Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 14 of 19
Found at i:2130375 original size:19 final size:19
Alignment explanation
Indices: 2130351--2130443 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 19
2130341 TTTAAATTAT
2130351 ATTTAAATAAAATTTTTTA
1 ATTTAAATAAAATTTTTTA
* * *
2130370 ATTTAAATTAATTTTATTTT
1 ATTTAAATAAAATTT-TTTA
**
2130390 ATTTAAAATATTATTTTTT-
1 ATTT-AAATAAAATTTTTTA
* * *
2130409 ATTGAAATATATAA-ATATTA
1 ATTTAAATA-A-AATTTTTTA
2130429 ATTTAAAT-AAATTTT
1 ATTTAAATAAAATTTT
2130444 AAATTTTTTT
Statistics
Matches: 53, Mismatches: 15, Indels: 13
0.65 0.19 0.16
Matches are distributed among these distances:
17 2 0.04
18 7 0.13
19 19 0.36
20 18 0.34
21 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (19 bp):
ATTTAAATAAAATTTTTTA
Found at i:2130395 original size:20 final size:19
Alignment explanation
Indices: 2130350--2130396 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2130340 ATTTAAATTA
2130350 TATTTAAATAAAATTTTTT
1 TATTTAAATAAAATTTTTT
* * *
2130369 AATTTAAATTAATTTTATTT
1 TATTTAAATAAAATTT-TTT
2130389 TATTTAAA
1 TATTTAAA
2130397 ATATTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAAATAAAATTTTTT
Found at i:2131319 original size:2 final size:2
Alignment explanation
Indices: 2131312--2131350 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2131302 CACCTGCATC
2131312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2131351 AAATATTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2131401 original size:35 final size:36
Alignment explanation
Indices: 2131343--2131428 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
2131333 TATATATATA
* * *
2131343 TATATATAAAATATTAAATTATTAAC-GTATCA-AAATT
1 TATATA-AAAATA-AAAAATATTAACAATATCATAAA-T
* *
2131380 TATATAAAAATAAAAAATATTATCAATATTATAAAT
1 TATATAAAAATAAAAAATATTAACAATATCATAAAT
2131416 TATATAAAAATAA
1 TATATAAAAATAA
2131429 TATAAATACA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
35 9 0.21
36 24 0.57
37 9 0.21
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (36 bp):
TATATAAAAATAAAAAATATTAACAATATCATAAAT
Found at i:2131424 original size:29 final size:28
Alignment explanation
Indices: 2131392--2131446 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2131382 TATAAAAATA
* * *
2131392 AAAAATATTATCAATATTATAAATTATAT
1 AAAAATAATATAAATA-CATAAATTATAT
2131421 AAAAATAATATAAATACATAAATTAT
1 AAAAATAATATAAATACATAAATTAT
2131447 TAGATCGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAAATAATATAAATACATAAATTATAT
Found at i:2131976 original size:28 final size:28
Alignment explanation
Indices: 2131928--2131981 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
2131918 TATGTACTTT
*
2131928 TATTTATTAATATAAAAATAACTTTTAA
1 TATTTATTAATATAAAAATAAATTTTAA
2131956 TATTT-TTAA-ATAATAAGATAAATTTT
1 TATTTATTAATATAA-AA-ATAAATTTT
2131982 CAAACGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
27 6 0.26
28 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TATTTATTAATATAAAAATAAATTTTAA
Found at i:2132262 original size:13 final size:14
Alignment explanation
Indices: 2132244--2132276 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2132234 TACATATTTT
2132244 AATATAA-TTATAA
1 AATATAACTTATAA
*
2132257 AATATAACTTTTAA
1 AATATAACTTATAA
2132271 AATATA
1 AATATA
2132277 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATAACTTATAA
Found at i:2132524 original size:38 final size:38
Alignment explanation
Indices: 2132447--2132525 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
2132437 TATTTAAATT
* *
2132447 AATTTATTTTAATTTAAATTATTATTTAATTAATAAAA
1 AATTTATTTTAATTTAAATTATAATTTAATAAATAAAA
* *
2132485 AATTTATTTTTATTTAAATT-TAATTATAAAAATATAAAA
1 AATTTATTTTAATTTAAATTATAATT-TAATAA-ATAAAA
2132524 AA
1 AA
2132526 ATCAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 4 0.11
38 23 0.66
39 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
AATTTATTTTAATTTAAATTATAATTTAATAAATAAAA
Found at i:2133313 original size:14 final size:14
Alignment explanation
Indices: 2133294--2133323 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2133284 TAAATTTCAC
2133294 ATAAAATATTAAAT
1 ATAAAATATTAAAT
2133308 ATAAAATATTAAAT
1 ATAAAATATTAAAT
2133322 AT
1 AT
2133324 GAAGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAAATATTAAAT
Found at i:2133868 original size:18 final size:18
Alignment explanation
Indices: 2133847--2133890 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2133837 TTATTAAATT
*
2133847 AAAATTATTTAAATTATA
1 AAAATTATTTAAAATATA
2133865 AAAATTATTTAAAATATA
1 AAAATTATTTAAAATATA
2133883 AATAATTA
1 AA-AATTA
2133891 CGAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTATTTAAAATATA
Found at i:2135147 original size:63 final size:63
Alignment explanation
Indices: 2135048--2135167 Score: 222
Period size: 63 Copynumber: 1.9 Consensus size: 63
2135038 AAAAAAATAG
2135048 TAAATCACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAAAATTAC
1 TAAATCACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAAAATTAC
* *
2135111 TAAATCACATTATATTTTAATGTAAGACAAATGGGATTATTATAAATGCTAAAATAA
1 TAAATCACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAA
2135168 TAATAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (63 bp):
TAAATCACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAAAATTAC
Found at i:2135192 original size:63 final size:63
Alignment explanation
Indices: 2135054--2135180 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 63
2135044 ATAGTAAATC
* **
2135054 ACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAAAATTACTAAATC
1 ACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAAAATTACAAAAAA
* *
2135117 ACATTATATTTTAATGTAAGACAAATGGGATTATTATAAATGCTAAAATAATAA-TA-AAAAAA
1 ACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAA-AATTACAAAAAA
2135179 AC
1 AC
2135181 TTGTCATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
62 5 0.09
63 51 0.88
64 2 0.03
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.32
Consensus pattern (63 bp):
ACATTATATTTTAATGTAAGAAAAATGGGATTATTACAAATGCTAAAATAAAATTACAAAAAA
Found at i:2135312 original size:31 final size:30
Alignment explanation
Indices: 2135230--2135333 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
2135220 TATTACTTTC
*
2135230 AAATAAA-TTCTTAATTTTTAGATTT-TACATT
1 AAATAAACTT-TTAACTTTTA-ATTTATAC-TT
*
2135261 CAAATAAA-TTTTAACATTTAATTTATACTT
1 -AAATAAACTTTTAACTTTTAATTTATACTT
*
2135291 AAATAAACCTTTTAACTTTTAATTTAAACTT
1 AAATAAA-CTTTTAACTTTTAATTTATACTT
2135322 AAATAAATCTTT
1 AAATAAA-CTTT
2135334 AAATATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 7 0.11
30 6 0.09
31 42 0.66
32 9 0.14
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (30 bp):
AAATAAACTTTTAACTTTTAATTTATACTT
Found at i:2135524 original size:30 final size:30
Alignment explanation
Indices: 2135470--2135535 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2135460 TTTTTTAGTA
**
2135470 TTTTAACCTTTAATTTGTACTTAAACAAAT
1 TTTTAACCTTTAATTTAAACTTAAACAAAT
* * *
2135500 TTTTAACTTTTAATTTAAATTTAAATAAAT
1 TTTTAACCTTTAATTTAAACTTAAACAAAT
*
2135530 CTTTAA
1 TTTTAA
2135536 TATAAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTTAACCTTTAATTTAAACTTAAACAAAT
Found at i:2135639 original size:198 final size:201
Alignment explanation
Indices: 2135268--2135644 Score: 573
Period size: 198 Copynumber: 1.9 Consensus size: 201
2135258 ATTCAAATAA
*
2135268 ATTTTAACATTTAATTTATACTTAAATAAACCTTTTAACTTTTAATTTAAACTTAAATAAATCTT
1 ATTTTAACATTTAATTTATACTTAAACAAACCTTTTAACTTTTAATTTAAACTTAAATAAATCTT
*
2135333 TAAATATAAATCAATATTTATTTATATAAAACTTGTTTGCGTAAAAAATGAACAAATAAAAATTT
66 TAAATATAAATCAATATTTATTTATATAAAACTTGTTTGCGTAAAAAATAAACAAATAAAAATTT
* * *
2135398 ATTCGAATACAATAAAATCATGAAAACCTACTTAAGAAAAGAAAAGAAATTTTTTTTTTAACTTT
131 ATTCGAATACAACAAAATCATAAAAACCAACTTAAGAAAAGAAAAGAAATTTTTTTTTTAACTTT
2135463 TTTAGT
196 TTTAGT
* * * *
2135469 ATTTTAACCTTTAATTTGTACTTAAACAAA-TTTTTAACTTTTAATTTAAATTTAAATAAATCTT
1 ATTTTAACATTTAATTTATACTTAAACAAACCTTTTAACTTTTAATTTAAACTTAAATAAATCTT
* * * ***
2135533 T-AATATAAATTAATATTTATTTATATGAAGCTTGTTTAG-GT-AAAAATAAAGGGATAAAAATT
66 TAAATATAAATCAATATTTATTTATATAAAACTTGTTT-GCGTAAAAAATAAACAAATAAAAATT
*
2135595 TATTCGGATACAACAAAATCATAAAAACCAACTTAAGAAAAGAAAAGAAA
130 TATTCGAATACAACAAAATCATAAAAACCAACTTAAGAAAAGAAAAGAAA
