alignment explanation
Indices: 39003162--39003301 Score: 217
Period size: 64 Copynumber: 2.2 Consensus size: 64
39003152 ATATACGTTG
*
39003162 CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATGTATATATATACTTATATTA
1 CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATATATATATATACTTATATTA
* ** * * *
39003226 CCGAAATGAATTGTATAGGTATGCACCTATTGCCGAATTGAATTATATATGTATACTTATATTG
1 CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATATATATATATACTTATATTA
39003290 CCGAATTGAATT
1 CCGAATTGAATT
39003302 TTATTTGTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (64 bp):
CCGAATTGAATTGTATAGGTACACACCTATTGCCGAATTGAAATATATATATATACTTATATTA
Found at i:39003311 original size:32 final size:32
Alignment explanation
Indices: 39003159--39003322 Score: 159
Period size: 32 Copynumber: 5.1 Consensus size: 32
39003149 CGAATATACG
* * ***
39003159 TTGCCGAATTGAATTGTATAGGTACACACCTA
1 TTGCCGAATTGAATTGTATATGTATACTTATA
* *
39003191 TTGCCGAATTGAAATGTATATATATACTTATA
1 TTGCCGAATTGAATTGTATATGTATACTTATA
* * * * ***
39003223 TTACCGAAATGAATTGTATAGGTATGCACCTA
1 TTGCCGAATTGAATTGTATATGTATACTTATA
*
39003255 TTGCCGAATTGAATTATATATGTATACTTATA
1 TTGCCGAATTGAATTGTATATGTATACTTATA
* *
39003287 TTGCCGAATTGAATTTTATTTGTATA-TATATA
1 TTGCCGAATTGAATTGTATATGTATACT-TATA
39003319 TTGC
1 TTGC
39003323 TGATTTGATT
Statistics
Matches: 105, Mismatches: 26, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
31 1 0.01
32 104 0.99
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (32 bp):
TTGCCGAATTGAATTGTATATGTATACTTATA
Found at i:39004366 original size:16 final size:17
Alignment explanation
Indices: 39004345--39004377 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39004335 TTGAGCAAGT
*
39004345 AAAATG-TGTTTGGTTA
1 AAAATGTTGTTTAGTTA
39004361 AAAATGTTGTTTAGTTA
1 AAAATGTTGTTTAGTTA
39004378 CGAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (17 bp):
AAAATGTTGTTTAGTTA
Found at i:39010354 original size:29 final size:30
Alignment explanation
Indices: 39010295--39010352 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39010285 TCCGAGCCTT
* *
39010295 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATATAATTATGAAAAAGTTTA
* *
39010325 GGGGCAAAATTATAATTTTGAAAAAGTT
1 GGGGCAAAAATATAATTATGAAAAAGTT
39010353 AGAGTCGAGG
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:0.43, C:0.05, G:0.22, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAATATAATTATGAAAAAGTTTA
Found at i:39010582 original size:13 final size:13
Alignment explanation
Indices: 39010564--39010595 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39010554 TTTCCAGCAA
39010564 TTATGAATTTATT
1 TTATGAATTTATT
39010577 TTATGAATTTATT
1 TTATGAATTTATT
*
39010590 TGATGA
1 TTATGA
39010596 TGATCCAAGC
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:39010801 original size:50 final size:50
Alignment explanation
Indices: 39010690--39010938 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
39010680 ATTTGGGTAA
* * *
39010690 AGAGATCCCATGTAAGACTATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC---A-A-GATG
* *
39010746 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
39010796 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** * * * *
39010846 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGAATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** *
39010896 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39010939 TGTTATGATC
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 97 0.56
51 34 0.20
52 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:39010888 original size:100 final size:103
Alignment explanation
Indices: 39010690--39010939 Score: 326
Period size: 100 Copynumber: 2.4 Consensus size: 103
39010680 ATTTGGGTAA
* *
39010690 AGAGATCCCATGTAAGACTATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA--ATGAGAGGTCCC
* ** *
39010755 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
63 ACGTAAGACCATGTCTGGGACATGGAATGGGCACCAAGATG
* * *
39010796 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAG-ATGAGAGGTCCCCCG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCACG
* *
39010858 TAAGACCATGTCTGGGACATGGAATGGGCACCGATATG
66 TAAGACCATGTCTGGGACATGGAATGGGCACCAAGATG
* *
39010896 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39010940 GTTATGATCA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 47 0.37
101 37 0.29
103 3 0.02
105 2 0.02
106 39 0.30
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCACG
TAAGACCATGTCTGGGACATGGAATGGGCACCAAGATG
Found at i:39014612 original size:40 final size:40
Alignment explanation
Indices: 39014551--39014683 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 40
39014541 CGAAAGTTGC
* *
39014551 GCCCAGCACTAGTCGGGTAAACCGACAAATATAATGGTGT
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* * **
39014591 GCCCAACACTAGTCAGATAAACTGACAAAGGT--T-GTG-
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* * *
39014627 G-CCAGCGCTAGTCGGGTAAACCGACAAATATAATGGTGT
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* *
39014666 GTCCAGCACTAGTTAGAT
1 GCCCAGCACTAGTCAGAT
39014684 GTACCAACGA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
35 23 0.32
36 1 0.01
37 4 0.06
38 4 0.06
39 1 0.01
40 38 0.54
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (40 bp):
GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
Found at i:39014612 original size:75 final size:73
Alignment explanation
Indices: 39014512--39014727 Score: 263
Period size: 75 Copynumber: 2.9 Consensus size: 73
39014502 GTATAAAAAA
*
39014512 GTGTGCCCAGCACTAGTCAGGTAAACTGACGAAAGTTGCGCCCAGCACTAGTCGGGTAAACCGAC
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGAAAGTTGCG-CCAGC-CTAGTCGGGTAAACCGAC
39014577 AAATATAATG
64 AAATATAATG
* *
39014587 GTGTGCCCAACACTAGTCAGATAAACTGAC-AAAGGTTGTGGCCAGCGCTAGTCGGGTAAACCGA
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGAAA-GTTG-CGCCAGC-CTAGTCGGGTAAACCGA
39014651 CAAATATAATG
63 CAAATATAATG
* * ** ** * * *
39014662 GTGTGTCCAGCACTAGTTAGATGTACCAACGATGAGTTGCGCCAGCGTAGTCGAGTAAACCGACA
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGA-AAGTTGCGCCAGCCTAGTCGGGTAAACCGACA
39014727 A
65 A
39014728 TATCGATTGC
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
74 21 0.17
75 94 0.77
76 6 0.05
77 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (73 bp):
GTGTGCCCAGCACTAGTCAGATAAACTGACGAAAGTTGCGCCAGCCTAGTCGGGTAAACCGACAA
ATATAATG
Found at i:39014647 original size:35 final size:34
Alignment explanation
Indices: 39014509--39014654 Score: 123
Period size: 35 Copynumber: 4.1 Consensus size: 34
39014499 CAGGTATAAA
*
39014509 AAAG-TGTGCCCAGCACTAGTCAGGTAAACTGAC
1 AAAGTTGTGCCCAGCACTAGTCAGGTAAACCGAC
