Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 17 of 25
Found at i:2392710 original size:43 final size:44
Alignment explanation
Indices: 2392663--2392760 Score: 105
Period size: 43 Copynumber: 2.3 Consensus size: 44
2392653 ATTTATTTTA
* * *
2392663 TATTTTA-TATAATTTTTTTATAATTAA-TTT-TTAATTTTAAATT
1 TATTTTATTA-AATATTTTTA-AATAAATTTTATTAATTATAAATT
*
2392706 TA-TTTATTAAATATTTTTAAATAAATTTTATTAATTATAATTT
1 TATTTTATTAAATATTTTTAAATAAATTTTATTAATTATAAATT
*
2392749 TATTTAATTAAA
1 TATTTTATTAAA
2392761 AAATTTATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
41 5 0.11
42 16 0.35
43 17 0.37
44 8 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (44 bp):
TATTTTATTAAATATTTTTAAATAAATTTTATTAATTATAAATT
Found at i:2392715 original size:19 final size:19
Alignment explanation
Indices: 2392678--2392715 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2392668 TATATAATTT
2392678 TTTTATAATTAATTTTTAA
1 TTTTATAATTAATTTTTAA
*
2392697 TTTTA-AATTTATTTATTAA
1 TTTTATAATTAATTT-TTAA
2392716 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATAATTAATTTTTAA
Found at i:2393895 original size:21 final size:21
Alignment explanation
Indices: 2393869--2393909 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2393859 ATATTAAAAA
2393869 ATATTTTA-TATTAATATTTAT
1 ATATTTTATTATTAA-ATTTAT
2393890 ATATTTTATTATTAAATTTA
1 ATATTTTATTATTAAATTTA
2393910 AATAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATTATTAAATTTAT
Found at i:2394167 original size:17 final size:16
Alignment explanation
Indices: 2394132--2394228 Score: 55
Period size: 16 Copynumber: 6.2 Consensus size: 16
2394122 ATGCTCATGT
* *
2394132 TTTAT-TTATATTATT
1 TTTATATTATAATATA
2394147 TTTATATTATAATCATA
1 TTTATATTATAAT-ATA
* * *
2394164 TTTAAAATATTATATA
1 TTTATATTATAATATA
2394180 TTT-TATTAT-ATAT-
1 TTTATATTATAATATA
*
2394193 TTTGACA-TATTAATA-A
1 TTT-ATATTA-TAATATA
2394209 TTTATATTAT-ATATAA
1 TTTATATTATAATAT-A
2394225 TTTA
1 TTTA
2394229 ATATATTTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.05
14 9 0.14
15 14 0.22
16 25 0.40
17 12 0.19
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTATATTATAATATA
Found at i:2394188 original size:12 final size:12
Alignment explanation
Indices: 2394171--2394195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2394161 ATATTTAAAA
2394171 TATTATATATTT
1 TATTATATATTT
2394183 TATTATATATTT
1 TATTATATATTT
2394195 T
1 T
2394196 GACATATTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTATATATTT
Found at i:2394192 original size:28 final size:29
Alignment explanation
Indices: 2394161--2394222 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
2394151 TATTATAATC
2394161 ATATTTAAAATATT-ATATATTT-TATTAT
1 ATATTTAAAATATTAATA-ATTTATATTAT
* *
2394189 ATATTTTGACATATTAATAATTTATATTAT
1 ATA-TTTAAAATATTAATAATTTATATTAT
2394219 ATAT
1 ATAT
2394223 AATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 3 0.10
29 14 0.48
30 12 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
ATATTTAAAATATTAATAATTTATATTAT
Found at i:2396134 original size:22 final size:23
Alignment explanation
Indices: 2396101--2396148 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2396091 CTAAAAACTC
* * *
2396101 TTAAAAATAATTTTTTATATTTT
1 TTAAAAATAATTATTAATAATTT
2396124 TTAAAAA-AATTATTAATAATTT
1 TTAAAAATAATTATTAATAATTT
2396146 TTA
1 TTA
2396149 TCTTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAAAATAATTATTAATAATTT
Found at i:2396309 original size:2 final size:2
Alignment explanation
Indices: 2396302--2396346 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2396292 CCCAAAAGTC
2396302 TA TA TA TA TA TA 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 TA TA TA
2396344 TA T
1 TA T
2396347 TCTTAAATAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2397269 original size:20 final size:19
Alignment explanation
Indices: 2397206--2397294 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 19
2397196 AAATTAATAA
* *
2397206 ATTAATTACATAAAACATT
1 ATTAATTATATAAAATATT
2397225 ATTAATTACT-TATAAATATT
1 ATTAATTA-TATA-AAATATT
2397245 ATTAATTATATAAAATATT
1 ATTAATTATATAAAATATT
2397264 A-T--TTA-ATAAAATATT
1 ATTAATTATATAAAATATT
* *
2397279 ATAAAATTACATAAAA
1 AT-TAATTATATAAAA
2397295 ATAATTATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
15 11 0.19
16 3 0.05
18 1 0.02
19 22 0.37
20 22 0.37
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTAATTATATAAAATATT
Found at i:2397274 original size:15 final size:16
Alignment explanation
Indices: 2397244--2397280 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2397234 TTATAAATAT
*
2397244 TATTAATTATATAAAA
1 TATTATTTATATAAAA
2397260 TATTATTTA-ATAAAA
1 TATTATTTATATAAAA
2397275 TATTAT
1 TATTAT
2397281 AAAATTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTATTTATATAAAA
Found at i:2398017 original size:2 final size:2
Alignment explanation
Indices: 2398012--2398038 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2398002 TATAACATAA
2398012 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 A
2398039 GATACTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2401496 original size:126 final size:126
Alignment explanation
Indices: 2401322--2401558 Score: 413
Period size: 126 Copynumber: 1.9 Consensus size: 126
2401312 TTGATAATGA
* *
2401322 TTTTTAAAAAAAAAAAAAAGAAAGAGTGAACAATGGTATGTCCCTACCAAGTAAGTCCAAACTGG
1 TTTTGAAAAAAAAAAAAAAGAAAGAGTGAACAATGGTATATCCCTACCAAGTAAGTCCAAACTGG
2401387 CCAATTTCCCATGTCGGATATCCGACTCCAAAGTAGCCTAGCCTATTGCTTATTCTTTTTC
66 CCAATTTCCCATGTCGGATATCCGACTCCAAAGTAGCCTAGCCTATTGCTTATTCTTTTTC
* *
2401448 TTTTGAAAAATAAAAAGAAAGAAAGAGTGAGCAA-GGTATATCCCTACCAAGTAAGTCCAAACTG
1 TTTTGAAAAA-AAAAAAAAAGAAAGAGTGAACAATGGTATATCCCTACCAAGTAAGTCCAAACTG
*
2401512 GCCAATTTTCCATGTCGGATATCCGACTCCAAAGTAGCCTAGCCTAT
65 GCCAATTTCCCATGTCGGATATCCGACTCCAAAGTAGCCTAGCCTAT
2401559 GCTGAAAGTC
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
126 84 0.80
127 21 0.20
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (126 bp):
TTTTGAAAAAAAAAAAAAAGAAAGAGTGAACAATGGTATATCCCTACCAAGTAAGTCCAAACTGG
CCAATTTCCCATGTCGGATATCCGACTCCAAAGTAGCCTAGCCTATTGCTTATTCTTTTTC
Found at i:2401907 original size:18 final size:18
Alignment explanation
Indices: 2401884--2401918 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2401874 GATATCTTGA
*
2401884 TAAAATAATTATAAATTT
1 TAAAATAATTAAAAATTT
*
2401902 TAAAATTATTAAAAATT
1 TAAAATAATTAAAAATT
2401919 ATAATTACAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATAATTAAAAATTT
Found at i:2402590 original size:20 final size:20
Alignment explanation
Indices: 2402558--2402612 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
2402548 ATGATTTAGT
*
2402558 AATTTTGTAAAAAAATATTA
1 AATTTTTTAAAAAAATATTA
* *
2402578 AGTTTTTTTAAAAAAATGTTA
1 A-ATTTTTTAAAAAAATATTA
2402599 AATTTTTTAAAAAA
1 AATTTTTTAAAAAA
2402613 TACTAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AATTTTTTAAAAAAATATTA
Found at i:2402782 original size:24 final size:23
Alignment explanation
Indices: 2402729--2402788 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
2402719 TAATAAATAA
*
2402729 AATACTTAATTTTTTTAATTAATT
1 AATA-TTAATTTATTTAATTAATT
2402753 AA-ATTAATATTATTTAATTTAA-T
1 AATATTAAT-TTATTTAA-TTAATT
2402776 AATATTAAATTTA
1 AATATT-AATTTA
2402789 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 12 0.39
25 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATTAATTTATTTAATTAATT
Found at i:2402792 original size:15 final size:15
Alignment explanation
Indices: 2402750--2402792 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2402740 TTTTTAATTA
*
2402750 ATTAAA-TTAATATT
1 ATTAAATTTAATAAT
*
2402764 ATTTAATTTAATAAT
1 ATTAAATTTAATAAT
2402779 ATTAAATTTAATAA
1 ATTAAATTTAATAA
2402793 AAAATTTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATTTAATAAT
Found at i:2403671 original size:3 final size:3