2135645 AATTAGAAAA
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
198 63 0.40
199 35 0.22
200 34 0.21
201 27 0.17
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.38
Consensus pattern (201 bp):
ATTTTAACATTTAATTTATACTTAAACAAACCTTTTAACTTTTAATTTAAACTTAAATAAATCTT
TAAATATAAATCAATATTTATTTATATAAAACTTGTTTGCGTAAAAAATAAACAAATAAAAATTT
ATTCGAATACAACAAAATCATAAAAACCAACTTAAGAAAAGAAAAGAAATTTTTTTTTTAACTTT
TTTAGT
Found at i:2135970 original size:9 final size:9
Alignment explanation
Indices: 2135956--2135999 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
2135946 TTGGGGGGTT
2135956 TTATTAATA
1 TTATTAATA
2135965 TTATTAATA
1 TTATTAATA
*
2135974 TTAATAATA
1 TTATTAATA
* * *
2135983 ATAATATTA
1 TTATTAATA
2135992 TTATTAAT
1 TTATTAAT
2136000 TAAGAGTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTATTAATA
Found at i:2140955 original size:14 final size:15
Alignment explanation
Indices: 2140938--2140967 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2140928 AATACCAAAA
2140938 TAAAATT-ACATCAT
1 TAAAATTCACATCAT
2140952 TAAAATTCACATCAT
1 TAAAATTCACATCAT
2140967 T
1 T
2140968 TCTTAAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATTCACATCAT
Found at i:2142382 original size:17 final size:17
Alignment explanation
Indices: 2142343--2142384 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
2142333 ATTTATTATC
2142343 ATAT-TAATA-AATAAT
1 ATATATAATATAATAAT
2142358 A-A-ATAATATAATAAT
1 ATATATAATATAATAAT
2142373 ATATATAATATA
1 ATATATAATATA
2142385 TTTAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 1 0.04
17 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATAATATAATAAT
Found at i:2142746 original size:31 final size:33
Alignment explanation
Indices: 2142697--2142769 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
2142687 ATATTTATGG
* * * *
2142697 TAATATTAAAATATTATTTTTATTTTTATAATTA
1 TAAT-TTAAAATAATATTTTTATTATTAAAATAA
2142731 -AATTTAAAA-AATATTTTTATTATTAAAATAA
1 TAATTTAAAATAATATTTTTATTATTAAAATAA
2142762 TAATTTAA
1 TAATTTAA
2142770 GTTGAAACGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 18 0.53
32 13 0.38
33 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TAATTTAAAATAATATTTTTATTATTAAAATAA
Found at i:2142830 original size:27 final size:28
Alignment explanation
Indices: 2142778--2142832 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
2142768 AAGTTGAAAC
*
2142778 GATTTAAATTTATTAAAATATTATTTAA
1 GATTTAAATTTATTAAAATATAATTTAA
*
2142806 GATTT-AATTTATATAAATTA-AATTTAA
1 GATTTAAATTTAT-TAAAATATAATTTAA
2142833 CAAATCGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
GATTTAAATTTATTAAAATATAATTTAA
Found at i:2144129 original size:246 final size:243
Alignment explanation
Indices: 2143305--2144520 Score: 1241
Period size: 246 Copynumber: 5.0 Consensus size: 243
2143295 TCGGAATAAG
* * * * *
2143305 CAGAAATGGGTTGTGGTGAATCAAAACACGTCGCGACTGAAAACACGATCAGCCGGAAGAATTCG
1 CAGAAATGGGCTGTGGTGAATCAAAACACGTCGCGACCG-AAACACCATCAGCCGGAAAAATTCA
* * * * *
2143370 AGAGCAGGATCCAGGAGGGGTAATAGAGCCCCGGAAACCACTGAAGCAAGAAGCGAACTTGATAG
65 AGAGCAGGATCCAAGAGGGGTAA-A-A-CCCCGGAAACCATTGAAGAAACAAGCAAACTTGATAG
* * *
2143435 AAACACGAGCTCGTTAATGAACGAGAAAGGCAAAAGTGTCA-ATCAGGAC-C--CTGGTGCAGAC
127 AAACACGAGCTCATTAATGAAAGAGGAAGGCAAAAGTGTCATATCAGGACTCTGCTGGTGCAGAC
* * * * *
2143496 AATTCCAGGGGTATGGCTGATGGAAATGGTATAGTTGAAAGCACAGGATATGA
192 AATTCCAGGGTTGTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAATAT-A
* * *
2143549 -AGAAATGGGCTGTGGTGAATCGAAACACGTCGCGACCGGAAACACCATCAGCCGGAAGAATTCG
1 CAGAAATGGGCTGTGGTGAATCAAAACACGTCGCGACC-GAAACACCATCAGCCGGAAAAATTCA
* * *
2143613 AGAGCAGGATCCAATGAGGGGCAAAACCCCGGAAACCATTGAAGCAACAAGCAGACTTGATAGAA
65 AGAGCAGGATCCAA-GAGGGGTAAAACCCCGGAAACCATTGAAGAAACAAGCAAACTTGATAGAA
* * * * * * * *
2143678 ACAGGAGCTCATTGATGAAAGGGGACGGCAAAAGCGTCA-ATCAAGACTCTGCTAGTGCAAACAA
129 ACACGAGCTCATTAATGAAAGAGGAAGGCAAAAGTGTCATATCAGGACTCTGCTGGTGCAGACAA
* * * * * * *
2143742 TTCCAGGGCTGTGGTTGCCGATGGGAATGGCCTAGCTAAAAGCACGGAATATG
194 TTCCAGGG-T-T-GTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAATATA
* *
2143795 CAGAAATAGGCTGTGATGGTGAATCAAAACACGTCG-GA---AAA-ACCATCAGTCGGAAAAATT
1 CAGAAATGGGC--TG-TGGTGAATCAAAACACGTCGCGACCGAAACACCATCAGCCGGAAAAATT
*
2143855 CAAGAGCAGGATCCAAGAGGGGTAAAACCCCTGAAACCATTGAAGAAACAAGCAAACTTGATAGA
63 CAAGAGCAGGATCCAAGAGGGGTAAAACCCCGGAAACCATTGAAGAAACAAGCAAACTTGATAGA
* * * * *
2143920 AGCACAAGCTCATTAATGAAAAAGGAAGGCAAAAGTGACAATGATCAAGACTCTGCTGGTGCAGA
128 AACACGAGCTCATTAATGAAAGAGGAAGGCAAAAGTGTC-AT-ATCAGGACTCTGCTGGTGCAGA
*
2143985 CAATTCCAGGGTTGTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAGTATA
191 CAATTCCAGGGTTGTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAATATA
* * *
2144038 CAGAAATGGGCTGTGGTGAATCAAAACACGTGGCGACCGATAACACCGTCAGTCGGAAAAATTCA
1 CAGAAATGGGCTGTGGTGAATCAAAACACGTCGCGACCGA-AACACCATCAGCCGGAAAAATTCA
* *
2144103 AGAGCAGGATCCAAGAGGGTTAAAACCCCGGAAACCATTGAAGAAACAAGCAAACTTGATAAAAA
65 AGAGCAGGATCCAAGAGGGGTAAAACCCCGGAAACCATTGAAGAAACAAGCAAACTTGATAGAAA
* * * * *
2144168 CACAAGCTTATCAATGAAAGAGGAAGGTAAAAGTGTCGATGATCAGGACTCTGCTGATGCAGACA
130 CACGAGCTCATTAATGAAAGAGGAAGGCAAAAGTGTC-AT-ATCAGGACTCTGCTGGTGCAGACA
* ** * * * * *
2144233 TTTCCAGGACTGTGGCTAATGGAAATGGCGTCGCTGAAGGCACAGAATATG
193 ATTCCAGGGTTGTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAATATA
* * * * * * * * *
2144284 CAGAAACGCGCTATGATGAATCAAAACAAGTTGTGACTGAAAACACCATCAGCC-AAAATAATTC
1 CAGAAATGGGCTGTGGTGAATCAAAACACGTCGCGACCG-AAACACCATCAGCCGGAAA-AATTC
* * * **** * *
2144348 AAGAGCAGAATTACAGGAAGCCAACAAAACCCCAGAAACCATTGAAGAAACAAGGAAACTTGATA
64 AAGAGCAGGA-TCCAAG-AG-GGGTAAAACCCCGGAAACCATTGAAGAAACAAGCAAACTTGATA
* * *
2144413 GAAACACGAGCTC----A-G-TAGAGGAAGGCAAAAGTGTCAATTACCAGGAC-C--CAGGTGCA
126 GAAACACGAGCTCATTAATGAAAGAGGAAGGCAAAAGTGTC-A-TATCAGGACTCTGCTGGTGCA
* * * *
2144469 AACAATCCCAAGGTTGTGGCTGATGGAAATGACATAGCTGAAAGCACAGAAT
189 GACAATTCCAGGGTTGTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAAT
2144521 TGAAGAAACA
Statistics
Matches: 820, Mismatches: 125, Indels: 58
0.82 0.12 0.06
Matches are distributed among these distances:
240 66 0.08
241 77 0.09
242 3 0.00
243 215 0.26
244 65 0.08
245 10 0.01
246 268 0.33
247 43 0.05
248 2 0.00
249 52 0.06
250 19 0.02
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.16
Consensus pattern (243 bp):
CAGAAATGGGCTGTGGTGAATCAAAACACGTCGCGACCGAAACACCATCAGCCGGAAAAATTCAA
GAGCAGGATCCAAGAGGGGTAAAACCCCGGAAACCATTGAAGAAACAAGCAAACTTGATAGAAAC
ACGAGCTCATTAATGAAAGAGGAAGGCAAAAGTGTCATATCAGGACTCTGCTGGTGCAGACAATT
CCAGGGTTGTGGCTGATGGAAATGGCATAGCTGAAAGCACAGAATATA
Found at i:2145047 original size:2 final size:2
Alignment explanation
Indices: 2145040--2145072 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2145030 TCTGATATGA
*
2145040 AT AT AT AT AT AT AT AT AT AT AT -T AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2145073 TAAATCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2145744 original size:29 final size:30
Alignment explanation
Indices: 2145688--2145750 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
2145678 AAAATTATTT
* * *
2145688 AATTAATTTTTATTATTTTTTAATTTAATA
1 AATTAATTTTTATAATTTATTAATTTAAAA
2145718 AATT-ATTTTTATAAGTTTATTAA-TTAAAA
1 AATTAATTTTTATAA-TTTATTAATTTAAAA
2145747 AATT
1 AATT
2145751 TCATTACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
AATTAATTTTTATAATTTATTAATTTAAAA
Found at i:2146684 original size:25 final size:26
Alignment explanation
Indices: 2146649--2146712 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
2146639 TTCTTTTAAT
2146649 ATTATGTAAATATAATTAAAA-TATAA
1 ATTAT-TAAATATAATTAAAATTATAA
*
2146675 ATTATTAAATAT-ATTAAAATTTTAA
1 ATTATTAAATATAATTAAAATTATAA
2146700 A-TA-TAAATATAAT
1 ATTATTAAATATAAT
2146713 ATATATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 7 0.20
24 11 0.31
25 12 0.34
26 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTATTAAATATAATTAAAATTATAA
Found at i:2146692 original size:17 final size:17
Alignment explanation
Indices: 2146663--2146704 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2146653 TGTAAATATA
2146663 ATTAAA-ATAT-AAATT
1 ATTAAATATATAAAATT
2146678 ATTAAATATATTAAAATT
1 ATTAAATATA-TAAAATT
2146696 -TTAAATATA
1 ATTAAATATA
2146705 AATATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 10 0.42