* *
39014542 GAAAGTTGCGCCCAGCACTAGTCGGGTAAACCGAC
1 -AAAGTTGTGCCCAGCACTAGTCAGGTAAACCGAC
* * * *
39014577 AAATATAATGGTGTGCCCAACACTAGTCAGATAAACTGAC
1 ----A-AA-GTTGTGCCCAGCACTAGTCAGGTAAACCGAC
* * *
39014617 AAAGGTTGTGGCCAGCGCTAGTCGGGTAAACCGAC
1 AAA-GTTGTGCCCAGCACTAGTCAGGTAAACCGAC
39014652 AAA
1 AAA
39014655 TATAATGGTG
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
34 4 0.05
35 55 0.62
36 1 0.01
38 1 0.01
39 2 0.02
40 25 0.28
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (34 bp):
AAAGTTGTGCCCAGCACTAGTCAGGTAAACCGAC
Found at i:39015096 original size:35 final size:35
Alignment explanation
Indices: 39015050--39015131 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 35
39015040 CTGGCCCGGT
*
39015050 CCGAAATATGGGAGGGTTCAGATAAAAATACAGGC
1 CCGAAATATGGGAGGGTCCAGATAAAAATACAGGC
* *
39015085 CCGAAATATGGGAGGGTCCAGGTAAAAATATAGGC
1 CCGAAATATGGGAGGGTCCAGATAAAAATACAGGC
39015120 CCGAAATATGGG
1 CCGAAATATGGG
39015132 TTTGGGCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (35 bp):
CCGAAATATGGGAGGGTCCAGATAAAAATACAGGC
Found at i:39017872 original size:18 final size:18
Alignment explanation
Indices: 39017849--39017911 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
39017839 GAATATAATA
39017849 ATAATAATAATCATCATT
1 ATAATAATAATCATCATT
* *
39017867 ATAATAATAA-CATTAAT
1 ATAATAATAATCATCATT
* *
39017884 ATTAATAATCAT-ATCATG
1 A-TAATAATAATCATCATT
*
39017902 GTAATAATAA
1 ATAATAATAA
39017912 ATAAATGATG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (18 bp):
ATAATAATAATCATCATT
Found at i:39018163 original size:15 final size:15
Alignment explanation
Indices: 39018131--39018169 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
39018121 AGTAATACAT
39018131 AAATATAAATAGATAA
1 AAATA-AAATAGATAA
39018147 AAATAAAATA-ATAAA
1 AAATAAAATAGAT-AA
39018162 AAATAAAA
1 AAATAAAA
39018170 CAAATAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAATAGATAA
Found at i:39018285 original size:18 final size:18
Alignment explanation
Indices: 39018262--39018298 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39018252 ATAAGTAAAT
39018262 AAATAAATAAAAGAATTA
1 AAATAAATAAAAGAATTA
*
39018280 AAATAAATAAAAGACTTA
1 AAATAAATAAAAGAATTA
39018298 A
1 A
39018299 TCATAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAGAATTA
Found at i:39018647 original size:47 final size:48
Alignment explanation
Indices: 39018578--39018672 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 48
39018568 CTTCTTAAGA
* *
39018578 AAAAACACGTGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGTCGCG
1 AAAAACACGAGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGCCGCG
*
39018626 AAAAA-ACGAGGATCCCAGAAGTAGATCAGGTCGGGCCACCGGCCGCG
1 AAAAACACGAGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGCCGCG
39018673 GCAAAACAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 39 0.89
48 5 0.11
ACGTcount: A:0.32, C:0.27, G:0.31, T:0.11
Consensus pattern (48 bp):
AAAAACACGAGGATCCCAGAAGTAGATCAGGTCAGGCCACCGGCCGCG
Found at i:39021172 original size:18 final size:20
Alignment explanation
Indices: 39021135--39021184 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
39021125 TAAACTATAA
*
39021135 ATTTTGAAATTTTCATAAA-T
1 ATTTTG-AATTTTCAAAAATT
39021155 ATTTTGAATTTT-AAAAATT
1 ATTTTGAATTTTCAAAAATT
39021174 ATTTTG-ATTTT
1 ATTTTGAATTTT
39021185 TTTTCGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTCAAAAATT
Found at i:39025552 original size:23 final size:23
Alignment explanation
Indices: 39025493--39025557 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
39025483 TCTAGTAGTT
39025493 TTTTAAATTATTTTAAAAATTACAA
1 TTTTAAATT-TTTT-AAAATTACAA
* * *
39025518 ATTT-CATATTTTTAAAATTAGAA
1 TTTTAAAT-TTTTTAAAATTACAA
39025541 TTTTAAATTTTTTAAAA
1 TTTTAAATTTTTTAAAA
39025558 AGACTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 21 0.64
24 8 0.24
25 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTAAATTTTTTAAAATTACAA
Found at i:39027389 original size:2 final size:2
Alignment explanation
Indices: 39027382--39027409 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39027372 TTTAAAAAGT
39027382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39027410 CGGGAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39027452 original size:16 final size:16
Alignment explanation
Indices: 39027415--39027457 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
39027405 ATATACGGGA
*
39027415 AATTTT-AAATAAATT
1 AATTTTAAAATAAACT
*
39027430 AA-ATTAAAATAAACT
1 AATTTTAAAATAAACT
39027445 AATTTTAAAATAA
1 AATTTTAAAATAA
39027458 CATATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTTTAAAATAAACT
Found at i:39028241 original size:18 final size:18
Alignment explanation
Indices: 39028208--39028242 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39028198 AAAATGAATC
**
39028208 AAAACCAAAACCGAAAAG
1 AAAACCAAAAAAGAAAAG
39028226 AAAACCAAAAAAGAAAA
1 AAAACCAAAAAAGAAAA
39028243 AAAGGAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAACCAAAAAAGAAAAG
Found at i:39035214 original size:17 final size:17
Alignment explanation
Indices: 39035192--39035240 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
39035182 CCTGGGCAGT
*
39035192 AGAAGAAGAAGAGAATA
1 AGAAGAAGAAGAGAAGA
*
39035209 AGAAGAATAAGAGAAGA
1 AGAAGAAGAAGAGAAGA
39035226 A-ATAGAAGAAGAGAA
1 AGA-AGAAGAAGAGAA
39035241 AATGGAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAGA
Found at i:39036318 original size:21 final size:21
Alignment explanation
Indices: 39036292--39036334 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39036282 CAACGTGGCA
39036292 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
*
39036313 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACATCAGCT
39036334 A
1 A
39036335 TCCCATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:39038749 original size:22 final size:22
Alignment explanation
Indices: 39038724--39038794 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
39038714 TAACTAAACC
39038724 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
39038746 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
39038768 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
39038790 CTCAT
1 CTCAT
39038795 TAATAATAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:39039902 original size:50 final size:51
Alignment explanation
Indices: 39039816--39040009 Score: 153
Period size: 50 Copynumber: 3.8 Consensus size: 51
39039806 CGATTTCTTA
* *
39039816 TCGTAAGCCTCCCCCCATGCGTCTAGGAGTAGGGATATTATTAAACATCGT
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* * * ** *
39039867 TCGTAAGTCT-CCCTCATGCGTCTATGAGCAAGGATATTATTAAACCCCAT