Alignment explanation
Indices: 2403663--2403692 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2403653 ATCGATGGCC
2403663 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2403693 GCCTTGGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2404924 original size:17 final size:17
Alignment explanation
Indices: 2404886--2404924 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2404876 TAAAATTAAT
*
2404886 AAATATATTAATATATA
1 AAATTTATTAATATATA
2404903 AAATTTATTCAATAT-TA
1 AAATTTATT-AATATATA
2404920 AAATT
1 AAATT
2404925 AGATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATTAATATATA
Found at i:2406850 original size:18 final size:19
Alignment explanation
Indices: 2406819--2406857 Score: 55
Period size: 17 Copynumber: 2.1 Consensus size: 19
2406809 AAAGTTAACA
2406819 ATATATTTATATAAATTTTT
1 ATATATTTATAT-AATTTTT
2406839 ATATA-TTA-ATAATTTTT
1 ATATATTTATATAATTTTT
2406856 AT
1 AT
2406858 TAAATAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 2 0.11
19 3 0.16
20 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATATTTATATAATTTTT
Found at i:2414809 original size:2 final size:2
Alignment explanation
Indices: 2414802--2414826 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2414792 ATATCAAGAT
2414802 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
2414827 CATCATTTGA
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:2415522 original size:15 final size:15
Alignment explanation
Indices: 2415502--2415530 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2415492 ATGGTGGATA
2415502 TAATGAATATTATTG
1 TAATGAATATTATTG
2415517 TAATGAATATTATT
1 TAATGAATATTATT
2415531 CGTACATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TAATGAATATTATTG
Found at i:2418380 original size:24 final size:24
Alignment explanation
Indices: 2418353--2418398 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2418343 TGGGTTTTAT
*
2418353 AGAGATAAACTTGGAGAGAGAGTA
1 AGAGATAAACTTGGAGAAAGAGTA
* *
2418377 AGAGATGAAGTTGGAGAAAGAG
1 AGAGATAAACTTGGAGAAAGAG
2418399 AGTGAAGTAG
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:0.02, G:0.37, T:0.15
Consensus pattern (24 bp):
AGAGATAAACTTGGAGAAAGAGTA
Found at i:2418702 original size:25 final size:25
Alignment explanation
Indices: 2418610--2418687 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
2418600 AACATATTTA
* *
2418610 TAAATATTATTTTGTAAATTATACTTT
1 TAAATATTATTTT-TAAA-TATAATTC
*
2418637 TAAA-ATTATTATTTCTAATATAATTC
1 TAAATATTATT-TTT-AAATATAATTC
2418663 TAAATATTATTTTTAAATATAATTC
1 TAAATATTATTTTTAAATATAATTC
2418688 ATTAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 10 0.23
26 20 0.45
27 14 0.32
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAATATTATTTTTAAATATAATTC
Found at i:2418707 original size:25 final size:25
Alignment explanation
Indices: 2418610--2418707 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 25
2418600 AACATATTTA
* *
2418610 TAAATATTATTTTGTAAATTATACTT-T
1 TAAA-ATTATTTT-TATA-TATAATTCT
*
2418637 TAAAATTATTATTTCTAATATAATTC-
1 TAAAATTATT-TTTAT-ATATAATTCT
*
2418663 TAAATATTATTTTTAAATATAATTCAT
1 TAAA-ATTATTTTTATATATAATTC-T
2418690 TAAAA-TATTTTTATATAT
1 TAAAATTATTTTTATATAT
2418708 TCATTTTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
25 21 0.36
26 21 0.36
27 17 0.29
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAAATTATTTTTATATATAATTCT
Found at i:2420923 original size:26 final size:25
Alignment explanation
Indices: 2420867--2420928 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
2420857 TAATTAGAAT
2420867 ACAATTATA-ATACGTACACTAACA
1 ACAATTATATATACGTACACTAACA
* * *
2420891 AGAAATTATATGTACGTACACTAATGA
1 A-CAATTATATATACGTACACTAA-CA
2420918 ACAATTATATA
1 ACAATTATATA
2420929 AAGGCATGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 1 0.03
25 7 0.23
26 20 0.67
27 2 0.07
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (25 bp):
ACAATTATATATACGTACACTAACA
Found at i:2421126 original size:21 final size:23
Alignment explanation
Indices: 2421084--2421133 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2421074 TCTTAAAAAC
* *
2421084 AAAATATTATGAAAAATAATAAT
1 AAAATATTATAAAAAATAATAAA
2421107 AAAAT-TTATAAAAAAT-ATAAA
1 AAAATATTATAAAAAATAATAAA
2421128 AAAATA
1 AAAATA
2421134 CCTTTAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATATTATAAAAAATAATAAA
Found at i:2426432 original size:27 final size:27
Alignment explanation
Indices: 2426402--2426464 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
2426392 TTTATTTATA
*
2426402 AAAAATGGTGGTTACTTTGTGTTTGTC
1 AAAAATGGTGGTTACTTTGTATTTGTC
* *
2426429 AAAAATGGTGGTTTCTTTTTATTTGTC
1 AAAAATGGTGGTTACTTTGTATTTGTC
2426456 AAAAATGGT
1 AAAAATGGT
2426465 AGCATGTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.44
Consensus pattern (27 bp):
AAAAATGGTGGTTACTTTGTATTTGTC
Found at i:2428014 original size:136 final size:136
Alignment explanation
Indices: 2427801--2428075 Score: 541
Period size: 136 Copynumber: 2.0 Consensus size: 136
2427791 TTATTTGGAT
*
2427801 CAATCTTTAACACCCCGAGGCATTCATAGTAGGTAAAGGATCAGAGATATGTGGGGACGCCCAAT
1 CAATCTTTAACACCCCGAGGCATTCATAGTAGGTAAAGGATCAGAGATATGTGGGGACGCCCAAC
2427866 GAAAATGAACTTTCAGATTATTGGAGCTTTTTGGCAAATGCAAATCTATTTCCCATCACCCTTCG
66 GAAAATGAACTTTCAGATTATTGGAGCTTTTTGGCAAATGCAAATCTATTTCCCATCACCCTTCG
2427931 TGGGGG
131 TGGGGG
2427937 CAATCTTTAACACCCCGAGGCATTCATAGTAGGTAAAGGATCAGAGATATGTGGGGACGCCCAAC
1 CAATCTTTAACACCCCGAGGCATTCATAGTAGGTAAAGGATCAGAGATATGTGGGGACGCCCAAC
2428002 GAAAATGAACTTTCAGATTATTGGAGCTTTTTGGCAAATGCAAATCTATTTCCCATCACCCTTCG
66 GAAAATGAACTTTCAGATTATTGGAGCTTTTTGGCAAATGCAAATCTATTTCCCATCACCCTTCG
2428067 TGGGGG
131 TGGGGG
2428073 CAA
1 CAA
2428076 GGTGTTCAGA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 138 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (136 bp):
CAATCTTTAACACCCCGAGGCATTCATAGTAGGTAAAGGATCAGAGATATGTGGGGACGCCCAAC
GAAAATGAACTTTCAGATTATTGGAGCTTTTTGGCAAATGCAAATCTATTTCCCATCACCCTTCG
TGGGGG
Found at i:2429981 original size:13 final size:13
Alignment explanation
Indices: 2429963--2429988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2429953 CAATTTTTTG
2429963 TGTATCGATACAT
1 TGTATCGATACAT
2429976 TGTATCGATACAT
1 TGTATCGATACAT
2429989 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2430728 original size:21 final size:21
Alignment explanation
Indices: 2430687--2430730 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2430677 CTCCCCTTTA
* *
2430687 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
2430708 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
2430729 TC
1 TC
2430731 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:2432556 original size:13 final size:13
Alignment explanation
Indices: 2432538--2432576 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2432528 ATAATCACCC
2432538 TGTATCGATACAA
1 TGTATCGATACAA
2432551 TGTATCGATACAA
1 TGTATCGATACAA
2432564 TGTATCGATACAA
1 TGTATCGATACAA
2432577 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2434643 original size:15 final size:15
Alignment explanation
Indices: 2434623--2434652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2434613 ATTTCGTTTG
*
2434623 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2434638 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2434653 AGACATTTTT
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:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2436486 original size:21 final size:21
Alignment explanation
Indices: 2436457--2436501 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2436447 AAGTTTTCAT
*
2436457 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2436477 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2436499 TTT
1 TTT
2436502 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2438734 original size:13 final size:13