18 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAAATATATAAAATT
Found at i:2146729 original size:31 final size:31
Alignment explanation
Indices: 2146667--2146727 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
2146657 AATATAATTA
2146667 AAATATAAATTATTAAATATATTAAAATTTT
1 AAATATAAATTATTAAATATATTAAAATTTT
*
2146698 AAATATAAA-TA-TAATATATATTAATATTTT
1 AAATATAAATTATTAA-ATATATTAAAATTTT
2146728 TATTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 3 0.11
30 16 0.57
31 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATATAAATTATTAAATATATTAAAATTTT
Found at i:2147049 original size:2 final size:2
Alignment explanation
Indices: 2147042--2147090 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2147032 TCAGAAACCT
*
2147042 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2147084 AG AG AG A
1 AG AG AG A
2147091 TTGGATGGCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:2150304 original size:18 final size:17
Alignment explanation
Indices: 2150271--2150313 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2150261 GCTAACAGTT
2150271 TAAATTTAAATATAATA
1 TAAATTTAAATATAATA
*
2150288 TAAATTATAAATGTAATA
1 TAAATT-TAAATATAATA
2150306 -AAATTTAA
1 TAAATTTAA
2150314 TAATATATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 11 0.46
18 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATATAATA
Found at i:2150647 original size:18 final size:18
Alignment explanation
Indices: 2150605--2150658 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
2150595 ATTCATGTGA
*
2150605 TTAT-ATTAT-AATTATA
1 TTATAATTATAAATTATT
2150621 TTA-AATTATAAATTATT
1 TTATAATTATAAATTATT
*
2150638 TTATAATTATAAAATATT
1 TTATAATTATAAATTATT
2150656 TTA
1 TTA
2150659 ATATATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 8 0.24
17 9 0.27
18 16 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAATTATAAATTATT
Found at i:2150752 original size:10 final size:12
Alignment explanation
Indices: 2150734--2150769 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
2150724 ATAATTATTT
2150734 TTATATTTTAT-
1 TTATATTTTATA
2150745 TT-TATTTTATA
1 TTATATTTTATA
2150756 TTATATTTTA-A
1 TTATATTTTATA
2150767 TTA
1 TTA
2150770 AGCATTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.35
11 8 0.35
12 7 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:2150754 original size:17 final size:17
Alignment explanation
Indices: 2150732--2150765 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2150722 ATATAATTAT
*
2150732 TTTTATATTTTATTTTA
1 TTTTATATTATATTTTA
2150749 TTTTATATTATATTTTA
1 TTTTATATTATATTTTA
2150766 ATTAAGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATATTATATTTTA
Found at i:2151738 original size:20 final size:20
Alignment explanation
Indices: 2151715--2151752 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2151705 AATATTACAT
2151715 AAATATATATTAATATATTA
1 AAATATATATTAATATATTA
*
2151735 AAATTTATATTAATATAT
1 AAATATATATTAATATAT
2151753 AATATATTAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATATATTAATATATTA
Found at i:2151775 original size:20 final size:20
Alignment explanation
Indices: 2151719--2151780 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
2151709 TTACATAAAT
2151719 ATATATT-AATAT-ATTA-A
1 ATATATTAAATATAATTATA
*
2151736 A-AT-TTATAT-TAATATATA
1 ATATATTAAATATAAT-TATA
2151754 ATATATTAAATATAATTATA
1 ATATATTAAATATAATTATA
2151774 ATATATT
1 ATATATT
2151781 TATCGTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
15 3 0.08
16 6 0.17
17 3 0.08
18 2 0.06
19 2 0.06
20 16 0.44
21 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATTAAATATAATTATA
Found at i:2151775 original size:27 final size:27
Alignment explanation
Indices: 2151700--2151779 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
2151690 TCTAAAAATA
*
2151700 ATATAA-ATATTACATA-AA-TAT-AT
1 ATATAATATATTAAATATAATTATAAT
*
2151723 AT-TAATATATTAAA-AT-TTATATTAAT
1 ATATAATATATTAAATATAAT-TA-TAAT
2151749 ATATAATATATTAAATATAATTATAAT
1 ATATAATATATTAAATATAATTATAAT
2151776 ATAT
1 ATAT
2151780 TTATCGTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
22 4 0.09
23 9 0.20
24 2 0.04
25 1 0.02
26 4 0.09
27 20 0.44
28 4 0.09
29 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATAATATATTAAATATAATTATAAT
Found at i:2152300 original size:3 final size:3
Alignment explanation
Indices: 2152292--2152318 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2152282 ATTTTAGATA
2152292 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2152319 ATGATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2152466 original size:19 final size:20
Alignment explanation
Indices: 2152435--2152473 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2152425 ATTAACTATT
2152435 AATATATTAATATTTATAAA
1 AATATATTAATATTTATAAA
*
2152455 AATATA-TAATATTTTTAAA
1 AATATATTAATATTTATAAA
2152474 TATAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAATATTTATAAA
Found at i:2152482 original size:19 final size:19
Alignment explanation
Indices: 2152442--2152482 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2152432 ATTAATATAT
*
2152442 TAATATTTATAAAAATATA
1 TAATATTTATAAAAATAAA
* *
2152461 TAATATTTTTAAATATAAA
1 TAATATTTATAAAAATAAA
2152480 TAA
1 TAA
2152483 AATATGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTTATAAAAATAAA
Found at i:2159167 original size:92 final size:92
Alignment explanation
Indices: 2159059--2159242 Score: 341
Period size: 92 Copynumber: 2.0 Consensus size: 92
2159049 AGACTCAAGG
** *
2159059 TATCGGTTATCACCACTTTATAATCCGGTAAAATTAATATGGATAATTTCAGATAATGATACAAG
1 TATCGGTTATCACCACTTTATAATCCACTAAAATTAATATGAATAATTTCAGATAATGATACAAG
2159124 AAACAAGAGCTCAAACCAAACTTTACA
66 AAACAAGAGCTCAAACCAAACTTTACA
2159151 TATCGGTTATCACCACTTTATAATCCACTAAAATTAATATGAATAATTTCAGATAATGATACAAG
1 TATCGGTTATCACCACTTTATAATCCACTAAAATTAATATGAATAATTTCAGATAATGATACAAG
2159216 AAACAAGAGCTCAAACCAAACTTTACA
66 AAACAAGAGCTCAAACCAAACTTTACA
2159243 AGCATAAGCA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (92 bp):
TATCGGTTATCACCACTTTATAATCCACTAAAATTAATATGAATAATTTCAGATAATGATACAAG
AAACAAGAGCTCAAACCAAACTTTACA
Found at i:2160617 original size:27 final size:28
Alignment explanation
Indices: 2160564--2160720 Score: 90
Period size: 27 Copynumber: 5.3 Consensus size: 28
2160554 TCTGATTATA
* * *
2160564 TTATAATTATATTAAATTATAAAATATT
1 TTATATTTATATTAAATTTTAATATATT
2160592 TTATATTTATA-TAAATTTTAATATA-T
1 TTATATTTATATTAAATTTTAATATATT
*
2160618 TAATAATTTATATTAAATATATTTTAATATATT
1 TTAT-ATTTATATT--A-A-ATTTTAATATATT
*
2160651 TAAAATAATAATTTATA-TAATTATTTTAGTATATT
1 T----T-AT-ATTTATATTAA--ATTTTAATATATT
* *
2160686 TTATA-TTATATTATATTTTAAT-TAATA
1 TTATATTTATATTAAATTTTAATAT-ATT
2160713 TTATATTT
1 TTATATTT
2160721 TAATTTAGTG
Statistics
Matches: 104, Mismatches: 9, Indels: 32
0.72 0.06 0.22
Matches are distributed among these distances:
26 5 0.05
27 33 0.32
28 18 0.17
29 3 0.03
30 3 0.03
31 2 0.02
32 11 0.11
33 2 0.02
34 1 0.01
35 15 0.14
37 1 0.01
38 10 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
TTATATTTATATTAAATTTTAATATATT
Found at i:2160645 original size:32 final size:33
Alignment explanation
Indices: 2160586--2160650 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
2160576 TAAATTATAA
* *
2160586 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTAAATAAATTTTAATATATT
*
2160619 AATAATTTATA-TTAAATATATTTTAATATATT
1 AATAATTTATATTTAAATAAATTTTAATATATT
2160651 TAAAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AATAATTTATATTTAAATAAATTTTAATATATT
Found at i:2160648 original size:10 final size:10
Alignment explanation
Indices: 2160593--2160688 Score: 50
Period size: 10 Copynumber: 8.9 Consensus size: 10
2160583 TAAAATATTT
2160593 TATA-TTTATA
1 TATATTTTA-A
*
2160603 TAAATTTTAA
1 TATATTTTAA
*
2160613 TATATTAATAA
1 TATATT-TTAA
* *
2160624 TTTATATTAAA
1 TATAT-TTTAA
2160635 TATATTTTAA
1 TATATTTTAA
*
2160645 TATATTTAAAA
1 TATATTT-TAA
*
2160656 TAATAATTTATA
1 T-ATATTTTA-A
*
2160668 TAATTATTTTAG
1 T-A-TATTTTAA
2160680 TATATTTTA
1 TATATTTTA
2160689 TATTATATTA
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
10 27 0.41
11 22 0.33
12 11 0.17
13 6 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
TATATTTTAA
Found at i:2160697 original size:22 final size:22
Alignment explanation