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* * ** ** * * * **
39039917 TTGTAAG-CTTCCCTTATATGTCTAGGAACAGGGGTATTATTAAACCCCG-
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* *
39039966 TCTGTAAGCCTCCCTCCATGCGTCTGGGAGC-AGGATATTCATTA
1 TC-GTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATT-ATTA
39040010 CTCTCCACGA
Statistics
Matches: 111, Mismatches: 28, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
49 3 0.03
50 81 0.73
51 27 0.24
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (51 bp):
TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
Found at i:39040152 original size:58 final size:58
Alignment explanation
Indices: 39040089--39040221 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 58
39040079 GAGCTCTTGG
* * * * *
39040089 CGGAGGTGAGACATATCTTCTATATTTGGGACCCTCCAG-GAACCCTTTGGGCTCTCAA
1 CGGAGGTGAGGCATATCTTCTACATTCGAGACCCTCC-GTGAACCCTTTAGGCTCTCAA
* * *
39040147 CGGAGGTGAGGCGTATCTTCTACATTCGAGCCCCTCCGTGAACCCTTTAGGCTTTCAA
1 CGGAGGTGAGGCATATCTTCTACATTCGAGACCCTCCGTGAACCCTTTAGGCTCTCAA
*
39040205 TGGAGGTGAGGCATATC
1 CGGAGGTGAGGCATATC
39040222 ATCTTCATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 1 0.02
58 63 0.98
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (58 bp):
CGGAGGTGAGGCATATCTTCTACATTCGAGACCCTCCGTGAACCCTTTAGGCTCTCAA
Found at i:39042858 original size:24 final size:25
Alignment explanation
Indices: 39042831--39042879 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
39042821 TAACAGGTAA
*
39042831 CTCCGAAGAGCTAT-TATCAGGAAG
1 CTCCGAAGAGCCATATATCAGGAAG
* *
39042855 CTCCGGATAGCCATATATCAGGAAG
1 CTCCGAAGAGCCATATATCAGGAAG
39042880 TTCAAGTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
CTCCGAAGAGCCATATATCAGGAAG
Found at i:39051383 original size:16 final size:16
Alignment explanation
Indices: 39051362--39051403 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
39051352 TCAATATCCA
39051362 ATTATCATATTCACAC
1 ATTATCATATTCACAC
* *
39051378 ATTATCACATTTACAC
1 ATTATCATATTCACAC
39051394 A-TAT-ATATTC
1 ATTATCATATTC
39051404 TTTTCAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.18
15 3 0.14
16 15 0.68
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATCATATTCACAC
Found at i:39057078 original size:19 final size:19
Alignment explanation
Indices: 39057054--39057166 Score: 181
Period size: 19 Copynumber: 5.8 Consensus size: 19
39057044 AATTTTTGAG
39057054 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
39057073 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
39057092 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
39057113 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
39057132 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
39057151 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
39057167 ATATATGATT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 68 0.79
21 18 0.21
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:39057107 original size:40 final size:40
Alignment explanation
Indices: 39057055--39057166 Score: 201
Period size: 40 Copynumber: 2.9 Consensus size: 40
39057045 ATTTTTGAGG
*
39057055 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
39057095 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
39057135 ATAT--AATCTTAGATATGATATGCAATCTTAGA
1 ATATGCAATCTTAGATATGATATGCAATCTTAGA
39057167 ATATATGATT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
38 28 0.39
40 43 0.61
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
Found at i:39057126 original size:59 final size:56
Alignment explanation
Indices: 39057054--39057173 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 56
39057044 AATTTTTGAG
*
39057054 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATACAATCCTAGATATG--ATATGCAATCTTAGA-AT
* *
39057113 GATATGCAATCTTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAAT
1 GATATGCAATCTTAGATATGATATACAATCCTAGATATGATATGCAATCTTAGAAT
39057169 -ATATG
1 GATATG
39057174 ATTTTGTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.03
57 15 0.26
59 36 0.62
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (56 bp):
GATATGCAATCTTAGATATGATATACAATCCTAGATATGATATGCAATCTTAGAAT
Found at i:39057989 original size:25 final size:26
Alignment explanation
Indices: 39057938--39057991 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39057928 AACATGATAT
*
39057938 TTTTTTTTAACGAATATTTTCCTATA
1 TTTTTTTAAACGAATATTTTCCTATA
* *
39057964 TTTTTTTAAAGGAATATTTTTC-ATA
1 TTTTTTTAAACGAATATTTTCCTATA
39057989 TTT
1 TTT
39057992 ATTATGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (26 bp):
TTTTTTTAAACGAATATTTTCCTATA
Found at i:39058839 original size:98 final size:98
Alignment explanation
Indices: 39058670--39058866 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
39058660 NNNNNNNTAA
* *
39058670 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
39058735 TTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
*
39058768 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
39058833 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
39058866 T
1 T
39058867 TTTATTGTAC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGAATGTTCTTTTAAAG
Found at i:39060054 original size:24 final size:24
Alignment explanation
Indices: 39060027--39060072 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39060017 AGAACAATCC
* *
39060027 CAAAAGGAAATGCACGAGCAGCTT
1 CAAAAGCAAATGAACGAGCAGCTT
*
39060051 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAACGAGCAGC
39060073 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAACGAGCAGCTT
Found at i:39063704 original size:133 final size:133
Alignment explanation
Indices: 39063466--39064144 Score: 909
Period size: 133 Copynumber: 5.1 Consensus size: 133
39063456 GTAGAGCAGG
39063466 TTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
1 TTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
*
39063531 CTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAATGGAAT
66 CTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
39063596 AGA
131 AGA
* *
39063599 TTAAAGATAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCAGATTTTAC
1 TTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
* *
39063664 CTCCCTGTCGTTATAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAAT
66 CTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
39063729 AGA
131 AGA
* *
39063732 TTAAAGATAGCAGATCTTGGCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGTGGATTTTAC
1 TTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
*
39063797 CTCCCTGTGGTTATAGTGAAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