Alignment explanation
Indices: 2438716--2438741 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2438706 CAATTTTTTG
2438716 TGTATCGATACAT
1 TGTATCGATACAT
2438729 TGTATCGATACAT
1 TGTATCGATACAT
2438742 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2445379 original size:15 final size:16
Alignment explanation
Indices: 2445359--2445393 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2445349 AAGGCAAGAA
2445359 AAAAAATAAA-AAATG
1 AAAAAATAAAGAAATG
2445374 AAAAAATAAATGAAATG
1 AAAAAATAAA-GAAATG
2445391 AAA
1 AAA
2445394 GATATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAGAAATG
Found at i:2446666 original size:6 final size:5
Alignment explanation
Indices: 2446644--2446702 Score: 59
Period size: 5 Copynumber: 11.6 Consensus size: 5
2446634 TTTTTCTATT
* *
2446644 AAAATG AAAAG AAAAG AATAAG AGAAG AAAAG AAAA- AAAAG GAAA- AAAAG
1 AAAA-G AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
2446694 AAAAAG AAA
1 -AAAAG AAA
2446703 GAGGGAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
4 7 0.16
5 25 0.56
6 13 0.29
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:2446688 original size:10 final size:9
Alignment explanation
Indices: 2446650--2446704 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
2446640 TATTAAAATG
2446650 AAAAGAAAA
1 AAAAGAAAA
*
2446659 GAATAAGAGAAG
1 -AA-AAGA-AAA
2446671 AAAAGAAAA
1 AAAAGAAAA
*
2446680 AAAAGGAAA
1 AAAAGAAAA
2446689 AAAAGAAAA
1 AAAAGAAAA
2446698 AGAAAGA
1 A-AAAGA
2446705 GGGAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 19 0.50
10 11 0.29
11 6 0.16
12 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:2446713 original size:21 final size:19
Alignment explanation
Indices: 2446650--2446713 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
2446640 TATTAAAATG
*
2446650 AAAAGAAAAGAATAAGAGAA
1 AAAAGAAAAGAA-AAGGGAA
*
2446670 GAAAAGAAAA-AAAAGGAAA
1 -AAAAGAAAAGAAAAGGGAA
2446689 AAAAGAAAAAGAAAGAGGGAA
1 AAAAG-AAAAGAAA-AGGGAA
2446710 AAAA
1 AAAA
2446714 TTGAGTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.14
19 9 0.24
20 5 0.14
21 18 0.49
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAGAAAAGGGAA
Found at i:2447263 original size:20 final size:20
Alignment explanation
Indices: 2447210--2447339 Score: 68
Period size: 20 Copynumber: 6.2 Consensus size: 20
2447200 ATTCAACATC
*
2447210 AATTTTAAATATTTTTTAGATAT
1 AATTTT-AA-ATTTTTTA-ATAA
2447233 AATGTTT-AATTTTTTAATAA
1 AAT-TTTAAATTTTTTAATAA
**
2447253 AATTTTAAATTTAAT-ATAA
1 AATTTTAAATTTTTTAATAA
* * * * * *
2447272 TATATT-AATTATTCAACATC
1 AATTTTAAATTTTTTAATA-A
*
2447292 AATTTTAAATATTTTTTGAATAT
1 AATTTT-AA-ATTTTTT-AATAA
*
2447315 AATTTTTAATTTTTTAATAA
1 AATTTTAAATTTTTTAATAA
2447335 AATTT
1 AATTT
2447340 AAAGAATTAA
Statistics
Matches: 80, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
18 4 0.05
19 13 0.16
20 25 0.31
21 15 0.19
22 3 0.04
23 14 0.17
24 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTTTAAATTTTTTAATAA
Found at i:2447286 original size:82 final size:83
Alignment explanation
Indices: 2447174--2447339 Score: 291
Period size: 82 Copynumber: 2.0 Consensus size: 83
2447164 ATATCATTCA
2447174 TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTT-AGATATAATGT
1 TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTTGA-ATATAATGT
2447238 TTAATTTTTTAATAAAATT
65 TTAATTTTTTAATAAAATT
* *
2447257 TTAAATTTAATATAAT-ATATTAATTATTCAACATCAATTTTAAATATTTTTTGAATATAATTTT
1 TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTTGAATATAATGTT
2447321 TAATTTTTTAATAAAATT
66 TAATTTTTTAATAAAATT
2447339 T
1 T
2447340 AAAGAATTAA
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
82 63 0.79
83 17 0.21
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (83 bp):
TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTTGAATATAATGTT
TAATTTTTTAATAAAATT
Found at i:2447387 original size:29 final size:29
Alignment explanation
Indices: 2447330--2447387 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
2447320 TTAATTTTTT
* *
2447330 AATAAAATTTAAAGAATTAAATTATTTAA
1 AATAAAATTTAAAGAATTAAACTAATTAA
2447359 AATAAAATATT-AA-AATTATAACTAATTAA
1 AATAAAAT-TTAAAGAATTA-AACTAATTAA
2447388 TATTATCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.20
29 18 0.72
30 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
AATAAAATTTAAAGAATTAAACTAATTAA
Found at i:2447548 original size:15 final size:15
Alignment explanation
Indices: 2447528--2447558 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2447518 TAATTTTATA
2447528 TAAATTATATTATCT
1 TAAATTATATTATCT
2447543 TAAATTATATTATCT
1 TAAATTATATTATCT
2447558 T
1 T
2447559 TCATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATTATATTATCT
Found at i:2451052 original size:19 final size:19
Alignment explanation
Indices: 2451028--2451067 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2451018 TTGTTCTCTT
*
2451028 ATCGCAAATCAGATCATTG
1 ATCGCAAATCAGATAATTG
2451047 ATCGCAAATCAGATAATTG
1 ATCGCAAATCAGATAATTG
2451066 AT
1 AT
2451068 TTACTGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (19 bp):
ATCGCAAATCAGATAATTG
Found at i:2452697 original size:21 final size:21
Alignment explanation
Indices: 2452672--2452725 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2452662 TTCAATAATT
*
2452672 TGTATCGATACAAT-AGGGTAA
1 TGTATCGATACAATAAGTG-AA
2452693 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
2452713 TATATCGATACAA
1 TGTATCGATACAA
2452726 GTCTGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:2452860 original size:52 final size:52
Alignment explanation
Indices: 2452781--2452917 Score: 220
Period size: 52 Copynumber: 2.6 Consensus size: 52
2452771 TCTGGAATGA
** *
2452781 AAATGTATTGATGCATTCTTCATTGTATCGATACATTCTAGGTTTTTGACCC
1 AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACCC
*
2452833 AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACTC
1 AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACCC
* *
2452885 AAATGTATAAATACATTCATCAATGTATCGATA
1 AAATGTATAAATGCATTCTTCAATGTATCGATA
2452918 TATGCAAGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (52 bp):
AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACCC
Found at i:2458591 original size:78 final size:78
Alignment explanation
Indices: 2458498--2458904 Score: 326
Period size: 79 Copynumber: 5.2 Consensus size: 78
2458488 AAATTTAATA
* * * * * *
2458498 TTTTAGAGATAAAAATGAAGTTGGAGTATCCCCTCGAAAATATCAGGGTTGGAATATCTTCTATG
1 TTTTAGAAAT-AAAATGAAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATG
2458563 AT-AGAAAATCGGTG
65 ATGA-AAAATCGGTG
* *** * *
2458577 TTTTAGAAATAAAATCAAGGTTGGAGTATCTTTTTGAAAATAACGGGGTTAGAGTAT-CTCCGAT
1 TTTTAGAAATAAAATGAA-GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCT-CGAT
**
2458641 -AGTGAAAAATCAATG
64 GA-TGAAAAATCGGTG
* * * * *
2458656 TTTTAGAAATAAAATCG-AGTTGGAGTATTCTCTC-AGAAATAACGAGGTTCGAGTATCCTCAAT
1 TTTTAGAAATAAAAT-GAAGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCTCGAT
* ** *
2458719 GGTGAAAAATTAGTA
64 GATGAAAAATCGGTG
* * * *
2458734 TTTTAGAAATAAAATCAGGGTTGGAGTATCCCTTCAAAAAT-ACTGGGGTTGGAGTATCCTCGAT
1 TTTTAGAAATAAAATGA-AGTTGGAGTATCCCCTCGAAAATAAC-GGGGTTGGAGTATCCTCGAT
* *
2458798 -AGTGAAAAATAGATG
64 GA-TGAAAAATCGGTG
** * * *
2458813 TTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTA-CCCCGATG
1 TTTTAGAAATAAAAT-GAAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATG
* * *
2458877 GTGGAAAATCGGTA
65 ATGAAAAATCGGTG
2458891 TTTTAGAAATAAAA
1 TTTTAGAAATAAAA
2458905 ACATTAATGA
Statistics
Matches: 261, Mismatches: 51, Indels: 33
0.76 0.15 0.10
Matches are distributed among these distances:
77 1 0.00
78 98 0.38
79 158 0.61
80 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (78 bp):
TTTTAGAAATAAAATGAAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGA
TGAAAAATCGGTG