Indices: 2160658--2160722 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
2160648 ATTTAAAATA
*
2160658 ATAATTTATATAATTATTTTAGT
1 ATAATTTATATTA-TATTTTAGT
* * *
2160681 ATATTTTATATTATATTATATT
1 ATAATTTATATTATATTTTAGT
* *
2160703 TTAATTAATATTATATTTTA
1 ATAATTTATATTATATTTTA
2160723 ATTTAGTGTC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATAATTTATATTATATTTTAGT
Found at i:2160700 original size:17 final size:17
Alignment explanation
Indices: 2160559--2160722 Score: 77
Period size: 16 Copynumber: 10.2 Consensus size: 17
2160549 AACCATCTGA
2160559 TTATATTATAATTATA--
1 TTATATTAT-ATTATATT
* **
2160575 TTAAATTATAAAATATT
1 TTATATTATATTATATT
*
2160592 TTATATT-TATATAAATT
1 TTATATTATAT-TATATT
*
2160609 TTA-A-TATATTAATAAT
1 TTATATTATATT-ATATT
*
2160625 TTATATTA-AATATATT
1 TTATATTATATTATATT
**
2160641 TTA-A-TATATT-TAAA
1 TTATATTATATTATATT
* * *
2160655 ATA-ATAAT-TTATATAA
1 TTATATTATATTATAT-T
*
2160671 TTAT-TT-TAGTATATT
1 TTATATTATATTATATT
2160686 TTATATTATATTATATT
1 TTATATTATATTATATT
2160703 TTA-ATTAATATTATATT
1 TTATATT-ATATTATATT
2160720 TTA
1 TTA
2160723 ATTTAGTGTC
Statistics
Matches: 110, Mismatches: 22, Indels: 31
0.67 0.13 0.19
Matches are distributed among these distances:
14 9 0.08
15 18 0.16
16 41 0.37
17 40 0.36
18 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:2160723 original size:17 final size:16
Alignment explanation
Indices: 2160563--2160725 Score: 81
Period size: 17 Copynumber: 10.2 Consensus size: 16
2160553 ATCTGATTAT
*
2160563 ATTATAATTATA-TTAA
1 ATTAT-ATTATATTTTA
**
2160579 ATTATAAAATATTTTA
1 ATTATATTATATTTTA
*
2160595 TATT-TATATAAATTTTA
1 -ATTATAT-TATATTTTA
*
2160612 A-TATATTAATAATTTA
1 ATTATATT-ATATTTTA
*
2160628 TATTA-AATATATTTTA
1 -ATTATATTATATTTTA
***
2160644 A-TATATT-TAAAATA
1 ATTATATTATATTTTA
* *
2160658 ATAAT-TTATATAATT-
1 ATTATATTATAT-TTTA
* *
2160673 ATTTTAGTATATTTTA
1 ATTATATTATATTTTA
2160689 TATTATATTATATTTTA
1 -ATTATATTATATTTTA
2160706 ATTAATATTATATTTTA
1 ATT-ATATTATATTTTA
2160723 ATT
1 ATT
2160726 TAGTGTCGTG
Statistics
Matches: 109, Mismatches: 23, Indels: 29
0.68 0.14 0.18
Matches are distributed among these distances:
14 9 0.08
15 18 0.17
16 37 0.34
17 43 0.39
18 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
ATTATATTATATTTTA
Found at i:2161621 original size:20 final size:18
Alignment explanation
Indices: 2161596--2161634 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
2161586 GACAGCTTTA
2161596 AATAAAAATAGTTAAAATAT
1 AATAAAAATA--TAAAATAT
2161616 AATAAAAATATAAAATAT
1 AATAAAAATATAAAATAT
2161634 A
1 A
2161635 TTAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AATAAAAATATAAAATAT
Found at i:2161635 original size:20 final size:21
Alignment explanation
Indices: 2161596--2161640 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2161586 GACAGCTTTA
*
2161596 AATAAAAATAGTTAAAATA-T
1 AATAAAAATAGTAAAAATATT
2161616 AATAAAAATA-TAAAATATATT
1 AATAAAAATAGTAAAA-ATATT
2161637 AATA
1 AATA
2161641 TTTTAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AATAAAAATAGTAAAAATATT
Found at i:2161931 original size:19 final size:21
Alignment explanation
Indices: 2161891--2161933 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
2161881 TATTCTAGAT
2161891 TTTTTCTTAAAAAATTATTAA
1 TTTTTCTTAAAAAATTATTAA
2161912 TTTTT-TTAAAAAATTA-TAA
1 TTTTTCTTAAAAAATTATTAA
2161931 TTT
1 TTT
2161934 AATTAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTCTTAAAAAATTATTAA
Found at i:2161939 original size:19 final size:20
Alignment explanation
Indices: 2161897--2161940 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2161887 AGATTTTTTC
**
2161897 TTAAAAAATTATTAATTTTT
1 TTAAAAAATTATTAATTTAA
2161917 TTAAAAAATTA-TAATTTAA
1 TTAAAAAATTATTAATTTAA
2161936 TTAAA
1 TTAAA
2161941 TTGATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAAATTATTAATTTAA
Found at i:2162361 original size:29 final size:28
Alignment explanation
Indices: 2162318--2162373 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2162308 ATTATTACAT
2162318 AATATAAAAAAATTAAAATATAATATAAA
1 AATATAAAAAAATTAAAAT-TAATATAAA
* * *
2162347 AATATAAATATATTAAAATTTATATAA
1 AATATAAAAAAATTAAAATTAATATAA
2162374 TATTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
AATATAAAAAAATTAAAATTAATATAAA
Found at i:2162376 original size:17 final size:17
Alignment explanation
Indices: 2162335--2162379 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2162325 AAAAATTAAA
*
2162335 ATATAATATAAAAATAT
1 ATATAATATTAAAATAT
* *
2162352 AAAT-ATATTAAAATTT
1 ATATAATATTAAAATAT
2162368 ATATAATATTAA
1 ATATAATATTAA
2162380 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATTAAAATAT
Found at i:2162406 original size:17 final size:18
Alignment explanation
Indices: 2162349--2162419 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 18
2162339 AATATAAAAA
*
2162349 TATAAATATATTAA-AATT
1 TATAAATATA-TAATATTT
*
2162367 TATATAATAT-TAAT-TAT
1 TATA-AATATATAATATTT
2162384 TA-AAAT-TAATAA-ATTT
1 TATAAATAT-ATAATATTT
2162400 TATAAATATATAATATTT
1 TATAAATATATAATATTT
2162418 TA
1 TA
2162420 AATATAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
14 1 0.02
15 3 0.07
16 8 0.19
17 14 0.33
18 11 0.26
19 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATAAATATATAATATTT
Found at i:2167093 original size:20 final size:20
Alignment explanation
Indices: 2167043--2167102 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
2167033 TTTTACATAA
2167043 AAATATTTA-ATTATTATTTT
1 AAAT-TTTATATTATTATTTT
***
2167063 AAATGAAATATTATTATTTT
1 AAATTTTATATTATTATTTT
*
2167083 TAATTTTATA-T-TTATTTT
1 AAATTTTATATTATTATTTT
2167101 AA
1 AA
2167103 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 8 0.26
19 2 0.06
20 21 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
AAATTTTATATTATTATTTT
Found at i:2172086 original size:14 final size:13
Alignment explanation
Indices: 2172053--2172105 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
2172043 TTTTAATTTT
* *
2172053 ATTATATATAAAA
1 ATTATATTTAATA
2172066 ATTATATTTATATA
1 ATTATATTTA-ATA
*
2172080 TTTATATTTAATA
1 ATTATATTTAATA
*
2172093 ATTATATTAAATA
1 ATTATATTTAATA
2172106 TAAATATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTATATTTAATA
Found at i:2172113 original size:32 final size:32
Alignment explanation
Indices: 2172077--2172149 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
2172067 TTATATTTAT
*
2172077 ATATTTATATTT-AATAATTATATTAAATATAA
1 ATATTTAAATTTGAA-AATTATATTAAATATAA
* *
2172109 ATATTTAAATTTGAAAATTCTTTTAAATA-ATA
1 ATATTTAAATTTGAAAATTATATTAAATATA-A
2172141 AT-TTTAAAT
1 ATATTTAAAT
2172150 ATTTTTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 8 0.22
32 26 0.72
33 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (32 bp):
ATATTTAAATTTGAAAATTATATTAAATATAA
Found at i:2172182 original size:25 final size:26
Alignment explanation
Indices: 2172133--2172184 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
2172123 AAATTCTTTT
**
2172133 AAATAATAATTTTAAATATTTTTATA
1 AAATAATAATTTTAAATATACTTATA
2172159 AAATAATAA-TTTAAATATACTTATA
1 AAATAATAATTTTAAATATACTTATA
2172184 A
1 A
2172185 GTCAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATAATAATTTTAAATATACTTATA
Found at i:2173481 original size:20 final size:20
Alignment explanation
Indices: 2173458--2173499 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2173448 TAATTATTTT
2173458 TAAAATATT-ATATATTT-A
1 TAAAATATTAATATATTTAA
*
2173476 TATAAATTTTAATATATTTAA
1 TA-AAATATTAATATATTTAA
2173497 TAA
1 TAA
2173500 TTTTATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.10
19 6 0.30
20 9 0.45
21 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATATTAATATATTTAA
Found at i:2173501 original size:18 final size:20
Alignment explanation
Indices: 2173467--2173510 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
2173457 TTAAAATATT
2173467 ATATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
2173487 ATATATTTA-AT-AATTTTA
1 ATATATTTATATAAATTTTA
*
2173505 TTATAT
1 ATATAT
2173511 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 2 0.09
20 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:2173510 original size:20 final size:22
Alignment explanation
Indices: 2173463--2173511 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
2173453 ATTTTTAAAA
2173463 TATTATATATTTATATAAATTT