66 CTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
39063862 AGA
131 AGA
* ** ** * * *
39063865 TTGAAGATTTCAGATCTTATCTCCCTAAGCATT---AGTGGAGCAGATCGAAGATGGCGGATTTT
1 TTAAAGATAGCAGATCTTGCCTTCCT--GCATTGACAGCGAAGCAGATCGAAGATGGCGGATTTT
* * *
39063927 ACCTCCCTATGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGGCAACAGTGGA
64 ACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
39063992 ATAGA
129 ATAGA
* ** ** * * ** *
39063997 TTGAAGATTTCAGATCTTATCTCCCTAAAGCAGT-AGTG-GGAGCAGATCGAAGATGGCGGATTT
1 TTAAAGATAGCAGATCTTGCCTTCCT---GCATTGACAGCGAAGCAGATCGAAGATGGCGGA-TT
* * * ** *
39064060 TTACCTCCCCTGGGGTTATAGTGGAGTACATTGAAAGCCAATAATTCTATTTCCCTAAGCAACAG
62 TTACCT-CCCTGTGGTTATAGTGGAGTACATTG-AAGCCAGTAATTCTACTTCCCTGGGCAGCAG
39064125 TGGAAATAAGA
125 TGG-AAT-AGA
39064136 TTGAAAGAT
1 TT-AAAGAT
39064145 TTTCAGATCT
Statistics
Matches: 500, Mismatches: 35, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
132 118 0.24
133 280 0.56
134 22 0.04
135 14 0.03
136 24 0.05
137 29 0.06
138 3 0.01
139 5 0.01
140 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (133 bp):
TTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATGGCGGATTTTAC
CTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
AGA
Found at i:39065606 original size:98 final size:98
Alignment explanation
Indices: 39065466--39065662 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
39065456 TAAAAAATAA
* *
39065466 TAAAGGAAATATTCCAAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
39065531 TTAAATCTTGGATAAGTGGATTTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* * *
39065564 TAAATGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
39065629 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
39065662 T
1 T
39065663 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:39066628 original size:17 final size:18
Alignment explanation
Indices: 39066539--39066628 Score: 53
Period size: 17 Copynumber: 4.9 Consensus size: 18
39066529 TACTAATTAC
*
39066539 AAATATTTAAATATTTAA-
1 AAATATTTATA-ATTTAAT
39066557 AATATAGTTTATATATTTTAATT
1 AA-ATA-TTTATA-A-TTTAA-T
*
39066580 AAAT-TTTATAA-ATAAT
1 AAATATTTATAATTTAAT
* **
39066596 TAATATTTATTGTTTAA-
1 AAATATTTATAATTTAAT
39066613 AAATATTTATAATTTA
1 AAATATTTATAATTTA
39066629 TATTTTATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.07
17 21 0.38
18 5 0.09
19 4 0.07
20 13 0.23
21 5 0.09
22 2 0.04
23 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AAATATTTATAATTTAAT
Found at i:39066635 original size:24 final size:24
Alignment explanation
Indices: 39066569--39066635 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
39066559 TATAGTTTAT
* *
39066569 ATATTT-TAA-TTAAATTTTATAA
1 ATATTTATAATTTATATTTTAAAA
*
39066591 ATAATTA-ATATTTAT-TGTTTAAAA
1 ATATTTATA-ATTTATAT-TTTAAAA
39066615 ATATTTATAATTTATATTTTA
1 ATATTTATAATTTATATTTTA
39066636 TATATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
22 6 0.17
23 2 0.06
24 25 0.71
25 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
ATATTTATAATTTATATTTTAAAA
Found at i:39071365 original size:18 final size:18
Alignment explanation
Indices: 39071334--39071392 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
39071324 GCAGAGTACA
39071334 GATGAAGA-GAATGAAGGT
1 GATGAAGATG-ATGAAGGT
*
39071352 GATGAAGATGATGATGATGAT
1 GATGAAGATGATGA--A-GGT
39071373 GATGACA-ATGATGAAGGT
1 GATGA-AGATGATGAAGGT
39071391 GA
1 GA
39071393 AGATGACAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 16 0.47
19 2 0.06
20 1 0.03
21 14 0.41
22 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.36, T:0.22
Consensus pattern (18 bp):
GATGAAGATGATGAAGGT
Found at i:39073888 original size:218 final size:217
Alignment explanation
Indices: 39073510--39073943 Score: 841
Period size: 218 Copynumber: 2.0 Consensus size: 217
39073500 AATATTGTGC
39073510 TATTGTACTGTTGAATAATAGTCTTTCTCCTGTCTATATGTTGCACTGTTTTCTAGTTTTTATCT
1 TATTGTACTGTTGAATAATAGTCTTTCTCCTGTCTATATGTTGCACTGTTTTCTAGTTTTTATCT
39073575 ACCCATGGTTGCCCCCTTTTTCGCTTTAAGGATTGGAAGATATTTTTACTTAATCTATAGTTCTA
66 ACCCATGGTTGCCCCCTTTTTCGCTTTAAGGATTGGAAGATATTTTTACTTAATCTATAGTTCTA
39073640 GCGTCATGTAGGAAAAATCTTATATATCATCTCTCATGTTAATTTGTGGCTTCTTCCACTAGTTT
131 GCGTCATGTAGGAAAAATCTTATATATCATCTCTCATGTTAATTTGTGGCTTCTTCCACTAGTTT
39073705 AGTTGAACCTCTGTCTCTCATGT
196 AGTTGAACCTCTGTCT-TCATGT
*
39073728 TATTGTACTGTTGAATAATAGTCTTTCTCCTGTCTATATGTTGCGCTGTTTTCTAGTTTTTATCT
1 TATTGTACTGTTGAATAATAGTCTTTCTCCTGTCTATATGTTGCACTGTTTTCTAGTTTTTATCT
*
39073793 ACCCATGGTTGCCCCCTTTTTCGCTTTAAGGATTGGAAGATATTTTTACTTAATCTATTGTTCTA
66 ACCCATGGTTGCCCCCTTTTTCGCTTTAAGGATTGGAAGATATTTTTACTTAATCTATAGTTCTA
39073858 GCGTCATGTAGGAAAAATCTTATATATCATCTCTCATGTTAATTTGTGGCTTCTTCCACTAGTTT
131 GCGTCATGTAGGAAAAATCTTATATATCATCTCTCATGTTAATTTGTGGCTTCTTCCACTAGTTT
39073923 AGTTGAACCTCTGTCTTCATG
196 AGTTGAACCTCTGTCTTCATG
39073944 AATTTTAAAT
Statistics
Matches: 214, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
217 5 0.02
218 209 0.98
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (217 bp):
TATTGTACTGTTGAATAATAGTCTTTCTCCTGTCTATATGTTGCACTGTTTTCTAGTTTTTATCT
ACCCATGGTTGCCCCCTTTTTCGCTTTAAGGATTGGAAGATATTTTTACTTAATCTATAGTTCTA
GCGTCATGTAGGAAAAATCTTATATATCATCTCTCATGTTAATTTGTGGCTTCTTCCACTAGTTT
AGTTGAACCTCTGTCTTCATGT
Found at i:39078354 original size:31 final size:31
Alignment explanation
Indices: 39078280--39078355 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
39078270 GGTATTGTCG
* *
39078280 TTAAAAACTATTTTCATTTGAGGCAATACCA
1 TTAAAAACTGTTTTCATTTCAGGCAATACCA
** * * **
39078311 TTAAAATTTGTTTTCATTTCAGGTAGTTTCA
1 TTAAAAACTGTTTTCATTTCAGGCAATACCA
39078342 TTAAAAACTGTTTT
1 TTAAAAACTGTTTT
39078356 TGTAATAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (31 bp):
TTAAAAACTGTTTTCATTTCAGGCAATACCA
Found at i:39080975 original size:14 final size:14
Alignment explanation
Indices: 39080956--39080983 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39080946 TAGTAAATTA
39080956 TTAAAAATATATAT
1 TTAAAAATATATAT
39080970 TTAAAAATATATAT
1 TTAAAAATATATAT
39080984 CATTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:39089175 original size:2 final size:2
Alignment explanation
Indices: 39089112--39089161 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
39089102 CAAGAGGTCA
39089112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39089154 AT AT AT AT
1 AT AT AT AT
39089162 GCGCATTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39098466 original size:16 final size:16
Alignment explanation
Indices: 39098417--39098469 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
39098407 TTGGTTGGCT
*
39098417 GTAATGGAATAGATGT
1 GTAATGGAATAGATGC
39098433 GTAATGGAATAGATGC
1 GTAATGGAATAGATGC