Found at i:2458677 original size:157 final size:154
Alignment explanation
Indices: 2458484--2458904 Score: 447
Period size: 157 Copynumber: 2.7 Consensus size: 154
2458474 CATCTCTCGA
* * *
2458484 TGAAAAATTTAATATTTTAGAGATAAAAAT-GAAGTTGGAGTATCCCCTCGAAAATATCAGGGTT
1 TGAAAAA--TAATGTTTTAGAAAT-AAAATCG-AGTTGGAGTATCCCCTCGAAAATAAC-GGGTT
* * * * * ** **
2458548 GGAATATCTTCTATGATAGAAAATCGGTGTTTTAGAAATAAAATCAAGGTTGGAGTATCTTTTTG
61 GGAGTATCCTCAATGGT-GAAAATCGGTATTTTAGAAATAAAATCAAGGTTGGAGTATCCCTTCA
2458613 AAAATAAC-GGGGTTAGAGTAT-CTCCGATAG
125 AAAAT-ACTGGGGTTAGAGTATCCT-CGATAG
* * *
2458643 TGAAAAATCAATGTTTTAGAAATAAAATCGAGTTGGAGTATTCTCTC-AGAAATAACGAGGTTCG
1 TGAAAAAT-AATGTTTTAGAAATAAAATCGAGTTGGAGTATCCCCTCGA-AAATAACG-GGTTGG
** *
2458707 AGTATCCTCAATGGTGAAAAATTAGTATTTTAGAAATAAAATCAGGGTTGGAGTATCCCTTCAAA
63 AGTATCCTCAATGGTG-AAAATCGGTATTTTAGAAATAAAATCAAGGTTGGAGTATCCCTTCAAA
*
2458772 AATACTGGGGTTGGAGTATCCTCGATAG
127 AATACTGGGGTTAGAGTATCCTCGATAG
* * *
2458800 TGAAAAATAGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGG
1 TGAAAAATA-ATGTTTTAGAAATAAAATC-GAGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGG
* *
2458865 AGTA-CCCCGATGGTGGAAAATCGGTATTTTAGAAATAAAA
63 AGTATCCTCAATGGT-GAAAATCGGTATTTTAGAAATAAAA
2458905 ACATTAATGA
Statistics
Matches: 221, Mismatches: 29, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
156 6 0.03
157 161 0.73
158 46 0.21
159 8 0.04
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (154 bp):
TGAAAAATAATGTTTTAGAAATAAAATCGAGTTGGAGTATCCCCTCGAAAATAACGGGTTGGAGT
ATCCTCAATGGTGAAAATCGGTATTTTAGAAATAAAATCAAGGTTGGAGTATCCCTTCAAAAATA
CTGGGGTTAGAGTATCCTCGATAG
Found at i:2461290 original size:50 final size:49
Alignment explanation
Indices: 2461227--2461360 Score: 164
Period size: 48 Copynumber: 2.7 Consensus size: 49
2461217 AAAATATCTG
* * *
2461227 AATGCATCGATACATTGAGAAATGTATCGATACATTTAGGTAAAACCTAA
1 AATGTATCGATACAATGAGAAATGTATCGATACATTTAGGT-AAACCCAA
* * *
2461277 AATGTATCGATACAATGAGAAATGTATCGATA-ATCTGGGTAAACCCAG
1 AATGTATCGATACAATGAGAAATGTATCGATACATTTAGGTAAACCCAA
* *
2461325 AATGTATCAATATAATGA-AGAATGTATCGATACATT
1 AATGTATCGATACAATGAGA-AATGTATCGATACATT
2461361 CTGGGTTTAC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.01
48 34 0.47
49 8 0.11
50 30 0.41
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (49 bp):
AATGTATCGATACAATGAGAAATGTATCGATACATTTAGGTAAACCCAA
Found at i:2461390 original size:49 final size:49
Alignment explanation
Indices: 2461247--2461401 Score: 183
Period size: 49 Copynumber: 3.2 Consensus size: 49
2461237 TACATTGAGA
* * *
2461247 AATGTATCGATACATT-TAGGTAAAACCTAAAATGTATCGATACAATG-AG
1 AATGTATCGATACATTCTGGGT-AAACCT-AGATGTATCGATATAATGAAG
* *
2461296 AAATGTATCGATA-A-TCTGGGTAAACCCAGAATGTATCAATATAATGAAG
1 -AATGTATCGATACATTCTGGGTAAACCTAG-ATGTATCGATATAATGAAG
**
2461345 AATGTATCGATACATTCTGGGTTTACCTAGATGTATCGATATAATGAAG
1 AATGTATCGATACATTCTGGGTAAACCTAGATGTATCGATATAATGAAG
2461394 AATGTATC
1 AATGTATC
2461402 ATTACAAATT
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
47 1 0.01
48 32 0.35
49 34 0.37
50 24 0.26
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (49 bp):
AATGTATCGATACATTCTGGGTAAACCTAGATGTATCGATATAATGAAG
Found at i:2461927 original size:20 final size:20
Alignment explanation
Indices: 2461903--2461954 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2461893 GGAAGAATAA
* *
2461903 AAAAGAAAAAGAAA-GAGAG
1 AAAAGAAAAAAAAATGAAAG
2461922 AGAAAGAAAAAAAAATGAAAG
1 A-AAAGAAAAAAAAATGAAAG
2461943 AAAAGAAAAAAA
1 AAAAGAAAAAAA
2461955 TTTTGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 23 0.79
21 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAAAAATGAAAG
Found at i:2461943 original size:15 final size:16
Alignment explanation
Indices: 2461923--2461952 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2461913 GAAAGAGAGA
2461923 GAAAGAAAA-AAAAAT
1 GAAAGAAAAGAAAAAT
2461938 GAAAGAAAAGAAAAA
1 GAAAGAAAAGAAAAA
2461953 AATTTTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
GAAAGAAAAGAAAAAT
Found at i:2476897 original size:1 final size:1
Alignment explanation
Indices: 2476887--2476978 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
2476877 TGGCAATTGG
* * * ** * * * **
2476887 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAACAAAAAAAAGGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2476952 AAGAAAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2476979 GTGAAGATTT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:2476935 original size:33 final size:33
Alignment explanation
Indices: 2476888--2476977 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
2476878 GGCAATTGGA
2476888 AAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAGGAAAAAG
2476922 AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
2476955 -AAAAAAAAAA-AAAACAAAAAAAA
1 AAAAAAAAAAACAAAACAAAAAAAA
2476978 AGTGAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
31 13 0.23
32 10 0.18
33 29 0.52
34 4 0.07
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
Found at i:2485250 original size:30 final size:28
Alignment explanation
Indices: 2485211--2485295 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 28
2485201 ATTGATAATA
2485211 AAATTAATAAATTAAATATAATTATTTGT
1 AAATTAATAAATTAAATATAATTATTT-T
*
2485240 AAATTTAATAAATATTAAATAAAATT-TTTT
1 AAA-TTAAT-AA-ATTAAATATAATTATTTT
* *
2485270 ACAAATAA-ATATTAAATATAATTATT
1 A-AATTAATAAATTAAATATAATTATT
2485296 CATAATTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
27 12 0.26
28 3 0.06
29 3 0.06
30 10 0.21
31 7 0.15
32 12 0.26
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTAATAAATTAAATATAATTATTTT
Found at i:2487159 original size:14 final size:14
Alignment explanation
Indices: 2487140--2487169 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2487130 GTTTATTCAA
2487140 AATTTTATAATCAC
1 AATTTTATAATCAC
2487154 AATTTTATAATCAC
1 AATTTTATAATCAC
2487168 AA
1 AA
2487170 CTATGCGTGA
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:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTTTATAATCAC
Found at i:2490131 original size:13 final size:13
Alignment explanation
Indices: 2490113--2490139 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2490103 TACAAAAATG
2490113 TATCATATAGATA
1 TATCATATAGATA
2490126 TATCATATAGATA
1 TATCATATAGATA
2490139 T
1 T
2490140 GTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TATCATATAGATA
Found at i:2490192 original size:12 final size:12
Alignment explanation
Indices: 2490166--2490198 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2490156 ATATTTTATG
*
2490166 TATTT-AAAAAT
1 TATTTAAAAAAA
2490177 TATTTAAAAAAA
1 TATTTAAAAAAA
2490189 TATTTAAAAA
1 TATTTAAAAA
2490199 TTTATTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TATTTAAAAAAA
Found at i:2490204 original size:12 final size:11
Alignment explanation
Indices: 2490166--2490200 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2490156 ATATTTTATG
2490166 TATTTAAAAAT
1 TATTTAAAAAT
*
2490177 TATTTAAAAAAA
1 TATTT-AAAAAT
2490189 TATTTAAAAAT
1 TATTTAAAAAT
2490200 T
1 T
2490201 TATTAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:2491036 original size:17 final size:17
Alignment explanation
Indices: 2491016--2491048 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2491006 AATTTTTTTA
2491016 AAAGATAAAAAA-AAAGG
1 AAAGA-AAAAAAGAAAGG
2491033 AAAGAAAAAAAGAAAG
1 AAAGAAAAAAAGAAAG
2491049 AGATCTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAGAAAAAAAGAAAGG
Found at i:2492403 original size:14 final size:15
Alignment explanation
Indices: 2492377--2492405 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2492367 CTAGCAGAGA
2492377 AGCACATAATCTCAC
1 AGCACATAATCTCAC
2492392 AGCACA-AATCTCAC
1 AGCACATAATCTCAC
2492406 CATCTACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.34, G:0.07, T:0.17
Consensus pattern (15 bp):