1 TATTATATATTTATATAAATTT
2173485 TA--ATATATTTA-AT-AATTT
1 TATTATATATTTATATAAATTT
2173503 TATTATATA
1 TATTATATA
2173512 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.28
19 2 0.08
20 14 0.56
22 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATATATTTATATAAATTT
Found at i:2174448 original size:19 final size:19
Alignment explanation
Indices: 2174424--2174464 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2174414 AAGTAACGAT
2174424 TTAAA-TAATAATTATAATA
1 TTAAATTAA-AATTATAATA
*
2174443 TTAAATTAAAATTATATTA
1 TTAAATTAAAATTATAATA
2174462 TTA
1 TTA
2174465 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATTAAAATTATAATA
Found at i:2174483 original size:17 final size:17
Alignment explanation
Indices: 2174457--2174516 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
2174447 ATTAAAATTA
*
2174457 TATTATTATTTTTTAAT
1 TATTAATATTTTTTAAT
2174474 TATTAATATTTATTATAAT
1 TATTAATATTT-TT-TAAT
* * *
2174493 TAATAATAATTTATAAT
1 TATTAATATTTTTTAAT
2174510 TA-TAATA
1 TATTAATA
2174517 AATATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 5 0.14
17 16 0.43
18 3 0.08
19 13 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTAATATTTTTTAAT
Found at i:2174515 original size:19 final size:19
Alignment explanation
Indices: 2174431--2174517 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
2174421 GATTTAAATA
* *
2174431 ATAATTATAATATTAAATT
1 ATAATTATAATAATAATTT
* * * *
2174450 AAAATTATATTATTATTTT
1 ATAATTATAATAATAATTT
*
2174469 TTAATTAT--TAAT-ATTT
1 ATAATTATAATAATAATTT
* *
2174485 ATTATAATTAATAATAATTT
1 ATAATTA-TAATAATAATTT
2174505 ATAATTATAATAA
1 ATAATTATAATAA
2174518 ATATAATATA
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
16 7 0.14
17 4 0.08
19 31 0.61
20 9 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAATTATAATAATAATTT
Found at i:2174527 original size:20 final size:22
Alignment explanation
Indices: 2174485--2174531 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
2174475 ATTAATATTT
*
2174485 ATTATAATTAATAATAATTTATA
1 ATTATAATAAATAATAA-TTATA
2174508 ATTATAATAAAT-ATAA-TATA
1 ATTATAATAAATAATAATTATA
2174528 ATTA
1 ATTA
2174532 AAAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
22 4 0.17
23 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATAATAAATAATAATTATA
Found at i:2174533 original size:15 final size:15
Alignment explanation
Indices: 2174487--2174529 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2174477 TAATATTTAT
*
2174487 TATAATTAATAATAATT
1 TATAATT-ATAATAA-A
2174504 TATAATTATAATAAA
1 TATAATTATAATAAA
2174519 TATAA-TATAAT
1 TATAATTATAAT
2174530 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 7 0.28
17 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATTATAATAAA
Found at i:2174882 original size:20 final size:19
Alignment explanation
Indices: 2174863--2174955 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
2174853 AAATTTAAAT
2174863 TATTTTTAATAAATAAAAA
1 TATTTTTAATAAATAAAAA
*
2174882 TA-TTTTAATATTAATATAAA
1 TATTTTTAATA--AATAAAAA
** * *
2174902 -ATTTTTAATATTTTAATA
1 TATTTTTAATAAATAAAAA
*
2174920 TATTTTAAAT-AATAAATAAA
1 TATTTTTAATAAAT-AA-AAA
*
2174940 TTTTTTTAATAAATAA
1 TATTTTTAATAAATAA
2174956 TTTTTTTTAT
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
18 12 0.22
19 12 0.22
20 27 0.50
21 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTTTTAATAAATAAAAA
Found at i:2174911 original size:38 final size:39
Alignment explanation
Indices: 2174858--2174955 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 39
2174848 TTTTTAAATT
*
2174858 TAAATTATTTTTAATAAATAAAAATATTTT-AATATTAATA
1 TAAA-TATTTTTAATAAATAAAAATATTTTAAATAATAA-A
** * *
2174898 TAAA-ATTTTTAATATTTTAATATATTTTAAATAATAAA
1 TAAATATTTTTAATAAATAAAAATATTTTAAATAATAAA
*
2174936 TAAATTTTTTTAATAAATAA
1 TAAATATTTTTAATAAATAA
2174956 TTTTTTTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
38 25 0.53
39 18 0.38
40 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
TAAATATTTTTAATAAATAAAAATATTTTAAATAATAAA
Found at i:2174931 original size:57 final size:54
Alignment explanation
Indices: 2174839--2174943 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 54
2174829 GAATAGAGTG
* *
2174839 AATATAATATTTTTAAATTTAAATTATTTTTAATAAATAAA-AATATTTTAATATT
1 AATATAAAATTTTTAAATTTAAATTATTTTAAAT-AATAAATAA-ATTTTAATATT
*
2174894 AATATAAAATTTTTAATATTTTAATATATTTTAAATAATAAATAAATTTT
1 AATATAAAATTTTTAA-ATTTAAAT-TATTTTAAATAATAAATAAATTTT
2174944 TTTAATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
55 15 0.34
56 18 0.41
57 11 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (54 bp):
AATATAAAATTTTTAAATTTAAATTATTTTAAATAATAAATAAATTTTAATATT
Found at i:2174951 original size:17 final size:17
Alignment explanation
Indices: 2174929--2174964 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2174919 ATATTTTAAA
2174929 TAATAAATAAATTTTTT
1 TAATAAATAAATTTTTT
*
2174946 TAATAAATAATTTTTTT
1 TAATAAATAAATTTTTT
2174963 TA
1 TA
2174965 TTGTTAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATAAATAAATTTTTT
Found at i:2177479 original size:2 final size:2
Alignment explanation
Indices: 2177467--2177501 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2177457 TTTAGGGGTT
2177467 TA TA T- TA 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 TA TA TA TA
2177502 AACCGAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2178366 original size:171 final size:168
Alignment explanation
Indices: 2178162--2178705 Score: 446
Period size: 171 Copynumber: 3.2 Consensus size: 168
2178152 AATTACTTTT
* *
2178162 TAAATATATTTTATTATTAAAAATTTAAAATTATCTGATAAAGATTTAAAAATATT-AAAATCTA
1 TAAATATATTTTATTATTAAAAATCTAAAATTATCTGATAAATATTTAAAAATATTAAAAATCTA
* * * *
2178226 AAATTATATAAAATAAATTTTTATATTTAAGAAATTATTGTATTTTAATAGGAATATG-TCAATA
66 AAATTATATAAAATAAATTTTTATACTTAAG-AACTATTATATTTTAATACGAA-A-GATCAATA
* * ** *
2178290 TATATTTTTTAAAATTTATTATTTTTTAATTTTTTAA-CTTAG
128 TATATTTTTTAAAACTTATTAATTCATAA-TTTTTAATC-CAG
* *
2178332 TAAATA-AATTTATTATTTAAAACATCAAAAATTATCTTGA-AAATATTTAAAAA-ATTAAAAAA
1 TAAATATATTTTATTA-TTAAAA-ATCTAAAATTATC-TGATAAATATTTAAAAATATT--AAAA
** * * *
2178394 AAGTAAAATTATAT-AAATAATTTGTTTATGCTTAAGAACTGTTATATTTTAATACGAAAGAATC
61 ATCTAAAATTATATAAAATAAATT-TTTATACTTAAGAACTATTATATTTTAATACGAAAG-ATC
* * *
2178458 AATTTATATTTTTTTAGACTTATTAATTCATAATTTTTAATCCAG
124 AATATATATTTTTTAAAACTTATTAATTCATAATTTTTAATCCAG
** * * *
2178503 TAAATATATTTTATTATTAAAATATCTAAAATTATAAGGTAAATATTTAAAAATTTTCAAAATCT
1 TAAATATATTTTATTATTAAAA-ATCTAAAATTATCTGATAAATATTTAAAAATATTAAAAATCT
* * * * *
2178568 AAAATTATGTAAAA-AAAATTTT-T-CTTGAGAAACTGTCATATTTTAATACGAAA-ATTTCAAT
65 AAAATTATATAAAATAAATTTTTATACTTAAG-AACTATTATATTTTAATACGAAAGA--TCAAT
* * * * * ** *
2178629 TTATGTTTTCTTTTAAACTTAATATTTTTTAATTTTTAATCTA-
127 ATAT-ATTT-TTTAAAACTTATTAATTCATAATTTTTAATCCAG
* * * *
2178672 AAAATTTAATTTATTATTAAATTATCTAAAATTA
1 TAAATATATTTTATTATTAAA-AATCTAAAATTA
2178706 CCTGTTAGTT
Statistics
Matches: 307, Mismatches: 47, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
166 1 0.00
167 5 0.02
168 32 0.10
169 43 0.14
170 61 0.20
171 72 0.23
172 68 0.22
173 25 0.08
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (168 bp):
TAAATATATTTTATTATTAAAAATCTAAAATTATCTGATAAATATTTAAAAATATTAAAAATCTA
AAATTATATAAAATAAATTTTTATACTTAAGAACTATTATATTTTAATACGAAAGATCAATATAT
ATTTTTTAAAACTTATTAATTCATAATTTTTAATCCAG
Found at i:2179118 original size:14 final size:15
Alignment explanation
Indices: 2179094--2179130 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2179084 AATATATTTA
*
2179094 AAAAATAAATAAATT
1 AAAAATAAATAAACT
2179109 AAAAAT-AATAAACT
1 AAAAATAAATAAACT
2179123 -AAAATAAA
1 AAAAATAAA
2179131 AACTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAATAAATAAACT
Found at i:2179118 original size:18 final size:18
Alignment explanation
Indices: 2179076--2179132 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
2179066 TAAATATTTT
* *
2179076 AATAATAAAATATATTTAA
1 AATAAT-AAATAAATTAAA
2179095 AA-AATAAATAAATTAAA
1 AATAATAAATAAATTAAA
*
2179112 AATAATAAACTAAAATAAA
1 AATAATAAA-TAAATTAAA
2179131 AA
1 AA
2179133 CTTTAAAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 12 0.36
18 9 0.27
19 12 0.36
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAATAAATAAATTAAA
Found at i:2179130 original size:19 final size:17
Alignment explanation
Indices: 2179093--2179132 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
2179083 AAATATATTT
*
2179093 AAAAAATAAATAAATTA
1 AAAAAATAAATAAAATA
2179110 AAAATAATAAACTAAAATA
1 AAAA-AATAAA-TAAAATA
2179129 AAAA
1 AAAA
2179133 CTTTAAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAAATAAATAAAATA
Found at i:2179255 original size:29 final size:29
Alignment explanation
Indices: 2179212--2179290 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
2179202 GTCAAGCGAG
*
2179212 TAAAATAATAATATTTTAATAAATAATTT
1 TAAAATAATATTATTTTAATAAATAATTT
* *
2179241 TAAAATAATATTATTTTAATAATTTATTT
1 TAAAATAATATTATTTTAATAAATAATTT
* *
2179270 TAAAATTAAAATTACTTTAAT
1 TAAAA-TAATATTATTTTAAT
2179291 TAATCTACCC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 31 0.70
30 13 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAAATAATATTATTTTAATAAATAATTT
Found at i:2179261 original size:14 final size:14
Alignment explanation
Indices: 2179215--2179272 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 14
2179205 AAGCGAGTAA
*
2179215 AATAATAATATTTT
1 AATAATATTATTTT
*
2179229 AATAA-ATAATTTT
1 AATAATATTATTTT
2179242 AAAATAATATTATTTT
1 --AATAATATTATTTT
2179258 AATAAT-TTATTTT
1 AATAATATTATTTT
2179271 AA
1 AA
2179273 AATTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 15 0.39
14 11 0.29
15 5 0.13
16 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:2179460 original size:12 final size:12
Alignment explanation
Indices: 2179439--2179474 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2179429 CGGTAAAAAG
2179439 TAAT-TAAAATA
1 TAATATAAAATA
2179450 TAATATAAAATA
1 TAATATAAAATA
2179462 TAATAT-AAATA
1 TAATATAAAATA
2179473 TA
1 TA
2179475 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:2179480 original size:20 final size:20
Alignment explanation
Indices: 2179452--2179490 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2179442 TTAAAATATA
2179452 ATATAAAATATAATATAAAT
1 ATATAAAATATAATATAAAT
* * *
2179472 ATATTAAATTTTATATAAA
1 ATATAAAATATAATATAAA
2179491 ATAAATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAAATATAATATAAAT
Found at i:2181983 original size:16 final size:17
Alignment explanation
Indices: 2181951--2181987 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2181941 GGATTTTTAA
2181951 ATTTTGAACTCATTTTG
1 ATTTTGAACTCATTTTG
*
2181968 ATTTTGAA-TTATTTTG
1 ATTTTGAACTCATTTTG
2181984 ATTT
1 ATTT
2181988 AAGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (17 bp):
ATTTTGAACTCATTTTG
Found at i:2182010 original size:15 final size:15
Alignment explanation
Indices: 2181962--2182011 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
2181952 TTTTGAACTC
*
2181962 ATTTTGATTTTGAATT
1 ATTTTGA-TTTAAATT
2181978 ATTTTGATTTAAGA-T
1 ATTTTGATTTAA-ATT
2181993 ATTTTGATTTAAATT
1 ATTTTGATTTAAATT
2182008 ATTT
1 ATTT
2182012 CAGTTTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 22 0.71
16 8 0.26
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (15 bp):
ATTTTGATTTAAATT
Found at i:2183154 original size:14 final size:14
Alignment explanation
Indices: 2183135--2183188 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
2183125 AAAAATATAA
2183135 ATTATTATTTAATT
1 ATTATTATTTAATT
*
2183149 ATTATTATTTTA-T
1 ATTATTATTTAATT
*
2183162 ATT-TAATTT-ATT
1 ATTATTATTTAATT
* *
2183174 ATTTTTATTAAATT
1 ATTATTATTTAATT
2183188 A
1 A
2183189 AATATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
13 8 0.24
14 15 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTATTATTTAATT
Found at i:2183187 original size:18 final size:19
Alignment explanation
Indices: 2183150--2183187 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2183140 TATTTAATTA
*
2183150 TTATTATTTTATATTTAAT
1 TTATTATTTTATATTAAAT
2183169 TTATTATTTT-TATTAAAT
1 TTATTATTTTATATTAAAT
2183187 T
1 T
2183188 AAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTTTATATTAAAT
Found at i:2183189 original size:22 final size:21
Alignment explanation
Indices: 2183143--2183195 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
2183133 AAATTATTAT
*
2183143 TTAATTATTATTATTTTATAT
1 TTAATTATTATTATTTTATAA
*
2183164 TTAATTTATTATTTTTATTA-AA
1 TTAA-TTATTATTATT-TTATAA
*
2183186 TTAAATATTA
1 TTAATTATTA
2183196 ATTTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.33
22 15 0.56
23 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATTATTATTATTTTATAA
Found at i:2184023 original size:5 final size:5
Alignment explanation
Indices: 2184013--2184040 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2184003 TATTATTTAA
2184013 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
2184041 GATCCAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:2185244 original size:13 final size:14
Alignment explanation
Indices: 2185221--2185249 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2185211 ATATTCATAT
2185221 TAAATATATATTCG
1 TAAATATATATTCG
2185235 TAAATA-ATATTCG
1 TAAATATATATTCG
2185248 TA
1 TA
2185250 TCTGAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
TAAATATATATTCG
Found at i:2186930 original size:36 final size:36
Alignment explanation
Indices: 2186884--2186954 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
2186874 TCCTCCTCCT
2186884 CCACCAGCACCGCCTCCAAAACCTCCACCGGCACCA
1 CCACCAGCACCGCCTCCAAAACCTCCACCGGCACCA
* * ** *
2186920 CCACCTGCACCTCCTCCAAGTCCTCCTCCGGCACC
1 CCACCAGCACCGCCTCCAAAACCTCCACCGGCACC
2186955 GCCTCCGACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.56, G:0.11, T:0.11
Consensus pattern (36 bp):
CCACCAGCACCGCCTCCAAAACCTCCACCGGCACCA
Found at i:2186987 original size:66 final size:66
Alignment explanation
Indices: 2186851--2186978 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
2186841 ACCTCCAAAC
* * *
2186851 CCACCACCTGCGCCGCCTCCAAGTCCTCCTCCTCCACCAGCACCGCCTCCAAAACCTCCACCGGC
1 CCACCACCTGCACCGCCTCCAAGTCCTCCTCCGCCACCAGCACCGACTCCAAAACCTCCACCGGC
2186916 A
66 A
* * * * *
2186917 CCACCACCTGCACCTCCTCCAAGTCCTCCTCCGGCACC-GCCTCCGACTCCTATACCTCCACC
1 CCACCACCTGCACCGCCTCCAAGTCCTCCTCCGCCACCAG-CACCGACTCCAAAACCTCCACC
2186979 TTTTCCACCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.18, C:0.56, G:0.11, T:0.15
Consensus pattern (66 bp):
CCACCACCTGCACCGCCTCCAAGTCCTCCTCCGCCACCAGCACCGACTCCAAAACCTCCACCGGC
A
Found at i:2187038 original size:78 final size:78
Alignment explanation
Indices: 2186916--2187065 Score: 194
Period size: 78 Copynumber: 1.9 Consensus size: 78
2186906 CTCCACCGGC
* * * * * *
2186916 ACCACCACCTGCACCTCCTCCAAGTCCTCCTCCGGCACCGCCTCCGACTCCTATACCTCCACCTT
1 ACCACCACCTGCACCTCCTCCAAGACCACCGCCAGCACCACCTCCAACTCCTATACCTCCACCTT
*
2186981 TTCCACCTCCAAA
66 TGCCACCTCCAAA
* * *
2186994 ACCACCACCTGCACCTCCTCC-GGCACCACCGCCAGCTCCACCTCCAACTCCTATGCCTCCACCT
1 ACCACCACCTGCACCTCCTCCAAG-ACCACCGCCAGCACCACCTCCAACTCCTATACCTCCACCT
2187058 TTGCCACC
65 TTGCCACC
2187066 ACCGATTCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 1 0.02
78 60 0.98
ACGTcount: A:0.19, C:0.54, G:0.09, T:0.19
Consensus pattern (78 bp):
ACCACCACCTGCACCTCCTCCAAGACCACCGCCAGCACCACCTCCAACTCCTATACCTCCACCTT
TGCCACCTCCAAA
Found at i:2187143 original size:30 final size:30
Alignment explanation
Indices: 2187109--2187410 Score: 376
Period size: 30 Copynumber: 10.5 Consensus size: 30
2187099 AAAACCACCA
* * *
2187109 CCAGCACCACCCCCACCGCCAAGTCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
*
2187139 CCAGCTCCACCTCCGCCACCAAGTCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
*
2187169 CCAGCTCCACCTCCACCGCCAAGTCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
*
2187199 CCAGCTCCACCTCCGCCACCAAGTCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
*
2187229 CCAGCGCCACCTCCACCACCAAGTCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
*
2187259 CCAG------CTCCACCACCAAGCCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
*
2187283 CCAGCTCCACCTCCACCACCAAGCCCTCCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
2187313 CCAGCTCCACCTCCACCACCAAG--C-CCT
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
* * *
2187340 CCA---CCAGCTCCACCACCAAGCCCTCCA
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
* * * *
2187367 CCAACTCCACCTCCACCACCGAGCCCTCCA
1 CCAGCTCCACCTCCACCACCAAGTCCTCCT
2187397 CCAGCTCCACCTCC
1 CCAGCTCCACCTCC
2187411 CAAACCTCCA