*
39098449 GTAATGGAATAGAGGC
1 GTAATGGAATAGATGC
39098465 GTAAT
1 GTAAT
39098470 AGGTAATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGATGC
Found at i:39098504 original size:45 final size:44
Alignment explanation
Indices: 39098449--39098536 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
39098439 GAATAGATGC
* *
39098449 GTAATGGAATAGAGGCGTAATAGGTAATCTTTTGTTTGATTGAAT
1 GTAATGGAATAGAGGCATAAT-GGTAATCTTGTGTTTGATTGAAT
* * *
39098494 GTAATTGAATAGAGGCATAATGGTATTCTTGTGTTTGGTTGAA
1 GTAATGGAATAGAGGCATAATGGTAATCTTGTGTTTGATTGAA
39098537 AGGAATAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 19 0.50
45 19 0.50
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.39
Consensus pattern (44 bp):
GTAATGGAATAGAGGCATAATGGTAATCTTGTGTTTGATTGAAT
Found at i:39098685 original size:18 final size:18
Alignment explanation
Indices: 39098656--39098716 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
39098646 GCTTATTAAT
39098656 ATAAATAATATATAATTTA
1 ATAAA-AATATATAATTTA
*
39098675 ATAAAAATATATAAGTTA
1 ATAAAAATATATAATTTA
39098693 AT-AAAATATATGAATTTA
1 ATAAAAATATAT-AATTTA
*
39098711 CTAAAA
1 ATAAAA
39098717 TCATAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 9 0.24
18 20 0.54
19 8 0.22
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAATATATAATTTA
Found at i:39102179 original size:51 final size:52
Alignment explanation
Indices: 39102101--39102201 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 52
39102091 AATTTATCAC
* *
39102101 ATTAAAAAATTTATTTTTTCTTATTTT-GGAATACTGATGGCCGACACCAAGT
1 ATTAAAAAATTTATGTTTTCTTATTTTGGGAAT-CAGATGGCCGACACCAAGT
*
39102153 ATTAAAAAA-TTA-GTTTTCTTAATTTTGGGAATCAGATGGCTGACACCAA
1 ATTAAAAAATTTATGTTTTCTT-ATTTTGGGAATCAGATGGCCGACACCAA
39102202 ACCCTGTGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
50 7 0.16
51 23 0.52
52 14 0.32
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (52 bp):
ATTAAAAAATTTATGTTTTCTTATTTTGGGAATCAGATGGCCGACACCAAGT
Found at i:39102561 original size:14 final size:14
Alignment explanation
Indices: 39102542--39102573 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39102532 TAATTTCTAT
39102542 ATTTTCGTGTATTA
1 ATTTTCGTGTATTA
39102556 ATTTTCGTGTATTA
1 ATTTTCGTGTATTA
39102570 ATTT
1 ATTT
39102574 AGTATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (14 bp):
ATTTTCGTGTATTA
Found at i:39102799 original size:90 final size:90
Alignment explanation
Indices: 39102686--39103011 Score: 492
Period size: 90 Copynumber: 3.6 Consensus size: 90
39102676 TTGTATCTGC
*
39102686 AAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
39102751 TCTGTTTGTAGTTTGTTGGGTGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
** * * * * * *
39102776 AAATTTAATTTAGTATGTGTTATATATAGTTTGAATTTAAAATTTTCGTGCACTAATGTTATCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
* *
39102841 TCAGTTTGTAGTTTGTTGGATGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
*
39102866 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCATGTATTAATTTTACCCA
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
39102931 TCTGTTTGTAGTTTGTTGGGTGTTT
66 TCTGTTTGTAGTTTGTTGGGTGTTT
* * * * *
39102956 AAATTTAATTTAGTGCGTATTATAT-TTGTTTGAATTTTATATTTTTGTGTATTAAT
1 AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAT
39103012 ATTCTAGAAT
Statistics
Matches: 210, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
89 26 0.12
90 184 0.88
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (90 bp):
AAATTTAATTTAGTCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCCA
TCTGTTTGTAGTTTGTTGGGTGTTT
Found at i:39106102 original size:25 final size:25
Alignment explanation
Indices: 39106023--39106102 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
39106013 TCTTTCGAGC
* *
39106023 CATATAACGGGAAGCTCATATGAGT
1 CATATAACGGGAAGCTTATAAGAGT
* * * ** *
39106048 CATGTAAAGGGAAACTTATCCG-GG
1 CATATAACGGGAAGCTTATAAGAGT
39106072 CGATATAACGGGAAGCTTATAAGAGT
1 C-ATATAACGGGAAGCTTATAAGAGT
39106098 CATAT
1 CATAT
39106103 TCAAAAAACT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.90
26 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (25 bp):
CATATAACGGGAAGCTTATAAGAGT
Found at i:39106185 original size:25 final size:25
Alignment explanation
Indices: 39106157--39106207 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
39106147 ATTAATCAGA
*
39106157 AAGCTCCAGATAGCCATATATCGGG
1 AAGCTCCAGAGAGCCATATATCGGG
* *
39106182 AAGCTCCGGAGAGCTATATATCGGG
1 AAGCTCCAGAGAGCCATATATCGGG
39106207 A
1 A
39106208 CACTCATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (25 bp):
AAGCTCCAGAGAGCCATATATCGGG
Found at i:39106308 original size:25 final size:25
Alignment explanation
Indices: 39106280--39106339 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
39106270 AAAGAGCTAT
39106280 TAACGGGAAGAT-TGCAAGAACCATA
1 TAACGGGAAGATCT-CAAGAACCATA
* * *
39106305 TAACAGGAAGCTCTTAAGAACCATA
1 TAACGGGAAGATCTCAAGAACCATA
*
39106330 TACCGGGAAG
1 TAACGGGAAG
39106340 CTCGAGAGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (25 bp):
TAACGGGAAGATCTCAAGAACCATA
Found at i:39106340 original size:25 final size:25
Alignment explanation
Indices: 39106295--39106342 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39106285 GGAAGATTGC
39106295 AAGAACCATATAACAGGAAGCTCTT
1 AAGAACCATATAACAGGAAGCTCTT
* *
39106320 AAGAACCATATACCGGGAAGCTC
1 AAGAACCATATAACAGGAAGCTC
39106343 GAGAGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (25 bp):
AAGAACCATATAACAGGAAGCTCTT
Found at i:39108634 original size:5 final size:5
Alignment explanation
Indices: 39108626--39108680 Score: 65
Period size: 5 Copynumber: 10.0 Consensus size: 5
39108616 AACTTTTTTT
39108626 TTTCA TTTCA TTTCTA CTTTCA TTTCCA TTTCA TTTCA TTTACA TTTTCA
1 TTTCA TTTCA TTTC-A -TTTCA TTT-CA TTTCA TTTCA TTT-CA -TTTCA
39108676 TTTCA
1 TTTCA
39108681 CTTAAATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 27 0.60
6 11 0.24
7 7 0.16
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.58
Consensus pattern (5 bp):
TTTCA
Found at i:39108648 original size:12 final size:11
Alignment explanation
Indices: 39108629--39108680 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
39108619 TTTTTTTTTT
39108629 CATTTCATTTC
1 CATTTCATTTC
*
39108640 TACTTTCATTTC
1 CA-TTTCATTTC
39108652 CATTTCATTT-
1 CATTTCATTTC
*
39108662 CATTTACATTTT
1 CATTT-CATTTC
39108674 CATTTCA
1 CATTTCA
39108681 CTTAAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 16 0.44
12 15 0.42
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (11 bp):
CATTTCATTTC
Found at i:39108659 original size:28 final size:28
Alignment explanation
Indices: 39108626--39108679 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