AGCACATAATCTCAC
Found at i:2492474 original size:2 final size:2
Alignment explanation
Indices: 2492469--2492499 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2492459 TCTTTTTCAT
*
2492469 AC AC AC AC AC AC AC AC AC AC AC AC CC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2492500 TGTGTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2496421 original size:2 final size:2
Alignment explanation
Indices: 2496414--2496446 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2496404 TCAAAACGTC
*
2496414 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2496447 ACTCTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2498985 original size:28 final size:27
Alignment explanation
Indices: 2498927--2498995 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
2498917 CACCTATTTG
* **
2498927 TTTGTCAAAAATGGTGATTATTTTGTA
1 TTTGTCAAAAATGGTGATTACTTTAAA
* *
2498954 TTTGTCAAAAATGGTAGTTTCCTTTAAA
1 TTTGTCAAAAATGGT-GATTACTTTAAA
*
2498982 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
2498996 AAGCTTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGATTACTTTAAA
Found at i:2501599 original size:21 final size:22
Alignment explanation
Indices: 2501570--2501615 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2501560 TGTTCAGACA
** *
2501570 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2501592 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2501613 AGT
1 AGT
2501616 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2504836 original size:27 final size:27
Alignment explanation
Indices: 2504798--2504911 Score: 75
Period size: 27 Copynumber: 4.4 Consensus size: 27
2504788 ATCCTCCTCC
*
2504798 ATTTT-AC-AATAAAAATTAGCCATCA
1 ATTTTGACAAATAAAAATAAGCCATCA
2504823 ATTTTGACAAAT---AATAAGCCAT-A
1 ATTTTGACAAATAAAAATAAGCCATCA
* *
2504846 ATTTTTGACAAACAAAAAGGAA-CCATCA
1 A-TTTTGACAAATAAAAA-TAAGCCATCA
* * *
2504874 TTTTTGACAAATACAAAGTAA-CCA-CC
1 ATTTTGACAAATA-AAAATAAGCCATCA
2504900 ATTGTTGACAAA
1 ATT-TTGACAAA
2504912 CACAAAGGGT
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.03
24 19 0.27
25 5 0.07
26 5 0.07
27 33 0.47
28 6 0.09
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (27 bp):
ATTTTGACAAATAAAAATAAGCCATCA
Found at i:2504843 original size:24 final size:24
Alignment explanation
Indices: 2504815--2504891 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
2504805 AATAAAAATT
*
2504815 AGCCATCAATTTTGACAAATAATA
1 AGCCATCAATTTTGACAAATAAAA
*
2504839 AGCCAT-AATTTTTGACAAACAAAA
1 AGCCATCAA-TTTTGACAAATAAAA
* *
2504863 AGGAACCATCATTTTTGACAAATACAA
1 A-G--CCATCAATTTTGACAAATAAAA
2504890 AG
1 AG
2504892 TAACCACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.05
24 20 0.47
25 1 0.02
26 1 0.02
27 18 0.42
28 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (24 bp):
AGCCATCAATTTTGACAAATAAAA
Found at i:2504916 original size:27 final size:27
Alignment explanation
Indices: 2504850--2504919 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
2504840 GCCATAATTT
* * *
2504850 TTGACAAACAAAAAGGAACCATCATTT
1 TTGACAAACACAAAGGAACCACCATTG
* *
2504877 TTGACAAATACAAAGTAACCACCATTG
1 TTGACAAACACAAAGGAACCACCATTG
2504904 TTGACAAACACAAAGG
1 TTGACAAACACAAAGG
2504920 GTAGCTTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (27 bp):
TTGACAAACACAAAGGAACCACCATTG
Found at i:2512869 original size:24 final size:24
Alignment explanation
Indices: 2512841--2512886 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2512831 AATAAAAATT
2512841 AGCCACCAA-TTTTGACAAACAATA
1 AGCCA-CAATTTTTGACAAACAATA
* *
2512865 AGCCATAATTTTTTACAAACAA
1 AGCCACAATTTTTGACAAACAA
2512887 AAAAGAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (24 bp):
AGCCACAATTTTTGACAAACAATA
Found at i:2512922 original size:27 final size:26
Alignment explanation
Indices: 2512879--2512944 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
2512869 ATAATTTTTT
* * *
2512879 ACAAACAAAAAAGAACCATCATTTTTG
1 ACAAAC-ACAAAGAACCACCATTGTTG
*
2512906 ACAAATACAAAGTAACCACCATTGTTG
1 ACAAACACAAAG-AACCACCATTGTTG
2512933 ACAAACACAAAG
1 ACAAACACAAAG
2512945 GGTAGTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.52, C:0.21, G:0.09, T:0.18
Consensus pattern (26 bp):
ACAAACACAAAGAACCACCATTGTTG
Found at i:2514067 original size:31 final size:31
Alignment explanation
Indices: 2514029--2514089 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2514019 ATAAATAAAA
2514029 TATATAGTAATATAGTAA-TGTAAAATATATT
1 TATATAGTAATATAGTAACT-TAAAATATATT
*
2514060 TATATAGTAATATCGTAACTTAAAATATAT
1 TATATAGTAATATAGTAACTTAAAATATAT
2514090 CATAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (31 bp):
TATATAGTAATATAGTAACTTAAAATATATT
Found at i:2514248 original size:21 final size:21
Alignment explanation
Indices: 2514224--2514263 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2514214 AAATGTATAT
**
2514224 TTGGATAAAATGATACATTGA
1 TTGGATAAAAAAATACATTGA
2514245 TTGGATAAAAAAATACATT
1 TTGGATAAAAAAATACATT
2514264 TTTTTGAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (21 bp):
TTGGATAAAAAAATACATTGA
Found at i:2518117 original size:11 final size:12
Alignment explanation
Indices: 2518101--2518129 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2518091 TGGTATTACC
2518101 TTATATCATAT-
1 TTATATCATATG
2518112 TTATATCATATG
1 TTATATCATATG
2518124 TTATAT
1 TTATAT
2518130 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (12 bp):
TTATATCATATG
Found at i:2519850 original size:186 final size:186
Alignment explanation
Indices: 2519529--2519877 Score: 502
Period size: 186 Copynumber: 1.9 Consensus size: 186
2519519 CTATAAAGGG
* * * *
2519529 GTAGTCAATGTAGGATATTTAGGCATATGGATAAAACTTGCCCCGAAAAGCTTACTAAGATCCAG
1 GTAGTCAATGCAGGATATATAGGCATATGGATAAAACTTGCCCCGAAAAGCCTACCAAGATCCAG
* * * *
2519594 TGCCCAAATGAGCAAGCCCTTGAGGGTGAGAAAGCACAGGGGAGAGATTTAGAGTCACTTGGAAG
66 TGCCCAAATGAGCAAGCCCTTAAGGGTAAGAAAGCACAAGGGAGAGATTTAGAATCACTTGGAAG
* *
2519659 AAATAAAGAAGTAGATTTTGCCTTAAAAAAGGAGTTGCCTTGAATACCATAGAGGT
131 AAATAAAGAAATAGATGTTGCCTTAAAAAAGGAGTTGCCTTGAATACCATAGAGGT
* * * **
2519715 GTAGTCAATGCAGGATATATAGGCATCTGGATAAAGCTTGCCTC-AAGAAGCCTACCAAGATCTG
1 GTAGTCAATGCAGGATATATAGGCATATGGATAAAACTTGCCCCGAA-AAGCCTACCAAGATCCA
* * * * *
2519779 GTGCCCGAATGAGCAAGCCCTTAAGGGTAAGAGAGCACAAGGGAGGGATTTAGAATCACTTTGAG
65 GTGCCCAAATGAGCAAGCCCTTAAGGGTAAGAAAGCACAAGGGAGAGATTTAGAATCACTTGGAA
2519844 GAAATAAAGAAATAGATGTTGCCTTAAAAAAGGA
130 GAAATAAAGAAATAGATGTTGCCTTAAAAAAGGA
2519878 AGTACGAATT
Statistics
Matches: 142, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
185 2 0.01
186 140 0.99
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.22
Consensus pattern (186 bp):
GTAGTCAATGCAGGATATATAGGCATATGGATAAAACTTGCCCCGAAAAGCCTACCAAGATCCAG
TGCCCAAATGAGCAAGCCCTTAAGGGTAAGAAAGCACAAGGGAGAGATTTAGAATCACTTGGAAG
AAATAAAGAAATAGATGTTGCCTTAAAAAAGGAGTTGCCTTGAATACCATAGAGGT
Found at i:2524287 original size:2 final size:2
Alignment explanation
Indices: 2524275--2524318 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2524265 GACAACAAAA
2524275 AT AT A- 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
2524316 AT A
1 AT A
2524319 CACACATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2524820 original size:2 final size:2
Alignment explanation
Indices: 2524813--2524852 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2524803 AACTCATAAA
*
2524813 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG 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
2524853 TCCATTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2525060 original size:9 final size:9
Alignment explanation
Indices: 2525048--2525072 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2525038 GCGCAACATT
2525048 ACTTGCAGC
1 ACTTGCAGC
2525057 ACTTGCAGC
1 ACTTGCAGC
2525066 ACTTGCA
1 ACTTGCA