Statistics
Matches: 244, Mismatches: 16, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
24 39 0.16
26 1 0.00
27 11 0.05
28 1 0.00
30 192 0.79
ACGTcount: A:0.20, C:0.59, G:0.09, T:0.13
Consensus pattern (30 bp):
CCAGCTCCACCTCCACCACCAAGTCCTCCT
Found at i:2187167 original size:84 final size:84
Alignment explanation
Indices: 2187090--2187410 Score: 381
Period size: 84 Copynumber: 3.8 Consensus size: 84
2187080 CTCCACCTTT
* * * * * * * *
2187090 TCCACCTCCAAAACCACCACCAGCACCACCCCCACCGCCAAGTCCTCCTCCAGCTCCACCTCCGC
1 TCCACCACCAAACCCTCCACCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCACCTCCAC
*
2187155 CACCAAGTCCTCCTCCAGC
66 CACCAAGTCCTCCACCAGC
** * * * *
2187174 TCCACCTCCACCGCCAAGTCCTCCTCCAGCTCCACCTCCGCCACCAAGTCCTCCTCCAGCGCCAC
1 TCCA---CCA---CCAAACCCTCCACCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCAC
*
2187239 CTCCACCACCAAGTCCTCCTCCAGC
60 CTCCACCACCAAGTCCTCCACCAGC
* *
2187264 TCCACCACCAAGCCCTCCTCCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCACCTCCAC
1 TCCACCACCAAACCCTCCACCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCACCTCCAC
*
2187329 CACCAAGCCCTCCACCAGC
66 CACCAAGTCCTCCACCAGC
* * * *
2187348 TCCACCACCAAGCCCTCCACCAACTCCACCTCCACCACCGAGCCCTCCACCAGCTCCACCTCC
1 TCCACCACCAAACCCTCCACCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCACCTCC
2187411 CAAACCTCCA
Statistics
Matches: 210, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
84 134 0.64
87 5 0.02
90 71 0.34
ACGTcount: A:0.21, C:0.58, G:0.08, T:0.13
Consensus pattern (84 bp):
TCCACCACCAAACCCTCCACCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCACCTCCAC
CACCAAGTCCTCCACCAGC
Found at i:2187343 original size:12 final size:12
Alignment explanation
Indices: 2187328--2187370 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
2187318 TCCACCTCCA
2187328 CCACCAAGCCCT
1 CCACCAAGCCCT
*
2187340 CCACC-AGCTCCA
1 CCACCAAGC-CCT
2187352 CCACCAAGCCCT
1 CCACCAAGCCCT
2187364 CCACCAA
1 CCACCAA
2187371 CTCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.28, C:0.58, G:0.07, T:0.07
Consensus pattern (12 bp):
CCACCAAGCCCT
Found at i:2187476 original size:54 final size:54
Alignment explanation
Indices: 2187263--2187477 Score: 173
Period size: 54 Copynumber: 3.8 Consensus size: 54
2187253 CCTCCTCCAG
* * * * * *
2187263 CTCCACCACCAAGCCCTCCTCCAGCTCCACCTCCACCACCAAGCCCTCCTCCAGCTCCAC
1 CTCCACCACCAAGCCCTCCACCAGCTCCA---CCACCA--AA-ACCACCTACAACACCAC
** * *
2187323 CTCCACCACCAAGCCCTCCACCAGCTCCACCACCAAGCCCTCC-ACCAACTCCAC
1 CTCCACCACCAAGCCCTCCACCAGCTCCACCACCAAAACCACCTA-CAACACCAC
* * *
2187377 CTCCACCACCGAGCCCTCCACCAGCTCCACCTCCCAAACCTCCACCTA-AACCACCAC
1 CTCCACCACCAAGCCCTCCACCAGCTCCACC-ACCAAA--ACCACCTACAA-CACCAC
* * *
2187434 CACCACCACCAAGCCCTCCTCCAGCACCACCACCAAAACCACCT
1 CTCCACCACCAAGCCCTCCACCAGCTCCACCACCAAAACCACCT
2187478 CCAAGGTTCT
Statistics
Matches: 133, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
54 50 0.38
55 5 0.04
56 7 0.05
57 42 0.32
58 1 0.01
60 28 0.21
ACGTcount: A:0.26, C:0.59, G:0.06, T:0.10
Consensus pattern (54 bp):
CTCCACCACCAAGCCCTCCACCAGCTCCACCACCAAAACCACCTACAACACCAC
Found at i:2187478 original size:24 final size:24
Alignment explanation
Indices: 2187434--2187480 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2187424 AAACCACCAC
** *
2187434 CACCACCACCAAGCCCTCCTCCAG
1 CACCACCACCAAAACCACCTCCAG
2187458 CACCACCACCAAAACCACCTCCA
1 CACCACCACCAAAACCACCTCCA
2187481 AGGTTCTCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.57, G:0.04, T:0.06
Consensus pattern (24 bp):
CACCACCACCAAAACCACCTCCAG
Found at i:2189094 original size:14 final size:15
Alignment explanation
Indices: 2189052--2189095 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
2189042 ATTTGAATAT
2189052 TATTATATTTGTATTA
1 TATTATATTT-TATTA
*
2189068 TA-TATATTATATTA
1 TATTATATTTTATTA
2189082 TATTAT-TTTTATTA
1 TATTATATTTTATTA
2189096 ATAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 14 0.56
15 9 0.36
16 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TATTATATTTTATTA
Found at i:2189118 original size:10 final size:10
Alignment explanation
Indices: 2189103--2189144 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2189093 TTAATAAAAA
2189103 TTTTATATAT
1 TTTTATATAT
*
2189113 TTTTATATAAA
1 TTTTATAT-AT
2189124 TTTTA-ATAT
1 TTTTATATAT
*
2189133 ATTTATATAT
1 TTTTATATAT
2189143 TT
1 TT
2189145 AAATTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 5 0.19
10 15 0.58
11 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTATATAT
Found at i:2189135 original size:22 final size:21
Alignment explanation
Indices: 2189100--2189142 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2189090 TTATTAATAA
*
2189100 AAATTTTATATATTTTTATAT
1 AAATTTTATATATTTATATAT
2189121 AAATTTTAATATATTTATATAT
1 AAATTTT-ATATATTTATATAT
2189143 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTTTATATATTTATATAT
Found at i:2189137 original size:20 final size:21
Alignment explanation
Indices: 2189065--2189141 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
2189055 TATATTTGTA
* *
2189065 TTATATATA-TTATAT-TATA
1 TTATATATATTTATATAAATT
* * * *
2189084 TTATTTTTATTAATAAAAATT
1 TTATATATATTTATATAAATT
*
2189105 TTATATATTTTTATATAAATT
1 TTATATATATTTATATAAATT
2189126 TTA-ATATATTTATATA
1 TTATATATATTTATATA
2189142 TTTAAATTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 7 0.16
20 16 0.36
21 21 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATATATTTATATAAATT
Found at i:2191004 original size:13 final size:13
Alignment explanation
Indices: 2190988--2191012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2190978 ATGGCACTTG
2190988 GTCCATCATATTA
1 GTCCATCATATTA
2191001 GTCCATCATATT
1 GTCCATCATATT
2191013 GAATTAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (13 bp):
GTCCATCATATTA
Found at i:2195668 original size:2 final size:2
Alignment explanation
Indices: 2195661--2195692 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2195651 TTTCCCAAAA
*
2195661 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2195693 AGAAGCTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2196149 original size:32 final size:33
Alignment explanation
Indices: 2196087--2196176 Score: 92
Period size: 32 Copynumber: 2.7 Consensus size: 33
2196077 TTTATATTAT
* * *
2196087 AAATATTTAAAATATTATATATTTATATAAATTTTA
1 AAATA-TTAATATATT-TATA-TTAGATAAAATTTA
* *
2196123 ATATATTAATA-ATTTTTATTAGATAAAATTTA
1 AAATATTAATATATTTATATTAGATAAAATTTA
*
2196155 AAATATTTATATATTTATATTA
1 AAATATTAATATATTTATATTA
2196177 TATTATTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
32 21 0.47
33 12 0.27
34 3 0.07
35 5 0.11
36 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
AAATATTAATATATTTATATTAGATAAAATTTA
Found at i:2196313 original size:28 final size:27
Alignment explanation
Indices: 2196282--2196335 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
2196272 CATTCGGTTC
*
2196282 AAATTATTTAATTTTAAATTT-TTTATTT
1 AAATAATTTAA-TTT-AATTTATTTATTT
2196310 AAATAATTTAATTTAATTTATTTATT
1 AAATAATTTAATTTAATTTATTTATT
2196336 CACTTGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 9 0.38
28 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
AAATAATTTAATTTAATTTATTTATTT
Found at i:2196945 original size:11 final size:11
Alignment explanation
Indices: 2196878--2196947 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 11
2196868 ATAATCAAAT
*
2196878 TTTAAATTAAA
1 TTTAATTTAAA
2196889 -TTAATTTAAA
1 TTTAATTTAAA
* *
2196899 -TAAATATAAA
1 TTTAATTTAAA
2196909 TATT-A-TTAATA
1 T-TTAATTTAA-A
*
2196920 TTTTATTTAAA
1 TTTAATTTAAA
2196931 TTTAATTTAAA
1 TTTAATTTAAA
2196942 TTTAAT
1 TTTAAT
2196948 ATAATTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
10 22 0.46
11 21 0.44
12 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:2197351 original size:20 final size:19
Alignment explanation
Indices: 2197312--2197352 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2197302 TGTTATATTT
*
2197312 TTAAAATTAAAATTTTTAA
1 TTAAAATTAAAATTTATAA
*
2197331 TTAAATTTAATAATTTATAA
1 TTAAAATTAA-AATTTATAA
2197351 TT
1 TT
2197353 GTATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATTAAAATTTATAA
Found at i:2197420 original size:17 final size:16
Alignment explanation
Indices: 2197396--2197430 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2197386 AATATATATA