39108616 AACTTTTTTT
39108626 TTTCATTTCATTT-CTACTTTCATTTCCA
1 TTTCATTTCATTTAC-ACTTTCATTTCCA
*
39108654 TTTCATTTCATTTACATTTTCATTTC
1 TTTCATTTCATTTACACTTTCATTTC
39108680 ACTTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTCATTTCATTTACACTTTCATTTCCA
Found at i:39108713 original size:21 final size:20
Alignment explanation
Indices: 39108682--39108734 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
39108672 TTCATTTCAC
39108682 TTAAA-TTATTTTTT-TCCAT
1 TTAAATTTATTTTTTCT-CAT
39108701 TTAAATTTAATTTTTTCTCAT
1 TTAAATTT-ATTTTTTCTCAT
*
39108722 TTCAATTT-TTTTT
1 TTAAATTTATTTTT
39108735 CATTTCAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.33
20 2 0.07
21 17 0.57
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAAATTTATTTTTTCTCAT
Found at i:39108716 original size:20 final size:21
Alignment explanation
Indices: 39108682--39108729 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
39108672 TTCATTTCAC
*
39108682 TTAAA-TTATTTTTTTC-CAT
1 TTAAATTTAATTTTTTCTCAT
39108701 TTAAATTTAATTTTTTCTCAT
1 TTAAATTTAATTTTTTCTCAT
*
39108722 TTCAATTT
1 TTAAATTT
39108730 TTTTTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 10 0.40
21 10 0.40
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAAATTTAATTTTTTCTCAT
Found at i:39108730 original size:16 final size:16
Alignment explanation
Indices: 39108705--39108763 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
39108695 TTCCATTTAA
*
39108705 ATTT-AATTTTTTCTC
1 ATTTCAATTTTTTTTC
39108720 ATTTCAATTTTTTTTC
1 ATTTCAATTTTTTTTC
*
39108736 ATTTCAGTTTTTTTTTTC
1 ATTTCA--ATTTTTTTTC
39108754 ATTTCAATTT
1 ATTTCAATTT
39108764 GTAATTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 4 0.11
16 19 0.50
18 15 0.39
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTTCAATTTTTTTTC
Found at i:39108730 original size:57 final size:57
Alignment explanation
Indices: 39108659--39108791 Score: 130
Period size: 57 Copynumber: 2.3 Consensus size: 57
39108649 TTCCATTTCA
39108659 TTTCATTTACATTTTCATTTCACTTAAATTATTTTTTTCCATTT-AAATT-TAATTT-T
1 TTTCATTTA-ATTTTCATTTCACTTAAATT-TTTTTTTCCATTTCAAATTGTAATTTAT
* * * * * *
39108715 TTCTCATTTCAATTTT-TTTTCATTTCAGTTTTTTTTTTCATTTCAATTTGTAATTTAT
1 TT-TCATTT-AATTTTCATTTCACTTAAATTTTTTTTTCCATTTCAAATTGTAATTTAT
*
39108773 TTTCATTTAAACTTTCATT
1 TTTCATTT-AATTTTCATT
39108792 CCATTTCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
55 12 0.19
56 16 0.26
57 28 0.45
58 6 0.10
ACGTcount: A:0.23, C:0.13, G:0.02, T:0.62
Consensus pattern (57 bp):
TTTCATTTAATTTTCATTTCACTTAAATTTTTTTTTCCATTTCAAATTGTAATTTAT
Found at i:39108732 original size:18 final size:17
Alignment explanation
Indices: 39108620--39108763 Score: 80
Period size: 17 Copynumber: 8.2 Consensus size: 17
39108610 CCTTTCAACT
39108620 TTTTTTTTTCATTTC-A
1 TTTTTTTTTCATTTCAA
** *
39108636 TTTCTACTTTCATTTCCA
1 TTT-TTTTTTCATTTCAA
**
39108654 -TTTCATTTCATTT-ACA
1 TTTTTTTTTCATTTCA-A
** * *
39108670 TTTTCATTTCACTTAAA
1 TTTTTTTTTCATTTCAA
*
39108687 TTATTTTTTTCCATTTAAA
1 TT-TTTTTTT-CATTTCAA
39108706 TTTAATTTTTTCTCATTTCAA
1 -TT--TTTTTT-TCATTTCAA
*
39108727 -TTTTTTTTCATTTCAGT
1 TTTTTTTTTCATTTCA-A
39108744 TTTTTTTTTCATTTCAA
1 TTTTTTTTTCATTTCAA
39108761 TTT
1 TTT
39108764 GTAATTTATT
Statistics
Matches: 104, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
16 21 0.20
17 36 0.35
18 22 0.21
19 8 0.08
20 2 0.02
21 14 0.13
22 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTTTTTTCATTTCAA
Found at i:39109046 original size:21 final size:21
Alignment explanation
Indices: 39109004--39109046 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
39108994 TGTCAGGGTC
*
39109004 ATTTAAAATTTTTCATATTTT
1 ATTTAAAATTTTTCATAATTT
*
39109025 ATTTAAATTTTTTC-TCAATTT
1 ATTTAAAATTTTTCAT-AATTT
39109046 A
1 A
39109047 AAAATCATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAAATTTTTCATAATTT
Found at i:39109292 original size:27 final size:27
Alignment explanation
Indices: 39109232--39109434 Score: 129
Period size: 27 Copynumber: 8.0 Consensus size: 27
39109222 CCTTTCTTTC
*
39109232 TTTTTTTCATTTAATTT-AATT-TCATT
1 TTTTTTTCATTTCATTTAAATTATC-TT
**
39109258 TCCATTTTCATTTCATTTAAATTATC--
1 T-TTTTTTCATTTCATTTAAATTATCTT
*
39109284 TTTTTTT--TTTCATTTAAATTTAAC-T
1 TTTTTTTCATTTCATTTAAA-TTATCTT
* **
39109309 TTTTTCTCATTTTGTTTAAATTATC--
1 TTTTTTTCATTTCATTTAAATTATCTT
*
39109334 TTTTTTTC----CATTTAAATT-TAATT
1 TTTTTTTCATTTCATTTAAATTAT-CTT
*
39109357 TTTTTCTCATTTCATTTAAATTATCTT
1 TTTTTTTCATTTCATTTAAATTATCTT
*
39109384 TTTTTTTCATTT-A---AATTTAAT-TT
1 TTTTTTTCATTTCATTTAAATT-ATCTT
*
39109407 TTTTTCTCATTTCATTTAAATTATCTT
1 TTTTTTTCATTTCATTTAAATTATCTT
39109434 T
1 T
39109435 CTTTCCATTT
Statistics
Matches: 136, Mismatches: 20, Indels: 41
0.69 0.10 0.21
Matches are distributed among these distances:
20 1 0.01
21 8 0.06
23 35 0.26
24 7 0.05
25 17 0.12
26 9 0.07
27 52 0.38
28 5 0.04
29 2 0.01
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTTTCATTTCATTTAAATTATCTT
Found at i:39109346 original size:48 final size:49
Alignment explanation
Indices: 39109265--39109461 Score: 281
Period size: 49 Copynumber: 4.0 Consensus size: 49
39109255 ATTTCCATTT
* *
39109265 TCATTTCATTTAAATTATCTTTTTTTTTTCATTTAAATTTAACTTTTTTC
1 TCATTTCATTTAAATTATC-TTTTTTTTCCATTTAAATTTAATTTTTTTC
**
39109315 TCATTTTGTTTAAATTATC-TTTTTTTCCATTTAAATTTAATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTTCCATTTAAATTTAATTTTTTTC
*
39109363 TCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAATTTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTTCCATTTAAATTTAA-TTTTTTTC
* * *
39109413 TCATTTCATTTAAATTATC-TTTCTTTCCATTTTAATTTATGTTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTTCCATTTAAATTTA-ATTTTTTTC
39109462 ATATTAATTT
Statistics
Matches: 133, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
48 44 0.33
49 45 0.34
50 44 0.33
ACGTcount: A:0.23, C:0.12, G:0.01, T:0.64
Consensus pattern (49 bp):
TCATTTCATTTAAATTATCTTTTTTTTCCATTTAAATTTAATTTTTTTC
Found at i:39109377 original size:98 final size:99
Alignment explanation
Indices: 39109265--39109461 Score: 317
Period size: 98 Copynumber: 2.0 Consensus size: 99
39109255 ATTTCCATTT
**
39109265 TCATTTCATTTAAATTATCTTTTTTTTTTCATTTAAATTTAA-CTTTTTTCTCATTTTGTTTAAA
1 TCATTTCATTTAAATTATC-TTTTTTTTTCATTTAAATTTAATCTTTTTTCTCATTTCATTTAAA
*
39109329 TTATCTTTTTTTCCATTTAAATTTA-ATTTTTTTC
65 TTATCTTTCTTTCCATTTAAATTTATATTTTTTTC
*
39109363 TCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAATTTTTTTTCTCATTTCATTTAAAT
1 TCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAATCTTTTTTCTCATTTCATTTAAAT
* *
39109428 TATCTTTCTTTCCATTTTAATTTATGTTTTTTTC
66 TATCTTTCTTTCCATTTAAATTTATATTTTTTTC