2525073 CTTGCCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (9 bp):
ACTTGCAGC
Found at i:2527026 original size:18 final size:17
Alignment explanation
Indices: 2527000--2527033 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2526990 TAATTTAAAC
*
2527000 ATAATTATATATAATATG
1 ATAAATATATA-AATATG
2527018 ATAAATATATAAATAT
1 ATAAATATATAAATAT
2527034 AAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATAAATATATAAATATG
Found at i:2527446 original size:6 final size:6
Alignment explanation
Indices: 2527427--2527456 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2527417 CACCTTTCAG
*
2527427 ATACCA ATATCA ATACCA ATACCA ATACCA
1 ATACCA ATACCA ATACCA ATACCA ATACCA
2527457 TGTATTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (6 bp):
ATACCA
Found at i:2529971 original size:2 final size:2
Alignment explanation
Indices: 2529964--2530000 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2529954 AACTATCACT
2529964 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
2530001 TTGGTTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2531076 original size:21 final size:22
Alignment explanation
Indices: 2531042--2531082 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2531032 AAAATCAAAA
2531042 TAATATAAATAAATATGAAAAGT
1 TAATATAAATAAATAT-AAAAGT
2531065 TAAT-TAAA-AAATATAAAA
1 TAATATAAATAAATATAAAA
2531083 TATTTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 4 0.22
23 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
TAATATAAATAAATATAAAAGT
Found at i:2531153 original size:17 final size:18
Alignment explanation
Indices: 2531127--2531160 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2531117 TTTAAAATAG
*
2531127 TTAATAATTTATGTTATA
1 TTAATAATTTATATTATA
2531145 TTAAT-ATTTATATTAT
1 TTAATAATTTATATTAT
2531161 TGATATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTAATAATTTATATTATA
Found at i:2532052 original size:18 final size:17
Alignment explanation
Indices: 2532029--2532073 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
2532019 CAAGACTTAA
2532029 TATTTTTAAAATAAATTT
1 TATTTTTAAAATAAA-TT
* **
2532047 TATTTTTTATCTAAATT
1 TATTTTTAAAATAAATT
2532064 TATTTTTAAA
1 TATTTTTAAA
2532074 TTTAATATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTAAAATAAATT
Found at i:2532850 original size:23 final size:24
Alignment explanation
Indices: 2532807--2532851 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2532797 TATTAAAATC
*
2532807 TATTTTCATAATAATATTTATACA
1 TATTTTCATAATAATACTTATACA
2532831 TATTTT-ATAATTAA-ACTTATA
1 TATTTTCATAA-TAATACTTATA
2532852 TAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTTTCATAATAATACTTATACA
Found at i:2532962 original size:12 final size:12
Alignment explanation
Indices: 2532929--2532982 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
2532919 TATTTATGTA
* *
2532929 ATATTTTATATC
1 ATATTTTATTTT
2532941 ATATTTTATTTT
1 ATATTTTATTTT
2532953 ATATTTTATTTT
1 ATATTTTATTTT
2532965 AATTATTTT-TTTT
1 -A-TATTTTATTTT
2532978 ATATT
1 ATATT
2532983 GTATCAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
11 4 0.11
12 23 0.61
13 5 0.13
14 6 0.16
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTTTATTTT
Found at i:2533571 original size:36 final size:36
Alignment explanation
Indices: 2533517--2533593 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
2533507 CAACTTGATG
*
2533517 TATTATTAAATTTGTAAATATTTATTTAATTAATTT
1 TATTATTAAATTTATAAATATTTATTTAATTAATTT
*
2533553 TATTATTATATTTATAAATATTTATTTAATTAATTT
1 TATTATTAAATTTATAAATATTTATTTAATTAATTT
2533589 TATTA
1 TATTA
2533594 AAAGTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (36 bp):
TATTATTAAATTTATAAATATTTATTTAATTAATTT
Found at i:2533576 original size:22 final size:21
Alignment explanation
Indices: 2533535--2533578 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
2533525 AATTTGTAAA
*
2533535 TATTTATTTAATTAATTTTAT
1 TATTTATTTAATAAATTTTAT
2533556 TATTATATTT-ATAAATATTTAT
1 TATT-TATTTAATAAAT-TTTAT
2533578 T
1 T
2533579 TAATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTATTTAATAAATTTTAT
Found at i:2533645 original size:23 final size:23
Alignment explanation
Indices: 2533601--2533645 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2533591 TTAAAAGTAA
* *
2533601 AAATATTAAAATATTTCCTTTTG
1 AAATATTAAAATATATACTTTTG
*
2533624 AAATATTAAAATATATATTTTT
1 AAATATTAAAATATATACTTTT
2533646 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATATTAAAATATATACTTTTG
Found at i:2534936 original size:28 final size:28
Alignment explanation
Indices: 2534900--2535049 Score: 103
Period size: 28 Copynumber: 5.4 Consensus size: 28
2534890 GACATGTGTT
* *
2534900 TAAGATAATATGAATAAGTTTGTCTTAA
1 TAAGATAATATGAATAAGATTATCTTAA
*
2534928 TAAGATAATATGGATAAGATTATCTTAA
1 TAAGATAATATGAATAAGATTATCTTAA
* * * **
2534956 CAAGATAATAT--CTAA-ATTAAACTGTGT
1 TAAGATAATATGAATAAGATT-ATCT-TAA
* *
2534983 TAAGATAAAATGGATAA-ACTTATCTTAA
1 TAAGATAATATGAATAAGA-TTATCTTAA
* *
2535011 CAAGATAATATGAATAA-ACTTATTTTAA
1 TAAGATAATATGAATAAGA-TTATCTTAA
* *
2535039 CAAAATAATAT
1 TAAGATAATAT
2535050 CTAAAGTAAA
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.03
26 6 0.06
27 10 0.10
28 70 0.71
29 7 0.07
30 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (28 bp):
TAAGATAATATGAATAAGATTATCTTAA
Found at i:2535016 original size:83 final size:85
Alignment explanation
Indices: 2534816--2535146 Score: 293
Period size: 83 Copynumber: 4.0 Consensus size: 85
2534806 ATGTCTTAAC
** * * * * *
2534816 AAGATAACGTGGATAAATTTATCTTAATAATACAA-AGTGAATAAGGTTATGTTAATAAGATAAT
1 AAGATAAAATGGATAAATTTATCTTAATAAGATAATA-TGAATAAGATTATCTTAACAAGATAAT
* *
2534880 GTCTAAAGTAGACATGTGTTT
65 ATCTAAAGTAAACATGTGTTT
* * * * *
2534901 AAGATAATATGAATAAGTTTGTCTTAATAAGATAATATGGATAAGATTATCTTAACAAGATAATA
1 AAGATAAAATGGATAAATTTATCTTAATAAGATAATATGAATAAGATTATCTTAACAAGATAATA
*
2534966 TCTAAATTAAAC-TGTG-TT
66 TCTAAAGTAAACATGTGTTT
* * * *
2534984 AAGATAAAATGGATAAACTTATCTTAACAAGATAATATGAATAA-ACTTATTTTAACAAAATAAT
1 AAGATAAAATGGATAAATTTATCTTAATAAGATAATATGAATAAGA-TTATCTTAACAAGATAAT
*
2535048 ATCTAAAGTAAACAT-TTTTT
65 ATCTAAAGTAAACATGTGTTT
* * ** * * * *
2535068 AA-AT-TAA--GTTATTTTAATATCTTAATAAGACAATATGAATAAGATTGTCTTAATAAGAAAA
1 AAGATAAAATGGATAAATT--TATCTTAATAAGATAATATGAATAAGATTATCTTAACAAGATAA
* *
2535129 TGTCTAAAGCAAACATGT
64 TATCTAAAGTAAACATGT
2535147 TCAGATAAAT
Statistics
Matches: 199, Mismatches: 39, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
80 4 0.02
82 52 0.26
83 72 0.36
84 9 0.05
85 61 0.31
86 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (85 bp):
AAGATAAAATGGATAAATTTATCTTAATAAGATAATATGAATAAGATTATCTTAACAAGATAATA
TCTAAAGTAAACATGTGTTT
Found at i:2535851 original size:49 final size:49
Alignment explanation
Indices: 2535793--2535893 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
2535783 ATGGCCTTAC
2535793 ATGCTGATTCTTGATAATAAGCAATCTAGTTGATTTATGGCTTGATTTG
1 ATGCTGATTCTTGATAATAAGCAATCTAGTTGATTTATGGCTTGATTTG
2535842 ATGCTGATTCTTGATAATAAGCAATCTAGTTGATTTATGGCTTGATTTG
1 ATGCTGATTCTTGATAATAAGCAATCTAGTTGATTTATGGCTTGATTTG
2535891 ATG
1 ATG
2535894 ACTTTTGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (49 bp):
ATGCTGATTCTTGATAATAAGCAATCTAGTTGATTTATGGCTTGATTTG
Found at i:2538409 original size:21 final size:21
Alignment explanation
Indices: 2538385--2538426 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2538375 ACTAAGATAA
2538385 ATAA-AAAAAAATAATAAAATT
1 ATAATAAAAAAATAA-AAAATT
*
2538406 ATAATTAAAAAATAAAAAATT
1 ATAATAAAAAAATAAAAAATT
2538427 CCTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
ATAATAAAAAAATAAAAAATT
Found at i:2538731 original size:14 final size:15
Alignment explanation
Indices: 2538714--2538745 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2538704 ATATTTTTAA
2538714 AAAATTT-AAATTTT
1 AAAATTTAAAATTTT
2538728 AAAATTTAAAATTTT
1 AAAATTTAAAATTTT