2197396 ATATAAATTATTAAAT
1 ATATAAATTATTAAAT
*
2197412 ATATCAAATTTTTAAAT
1 ATAT-AAATTATTAAAT
2197429 AT
1 AT
2197431 GAATATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATAAATTATTAAAT
Found at i:2199273 original size:12 final size:13
Alignment explanation
Indices: 2199251--2199279 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2199241 ATTATGTTAT
2199251 ATTTTTAAATTAA
1 ATTTTTAAATTAA
2199264 ATTTTT-AATTAA
1 ATTTTTAAATTAA
2199276 ATTT
1 ATTT
2199280 AATAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTAAATTAA
Found at i:2201207 original size:12 final size:12
Alignment explanation
Indices: 2201190--2201214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2201180 CTATCGTATA
2201190 TAAAAAATATTT
1 TAAAAAATATTT
2201202 TAAAAAATATTT
1 TAAAAAATATTT
2201214 T
1 T
2201215 TTTTATTTCT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:2201548 original size:5 final size:5
Alignment explanation
Indices: 2201534--2201573 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
2201524 CAAAAGAAAG
2201534 AAAA- AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAA
2201574 GCAGCAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
7 5 0.15
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:2201551 original size:12 final size:12
Alignment explanation
Indices: 2201543--2201568 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2201533 GAAAAAAAAT
2201543 AAAATAAAATAA
1 AAAATAAAATAA
2201555 AAAATAAAATAA
1 AAAATAAAATAA
2201567 AA
1 AA
2201569 TAAAAGCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:2201558 original size:17 final size:17
Alignment explanation
Indices: 2201536--2201573 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2201526 AAAGAAAGAA
2201536 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
2201553 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
2201570 AAAA
1 AAAA
2201574 GCAGCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAAATAAAATAAAAT
Found at i:2202270 original size:90 final size:89
Alignment explanation
Indices: 2202174--2202350 Score: 248
Period size: 90 Copynumber: 2.0 Consensus size: 89
2202164 ACTCGTATCT
* * ** * * *
2202174 AACACTTATGTTCGACACATATTCGGATACAAGTATGTAAGTATAATC-CTCTAATATTAAAAAA
1 AACACTTATATCCGACACATATTCCAATACAAATACGTAAGTATAATCTCTCAAATATT-AAAAA
2202238 AAAAACCTTCAAAAAAATCAAACACC
65 AAAAA-CTTCAAAAAAATCAAACACC
* *
2202264 AACACTTATATCCGACACATATTCCAATACAAATACGTGAGTATAATCTTTCAAATATTAAAAAA
1 AACACTTATATCCGACACATATTCCAATACAAATACGTAAGTATAATCTCTCAAATATTAAAAAA
2202329 AAAACTTCAAAAAAATCAAACA
66 AAAACTTCAAAAAAATCAAACA
2202351 TACACGTATC
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
89 18 0.23
90 51 0.66
91 8 0.10
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (89 bp):
AACACTTATATCCGACACATATTCCAATACAAATACGTAAGTATAATCTCTCAAATATTAAAAAA
AAAACTTCAAAAAAATCAAACACC
Found at i:2208330 original size:2 final size:2
Alignment explanation
Indices: 2208323--2208347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2208313 CAACTTTATT
2208323 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2208348 TTTTAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2208615 original size:20 final size:18
Alignment explanation
Indices: 2208555--2208616 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 18
2208545 TTGTGTAGGC
*
2208555 TTTAAATTT-TTTAATTT
1 TTTAATTTTATTTAATTT
*
2208572 TTTAATTTTGATTTAAATAT
1 TTTAATTTT-ATTT-AATTT
2208592 TTTAATTTTATTTAGATTT
1 TTTAATTTTATTTA-ATTT
2208611 ATTTAA
1 -TTTAA
2208617 ATATCTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.22
18 1 0.03
19 10 0.27
20 18 0.49
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTAATTTTATTTAATTT
Found at i:2208656 original size:30 final size:30
Alignment explanation
Indices: 2208622--2208688 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
2208612 TTTAAATATC
***
2208622 TATTTTAGGATTTAAATTTTTTTAAAAAA-A
1 TATTTTAGGA-TTAAATTTAAATAAAAAATA
*
2208652 TATTTTTATGATTAAATTTAAATAAAAAATA
1 TA-TTTTAGGATTAAATTTAAATAAAAAATA
2208683 TATTTT
1 TATTTT
2208689 TATTAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
TATTTTAGGATTAAATTTAAATAAAAAATA
Found at i:2209315 original size:11 final size:10
Alignment explanation
Indices: 2209293--2209385 Score: 59
Period size: 10 Copynumber: 9.1 Consensus size: 10
2209283 TCATTTAAAA
2209293 TTTAAATTAT
1 TTTAAATTAT
2209303 TTTAAATTTAT
1 TTTAAA-TTAT
*
2209314 TTTTAATTAATT
1 TTTAAATT-A-T
2209326 ATTTAAATTAT
1 -TTTAAATTAT
2209337 TTTAAA--A-
1 TTTAAATTAT
* *
2209344 TTAAATATTTT
1 TTTAA-ATTAT
*
2209355 TTTAATTTAT
1 TTTAAATTAT
*
2209365 ATT-AATTAAT
1 TTTAAATT-AT
2209375 TTTAAATTAT
1 TTTAAATTAT
2209385 T
1 T
2209386 AATTTTTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
9 3 0.05
10 26 0.41
11 19 0.30
12 2 0.03
13 7 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTAAATTAT
Found at i:2209374 original size:50 final size:49
Alignment explanation
Indices: 2209286--2209385 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 49
2209276 TGATGAATCA
*
2209286 TTTAAAATTTAAATTATTTTAAATTTATTTTTAATTAATTATTTAAATTAT
1 TTTAAAATTTAAATTATTTTAAATTTATTATTAATTAA-T-TTTAAATTAT
* *
2209337 TTTAAAA-TTAAATATTTTTTTAATTTA-TATTAATTAATTTTAAATTAT
1 TTTAAAATTTAAAT-TATTTTAAATTTATTATTAATTAATTTTAAATTAT
2209385 T
1 T
2209386 AATTTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
48 11 0.24
49 1 0.02
50 15 0.33
51 18 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (49 bp):
TTTAAAATTTAAATTATTTTAAATTTATTATTAATTAATTTTAAATTAT
Found at i:2209668 original size:16 final size:18
Alignment explanation
Indices: 2209641--2209674 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2209631 TTTTTAAAAT
2209641 AAAATTATAATAT-TAAA
1 AAAATTATAATATGTAAA
2209658 AAAATTA-AATATGTAAA
1 AAAATTATAATATGTAAA
2209675 CGGATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAATTATAATATGTAAA
Found at i:2215614 original size:25 final size:24
Alignment explanation
Indices: 2215572--2215621 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
2215562 ATTTTAATTT
2215572 TTAAAATTTTAAAAAATAAAAATA
1 TTAAAATTTTAAAAAATAAAAATA
* *
2215596 TTAAATTTATTAAAAAATAAATATA
1 TTAAAATT-TTAAAAAATAAAAATA
2215621 T
1 T
2215622 ATATCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAATTTTAAAAAATAAAAATA
Found at i:2215912 original size:19 final size:18
Alignment explanation
Indices: 2215888--2215929 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
2215878 TATAAATACG
2215888 AATATAATAAAAATTATTA
1 AATATAATAAAAATT-TTA
*
2215907 AATAT-ATTAAAATTTTA
1 AATATAATAAAAATTTTA
2215924 AATATA
1 AATATA
2215930 GTTATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATAAAAATTTTA
Found at i:2216831 original size:10 final size:10
Alignment explanation
Indices: 2216812--2216854 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
2216802 TGAAGTAATA
2216812 ATTTTAAATT
1 ATTTTAAATT
*
2216822 ATTTTTAATT
1 ATTTTAAATT
2216832 CAAATTTTAAATT
1 ---ATTTTAAATT
2216845 ATTTTAAATT
1 ATTTTAAATT
2216855 CGAATAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:2216837 original size:23 final size:23
Alignment explanation
Indices: 2216811--2216855 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2216801 TTGAAGTAAT
*
2216811 AATTTTAAATTATTTTTAATTCA
1 AATTTTAAATTATTTTAAATTCA
2216834 AATTTTAAATTATTTTAAATTC
1 AATTTTAAATTATTTTAAATTC
2216856 GAATAGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
AATTTTAAATTATTTTAAATTCA
Found at i:2217161 original size:13 final size:13
Alignment explanation
Indices: 2217130--2217164 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2217120 CACTAATAGT
2217130 TATATATTTTTAAA
1 TATAT-TTTTTAAA
2217144 T-TATTTTTTAAA
1 TATATTTTTTAAA
2217156 TATATTTTT
1 TATATTTTT
2217165 ATTAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.45
13 10 0.50
14 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATATTTTTTAAA
Found at i:2217165 original size:12 final size:12
Alignment explanation
Indices: 2217131--2217165 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2217121 ACTAATAGTT
2217131 ATATATTTTTAA
1 ATATATTTTTAA
2217143 AT-TATTTTTTAA
1 ATATA-TTTTTAA
2217155 ATATATTTTTA
1 ATATATTTTTA
2217166 TTAATCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATATTTTTAA
Done.