39109462 ATATTAATTT
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 22 0.24
98 61 0.67
99 8 0.09
ACGTcount: A:0.23, C:0.12, G:0.01, T:0.64
Consensus pattern (99 bp):
TCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAATCTTTTTTCTCATTTCATTTAAAT
TATCTTTCTTTCCATTTAAATTTATATTTTTTTC
Found at i:39109468 original size:21 final size:21
Alignment explanation
Indices: 39109349--39109471 Score: 63
Period size: 21 Copynumber: 5.4 Consensus size: 21
39109339 TTCCATTTAA
39109349 ATTTAATTT-T-TTTCTCATTTC
1 ATTTAATTTATCTTTCT--TTTC
* *
39109370 ATTTAAATTATCTTTTTTTTTC
1 ATTTAATTTATC-TTTCTTTTC
*
39109392 ATTTAAATTTAATTTTTTTTCTCATTTC
1 ATTT-AATTT-A---TCTTTCT--TTTC
* *
39109420 ATTTAAATTATCTTTCTTTCC
1 ATTTAATTTATCTTTCTTTTC
*
39109441 ATTTTAATTTATGTTT-TTTTC
1 A-TTTAATTTATCTTTCTTTTC
39109462 ATATTAATTT
1 AT-TTAATTT
39109472 TTCTCTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
20 1 0.01
21 24 0.30
22 21 0.27
23 10 0.13
24 5 0.06
26 5 0.06
27 5 0.06
28 8 0.10
ACGTcount: A:0.24, C:0.11, G:0.01, T:0.65
Consensus pattern (21 bp):
ATTTAATTTATCTTTCTTTTC
Found at i:39109733 original size:44 final size:44
Alignment explanation
Indices: 39109494--39109730 Score: 339
Period size: 44 Copynumber: 5.4 Consensus size: 44
39109484 AATTTATTTC
** * * *
39109494 ATTTAATGTGTTTTAAGTTAAATATGTAAGTCTGTTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
*
39109538 ATTTAACGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
*
39109582 GTTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* * *
39109626 GTTTAATGTGTTCTAAAATAAATATGTATGTATATTGTATTTTA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* * *
39109670 ATTTAATGTGCTTTAAATTAAATATGCATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* *
39109714 ATTTAACGTATTTTAAA
1 ATTTAATGTGTTTTAAA
39109731 TTAGGAACAA
Statistics
Matches: 174, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 174 1.00
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (44 bp):
ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
Found at i:39113590 original size:46 final size:44
Alignment explanation
Indices: 39113539--39113686 Score: 128
Period size: 45 Copynumber: 3.3 Consensus size: 44
39113529 TTTTGACATA
*
39113539 TAGTATTATTTAATATTTAAGCT-TAAC-ATTGTTTTAAATTTATCAT
1 TAGTATTATTTAATATTTAA--TAT-ACTATTATTTTAAA-TTATCAT
*
39113585 TAGTATTATTTTAATATTTAATATACTATTATTTTAAATTATTAT
1 TAGTATTA-TTTAATATTTAATATACTATTATTTTAAATTATCAT
* *
39113630 TAATATTATTTAA-ATTTATCATATA-TCAATATTTT-AATT-TCAT
1 TAGTATTATTTAATATTTA--ATATACT-ATTATTTTAAATTATCAT
*
39113673 TATGTACTATTTAA
1 TA-GTATTATTTAA
39113687 AAAAAAACTT
Statistics
Matches: 88, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
43 10 0.11
44 19 0.22
45 28 0.32
46 19 0.22
47 12 0.14
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (44 bp):
TAGTATTATTTAATATTTAATATACTATTATTTTAAATTATCAT
Found at i:39113648 original size:22 final size:23
Alignment explanation
Indices: 39113561--39113648 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
39113551 ATATTTAAGC
* * *
39113561 TTAACATTGTTTTAAATTTATCA
1 TTAATATTATTTTAAATTTATTA
* *
39113584 TTAGTATTATTTTAATATTTAATA
1 TTAATATTATTTTAA-ATTTATTA
*
39113608 -TACTATTATTTTAAA-TTATTA
1 TTAATATTATTTTAAATTTATTA
39113629 TTAATATTA-TTTAAATTTAT
1 TTAATATTATTTTAAATTTAT
39113649 CATATATCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 11 0.20
22 12 0.22
23 25 0.46
24 6 0.11
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATTATTTTAAATTTATTA
Found at i:39121108 original size:19 final size:20
Alignment explanation
Indices: 39121063--39121115 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
39121053 CATATACGAA
*
39121063 ATATAAATTTTAATTTAAAT
1 ATATAAATTATAATTTAAAT
* *
39121083 ATATAAATTATATTTTAAGT
1 ATATAAATTATAATTTAAAT
*
39121103 AT-TAAAATATAAT
1 ATATAAATTATAAT
39121116 AATTACAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATAAATTATAATTTAAAT
Found at i:39121550 original size:31 final size:32
Alignment explanation
Indices: 39121512--39121578 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
39121502 CTTTAAATCC
39121512 ATACATTTGAATCAAAATCAAAATTT-TATGT
1 ATACATTTGAATCAAAATCAAAATTTATATGT
*
39121543 ATACATTTGAATTAAAATCAAAATTTAATATGT
1 ATACATTTGAATCAAAATCAAAATTT-ATATGT
39121576 ATA
1 ATA
39121579 ATTGCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 25 0.76
33 8 0.24
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (32 bp):
ATACATTTGAATCAAAATCAAAATTTATATGT
Found at i:39122145 original size:28 final size:28
Alignment explanation
Indices: 39122113--39122172 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
39122103 GACGTGTAAC
*
39122113 ATAAAATGTAAAT-TTAAG-TACTAAATTA
1 ATAAAA-G-AAATCTTAAGATACCAAATTA
*
39122141 ATAAAAGAAATCTTAAGATACCAAATTC
1 ATAAAAGAAATCTTAAGATACCAAATTA
39122169 ATAA
1 ATAA
39122173 TTTCCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 18 0.64
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (28 bp):
ATAAAAGAAATCTTAAGATACCAAATTA
Found at i:39125122 original size:15 final size:15
Alignment explanation
Indices: 39125078--39125124 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
39125068 TTACTCTTCA
39125078 AATTTTTTAAA-TTT
1 AATTTTTTAAATTTT
*
39125092 AATTTTTAAGAATTTT
1 AATTTTTTA-AATTTT
*
39125108 TATTTTTTAAATTTT
1 AATTTTTTAAATTTT
39125123 AA
1 AA
39125125 ATTCAGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.30
15 9 0.33
16 10 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
AATTTTTTAAATTTT
Found at i:39130235 original size:11 final size:11
Alignment explanation
Indices: 39130219--39130249 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39130209 TATATATATT
39130219 TAAAAATTATA
1 TAAAAATTATA
*
39130230 TAAAAATAATA
1 TAAAAATTATA
39130241 TAAAAATTA
1 TAAAAATTA
39130250 ATACGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:39130480 original size:21 final size:20
Alignment explanation
Indices: 39130456--39130497 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
39130446 GTACAAAACT
39130456 ATAAAAATTACAAAAATATTA
1 ATAAAAATTAC-AAAATATTA
**
39130477 ATAATTATTACAAAATATTA
1 ATAAAAATTACAAAATATTA
39130497 A
1 A
39130498 CATGGCTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAATTACAAAATATTA
Found at i:39130544 original size:15 final size:15
Alignment explanation
Indices: 39130524--39130562 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
39130514 AATAATTAGT
39130524 AAAAATTATAAATTA
1 AAAAATTATAAATTA
39130539 AAAAATTATAAATTA
1 AAAAATTATAAATTA
*
39130554 TAAAATTAT
1 AAAAATTAT
39130563 TAATACTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAATTATAAATTA
Found at i:39130562 original size:8 final size:8