2538743 AAA
1 AAA
2538746 TCAAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTTAAAATTTT
Found at i:2538731 original size:15 final size:15
Alignment explanation
Indices: 2538686--2538745 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
2538676 GTATTAGAGT
*
2538686 TTTAAATTCATAAAAA
1 TTTAAATT-TTAAAAA
*
2538702 -TTATATTTTTAAAAAA
1 TTTA-AATTTT-AAAAA
2538718 TTTAAATTTT-AAAA
1 TTTAAATTTTAAAAA
2538732 TTTAAAATTTTAAA
1 TTT-AAATTTTAAA
2538746 TCAAATTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 7 0.19
15 11 0.31
16 15 0.42
17 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATTTTAAAAA
Found at i:2539832 original size:12 final size:13
Alignment explanation
Indices: 2539815--2539855 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
2539805 CGAAATATTC
2539815 TAAATT-TTAAAA
1 TAAATTATTAAAA
2539827 TAAATTATTAAAA
1 TAAATTATTAAAA
2539840 TAATATTATTATAAA
1 TAA-ATTATTA-AAA
2539855 T
1 T
2539856 TTTTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 7 0.27
15 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAATTATTAAAA
Found at i:2539849 original size:14 final size:14
Alignment explanation
Indices: 2539821--2539877 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
2539811 ATTCTAAATT
2539821 TTAAAATAA-ATTA
1 TTAAAATAATATTA
2539834 TTAAAATAATATTA
1 TTAAAATAATATTA
* *
2539848 TTATAAAT-TTTTTA
1 TTA-AAATAATATTA
* *
2539862 TTTAAATATTATTA
1 TTAAAATAATATTA
2539876 TT
1 TT
2539878 TTACTCTCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 13 0.35
14 20 0.54
15 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAAAATAATATTA
Found at i:2540181 original size:16 final size:18
Alignment explanation
Indices: 2540145--2540181 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2540135 TTTCATAACT
2540145 TTTTATTCAGTAAATATA
1 TTTTATTCAGTAAATATA
*
2540163 TTTTATT-ATTAAA-ATA
1 TTTTATTCAGTAAATATA
2540179 TTT
1 TTT
2540182 AAAATTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTATTCAGTAAATATA
Found at i:2540224 original size:15 final size:15
Alignment explanation
Indices: 2540204--2540234 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2540194 TAAATATTTT
*
2540204 AAAATATTAAAATAA
1 AAAATATAAAAATAA
2540219 AAAATATAAAAATAA
1 AAAATATAAAAATAA
2540234 A
1 A
2540235 TTTTTATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATATAAAAATAA
Found at i:2540646 original size:160 final size:160
Alignment explanation
Indices: 2540412--2540821 Score: 404
Period size: 169 Copynumber: 2.5 Consensus size: 160
2540402 TAATTTGACA
* *
2540412 CTTTTATATTAAAATACGATAATTTTTTAAGTATAAAAATTATTTTACATAATTTTAGATTTT-A
1 CTTTTATATTAAAATACAATAATTTCTTAAGTATAAAAATTATTTTACATAATTTTAGATTTTAA
* * **
2540476 ATATTTTTAAATATTT-TTTGAATAA-TTT-ATATTTTAATAATAAAATACATTTAGT-GAGTTA
66 AAATTTTAAAATATTTATCAG-ATAATTTTAATATTTTAATAATAAAATACATTTA-TCGAGTT-
*
2540537 AAAAATTATGAAATAATAAATCTATACATTGGTG
128 -AAAATTACGAAATAATAAATCTATACATTGGTG
* * * * *
2540571 CTTTTGTATT-AAATACAATCATTTCTTAAGTGTAAAAAGTTTATTTTTCATAATTTTAGGTTTT
1 CTTTTATATTAAAATACAATAATTTCTTAAGTATAAAAA--TTATTTTACATAATTTTAGATTTT
*
2540635 AAAAATTTTAAAATATTTATCAGATAATTTTAGATATTTTAATAATAAAATATATTTATCGAGTT
64 AAAAATTTTAAAATATTTATCAGATAATTTTA-ATATTTTAATAATAAAATACATTTATCGAGTT
* * * * * *
2540700 AACATTACGAAATAATAAGTCTCAAAAAAAT-GTAAACT
128 AAAATTACGAAATAATAAATCT--ATACATTGGT----G
*
2540738 CATACTTTCATATTAAAATAC-ATAATTTCTTAAGTATAAAAATTATTTTACATAATTTTAAATT
1 C-T--TTT-ATATTAAAATACAATAATTTCTTAAGTATAAAAATTATTTTACATAATTTTAGATT
* * *
2540802 TTAATATTTTTTAAATATTT
62 TTAAAAATTTTAAAATATTT
2540822 TTTGAAAATT
Statistics
Matches: 204, Mismatches: 28, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
158 24 0.12
159 9 0.04
160 22 0.11
161 19 0.09
162 24 0.12
163 3 0.01
164 33 0.16
167 1 0.00
168 1 0.00
169 36 0.18
170 3 0.01
171 23 0.11
172 6 0.03
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (160 bp):
CTTTTATATTAAAATACAATAATTTCTTAAGTATAAAAATTATTTTACATAATTTTAGATTTTAA
AAATTTTAAAATATTTATCAGATAATTTTAATATTTTAATAATAAAATACATTTATCGAGTTAAA
ATTACGAAATAATAAATCTATACATTGGTG
Found at i:2541830 original size:20 final size:20
Alignment explanation
Indices: 2541805--2541843 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
2541795 TTTGAATTAT
2541805 TTTAAT-TTGAAAACAAATGA
1 TTTAATCTTGAAAA-AAATGA
2541825 TTTAATGCTTGAAAAAAAT
1 TTTAAT-CTTGAAAAAAAT
2541844 TTATACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (20 bp):
TTTAATCTTGAAAAAAATGA
Found at i:2543732 original size:48 final size:48
Alignment explanation
Indices: 2543628--2543739 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
2543618 TTTTTTACAT
* * * *
2543628 GAGTTATTCTAAACAAAAGCTATTATCTATAAGATTTGTTTTGAACAA
1 GAGTTATTCTAAACAAAAGCTATTATCTACAAAAATTGTTTTAAACAA
* ** * * * *
2543676 AAACTATTCTAAGCAAGAGTTATTATTTACAAAAATTGTTTTAAACAA
1 GAGTTATTCTAAACAAAAGCTATTATCTACAAAAATTGTTTTAAACAA
2543724 GAGTTATTCTAAACAA
1 GAGTTATTCTAAACAA
2543740 TAATTATTTT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (48 bp):
GAGTTATTCTAAACAAAAGCTATTATCTACAAAAATTGTTTTAAACAA
Found at i:2545164 original size:15 final size:16
Alignment explanation
Indices: 2545134--2545178 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2545124 CATATTTATT
2545134 TATTAATTTCTTTAAAAA
1 TATT-ATTT-TTTAAAAA
2545152 TA-TATTTTTTAAAAA
1 TATTATTTTTTAAAAA
2545167 TATTATTTTTTA
1 TATTATTTTTTA
2545179 CCTACATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.38
16 13 0.50
17 1 0.04
18 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATTTTTTAAAAA
Found at i:2545616 original size:13 final size:13
Alignment explanation
Indices: 2545598--2545623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2545588 CACTCATATT
2545598 ATATTTTTTAAAA
1 ATATTTTTTAAAA
2545611 ATATTTTTTAAAA
1 ATATTTTTTAAAA
2545624 TTTAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTTTTAAAA
Found at i:2545632 original size:14 final size:14
Alignment explanation
Indices: 2545602--2545644 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2545592 CATATTATAT
* *
2545602 TTTTTAAAA-ATAT
1 TTTTTAAAATTTAA
2545615 TTTTTAAAATTTAA
1 TTTTTAAAATTTAA
2545629 TTTTTAATAATTTAA
1 TTTTTAA-AATTTAA
2545644 T
1 T
2545645 CTTAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 9 0.35
14 9 0.35
15 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAAATTTAA
Found at i:2545711 original size:19 final size:20
Alignment explanation
Indices: 2545687--2545730 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
2545677 ATATGTTTTA
*
2545687 ATATTTATATTATA-ATATT
1 ATATTTATATGATATATATT
2545706 ATATTTATATGATATATATT
1 ATATTTATATGATATATATT
2545726 -TATTT
1 ATATTT
2545731 TTTATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATTTATATGATATATATT
Found at i:2546789 original size:16 final size:16
Alignment explanation
Indices: 2546770--2546808 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2546760 TTACTTTGAA
*
2546770 TTATTTTAATTTTAAG
1 TTATTTTAAATTTAAG
*
2546786 TTATTTTAAATTTAAT
1 TTATTTTAAATTTAAG
2546802 TTATTTT
1 TTATTTT
2546809 GAGTTCAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATTTTAAATTTAAG
Found at i:2547006 original size:16 final size:16
Alignment explanation
Indices: 2546960--2547042 Score: 76
Period size: 16 Copynumber: 5.1 Consensus size: 16
2546950 TCAATTCGAG
*
2546960 TTTAAATCATTTCAAA
1 TTTAAATCATTTTAAA
* * * *
2546976 TTTAGATTATCTTAAG
1 TTTAAATCATTTTAAA
2546992 TTTAAATCATTTTAAA
1 TTTAAATCATTTTAAA
* **
2547008 TTTAAATTATTTTTTA
1 TTTAAATCATTTTAAA
*
2547024 TTTAAATTATTTTTAAA
1 TTTAAATCA-TTTTAAA
2547041 TT
1 TT
2547043 CATATTTATT
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
16 45 0.87
17 7 0.13
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAAATCATTTTAAA
Found at i:2547076 original size:16 final size:16
Alignment explanation
Indices: 2546992--2547076 Score: 52
Period size: 16 Copynumber: 5.3 Consensus size: 16
2546982 TTATCTTAAG
* * *
2546992 TTTAAATCATTTTAAA
1 TTTAAATTATTTTTAT
2547008 TTTAAATTATTTTT-T
1 TTTAAATTATTTTTAT
*
2547023 ATTTAAATTATTTTTAA
1 -TTTAAATTATTTTTAT
* *
2547040 ATT-CA-TATTTATTGAT
1 TTTAAATTATTT-TT-AT
2547056 TTTAAATTATTTATT-T
1 TTTAAATTATTT-TTAT
2547072 TTTAA
1 TTTAA
2547077 TCAAATTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 5 0.09
15 3 0.06
16 37 0.69
17 1 0.02
18 8 0.15
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (16 bp):
TTTAAATTATTTTTAT
Found at i:2547468 original size:2 final size:2
Alignment explanation
Indices: 2547463--2547489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2547453 ATATATATAT
2547463 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2547490 AAAGGAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2547883 original size:26 final size:27
Alignment explanation
Indices: 2547832--2547883 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2547822 ATTTTTTTAT
*
2547832 TATTTAAAATATTATAAATTTATATAA
1 TATTTAAAAAATTATAAATTTATATAA
*
2547859 TATTTAAAAAATT-TAAATTTGTATA
1 TATTTAAAAAATTATAAATTTATATA
2547884 TTCATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTTAAAAAATTATAAATTTATATAA
Found at i:2547951 original size:24 final size:23
Alignment explanation
Indices: 2547893--2547959 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
2547883 ATTCATTATA
*
2547893 TATTTATTTTTTGATATTTTATTT
1 TATTTA-TTTTTAATATTTTATTT
*
2547917 TAATTAATTTTTAATATTTTATTT
1 T-ATTTATTTTTAATATTTTATTT
2547941 GT-TTTATTTTTATATATTT
1 -TATTTATTTTTA-ATATTT
2547960 AAAGTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 9 0.24
24 23 0.62
25 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (23 bp):
TATTTATTTTTAATATTTTATTT
Found at i:2548814 original size:17 final size:18
Alignment explanation
Indices: 2548780--2548823 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2548770 TTTTAATTTT
*
2548780 AAATTT-AATTAC-ATAA
1 AAATTTAAATTACAAAAA
*
2548796 AAATTTAAATTATAAAAA
1 AAATTTAAATTACAAAAA
2548814 AAATTTAAAT
1 AAATTTAAAT
2548824 AAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.25
17 5 0.21
18 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTTAAATTACAAAAA
Found at i:2548890 original size:26 final size:27
Alignment explanation
Indices: 2548843--2548898 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
2548833 TTATTTAATG
2548843 TAATTTAACTTAAATTTATATAATTAT
1 TAATTTAACTTAAATTTATATAATTAT
2548870 TAATTTAA-TTAAATATT-TATAATTAT
1 TAATTTAACTTAAAT-TTATATAATTAT
2548896 TAA
1 TAA
2548899 AAATATCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATTTAACTTAAATTTATATAATTAT
Found at i:2556345 original size:2 final size:2
Alignment explanation
Indices: 2556338--2556367 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2556328 CTACTCTGTG
2556338 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
2556368 GTCTTGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2561186 original size:2 final size:2
Alignment explanation
Indices: 2561179--2561208 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2561169 ACCCTAAATA
2561179 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
2561209 TAATTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2561753 original size:3 final size:3
Alignment explanation
Indices: 2561745--2561793 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2561735 AATTTTCAAT
2561745 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2561793 A
1 A
2561794 ATTTTTAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2569005 original size:22 final size:23
Alignment explanation
Indices: 2568980--2569024 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2568970 GTTCACGAAT
2568980 AAACTCGTTT-ATAAATCATTTA
1 AAACTCGTTTAATAAATCATTTA
*
2569002 AAACTCGTTTAATAAATTATTTA
1 AAACTCGTTTAATAAATCATTTA
2569025 TAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (23 bp):
AAACTCGTTTAATAAATCATTTA
Found at i:2569336 original size:34 final size:34
Alignment explanation
Indices: 2569273--2569355 Score: 80
Period size: 36 Copynumber: 2.4 Consensus size: 34
2569263 TCACTTAATT
**
2569273 TAAATGAACAAACATAAATATGTCTAATTTTAAA
1 TAAATGAACAAACATAAATATGTAAAATTTTAAA
*
2569307 TAAATGAATACAAACATAAAT-T-TAAAATTTTTTAA
1 TAAATG-A-ACAAACATAAATATGTAAAA-TTTTAAA
2569342 TGAATATGAACAAA
1 T-AA-ATGAACAAA
2569356 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
34 9 0.22
35 14 0.34
36 15 0.37
37 3 0.07
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (34 bp):
TAAATGAACAAACATAAATATGTAAAATTTTAAA
Found at i:2570472 original size:50 final size:50
Alignment explanation
Indices: 2570381--2570668 Score: 468
Period size: 50 Copynumber: 5.7 Consensus size: 50
2570371 TATACTTAGA
** *
2570381 GTCAACAATTATGGCCACCTTTTCTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACC-TCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
2570432 GTCAACAATAATGGCCATCTCCTTCTATTGTCAAAGGTTGGTGAATAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2570482 GTCAACAATTATGGCCACCTCCCTCTATTATCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
2570532 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
2570582 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2570632 ATCAACAATTATGGCCACCTCTCTCTATTGTCAAAGG
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGG
2570669 CACTTTCCAT
Statistics
Matches: 221, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 204 0.92
51 17 0.08
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2575115 original size:50 final size:50
Alignment explanation
Indices: 2575053--2575289 Score: 411
Period size: 50 Copynumber: 4.7 Consensus size: 50
2575043 TATACTTAGA
* **
2575053 GTCAACAATTATGACCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
2575103 GTTAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
2575153 GTCAATAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
2575203 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
2575253 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGG
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGG
2575290 CACTTTCCAT
Statistics
Matches: 176, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 176 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2578819 original size:155 final size:154
Alignment explanation
Indices: 2578621--2579011 Score: 389
Period size: 155 Copynumber: 2.5 Consensus size: 154
2578611 GTATCCTAAT
** *
2578621 AACCCTAATGGAC-TTAAAAATGA-TATAGATGGGATGAACCTATCCTAAATACGCACCTTCGAC
1 AACCCTAAAAGACTTTAAAAA-GACTATAGATGGGATGAAACTATCCTAAATACGCACCTTCGAC
* * *
2578684 ATAAAAGTAGACCCGGTGACGACCTAAAAGTTAGTT-TAAAAAATTACGAAAATACCCCTATGAG
65 ATAAAAGCAGACCCGATGACGACCTAAAACTTAGTTCTAAAAAATTACGAAAATACCCCTA-GAG
*
2578748 TATA-CTTTCGACGTAAAAGTATCTCGAC
129 GATATC-TTCGACGT-AAAGTA-CTCGAC
* * * * * * * * *
2578776 AACCTTAAAGGA-TTTAAAAAGACTAGAGATGGAATGAAACTATCTTAAATGCCCACCTTTGGCA
1 AACCCTAAAAGACTTTAAAAAGACTATAGATGGGATGAAACTATCCTAAATACGCACCTTCGACA
* * ** ** *
2578840 TAAAAGCGGACCCGATGATGAGTTAGGACTTGGTTCTAAAAAATTACGAAAATACCCCTAGAGGA
66 TAAAAGCAGACCCGATGACGACCTAAAACTTAGTTCTAAAAAATTACGAAAATACCCCTAGAGGA
** *
2578905 TATCTTCGACGTGGAGTACTCGAT
131 TATCTTCGACGTAAAGTACTCGAC
* * * * ** *
2578929 ACCCCTAAAAGACTTTAAAAGGACTATAAAAGGGATGAGTCTATCCTAAATACGTACCTTC-AGC
1 AACCCTAAAAGACTTTAAAAAGACTATAGATGGGATGAAACTATCCTAAATACGCACCTTCGA-C
2578993 ATAAAAGCAGACCCGATGA
65 ATAAAAGCAGACCCGATGA
2579012 TAACCTAATA
Statistics
Matches: 189, Mismatches: 41, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
153 14 0.07
154 61 0.32
155 89 0.47
156 25 0.13
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (154 bp):
AACCCTAAAAGACTTTAAAAAGACTATAGATGGGATGAAACTATCCTAAATACGCACCTTCGACA
TAAAAGCAGACCCGATGACGACCTAAAACTTAGTTCTAAAAAATTACGAAAATACCCCTAGAGGA
TATCTTCGACGTAAAGTACTCGAC
Done.