Alignment explanation
Indices: 39130525--39130562 Score: 53
Period size: 7 Copynumber: 5.0 Consensus size: 8
39130515 ATAATTAGTA
39130525 AAAATTAT
1 AAAATTAT
*
39130533 -AAATTAA
1 AAAATTAT
39130540 AAAATTAT
1 AAAATTAT
39130548 -AAATTAT
1 AAAATTAT
39130555 AAAATTAT
1 AAAATTAT
39130563 TAATACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:39132517 original size:20 final size:19
Alignment explanation
Indices: 39132483--39132533 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
39132473 TTCATTCTAG
* *
39132483 ATGTATATATTTTTATTAA
1 ATGTAAATATTTTTAATAA
39132502 ATGTAAATACTTTTTAATAA
1 ATGTAAATA-TTTTTAATAA
*
39132522 ATTTAAA-ATTTT
1 ATGTAAATATTTT
39132534 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 15 0.54
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATGTAAATATTTTTAATAA
Found at i:39140043 original size:95 final size:97
Alignment explanation
Indices: 39139829--39140075 Score: 369
Period size: 95 Copynumber: 2.6 Consensus size: 97
39139819 AATAAAGTAA
* * * *
39139829 TGGCGCTATTTAGAATGACTCCACCAAATAAAATATTATTTTAAAAAAATTTAAATATAAAAAAA
1 TGGCGCCATTTAGAATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATATAAAAAAA
39139894 TAGATTTTTTAAAAAAAGTCTTAAAATGAATTGG
66 TAGA--TTTTAAAAAAAGTCTTAAAATGAATTGG
39139928 TGGCGCCATTTAGAATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATAT-AAAAAA
1 TGGCGCCATTTAGAATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATATAAAAAAA
39139992 TAGA-TTTAAAAAAAGTCTTAAAATGAATTGG
66 TAGATTTTAAAAAAAGTCTTAAAATGAATTGG
* **
39140023 TGGCGCCATTTAGAATGGCTCTACCAAA-AAGAATA-TACATTT-AAAATTTTAAA
1 TGGCGCCATTTAGAATGGCTCCACCAAATAA-AATATTATTTTTAAAAATTTTAAA
39140076 AAATAAGTAA
Statistics
Matches: 140, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
93 11 0.08
94 7 0.05
95 58 0.41
98 10 0.07
99 54 0.39
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.32
Consensus pattern (97 bp):
TGGCGCCATTTAGAATGGCTCCACCAAATAAAATATTATTTTTAAAAATTTTAAATATAAAAAAA
TAGATTTTAAAAAAAGTCTTAAAATGAATTGG
Found at i:39145408 original size:25 final size:24
Alignment explanation
Indices: 39145331--39145457 Score: 127
Period size: 25 Copynumber: 5.3 Consensus size: 24
39145321 CACTAATGAA
*
39145331 CAGAGAGCACTGAAGTGCTAT-A-
1 CAGAGAGCACTGACGTGCTATAAT
* *
39145353 CAGAGAGCACAGATGTGCTA-AA-
1 CAGAGAGCACTGACGTGCTATAAT
39145375 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTA-TAAT
* * *
39145400 CAAAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTGACGTGCT-ATAAT
**
39145425 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCT-ATAAT
39145450 CAGAGAGC
1 CAGAGAGC
39145458 GCGCTAAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
22 37 0.41
24 2 0.02
25 50 0.56
26 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTATAAT
Found at i:39166749 original size:16 final size:16
Alignment explanation
Indices: 39166725--39166760 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39166715 GATTTGCTAT
*
39166725 TACACCTCTAATCCAA
1 TACAACTCTAATCCAA
39166741 TACAACTCTAATCCAA
1 TACAACTCTAATCCAA
39166757 TACA
1 TACA
39166761 GTGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (16 bp):
TACAACTCTAATCCAA
Found at i:39167478 original size:53 final size:53
Alignment explanation
Indices: 39167393--39167497 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
39167383 ATCAAATTCT
*
39167393 CATATTACTCATTTTGATATATTTATTGTGTT-AAATATTGAGATTTAATGGATC
1 CATATTACTCA-TTTGATATATCTATTGTGTTAAAAT-TTGAGATTTAATGGATC
* *
39167447 CATATTACTCGA-TTGATTTATCTATTTTGTTAAAATTTGAGATTTAATGGA
1 CATATTACTC-ATTTGATATATCTATTGTGTTAAAATTTGAGATTTAATGGA
39167498 GCAATTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 31 0.67
54 14 0.30
55 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (53 bp):
CATATTACTCATTTGATATATCTATTGTGTTAAAATTTGAGATTTAATGGATC
Found at i:39167602 original size:54 final size:54
Alignment explanation
Indices: 39167520--39167625 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
39167510 ACCAAACCCT
* *
39167520 TATATTACTCGTTTTGGTCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
1 TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
* *
39167574 TATATTACTCATTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGA
1 TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGA
39167626 GCAATTAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (54 bp):
TATATTACTCATTTTGATCCATCTATTGTGTTAAATATTGAGATTTAATGGATC
Found at i:39167610 original size:127 final size:128
Alignment explanation
Indices: 39167362--39167696 Score: 448
Period size: 127 Copynumber: 2.6 Consensus size: 128
39167352 CTAATCAAAT
* * ** * * *
39167362 TTTAATGGAGCGATTAAATCCATCAAATTCTCATATTACTCATTTTGATATATTTATTGTGTTAA
1 TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
* *
39167427 ATATTGAGATTTAATGGATCCATATTACTCGATTGATTTATCTATTTTGTTAAAA-TTTGAGA
66 ATATTGAGATTTAATGGATCCATATTACTCGATTGATCTATCTATTGTGTTAAAATTTTGAGA
* * * *
39167489 TTTAATGGAGCAATTAAATTCACCAAACCCTTATATTACTCGTTTTGGTCCATCTATTGTGTTAA
1 TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
*
39167554 ATATTGAGATTTAATGGATCTATATTACTC-ATTTTGATCTATCTATTGTGTT-AAATTTTGAGA
66 ATATTGAGATTTAATGGATCCATATTACTCGA--TTGATCTATCTATTGTGTTAAAATTTTGAGA
* *
39167617 TTTAATGGAGCAATTAACTCCACCAAACCC-CA-A-TACTCGTTTTCATCTATCTATTGTGTTAA
1 TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
* *
39167679 ATTTTGAGATTTTATGGA
66 ATATTGAGATTTAATGGA
39167697 GCGATTAAAT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
125 42 0.23
126 2 0.01
127 87 0.48
128 52 0.28
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (128 bp):
TTTAATGGAGCAATTAAATCCACCAAACCCTCATATTACTCGTTTTGATCTATCTATTGTGTTAA
ATATTGAGATTTAATGGATCCATATTACTCGATTGATCTATCTATTGTGTTAAAATTTTGAGA
Found at i:39167761 original size:76 final size:72
Alignment explanation
Indices: 39167576--39167769 Score: 264
Period size: 71 Copynumber: 2.7 Consensus size: 72
39167566 AATGGATCTA
* *
39167576 TATTACTCATTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAACTCCACC
1 TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
39167641 AAACCCC
66 AAACCCC
* * * *
39167648 -AATACTCGTTTTCATCTATCTATTGTGTTAAATTTTGAGATTTTATGGAGCGATTAAATCCACC
1 TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
39167712 AAACCCCGCC
66 AAA--CC-CC
* * *
39167722 GTATTATTCGTTTTGATCTATCTAATGTGTTGAATTTTGAGATTTAAT
1 -TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAAT
39167770 TTTTAAGTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 61 0.58
73 2 0.02
74 2 0.02
76 40 0.38
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (72 bp):
TATTACTCGTTTTGATCTATCTATTGTGTTAAATTTTGAGATTTAATGGAGCAATTAAATCCACC
AAACCCC
Done.